From 29dc4b30fc93a7fde77793033b43fdf30f6abbcd Mon Sep 17 00:00:00 2001
From: Eric Boittier <ericdavid.boittier@unibas.ch>
Date: Wed, 23 Nov 2022 10:45:09 +0100
Subject: [PATCH] cleaning dir
---
.DS_Store | Bin 6148 -> 0 bytes
.../8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d | 0
.../bac1bbdfef47272490e8c91d5267120512437532 | 7 -
.idea/workspace.xml | 45 -
.ipynb_checkpoints/cdna-checkpoint.ipynb | 1186 -----------------
.../copy_numbers-checkpoint.csv | 0
6 files changed, 1238 deletions(-)
delete mode 100644 .DS_Store
delete mode 100644 .idea/sonarlint/issuestore/8/e/8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d
delete mode 100644 .idea/sonarlint/issuestore/b/a/bac1bbdfef47272490e8c91d5267120512437532
delete mode 100644 .idea/workspace.xml
delete mode 100644 .ipynb_checkpoints/cdna-checkpoint.ipynb
delete mode 100644 .ipynb_checkpoints/copy_numbers-checkpoint.csv
diff --git a/.DS_Store b/.DS_Store
deleted file mode 100644
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diff --git a/.idea/sonarlint/issuestore/8/e/8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d b/.idea/sonarlint/issuestore/8/e/8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d
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deleted file mode 100644
index 73a7b14..0000000
--- a/.idea/sonarlint/issuestore/b/a/bac1bbdfef47272490e8c91d5267120512437532
+++ /dev/null
@@ -1,7 +0,0 @@
-
-� python:S101 "bRename class "cDNA_Gen" to match the regular expression ^_?([A-Z_][a-zA-Z0-9]*|[a-z_][a-z0-9_]*)$.(����8Ų���0
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-� python:S101M"cRename class "GTF_entry" to match the regular expression ^_?([A-Z_][a-zA-Z0-9]*|[a-z_][a-z0-9_]*)$.(։�������8ʲ���0
-; python:S2772a" Remove this unneeded "pass".(�۾8ʲ���0
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diff --git a/.idea/workspace.xml b/.idea/workspace.xml
deleted file mode 100644
index 8a987c1..0000000
--- a/.idea/workspace.xml
+++ /dev/null
@@ -1,45 +0,0 @@
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- <option name="HIGHLIGHT_CONFLICTS" value="true" />
- <option name="HIGHLIGHT_NON_ACTIVE_CHANGELIST" value="false" />
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- </component>
- <component name="Git.Settings">
- <option name="RECENT_GIT_ROOT_PATH" value="$PROJECT_DIR$" />
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- </component>
- <component name="ProjectId" id="2GzM5DMpjLKSe0zWWtlaBWfsqTD" />
- <component name="ProjectLevelVcsManager" settingsEditedManually="true" />
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diff --git a/.ipynb_checkpoints/cdna-checkpoint.ipynb b/.ipynb_checkpoints/cdna-checkpoint.ipynb
deleted file mode 100644
index fff378b..0000000
--- a/.ipynb_checkpoints/cdna-checkpoint.ipynb
+++ /dev/null
@@ -1,1186 +0,0 @@
-{
- "cells": [
- {
- "cell_type": "code",
- "execution_count": 1,
- "id": "451af95e-82e7-4c64-a4f2-391d7ad5b8c1",
- "metadata": {},
- "outputs": [],
- "source": [
- "import sys\n",
- "\n",
- "def translate(res):\n",
- " translate_dict = {\"A\": \"T\", \"U\": \"A\", \"G\": \"C\", \"C\":\"G\"}\n",
- " if res not in translate_dict.keys():\n",
- " print(\"cDNA residue not A,T,U or G \")\n",
- " sys.exit(1)\n",
- " return translate_dict[res]\n",
- "\n",
- "class cDNA_Gen:\n",
- " def __init__(self, \n",
- " fasta, \n",
- " gtf, \n",
- " cpn, \n",
- " output_fasta = \"cDNA.fasta\",\n",
- " output_csv = \"cDNA.csv\"\n",
- " ):\n",
- " # inputs\n",
- " self.fasta = fasta\n",
- " self.gtf = gtf\n",
- " self.cpn = cpn\n",
- " self.output_fasta = output_fasta\n",
- " self.output_csv = output_csv\n",
- " # variables\n",
- " self.prime_sites = []\n",
- " self.fasta_seq = \"\"\n",
- " self.fasta_id = \"\"\n",
- " self.copy_numbers = {}\n",
- " \n",
- " self.run()\n",
- " \n",
- " def run(self):\n",
- " self.read_fasta()\n",
- " self.read_gtf()\n",
- " \n",
- " def order_priming_sites(self):\n",
- " pass\n",
- " \n",
- " def generate_cdna(self):\n",
- " pass\n",
- " \n",
- " \n",
- " def read_fasta(self):\n",
- " fasta = open(self.fasta).readlines()\n",
- " self.fasta_id = fasta[0]\n",
- " print(fasta[0])\n",
- " self.fasta_seq = \"\".join([_.rstrip() for _ in fasta[1:]])\n",
- " \n",
- " \n",
- " def read_gtf(self):\n",
- " with open(self.gtf) as gtf_file:\n",
- " gtf_lines = gtf_file.readlines()\n",
- " for line in gtf_lines[:1000]:\n",
- " if not line.startswith(\"#\"):\n",
- " temp_gtf = GTF_entry(line)\n",
- " temp_gtf.set_sequence(self.fasta_seq)\n",
- " self.prime_sites.append(temp_gtf)\n",
- "\n",
- " def write_fasta(self):\n",
- " pass\n",
- " \n",
- " def read_copy_numbers(self):\n",
- " with open(self.cpn) as cpn_file:\n",
- " cpn_lines = cpn_file.readlines()\n",
- " for line in cpn_lines:\n",
- " csv = line.split(\",\")\n",
- " trans_id = csv[0]\n",
- " if trans_id:\n",
- " gene_id = csv[1]\n",
- " count = csv[2]\n",
- " self.copy_numbers[gene_id] = count\n",
- " \n",
- " \n",
- " def return_output(self):\n",
- " return self.output_fasta, self.output_csv\n",
- " \n",
- "\n",
- "class GTF_entry:\n",
- " def __init__(self, string):\n",
- " self.string = string\n",
- " self.values = self.string.split(\"\\t\")\n",
- " self.start = int(self.values[3])\n",
- " self.end = int(self.values[4])\n",
- " self.score = float(0.5) #self.values[5]\n",
- " self.sequence = \"no sequence set\"\n",
- " self.length = self.end - self.start\n",
- " \n",
- " def __repr__(self):\n",
- " return self.sequence[:10] + \"...\" + f\" len={self.length} score={self.score}\"\n",
- " \n",
- " def set_sequence(self, full_sequence):\n",
- " self.sequence = full_sequence[self.start:self.end]\n",
- " \n",
- " \n",
- "if __name__ == \"__main__\":\n",
- " import argparse\n",
- " pass\n",
- " \n",
- " "
- ]
- },
- {
- "cell_type": "code",
- "execution_count": 2,
- "id": "84d36302-f645-43a9-a5a6-b4f3d913f734",
- "metadata": {},
- "outputs": [],
- "source": [
- "fasta = \"/Users/ericboittier/Downloads/Homo_sapiens.GRCh38.dna.primary_assembly.fa\"\n",
- "gtf = \"/Users/ericboittier/Downloads/Homo_sapiens.GRCh38.107.gtf\""
- ]
- },
- {
- "cell_type": "code",
- "execution_count": 3,
- "id": "c7a3c6f2-c8f3-466e-80aa-05ae982680f1",
- "metadata": {},
- "outputs": [
- {
- "name": "stdout",
- "output_type": "stream",
- "text": [
- ">1 dna:chromosome chromosome:GRCh38:1:1:248956422:1 REF\n",
- "\n"
- ]
- }
- ],
- "source": [
- "cdna_gen = cDNA_Gen(fasta, gtf, gtf)"
- ]
- },
- {
- "cell_type": "code",
- "execution_count": 4,
- "id": "f03693e4-82e8-4a48-9163-1146941ac095",
- "metadata": {},
- "outputs": [
- {
- "data": {
- "text/plain": [
- "[TTTCGCCTGC... len=26083 score=0.5,\n",
- " TTTCGCCTGC... len=26083 score=0.5,\n",
- " TTTCGCCTGC... len=324 score=0.5,\n",
- " TGTCGTGGCT... len=204 score=0.5,\n",
- " TG... len=2 score=0.5,\n",
- " TTACGCCAAG... len=76 score=0.5,\n",
- " TTACGCCAAG... len=76 score=0.5,\n",
- " AGTATGAGGC... len=101 score=0.5,\n",
- " AGTATGAGGC... len=101 score=0.5,\n",
- " GGGCCCAGTA... len=59 score=0.5,\n",
- " GGGCCCAGTA... len=59 score=0.5,\n",
- " AACTTCTCAA... len=69 score=0.5,\n",
- " AACTTCTCAA... len=69 score=0.5,\n",
- " CACCGTGGAG... len=165 score=0.5,\n",
- " CACCGTGGAG... len=165 score=0.5,\n",
- " ACGGCTGGCA... len=69 score=0.5,\n",
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- " TGGCTGGGCT... len=155 score=0.5,\n",
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- " TCAGCCGGCG... len=56 score=0.5,\n",
- " CCAGCCTGGA... len=125 score=0.5,\n",
- " CCAGCCTGGA... len=125 score=0.5,\n",
- " AACTCGCCCT... len=124 score=0.5,\n",
- " AACTCGCCCT... len=124 score=0.5,\n",
- " CTCCTGCTCT... len=51 score=0.5,\n",
- " CTCCTGCTCT... len=51 score=0.5,\n",
- " AGGAGATAAG... len=70 score=0.5,\n",
- " AGGAGATAAG... len=70 score=0.5,\n",
- " TTCATGCTGG... len=167 score=0.5,\n",
- " TTCATGCTGG... len=167 score=0.5,\n",
- " CGCCTGAAGC... len=108 score=0.5,\n",
- " CGCCTGAAGC... len=108 score=0.5,\n",
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- " CCACGGCATA... len=329 score=0.5,\n",
- " AG... len=2 score=0.5,\n",
- " TTTCGCCTGC... len=119 score=0.5,\n",
- " CACTGGCTAG... len=2030 score=0.5,\n",
- " AGTGTCACTC... len=19822 score=0.5,\n",
- " AGTGTCACTC... len=719 score=0.5,\n",
- " GGGCCCAGTA... len=59 score=0.5,\n",
- " AACTTCTCAA... len=69 score=0.5,\n",
- " CACCGTGGAG... len=165 score=0.5,\n",
- " ACGGCTGGCA... len=69 score=0.5,\n",
- " TGGCTGGGCT... len=155 score=0.5,\n",
- " TCAGCCGGCG... len=56 score=0.5,\n",
- " CCAGCCTGGA... len=125 score=0.5,\n",
- " AACTCGCCCT... len=124 score=0.5,\n",
- " CTCCTGCTCT... len=51 score=0.5,\n",
- " AGGAGATAAG... len=70 score=0.5,\n",
- " TTCATGCTGG... len=167 score=0.5,\n",
- " CGCCTGAAGC... len=108 score=0.5,\n",
- " CCACGGCATA... len=2363 score=0.5,\n",
- " GGGCCCAGTA... len=3613 score=0.5,\n",
- " GGGCCCAGTA... len=59 score=0.5,\n",
- " AACTTCTCAA... len=69 score=0.5,\n",
- " CACCGTGGAG... len=165 score=0.5,\n",
- " ACGGCTGGCA... len=117 score=0.5,\n",
- " AATAAGCCAG... len=12717 score=0.5,\n",
- " AATAAGCCAG... len=1686 score=0.5,\n",
- " TCAGCCGGCG... len=56 score=0.5,\n",
- " CCAGCCTGGA... len=125 score=0.5,\n",
- " AACTCGCCCT... len=124 score=0.5,\n",
- " CTCCTGCTCT... len=51 score=0.5,\n",
- " AGGAGATAAG... len=70 score=0.5,\n",
- " CCCAGTCACG... len=119 score=0.5,\n",
- " TTCATGCTGG... len=167 score=0.5,\n",
- " CGCCTGAAGC... len=108 score=0.5,\n",
- " CCACGGCATA... len=717 score=0.5,\n",
- " GCCGGCCTTG... len=11632 score=0.5,\n",
- " GCCGGCCTTG... len=602 score=0.5,\n",
- " TCAGCCGGCG... len=453 score=0.5,\n",
- " AACTCGCCCT... len=124 score=0.5,\n",
- " AGGAGATAAG... len=1467 score=0.5,\n",
- " CCACGGCATA... len=716 score=0.5,\n",
- " CTGGCCACCG... len=24417 score=0.5,\n",
- " CTGGCCACCG... len=305 score=0.5,\n",
- " TGTCGTGGCT... len=204 score=0.5,\n",
- " TG... len=2 score=0.5,\n",
- " TTACGCCAAG... len=76 score=0.5,\n",
- " TTACGCCAAG... len=76 score=0.5,\n",
- " AACTTCTCAA... len=41 score=0.5,\n",
- " AACTTCTCAA... len=41 score=0.5,\n",
- " CGTCCGAGCA... len=37 score=0.5,\n",
- " CGTCCGAGCA... len=37 score=0.5,\n",
- " ACGGCTGGCA... len=69 score=0.5,\n",
- " ACGGCTGGCA... len=69 score=0.5,\n",
- " TGGCTGGGCT... len=155 score=0.5,\n",
- " TGGCTGGGCT... len=155 score=0.5,\n",
- " TCAGCCGGCG... len=56 score=0.5,\n",
- " TCAGCCGGCG... len=56 score=0.5,\n",
- " CCAGCCTGGA... len=125 score=0.5,\n",
- " CCAGCCTGGA... len=125 score=0.5,\n",
- " AACTCGCCCT... len=124 score=0.5,\n",
- " AACTCGCCCT... len=122 score=0.5,\n",
- " CTCCTGCTCT... len=51 score=0.5,\n",
- " AGGAGATAAG... len=70 score=0.5,\n",
- " TTCATGCTGG... len=167 score=0.5,\n",
- " CGCCTGAAGC... len=108 score=0.5,\n",
- " CCACGGCATA... len=716 score=0.5,\n",
- " CTGGCCACCG... len=100 score=0.5,\n",
- " G... len=1 score=0.5,\n",
- " CTCCTGCTCT... len=51 score=0.5,\n",
- " AGGAGATAAG... len=70 score=0.5,\n",
- " TTCATGCTGG... len=167 score=0.5,\n",
- " CGCCTGAAGC... len=108 score=0.5,\n",
- " CCACGGCATA... len=716 score=0.5,\n",
- " CACCCCCGGC... len=8215 score=0.5,\n",
- " CACCCCCGGC... len=8215 score=0.5,\n",
- " CACCCCCGGC... len=121 score=0.5,\n",
- " AAGGGGACCC... len=203 score=0.5,\n",
- " TTGACCTTCA... len=371 score=0.5,\n",
- " TTGACCTTCA... len=371 score=0.5,\n",
- " TTGACCTTCA... len=371 score=0.5,\n",
- " AAGAAGCCTG... len=702 score=0.5,\n",
- " AAGAAGCCTG... len=702 score=0.5,\n",
- " AAGAAGCCTG... len=702 score=0.5,\n",
- " TGACCCACCA... len=546 score=0.5,\n",
- " TGACCCACCA... len=546 score=0.5,\n",
- " TGACCCACCA... len=546 score=0.5,\n",
- " ATTGGAGGAA... len=1478 score=0.5,\n",
- " ATTGGAGGAA... len=1478 score=0.5,\n",
- " ATTGGAGGAA... len=50 score=0.5,\n",
- " TGTGTGGTGA... len=84 score=0.5,\n",
- " TCAGAGCCCA... len=77 score=0.5,\n",
- " CAGGGCCATC... len=161 score=0.5,\n",
- " AGTAGGCCTC... len=193 score=0.5,\n",
- " AAATGCCGTC... len=2973 score=0.5,\n",
- " AAATGCCGTC... len=2973 score=0.5,\n",
- " AAATGCCGTC... len=90 score=0.5,\n",
- " AGCCACCCCA... len=125 score=0.5,\n",
- " AGAACGGCAT... len=408 score=0.5,\n",
- " GTGTCCAAAC... len=369453 score=0.5,\n",
- " GTGTCCAAAC... len=365174 score=0.5,\n",
- " GTGTCCAAAC... len=128 score=0.5,\n",
- " TGCGATCCAA... len=36 score=0.5,\n",
- " TG... len=2 score=0.5,\n",
- " TGACGGTGAC... len=349 score=0.5,\n",
- " TGACGGTGAC... len=349 score=0.5,\n",
- " AAATACTGAC... len=50 score=0.5,\n",
- " AAATACTGAC... len=50 score=0.5,\n",
- " AGATCTCCGA... len=137 score=0.5,\n",
- " AGATCTCCGA... len=137 score=0.5,\n",
- " TTTACTATAA... len=102 score=0.5,\n",
- " TTTACTATAA... len=102 score=0.5,\n",
- " GGAGCCCACG... len=207 score=0.5,\n",
- " GGAGCCCACG... len=207 score=0.5,\n",
- " CTGGAGCAGC... len=147 score=0.5,\n",
- " CTGGAGCAGC... len=147 score=0.5,\n",
- " TGTTCACGGA... len=153 score=0.5,\n",
- " TGTTCACGGA... len=153 score=0.5,\n",
- " TGAGGTCTGC... len=1416 score=0.5,\n",
- " TGAGGTCTGC... len=1416 score=0.5,\n",
- " AGGGTAGAAA... len=87 score=0.5,\n",
- " AGGGTAGAAA... len=87 score=0.5,\n",
- " TGTCAGCCAT... len=169 score=0.5,\n",
- " TGTCAGCCAT... len=169 score=0.5,\n",
- " TACTGTGGGA... len=77 score=0.5,\n",
- " TACTGTGGGA... len=77 score=0.5,\n",
- " TGTAAGTACT... len=169 score=0.5,\n",
- " TGTAAGTACT... len=169 score=0.5,\n",
- " GAGCCAGCAC... len=174 score=0.5,\n",
- " GAGCCAGCAC... len=174 score=0.5,\n",
- " GCGGACATGC... len=236 score=0.5,\n",
- " GCGGACATGC... len=236 score=0.5,\n",
- " CATATGCAAT... len=665 score=0.5,\n",
- " CATATGCAA... len=9 score=0.5,\n",
- " GA... len=2 score=0.5,\n",
- " GTGTCCAAAC... len=91 score=0.5,\n",
- " GCTGTCCCTT... len=652 score=0.5,\n",
- " ATGCTGGGGA... len=117408 score=0.5,\n",
- " ATGCTGGGGA... len=113 score=0.5,\n",
- " TGACGGTGAC... len=466 score=0.5,\n",
- " AAGATAGTGT... len=366224 score=0.5,\n",
- " AAGATAGTGT... len=99 score=0.5,\n",
- " TGCGATCCAA... len=36 score=0.5,\n",
- " TG... len=2 score=0.5,\n",
- " TGACGGTGAC... len=349 score=0.5,\n",
- " TGACGGTGAC... len=349 score=0.5,\n",
- " AAATACTGAC... len=50 score=0.5,\n",
- " AAATACTGAC... len=50 score=0.5,\n",
- " TCTCCGAAGA... len=134 score=0.5,\n",
- " TCTCCGAAGA... len=134 score=0.5,\n",
- " TTTACTATAA... len=102 score=0.5,\n",
- " TTTACTATAA... len=102 score=0.5,\n",
- " GGAGCCCACG... len=207 score=0.5,\n",
- " GGAGCCCACG... len=207 score=0.5,\n",
- " CTGGAGCAGC... len=147 score=0.5,\n",
- " CTGGAGCAGC... len=147 score=0.5,\n",
- " TGTTCACGGA... len=153 score=0.5,\n",
- " TGTTCACGGA... len=153 score=0.5,\n",
- " TGAGGTCTGC... len=1416 score=0.5,\n",
- " TGAGGTCTGC... len=1416 score=0.5,\n",
- " AGGGTAGAAA... len=87 score=0.5,\n",
- " AGGGTAGAAA... len=87 score=0.5,\n",
- " TGTCAGCCAT... len=169 score=0.5,\n",
- " TGTCAGCCAT... len=169 score=0.5,\n",
- " TACTGTGGGA... len=77 score=0.5,\n",
- " TACTGTGGGA... len=77 score=0.5,\n",
- " TGTAAGTACT... len=169 score=0.5,\n",
- " TGTAAGTACT... len=169 score=0.5,\n",
- " GAGCCAGCAC... len=174 score=0.5,\n",
- " GAGCCAGCAC... len=174 score=0.5,\n",
- " GCGGACATGC... len=236 score=0.5,\n",
- " GCGGACATGC... len=236 score=0.5,\n",
- " TGTGCTGAGG... len=174 score=0.5,\n",
- " TGTGCTGAGG... len=174 score=0.5,\n",
- " GTTCTCTGGA... len=1687 score=0.5,\n",
- " GTTCTCTGGA... len=74 score=0.5,\n",
- " GA... len=2 score=0.5,\n",
- " AAGATAGTGT... len=62 score=0.5,\n",
- " GGGCTGGGCA... len=1609 score=0.5,\n",
- " CTGCTTCTGG... len=365131 score=0.5,\n",
- " CTGCTTCTGG... len=85 score=0.5,\n",
- " TGCGATCCAA... len=36 score=0.5,\n",
- " TG... len=2 score=0.5,\n",
- " TGACGGTGAC... len=349 score=0.5,\n",
- " TGACGGTGAC... len=349 score=0.5,\n",
- " AAATACTGAC... len=50 score=0.5,\n",
- " AAATACTGAC... len=50 score=0.5,\n",
- " AGATCTCCGA... len=137 score=0.5,\n",
- " AGATCTCCGA... len=137 score=0.5,\n",
- " TTTACTATAA... len=102 score=0.5,\n",
- " TTTACTATAA... len=102 score=0.5,\n",
- " GGAGCCCACG... len=207 score=0.5,\n",
- " GGAGCCCACG... len=207 score=0.5,\n",
- " CTGGAGCAGC... len=147 score=0.5,\n",
- " CTGGAGCAGC... len=147 score=0.5,\n",
- " TGTTCACGGA... len=153 score=0.5,\n",
- " TGTTCACGGA... len=153 score=0.5,\n",
- " TGAGGTCTGC... len=1416 score=0.5,\n",
- " TGAGGTCTGC... len=1416 score=0.5,\n",
- " GTAGAAAAGC... len=84 score=0.5,\n",
- " GTAGAAAAGC... len=84 score=0.5,\n",
- " TGTCAGCCAT... len=169 score=0.5,\n",
- " TGTCAGCCAT... len=169 score=0.5,\n",
- " TACTGTGGGA... len=77 score=0.5,\n",
- " TACTGTGGGA... len=77 score=0.5,\n",
- " TGTAAGTACT... len=169 score=0.5,\n",
- " TGTAAGTACT... len=169 score=0.5,\n",
- " GAGCCAGCAC... len=174 score=0.5,\n",
- " GAGCCAGCAC... len=174 score=0.5,\n",
- " GCGGACATGC... len=236 score=0.5,\n",
- " GCGGACATGC... len=236 score=0.5,\n",
- " CATATGCAAT... len=665 score=0.5,\n",
- " CATATGCAA... len=9 score=0.5,\n",
- " GA... len=2 score=0.5,\n",
- " CTGCTTCTGG... len=48 score=0.5,\n",
- " GCTGTCCCTT... len=652 score=0.5,\n",
- " GTGTGTGGCT... len=369418 score=0.5,\n",
- " GTGTGTGGCT... len=93 score=0.5,\n",
- " TGCGATCCAA... len=36 score=0.5,\n",
- " TG... len=2 score=0.5,\n",
- " TGACGGTGAC... len=349 score=0.5,\n",
- " TGACGGTGAC... len=349 score=0.5,\n",
- " AAATACTGAC... len=50 score=0.5,\n",
- " AAATACTGAC... len=50 score=0.5,\n",
- " TCTCCGAAGA... len=134 score=0.5,\n",
- " TCTCCGAAGA... len=134 score=0.5,\n",
- " TTTACTATAA... len=102 score=0.5,\n",
- " TTTACTATAA... len=102 score=0.5,\n",
- " GGAGCCCACG... len=207 score=0.5,\n",
- " GGAGCCCACG... len=207 score=0.5,\n",
- " CTGGAGCAGC... len=147 score=0.5,\n",
- " CTGGAGCAGC... len=147 score=0.5,\n",
- " TGTTCACGGA... len=153 score=0.5,\n",
- " TGTTCACGGA... len=153 score=0.5,\n",
- " TGAGGTCTGC... len=1416 score=0.5,\n",
- " TGAGGTCTGC... len=1416 score=0.5,\n",
- " AGGGTAGAAA... len=87 score=0.5,\n",
- " AGGGTAGAAA... len=87 score=0.5,\n",
- " TGTCAGCCAT... len=169 score=0.5,\n",
- " TGTCAGCCAT... len=169 score=0.5,\n",
- " TACTGTGGGA... len=77 score=0.5,\n",
- " TACTGTGGGA... len=77 score=0.5,\n",
- " TGTAAGTACT... len=169 score=0.5,\n",
- " TGTAAGTACT... len=169 score=0.5,\n",
- " GAGCCAGCAC... len=174 score=0.5,\n",
- " GAGCCAGCAC... len=174 score=0.5,\n",
- " GCGGACATGC... len=236 score=0.5,\n",
- " GCGGACATGC... len=236 score=0.5,\n",
- " TGTGCTGAGG... len=174 score=0.5,\n",
- " TGTGCTGAGG... len=174 score=0.5,\n",
- " CATATGCAAT... len=4944 score=0.5,\n",
- " CATATGCAAT... len=131 score=0.5,\n",
- " GA... len=2 score=0.5,\n",
- " GTGTGTGGCT... len=56 score=0.5,\n",
- " GGGCTGGGCA... len=4809 score=0.5,\n",
- " AGCACAAGGC... len=195994 score=0.5,\n",
- " AGCACAAGGC... len=164 score=0.5,\n",
- " AAATACTGAC... len=50 score=0.5,\n",
- " TCTCCGAAGA... len=134 score=0.5,\n",
- " TTTACTATAA... len=102 score=0.5,\n",
- " GGAGCCCACG... len=207 score=0.5,\n",
- " CTGGAGCAGC... len=147 score=0.5,\n",
- " TGTTCACGGA... len=153 score=0.5,\n",
- " TGAGGTCTGC... len=1416 score=0.5,\n",
- " AGGGTAGAAA... len=87 score=0.5,\n",
- " TGTCAGCCAT... len=169 score=0.5,\n",
- " TACTGTGGGA... len=77 score=0.5,\n",
- " TGTAAGTACT... len=169 score=0.5,\n",
- " GAGCCAGCAC... len=174 score=0.5,\n",
- " GCGGACATGC... len=236 score=0.5,\n",
- " TGTGCTGAGG... len=174 score=0.5,\n",
- " CATATGCAAT... len=248 score=0.5,\n",
- " CAAAGGTAGG... len=142786 score=0.5,\n",
- " CAAAG... len=5 score=0.5,\n",
- " CAAAG... len=5 score=0.5,\n",
- " TCTCCGAAGA... len=134 score=0.5,\n",
- " TCTCCGAAGA... len=134 score=0.5,\n",
- " TGAAAGTGAA... len=242 score=0.5,\n",
- " TGAAAGTGAA... len=17 score=0.5,\n",
- " GA... len=2 score=0.5,\n",
- " GGAAAATTGG... len=221 score=0.5,\n",
- " TTTACTATAA... len=37802 score=0.5,\n",
- " TTTACTATAA... len=102 score=0.5,\n",
- " TTTACTATAA... len=102 score=0.5,\n",
- " GGAGCCCACG... len=207 score=0.5,\n",
- " GGAGCCCACG... len=207 score=0.5,\n",
- " CTGGAGCAGC... len=147 score=0.5,\n",
- " CTGGAGCAGC... len=147 score=0.5,\n",
- " TGTTCACGGA... len=153 score=0.5,\n",
- " TGTTCACGGA... len=153 score=0.5,\n",
- " TGAGGTCTGC... len=1416 score=0.5,\n",
- " TGAGGTCTGC... len=1416 score=0.5,\n",
- " GTAGAAAAGC... len=84 score=0.5,\n",
- " GTAGAAAAGC... len=84 score=0.5,\n",
- " TGTCAGCCAT... len=169 score=0.5,\n",
- " TGTCAGCCAT... len=169 score=0.5,\n",
- " TACTGTGGGA... len=77 score=0.5,\n",
- " TACTGTGGGA... len=77 score=0.5,\n",
- " TGTAAGTACT... len=169 score=0.5,\n",
- " TGTAAGTACT... len=169 score=0.5,\n",
- " GAGCCAGCAC... len=174 score=0.5,\n",
- " GAGCCAGCAC... len=174 score=0.5,\n",
- " GCGGACATGC... len=236 score=0.5,\n",
- " GCGGACATGC... len=236 score=0.5,\n",
- " TGTGCTGAGG... len=174 score=0.5,\n",
- " TGTGCTGAGG... len=174 score=0.5,\n",
- " CATATGCAAT... len=616 score=0.5,\n",
- " CATATGCAAT... len=131 score=0.5,\n",
- " GA... len=2 score=0.5,\n",
- " GGGCTGGGCA... len=481 score=0.5,\n",
- " GCCGGCCCCG... len=9176 score=0.5,\n",
- " GCCGGCCCCG... len=140 score=0.5,\n",
- " TGTAAGTACT... len=169 score=0.5,\n",
- " GAGCCAGCAC... len=174 score=0.5,\n",
- " GCGGACATGC... len=236 score=0.5,\n",
- " CATATGCAAT... len=418 score=0.5,\n",
- " ACAGGCGCCC... len=856 score=0.5,\n",
- " ACAGGCGCCC... len=534 score=0.5,\n",
- " GAGCCAGCAC... len=21 score=0.5,\n",
- " TTAATCCCCT... len=1043 score=0.5,\n",
- " TTAATCCCCT... len=1043 score=0.5,\n",
- " TTAATCCCCT... len=1043 score=0.5,\n",
- " TTGTTTGCTT... len=5466 score=0.5,\n",
- " TTGTTTGCTT... len=5466 score=0.5,\n",
- " TTTCTTCTGT... len=452 score=0.5,\n",
- " AAAATCCCTG... len=628 score=0.5,\n",
- " TGTGCAGCTT... len=65 score=0.5,\n",
- " TTGTTTGCTT... len=76 score=0.5,\n",
- " TTTACCAAGT... len=9833 score=0.5,\n",
- " TTTACCAAGT... len=8600 score=0.5,\n",
- " CGCCAGGCTG... len=173 score=0.5,\n",
- " CGCCAGGCTG... len=111 score=0.5,\n",
- " AT... len=2 score=0.5,\n",
- " TGCAAGTGTG... len=80 score=0.5,\n",
- " TGCAAGTGTG... len=80 score=0.5,\n",
- " TACGTGATCC... len=406 score=0.5,\n",
- " TACGTGATCC... len=406 score=0.5,\n",
- " TGCGGTGAGA... len=235 score=0.5,\n",
- " TGCGGTGAGA... len=235 score=0.5,\n",
- " TTGCTGCTGC... len=135 score=0.5,\n",
- " TTGCTGCTGC... len=135 score=0.5,\n",
- " TTTACCAAGT... len=1870 score=0.5,\n",
- " CGGTAGTGCC... len=65 score=0.5,\n",
- " CA... len=2 score=0.5,\n",
- " GCCGCGGGTT... len=61 score=0.5,\n",
- " TTTACCAAGT... len=1801 score=0.5,\n",
- " GATTTTACCT... len=8590 score=0.5,\n",
- " CGCCAGGCTG... len=173 score=0.5,\n",
- " CGCCAGGCTG... len=111 score=0.5,\n",
- " AT... len=2 score=0.5,\n",
- " TGCAAGTGTG... len=80 score=0.5,\n",
- " TGCAAGTGTG... len=80 score=0.5,\n",
- " TACGTGATCC... len=406 score=0.5,\n",
- " TACGTGATCC... len=406 score=0.5,\n",
- " TGCGGTGAGA... len=175 score=0.5,\n",
- " TGCGGTGAGA... len=175 score=0.5,\n",
- " TTGCTGCTGC... len=135 score=0.5,\n",
- " TTGCTGCTGC... len=135 score=0.5,\n",
- " GATTTTACCT... len=1860 score=0.5,\n",
- " CGGTAGTGCC... len=65 score=0.5,\n",
- " CA... len=2 score=0.5,\n",
- " GCCGCGGGTT... len=61 score=0.5,\n",
- " GATTTTACCT... len=1791 score=0.5,\n",
- " GAAAGGTGAC... len=8395 score=0.5,\n",
- " CGCCAGGCTG... len=65 score=0.5,\n",
- " CGCCAGGCTG... len=65 score=0.5,\n",
- " TGCAAGTGTG... len=80 score=0.5,\n",
- " TGCAAGTGTG... len=80 score=0.5,\n",
- " TACGTGATCC... len=406 score=0.5,\n",
- " TACGTGATCC... len=406 score=0.5,\n",
- " TGCGGTGAGA... len=175 score=0.5,\n",
- " TGCGGTGAGA... len=175 score=0.5,\n",
- " TTGCTGCTGC... len=135 score=0.5,\n",
- " TTGCTGCTGC... len=135 score=0.5,\n",
- " CCCAGGACCT... len=803 score=0.5,\n",
- " CGGTAGTGCC... len=65 score=0.5,\n",
- " CA... len=2 score=0.5,\n",
- " TTGACTAACC... len=278 score=0.5,\n",
- " GAAAGGTGAC... len=310 score=0.5,\n",
- " CCCAGGACCT... len=734 score=0.5,\n",
- " TTGACTAACC... len=278 score=0.5,\n",
- " GAAAGGTGAC... len=310 score=0.5,\n",
- " TAAAGATGCC... len=7702 score=0.5,\n",
- " CGCCAGGCTG... len=149 score=0.5,\n",
- " CGCCAGGCTG... len=111 score=0.5,\n",
- " AT... len=2 score=0.5,\n",
- " TGCAAGTGTG... len=80 score=0.5,\n",
- " TGCAAGTGTG... len=80 score=0.5,\n",
- " TACGTGATCC... len=406 score=0.5,\n",
- " TACGTGATCC... len=406 score=0.5,\n",
- " TGCGGTGAGA... len=175 score=0.5,\n",
- " TGCGGTGAGA... len=175 score=0.5,\n",
- " TTGCTGCTGC... len=135 score=0.5,\n",
- " TTGCTGCTGC... len=135 score=0.5,\n",
- " TAAAGATGCC... len=990 score=0.5,\n",
- " CGGTAGTGCC... len=59 score=0.5,\n",
- " CA... len=2 score=0.5,\n",
- " GCCGCGGGTT... len=37 score=0.5,\n",
- " TAAAGATGCC... len=927 score=0.5,\n",
- " AGAACAGGTG... len=6017 score=0.5,\n",
- " CGCCAGGCTG... len=144 score=0.5,\n",
- " CGCCAGGCTG... len=111 score=0.5,\n",
- " AT... len=2 score=0.5,\n",
- " TGCAAGTGTG... len=80 score=0.5,\n",
- " TGCAAGTGTG... len=80 score=0.5,\n",
- " TGATCCCCGT... len=402 score=0.5,\n",
- " TGATCCCCGT... len=402 score=0.5,\n",
- " TGCGGTGAGA... len=175 score=0.5,\n",
- " GTCCTCTCCG... len=30 score=0.5,\n",
- " CA... len=2 score=0.5,\n",
- " AGAACAGGTG... len=101 score=0.5,\n",
- " GCCGCGGGTT... len=32 score=0.5,\n",
- " TGCGGTGAGA... len=141 score=0.5,\n",
- " AGAACAGGTG... len=101 score=0.5,\n",
- " AGGCAGGCGA... len=5267 score=0.5,\n",
- " TGAATGGCTG... len=200 score=0.5,\n",
- " TGCAAGTGTG... len=80 score=0.5,\n",
- " AGGCAGGCGA... len=328 score=0.5,\n",
- " AGGCAGGCGA... len=89 score=0.5,\n",
- " AT... len=2 score=0.5,\n",
- " TGAATGGCTG... len=200 score=0.5,\n",
- " TGCAAGTGTG... len=80 score=0.5,\n",
- " CAGCGCCGCG... len=238 score=0.5,\n",
- " CTGCTGCTCA... len=1421 score=0.5,\n",
- " AGCCCCCCGG... len=326 score=0.5,\n",
- " CTGCTGCTCA... len=275 score=0.5,\n",
- " CGTGTGGTGA... len=2232 score=0.5,\n",
- " TTAGCGTGAG... len=206 score=0.5,\n",
- " AGGCCAGAGG... len=74 score=0.5,\n",
- " TA... len=2 score=0.5,\n",
- " CGGGCCAGCT... len=190 score=0.5,\n",
- " CGTGTGGTGA... len=254 score=0.5,\n",
- " TTAGCGTGAG... len=128 score=0.5,\n",
- " CGGGCCAGCT... len=190 score=0.5,\n",
- " CGTGTGGTGA... len=254 score=0.5,\n",
- " TGCAGTGTCA... len=3759 score=0.5,\n",
- " CGCCAGGCTG... len=123 score=0.5,\n",
- " CGCCAGGCTG... len=111 score=0.5,\n",
- " AT... len=2 score=0.5,\n",
- " TTAGCGTGAG... len=238 score=0.5,\n",
- " AGGCCAGAGG... len=106 score=0.5,\n",
- " TA... len=2 score=0.5,\n",
- " TGCAAGTGTG... len=80 score=0.5,\n",
- " TGCAGTGTCA... len=103 score=0.5,\n",
- " GCCGCGGGTT... len=11 score=0.5,\n",
- " TTAGCGTGAG... len=128 score=0.5,\n",
- " TGCAAGTGTG... len=80 score=0.5,\n",
- " TGCAGTGTCA... len=103 score=0.5,\n",
- " TTGCCCTCTT... len=2406 score=0.5,\n",
- " TTGCCCTCTT... len=2406 score=0.5,\n",
- " TTGCCCTCTT... len=2406 score=0.5,\n",
- " GAAGCGGAGG... len=213 score=0.5,\n",
- " GAAGCGGAGG... len=213 score=0.5,\n",
- " TGTTCGCCGA... len=1542 score=0.5,\n",
- " TGTTCGCCGA... len=1542 score=0.5,\n",
- " TGTTCGCCGA... len=1542 score=0.5,\n",
- " AAATCACGTT... len=101817 score=0.5,\n",
- " AAATCACGTT... len=6869 score=0.5,\n",
- " TTCCTCAATG... len=129 score=0.5,\n",
- " AAATCACGTT... len=1161 score=0.5,\n",
- " GTCTAAAATT... len=10903 score=0.5,\n",
- " TTGGTTGTGT... len=149 score=0.5,\n",
- " TCGAGGCAGC... len=901 score=0.5,\n",
- " TAAGTCGCAG... len=84 score=0.5,\n",
- " GTCTAAAATT... len=1112 score=0.5,\n",
- " CATTGCAAAA... len=101537 score=0.5,\n",
- " CCCATCCCCT... len=336 score=0.5,\n",
- " TTGGTTGTGT... len=134 score=0.5,\n",
- " TCGAGGCAGC... len=901 score=0.5,\n",
- " CATTGCAAAA... len=881 score=0.5,\n",
- " ACACATATAT... len=10292 score=0.5,\n",
- " TTGGTTGTGT... len=149 score=0.5,\n",
- " TCGAGGCAGC... len=901 score=0.5,\n",
- " ACACATATAT... len=501 score=0.5,\n",
- " CCCAATTTTG... len=456 score=0.5,\n",
- " CCCAATTTTG... len=456 score=0.5,\n",
- " GGAAAAATAT... len=34487 score=0.5,\n",
- " TTCAAGTTTG... len=157 score=0.5,\n",
- " TTTTCCTGGA... len=104 score=0.5,\n",
- " TTGGTTGTGT... len=149 score=0.5,\n",
- " GGAAAAATAT... len=5189 score=0.5,\n",
- " AGGGCTGGTG... len=1696 score=0.5,\n",
- " AGGGCTGGTG... len=1696 score=0.5,\n",
- " AGGGCTGGTG... len=1696 score=0.5,\n",
- " CTCCTCCCGG... len=81894 score=0.5,\n",
- " CTCCTCCCGG... len=81894 score=0.5,\n",
- " CTCCTCCCGG... len=1416 score=0.5,\n",
- " TGGAGGCGGC... len=968 score=0.5,\n",
- " TG... len=2 score=0.5,\n",
- " TCTCCTCTGA... len=125 score=0.5,\n",
- " TCTCCTCTGA... len=125 score=0.5,\n",
- " GCCTGGGCTG... len=115 score=0.5,\n",
- " GCCTGGGCTG... len=115 score=0.5,\n",
- " TTCTACTCCT... len=262 score=0.5,\n",
- " TTCTACTCCT... len=262 score=0.5,\n",
- " CACCTCCTCC... len=292 score=0.5,\n",
- " CACCTCCTCC... len=292 score=0.5,\n",
- " AGCTGGAGTT... len=230 score=0.5,\n",
- " AGCTGGAGTT... len=230 score=0.5,\n",
- " TCGAAGACCT... len=3636 score=0.5,\n",
- " TCGAAGACCT... len=185 score=0.5,\n",
- " AG... len=2 score=0.5,\n",
- " CTCCTCCCGG... len=447 score=0.5,\n",
- " TTCCGTGCCT... len=3447 score=0.5,\n",
- " GCGGCTGTGC... len=70559 score=0.5,\n",
- " GCGGCTGTGC... len=190 score=0.5,\n",
- " TCTCCTCTGA... len=60 score=0.5,\n",
- " GGGGGGCGCG... len=55380 score=0.5,\n",
- " GGGGGGCGCG... len=75 score=0.5,\n",
- " TCTCCTCTGA... len=125 score=0.5,\n",
- " GCCTGGGCTG... len=91 score=0.5,\n",
- " TGTCTGGCCT... len=722 score=0.5,\n",
- " TGTCTGGCCT... len=462 score=0.5,\n",
- " CACCTCCTCC... len=75 score=0.5,\n",
- " CATGAATTCA... len=336 score=0.5,\n",
- " CATGAATTCA... len=336 score=0.5,\n",
- " CATGAATTCA... len=336 score=0.5,\n",
- " GCAAGTTCAT... len=1031 score=0.5,\n",
- " GCAAGTTCAT... len=1031 score=0.5,\n",
- " GCAAGTTCAT... len=216 score=0.5,\n",
- " GTGAAAGTTT... len=197 score=0.5,\n",
- " GAAGACTCCT... len=423 score=0.5,\n",
- " GAAGACTCCT... len=423 score=0.5,\n",
- " GAAGACTCCT... len=423 score=0.5,\n",
- " TTTGACCTCC... len=4477 score=0.5,\n",
- " TTTGACCTCC... len=4353 score=0.5,\n",
- " GCTTTCCCGC... len=37 score=0.5,\n",
- " TCCCGAGAAG... len=638 score=0.5,\n",
- " TTCAATACTG... len=53 score=0.5,\n",
- " TCCTGCACCC... len=143 score=0.5,\n",
- " TCCTCATCGT... len=175 score=0.5,\n",
- " TTTGACCTCC... len=594 score=0.5,\n",
- " CGCCATCCTC... len=4339 score=0.5,\n",
- " GCTTTCCCGC... len=37 score=0.5,\n",
- " TCCCGAGAAG... len=638 score=0.5,\n",
- " TCCTGCACCC... len=143 score=0.5,\n",
- " CGCCATCCTC... len=580 score=0.5,\n",
- " TTGCTCACTT... len=1880 score=0.5,\n",
- " GCTTTCCCGC... len=161 score=0.5,\n",
- " TCCCGAGAAG... len=638 score=0.5,\n",
- " TTGCTCACTT... len=184 score=0.5,\n",
- " TTGCTCACTT... len=1880 score=0.5,\n",
- " TCCCGAGAAG... len=1067 score=0.5,\n",
- " TTGCTCACTT... len=184 score=0.5,\n",
- " ATCTTGTTGA... len=371 score=0.5,\n",
- " ATCTTGTTGA... len=371 score=0.5,\n",
- " ATCTTGTTGA... len=371 score=0.5,\n",
- " TCCCCCACAC... len=158470 score=0.5,\n",
- " TCCCCCACAC... len=64284 score=0.5,\n",
- " TCCCCCACAC... len=292 score=0.5,\n",
- " CAAGCTCTAC... len=47 score=0.5,\n",
- " TTTCAGAGCC... len=103 score=0.5,\n",
- " TTGCCACGGC... len=359 score=0.5,\n",
- " GTCAGGCCTC... len=155808 score=0.5,\n",
- " GTCAGGCCTC... len=52 score=0.5,\n",
- " TGGCGTCCTC... len=35 score=0.5,\n",
- " TG... len=2 score=0.5,\n",
- " CAAGCTCTAC... len=47 score=0.5,\n",
- " CAAGCTCTAC... len=47 score=0.5,\n",
- " TTGCCACGGC... len=84 score=0.5,\n",
- " TTGCCACGGC... len=84 score=0.5,\n",
- " GCTGACAGAT... len=128 score=0.5,\n",
- " GCTGACAGAT... len=128 score=0.5,\n",
- " TCCCGCAGGC... len=85 score=0.5,\n",
- " TCCCGCAGGC... len=85 score=0.5,\n",
- " AATACCTGCT... len=102 score=0.5,\n",
- " AATACCTGCT... len=102 score=0.5,\n",
- " GACTCAGTTA... len=97 score=0.5,\n",
- " GACTCAGTTA... len=97 score=0.5,\n",
- " CCACCACATC... len=91 score=0.5,\n",
- " CCACCACATC... len=91 score=0.5,\n",
- " AGGCAGTTCC... len=1227 score=0.5,\n",
- " AGGCAGTTCC... len=453 score=0.5,\n",
- " AG... len=2 score=0.5,\n",
- " GTCAGGCCTC... len=16 score=0.5,\n",
- " GCTGCGCCTG... len=770 score=0.5,\n",
- " AGGCAGAGCA... len=148304 score=0.5,\n",
- " AGGCAGAGCA... len=20 score=0.5,\n",
- " AGGCAGAGCA... len=20 score=0.5,\n",
- " CAAGCTCTAC... len=47 score=0.5,\n",
- " CAAGCTCTAC... len=47 score=0.5,\n",
- " TTGCCACGGC... len=84 score=0.5,\n",
- " TTGCCACGGC... len=84 score=0.5,\n",
- " GCTGACAGAT... len=128 score=0.5,\n",
- " GCTGACAGAT... len=128 score=0.5,\n",
- " TCCCGCAGGC... len=85 score=0.5,\n",
- " TCCCGCAGGC... len=85 score=0.5,\n",
- " AATACCTGCT... len=267 score=0.5,\n",
- " AATACCTGCT... len=110 score=0.5,\n",
- " AA... len=2 score=0.5,\n",
- " GACTCCATCA... len=153 score=0.5,\n",
- " ATGGGTGCGC... len=401 score=0.5,\n",
- " ATGGGTGCGC... len=172 score=0.5,\n",
- " TTGCCACGGC... len=76 score=0.5,\n",
- " CATCCAGATG... len=22535 score=0.5,\n",
- " CATCCAGATG... len=22528 score=0.5,\n",
- " CATCCAGATG... len=148 score=0.5,\n",
- " ACAGTGCCTG... len=957 score=0.5,\n",
- " AGGGAGGCCC... len=12204 score=0.5,\n",
- " AGGGAGGCCC... len=125 score=0.5,\n",
- " ATAGTGCACA... len=122 score=0.5,\n",
- " TCTTGGCTCC... len=297 score=0.5,\n",
- " TTTGGAGTAA... len=366 score=0.5,\n",
- " TTGCCAAAAG... len=11873 score=0.5,\n",
- " TTGCCAAAAG... len=81 score=0.5,\n",
- " ATAGTGCACA... len=122 score=0.5,\n",
- " TCTTGGCTCC... len=297 score=0.5,\n",
- " AAATAATCAC... len=95 score=0.5,\n",
- " AGCTTTGGAG... len=82 score=0.5,\n",
- " CCAACAGCGA... len=22503 score=0.5,\n",
- " CCAACAGCGA... len=116 score=0.5,\n",
- " ATAGTGCACA... len=122 score=0.5,\n",
- " ACAGTGCCTG... len=964 score=0.5,\n",
- " TGGGTGTCTG... len=22520 score=0.5,\n",
- " TGGGTGTCTG... len=140 score=0.5,\n",
- " ATAGTGCACA... len=122 score=0.5,\n",
- " ACAGTGCCTG... len=138 score=0.5,\n",
- " CCTCGGGGGA... len=309 score=0.5,\n",
- " AGGGAGGCCC... len=22505 score=0.5,\n",
- " AGGGAGGCCC... len=125 score=0.5,\n",
- " TCAATCAAAG... len=128 score=0.5,\n",
- " ACAGTGCCTG... len=957 score=0.5,\n",
- " ACAGCGATGG... len=13578 score=0.5,\n",
- " ACAGCGATGG... len=113 score=0.5,\n",
- " ATAGTGCACA... len=122 score=0.5,\n",
- " AAATAATCAC... len=95 score=0.5,\n",
- " AATTGGCTCA... len=1197 score=0.5,\n",
- " CCACAAGGGA... len=22517 score=0.5,\n",
- " CCACAAGGGA... len=130 score=0.5,\n",
- " ACAGTGCCTG... len=964 score=0.5,\n",
- " GGGAGAGGAG... len=12662 score=0.5,\n",
- " GGGAGAGGAG... len=12662 score=0.5,\n",
- " GGGAGAGGAG... len=322 score=0.5,\n",
- " TACACGGAGC... len=34 score=0.5,\n",
- " TGTCTCCACA... len=236 score=0.5,\n",
- " TTTATCCTGA... len=100 score=0.5,\n",
- " GGTCTTGAAT... len=695 score=0.5,\n",
- " TTACTGGAGT... len=12636 score=0.5,\n",
- " TTACTGGAGT... len=581 score=0.5,\n",
- " TACACGGAGC... len=34 score=0.5,\n",
- " TGTCTCCACA... len=236 score=0.5,\n",
- " TCAGATAAAT... len=427 score=0.5,\n",
- " TTTATCCTGA... len=100 score=0.5,\n",
- " GGTCTTGAAT... len=693 score=0.5,\n",
- " GCAGTGTGTT... len=12645 score=0.5,\n",
- " GCAGTGTGTT... len=307 score=0.5,\n",
- " TACACGGAGC... len=34 score=0.5,\n",
- " TGTCTCCACA... len=236 score=0.5,\n",
- " CCTGAGACCG... len=133 score=0.5,\n",
- " TTTATCCTGA... len=100 score=0.5,\n",
- " GGTCTTGAAT... len=693 score=0.5,\n",
- " GCAGTGTGTT... len=12645 score=0.5,\n",
- " GCAGTGTGTT... len=307 score=0.5,\n",
- " TACACGGAGC... len=34 score=0.5,\n",
- " TGTCTCCACA... len=236 score=0.5,\n",
- " TCAGATAAAT... len=427 score=0.5,\n",
- " TTTATCCTGA... len=100 score=0.5,\n",
- " GGTCTTGAAT... len=693 score=0.5,\n",
- " GTGTCTCCAC... len=8378 score=0.5,\n",
- " GTGTCTCCAC... len=237 score=0.5,\n",
- " GCATTAGTTC... len=311 score=0.5,\n",
- " TTTATCCTGA... len=100 score=0.5,\n",
- " GGTCTTGAAT... len=695 score=0.5,\n",
- " GCATTTTTCT... len=4800 score=0.5,\n",
- " GCATTTTTCT... len=551 score=0.5,\n",
- " TACACGGAGC... len=34 score=0.5,\n",
- " TGTCTCCACA... len=236 score=0.5,\n",
- " GCCTTCTTCC... len=159 score=0.5,\n",
- " CCATTATGCC... len=5967 score=0.5,\n",
- " CCATTATGCC... len=210 score=0.5,\n",
- " TACACGGAGC... len=34 score=0.5,\n",
- " TGTCTCCACA... len=236 score=0.5,\n",
- " ACCCCCCATT... len=285 score=0.5,\n",
- " TACACGGAGC... len=9134 score=0.5,\n",
- " TACACGGAGC... len=34 score=0.5,\n",
- " TGTCTCCACA... len=236 score=0.5,\n",
- " GCATTAGTTC... len=311 score=0.5,\n",
- " GGTCTTGAAT... len=693 score=0.5,\n",
- " AGGCATTTTT... len=6028 score=0.5,\n",
- " AGGCATTTTT... len=270 score=0.5,\n",
- " TACACGGAGC... len=34 score=0.5,\n",
- " TGTCTCCACA... len=236 score=0.5,\n",
- " TTCTCTCCAT... len=309 score=0.5,\n",
- " CCAGCGCAAT... len=4785 score=0.5,\n",
- " CCAGCGCAAT... len=253 score=0.5,\n",
- " TACACGGAGC... len=34 score=0.5,\n",
- " TGTCTCCACA... len=236 score=0.5,\n",
- " GCCTTCTTCC... len=159 score=0.5,\n",
- " CCATTATGCC... len=12548 score=0.5,\n",
- " CCATTATGCC... len=210 score=0.5,\n",
- " TACACGGAGC... len=34 score=0.5,\n",
- " TGTCTCCACA... len=236 score=0.5,\n",
- " GCATTAGTTC... len=311 score=0.5,\n",
- " TTTATCCTGA... len=100 score=0.5,\n",
- " GGTCTTGAAT... len=693 score=0.5,\n",
- " ACCAGCGCAA... len=12592 score=0.5,\n",
- " ACCAGCGCAA... len=537 score=0.5,\n",
- " TACACGGAGC... len=34 score=0.5,\n",
- " TGTCTCCACA... len=236 score=0.5,\n",
- " TTTATCCTGA... len=100 score=0.5,\n",
- " GGTCTTGAAT... len=693 score=0.5,\n",
- " CTCTTAACCA... len=6017 score=0.5,\n",
- " CTCTTAACCA... len=543 score=0.5,\n",
- " TACACGGAGC... len=34 score=0.5,\n",
- " TGTCTCCACA... len=236 score=0.5,\n",
- " TTCTCTCCAT... len=308 score=0.5,\n",
- " TAATAATCAC... len=162 score=0.5,\n",
- " TAATAATCAC... len=162 score=0.5,\n",
- " TAATAATCAC... len=162 score=0.5,\n",
- " TGCCCCAACT... len=206 score=0.5,\n",
- " TGCCCCAACT... len=206 score=0.5,\n",
- " TGCCCCAACT... len=206 score=0.5,\n",
- " TGGCACATGC... len=681 score=0.5,\n",
- " TGGCACATGC... len=681 score=0.5,\n",
- " TGGCACATGC... len=681 score=0.5,\n",
- " TTATGTCAGG... len=4440 score=0.5,\n",
- " TTATGTCAGG... len=4440 score=0.5,\n",
- " ATCAAACACC... len=166 score=0.5,\n",
- " TATCTTCATC... len=47 score=0.5,\n",
- " TGTAATCCCA... len=122 score=0.5,\n",
- " TTATGTCAGG... len=110 score=0.5,\n",
- " CCCTTTGCTG... len=79552 score=0.5,\n",
- " CCCTTTGCTG... len=53824 score=0.5,\n",
- " CCCTTTGCTG... len=57 score=0.5,\n",
- " TGTGTGATGC... len=291 score=0.5,\n",
- " TGATGGCTCC... len=114 score=0.5,\n",
- " TG... len=2 score=0.5,\n",
- " GGAGCGGTGC... len=146 score=0.5,\n",
- " GGAGCGGTGC... len=146 score=0.5,\n",
- " CTCCATCGAC... len=70 score=0.5,\n",
- " CTCCATCGAC... len=70 score=0.5,\n",
- " CCCTTTGCTG... len=57 score=0.5,\n",
- " TGTGTGATGC... len=176 score=0.5,\n",
- " ACGGGCGGGC... len=38067 score=0.5,\n",
- " ACGGGCGGGC... len=203 score=0.5,\n",
- " TGGAAGAGCC... len=42 score=0.5,\n",
- " TG... len=2 score=0.5,\n",
- " GGAGCGGTGC... len=146 score=0.5,\n",
- " GGAGCGGTGC... len=146 score=0.5,\n",
- " CTCCATCGAC... len=244 score=0.5,\n",
- " CTCCATCGAC... len=244 score=0.5,\n",
- " GGCTGAAGCA... len=128 score=0.5,\n",
- " GGCTGAAGCA... len=128 score=0.5,\n",
- " AAGCGGACAC... len=170 score=0.5,\n",
- " AAGCGGACAC... len=170 score=0.5,\n",
- " TGGCGGGTGT... len=93 score=0.5,\n",
- " TGGCGGGTGT... len=93 score=0.5,\n",
- " CTTCACCAAC... len=203 score=0.5,\n",
- " CTTCACCAAC... len=203 score=0.5,\n",
- " GGACTGCTGG... len=120 score=0.5,\n",
- " GGACTGCTGG... len=120 score=0.5,\n",
- " TACCCAGTGA... len=171 score=0.5,\n",
- " TACCCAGTGA... len=171 score=0.5,\n",
- " GGAAGAAGCT... len=107 score=0.5,\n",
- " GGAAGAAGCT... len=107 score=0.5,\n",
- " CATCCACCAA... len=143 score=0.5,\n",
- " CATCCACCAA... len=143 score=0.5,\n",
- " GCAAGGCTGA... len=92 score=0.5,\n",
- " GCAAGGCTGA... len=92 score=0.5,\n",
- " AGAAGGGCAG... len=82 score=0.5,\n",
- " AGAAGGGCAG... len=82 score=0.5,\n",
- " GCGACCCGGC... len=97 score=0.5,\n",
- " GCGACCCGGC... len=97 score=0.5,\n",
- " GGCGTCCAGC... len=182 score=0.5,\n",
- " GGCGTCCAGC... len=182 score=0.5,\n",
- " TGCCCTGAAC... len=107 score=0.5,\n",
- " TGCCCTGAAC... len=107 score=0.5,\n",
- " CGTGTTCAAC... len=124 score=0.5,\n",
- " CGTGTTCAAC... len=124 score=0.5,\n",
- " TCATCGACCC... len=84 score=0.5,\n",
- " TCATCGACCC... len=84 score=0.5,\n",
- " GTTCAACCCC... len=146 score=0.5,\n",
- " GTTCAACCCC... len=146 score=0.5,\n",
- " CTACAGACAC... len=79 score=0.5,\n",
- " CTACAGACAC... len=79 score=0.5,\n",
- " TCAAGCAGGC... len=798 score=0.5,\n",
- " TCAAGCAGGC... len=798 score=0.5,\n",
- " TAGGAACTGA... len=1909 score=0.5,\n",
- " TAGGAAC... len=7 score=0.5,\n",
- " GA... len=2 score=0.5,\n",
- " ACGGGCGGGC... len=160 score=0.5,\n",
- " AGCGGCGAGT... len=1898 score=0.5,\n",
- " CGGCTGCGTC... len=29210 score=0.5,\n",
- " CGGCTGCGTC... len=397 score=0.5,\n",
- " TGTCTGGTCC... len=123 score=0.5,\n",
- " TG... len=2 score=0.5,\n",
- " GGAGCGGTGC... len=146 score=0.5,\n",
- " GGAGCGGTGC... len=146 score=0.5,\n",
- " CTCCATCGAC... len=244 score=0.5,\n",
- " CTCCATCGAC... len=244 score=0.5,\n",
- " GGCTGAAGCA... len=128 score=0.5,\n",
- " GGCTGAAGCA... len=128 score=0.5,\n",
- " AAGCGGACAC... len=170 score=0.5,\n",
- " AAGCGGACAC... len=170 score=0.5,\n",
- " TGGCGGGTGT... len=93 score=0.5,\n",
- " TGGCGGGTGT... len=93 score=0.5,\n",
- " CTTCACCAAC... len=203 score=0.5,\n",
- " CTTCACCAAC... len=203 score=0.5,\n",
- " GGACTGCTGG... len=120 score=0.5,\n",
- " GGACTGCTGG... len=120 score=0.5,\n",
- " TACCCAGTGA... len=171 score=0.5,\n",
- " TACCCAGTGA... len=171 score=0.5,\n",
- " GGAAGAAGCT... len=107 score=0.5,\n",
- " GGAAGAAGCT... len=107 score=0.5,\n",
- " CATCCACCAA... len=143 score=0.5,\n",
- " CATCCACCAA... len=143 score=0.5,\n",
- " GCAAGGCTGA... len=92 score=0.5,\n",
- " GCAAGGCTGA... len=92 score=0.5,\n",
- " AGAAGGGCAG... len=82 score=0.5,\n",
- " AGAAGGGCAG... len=82 score=0.5,\n",
- " GCGACCCGGC... len=97 score=0.5,\n",
- " GCGACCCGGC... len=97 score=0.5,\n",
- " GGCGTCCAGC... len=182 score=0.5,\n",
- " GGCGTCCAGC... len=182 score=0.5,\n",
- " TGCCCTGAAC... len=107 score=0.5,\n",
- " TGCCCTGAAC... len=107 score=0.5,\n",
- " CGTGTTCAAC... len=124 score=0.5,\n",
- " CGTGTTCAAC... len=124 score=0.5,\n",
- " TCATCGACCC... len=84 score=0.5,\n",
- " TCATCGACCC... len=84 score=0.5,\n",
- " GTTCAACCCC... len=146 score=0.5,\n",
- " GTTCAACCCC... len=146 score=0.5,\n",
- " CTACAGACAC... len=79 score=0.5,\n",
- " CTACAGACAC... len=79 score=0.5,\n",
- " TCAAGCAGGC... len=297 score=0.5,\n",
- " TCAAGCAGGC... len=297 score=0.5,\n",
- " CACCCGCCCC... len=1603 score=0.5,\n",
- " CACCCGCCCC... len=1288 score=0.5,\n",
- " GA... len=2 score=0.5,\n",
- " CGGCTGCGTC... len=273 score=0.5,\n",
- " CGTCAGTGGT... len=311 score=0.5,\n",
- " ACAGGGAACG... len=26440 score=0.5,\n",
- " ACAGGGAACG... len=888 score=0.5,\n",
- " GGCTGAAGCA... len=128 score=0.5,\n",
- " AAGCGGACAC... len=170 score=0.5,\n",
- " TGGCGGGTGT... len=93 score=0.5,\n",
- " CTTCACCAAC... len=203 score=0.5,\n",
- " GGACTGCTGG... len=120 score=0.5,\n",
- " TACCCAGTGA... len=171 score=0.5,\n",
- " GGAAGAAGCT... len=107 score=0.5,\n",
- " CATCCACCAA... len=143 score=0.5,\n",
- " GCAAGGCTGA... len=92 score=0.5,\n",
- " AGAAGGGCAG... len=82 score=0.5,\n",
- " GCGACCCGGC... len=97 score=0.5,\n",
- " GGCGTCCAGC... len=182 score=0.5,\n",
- " TGCCCTGAAC... len=107 score=0.5,\n",
- " CGTGTTCAAC... len=124 score=0.5,\n",
- " TCATCGACCC... len=84 score=0.5,\n",
- " GTTCAACCCC... len=146 score=0.5,\n",
- " CTACAGACAC... len=79 score=0.5,\n",
- " TCAAGCAGGC... len=3418 score=0.5,\n",
- " GCGCGCACCT... len=25388 score=0.5,\n",
- " GCGCGCACCT... len=90 score=0.5,\n",
- " GCGCGCACCT... len=90 score=0.5,\n",
- " GGCTGAAGCA... len=128 score=0.5,\n",
- " GGCTGAAGCA... len=128 score=0.5,\n",
- " AAGCGGACAC... len=170 score=0.5,\n",
- " AAGCGGACAC... len=170 score=0.5,\n",
- " TGGCGGGTGT... len=93 score=0.5,\n",
- " TGGCGGGTGT... len=93 score=0.5,\n",
- " CTTCACCAAC... len=203 score=0.5,\n",
- " CTTCACCAAC... len=203 score=0.5,\n",
- " GGACTGCTGG... len=120 score=0.5,\n",
- " GGACTGCTGG... len=120 score=0.5,\n",
- " TACCCAGTGA... len=171 score=0.5,\n",
- " TACCCAGTGA... len=171 score=0.5,\n",
- " GGAAGAAGCT... len=107 score=0.5,\n",
- " GGAAGAAGCT... len=107 score=0.5,\n",
- " CATCCACCAA... len=143 score=0.5,\n",
- " CATCCACCAA... len=143 score=0.5,\n",
- " GCAAGGCTGA... len=92 score=0.5,\n",
- " GCAAGGCTGA... len=92 score=0.5,\n",
- " AGAAGGGCAG... len=82 score=0.5,\n",
- " AGAAGGGCAG... len=82 score=0.5,\n",
- " GCGACCCGGC... len=97 score=0.5,\n",
- " GCGACCCGGC... len=97 score=0.5,\n",
- " GGCGTCCAGC... len=182 score=0.5,\n",
- " GGCGTCCAGC... len=182 score=0.5,\n",
- " CGTGTTCAAC... len=124 score=0.5,\n",
- " CGTGTTCAAC... len=124 score=0.5,\n",
- " TCATCGACCC... len=84 score=0.5,\n",
- " TCATCGACCC... len=84 score=0.5,\n",
- " GTTCAACCCC... len=146 score=0.5,\n",
- " GTTCAACCCC... len=146 score=0.5,\n",
- " CTACAGACAC... len=79 score=0.5,\n",
- " CTACAGACAC... len=79 score=0.5,\n",
- " TCAAGCAGGC... len=297 score=0.5,\n",
- " TCAAGCAGGC... len=297 score=0.5,\n",
- " CACCCGCCCC... len=1354 score=0.5,\n",
- " CACCCGCCCC... len=1288 score=0.5,\n",
- " GA... len=2 score=0.5,\n",
- " CGTCAGTGGT... len=62 score=0.5,\n",
- " TGGGGGAACC... len=7746 score=0.5,\n",
- " TGGGGGAACC... len=865 score=0.5,\n",
- " TCATCGACCC... len=84 score=0.5,\n",
- " GTTCAACCCC... len=146 score=0.5,\n",
- " CTACAGACAC... len=5887 score=0.5,\n",
- " GTGGGGGCCA... len=6881 score=0.5,\n",
- " GTGGGGGCCA... len=181 score=0.5,\n",
- " GTTCAACCCC... len=146 score=0.5,\n",
- " CTACAGACAC... len=79 score=0.5,\n",
- " TCAAGCAGGC... len=297 score=0.5,\n",
- " TAGGAACTGA... len=26 score=0.5,\n",
- " CACCCGCCCC... len=1606 score=0.5,\n",
- " TCCTTTGCTC... len=29243 score=0.5,\n",
- " TCCTTTGCTC... len=423 score=0.5,\n",
- " TGTCTGGTCC... len=123 score=0.5,\n",
- " TG... len=2 score=0.5,\n",
- " GGAGCGGTGC... len=146 score=0.5,\n",
- " GGAGCGGTGC... len=146 score=0.5,\n",
- " CTCCATCGAC... len=243 score=0.5,\n",
- " CTCCATCGAC... len=243 score=0.5,\n",
- " TGGCTGAAGC... len=129 score=0.5,\n",
- " TGGCTGAAGC... len=129 score=0.5,\n",
- " AAGCGGACAC... len=170 score=0.5,\n",
- " AAGCGGACAC... len=170 score=0.5,\n",
- " TGGCGGGTGT... len=93 score=0.5,\n",
- " TGGCGGGTGT... len=93 score=0.5,\n",
- " CTTCACCAAC... len=203 score=0.5,\n",
- " CTTCACCAAC... len=203 score=0.5,\n",
- " GGACTGCTGG... len=120 score=0.5,\n",
- " GGACTGCTGG... len=120 score=0.5,\n",
- " TACCCAGTGA... len=171 score=0.5,\n",
- " TACCCAGTGA... len=171 score=0.5,\n",
- " GGAAGAAGCT... len=107 score=0.5,\n",
- " GGAAGAAGCT... len=107 score=0.5,\n",
- " CATCCACCAA... len=143 score=0.5,\n",
- " CATCCACCAA... len=143 score=0.5,\n",
- " GCAAGGCTGA... len=92 score=0.5,\n",
- " GCAAGGCTGA... len=92 score=0.5,\n",
- " AGAAGGGCAG... len=82 score=0.5,\n",
- " AGAAGGGCAG... len=82 score=0.5,\n",
- " GCGACCCGGC... len=97 score=0.5,\n",
- " GCGACCCGGC... len=97 score=0.5,\n",
- " GGCGTCCAGC... len=182 score=0.5,\n",
- " GGCGTCCAGC... len=182 score=0.5,\n",
- " TGCCCTGAAC... len=107 score=0.5,\n",
- " TGCCCTGAAC... len=107 score=0.5,\n",
- " CGTGTTCAAC... len=124 score=0.5,\n",
- " CGTGTTCAAC... len=124 score=0.5,\n",
- " TCATCGACCC... len=84 score=0.5,\n",
- " TCATCGACCC... len=84 score=0.5,\n",
- " GTTCAACCCC... len=146 score=0.5,\n",
- " GTTCAACCCC... len=146 score=0.5,\n",
- " CTACAGACAC... len=79 score=0.5,\n",
- " CTACAGACAC... len=79 score=0.5,\n",
- " TCAAGCAGGC... len=297 score=0.5,\n",
- " TCAAGCAGGC... len=297 score=0.5,\n",
- " CACCCGCCCC... len=1610 score=0.5,\n",
- " CACCCGCCCC... len=1288 score=0.5,\n",
- " GA... len=2 score=0.5,\n",
- " TCCTTTGCTC... len=299 score=0.5,\n",
- " CGTCAGTGGT... len=318 score=0.5,\n",
- " TTTACCTCTG... len=9344 score=0.5,\n",
- " TTTACCTCTG... len=9344 score=0.5,\n",
- " CTCTGTGTCC... len=191 score=0.5,\n",
- " TGCTTCTGAA... len=135 score=0.5,\n",
- " TTTACCTCTG... len=135 score=0.5,\n",
- " CACAGAAGTC... len=76638 score=0.5,\n",
- " CACAGAAGTC... len=76638 score=0.5,\n",
- " CACAGAAGTC... len=177 score=0.5,\n",
- " CAATACTGAA... len=842 score=0.5]"
- ]
- },
- "execution_count": 4,
- "metadata": {},
- "output_type": "execute_result"
- }
- ],
- "source": [
- "cdna_gen.prime_sites"
- ]
- },
- {
- "cell_type": "code",
- "execution_count": null,
- "id": "871cd34d-3291-446e-8173-7b444d768865",
- "metadata": {},
- "outputs": [],
- "source": []
- }
- ],
- "metadata": {
- "kernelspec": {
- "display_name": "Python 3 (ipykernel)",
- "language": "python",
- "name": "python3"
- },
- "language_info": {
- "codemirror_mode": {
- "name": "ipython",
- "version": 3
- },
- "file_extension": ".py",
- "mimetype": "text/x-python",
- "name": "python",
- "nbconvert_exporter": "python",
- "pygments_lexer": "ipython3",
- "version": "3.9.13"
- }
- },
- "nbformat": 4,
- "nbformat_minor": 5
-}
diff --git a/.ipynb_checkpoints/copy_numbers-checkpoint.csv b/.ipynb_checkpoints/copy_numbers-checkpoint.csv
deleted file mode 100644
index e69de29..0000000
--
GitLab