Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NC_045038
Parameters: 2 7 7 80 10 50 500
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 500
Length: 607282
ACGTcount: A:0.27, C:0.23, G:0.23, T:0.28
Found at i:32429 original size:20 final size:20
Alignment explanation
Indices: 32401--32440 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
32391 CATATTAAAG
*
32401 AGTGAAATTCCAGTTTCTCT
1 AGTGAAATTACAGTTTCTCT
* *
32421 AGTGGAATTAGAGTTTCTCT
1 AGTGAAATTACAGTTTCTCT
32441 CTTCCTAAAC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.25, C:0.15, G:0.20, T:0.40
Consensus pattern (20 bp):
AGTGAAATTACAGTTTCTCT
Left flanking sequence: Indices 31901 -- 32400
TTGATTCCTAACCTTCAGCGGAGTTAGGAATTCAAGGTCTAAGTAGAAGCTTCACCTCCGACCTG
TGCTATCCATTCTAGTCTAGTGCGCCTAGGACTGTGAAGACTGAAGCTAAGTACTGCTTTACGGA
ATGCAGCAGTTCACTTTCTAACATATACAAGCTAGCGCTTTCTTACTAACAACGTATTCAGGAAT
AGCCTTTACTAAAATAAAGGCTTCTAGAAAGCGCTTTAACGATATCTCTTTCGGACCCTCTTCTT
TCTCTCTGCGCGGAGGCTAGCGCATCTTTCACAGGGAACAGTCTTATAGGGAAGACAATAAGATT
CCTAGGCTTGAAAGTGGAAGTAGCAATCCCTCTTTCAAGGTCTTTCTATCTTGCCTCATTCCCGG
GAAAATCAATCTCCTCGTTGGGAGGTAGGTTCGGGTATGGTACTACGCTTCTTGACACATGTCAT
GCTGGATTTGAAGGAATAGAAATGAAAGTTGAATTCATATTAAAG
Right flanking sequence: Indices 32441 -- 32940
CTTCCTAAACTAGAAATACATGCTTGTAGGCTTTCTTTCCCCATATCTTCCCGAGTAGTGTACCG
TCCGGTCCCTACCACTACTTCCTTTACTTCGATCCGGAATTCCCCTGAACCAGGGGATTCTCTTC
GCTTTCAGGCCAATCAATCCGTCTATAAATAACAGTTATGAAACAGCCTTCTTCTACTCTATAGT
TTAGAAGTGGAATCATTGGTTCTCGGGAAAGAACCCCGCTTTTCAATTCCTTCTTGTGTTTGGGA
GTAGAAGAGCGAAGGCTTGTTTGTGGCCAGAGTTTCCTCGTTATGCGTTGGACAGCAACAATAAG
CTGATTACGGGATGGAGCCTTGATTGGTTTCAGGACCGTATAGGCCGATGGTTGCCCTCCTGTGA
GGAGTTTAAGATCCCTCCTATTCCGGGTAGACTCGGGGCTTCGTTAGAAGGTGGCGGCAAGCGCC
GTATATTCGCCATTGGGAACTACGTTAATCAGAGGTTGTTACACC
Found at i:36076 original size:13 final size:13
Alignment explanation
Indices: 36058--36084 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
36048 GAGTGCTTTG
36058 AATTAATAGCATC
1 AATTAATAGCATC
36071 AATTAATAGCATC
1 AATTAATAGCATC
36084 A
1 A
36085 CTTCTACCAC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.48, C:0.15, G:0.07, T:0.30
Consensus pattern (13 bp):
AATTAATAGCATC
Left flanking sequence: Indices 35558 -- 36057
TCGCAATGAACAAAATGAGACGTTTGCTTGCTTCACCGCCAACAAAGAGGCCCACTAGGATGCTC
TCTTGGATTGGGTGTGGGATAGGATGCCTATACATCCACTTTCATAGCATAGCTGGTTCATTGAT
AGCAGTTGTATGGCTTTTCTAGCAGCTTTCTATATAATATAGTATAGGAGGCTAACTATAGAGCA
GTTATATTACTTTCATAGCGTTTAGTAGTTGTAGGGATAGGTAGCTACAAGTAGTGCTTGAATGG
GAAGACTCTCTTGACTTCTTTTCTTTCAATAAGGAGTGCTTGAAACATAGCTAACCCTTCTTAAG
GCAAGAGTGCTTGAAGAGAAAGCTACCCAAAGGAGAAGCAGTATACGAAAGGTCTAAGTCTTACA
TAGTTGTCTTTGTCTCCTTGGTACCCCTCCCTCTTATTCTTATTCTTCCTCTGTAATAGCTGCCT
CGCTAGCGAAGAGTCTTCCAAGCCCTGAGCGCGCTGAGTGCTTTG
Right flanking sequence: Indices 36085 -- 36584
CTTCTACCACTTGCATAGCATATCGGTAGTAGCTACAAGACAAAAAACTAACTCAAGAACGCAAG
AGAAGTGCTTTTAAAATGGTAGAGCTAGAAGAAAGCATCTACTAAGCTAACCATCTAATCTAAGC
AGTAGTATCTCAACTCAAGGAATAGCTTTCCCGCAAGAGGAAAGAGCATCTATCTACACAGTTAG
CTGCCCCTACTTTACTTTGGGCTATTGCCTTAGCTAGGTTGGCTCCTAGGCTAAAGCAACTGTAC
AACAGGCGATGCCTCGCAGCATGGAATGTTCTTTCTTCTTCCTCTGGGCTCTGGAATGGAAGAAT
TGGTTCAGCATCAACCCCGGGATTCTTTCCCCGACTACAAGAAAAGAAAGCCTTGCTTGCTTCTA
ATTTCGTTTGGCATTCTAAGGAGAAACTTCCCCGTAGGCTCGATTCGGTTCCATCCTAAACCTTC
TATCCTACGTCTTATCACTCGGAATCGCATTCTATCACACTGGTG
Found at i:42181 original size:29 final size:29
Alignment explanation
Indices: 42139--42204 Score: 132
Period size: 29 Copynumber: 2.3 Consensus size: 29
42129 TGTCTTACTT
42139 CCTGGCCCTATCAGACCAGTGACTAAATA
1 CCTGGCCCTATCAGACCAGTGACTAAATA
42168 CCTGGCCCTATCAGACCAGTGACTAAATA
1 CCTGGCCCTATCAGACCAGTGACTAAATA
42197 CCTGGCCC
1 CCTGGCCC
42205 GGCTTTGACT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 37 1.00
ACGTcount: A:0.27, C:0.35, G:0.18, T:0.20
Consensus pattern (29 bp):
CCTGGCCCTATCAGACCAGTGACTAAATA
Left flanking sequence: Indices 41639 -- 42138
TAAATTCCATGTCAAATTAAATGGAAGATTTAATTATACCTACTTATTGATATTACGGCTGCTTT
CTTTCAAAAAAAGATAGCTACTACTCCGAGTTAGTACTCTACTCCTAGTAAAGGAAAGACTACTG
ACCTTATTCGTGAACTTAATGGGATTGATTAGGTAGGCTATAGCCCACACCACTATTCTATGGGC
TAGGCGATTCCTCTTCTATTCTAGAGGATAACTAGTCTAGACCTGGGAAAGCCTTAAAGGGAAGC
TTACTTATTCGTCTTCCCCTTCTAGAAAACTATTCTAGAGGCTTCCTCTTATAGGAAACACTATT
CTCTAGTCTTATTACTAGTCTTGAACAGGTAAAGCCTTAAAAGCTTCCTTTGGGTGATCAAAGAT
GAGAATCAAGGCTACTCGCCCCCCTATTACTAATGTATTAGGGGTCCTATTACTATTAGAAAGAA
GGATGACTGTTACTGTATGTCCCTTAACTAAATAATGTCTTACTT
Right flanking sequence: Indices 42205 -- 42704
GGCTTTGACTACTGACTTTCCTTACTGCAATAAGCCCAGGACCTTCAGTCTTGCGGTGTGGCCCT
TCAGAGGTATTCTATGAATAGTGAACAGACAATTCACCTCCCTTTCCGGTCTCACTTCACCACTC
TGGCATTCCTAGGCGTATTCCTTCTTTTCATCGTAAGATGATAAGTAGGAGGGGCGAAACTGCGG
ATCAACTGGTTCGCTTTTCCTCTTTTTTCTATTTCGATGTTTTCGTTATCCAAGTTTATTATTCT
TAGAAAGAAAGGACGATTTGGGTACGATTCTATCGTGAAGAGGCCGTCCTCTGTCCCTGAAGATC
TATTTAACGATCTCATACAGGTATTTCTAGATTAGTTGAAAGGTATGTTCCCGGGGCTCTTAGCC
TTATGTTTACAGGTAGATCTCTTAGGACTGGTATGACTCTTATACACGTAGTATTGAAGAAAGAG
GGCTATAAATTCCTTAGGTTATCCCAAAGGCAACCTTCTTACTGG
Found at i:49407 original size:25 final size:27
Alignment explanation
Indices: 49364--49421 Score: 66
Period size: 25 Copynumber: 2.2 Consensus size: 27
49354 AGTGAATCGT
*
49364 AAGGCCTCCAAATAGTTG-ACCAGC-A
1 AAGGCCTCCAAATACTTGAACCAGCGA
* * *
49389 AAGGCCTCCCATTACTTGAACCGGCGA
1 AAGGCCTCCAAATACTTGAACCAGCGA
49416 AAGGCC
1 AAGGCC
49422 CCTCTTAGCA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
25 15 0.56
26 5 0.19
27 7 0.26
ACGTcount: A:0.31, C:0.31, G:0.22, T:0.16
Consensus pattern (27 bp):
AAGGCCTCCAAATACTTGAACCAGCGA
Left flanking sequence: Indices 48864 -- 49363
ACTTCGTTCTGTACGGGATAAGGAGCGAAAAGCGCAGCATGGCAATCGGAGACAAGTAAAGTTCA
GTAATAAATTGGATAGATAGATTCGTGAGTAGTGTAATCATAGAGGATAAGGTGACAGGATTGGT
AATCTACTCTTCATGGGTACCGGAGATCGTCTCCTCGGCTGTTAGGTTAAGTGTTCATCGTCACT
TGAGTACAAGTACATGATGGTCGTCCTATGAGTGAATGCGCTTCAGTCTAAGGTCAAAATTGCTT
GAGCTGATAAAGTTGTAAGGCTGAAGTACCCAAGCCTAGGGTTTAAGCGGATGCCCCAAGGCTCT
CTTCGTAATGGCTGGTGGCAACGCTAATGGATTGGACGACAGGTACGATAAGCTCACTGCCAGGA
TATAACCATTCTTGTCCCGAAGAAAAGCAGATGTTGATGACTCCGAGATAGATGACCGGATCGGC
AACGGACGTTGACGAGCAAGATCCCTCTGCCATTGAGTGAATCGT
Right flanking sequence: Indices 49422 -- 49921
CCTCTTAGCAGGATCGTCTTCAGATGTTATCAACGAATCGTCTCTTGCAGGAGTTGTGGAATATA
GTATTTGTCCCGTGAGTGTGAGTGGCTTTTCTCTTTTGGTTGTGGATTGCGTGCAGCTTGACTTC
TTTCTTCCACATAGGCTAGCTTCCTTGCTTGCATGCCTTGTGGCGAACTAGACTGAAAATTTTGT
ATATAAAGAAAAATTCTTTCTTCTTGTGTGATACAAGAAAGACCTCGAGACTGACAAGATGGGTC
CTTTAGGTAATAGATCACTGAAGGAAAGGTTGGTCATAAATTTGGAGAGTTTGCTTCTACACGGA
AACGAAGACTGTCGAGAACAAATATTTAACCGGGAAGAAAAAAGGGGAAAAAGTAAATAAAGTCT
AAGCAGCGCATATGGCACGAAAAGGAAATCCGATTTCGGTAAGACTCGATCTGAATCGTAGTTCA
GATTCAAGTCGGTTCAGTGAGGGCGACCGCGAAAGTCACCGAATG
Found at i:65108 original size:12 final size:12
Alignment explanation
Indices: 65091--65115 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
65081 CCTTATCCTT
65091 ATTATATCAATA
1 ATTATATCAATA
65103 ATTATATCAATA
1 ATTATATCAATA
65115 A
1 A
65116 AGTACTAAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.52, C:0.08, G:0.00, T:0.40
Consensus pattern (12 bp):
ATTATATCAATA
Left flanking sequence: Indices 64591 -- 65090
AGAGCTTACCCGGCGGAGAAAGGCTATTCATAGCGCTTCACACCTTTTGTATCAGCATTGGCGGC
TAAGCCACATTTGCTTTTTTATTTCTAGTCCCTCACCCCAGGTATCAAGTGCGAGGTTATCTTGG
TTTGGGTCTATGCCCATTCGCCTAAGACCATCATTGCCCGCACCTCTTATTCGTATCAGGTTCCA
TCCTCTCTTTCCGGTGGTGCAGTGGGCGAAGTCCTATCAGGGGCATTTTACTTTTTTGGGTTGGA
AGGCCTGGCATTCAATCAAAGCAGCGGAGTCGAAAAAGAAGGTTCGTAGAACCGTACGAGCCCAA
CAAAAAGCACTTTCTTTTATCTAAATAGACGTAGAACTTCCAGTTCTACTTTCTCCATTTTGAGC
TTCTCCGTACATCACCTTCTTCCTTACTTGAGCTTCCTCTGGTCGCCTTCCTTCGGTCTCCTATT
GGAATATCTTGGAAGCTCATAAGCAGTAGTAAACCCCTTATCCTT
Right flanking sequence: Indices 65116 -- 65615
AGTACTAAATAAGAGACTTCTATTTAGAATCTTTTTAGTACACTGAAACTATGTCTTATGGTAAG
CGGACGCCACCTTTCTCGTCGGCGATCACCGTGAGATCTCTTGAGTGGTAATAAAAAAAGGAAAT
GGCACGTATCCTTTCACCAGTACTTCTTCAAAAAATTCCCCCATTGCTCCCTTTGTCACAAGTTC
TAAGAAATCATCAGTAACTATATACTATGTTATGTCGGTTAGTCTGACTTCCTTTTAGGGCACGA
AGGAATAACCAATAGAATCAGGGTGCTCAATCTTCCTCTCACGAGGACAAAAGCATGCTTCGCAA
TCAAGCTAGAAAAAGACTCATCTGCGAAGACTAATAAAGAGAGTCCTTTACTCTAAAGTAAAGAA
TCAGTTTACTACTGCCTTCCTCTCGGGCGCACTTCATTTCTAATCATTCAGTCTGATTTCCATCC
TATCGCTCTTTCTTTAAAAGTAACTTTTACTGACGTCAGAAGATC
Found at i:167654 original size:24 final size:24
Alignment explanation
Indices: 167613--167660 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
167603 TTCGGATTCC
* *
167613 TTACTTGGGGCTGATGAGGATGAG
1 TTACTTCGGGCTCATGAGGATGAG
* *
167637 TTACTTCGGGCTCCTGAGGGTGAG
1 TTACTTCGGGCTCATGAGGATGAG
167661 GAATTTATCC
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.17, C:0.15, G:0.40, T:0.29
Consensus pattern (24 bp):
TTACTTCGGGCTCATGAGGATGAG
Left flanking sequence: Indices 167113 -- 167612
AGTGTGAAATTGTCAGTTTCCTCCTCTTTTTGAGGCTGAGAGATCATATGGGGAAGACAATTCTC
ATTTCTTAGTTACAATAAAGAAGCCCTTCTCAAGGAAGTGAGCCAAGAGCCACTCATCTGAGCCA
GCGGATTCGAATTCAGCTGTGCCGGTGCGCAAAGCAAGCACGCTTAGACTGCGATGTGCAATCTT
TGGTCTGCCTATCATTGTCCATTAAGGGCTGACTCCGCTAGGCAAGAGGACCACTACTGGGATTA
TTTAACTACTAACTGATGACCAGGGGACTACTCTGTCTGCTTTTTCCACTACTGATATTGACTGA
CCTGTTGAGAAGATAGCTGCAAGAAAAAGAAAAGAAGTAGAGTTAGATTGTGTTCTAGTATGTAA
GCATCTCTATCCTTGGTCGATTCGTCTGCTCATTCAGCCTACGATTCTTATCCAATTGCTTCTTC
CGATAAGTCTTATGAAATGAATTCGGCTATAGGCATTCGGATTCC
Right flanking sequence: Indices 167661 -- 168160
GAATTTATCCCTGAAGCCGTTGATCCAGAAAGATAATTACCACCATCAGATGATGACCCCTCAGA
GATAGAAGTCCAAATCCGTTATTTTGACCTTGACCTGCCTCTTCCCCAATGGGCACAAGATGCTA
CAAACTATCATACACGGGCCACTCAAGAGTTCATATCCAATCTGGACTTCTACTTTAGGCAACGG
AATCGTGCAGAGATTCTCTACCGAATCGAACTCAAGCTCCTAGCTAAAGACCACCTGAAAGAGGA
GCGGATCGGAATTAGGCCTGATAATATAGCTTTTCCTTGACGAGCTCATCTCAAAAGTATAGTAA
GATATACGAAAGGAAGAATGTAGAACTGCAAGAAGTCACTTCCAAGGATACAACTGCTGGGATTG
CGAGACTCCCGGAAAGACATGCAAATACATTCGCGCGGCTACAATAGAGTTCTTTTACTGTGTCA
ACCTGCTTAATGAATGGTTTGGGGCTTTCGTTAACAGTCCCTATG
Found at i:175577 original size:16 final size:16
Alignment explanation
Indices: 175556--175590 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
175546 TGCGGATAGC
*
175556 CAATAAAGTTAGTAGT
1 CAATAAAGTAAGTAGT
175572 CAATAAAGTAAGTAGT
1 CAATAAAGTAAGTAGT
175588 CAA
1 CAA
175591 GGATGTTAGG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.49, C:0.09, G:0.17, T:0.26
Consensus pattern (16 bp):
CAATAAAGTAAGTAGT
Left flanking sequence: Indices 175056 -- 175555
CTCCAAGTGGGGATGGAACTCAATAATCTTTCCCTATTAGCTTCTTCCTTAGTTACTCTTTTTCT
TTCCCTAAGGCGGTATAAGAATAAAATAAGTAAGGAAAGCAGGTCCAGAAAGCTTATTATCGTAT
TCCCACGGCCTTTAATCTATTACAGAACTTAGACATCTACATCTTCTAAACTAAGAGTTAGAGAC
ATTAGATAGATATCTTATCTCAGGATAAATAGAAGCTGAAAATACTAAAGGTCTAAATTCCACTA
CTGCGACTGGTACGAAAGCTGGTGGAAATGGAATGGGACTACTGCCACTGAAGAAGATGATCTTG
CTTAATTGAATTGTTTCGTAGACTCGGTTTCCGTTACTGAATCGGATGCTTGAACCCTATTTTAT
TTTATTCGCTTAATTGGAAGAGTCCGCGAGGCAGACCCGGAGAAAGATAAAATAGCCTAAGAGTC
AGTCCTGTGCTTATGGCAGGAGAAGAAGGGAAGTCTGCGGATAGC
Right flanking sequence: Indices 175591 -- 176090
GGATGTTAGGGCCTTTCCTCCTTCCCAATTAGTATCATATAGAGCCATAAATGGGCATTAGGTTC
CGGAGATCTATTTTAGGACGAAGAATAGGATGAAAACTACTATCTACGCTTGATGTTGCCCAACA
GGCTGAAAATAAAAATAAGAAGGATAAGCCTATAACTAGGGGTTCAATCACTTGAAAGTTCCTTC
TATTTTACTCTTTGACTCGCTTTCTTTTCAATAGCTCCAAGTATATTCATAGTACGCTCCCGCTA
CTCATAGAAGTGCCTAGCTCAATGGATAAGGGAGAAGCTTGTAATAAGAGAGAAGACAAGAAAGG
AAGAGGGGTGATCCCCGATGGGCAGAACGATATTAGCAAGTGCCTATACCAGTGACGATTTAGAT
GAAAAGGCGAGTCGGGTTTCACCACATATGTGTAGTATCCGGCCCCGCGCAAACGTAGACTAACT
CTTAAAGAGCGGTTTCCGTACTTATTCATCACTGCCATAGTTCCT
Found at i:241810 original size:8 final size:8
Alignment explanation
Indices: 241797--241829 Score: 57
Period size: 8 Copynumber: 4.1 Consensus size: 8
241787 CCCTTTAGAG
241797 AACAAGCA
1 AACAAGCA
*
241805 AACAAGTA
1 AACAAGCA
241813 AACAAGCA
1 AACAAGCA
241821 AACAAGCA
1 AACAAGCA
241829 A
1 A
241830 CGGACTGAGC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
8 23 1.00
ACGTcount: A:0.64, C:0.21, G:0.12, T:0.03
Consensus pattern (8 bp):
AACAAGCA
Left flanking sequence: Indices 241297 -- 241796
CGCTTTTCGTTTATGAAAAGGGGAAAGGCCTTTTTCAGCTTGCTGCTCGTTTTCTCGCTTCCGAG
AGGCGAAGGGATTGGATTTCACCTATGATCAGATCAGTGGGCAACCATAGTTTACTTTTTTCGTG
GTGTTGTTGAAAGCGAATTTGTAAGTAGGCCTCGCTTTTCGGAGCTGCTCCCAGCTCACACTATG
GTGGAGGAGGTGCCGTGAAGATCTAGGAGTGTGAGCAGTACGAGCTGAAAGGCTCCCATACTGTT
TGGAGGGCAGGGGGCATAGATGCCAAACAAACCTGACCCCTATCTATCGTCGTAGAAGCTGTTCC
TAGGAAAGATTATGGTTCTCGGGTTAAATCTCTATTAATACCAGATACAGGGGAAGCTAAAGCGG
AAATGAAAGAGTAGGGTGAGGGATAAGGGGGGAAGCCACTAAATGGAAGGCTTCGCTCGCTCGCT
CTAACGCTCGTTTAGTAGACAGCGAGTGGAGTGGCCCCTTTAGAG
Right flanking sequence: Indices 241830 -- 242329
CGGACTGAGCGCAGACGCGCGAAAGCCGTAGCCGCGCAGTCGTTTTCTTGCTAGGGGCGAGTACT
ACACGAGCTCGTAAGTCAAGTACGGAACGAGCCTTGTCTACGAAGCAGAGCGACCTCGTCTTGCT
TGCTTCTGGCGAAGCTTCTAGCACTAGATAATAGGAATTTTTTTATGGGATGGGAGGAATAGTAC
TTTTAAGGCCGACCACTACATAGGAGCGATAGCGAAGCCAAGCCGTATAAAGGCGAGCAGCCCTT
ATAGCAAACGGCCTACTTATAGCCCTATTTTTCCTTTCTTCGGGGACTTCAACGACGAGCCTTAC
AAGCGGCAATTCTTCACGTTTTCCTCAGACAGTGGGAATGAATTCTATTACTTGATTGACATTGA
GAGATATTTTTACCACACCGAAAAAGAAATATGCCGATATGCTTGATGTACCAGCCAAGCCAGCT
CGACCGTATACAGTATAAGGGATTCGCCTTTGCCTCAGACAGAAG
Found at i:267053 original size:30 final size:30
Alignment explanation
Indices: 267017--267084 Score: 136
Period size: 30 Copynumber: 2.3 Consensus size: 30
267007 ATAGCATTTC
267017 GTACAGATGGACATATATATATAGTACCAG
1 GTACAGATGGACATATATATATAGTACCAG
267047 GTACAGATGGACATATATATATAGTACCAG
1 GTACAGATGGACATATATATATAGTACCAG
267077 GTACAGAT
1 GTACAGAT
267085 AGAGATTTCA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 38 1.00
ACGTcount: A:0.40, C:0.13, G:0.21, T:0.26
Consensus pattern (30 bp):
GTACAGATGGACATATATATATAGTACCAG
Left flanking sequence: Indices 266517 -- 267016
GCACAGTTGAATCGAGGTATGAAAGGATTGAACCAGAGCCGAGGGTGCACACTGCCTTCTTAACT
GCCAACTCCTTCTTAAGCGCTTTCGGGAAAGGAAGGAGACATTTAAATCAAGAAAGATAAAGGAA
GGGGATGGGATAGTCGCTTACAGAAGGGCAGAGAGATCTTATTCAATGCGATAGAAAGAAGGCTT
GACAAATGGAGCGAGGAGCAGGGGCTTGTCTACCTCGGGCACATCGTTGGAGAAGGACAGTTATC
GACCCAACCAGAGTCAAAGCCATTGTGGACTGGAACAAAACGAGAAATGTGACTGTGACAAGGAA
CAAGAGTAAGTTCCCAGTGGTGAGTAAGGAGTAGGCTTTTAAGGTTAGGGTAACGAGAGAATAGG
GCTGACAGTTACTCATCTTGAGTAAGATAGGGAAAAACCACTTCTTGGACTTGTTTTCTTTCAGA
GTGAAGAACATGGATTGCGGAGGCCGGCGGCACAGATAGCATTTC
Right flanking sequence: Indices 267085 -- 267584
AGAGATTTCACTAGCACCAGTTTTTTACCTATAGCTATAAGCGGGGGAAGCTGAAGCTAGATCTG
TCACGTATGAAGGAAAGAAGGACGTTAGATACCTCTTGGGCGTAGATAGGAGACCTGATCATACT
CTTTACTCTCATCAATAGTGACGTTATGATTGTCGTTATTCTATTCCGATGGATTGACTGGTGCC
CCAAACTCCTCTCTTTGGCTTATATCCATAGTCTGACCCGACCTGCTTTGAATGATTCAAACGAG
CTTTTCACTCGAAAAAGAAGGAGAGTTGAACTTGTTGCATGCATCCTCTACTATGAAAGCTTACC
TGGAATAAGGAATAAAAACCTGATCATCTGCTTTAATTTCGTTTCAAGCATTTTTGAACTCGTTT
AGGGAATTGATTGATCGAGTCCAATCAATGGGGTCTCAGGTAAGCCCCTTCGGGCCCTTTCACTT
TTTTTCAAAGCAGGAACCTCTTCCAATTTCACAGAATATACATAG
Found at i:350674 original size:34 final size:34
Alignment explanation
Indices: 350629--350739 Score: 94
Period size: 34 Copynumber: 3.4 Consensus size: 34
350619 AACTAACCTC
*
350629 GCGCTAGCGCGCTACATCAAGCAAGAAAACGACT
1 GCGCTAACGCGCTACATCAAGCAAGAAAACGACT
* *
350663 GCGCTAACGCGC-AC-TTAA-C-AG-TAA-G--T
1 GCGCTAACGCGCTACATCAAGCAAGAAAACGACT
* * *
350689 TCGCTAACGCGCGCTACACCGAGCAAGAAAACGACT
1 GCGCTAA--CGCGCTACATCAAGCAAGAAAACGACT
350725 GCGCTAACGCGCTAC
1 GCGCTAACGCGCTAC
350740 GGCTTTCGCG
Statistics
Matches: 58, Mismatches: 9, Indels: 20
0.67 0.10 0.23
Matches are distributed among these distances:
26 7 0.12
28 6 0.10
29 4 0.07
30 3 0.05
31 2 0.03
32 5 0.09
33 4 0.07
34 20 0.34
36 7 0.12
ACGTcount: A:0.32, C:0.32, G:0.23, T:0.14
Consensus pattern (34 bp):
GCGCTAACGCGCTACATCAAGCAAGAAAACGACT
Left flanking sequence: Indices 350129 -- 350628
CGACACCGATGGGAATGCATGCTACGAAAGATAGGGTCGAGTCTGATACATCAACCGTCTACTCA
ATATCCTTGTATGAGTCCACAATCACTACACGAGATGAACCTTGGTTTGGTGAATTGAAGTTGGC
CTTAGGTGTAATAGGACTCCCAGTTACTGCGCGCGATCGTATACTGAGGTGCTCCCCGCCGGTTG
TTGGAACGACGCGAGCCGGGCCGGGCCTAAATTCAGAAAGATGAAGGGTCCAAAAGTAAATCAAA
ATAGGGGGTTCAAAATTCCCCATCTCATTGGGGGCGGAAAACGAATCGACATCTCGATGTGATAC
AGCCTTTTCTATTTTAGTTGGGAAAGAACGGCGAAGTCCATCCGAACCGTCCAATGAAGAATAAG
AGGAGAGCAAAGCGCCAATGGCGCGCGAAGCGCATGCGGAACGGGCACGGAGAAAAATGAGTGTG
GAGGATAAGCTTCCAGCTTTATCGCTCCTCTCCTTAACTAACCTC
Right flanking sequence: Indices 350740 -- 351239
GGCTTTCGCGCGTCTGCGCTCAGTCCGTTGCTTGTTAGCTTGTTTACTTGTTTGCTTCTTTCCTT
AGTTTCACACTAAGCTCTTCGATCCTTATTGAAAACGAAAGCGAGTTTCGCTCATTCCCTTCGCT
TCCTGGGCCCAAAGCAGTGCAGTCTTTCCTGGCCAAATCAAGGATTTGGGGCTTCTTGCTACGCT
ACTTAACTATAGAAATCCATTTCTAGTAGTAATATATATGAATAGAAAGATAGATCCATCCATCT
ATCCTATCCGATTTCGATTTTTATATCTAAAAAAGAATCGATTTCATTCAACGTTTGATTCAAAG
AACTGCGCTTAGCCCCCCCGCTCATGAAACGGCTCTGCTGCAATGGATGGCAGAGGGTCCGTAGT
ACCCAAAGCACTGGAGTGGTCCAGTAGCCGGGAAGGGGCCTAGAAGTGCCTACTACTACACCACA
CTACACTTGGCTCTACACATTTACAGAGCTAACCCCTGTCCCTGG
Found at i:414717 original size:29 final size:29
Alignment explanation
Indices: 414675--414742 Score: 136
Period size: 29 Copynumber: 2.3 Consensus size: 29
414665 TCGGTCGAGC
414675 ACTTCGTTCCAGATACTGATCGTATCAGT
1 ACTTCGTTCCAGATACTGATCGTATCAGT
414704 ACTTCGTTCCAGATACTGATCGTATCAGT
1 ACTTCGTTCCAGATACTGATCGTATCAGT
414733 ACTTCGTTCC
1 ACTTCGTTCC
414743 TTACTTTAAC
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 39 1.00
ACGTcount: A:0.22, C:0.26, G:0.16, T:0.35
Consensus pattern (29 bp):
ACTTCGTTCCAGATACTGATCGTATCAGT
Left flanking sequence: Indices 414175 -- 414674
AGAGTTTGGTTACCAAGTTCAGTTACCATAAAAGTGCAACGTACTTAGTGCTTGCACTAAGGTAA
GTATAGAGCTGACTTGTTAAAGTCTGGATTATAGATGCTTACTCGTCAGAGTAAGGTAATTTCTT
ACTTATATATATAATATAAGGAACGAAGAACAGACTTGTTAGAGTCTGGAGAGGTATCATGAAAT
ACTGACTCTTACGAGTGTCTGGGGCGTAGCCACTCGAGTCGTACCTTTTAGCTTAAGTTAGAGTG
AGTAGCCCACGGGTGTGGGATACGAGCGTTCTTCTTACTTATGTAATTTCTGTAAGTGATCGAGG
TAATTTATTACTTAGTACTTGTGCTAAGGTAATAAATTGCTCGAACAAAGTGAGAGGGGCGTAGC
GCTTACGCTAAGGTTAATGGGAAGCGATCGAAGGGGGCAATGGGTACCCGAGTGAGCGTAAACAG
TACGCGGGCTCCTAACTAACTACTAGCTATCCCTTTCGGTCGAGC
Right flanking sequence: Indices 414743 -- 415242
TTACTTTAACAAGTAAGCACTTCTCGATCCTCTCCAACCAGTCGAGCTTCTTCTCTCCCTTTGTT
CGTACCTTACTTTCCCAAGTAAGCATTTCTCTATCCTTAGCGTAAACACGTCGTACTTCATACCG
AAAGGGAGGCCCCTGCTAGCTCCACGCGGGAAGAAGTCTGACAAGTCTCTTATTAGAGCCGGGTA
GCCAAGCTAATCCGATGAGGGGGGCATGCTTTTTCTTTTAGGATGGATGCAACGGAGATGGCAGT
AACGTATTCCTAAAGATGACCGGAGGAGTCAATCGAAATTGAACCTGGAATACTAGACATGCAAC
TCTCAAAAAAGGAATGCAAATAGAAGGATCCGACCATCCATCTTCCTTCCCCAAGAAAGGCGGCA
TTGAGCTAACATCTCCGCGCCCAACTCTTTTGGTTCAACGAAGTACTCCCATTCTCCGACTTTTT
AACTCCCTGGAGGGACAGAGGACACAATAAAAAGCCTTTGGATGT
Found at i:522698 original size:18 final size:18
Alignment explanation
Indices: 522677--522719 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
522667 CAACCTTGTT
522677 GACTATGACAACAG-TCGC
1 GACTATGA-AACAGATCGC
522695 GACTAT-AAACAGACTCGC
1 GACTATGAAACAGA-TCGC
522713 GACTATG
1 GACTATG
522720 GCAGGGCGGT
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
16 5 0.23
17 1 0.05
18 16 0.73
ACGTcount: A:0.35, C:0.26, G:0.21, T:0.19
Consensus pattern (18 bp):
GACTATGAAACAGATCGC
Left flanking sequence: Indices 522177 -- 522676
TACCGTCTAGCCGTTGGTACTCCGCATCTTCACGGAGAATTCAATTTCACCGGGTCCATGTCGGA
GACAGCGGGGCAGTCGTTACACCATTCGTGCAGGTCGCTACTTATGCGACAAGGAATTTCGCTAC
CTTAGGACAGTTAGAGTTACTGCCGCCGTTTACCGGGGCTTCCATTCAAAGCTTATAACACTTCT
CCTTCCGACCTTCCAGCACCGGGCAGGTGTCAGACTCTATACATCGTGTTACCACTTAGCAGAGT
CCTGTGTTTTTAATAAACAGTCGCTACCCCCTGGTATGTGCCGCTTTCCTAATCAAAAGATAGGA
GAGCACCCCTTCTCCCGAAGTTACGGGGTCATTTTGCCGAGTTCCTTCGACATGGTTCTCTCAAG
CGCCCTAGTATACTCTACTTGTTCACCTGTGTCGGTTTGGGGTACGGTCAGTTCACCGGGAGGAT
CGCCCTCCCAATTCGAAGTTTTTTCCTGGAAGTTTCAACCTTGTT
Right flanking sequence: Indices 522720 -- 523219
GCAGGGCGGTACGCTCTGCTCTCTCGCGACCCCTACTCTAATCAAAAGACTAAAGGCCCCTACTG
AAGATTGAAAAGGCGAGCACTGAAATGAGAAAGGCTTGTAGACTCGTGACGCTGAACGACACATT
CTAAAACTAAACACTAGAAAGTGCTTCGAAAGGTGTCAGAGCAGGTGCGCGGAGCCCGGCATGTT
CGCCTGCTGGGCCGAGTGTTCGCCCACTTCAGAGTCTTCGCCTTTAGATAACAAAAAGTGTCCGC
CCCTTACCGCTCCGTGGGGTCGCCAAACTACGACGAGACTTTCTCCTTACTCTAACAAGTAAGCA
AGTAAACTACCTTTTGAAGCGCCAGTCGCGTAGGGCGACCGGGCCAGGCCGAGTCAGAAAGGCTT
TGATGACTCAAGGTTCATATTAGGGAAAGGAGAGTGAGGGGAAGAGGGGGCAGCCCTCGGCCCGA
TCATCCAATTCACTCCAACAGACAGGCATGGTTCTGTAGTCAAAG
Found at i:562801 original size:17 final size:19
Alignment explanation
Indices: 562774--562823 Score: 59
Period size: 19 Copynumber: 2.7 Consensus size: 19
562764 TGAGTCTCCT
562774 TCCCTTTCATTC-GCTTCC
1 TCCCTTTCATTCAGCTTCC
562792 TCCC-TTCATTCAAGCTTCC
1 TCCCTTTCATTC-AGCTTCC
* *
562811 TCTCTTTCTTTCA
1 TCCCTTTCATTCA
562824 TCGGCGAACA
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
17 7 0.26
18 4 0.15
19 10 0.37
20 6 0.22
ACGTcount: A:0.10, C:0.40, G:0.04, T:0.46
Consensus pattern (19 bp):
TCCCTTTCATTCAGCTTCC
Left flanking sequence: Indices 562274 -- 562773
TACCTTGAATGGATCTATTCCCTTAGTCTGTGTGTGCTTACCGTTCTAGCATCATCCCCCTCTCG
CTTAGTTCTAGGTATGAATACATCGAGGCCTTCTGGGAATGATAAAGATGTTATGTATGTGGTTC
TATGGCAAAAGGAAGCAGATATTTGCTTGGCAGTCCCTGGTCGAATCAAAATTGTCGCCCTACAC
GATGAGGGTTGTAATCTACCTCAGGGCGTATTAGGTTTTTATATTTTCTTACCTGATTTTTCATA
ATGCTGCTAGTCAAGTTCGATAAAGAATATAAAATAAAGAATTGACTCTTTCGCAGTGCGGGAGG
ACCTTTTTTTGAATTGAATCTTGAAAGCCTTGTCATAGACTTCGGGGCCTTCCACTTGCTTGACC
CCTGAAAAGAAGGCCTCCAGACATGGAATTGAATGTGAATCTCTTCCGCTGAGATCGGGCTTACT
CTATGCCATCTATCCTTTGCTTTCCTGTTAGCCGTTGAGTCTCCT
Right flanking sequence: Indices 562824 -- 563323
TCGGCGAACAGGTGGGATGCATTGACACGACTCCACCTATTGAATAGAGAGAGGGCCTCTTACTA
ACGAGCGATTCTGGCTTTACATCTCCATGTTGATTTGAATATATCGAAAAAGGCAAAGGCTAATC
CCACAGAATCTTCGGGCTCTCCTCAATCTCACAGGTATCCGTGACCTAATTAATACTGGATTCAG
GGATATATAGCTCTGGTACCTGTGAGACTGGACTTGAAAACTGTGCCGGGGAAGATGAAAACCGA
TGGATGTGTTTACGGGCACTAAGCTATGTATATTCTGTGAAATTGGAAGAGGTTCCTGCTTTGTT
TGGATTAAAAAAAAAAAGGGCCCTTTTGGGCTTACCTGAGACCCCTTTTCTTTTATTGGATTCAA
TCCATTCCATCAAAGGAAAGAGTTCAAAAATGCTTGAAACGAAATGATGCTAAAGCGGATGATCA
GGATTCTAAACCTTCTTCCAGTTAAGTTTTCTTTCATAATAGAGG
Found at i:604423 original size:18 final size:18
Alignment explanation
Indices: 604402--604444 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
604392 CAACCTTGTT
604402 GACTATGACAACAG-TCGC
1 GACTATGA-AACAGATCGC
604420 GACTAT-AAACAGACTCGC
1 GACTATGAAACAGA-TCGC
604438 GACTATG
1 GACTATG
604445 GCAGGGCGGT
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
16 5 0.23
17 1 0.05
18 16 0.73
ACGTcount: A:0.35, C:0.26, G:0.21, T:0.19
Consensus pattern (18 bp):
GACTATGAAACAGATCGC
Left flanking sequence: Indices 603902 -- 604401
TACCGTCTAGCCGTTGGTACTCCGCATCTTCACGGAGAATTCAATTTCACCGGGTCCATGTCGGA
GACAGCGGGGCAGTCGTTACACCATTCGTGCAGGTCGCTACTTATGCGACAAGGAATTTCGCTAC
CTTAGGACAGTTAGAGTTACTGCCGCCGTTTACCGGGGCTTCCATTCAAAGCTTATAACACTTCT
CCTTCCGACCTTCCAGCACCGGGCAGGTGTCAGACTCTATACATCGTGTTACCACTTAGCAGAGT
CCTGTGTTTTTAATAAACAGTCGCTACCCCCTGGTATGTGCCGCTTTCCTAATCAAAAGATAGGA
GAGCACCCCTTCTCCCGAAGTTACGGGGTCATTTTGCCGAGTTCCTTCGACATGGTTCTCTCAAG
CGCCCTAGTATACTCTACTTGTTCACCTGTGTCGGTTTGGGGTACGGTCAGTTCACCGGGAGGAT
CGCCCTCCCAATTCGAAGTTTTTTCCTGGAAGTTTCAACCTTGTT
Right flanking sequence: Indices 604445 -- 604944
GCAGGGCGGTACGCTCTGCTCTCTCGCGACCCCTACTCTAATCAAAAGACTAAAGGCCCCTACTG
AAGATTGAAAAGGCGAGCACTGAAATGAGAAAGGCTTGTAGACTCGTGACGCTGAACGACACATT
CTAAAACTAAACACTAGAAAGTGCTTCGAAAGGTGTCAGAGCAGGTGCGCGGAGCCCGGCATGTT
CGCCTGCTGGGCCGAGTGTTCGCCCACTTCAGAGTCTTCGCCTTTAGATAACAAAAAGTGTCCGC
CCCTTACCGCTCCGTGGGGTCGCCAAACTACGACGAGACTTTCTCCTTACTCTAACAAGTAAGCA
AGTAAACTACCTTTTGAAGCGCCAGTCGCGTAGGGCGACCGGGCCAGGCCGAGTCAGAAAGGCTT
TGATGACTCAAGGTTCATATTAGGGAAAGGAGAGTGAGGGGAAGAGGGGGCAGCCCTCGGCCCGA
TCATCCAATTCACTCCAACAGACAGGCATGGTTCTGTAGTCAAAG
Done.