Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NC_012116
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: 476890
ACGTcount: A:0.28, C:0.23, G:0.22, T:0.27
Found at i:3577 original size:17 final size:17
Alignment explanation
Indices: 3533--3579 Score: 60
Period size: 16 Copynumber: 2.8 Consensus size: 17
3523 GCAGTAAATG
*
3533 GAATGAAACTAAGCAAGA
1 GAATG-AACTAACCAAGA
*
3551 G-ATCAACTAACCAAGA
1 GAATGAACTAACCAAGA
3567 GAATGAACTAACC
1 GAATGAACTAACC
3580 CCAAGGGATG
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
16 12 0.48
17 12 0.48
18 1 0.04
ACGTcount: A:0.51, C:0.19, G:0.17, T:0.13
Consensus pattern (17 bp):
GAATGAACTAACCAAGA
Left flanking sequence: Indices 3033 -- 3532
TCTCTAAGCAGCCAAGGCCAAGAGCAAGCAGGAGTAGTACTATCCGCCTAGAAAGATTCATTCGA
TAAAGAGAATGCGAGTAGGCAGGAGATCAATAGACACAGAAAGAGAAGACCAAAAGGAGCAGAAG
GCACTCAGTTGTTTATGTGAAATAAAGAAGCAGCAGGTTACACTTTTACACTTTCCCGAAGAAAG
CTAAAAGCAAGAAGATGAAAGATGGGATGAGATGCTAGCCTTAGCGCAGAAGATCAATCATTGAG
CCTTAGGCCACTACCGAGCAGCAATGGAGGATCATAACACTTGAGAGATGATCCCTACTGGAAAA
GGCGGAGACAATACCTCTTGTTGCGACAAATCTCATTTAAAAAGCCCATTTATCAATCACATTTT
CAGGCACACCAGTCAAAGAGCCATCGGACCCATGAAAGTCCCCTTTTTTGACTAATATACACGCC
CTTTGCCAGGATGTCTTTCATCAAGCAAAAGAGGGGCAGTAAATG
Right flanking sequence: Indices 3580 -- 4079
CCAAGGGATGATCTCAGATTGAAATCCAAGGCATGGTCTCATTGAAAGTTTAGGGCCAATACAAA
TCAAAAAAAGCATTTTGAAGGGGGTATGATCCCAGGATGGATTGTCAGTAATTGTGGACGAAGCA
GCGGGCATACCAGAAATGGATTGTCAGGAATGGTAGATGGAGCAAGGATGCATAGCAGGCTTAAA
ACACGACAGAAGTAGGACGCACTGAGGCCGAGCTTTCCTCTACTACTCATTGGAGCTAGCATACG
CAATTTTCCGTTGAAGGGTTCAACTATCAGGGCGGCCATTTCGAGCGAGATTCATTTTCAAGAGT
AATGAGCCTACGCCTATTTCATGACTCCCGAAGAGCTCATCAAAGAGCTAAGGGATGAGAAAAGG
AGGAGGCGGAATTTCTTTCAACTATAACATTTATTACAACATCTTACAACACTTAATATTACAGA
AAATGACAGAGAATTCGGTAAGGGGATAGAAGCACATCCTGCACC
Found at i:105649 original size:15 final size:15
Alignment explanation
Indices: 105626--105660 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
105616 GCACCCTACC
*
105626 AAGGCTAAGAAGCCG
1 AAGGCTAAGAAGCCA
*
105641 AAGGGTAAGAAGCCA
1 AAGGCTAAGAAGCCA
105656 AAGGC
1 AAGGC
105661 CAATGACACT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.43, C:0.17, G:0.34, T:0.06
Consensus pattern (15 bp):
AAGGCTAAGAAGCCA
Left flanking sequence: Indices 105126 -- 105625
GCATTCTAATGCGCGTCAGACCCCTCCCAAGGAAGAAGGTAAAGGCAGCAGCTCGGGAAGCTTCT
TGCGTGCGTGCTTGGCTTCAACATTCTCGAGTCATTGATAGAGTGGTGGAACTCCGCTTGTTAGG
AGTGAGTTTAGTTACGAGCAAGAAAGAGATGCGCGTCCTATTGGAAAGGCCTACGTTAGCGCATA
CGATTGATTTTATTTGAATGTGGTCACATTCTAAGCGAGGGGCCGTTGACTATTGACAGACTGTA
ACAAGCAGGTATTATGCTTCTTCCTCATCCACTTGATCGGGGGAATTCGCTTCCGCATCCCCTGA
ATGAACGTATCAAACCGATCCTTAAGCTAGTCTGGAGTCAGAAATGGCTAAACTGCGTGAAGAGA
TTCAATCGCAGTCTGCTGCTAAGCTTCCTGAGGCACCAGTGATGCGCCCTCTTACTGAATCCCCA
ACGGTATTAGAGGTGCCCCAACCTACTCTGTCCAAGCACCCTACC
Right flanking sequence: Indices 105661 -- 106160
CAATGACACTAGCTAACCACAACTGAGAGAGCTACCCTAGATGAATTAGTTGCGGCAAGAGCGGT
AATAGTACCGGCATAAGAAGTTGGAAAGGTCCCTTTGTAGCATACTTTACAGAAGAATCTTACTC
ATCCTCAAAAGTTCGGTTAGTAGTTTCAGAGGCATCGAGTTCAAAATCAAAGGCTGATTACCGTG
GAAAGGCACTTTCAAAGGCTATCTATCCCCCATTCTACCAGCAAACCAGTTAACAAGGAGATAGT
AATCCCACGCCTAAAGGAAGCAAGGTGAGGATAGAAGAAGCCAACCTGCCAACAAGTAAGCCCCC
TCTTTCGAGTTCTAGAGCTAGAGTAAGGTATGTATGCGTAGTTAGTAATTCCCCTTTTTCTAGAG
CAAGAGTTGGGAAAATCACTCATGATAGAGTCAGTCAGTTCGTCATGCTATTTTAACCCCGGTGC
TAGAATAGATAGAGATAGAGTTAGTAAGCCAATTAGTCTATCCGT
Found at i:125153 original size:22 final size:22
Alignment explanation
Indices: 125128--125224 Score: 194
Period size: 22 Copynumber: 4.4 Consensus size: 22
125118 CCTTACTCCC
125128 TTCGCTCCTCTCCAACCTGGCT
1 TTCGCTCCTCTCCAACCTGGCT
125150 TTCGCTCCTCTCCAACCTGGCT
1 TTCGCTCCTCTCCAACCTGGCT
125172 TTCGCTCCTCTCCAACCTGGCT
1 TTCGCTCCTCTCCAACCTGGCT
125194 TTCGCTCCTCTCCAACCTGGCT
1 TTCGCTCCTCTCCAACCTGGCT
125216 TTCGCTCCT
1 TTCGCTCCT
125225 ACGCTACGAA
Statistics
Matches: 75, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 75 1.00
ACGTcount: A:0.08, C:0.45, G:0.13, T:0.33
Consensus pattern (22 bp):
TTCGCTCCTCTCCAACCTGGCT
Left flanking sequence: Indices 124628 -- 125127
AGATAAATGAAAGAAGAAAAATGAACCACCTCTCGTACATAACTAATCAGCCTAAGTTTTTGATA
TTCTTAGATAGACGATCGGGACTCTGACTCCGAAAGAGAAAGAAAGCTCTCCGACCTGAGTTGGT
AGGCGTCACTTTCGCACCTAGTGAATTGGTTGACTTGTCTTTCTCCCAACCACCGTTAGGAACAG
GACGTAGCTGCCTAACCCGCTCCCCCCTGTAGTTATGGAAGGTATTGGAATCTCAGTCATAGTCT
CTCTCACGATACGCCTTGGGACTGTAGGCAGAAGGCGTAGCTCTAACTCTAACATTCCAAGCGAA
TCAAAGAAAAGAAAGACTTGAGGAGGGGCAGATGTGACTTTGTGTTCATCTTCTATCTGAGAAGT
AAGCTAACAAGAAAACAGACTAACTTACTTAAGAGAAAGGACCGACACTAGTAGCTTCTTTTCGG
GTAGACAGAGCGAATCCAATGGTACACAGACTCCGCCTTACTCCC
Right flanking sequence: Indices 125225 -- 125724
ACGCTACGAACACACCGGATATTGAAAAGAGCGCTTACTCTTCTTGCAGCGGAGTCGTTCACAAG
AGAAAGACTAGCTGTGGATTCAATAGCAGTTTTTTTCTAAAACAGTAAGAACGCATTCAATGTCA
TCTCTTCCTAAGTTTCTTAATGTTGTCAAGTAAGGTAGGTCTCAGTCTAGCTGTCCTCCTAACAG
CAGTCTATTCTTCTATCTTTGCGGTGTGGTAAGTAAGTATTGTATTGTGTAGCGAGGTTCTCTTG
GTTGGGGTCTATGCCCATTCGCCTCTCTTGCCCGGTCGAGAACTAAATTAAGCGAGATTCCAGCC
CTCCTTCCTTGCATCCAACTTTTTATGGCAGCAGTCGATTGGATTACTAGGCATCCCTTGATAGC
ACGAATTGGGTGCGATTGCCCTCAGTTCTTCCGTCCTTCCCACAGCACAGCGCTAATGCCGACTG
CAAGGGCCTCCCCCTCTCTTTGAGATTCTCGGAATTTCCCAAAAG
Found at i:158606 original size:19 final size:19
Alignment explanation
Indices: 158582--158618 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
158572 CCTACCCCAC
158582 CAAAAA-AAAAAGAAGATAT
1 CAAAAAGAAAAA-AAGATAT
158601 CAAAAAGAAAAAAAGATA
1 CAAAAAGAAAAAAAGATA
158619 GACACTCGAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 12 0.71
20 5 0.29
ACGTcount: A:0.76, C:0.05, G:0.11, T:0.08
Consensus pattern (19 bp):
CAAAAAGAAAAAAAGATAT
Left flanking sequence: Indices 158082 -- 158581
CGTAAATTTAAAACTGAACTCAGCCTTTTTTGCCCGCCCACTTACCCCTTCTTCATGATCCGCTG
CCGCGTGTCCGTTATATGAGAATACCTTTGCTCGAAATGGATTCCGTTAGCAAAAAACGGAATAT
GATGCCTGCTACTGTGACTGCCAGTGCTCTTGCCCTATTTGGGCTCCCACTCCCCCACTCATCTC
CTCTAACATTGACACGATCCGCTCCACCTTTTCAGGAGCGGGTCGCCTAAGATGCTCCTCTTTCC
GCAATTCGCAGATGAGTTCCCCCCTTTCCGGAAATCCATCAGCAACTACAGGCGCTTGCTGTCCT
CCTACTACTGGCGGGGCCGGCTGGTCATCTACCATCGGTGGCGCCAGAGTCAATTCGAAATTCAC
ATCACCCACTTCTGGAATGGGTTGACCAAGAACCAACTCAAAATTGAGCCCTGATTGAGGCTCCA
TTACATATGATGAAAACAAACTAGCCCAGTCGGGTCCTACCCCAC
Right flanking sequence: Indices 158619 -- 159118
GACACTCGAAGGAAGAAGAAAAAGAAAAGTGTCTTTCGAAGGATATTCATGATATTAGGTTAGAT
TTCTGTTTTTTCGCTCTGCTGGCGGAGCGGTATACCGAAAAAAGAGAGACTTCTGGGCTCGCAAT
AAAGCTAAGGTCCTGATCGAGCAACTAGTAGTCCTATCTATCCACCTCTCCAAACACAATATCTT
GAGTACCTATGATGGTGACCACATCTGCTGGCATGTGATGTTTGGACATAGAATCGAGTCCTTGT
GAATGGGCAGAGCCGGGTGCTCTTATTTTACGACGGTAGGGACGATTGCTTCCATTACTGACCAG
AAAGACACCAAATTCTCCTTTAGGTGCTTCAACTGCGGTATAGGTAGAAGGAGCTGGTACGGAAA
AACCTTCTGTATAAAGTTCGAAATGGTGAATTGAGGTAGAGTAGACCGATGATCCTGTAGTCATT
TGGCCGGCTATTGAAAGAAAAAAGCTTGCATCTGCTCCCCCTATT
Found at i:237337 original size:12 final size:12
Alignment explanation
Indices: 237320--237359 Score: 55
Period size: 12 Copynumber: 3.3 Consensus size: 12
237310 CTTTTGATCG
237320 AAAAAGAAAGAA
1 AAAAAGAAAGAA
237332 AAAAAGAAAGAA
1 AAAAAGAAAGAA
*
237344 AAGAGAGAAA-AA
1 AA-AAAGAAAGAA
237356 AAAA
1 AAAA
237360 GAATCAAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
11 1 0.04
12 18 0.72
13 6 0.24
ACGTcount: A:0.82, C:0.00, G:0.17, T:0.00
Consensus pattern (12 bp):
AAAAAGAAAGAA
Left flanking sequence: Indices 236820 -- 237319
GAGCCTCCTTTCTTCTCGGTCCACAGAGAGAAAATGTAGGACTAGTGCCAACAGTTAATCACGGA
AGAAAGGACTCACTGAGCCGAGATCACTAACTAATACTAATAGAATAGAAAAGAACTGTCTTTTC
TGTATACTACTCTCCCCGGTTCCGTTGCTACTGCGGGCTTTACGCAATCGATCGGATCATATAGA
TATCCCTTCAACACAACATAGGTCGTCGAAAGGATCTCGGAGACCCACCAAAGCACGAAAGCCAG
GATCTTTCAGAAAATGGATTCCTATTCGAAGAGTGCATAACCGCATGGATAAGCTCACACTAAAC
CGAGAATTTTGGATCAAATTCGGGATTTTCCTTGTCAGTAAGGAATTGGAATGTATGAATATCGA
TTCATATAGATAGAGAAGAAAAGGTTCTCTATTGATTCAAGTGCTGTCCCTATGGGATAGGGATA
GAGAAAGAGGAAAAAACCGAAGATTTCACATAGTGCTTTTGATCG
Right flanking sequence: Indices 237360 -- 237859
GAATCAAAAAAGAAGTCAATCAAAATGAAGTAGAAGAACCCAGATTCCAAATGAACAAATTCAAA
CTTGAAAAAGTGTCTTTCTTATTCTCGAAGAATGAGGGGCAAAGGGATTGATCGAGAAAGATCTC
TTGTTCTTATTATAAGATCGTGTGATTGGATCCGCAGATGTTTGGTAAAAAGAAGAATCTTCTAC
TTTGAAAAGAATAAAAATGGAAAGTGTTCAATTGGAACATGAAAACGTGACTGAGTTTGTCCGTT
TTACTCTTCGGGACGGAGTGGAAGAAGGGAGGAGATTCTCGAACGAGGAAAAGGACCCAATGACT
TCGAAAGAATTGAACGAGGAGCCGTATGAGGTTCAAATCTCATGTACGGTTCTGTAGAGTGGCAG
TAAGGGTGACTTATCTGTAAACTTTTCCACTATCACCCCCAAAAAACCAAACTCTGCCTTACGTA
AAGTTGCCAGAGTACGATTAACCTCTGGATTTGAAATCACTGCTT
Found at i:253328 original size:20 final size:19
Alignment explanation
Indices: 253292--253333 Score: 59
Period size: 20 Copynumber: 2.2 Consensus size: 19
253282 GACGATCTGG
253292 CTAATTATATATACTTCTAT
1 CTAATTATATATACTTCT-T
253312 CTAATTATATACT-CTTCTT
1 CTAATTATATA-TACTTCTT
253331 CTA
1 CTA
253334 TTAGAAAGGC
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 4 0.19
20 16 0.76
21 1 0.05
ACGTcount: A:0.31, C:0.19, G:0.00, T:0.50
Consensus pattern (19 bp):
CTAATTATATATACTTCTT
Left flanking sequence: Indices 252792 -- 253291
GCAATTCAGTTTCAAATGGTTTGAGCTTGGAAACAACCTGCTATCTATCGATAGGCGAGAACAGA
CTGCTATTGGCTGCTTCGCCTATCTATTCTATTATGGCCGGCTTGGAGACATCAGAGGAAGACCA
TCATCTCTATCCGGGTACGATCATAGCTTCATTCATTCGTTGAACCTTGGGGATAACCATTAGCA
TTGAGGTCAATCACCACACCACCTCTATCATACATACGACATTACATGACGCGAGAGTGCATGGT
CAACACAGACCTAAAACGCCTAGGTTCCGCTTGCAGCCAATACAACCACAACCGGCACTTGCACG
AGATTCAACAACCGAAACTACTGGTAGTCCCGAGGAGACGGCATCCTCCTATAATAGTTAGCAGT
ACTGAAGAAGCGAGCCCTATCAGAGAAAGAAAAGGACCCCCTTTTCAAAAAGAAAGGAAGTCGCT
AGCTAGATGTCAAAGGTGATTCTGTTCATGCTTCAGACGATCTGG
Right flanking sequence: Indices 253334 -- 253833
TTAGAAAGGCGAACTTATAGGCCTGTTTTAGCTCCTTTCCATAAGCGGTTAGGTTGACTTTGGAA
AGGCTACTAAGGACCGGGAAGGATTCATGGAGAACGAATCTATCTTACTGGAATCTATTTCTACC
ACTACTTGGGAGGGCTGATCATAGACCTATATTAATGACAACCAAGGATAAGCCCTATACCTTTG
AGGATGGATCAACAATGGCTTCTGAATGCAGAATGTATACAATGAATTTGATTGAGGAATGAAAC
TCCCAAGAATTTGAAAGCTCCTGCCTACTGCTTTAACCGAAGACTAGTACTAGTAGCAGTAGCAA
TTCAACAACGACTAAAGGCCCTGACTGCTGATTTCATTCAAAAGCGAAGGAAATTTCATTACAAA
ACAAGCGGAAAATACGTGAATGGAAAAGGAAGATTGGAACAAGCAATTGAGAGAGAACCACATGC
AGAACACATAGAGGACTATTGTATGTATAGAAGATTGGAAGCTCA
Found at i:319983 original size:2 final size:2
Alignment explanation
Indices: 319976--320007 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
319966 GGGGCCCTAC
319976 TA TA TA TA TA -A TA TA TA TA TA TA -A TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
320008 GTACCCTTTC
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
1 2 0.07
2 26 0.93
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Left flanking sequence: Indices 319476 -- 319975
AAGCTCATCTGACCCCAAGGTAGTACGTATCCTATAAAAGCTGTCACAATCATTAATAGGAAGAT
AACAACTCCGAGACACCAAACAAATTCCCTAGGACTGCTATAACTCGCATGATATAGACCACGAA
AAAGATGAAGGTAAACCACAATGAGAAACATACTTGCCCCATTAGCATGCATATAACGGAGCAAC
CAGCCCCCTTCAACATCTCTCATAATGTGTTCTACGCTGTTGAAAGCTAGATCCACATGAGGTGT
GTAATGCATAGCTAAAAAAACGCCAGTCACTATTTGAATGACTAAACAAAGACCAGCTAACGGAC
CGAACCCCCACCAATAACTAAGATTGCTCGGGGTTGGATAATCTATCAAATGCTGATTAAGTGTG
GAGGATATAGGCTGTTTAAGAAGAGAGAATCGTTGGTTCCTTATAGTCATTTCTCTTTCCTATCG
TGACTACTCTTGTTCCCCCACCTTTTGAGCGTTCTGGGGCCCTAC
Right flanking sequence: Indices 320008 -- 320507
GTACCCTTTCTTTGACTTTTGAAGGATGGAGGGGGTATACAGCGAAAGAAGCGTCGAATGGGTCA
TCCTGGGTTACTGAAGGGTCGTCCGACCGCTCGGTGACCGAATCAGAGAGGTTTTTACCGCTTTC
TCTTCTCTCCAGCACTCTTGGACTGATCATCTTGCTGCAACAAAGCAAGCTTAGGAATGAATCTA
ATGGAAATTTAGGTCTCTGTCCGCTTGGAAGATTATTCTTTCCTCTTCGGTGAAAGAGGGAAAAG
GTGTGTGGGAGAAAGAATGATAAAAGGAGAGAAGATCTCGTCCGCCAAGCGGGACAGAGTGCGAC
CCCTAAGCAATTGGAGGTTCTCGCTCATCTCTTGGGGGTCCATATCATCTTCAAACTTTTCCTCT
TCCATTAGCATAGCTAAATTTGAAGAGGATGACTCAGCGTCAGGAAAAGTAAGCCCCCCTTTGCC
TTGATTGAATTTGGCTTCGCTGCGCCCTGAATCAATCAAAAAGCT
Found at i:319994 original size:13 final size:13
Alignment explanation
Indices: 319976--320007 Score: 64
Period size: 13 Copynumber: 2.5 Consensus size: 13
319966 GGGGCCCTAC
319976 TATATATATAATA
1 TATATATATAATA
319989 TATATATATAATA
1 TATATATATAATA
320002 TATATA
1 TATATA
320008 GTACCCTTTC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (13 bp):
TATATATATAATA
Left flanking sequence: Indices 319476 -- 319975
AAGCTCATCTGACCCCAAGGTAGTACGTATCCTATAAAAGCTGTCACAATCATTAATAGGAAGAT
AACAACTCCGAGACACCAAACAAATTCCCTAGGACTGCTATAACTCGCATGATATAGACCACGAA
AAAGATGAAGGTAAACCACAATGAGAAACATACTTGCCCCATTAGCATGCATATAACGGAGCAAC
CAGCCCCCTTCAACATCTCTCATAATGTGTTCTACGCTGTTGAAAGCTAGATCCACATGAGGTGT
GTAATGCATAGCTAAAAAAACGCCAGTCACTATTTGAATGACTAAACAAAGACCAGCTAACGGAC
CGAACCCCCACCAATAACTAAGATTGCTCGGGGTTGGATAATCTATCAAATGCTGATTAAGTGTG
GAGGATATAGGCTGTTTAAGAAGAGAGAATCGTTGGTTCCTTATAGTCATTTCTCTTTCCTATCG
TGACTACTCTTGTTCCCCCACCTTTTGAGCGTTCTGGGGCCCTAC
Right flanking sequence: Indices 320008 -- 320507
GTACCCTTTCTTTGACTTTTGAAGGATGGAGGGGGTATACAGCGAAAGAAGCGTCGAATGGGTCA
TCCTGGGTTACTGAAGGGTCGTCCGACCGCTCGGTGACCGAATCAGAGAGGTTTTTACCGCTTTC
TCTTCTCTCCAGCACTCTTGGACTGATCATCTTGCTGCAACAAAGCAAGCTTAGGAATGAATCTA
ATGGAAATTTAGGTCTCTGTCCGCTTGGAAGATTATTCTTTCCTCTTCGGTGAAAGAGGGAAAAG
GTGTGTGGGAGAAAGAATGATAAAAGGAGAGAAGATCTCGTCCGCCAAGCGGGACAGAGTGCGAC
CCCTAAGCAATTGGAGGTTCTCGCTCATCTCTTGGGGGTCCATATCATCTTCAAACTTTTCCTCT
TCCATTAGCATAGCTAAATTTGAAGAGGATGACTCAGCGTCAGGAAAAGTAAGCCCCCCTTTGCC
TTGATTGAATTTGGCTTCGCTGCGCCCTGAATCAATCAAAAAGCT
Found at i:361432 original size:15 final size:15
Alignment explanation
Indices: 361412--361442 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
361402 CTAAAAGATC
361412 AAAGAGAGGAAAGGA
1 AAAGAGAGGAAAGGA
361427 AAAGAGAGGAAAGGA
1 AAAGAGAGGAAAGGA
361442 A
1 A
361443 GAGGACAATT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.61, C:0.00, G:0.39, T:0.00
Consensus pattern (15 bp):
AAAGAGAGGAAAGGA
Left flanking sequence: Indices 360912 -- 361411
GGTCAACGTCCATTGCCGATCCGGTCGTCCATCTCGGAGTCATCAACATCTCTGTTATCGGATAT
GAGTGGTCTTACCCCATAGAAAGCTTGATCTATCTGCCCCACCATTTTGTCGTATGCCTTTCGAT
CCGTCCAGTGAGAGACCTTCGGACCGAAGCATTTCCATTGCACGGATACCCAATCCTACAACTTG
CTCAGTTTTCCATGTCCAGACGTACGGACATAACTTTGATTAAGAAGTGAAGCCATCGTATAGCC
CAACTTGTGACTACTAGTATAGCTACCGAACATAGAAACCCAGGGAGATGAGCCCCGGTACTCGA
TAAGAGTAGACTGCCGGTTGTCTCTTCCTTTTCAAAACAATCCATGAAACTTGTTAGACTACGCT
ACTCTCTCTTTGATGAGATAGCACAAAAAAAGGCTGAAGAAATGAGAAAAAAGAGCATACAACAA
AGCTCAGCTTCATTTTGATTTCATTCTTCTTTCCCCTAAAAGATC
Right flanking sequence: Indices 361443 -- 361942
GAGGACAATTCAGTTGTTAGTTGGAGTTCCTCTTTCAAGACAATAAGCAGTCTACGGTCTCGACA
CCGAAAGTAGGATATCACTGTATTCCCTCTTTTCCTCGGGAGTCAGAAGTGAATCAGGGACTTGC
CATGGACACGAGTGAACGGATTCAAGATAGAGTTGAAACCGCTTACTAGTAGTGAGGAGGGAAAG
CAGCCTCGCTCAGCGCGAAATAGCGTCTATATAGAATCAAAGTTCCACATCGTTGTGACTCCTAG
ACAAGAGTTCGAATAGAATCCCCTAACAGAGGTGTGGATGTCTTTGGGGTGAGGCATGAAAGGAG
TAGGGCCACGGTTAGCCGGCAGCGGGTCAAGAAAGAGACAAAACTTGAGCGAGGAACGGGCTCCG
CCCTAGTTCTTAAGGCGAAGTCTCACATGAAAGACAATTTCAAAAGACTCGGCTCGAAAAGGAGA
AAAACCCGTCCTCCGGGAAAAGACAGCAAGAGATTGTGTAGAAAG
Found at i:373263 original size:24 final size:21
Alignment explanation
Indices: 373235--373303 Score: 75
Period size: 21 Copynumber: 3.1 Consensus size: 21
373225 ACAAAAAAGA
373235 TTTGTCTAAGTCACTTCGTTTCTT
1 TTTGTCTAAGTCACTTC--TT-TT
* *
373259 TTTGTCCAAGTTACTTCTTTT
1 TTTGTCTAAGTCACTTCTTTT
* *
373280 TTTGTCTAACTCACTTCCTTT
1 TTTGTCTAAGTCACTTCTTTT
373301 TTT
1 TTT
373304 CTTTGTGAGT
Statistics
Matches: 39, Mismatches: 6, Indels: 3
0.81 0.12 0.06
Matches are distributed among these distances:
21 22 0.56
22 2 0.05
24 15 0.38
ACGTcount: A:0.13, C:0.22, G:0.09, T:0.57
Consensus pattern (21 bp):
TTTGTCTAAGTCACTTCTTTT
Left flanking sequence: Indices 372735 -- 373234
GATTTGGAAGATCCAAAACCAAAAAGAGTGGTATTTGCTAGCAACAACATAATGGAGGCAGTCAA
TCAATATAGATTGATCCGAAATCTGATTCAAATCCAATATAGCACCTATGGGTACATAAGAAATG
TATTGAATCGATTCTTTTTAATGAATAGATCCGATCGCAACTTCGAATATGGAATAAAAAGGGAT
CAAATAGGAAATGAGACTCTGAATCATAGAACTATAATGAAATATACGATCAACCAACATTTCTC
GAATTTGAAAAAGAGTCAGAAGAAATGGTTCGATCCTCTTCTTTTTCTTTCTCGAACCGAGAGAT
CCATAAATCGGGATCCTAATGCATATAGATACAAATGGTCCAATGGGAGCAAGAATTTCCAGGAG
CATTTGGAACATTTCGTTTCTGAGCAGAAGAGCCGTTTTCAAGTAGTGTTCGATCGATTACGTAT
TAATCAATATTCGATTGATTGGTCTGAGGTTATTGACAAAAAAGA
Right flanking sequence: Indices 373304 -- 373803
CTTTGTGAGTTTCGAGAATATCCCCATTCATAGGTCTGAGATCCACATCTATGAATTGAAAGGTC
CGAACGATCAACTCTGCAATCAGTTGTTAGAATCAATAGGTCTTCAAATCGTTCATTTGATAAAA
TTGAAACCTTTCTTATTGGATGATCATAAGACTTCTCAAAAATCTAAATTCTTGATCAATGGAGG
AACAATATCACCATTTTTGTTCAATAAGATACCAAAGTGGATGATTGACTCATTCCATACTAGAA
AGAATCGCAGGAAAGATTTTGATAACACGGATTCCTATTTCTCAATGATATCCCACGATCAAGAC
AATTGGCTGAATCCCGTGAAACCATTTCATAGAAGTTCATTGATATCTTCTTTTTATAAAGCAAA
TCGACTTCGATTCTTGAATAATCCACATCACTTCTGCTTCTATTGTAACAAAAGATTCCCTTTTT
ATGTGGAAAAGGCCCGTATCAAGAATTCTGATTTTACGTATGGAC
Found at i:375698 original size:18 final size:18
Alignment explanation
Indices: 375675--375734 Score: 102
Period size: 18 Copynumber: 3.3 Consensus size: 18
375665 TTGATGATAT
375675 CGATATTGATGCTAGTGA
1 CGATATTGATGCTAGTGA
*
375693 CGATATTGATGCTAGTAA
1 CGATATTGATGCTAGTGA
*
375711 CGATATTGATGATAGTGA
1 CGATATTGATGCTAGTGA
375729 CGATAT
1 CGATAT
375735 CGATCGTGAA
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 39 1.00
ACGTcount: A:0.32, C:0.10, G:0.25, T:0.33
Consensus pattern (18 bp):
CGATATTGATGCTAGTGA
Left flanking sequence: Indices 375175 -- 375674
ATTCGATTGATGATAAAGAAAGAGAATTCTTGGTTCAGTTCTCCACCTTAACGGAAGAAAAAAGG
ATTGATCCAATTCTATTGAGTCTGACTCATAGTGATCATTTATCAAAGAATGACTCTGGTTATCA
AATGATTGAACAACCGGGAACAATTGACTTACGAGACTTAGTTGACATTCATAAAAAGTCTCTAA
TGAATTATGAGTTCAATACATCCTGTTTAGTAGAAAGACGGATATTCCTTGCTCATTATCAGACA
ATCACTTATTCACAAACTTCGTGTGGGGCTAATAGTTTTCATTTCCCGTCTCATGGAAAAGCCTT
TTCGCTCCGCTTAGCCCTATCCCCCTCTAGGGCCTATTTTAGTGATAGGTTCTATAGGAACCGGA
CGATCCTATTTGGTCAAATACCTAGCGACAAACTCCTATGTTCCTTTCATTACAGTATTTCTGAA
CAAGTTCCTGGATAACAAGCCTAAAGGTTTTTTTATTGATGATAT
Right flanking sequence: Indices 375735 -- 376234
CGATCGTGAACTTGATACGGAGCTGGAGCTTCTAACTATGATGAATGCGCTAACTATGGATATGA
TGTCGGAAATAGACCGATTTTATATCACCCTTCAATTCGAATTAGCAAAAGCAATGTCTCCTTGC
ATAATATGGATTCCAAACATTCATGATCTGGATGTGAATGAGTCGAATTACTTATCCCTCGGTCT
ATTAGTGAACTCTCTCTCCAGGGATTGTGAAAGATGTTCCACTAGAAAGATTCTTGTTATTGCTT
CGACTCATATTCCCAAAAAAGTGGATCCCGCTCTAATAGCCCCGAATAAATGAAATACATGCATT
AAGATACGAAGGCTTCTTATTCCACAACAACGAAAGCACTTTTTCACTCTTTCATATACTAGGGG
ATTTCACTTGGAAAAGCAAATGTTCCATACTAATGGATTCGAGTCCATAACCATGGGTTCCAATG
CACGAGATCTTGTAGCACTTACCAATGAGGCCCTATCGATTAGTA
Found at i:378320 original size:13 final size:13
Alignment explanation
Indices: 378302--378327 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
378292 TCTACCCTTG
378302 TGTGATTCCTGTT
1 TGTGATTCCTGTT
378315 TGTGATTCCTGTT
1 TGTGATTCCTGTT
378328 GAAGCATATA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.08, C:0.15, G:0.23, T:0.54
Consensus pattern (13 bp):
TGTGATTCCTGTT
Left flanking sequence: Indices 377802 -- 378301
CCATTGGAAAATCAAAAATACGCATGTCGGATGAAATGGTTGTTGCTATCTGCTCTAATAACGAA
TCATTGGTTTAACTGAATAACTAAATCAAATAGATAGACCTTTCTCTTCGTCTCAGGTCGATGGA
TCTTCTCAATTGGAAGATCTCCTATATGGATAATACACATTCCAGTTGACCAAGCCTAATTCTAA
TTGTTTTGTTCCGAAGCAAAGATATCCACGGGGCGGTTCGCCCTATTCAGATATTCACGACCAAG
AAGTACTGGATTCTCTTTCGGATAGGTCCTGAAAGGAGAAGGAAGGCTGGAATGCCACCAGGCGT
CTATTATTGAATTCACCCGACCCGATAGTACCAATTTTGTTTTGGGAACGTCCAGTGCCAAAGTC
ACTGAATGGGTAAGTCGCCAATCCCTAAAACGGACTGTGTAATGTACTTTATCTGCTGGGTTACG
GGGGGGCATTTTACCATAGGTTTATATTGTATCAATCTACCCTTG
Right flanking sequence: Indices 378328 -- 378827
GAAGCATATACTGGGGGGGGGGCGCAGGGCGGACGATTTCAAAGCGGACTCCCCATTCATTAGAT
AGAGAAAGAGAAGATCGCCAAGATTTCGTGATCCACTGCCGAACTTATTCCAATTCAATGAGCAT
TTCAATATTATGCCTTGAAGAGGACTCGAACCTCCACGCTCTTTAGCACGAGATTTTGAGTCTCG
CGTGTCTACCATTTCACCACCAAGGCATTTTGAAAGTGAATCGTATTCCATGAATATGATATCTA
TCTAGTGTGATGTATGGAATATATGACAAAGGTGGAGTGTTGGAGTATTTCTATTGATCGGTCAT
GTCATATAGGCCCGAGTCGGACATCCAATTGCTTCGATTTGAATTATCCGGAGGATGTCTTATAT
ATATTAATTATCAAAAAGATGGACAATCAAACCTATTTCTCGATTCAATAGAAGCCCAAAGAGGT
GAATAGGGTCCCAAATAACGAGAGATATGTAAAAAGTAGGTCCGA
Found at i:383096 original size:39 final size:38
Alignment explanation
Indices: 383042--383122 Score: 153
Period size: 39 Copynumber: 2.1 Consensus size: 38
383032 CCCATCCTTC
383042 AATATCATGATTGGGTCGACCAGGCCAGATCATGAGTGA
1 AATATCATGATTGGGTCGACCAGGCCAGATCATGAGT-A
383081 AATATCATGATTGGGTCGACCAGGCCAGATCATGAGTA
1 AATATCATGATTGGGTCGACCAGGCCAGATCATGAGTA
383119 AATA
1 AATA
383123 GAAAATCTAA
Statistics
Matches: 42, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
38 5 0.12
39 37 0.88
ACGTcount: A:0.33, C:0.17, G:0.26, T:0.23
Consensus pattern (38 bp):
AATATCATGATTGGGTCGACCAGGCCAGATCATGAGTA
Left flanking sequence: Indices 382542 -- 383041
AATCTATCTCTCAGCGATTCTTTTCTCCGCCAATAACCCCTTCCCAACCAGCCCGCCCGATCTAT
TTTGTAAGATCGGCTAATTTAAAGGGGTTAATCTGGTCCGAAGTTGTCGGAACGAATCGTTTGCT
TTATCAAACAAAGCGGGGGTCTTGGTTGGCCCCCTATTTTCAACCATTATAGCTGGCGTCGACCC
GCTTTGCGATACGGACGGACACGAAGAAGAACGCAGGCAGCGAAAATGCAAAAGAGAAGACCAAA
GATTCCCGCCCCAGAGCATGTTCTTGACTCAACCACAAATCTGTTGAATGAAGGTAGCTTGCTTA
CTCTCAGCCACTAGTTAGAAGGAAATCCCTTGACTTCGTTTATGCCCTTATGCAGTAAAGAAAGC
AAGTGAGGCGGGCTAAGATTCCATTCGAAGTAAGGTAACAGGATTCGATGTTGCACCATCTTCCA
CTCTTCTCGGGATCTGGAGTTTTTCGAGAAAAGGTCCCATCCTTC
Right flanking sequence: Indices 383123 -- 383622
GAAAATCTAAAACGTACATAGCTGTTCCAGCTGAAATACTTGGAATAATTCTACCACTTCTACTA
GGAGTAGCCTTTTTAGTGCTAGCTGAACGTAAAGTAATGGCTTTTGTGCAACGTCGAAAGGGTCC
TGATGTAGTGGGATCGTTCGGATTGTTACAACCTCTAGCAGATGGTTCGAAATTGATTCTAAAAG
AACCTATTTCACCAAGTAGTGCGAATTTCTTCCTTTTTAGAATGGCTCCAGTGGCTACATTTATG
TTAAGTCTGGTCGCTCGGGCCGTTGTACCTTTTGATTATGGTATGGTATTGTCAGATCCGAACAT
AGGGCTACTTTATTTGTTTGCCATATCTTCGCTAGGTGTTTATGGAATTATTATTGCAGGTCGGT
CTAGTAATTAGGGGGCGGCCGTTCGGTCGCCTATGATAAACGGACCAATAGGTCAAAAATGGGTT
TGTGCCGCAGGTGTTGAACGATCTACTCTACACAGGTGTGGGCTT
Found at i:436531 original size:36 final size:36
Alignment explanation
Indices: 436482--436570 Score: 142
Period size: 36 Copynumber: 2.5 Consensus size: 36
436472 TGTTCCCAGT
* *
436482 GCAATAACCGTTCCCAGTACTTTTCTTCTTCCTAGA
1 GCAATAACTGTTCCCAGTACTTTTCTTCTTCCTAAA
436518 GCAATAACTGTTCCCAGTACTTTTCTTCTTCCTAAA
1 GCAATAACTGTTCCCAGTACTTTTCTTCTTCCTAAA
* *
436554 GAAAGAACTGTTCCCAG
1 GCAATAACTGTTCCCAG
436571 AACAAGTGGT
Statistics
Matches: 49, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
36 49 1.00
ACGTcount: A:0.26, C:0.28, G:0.12, T:0.34
Consensus pattern (36 bp):
GCAATAACTGTTCCCAGTACTTTTCTTCTTCCTAAA
Left flanking sequence: Indices 435982 -- 436481
GATCTATCTAAGACAAGTAGAAGCATTAGGCTAAAAGCAATATCTTTTTTCATTGGTACTTGCAT
TTTAGCTCTGACCCTGGGGGAATCCGTCTCCCAGCACGGGGTATATCTGAATCTTAGAGAATTTG
ATTTTCATTCTTTGATGAAGGCTTAGAGAGGTTCTCTAGAGTTTCTTTTTTAGTTTCATGATTCT
ACTTTAGGTCCACACTCGAGAGCAAGTCTTCGCAATGGTACTTGATTTTCTTTCCCATTACTTCG
CAGGTAAAAAACCAGCCTACTGGTAAATGTTGTGTCTCTTTAGTGCCGTTGCCTTGAGCGTAACG
TAACTAATATATATATCTAAGAATGGAATGGAAAATGAACACTCTTTTAGTGGCTCTTAAGAAAG
CCATTTCTTGATCAAACTACGAACAACAGCCGACTATGAGAAGTCATGAGCAAACCCATGTTTCC
GTTCCCAGTACTATGAGTCTTCCTAGAGCAATAAGTGTTCCCAGT
Right flanking sequence: Indices 436571 -- 437070
AACAAGTGGTTCTTCTCTCACTAGAAGTGGTTTGACACCTACTCTATTAGAGAGAGAGCAATTAG
AGTATGGCTTGGCAGAAGAGAAAATGAGGACCTTTCTCGCACAAGGTAAAGGAATCAATCCTGTA
AAACTGACAAAGAAATTGATGGGTATTGAGTCAACTAGCTATCTAGAATTTCTTAATAAAAAAAC
CATCGGGTTGGCACATCCCCGATCCTTTGACTTATGCGAGAGAGGCCTTAGTAAGATAATCCAAG
ACCAAGCTGTAAGGCAAGATGTTTTGGTGAGAGATGTGAGTCCGGCTGTAAGGCAAGATGTTTTG
GTGAGTCCGCAGGGGCAAGGCTCTTGCCTATCGGGGCTAGAGTTGGTCATAGTAGATGGTCTGGT
GACTATTTTGCCGACGCTCATTTATGGTTCTATCCTTTTTTGGGACTATTTGCCTGATGCGAGTC
AGGCCCCTGTTATAGAAGAATTACTGCAGTTGGAGGAGACTGTTC
Done.