Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NC_064134
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: 194298
ACGTcount: A:0.27, C:0.23, G:0.23, T:0.27
Found at i:3509 original size:28 final size:28
Alignment explanation
Indices: 3469--3524 Score: 112
Period size: 28 Copynumber: 2.0 Consensus size: 28
3459 GAAAGGGCCG
3469 CTTGCTTCACTTCATTTTTCTATAGAAT
1 CTTGCTTCACTTCATTTTTCTATAGAAT
3497 CTTGCTTCACTTCATTTTTCTATAGAAT
1 CTTGCTTCACTTCATTTTTCTATAGAAT
3525 AAAATAATAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.21, C:0.21, G:0.07, T:0.50
Consensus pattern (28 bp):
CTTGCTTCACTTCATTTTTCTATAGAAT
Left flanking sequence: Indices 2969 -- 3468
CCAGCAGGCCCTACCTTAAAATGTCCCCAGACAGCCAGCCCTCACCAGGCTGCTAGCATTGCTAA
ATGCTCCGCCACGAAGCAAGCTCTCCCGAATACGACAGATGCAGAAGTGGGGAAGCCGGAAGTGG
CTAAAGAAGTCGGAGGAAGAAAGTAGTTGGACAACTGTATACACGAGGGTACATTAGTCTTCTGG
GAATTGGCAACATTGACAGAAAGGGGAAAGGGTAGGAATACACTTTTTTAGGTGTAGCTATACTA
AAGTAGTTGGCCTAACCTTCGGTTCCCGTAACCAAGTTTTTCTTTCTCATTCCTTATGTACTTTT
TCTTACTTCATCCATACTTTTTGACTTTTTCTGAAGTGTGGGGCAAACGGCGCCCTCTACTTCTA
CTTCTAACTAAAGGCGAAGAGCCGGCATTGCAAGCAAATAGAGAGCCTCCGCCCGTTTGATCGGT
TGCGAGCCGGAAAGCGTACCGGCAGTTTGAGTCGCGAAAGGGCCG
Right flanking sequence: Indices 3525 -- 4024
AAAATAATATATATAATTGAATTCTATATCTATCTATAAACAAAAAAGATATATATAATCTTTTG
ATTTTTCCAATTGTTCATTCCTGGGGAGAGGAAGAAGCAGATAGAGCAAAGGCCTCCTCTTTCCG
TTCGCTCTTCCCGAAGTGAGCGAATTGCATGTAGAGATCCGTAGGGGCTTATAGTTTAATTGGTT
GAAACGTACCGCTCATAACGGTGATATTGTAGGTTCGAGCCCTACTAAGCCTACCACCCCCTGCT
CTTCTCTTTCAGCCCTTGCTGGTGAAAGTCTTAGAATGAATGTTGGCCTAGATAGAGGAATAAAA
ACTAGCTCGACCGGAAGGGAGAGGATAGGCGAATCAGTAACTGAAATGAAAGCTGGAGTAAGACA
GTCAGTTGGAGAGCTAGCATGAAGAAGTAGGAAGGGATATTCGAAAGGCAGAAGGGTAAGAGCTA
GAAGGCTGTCTTTGAGGATAGGATGGTCGGACAAGGAATCCAACC
Found at i:16453 original size:25 final size:25
Alignment explanation
Indices: 16425--16475 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
16415 TAATTTGCCT
16425 AGTGAGAAAGCCAGGAAAAGACCCA
1 AGTGAGAAAGCCAGGAAAAGACCCA
16450 AGTGAGAAAGCCAGGAAAAGACCCA
1 AGTGAGAAAGCCAGGAAAAGACCCA
16475 A
1 A
16476 CAGACATACA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.49, C:0.20, G:0.27, T:0.04
Consensus pattern (25 bp):
AGTGAGAAAGCCAGGAAAAGACCCA
Left flanking sequence: Indices 15925 -- 16424
CAGCACCATCTCCATACCTTCCTTCCGTATCCGAGGTGGGCTCTTTCATCGGCCTCTCTTGGAGT
TGCCCGAGTGAAATGGAACGCTCTTCATTCGCAGGCAGTTACGGGGACTTTGCTTTTAGCTTTTA
GCCTTCCTAGCTAGCCGACAAAGGTCGAACTTTCTTACTTCTTTATTGAAAGCGAAAGAGAAAAC
TGACTTACTGAACTTTTTTATTGAAAGGGTATAACTAACTGGCTGGCACCTTACGAAGTAGTATA
CTTATTTTGTTTAGTAGTAGGAGGCTTCACATACTCTTACTACTCGAGAGATAGGGTAGCACCCC
CCATCCCGAAGTGACGAAGATGAAAAGTGCTTTTGCTAACTCTTTCTCGTCTTCAAAAAAGTATC
AAAATGCAGTTATATAAGCTATCACTTTTTCAATTCAAGATCAGCTCATCGAAGGGAAAAGTGAG
AGTATCAAAATGCAGTTATATGAGCATCGACTTTCTAATTTGCCT
Right flanking sequence: Indices 16476 -- 16975
CAGACATACAAACTCACTCTCCAGGGGCAGCTGAGGAAGGCAAGATTGATTAGGAGGTGGGGCAA
CTAGCTAGCCTTAAACCCCCAGCAAGCCATAGGGGTAGGCGGAAGACTTTCTCCTCTCGCTGCAA
GAAAAGCCCTTTTATCGATCTTGATTATATGCCGTAGTACCTACCCCTCACCTGGCCTGCGAGGG
GCTTCAAAGGCTCACAATGCCCCTTTTTAATAAGTTAGTTAGGACTTGCCTGCATCTCCCCATTC
AATAGGCTAAGCAGCTAGCACCTTGCCGGTCTTGGTTTTGTCTCAGCAGAGTGCGTGGATGGGAC
GCCGGGGACGGTGCCCCTTCCTCTGTAGGTACTACGGCCTAGCCCAAACTTTTAGACTGATTTGG
GCTAAGCAAGTTTATACGCCTTCGCAGCCCCTACTTCAATTAAGGCAAGCTTTCCTTTATTAGTA
AAGGGGTCTAGTGCATGGAGATTGACCCAGCTCTTAGCCTGAGCT
Found at i:24863 original size:21 final size:21
Alignment explanation
Indices: 24778--24863 Score: 97
Period size: 21 Copynumber: 4.2 Consensus size: 21
24768 TTCACGGGGG
*
24778 TTTCTTCTCATCAGTCTTTGT
1 TTTCTCCTCATCAGTCTTTGT
* * * *
24799 TTT-T-CACGTCAGTATTTGC
1 TTTCTCCTCATCAGTCTTTGT
24818 TTTCTCCTCATCAGTCTTT-T
1 TTTCTCCTCATCAGTCTTTGT
24838 GTTTCTCCTCATCAGTCTTTGT
1 -TTTCTCCTCATCAGTCTTTGT
24860 TTTC
1 TTTC
24864 ATGTCAGTCT
Statistics
Matches: 53, Mismatches: 8, Indels: 8
0.77 0.12 0.12
Matches are distributed among these distances:
19 14 0.26
20 2 0.04
21 36 0.68
22 1 0.02
ACGTcount: A:0.10, C:0.26, G:0.10, T:0.53
Consensus pattern (21 bp):
TTTCTCCTCATCAGTCTTTGT
Left flanking sequence: Indices 24278 -- 24777
GATTCCATATTCTATGCCAATAGACTCGTGACATCCATGTACTGAGTCGTCAAATGAGCCACGTT
AAGAAAGCCCAAGTTATACGCATTGGCCCACAGGGTGCCCCACCCAATAGGGCCCGAATGAAAGA
CCCAAGCCTACATGAACCATCACAAAGAAAGTCCTCAAAATGGTCCTGTTTCGATGAAACCTCGA
TGAAAGCCCGCAGAAGGGCCAAAGCACAACAAGCCTACCCATCATCAAAGCAAGCCCCAATGCAA
GAACTCCCTTTATATGAAGTTCTTCCGTACGTCTTGGATGTCCTTGATGCTTCATTCATCTCCGA
TCCCTTCTCAACTCAAACTTGTTTTTAGGCATGCAATAAATAGACACTGGTTCTTACCTCTTTCC
TATCTATACTCAATTTTAGGCTAGCTATAAGATTCAAGGTTGGTACTAAAATACTTGTTGATCAC
ATTCATGGAGGAGATGCACAGAGGGCTCTAGTCTTTTCACGGGGG
Right flanking sequence: Indices 24864 -- 25363
ATGTCAGTCTTTTTCTCGACTAATGTTTGGTTAGTGACCCCTGTCTGTACTTCAATCTGTGATTT
CAACTTGGCAATCTCTCTATTCCTCTCTTCTAATTTCTCATTGAGTCTCTCATTCTCAAGATGGA
GTACTCTATCACTTAGTGATGAAATCACTTTTCTACTAATGTAGTCTATGTTAGACAAGTCATGT
ATAGCAATAGGCTCAGTATCCACCCAGTTCTTATTACTGTCATATACGGGTAACCTCTTAGACCC
CTCTTTCAGACCTAAACTGAAGATGATTTCTTTATTTTTGATCTCCAAACTTTCCCAATCAATCC
TGAATTTTGCATCCACCTTGACCTGCACCCTTCTCGATGGTTCTGCGTACTGTTTCTCAAACCAT
TCGGGAGTGACCTTATCTTTAGCAGGTCCCTTGTATTTTTTGACTGTGCTTCCTTCCAAGGTGTA
GTAACTATAAGCTTTTGGTGCAAGAAAGAAACCTTTCACAATTTG
Found at i:24872 original size:18 final size:21
Alignment explanation
Indices: 24785--24875 Score: 77
Period size: 21 Copynumber: 4.6 Consensus size: 21
24775 GGGTTTCTTC
*
24785 TCATCAGTCTTTG-TTTTTCA
1 TCATCAGTCTTTGCTTTCTCA
* * *
24805 -CGTCAGTATTTGCTTTCTCC
1 TCATCAGTCTTTGCTTTCTCA
*
24825 TCATCAGTCTTTTG-TTTCTCC
1 TCATCAGTC-TTTGCTTTCTCA
24846 TCATCAGTCTTTG-TTT-TCA
1 TCATCAGTCTTTGCTTTCTCA
*
24865 T-GTCAGTCTTT
1 TCATCAGTCTTT
24876 TTCTCGACTA
Statistics
Matches: 60, Mismatches: 8, Indels: 8
0.79 0.11 0.11
Matches are distributed among these distances:
18 9 0.15
19 13 0.22
20 12 0.20
21 22 0.37
22 4 0.07
ACGTcount: A:0.12, C:0.24, G:0.12, T:0.52
Consensus pattern (21 bp):
TCATCAGTCTTTGCTTTCTCA
Left flanking sequence: Indices 24285 -- 24784
TATTCTATGCCAATAGACTCGTGACATCCATGTACTGAGTCGTCAAATGAGCCACGTTAAGAAAG
CCCAAGTTATACGCATTGGCCCACAGGGTGCCCCACCCAATAGGGCCCGAATGAAAGACCCAAGC
CTACATGAACCATCACAAAGAAAGTCCTCAAAATGGTCCTGTTTCGATGAAACCTCGATGAAAGC
CCGCAGAAGGGCCAAAGCACAACAAGCCTACCCATCATCAAAGCAAGCCCCAATGCAAGAACTCC
CTTTATATGAAGTTCTTCCGTACGTCTTGGATGTCCTTGATGCTTCATTCATCTCCGATCCCTTC
TCAACTCAAACTTGTTTTTAGGCATGCAATAAATAGACACTGGTTCTTACCTCTTTCCTATCTAT
ACTCAATTTTAGGCTAGCTATAAGATTCAAGGTTGGTACTAAAATACTTGTTGATCACATTCATG
GAGGAGATGCACAGAGGGCTCTAGTCTTTTCACGGGGGTTTCTTC
Right flanking sequence: Indices 24876 -- 25375
TTCTCGACTAATGTTTGGTTAGTGACCCCTGTCTGTACTTCAATCTGTGATTTCAACTTGGCAAT
CTCTCTATTCCTCTCTTCTAATTTCTCATTGAGTCTCTCATTCTCAAGATGGAGTACTCTATCAC
TTAGTGATGAAATCACTTTTCTACTAATGTAGTCTATGTTAGACAAGTCATGTATAGCAATAGGC
TCAGTATCCACCCAGTTCTTATTACTGTCATATACGGGTAACCTCTTAGACCCCTCTTTCAGACC
TAAACTGAAGATGATTTCTTTATTTTTGATCTCCAAACTTTCCCAATCAATCCTGAATTTTGCAT
CCACCTTGACCTGCACCCTTCTCGATGGTTCTGCGTACTGTTTCTCAAACCATTCGGGAGTGACC
TTATCTTTAGCAGGTCCCTTGTATTTTTTGACTGTGCTTCCTTCCAAGGTGTAGTAACTATAAGC
TTTTGGTGCAAGAAAGAAACCTTTCACAATTTGATCTTCCAGCTT
Found at i:32429 original size:25 final size:25
Alignment explanation
Indices: 32401--32450 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
32391 ATTCAACTCC
32401 TGAGAGATTCTATAGTTCCTGAGCT
1 TGAGAGATTCTATAGTTCCTGAGCT
32426 TGAGAGATTCTATAGTTCCTGAGCT
1 TGAGAGATTCTATAGTTCCTGAGCT
32451 ACCCCAATTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.24, C:0.16, G:0.24, T:0.36
Consensus pattern (25 bp):
TGAGAGATTCTATAGTTCCTGAGCT
Left flanking sequence: Indices 31901 -- 32400
TTAACAATTCATGGCATGAATTAGAGTTGAAGGAAGAAAGACATGAAATGCTAGAAAGATGGAAT
CTATGAATGAGCTCTTTCGTCTAAGCCTAGAACTAGGCAAGAGCAAGGAATGGACTTTAAGTGAG
TGAAAACCGGAAGGAGGGGACAAAGGTCAGTTCTATAAGGCAAGAAAGCAAGATCAGAAGAAGGA
GCAATGCAGAATAACTAAGCATGACAAGGAGAGGATAGCTAGACTTTCAAAGACAGTAGCAATGG
CAAGGAGACTAATCCCGATATTCTTTCCCTAGCAATTGGAGGATTCTATTGATCCAAGACCTGTA
TGTAGACCTGGGCCTCCCCCGCTTTCAGTTAAGGCCAGAAAGAATTATCTTACCTTTCTCTTCTG
TCAGTCTTTGAAGTTTCCTTTCTTTGAAAACCAAGGATGAAGCTAGAATGTGGAGTACGGACTTA
TCATGCTTCCCAATTCCACTAGCATAAAAGAGTTTATTCAACTCC
Right flanking sequence: Indices 32451 -- 32950
ACCCCAATTTGATGAGAATGAGGGAAGAAGTCCTTAGCTATTCCTTTGGCCTATAATAAGAAAGG
TCCATCAAGACTCAGAAATTACCCTCGATCTTTTCAATCCCTCTAGTAGAGAATTCTTAGCCTTC
GTCTTAGAAACTGAGCTCTCACAAAGCAAGTCATTACTTATTGTTTACACACACTTTCTATTTTA
CTTAGCCTACTTCTTTATCATTAGATCAATTAGGCAGGGGAAGACTCTGTGTACTAACTTTCTCT
TCTTTCTTCTTCTTTGAAATCCCTTGCCACTTCCCTTCTTTGCTAGCACGTACCTGTCTTTGCTT
TGCACAAGAGATCCCCCTACTCTTCACACCCCTCTAGTCCTGATCTTGCTTATGCATTACTTGGG
AAGGATTGCCCTATCCCTTTGTTGGGGGCTTTGGCTACCCTACCTCATTCCCTTCACAAGCCAAG
GACAAGATGAATCTATTGCCCTGCCTCCAAGAGAAGAAATGGCAC
Found at i:34050 original size:21 final size:21
Alignment explanation
Indices: 34026--34069 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
34016 TCTTTGAGAG
*
34026 CATAAAGAGGGCCTTATAATT
1 CATAAAGAGGGCCTTAGAATT
*
34047 CATAAAGAGGGTCTTAGAATT
1 CATAAAGAGGGCCTTAGAATT
34068 CA
1 CA
34070 AACTAGATAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.39, C:0.14, G:0.20, T:0.27
Consensus pattern (21 bp):
CATAAAGAGGGCCTTAGAATT
Left flanking sequence: Indices 33526 -- 34025
AGATTCCCCTTTCGATTGGAGTTCTACGGTGGGAAAGAAAGTAAGGAGTTAGAGCTCGGAAGTGA
GAACTAGCTTATAGGAGCGAAGCCACTCGACCAGAGGGAGAGGAATGAGTACTCTCTCTCCTCAT
TCAAAGAAGATAGAGGAATTCCCCAGTACTGCTATAACTATAGGGGGAGAAGTGAGAACTAGCTA
GACCATATTTACTTTTATATAGGCTCGACCTTAAAAGAGGGAGTAAAAACTTACTTATAGGGGTT
GCCAGTCATAGCTATAGGAAGAGGGAATCCAACTATCGCAATTCAATCATAGGGCTAAACTGTGC
TTGATTAGTACCGGCTTTCGTTGAACTGAACAAGCGAAATGAGAATGTCAGTCTAGTGCTAAAAA
GGGCGAATAGCAATCGGGCTAAATGCATGGCTTCGACTCCTAATTCTACCTTTAAAGGGCTTCGT
TTCGGCCTATGGAATCTCAGTTCTGTAAAAGCCGGTCTTTGAGAG
Right flanking sequence: Indices 34070 -- 34569
AACTAGATATCGGATGAAAGTGGTATGACAACCTCAAACCCCGGTCCCATGGGGAGAGTTTTCTA
TTTGAGTTTCGGAAAAGAAAGGAGAAAGGACTTTTGAAGCTTGCTGACTAGGGTTGGAAGCGAAA
TTCAGTCTTCGCCATAACATAAGAAAGTCGTGGAGTGCATAAGCCCCTTTAGAGATAGGGGCTAC
TTTCTTGTGGTAGTCATTGCGAATGAGCAAGTAGGGGGCGGCAACTAAAGAGGTAGCGAGACTGA
CCGCAATTGCAGGAATAGGTTGACTTTCTTTCATTTTGGTTATGGAAAGTGAAAGTTCTTTCGTT
TAGTACGAGATCGCTTCACACCTCGCGGTGCTTACACCTCTCGCCTATCGAAGTTCTGTTCAAAA
ACCTCGTCCGAGAACTTGTATAGAGAAGGATTTCCCGCGGCGCAGCAGTTCTTCCATACCAACTT
AGCTGCCCGGCGCTGCTATTGGCATAACAACCGGTACACCATAGG
Found at i:35701 original size:18 final size:18
Alignment explanation
Indices: 35680--35722 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
35670 CAACCTTGTT
35680 GACTATGACAACAG-TCGC
1 GACTATGA-AACAGATCGC
35698 GACTAT-AAACAGACTCGC
1 GACTATGAAACAGA-TCGC
35716 GACTATG
1 GACTATG
35723 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 35180 -- 35679
TACCGTCTAGCCGTTGGTACTCCGCATCTTCACGGAGAATTCAATTTCACCGGGTCCATGTCGGA
GACAGCGGGGCAGTCGTTACACCATTCGTGCAGGTCGCTACTTATGCGACAAGGAATTTCGCTAC
CTTAGGACAGTTAGAGTTACTGCCGCCGTTTACCGGGGCTTCCATTCAAAGCTTATAACACTTCT
CCTTCCGACTTTCCAGCACCGGGCAGGTGTCAGACTCTATACATCGTGTTACCACTTAGCAGAGT
CCTGTGTTTTTAATAAACAGTCGCTACCCCCTGGTATGTGCCGCTTTCCTAATCAAAAGATAGGA
GAGCACCCCTTCTCCCGAAGTTACGGGGTCATTTTGCCGAGTTCCTTCGACATGGTTCTCTCAAG
CGCCCTAGTATACTCTACTTGTTCACCTGTGTCGGTTTGGGGTACGGTCAGTTCACCGGGAGGAT
CGCCCTCCCAATTCGAAGTTTTTTCCTGGAAGTTTCAACCTTGTT
Right flanking sequence: Indices 35723 -- 36222
GCAGGGCGGTACGCTCTGCTCTCTCGCGACCCCTACTCTAATCAAAAGACTAAAGGCCCCTACTG
AAGATTCAAAGGGCGAGCACTGAAATGAGAAAGGCTTGTAGACTCGTGACGCTGAACGAGACATT
CGAAAACTAAAGCGCACACTAGAAAGTGCTTCGAAAGGTGTCAGCAGGTGCGCGGAGCCGGAGCC
CGGCATGTTCGCCCGCTGGGCCGAGTGTTCGCCCACTTCAGAGTCTTCGCCTTTAGATAACAAAA
AGTGTCCGCCCCTTAGGTCGCCAAACTACGACGAGAGTTTCGCCTTTTGAAGCGCCAGTCGCGTA
GGGCGACCGGGCCAGGCCGAGTCAGAAAGGCTTTGATGACTCAAGGTTCATATTAGGGAAAGGAG
AGTGAGGGGAAGAGGGGGCAGCCCTCGGCCCGATCATCCAATTCGCTCCAACAGACAGGCATGGT
TCTGTAGTCAAAGCAACTTCGTCACTTTCGTGTACCCATCGGACG
Found at i:84445 original size:19 final size:19
Alignment explanation
Indices: 84423--84460 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
84413 CTGGACTATT
84423 CAAAATAGAATAGACTGGA
1 CAAAATAGAATAGACTGGA
84442 CAAAATAGAATAGACTGGA
1 CAAAATAGAATAGACTGGA
84461 TTAGCGAGAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.53, C:0.11, G:0.21, T:0.16
Consensus pattern (19 bp):
CAAAATAGAATAGACTGGA
Left flanking sequence: Indices 83923 -- 84422
CATCTCTATTTCATGGGCCGAAGGCTAAGGCTTATTATATAATAGTAAGTAAACTGGTTAGCTTT
AGGACTAGACAACCCCGCCGGGAGCCAAGAGAAGTAAGCTTAGGCTGCACATGTTAGATCCGATT
CCAATTTGACGAATTACCCTCTTATGTCAAATCTGAAAAGAACCTATTCCTATTCGTCGTAAACA
AAAGGCATATTAAACAAAGGTCTTACGGAGTCTTGTCCTAAAGTCCCACGCATGCCTGCTCTTCG
TATATAGAGACACGATTCTTGGCATCCTGCCTTTAAAGAGGCGCTTCGATAGACGATCAGTTATC
AGTCTAGTTCGACACCTTGTTCTCAACTGAACTAGTAGACAGACGCCTCTGGGCATTTCTCAAAA
GAGTTAGATCCGCCTAATCAATGTAGTAGTTCAGCTATTCCTTTGACAGACAGTGAAAGTTTCAG
GCAAAGACAGAGGATCCGATCCTGTAGTCAACTACCTGGACTATT
Right flanking sequence: Indices 84461 -- 84960
TTAGCGAGATCCGTTTTCATCCGAACCCCATCTTGTTAAGCCTAAGAGGCACGAGCTATATCTTA
CATACTCTATTGTCCGATCATAGCCGTCTGAGAGTCCTGCCCGAGCAGGAGGAGCATCCAATCCA
TACCTAGGTAGAGGAAGCTGATCTGCCGTATGCACTTCCGACTGACACAATCGACAGCTTGAGGA
ATAAATGTGCTTTAATACTTTCCGAGTTTTGCAAGAATAATAATCGTGAACATGAGACCTTCGTC
GACATCATACAAGAACTGACCTTAAAAAACAAGATAAGCGAAGGCGATTCACTTTCGCGTGAGGA
CTTTATTCACATTTTACGGACTTATTACGGCTTACAGAATTCGGAGATAGTGGGGATAGATGGGC
TAGGAAATATGAAGAGCTAACGGGATGCTTACCGACTGAACGAACTTCGGCAAAAGGAAATGAAA
CGGGCGGGCGAAATGACGTGAGAGAAAGAACCTCTTAGTGGAGTC
Found at i:115271 original size:18 final size:17
Alignment explanation
Indices: 115241--115274 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
115231 CGTTCCTCTC
*
115241 GCTCCAACTACAATGGA
1 GCTCCAACAACAATGGA
115258 GCTCGCAACAACAATGG
1 GCTC-CAACAACAATGG
115275 GCGAAATCAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 4 0.27
18 11 0.73
ACGTcount: A:0.35, C:0.29, G:0.21, T:0.15
Consensus pattern (17 bp):
GCTCCAACAACAATGGA
Left flanking sequence: Indices 114741 -- 115240
TTATAGTGCTTGGGTGAGAACGGATCAAAGTGTTCGCTCTTGGTTGAATGCGACACTCTCAGTGG
ACATGTTGACGGAAGTCTACAATAGAATATGAAAACAAAACATATATGGATGTTTGGATGGCTTT
AGAGCAAAGATTTGTTGATCAGTCCACGGCTAAAGAAATGAAATTGAAGTTCGATATTCAGAATA
ACAGGAAAGGTAACAAGCCTATGGATGCCTATTTACGGGAACTGAAGTCTATGGTTGATGCCTTG
GCTGCTATCAACTCTCTTCTATGTCCCCAAAGGATATAGTTTTCACTACAAAGCCCTTTGAATAT
GAAGCTTTTGTTACAAGCATCTCCGACTCTAAGACTGTTCCATCGTTTGAGGAGCTGCGGACTAA
GGTCCTTAACCAAGAATCGCGTCTTCATCGCATACAAGCTGCACAACACAGTGAGCAGCAATCAG
CCTTTGTGTCTCAGACTTCAGCTGCTTCTGATAATCGTTCCTCTC
Right flanking sequence: Indices 115275 -- 115774
GCGAAATCAACAACTGATTCCCCGCATTGCTCTTCCAAGCCCTTATTCCCAAGTTACCTTAACTA
GTTCTCCGCACCTGTCTGTAACGGACCCTCTGCCTTTAGCTACAAATAAAGACTCTCAAGAATTA
TGGGACTGTCTTAGAGGCCTGAATCCTTTGGATAGTGGTCAGGAAGATACCTTTAACCCCTGAAC
ACACTGGCAGATCACCTGGCAGTGCTTGGCCTTTGATGGCTTTGATAGTCTTGAAAACAATGTAG
TATTCCGCCAGGAGCATTTGCCACCTTGCTATCCCCCCAGAGAGAGAGGCTTTCTCGAATATGTA
TTTCAGTGCGCCCATGCGAGCGATGAGCCAAGTTGCGTGATAAAGCATGTACTGCCAGAGCAGCC
CAAGCGAATGCGCAGCACGTCCGTTCTAGTGCTGAATATCTGTTCTCGTAATCCGTGAACTTCTT
TCTCAGTTAGTTCGTGGGATCGGCATCTCCTGAATGGCTTTCACC
Found at i:127771 original size:36 final size:36
Alignment explanation
Indices: 127724--127832 Score: 218
Period size: 36 Copynumber: 3.0 Consensus size: 36
127714 CGCTGTTCTA
127724 GCTCCGGATCGGGCACTGCGGGCGGATTTGCCTCGG
1 GCTCCGGATCGGGCACTGCGGGCGGATTTGCCTCGG
127760 GCTCCGGATCGGGCACTGCGGGCGGATTTGCCTCGG
1 GCTCCGGATCGGGCACTGCGGGCGGATTTGCCTCGG
127796 GCTCCGGATCGGGCACTGCGGGCGGATTTGCCTCGG
1 GCTCCGGATCGGGCACTGCGGGCGGATTTGCCTCGG
127832 G
1 G
127833 GGCATTAGCC
Statistics
Matches: 73, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 73 1.00
ACGTcount: A:0.08, C:0.30, G:0.42, T:0.19
Consensus pattern (36 bp):
GCTCCGGATCGGGCACTGCGGGCGGATTTGCCTCGG
Left flanking sequence: Indices 127224 -- 127723
ACCCTACCCTTTCATTTCCGCTTAAGCTTCCCCGGTTTGGGGGATTAATTGATTGGATACCCGAG
AACCATAATCTTTCCTAGGAACAGCTTCTACGACGATAGATAGGGGTCAGGTTTGTTTGGCATCT
ATGCCCCCCCCCTGCCCTCCAAACAGTATGGGAGCCTTTCAGCTCGTACTGCTCACACCCCTAGA
TCTTCATGGCACCTCCCCCTTACCACAAACCTTTTAGGAACCCGACCCCTATGGATGGTCGTGGT
CCCATTCTGTCATCGCTGCCTCAAGTAACTTAGCTGCTTGGGAAGCACCACCAACATTATTCTGA
ATCTCAAGCAATACAGACATGGTATCCTCTATGTGATTTAACCTCGTCATCGTAGAGGTATCAAT
TTGAAGCCGATGTCGCACACTGGAGATCAAGGTTAATGCCGGTCTGTTACGCATGAAGGCCCCCA
GGAATTGGGGCACTGCGTTGTGCAACTCCTGGCGTCGCTGTTCTA
Right flanking sequence: Indices 127833 -- 128332
GGCATTAGCCGCTTCCACCGCCCCCCAGTCAACCCAGGTTTCCCAGGAATGTGAAGAACTCTCTG
GGGATGCCATCATAGCGATGATAGATAGGGGTCAGGTTTGTTTGGCATCTATGCCCCCCCCTGCC
CTCCAAACAGTATGGGAGCCTTTCAGCTCGTACTGCTCACACCCCTAGATCTTCGCGGCACCTCC
TCCACCATAGTGTGAGCTGGGAGCTGCTCCGAAAGGCGAGGCCTACTTAAATAAGTAATGAGCTT
TCAACAACGTTAACAACACTACGAAAAAAGTAAACTATGGTTGCCCACTGATATGACCATAGGGG
AAATCTAACCCCTTCTCTGCTCCTTTACTGACCCTTTCCTTCGCTACTAGGAGAGTCGCTAGCTT
GCTTCATTATATTCTATAAGCGGAGCGACTTGTCGAGTCTACGAAGCTTCGTAGTTGCTTCCCCC
CTCCCCCCTTTCTTTTGCCCCGCCATGCCACTAGATCCATAATGA
Found at i:127821 original size:18 final size:18
Alignment explanation
Indices: 127728--127822 Score: 58
Period size: 18 Copynumber: 5.3 Consensus size: 18
127718 GTTCTAGCTC
127728 CGGATCGGGCACTGCGGG
1 CGGATCGGGCACTGCGGG
**
127746 CGGAT-TTGC-CT-CGGG
1 CGGATCGGGCACTGCGGG
127761 CTCCGGATCGGGCACTGCGGG
1 ---CGGATCGGGCACTGCGGG
**
127782 CGGAT-TTGC-CT-CGGG
1 CGGATCGGGCACTGCGGG
127797 CTCCGGATCGGGCACTGCGGG
1 ---CGGATCGGGCACTGCGGG
127818 CGGAT
1 CGGAT
127823 TTGCCTCGGG
Statistics
Matches: 57, Mismatches: 8, Indels: 24
0.64 0.09 0.27
Matches are distributed among these distances:
15 8 0.14
16 4 0.07
17 4 0.07
18 25 0.44
19 4 0.07
20 4 0.07
21 8 0.14
ACGTcount: A:0.09, C:0.29, G:0.43, T:0.18
Consensus pattern (18 bp):
CGGATCGGGCACTGCGGG
Left flanking sequence: Indices 127228 -- 127727
TACCCTTTCATTTCCGCTTAAGCTTCCCCGGTTTGGGGGATTAATTGATTGGATACCCGAGAACC
ATAATCTTTCCTAGGAACAGCTTCTACGACGATAGATAGGGGTCAGGTTTGTTTGGCATCTATGC
CCCCCCCCTGCCCTCCAAACAGTATGGGAGCCTTTCAGCTCGTACTGCTCACACCCCTAGATCTT
CATGGCACCTCCCCCTTACCACAAACCTTTTAGGAACCCGACCCCTATGGATGGTCGTGGTCCCA
TTCTGTCATCGCTGCCTCAAGTAACTTAGCTGCTTGGGAAGCACCACCAACATTATTCTGAATCT
CAAGCAATACAGACATGGTATCCTCTATGTGATTTAACCTCGTCATCGTAGAGGTATCAATTTGA
AGCCGATGTCGCACACTGGAGATCAAGGTTAATGCCGGTCTGTTACGCATGAAGGCCCCCAGGAA
TTGGGGCACTGCGTTGTGCAACTCCTGGCGTCGCTGTTCTAGCTC
Right flanking sequence: Indices 127823 -- 128322
TTGCCTCGGGGGCATTAGCCGCTTCCACCGCCCCCCAGTCAACCCAGGTTTCCCAGGAATGTGAA
GAACTCTCTGGGGATGCCATCATAGCGATGATAGATAGGGGTCAGGTTTGTTTGGCATCTATGCC
CCCCCCTGCCCTCCAAACAGTATGGGAGCCTTTCAGCTCGTACTGCTCACACCCCTAGATCTTCG
CGGCACCTCCTCCACCATAGTGTGAGCTGGGAGCTGCTCCGAAAGGCGAGGCCTACTTAAATAAG
TAATGAGCTTTCAACAACGTTAACAACACTACGAAAAAAGTAAACTATGGTTGCCCACTGATATG
ACCATAGGGGAAATCTAACCCCTTCTCTGCTCCTTTACTGACCCTTTCCTTCGCTACTAGGAGAG
TCGCTAGCTTGCTTCATTATATTCTATAAGCGGAGCGACTTGTCGAGTCTACGAAGCTTCGTAGT
TGCTTCCCCCCTCCCCCCTTTCTTTTGCCCCGCCATGCCACTAGA
Found at i:137388 original size:20 final size:20
Alignment explanation
Indices: 137363--137403 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
137353 TGTAAGTGTT
137363 AGAAAGA-GTAAGTTAAGTAA
1 AGAAAGATGTAAGTTAA-TAA
*
137383 AGAAAGATGTCAGTTAATAA
1 AGAAAGATGTAAGTTAATAA
137403 A
1 A
137404 TCAGGGGACC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 11 0.58
21 8 0.42
ACGTcount: A:0.54, C:0.02, G:0.22, T:0.22
Consensus pattern (20 bp):
AGAAAGATGTAAGTTAATAA
Left flanking sequence: Indices 136863 -- 137362
AAGTGATCCAAGCTGGAAGTGAGCCGGAGTTCGTAGGCTAAGTGAACGGGGAGCAACGGCTGATC
GAAAAGCGAAGATAGGCGCATAGTTCAGTGATCTACAAGAGTGGTAGAGGTCCCGATCAGGTTGT
TTTAACAAGCTAGTTAGGCCAGATAGGCTAAACTAGTAGTTCGTAGTTCCCCAGGCCAGCGGTCT
CGCTATTCCTGATGATCAGGTTAGGCAAGCTAATCACGCCTGCTGCGTCAAACCTTCATTGAATG
GGAATGAAAATTCGACGGCATCTAACTACCTAAACCTAAGGCGAATACGTGAACAGAGACTTCTC
TCTGCTGCTGTAGCTGCTAGGATACTAAAATTGTCTGCTTCAGCTAACCACACGGCGTTCAGTCG
CCCAAACACACGAACATACTATACAAAGAAGGAGAGGCAAGCGCTGAGTCTTAAATTAGATTACC
CCTCTGATTTGTCACCCGCTGAGCTAACGTCGAGATGTAAGTGTT
Right flanking sequence: Indices 137404 -- 137903
TCAGGGGACCCAGCCTCACTAAGGTTAACGGATTGTCTACCATTCGCTCAGCTTCGGAAAGCCCT
GTGGAGGCCTACAAAGAAAGGCACAACGCTTATGTTGCATGCAATATCTTGGAATCTGCTTCGAT
ATAAGTCGGATGGATAGTTTTTTAGATGAAAAAAGAATCAAATAGCAGCGAGACTAAATGGTTTT
AAGTCGAATAAAGGGCCTAGGAGTCATAAGCAAAAGCAAGATAGAAGCCTTAAAAATCCACACAT
ATATAAGTATAAGCTCTACTAAATCTAGATAACTAGAATTCCAAGGGACCAGAAATCCTGCCCGT
AGATGGCCGAAACAGAGCTTCGGAGGGGCTATGCTGCTTACTGTAACTGTCAAATTTGATTCCCT
TCCCTTTTTGCCGGAGCAGGACACACATAAAAAAGAGAAATGGCAAAAAAAAGACCTCCTACACG
CACGGGAACCAGAACAAAAGAAGGAGATAGGATCCACCTGCACGC
Found at i:177460 original size:16 final size:16
Alignment explanation
Indices: 177435--177474 Score: 55
Period size: 16 Copynumber: 2.6 Consensus size: 16
177425 AAAGTGGAAA
*
177435 CTTTCCGCGGGATCCT
1 CTTTCTGCGGGATCCT
*
177451 CTTTCTGCGGGATGCT
1 CTTTCTGCGGGATCCT
177467 CTTT-TGCG
1 CTTTCTGCG
177475 CTACGATGGA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 4 0.18
16 18 0.82
ACGTcount: A:0.05, C:0.30, G:0.28, T:0.38
Consensus pattern (16 bp):
CTTTCTGCGGGATCCT
Left flanking sequence: Indices 176935 -- 177434
ACTAACCGAGCCAAGCCCAGTTCCCGCCGATAGGCGCAGGTAGCTTGCTTCCAAGCCTTGCCTTA
TATGATAGTTGTGGCCATGGCCCGAAGGAGCCTTAAGCACTTGTACAATGCTTCAAGTCAAGGCT
CCCTCCCACTCGTTGCCCAGAGCCTTGACTTTCCATGTTTTTAGTCAAATGCGCGCTAGCGCGCT
ACAACTAGCACTTTTTTCTCTGATAGGCTCGCTTCTTCAAGCTCCGACCCTTATTGAAAAAAAAA
AAGCGCTAACGCGCCTTTACTTTTTTTTATTATATAATACCTTCTTTCTACTTCTTTCTCAAAGT
CAAGCAAGCAACCTTTCGCCTTTCTTTTTTTGAGGAGATATAAAAAGAAGCAACCTTACTAAGCA
AACGTAGGCTTGGGCTCGAAAGCAAGAAGCAATGGCTTTCGCGCTTGTTGGAGCTATTAAGCATC
TTAGACTATTCCATTCCATTTTGAAGCTGGACAGAAAAGTGGAAA
Right flanking sequence: Indices 177475 -- 177974
CTACGATGGACTTTTTTACTCTTTAAGTGCGCCACTCCTTCTTTTGTCCTGTATCTGTAGCTGCT
TTTCCCGCACTCTCTTTTATCCCGCCGAAGGTCCCCCTTACGTAATAGGGGTTAAGTTAAGGGGG
GTGCACACCGTGGTCAAATCTGCATGAAAAACCGCGGGGAATCATTAGTATTAAGTATTATGCTC
CCGCACCCCCTATCTCTTAAAGGCTCTGCGCTCCCGCATTCTGATTGATCCTGTGCAATGTTGTA
ATCCTGCTGTTCCTTTATCCCCCGCTCCGCAGCTGCTGGAGACTTAGTCATATTTTGAGCCTTTT
GCGGTACTGATTGATGTTATGGGGGATTACTTGGGTTGGCCGGACTGTTTGTTTGCGAAGGCCGA
AGGACTTAAAAATGAGGTTTTTGGTGTTATTGGACAGAATTGGTGCCGTTTTCCCACGCCTCATT
TTCCATAATATGATTATGAGCTGCAGAACGCTTGAAGCTGGAATT
Found at i:184496 original size:39 final size:39
Alignment explanation
Indices: 184442--184520 Score: 140
Period size: 39 Copynumber: 2.0 Consensus size: 39
184432 CAATTTTCTA
*
184442 TTCACTCATGATCTGGCCTAGTCGACCCGATCATGATAT
1 TTCACTCATGATCTGGCCTAGTCGACCCAATCATGATAT
*
184481 TTCACTCATGATCTGGCCTGGTCGACCCAATCATGATAT
1 TTCACTCATGATCTGGCCTAGTCGACCCAATCATGATAT
184520 T
1 T
184521 GAAGGATGGG
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
39 38 1.00
ACGTcount: A:0.23, C:0.28, G:0.18, T:0.32
Consensus pattern (39 bp):
TTCACTCATGATCTGGCCTAGTCGACCCAATCATGATAT
Left flanking sequence: Indices 183942 -- 184441
GCCCACACCTGTGTAGAGTGGATCGTTCAACACCTGCGGCACAAACCCATTTTTGACCTATTGGT
CCTAGTATCATAGGCGACCGAACGGCCGCCCCCTAATTACTAGACCGACCTGCTATAATAATTCC
ATAAACACCTAGCGAAGATATGGCAAACAAATAAAGTAGCCCTATGTTCGGATCTGACAATACCA
TACCATAATCAAAAGGTACAACGGCCCGGGCGACCAGACTTAACATAAATGTAGCCACTGGAGCC
ATTCTAAAAAGGGAGAAATTTGCACTACTTGGTGAAATAGGTTCTTTTATAATCAATTTAAAACC
ATCTGCTAGAGGTTGTAACAATCCAAACGATCCCACTACATCAGGACCCTTTCGACGTTGCACAA
AAGCCATTACTTTACGTTCAGCTAGCACTAAAAAGGCTACTCCTAGTAGAAGTGGTAGAATTATT
CCAAGTATTTCAGCTGGAACTGCTATGTACATTTTCAATTTTCTA
Right flanking sequence: Indices 184521 -- 185020
GAAGGATGGGACCTTTTCTCGAAAAAGAAAGGAGATTCTATTTCTTCTTCCAAGCCCTTCTTAGA
AGATGCAGTCAGTAAGCTCTCACTTATCTTCTTCATTTACGAAAATAGATAGATAAGAAAAGATG
TCAGCCTCTCTTTTCTCGCGGAACACTCACTTAATGGGGCTATTTGAATTGGAAGACAACGACAA
AAGTGAAAGAAGGAGGTCTATTTCGTTGATCGATGTCAATGGACCAAGAAATCTGTCCTTTGCTG
AAAGCTCATAGGGTAAGAAGAATTGAAAGGTAGGTTTTGTCAGTGATTAAATGGAAAGGTCAGCT
GGAGCGAAAACCAATCAAACTCAGAAAGATAGGTAGATCGAGCGCGCTGAGGGAAATTCGAGAGA
TCCGGAGACATGGCCACTACTGGCCTACGGTCCTTGCAGATTACATAGCACATGCTAAGAGCTGC
GATGCCTGCCAGAGGTATGCAGGAATCCAGCACAAGCCGGCTTCC
Found at i:192117 original size:25 final size:25
Alignment explanation
Indices: 192089--192139 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
192079 TAATTTGCCT
192089 AGTGAGAAAGCCAGGAAAAGACCCA
1 AGTGAGAAAGCCAGGAAAAGACCCA
192114 AGTGAGAAAGCCAGGAAAAGACCCA
1 AGTGAGAAAGCCAGGAAAAGACCCA
192139 A
1 A
192140 CAGACATACA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.49, C:0.20, G:0.27, T:0.04
Consensus pattern (25 bp):
AGTGAGAAAGCCAGGAAAAGACCCA
Left flanking sequence: Indices 191589 -- 192088
ACTTTCGGTGGACGTGGAGCCAACGAGTTCAGTCGAACAGCGTAACGAGTCTAAGGTTACAGAAG
CGTTCGCCAACTTTGATAGGCATAGCATTGCAAGCAAATAGAGCAGAGAGCTTACCCTTTCTTTC
TATTAGAGTCGTGAGCTTGTTGTAGTCGGTCCTAAAGGGAGAACCTTTCTGCTTACTTGCTATAT
CCCCGCGTCCTTGCACGGCTCGTTCTTCGCTTCCCCCTCTCCCCCAGGCCATATGGAGTATAGCC
AAGTGGTAAGGCATCGGTTTTTGGTACCGGCATGCAAAGGTTCGAATCCTTTTACTCCAGATTCT
CAACAGATCAAACAAGCTAAAGAGAAAGAAAGCAATAGAAAAAAGAAAGAGAAGGGAAAAGTATC
AAAATGCAGTTATATAAGCTATCACTTTTTCAATTCAAGATCAGCTCATCGAAGGGAAAAGTGAG
AGTATCAAAATGCAGTTATATGAGCATCGACTTTCTAATTTGCCT
Right flanking sequence: Indices 192140 -- 192639
CAGACATACAAACTCACTCTCCAGGGGCAGCTGAGGAAGGCAAGATTGATTAGGAGGTGGGGCAA
CTAGCTAGCCTTAGTAGTCAGGACGGAAGTCATACAACCTAGCTCCGGAGTTCATACATTTTTCA
TGCTTTCGGACGGCTCACTCTCAATTTCTTTAAGGTGCTAGCTGCTTAGCTTTACTAGAAGGTCG
ATGAGCTGGGTCAATCTCCATGCCCTTATCTTCTTCAAGCCCTTAAGGCAAAGAAGTCAACTAGC
GGTCTAGGAAGGCTAAGAAGGCAACTAGCTGCTTAGCCAACGACGATGAAGGTTAGTAACTCTCC
TTAAGGTCGATGCTAAAGAGCGTACTTAACACCAACCCCGGGCAAGCACCCAGGAAGGAAGACTA
ACAAGCTCGCCCTATTCAATAGGGGCTTAGCGAGTGTTTGAAGCCTCCTATCTCTTAAAGCTAAG
GTCCTAGCTTTAGGGGCTAGGGGCGTTTAGCAGACTTCTAGGCCT
Done.