Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NC_035157
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: 779361
ACGTcount: A:0.28, C:0.22, G:0.22, T:0.28
Found at i:30851 original size:18 final size:18
Alignment explanation
Indices: 30828--30874 Score: 76
Period size: 18 Copynumber: 2.6 Consensus size: 18
30818 CGTGAAAGAT
*
30828 CGGGCTTAGAATCGGGAA
1 CGGGCTTAGAATCAGGAA
30846 CGGGCTTAGAATCAGGAA
1 CGGGCTTAGAATCAGGAA
*
30864 CGGGCATAGAA
1 CGGGCTTAGAA
30875 CGGAAAATGA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.32, C:0.17, G:0.36, T:0.15
Consensus pattern (18 bp):
CGGGCTTAGAATCAGGAA
Left flanking sequence: Indices 30328 -- 30827
CTACTTAATTAAGCCTTTTTCTTTCCGAGGACAGCACAGGGCTCAGCACTCAAACTGTATAGGTT
TCCGCATTTGGAGGGACAACTACGGCTTATCCATAAGCAAGGGCCTGGCCTGAAACTGACTAAAA
AGATACCGCCCCAGCTGAATAAGTATACTAGTAGAGTAGTCTCCTGTAGAGAGATTAGATAGGCG
AAGGGGAACAAAGCTATTTATTCTCTAGAATCTTAAGATAAATCTATCTATTATCATTAGCTCTT
TCAGGGAAATACCTATAGATTACTGGTAGGGATGGAACATAACTCCCAGAAAGGAAAACTTCCAC
TGCCCTAGCTTTTGACCTTGACCTAACCCTTTAACAACCTAGACCTAGCTATTAACCTGTGCCTG
CCCTAGCCGTCTTTGATCTAGCTGGCTTGAGAAAGAAAATCCCAGATAAAAGCGGGACCACCCAC
AGGCATAGTGACCAAATAGACCCTCTCTTGTAGCTCGTGAAAGAT
Right flanking sequence: Indices 30875 -- 31374
CGGAAAATGAGCCTGTTAACTACTTGCCAGGTTCGCCTACCTTATTAGATTCGGCCTACAGAACT
TATTGGATTTACTTACATTCCTGTTTTTTAGATAACTTCTTCACTGACAACTTCTTTGATTCATC
GCCCATCGATCAAAAGAAAGACTAACGGCCTAAAAGCTTCCTTCGCCTGAGACTGAGCTTACCTT
GCCCACTTGAATGTACTATCTATTTGAGTTCTATTTTCAGTTTCGTGGCTGGATTAGAAGTTCGA
CTGAGCTATAGTCTCCGGACTAGTTGAACACTGACTCTTATTCCACTACTAGAAGTCCTTCTTCT
TATCGATTTGAGTGAGATTGAATCTTGAGCCCCCATCCTTGCTTTGATTTCCATTTATCTTCTCC
ACGGATGAACACCGGAATGGATTGATCTGACTCAATCTCTTTCTTCATGTCTCGCCCTGAAGATC
GAATTCCGTATTTACATTGATTTGACCTACCTTCTGCAATAGTGA
Found at i:64431 original size:18 final size:17
Alignment explanation
Indices: 64404--64440 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 17
64394 TCCCAGCTCC
*
64404 TGCCTTGCTTGCTTTCTT
1 TGCCTGGCTTGC-TTCTT
64422 TGCCTGGCTTGCTTCTT
1 TGCCTGGCTTGCTTCTT
64439 TG
1 TG
64441 TGTTTCATAG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 7 0.39
18 11 0.61
ACGTcount: A:0.00, C:0.27, G:0.22, T:0.51
Consensus pattern (17 bp):
TGCCTGGCTTGCTTCTT
Left flanking sequence: Indices 63904 -- 64403
CCCAGGGTTGACTCCCTTCACTAGTCAACGAAGTGCATCTACGGATGTAGGCACATTCTTGCTTG
ATCATTTGCTCTCACTAGACCGCCCTAGAGTACGATACTGGTTCGCCATAGGTTCGAAGGGCTGT
CTCTTGTGTGCGATGGTTGGGTATGAATGGAGCTTGCTCGGTAGAAAGGAGAGTAACCTTTGGGT
AATATAATATAATTTACTCATTCCTTCATAATGAAATATTCTACTCTTTTCTTTCTCCGTGGATT
CCTTGAGGATTGATCTGTTGTTGGATCCGTTGATGGATCGACCCTCCCTAACCACCCTATTTTTG
AGCACAGGCAGGTTTGAAGTGAAGGGATAGAATCCTGTACGTAGAAGGCTGAACCCATAACTCGT
GATTCGTAGCTTACAACCTATCCTTTCTCATCTTTGCTTACCGCTTCGCCCCCTTGCTCAAGTAT
GAGTCCTAAAGGTAAGGCAAGAAAGAGATTCTCAATCCCAGCTCC
Right flanking sequence: Indices 64441 -- 64940
TGTTTCATAGTGACTAATCTACCTATTCCTATGCTGGCAGGGGACTCAAGGTTGGCAGGGTTGTC
TCTAGGGTTGGGAATGAGACTATGAAACTCTTTCCTTTCCCGCCGGTAAGCAAGCAAGTCAAAAC
GCTAACACTGATGAGCTTGCTCTAATGAAACTACTAACACTCAGACTAGGGACAGGGGCTCAGAC
CCTGTTGCCTAGAAGAAGGAGATTCTATTTAGTTAGTCGGGTCTTAACAAGGAGCTAATGGATGC
ACTAACATATCGCCCCGTGTCCTAATAGTTATCTTACTACTGGAGTTAGATTGACTCCTTGGGTC
GGGCACCAAGGGAAGGATTAGTTCATATCCTAAACACCTATCGATTGTGTTAGTGAGTAAGTAAT
CACCCCCCGTGTATCCTTATAGAGTTCAGTTTAGTGCTTCTTACTGGTTGGGGTGGAGTCTAGCT
ACTACTACACGAGTCCCACACACCACTCCACAGCTCTAGGCTTTC
Found at i:73338 original size:13 final size:13
Alignment explanation
Indices: 73320--73345 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
73310 TAAGGAAGGC
73320 CTTGCCTTATTAG
1 CTTGCCTTATTAG
73333 CTTGCCTTATTAG
1 CTTGCCTTATTAG
73346 AGAGATATAG
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:0.15, C:0.23, G:0.15, T:0.46
Consensus pattern (13 bp):
CTTGCCTTATTAG
Left flanking sequence: Indices 72820 -- 73319
CTCAGACTCGCAGAAGACAAGTGAAAAGTATCTCGAGGTTTCTCCGCTTCTTGTTTCAAAATATC
GCAAAAATTCAGCGCTCTAAAAAAAAGGCCGGAAGGCCCCAGGACCCCCACCCCACGGCCCCTAT
GCCAAAGCAGTTGAGTGCAAGGAGGTCAGAGCAGAGGAGCTTCCCGGGTAGCAAGCTAGTTAGGA
GAGAATTCACCTATGGATTATTAAGTAGGTAGGAAAGCACGATAGGAGGCATGTCTCAGGCCTAG
GTGACAGCGGAGAACTTTAGAGGTAGGCTGGAAGGAAAGAGAAAGGCTAGGAGCTAGGCTAAATA
CGGAAGTAAATTCGTCTTTCGTCTGTATTGTGATCCCATGCCAGGACGAAGAAATCAAAGGATTT
ATAGTCATGCTCATGGAAGTATTGACTGGTTTAACGCTCATACCAATACGGCAGAGCATTTTTTC
TTAACTATTGAAAAAGCTCTTGATTTTTTCGGTTTTAAGGAAGGC
Right flanking sequence: Indices 73346 -- 73845
AGAGATATAGCCACCATAGACTAGCTCGTCTGTAGGGCTATGATCAGGCCATGCGGTCTAGAGAT
CTAGTTGACGCTTGGAAGAAACGGATATCCTTTCGAGAGAGAACGTGGCCATCCCGACCTGGAAG
GACTTTTATACTTCCTGCTTTGAGTGGGCCAGAAAGACAGATCAGTTCGTTTGCAACAGATCTTG
GAAGAAAATCAACAGAAAGAAGGTTGAGTGATAGACGAGGGGTTGTTTTCAGATGACGAAGTATT
CGTCAGCGATAGGGCTTCGCGCCTGAGAACAAAAAAAATGAAGGAAAAAAAAAGGCTTACAGAGG
ATTTCCAATAAGAAAAGGAAGAAGACCCCCATAGAACTCAAAGCGGAGGGGCTCTTCCTCAGAAT
GACGATGTGTGAGTTGCTTTTGTGAGGGGATAAAAGAGGTATGAAGAAAGTTGGCCAAGGTCATA
AGGTAAGGCCAAAGGTATTGGTGCATCTTTTTCTAGAAGTGGTCA
Found at i:115127 original size:22 final size:22
Alignment explanation
Indices: 115088--115130 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
115078 CTTCATCCGA
*
115088 ATAAGGAAGAGACAGGTACAAT
1 ATAAGGAAGAAACAGGTACAAT
* *
115110 ATAAGGAATAAACTGGTACAA
1 ATAAGGAAGAAACAGGTACAA
115131 GGAGTCCAGC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.51, C:0.09, G:0.23, T:0.16
Consensus pattern (22 bp):
ATAAGGAAGAAACAGGTACAAT
Left flanking sequence: Indices 114588 -- 115087
GTGAAACAAAGGAATGCTCCGTCAATTAAGTATTACCGGGGCCCCTTCTCCCTTATTCGCTCCTA
GGAATTAAGGGGAATAGGGCGCCTCGATTCAGTAGTTACAGGCCCGGGGCCTATATCTAGATTAG
AGGAATTAAATCGAGGAAGAAAAGGGAGCTGCGGATAAGGACAAGTCCGATCAGAACTACTACAC
AACCTTCAATGACTCTAACAAAAAACCTTGATGAATTAGATTAGAAAGGAAAGAAAGAGAAAAGG
AAGAAGAAAATAAATTATCCTAAGGAAATGAAACTAATAACAAATAGGATAATAGAGAGAAAGAA
CAACTTAAAGCTCATAGCATGCTAGCCGCCCTAGCTACTAGAGCGCTTAGCTAACAGCTCTTGGC
TCAGAAAGAATAGCTCCTAGGGCTAAAATTTTTTTATAAATTACCCGCTCAATCAGATAGGACGA
CCTACTCCTTAGTTGAACCGGACTTTGCCACTCACCTTCATCCGA
Right flanking sequence: Indices 115131 -- 115630
GGAGTCCAGCTGAACCACCCAGATCCGCTTCTTTCATCAAGCAACACAGCCTAGTCTAACCCGAG
CCCGAGTTCGTATTGGTAAATTTCGGGTCAGCAGGCAAAGGAAAGGGAACACCCACGTTCTACTT
TAATTAAGATGTGGTACAGTACTCTTCCCATGTTAAACTGCCCTGCCTTTCTAAAGGCCTGGTAC
ATCTTTTTTTTTTAAACCTATTCTCGACCCTCCTTCCTACCCCACCCACCGCTCTTCCTTTGAGG
CAAAAGTCTCTCTTATTCGACCAGAAGAGCCTTCTTCTTCATTTCACCTATGGACTTTTTCCACG
TAGCAACTTCCATACTGCACGAAGTCTTCTTCGGGAATGGCTTACCGCTCCGTGGGAATTGGATT
TAGTCCCGCGCGCTCCTGAAATGGGGGCTCTTTCCTCGGTGCGAAGGATCAAACCCTACGCCCAC
TGCCCTTGTTCCAAGATCTCACTTCATTCACGTATCCGCATCTGC
Found at i:122198 original size:19 final size:19
Alignment explanation
Indices: 122165--122203 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
122155 GAAGAAAGCG
** *
122165 TAAAAAAGAGCTTCCTCTA
1 TAAAAAAGAAATTCCCCTA
122184 TAAAAAAGAAATTCCCCTA
1 TAAAAAAGAAATTCCCCTA
122203 T
1 T
122204 CACCCGAGGG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.46, C:0.21, G:0.08, T:0.26
Consensus pattern (19 bp):
TAAAAAAGAAATTCCCCTA
Left flanking sequence: Indices 121665 -- 122164
AGTGATTGTTAAAAAGCTTCCTTTAACAATTAGATTAGGATCGGAGAAGTAAGCCAAGTCAAGTC
AAGGAAGATGCCCACTACTTATATAATAATAAATTTCCAGCCTCTAAACTAAAGGCTTTGAGCAA
GAAAAGGGATTGATATAGAGCATCGTGCTGATCGATGCGCGAAATACCCGGTTTTATAGTCAAAA
GATCTGCTAGCTATGGAGAAAGTATCCCGTCGACCTTCCTTCGATGACATCTCTGGACCAAGGTT
CCGGGCGTAGAATCCGCGTTAGTATCTGAAATGGATCAGTAGTCTCTCACAGAGTCCTCTCTTAC
GCTTAAGGCATCAAAAATAGAAACGAATCTGAGCTGGCTTTCAAGAAGGTATGTATAGCAGTAAG
ACTCGTAGGCGGACTAAGAGCTCTTGTCTTAGGCTGTTCTCAAATCCACACTTTCGGAATAGAAT
GGCTTGTTTTCAAGGTAACTAGAAATTGCATAAGAGAAGAAAGCG
Right flanking sequence: Indices 122204 -- 122703
CACCCGAGGGAACTCACTTAATCCTCATCTCTTGAACTCACTGAAACCAAGCCAATGGAGATTGG
CGGGTAAGATGCTGGAAATAGACTTCGCCGAATCCCTTTTCATTACATCCAACCGTCTGCTACTT
CTGCTACCGCAGCCCTTGCGACTTGATTGGTCCCCTTCCACTTCCCCCATTGTCAACTCGCTTGC
CCCGGCGTGAAGAACTCTCTCACGGAAGTGACTTCGACCAAGCATCTCGATTCAACTACAAGCCT
GCTATTCACTCGCTTTCGACGTTTCAAGTCGGATCTTGCCTTCACTCCTAAAGGAAGAAAACCTC
ACCTCAGAGCTTCACAAGAGCAGTCGAAAGAGCAAACTGATTCAACTTGAGCTATTCTTATTATT
GTGACAAGATCTGGAATTGCCTCTACGCTTTTTTCCTTTGCAACTTGCTACTAATGTCATACCGC
ATTCAGTCTAATTGGCCCAGCTCTCCTCTTTTCTTTGGTCAAGCC
Found at i:274059 original size:18 final size:18
Alignment explanation
Indices: 274019--274061 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
274009 AGCGCCCTGC
274019 CATAGTCGCGAGTCTGTTT
1 CATAGTCGCGAG-CTGTTT
274038 -ATAGTCGCGA-CTGTTGT
1 CATAGTCGCGAGCTGTT-T
274055 CATAGTC
1 CATAGTC
274062 AACAAGGTCA
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:0.19, C:0.21, G:0.26, T:0.35
Consensus pattern (18 bp):
CATAGTCGCGAGCTGTTT
Left flanking sequence: Indices 273519 -- 274018
ACCCCCGAAAGGGCTGCCGTCCGATGGGTACACGAAAGTGACGAAGTTGCTTTGACTACAGAACC
ATGCCTGTCTGTTGGAGCGAATTGGATGATCGGGCCGAGCCCCCTCTTCCCCGTGCTCTCCTTTC
CCTAATATGAACCTCACGTCATCAATTTCTGACTCGGCCTGGCCCGGTCGCCCTACGCGACTGGC
GCTTCAAAAGGCGAAACTCTCGTCGTAGTTTGGCGACCTGACGGGGCTCCCACTTTTTGTTATCT
AAAGGCGAAGACTCAGAAGTGGGCGTCGACTCGGCCCAGCGGGCGAACATGCCGGGCTCCGGCTC
CGCGCACCTGCCCTTTCGAAGCACTTTCTAGTGTGCGCTTTAGTTTTCGAATGTGTTGTTCAGCG
TCACGAGTCTACAAGCCTTTCGTGTTTCAGTGCTCGCCTTCATAATCTTCAGTAGGGGCCGTCTA
GTCTTTTGATTAGAGTAGGGGTCGCGAGAGAGCAGAGCGCCCTGC
Right flanking sequence: Indices 274062 -- 274561
AACAAGGTCACAACTTCCAGGAAAAAACTTCGAATTGGGAGGGCGATCCTCCCGGTGAACTGACC
GTACCCCAAACCGACACAGGTGAACAAGTAGAGTATACTAGGGCGCTTGAGAGAACCATGTCGAA
GGAACTCGGCAAAATGACCCCGTAACTTCGGGAGAAGGGGTGCTCTCCTATCTTTTGATTAGGAA
AGCGGCACATACCAGGGGGTAGCGACTGTTTATTAAAAACACAGGACTCTGCTAAGTGGTAACAC
GATGTATAGAGTCTGACACCTGCCCGGTGCTGGAAGGTCGGAAGGAGAAGTGTTATAAGCTTTGA
ATGGAAGCCCCGGTAAACGGCGGCAGTAACTCTAACTGTCCTAAGGTAGCGAAATTCCTTGTCGC
ATAAGTAGCGACCTGCACGAATGGTGTAACGACTGCCCCGCTGTCTCCGACATGGACCCGGTGAA
ATTGAATTCTCCGTGAAGATGCGGAGTACCAACGGCTAGACGGTA
Found at i:293191 original size:33 final size:33
Alignment explanation
Indices: 293149--293216 Score: 109
Period size: 33 Copynumber: 2.1 Consensus size: 33
293139 ACAGAGGTGA
* * *
293149 CTAATACAGACGAGGAGAAAGAGAAACCGATAC
1 CTAATACAGACGACGAGAAAAAGAAACCGAAAC
293182 CTAATACAGACGACGAGAAAAAGAAACCGAAAC
1 CTAATACAGACGACGAGAAAAAGAAACCGAAAC
293215 CT
1 CT
293217 CCTTGAAAGA
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.50, C:0.21, G:0.21, T:0.09
Consensus pattern (33 bp):
CTAATACAGACGACGAGAAAAAGAAACCGAAAC
Left flanking sequence: Indices 292649 -- 293148
TGCCCAGAGGAGGATGCTAGTGAGTTGTTAAGGAACTTCTTGCATTGCACATAGGGAAGGTGCGG
AGCGGTTCTTTATCTTATCATTGCCCTAAGGTAAGGCTTGGAACTGAACTGCAAGTATATAAGAA
AGGATATTGCTAAGAGTTAGCAGTCGAAGGGAGTTTGAACTGTGAAGGAATTACCGGTGCGCACA
GAGAAGGGGGAGAGAATACAGAAAATACGCCCTTGACTATACGGAGGATAAGAAATTAGGCAGGA
CTGATTTCCCTTCTTATCTTATTGTTGAGACAGGAAAGCAGTCAAGCGAATCGACGCATCTATCA
GCAGTAGGAGTAGGACGTAGCGCATAAGAGGGTCTTAGGAATCGATCTAGATGCCCAGAAGAGGA
TGCTATCGAATGCCCTCTTTGACGGGCTTGTGCAAGAAGCCGATTATTCTACCATCTTTTCCAAT
AGTGCCATTTTATTGATGCTATCGAAGAAGAACCAACAGAGGTGA
Right flanking sequence: Indices 293217 -- 293716
CCTTGAAAGAAGGAAAAATGCCACATCAGTAAGAGAAGTGGGCAAAAAAGCTGCTCTCCTATTTG
GACCACCTTCCACCCTGTCTCCCTCTCCATACATACAGAACCGTAGTTTATGGTCTCTTGTGTTT
ACAGCCCATTCTTCACCTTTCCTATAGCCAGCAAATCAAGGAGATACGGCTTAAAAGCCTACGCG
CGTCAGGTTGTTCGGCTTCGGCCCTTCCTACACGTGACTACACGGAATTAACTTTACTTTACGGT
ACGGAACTAGATATGAATTTCATCCTCTGTTGGCGAGATCAGAGGCAACGGTGGCAGCAGCTGTG
GATTCTGTTGATTCTTCATCTCCTCGCTTGACGCTCTCTTCAATTGCAGATCCTGAACCTTCGGT
CAAGTTGCTTTTCTATCCTGAACTTTCGGCTAAAGTGGCTTCCTCCTCTCTTCTCTTGAACTTTC
GTTCAAGTGGCTTCCTGTAGGGGCCTTTGAACGGGCCTTGGTGGG
Found at i:372565 original size:24 final size:24
Alignment explanation
Indices: 372538--372585 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
372528 AACTTGCAAA
*
372538 CATAACCAGGCAGTGAGGGATCTT
1 CATAACCAGGCAGTGAGGAATCTT
* *
372562 CATACCCAGGCGGTGAGGAATCTT
1 CATAACCAGGCAGTGAGGAATCTT
372586 AAGGGGAGGG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.27, C:0.23, G:0.29, T:0.21
Consensus pattern (24 bp):
CATAACCAGGCAGTGAGGAATCTT
Left flanking sequence: Indices 372038 -- 372537
AAATCAGGTCTTGTAATATACTGCAGGGCTCCAACGATGCTTCTGTACAGAGATGGATTATGAAA
TGGAGTAGAAGAGACTGCAGCAGAGGACTTATTTTAAAGTTAATTGGAGAAGAGCAGGGCTTACA
ATTCAGCATAGCAGCTCTCTGGAGGAGATCCAACGCATATTTTTGCTGTGTTAAAAAAAGTCCAC
GATCATTCTTGTCTTGAGTACCTCAATGCCAAGAAAATAGTTCAAGTTCCCGAGGTTCTTTATAG
CAAACTGAGCACTTAATTCAGTGATTAGAGTGGAGATATAAGAGGTATCACTGCCAGTTATAATA
ATATCATCCACATAAACCGCAAGAATTGTAGTTCGCAAACTGTTAGTTTGAATAAATAACGAGGA
ATCACTACGGCTCATAAGAAAGCCTTTACTGATTAAACAGCTATAAAACTTATCATACCAAGCGC
GTGATGCCTGTTTAAGACCATACAATGCTTTCTGCAACTTGCAAA
Right flanking sequence: Indices 372586 -- 373085
AAGGGGAGGGGTTGGTAGTGAAGGGAAGTCCAGGGCTGTGTCTGATCAGCTTACTGGGATAATTC
CAGGCGAGGGAGTATTGGTAAGGTTATGGAGGAAAGAGGAAATAGGATTTTGGGCATCTCTCGTT
GCTTCGGATTTTGATGATAAATAAGCTTCTCACAGATATTTACTTTTAGATAGATACCAGCATAG
TATCTTAATTAGCAGTTTCTTGAACTTGGTTGCACTCGTAAAGCAGCTTAAGAGAGCAACGAAAG
ACGGAGCGGTGATATTTCCTGACTAGCAAGTGGAGGATCATTCCAGGCTCTAATTCAGTCTCTGA
TGGCGTAGCTGATGTGTCATGCTAGGAAGCTGAGCTAGGGCATTTCTTCTTTCGGTTTAAGTGTT
CTAAGAAGTGAAAACCCTCCTCTCCGCTTCTGGCAGCATAGAAGGAAGCTTGGGGGAAAGGTCTA
AGTGCAAGCATTGAGTCAAACTGATTCAGGTATAGCAATGTAGTT
Found at i:393551 original size:27 final size:28
Alignment explanation
Indices: 393512--393565 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 28
393502 CTAATGTCGT
*
393512 TCTCTGGCAATGC-TATGCTGGAGGGAA
1 TCTCTGGCAATGCAAATGCTGGAGGGAA
* *
393539 TCTCTGGCTATGCAAATGGTGGAGGGA
1 TCTCTGGCAATGCAAATGCTGGAGGGA
393566 TTATGAAGTC
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
27 12 0.52
28 11 0.48
ACGTcount: A:0.22, C:0.17, G:0.35, T:0.26
Consensus pattern (28 bp):
TCTCTGGCAATGCAAATGCTGGAGGGAA
Left flanking sequence: Indices 393012 -- 393511
CAAGCCAAGAGGGAAAGAAGTTTGCAGGTAGCTGTTAGACGTCGCTCCTAGAGCAGAAAGAAGTC
AACCATCAAGAGATCCTAGAAGATCAAGAGAAAGAATTTATCACAGGACTCAAAATCTTCCCCTT
CCGATTAACAATCTCTTCCTTCCATTATGAAGATTCATTTATGAATTCTGAACGTTCATCTCTCT
TTTAGTAGTAGTCGGAGTACTGGGGAATATCTTATCGTCAGAGAAGTCAAAAAGGAAATGCCAAC
TTTCCTTTCCCTCCTAAGCTCCTCATTTCACACAATAAACTATTTTCCGACATTTCTTTTCTTTA
CTTCACTCGCTTTCGAGTCGACGAAGAAAAGAAGATTAACAACACCTTATGGAGATAGCTTGCCT
TCACTCTCACAGCTTGTGTGCCGTGGAAGGGGAAGGTCTTGCTTCCTCTCGTGCCTTTAAAAAAA
GTACCCATACCATTATGATCACCTTTAGAGTAAAACTAATGTCGT
Right flanking sequence: Indices 393566 -- 394065
TTATGAAGTCTTTGGGTAATGGCACTAAGCTTAATACACTTAGGAAATCCCTAGATAGAGAATGA
CCTTAAAAGGAACAAAGCTCTATTAAATCCACGGATAGAGACCTTAAAAGGAACAAAGCTCTATT
AAATGCCGGTCTCCTGCTGTATGTTTTTCTTTTTATTCTCTTACATAAAATTAAGGACATAGTGT
CCGAAAACCTCTCATAGCAGGTGTTAAGTCTAAATCAGACTGAGACTGATGGTCCAGGGTAGCGA
CACCTGAAATCGTATTAATAAGCTCAGGGTTTCACTCAGATCTTTGTGTGGCAGAACGCCAAATA
GGGTGGCTTGCCACACCTGAGCTCAGGGTTTTACTCTGATCTTTGTGTGGCAGAACGCCAAGCCA
AGGGGAAGAACGCCAAGACAAGGGTTGCGACAACTGAAATCTTATTAATAACCTCAGGGAAAGCC
AGGGTTTTACTCGGATTTTAAAGAAAAACAAAAAAAAATATGTTA
Found at i:393967 original size:20 final size:20
Alignment explanation
Indices: 393942--393979 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
393932 TTTGTGTGGC
*
393942 AGAACGCCAAGCCAAGGGGA
1 AGAACGCCAAGACAAGGGGA
393962 AGAACGCCAAGACAAGGG
1 AGAACGCCAAGACAAGGG
393980 TTGCGACAAC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.42, C:0.24, G:0.34, T:0.00
Consensus pattern (20 bp):
AGAACGCCAAGACAAGGGGA
Left flanking sequence: Indices 393442 -- 393941
GCTTCCTCTCGTGCCTTTAAAAAAAGTACCCATACCATTATGATCACCTTTAGAGTAAAACTAAT
GTCGTTCTCTGGCAATGCTATGCTGGAGGGAATCTCTGGCTATGCAAATGGTGGAGGGATTATGA
AGTCTTTGGGTAATGGCACTAAGCTTAATACACTTAGGAAATCCCTAGATAGAGAATGACCTTAA
AAGGAACAAAGCTCTATTAAATCCACGGATAGAGACCTTAAAAGGAACAAAGCTCTATTAAATGC
CGGTCTCCTGCTGTATGTTTTTCTTTTTATTCTCTTACATAAAATTAAGGACATAGTGTCCGAAA
ACCTCTCATAGCAGGTGTTAAGTCTAAATCAGACTGAGACTGATGGTCCAGGGTAGCGACACCTG
AAATCGTATTAATAAGCTCAGGGTTTCACTCAGATCTTTGTGTGGCAGAACGCCAAATAGGGTGG
CTTGCCACACCTGAGCTCAGGGTTTTACTCTGATCTTTGTGTGGC
Right flanking sequence: Indices 393980 -- 394479
TTGCGACAACTGAAATCTTATTAATAACCTCAGGGAAAGCCAGGGTTTTACTCGGATTTTAAAGA
AAAACAAAAAAAAATATGTTATATAATATGAGGAAGAATGCTAATTCTTTGTGTTGCAGAACGAA
ATTAAATCAATACATGAGTATTATATATAAGAGGGTTTTTTGTGTTAATAACTTCCAATTGTTGA
ATCGCAAGGTTCATATAGAATGGCATAAGCATAAGTGGGATAATACTTTATTGGGTATGGAACAA
ATTAATTGGCTTGCAATGAAATTATTTTTGAATTATTTGTTGATACCCAGAAAGGTGAATGACCC
CGCTCAAAGGGCTCAAAGGATCTTATCCAAGCATCCAGGAGGTGTCTTATTCACCAAAGTGAAAC
ACCAGCACTTGCGCAAAACGCCTGACAAAGGTCTGGCCGACGTATTAACTTTTTGGGTCTCAGAT
TTATTCGATTCTTCTTTCAAGACACGAGTCGATTTAATGCTCACT
Found at i:403441 original size:21 final size:21
Alignment explanation
Indices: 403382--403433 Score: 68
Period size: 21 Copynumber: 2.5 Consensus size: 21
403372 GCCAATACCC
* * * *
403382 GCAATCAAGTCATACTCAACA
1 GCAATCAAGTTAAAATCACCA
403403 GCAATCAAGTTAAAATCACCA
1 GCAATCAAGTTAAAATCACCA
403424 GCAATCAAGT
1 GCAATCAAGT
403434 AAGCATCAAC
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.44, C:0.25, G:0.12, T:0.19
Consensus pattern (21 bp):
GCAATCAAGTTAAAATCACCA
Left flanking sequence: Indices 402882 -- 403381
AGGGTCCTCTTGGAAATCCTGCTCCTTCTACGGCTGCTAGTATCCTTGTTCTTCTACTCGCAGGC
AGGGCTGCTCTTGCTATTGTTGCTAGGATCCTCTTATCCTATTGGTTGCTAGTCCCGGGCTTCTA
GGACAAAGTGTAAAGAGAAGAGTTAGAGTTCTTCCTCTTTCTCCCCTATCACTTAAAGGGAGATG
GCCTAATTTCTATTCTATCTATGGATCGAGAATAATCGTCAGTTTGAGGCCTGTCTTTGAACATA
AGGCATGAGAATCCTTCTCAGCGGAGTCTCTGTGTGTTGAGATCGAGGGTAGTTTGATTCTGGGA
ACCGAGCCGGCTTCGGCCAACGAATGAAGTTCTTTAGTAGGTTATCCGGGCATAGTTGAGTTAGG
AGCGAGGGAGTTCCATTTACTAGCTATATCCTCTTATTCTCGGGAAAGGGCAGTTCCAGCTAGGG
CTAGAGGACAGTCACATTCCTATTAGTAGGTTGAGGCCAATACCC
Right flanking sequence: Indices 403434 -- 403933
AAGCATCAACTGCTTTACCGTATAACAGTTCCTTGAGCAGATGTGATTGCAAATCTTCTACTACC
AAAGAATCTCTATCCGTCCCCCATATGCCCTTCGTTCTCCTGTCGTATGGATGTCTGTTTTCCCC
CCCCCCCTTCAATGCTGTCGCATTCTTGCCCCTTTTCGGTATGGTCCTTTCATTCAGGCCTTTCC
TTATGCACCGATGGTTTCATGATTCCTTGAAAAAAAAAATGTTTGCGAGCGTCAAAGCACCTAAC
CATACCTACTACACCATGCACTCCGCCGGTAAGCAGCCCGGACATGAAAGAAAGTGCATTTGGAA
GCATATGTGTGCCACTTTGGCACGAGATTTCAGCTCTACTTTGACTTTCATGGTTCCACTGTTCG
TCGAGATCCCTTGAGTGCTACTAAATGTAGAGAAAGACATTCATAGCTTGAACCTTCTGGTCACT
TCATTCCCTTTACATAAAAAAAGGTTTTGCTTGCTTTTCCACCTA
Found at i:458494 original size:17 final size:17
Alignment explanation
Indices: 458472--458516 Score: 54
Period size: 17 Copynumber: 2.6 Consensus size: 17
458462 TGGGGAAGAA
*
458472 AGGAAATCTGTCTTTAT
1 AGGAAATCTGTATTTAT
* *
458489 AGGAAATTTATATTTAT
1 AGGAAATCTGTATTTAT
*
458506 AGGGAATCTGT
1 AGGAAATCTGT
458517 GCTTACTAAG
Statistics
Matches: 22, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.33, C:0.07, G:0.20, T:0.40
Consensus pattern (17 bp):
AGGAAATCTGTATTTAT
Left flanking sequence: Indices 457972 -- 458471
CTCCCTGTCAGCTCCCTTCAACCATACATATATCTTAAATCTAGCTGGGTGCATGCAGACGTTTG
CGGACATCACCTATGGTGAATTTCCCGAAGCACATCTCGTTGGATGGATGTCGTTGCCGCGAAGT
GAGCTGGGCCACCTTCTGAGCGGAAGTGCCTTTGTAGCCTAGATCGTGCTCAGCTGGATAGGTTC
TTACTCTTACTTACGGATCGAAATAACAAAAGAAAGAACTAGAGCCCTGCTGTTCTAAAGCACAA
GTAAGGGCTTTTTTGTTCTACCAGAGAGAGTCTATTCTCACACTGAATCAATCATTCGAAGGGTC
GGGGAAGGAAGCGATGATCGGTCTATCCCATTAAGCGTAATCCCGTTAGCCAATGAAAGGACTAC
CTTTCTTGGACTGTGAGCGACGACACCAGATCAGAGCTAAGCGAGAAACGAGAAGCTGCGGTGAA
TCAATCAGTATTAGCTAAGGCAAGCATTCTAATTCTGGGGAAGAA
Right flanking sequence: Indices 458517 -- 459016
GCTTACTAAGCCTTTGTTTGAAGGACCGGTCTGAAAGTGCAAGACTAGCTGGACCCGGACTGACT
AATCGCTAAGAGCTCGTCCCGAGAGAACTCTCAGTACGGCATTCAGTAAGAAGTTAGCCAAGTTC
TGTTAGCCGTTACGTTAGGGTGACTCGAGAAAGTTTGAAAGGGAATTCCGATAGCCCTTAAGCTT
CAAGCTATCCGGCTTCAAGCCGTGAAGGAGGAATCCGAGTTACATCCTCTTAAAATAAGGAAGAT
CGTTCATCAGCGCTTTCAGTAACTAAGAGTCAATCAGGTGCGTAATCAAGCTCATCTCATTACTT
AGGATCTCACTCTCTCAATCTCCTATCTGGATTCTTTGCTTAGTCAGAGTTGAATCTTATAATAA
GGACAAGAAAGACTGGCATTCAGGTAAGGCATGATTCGGAAGATAGTGAATCTCTCCTTACTTGA
CTCTAGAAAGCTCTTTCTTTGCAAGTGGCAAGCAAGACTATGGTT
Found at i:573416 original size:35 final size:35
Alignment explanation
Indices: 573365--573444 Score: 151
Period size: 35 Copynumber: 2.3 Consensus size: 35
573355 GGCCCTTTTG
573365 CGACTCAAACTGCCGGTACGCTTTCCGGCTCGCAA
1 CGACTCAAACTGCCGGTACGCTTTCCGGCTCGCAA
*
573400 CGACGCAAACTGCCGGTACGCTTTCCGGCTCGCAA
1 CGACTCAAACTGCCGGTACGCTTTCCGGCTCGCAA
573435 CGACTCAAAC
1 CGACTCAAAC
573445 GGGCGGAGGC
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
35 43 1.00
ACGTcount: A:0.23, C:0.38, G:0.23, T:0.17
Consensus pattern (35 bp):
CGACTCAAACTGCCGGTACGCTTTCCGGCTCGCAA
Left flanking sequence: Indices 572865 -- 573364
ACCTCCGATCAGACAGAAAGATGCGATCGTTAGAGATTCGACGATTCCCGGTTGGACCTATTCAA
GCGATTGAACGAGATACTCGACAACTAGAAAGACGCACTTGAATACTGAATGCTATGAGTCGAGA
GAGAAAGAATGAATATCACCAACCATAAAGACGATAAAAGAAGGCACTCCCGTTCCCCCGAAATC
ATCTTCTGTGCGTGGTTATCCAATCATGATGTGGTAGGCTTAGTAGGGCTCGAACCTACAATCTA
ACCGTTATGAGCGGTACGTTTCAACCAATTAAACTATAAGCCCCTACGGATCTCTACATGCAATT
CGCTCACTTCGGGAAGAGCGGACGGAAGGCGACGGGGAGGCCTTTGCTCTATCTGCTTCTTCCTC
TTCTCAGGAATGAAGAATTAGATAAAAAAAAATGGATTATATTATTATATATATAATATTCTATA
TCTATTATTAGAATTAATAATATAATTAAGCAAGCGGCCCTTTTG
Right flanking sequence: Indices 573445 -- 573944
GGGCGGAGGCTCTCTATTTGCTTGCACTGCCGGCTGTTCGCCTTTAGTTAGAAGTAGAAGTCGCT
CTTTGCCCCACACTTCTAAAAAAGTATGGATTAATTAAGTAAGAAAAAAAAACTTGGTTACGGGA
ACCGAAGGTTAGGCCGACTACTTACTTTCTCCTTACCCTTAACAGGATTGTCTCCTACCGATCGA
GGAAAGGCTTAGAATCCATGCTTTGACCGGTAATGTCCAATCTAAGAACGTCTTGTGCCTTTTCC
TGGGCCCCCTTCATTCTGACTTAGCTAATTAAATTATTTCTATTTCTAATGGGCTTATACTTTTT
TCTATATCCCCTGAGAAAAGAAAGTCCTGCTATATCTAATGTATTTTTTCCAGGACCGCTTGCTT
CTGATCGCGCTTTAGAGTCTGTGCCGGTTGATGATCCTCAGTCGCAAGGTCAAAGAGGGTCTGAT
TTCTAGCATCTATGAAATCACTAAGTCTGGTAGGCTTCTGCACAT
Found at i:613141 original size:20 final size:20
Alignment explanation
Indices: 613116--613154 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
613106 AGGTAACTCG
613116 AGAGTA-GAAAGAACTAGAAT
1 AGAGTATGAAAGAAC-AGAAT
*
613136 AGAGTATGACAGAACAGAA
1 AGAGTATGAAAGAACAGAA
613155 CCAGTAGCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 10 0.59
21 7 0.41
ACGTcount: A:0.54, C:0.08, G:0.26, T:0.13
Consensus pattern (20 bp):
AGAGTATGAAAGAACAGAAT
Left flanking sequence: Indices 612616 -- 613115
GATCTTCTTTCTCCGTTGTGAAAGGAGTTGGTTCCGTAGTTTTAGAATTCGGCTGATCCCAAGTA
CTCCATCTCCATCATTGCATATTTTTATATAGAAAGTAAAGAAGAAAAGGCATAACCAGAAGAAT
TGTGTAAAATAAGTAAATTTATCCAGTTGAGGCATGATTGATTTGAGAAAAAATAAATTCTTACT
TCCAGAAAGAAGGAGCTCCCTTCCTGTACGAGTAAACAATAGATAAGGTTTGCTTGTTGGTTGTT
GACCAACAGAAAGCATGGGATGCCCCACAACAAATAGATGGGAGCAGGAAATCTTTATCATTCGG
CGTAGTGCAGCTTATATAGAAGGGGCAAAGCGCTGTTCGTGGCACAGCTTTCTTATATTACGATA
TTTTCATTGATCGTAGCTAATTAGGTGGCAACAACCGAAGAAGCAGAAGAAGTAGCTGCTACCGC
TTCGTGGGCTTCTTCTTTTTCTGAGTCTGCTCGAAAGGTAACTCG
Right flanking sequence: Indices 613155 -- 613654
CCAGTAGCTTTGAGCTTTCACGTGTTTCAGCTCTTGTTCACAATCCAGCTGCTATTGAATCAGCG
TAAGGAGATGCCGATGAGGGTACAATAGAGAAAAGAATGAGCTTTTGTTCAGAGCTTGAATCAGA
ATATCCTTCAGTAACTCCAGGATTCCCCTGGTAGGGCATACAGGACATACCAGGTGAGAAGTTCG
GGCGGAAAGATAGATCGAGTTTACTTTACCCTCTTGATTGACTTTCACTTTAGGACTGAAAGATA
GCAAAGGAAATGGCAGCAGTGCTTTATATAACTGCTTTTAGGTCTTCGTTGATCACTTCTGCTTA
ATTCTCTTTCGAAACCTAGAAAGCGAGAAAGAGAATAGTGAACGACTCCGATGCTATTTCTATTT
AATATTTAAGAAGATGGAGGAATAAGCGATGCTGCTAAGATCCGCAGTCGATTTAGCTCTTGAGG
GAAGGGAAAGGCGTAATTTGATGGGCTTTTAGGACTGGCCCGGAG
Found at i:684596 original size:19 final size:19
Alignment explanation
Indices: 684561--684599 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
684551 GAGCAAGCCC
*
684561 AAACAGAAGCAACAAGAAA
1 AAACAGAAGCAAAAAGAAA
684580 AAACA-AAGCAAGAAAGAAA
1 AAACAGAAGCAA-AAAGAAA
684599 A
1 A
684600 CAGCTCTTTG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 6 0.33
19 12 0.67
ACGTcount: A:0.72, C:0.13, G:0.15, T:0.00
Consensus pattern (19 bp):
AAACAGAAGCAAAAAGAAA
Left flanking sequence: Indices 684061 -- 684560
GATCTTCACTGGTCGGAGGCTAAGAGCTTTCTTTGACTCTGAGTCATATGGGATGGGTCCCTACT
CTCACTATGGCATAGTGGCCCAACGGTTCCTATGAAAGTCATAGCCGGACCTACTCTCCTCTCGC
CGATGGTTTGAGAGTTGCGTTGGCGTGACGCTAATCTACTTTCGAGTGCTTGAGTTTCACTCATG
TAGAGATAACGAAGGGAAAGGGCATTTGAGGGAGAGCCCAACCCAAGGGAAGGGGCAAAGAAAGG
ACCTGAGCACATTGACATCGAAGAAAAGGCCAATGAAAATAGGGAAAGTCCTATTCAAGCCGCTT
TACCGACGAGGTTAAAGAGCGGTAGCCCCTCCTTCGAGCAAGCAAGCGGCACTAAAAGCAGGATG
AAAGCAAGCAAGGAGTGTAAGCCACTTGCCCGATAGGGTAAGGAGCGGAGACCCTTCCTTCATTC
ATTAAGTTTAGGGATTTGAGTCAGGGATAACAGAGGAGCAAGCCC
Right flanking sequence: Indices 684600 -- 685099
CAGCTCTTTGTCTTACTGTGCCCGAGGAAGGGAAGAAAGAAGATGACAGACAAAGCACAACGGAG
GAATGAACTTCAAGCATGGAGGGGGAAAGTAACGGCACTCAAAGCTGTCTTCCATCAACCAAGCA
TGAAACAGAAGCCATGGACTAAGATGACTGGACAGGAGCGATAAGCAGCTATCAGCCACTCGAAC
CAAGTTAGAGGTTTTTTTCATGAGAGTCTTTCTAACATTCTTCACCTGAACCCGGGAACAGCTTT
GACTTAGATACTCTATTGTCAGATAGTTGAATGGCACCGGGAATGGATTAGGGAGCAAAGGAGAT
TAGGGAAAGTCCTCTGAAAGCCCTTTTTCCAACTGAGAGGGGCAGGAGAAGGATAGAAAGGTAGT
TTCCTCCAGCAAGAGGGATGACTTCTTCCTTTCCGCAAATAACAAGCGCTTTTCTTCGCCACATC
GCGTATAACGGGAATCGAACCCCCCTGCTGCTGGCGGGCGGATGG
Done.