Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold246
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 866086
ACGTcount: A:0.32, C:0.16, G:0.15, T:0.32
Warning! 37936 characters in sequence are not A, C, G, or T
File 3 of 4
Found at i:503772 original size:18 final size:18
Alignment explanation
Indices: 503650--503840 Score: 100
Period size: 18 Copynumber: 11.0 Consensus size: 18
503640 TAAGTATAAT
*
503650 TAAGTTATGCAAGTTATG
1 TAAGTTATGTAAGTTATG
* * * *
503668 ATATGATATAT-ATTTATG
1 -TAAGTTATGTAAGTTATG
* *
503686 T-A-TTATGTAAATTACG
1 TAAGTTATGTAAGTTATG
*
503702 TAAGTTATG-AGAGTTATA
1 TAAGTTATGTA-AGTTATG
*
503720 TAAGTTATG-ATA-TTATA
1 TAAGTTATGTA-AGTTATG
*
503737 TATATTTATGT-A-TTATG
1 TA-AGTTATGTAAGTTATG
503754 TAAGCTT-TGTAAGTTATG
1 TAAG-TTATGTAAGTTATG
*
503772 TGAGTTATGTAAGTTATG
1 TAAGTTATGTAAGTTATG
* * * *
503790 TATGATATAT-ATTTATG
1 TAAGTTATGTAAGTTATG
*
503807 T-A-TCATGTAAGTTATG
1 TAAGTTATGTAAGTTATG
*
503823 TGAGTTATGTAAGTTATG
1 TAAGTTATGTAAGTTATG
503841 ATATGATATA
Statistics
Matches: 130, Mismatches: 29, Indels: 27
0.70 0.16 0.15
Matches are distributed among these distances:
15 7 0.05
16 17 0.13
17 30 0.23
18 70 0.54
19 6 0.05
ACGTcount: A:0.34, C:0.02, G:0.18, T:0.46
Consensus pattern (18 bp):
TAAGTTATGTAAGTTATG
Found at i:503822 original size:51 final size:52
Alignment explanation
Indices: 503761--503869 Score: 202
Period size: 51 Copynumber: 2.1 Consensus size: 52
503751 ATGTAAGCTT
503761 TGTAAGTTATGTGAGTTATGTAAGTTATG-TATGATATATATTTATGTATCA
1 TGTAAGTTATGTGAGTTATGTAAGTTATGATATGATATATATTTATGTATCA
*
503812 TGTAAGTTATGTGAGTTATGTAAGTTATGATATGATATATATTTATGTATTA
1 TGTAAGTTATGTGAGTTATGTAAGTTATGATATGATATATATTTATGTATCA
503864 TGTAAG
1 TGTAAG
503870 NNNNNNNNNN
Statistics
Matches: 56, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
51 29 0.52
52 27 0.48
ACGTcount: A:0.32, C:0.01, G:0.20, T:0.47
Consensus pattern (52 bp):
TGTAAGTTATGTGAGTTATGTAAGTTATGATATGATATATATTTATGTATCA
Found at i:504138 original size:24 final size:25
Alignment explanation
Indices: 504097--504147 Score: 61
Period size: 24 Copynumber: 2.1 Consensus size: 25
504087 AGGTTAGATA
*
504097 TTAAAAATATATGTTTTA-AGTTAT
1 TTAAAAATATATGATTTATAGTTAT
*
504121 TTAAAAATATAAT-ATTTATATTTAT
1 TTAAAAATAT-ATGATTTATAGTTAT
504146 TT
1 TT
504148 TTAAAATTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
24 14 0.61
25 9 0.39
ACGTcount: A:0.43, C:0.00, G:0.04, T:0.53
Consensus pattern (25 bp):
TTAAAAATATATGATTTATAGTTAT
Found at i:505731 original size:24 final size:23
Alignment explanation
Indices: 505695--505770 Score: 75
Period size: 23 Copynumber: 3.3 Consensus size: 23
505685 CAAGTCTGTT
* *
505695 GGGAATTTAGGGAAATGAAATTG
1 GGGAAATTGGGGAAATGAAATTG
505718 GGGAAATTGGGGGAAAATG-AATT-
1 GGGAAATT-GGGG-AAATGAAATTG
* * *
505741 GGAAAATTGGGGAAATAAAATCG
1 GGGAAATTGGGGAAATGAAATTG
505764 GGGAAAT
1 GGGAAAT
505771 CTGAGTGGGG
Statistics
Matches: 43, Mismatches: 6, Indels: 8
0.75 0.11 0.14
Matches are distributed among these distances:
21 4 0.09
22 7 0.16
23 20 0.47
24 7 0.16
25 5 0.12
ACGTcount: A:0.42, C:0.01, G:0.36, T:0.21
Consensus pattern (23 bp):
GGGAAATTGGGGAAATGAAATTG
Found at i:505734 original size:164 final size:165
Alignment explanation
Indices: 505463--505789 Score: 496
Period size: 164 Copynumber: 2.0 Consensus size: 165
505453 TGAATAGAGG
* * * *
505463 AAGCGGGTGACAGAGCGACCGCTAGAGTGGAGACGACTGCGACGGCAACGGTGTTGGATAGGTCA
1 AAGCGGGTGACAGAGCGACCGCCAGAGTGGAGACGACTGCGACGGCAACGGCGTTGGACAAGTCA
*
505528 GTTGGGAATTTGGGAAAATGAAATCGGGGAAATTGGGGGAAAAGGAATTGGGAAATTAGGGAAAT
66 GTTGGGAATTTGGGAAAATGAAATCGGGGAAATTGGGGGAAAAGGAATTGGAAAATTAGGGAAAT
505593 AAAATC-GGGAAATCTGAGTGAGGGAAAACTAAGT
131 AAAATCGGGGAAATCTGAGTGAGGGAAAACTAAGT
* * * * * *
505627 AAGCGGGTGACAGAGTGACTGCCAGAGTGGAGACGATTGCGACGGTAGCGGCGTTGGACAAGTCT
1 AAGCGGGTGACAGAGCGACCGCCAGAGTGGAGACGACTGCGACGGCAACGGCGTTGGACAAGTCA
* * *
505692 GTTGGGAATTTAGGG-AAATGAAATTGGGGAAATTGGGGGAAAATGAATTGGAAAATTGGGGAAA
66 GTTGGGAATTT-GGGAAAATGAAATCGGGGAAATTGGGGGAAAAGGAATTGGAAAATTAGGGAAA
*
505756 TAAAATCGGGGAAATCTGAGTGGGGGAAAACTAA
130 TAAAATCGGGGAAATCTGAGTGAGGGAAAACTAA
505790 CAAAATTCGG
Statistics
Matches: 146, Mismatches: 15, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
164 118 0.81
165 28 0.19
ACGTcount: A:0.34, C:0.10, G:0.37, T:0.19
Consensus pattern (165 bp):
AAGCGGGTGACAGAGCGACCGCCAGAGTGGAGACGACTGCGACGGCAACGGCGTTGGACAAGTCA
GTTGGGAATTTGGGAAAATGAAATCGGGGAAATTGGGGGAAAAGGAATTGGAAAATTAGGGAAAT
AAAATCGGGGAAATCTGAGTGAGGGAAAACTAAGT
Found at i:506384 original size:8 final size:7
Alignment explanation
Indices: 506258--506531 Score: 88
Period size: 7 Copynumber: 38.7 Consensus size: 7
506248 ATGTTTTTAG
506258 CTAAACC
1 CTAAACC
* **
506265 ATAAATA
1 CTAAACC
506272 CTAAACC
1 CTAAACC
*
506279 CTAAACA
1 CTAAACC
*
506286 CTAAATC
1 CTAAACC
*
506293 ATAAACC
1 CTAAACC
*
506300 CTAAGCC
1 CTAAACC
506307 ACTAAACC
1 -CTAAACC
*
506315 CTAAAAC
1 CTAAACC
* **
506322 ATAAAAT
1 CTAAACC
*
506329 TTAAACC
1 CTAAACC
*
506336 TTAAACC
1 CTAAACC
* *
506343 TTAATCTC
1 CTAAAC-C
*
506351 CTAACCC
1 CTAAACC
506358 CTAAACC
1 CTAAACC
*
506365 CTAAGCC
1 CTAAACC
506372 C-ATAACC
1 CTA-AACC
*
506379 CTATAAATC
1 C--TAAACC
*
506388 CTAAGCTC
1 CTAAAC-C
506396 CT-AACC
1 CTAAACC
*
506402 CTTAACC
1 CTAAACC
* *
506409 CTTACACA
1 C-TAAACC
*
506417 CTAAACA
1 CTAAACC
506424 CTAAACC
1 CTAAACC
*
506431 ATAAA-C
1 CTAAACC
*
506437 CTACACC
1 CTAAACC
506444 CTAAACC
1 CTAAACC
* *
506451 GTAAACA
1 CTAAACC
*
506458 CTAAACT
1 CTAAACC
* *
506465 CTTAACA
1 CTAAACC
*
506472 CTAAATC
1 CTAAACC
*
506479 ATAAACC
1 CTAAACC
* **
506486 TTAAATT
1 CTAAACC
*
506493 TTAAACC
1 CTAAACC
* **
506500 CCAAATA
1 CTAAACC
*
506507 ATAAA-C
1 CTAAACC
*
506513 CTACACC
1 CTAAACC
506520 CTAAACC
1 CTAAACC
506527 CTAAA
1 CTAAA
506532 TGTATATATT
Statistics
Matches: 191, Mismatches: 65, Indels: 22
0.69 0.23 0.08
Matches are distributed among these distances:
6 11 0.06
7 157 0.82
8 18 0.09
9 4 0.02
10 1 0.01
ACGTcount: A:0.45, C:0.32, G:0.01, T:0.22
Consensus pattern (7 bp):
CTAAACC
Found at i:506390 original size:23 final size:23
Alignment explanation
Indices: 506337--506410 Score: 75
Period size: 23 Copynumber: 3.3 Consensus size: 23
506327 ATTTAAACCT
* * *
506337 TAAACCTTAATCTCCTAACCC-C
1 TAAACCCTAAGCTCCTAACCCTA
506359 TAAACCCTAAGC-CCATAACCCTA
1 TAAACCCTAAGCTCC-TAACCCTA
*
506382 TAAATCCTAAGCTCCTAACCCT-
1 TAAACCCTAAGCTCCTAACCCTA
506404 T-AACCCT
1 TAAACCCT
506411 TACACACTAA
Statistics
Matches: 44, Mismatches: 5, Indels: 7
0.79 0.09 0.12
Matches are distributed among these distances:
21 7 0.16
22 17 0.39
23 18 0.41
24 2 0.05
ACGTcount: A:0.34, C:0.39, G:0.03, T:0.24
Consensus pattern (23 bp):
TAAACCCTAAGCTCCTAACCCTA
Found at i:506462 original size:27 final size:27
Alignment explanation
Indices: 506411--506490 Score: 69
Period size: 27 Copynumber: 2.9 Consensus size: 27
506401 CCTTAACCCT
506411 TACACACTAAACACTAAACCATAAACC
1 TACACACTAAACACTAAACCATAAACC
*
506438 TACACCCTAAAC-CGTAAA-CACTAAACTC
1 TACACACTAAACAC-TAAACCA-TAAAC-C
*
506466 TTA-ACACTAAATCA-TAAACCTTAAA
1 -TACACACTAAA-CACTAAACCATAAA
506491 TTTTAAACCC
Statistics
Matches: 43, Mismatches: 3, Indels: 13
0.73 0.05 0.22
Matches are distributed among these distances:
26 3 0.07
27 20 0.47
28 16 0.37
29 4 0.09
ACGTcount: A:0.49, C:0.30, G:0.01, T:0.20
Consensus pattern (27 bp):
TACACACTAAACACTAAACCATAAACC
Found at i:507206 original size:39 final size:41
Alignment explanation
Indices: 507163--507311 Score: 191
Period size: 40 Copynumber: 3.7 Consensus size: 41
507153 TTTGAAAAAA
* **
507163 GCCGCTAATGCTTGATCTATAGC-GCGTTTTTTTTA-AAGC
1 GCCGCTAATGCTCGATCTATAGCAGCGTTTTTTCAAGAAGC
*
507202 GCCGCTAATGCTCGATCTATAGCAGAG-TTTTTCAAGAAGC
1 GCCGCTAATGCTCGATCTATAGCAGCGTTTTTTCAAGAAGC
*
507242 GCCGCTAATGCTCGATCTATAAC-GAC-TTTTTTCAAGAAGC
1 GCCGCTAATGCTCGATCTATAGCAG-CGTTTTTTCAAGAAGC
* *
507282 GCCGCTAATGTTCGATCTATAGCGGCGTTT
1 GCCGCTAATGCTCGATCTATAGCAGCGTTT
507312 GAATAACAAA
Statistics
Matches: 96, Mismatches: 8, Indels: 10
0.84 0.07 0.09
Matches are distributed among these distances:
39 29 0.30
40 63 0.66
41 4 0.04
ACGTcount: A:0.23, C:0.23, G:0.21, T:0.32
Consensus pattern (41 bp):
GCCGCTAATGCTCGATCTATAGCAGCGTTTTTTCAAGAAGC
Found at i:509122 original size:21 final size:21
Alignment explanation
Indices: 509073--509114 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
509063 AACTCGAAAT
*
509073 AAAT-TTTATTTATTTTTCAAA
1 AAATATTT-TTTATTGTTCAAA
509094 AAATATTTTTTATTGTTCAAA
1 AAATATTTTTTATTGTTCAAA
509115 TTATATTTGA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 16 0.84
22 3 0.16
ACGTcount: A:0.38, C:0.05, G:0.02, T:0.55
Consensus pattern (21 bp):
AAATATTTTTTATTGTTCAAA
Found at i:509686 original size:28 final size:28
Alignment explanation
Indices: 509640--509693 Score: 74
Period size: 28 Copynumber: 1.9 Consensus size: 28
509630 CAAATGCCTA
*
509640 TTTTTGTAATTATTCTATTTTCTATACC
1 TTTTTGTAATTAATCTATTTTCTATACC
*
509668 TTTTTAGTAATTAAT-TATTTTTTATA
1 TTTTT-GTAATTAATCTATTTTCTATA
509694 TTATTTAGGT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
28 15 0.65
29 8 0.35
ACGTcount: A:0.26, C:0.07, G:0.04, T:0.63
Consensus pattern (28 bp):
TTTTTGTAATTAATCTATTTTCTATACC
Found at i:509689 original size:29 final size:27
Alignment explanation
Indices: 509640--509693 Score: 65
Period size: 29 Copynumber: 1.9 Consensus size: 27
509630 CAAATGCCTA
*
509640 TTTTTGTAATTATTCTATTTTCTATACC
1 TTTTTGTAATTATTATATTTT-TATACC
509668 TTTTTAGTAATTAATTAT-TTTTTATA
1 TTTTT-GTAATT-ATTATATTTTTATA
509694 TTATTTAGGT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
28 9 0.39
29 10 0.43
30 4 0.17
ACGTcount: A:0.26, C:0.07, G:0.04, T:0.63
Consensus pattern (27 bp):
TTTTTGTAATTATTATATTTTTATACC
Found at i:514376 original size:16 final size:17
Alignment explanation
Indices: 514355--514390 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
514345 TTTGTTTTTT
*
514355 TTTGGGC-TAGGTTTGG
1 TTTGGGCTTAGGTTTAG
514371 TTTGGGCTTAGGTTTAG
1 TTTGGGCTTAGGTTTAG
514388 TTT
1 TTT
514391 ATTGGGTTTG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 7 0.39
17 11 0.61
ACGTcount: A:0.08, C:0.06, G:0.36, T:0.50
Consensus pattern (17 bp):
TTTGGGCTTAGGTTTAG
Found at i:516621 original size:20 final size:20
Alignment explanation
Indices: 516598--516639 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
516588 TTTCATATTT
516598 AAAATTGTAAATCTCATTCC
1 AAAATTGTAAATCTCATTCC
516618 AAAATTGTAAATCTCATTCC
1 AAAATTGTAAATCTCATTCC
516638 AA
1 AA
516640 CATAATTATT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.43, C:0.19, G:0.05, T:0.33
Consensus pattern (20 bp):
AAAATTGTAAATCTCATTCC
Found at i:516795 original size:28 final size:28
Alignment explanation
Indices: 516741--516809 Score: 86
Period size: 28 Copynumber: 2.4 Consensus size: 28
516731 ACAAAATATT
* *
516741 TTTTATAATATTAAAAATTAGACTTAAA
1 TTTTAAAATATTAAAAATAAGACTTAAA
516769 TTTTAAAATATTAAAAATAAAGA-TTAAA
1 TTTTAAAATATTAAAAAT-AAGACTTAAA
516797 TTATTGAAAATAT
1 TT-TT-AAAATAT
516810 AAGTTGAGAG
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
28 24 0.67
29 5 0.14
30 7 0.19
ACGTcount: A:0.54, C:0.01, G:0.04, T:0.41
Consensus pattern (28 bp):
TTTTAAAATATTAAAAATAAGACTTAAA
Found at i:518943 original size:3 final size:3
Alignment explanation
Indices: 518935--518968 Score: 52
Period size: 3 Copynumber: 11.7 Consensus size: 3
518925 TTTATATTGT
*
518935 TTA TTA TTA TAA TTA TTA TTA -TA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
518969 GTATTTATAT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
2 2 0.07
3 26 0.93
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:518965 original size:14 final size:14
Alignment explanation
Indices: 518935--518973 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
518925 TTTATATTGT
518935 TTATTATTATA--A
1 TTATTATTATATTA
518947 TTATTATTATATTA
1 TTATTATTATATTA
*
518961 TTATTATTGTATT
1 TTATTATTATATT
518974 TATATGTGTG
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
12 11 0.46
14 13 0.54
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.64
Consensus pattern (14 bp):
TTATTATTATATTA
Found at i:519007 original size:16 final size:16
Alignment explanation
Indices: 518988--519018 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
518978 TGTGTGCGCC
*
518988 TATATATATATATTAA
1 TATACATATATATTAA
519004 TATACATATATATTA
1 TATACATATATATTA
519019 TAAATGTTTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (16 bp):
TATACATATATATTAA
Found at i:524972 original size:56 final size:58
Alignment explanation
Indices: 524905--525026 Score: 178
Period size: 56 Copynumber: 2.1 Consensus size: 58
524895 TTCAACATGA
* *
524905 GAACAATTGTCAAGTCCAATG-ACTAACTTGGACAAAAAAA-TTT-AAGCCCAATAAAG
1 GAACAATTGTCAAGTCC-AGGAACTAACTTGGACAAAAAAATTTTAAACCCCAATAAAG
* *
524961 GAACAATTGTCAAGTTCAGGAACTAACTTGGACAAAAAAATTTTAAACCCCAATATAG
1 GAACAATTGTCAAGTCCAGGAACTAACTTGGACAAAAAAATTTTAAACCCCAATAAAG
525019 GAACAATT
1 GAACAATT
525027 ACCAAGTTCA
Statistics
Matches: 59, Mismatches: 4, Indels: 4
0.88 0.06 0.06
Matches are distributed among these distances:
55 2 0.03
56 35 0.59
57 3 0.05
58 19 0.32
ACGTcount: A:0.46, C:0.17, G:0.14, T:0.23
Consensus pattern (58 bp):
GAACAATTGTCAAGTCCAGGAACTAACTTGGACAAAAAAATTTTAAACCCCAATAAAG
Found at i:525033 original size:58 final size:56
Alignment explanation
Indices: 524926--525037 Score: 170
Period size: 58 Copynumber: 2.0 Consensus size: 56
524916 AAGTCCAATG
* **
524926 ACTAACTTGGACAAAAAAATTTAAGCCCAATAAAGGAACAATTGTCAAGTTCAGGA
1 ACTAACTTGGACAAAAAAATTTAACCCCAATAAAGGAACAATTACCAAGTTCAGGA
*
524982 ACTAACTTGGACAAAAAAATTTTAAACCCCAATATAGGAACAATTACCAAGTTCAG
1 ACTAACTTGGACAAAAAAA-TTT-AACCCCAATAAAGGAACAATTACCAAGTTCAG
525038 ATCCAAAATA
Statistics
Matches: 50, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
56 19 0.38
57 3 0.06
58 28 0.56
ACGTcount: A:0.46, C:0.18, G:0.13, T:0.22
Consensus pattern (56 bp):
ACTAACTTGGACAAAAAAATTTAACCCCAATAAAGGAACAATTACCAAGTTCAGGA
Found at i:529331 original size:14 final size:14
Alignment explanation
Indices: 529312--529367 Score: 76
Period size: 14 Copynumber: 3.8 Consensus size: 14
529302 AAAAAGGTTG
529312 TAACAGTTAGTAGT
1 TAACAGTTAGTAGT
529326 TAACAGTTAGTAGT
1 TAACAGTTAGTAGT
*
529340 TAATAGTTGTAGTTAGT
1 TAACAG-T-TAG-TAGT
529357 TAACAGTTAGT
1 TAACAGTTAGT
529368 TATTAGCTTG
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
14 20 0.54
15 4 0.11
16 4 0.11
17 9 0.24
ACGTcount: A:0.34, C:0.05, G:0.21, T:0.39
Consensus pattern (14 bp):
TAACAGTTAGTAGT
Found at i:534830 original size:25 final size:25
Alignment explanation
Indices: 534802--534866 Score: 62
Period size: 25 Copynumber: 2.6 Consensus size: 25
534792 TCTATTCAAT
534802 TATAAATAAATTAATATTTAAAAAA
1 TATAAATAAATTAATATTTAAAAAA
* *
534827 TAT-AGTAAAATTTA-ATTTAAAAAA
1 TATAAAT-AAATTAATATTTAAAAAA
* *
534851 TCATAAACAATTTAAT
1 T-ATAAATAAATTAAT
534867 TTAAACATGG
Statistics
Matches: 30, Mismatches: 6, Indels: 7
0.70 0.14 0.16
Matches are distributed among these distances:
24 13 0.43
25 16 0.53
26 1 0.03
ACGTcount: A:0.58, C:0.03, G:0.02, T:0.37
Consensus pattern (25 bp):
TATAAATAAATTAATATTTAAAAAA
Found at i:534844 original size:24 final size:24
Alignment explanation
Indices: 534817--534871 Score: 78
Period size: 24 Copynumber: 2.3 Consensus size: 24
534807 ATAAATTAAT
534817 ATTTAAAAAAT-ATAGTAA-AATTTA
1 ATTTAAAAAATCATA--AACAATTTA
534841 ATTTAAAAAATCATAAACAATTTA
1 ATTTAAAAAATCATAAACAATTTA
534865 ATTTAAA
1 ATTTAAA
534872 CATGGTTAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
23 2 0.07
24 24 0.83
25 3 0.10
ACGTcount: A:0.58, C:0.04, G:0.02, T:0.36
Consensus pattern (24 bp):
ATTTAAAAAATCATAAACAATTTA
Found at i:536592 original size:22 final size:22
Alignment explanation
Indices: 536567--536608 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
536557 TTTATTTTAA
*
536567 TGAATTTTTAATGATTTTTTGG
1 TGAATTTTTAATAATTTTTTGG
536589 TGAATTTTTAATAATTTTTT
1 TGAATTTTTAATAATTTTTT
536609 TAAATATATA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.26, C:0.00, G:0.12, T:0.62
Consensus pattern (22 bp):
TGAATTTTTAATAATTTTTTGG
Found at i:536608 original size:11 final size:11
Alignment explanation
Indices: 536561--536607 Score: 60
Period size: 11 Copynumber: 4.4 Consensus size: 11
536551 TATTTTTTTA
536561 TTTTAATGAAT
1 TTTTAATGAAT
*
536572 TTTTAATGATT
1 TTTTAATGAAT
**
536583 TTTTGGTGAAT
1 TTTTAATGAAT
536594 TTTTAAT-AAT
1 TTTTAATGAAT
536604 TTTT
1 TTTT
536608 TTAAATATAT
Statistics
Matches: 30, Mismatches: 6, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
10 7 0.23
11 23 0.77
ACGTcount: A:0.28, C:0.00, G:0.11, T:0.62
Consensus pattern (11 bp):
TTTTAATGAAT
Found at i:542341 original size:13 final size:13
Alignment explanation
Indices: 542307--542343 Score: 56
Period size: 14 Copynumber: 2.8 Consensus size: 13
542297 AGATATTTGT
*
542307 AATTTGAAAACTT
1 AATTTGAAAACTC
542320 AAGTTTGAAAACTC
1 AA-TTTGAAAACTC
542334 AATTTGAAAA
1 AATTTGAAAA
542344 TTTGGAAACT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 10 0.45
14 12 0.55
ACGTcount: A:0.49, C:0.08, G:0.11, T:0.32
Consensus pattern (13 bp):
AATTTGAAAACTC
Found at i:542605 original size:34 final size:34
Alignment explanation
Indices: 542567--542767 Score: 159
Period size: 34 Copynumber: 5.9 Consensus size: 34
542557 AATTACAAAA
** * *
542567 CTATTCACTTGTCTTTTCTTGGAGGGAATATTTC
1 CTATTCACTCATCATTTCTTGCAGGGAATATTTC
* ** * * *
542601 CTATTCACGCATTTTTTTGTTGCAGGGAATCTCTC
1 CTATTCACTCA-TCATTTCTTGCAGGGAATATTTC
* * * *
542636 TTGTTCACACATCATTTCTTGCAGGGAATCTTTC
1 CTATTCACTCATCATTTCTTGCAGGGAATATTTC
*
542670 CTATTCACGCATCATTTCTTGCAGGGAATATTTC
1 CTATTCACTCATCATTTCTTGCAGGGAATATTTC
* * * * * *
542704 CTGTTCACGCATTATTTTGTTGCAGGGAATCTCTC
1 CTATTCACTCATCA-TTTCTTGCAGGGAATATTTC
* * * *
542739 ATGTTCACACATCATTTCTTGTAGGGAAT
1 CTATTCACTCATCATTTCTTGCAGGGAAT
542768 CTCTCATGTT
Statistics
Matches: 136, Mismatches: 29, Indels: 4
0.80 0.17 0.02
Matches are distributed among these distances:
34 82 0.60
35 54 0.40
ACGTcount: A:0.20, C:0.21, G:0.17, T:0.41
Consensus pattern (34 bp):
CTATTCACTCATCATTTCTTGCAGGGAATATTTC
Found at i:542681 original size:69 final size:69
Alignment explanation
Indices: 542580--542779 Score: 231
Period size: 69 Copynumber: 2.9 Consensus size: 69
542570 TTCACTTGTC
* * ** * *
542580 TTTTCTTGGAGGGAATATTTCCTATTCACGCATTTTTTTGTTGCAGGGAATCTCTCTTGTTCACA
1 TTTTCTTGCAGGGAATCTTTCCTATTCACGCA-TCATTTCTTGCAGGGAATCTCTCATGTTCACA
542645 CATCA
65 CATCA
* * * *
542650 -TTTCTTGCAGGGAATCTTTCCTATTCACGCATCATTTCTTGCAGGGAATATTTCCTGTTCACGC
1 TTTTCTTGCAGGGAATCTTTCCTATTCACGCATCATTTCTTGCAGGGAATCTCTCATGTTCACAC
*
542714 ATTA
66 ATCA
* * * * * *
542718 TTTTGTTGCAGGGAATCTCTCATGTTCACACATCATTTCTTGTAGGGAATCTCTCATGTTCA
1 TTTTCTTGCAGGGAATCTTTCCTATTCACGCATCATTTCTTGCAGGGAATCTCTCATGTTCA
542780 TTCGTCATTT
Statistics
Matches: 110, Mismatches: 19, Indels: 3
0.83 0.14 0.02
Matches are distributed among these distances:
68 29 0.26
69 81 0.74
ACGTcount: A:0.20, C:0.21, G:0.17, T:0.41
Consensus pattern (69 bp):
TTTTCTTGCAGGGAATCTTTCCTATTCACGCATCATTTCTTGCAGGGAATCTCTCATGTTCACAC
ATCA
Found at i:542746 original size:103 final size:103
Alignment explanation
Indices: 542581--542769 Score: 333
Period size: 103 Copynumber: 1.8 Consensus size: 103
542571 TCACTTGTCT
* * *
542581 TTTCTTGGAGGGAATATTTCCTATTCACGCATTTTTTTGTTGCAGGGAATCTCTCTTGTTCACAC
1 TTTCTTGCAGGGAATATTTCCTATTCACGCATTATTTTGTTGCAGGGAATCTCTCATGTTCACAC
542646 ATCATTTCTTGCAGGGAATCTTTCCTATTCACGCATCA
66 ATCATTTCTTGCAGGGAATCTTTCCTATTCACGCATCA
*
542684 TTTCTTGCAGGGAATATTTCCTGTTCACGCATTATTTTGTTGCAGGGAATCTCTCATGTTCACAC
1 TTTCTTGCAGGGAATATTTCCTATTCACGCATTATTTTGTTGCAGGGAATCTCTCATGTTCACAC
*
542749 ATCATTTCTTGTAGGGAATCT
66 ATCATTTCTTGCAGGGAATCT
542770 CTCATGTTCA
Statistics
Matches: 81, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
103 81 1.00
ACGTcount: A:0.21, C:0.21, G:0.17, T:0.41
Consensus pattern (103 bp):
TTTCTTGCAGGGAATATTTCCTATTCACGCATTATTTTGTTGCAGGGAATCTCTCATGTTCACAC
ATCATTTCTTGCAGGGAATCTTTCCTATTCACGCATCA
Found at i:542791 original size:34 final size:34
Alignment explanation
Indices: 542620--542779 Score: 203
Period size: 34 Copynumber: 4.7 Consensus size: 34
542610 CATTTTTTTG
*
542620 TTGCAGGGAATCTCTCTTGTTCACACATCATTTC
1 TTGCAGGGAATCTCTCATGTTCACACATCATTTC
* * * *
542654 TTGCAGGGAATCTTTCCTATTCACGCATCATTTC
1 TTGCAGGGAATCTCTCATGTTCACACATCATTTC
* * * * * *
542688 TTGCAGGGAATATTTCCTGTTCACGCATTATTTTG
1 TTGCAGGGAATCTCTCATGTTCACACATCA-TTTC
542723 TTGCAGGGAATCTCTCATGTTCACACATCATTTC
1 TTGCAGGGAATCTCTCATGTTCACACATCATTTC
*
542757 TTGTAGGGAATCTCTCATGTTCA
1 TTGCAGGGAATCTCTCATGTTCA
542780 TTCGTCATTT
Statistics
Matches: 110, Mismatches: 15, Indels: 2
0.87 0.12 0.02
Matches are distributed among these distances:
34 82 0.75
35 28 0.25
ACGTcount: A:0.21, C:0.23, G:0.17, T:0.39
Consensus pattern (34 bp):
TTGCAGGGAATCTCTCATGTTCACACATCATTTC
Found at i:545692 original size:21 final size:23
Alignment explanation
Indices: 545668--545710 Score: 54
Period size: 21 Copynumber: 2.0 Consensus size: 23
545658 TTAATTTTTT
*
545668 AAAACATATTT-CTTCT-TTTAC
1 AAAACAGATTTGCTTCTGTTTAC
*
545689 AAAAGAGATTTGCTTCTGTTTA
1 AAAACAGATTTGCTTCTGTTTA
545711 TAATTAATTA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 9 0.50
22 5 0.28
23 4 0.22
ACGTcount: A:0.33, C:0.14, G:0.09, T:0.44
Consensus pattern (23 bp):
AAAACAGATTTGCTTCTGTTTAC
Found at i:553582 original size:26 final size:25
Alignment explanation
Indices: 553553--553615 Score: 65
Period size: 26 Copynumber: 2.4 Consensus size: 25
553543 TTATTTAAAT
*
553553 TTAATTATAAATGATATATTAACAT-A
1 TTAATTATAAATAATA-ATTAA-ATAA
* *
553579 TTAATATAAAAATAATAATTTAATAA
1 TTAAT-TATAAATAATAATTAAATAA
553605 TTAATTATAAA
1 TTAATTATAAA
553616 AAGATTAATA
Statistics
Matches: 31, Mismatches: 4, Indels: 5
0.77 0.10 0.12
Matches are distributed among these distances:
25 7 0.23
26 15 0.48
27 9 0.29
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.41
Consensus pattern (25 bp):
TTAATTATAAATAATAATTAAATAA
Found at i:563169 original size:25 final size:24
Alignment explanation
Indices: 563141--563200 Score: 57
Period size: 26 Copynumber: 2.4 Consensus size: 24
563131 AATCTCCGTT
**
563141 AAGCTCAAGTCTAGCTTTGAGTCTC
1 AAGCTCAAGTCTAGAGTTGAG-CTC
* * *
563166 AAGCCTCAAATTTTGAGTTGAGCTC
1 AAG-CTCAAGTCTAGAGTTGAGCTC
563191 AAGCTCAAGT
1 AAGCTCAAGT
563201 TTCTTACCGC
Statistics
Matches: 28, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
24 6 0.21
25 9 0.32
26 13 0.46
ACGTcount: A:0.28, C:0.22, G:0.20, T:0.30
Consensus pattern (24 bp):
AAGCTCAAGTCTAGAGTTGAGCTC
Found at i:568207 original size:25 final size:25
Alignment explanation
Indices: 568173--568227 Score: 83
Period size: 25 Copynumber: 2.2 Consensus size: 25
568163 TAAGAGTGGT
*
568173 CAAAATAAAATCACAAAACTATGGA
1 CAAAATAAAATCACAAAACTATAGA
* *
568198 CAAAATAAAATCACGAAACTGTAGA
1 CAAAATAAAATCACAAAACTATAGA
568223 CAAAA
1 CAAAA
568228 CCATAATAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.60, C:0.16, G:0.09, T:0.15
Consensus pattern (25 bp):
CAAAATAAAATCACAAAACTATAGA
Found at i:569564 original size:30 final size:30
Alignment explanation
Indices: 569529--569590 Score: 115
Period size: 30 Copynumber: 2.1 Consensus size: 30
569519 AGATTAATAG
569529 ATGCACATATAGTGAAATTTTATTAATTTT
1 ATGCACATATAGTGAAATTTTATTAATTTT
*
569559 ATGCACATATAGTGAATTTTTATTAATTTT
1 ATGCACATATAGTGAAATTTTATTAATTTT
569589 AT
1 AT
569591 AAGTTGGATT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.35, C:0.06, G:0.10, T:0.48
Consensus pattern (30 bp):
ATGCACATATAGTGAAATTTTATTAATTTT
Found at i:570232 original size:5 final size:5
Alignment explanation
Indices: 570218--570282 Score: 55
Period size: 5 Copynumber: 12.8 Consensus size: 5
570208 ACAAATAAAT
* *
570218 AAAAG AAAAAG AAAA- AAAAG -AAAG ACAAG CAAAACG AAACAG AAAGG
1 AAAAG -AAAAG AAAAG AAAAG AAAAG AAAAG -AAAA-G AAA-AG AAAAG
570265 AAAAG -AAAG AAAAG AAAA
1 AAAAG AAAAG AAAAG AAAA
570283 AGGGAAAGGG
Statistics
Matches: 49, Mismatches: 4, Indels: 13
0.74 0.06 0.20
Matches are distributed among these distances:
4 12 0.24
5 20 0.41
6 15 0.31
7 2 0.04
ACGTcount: A:0.75, C:0.06, G:0.18, T:0.00
Consensus pattern (5 bp):
AAAAG
Found at i:570273 original size:10 final size:9
Alignment explanation
Indices: 570219--570281 Score: 54
Period size: 9 Copynumber: 6.3 Consensus size: 9
570209 CAAATAAATA
570219 AAAGAAAAAG
1 AAAG-AAAAG
*
570229 AAAAAAAAG
1 AAAGAAAAG
*
570238 AAAGACAAG
1 AAAGAAAAG
570247 CAAAACGAAACAG
1 --AAA-GAAA-AG
570260 AAAGGAAAAG
1 AAA-GAAAAG
570270 AAAGAAAAG
1 AAAGAAAAG
570279 AAA
1 AAA
570282 AAGGGAAAGG
Statistics
Matches: 44, Mismatches: 5, Indels: 9
0.76 0.09 0.16
Matches are distributed among these distances:
9 21 0.48
10 8 0.18
11 10 0.23
12 3 0.07
13 2 0.05
ACGTcount: A:0.75, C:0.06, G:0.19, T:0.00
Consensus pattern (9 bp):
AAAGAAAAG
Found at i:571279 original size:40 final size:37
Alignment explanation
Indices: 571165--571292 Score: 136
Period size: 40 Copynumber: 3.4 Consensus size: 37
571155 ACTTCGAGTT
**
571165 GATGAGACACTGGGTGTCAATTTACTTCGGTTTAACC
1 GATGAGACACTGGGTGTCAATTTACTTCGAATTAACC
* *
571202 G-TGAGGCACT-GGTGCCAATTTACTTC-AAGTTAACC
1 GATGAGACACTGGGTGTCAATTTACTTCGAA-TTAACC
* *
571237 GATGAGACACTAGGTGTCAATTTATTACTTCGAATTATCC
1 GATGAGACACTGGGTGTCAA--T-TTACTTCGAATTAACC
*
571277 GATGAGGCACTGGGTG
1 GATGAGACACTGGGTG
571293 CCAAACTGGT
Statistics
Matches: 75, Mismatches: 9, Indels: 11
0.79 0.09 0.12
Matches are distributed among these distances:
35 22 0.29
36 16 0.21
37 8 0.11
39 1 0.01
40 26 0.35
41 2 0.03
ACGTcount: A:0.26, C:0.19, G:0.25, T:0.30
Consensus pattern (37 bp):
GATGAGACACTGGGTGTCAATTTACTTCGAATTAACC
Found at i:575866 original size:15 final size:15
Alignment explanation
Indices: 575843--575880 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
575833 TCATCTCCCC
*
575843 TTGAGTCCACTACAA
1 TTGACTCCACTACAA
*
575858 TTGACTCCACTACCA
1 TTGACTCCACTACAA
575873 TTGACTCC
1 TTGACTCC
575881 TCTGGAAAAC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.26, C:0.34, G:0.11, T:0.29
Consensus pattern (15 bp):
TTGACTCCACTACAA
Found at i:581048 original size:13 final size:15
Alignment explanation
Indices: 581019--581050 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
581009 TGGTTTTGAA
581019 GTTTTTTATATTAGG
1 GTTTTTTATATTAGG
581034 GTTTTTTA-ATT-GG
1 GTTTTTTATATTAGG
581047 GTTT
1 GTTT
581051 AAATTTGGTG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
13 6 0.35
14 3 0.18
15 8 0.47
ACGTcount: A:0.16, C:0.00, G:0.22, T:0.62
Consensus pattern (15 bp):
GTTTTTTATATTAGG
Found at i:591297 original size:10 final size:10
Alignment explanation
Indices: 591282--591312 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
591272 TAAAGACCTC
591282 TTTTAATTTT
1 TTTTAATTTT
591292 TTTTAATTTT
1 TTTTAATTTT
*
591302 CTTTAATTTT
1 TTTTAATTTT
591312 T
1 T
591313 AATAACTATT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.19, C:0.03, G:0.00, T:0.77
Consensus pattern (10 bp):
TTTTAATTTT
Found at i:594677 original size:21 final size:21
Alignment explanation
Indices: 594652--594697 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
594642 GGGGTCTACG
594652 CGCCCATGTGAAGGCCACACA
1 CGCCCATGTGAAGGCCACACA
* * **
594673 CGCCCGTGTGGAGGGGACACA
1 CGCCCATGTGAAGGCCACACA
594694 CGCC
1 CGCC
594698 ATTGTGAGCA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.22, C:0.37, G:0.33, T:0.09
Consensus pattern (21 bp):
CGCCCATGTGAAGGCCACACA
Found at i:597214 original size:13 final size:13
Alignment explanation
Indices: 597196--597235 Score: 53
Period size: 13 Copynumber: 2.8 Consensus size: 13
597186 ATTCTGAATG
597196 TTTTAATATTTAA
1 TTTTAATATTTAA
597209 TTTTAATAATTTAA
1 TTTTAAT-ATTTAA
597223 TAATTTAATATTT
1 T--TTTAATATTT
597236 TAAAAAATTA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
13 7 0.29
14 7 0.29
15 4 0.17
16 6 0.25
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (13 bp):
TTTTAATATTTAA
Found at i:597223 original size:8 final size:8
Alignment explanation
Indices: 597197--597238 Score: 54
Period size: 8 Copynumber: 5.6 Consensus size: 8
597187 TTCTGAATGT
597197 TTTAAT-A
1 TTTAATAA
597204 TTTAAT--
1 TTTAATAA
597210 TTTAATAA
1 TTTAATAA
597218 TTTAATAA
1 TTTAATAA
*
597226 TTTAATAT
1 TTTAATAA
597234 TTTAA
1 TTTAA
597239 AAAATTAAAA
Statistics
Matches: 32, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
6 6 0.19
7 6 0.19
8 20 0.62
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (8 bp):
TTTAATAA
Found at i:600905 original size:41 final size:41
Alignment explanation
Indices: 600860--600944 Score: 161
Period size: 41 Copynumber: 2.1 Consensus size: 41
600850 AGAATACACA
600860 TATTTTTAACTAATAAATGTAAATCAATTTATAACTATAAT
1 TATTTTTAACTAATAAATGTAAATCAATTTATAACTATAAT
*
600901 TATTTTTAACTAATAAATGTAAATCAATTTATAATTATAAT
1 TATTTTTAACTAATAAATGTAAATCAATTTATAACTATAAT
600942 TAT
1 TAT
600945 CACAACTTTT
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 43 1.00
ACGTcount: A:0.46, C:0.06, G:0.02, T:0.46
Consensus pattern (41 bp):
TATTTTTAACTAATAAATGTAAATCAATTTATAACTATAAT
Found at i:600931 original size:23 final size:23
Alignment explanation
Indices: 600864--600931 Score: 60
Period size: 23 Copynumber: 3.2 Consensus size: 23
600854 TACACATATT
600864 TTTAACTAATAAATGTAAATCAA
1 TTTAACTAATAAATGTAAATCAA
*
600887 TTT-A-TAACTATAAT-T--AT--T
1 TTTAACTAA-TA-AATGTAAATCAA
600905 TTTAACTAATAAATGTAAATCAA
1 TTTAACTAATAAATGTAAATCAA
600928 TTTA
1 TTTA
600932 TAATTATAAT
Statistics
Matches: 34, Mismatches: 2, Indels: 18
0.63 0.04 0.33
Matches are distributed among these distances:
18 6 0.18
19 4 0.12
20 5 0.15
21 5 0.15
22 4 0.12
23 10 0.29
ACGTcount: A:0.47, C:0.07, G:0.03, T:0.43
Consensus pattern (23 bp):
TTTAACTAATAAATGTAAATCAA
Found at i:620655 original size:55 final size:55
Alignment explanation
Indices: 620589--620697 Score: 200
Period size: 55 Copynumber: 2.0 Consensus size: 55
620579 TCTGTGATAT
*
620589 ATTTCTTTGTGTTTCATTTGGATTACTAGTACTTTAGATTATGCCTTTGCTTGGA
1 ATTTCTTTGTGTTTCATTTGGATTACTAGTACTTTAGATTAAGCCTTTGCTTGGA
*
620644 ATTTCTTTGTGTTTCGTTTGGATTACTAGTACTTTAGATTAAGCCTTTGCTTGG
1 ATTTCTTTGTGTTTCATTTGGATTACTAGTACTTTAGATTAAGCCTTTGCTTGG
620698 TGCTTTAGAT
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
55 52 1.00
ACGTcount: A:0.17, C:0.13, G:0.19, T:0.50
Consensus pattern (55 bp):
ATTTCTTTGTGTTTCATTTGGATTACTAGTACTTTAGATTAAGCCTTTGCTTGGA
Found at i:638743 original size:17 final size:17
Alignment explanation
Indices: 638716--638748 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
638706 TGTATTCATT
638716 AAAATAGTATTATTTTAA
1 AAAATAGTATT-TTTTAA
638734 AAAATA-TATTTTTTA
1 AAAATAGTATTTTTTA
638749 TGTTTTTTTC
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 5 0.33
17 4 0.27
18 6 0.40
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (17 bp):
AAAATAGTATTTTTTAA
Found at i:638920 original size:18 final size:17
Alignment explanation
Indices: 638894--638928 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
638884 ACTCCAGTTT
638894 GAAGAAAAAAAACAAAGA
1 GAAGAAAAAAAA-AAAGA
*
638912 GAAGTAAAAAAAAAAGA
1 GAAGAAAAAAAAAAAGA
638929 TGTGAAATAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.77, C:0.03, G:0.17, T:0.03
Consensus pattern (17 bp):
GAAGAAAAAAAAAAAGA
Found at i:650432 original size:99 final size:100
Alignment explanation
Indices: 650287--650485 Score: 373
Period size: 99 Copynumber: 2.0 Consensus size: 100
650277 GTTGGTAATA
650287 AAAAAGATGCCAACTATCTTCTCTTTCATATCAATCATTTCTTAATATTTAAA-AAAGTATTTTA
1 AAAAAGATGCCAACTATCTTCTCTTTCATATCAATCATTTCTTAATATTTAAACAAAGTATTTTA
*
650351 CTTTTGCTAATTAAGAAATAGTTACCACTCATGAT
66 CTTTTGCTAATTAAGAAATAGTTACAACTCATGAT
*
650386 AAAAAGATGCCAACTATCTTCTCTTTCATATCAATCATTTTTTAATATTTAAACAAAGTATTTTA
1 AAAAAGATGCCAACTATCTTCTCTTTCATATCAATCATTTCTTAATATTTAAACAAAGTATTTTA
650451 CTTTTGCTAATTAAGAAATAGTTACAACTCATGAT
66 CTTTTGCTAATTAAGAAATAGTTACAACTCATGAT
650486 TTCTTCTTCT
Statistics
Matches: 97, Mismatches: 2, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
99 52 0.54
100 45 0.46
ACGTcount: A:0.38, C:0.16, G:0.07, T:0.40
Consensus pattern (100 bp):
AAAAAGATGCCAACTATCTTCTCTTTCATATCAATCATTTCTTAATATTTAAACAAAGTATTTTA
CTTTTGCTAATTAAGAAATAGTTACAACTCATGAT
Found at i:650916 original size:13 final size:14
Alignment explanation
Indices: 650884--650917 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
650874 ACAATTACTT
*
650884 TATTCAAAACAACG
1 TATTCAAAACAACA
650898 TATTCAAAACAA-A
1 TATTCAAAACAACA
650911 TATTCAA
1 TATTCAA
650918 CATATTACCT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 7 0.37
14 12 0.63
ACGTcount: A:0.53, C:0.18, G:0.03, T:0.26
Consensus pattern (14 bp):
TATTCAAAACAACA
Found at i:651190 original size:21 final size:21
Alignment explanation
Indices: 651166--651213 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
651156 GCGGGGGTTA
*
651166 TGGTTGCTCCGGT-GGGGATTC
1 TGGTTGCTCCGGTAGGGTA-TC
*
651187 TGGTTCCTCCGGTAGGGTATC
1 TGGTTGCTCCGGTAGGGTATC
651208 TGGTTG
1 TGGTTG
651214 TCGATGTTGG
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
21 19 0.83
22 4 0.17
ACGTcount: A:0.06, C:0.19, G:0.40, T:0.35
Consensus pattern (21 bp):
TGGTTGCTCCGGTAGGGTATC
Found at i:651480 original size:18 final size:18
Alignment explanation
Indices: 651454--651496 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
651444 GACTCGAAAA
* * *
651454 AGGAAACATATAAGGGTT
1 AGGATACATAAAAGGGCT
651472 AGGATACATAAAAGGGCT
1 AGGATACATAAAAGGGCT
651490 AGGATAC
1 AGGATAC
651497 GCACCTGGCA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.44, C:0.09, G:0.28, T:0.19
Consensus pattern (18 bp):
AGGATACATAAAAGGGCT
Found at i:653356 original size:11 final size:10
Alignment explanation
Indices: 653342--653395 Score: 65
Period size: 11 Copynumber: 5.1 Consensus size: 10
653332 AAATAGGGAT
653342 TTGAGAGAAA
1 TTGAGAGAAA
653352 TTTGAGAGGAAA
1 -TTGAGA-GAAA
653364 TTGAGAGCAAA
1 TTGAGAG-AAA
653375 TTGAGAGGAAA
1 TTGAGA-GAAA
653386 TT-AGAGAAA
1 TTGAGAGAAA
653395 T
1 T
653396 GATTTAATTA
Statistics
Matches: 40, Mismatches: 0, Indels: 8
0.83 0.00 0.17
Matches are distributed among these distances:
9 5 0.12
10 4 0.10
11 26 0.65
12 5 0.12
ACGTcount: A:0.46, C:0.02, G:0.30, T:0.22
Consensus pattern (10 bp):
TTGAGAGAAA
Found at i:653370 original size:22 final size:22
Alignment explanation
Indices: 653342--653395 Score: 85
Period size: 22 Copynumber: 2.5 Consensus size: 22
653332 AAATAGGGAT
653342 TTGAGAGAAATTTGAGAGGAAA
1 TTGAGAGAAATTTGAGAGGAAA
653364 TTGAGAGCAAA-TTGAGAGGAAA
1 TTGAGAG-AAATTTGAGAGGAAA
653386 TT-AGAGAAAT
1 TTGAGAGAAAT
653396 GATTTAATTA
Statistics
Matches: 30, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
20 3 0.10
21 4 0.13
22 20 0.67
23 3 0.10
ACGTcount: A:0.46, C:0.02, G:0.30, T:0.22
Consensus pattern (22 bp):
TTGAGAGAAATTTGAGAGGAAA
Found at i:656676 original size:70 final size:70
Alignment explanation
Indices: 656599--656733 Score: 270
Period size: 70 Copynumber: 1.9 Consensus size: 70
656589 TCATTGAATA
656599 TGATGACCAAGGTCTGGTAAAATAATAGTCTTTCTAATATTTGTTGAATTTTAATATTATAAATT
1 TGATGACCAAGGTCTGGTAAAATAATAGTCTTTCTAATATTTGTTGAATTTTAATATTATAAATT
656664 ATTAT
66 ATTAT
656669 TGATGACCAAGGTCTGGTAAAATAATAGTCTTTCTAATATTTGTTGAATTTTAATATTATAAATT
1 TGATGACCAAGGTCTGGTAAAATAATAGTCTTTCTAATATTTGTTGAATTTTAATATTATAAATT
656734 GATGTGGATT
Statistics
Matches: 65, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
70 65 1.00
ACGTcount: A:0.36, C:0.07, G:0.13, T:0.44
Consensus pattern (70 bp):
TGATGACCAAGGTCTGGTAAAATAATAGTCTTTCTAATATTTGTTGAATTTTAATATTATAAATT
ATTAT
Found at i:657525 original size:2 final size:2
Alignment explanation
Indices: 657518--657554 Score: 56
Period size: 2 Copynumber: 18.5 Consensus size: 2
657508 CTTCATATTC
* *
657518 AT AT AT AT AC AT AT AT AT AT AT AT AT AT AT TT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
657555 ACAATTGAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:657977 original size:2 final size:2
Alignment explanation
Indices: 657970--658002 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
657960 TCTTTCCATT
657970 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
658003 GTTTTCACTG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:658281 original size:2 final size:2
Alignment explanation
Indices: 658274--658308 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
658264 TCTTTACAGT
658274 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
658309 GTTCTTACTG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:664908 original size:21 final size:19
Alignment explanation
Indices: 664872--664911 Score: 53
Period size: 21 Copynumber: 2.0 Consensus size: 19
664862 CACTAAAAGA
*
664872 CAAATTTTTTTTTTATTTT
1 CAAATTTTTTTATTATTTT
664891 CAAATATTATTTTATTATTTT
1 CAAAT-TT-TTTTATTATTTT
664912 TTCTCCCTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 5 0.28
20 2 0.11
21 11 0.61
ACGTcount: A:0.28, C:0.05, G:0.00, T:0.68
Consensus pattern (19 bp):
CAAATTTTTTTATTATTTT
Found at i:664970 original size:14 final size:14
Alignment explanation
Indices: 664934--664963 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
664924 TGCTACCATT
*
664934 TTACTATTATGTTG
1 TTACTATTTTGTTG
664948 TTACTATTTTGTTG
1 TTACTATTTTGTTG
664962 TT
1 TT
664964 TTTATTTAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.17, C:0.07, G:0.13, T:0.63
Consensus pattern (14 bp):
TTACTATTTTGTTG
Found at i:665033 original size:30 final size:30
Alignment explanation
Indices: 664998--665057 Score: 111
Period size: 30 Copynumber: 2.0 Consensus size: 30
664988 TATTTTATTA
664998 TTAATTTTGTTATTATTTTAAAGACATTTG
1 TTAATTTTGTTATTATTTTAAAGACATTTG
*
665028 TTAATTTTGTTATTATTTTAGAGACATTTG
1 TTAATTTTGTTATTATTTTAAAGACATTTG
665058 CTTGTTAAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.28, C:0.03, G:0.12, T:0.57
Consensus pattern (30 bp):
TTAATTTTGTTATTATTTTAAAGACATTTG
Found at i:688897 original size:31 final size:31
Alignment explanation
Indices: 688830--688890 Score: 79
Period size: 31 Copynumber: 2.0 Consensus size: 31
688820 TATAAAATGG
* * *
688830 ACATTAAACTATTCAAAAGTTTTCATTTAAT
1 ACATTGAACTATTCAAAAATTCTCATTTAAT
688861 ACATTGAACTATTCAAAAAATTCT-ATTTAA
1 ACATTGAACTATTC-AAAAATTCTCATTTAA
688891 ACCATTGGGT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
31 19 0.73
32 7 0.27
ACGTcount: A:0.44, C:0.13, G:0.03, T:0.39
Consensus pattern (31 bp):
ACATTGAACTATTCAAAAATTCTCATTTAAT
Found at i:694128 original size:27 final size:29
Alignment explanation
Indices: 694090--694148 Score: 86
Period size: 28 Copynumber: 2.1 Consensus size: 29
694080 TTGTTCATAG
*
694090 TTTTGTGA-TTTTATTTTGTC-AATATTT
1 TTTTGTGATTTTTATTTTGTCTAATATGT
*
694117 TTTTGTGGTTTTTATTTTGTCTAATATGT
1 TTTTGTGATTTTTATTTTGTCTAATATGT
694146 TTT
1 TTT
694149 CTTTTAAGTA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
27 7 0.25
28 12 0.43
29 9 0.32
ACGTcount: A:0.15, C:0.03, G:0.14, T:0.68
Consensus pattern (29 bp):
TTTTGTGATTTTTATTTTGTCTAATATGT
Found at i:695483 original size:19 final size:19
Alignment explanation
Indices: 695452--695489 Score: 60
Period size: 19 Copynumber: 2.0 Consensus size: 19
695442 TATAGAAATG
695452 ATTTTTTATAATTTTTATA
1 ATTTTTTATAATTTTTATA
695471 ATTTCTTTA-AATTTTTATA
1 ATTT-TTTATAATTTTTATA
695490 TTAAACAATT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 14 0.78
20 4 0.22
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.66
Consensus pattern (19 bp):
ATTTTTTATAATTTTTATA
Found at i:698107 original size:45 final size:44
Alignment explanation
Indices: 698030--698336 Score: 294
Period size: 45 Copynumber: 6.8 Consensus size: 44
698020 CGCCACCATA
* * * * *
698030 TGAACATAAACCTCCGGTTTATGAACCACCAAAGAAGGAGAAGCC
1 TGAACCTAAACCACCAGTTTAT-AACCTCCAAAGAAGGAAAAGCC
* * *
698075 TGAACCTAAGCCACCAGTTTATACACCTCCAAAGAAAGAGAAGCC
1 TGAACCTAAACCACCAGTTTATA-ACCTCCAAAGAAGGAAAAGCC
* *
698120 TGAACCGAAACCACCAGTATATGAACCTCCAAAGAAGGAAAAGCC
1 TGAACCTAAACCACCAGTTTAT-AACCTCCAAAGAAGGAAAAGCC
* * * * *
698165 TGAGCCTAAACCACCGGTTTATACACCACCAAAGAAAGAAAAGCA
1 TGAACCTAAACCACCAGTTTATA-ACCTCCAAAGAAGGAAAAGCC
* * * * *
698210 TGAACAC-AAGCCACCGGTGTATGAACCACCAAAGAAGGAAAAACC
1 TGAAC-CTAAACCACCAGTTTAT-AACCTCCAAAGAAGGAAAAGCC
* * * *
698255 TGAGCCTAAACCACCAGTTTATGCACCTCCAAAGAAAGAAAAACC
1 TGAACCTAAACCACCAGTTTAT-AACCTCCAAAGAAGGAAAAGCC
*
698300 AGAA-CTCAAACCACCAGTTTATAAGCCTCCAAAGAAG
1 TGAACCT-AAACCACCAGTTTATAA-CCTCCAAAGAAG
698337 CCACCAGTGT
Statistics
Matches: 219, Mismatches: 35, Indels: 16
0.81 0.13 0.06
Matches are distributed among these distances:
44 6 0.03
45 210 0.96
46 3 0.01
ACGTcount: A:0.43, C:0.27, G:0.17, T:0.14
Consensus pattern (44 bp):
TGAACCTAAACCACCAGTTTATAACCTCCAAAGAAGGAAAAGCC
Found at i:698152 original size:90 final size:90
Alignment explanation
Indices: 698030--698336 Score: 384
Period size: 90 Copynumber: 3.4 Consensus size: 90
698020 CGCCACCATA
* * * * * * *
698030 TGAACATAAACCTCCGGTTTATGAACCACCAAAGAAGGAGAAGCCTGAACCTAAGCCACCAGTTT
1 TGAACACAAACCACCAGTATATGAACCACCAAAGAAGGAAAAGCCTGAGCCTAAACCACCAGTTT
*
698095 ATACACCTCCAAAGAAAGAGAAGCC
66 ATACACCTCCAAAGAAAGAAAAGCC
* *
698120 TGAAC-CGAAACCACCAGTATATGAACCTCCAAAGAAGGAAAAGCCTGAGCCTAAACCACCGGTT
1 TGAACAC-AAACCACCAGTATATGAACCACCAAAGAAGGAAAAGCCTGAGCCTAAACCACCAGTT
* *
698184 TATACACCACCAAAGAAAGAAAAGCA
65 TATACACCTCCAAAGAAAGAAAAGCC
* * * *
698210 TGAACACAAGCCACCGGTGTATGAACCACCAAAGAAGGAAAAACCTGAGCCTAAACCACCAGTTT
1 TGAACACAAACCACCAGTATATGAACCACCAAAGAAGGAAAAGCCTGAGCCTAAACCACCAGTTT
* *
698275 ATGCACCTCCAAAGAAAGAAAAACC
66 ATACACCTCCAAAGAAAGAAAAGCC
* * * *
698300 AGAACTCAAACCACCAGTTTAT-AAGCCTCCAAAGAAG
1 TGAACACAAACCACCAGTATATGAA-CCACCAAAGAAG
698337 CCACCAGTGT
Statistics
Matches: 186, Mismatches: 28, Indels: 6
0.85 0.13 0.03
Matches are distributed among these distances:
89 2 0.01
90 183 0.98
91 1 0.01
ACGTcount: A:0.43, C:0.27, G:0.17, T:0.14
Consensus pattern (90 bp):
TGAACACAAACCACCAGTATATGAACCACCAAAGAAGGAAAAGCCTGAGCCTAAACCACCAGTTT
ATACACCTCCAAAGAAAGAAAAGCC
Found at i:698223 original size:135 final size:133
Alignment explanation
Indices: 698031--698335 Score: 344
Period size: 135 Copynumber: 2.2 Consensus size: 133
698021 GCCACCATAT
* * * * *
698031 GAACATAAACCTCCGGTTTATGAACCACCAAAGAAGGAGAAGCCTGAACCTAAGCCACCAGTTTA
1 GAAC-TAAACCACCGGTTTAT-AACCACCAAAGAAAGAAAAGCATGAACCTAAGCCACCAGTGTA
* * * *
698096 T-ACACCTCCAAAGAAAGAGAAGCCTGAACCGAAACCACCAGTATATGAACCTCCAAAGAAGGAA
64 TGA-ACCACCAAAGAAAGAAAAACCTGAACCGAAACCACCAGTATATGAACCTCCAAAGAAAGAA
* *
698160 AAGCCT
128 AAACCA
* *
698166 GAGCCTAAACCACCGGTTTATACACCACCAAAGAAAGAAAAGCATGAACAC-AAGCCACCGGTGT
1 GA-ACTAAACCACCGGTTTATA-ACCACCAAAGAAAGAAAAGCATGAAC-CTAAGCCACCAGTGT
* * * * *
698230 ATGAACCACCAAAGAAGGAAAAACCTGAGCCTAAACCACCAGTTTATGCACCTCCAAAGAAAGAA
63 ATGAACCACCAAAGAAAGAAAAACCTGAACCGAAACCACCAGTATATGAACCTCCAAAGAAAGAA
698295 AAACCA
128 AAACCA
* *
698301 GAACTCAAACCACCAGTTTATAAGCCTCCAAAGAA
1 GAACT-AAACCACCGGTTTATAA-CCACCAAAGAA
698336 GCCACCAGTG
Statistics
Matches: 143, Mismatches: 21, Indels: 12
0.81 0.12 0.07
Matches are distributed among these distances:
134 4 0.03
135 136 0.95
136 3 0.02
ACGTcount: A:0.43, C:0.27, G:0.16, T:0.13
Consensus pattern (133 bp):
GAACTAAACCACCGGTTTATAACCACCAAAGAAAGAAAAGCATGAACCTAAGCCACCAGTGTATG
AACCACCAAAGAAAGAAAAACCTGAACCGAAACCACCAGTATATGAACCTCCAAAGAAAGAAAAA
CCA
Found at i:701917 original size:10 final size:10
Alignment explanation
Indices: 701902--701954 Score: 56
Period size: 10 Copynumber: 5.2 Consensus size: 10
701892 TCTTATGTTT
701902 TTTCTTCTTC
1 TTTCTTCTTC
701912 TTTCTT-TCTC
1 TTTCTTCT-TC
*
701922 TTTCTCCTTC
1 TTTCTTCTTC
701932 -TTCTTCTTC
1 TTTCTTCTTC
701941 TTTCGGTTCTTC
1 TTTC--TTCTTC
701953 TT
1 TT
701955 CCTTGTCCTT
Statistics
Matches: 36, Mismatches: 2, Indels: 8
0.78 0.04 0.17
Matches are distributed among these distances:
9 9 0.25
10 18 0.50
11 1 0.03
12 8 0.22
ACGTcount: A:0.00, C:0.30, G:0.04, T:0.66
Consensus pattern (10 bp):
TTTCTTCTTC
Found at i:702572 original size:22 final size:22
Alignment explanation
Indices: 702516--702575 Score: 79
Period size: 21 Copynumber: 2.8 Consensus size: 22
702506 CTATTCATCA
702516 AATTTGAGCCACACGGGCATGT
1 AATTTGAGCCACACGGGCATGT
* *
702538 -GTCT-AGGCCACACGGGCATGT
1 AATTTGA-GCCACACGGGCATGT
702559 AATTTGAGCCACACGGG
1 AATTTGAGCCACACGGG
702576 TCGGGTCTCG
Statistics
Matches: 31, Mismatches: 4, Indels: 6
0.76 0.10 0.15
Matches are distributed among these distances:
20 1 0.03
21 17 0.55
22 12 0.39
23 1 0.03
ACGTcount: A:0.25, C:0.25, G:0.30, T:0.20
Consensus pattern (22 bp):
AATTTGAGCCACACGGGCATGT
Found at i:703775 original size:44 final size:44
Alignment explanation
Indices: 703712--703878 Score: 183
Period size: 44 Copynumber: 3.7 Consensus size: 44
703702 TCATCCTAAC
*
703712 CCACTGCATCTTCAGGGAGATAAGATTTATAGCTTTAATCTGCT
1 CCACTGCAACTTCAGGGAGATAAGATTTATAGCTTTAATCTGCT
* * *
703756 CCACTGCAATTTCAGGGAGATAAGATTTGTAGCTTTAATTTGCT
1 CCACTGCAACTTCAGGGAGATAAGATTTATAGCTTTAATCTGCT
* * * * *
703800 CCATTACAACTTCAGAGAGATAAGATTCGCCATGGTAAG-TTCAATCTGCT
1 CCACTGCAACTTCAGGGAGATAAGATT-----T-AT-AGCTTTAATCTGCT
703850 CCACTGCAACTTCAGGGAGATAAGATTTA
1 CCACTGCAACTTCAGGGAGATAAGATTTA
703879 CTATGGTGAC
Statistics
Matches: 102, Mismatches: 14, Indels: 14
0.78 0.11 0.11
Matches are distributed among these distances:
44 63 0.62
45 1 0.01
49 1 0.01
50 35 0.34
51 2 0.02
ACGTcount: A:0.30, C:0.20, G:0.19, T:0.31
Consensus pattern (44 bp):
CCACTGCAACTTCAGGGAGATAAGATTTATAGCTTTAATCTGCT
Found at i:703904 original size:50 final size:50
Alignment explanation
Indices: 703797--703911 Score: 124
Period size: 50 Copynumber: 2.3 Consensus size: 50
703787 GCTTTAATTT
* * * * *
703797 GCTCCATTACAACTTCAGAGAGATAAGATTCGCCATGGTAAGTTCAATCT
1 GCTCCACTACAACTTCAGAGAGATAAGATTCACCATGGTAACTTCAACCC
* * * * *
703847 GCTCCACTGCAACTTCAGGGAGATAAGATTTACTATGGTGACTTCAACCC
1 GCTCCACTACAACTTCAGAGAGATAAGATTCACCATGGTAACTTCAACCC
703897 GAC-CCACTACAACTT
1 G-CTCCACTACAACTT
703912 TAAGGGTATA
Statistics
Matches: 53, Mismatches: 11, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
50 52 0.98
51 1 0.02
ACGTcount: A:0.30, C:0.26, G:0.17, T:0.26
Consensus pattern (50 bp):
GCTCCACTACAACTTCAGAGAGATAAGATTCACCATGGTAACTTCAACCC
Found at i:715582 original size:14 final size:15
Alignment explanation
Indices: 715558--715587 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
715548 ATAAGTAGAT
715558 AAATAGATAATAATA
1 AAATAGATAATAATA
715573 AAATAG-TAATAATA
1 AAATAGATAATAATA
715587 A
1 A
715588 TAGTAAAGGC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 9 0.60
15 6 0.40
ACGTcount: A:0.67, C:0.00, G:0.07, T:0.27
Consensus pattern (15 bp):
AAATAGATAATAATA
Found at i:715692 original size:4 final size:4
Alignment explanation
Indices: 715683--715802 Score: 68
Period size: 4 Copynumber: 29.5 Consensus size: 4
715673 GTGAAGGAAT
* * *
715683 AATA AATA AATG AATA AA-A GAATTAA AATA AA-A AAGTA AATA GATG
1 AATA AATA AATA AATA AATA -AA-T-A AATA AATA AA-TA AATA AATA
* * * *
715729 AAT- AATA TATA AATA AATA AGTA AATA AATG AATAA AATAA AAGA AAT-
1 AATA AATA AATA AATA AATA AATA AATA AATA AAT-A AAT-A AATA AATA
* * *
715777 AATA AATA AGTA AATC AATG AATA AA
1 AATA AATA AATA AATA AATA AATA AA
715803 AGAATTAAAA
Statistics
Matches: 89, Mismatches: 18, Indels: 18
0.71 0.14 0.14
Matches are distributed among these distances:
3 10 0.11
4 65 0.73
5 11 0.12
6 2 0.02
7 1 0.01
ACGTcount: A:0.68, C:0.01, G:0.08, T:0.23
Consensus pattern (4 bp):
AATA
Found at i:715751 original size:31 final size:30
Alignment explanation
Indices: 715680--715785 Score: 117
Period size: 31 Copynumber: 3.4 Consensus size: 30
715670 AAAGTGAAGG
715680 AATAA-TAAATAAATGAATAAAAGAATTAAAATA
1 AATAAGTAAATAAATGAAT--AA-AA-TAAAATA
* * *
715713 AAAAAGTAAATAGATGAATAATATATAAATA
1 AATAAGTAAATAAATGAATAAAATA-AAATA
*
715744 AATAAGTAAATAAATGAATAAAATAAAAGA
1 AATAAGTAAATAAATGAATAAAATAAAATA
715774 AATAA-TAAATAA
1 AATAAGTAAATAA
715786 GTAAATCAAT
Statistics
Matches: 64, Mismatches: 7, Indels: 8
0.81 0.09 0.10
Matches are distributed among these distances:
29 7 0.11
30 11 0.17
31 28 0.44
32 2 0.03
33 4 0.06
34 12 0.19
ACGTcount: A:0.69, C:0.00, G:0.08, T:0.24
Consensus pattern (30 bp):
AATAAGTAAATAAATGAATAAAATAAAATA
Found at i:715779 original size:45 final size:46
Alignment explanation
Indices: 715729--715817 Score: 119
Period size: 45 Copynumber: 2.0 Consensus size: 46
715719 TAAATAGATG
* *
715729 AATAATATATAAATAAAT-AAGTAAATAAATGAA-TAAAATAAAAGA
1 AATAATAAATAAATAAATCAA-TAAATAAAAGAATTAAAATAAAAGA
* *
715774 AATAATAAATAAGTAAATCAATGAATAAAAGAATTAAAATAAAA
1 AATAATAAATAAATAAATCAATAAATAAAAGAATTAAAATAAAA
715818 AAGGACTTAA
Statistics
Matches: 38, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
45 26 0.68
46 12 0.32
ACGTcount: A:0.69, C:0.01, G:0.07, T:0.24
Consensus pattern (46 bp):
AATAATAAATAAATAAATCAATAAATAAAAGAATTAAAATAAAAGA
Found at i:717543 original size:29 final size:30
Alignment explanation
Indices: 717494--717559 Score: 82
Period size: 29 Copynumber: 2.2 Consensus size: 30
717484 ATTAAATTTG
717494 AATTTTTAAAATTAAAAATATAAAAAATAA
1 AATTTTTAAAATTAAAAATATAAAAAATAA
* *
717524 AATTTTTGAAAA-T-AATATATAAAAAATTA
1 AATTTTT-AAAATTAAAAATATAAAAAATAA
*
717553 ATTTTTT
1 AATTTTT
717560 TAATTTTTAA
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
29 20 0.62
30 8 0.25
31 4 0.12
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.41
Consensus pattern (30 bp):
AATTTTTAAAATTAAAAATATAAAAAATAA
Found at i:721981 original size:15 final size:15
Alignment explanation
Indices: 721942--721973 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
721932 TATGCGTACA
721942 AAATATAAAAGACAT
1 AAATATAAAAGACAT
*
721957 AAATACAAAAGACAT
1 AAATATAAAAGACAT
721972 AA
1 AA
721974 TAGTAAAATG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.69, C:0.09, G:0.06, T:0.16
Consensus pattern (15 bp):
AAATATAAAAGACAT
Found at i:724832 original size:9 final size:9
Alignment explanation
Indices: 724818--724848 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
724808 TTTGGTTAAA
724818 AATTAACCG
1 AATTAACCG
724827 AATTAACCG
1 AATTAACCG
*
724836 AATTACCCG
1 AATTAACCG
724845 AATT
1 AATT
724849 GAATCACTAC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.42, C:0.23, G:0.10, T:0.26
Consensus pattern (9 bp):
AATTAACCG
Found at i:724878 original size:17 final size:17
Alignment explanation
Indices: 724856--724918 Score: 54
Period size: 17 Copynumber: 3.5 Consensus size: 17
724846 ATTGAATCAC
724856 TACATAATTAAAAATAT
1 TACATAATTAAAAATAT
*** *
724873 TACATAAGTCTTTGAATCAC
1 TACATAA-T-TAAAAAT-AT
*
724893 TACATAATTAAAAACAT
1 TACATAATTAAAAATAT
724910 TACATAATT
1 TACATAATT
724919 CTTGAAATTA
Statistics
Matches: 34, Mismatches: 9, Indels: 6
0.69 0.18 0.12
Matches are distributed among these distances:
17 17 0.50
18 4 0.12
19 5 0.15
20 8 0.24
ACGTcount: A:0.49, C:0.13, G:0.03, T:0.35
Consensus pattern (17 bp):
TACATAATTAAAAATAT
Found at i:724894 original size:37 final size:37
Alignment explanation
Indices: 724847--724921 Score: 132
Period size: 37 Copynumber: 2.0 Consensus size: 37
724837 ATTACCCGAA
*
724847 TTGAATCACTACATAATTAAAAATATTACATAAGTCT
1 TTGAATCACTACATAATTAAAAACATTACATAAGTCT
*
724884 TTGAATCACTACATAATTAAAAACATTACATAATTCT
1 TTGAATCACTACATAATTAAAAACATTACATAAGTCT
724921 T
1 T
724922 GAAATTAACA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
37 36 1.00
ACGTcount: A:0.45, C:0.15, G:0.04, T:0.36
Consensus pattern (37 bp):
TTGAATCACTACATAATTAAAAACATTACATAAGTCT
Found at i:725120 original size:38 final size:39
Alignment explanation
Indices: 725053--725126 Score: 114
Period size: 38 Copynumber: 1.9 Consensus size: 39
725043 ACTTAAGAGT
* *
725053 TAGACTTTAGTTTTATTTTTATTATGTT-GGTAATTGGG
1 TAGACTTTAGTTTTAGTTTTATTAGGTTGGGTAATTGGG
*
725091 TAGACTTTAGTTTTAGTTTTATTGGGTTGGGTAATT
1 TAGACTTTAGTTTTAGTTTTATTAGGTTGGGTAATT
725127 AGGTTGGGTT
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
38 25 0.78
39 7 0.22
ACGTcount: A:0.20, C:0.03, G:0.23, T:0.54
Consensus pattern (39 bp):
TAGACTTTAGTTTTAGTTTTATTAGGTTGGGTAATTGGG
Found at i:725133 original size:13 final size:13
Alignment explanation
Indices: 725111--725167 Score: 77
Period size: 13 Copynumber: 4.7 Consensus size: 13
725101 TTTTAGTTTT
725111 ATTGGGTTGGGTA
1 ATTGGGTTGGGTA
*
725124 ATTAGGTTGGG--
1 ATTGGGTTGGGTA
725135 -TTGGGTT-GGTA
1 ATTGGGTTGGGTA
725146 ATTGGGTTGGGTA
1 ATTGGGTTGGGTA
725159 ATTGGGTTG
1 ATTGGGTTG
725168 AGTTGGATAA
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
9 2 0.05
10 6 0.16
12 7 0.18
13 23 0.61
ACGTcount: A:0.14, C:0.00, G:0.46, T:0.40
Consensus pattern (13 bp):
ATTGGGTTGGGTA
Found at i:725135 original size:18 final size:18
Alignment explanation
Indices: 725112--725179 Score: 66
Period size: 18 Copynumber: 3.8 Consensus size: 18
725102 TTTAGTTTTA
725112 TTGGGTTGGGTAATTAGG
1 TTGGGTTGGGTAATTAGG
*** *
725130 TTGGGTTGGGTTGGTA-A
1 TTGGGTTGGGTAATTAGG
*
725147 TTGGGTTGGGTAATTGGG
1 TTGGGTTGGGTAATTAGG
* *
725165 TTGAGTTGGATAATT
1 TTGGGTTGGGTAATT
725180 TTATTTATTA
Statistics
Matches: 38, Mismatches: 11, Indels: 2
0.75 0.22 0.04
Matches are distributed among these distances:
17 12 0.32
18 26 0.68
ACGTcount: A:0.16, C:0.00, G:0.43, T:0.41
Consensus pattern (18 bp):
TTGGGTTGGGTAATTAGG
Found at i:725145 original size:22 final size:23
Alignment explanation
Indices: 725112--725157 Score: 76
Period size: 22 Copynumber: 2.0 Consensus size: 23
725102 TTTAGTTTTA
725112 TTGGGTTGGGTAATTAGGTTGGG
1 TTGGGTTGGGTAATTAGGTTGGG
*
725135 TTGGGTT-GGTAATTGGGTTGGG
1 TTGGGTTGGGTAATTAGGTTGGG
725157 T
1 T
725158 AATTGGGTTG
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
22 15 0.68
23 7 0.32
ACGTcount: A:0.11, C:0.00, G:0.48, T:0.41
Consensus pattern (23 bp):
TTGGGTTGGGTAATTAGGTTGGG
Found at i:726227 original size:54 final size:53
Alignment explanation
Indices: 726100--726268 Score: 223
Period size: 54 Copynumber: 3.2 Consensus size: 53
726090 AAAGGTTGTT
* * ** *
726100 AAATGACTGAAATACCCCCATAAGGTAGAATGACGGAAATA-CCCTATAGGGTA
1 AAATGACCGAAATACCCCCAT-AGGTAAAATGACCAAAATACCCCTATAAGGTA
*
726153 AAATGACCGAAATACCCCCATAGGATAAAATGACCAAAATACCCCCATAAGGTA
1 AAATGACCGAAATACCCCCATAGG-TAAAATGACCAAAATACCCCTATAAGGTA
* * *
726207 AAATGACCGTAATACCCCCATAGGTTTAAATGACCAAAATACCCCTGTAAGGTA
1 AAATGACCGAAATACCCCCATAGG-TAAAATGACCAAAATACCCCTATAAGGTA
726261 AAATGACC
1 AAATGACC
726269 ATAATGCCCC
Statistics
Matches: 103, Mismatches: 11, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
52 3 0.03
53 33 0.32
54 67 0.65
ACGTcount: A:0.43, C:0.23, G:0.16, T:0.18
Consensus pattern (53 bp):
AAATGACCGAAATACCCCCATAGGTAAAATGACCAAAATACCCCTATAAGGTA
Found at i:726269 original size:27 final size:27
Alignment explanation
Indices: 726100--726268 Score: 200
Period size: 27 Copynumber: 6.3 Consensus size: 27
726090 AAAGGTTGTT
*
726100 AAATGACTGAAATACCCCCATAAGGTA
1 AAATGACCGAAATACCCCCATAAGGTA
* * * *
726127 GAATGACGGAAATA-CCCTATAGGGTA
1 AAATGACCGAAATACCCCCATAAGGTA
726153 AAATGACCGAAATACCCCCAT-AGGATA
1 AAATGACCGAAATACCCCCATAAGG-TA
*
726180 AAATGACCAAAATACCCCCATAAGGTA
1 AAATGACCGAAATACCCCCATAAGGTA
* *
726207 AAATGACCGTAATACCCCCAT-AGGTTT
1 AAATGACCGAAATACCCCCATAAGG-TA
* **
726234 AAATGACCAAAATACCCCTGTAAGGTA
1 AAATGACCGAAATACCCCCATAAGGTA
726261 AAATGACC
1 AAATGACC
726269 ATAATGCCCC
Statistics
Matches: 120, Mismatches: 17, Indels: 10
0.82 0.12 0.07
Matches are distributed among these distances:
26 27 0.22
27 87 0.73
28 6 0.05
ACGTcount: A:0.43, C:0.23, G:0.16, T:0.18
Consensus pattern (27 bp):
AAATGACCGAAATACCCCCATAAGGTA
Found at i:726287 original size:27 final size:27
Alignment explanation
Indices: 726149--726289 Score: 101
Period size: 27 Copynumber: 5.2 Consensus size: 27
726139 TACCCTATAG
* *
726149 GGTAAAATGACCGAAATACCCC--CATA
1 GGTAAAATGACCAAAATACCCCTGGA-A
***
726175 GGATAAAATGACCAAAATACCCCCATAA
1 GG-TAAAATGACCAAAATACCCCTGGAA
** *
726203 GGTAAAATGACCGTAATACCCC--CATA
1 GGTAAAATGACCAAAATACCCCTGGA-A
* *
726229 GGTTTAAATGACCAAAATACCCCTGTAA
1 GG-TAAAATGACCAAAATACCCCTGGAA
* * *
726257 GGTAAAATGACCATAATGCCCCTGGAG
1 GGTAAAATGACCAAAATACCCCTGGAA
726284 GGTAAA
1 GGTAAA
726290 TTACTATTTT
Statistics
Matches: 94, Mismatches: 14, Indels: 13
0.78 0.12 0.11
Matches are distributed among these distances:
25 1 0.01
26 5 0.05
27 80 0.85
28 6 0.06
29 2 0.02
ACGTcount: A:0.41, C:0.23, G:0.17, T:0.18
Consensus pattern (27 bp):
GGTAAAATGACCAAAATACCCCTGGAA
Found at i:726342 original size:24 final size:24
Alignment explanation
Indices: 726310--726420 Score: 109
Period size: 24 Copynumber: 4.6 Consensus size: 24
726300 GCCCCTCGAG
* *
726310 TGTAAATGATTGATTTGTATGTGA
1 TGTAAATGACTGATTTGTCTGTGA
* *
726334 TGTAAATGACTGATGTGCCTGTGA
1 TGTAAATGACTGATTTGTCTGTGA
* *
726358 TTTAAATGATTGATTTGTCTGTGAA
1 TGTAAATGACTGATTTGTCTGTG-A
726383 TGGT--ATGACTGATTTGTCTGTGA
1 T-GTAAATGACTGATTTGTCTGTGA
* **
726406 TTTGTATGACTGATT
1 TGTAAATGACTGATT
726421 CTGAGTATGG
Statistics
Matches: 72, Mismatches: 11, Indels: 8
0.79 0.12 0.09
Matches are distributed among these distances:
22 1 0.01
23 2 0.03
24 66 0.92
25 2 0.03
26 1 0.01
ACGTcount: A:0.24, C:0.06, G:0.25, T:0.44
Consensus pattern (24 bp):
TGTAAATGACTGATTTGTCTGTGA
Found at i:726365 original size:48 final size:48
Alignment explanation
Indices: 726312--726408 Score: 135
Period size: 48 Copynumber: 2.0 Consensus size: 48
726302 CCCTCGAGTG
726312 TAAATGATTGATTTGTATGTG-AT-GTAAATGACTGATGTGCCTGTGATT
1 TAAATGATTGATTTGTATGTGAATGGT--ATGACTGATGTGCCTGTGATT
* * *
726360 TAAATGATTGATTTGTCTGTGAATGGTATGACTGATTTGTCTGTGATT
1 TAAATGATTGATTTGTATGTGAATGGTATGACTGATGTGCCTGTGATT
726408 T
1 T
726409 GTATGACTGA
Statistics
Matches: 44, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
48 40 0.91
49 2 0.05
50 2 0.05
ACGTcount: A:0.25, C:0.06, G:0.25, T:0.44
Consensus pattern (48 bp):
TAAATGATTGATTTGTATGTGAATGGTATGACTGATGTGCCTGTGATT
Found at i:726522 original size:27 final size:27
Alignment explanation
Indices: 726484--726548 Score: 73
Period size: 27 Copynumber: 2.4 Consensus size: 27
726474 ATGGAAGAAG
*
726484 TACTG-TACTGGTGGCTCT-GCCACA-A
1 TACTGTTACTGGTAGCT-TGGCCACATA
726509 TCACTGTTACTGGTAGCTTGGCCACATA
1 T-ACTGTTACTGGTAGCTTGGCCACATA
*
726537 TACTATTACTGG
1 TACTGTTACTGG
726549 CATTTTTGCT
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
25 1 0.03
26 5 0.15
27 26 0.76
28 2 0.06
ACGTcount: A:0.22, C:0.25, G:0.22, T:0.32
Consensus pattern (27 bp):
TACTGTTACTGGTAGCTTGGCCACATA
Found at i:726636 original size:32 final size:32
Alignment explanation
Indices: 726595--726729 Score: 123
Period size: 32 Copynumber: 4.3 Consensus size: 32
726585 GCAATGCTAT
* *
726595 TGATGGCTTTGTGCCGATTATATGACTGTTAC
1 TGATGGCTTTGTGCCGATCATATCACTGTTAC
* *
726627 TGATGGCTTTGTGCCGATGATATTA-TCGTTAC
1 TGATGGCTTTGTGCCGATCATATCACT-GTTAC
* * * * *
726659 TGATAGATGTGTGCCAATCATATCACTGCTAC
1 TGATGGCTTTGTGCCGATCATATCACTGTTAC
* * *
726691 TGATGGCTTTGTGTCAATCATATTA-TG-TAC
1 TGATGGCTTTGTGCCGATCATATCACTGTTAC
*
726721 TTATGGCTT
1 TGATGGCTT
726730 GTAGCCATTC
Statistics
Matches: 86, Mismatches: 15, Indels: 6
0.80 0.14 0.06
Matches are distributed among these distances:
30 11 0.13
31 3 0.03
32 71 0.83
33 1 0.01
ACGTcount: A:0.21, C:0.16, G:0.22, T:0.40
Consensus pattern (32 bp):
TGATGGCTTTGTGCCGATCATATCACTGTTAC
Found at i:726751 original size:22 final size:22
Alignment explanation
Indices: 726721--726767 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
726711 TATTATGTAC
* * *
726721 TTATGGCTTGTAGCCATTCTGT
1 TTATAGCTTATAGCCATCCTGT
*
726743 TTATAGCTTATAGCTATCCTGT
1 TTATAGCTTATAGCCATCCTGT
726765 TTA
1 TTA
726768 CGGCTCTTAG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.19, C:0.17, G:0.17, T:0.47
Consensus pattern (22 bp):
TTATAGCTTATAGCCATCCTGT
Found at i:731634 original size:231 final size:235
Alignment explanation
Indices: 731383--731867 Score: 825
Period size: 241 Copynumber: 2.0 Consensus size: 235
731373 GTATAGAGGC
731383 TAAATCCTAATTTAGACATAATAGAGAGGTCAAAATTAAAATTTAACATTTTTTAAAATGC-AAA
1 TAAATCCTAATTTAGACATAATAGAGAGGTCAAAATTAAAATTTAACATTTTTTAAAATGCAAAA
731447 AAAAAAG-AAA-AAAAGAAAAGGAAAGCACCATGGTGGTGCATGTGTAAACAAAGGACTTACTTT
66 AAAAAAGAAAAGAAAAGAAAAGGAAAGCACCATGGTGGTGCATGTGTAAACAAAGGACTTACTTT
731510 TATATAGACTTATATGGATTAAATAGAATTAAATCCGAATTTAAGTATGGAGTGTGAATTCATTC
131 TATATAGACTTATATGGATTAAATAGAATTAAATCCGAATTTAAGTATGGAGTGTGAATTCATTC
731575 -GAAATGATAAGAAGAAATAAGAAAATAATATAATTGATG
196 TGAAATGATAAGAAGAAATAAGAAAATAATATAATTGATG
731614 TAAATCCTAATTTAGACATAATAGAGAGGTCAAAATTAAAATTTAACATTTTTTAAAATGCAAAA
1 TAAATCCTAATTTAGACATAATAGAGAGGTCAAAATTAAAATTTAACATTTTTTAAAATGC--AA
*
731679 AAAAAAAAGAAAAAAAAAGAAAAGAAAAGGAAAGCACCATGGTGGTGCATGTGTAAACAAAGGAT
64 AAAAAAAAG-----AAAAGAAAAGAAAAGGAAAGCACCATGGTGGTGCATGTGTAAACAAAGGAC
731744 TTACTTTTATATAGACTTATATGGATTAAATAGAATTAAATCCGAATTTAAGTATGGAGTGTGAA
124 TTACTTTTATATAGACTTATATGGATTAAATAGAATTAAATCCGAATTTAAGTATGGAGTGTGAA
*
731809 TTCATTCGTATTGAAATGATATGAAGAAATAAGAAAATAATATAATTGATG
189 TTCATTC----TGAAATGATAAGAAGAAATAAGAAAATAATATAATTGATG
731860 TAAATCCT
1 TAAATCCT
731868 TGATAATATG
Statistics
Matches: 237, Mismatches: 2, Indels: 15
0.93 0.01 0.06
Matches are distributed among these distances:
231 61 0.26
234 10 0.04
240 3 0.01
241 117 0.49
246 46 0.19
ACGTcount: A:0.48, C:0.08, G:0.16, T:0.28
Consensus pattern (235 bp):
TAAATCCTAATTTAGACATAATAGAGAGGTCAAAATTAAAATTTAACATTTTTTAAAATGCAAAA
AAAAAAGAAAAGAAAAGAAAAGGAAAGCACCATGGTGGTGCATGTGTAAACAAAGGACTTACTTT
TATATAGACTTATATGGATTAAATAGAATTAAATCCGAATTTAAGTATGGAGTGTGAATTCATTC
TGAAATGATAAGAAGAAATAAGAAAATAATATAATTGATG
Found at i:731691 original size:10 final size:10
Alignment explanation
Indices: 731678--731707 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
731668 AAAATGCAAA
731678 AAAAAAAAAG
1 AAAAAAAAAG
731688 AAAAAAAAAG
1 AAAAAAAAAG
*
731698 AAAAGAAAAG
1 AAAAAAAAAG
731708 GAAAGCACCA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.87, C:0.00, G:0.13, T:0.00
Consensus pattern (10 bp):
AAAAAAAAAG
Found at i:731712 original size:15 final size:15
Alignment explanation
Indices: 731675--731706 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
731665 TTTAAAATGC
731675 AAAAAAAA-AAAAGA
1 AAAAAAAAGAAAAGA
731689 AAAAAAAAGAAAAGA
1 AAAAAAAAGAAAAGA
731704 AAA
1 AAA
731707 GGAAAGCACC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 8 0.47
15 9 0.53
ACGTcount: A:0.91, C:0.00, G:0.09, T:0.00
Consensus pattern (15 bp):
AAAAAAAAGAAAAGA
Found at i:733091 original size:45 final size:45
Alignment explanation
Indices: 733037--733417 Score: 453
Period size: 45 Copynumber: 8.5 Consensus size: 45
733027 CTGTCTATGA
* * *
733037 ACCACCAAAGAAGGAAAAGCCTGAGCCTAAGCCACCAGTTTATAC
1 ACCACCAAAGAAGGAGAAGCCTGAGCCCAAACCACCAGTTTATAC
* * * *
733082 ACCTCCAAAGAAAGAGAAGCCTGAACCCAAACCACCAGTATATGA-
1 ACCACCAAAGAAGGAGAAGCCTGAGCCCAAACCACCAGTTTAT-AC
* * * *
733127 ACCTCCAAAGAAGGAAAAGCCTGAGCCTAAGCCACCAGTTTATAC
1 ACCACCAAAGAAGGAGAAGCCTGAGCCCAAACCACCAGTTTATAC
* *
733172 ACCACCAAAGAAAGAGAAGCCTGAGCCCAAACCACCAGTATATGA-
1 ACCACCAAAGAAGGAGAAGCCTGAGCCCAAACCACCAGTTTAT-AC
* * * * *
733217 ACCTCCAAAGAAGGAAAAGCCTGAACCTAAGCCACCAGTTTATAC
1 ACCACCAAAGAAGGAGAAGCCTGAGCCCAAACCACCAGTTTATAC
* *
733262 ACCACCAAAGAAAGAGAAGCCTGAGCCCAAACCACCAGTATATGA-
1 ACCACCAAAGAAGGAGAAGCCTGAGCCCAAACCACCAGTTTAT-AC
* * * *
733307 ACCCCCAAAGAAGGAAAAGCCTGAGCCTAAGCCACCAGTTTATAC
1 ACCACCAAAGAAGGAGAAGCCTGAGCCCAAACCACCAGTTTATAC
* * * **
733352 ACCACCAAAGAAAGAGCAGCCTGAGCCCAAACCACCAGTGTATGG
1 ACCACCAAAGAAGGAGAAGCCTGAGCCCAAACCACCAGTTTATAC
733397 ACCACCAAAGAAGGAGAAGCC
1 ACCACCAAAGAAGGAGAAGCC
733418 ACCGGCTTAT
Statistics
Matches: 280, Mismatches: 50, Indels: 12
0.82 0.15 0.04
Matches are distributed among these distances:
44 3 0.01
45 274 0.98
46 3 0.01
ACGTcount: A:0.41, C:0.29, G:0.18, T:0.11
Consensus pattern (45 bp):
ACCACCAAAGAAGGAGAAGCCTGAGCCCAAACCACCAGTTTATAC
Found at i:733135 original size:90 final size:90
Alignment explanation
Indices: 733032--733417 Score: 682
Period size: 90 Copynumber: 4.3 Consensus size: 90
733022 GCCCCCTGTC
*
733032 TATGAACCACCAAAGAAGGAAAAGCCTGAGCCTAAGCCACCAGTTTATACACCTCCAAAGAAAGA
1 TATGAACCACCAAAGAAGGAAAAGCCTGAGCCTAAGCCACCAGTTTATACACCACCAAAGAAAGA
*
733097 GAAGCCTGAACCCAAACCACCAGTA
66 GAAGCCTGAGCCCAAACCACCAGTA
*
733122 TATGAACCTCCAAAGAAGGAAAAGCCTGAGCCTAAGCCACCAGTTTATACACCACCAAAGAAAGA
1 TATGAACCACCAAAGAAGGAAAAGCCTGAGCCTAAGCCACCAGTTTATACACCACCAAAGAAAGA
733187 GAAGCCTGAGCCCAAACCACCAGTA
66 GAAGCCTGAGCCCAAACCACCAGTA
* *
733212 TATGAACCTCCAAAGAAGGAAAAGCCTGAACCTAAGCCACCAGTTTATACACCACCAAAGAAAGA
1 TATGAACCACCAAAGAAGGAAAAGCCTGAGCCTAAGCCACCAGTTTATACACCACCAAAGAAAGA
733277 GAAGCCTGAGCCCAAACCACCAGTA
66 GAAGCCTGAGCCCAAACCACCAGTA
*
733302 TATGAACCCCCAAAGAAGGAAAAGCCTGAGCCTAAGCCACCAGTTTATACACCACCAAAGAAAGA
1 TATGAACCACCAAAGAAGGAAAAGCCTGAGCCTAAGCCACCAGTTTATACACCACCAAAGAAAGA
* *
733367 GCAGCCTGAGCCCAAACCACCAGTG
66 GAAGCCTGAGCCCAAACCACCAGTA
* *
733392 TATGGACCACCAAAGAAGGAGAAGCC
1 TATGAACCACCAAAGAAGGAAAAGCC
733418 ACCGGCTTAT
Statistics
Matches: 285, Mismatches: 11, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
90 285 1.00
ACGTcount: A:0.41, C:0.29, G:0.18, T:0.12
Consensus pattern (90 bp):
TATGAACCACCAAAGAAGGAAAAGCCTGAGCCTAAGCCACCAGTTTATACACCACCAAAGAAAGA
GAAGCCTGAGCCCAAACCACCAGTA
Found at i:734025 original size:17 final size:17
Alignment explanation
Indices: 734003--734036 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
733993 TCTAAGGCAA
*
734003 TGATGAATATTATTCCG
1 TGATGAAAATTATTCCG
734020 TGATGAAAATTATTCCG
1 TGATGAAAATTATTCCG
734037 ACCCTTCATG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.32, C:0.12, G:0.18, T:0.38
Consensus pattern (17 bp):
TGATGAAAATTATTCCG
Found at i:735580 original size:22 final size:22
Alignment explanation
Indices: 735555--735606 Score: 63
Period size: 21 Copynumber: 2.4 Consensus size: 22
735545 AAATTTATAG
*
735555 TTAAAATTTA-ATTAGTAAATTT
1 TTAAAATTTAGAATA-TAAATTT
*
735577 TT-AAATTTAGAATATATATTT
1 TTAAAATTTAGAATATAAATTT
735598 TTAAAATTT
1 TTAAAATTT
735607 TCGTATGAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
21 15 0.58
22 11 0.42
ACGTcount: A:0.44, C:0.00, G:0.04, T:0.52
Consensus pattern (22 bp):
TTAAAATTTAGAATATAAATTT
Found at i:736072 original size:20 final size:20
Alignment explanation
Indices: 736038--736079 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
736028 AACTATTTAA
** *
736038 ATAATATTATTTGAATAGTT
1 ATAATATTAAATGAATAATT
736058 ATAATATTAAATGAATAATT
1 ATAATATTAAATGAATAATT
736078 AT
1 AT
736080 GGGTTTATTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.48, C:0.00, G:0.07, T:0.45
Consensus pattern (20 bp):
ATAATATTAAATGAATAATT
Found at i:742092 original size:19 final size:18
Alignment explanation
Indices: 742070--742108 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 18
742060 CTTAGTAAAT
*
742070 AAATTTATACAAGTTTCTC
1 AAATATATACAAGTTT-TC
*
742089 AAATATATAGAAGTTTTC
1 AAATATATACAAGTTTTC
742107 AA
1 AA
742109 GACTTGCTAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 4 0.22
19 14 0.78
ACGTcount: A:0.44, C:0.10, G:0.08, T:0.38
Consensus pattern (18 bp):
AAATATATACAAGTTTTC
Found at i:743506 original size:64 final size:64
Alignment explanation
Indices: 743405--743532 Score: 238
Period size: 64 Copynumber: 2.0 Consensus size: 64
743395 AGGTTGAGAG
743405 ACTAAAATGGACAAGGATCAATTAGCCAATTACCCTAAGCTAAATTGAAAAAAAAATTCTTAGT
1 ACTAAAATGGACAAGGATCAATTAGCCAATTACCCTAAGCTAAATTGAAAAAAAAATTCTTAGT
* *
743469 ACTAAAATGGACAAGGATCAATTAGCCAATTACCCTAAGCTAATTTTAAAAAAAAATTCTTAGT
1 ACTAAAATGGACAAGGATCAATTAGCCAATTACCCTAAGCTAAATTGAAAAAAAAATTCTTAGT
743533 CACTTTCATT
Statistics
Matches: 62, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
64 62 1.00
ACGTcount: A:0.46, C:0.16, G:0.12, T:0.27
Consensus pattern (64 bp):
ACTAAAATGGACAAGGATCAATTAGCCAATTACCCTAAGCTAAATTGAAAAAAAAATTCTTAGT
Found at i:744267 original size:20 final size:20
Alignment explanation
Indices: 744242--744282 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
744232 TAATCATGAC
744242 TAAGCCTTGTGTATCCGTAG
1 TAAGCCTTGTGTATCCGTAG
744262 TAAGCCTTGTGTATCCGTAG
1 TAAGCCTTGTGTATCCGTAG
744282 T
1 T
744283 CCAAAATTTC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.20, C:0.20, G:0.24, T:0.37
Consensus pattern (20 bp):
TAAGCCTTGTGTATCCGTAG
Found at i:744698 original size:45 final size:45
Alignment explanation
Indices: 744649--745002 Score: 369
Period size: 45 Copynumber: 7.9 Consensus size: 45
744639 CTATGAACCT
* * *
744649 CCAAAGAAGGAAAAACCTGAACCTAAACCACCAGTTTATACACCA
1 CCAAAGAAAGAAAAGCCTGAACCCAAACCACCAGTTTATACACCA
* * * * *
744694 CCAAAGAAAGAGAAGCCAGAACCCAAGCCACCAGTATATGA-ATCA
1 CCAAAGAAAGAAAAGCCTGAACCCAAACCACCAGTTTAT-ACACCA
* *
744739 CCAAA-AAAGGAAAAGCCCGAA-CCAAAGCCACCAGTTTATACACCT
1 CCAAAGAAA-GAAAAGCCTGAACCCAAA-CCACCAGTTTATACACCA
* * *
744784 CCAAAGAAAGAGAAGCCTGAACACAAACCACCAGTATATGA-ACCA
1 CCAAAGAAAGAAAAGCCTGAACCCAAACCACCAGTTTAT-ACACCA
* * * * *
744829 CCAAAGAAGGAAAAGCCTGAGCCTAAGCCACCAGTTTATACCCCA
1 CCAAAGAAAGAAAAGCCTGAACCCAAACCACCAGTTTATACACCA
* * *
744874 CCAAAGAAAGAGAAGCCTGAACCCAAGCCACCAGTGTATGA-ACCA
1 CCAAAGAAAGAAAAGCCTGAACCCAAACCACCAGTTTAT-ACACCA
* * * *
744919 CCAAAGAAGGAAAAGCCT-AAGCCTAAGCCACCGGTTTATACACCA
1 CCAAAGAAAGAAAAGCCTGAA-CCCAAACCACCAGTTTATACACCA
* *
744964 CCAAAGAAAGAAAAACCAGAACCCAAACCACCAGTTTAT
1 CCAAAGAAAGAAAAGCCTGAACCCAAACCACCAGTTTAT
745003 CAACCTCCGA
Statistics
Matches: 253, Mismatches: 44, Indels: 24
0.79 0.14 0.07
Matches are distributed among these distances:
44 12 0.05
45 229 0.91
46 12 0.05
ACGTcount: A:0.45, C:0.29, G:0.16, T:0.11
Consensus pattern (45 bp):
CCAAAGAAAGAAAAGCCTGAACCCAAACCACCAGTTTATACACCA
Found at i:744781 original size:90 final size:90
Alignment explanation
Indices: 744628--745017 Score: 505
Period size: 90 Copynumber: 4.3 Consensus size: 90
744618 TTATGAACAT
* * * * *
744628 AAGCCACCTGTCTATGAACCTCCAAAGAAGGAAAAACCTGAACCTAAA-CCACCAGTTTATACAC
1 AAGCCACCAGTATATGAACCACCAAAGAAGGAAAAGCCCGAACC-AAAGCCACCAGTTTATACAC
744692 CACCAAAGAAAGAGAAGCCAGAACCC
65 CACCAAAGAAAGAGAAGCCAGAACCC
* *
744718 AAGCCACCAGTATATGAATCACCAAAAAAGGAAAAGCCCGAACCAAAGCCACCAGTTTATACACC
1 AAGCCACCAGTATATGAACCACCAAAGAAGGAAAAGCCCGAACCAAAGCCACCAGTTTATACACC
* * *
744783 TCCAAAGAAAGAGAAGCCTGAACAC
66 ACCAAAGAAAGAGAAGCCAGAACCC
* * * * *
744808 AAACCACCAGTATATGAACCACCAAAGAAGGAAAAGCCTGAGCCTAAGCCACCAGTTTATACCCC
1 AAGCCACCAGTATATGAACCACCAAAGAAGGAAAAGCCCGAACCAAAGCCACCAGTTTATACACC
*
744873 ACCAAAGAAAGAGAAGCCTGAACCC
66 ACCAAAGAAAGAGAAGCCAGAACCC
* * * *
744898 AAGCCACCAGTGTATGAACCACCAAAGAAGGAAAAG-CCTAAGCCTAAGCCACCGGTTTATACAC
1 AAGCCACCAGTATATGAACCACCAAAGAAGGAAAAGCCCGAA-CCAAAGCCACCAGTTTATACAC
* *
744962 CACCAAAGAAAGAAAAACCAGAACCC
65 CACCAAAGAAAGAGAAGCCAGAACCC
* * * * *
744988 AAACCACCAGTTTATCAACCTCCGAAGAAG
1 AAGCCACCAGTATATGAACCACCAAAGAAG
745018 CCACCAGTTT
Statistics
Matches: 264, Mismatches: 34, Indels: 4
0.87 0.11 0.01
Matches are distributed among these distances:
89 5 0.02
90 259 0.98
ACGTcount: A:0.44, C:0.29, G:0.16, T:0.12
Consensus pattern (90 bp):
AAGCCACCAGTATATGAACCACCAAAGAAGGAAAAGCCCGAACCAAAGCCACCAGTTTATACACC
ACCAAAGAAAGAGAAGCCAGAACCC
Found at i:744949 original size:180 final size:180
Alignment explanation
Indices: 744621--745017 Score: 562
Period size: 180 Copynumber: 2.2 Consensus size: 180
744611 CCCCACCTTA
* * * *
744621 TGAACATAAGCCACCTGTCTATGAACCTCCAAAGAAGGAAAAACCTGAACCTAAACCACCAGTTT
1 TGAACACAAACCACCAGTATATGAACCTCCAAAGAAGGAAAAACCTGAACCTAAACCACCAGTTT
*
744686 ATACACCACCAAAGAAAGAGAAGCCAGAACCCAAGCCACCAGTATATGAATCACCAAAAAAGGAA
66 ATACACCACCAAAGAAAGAGAAGCCAGAACCCAAGCCACCAGTATATGAACCACCAAAAAAGGAA
* * *
744751 AAGCCCGAACCAAAGCCACCAGTTTATACACCTCCAAAGAAAGAGAAGCC
131 AAGCCCGAACCAAAGCCACCAGTTTATACACCACCAAAGAAAGAAAAACC
* * * *
744801 TGAACACAAACCACCAGTATATGAACCACCAAAGAAGGAAAAGCCTGAGCCTAAGCCACCAGTTT
1 TGAACACAAACCACCAGTATATGAACCTCCAAAGAAGGAAAAACCTGAACCTAAACCACCAGTTT
* * * *
744866 ATACCCCACCAAAGAAAGAGAAGCCTGAACCCAAGCCACCAGTGTATGAACCACCAAAGAAGGAA
66 ATACACCACCAAAGAAAGAGAAGCCAGAACCCAAGCCACCAGTATATGAACCACCAAAAAAGGAA
* * *
744931 AAG-CCTAAGCCTAAGCCACCGGTTTATACACCACCAAAGAAAGAAAAACC
131 AAGCCCGAA-CCAAAGCCACCAGTTTATACACCACCAAAGAAAGAAAAACC
* * * * *
744981 AGAACCCAAACCACCAGTTTATCAACCTCCGAAGAAG
1 TGAACACAAACCACCAGTATATGAACCTCCAAAGAAG
745018 CCACCAGTTT
Statistics
Matches: 191, Mismatches: 25, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
179 4 0.02
180 187 0.98
ACGTcount: A:0.44, C:0.29, G:0.16, T:0.12
Consensus pattern (180 bp):
TGAACACAAACCACCAGTATATGAACCTCCAAAGAAGGAAAAACCTGAACCTAAACCACCAGTTT
ATACACCACCAAAGAAAGAGAAGCCAGAACCCAAGCCACCAGTATATGAACCACCAAAAAAGGAA
AAGCCCGAACCAAAGCCACCAGTTTATACACCACCAAAGAAAGAAAAACC
Found at i:749091 original size:340 final size:341
Alignment explanation
Indices: 748459--749140 Score: 1357
Period size: 340 Copynumber: 2.0 Consensus size: 341
748449 TTAATAAAAT
748459 ATTTAAAAATATTTTTAATTGATATTTATATAGTTTTATAATTAAATTTAAATAATATAAATATT
1 ATTTAAAAATATTTTTAATTGATATTTATATAGTTTTATAATTAAATTTAAATAATATAAATATT
748524 TTTTTCTTATTTAAATTGAATTATGACCAGGTTGAGCCGGTTTGAGGTGCAAAAATATTTGTCCA
66 TTTTTCTTATTTAAATTGAATTATGACCAGGTTGAGCCGGTTTGAGGTGCAAAAATATTTGTCCA
748589 AGCTCGACTTAAGTCGGACTAAGCCTATTGGGCTACCCAGCCCTTGATCAGGTTTAGTTACTGTC
131 AGCTCGACTTAAGTCGGACTAAGCCTATTGGGCTACCCAGCCCTTGATCAGGTTTAGTTACTGTC
748654 AAAACCTTTTTTAAAATCGACTTTTTATTTTAAAACAAAAGAAAATGGGATCGCCATCAATCATT
196 AAAACCTTTTTTAAAATCGACTTTTTATTTTAAAACAAAAGAAAATGGGATCGCCATCAATCATT
748719 TTTATGAGGTGTGATCGGATCACCTCATAATTTTAATAAAAGGTTTGATTTATTAAAATGATTTT
261 TTTATGAGGTGTGATCGGATCACCTCATAATTTTAATAAAAGGTTTGATTTATTAAAATGATTTT
748784 CAGTCTACAAAAATCC
326 CAGTCTACAAAAATCC
748800 ATTTAAAAATA-TTTTAATTGATATTTATATAGTTTTATAATTAAATTTAAATAATATAAATATT
1 ATTTAAAAATATTTTTAATTGATATTTATATAGTTTTATAATTAAATTTAAATAATATAAATATT
748864 TTTTTCTTATTTAAATTGAATTATGACCAGGTTGAGCCGGTTTGAGGTGCAAAAATATTTGTCCA
66 TTTTTCTTATTTAAATTGAATTATGACCAGGTTGAGCCGGTTTGAGGTGCAAAAATATTTGTCCA
748929 AGCTCGACTTAAGTCGGACTAAGCCTATTGGGCTACCCAGCCCTTGATCAGGTTTAGTTACTGTC
131 AGCTCGACTTAAGTCGGACTAAGCCTATTGGGCTACCCAGCCCTTGATCAGGTTTAGTTACTGTC
748994 AAAACCTTTTTTAAAATCGACTTTTTATTTTAAAACAAAAGAAAATGGGATCGCCATCAATCATT
196 AAAACCTTTTTTAAAATCGACTTTTTATTTTAAAACAAAAGAAAATGGGATCGCCATCAATCATT
749059 TTTATGAGGTGTGATCGGATCACCTCATAATTTTAATAAAAGGTTTGATTTATTAAAATGATTTT
261 TTTATGAGGTGTGATCGGATCACCTCATAATTTTAATAAAAGGTTTGATTTATTAAAATGATTTT
749124 CAGTCTACAAAAATCC
326 CAGTCTACAAAAATCC
749140 A
1 A
749141 AGAGATAGGT
Statistics
Matches: 341, Mismatches: 0, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
340 330 0.97
341 11 0.03
ACGTcount: A:0.34, C:0.13, G:0.14, T:0.38
Consensus pattern (341 bp):
ATTTAAAAATATTTTTAATTGATATTTATATAGTTTTATAATTAAATTTAAATAATATAAATATT
TTTTTCTTATTTAAATTGAATTATGACCAGGTTGAGCCGGTTTGAGGTGCAAAAATATTTGTCCA
AGCTCGACTTAAGTCGGACTAAGCCTATTGGGCTACCCAGCCCTTGATCAGGTTTAGTTACTGTC
AAAACCTTTTTTAAAATCGACTTTTTATTTTAAAACAAAAGAAAATGGGATCGCCATCAATCATT
TTTATGAGGTGTGATCGGATCACCTCATAATTTTAATAAAAGGTTTGATTTATTAAAATGATTTT
CAGTCTACAAAAATCC
Found at i:752690 original size:74 final size:74
Alignment explanation
Indices: 752569--752712 Score: 218
Period size: 74 Copynumber: 1.9 Consensus size: 74
752559 TCTTTTCAAA
* * * * *
752569 CTCAAGTTATAAACGATCTCGGGAATTAAGAAGAAATCGTGTCCTAACTTATTGGGCATGATCCC
1 CTCAAGTTATAAACGATCTCAGGAATGAAGAAGAAATCGCGTCCTAACTTACTGAGCATGATCCC
752634 TTTTTTTTT
66 TTTTTTTTT
*
752643 CTCAAGTTTTAAACGATCTCAGGAATGAAGAA-AAGATCGCGTCCTAACTTACTGAGCATGATCC
1 CTCAAGTTATAAACGATCTCAGGAATGAAGAAGAA-ATCGCGTCCTAACTTACTGAGCATGATCC
752707 CTTTTT
65 CTTTTT
752713 AAAATCCGAA
Statistics
Matches: 63, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
73 2 0.03
74 61 0.97
ACGTcount: A:0.30, C:0.19, G:0.17, T:0.33
Consensus pattern (74 bp):
CTCAAGTTATAAACGATCTCAGGAATGAAGAAGAAATCGCGTCCTAACTTACTGAGCATGATCCC
TTTTTTTTT
Found at i:753903 original size:45 final size:45
Alignment explanation
Indices: 753854--754136 Score: 331
Period size: 45 Copynumber: 6.3 Consensus size: 45
753844 CGGTTTATAC
* * *
753854 ACCTCCAAAAAAAGAGAAGCCTGAACCCAAACCACCAGTGTATGA
1 ACCTCCAAAGAAAGAGAAACCTGAACCCAAACCACCAGTATATGA
* * *
753899 ACCTCCAAAGAAGGAGAAGCCTGAACCTAAACCACCAGTATATGA
1 ACCTCCAAAGAAAGAGAAACCTGAACCCAAACCACCAGTATATGA
* * * * * *
753944 ACCTCCAAAGAAGGAGAAACCTGAGCCAAAATCACCGGTTTAT-A
1 ACCTCCAAAGAAAGAGAAACCTGAACCCAAACCACCAGTATATGA
753988 CACCTCCAAAGAAAGAGAAACCTGAACCCAAACCACCAGTATATGA
1 -ACCTCCAAAGAAAGAGAAACCTGAACCCAAACCACCAGTATATGA
* * * * * *
754034 ACCTCCAAAGAAGGAGAAGCCCG-AGCCAAAGCCACCGGTTTAT-A
1 ACCTCCAAAGAAAGAGAAACCTGAACCCAAA-CCACCAGTATATGA
* *
754078 CACCTCCAAAGAAAGAGAAACCTGAACCCAAACCACCAATGTATGA
1 -ACCTCCAAAGAAAGAGAAACCTGAACCCAAACCACCAGTATATGA
754124 ACCTCCAAA-AAAG
1 ACCTCCAAAGAAAG
754137 CCTCCAATGT
Statistics
Matches: 203, Mismatches: 29, Indels: 13
0.83 0.12 0.05
Matches are distributed among these distances:
44 12 0.06
45 183 0.90
46 8 0.04
ACGTcount: A:0.43, C:0.29, G:0.16, T:0.12
Consensus pattern (45 bp):
ACCTCCAAAGAAAGAGAAACCTGAACCCAAACCACCAGTATATGA
Found at i:753934 original size:90 final size:90
Alignment explanation
Indices: 753854--754237 Score: 398
Period size: 90 Copynumber: 4.1 Consensus size: 90
753844 CGGTTTATAC
* * * * * *
753854 ACCTCCAAAAAAAGAGAAGCCTGAACCCAAACCACCAGTGTATGA-ACCTCCAAAGAAGGAGAAG
1 ACCTCCAAAGAAGGAGAAGCCTGAACCCAAACCACCGGTTTAT-ACACCTCCAAAGAAAGAGAAA
*
753918 CCTGAACCTAAACCACCAGTATATGA
65 CCTGAACCCAAACCACCAGTATATGA
* * * *
753944 ACCTCCAAAGAAGGAGAAACCTGAGCCAAAATCACCGGTTTATACACCTCCAAAGAAAGAGAAAC
1 ACCTCCAAAGAAGGAGAAGCCTGAACCCAAACCACCGGTTTATACACCTCCAAAGAAAGAGAAAC
754009 CTGAACCCAAACCACCAGTATATGA
66 CTGAACCCAAACCACCAGTATATGA
* *
754034 ACCTCCAAAGAAGGAGAAGCCCG-AGCCAAAGCCACCGGTTTATACACCTCCAAAGAAAGAGAAA
1 ACCTCCAAAGAAGGAGAAGCCTGAACCCAAA-CCACCGGTTTATACACCTCCAAAGAAAGAGAAA
* *
754098 CCTGAACCCAAACCACCAATGTATGA
65 CCTGAACCCAAACCACCAGTATATGA
*
754124 ACCTCCAAAAAAGCCTCCAATGTACGAA-CCT-AAGCCACCAAAGCCACCGGTTTATACACCTCC
1 ACCTCC---AAAG-----AA-GGA-GAAGCCTGAA--C-CCAAA-CCACCGGTTTATACACCTCC
* * *
754187 AAAGAAAAAGAAACCTGATGAACCCAAACCACCAATGTATGA
52 AAAGAAAGAGAAACC---TGAACCCAAACCACCAGTATATGA
754229 ACCTCCAAA
1 ACCTCCAAA
754238 AAAGCCTCCA
Statistics
Matches: 252, Mismatches: 23, Indels: 26
0.84 0.08 0.09
Matches are distributed among these distances:
89 5 0.02
90 160 0.63
93 4 0.02
98 2 0.01
99 5 0.02
100 3 0.01
102 43 0.17
105 30 0.12
ACGTcount: A:0.42, C:0.30, G:0.15, T:0.13
Consensus pattern (90 bp):
ACCTCCAAAGAAGGAGAAGCCTGAACCCAAACCACCGGTTTATACACCTCCAAAGAAAGAGAAAC
CTGAACCCAAACCACCAGTATATGA
Found at i:754013 original size:135 final size:135
Alignment explanation
Indices: 753841--754102 Score: 420
Period size: 135 Copynumber: 1.9 Consensus size: 135
753831 GAACCTAAGC
* *
753841 CACCGGTTTATACACCTCCAAAAAAAGAGAAGCCTGAACCCAAACCACCAGTGTATGAACCTCCA
1 CACCGGTTTATACACCTCCAAAAAAAGAGAAACCTGAACCCAAACCACCAGTATATGAACCTCCA
* *
753906 AAGAAGGAGAAGCCTGAACCTAAA-CCACCAGTATATGA-ACCTCCAAAGAAGGAGAAACCTGAG
66 AAGAAGGAGAAGCCCGAACC-AAAGCCACCAGTATAT-ACACCTCCAAAGAAAGAGAAACCTGAG
753969 CCAAAAT
129 CCAAAAT
*
753976 CACCGGTTTATACACCTCCAAAGAAAGAGAAACCTGAACCCAAACCACCAGTATATGAACCTCCA
1 CACCGGTTTATACACCTCCAAAAAAAGAGAAACCTGAACCCAAACCACCAGTATATGAACCTCCA
* * *
754041 AAGAAGGAGAAGCCCGAGCCAAAGCCACCGGTTTATACACCTCCAAAGAAAGAGAAACCTGA
66 AAGAAGGAGAAGCCCGAACCAAAGCCACCAGTATATACACCTCCAAAGAAAGAGAAACCTGA
754103 ACCCAAACCA
Statistics
Matches: 117, Mismatches: 8, Indels: 4
0.91 0.06 0.03
Matches are distributed among these distances:
134 4 0.03
135 113 0.97
ACGTcount: A:0.42, C:0.28, G:0.17, T:0.13
Consensus pattern (135 bp):
CACCGGTTTATACACCTCCAAAAAAAGAGAAACCTGAACCCAAACCACCAGTATATGAACCTCCA
AAGAAGGAGAAGCCCGAACCAAAGCCACCAGTATATACACCTCCAAAGAAAGAGAAACCTGAGCC
AAAAT
Found at i:754128 original size:135 final size:134
Alignment explanation
Indices: 753849--754136 Score: 393
Period size: 135 Copynumber: 2.1 Consensus size: 134
753839 GCCACCGGTT
* *
753849 TATACACCTCCAAAAAAAGAGAAGCCTGAACCCAAACCACCAGTGTATGAACCTCCAAAGAAGGA
1 TATACACCTCC-AAAAAAGAGAAACCTGAACCCAAACCACCAGTATATGAACCTCCAAAGAAGGA
* * * *
753914 GAAGCCTGAACCTAAACCACCAGTATATGAACCTCCAAAGAAGGAGAAACCTGAGCCAAAATCAC
65 GAAGCCCGAACCTAAACCACCAGTATATGAACCTCCAAAGAAAGAGAAACCTGAACCAAAACCAC
** *
753979 CGGTT
130 CAATG
753984 TATACACCTCCAAAGAAAGAGAAACCTGAACCCAAACCACCAGTATATGAACCTCCAAAGAAGGA
1 TATACACCTCCAAA-AAAGAGAAACCTGAACCCAAACCACCAGTATATGAACCTCCAAAGAAGGA
* * * *
754049 GAAGCCCGAGCC-AAAGCCACCGGTTTAT-ACACCTCCAAAGAAAGAGAAACCTGAACCCAAACC
65 GAAGCCCGAACCTAAA-CCACCAGTATATGA-ACCTCCAAAGAAAGAGAAACCTGAACCAAAACC
754112 ACCAATG
128 ACCAATG
754119 TATGA-ACCTCCAAAAAAG
1 TAT-ACACCTCCAAAAAAG
754137 CCTCCAATGT
Statistics
Matches: 136, Mismatches: 13, Indels: 9
0.86 0.08 0.06
Matches are distributed among these distances:
134 11 0.08
135 124 0.91
136 1 0.01
ACGTcount: A:0.43, C:0.28, G:0.16, T:0.12
Consensus pattern (134 bp):
TATACACCTCCAAAAAAGAGAAACCTGAACCCAAACCACCAGTATATGAACCTCCAAAGAAGGAG
AAGCCCGAACCTAAACCACCAGTATATGAACCTCCAAAGAAAGAGAAACCTGAACCAAAACCACC
AATG
Found at i:754171 original size:57 final size:56
Alignment explanation
Indices: 754105--754396 Score: 200
Period size: 57 Copynumber: 5.4 Consensus size: 56
754095 AAACCTGAAC
754105 CCAAACCACCAATGTATGAACCTCCAAAAAAGCCTCCAATGTACGAACCTAAGCCA
1 CCAAACCACCAATGTATGAACCTCCAAAAAAGCCTCCAATGTACGAACCTAAGCCA
** * * *
754161 CCAAAGCCACCGGTTTAT-ACACCTCCAAAGAAA------AA-G-A--AACCTGATG-AA
1 CCAAA-CCACCAATGTATGA-ACCTCCAAA-AAAGCCTCCAATGTACGAACCT-AAGCCA
*
754209 CCCAAACCACCAATGTATGAACCTCCAAAAAAGCCTCCAATGTACGACCCTAAGCCA
1 -CCAAACCACCAATGTATGAACCTCCAAAAAAGCCTCCAATGTACGAACCTAAGCCA
* ** * * *
754266 CCAAAGCCGCCGGTTTAT-ACACCTCCAAAGAAA------AA-G-A--AACCTGATG-AA
1 CCAAA-CCACCAATGTATGA-ACCTCCAAA-AAAGCCTCCAATGTACGAACCT-AAGCCA
754314 CCCAAACCACCAATGTATGAACCTCCAAAAAAGCCTCCAATGTACGAACCTAAGCCA
1 -CCAAACCACCAATGTATGAACCTCCAAAAAAGCCTCCAATGTACGAACCTAAGCCA
*
754371 CCAAAACCACCAATGTATCAACCTCC
1 CC-AAACCACCAATGTATGAACCTCC
754397 CAACAACCCA
Statistics
Matches: 176, Mismatches: 25, Indels: 69
0.65 0.09 0.26
Matches are distributed among these distances:
47 6 0.03
48 46 0.26
49 16 0.09
50 2 0.01
51 2 0.01
52 4 0.02
53 4 0.02
54 2 0.01
55 2 0.01
56 18 0.10
57 68 0.39
58 6 0.03
ACGTcount: A:0.41, C:0.33, G:0.12, T:0.14
Consensus pattern (56 bp):
CCAAACCACCAATGTATGAACCTCCAAAAAAGCCTCCAATGTACGAACCTAAGCCA
Found at i:754202 original size:48 final size:48
Alignment explanation
Indices: 754150--754307 Score: 108
Period size: 48 Copynumber: 3.1 Consensus size: 48
754140 CCAATGTACG
754150 AACCTAAGCCACCAAAGCCACCGGTTTATACACCTCCAAAGAAAAAGA
1 AACCTAAGCCACCAAAGCCACCGGTTTATACACCTCCAAAGAAAAAGA
* * ** *
754198 AACCTGATG-AACCCAAA-CCACCAATGTATGA-ACCTCCAAA-AAAGCCTCCAATGTA
1 AACCT-AAGCCA-CCAAAGCCACCGGTTTAT-ACACCTCCAAAGAAA------AA-G-A
* *
754253 CGACCCTAAGCCACCAAAGCCGCCGGTTTATACACCTCCAAAGAAAAAGA
1 --AACCTAAGCCACCAAAGCCACCGGTTTATACACCTCCAAAGAAAAAGA
754303 AACCT
1 AACCT
754308 GATGAACCCA
Statistics
Matches: 80, Mismatches: 13, Indels: 34
0.63 0.10 0.27
Matches are distributed among these distances:
47 3 0.04
48 28 0.35
49 8 0.10
50 1 0.01
51 1 0.01
52 2 0.03
53 2 0.03
54 1 0.01
55 1 0.01
56 8 0.10
57 22 0.28
58 3 0.04
ACGTcount: A:0.41, C:0.32, G:0.13, T:0.14
Consensus pattern (48 bp):
AACCTAAGCCACCAAAGCCACCGGTTTATACACCTCCAAAGAAAAAGA
Found at i:754385 original size:30 final size:26
Alignment explanation
Indices: 754317--754411 Score: 75
Period size: 27 Copynumber: 3.4 Consensus size: 26
754307 TGATGAACCC
*
754317 AAACCACCAATGTATGAACCTCCAAA
1 AAACCACCAATGTACGAACCTCCAAA
* *
754343 AAAGCCTCCAATGTACGAACCTAAGCCACCA
1 AAA-CCACCAATGTACGAACCT---CCA-AA
*
754374 AAACCACCAATGTATC-AACCTCCCAAC
1 AAACCACCAATGTA-CGAACCT-CCAAA
*
754401 AACCCACCAAT
1 AAACCACCAAT
754412 ATATGAGCCC
Statistics
Matches: 55, Mismatches: 8, Indels: 11
0.74 0.11 0.15
Matches are distributed among these distances:
26 3 0.05
27 26 0.47
28 3 0.05
30 18 0.33
31 5 0.09
ACGTcount: A:0.42, C:0.37, G:0.07, T:0.14
Consensus pattern (26 bp):
AAACCACCAATGTACGAACCTCCAAA
Found at i:754429 original size:57 final size:57
Alignment explanation
Indices: 754317--754439 Score: 138
Period size: 57 Copynumber: 2.2 Consensus size: 57
754307 TGATGAACCC
* * * * * *
754317 AAACCACCAATGTATGAACCTCCAAAAAAGCCTCCAATGTACGAACCTAAGCCACCA
1 AAACCACCAATGTATCAACCTCCAAAAAACCCACCAATATACGAACCCAAACCACCA
* * * * *
754374 AAACCACCAATGTATCAACCTCCCAACAACCCACCAATATATGAGCCCAAACCACCT
1 AAACCACCAATGTATCAACCTCCAAAAAACCCACCAATATACGAACCCAAACCACCA
*
754431 AAGCCACCA
1 AAACCACCA
754440 GTTTATGCAC
Statistics
Matches: 54, Mismatches: 12, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
57 54 1.00
ACGTcount: A:0.41, C:0.37, G:0.08, T:0.13
Consensus pattern (57 bp):
AAACCACCAATGTATCAACCTCCAAAAAACCCACCAATATACGAACCCAAACCACCA
Found at i:754429 original size:105 final size:105
Alignment explanation
Indices: 754059--754381 Score: 589
Period size: 105 Copynumber: 3.1 Consensus size: 105
754049 GAAGCCCGAG
*
754059 CCAAAGCCACCGGTTTATACACCTCCAAAGAAAGAGAAACC---TGAACCCAAACCACCAATGTA
1 CCAAAGCCACCGGTTTATACACCTCCAAAGAAAAAGAAACCTGATGAACCCAAACCACCAATGTA
754121 TGAACCTCCAAAAAAGCCTCCAATGTACGAACCTAAGCCA
66 TGAACCTCCAAAAAAGCCTCCAATGTACGAACCTAAGCCA
754161 CCAAAGCCACCGGTTTATACACCTCCAAAGAAAAAGAAACCTGATGAACCCAAACCACCAATGTA
1 CCAAAGCCACCGGTTTATACACCTCCAAAGAAAAAGAAACCTGATGAACCCAAACCACCAATGTA
*
754226 TGAACCTCCAAAAAAGCCTCCAATGTACGACCCTAAGCCA
66 TGAACCTCCAAAAAAGCCTCCAATGTACGAACCTAAGCCA
*
754266 CCAAAGCCGCCGGTTTATACACCTCCAAAGAAAAAGAAACCTGATGAACCCAAACCACCAATGTA
1 CCAAAGCCACCGGTTTATACACCTCCAAAGAAAAAGAAACCTGATGAACCCAAACCACCAATGTA
754331 TGAACCTCCAAAAAAGCCTCCAATGTACGAACCTAAGCCA
66 TGAACCTCCAAAAAAGCCTCCAATGTACGAACCTAAGCCA
*
754371 CCAAAACCACC
1 CCAAAGCCACC
754382 AATGTATCAA
Statistics
Matches: 212, Mismatches: 6, Indels: 3
0.96 0.03 0.01
Matches are distributed among these distances:
102 40 0.19
105 172 0.81
ACGTcount: A:0.41, C:0.33, G:0.12, T:0.14
Consensus pattern (105 bp):
CCAAAGCCACCGGTTTATACACCTCCAAAGAAAAAGAAACCTGATGAACCCAAACCACCAATGTA
TGAACCTCCAAAAAAGCCTCCAATGTACGAACCTAAGCCA
Found at i:757871 original size:12 final size:12
Alignment explanation
Indices: 757854--757879 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
757844 AAATAATATT
757854 TTGATTACTTTA
1 TTGATTACTTTA
757866 TTGATTACTTTA
1 TTGATTACTTTA
757878 TT
1 TT
757880 TTGCAGCGGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.23, C:0.08, G:0.08, T:0.62
Consensus pattern (12 bp):
TTGATTACTTTA
Found at i:758361 original size:70 final size:70
Alignment explanation
Indices: 758288--758437 Score: 178
Period size: 70 Copynumber: 2.2 Consensus size: 70
758278 ATTTTCTTCT
*
758288 TTTTTTTAAAA-AAAAAAGAAAGAAAACACGAAGATTTTGAAACACGAGAATTTTTTTGAAAACA
1 TTTTTTTAAAACAAAAAAGAAAGAAAACACGAAAATTTTGAAACACGAGAATTTTTTTGAAAACA
758352 CGAAA
66 CGAAA
* ** ***** * *
758357 -TTTTTGAAACACGGAAATTTTTGGAAACATGAAAATTTTGAAACACGAGAATTTTTTTGAAAAC
1 TTTTTTTAAA-ACAAAAAAGAAAGAAAACACGAAAATTTTGAAACACGAGAATTTTTTTGAAAAC
758421 ACGAAA
65 ACGAAA
758427 TTTTTTTAAAA
1 TTTTTTTAAAA
758438 GAAATATCGT
Statistics
Matches: 66, Mismatches: 12, Indels: 5
0.80 0.14 0.06
Matches are distributed among these distances:
68 8 0.12
69 1 0.02
70 49 0.74
71 8 0.12
ACGTcount: A:0.47, C:0.09, G:0.13, T:0.31
Consensus pattern (70 bp):
TTTTTTTAAAACAAAAAAGAAAGAAAACACGAAAATTTTGAAACACGAGAATTTTTTTGAAAACA
CGAAA
Done.