Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011984.1 Kokia drynarioides strain JFW-HI SEQ_126982, whole genome shotgun sequence
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: 103040
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Warning! 4 characters in sequence are not A, C, G, or T
Found at i:598 original size:26 final size:28
Alignment explanation
Indices: 555--610 Score: 71
Period size: 29 Copynumber: 2.0 Consensus size: 28
545 ATTTTACGAA
*
555 TTGTTTTAATATCGTTTTTAA-TTTATTTG
1 TTGTTTTAATA-C-TTTTTAACTATATTTG
584 TTGTTTTAATA-TTTTTAACTATATTTG
1 TTGTTTTAATACTTTTTAACTATATTTG
611 ATATATCATA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
26 7 0.28
27 7 0.28
29 11 0.44
ACGTcount: A:0.23, C:0.04, G:0.09, T:0.64
Consensus pattern (28 bp):
TTGTTTTAATACTTTTTAACTATATTTG
Found at i:3220 original size:25 final size:24
Alignment explanation
Indices: 3176--3222 Score: 60
Period size: 25 Copynumber: 1.9 Consensus size: 24
3166 TTTCATCAAC
*
3176 CAAAAAAAAATAAAACTCAAATAA
1 CAAAAAAAAACAAAACTCAAATAA
3200 CAAAACAAAAACAAATA-TCAAAT
1 CAAAA-AAAAACAAA-ACTCAAAT
3223 GCCGAAATTG
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
24 5 0.25
25 14 0.70
26 1 0.05
ACGTcount: A:0.72, C:0.15, G:0.00, T:0.13
Consensus pattern (24 bp):
CAAAAAAAAACAAAACTCAAATAA
Found at i:3533 original size:27 final size:26
Alignment explanation
Indices: 3480--3535 Score: 67
Period size: 27 Copynumber: 2.1 Consensus size: 26
3470 TCAGCTAATT
****
3480 CATGATTTTTATCATATCATTTTAAG
1 CATGATTTTTATCATATCAAAACAAG
3506 CATGATTTTTAATCATATCAAAACAAG
1 CATGATTTTT-ATCATATCAAAACAAG
3533 CAT
1 CAT
3536 CCATTTCAAT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
26 10 0.40
27 15 0.60
ACGTcount: A:0.38, C:0.14, G:0.07, T:0.41
Consensus pattern (26 bp):
CATGATTTTTATCATATCAAAACAAG
Found at i:8409 original size:3 final size:3
Alignment explanation
Indices: 8403--8429 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
8393 GGAAGAAGTT
8403 GAA GAA GAA GAA GAA GAA GAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA
8430 AGAGAGGGAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:8649 original size:5 final size:6
Alignment explanation
Indices: 8634--8658 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
8624 GTGTTGGGAC
8634 AAAAAT AAAAAT AAAAAT AAAAAT A
1 AAAAAT AAAAAT AAAAAT AAAAAT A
8659 GGAGACAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (6 bp):
AAAAAT
Found at i:11484 original size:9 final size:9
Alignment explanation
Indices: 11465--11507 Score: 61
Period size: 9 Copynumber: 4.7 Consensus size: 9
11455 TTAAAAAAAA
11465 AATTATTTAT
1 AATT-TTTAT
11475 AATTTTTAT
1 AATTTTTAT
11484 AATTTTTAAT
1 AATTTTT-AT
11494 AATTTTTA-
1 AATTTTTAT
11502 AATTTT
1 AATTTT
11508 GAAGGGACTC
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
8 6 0.19
9 13 0.41
10 13 0.41
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (9 bp):
AATTTTTAT
Found at i:11501 original size:10 final size:10
Alignment explanation
Indices: 11473--11502 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
11463 AAAATTATTT
11473 ATAATTTTT-
1 ATAATTTTTA
11482 ATAATTTTTA
1 ATAATTTTTA
11492 ATAATTTTTA
1 ATAATTTTTA
11502 A
1 A
11503 ATTTTGAAGG
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 9 0.45
10 11 0.55
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (10 bp):
ATAATTTTTA
Found at i:20803 original size:21 final size:20
Alignment explanation
Indices: 20764--20805 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
20754 GTTTTGAGCA
*
20764 ATTTATTTTTTTATTCTTTT
1 ATTTATTTTTATATTCTTTT
*
20784 ATTTATTTTATATGTTCTTTT
1 ATTTATTTT-TATATTCTTTT
20805 A
1 A
20806 ACTTTTTTTC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 9 0.47
21 10 0.53
ACGTcount: A:0.19, C:0.05, G:0.02, T:0.74
Consensus pattern (20 bp):
ATTTATTTTTATATTCTTTT
Found at i:34466 original size:6 final size:6
Alignment explanation
Indices: 34441--34531 Score: 57
Period size: 6 Copynumber: 15.5 Consensus size: 6
34431 TTTAAATTGG
** * **
34441 TTTAAA TTTATT TTTGAA TTTAAA TTT--A TGTTAAA TTTAAA TTTATCTT
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA T-TTAAA TTTAAA TTTA--AA
**
34490 TTTAAA TTTAAA TTT-GC TTTAAA TTTAAA TTT-AA -TTAAA TTT
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTT
34532 GAATGGATTT
Statistics
Matches: 63, Mismatches: 14, Indels: 16
0.68 0.15 0.17
Matches are distributed among these distances:
4 4 0.06
5 9 0.14
6 44 0.70
7 2 0.03
8 4 0.06
ACGTcount: A:0.37, C:0.02, G:0.03, T:0.57
Consensus pattern (6 bp):
TTTAAA
Found at i:34479 original size:17 final size:17
Alignment explanation
Indices: 34441--34531 Score: 94
Period size: 17 Copynumber: 5.2 Consensus size: 17
34431 TTTAAATTGG
*
34441 TTTAAATTTATTTTTGAA
1 TTTAAATTTA-TTTTAAA
*
34459 TTTAAATTTATGTTAAA
1 TTTAAATTTATTTTAAA
34476 TTTAAATTTATCTTTTTAAA
1 TTTAAATTTA---TTTTAAA
**
34496 TTTAAATTTGCTTTAAA
1 TTTAAATTTATTTTAAA
*
34513 TTTAAATTTA-ATTAAA
1 TTTAAATTTATTTTAAA
34529 TTT
1 TTT
34532 GAATGGATTT
Statistics
Matches: 63, Mismatches: 7, Indels: 8
0.81 0.09 0.10
Matches are distributed among these distances:
16 8 0.13
17 30 0.48
18 10 0.16
20 15 0.24
ACGTcount: A:0.37, C:0.02, G:0.03, T:0.57
Consensus pattern (17 bp):
TTTAAATTTATTTTAAA
Found at i:34500 original size:37 final size:35
Alignment explanation
Indices: 34441--34522 Score: 112
Period size: 37 Copynumber: 2.3 Consensus size: 35
34431 TTTAAATTGG
*
34441 TTTAAATTTATTTTTGAATTTAAATTT-ATGTTAAA
1 TTTAAATTTATTTTTAAATTTAAATTTGAT-TTAAA
*
34476 TTTAAATTTATCTTTTTAAATTTAAATTTGCTTTAAA
1 TTTAAATTTA--TTTTTAAATTTAAATTTGATTTAAA
34513 TTTAAATTTA
1 TTTAAATTTA
34523 ATTAAATTTG
Statistics
Matches: 42, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
35 10 0.24
37 31 0.74
38 1 0.02
ACGTcount: A:0.37, C:0.02, G:0.04, T:0.57
Consensus pattern (35 bp):
TTTAAATTTATTTTTAAATTTAAATTTGATTTAAA
Found at i:35266 original size:33 final size:33
Alignment explanation
Indices: 35226--35332 Score: 92
Period size: 33 Copynumber: 3.2 Consensus size: 33
35216 AAAATGTCAT
* *
35226 TAATAATATTATTAATTAT-ATTAGCAATAATAA
1 TAATAATATTACTAA-TATCATTAACAATAATAA
*
35259 TAATAATATTACTAATATCATTAACAATATTAA
1 TAATAATATTACTAATATCATTAACAATAATAA
* * * * * * *
35292 TGACAATAATAATAATGA-CATCAATAATAATAT
1 TAATAATATTACTAAT-ATCATTAACAATAATAA
35325 TAATAATA
1 TAATAATA
35333 GCATTAATTA
Statistics
Matches: 59, Mismatches: 13, Indels: 4
0.78 0.17 0.05
Matches are distributed among these distances:
32 3 0.05
33 55 0.93
34 1 0.02
ACGTcount: A:0.53, C:0.07, G:0.03, T:0.37
Consensus pattern (33 bp):
TAATAATATTACTAATATCATTAACAATAATAA
Found at i:35307 original size:15 final size:15
Alignment explanation
Indices: 35283--35322 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
35273 ATATCATTAA
*
35283 CAATATTAATGACAAT
1 CAATAATAATGAC-AT
35299 -AATAATAATGACAT
1 CAATAATAATGACAT
35313 CAATAATAAT
1 CAATAATAAT
35323 ATTAATAATA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
14 2 0.09
15 20 0.91
ACGTcount: A:0.55, C:0.10, G:0.05, T:0.30
Consensus pattern (15 bp):
CAATAATAATGACAT
Found at i:35329 original size:12 final size:12
Alignment explanation
Indices: 35224--35332 Score: 56
Period size: 12 Copynumber: 8.8 Consensus size: 12
35214 CGAAAATGTC
*
35224 ATTAATAATATT
1 ATTAATAATAAT
* *
35236 ATTAATTATATT
1 ATTAATAATAAT
**
35248 AGCAATAATAAT
1 ATTAATAATAAT
*
35260 AATAATATTACTAAT
1 ATTAATA--A-TAAT
* * *
35275 ATCATTAACAAT
1 ATTAATAATAAT
* *
35287 ATTAATGACAAT
1 ATTAATAATAAT
* * *
35299 AATAATAATGAC
1 ATTAATAATAAT
*
35311 ATCAATAATAAT
1 ATTAATAATAAT
35323 ATTAATAATA
1 ATTAATAATA
35333 GCATTAATTA
Statistics
Matches: 70, Mismatches: 24, Indels: 6
0.70 0.24 0.06
Matches are distributed among these distances:
12 60 0.86
13 1 0.01
14 1 0.01
15 8 0.11
ACGTcount: A:0.53, C:0.06, G:0.03, T:0.38
Consensus pattern (12 bp):
ATTAATAATAAT
Found at i:36471 original size:59 final size:58
Alignment explanation
Indices: 36376--36866 Score: 606
Period size: 59 Copynumber: 8.3 Consensus size: 58
36366 CCTTAGGCTG
* *
36376 TCCAAAAATTACCATTTTACCCCCAAACTTCTAAAAATTCCATTTTTAACCCCAAAACT
1 TCCAAAAATTACCATTTTA-CCCCAAACTTCCAAAAATCCCATTTTTAACCCCAAAACT
* * * *
36435 ACCAAAAATTACCATTTTACCCTCGAAGTTCCAAAAATCCCATTTTTGACCCCAAAACT
1 TCCAAAAATTACCATTTTACCC-CAAACTTCCAAAAATCCCATTTTTAACCCCAAAACT
* * * *
36494 TCCAAAAATTACCATTTTATCCCCGAACTTCCAAAAATCCCATTTTTGACCTCGAAACT
1 TCCAAAAATTACCATTTTA-CCCCAAACTTCCAAAAATCCCATTTTTAACCCCAAAACT
* ** *
36553 TCCAAAAAATACCATTTTACCCCTAAACTTCCAAAAATCCCATTTTTAACCTTAAAATT
1 TCCAAAAATTACCATTTTACCCC-AAACTTCCAAAAATCCCATTTTTAACCCCAAAACT
** * * *
36612 TCCAAAAATTGGCATTTTACCCCTAAACTTCCAAAAATCCCATTTTTGACCTCGAAACT
1 TCCAAAAATTACCATTTTACCCC-AAACTTCCAAAAATCCCATTTTTAACCCCAAAACT
* * *
36671 TCCAAAAATCACTATTTTACCCCCGAACTTCCAAAAATCCCATTTTTAACCCCAAAACT
1 TCCAAAAATTACCATTTTA-CCCCAAACTTCCAAAAATCCCATTTTTAACCCCAAAACT
* * * *
36730 TCTAAAAATTACCATTTTACCTTCAAACTT-CAAAAATCCCATTTTTAACCTCGAAACT
1 TCCAAAAATTACCATTTTACC-CCAAACTTCCAAAAATCCCATTTTTAACCCCAAAACT
* * * * *
36788 TCCAAAAATCACCATTTTACCCCTGAACTTCCTAAAATCCCATTTTTGACCCCGAAACT
1 TCCAAAAATTACCATTTTACCCC-AAACTTCCAAAAATCCCATTTTTAACCCCAAAACT
*
36847 TCCAAAAAATTACTATTTTA
1 TCC-AAAAATTACCATTTTA
36867 TTCCCGGATG
Statistics
Matches: 377, Mismatches: 47, Indels: 15
0.86 0.11 0.03
Matches are distributed among these distances:
57 1 0.00
58 59 0.16
59 296 0.79
60 21 0.06
ACGTcount: A:0.37, C:0.30, G:0.03, T:0.31
Consensus pattern (58 bp):
TCCAAAAATTACCATTTTACCCCAAACTTCCAAAAATCCCATTTTTAACCCCAAAACT
Found at i:36672 original size:177 final size:177
Alignment explanation
Indices: 36376--36986 Score: 725
Period size: 177 Copynumber: 3.5 Consensus size: 177
36366 CCTTAGGCTG
* * * * *
36376 TCCAAAAATTACCATTTTACCCCCAAACTTCTAAAAATTCCATTTTTAACCCCAAAACTACCAAA
1 TCCAAAAATTACCATTTTACCCCTAAACTTCCAAAAATCCCATTTTTAACCTCAAAACTTCCAAA
* *
36441 AATTACCATTTTA-CCCTCGAAGTTCCAAAAATCCCATTTTTGACCCCAAAACTTCCAAAAATTA
66 AATTACCATTTTACCCCT-GAACTTCCAAAAATCCCATTTTTGACCCCGAAACTTCCAAAAATTA
*
36505 CCATTTTATCCCCGAACTTCCAAAAATCCCATTTTTGACCTCGAAACT
130 CTATTTTATCCCCGAACTTCCAAAAATCCCATTTTTGACCTCGAAACT
* * *
36553 TCCAAAAAATACCATTTTACCCCTAAACTTCCAAAAATCCCATTTTTAACCTTAAAATTTCCAAA
1 TCCAAAAATTACCATTTTACCCCTAAACTTCCAAAAATCCCATTTTTAACCTCAAAACTTCCAAA
** * * *
36618 AATTGGCATTTTACCCCTAAACTTCCAAAAATCCCATTTTTGACCTCGAAACTTCCAAAAATCAC
66 AATTACCATTTTACCCCTGAACTTCCAAAAATCCCATTTTTGACCCCGAAACTTCCAAAAATTAC
* * * *
36683 TATTTTACCCCCGAACTTCCAAAAATCCCATTTTTAACCCCAAAACT
131 TATTTTATCCCCGAACTTCCAAAAATCCCATTTTTGACCTCGAAACT
* * *
36730 TCTAAAAATTACCATTTTA-CCTTCAAACTT-CAAAAATCCCATTTTTAACCTCGAAACTTCCAA
1 TCCAAAAATTACCATTTTACCCCT-AAACTTCCAAAAATCCCATTTTTAACCTCAAAACTTCCAA
* *
36793 AAATCACCATTTTACCCCTGAACTTCCTAAAATCCCATTTTTGACCCCGAAACTTCCAAAAAATT
65 AAATTACCATTTTACCCCTGAACTTCCAAAAATCCCATTTTTGACCCCGAAACTTCC-AAAAATT
* * * * *
36858 ACTATTTTATTCCCGGA-TGTCCGAAGA-CTCCGTTTTTGACCTCGAAAC-
129 ACTATTTTATCCCCGAACT-TCCAAAAATC-CCATTTTTGACCTCGAAACT
* * * ** ** * * ** *
36906 TCCCAAAGTTACCCTTTTACCCCCGAA-TGT-TTAAAATTCCATTTTTAACCTCGAATTTTCCTA
1 TCCAAAAATTACCATTTTACCCCTAAACT-TCCAAAAATCCCATTTTTAACCTCAAAACTTCCAA
*
36969 AAATTACCATTTTGCCCC
65 AAATTACCATTTTACCCC
36987 GTGCACCCGA
Statistics
Matches: 370, Mismatches: 57, Indels: 15
0.84 0.13 0.03
Matches are distributed among these distances:
175 1 0.00
176 147 0.40
177 218 0.59
178 4 0.01
ACGTcount: A:0.35, C:0.30, G:0.05, T:0.31
Consensus pattern (177 bp):
TCCAAAAATTACCATTTTACCCCTAAACTTCCAAAAATCCCATTTTTAACCTCAAAACTTCCAAA
AATTACCATTTTACCCCTGAACTTCCAAAAATCCCATTTTTGACCCCGAAACTTCCAAAAATTAC
TATTTTATCCCCGAACTTCCAAAAATCCCATTTTTGACCTCGAAACT
Found at i:36952 original size:28 final size:30
Alignment explanation
Indices: 36920--36981 Score: 74
Period size: 28 Copynumber: 2.1 Consensus size: 30
36910 AAAGTTACCC
*
36920 TTTTACCCCCGAATGTT-TAAAATT-CCAT
1 TTTTAACCCCGAATGTTCTAAAATTACCAT
* *
36948 TTTTAACCTCGAATTTTCCTAAAATTACCAT
1 TTTTAACCCCGAATGTT-CTAAAATTACCAT
36979 TTT
1 TTT
36982 GCCCCGTGCA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
28 14 0.50
30 7 0.25
31 7 0.25
ACGTcount: A:0.29, C:0.23, G:0.05, T:0.44
Consensus pattern (30 bp):
TTTTAACCCCGAATGTTCTAAAATTACCAT
Found at i:48777 original size:86 final size:86
Alignment explanation
Indices: 48668--48877 Score: 285
Period size: 86 Copynumber: 2.4 Consensus size: 86
48658 TGATAAAAAG
* * * * *
48668 GTTAGCTTCTTGATGAAATACTGAGAAGTGGACTAAATTCGTGTTCCTGGTGAGATACAGAGAAG
1 GTTAGCTTCCTGATGAAATACTGAGAAGTGGACCAAATTCATCTTCCTGATGAGATACAGAGAAG
* *
48733 CGGATTGAAACAGACGACGCA
66 CGGATTGAAACAAAAGACGCA
*
48754 GTTAGCTTCCTGATGAAATACTGAGAAGTGGACCAAATTCATCTTCCTGATGAGATACAGAGAGG
1 GTTAGCTTCCTGATGAAATACTGAGAAGTGGACCAAATTCATCTTCCTGATGAGATACAGAGAAG
*
48819 CGGATTGAAACAAAAGATGCA
66 CGGATTGAAACAAAAGACGCA
* * * * **
48840 GTCATCTTCCCGATGAGATACTGAGAAGAAGACCAAAT
1 GTTAGCTTCCTGATGAAATACTGAGAAGTGGACCAAAT
48878 CAAACCCACG
Statistics
Matches: 109, Mismatches: 15, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
86 109 1.00
ACGTcount: A:0.35, C:0.17, G:0.25, T:0.23
Consensus pattern (86 bp):
GTTAGCTTCCTGATGAAATACTGAGAAGTGGACCAAATTCATCTTCCTGATGAGATACAGAGAAG
CGGATTGAAACAAAAGACGCA
Found at i:49756 original size:13 final size:13
Alignment explanation
Indices: 49740--49773 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
49730 TTAATATTTA
49740 AAATTAAAAGCCC
1 AAATTAAAAGCCC
*
49753 AAATTAAAAGTCC
1 AAATTAAAAGCCC
*
49766 AAAATAAA
1 AAATTAAA
49774 TACAAAGTCC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.62, C:0.15, G:0.06, T:0.18
Consensus pattern (13 bp):
AAATTAAAAGCCC
Found at i:50444 original size:15 final size:15
Alignment explanation
Indices: 50420--50459 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
50410 ATATCATTAA
*
50420 CAATATTAATGACAAT
1 CAATAATAATGAC-AT
50436 -AATAATAATGACAT
1 CAATAATAATGACAT
50450 CAATAATAAT
1 CAATAATAAT
50460 ATTAATAATA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
14 2 0.09
15 20 0.91
ACGTcount: A:0.55, C:0.10, G:0.05, T:0.30
Consensus pattern (15 bp):
CAATAATAATGACAT
Found at i:50466 original size:12 final size:12
Alignment explanation
Indices: 50388--50469 Score: 56
Period size: 12 Copynumber: 6.8 Consensus size: 12
50378 CGAAAATGTC
*
50388 ATTAATAATATT
1 ATTAATAATAAT
* *
50400 ATTATTACTAAT
1 ATTAATAATAAT
* * *
50412 ATCATTAACAAT
1 ATTAATAATAAT
* *
50424 ATTAATGACAAT
1 ATTAATAATAAT
* * *
50436 AATAATAATGAC
1 ATTAATAATAAT
*
50448 ATCAATAATAAT
1 ATTAATAATAAT
50460 ATTAATAATA
1 ATTAATAATA
50470 GCATTAATTA
Statistics
Matches: 51, Mismatches: 19, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
12 51 1.00
ACGTcount: A:0.52, C:0.07, G:0.02, T:0.38
Consensus pattern (12 bp):
ATTAATAATAAT
Found at i:51570 original size:29 final size:30
Alignment explanation
Indices: 51533--51671 Score: 137
Period size: 29 Copynumber: 4.7 Consensus size: 30
51523 CCCTAGGCTA
51533 TCCAAAAATTACCATTTTACCCCCG-AACT
1 TCCAAAAATTACCATTTTACCCCCGAAACT
* *
51562 TCCTAAAA-T-CTCATTTTTGA-CCTCGAAACT
1 TCCAAAAATTAC-CA-TTTT-ACCCCCGAAACT
51592 TCCAAAAATTACCATTTTACCCCC-AAACT
1 TCCAAAAATTACCATTTTACCCCCGAAACT
* * *
51621 TCCTAAAA-TCCCATTTTTAACCCCGAAACT
1 TCCAAAAATTACCA-TTTTACCCCCGAAACT
*
51651 TCCAAAAAATTACTATTTTAC
1 TCC-AAAAATTACCATTTTAC
51672 TCTTGGATGT
Statistics
Matches: 88, Mismatches: 11, Indels: 20
0.74 0.09 0.17
Matches are distributed among these distances:
27 1 0.01
28 7 0.08
29 37 0.42
30 27 0.31
31 12 0.14
32 4 0.05
ACGTcount: A:0.35, C:0.30, G:0.03, T:0.32
Consensus pattern (30 bp):
TCCAAAAATTACCATTTTACCCCCGAAACT
Found at i:51594 original size:30 final size:29
Alignment explanation
Indices: 51547--51658 Score: 113
Period size: 30 Copynumber: 3.8 Consensus size: 29
51537 AAAATTACCA
*
51547 TTTTACCCCCG-AACTTCCTAAAATCTCAT
1 TTTTA-CCCCGAAACTTCCAAAAATCTCAT
*
51576 TTTTGACCTCGAAACTTCCAAAAAT-TACCA-
1 TTTT-ACCCCGAAACTTCCAAAAATCT--CAT
* * *
51606 TTTTACCCCCAAACTTCCTAAAATCCCAT
1 TTTTACCCCGAAACTTCCAAAAATCTCAT
51635 TTTTAACCCCGAAACTTCCAAAAA
1 TTTT-ACCCCGAAACTTCCAAAAA
51659 ATTACTATTT
Statistics
Matches: 68, Mismatches: 8, Indels: 13
0.76 0.09 0.15
Matches are distributed among these distances:
28 2 0.03
29 30 0.44
30 34 0.50
31 2 0.03
ACGTcount: A:0.34, C:0.32, G:0.04, T:0.30
Consensus pattern (29 bp):
TTTTACCCCGAAACTTCCAAAAATCTCAT
Found at i:51625 original size:59 final size:59
Alignment explanation
Indices: 51533--51671 Score: 224
Period size: 59 Copynumber: 2.3 Consensus size: 59
51523 CCCTAGGCTA
* * * *
51533 TCCAAAAATTACCATTTTACCCCCGAACTTCCTAAAATCTCATTTTTGACCTCGAAACT
1 TCCAAAAATTACCATTTTACCCCCAAACTTCCTAAAATCCCATTTTTAACCCCGAAACT
51592 TCCAAAAATTACCATTTTACCCCCAAACTTCCTAAAATCCCATTTTTAACCCCGAAACT
1 TCCAAAAATTACCATTTTACCCCCAAACTTCCTAAAATCCCATTTTTAACCCCGAAACT
*
51651 TCCAAAAAATTACTATTTTAC
1 TCC-AAAAATTACCATTTTAC
51672 TCTTGGATGT
Statistics
Matches: 74, Mismatches: 5, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
59 58 0.78
60 16 0.22
ACGTcount: A:0.35, C:0.30, G:0.03, T:0.32
Consensus pattern (59 bp):
TCCAAAAATTACCATTTTACCCCCAAACTTCCTAAAATCCCATTTTTAACCCCGAAACT
Found at i:51761 original size:28 final size:30
Alignment explanation
Indices: 51725--51785 Score: 81
Period size: 28 Copynumber: 2.1 Consensus size: 30
51715 AAGTTACCCA
*
51725 TTTACCCCCGAATGTTT-AAAATT-CCATT
1 TTTAACCCCGAATGTTTCAAAATTACCATT
*
51753 TTTAACCCCGAATTTTTCCAAAATTACCATT
1 TTTAACCCCGAATGTTT-CAAAATTACCATT
51784 TT
1 TT
51786 ACCCCGTGCA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
28 15 0.54
30 6 0.21
31 7 0.25
ACGTcount: A:0.30, C:0.25, G:0.05, T:0.41
Consensus pattern (30 bp):
TTTAACCCCGAATGTTTCAAAATTACCATT
Found at i:65597 original size:11 final size:10
Alignment explanation
Indices: 65580--65633 Score: 54
Period size: 11 Copynumber: 5.1 Consensus size: 10
65570 TAATTGTAAT
65580 ATAATAATAAA
1 ATAATAA-AAA
*
65591 ATGATAACAAA
1 ATAATAA-AAA
65602 ATAATAAAAAA
1 ATAAT-AAAAA
* *
65613 AAAATAACAA
1 ATAATAAAAA
65623 ATAATAAAAA
1 ATAATAAAAA
65633 A
1 A
65634 CAACAACAAT
Statistics
Matches: 35, Mismatches: 7, Indels: 3
0.78 0.16 0.07
Matches are distributed among these distances:
10 13 0.37
11 20 0.57
12 2 0.06
ACGTcount: A:0.76, C:0.04, G:0.02, T:0.19
Consensus pattern (10 bp):
ATAATAAAAA
Found at i:65605 original size:22 final size:20
Alignment explanation
Indices: 65580--65633 Score: 63
Period size: 22 Copynumber: 2.5 Consensus size: 20
65570 TAATTGTAAT
**
65580 ATAATAATAAAATGATAACAAA
1 ATAATAA-AAAAAAATAAC-AA
65602 ATAATAAAAAAAAAATAACAA
1 ATAAT-AAAAAAAAATAACAA
65623 ATAATAAAAAA
1 ATAATAAAAAA
65634 CAACAACAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
20 6 0.21
21 7 0.24
22 14 0.48
23 2 0.07
ACGTcount: A:0.76, C:0.04, G:0.02, T:0.19
Consensus pattern (20 bp):
ATAATAAAAAAAAATAACAA
Found at i:70433 original size:2 final size:2
Alignment explanation
Indices: 70428--70459 Score: 55
Period size: 2 Copynumber: 15.5 Consensus size: 2
70418 ACACACACAC
70428 AT AT AT AT AT AT AT AT AT AT AT AT AT CAT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT A
70460 CAAAATATTA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 27 0.93
3 2 0.07
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:70471 original size:21 final size:22
Alignment explanation
Indices: 70442--70482 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
70432 ATATATATAT
*
70442 ATATATATATATCATATACAAA
1 ATATATATATATAATATACAAA
*
70464 ATAT-TATATTTAATATACA
1 ATATATATATATAATATACA
70483 TAGAAAAAGT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 13 0.76
22 4 0.24
ACGTcount: A:0.51, C:0.07, G:0.00, T:0.41
Consensus pattern (22 bp):
ATATATATATATAATATACAAA
Found at i:70479 original size:26 final size:26
Alignment explanation
Indices: 70434--70505 Score: 65
Period size: 26 Copynumber: 2.6 Consensus size: 26
70424 ACACATATAT
* *
70434 ATATATATATATATATATATCATATACAAA
1 ATAT-TATATTTA-ATATA-CATAGA-AAA
70464 ATATTATATTTAATATACATAGAAAA
1 ATATTATATTTAATATACATAGAAAA
*
70490 A-GTTATACTTTAATAT
1 ATATTATA-TTTAATAT
70506 GCAAGATTTT
Statistics
Matches: 38, Mismatches: 3, Indels: 6
0.81 0.06 0.13
Matches are distributed among these distances:
25 5 0.13
26 12 0.32
27 5 0.13
28 5 0.13
29 7 0.18
30 4 0.11
ACGTcount: A:0.50, C:0.06, G:0.03, T:0.42
Consensus pattern (26 bp):
ATATTATATTTAATATACATAGAAAA
Found at i:73207 original size:16 final size:15
Alignment explanation
Indices: 73172--73227 Score: 58
Period size: 15 Copynumber: 3.5 Consensus size: 15
73162 TTAAAATGAC
73172 TAAATAAAAAATCAA
1 TAAATAAAAAATCAA
**
73187 TAAATAAAAAATGTA
1 TAAATAAAAAATCAA
*
73202 TAAAATATTAAAATACAA
1 T-AAATA-AAAAAT-CAA
73220 TAAATAAA
1 TAAATAAA
73228 TTTTTTTTAA
Statistics
Matches: 32, Mismatches: 6, Indels: 5
0.74 0.14 0.12
Matches are distributed among these distances:
15 14 0.44
16 6 0.19
17 10 0.31
18 2 0.06
ACGTcount: A:0.70, C:0.04, G:0.02, T:0.25
Consensus pattern (15 bp):
TAAATAAAAAATCAA
Found at i:79699 original size:19 final size:19
Alignment explanation
Indices: 79664--79702 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
79654 CTGTCATCTC
*
79664 TTTTTTCTGTTGTTCTTTT
1 TTTTTTCTCTTGTTCTTTT
79683 TTTTTTCTTCTTG-TCTTTT
1 TTTTTTC-TCTTGTTCTTTT
79702 T
1 T
79703 ATCTCCAAGT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 14 0.78
20 4 0.22
ACGTcount: A:0.00, C:0.13, G:0.08, T:0.79
Consensus pattern (19 bp):
TTTTTTCTCTTGTTCTTTT
Found at i:89440 original size:23 final size:23
Alignment explanation
Indices: 89315--89441 Score: 121
Period size: 23 Copynumber: 5.4 Consensus size: 23
89305 ACACTAGCGC
*
89315 GCTCTCTGTTTAGCAC-GTCTCGT
1 GCTCTCTGTTTAGCACTGTGT-GT
** *
89338 GCTCTCTGTTATTAATACTGTGCGT
1 GCTCTCTG-T-TTAGCACTGTGTGT
* *
89363 GCTCTCTGATTAGCACTTTGTGT
1 GCTCTCTGTTTAGCACTGTGTGT
* * ** *
89386 ACTCTCTGATTAGTGCTTTGTGT
1 GCTCTCTGTTTAGCACTGTGTGT
89409 GCTCTCTGTTTAGCACTGTGTGT
1 GCTCTCTGTTTAGCACTGTGTGT
89432 GCTCTCTGTT
1 GCTCTCTGTT
89442 GCCCAGCACT
Statistics
Matches: 84, Mismatches: 17, Indels: 6
0.79 0.16 0.06
Matches are distributed among these distances:
23 66 0.79
24 1 0.01
25 15 0.18
26 2 0.02
ACGTcount: A:0.11, C:0.23, G:0.22, T:0.44
Consensus pattern (23 bp):
GCTCTCTGTTTAGCACTGTGTGT
Found at i:89501 original size:18 final size:18
Alignment explanation
Indices: 89478--89516 Score: 78
Period size: 18 Copynumber: 2.2 Consensus size: 18
89468 CTCTCTGTTT
89478 GTTCCGTATATCCTAACG
1 GTTCCGTATATCCTAACG
89496 GTTCCGTATATCCTAACG
1 GTTCCGTATATCCTAACG
89514 GTT
1 GTT
89517 TATACGTGTG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.21, C:0.26, G:0.18, T:0.36
Consensus pattern (18 bp):
GTTCCGTATATCCTAACG
Found at i:90445 original size:3 final size:3
Alignment explanation
Indices: 90437--90461 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
90427 CTCAGACGTC
90437 GAT GAT GAT GAT GAT GAT GAT GAT G
1 GAT GAT GAT GAT GAT GAT GAT GAT G
90462 GATTGTAATC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.36, T:0.32
Consensus pattern (3 bp):
GAT
Found at i:91436 original size:16 final size:16
Alignment explanation
Indices: 91397--91442 Score: 53
Period size: 15 Copynumber: 3.0 Consensus size: 16
91387 ATGTTTATAT
91397 TTTTATTTTGG-TCAC
1 TTTTATTTTGGATCAC
*
91412 -TTAATTTTTGGATCAC
1 TTTTA-TTTTGGATCAC
91428 TTTTATTTT-GATCAC
1 TTTTATTTTGGATCAC
91443 AAAAAAATTA
Statistics
Matches: 26, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
14 3 0.12
15 12 0.46
16 8 0.31
17 3 0.12
ACGTcount: A:0.20, C:0.13, G:0.11, T:0.57
Consensus pattern (16 bp):
TTTTATTTTGGATCAC
Found at i:92120 original size:21 final size:20
Alignment explanation
Indices: 92078--92121 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 20
92068 TGTTAAGCAT
*
92078 AATTTAAAAATATAAAATAA
1 AATTTAAAAATATAAAAGAA
* *
92098 AATTTCAAAAATTTAGAAGAA
1 AATTT-AAAAATATAAAAGAA
92119 AAT
1 AAT
92122 AAAATTAATT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
20 5 0.25
21 15 0.75
ACGTcount: A:0.64, C:0.02, G:0.05, T:0.30
Consensus pattern (20 bp):
AATTTAAAAATATAAAAGAA
Found at i:94353 original size:31 final size:31
Alignment explanation
Indices: 94283--94354 Score: 85
Period size: 30 Copynumber: 2.4 Consensus size: 31
94273 TTGAATAATT
* * * *
94283 TATATTTTTA-TAATTTTTAAAAAGTTAAAT
1 TATAATTTTATTAATTTTAAAAAAATTAAAA
*
94313 TA-AAATTTATTAATTTTAAAAAAATTAAAA
1 TATAATTTTATTAATTTTAAAAAAATTAAAA
94343 TATAATTTTATT
1 TATAATTTTATT
94355 TTTGTTGCTT
Statistics
Matches: 34, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
29 5 0.15
30 21 0.62
31 8 0.24
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.50
Consensus pattern (31 bp):
TATAATTTTATTAATTTTAAAAAAATTAAAA
Found at i:95875 original size:19 final size:19
Alignment explanation
Indices: 95838--95880 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 19
95828 ATTCAATATG
95838 AAAATTTTAACAAAATAAA
1 AAAATTTTAACAAAATAAA
* ** *
95857 TAAATTTTATTAAATTAAA
1 AAAATTTTAACAAAATAAA
95876 AAAAT
1 AAAAT
95881 CAACTTCTTG
Statistics
Matches: 19, Mismatches: 5, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (19 bp):
AAAATTTTAACAAAATAAA
Done.