Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01015017.1 Kokia drynarioides strain JFW-HI SEQ_130061, 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: 111398
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 81 characters in sequence are not A, C, G, or T
Found at i:4393 original size:21 final size:22
Alignment explanation
Indices: 4364--4404 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
4354 AAATAAGGAG
*
4364 AAAATAACAAAAAAATAGCATT
1 AAAATAACAAAAAAAGAGCATT
4386 AAAA-AACAAAAAAAGAGCA
1 AAAATAACAAAAAAAGAGCA
4405 GATTTTTTTG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 14 0.78
22 4 0.22
ACGTcount: A:0.73, C:0.10, G:0.07, T:0.10
Consensus pattern (22 bp):
AAAATAACAAAAAAAGAGCATT
Found at i:25001 original size:688 final size:689
Alignment explanation
Indices: 23976--25324 Score: 2439
Period size: 688 Copynumber: 2.0 Consensus size: 689
23966 GGGAATTGGG
* *
23976 ATCCTACTCAGAAGTTCGAAAATCTTGACTTTCTAGCCATGTGTCTTCGGCGTGAAATTAGAAAA
1 ATCCTACTCAGAAGTTCGAAAATCTTGACTTTCTAACCATATGTCTTCGGCGTGAAATTAGAAAA
*
24041 AAATTTTAAGGTGATCGGAATTAAATTGTATATTTTTATAATAATAAAATTGAAATTTCGTTATT
66 AAAATTTAAGGTGATCGGAATTAAATTGTATATTTTTATAATAATAAAATTGAAATTTCGTTATT
*
24106 TAAATAGTTTATATCTTTATCATTTTAAAAAACTAAATTAAAAGTATTTTTATTTTAAAAGATTA
131 TAAATAGTTTATATCTTTATCATTTTAAAAAACTAAATTAAAAGTATTCTTATTTTAAAAGATTA
* *
24171 AAATACAATTTTATAACATACTAATTTAAAATTTTATGAATAATAAAGAGACTAAAATTAAAATT
196 AAATACAATTTTATAACATACTAATTTAAAATTTTATGAATAAAAAAGAGACTAAAATTAAAAAT
* * *
24236 TTTTATTTTAAAAAATCAAAGCACCTACCAATCCTTAACTCTACCCCTATGTGTTTCTGACTCCA
261 TTTTATTTTAAAAAATCAAAGCACCTACCAACCCCTAACTCTACCCCTATGTGTTTCTCACTCCA
* *
24301 TTAGAGTAGAAATAAAATAATTAAAATCAAGAACAAAACCATCTTAATATTTTTCAATATGATCT
326 TTAGAGTAGAAATAAAATAATCAAAACCAAGAACAAAACCATCTTAATATTTTTCAATATGATCT
*
24366 CTCGATAGTTAAATTGGATTTTGATTAATTTATATGTGAAAT-AAAAAAAACTCTTTAAATACTT
391 CTCGATAGTTAAATTGGATTTTGATTAATTTATATGTGAAATAAAAAAAAACTCTATAAATACTT
* *
24430 ATTTTTTGATCATTTATAAGACTTAAACCCTAAGCATTCAACTTCTTATCACTCGAGTAATTTGA
456 ATTTTTTGATCATTTATAAGACTTAAACCCGAAACATTCAACTTCTTATCACTCGAGTAATTTGA
24495 ATTAAAAAATAAATGAAATTTATTGCAATATTATCAATAATTGAAAAAAGGAAAAGAGCAAAATA
521 ATTAAAAAATAAATGAAATTTATTGCAATATTATCAATAATTGAAAAAAGGAAAAGAGCAAAATA
24560 TCCACAATTGTCAAGTAGACATTGTTGTCATATCCATATTGGTAGATGAATGCGACAACTAGACA
586 TCCACAATTGTCAAGTAGACATTGTTGTCATATCCATATTGGTAGATGAATGCGACAACTAGACA
24625 TTAAAGTTGCAATCTCCAAATCATGAAGAGAAGTATACT
651 TTAAAGTTGCAATCTCCAAATCATGAAGAGAAGTATACT
* *
24664 ATCCTACTCAGAAGTTCGAAAATCTTGACTTTCTAACCATATGTCTTTGGGGTGAAATTAGAAAA
1 ATCCTACTCAGAAGTTCGAAAATCTTGACTTTCTAACCATATGTCTTCGGCGTGAAATTAGAAAA
*
24729 AAAATTTAAGGTGATCGGAATTAAATTGTATATTTTTATAATAATCAAATTGAAATTTCGTTATT
66 AAAATTTAAGGTGATCGGAATTAAATTGTATATTTTTATAATAATAAAATTGAAATTTCGTTATT
* * *
24794 TGAATAGTTTATATCTTTATCATTTTAAAAAATTAAATTAAAAGTATTCTTATTTTAAAAGATTG
131 TAAATAGTTTATATCTTTATCATTTTAAAAAACTAAATTAAAAGTATTCTTATTTTAAAAGATTA
*
24859 AAGTACAATTTTATAACATACTAATTTAAAATTTTATGAATAAAAAAGAGACTAAAATTAAAAAT
196 AAATACAATTTTATAACATACTAATTTAAAATTTTATGAATAAAAAAGAGACTAAAATTAAAAAT
* *
24924 TTTTATTTTAAAAAATCAAATCACTTACCAACCCCTAACTCTACCCCTATGTGTTTCTCACTCCA
261 TTTTATTTTAAAAAATCAAAGCACCTACCAACCCCTAACTCTACCCCTATGTGTTTCTCACTCCA
*
24989 TTAGAGTAGAAATCAAATAATCAAAACCAAGAACAAAACCATCTTAATATTTTTCAATATGATCT
326 TTAGAGTAGAAATAAAATAATCAAAACCAAGAACAAAACCATCTTAATATTTTTCAATATGATCT
* *
25054 CTCGATAGTTAAATTGGGTTTTGATTAATTTATATTTGAAATAAAAAAAAACTCTATAAATACTT
391 CTCGATAGTTAAATTGGATTTTGATTAATTTATATGTGAAATAAAAAAAAACTCTATAAATACTT
* *
25119 ATTTTTTTATCATTTATAAGACTTAAACCCGAAACATTCAACTTCTTATCACTCGAGTATTTTGA
456 ATTTTTTGATCATTTATAAGACTTAAACCCGAAACATTCAACTTCTTATCACTCGAGTAATTTGA
25184 ATTAAAAAATAAATGAAATTTATTGCAATATTATCAATAATTGAAAAAAGGAAAAGAGCAAAATA
521 ATTAAAAAATAAATGAAATTTATTGCAATATTATCAATAATTGAAAAAAGGAAAAGAGCAAAATA
25249 TCCACAATTGTCAAGTAGACATTGTTGTCATATCCATATTGGTAGATGAATGCGACAACTAGACA
586 TCCACAATTGTCAAGTAGACATTGTTGTCATATCCATATTGGTAGATGAATGCGACAACTAGACA
25314 TTAAAGTTGCA
651 TTAAAGTTGCA
25325 CCCAATTAGC
Statistics
Matches: 632, Mismatches: 28, Indels: 1
0.96 0.04 0.00
Matches are distributed among these distances:
688 409 0.65
689 223 0.35
ACGTcount: A:0.41, C:0.13, G:0.10, T:0.36
Consensus pattern (689 bp):
ATCCTACTCAGAAGTTCGAAAATCTTGACTTTCTAACCATATGTCTTCGGCGTGAAATTAGAAAA
AAAATTTAAGGTGATCGGAATTAAATTGTATATTTTTATAATAATAAAATTGAAATTTCGTTATT
TAAATAGTTTATATCTTTATCATTTTAAAAAACTAAATTAAAAGTATTCTTATTTTAAAAGATTA
AAATACAATTTTATAACATACTAATTTAAAATTTTATGAATAAAAAAGAGACTAAAATTAAAAAT
TTTTATTTTAAAAAATCAAAGCACCTACCAACCCCTAACTCTACCCCTATGTGTTTCTCACTCCA
TTAGAGTAGAAATAAAATAATCAAAACCAAGAACAAAACCATCTTAATATTTTTCAATATGATCT
CTCGATAGTTAAATTGGATTTTGATTAATTTATATGTGAAATAAAAAAAAACTCTATAAATACTT
ATTTTTTGATCATTTATAAGACTTAAACCCGAAACATTCAACTTCTTATCACTCGAGTAATTTGA
ATTAAAAAATAAATGAAATTTATTGCAATATTATCAATAATTGAAAAAAGGAAAAGAGCAAAATA
TCCACAATTGTCAAGTAGACATTGTTGTCATATCCATATTGGTAGATGAATGCGACAACTAGACA
TTAAAGTTGCAATCTCCAAATCATGAAGAGAAGTATACT
Found at i:30487 original size:29 final size:29
Alignment explanation
Indices: 30400--30737 Score: 337
Period size: 29 Copynumber: 11.6 Consensus size: 29
30390 AATTCAGGTT
* *
30400 TAAAAAGGGAATTTTTGGAAGTTTCGAGG
1 TAAAAATGGAATTTTTGGAAGTTTCGGGG
* * * *
30429 TCAAAAATGGGATTTGTAGAA-TTTGGGGG
1 T-AAAAATGGAATTTTTGGAAGTTTCGGGG
* *
30458 TAAAAATGGAATTTTTAGAAGTTTTGGGG
1 TAAAAATGGAATTTTTGGAAGTTTCGGGG
* * **
30487 TCAAAATGGGATTTTTGGAAGTTTTTGGG
1 TAAAAATGGAATTTTTGGAAGTTTCGGGG
* * * *
30516 TCAAAAATGGGATTTTTTGAATTTTGGGGG
1 T-AAAAATGGAATTTTTGGAAGTTTCGGGG
* *
30546 T-AAAATGGAATTTTTGGAAGTTTCAAGGT
1 TAAAAATGGAATTTTTGGAAGTTTC-GGGG
*
30575 TAAAAATGGGATTTTTGGAAG-TTCGAGGG
1 TAAAAATGGAATTTTTGGAAGTTTCG-GGG
*
30604 TAAAAATAGAATTTTTGGAAGTTTCGGGG
1 TAAAAATGGAATTTTTGGAAGTTTCGGGG
* *
30633 T-CAAATGGGATTTTTGGAAG-TTCGGGGG
1 TAAAAATGGAATTTTTGGAAGTTTC-GGGG
* *
30661 TGAAGATGGAATTTTTGGAAGTTTCGGGG
1 TAAAAATGGAATTTTTGGAAGTTTCGGGG
*
30690 TTAAAAATGGGATTTTTGGAAG-TTCGGGGG
1 -TAAAAATGGAATTTTTGGAAGTTTC-GGGG
*
30720 TGAAAATGGAATTTTTGG
1 TAAAAATGGAATTTTTGG
30738 GTAGTTTAGG
Statistics
Matches: 257, Mismatches: 40, Indels: 24
0.80 0.12 0.07
Matches are distributed among these distances:
27 3 0.01
28 57 0.22
29 111 0.43
30 86 0.33
ACGTcount: A:0.30, C:0.03, G:0.32, T:0.35
Consensus pattern (29 bp):
TAAAAATGGAATTTTTGGAAGTTTCGGGG
Found at i:30507 original size:87 final size:87
Alignment explanation
Indices: 30400--30748 Score: 384
Period size: 87 Copynumber: 4.0 Consensus size: 87
30390 AATTCAGGTT
* *
30400 TAAAAA-GGGAATTTTTGGAAGTTTCGAGGTCAAAAATGGGATTTGTAGAA-TTTGGGGGTAAAA
1 TAAAAATGGG-ATTTTTGGAAGTTTCGAGGTCAAAAATGGGATTTTTGGAAGTTTGGGGGT-AAA
* *
30463 ATGGAATTTTTAGAAGTTTTGGGG
64 ATGGAATTTTTGGAAGTTTAGGGG
* * * *
30487 TCAAAATGGGATTTTTGGAAGTTTTTG-GGTCAAAAATGGGATTTTTTGAATTTTGGGGGTAAAA
1 TAAAAATGGGATTTTTGGAAG-TTTCGAGGTCAAAAATGGGATTTTTGGAAGTTTGGGGGTAAAA
* *
30551 TGGAATTTTTGGAAGTTTCAAGGT
65 TGGAATTTTTGGAAGTTT-AGGGG
* * * *
30575 TAAAAATGGGATTTTTGGAAG-TTCGAGGGT-AAAAATAGAATTTTTGGAAGTTTCGGGGTCAAA
1 TAAAAATGGGATTTTTGGAAGTTTCGA-GGTCAAAAATGGGATTTTTGGAAGTTTGGGGGTAAAA
* **
30638 TGGGATTTTTGGAAGTTCGGGGG
65 TGGAATTTTTGGAAGTTTAGGGG
* * * * * *
30661 TGAAGATGGAATTTTTGGAAGTTTCGGGGTTAAAAATGGGATTTTTGGAAGTTCGGGGGTGAAAA
1 TAAAAATGGGATTTTTGGAAGTTTCGAGGTCAAAAATGGGATTTTTGGAAGTTTGGGGGT-AAAA
*
30726 TGGAATTTTTGGGTAGTTTAGGG
65 TGGAATTTTT-GGAAGTTTAGGG
30749 ACCTCTAGGG
Statistics
Matches: 218, Mismatches: 34, Indels: 18
0.81 0.13 0.07
Matches are distributed among these distances:
86 26 0.12
87 130 0.60
88 53 0.24
89 9 0.04
ACGTcount: A:0.29, C:0.03, G:0.32, T:0.35
Consensus pattern (87 bp):
TAAAAATGGGATTTTTGGAAGTTTCGAGGTCAAAAATGGGATTTTTGGAAGTTTGGGGGTAAAAT
GGAATTTTTGGAAGTTTAGGGG
Found at i:32475 original size:6 final size:6
Alignment explanation
Indices: 32460--32532 Score: 64
Period size: 6 Copynumber: 12.7 Consensus size: 6
32450 TGTAATTGAT
* * *
32460 TTTAAA TTTAAG TTTAAA ATT--A TTTCAAA TTTAAA -CTAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTT-AAA TTTAAA TTTAAA TTTAAA
* *
32506 TTTAAA TTTAAA -GTAAA TTTAAT TTTA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTA
32533 GAAATAAATC
Statistics
Matches: 53, Mismatches: 9, Indels: 10
0.74 0.12 0.14
Matches are distributed among these distances:
4 3 0.06
5 8 0.15
6 38 0.72
7 4 0.08
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.48
Consensus pattern (6 bp):
TTTAAA
Found at i:32477 original size:12 final size:11
Alignment explanation
Indices: 32460--32530 Score: 63
Period size: 11 Copynumber: 6.3 Consensus size: 11
32450 TGTAATTGAT
32460 TTTAAATTTAA
1 TTTAAATTTAA
*
32471 GTTTAAAATT-A
1 -TTTAAATTTAA
32482 TTTCAAATTTAA
1 TTT-AAATTTAA
**
32494 ACTAAATTTAAA
1 TTTAAATTT-AA
32506 TTTAAATTTAA
1 TTTAAATTTAA
**
32517 AGTAAATTTAA
1 TTTAAATTTAA
32528 TTT
1 TTT
32531 TAGAAATAAA
Statistics
Matches: 46, Mismatches: 10, Indels: 7
0.73 0.16 0.11
Matches are distributed among these distances:
10 3 0.07
11 24 0.52
12 19 0.41
ACGTcount: A:0.46, C:0.03, G:0.03, T:0.48
Consensus pattern (11 bp):
TTTAAATTTAA
Found at i:32506 original size:17 final size:17
Alignment explanation
Indices: 32462--32511 Score: 57
Period size: 17 Copynumber: 2.9 Consensus size: 17
32452 TAATTGATTT
*
32462 TAAATTTAAGTTTAAAA
1 TAAATTTAAATTTAAAA
* *
32479 T-TATTTCAAATTTAAAC
1 TAAATTT-AAATTTAAAA
32496 TAAATTTAAATTTAAA
1 TAAATTTAAATTTAAA
32512 TTTAAAGTAA
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
16 4 0.15
17 19 0.70
18 4 0.15
ACGTcount: A:0.50, C:0.04, G:0.02, T:0.44
Consensus pattern (17 bp):
TAAATTTAAATTTAAAA
Found at i:32512 original size:23 final size:23
Alignment explanation
Indices: 32481--32532 Score: 77
Period size: 23 Copynumber: 2.2 Consensus size: 23
32471 GTTTAAAATT
32481 ATTTCAAATTTAAACTAAATTTAA
1 ATTT-AAATTTAAACTAAATTTAA
*
32505 ATTTAAATTTAAAGTAAATTTAA
1 ATTTAAATTTAAACTAAATTTAA
*
32528 TTTTA
1 ATTTA
32533 GAAATAAATC
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
23 22 0.85
24 4 0.15
ACGTcount: A:0.48, C:0.04, G:0.02, T:0.46
Consensus pattern (23 bp):
ATTTAAATTTAAACTAAATTTAA
Found at i:32522 original size:17 final size:18
Alignment explanation
Indices: 32502--32546 Score: 56
Period size: 17 Copynumber: 2.6 Consensus size: 18
32492 AAACTAAATT
*
32502 TAAATTTAAATTTA-AAG
1 TAAATTTAAATTTAGAAA
*
32519 TAAATTTAATTTTAGAAA
1 TAAATTTAAATTTAGAAA
*
32537 TAAATCTAAA
1 TAAATTTAAA
32547 ATCCATCTAA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
17 13 0.57
18 10 0.43
ACGTcount: A:0.53, C:0.02, G:0.04, T:0.40
Consensus pattern (18 bp):
TAAATTTAAATTTAGAAA
Found at i:32540 original size:23 final size:23
Alignment explanation
Indices: 32481--32546 Score: 62
Period size: 23 Copynumber: 2.8 Consensus size: 23
32471 GTTTAAAATT
*
32481 ATTTCAAATTTAAACTAAATTTAA
1 ATTT-AAATATAAACTAAATTTAA
* *
32505 ATTTAAATTTAAAGTAAATTTAA
1 ATTTAAATATAAACTAAATTTAA
*
32528 TTTTAGAA-ATAAATCTAAA
1 ATTTA-AATATAAA-CTAAA
32547 ATCCATCTAA
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
23 26 0.72
24 10 0.28
ACGTcount: A:0.52, C:0.05, G:0.03, T:0.41
Consensus pattern (23 bp):
ATTTAAATATAAACTAAATTTAA
Found at i:32622 original size:3 final size:3
Alignment explanation
Indices: 32614--32652 Score: 53
Period size: 3 Copynumber: 13.0 Consensus size: 3
32604 GGCTTCAACA
*
32614 ATT ATT ATT ATT ATT ATT ATT ATT -TT CATC ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT -ATT ATT ATT ATT
32653 GTGGATTTTT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
2 2 0.06
3 29 0.91
4 1 0.03
ACGTcount: A:0.31, C:0.05, G:0.00, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:34716 original size:29 final size:30
Alignment explanation
Indices: 34684--34744 Score: 88
Period size: 29 Copynumber: 2.0 Consensus size: 30
34674 AAAAATTTTG
34684 TGTATAAAATTGCACA-AAACCAAAGTTCA
1 TGTATAAAATTGCACATAAACCAAAGTTCA
* *
34713 TGTATACAATTGCACATTAAACCATAGTTCA
1 TGTATAAAATTGCACA-TAAACCAAAGTTCA
34744 T
1 T
34745 AATAATTTCA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
29 15 0.54
31 13 0.46
ACGTcount: A:0.43, C:0.18, G:0.10, T:0.30
Consensus pattern (30 bp):
TGTATAAAATTGCACATAAACCAAAGTTCA
Found at i:35334 original size:22 final size:23
Alignment explanation
Indices: 35309--35377 Score: 59
Period size: 24 Copynumber: 2.8 Consensus size: 23
35299 AAAAATCTTT
35309 TTAAAAATTATAAAATTTTAA-A
1 TTAAAAATTATAAAATTTTAATA
* *
35331 TTAATAAAAATAAAATTACATTTTAATA
1 TT-A-AAAATTATAA--A-ATTTTAATA
*
35359 TTAAAAATGATAAAATTTT
1 TTAAAAATTATAAAATTTT
35378 GAGTTAATCT
Statistics
Matches: 36, Mismatches: 5, Indels: 11
0.69 0.10 0.21
Matches are distributed among these distances:
22 2 0.06
23 6 0.17
24 9 0.25
26 8 0.22
27 8 0.22
28 3 0.08
ACGTcount: A:0.57, C:0.01, G:0.01, T:0.41
Consensus pattern (23 bp):
TTAAAAATTATAAAATTTTAATA
Found at i:35371 original size:28 final size:27
Alignment explanation
Indices: 35323--35375 Score: 72
Period size: 28 Copynumber: 1.9 Consensus size: 27
35313 AAATTATAAA
35323 ATTTTAAATTAATAAAAATAAAATTAC
1 ATTTTAAATTAATAAAAATAAAATTAC
*
35350 ATTTTAATATTAA-AAATGATAAAATT
1 ATTTTAA-ATTAATAAA-AATAAAATT
35376 TTGAGTTAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
27 10 0.43
28 13 0.57
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.40
Consensus pattern (27 bp):
ATTTTAAATTAATAAAAATAAAATTAC
Found at i:36329 original size:29 final size:27
Alignment explanation
Indices: 36276--36329 Score: 63
Period size: 27 Copynumber: 1.9 Consensus size: 27
36266 CGAAAGAAAA
* * *
36276 AAATTTTAGGAATTAAAATTAAATTGT
1 AAATTTTACGAAGTAAAAATAAATTGT
36303 AAATTTTACGATAGTAAAAATATAATT
1 AAATTTTACGA-AGTAAAAATA-AATT
36330 TTATTATTGA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
27 10 0.45
28 8 0.36
29 4 0.18
ACGTcount: A:0.50, C:0.02, G:0.09, T:0.39
Consensus pattern (27 bp):
AAATTTTACGAAGTAAAAATAAATTGT
Found at i:44499 original size:29 final size:29
Alignment explanation
Indices: 44412--44749 Score: 337
Period size: 29 Copynumber: 11.6 Consensus size: 29
44402 AATTCAGGTT
* *
44412 TAAAAAGGGAATTTTTGGAAGTTTCGAGG
1 TAAAAATGGAATTTTTGGAAGTTTCGGGG
* * * *
44441 TCAAAAATGGGATTTGTAGAA-TTTGGGGG
1 T-AAAAATGGAATTTTTGGAAGTTTCGGGG
* *
44470 TAAAAATGGAATTTTTAGAAGTTTTGGGG
1 TAAAAATGGAATTTTTGGAAGTTTCGGGG
* * **
44499 TCAAAATGGGATTTTTGGAAGTTTTTGGG
1 TAAAAATGGAATTTTTGGAAGTTTCGGGG
* * * *
44528 TCAAAAATGGGATTTTTTGAATTTTGGGGG
1 T-AAAAATGGAATTTTTGGAAGTTTCGGGG
* *
44558 T-AAAATGGAATTTTTGGAAGTTTCAAGGT
1 TAAAAATGGAATTTTTGGAAGTTTC-GGGG
*
44587 TAAAAATGGGATTTTTGGAAG-TTCGAGGG
1 TAAAAATGGAATTTTTGGAAGTTTCG-GGG
*
44616 TAAAAATAGAATTTTTGGAAGTTTCGGGG
1 TAAAAATGGAATTTTTGGAAGTTTCGGGG
* *
44645 T-CAAATGGGATTTTTGGAAG-TTCGGGGG
1 TAAAAATGGAATTTTTGGAAGTTTC-GGGG
* *
44673 TGAAGATGGAATTTTTGGAAGTTTCGGGG
1 TAAAAATGGAATTTTTGGAAGTTTCGGGG
*
44702 TTAAAAATGGGATTTTTGGAAG-TTCGGGGG
1 -TAAAAATGGAATTTTTGGAAGTTTC-GGGG
*
44732 TGAAAATGGAATTTTTGG
1 TAAAAATGGAATTTTTGG
44750 GTAGTTTAGG
Statistics
Matches: 257, Mismatches: 40, Indels: 24
0.80 0.12 0.07
Matches are distributed among these distances:
27 3 0.01
28 57 0.22
29 111 0.43
30 86 0.33
ACGTcount: A:0.30, C:0.03, G:0.32, T:0.35
Consensus pattern (29 bp):
TAAAAATGGAATTTTTGGAAGTTTCGGGG
Found at i:44519 original size:87 final size:87
Alignment explanation
Indices: 44412--44760 Score: 384
Period size: 87 Copynumber: 4.0 Consensus size: 87
44402 AATTCAGGTT
* *
44412 TAAAAA-GGGAATTTTTGGAAGTTTCGAGGTCAAAAATGGGATTTGTAGAA-TTTGGGGGTAAAA
1 TAAAAATGGG-ATTTTTGGAAGTTTCGAGGTCAAAAATGGGATTTTTGGAAGTTTGGGGGT-AAA
* *
44475 ATGGAATTTTTAGAAGTTTTGGGG
64 ATGGAATTTTTGGAAGTTTAGGGG
* * * *
44499 TCAAAATGGGATTTTTGGAAGTTTTTG-GGTCAAAAATGGGATTTTTTGAATTTTGGGGGTAAAA
1 TAAAAATGGGATTTTTGGAAG-TTTCGAGGTCAAAAATGGGATTTTTGGAAGTTTGGGGGTAAAA
* *
44563 TGGAATTTTTGGAAGTTTCAAGGT
65 TGGAATTTTTGGAAGTTT-AGGGG
* * * *
44587 TAAAAATGGGATTTTTGGAAG-TTCGAGGGT-AAAAATAGAATTTTTGGAAGTTTCGGGGTCAAA
1 TAAAAATGGGATTTTTGGAAGTTTCGA-GGTCAAAAATGGGATTTTTGGAAGTTTGGGGGTAAAA
* **
44650 TGGGATTTTTGGAAGTTCGGGGG
65 TGGAATTTTTGGAAGTTTAGGGG
* * * * * *
44673 TGAAGATGGAATTTTTGGAAGTTTCGGGGTTAAAAATGGGATTTTTGGAAGTTCGGGGGTGAAAA
1 TAAAAATGGGATTTTTGGAAGTTTCGAGGTCAAAAATGGGATTTTTGGAAGTTTGGGGGT-AAAA
*
44738 TGGAATTTTTGGGTAGTTTAGGG
65 TGGAATTTTT-GGAAGTTTAGGG
44761 ACCTCTAGGG
Statistics
Matches: 218, Mismatches: 34, Indels: 18
0.81 0.13 0.07
Matches are distributed among these distances:
86 26 0.12
87 130 0.60
88 53 0.24
89 9 0.04
ACGTcount: A:0.29, C:0.03, G:0.32, T:0.35
Consensus pattern (87 bp):
TAAAAATGGGATTTTTGGAAGTTTCGAGGTCAAAAATGGGATTTTTGGAAGTTTGGGGGTAAAAT
GGAATTTTTGGAAGTTTAGGGG
Found at i:46487 original size:6 final size:6
Alignment explanation
Indices: 46472--46544 Score: 64
Period size: 6 Copynumber: 12.7 Consensus size: 6
46462 TGTAATTGAT
* * *
46472 TTTAAA TTTAAG TTTAAA ATT--A TTTCAAA TTTAAA -CTAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTT-AAA TTTAAA TTTAAA TTTAAA
* *
46518 TTTAAA TTTAAA -GTAAA TTTAAT TTTA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTA
46545 GAAATAAATC
Statistics
Matches: 53, Mismatches: 9, Indels: 10
0.74 0.12 0.14
Matches are distributed among these distances:
4 3 0.06
5 8 0.15
6 38 0.72
7 4 0.08
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.48
Consensus pattern (6 bp):
TTTAAA
Found at i:46489 original size:12 final size:11
Alignment explanation
Indices: 46472--46542 Score: 63
Period size: 11 Copynumber: 6.3 Consensus size: 11
46462 TGTAATTGAT
46472 TTTAAATTTAA
1 TTTAAATTTAA
*
46483 GTTTAAAATT-A
1 -TTTAAATTTAA
46494 TTTCAAATTTAA
1 TTT-AAATTTAA
**
46506 ACTAAATTTAAA
1 TTTAAATTT-AA
46518 TTTAAATTTAA
1 TTTAAATTTAA
**
46529 AGTAAATTTAA
1 TTTAAATTTAA
46540 TTT
1 TTT
46543 TAGAAATAAA
Statistics
Matches: 46, Mismatches: 10, Indels: 7
0.73 0.16 0.11
Matches are distributed among these distances:
10 3 0.07
11 24 0.52
12 19 0.41
ACGTcount: A:0.46, C:0.03, G:0.03, T:0.48
Consensus pattern (11 bp):
TTTAAATTTAA
Found at i:46518 original size:17 final size:17
Alignment explanation
Indices: 46474--46523 Score: 57
Period size: 17 Copynumber: 2.9 Consensus size: 17
46464 TAATTGATTT
*
46474 TAAATTTAAGTTTAAAA
1 TAAATTTAAATTTAAAA
* *
46491 T-TATTTCAAATTTAAAC
1 TAAATTT-AAATTTAAAA
46508 TAAATTTAAATTTAAA
1 TAAATTTAAATTTAAA
46524 TTTAAAGTAA
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
16 4 0.15
17 19 0.70
18 4 0.15
ACGTcount: A:0.50, C:0.04, G:0.02, T:0.44
Consensus pattern (17 bp):
TAAATTTAAATTTAAAA
Found at i:46524 original size:23 final size:23
Alignment explanation
Indices: 46493--46544 Score: 77
Period size: 23 Copynumber: 2.2 Consensus size: 23
46483 GTTTAAAATT
46493 ATTTCAAATTTAAACTAAATTTAA
1 ATTT-AAATTTAAACTAAATTTAA
*
46517 ATTTAAATTTAAAGTAAATTTAA
1 ATTTAAATTTAAACTAAATTTAA
*
46540 TTTTA
1 ATTTA
46545 GAAATAAATC
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
23 22 0.85
24 4 0.15
ACGTcount: A:0.48, C:0.04, G:0.02, T:0.46
Consensus pattern (23 bp):
ATTTAAATTTAAACTAAATTTAA
Found at i:46534 original size:17 final size:18
Alignment explanation
Indices: 46514--46558 Score: 56
Period size: 17 Copynumber: 2.6 Consensus size: 18
46504 AAACTAAATT
*
46514 TAAATTTAAATTTA-AAG
1 TAAATTTAAATTTAGAAA
*
46531 TAAATTTAATTTTAGAAA
1 TAAATTTAAATTTAGAAA
*
46549 TAAATCTAAA
1 TAAATTTAAA
46559 ATCCATCTAA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
17 13 0.57
18 10 0.43
ACGTcount: A:0.53, C:0.02, G:0.04, T:0.40
Consensus pattern (18 bp):
TAAATTTAAATTTAGAAA
Found at i:46552 original size:23 final size:23
Alignment explanation
Indices: 46493--46558 Score: 62
Period size: 23 Copynumber: 2.8 Consensus size: 23
46483 GTTTAAAATT
*
46493 ATTTCAAATTTAAACTAAATTTAA
1 ATTT-AAATATAAACTAAATTTAA
* *
46517 ATTTAAATTTAAAGTAAATTTAA
1 ATTTAAATATAAACTAAATTTAA
*
46540 TTTTAGAA-ATAAATCTAAA
1 ATTTA-AATATAAA-CTAAA
46559 ATCCATCTAA
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
23 26 0.72
24 10 0.28
ACGTcount: A:0.52, C:0.05, G:0.03, T:0.41
Consensus pattern (23 bp):
ATTTAAATATAAACTAAATTTAA
Found at i:46634 original size:3 final size:3
Alignment explanation
Indices: 46626--46664 Score: 53
Period size: 3 Copynumber: 13.0 Consensus size: 3
46616 GGCTTCAACA
*
46626 ATT ATT ATT ATT ATT ATT ATT ATT -TT CATC ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT -ATT ATT ATT ATT
46665 GTGGATTTTT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
2 2 0.06
3 29 0.91
4 1 0.03
ACGTcount: A:0.31, C:0.05, G:0.00, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:48728 original size:29 final size:30
Alignment explanation
Indices: 48696--48756 Score: 88
Period size: 29 Copynumber: 2.0 Consensus size: 30
48686 AAAAATTTTG
48696 TGTATAAAATTGCACA-AAACCAAAGTTCA
1 TGTATAAAATTGCACATAAACCAAAGTTCA
* *
48725 TGTATACAATTGCACATTAAACCATAGTTCA
1 TGTATAAAATTGCACA-TAAACCAAAGTTCA
48756 T
1 T
48757 AATAATTTCA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
29 15 0.54
31 13 0.46
ACGTcount: A:0.43, C:0.18, G:0.10, T:0.30
Consensus pattern (30 bp):
TGTATAAAATTGCACATAAACCAAAGTTCA
Found at i:49346 original size:22 final size:23
Alignment explanation
Indices: 49321--49389 Score: 59
Period size: 24 Copynumber: 2.8 Consensus size: 23
49311 AAAAATCTTT
49321 TTAAAAATTATAAAATTTTAA-A
1 TTAAAAATTATAAAATTTTAATA
* *
49343 TTAATAAAAATAAAATTACATTTTAATA
1 TT-A-AAAATTATAA--A-ATTTTAATA
*
49371 TTAAAAATGATAAAATTTT
1 TTAAAAATTATAAAATTTT
49390 GAGTTAATCT
Statistics
Matches: 36, Mismatches: 5, Indels: 11
0.69 0.10 0.21
Matches are distributed among these distances:
22 2 0.06
23 6 0.17
24 9 0.25
26 8 0.22
27 8 0.22
28 3 0.08
ACGTcount: A:0.57, C:0.01, G:0.01, T:0.41
Consensus pattern (23 bp):
TTAAAAATTATAAAATTTTAATA
Found at i:49383 original size:28 final size:27
Alignment explanation
Indices: 49335--49387 Score: 72
Period size: 28 Copynumber: 1.9 Consensus size: 27
49325 AAATTATAAA
49335 ATTTTAAATTAATAAAAATAAAATTAC
1 ATTTTAAATTAATAAAAATAAAATTAC
*
49362 ATTTTAATATTAA-AAATGATAAAATT
1 ATTTTAA-ATTAATAAA-AATAAAATT
49388 TTGAGTTAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
27 10 0.43
28 13 0.57
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.40
Consensus pattern (27 bp):
ATTTTAAATTAATAAAAATAAAATTAC
Found at i:50341 original size:29 final size:27
Alignment explanation
Indices: 50288--50341 Score: 63
Period size: 27 Copynumber: 1.9 Consensus size: 27
50278 CGAAAGAAAA
* * *
50288 AAATTTTAGGAATTAAAATTAAATTGT
1 AAATTTTACGAAGTAAAAATAAATTGT
50315 AAATTTTACGATAGTAAAAATATAATT
1 AAATTTTACGA-AGTAAAAATA-AATT
50342 TTATTATTGA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
27 10 0.45
28 8 0.36
29 4 0.18
ACGTcount: A:0.50, C:0.02, G:0.09, T:0.39
Consensus pattern (27 bp):
AAATTTTACGAAGTAAAAATAAATTGT
Found at i:56922 original size:18 final size:17
Alignment explanation
Indices: 56901--56946 Score: 65
Period size: 18 Copynumber: 2.5 Consensus size: 17
56891 TAGAAATATA
56901 AAAATATTTAAAACGTTC
1 AAAA-ATTTAAAACGTTC
56919 AAAAATTATAAAACGTTC
1 AAAAATT-TAAAACGTTC
56937 ATAAAATTTA
1 A-AAAATTTA
56947 GAAAAATCGA
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
17 3 0.12
18 17 0.65
19 6 0.23
ACGTcount: A:0.54, C:0.09, G:0.04, T:0.33
Consensus pattern (17 bp):
AAAAATTTAAAACGTTC
Found at i:80978 original size:60 final size:61
Alignment explanation
Indices: 80869--81000 Score: 171
Period size: 60 Copynumber: 2.2 Consensus size: 61
80859 AAATCCAAGT
*
80869 TAGTTGGGTGACCAAAAAAGAAAAAAATTGAATAGTTAGGTGACTATTTTATAACTTTTCA
1 TAGTTGGGTGACCAAAAAAGAAAAAAACTGAATAGTTAGGTGACTATTTTATAACTTTTCA
*** * *
80930 T-GATTGGGTGACCAAAAAAGAAATTTACT-AATAGTTGGGTGA-TCATTTTGTAACTTTTCA
1 TAG-TTGGGTGACCAAAAAAGAAAAAAACTGAATAGTTAGGTGACT-ATTTTATAACTTTTCA
80990 TAGTTGGGTGA
1 TAGTTGGGTGA
81001 AAAAAAAAAT
Statistics
Matches: 62, Mismatches: 6, Indels: 7
0.83 0.08 0.09
Matches are distributed among these distances:
59 1 0.02
60 37 0.60
61 24 0.39
ACGTcount: A:0.36, C:0.08, G:0.21, T:0.35
Consensus pattern (61 bp):
TAGTTGGGTGACCAAAAAAGAAAAAAACTGAATAGTTAGGTGACTATTTTATAACTTTTCA
Found at i:90957 original size:53 final size:53
Alignment explanation
Indices: 90894--91000 Score: 214
Period size: 53 Copynumber: 2.0 Consensus size: 53
90884 CGATGCTCAA
90894 ATCCTACGCCTTGTCTTTCTTTAGTAACTCGATCAAAGGTGCGGCTATTTTGG
1 ATCCTACGCCTTGTCTTTCTTTAGTAACTCGATCAAAGGTGCGGCTATTTTGG
90947 ATCCTACGCCTTGTCTTTCTTTAGTAACTCGATCAAAGGTGCGGCTATTTTGG
1 ATCCTACGCCTTGTCTTTCTTTAGTAACTCGATCAAAGGTGCGGCTATTTTGG
91000 A
1 A
91001 GTAGCCTTTG
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
53 54 1.00
ACGTcount: A:0.20, C:0.22, G:0.21, T:0.37
Consensus pattern (53 bp):
ATCCTACGCCTTGTCTTTCTTTAGTAACTCGATCAAAGGTGCGGCTATTTTGG
Found at i:93245 original size:39 final size:39
Alignment explanation
Indices: 93202--93282 Score: 162
Period size: 39 Copynumber: 2.1 Consensus size: 39
93192 TTACGGCTTG
93202 CTTGTAAATGACAAGCTCACTTCGAAGATCCTTGATCTC
1 CTTGTAAATGACAAGCTCACTTCGAAGATCCTTGATCTC
93241 CTTGTAAATGACAAGCTCACTTCGAAGATCCTTGATCTC
1 CTTGTAAATGACAAGCTCACTTCGAAGATCCTTGATCTC
93280 CTT
1 CTT
93283 CACCAACTCG
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 42 1.00
ACGTcount: A:0.27, C:0.26, G:0.15, T:0.32
Consensus pattern (39 bp):
CTTGTAAATGACAAGCTCACTTCGAAGATCCTTGATCTC
Found at i:100860 original size:31 final size:30
Alignment explanation
Indices: 100792--100860 Score: 77
Period size: 31 Copynumber: 2.2 Consensus size: 30
100782 GATGATGATT
*
100792 GGACTATAATTTTTAAATTGAAAAAGTATAG
1 GGACTA-AATTTTTAAATTGAAAAAGTACAG
* *
100823 GAACTAAA-TTTTAAATTCTAAATAAGTACAG
1 GGACTAAATTTTTAAATT-GAAA-AAGTACAG
100854 GGACTAA
1 GGACTAA
100861 CAACAGAATT
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
29 9 0.28
30 5 0.16
31 18 0.56
ACGTcount: A:0.46, C:0.07, G:0.14, T:0.32
Consensus pattern (30 bp):
GGACTAAATTTTTAAATTGAAAAAGTACAG
Found at i:102255 original size:22 final size:20
Alignment explanation
Indices: 102222--102261 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 20
102212 ATTTTAATTT
102222 TATAAAAATAAAATAAAAAAG
1 TATAAAAATAAAA-AAAAAAG
102243 TATAAAAATTAAAAAAAAA
1 TATAAAAA-TAAAAAAAAA
102262 TTAGCATGAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 13 0.72
22 5 0.28
ACGTcount: A:0.78, C:0.00, G:0.03, T:0.20
Consensus pattern (20 bp):
TATAAAAATAAAAAAAAAAG
Found at i:108107 original size:16 final size:16
Alignment explanation
Indices: 108086--108130 Score: 58
Period size: 14 Copynumber: 2.9 Consensus size: 16
108076 AATGGAATGA
108086 AAATAAATTTTTAATT
1 AAATAAATTTTTAATT
108102 AAATAAA--TTTAATT
1 AAATAAATTTTTAATT
*
108116 AATTAAAATTTTTAA
1 AAAT-AAATTTTTAA
108131 ATCCTAAACT
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
14 10 0.40
15 3 0.12
16 7 0.28
17 5 0.20
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (16 bp):
AAATAAATTTTTAATT
Found at i:110027 original size:30 final size:31
Alignment explanation
Indices: 109993--110055 Score: 85
Period size: 31 Copynumber: 2.1 Consensus size: 31
109983 TATCATTTAA
*
109993 TACTTAAATT-TAATTT-AATATTCAATTTGG
1 TACTTAAATTGT-ATTTCAAGATTCAATTTGG
*
110023 TACTTAAATTGTGTTTCAAGATTCAATTTGG
1 TACTTAAATTGTATTTCAAGATTCAATTTGG
110054 TA
1 TA
110056 TTCATACCAA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
30 13 0.45
31 16 0.55
ACGTcount: A:0.33, C:0.08, G:0.11, T:0.48
Consensus pattern (31 bp):
TACTTAAATTGTATTTCAAGATTCAATTTGG
Done.