Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01010018.1 Kokia drynarioides strain JFW-HI SEQ_124783, 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: 103170
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.33
Found at i:453 original size:11 final size:11
Alignment explanation
Indices: 437--467 Score: 55
Period size: 10 Copynumber: 2.9 Consensus size: 11
427 TTCTGATTTT
437 GAAAAATTATA
1 GAAAAATTATA
448 GAAAAATT-TA
1 GAAAAATTATA
458 GAAAAATTAT
1 GAAAAATTAT
468 TAGAGACTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
10 10 0.53
11 9 0.47
ACGTcount: A:0.61, C:0.00, G:0.10, T:0.29
Consensus pattern (11 bp):
GAAAAATTATA
Found at i:459 original size:10 final size:10
Alignment explanation
Indices: 432--465 Score: 50
Period size: 10 Copynumber: 3.3 Consensus size: 10
422 CCCTGTTCTG
*
432 ATTTTGAAAA
1 ATTTAGAAAA
442 ATTATAGAAAA
1 ATT-TAGAAAA
453 ATTTAGAAAA
1 ATTTAGAAAA
463 ATT
1 ATT
466 ATTAGAGACT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
10 13 0.59
11 9 0.41
ACGTcount: A:0.56, C:0.00, G:0.09, T:0.35
Consensus pattern (10 bp):
ATTTAGAAAA
Found at i:1101 original size:23 final size:22
Alignment explanation
Indices: 1087--1193 Score: 117
Period size: 23 Copynumber: 4.7 Consensus size: 22
1077 TTACTGTTCA
*
1087 GCACTGTGTGTGCTTACTGTTT
1 GCACTGTGTGTGCTTACTGATT
*
1109 CGCACT-TCGTGTGCCTACTGATTT
1 -GCACTGT-GTGTGCTTACTGA-TT
* * * *
1133 GCGCTATGTGCGCCTACTGATT
1 GCACTGTGTGTGCTTACTGATT
1155 GCACTGTGTGTGCTTACTGGATT
1 GCACTGTGTGTGCTTACT-GATT
1178 GCACTGTGTGTGCTTA
1 GCACTGTGTGTGCTTA
1194 TTGTTTCCCT
Statistics
Matches: 72, Mismatches: 8, Indels: 8
0.82 0.09 0.09
Matches are distributed among these distances:
22 17 0.24
23 52 0.72
24 3 0.04
ACGTcount: A:0.12, C:0.22, G:0.27, T:0.38
Consensus pattern (22 bp):
GCACTGTGTGTGCTTACTGATT
Found at i:9584 original size:19 final size:20
Alignment explanation
Indices: 9546--9584 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
9536 AGTGATTTTT
* *
9546 GAAAAATTAATTTTGATCAA
1 GAAAAATTAAATTAGATCAA
9566 GAAAAATTAAATTAG-TCAA
1 GAAAAATTAAATTAGATCAA
9585 ATTGATTAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 4 0.24
20 13 0.76
ACGTcount: A:0.54, C:0.05, G:0.10, T:0.31
Consensus pattern (20 bp):
GAAAAATTAAATTAGATCAA
Found at i:9766 original size:20 final size:18
Alignment explanation
Indices: 9742--9843 Score: 79
Period size: 20 Copynumber: 5.7 Consensus size: 18
9732 AATAATATTT
9742 TATTAATTTAATATTAAA
1 TATTAATTTAATATTAAA
*
9760 GTGATTATTTTAATATTAAA
1 -T-ATTAATTTAATATTAAA
*
9780 T-TTAATTTAATATT-TA
1 TATTAATTTAATATTAAA
* * *
9796 TCTTGA-TGAATATT--A
1 TATTAATTTAATATTAAA
9811 TATTAATTTAATATTAAA
1 TATTAATTTAATATTAAA
9829 GTGATTAAGTTTAAT
1 -T-ATTAA-TTTAAT
9844 CATAGTTGAA
Statistics
Matches: 67, Mismatches: 8, Indels: 14
0.75 0.09 0.16
Matches are distributed among these distances:
15 5 0.07
16 16 0.24
17 15 0.22
18 1 0.01
19 3 0.04
20 21 0.31
21 6 0.09
ACGTcount: A:0.41, C:0.01, G:0.07, T:0.51
Consensus pattern (18 bp):
TATTAATTTAATATTAAA
Found at i:9774 original size:68 final size:69
Alignment explanation
Indices: 9700--9835 Score: 220
Period size: 68 Copynumber: 2.0 Consensus size: 69
9690 ATTTGAATAG
* *
9700 TTTAATATTAAATTAAATTTAATACTTATTTTAAT-AATATTTTATTAATTTAATATTAAAGTGA
1 TTTAATATTAAATTAAATTTAATACTTATCTTAATGAATATTATATTAATTTAATATTAAAGTGA
9764 TTAT
66 TTAT
* * *
9768 TTTAATATTAAATTTAATTTAATATTTATCTTGATGAATATTATATTAATTTAATATTAAAGTGA
1 TTTAATATTAAATTAAATTTAATACTTATCTTAATGAATATTATATTAATTTAATATTAAAGTGA
9833 TTA
66 TTA
9836 AGTTTAATCA
Statistics
Matches: 62, Mismatches: 5, Indels: 1
0.91 0.07 0.01
Matches are distributed among these distances:
68 31 0.50
69 31 0.50
ACGTcount: A:0.42, C:0.01, G:0.04, T:0.52
Consensus pattern (69 bp):
TTTAATATTAAATTAAATTTAATACTTATCTTAATGAATATTATATTAATTTAATATTAAAGTGA
TTAT
Found at i:16340 original size:25 final size:25
Alignment explanation
Indices: 16280--16380 Score: 71
Period size: 25 Copynumber: 4.0 Consensus size: 25
16270 AGATGATGAA
* * * *
16280 GATATTTTGTTTGCCTCGTAAAAGC
1 GATATTCTGTCTGACTCGTAAGAGC
* *
16305 GATATTTTGTCT-AGCTCGTAAGAGT
1 GATATTCTGTCTGA-CTCGTAAGAGC
* *
16330 GATGTTCTGTCTGACTCGTAAGATC
1 GATATTCTGTCTGACTCGTAAGAGC
* *
16355 GATACTT-TATCTGGACTCATAAGAGC
1 GATA-TTCTGTCT-GACTCGTAAGAGC
16381 TAAACTTTGT
Statistics
Matches: 60, Mismatches: 12, Indels: 7
0.76 0.15 0.09
Matches are distributed among these distances:
25 46 0.77
26 14 0.23
ACGTcount: A:0.25, C:0.17, G:0.22, T:0.37
Consensus pattern (25 bp):
GATATTCTGTCTGACTCGTAAGAGC
Found at i:18920 original size:16 final size:16
Alignment explanation
Indices: 18899--18930 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
18889 ATAAATTTTT
*
18899 ATGTTAAAGGACTAAA
1 ATGTTAAAGGAATAAA
18915 ATGTTAAAGGAATAAA
1 ATGTTAAAGGAATAAA
18931 TTTGTAAGGA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.53, C:0.03, G:0.19, T:0.25
Consensus pattern (16 bp):
ATGTTAAAGGAATAAA
Found at i:19683 original size:24 final size:25
Alignment explanation
Indices: 19649--19720 Score: 101
Period size: 24 Copynumber: 2.9 Consensus size: 25
19639 TGGTTAAACT
*
19649 CTATCTGGGCTCGTAAGAGCTAA-C
1 CTATCTGGGCTCGTATGAGCTAATC
* *
19673 CTATCTCGGCTCGTATGAGCTAATT
1 CTATCTGGGCTCGTATGAGCTAATC
*
19698 CTGTCTGGGCTCGTATGAGCTAA
1 CTATCTGGGCTCGTATGAGCTAA
19721 ATTTTTGGAA
Statistics
Matches: 42, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
24 21 0.50
25 21 0.50
ACGTcount: A:0.21, C:0.24, G:0.25, T:0.31
Consensus pattern (25 bp):
CTATCTGGGCTCGTATGAGCTAATC
Found at i:19857 original size:17 final size:17
Alignment explanation
Indices: 19830--19876 Score: 76
Period size: 17 Copynumber: 2.6 Consensus size: 17
19820 ATAATTGTTC
19830 TTATGAACTTACTAAGCT
1 TTAT-AACTTACTAAGCT
19848 TTATAACTTACTAAGCT
1 TTATAACTTACTAAGCT
19865 TTATAAGCTTAC
1 TTATAA-CTTAC
19877 CTGTGTATCT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
17 19 0.68
18 9 0.32
ACGTcount: A:0.34, C:0.17, G:0.09, T:0.40
Consensus pattern (17 bp):
TTATAACTTACTAAGCT
Found at i:29260 original size:12 final size:12
Alignment explanation
Indices: 29243--29268 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
29233 CTAAAGAAAA
29243 AGGAAGAAGAAG
1 AGGAAGAAGAAG
29255 AGGAAGAAGAAG
1 AGGAAGAAGAAG
29267 AG
1 AG
29269 AATAAAGAGA
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:0.58, C:0.00, G:0.42, T:0.00
Consensus pattern (12 bp):
AGGAAGAAGAAG
Found at i:29714 original size:18 final size:18
Alignment explanation
Indices: 29668--29717 Score: 59
Period size: 18 Copynumber: 2.8 Consensus size: 18
29658 TTCTTTTAGA
29668 TATTTTCA-TGCATTTTT
1 TATTTTCACTGCATTTTT
* *
29685 TATTGTCTCTGCATTTTAT
1 TATTTTCACTGCATTTT-T
29704 T-TTTTCACTGCATT
1 TATTTTCACTGCATT
29718 CCTTTTGTTA
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
17 6 0.22
18 19 0.70
19 2 0.07
ACGTcount: A:0.16, C:0.16, G:0.08, T:0.60
Consensus pattern (18 bp):
TATTTTCACTGCATTTTT
Found at i:35285 original size:21 final size:20
Alignment explanation
Indices: 35234--35293 Score: 66
Period size: 21 Copynumber: 2.9 Consensus size: 20
35224 AAGTCAACGA
*
35234 TCAAAGTCAATGGTCAATGG
1 TCAAAGTCAACGGTCAATGG
*
35254 TCAACGATCAACGGTCAATGG
1 TCAAAG-TCAACGGTCAATGG
*
35275 TTTAAAGTCAACAGGTCAA
1 -TCAAAGTCAAC-GGTCAA
35294 CCAATGGGTC
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
20 5 0.15
21 18 0.55
22 10 0.30
ACGTcount: A:0.37, C:0.18, G:0.22, T:0.23
Consensus pattern (20 bp):
TCAAAGTCAACGGTCAATGG
Found at i:36554 original size:13 final size:13
Alignment explanation
Indices: 36522--36560 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 13
36512 TATCTTTAAC
*
36522 TTAGATTAATTTAGT
1 TTAGATTAA--TACT
36537 TTAGATTAATACT
1 TTAGATTAATACT
36550 TTAGATTAATA
1 TTAGATTAATA
36561 TCCTTCAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 14 0.61
15 9 0.39
ACGTcount: A:0.38, C:0.03, G:0.10, T:0.49
Consensus pattern (13 bp):
TTAGATTAATACT
Found at i:38347 original size:37 final size:37
Alignment explanation
Indices: 38294--38384 Score: 96
Period size: 37 Copynumber: 2.4 Consensus size: 37
38284 TTACAAAAAT
38294 AATATTATTTTAATAGT-TTAATATTAAATTAA-ATTA
1 AATATTATTTTAATAGTATT-ATATTAAATTAATATTA
* * *
38330 AATATTTATTTTGATAGTATTTTATTAATTTAATATTA
1 AATA-TTATTTTAATAGTATTATATTAAATTAATATTA
*
38368 AAGTTATTATCTTAATA
1 AA--TATTATTTTAATA
38385 ATAAATTTAA
Statistics
Matches: 45, Mismatches: 5, Indels: 7
0.79 0.09 0.12
Matches are distributed among these distances:
36 4 0.09
37 22 0.49
38 8 0.18
39 9 0.20
40 2 0.04
ACGTcount: A:0.42, C:0.01, G:0.04, T:0.53
Consensus pattern (37 bp):
AATATTATTTTAATAGTATTATATTAAATTAATATTA
Found at i:38374 original size:20 final size:19
Alignment explanation
Indices: 38351--38400 Score: 52
Period size: 20 Copynumber: 2.7 Consensus size: 19
38341 TGATAGTATT
*
38351 TTATTAATTTAATATTAAA
1 TTATTAATTTAATAATAAA
38370 GTTATT-ATCTTAATAATAAA
1 -TTATTAAT-TTAATAATAAA
38390 -T-TTAATTTAAT
1 TTATTAATTTAAT
38401 GTTTATCTTG
Statistics
Matches: 27, Mismatches: 1, Indels: 7
0.77 0.03 0.20
Matches are distributed among these distances:
17 7 0.26
18 3 0.11
19 2 0.07
20 15 0.56
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.52
Consensus pattern (19 bp):
TTATTAATTTAATAATAAA
Found at i:38652 original size:25 final size:26
Alignment explanation
Indices: 38602--38649 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 26
38592 AGTTGTAGAG
38602 AGAAAATTCTCTGAAGAGATTATTTT
1 AGAAAATTCTCTGAAGAGATTATTTT
38628 AGAAAA-TCTCT--AGAGA-TATTTT
1 AGAAAATTCTCTGAAGAGATTATTTT
38650 TTTTATTTAC
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
22 6 0.27
23 5 0.23
25 5 0.23
26 6 0.27
ACGTcount: A:0.40, C:0.08, G:0.15, T:0.38
Consensus pattern (26 bp):
AGAAAATTCTCTGAAGAGATTATTTT
Found at i:40701 original size:52 final size:52
Alignment explanation
Indices: 40553--40882 Score: 484
Period size: 52 Copynumber: 6.4 Consensus size: 52
40543 GTCTGATAAT
*
40553 TATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATGAGGTTCGATGAC
1 TATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATGAGGTCCGATGAC
* *
40605 TATGTGTCATCATGAGTA-ATGAATCCTTTAAGGATTATGAGGTCCGATGAC
1 TATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATGAGGTCCGATGAC
*
40656 TATGTGTCATCGTGAGTATATGAATCCTATACGGATTATGAGGTCCGATGAC
1 TATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATGAGGTCCGATGAC
* * * *
40708 TATCTATCATCGTGAATATATGAATCATTTACGGATTATGAGGTCCGATGAC
1 TATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATGAGGTCCGATGAC
* * * *
40760 TATGTGTCATTGTGACTATATGAATCCTTTACGGATTATGAGATTCGATGAC
1 TATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATGAGGTCCGATGAC
* * * *
40812 TATGTGTCATCGTGAGCATATGGATCCTTTTTCGGATT-TAAGGTCCGATGAC
1 TATGTGTCATCGTGAGTATATGAATCC-TTTACGGATTATGAGGTCCGATGAC
*
40864 TTTGTGTCATCGTGAGTAT
1 TATGTGTCATCGTGAGTAT
40883 TAAATGGGAA
Statistics
Matches: 248, Mismatches: 28, Indels: 4
0.89 0.10 0.01
Matches are distributed among these distances:
51 48 0.19
52 191 0.77
53 9 0.04
ACGTcount: A:0.26, C:0.15, G:0.23, T:0.36
Consensus pattern (52 bp):
TATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATGAGGTCCGATGAC
Found at i:45958 original size:52 final size:52
Alignment explanation
Indices: 45875--46269 Score: 587
Period size: 52 Copynumber: 7.6 Consensus size: 52
45865 TAAATTAAAA
45875 AGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATG
1 AGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATG
* *
45927 AGGTTCGATGACTATGTGTCATCATGAGTATATGAATCCTTTACGGATTATG
1 AGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATG
* *
45979 AGGTCCGATGACTATGTGTCATCATGAGTATATGAATCTTTTACGGATTATG
1 AGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATG
* * *
46031 AGGTCCGATGACTATGTGTTATCGTGAATATATGAATCTTTTACGGATTATG
1 AGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATG
46083 AGGTCCGATGA-TAATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATG
1 AGGTCCGATGACT-ATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATG
* *
46135 AGATCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTATGGATTATG
1 AGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATG
* * * * *
46187 AGGTCTGATGACTATGTGTCATCGTGAGCATATGGATCCTCTTTCGGATT-TA
1 AGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCT-TTACGGATTATG
* ** * *
46239 AAGTATGATGACTTTGTGTCATCGTAAGTAT
1 AGGTCCGATGACTATGTGTCATCGTGAGTAT
46270 TAAATGGGAA
Statistics
Matches: 316, Mismatches: 24, Indels: 6
0.91 0.07 0.02
Matches are distributed among these distances:
51 1 0.00
52 307 0.97
53 8 0.03
ACGTcount: A:0.26, C:0.14, G:0.24, T:0.36
Consensus pattern (52 bp):
AGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATG
Found at i:47825 original size:30 final size:30
Alignment explanation
Indices: 47789--47883 Score: 154
Period size: 30 Copynumber: 3.2 Consensus size: 30
47779 TCAAATTGGT
*
47789 CTTATTTTTCATTTTAGAATATTTAGTTTC
1 CTTATTTTTCATTTGAGAATATTTAGTTTC
*
47819 CTTATTTTTCATTTGAGAATATTTAGCTTC
1 CTTATTTTTCATTTGAGAATATTTAGTTTC
* *
47849 CTTATTTTTCGTTTGAGAATATTCAGTTTC
1 CTTATTTTTCATTTGAGAATATTTAGTTTC
47879 CTTAT
1 CTTAT
47884 AAAAAAAACT
Statistics
Matches: 60, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
30 60 1.00
ACGTcount: A:0.22, C:0.13, G:0.09, T:0.56
Consensus pattern (30 bp):
CTTATTTTTCATTTGAGAATATTTAGTTTC
Found at i:48460 original size:13 final size:13
Alignment explanation
Indices: 48443--48491 Score: 53
Period size: 13 Copynumber: 3.8 Consensus size: 13
48433 AAACATGGAG
*
48443 CTAAGTGATACCG
1 CTAAGTGATACCA
*
48456 CTAAGTGGTACCA
1 CTAAGTGATACCA
* *
48469 CTAACTGACACCA
1 CTAAGTGATACCA
*
48482 CTAATTGATA
1 CTAAGTGATA
48492 TTTCTCAGTG
Statistics
Matches: 29, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
13 29 1.00
ACGTcount: A:0.35, C:0.24, G:0.16, T:0.24
Consensus pattern (13 bp):
CTAAGTGATACCA
Found at i:52684 original size:18 final size:18
Alignment explanation
Indices: 52661--52707 Score: 55
Period size: 16 Copynumber: 2.7 Consensus size: 18
52651 AAAATCCATT
52661 TAAAAACTTTA-AAAAGTA
1 TAAAAACTTTATAAAA-TA
52679 TAAAAA--TTATAAAATA
1 TAAAAACTTTATAAAATA
*
52695 TAAAAACTATATA
1 TAAAAACTTTATA
52708 TATATATATA
Statistics
Matches: 25, Mismatches: 1, Indels: 6
0.78 0.03 0.19
Matches are distributed among these distances:
16 11 0.44
17 4 0.16
18 10 0.40
ACGTcount: A:0.64, C:0.04, G:0.02, T:0.30
Consensus pattern (18 bp):
TAAAAACTTTATAAAATA
Found at i:52988 original size:29 final size:29
Alignment explanation
Indices: 52928--52987 Score: 79
Period size: 28 Copynumber: 2.1 Consensus size: 29
52918 TAAAATATAG
* * *
52928 AAAATTA-CAAAATTATTATGAATGACAT
1 AAAATTATAAAAATTATTATGAATAACAA
52956 AAAATTATAAAAATTATTA-GAATAACAA
1 AAAATTATAAAAATTATTATGAATAACAA
52984 AAAA
1 AAAA
52988 AGTATAGAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
28 18 0.64
29 10 0.36
ACGTcount: A:0.62, C:0.05, G:0.05, T:0.28
Consensus pattern (29 bp):
AAAATTATAAAAATTATTATGAATAACAA
Found at i:52993 original size:29 final size:30
Alignment explanation
Indices: 52936--52999 Score: 78
Period size: 29 Copynumber: 2.2 Consensus size: 30
52926 AGAAAATTAC
* * *
52936 AAAATTATTATGAATGACATAAAATTATA-
1 AAAATTATTATGAATAACAAAAAAGTATAG
52965 AAAATTATTA-GAATAACAAAAAAAGTATAG
1 AAAATTATTATGAATAAC-AAAAAAGTATAG
52995 AAAAT
1 AAAAT
53000 AAAAAAATTT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
28 6 0.20
29 19 0.63
30 5 0.17
ACGTcount: A:0.61, C:0.03, G:0.08, T:0.28
Consensus pattern (30 bp):
AAAATTATTATGAATAACAAAAAAGTATAG
Found at i:53055 original size:20 final size:20
Alignment explanation
Indices: 53032--53071 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
53022 TACGAAAAGA
*
53032 TATTTAAAAA-TATAGAAAAT
1 TATTAAAAAATTATA-AAAAT
53052 TATTAAAAAATTATAAAAAT
1 TATTAAAAAATTATAAAAAT
53072 ATAGAAAAGT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 14 0.78
21 4 0.22
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.35
Consensus pattern (20 bp):
TATTAAAAAATTATAAAAAT
Found at i:53486 original size:18 final size:18
Alignment explanation
Indices: 53450--53487 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
53440 TAAATTTGCG
*
53450 TTATAATTTTTATGTTAT
1 TTATAATTTTTATGATAT
53468 TTATAATATTTTAT-ATAT
1 TTATAAT-TTTTATGATAT
53486 TT
1 TT
53488 TTTTAAAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 12 0.67
19 6 0.33
ACGTcount: A:0.32, C:0.00, G:0.03, T:0.66
Consensus pattern (18 bp):
TTATAATTTTTATGATAT
Found at i:53557 original size:14 final size:15
Alignment explanation
Indices: 53530--53623 Score: 56
Period size: 16 Copynumber: 6.2 Consensus size: 15
53520 ATTTTTCATA
53530 ATTTATATATTTTTT
1 ATTTATATATTTTTT
53545 ATTTATA-ATTTTTT
1 ATTTATATATTTTTT
53559 ACACTTT-TATA-TTTTT
1 --A-TTTATATATTTTTT
*
53575 A-TTAT-T-TTTTAAT
1 ATTTATATATTTT-TT
*
53588 ATTTATATATTGTTATA
1 ATTTATATATT-TT-TT
*
53605 ATTATCTATATTTTTT
1 ATT-TATATATTTTTT
53621 ATT
1 ATT
53624 ATTTTTAATC
Statistics
Matches: 62, Mismatches: 5, Indels: 23
0.69 0.06 0.26
Matches are distributed among these distances:
12 6 0.10
13 3 0.05
14 12 0.19
15 8 0.13
16 14 0.23
17 12 0.19
18 7 0.11
ACGTcount: A:0.29, C:0.03, G:0.01, T:0.67
Consensus pattern (15 bp):
ATTTATATATTTTTT
Found at i:53917 original size:13 final size:13
Alignment explanation
Indices: 53899--53923 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
53889 TATTTCAAAC
53899 TATACATAAATTA
1 TATACATAAATTA
53912 TATACATAAATT
1 TATACATAAATT
53924 TTCATTTTGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.52, C:0.08, G:0.00, T:0.40
Consensus pattern (13 bp):
TATACATAAATTA
Found at i:54597 original size:24 final size:25
Alignment explanation
Indices: 54570--54616 Score: 60
Period size: 25 Copynumber: 1.9 Consensus size: 25
54560 TGAGATAAAT
54570 TTTAAAAG-TAAATATGAATTTTGG
1 TTTAAAAGTTAAATATGAATTTTGG
* * *
54594 TTTAATAGTTATATATGATTTTT
1 TTTAAAAGTTAAATATGAATTTT
54617 TATTTTGTGT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
24 7 0.37
25 12 0.63
ACGTcount: A:0.36, C:0.00, G:0.13, T:0.51
Consensus pattern (25 bp):
TTTAAAAGTTAAATATGAATTTTGG
Found at i:56744 original size:16 final size:16
Alignment explanation
Indices: 56723--56762 Score: 62
Period size: 16 Copynumber: 2.5 Consensus size: 16
56713 TCACACTCTC
56723 CTAAGGGTCCATTCCA
1 CTAAGGGTCCATTCCA
*
56739 CTAAGGGTTCATTCCA
1 CTAAGGGTCCATTCCA
*
56755 ATAAGGGT
1 CTAAGGGT
56763 ATGAATCCTA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.28, C:0.23, G:0.23, T:0.28
Consensus pattern (16 bp):
CTAAGGGTCCATTCCA
Found at i:56782 original size:128 final size:128
Alignment explanation
Indices: 56645--56901 Score: 487
Period size: 128 Copynumber: 2.0 Consensus size: 128
56635 TCCTTGATCT
*
56645 ATCCATCCATCTTACACATCTTTGGGCTTTTTTTTCCACCATGGAAGCTTCCACTAAGGGTACAA
1 ATCCATCCATCTTACACATCTTTGGGCTTTTTCTTCCACCATGGAAGCTTCCACTAAGGGTACAA
*
56710 CTTTCACACTCTCCTAAGGGTCCATTCCACTAAGGGTTCATTCCAATAAGGGTATGAATCCTA
66 CTTTCACACTCTCCTAAGGGTCCATTCCACTAAGAGTTCATTCCAATAAGGGTATGAATCCTA
*
56773 ATCCATCCATCTTACACATCTTTGGGCTTTTTCTTCCACCATGGAAGCTTCCACTAAGGGTTCAA
1 ATCCATCCATCTTACACATCTTTGGGCTTTTTCTTCCACCATGGAAGCTTCCACTAAGGGTACAA
56838 CTTTCACACTCTCCTAAGGGTCCATTCCACTAAGAGTTCATTCCAATAAGGGTATGAATCCTA
66 CTTTCACACTCTCCTAAGGGTCCATTCCACTAAGAGTTCATTCCAATAAGGGTATGAATCCTA
56901 A
1 A
56902 AGACACAACT
Statistics
Matches: 126, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
128 126 1.00
ACGTcount: A:0.26, C:0.28, G:0.14, T:0.32
Consensus pattern (128 bp):
ATCCATCCATCTTACACATCTTTGGGCTTTTTCTTCCACCATGGAAGCTTCCACTAAGGGTACAA
CTTTCACACTCTCCTAAGGGTCCATTCCACTAAGAGTTCATTCCAATAAGGGTATGAATCCTA
Found at i:58166 original size:24 final size:23
Alignment explanation
Indices: 58122--58166 Score: 54
Period size: 24 Copynumber: 1.9 Consensus size: 23
58112 AAAAATATAA
* * *
58122 TTTTATTATTTTAATAGATTATT
1 TTTTATAATTTTAAAAAATTATT
58145 TTTTATAATTTTTAAAAAATTA
1 TTTTATAA-TTTTAAAAAATTA
58167 AATTAAATTT
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
23 7 0.39
24 11 0.61
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (23 bp):
TTTTATAATTTTAAAAAATTATT
Found at i:58361 original size:8 final size:8
Alignment explanation
Indices: 58339--58405 Score: 50
Period size: 7 Copynumber: 8.1 Consensus size: 8
58329 GCTATGAACA
58339 TATATTTT
1 TATATTTT
*
58347 AAT-TTTT
1 TATATTTT
58354 TATATTTT
1 TATATTTT
58362 TATAATTTT
1 TAT-ATTTT
58371 TACTATTTT
1 TA-TATTTT
*
58380 GTATAATTATC
1 -TAT-ATT-TT
58391 TAT-TTTT
1 TATATTTT
58398 TA-ATTTT
1 TATATTTT
58405 T
1 T
58406 TATAATTAAT
Statistics
Matches: 48, Mismatches: 4, Indels: 15
0.72 0.06 0.22
Matches are distributed among these distances:
7 14 0.29
8 11 0.23
9 13 0.27
10 9 0.19
11 1 0.02
ACGTcount: A:0.27, C:0.03, G:0.01, T:0.69
Consensus pattern (8 bp):
TATATTTT
Found at i:58372 original size:25 final size:25
Alignment explanation
Indices: 58343--58417 Score: 80
Period size: 27 Copynumber: 3.0 Consensus size: 25
58333 TGAACATATA
* *
58343 TTTTAATTTTTTATATTTTTATAAT
1 TTTTAATTTTTTATAATTATATAAT
* * *
58368 TTTTACTATTTTGTATAATTATCTATT
1 TTTTA--ATTTTTTATAATTATATAAT
58395 TTTTAATTTTTTATAATTA-ATAA
1 TTTTAATTTTTTATAATTATATAA
58418 AAATTTAATT
Statistics
Matches: 40, Mismatches: 8, Indels: 5
0.75 0.15 0.09
Matches are distributed among these distances:
24 2 0.05
25 18 0.45
27 20 0.50
ACGTcount: A:0.31, C:0.03, G:0.01, T:0.65
Consensus pattern (25 bp):
TTTTAATTTTTTATAATTATATAAT
Found at i:58384 original size:19 final size:17
Alignment explanation
Indices: 58350--58405 Score: 62
Period size: 17 Copynumber: 3.3 Consensus size: 17
58340 ATATTTTAAT
58350 TTTTTATATTTTTATAA
1 TTTTTATATTTTTATAA
58367 TTTTTACTATTTTGTATAA
1 TTTTTA-TATTTT-TATAA
* *
58386 -TTATCTATTTTT-TAA
1 TTTTTATATTTTTATAA
58401 TTTTT
1 TTTTT
58406 TATAATTAAT
Statistics
Matches: 33, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
15 3 0.09
16 4 0.12
17 12 0.36
18 9 0.27
19 5 0.15
ACGTcount: A:0.25, C:0.04, G:0.02, T:0.70
Consensus pattern (17 bp):
TTTTTATATTTTTATAA
Found at i:59658 original size:20 final size:23
Alignment explanation
Indices: 59612--59664 Score: 58
Period size: 23 Copynumber: 2.4 Consensus size: 23
59602 AATTAATGTC
* *
59612 TTTTATTATTATTTGATAACATC
1 TTTTAATATTATTTGATAACATA
59635 TTTTAATATTATTT-A-AA-ATA
1 TTTTAATATTATTTGATAACATA
*
59655 TTTTAGTATT
1 TTTTAATATT
59665 TATTATTTTT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
20 11 0.41
21 2 0.07
22 1 0.04
23 13 0.48
ACGTcount: A:0.34, C:0.04, G:0.04, T:0.58
Consensus pattern (23 bp):
TTTTAATATTATTTGATAACATA
Found at i:60190 original size:25 final size:24
Alignment explanation
Indices: 60162--60216 Score: 74
Period size: 25 Copynumber: 2.2 Consensus size: 24
60152 AAAAATATAG
*
60162 TTAATAAATAAATACAATTTTATT
1 TTAATAAAGAAATACAATTTTATT
* *
60186 CTTAAAAAAGAGATACAATTTTATT
1 -TTAATAAAGAAATACAATTTTATT
60211 TTAATA
1 TTAATA
60217 TCATTTTTAA
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
24 5 0.19
25 21 0.81
ACGTcount: A:0.49, C:0.05, G:0.04, T:0.42
Consensus pattern (24 bp):
TTAATAAAGAAATACAATTTTATT
Found at i:63178 original size:27 final size:27
Alignment explanation
Indices: 63114--63189 Score: 70
Period size: 27 Copynumber: 2.9 Consensus size: 27
63104 CTACCATTTT
63114 CTAATTAA--AATAATAATAAATATTTAA
1 CTAATTAATTAATAA-AAT-AATATTTAA
* *
63141 GTAA-AATATTAATAAAATAATATTTAA
1 CTAATTA-ATTAATAAAATAATATTTAA
*
63168 CTAATTAATTAATGAAA-AATAT
1 CTAATTAATTAATAAAATAATAT
63190 CTCCAAATAT
Statistics
Matches: 40, Mismatches: 5, Indels: 9
0.74 0.09 0.17
Matches are distributed among these distances:
26 6 0.15
27 25 0.62
28 4 0.10
29 5 0.12
ACGTcount: A:0.58, C:0.03, G:0.03, T:0.37
Consensus pattern (27 bp):
CTAATTAATTAATAAAATAATATTTAA
Found at i:71493 original size:29 final size:31
Alignment explanation
Indices: 71446--71507 Score: 74
Period size: 29 Copynumber: 2.1 Consensus size: 31
71436 TTGATTTAAT
* * *
71446 GTGCAATTATATACATG-AACTTTAATT-TG
1 GTGCAATCATACACATGAAACTCTAATTGTG
*
71475 GTGCAATCATACACGTGAAACTCTAATTGTG
1 GTGCAATCATACACATGAAACTCTAATTGTG
71506 GT
1 GT
71508 TCAAAAGTAT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
29 14 0.52
30 9 0.33
31 4 0.15
ACGTcount: A:0.32, C:0.15, G:0.18, T:0.35
Consensus pattern (31 bp):
GTGCAATCATACACATGAAACTCTAATTGTG
Found at i:72416 original size:17 final size:19
Alignment explanation
Indices: 72394--72432 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
72384 CGAGAATTAT
72394 TATTTT-TAAAAAT-ATAA
1 TATTTTATAAAAATCATAA
*
72411 TATTTTATAAAGATCATAA
1 TATTTTATAAAAATCATAA
72430 TAT
1 TAT
72433 ATTGGGTTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 6 0.32
18 6 0.32
19 7 0.37
ACGTcount: A:0.49, C:0.03, G:0.03, T:0.46
Consensus pattern (19 bp):
TATTTTATAAAAATCATAA
Found at i:76594 original size:20 final size:20
Alignment explanation
Indices: 76548--76601 Score: 56
Period size: 20 Copynumber: 2.6 Consensus size: 20
76538 ACAGATTAAT
*
76548 TAAATATTATTAAAAAAATAA
1 TAAA-ATTATTAAAAAAAAAA
*
76569 TTAAATTA-TAAAAATAAAAA
1 TAAAATTATTAAAAA-AAAAA
*
76589 TAAAATAATTAAA
1 TAAAATTATTAAA
76602 TTAAACGAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
19 6 0.22
20 14 0.52
21 7 0.26
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (20 bp):
TAAAATTATTAAAAAAAAAA
Done.