Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013242.1 Kokia drynarioides strain JFW-HI SEQ_128261, 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: 58535
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.34
Warning! 2 characters in sequence are not A, C, G, or T
Found at i:4764 original size:32 final size:33
Alignment explanation
Indices: 4728--4792 Score: 87
Period size: 32 Copynumber: 2.0 Consensus size: 33
4718 TCCAAAGCAT
* * *
4728 TTTTTGTCTCAAAAG-AATTTTGCTTAGCAATA
1 TTTTTATCTCAAAAGTAATTTTGATAAGCAATA
*
4760 TTTTTATCTCAAAAGTGATTTTGATAAGCAATA
1 TTTTTATCTCAAAAGTAATTTTGATAAGCAATA
4793 CTAAGCAGAC
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
32 14 0.50
33 14 0.50
ACGTcount: A:0.34, C:0.11, G:0.12, T:0.43
Consensus pattern (33 bp):
TTTTTATCTCAAAAGTAATTTTGATAAGCAATA
Found at i:8357 original size:22 final size:23
Alignment explanation
Indices: 8331--8375 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
8321 AAAAATAATG
8331 AAATTAT-ATTTTTATTATTTTA
1 AAATTATGATTTTTATTATTTTA
* *
8353 AAATTATGATTTTTTTTTTTTTA
1 AAATTATGATTTTTATTATTTTA
8376 GTTTTACCCC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 7 0.35
23 13 0.65
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (23 bp):
AAATTATGATTTTTATTATTTTA
Found at i:15815 original size:29 final size:30
Alignment explanation
Indices: 15755--15817 Score: 92
Period size: 29 Copynumber: 2.1 Consensus size: 30
15745 CTGGTTAACA
15755 ACACAAAATTTGATTTAATGTATAATATTAT
1 ACACAAAATTTGATTT-ATGTATAATATTAT
* *
15786 ACACAAACTTTGATTT-TGTATAATTTTAT
1 ACACAAAATTTGATTTATGTATAATATTAT
15815 ACA
1 ACA
15818 GGAATTATTA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
29 15 0.50
31 15 0.50
ACGTcount: A:0.41, C:0.10, G:0.06, T:0.43
Consensus pattern (30 bp):
ACACAAAATTTGATTTATGTATAATATTAT
Found at i:16086 original size:22 final size:24
Alignment explanation
Indices: 16050--16094 Score: 67
Period size: 22 Copynumber: 2.0 Consensus size: 24
16040 CCCATAACTT
16050 AATTATGTGATATTAAAT-TTGTA
1 AATTATGTGATATTAAATATTGTA
*
16073 AATTAT-TTATATTAAATATTGT
1 AATTATGTGATATTAAATATTGT
16095 TATGTTATCT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 10 0.50
23 10 0.50
ACGTcount: A:0.40, C:0.00, G:0.09, T:0.51
Consensus pattern (24 bp):
AATTATGTGATATTAAATATTGTA
Found at i:18854 original size:12 final size:12
Alignment explanation
Indices: 18837--18882 Score: 56
Period size: 12 Copynumber: 3.8 Consensus size: 12
18827 TCTCGAACAA
18837 GCTCATTTATTG
1 GCTCATTTATTG
**
18849 GCTCATTTATAA
1 GCTCATTTATTG
18861 GCTCATTTATTG
1 GCTCATTTATTG
* *
18873 ACTCGTTTAT
1 GCTCATTTAT
18883 GATTCGTTTA
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
12 28 1.00
ACGTcount: A:0.22, C:0.17, G:0.13, T:0.48
Consensus pattern (12 bp):
GCTCATTTATTG
Found at i:18866 original size:24 final size:24
Alignment explanation
Indices: 18835--18882 Score: 78
Period size: 24 Copynumber: 2.0 Consensus size: 24
18825 GTTCTCGAAC
*
18835 AAGCTCATTTATTGGCTCATTTAT
1 AAGCTCATTTATTGACTCATTTAT
*
18859 AAGCTCATTTATTGACTCGTTTAT
1 AAGCTCATTTATTGACTCATTTAT
18883 GATTCGTTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.25, C:0.17, G:0.12, T:0.46
Consensus pattern (24 bp):
AAGCTCATTTATTGACTCATTTAT
Found at i:19040 original size:23 final size:24
Alignment explanation
Indices: 18986--19042 Score: 62
Period size: 24 Copynumber: 2.4 Consensus size: 24
18976 ATTAATATTA
*
18986 TTCGTGGACATGTTCAATTATATG
1 TTCGTGAACATGTTCAATTATATG
** **
19010 TTTATGAACATGTTCGTTTA-ATG
1 TTCGTGAACATGTTCAATTATATG
19033 TTCGTGAACA
1 TTCGTGAACA
19043 CGTTTGATTA
Statistics
Matches: 26, Mismatches: 7, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
23 11 0.42
24 15 0.58
ACGTcount: A:0.26, C:0.12, G:0.19, T:0.42
Consensus pattern (24 bp):
TTCGTGAACATGTTCAATTATATG
Found at i:23078 original size:18 final size:19
Alignment explanation
Indices: 23051--23091 Score: 52
Period size: 18 Copynumber: 2.3 Consensus size: 19
23041 TAATTAAAAA
23051 ATTA-ATAAAA-AATATTAT
1 ATTATATAAAATAA-ATTAT
23069 -TTATATAAAATAAATTAT
1 ATTATATAAAATAAATTAT
23087 ATTAT
1 ATTAT
23092 TACGATGATA
Statistics
Matches: 20, Mismatches: 0, Indels: 5
0.80 0.00 0.20
Matches are distributed among these distances:
17 3 0.15
18 11 0.55
19 6 0.30
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (19 bp):
ATTATATAAAATAAATTAT
Found at i:23623 original size:21 final size:22
Alignment explanation
Indices: 23576--23617 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
23566 AATATAATAA
23576 CAAAATGACAACAAAACAACAT
1 CAAAATGACAACAAAACAACAT
*
23598 CAAAATGGCAAC-AAACAACA
1 CAAAATGACAACAAAACAACA
23618 ATAAAAATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 8 0.42
22 11 0.58
ACGTcount: A:0.62, C:0.24, G:0.07, T:0.07
Consensus pattern (22 bp):
CAAAATGACAACAAAACAACAT
Found at i:23624 original size:22 final size:22
Alignment explanation
Indices: 23577--23625 Score: 64
Period size: 22 Copynumber: 2.2 Consensus size: 22
23567 ATATAATAAC
*
23577 AAAATGACAACAAAACAACATC
1 AAAATGACAACAAAACAACATA
*
23599 AAAATGGCAAC-AAACAACAATA
1 AAAATGACAACAAAACAAC-ATA
23621 AAAAT
1 AAAAT
23626 TTAGGCAAGT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 7 0.29
22 17 0.71
ACGTcount: A:0.65, C:0.18, G:0.06, T:0.10
Consensus pattern (22 bp):
AAAATGACAACAAAACAACATA
Found at i:29998 original size:30 final size:31
Alignment explanation
Indices: 29942--30011 Score: 83
Period size: 30 Copynumber: 2.3 Consensus size: 31
29932 TAGTAATGGT
*
29942 AAAATTGTACTTTAACCCGTCTAAAATGATA
1 AAAATTGTAATTTAACCCGTCTAAAATGATA
* *
29973 AAAATT-TAATTTAACCC-TTTAAAAATTATA
1 AAAATTGTAATTTAACCCGTCT-AAAATGATA
30003 AAAA-TGTAA
1 AAAATTGTAA
30012 ACTATTAAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
29 3 0.09
30 25 0.74
31 6 0.18
ACGTcount: A:0.49, C:0.11, G:0.06, T:0.34
Consensus pattern (31 bp):
AAAATTGTAATTTAACCCGTCTAAAATGATA
Found at i:30467 original size:39 final size:40
Alignment explanation
Indices: 30405--30485 Score: 92
Period size: 39 Copynumber: 2.0 Consensus size: 40
30395 TTTTCAAGAT
* * * *
30405 TTAGTATTAATATTTAGGGTTTAACATTTAATATTTAAAA
1 TTAGTATTAAAATTTAAGGTTTAACATCTAAGATTTAAAA
* * *
30445 TTAGTA-TAAAATTTAAGTTTTAAGATCTAAGATTTGAAA
1 TTAGTATTAAAATTTAAGGTTTAACATCTAAGATTTAAAA
30484 TT
1 TT
30486 TTAAAATTTT
Statistics
Matches: 34, Mismatches: 7, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
39 28 0.82
40 6 0.18
ACGTcount: A:0.41, C:0.02, G:0.11, T:0.46
Consensus pattern (40 bp):
TTAGTATTAAAATTTAAGGTTTAACATCTAAGATTTAAAA
Found at i:32581 original size:17 final size:17
Alignment explanation
Indices: 32547--32579 Score: 59
Period size: 16 Copynumber: 2.0 Consensus size: 17
32537 ATAAGTGTTG
32547 AATTTATTAATATATTT
1 AATTTATTAATATATTT
32564 AATTT-TTAATATATTT
1 AATTTATTAATATATTT
32580 TATAAGACAC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 11 0.69
17 5 0.31
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (17 bp):
AATTTATTAATATATTT
Found at i:33949 original size:21 final size:22
Alignment explanation
Indices: 33908--33959 Score: 65
Period size: 21 Copynumber: 2.4 Consensus size: 22
33898 ACTTAACAAG
33908 ATAAATATTAGATTAAAATTAAT
1 ATAAATATTA-ATTAAAATTAAT
33931 ATTAAATATT-ATT-AAATTAAT
1 A-TAAATATTAATTAAAATTAAT
33952 A-AAATATT
1 ATAAATATT
33960 TATCTACAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
19 7 0.25
21 9 0.32
22 3 0.11
23 1 0.04
24 8 0.29
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (22 bp):
ATAAATATTAATTAAAATTAAT
Found at i:36047 original size:14 final size:13
Alignment explanation
Indices: 36009--36047 Score: 51
Period size: 13 Copynumber: 2.9 Consensus size: 13
35999 AGTTTAGCAT
*
36009 TGTTTTTAAAAAG
1 TGTTTTGAAAAAG
*
36022 TGTTTTGGAAAAG
1 TGTTTTGAAAAAG
36035 TGATTTTGAAAAA
1 TG-TTTTGAAAAA
36048 TACTTTTAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
13 13 0.59
14 9 0.41
ACGTcount: A:0.38, C:0.00, G:0.21, T:0.41
Consensus pattern (13 bp):
TGTTTTGAAAAAG
Found at i:36441 original size:23 final size:24
Alignment explanation
Indices: 36406--36454 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
36396 AGTGCTTTTG
36406 AAAAAGCCAAAAATTTTATTCAAA
1 AAAAAGCCAAAAATTTTATTCAAA
36430 AAAAAGCCAAAAATTTTATTCAAA
1 AAAAAGCCAAAAATTTTATTCAAA
36454 A
1 A
36455 GTTACTTATT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.59, C:0.12, G:0.04, T:0.24
Consensus pattern (24 bp):
AAAAAGCCAAAAATTTTATTCAAA
Found at i:38637 original size:30 final size:30
Alignment explanation
Indices: 38545--38655 Score: 134
Period size: 30 Copynumber: 3.7 Consensus size: 30
38535 ATACAACTCT
38545 TAAATGCAGCTCGTGCGACTACAACCCGTG
1 TAAATGCAGCTCGTGCGACTACAACCCGTG
* * * * * *
38575 TAAAT-CAGAGTTCCTACTACTGCAATCCGTG
1 TAAATGC--AGCTCGTGCGACTACAACCCGTG
38606 TAAATGCAGCTCGTGCGACTACAACCCGTG
1 TAAATGCAGCTCGTGCGACTACAACCCGTG
*
38636 TAAATACAGCTCGTGCGACT
1 TAAATGCAGCTCGTGCGACT
38656 GTAGTTTGTC
Statistics
Matches: 65, Mismatches: 13, Indels: 6
0.77 0.15 0.07
Matches are distributed among these distances:
29 1 0.02
30 41 0.63
31 22 0.34
32 1 0.02
ACGTcount: A:0.28, C:0.28, G:0.21, T:0.23
Consensus pattern (30 bp):
TAAATGCAGCTCGTGCGACTACAACCCGTG
Found at i:38734 original size:33 final size:33
Alignment explanation
Indices: 38678--38741 Score: 94
Period size: 33 Copynumber: 1.9 Consensus size: 33
38668 AATGCAACAA
*
38678 TTTATGTGACTGCAATCCATGTAAATGTAGCAG
1 TTTATGCGACTGCAATCCATGTAAATGTAGCAG
*
38711 TTTATGCGACTGCAA-CTCTTGTAAATGTAGC
1 TTTATGCGACTGCAATC-CATGTAAATGTAGC
38742 TTGTGTGACT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
32 1 0.04
33 27 0.96
ACGTcount: A:0.28, C:0.17, G:0.20, T:0.34
Consensus pattern (33 bp):
TTTATGCGACTGCAATCCATGTAAATGTAGCAG
Found at i:41697 original size:25 final size:23
Alignment explanation
Indices: 41657--41719 Score: 69
Period size: 23 Copynumber: 2.7 Consensus size: 23
41647 AAAAGTATTA
41657 TAAAATTTAT--AATTTAGTTC-T
1 TAAAATTTATAAAATTTA-TTCTT
41678 TAAAATTATTATAAAATTTATTCTT
1 TAAAA-T-TTATAAAATTTATTCTT
*
41703 TATAATTTATAAAATTT
1 TAAAATTTATAAAATTT
41720 TAAAATAGTA
Statistics
Matches: 36, Mismatches: 1, Indels: 8
0.80 0.02 0.18
Matches are distributed among these distances:
21 5 0.14
22 1 0.03
23 15 0.42
24 4 0.11
25 11 0.31
ACGTcount: A:0.43, C:0.03, G:0.02, T:0.52
Consensus pattern (23 bp):
TAAAATTTATAAAATTTATTCTT
Found at i:42493 original size:19 final size:18
Alignment explanation
Indices: 42471--42521 Score: 59
Period size: 19 Copynumber: 2.8 Consensus size: 18
42461 AAATTCTTTT
*
42471 TAAAAATTTAAAAAAATCA
1 TAAAAATTTAAAAAAA-AA
42490 TAAAAA-TTAAAATAAAAA
1 TAAAAATTTAAAA-AAAAA
*
42508 TAAAATTTTAAAAA
1 TAAAAATTTAAAAA
42522 TAGATAAAAG
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
18 13 0.46
19 15 0.54
ACGTcount: A:0.71, C:0.02, G:0.00, T:0.27
Consensus pattern (18 bp):
TAAAAATTTAAAAAAAAA
Found at i:42494 original size:18 final size:17
Alignment explanation
Indices: 42473--42521 Score: 53
Period size: 18 Copynumber: 2.7 Consensus size: 17
42463 ATTCTTTTTA
*
42473 AAAATTTAAAAAAATCAT
1 AAAATTTAAAAAAA-AAT
*
42491 AAAAATTAAAATAAAAAT
1 AAAATTTAAAA-AAAAAT
42509 AAAATTTTAAAAA
1 AAAA-TTTAAAAA
42522 TAGATAAAAG
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
18 17 0.65
19 9 0.35
ACGTcount: A:0.71, C:0.02, G:0.00, T:0.27
Consensus pattern (17 bp):
AAAATTTAAAAAAAAAT
Found at i:45219 original size:29 final size:29
Alignment explanation
Indices: 45149--45462 Score: 249
Period size: 29 Copynumber: 10.8 Consensus size: 29
45139 ATTCGGGGTT
* *
45149 TAAAAATGGAATTTTTAGACA--TTCAAGGG
1 TAAAAATGGAA-TTTTGGA-AGTTTCGAGGG
* *
45178 T-AAAAGGGTAATTTT-GATAGTTTTGAGGG
1 TAAAAATGG-AATTTTGGA-AGTTTCGAGGG
*
45207 TAAAAATGGAA-TTTGGAAGTTTCGGGGG
1 TAAAAATGGAATTTTGGAAGTTTCGAGGG
*
45235 CAAAAATGGAATTTTTGGAAGTTTC-AGGG
1 TAAAAATGGAA-TTTTGGAAGTTTCGAGGG
* * * *
45264 CAAAAATGGGATTTTTGGAAGTTTTG-GGT
1 TAAAAAT-GGAATTTTGGAAGTTTCGAGGG
* *
45293 TAAAAAGGGATTTTTGGAAGTTTCGA-GG
1 TAAAAATGGAATTTTGGAAGTTTCGAGGG
*
45321 TCAAAAATAGAATTTTTGGAA-TTTCGAGGG
1 T-AAAAATGGAA-TTTTGGAAGTTTCGAGGG
*
45351 T-AAAATGGAATTTTTGGAAGTTTAG-GGG
1 TAAAAATGGAA-TTTTGGAAGTTTCGAGGG
* *
45379 TAAAAATAGAATTTATGGAAGTTTTGA-GG
1 TAAAAATGGAATTT-TGGAAGTTTCGAGGG
**
45408 TCAAAAATAAAATTTTTGGAAG-TTCGAGGG
1 T-AAAAATGGAA-TTTTGGAAGTTTCGAGGG
*
45438 TAAAAATGGAATTTTTAGAAGTTTC
1 TAAAAATGGAA-TTTTGGAAGTTTC
45463 AAGGTCAAAA
Statistics
Matches: 236, Mismatches: 28, Indels: 41
0.77 0.09 0.13
Matches are distributed among these distances:
27 3 0.01
28 75 0.32
29 102 0.43
30 53 0.22
31 3 0.01
ACGTcount: A:0.35, C:0.04, G:0.27, T:0.34
Consensus pattern (29 bp):
TAAAAATGGAATTTTGGAAGTTTCGAGGG
Found at i:45287 original size:87 final size:86
Alignment explanation
Indices: 45196--45461 Score: 340
Period size: 87 Copynumber: 3.1 Consensus size: 86
45186 TAATTTTGAT
* * *
45196 AGTTTTGAGGGTAAAAATGGAATTTGGAAGTTTCGGGGGCAAAAATGGAATTTTTGGAAGTTTC-
1 AGTTTTG-GGGTAAAAATGGAATTTGGAAGTTTCGAGGTCAAAAATAGAATTTTTGGAAGTTTCG
*
45260 AGGGCAAAAATGGGATTTTTGGA
65 AGGG-AAAAATGGAATTTTTGGA
* * *
45283 AGTTTTGGGTTAAAAAGGGATTTTTGGAAGTTTCGAGGTCAAAAATAGAATTTTTGGAA-TTTCG
1 AGTTTTGGGGTAAAAATGGA-ATTTGGAAGTTTCGAGGTCAAAAATAGAATTTTTGGAAGTTTCG
*
45347 AGGGTAAAATGGAATTTTTGGA
65 AGGGAAAAATGGAATTTTTGGA
* * * *
45369 AGTTTAGGGGTAAAAATAGAATTTATGGAAGTTTTGAGGTCAAAAATAAAATTTTTGGAAG-TTC
1 AGTTTTGGGGTAAAAATGGAA-TT-TGGAAGTTTCGAGGTCAAAAATAGAATTTTTGGAAGTTTC
*
45433 GAGGGTAAAAATGGAATTTTTAGA
64 GAGGG-AAAAATGGAATTTTTGGA
45457 AGTTT
1 AGTTT
45462 CAAGGTCAAA
Statistics
Matches: 156, Mismatches: 17, Indels: 11
0.85 0.09 0.06
Matches are distributed among these distances:
86 49 0.31
87 86 0.55
88 21 0.13
ACGTcount: A:0.35, C:0.03, G:0.28, T:0.34
Consensus pattern (86 bp):
AGTTTTGGGGTAAAAATGGAATTTGGAAGTTTCGAGGTCAAAAATAGAATTTTTGGAAGTTTCGA
GGGAAAAATGGAATTTTTGGA
Found at i:47203 original size:6 final size:6
Alignment explanation
Indices: 47193--47256 Score: 69
Period size: 6 Copynumber: 11.0 Consensus size: 6
47183 TAATGGACTT
* * *
47193 TTTAAT TTTAAA ATTAAA TTTAAA TTTAAA ATT-AA TTTAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
* *
47240 -ATAAA TCTAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA
47257 ATAAATTAAA
Statistics
Matches: 48, Mismatches: 8, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
5 8 0.17
6 40 0.83
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (6 bp):
TTTAAA
Found at i:47231 original size:17 final size:17
Alignment explanation
Indices: 47193--47263 Score: 106
Period size: 17 Copynumber: 4.1 Consensus size: 17
47183 TAATGGACTT
*
47193 TTTAATTTTAAAATTAAA
1 TTTAAATTTAAAA-TAAA
*
47211 TTTAAATTTAAAATTAA
1 TTTAAATTTAAAATAAA
47228 TTTAAATTTAAAATAAA
1 TTTAAATTTAAAATAAA
*
47245 TCTAAATTTAAAATAAA
1 TTTAAATTTAAAATAAA
47262 TT
1 TT
47264 AAAAAGGAAC
Statistics
Matches: 48, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
17 36 0.75
18 12 0.25
ACGTcount: A:0.54, C:0.01, G:0.00, T:0.45
Consensus pattern (17 bp):
TTTAAATTTAAAATAAA
Found at i:49491 original size:51 final size:51
Alignment explanation
Indices: 49408--49645 Score: 316
Period size: 51 Copynumber: 4.6 Consensus size: 51
49398 CTATAAACGA
*
49408 AAAGGTCCGATGACTAAGAGTCATCGTGAGTAAATGAATCCTTTACGGATT
1 AAAGGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTACGGATT
** *
49459 AAAACTCCGATGACTAAGTGTCATCGTAAGTAAATGAATCCTTTACGGATT
1 AAAGGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTACGGATT
* * *
49510 AAAGGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCATGATGGATT
1 AAAGGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTACGGATT
* * * * **
49561 AAAGGTCCGATGACTCAGTGTCATCGTGAGTATATGAATTCCTATATGGAAC
1 AAAGGTCCGATGACTAAGTGTCATCGTGAGTAAATGAA-TCCTTTACGGATT
*
49613 AAGAGGTCCGATGACTATA-TGTCATTGTGAGTA
1 AA-AGGTCCGATGACTA-AGTGTCATCGTGAGTA
49646 TTAAATGAAA
Statistics
Matches: 165, Mismatches: 19, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
51 128 0.78
52 10 0.06
53 26 0.16
54 1 0.01
ACGTcount: A:0.33, C:0.16, G:0.23, T:0.29
Consensus pattern (51 bp):
AAAGGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTACGGATT
Found at i:56709 original size:21 final size:22
Alignment explanation
Indices: 56684--56728 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 22
56674 TGATTTTATC
* *
56684 AAATTCTGAAAT-TTAATTAAA
1 AAATTCTAAAATATAAATTAAA
*
56705 AAATTTTAAAATATAAATTAAA
1 AAATTCTAAAATATAAATTAAA
56727 AA
1 AA
56729 GAAAATTTAC
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
21 10 0.50
22 10 0.50
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.36
Consensus pattern (22 bp):
AAATTCTAAAATATAAATTAAA
Found at i:56901 original size:21 final size:17
Alignment explanation
Indices: 56863--56899 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
56853 ATACGCGTTT
56863 ATTTATTAAAAATTTTA
1 ATTTATTAAAAATTTTA
56880 ATTTATTAAATAA-TTTA
1 ATTTATTAAA-AATTTTA
56897 ATT
1 ATT
56900 AAGTTATAGA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 17 0.89
18 2 0.11
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTATTAAAAATTTTA
Found at i:57302 original size:18 final size:19
Alignment explanation
Indices: 57265--57309 Score: 67
Period size: 19 Copynumber: 2.5 Consensus size: 19
57255 CTCAATAAAC
57265 TTAAATTTATTTTAAAATT
1 TTAAATTTATTTTAAAATT
*
57284 TTAAGTTTATTTT-AAA-T
1 TTAAATTTATTTTAAAATT
57301 TTAAATTTA
1 TTAAATTTA
57310 GCTGAAATTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
17 9 0.38
18 3 0.12
19 12 0.50
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (19 bp):
TTAAATTTATTTTAAAATT
Found at i:57309 original size:17 final size:17
Alignment explanation
Indices: 57260--57339 Score: 88
Period size: 17 Copynumber: 4.6 Consensus size: 17
57250 CTGGGCTCAA
*
57260 TAAACTTAAATTTATTT
1 TAAATTTAAATTTATTT
*
57277 TAAAATTTTAAGTTTATTT
1 T-AAA-TTTAAATTTATTT
**
57296 TAAATTTAAATTTAGCT
1 TAAATTTAAATTTATTT
* *
57313 GAAATTTAAATTTATTA
1 TAAATTTAAATTTATTT
57330 TAAATTTAAA
1 TAAATTTAAA
57340 CTTAAAATTT
Statistics
Matches: 51, Mismatches: 10, Indels: 4
0.78 0.15 0.06
Matches are distributed among these distances:
17 33 0.65
18 6 0.12
19 12 0.24
ACGTcount: A:0.44, C:0.03, G:0.04, T:0.50
Consensus pattern (17 bp):
TAAATTTAAATTTATTT
Done.