Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014216.1 Kokia drynarioides strain JFW-HI SEQ_129249, 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: 35895
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.35
Warning! 5 characters in sequence are not A, C, G, or T
Found at i:1452 original size:28 final size:27
Alignment explanation
Indices: 1404--1486 Score: 112
Period size: 28 Copynumber: 3.0 Consensus size: 27
1394 GATATCCAAT
*
1404 TTACTCCCTGTTGACCTAAAGGTCATGC
1 TTACT-CCTGTTGACCCAAAGGTCATGC
*
1432 TTACTCCATGTTAACCCAAAGGTCATGC
1 TTACTCC-TGTTGACCCAAAGGTCATGC
*
1460 TTACTTCCTGTTGACACAAAGGTCATG
1 TTAC-TCCTGTTGACCCAAAGGTCATG
1487 ATGGTCATTT
Statistics
Matches: 49, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
27 2 0.04
28 44 0.90
29 3 0.06
ACGTcount: A:0.25, C:0.27, G:0.17, T:0.31
Consensus pattern (27 bp):
TTACTCCTGTTGACCCAAAGGTCATGC
Found at i:5952 original size:49 final size:49
Alignment explanation
Indices: 5902--6586 Score: 318
Period size: 49 Copynumber: 14.0 Consensus size: 49
5892 CCTTCTTTGG
* * * * *
5902 TTTTAAGGTGTCAGATCCGCCATCGTGGCTTCAATCTATCCCTCTTTGG
1 TTTTAAGGTGTTAGATCCGCCATTGTGGCTTCAACCTATCCCTCTTCGA
* * * * **
5951 TTTTAAGGTATTAGGTTCGCCATCGTAACTTCAACCTATCCCTCTTCGA
1 TTTTAAGGTGTTAGATCCGCCATTGTGGCTTCAACCTATCCCTCTTCGA
* * * * * * * * *
6000 TTTCAAGGTGTAAGATTCGTCGTTATGACTTCAATCTTTCCCTCTTCGA
1 TTTTAAGGTGTTAGATCCGCCATTGTGGCTTCAACCTATCCCTCTTCGA
* * * * *
6049 TTTTAAGGTGTTA-AGTCTGCCGTTATGGCTTTAACCTAACCCTCTTCGA
1 TTTTAAGGTGTTAGA-TCCGCCATTGTGGCTTCAACCTATCCCTCTTCGA
* * * * *
6098 TTTTAAGGTGTTA-AGTCCACCATTGCGGCTTGAACCTATTCCTCTTTGA
1 TTTTAAGGTGTTAGA-TCCGCCATTGTGGCTTCAACCTATCCCTCTTCGA
* * * * * * * ** *
6147 TTTTAAGGTGTAAGATTCGTCGTTGCGACTTTAATTTTTTCCCTCTTCGA
1 TTTTAAGGTGTTAGATCCGCCATTGTGGCTTCAA-CCTATCCCTCTTCGA
* * * * ** * * *
6197 TTTTAGGGTGTTAGGTCCACCGTTACGACTTCAACCTATCCCTATTCAA
1 TTTTAAGGTGTTAGATCCGCCATTGTGGCTTCAACCTATCCCTCTTCGA
* * ** * **
6246 TTTTAAGGTG-TAAAGTCCACTGTTGTGACTTCAACCTATCCCTCTTTAA
1 TTTTAAGGTGTTAGA-TCCGCCATTGTGGCTTCAACCTATCCCTCTTCGA
* * ** ** * * * *
6295 TTTTAATGTG-TAGGATCCACTGTTACGACTTCAATCTTTCACTCTTCGA
1 TTTTAAGGTGTTA-GATCCGCCATTGTGGCTTCAACCTATCCCTCTTCGA
* * *** *** * ** *
6344 TTTTAGGGTGTTAAATTTACCATTACAGCTTTAATTTATCCCTCTTTGA
1 TTTTAAGGTGTTAGATCCGCCATTGTGGCTTCAACCTATCCCTCTTCGA
* * * * ** * *
6393 TTTTAGGGTGTTAGGTCTGCCGTTACGGCTTCAACCTATCCCCCTT-TA
1 TTTTAAGGTGTTAGATCCGCCATTGTGGCTTCAACCTATCCCTCTTCGA
* *** * * * *
6441 GTTTTAAGGTGTAAGATCCGTTGTTATGGCTTCAATCTTTCCCTCTTTGA
1 -TTTTAAGGTGTTAGATCCGCCATTGTGGCTTCAACCTATCCCTCTTCGA
* * * * * * * **
6491 TTTTAAGGTGTTAGATCTGTCGTTGCGGCTTCAATCTATTCCTTTTTTA
1 TTTTAAGGTGTTAGATCCGCCATTGTGGCTTCAACCTATCCCTCTTCGA
* * * *
6540 TTATAAGGTGTTAGGTCCACCATTGCGGCTTCAACCTATCCCTCTTC
1 TTTTAAGGTGTTAGATCCGCCATTGTGGCTTCAACCTATCCCTCTTC
6587 AACTCTAGGA
Statistics
Matches: 492, Mismatches: 136, Indels: 16
0.76 0.21 0.02
Matches are distributed among these distances:
48 4 0.01
49 447 0.91
50 41 0.08
ACGTcount: A:0.20, C:0.23, G:0.17, T:0.40
Consensus pattern (49 bp):
TTTTAAGGTGTTAGATCCGCCATTGTGGCTTCAACCTATCCCTCTTCGA
Found at i:6134 original size:147 final size:147
Alignment explanation
Indices: 5928--6586 Score: 604
Period size: 147 Copynumber: 4.5 Consensus size: 147
5918 CCGCCATCGT
* * * * * * * * ***
5928 GGCTTCAATCTATCCCTCTTTGGTTTTAAGGTATTAGGTTCGCCATCGTAACTTCAACCTATCCC
1 GGCTTCAACCTATCCCTCTTCGATTTTAAGGTGTTAAGTCCACCATTGCGGCTTCAACCTATCCC
* *
5993 TCTTCGATTTCAAGGTGTAAGATTCGTCGTTATGACTTCAATCTTTCCCTCTTCGATTTTAAGGT
66 TCTTCGATTTTAAGGTGTAAGATTCGTCGTTACGACTTCAATCTTTCCCTCTTCGATTTTAAGGT
* *
6058 GTTAAGTCTGCCGTTAT
131 GTTAAGTCTACCGTTAC
* * * *
6075 GGCTTTAACCTAACCCTCTTCGATTTTAAGGTGTTAAGTCCACCATTGCGGCTTGAACCTATTCC
1 GGCTTCAACCTATCCCTCTTCGATTTTAAGGTGTTAAGTCCACCATTGCGGCTTCAACCTATCCC
* * * * *
6140 TCTTTGATTTTAAGGTGTAAGATTCGTCGTTGCGACTTTAATTTTTTCCCTCTTCGATTTTAGGG
66 TCTTCGATTTTAAGGTGTAAGATTCGTCGTTACGACTTCAA-TCTTTCCCTCTTCGATTTTAAGG
* *
6205 TGTTAGGTCCACCGTTAC
130 TGTTAAGTCTACCGTTAC
* * * * ** * *
6223 GACTTCAACCTATCCCTATTCAATTTTAAGGTGTAAAGTCCACTGTTGTGACTTCAACCTATCCC
1 GGCTTCAACCTATCCCTCTTCGATTTTAAGGTGTTAAGTCCACCATTGCGGCTTCAACCTATCCC
** * * ** * *
6288 TCTTTAATTTTAATGTGTAGGA-TCCACTGTTACGACTTCAATCTTTCACTCTTCGATTTTAGGG
66 TCTTCGATTTTAAGGTGTAAGATTCGTC-GTTACGACTTCAATCTTTCCCTCTTCGATTTTAAGG
* * *
6352 TGTTAAATTTACCATTAC
130 TGTTAAGTCTACCGTTAC
* * ** * * * ** * *
6370 AGCTTTAATTTATCCCTCTTTGATTTTAGGGTGTTAGGTCTGCCGTTACGGCTTCAACCTATCCC
1 GGCTTCAACCTATCCCTCTTCGATTTTAAGGTGTTAAGTCCACCATTGCGGCTTCAACCTATCCC
* * * * * * *
6435 CCTT-TAGTTTTAAGGTGTAAGATCCGTTGTTATGGCTTCAATCTTTCCCTCTTTGATTTTAAGG
66 TCTTCGA-TTTTAAGGTGTAAGATTCGTCGTTACGACTTCAATCTTTCCCTCTTCGATTTTAAGG
** *
6499 TGTT-AGATCTGTCGTTGC
130 TGTTAAG-TCTACCGTTAC
* * * ** * *
6517 GGCTTCAATCTATTCCTTTTTTATTATAAGGTGTTAGGTCCACCATTGCGGCTTCAACCTATCCC
1 GGCTTCAACCTATCCCTCTTCGATTTTAAGGTGTTAAGTCCACCATTGCGGCTTCAACCTATCCC
6582 TCTTC
66 TCTTC
6587 AACTCTAGGA
Statistics
Matches: 405, Mismatches: 101, Indels: 11
0.78 0.20 0.02
Matches are distributed among these distances:
146 2 0.00
147 284 0.70
148 119 0.29
ACGTcount: A:0.20, C:0.23, G:0.17, T:0.41
Consensus pattern (147 bp):
GGCTTCAACCTATCCCTCTTCGATTTTAAGGTGTTAAGTCCACCATTGCGGCTTCAACCTATCCC
TCTTCGATTTTAAGGTGTAAGATTCGTCGTTACGACTTCAATCTTTCCCTCTTCGATTTTAAGGT
GTTAAGTCTACCGTTAC
Found at i:6142 original size:98 final size:98
Alignment explanation
Indices: 5986--6504 Score: 382
Period size: 98 Copynumber: 5.3 Consensus size: 98
5976 TAACTTCAAC
* * * * * ** * * *
5986 CTATCCCTCTTCGATTTCAAGGTGTAAGATTCGTCGTTATGACTTCAATCTTTCCCTCTTCGATT
1 CTATCCCTCTTTGATTTTAAGGTGTTAGGTCCACCGTTACGACTTCAACCTATCCCTCTTCGATT
*
6051 TTAAGGTGTTAAGTCTGCCGTTATGGCTTTAAC
66 TTAAGGTGTTAAGTCTGCCGTTATGGCTTTAAT
* * * * * * * * *
6084 CTAACCCTCTTCGATTTTAAGGTGTTAAGTCCACCATTGCGGCTTGAACCTATTCCTCTTTGATT
1 CTATCCCTCTTTGATTTTAAGGTGTTAGGTCCACCGTTACGACTTCAACCTATCCCTCTTCGATT
* ** *
6149 TTAAGGTG-TAAGAT-TCGTCGTTGCGACTTTAATT
66 TTAAGGTGTTAAG-TCT-GCCGTTATGGCTTTAA-T
* * * * * *
6183 TTTTCCCTCTTCGATTTTAGGGTGTTAGGTCCACCGTTACGACTTCAACCTATCCCTATTCAATT
1 CTATCCCTCTTTGATTTTAAGGTGTTAGGTCCACCGTTACGACTTCAACCTATCCCTCTTCGATT
* ** * * * * *
6248 TTAAGGTGTAAAGTCCACTGTTGTGACTTCAAC
66 TTAAGGTGTTAAGTCTGCCGTTATGGCTTTAAT
* * * * * *
6281 CTATCCCTCTTTAATTTTAATGTG-TAGGATCCACTGTTACGACTTCAATCTTTCACTCTTCGAT
1 CTATCCCTCTTTGATTTTAAGGTGTTAGG-TCCACCGTTACGACTTCAACCTATCCCTCTTCGAT
* * * * * **
6345 TTTAGGGTGTTAAATTTACCATTACAGCTTTAAT
65 TTTAAGGTGTTAAGTCTGCCGTTATGGCTTTAAT
* * ** * * *
6379 TTATCCCTCTTTGATTTTAGGGTGTTAGGTCTGCCGTTACGGCTTCAACCTATCCCCCTT-TAGT
1 CTATCCCTCTTTGATTTTAAGGTGTTAGGTCCACCGTTACGACTTCAACCTATCCCTCTTCGA-T
* ** *
6443 TTTAAGGTG-TAAGATCCGTTGTTATGGCTTCAAT
65 TTTAAGGTGTTAAG-TCTGCCGTTATGGCTTTAAT
*
6477 CTTTCCCTCTTTGATTTTAAGGTGTTAG
1 CTATCCCTCTTTGATTTTAAGGTGTTAG
6505 ATCTGTCGTT
Statistics
Matches: 317, Mismatches: 95, Indels: 18
0.74 0.22 0.04
Matches are distributed among these distances:
97 13 0.04
98 225 0.71
99 76 0.24
100 3 0.01
ACGTcount: A:0.20, C:0.22, G:0.17, T:0.41
Consensus pattern (98 bp):
CTATCCCTCTTTGATTTTAAGGTGTTAGGTCCACCGTTACGACTTCAACCTATCCCTCTTCGATT
TTAAGGTGTTAAGTCTGCCGTTATGGCTTTAAT
Found at i:14223 original size:13 final size:13
Alignment explanation
Indices: 14205--14229 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
14195 TTGTGATCCG
14205 TTGCATTTTATTT
1 TTGCATTTTATTT
14218 TTGCATTTTATT
1 TTGCATTTTATT
14230 GTATGTATGT
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:0.16, C:0.08, G:0.08, T:0.68
Consensus pattern (13 bp):
TTGCATTTTATTT
Found at i:19272 original size:29 final size:28
Alignment explanation
Indices: 19238--19298 Score: 79
Period size: 28 Copynumber: 2.1 Consensus size: 28
19228 AAATGAGACT
19238 TTTTGGA-TACTCGAGGGGCAAAATGGTAA
1 TTTTGGACT-CTCG-GGGGCAAAATGGTAA
* *
19267 TTTTGGACTTTTGGGGGCAAAATGGTAA
1 TTTTGGACTCTCGGGGGCAAAATGGTAA
19295 TTTT
1 TTTT
19299 TGGAAAATTT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
28 19 0.66
29 9 0.31
30 1 0.03
ACGTcount: A:0.26, C:0.08, G:0.30, T:0.36
Consensus pattern (28 bp):
TTTTGGACTCTCGGGGGCAAAATGGTAA
Found at i:19312 original size:29 final size:28
Alignment explanation
Indices: 19252--19312 Score: 86
Period size: 28 Copynumber: 2.1 Consensus size: 28
19242 GGATACTCGA
**
19252 GGGGCAAAATGGTAATTTTGGACTTTTG
1 GGGGCAAAATGGTAATTTTGGAAATTTG
19280 GGGGCAAAATGGTAATTTTTGGAAAATTTG
1 GGGGCAAAATGGTAA-TTTTGG-AAATTTG
19310 GGG
1 GGG
19313 TTAAAAATGA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
28 15 0.52
29 6 0.21
30 8 0.28
ACGTcount: A:0.28, C:0.05, G:0.34, T:0.33
Consensus pattern (28 bp):
GGGGCAAAATGGTAATTTTGGAAATTTG
Found at i:19414 original size:58 final size:57
Alignment explanation
Indices: 19352--19473 Score: 129
Period size: 58 Copynumber: 2.1 Consensus size: 57
19342 TAAAACGATA
*
19352 AATTTTAGAAAAATCAGGATCAAAAACGGAATTTTTTGACA-TTCGAGGGTAAAATGGT
1 AATTTTAGAAAAATCAGGATCAAAAACGGAA-TTTTGGA-AGTTCGAGGGTAAAATGGT
* *** * * **
19410 AATTTTTGGAAGTTTCGGGATTAAAATTGGAATTTTGGAAGTTCGAGGGTAAAATGGT
1 AA-TTTTAGAAAAATCAGGATCAAAAACGGAATTTTGGAAGTTCGAGGGTAAAATGGT
19468 AATTTT
1 AATTTT
19474 CAAAAGTTTC
Statistics
Matches: 53, Mismatches: 9, Indels: 5
0.79 0.13 0.07
Matches are distributed among these distances:
57 5 0.09
58 27 0.51
59 21 0.40
ACGTcount: A:0.36, C:0.06, G:0.24, T:0.34
Consensus pattern (57 bp):
AATTTTAGAAAAATCAGGATCAAAAACGGAATTTTGGAAGTTCGAGGGTAAAATGGT
Found at i:19442 original size:59 final size:58
Alignment explanation
Indices: 19373--19747 Score: 386
Period size: 59 Copynumber: 6.4 Consensus size: 58
19363 AATCAGGATC
* * *
19373 AAAAACGGAATTTTTTGACA-TTCGAGGGT-AAAATGGTAATTTTTGGAAGTTTCGGGATT
1 AAAAATGGAATTTTTGGA-AGTTCGAGGGTAAAAAT-GTAATTTTTGAAAGTTTCGGG-TT
* **
19432 AAAATTGGAA-TTTTGGAAGTTCGAGGGT-AAAATGGTAATTTTCAAAAGTTTCGAGGTT
1 AAAAATGGAATTTTTGGAAGTTCGAGGGTAAAAAT-GTAATTTTTGAAAGTTTCG-GGTT
* ** *
19490 AAAAATAGAATTTTTATAAGTTCGAGGGTAAAAATGTAATTTTTG-AAGTTTTGGGGTT
1 AAAAATGGAATTTTTGGAAGTTCGAGGGTAAAAATGTAATTTTTGAAAG-TTTCGGGTT
* * * * *
19548 AAGAATGTAATTTTTGGAAGTTCGAGGGTAAAAATATAATTTTTGGAAGTTTCGAGGTA
1 AAAAATGGAATTTTTGGAAGTTCGAGGGTAAAAATGTAATTTTTGAAAGTTTCG-GGTT
* * * *
19607 AAAAATGGATTTTTTGGAAGTTCG-GGAGTAAAAATGTAATTTTCGAAAGTTTCGGAATC
1 AAAAATGGAATTTTTGGAAGTTCGAGG-GTAAAAATGTAATTTTTGAAAGTTTCGG-GTT
* * *
19666 AAAAATGGAATTTTTGGAAGTTC-AGGGGTAAAATTGTAATTTTTGAAAGTTTTAGGGTC
1 AAAAATGGAATTTTTGGAAGTTCGA-GGGTAAAAATGTAATTTTTGAAAG-TTTCGGGTT
*
19725 AAAAATGGAGTTTTTGGATAGTT
1 AAAAATGGAATTTTTGGA-AGTT
19748 TAGGGACTTT
Statistics
Matches: 268, Mismatches: 35, Indels: 25
0.82 0.11 0.08
Matches are distributed among these distances:
57 1 0.00
58 100 0.37
59 151 0.56
60 16 0.06
ACGTcount: A:0.35, C:0.04, G:0.25, T:0.36
Consensus pattern (58 bp):
AAAAATGGAATTTTTGGAAGTTCGAGGGTAAAAATGTAATTTTTGAAAGTTTCGGGTT
Found at i:19444 original size:30 final size:29
Alignment explanation
Indices: 19402--19748 Score: 233
Period size: 29 Copynumber: 11.8 Consensus size: 29
19392 ATTCGAGGGT
19402 AAAATGGTAATTTTTGGAAGTTTCGGGATTA
1 AAAATGG-AATTTTTGGAAGTTTCGGG-TTA
* *
19433 AAATTGGAA-TTTTGGAAG-TTCGAGGGT-
1 AAAATGGAATTTTTGGAAGTTTCG-GGTTA
***
19460 AAAATGGTAATTTTCAAAAGTTTCGAGGTTA
1 AAAATGG-AATTTTTGGAAGTTTCG-GGTTA
* ** *
19491 AAAATAGAATTTTTATAAG-TTCGAGGGTA
1 AAAATGGAATTTTTGGAAGTTTCG-GGTTA
* *
19520 AAAATGTAATTTTT-GAAGTTTTGGGGTTA
1 AAAATGGAATTTTTGGAAG-TTTCGGGTTA
* * *
19549 AGAATGTAATTTTTGGAAG-TTCGAGGGTA
1 AAAATGGAATTTTTGGAAGTTTCG-GGTTA
** *
19578 AAAATATAATTTTTGGAAGTTTCGAGGTAA
1 AAAATGGAATTTTTGGAAGTTTCG-GGTTA
* *
19608 AAAATGGATTTTTTGGAAG-TTCGGGAGTA
1 AAAATGGAATTTTTGGAAGTTTCGGG-TTA
* * * * *
19637 AAAATGTAATTTTCGAAAGTTTCGGAATCA
1 AAAATGGAATTTTTGGAAGTTTCGG-GTTA
*
19667 AAAATGGAATTTTTGGAAG-TTCAGGGGTA
1 AAAATGGAATTTTTGGAAGTTTC-GGGTTA
* * * * *
19696 AAATTGTAATTTTTGAAAGTTTTAGGGTCA
1 AAAATGGAATTTTTGGAAG-TTTCGGGTTA
*
19726 AAAATGGAGTTTTTGGATAGTTT
1 AAAATGGAATTTTTGGA-AGTTT
19749 AGGGACTTTT
Statistics
Matches: 248, Mismatches: 51, Indels: 35
0.74 0.15 0.10
Matches are distributed among these distances:
27 6 0.02
28 15 0.06
29 116 0.47
30 95 0.38
31 16 0.06
ACGTcount: A:0.35, C:0.04, G:0.25, T:0.37
Consensus pattern (29 bp):
AAAATGGAATTTTTGGAAGTTTCGGGTTA
Found at i:19461 original size:117 final size:118
Alignment explanation
Indices: 19285--19698 Score: 370
Period size: 117 Copynumber: 3.5 Consensus size: 118
19275 TTTTGGGGGC
* * * * * *
19285 AAAATGGTAATTTTTGGAAAATTT-GGGGTTAAAAAT-GAAATTTTAGATA-TCCGGGGGTAAAA
1 AAAAT-GTAATTTTTGG-AAGTTTCGGGATTAAAAATGGAATTTTTGGA-AGTTCGAGGGTAAAA
* ** * *
19347 CGATAAATTTTAGAAAAATC-AGGATCAAAAACGGAATTTTTTGACA-TTCGAGGGT-
63 AGATAAATTTTAGAAATTTCGAGG-TAAAAAATGGAATTTTTTGA-AGTTCGAGGGTA
* *
19402 AAAATGGTAATTTTTGGAAGTTTCGGGATTAAAATTGGAA-TTTTGGAAGTTCGAGGGTAAAATG
1 AAAAT-GTAATTTTTGGAAGTTTCGGGATTAAAAATGGAATTTTTGGAAGTTCGAGGGTAAAAAG
* * *
19466 GT-AATTTTCA-AAAGTTTCGAGGTTAAAAATAGAATTTTTAT-AAGTTCGAGGGTA
65 ATAAATTTT-AGAAA-TTTCGAGGTAAAAAATGGAATTTTT-TGAAGTTCGAGGGTA
* * * * *
19520 AAAATGTAATTTTT-GAAGTTTTGGGGTTAAGAATGTAATTTTTGGAAGTTCGAGGGTAAAAATA
1 AAAATGTAATTTTTGGAAGTTTCGGGATTAAAAATGGAATTTTTGGAAGTTCGAGGGTAAAAAGA
* * *
19584 TAATTTTTGGAAGTTTCGAGGTAAAAAATGG-ATTTTTTGGAAGTTCG-GGAGTA
66 TAAATTTTAGAAATTTCGAGGTAAAAAATGGAATTTTTT-GAAGTTCGAGG-GTA
* * * *
19637 AAAATGTAATTTTCGAAAGTTTCGGAATCAAAAATGGAATTTTTGGAAGTTC-AGGGGTAAAA
1 AAAATGTAATTTTTGGAAGTTTCGGGATTAAAAATGGAATTTTTGGAAGTTCGA-GGGTAAAA
19699 TTGTAATTTT
Statistics
Matches: 246, Mismatches: 34, Indels: 33
0.79 0.11 0.11
Matches are distributed among these distances:
115 1 0.00
116 43 0.17
117 145 0.59
118 57 0.23
ACGTcount: A:0.37, C:0.05, G:0.24, T:0.34
Consensus pattern (118 bp):
AAAATGTAATTTTTGGAAGTTTCGGGATTAAAAATGGAATTTTTGGAAGTTCGAGGGTAAAAAGA
TAAATTTTAGAAATTTCGAGGTAAAAAATGGAATTTTTTGAAGTTCGAGGGTA
Found at i:21563 original size:17 final size:17
Alignment explanation
Indices: 21537--21632 Score: 77
Period size: 17 Copynumber: 5.6 Consensus size: 17
21527 CTTTTTAATT
* *
21537 AATTTTAATTTACAGTA
1 AATTTAAATTTAAAGTA
21554 AATTTAAATTTAAAGTA
1 AATTTAAATTTAAAGTA
* * **
21571 AATTTAAACTCAAAAAA
1 AATTTAAATTTAAAGTA
*
21588 GAATTTAAATTTAGAA-CA
1 -AATTTAAATTTA-AAGTA
* *
21606 AATTCAAACTTAAAGTA
1 AATTTAAATTTAAAGTA
*
21623 AATTAAAATT
1 AATTTAAATT
21633 AAAAATTGGA
Statistics
Matches: 62, Mismatches: 14, Indels: 6
0.76 0.17 0.07
Matches are distributed among these distances:
16 2 0.03
17 47 0.76
18 11 0.18
19 2 0.03
ACGTcount: A:0.53, C:0.06, G:0.05, T:0.35
Consensus pattern (17 bp):
AATTTAAATTTAAAGTA
Found at i:23149 original size:62 final size:62
Alignment explanation
Indices: 23060--23453 Score: 625
Period size: 62 Copynumber: 6.4 Consensus size: 62
23050 CATAAAGCTT
* *
23060 CGATGATTTTGTGTCATTGTGAGTATTAAATGAGAAATGAATCCTATTACAGATTAAAGGTC
1 CGATGACTTTGTGTCATCGTGAGTATTAAATGAGAAATGAATCCTATTACAGATTAAAGGTC
* * *
23122 CAATGACTTTGTGTCATCGTGAGTATTAAATGAGAAATGAATCCTTTTACAGATTAAAGGTT
1 CGATGACTTTGTGTCATCGTGAGTATTAAATGAGAAATGAATCCTATTACAGATTAAAGGTC
*
23184 CGATGAC--TGTGTCATCGTGAGTATTAAATGAGAAATGAATCCTATTACGGATTAAAGGTC
1 CGATGACTTTGTGTCATCGTGAGTATTAAATGAGAAATGAATCCTATTACAGATTAAAGGTC
* * *
23244 CGATGAATTTGTGTCATCGTGAGTATTAAATGAGAAATGAATCCCATTAC-GTATTAAAGGTT
1 CGATGACTTTGTGTCATCGTGAGTATTAAATGAGAAATGAATCCTATTACAG-ATTAAAGGTC
**
23306 CGATGACTTTGTGTCATCGTGAGTATTAAATGAGAAATGAATCCTATTATGGATTAAAGGTC
1 CGATGACTTTGTGTCATCGTGAGTATTAAATGAGAAATGAATCCTATTACAGATTAAAGGTC
*
23368 CGATGACTTTGTGTCATCGTGAGTATTAAATGAGAAATGAATCCTATTA-TGAATTAAAGGTC
1 CGATGACTTTGTGTCATCGTGAGTATTAAATGAGAAATGAATCCTATTACAG-ATTAAAGGTC
*
23430 CGATGACTTTGTGTCATCATGAGT
1 CGATGACTTTGTGTCATCGTGAGT
23454 TATCAGATGT
Statistics
Matches: 309, Mismatches: 18, Indels: 10
0.92 0.05 0.03
Matches are distributed among these distances:
60 56 0.18
61 2 0.01
62 250 0.81
63 1 0.00
ACGTcount: A:0.33, C:0.12, G:0.22, T:0.34
Consensus pattern (62 bp):
CGATGACTTTGTGTCATCGTGAGTATTAAATGAGAAATGAATCCTATTACAGATTAAAGGTC
Found at i:25288 original size:5 final size:5
Alignment explanation
Indices: 25273--25332 Score: 70
Period size: 5 Copynumber: 12.2 Consensus size: 5
25263 TTCACATTTC
** *
25273 TTTATT TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT TTCCT TAT-T TTTA-
1 TTTA-T TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT
25322 TTTAT TTTAT T
1 TTTAT TTTAT T
25333 ATTTCTTTGA
Statistics
Matches: 47, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
4 7 0.15
5 36 0.77
6 4 0.09
ACGTcount: A:0.18, C:0.03, G:0.00, T:0.78
Consensus pattern (5 bp):
TTTAT
Found at i:26705 original size:126 final size:125
Alignment explanation
Indices: 26479--26730 Score: 486
Period size: 126 Copynumber: 2.0 Consensus size: 125
26469 TTGCACTAGG
26479 AGGGTTTGATTTTCTTGGGTCCCTATGTGACTCGATTGGCGAGACATTTTGAGCTACTCGACACA
1 AGGGTTTGATTTTCTTGGGTCCCTATGTGACTCGATTGGCGAGACATTTTGAGCTACTCGACACA
26544 CCGGAGTAGACAACCTCTTTTACACTGATTGGACGGATGGTCCTGTAAGGATAATTTATT
66 CCGGAGTAGACAACCTCTTTTACACTGATTGGACGGATGGTCCTGTAAGGATAATTTATT
26604 ANGGGTTTGATTTTCTTGGGTCCCTATGTGACTCGATTGGCGAGACATTTTGAGCTACTCGACAC
1 A-GGGTTTGATTTTCTTGGGTCCCTATGTGACTCGATTGGCGAGACATTTTGAGCTACTCGACAC
*
26669 ACCGGTGTAGACAACCTCTTTTACACTGATTGGACGGATGGTCCTGTAAGGATAATTTATT
65 ACCGGAGTAGACAACCTCTTTTACACTGATTGGACGGATGGTCCTGTAAGGATAATTTATT
26730 A
1 A
26731 TGAGTCATAT
Statistics
Matches: 125, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
125 1 0.01
126 124 0.99
ACGTcount: A:0.23, C:0.19, G:0.25, T:0.33
Consensus pattern (125 bp):
AGGGTTTGATTTTCTTGGGTCCCTATGTGACTCGATTGGCGAGACATTTTGAGCTACTCGACACA
CCGGAGTAGACAACCTCTTTTACACTGATTGGACGGATGGTCCTGTAAGGATAATTTATT
Found at i:28102 original size:11 final size:10
Alignment explanation
Indices: 28080--28122 Score: 50
Period size: 11 Copynumber: 4.0 Consensus size: 10
28070 AAGATGAATT
28080 GAAAACAAAAA
1 GAAAA-AAAAA
28091 GAAGAAAAAAA
1 GAA-AAAAAAA
*
28102 GAAAACAAAA
1 GAAAAAAAAA
28112 GAAAACAAAAA
1 GAAAA-AAAAA
28123 AATATATATT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
10 11 0.39
11 15 0.54
12 2 0.07
ACGTcount: A:0.81, C:0.07, G:0.12, T:0.00
Consensus pattern (10 bp):
GAAAAAAAAA
Found at i:28111 original size:10 final size:10
Alignment explanation
Indices: 28080--28121 Score: 57
Period size: 10 Copynumber: 4.0 Consensus size: 10
28070 AAGATGAATT
28080 GAAAACAAAAA
1 GAAAAC-AAAA
*
28091 GAAGAAAAAAA
1 GAA-AACAAAA
28102 GAAAACAAAA
1 GAAAACAAAA
28112 GAAAACAAAA
1 GAAAACAAAA
28122 AAATATATAT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
10 16 0.57
11 10 0.36
12 2 0.07
ACGTcount: A:0.81, C:0.07, G:0.12, T:0.00
Consensus pattern (10 bp):
GAAAACAAAA
Found at i:28121 original size:22 final size:22
Alignment explanation
Indices: 28080--28123 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
28070 AAGATGAATT
*
28080 GAAAACAAAAAGAAGAAAAAAA
1 GAAAACAAAAAGAAAAAAAAAA
28102 GAAAAC-AAAAGAAAACAAAAAA
1 GAAAACAAAAAGAAAA-AAAAAA
28124 ATATATATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 8 0.40
22 12 0.60
ACGTcount: A:0.82, C:0.07, G:0.11, T:0.00
Consensus pattern (22 bp):
GAAAACAAAAAGAAAAAAAAAA
Found at i:30490 original size:48 final size:48
Alignment explanation
Indices: 30427--30545 Score: 148
Period size: 48 Copynumber: 2.4 Consensus size: 48
30417 GACTATTCAC
* * *
30427 ATAAAAAATATTTAAAAATTAATTAAGTTATAAAAATAATATAAAATAA
1 ATAAATAATA-TTAAAAATTAATTAAATTATAAAAATAAAATAAAATAA
* * **
30476 TTAAATATTATTAAAAAACAATTAAATTATAAAAATAAAATAAAATAA
1 ATAAATAATATTAAAAATTAATTAAATTATAAAAATAAAATAAAATAA
*
30524 ATAAATAATATAAAATAATTAA
1 ATAAATAATATTAAA-AATTAA
30546 AATTAACTCT
Statistics
Matches: 57, Mismatches: 12, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
48 46 0.81
49 11 0.19
ACGTcount: A:0.66, C:0.01, G:0.01, T:0.32
Consensus pattern (48 bp):
ATAAATAATATTAAAAATTAATTAAATTATAAAAATAAAATAAAATAA
Found at i:30525 original size:9 final size:9
Alignment explanation
Indices: 30507--30548 Score: 50
Period size: 9 Copynumber: 4.6 Consensus size: 9
30497 TTAAATTATA
30507 AAAATAAAAT
1 AAAAT-AAAT
30517 AAAATAAAT
1 AAAATAAAT
30526 -AAATAATAT
1 AAAATAA-AT
*
30535 AAAATAATT
1 AAAATAAAT
30544 AAAAT
1 AAAAT
30549 TAACTCTTAC
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
8 6 0.21
9 12 0.41
10 11 0.38
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (9 bp):
AAAATAAAT
Found at i:30546 original size:18 final size:17
Alignment explanation
Indices: 30456--30542 Score: 60
Period size: 18 Copynumber: 5.3 Consensus size: 17
30446 TAATTAAGTT
30456 ATAA-AAATAATATAAA
1 ATAATAAATAATATAAA
*
30472 ATAATTAAATATTATTAAA
1 ATAA-TAAATAATA-TAAA
* * *
30491 A-AACAATTAA-AT--T
1 ATAATAAATAATATAAA
*
30504 ATAA-AAATAAAATAAA
1 ATAATAAATAATATAAA
30520 ATAAATAAATAATATAAA
1 AT-AATAAATAATATAAA
30538 ATAAT
1 ATAAT
30543 TAAAATTAAC
Statistics
Matches: 54, Mismatches: 8, Indels: 17
0.68 0.10 0.22
Matches are distributed among these distances:
13 6 0.11
14 4 0.07
15 1 0.02
16 7 0.13
17 9 0.17
18 22 0.41
19 5 0.09
ACGTcount: A:0.69, C:0.01, G:0.00, T:0.30
Consensus pattern (17 bp):
ATAATAAATAATATAAA
Found at i:30723 original size:11 final size:11
Alignment explanation
Indices: 30695--30747 Score: 61
Period size: 11 Copynumber: 4.7 Consensus size: 11
30685 TGAGAGCTTT
30695 AGAGAAAAGTTG
1 AGAGAAAA-TTG
30707 AGAGAAAATTG
1 AGAGAAAATTG
* *
30718 ATAGAAATTTG
1 AGAGAAAATTG
*
30729 AGAGAAACTTG
1 AGAGAAAATTG
*
30740 AGTGAAAA
1 AGAGAAAA
30748 ATAAAAGGGG
Statistics
Matches: 35, Mismatches: 6, Indels: 1
0.83 0.14 0.02
Matches are distributed among these distances:
11 27 0.77
12 8 0.23
ACGTcount: A:0.51, C:0.02, G:0.26, T:0.21
Consensus pattern (11 bp):
AGAGAAAATTG
Found at i:31348 original size:18 final size:17
Alignment explanation
Indices: 31321--31354 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
31311 ATAATATTAA
31321 TTATATTTATAAAATCT
1 TTATATTTATAAAATCT
*
31338 TTATATATTATATAATC
1 TTATAT-TTATAAAATC
31355 ATAAACATTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.41, C:0.06, G:0.00, T:0.53
Consensus pattern (17 bp):
TTATATTTATAAAATCT
Found at i:31419 original size:19 final size:19
Alignment explanation
Indices: 31395--31434 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
31385 ATTATGTTAT
* *
31395 ATAAAACATTTCTATTAAA
1 ATAAAACATTTATATAAAA
31414 ATAAAACATTTATATAAAA
1 ATAAAACATTTATATAAAA
31433 AT
1 AT
31435 TTTGTTTTAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.57, C:0.07, G:0.00, T:0.35
Consensus pattern (19 bp):
ATAAAACATTTATATAAAA
Found at i:32022 original size:18 final size:18
Alignment explanation
Indices: 31999--32035 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
31989 AATACGAGAA
31999 TATTTTAATTTTTTTATT
1 TATTTTAATTTTTTTATT
32017 TATTTTAATTTTTTTATT
1 TATTTTAATTTTTTTATT
32035 T
1 T
32036 CAATAAAATA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (18 bp):
TATTTTAATTTTTTTATT
Found at i:32519 original size:13 final size:13
Alignment explanation
Indices: 32476--32523 Score: 51
Period size: 13 Copynumber: 3.4 Consensus size: 13
32466 TTTAAAATTA
*
32476 TTAAAATTATTTTT
1 TTAAAAATA-TTTT
32490 TTAAAATATAAATTTT
1 TTAAAA-AT--ATTTT
32506 TTAAAAATATTTT
1 TTAAAAATATTTT
32519 TTAAA
1 TTAAA
32524 TATAAAATTA
Statistics
Matches: 30, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
13 10 0.33
14 6 0.20
15 3 0.10
16 10 0.33
17 1 0.03
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (13 bp):
TTAAAAATATTTT
Found at i:32520 original size:15 final size:14
Alignment explanation
Indices: 32476--32520 Score: 54
Period size: 14 Copynumber: 3.1 Consensus size: 14
32466 TTTAAAATTA
*
32476 TTAAAATTATTTTT
1 TTAAAAATATTTTT
*
32490 TTAAAATATAAATTTT
1 TTAAAA-AT-ATTTTT
32506 TTAAAAATATTTTT
1 TTAAAAATATTTTT
32520 T
1 T
32521 AAATATAAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
14 12 0.46
15 3 0.12
16 11 0.42
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (14 bp):
TTAAAAATATTTTT
Found at i:32527 original size:28 final size:30
Alignment explanation
Indices: 32468--32538 Score: 101
Period size: 28 Copynumber: 2.4 Consensus size: 30
32458 CAAATGATTT
*
32468 TAAAATTATTAAAATTATTTTTTTAAAATA
1 TAAAATTATTAAAAATATTTTTTTAAAATA
* *
32498 TAAATTTTTTAAAAATA-TTTTTT-AAATA
1 TAAAATTATTAAAAATATTTTTTTAAAATA
32526 TAAAATTATTAAA
1 TAAAATTATTAAA
32539 TTATTTAATT
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
28 16 0.44
29 6 0.17
30 14 0.39
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (30 bp):
TAAAATTATTAAAAATATTTTTTTAAAATA
Found at i:32620 original size:18 final size:18
Alignment explanation
Indices: 32568--32623 Score: 59
Period size: 18 Copynumber: 3.4 Consensus size: 18
32558 ATCTTCTTCC
32568 CCATTTTTCCATCTAACA
1 CCATTTTTCCATCTAACA
* *
32586 CCA---CTCCTTCT--CA
1 CCATTTTTCCATCTAACA
32599 CCATTTTTCCATCTAACA
1 CCATTTTTCCATCTAACA
32617 CCATTTT
1 CCATTTT
32624 CTCATTGAAT
Statistics
Matches: 29, Mismatches: 4, Indels: 10
0.67 0.09 0.23
Matches are distributed among these distances:
13 5 0.17
15 6 0.21
16 6 0.21
18 12 0.41
ACGTcount: A:0.23, C:0.38, G:0.00, T:0.39
Consensus pattern (18 bp):
CCATTTTTCCATCTAACA
Found at i:32877 original size:24 final size:24
Alignment explanation
Indices: 32845--32891 Score: 85
Period size: 24 Copynumber: 2.0 Consensus size: 24
32835 TGAAGTTTTT
32845 TATTTATTTCTCGAGAAAATACTC
1 TATTTATTTCTCGAGAAAATACTC
*
32869 TATTTATTTCTCGGGAAAATACT
1 TATTTATTTCTCGAGAAAATACT
32892 AAATTCATAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.32, C:0.15, G:0.11, T:0.43
Consensus pattern (24 bp):
TATTTATTTCTCGAGAAAATACTC
Found at i:33260 original size:11 final size:11
Alignment explanation
Indices: 33244--33297 Score: 53
Period size: 11 Copynumber: 5.3 Consensus size: 11
33234 TATATTTTAA
33244 AAATTAATTTT
1 AAATTAATTTT
33255 AAATTAATTTT
1 AAATTAATTTT
* *
33266 ATATT--TTTA
1 AAATTAATTTT
*
33275 AAAATAATTTT
1 AAATTAATTTT
33286 -AA-TAATTTT
1 AAATTAATTTT
33295 AAA
1 AAA
33298 ATTATTTGTT
Statistics
Matches: 35, Mismatches: 5, Indels: 7
0.74 0.11 0.15
Matches are distributed among these distances:
9 13 0.37
10 4 0.11
11 18 0.51
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (11 bp):
AAATTAATTTT
Found at i:33269 original size:31 final size:29
Alignment explanation
Indices: 33222--33295 Score: 107
Period size: 31 Copynumber: 2.5 Consensus size: 29
33212 GATGAAGATG
33222 ATTTTAATAA-TTTATA-TTTTAAAAATTA
1 ATTTTAATAATTTTATATTTTTAAAAA-TA
33250 ATTTTAAATTAATTTTATATTTTTAAAAATA
1 ATTTT-AA-TAATTTTATATTTTTAAAAATA
33281 ATTTTAATAATTTTA
1 ATTTTAATAATTTTA
33296 AAATTATTTG
Statistics
Matches: 42, Mismatches: 0, Indels: 7
0.86 0.00 0.14
Matches are distributed among these distances:
28 5 0.12
29 10 0.24
30 5 0.12
31 13 0.31
32 9 0.21
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (29 bp):
ATTTTAATAATTTTATATTTTTAAAAATA
Found at i:33275 original size:19 final size:20
Alignment explanation
Indices: 33248--33304 Score: 71
Period size: 20 Copynumber: 2.9 Consensus size: 20
33238 TTTTAAAAAT
*
33248 TAATTTTAAATTAATTTT-A
1 TAATTTTAAAATAATTTTAA
*
33267 TATTTTTAAAAATAATTTTAA
1 TAATTTT-AAAATAATTTTAA
*
33288 TAATTTTAAAATTATTT
1 TAATTTTAAAATAATTT
33305 GTTGATGTGA
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
19 6 0.19
20 19 0.59
21 7 0.22
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (20 bp):
TAATTTTAAAATAATTTTAA
Found at i:33284 original size:20 final size:21
Alignment explanation
Indices: 33248--33298 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
33238 TTTTAAAAAT
*
33248 TAATTTT-AAATTAATTTT-A
1 TAATTTTAAAAATAATTTTAA
*
33267 TATTTTTAAAAATAATTTTAA
1 TAATTTTAAAAATAATTTTAA
33288 TAATTTTAAAA
1 TAATTTTAAAA
33299 TTATTTGTTG
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
19 6 0.22
20 10 0.37
21 11 0.41
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (21 bp):
TAATTTTAAAAATAATTTTAA
Done.