Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013635.1 Kokia drynarioides strain JFW-HI SEQ_128663, 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: 122795
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.34
Warning! 15 characters in sequence are not A, C, G, or T
Found at i:3277 original size:23 final size:23
Alignment explanation
Indices: 3249--3313 Score: 78
Period size: 25 Copynumber: 2.7 Consensus size: 23
3239 ACACTAGTGC
3249 GCTCTCTGTTTAGCAC-GTCTCGT
1 GCTCTCTGTTTAGCACTGTCT-GT
*
3272 GCTCTCTGTTATTAGCACTGTGTGT
1 GCTCTCTG-T-TTAGCACTGTCTGT
*
3297 GCTCTCTGATTAGCACT
1 GCTCTCTGTTTAGCACT
3314 TTGATTAGTA
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
23 16 0.43
24 1 0.03
25 17 0.46
26 3 0.08
ACGTcount: A:0.12, C:0.26, G:0.22, T:0.40
Consensus pattern (23 bp):
GCTCTCTGTTTAGCACTGTCTGT
Found at i:3286 original size:25 final size:24
Alignment explanation
Indices: 3249--3313 Score: 82
Period size: 23 Copynumber: 2.8 Consensus size: 24
3239 ACACTAGTGC
3249 GCTCTCTGT-TTAGCAC-GTCTCGT
1 GCTCTCTGTATTAGCACTGTCT-GT
*
3272 GCTCTCTGTTATTAGCACTGTGTGT
1 GCTCTCTG-TATTAGCACTGTCTGT
3297 GCTCTCTG-ATTAGCACT
1 GCTCTCTGTATTAGCACT
3314 TTGATTAGTA
Statistics
Matches: 38, Mismatches: 1, Indels: 6
0.84 0.02 0.13
Matches are distributed among these distances:
23 17 0.45
24 1 0.03
25 17 0.45
26 3 0.08
ACGTcount: A:0.12, C:0.26, G:0.22, T:0.40
Consensus pattern (24 bp):
GCTCTCTGTATTAGCACTGTCTGT
Found at i:3331 original size:35 final size:35
Alignment explanation
Indices: 3282--3348 Score: 98
Period size: 35 Copynumber: 1.9 Consensus size: 35
3272 GCTCTCTGTT
*
3282 ATTAGCACTGTGTGTGCTCTCTGATTAGCACTTTG
1 ATTAGCACTGTGTGTACTCTCTGATTAGCACTTTG
* * *
3317 ATTAGTACTTTGTGTACTCTCTGTTTAGCACT
1 ATTAGCACTGTGTGTACTCTCTGATTAGCACT
3349 GTGTGTGCTC
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
35 28 1.00
ACGTcount: A:0.18, C:0.19, G:0.19, T:0.43
Consensus pattern (35 bp):
ATTAGCACTGTGTGTACTCTCTGATTAGCACTTTG
Found at i:3353 original size:23 final size:23
Alignment explanation
Indices: 3318--3364 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
3308 AGCACTTTGA
* *
3318 TTAGTACTTTGTGTACTCTCTGT
1 TTAGCACTGTGTGTACTCTCTGT
*
3341 TTAGCACTGTGTGTGCTCTCTGT
1 TTAGCACTGTGTGTACTCTCTGT
3364 T
1 T
3365 GCCCAGCATT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.11, C:0.19, G:0.21, T:0.49
Consensus pattern (23 bp):
TTAGCACTGTGTGTACTCTCTGT
Found at i:21534 original size:22 final size:21
Alignment explanation
Indices: 21508--21549 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
21498 TTAAAAATTC
21508 ATAAATATTATTAATTTTTTTA
1 ATAAA-ATTATTAATTTTTTTA
* *
21530 ATAAAATTTTTGATTTTTTT
1 ATAAAATTATTAATTTTTTT
21550 GTTTCAGTAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 13 0.72
22 5 0.28
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (21 bp):
ATAAAATTATTAATTTTTTTA
Found at i:22616 original size:22 final size:22
Alignment explanation
Indices: 22588--22633 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
22578 ATACATAAGT
22588 AATCGTCAACCCG-GATCCTAAA
1 AATCGTCAACCCGAG-TCCTAAA
*
22610 AATCGTCAACTCGAGTCCTAAA
1 AATCGTCAACCCGAGTCCTAAA
22632 AA
1 AA
22634 GGATCCGGGT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 21 0.95
23 1 0.05
ACGTcount: A:0.39, C:0.28, G:0.13, T:0.20
Consensus pattern (22 bp):
AATCGTCAACCCGAGTCCTAAA
Found at i:23785 original size:29 final size:28
Alignment explanation
Indices: 23752--23811 Score: 68
Period size: 28 Copynumber: 2.1 Consensus size: 28
23742 TTATTACATG
23752 TTTTTGTTCACAT-AGTGAATTTGCCCTAA
1 TTTTT-TT-ACATGAGTGAATTTGCCCTAA
***
23781 TTTTTTTTGGTGAGTGAATTTGCCCTAA
1 TTTTTTTACATGAGTGAATTTGCCCTAA
23809 TTT
1 TTT
23812 AATCAAATCT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
27 1 0.04
28 21 0.78
29 5 0.19
ACGTcount: A:0.20, C:0.13, G:0.17, T:0.50
Consensus pattern (28 bp):
TTTTTTTACATGAGTGAATTTGCCCTAA
Found at i:24314 original size:21 final size:21
Alignment explanation
Indices: 24290--24330 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
24280 TAGCATAATC
*
24290 CAAATATAAAATTTAGAAATT
1 CAAACATAAAATTTAGAAATT
* *
24311 CAAACATAAAGTTTATAAAT
1 CAAACATAAAATTTAGAAAT
24331 CTAAATTACT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.56, C:0.07, G:0.05, T:0.32
Consensus pattern (21 bp):
CAAACATAAAATTTAGAAATT
Found at i:34803 original size:83 final size:83
Alignment explanation
Indices: 34664--34835 Score: 344
Period size: 83 Copynumber: 2.1 Consensus size: 83
34654 TGATAGTGTT
34664 ACCAAAACAAGAAACATGGATTGATAATTACAACAATTTAGTTTAAGTATCTCTTTCTAACCAAT
1 ACCAAAACAAGAAACATGGATTGATAATTACAACAATTTAGTTTAAGTATCTCTTTCTAACCAAT
34729 TATTGATGTCCAATGGGA
66 TATTGATGTCCAATGGGA
34747 ACCAAAACAAGAAACATGGATTGATAATTACAACAATTTAGTTTAAGTATCTCTTTCTAACCAAT
1 ACCAAAACAAGAAACATGGATTGATAATTACAACAATTTAGTTTAAGTATCTCTTTCTAACCAAT
34812 TATTGATGTCCAATGGGA
66 TATTGATGTCCAATGGGA
34830 ACCAAA
1 ACCAAA
34836 TGTTTAGGAT
Statistics
Matches: 89, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
83 89 1.00
ACGTcount: A:0.41, C:0.16, G:0.13, T:0.30
Consensus pattern (83 bp):
ACCAAAACAAGAAACATGGATTGATAATTACAACAATTTAGTTTAAGTATCTCTTTCTAACCAAT
TATTGATGTCCAATGGGA
Found at i:35102 original size:6 final size:6
Alignment explanation
Indices: 35091--35119 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
35081 AGGCAGCTCT
35091 TTGGCA TTGGCA TTGGCA TTGGCA TTGGC
1 TTGGCA TTGGCA TTGGCA TTGGCA TTGGC
35120 CTATCCAGGG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.14, C:0.17, G:0.34, T:0.34
Consensus pattern (6 bp):
TTGGCA
Found at i:37657 original size:21 final size:20
Alignment explanation
Indices: 37629--37670 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
37619 GTTTAGAAAT
*
37629 ATTTCCTAAAAAATTTTAAA
1 ATTTCCTAAAAAATATTAAA
*
37649 ATTTGCCTAAATAATATTAAA
1 ATTT-CCTAAAAAATATTAAA
37670 A
1 A
37671 GACTATCAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 4 0.21
21 15 0.79
ACGTcount: A:0.50, C:0.10, G:0.02, T:0.38
Consensus pattern (20 bp):
ATTTCCTAAAAAATATTAAA
Found at i:39555 original size:88 final size:88
Alignment explanation
Indices: 39406--39581 Score: 343
Period size: 88 Copynumber: 2.0 Consensus size: 88
39396 GGAGAGGGGC
39406 GGTGACGGGGGTATCATTGTTTCCGTGTGGAAATAGGGGGGATTTTCTCACATTGGTGGTGAAAG
1 GGTGACGGGGGTATCATTGTTTCCGTGTGGAAATAGGGGGGATTTTCTCACATTGGTGGTGAAAG
39471 GGACCCATTTTCCTTGGTTTCTT
66 GGACCCATTTTCCTTGGTTTCTT
*
39494 GGTGACGGGGGTATCATTTTTTCCGTGTGGAAATAGGGGGGATTTTCTCACATTGGTGGTGAAAG
1 GGTGACGGGGGTATCATTGTTTCCGTGTGGAAATAGGGGGGATTTTCTCACATTGGTGGTGAAAG
39559 GGACCCATTTTCCTTGGTTTCTT
66 GGACCCATTTTCCTTGGTTTCTT
39582 TATTACGTCT
Statistics
Matches: 87, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
88 87 1.00
ACGTcount: A:0.17, C:0.15, G:0.32, T:0.36
Consensus pattern (88 bp):
GGTGACGGGGGTATCATTGTTTCCGTGTGGAAATAGGGGGGATTTTCTCACATTGGTGGTGAAAG
GGACCCATTTTCCTTGGTTTCTT
Found at i:40874 original size:34 final size:34
Alignment explanation
Indices: 40835--40908 Score: 114
Period size: 35 Copynumber: 2.2 Consensus size: 34
40825 TTAAAAGTTG
*
40835 AAATTTTTGGA-CCCTTAAAAATTTGTAAAAAAA
1 AAATTTTTGGATCCCTTAAAAATTTATAAAAAAA
*
40868 ATAATTTTTGGATCCCTTAAAAATTTATAAAACAA
1 A-AATTTTTGGATCCCTTAAAAATTTATAAAAAAA
40903 AAATTT
1 AAATTT
40909 GGACCTCTTT
Statistics
Matches: 37, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
33 1 0.03
34 15 0.41
35 21 0.57
ACGTcount: A:0.47, C:0.09, G:0.07, T:0.36
Consensus pattern (34 bp):
AAATTTTTGGATCCCTTAAAAATTTATAAAAAAA
Found at i:41404 original size:22 final size:22
Alignment explanation
Indices: 41369--41430 Score: 63
Period size: 22 Copynumber: 2.7 Consensus size: 22
41359 ATTTAATGCC
41369 TTAATTGATAAAA-TACTAATACT
1 TTAA-TGATAAAATTA-TAATACT
* *
41392 TTAATGATTAAATTATAATATT
1 TTAATGATAAAATTATAATACT
41414 TTAATGTATGAAAATTA
1 TTAATG-AT-AAAATTA
41431 ATTTAGAATA
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
22 19 0.58
23 8 0.24
24 6 0.18
ACGTcount: A:0.47, C:0.03, G:0.06, T:0.44
Consensus pattern (22 bp):
TTAATGATAAAATTATAATACT
Found at i:44269 original size:2 final size:2
Alignment explanation
Indices: 44262--44289 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
44252 TAACCTTATT
44262 TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC
44290 CTTCTTTGTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:52255 original size:18 final size:17
Alignment explanation
Indices: 52224--52257 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
52214 TTGAATTATT
*
52224 TTAAATATAGATAAATA
1 TTAAATATACATAAATA
52241 TTAAATTATACATAAAT
1 TTAAA-TATACATAAAT
52258 TTTTATTACA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.56, C:0.03, G:0.03, T:0.38
Consensus pattern (17 bp):
TTAAATATACATAAATA
Found at i:54158 original size:3 final size:3
Alignment explanation
Indices: 54152--54177 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
54142 CCCCCAAAAA
54152 AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AA
54178 GCAGACCTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:61322 original size:20 final size:19
Alignment explanation
Indices: 61297--61337 Score: 55
Period size: 20 Copynumber: 2.1 Consensus size: 19
61287 TACCCTTTTT
*
61297 TTTTTTTTTTAATTTCATCA
1 TTTTTTTATTAATTTC-TCA
*
61317 TTTTTTTATTATTTTCTCA
1 TTTTTTTATTAATTTCTCA
61336 TT
1 TT
61338 CACTATTTGT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 5 0.26
20 14 0.74
ACGTcount: A:0.17, C:0.10, G:0.00, T:0.73
Consensus pattern (19 bp):
TTTTTTTATTAATTTCTCA
Found at i:63484 original size:26 final size:26
Alignment explanation
Indices: 63411--63474 Score: 94
Period size: 26 Copynumber: 2.5 Consensus size: 26
63401 ACCAAAGTAC
* * *
63411 TAACAAAGAGCACATA-AGTGTTGGG
1 TAACAGAGAGCACACACAGTGCTGGG
63436 TAACAGAGAGCACACACAGTGCTGGG
1 TAACAGAGAGCACACACAGTGCTGGG
63462 TAACAGAGAGCAC
1 TAACAGAGAGCAC
63475 GAGACGTGCT
Statistics
Matches: 35, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
25 14 0.40
26 21 0.60
ACGTcount: A:0.39, C:0.19, G:0.28, T:0.14
Consensus pattern (26 bp):
TAACAGAGAGCACACACAGTGCTGGG
Found at i:71141 original size:2 final size:2
Alignment explanation
Indices: 71134--71170 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
71124 AAAACCCGTT
*
71134 AG AG AG AG AT AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
71171 TTGCTTGATC
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.46, T:0.03
Consensus pattern (2 bp):
AG
Found at i:73862 original size:10 final size:10
Alignment explanation
Indices: 73849--73891 Score: 50
Period size: 10 Copynumber: 4.1 Consensus size: 10
73839 CCAAAAAAAT
73849 TTAAAAATTA
1 TTAAAAATTA
*
73859 TTAAAAATCA
1 TTAAAAATTA
*
73869 TTAAAAATATC
1 TTAAAAAT-TA
73880 TATAAAAATTA
1 T-TAAAAATTA
73891 T
1 T
73892 AAATTTTTTT
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
10 17 0.63
11 3 0.11
12 7 0.26
ACGTcount: A:0.58, C:0.05, G:0.00, T:0.37
Consensus pattern (10 bp):
TTAAAAATTA
Found at i:73953 original size:21 final size:20
Alignment explanation
Indices: 73914--73953 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
73904 AAATAACTAA
*
73914 AAATATTAAAAAATGTAAAC
1 AAATATTAAAAAATATAAAC
*
73934 AAATATTTAAAAATTATAAA
1 AAATA-TTAAAAAATATAAA
73954 AAAGAAATTC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.65, C:0.03, G:0.03, T:0.30
Consensus pattern (20 bp):
AAATATTAAAAAATATAAAC
Found at i:85323 original size:21 final size:21
Alignment explanation
Indices: 85293--85360 Score: 66
Period size: 21 Copynumber: 3.1 Consensus size: 21
85283 CTCACAAAGA
*
85293 AAAAAG-GAAGTGAGTTAGAC
1 AAAAAGAGAAGTGACTTAGAC
** *
85313 AAAAAGAGAAGCAACTTGGAC
1 AAAAAGAGAAGTGACTTAGAC
85334 AAAAAGAAACGAAGTGACTTAGAC
1 AAAAAG--A-GAAGTGACTTAGAC
85358 AAA
1 AAA
85361 TCTTTTTTGT
Statistics
Matches: 37, Mismatches: 7, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
20 6 0.16
21 16 0.43
23 1 0.03
24 14 0.38
ACGTcount: A:0.54, C:0.10, G:0.24, T:0.12
Consensus pattern (21 bp):
AAAAAGAGAAGTGACTTAGAC
Found at i:86432 original size:21 final size:21
Alignment explanation
Indices: 86384--86442 Score: 61
Period size: 20 Copynumber: 2.9 Consensus size: 21
86374 CCCAAGTGTG
86384 TTATTTAATAAAAATTATGAT
1 TTATTTAATAAAAATTATGAT
* *
86405 TTA-TTAATTAAAGTTAT-ACT
1 TTATTTAATAAAAATTATGA-T
86425 TTATTTAA-AAATAATTAT
1 TTATTTAATAAA-AATTAT
86443 AAAAATATAT
Statistics
Matches: 31, Mismatches: 4, Indels: 6
0.76 0.10 0.15
Matches are distributed among these distances:
19 1 0.03
20 18 0.58
21 12 0.39
ACGTcount: A:0.46, C:0.02, G:0.03, T:0.49
Consensus pattern (21 bp):
TTATTTAATAAAAATTATGAT
Found at i:98447 original size:23 final size:21
Alignment explanation
Indices: 98405--98449 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 21
98395 AAATGTTAAA
*
98405 ATATATTTTATTTGATATTTG
1 ATATATTTTATTTGAAATTTG
*
98426 ATATATTTTTATATTTAAATTTG
1 ATATA-TTTTAT-TTGAAATTTG
98449 A
1 A
98450 ATTTAAAATA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 5 0.25
22 6 0.30
23 9 0.45
ACGTcount: A:0.33, C:0.00, G:0.07, T:0.60
Consensus pattern (21 bp):
ATATATTTTATTTGAAATTTG
Found at i:114220 original size:15 final size:16
Alignment explanation
Indices: 114195--114228 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
114185 AAAATGTAAT
114195 TTTATTATTTTAATAA
1 TTTATTATTTTAATAA
*
114211 TTTA-TATTTTTATAA
1 TTTATTATTTTAATAA
114226 TTT
1 TTT
114229 TTAAAAGATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 13 0.76
16 4 0.24
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (16 bp):
TTTATTATTTTAATAA
Found at i:116264 original size:17 final size:17
Alignment explanation
Indices: 116242--116274 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
116232 TCTCTTGACC
116242 TTTAACTTTTCATATTT
1 TTTAACTTTTCATATTT
116259 TTTAACTTTTCATATT
1 TTTAACTTTTCATATT
116275 CTTGTAACTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.24, C:0.12, G:0.00, T:0.64
Consensus pattern (17 bp):
TTTAACTTTTCATATTT
Done.