Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01001760.1 Kokia drynarioides strain JFW-HI SEQ_113477, 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: 57826
ACGTcount: A:0.36, C:0.15, G:0.14, T:0.36
Warning! 26 characters in sequence are not A, C, G, or T
Found at i:7824 original size:61 final size:62
Alignment explanation
Indices: 7724--7849 Score: 236
Period size: 61 Copynumber: 2.0 Consensus size: 62
7714 TTTCTTTGCT
*
7724 TTTACCCATCATAGTCTTCTCTAATCATAATTGTTGCTTTTAAGTGTATTAGGCTAATTTTC
1 TTTACCCATCATAGTCTTCTCTAATCATAATTGCTGCTTTTAAGTGTATTAGGCTAATTTTC
7786 TTTA-CCATCATAGTCTTCTCTAATCATAATTGCTGCTTTTAAGTGTATTAGGCTAATTTTC
1 TTTACCCATCATAGTCTTCTCTAATCATAATTGCTGCTTTTAAGTGTATTAGGCTAATTTTC
7847 TTT
1 TTT
7850 CAAGTTTTAT
Statistics
Matches: 63, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
61 59 0.94
62 4 0.06
ACGTcount: A:0.24, C:0.17, G:0.11, T:0.48
Consensus pattern (62 bp):
TTTACCCATCATAGTCTTCTCTAATCATAATTGCTGCTTTTAAGTGTATTAGGCTAATTTTC
Found at i:12264 original size:120 final size:120
Alignment explanation
Indices: 12051--12410 Score: 666
Period size: 120 Copynumber: 3.0 Consensus size: 120
12041 TGGTATGTTA
12051 ATTTAGAATGGTATAATGTAGGCGATGAAAAACTGTAATAAAAATCAAATTTCATGAATAAATTT
1 ATTTAGAATGGTATAATGTAGGCGATGAAAAACTGTAATAAAAATCAAATTTCATGAATAAATTT
*
12116 ACACCCGAACGTTATCGAATTGCATATATTACATCAGAGTTTCTATATATATTTG
66 ACACCCGAACGTTATCGAATTGCATATATTATATCAGAGTTTCTATATATATTTG
*
12171 ATTTAGAATGGTATAATGTAGGCGATGAAAAACTGTAATAAAAATCAAATTTCACGAATAAATTT
1 ATTTAGAATGGTATAATGTAGGCGATGAAAAACTGTAATAAAAATCAAATTTCATGAATAAATTT
* *
12236 ACATCCGAACGTTATCGAATTGCATATATTATATCAGAGTTTCTATATGTATTTG
66 ACACCCGAACGTTATCGAATTGCATATATTATATCAGAGTTTCTATATATATTTG
**
12291 ATTTAGAATGGTATAATGTAGGCGATGAAAAACTGTAATAAAAATCAAATTTCATGAATAAGCTT
1 ATTTAGAATGGTATAATGTAGGCGATGAAAAACTGTAATAAAAATCAAATTTCATGAATAAATTT
12356 ACACCCGAACGTTATCGAATTGCATATATTATATCAGAGTTTCTATATATATTTG
66 ACACCCGAACGTTATCGAATTGCATATATTATATCAGAGTTTCTATATATATTTG
12411 GGAGATTTAA
Statistics
Matches: 231, Mismatches: 9, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
120 231 1.00
ACGTcount: A:0.39, C:0.11, G:0.15, T:0.34
Consensus pattern (120 bp):
ATTTAGAATGGTATAATGTAGGCGATGAAAAACTGTAATAAAAATCAAATTTCATGAATAAATTT
ACACCCGAACGTTATCGAATTGCATATATTATATCAGAGTTTCTATATATATTTG
Found at i:15436 original size:29 final size:27
Alignment explanation
Indices: 15400--15454 Score: 92
Period size: 29 Copynumber: 2.0 Consensus size: 27
15390 TGACAAAAAA
15400 TATAAAAATCATAAAAAATTATAAAATTT
1 TATAAAAATCATAAAAAA--ATAAAATTT
15429 TATAAAAATCATAAAAAAATAAAATT
1 TATAAAAATCATAAAAAAATAAAATT
15455 CATCAAAAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
27 8 0.31
29 18 0.69
ACGTcount: A:0.65, C:0.04, G:0.00, T:0.31
Consensus pattern (27 bp):
TATAAAAATCATAAAAAAATAAAATTT
Found at i:15452 original size:17 final size:18
Alignment explanation
Indices: 15430--15464 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
15420 ATAAAATTTT
15430 ATAAAAATCAT-AAAAAA
1 ATAAAAATCATCAAAAAA
*
15447 ATAAAATTCATCAAAAAA
1 ATAAAAATCATCAAAAAA
15465 GCCTTTTAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 10 0.62
18 6 0.38
ACGTcount: A:0.71, C:0.09, G:0.00, T:0.20
Consensus pattern (18 bp):
ATAAAAATCATCAAAAAA
Found at i:15464 original size:29 final size:28
Alignment explanation
Indices: 15403--15464 Score: 72
Period size: 29 Copynumber: 2.1 Consensus size: 28
15393 CAAAAAATAT
* *
15403 AAAAATCATAAAAAATTATAAAATTTTAT
1 AAAAATCATAAAAAA-TATAAAATTTCAA
15432 AAAAATCATAAAAAA-ATAAAATTCATCAA
1 AAAAATCATAAAAAATATAAAATT--TCAA
15461 AAAA
1 AAAA
15465 GCCTTTTAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
27 8 0.28
29 21 0.72
ACGTcount: A:0.68, C:0.06, G:0.00, T:0.26
Consensus pattern (28 bp):
AAAAATCATAAAAAATATAAAATTTCAA
Found at i:25581 original size:20 final size:21
Alignment explanation
Indices: 25556--25608 Score: 56
Period size: 20 Copynumber: 2.6 Consensus size: 21
25546 TATTAAAAAT
25556 ATAAAATTAATAAATA-TTTA
1 ATAAAATTAATAAATAGTTTA
* *
25576 ATAAAAATAAT-TATAGTTTA
1 ATAAAATTAATAAATAGTTTA
*
25596 AAAAAATATAATA
1 ATAAAAT-TAATA
25609 TTAATGAGTT
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
19 3 0.12
20 19 0.73
21 4 0.15
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (21 bp):
ATAAAATTAATAAATAGTTTA
Found at i:27738 original size:6 final size:6
Alignment explanation
Indices: 27729--27756 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
27719 ATAATTTCTA
27729 TTTTAT TTTTAT TTTTAT TTTTAT TTTT
1 TTTTAT TTTTAT TTTTAT TTTTAT TTTT
27757 TATATTCGTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.14, C:0.00, G:0.00, T:0.86
Consensus pattern (6 bp):
TTTTAT
Found at i:27741 original size:11 final size:11
Alignment explanation
Indices: 27722--27755 Score: 50
Period size: 12 Copynumber: 3.0 Consensus size: 11
27712 TAGTATTATA
*
27722 ATTTCTATTTT
1 ATTTTTATTTT
27733 ATTTTTATTTTT
1 ATTTTTA-TTTT
27745 ATTTTTATTTT
1 ATTTTTATTTT
27756 TTATATTCGT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
11 10 0.48
12 11 0.52
ACGTcount: A:0.18, C:0.03, G:0.00, T:0.79
Consensus pattern (11 bp):
ATTTTTATTTT
Found at i:28521 original size:3 final size:3
Alignment explanation
Indices: 28513--28538 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
28503 GTTCTCTGAG
28513 GAA GAA GAA GAA GAA GAA GAA GAA GA
1 GAA GAA GAA GAA GAA GAA GAA GAA GA
28539 TTATTGTGTT
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:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:31479 original size:2 final size:2
Alignment explanation
Indices: 31474--31501 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
31464 AAAAAAAAAA
31474 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
31502 GATCAAAACC
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:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:41272 original size:23 final size:22
Alignment explanation
Indices: 41246--41288 Score: 59
Period size: 23 Copynumber: 1.9 Consensus size: 22
41236 TTGAATTCAG
41246 AAATTTGAAAAATAATAAAATTA
1 AAATTTGAAAAATAA-AAAATTA
* *
41269 AAATTTTAAAATTAAAAAAT
1 AAATTTGAAAAATAAAAAAT
41289 GTAAGGACTA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 5 0.28
23 13 0.72
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (22 bp):
AAATTTGAAAAATAAAAAATTA
Found at i:41513 original size:24 final size:24
Alignment explanation
Indices: 41463--41513 Score: 59
Period size: 24 Copynumber: 2.1 Consensus size: 24
41453 TAAAACTTTT
* **
41463 TTTAAATTTGACTTCTTATTATTA
1 TTTAAATTTGACTTATTATTAAAA
41487 TTTAAATTTGA-TTATTATATAAAA
1 TTTAAATTTGACTTATTAT-TAAAA
41511 TTT
1 TTT
41514 TAAAAAAACA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
23 6 0.26
24 17 0.74
ACGTcount: A:0.35, C:0.04, G:0.04, T:0.57
Consensus pattern (24 bp):
TTTAAATTTGACTTATTATTAAAA
Found at i:42095 original size:16 final size:17
Alignment explanation
Indices: 42074--42109 Score: 65
Period size: 16 Copynumber: 2.2 Consensus size: 17
42064 GTTACATGTC
42074 TTTTTTTATTCTTT-TT
1 TTTTTTTATTCTTTCTT
42090 TTTTTTTATTCTTTCTT
1 TTTTTTTATTCTTTCTT
42107 TTT
1 TTT
42110 CAGTTCATTA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 14 0.74
17 5 0.26
ACGTcount: A:0.06, C:0.08, G:0.00, T:0.86
Consensus pattern (17 bp):
TTTTTTTATTCTTTCTT
Found at i:45246 original size:24 final size:24
Alignment explanation
Indices: 45219--45264 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
45209 GTGATAAAGA
45219 TAAATTAGTTTTT-CTAGTAAAAAT
1 TAAATTAGTTTTTCCTA-TAAAAAT
*
45243 TAAATTATTTTTTCCTATAAAA
1 TAAATTAGTTTTTCCTATAAAA
45265 GCCCAAGTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
24 17 0.85
25 3 0.15
ACGTcount: A:0.41, C:0.07, G:0.04, T:0.48
Consensus pattern (24 bp):
TAAATTAGTTTTTCCTATAAAAAT
Found at i:47037 original size:6 final size:6
Alignment explanation
Indices: 47028--47059 Score: 64
Period size: 6 Copynumber: 5.3 Consensus size: 6
47018 ATCACCATCC
47028 CTTTCT CTTTCT CTTTCT CTTTCT CTTTCT CT
1 CTTTCT CTTTCT CTTTCT CTTTCT CTTTCT CT
47060 CTCCTCTATC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (6 bp):
CTTTCT
Found at i:54283 original size:25 final size:26
Alignment explanation
Indices: 54234--54283 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 26
54224 GATTGAATTT
*
54234 AAATAATAATGTAAATATTACAAAAC
1 AAATAATAATGTAAATATTAAAAAAC
* *
54260 AAATACTAAT-TAAATTTTAAAAAA
1 AAATAATAATGTAAATATTAAAAAA
54284 ACTAAACTTG
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
25 12 0.57
26 9 0.43
ACGTcount: A:0.62, C:0.06, G:0.02, T:0.30
Consensus pattern (26 bp):
AAATAATAATGTAAATATTAAAAAAC
Found at i:55551 original size:2 final size:2
Alignment explanation
Indices: 55541--55575 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
55531 TTTATAGAAC
55541 AT AT A- AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
55576 TTATCCATAT
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Done.