Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013264.1 Kokia drynarioides strain JFW-HI SEQ_128285, 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: 94570
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
Warning! 95 characters in sequence are not A, C, G, or T
Found at i:5471 original size:18 final size:16
Alignment explanation
Indices: 5440--5480 Score: 57
Period size: 16 Copynumber: 2.5 Consensus size: 16
5430 AAATTTATTT
5440 TTAAAAATTAAAATTA
1 TTAAAAATTAAAATTA
5456 TTAAAAAGTATAAAATTA
1 TTAAAAA-T-TAAAATTA
5474 -TAAAAAT
1 TTAAAAAT
5481 ATTTTTCAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
16 8 0.35
17 7 0.30
18 8 0.35
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.34
Consensus pattern (16 bp):
TTAAAAATTAAAATTA
Found at i:5471 original size:47 final size:45
Alignment explanation
Indices: 5400--5492 Score: 116
Period size: 47 Copynumber: 2.0 Consensus size: 45
5390 ATTAATTTTT
* *
5400 TTAAAATTTTAAAAATTCAAAAAATGTATAAAATTTATTTTTAAAAA
1 TTAAAATTTTAAAAAGTCAAAAAAT-TATAAAA-ATATTTTTAAAAA
* *
5447 TTAAAATTATTAAAAAGT-ATAAAATTATAAAAATATTTTTCAAAA
1 TTAAAATT-TTAAAAAGTCAAAAAATTATAAAAATATTTTTAAAAA
5492 T
1 T
5493 ATATTTTTTA
Statistics
Matches: 41, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
45 12 0.29
46 7 0.17
47 14 0.34
48 8 0.20
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.40
Consensus pattern (45 bp):
TTAAAATTTTAAAAAGTCAAAAAATTATAAAAATATTTTTAAAAA
Found at i:8435 original size:55 final size:55
Alignment explanation
Indices: 8369--8475 Score: 196
Period size: 55 Copynumber: 1.9 Consensus size: 55
8359 ATACTTTGAC
*
8369 TATAAACTATTAAAATGGTGAAATTGTATTTTTACTATTGTAAAAATTATAAAGA
1 TATAAACTATTAAAATGGTGAAATTGCATTTTTACTATTGTAAAAATTATAAAGA
*
8424 TATAAACTATTAAAATGGTGAAATTGCATTTTTATTATTGTAAAAATTATAA
1 TATAAACTATTAAAATGGTGAAATTGCATTTTTACTATTGTAAAAATTATAA
8476 TTTAATTTCG
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
55 50 1.00
ACGTcount: A:0.45, C:0.04, G:0.10, T:0.41
Consensus pattern (55 bp):
TATAAACTATTAAAATGGTGAAATTGCATTTTTACTATTGTAAAAATTATAAAGA
Found at i:17308 original size:20 final size:20
Alignment explanation
Indices: 17269--17320 Score: 59
Period size: 20 Copynumber: 2.6 Consensus size: 20
17259 GTATTTCTAT
* **
17269 ATAAAAAAAATCAATTTTAA
1 ATAAAAAAAATAAAGATTAA
17289 ATAAAAAAAATAAAGATTAA
1 ATAAAAAAAATAAAGATTAA
* *
17309 ATTAACAAAATA
1 ATAAAAAAAATA
17321 TATATATATA
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.69, C:0.04, G:0.02, T:0.25
Consensus pattern (20 bp):
ATAAAAAAAATAAAGATTAA
Found at i:25020 original size:7 final size:6
Alignment explanation
Indices: 24999--25040 Score: 66
Period size: 6 Copynumber: 6.7 Consensus size: 6
24989 ACCGTTCTAG
24999 TTTTCT TTTTCT TTTTCTT TTTTCT TTTTCTT TTTTCT TTTT
1 TTTTCT TTTTCT TTTTC-T TTTTCT TTTTC-T TTTTCT TTTT
25041 AATTTCCAAT
Statistics
Matches: 34, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
6 22 0.65
7 12 0.35
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (6 bp):
TTTTCT
Found at i:25022 original size:13 final size:13
Alignment explanation
Indices: 24999--25040 Score: 77
Period size: 13 Copynumber: 3.3 Consensus size: 13
24989 ACCGTTCTAG
24999 TTTTC-TTTTTCT
1 TTTTCTTTTTTCT
25011 TTTTCTTTTTTCT
1 TTTTCTTTTTTCT
25024 TTTTCTTTTTTCT
1 TTTTCTTTTTTCT
25037 TTTT
1 TTTT
25041 AATTTCCAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
12 5 0.17
13 24 0.83
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (13 bp):
TTTTCTTTTTTCT
Found at i:30341 original size:23 final size:21
Alignment explanation
Indices: 30310--30435 Score: 81
Period size: 23 Copynumber: 5.5 Consensus size: 21
30300 CACTAGCGCA
*
30310 CTCTTTGTTTAGCACGTCTCGTG
1 CTCTCTGTTTAGCACGT-T-GTG
30333 CTCTCTGTTATTAGCACTGTGTGTG
1 CTCTCTG-T-TTAGCAC-GT-TGTG
* * *
30358 CTCTTTGATTAGCACTTTGTGTG
1 CTCTCTGTTTAGCAC-GT-TGTG
* * *
30381 CTCTCTGATTAGTACTTTGTG
1 CTCTCTGTTTAGCACGTTGTG
*
30402 TACTCTCTGTTTAGCATTGTTGTG
1 --CTCTCTGTTTAGCA-CGTTGTG
30426 CTCTCTGTTT
1 CTCTCTGTTT
30436 CCCAATACCT
Statistics
Matches: 86, Mismatches: 11, Indels: 13
0.78 0.10 0.12
Matches are distributed among these distances:
21 4 0.05
22 12 0.14
23 45 0.52
24 6 0.07
25 16 0.19
26 3 0.03
ACGTcount: A:0.11, C:0.21, G:0.21, T:0.48
Consensus pattern (21 bp):
CTCTCTGTTTAGCACGTTGTG
Found at i:30416 original size:46 final size:46
Alignment explanation
Indices: 30330--30433 Score: 122
Period size: 46 Copynumber: 2.2 Consensus size: 46
30320 AGCACGTCTC
* *
30330 GTGCTCTCTGTTATTAGCACTGTGTGTGCTCTTTGATTAGCACTT-TGT
1 GTGCTCTCTG-TATTAGCACTGTGTGTACTCTCTGATTAGCA-TTGT-T
* * *
30378 GTGCTCTCTG-ATTAGTACTTTGTGTACTCTCTGTTTAGCATTGTT
1 GTGCTCTCTGTATTAGCACTGTGTGTACTCTCTGATTAGCATTGTT
30423 GTGCTCTCTGT
1 GTGCTCTCTGT
30434 TTCCCAATAC
Statistics
Matches: 49, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
45 13 0.27
46 26 0.53
48 10 0.20
ACGTcount: A:0.12, C:0.19, G:0.22, T:0.47
Consensus pattern (46 bp):
GTGCTCTCTGTATTAGCACTGTGTGTACTCTCTGATTAGCATTGTT
Found at i:35686 original size:17 final size:18
Alignment explanation
Indices: 35644--35687 Score: 54
Period size: 17 Copynumber: 2.4 Consensus size: 18
35634 TATCATTAAT
35644 AATTCAATTTTAATATAAA
1 AATTCAA-TTTAATATAAA
* *
35663 TATTCAATTTATTA-AAA
1 AATTCAATTTAATATAAA
35680 AATTCAAT
1 AATTCAAT
35688 ACTATAAATA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
17 10 0.45
18 6 0.27
19 6 0.27
ACGTcount: A:0.50, C:0.07, G:0.00, T:0.43
Consensus pattern (18 bp):
AATTCAATTTAATATAAA
Found at i:36324 original size:22 final size:21
Alignment explanation
Indices: 36288--36347 Score: 93
Period size: 22 Copynumber: 2.8 Consensus size: 21
36278 TATATTGTTG
*
36288 TTTTGGTGTTTTTTTTTACTA
1 TTTTGGTGTTGTTTTTTACTA
*
36309 TTTTGATTGTTGTTTTTTACTA
1 TTTTG-GTGTTGTTTTTTACTA
36331 TTTTGGTGTTGTTTTTT
1 TTTTGGTGTTGTTTTTT
36348 TTGTTATTTT
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
21 16 0.46
22 19 0.54
ACGTcount: A:0.08, C:0.03, G:0.17, T:0.72
Consensus pattern (21 bp):
TTTTGGTGTTGTTTTTTACTA
Found at i:36342 original size:24 final size:23
Alignment explanation
Indices: 36288--36369 Score: 82
Period size: 24 Copynumber: 3.7 Consensus size: 23
36278 TATATTGTTG
36288 TTTTGGTG-T-TTTTTTTTACTA
1 TTTTGGTGTTGTTTTTTTTACTA
*
36309 TTTT-G-ATTGTTGTTTTTTACTA
1 TTTTGGTGTTGTT-TTTTTTACTA
**
36331 TTTTGGTGTTGTTTTTTTTGTTA
1 TTTTGGTGTTGTTTTTTTTACTA
*
36354 TTTTTGCTGTTGTTTT
1 -TTTTGGTGTTGTTTT
36370 GATTGTTATT
Statistics
Matches: 50, Mismatches: 5, Indels: 9
0.78 0.08 0.14
Matches are distributed among these distances:
20 2 0.04
21 6 0.12
22 14 0.28
23 9 0.18
24 19 0.38
ACGTcount: A:0.07, C:0.04, G:0.17, T:0.72
Consensus pattern (23 bp):
TTTTGGTGTTGTTTTTTTTACTA
Found at i:36352 original size:12 final size:12
Alignment explanation
Indices: 36337--36388 Score: 50
Period size: 12 Copynumber: 4.3 Consensus size: 12
36327 ACTATTTTGG
*
36337 TGTTGTTTTTTT
1 TGTTATTTTTTT
**
36349 TGTTATTTTTGC
1 TGTTATTTTTTT
* **
36361 TGTTGTTTTGAT
1 TGTTATTTTTTT
36373 TGTTATTTTTTT
1 TGTTATTTTTTT
36385 TGTT
1 TGTT
36389 CGAATGTTAT
Statistics
Matches: 30, Mismatches: 10, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
12 30 1.00
ACGTcount: A:0.06, C:0.02, G:0.17, T:0.75
Consensus pattern (12 bp):
TGTTATTTTTTT
Found at i:36388 original size:24 final size:24
Alignment explanation
Indices: 36331--36382 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
36321 TTTTTTACTA
* **
36331 TTTTGGTGTTGTTTTTTTTGTTAT
1 TTTTGCTGTTGTTTTGATTGTTAT
36355 TTTTGCTGTTGTTTTGATTGTTAT
1 TTTTGCTGTTGTTTTGATTGTTAT
36379 TTTT
1 TTTT
36383 TTTGTTCGAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.06, C:0.02, G:0.19, T:0.73
Consensus pattern (24 bp):
TTTTGCTGTTGTTTTGATTGTTAT
Found at i:41005 original size:6 final size:6
Alignment explanation
Indices: 40997--41026 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
40987 AAGTGGGGAT
*
40997 GGAGAT GGAGAC GGAGAC GGAGAC GGAGAC
1 GGAGAC GGAGAC GGAGAC GGAGAC GGAGAC
41027 CCAGAAATCT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.33, C:0.13, G:0.50, T:0.03
Consensus pattern (6 bp):
GGAGAC
Found at i:43869 original size:19 final size:19
Alignment explanation
Indices: 43847--43884 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
43837 AATTGCCGTC
*
43847 ATTCATCGTAATTAAATTT
1 ATTCATCGTAATCAAATTT
43866 ATTCATCGTAATCAAATTT
1 ATTCATCGTAATCAAATTT
43885 GTTATTATCT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.37, C:0.13, G:0.05, T:0.45
Consensus pattern (19 bp):
ATTCATCGTAATCAAATTT
Found at i:44088 original size:18 final size:18
Alignment explanation
Indices: 44053--44097 Score: 51
Period size: 17 Copynumber: 2.6 Consensus size: 18
44043 AATTCAATTT
44053 TAATATAAATATTCAATA
1 TAATATAAATATTCAATA
*
44071 TAAT-TAAATAATT-TA-A
1 TAATATAAAT-ATTCAATA
44087 TAATATAAATA
1 TAATATAAATA
44098 GTAAAAAAAC
Statistics
Matches: 24, Mismatches: 1, Indels: 6
0.77 0.03 0.19
Matches are distributed among these distances:
16 6 0.25
17 11 0.46
18 7 0.29
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (18 bp):
TAATATAAATATTCAATA
Found at i:44878 original size:17 final size:17
Alignment explanation
Indices: 44856--44901 Score: 58
Period size: 17 Copynumber: 2.7 Consensus size: 17
44846 TTTTTAAAAA
44856 AATATTTATATTATTTT
1 AATATTTATATTATTTT
*
44873 AATATTTA-ATAATTTT
1 AATATTTATATTATTTT
*
44889 ATATATTTTTATT
1 A-ATATTTATATT
44902 TATTAAAATT
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
16 8 0.33
17 14 0.58
18 2 0.08
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (17 bp):
AATATTTATATTATTTT
Found at i:44895 original size:25 final size:25
Alignment explanation
Indices: 44854--44919 Score: 71
Period size: 25 Copynumber: 2.6 Consensus size: 25
44844 AATTTTTAAA
44854 AAAATATTTATATTATTTTAATAT-TT
1 AAAAT-TTTATA-TATTTTAATATATT
* *
44880 AATAATTTTATATATTTTTATTTATT
1 AA-AATTTTATATATTTTAATATATT
*
44906 AAAATTTTACATAT
1 AAAATTTTATATAT
44920 GATTATCTTA
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
25 20 0.57
26 12 0.34
27 3 0.09
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.58
Consensus pattern (25 bp):
AAAATTTTATATATTTTAATATATT
Found at i:48261 original size:11 final size:11
Alignment explanation
Indices: 48245--48271 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
48235 ATGATTCCTT
48245 AAAAAAGAAAA
1 AAAAAAGAAAA
48256 AAAAAAGAAAA
1 AAAAAAGAAAA
48267 AAAAA
1 AAAAA
48272 CTGTTGCAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.93, C:0.00, G:0.07, T:0.00
Consensus pattern (11 bp):
AAAAAAGAAAA
Found at i:51541 original size:17 final size:18
Alignment explanation
Indices: 51509--51547 Score: 62
Period size: 17 Copynumber: 2.2 Consensus size: 18
51499 CAAAATCTTA
*
51509 TTTATTAATCATATATTT
1 TTTATAAATCATATATTT
51527 TTTATAAAT-ATATATTT
1 TTTATAAATCATATATTT
51544 TTTA
1 TTTA
51548 CATAATTCTA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
17 12 0.60
18 8 0.40
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.62
Consensus pattern (18 bp):
TTTATAAATCATATATTT
Found at i:66433 original size:16 final size:16
Alignment explanation
Indices: 66412--66444 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
66402 AGTATTTTTG
66412 TAAT-AATTATTAATTT
1 TAATAAATTA-TAATTT
66428 TAATAAATTATAATTT
1 TAATAAATTATAATTT
66444 T
1 T
66445 TTATAGTTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 11 0.69
17 5 0.31
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (16 bp):
TAATAAATTATAATTT
Found at i:73092 original size:81 final size:81
Alignment explanation
Indices: 72957--73123 Score: 307
Period size: 81 Copynumber: 2.1 Consensus size: 81
72947 TATCCCCATA
*
72957 AGTTTGTGTGACTGAAAGCAGCGCCACATTATTACTTTTTTATTGTCGATTTATTCAATAAAGGA
1 AGTTTGTGTGACTGAAAGCAGCGCCACATTATTACTTTTTTATTGTCAATTTATTCAATAAAGGA
*
73022 GTTAAATTCTCTGTAT
66 ATTAAATTCTCTGTAT
*
73038 AGTTTGTGTGATTGAAAGCAGCGCCACATTATTACTTTTTTATTGTCAATTTATTCAATAAAGGA
1 AGTTTGTGTGACTGAAAGCAGCGCCACATTATTACTTTTTTATTGTCAATTTATTCAATAAAGGA
73103 ATTAAATTCTCTGTAT
66 ATTAAATTCTCTGTAT
73119 AGTTT
1 AGTTT
73124 ACTCCGCCCT
Statistics
Matches: 83, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
81 83 1.00
ACGTcount: A:0.29, C:0.13, G:0.16, T:0.42
Consensus pattern (81 bp):
AGTTTGTGTGACTGAAAGCAGCGCCACATTATTACTTTTTTATTGTCAATTTATTCAATAAAGGA
ATTAAATTCTCTGTAT
Found at i:89752 original size:24 final size:24
Alignment explanation
Indices: 89724--89782 Score: 82
Period size: 24 Copynumber: 2.5 Consensus size: 24
89714 TAGATTAATA
*
89724 AGAGTTTGACTCAAACAAATAAAC
1 AGAGTTTAACTCAAACAAATAAAC
* * *
89748 AGAGTTTAATTGAAACAAATAAAT
1 AGAGTTTAACTCAAACAAATAAAC
89772 AGAGTTTAACT
1 AGAGTTTAACT
89783 AAAAGATTAT
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.49, C:0.10, G:0.14, T:0.27
Consensus pattern (24 bp):
AGAGTTTAACTCAAACAAATAAAC
Found at i:90488 original size:2 final size:2
Alignment explanation
Indices: 90481--90506 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
90471 ACTTTCACTC
90481 GT GT GT GT GT GT GT GT GT GT GT GT GT
1 GT GT GT GT GT GT GT GT GT GT GT GT GT
90507 ATATATATAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
GT
Done.