Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013013.1 Kokia drynarioides strain JFW-HI SEQ_128031, 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: 99654
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Warning! 57 characters in sequence are not A, C, G, or T
Found at i:5494 original size:19 final size:20
Alignment explanation
Indices: 5470--5509 Score: 64
Period size: 19 Copynumber: 2.0 Consensus size: 20
5460 AGATTAAACT
*
5470 TTAATTAATT-ATAATTAAC
1 TTAATTAATTAACAATTAAC
5489 TTAATTAATTAACAATTAAC
1 TTAATTAATTAACAATTAAC
5509 T
1 T
5510 AATGTTAACC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 10 0.53
20 9 0.47
ACGTcount: A:0.47, C:0.07, G:0.00, T:0.45
Consensus pattern (20 bp):
TTAATTAATTAACAATTAAC
Found at i:12479 original size:19 final size:20
Alignment explanation
Indices: 12455--12494 Score: 64
Period size: 19 Copynumber: 2.0 Consensus size: 20
12445 AGATTAAACT
*
12455 TTAATTAATT-ATAATTAAC
1 TTAATTAATTAACAATTAAC
12474 TTAATTAATTAACAATTAAC
1 TTAATTAATTAACAATTAAC
12494 T
1 T
12495 AATGTTAACC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 10 0.53
20 9 0.47
ACGTcount: A:0.47, C:0.07, G:0.00, T:0.45
Consensus pattern (20 bp):
TTAATTAATTAACAATTAAC
Found at i:26788 original size:21 final size:22
Alignment explanation
Indices: 26746--26785 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
26736 CAAACTAATG
26746 AAACAAGACTAAAAATACAACT
1 AAACAAGACTAAAAATACAACT
26768 AAACAA-ACTAAAAA-ACAA
1 AAACAAGACTAAAAATACAA
26786 ACTGGACCAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 4 0.22
21 8 0.44
22 6 0.33
ACGTcount: A:0.70, C:0.17, G:0.03, T:0.10
Consensus pattern (22 bp):
AAACAAGACTAAAAATACAACT
Found at i:33400 original size:20 final size:20
Alignment explanation
Indices: 33351--33403 Score: 72
Period size: 20 Copynumber: 2.7 Consensus size: 20
33341 TTTTTATAAA
*
33351 TATTTTGAA-TTTTGAAAGT
1 TATTTTGAATTTTTGAAAAT
**
33370 TATTTAAAATTTTTGAAAAT
1 TATTTTGAATTTTTGAAAAT
33390 TATTTTGAATTTTT
1 TATTTTGAATTTTT
33404 TTGTAATTTT
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
19 7 0.25
20 21 0.75
ACGTcount: A:0.34, C:0.00, G:0.09, T:0.57
Consensus pattern (20 bp):
TATTTTGAATTTTTGAAAAT
Found at i:35246 original size:30 final size:31
Alignment explanation
Indices: 35212--35278 Score: 93
Period size: 30 Copynumber: 2.2 Consensus size: 31
35202 GTTACATTTA
*
35212 ACAAAACAGTCACTCAA-CT-TTGAAAATGTG
1 ACAAAACAGTCACTAAAGCTATTGAAAA-GTG
*
35242 ACAAAACAGTCACTAAAGTTATTGAAAAGTG
1 ACAAAACAGTCACTAAAGCTATTGAAAAGTG
35273 ACAAAA
1 ACAAAA
35279 TAATCCTCTA
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
30 16 0.48
31 10 0.30
32 7 0.21
ACGTcount: A:0.49, C:0.16, G:0.13, T:0.21
Consensus pattern (31 bp):
ACAAAACAGTCACTAAAGCTATTGAAAAGTG
Found at i:41619 original size:2 final size:2
Alignment explanation
Indices: 41612--41654 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
41602 AGTAGAAACA
41612 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
41654 A
1 A
41655 AAAAAAACTC
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:41773 original size:22 final size:21
Alignment explanation
Indices: 41734--41774 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
41724 ATTAAATTAA
*
41734 AATAAAAATTTTAGTTTTTTC
1 AATAAAAATTTTACTTTTTTC
41755 AATAAAAATTTTAACTTTTT
1 AATAAAAATTTT-ACTTTTT
41775 AGAGCACTGT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 12 0.67
22 6 0.33
ACGTcount: A:0.41, C:0.05, G:0.02, T:0.51
Consensus pattern (21 bp):
AATAAAAATTTTACTTTTTTC
Found at i:42319 original size:30 final size:31
Alignment explanation
Indices: 42283--42373 Score: 148
Period size: 32 Copynumber: 2.9 Consensus size: 31
42273 GAAATTTCGA
*
42283 TTTTTTTTGAAACACATTCAAAGAATTGA-T
1 TTTTTTTTAAAACACATTCAAAGAATTGATT
*
42313 TTTTTTTAAAAACACATTCAAAGAATTGATTT
1 TTTTTTTTAAAACACATTCAAAGAATTGA-TT
42345 TTTTTTTTAAAACACATTCAAAGAATTGA
1 TTTTTTTTAAAACACATTCAAAGAATTGA
42374 CAATTTTTTT
Statistics
Matches: 56, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
30 27 0.48
32 29 0.52
ACGTcount: A:0.40, C:0.10, G:0.08, T:0.43
Consensus pattern (31 bp):
TTTTTTTTAAAACACATTCAAAGAATTGATT
Found at i:42381 original size:32 final size:30
Alignment explanation
Indices: 42282--42386 Score: 140
Period size: 32 Copynumber: 3.4 Consensus size: 30
42272 AGAAATTTCG
*
42282 ATTTTTTTTGAAACACATTCAAAGAATTG-
1 ATTTTTTTTAAAACACATTCAAAGAATTGA
42311 ATTTTTTTTAAAAACACATTCAAAGAATTGA
1 ATTTTTTTT-AAAACACATTCAAAGAATTGA
*
42342 TTTTTTTTTTTAAAACACATTCAAAGAATTGA
1 --ATTTTTTTTAAAACACATTCAAAGAATTGA
*
42374 CAATTTTTTTAAA
1 -ATTTTTTTTAAA
42387 GGAAGAATTG
Statistics
Matches: 67, Mismatches: 5, Indels: 6
0.86 0.06 0.08
Matches are distributed among these distances:
29 9 0.13
30 19 0.28
31 10 0.15
32 21 0.31
33 8 0.12
ACGTcount: A:0.40, C:0.10, G:0.07, T:0.44
Consensus pattern (30 bp):
ATTTTTTTTAAAACACATTCAAAGAATTGA
Found at i:48223 original size:4 final size:4
Alignment explanation
Indices: 48214--48248 Score: 52
Period size: 4 Copynumber: 8.2 Consensus size: 4
48204 TCTCATTATT
48214 ATAA ATAA ATAA TATAA ATAA ATAA ATAA TATAA A
1 ATAA ATAA ATAA -ATAA ATAA ATAA ATAA -ATAA A
48249 AGGCATTAGG
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
4 21 0.72
5 8 0.28
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (4 bp):
ATAA
Found at i:48231 original size:13 final size:13
Alignment explanation
Indices: 48213--48248 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
48203 TTCTCATTAT
48213 TATAAATAAATAA
1 TATAAATAAATAA
48226 TATAAATAAATAA
1 TATAAATAAATAA
48239 -ATAATATAAA
1 TATAA-ATAAA
48249 AGGCATTAGG
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
12 4 0.18
13 18 0.82
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (13 bp):
TATAAATAAATAA
Found at i:48236 original size:17 final size:17
Alignment explanation
Indices: 48214--48248 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
48204 TCTCATTATT
48214 ATAAATAAATAATATAA
1 ATAAATAAATAATATAA
48231 ATAAATAAATAATATAA
1 ATAAATAAATAATATAA
48248 A
1 A
48249 AGGCATTAGG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (17 bp):
ATAAATAAATAATATAA
Found at i:49215 original size:31 final size:32
Alignment explanation
Indices: 49172--49236 Score: 89
Period size: 31 Copynumber: 2.1 Consensus size: 32
49162 TTACTTTGAT
* *
49172 TTGATCAATTTTAG-TTCATGTAC-TTTTCAAA
1 TTGAGCAATTTTAGTTTC-TATACTTTTTCAAA
49203 TTGAGCAATTTTAGTTTCTATACTTTTTCAAA
1 TTGAGCAATTTTAGTTTCTATACTTTTTCAAA
49235 TT
1 TT
49237 TTTAAATTTT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
31 17 0.57
32 13 0.43
ACGTcount: A:0.28, C:0.12, G:0.09, T:0.51
Consensus pattern (32 bp):
TTGAGCAATTTTAGTTTCTATACTTTTTCAAA
Found at i:53247 original size:2 final size:2
Alignment explanation
Indices: 53242--53273 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
53232 TAAATTCATT
53242 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
53274 TATATATATA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:56925 original size:22 final size:22
Alignment explanation
Indices: 56900--56941 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
56890 ATAATTTAAA
*
56900 TAAAATTATTATGTATTTTTTT
1 TAAAATTATTATATATTTTTTT
*
56922 TAAAATTTTTATATATTTTT
1 TAAAATTATTATATATTTTT
56942 ATGAGATTAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.64
Consensus pattern (22 bp):
TAAAATTATTATATATTTTTTT
Found at i:59108 original size:34 final size:34
Alignment explanation
Indices: 59033--59109 Score: 81
Period size: 34 Copynumber: 2.2 Consensus size: 34
59023 TATTTGAAAT
59033 TGATGAATTTAAAATTAATAAAAATACATGAAATAA
1 TGAT-AATTTAAAATTAATAAAAATACA-GAAATAA
59069 T-ATAATTTAAAATTGAAATAAAAAATA-A-AAA-AA
1 TGATAATTTAAAATT--AAT-AAAAATACAGAAATAA
59102 TGATAATT
1 TGATAATT
59110 ATACATGATA
Statistics
Matches: 37, Mismatches: 0, Indels: 10
0.79 0.00 0.21
Matches are distributed among these distances:
33 3 0.08
34 20 0.54
35 2 0.05
36 5 0.14
37 7 0.19
ACGTcount: A:0.61, C:0.01, G:0.06, T:0.31
Consensus pattern (34 bp):
TGATAATTTAAAATTAATAAAAATACAGAAATAA
Found at i:74152 original size:21 final size:22
Alignment explanation
Indices: 74123--74174 Score: 61
Period size: 21 Copynumber: 2.4 Consensus size: 22
74113 TTGTTTTTAA
* *
74123 TTTTCTTTTCTATTTT-TGTTC
1 TTTTTTTTTCTATTTTCTCTTC
* *
74144 TTTTTTTTTCTCTTTTCTCTTT
1 TTTTTTTTTCTATTTTCTCTTC
74166 TTTTTTTTT
1 TTTTTTTTT
74175 TCCTCTTCCT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
21 14 0.54
22 12 0.46
ACGTcount: A:0.02, C:0.13, G:0.02, T:0.83
Consensus pattern (22 bp):
TTTTTTTTTCTATTTTCTCTTC
Found at i:74180 original size:17 final size:19
Alignment explanation
Indices: 74142--74181 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
74132 CTATTTTTGT
*
74142 TCTTTTTTTTTCTCTTTTC
1 TCTTTTTTTTTCTCTTTCC
74161 TCTTTTTTTTT-T-TTTCC
1 TCTTTTTTTTTCTCTTTCC
74178 TCTT
1 TCTT
74182 CCTCCTCTTC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 8 0.40
18 1 0.05
19 11 0.55
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (19 bp):
TCTTTTTTTTTCTCTTTCC
Found at i:74532 original size:27 final size:28
Alignment explanation
Indices: 74473--74534 Score: 74
Period size: 27 Copynumber: 2.3 Consensus size: 28
74463 TATTATTGTT
* * *
74473 ATTAAATTTTAATAAGATTATTAAGATA
1 ATTAAATTTTAATAAAAATAATAAGATA
74501 ATTAAA-TTTAATAAAAATAATAA-ATA
1 ATTAAATTTTAATAAAAATAATAAGATA
*
74527 ATTTAATT
1 ATTAAATT
74535 ATATTTTAAC
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
26 8 0.28
27 15 0.52
28 6 0.21
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.42
Consensus pattern (28 bp):
ATTAAATTTTAATAAAAATAATAAGATA
Found at i:85335 original size:23 final size:23
Alignment explanation
Indices: 85292--85337 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
85282 AATATGTATT
* *
85292 TTTATAAAAAATATTATTTTTTA
1 TTTATAAAAAATATGAATTTTTA
85315 TTTAT-AAAAATAATGAATTTTTA
1 TTTATAAAAAAT-ATGAATTTTTA
85338 GTAATTTTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 6 0.30
23 14 0.70
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (23 bp):
TTTATAAAAAATATGAATTTTTA
Found at i:86433 original size:31 final size:31
Alignment explanation
Indices: 86398--86484 Score: 115
Period size: 31 Copynumber: 2.9 Consensus size: 31
86388 ATGATTAAAT
* *
86398 CACAATTAAAGTTTCAAGTATACATTTGAAC
1 CACAATTAAAGTTTCATGTATACAATTGAAC
* * *
86429 CACAATTAAAATTTCATGTATATAATTGCAC
1 CACAATTAAAGTTTCATGTATACAATTGAAC
86460 CA-AATTAAAG-TTCATGTATACAATT
1 CACAATTAAAGTTTCATGTATACAATT
86485 ACACATTAAA
Statistics
Matches: 49, Mismatches: 7, Indels: 2
0.84 0.12 0.03
Matches are distributed among these distances:
29 14 0.29
30 7 0.14
31 28 0.57
ACGTcount: A:0.43, C:0.15, G:0.08, T:0.34
Consensus pattern (31 bp):
CACAATTAAAGTTTCATGTATACAATTGAAC
Found at i:87342 original size:26 final size:27
Alignment explanation
Indices: 87294--87345 Score: 79
Period size: 26 Copynumber: 2.0 Consensus size: 27
87284 AAATAACTAA
87294 AATTTTAAAATAATCTATTTTAAATAC
1 AATTTTAAAATAATCTATTTTAAATAC
* *
87321 AATTTTAATA-AATGTATTTTAAATA
1 AATTTTAAAATAATCTATTTTAAATA
87346 AATAAAAAAG
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 14 0.61
27 9 0.39
ACGTcount: A:0.48, C:0.04, G:0.02, T:0.46
Consensus pattern (27 bp):
AATTTTAAAATAATCTATTTTAAATAC
Found at i:88809 original size:2 final size:2
Alignment explanation
Indices: 88802--88833 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
88792 ATTTTCCACT
88802 TC TC 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 TC TC
88834 CCCTTTGTTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:99594 original size:4 final size:4
Alignment explanation
Indices: 99585--99637 Score: 61
Period size: 4 Copynumber: 12.8 Consensus size: 4
99575 AAATAAACGG
* * *
99585 GAAA GAAA GAAA GGAAA GAAA GAAA GAAA GGAA GAAG GAGAG GAAA GAAA
1 GAAA GAAA GAAA -GAAA GAAA GAAA GAAA GAAA GAAA GA-AA GAAA GAAA
99635 GAA
1 GAA
99638 GAAGGAGAGG
Statistics
Matches: 43, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
4 35 0.81
5 8 0.19
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (4 bp):
GAAA
Found at i:99607 original size:17 final size:17
Alignment explanation
Indices: 99585--99617 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
99575 AAATAAACGG
99585 GAAAGAAAGAAAGGAAA
1 GAAAGAAAGAAAGGAAA
99602 GAAAGAAAGAAAGGAA
1 GAAAGAAAGAAAGGAA
99618 GAAGGAGAGG
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:0.70, C:0.00, G:0.30, T:0.00
Consensus pattern (17 bp):
GAAAGAAAGAAAGGAAA
Found at i:99640 original size:20 final size:20
Alignment explanation
Indices: 99584--99650 Score: 82
Period size: 20 Copynumber: 3.2 Consensus size: 20
99574 CAAATAAACG
*
99584 GGAAAGAAAGAAAGGAAAGA-A
1 GGAAAGAAAG-AA-GAAGGAGA
*
99605 AGAAAGAAAGGAAGAAGGAGA
1 GGAAAGAAA-GAAGAAGGAGA
99626 GGAAAGAAAGAAGAAGGAGA
1 GGAAAGAAAGAAGAAGGAGA
99646 GGAAA
1 GGAAA
99651 ATAA
Statistics
Matches: 41, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
20 21 0.51
21 19 0.46
22 1 0.02
ACGTcount: A:0.63, C:0.00, G:0.37, T:0.00
Consensus pattern (20 bp):
GGAAAGAAAGAAGAAGGAGA
Done.