Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01015191.1 Kokia drynarioides strain JFW-HI SEQ_130235, 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: 85681
ACGTcount: A:0.34, C:0.16, G:0.15, T:0.35
Warning! 211 characters in sequence are not A, C, G, or T
Found at i:203 original size:21 final size:20
Alignment explanation
Indices: 179--223 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 20
169 TTCTTCCCCT
179 TCTTCTTTATTTCTTTCTTTC
1 TCTTCTTTATTTCTTT-TTTC
* *
200 TCTTTTTTCTTTCTTTTTTC
1 TCTTCTTTATTTCTTTTTTC
220 -CTTC
1 TCTTC
224 AATATTCGTT
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
19 3 0.14
20 4 0.19
21 14 0.67
ACGTcount: A:0.02, C:0.24, G:0.00, T:0.73
Consensus pattern (20 bp):
TCTTCTTTATTTCTTTTTTC
Found at i:210 original size:17 final size:18
Alignment explanation
Indices: 182--215 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
172 TTCCCCTTCT
182 TCTTTATTTCTTTCTTTC
1 TCTTTATTTCTTTCTTTC
200 TCTTT-TTTCTTTCTTT
1 TCTTTATTTCTTTCTTT
216 TTTCCTTCAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 11 0.69
18 5 0.31
ACGTcount: A:0.03, C:0.21, G:0.00, T:0.76
Consensus pattern (18 bp):
TCTTTATTTCTTTCTTTC
Found at i:1071 original size:31 final size:30
Alignment explanation
Indices: 1034--1094 Score: 88
Period size: 31 Copynumber: 2.0 Consensus size: 30
1024 AAATGTTATG
1034 TTTTAGTCACTTA-CGTTAACATGTTGTAACA
1 TTTTAGTCACTTACCGTTAACA-G-TGTAACA
1065 TTTTAGTCACTTAGCCGTTAACAGTGTAAC
1 TTTTAGTCACTTA-CCGTTAACAGTGTAAC
1095 GGTAAGCTGA
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
31 19 0.68
32 1 0.04
33 8 0.29
ACGTcount: A:0.28, C:0.18, G:0.15, T:0.39
Consensus pattern (30 bp):
TTTTAGTCACTTACCGTTAACAGTGTAACA
Found at i:8553 original size:21 final size:21
Alignment explanation
Indices: 8529--8568 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
8519 GAATCTATAA
*
8529 TAAAATTATTCAAAAAAATAT
1 TAAAAATATTCAAAAAAATAT
* *
8550 TAAAAATATTTAACAAAAT
1 TAAAAATATTCAAAAAAAT
8569 GATTGATTGA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.62, C:0.05, G:0.00, T:0.33
Consensus pattern (21 bp):
TAAAAATATTCAAAAAAATAT
Found at i:11720 original size:29 final size:30
Alignment explanation
Indices: 11685--11750 Score: 98
Period size: 30 Copynumber: 2.2 Consensus size: 30
11675 TGGGTTAACG
11685 TGCAATTGTATACAT-AAACTTTGATTTGA
1 TGCAATTGTATACATAAAACTTTGATTTGA
* *
11714 TGCAATTTTATACATAAAATTTTGATTTGA
1 TGCAATTGTATACATAAAACTTTGATTTGA
*
11744 TCCAATT
1 TGCAATT
11751 CTTGTAAATT
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
29 14 0.42
30 19 0.58
ACGTcount: A:0.35, C:0.11, G:0.11, T:0.44
Consensus pattern (30 bp):
TGCAATTGTATACATAAAACTTTGATTTGA
Found at i:11994 original size:29 final size:30
Alignment explanation
Indices: 11945--12005 Score: 79
Period size: 29 Copynumber: 2.0 Consensus size: 30
11935 TAACTACACC
* *
11945 AAATTAAAATTCATATATATAATTTTACAAT
1 AAATTAAAATT-ATATATATAATCTTAAAAT
*
11976 AAATTAAAATT-TATGTATAATCTTAAAAT
1 AAATTAAAATTATATATATAATCTTAAAAT
12005 A
1 A
12006 TATTTTTTTC
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
29 16 0.59
31 11 0.41
ACGTcount: A:0.52, C:0.05, G:0.02, T:0.41
Consensus pattern (30 bp):
AAATTAAAATTATATATATAATCTTAAAAT
Found at i:13221 original size:23 final size:26
Alignment explanation
Indices: 13186--13238 Score: 67
Period size: 25 Copynumber: 2.2 Consensus size: 26
13176 CAATTCATCC
*
13186 AATTTAATTAAATA-AAT-TATTAAA
1 AATTTAATAAAATAGAATATATTAAA
*
13210 AATTT-ATAAAATAGAGTATATTAAA
1 AATTTAATAAAATAGAATATATTAAA
13235 AATT
1 AATT
13239 CAGTTTAATC
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
23 7 0.28
24 7 0.28
25 11 0.44
ACGTcount: A:0.57, C:0.00, G:0.04, T:0.40
Consensus pattern (26 bp):
AATTTAATAAAATAGAATATATTAAA
Found at i:14003 original size:18 final size:19
Alignment explanation
Indices: 13968--14002 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
13958 TACTGAACAA
13968 TTTTATCTTTTTTCTTTTC
1 TTTTATCTTTTTTCTTTTC
13987 TTTT-TCTTTTTT-TTTT
1 TTTTATCTTTTTTCTTTT
14003 TGCAAATTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 4 0.25
18 8 0.50
19 4 0.25
ACGTcount: A:0.03, C:0.11, G:0.00, T:0.86
Consensus pattern (19 bp):
TTTTATCTTTTTTCTTTTC
Found at i:19895 original size:31 final size:31
Alignment explanation
Indices: 19845--19929 Score: 102
Period size: 31 Copynumber: 2.8 Consensus size: 31
19835 ATAAAGACGT
*
19845 AACC-TTTC-AAAATGATCAAATAAGAGCCA
1 AACCTTTTCAAAAATGCTCAAATAAGAGCCA
* * *
19874 AATCTTTTCAAAAATGCTCAAATAAGGGTCA
1 AACCTTTTCAAAAATGCTCAAATAAGAGCCA
**
19905 AACCTTTTCAAAAGGGCTCAAATAA
1 AACCTTTTCAAAAATGCTCAAATAA
19930 TGACTTCTCA
Statistics
Matches: 47, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
29 3 0.06
30 4 0.09
31 40 0.85
ACGTcount: A:0.45, C:0.19, G:0.12, T:0.25
Consensus pattern (31 bp):
AACCTTTTCAAAAATGCTCAAATAAGAGCCA
Found at i:33879 original size:10 final size:10
Alignment explanation
Indices: 33864--33933 Score: 56
Period size: 9 Copynumber: 7.0 Consensus size: 10
33854 TCAAGAAAAT
*
33864 TTAAAAATTG
1 TTAAAAATTA
*
33874 TTAAAAAATCA
1 TT-AAAAATTA
*
33885 TTAAAAATATC
1 TTAAAAAT-TA
33896 TATAAAAATTA
1 T-TAAAAATTA
33907 TT-AAAA-TA
1 TTAAAAATTA
*
33915 TTTAAAATTA
1 TTAAAAATTA
33925 -TAAAAATTA
1 TTAAAAATTA
33934 AAATAACTGA
Statistics
Matches: 49, Mismatches: 6, Indels: 11
0.74 0.09 0.17
Matches are distributed among these distances:
8 4 0.08
9 16 0.33
10 11 0.22
11 11 0.22
12 7 0.14
ACGTcount: A:0.59, C:0.03, G:0.01, T:0.37
Consensus pattern (10 bp):
TTAAAAATTA
Found at i:37710 original size:4 final size:4
Alignment explanation
Indices: 37703--37727 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
37693 TAATGATACT
37703 ATAA ATAA ATAA ATAA ATAA ATAA A
1 ATAA ATAA ATAA ATAA ATAA ATAA A
37728 ATTAGTAGAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (4 bp):
ATAA
Found at i:40282 original size:18 final size:20
Alignment explanation
Indices: 40242--40292 Score: 70
Period size: 19 Copynumber: 2.6 Consensus size: 20
40232 AAAATAACAA
* *
40242 AAAATTTTAAAATAATTTTT
1 AAAATTTCAAAATAATTTAT
40262 AAAA-TTCAAAAT-ATTTAT
1 AAAATTTCAAAATAATTTAT
40280 AAAATTTCAAAAT
1 AAAATTTCAAAAT
40293 TTATATTTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
18 9 0.32
19 15 0.54
20 4 0.14
ACGTcount: A:0.55, C:0.04, G:0.00, T:0.41
Consensus pattern (20 bp):
AAAATTTCAAAATAATTTAT
Found at i:40318 original size:10 final size:10
Alignment explanation
Indices: 40303--40340 Score: 51
Period size: 10 Copynumber: 3.7 Consensus size: 10
40293 TTATATTTTT
40303 TAAAAAATTA
1 TAAAAAATTA
40313 TAAAAAATT-
1 TAAAAAATTA
40322 TAAAAAATATA
1 TAAAAAAT-TA
40333 TAATAAAA
1 TAA-AAAA
40341 GTTAAAATTT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
9 8 0.32
10 10 0.40
11 3 0.12
12 4 0.16
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (10 bp):
TAAAAAATTA
Found at i:40325 original size:19 final size:21
Alignment explanation
Indices: 40301--40347 Score: 71
Period size: 19 Copynumber: 2.3 Consensus size: 21
40291 ATTTATATTT
40301 TTTAAAAAAT-TATAA-AAAA
1 TTTAAAAAATATATAATAAAA
40320 TTTAAAAAATATATAATAAAA
1 TTTAAAAAATATATAATAAAA
*
40341 GTTAAAA
1 TTTAAAA
40348 TTTTAAAAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
19 10 0.40
20 5 0.20
21 10 0.40
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.32
Consensus pattern (21 bp):
TTTAAAAAATATATAATAAAA
Found at i:43082 original size:2 final size:2
Alignment explanation
Indices: 43077--43106 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
43067 AAAAAAAAAA
43077 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
43107 GATGTGTTAC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:48316 original size:19 final size:19
Alignment explanation
Indices: 48276--48321 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
48266 TTTCATATAT
* *
48276 ATATTTTTTTAATTTTCGA
1 ATATTTTTATAATTTTCAA
*
48295 ATATTTTTATAATTTTTAA
1 ATATTTTTATAATTTTCAA
48314 ATAATTTT
1 AT-ATTTT
48322 GGACTTGGAC
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
19 18 0.78
20 5 0.22
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.63
Consensus pattern (19 bp):
ATATTTTTATAATTTTCAA
Found at i:52262 original size:2 final size:2
Alignment explanation
Indices: 52255--52287 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
52245 CTAAAATGTA
52255 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
52288 ATAACATACC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:52843 original size:12 final size:13
Alignment explanation
Indices: 52822--52847 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
52812 AATTCATCAA
52822 TTTTCTTTTTTTT
1 TTTTCTTTTTTTT
52835 TTTTCTTTTTTTT
1 TTTTCTTTTTTTT
52848 AAATCTAAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.00, C:0.08, G:0.00, T:0.92
Consensus pattern (13 bp):
TTTTCTTTTTTTT
Found at i:57186 original size:2 final size:2
Alignment explanation
Indices: 57175--57203 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
57165 TATCAAATTG
57175 AT AT -T 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
57204 TTTACAACAA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:62402 original size:10 final size:10
Alignment explanation
Indices: 62389--62437 Score: 53
Period size: 10 Copynumber: 4.7 Consensus size: 10
62379 ATTAAGAAAT
62389 ATTTTTTATA
1 ATTTTTTATA
62399 ATTTTTTAATA
1 ATTTTTT-ATA
**
62410 ATTTTTGCTA
1 ATTTTTTATA
*
62420 ATTTTTAATA
1 ATTTTTTATA
62430 ATTGTTTT
1 ATT-TTTT
62438 TGAAATTTAA
Statistics
Matches: 32, Mismatches: 5, Indels: 3
0.80 0.12 0.08
Matches are distributed among these distances:
10 20 0.62
11 12 0.38
ACGTcount: A:0.29, C:0.02, G:0.04, T:0.65
Consensus pattern (10 bp):
ATTTTTTATA
Found at i:62414 original size:20 final size:20
Alignment explanation
Indices: 62389--62432 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 20
62379 ATTAAGAAAT
*
62389 ATTTTTTATAATTTTTTAATA
1 ATTTTTGATAA-TTTTTAATA
*
62410 ATTTTTGCTAATTTTTAATA
1 ATTTTTGATAATTTTTAATA
62430 ATT
1 ATT
62433 GTTTTTGAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 12 0.57
21 9 0.43
ACGTcount: A:0.32, C:0.02, G:0.02, T:0.64
Consensus pattern (20 bp):
ATTTTTGATAATTTTTAATA
Found at i:68190 original size:16 final size:16
Alignment explanation
Indices: 68169--68202 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
68159 TGCATCCTTG
68169 TGATTAATTCTATTCA
1 TGATTAATTCTATTCA
68185 TGATTAATTCTATTCA
1 TGATTAATTCTATTCA
68201 TG
1 TG
68203 TTTTATTATT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.29, C:0.12, G:0.09, T:0.50
Consensus pattern (16 bp):
TGATTAATTCTATTCA
Found at i:75227 original size:12 final size:12
Alignment explanation
Indices: 75210--75240 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
75200 AAATATACTT
75210 AAAAACATTAAA
1 AAAAACATTAAA
*
75222 ATAAACATTAAA
1 AAAAACATTAAA
75234 AAAAACA
1 AAAAACA
75241 AATTTAAAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.74, C:0.10, G:0.00, T:0.16
Consensus pattern (12 bp):
AAAAACATTAAA
Found at i:75468 original size:24 final size:24
Alignment explanation
Indices: 75420--75492 Score: 87
Period size: 24 Copynumber: 3.0 Consensus size: 24
75410 AAACAGAAGC
75420 AAAACTAACAAAAAT-G-ACAATAAAA
1 AAAAC-AACAAAAATAGTA-AA-AAAA
75445 AAAACAACAAAAATAGTAAAAAAA
1 AAAACAACAAAAATAGTAAAAAAA
* *
75469 AAAGCAACCAAAATAGTAAAAAAA
1 AAAACAACAAAAATAGTAAAAAAA
75493 TGGCAATATA
Statistics
Matches: 44, Mismatches: 2, Indels: 5
0.86 0.04 0.10
Matches are distributed among these distances:
24 35 0.80
25 8 0.18
26 1 0.02
ACGTcount: A:0.74, C:0.11, G:0.05, T:0.10
Consensus pattern (24 bp):
AAAACAACAAAAATAGTAAAAAAA
Found at i:75498 original size:23 final size:24
Alignment explanation
Indices: 75441--75492 Score: 88
Period size: 24 Copynumber: 2.2 Consensus size: 24
75431 AAATGACAAT
75441 AAAAAAAA-CAACAAAAATAGTAA
1 AAAAAAAAGCAACAAAAATAGTAA
*
75464 AAAAAAAAGCAACCAAAATAGTAA
1 AAAAAAAAGCAACAAAAATAGTAA
75488 AAAAA
1 AAAAA
75493 TGGCAATATA
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
23 8 0.30
24 19 0.70
ACGTcount: A:0.77, C:0.10, G:0.06, T:0.08
Consensus pattern (24 bp):
AAAAAAAAGCAACAAAAATAGTAA
Found at i:77292 original size:70 final size:71
Alignment explanation
Indices: 77191--77344 Score: 292
Period size: 70 Copynumber: 2.2 Consensus size: 71
77181 TCAAAACATC
77191 AAAATCAATTAATAAATGATTGAATTTTTTTTATCTCTCGATAACGTCAATTGTTTTATTACTAT
1 AAAATCAATTAATAAATGATTGAATTTTTTTTATCTCTCGATAACGTCAATTGTTTTATTACTAT
77256 AATATT
66 AATATT
77262 -AAATCAATTAATAAATGATTGAATTTTTTTTATCTCTCGATAACGTCAATTGTTTTATTACTAT
1 AAAATCAATTAATAAATGATTGAATTTTTTTTATCTCTCGATAACGTCAATTGTTTTATTACTAT
77326 AATATT
66 AATATT
*
77332 AAAATTAATTAAT
1 AAAATCAATTAAT
77345 TTAATCTTCT
Statistics
Matches: 81, Mismatches: 1, Indels: 2
0.96 0.01 0.02
Matches are distributed among these distances:
70 70 0.86
71 11 0.14
ACGTcount: A:0.38, C:0.09, G:0.06, T:0.46
Consensus pattern (71 bp):
AAAATCAATTAATAAATGATTGAATTTTTTTTATCTCTCGATAACGTCAATTGTTTTATTACTAT
AATATT
Found at i:78365 original size:6 final size:7
Alignment explanation
Indices: 78349--78374 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
78339 TTCCAAGTCA
78349 TTTTTCT
1 TTTTTCT
78356 TTTTTCT
1 TTTTTCT
78363 TTTTTCT
1 TTTTTCT
78370 TTTTT
1 TTTTT
78375 TAAATCCAAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (7 bp):
TTTTTCT
Done.