Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01001964.1 Kokia drynarioides strain JFW-HI SEQ_113801, 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: 31001
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Found at i:11237 original size:73 final size:73
Alignment explanation
Indices: 11118--11265 Score: 251
Period size: 73 Copynumber: 2.0 Consensus size: 73
11108 GGAAGAGACA
* * *
11118 TACTTTCATTCGAGGATGTAAAGGGTCATTTTTTGAGTAAAGACAAGTTCAACAATGAGTTTGGT
1 TACTTTCATTCGAGGATGTAAAGGGTCATTTGTTGAGCAAAGACAAGTTCAACAAAGAGTTTGGT
11183 TCTAATAG
66 TCTAATAG
* *
11191 TACTTTCATTCGAGGATGTGAAGGGTCATTTGTTGAGCAAATACAAGTTCAACAAAGAGTTTGGT
1 TACTTTCATTCGAGGATGTAAAGGGTCATTTGTTGAGCAAAGACAAGTTCAACAAAGAGTTTGGT
11256 TCTAATAG
66 TCTAATAG
11264 TA
1 TA
11266 AGGTAGATAA
Statistics
Matches: 70, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
73 70 1.00
ACGTcount: A:0.32, C:0.11, G:0.22, T:0.34
Consensus pattern (73 bp):
TACTTTCATTCGAGGATGTAAAGGGTCATTTGTTGAGCAAAGACAAGTTCAACAAAGAGTTTGGT
TCTAATAG
Found at i:12255 original size:23 final size:24
Alignment explanation
Indices: 12208--12257 Score: 75
Period size: 24 Copynumber: 2.1 Consensus size: 24
12198 AAAAATAATC
* *
12208 TTTCAGTTAAGCTCTATTTATTTA
1 TTTCAATTAAACTCTATTTATTTA
12232 TTTCAATTAAACTCTA-TTATTTA
1 TTTCAATTAAACTCTATTTATTTA
12255 TTT
1 TTT
12258 GAGTCAAACT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
23 10 0.42
24 14 0.58
ACGTcount: A:0.28, C:0.12, G:0.04, T:0.56
Consensus pattern (24 bp):
TTTCAATTAAACTCTATTTATTTA
Found at i:12266 original size:23 final size:23
Alignment explanation
Indices: 12219--12274 Score: 67
Period size: 23 Copynumber: 2.3 Consensus size: 23
12209 TTCAGTTAAG
*
12219 CTCTATTTATTTATTTCAATTAAA
1 CTCTA-TTATTTATTTCAATCAAA
* *
12243 CTCTATTATTTATTTGAGTCAAA
1 CTCTATTATTTATTTCAATCAAA
12266 CTCTTATTA
1 CTC-TATTA
12275 CTCTATATTA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
23 18 0.64
24 10 0.36
ACGTcount: A:0.30, C:0.14, G:0.04, T:0.52
Consensus pattern (23 bp):
CTCTATTATTTATTTCAATCAAA
Found at i:18172 original size:10 final size:10
Alignment explanation
Indices: 18126--18250 Score: 69
Period size: 10 Copynumber: 12.5 Consensus size: 10
18116 TTGTAAAAAA
*
18126 ATTAAATATT
1 ATTAAAAATT
*
18136 GTTAAAAA-T
1 ATTAAAAATT
*
18145 ATTTTAAAATT
1 A-TTAAAAATT
*
18156 -GTAAAAAGTT
1 ATTAAAAA-TT
18166 ATTAAAAATT
1 ATTAAAAATT
18176 A-TAAAACATT
1 ATTAAAA-ATT
* *
18186 ATTTAAAGTT
1 ATTAAAAATT
*
18196 TTTAAAAATT
1 ATTAAAAATT
*
18206 AATAAAAATT
1 ATTAAAAATT
* *
18216 -GTGAAAATT
1 ATTAAAAATT
18225 ATTTAAAAATT
1 A-TTAAAAATT
* * *
18236 GTAAAAAATA
1 ATTAAAAATT
18246 ATTAA
1 ATTAA
18251 TCGGCAATTT
Statistics
Matches: 84, Mismatches: 23, Indels: 16
0.68 0.19 0.13
Matches are distributed among these distances:
9 18 0.21
10 48 0.57
11 18 0.21
ACGTcount: A:0.54, C:0.01, G:0.06, T:0.39
Consensus pattern (10 bp):
ATTAAAAATT
Found at i:18201 original size:60 final size:58
Alignment explanation
Indices: 18051--18242 Score: 198
Period size: 60 Copynumber: 3.3 Consensus size: 58
18041 ATTAAAAACA
* *
18051 TTAAAAATTGTAAAAATATTTAAATTATTAAAAA-A-TTTAAGAATTGTAAAAAGAATAT
1 TTAAAAATTGTAAAAATATTTAAATTTTTAAAAATATTTTAA-AATTGTAAAAAG-TTAT
* *
18109 TTTAAAATTGTAAAAA-AATTAAATATTGTTAAAAATATTTTAAAATTGTAAAAAGTTA-
1 TTAAAAATTGTAAAAATATTTAAAT-TT-TTAAAAATATTTTAAAATTGTAAAAAGTTAT
* * * *
18167 TTAAAAATTATAAAACATTATTTAAAGTTTTTAAAAAT-TAATAAAAATTGTGAAAA-TTAT
1 TTAAAAATTGTAAAA-A-TATTTAAA-TTTTTAAAAATAT-TTTAAAATTGTAAAAAGTTAT
18227 TTAAAAATTGTAAAAA
1 TTAAAAATTGTAAAAA
18243 ATAATTAATC
Statistics
Matches: 113, Mismatches: 11, Indels: 19
0.79 0.08 0.13
Matches are distributed among these distances:
57 7 0.06
58 29 0.26
59 15 0.13
60 48 0.42
61 13 0.12
62 1 0.01
ACGTcount: A:0.55, C:0.01, G:0.06, T:0.38
Consensus pattern (58 bp):
TTAAAAATTGTAAAAATATTTAAATTTTTAAAAATATTTTAAAATTGTAAAAAGTTAT
Found at i:18230 original size:30 final size:29
Alignment explanation
Indices: 18154--18242 Score: 83
Period size: 30 Copynumber: 3.0 Consensus size: 29
18144 TATTTTAAAA
18154 TTGTAAAAAGTTA-TTAAAAATTATAAAACA
1 TTGTAAAAA-TTATTTAAAAATTATAAAA-A
* * *
18184 TTATTTAAAGTT-TTTAAAAATTAATAAAAA
1 TT-GTAAAAATTATTTAAAAATT-ATAAAAA
* *
18214 TTGTGAAAATTATTTAAAAATTGTAAAAA
1 TTGTAAAAATTATTTAAAAATTATAAAAA
18243 ATAATTAATC
Statistics
Matches: 48, Mismatches: 7, Indels: 9
0.75 0.11 0.14
Matches are distributed among these distances:
29 12 0.25
30 26 0.54
31 10 0.21
ACGTcount: A:0.54, C:0.01, G:0.07, T:0.38
Consensus pattern (29 bp):
TTGTAAAAATTATTTAAAAATTATAAAAA
Found at i:18243 original size:30 final size:28
Alignment explanation
Indices: 18072--18244 Score: 79
Period size: 30 Copynumber: 5.9 Consensus size: 28
18062 AAAAATATTT
* *
18072 AAATTATTAAAAAATTT-AAGAATTGTAA
1 AAATTATTTAAAAATTTAAAAAATTGT-A
* * *
18100 AAAGAATATTTTAAAATTGTAAAAAAAT-TA
1 AA--ATTATTTAAAAATT-TAAAAAATTGTA
* **
18130 AATATT-GTTAAAAATATTTTAAAATTGTAA
1 AA-ATTATTTAAAAAT-TTAAAAAATTGT-A
18160 AAAGTTA-TTAAAAATTATAAAACATTATT-TA
1 AAA-TTATTTAAAAATT-TAAAA-A--ATTGTA
* *
18191 AAGTT-TTTAAAAATTAATAAAAATTGTGA
1 AAATTATTTAAAAATTTA-AAAAATTGT-A
18220 AAATTATTTAAAAATTGTAAAAAAT
1 AAATTATTTAAAAATT-TAAAAAAT
18245 AATTAATCGG
Statistics
Matches: 108, Mismatches: 18, Indels: 36
0.67 0.11 0.22
Matches are distributed among these distances:
27 3 0.03
28 16 0.15
29 13 0.12
30 60 0.56
31 7 0.06
32 6 0.06
33 3 0.03
ACGTcount: A:0.55, C:0.01, G:0.06, T:0.38
Consensus pattern (28 bp):
AAATTATTTAAAAATTTAAAAAATTGTA
Found at i:18244 original size:40 final size:39
Alignment explanation
Indices: 18050--18250 Score: 171
Period size: 40 Copynumber: 5.1 Consensus size: 39
18040 AATTAAAAAC
*
18050 ATTAAAAATTGT-AAAAATATTT-AAATTATTAAAAAA-T
1 ATTAAAAATTGTAAAAAATATTTAAAATT-GTAAAAAATT
*
18087 -TTAAGAATTGTAAAAAGAATATTTTAAAATTGTAAAAAA--
1 ATTAAAAATTGT-AAAA-AATA-TTTAAAATTGTAAAAAATT
* * *
18126 ATTAAATATTGTTAAAAATATTTTAAAATTGTAAAAAGTT
1 ATTAAAAATTGTAAAAAATA-TTTAAAATTGTAAAAAATT
* * * * *
18166 ATTAAAAATTATAAAACATTATTTAAAGTTTTTAAAAATT
1 ATTAAAAATTGTAAAA-AATATTTAAAATTGTAAAAAATT
* * * *
18206 AATAAAAATTGTGAAAATTATTTAAAAATTGTAAAAAATA
1 ATTAAAAATTGTAAAAAATATTT-AAAATTGTAAAAAATT
18246 ATTAA
1 ATTAA
18251 TCGGCAATTT
Statistics
Matches: 132, Mismatches: 22, Indels: 17
0.77 0.13 0.10
Matches are distributed among these distances:
36 10 0.08
38 24 0.18
39 14 0.11
40 76 0.58
41 8 0.06
ACGTcount: A:0.56, C:0.00, G:0.06, T:0.38
Consensus pattern (39 bp):
ATTAAAAATTGTAAAAAATATTTAAAATTGTAAAAAATT
Found at i:18250 original size:20 final size:20
Alignment explanation
Indices: 18050--18250 Score: 121
Period size: 20 Copynumber: 10.2 Consensus size: 20
18040 AATTAAAAAC
18050 ATTAAAAATTGT-AAAAAT-
1 ATTAAAAATTGTAAAAAATA
* *
18068 ATT-TAAATTATTAAAAAAT-
1 ATTAAAAATT-GTAAAAAATA
*
18087 -TTAAGAATTGTAAAAAGAATA
1 ATTAAAAATTGT-AAAA-AATA
* *
18108 TTTTAAAATTGT-AAAAA-A
1 ATTAAAAATTGTAAAAAATA
* *
18126 ATTAAATATTGTTAAAAATA
1 ATTAAAAATTGTAAAAAATA
* * * *
18146 TTTTAAAATTGTAAAAAGTT
1 ATTAAAAATTGTAAAAAATA
* *
18166 ATTAAAAATTATAAAACATTA
1 ATTAAAAATTGTAAAA-AATA
* ** * *
18187 TTTAAAGTTTTTAAAAATTA
1 ATTAAAAATTGTAAAAAATA
* *
18207 A-TAAAAATTGTGAAAATTA
1 ATTAAAAATTGTAAAAAATA
*
18226 TTTAAAAATTGTAAAAAATA
1 ATTAAAAATTGTAAAAAATA
18246 ATTAA
1 ATTAA
18251 TCGGCAATTT
Statistics
Matches: 138, Mismatches: 34, Indels: 20
0.72 0.18 0.10
Matches are distributed among these distances:
17 5 0.04
18 17 0.12
19 35 0.25
20 58 0.42
21 14 0.10
22 9 0.07
ACGTcount: A:0.56, C:0.00, G:0.06, T:0.38
Consensus pattern (20 bp):
ATTAAAAATTGTAAAAAATA
Found at i:18301 original size:10 final size:10
Alignment explanation
Indices: 18286--18382 Score: 65
Period size: 10 Copynumber: 9.6 Consensus size: 10
18276 TTATTTACTG
18286 TTTTTAATAA
1 TTTTTAATAA
*
18296 TTTTTAACAA
1 TTTTTAATAA
* **
18306 ATTAAAATAA
1 TTTTTAATAA
18316 TGTTTT-ATAA
1 T-TTTTAATAA
18326 TTTTTAATAA
1 TTTTTAATAA
18336 TTTTT--TACA
1 TTTTTAATA-A
* *
18345 GTTTTAAAATA
1 TTTTTAATA-A
*
18356 TTTTTAACAA
1 TTTTTAATAA
*
18366 TATTTAATAA
1 TTTTTAATAA
18376 TTGTTTA
1 TT-TTTA
18383 CAATATTTAA
Statistics
Matches: 65, Mismatches: 16, Indels: 11
0.71 0.17 0.12
Matches are distributed among these distances:
8 2 0.03
9 9 0.14
10 39 0.60
11 15 0.23
ACGTcount: A:0.40, C:0.03, G:0.03, T:0.54
Consensus pattern (10 bp):
TTTTTAATAA
Found at i:18349 original size:20 final size:20
Alignment explanation
Indices: 18265--18409 Score: 109
Period size: 20 Copynumber: 7.3 Consensus size: 20
18255 CAATTTCACG
* * *
18265 ATTTTTAATACTTATTTACT
1 ATTTTTAATAATTTTTTACA
* *
18285 GTTTTTAATAATTTTTAACA
1 ATTTTTAATAATTTTTTACA
* ** * *
18305 AATTAAAATAATGTTTTATA
1 ATTTTTAATAATTTTTTACA
18325 ATTTTTAATAATTTTTTAC-
1 ATTTTTAATAATTTTTTACA
*
18344 AGTTTTAA-AATATTTTTAACA
1 ATTTTTAATAAT-TTTTT-ACA
* *
18365 ATATTTAATAATTGTTTACA
1 ATTTTTAATAATTTTTTACA
* *
18385 ATATTTAAT-CTTTTTT-CA
1 ATTTTTAATAATTTTTTACA
18403 ATTTTTA
1 ATTTTTA
18410 TTTTTTTAAT
Statistics
Matches: 97, Mismatches: 24, Indels: 10
0.74 0.18 0.08
Matches are distributed among these distances:
18 11 0.11
19 17 0.18
20 56 0.58
21 10 0.10
22 3 0.03
ACGTcount: A:0.37, C:0.06, G:0.03, T:0.55
Consensus pattern (20 bp):
ATTTTTAATAATTTTTTACA
Found at i:18375 original size:60 final size:61
Alignment explanation
Indices: 18265--18381 Score: 150
Period size: 60 Copynumber: 1.9 Consensus size: 61
18255 CAATTTCACG
* * *
18265 ATTTTTAATACTTATTTACTGTTTTTAATAATTTTTAACAAATTAAAATAA-TGTTTTATA
1 ATTTTTAATAATTATTTACAGTTTTAAATAATTTTTAACAAATTAAAATAATTGTTTTATA
* *
18325 ATTTTTAATAATTTTTTACAGTTTTAAA-ATATTTTTAACAATATT-TAATAATTGTTT
1 ATTTTTAATAATTATTTACAGTTTTAAATA-ATTTTTAACAA-ATTAAAATAATTGTTT
18382 ACAATATTTA
Statistics
Matches: 49, Mismatches: 5, Indels: 5
0.83 0.08 0.08
Matches are distributed among these distances:
59 1 0.02
60 40 0.82
61 8 0.16
ACGTcount: A:0.38, C:0.04, G:0.03, T:0.55
Consensus pattern (61 bp):
ATTTTTAATAATTATTTACAGTTTTAAATAATTTTTAACAAATTAAAATAATTGTTTTATA
Found at i:18409 original size:18 final size:17
Alignment explanation
Indices: 18363--18433 Score: 65
Period size: 17 Copynumber: 4.0 Consensus size: 17
18353 ATATTTTTAA
*
18363 CAATATTTAATAATTGTTTA
1 CAATATTTAAT--TT-TTTT
18383 CAATATTTAATCTTTTTT
1 CAATATTTAAT-TTTTTT
*
18401 CAAT-TTTTATTTTTTT
1 CAATATTTAATTTTTTT
18417 -AATACTTTAATTTTTTT
1 CAATA-TTTAATTTTTTT
18434 ACTTGTTATA
Statistics
Matches: 45, Mismatches: 4, Indels: 7
0.80 0.07 0.12
Matches are distributed among these distances:
15 3 0.07
16 6 0.13
17 16 0.36
18 7 0.16
19 2 0.04
20 11 0.24
ACGTcount: A:0.30, C:0.07, G:0.01, T:0.62
Consensus pattern (17 bp):
CAATATTTAATTTTTTT
Found at i:22111 original size:58 final size:58
Alignment explanation
Indices: 22021--22153 Score: 266
Period size: 58 Copynumber: 2.3 Consensus size: 58
22011 ACACATGTAT
22021 GTATCAGCTCCTTGAGAGGTAACAATTCTTGCTTGCATGATTATATCCCTAATTTACA
1 GTATCAGCTCCTTGAGAGGTAACAATTCTTGCTTGCATGATTATATCCCTAATTTACA
22079 GTATCAGCTCCTTGAGAGGTAACAATTCTTGCTTGCATGATTATATCCCTAATTTACA
1 GTATCAGCTCCTTGAGAGGTAACAATTCTTGCTTGCATGATTATATCCCTAATTTACA
22137 GTATCAGCTCCTTGAGA
1 GTATCAGCTCCTTGAGA
22154 TGAAAGTAGT
Statistics
Matches: 75, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
58 75 1.00
ACGTcount: A:0.27, C:0.21, G:0.17, T:0.35
Consensus pattern (58 bp):
GTATCAGCTCCTTGAGAGGTAACAATTCTTGCTTGCATGATTATATCCCTAATTTACA
Found at i:23093 original size:6 final size:6
Alignment explanation
Indices: 23084--23126 Score: 50
Period size: 6 Copynumber: 7.2 Consensus size: 6
23074 GGGCCATGAC
* * * *
23084 CATGGT CATGGT CACGGT CATGGC CATGAT CACGGT CATGGT C
1 CATGGT CATGGT CATGGT CATGGT CATGGT CATGGT CATGGT C
23127 CTAGCCATAG
Statistics
Matches: 29, Mismatches: 8, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.19, C:0.26, G:0.30, T:0.26
Consensus pattern (6 bp):
CATGGT
Found at i:23111 original size:18 final size:18
Alignment explanation
Indices: 23084--23124 Score: 64
Period size: 18 Copynumber: 2.3 Consensus size: 18
23074 GGGCCATGAC
* *
23084 CATGGTCATGGTCACGGT
1 CATGGCCATGATCACGGT
23102 CATGGCCATGATCACGGT
1 CATGGCCATGATCACGGT
23120 CATGG
1 CATGG
23125 TCCTAGCCAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.20, C:0.24, G:0.32, T:0.24
Consensus pattern (18 bp):
CATGGCCATGATCACGGT
Found at i:23218 original size:3 final size:3
Alignment explanation
Indices: 23210--23237 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
23200 AGGAGAACAC
23210 CAT CAT CAT CAT CAT CAT CAT CAT CAT C
1 CAT CAT CAT CAT CAT CAT CAT CAT CAT C
23238 CCGAGGGGCA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.32, C:0.36, G:0.00, T:0.32
Consensus pattern (3 bp):
CAT
Found at i:24032 original size:61 final size:61
Alignment explanation
Indices: 23949--24073 Score: 205
Period size: 61 Copynumber: 2.0 Consensus size: 61
23939 TCCATGTTTG
* * * *
23949 ATTGCCTGAGCTTGAAGCAAAAGACTGATATTCAATTCAATAATACATATTAATGTAGTGA
1 ATTGCCTGAACTTGAAGAAAAAGACAGATATTCAATTCAATAACACATATTAATGTAGTGA
*
24010 ATTGCTTGAACTTGAAGAAAAAGACAGATATTCAATTCAATAACACATATTAATGTAGTGA
1 ATTGCCTGAACTTGAAGAAAAAGACAGATATTCAATTCAATAACACATATTAATGTAGTGA
24071 ATT
1 ATT
24074 TGAAGGCAAA
Statistics
Matches: 59, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
61 59 1.00
ACGTcount: A:0.42, C:0.12, G:0.15, T:0.31
Consensus pattern (61 bp):
ATTGCCTGAACTTGAAGAAAAAGACAGATATTCAATTCAATAACACATATTAATGTAGTGA
Found at i:30495 original size:24 final size:23
Alignment explanation
Indices: 30467--30513 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 23
30457 TTAAATTTAC
*
30467 TTAAAATTTAAATTTATTATAAAT
1 TTAAAATTTAAATCTATT-TAAAT
30491 TTAAAATTTAAATCTATTTAAAT
1 TTAAAATTTAAATCTATTTAAAT
30514 CAAGTCCAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
23 5 0.23
24 17 0.77
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (23 bp):
TTAAAATTTAAATCTATTTAAAT
Found at i:30512 original size:17 final size:17
Alignment explanation
Indices: 30421--30500 Score: 108
Period size: 17 Copynumber: 4.6 Consensus size: 17
30411 TCCAACAAAG
*
30421 ATTTAAATTTATTTTAA
1 ATTTAAATTTATTATAA
*
30438 AATTAAATTTATTATAA
1 ATTTAAATTTATTATAA
*
30455 GTTTAAATTTACTTA-AA
1 ATTTAAATTTA-TTATAA
30472 ATTTAAATTTATTATAA
1 ATTTAAATTTATTATAA
30489 ATTTAAAATTTA
1 ATTT-AAATTTA
30501 AATCTATTTA
Statistics
Matches: 55, Mismatches: 5, Indels: 5
0.85 0.08 0.08
Matches are distributed among these distances:
16 3 0.05
17 42 0.76
18 10 0.18
ACGTcount: A:0.46, C:0.01, G:0.01, T:0.51
Consensus pattern (17 bp):
ATTTAAATTTATTATAA
Done.