Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011898.1 Kokia drynarioides strain JFW-HI SEQ_126895, 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: 30002
ACGTcount: A:0.34, C:0.18, G:0.18, T:0.30
Found at i:8246 original size:168 final size:168
Alignment explanation
Indices: 7963--8277 Score: 513
Period size: 168 Copynumber: 1.9 Consensus size: 168
7953 ACAAATGACG
* *
7963 CGGTCATCTTCCTGATGAGATATTAAGAAGAAGACCAAATCAAACCTACGCTCGATGTGAGCAAA
1 CGGTCATCTTCCTGATGAGATATTAAGAAAAAGACCAAATCAAACCCACGCTCGATGTGAGCAAA
* * *
8028 TATTCTAACCCCAGCTTCCTGATGAGACACCGAGAAGCAGGTCAAAGCAATAAACAATTAGCTTC
66 TATTCGAACCCCAGCTTCCTGATGAGACACCGAGAAGCAGATCAAAGCAATAAACAATTAACTTC
8093 CTGATGAGATACAGAGAAACAGATTGAAATAAATGGCA
131 CTGATGAGATACAGAGAAACAGATTGAAATAAATGGCA
*
8131 CGGTCATCTTCCTGATGATATATTAAGAAAAAGACCAAATCAAACCCACGCTCGATGTGAGCAAA
1 CGGTCATCTTCCTGATGAGATATTAAGAAAAAGACCAAATCAAACCCACGCTCGATGTGAGCAAA
* * * ***
8196 TCTTCGAATCCCAGCTTCCTGATGAGACACCGAGAAGCAGATCGAAGCAATAAATGGTTAACTTC
66 TATTCGAACCCCAGCTTCCTGATGAGACACCGAGAAGCAGATCAAAGCAATAAACAATTAACTTC
*
8261 CTGATGAGATACTGAGA
131 CTGATGAGATACAGAGA
8278 GGTGGACCAA
Statistics
Matches: 134, Mismatches: 13, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
168 134 1.00
ACGTcount: A:0.37, C:0.22, G:0.20, T:0.22
Consensus pattern (168 bp):
CGGTCATCTTCCTGATGAGATATTAAGAAAAAGACCAAATCAAACCCACGCTCGATGTGAGCAAA
TATTCGAACCCCAGCTTCCTGATGAGACACCGAGAAGCAGATCAAAGCAATAAACAATTAACTTC
CTGATGAGATACAGAGAAACAGATTGAAATAAATGGCA
Found at i:8440 original size:197 final size:197
Alignment explanation
Indices: 8161--8548 Score: 641
Period size: 197 Copynumber: 2.0 Consensus size: 197
8151 TATTAAGAAA
*
8161 AAGACCAAATCAAACCCACGCTCGATGTGAGCAAATCTTCGAATCCCAGCTTCCTGATGAGACAC
1 AAGACCAAATCAAACCCACGCTCGATGTGAGCAAATCTTCGAAGCCCAGCTTCCTGATGAGACAC
* * * *
8226 CGAGAAGCAGATCGAAGCAATAAATGGTTAACTTCCTGATGAGATACTGAGAGGTGGACCAAATT
66 CAAGAAGCAGATCGAAGCAATAAACGGTTAACTTCCTGATGAGATACTGAGAAGTGAACCAAATT
* * ** *
8291 TGTCTTCTTGATGAGATACAGAGAAGCGGATTGAAACAAACGACGCGGTCATCTTCCTGATCGGA
131 CGTCTTCCTGATGAGATACAGAGAAGCAAATTGAAACAAACGACGCGATCATCTTCCTGATCGGA
8356 AG
196 AG
*
8358 AAGACCAAATCAAACTCACGCTCGATGTGAGCAAATCTTCGAAGCCCAGCTTCCTGATGAGACAC
1 AAGACCAAATCAAACCCACGCTCGATGTGAGCAAATCTTCGAAGCCCAGCTTCCTGATGAGACAC
* *
8423 CAAGAAGCAGGTCGAAGCAATAAACGGTTAGCTTCCTGATGAGATACTGAGAAGTGAACCAAATT
66 CAAGAAGCAGATCGAAGCAATAAACGGTTAACTTCCTGATGAGATACTGAGAAGTGAACCAAATT
* *
8488 CGTCTTCCTGATGAGATACAGAGAAGCAAATTGAAACAAATGGCGCGATCATCTTCCTGAT
131 CGTCTTCCTGATGAGATACAGAGAAGCAAATTGAAACAAACGACGCGATCATCTTCCTGAT
8549 GAGATACTGA
Statistics
Matches: 176, Mismatches: 15, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
197 176 1.00
ACGTcount: A:0.34, C:0.22, G:0.22, T:0.21
Consensus pattern (197 bp):
AAGACCAAATCAAACCCACGCTCGATGTGAGCAAATCTTCGAAGCCCAGCTTCCTGATGAGACAC
CAAGAAGCAGATCGAAGCAATAAACGGTTAACTTCCTGATGAGATACTGAGAAGTGAACCAAATT
CGTCTTCCTGATGAGATACAGAGAAGCAAATTGAAACAAACGACGCGATCATCTTCCTGATCGGA
AG
Found at i:8504 original size:37 final size:37
Alignment explanation
Indices: 8454--8599 Score: 139
Period size: 37 Copynumber: 3.6 Consensus size: 37
8444 AAACGGTTAG
*
8454 CTTCCTGATGAGATACTGAGAAGTGAACCAAATTCGT
1 CTTCCTGATGAGATACAGAGAAGTGAACCAAATTCGT
* *
8491 CTTCCTGATGAGATACAGAGAAGCAAATTGAAACAAATGGCGCGATCAT
1 CTTCCTGATGAGATACAGAGAAG-----TGAACCAAAT-------TCGT
* *
8540 CTTCCTGATGAGATACTGAGAATTGAACCAAATTCGT
1 CTTCCTGATGAGATACAGAGAAGTGAACCAAATTCGT
8577 CTTCCTGATGAGATACAGAGAAG
1 CTTCCTGATGAGATACAGAGAAG
8600 CAGATTGAAA
Statistics
Matches: 88, Mismatches: 9, Indels: 24
0.73 0.07 0.20
Matches are distributed among these distances:
37 46 0.52
42 9 0.10
44 9 0.10
49 24 0.27
ACGTcount: A:0.35, C:0.18, G:0.22, T:0.25
Consensus pattern (37 bp):
CTTCCTGATGAGATACAGAGAAGTGAACCAAATTCGT
Found at i:8559 original size:86 final size:86
Alignment explanation
Indices: 8454--8648 Score: 318
Period size: 86 Copynumber: 2.3 Consensus size: 86
8444 AAACGGTTAG
8454 CTTCCTGATGAGATACTGAGAAGTGAACCAAATTCGTCTTCCTGATGAGATACAGAGAAGCAAAT
1 CTTCCTGATGAGATACTGAGAAGTGAACCAAATTCGTCTTCCTGATGAGATACAGAGAAGCAAAT
* *
8519 TGAAACAAATGGCGCGATCAT
66 TGAAACAAACGACGCGATCAT
* *
8540 CTTCCTGATGAGATACTGAGAATTGAACCAAATTCGTCTTCCTGATGAGATACAGAGAAGCAGAT
1 CTTCCTGATGAGATACTGAGAAGTGAACCAAATTCGTCTTCCTGATGAGATACAGAGAAGCAAAT
* *
8605 TGAAACAAACGACGTGGTCAT
66 TGAAACAAACGACGCGATCAT
* *
8626 CTTCCTAATGCGATACTGAGAAG
1 CTTCCTGATGAGATACTGAGAAG
8649 AAGACCAAAT
Statistics
Matches: 100, Mismatches: 9, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
86 100 1.00
ACGTcount: A:0.35, C:0.19, G:0.22, T:0.24
Consensus pattern (86 bp):
CTTCCTGATGAGATACTGAGAAGTGAACCAAATTCGTCTTCCTGATGAGATACAGAGAAGCAAAT
TGAAACAAACGACGCGATCAT
Found at i:9221 original size:34 final size:34
Alignment explanation
Indices: 9177--9257 Score: 117
Period size: 34 Copynumber: 2.4 Consensus size: 34
9167 AGGGCCCAAC
* * *
9177 AAATTTAAATTTATTTTAAAATTAGGTTTATTTT
1 AAATTTAAATTTATTTGAAAATTAAGTTTATTAT
* *
9211 GAATTTAAATTTATTTGAAATTTAAGTTTATTAT
1 AAATTTAAATTTATTTGAAAATTAAGTTTATTAT
9245 AAATTTAAATTTA
1 AAATTTAAATTTA
9258 AAATTTATTT
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
34 41 1.00
ACGTcount: A:0.41, C:0.00, G:0.06, T:0.53
Consensus pattern (34 bp):
AAATTTAAATTTATTTGAAAATTAAGTTTATTAT
Found at i:9264 original size:24 final size:25
Alignment explanation
Indices: 9223--9271 Score: 66
Period size: 24 Copynumber: 2.0 Consensus size: 25
9213 ATTTAAATTT
*
9223 ATTTGAAATTTAAGTTTA-TTATAA
1 ATTTGAAATTTAAATTTATTTATAA
9247 ATTT-AAATTTAAAATTTATTTATAA
1 ATTTGAAATTT-AAATTTATTTATAA
9272 TGTCCAAGTA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
23 6 0.27
24 10 0.45
25 6 0.27
ACGTcount: A:0.45, C:0.00, G:0.04, T:0.51
Consensus pattern (25 bp):
ATTTGAAATTTAAATTTATTTATAA
Found at i:9268 original size:17 final size:17
Alignment explanation
Indices: 9177--9257 Score: 99
Period size: 17 Copynumber: 4.8 Consensus size: 17
9167 AGGGCCCAAC
9177 AAATTTAAATTTATTTT
1 AAATTTAAATTTATTTT
* **
9194 AAAATTAGGTTTATTTT
1 AAATTTAAATTTATTTT
* *
9211 GAATTTAAATTTATTTG
1 AAATTTAAATTTATTTT
* *
9228 AAATTTAAGTTTATTAT
1 AAATTTAAATTTATTTT
9245 AAATTTAAATTTA
1 AAATTTAAATTTA
9258 AAATTTATTT
Statistics
Matches: 51, Mismatches: 13, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
17 51 1.00
ACGTcount: A:0.41, C:0.00, G:0.06, T:0.53
Consensus pattern (17 bp):
AAATTTAAATTTATTTT
Found at i:11084 original size:29 final size:29
Alignment explanation
Indices: 11042--11400 Score: 249
Period size: 29 Copynumber: 12.2 Consensus size: 29
11032 CCTTGGAGGT
*
11042 CCCT-AAACCTTCCAAAAATTTCGTTTTTA
1 CCCTCAAA-CTTCCAAAAATTTCATTTTTA
* **
11071 CCCTCGAACTTCCAAAAATCCCATTTTTGA
1 CCCTCAAACTTCCAAAAATTTCATTTTT-A
11101 -CCTCGAAACTTCCAAAAATTAT-ATTTTTA
1 CCCTC-AAACTTCCAAAAATT-TCATTTTTA
**
11130 CCC-CAAAACTTCCAAAAATACCATTTTTGA
1 CCCTC-AAACTTCCAAAAATTTCATTTTT-A
11160 -CCTCAAAACTTCCAAAAA-TTCAATTTTTA
1 CCCTC-AAACTTCCAAAAATTTC-ATTTTTA
* * * *
11189 CCCCCAAACTTTCAAAAATCTCATTTTAA
1 CCCTCAAACTTCCAAAAATTTCATTTTTA
* *
11218 CCCTAAAACTTCCAAAAA-TTCTAATTTTA
1 CCCTCAAACTTCCAAAAATTTC-ATTTTTA
* * * *
11247 CCCCCAAACTCCCAAAAATCTCTTTTTTAA
1 CCCTCAAACTTCCAAAAATTTCATTTTT-A
11277 CCC-CAAAACTTCCAAAAA-TTCTATTTTTGA
1 CCCTC-AAACTTCCAAAAATTTC-ATTTTT-A
* *
11307 -CTTCAAAACTTCC-AAAATTTCCATTATTA
1 CCCTC-AAACTTCCAAAAATTT-CATTTTTA
** **
11336 CCCTTGAACTTCCAAAAAATCCCATTTTTGA
1 CCCTCAAACTTCC-AAAAATTTCATTTTT-A
*
11367 CCC-CTAAACTTCCAAAAATTACCATTTTT-
1 CCCTC-AAACTTCCAAAAATT-TCATTTTTA
11396 CCCTC
1 CCCTC
11401 GGATGTCGAA
Statistics
Matches: 261, Mismatches: 43, Indels: 51
0.74 0.12 0.14
Matches are distributed among these distances:
28 2 0.01
29 127 0.49
30 107 0.41
31 25 0.10
ACGTcount: A:0.36, C:0.29, G:0.02, T:0.33
Consensus pattern (29 bp):
CCCTCAAACTTCCAAAAATTTCATTTTTA
Found at i:11113 original size:30 final size:29
Alignment explanation
Indices: 11050--11395 Score: 311
Period size: 30 Copynumber: 11.7 Consensus size: 29
11040 GTCCCTAAAC
* * *
11050 CTTCCAAAAATTTCGTTTTTACCCTC-GAA
1 CTTCCAAAAATTCCATTTTTACCC-CAAAA
* * *
11079 CTTCCAAAAATCCCATTTTTGACCTCGAAA
1 CTTCCAAAAATTCCATTTTT-ACCCCAAAA
**
11109 CTTCCAAAAATTATATTTTTACCCCAAAA
1 CTTCCAAAAATTCCATTTTTACCCCAAAA
* *
11138 CTTCCAAAAATACCATTTTTGACCTCAAAA
1 CTTCCAAAAATTCCATTTTT-ACCCCAAAA
* *
11168 CTTCCAAAAATTCAATTTTTACCCCCAAA
1 CTTCCAAAAATTCCATTTTTACCCCAAAA
* * *
11197 CTTTCAAAAA-TCTCATTTTAACCCTAAAA
1 CTTCCAAAAATTC-CATTTTTACCCCAAAA
* * *
11226 CTTCCAAAAATTCTAATTTTACCCCCAAA
1 CTTCCAAAAATTCCATTTTTACCCCAAAA
* *
11255 CTCCCAAAAA-TCTCTTTTTTAACCCCAAAA
1 CTTCCAAAAATTC-CATTTTT-ACCCCAAAA
* **
11285 CTTCCAAAAATTCTATTTTTGACTTCAAAA
1 CTTCCAAAAATTCCATTTTT-ACCCCAAAA
* * ***
11315 CTTCCAAAATTTCCATTATTACCCTTGAA
1 CTTCCAAAAATTCCATTTTTACCCCAAAA
* *
11344 CTTCCAAAAAATCCCATTTTTGACCCCTAAA
1 CTTCC-AAAAATTCCATTTTT-ACCCCAAAA
11375 CTTCCAAAAATTACCATTTTT
1 CTTCCAAAAATT-CCATTTTT
11396 CCCTCGGATG
Statistics
Matches: 252, Mismatches: 54, Indels: 20
0.77 0.17 0.06
Matches are distributed among these distances:
28 4 0.02
29 112 0.44
30 114 0.45
31 22 0.09
ACGTcount: A:0.36, C:0.28, G:0.02, T:0.34
Consensus pattern (29 bp):
CTTCCAAAAATTCCATTTTTACCCCAAAA
Found at i:11142 original size:59 final size:59
Alignment explanation
Indices: 11050--11395 Score: 333
Period size: 59 Copynumber: 5.8 Consensus size: 59
11040 GTCCCTAAAC
* * * *
11050 CTTCCAAAAATT-TCGTTTTTACCCTC-GAACTTCCAAAAATCCCATTTTTGACCTCGAAA
1 CTTCCAAAAATTCT-ATTTTTACCC-CAAAACTTCCAAAAATCCCATTTTTAACCTCAAAA
* * *
11109 CTTCCAAAAATTATATTTTTACCCCAAAACTTCCAAAAATACCATTTTTGACCTCAAAA
1 CTTCCAAAAATTCTATTTTTACCCCAAAACTTCCAAAAATCCCATTTTTAACCTCAAAA
* * * *
11168 CTTCCAAAAATTCAATTTTTACCCCCAAACTTTCAAAAATCTCA-TTTTAACC-CTAAAA
1 CTTCCAAAAATTCTATTTTTACCCCAAAACTTCCAAAAATCCCATTTTTAACCTC-AAAA
* * * * * *
11226 CTTCCAAAAATTCTAATTTTACCCCCAAACTCCCAAAAATCTCTTTTTTAACCCCAAAA
1 CTTCCAAAAATTCTATTTTTACCCCAAAACTTCCAAAAATCCCATTTTTAACCTCAAAA
** * * * * **
11285 CTTCCAAAAATTCTATTTTTGACTTCAAAACTTCCAAAATTTCCATTATTACCCT-TGAA
1 CTTCCAAAAATTCTATTTTT-ACCCCAAAACTTCCAAAAATCCCATTTTTAACCTCAAAA
* * * *
11344 CTTCCAAAAAATCCCATTTTTGACCCCTAAACTTCCAAAAATTACCATTTTT
1 CTTCC-AAAAATTCTATTTTT-ACCCCAAAACTTCCAAAAA-TCCCATTTTT
11396 CCCTCGGATG
Statistics
Matches: 241, Mismatches: 38, Indels: 14
0.82 0.13 0.05
Matches are distributed among these distances:
57 1 0.00
58 51 0.21
59 127 0.53
60 54 0.22
61 8 0.03
ACGTcount: A:0.36, C:0.28, G:0.02, T:0.34
Consensus pattern (59 bp):
CTTCCAAAAATTCTATTTTTACCCCAAAACTTCCAAAAATCCCATTTTTAACCTCAAAA
Found at i:14319 original size:16 final size:15
Alignment explanation
Indices: 14269--14325 Score: 62
Period size: 15 Copynumber: 3.8 Consensus size: 15
14259 GTATTTCACC
*
14269 AAAAAAAAGAGAGAA
1 AAAAAAAAGAAAGAA
*
14284 AAAAAAAAGGAAAGGA
1 AAAAAAAA-GAAAGAA
*
14300 AAAGAAAAGAAA-AA
1 AAAAAAAAGAAAGAA
*
14314 AAAAAGAAGAAA
1 AAAAAAAAGAAA
14326 AATGAGAAGG
Statistics
Matches: 35, Mismatches: 6, Indels: 3
0.80 0.14 0.07
Matches are distributed among these distances:
14 11 0.31
15 12 0.34
16 12 0.34
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (15 bp):
AAAAAAAAGAAAGAA
Found at i:15515 original size:23 final size:23
Alignment explanation
Indices: 15489--15536 Score: 96
Period size: 23 Copynumber: 2.1 Consensus size: 23
15479 TCGATGTGTT
15489 AGGCCAAACACGTTTCCTTATCA
1 AGGCCAAACACGTTTCCTTATCA
15512 AGGCCAAACACGTTTCCTTATCA
1 AGGCCAAACACGTTTCCTTATCA
15535 AG
1 AG
15537 TAGAGAGGTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.31, C:0.29, G:0.15, T:0.25
Consensus pattern (23 bp):
AGGCCAAACACGTTTCCTTATCA
Found at i:25762 original size:12 final size:12
Alignment explanation
Indices: 25721--25772 Score: 50
Period size: 12 Copynumber: 4.2 Consensus size: 12
25711 CCTTTTTTTC
*
25721 TTTTTTTTTTAAA
1 TTTTTATTTT-AA
* *
25734 TATTTACTTTAA
1 TTTTTATTTTAA
* *
25746 ATTTTATTTTTA
1 TTTTTATTTTAA
25758 TTTTTATTTTAA
1 TTTTTATTTTAA
25770 TTT
1 TTT
25773 AACCCTTAGA
Statistics
Matches: 30, Mismatches: 9, Indels: 1
0.75 0.22 0.03
Matches are distributed among these distances:
12 23 0.77
13 7 0.23
ACGTcount: A:0.25, C:0.02, G:0.00, T:0.73
Consensus pattern (12 bp):
TTTTTATTTTAA
Done.