Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014211.1 Kokia drynarioides strain JFW-HI SEQ_129244, 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: 17910
ACGTcount: A:0.34, C:0.18, G:0.20, T:0.28
Warning! 5 characters in sequence are not A, C, G, or T
Found at i:1128 original size:59 final size:59
Alignment explanation
Indices: 995--1423 Score: 554
Period size: 59 Copynumber: 7.3 Consensus size: 59
985 AAACTATCTA
* * * * * *
995 AAAATTACCATTTTACCCCCGAACTTCCAAAAATTCCA-TTTTGACCCTAAAACTTCTT
1 AAAATTACCATTTTACCCTCAAACTTCCAAAAATCCCATTTTTAACCCCAAAACTTCCT
*
1053 AAAATTACCATTTTACCCTCAAACTTTCAAAAATCCCATTTTTAACCCCAAAACTTCCT
1 AAAATTACCATTTTACCCTCAAACTTCCAAAAATCCCATTTTTAACCCCAAAACTTCCT
* *
1112 AAAATTACCATTTTACCCTCGAACTTCCAAAAATCCCATTTTTGACCCCAAAACTTCCT
1 AAAATTACCATTTTACCCTCAAACTTCCAAAAATCCCATTTTTAACCCCAAAACTTCCT
* * *
1171 AAAATTACCATTTTACCCTCAAACTTCCAAAAATCCCATTTTTAACCTCGAACCTTCCT
1 AAAATTACCATTTTACCCTCAAACTTCCAAAAATCCCATTTTTAACCCCAAAACTTCCT
* * * *
1230 AAAATTATCATTTTACCCCCAAACTTCCAAAAATCCCATTTTTGACCCCAAAACTTCCG
1 AAAATTACCATTTTACCCTCAAACTTCCAAAAATCCCATTTTTAACCCCAAAACTTCCT
* * * * *
1289 AAAATTACCATTTTACCCTCAAACTTCTAAAAGTCCCATTTTTTACCCTAAAACTTCCA
1 AAAATTACCATTTTACCCTCAAACTTCCAAAAATCCCATTTTTAACCCCAAAACTTCCT
* * * * * * ** * * *
1348 AAAATTACCATTTTACCCCCGAACTTTCGAAAGTCTCATTTTTAACATCGACACTTCCAA
1 AAAATTACCATTTTACCCTCAAACTTCCAAAAATCCCATTTTTAACCCCAAAACTTCC-T
1408 AAAATTACCATTTTAC
1 AAAATTACCATTTTAC
1424 TCTCGGATGT
Statistics
Matches: 328, Mismatches: 41, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
58 34 0.10
59 277 0.84
60 17 0.05
ACGTcount: A:0.35, C:0.30, G:0.03, T:0.32
Consensus pattern (59 bp):
AAAATTACCATTTTACCCTCAAACTTCCAAAAATCCCATTTTTAACCCCAAAACTTCCT
Found at i:13656 original size:201 final size:201
Alignment explanation
Indices: 13306--14026 Score: 875
Period size: 201 Copynumber: 3.6 Consensus size: 201
13296 ATGTAACCAT
* * * * *
13306 CTTCTTGATGAGACACTAAGAAGCAGGTCGAAGCGATGAAAGGTTAGCTTCCTGATGAGATACTA
1 CTTCCTGATGAGACACTGAGAAGCAGGTCGAAGCAATAAAAGGTTAGCTTCCTAATGAGATACTA
** * *
13371 AGAAGTGAACCAAATTCGCCTTCCTGATGAGATACAGAGAAGCGTGTTGAAACAAGTGACGCGGT
66 AGAAGTGAACCAAATTCGCCTTCCTGATGAGATACAGAGAAGCGAATTGAAACAAGCGACGCGAT
** * *
13436 CATCTTCCTGATGAGACACTGAGAAGAAGACCCAAGTGAGGCTTGATATGAGCAAAATCTTCGAA
131 CATCTTCCTGATGAGACACTGAGAAGAAGACCCAAACGAGGCTTAAAATGAGCAAAATCTTCGAA
*
13501 CCCTAG
196 CCCCAG
* *
13507 CTTCCTGATGAGACACTGAGAAGCAGGTCGAAGCAATGAAAGGTTAGCTTCCTAATGAGATACTG
1 CTTCCTGATGAGACACTGAGAAGCAGGTCGAAGCAATAAAAGGTTAGCTTCCTAATGAGATACTA
* *
13572 AGAAGTGAACCAAATTCGCCTTCCTGATGAGATACAGAGAAGCGAGTTGTAACAAGCGACGCGAT
66 AGAAGTGAACCAAATTCGCCTTCCTGATGAGATACAGAGAAGCGAATTGAAACAAGCGACGCGAT
* * * * * *
13637 CATCTTCCTGATAAGACACTGAGAAGAAGACTCAAACGATGCTCAAAGTGAGCAAAATCTTCTAA
131 CATCTTCCTGATGAGACACTGAGAAGAAGACCCAAACGAGGCTTAAAATGAGCAAAATCTTCGAA
13702 CCCCAG
196 CCCCAG
* * * *
13708 CTTCCTGATGAGACACTGAGAAGTAGGTCGAAGCGATAAAAGGTTAGCTTCCTGATGAGATACTG
1 CTTCCTGATGAGACACTGAGAAGCAGGTCGAAGCAATAAAAGGTTAGCTTCCTAATGAGATACTA
* * * *** * *
13773 AGAAGTGAACCAAATTTGTCTTCCTGATGAGATACAGAGGAGCGAATTGAAACAAANNNNNATGT
66 AGAAGTGAACCAAATTCGCCTTCCTGATGAGATACAGAGAAGCGAATTGAAAC-AA--GCGACGC
* * * * * * *
13838 GATCATCTTCCTGACGAGGCACGGAGAAGAAGGCCCAAACGAGGCTCAAAACGAGCAAAATCTTT
128 GATCATCTTCCTGATGAGACACTGAGAAGAAGACCCAAACGAGGCTTAAAATGAGCAAAATCTTC
13903 GAACCCCAG
193 GAACCCCAG
* * * *
13912 CTT-CT--T--G--ATTGAGAGGCAGGTTGAAGCAATAAAATGGTTAGCTT-CTAGATAAGATAC
1 CTTCCTGATGAGACACTGAGAAGCAGGTCGAAGCAATAAAA-GGTTAGCTTCCTA-ATGAGATAC
* * *
13969 TAAGAAG-CAGACCAAATTCGTCTTCCTAATGAGATACAGAGAAGCGAATTGAAACAAG
64 TAAGAAGTGA-ACCAAATTCGCCTTCCTGATGAGATACAGAGAAGCGAATTGAAACAAG
14027 TGATAAAAGG
Statistics
Matches: 456, Mismatches: 58, Indels: 18
0.86 0.11 0.03
Matches are distributed among these distances:
197 27 0.06
198 65 0.14
199 1 0.00
201 291 0.64
202 2 0.00
203 2 0.00
204 68 0.15
ACGTcount: A:0.35, C:0.19, G:0.24, T:0.21
Consensus pattern (201 bp):
CTTCCTGATGAGACACTGAGAAGCAGGTCGAAGCAATAAAAGGTTAGCTTCCTAATGAGATACTA
AGAAGTGAACCAAATTCGCCTTCCTGATGAGATACAGAGAAGCGAATTGAAACAAGCGACGCGAT
CATCTTCCTGATGAGACACTGAGAAGAAGACCCAAACGAGGCTTAAAATGAGCAAAATCTTCGAA
CCCCAG
Found at i:14440 original size:11 final size:11
Alignment explanation
Indices: 14423--14499 Score: 66
Period size: 11 Copynumber: 6.9 Consensus size: 11
14413 GGGGCCTTTT
*
14423 TTTAATTT-AT
1 TTTAATTTAAA
*
14433 TTTAAATTTAGA
1 TTT-AATTTAAA
*
14445 TTTATTTTAAA
1 TTTAATTTAAA
* **
14456 TTTAAATTATC
1 TTTAATTTAAA
*
14467 TTAAATTTAAA
1 TTTAATTTAAA
14478 TTTAATTTAAA
1 TTTAATTTAAA
14489 TTTAAATTTAA
1 TTT-AATTTAA
14500 TTTCAAAGTT
Statistics
Matches: 51, Mismatches: 13, Indels: 4
0.75 0.19 0.06
Matches are distributed among these distances:
10 3 0.06
11 38 0.75
12 10 0.20
ACGTcount: A:0.42, C:0.01, G:0.01, T:0.56
Consensus pattern (11 bp):
TTTAATTTAAA
Found at i:14447 original size:6 final size:6
Alignment explanation
Indices: 14433--14512 Score: 73
Period size: 6 Copynumber: 14.0 Consensus size: 6
14423 TTTAATTTAT
* *
14433 TTTAAA TTTAGA TTT-AT TTTAAA TTTAAA -TT--A TCTTAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA T-TTAAA TTTAAA
*
14478 TTT-AA TTTAAA TTTAAA TTT-AA TTTCAAA GTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTT-AAA TTTAAA
14513 AAGTCGAAAG
Statistics
Matches: 61, Mismatches: 5, Indels: 16
0.74 0.06 0.20
Matches are distributed among these distances:
3 1 0.02
5 17 0.28
6 37 0.61
7 6 0.10
ACGTcount: A:0.44, C:0.03, G:0.03, T:0.51
Consensus pattern (6 bp):
TTTAAA
Found at i:14460 original size:33 final size:33
Alignment explanation
Indices: 14423--14498 Score: 107
Period size: 33 Copynumber: 2.3 Consensus size: 33
14413 GGGGCCTTTT
* * *
14423 TTTAATTTATTTTAAATTTAGATTTATTTTAAA
1 TTTAATTTATCTTAAATTTAAATTTAATTTAAA
*
14456 TTTAAATTATCTTAAATTTAAATTTAATTTAAA
1 TTTAATTTATCTTAAATTTAAATTTAATTTAAA
14489 TTTAAATTTA
1 TTT-AATTTA
14499 ATTTCAAAGT
Statistics
Matches: 37, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
33 32 0.86
34 5 0.14
ACGTcount: A:0.41, C:0.01, G:0.01, T:0.57
Consensus pattern (33 bp):
TTTAATTTATCTTAAATTTAAATTTAATTTAAA
Found at i:14499 original size:17 final size:17
Alignment explanation
Indices: 14426--14512 Score: 106
Period size: 17 Copynumber: 5.1 Consensus size: 17
14416 GCCTTTTTTT
*
14426 AATTTATTTTAAATTTA
1 AATTTAATTTAAATTTA
* *
14443 GATTTATTTTAAATTTA
1 AATTTAATTTAAATTTA
14460 AA-TT-ATCTTAAATTTA
1 AATTTAAT-TTAAATTTA
14476 AATTTAATTTAAATTTA
1 AATTTAATTTAAATTTA
*
14493 AATTTAATTTCAAAGTTA
1 AATTTAATTT-AAATTTA
14511 AA
1 AA
14513 AAGTCGAAAG
Statistics
Matches: 62, Mismatches: 4, Indels: 7
0.85 0.05 0.10
Matches are distributed among these distances:
15 1 0.02
16 13 0.21
17 38 0.61
18 10 0.16
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.52
Consensus pattern (17 bp):
AATTTAATTTAAATTTA
Found at i:15817 original size:96 final size:96
Alignment explanation
Indices: 15644--15824 Score: 217
Period size: 96 Copynumber: 1.9 Consensus size: 96
15634 AGGATATCCA
* * * *
15644 ATTATCTCGATTTGAAGAAAGGTTGCACCTAGTAAGTTAAGGCGCAATATTTTAGAATCGAAGAT
1 ATTATCTCGATTTGAAGAAAGATTGCACCTAATAAGTTAAGGCACAATATTTTAGAATCGAAGAA
*
15709 AAGGAAACATTGCCTCGATTAAGGGTATTCG
66 AAAGAAACATTGCCTCGATTAAGGGTATTCG
* * *
15740 ATTATTTCGATTTGAAGGAAA-ATTGCACCTAATGAGTTAAGGCACAA-ATTTTTGAAACTCGAA
1 ATTATCTCGATTTGAA-GAAAGATTGCACCTAATAAGTTAAGGCACAATATTTTAG-AA-TCGAA
*
15803 -ACAAAAG-AATATTGCCTCGATT
63 GA-AAAAGAAACATTGCCTCGATT
15825 TTTGAAACTT
Statistics
Matches: 72, Mismatches: 9, Indels: 8
0.81 0.10 0.09
Matches are distributed among these distances:
95 6 0.08
96 54 0.75
97 12 0.17
ACGTcount: A:0.36, C:0.14, G:0.20, T:0.30
Consensus pattern (96 bp):
ATTATCTCGATTTGAAGAAAGATTGCACCTAATAAGTTAAGGCACAATATTTTAGAATCGAAGAA
AAAGAAACATTGCCTCGATTAAGGGTATTCG
Found at i:16148 original size:29 final size:27
Alignment explanation
Indices: 16105--16370 Score: 139
Period size: 29 Copynumber: 9.0 Consensus size: 27
16095 AATTTAAAAC
16105 GTTCGAGTGTAAAAATGGTAATTTT-GAGA
1 GTTCGAG-GT-AAAATGGTAATTTTGGA-A
*
16134 GTTTCGAGGTCAAAAATGAG-ATTTTTGGAA
1 G-TTCGAGGT--AAAATG-GTAATTTTGGAA
*
16164 GTTCGGGGTAAAATGGTAATTTTTGGAA
1 GTTCGAGGTAAAATGGTAA-TTTTGGAA
* *
16192 GGTT-TAGGGACTAAAAATTGG-ATTTTTGGAA
1 -GTTCGA-GG--T-AAAA-TGGTAATTTTGGAA
* *
16223 GTTTAGGGGTAAAATGGTAATTCTTGGAA
1 G-TTCGAGGTAAAATGGTAATT-TTGGAA
16252 GATTCGAGGTCAAAAATGG-AATTTTAGGAA
1 G-TTCGAGGT--AAAATGGTAATTTT-GGAA
* * *
16282 GTTTAGGGGTAAAATAGTAATTTTTGGAA
1 G-TTCGAGGTAAAATGGTAA-TTTTGGAA
* *
16311 GATTCGGGGTTGAAAATGG-GATTTTAGGAA
1 G-TTCGAGG-T-AAAATGGTAATTTT-GGAA
16341 GTTCGAGGGTAAAATGGTAATTTTTGGAA
1 GTTCGA-GGTAAAATGGTAA-TTTTGGAA
16370 G
1 G
16371 GTTTAGGGAC
Statistics
Matches: 188, Mismatches: 22, Indels: 54
0.71 0.08 0.20
Matches are distributed among these distances:
26 1 0.01
27 10 0.05
28 28 0.15
29 59 0.31
30 53 0.28
31 29 0.15
32 5 0.03
33 3 0.02
ACGTcount: A:0.33, C:0.04, G:0.30, T:0.33
Consensus pattern (27 bp):
GTTCGAGGTAAAATGGTAATTTTGGAA
Found at i:16216 original size:59 final size:58
Alignment explanation
Indices: 16145--16380 Score: 253
Period size: 59 Copynumber: 4.0 Consensus size: 58
16135 TTTCGAGGTC
* * *
16145 AAAAATGAGATTTTTGGAAG-TTCGGGGTAAAATGGTAATTTTTGGAAGGTTTAGGGACT
1 AAAAATG-GATTTTAGGAAGTTTAGGGGTAAAATGGTAATTTTTGGAA-GATTAGGGACT
* * * *
16204 AAAAATTGGATTTTTGGAAGTTTAGGGGTAAAATGGTAATTCTTGGAAGATTCGAGGTC-
1 AAAAA-TGGATTTTAGGAAGTTTAGGGGTAAAATGGTAATTTTTGGAAGATTAG-GGACT
* * **
16263 AAAAATGGAATTTTAGGAAGTTTAGGGGTAAAATAGTAATTTTTGGAAGATTCGGGGTT
1 AAAAATGG-ATTTTAGGAAGTTTAGGGGTAAAATGGTAATTTTTGGAAGATTAGGGACT
* * *
16322 GAAAATGGGATTTTAGGAAG-TTCGAGGGTAAAATGGTAATTTTTGGAAGGTTTAGGGAC
1 AAAAAT-GGATTTTAGGAAGTTTAG-GGGTAAAATGGTAATTTTTGGAA-GATTAGGGAC
16381 CTTCGAGGTA
Statistics
Matches: 152, Mismatches: 17, Indels: 15
0.83 0.09 0.08
Matches are distributed among these distances:
58 8 0.05
59 106 0.70
60 38 0.25
ACGTcount: A:0.33, C:0.03, G:0.31, T:0.33
Consensus pattern (58 bp):
AAAAATGGATTTTAGGAAGTTTAGGGGTAAAATGGTAATTTTTGGAAGATTAGGGACT
Found at i:16264 original size:118 final size:117
Alignment explanation
Indices: 16116--16370 Score: 320
Period size: 118 Copynumber: 2.2 Consensus size: 117
16106 TTCGAGTGTA
* * *
16116 AAAATGGTAATTTT-GAGAGTTTCGAGGTCAAAAAT-GAGATTTTTGGAAG-TTCGGGGTAAAAT
1 AAAATGGTAATTTTGGA-AGATTCGAGGTCAAAAATGGA-ATTTTAGGAAGTTTAGGGGTAAAAT
* * * *
16178 GGTAATTTTTGGAAGGTTTAGGGACTAAAAATTGGATTTTTGGAAGTTTAG-GGGT
64 AGTAATTTTTGGAA-GATTAGGGACTAAAAATGGGATTTTAGGAAG-TTAGAGGGT
16233 AAAATGGTAATTCTTGGAAGATTCGAGGTCAAAAATGGAATTTTAGGAAGTTTAGGGGTAAAATA
1 AAAATGGTAATT-TTGGAAGATTCGAGGTCAAAAATGGAATTTTAGGAAGTTTAGGGGTAAAATA
* ** * *
16298 GTAATTTTTGGAAGATTCGGGGTTGAAAATGGGATTTTAGGAAGTTCGAGGGT
65 GTAATTTTTGGAAGATTAGGGACTAAAAATGGGATTTTAGGAAGTTAGAGGGT
16351 AAAATGGTAATTTTTGGAAG
1 AAAATGGTAA-TTTTGGAAG
16371 GTTTAGGGAC
Statistics
Matches: 120, Mismatches: 12, Indels: 11
0.84 0.08 0.08
Matches are distributed among these distances:
117 15 0.12
118 74 0.62
119 31 0.26
ACGTcount: A:0.33, C:0.04, G:0.30, T:0.33
Consensus pattern (117 bp):
AAAATGGTAATTTTGGAAGATTCGAGGTCAAAAATGGAATTTTAGGAAGTTTAGGGGTAAAATAG
TAATTTTTGGAAGATTAGGGACTAAAAATGGGATTTTAGGAAGTTAGAGGGT
Found at i:16378 original size:29 final size:28
Alignment explanation
Indices: 16154--16378 Score: 179
Period size: 29 Copynumber: 7.6 Consensus size: 28
16144 CAAAAATGAG
**
16154 ATTTTTGGAAGTTCGGGGTAAAATGGTA
1 ATTTTTGGAAGTTTAGGGTAAAATGGTA
16182 ATTTTTGGAAGGTTTAGGGACTAAAAATTGG--
1 ATTTTTGGAA-GTTTAGGG--T-AAAA-TGGTA
16213 ATTTTTGGAAGTTTAGGGGTAAAATGGTA
1 ATTTTTGGAAGTTTA-GGGTAAAATGGTA
* * *
16242 ATTCTTGGAAGATTCGAGGTCAAAAATGG-A
1 ATTTTTGGAAGTTTAG-GGT--AAAATGGTA
* *
16272 ATTTTAGGAAGTTTAGGGGTAAAATAGTA
1 ATTTTTGGAAGTTTA-GGGTAAAATGGTA
** *
16301 ATTTTTGGAAGATTCGGGGTTGAAAATGG-G
1 ATTTTTGGAAG-TTTAGGG-T-AAAATGGTA
* *
16331 ATTTTAGGAAGTTCGAGGGTAAAATGGTA
1 ATTTTTGGAAGTT-TAGGGTAAAATGGTA
16360 ATTTTTGGAAGGTTTAGGG
1 ATTTTTGGAA-GTTTAGGG
16379 ACCTTCGAGG
Statistics
Matches: 157, Mismatches: 21, Indels: 37
0.73 0.10 0.17
Matches are distributed among these distances:
27 3 0.02
28 28 0.18
29 52 0.33
30 39 0.25
31 28 0.18
32 4 0.03
33 3 0.02
ACGTcount: A:0.32, C:0.03, G:0.31, T:0.34
Consensus pattern (28 bp):
ATTTTTGGAAGTTTAGGGTAAAATGGTA
Done.