Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012168.1 Kokia drynarioides strain JFW-HI SEQ_127169, 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: 17724
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
Found at i:4628 original size:69 final size:68
Alignment explanation
Indices: 4555--4732 Score: 194
Period size: 71 Copynumber: 2.6 Consensus size: 68
4545 AAAAATAATT
* * *
4555 GAGATGAAAACCCATAAAGGGCATCTTGAAATAAAAAAACAAACAAAAAAATGAAGAGAAAAAGA
1 GAGATGAAAACCCGTAAAGGGCATCTTGAAATAAAAAAAAAAACAAAAAAA-GAAAAGAAAAAGA
*
4620 GGTC
65 AGTC
* * * * * *
4624 GAGATGAAAACTCGTAAAGGACATCTTGAAACCCAAACAAAAAAAAGAAAGAAAGAAAAGAATAA
1 GAGATGAAAACCCGTAAAGGGCATCTTGAAA--TAAA-AAAAAAAACAAAAAAAGAAAAGAAAAA
4689 GAAGTC
63 GAAGTC
* * * *
4695 GAGATGAAAACCCGCAAAGAGCATCTCGAAATGAAAAA
1 GAGATGAAAACCCGTAAAGGGCATCTTGAAATAAAAAA
4733 TAATAAAAAT
Statistics
Matches: 89, Mismatches: 17, Indels: 7
0.79 0.15 0.06
Matches are distributed among these distances:
68 3 0.03
69 30 0.34
71 43 0.48
72 13 0.15
ACGTcount: A:0.56, C:0.13, G:0.19, T:0.11
Consensus pattern (68 bp):
GAGATGAAAACCCGTAAAGGGCATCTTGAAATAAAAAAAAAAACAAAAAAAGAAAAGAAAAAGAA
GTC
Found at i:5974 original size:5 final size:5
Alignment explanation
Indices: 5944--6040 Score: 96
Period size: 5 Copynumber: 19.8 Consensus size: 5
5934 TTTCACCCAA
*
5944 AAAAG AAGAAG AAGAAG AAAAA AAAAG AAAAG AAAAG AAGAA- AAAAG
1 AAAAG AA-AAG AA-AAG AAAAG AAAAG AAAAG AAAAG AA-AAG AAAAG
* * *
5991 AAAAG AAAAG AAAAG AAAA- AAGA- AAAAG -AAA- AAAAT AAGAG AAAAG
1 AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG
6037 AAAA
1 AAAA
6041 TGAGAAGGAG
Statistics
Matches: 79, Mismatches: 7, Indels: 12
0.81 0.07 0.12
Matches are distributed among these distances:
4 14 0.18
5 52 0.66
6 13 0.16
ACGTcount: A:0.80, C:0.00, G:0.19, T:0.01
Consensus pattern (5 bp):
AAAAG
Found at i:6045 original size:13 final size:12
Alignment explanation
Indices: 5949--6046 Score: 87
Period size: 12 Copynumber: 8.0 Consensus size: 12
5939 CCCAAAAAAG
5949 AAGAAGAAGAAGAA
1 AAGAA-AAG-AGAA
5963 AA-AAAA-AGAA
1 AAGAAAAGAGAA
5973 AAGAAAAGAAGAA
1 AAGAAAAG-AGAA
*
5986 AA-AAGAAAAGAA
1 AAGAA-AAGAGAA
*
5998 AAGAAAAGAAAA
1 AAGAAAAGAGAA
6010 AAGAAAA-AGAA
1 AAGAAAAGAGAA
*
6021 AAAAATAAGAGAA
1 AAGAA-AAGAGAA
6034 AAGAAAATGAGAA
1 AAGAAAA-GAGAA
6047 GGAGAGTCCG
Statistics
Matches: 70, Mismatches: 6, Indels: 17
0.75 0.06 0.18
Matches are distributed among these distances:
10 6 0.09
11 11 0.16
12 26 0.37
13 25 0.36
14 2 0.03
ACGTcount: A:0.79, C:0.00, G:0.19, T:0.02
Consensus pattern (12 bp):
AAGAAAAGAGAA
Found at i:6396 original size:19 final size:20
Alignment explanation
Indices: 6354--6397 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
6344 TGTTTCTTAT
*
6354 TTTTTACCAACATTTGTCAT
1 TTTTTACCAACATTTGTCAA
*
6374 TTTTTACCAATATTTG-CAA
1 TTTTTACCAACATTTGTCAA
6393 TTTTT
1 TTTTT
6398 GGCCATTGTT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 7 0.32
20 15 0.68
ACGTcount: A:0.25, C:0.16, G:0.05, T:0.55
Consensus pattern (20 bp):
TTTTTACCAACATTTGTCAA
Found at i:6397 original size:20 final size:20
Alignment explanation
Indices: 6352--6389 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
6342 AATGTTTCTT
6352 ATTTTTTACCAACATTTGTC
1 ATTTTTTACCAACATTTGTC
*
6372 ATTTTTTACCAATATTTG
1 ATTTTTTACCAACATTTG
6390 CAATTTTTGG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.26, C:0.16, G:0.05, T:0.53
Consensus pattern (20 bp):
ATTTTTTACCAACATTTGTC
Found at i:7273 original size:100 final size:100
Alignment explanation
Indices: 6989--7609 Score: 683
Period size: 100 Copynumber: 6.2 Consensus size: 100
6979 CAATAAATTT
* * * * * * * * *
6989 TATA-CCCTAAAGTTGCAGTGGAGCGAATTAAAACTAACAATAGTAAATCTCAATCTTCACTAAA
1 TATACCCCTAAAGTTGTAGAGGGGTGAATTAAAACTAACAGTAGCAGATCTCAATCTCCACTGAA
* *
7053 GTTGCAGTGAAATGGAGTGAAGCCACACCAAATCC
66 GTTGCAATGGAATGGAGTGAAGCCACACCAAATCC
* * * * *
7088 TATACCCTTAAAGTTATAGAGGGGGCGAATTAAAACTAACAGTAGCAAATCTCAATCTCCATTGA
1 TATACCCCTAAAGTTGTAGA-GGGGTGAATTAAAACTAACAGTAGCAGATCTCAATCTCCACTGA
* * *
7153 AGTTGCAGTGGAATGAAGTGAAGTCACACCAAATCC
65 AGTTGCAATGGAATGGAGTGAAGCCACACCAAATCC
* * * * *
7189 TATACCCTTAAAGTTGTAGAGGGGTGAATTAGAATTAATAGTAGCAGATCTTAATCTCCACTGAA
1 TATACCCCTAAAGTTGTAGAGGGGTGAATTAAAACTAACAGTAGCAGATCTCAATCTCCACTGAA
*
7254 GTTGCAATGGAATGGAGTGAAGCCATACCAAATCC
66 GTTGCAATGGAATGGAGTGAAGCCACACCAAATCC
* * * *
7289 TACACCCCTAAAGTTGTAG-GGGGAT-AGATTTAAACTAACAGTAGTAGATCTCAATCTCTACTG
1 TATACCCCTAAAGTTGTAGAGGGG-TGA-ATTAAAACTAACAGTAGCAGATCTCAATCTCCACTG
* * * * *
7352 AATTTGTAATGGAATGAAGTGAAGCCACACAAAATCT
64 AAGTTGCAATGGAATGGAGTGAAGCCACACCAAATCC
** * * *
7389 TATACCCCTAAAGTTACAGAGGGATGGATTAAAACTAACAGTAGCAGATCTCAATCTTCACTGAA
1 TATACCCCTAAAGTTGTAGAGGGGTGAATTAAAACTAACAGTAGCAGATCTCAATCTCCACTGAA
** * *
7454 GTTGCGGTGGAATGGAATGAAGTCACACCAAATCC
66 GTTGCAATGGAATGGAGTGAAGCCACACCAAATCC
* * * * * * *
7489 TATACCCTTAAAGTTTTAGAGGGG-CAGATCAAAACTAACAGTAGCAGGTCTCAATCTCTATTGA
1 TATACCCCTAAAGTTGTAGAGGGGTGA-ATTAAAACTAACAGTAGCAGATCTCAATCTCCACTGA
*
7553 AGTTGCAATGGAATGGAGTGAAGTTACACCACCAAATCC
65 AGTTGCAATGGAATGGAGTGAAG--CCA-CACCAAATCC
*
7592 TATACCCCTGAAGTTGTA
1 TATACCCCTAAAGTTGTA
7610 ATAGGTCAGA
Statistics
Matches: 436, Mismatches: 76, Indels: 16
0.83 0.14 0.03
Matches are distributed among these distances:
99 9 0.02
100 307 0.70
101 93 0.21
102 2 0.00
103 25 0.06
ACGTcount: A:0.36, C:0.19, G:0.20, T:0.25
Consensus pattern (100 bp):
TATACCCCTAAAGTTGTAGAGGGGTGAATTAAAACTAACAGTAGCAGATCTCAATCTCCACTGAA
GTTGCAATGGAATGGAGTGAAGCCACACCAAATCC
Found at i:7556 original size:300 final size:303
Alignment explanation
Indices: 7019--7609 Score: 809
Period size: 300 Copynumber: 2.0 Consensus size: 303
7009 GAGCGAATTA
* * *
7019 AAACTAACAATAGTAAATCTCAATCTTCACTAAAGTTGCAGTGAAATGGAGTGAAGCCACACCAA
1 AAACTAACAATAGTAAATCTCAATCTTCACTAAAGTTGCAATGAAATGAAGTGAAGCCACACAAA
* *
7084 ATCCTATACCCTTAAAGTTATAGAGGGGGCGAATTAAAACTAACAGTAGCAAATCTCAATCTCCA
66 ATCCTATACCCCTAAAGTTACAGAGGGGGCGAATTAAAACTAACAGTAGCAAATCTCAATCTCCA
* *
7149 TTGAAGTTGCAGTGGAATGAAGTGAAGTCACACCAAATCCTATACCCTTAAAGTTGTAGAGGGGT
131 CTGAAGTTGCAGTGGAATGAAGTGAAGTCACACCAAATCCTATACCCTTAAAGTTGTAGAGGGGA
* * * * * *
7214 GAATTAGAATTAATAGTAGCAGATCTTAATCTCCACTGAAGTTGCAATGGAATGGAGTGAAG-CC
196 GAATCAAAACTAACAGTAGCAGATCTCAATCTCCACTGAAGTTGCAATGGAATGGAGTGAAGTAC
*
7278 A-TACCAAATCCTACACCCCTAAAGTTGTAGGGGGATAGATTT
261 ACCACCAAATCCTACACCCCTAAAGTTGTAGGGGGATAGATTT
* * * * * *
7320 AAACTAACAGTAGTAGATCTCAATC-TCTACTGAATTTGTAATGGAATGAAGTGAAGCCACACAA
1 AAACTAACAATAGTAAATCTCAATCTTC-ACTAAAGTTGCAATGAAATGAAGTGAAGCCACACAA
* * * *
7384 AATCTTATACCCCTAAAGTTACAGAGGGATG-G-ATTAAAACTAACAGTAGCAGATCTCAATCTT
65 AATCCTATACCCCTAAAGTTACAGAGGG-GGCGAATTAAAACTAACAGTAGCAAATCTCAATCTC
* *
7447 CACTGAAGTTGCGGTGGAATGGAA-TGAAGTCACACCAAATCCTATACCCTTAAAGTTTTAGAGG
129 CACTGAAGTTGCAGTGGAAT-GAAGTGAAGTCACACCAAATCCTATACCCTTAAAGTTGTAGAGG
* * *
7511 GGCAG-ATCAAAACTAACAGTAGCAGGTCTCAATCTCTATTGAAGTTGCAATGGAATGGAGTGAA
193 GG-AGAATCAAAACTAACAGTAGCAGATCTCAATCTCCACTGAAGTTGCAATGGAATGGAGTGAA
* *
7575 GTTACACCACCAAATCCTATACCCCTGAAGTTGTA
257 G-TACACCACCAAATCCTACACCCCTAAAGTTGTA
7610 ATAGGTCAGA
Statistics
Matches: 252, Mismatches: 31, Indels: 12
0.85 0.11 0.04
Matches are distributed among these distances:
300 142 0.56
301 82 0.33
302 3 0.01
303 25 0.10
ACGTcount: A:0.37, C:0.19, G:0.20, T:0.25
Consensus pattern (303 bp):
AAACTAACAATAGTAAATCTCAATCTTCACTAAAGTTGCAATGAAATGAAGTGAAGCCACACAAA
ATCCTATACCCCTAAAGTTACAGAGGGGGCGAATTAAAACTAACAGTAGCAAATCTCAATCTCCA
CTGAAGTTGCAGTGGAATGAAGTGAAGTCACACCAAATCCTATACCCTTAAAGTTGTAGAGGGGA
GAATCAAAACTAACAGTAGCAGATCTCAATCTCCACTGAAGTTGCAATGGAATGGAGTGAAGTAC
ACCACCAAATCCTACACCCCTAAAGTTGTAGGGGGATAGATTT
Found at i:9085 original size:31 final size:30
Alignment explanation
Indices: 9045--9121 Score: 84
Period size: 31 Copynumber: 2.6 Consensus size: 30
9035 CCATTTGGTC
* *
9045 CTTTCTCATTTTTAATTTGTTTCAATTTAG
1 CTTTTTCATTTTTAATTTATTTCAATTTAG
* * *
9075 TCTTTTTCATTTTTTATTTATTTTAATTTCG
1 -CTTTTTCATTTTTAATTTATTTCAATTTAG
*
9106 CTTTTT-AATTTTAATT
1 CTTTTTCATTTTTAATT
9122 GCTTTACAAT
Statistics
Matches: 39, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
29 8 0.21
30 6 0.15
31 25 0.64
ACGTcount: A:0.19, C:0.10, G:0.04, T:0.66
Consensus pattern (30 bp):
CTTTTTCATTTTTAATTTATTTCAATTTAG
Found at i:9227 original size:5 final size:5
Alignment explanation
Indices: 9217--9262 Score: 56
Period size: 5 Copynumber: 8.8 Consensus size: 5
9207 TTCTTGTAAT
* *
9217 TTTTA TTTTA TTTTA ATTTA GTTTAA TTTTA TTTTA TTTCTA TTTT
1 TTTTA TTTTA TTTTA TTTTA -TTTTA TTTTA TTTTA TTT-TA TTTT
9263 TAATTTGTAC
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
5 27 0.77
6 8 0.23
ACGTcount: A:0.22, C:0.02, G:0.02, T:0.74
Consensus pattern (5 bp):
TTTTA
Found at i:9235 original size:11 final size:11
Alignment explanation
Indices: 9215--9268 Score: 58
Period size: 11 Copynumber: 4.9 Consensus size: 11
9205 GGTTCTTGTA
*
9215 ATTTTTATTTT
1 ATTTTAATTTT
9226 ATTTTAA-TTT
1 ATTTTAATTTT
*
9236 AGTTTAATTTT
1 ATTTTAATTTT
9247 ATTTT-ATTTCT
1 ATTTTAATTT-T
9258 ATTTTTAATTT
1 A-TTTTAATTT
9269 GTACCTTTAA
Statistics
Matches: 36, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
10 13 0.36
11 15 0.42
12 4 0.11
13 4 0.11
ACGTcount: A:0.24, C:0.02, G:0.02, T:0.72
Consensus pattern (11 bp):
ATTTTAATTTT
Found at i:9236 original size:10 final size:10
Alignment explanation
Indices: 9217--9268 Score: 50
Period size: 10 Copynumber: 4.9 Consensus size: 10
9207 TTCTTGTAAT
*
9217 TTTTATTTTA
1 TTTTAATTTA
9227 TTTTAATTTA
1 TTTTAATTTA
*
9237 GTTTAATTTTA
1 TTTTAA-TTTA
*
9248 TTTTATTTCTA
1 TTTTAATT-TA
9259 TTTTTAATTT
1 -TTTTAATTT
9269 GTACCTTTAA
Statistics
Matches: 34, Mismatches: 5, Indels: 5
0.77 0.11 0.11
Matches are distributed among these distances:
10 16 0.47
11 11 0.32
12 7 0.21
ACGTcount: A:0.23, C:0.02, G:0.02, T:0.73
Consensus pattern (10 bp):
TTTTAATTTA
Found at i:9247 original size:16 final size:17
Alignment explanation
Indices: 9226--9268 Score: 52
Period size: 16 Copynumber: 2.6 Consensus size: 17
9216 TTTTTATTTT
9226 ATTTTAATTTAGTT-TA
1 ATTTTAATTTAGTTCTA
* *
9242 ATTTTATTTTATTTCTA
1 ATTTTAATTTAGTTCTA
*
9259 TTTTTAATTT
1 ATTTTAATTT
9269 GTACCTTTAA
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
16 12 0.55
17 10 0.45
ACGTcount: A:0.26, C:0.02, G:0.02, T:0.70
Consensus pattern (17 bp):
ATTTTAATTTAGTTCTA
Found at i:9285 original size:30 final size:30
Alignment explanation
Indices: 9244--9307 Score: 78
Period size: 30 Copynumber: 2.1 Consensus size: 30
9234 TTAGTTTAAT
* *
9244 TTTATTTTATTT-CTATTTTTAATTT-GTACC
1 TTTAATTTATTTGC-ATTTTCAATTTAGT-CC
9274 TTTAATTTATTTGCATTTTCAATTTAGTCC
1 TTTAATTTATTTGCATTTTCAATTTAGTCC
9304 TTTA
1 TTTA
9308 CTTAATTTTG
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
30 27 0.90
31 3 0.10
ACGTcount: A:0.22, C:0.11, G:0.05, T:0.62
Consensus pattern (30 bp):
TTTAATTTATTTGCATTTTCAATTTAGTCC
Found at i:9449 original size:17 final size:17
Alignment explanation
Indices: 9427--9459 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
9417 TAGTCTTTAA
9427 TTTTTATTTATTTATTG
1 TTTTTATTTATTTATTG
9444 TTTTTATTTATTTATT
1 TTTTTATTTATTTATT
9460 TGTTACTTAT
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:0.18, C:0.00, G:0.03, T:0.79
Consensus pattern (17 bp):
TTTTTATTTATTTATTG
Found at i:9474 original size:3 final size:3
Alignment explanation
Indices: 9466--9508 Score: 79
Period size: 3 Copynumber: 14.7 Consensus size: 3
9456 TATTTGTTAC
9466 TTA TTA TTA TTA TTA -TA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
9509 TAGTCCTTTA
Statistics
Matches: 39, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 2 0.05
3 37 0.95
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:11030 original size:18 final size:18
Alignment explanation
Indices: 11009--11066 Score: 64
Period size: 18 Copynumber: 3.3 Consensus size: 18
10999 TTATCAAAAG
*
11009 ATATATTAATTAATGATA
1 ATATATTAATTAATAATA
* *
11027 ATATAATAATAAATAATA
1 ATATATTAATTAATAATA
* *
11045 ATAT-TTTATTATTAATA
1 ATATATTAATTAATAATA
11062 ATATA
1 ATATA
11067 AAATATAAGA
Statistics
Matches: 32, Mismatches: 7, Indels: 2
0.78 0.17 0.05
Matches are distributed among these distances:
17 13 0.41
18 19 0.59
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (18 bp):
ATATATTAATTAATAATA
Done.