Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01006659.1 Kokia drynarioides strain JFW-HI SEQ_121251, 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: 35296
ACGTcount: A:0.35, C:0.17, G:0.15, T:0.34
Found at i:3301 original size:25 final size:24
Alignment explanation
Indices: 3273--3321 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 24
3263 TGAAAATATC
3273 TGAAAA-TTCAATTAATTAAAAAAAA
1 TGAAAATTTCAA--AATTAAAAAAAA
*
3298 TGAAAATTTTAAAATTAAAAAAAA
1 TGAAAATTTCAAAATTAAAAAAAA
3322 AAAAAAAAGG
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
24 12 0.55
25 6 0.27
26 4 0.18
ACGTcount: A:0.65, C:0.02, G:0.04, T:0.29
Consensus pattern (24 bp):
TGAAAATTTCAAAATTAAAAAAAA
Found at i:6113 original size:144 final size:144
Alignment explanation
Indices: 5924--6213 Score: 535
Period size: 144 Copynumber: 2.0 Consensus size: 144
5914 CCATCAACTA
5924 ATACAAACTATAGCTATAATTTTAAAATCTAAATCACTTAGGGTCTCAGTTGGTAAATTTTCTTT
1 ATACAAACTATAGCTATAATTTTAAAATCTAAATCACTTAGGGTCTCAGTTGGTAAATTTTCTTT
* *
5989 CTTTCTCTTTTTAACATATGAGGTGGATACTGGATAGGGATAGGATTGTCTCTCATTCTGTCTTT
66 CTTTCTCTTTTTAACATATGAGGTGGATACTGGATAGGGATAAGATTGTCTCTCATTCTGTCGTT
6054 TTTCTTGATAAAAG
131 TTTCTTGATAAAAG
* *
6068 ATACAAACTATCGCTATAATTTTAAAATCTAAATCACTTAGGGTCTTAGTTGGTAAATTTTCTTT
1 ATACAAACTATAGCTATAATTTTAAAATCTAAATCACTTAGGGTCTCAGTTGGTAAATTTTCTTT
*
6133 CTTTCTTTTTTTAACATATGAGGTGGATACTGGATAGGGATAAGATTGTCTCTCATTCTGTCGTT
66 CTTTCTCTTTTTAACATATGAGGTGGATACTGGATAGGGATAAGATTGTCTCTCATTCTGTCGTT
6198 TTTCTTGATAAAAG
131 TTTCTTGATAAAAG
6212 AT
1 AT
6214 TGTATCTAAG
Statistics
Matches: 141, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
144 141 1.00
ACGTcount: A:0.29, C:0.13, G:0.16, T:0.42
Consensus pattern (144 bp):
ATACAAACTATAGCTATAATTTTAAAATCTAAATCACTTAGGGTCTCAGTTGGTAAATTTTCTTT
CTTTCTCTTTTTAACATATGAGGTGGATACTGGATAGGGATAAGATTGTCTCTCATTCTGTCGTT
TTTCTTGATAAAAG
Found at i:9351 original size:19 final size:20
Alignment explanation
Indices: 9323--9378 Score: 69
Period size: 20 Copynumber: 2.9 Consensus size: 20
9313 TAAAAACAAG
* *
9323 TATACCAAAATTTTTAA-AT
1 TATACTAAAATTTCTAACAT
9342 TATACTAAAATTTCTAACAT
1 TATACTAAAATTTCTAACAT
* *
9362 TATATTAAAATATCTAA
1 TATACTAAAATTTCTAA
9379 TACTATATCA
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
19 15 0.47
20 17 0.53
ACGTcount: A:0.48, C:0.11, G:0.00, T:0.41
Consensus pattern (20 bp):
TATACTAAAATTTCTAACAT
Found at i:9385 original size:20 final size:20
Alignment explanation
Indices: 9342--9386 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
9332 ATTTTTAAAT
* * *
9342 TATACTAAAATTTCTAACAT
1 TATATTAAAATATCTAACAC
*
9362 TATATTAAAATATCTAATAC
1 TATATTAAAATATCTAACAC
9382 TATAT
1 TATAT
9387 CAACACCAAA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.47, C:0.11, G:0.00, T:0.42
Consensus pattern (20 bp):
TATATTAAAATATCTAACAC
Found at i:14877 original size:12 final size:12
Alignment explanation
Indices: 14862--14887 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
14852 AATTCTTCAA
14862 ACACATAAAAAT
1 ACACATAAAAAT
14874 ACACATAAAAAT
1 ACACATAAAAAT
14886 AC
1 AC
14888 TTCACTGTAC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.65, C:0.19, G:0.00, T:0.15
Consensus pattern (12 bp):
ACACATAAAAAT
Found at i:15165 original size:37 final size:37
Alignment explanation
Indices: 15091--15182 Score: 139
Period size: 37 Copynumber: 2.5 Consensus size: 37
15081 GTTCTTGGAC
* * **
15091 CACCGGCACAAAGCTTTGCTAGGCACATAGCTTGAATA
1 CACCGGCACAAAGC-TTGCTAGGCACACAACCCGAATA
15129 CACCGGCACAAAGCTTGCTAGGCACACAACCCGAATA
1 CACCGGCACAAAGCTTGCTAGGCACACAACCCGAATA
15166 CACCGGCACAAAGCTTG
1 CACCGGCACAAAGCTTG
15183 ATACACCGGC
Statistics
Matches: 50, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
37 36 0.72
38 14 0.28
ACGTcount: A:0.33, C:0.32, G:0.21, T:0.15
Consensus pattern (37 bp):
CACCGGCACAAAGCTTGCTAGGCACACAACCCGAATA
Found at i:15188 original size:20 final size:20
Alignment explanation
Indices: 15163--15323 Score: 234
Period size: 20 Copynumber: 8.1 Consensus size: 20
15153 CACAACCCGA
*
15163 ATACACCGGCACAAAGCTTG
1 ATACACCGGCACAAAGCCTG
*
15183 ATACACCGGCACTAAGCCTG
1 ATACACCGGCACAAAGCCTG
* *
15203 ATACACCGGCACGAAGCCTA
1 ATACACCGGCACAAAGCCTG
* *
15223 AAACACCGGCACGAAGCCTG
1 ATACACCGGCACAAAGCCTG
15243 ATACACCGGCACGAAA-CCTG
1 ATACACCGGCAC-AAAGCCTG
15263 ATACACCGGCACAAAGCCTG
1 ATACACCGGCACAAAGCCTG
* *
15283 AAACACCGGCACAAAGCCTA
1 ATACACCGGCACAAAGCCTG
15303 ATACACCGGCACAAAGCCTG
1 ATACACCGGCACAAAGCCTG
15323 A
1 A
15324 ATACTTAGAA
Statistics
Matches: 127, Mismatches: 12, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
19 3 0.02
20 122 0.96
21 2 0.02
ACGTcount: A:0.36, C:0.34, G:0.20, T:0.10
Consensus pattern (20 bp):
ATACACCGGCACAAAGCCTG
Found at i:15630 original size:20 final size:20
Alignment explanation
Indices: 15605--15707 Score: 138
Period size: 20 Copynumber: 5.2 Consensus size: 20
15595 CAATGGGCAC
15605 GAAACACCGGCACAAAGCCT
1 GAAACACCGGCACAAAGCCT
15625 GAAACACCGGCACAAAGCCT
1 GAAACACCGGCACAAAGCCT
* * *
15645 GATACACAGGCACGAAGCCT
1 GAAACACCGGCACAAAGCCT
*
15665 -AATACACCGGCACGAAGCCT
1 GAA-ACACCGGCACAAAGCCT
15685 -AATACACCGGCACAAAGCCT
1 GAA-ACACCGGCACAAAGCCT
15705 GAA
1 GAA
15708 TACTTAGAAT
Statistics
Matches: 75, Mismatches: 6, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
19 1 0.01
20 72 0.96
21 2 0.03
ACGTcount: A:0.39, C:0.33, G:0.20, T:0.08
Consensus pattern (20 bp):
GAAACACCGGCACAAAGCCT
Found at i:15672 original size:40 final size:41
Alignment explanation
Indices: 15608--15710 Score: 156
Period size: 40 Copynumber: 2.6 Consensus size: 41
15598 TGGGCACGAA
*
15608 ACACCGGCACAAAGCCTGAA-ACACCGGCACAAAGCCTGAT
1 ACACCGGCACAAAGCCTGAATACACCGGCACAAAGCCTAAT
* * *
15648 ACACAGGCACGAAGCCT-AATACACCGGCACGAAGCCTAAT
1 ACACCGGCACAAAGCCTGAATACACCGGCACAAAGCCTAAT
15688 ACACCGGCACAAAGCCTGAATAC
1 ACACCGGCACAAAGCCTGAATAC
15711 TTAGAATCAA
Statistics
Matches: 55, Mismatches: 6, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
39 2 0.04
40 48 0.87
41 5 0.09
ACGTcount: A:0.38, C:0.34, G:0.19, T:0.09
Consensus pattern (41 bp):
ACACCGGCACAAAGCCTGAATACACCGGCACAAAGCCTAAT
Found at i:15930 original size:383 final size:379
Alignment explanation
Indices: 15223--15980 Score: 1394
Period size: 383 Copynumber: 2.0 Consensus size: 379
15213 ACGAAGCCTA
* * *
15223 AAACACCGGCACGAAGCCTGATACACCGGCACGAAACCTGATACACCGGCACAAAGCCTGAAACA
1 AAACACCGGCACAAAGCCTGAAACACCGGCACGAAACCTGATACACAGGCACAAAGCCTGAAACA
15288 CCGGCACAAAGCCTAATACACCGGCACAAAGCCTGAATACTTAGAATCAATTGTACCAATCCACA
66 CCGGCACAAAGCCTAATACACCGGCACAAAGCCTGAATACTTAGAATCAATTGTACCAATCCACA
15353 TAGAATGGTACATGTCAACAAATAACCATTCCTTATATAAAAATCTATAATTCAACAATGAACAA
131 TAGAATGGTACATGTCAACAAATAACCATTCCTTATATAAAAATCTATAATTCAACAATGAACAA
15418 TCACAAAATAAATTTATAATTTCACATAATAACAAAACGAACTTACCTAATTACATGATTAACAA
196 TCACAAAATAAATTTATAATTTCACATAATAACAAAACGAACTTACCTAATTACATGATTAACAA
15483 TTTCTCCTTTCATGGTTCAACCATTTAACAACAGATGACTATGAGTATTTCTTGATCTATTCCAT
261 TTTCTCCTTTCATGGTTCAACCATTTAACAACAGATGACTATGAGTATTTCTTGATCTATTCCAT
15548 AATCATACTTGTATATATATATATATATATATTCATAATTTTCCATCCAATGGGCACG
326 AATCATACTTG----TATATATATATATATATTCATAATTTTCCATCCAATGGGCACG
*
15606 AAACACCGGCACAAAGCCTGAAACACCGGCAC-AAAGCCTGATACACAGGCACGAAGCCT-AATA
1 AAACACCGGCACAAAGCCTGAAACACCGGCACGAAA-CCTGATACACAGGCACAAAGCCTGAA-A
*
15669 CACCGGCACGAAGCCTAATACACCGGCACAAAGCCTGAATACTTAGAATCAATTGTACCAATCCA
64 CACCGGCACAAAGCCTAATACACCGGCACAAAGCCTGAATACTTAGAATCAATTGTACCAATCCA
15734 CATAGAATGGTACATGTCAACAAATAACCATTCCTTATATAAAAATCTATAATTCAACAATGAAC
129 CATAGAATGGTACATGTCAACAAATAACCATTCCTTATATAAAAATCTATAATTCAACAATGAAC
15799 AATCACAAAATAAATTTATAATTTCACATAATAACAAAACGAACTTACCTAATTACATGATTAAC
194 AATCACAAAATAAATTTATAATTTCACATAATAACAAAACGAACTTACCTAATTACATGATTAAC
*
15864 AATTTCTCCTTTCATGGTTCAACCATTTAACAACAGATGACTGTGAGTATTTCTTGATCTATTCC
259 AATTTCTCCTTTCATGGTTCAACCATTTAACAACAGATGACTATGAGTATTTCTTGATCTATTCC
15929 ATAATCATACTTGTATATATATATATATATTCATAATTTTCCATCCAATGGG
324 ATAATCATACTTGTATATATATATATATATTCATAATTTTCCATCCAATGGG
15981 ATTATCCAAT
Statistics
Matches: 367, Mismatches: 6, Indels: 8
0.96 0.02 0.02
Matches are distributed among these distances:
379 39 0.11
382 5 0.01
383 323 0.88
ACGTcount: A:0.40, C:0.23, G:0.11, T:0.27
Consensus pattern (379 bp):
AAACACCGGCACAAAGCCTGAAACACCGGCACGAAACCTGATACACAGGCACAAAGCCTGAAACA
CCGGCACAAAGCCTAATACACCGGCACAAAGCCTGAATACTTAGAATCAATTGTACCAATCCACA
TAGAATGGTACATGTCAACAAATAACCATTCCTTATATAAAAATCTATAATTCAACAATGAACAA
TCACAAAATAAATTTATAATTTCACATAATAACAAAACGAACTTACCTAATTACATGATTAACAA
TTTCTCCTTTCATGGTTCAACCATTTAACAACAGATGACTATGAGTATTTCTTGATCTATTCCAT
AATCATACTTGTATATATATATATATATTCATAATTTTCCATCCAATGGGCACG
Found at i:24718 original size:2 final size:2
Alignment explanation
Indices: 24713--24737 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
24703 GAAAGTTTTT
24713 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
24738 TCGTAATTTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:29343 original size:2 final size:2
Alignment explanation
Indices: 29336--29361 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
29326 ATACGTCTTT
29336 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
29362 ACGAATGTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:29756 original size:43 final size:43
Alignment explanation
Indices: 29657--29979 Score: 342
Period size: 43 Copynumber: 7.3 Consensus size: 43
29647 TTATGAGAAA
* * * ** *
29657 AAACGCCGCTAAAGAATATGGTTTTTAGCTGCG-TTTTACTAC
1 AAACGCCGCTAAAGAACATGGTCTTTAGCGGCGCTTTCCCCAC
* * * *
29699 AAACGCCGCTAAAGAACATGATCTTTAGCGGAGCTTTCACCAT
1 AAACGCCGCTAAAGAACATGGTCTTTAGCGGCGCTTTCCCCAC
* **
29742 AAACGTCGCTAAAGAACATGGTCTTTAGCGGCGCTTTTGCCAC
1 AAACGCCGCTAAAGAACATGGTCTTTAGCGGCGCTTTCCCCAC
* * *
29785 AAACGTCGTTAAAGAACATGGTCTTTAGCGGCGTTTTCCCCAC
1 AAACGCCGCTAAAGAACATGGTCTTTAGCGGCGCTTTCCCCAC
* * *
29828 AAATGCCACGAAAGAACATGGTCTTTAGCGGCGCTTTCCCCAC
1 AAACGCCGCTAAAGAACATGGTCTTTAGCGGCGCTTTCCCCAC
*
29871 AAACGCCGCTAAAGACCGCTAAAGAACATGGTCTTTAGCGGTGCTTTCCCCAC
1 AAA-----C----G-CCGCTAAAGAACATGGTCTTTAGCGGCGCTTTCCCCAC
*
29924 AAACGCCGCTAAAGAACATGGTTTTTAGCGGCGCTTTCCCCAC
1 AAACGCCGCTAAAGAACATGGTCTTTAGCGGCGCTTTCCCCAC
* *
29967 AAATGCGGCTAAA
1 AAACGCCGCTAAA
29980 TTAATAGATT
Statistics
Matches: 238, Mismatches: 32, Indels: 21
0.82 0.11 0.07
Matches are distributed among these distances:
42 28 0.12
43 169 0.71
44 1 0.00
48 1 0.00
52 1 0.00
53 38 0.16
ACGTcount: A:0.28, C:0.26, G:0.21, T:0.24
Consensus pattern (43 bp):
AAACGCCGCTAAAGAACATGGTCTTTAGCGGCGCTTTCCCCAC
Found at i:29918 original size:53 final size:53
Alignment explanation
Indices: 29838--29938 Score: 193
Period size: 53 Copynumber: 1.9 Consensus size: 53
29828 AAATGCCACG
29838 AAAGAACATGGTCTTTAGCGGCGCTTTCCCCACAAACGCCGCTAAAGACCGCT
1 AAAGAACATGGTCTTTAGCGGCGCTTTCCCCACAAACGCCGCTAAAGACCGCT
*
29891 AAAGAACATGGTCTTTAGCGGTGCTTTCCCCACAAACGCCGCTAAAGA
1 AAAGAACATGGTCTTTAGCGGCGCTTTCCCCACAAACGCCGCTAAAGA
29939 ACATGGTTTT
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
53 47 1.00
ACGTcount: A:0.30, C:0.30, G:0.21, T:0.20
Consensus pattern (53 bp):
AAAGAACATGGTCTTTAGCGGCGCTTTCCCCACAAACGCCGCTAAAGACCGCT
Found at i:29958 original size:96 final size:96
Alignment explanation
Indices: 29794--29979 Score: 300
Period size: 96 Copynumber: 1.9 Consensus size: 96
29784 CAAACGTCGT
* *
29794 TAAAGAACATGGTCTTTAGCGGCGTTTTCCCCACAAATGCCACGAAAGAACATGGTCTTTAGCGG
1 TAAAGAACATGGTCTTTAGCGGCGCTTTCCCCACAAACGCCACGAAAGAACATGGTCTTTAGCGG
29859 CGCTTTCCCCACAAACGCCGCTAAAGACCGC
66 CGCTTTCCCCACAAACGCCGCTAAAGACCGC
* * * *
29890 TAAAGAACATGGTCTTTAGCGGTGCTTTCCCCACAAACGCCGCTAAAGAACATGGTTTTTAGCGG
1 TAAAGAACATGGTCTTTAGCGGCGCTTTCCCCACAAACGCCACGAAAGAACATGGTCTTTAGCGG
* *
29955 CGCTTTCCCCACAAATGCGGCTAAA
66 CGCTTTCCCCACAAACGCCGCTAAA
29980 TTAATAGATT
Statistics
Matches: 82, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
96 82 1.00
ACGTcount: A:0.28, C:0.28, G:0.21, T:0.23
Consensus pattern (96 bp):
TAAAGAACATGGTCTTTAGCGGCGCTTTCCCCACAAACGCCACGAAAGAACATGGTCTTTAGCGG
CGCTTTCCCCACAAACGCCGCTAAAGACCGC
Found at i:33148 original size:22 final size:22
Alignment explanation
Indices: 33120--33184 Score: 78
Period size: 22 Copynumber: 3.0 Consensus size: 22
33110 GGTTGTTTTT
33120 TATAATTAAATATTTAATTAAA
1 TATAATTAAATATTTAATTAAA
* * *
33142 TATAATTAAATAATTAAAT-AT
1 TATAATTAAATATTTAATTAAA
*
33163 TTTAAATTAAATATTTAATTAA
1 TAT-AATTAAATATTTAATTAA
33185 CTAATACTAT
Statistics
Matches: 35, Mismatches: 6, Indels: 3
0.80 0.14 0.07
Matches are distributed among these distances:
21 3 0.09
22 31 0.89
23 1 0.03
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (22 bp):
TATAATTAAATATTTAATTAAA
Found at i:33172 original size:14 final size:15
Alignment explanation
Indices: 33117--33178 Score: 60
Period size: 14 Copynumber: 4.2 Consensus size: 15
33107 TTGGGTTGTT
33117 TTTTATAATTAAATA
1 TTTTATAATTAAATA
33132 --TT-TAATTAAATA
1 TTTTATAATTAAATA
*
33144 TAATTAAATAATTAAATA
1 T--TT-TATAATTAAATA
33162 TTTTA-AATTAAATA
1 TTTTATAATTAAATA
33176 TTT
1 TTT
33179 AATTAACTAA
Statistics
Matches: 39, Mismatches: 2, Indels: 13
0.72 0.04 0.24
Matches are distributed among these distances:
12 10 0.26
13 2 0.05
14 12 0.31
15 1 0.03
16 3 0.08
18 11 0.28
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (15 bp):
TTTTATAATTAAATA
Found at i:34842 original size:21 final size:21
Alignment explanation
Indices: 34816--34866 Score: 93
Period size: 21 Copynumber: 2.4 Consensus size: 21
34806 AAGATAAGAC
34816 TGAAGAAGAGAAGGGCGTGCA
1 TGAAGAAGAGAAGGGCGTGCA
*
34837 TGAAGAAGGGAAGGGCGTGCA
1 TGAAGAAGAGAAGGGCGTGCA
34858 TGAAGAAGA
1 TGAAGAAGA
34867 AGGTAATTTC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.39, C:0.08, G:0.43, T:0.10
Consensus pattern (21 bp):
TGAAGAAGAGAAGGGCGTGCA
Done.