Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01002542.1 Kokia drynarioides strain JFW-HI SEQ_114723, 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: 37967
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.34
Warning! 13 characters in sequence are not A, C, G, or T
Found at i:551 original size:21 final size:22
Alignment explanation
Indices: 516--556 Score: 59
Period size: 21 Copynumber: 1.9 Consensus size: 22
506 ACGAATTAAT
516 ATTAAATAAGAAAAA-TAAATA
1 ATTAAATAAGAAAAACTAAATA
537 ATTAAATAA-ATAAAACTAAA
1 ATTAAATAAGA-AAAACTAAA
557 AGTGATTGAA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 1 0.06
21 13 0.72
22 4 0.22
ACGTcount: A:0.71, C:0.02, G:0.02, T:0.24
Consensus pattern (22 bp):
ATTAAATAAGAAAAACTAAATA
Found at i:13764 original size:30 final size:30
Alignment explanation
Indices: 13728--13798 Score: 142
Period size: 30 Copynumber: 2.4 Consensus size: 30
13718 AGCATGCTTG
13728 TAATGTGATTACGCGCTATCATCAGAAATT
1 TAATGTGATTACGCGCTATCATCAGAAATT
13758 TAATGTGATTACGCGCTATCATCAGAAATT
1 TAATGTGATTACGCGCTATCATCAGAAATT
13788 TAATGTGATTA
1 TAATGTGATTA
13799 TATAACAATA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 41 1.00
ACGTcount: A:0.34, C:0.14, G:0.17, T:0.35
Consensus pattern (30 bp):
TAATGTGATTACGCGCTATCATCAGAAATT
Found at i:14712 original size:29 final size:29
Alignment explanation
Indices: 14670--14727 Score: 71
Period size: 29 Copynumber: 2.0 Consensus size: 29
14660 TTATAGGGAC
*
14670 TGGATTAAATTAGTCCCTCTACTACTAAA
1 TGGATCAAATTAGTCCCTCTACTACTAAA
* * * *
14699 TGGATCAATTTAGTTCTTGTACTACTAAA
1 TGGATCAAATTAGTCCCTCTACTACTAAA
14728 ATAAGTCCAA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
29 24 1.00
ACGTcount: A:0.33, C:0.17, G:0.12, T:0.38
Consensus pattern (29 bp):
TGGATCAAATTAGTCCCTCTACTACTAAA
Found at i:14939 original size:30 final size:30
Alignment explanation
Indices: 14905--14968 Score: 76
Period size: 29 Copynumber: 2.2 Consensus size: 30
14895 TTCGACTTAT
** * *
14905 TTGATTCTTTTTACCAGTATAGGGACTAAA
1 TTGATTCCATTTACCAATAGAGGGACTAAA
*
14935 TTGA-TCCATTTACTAATAGAGGGACTAAA
1 TTGATTCCATTTACCAATAGAGGGACTAAA
14964 TTGAT
1 TTGAT
14969 CCAATCCACA
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
29 24 0.86
30 4 0.14
ACGTcount: A:0.33, C:0.12, G:0.17, T:0.38
Consensus pattern (30 bp):
TTGATTCCATTTACCAATAGAGGGACTAAA
Found at i:18234 original size:222 final size:222
Alignment explanation
Indices: 17848--18411 Score: 871
Period size: 222 Copynumber: 2.5 Consensus size: 222
17838 CTTTGATATC
*
17848 CTTTCCTGCTCCACCAATAGCTGCTCTTTCAAACATGCATCTACTTTTGCAAAAATTATTTCTTT
1 CTTTCCTGCTCCACCAATAGCTGCTCTTTCAAACATGCATCTACTTTTGCAAAAATCATTTCTTT
* * * * * *
17913 CTTTAAACCATCAATGACAGCATAAGCATTGGTAAGATTTTTTCCAGTGTCTGCTTCCTTCTCGT
66 CTTTAAACCATCAGTGACAGCATAAGCATTGGTAAGCTTTTTCCCAGAGTCAGCTTCCTTCTCAT
* * * * *
17978 CCAAATTCTGGAGAAGCAGACAGTTTTCTTTCTTCATCTTTCTTAACTCAATTTGTGCTTCTTCA
131 CCAAATCCTGGAGAAGCAGACAGTTCTCTTTCTTCAACATTCTTAACTCAATCTGTGCTTCTTCA
*
18043 ACTTTTTCTTGTAGAAAAGACAACTCA
196 ACTTTTTCTTGGAGAAAAGACAACTCA
*
18070 CTTTCCTGCTCCACCAATAGCTGCTCTTTCAAACATGCATCTACTTTTGCGAAAATCATTTCTTT
1 CTTTCCTGCTCCACCAATAGCTGCTCTTTCAAACATGCATCTACTTTTGCAAAAATCATTTCTTT
* * * *
18135 CTTTAAACCATCAGTGACAG-AGTAGGCATTGGCAAGCTTTTTGCCAGAGTCAGCTTTCTTCTCA
66 CTTTAAACCATCAGTGACAGCA-TAAGCATTGGTAAGCTTTTTCCCAGAGTCAGCTTCCTTCTCA
*
18199 TCCAAATCCTGGAGAAGTAGACAGTTCTCTTTCTTCAACATTCTTAACTCAATCTGTGCTTCTTC
130 TCCAAATCCTGGAGAAGCAGACAGTTCTCTTTCTTCAACATTCTTAACTCAATCTGTGCTTCTTC
*
18264 AACTTTTTCTTGGAGAATAGACAACTCA
195 AACTTTTTCTTGGAGAAAAGACAACTCA
* * * * *
18292 CTTTCCCGCTCCACCAATAGCTGCTCCTTCAAACATGCATCTAATTTTGTAAAAGTCATTTCTTT
1 CTTTCCTGCTCCACCAATAGCTGCTCTTTCAAACATGCATCTACTTTTGCAAAAATCATTTCTTT
18357 CTTTAAACCATCAAG-GACAGCATAAGCATTGGTAAGCTTTTTCCCAGAGTCAGCT
66 CTTTAAACCATC-AGTGACAGCATAAGCATTGGTAAGCTTTTTCCCAGAGTCAGCT
18412 AAGTGGACAA
Statistics
Matches: 311, Mismatches: 28, Indels: 6
0.90 0.08 0.02
Matches are distributed among these distances:
221 1 0.00
222 307 0.99
223 3 0.01
ACGTcount: A:0.26, C:0.25, G:0.13, T:0.36
Consensus pattern (222 bp):
CTTTCCTGCTCCACCAATAGCTGCTCTTTCAAACATGCATCTACTTTTGCAAAAATCATTTCTTT
CTTTAAACCATCAGTGACAGCATAAGCATTGGTAAGCTTTTTCCCAGAGTCAGCTTCCTTCTCAT
CCAAATCCTGGAGAAGCAGACAGTTCTCTTTCTTCAACATTCTTAACTCAATCTGTGCTTCTTCA
ACTTTTTCTTGGAGAAAAGACAACTCA
Found at i:21239 original size:384 final size:381
Alignment explanation
Indices: 20501--21648 Score: 1882
Period size: 381 Copynumber: 3.0 Consensus size: 381
20491 CGTTCTTAGC
20501 TTAGACAGCTCCTCCTGTGTCTTCAAAATGTCATTCTCCACCATATCTTCAAGCTTTTGTTCAAT
1 TTAGACAGCTCCTCCTGTGTCTTCAAAATGTCATTCTCCACCATATCTTCAAGCTTTTGTTCAAT
* * * * ** * * *
20566 AGCAGCAGCATGCTGCTCCTCCTCAAAAAGCCTTTTCCGGAGATCAGTGCAAACTTCCTCTGACT
66 AGCAGCAGCACGCTGCTCCTCCTCCAGAAGCCTCTGGCGAAGTTCAGTGCAAGCTTCCTCTGACT
* * *
20631 TTGCAACTTCAATTTCAAGGGAACGAATATGTTTTTCTGCTTCTTCAATCATGGTAGCTTGGTCG
131 TTTCAACTTCAGTTTCAAGGGAATGAATATGTTTTTCTGCTTCTTCAATCATGGTAGCTTGGTCG
* * *** * * ***
20696 ATTAGAAGAGCATCCTTACTCAAGATCATCTCTGCTGATTCAGCAAGTTGCGAATCCTTACCCTT
196 ATCAAAAGAGCATCCTTACTCAAGATTGCCTCCGCTGATTCTGCAAGTTGTTCATCCTTACCCTT
* * * *
20761 CAATGCACTGAGATGATGATGGTTTGCCTCTGATAATCTATTCACAAGTAAAAAAGCAGCAGTTG
261 CAATGCATTGAGATGATTATGGTTTGCCTCTGATAATCTATTCACAAGTACAAAAGCAACAGTTG
* *
20826 CACAAGTAGATGCATTTCTTAGATCATCTTCAGCCATCTTCATTCTGTCCTCAAGT
326 CACAAGTAGATGCATTTCTCAGGTCATCTTCAGCCATCTTCATTCTGTCCTCAAGT
*
20882 TTAGACAGCTCCTCCTGTGTCTTCATCAAAAAGTCATTCTCCACCATATCTTCAAGCTTTTGTTC
1 TTAGACAGCTCCTCCTGTGTC-T--TCAAAATGTCATTCTCCACCATATCTTCAAGCTTTTGTTC
*
20947 AATAGCAGCAGCACGCTGCTCCTCCTCCAGAAGCCTCCGGCGAAGTTCAGTGCAAGCTTCCTCTG
63 AATAGCAGCAGCACGCTGCTCCTCCTCCAGAAGCCTCTGGCGAAGTTCAGTGCAAGCTTCCTCTG
*
21012 ACTTTTCAACTTCAGTTTCAAGGGAATGAATATGTGTTTCTGCTTCTTCAATCATGGTAGCTTGG
128 ACTTTTCAACTTCAGTTTCAAGGGAATGAATATGTTTTTCTGCTTCTTCAATCATGGTAGCTTGG
*
21077 TCGATCAAAAGAGCATCCTTACTCAAGATTGCCTCCGCTGATTCTGCAAGTTGTTCATCCTTACA
193 TCGATCAAAAGAGCATCCTTACTCAAGATTGCCTCCGCTGATTCTGCAAGTTGTTCATCCTTACC
21142 CTTCAATGCATTGAGATGATTATGGTTTGCCTCTGATAATCTATTCACAAGTACAAAAGCAACAG
258 CTTCAATGCATTGAGATGATTATGGTTTGCCTCTGATAATCTATTCACAAGTACAAAAGCAACAG
* *
21207 TTGCACAAGTAGATGCATTTCTCAGGTCATCTTCAGCCATCTTCATTCTGTCCTTAAGA
323 TTGCACAAGTAGATGCATTTCTCAGGTCATCTTCAGCCATCTTCATTCTGTCCTCAAGT
* * *
21266 TTAGACTGCTCCTCCTGTGACTTCAAAATGTCATTCTCCACCATATCTTCAAGCTTTTCTTCAAT
1 TTAGACAGCTCCTCCTGTGTCTTCAAAATGTCATTCTCCACCATATCTTCAAGCTTTTGTTCAAT
* *
21331 AGCAGCAGCACGCTCCTCCTCCTCCAGAAGCCTCTGGCTAAGTTCAGTGCAAGCTTCCTCTGACT
66 AGCAGCAGCACGCTGCTCCTCCTCCAGAAGCCTCTGGCGAAGTTCAGTGCAAGCTTCCTCTGACT
*
21396 TTTCAACTTCAGTTTCAAGGGAATGAATATGTTTTTCTTCTTCTTCAATCATGGTAGCTTGGTCG
131 TTTCAACTTCAGTTTCAAGGGAATGAATATGTTTTTCTGCTTCTTCAATCATGGTAGCTTGGTCG
*
21461 ATCAAAAGAGCATCCTTACTCAAGATTGCCTTCGCTGATTCTGCAAGTTGTTCATCCTTACCCTT
196 ATCAAAAGAGCATCCTTACTCAAGATTGCCTCCGCTGATTCTGCAAGTTGTTCATCCTTACCCTT
*
21526 CAATGCATTAAGATGATTATGGTTTGCCTCTGATAATCTATTCACAAGTACAAAAGCAACAGTTG
261 CAATGCATTGAGATGATTATGGTTTGCCTCTGATAATCTATTCACAAGTACAAAAGCAACAGTTG
*
21591 CACAAGTAGATGTATTTCTCAGGTCATCTTCAGCCATCTTCATTCTGTCCTCAAGT
326 CACAAGTAGATGCATTTCTCAGGTCATCTTCAGCCATCTTCATTCTGTCCTCAAGT
21647 TT
1 TT
21649 TCTAATGATT
Statistics
Matches: 715, Mismatches: 49, Indels: 6
0.93 0.06 0.01
Matches are distributed among these distances:
381 369 0.52
382 1 0.00
383 1 0.00
384 344 0.48
ACGTcount: A:0.25, C:0.25, G:0.16, T:0.33
Consensus pattern (381 bp):
TTAGACAGCTCCTCCTGTGTCTTCAAAATGTCATTCTCCACCATATCTTCAAGCTTTTGTTCAAT
AGCAGCAGCACGCTGCTCCTCCTCCAGAAGCCTCTGGCGAAGTTCAGTGCAAGCTTCCTCTGACT
TTTCAACTTCAGTTTCAAGGGAATGAATATGTTTTTCTGCTTCTTCAATCATGGTAGCTTGGTCG
ATCAAAAGAGCATCCTTACTCAAGATTGCCTCCGCTGATTCTGCAAGTTGTTCATCCTTACCCTT
CAATGCATTGAGATGATTATGGTTTGCCTCTGATAATCTATTCACAAGTACAAAAGCAACAGTTG
CACAAGTAGATGCATTTCTCAGGTCATCTTCAGCCATCTTCATTCTGTCCTCAAGT
Found at i:33065 original size:23 final size:23
Alignment explanation
Indices: 33035--33086 Score: 68
Period size: 23 Copynumber: 2.3 Consensus size: 23
33025 AACGCTAGCA
* *
33035 TGCTTACTGTTTCGTACTTAGTG
1 TGCTTACTGTTACGCACTTAGTG
*
33058 TGCTTACTGTTACGCACTTCGTG
1 TGCTTACTGTTACGCACTTAGTG
*
33081 GGCTTA
1 TGCTTA
33087 TTGATTTGCG
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.13, C:0.21, G:0.23, T:0.42
Consensus pattern (23 bp):
TGCTTACTGTTACGCACTTAGTG
Found at i:33142 original size:23 final size:23
Alignment explanation
Indices: 33100--33157 Score: 91
Period size: 23 Copynumber: 2.6 Consensus size: 23
33090 ATTTGCGCTA
*
33100 TGTGGGCCTACT-GATTGCACTG
1 TGTGTGCCTACTGGATTGCACTG
33122 TGTGTGCCTACTGGATTGCACTG
1 TGTGTGCCTACTGGATTGCACTG
*
33145 TGTGTGCTTACTG
1 TGTGTGCCTACTG
33158 TTTCCCCAGC
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
22 11 0.33
23 22 0.67
ACGTcount: A:0.12, C:0.21, G:0.31, T:0.36
Consensus pattern (23 bp):
TGTGTGCCTACTGGATTGCACTG
Done.