Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01005291.1 Kokia drynarioides strain JFW-HI SEQ_119217, 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: 12976
ACGTcount: A:0.33, C:0.13, G:0.18, T:0.36
Found at i:179 original size:18 final size:19
Alignment explanation
Indices: 156--199 Score: 63
Period size: 18 Copynumber: 2.4 Consensus size: 19
146 ATTATGCATG
* *
156 TATATATAGTTTGT-TCTT
1 TATATATAGTATGTATATT
174 TATATATAGTATGTATATT
1 TATATATAGTATGTATATT
193 TATATAT
1 TATATAT
200 TTTAATCTCT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 13 0.57
19 10 0.43
ACGTcount: A:0.32, C:0.02, G:0.09, T:0.57
Consensus pattern (19 bp):
TATATATAGTATGTATATT
Found at i:4119 original size:787 final size:788
Alignment explanation
Indices: 2599--4177 Score: 2944
Period size: 787 Copynumber: 2.0 Consensus size: 788
2589 TGGCACCGAT
* *
2599 AAACTTTCACTCTTGTTCTTTCATTTCCTCTAATTTCTTTTTCATAGAGAAGTCCTCAAATCTCG
1 AAACTTTCACTCTTGTTCTTTCATTTCCTCTAATTTCTTTTTCACAAAGAAGTCCTCAAATCTCG
* * * *
2664 CTAGGATTCTCCTCCGTCGGTCACCTTGCTTTGATGCCGTCATCGTCTTTTTCATTGTCGTCACC
66 CTAGGATTCTCCTCCGTCGGTCACCTTGCTTTGATGCCATCATCATCTGTTTCACTGTCGTCACC
* *
2729 AATCGGAGAAGCACCGTACGACTTTCCTTTCTCTCTTGCTTCTACTCTTATTCTTTTCTACTCTA
131 AATCGGAGAAGCACCGTACAACTTTCCTTTCTCTCCTGCTTCTACTCTTATTCTTTTCTACTCTA
* *
2794 TTTTTTGTTTTCAAAACCCTTGGCTGTCGCTACTCTTTTTGGGTCTGCCATGCATGCTGCTCTTT
196 TTTTTTATTTTCAAAACCATTGGCTGTCGCTACTCTTTTTGGGTCTGCCATGCATGCTGCTCTTT
*
2859 CTGGGAAGCTTGAATGTTTTTTAAAGTGGGGTGAAATTGCTGAAAAAATTTGGGAAGATTACAAG
261 CTGGGAAGCTTGAACGTTTTTTAAAGTGGGGTGAAATTGCTGAAAAAATTTGGGAAGATTACAAG
* * *
2924 TTGATTTGTGAATTTGATTAGTTTAATTGTTTTAATTTTATTGTCATCTTCTTAGGTTTTGGTTG
326 TAGATTTGTGAATTTGATCAGTTTAATTGTTTTAATTTTATTGTCATCTTCTTAGGTCTTGGTTG
2989 ATGTTGTGAACATATTTTGCTTGTTCATGCTATCCTCCAACAATGGCTAGATTTATGGTTCGAAT
391 ATGTTGTGAACATATTTTGCTTGTTCATGCTATCCTCCAACAATGGCTAGATTTATGGTTCGAAT
*
3054 TTTTACATAATTTAATCAAATTTAACTTGTTTCATATTTACAGTTGCGCTAAACTTAGAAATGTT
456 TTTTACATAATTTAATCAAATTTAACTTGTTTCATATTTACAGTTGCGCTAAACTTAGAAATATT
3119 CTTAAATTTTTTTCAAACAAACCCAAAAATGTTGAATGAATTTGGAAATGTTGAATGAATTCAAA
521 CTTAAATTTTTTTCAAACAAACCCAAAAATGTTGAATGAATTTGGAAATGTTGAATGAATTCAAA
3184 AAAGAAAAAGGTAAAATGACGAGGGGAAGAAAGAAGAGAAAGGAATACTTGGAAAAAGAATAAAA
586 AAAGAAAAAGGTAAAATGACGAGGGGAAGAAAGAAGAGAAAGGAATACTTGGAAAAAGAATAAAA
*
3249 TAAGAAAAAAATGTTCTTAAATTTCTCAAAGAAACCCAAAAATATGAAATGAATCCAGAAAATGA
651 TAAGAAAAAAATGTTCTTAAATTTCTCAAAGAAACCCAAAAATATGAAATAAATCCAGAAAATGA
3314 AAACACGATGTCAAAAGAGAAAGAATGAAGAAGAAAGGAATAAC-AAAAAAGGAAATAAGAAAAA
716 AAACACGATGTCAAAAGAGAAAGAATGAAGAAGAAAGGAATAACAAAAAAAGGAAATAAGAAAAA
3378 ATAGAAAG
781 ATAGAAAG
* *
3386 AAACTTTCACTCTTGTTCTTTCATTTCCTGTAATTTTTTTTTCACAAAGAAGTCCTCAAATCTCG
1 AAACTTTCACTCTTGTTCTTTCATTTCCTCTAATTTCTTTTTCACAAAGAAGTCCTCAAATCTCG
*
3451 CTAGGATTCTCCTCCGTCGGTCACCTTGCTTTGATGTCATCATCATCTGTTTCACTGTCGTCACC
66 CTAGGATTCTCCTCCGTCGGTCACCTTGCTTTGATGCCATCATCATCTGTTTCACTGTCGTCACC
3516 AATCGGAGAAGCACCGTACAACTTTCCTTTCTCTCCTGCTTCTACTCTTATTCTTTTCTACTCTA
131 AATCGGAGAAGCACCGTACAACTTTCCTTTCTCTCCTGCTTCTACTCTTATTCTTTTCTACTCTA
3581 TTTTTTATTTTCAAAACCATTGGCTGTCGCTACTCTTTTTGGGTCTGCCATGCATGCTGCTCTTT
196 TTTTTTATTTTCAAAACCATTGGCTGTCGCTACTCTTTTTGGGTCTGCCATGCATGCTGCTCTTT
3646 CTGGGAAGCTTGAACGTTTTTTAAAGTGGGGTGAAATTGCTGAAAAAATTTGGGAAGATTACAAG
261 CTGGGAAGCTTGAACGTTTTTTAAAGTGGGGTGAAATTGCTGAAAAAATTTGGGAAGATTACAAG
* *
3711 TAGATTTGTGAATTTGATCAGTTTAATTGTTTTAATTTTCTTGTCATTTTCTTAGGTCTTGGTTG
326 TAGATTTGTGAATTTGATCAGTTTAATTGTTTTAATTTTATTGTCATCTTCTTAGGTCTTGGTTG
3776 ATGTTGTGAACATATTTTGCTTGTTCATGCTATCCTCCAACAATGGCTAGATTTATGGTTCGAAT
391 ATGTTGTGAACATATTTTGCTTGTTCATGCTATCCTCCAACAATGGCTAGATTTATGGTTCGAAT
3841 TTTTACATAATTTAATCAAATTTAACTTGTTTCATATTTACAGTTGCGCTAAACTTAGAAATATT
456 TTTTACATAATTTAATCAAATTTAACTTGTTTCATATTTACAGTTGCGCTAAACTTAGAAATATT
3906 CTTAAATTTTTTTCAAACAAACCCAAAAATGTTGAATGAATTTGGAAATGTTGAATGAATTCAAA
521 CTTAAATTTTTTTCAAACAAACCCAAAAATGTTGAATGAATTTGGAAATGTTGAATGAATTCAAA
3971 AAAGAAAAAGGTAAAATGACGAGGGGAAGAAAGAAGAGAAAGGAATACTTGGAAAAAGAATAAAA
586 AAAGAAAAAGGTAAAATGACGAGGGGAAGAAAGAAGAGAAAGGAATACTTGGAAAAAGAATAAAA
4036 TAAGAAAAAAATGTTCTTAAATTTCTCAAAGAAACCCAAAAATATGAAATAAATCCAGAAAATGA
651 TAAGAAAAAAATGTTCTTAAATTTCTCAAAGAAACCCAAAAATATGAAATAAATCCAGAAAATGA
*
4101 AAACACGATGTGAAAAGAGAAAGAATGAAGAAGAAAGGAATAACAAAAAAAAGGAAATAAGAAAA
716 AAACACGATGTCAAAAGAGAAAGAATGAAGAAGAAAGGAATAAC-AAAAAAAGGAAATAAGAAAA
4166 AATAGAAAG
780 AATAGAAAG
4175 AAA
1 AAA
4178 ATGAAAATTA
Statistics
Matches: 768, Mismatches: 22, Indels: 2
0.97 0.03 0.00
Matches are distributed among these distances:
787 737 0.96
789 31 0.04
ACGTcount: A:0.34, C:0.15, G:0.17, T:0.34
Consensus pattern (788 bp):
AAACTTTCACTCTTGTTCTTTCATTTCCTCTAATTTCTTTTTCACAAAGAAGTCCTCAAATCTCG
CTAGGATTCTCCTCCGTCGGTCACCTTGCTTTGATGCCATCATCATCTGTTTCACTGTCGTCACC
AATCGGAGAAGCACCGTACAACTTTCCTTTCTCTCCTGCTTCTACTCTTATTCTTTTCTACTCTA
TTTTTTATTTTCAAAACCATTGGCTGTCGCTACTCTTTTTGGGTCTGCCATGCATGCTGCTCTTT
CTGGGAAGCTTGAACGTTTTTTAAAGTGGGGTGAAATTGCTGAAAAAATTTGGGAAGATTACAAG
TAGATTTGTGAATTTGATCAGTTTAATTGTTTTAATTTTATTGTCATCTTCTTAGGTCTTGGTTG
ATGTTGTGAACATATTTTGCTTGTTCATGCTATCCTCCAACAATGGCTAGATTTATGGTTCGAAT
TTTTACATAATTTAATCAAATTTAACTTGTTTCATATTTACAGTTGCGCTAAACTTAGAAATATT
CTTAAATTTTTTTCAAACAAACCCAAAAATGTTGAATGAATTTGGAAATGTTGAATGAATTCAAA
AAAGAAAAAGGTAAAATGACGAGGGGAAGAAAGAAGAGAAAGGAATACTTGGAAAAAGAATAAAA
TAAGAAAAAAATGTTCTTAAATTTCTCAAAGAAACCCAAAAATATGAAATAAATCCAGAAAATGA
AAACACGATGTCAAAAGAGAAAGAATGAAGAAGAAAGGAATAACAAAAAAAGGAAATAAGAAAAA
ATAGAAAG
Found at i:4173 original size:16 final size:17
Alignment explanation
Indices: 4134--4167 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
4124 AATGAAGAAG
4134 AAAGG-AATAACAAAAA
1 AAAGGAAATAACAAAAA
*
4150 AAAGGAAATAAGAAAAA
1 AAAGGAAATAACAAAAA
4167 A
1 A
4168 TAGAAAGAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 5 0.31
17 11 0.69
ACGTcount: A:0.76, C:0.03, G:0.15, T:0.06
Consensus pattern (17 bp):
AAAGGAAATAACAAAAA
Found at i:9501 original size:50 final size:48
Alignment explanation
Indices: 9437--9530 Score: 143
Period size: 50 Copynumber: 1.9 Consensus size: 48
9427 TGTGTGAATT
* *
9437 TGTGATTTTATGATTTAGGTGCAGTACTCACACGGTCTGGTACACGGCTG
1 TGTGAATTTATGATTTAGGTGCAGTACT--CACGGTCTGGCACACGGCTG
*
9487 TGTGAATTTGTGATTTAGGTGCAGTACTCACGGTCTGGCACACG
1 TGTGAATTTATGATTTAGGTGCAGTACTCACGGTCTGGCACACG
9531 TCCTGGTACA
Statistics
Matches: 41, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
48 15 0.37
50 26 0.63
ACGTcount: A:0.20, C:0.18, G:0.29, T:0.33
Consensus pattern (48 bp):
TGTGAATTTATGATTTAGGTGCAGTACTCACGGTCTGGCACACGGCTG
Done.