Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014512.1 Kokia drynarioides strain JFW-HI SEQ_129551, 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: 10858
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33
Found at i:2835 original size:674 final size:674
Alignment explanation
Indices: 1541--3566 Score: 3854
Period size: 674 Copynumber: 3.0 Consensus size: 674
1531 GGAGCATTTT
*
1541 TTTCTTGTAGAGTTTGCATACAATAATAGTTTTCAGTCGAGCATTCAGATGGCTCCATATGTGGC
1 TTTCTTGTAGTGTTTGCATACAATAATAGTTTTCAGTCGAGCATTCAGATGGCTCCATATGTGGC
* * *
1606 TTTGTATGGATGCAAGTGTAGAACACCCTTGTGTTAGACCGAGCTGAGTGAGAAGAAGGTGATAA
66 TTTGTATGGACGCAAGTGTAGAACACCCTTGTGTTAGATCGAGCTGAGTGAGAAGAAGCTGATAA
1671 GGCTGGAAATAGTGCATGAAACTAAAGATATGGTGAAGATTATTCGAGATTAATTAAAAGAAGCT
131 GGCTGGAAATAGTGCATGAAACTAAAGATATGGTGAAGATTATTCGAGATTAATTAAAAGAAGCT
* * *
1736 TATGATGGGCAAAAGTCGTATTCTGACTTGAAGAGGAAGGACATTGAGTTCAATGTCGAAGATCA
196 TATGATAGGCAGAAGTCGTATTCTGACTTGAAGAGGAAGGACAATGAGTTCAATGTCGAAGATCA
* * *
1801 AGTTTTCTTATATGTCTCACCGTGGAAAAAAGGTATTACGGTTTGGTTGTAAATGGAATTTAAGC
261 AGTTTTCTTAAATGTCTCACCGTGGAAAAAAGGTATTAAGGTTTGGTTGTAAAGGGAATTTAAGC
*
1866 CTTAGATTTATTGGACCCTATTACATCATCAAGAGAGTAGGATCGGTAGTGTATCAGTTAGAATT
326 CCTAGATTTATTGGACCCTATTACATCATCAAGAGAGTAGGATCGGTAGTGTATCAGTTAGAATT
* *
1931 GCCTTCAAAATTGGATCTTATATATGATGTATTTCATGTGTCCATGTTAAGGCATTATAGATTTG
391 GCCTTCAAAATTGGATCTTATATATGACGTATTTCATGTGTCCATGTTAAGGCATTCTAGATTTG
* *
1996 ACCCTTCGCATATTGTGTCGATTTAGGAAATAGAGGTTCGATCGGACTTATCTTTCAAAGAAGAA
456 ACCCTTCTCATATTGTGTCGATTTAGGAAATAGAGGTTCGATCAGACTTATCTTTCAAAGAAGAA
2061 CTGATACAAATATTAGAGAGAGAAGTCAAGGTATTACTAAGGAAGCATATTCCTCTCGTAAAGGT
521 CTGATACAAATATTAGAGAGAGAAGTCAAGGTATTACTAAGGAAGCATATTCCTCTCGTAAAGGT
* *
2126 TCTTTGGAGAAATCACGGTTCCAATGACGCTACTTTAGAACCAAAAGATGGATGCAATAACAATA
586 TCTTTGAAGAAATCACGGTTCCAATGACACTACTTTAGAACCAAAAGATGGATGCAATAACAATA
2191 TCGTCACTTATTCTCGCCAGGTAA
651 TCGTCACTTATTCTCGCCAGGTAA
2215 TTTCTTGTAGTGTTTGCATACAATAATAGTTTTCAGTCGAGCATTCAGATGGCTCCATATGTGGC
1 TTTCTTGTAGTGTTTGCATACAATAATAGTTTTCAGTCGAGCATTCAGATGGCTCCATATGTGGC
2280 TTTGTATGGACGCAAGTGTAGAACACCCTTGTGTTAGATCGAGCTGAGTGAGAAGAAGCTGATAA
66 TTTGTATGGACGCAAGTGTAGAACACCCTTGTGTTAGATCGAGCTGAGTGAGAAGAAGCTGATAA
*
2345 GGCTGGAAATAGTGCATGAAACTAAAGATATGGTGAAGATTATTTGAGATTAATTAAAAGAAGCT
131 GGCTGGAAATAGTGCATGAAACTAAAGATATGGTGAAGATTATTCGAGATTAATTAAAAGAAGCT
2410 TATGATAGGCAGAAGTCGTATTCTGACTTGAAGAGGAAGGACAATGAGTTCAATGTCGAAGATCA
196 TATGATAGGCAGAAGTCGTATTCTGACTTGAAGAGGAAGGACAATGAGTTCAATGTCGAAGATCA
2475 AGTTTTCTTAAATGTCTCACCGTGGAAAAAAGGTATTAAGGTTTGGTTGTAAAGGGAATTTAAGC
261 AGTTTTCTTAAATGTCTCACCGTGGAAAAAAGGTATTAAGGTTTGGTTGTAAAGGGAATTTAAGC
2540 CCTAGATTTATTGGACCCTATTACATCATCAAGAGAGTAGGATCGGTAGTGTATCAGTTAGAATT
326 CCTAGATTTATTGGACCCTATTACATCATCAAGAGAGTAGGATCGGTAGTGTATCAGTTAGAATT
2605 GCCTTCAAAATTGGATCTTATATATGACGTATTTCATGTGTCCATGTTAAGGCATTCTAGATTTG
391 GCCTTCAAAATTGGATCTTATATATGACGTATTTCATGTGTCCATGTTAAGGCATTCTAGATTTG
2670 ACCCTTCTCATATTGTGTCGATTTAGGAAATAGAGGTTCGATCAGACTTATCTTTCAAAGAAGAA
456 ACCCTTCTCATATTGTGTCGATTTAGGAAATAGAGGTTCGATCAGACTTATCTTTCAAAGAAGAA
2735 CTGATACAAATATTAGAGAGAGAAGTCAAGGTATTACTAAGGAAGCATATTCCTCTCGTAAAGGT
521 CTGATACAAATATTAGAGAGAGAAGTCAAGGTATTACTAAGGAAGCATATTCCTCTCGTAAAGGT
2800 TCTTTGAAGAAATCACGGTTCCAATGACACTACTTTAGAACCAAAAGATGGATGCAATAACAATA
586 TCTTTGAAGAAATCACGGTTCCAATGACACTACTTTAGAACCAAAAGATGGATGCAATAACAATA
2865 TCGTCACTTATTCTCGCCAGGTAA
651 TCGTCACTTATTCTCGCCAGGTAA
*
2889 TTTCTTGTAGTGTTTGCATACAATAATAGTTTTCAGTCGAGCATTCAGATGGCTCCATATATGGC
1 TTTCTTGTAGTGTTTGCATACAATAATAGTTTTCAGTCGAGCATTCAGATGGCTCCATATGTGGC
*
2954 TTTGTATGGACGCAAGTGTAGAACACCCTTGTGTTAGATCGAGCTAAGTGAGAAGAAGCTGATAA
66 TTTGTATGGACGCAAGTGTAGAACACCCTTGTGTTAGATCGAGCTGAGTGAGAAGAAGCTGATAA
3019 GGCTGGAAATAGTGCATGAAACTAAAGATATGGTGAAGATTATTCGAGATTAATTAAAAGAAGCT
131 GGCTGGAAATAGTGCATGAAACTAAAGATATGGTGAAGATTATTCGAGATTAATTAAAAGAAGCT
3084 TATGATAGGCAGAAGTCGTATTCTGACTTGAAGAGGAAGGACAATGAGTTCAATGTCGAAGATCA
196 TATGATAGGCAGAAGTCGTATTCTGACTTGAAGAGGAAGGACAATGAGTTCAATGTCGAAGATCA
* *
3149 AGTTTTCTTAAATGTCTCACCATGGAAAAACGGTATTAAGGTTTGGTTGTAAAGGGAATTTAAGC
261 AGTTTTCTTAAATGTCTCACCGTGGAAAAAAGGTATTAAGGTTTGGTTGTAAAGGGAATTTAAGC
3214 CCTAGATTTATTGGACCCTATTACATCATCAAGAGAGTAGGATCGGTAGTGTATCAGTTAGAATT
326 CCTAGATTTATTGGACCCTATTACATCATCAAGAGAGTAGGATCGGTAGTGTATCAGTTAGAATT
3279 GCCTTCAAAATTGGATCTTATATATGACGTATTTCATGTGTCCATGTTAAGGCATTCTAGATTTG
391 GCCTTCAAAATTGGATCTTATATATGACGTATTTCATGTGTCCATGTTAAGGCATTCTAGATTTG
3344 ACCCTTCTCATATTGTGTCGATTTAGGAAATAGAGGTTCGATCAGACTTATCTTTCAAAGAAGAA
456 ACCCTTCTCATATTGTGTCGATTTAGGAAATAGAGGTTCGATCAGACTTATCTTTCAAAGAAGAA
3409 CTGATACAAATATTAGAGAGAGAAGTCAAGGTATTACTAAGGAAGCATATTCCTCTCGTAAAGGT
521 CTGATACAAATATTAGAGAGAGAAGTCAAGGTATTACTAAGGAAGCATATTCCTCTCGTAAAGGT
3474 TCTTTGAAGAAATCACGGTTCCAATGACACTACTTTAGAACCAAAAGATGGATGCAATAACAATA
586 TCTTTGAAGAAATCACGGTTCCAATGACACTACTTTAGAACCAAAAGATGGATGCAATAACAATA
3539 TCGTCACTTATTCTCGCCAGGTAA
651 TCGTCACTTATTCTCGCCAGGTAA
3563 TTTC
1 TTTC
3567 GAGGATAAAA
Statistics
Matches: 1329, Mismatches: 23, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
674 1329 1.00
ACGTcount: A:0.33, C:0.14, G:0.22, T:0.31
Consensus pattern (674 bp):
TTTCTTGTAGTGTTTGCATACAATAATAGTTTTCAGTCGAGCATTCAGATGGCTCCATATGTGGC
TTTGTATGGACGCAAGTGTAGAACACCCTTGTGTTAGATCGAGCTGAGTGAGAAGAAGCTGATAA
GGCTGGAAATAGTGCATGAAACTAAAGATATGGTGAAGATTATTCGAGATTAATTAAAAGAAGCT
TATGATAGGCAGAAGTCGTATTCTGACTTGAAGAGGAAGGACAATGAGTTCAATGTCGAAGATCA
AGTTTTCTTAAATGTCTCACCGTGGAAAAAAGGTATTAAGGTTTGGTTGTAAAGGGAATTTAAGC
CCTAGATTTATTGGACCCTATTACATCATCAAGAGAGTAGGATCGGTAGTGTATCAGTTAGAATT
GCCTTCAAAATTGGATCTTATATATGACGTATTTCATGTGTCCATGTTAAGGCATTCTAGATTTG
ACCCTTCTCATATTGTGTCGATTTAGGAAATAGAGGTTCGATCAGACTTATCTTTCAAAGAAGAA
CTGATACAAATATTAGAGAGAGAAGTCAAGGTATTACTAAGGAAGCATATTCCTCTCGTAAAGGT
TCTTTGAAGAAATCACGGTTCCAATGACACTACTTTAGAACCAAAAGATGGATGCAATAACAATA
TCGTCACTTATTCTCGCCAGGTAA
Found at i:7347 original size:48 final size:48
Alignment explanation
Indices: 7275--7372 Score: 151
Period size: 48 Copynumber: 2.0 Consensus size: 48
7265 AAGTACATTT
* *
7275 AGGGATGGTTAATAATAAAACTTCTCTCTTGGACCAGCATATCCTCTA
1 AGGGATGGTTAATAATAAAACTTCTCACTTGGACCAGCACATCCTCTA
* * *
7323 AGGGATGGTTAATAATAAAGCTTCTCAGTTGGACCAGCACATCTTCTA
1 AGGGATGGTTAATAATAAAACTTCTCACTTGGACCAGCACATCCTCTA
7371 AG
1 AG
7373 ATCCCTTTTG
Statistics
Matches: 45, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
48 45 1.00
ACGTcount: A:0.32, C:0.19, G:0.19, T:0.30
Consensus pattern (48 bp):
AGGGATGGTTAATAATAAAACTTCTCACTTGGACCAGCACATCCTCTA
Done.