Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01010878.1 Kokia drynarioides strain JFW-HI SEQ_125846, 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: 1859
ACGTcount: A:0.39, C:0.14, G:0.17, T:0.25
Warning! 95 characters in sequence are not A, C, G, or T
Found at i:386 original size:216 final size:213
Alignment explanation
Indices: 4--553 Score: 730
Period size: 216 Copynumber: 2.6 Consensus size: 213
1 GAC
*
4 GTAAATAAGTTTTAAATTCAAAGACCAAAAGTTGTTTACAAAATGACAAAGCATTTGGACCAAAT
1 GTAAATAAGTTTTAAATT-AAAAACCAAAAGTTGTTTACAAAATGACAAA-CATTTGGACCAAAT
* * *
69 GATACGA-TTTCTCGAGAATGGAATGTTCGAAAAATTACTCGAAGGAATGGATCGTCATGAATAC
64 GATGCGATTTTC-CGAGCATGGAATGTTCGAAAAATTACTCAAAGGAATGGATCGTCATGAATAC
* * * * **
133 TTTAAGGAGCCAAAGTTATAAAATAACTTGAAAAAGTTTGACAAGTTTGGAAGTTCGTCCAAGAA
128 TTTAAGGAACCAAAGTTATAAAAGAACTCGAAAAAGTTTCACAAGTTCAGAAGTTCGTCCAAGAA
198 CCAAAAGAGAAACAAGTCTCACT
193 CCAAAAGAGAAACAA-TCTCA-T
* *
221 -TAAATAAGTTTTTTAATTAAAAACCCAAAAGTTGTTTGC-AAATGACAAACTATTTGGACCAAA
1 GTAAATAAG-TTTTAAATTAAAAA-CCAAAAGTTGTTTACAAAATGACAAAC-ATTTGGACCAAA
* *
284 TGATGCGATTTTCCAAGCATGGAATGTTCGAAAAATTACGCAAAGGAATGGATCGTCATGAATAC
63 TGATGCGATTTTCCGAGCATGGAATGTTCGAAAAATTACTCAAAGGAATGGATCGTCATGAATAC
* *
349 TTTAAGGAACCAAAGTTATAAAAGAACTCGTAAAAGTTTCACAAGTTCATAAGTTCGTCCAAGAA
128 TTTAAGGAACCAAAGTTATAAAAGAACTCGAAAAAGTTTCACAAGTTCAGAAGTTCGTCCAAGAA
* *
414 CCAAAAGTGAAACAATCTGAT
193 CCAAAAGAGAAACAATCTCAT
* ** * *
435 GCAAATAAGTTTTAAATTCAAAGGCCAAAAGTT-TTTACAAAAATGACAACCGTTTGGACCAAAT
1 GTAAATAAGTTTTAAATT-AAAAACCAAAAGTTGTTTAC-AAAATGACAAACATTTGGACCAAAT
* * * * *
499 GATGCGATTTCCCGAGCATCGAATGCTCGAAATATTGCTCAAAGGAATGGATCGT
64 GATGCGATTTTCCGAGCATGGAATGTTCGAAAAATTACTCAAAGGAATGGATCGT
554 TTTGAACACT
Statistics
Matches: 293, Mismatches: 32, Indels: 19
0.85 0.09 0.06
Matches are distributed among these distances:
213 4 0.01
214 78 0.27
215 25 0.09
216 160 0.55
217 26 0.09
ACGTcount: A:0.41, C:0.15, G:0.18, T:0.26
Consensus pattern (213 bp):
GTAAATAAGTTTTAAATTAAAAACCAAAAGTTGTTTACAAAATGACAAACATTTGGACCAAATGA
TGCGATTTTCCGAGCATGGAATGTTCGAAAAATTACTCAAAGGAATGGATCGTCATGAATACTTT
AAGGAACCAAAGTTATAAAAGAACTCGAAAAAGTTTCACAAGTTCAGAAGTTCGTCCAAGAACCA
AAAGAGAAACAATCTCAT
Found at i:1233 original size:217 final size:215
Alignment explanation
Indices: 661--1859 Score: 1635
Period size: 216 Copynumber: 5.5 Consensus size: 215
651 NNNNNNNNNN
*
661 GTTGTTTACAAATGACAAACTATTTGGACCAAATGATGCGATTTCACAAGCATGGAATGTTCGAA
1 GTTGTTTACAAATGACAAACTATTTGGACCAAATGATGCGATTTCCCAAGCATGGAATGTTCGAA
* *
726 AAATTACTCGAAGGAAT-GATCGTCTTGAATACTTTAAGGAACCAAAGTTATAAAAGAACTCGTA
66 AAATTGCTCGAAGGAATGGATCGTCATGAATACTTTAAGGAACCAAAGTTATAAAAGAACTCGTA
* ** * * * * *
790 AAAGTTTCACAAGTTCATAAGTTCGTCCATGAAACAAAAGAGAAACAATTCTAACGTAAATAAGT
131 AAAGTTTGACAAGTTTGTAAGTTCATCCAAGAACCAAAAGAGAAACAAGTCTCACGTAAATAAGT
* * *
855 TTTAAATTCAAAGACCAAAA
196 TTTTAATTTAAAAACCAAAA
* * *
875 GTTGTTTACAAAATGACAAACCATTTGGACCAAATGATGCGATTTCCCAAGAAGGGAATGTTCGA
1 GTTGTTTAC-AAATGACAAACTATTTGGACCAAATGATGCGATTTCCCAAGCATGGAATGTTCGA
* * * *
940 AAAATGGCTTGAAGGAATGGATCATCATGAATACTTTAAGTAACCAAAGTTATAAAAGAACTCGT
65 AAAATTGCTCGAAGGAATGGATCGTCATGAATACTTTAAGGAACCAAAGTTATAAAAGAACTCGT
* * * * *
1005 AAAAGTTTGACAAGTTTGGAAGTTCGTCCAAGAACCAAAAGAGAAACAAGTCTCTCCTAGATAAG
130 AAAAGTTTGACAAGTTTGTAAGTTCATCCAAGAACCAAAAGAGAAACAAGTCTCACGTAAATAAG
1070 TTTTTAATTTAAAAACCAAAA
195 TTTTTAATTTAAAAACCAAAA
* * * *
1091 GTTGTTTACAAAATGACAAGCTATTTTGGACCAAATGGTGCGATTTCCCAAGCATGGAATGCTCA
1 GTTGTTTAC-AAATGACAAACTA-TTTGGACCAAATGATGCGATTTCCCAAGCATGGAATGTTCG
* ** *
1156 AAAAATTGCTCAAAGGAATGGATCGTTTTGAATACTTTAAGGAATCAAAGTTATAAAAGAACTCG
64 AAAAATTGCTCGAAGGAATGGATCGTCATGAATACTTTAAGGAACCAAAGTTATAAAAGAACTCG
* * * * * *
1221 CAACATTTTGACAAGCTTGTAAGTTCACCCAAGAACCAAAAGAGAAACAAGTCTCACTTAAATAA
129 TAAAAGTTTGACAAGTTTGTAAGTTCATCCAAGAACCAAAAGAGAAACAAGTCTCACGTAAATAA
1286 GTTTTTTAATTTAAAAACCAAAA
194 G-TTTTTAATTTAAAAACCAAAA
*
1309 GTTGTTTACAAATGACAAACTATTTGGACCAAATGATGCGATTTCCCGAGCATGGAATGTTCGAA
1 GTTGTTTACAAATGACAAACTATTTGGACCAAATGATGCGATTTCCCAAGCATGGAATGTTCGAA
* *
1374 AAATGGCTCGAAGGAATGGATCGTCATGAATACGTTAAGGAACCAAAGTTATAAAAGAACTCGTA
66 AAATTGCTCGAAGGAATGGATCGTCATGAATACTTTAAGGAACCAAAGTTATAAAAGAACTCGTA
* * * * *
1439 AAAGTTTGACAAATTTGGAAGTTCATCCAAGAACCAAAAGAGATACAATTCTGACGTAAATAAGT
131 AAAGTTTGACAAGTTTGTAAGTTCATCCAAGAACCAAAAGAGAAACAAGTCTCACGTAAATAAGT
* *
1504 TTTTAATTCAAAGACCAAAA
196 TTTTAATTTAAAAACCAAAA
* ** * * * *
1524 GTTGGTTACAAAAATGACAAACCGTTTGGACCAAATGATGTGATTTCCCGAGCATCGAATGCTCG
1 GTTGTTTAC--AAATGACAAACTATTTGGACCAAATGATGCGATTTCCCAAGCATGGAATGTTCG
* ** * * * *
1589 AAAAATTGCTCAAAGGAATGGATCGTTTTGAATACTTTAAGGAATCAAAGTAAAAAAAGAGCTCG
64 AAAAATTGCTCGAAGGAATGGATCGTCATGAATACTTTAAGGAACCAAAGTTATAAAAGAACTCG
** * * * * *
1654 TATTATTTTGAGAAGCTCGTAAGTTCATCCAAGAACCAAAAGAGAAACAAGTCTCACTTAAATAA
129 TAAAAGTTTGACAAGTTTGTAAGTTCATCCAAGAACCAAAAGAGAAACAAGTCTCACGTAAATAA
*
1719 TTTTTTTAATTTAAAAACCAAAA
194 -GTTTTTAATTTAAAAACCAAAA
* * * *
1742 GTTGTTTGCAAATAACAAACTATTGGGACCAAAAGATGCGATTTCCCAAGCATGGAATGTTCGAA
1 GTTGTTTACAAATGACAAACTATTTGGACCAAATGATGCGATTTCCCAAGCATGGAATGTTCGAA
*
1807 AAATTACTCGAAGGAATGGATCGTCATGAATACTTTAAGGAACCAAAGTTATA
66 AAATTGCTCGAAGGAATGGATCGTCATGAATACTTTAAGGAACCAAAGTTATA
Statistics
Matches: 857, Mismatches: 121, Indels: 12
0.87 0.12 0.01
Matches are distributed among these distances:
214 9 0.01
215 93 0.11
216 380 0.44
217 319 0.37
218 56 0.07
ACGTcount: A:0.41, C:0.15, G:0.18, T:0.27
Consensus pattern (215 bp):
GTTGTTTACAAATGACAAACTATTTGGACCAAATGATGCGATTTCCCAAGCATGGAATGTTCGAA
AAATTGCTCGAAGGAATGGATCGTCATGAATACTTTAAGGAACCAAAGTTATAAAAGAACTCGTA
AAAGTTTGACAAGTTTGTAAGTTCATCCAAGAACCAAAAGAGAAACAAGTCTCACGTAAATAAGT
TTTTAATTTAAAAACCAAAA
Found at i:1556 original size:433 final size:432
Alignment explanation
Indices: 661--1859 Score: 1749
Period size: 433 Copynumber: 2.8 Consensus size: 432
651 NNNNNNNNNN
* * * *
661 GTTGTTTAC-AAATGACAAACTATTTGGACCAAATGATGCGATTTCACAAGCATGGAATGTTCGA
1 GTTGGTTACAAAATGACAAACAATTTGGACCAAATGATGCGATTTCCCAAGCATGGAATGCTCGA
* * * *
725 AAAATTACTCGAAGGAAT-GATCGTCTTGAATACTTTAAGGAACCAAAGTTATAAAAGAACTCGT
66 AAAATTGCTCAAAGGAATGGATCGTTTTGAATACTTTAAGGAATCAAAGTTATAAAAGAACTCGT
* * * * * * * * *
789 AAAAGTTTCACAAG-TTCATAAGTTCGTCCATGAAACAAAAGAGAAACAATTCTAACGTAAATAA
131 AAAATTTTGACAAGCTT-GTAAGTTCATCCAAGAACCAAAAGAGAAACAAGTCTCACTTAAATAA
* * * *
853 G-TTTTAAATTCAAAGACCAAAAGTTGTTTACAAAATGACAAACCATTTGGACCAAATGATGCGA
195 GTTTTTTAATTTAAAAACCAAAAGTTGTTTAC-AAATGACAAACTATTTGGACCAAATGATGCGA
* * * * *
917 TTTCCCAAGAAGGGAATGTTCGAAAAATGGCTTGAAGGAATGGATCATCATGAATACTTTAAGTA
259 TTTCCCAAGCATGGAATGTTCGAAAAATGGCTCGAAGGAATGGATCGTCATGAATACTTTAAGGA
* *
982 ACCAAAGTTATAAAAGAACTCGTAAAAGTTTGACAAGTTTGGAAGTTCGTCCAAGAACCAAAAGA
324 ACCAAAGTTATAAAAGAACTCGTAAAAGTTTGACAAATTTGGAAGTTCATCCAAGAACCAAAAGA
* * *
1047 GAAACAAGTCTCTCCTAGATAAGTTTTTAATTTAAAAACCAAAA
389 GAAACAAGTCTCACCTAAATAAGTTTTTAATTCAAAAACCAAAA
* * * * *
1091 GTTGTTTACAAAATGACAAGCTATTTTGGACCAAATGGTGCGATTTCCCAAGCATGGAATGCTCA
1 GTTGGTTACAAAATGACAAAC-AATTTGGACCAAATGATGCGATTTCCCAAGCATGGAATGCTCG
1156 AAAAATTGCTCAAAGGAATGGATCGTTTTGAATACTTTAAGGAATCAAAGTTATAAAAGAACTCG
65 AAAAATTGCTCAAAGGAATGGATCGTTTTGAATACTTTAAGGAATCAAAGTTATAAAAGAACTCG
* * *
1221 CAACATTTTGACAAGCTTGTAAGTTCACCCAAGAACCAAAAGAGAAACAAGTCTCACTTAAATAA
130 TAAAATTTTGACAAGCTTGTAAGTTCATCCAAGAACCAAAAGAGAAACAAGTCTCACTTAAATAA
1286 GTTTTTTAATTTAAAAACCAAAAGTTGTTTACAAATGACAAACTATTTGGACCAAATGATGCGAT
195 GTTTTTTAATTTAAAAACCAAAAGTTGTTTACAAATGACAAACTATTTGGACCAAATGATGCGAT
* *
1351 TTCCCGAGCATGGAATGTTCGAAAAATGGCTCGAAGGAATGGATCGTCATGAATACGTTAAGGAA
260 TTCCCAAGCATGGAATGTTCGAAAAATGGCTCGAAGGAATGGATCGTCATGAATACTTTAAGGAA
1416 CCAAAGTTATAAAAGAACTCGTAAAAGTTTGACAAATTTGGAAGTTCATCCAAGAACCAAAAGAG
325 CCAAAGTTATAAAAGAACTCGTAAAAGTTTGACAAATTTGGAAGTTCATCCAAGAACCAAAAGAG
* * * * *
1481 ATACAATTCTGACGTAAATAAGTTTTTAATTCAAAGACCAAAA
390 AAACAAGTCTCACCTAAATAAGTTTTTAATTCAAAAACCAAAA
** * * *
1524 GTTGGTTACAAAAATGACAAACCGTTTGGACCAAATGATGTGATTTCCCGAGCATCGAATGCTCG
1 GTTGGTTAC-AAAATGACAAACAATTTGGACCAAATGATGCGATTTCCCAAGCATGGAATGCTCG
* * *
1589 AAAAATTGCTCAAAGGAATGGATCGTTTTGAATACTTTAAGGAATCAAAGTAAAAAAAGAGCTCG
65 AAAAATTGCTCAAAGGAATGGATCGTTTTGAATACTTTAAGGAATCAAAGTTATAAAAGAACTCG
** * *
1654 TATTATTTTGAGAAGCTCGTAAGTTCATCCAAGAACCAAAAGAGAAACAAGTCTCACTTAAATAA
130 TAAAATTTTGACAAGCTTGTAAGTTCATCCAAGAACCAAAAGAGAAACAAGTCTCACTTAAATAA
* * * * *
1719 TTTTTTTAATTTAAAAACCAAAAGTTGTTTGCAAATAACAAACTATTGGGACCAAAAGATGCGAT
195 GTTTTTTAATTTAAAAACCAAAAGTTGTTTACAAATGACAAACTATTTGGACCAAATGATGCGAT
**
1784 TTCCCAAGCATGGAATGTTCGAAAAATTACTCGAAGGAATGGATCGTCATGAATACTTTAAGGAA
260 TTCCCAAGCATGGAATGTTCGAAAAATGGCTCGAAGGAATGGATCGTCATGAATACTTTAAGGAA
1849 CCAAAGTTATA
325 CCAAAGTTATA
Statistics
Matches: 692, Mismatches: 71, Indels: 9
0.90 0.09 0.01
Matches are distributed among these distances:
430 9 0.01
431 10 0.01
432 54 0.08
433 579 0.84
434 40 0.06
ACGTcount: A:0.41, C:0.15, G:0.18, T:0.27
Consensus pattern (432 bp):
GTTGGTTACAAAATGACAAACAATTTGGACCAAATGATGCGATTTCCCAAGCATGGAATGCTCGA
AAAATTGCTCAAAGGAATGGATCGTTTTGAATACTTTAAGGAATCAAAGTTATAAAAGAACTCGT
AAAATTTTGACAAGCTTGTAAGTTCATCCAAGAACCAAAAGAGAAACAAGTCTCACTTAAATAAG
TTTTTTAATTTAAAAACCAAAAGTTGTTTACAAATGACAAACTATTTGGACCAAATGATGCGATT
TCCCAAGCATGGAATGTTCGAAAAATGGCTCGAAGGAATGGATCGTCATGAATACTTTAAGGAAC
CAAAGTTATAAAAGAACTCGTAAAAGTTTGACAAATTTGGAAGTTCATCCAAGAACCAAAAGAGA
AACAAGTCTCACCTAAATAAGTTTTTAATTCAAAAACCAAAA
Done.