Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01000753.1 Kokia drynarioides strain JFW-HI SEQ_111797, 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, 931
Length: 1553
ACGTcount: A:0.40, C:0.16, G:0.17, T:0.27
Found at i:804 original size:432 final size:431
Alignment explanation
Indices: 7--1553 Score: 2186
Period size: 432 Copynumber: 3.6 Consensus size: 431
1 TCACTT
* ** * *
7 AATAAGTTTTTAATTGAAAGATCAAAACATGTTTACAAAATGA-AAATCTATTTAGACCAAATGA
1 AATAAGTTTTTAATTTAAAGGCCAAAACTTGTTTACAAAATGACAAA-CTTTTTAGACCAAATGA
* ** * * * *
71 TGCGATTTCCCTCGCATGGAATGTTCGAAAAATTACTCAAAGGAATGGA---TC--G--T-C-TT
65 TGCGACTTCCCGAGCATGTAATGTTCGAAAAATTGCTCGAAGGATTGGATCGTCTTGCATACATT
* *
127 ---GAACCAAAGCTATAAAAGAGCTAGTAAAAGTTCGACAAGTTCAGAAGTTCGTCCAAGAACCA
130 AAGGAACCGAAGCTATAAAAGAACTAGTAAAAGTTCGACAAGTTCAGAAGTTCGTCCAAGAACCA
* * * *
189 ATAGAGACACAGTTCTCTCGTAAATAAGTTTTTAATTCAAAGATCGAAACATGTTTACAAAATGA
195 AGAGAGACACAATTCTCACGTAAATAAGTTTTTAATTCAAAGATCAAAACATGTTTACAAAATGA
* * * **
254 AAAGCTATTTAGACCAAATGATAAGATTTCCCTCACATGGAATGTTTGGAAAATTACTCGAAGGA
260 AAAACTATTTAGACCAAATGATACGATTTCCCTCGCATGGAATGTTCAGAAAATTACTCGAAGGA
* * *
319 ATGGATCATCTTGAACACTTTAAGGAACTGGATTTAAAAAAGAACTAGTAAAAGTTTGACAAGTT
325 ATGGATCGTCTTGAACACTTTAAGGAAC-GGATTTAAAAAAGAACTCGTAAAAGTTTGACAATTT
* *
384 CGGAAGTTCGTCCAACAACCAAGAGAGAAACAATTCTAACGTA
389 TGTAAGTTCGTCCAACAACCAAGAGAGAAACAATTCTAACGTA
* *
427 AATAAGTTTTTAATTTAAAGGCCAAAACTTTTTTACAAAATGACAAACCTTTTAGACCAAATGAT
1 AATAAGTTTTTAATTTAAAGGCCAAAACTTGTTTACAAAATGACAAACTTTTTAGACCAAATGAT
* * * * * *
492 GCTACTTCTCGAGCATGTAATGTTCGGAAAATTTCTCGAAGGATTGGATTGTCTTGCATACTTTA
66 GCGACTTCCCGAGCATGTAATGTTCGAAAAATTGCTCGAAGGATTGGATCGTCTTGCATACATTA
* * * * *
557 AGGAACCGAAGCTATAAATGAACTCGTAAAAGTTCGACAAGTTCGGAAGTTCATCCGAGAACCAA
131 AGGAACCGAAGCTATAAAAGAACTAGTAAAAGTTCGACAAGTTCAGAAGTTCGTCCAAGAACCAA
* * *
622 GAGAGAAACAATTCTCACGTAAATCAGTTTATAATTCAAAGATCAAAACATGTTTACAAAATGAA
196 GAGAGACACAATTCTCACGTAAATAAGTTTTTAATTCAAAGATCAAAACATGTTTACAAAATGAA
* * * *
687 AAACTATTTAGACCAAATGATGCGACTTCCGTCGCATGGAATGTTCCGAAAATTACTCGAAGGAA
261 AAACTATTTAGACCAAATGATACGATTTCCCTCGCATGGAATGTTCAGAAAATTACTCGAAGGAA
*
752 TGGATCGTCTTGAACACTTTAAGGAATCGAATTTAAAAAAGAACTCGTAAAAGTTTGACAATTTT
326 TGGATCGTCTTGAACACTTTAAGGAA-CGGATTTAAAAAAGAACTCGTAAAAGTTTGACAATTTT
* *
817 GTAAGTTCGTCCTACAACCAAGAGAGAAACAATTCTCACGTA
390 GTAAGTTCGTCCAACAACCAAGAGAGAAACAATTCTAACGTA
* * *
859 AATAAGTTTTTAATTTAAAGGCCAAAACCTGTTTACAAAATAACAAACTTTTTATACCAAATGAT
1 AATAAGTTTTTAATTTAAAGGCCAAAACTTGTTTACAAAATGACAAACTTTTTAGACCAAATGAT
* * * * *
924 GCGACTTCCCGAGCATGTAATGCTCGAAAAATTGCTCAAAGGATTGTATCGTCTTGAATACGTTA
66 GCGACTTCCCGAGCATGTAATGTTCGAAAAATTGCTCGAAGGATTGGATCGTCTTGCATACATTA
* * * * *
989 AGGAACCGAAACTATAAAAGTACTAGTAAAAGTTCAACAAGTTCAGAAGTTCGTCCAAAAACCAG
131 AGGAACCGAAGCTATAAAAGAACTAGTAAAAGTTCGACAAGTTCAGAAGTTCGTCCAAGAACCAA
* * * *
1054 GACAGACAGAATTCTCACGTAAATAAGTTTTTAATTCAGAGATCAAAACTTGTTTACAAAATGAA
196 GAGAGACACAATTCTCACGTAAATAAGTTTTTAATTCAAAGATCAAAACATGTTTACAAAATGAA
* *
1119 AAACTAATTAGACCAAATGATACGATTTCCCTCGCATGGAATGTTCAGAAAATTAATCGAAGGAA
261 AAACTATTTAGACCAAATGATACGATTTCCCTCGCATGGAATGTTCAGAAAATTACTCGAAGGAA
* *
1184 TGGATCGTCTTGAACACTTTAAGGAACCGGATTTAAAAAAGAACGCGTAAAAGATTGACAATTTT
326 TGGATCGTCTTGAACACTTTAAGGAA-CGGATTTAAAAAAGAACTCGTAAAAGTTTGACAATTTT
* *
1249 GTAAGCTCGTCCAACAACAAAGAGAGAAACAATTCTAACGTA
390 GTAAGTTCGTCCAACAACCAAGAGAGAAACAATTCTAACGTA
* * *
1291 AATAAGTTTTTAATTCAAAGGCCAAAACTTGTTTGCAAAATGAAAAACTTTTTAGACCAAATGAT
1 AATAAGTTTTTAATTTAAAGGCCAAAACTTGTTTACAAAATGACAAACTTTTTAGACCAAATGAT
* * *
1356 GCGACTTCCCGAGCAAGTAATGTTTGAAAAATTGCTCGAAGGATTGGATCGTCCT-CAATACATT
66 GCGACTTCCCGAGCATGTAATGTTCGAAAAATTGCTCGAAGGATTGGATCGTCTTGC-ATACATT
* * * *
1420 AAGGAATCGAAGCTATAAAAGAACTCGTAAAAGTTCGACAAGTTCGGAAGTTCGTCCAGGAACCA
130 AAGGAACCGAAGCTATAAAAGAACTAGTAAAAGTTCGACAAGTTCAGAAGTTCGTCCAAGAACCA
*
1485 AGAGAGACACAATTCTCACGTAAATAAGTTTTTAATTCAAAGATCAAAACTTGTTTACAAAATGA
195 AGAGAGACACAATTCTCACGTAAATAAGTTTTTAATTCAAAGATCAAAACATGTTTACAAAATGA
1550 AAAA
260 AAAA
Statistics
Matches: 993, Mismatches: 119, Indels: 18
0.88 0.11 0.02
Matches are distributed among these distances:
420 92 0.09
421 3 0.00
423 2 0.00
425 1 0.00
427 1 0.00
428 1 0.00
429 2 0.00
432 890 0.90
433 1 0.00
ACGTcount: A:0.40, C:0.16, G:0.17, T:0.27
Consensus pattern (431 bp):
AATAAGTTTTTAATTTAAAGGCCAAAACTTGTTTACAAAATGACAAACTTTTTAGACCAAATGAT
GCGACTTCCCGAGCATGTAATGTTCGAAAAATTGCTCGAAGGATTGGATCGTCTTGCATACATTA
AGGAACCGAAGCTATAAAAGAACTAGTAAAAGTTCGACAAGTTCAGAAGTTCGTCCAAGAACCAA
GAGAGACACAATTCTCACGTAAATAAGTTTTTAATTCAAAGATCAAAACATGTTTACAAAATGAA
AAACTATTTAGACCAAATGATACGATTTCCCTCGCATGGAATGTTCAGAAAATTACTCGAAGGAA
TGGATCGTCTTGAACACTTTAAGGAACGGATTTAAAAAAGAACTCGTAAAAGTTTGACAATTTTG
TAAGTTCGTCCAACAACCAAGAGAGAAACAATTCTAACGTA
Found at i:1553 original size:216 final size:216
Alignment explanation
Indices: 127--1553 Score: 1689
Period size: 216 Copynumber: 6.6 Consensus size: 216
117 GGATCGTCTT
* * * * * *
127 GAACCAAAGCTATAAAAGAGCTAGTAAAAGTTCGACAAGTTCAGAAGTTCGTCCAAGAACCAATA
1 GAACCGAAGCTATAAAAGAACTCGTAAAAGTTCGACAAGTTCGGAAGTTCGTCCAACAACCAAGA
* * * * *
192 GAGACACAGTTCTCTCGTAAATAAGTTTTTAATTCAAAGATCGAAACATGTTTACAAAATGAAAA
66 GAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGATCAAAACTTGTTTACAAAATGAAAA
* ** * * * *
257 GCTATTTAGACCAAATGATAAGATTTCCCTCA-CATGGAATGTTTGGAAAATTACTCGAAGGAAT
131 ACTATTTAGACCAAATGATGCGACTTCCC-GAGCATGGAATGTTCGAAAAATTACTCGAAGGAAT
*
321 GGATCATCTTGAACACTTTAAG
195 GGATCGTCTTGAACACTTTAAG
* * ** * * *
343 GAACTGGATTTAAAAAAGAACTAGTAAAAGTTTGACAAGTTCGGAAGTTCGTCCAACAACCAAGA
1 GAACCGAAGCTATAAAAGAACTCGTAAAAGTTCGACAAGTTCGGAAGTTCGTCCAACAACCAAGA
* * ** *
408 GAGAAACAATTCTAACGTAAATAAGTTTTTAATTTAAAGGCCAAAACTTTTTTACAAAATGACAA
66 GAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGATCAAAACTTGTTTACAAAATGA-AA
* * * * * * *
473 ACCT-TTTAGACCAAATGATGCTACTTCTCGAGCATGTAATGTTCGGAAAATTTCTCGAAGGATT
130 AACTATTTAGACCAAATGATGCGACTTCCCGAGCATGGAATGTTCGAAAAATTACTCGAAGGAAT
* * *
537 GGATTGTCTTGCATACTTTAAG
195 GGATCGTCTTGAACACTTTAAG
* * * *
559 GAACCGAAGCTATAAATGAACTCGTAAAAGTTCGACAAGTTCGGAAGTTCATCCGAGAACCAAGA
1 GAACCGAAGCTATAAAAGAACTCGTAAAAGTTCGACAAGTTCGGAAGTTCGTCCAACAACCAAGA
* * *
624 GAGAAACAATTCTCACGTAAATCAGTTTATAATTCAAAGATCAAAACATGTTTACAAAATGAAAA
66 GAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGATCAAAACTTGTTTACAAAATGAAAA
*
689 ACTATTTAGACCAAATGATGCGACTT-CCGTCGCATGGAATGTTCCG-AAAATTACTCGAAGGAA
131 ACTATTTAGACCAAATGATGCGACTTCCCG-AGCATGGAATGTT-CGAAAAATTACTCGAAGGAA
752 TGGATCGTCTTGAACACTTTAAG
194 TGGATCGTCTTGAACACTTTAAG
* ** * * * * * *
775 GAATCGAATTTAAAAAAGAACTCGTAAAAGTTTGACAATTTTGTAAGTTCGTCCTACAACCAAGA
1 GAACCGAAGCTATAAAAGAACTCGTAAAAGTTCGACAAGTTCGGAAGTTCGTCCAACAACCAAGA
* ** *
840 GAGAAACAATTCTCACGTAAATAAGTTTTTAATTTAAAGGCCAAAACCTGTTTACAAAAT-AACA
66 GAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGATCAAAACTTGTTTACAAAATGAA-A
* * * * * * *
904 AACTTTTTATACCAAATGATGCGACTTCCCGAGCATGTAATGCTCGAAAAATTGCTCAAAGGATT
130 AACTATTTAGACCAAATGATGCGACTTCCCGAGCATGGAATGTTCGAAAAATTACTCGAAGGAAT
* * *
969 GTATCGTCTTGAATACGTTAAG
195 GGATCGTCTTGAACACTTTAAG
* * * * * * *
991 GAACCGAAACTATAAAAGTACTAGTAAAAGTTCAACAAGTTCAGAAGTTCGTCCAAAAACCAGGA
1 GAACCGAAGCTATAAAAGAACTCGTAAAAGTTCGACAAGTTCGGAAGTTCGTCCAACAACCAAGA
* * * *
1056 CAGACAGAATTCTCACGTAAATAAGTTTTTAATTCAGAGATCAAAACTTGTTTACAAAATGAAAA
66 GAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGATCAAAACTTGTTTACAAAATGAAAA
* * * ** *
1121 ACTAATTAGACCAAATGATACGATTTCCCTCGCATGGAATGTTC-AGAAAATTAATCGAAGGAAT
131 ACTATTTAGACCAAATGATGCGACTTCCCGAGCATGGAATGTTCGA-AAAATTACTCGAAGGAAT
1185 GGATCGTCTTGAACACTTTAAG
195 GGATCGTCTTGAACACTTTAAG
* ** * * * * * * *
1207 GAACCGGATTTAAAAAAGAACGCGTAAAAGATT-GACAATTTTGTAAGCTCGTCCAACAACAAAG
1 GAACCGAAGCTATAAAAGAACTCGTAAAAG-TTCGACAAGTTCGGAAGTTCGTCCAACAACCAAG
* ** *
1271 AGAGAAACAATTCTAACGTAAATAAGTTTTTAATTCAAAGGCCAAAACTTGTTTGCAAAATGAAA
65 AGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGATCAAAACTTGTTTACAAAATGAAA
* * * * * *
1336 AACTTTTTAGACCAAATGATGCGACTTCCCGAGCAAGTAATGTTTGAAAAATTGCTCGAAGGATT
130 AACTATTTAGACCAAATGATGCGACTTCCCGAGCATGGAATGTTCGAAAAATTACTCGAAGGAAT
* * * *
1401 GGATCGTCCTCAATACATTAAG
195 GGATCGTCTTGAACACTTTAAG
* **
1423 GAATCGAAGCTATAAAAGAACTCGTAAAAGTTCGACAAGTTCGGAAGTTCGTCCAGGAACCAAGA
1 GAACCGAAGCTATAAAAGAACTCGTAAAAGTTCGACAAGTTCGGAAGTTCGTCCAACAACCAAGA
*
1488 GAGACACAATTCTCACGTAAATAAGTTTTTAATTCAAAGATCAAAACTTGTTTACAAAATGAAAA
66 GAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGATCAAAACTTGTTTACAAAATGAAAA
1553 A
131 A
Statistics
Matches: 1007, Mismatches: 191, Indels: 26
0.82 0.16 0.02
Matches are distributed among these distances:
215 15 0.01
216 977 0.97
217 15 0.01
ACGTcount: A:0.40, C:0.16, G:0.17, T:0.27
Consensus pattern (216 bp):
GAACCGAAGCTATAAAAGAACTCGTAAAAGTTCGACAAGTTCGGAAGTTCGTCCAACAACCAAGA
GAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGATCAAAACTTGTTTACAAAATGAAAA
ACTATTTAGACCAAATGATGCGACTTCCCGAGCATGGAATGTTCGAAAAATTACTCGAAGGAATG
GATCGTCTTGAACACTTTAAG
Done.