Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013860.1 Kokia drynarioides strain JFW-HI SEQ_128888, 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, 842
Length: 1404
ACGTcount: A:0.39, C:0.17, G:0.16, T:0.28
Found at i:387 original size:216 final size:215
Alignment explanation
Indices: 13--1404 Score: 1450
Period size: 216 Copynumber: 6.4 Consensus size: 215
3 CGTCCAAGAG
* * * * * ***
13 CAAGAGAGACACATTTCACACTTAAATAATTTTTTAATTCAAAGATTAAAACTTGTTTACAAAAT
1 CAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGGCAAAAACTTGTTTACAAAAT
* *
78 GA-AAAACTATTTAGACCAAATGATGCGATTTCCCTCGCATGGAATGTTCGATAAATTACTCGAA
66 GACAAACCTA-TTAGACCAAATGATGCGACTTCCCTCGCATGGAATGTTCGA-AAATTACTCGAA
* *
142 GAAATGGATCGTCTTGAACACTTTAAGGAACTGGGTTTAAAAAAGAACTAGTAAAAGTTTGACAA
129 GGAATGGATCGTCTTGAACACTTTAAGGAACTGGATTTAAAAAAGAACTAGTAAAAGTTTGACAA
* * *
207 GTTCGGAAGTTCGTCCACCAAC
194 GTTCGTAAGTTCATCCAACAAC
* *
229 CAAGAGAGAAACAATTGTCATGTAAATAAGTTTTTAATTCAAAGGCAAAAACTTGTTTACAAAAT
1 CAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGGCAAAAACTTGTTTACAAAAT
* * * * * *
294 GACAAACCTATTAGACGAAACGATGTGACTTCCCGT-GCATGTAATGTTCGGAAAATTGCTCGAT
66 GACAAACCTATTAGACCAAATGATGCGACTTCCC-TCGCATGGAATGTTC-GAAAATTACTCGAA
* * * * * * * ** * * * * *
358 GTATTGTATCGTCTTGCATACTTTAAGGAACCGAAGCTATAAAACAAGTCA-TAAAAGTTCGGCA
129 GGAATGGATCGTCTTGAACACTTTAAGGAACTGGATTTAAAAAAGAACT-AGTAAAAGTTTGACA
* *
422 AGTTCGTATGTTCATCCAAGAAC
193 AGTTCGTAAGTTCATCCAACAAC
* ** * * * *
445 CAAGAGAGAAATAATTCTTGCGTCAATAAGTTTATAATTCAAAGATC-AAAACATGTTTACAAAA
1 CAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAG-GCAAAAACTTGTTTACAAAA
* * * * *
509 TCAAAAAACTATTTAGACCAAATGATGCGATTTCCCTCGCATGGAATGTTTCGAAAATTACTCGT
65 TGACAAACCTA-TTAGACCAAATGATGCGACTTCCCTCGCATGGAATG-TTCGAAAATTACTCGA
* *
574 AGGAATGGATCGTCTTGAACACTTTAAGGAACTGGATTTGAAAAAGAACTAGTAAAAGTTTGAAA
128 AGGAATGGATCGTCTTGAACACTTTAAGGAACTGGATTTAAAAAAGAACTAGTAAAAGTTTGACA
* * * * *
639 AGATCGGAAGTACATCTAACGAC
193 AGTTCGTAAGTTCATCCAACAAC
* * * * *
662 CAAGAGAGAATCACTTCTCACGTAAATAAGTTTTTAATTCAAAGGCCAAAACATATTTACAAAAT
1 CAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGGCAAAAACTTGTTTACAAAAT
* * * ** * * *
727 GACAAACTTTTTAGACCAAACGATGCGACTTCCCGAGCATGTAACGTTCAGAAAATTTCTTCG-A
66 GACAAACCTATTAGACCAAATGATGCGACTTCCCTCGCATGGAATGTTC-GAAAATTAC-TCGAA
* * * * * * *
791 GCAATGGATCGT-TCTAAACACTTTATGGAATTAGATTTATAAAAGAACTCGTAAAAGTTTGACA
129 GGAATGGATCGTCT-TGAACACTTTAAGGAACTGGATTTAAAAAAGAACTAGTAAAAGTTTGACA
*
855 ATTTCGTAAGTTCATCCAACAAC
193 AGTTCGTAAGTTCATCCAACAAC
878 CAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGGCAAAAACTTGTTTACAAAAT
1 CAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGGCAAAAACTTGTTTACAAAAT
* * * * * *
943 GACAAACCTTTTAGACCAAATGATGCTACTTCCC-CAGCATGTAATGTTCGAAAAATTGCACAAA
66 GACAAACCTATTAGACCAAATGATGCGACTTCCCTC-GCATGGAATGTTCG-AAAATTACTCGAA
* * * * * ** * * * ** *
1007 GGATTGGATCGTCTTGCATACTTTAAGGAACCGAAGCTATAAATGAACTCGTAAAAGTTCAACAT
129 GGAATGGATCGTCTTGAACACTTTAAGGAACTGGATTTAAAAAAGAACTAGTAAAAGTTTGACAA
* * **
1072 GTTCGAAATTTCATCCAAGTAC
194 GTTCGTAAGTTCATCCAACAAC
* * * * *
1094 CAAGAGAGAAACAATTCTCACATAAATAAGTTTTTAATTCAAAGATCAAAAACATGTTCATAAAA
1 CAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAG-GCAAAAACTTGTTTACAAAA
* * * * * *
1159 TGA-AAAACTATTTAAACCAAATGATGCGATTTTCATCGCATGGAATATTTCGAAAATTACTCGA
65 TGACAAACCTA-TTAGACCAAATGATGCGACTTCCCTCGCATGGAAT-GTTCGAAAATTACTCGA
* * * * * *
1223 AGGAATGGATCGTCTTGAATACTTTCAGGAACTAGATTTAAAAAACAACTCGTAAAAGTTTCACA
128 AGGAATGGATCGTCTTGAACACTTTAAGGAACTGGATTTAAAAAAGAACTAGTAAAAGTTTGACA
* * *
1288 ATTTCGTAAGCTCATCCATCAAC
193 AGTTCGTAAGTTCATCCAACAAC
* *
1311 CAAGAGAGATACAATTCTCACGTAAATAAGTTTTTAATTCAAAGGCCAAAACTTGTTTACAAAAT
1 CAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGGCAAAAACTTGTTTACAAAAT
* *
1376 GACAAACTTTTTAGACCAAATGATGCGAC
66 GACAAACCTATTAGACCAAATGATGCGAC
Statistics
Matches: 953, Mismatches: 201, Indels: 44
0.80 0.17 0.04
Matches are distributed among these distances:
215 6 0.01
216 595 0.62
217 344 0.36
218 8 0.01
ACGTcount: A:0.39, C:0.17, G:0.16, T:0.28
Consensus pattern (215 bp):
CAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGGCAAAAACTTGTTTACAAAAT
GACAAACCTATTAGACCAAATGATGCGACTTCCCTCGCATGGAATGTTCGAAAATTACTCGAAGG
AATGGATCGTCTTGAACACTTTAAGGAACTGGATTTAAAAAAGAACTAGTAAAAGTTTGACAAGT
TCGTAAGTTCATCCAACAAC
Found at i:885 original size:433 final size:426
Alignment explanation
Indices: 13--1403 Score: 1561
Period size: 433 Copynumber: 3.2 Consensus size: 426
3 CGTCCAAGAG
* * * * * *
13 CAAGAGAGACACATTTCACACTTAAATAATTTTTTAATTCAAAGATTAAAACTTGTTTACAAAAT
1 CAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGATCAAAACTTGTTTACAAAAT
*
78 GAAAAACTATTTAGACCAAATGATGCGATTTCCCTCGCATGGAATGTTCGATAAATTACTCGAAG
66 AAAAAACTATTTAGACCAAATGATGCGATTTCCCTCGCATGGAATGTTCGA-AAATTACTCGAAG
* * *
143 AAATGGATCGTCTTGAACACTTTAAGGAACTGGGTTTAAAAAAGAACTAGTAAAAGTTTGACAAG
130 GAATGGATCGTCTTGAACACTTTAAGGAACTGGATTT-AAAAAGAACTAGTAAAAGTTTGAAAAG
* * * * *
208 TTCGGAAGTTCGTCCACCAACCAAGAGAGAAACAATTGTCATGTAAATAAGTTTTTAATTCAAAG
194 TTCGGAAGTTCATCCAACGACCAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAG
* * * * * *
273 GCAAAAACTTGTTTACAAAATGACAAACCTATTAGACGAAACGATGTGACTTCCCGTGCATGTAA
259 GCAAAAACATGTTTACAAAATGACAAACTTTTTAGACCAAACGATGCGACTTCCCGAGCATGTAA
* * * * * * ** **
338 TGTTCGGAAAATTGCTCGATGTATTGTATCGTCTTGCATACTTTAAGGAACCGAAGCTATAAAAC
324 AGTTC-GAAAATTACTCGA-GCAATGGATCGTCTTGAATACTTT-AGGAATAG-ATTTATAAAAC
* * * * * * *
403 AAGTCATAAAAGTTCGGCAAGTTCGTATGTTCATCCAAGAAC
385 AACTCGTAAAAGTTTGACAATTTCGTAAGTTCATCCAACAAC
* ** * * *
445 CAAGAGAGAAATAATTCTTGCGTCAATAAGTTTATAATTCAAAGATCAAAACATGTTTACAAAAT
1 CAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGATCAAAACTTGTTTACAAAAT
*
510 CAAAAAACTATTTAGACCAAATGATGCGATTTCCCTCGCATGGAATGTTTCGAAAATTACTCGTA
66 -AAAAAACTATTTAGACCAAATGATGCGATTTCCCTCGCATGGAATG-TTCGAAAATTACTCGAA
575 GGAATGGATCGTCTTGAACACTTTAAGGAACTGGATTTGAAAAAGAACTAGTAAAAGTTTGAAAA
129 GGAATGGATCGTCTTGAACACTTTAAGGAACTGGATTT-AAAAAGAACTAGTAAAAGTTTGAAAA
* * * * *
640 GATCGGAAGTACATCTAACGACCAAGAGAGAATCACTTCTCACGTAAATAAGTTTTTAATTCAAA
193 GTTCGGAAGTTCATCCAACGACCAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAA
* *
705 GGCCAAAACATATTTACAAAATGACAAACTTTTTAGACCAAACGATGCGACTTCCCGAGCATGTA
258 GGCAAAAACATGTTTACAAAATGACAAACTTTTTAGACCAAACGATGCGACTTCCCGAGCATGTA
* * * *
770 ACGTTCAGAAAATTTCTTCGAGCAATGGATCGT-TCTAAACACTTTATGGAATTAGATTTATAAA
323 AAGTTC-GAAAATTAC-TCGAGCAATGGATCGTCT-TGAATACTTTA-GGAA-TAGATTTATAAA
*
834 AGAACTCGTAAAAGTTTGACAATTTCGTAAGTTCATCCAACAAC
383 ACAACTCGTAAAAGTTTGACAATTTCGTAAGTTCATCCAACAAC
*
878 CAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAG-GCAAAAACTTGTTTACAAAA
1 CAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGATC-AAAACTTGTTTACAAAA
* * * * * * * *
942 TGACAAACCT-TTTAGACCAAATGATGCTACTTCCC-CAGCATGTAATGTTCGAAAAATTGCACA
65 T-AAAAAACTATTTAGACCAAATGATGCGATTTCCCTC-GCATGGAATGTTCG-AAAATTACTCG
* * * * * ** * * *
1005 AAGGATTGGATCGTCTTGCATACTTTAAGGAACCGAAGCTATAAATGAACTCGTAAAAG-TTCAA
127 AAGGAATGGATCGTCTTGAACACTTTAAGGAACTGGATTTA-AAAAGAACTAGTAAAAGTTTGAA
* * * *
1069 CATGTTCGAAATTTCATCCAA-GTACCAAGAGAGAAACAATTCTCACATAAATAAGTTTTTAATT
191 -AAGTTCGGAAGTTCATCCAACG-ACCAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATT
* * * * * * * * * ***
1133 CAAAGATCAAAAACATGTTCATAAAATGAAAAACTATTTAAACCAAATGATGCGATTTTCATCGC
254 CAAAG-GCAAAAACATGTTTACAAAATGACAAACTTTTTAGACCAAACGATGCGACTTCCCGAGC
* * *
1198 ATGGAATATTTCGAAAATTACTCGAAGGAATGGATCGTCTTGAATACTTTCAGGAACTAGATTTA
318 ATGTAA-AGTTCGAAAATTACTCG-AGCAATGGATCGTCTTGAATACTTT-AGGAA-TAGATTTA
* * * *
1263 AAAAACAACTCGTAAAAGTTTCACAATTTCGTAAGCTCATCCATCAAC
379 TAAAACAACTCGTAAAAGTTTGACAATTTCGTAAGTTCATCCAACAAC
* **
1311 CAAGAGAGATACAATTCTCACGTAAATAAGTTTTTAATTCAAAGGCCAAAACTTGTTTACAAAAT
1 CAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGATCAAAACTTGTTTACAAAAT
* * *
1376 GACAAACTTTTTAGACCAAATGATGCGA
66 AAAAAACTATTTAGACCAAATGATGCGA
1404 C
Statistics
Matches: 813, Mismatches: 127, Indels: 37
0.83 0.13 0.04
Matches are distributed among these distances:
431 11 0.01
432 207 0.25
433 579 0.71
434 16 0.02
ACGTcount: A:0.39, C:0.17, G:0.16, T:0.28
Consensus pattern (426 bp):
CAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGATCAAAACTTGTTTACAAAAT
AAAAAACTATTTAGACCAAATGATGCGATTTCCCTCGCATGGAATGTTCGAAAATTACTCGAAGG
AATGGATCGTCTTGAACACTTTAAGGAACTGGATTTAAAAAGAACTAGTAAAAGTTTGAAAAGTT
CGGAAGTTCATCCAACGACCAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGGC
AAAAACATGTTTACAAAATGACAAACTTTTTAGACCAAACGATGCGACTTCCCGAGCATGTAAAG
TTCGAAAATTACTCGAGCAATGGATCGTCTTGAATACTTTAGGAATAGATTTATAAAACAACTCG
TAAAAGTTTGACAATTTCGTAAGTTCATCCAACAAC
Found at i:1255 original size:649 final size:649
Alignment explanation
Indices: 13--1404 Score: 1911
Period size: 649 Copynumber: 2.1 Consensus size: 649
3 CGTCCAAGAG
* * * * ***
13 CAAGAGAGACA-CATTTCACACTTAAATAATTTTTTAATTCAAAGATTAAAACTTGTTTACAAAA
1 CAAGAGAGA-ATCAATTCTCACGTAAATAAGTTTTTAATTCAAAGGCCAAAACTTGTTTACAAAA
* * * ** *
77 TGAAAAACTATTTAGACCAAATGATGCGATTTCCCTCGCATGGAATGTTCGATAAATTACTCGAA
65 TGACAAACTTTTTAGACCAAATGATGCGACTTCCCGAGCATGGAACGTTCGATAAATTACTCGAA
* * *
142 GAAATGGATCGTCTTGAACACTTTAAGGAACTGGGTTTAAAAAAGAACTAGTAAAAGTTTGACAA
130 GAAATGGATCGTCTTAAACACTTTAAGGAACTAGATTTAAAAAAGAACTAGTAAAAGTTTGACAA
* * * *
207 GTTCGGAAGTTCGTCCACCAACCAAGAGAGAAACAATTGTCATGTAAATAAGTTTTTAATTCAAA
195 GTTCGGAAGTTCATCCAACAACCAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAA
* **
272 GGCAAAAACTTGTTTACAAAATGACAAACCTATTAGACGAAACGATGTGACTTCCCGTGCATGTA
260 GGCAAAAACTTGTTTACAAAATGACAAACCTATTAGACCAAACGATGTGACTTCCCCAGCATGTA
* * * * * *
337 ATGTTCGGAAAATTGCTCGATGTATTGTATCGTCTTGCATACTTTAAGGAACCGAAGCTATAAAA
325 ATGTTCGAAAAATTGCACAAAGGATTGGATCGTCTTGCATACTTTAAGGAACCGAAGCTATAAAA
* ** * * ** *
402 CAAGTCATAAAAGTTCGGCAAGTTCGTATGTTCATCCAAGAACCAAGAGAGAAATAATTCTTGCG
390 CAACTCATAAAAGTTCAACAAGTTCGAATGTTCATCCAAGAACCAAGAGAGAAACAATTCTCACA
* * *
467 TCAATAAGTTTATAATTCAAAGATCAAAACATGTTTACAAAATCAAAAAACTATTTAGACCAAAT
455 TAAATAAGTTTATAATTCAAAGATCAAAACATGTTCACAAAATCAAAAAACTATTTAAACCAAAT
* * *
532 GATGCGATTTCCCTCGCATGGAATGTTTCGAAAATTACTCGTAGGAATGGATCGTCTTGAACACT
520 GATGCGATTTCCATCGCATGGAATATTTCGAAAATTACTCGAAGGAATGGATCGTCTTGAACACT
* * * * * *
597 TTAAGGAACTGGATTTGAAAAAGAACTAGTAAAAGTTTGAAAAGATCGGAAG-TACATCTAACGA
585 TTAAGGAACTAGATTTAAAAAACAACTAGTAAAAGTTTCAAAAGATCGGAAGCT-CATCCAACAA
661 C
649 C
* * *
662 CAAGAGAGAATCACTTCTCACGTAAATAAGTTTTTAATTCAAAGGCCAAAACATATTTACAAAAT
1 CAAGAGAGAATCAATTCTCACGTAAATAAGTTTTTAATTCAAAGGCCAAAACTTGTTTACAAAAT
* * *
727 GACAAACTTTTTAGACCAAACGATGCGACTTCCCGAGCATGTAACGTTCAGA-AAATTTCTTCG-
66 GACAAACTTTTTAGACCAAATGATGCGACTTCCCGAGCATGGAACGTTC-GATAAATTAC-TCGA
* * * * *
790 AGCAATGGATCGT-TCTAAACACTTTATGGAATTAGATTTATAAAAGAACTCGTAAAAGTTTGAC
129 AGAAATGGATCGTCT-TAAACACTTTAAGGAACTAGATTTAAAAAAGAACTAGTAAAAGTTTGAC
* *
854 AATTTCGTAAGTTCATCCAACAACCAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCA
193 AAGTTCGGAAGTTCATCCAACAACCAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCA
* *
919 AAGGCAAAAACTTGTTTACAAAATGACAAACCTTTTAGACCAAATGATGCT-ACTTCCCCAGCAT
258 AAGGCAAAAACTTGTTTACAAAATGACAAACCTATTAGACCAAACGATG-TGACTTCCCCAGCAT
983 GTAATGTTCGAAAAATTGCACAAAGGATTGGATCGTCTTGCATACTTTAAGGAACCGAAGCTATA
322 GTAATGTTCGAAAAATTGCACAAAGGATTGGATCGTCTTGCATACTTTAAGGAACCGAAGCTATA
** * * *
1048 AATGAACTCGTAAAAGTTCAACATGTTCGAAAT-TTCATCCAAGTACCAAGAGAGAAACAATTCT
387 AAACAACTCATAAAAGTTCAACAAGTTCG-AATGTTCATCCAAGAACCAAGAGAGAAACAATTCT
* * *
1112 CACATAAATAAGTTTTTAATTCAAAGATCAAAAACATGTTCATAAAAT-GAAAAACTATTTAAAC
451 CACATAAATAAGTTTATAATTCAAAGATC-AAAACATGTTCACAAAATCAAAAAACTATTTAAAC
*
1176 CAAATGATGCGATTTTCATCGCATGGAATATTTCGAAAATTACTCGAAGGAATGGATCGTCTTGA
515 CAAATGATGCGATTTCCATCGCATGGAATATTTCGAAAATTACTCGAAGGAATGGATCGTCTTGA
* * * * ** *
1241 ATACTTTCAGGAACTAGATTTAAAAAACAACTCGTAAAAGTTTCACAATTTCGTAAGCTCATCCA
580 ACACTTTAAGGAACTAGATTTAAAAAACAACTAGTAAAAGTTTCAAAAGATCGGAAGCTCATCCA
*
1306 TCAAC
645 ACAAC
1311 CAAGAGAG-ATACAATTCTCACGTAAATAAGTTTTTAATTCAAAGGCCAAAACTTGTTTACAAAA
1 CAAGAGAGAAT-CAATTCTCACGTAAATAAGTTTTTAATTCAAAGGCCAAAACTTGTTTACAAAA
1375 TGACAAACTTTTTAGACCAAATGATGCGAC
65 TGACAAACTTTTTAGACCAAATGATGCGAC
Statistics
Matches: 650, Mismatches: 84, Indels: 18
0.86 0.11 0.02
Matches are distributed among these distances:
648 4 0.01
649 621 0.96
650 25 0.04
ACGTcount: A:0.39, C:0.17, G:0.16, T:0.28
Consensus pattern (649 bp):
CAAGAGAGAATCAATTCTCACGTAAATAAGTTTTTAATTCAAAGGCCAAAACTTGTTTACAAAAT
GACAAACTTTTTAGACCAAATGATGCGACTTCCCGAGCATGGAACGTTCGATAAATTACTCGAAG
AAATGGATCGTCTTAAACACTTTAAGGAACTAGATTTAAAAAAGAACTAGTAAAAGTTTGACAAG
TTCGGAAGTTCATCCAACAACCAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAG
GCAAAAACTTGTTTACAAAATGACAAACCTATTAGACCAAACGATGTGACTTCCCCAGCATGTAA
TGTTCGAAAAATTGCACAAAGGATTGGATCGTCTTGCATACTTTAAGGAACCGAAGCTATAAAAC
AACTCATAAAAGTTCAACAAGTTCGAATGTTCATCCAAGAACCAAGAGAGAAACAATTCTCACAT
AAATAAGTTTATAATTCAAAGATCAAAACATGTTCACAAAATCAAAAAACTATTTAAACCAAATG
ATGCGATTTCCATCGCATGGAATATTTCGAAAATTACTCGAAGGAATGGATCGTCTTGAACACTT
TAAGGAACTAGATTTAAAAAACAACTAGTAAAAGTTTCAAAAGATCGGAAGCTCATCCAACAAC
Done.