Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01010775.1 Kokia drynarioides strain JFW-HI SEQ_125738, 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: 1698
ACGTcount: A:0.41, C:0.15, G:0.16, T:0.28
Found at i:443 original size:216 final size:216
Alignment explanation
Indices: 1--1100 Score: 1350
Period size: 216 Copynumber: 5.1 Consensus size: 216
* *
1 AAGAACCAAGAGAGACACAATTCTCACGTAAATAAGTTTTTAATTCAAAGATCAAAACTTGTCTA
1 AAGAACCAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGATCAAAACTTGTTTA
* * ** ** * * *
66 CAAAATGAAAAATTATTTAAACCAAATGATGCGATTTTTCGAGAATGGATTGTTCAAAAACTGT-
66 CAAAATGAAAAACTATTTAGACCAAATGATGCGATTTCCCTCGCATGGAATGTTCAAAAAAT-TA
* * *
130 -TAGAAGGAATGGATCATCTTGAATACTTTAATGAACTGAAGCTATAAAAGAACTCGTAAAAGTT
130 CTCGAAGGAATGGATCGTCTTGAACACTTTAATGAACTGAAGCTATAAAAGAACTCGTAAAAGTT
* *
194 TCTAAATTTCAGAATTTCGTCC
195 TGTCAATTTCAGAATTTCGTCC
* *
216 AAAAACCAAGAGAGAAACAATTCTCACGGAAATAAGTTTTTAATTCAAAGATCAAAACTTGTTTA
1 AAGAACCAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGATCAAAACTTGTTTA
* * * * ***
281 CAAAATAAAAAACTATTTAGACTAAATGATACGATTTCCCTCGTATGGAATGTTCGGTAAATTAC
66 CAAAATGAAAAACTATTTAGACCAAATGATGCGATTTCCCTCGCATGGAATGTTCAAAAAATTAC
*
346 TCGAAGGAATGGATCGTCTTGAACACTTTAATGAACTGAAGCTATAAAAGAACTCATAAAAGTTT
131 TCGAAGGAATGGATCGTCTTGAACACTTTAATGAACTGAAGCTATAAAAGAACTCGTAAAAGTTT
* *
411 GTCAATTTTAGAATTTCATCC
196 GTCAATTTCAGAATTTCGTCC
* * *
432 AAGAGCCAAGAGGGAAACAATTATCACGTAAATAAGTTTTTAATTCAAAGATCAAAACTTGTTTA
1 AAGAACCAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGATCAAAACTTGTTTA
* * * *
497 CAAAATGGAAAACTGTTTAGACCAAATGATACGATTTCCCTCGCATGGAATGTTCCAAAAATTAC
66 CAAAATGAAAAACTATTTAGACCAAATGATGCGATTTCCCTCGCATGGAATGTTCAAAAAATTAC
* * ** *
562 -CGGAAGGAATGGATCGTCTTGAGCACTTTAA-GAAAC-CAGATTTAAAAAAGAACTCGTAAAAG
131 TC-GAAGGAATGGATCGTCTTGAACACTTTAATG-AACTGA-AGCTATAAAAGAACTCGTAAAAG
* * * * *
624 TTTGACAAGTTCGGAAGTTCGTAC
193 TTTGTCAATTTCAGAATTTCGTCC
* * * ** *
648 AACAACCAAGAGAGAAACAATTCTCACGTCAACAAGTTTTTAATTCAAAGGCCAAAACATGTTTA
1 AAGAACCAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGATCAAAACTTGTTTA
** * * * ** * *
713 CAAAATGACGAACTTTTTAGATCAAATGATGCGAGTTCCCAAGCATGTAATGTTCAAAAAATTGC
66 CAAAATGAAAAACTATTTAGACCAAATGATGCGATTTCCCTCGCATGGAATGTTCAAAAAATTAC
* * * * * * * * * *
778 TTGAAGGATTGGATCGTCTTGAATACTTTAAGGAACCGAAGTTATAAAAGAAATAGTAACAGTTC
131 TCGAAGGAATGGATCGTCTTGAACACTTTAATGAACTGAAGCTATAAAAGAACTCGTAAAAGTTT
* * *
843 GACAATTTCAAAAGTTCGTCC
196 GTCAATTTCAGAATTTCGTCC
* * * *
864 AATAACCAAGAGAGACACAATTTTCACGTAAATAAGCTTTTAATTCAAAGATCAAAACTTGTTTA
1 AAGAACCAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGATCAAAACTTGTTTA
*
929 CAAAATGAAAAACTATTTAGACCAAATGATGCGATTTCCCTCAG-ATGGAATGTTCACAAAATTA
66 CAAAATGAAAAACTATTTAGACCAAATGATGCGATTTCCCTC-GCATGGAATGTTCAAAAAATTA
* *
993 CTCGAAGGAATGGATCGTCTTGAACACTTGAATGAACAT-AAGCTATGAAAGAACTCGTAAAAGT
130 CTCGAAGGAATGGATCGTCTTGAACACTTTAATGAAC-TGAAGCTATAAAAGAACTCGTAAAAGT
*
1057 TTGTCAATTTTAGAATTTCGTCC
194 TTGTCAATTTCAGAATTTCGTCC
* *
1080 AGGAACCAAGGGAGAAACAAT
1 AAGAACCAAGAGAGAAACAAT
1101 CGAAGTTATA
Statistics
Matches: 747, Mismatches: 128, Indels: 19
0.84 0.14 0.02
Matches are distributed among these distances:
214 1 0.00
215 111 0.15
216 632 0.85
217 3 0.00
ACGTcount: A:0.41, C:0.15, G:0.16, T:0.28
Consensus pattern (216 bp):
AAGAACCAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGATCAAAACTTGTTTA
CAAAATGAAAAACTATTTAGACCAAATGATGCGATTTCCCTCGCATGGAATGTTCAAAAAATTAC
TCGAAGGAATGGATCGTCTTGAACACTTTAATGAACTGAAGCTATAAAAGAACTCGTAAAAGTTT
GTCAATTTCAGAATTTCGTCC
Found at i:1333 original size:287 final size:286
Alignment explanation
Indices: 814--1387 Score: 830
Period size: 287 Copynumber: 2.0 Consensus size: 286
804 TTTAAGGAAC
* * *
814 CGAAGTTATAAAAGAAATAGTAACAGTTCGACAATTTCAAAAGTTCGTCCAATAACCAAGAGAGA
1 CGAAGTTATAAAAGAAACAGTAACAGTTCGACAAGTTCAAAAGTTCGTCCAAGAACCAAGAGAGA
*
879 CACAATTTTCACGTAAATAAGCTTTTAATTCAAAGATCAAAACTTGTTTACAAAATGAAAAACTA
66 CACAATTCTCACGTAAATAAGCTTTTAATTCAAAGATCAAAACTTGTTTACAAAATGAAAAACTA
* * *
944 TTTAGACCAAATGATGCGATTTCCCTCAGATGGAATGTTCACAAAATTACTCGAAGGAATGGATC
131 TTTAGACCAAATGATACGATTT-CCTCAGATGGAATGTTCACAAAACTACTAGAAGGAATGGATC
* * *
1009 GTCTTGAACACTTGAATGAACATAAGCTATGAAAGAACTCGTAAAAGTTTGTCAATTTTAGAATT
195 GTCTTGAACACTTGAATGAACATAAGCTATAAAAGAACCCGTAAAAGTTTGTCAATTTCAGAATT
* *
1074 TCGTCCAGGAACCAAGGGAGAAACAAT
260 TCGTCCAAGAACCAAGAGAGAAACAAT
* * *
1101 CGAAGTTATAAAAGAACCAGTAACAGTTTGACAAGTTCGAAAGTTCGTCCAAGAACCAAGAGAGA
1 CGAAGTTATAAAAGAAACAGTAACAGTTCGACAAGTTCAAAAGTTCGTCCAAGAACCAAGAGAGA
* *
1166 CACAATTCTCACGTAAATAAGTTTTTAATTCAAAGATCAAAACTTGTTTAGAAAATGAAAAACTA
66 CACAATTCTCACGTAAATAAGCTTTTAATTCAAAGATCAAAACTTGTTTACAAAATGAAAAACTA
* * * *
1231 TTTAGACCAAATGATACGATTT-GTCGAGAATGGATTGTTCGA-AAAGCTGCTAGAAGGAATGGA
131 TTTAGACCAAATGATACGATTTCCTC-AG-ATGGAATGTTC-ACAAAACTACTAGAAGGAATGGA
* * * * * *
1294 TTGTCTTGAATACTTTAATTAAC-TGATGTTATAAAAGAACCCGTAAAAGTTTGTCAATTTCAGA
193 TCGTCTTGAACACTTGAATGAACAT-AAGCTATAAAAGAACCCGTAAAAGTTTGTCAATTTCAGA
*
1358 ATTTCGTCTAAGAACCAAGAGAGAAACAAT
257 ATTTCGTCCAAGAACCAAGAGAGAAACAAT
1388 TTTCATGTAA
Statistics
Matches: 255, Mismatches: 28, Indels: 8
0.88 0.10 0.03
Matches are distributed among these distances:
285 2 0.01
286 3 0.01
287 249 0.98
288 1 0.00
ACGTcount: A:0.41, C:0.15, G:0.17, T:0.27
Consensus pattern (286 bp):
CGAAGTTATAAAAGAAACAGTAACAGTTCGACAAGTTCAAAAGTTCGTCCAAGAACCAAGAGAGA
CACAATTCTCACGTAAATAAGCTTTTAATTCAAAGATCAAAACTTGTTTACAAAATGAAAAACTA
TTTAGACCAAATGATACGATTTCCTCAGATGGAATGTTCACAAAACTACTAGAAGGAATGGATCG
TCTTGAACACTTGAATGAACATAAGCTATAAAAGAACCCGTAAAAGTTTGTCAATTTCAGAATTT
CGTCCAAGAACCAAGAGAGAAACAAT
Found at i:1505 original size:216 final size:216
Alignment explanation
Indices: 1105--1693 Score: 658
Period size: 216 Copynumber: 2.7 Consensus size: 216
1095 AACAATCGAA
* * *
1105 GTTATAAAAGAACCAGTAACAGTTTGACAAGTTC-GAAAGTTCGTCCAAGAACCAAGAGAGACAC
1 GTTATAAAAGAACCCGTAAAAGTTTGACAAGTTCAGAAAGTTCGTCCAAGAACCAAGAGAGAAAC
*
1169 AATTCTCACGTAAATAAGTTTTTAATTCAAAGATCAAAACTTGTTTA-GAAAATGAAAAACTATT
66 AATTTTCA-GTAAATAAGTTTTTAATTCAAAGAT-AAAACTTGTTTACG-AAATGAAAAACTATT
* ** * * * *
1233 TAGACCAAATGATACGATTTGTCGAGAATGGATTGTTCGAAAAGCTGCTAGAAGGAATGGATTGT
128 TAGACCAAATGATGCGATTTCCCGAGAATGGAATGTTCGAAAAGCTACCAGAAGGAATGGATCGT
* * * ** *
1298 CTTGAATACTTTAATTAA-CTGAT
193 CTTGAACAATCTAAGGAACCGGAT
* * * *
1321 GTTATAAAAGAACCCGTAAAAGTTTGTCAATTTCAG-AATTTCGTCTAAGAACCAAGAGAGAAAC
1 GTTATAAAAGAACCCGTAAAAGTTTGACAAGTTCAGAAAGTTCGTCCAAGAACCAAGAGAGAAAC
* *
1385 AATTTTCATGTAAATATGTTTTTAATTCGAAGATAATAACTTGTTTACGAAATGAAAAACTATTT
66 AATTTTCA-GTAAATAAGTTTTTAATTCAAAGATAA-AACTTGTTTACGAAATGAAAAACTATTT
** * * *
1450 AGACCAAATGATGCGATTTCCCTTGCATGGAATGTTTCGAAAA-TTACCCGAAGGAATGGATCGT
129 AGACCAAATGATGCGATTTCCCGAGAATGGAATG-TTCGAAAAGCTACCAGAAGGAATGGATCGT
1514 CTTGAACAATCTAAGGAACCGGAT
193 CTTGAACAATCTAAGGAACCGGAT
* * * * * *
1538 -ATAGAAAAGAACTCGTAAAATTTTGACAAGTT-AGAAAGTTCGTCCAACAA-CAGAGAAAGAAA
1 GTTATAAAAGAACCCGTAAAAGTTTGACAAGTTCAGAAAGTTCGTCCAAGAACCA-AGAGAGAAA
** *
1600 CAATTCTCTCA-TAAATAAGTTTTTAATTCAAAGGCCAAAACTTGTTTAC-AAAGTGAAAAACTT
65 CAATT-T-TCAGTAAATAAGTTTTTAATTCAAA-GATAAAACTTGTTTACGAAA-TGAAAAACTA
* *
1663 TTTAGACCAAATGATGCGACTTCCCAAGAAT
126 TTTAGACCAAATGATGCGATTTCCCGAGAAT
1694 ATAAT
Statistics
Matches: 314, Mismatches: 48, Indels: 22
0.82 0.12 0.06
Matches are distributed among these distances:
215 9 0.03
216 284 0.90
217 18 0.06
218 3 0.01
ACGTcount: A:0.40, C:0.15, G:0.17, T:0.29
Consensus pattern (216 bp):
GTTATAAAAGAACCCGTAAAAGTTTGACAAGTTCAGAAAGTTCGTCCAAGAACCAAGAGAGAAAC
AATTTTCAGTAAATAAGTTTTTAATTCAAAGATAAAACTTGTTTACGAAATGAAAAACTATTTAG
ACCAAATGATGCGATTTCCCGAGAATGGAATGTTCGAAAAGCTACCAGAAGGAATGGATCGTCTT
GAACAATCTAAGGAACCGGAT
Found at i:1554 original size:503 final size:502
Alignment explanation
Indices: 607--1562 Score: 1276
Period size: 503 Copynumber: 1.9 Consensus size: 502
597 CCAGATTTAA
*
607 AAAAGAACTCGTAAAAGTTTGACAAGTTCGGAAGTTCGTACAACAACCAAGAGAGAAACAATTCT
1 AAAAGAACTCGTAAAAGTTTGACAAGTTCGAAAGTTCGTACAACAACCAAGAGAGAAACAATTCT
* * ** * *
672 CACGTCAACAAGTTTTTAATTCAAAGGCCAAAACATGTTTACAAAATGACGAACTTTTTAGATCA
66 CACGTAAACAAGTTTTTAATTCAAAGACCAAAACATGTTTACAAAATGAAAAACTATTTAGACCA
* * * * * *
737 AATGATGCGAGTTCCCAAGCATGTAATGTTCAAAAAATTGCTTGAAGGATTGGATCGTCTTGAAT
131 AATGATACGAGTTCCCAAGAATGGAATGTTCAAAAAACTGCTAGAAGGAATGGATCGTCTTGAAT
* * *
802 ACTTTAAGGAACCGAAGTTATAAAAGAAATAGTAACAGTTCGACAATTTCAAAAGTTCGTCCAAT
196 ACTTTAAGGAACCGAAGTTATAAAAGAAACAGTAAAAGTTCGACAATTTCAAAAGTTCGTCCAAG
*
867 AACCAAGAGAGACACAATTTTCACGTAAATAAGCTTTTAATTCAAAGATCAAAACTTGTTTACAA
261 AACCAAGAGAGAAACAATTTTCACGTAAATAAGCTTTTAATTCAAAGATCAAAACTTGTTTACAA
*
932 AATGAAAAACTATTTAGACCAAATGATGCGATTTCCCTCAGATGGAATGTTCACAAAATTACTCG
326 AATGAAAAACTATTTAGACCAAATGATGCGATTTCCCTCAGATGGAATGTTCACAAAATTACCCG
* * *
997 AAGGAATGGATCGTCTTGAACACTTGAATGAACATAAGCTATGAAAGAACTCGTAAAAGTTTGTC
391 AAGGAATGGATCGTCTTGAACAATTGAAGGAACA-AAGATATGAAAGAACTCGTAAAAGTTTGTC
1062 AATTTTAGAATTTCGTCCAGGAACCAAGGGAGAAACAATCGAAGTTAT
455 AATTTTAGAATTTCGTCCAGGAACCAAGGGAGAAACAATCGAAGTTAT
* * * *
1110 AAAAGAAC-CAGTAACAGTTTGACAAGTTCGAAAGTTCGTCCAAGAACCAAGAGAGACACAATTC
1 AAAAGAACTC-GTAAAAGTTTGACAAGTTCGAAAGTTCGTACAACAACCAAGAGAGAAACAATTC
* * * *
1174 TCACGTAAATAAGTTTTTAATTCAAAGATCAAAACTTGTTTAGAAAATGAAAAACTATTTAGACC
65 TCACGTAAACAAGTTTTTAATTCAAAGACCAAAACATGTTTACAAAATGAAAAACTATTTAGACC
* ** * * * * *
1239 AAATGATACGATTTGTCGAGAATGGATTGTTCGAAAAGCTGCTAGAAGGAATGGATTGTCTTGAA
130 AAATGATACGAGTTCCCAAGAATGGAATGTTCAAAAAACTGCTAGAAGGAATGGATCGTCTTGAA
** * * * * * * * * *
1304 TACTTTAATTAACTGATGTTATAAAAGAACCCGTAAAAGTTTGTCAATTTCAGAATTTCGTCTAA
195 TACTTTAAGGAACCGAAGTTATAAAAGAAACAGTAAAAGTTCGACAATTTCAAAAGTTCGTCCAA
* * * *
1369 GAACCAAGAGAGAAACAATTTTCATGTAAATATGTTTTTAATTCGAAGAT-AATAACTTGTTTAC
260 GAACCAAGAGAGAAACAATTTTCACGTAAATAAGCTTTTAATTCAAAGATCAA-AACTTGTTTAC
* * *
1433 GAAATGAAAAACTATTTAGACCAAATGATGCGATTTCCCT-TGCATGGAATGTTTC-GAAAATTA
324 AAAATGAAAAACTATTTAGACCAAATGATGCGATTTCCCTCAG-ATGGAATG-TTCACAAAATTA
** *
1496 CCCGAAGGAATGGATCGTCTTGAACAATCT-AAGGAAC-CGGATATAGAAAAGAACTCGTAAAAT
387 CCCGAAGGAATGGATCGTCTTGAACAAT-TGAAGGAACAAAGATAT-G-AAAGAACTCGTAAAAG
1559 TTTG
449 TTTG
1563 ACAAGTTAGA
Statistics
Matches: 388, Mismatches: 58, Indels: 14
0.84 0.13 0.03
Matches are distributed among these distances:
501 4 0.01
502 5 0.01
503 375 0.97
504 4 0.01
ACGTcount: A:0.40, C:0.15, G:0.17, T:0.28
Consensus pattern (502 bp):
AAAAGAACTCGTAAAAGTTTGACAAGTTCGAAAGTTCGTACAACAACCAAGAGAGAAACAATTCT
CACGTAAACAAGTTTTTAATTCAAAGACCAAAACATGTTTACAAAATGAAAAACTATTTAGACCA
AATGATACGAGTTCCCAAGAATGGAATGTTCAAAAAACTGCTAGAAGGAATGGATCGTCTTGAAT
ACTTTAAGGAACCGAAGTTATAAAAGAAACAGTAAAAGTTCGACAATTTCAAAAGTTCGTCCAAG
AACCAAGAGAGAAACAATTTTCACGTAAATAAGCTTTTAATTCAAAGATCAAAACTTGTTTACAA
AATGAAAAACTATTTAGACCAAATGATGCGATTTCCCTCAGATGGAATGTTCACAAAATTACCCG
AAGGAATGGATCGTCTTGAACAATTGAAGGAACAAAGATATGAAAGAACTCGTAAAAGTTTGTCA
ATTTTAGAATTTCGTCCAGGAACCAAGGGAGAAACAATCGAAGTTAT
Done.