Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01002690.1 Kokia drynarioides strain JFW-HI SEQ_114959, 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: 2374
ACGTcount: A:0.40, C:0.14, G:0.18, T:0.28
Found at i:403 original size:216 final size:213
Alignment explanation
Indices: 1--1917 Score: 1942
Period size: 216 Copynumber: 9.0 Consensus size: 213
** * *
1 TGTAAGGAACCGAAGTTATAAAAGAACTCGTAAAAGCGTGACAAGTTCGGAAGTTTGCCCAAGAA
1 TGTAAGGAACCGAAGTTATAAAAGAACTCGTAAAAGTTTGA-AAGTTCGGAAGTTCGTCCAAGAA
* * * *
66 CCAAGAGA-AAA-AATTCTCAAGTAAATAAGTTTTTGATTCAAAGACCGAAACTTGTTTTCAAAA
65 CCAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTC-AAGACCAAAACTTGTTTACAAAA
* * * * * * * *
129 TGACAAAC-ACTTTAGACCAAAAGCTGCTA-TTTCTCAAGAATAGAATATTTAGAAAATTGCTCG
129 TGACAAACTA-TTTAGACCAAATGATGCGATTTTC-CGAGCATGGAATGTTCA-AAAATTGCTCG
*
192 AAGGAATGGATCATCTTGAATAC
191 AAGGAATGGATCGTCTTGAATAC
* * * *
215 TGTAAGGAACCGAAGATATGAAAGAACTCGTAAAAGTTTGACTAGTTCGAAAGTTCGTCCAAGAA
1 TGTAAGGAACCGAAGTTATAAAAGAACTCGTAAAAGTTTGA-AAGTTCGGAAGTTCGTCCAAGAA
* *
280 CCAAGAGAGAAATAATTCTCACGTAAATAAGTTTTTAATTCAAGCAGCAAAACCTT-TTTACAAA
65 CCAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAG-ACCAAAA-CTTGTTTACAAA
*
344 ATGACAAACTATTTAGACCAAATGATGCGATTTTCCAAGCATGGAATGTTCGAAAAATTGCTCGA
128 ATGACAAACTATTTAGACCAAATGATGCGATTTTCCGAGCATGGAATGTTC-AAAAATTGCTCGA
*
409 AGGAATGGATCGTCTTGAATGC
192 AGGAATGGATCGTCTTGAATAC
* * * *
431 TTTATGGAACTGAAATTATAAAAGAACTCGTAAAAGTTTGACAAGTTCGGAAGTTCGTCCAAGAA
1 TGTAAGGAACCGAAGTTATAAAAGAACTCGTAAAAGTTTGA-AAGTTCGGAAGTTCGTCCAAGAA
* * * * ** *
496 CTAAAAGAGAAACAATTCTCGCGTAAATAAGTATTTAATTCAAAGACCAAAGGTTGTTCACAAAA
65 CCAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTC-AAGACCAAAACTTGTTTACAAAA
* * * *
561 TGATAAACTATTTAGACAAAATTATGCGATTTT-CGAGCATGGAATGTTCAGAAAATAGCTCGAA
129 TGACAAACTATTTAGACCAAATGATGCGATTTTCCGAGCATGGAATGTTCA-AAAATTGCTCGAA
* * *
625 GGAATGGATCATCTTGACTAT
193 GGAATGGATCGTCTTGAATAC
** * * *
646 TGTAAGGAACC-------T---AG---TCGTAAAAGTATAAAAAGTTCGGAAGTTCATCCAACAG
1 TGTAAGGAACCGAAGTTATAAAAGAACTCGTAAAAGT-TTGAAAGTTCGGAAGTTCGTCCAAGAA
*** * * *
698 CC-A-AGAGAAACAATTCTCACGTAAATAAGTTTTCGCTTTAAAGACCAAAACTTGTTTACCAGA
65 CCAAGAGAGAAACAATTCTCACGTAAATAAGTTTT-TAATTCAAGACCAAAACTTGTTTACAAAA
* * * ** * *
761 CGAAAAACTATTTAGACTAAATGATGCGATTACCCGAGAATGGAGTGTTC-AAAATTGCT-GAAA
129 TGACAAACTATTTAGACCAAATGATGCGATTTTCCGAGCATGGAATGTTCAAAAATTGCTCG-AA
824 GGAATGGAT-GTTCTTGAATAC
193 GGAATGGATCG-TCTTGAATAC
* * * *
845 T-TCAAGGAATCTG-AGTTATAAAAGAACTAGTAAAGGTTTGTAAAGTTTGGAAGTTCGTCCAAG
1 TGT-AAGGAA-CCGAAGTTATAAAAGAACTCGTAAAAGTTTG-AAAGTTCGGAAGTTCGTCCAAG
* * * * *
908 AACAAAGAGAGAGAAAAAATTCTAACGTAAATAAGTTTTTAATTTAAAGA-GAAAACTTGTTTAC
63 AAC-CA-AGAGAGAAACAATTCTCACGTAAATAAGTTTTTAA-TTCAAGACCAAAACTTGTTTAC
* * *
972 AAAATGACAAACAATTTAGA-AAAATGATGCGATTTTCCGAGCATAGAATGTT-AAGAAAGTTGC
125 AAAATGACAAACTATTTAGACCAAATGATGCGATTTTCCGAGCATGGAATGTTCAA-AAA-TTGC
* *
1035 TAGAAGGAATGTATCGTCTTGAATAC
188 TCGAAGGAATGGATCGTCTTGAATAC
* * *
1061 TGTAAGGAACCGAAGTTATAAAAGAACTCGTAAAAGTTTGATTAGTTCGAAAGTTGGTCCAAGAA
1 TGTAAGGAACCGAAGTTATAAAAGAACTCGTAAAAGTTTGA-AAGTTCGGAAGTTCGTCCAAGAA
* * *
1126 CCAAGAGAGAAATAATTCTCACGTAAATAAGTTTTTAATTTAAGCAACAAAAACTT-TTTACAAA
65 CCAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAG--ACCAAAACTTGTTTACAAA
* *
1190 ATGACAAACAATTTAGACCAAATGGTGCGATTTTCCGAGCATGGAATGTTCGAAAAATTGCTCGA
128 ATGACAAACTATTTAGACCAAATGATGCGATTTTCCGAGCATGGAATGTTC-AAAAATTGCTCGA
1255 AGGAATGGATCGTCTTGAATAC
192 AGGAATGGATCGTCTTGAATAC
* * * * *
1277 TTTATGGAACTGAAATTATAAAAGAACTCGTAAAAGTTTGATAAGTTTGGAAGTTCGTCCAAGAA
1 TGTAAGGAACCGAAGTTATAAAAGAACTCGTAAAAGTTTGA-AAGTTCGGAAGTTCGTCCAAGAA
* * * * *
1342 CCAAAAGAGAAACAATTCTCATGTAAATAAGTATTTAATTCAAAGACCAAAAGTTTTTTACAAAA
65 CCAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTC-AAGACCAAAACTTGTTTACAAAA
* *
1407 TGACAAACTATTTCGACCAAAATGATGCGA-TTTCCTGAGCATGGAATGTTCAAAAAATTGCTTG
129 TGACAAACTATTTAGACC-AAATGATGCGATTTTCC-GAGCATGGAATGTTC-AAAAATTGCTCG
*
1471 ATGGAATGGATCGTCTTGAATAC
191 AAGGAATGGATCGTCTTGAATAC
* * * * *
1494 TGCAAGGAA-CGGAGTTATAAAAGAACTCGTAAAAGTTTGAAATGTTCTGAAGTTCGTCCAATAG
1 TGTAAGGAACCGAAGTTATAAAAGAACTCGTAAAAGTTTGAAA-GTTCGGAAGTTCGTCCAAGAA
* * * ** * * *
1558 CC-A-AGA-AAA-AATCCTCAGGAAAAT-A-TTTCTTGTTTTAATGATCAAAACTCGTTTACAAA
65 CCAAGAGAGAAACAATTCTCACGTAAATAAGTTT-TTAATTCAA-GACCAAAACTTGTTTACAAA
* * * * * * * *
1617 ATTA-AGACCTATTTAAACTAAATGATGCGATTTCCCGAGAATGGAATGTTCAAAAATTCCTCAA
128 ATGACA-AACTATTTAGACCAAATGATGCGATTTTCCGAGCATGGAATGTTCAAAAATTGCTCGA
1681 AGGAATGGATCGTCTTGAATAC
192 AGGAATGGATCGTCTTGAATAC
* * * * *
1703 TTTAAGGAACCGGAGTTATAAATGAACTCGTAAAAGTTTGAAAAGTTTGGAAGTTCATCCAAGAA
1 TGTAAGGAACCGAAGTTATAAAAGAACTCGTAAAAGTTTG-AAAGTTCGGAAGTTCGTCCAAGAA
* * * *
1768 CAAAGAGAGAGAAACAATTCTCACGTAAATAAGTTTTAAATTTAAAGACGAAAACTTGTTTACAA
65 C-CA-AGAGAGAAACAATTCTCACGTAAATAAGTTTTTAA-TTCAAGACCAAAACTTGTTTACAA
* * * * *
1833 AATG---AACAATTTAGA-AAAATGATGCGATTTTTCGAGCATAGAATGTT-AAGAAAGTTGCTA
127 AATGACAAACTATTTAGACCAAATGATGCGATTTTCCGAGCATGGAATGTTCAA-AAA-TTGCTC
* *
1893 GAAGGAATGTATCGTCTTCAATAC
190 GAAGGAATGGATCGTCTTGAATAC
1917 T
1 T
1918 ACTCGTAAAA
Statistics
Matches: 1421, Mismatches: 211, Indels: 142
0.80 0.12 0.08
Matches are distributed among these distances:
198 2 0.00
199 34 0.02
200 74 0.05
201 17 0.01
202 31 0.02
203 2 0.00
205 2 0.00
206 1 0.00
208 1 0.00
209 40 0.03
210 76 0.05
211 41 0.03
212 43 0.03
213 39 0.03
214 166 0.12
215 136 0.10
216 601 0.42
217 106 0.07
218 9 0.01
ACGTcount: A:0.40, C:0.14, G:0.18, T:0.28
Consensus pattern (213 bp):
TGTAAGGAACCGAAGTTATAAAAGAACTCGTAAAAGTTTGAAAGTTCGGAAGTTCGTCCAAGAAC
CAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAGACCAAAACTTGTTTACAAAATG
ACAAACTATTTAGACCAAATGATGCGATTTTCCGAGCATGGAATGTTCAAAAATTGCTCGAAGGA
ATGGATCGTCTTGAATAC
Found at i:2345 original size:216 final size:216
Alignment explanation
Indices: 1971--2371 Score: 515
Period size: 216 Copynumber: 1.9 Consensus size: 216
1961 AGTGAAACAA
* * * * *
1971 TTCTCACATAAATAAGTTTTTGATTCAAAGACCAAAACTTGTTTTCAAAATGACAAACTCTTTAG
1 TTCTCACATAAATAAGTTATTAATTCAAAGAACAAAACTTGTTTACAAAATGACAAACTATTTAG
* * * *
2036 ACCAAATGCTGCTATTTCTCAAGAATAGAATGTTAAGAAAGTTGCTAGAAGGAATGTATCGTCTT
66 ACCAAATGATGCGATTTCTCAAGAATAGAATGTTAAGAAAATTGCTAGAAGGAATGGATCGTCTT
* * * **
2101 GAATACTGTAAGGAACCGAAGTTATAAAAGAACTTGTAAAAGTTTGACT-AGTTCGAAAGTTGGT
131 GAATACTGTAAGAAACCAAAATTATAAAAGAACTCCTAAAAGTTTGA-TAAGTTCGAAAGTTGGT
2165 CCTTGGACCAAGAGAGAAATAT
195 CCTTGGACCAAGAGAGAAATAT
*
2187 TTCTCACGTAAATAAGTTATTAATTC-AAGCAACAAAACCTT-TTTACAAAATGACAAACTATTT
1 TTCTCACATAAATAAGTTATTAATTCAAAG-AACAAAA-CTTGTTTACAAAATGACAAACTATTT
* * * * *
2250 AGACCAAATGATGCGATTT-TCCGAGCATGGAATGTT-CGAATAATTGCTCGAAGGAATGGATCG
64 AGACCAAATGATGCGATTTCT-CAAGAATAGAATGTTAAGAA-AATTGCTAGAAGGAATGGATCG
* * *
2313 TCTTGAATACTTTACGAAACTAAAATTATAAAAGAACTCCTAAAAGTTTGATAAGTTCG
127 TCTTGAATACTGTAAGAAACCAAAATTATAAAAGAACTCCTAAAAGTTTGATAAGTTCG
2372 GAA
Statistics
Matches: 157, Mismatches: 23, Indels: 10
0.83 0.12 0.05
Matches are distributed among these distances:
215 8 0.05
216 146 0.93
217 3 0.02
ACGTcount: A:0.38, C:0.15, G:0.17, T:0.30
Consensus pattern (216 bp):
TTCTCACATAAATAAGTTATTAATTCAAAGAACAAAACTTGTTTACAAAATGACAAACTATTTAG
ACCAAATGATGCGATTTCTCAAGAATAGAATGTTAAGAAAATTGCTAGAAGGAATGGATCGTCTT
GAATACTGTAAGAAACCAAAATTATAAAAGAACTCCTAAAAGTTTGATAAGTTCGAAAGTTGGTC
CTTGGACCAAGAGAGAAATAT
Done.