Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013072.1 Kokia drynarioides strain JFW-HI SEQ_128090, 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: 2103
ACGTcount: A:0.40, C:0.14, G:0.17, T:0.27
Warning! 50 characters in sequence are not A, C, G, or T
Found at i:97 original size:37 final size:37
Alignment explanation
Indices: 47--121 Score: 132
Period size: 37 Copynumber: 2.0 Consensus size: 37
37 AATGACAAAC
*
47 TATTTAGACCAAATTATGCGATTTCCCGAGCATGGAA
1 TATTTAGACCAAATTATGCAATTTCCCGAGCATGGAA
*
84 TATTTAGACCAAATTATGCAATTTCTCGAGCATGGAA
1 TATTTAGACCAAATTATGCAATTTCCCGAGCATGGAA
121 T
1 T
122 GTTCGGAAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
37 36 1.00
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.32
Consensus pattern (37 bp):
TATTTAGACCAAATTATGCAATTTCCCGAGCATGGAA
Found at i:458 original size:216 final size:216
Alignment explanation
Indices: 84--1203 Score: 1382
Period size: 216 Copynumber: 5.2 Consensus size: 216
74 GAGCATGGAA
* * * *
84 TATTTAGACCAAATTATGCAATTTCTCGAGCATGGAATGTTCGGAAAATTGCTC-GAAGCAATGG
1 TATTTAGACCAAATTATGCGATTTCCCGAGCATGGAATGTTCGAAAAATTGCTCAG-AGGAATGG
* * *
148 ATCATCTTGAATACTTGAAGGACCCGAAGTTATAAAAG-AACTAGTAAAAGTTTGACAAATTTGA
65 ATCATCTTGAATACTTGAAGGAACCGAAGTTA-AAAAGTAACTAGTAAAAGTTTGACAAGTTCGA
212 AAGTTCGTACAAAGACAAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGACAAA
129 AAGTTCGTACAAAGACAAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGACAAA
277 AACTTGTTTACAAAATGACAAAC
194 AACTTGTTTACAAAATGACAAAC
*
300 TATTTAGACCAAATTATGCGATTTCCCGAGCATGGAATGTTCGAAAAATTGCTCAGAGGAATAGA
1 TATTTAGACCAAATTATGCGATTTCCCGAGCATGGAATGTTCGAAAAATTGCTCAGAGGAATGGA
** * * * * * * *
365 TTTTGTTGAATACTTCAGGGAATCAAAGTTAAAAAGTAACTCGTAAAAGTTTAACAAGTTCGAAA
66 TCATCTTGAATACTTGAAGGAACCGAAGTTAAAAAGTAACTAGTAAAAGTTTGACAAGTTCGAAA
* * *
430 GTTCGTACAAAGATAAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTATTTCAAAGACCAAAA
131 GTTCGTACAAAGACAAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGACAAAAA
*
495 CTTGTTTGCAAAATGACAAAC
196 CTTGTTTACAAAATGACAAAC
* * * * * * * *
516 TAATTAGGCCAAATGATTCGATCTCCCGAGCATGAAATGTAT-GAAAAATTGTTC-GAAAGAATG
1 TATTTAGACCAAATTATGCGATTTCCCGAGCATGGAATGT-TCGAAAAATTGCTCAG-AGGAATG
* * *
579 GATCATCTTGAATTCTTTAAGGATCCGAAGTTATAAAAG-AACTAGTAAAAGTTTGACAAGTTCG
64 GATCATCTTGAATACTTGAAGGAACCGAAGTTA-AAAAGTAACTAGTAAAAGTTTGACAAGTTCG
* * * *
643 AAAGTTCGT-CCAAGAACAAAGAGAGAAACAATTCTCTCGTAAGTAAGTTTTTAATTCAAAGACG
128 AAAGTTCGTACAAAG-ACAAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGACA
**
707 AAAACTTGGATACAAAATGACAAAC
192 AAAACTTGTTTACAAAATGACAAAC
** * * * * *
732 TATTTAGACC-AATTGAAACGATTTCCCAAGGATGGATTATTC-AGAAAATTGCTCAAAGGAATG
1 TATTTAGACCAAATT-ATGCGATTTCCCGAGCATGGAATGTTCGA-AAAATTGCTCAGAGGAATG
* * * * * * * * *
795 GATCTTGTTGAATACTTTAGGGAACTGAAGTTAAAAAATAACTCGTAAAAGATTCACAAGTTCGA
64 GATCATCTTGAATACTTGAAGGAACCGAAGTTAAAAAGTAACTAGTAAAAGTTTGACAAGTTCGA
* *
860 AAGTTCGT-CCAAGAACAAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGTGC-
129 AAGTTCGTACAAAG-ACAAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAG-ACA
* *
923 AAAACTTGTTTGCCAAAATGACAAAT
192 AAAACTTGTTT-ACAAAATGACAAAC
* * * * * * * *
949 TATTTAGACCAAATAATACGATTTACCGAGCACGGAATGTTCGGAAATTTGCATGA-AGCAATGG
1 TATTTAGACCAAATTATGCGATTTCCCGAGCATGGAATGTTCGAAAAATTGC-TCAGAGGAATGG
* * * *
1013 ATCGTCTTGAATACTTGAAGGAACCCAAAGTTATAAA-TGAACTAGTAAAAGTTTGACAAGTTTG
65 ATCATCTTGAATACTTGAAGGAA-CCGAAGTTAAAAAGT-AACTAGTAAAAGTTTGACAAGTTCG
*
1077 AAAGTTCGTACAGAGACAAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGACAA
128 AAAGTTCGTACAAAGACAAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGACAA
1142 AAACTTGTTTACAAAATGACAAAC
193 AAACTTGTTTACAAAATGACAAAC
*
1166 TATTTAGACCAAATTATGCGATATCCCGAGCATGGAAT
1 TATTTAGACCAAATTATGCGATTTCCCGAGCATGGAAT
1204 ATTTAGACCA
Statistics
Matches: 770, Mismatches: 114, Indels: 39
0.83 0.12 0.04
Matches are distributed among these distances:
215 19 0.02
216 516 0.67
217 130 0.17
218 102 0.13
219 3 0.00
ACGTcount: A:0.41, C:0.14, G:0.17, T:0.27
Consensus pattern (216 bp):
TATTTAGACCAAATTATGCGATTTCCCGAGCATGGAATGTTCGAAAAATTGCTCAGAGGAATGGA
TCATCTTGAATACTTGAAGGAACCGAAGTTAAAAAGTAACTAGTAAAAGTTTGACAAGTTCGAAA
GTTCGTACAAAGACAAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGACAAAAA
CTTGTTTACAAAATGACAAAC
Found at i:919 original size:432 final size:433
Alignment explanation
Indices: 110--1206 Score: 1584
Period size: 432 Copynumber: 2.5 Consensus size: 433
100 TGCAATTTCT
*
110 CGAGCATGGAATGTTCGGAAAATTGCTCGAAGCAATGGATCATCTTGAATACTTGAAGGACCCGA
1 CGAGCATGGAATGTTCGGAAAATTGATCGAAGCAATGGATCATCTTGAATACTTGAAGGACCCGA
*
175 AGTTATAAAAGAACTAGTAAAAGTTTGACAAATTTGAAAGTTCGTACAA-AGACAAAGAGAGAAA
66 AGTTATAAAAGAACTAGTAAAAGTTTGACAAGTTTGAAAGTTCGTACAAGAGACAAAGAGAGAAA
239 CAATTCTCACGTAAATAAGTTTTTAATTCAAAGACAAAAACTTGTTTACAAAATGACAAACTATT
131 CAATTCTCACGTAAATAAGTTTTTAATTCAAAGACAAAAACTTGTTTACAAAATGACAAACTATT
** * * * *
304 TAGACCAAATTATGCGATTTCCCGAGCATGGAATGTTCGAAAAATTGCTCAGAGGAATAGATTTT
196 TAGACC-AATTAAACGATTTCCCAAGCATGGAATATTCGAAAAATTGCTCAAAGGAATAGATCTT
* *
369 GTTGAATACTTCAGGGAATCAAAGTTAAAAAGTAACTCGTAAAAGTTTAACAAGTTCGAAAGTTC
260 GTTGAATACTTCAGGGAATCAAAGTTAAAAAATAACTCGTAAAAGATTAACAAGTTCGAAAGTTC
* *
434 GTACAAAGATAAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTATTTCAAAGACCAAAACTTG
325 GTACAAAGACAAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGACCAAAACTTG
* * * *
499 TTTG-CAAAATGACAAACTAATTAGGCCAAATGATTCGATCTCC
390 TTTGCCAAAATGACAAACTAATTAGACCAAATAATACGATCTAC
* * * * * *
542 CGAGCATGAAATGTAT-GAAAAATTGTTCGAAAG-AATGGATCATCTTGAATTCTTTAAGGATCC
1 CGAGCATGGAATGT-TCGGAAAATTGATCG-AAGCAATGGATCATCTTGAATACTTGAAGGACCC
* *
605 GAAGTTATAAAAGAACTAGTAAAAGTTTGACAAGTTCGAAAGTTCGTCCAAGA-ACAAAGAGAGA
64 GAAGTTATAAAAGAACTAGTAAAAGTTTGACAAGTTTGAAAGTTCGTACAAGAGACAAAGAGAGA
* * * **
669 AACAATTCTCTCGTAAGTAAGTTTTTAATTCAAAGACGAAAACTTGGATACAAAATGACAAACTA
129 AACAATTCTCACGTAAATAAGTTTTTAATTCAAAGACAAAAACTTGTTTACAAAATGACAAACTA
* * *
734 TTTAGACCAATTGAAACGATTTCCCAAGGATGGATTATTC-AGAAAATTGCTCAAAGGAATGGAT
194 TTTAGACCAATT-AAACGATTTCCCAAGCATGGAATATTCGA-AAAATTGCTCAAAGGAATAGAT
* * *
798 CTTGTTGAATACTTTAGGGAA-CTGAAGTTAAAAAATAACTCGTAAAAGATTCACAAGTTCGAAA
257 CTTGTTGAATACTTCAGGGAATC-AAAGTTAAAAAATAACTCGTAAAAGATTAACAAGTTCGAAA
* **
862 GTTCGT-CCAAGAACAAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGTGCAAA
321 GTTCGTACAAAG-ACAAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGACCAAA
* * *
926 ACTTGTTTGCCAAAATGACAAATTATTTAGACCAAATAATACGATTTAC
385 ACTTGTTTGCCAAAATGACAAACTAATTAGACCAAATAATACGATCTAC
* * *
975 CGAGCACGGAATGTTCGGAAATTTGCAT-GAAGCAATGGATCGTCTTGAATACTTGAAGGAACCC
1 CGAGCATGGAATGTTCGGAAAATTG-ATCGAAGCAATGGATCATCTTGAATACTTGAAGG-ACCC
* *
1039 AAAGTTATAAATGAACTAGTAAAAGTTTGACAAGTTTGAAAGTTCGTAC-AGAGACAAAGAGAGA
64 GAAGTTATAAAAGAACTAGTAAAAGTTTGACAAGTTTGAAAGTTCGTACAAGAGACAAAGAGAGA
1103 AACAATTCTCACGTAAATAAGTTTTTAATTCAAAGACAAAAACTTGTTTACAAAATGACAAACTA
129 AACAATTCTCACGTAAATAAGTTTTTAATTCAAAGACAAAAACTTGTTTACAAAATGACAAACTA
** * *
1168 TTTAGACCAAATTATGCGATATCCCGAGCATGGAATATT
194 TTTAGACC-AATTAAACGATTTCCCAAGCATGGAATATT
1207 TAGACCAAAT
Statistics
Matches: 587, Mismatches: 64, Indels: 26
0.87 0.09 0.04
Matches are distributed among these distances:
431 10 0.02
432 342 0.58
433 83 0.14
434 148 0.25
435 4 0.01
ACGTcount: A:0.41, C:0.14, G:0.18, T:0.27
Consensus pattern (433 bp):
CGAGCATGGAATGTTCGGAAAATTGATCGAAGCAATGGATCATCTTGAATACTTGAAGGACCCGA
AGTTATAAAAGAACTAGTAAAAGTTTGACAAGTTTGAAAGTTCGTACAAGAGACAAAGAGAGAAA
CAATTCTCACGTAAATAAGTTTTTAATTCAAAGACAAAAACTTGTTTACAAAATGACAAACTATT
TAGACCAATTAAACGATTTCCCAAGCATGGAATATTCGAAAAATTGCTCAAAGGAATAGATCTTG
TTGAATACTTCAGGGAATCAAAGTTAAAAAATAACTCGTAAAAGATTAACAAGTTCGAAAGTTCG
TACAAAGACAAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGACCAAAACTTGT
TTGCCAAAATGACAAACTAATTAGACCAAATAATACGATCTAC
Found at i:1216 original size:37 final size:37
Alignment explanation
Indices: 1166--1258 Score: 186
Period size: 37 Copynumber: 2.5 Consensus size: 37
1156 AATGACAAAC
1166 TATTTAGACCAAATTATGCGATATCCCGAGCATGGAA
1 TATTTAGACCAAATTATGCGATATCCCGAGCATGGAA
1203 TATTTAGACCAAATTATGCGATATCCCGAGCATGGAA
1 TATTTAGACCAAATTATGCGATATCCCGAGCATGGAA
1240 TATTTAGACCAAATTATGC
1 TATTTAGACCAAATTATGC
1259 NNNNNNNNNN
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 56 1.00
ACGTcount: A:0.35, C:0.18, G:0.17, T:0.29
Consensus pattern (37 bp):
TATTTAGACCAAATTATGCGATATCCCGAGCATGGAA
Found at i:1636 original size:37 final size:37
Alignment explanation
Indices: 1586--1697 Score: 197
Period size: 37 Copynumber: 3.0 Consensus size: 37
1576 AATGACAAAC
1586 TATTTAGACCAAATTATGCGATATCCCGAGCATGGAA
1 TATTTAGACCAAATTATGCGATATCCCGAGCATGGAA
1623 TATTTAGACCAAATTATGCGATATCCCGAGCATGGAA
1 TATTTAGACCAAATTATGCGATATCCCGAGCATGGAA
* * *
1660 TATTTAGACCAAATTATGCAATTTCCTGAGCATGGAA
1 TATTTAGACCAAATTATGCGATATCCCGAGCATGGAA
1697 T
1 T
1698 GTTCGGAAAA
Statistics
Matches: 72, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
37 72 1.00
ACGTcount: A:0.35, C:0.18, G:0.18, T:0.29
Consensus pattern (37 bp):
TATTTAGACCAAATTATGCGATATCCCGAGCATGGAA
Found at i:1890 original size:290 final size:291
Alignment explanation
Indices: 1369--1913 Score: 925
Period size: 290 Copynumber: 1.9 Consensus size: 291
1359 AATGACAAAT
* *
1369 TATTTAGACCAAATAATACGATTTACCGAGCACGGAATGTTCGGAAATTTGCATGAAGCAATGGA
1 TATTTAGACCAAATAATACAATTTACCGAGCACGGAATGTTCGGAAAATTGCATGAAGCAATGGA
* * *
1434 TCGTCTTGAATACTTGAAGGAACCCAAAGTTATAAATGAACTAGTAAAAGTTTGACAAGTTTGAA
66 TCATCTTGAATACTTGAAGGAACCCAAAGTTATAAAAGAACTAGTAAAAGTTTGACAAATTTGAA
*
1499 AGTTCGTACAGAGACAAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGACAAAA
131 AGTTCGTACAAAGACAAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGACAAAA
1564 ACTTGTTTACAAAATGACAAACTATTTAGACCAAATTATGCGATATCCCGAGCATGGAATATTTA
196 ACTTGTTTACAAAATGACAAACTATTTAGACCAAATTATGCGATATCCCGAGCATGGAATATTTA
1629 GACCAAATTATGCGATATCCCGAGCATGGAA
261 GACCAAATTATGCGATATCCCGAGCATGGAA
* * *
1660 TATTTAGACCAAATTATGCAATTT-CCTGAGCATGGAATGTTCGGAAAATTGC-TCGAAGCAATG
1 TATTTAGACCAAATAATACAATTTACC-GAGCACGGAATGTTCGGAAAATTGCAT-GAAGCAATG
* * *
1723 GATTATCTTTAATACTTGAAGG-ACCCGAAGTTATAAAAGAACTAGTAAAAGTTTGACAAATTTG
64 GATCATCTTGAATACTTGAAGGAACCCAAAGTTATAAAAGAACTAGTAAAAGTTTGACAAATTTG
*
1787 ATAGTTCGTACAAAGACAAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGACAA
129 AAAGTTCGTACAAAGACAAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGACAA
*
1852 AAACTTGTTTACAAAATGACAAACTATTTAGACCAAATTATGCGATTTCCCGAGCATGGAAT
194 AAACTTGTTTACAAAATGACAAACTATTTAGACCAAATTATGCGATATCCCGAGCATGGAAT
1914 GTTCAGAAAA
Statistics
Matches: 238, Mismatches: 14, Indels: 5
0.93 0.05 0.02
Matches are distributed among these distances:
290 166 0.70
291 72 0.30
ACGTcount: A:0.40, C:0.15, G:0.17, T:0.28
Consensus pattern (291 bp):
TATTTAGACCAAATAATACAATTTACCGAGCACGGAATGTTCGGAAAATTGCATGAAGCAATGGA
TCATCTTGAATACTTGAAGGAACCCAAAGTTATAAAAGAACTAGTAAAAGTTTGACAAATTTGAA
AGTTCGTACAAAGACAAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGACAAAA
ACTTGTTTACAAAATGACAAACTATTTAGACCAAATTATGCGATATCCCGAGCATGGAATATTTA
GACCAAATTATGCGATATCCCGAGCATGGAA
Found at i:2034 original size:216 final size:216
Alignment explanation
Indices: 1660--2103 Score: 660
Period size: 216 Copynumber: 2.1 Consensus size: 216
1650 GAGCATGGAA
* * *
1660 TATTTAGACCAAATTATGCAATTTCCTGAGCATGGAATGTTCGGAAAATTGCTCGAAGCAATGGA
1 TATTTAGACCAAATTATGCAATTTCCCGAGCATGGAATGTTCAGAAAATTGCTCGAAGCAATAGA
* * * * *
1725 TTATCTTTAATACTTGAAGGACCCGAAGTTATAAAAGAACTAGTAAAAGTTTGACAAATTTGATA
66 TTATCTTGAATACTTCAAGGAACCGAAGTTATAAAAGAACTAGTAAAAGTTTGACAAATTCGAAA
1790 GTTCGTACAAAGACAAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGACAAAAA
131 GTTCGTACAAAGACAAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGACAAAAA
1855 CTTGTTTACAAAATGACAAAC
196 CTTGTTTACAAAATGACAAAC
* *
1876 TATTTAGACCAAATTATGCGATTTCCCGAGCATGGAATGTTCAGAAAATTGCTC-AGAGGAATAG
1 TATTTAGACCAAATTATGCAATTTCCCGAGCATGGAATGTTCAGAAAATTGCTCGA-AGCAATAG
* * * * *
1940 ATCT-TGTTGAATACTTCAGGGAATCGAAGTTA-AAAAGTAACTCGTAAAAGTTTGACAAGTTCG
65 AT-TATCTTGAATACTTCAAGGAACCGAAGTTATAAAAG-AACTAGTAAAAGTTTGACAAATTCG
* *
2003 AAAGTTCGTACAAAGATAAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGACCA
128 AAAGTTCGTACAAAGACAAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGACAA
*
2068 AAACTTGTTTGCAAAATGACAAAC
193 AAACTTGTTTACAAAATGACAAAC
* *
2092 TAATTAGGCCAA
1 TATTTAGACCAA
Statistics
Matches: 205, Mismatches: 20, Indels: 6
0.89 0.09 0.03
Matches are distributed among these distances:
215 6 0.03
216 198 0.97
217 1 0.00
ACGTcount: A:0.41, C:0.14, G:0.17, T:0.28
Consensus pattern (216 bp):
TATTTAGACCAAATTATGCAATTTCCCGAGCATGGAATGTTCAGAAAATTGCTCGAAGCAATAGA
TTATCTTGAATACTTCAAGGAACCGAAGTTATAAAAGAACTAGTAAAAGTTTGACAAATTCGAAA
GTTCGTACAAAGACAAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGACAAAAA
CTTGTTTACAAAATGACAAAC
Done.