Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013182.1 Kokia drynarioides strain JFW-HI SEQ_128201, 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: 3243
ACGTcount: A:0.36, C:0.21, G:0.19, T:0.24
Found at i:1170 original size:203 final size:204
Alignment explanation
Indices: 919--1450 Score: 647
Period size: 203 Copynumber: 2.6 Consensus size: 204
909 GCAATAAATG
919 GTTAGCTTCCTGATGAGATACGGAGAAGTAGACCAAATTCGTCTTCCTGATGAGATACAGAGAAG
1 GTTAGCTTCCTGATGAGATACGGAGAAGTAGACCAAATTCGTCTTCCTGATGAGATACAGAGAAG
* *
984 CGGATTGAAACGAACAACGCGGTCATCTTCCTAATGAGATACTGAGAAGAAGACCAAACCAAACT
66 CGGATTGAAACAAACGACGCGGTCATCTTCCTAATGAGATACTGAGAAGAAGACCAAA--AAAC-
* * * *
1049 AAACCCATGCTCGACATG-AGC-AAATCTTCGAACCAC-AGCTCCCTGATG-AGATACTGAGAAG
128 AAACCCACGCTC-A-AAGAAACAAAATCTTCGAACCACGAGCTCCCTGA-GAAGATACTGAAAAG
*
1110 C-GTGTCG-AAT-TAA
190 CAG-GTCGAAATACAA
1123 -TTAGCTTCCTGATGAGATACGGAGAAGTAGACCAAATTCGTCTTCCTGATGAGATACAGAGAAG
1 GTTAGCTTCCTGATGAGATACGGAGAAGTAGACCAAATTCGTCTTCCTGATGAGATACAGAGAAG
* * * *
1187 CGGA-TAAAACAAACGACGCGGTCATCTTCCTAATGAGATATTGAGAAGAAGACC--AAATCGAA
66 CGGATTGAAACAAACGACGCGGTCATCTTCCTAATGAGATACTGAGAAGAAGACCAAAAAACAAA
* *
1249 CCCACGCTCAAAGCAAACAAAATCTTCGAACCCCGAGCTTCCTGAGAAGATACTGAAAAGCAGGT
131 CCCACGCTCAAAG-AAACAAAATCTTCGAACCACGAGCTCCCTGAGAAGATACTGAAAAGCAGGT
1314 CGAACCAATACAA
195 CG-A--AATACAA
* * * * * *
1327 GGTTAGCTTCCTGATGAGATACTGAGAAGT-GAACCAAACTCGTATTCCTGATAAGGTATAGAGA
1 -GTTAGCTTCCTGATGAGATACGGAGAAGTAG-ACCAAATTCGTCTTCCTGATGAGATACAGAGA
* * * * *
1391 AGCGAATTGAAACAAACGATGCAGTCATCTTCCTGATAAGATACTGAGAAGAAGACCAAA
64 AGCGGATTGAAACAAACGACGCGGTCATCTTCCTAATGAGATACTGAGAAGAAGACCAAA
1451 TCAATAATAC
Statistics
Matches: 285, Mismatches: 26, Indels: 29
0.84 0.08 0.09
Matches are distributed among these distances:
195 2 0.01
196 1 0.00
197 12 0.04
198 18 0.06
199 26 0.09
200 2 0.01
202 46 0.16
203 71 0.25
204 2 0.01
205 1 0.00
206 59 0.21
207 44 0.15
209 1 0.00
ACGTcount: A:0.37, C:0.21, G:0.22, T:0.20
Consensus pattern (204 bp):
GTTAGCTTCCTGATGAGATACGGAGAAGTAGACCAAATTCGTCTTCCTGATGAGATACAGAGAAG
CGGATTGAAACAAACGACGCGGTCATCTTCCTAATGAGATACTGAGAAGAAGACCAAAAAACAAA
CCCACGCTCAAAGAAACAAAATCTTCGAACCACGAGCTCCCTGAGAAGATACTGAAAAGCAGGTC
GAAATACAA
Found at i:1831 original size:198 final size:203
Alignment explanation
Indices: 1587--2117 Score: 659
Period size: 198 Copynumber: 2.6 Consensus size: 203
1577 GAAATAAATG
*
1587 GTTAGCTTCCTGATGAGATACGGAGAAGTAGACCAAATTCGTCTTCCTGATGAGATACAGAGAAG
1 GTTAGCTTCCTGATGAGATACGGAGAAGTAGACCAAATTCGTCTTCCTGATGAGATATAGAGAAG
* *
1652 CGAATTGAAACGAACAATGCGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAACC
66 CGAATTGAAACAAACGATGCGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAACC
** * * *
1717 CATTCTCGACATG-AGC-AAATCTTCGAA-CCACAGCTCCCTGATG-AGATACTGAGAAGC-GTG
131 CACGCTC-A-AAGAAACAAAATCTTCGAACCCACAGCTCCCTGA-GAAGATACTGAAAAGCAG-G
*
1777 TCG-A-AGT-AA
192 TCGAACAATAAA
* *
1786 -TTAGTTTCCTGATGAGATACGGAGAAGTAGACCAAATTTGTCTTCCTGATGAGATATAGAGAAG
1 GTTAGCTTCCTGATGAGATACGGAGAAGTAGACCAAATTCGTCTTCCTGATGAGATATAGAGAAG
* * * * * * * *
1850 TGGA-TAAAACAAACGACGCGGTCATCTTCCTAATGAGATATTGAGAAGAAGAGCAAATCGAACC
66 CGAATTGAAACAAACGATGCGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAACC
* *
1914 CACGCTCAAAGCAAACAAAATCTTCGAACCCCCAGCTTCCTGAGAAGATACTGAAAAGCAGGTCG
131 CACGCTCAAAG-AAACAAAATCTTCGAACCCACAGCTCCCTGAGAAGATACTGAAAAGCAGGTCG
1979 AACCAATACAA
195 AA-CAATA-AA
* ** * * * *
1990 GGTTAGCTTCCTTATGAGATATTGAGAAGTAAACCAAACTCGTATTCCTGATGAGGTATAGAGAA
1 -GTTAGCTTCCTGATGAGATACGGAGAAGTAGACCAAATTCGTCTTCCTGATGAGATATAGAGAA
*
2055 GCGAATTGAAACAAACGATGCAGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAA
65 GCGAATTGAAACAAACGATGCGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAA
2118 TAAAACAGAA
Statistics
Matches: 279, Mismatches: 39, Indels: 20
0.83 0.12 0.06
Matches are distributed among these distances:
195 2 0.01
196 1 0.00
197 59 0.21
198 75 0.27
199 29 0.10
200 2 0.01
202 2 0.01
204 2 0.01
206 57 0.20
207 50 0.18
ACGTcount: A:0.37, C:0.20, G:0.22, T:0.22
Consensus pattern (203 bp):
GTTAGCTTCCTGATGAGATACGGAGAAGTAGACCAAATTCGTCTTCCTGATGAGATATAGAGAAG
CGAATTGAAACAAACGATGCGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAACC
CACGCTCAAAGAAACAAAATCTTCGAACCCACAGCTCCCTGAGAAGATACTGAAAAGCAGGTCGA
ACAATAAA
Found at i:2059 original size:663 final size:666
Alignment explanation
Indices: 788--2120 Score: 2447
Period size: 663 Copynumber: 2.0 Consensus size: 666
778 GGCAAATTGC
*
788 AATACCCACAAAACAACGCGGTCATCTTCCTGATGAGATATTGAGAAGAAGACCAAACCAAGCCC
1 AATACCCACAAAACAACACGGTCATCTTCCTGATGAGATATTGAGAAGAAGACCAAACCAAGCCC
*
853 ACGCATGATGTCTTCGAATCCCAGCTTCCTGATGACACACCGAGAAGCAGATCGGAGCAATAAAT
66 ACGCATGATGTCTTCGAATCCCAGCTTCCTGATGACACACCGAGAAGCAGATCGGAGAAATAAAT
918 GGTTAGCTTCCTGATGAGATACGGAGAAGTAGACCAAATTCGTCTTCCTGATGAGATACAGAGAA
131 GGTTAGCTTCCTGATGAGATACGGAGAAGTAGACCAAATTCGTCTTCCTGATGAGATACAGAGAA
*
983 GCGGATTGAAACGAACAACGCGGTCATCTTCCTAATGAGATACTGAGAAGAAGACCAAACCAAAC
196 GCGAATTGAAACGAACAACGCGGTCATCTTCCTAATGAGATACTGAGAAGAAGACC-AA-CAAAC
1048 TAAACCCATGCTCGACATGAGCAAATCTTCGAACCACAGCTCCCTGATGAGATACTGAGAAGCGT
259 TAAACCCATGCTCGACATGAGCAAATCTTCGAACCACAGCTCCCTGATGAGATACTGAGAAGCGT
*
1113 GTCGAATTAATTAGCTTCCTGATGAGATACGGAGAAGTAGACCAAATTCGTCTTCCTGATGAGAT
324 GTCGAAGTAATTAGCTTCCTGATGAGATACGGAGAAGTAGACCAAATTCGTCTTCCTGATGAGAT
1178 ACAGAGAAGCGGATAAAACAAACGACGCGGTCATCTTCCTAATGAGATATTGAGAAGAAGACCAA
389 ACAGAGAAGCGGATAAAACAAACGACGCGGTCATCTTCCTAATGAGATATTGAGAAGAAGACCAA
*
1243 ATCGAACCCACGCTCAAAGCAAACAAAATCTTCGAACCCCGAGCTTCCTGAGAAGATACTGAAAA
454 ATCGAACCCACGCTCAAAGCAAACAAAATCTTCGAACCCCCAGCTTCCTGAGAAGATACTGAAAA
*
1308 GCAGGTCGAACCAATACAAGGTTAGCTTCCTGATGAGATACTGAGAAGTGAACCAAACTCGTATT
519 GCAGGTCGAACCAATACAAGGTTAGCTTCCTGATGAGATACTGAGAAGTAAACCAAACTCGTATT
1373 CCTGATAAGGTATAGAGAAGCGAATTGAAACAAACGATGCAGTCATCTTCCTGATAAGATACTGA
584 CCTGATAAGGTATAGAGAAGCGAATTGAAACAAACGATGCAGTCATCTTCCTGATAAGATACTGA
1438 GAAGAAGACCAAATCAAT
649 GAAGAAGACCAAATCAAT
1456 AATACCCACAAAACAACACGGTCATCTTCCTGATGAGATATTGAGAAGAAGACCAAACCAAGCCC
1 AATACCCACAAAACAACACGGTCATCTTCCTGATGAGATATTGAGAAGAAGACCAAACCAAGCCC
*
1521 GCGCATGATGTCTTCGAATCCCAGCTTCCTGATGACACACCGAGAAGCAGATCGGAGAAATAAAT
66 ACGCATGATGTCTTCGAATCCCAGCTTCCTGATGACACACCGAGAAGCAGATCGGAGAAATAAAT
1586 GGTTAGCTTCCTGATGAGATACGGAGAAGTAGACCAAATTCGTCTTCCTGATGAGATACAGAGAA
131 GGTTAGCTTCCTGATGAGATACGGAGAAGTAGACCAAATTCGTCTTCCTGATGAGATACAGAGAA
* * *
1651 GCGAATTGAAACGAACAATGCGGTCATCTTCCTGATGAGATACTGAGAAGAAGACC-A-AATC-A
196 GCGAATTGAAACGAACAACGCGGTCATCTTCCTAATGAGATACTGAGAAGAAGACCAACAAACTA
*
1713 AACCCATTCTCGACATGAGCAAATCTTCGAACCACAGCTCCCTGATGAGATACTGAGAAGCGTGT
261 AACCCATGCTCGACATGAGCAAATCTTCGAACCACAGCTCCCTGATGAGATACTGAGAAGCGTGT
* * *
1778 CGAAGTAATTAGTTTCCTGATGAGATACGGAGAAGTAGACCAAATTTGTCTTCCTGATGAGATAT
326 CGAAGTAATTAGCTTCCTGATGAGATACGGAGAAGTAGACCAAATTCGTCTTCCTGATGAGATAC
* *
1843 AGAGAAGTGGATAAAACAAACGACGCGGTCATCTTCCTAATGAGATATTGAGAAGAAGAGCAAAT
391 AGAGAAGCGGATAAAACAAACGACGCGGTCATCTTCCTAATGAGATATTGAGAAGAAGACCAAAT
1908 CGAACCCACGCTCAAAGCAAACAAAATCTTCGAACCCCCAGCTTCCTGAGAAGATACTGAAAAGC
456 CGAACCCACGCTCAAAGCAAACAAAATCTTCGAACCCCCAGCTTCCTGAGAAGATACTGAAAAGC
* *
1973 AGGTCGAACCAATACAAGGTTAGCTTCCTTATGAGATATTGAGAAGTAAACCAAACTCGTATTCC
521 AGGTCGAACCAATACAAGGTTAGCTTCCTGATGAGATACTGAGAAGTAAACCAAACTCGTATTCC
* *
2038 TGATGAGGTATAGAGAAGCGAATTGAAACAAACGATGCAGTCATCTTCCTGATGAGATACTGAGA
586 TGATAAGGTATAGAGAAGCGAATTGAAACAAACGATGCAGTCATCTTCCTGATAAGATACTGAGA
2103 AGAAGACCAAATCAAT
651 AGAAGACCAAATCAAT
2119 AA
1 AA
2121 AACAGAACTC
Statistics
Matches: 645, Mismatches: 20, Indels: 5
0.96 0.03 0.01
Matches are distributed among these distances:
663 396 0.61
664 3 0.00
666 1 0.00
668 245 0.38
ACGTcount: A:0.37, C:0.22, G:0.21, T:0.20
Consensus pattern (666 bp):
AATACCCACAAAACAACACGGTCATCTTCCTGATGAGATATTGAGAAGAAGACCAAACCAAGCCC
ACGCATGATGTCTTCGAATCCCAGCTTCCTGATGACACACCGAGAAGCAGATCGGAGAAATAAAT
GGTTAGCTTCCTGATGAGATACGGAGAAGTAGACCAAATTCGTCTTCCTGATGAGATACAGAGAA
GCGAATTGAAACGAACAACGCGGTCATCTTCCTAATGAGATACTGAGAAGAAGACCAACAAACTA
AACCCATGCTCGACATGAGCAAATCTTCGAACCACAGCTCCCTGATGAGATACTGAGAAGCGTGT
CGAAGTAATTAGCTTCCTGATGAGATACGGAGAAGTAGACCAAATTCGTCTTCCTGATGAGATAC
AGAGAAGCGGATAAAACAAACGACGCGGTCATCTTCCTAATGAGATATTGAGAAGAAGACCAAAT
CGAACCCACGCTCAAAGCAAACAAAATCTTCGAACCCCCAGCTTCCTGAGAAGATACTGAAAAGC
AGGTCGAACCAATACAAGGTTAGCTTCCTGATGAGATACTGAGAAGTAAACCAAACTCGTATTCC
TGATAAGGTATAGAGAAGCGAATTGAAACAAACGATGCAGTCATCTTCCTGATAAGATACTGAGA
AGAAGACCAAATCAAT
Found at i:2376 original size:17 final size:17
Alignment explanation
Indices: 2354--2408 Score: 83
Period size: 17 Copynumber: 3.2 Consensus size: 17
2344 AGAAATTGAA
2354 TTTATTTTAAATTTAAG
1 TTTATTTTAAATTTAAG
2371 TTTATTTTAAATTTAAG
1 TTTATTTTAAATTTAAG
* * *
2388 TTTATTATAAAATTAAA
1 TTTATTTTAAATTTAAG
2405 TTTA
1 TTTA
2409 GAAAAGTCCA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
17 35 1.00
ACGTcount: A:0.40, C:0.00, G:0.04, T:0.56
Consensus pattern (17 bp):
TTTATTTTAAATTTAAG
Found at i:3109 original size:30 final size:30
Alignment explanation
Indices: 3073--3141 Score: 95
Period size: 30 Copynumber: 2.3 Consensus size: 30
3063 AAATATTTAT
* *
3073 TAATAATAATTTTTTTTAAAACAATAAT-AA
1 TAATAATAATATCTTTTAAAA-AATAATCAA
*
3103 TAATAATAATATCTTTTAAAAAATAATCAT
1 TAATAATAATATCTTTTAAAAAATAATCAA
3133 TAATAATAA
1 TAATAATAA
3142 AAAAGGCATT
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
29 6 0.17
30 29 0.83
ACGTcount: A:0.55, C:0.04, G:0.00, T:0.41
Consensus pattern (30 bp):
TAATAATAATATCTTTTAAAAAATAATCAA
Done.