Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01008182.1 Kokia drynarioides strain JFW-HI SEQ_122841, 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, 798
Length: 1331
ACGTcount: A:0.40, C:0.14, G:0.17, T:0.28
Found at i:650 original size:216 final size:216
Alignment explanation
Indices: 1--1331 Score: 1463
Period size: 216 Copynumber: 6.2 Consensus size: 216
* * * * *
1 TTTTAATTCAACGACCAAAACCTGTTTA-ATAAATGACAATCTATTTAGACCAAATGCTGTGATT
1 TTTTAATTCAAAGACCAAAACTTGTTTACA-AAATGACAAACTATTTAGACCAAATGATGCGATT
* * ** * * * *
65 TCTTGAGCAAGGAATGTTTGGAAAACTGCTCGAAGGACTGGATCGCCTTCAATACTTTAAGGAAT
65 TCTCGAGCATGGAATGTTCAGAAAATTGCTCGAAGGAATGGATCGTCTTGAATACTTTAAGGAAT
* * * * * * *
130 GGAAGTTATAAAATAAGTCGTAAAAGTTTGACACGTTTGAAAGTTCATCCAAGAAGAAAGAGAGA
130 CGAAGTTATAAAAGAACTCGTAAAAGTTTGACAAGTTAGAAAGTTCGTCCAAGAACAAAGAGAGA
*
195 AACAATTCTCACGCAAATAAGT
195 AACAATTCTCACGTAAATAAGT
* * * * * *
217 TTTTTATTCCAAGACCAAAACTTGTTTACGAAATGACAAACTCTTTAGACCGAATGATGCAATTT
1 TTTTAATTCAAAGACCAAAACTTGTTTACAAAATGACAAACTATTTAGACCAAATGATGCGATTT
* * * * *
282 TTTGAGCATGGAATGTTCAGAAAA-TACTCAAAGGAATGGGTCGTCTTGAATACTTTAAGGAAGT
66 CTCGAGCATGGAATGTTCAGAAAATTGCTCGAAGGAATGGATCGTCTTGAATACTTTAAGGAA-T
* * * * * * *
346 -TAAGTTATAAAAGATCTCCTAAAAGTTTGACAAGTTCAG-GAGTTCGTCCATGAACCAAGAGTG
130 CGAAGTTATAAAAGAACTCGTAAAAGTTTGACAAGTT-AGAAAGTTCGTCCAAGAACAAAGAGAG
** *
409 ATGCAATTCTCTCGTAAATAAGT
194 AAACAATTCTCACGTAAATAAGT
** * *
432 TTTTAATTCAAAGACCAAAACTTGTAAACAAAATGACAAAATATTTAAACCAAATGATGCGATTT
1 TTTTAATTCAAAGACCAAAACTTGTTTACAAAATGACAAACTATTTAGACCAAATGATGCGATTT
* * * * ** * * *
497 CTCAAGCACGGAATGTTCAGAAAATTGCTCTAACGAATGTTTCTTGTTGAATACTTTAGGGAATC
66 CTCGAGCATGGAATGTTCAGAAAATTGCTCGAAGGAATGGATCGTCTTGAATACTTTAAGGAATC
* * * *
562 GAAGTTAAAAAATAACTCGTAAAAGTTTGACAAGTTAGAAAGTTTGTAC-AGAGACAAAGAGAGA
131 GAAGTTATAAAAGAACTCGTAAAAGTTTGACAAGTTAGAAAGTTCGTCCAAGA-ACAAAGAGAGA
626 AACAATTCTCACGTAAATAAGT
195 AACAATTCTCACGTAAATAAGT
* * ** * *
648 TTTTAATTCAATGACCAAAATTTGTTTTTAAAATGACAAACCATTTAGGCCAAATGATGCGATTT
1 TTTTAATTCAAAGACCAAAACTTGTTTACAAAATGACAAACTATTTAGACCAAATGATGCGATTT
* * * *
713 GC-CGAGCATAGAATATTTAGAAAATTGCTCGAAGGAATGGATAGTCTTGAATACTTTAAGG-AT
66 -CTCGAGCATGGAATGTTCAGAAAATTGCTCGAAGGAATGGATCGTCTTGAATACTTTAAGGAAT
* * *
776 AAGAAGTTATAAAAGAACTAGTAAAAGTTTGACAAGCTT-GAAAGTTCATCCAAGAACAAAGAGA
130 -CGAAGTTATAAAAGAACTCGTAAAAGTTTGACAAG-TTAGAAAGTTCGTCCAAGAACAAAGAGA
*
840 GAAACAATTCTCACGTAAATAACT
193 GAAACAATTCTCACGTAAATAAGT
* * *
864 TTTTAATTCAAAGACCAGAACTTGTTTACAAAATGACAAACTATTTAGATCAAATGATGCAATTT
1 TTTTAATTCAAAGACCAAAACTTGTTTACAAAATGACAAACTATTTAGACCAAATGATGCGATTT
* * * * * *
929 CCCAAGGATGGAATGTTC-GAAAAATTGCTCTAGAA--AATGGATCTTGTTGAATACTTTAGGGA
66 CTCGAGCATGGAATGTTCAG-AAAATTGCTC--GAAGGAATGGATCGTCTTGAATACTTTAAGGA
* * * * *
991 ATTGAAGTTAAAAAATAACTCGTAAAAGTTTGAGAAGTTCGAAAGTTCGTCCAAGAACAAAGAGA
128 ATCGAAGTTATAAAAGAACTCGTAAAAGTTTGACAAGTTAGAAAGTTCGTCCAAGAACAAAGAGA
1056 GAAACAATTCTCACGT-AATAAGT
193 GAAACAATTCTCACGTAAATAAGT
* * * * * * *
1079 TTTTAATTTAAAGGCAAAAACCTGTTTGCAAAACGACAAATTATTTAGACCAAATGATGCGATTT
1 TTTTAATTCAAAGACCAAAACTTGTTTACAAAATGACAAACTATTTAGACCAAATGATGCGATTT
* ** *
1144 CTCGAGCATGGAATGTTTAGAAAATTGCTCGAAAAAATAGATCGTCTTGAATACTTTAAGG-ATC
66 CTCGAGCATGGAATGTTCAGAAAATTGCTCGAAGGAATGGATCGTCTTGAATACTTTAAGGAAT-
* *
1208 CAAAGTTATAAAAGAAC-CAGTAAAAGTTTGAC-AGCTTCGAAAGTTCGTCCAAGAACAAA-AGG
130 CGAAGTTATAAAAGAACTC-GTAAAAGTTTGACAAG-TTAGAAAGTTCGTCCAAGAACAAAGA-G
* *
1270 AGAAACAATTGTCACGTAAATAAGA
192 AGAAACAATTCTCACGTAAATAAGT
* * *
1295 TTTAAATTCAACGACCAAAACCTGTTTA-ACAAATGAC
1 TTTTAATTCAAAGACCAAAACTTGTTTACA-AAATGAC
Statistics
Matches: 927, Mismatches: 162, Indels: 52
0.81 0.14 0.05
Matches are distributed among these distances:
213 3 0.00
214 6 0.01
215 359 0.39
216 548 0.59
217 8 0.01
218 3 0.00
ACGTcount: A:0.40, C:0.14, G:0.17, T:0.28
Consensus pattern (216 bp):
TTTTAATTCAAAGACCAAAACTTGTTTACAAAATGACAAACTATTTAGACCAAATGATGCGATTT
CTCGAGCATGGAATGTTCAGAAAATTGCTCGAAGGAATGGATCGTCTTGAATACTTTAAGGAATC
GAAGTTATAAAAGAACTCGTAAAAGTTTGACAAGTTAGAAAGTTCGTCCAAGAACAAAGAGAGAA
ACAATTCTCACGTAAATAAGT
Found at i:1235 original size:647 final size:646
Alignment explanation
Indices: 1--1331 Score: 1639
Period size: 647 Copynumber: 2.1 Consensus size: 646
* * * *
1 TTTTAATTCAACGACCAAAACCTGTTTAATAAATGACAATCTATTTAGACCAAATGCTGTGATTT
1 TTTTAATTCAACGACCAAAACCTGTTTAATAAATGACAAACCATTTAGACCAAATGATGCGATTT
* * * * * *
66 CTTGAGCAAGGAATGTTTGGAAAACTGCTCGAAGGACTGGATCGCCTTCAATACTTTAAGGAATG
66 CTCGAGCAAGGAATATTTAGAAAACTGCTCGAAGGAATGGATAGCCTTCAATACTTTAAGGAATA
* * * * * *
131 GAAGTTATAAAATAAGTCGTAAAAGTTTGACACGTTTGAAAGTTCATCCAAGAAGAAAGAGAGAA
131 GAAGTTATAAAAGAACTAGTAAAAGTTTGACAAGCTTGAAAGTTCATCCAAGAACAAAGAGAGAA
* * * * *
196 ACAATTCTCACGCAAATAAGTTTTTTATTCCAAGACCAAAACTTGTTTACGAAATGACAAACTCT
196 ACAATTCTCACGCAAATAACTTTTTAATTCAAAGACCAAAACTTGTTTACAAAATGACAAACTAT
* **** *
261 TTAGACCGAATGATGCAATTTTTTGAGCATGGAATGTTCAGAAAATACTCAAAGGAATGGGTCGT
261 TTAGACCAAATGATGCAATTTCCCAAGCATGGAATGTTCAGAAAATACTCAAA-GAATGGATCGT
* * *
326 CTTGAATACTTTAAGGAAGTTAAGTTATAAAAGATCTCCTAAAAGTTTGACAAGTTCAGGAGTTC
325 CTTGAATACTTTAAGGAAGTTAAGTTAAAAAAGAACTCCTAAAAGTTTGACAAGTTCAGAAGTTC
* * * ** * * *
391 GTCCATGAACCAAGAGTGATGCAATTCTCTCGTAAATAAGTTTTTAATTCAAAGACCAAAACTTG
390 GTCCAAGAACAAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGACAAAAACCTG
*
456 TAAACAAAATGACAAAATATTTAAACCAAATGATGCGATTTCTCAAGCACGGAATGTTCAGAAAA
455 TAAACAAAACGACAAAATATTTAAACCAAATGATGCGATTTCTCAAGCACGGAATGTTCAGAAAA
* ** * * * * * *
521 TTGCTCTAACGAATGTTTCTTGTTGAATACTTTAGGGAATCGAAGTTAAAAAATAACTCGTAAAA
520 TTGCTCGAAAAAATGTATCGTCTTGAATACTTTAAGGAATCAAAGTTAAAAAAGAACTCGTAAAA
* *
586 GTTTGACAAG-TTAGAAAGTTTGTAC-AGAGAC-AAAGAGAGAAACAATTCTCACGTAAATAAGT
585 GTTTGAC-AGCTTAGAAAGTTCGTACAAGA-ACAAAAG-GAGAAACAATTCTCACGTAAATAAGA
* ** * *
648 TTTTAATTCAATGACCAAAATTTGTTT-TTAAAATGACAAACCATTTAGGCCAAATGATGCGATT
1 TTTTAATTCAACGACCAAAACCTGTTTAAT-AAATGACAAACCATTTAGACCAAATGATGCGATT
* * *
712 TGC-CGAGCATA-GAATATTTAGAAAATTGCTCGAAGGAATGGATAGTCTTGAATACTTTAAGG-
65 T-CTCGAGCA-AGGAATATTTAGAAAACTGCTCGAAGGAATGGATAGCCTTCAATACTTTAAGGA
774 ATAAGAAGTTATAAAAGAACTAGTAAAAGTTTGACAAGCTTGAAAGTTCATCCAAGAACAAAGAG
128 AT-AGAAGTTATAAAAGAACTAGTAAAAGTTTGACAAGCTTGAAAGTTCATCCAAGAACAAAGAG
* *
839 AGAAACAATTCTCACGTAAATAACTTTTTAATTCAAAGACCAGAACTTGTTTACAAAATGACAAA
192 AGAAACAATTCTCACGCAAATAACTTTTTAATTCAAAGACCAAAACTTGTTTACAAAATGACAAA
* * *
904 CTATTTAGATCAAATGATGCAATTTCCCAAGGATGGAATGTTC-GAAAAATTGCTCTAGAA-AAT
257 CTATTTAGACCAAATGATGCAATTTCCCAAGCATGGAATGTTCAG-AAAA-TACTC-A-AAGAAT
* * * * * *
967 GGATCTTGTTGAATACTTTAGGGAA-TTGAAGTTAAAAAATAACTCGTAAAAGTTTGAGAAGTTC
318 GGATCGTCTTGAATACTTTAAGGAAGTT-AAGTTAAAAAAGAACTCCTAAAAGTTTGACAAGTTC
* *
1031 -GAAAGTTCGTCCAAGAACAAAGAGAGAAACAATTCTCACGT-AATAAGTTTTTAATTTAAAGGC
382 AG-AAGTTCGTCCAAGAACAAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGAC
*** * * * *
1094 AAAAACCTGTTTGCAAAACGACAAATTATTTAGACCAAATGATGCGATTTCTCGAGCATGGAATG
446 AAAAACCTGTAAACAAAACGACAAAATATTTAAACCAAATGATGCGATTTCTCAAGCACGGAATG
* *
1159 TTTAGAAAATTGCTCGAAAAAATAG-ATCGTCTTGAATACTTTAAGG-ATCCAAAGTTATAAAAG
511 TTCAGAAAATTGCTCGAAAAAAT-GTATCGTCTTGAATACTTTAAGGAAT-CAAAGTTAAAAAAG
* * *
1222 AAC-CAGTAAAAGTTTGACAGCTTCGAAAGTTCGTCCAAGAACAAAAGGAGAAACAATTGTCACG
574 AACTC-GTAAAAGTTTGACAGCTTAGAAAGTTCGTACAAGAACAAAAGGAGAAACAATTCTCACG
1286 TAAATAAGA
638 TAAATAAGA
* *
1295 TTTAAATTCAACGACCAAAACCTGTTTAACAAATGAC
1 TTTTAATTCAACGACCAAAACCTGTTTAATAAATGAC
Statistics
Matches: 578, Mismatches: 89, Indels: 34
0.82 0.13 0.05
Matches are distributed among these distances:
646 9 0.02
647 465 0.80
648 101 0.17
649 1 0.00
650 2 0.00
ACGTcount: A:0.40, C:0.14, G:0.17, T:0.28
Consensus pattern (646 bp):
TTTTAATTCAACGACCAAAACCTGTTTAATAAATGACAAACCATTTAGACCAAATGATGCGATTT
CTCGAGCAAGGAATATTTAGAAAACTGCTCGAAGGAATGGATAGCCTTCAATACTTTAAGGAATA
GAAGTTATAAAAGAACTAGTAAAAGTTTGACAAGCTTGAAAGTTCATCCAAGAACAAAGAGAGAA
ACAATTCTCACGCAAATAACTTTTTAATTCAAAGACCAAAACTTGTTTACAAAATGACAAACTAT
TTAGACCAAATGATGCAATTTCCCAAGCATGGAATGTTCAGAAAATACTCAAAGAATGGATCGTC
TTGAATACTTTAAGGAAGTTAAGTTAAAAAAGAACTCCTAAAAGTTTGACAAGTTCAGAAGTTCG
TCCAAGAACAAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGACAAAAACCTGT
AAACAAAACGACAAAATATTTAAACCAAATGATGCGATTTCTCAAGCACGGAATGTTCAGAAAAT
TGCTCGAAAAAATGTATCGTCTTGAATACTTTAAGGAATCAAAGTTAAAAAAGAACTCGTAAAAG
TTTGACAGCTTAGAAAGTTCGTACAAGAACAAAAGGAGAAACAATTCTCACGTAAATAAGA
Found at i:1305 original size:431 final size:431
Alignment explanation
Indices: 1--1331 Score: 1522
Period size: 431 Copynumber: 3.1 Consensus size: 431
* * ** * * **
1 TTTTAATTCAACGACCAAAACCTGTTTA-ATAAATGACAATCTATTTAGACCAAATGCTGTGATT
1 TTTTAATTCAAAGACCAAAACTTGTTTACA-AAATGACAAAATATTTAAACCAAATGATGCAATT
*** * ** * * ** * *** * *
65 TCTTGAGCAAGGAATGTTTGGAAAACTGCTCGAAGGACTGGATCGCCTTCAATACTTTAAGGAAT
65 TCCCAAGCACGGAATGTTCAGAAAATTGCTCTAACAAATGGATCTTGTTGAATACTTTAGGGAAT
* * * * * * *
130 GGAAGTTATAAAATAAGTCGTAAAAGTTTGACACGTTTGAAAGTTCATCCAAGAAGAAAGAGAGA
130 CGAAGTTAAAAAATAACTCGTAAAAGTTTGACAAGTTAGAAAGTTCGTCCAAGAACAAAGAGAGA
* * * * *
195 AACAATTCTCACGCAAATAAGTTTTTTATTCCAAGACCAAAACTTGTTTACGAAATGACAAACTC
195 AACAATTCTCACG-TAATAAGTTTTTAATTCAAAGACCAAAACTTGTTTACAAAATGACAAACTA
* * * * * * *
260 TTTAGACCGAATGATGCAATTTTTTGAGCATGGAATGTTCAGAAAA-TACTC-AAAGGAATGGGT
259 TTTAGACCAAATGATGCGATTTCTCGAGCATGGAATGTTTAGAAAATTGCTCGAAA-GAATGGAT
* * *
323 CGTCTTGAATACTTTAAGGA-AGTTAAGTTATAAAAGATCTC-CTAAAAGTTTGACAAG-TTC-A
323 CGTCTTGAATACTTTAAGGATA--AAAGTTATAAAAGAAC-CAGTAAAAGTTTGACAAGCTTCGA
* * * * ** *
384 GGAGTTCGTCCATGAACCAAGAGTGATGCAATTCTCTCGTAAATAAGT
385 -AAGTTCGTCCAAGAACAAAGAGAGAAACAATTCTCACGTAAATAAGT
** *
432 TTTTAATTCAAAGACCAAAACTTGTAAACAAAATGACAAAATATTTAAACCAAATGATGCGATTT
1 TTTTAATTCAAAGACCAAAACTTGTTTACAAAATGACAAAATATTTAAACCAAATGATGCAATTT
* * **
497 CTCAAGCACGGAATGTTCAGAAAATTGCTCTAACGAATGTTTCTTGTTGAATACTTTAGGGAATC
66 CCCAAGCACGGAATGTTCAGAAAATTGCTCTAACAAATGGATCTTGTTGAATACTTTAGGGAATC
* *
562 GAAGTTAAAAAATAACTCGTAAAAGTTTGACAAGTTAGAAAGTTTGTAC-AGAGACAAAGAGAGA
131 GAAGTTAAAAAATAACTCGTAAAAGTTTGACAAGTTAGAAAGTTCGTCCAAGA-ACAAAGAGAGA
* * ** *
626 AACAATTCTCACGTAAATAAGTTTTTAATTCAATGACCAAAATTTGTTTTTAAAATGACAAACCA
195 AACAATTCTCACGT-AATAAGTTTTTAATTCAAAGACCAAAACTTGTTTACAAAATGACAAACTA
* * * *
691 TTTAGGCCAAATGATGCGATTTGC-CGAGCATAGAATATTTAGAAAATTGCTCGAAGGAATGGAT
259 TTTAGACCAAATGATGCGATTT-CTCGAGCATGGAATGTTTAGAAAATTGCTCGAAAGAATGGAT
* *
755 AGTCTTGAATACTTTAAGGATAAGAAGTTATAAAAGAACTAGTAAAAGTTTGACAAGCTT-GAAA
323 CGTCTTGAATACTTTAAGGATAA-AAGTTATAAAAGAACCAGTAAAAGTTTGACAAGCTTCGAAA
* *
819 GTTCATCCAAGAACAAAGAGAGAAACAATTCTCACGTAAATAACT
387 GTTCGTCCAAGAACAAAGAGAGAAACAATTCTCACGTAAATAAGT
* * * *
864 TTTTAATTCAAAGACCAGAACTTGTTTACAAAATGACAAACTATTTAGATCAAATGATGCAATTT
1 TTTTAATTCAAAGACCAAAACTTGTTTACAAAATGACAAAATATTTAAACCAAATGATGCAATTT
* *
929 CCCAAGGATGGAATGTTC-GAAAAATTGCTCTAGA-AAATGGATCTTGTTGAATACTTTAGGGAA
66 CCCAAGCACGGAATGTTCAG-AAAATTGCTCTA-ACAAATGGATCTTGTTGAATACTTTAGGGAA
* * *
992 TTGAAGTTAAAAAATAACTCGTAAAAGTTTGAGAAGTTCGAAAGTTCGTCCAAGAACAAAGAGAG
129 TCGAAGTTAAAAAATAACTCGTAAAAGTTTGACAAGTTAGAAAGTTCGTCCAAGAACAAAGAGAG
* * * * * * *
1057 AAACAATTCTCACGTAATAAGTTTTTAATTTAAAGGCAAAAACCTGTTTGCAAAACGACAAATTA
194 AAACAATTCTCACGTAATAAGTTTTTAATTCAAAGACCAAAACTTGTTTACAAAATGACAAACTA
* *
1122 TTTAGACCAAATGATGCGATTTCTCGAGCATGGAATGTTTAGAAAATTGCTCGAAAAAATAGATC
259 TTTAGACCAAATGATGCGATTTCTCGAGCATGGAATGTTTAGAAAATTGCTCGAAAGAATGGATC
*
1187 GTCTTGAATACTTTAAGGATCCAAAGTTATAAAAGAACCAGTAAAAGTTTGAC-AGCTTCGAAAG
324 GTCTTGAATACTTTAAGGAT-AAAAGTTATAAAAGAACCAGTAAAAGTTTGACAAGCTTCGAAAG
* *
1251 TTCGTCCAAGAACAAA-AGGAGAAACAATTGTCACGTAAATAAGA
388 TTCGTCCAAGAACAAAGA-GAGAAACAATTCTCACGTAAATAAGT
* * *
1295 TTTAAATTCAACGACCAAAACCTGTTTA-ACAAATGAC
1 TTTTAATTCAAAGACCAAAACTTGTTTACA-AAATGAC
Statistics
Matches: 766, Mismatches: 115, Indels: 38
0.83 0.13 0.04
Matches are distributed among these distances:
430 11 0.01
431 464 0.61
432 281 0.37
433 10 0.01
ACGTcount: A:0.40, C:0.14, G:0.17, T:0.28
Consensus pattern (431 bp):
TTTTAATTCAAAGACCAAAACTTGTTTACAAAATGACAAAATATTTAAACCAAATGATGCAATTT
CCCAAGCACGGAATGTTCAGAAAATTGCTCTAACAAATGGATCTTGTTGAATACTTTAGGGAATC
GAAGTTAAAAAATAACTCGTAAAAGTTTGACAAGTTAGAAAGTTCGTCCAAGAACAAAGAGAGAA
ACAATTCTCACGTAATAAGTTTTTAATTCAAAGACCAAAACTTGTTTACAAAATGACAAACTATT
TAGACCAAATGATGCGATTTCTCGAGCATGGAATGTTTAGAAAATTGCTCGAAAGAATGGATCGT
CTTGAATACTTTAAGGATAAAAGTTATAAAAGAACCAGTAAAAGTTTGACAAGCTTCGAAAGTTC
GTCCAAGAACAAAGAGAGAAACAATTCTCACGTAAATAAGT
Done.