Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01005233.1 Kokia drynarioides strain JFW-HI SEQ_119120, 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, 631
Length: 1053
ACGTcount: A:0.38, C:0.15, G:0.18, T:0.29
Found at i:442 original size:216 final size:217
Alignment explanation
Indices: 1--989 Score: 1090
Period size: 216 Copynumber: 4.6 Consensus size: 217
* * * * **
1 GTTTGACACGTTCGAAAGTTCTTCCAAGAAGAAAGAGAGAAACAATTCTCACACAAATAAG-TTT
1 GTTTGACAAGTTCGGAAGTTCGTCCAAGAACAAAGAGAGAAACAATTCTCACGTAAATAAGTTTT
* * ** * *
65 TAATTCCAAGACCAAAACTTCTTTAGGAAATG-CTATACTATTTAGACCAAATGATGC-AGTTCC
66 TAATTCAAAGACCAAAACTTGTTTACAAAATGAC-AAACTATTTAGACCAAATGATGCGA-TTTC
* * * * *
128 CCGAGCATGGAATGTTCAGAAAAA-TGCTCAAAGGAAT-GAGTCATCTTGAATACTTTAAGGAAG
129 TCGAGCATGGAATGTTCAGAAAAATTGCTCTAAGGAATGGA-TCTTCTTGAATACTTTAGGGAAC
** * * * * *
191 TTAAGCTATAAAAGATCTCCTCAAA
193 CAAAGTTAAAAAAGAACTCGTAAAA
* * * * * * * * *
216 GTTGGACAAGTTCGGGAGTTCGTCCATGGACCAAGAGTGATACAATTCTCTCGTAAATAGGTTTT
1 GTTTGACAAGTTCGGAAGTTCGTCCAAGAACAAAGAGAGAAACAATTCTCACGTAAATAAGTTTT
*
281 TAATTCAAAGACTAAAACTTGTTTACAAAATGACAAACTATTTAGACCAAATGATGCGATTTCTC
66 TAATTCAAAGACCAAAACTTGTTTACAAAATGACAAACTATTTAGACCAAATGATGCGATTTCTC
* * *
346 GAGCGTGGAATGTTCAG-AAAATTGCTCTAAGGAATGGATCTTGTTGAATACTTTAGGGAACCGA
131 GAGCATGGAATGTTCAGAAAAATTGCTCTAAGGAATGGATCTTCTTGAATACTTTAGGGAACCAA
* * *
410 TGTTAAAAAATAACTTGTAAAA
196 AGTTAAAAAAGAACTCGTAAAA
** * * * *
432 GTTTGACAAGTTCAAAAGTTTGTACAA-AGACAAAGTGAGAAACAATTCTCACCTAAATAAGTTT
1 GTTTGACAAGTTCGGAAGTTCGTCCAAGA-ACAAAGAGAGAAACAATTCTCACGTAAATAAGTTT
* * * *
496 TTAATTCAAAGAGCAAAACTTTTTTGCAAAATGACAAACTATTTAGACCAAATGATGTGATTTCT
65 TTAATTCAAAGACCAAAACTTGTTTACAAAATGACAAACTATTTAGACCAAATGATGCGATTTCT
* * * *
561 CGAGCATGGAATGTT-TGAAAAATTGCTCGTAA-GAATGGATCGTCTCGAATACTTT-GAGGATC
130 CGAGCATGGAATGTTCAGAAAAATTGCTC-TAAGGAATGGATCTTCTTGAATACTTTAG-GGAAC
** * *
623 CAAAGTTATCAACGAACTAGTAAAA
193 CAAAGTTAAAAAAGAACTCGTAAAA
* * **
648 GTTTGACAAGCTCGTAAGTTCGTCCAAGAACAAAGAGAGAATTAATTCTCACGTAAATAAGTTTT
1 GTTTGACAAGTTCGGAAGTTCGTCCAAGAACAAAGAGAGAAACAATTCTCACGTAAATAAGTTTT
* * * *
713 TAATTCAAAGATCAAAACTTGTTTACAAAATGAC--A-TATTTAGATCAAATGATGCAATTTCCC
66 TAATTCAAAGACCAAAACTTGTTTACAAAATGACAAACTATTTAGACCAAATGATGCGATTTCTC
* * * * *
775 GAGCATGGAATGTTC-GAAAAATTGCTTTATGGAATGGATTTTGTTGAATGCTTTAGGGAACCAA
131 GAGCATGGAATGTTCAGAAAAATTGCTCTAAGGAATGGATCTTCTTGAATACTTTAGGGAACCAA
*
839 AGTTAAAAAATAACTCGTAAAA
196 AGTTAAAAAAGAACTCGTAAAA
* * * * *
861 GTTTGACCAGTTTGGAAGTTTGTCCAAGAAGAAAGAGAGAAACAATTCTCACGTAAATAAATTTT
1 GTTTGACAAGTTCGGAAGTTCGTCCAAGAACAAAGAGAGAAACAATTCTCACGTAAATAAGTTTT
* * *
926 TAATTCAACA-ACCAAAACTTGTTTACAAAATAACAATCTATTTTGACCAAATGATGCGATTTCT
66 TAATTCAA-AGACCAAAACTTGTTTACAAAATGACAAACTATTTAGACCAAATGATGCGATTTCT
990 TTTTTAGCAA
Statistics
Matches: 640, Mismatches: 117, Indels: 33
0.81 0.15 0.04
Matches are distributed among these distances:
212 2 0.00
213 176 0.28
214 3 0.00
215 52 0.08
216 399 0.62
217 8 0.01
ACGTcount: A:0.38, C:0.15, G:0.17, T:0.29
Consensus pattern (217 bp):
GTTTGACAAGTTCGGAAGTTCGTCCAAGAACAAAGAGAGAAACAATTCTCACGTAAATAAGTTTT
TAATTCAAAGACCAAAACTTGTTTACAAAATGACAAACTATTTAGACCAAATGATGCGATTTCTC
GAGCATGGAATGTTCAGAAAAATTGCTCTAAGGAATGGATCTTCTTGAATACTTTAGGGAACCAA
AGTTAAAAAAGAACTCGTAAAA
Found at i:920 original size:429 final size:429
Alignment explanation
Indices: 1--1053 Score: 1205
Period size: 432 Copynumber: 2.4 Consensus size: 429
* * *
1 GTTTGACACGTTCGAAAGTTCT-TCCAAGAAGAAAGAGAGAAACAATTCTCACACAAATAAG-TT
1 GTTTGACAAGTTCAAAAGTT-TGTCCAAGAAGAAAGAGAGAAACAATTCTCACATAAATAAGTTT
* * * * * *
64 TTAATTCCAAGACCAAAACTTCTTTAG-GAAATG-CTATACTATTTAGACCAAATGATGCAGTTC
65 TTAATTCAAAGACCAAAACTT-TTTTGCAAAATGAC-AAACTATTTAGACCAAATGATGGA-TTT
* * * * *
127 CCCGAGCATGGAATGTTCAGAAAAATGCTCAAAGGAAT-GAGTCATCTTGAATACTTTAAGGAAG
127 CTCGAGCATGGAATGTT-TGAAAAATGCTCGAAGGAATGGA-TCGTCTTGAATACTTTAAGGAAC
** * * * * * * * * *
191 TTAAGCTATAAAAGATCTCCTCAAAGTTGGACAAGTTCGGGAGTTCGTCCATGGACCAAGAGTGA
190 CAAAGCTATAAAAGAACTACTAAAAGTTGGACAAGCTCGGAAGTTCGTCCAAGAACAAAGAGAGA
* *
256 TACAATTCTCTCGTAAATAGGTTTTTAATTCAAAGACTAAAACTTGTTTACAAAATGACAAACTA
255 TACAATTCTCACGTAAATAAGTTTTTAATTCAAAGACTAAAACTTGTTTACAAAATGAC-AACTA
* * *
321 TTTAGACCAAATGATGCGATTTCTCGAGCGTGGAATGTTCAGAAAATTGCTCTAAGGAATGGATC
319 TTTAGACCAAATGATGCAATTTCCCGAGCATGGAATGTTCAGAAAATTGCTCTAAGGAATGGATC
* * *
386 TTGTTGAATACTTTAGGGAACCGATGTTAAAAAATAACTTGTAAAA
384 TTGTTGAATACTTTAGGGAACCAAAGTTAAAAAATAACTCGTAAAA
* * * *
432 GTTTGACAAGTTCAAAAGTTTGTACAA-AGACAAAGTGAGAAACAATTCTCACCTAAATAAGTTT
1 GTTTGACAAGTTCAAAAGTTTGTCCAAGA-AGAAAGAGAGAAACAATTCTCACATAAATAAGTTT
*
496 TTAATTCAAAGAGCAAAACTTTTTTGCAAAATGACAAACTATTTAGACCAAATGATGTGATTTCT
65 TTAATTCAAAGACCAAAACTTTTTTGCAAAATGACAAACTATTTAGACCAAATGATG-GATTTCT
* * *
561 CGAGCATGGAATGTTTGAAAAATTGCTCGTAA-GAATGGATCGTCTCGAATACTTTGAGGATCCA
129 CGAGCATGGAATGTTTGAAAAA-TGCTCG-AAGGAATGGATCGTCTTGAATACTTTAAGGAACCA
* * * * * *
625 AAGTTATCAACGAACTAGTAAAAGTTTGACAAGCTCGTAAGTTCGTCCAAGAACAAAGAGAGA-A
192 AAGCTATAAAAGAACTACTAAAAGTTGGACAAGCTCGGAAGTTCGTCCAAGAACAAAGAGAGATA
*
689 TTAATTCTCACGTAAATAAGTTTTTAATTCAAAGA-TCAAAACTTGTTTACAAAATGAC-A-TAT
257 -CAATTCTCACGTAAATAAGTTTTTAATTCAAAGACT-AAAACTTGTTTACAAAATGACAACTAT
* * * *
751 TTAGATCAAATGATGCAATTTCCCGAGCATGGAATGTTC-GAAAAATTGCTTTATGGAATGGATT
320 TTAGACCAAATGATGCAATTTCCCGAGCATGGAATGTTCAG-AAAATTGCTCTAAGGAATGGATC
*
815 TTGTTGAATGCTTTAGGGAACCAAAGTTAAAAAATAACTCGTAAAA
384 TTGTTGAATACTTTAGGGAACCAAAGTTAAAAAATAACTCGTAAAA
* *** * *
861 GTTTGACCAGTTTGGAAGTTTGTCCAAGAAGAAAGAGAGAAACAATTCTCACGTAAATAAATTTT
1 GTTTGACAAGTTCAAAAGTTTGTCCAAGAAGAAAGAGAGAAACAATTCTCACATAAATAAGTTTT
* * * * *
926 TAATTCAACA-ACCAAAACTTGTTTACAAAATAACAATCTATTTTGACCAAATGATGCGATTTCT
66 TAATTCAA-AGACCAAAACTTTTTTGCAAAATGACAAACTATTTAGACCAAATGATG-GATTTC-
** * * * *
990 TTTTTAGCAAGGAATGTTTGGAAAACTGCTCGAAGGAATGGATCGCCTTGAATGCTTTAAGGAA
128 --TCGAGCATGGAATGTTT-GAAAAATGCTCGAAGGAATGGATCGTCTTGAATACTTTAAGGAA
Statistics
Matches: 525, Mismatches: 78, Indels: 37
0.82 0.12 0.06
Matches are distributed among these distances:
428 1 0.00
429 208 0.40
430 5 0.01
431 64 0.12
432 236 0.45
433 11 0.02
ACGTcount: A:0.38, C:0.15, G:0.18, T:0.29
Consensus pattern (429 bp):
GTTTGACAAGTTCAAAAGTTTGTCCAAGAAGAAAGAGAGAAACAATTCTCACATAAATAAGTTTT
TAATTCAAAGACCAAAACTTTTTTGCAAAATGACAAACTATTTAGACCAAATGATGGATTTCTCG
AGCATGGAATGTTTGAAAAATGCTCGAAGGAATGGATCGTCTTGAATACTTTAAGGAACCAAAGC
TATAAAAGAACTACTAAAAGTTGGACAAGCTCGGAAGTTCGTCCAAGAACAAAGAGAGATACAAT
TCTCACGTAAATAAGTTTTTAATTCAAAGACTAAAACTTGTTTACAAAATGACAACTATTTAGAC
CAAATGATGCAATTTCCCGAGCATGGAATGTTCAGAAAATTGCTCTAAGGAATGGATCTTGTTGA
ATACTTTAGGGAACCAAAGTTAAAAAATAACTCGTAAAA
Done.