Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012367.1 Kokia drynarioides strain JFW-HI SEQ_127371, 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, 890
Length: 1484
ACGTcount: A:0.36, C:0.13, G:0.18, T:0.27
Warning! 105 characters in sequence are not A, C, G, or T
Found at i:393 original size:216 final size:216
Alignment explanation
Indices: 3--852 Score: 1029
Period size: 216 Copynumber: 3.9 Consensus size: 216
1 AT
*
3 GAGAGAAACAACTCTCACGTAAATAAGTTTTTCATTCAAAGACCAAAAGTTGTTTAGAAAATGAC
1 GAGAGAAACAACTCTCACGTAAATAAGTTTTTAATTCAAAGACCAAAAGTTGTTTAGAAAATGAC
* * * * * **
68 AAAGTATTTAGTCCAAATAATGCGATTTCCCGAGCATGGAATG-TTGAAAAAATTGCTCTAAGGA
66 AAACTATTTAGACAAAATGATGCGATTTCCCGAGCATGGAATGTTTG-GAAAATTGCTGGAAGGA
* * * * * * * *
132 ATGGATTGTCTTGAATACTTTAA-GAAATCGAAGTTATAGAAGAACTCGTAAGAGTTTGTCAAGT
130 ATGGATCGTCGTGAATACTTTAAGGAACT-GAAGTTCTAAAAGAACTCGTAAAACTTCGTCAAGT
* * *
196 TTGGAAGTTCGTCTAAGAACCAA
194 TCGGAAGTTCGTCCAAGAACAAA
* * * *
219 GACAGAAACAACTCTCACATAAATAGGTTTTTAATTCAAAGACCAAAAGTTGTGTAGAAAATGAC
1 GAGAGAAACAACTCTCACGTAAATAAGTTTTTAATTCAAAGACCAAAAGTTGTTTAGAAAATGAC
* * *
284 AAACTATTTGGACAAAATGATGCGATTTCCCGTGCATGGAATGTTTGGAAAATTGATGGAAGGAA
66 AAACTATTTAGACAAAATGATGCGATTTCCCGAGCATGGAATGTTTGGAAAATTGCTGGAAGGAA
*
349 TGGATCGTCGTGAATACTTTAAGGAACTGAAGTTCTAAAAGAACTCGTAAAACTTCGTAAAGTTC
131 TGGATCGTCGTGAATACTTTAAGGAACTGAAGTTCTAAAAGAACTCGTAAAACTTCGTCAAGTTC
*
414 GAAAGTTCGTCCAAGAACAAA
196 GGAAGTTCGTCCAAGAACAAA
* * * * *** *
435 GGGAGAAACTACTCTCACGTAATTAACTTTTTAATTTGTAGACCAAAAGTTGTTTACAAAATGAC
1 GAGAGAAACAACTCTCACGTAAATAAGTTTTTAATTCAAAGACCAAAAGTTGTTTAGAAAATGAC
* ** * * * * **
500 AAACTATTTAGACTAAATTTTGTGATATTCACGAGCTTGAAATGTTCAGAAAATTGCTGGAAGGA
66 AAACTATTTAGACAAAATGATGCGAT-TTCCCGAGCATGGAATGTTTGGAAAATTGCTGGAAGGA
* *
565 ATGGATTGTCGTGAATACTTTGAGGAACTGAAGTTCTAAAAGAACTCGTAAAACTTCGTCAAGTT
130 ATGGATCGTCGTGAATACTTTAAGGAACTGAAGTTCTAAAAGAACTCGTAAAACTTCGTCAAGTT
*
630 CGGAAGTTCATCCAAGAACAAA
195 CGGAAGTTCGTCCAAGAACAAA
* * * *
652 GAGAGAAACAACGAACTCGTAAATAACTTTTAATTTATAGGTTTTTAATTAAAAGACCAAAAGTT
1 GAGAG--A-AAC-AACTC-----TCAC--GTAA---ATAAGTTTTTAATTCAAAGACCAAAAGTT
**
717 GTTTAGAAAATGACAAACTATTTAGACAAAATGATGCGATTTCCCGTCCATGGAATGTTTGGAAA
52 GTTTAGAAAATGACAAACTATTTAGACAAAATGATGCGATTTCCCGAGCATGGAATGTTTGGAAA
* *
782 ATTGCTAGAAGGAATGGATCGTCATGAATACTTTAAGGAACTGAAGTTCTAAAAGAACTCGTAAA
117 ATTGCTGGAAGGAATGGATCGTCGTGAATACTTTAAGGAACTGAAGTTCTAAAAGAACTCGTAAA
847 ACTTCG
182 ACTTCG
853 NNNNNNNNNN
Statistics
Matches: 534, Mismatches: 83, Indels: 20
0.84 0.13 0.03
Matches are distributed among these distances:
216 253 0.47
217 124 0.23
219 1 0.00
220 3 0.01
221 4 0.01
226 3 0.01
228 3 0.01
230 85 0.16
231 58 0.11
ACGTcount: A:0.39, C:0.14, G:0.19, T:0.28
Consensus pattern (216 bp):
GAGAGAAACAACTCTCACGTAAATAAGTTTTTAATTCAAAGACCAAAAGTTGTTTAGAAAATGAC
AAACTATTTAGACAAAATGATGCGATTTCCCGAGCATGGAATGTTTGGAAAATTGCTGGAAGGAA
TGGATCGTCGTGAATACTTTAAGGAACTGAAGTTCTAAAAGAACTCGTAAAACTTCGTCAAGTTC
GGAAGTTCGTCCAAGAACAAA
Found at i:824 original size:447 final size:432
Alignment explanation
Indices: 5--852 Score: 1158
Period size: 447 Copynumber: 1.9 Consensus size: 432
1 ATGA
* * *
5 GAGAAACAACTCTCACGTAAATAAGTTTTTCATTCAAAGACCAAAAGTTGTTTAGAAAATGACAA
1 GAGAAACAACTCTCACGTAAATAACTTTTTAATTCAAAGACCAAAAGTTGTTTACAAAATGACAA
* * * * * *
70 AGTATTTAGTCCAAATAATGCGATTTCCCGAGCATGGAATGTTGAAAAAATTGCTCTAAGGAATG
66 ACTATTTAGACCAAATAATGCGATTTCACGAGCATGAAATGTTCAAAAAATTGCTCGAAGGAATG
* * * * * *
135 GATTGTCTTGAATACTTTAAGAAATCGAAGTTATAGAAGAACTCGTAAGAGTTTGTCAAGTTTGG
131 GATTGTCGTGAATACTTTAAGAAATCGAAGTTATAAAAGAACTCGTAAAACTTCGTCAAGTTCGG
* * * * *
200 AAGTTCGTCTAAGAACCAAGACAGAAACAACTCTCACATAAATAGGTTTTTAATTCAAAGACCAA
196 AAGTTCATCCAAGAACAAAGACAGAAACAACTCTAACATAAATAGGTTTTTAATTAAAAGACCAA
* *
265 AAGTTGTGTAGAAAATGACAAACTATTTGGACAAAATGATGCGATTTCCCGTGCATGGAATGTTT
261 AAGTTGTGTAGAAAATGACAAACTATTTAGACAAAATGATGCGATTTCCCGTCCATGGAATGTTT
* *
330 GGAAAATTGATGGAAGGAATGGATCGTCGTGAATACTTTAAGGAACTGAAGTTCTAAAAGAACTC
326 GGAAAATTGATAGAAGGAATGGATCGTCATGAATACTTTAAGGAACTGAAGTTCTAAAAGAACTC
395 GTAAAACTTCGTAAAGTTCGAAAGTTCGTCCAAGAACAAAGG
391 GTAAAACTTCGTAAAGTTCGAAAGTTCGTCCAAGAACAAAGG
* * ***
437 GAGAAACTACTCTCACGTAATTAACTTTTTAATTTGTAGACCAAAAGTTGTTTACAAAATGACAA
1 GAGAAACAACTCTCACGTAAATAACTTTTTAATTCAAAGACCAAAAGTTGTTTACAAAATGACAA
* ** * * * *
502 ACTATTTAGACTAAATTTTGTGATATTCACGAGCTTGAAATGTTCAGAAAATTGCTGGAAGGAAT
66 ACTATTTAGACCAAATAATGCGAT-TTCACGAGCATGAAATGTTCAAAAAATTGCTCGAAGGAAT
* * *
567 GGATTGTCGTGAATACTTTGAGGAA-CTGAAGTTCTAAAAGAACTCGTAAAACTTCGTCAAGTTC
130 GGATTGTCGTGAATACTTTAAGAAATC-GAAGTTATAAAAGAACTCGTAAAACTTCGTCAAGTTC
* *
631 GGAAGTTCATCCAAGAACAAAGAGAGAAACAACGAACTCGTAAATAACTTTTAATTTATAGGTTT
194 GGAAGTTCATCCAAGAACAAAGACAG--A-AAC-AACTC-----TAAC--ATAA---ATAGGTTT
*
696 TTAATTAAAAGACCAAAAGTTGTTTAGAAAATGACAAACTATTTAGACAAAATGATGCGATTTCC
245 TTAATTAAAAGACCAAAAGTTGTGTAGAAAATGACAAACTATTTAGACAAAATGATGCGATTTCC
*
761 CGTCCATGGAATGTTTGGAAAATTGCTAGAAGGAATGGATCGTCATGAATACTTTAAGGAACTGA
310 CGTCCATGGAATGTTTGGAAAATTGATAGAAGGAATGGATCGTCATGAATACTTTAAGGAACTGA
826 AGTTCTAAAAGAACTCGTAAAACTTCG
375 AGTTCTAAAAGAACTCGTAAAACTTCG
853 NNNNNNNNNN
Statistics
Matches: 357, Mismatches: 43, Indels: 17
0.86 0.10 0.04
Matches are distributed among these distances:
432 76 0.21
433 108 0.30
435 1 0.00
436 3 0.01
437 5 0.01
442 3 0.01
444 3 0.01
447 158 0.44
ACGTcount: A:0.39, C:0.14, G:0.19, T:0.28
Consensus pattern (432 bp):
GAGAAACAACTCTCACGTAAATAACTTTTTAATTCAAAGACCAAAAGTTGTTTACAAAATGACAA
ACTATTTAGACCAAATAATGCGATTTCACGAGCATGAAATGTTCAAAAAATTGCTCGAAGGAATG
GATTGTCGTGAATACTTTAAGAAATCGAAGTTATAAAAGAACTCGTAAAACTTCGTCAAGTTCGG
AAGTTCATCCAAGAACAAAGACAGAAACAACTCTAACATAAATAGGTTTTTAATTAAAAGACCAA
AAGTTGTGTAGAAAATGACAAACTATTTAGACAAAATGATGCGATTTCCCGTCCATGGAATGTTT
GGAAAATTGATAGAAGGAATGGATCGTCATGAATACTTTAAGGAACTGAAGTTCTAAAAGAACTC
GTAAAACTTCGTAAAGTTCGAAAGTTCGTCCAAGAACAAAGG
Done.