Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01009779.1 Kokia drynarioides strain JFW-HI SEQ_124500, 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: 2447
ACGTcount: A:0.36, C:0.13, G:0.18, T:0.27
Warning! 143 characters in sequence are not A, C, G, or T
Found at i:479 original size:217 final size:216
Alignment explanation
Indices: 103--1551 Score: 1936
Period size: 217 Copynumber: 6.7 Consensus size: 216
93 AGAACTCGTA
* ** * * * * *
103 AAACAACTATCACGTAAATAGGTTGTTAATTAAAAGACCAAAAGTTGTTTAGAAAATGACAATCT
1 AAACAACGATCACGTAAATAACTTTTTAATTTATAGACCAAAAGTTGTTTACAAAATGACAAACT
* * *
168 ATTTAGACAAAATGATGCGATTTCCCGTGCATGGAATGTTTGGAAAATTGCTGGAAGGAATGGAT
66 ATTTAGACTAAATGATGCGATTTCACGAGCATGGAATGTTTGGAAAATTGCTGGAAGGAATGGAT
* *
233 CGTCGTGAATACTTTAAGGAACTGAAGTTCTAAAAGAACTGGTAAAACTTCGTCAAGTTCGGAAG
131 TGTCGTGAATACTTTAAGGAACTGAAGTTCTAAAAGAACTCGTAAAACTTCGTCAAGTTCGGAAG
*
298 TTCGTCCAAGAACAAAGGGAG
196 TTCGTCCAAGAACAAAGAGAG
* * *
319 AAACAACGATCATGTAAATAACTTTTTAATTTGTAGACCAAAAGTTGTTTACAAAATAACAAACT
1 AAACAACGATCACGTAAATAACTTTTTAATTTATAGACCAAAAGTTGTTTACAAAATGACAAACT
* * * * * ** * * *
384 ATTTAGACTAAATTATGTGATTTTCCCGAGCATGAAATCTTCAGAAAATTGCTCGAAGCAATGAA
66 ATTTAGACTAAATGATGCGA-TTTCACGAGCATGGAATGTTTGGAAAATTGCTGGAAGGAATGGA
* * * * *
449 TCGTCATGAATACTTTATGGAACTGAAGTTCTAAAAGAACTCGTAAAACTTCGTAAAGTTCGAAA
130 TTGTCGTGAATACTTTAAGGAACTGAAGTTCTAAAAGAACTCGTAAAACTTCGTCAAGTTCGGAA
*
514 GTTCGTCCAAGAACAAAGGGAG
195 GTTCGTCCAAGAACAAAGAGAG
* ** *
536 AAACTACTCTCACGTAAATAACTTTTTAATTTGTAGACCAAAAGTTGTTTACAAAATGACAAACT
1 AAACAACGATCACGTAAATAACTTTTTAATTTATAGACCAAAAGTTGTTTACAAAATGACAAACT
** * * * * **
601 ATTTAGACTAAATTTTGTGATATTCAGGAGCTTGAAATGTTCAGAAAATTGCTGGAAGGAATGGA
66 ATTTAGACTAAATGATGCGAT-TTCACGAGCATGGAATGTTTGGAAAATTGCTGGAAGGAATGGA
*
666 TTGTCGTGAATACTTTGAGGAACTGAAGTTCTAAAAGAACTCGTAAAACTTCGTCAAGTTCGGAA
130 TTGTCGTGAATACTTTAAGGAACTGAAGTTCTAAAAGAACTCGTAAAACTTCGTCAAGTTCGGAA
*
731 GTTCATCCAAGAACAAAGAGAG
195 GTTCGTCCAAGAACAAAGAGAG
* *
753 AAACAACGAACTCGTAAATAAC-TTTTAATTTATAGACCAAAAGTTGTTTACAAAATGACAAACT
1 AAACAACGATCACGTAAATAACTTTTTAATTTATAGACCAAAAGTTGTTTACAAAATGACAAACT
* * * * *
817 ATTTAGACCAAAGGATGCGATTTCACGAGCGTGGAATGTTTGGAAAATTGCTTGATGGAATGGAT
66 ATTTAGACTAAATGATGCGATTTCACGAGCATGGAATGTTTGGAAAATTGCTGGAAGGAATGGAT
* * * * * * *
882 TGTCATGAATACTTTAAGGAA-TGAATGTTATAGATGAACTGGTAAAAGTT-TTCCAAGTT-GAG
131 TGTCGTGAATACTTTAAGGAACTGAA-GTTCTAAAAGAACTCGTAAAACTTCGT-CAAGTTCG-G
* * *
944 AAGTTCGTCCGAGAACCATGAGAG
193 AAGTTCGTCCAAGAACAAAGAGAG
** * * * * *
968 AAACAACTCTCACGTAAATAAGTTTTTAATTCAAAGACCAAAAGTTGTGTAGAAAATGACAAACT
1 AAACAACGATCACGTAAATAACTTTTTAATTTATAGACCAAAAGTTGTTTACAAAATGACAAACT
* * * *
1033 ATTTGGACAAAATGATGCGATTTCCCGTGCATGGAATGTTTGGAAAATTGCTGGAAGGAATGGAT
66 ATTTAGACTAAATGATGCGATTTCACGAGCATGGAATGTTTGGAAAATTGCTGGAAGGAATGGAT
* * *
1098 CGTCGTGAATACTTTAAGGAACTGAAGTTCTAAAAGAACTCGTAAAACTTCGTAAAGTTCGAAAG
131 TGTCGTGAATACTTTAAGGAACTGAAGTTCTAAAAGAACTCGTAAAACTTCGTCAAGTTCGGAAG
*
1163 TTCGTCCAAGAACAAAGGGAG
196 TTCGTCCAAGAACAAAGAGAG
* ** *
1184 AAACTACTCTCACGTAAATAACTTTTTAATTTGTAGACCAAAAGTTGTTTACAAAATGACAAACT
1 AAACAACGATCACGTAAATAACTTTTTAATTTATAGACCAAAAGTTGTTTACAAAATGACAAACT
** * * * **
1249 ATTTAGACTAAATTTTGTGATATTCACGAGCTTGAAATGTTCAGAAAATTGCTGGAAGGAATGGA
66 ATTTAGACTAAATGATGCGAT-TTCACGAGCATGGAATGTTTGGAAAATTGCTGGAAGGAATGGA
*
1314 TTGTCGTGAATACTTTGAGGAACTGAAGTTCTAAAAGAACTCGTAAAACTTCGTCAAGTTCGGAA
130 TTGTCGTGAATACTTTAAGGAACTGAAGTTCTAAAAGAACTCGTAAAACTTCGTCAAGTTCGGAA
*
1379 GTTCATCCAAGAACAAAGAGAG
195 GTTCGTCCAAGAACAAAGAGAG
* *
1401 AAACAACGAACTCGTAAATAAC-TTTTAATTTATAGACCAAAAGTTGTTTACAAAATGACAAACT
1 AAACAACGATCACGTAAATAACTTTTTAATTTATAGACCAAAAGTTGTTTACAAAATGACAAACT
* *
1465 ATTTAGACCAAATGATGCGATTTCACGAGCATGGAATGTTTGGAAAATTGCTTGAAGGAATGGAT
66 ATTTAGACTAAATGATGCGATTTCACGAGCATGGAATGTTTGGAAAATTGCTGGAAGGAATGGAT
*
1530 TGTCATGAATACTTTAAGGAAC
131 TGTCGTGAATACTTTAAGGAAC
1552 GAATGTTATA
Statistics
Matches: 1073, Mismatches: 150, Indels: 21
0.86 0.12 0.02
Matches are distributed among these distances:
214 6 0.01
215 178 0.17
216 419 0.39
217 470 0.44
ACGTcount: A:0.38, C:0.14, G:0.20, T:0.28
Consensus pattern (216 bp):
AAACAACGATCACGTAAATAACTTTTTAATTTATAGACCAAAAGTTGTTTACAAAATGACAAACT
ATTTAGACTAAATGATGCGATTTCACGAGCATGGAATGTTTGGAAAATTGCTGGAAGGAATGGAT
TGTCGTGAATACTTTAAGGAACTGAAGTTCTAAAAGAACTCGTAAAACTTCGTCAAGTTCGGAAG
TTCGTCCAAGAACAAAGAGAG
Found at i:1373 original size:648 final size:649
Alignment explanation
Indices: 128--1601 Score: 2461
Period size: 648 Copynumber: 2.3 Consensus size: 649
118 AAATAGGTTG
* * * * * *
128 TTAATTAAAAGACCAAAAGTTGTTTAGAAAATGACAATCTATTTAGACAAAATGATGCGATTTCC
1 TTAATTTATAGACCAAAAGTTGTTTACAAAATGACAAACTATTTAGACCAAATGATGCGATTTCA
* * * *
193 CGTGCATGGAATGTTTGGAAAATTGCTGGAAGGAATGGATCGTCGTGAATACTTTAAGGAACTGA
66 CGAGCATGGAATGTTTGGAAAATTGCTTGAAGGAATGGATTGTCATGAATACTTTAAGGAA-TGA
* * * * * *
258 A-GTTCTAAAAGAACTGGTAAAACTTCGT-CAAGTTCG-GAAGTTCGTCCAAGAACAAAGGGAGA
130 ATGTTATAGATGAACTGGTAAAAGTT-TTCCAAGTT-GAGAAGTTCGTCCAAGAACAAAGAGAGA
* *** *
320 AACAACGATCATGTAAATAACTTTTTAATTTGTAGACCAAAAGTTGTTTACAAAATAACAAACTA
193 AACAACGATCACGTAAATAACTTTTTAATTCAAAGACCAAAAGTTGTGTACAAAATAACAAACTA
* * *
385 TTTAGACTAAATTATGTGATTTTCCCGAGCATGAAATCTTCAGAAAATTGCTCGAAGCAATGAAT
258 TTTAGACAAAATGATGCGATTTTCCCGAGCATGAAATCTTCAGAAAATTGCTCGAAGCAATGAAT
*
450 CGTCATGAATACTTTATGGAACTGAAGTTCTAAAAGAACTCGTAAAACTTCGTAAAGTTCGAAAG
323 CGTCATGAATACTTTAAGGAACTGAAGTTCTAAAAGAACTCGTAAAACTTCGTAAAGTTCGAAAG
515 TTCGTCCAAGAACAAAGGGAGAAACTACTCTCACGTAAATAACTTTTTAATTTGTAGACCAAAAG
388 TTCGTCCAAGAACAAAGGGAGAAACTACTCTCACGTAAATAACTTTTTAATTTGTAGACCAAAAG
*
580 TTGTTTACAAAATGACAAACTATTTAGACTAAATTTTGTGATATTCAGGAGCTTGAAATGTTCAG
453 TTGTTTACAAAATGACAAACTATTTAGACTAAATTTTGTGATATTCACGAGCTTGAAATGTTCAG
645 AAAATTGCTGGAAGGAATGGATTGTCGTGAATACTTTGAGGAACTGAAGTTCTAAAAGAACTCGT
518 AAAATTGCTGGAAGGAATGGATTGTCGTGAATACTTTGAGGAACTGAAGTTCTAAAAGAACTCGT
710 AAAACTTCGTCAAGTTCGGAAGTTCATCCAAGAACAAAGAGAGAAACAACGAACTCGTAAATAAC
583 AAAACTTCGTCAAGTTCGGAAGTTCATCCAAGAACAAAGAGAGAAACAACGAACTCGTAAATAAC
775 TT
648 TT
*
777 TTAATTTATAGACCAAAAGTTGTTTACAAAATGACAAACTATTTAGACCAAAGGATGCGATTTCA
1 TTAATTTATAGACCAAAAGTTGTTTACAAAATGACAAACTATTTAGACCAAATGATGCGATTTCA
* *
842 CGAGCGTGGAATGTTTGGAAAATTGCTTGATGGAATGGATTGTCATGAATACTTTAAGGAATGAA
66 CGAGCATGGAATGTTTGGAAAATTGCTTGAAGGAATGGATTGTCATGAATACTTTAAGGAATGAA
* * *
907 TGTTATAGATGAACTGGTAAAAGTTTTCCAAGTTGAGAAGTTCGTCCGAGAACCATGAGAGAAAC
131 TGTTATAGATGAACTGGTAAAAGTTTTCCAAGTTGAGAAGTTCGTCCAAGAACAAAGAGAGAAAC
** * * *
972 AACTCTCACGTAAATAAGTTTTTAATTCAAAGACCAAAAGTTGTGTAGAAAATGACAAACTATTT
196 AACGATCACGTAAATAACTTTTTAATTCAAAGACCAAAAGTTGTGTACAAAATAACAAACTATTT
* * * * ** * * *
1037 GGACAAAATGATGCGA-TTTCCCGTGCATGGAATGTTTGGAAAATTGCTGGAAGGAATGGATCGT
261 AGACAAAATGATGCGATTTTCCCGAGCATGAAATCTTCAGAAAATTGCTCGAAGCAATGAATCGT
*
1101 CGTGAATACTTTAAGGAACTGAAGTTCTAAAAGAACTCGTAAAACTTCGTAAAGTTCGAAAGTTC
326 CATGAATACTTTAAGGAACTGAAGTTCTAAAAGAACTCGTAAAACTTCGTAAAGTTCGAAAGTTC
1166 GTCCAAGAACAAAGGGAGAAACTACTCTCACGTAAATAACTTTTTAATTTGTAGACCAAAAGTTG
391 GTCCAAGAACAAAGGGAGAAACTACTCTCACGTAAATAACTTTTTAATTTGTAGACCAAAAGTTG
1231 TTTACAAAATGACAAACTATTTAGACTAAATTTTGTGATATTCACGAGCTTGAAATGTTCAGAAA
456 TTTACAAAATGACAAACTATTTAGACTAAATTTTGTGATATTCACGAGCTTGAAATGTTCAGAAA
1296 ATTGCTGGAAGGAATGGATTGTCGTGAATACTTTGAGGAACTGAAGTTCTAAAAGAACTCGTAAA
521 ATTGCTGGAAGGAATGGATTGTCGTGAATACTTTGAGGAACTGAAGTTCTAAAAGAACTCGTAAA
1361 ACTTCGTCAAGTTCGGAAGTTCATCCAAGAACAAAGAGAGAAACAACGAACTCGTAAATAACTT
586 ACTTCGTCAAGTTCGGAAGTTCATCCAAGAACAAAGAGAGAAACAACGAACTCGTAAATAACTT
1425 TTAATTTATAGACCAAAAGTTGTTTACAAAATGACAAACTATTTAGACCAAATGATGCGATTTCA
1 TTAATTTATAGACCAAAAGTTGTTTACAAAATGACAAACTATTTAGACCAAATGATGCGATTTCA
*
1490 CGAGCATGGAATGTTTGGAAAATTGCTTGAAGGAATGGATTGTCATGAATACTTTAAGGAACGAA
66 CGAGCATGGAATGTTTGGAAAATTGCTTGAAGGAATGGATTGTCATGAATACTTTAAGGAATGAA
1555 TGTTATAGATGAACTGGTAAAAGTTTTCCAAGTTGAGAAGTTCGTCC
131 TGTTATAGATGAACTGGTAAAAGTTTTCCAAGTTGAGAAGTTCGTCC
1602 NNNNNNNNNN
Statistics
Matches: 771, Mismatches: 51, Indels: 7
0.93 0.06 0.01
Matches are distributed among these distances:
648 540 0.70
649 231 0.30
ACGTcount: A:0.38, C:0.14, G:0.20, T:0.28
Consensus pattern (649 bp):
TTAATTTATAGACCAAAAGTTGTTTACAAAATGACAAACTATTTAGACCAAATGATGCGATTTCA
CGAGCATGGAATGTTTGGAAAATTGCTTGAAGGAATGGATTGTCATGAATACTTTAAGGAATGAA
TGTTATAGATGAACTGGTAAAAGTTTTCCAAGTTGAGAAGTTCGTCCAAGAACAAAGAGAGAAAC
AACGATCACGTAAATAACTTTTTAATTCAAAGACCAAAAGTTGTGTACAAAATAACAAACTATTT
AGACAAAATGATGCGATTTTCCCGAGCATGAAATCTTCAGAAAATTGCTCGAAGCAATGAATCGT
CATGAATACTTTAAGGAACTGAAGTTCTAAAAGAACTCGTAAAACTTCGTAAAGTTCGAAAGTTC
GTCCAAGAACAAAGGGAGAAACTACTCTCACGTAAATAACTTTTTAATTTGTAGACCAAAAGTTG
TTTACAAAATGACAAACTATTTAGACTAAATTTTGTGATATTCACGAGCTTGAAATGTTCAGAAA
ATTGCTGGAAGGAATGGATTGTCGTGAATACTTTGAGGAACTGAAGTTCTAAAAGAACTCGTAAA
ACTTCGTCAAGTTCGGAAGTTCATCCAAGAACAAAGAGAGAAACAACGAACTCGTAAATAACTT
Done.