Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01009802.1 Kokia drynarioides strain JFW-HI SEQ_124523, 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: 4819
ACGTcount: A:0.31, C:0.19, G:0.18, T:0.33
Found at i:331 original size:29 final size:29
Alignment explanation
Indices: 291--598 Score: 213
Period size: 30 Copynumber: 10.5 Consensus size: 29
281 GAGGTCCCTA
291 AACTATCCAAAAATTCTATTTTTACCCTCG
1 AACT-TCCAAAAATTCTATTTTTACCCTCG
* *
321 AACTT-CAAAAATT-TCATTTCTAACCC-CAA
1 AACTTCCAAAAATTCT-ATTT-TTACCCTC-G
* *
350 AACTTCTAAAAATTCCATTTTTACCCTCG
1 AACTTCCAAAAATTCTATTTTTACCCTCG
* *
379 AACTTTCGAAAA-TCTTATTTTTGACCC-CG
1 AACTTCCAAAAATTC-TATTTTT-ACCCTCG
* * * *
408 AAATTTCCAAAAATTTTGTTTTTACCCTCT
1 -AACTTCCAAAAATTCTATTTTTACCCTCG
* * ***
438 AACTTCCAAAAATCCCATTTTTAACCCAAA
1 AACTTCCAAAAATTCTATTTTT-ACCCTCG
468 AACTTCCAAAAATTAC-ATTTTTACCCTCG
1 AACTTCCAAAAATT-CTATTTTTACCCTCG
* * **
497 AGCTTCCAAAAATCCCT-TTTTTGACCCTAA
1 AACTTCCAAAAAT-TCTATTTTT-ACCCTCG
* * * *
527 AACTTCCAAAAATACCA-TTTTACCCCCA
1 AACTTCCAAAAATTCTATTTTTACCCTCG
555 AACTTCCAAAAATATC-ATTTTTGACCC-CG
1 AACTTCCAAAAAT-TCTATTTTT-ACCCTCG
584 AAACTTCCAAAAATT
1 -AACTTCCAAAAATT
599 ACCTTTTTGC
Statistics
Matches: 218, Mismatches: 39, Indels: 43
0.73 0.13 0.14
Matches are distributed among these distances:
27 1 0.00
28 34 0.16
29 88 0.40
30 93 0.43
31 2 0.01
ACGTcount: A:0.35, C:0.27, G:0.04, T:0.34
Consensus pattern (29 bp):
AACTTCCAAAAATTCTATTTTTACCCTCG
Found at i:561 original size:58 final size:60
Alignment explanation
Indices: 290--673 Score: 353
Period size: 59 Copynumber: 6.5 Consensus size: 60
280 GGAGGTCCCT
* ** * *
290 AAACTATCCAAAAATT-CTATTTTTACCCTCGAACTT-CAAAAATTTCATTTCTAACCCCA
1 AAACT-TCCAAAAATTACCATTTTTACCCTCGAACTTCCAAAAATCCCATTTTTGACCCCA
* * * ** *
349 AAACTTCTAAAAATT-CCATTTTTACCCTCGAACTTTCGAAAATCTTATTTTTGACCCCG
1 AAACTTCCAAAAATTACCATTTTTACCCTCGAACTTCCAAAAATCCCATTTTTGACCCCA
* *** * * *
408 AAATTTCCAAAAATT-TTGTTTTTACCCTCTAACTTCCAAAAATCCCATTTTTAACCCAA
1 AAACTTCCAAAAATTACCATTTTTACCCTCGAACTTCCAAAAATCCCATTTTTGACCCCA
* * *
467 AAACTTCCAAAAATTA-CATTTTTACCCTCGAGCTTCCAAAAATCCCTTTTTTGACCCTA
1 AAACTTCCAAAAATTACCATTTTTACCCTCGAACTTCCAAAAATCCCATTTTTGACCCCA
* * ** *
526 AAACTTCCAAAAA-TACCA-TTTTACCCCCAAACTTCCAAAAATATCATTTTTGACCCCG
1 AAACTTCCAAAAATTACCATTTTTACCCTCGAACTTCCAAAAATCCCATTTTTGACCCCA
* * * * *
584 AAACTTCCAAAAATTACC-TTTTTGCCCTCGGA-TGTCCAAAAA-CTCCATTTTCGACCTCG
1 AAACTTCCAAAAATTACCATTTTTACCCTCGAACT-TCCAAAAATC-CCATTTTTGACCCCA
*
643 AAAC-TCTC-AAAATTACC-CTTTTACCCTCGAA
1 AAACTTC-CAAAAATTACCATTTTTACCCTCGAA
674 TGTCTAAAGA
Statistics
Matches: 269, Mismatches: 48, Indels: 17
0.81 0.14 0.05
Matches are distributed among these distances:
58 98 0.36
59 171 0.64
ACGTcount: A:0.34, C:0.28, G:0.05, T:0.33
Consensus pattern (60 bp):
AAACTTCCAAAAATTACCATTTTTACCCTCGAACTTCCAAAAATCCCATTTTTGACCCCA
Found at i:647 original size:117 final size:115
Alignment explanation
Indices: 290--670 Score: 340
Period size: 117 Copynumber: 3.2 Consensus size: 115
280 GGAGGTCCCT
* * * * *
290 AAACTATCCAAAAATTCTATTTTTACCCTCGAACTT-CAAAAATTTCATTTCTAACCCCAAAACT
1 AAACT-TCCAAAAATACCA-TTTTACCCTCAAACTTCCAAAAATATCATTTTTAACCCCAAAACT
* * * * *
354 TCTAAAAATT-CCATTTTTACCCTCGAACTTTCGAAAA-TCTTATTTTTGACCCCG
64 TCCAAAAATTACC-TTTTTACCCTCGGA-TTCCAAAAACTC-CATTTTTGA-CCCG
* **** * ** *
408 AAATTTCCAAAAATTTTGTTTTTACCCTCTAACTTCCAAAAATCCCATTTTTAACCCAAAAACTT
1 AAACTTCCAAAAA-TACCATTTTACCCTCAAACTTCCAAAAATATCATTTTTAACCCCAAAACTT
* * * *
473 CCAAAAATTACATTTTTACCCTCGAGCTTCCAAAAA-TCCCTTTTTTGACCCTA
65 CCAAAAATTACCTTTTTACCCTCG-GATTCCAAAAACT-CCATTTTTGACCC-G
* * *
526 AAACTTCCAAAAATACCATTTTACCCCCAAACTTCCAAAAATATCATTTTTGACCCCGAAACTTC
1 AAACTTCCAAAAATACCATTTTACCCTCAAACTTCCAAAAATATCATTTTTAACCCCAAAACTTC
* *
591 CAAAAATTACCTTTTTGCCCTCGGATGTCCAAAAACTCCATTTTCGACCTCG
66 CAAAAATTACCTTTTTACCCTCGGAT-TCCAAAAACTCCATTTTTGACC-CG
* *
643 AAAC-TCTCAAAATTACCCTTTTACCCTC
1 AAACTTC-CAAAAATACCATTTTACCCTC
671 GAATGTCTAA
Statistics
Matches: 214, Mismatches: 39, Indels: 21
0.78 0.14 0.08
Matches are distributed among these distances:
116 4 0.02
117 128 0.60
118 80 0.37
119 2 0.01
ACGTcount: A:0.34, C:0.29, G:0.04, T:0.33
Consensus pattern (115 bp):
AAACTTCCAAAAATACCATTTTACCCTCAAACTTCCAAAAATATCATTTTTAACCCCAAAACTTC
CAAAAATTACCTTTTTACCCTCGGATTCCAAAAACTCCATTTTTGACCCG
Found at i:699 original size:58 final size:59
Alignment explanation
Indices: 427--723 Score: 147
Period size: 59 Copynumber: 5.1 Consensus size: 59
417 AAAATTTTGT
* * *
427 TTTTACCCTCTAACT-TCCAAAAA-TCCCATTTTTAACC-CAAAAACTTC-CAAAAATTA-CA
1 TTTTACCCTCGAA-TGTCCAAAAACT-CCATTTTCAACCTC--AAACTTCTCCAAAATTACCA
* * * * * *
485 TTTTTACCCTCGAGCT-TCCAAAAA-TCCCTTTTTTGACCCTAAAAC-T-TCCAAAAATACCA
1 -TTTTACCCTCGA-ATGTCCAAAAACT-CC-ATTTTCAACCTCAAACTTCTCCAAAATTACCA
* * * ** * * *
544 TTTTACCCCCAAACT-TCCAAAAA-TATCATTTTTGACCCCGAAACTTC-CAAAAATTACCT
1 TTTTACCCTCGAA-TGTCCAAAAACT-CCATTTTCAACCTC-AAACTTCTCCAAAATTACCA
* * * *
603 TTTTGCCCTCGGATGTCCAAAAACTCCATTTTCGACCTCGAAAC-TCT-CAAAATTACCC
1 TTTTACCCTCGAATGTCCAAAAACTCCATTTTCAACCTC-AAACTTCTCCAAAATTACCA
* * * *
661 TTTTACCCTCGAATGTCTAAAGATTCCATTCTT-AACCTCAAACTTTTCCAAAATTACCA
1 TTTTACCCTCGAATGTCCAAAAACTCCATT-TTCAACCTCAAACTTCTCCAAAATTACCA
720 TTTT
1 TTTT
724 GCCTCCGGGT
Statistics
Matches: 184, Mismatches: 39, Indels: 30
0.73 0.15 0.12
Matches are distributed among these distances:
57 10 0.05
58 77 0.42
59 89 0.48
60 8 0.04
ACGTcount: A:0.33, C:0.30, G:0.05, T:0.33
Consensus pattern (59 bp):
TTTTACCCTCGAATGTCCAAAAACTCCATTTTCAACCTCAAACTTCTCCAAAATTACCA
Done.