Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012554.1 Kokia drynarioides strain JFW-HI SEQ_127563, 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: 17272
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.33
Found at i:5158 original size:24 final size:24
Alignment explanation
Indices: 5079--5158 Score: 70
Period size: 24 Copynumber: 3.3 Consensus size: 24
5069 ATGTGACTAC
* * **
5079 TCCAAAGAAACCAAGTGTGGGAAA
1 TCCAAGGAGACCAAGTGTGAAAAA
* * * * *
5103 TCCGAGCAGATCAGGTGTGAAATA
1 TCCAAGGAGACCAAGTGTGAAAAA
*
5127 TCCCAGGAGACCAAGTGTGAAAAA
1 TCCAAGGAGACCAAGTGTGAAAAA
5151 TCCAAGGA
1 TCCAAGGA
5159 AAGATGAAAA
Statistics
Matches: 41, Mismatches: 15, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
24 41 1.00
ACGTcount: A:0.40, C:0.19, G:0.26, T:0.15
Consensus pattern (24 bp):
TCCAAGGAGACCAAGTGTGAAAAA
Found at i:13337 original size:23 final size:24
Alignment explanation
Indices: 13307--13375 Score: 72
Period size: 23 Copynumber: 3.0 Consensus size: 24
13297 TTTTATTATT
*
13307 TTAAATTTAGATTT-ATTTTAAAT
1 TTAAATTTAGATTTAAATTTAAAT
* *
13330 TTAGATTTA-TTTTAAATTTAAAT
1 TTAAATTTAGATTTAAATTTAAAT
*
13353 TTAAATTT-GATTTCAAAATTAAA
1 TTAAATTTAGATTT-AAATTTAAA
13376 AAAGTCCAAA
Statistics
Matches: 37, Mismatches: 6, Indels: 5
0.77 0.12 0.10
Matches are distributed among these distances:
22 3 0.08
23 26 0.70
24 8 0.22
ACGTcount: A:0.42, C:0.01, G:0.04, T:0.52
Consensus pattern (24 bp):
TTAAATTTAGATTTAAATTTAAAT
Found at i:13348 original size:7 final size:6
Alignment explanation
Indices: 13306--13360 Score: 60
Period size: 6 Copynumber: 9.5 Consensus size: 6
13296 TTTTTATTAT
* * * *
13306 TTTAAA TTTAGA TTT-AT TTTAAA TTTAGA TTT-AT TTTAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
13352 TTTAAA TTT
1 TTTAAA TTT
13361 GATTTCAAAA
Statistics
Matches: 39, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
5 6 0.15
6 33 0.85
ACGTcount: A:0.38, C:0.00, G:0.04, T:0.58
Consensus pattern (6 bp):
TTTAAA
Found at i:13365 original size:17 final size:17
Alignment explanation
Indices: 13302--13355 Score: 99
Period size: 17 Copynumber: 3.2 Consensus size: 17
13292 CTTTTTTTTA
13302 TTATTTTAAATTTAGAT
1 TTATTTTAAATTTAGAT
13319 TTATTTTAAATTTAGAT
1 TTATTTTAAATTTAGAT
*
13336 TTATTTTAAATTTAAAT
1 TTATTTTAAATTTAGAT
13353 TTA
1 TTA
13356 AATTTGATTT
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
17 36 1.00
ACGTcount: A:0.37, C:0.00, G:0.04, T:0.59
Consensus pattern (17 bp):
TTATTTTAAATTTAGAT
Found at i:15492 original size:30 final size:29
Alignment explanation
Indices: 15238--15512 Score: 276
Period size: 29 Copynumber: 9.5 Consensus size: 29
15228 AAACTATCTG
* *
15238 AAAATTACCA-TTTTACCCCTAAACTTCTA
1 AAAATT-CCATTTTTACCCCAAAACTTCCA
* *
15267 AAAA-TCTCATTTTTGACCCTAAAACATCCA
1 AAAATTC-CATTTTT-ACCCCAAAACTTCCA
* *
15297 AAAATTAACA-TTTTACCCCTAAACTTCCA
1 AAAATT-CCATTTTTACCCCAAAACTTCCA
* *
15326 AAAATCCCATTTTTGACCTCAAAACTTCCA
1 AAAATTCCATTTTT-ACCCCAAAACTTCCA
15356 AAAATTCCA-TTTTACCCC-AAACTTCCA
1 AAAATTCCATTTTTACCCCAAAACTTCCA
* *
15383 AAAATCCCATTTTGACCCCAAAACTTCCA
1 AAAATTCCATTTTTACCCCAAAACTTCCA
* *
15412 AAAATTTCATTTTTACCCTC-AAACTTCTA
1 AAAATTCCATTTTTACCC-CAAAACTTCCA
* * *
15441 AATATCCCATTTTTACCCCGAAACTTCCA
1 AAAATTCCATTTTTACCCCAAAACTTCCA
* **
15470 AAAATTCTATTTTTACCCCCGAACTTCCA
1 AAAATTCCATTTTTACCCCAAAACTTCCA
15499 AAAA-TCTCATTTTT
1 AAAATTC-CATTTTT
15513 GATCCCGAAA
Statistics
Matches: 204, Mismatches: 30, Indels: 24
0.79 0.12 0.09
Matches are distributed among these distances:
27 18 0.09
28 20 0.10
29 122 0.60
30 41 0.20
31 3 0.01
ACGTcount: A:0.36, C:0.29, G:0.02, T:0.33
Consensus pattern (29 bp):
AAAATTCCATTTTTACCCCAAAACTTCCA
Found at i:15549 original size:58 final size:58
Alignment explanation
Indices: 15238--15547 Score: 348
Period size: 58 Copynumber: 5.3 Consensus size: 58
15228 AAACTATCTG
* * * *
15238 AAAATTACCATTTTACCCCTAAACTTCTAAAAATCTCATTTTTGACCCTAAAACATCCA
1 AAAATTACCATTTTACCCCCAAACTTCCAAAAATCCCATTTTTGACCC-AAAACTTCCA
* *
15297 AAAATTAACATTTTACCCCTAAACTTCCAAAAATCCCATTTTTGACCTCAAAACTTCCA
1 AAAATTACCATTTTACCCCCAAACTTCCAAAAATCCCATTTTTGACC-CAAAACTTCCA
15356 AAAATT-CCATTTTA-CCCCAAACTTCCAAAAATCCCA-TTTTGACCCCAAAACTTCCA
1 AAAATTACCATTTTACCCCCAAACTTCCAAAAATCCCATTTTTGA-CCCAAAACTTCCA
* * * * *
15412 AAAATT-TCATTTTTACCCTCAAACTTCTAAATATCCCATTTTT-ACCCCGAAACTTCCA
1 AAAATTACCA-TTTTACCCCCAAACTTCCAAAAATCCCATTTTTGA-CCCAAAACTTCCA
* * * *
15470 AAAATT-CTATTTTTACCCCCGAACTTCCAAAAATCTCATTTTTGATCCCGAAAC-TCTC-
1 AAAATTACCA-TTTTACCCCCAAACTTCCAAAAATCCCATTTTTGA-CCCAAAACTTC-CA
*
15528 AAAATTACCCTTTTACCCCC
1 AAAATTACCATTTTACCCCC
15548 GATGTCTAAA
Statistics
Matches: 222, Mismatches: 21, Indels: 17
0.85 0.08 0.07
Matches are distributed among these distances:
56 25 0.11
57 28 0.13
58 94 0.42
59 74 0.33
60 1 0.00
ACGTcount: A:0.35, C:0.30, G:0.02, T:0.32
Consensus pattern (58 bp):
AAAATTACCATTTTACCCCCAAACTTCCAAAAATCCCATTTTTGACCCAAAACTTCCA
Found at i:15601 original size:173 final size:173
Alignment explanation
Indices: 15238--15604 Score: 392
Period size: 173 Copynumber: 2.1 Consensus size: 173
15228 AAACTATCTG
* *
15238 AAAATTACCATTTTACCCCTAAACTTCTAAAAATCTCATTTTTGACCCTAAAACATCCAAAAATT
1 AAAATTACCATTTTACCCCTAAACTTCTAAAAATCCCATTTTTGACCCCAAAACATCCAAAAATT
*
15303 AACATTTTACCCCTAAACTTCCAAAAATCCCATTTTTGACCTCAAAACTTCCAAAAATTCCATTT
66 -ACATTTTACCCCCAAACTTCCAAAAATCCCATTTTTGACCTCAAAACTTCCAAAAATTCCATTT
*
15368 TACCCCAAACTTCCAAAAATCCCATTTTGACCCCAAAACTTCCA
130 TACCCCAAACTTCCAAAAATCCCATTTTAACCCCAAAACTTCCA
* * * *
15412 AAAATT-TCATTTTTA-CCCTCAAACTTCTAAATATCCCATTTTT-ACCCCGAAACTTCCAAAAA
1 AAAATTACCA-TTTTACCCCT-AAACTTCTAAAAATCCCATTTTTGACCCCAAAACATCCAAAAA
* * *
15474 TT-CTATTTTTACCCCCGAACTTCCAAAAATCTCATTTTTGATCC-CGAAAC-TCTC-AAAATTA
64 TTAC-A-TTTTACCCCCAAACTTCCAAAAATCCCATTTTTGA-CCTCAAAACTTC-CAAAAATT-
* ** * * * * ** *
15535 CCCTTTTACCCCCGA-TGT-CTAAAATTCTATTTTTAACCCCGAATTTTCCC
124 CCATTTTACCCCAAACT-TCCAAAAATCCCA-TTTTAACCCCAAAACTTCCA
15585 AAAATTACCATTTTACCCCT
1 AAAATTACCATTTTACCCCT
15605 GTGCATCTGA
Statistics
Matches: 160, Mismatches: 22, Indels: 22
0.78 0.11 0.11
Matches are distributed among these distances:
171 1 0.01
172 18 0.11
173 101 0.63
174 40 0.25
ACGTcount: A:0.35, C:0.30, G:0.03, T:0.33
Consensus pattern (173 bp):
AAAATTACCATTTTACCCCTAAACTTCTAAAAATCCCATTTTTGACCCCAAAACATCCAAAAATT
ACATTTTACCCCCAAACTTCCAAAAATCCCATTTTTGACCTCAAAACTTCCAAAAATTCCATTTT
ACCCCAAACTTCCAAAAATCCCATTTTAACCCCAAAACTTCCA
Done.