Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013326.1 Kokia drynarioides strain JFW-HI SEQ_128348, 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: 3993
ACGTcount: A:0.32, C:0.19, G:0.16, T:0.33
Found at i:1094 original size:29 final size:29
Alignment explanation
Indices: 1062--1147 Score: 93
Period size: 30 Copynumber: 2.9 Consensus size: 29
1052 CCAGGGAGGT
*
1062 CTCTAAACTTTTAAAAATTTTATTTTTAA
1 CTCTAAACTTTTAAAAATTTCATTTTTAA
* *
1091 CTCTGAATCTTTTAAAAATTATCA-TTTTAC
1 CTCT-AAACTTTTAAAAATT-TCATTTTTAA
* * *
1121 CTCCAAACTTCTAAAAATCTCATTTTT
1 CTCTAAACTTTTAAAAATTTCATTTTT
1148 TAACCTCGAA
Statistics
Matches: 47, Mismatches: 7, Indels: 6
0.78 0.12 0.10
Matches are distributed among these distances:
28 3 0.06
29 20 0.43
30 22 0.47
31 2 0.04
ACGTcount: A:0.35, C:0.17, G:0.01, T:0.47
Consensus pattern (29 bp):
CTCTAAACTTTTAAAAATTTCATTTTTAA
Found at i:1486 original size:29 final size:29
Alignment explanation
Indices: 1145--1486 Score: 251
Period size: 29 Copynumber: 11.6 Consensus size: 29
1135 AAATCTCATT
*
1145 TTTTAACCTCGAATCTTCCAAAAATTACCA
1 TTTTACCCTCGAA-CTTCCAAAAATTACCA
* * * *
1175 TTCTA-CCTCTAAACTTACAAAAA-TCCCA
1 TTTTACCCTC-GAACTTCCAAAAATTACCA
* *
1203 TTTTTAACCTCGAACCTTCCAAAAATTATCA
1 -TTTTACCCTCGAA-CTTCCAAAAATTACCA
* * * *
1234 TTCTACCCCCAAACTT-CAAAAAAT-CTCA
1 TTTTACCCTCGAACTTCCAAAAATTAC-CA
* *
1262 TTTTTAATCCCT-AAACTTCCAACAATTACCA
1 -TTTT-A-CCCTCGAACTTCCAAAAATTACCA
* *
1293 TTTTACCCCCGAACTTCCAAAAA-TCCCA
1 TTTTACCCTCGAACTTCCAAAAATTACCA
1321 TTTTTAACCC-CGAACCTTCCAAAAATTACCA
1 -TTTT-ACCCTCGAA-CTTCCAAAAATTACCA
*
1352 TTTTACCC-CTAAACTTCCAAAAA-T-CCA
1 TTTTACCCTC-GAACTTCCAAAAATTACCA
*
1379 TTTTTAACCC-CGAACCTTCC-AAAATTACTA
1 -TTTT-ACCCTCGAA-CTTCCAAAAATTACCA
* * *
1409 TTTTACCCTCAAACTTCCAAAAAGTCCCA
1 TTTTACCCTCGAACTTCCAAAAATTACCA
1438 TTTTTGACCC-CGAACCTTCCAAAAATTACCA
1 -TTTT-ACCCTCGAA-CTTCCAAAAATTACCA
1469 TTTTACCCTCGAACTTCC
1 TTTTACCCTCGAACTTCC
1487 GGAAGGTCTC
Statistics
Matches: 250, Mismatches: 34, Indels: 57
0.73 0.10 0.17
Matches are distributed among these distances:
27 3 0.01
28 40 0.16
29 94 0.38
30 76 0.30
31 36 0.14
32 1 0.00
ACGTcount: A:0.35, C:0.32, G:0.03, T:0.31
Consensus pattern (29 bp):
TTTTACCCTCGAACTTCCAAAAATTACCA
Found at i:1503 original size:59 final size:59
Alignment explanation
Indices: 1104--1486 Score: 488
Period size: 59 Copynumber: 6.5 Consensus size: 59
1094 TGAATCTTTT
* * * * *
1104 AAAAATTATCATTTTA-CCTCCAAACTTCTAAAAATCTCATTTTTTAACCTCGAATCTTCC
1 AAAAATTACCATTTTACCCT-CAAACTTCCAAAAATCCCA-TTTTTAACCCCGAACCTTCC
* * *
1164 AAAAATTACCATTCTA-CCTCTAAACTTACAAAAATCCCATTTTTAACCTCGAACCTTCC
1 AAAAATTACCATTTTACCCTC-AAACTTCCAAAAATCCCATTTTTAACCCCGAACCTTCC
* * * * * * * *
1223 AAAAATTATCATTCTACCCCCAAACTTCAAAAAATCTCATTTTTAATCCCTAAACTTCC
1 AAAAATTACCATTTTACCCTCAAACTTCCAAAAATCCCATTTTTAACCCCGAACCTTCC
* * *
1282 AACAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTAACCCCGAACCTTCC
1 AAAAATTACCATTTTACCCTCAAACTTCCAAAAATCCCATTTTTAACCCCGAACCTTCC
1341 AAAAATTACCATTTTACCC-CTAAACTTCCAAAAAT-CCATTTTTAACCCCGAACCTTCC
1 AAAAATTACCATTTTACCCTC-AAACTTCCAAAAATCCCATTTTTAACCCCGAACCTTCC
* *
1399 -AAAATTACTATTTTACCCTCAAACTTCCAAAAAGTCCCATTTTTGACCCCGAACCTTCC
1 AAAAATTACCATTTTACCCTCAAACTTCCAAAAA-TCCCATTTTTAACCCCGAACCTTCC
*
1458 AAAAATTACCATTTTACCCTCGAACTTCC
1 AAAAATTACCATTTTACCCTCAAACTTCC
1487 GGAAGGTCTC
Statistics
Matches: 286, Mismatches: 30, Indels: 14
0.87 0.09 0.04
Matches are distributed among these distances:
57 30 0.10
58 26 0.09
59 169 0.59
60 61 0.21
ACGTcount: A:0.35, C:0.31, G:0.02, T:0.31
Consensus pattern (59 bp):
AAAAATTACCATTTTACCCTCAAACTTCCAAAAATCCCATTTTTAACCCCGAACCTTCC
Found at i:2430 original size:26 final size:26
Alignment explanation
Indices: 2400--2462 Score: 67
Period size: 24 Copynumber: 2.5 Consensus size: 26
2390 TTAATTTTAA
*
2400 TTTGATGTAATTTATATAAAAAAAAC
1 TTTGATATAATTTATATAAAAAAAAC
* *
2426 TTTGA-ATAA-ATATATAAATAAAAC
1 TTTGATATAATTTATATAAAAAAAAC
* *
2450 TTTAATTTAATTT
1 TTTGATATAATTT
2463 TAAATTGAAT
Statistics
Matches: 29, Mismatches: 6, Indels: 4
0.74 0.15 0.10
Matches are distributed among these distances:
24 17 0.59
25 6 0.21
26 6 0.21
ACGTcount: A:0.49, C:0.03, G:0.05, T:0.43
Consensus pattern (26 bp):
TTTGATATAATTTATATAAAAAAAAC
Done.