Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01010784.1 Kokia drynarioides strain JFW-HI SEQ_125750, 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: 3329
ACGTcount: A:0.30, C:0.20, G:0.16, T:0.32
Warning! 50 characters in sequence are not A, C, G, or T
Found at i:1294 original size:30 final size:29
Alignment explanation
Indices: 1236--1524 Score: 323
Period size: 30 Copynumber: 9.8 Consensus size: 29
1226 CCCTAAATTG
1236 TCTAAAAATCCCATTTTTACCCCAAAACT
1 TCTAAAAATCCCATTTTTACCCCAAAACT
*
1265 TCTAAAAATCCCATTTTTAACCTCAAAACT
1 TCTAAAAATCCCATTTTT-ACCCCAAAACT
* *
1295 TCCAAAAATCCCATTTTTACCCCCAAACT
1 TCTAAAAATCCCATTTTTACCCCAAAACT
*
1324 TCTAAAAATCCAATTTTTAACCCCAAAACT
1 TCTAAAAATCCCATTTTT-ACCCCAAAACT
*
1354 TCTAAAAATCCCATTTTTAACCCCAAAGCT
1 TCTAAAAATCCCATTTTT-ACCCCAAAACT
* * * *
1384 TTTAAAAATCCTAATTTTAACCCC-AAAGT
1 TCTAAAAATCC-CATTTTTACCCCAAAACT
* **
1413 TCTAAAAATTCCATTTTTACCCCCGAACT
1 TCTAAAAATCCCATTTTTACCCCAAAACT
* *
1442 ACCAAAAATCCCATTTTTTACCCCAAAACT
1 TCTAAAAATCCCA-TTTTTACCCCAAAACT
* **
1472 T-TCAAAAGGT-CCATTTTTACCCCCGAACT
1 TCT-AAAA-ATCCCATTTTTACCCCAAAACT
*
1501 TCTAGAAATCCCATTTTTGACCCC
1 TCTAAAAATCCCATTTTT-ACCCC
1525 GAATTTTCCC
Statistics
Matches: 218, Mismatches: 32, Indels: 19
0.81 0.12 0.07
Matches are distributed among these distances:
28 11 0.05
29 94 0.43
30 107 0.49
31 6 0.03
ACGTcount: A:0.36, C:0.30, G:0.03, T:0.31
Consensus pattern (29 bp):
TCTAAAAATCCCATTTTTACCCCAAAACT
Found at i:1311 original size:59 final size:59
Alignment explanation
Indices: 1239--1524 Score: 360
Period size: 59 Copynumber: 4.8 Consensus size: 59
1229 TAAATTGTCT
* *
1239 AAAAATCCCATTTTTACCCCAAAACTTCTAAAAATCCCATTTTTAACCTCAAAACTTCC
1 AAAAATCCCATTTTTACCCCCAAACTTCTAAAAATCCCATTTTTAACCCCAAAACTTCC
* *
1298 AAAAATCCCATTTTTACCCCCAAACTTCTAAAAATCCAATTTTTAACCCCAAAACTTCT
1 AAAAATCCCATTTTTACCCCCAAACTTCTAAAAATCCCATTTTTAACCCCAAAACTTCC
* * * * * *
1357 AAAAATCCCATTTTTAACCCCAAAGCTTTTAAAAATCCTAATTTTAACCCC-AAAGTTCT
1 AAAAATCCCATTTTTACCCCCAAA-CTTCTAAAAATCCCATTTTTAACCCCAAAACTTCC
* * * * * *
1416 AAAAATTCCATTTTTACCCCCGAACTACCAAAAATCCCATTTTTTACCCCAAAACTTTC
1 AAAAATCCCATTTTTACCCCCAAACTTCTAAAAATCCCATTTTTAACCCCAAAACTTCC
* * * *
1475 AAAAGGT-CCATTTTTACCCCCGAACTTCTAGAAATCCCATTTTTGACCCC
1 AAAA-ATCCCATTTTTACCCCCAAACTTCTAAAAATCCCATTTTTAACCCC
1525 GAATTTTCCC
Statistics
Matches: 198, Mismatches: 26, Indels: 6
0.86 0.11 0.03
Matches are distributed among these distances:
58 20 0.10
59 154 0.78
60 24 0.12
ACGTcount: A:0.36, C:0.30, G:0.03, T:0.31
Consensus pattern (59 bp):
AAAAATCCCATTTTTACCCCCAAACTTCTAAAAATCCCATTTTTAACCCCAAAACTTCC
Found at i:1527 original size:29 final size:28
Alignment explanation
Indices: 1236--1524 Score: 294
Period size: 29 Copynumber: 9.8 Consensus size: 28
1226 CCCTAAATTG
1236 TCTAAAAATCCCATTTTTACCCCAAAACT
1 TCTAAAAATCCCATTTTTACCCC-AAACT
*
1265 TCTAAAAATCCCATTTTTAACCTCAAAACT
1 TCTAAAAATCCCATTTTT-ACC-CCAAACT
*
1295 TCCAAAAATCCCATTTTTACCCCCAAACT
1 TCTAAAAATCCCATTTTTA-CCCCAAACT
*
1324 TCTAAAAATCCAATTTTTAACCCCAAAACT
1 TCTAAAAATCCCATTTTT-ACCCC-AAACT
1354 TCTAAAAATCCCATTTTTAACCCCAAAGCT
1 TCTAAAAATCCCATTTTT-ACCCCAAA-CT
* * * *
1384 TTTAAAAATCCTAATTTTAACCCCAAAGT
1 TCTAAAAATCC-CATTTTTACCCCAAACT
* *
1413 TCTAAAAATTCCATTTTTACCCCCGAACT
1 TCTAAAAATCCCATTTTTA-CCCCAAACT
* *
1442 ACCAAAAATCCCATTTTTTACCCCAAAACT
1 TCTAAAAATCCCA-TTTTTACCCC-AAACT
* *
1472 T-TCAAAAGGT-CCATTTTTACCCCCGAACT
1 TCT-AAAA-ATCCCATTTTTA-CCCCAAACT
*
1501 TCTAGAAATCCCATTTTTGACCCC
1 TCTAAAAATCCCATTTTT-ACCCC
1525 GAATTTTCCC
Statistics
Matches: 218, Mismatches: 26, Indels: 32
0.79 0.09 0.12
Matches are distributed among these distances:
28 7 0.03
29 105 0.48
30 99 0.45
31 7 0.03
ACGTcount: A:0.36, C:0.30, G:0.03, T:0.31
Consensus pattern (28 bp):
TCTAAAAATCCCATTTTTACCCCAAACT
Done.