Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012382.1 Kokia drynarioides strain JFW-HI SEQ_127386, 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: 9648
ACGTcount: A:0.33, C:0.18, G:0.14, T:0.34
Warning! 79 characters in sequence are not A, C, G, or T
Found at i:1253 original size:59 final size:59
Alignment explanation
Indices: 1157--1587 Score: 616
Period size: 59 Copynumber: 7.3 Consensus size: 59
1147 CCCTAGAGGT
* * * * * *
1157 CCCTAAACTTTCTAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCTATTTTTAA
1 CCCTGAACCTTCTAAAAATTACCATTTTACCCTCGAACTTCCAAAAACCCCATTTTTGA
* * *
1216 CCCTAAACATTCTAAAAATTATCATTTTACCCTCGAACTTCCAAAAACCCCATTTTTGA
1 CCCTGAACCTTCTAAAAATTACCATTTTACCCTCGAACTTCCAAAAACCCCATTTTTGA
* * * *
1275 CCCCGAACCTTCAAAAAATTAACATTTTACCCTCAAACTTCCAAAAACCCCATTTTTGA
1 CCCTGAACCTTCTAAAAATTACCATTTTACCCTCGAACTTCCAAAAACCCCATTTTTGA
* * * *
1334 CCCCGAACCTTCTATAAATTACCATATTATCCTCGAACTTCCAAAAACCCCATTTTTGA
1 CCCTGAACCTTCTAAAAATTACCATTTTACCCTCGAACTTCCAAAAACCCCATTTTTGA
1393 -CCTCGAACCTTCTAAAAATTACCATTTTACCCTCGAACTTCCAAAAACCCCATTTTTGA
1 CCCT-GAACCTTCTAAAAATTACCATTTTACCCTCGAACTTCCAAAAACCCCATTTTTGA
*
1452 -CCTCGAACCTTCTAAAAATTACCATTTTACCCCCGAACTTCCAAAAACCCCATTTTTGA
1 CCCT-GAACCTTCTAAAAATTACCATTTTACCCTCGAACTTCCAAAAACCCCATTTTTGA
* * *
1511 CCTTGAACCTTCTAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGA
1 CCCTGAACCTTCTAAAAATTACCATTTTACCCTCGAACTTCCAAAAACCCCATTTTTGA
* *
1570 CCCCGAA-CTTCCAAAAAT
1 CCCTGAACCTTCTAAAAAT
1588 CTCATTTTTG
Statistics
Matches: 342, Mismatches: 28, Indels: 5
0.91 0.07 0.01
Matches are distributed among these distances:
58 12 0.04
59 328 0.96
60 2 0.01
ACGTcount: A:0.34, C:0.32, G:0.04, T:0.30
Consensus pattern (59 bp):
CCCTGAACCTTCTAAAAATTACCATTTTACCCTCGAACTTCCAAAAACCCCATTTTTGA
Found at i:1626 original size:29 final size:29
Alignment explanation
Indices: 1170--1625 Score: 296
Period size: 29 Copynumber: 15.5 Consensus size: 29
1160 TAAACTTTCT
1170 AAAAATTACCA-TTTT-ACCCCCGAACTTCC
1 AAAAA-TACCATTTTTGA-CCCCGAACTTCC
* ** *
1199 AAAAAT-CCTATTTTTAACCCTAAACATTCT
1 AAAAATACC-ATTTTTGACCCCGAAC-TTCC
*
1229 AAAAATTATCA-TTTT-ACCCTCGAACTTCC
1 AAAAA-TACCATTTTTGACCC-CGAACTTCC
** *
1258 AAAAACCCCATTTTTGACCCCGAACCTTCA
1 AAAAATACCATTTTTGACCCCGAA-CTTCC
* *
1288 AAAAATTAACA-TTTT-ACCCTCAAACTTCC
1 AAAAA-TACCATTTTTGACCC-CGAACTTCC
** *
1317 AAAAACCCCATTTTTGACCCCGAACCTTCT
1 AAAAATACCATTTTTGACCCCGAA-CTTCC
* * *
1347 ATAAATTACCA-TATT-ATCCTCGAACTTCC
1 A-AAAATACCATTTTTGA-CCCCGAACTTCC
** * *
1376 AAAAACCCCATTTTTGACCTCGAACCTTCT
1 AAAAATACCATTTTTGACCCCGAA-CTTCC
1406 AAAAATTACCA-TTTT-ACCCTCGAACTTCC
1 AAAAA-TACCATTTTTGACCC-CGAACTTCC
** * *
1435 AAAAACCCCATTTTTGACCTCGAACCTTCT
1 AAAAATACCATTTTTGACCCCGAA-CTTCC
1465 AAAAATTACCA-TTTT-ACCCCCGAACTTCC
1 AAAAA-TACCATTTTTGA-CCCCGAACTTCC
** ** *
1494 AAAAACCCCATTTTTGACCTTGAACCTTCT
1 AAAAATACCATTTTTGACCCCGAA-CTTCC
1524 AAAAATTACCA-TTTT-ACCCCCGAACTTCC
1 AAAAA-TACCATTTTTGA-CCCCGAACTTCC
*
1553 AAAAATCCCATTTTTGACCCCGAACTTCC
1 AAAAATACCATTTTTGACCCCGAACTTCC
* *
1582 AAAAAT-CTCATTTTTGACTCCGAACCTTTC
1 AAAAATAC-CATTTTTGACCCCGAA-CTTCC
*
1612 AAAACTACCATTTT
1 AAAAATACCATTTT
1626 GCCCCCGTGC
Statistics
Matches: 332, Mismatches: 58, Indels: 73
0.72 0.13 0.16
Matches are distributed among these distances:
27 2 0.01
28 23 0.07
29 157 0.47
30 129 0.39
31 20 0.06
32 1 0.00
ACGTcount: A:0.34, C:0.31, G:0.04, T:0.31
Consensus pattern (29 bp):
AAAAATACCATTTTTGACCCCGAACTTCC
Found at i:3122 original size:30 final size:30
Alignment explanation
Indices: 3088--3170 Score: 125
Period size: 30 Copynumber: 2.7 Consensus size: 30
3078 TTAAAACCAA
3088 GTCAAATTTGAATTTTTGAAAAGTTCAAGG
1 GTCAAATTTGAATTTTTGAAAAGTTCAAGG
3118 GTCAAATTTGAATTTTT-AGAAAGTTCAAGG
1 GTCAAATTTGAATTTTTGA-AAAGTTCAAGG
3148 GTCAAATTAT-AATTTTTGGAAAA
1 GTCAAATT-TGAATTTTT-GAAAA
3171 TTTGAGGGTA
Statistics
Matches: 49, Mismatches: 0, Indels: 7
0.88 0.00 0.12
Matches are distributed among these distances:
29 1 0.02
30 43 0.88
31 4 0.08
32 1 0.02
ACGTcount: A:0.39, C:0.06, G:0.18, T:0.37
Consensus pattern (30 bp):
GTCAAATTTGAATTTTTGAAAAGTTCAAGG
Found at i:4223 original size:16 final size:16
Alignment explanation
Indices: 4202--4234 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
4192 ATTTATATTC
4202 ATAAAAT-AATAAATAA
1 ATAAAATGAA-AAATAA
4218 ATAAAATGAAAAATAA
1 ATAAAATGAAAAATAA
4234 A
1 A
4235 ATTGGGTTTC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 14 0.88
17 2 0.12
ACGTcount: A:0.76, C:0.00, G:0.03, T:0.21
Consensus pattern (16 bp):
ATAAAATGAAAAATAA
Found at i:8406 original size:9 final size:9
Alignment explanation
Indices: 8392--8426 Score: 61
Period size: 9 Copynumber: 3.8 Consensus size: 9
8382 AAACGAATTT
8392 AAATTTTTA
1 AAATTTTTA
8401 AAATTTTTA
1 AAATTTTTA
8410 AAATTTTTAA
1 AAATTTTT-A
8420 AAATTTT
1 AAATTTT
8427 CAATTTTAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
9 17 0.68
10 8 0.32
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (9 bp):
AAATTTTTA
Done.