Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013564.1 Kokia drynarioides strain JFW-HI SEQ_128590, 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: 25379
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:5588 original size:27 final size:28
Alignment explanation
Indices: 5542--5594 Score: 72
Period size: 27 Copynumber: 1.9 Consensus size: 28
5532 ATATATATAT
* *
5542 AAGAAATAAAAGAATAAAGAA-AGAAAA
1 AAGAAACAAAAGAAGAAAGAACAGAAAA
*
5569 AAGAAACAAAAGAAGGAAGAACAGAA
1 AAGAAACAAAAGAAGAAAGAACAGAA
5595 GCTCAAACGA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
27 18 0.82
28 4 0.18
ACGTcount: A:0.74, C:0.04, G:0.19, T:0.04
Consensus pattern (28 bp):
AAGAAACAAAAGAAGAAAGAACAGAAAA
Found at i:12279 original size:18 final size:18
Alignment explanation
Indices: 12256--12294 Score: 69
Period size: 18 Copynumber: 2.2 Consensus size: 18
12246 CTGGAAGGCC
12256 TTAGTGAGAACATCAGGG
1 TTAGTGAGAACATCAGGG
*
12274 TTAGTGAGATCATCAGGG
1 TTAGTGAGAACATCAGGG
12292 TTA
1 TTA
12295 ATGGTAGGCT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.31, C:0.10, G:0.31, T:0.28
Consensus pattern (18 bp):
TTAGTGAGAACATCAGGG
Found at i:18439 original size:25 final size:25
Alignment explanation
Indices: 18404--18456 Score: 97
Period size: 25 Copynumber: 2.1 Consensus size: 25
18394 TGACTTGTAC
*
18404 AAGCTTTTAAGCTGTTAAGTCAACT
1 AAGCTTCTAAGCTGTTAAGTCAACT
18429 AAGCTTCTAAGCTGTTAAGTCAACT
1 AAGCTTCTAAGCTGTTAAGTCAACT
18454 AAG
1 AAG
18457 TCACATCCTT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Consensus pattern (25 bp):
AAGCTTCTAAGCTGTTAAGTCAACT
Found at i:18635 original size:20 final size:20
Alignment explanation
Indices: 18612--18701 Score: 85
Period size: 20 Copynumber: 4.5 Consensus size: 20
18602 CTCTGCCAAC
*
18612 TGCTTGCTAATACTGCTCGA
1 TGCTTGCTGATACTGCTCGA
*
18632 TGC-TGCCTGATATTGCTCGA
1 TGCTTG-CTGATACTGCTCGA
* *
18652 TGC-TGTTGATGCTGCTCGA
1 TGCTTGCTGATACTGCTCGA
** *
18671 TGCTACCTGATGCTGCTCGA
1 TGCTTGCTGATACTGCTCGA
*
18691 TGCTGGCTGAT
1 TGCTTGCTGAT
18702 GCACTTGGCT
Statistics
Matches: 58, Mismatches: 10, Indels: 4
0.81 0.14 0.06
Matches are distributed among these distances:
19 16 0.28
20 42 0.72
ACGTcount: A:0.14, C:0.24, G:0.27, T:0.34
Consensus pattern (20 bp):
TGCTTGCTGATACTGCTCGA
Found at i:18674 original size:10 final size:10
Alignment explanation
Indices: 18624--18695 Score: 69
Period size: 10 Copynumber: 7.3 Consensus size: 10
18614 CTTGCTAATA
18624 CTGCTCGATG
1 CTGCTCGATG
*
18634 CTGC-CTGATA
1 CTGCTC-GATG
*
18644 TTGCTCGATG
1 CTGCTCGATG
*
18654 CTG-TTGATG
1 CTGCTCGATG
18663 CTGCTCGATG
1 CTGCTCGATG
*
18673 CTAC-CTGATG
1 CTGCTC-GATG
18683 CTGCTCGATG
1 CTGCTCGATG
18693 CTG
1 CTG
18696 GCTGATGCAC
Statistics
Matches: 49, Mismatches: 8, Indels: 10
0.73 0.12 0.15
Matches are distributed among these distances:
9 10 0.20
10 37 0.76
11 2 0.04
ACGTcount: A:0.12, C:0.26, G:0.28, T:0.33
Consensus pattern (10 bp):
CTGCTCGATG
Found at i:18702 original size:20 final size:20
Alignment explanation
Indices: 18624--18703 Score: 108
Period size: 20 Copynumber: 4.0 Consensus size: 20
18614 CTTGCTAATA
*
18624 CTGCTCGATGCTGCCTGATA
1 CTGCTCGATGCTGCCTGATG
* *
18644 TTGCTCGATGCTG-TTGATG
1 CTGCTCGATGCTGCCTGATG
*
18663 CTGCTCGATGCTACCTGATG
1 CTGCTCGATGCTGCCTGATG
*
18683 CTGCTCGATGCTGGCTGATG
1 CTGCTCGATGCTGCCTGATG
18703 C
1 C
18704 ACTTGGCTCA
Statistics
Matches: 51, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
19 15 0.29
20 36 0.71
ACGTcount: A:0.12, C:0.26, G:0.29, T:0.33
Consensus pattern (20 bp):
CTGCTCGATGCTGCCTGATG
Found at i:19398 original size:30 final size:26
Alignment explanation
Indices: 19368--19427 Score: 95
Period size: 26 Copynumber: 2.3 Consensus size: 26
19358 GAGTGTGATT
*
19368 GATTGTAATGTCTAATACAGTGCCGA
1 GATTGTGATGTCTAATACAGTGCCGA
19394 GATTGTGATGTCTAATACAGTGCCGA
1 GATTGTGATGTCTAATACAGTGCCGA
*
19420 -ATGGTGAT
1 GATTGTGAT
19428 TATGCCCGTC
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
25 7 0.22
26 25 0.78
ACGTcount: A:0.28, C:0.13, G:0.27, T:0.32
Consensus pattern (26 bp):
GATTGTGATGTCTAATACAGTGCCGA
Done.