Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01010554.1 Kokia drynarioides strain JFW-HI SEQ_125474, 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: 11080
ACGTcount: A:0.31, C:0.15, G:0.19, T:0.35
Warning! 50 characters in sequence are not A, C, G, or T
Found at i:797 original size:29 final size:28
Alignment explanation
Indices: 739--820 Score: 112
Period size: 29 Copynumber: 2.9 Consensus size: 28
729 ACGTTAACAA
* *
739 GACACCCCCACATTT-TAAGTGGTTTTAG
1 GACA-CCCCACATTTCCAAGTGGTTCTAG
767 GACACACCCACATTTCCAAGTGGTTCTAG
1 GACAC-CCCACATTTCCAAGTGGTTCTAG
796 GACACCCTCACATTTCCAAGTGGTT
1 GACACCC-CACATTTCCAAGTGGTT
821 GTCTCGTCTC
Statistics
Matches: 49, Mismatches: 2, Indels: 5
0.88 0.04 0.09
Matches are distributed among these distances:
27 1 0.02
28 15 0.31
29 33 0.67
ACGTcount: A:0.26, C:0.29, G:0.17, T:0.28
Consensus pattern (28 bp):
GACACCCCACATTTCCAAGTGGTTCTAG
Found at i:3047 original size:11 final size:12
Alignment explanation
Indices: 3030--3062 Score: 50
Period size: 11 Copynumber: 2.8 Consensus size: 12
3020 TATAAAAAAT
3030 ATAAATTTAAT-
1 ATAAATTTAATA
*
3041 TTAAATTTAATA
1 ATAAATTTAATA
3053 ATAAATTTAA
1 ATAAATTTAA
3063 AAACAAATAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
11 10 0.53
12 9 0.47
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (12 bp):
ATAAATTTAATA
Found at i:3489 original size:23 final size:23
Alignment explanation
Indices: 3463--3513 Score: 75
Period size: 23 Copynumber: 2.2 Consensus size: 23
3453 CAGAAGTTTT
*
3463 ACAAACATAATGACAAGAGAGTA
1 ACAAACATAATGACAAGAAAGTA
* *
3486 ACAAACATAATGATAAGAAAGTT
1 ACAAACATAATGACAAGAAAGTA
3509 ACAAA
1 ACAAA
3514 ATAGTAATAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.59, C:0.12, G:0.14, T:0.16
Consensus pattern (23 bp):
ACAAACATAATGACAAGAAAGTA
Found at i:4700 original size:22 final size:25
Alignment explanation
Indices: 4673--4723 Score: 79
Period size: 25 Copynumber: 2.1 Consensus size: 25
4663 TATTTTTAAA
*
4673 ATTTTTT-GAAA-AATATTTTTATT
1 ATTTTTTAGAAAGAATATTTATATT
4696 ATTTTTTAGAAAGAATATTTATATT
1 ATTTTTTAGAAAGAATATTTATATT
4721 ATT
1 ATT
4724 AATTTAATAT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
23 7 0.28
24 4 0.16
25 14 0.56
ACGTcount: A:0.37, C:0.00, G:0.06, T:0.57
Consensus pattern (25 bp):
ATTTTTTAGAAAGAATATTTATATT
Found at i:4712 original size:25 final size:23
Alignment explanation
Indices: 4663--4723 Score: 77
Period size: 23 Copynumber: 2.6 Consensus size: 23
4653 ATGCTCATAT
**
4663 TATTTTTAAAATTTTTTGAAAAA
1 TATTTTTATTATTTTTTGAAAAA
4686 TATTTTTATTATTTTTTAGAAAGAA
1 TATTTTTATTATTTTTT-GAAA-AA
*
4711 TATTTATATTATT
1 TATTTTTATTATT
4724 AATTTAATAT
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
23 15 0.45
24 4 0.12
25 14 0.42
ACGTcount: A:0.38, C:0.00, G:0.05, T:0.57
Consensus pattern (23 bp):
TATTTTTATTATTTTTTGAAAAA
Found at i:4745 original size:20 final size:20
Alignment explanation
Indices: 4709--4746 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
4699 TTTTAGAAAG
*
4709 AATATTTATATTATTAATTT
1 AATATTTATAATATTAATTT
4729 AATATTTAATAAT-TTAAT
1 AATATTT-ATAATATTAAT
4747 ATGATTTTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
20 12 0.75
21 4 0.25
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (20 bp):
AATATTTATAATATTAATTT
Found at i:5881 original size:58 final size:58
Alignment explanation
Indices: 5791--5907 Score: 234
Period size: 58 Copynumber: 2.0 Consensus size: 58
5781 GCTAAATCCC
5791 ATTTGTTTTCCACAGTTGCCGAACATCTTTGATCACATCAACAACTTCATGTTGTTTT
1 ATTTGTTTTCCACAGTTGCCGAACATCTTTGATCACATCAACAACTTCATGTTGTTTT
5849 ATTTGTTTTCCACAGTTGCCGAACATCTTTGATCACATCAACAACTTCATGTTGTTTT
1 ATTTGTTTTCCACAGTTGCCGAACATCTTTGATCACATCAACAACTTCATGTTGTTTT
5907 A
1 A
5908 CCTAGAAATT
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
58 59 1.00
ACGTcount: A:0.25, C:0.22, G:0.12, T:0.41
Consensus pattern (58 bp):
ATTTGTTTTCCACAGTTGCCGAACATCTTTGATCACATCAACAACTTCATGTTGTTTT
Done.