Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01005700.1 Kokia drynarioides strain JFW-HI SEQ_119912, 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: 12352
ACGTcount: A:0.33, C:0.13, G:0.15, T:0.38
Found at i:446 original size:31 final size:33
Alignment explanation
Indices: 408--475 Score: 88
Period size: 34 Copynumber: 2.1 Consensus size: 33
398 TATTTGTTGG
408 TTTTTAG-TTAG-C-TGGTTTTAGTTTTGTTTTT
1 TTTTTAGTTTAGCCATGGTTTTA-TTTTGTTTTT
*
439 TTTTTAGTTTTGCCAATGGTTTTATTTTGTTTTT
1 TTTTTAGTTTAGCC-ATGGTTTTATTTTGTTTTT
473 TTT
1 TTT
476 GTTTCAATAA
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
31 7 0.22
32 3 0.09
33 1 0.03
34 13 0.41
35 8 0.25
ACGTcount: A:0.10, C:0.04, G:0.16, T:0.69
Consensus pattern (33 bp):
TTTTTAGTTTAGCCATGGTTTTATTTTGTTTTT
Found at i:2655 original size:22 final size:23
Alignment explanation
Indices: 2629--2671 Score: 70
Period size: 22 Copynumber: 1.9 Consensus size: 23
2619 TCAAAAGTTG
2629 TCAAAAAAAA-AATTTCATTTTA
1 TCAAAAAAAATAATTTCATTTTA
*
2651 TCAAAAAAAATTATTTCATTT
1 TCAAAAAAAATAATTTCATTT
2672 AATACACATG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 10 0.53
23 9 0.47
ACGTcount: A:0.51, C:0.09, G:0.00, T:0.40
Consensus pattern (23 bp):
TCAAAAAAAATAATTTCATTTTA
Found at i:3519 original size:30 final size:30
Alignment explanation
Indices: 3462--3522 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 30
3452 ATTTTTTTTA
**
3462 AATGTGTATAATTAAATCGAATCAAAATTT
1 AATGTGTATAATTAAATAAAATCAAAATTT
* *
3492 AATGTGTATAATTACATAAAATTAAAATTT
1 AATGTGTATAATTAAATAAAATCAAAATTT
3522 A
1 A
3523 TATATCAAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.49, C:0.05, G:0.08, T:0.38
Consensus pattern (30 bp):
AATGTGTATAATTAAATAAAATCAAAATTT
Found at i:3611 original size:22 final size:20
Alignment explanation
Indices: 3573--3613 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 20
3563 TACTTATCAT
*
3573 TGAAAATATTAATTTTTTTC
1 TGAAAATATTAAATTTTTTC
3593 TGAAAATAAATTAAATTTTTT
1 TGAAAAT--ATTAAATTTTTT
3614 ATTGTGATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 7 0.39
22 11 0.61
ACGTcount: A:0.41, C:0.02, G:0.05, T:0.51
Consensus pattern (20 bp):
TGAAAATATTAAATTTTTTC
Found at i:6662 original size:19 final size:20
Alignment explanation
Indices: 6618--6663 Score: 60
Period size: 19 Copynumber: 2.4 Consensus size: 20
6608 ATACATTAAT
*
6618 ATATTAAATTATATTCTGTC
1 ATATTAAATTATATACTGTC
*
6638 AT-TTAAATTA-ATACTTTC
1 ATATTAAATTATATACTGTC
6656 ATATTAAA
1 ATATTAAA
6664 AATATTTATT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
18 8 0.35
19 13 0.57
20 2 0.09
ACGTcount: A:0.41, C:0.09, G:0.02, T:0.48
Consensus pattern (20 bp):
ATATTAAATTATATACTGTC
Found at i:9592 original size:56 final size:56
Alignment explanation
Indices: 9513--9634 Score: 183
Period size: 57 Copynumber: 2.1 Consensus size: 56
9503 AAATTTTAAG
*
9513 TTTTTTTCAATAGAATTACTTGATTCTTTT-AATTTTTTTAATAATTATTTTGATTA
1 TTTTTTT-AATAGAATTACTTGATTCTTTTAAAATTTTTTAATAATTATTTTGATTA
* *
9569 TTTTGTTTAATAGAGTTATTTGATTCTTTTAAAATTTTTTAATAATTATTTTGATTA
1 TTTT-TTTAATAGAATTACTTGATTCTTTTAAAATTTTTTAATAATTATTTTGATTA
9626 TTTTATTTA
1 TTTT-TTTA
9635 TGGATTCAAT
Statistics
Matches: 60, Mismatches: 4, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
56 24 0.40
57 36 0.60
ACGTcount: A:0.29, C:0.03, G:0.07, T:0.61
Consensus pattern (56 bp):
TTTTTTTAATAGAATTACTTGATTCTTTTAAAATTTTTTAATAATTATTTTGATTA
Found at i:9593 original size:26 final size:24
Alignment explanation
Indices: 9544--9598 Score: 67
Period size: 26 Copynumber: 2.2 Consensus size: 24
9534 GATTCTTTTA
9544 ATTTTTTTAATAATTATTTTGATT
1 ATTTTTTTAATAATTATTTTGATT
9568 ATTTTGTTTAATAGAGTTA-TTTGATT
1 ATTTT-TTTAATA-A-TTATTTTGATT
*
9594 CTTTT
1 ATTTT
9599 AAAATTTTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
24 5 0.19
25 7 0.26
26 12 0.44
27 3 0.11
ACGTcount: A:0.25, C:0.02, G:0.09, T:0.64
Consensus pattern (24 bp):
ATTTTTTTAATAATTATTTTGATT
Found at i:9791 original size:11 final size:12
Alignment explanation
Indices: 9775--9803 Score: 51
Period size: 11 Copynumber: 2.5 Consensus size: 12
9765 CGTTGAAATC
9775 AAAAGAAAAA-A
1 AAAAGAAAAAGA
9786 AAAAGAAAAAGA
1 AAAAGAAAAAGA
9798 AAAAGA
1 AAAAGA
9804 GAGACATGTC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
11 10 0.59
12 7 0.41
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (12 bp):
AAAAGAAAAAGA
Found at i:9802 original size:6 final size:6
Alignment explanation
Indices: 9775--9803 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
9765 CGTTGAAATC
9775 AAAAGA AAAA-A AAAAGA AAAAGA AAAAGA
1 AAAAGA AAAAGA AAAAGA AAAAGA AAAAGA
9804 GAGACATGTC
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
5 5 0.23
6 17 0.77
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (6 bp):
AAAAGA
Found at i:10037 original size:15 final size:15
Alignment explanation
Indices: 9991--10041 Score: 54
Period size: 15 Copynumber: 3.5 Consensus size: 15
9981 ACAAAACAAT
*
9991 AATATAAATGATTAA
1 AATATAAATTATTAA
10006 AA-AGTAATATT-TT-A
1 AATA-TAA-ATTATTAA
10020 AATATAAATTATTAA
1 AATATAAATTATTAA
10035 AATATAA
1 AATATAA
10042 TTTGAAACAA
Statistics
Matches: 30, Mismatches: 1, Indels: 10
0.73 0.02 0.24
Matches are distributed among these distances:
13 3 0.10
14 9 0.30
15 16 0.53
16 2 0.07
ACGTcount: A:0.59, C:0.00, G:0.04, T:0.37
Consensus pattern (15 bp):
AATATAAATTATTAA
Done.