Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01010952.1 Kokia drynarioides strain JFW-HI SEQ_125920, 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: 20267
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Found at i:5740 original size:6 final size:6
Alignment explanation
Indices: 5729--5755 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
5719 TCCTTACTCT
5729 TTAAAA TTAAAA TTAAAA TTAAAA TTA
1 TTAAAA TTAAAA TTAAAA TTAAAA TTA
5756 GAAAACTAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (6 bp):
TTAAAA
Found at i:9664 original size:39 final size:40
Alignment explanation
Indices: 9620--9698 Score: 115
Period size: 39 Copynumber: 2.0 Consensus size: 40
9610 TTGATTGCTA
*
9620 TTTTTTGCTGTTTTGGTACT-GTGTTTTTACTATTTTGGT
1 TTTTTTACTGTTTTGGTACTAGTGTTTTTACTATTTTGGT
* * *
9659 TTTTTTACTGTTTTGGTGCTATTTTTTTTACTATTTTGGT
1 TTTTTTACTGTTTTGGTACTAGTGTTTTTACTATTTTGGT
9699 GTTGTTTTTA
Statistics
Matches: 35, Mismatches: 4, Indels: 1
0.88 0.10 0.03
Matches are distributed among these distances:
39 18 0.51
40 17 0.49
ACGTcount: A:0.09, C:0.08, G:0.18, T:0.66
Consensus pattern (40 bp):
TTTTTTACTGTTTTGGTACTAGTGTTTTTACTATTTTGGT
Found at i:9665 original size:17 final size:17
Alignment explanation
Indices: 9643--9675 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
9633 TGGTACTGTG
9643 TTTTTACTATTTTGGTT
1 TTTTTACTATTTTGGTT
*
9660 TTTTTACTGTTTTGGT
1 TTTTTACTATTTTGGT
9676 GCTATTTTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.09, C:0.06, G:0.15, T:0.70
Consensus pattern (17 bp):
TTTTTACTATTTTGGTT
Found at i:9683 original size:22 final size:22
Alignment explanation
Indices: 9605--9699 Score: 67
Period size: 22 Copynumber: 4.5 Consensus size: 22
9595 TGTTTTGATG
* *
9605 CTGTTTTGATTGCTA-TTTTTTG
1 CTGTTTTG-GTGCTATTTTTTTA
* * *
9627 CTGTTTTGGTACTGTGTTTTTA
1 CTGTTTTGGTGCTATTTTTTTA
*
9649 CTATTTT-G-G---TTTTTTTA
1 CTGTTTTGGTGCTATTTTTTTA
9666 CTGTTTTGGTGCTATTTTTTTTA
1 CTGTTTTGGTGCTA-TTTTTTTA
*
9689 CTATTTTGGTG
1 CTGTTTTGGTG
9700 TTGTTTTTAT
Statistics
Matches: 56, Mismatches: 10, Indels: 13
0.71 0.13 0.16
Matches are distributed among these distances:
17 13 0.23
18 1 0.02
19 1 0.02
21 4 0.07
22 19 0.34
23 18 0.32
ACGTcount: A:0.09, C:0.08, G:0.19, T:0.63
Consensus pattern (22 bp):
CTGTTTTGGTGCTATTTTTTTA
Found at i:9722 original size:21 final size:21
Alignment explanation
Indices: 9698--9785 Score: 65
Period size: 21 Copynumber: 4.0 Consensus size: 21
9688 ACTATTTTGG
*
9698 TGTTGTTTTTATTGTTATTTT
1 TGTTGTTTTGATTGTTATTTT
*
9719 TGTTGCTATTT--TCTATTATTTTT
1 TGTTG-T-TTTGAT-TGTTA-TTTT
9742 ACTGTTGTTTTGATTGTTATTTT
1 --TGTTGTTTTGATTGTTATTTT
* *
9765 GGTTGTTTGGA-TGTTATTTT
1 TGTTGTTTTGATTGTTATTTT
9785 T
1 T
9786 ATGCGTTTTT
Statistics
Matches: 54, Mismatches: 5, Indels: 17
0.71 0.07 0.22
Matches are distributed among these distances:
20 9 0.17
21 15 0.28
22 5 0.09
23 14 0.26
24 5 0.09
25 6 0.11
ACGTcount: A:0.11, C:0.03, G:0.17, T:0.68
Consensus pattern (21 bp):
TGTTGTTTTGATTGTTATTTT
Found at i:9779 original size:20 final size:21
Alignment explanation
Indices: 9745--9784 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
9735 TATTTTTACT
*
9745 GTTGTTTTGATTGTTATTTTG
1 GTTGTTTGGATTGTTATTTTG
9766 GTTGTTTGGA-TGTTATTTT
1 GTTGTTTGGATTGTTATTTT
9785 TATGCGTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 9 0.50
21 9 0.50
ACGTcount: A:0.10, C:0.00, G:0.25, T:0.65
Consensus pattern (21 bp):
GTTGTTTGGATTGTTATTTTG
Found at i:10759 original size:29 final size:29
Alignment explanation
Indices: 10699--10775 Score: 97
Period size: 29 Copynumber: 2.7 Consensus size: 29
10689 TTGTTTAAAG
*
10699 GTATGTTTATCTTTTA--TTTTTTGATTGT
1 GTATGTTTAT-TTTTATGTTTTTTGATTCT
*
10727 -TATGTTTATTTTTATGTTTTTTTATTCT
1 GTATGTTTATTTTTATGTTTTTTGATTCT
*
10755 GTATGTTTTTTTTTATGTTTT
1 GTATGTTTATTTTTATGTTTT
10776 GTTTGAAGGG
Statistics
Matches: 43, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
26 5 0.12
27 9 0.21
28 10 0.23
29 19 0.44
ACGTcount: A:0.13, C:0.03, G:0.12, T:0.73
Consensus pattern (29 bp):
GTATGTTTATTTTTATGTTTTTTGATTCT
Found at i:11041 original size:19 final size:19
Alignment explanation
Indices: 10999--11042 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
10989 ATTAATTACT
10999 TTTTTTACTTTTACTTTTA
1 TTTTTTACTTTTACTTTTA
* * * *
11018 ATTTTTATTTTTTCTTTTC
1 TTTTTTACTTTTACTTTTA
11037 TTTTTT
1 TTTTTT
11043 GTATGTTTAT
Statistics
Matches: 20, Mismatches: 5, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.11, C:0.09, G:0.00, T:0.80
Consensus pattern (19 bp):
TTTTTTACTTTTACTTTTA
Found at i:16719 original size:43 final size:43
Alignment explanation
Indices: 16658--16743 Score: 172
Period size: 43 Copynumber: 2.0 Consensus size: 43
16648 ATACTTATTC
16658 CTGGGTTTCTTCTAGTGAAACAAAATCATTGATTTTTAAGGTA
1 CTGGGTTTCTTCTAGTGAAACAAAATCATTGATTTTTAAGGTA
16701 CTGGGTTTCTTCTAGTGAAACAAAATCATTGATTTTTAAGGTA
1 CTGGGTTTCTTCTAGTGAAACAAAATCATTGATTTTTAAGGTA
16744 AGCTGCTGCT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 43 1.00
ACGTcount: A:0.30, C:0.12, G:0.19, T:0.40
Consensus pattern (43 bp):
CTGGGTTTCTTCTAGTGAAACAAAATCATTGATTTTTAAGGTA
Found at i:17175 original size:15 final size:14
Alignment explanation
Indices: 17132--17188 Score: 55
Period size: 14 Copynumber: 4.1 Consensus size: 14
17122 TAAAAATATC
* *
17132 ATAAATTCTTTAAA
1 ATAATTTCTTAAAA
17146 A-AA-TTCTTAAAA
1 ATAATTTCTTAAAA
17158 ATAATTTCTTAGAAA
1 ATAATTTCTTA-AAA
* *
17173 ATATTTTTTTAAAA
1 ATAATTTCTTAAAA
17187 AT
1 AT
17189 TAAAATATTA
Statistics
Matches: 37, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
12 9 0.24
13 4 0.11
14 12 0.32
15 12 0.32
ACGTcount: A:0.49, C:0.05, G:0.02, T:0.44
Consensus pattern (14 bp):
ATAATTTCTTAAAA
Done.