Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01001820.1 Kokia drynarioides strain JFW-HI SEQ_113562, 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: 16079
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Found at i:2208 original size:18 final size:18
Alignment explanation
Indices: 2185--2227 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
2175 TAATAGATTT
2185 TTAATTAAATAAATTT-AA
1 TTAATTAAA-AAATTTAAA
* *
2203 TTAATTGAAAATTTTAAA
1 TTAATTAAAAAATTTAAA
2221 TTAATTA
1 TTAATTA
2228 CACCCTTGAA
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
17 5 0.24
18 16 0.76
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (18 bp):
TTAATTAAAAAATTTAAA
Found at i:9480 original size:18 final size:18
Alignment explanation
Indices: 9457--9532 Score: 77
Period size: 18 Copynumber: 4.3 Consensus size: 18
9447 AATAATTTTT
*
9457 TAAAATTTTAAATATTTA
1 TAAAATTTTAAAAATTTA
9475 TAAAATTTTAAAAATTTA
1 TAAAATTTTAAAAATTTA
*
9493 T---ATTTTAAAAAAATTA
1 TAAAATTTT-AAAAATTTA
* *
9509 AAAAATTCTAAAGAATTTA
1 TAAAATTTTAAA-AATTTA
9528 TAAAA
1 TAAAA
9533 AAAAGTTAAA
Statistics
Matches: 47, Mismatches: 6, Indels: 9
0.76 0.10 0.15
Matches are distributed among these distances:
15 5 0.11
16 8 0.17
18 21 0.45
19 13 0.28
ACGTcount: A:0.57, C:0.01, G:0.01, T:0.41
Consensus pattern (18 bp):
TAAAATTTTAAAAATTTA
Found at i:9505 original size:26 final size:26
Alignment explanation
Indices: 9454--9520 Score: 73
Period size: 25 Copynumber: 2.6 Consensus size: 26
9444 CAAAATAATT
* *
9454 TTTTAAAATTTTAAATATTTATAAAA
1 TTTTAAAAATTTAAATATTTAAAAAA
*
9480 TTTTAAAAATTTATAT-TTTAAAAAA
1 TTTTAAAAATTTAAATATTTAAAAAA
* *
9505 ATTAAAAAATTCTAAA
1 TTTTAAAAATT-TAAA
9521 GAATTTATAA
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
25 17 0.50
26 17 0.50
ACGTcount: A:0.54, C:0.01, G:0.00, T:0.45
Consensus pattern (26 bp):
TTTTAAAAATTTAAATATTTAAAAAA
Found at i:9534 original size:30 final size:28
Alignment explanation
Indices: 9482--9556 Score: 77
Period size: 31 Copynumber: 2.7 Consensus size: 28
9472 TTATAAAATT
*
9482 TTAAAAATTT--ATATTTT-AAAAAAA-
1 TTAAAAATTTAAAAATTTTAAAAAAAAG
9506 TTAAAAAATTCTAAAGAATTTATAAAAAAAAG
1 TT-AAAAATT-TAAA-AATTT-TAAAAAAAAG
9538 TTAAAAATTTAAAAATTTT
1 TTAAAAATTTAAAAATTTT
9557 CTAAAATAAT
Statistics
Matches: 42, Mismatches: 1, Indels: 12
0.76 0.02 0.22
Matches are distributed among these distances:
24 2 0.05
25 7 0.17
26 1 0.02
28 2 0.05
29 9 0.21
30 5 0.12
31 14 0.33
32 2 0.05
ACGTcount: A:0.59, C:0.01, G:0.03, T:0.37
Consensus pattern (28 bp):
TTAAAAATTTAAAAATTTTAAAAAAAAG
Found at i:9546 original size:21 final size:22
Alignment explanation
Indices: 9508--9552 Score: 58
Period size: 23 Copynumber: 2.1 Consensus size: 22
9498 TAAAAAAATT
*
9508 AAAAAATTCTAAAGAATTTATAA
1 AAAAAAGTCTAAAGAATTTA-AA
9531 AAAAAAGT-TAAA-AATTTAAA
1 AAAAAAGTCTAAAGAATTTAAA
9551 AA
1 AA
9553 TTTTCTAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
20 4 0.19
21 6 0.29
22 4 0.19
23 7 0.33
ACGTcount: A:0.67, C:0.02, G:0.04, T:0.27
Consensus pattern (22 bp):
AAAAAAGTCTAAAGAATTTAAA
Found at i:9549 original size:8 final size:8
Alignment explanation
Indices: 9455--9555 Score: 57
Period size: 8 Copynumber: 12.4 Consensus size: 8
9445 AAAATAATTT
*
9455 TTTAAAAT
1 TTTAAAAA
*
9463 TTTAAATA
1 TTTAAAAA
9471 TTTATAAAA
1 TTTA-AAAA
9480 TTTTAAAAA
1 -TTTAAAAA
* *
9489 TTT-ATAT
1 TTTAAAAA
9496 TTTAAAAAAA
1 TTT--AAAAA
*
9506 TTAAAAAA
1 TTTAAAAA
9514 TTCTAAAGAA
1 TT-TAAA-AA
*
9524 TTTATAAA
1 TTTAAAAA
9532 ---AAAAA
1 TTTAAAAA
*
9537 GTTAAAAA
1 TTTAAAAA
9545 TTTAAAAA
1 TTTAAAAA
9553 TTT
1 TTT
9556 TCTAAAATAA
Statistics
Matches: 71, Mismatches: 12, Indels: 20
0.69 0.12 0.19
Matches are distributed among these distances:
5 4 0.06
7 5 0.07
8 37 0.52
9 13 0.18
10 12 0.17
ACGTcount: A:0.56, C:0.01, G:0.02, T:0.41
Consensus pattern (8 bp):
TTTAAAAA
Found at i:9562 original size:30 final size:31
Alignment explanation
Indices: 9499--9555 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 31
9489 TTTATATTTT
9499 AAAAAAATTAAAAAATTCTAAAGAATTTATA
1 AAAAAAATTAAAAAATTCTAAAGAATTTATA
9530 AAAAAAAGTT-AAAAATT-TAAA-AATTT
1 AAAAAAA-TTAAAAAATTCTAAAGAATTT
9556 TCTAAAATAA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
29 5 0.20
30 4 0.16
31 14 0.56
32 2 0.08
ACGTcount: A:0.65, C:0.02, G:0.04, T:0.30
Consensus pattern (31 bp):
AAAAAAATTAAAAAATTCTAAAGAATTTATA
Found at i:14139 original size:4 final size:4
Alignment explanation
Indices: 14132--14171 Score: 80
Period size: 4 Copynumber: 10.0 Consensus size: 4
14122 TGGTCGGTCG
14132 GGTT GGTT GGTT GGTT GGTT GGTT GGTT GGTT GGTT GGTT
1 GGTT GGTT GGTT GGTT GGTT GGTT GGTT GGTT GGTT GGTT
14172 CAATTCAATT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 36 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (4 bp):
GGTT
Done.