Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014071.1 Kokia drynarioides strain JFW-HI SEQ_129102, 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: 12251
ACGTcount: A:0.35, C:0.14, G:0.15, T:0.35
Found at i:176 original size:20 final size:21
Alignment explanation
Indices: 151--193 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
141 TACTTACTAC
151 TACTAAC-AACAAAATAAAAT
1 TACTAACTAACAAAATAAAAT
* *
171 TACTAACTAGCAAAATTAAAT
1 TACTAACTAACAAAATAAAAT
192 TA
1 TA
194 AAGTAAATTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 7 0.35
21 13 0.65
ACGTcount: A:0.58, C:0.14, G:0.02, T:0.26
Consensus pattern (21 bp):
TACTAACTAACAAAATAAAAT
Found at i:545 original size:4 final size:4
Alignment explanation
Indices: 538--615 Score: 54
Period size: 4 Copynumber: 19.0 Consensus size: 4
528 TTATTTTTTT
* * *
538 TTTC TTTC TCCTTC TTCC CTTTC TTCTC CTTC -TTC CTTC -TTC TTTC
1 TTTC TTTC T--TTC TTTC -TTTC TT-TC TTTC TTTC TTTC TTTC TTTC
*
584 TTTC TTTC TTTC TCTTT TTTC TTTC TTT- TTTC
1 TTTC TTTC TTTC T-TTC TTTC TTTC TTTC TTTC
616 CTTCATTTTT
Statistics
Matches: 61, Mismatches: 5, Indels: 16
0.74 0.06 0.20
Matches are distributed among these distances:
3 9 0.15
4 39 0.64
5 9 0.15
6 4 0.07
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (4 bp):
TTTC
Found at i:566 original size:18 final size:19
Alignment explanation
Indices: 538--584 Score: 69
Period size: 18 Copynumber: 2.5 Consensus size: 19
528 TTATTTTTTT
538 TTTCTTTCTCCTTCTTCCC
1 TTTCTTTCTCCTTCTTCCC
*
557 TTTC-TTCTCCTTCTTCCT
1 TTTCTTTCTCCTTCTTCCC
575 TCTTCTTTCT
1 T-TTCTTTCT
585 TTCTTTCTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
18 14 0.56
19 7 0.28
20 4 0.16
ACGTcount: A:0.00, C:0.38, G:0.00, T:0.62
Consensus pattern (19 bp):
TTTCTTTCTCCTTCTTCCC
Found at i:588 original size:18 final size:17
Alignment explanation
Indices: 537--612 Score: 64
Period size: 18 Copynumber: 4.2 Consensus size: 17
527 ATTATTTTTT
537 TTTTCTTTCTCCTTCTTCC
1 TTTTCTTTCT--TTCTTCC
* *
556 CTTTCTTCTCCTTCTTCC
1 TTTTCTT-TCTTTCTTCC
*
574 TTCTTCTTTCTTTCTTTC
1 TT-TTCTTTCTTTCTTCC
*
592 TTTCTCTTT-TTTCTTTC
1 TTT-TCTTTCTTTCTTCC
609 TTTT
1 TTTT
613 TTCCTTCATT
Statistics
Matches: 49, Mismatches: 5, Indels: 9
0.78 0.08 0.14
Matches are distributed among these distances:
16 1 0.02
17 12 0.24
18 23 0.47
19 11 0.22
20 2 0.04
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (17 bp):
TTTTCTTTCTTTCTTCC
Found at i:610 original size:32 final size:32
Alignment explanation
Indices: 535--615 Score: 85
Period size: 32 Copynumber: 2.6 Consensus size: 32
525 ACATTATTTT
*
535 TTTTTTCTTTC-TCCTTCTTCCCTTTCTTCTC
1 TTTTTTCTTTCTTCTTTCTTCCCTTTCTTCTC
* * * *
566 CTTCTTCCTTCTTCTTTCTT-TCTTTCTTTCTC
1 TTTTTTCTTTCTTCTTTCTTCCCTTTC-TTCTC
*
598 TTTTTTCTTTCTTTTTTC
1 TTTTTTCTTTCTTCTTTC
616 CTTCATTTTT
Statistics
Matches: 39, Mismatches: 9, Indels: 3
0.76 0.18 0.06
Matches are distributed among these distances:
31 13 0.33
32 26 0.67
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (32 bp):
TTTTTTCTTTCTTCTTTCTTCCCTTTCTTCTC
Found at i:612 original size:11 final size:11
Alignment explanation
Indices: 574--626 Score: 56
Period size: 11 Copynumber: 4.9 Consensus size: 11
564 TCCTTCTTCC
*
574 TTCTTCTTTCT
1 TTCTTTTTTCT
585 TTCTTTCTTTC-
1 TTCTTT-TTTCT
596 -TCTTTTTTCT
1 TTCTTTTTTCT
*
606 TTCTTTTTTCC
1 TTCTTTTTTCT
*
617 TTCATTTTTC
1 TTCTTTTTTC
627 GTTGGTCCCC
Statistics
Matches: 36, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
9 4 0.11
10 5 0.14
11 23 0.64
12 4 0.11
ACGTcount: A:0.02, C:0.25, G:0.00, T:0.74
Consensus pattern (11 bp):
TTCTTTTTTCT
Found at i:624 original size:21 final size:21
Alignment explanation
Indices: 557--624 Score: 61
Period size: 21 Copynumber: 3.1 Consensus size: 21
547 CCTTCTTCCC
*
557 TTTCTTCTCCTTC-TTCCTTCTT
1 TTTCTT-TCTTTCTTTCCTTC-T
579 CTTTCTTTCTTTCTTTCTCTT-T
1 -TTTCTTTCTTTCTTTC-CTTCT
601 TTTCTTTCTTT-TTTCCTTCAT
1 TTTCTTTCTTTCTTTCCTTC-T
622 TTT
1 TTT
625 TCGTTGGTCC
Statistics
Matches: 40, Mismatches: 1, Indels: 10
0.78 0.02 0.20
Matches are distributed among these distances:
19 3 0.08
20 4 0.10
21 15 0.38
22 6 0.15
23 9 0.22
24 3 0.08
ACGTcount: A:0.01, C:0.28, G:0.00, T:0.71
Consensus pattern (21 bp):
TTTCTTTCTTTCTTTCCTTCT
Found at i:825 original size:27 final size:27
Alignment explanation
Indices: 787--839 Score: 88
Period size: 27 Copynumber: 2.0 Consensus size: 27
777 CAAGTGGCAA
*
787 ATATTCCTCCATTGGTGTCGACACTTG
1 ATATTCCTCCATTGGTGCCGACACTTG
*
814 ATATTCCTCCATTGGTGCCGCCACTT
1 ATATTCCTCCATTGGTGCCGACACTT
840 CTTGTTCCTC
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.17, C:0.30, G:0.17, T:0.36
Consensus pattern (27 bp):
ATATTCCTCCATTGGTGCCGACACTTG
Found at i:847 original size:27 final size:27
Alignment explanation
Indices: 787--851 Score: 85
Period size: 27 Copynumber: 2.4 Consensus size: 27
777 CAAGTGGCAA
* *
787 ATATTCCTCCATTGGTGTCGACACTTG
1 ATATTCCTCCATTGGTGCCGACACTTC
*
814 ATATTCCTCCATTGGTGCCGCCACTTC
1 ATATTCCTCCATTGGTGCCGACACTTC
* *
841 TTGTTCCTCCA
1 ATATTCCTCCA
852 CTGGATGTCA
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
27 33 1.00
ACGTcount: A:0.15, C:0.32, G:0.15, T:0.37
Consensus pattern (27 bp):
ATATTCCTCCATTGGTGCCGACACTTC
Found at i:4301 original size:7 final size:7
Alignment explanation
Indices: 4289--4328 Score: 80
Period size: 7 Copynumber: 5.7 Consensus size: 7
4279 CCTGACAGTA
4289 AGTAATT
1 AGTAATT
4296 AGTAATT
1 AGTAATT
4303 AGTAATT
1 AGTAATT
4310 AGTAATT
1 AGTAATT
4317 AGTAATT
1 AGTAATT
4324 AGTAA
1 AGTAA
4329 AAAGAGAGTA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 33 1.00
ACGTcount: A:0.45, C:0.00, G:0.15, T:0.40
Consensus pattern (7 bp):
AGTAATT
Found at i:8345 original size:4 final size:4
Alignment explanation
Indices: 8336--8404 Score: 59
Period size: 4 Copynumber: 17.0 Consensus size: 4
8326 AAATAAACGG
* * * *
8336 GAAA GAAA GAAA GGAAA GAAA GAAA GAAA AAAA GGAA GAAG GAGAG GAAA
1 GAAA GAAA GAAA -GAAA GAAA GAAA GAAA GAAA GAAA GAAA GA-AA GAAA
* *
8386 GAAA G-GA GAAG GAAA GAAA
1 GAAA GAAA GAAA GAAA GAAA
8405 TGTTATGTAT
Statistics
Matches: 52, Mismatches: 10, Indels: 6
0.76 0.15 0.09
Matches are distributed among these distances:
3 2 0.04
4 42 0.81
5 8 0.15
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (4 bp):
GAAA
Found at i:8362 original size:21 final size:21
Alignment explanation
Indices: 8336--8404 Score: 77
Period size: 21 Copynumber: 3.2 Consensus size: 21
8326 AAATAAACGG
8336 GAAAGAAAGAAAGGAAAGAAA
1 GAAAGAAAGAAAGGAAAGAAA
* *
8357 GAAAGAAAAAAAGG-AAGAAG
1 GAAAGAAAGAAAGGAAAGAAA
*
8377 GAGAGGAAAGAAAGGAGAAGGAAA
1 GA-AAGAAAGAAAGGA-AA-GAAA
8401 GAAA
1 GAAA
8405 TGTTATGTAT
Statistics
Matches: 38, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
20 7 0.18
21 23 0.61
23 3 0.08
24 5 0.13
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (21 bp):
GAAAGAAAGAAAGGAAAGAAA
Found at i:8393 original size:14 final size:15
Alignment explanation
Indices: 8340--8404 Score: 59
Period size: 15 Copynumber: 4.5 Consensus size: 15
8330 AAACGGGAAA
8340 GAAAGAAAGGA-AA-
1 GAAAGAAAGGAGAAG
* *
8353 GAAAGAAAGAAAAAAAG
1 GAAAGAAAG--GAGAAG
8370 G-AAG-AAGGAG-AG
1 GAAAGAAAGGAGAAG
8382 GAAAGAAAGGAGAAG
1 GAAAGAAAGGAGAAG
8397 GAAAGAAA
1 GAAAGAAA
8405 TGTTATGTAT
Statistics
Matches: 42, Mismatches: 3, Indels: 12
0.74 0.05 0.21
Matches are distributed among these distances:
12 3 0.07
13 13 0.31
14 6 0.14
15 14 0.33
16 5 0.12
17 1 0.02
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (15 bp):
GAAAGAAAGGAGAAG
Done.