Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01005965.1 Kokia drynarioides strain JFW-HI SEQ_120369, 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: 37815
ACGTcount: A:0.34, C:0.15, G:0.17, T:0.34
Found at i:1568 original size:37 final size:37
Alignment explanation
Indices: 1513--1618 Score: 149
Period size: 37 Copynumber: 2.9 Consensus size: 37
1503 CATCTAAAAA
1513 ATTCAGGCTTTGTGCTTAGTAGGCTTCGTGCCGGTGT
1 ATTCAGGCTTTGTGCTTAGTAGGCTTCGTGCCGGTGT
* *
1550 ATTCGGGCTTTGTGCTTAGTAGGCTTCGTACCGGTGT
1 ATTCAGGCTTTGTGCTTAGTAGGCTTCGTGCCGGTGT
* * * * *
1587 ATTCAAGTTTTGTGCCTAGTAGGTTTTGTGCC
1 ATTCAGGCTTTGTGCTTAGTAGGCTTCGTGCC
1619 AATGATCAAA
Statistics
Matches: 60, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
37 60 1.00
ACGTcount: A:0.12, C:0.18, G:0.30, T:0.40
Consensus pattern (37 bp):
ATTCAGGCTTTGTGCTTAGTAGGCTTCGTGCCGGTGT
Found at i:2908 original size:17 final size:18
Alignment explanation
Indices: 2886--2919 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
2876 ACAATTGTAG
*
2886 TTTAAAT-TCTAATTATT
1 TTTAAATGTATAATTATT
2903 TTTAAATGTATAATTAT
1 TTTAAATGTATAATTAT
2920 CATAACTTCT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.38, C:0.03, G:0.03, T:0.56
Consensus pattern (18 bp):
TTTAAATGTATAATTATT
Found at i:8648 original size:21 final size:19
Alignment explanation
Indices: 8622--8674 Score: 70
Period size: 21 Copynumber: 2.6 Consensus size: 19
8612 GGAGTTTTTG
8622 GTATCGGTAGATGCATGACTT
1 GTATCGGTAGAT-CAT-ACTT
8643 GTATCGGTAGAAATCATACTT
1 GTATCGGTAG--ATCATACTT
8664 GTATCGGTAGA
1 GTATCGGTAGA
8675 GCTAACATAA
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
19 1 0.03
21 24 0.80
22 3 0.10
23 2 0.07
ACGTcount: A:0.28, C:0.13, G:0.26, T:0.32
Consensus pattern (19 bp):
GTATCGGTAGATCATACTT
Found at i:11137 original size:22 final size:22
Alignment explanation
Indices: 11095--11139 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
11085 CGATCAACGG
* *
11095 GTCAATGGGTTAAAGTCAATTA
1 GTCAATGGGTCAAAGCCAATTA
11117 GTCAATGGGTCAAA-CCAAATTA
1 GTCAATGGGTCAAAGCC-AATTA
11139 G
1 G
11140 GTTTAGGGTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 1 0.05
22 19 0.95
ACGTcount: A:0.38, C:0.13, G:0.22, T:0.27
Consensus pattern (22 bp):
GTCAATGGGTCAAAGCCAATTA
Found at i:11245 original size:15 final size:16
Alignment explanation
Indices: 11206--11245 Score: 50
Period size: 15 Copynumber: 2.7 Consensus size: 16
11196 TAGGCTTCAT
11206 GGTT-TTGGGTTATAG
1 GGTTATTGGGTTATAG
*
11221 GGTTA-AGGGTTA-AG
1 GGTTATTGGGTTATAG
11235 GGTTATTGGGT
1 GGTTATTGGGT
11246 CACTTCTTTG
Statistics
Matches: 21, Mismatches: 2, Indels: 4
0.78 0.07 0.15
Matches are distributed among these distances:
14 7 0.33
15 14 0.67
ACGTcount: A:0.17, C:0.00, G:0.42, T:0.40
Consensus pattern (16 bp):
GGTTATTGGGTTATAG
Found at i:14356 original size:17 final size:18
Alignment explanation
Indices: 14330--14366 Score: 58
Period size: 17 Copynumber: 2.1 Consensus size: 18
14320 AAAGTCCTCA
14330 AAACGAGTAATACA-AAT
1 AAACGAGTAATACATAAT
*
14347 AAACGGGTAATACATAAT
1 AAACGAGTAATACATAAT
14365 AA
1 AA
14367 TCCATCTAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 13 0.72
18 5 0.28
ACGTcount: A:0.57, C:0.11, G:0.14, T:0.19
Consensus pattern (18 bp):
AAACGAGTAATACATAAT
Found at i:21823 original size:37 final size:39
Alignment explanation
Indices: 21742--21824 Score: 91
Period size: 37 Copynumber: 2.2 Consensus size: 39
21732 TTAGTACGTC
21742 CGAAGTATAATATGCACTTCGAACCTCATCGATATAAAAT
1 CGAAGTAT-ATATGCACTTCGAACCTCATCGATATAAAAT
* ** * *
21782 -GAAGTAT-TATGCGCTTCGTGCCTCATCGGT-TTAAAT
1 CGAAGTATATATGCACTTCGAACCTCATCGATATAAAAT
21818 CGAAGTA
1 CGAAGTA
21825 AACATATAAA
Statistics
Matches: 37, Mismatches: 5, Indels: 5
0.79 0.11 0.11
Matches are distributed among these distances:
36 5 0.14
37 25 0.68
39 7 0.19
ACGTcount: A:0.33, C:0.19, G:0.18, T:0.30
Consensus pattern (39 bp):
CGAAGTATATATGCACTTCGAACCTCATCGATATAAAAT
Found at i:23612 original size:20 final size:19
Alignment explanation
Indices: 23587--23637 Score: 61
Period size: 19 Copynumber: 2.7 Consensus size: 19
23577 TTGAAGTCCA
23587 AAAATAAATAAATA-AATTAT
1 AAAATAAATAAA-ACAA-TAT
23607 AAAAT-AATAAAACAATAT
1 AAAATAAATAAAACAATAT
*
23625 AAAATATATAAAA
1 AAAATAAATAAAA
23638 TTATATTGTG
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
18 9 0.32
19 14 0.50
20 5 0.18
ACGTcount: A:0.73, C:0.02, G:0.00, T:0.25
Consensus pattern (19 bp):
AAAATAAATAAAACAATAT
Found at i:26763 original size:25 final size:24
Alignment explanation
Indices: 26724--26771 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 24
26714 CAAACCCAAT
26724 AACCCTAACTCGAACTCGTGTGACCC
1 AACCCTAACTCGAAC-CGT-TGACCC
*
26750 AACCC-AACTTGAACCGTTGACC
1 AACCCTAACTCGAACCGTTGACC
26772 ATTGACCATT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
23 5 0.24
24 3 0.14
25 8 0.38
26 5 0.24
ACGTcount: A:0.29, C:0.38, G:0.15, T:0.19
Consensus pattern (24 bp):
AACCCTAACTCGAACCGTTGACCC
Found at i:27412 original size:6 final size:6
Alignment explanation
Indices: 27403--27456 Score: 72
Period size: 6 Copynumber: 9.0 Consensus size: 6
27393 TATATTACCA
* * * *
27403 TGAGAT TGAGAT TGAGAT TAAGAT TGAGAC TGAGAT TGAGAC TGAGAC
1 TGAGAT TGAGAT TGAGAT TGAGAT TGAGAT TGAGAT TGAGAT TGAGAT
27451 TGAGAT
1 TGAGAT
27457 ATACATGTTA
Statistics
Matches: 42, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
6 42 1.00
ACGTcount: A:0.35, C:0.06, G:0.31, T:0.28
Consensus pattern (6 bp):
TGAGAT
Found at i:32618 original size:15 final size:17
Alignment explanation
Indices: 32588--32619 Score: 50
Period size: 15 Copynumber: 2.0 Consensus size: 17
32578 TTATTTCGAT
32588 TTAATTTCGATATAGTA
1 TTAATTTCGATATAGTA
32605 TTAATTT-G-TATAGTA
1 TTAATTTCGATATAGTA
32620 CTAGTATAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 7 0.47
16 1 0.07
17 7 0.47
ACGTcount: A:0.34, C:0.03, G:0.12, T:0.50
Consensus pattern (17 bp):
TTAATTTCGATATAGTA
Done.