Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01008369.1 Kokia drynarioides strain JFW-HI SEQ_123036, 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: 44990
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:7476 original size:24 final size:24
Alignment explanation
Indices: 7427--7477 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
7417 AATTCTAGTC
* *
7427 AATGCAAAATATATTTTGCTAATA
1 AATGCAAAATATATTATACTAATA
* *
7451 AATGCTAAATATATTATACTACTA
1 AATGCAAAATATATTATACTAATA
7475 AAT
1 AAT
7478 CTTTTAGAGA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.47, C:0.10, G:0.06, T:0.37
Consensus pattern (24 bp):
AATGCAAAATATATTATACTAATA
Found at i:9804 original size:24 final size:24
Alignment explanation
Indices: 9777--9823 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
9767 AAGCCTAATT
* *
9777 CTAATCAATTCAAAATATATTATG
1 CTAATAAATGCAAAATATATTATG
*
9801 CTAATAAATGCTAAATATATTAT
1 CTAATAAATGCAAAATATATTAT
9824 ACTACTAACT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.47, C:0.11, G:0.04, T:0.38
Consensus pattern (24 bp):
CTAATAAATGCAAAATATATTATG
Found at i:10046 original size:12 final size:12
Alignment explanation
Indices: 10031--10056 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
10021 ATAAATTAAA
10031 ATTTAAAAATAT
1 ATTTAAAAATAT
10043 ATTTAAAAATAT
1 ATTTAAAAATAT
10055 AT
1 AT
10057 AAATTAATTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (12 bp):
ATTTAAAAATAT
Found at i:11985 original size:26 final size:26
Alignment explanation
Indices: 11955--12016 Score: 72
Period size: 26 Copynumber: 2.3 Consensus size: 26
11945 AATTTATTTC
*
11955 TTTTATATATTTATAGTTTCTTATA-A
1 TTTTATATAATTATAG-TTCTTATATA
* *
11981 TTTTATAAAATTATAGTTCTTTTATA
1 TTTTATATAATTATAGTTCTTATATA
12007 TATTTATATA
1 T-TTTATATA
12017 CTTTTATAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
25 7 0.23
26 16 0.53
27 7 0.23
ACGTcount: A:0.34, C:0.03, G:0.03, T:0.60
Consensus pattern (26 bp):
TTTTATATAATTATAGTTCTTATATA
Found at i:12005 original size:19 final size:18
Alignment explanation
Indices: 11976--12026 Score: 57
Period size: 19 Copynumber: 2.8 Consensus size: 18
11966 TATAGTTTCT
*
11976 TATAATTTTATAAAATTA
1 TATACTTTTATAAAATTA
* * *
11994 TAGTTCTTTTATATATTTA
1 TA-TACTTTTATAAAATTA
12013 TATACTTTTATAAA
1 TATACTTTTATAAA
12027 TTTACAAAAT
Statistics
Matches: 26, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
18 12 0.46
19 14 0.54
ACGTcount: A:0.39, C:0.04, G:0.02, T:0.55
Consensus pattern (18 bp):
TATACTTTTATAAAATTA
Found at i:12022 original size:18 final size:18
Alignment explanation
Indices: 11976--12030 Score: 65
Period size: 18 Copynumber: 3.0 Consensus size: 18
11966 TATAGTTTCT
* *
11976 TATAATTTTATAAAATTA
1 TATACTTTTATAAATTTA
* *
11994 TAGTTCTTTTATATATTTA
1 TA-TACTTTTATAAATTTA
12013 TATACTTTTATAAATTTA
1 TATACTTTTATAAATTTA
12031 CAAAATTTTA
Statistics
Matches: 30, Mismatches: 6, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
18 16 0.53
19 14 0.47
ACGTcount: A:0.38, C:0.04, G:0.02, T:0.56
Consensus pattern (18 bp):
TATACTTTTATAAATTTA
Found at i:12024 original size:45 final size:45
Alignment explanation
Indices: 11952--12037 Score: 122
Period size: 45 Copynumber: 1.9 Consensus size: 45
11942 ACCAATTTAT
* *
11952 TTCTTTTATATATTTATAGTTTCTTATAATTTTATAAAATTATAG
1 TTCTTTTATATATTTATAGTTTCTTATAAATTTACAAAATTATAG
11997 TTCTTTTATATATTTATA-TACTT-TTATAAATTTACAAAATT
1 TTCTTTTATATATTTATAGT--TTCTTATAAATTTACAAAATT
12038 TTAAACTTTT
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
44 1 0.03
45 34 0.92
46 2 0.05
ACGTcount: A:0.35, C:0.06, G:0.02, T:0.57
Consensus pattern (45 bp):
TTCTTTTATATATTTATAGTTTCTTATAAATTTACAAAATTATAG
Found at i:12353 original size:19 final size:21
Alignment explanation
Indices: 12314--12354 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
12304 TAAAAAAAAC
*
12314 TATATACTTTTTAAATTAATT
1 TATATACTTTTTAAATGAATT
12335 TATATA-TTTTTAAA-GAATT
1 TATATACTTTTTAAATGAATT
12354 T
1 T
12355 TTAATCTATG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 5 0.26
20 8 0.42
21 6 0.32
ACGTcount: A:0.39, C:0.02, G:0.02, T:0.56
Consensus pattern (21 bp):
TATATACTTTTTAAATGAATT
Found at i:12494 original size:32 final size:33
Alignment explanation
Indices: 12458--12554 Score: 101
Period size: 32 Copynumber: 3.0 Consensus size: 33
12448 TAGTGATGAG
12458 GTACCAAAC-TGAGTGACGCAATACAAGTTAAT
1 GTACCAAACTTGAGTGACGCAATACAAGTTAAT
* * *
12490 GTACC-AACTTGGGTGATGGAATACAAGTTAAT
1 GTACCAAACTTGAGTGACGCAATACAAGTTAAT
* * * * *
12522 GTACC-ACCTTGGGTGAGGGAATAAAAGTTAAT
1 GTACCAAACTTGAGTGACGCAATACAAGTTAAT
12554 G
1 G
12555 GAGAGTTACT
Statistics
Matches: 58, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
31 3 0.05
32 55 0.95
ACGTcount: A:0.36, C:0.14, G:0.25, T:0.25
Consensus pattern (33 bp):
GTACCAAACTTGAGTGACGCAATACAAGTTAAT
Found at i:14390 original size:19 final size:18
Alignment explanation
Indices: 14352--14396 Score: 56
Period size: 19 Copynumber: 2.5 Consensus size: 18
14342 GAATTTAAGG
* *
14352 GAGAATTGAGAGATATTT
1 GAGAATTGAGAGAGAGTT
14370 GAGAATGTGAGAGAGAGTT
1 GAGAAT-TGAGAGAGAGTT
14389 GAG-ATTGA
1 GAGAATTGA
14397 ATTGCAAGAG
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
17 3 0.12
18 8 0.33
19 13 0.54
ACGTcount: A:0.38, C:0.00, G:0.36, T:0.27
Consensus pattern (18 bp):
GAGAATTGAGAGAGAGTT
Found at i:19306 original size:44 final size:44
Alignment explanation
Indices: 19207--19346 Score: 174
Period size: 44 Copynumber: 3.0 Consensus size: 44
19197 TAGTTGTGAA
* *
19207 TTTATTTCTTTTATATATTTATACATATTATTTTATAAATTTAT-TAAT
1 TTTAGTTCTTTTATATA-TT-T--ATATT-TTTTATAAATTTATAAAAT
*
19255 TTGTAGTTCTTTTATATATTTATATTTTTTATAAACTTATAAAAT
1 TT-TAGTTCTTTTATATATTTATATTTTTTATAAATTTATAAAAT
*
19300 TTTAGTTCTTTTATATATTTATATATATTTATAAATTTATAAAAT
1 TTTAGTTCTTTTATATATTTATAT-TTTTTATAAATTTATAAAAT
19345 TT
1 TT
19347 AAATTTTTAT
Statistics
Matches: 84, Mismatches: 5, Indels: 9
0.86 0.05 0.09
Matches are distributed among these distances:
44 35 0.42
45 30 0.36
47 1 0.01
48 4 0.05
49 14 0.17
ACGTcount: A:0.34, C:0.04, G:0.02, T:0.60
Consensus pattern (44 bp):
TTTAGTTCTTTTATATATTTATATTTTTTATAAATTTATAAAAT
Found at i:19426 original size:20 final size:20
Alignment explanation
Indices: 19403--19449 Score: 58
Period size: 21 Copynumber: 2.3 Consensus size: 20
19393 ACTTTTCAAA
19403 ATATTTGAAGTTTTTTTTAT
1 ATATTTGAAGTTTTTTTTAT
* *
19423 ATATTTTTAATTTTTTTTTAT
1 ATA-TTTGAAGTTTTTTTTAT
*
19444 AAATTT
1 ATATTT
19450 ATATTTTATA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
20 6 0.26
21 17 0.74
ACGTcount: A:0.28, C:0.00, G:0.04, T:0.68
Consensus pattern (20 bp):
ATATTTGAAGTTTTTTTTAT
Found at i:19450 original size:19 final size:21
Alignment explanation
Indices: 19413--19456 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 21
19403 ATATTTGAAG
**
19413 TTTTTTTTATATATTTTTA-A
1 TTTTTTTTATATAAATTTATA
19433 TTTTTTTT-TATAAATTTATA
1 TTTTTTTTATATAAATTTATA
19453 TTTT
1 TTTT
19457 ATATTTTAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 8 0.38
20 13 0.62
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (21 bp):
TTTTTTTTATATAAATTTATA
Found at i:21819 original size:49 final size:49
Alignment explanation
Indices: 21669--21821 Score: 139
Period size: 49 Copynumber: 3.1 Consensus size: 49
21659 GCACACAAAT
* * * * * * *
21669 TGTGTGTAATTTTGTAGCCCATGTGTG-TTGGCCATGTGGGGCATACGATCA
1 TGTGTG-AA-TTTGTAGCCCGTGTG-GATAGGCCATGTGGAGCACAAGACCG
*
21720 TGTGTGAATTTGTAGCCCGTGTGGATAGGCCATGTGGGGCACAAGACCG
1 TGTGTGAATTTGTAGCCCGTGTGGATAGGCCATGTGGAGCACAAGACCG
* ** * *
21769 TGTGTGATTTTGTAGCTTGTGTAGG-TAGGCCATGTGGAGCACACGGCCG
1 TGTGTGAATTTGTAGCCCGTGT-GGATAGGCCATGTGGAGCACAAGACCG
21818 TGTG
1 TGTG
21822 AAATCATGCA
Statistics
Matches: 88, Mismatches: 12, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
48 1 0.01
49 77 0.88
50 4 0.05
51 6 0.07
ACGTcount: A:0.18, C:0.16, G:0.35, T:0.31
Consensus pattern (49 bp):
TGTGTGAATTTGTAGCCCGTGTGGATAGGCCATGTGGAGCACAAGACCG
Found at i:24281 original size:18 final size:17
Alignment explanation
Indices: 24255--24298 Score: 52
Period size: 18 Copynumber: 2.5 Consensus size: 17
24245 ATGAACTTTC
*
24255 TTTTTTTTTTTAATTTG
1 TTTTATTTTTTAATTTG
*
24272 ATTTTATTTTTTATTTTG
1 -TTTTATTTTTTAATTTG
24290 TATTTATTT
1 T-TTTATTT
24299 GATTGGGCCC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
17 1 0.04
18 22 0.96
ACGTcount: A:0.16, C:0.00, G:0.05, T:0.80
Consensus pattern (17 bp):
TTTTATTTTTTAATTTG
Found at i:24616 original size:5 final size:5
Alignment explanation
Indices: 24599--24662 Score: 60
Period size: 5 Copynumber: 12.8 Consensus size: 5
24589 GGGATAGGGC
* * * *
24599 ATGAT ATGTT ATGAT ATGAT -TCATT ATGAT ATGAT ATGAT -TCATT ATGTT
1 ATGAT ATGAT ATGAT ATGAT ATGA-T ATGAT ATGAT ATGAT ATGA-T ATGAT
24649 ATGAT ATGAT ATGA
1 ATGAT ATGAT ATGA
24663 AACGTTTTGA
Statistics
Matches: 47, Mismatches: 8, Indels: 8
0.75 0.13 0.13
Matches are distributed among these distances:
4 4 0.09
5 40 0.85
6 3 0.06
ACGTcount: A:0.34, C:0.03, G:0.17, T:0.45
Consensus pattern (5 bp):
ATGAT
Found at i:24626 original size:20 final size:20
Alignment explanation
Indices: 24603--24658 Score: 103
Period size: 20 Copynumber: 2.8 Consensus size: 20
24593 TAGGGCATGA
24603 TATGTTATGATATGATTCAT
1 TATGTTATGATATGATTCAT
*
24623 TATGATATGATATGATTCAT
1 TATGTTATGATATGATTCAT
24643 TATGTTATGATATGAT
1 TATGTTATGATATGAT
24659 ATGAAACGTT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.32, C:0.04, G:0.16, T:0.48
Consensus pattern (20 bp):
TATGTTATGATATGATTCAT
Found at i:28662 original size:10 final size:11
Alignment explanation
Indices: 28646--28683 Score: 51
Period size: 10 Copynumber: 3.5 Consensus size: 11
28636 GTTCTCTTAA
28646 AATAATATAAT
1 AATAATATAAT
28657 -ATAATATAAT
1 AATAATATAAT
*
28667 AATAATAATAAC
1 AATAAT-ATAAT
28679 AATAA
1 AATAA
28684 ATTAATTGTT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
10 10 0.42
11 5 0.21
12 9 0.38
ACGTcount: A:0.66, C:0.03, G:0.00, T:0.32
Consensus pattern (11 bp):
AATAATATAAT
Found at i:29927 original size:20 final size:20
Alignment explanation
Indices: 29890--30019 Score: 156
Period size: 20 Copynumber: 6.5 Consensus size: 20
29880 GGGGTAGGAC
*
29890 ATGATATG-TTATGATATGAT
1 ATGATATGATT-TGTTATGAT
*
29910 ATGAT-TCGTTTTGTTATGAT
1 ATGATAT-GATTTGTTATGAT
* *
29930 ATGATATGATTTATTATGAA
1 ATGATATGATTTGTTATGAT
29950 ATGATATGATTTGTTATGAT
1 ATGATATGATTTGTTATGAT
* *
29970 GTGATATGATTCGTTATGAT
1 ATGATATGATTTGTTATGAT
* *
29990 ATGATAAGATTTGTTATGTT
1 ATGATATGATTTGTTATGAT
30010 ATGATATGAT
1 ATGATATGAT
30020 ATTCTAATTT
Statistics
Matches: 94, Mismatches: 13, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
19 1 0.01
20 90 0.96
21 3 0.03
ACGTcount: A:0.31, C:0.02, G:0.20, T:0.48
Consensus pattern (20 bp):
ATGATATGATTTGTTATGAT
Found at i:30037 original size:5 final size:5
Alignment explanation
Indices: 29890--30021 Score: 90
Period size: 5 Copynumber: 26.4 Consensus size: 5
29880 GGGGTAGGAC
* * * *
29890 ATGAT ATGTT ATGAT ATGAT ATGAT -TCGTT TTGTT ATGAT ATGAT ATGAT
1 ATGAT ATGAT ATGAT ATGAT ATGAT AT-GAT ATGAT ATGAT ATGAT ATGAT
* * * * * *
29940 -TTATT ATGAA ATGAT ATGAT TTGTT ATGAT GTGAT ATGAT -TCGTT ATGAT
1 ATGA-T ATGAT ATGAT ATGAT ATGAT ATGAT ATGAT ATGAT AT-GAT ATGAT
* * * *
29990 ATGAT AAGAT TTGTT ATGTT ATGAT ATGAT AT
1 ATGAT ATGAT ATGAT ATGAT ATGAT ATGAT AT
30022 TCTAATTTAT
Statistics
Matches: 98, Mismatches: 23, Indels: 12
0.74 0.17 0.09
Matches are distributed among these distances:
4 4 0.04
5 90 0.92
6 4 0.04
ACGTcount: A:0.31, C:0.02, G:0.20, T:0.48
Consensus pattern (5 bp):
ATGAT
Found at i:32705 original size:19 final size:19
Alignment explanation
Indices: 32681--32718 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
32671 ATGCTCTTTA
32681 ATCTTACTTATTACTTTCC
1 ATCTTACTTATTACTTTCC
32700 ATCTTACTTATTACTTTCC
1 ATCTTACTTATTACTTTCC
32719 TTAGAAATAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.21, C:0.26, G:0.00, T:0.53
Consensus pattern (19 bp):
ATCTTACTTATTACTTTCC
Found at i:37641 original size:18 final size:18
Alignment explanation
Indices: 37594--37641 Score: 69
Period size: 18 Copynumber: 2.7 Consensus size: 18
37584 GCTTGTCCTC
*
37594 AAGCAAACAAAACAAGAA
1 AAGCAAACAAAGCAAGAA
* *
37612 AAGCGAATAAAGCAAGAA
1 AAGCAAACAAAGCAAGAA
37630 AAGCAAACAAAG
1 AAGCAAACAAAG
37642 GAGCTTGAGT
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.67, C:0.15, G:0.17, T:0.02
Consensus pattern (18 bp):
AAGCAAACAAAGCAAGAA
Found at i:42253 original size:22 final size:22
Alignment explanation
Indices: 42223--42264 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
42213 TTGAGACTGA
* *
42223 CGTCGATGTCATGACAAAGAAC
1 CGTCCATGTCACGACAAAGAAC
*
42245 CGTCCATGTCACGAGAAAGA
1 CGTCCATGTCACGACAAAGA
42265 GTACAGAATT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.36, C:0.24, G:0.24, T:0.17
Consensus pattern (22 bp):
CGTCCATGTCACGACAAAGAAC
Done.