Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01001406.1 Kokia drynarioides strain JFW-HI SEQ_112894, 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: 63870
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.34
Warning! 2 characters in sequence are not A, C, G, or T
Found at i:2998 original size:24 final size:23
Alignment explanation
Indices: 2961--3022 Score: 81
Period size: 23 Copynumber: 2.7 Consensus size: 23
2951 AAAGAAGAGA
* *
2961 AAAATAAGTGAAAAGAACAAAAAG
1 AAAATGAGT-AAAAAAACAAAAAG
*
2985 AAAATGAGTAAAAATACAAAAAG
1 AAAATGAGTAAAAAAACAAAAAG
3008 AAAA-GAGTAAAAAAA
1 AAAATGAGTAAAAAAA
3023 GTGTGAAAAG
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
22 10 0.29
23 16 0.47
24 8 0.24
ACGTcount: A:0.73, C:0.03, G:0.15, T:0.10
Consensus pattern (23 bp):
AAAATGAGTAAAAAAACAAAAAG
Found at i:14418 original size:30 final size:30
Alignment explanation
Indices: 14382--14442 Score: 122
Period size: 30 Copynumber: 2.0 Consensus size: 30
14372 AGTTAACTCG
14382 TACAGGGATGATGGATCTAGAAGAAGGAAT
1 TACAGGGATGATGGATCTAGAAGAAGGAAT
14412 TACAGGGATGATGGATCTAGAAGAAGGAAT
1 TACAGGGATGATGGATCTAGAAGAAGGAAT
14442 T
1 T
14443 CACGAAGACA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.39, C:0.07, G:0.33, T:0.21
Consensus pattern (30 bp):
TACAGGGATGATGGATCTAGAAGAAGGAAT
Found at i:17709 original size:21 final size:20
Alignment explanation
Indices: 17680--17727 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 20
17670 AATAATATTT
17680 AATAAATTTATAAAATTTAAA
1 AATAAATTT-TAAAATTTAAA
* * *
17701 AATATATTTTTAGATTTAAA
1 AATAAATTTTAAAATTTAAA
*
17721 AAAAAAT
1 AATAAAT
17728 AAGATTTGAA
Statistics
Matches: 22, Mismatches: 5, Indels: 1
0.79 0.18 0.04
Matches are distributed among these distances:
20 14 0.64
21 8 0.36
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (20 bp):
AATAAATTTTAAAATTTAAA
Found at i:28708 original size:2 final size:2
Alignment explanation
Indices: 28701--28741 Score: 73
Period size: 2 Copynumber: 20.5 Consensus size: 2
28691 ATCCCTCAAT
*
28701 CA CA CA CA CA CA CA CA CA CA TA CA CA CA CA CA CA CA CA CA C
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA C
28742 TTATATATAT
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.49, G:0.00, T:0.02
Consensus pattern (2 bp):
CA
Found at i:37701 original size:15 final size:15
Alignment explanation
Indices: 37673--37740 Score: 50
Period size: 15 Copynumber: 4.5 Consensus size: 15
37663 TGGAAGATGT
**
37673 GAGCACTCGCGTTGC
1 GAGCACTCATGTTGC
37688 GAGCACTCATGTTGC
1 GAGCACTCATGTTGC
*
37703 G-GACACTCAT-TACGC
1 GAG-CACTCATGT-TGC
* *
37718 GAACACTGATGTTGC
1 GAGCACTCATGTTGC
*
37733 GAACACTC
1 GAGCACTC
37741 GCGTTTCGAG
Statistics
Matches: 42, Mismatches: 7, Indels: 8
0.74 0.12 0.14
Matches are distributed among these distances:
14 2 0.05
15 39 0.93
16 1 0.02
ACGTcount: A:0.24, C:0.29, G:0.25, T:0.22
Consensus pattern (15 bp):
GAGCACTCATGTTGC
Found at i:37710 original size:30 final size:30
Alignment explanation
Indices: 37676--37750 Score: 73
Period size: 30 Copynumber: 2.5 Consensus size: 30
37666 AAGATGTGAG
*
37676 CACTCGCGTTGCGAGCACTCATGTTGCGGA
1 CACTCGCGTTGCGAGCACTCATGTTGCGAA
* * *
37706 CACT--CATTACGCGAACACTGATGTTGCGAA
1 CACTCGCGTT--GCGAGCACTCATGTTGCGAA
*
37736 CACTCGCGTTTCGAG
1 CACTCGCGTTGCGAG
37751 AATGGAGGGT
Statistics
Matches: 34, Mismatches: 7, Indels: 8
0.69 0.14 0.16
Matches are distributed among these distances:
28 3 0.09
30 28 0.82
32 3 0.09
ACGTcount: A:0.21, C:0.29, G:0.25, T:0.24
Consensus pattern (30 bp):
CACTCGCGTTGCGAGCACTCATGTTGCGAA
Found at i:37911 original size:30 final size:30
Alignment explanation
Indices: 37875--37950 Score: 152
Period size: 30 Copynumber: 2.5 Consensus size: 30
37865 GGAAGACACT
37875 TCATGCATTCCATGCATTTTATACAACCCG
1 TCATGCATTCCATGCATTTTATACAACCCG
37905 TCATGCATTCCATGCATTTTATACAACCCG
1 TCATGCATTCCATGCATTTTATACAACCCG
37935 TCATGCATTCCATGCA
1 TCATGCATTCCATGCA
37951 ATGTGCTGTA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 46 1.00
ACGTcount: A:0.26, C:0.30, G:0.11, T:0.33
Consensus pattern (30 bp):
TCATGCATTCCATGCATTTTATACAACCCG
Found at i:38445 original size:17 final size:17
Alignment explanation
Indices: 38423--38477 Score: 101
Period size: 17 Copynumber: 3.2 Consensus size: 17
38413 ATTCGGCCAA
*
38423 CTACTCCGTTGAAACAG
1 CTACTCCGTTGAAGCAG
38440 CTACTCCGTTGAAGCAG
1 CTACTCCGTTGAAGCAG
38457 CTACTCCGTTGAAGCAG
1 CTACTCCGTTGAAGCAG
38474 CTAC
1 CTAC
38478 CACATTAACT
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
17 37 1.00
ACGTcount: A:0.25, C:0.31, G:0.20, T:0.24
Consensus pattern (17 bp):
CTACTCCGTTGAAGCAG
Found at i:42725 original size:31 final size:31
Alignment explanation
Indices: 42678--42814 Score: 110
Period size: 31 Copynumber: 4.5 Consensus size: 31
42668 TATGTATAAC
42678 ATTTGATA-CTAGAACTTGACA-TTTTCTCTTA
1 ATTTGATACCTA-AACTTGACACTTTT-TCTTA
* * * *
42709 ATTTGGTACCTAAACTT----TTTTTTGTCCA
1 ATTTGATACCTAAACTTGACACTTTTTCT-TA
42737 ATTTGATA-CTCAAACTTGACACTTTTTCTTA
1 ATTTGATACCT-AAACTTGACACTTTTTCTTA
*
42768 ATTTGATACCTAAAATTGACACTTTTT-TTA
1 ATTTGATACCTAAACTTGACACTTTTTCTTA
* * *
42798 AGTTGGTACTTAAACTT
1 ATTTGATACCTAAACTT
42815 TTTGGGGTCC
Statistics
Matches: 85, Mismatches: 12, Indels: 19
0.73 0.10 0.16
Matches are distributed among these distances:
27 4 0.05
28 18 0.21
30 16 0.19
31 36 0.42
32 11 0.13
ACGTcount: A:0.28, C:0.16, G:0.09, T:0.46
Consensus pattern (31 bp):
ATTTGATACCTAAACTTGACACTTTTTCTTA
Found at i:42830 original size:89 final size:91
Alignment explanation
Indices: 42678--42868 Score: 248
Period size: 89 Copynumber: 2.1 Consensus size: 91
42668 TATGTATAAC
* * ***
42678 ATTTGATA-CTAGAACTTGACATTTTCTCTTAATTTGGTACCTAAACTTTTTTTTGTCCAATTTG
1 ATTTGATACCTAGAAATTGACATTTTCTCTTAAGTTGGTACCTAAACTTTTTGGGGTCCAATTTG
*
42742 ATA-CTCAAACTTGACACTTTTTCTTA
66 ATACCT-AAACTTGACACTTTTTCCTA
*
42768 ATTTGATACCTA-AAATTGACACTTTT-T-TTAAGTTGGTACTTAAACTTTTTGGGGTCCAATTT
1 ATTTGATACCTAGAAATTGACA-TTTTCTCTTAAGTTGGTACCTAAACTTTTTGGGGTCCAATTT
**
42830 GATACCTAAACTTGACTGTTTTTCCTA
65 GATACCTAAACTTGACACTTTTTCCTA
42857 ATTTGATACCTA
1 ATTTGATACCTA
42869 CTTTTTTTAA
Statistics
Matches: 89, Mismatches: 9, Indels: 7
0.85 0.09 0.07
Matches are distributed among these distances:
89 63 0.71
90 19 0.21
91 7 0.08
ACGTcount: A:0.27, C:0.17, G:0.11, T:0.45
Consensus pattern (91 bp):
ATTTGATACCTAGAAATTGACATTTTCTCTTAAGTTGGTACCTAAACTTTTTGGGGTCCAATTTG
ATACCTAAACTTGACACTTTTTCCTA
Found at i:43182 original size:59 final size:58
Alignment explanation
Indices: 43033--43203 Score: 175
Period size: 58 Copynumber: 2.9 Consensus size: 58
43023 AAACTAAATC
* * * * * *
43033 TAAAAAGAAGCTTAGATACTAAATTAGGAAAAAATGTTAAGTTCAAGTACC-AAATTGGA
1 TAAAAA-AAGTTTAGGTACCAAATTAAGAAAAAGTG-TAAGTTCAAGTACCAAAATAGGA
* *
43092 TAAAAAAAGTTTAGTTACCAAATTAAAAAAAAGTGTAAGTTCAAGTACCAAAATAGG-
1 TAAAAAAAGTTTAGGTACCAAATTAAGAAAAAGTGTAAGTTCAAGTACCAAAATAGGA
* * * *
43149 TCAAAAAAGAGTTTAGGTATCAAATTAAGAAAAAGTGGAGAGTTCAGGTATCAAA
1 T-AAAAAA-AGTTTAGGTACCAAATTAAGAAAAAGTGTA-AGTTCAAGTACCAAA
43204 TGTTATATTA
Statistics
Matches: 95, Mismatches: 13, Indels: 7
0.83 0.11 0.06
Matches are distributed among these distances:
57 15 0.16
58 35 0.37
59 32 0.34
60 13 0.14
ACGTcount: A:0.50, C:0.08, G:0.18, T:0.25
Consensus pattern (58 bp):
TAAAAAAAGTTTAGGTACCAAATTAAGAAAAAGTGTAAGTTCAAGTACCAAAATAGGA
Found at i:47473 original size:30 final size:30
Alignment explanation
Indices: 47439--47500 Score: 124
Period size: 30 Copynumber: 2.1 Consensus size: 30
47429 GCAAGCTTAC
47439 TCAAAGGAAAAAGGATATCAAGATTCACTT
1 TCAAAGGAAAAAGGATATCAAGATTCACTT
47469 TCAAAGGAAAAAGGATATCAAGATTCACTT
1 TCAAAGGAAAAAGGATATCAAGATTCACTT
47499 TC
1 TC
47501 TTGGGCCGGT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.45, C:0.15, G:0.16, T:0.24
Consensus pattern (30 bp):
TCAAAGGAAAAAGGATATCAAGATTCACTT
Found at i:47885 original size:46 final size:46
Alignment explanation
Indices: 47801--47967 Score: 210
Period size: 46 Copynumber: 3.6 Consensus size: 46
47791 TCAAATCAAG
* * *
47801 TTGTCTTCCACAATTTCAGGGATTTGTTTTACTAGAGTGTAGGCAT
1 TTGTCTTCCATAATTTTAGGGATTTGTTTGACTAGAGTGTAGGCAT
* * *
47847 CTGTAC-TCCATAATTCTAGGGATTTGTTCGACTAGAGTGTAGGCAT
1 TTGT-CTTCCATAATTTTAGGGATTTGTTTGACTAGAGTGTAGGCAT
* * * * * *
47893 TTGTCTTCCACAATTTTAGGGATTTGTTTGGCTAAATTGTTGGTAT
1 TTGTCTTCCATAATTTTAGGGATTTGTTTGACTAGAGTGTAGGCAT
47939 TTGTCTTCCATAATTTTAGGGATTTGTTT
1 TTGTCTTCCATAATTTTAGGGATTTGTTT
47968 CTCTACCATC
Statistics
Matches: 103, Mismatches: 16, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
45 1 0.01
46 101 0.98
47 1 0.01
ACGTcount: A:0.21, C:0.14, G:0.22, T:0.44
Consensus pattern (46 bp):
TTGTCTTCCATAATTTTAGGGATTTGTTTGACTAGAGTGTAGGCAT
Found at i:47912 original size:23 final size:22
Alignment explanation
Indices: 47886--47965 Score: 74
Period size: 23 Copynumber: 3.5 Consensus size: 22
47876 GACTAGAGTG
*
47886 TAGGCATTTGTCTTCCACAATTT
1 TAGGGATTTGTCTTCCA-AATTT
*
47909 TAGGGATTTGT-TTGGCTAAATTGT
1 TAGGGATTTGTCTT--CCAAATT-T
*
47933 T-GGTATTTGTCTTCCATAATTT
1 TAGGGATTTGTCTTCCA-AATTT
47955 TAGGGATTTGT
1 TAGGGATTTGT
47966 TTCTCTACCA
Statistics
Matches: 46, Mismatches: 5, Indels: 12
0.73 0.08 0.19
Matches are distributed among these distances:
22 6 0.13
23 34 0.74
24 6 0.13
ACGTcount: A:0.20, C:0.11, G:0.21, T:0.47
Consensus pattern (22 bp):
TAGGGATTTGTCTTCCAAATTT
Found at i:51875 original size:14 final size:15
Alignment explanation
Indices: 51845--51878 Score: 54
Period size: 14 Copynumber: 2.4 Consensus size: 15
51835 TTTAAAATTT
51845 AAAT-TTAATATATA
1 AAATATTAATATATA
51859 AAATATTAATATA-A
1 AAATATTAATATATA
51873 AAATAT
1 AAATAT
51879 ATTCTTAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 11 0.58
15 8 0.42
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (15 bp):
AAATATTAATATATA
Found at i:52600 original size:20 final size:20
Alignment explanation
Indices: 52577--52615 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
52567 TTTATTTATT
52577 AAATAATAAT-TCTATAAATG
1 AAATAATAATCT-TATAAATG
52597 AAATAATAATCTTATAAAT
1 AAATAATAATCTTATAAAT
52616 AAAACTTTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 17 0.94
21 1 0.06
ACGTcount: A:0.56, C:0.05, G:0.03, T:0.36
Consensus pattern (20 bp):
AAATAATAATCTTATAAATG
Found at i:53142 original size:20 final size:19
Alignment explanation
Indices: 53114--53157 Score: 63
Period size: 20 Copynumber: 2.3 Consensus size: 19
53104 TATTAATTTG
53114 TTTATAAA-TTTATTATATT
1 TTTATAAATTTTA-TATATT
53133 TTTATAAAATTTTATATATT
1 TTTAT-AAATTTTATATATT
53153 TTTAT
1 TTTAT
53158 CGAAAAGTGA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 5 0.22
20 14 0.61
21 4 0.17
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (19 bp):
TTTATAAATTTTATATATT
Found at i:61206 original size:48 final size:48
Alignment explanation
Indices: 61150--61246 Score: 194
Period size: 48 Copynumber: 2.0 Consensus size: 48
61140 AGTAATACTA
61150 ACTGTAAGCGGTACTCTTGTTGTAGTAATCAAACATTGACAATAAATT
1 ACTGTAAGCGGTACTCTTGTTGTAGTAATCAAACATTGACAATAAATT
61198 ACTGTAAGCGGTACTCTTGTTGTAGTAATCAAACATTGACAATAAATT
1 ACTGTAAGCGGTACTCTTGTTGTAGTAATCAAACATTGACAATAAATT
61246 A
1 A
61247 TGTTAAACAA
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
48 49 1.00
ACGTcount: A:0.36, C:0.14, G:0.16, T:0.33
Consensus pattern (48 bp):
ACTGTAAGCGGTACTCTTGTTGTAGTAATCAAACATTGACAATAAATT
Done.