Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01003121.1 Kokia drynarioides strain JFW-HI SEQ_115694, 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: 55613
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Warning! 88 characters in sequence are not A, C, G, or T
Found at i:4505 original size:7 final size:7
Alignment explanation
Indices: 4493--4533 Score: 61
Period size: 6 Copynumber: 6.3 Consensus size: 7
4483 AGATTAAAAG
4493 AAAAGGA
1 AAAAGGA
4500 AAAAGGA
1 AAAAGGA
4507 AAAA-GA
1 AAAAGGA
4513 AAAA-GA
1 AAAAGGA
4519 AAAAGG-
1 AAAAGGA
4525 AAAAGGA
1 AAAAGGA
4532 AA
1 AA
4534 TTTATATTTT
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
6 18 0.56
7 14 0.44
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (7 bp):
AAAAGGA
Found at i:4508 original size:13 final size:13
Alignment explanation
Indices: 4488--4533 Score: 60
Period size: 13 Copynumber: 3.7 Consensus size: 13
4478 GGAAAAGATT
4488 AAAA-GAAAAGGA
1 AAAAGGAAAAGGA
*
4500 AAAAGGAAAAAGA
1 AAAAGGAAAAGGA
*
4513 AAAAGAAAAAGG-
1 AAAAGGAAAAGGA
4525 AAAAGGAAA
1 AAAAGGAAA
4534 TTTATATTTT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
12 12 0.41
13 17 0.59
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (13 bp):
AAAAGGAAAAGGA
Found at i:4510 original size:19 final size:19
Alignment explanation
Indices: 4488--4533 Score: 74
Period size: 19 Copynumber: 2.4 Consensus size: 19
4478 GGAAAAGATT
*
4488 AAAAGAAAAGGAAAAAGGA
1 AAAAGAAAAAGAAAAAGGA
4507 AAAAGAAAAAGAAAAAGGA
1 AAAAGAAAAAGAAAAAGGA
*
4526 AAAGGAAA
1 AAAAGAAA
4534 TTTATATTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (19 bp):
AAAAGAAAAAGAAAAAGGA
Found at i:4582 original size:29 final size:30
Alignment explanation
Indices: 4540--4597 Score: 100
Period size: 29 Copynumber: 2.0 Consensus size: 30
4530 GAAATTTATA
4540 TTTTATATTTTAAAAAATAA-ATTAAAATT
1 TTTTATATTTTAAAAAATAATATTAAAATT
*
4569 TTTTATATTTTAAAAAATAATTTTAAAAT
1 TTTTATATTTTAAAAAATAATATTAAAAT
4598 CATTTGTTGA
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
29 20 0.74
30 7 0.26
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (30 bp):
TTTTATATTTTAAAAAATAATATTAAAATT
Found at i:4893 original size:25 final size:24
Alignment explanation
Indices: 4821--4907 Score: 68
Period size: 25 Copynumber: 3.5 Consensus size: 24
4811 TATTAGGGGT
*
4821 TAAATTTAAATACTCAAATAATAAAA
1 TAAAATTAAATA-TCAAATAA-AAAA
* *
4847 -AAAACTCAAATATCAATTTAAAAAA
1 TAAAA-TTAAATATCAA-ATAAAAAA
* *
4872 TAAAATTAAATATCAAGATAAATAT
1 TAAAATTAAATATCAA-ATAAAAAA
*
4897 TATAATTAAAT
1 TAAAATTAAAT
4908 CAAGTACCAA
Statistics
Matches: 49, Mismatches: 9, Indels: 7
0.75 0.14 0.11
Matches are distributed among these distances:
25 36 0.73
26 13 0.27
ACGTcount: A:0.61, C:0.07, G:0.01, T:0.31
Consensus pattern (24 bp):
TAAAATTAAATATCAAATAAAAAA
Found at i:11491 original size:2 final size:2
Alignment explanation
Indices: 11484--11508 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
11474 TCTTCATTTA
11484 TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG T
11509 TAGGCACATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:23982 original size:13 final size:14
Alignment explanation
Indices: 23966--23998 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
23956 TTATAAAATT
23966 TAAATTTAAA-AAA
1 TAAATTTAAACAAA
23979 TAAATTTAAACAAA
1 TAAATTTAAACAAA
*
23993 AAAATT
1 TAAATT
23999 ATTTAAAATA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 10 0.56
14 8 0.44
ACGTcount: A:0.67, C:0.03, G:0.00, T:0.30
Consensus pattern (14 bp):
TAAATTTAAACAAA
Found at i:25823 original size:63 final size:63
Alignment explanation
Indices: 25724--25849 Score: 252
Period size: 63 Copynumber: 2.0 Consensus size: 63
25714 CACGAAGCAC
25724 CAAATCCAGTAATAAAACGATAGGAGCCCTTTGATATAACCGGTCAGCGAAACCTCCGACTGA
1 CAAATCCAGTAATAAAACGATAGGAGCCCTTTGATATAACCGGTCAGCGAAACCTCCGACTGA
25787 CAAATCCAGTAATAAAACGATAGGAGCCCTTTGATATAACCGGTCAGCGAAACCTCCGACTGA
1 CAAATCCAGTAATAAAACGATAGGAGCCCTTTGATATAACCGGTCAGCGAAACCTCCGACTGA
25850 AACGTGGTTG
Statistics
Matches: 63, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
63 63 1.00
ACGTcount: A:0.37, C:0.25, G:0.19, T:0.19
Consensus pattern (63 bp):
CAAATCCAGTAATAAAACGATAGGAGCCCTTTGATATAACCGGTCAGCGAAACCTCCGACTGA
Found at i:31346 original size:39 final size:39
Alignment explanation
Indices: 31303--31453 Score: 205
Period size: 39 Copynumber: 3.9 Consensus size: 39
31293 AAATGCCTGT
* * *
31303 GGGCCAGATGAGTTCCATATATCCTCAGCAAATGCCAAC
1 GGGCCAGATGGGTTCAATGTATCCTCAGCAAATGCCAAC
* * *
31342 GGGCCAAATGGGTTCAATGTATCCTCAGCAAGTGCC-AG
1 GGGCCAGATGGGTTCAATGTATCCTCAGCAAATGCCAAC
*
31380 GGGCCCAGATGGGTTCAATGTATCCTCAGCAAATGCCAGC
1 GGG-CCAGATGGGTTCAATGTATCCTCAGCAAATGCCAAC
* *
31420 TGGCCAGATGGGTTCAATGTATCCTCGGCAAATG
1 GGGCCAGATGGGTTCAATGTATCCTCAGCAAATG
31454 TATGGCAACC
Statistics
Matches: 98, Mismatches: 12, Indels: 4
0.86 0.11 0.04
Matches are distributed among these distances:
38 4 0.04
39 92 0.94
40 2 0.02
ACGTcount: A:0.26, C:0.25, G:0.26, T:0.22
Consensus pattern (39 bp):
GGGCCAGATGGGTTCAATGTATCCTCAGCAAATGCCAAC
Found at i:31435 original size:78 final size:78
Alignment explanation
Indices: 31306--31450 Score: 227
Period size: 78 Copynumber: 1.9 Consensus size: 78
31296 TGCCTGTGGG
*
31306 CCAGATGAGTTCCATATATCCTCAGCAAATGCCAACGGGCCAAATGGGTTCAATGTATCCTCAGC
1 CCAGATGAGTTCAATATATCCTCAGCAAATGCCAACGGGCCAAATGGGTTCAATGTATCCTCAGC
31371 AAGTGCCAGGGGC
66 AAGTGCCAGGGGC
* * * * * *
31384 CCAGATGGGTTCAATGTATCCTCAGCAAATGCCAGCTGGCCAGATGGGTTCAATGTATCCTCGGC
1 CCAGATGAGTTCAATATATCCTCAGCAAATGCCAACGGGCCAAATGGGTTCAATGTATCCTCAGC
31449 AA
66 AA
31451 ATGTATGGCA
Statistics
Matches: 60, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
78 60 1.00
ACGTcount: A:0.27, C:0.26, G:0.25, T:0.22
Consensus pattern (78 bp):
CCAGATGAGTTCAATATATCCTCAGCAAATGCCAACGGGCCAAATGGGTTCAATGTATCCTCAGC
AAGTGCCAGGGGC
Found at i:39649 original size:17 final size:16
Alignment explanation
Indices: 39607--39703 Score: 63
Period size: 17 Copynumber: 5.9 Consensus size: 16
39597 TACTAATTAC
* *
39607 ATAGCATATAAAAACA
1 ATAGAATATAAAAAGA
* *
39623 ACATAATATAATATAAGA
1 ATAGAATATAA-A-AAGA
*
39641 ATA-AATATAAAAATA
1 ATAGAATATAAAAAGA
* *
39656 CATAGCATATAAAAACA
1 -ATAGAATATAAAAAGA
*
39673 ATATAATATAATATAAGA
1 ATAGAATATAA-A-AAGA
39691 ATA-AATATAAAAA
1 ATAGAATATAAAAA
39704 TTATTCATGA
Statistics
Matches: 64, Mismatches: 11, Indels: 13
0.73 0.12 0.15
Matches are distributed among these distances:
15 5 0.08
16 22 0.34
17 26 0.41
18 11 0.17
ACGTcount: A:0.65, C:0.06, G:0.04, T:0.25
Consensus pattern (16 bp):
ATAGAATATAAAAAGA
Found at i:39663 original size:50 final size:50
Alignment explanation
Indices: 39604--39704 Score: 193
Period size: 50 Copynumber: 2.0 Consensus size: 50
39594 ATGTACTAAT
39604 TACATAGCATATAAAAACAACATAATATAATATAAGAATAAATATAAAAA
1 TACATAGCATATAAAAACAACATAATATAATATAAGAATAAATATAAAAA
*
39654 TACATAGCATATAAAAACAATATAATATAATATAAGAATAAATATAAAAA
1 TACATAGCATATAAAAACAACATAATATAATATAAGAATAAATATAAAAA
39704 T
1 T
39705 TATTCATGAA
Statistics
Matches: 50, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
50 50 1.00
ACGTcount: A:0.63, C:0.07, G:0.04, T:0.26
Consensus pattern (50 bp):
TACATAGCATATAAAAACAACATAATATAATATAAGAATAAATATAAAAA
Done.