Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01015026.1 Kokia drynarioides strain JFW-HI SEQ_130070, 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: 68521
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.33
Found at i:4053 original size:34 final size:34
Alignment explanation
Indices: 4010--4081 Score: 144
Period size: 34 Copynumber: 2.1 Consensus size: 34
4000 CTTTGCAGAC
4010 AACTCTATCATCACATAGAATTTCATTTTTCTTT
1 AACTCTATCATCACATAGAATTTCATTTTTCTTT
4044 AACTCTATCATCACATAGAATTTCATTTTTCTTT
1 AACTCTATCATCACATAGAATTTCATTTTTCTTT
4078 AACT
1 AACT
4082 ATCATGTCTA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 38 1.00
ACGTcount: A:0.31, C:0.21, G:0.03, T:0.46
Consensus pattern (34 bp):
AACTCTATCATCACATAGAATTTCATTTTTCTTT
Found at i:8742 original size:13 final size:13
Alignment explanation
Indices: 8724--8775 Score: 52
Period size: 12 Copynumber: 3.8 Consensus size: 13
8714 TCATAAATAG
8724 TTATAATATATAT
1 TTATAATATATAT
8737 TTATAATTAATATAATT
1 TTATAA-T-ATAT-A-T
8754 TTATAATAT-TAT
1 TTATAATATATAT
*
8766 TTAAAATATA
1 TTATAATATA
8776 AATAAATGAT
Statistics
Matches: 33, Mismatches: 1, Indels: 10
0.75 0.02 0.23
Matches are distributed among these distances:
12 9 0.27
13 7 0.21
14 2 0.06
15 6 0.18
16 2 0.06
17 7 0.21
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (13 bp):
TTATAATATATAT
Found at i:8749 original size:17 final size:17
Alignment explanation
Indices: 8727--8760 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
8717 TAAATAGTTA
8727 TAATAT-ATATTTATAAT
1 TAATATAAT-TTTATAAT
8744 TAATATAATTTTATAAT
1 TAATATAATTTTATAAT
8761 ATTATTTAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 14 0.88
18 2 0.12
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (17 bp):
TAATATAATTTTATAAT
Found at i:10061 original size:16 final size:15
Alignment explanation
Indices: 10020--10062 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 15
10010 CTTATATTTG
*
10020 TATATTTCATATCATC
1 TATATTT-ATATCATA
*
10036 TATTTTTATATCATA
1 TATATTTATATCATA
10051 TCATATTTATAT
1 T-ATATTTATAT
10063 AATACTTTGA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
15 8 0.35
16 15 0.65
ACGTcount: A:0.33, C:0.12, G:0.00, T:0.56
Consensus pattern (15 bp):
TATATTTATATCATA
Found at i:12646 original size:11 final size:11
Alignment explanation
Indices: 12630--12659 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
12620 AAAGTAGAAA
12630 AGGAAACTAGG
1 AGGAAACTAGG
*
12641 AGGAAACTGGG
1 AGGAAACTAGG
12652 AGGAAACT
1 AGGAAACT
12660 TCAAGGACCT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.43, C:0.10, G:0.37, T:0.10
Consensus pattern (11 bp):
AGGAAACTAGG
Found at i:13167 original size:16 final size:18
Alignment explanation
Indices: 13146--13178 Score: 52
Period size: 16 Copynumber: 1.9 Consensus size: 18
13136 CATGTCAAAA
13146 TAATATT-T-AAATTCAT
1 TAATATTGTAAAATTCAT
13162 TAATATTGTAAAATTCA
1 TAATATTGTAAAATTCA
13179 ATGAAAAATT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 7 0.47
17 1 0.07
18 7 0.47
ACGTcount: A:0.45, C:0.06, G:0.03, T:0.45
Consensus pattern (18 bp):
TAATATTGTAAAATTCAT
Found at i:19650 original size:12 final size:14
Alignment explanation
Indices: 19622--19667 Score: 58
Period size: 13 Copynumber: 3.2 Consensus size: 14
19612 ATATTTTAAT
19622 AAAATTCAAATTTA
1 AAAATTCAAATTTA
*
19636 AAAATT-AAATTAA
1 AAAATTCAAATTTA
19649 AAAATGTCAAATTCTA
1 AAAAT-TCAAATT-TA
19665 AAA
1 AAA
19668 TTAATGTGAA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
13 11 0.41
14 7 0.26
15 5 0.19
16 4 0.15
ACGTcount: A:0.61, C:0.07, G:0.02, T:0.30
Consensus pattern (14 bp):
AAAATTCAAATTTA
Found at i:19658 original size:28 final size:28
Alignment explanation
Indices: 19617--19702 Score: 90
Period size: 28 Copynumber: 3.0 Consensus size: 28
19607 TTATTATATT
19617 TTAATAAAAT-TCAAATTTAAAAATTAAA
1 TTAA-AAAATGTCAAATTTAAAAATTAAA
19645 TTAAAAAATGTCAAATTCT-AAAATT-AA
1 TTAAAAAATGTCAAATT-TAAAAATTAAA
*
19672 TGTGAAAAAATGT-TAATTTCAAAAATTAAA
1 T-T-AAAAAATGTCAAATTT-AAAAATTAAA
19702 T
1 T
19703 GTTCCTTTAC
Statistics
Matches: 50, Mismatches: 1, Indels: 12
0.79 0.02 0.19
Matches are distributed among these distances:
27 9 0.18
28 22 0.44
29 16 0.32
30 3 0.06
ACGTcount: A:0.56, C:0.05, G:0.05, T:0.35
Consensus pattern (28 bp):
TTAAAAAATGTCAAATTTAAAAATTAAA
Found at i:19679 original size:29 final size:27
Alignment explanation
Indices: 19617--19700 Score: 82
Period size: 29 Copynumber: 3.0 Consensus size: 27
19607 TTATTATATT
19617 TTAATAAAAT-TCAAATT-TAAAAATTAAA
1 TTAA-AAAATGTCAAATTCT-AAAATT-AA
19645 TTAAAAAATGTCAAATTCTAAAATTAA
1 TTAAAAAATGTCAAATTCTAAAATTAA
* * *
19672 TGTGAAAAAATGTTAATTTCAAAAATTAA
1 T-T-AAAAAATGTCAAATTCTAAAATTAA
19701 ATGTTCCTTT
Statistics
Matches: 49, Mismatches: 3, Indels: 7
0.83 0.05 0.12
Matches are distributed among these distances:
27 8 0.16
28 18 0.37
29 23 0.47
ACGTcount: A:0.56, C:0.05, G:0.05, T:0.35
Consensus pattern (27 bp):
TTAAAAAATGTCAAATTCTAAAATTAA
Found at i:22885 original size:21 final size:20
Alignment explanation
Indices: 22848--22886 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
22838 ATCCCGAATA
*
22848 TTGAACTCAAATCTTGAACT
1 TTGAACTCAAATATTGAACT
*
22868 TTGAACCTTAAATATTGAA
1 TTGAA-CTCAAATATTGAA
22887 TTAAGGTTTA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 5 0.31
21 11 0.69
ACGTcount: A:0.38, C:0.15, G:0.10, T:0.36
Consensus pattern (20 bp):
TTGAACTCAAATATTGAACT
Found at i:36094 original size:7 final size:7
Alignment explanation
Indices: 36077--36105 Score: 51
Period size: 7 Copynumber: 4.3 Consensus size: 7
36067 AACATATAAC
36077 ATTAAAT
1 ATTAAAT
36084 -TTAAAT
1 ATTAAAT
36090 ATTAAAT
1 ATTAAAT
36097 ATTAAAT
1 ATTAAAT
36104 AT
1 AT
36106 ATACAGGCAC
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
6 6 0.29
7 15 0.71
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (7 bp):
ATTAAAT
Found at i:38627 original size:17 final size:17
Alignment explanation
Indices: 38605--38639 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
38595 TTTAACTGTG
38605 GAAAAAAAACAAAAAAA
1 GAAAAAAAACAAAAAAA
* *
38622 GAAAAAAAGCAAATAAA
1 GAAAAAAAACAAAAAAA
38639 G
1 G
38640 TTTGTTTTGT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.80, C:0.06, G:0.11, T:0.03
Consensus pattern (17 bp):
GAAAAAAAACAAAAAAA
Found at i:39360 original size:12 final size:12
Alignment explanation
Indices: 39343--39368 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
39333 TAACTAGATG
39343 ATGATTATTATT
1 ATGATTATTATT
39355 ATGATTATTATT
1 ATGATTATTATT
39367 AT
1 AT
39369 TTTGAATTAA
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:0.35, C:0.00, G:0.08, T:0.58
Consensus pattern (12 bp):
ATGATTATTATT
Found at i:58342 original size:69 final size:69
Alignment explanation
Indices: 58222--58392 Score: 270
Period size: 69 Copynumber: 2.5 Consensus size: 69
58212 ACAATACTAG
* *
58222 CTACGATTATAAGTAATTTCTCGACATCAGAGACCACTCAGTCGCATTCCAATATGCAGTCAATT
1 CTACGATTATAAGTAATTTCTAGACATCAGAGACCACTCAGTCGCATTCCAAAATGCAGTCAATT
58287 ATAA
66 ATAA
* * * *
58291 CTATGATTGTAAGTAATTTCTAGACATCAGAGACCCCTCAGTTGCATTCCAAAATGCAGTCAATT
1 CTACGATTATAAGTAATTTCTAGACATCAGAGACCACTCAGTCGCATTCCAAAATGCAGTCAATT
58356 ATAA
66 ATAA
* *
58360 CTACGATTTTAAGTAATTTCTAGACATAAGAGA
1 CTACGATTATAAGTAATTTCTAGACATCAGAGA
58393 ACATCACTCA
Statistics
Matches: 93, Mismatches: 9, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
69 93 1.00
ACGTcount: A:0.36, C:0.20, G:0.14, T:0.30
Consensus pattern (69 bp):
CTACGATTATAAGTAATTTCTAGACATCAGAGACCACTCAGTCGCATTCCAAAATGCAGTCAATT
ATAA
Found at i:60251 original size:22 final size:22
Alignment explanation
Indices: 60217--60261 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
60207 TTGATATTGG
* *
60217 ATCAACATTATTTAATTCAAAA
1 ATCAACATGATTTAATTAAAAA
* *
60239 ATCATCATGATTTTATTAAAAA
1 ATCAACATGATTTAATTAAAAA
60261 A
1 A
60262 CAAGTATTGT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.49, C:0.11, G:0.02, T:0.38
Consensus pattern (22 bp):
ATCAACATGATTTAATTAAAAA
Found at i:60987 original size:12 final size:12
Alignment explanation
Indices: 60970--61009 Score: 53
Period size: 12 Copynumber: 3.3 Consensus size: 12
60960 AACAAATAAC
*
60970 TAAAATGTAATA
1 TAAAATATAATA
60982 TAAAATATAATA
1 TAAAATATAATA
* *
60994 TCAAATACAATA
1 TAAAATATAATA
61006 TAAA
1 TAAA
61010 TAAGTAAATG
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.62, C:0.05, G:0.03, T:0.30
Consensus pattern (12 bp):
TAAAATATAATA
Found at i:62818 original size:25 final size:25
Alignment explanation
Indices: 62790--62894 Score: 87
Period size: 23 Copynumber: 4.4 Consensus size: 25
62780 CGTCTCGTGC
62790 TCTCTGTTATTAGCACTGTGTGTGT
1 TCTCTGTTATTAGCACTGTGTGTGT
* *
62815 TCTCTG--ATTAGTACTTTGTGTAG-
1 TCTCTGTTATTAGCACTGTGTGT-GT
* * *
62838 TCTTTG-T-TTAGCAATGTGTGTGC
1 TCTCTGTTATTAGCACTGTGTGTGT
* *
62861 TCTCTGTTATCCAGCACT-TATGTGT
1 TCTCTGTTAT-TAGCACTGTGTGTGT
62886 TCTCTGTTA
1 TCTCTGTTA
62895 GTACTTTGGT
Statistics
Matches: 63, Mismatches: 11, Indels: 12
0.73 0.13 0.14
Matches are distributed among these distances:
22 1 0.02
23 34 0.54
24 2 0.03
25 21 0.33
26 5 0.08
ACGTcount: A:0.14, C:0.17, G:0.21, T:0.48
Consensus pattern (25 bp):
TCTCTGTTATTAGCACTGTGTGTGT
Found at i:62865 original size:71 final size:69
Alignment explanation
Indices: 62766--62915 Score: 196
Period size: 71 Copynumber: 2.1 Consensus size: 69
62756 CACTAGCGCG
* * * *
62766 CTCTCTGTTTAGC-ACGTCTCGTGCTCTCTGTTAT-TAGCACTGTGTGTGTTCTCTGATTAGTAC
1 CTCTCTGTTTAGCAATGTGT-GTGCTCTCTGTTATCCAGCACT-TATGTGTTCTCTG-TTAGTAC
62829 TTTGTGTA
63 TTTG-GTA
* *
62837 GTCTTTGTTTAGCAATGTGTGTGCTCTCTGTTATCCAGCACTTATGTGTTCTCTGTTAGTACTTT
1 CTCTCTGTTTAGCAATGTGTGTGCTCTCTGTTATCCAGCACTTATGTGTTCTCTGTTAGTACTTT
62902 GGTA
66 GGTA
62906 CTCTCTGTTT
1 CTCTCTGTTT
62916 GTTCCGTATA
Statistics
Matches: 69, Mismatches: 8, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
69 11 0.16
70 11 0.16
71 37 0.54
72 10 0.14
ACGTcount: A:0.13, C:0.20, G:0.21, T:0.47
Consensus pattern (69 bp):
CTCTCTGTTTAGCAATGTGTGTGCTCTCTGTTATCCAGCACTTATGTGTTCTCTGTTAGTACTTT
GGTA
Found at i:62868 original size:23 final size:23
Alignment explanation
Indices: 62765--62868 Score: 77
Period size: 23 Copynumber: 4.4 Consensus size: 23
62755 ACACTAGCGC
* *
62765 GCTCTCTGTTTAGC-ACGTCTCGT
1 GCTCTCTGTTTAGCAATGTGT-GT
*
62788 GCTCTCTGTTATTAGCACTGTGTGT
1 GCTCTCTG-T-TTAGCAATGTGTGT
* * * * *
62813 GTTCTCTGATTAGTACTTTGTGT
1 GCTCTCTGTTTAGCAATGTGTGT
*
62836 AG-TCTTTGTTTAGCAATGTGTGT
1 -GCTCTCTGTTTAGCAATGTGTGT
62859 GCTCTCTGTT
1 GCTCTCTGTT
62869 ATCCAGCACT
Statistics
Matches: 63, Mismatches: 13, Indels: 10
0.73 0.15 0.12
Matches are distributed among these distances:
22 1 0.02
23 43 0.68
24 2 0.03
25 14 0.22
26 3 0.05
ACGTcount: A:0.12, C:0.19, G:0.23, T:0.46
Consensus pattern (23 bp):
GCTCTCTGTTTAGCAATGTGTGT
Found at i:64935 original size:26 final size:26
Alignment explanation
Indices: 64886--64935 Score: 73
Period size: 26 Copynumber: 1.9 Consensus size: 26
64876 TAATAACGGA
*
64886 TTGCTCTATTATTATTATTTTGTTAC
1 TTGCTCTATTATTATTATTATGTTAC
* *
64912 TTGCTCTATTTTTATTGTTATGTT
1 TTGCTCTATTATTATTATTATGTT
64936 GGTATAGTTT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.16, C:0.10, G:0.10, T:0.64
Consensus pattern (26 bp):
TTGCTCTATTATTATTATTATGTTAC
Done.