Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01004497.1 Kokia drynarioides strain JFW-HI SEQ_117931, 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: 28074
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Found at i:71 original size:6 final size:6
Alignment explanation
Indices: 62--102 Score: 82
Period size: 6 Copynumber: 6.8 Consensus size: 6
52 GAAAAAGTAG
62 ATATAA ATATAA ATATAA ATATAA ATATAA ATATAA ATATA
1 ATATAA ATATAA ATATAA ATATAA ATATAA ATATAA ATATA
103 GAAATGAAAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 35 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (6 bp):
ATATAA
Found at i:4590 original size:60 final size:62
Alignment explanation
Indices: 4524--4639 Score: 164
Period size: 60 Copynumber: 1.9 Consensus size: 62
4514 TTTTTGATCT
* *
4524 AATTTGATACTTGAACTTGACACTTTTTCT-TGATTTGACACCTAA-ATTTTTTTTGGACAC
1 AATTTGATACCTGAACTTGACACTTTTTCTCTAATTTGACACCTAAGATTTTTTTTGGACAC
* * * *
4584 AATTTGATACCTGAACTTGACATTTTTTTTCTAATTTGGCACCTAAGCTTTTTTTT
1 AATTTGATACCTGAACTTGACACTTTTTCTCTAATTTGACACCTAAGATTTTTTTT
4640 TTTTTTAGAT
Statistics
Matches: 48, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
60 27 0.56
61 13 0.27
62 8 0.17
ACGTcount: A:0.25, C:0.16, G:0.11, T:0.47
Consensus pattern (62 bp):
AATTTGATACCTGAACTTGACACTTTTTCTCTAATTTGACACCTAAGATTTTTTTTGGACAC
Found at i:6614 original size:21 final size:21
Alignment explanation
Indices: 6590--6629 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
6580 TAATTTTTTG
6590 TTCATATTCGTTTATTTAAAA
1 TTCATATTCGTTTATTTAAAA
* *
6611 TTCATGTTCGTTTGTTTAA
1 TTCATATTCGTTTATTTAA
6630 TGTTCACGAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.25, C:0.10, G:0.10, T:0.55
Consensus pattern (21 bp):
TTCATATTCGTTTATTTAAAA
Found at i:6635 original size:21 final size:21
Alignment explanation
Indices: 6588--6635 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
6578 TTTAATTTTT
6588 TGTTCATATTCGTTTATTTAA
1 TGTTCATATTCGTTTATTTAA
** * *
6609 AATTCATGTTCGTTTGTTTAA
1 TGTTCATATTCGTTTATTTAA
6630 TGTTCA
1 TGTTCA
6636 CGAACATGTT
Statistics
Matches: 21, Mismatches: 6, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.23, C:0.10, G:0.12, T:0.54
Consensus pattern (21 bp):
TGTTCATATTCGTTTATTTAA
Found at i:6690 original size:23 final size:24
Alignment explanation
Indices: 6664--6723 Score: 68
Period size: 24 Copynumber: 2.5 Consensus size: 24
6654 TTAATCAAAT
*
6664 ATGTTCACAAACAT-TAAATGAAC
1 ATGTTCACAAACATATAAATAAAC
* *
6687 ATGTTCACTAACATATAATTAAAC
1 ATGTTCACAAACATATAAATAAAC
* *
6711 ATATTCACGAACA
1 ATGTTCACAAACA
6724 ATGTTAATGA
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
23 13 0.42
24 18 0.58
ACGTcount: A:0.47, C:0.18, G:0.07, T:0.28
Consensus pattern (24 bp):
ATGTTCACAAACATATAAATAAAC
Found at i:7522 original size:27 final size:29
Alignment explanation
Indices: 7492--7547 Score: 80
Period size: 27 Copynumber: 2.0 Consensus size: 29
7482 TTTTCTTAAG
* *
7492 TATTTATATTTT-TTGAAAATTA-AAAAA
1 TATTTAAATTTTATTAAAAATTAGAAAAA
7519 TATTTAAATTTTATTAAAAATTAGAAAAA
1 TATTTAAATTTTATTAAAAATTAGAAAAA
7548 AAATTATAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
27 11 0.44
28 9 0.36
29 5 0.20
ACGTcount: A:0.52, C:0.00, G:0.04, T:0.45
Consensus pattern (29 bp):
TATTTAAATTTTATTAAAAATTAGAAAAA
Found at i:7558 original size:9 final size:9
Alignment explanation
Indices: 7546--7615 Score: 63
Period size: 9 Copynumber: 7.7 Consensus size: 9
7536 AAATTAGAAA
7546 AAAAATTAT
1 AAAAATTAT
*
7555 -AAAATCAT
1 AAAAATTAT
7563 AAAAA-TAT
1 AAAAATTAT
*
7571 AAAAAATTGT
1 -AAAAATTAT
*
7581 AAAATTTTAT
1 AAAA-ATTAT
*
7591 AAAAATCATT
1 AAAAATTA-T
7601 AAAAATTAT
1 AAAAATTAT
7610 AAAAAT
1 AAAAAT
7616 GCATAAAAAA
Statistics
Matches: 48, Mismatches: 8, Indels: 10
0.73 0.12 0.15
Matches are distributed among these distances:
8 9 0.19
9 22 0.46
10 17 0.35
ACGTcount: A:0.64, C:0.03, G:0.01, T:0.31
Consensus pattern (9 bp):
AAAAATTAT
Found at i:7558 original size:10 final size:10
Alignment explanation
Indices: 7545--7614 Score: 51
Period size: 10 Copynumber: 7.5 Consensus size: 10
7535 AAAATTAGAA
7545 AAAAAATTAT
1 AAAAAATTAT
*
7555 --AAAATCAT
1 AAAAAATTAT
7563 -AAAAA-TAT
1 AAAAAATTAT
*
7571 AAAAAATTGT
1 AAAAAATTAT
**
7581 AAAATTTTAT
1 AAAAAATTAT
*
7591 -AAAAATCAT
1 AAAAAATTAT
*
7600 TAAAAATTAT
1 AAAAAATTAT
7610 AAAAA
1 AAAAA
7615 TGCATAAAAA
Statistics
Matches: 45, Mismatches: 11, Indels: 8
0.70 0.17 0.12
Matches are distributed among these distances:
8 9 0.20
9 15 0.33
10 21 0.47
ACGTcount: A:0.66, C:0.03, G:0.01, T:0.30
Consensus pattern (10 bp):
AAAAAATTAT
Found at i:7566 original size:19 final size:20
Alignment explanation
Indices: 7544--7625 Score: 66
Period size: 19 Copynumber: 4.3 Consensus size: 20
7534 AAAAATTAGA
7544 AAAAAAATTAT-AAAATCAT
1 AAAAAAATTATAAAAATCAT
* **
7563 AAAAATA-TA-AAAAATTGT
1 AAAAAAATTATAAAAATCAT
**
7581 -AAAATTTTATAAAAATCAT
1 AAAAAAATTATAAAAATCAT
*
7600 -TAAAAATTATAAAAATGCAT
1 AAAAAAATTATAAAAAT-CAT
7620 AAAAAA
1 AAAAAA
7626 TGTTCTTTAA
Statistics
Matches: 48, Mismatches: 10, Indels: 8
0.73 0.15 0.12
Matches are distributed among these distances:
17 5 0.10
18 10 0.21
19 26 0.54
20 3 0.06
21 4 0.08
ACGTcount: A:0.66, C:0.04, G:0.02, T:0.28
Consensus pattern (20 bp):
AAAAAAATTATAAAAATCAT
Found at i:7605 original size:57 final size:57
Alignment explanation
Indices: 7507--7624 Score: 136
Period size: 57 Copynumber: 2.1 Consensus size: 57
7497 ATATTTTTTG
* *
7507 AAAATTAAAAAATATTTAAATTTTATTAAAAATTAGAAAAAAAATTAT-AAAAT-CATA
1 AAAATTAAAAAATATTAAAATTTTATTAAAAATCAG--AAAAAATTATAAAAATGCATA
**
7564 AAAATATAAAAAAT-TGTAAAATTTTA-TAAAAATCATTAAAAATTATAAAAATGCATA
1 AAAAT-TAAAAAATAT-TAAAATTTTATTAAAAATCAGAAAAAATTATAAAAATGCATA
7621 AAAA
1 AAAA
7625 ATGTTCTTTA
Statistics
Matches: 53, Mismatches: 4, Indels: 8
0.82 0.06 0.12
Matches are distributed among these distances:
55 9 0.17
56 5 0.09
57 22 0.42
58 17 0.32
ACGTcount: A:0.64, C:0.03, G:0.03, T:0.31
Consensus pattern (57 bp):
AAAATTAAAAAATATTAAAATTTTATTAAAAATCAGAAAAAATTATAAAAATGCATA
Found at i:7621 original size:10 final size:9
Alignment explanation
Indices: 7546--7624 Score: 54
Period size: 9 Copynumber: 8.6 Consensus size: 9
7536 AAATTAGAAA
*
7546 AAAAATTAT
1 AAAAATCAT
7555 -AAAATCAT
1 AAAAATCAT
7563 AAAAAT-AT
1 AAAAATCAT
**
7571 AAAAAATTGT
1 -AAAAATCAT
* *
7581 AAAATTTTAT
1 AAAA-ATCAT
7591 AAAAATCATT
1 AAAAATCA-T
*
7601 AAAAATTAT
1 AAAAATCAT
7610 AAAAATGCAT
1 AAAAAT-CAT
7620 AAAAA
1 AAAAA
7625 ATGTTCTTTA
Statistics
Matches: 56, Mismatches: 8, Indels: 11
0.75 0.11 0.15
Matches are distributed among these distances:
8 9 0.16
9 24 0.43
10 23 0.41
ACGTcount: A:0.65, C:0.04, G:0.03, T:0.29
Consensus pattern (9 bp):
AAAAATCAT
Found at i:7828 original size:18 final size:19
Alignment explanation
Indices: 7788--7828 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 19
7778 GTAAGATAAT
* *
7788 TTTTTATATTTTTTTATGA
1 TTTTTATATTTCTTTATCA
7807 -TTTTATATTTCTTTA-CA
1 TTTTTATATTTCTTTATCA
7824 TTTTT
1 TTTTT
7829 TTGTAATTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 3
0.79 0.08 0.12
Matches are distributed among these distances:
17 1 0.05
18 18 0.95
ACGTcount: A:0.20, C:0.05, G:0.02, T:0.73
Consensus pattern (19 bp):
TTTTTATATTTCTTTATCA
Found at i:7911 original size:28 final size:28
Alignment explanation
Indices: 7847--8009 Score: 116
Period size: 29 Copynumber: 5.5 Consensus size: 28
7837 TTTTTACGAA
7847 TTTATAAAATTTTAATATTTTATATTTTATGATT
1 TTTATAAAATTTTAA-A--TT-T-TTTTAT-ATT
7881 TTTATAAAATTTTACAATTTTTTTATATT
1 TTTATAAAATTTTA-AATTTTTTTATATT
** * *
7910 TTT-TACTATTTATATATTTTTTTCTA-T
1 TTTATAAAATTT-TAAATTTTTTTATATT
*
7937 TTTATAATAAATTTTAAATATTTTTATATT
1 TTTAT-A-AAATTTTAAATTTTTTTATATT
* * *
7967 TTTATTAAAATTTAATAATTTTTATA-ACT
1 TTTA-TAAAATTTTA-AATTTTTTTATATT
*
7996 TTTATTAAATTTTA
1 TTTATAAAATTTTA
8010 TTTTTCATAA
Statistics
Matches: 106, Mismatches: 15, Indels: 22
0.74 0.10 0.15
Matches are distributed among these distances:
27 4 0.04
28 25 0.24
29 33 0.31
30 24 0.23
31 2 0.02
32 2 0.02
34 15 0.14
35 1 0.01
ACGTcount: A:0.35, C:0.02, G:0.01, T:0.62
Consensus pattern (28 bp):
TTTATAAAATTTTAAATTTTTTTATATT
Found at i:7925 original size:18 final size:17
Alignment explanation
Indices: 7901--7942 Score: 66
Period size: 18 Copynumber: 2.4 Consensus size: 17
7891 TTTACAATTT
7901 TTTTATATTTTTTACTA
1 TTTTATATTTTTTACTA
*
7918 TTTATATATTTTTTTCTA
1 TTT-TATATTTTTTACTA
7936 TTTTATA
1 TTTTATA
7943 ATAAATTTTA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 7 0.30
18 16 0.70
ACGTcount: A:0.24, C:0.05, G:0.00, T:0.71
Consensus pattern (17 bp):
TTTTATATTTTTTACTA
Found at i:9169 original size:5 final size:5
Alignment explanation
Indices: 9159--9184 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
9149 AAGAGACCTA
9159 AACAC AACAC AACAC AACAC AACAC A
1 AACAC AACAC AACAC AACAC AACAC A
9185 GTTAGCAACT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.62, C:0.38, G:0.00, T:0.00
Consensus pattern (5 bp):
AACAC
Found at i:16112 original size:104 final size:104
Alignment explanation
Indices: 15984--16296 Score: 590
Period size: 104 Copynumber: 3.0 Consensus size: 104
15974 CTAATACTAC
15984 TACTGAAATTGCTTCCTATTGACACAATCAACCTGAACTTCTCACTTTCACAAATGGATAACCAA
1 TACTGAAATTGCTTCCTATTGACACAATCAACCTGAACTTCTCACTTTCACAAATGGATAACCAA
16049 TAAACATAAAATGCCCACAACTTAGAATTTTAAGGCTAT
66 TAAACATAAAATGCCCACAACTTAGAATTTTAAGGCTAT
* *
16088 TACTGAAATTGCTTCCTATTGACACGATCAACCTGAACTTCTCACTTTCACAAATGGACAACCAA
1 TACTGAAATTGCTTCCTATTGACACAATCAACCTGAACTTCTCACTTTCACAAATGGATAACCAA
*
16153 TAAACATAAAATGCCCACAACTTAGAATTTTAAGGTTAT
66 TAAACATAAAATGCCCACAACTTAGAATTTTAAGGCTAT
*
16192 TACTGAAATTGCTTCCTATTGACACAATCAACCTGAGCTTCTCACTTTCACAAATGGATAACCAA
1 TACTGAAATTGCTTCCTATTGACACAATCAACCTGAACTTCTCACTTTCACAAATGGATAACCAA
16257 TAAACATAAAATGCCCACAACTTAGAATTTTAAGGCTAT
66 TAAACATAAAATGCCCACAACTTAGAATTTTAAGGCTAT
16296 T
1 T
16297 TTCAGTACCC
Statistics
Matches: 202, Mismatches: 7, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
104 202 1.00
ACGTcount: A:0.38, C:0.23, G:0.10, T:0.29
Consensus pattern (104 bp):
TACTGAAATTGCTTCCTATTGACACAATCAACCTGAACTTCTCACTTTCACAAATGGATAACCAA
TAAACATAAAATGCCCACAACTTAGAATTTTAAGGCTAT
Found at i:19173 original size:31 final size:31
Alignment explanation
Indices: 19138--19198 Score: 95
Period size: 31 Copynumber: 2.0 Consensus size: 31
19128 CTTTATGCAG
* *
19138 CACTATTTTAAATCATTTAAATATTATTTAC
1 CACTATATTAAATCATTTAAATATAATTTAC
*
19169 CACTATATTAAATTATTTAAATATAATTTA
1 CACTATATTAAATCATTTAAATATAATTTA
19199 TTATTATATT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.43, C:0.10, G:0.00, T:0.48
Consensus pattern (31 bp):
CACTATATTAAATCATTTAAATATAATTTAC
Found at i:19207 original size:31 final size:32
Alignment explanation
Indices: 19144--19236 Score: 93
Period size: 31 Copynumber: 3.0 Consensus size: 32
19134 GCAGCACTAT
* * ** *
19144 TTTAAATCATTTAAATATTATTTACCACTATA
1 TTTAAATTATTTAAATATAATTTATTATTATA
19176 -TTAAATTATTTAAATATAATTTATTATTATA
1 TTTAAATTATTTAAATATAATTTATTATTATA
* *
19207 TTTAAAAT-TTTAAA-ATATTTTATGTATTAT
1 TTTAAATTATTTAAATATAATTTAT-TATTAT
19237 TAATTTTAGA
Statistics
Matches: 52, Mismatches: 7, Indels: 5
0.81 0.11 0.08
Matches are distributed among these distances:
30 8 0.15
31 38 0.73
32 6 0.12
ACGTcount: A:0.42, C:0.04, G:0.01, T:0.53
Consensus pattern (32 bp):
TTTAAATTATTTAAATATAATTTATTATTATA
Found at i:27883 original size:10 final size:10
Alignment explanation
Indices: 27863--27893 Score: 53
Period size: 10 Copynumber: 3.0 Consensus size: 10
27853 CATTCAACCA
27863 TTTTGTGTTTT
1 TTTTGT-TTTT
27874 TTTTGTTTTT
1 TTTTGTTTTT
27884 TTTTGTTTTT
1 TTTTGTTTTT
27894 ATGATGCTCC
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 14 0.70
11 6 0.30
ACGTcount: A:0.00, C:0.00, G:0.13, T:0.87
Consensus pattern (10 bp):
TTTTGTTTTT
Done.