Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011486.1 Kokia drynarioides strain JFW-HI SEQ_126471, 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: 18364
ACGTcount: A:0.36, C:0.16, G:0.14, T:0.34
Found at i:1905 original size:11 final size:11
Alignment explanation
Indices: 1889--1918 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
1879 AGTTCAAACA
*
1889 CTTTTTTTTTT
1 CTTTTTTCTTT
1900 CTTTTTTCTTT
1 CTTTTTTCTTT
1911 CTTTTTTC
1 CTTTTTTC
1919 AATTCAAATT
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:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (11 bp):
CTTTTTTCTTT
Found at i:10202 original size:87 final size:85
Alignment explanation
Indices: 10058--10253 Score: 241
Period size: 87 Copynumber: 2.3 Consensus size: 85
10048 TGTTCAAATT
** * *
10058 TTTTCAAAAAAAGCAATTAAACTCTTCTTTTTTTCACTCAATTGAACACTTAGACTTTCAAAATG
1 TTTTCAAAAAAAGCAATTAGCCCCTACTTTTTTTCACTCAATTGAACACTTAGACTTTCAAAATG
* ** *
10123 CATCAAAAGGGTCCTCAAAC
66 CATCAAAAAGACCCTCAAAA
* * *
10143 TTCTTCAAAAAAAGCAATTGAGCCCCTACTTTTTTTCACTCAATTGGATACTT-GAACTTTTAAA
1 TT-TTCAAAAAAAGCAATT-AGCCCCTACTTTTTTTCACTCAATTGAACACTTAG-ACTTTCAAA
10207 ATGCATCAAAAAGACCCTCAAAA
63 ATGCATCAAAAAGACCCTCAAAA
*
10230 TTTTTAAAAAAAGCAATTAAGCCC
1 TTTTCAAAAAAAGCAATT-AGCCC
10254 TTGCTCTTAT
Statistics
Matches: 95, Mismatches: 13, Indels: 5
0.84 0.12 0.04
Matches are distributed among these distances:
85 2 0.02
86 37 0.39
87 56 0.59
ACGTcount: A:0.39, C:0.21, G:0.09, T:0.32
Consensus pattern (85 bp):
TTTTCAAAAAAAGCAATTAGCCCCTACTTTTTTTCACTCAATTGAACACTTAGACTTTCAAAATG
CATCAAAAAGACCCTCAAAA
Found at i:12536 original size:15 final size:15
Alignment explanation
Indices: 12516--12554 Score: 53
Period size: 14 Copynumber: 2.7 Consensus size: 15
12506 GCACATCAAA
*
12516 CAAGAATTAATATAT
1 CAAGAATTAATAAAT
*
12531 CAAGAA-TACTAAAT
1 CAAGAATTAATAAAT
12545 CAAGAATTAA
1 CAAGAATTAA
12555 GCACACATAA
Statistics
Matches: 20, Mismatches: 3, Indels: 2
0.80 0.12 0.08
Matches are distributed among these distances:
14 12 0.60
15 8 0.40
ACGTcount: A:0.56, C:0.10, G:0.08, T:0.26
Consensus pattern (15 bp):
CAAGAATTAATAAAT
Found at i:14056 original size:20 final size:19
Alignment explanation
Indices: 14033--14090 Score: 71
Period size: 19 Copynumber: 2.9 Consensus size: 19
14023 CTTTTTCTGA
14033 ATTTTCTTTTTTTTTTTTCG
1 ATTTT-TTTTTTTTTTTTCG
**
14053 ATTTTTTTCATTTTTTTCG
1 ATTTTTTTTTTTTTTTTCG
14072 ACTTTTTTTTCTTTTTTTT
1 A-TTTTTTTT-TTTTTTTT
14091 AAATAATAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
19 13 0.41
20 12 0.38
21 7 0.22
ACGTcount: A:0.07, C:0.10, G:0.03, T:0.79
Consensus pattern (19 bp):
ATTTTTTTTTTTTTTTTCG
Found at i:14058 original size:21 final size:19
Alignment explanation
Indices: 14012--14090 Score: 77
Period size: 21 Copynumber: 3.8 Consensus size: 19
14002 ATATTTTGTC
*
14012 TTTTTCTTCTTCTTTTTCTGAA
1 TTTTT-TTCTTTTTTTTC-G-A
*
14034 TTTTCTTTTTTTTTTTTCGA
1 TTTT-TTTCTTTTTTTTCGA
*
14054 TTTTTTTCATTTTTTTCGA
1 TTTTTTTCTTTTTTTTCGA
14073 CTTTTTTTTCTTTTTTTT
1 --TTTTTTTCTTTTTTTT
14091 AAATAATAAA
Statistics
Matches: 49, Mismatches: 5, Indels: 7
0.80 0.08 0.11
Matches are distributed among these distances:
19 13 0.27
20 5 0.10
21 16 0.33
22 14 0.29
23 1 0.02
ACGTcount: A:0.06, C:0.13, G:0.04, T:0.77
Consensus pattern (19 bp):
TTTTTTTCTTTTTTTTCGA
Found at i:14066 original size:19 final size:19
Alignment explanation
Indices: 14011--14089 Score: 70
Period size: 19 Copynumber: 3.8 Consensus size: 19
14001 CATATTTTGT
14011 CTTTTTCTTCTTCTTTTTCTGAA
1 CTTTTT-TTCTT-TTTTTC-G-A
* *
14034 TTTTCTTTTTTTTTTTTCGA
1 CTTT-TTTTCTTTTTTTCGA
14054 -TTTTTTTCATTTTTTTCGA
1 CTTTTTTTC-TTTTTTTCGA
14073 CTTTTTTTTCTTTTTTT
1 C-TTTTTTTCTTTTTTT
14090 TAAATAATAA
Statistics
Matches: 49, Mismatches: 3, Indels: 11
0.78 0.05 0.17
Matches are distributed among these distances:
18 4 0.08
19 13 0.27
20 8 0.16
21 9 0.18
22 6 0.12
23 7 0.14
24 2 0.04
ACGTcount: A:0.06, C:0.14, G:0.04, T:0.76
Consensus pattern (19 bp):
CTTTTTTTCTTTTTTTCGA
Found at i:15005 original size:5 final size:5
Alignment explanation
Indices: 14995--15049 Score: 56
Period size: 5 Copynumber: 9.8 Consensus size: 5
14985 ATTGCATAAT
14995 TAAAA TAAAA TTAAAAA TAAAA TAAAA TAAAA CTAAAAA TGAAAA TGAAAA
1 TAAAA TAAAA -T-AAAA TAAAA TAAAA TAAAA -T-AAAA T-AAAA T-AAAA
15046 TAAA
1 TAAA
15050 TATACTATTT
Statistics
Matches: 45, Mismatches: 1, Indels: 8
0.83 0.02 0.15
Matches are distributed among these distances:
5 22 0.49
6 15 0.33
7 8 0.18
ACGTcount: A:0.75, C:0.02, G:0.04, T:0.20
Consensus pattern (5 bp):
TAAAA
Found at i:15015 original size:6 final size:6
Alignment explanation
Indices: 14996--15049 Score: 58
Period size: 6 Copynumber: 9.3 Consensus size: 6
14986 TTGCATAATT
* * * *
14996 AAAATA AAATTA AAAAT- AAAAT- AAAATA AAACTA AAAATG AAAATG
1 AAAATA AAAATA AAAATA AAAATA AAAATA AAAATA AAAATA AAAATA
15042 AAAATA AA
1 AAAATA AA
15050 TATACTATTT
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
5 10 0.24
6 31 0.76
ACGTcount: A:0.76, C:0.02, G:0.04, T:0.19
Consensus pattern (6 bp):
AAAATA
Found at i:15015 original size:17 final size:16
Alignment explanation
Indices: 14995--15049 Score: 65
Period size: 17 Copynumber: 3.2 Consensus size: 16
14985 ATTGCATAAT
14995 TAAAATAAAATTAAAAA
1 TAAAATAAAA-TAAAAA
*
15012 TAAAATAAAATAAAAC
1 TAAAATAAAATAAAAA
*
15028 TAAAAATGAAAATGAAAA
1 T-AAAAT-AAAATAAAAA
15046 TAAA
1 TAAA
15050 TATACTATTT
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
16 6 0.18
17 18 0.55
18 9 0.27
ACGTcount: A:0.75, C:0.02, G:0.04, T:0.20
Consensus pattern (16 bp):
TAAAATAAAATAAAAA
Found at i:15081 original size:20 final size:19
Alignment explanation
Indices: 15056--15116 Score: 68
Period size: 20 Copynumber: 3.1 Consensus size: 19
15046 TAAATATACT
*
15056 ATTTTTTTTTGAATTTTTGA
1 ATTTTTTTTT-AATTTTTAA
**
15076 ATTTTTTAAATAATTTTTAA
1 ATTTTTT-TTTAATTTTTAA
15096 ATTTTTTTTTCAATTTTTAA
1 ATTTTTTTTT-AATTTTTAA
15116 A
1 A
15117 GACATGAAAG
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
19 1 0.03
20 32 0.94
21 1 0.03
ACGTcount: A:0.30, C:0.02, G:0.03, T:0.66
Consensus pattern (19 bp):
ATTTTTTTTTAATTTTTAA
Found at i:17939 original size:14 final size:13
Alignment explanation
Indices: 17921--17952 Score: 55
Period size: 14 Copynumber: 2.4 Consensus size: 13
17911 AATAAAAGGG
17921 AAAAAATTAAATT
1 AAAAAATTAAATT
17934 AGAAAAATTAAATT
1 A-AAAAATTAAATT
17948 AAAAA
1 AAAAA
17953 TGCAAATAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 5 0.28
14 13 0.72
ACGTcount: A:0.72, C:0.00, G:0.03, T:0.25
Consensus pattern (13 bp):
AAAAAATTAAATT
Found at i:17977 original size:18 final size:19
Alignment explanation
Indices: 17942--17984 Score: 61
Period size: 18 Copynumber: 2.3 Consensus size: 19
17932 TTAGAAAAAT
*
17942 TAAATTAAAAATGCAAATAA
1 TAAAATAAAAAT-CAAATAA
17962 TAAAATAAAAAT-AAATAA
1 TAAAATAAAAATCAAATAA
17980 TAAAA
1 TAAAA
17985 AAATGGCTAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 11 0.50
20 11 0.50
ACGTcount: A:0.72, C:0.02, G:0.02, T:0.23
Consensus pattern (19 bp):
TAAAATAAAAATCAAATAA
Done.