Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01004711.1 Kokia drynarioides strain JFW-HI SEQ_118280, 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: 23844
ACGTcount: A:0.36, C:0.16, G:0.15, T:0.33
Found at i:3394 original size:13 final size:13
Alignment explanation
Indices: 3364--3404 Score: 55
Period size: 13 Copynumber: 3.1 Consensus size: 13
3354 AAGCCGTCTC
*
3364 TTCTCTCTTCTTTT
1 TTCTCTCTT-TATT
*
3378 TTCTTTCTTTATT
1 TTCTCTCTTTATT
3391 TTCTCTCTTTATT
1 TTCTCTCTTTATT
3404 T
1 T
3405 CTGTCCCTAC
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
13 16 0.67
14 8 0.33
ACGTcount: A:0.05, C:0.22, G:0.00, T:0.73
Consensus pattern (13 bp):
TTCTCTCTTTATT
Found at i:5176 original size:18 final size:19
Alignment explanation
Indices: 5150--5188 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
5140 ATAATTTTTT
* *
5150 TTTTATTTAGATTTTTAAA
1 TTTTATTTAAAATTTTAAA
5169 TTTT-TTTAAAATTTTAAA
1 TTTTATTTAAAATTTTAAA
5187 TT
1 TT
5189 AGTAAAGATA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 14 0.78
19 4 0.22
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.64
Consensus pattern (19 bp):
TTTTATTTAAAATTTTAAA
Found at i:7413 original size:6 final size:6
Alignment explanation
Indices: 7402--7431 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
7392 GTAGAGGACT
7402 CCAACA CCAACA CCAACA CCAACA CCAACA
1 CCAACA CCAACA CCAACA CCAACA CCAACA
7432 TGGCATCACC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (6 bp):
CCAACA
Found at i:9526 original size:5 final size:5
Alignment explanation
Indices: 9516--9540 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
9506 TGACTGTGAA
9516 GAGAG GAGAG GAGAG GAGAG GAGAG
1 GAGAG GAGAG GAGAG GAGAG GAGAG
9541 CAGGATTTCT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.40, C:0.00, G:0.60, T:0.00
Consensus pattern (5 bp):
GAGAG
Found at i:19295 original size:78 final size:78
Alignment explanation
Indices: 19166--19321 Score: 276
Period size: 78 Copynumber: 2.0 Consensus size: 78
19156 GTGCAAAACC
* * * *
19166 CTGCTGATTGTAAGGCACATTCCCTTGCTGGTTCGGAGTGGTATTTCCTTGTCGATCATATCTTG
1 CTGCTGATTGTAAGGCACATACCATTGCTGGTTCGGAGAGGTATTTCCTTGTCGATCATACCTTG
19231 GTTGGTCAGGGTT
66 GTTGGTCAGGGTT
19244 CTGCTGATTGTAAGGCACATACCATTGCTGGTTCGGAGAGGTATTTCCTTGTCGATCATACCTTG
1 CTGCTGATTGTAAGGCACATACCATTGCTGGTTCGGAGAGGTATTTCCTTGTCGATCATACCTTG
19309 GTTGGTCAGGGTT
66 GTTGGTCAGGGTT
19322 TCTATTTTGT
Statistics
Matches: 74, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
78 74 1.00
ACGTcount: A:0.16, C:0.19, G:0.28, T:0.37
Consensus pattern (78 bp):
CTGCTGATTGTAAGGCACATACCATTGCTGGTTCGGAGAGGTATTTCCTTGTCGATCATACCTTG
GTTGGTCAGGGTT
Found at i:19942 original size:2 final size:2
Alignment explanation
Indices: 19935--19977 Score: 77
Period size: 2 Copynumber: 21.5 Consensus size: 2
19925 AAGCTCATAT
*
19935 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA AA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
19977 G
1 G
19978 GACCTGATGC
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
GA
Found at i:20547 original size:3 final size:3
Alignment explanation
Indices: 20539--20563 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
20529 ATAAAAAACT
20539 TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA T
20564 TAATTCTTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:20916 original size:19 final size:19
Alignment explanation
Indices: 20892--20928 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
20882 GTGATAAAAA
20892 AATAAAAAAAATAAAAATC
1 AATAAAAAAAATAAAAATC
**
20911 AATAAAAATTATAAAAAT
1 AATAAAAAAAATAAAAAT
20929 TATTAAATTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.76, C:0.03, G:0.00, T:0.22
Consensus pattern (19 bp):
AATAAAAAAAATAAAAATC
Found at i:20919 original size:10 final size:9
Alignment explanation
Indices: 20885--20928 Score: 54
Period size: 9 Copynumber: 4.9 Consensus size: 9
20875 ATGATATGTG
20885 ATAAAAA-A
1 ATAAAAATA
*
20893 ATAAAAAAA
1 ATAAAAATA
20902 ATAAAAATCA
1 ATAAAAAT-A
*
20912 ATAAAAATT
1 ATAAAAATA
20921 ATAAAAAT
1 ATAAAAAT
20929 TATTAAATTT
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
8 7 0.22
9 16 0.50
10 9 0.28
ACGTcount: A:0.77, C:0.02, G:0.00, T:0.20
Consensus pattern (9 bp):
ATAAAAATA
Found at i:21038 original size:11 final size:11
Alignment explanation
Indices: 20996--21038 Score: 52
Period size: 11 Copynumber: 4.0 Consensus size: 11
20986 TTGTAGAATT
20996 TTATAAAAAAA
1 TTATAAAAAAA
*
21007 TCAT-AAAAAA
1 TTATAAAAAAA
* *
21017 TTCTTAAAAAA
1 TTATAAAAAAA
21028 TTATAAAAAAA
1 TTATAAAAAAA
21039 GTAAAGAAAT
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
10 8 0.31
11 18 0.69
ACGTcount: A:0.67, C:0.05, G:0.00, T:0.28
Consensus pattern (11 bp):
TTATAAAAAAA
Found at i:21257 original size:18 final size:17
Alignment explanation
Indices: 21244--21325 Score: 62
Period size: 17 Copynumber: 4.7 Consensus size: 17
21234 TTTTTATGCA
21244 TTTTATAATTTTTATAAT
1 TTTTAT-ATTTTTATAAT
*
21262 TTTTATATTTTTATTAAA
1 TTTTATATTTTTA-TAAT
* *
21280 ATTTA-ATATTTTATAAC
1 TTTTATAT-TTTTATAAT
21297 TTTTATTGATTTTTAT--T
1 TTTTA-T-ATTTTTATAAT
*
21314 ATTTATATTTTT
1 TTTTATATTTTT
21326 TTGCCACGTG
Statistics
Matches: 53, Mismatches: 6, Indels: 13
0.74 0.08 0.18
Matches are distributed among these distances:
15 6 0.11
16 1 0.02
17 20 0.38
18 18 0.34
19 6 0.11
20 2 0.04
ACGTcount: A:0.30, C:0.01, G:0.01, T:0.67
Consensus pattern (17 bp):
TTTTATATTTTTATAAT
Found at i:21291 original size:26 final size:26
Alignment explanation
Indices: 21258--21325 Score: 68
Period size: 27 Copynumber: 2.7 Consensus size: 26
21248 ATAATTTTTA
21258 TAAT-TTTTATATTTTTATTAAAATT
1 TAATATTTTATATTTTTATTAAAATT
* * **
21283 TAATATTTTATAACTTTTATTGATTTT
1 TAATATTTTAT-ATTTTTATTAAAATT
*
21310 TATTA-TTTATATTTTT
1 TAATATTTTATATTTTT
21326 TTGCCACGTG
Statistics
Matches: 35, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
25 9 0.26
26 11 0.31
27 15 0.43
ACGTcount: A:0.31, C:0.01, G:0.01, T:0.66
Consensus pattern (26 bp):
TAATATTTTATATTTTTATTAAAATT
Found at i:21312 original size:10 final size:9
Alignment explanation
Indices: 21244--21327 Score: 57
Period size: 9 Copynumber: 9.4 Consensus size: 9
21234 TTTTTATGCA
*
21244 TTTTATAAT
1 TTTTATTAT
*
21253 TTTTATAAT
1 TTTTATTAT
21262 TTTTA-TAT
1 TTTTATTAT
*
21270 TTTTATTAAA
1 TTTTATT-AT
* *
21280 ATTTAATA-
1 TTTTATTAT
* *
21288 TTTTATAAC
1 TTTTATTAT
21297 TTTTATTGAT
1 TTTTATT-AT
21307 TTTTATTAT
1 TTTTATTAT
*
21316 TTATATT-T
1 TTTTATTAT
21324 TTTT
1 TTTT
21328 GCCACGTGTC
Statistics
Matches: 60, Mismatches: 11, Indels: 9
0.75 0.14 0.11
Matches are distributed among these distances:
8 16 0.27
9 30 0.50
10 14 0.23
ACGTcount: A:0.30, C:0.01, G:0.01, T:0.68
Consensus pattern (9 bp):
TTTTATTAT
Found at i:23450 original size:20 final size:20
Alignment explanation
Indices: 23401--23451 Score: 54
Period size: 18 Copynumber: 2.7 Consensus size: 20
23391 AATAAAATAG
*
23401 TTATTAATT-AAAAATATTT
1 TTATTAATTAAAAAATATAT
* *
23420 TTTTTGA--AAAAAATATAT
1 TTATTAATTAAAAAATATAT
23438 TTATTAATTAAAAA
1 TTATTAATTAAAAA
23452 TTAAAAAAGA
Statistics
Matches: 24, Mismatches: 5, Indels: 5
0.71 0.15 0.15
Matches are distributed among these distances:
18 14 0.58
19 5 0.21
20 5 0.21
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (20 bp):
TTATTAATTAAAAAATATAT
Done.