Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013433.1 Kokia drynarioides strain JFW-HI SEQ_128459, 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: 23990
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.34
Warning! 51 characters in sequence are not A, C, G, or T
Found at i:2887 original size:2 final size:2
Alignment explanation
Indices: 2880--2926 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
2870 TTATACAACC
2880 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2922 TA TA T
1 TA TA T
2927 GATTGAAAGA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:12236 original size:29 final size:29
Alignment explanation
Indices: 12193--12294 Score: 134
Period size: 30 Copynumber: 3.5 Consensus size: 29
12183 TTCGAGTAAA
* *
12193 AAAAATGAGATTTTTGGAAGTTCGGGGGT
1 AAAAATGGGAATTTTGGAAGTTCGGGGGT
* *
12222 AAAAATGGTAATTTTGGAAGTTACGGGGTT
1 AAAAATGGGAATTTTGGAAGTT-CGGGGGT
*
12252 AAAAATGGGATTTTTGGAAGTTCGGGGGT
1 AAAAATGGGAATTTTGGAAGTTCGGGGGT
*
12281 -AAAATGAGAATTTT
1 AAAAATGGGAATTTT
12295 TGAACAATTT
Statistics
Matches: 63, Mismatches: 9, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
28 12 0.19
29 25 0.40
30 26 0.41
ACGTcount: A:0.33, C:0.03, G:0.31, T:0.32
Consensus pattern (29 bp):
AAAAATGGGAATTTTGGAAGTTCGGGGGT
Found at i:12295 original size:29 final size:29
Alignment explanation
Indices: 12193--12296 Score: 133
Period size: 29 Copynumber: 3.6 Consensus size: 29
12183 TTCGAGTAAA
12193 AAAAAT-GAGATTTTTGGAAGTTCGGGGGT
1 AAAAATGGA-ATTTTTGGAAGTTCGGGGGT
*
12222 AAAAATGGTAA-TTTTGGAAGTTACGGGGTT
1 AAAAATGG-AATTTTTGGAAGTT-CGGGGGT
*
12252 AAAAATGGGATTTTTGGAAGTTCGGGGGT
1 AAAAATGGAATTTTTGGAAGTTCGGGGGT
12281 -AAAATGAGAATTTTTG
1 AAAAATG-GAATTTTTG
12297 AACAATTTAG
Statistics
Matches: 66, Mismatches: 4, Indels: 10
0.82 0.05 0.12
Matches are distributed among these distances:
28 6 0.09
29 32 0.48
30 27 0.41
31 1 0.02
ACGTcount: A:0.33, C:0.03, G:0.32, T:0.33
Consensus pattern (29 bp):
AAAAATGGAATTTTTGGAAGTTCGGGGGT
Found at i:13405 original size:15 final size:15
Alignment explanation
Indices: 13388--13443 Score: 60
Period size: 15 Copynumber: 3.7 Consensus size: 15
13378 TTATGTCATT
*
13388 AATATTATTATTATT
1 AATATTATTATTATA
**
13403 AATATTATTAAGA-A
1 AATATTATTATTATA
13417 AATATTTATTATTAATA
1 AATA-TTATTATT-ATA
13434 AATATTATTA
1 AATATTATTA
13444 AAACTGCTCG
Statistics
Matches: 33, Mismatches: 5, Indels: 5
0.77 0.12 0.12
Matches are distributed among these distances:
14 4 0.12
15 17 0.52
16 7 0.21
17 5 0.15
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (15 bp):
AATATTATTATTATA
Found at i:13426 original size:18 final size:16
Alignment explanation
Indices: 13405--13443 Score: 51
Period size: 18 Copynumber: 2.3 Consensus size: 16
13395 TTATTATTAA
13405 TATTATTAAGAAAATATT
1 TATTATTAA-AAAATA-T
*
13423 TATTATTAATAAATAT
1 TATTATTAAAAAATAT
13439 TATTA
1 TATTA
13444 AAACTGCTCG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 6 0.30
17 5 0.25
18 9 0.45
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (16 bp):
TATTATTAAAAAATAT
Found at i:14168 original size:6 final size:6
Alignment explanation
Indices: 14159--14248 Score: 73
Period size: 6 Copynumber: 15.5 Consensus size: 6
14149 TGAACTTTAT
* * *
14159 TTTAAA TTTATAA --TAAT TTTAAA TTTGAAA -ATAAA TTTAAA CTTAAA
1 TTTAAA TTTA-AA TTTAAA TTTAAA TTT-AAA TTTAAA TTTAAA TTTAAA
* * *
14206 TTTGAA TTTAAA -ATAAA TTTAAA TTTAAA -ATAAA TTTAAA TTT
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTT
14249 TTAAACAAAT
Statistics
Matches: 65, Mismatches: 12, Indels: 14
0.71 0.13 0.15
Matches are distributed among these distances:
4 1 0.02
5 13 0.20
6 46 0.71
7 5 0.08
ACGTcount: A:0.51, C:0.01, G:0.02, T:0.46
Consensus pattern (6 bp):
TTTAAA
Found at i:14179 original size:17 final size:17
Alignment explanation
Indices: 14159--14280 Score: 121
Period size: 17 Copynumber: 7.4 Consensus size: 17
14149 TGAACTTTAT
* *
14159 TTTAAATTTATAATAAT
1 TTTAAATTTAAAATAAA
14176 TTTAAATTTGAAAATAAA
1 TTTAAATTT-AAAATAAA
*
14194 TTTAAA-CT----TAAA
1 TTTAAATTTAAAATAAA
*
14206 TTTGAATTTAAAATAAA
1 TTTAAATTTAAAATAAA
14223 TTTAAATTTAAAATAAA
1 TTTAAATTTAAAATAAA
* *
14240 TTTAAATTTTTAAACAAA
1 TTTAAA-TTTAAAATAAA
14258 TTT-AATCTTAAAATAAA
1 TTTAAAT-TTAAAATAAA
14275 TTTAAA
1 TTTAAA
14281 AGGGAGTTTG
Statistics
Matches: 86, Mismatches: 10, Indels: 17
0.76 0.09 0.15
Matches are distributed among these distances:
12 9 0.10
13 1 0.01
16 1 0.01
17 49 0.57
18 26 0.30
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.43
Consensus pattern (17 bp):
TTTAAATTTAAAATAAA
Found at i:14194 original size:29 final size:28
Alignment explanation
Indices: 14161--14280 Score: 101
Period size: 29 Copynumber: 4.4 Consensus size: 28
14151 AACTTTATTT
*
14161 TAAATTTATAA-TAATTTTAAATTTGAAAA
1 TAAATTTA-AACTAAATTTAAATTT-AAAA
*
14190 TAAATTTAAACTTAAATTTGAATTTAAAA
1 TAAATTTAAAC-TAAATTTAAATTTAAAA
* *
14219 TAAATTTAAATTTAAA-ATAAATTT-AAA
1 TAAATTTAAA-CTAAATTTAAATTTAAAA
*
14246 T--TTTTAAAC-AAATTT-AATCTTAAAA
1 TAAATTTAAACTAAATTTAAAT-TTAAAA
14271 TAAATTTAAA
1 TAAATTTAAA
14281 AGGGAGTTTG
Statistics
Matches: 74, Mismatches: 9, Indels: 18
0.73 0.09 0.18
Matches are distributed among these distances:
23 6 0.08
24 3 0.04
25 10 0.14
27 10 0.14
28 8 0.11
29 26 0.35
30 11 0.15
ACGTcount: A:0.53, C:0.03, G:0.02, T:0.42
Consensus pattern (28 bp):
TAAATTTAAACTAAATTTAAATTTAAAA
Found at i:14198 original size:35 final size:34
Alignment explanation
Indices: 14159--14280 Score: 121
Period size: 35 Copynumber: 3.7 Consensus size: 34
14149 TGAACTTTAT
* *
14159 TTTAAATTTATAATAATTTTAAATTTGAAAATAAA
1 TTTAAATTTAAAATAAATTTAAATTT-AAAATAAA
* *
14194 TTTAAA-CT----TAAATTTGAATTTAAAATAAA
1 TTTAAATTTAAAATAAATTTAAATTTAAAATAAA
* *
14223 TTTAAATTTAAAATAAATTTAAATTTTTAAACAAA
1 TTTAAATTTAAAATAAATTTAAA-TTTAAAATAAA
14258 TTT-AATCTTAAAATAAATTTAAA
1 TTTAAAT-TTAAAATAAATTTAAA
14281 AGGGAGTTTG
Statistics
Matches: 73, Mismatches: 7, Indels: 14
0.78 0.07 0.15
Matches are distributed among these distances:
29 14 0.19
30 12 0.16
34 13 0.18
35 34 0.47
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.43
Consensus pattern (34 bp):
TTTAAATTTAAAATAAATTTAAATTTAAAATAAA
Found at i:14216 original size:12 final size:12
Alignment explanation
Indices: 14159--14248 Score: 73
Period size: 11 Copynumber: 7.8 Consensus size: 12
14149 TGAACTTTAT
14159 TTTAAATTTATAA
1 TTTAAATTTA-AA
*
14172 --TAATTTTAAA
1 TTTAAATTTAAA
*
14182 TTTGAAA-ATAAA
1 TTT-AAATTTAAA
*
14194 TTTAAACTTAAA
1 TTTAAATTTAAA
*
14206 TTTGAATTTAAA
1 TTTAAATTTAAA
*
14218 -ATAAATTTAAA
1 TTTAAATTTAAA
*
14229 TTTAAA-ATAAA
1 TTTAAATTTAAA
14240 TTTAAATTT
1 TTTAAATTT
14249 TTAAACAAAT
Statistics
Matches: 60, Mismatches: 11, Indels: 13
0.71 0.13 0.15
Matches are distributed among these distances:
10 2 0.03
11 29 0.48
12 27 0.45
13 2 0.03
ACGTcount: A:0.51, C:0.01, G:0.02, T:0.46
Consensus pattern (12 bp):
TTTAAATTTAAA
Found at i:19889 original size:21 final size:19
Alignment explanation
Indices: 19857--19896 Score: 53
Period size: 21 Copynumber: 2.0 Consensus size: 19
19847 GCGATGAGTA
*
19857 TTTTAAAATTGAAATTTTT
1 TTTTAAAATTGAAAATTTT
19876 TTTTCAAAACTTGAAAATTTT
1 TTTT-AAAA-TTGAAAATTTT
19897 ACTTCTTTCT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 4 0.22
20 4 0.22
21 10 0.56
ACGTcount: A:0.38, C:0.05, G:0.05, T:0.53
Consensus pattern (19 bp):
TTTTAAAATTGAAAATTTT
Found at i:20151 original size:26 final size:26
Alignment explanation
Indices: 20122--20176 Score: 110
Period size: 26 Copynumber: 2.1 Consensus size: 26
20112 TTACATGATT
20122 ATCAAGTGAGTAAATTTGTTATTTAC
1 ATCAAGTGAGTAAATTTGTTATTTAC
20148 ATCAAGTGAGTAAATTTGTTATTTAC
1 ATCAAGTGAGTAAATTTGTTATTTAC
20174 ATC
1 ATC
20177 TATTTATGTC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 29 1.00
ACGTcount: A:0.35, C:0.09, G:0.15, T:0.42
Consensus pattern (26 bp):
ATCAAGTGAGTAAATTTGTTATTTAC
Done.