Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168186.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_423, 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: 27371
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Found at i:16157 original size:2 final size:2
Alignment explanation
Indices: 16150--16185 Score: 63
Period size: 2 Copynumber: 17.5 Consensus size: 2
16140 TAATGTGATC
16150 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TCA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T-A TA TA T
16186 GGAAGCTCTT
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 31 0.94
3 2 0.06
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:16863 original size:22 final size:22
Alignment explanation
Indices: 16801--16857 Score: 82
Period size: 22 Copynumber: 2.6 Consensus size: 22
16791 TTCGATTTGA
16801 TTTAAAATTAATAAAATATTATTT
1 TTTAAAA-T-ATAAAATATTATTT
16825 TTTAAAATATAAAATATTA-TT
1 TTTAAAATATAAAATATTATTT
16846 TTT-AAATATAAA
1 TTTAAAATATAAA
16858 TTATATAAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
20 9 0.27
21 5 0.15
22 11 0.33
23 1 0.03
24 7 0.21
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (22 bp):
TTTAAAATATAAAATATTATTT
Found at i:17213 original size:28 final size:28
Alignment explanation
Indices: 17181--17245 Score: 78
Period size: 28 Copynumber: 2.3 Consensus size: 28
17171 CGTATAACAC
*
17181 AAAAATAAAATTTTAAAAATAATAATATT
1 AAAAATAAAATTTTAAAAATAAGAATA-T
* * *
17210 AAAAAT-TAATTTTAAAACTTAGAATAT
1 AAAAATAAAATTTTAAAAATAAGAATAT
17237 AAAAATAAA
1 AAAAATAAA
17246 TCAAAATTCA
Statistics
Matches: 30, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
27 7 0.23
28 17 0.57
29 6 0.20
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.32
Consensus pattern (28 bp):
AAAAATAAAATTTTAAAAATAAGAATAT
Found at i:17219 original size:16 final size:15
Alignment explanation
Indices: 17181--17244 Score: 55
Period size: 14 Copynumber: 4.5 Consensus size: 15
17171 CGTATAACAC
*
17181 AAAAATAA-AATTTT
1 AAAAATAATAATATT
17195 AAAAATAATAATATT
1 AAAAATAATAATATT
*
17210 AAAAAT--TAATTTT
1 AAAAATAATAATATT
* * *
17223 AAAACTTAGAATA-T
1 AAAAATAATAATATT
17237 AAAAATAA
1 AAAAATAA
17245 ATCAAAATTC
Statistics
Matches: 40, Mismatches: 7, Indels: 6
0.75 0.13 0.11
Matches are distributed among these distances:
13 11 0.28
14 15 0.38
15 14 0.35
ACGTcount: A:0.64, C:0.02, G:0.02, T:0.33
Consensus pattern (15 bp):
AAAAATAATAATATT
Found at i:17984 original size:20 final size:23
Alignment explanation
Indices: 17944--17984 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
17934 CATAAGCTTA
17944 TTCACCTTTAATATCTCTTCATC
1 TTCACCTTTAATATCTCTTCATC
17967 TTCA-CTTTAAT-T-TCTTCA
1 TTCACCTTTAATATCTCTTCA
17985 AAGTCATTGC
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 6 0.33
21 1 0.06
22 7 0.39
23 4 0.22
ACGTcount: A:0.22, C:0.27, G:0.00, T:0.51
Consensus pattern (23 bp):
TTCACCTTTAATATCTCTTCATC
Found at i:25310 original size:12 final size:13
Alignment explanation
Indices: 25290--25336 Score: 60
Period size: 13 Copynumber: 3.7 Consensus size: 13
25280 ATCGATTTAG
25290 ATATTTTATTAAA
1 ATATTTTATTAAA
25303 AT-TTTTATTAAA
1 ATATTTTATTAAA
* *
25315 TTATTTTAATAAA
1 ATATTTTATTAAA
*
25328 ATACTTTAT
1 ATATTTTAT
25337 AAATTTCACC
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
12 11 0.39
13 17 0.61
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (13 bp):
ATATTTTATTAAA
Found at i:25327 original size:13 final size:13
Alignment explanation
Indices: 25290--25339 Score: 50
Period size: 12 Copynumber: 4.0 Consensus size: 13
25280 ATCGATTTAG
*
25290 ATATTTTATTAAA
1 ATATTTTAATAAA
*
25303 AT-TTTTATTAAA
1 ATATTTTAATAAA
*
25315 TTATTTTAATAAA
1 ATATTTTAATAAA
*
25328 ATACTTT-ATAAA
1 ATATTTTAATAAA
25340 TTTCACCTAA
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
12 16 0.50
13 16 0.50
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (13 bp):
ATATTTTAATAAA
Found at i:25339 original size:25 final size:25
Alignment explanation
Indices: 25291--25341 Score: 68
Period size: 25 Copynumber: 2.0 Consensus size: 25
25281 TCGATTTAGA
* *
25291 TATTTTATTAAAATTTTTATTAAAT
1 TATTTTAATAAAATCTTTATTAAAT
25316 TATTTTAATAAAATACTTTA-TAAAT
1 TATTTTAATAAAAT-CTTTATTAAAT
25341 T
1 T
25342 TCACCTAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
25 19 0.83
26 4 0.17
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (25 bp):
TATTTTAATAAAATCTTTATTAAAT
Done.