Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167996.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_252, 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: 42392
ACGTcount: A:0.35, C:0.14, G:0.15, T:0.36
Found at i:1149 original size:22 final size:22
Alignment explanation
Indices: 1114--1156 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
1104 TCAATTGTGT
*
1114 ATAATATTGAAATTTTAATTTTA
1 ATAATATT-AAAATTTAATTTTA
1137 ATAA-ATTAAAATTTAATTTT
1 ATAATATTAAAATTTAATTTT
1157 TTATCATTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 12 0.63
22 3 0.16
23 4 0.21
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (22 bp):
ATAATATTAAAATTTAATTTTA
Found at i:6716 original size:2 final size:2
Alignment explanation
Indices: 6709--6740 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
6699 AAGTATTAGT
*
6709 TA TA TA TA TA TA TA TA TA TA TA TA TA AA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
6741 CACGCGCGAG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:7062 original size:21 final size:21
Alignment explanation
Indices: 7037--7077 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
7027 ATTTAAAATT
*
7037 ATTAAAATTTAAATTTTAATC
1 ATTAAAATTAAAATTTTAATC
7058 ATTAAAATTAAAATTTTAAT
1 ATTAAAATTAAAATTTTAAT
7078 ATTTGACAGA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.46
Consensus pattern (21 bp):
ATTAAAATTAAAATTTTAATC
Found at i:7240 original size:30 final size:29
Alignment explanation
Indices: 7172--7251 Score: 97
Period size: 30 Copynumber: 2.6 Consensus size: 29
7162 TTTTCTAAAA
*
7172 TAAAAAATAAATTAAAAATTTTTTTTGGATAT
1 TAAAAAAT-AATT--AAATCTTTTTTGGATAT
*
7204 TTAAAAATAATTAAATCTTTTTTGGATAAT
1 TAAAAAATAATTAAATCTTTTTTGGAT-AT
*
7234 TAAAAAACAATTAAATCT
1 TAAAAAATAATTAAATCT
7252 AACAAAGAAT
Statistics
Matches: 43, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
29 14 0.33
30 18 0.42
31 4 0.09
32 7 0.16
ACGTcount: A:0.50, C:0.04, G:0.05, T:0.41
Consensus pattern (29 bp):
TAAAAAATAATTAAATCTTTTTTGGATAT
Found at i:16814 original size:12 final size:12
Alignment explanation
Indices: 16797--16821 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
16787 CAATAATATA
16797 TAAAAATATTAT
1 TAAAAATATTAT
16809 TAAAAATATTAT
1 TAAAAATATTAT
16821 T
1 T
16822 TATAATTTAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (12 bp):
TAAAAATATTAT
Found at i:16979 original size:6 final size:6
Alignment explanation
Indices: 16963--17003 Score: 55
Period size: 6 Copynumber: 6.5 Consensus size: 6
16953 TGATAAAATT
*
16963 TTTTAA TTTTTAA TTTTGA TTTTACA TTTTAA TTTTAA TTT
1 TTTTAA -TTTTAA TTTTAA TTTTA-A TTTTAA TTTTAA TTT
17004 ATTAATTTTT
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
6 19 0.61
7 12 0.39
ACGTcount: A:0.27, C:0.02, G:0.02, T:0.68
Consensus pattern (6 bp):
TTTTAA
Found at i:17010 original size:8 final size:7
Alignment explanation
Indices: 16962--17016 Score: 55
Period size: 7 Copynumber: 8.1 Consensus size: 7
16952 GTGATAAAAT
16962 TTTTTAA
1 TTTTTAA
16969 TTTTTAA
1 TTTTTAA
*
16976 -TTTTGA
1 TTTTTAA
16982 -TTTTACA
1 TTTTTA-A
16989 -TTTTAA
1 TTTTTAA
16995 -TTTTAA
1 TTTTTAA
17001 TTTATTAA
1 TTT-TTAA
17009 TTTTTAA
1 TTTTTAA
17016 T
1 T
17017 AAAAAACTTA
Statistics
Matches: 43, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
6 16 0.37
7 20 0.47
8 7 0.16
ACGTcount: A:0.29, C:0.02, G:0.02, T:0.67
Consensus pattern (7 bp):
TTTTTAA
Found at i:26257 original size:11 final size:11
Alignment explanation
Indices: 26233--26271 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
26223 TATTTTTTTT
*
26233 ATTTTGTTAAA
1 ATTTTTTTAAA
*
26244 ATTTTTTTATA
1 ATTTTTTTAAA
26255 ATTTTTATTAAA
1 ATTTTT-TTAAA
26267 ATTTT
1 ATTTT
26272 AAATTATATC
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
11 15 0.62
12 9 0.38
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.64
Consensus pattern (11 bp):
ATTTTTTTAAA
Found at i:26260 original size:12 final size:12
Alignment explanation
Indices: 26234--26271 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
26224 ATTTTTTTTA
*
26234 TTTTGTTAAAAT
1 TTTTATTAAAAT
*
26246 TTTT-TTATAAT
1 TTTTATTAAAAT
26257 TTTTATTAAAAT
1 TTTTATTAAAAT
26269 TTT
1 TTT
26272 AAATTATATC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
11 10 0.43
12 13 0.57
ACGTcount: A:0.32, C:0.00, G:0.03, T:0.66
Consensus pattern (12 bp):
TTTTATTAAAAT
Found at i:28095 original size:20 final size:21
Alignment explanation
Indices: 28057--28095 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
28047 AATCAAAATG
28057 AAAAGACAAAAGAAATTGCTC
1 AAAAGACAAAAGAAATTGCTC
*
28078 AAAAGACGAAAG-AATTGC
1 AAAAGACAAAAGAAATTGC
28096 AGATGGGAGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 6 0.35
21 11 0.65
ACGTcount: A:0.56, C:0.13, G:0.18, T:0.13
Consensus pattern (21 bp):
AAAAGACAAAAGAAATTGCTC
Found at i:31721 original size:24 final size:23
Alignment explanation
Indices: 31676--31727 Score: 59
Period size: 23 Copynumber: 2.2 Consensus size: 23
31666 GAATTAGATT
* *
31676 TAAAAAATAAAAAAACCCAAATC
1 TAAAAAATAAAAAAAACAAAATC
*
31699 TAAAAAATAAAATAAAATAAAATC
1 TAAAAAATAAAA-AAAACAAAATC
*
31723 CAAAA
1 TAAAA
31728 TGTCTCAAAC
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
23 12 0.50
24 12 0.50
ACGTcount: A:0.73, C:0.12, G:0.00, T:0.15
Consensus pattern (23 bp):
TAAAAAATAAAAAAAACAAAATC
Found at i:32338 original size:328 final size:330
Alignment explanation
Indices: 31734--32397 Score: 1188
Period size: 328 Copynumber: 2.0 Consensus size: 330
31724 AAAATGTCTC
31734 AAACTAAAATAATCCAAAATCTGAAATTGTTTGAACCTAAAAAAATTCAAAACTCAAACTCAACT
1 AAACTAAAATAATCCAAAATCTGAAATTGTTTGAACCTAAAAAAATTCAAAACTCAAACTCAACT
31799 AAAATTCGAAAAGCATGCTAAAATAATTATATCTTTCATAAAATCTTTAAAAAAAAGAAAAAAGC
66 AAAATTCGAAAAGCATGCTAAAATAATTATATCTTTCATAAAATCTTT---AAAAAGAAAAAAGC
31864 TGACTAACCCGAATCTGGATTCAGTTATATTCCATCACGTATAAGCAAATGCAGCAAGCTTCCAA
128 TGACTAACCCGAATCTGGATTCAGTTATATTCCATCACGTATAAGCAAATGCAGCAAGCTTCCAA
**
31929 CATTAGCATTGTCTATTAAATAGTCAAAATTAAATATTGAAATTTACTGTACAATTTATTTGATA
193 CATTAGCATCATCTATTAAATAGTCAAAATTAAATATTGAAATTTACTGTACAATTTATTTGATA
* * *
31994 TTATATTGATAATTAAATATTAAATAAATGTTTTTGTTGGTTTTTTAAAGTATTTTACATTAATG
258 TTATATTGAAAATTAAATATTAAATAAATGTTTTTGTTGGTTTTTAAAAGTATTTTACATTAATA
32059 AAAGTGAA
323 AAAGTGAA
* *
32067 AAACTAAAATAATCCAAAATCTGAAATTGTTTGAACCTAAAAAAATTCAAAACTCGAATTCAACT
1 AAACTAAAATAATCCAAAATCTGAAATTGTTTGAACCTAAAAAAATTCAAAACTCAAACTCAACT
* *
32132 AAAATTCGAAAAGCATGCTAAAATAATTATATCTTTCATAAAATCTTT-TAAA-AAAAATGCTGA
66 AAAATTCGAAAAGCATGCTAAAATAATTATATCTTTCATAAAATCTTTAAAAAGAAAAAAGCTGA
32195 CTAACCCGAATCTGGATTCAGTTATATTCCATCACGTATAAGCAAATGCAGCAAGCTTCCAACAT
131 CTAACCCGAATCTGGATTCAGTTATATTCCATCACGTATAAGCAAATGCAGCAAGCTTCCAACAT
* *
32260 TAGCATCATCTATTAAATAGTTAAAATTAAATATTGAAATTTACTGTACAATTTATTTGATATTC
196 TAGCATCATCTATTAAATAGTCAAAATTAAATATTGAAATTTACTGTACAATTTATTTGATATTA
32325 TATTGAAAATTAAATATTAAATAAATGTTTTTGTTGGTTTTTAAAAGTATTTTACATTAATAAAA
261 TATTGAAAATTAAATATTAAATAAATGTTTTTGTTGGTTTTTAAAAGTATTTTACATTAATAAAA
32390 GTGAA
326 GTGAA
32395 AAA
1 AAA
32398 ATAGTTAAAA
Statistics
Matches: 320, Mismatches: 11, Indels: 5
0.95 0.03 0.01
Matches are distributed among these distances:
328 206 0.64
329 3 0.01
333 111 0.35
ACGTcount: A:0.44, C:0.13, G:0.10, T:0.34
Consensus pattern (330 bp):
AAACTAAAATAATCCAAAATCTGAAATTGTTTGAACCTAAAAAAATTCAAAACTCAAACTCAACT
AAAATTCGAAAAGCATGCTAAAATAATTATATCTTTCATAAAATCTTTAAAAAGAAAAAAGCTGA
CTAACCCGAATCTGGATTCAGTTATATTCCATCACGTATAAGCAAATGCAGCAAGCTTCCAACAT
TAGCATCATCTATTAAATAGTCAAAATTAAATATTGAAATTTACTGTACAATTTATTTGATATTA
TATTGAAAATTAAATATTAAATAAATGTTTTTGTTGGTTTTTAAAAGTATTTTACATTAATAAAA
GTGAA
Found at i:33248 original size:22 final size:22
Alignment explanation
Indices: 33220--33263 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
33210 GTGTATTGTC
33220 TTATAAACAAGTTACTAATATA
1 TTATAAACAAGTTACTAATATA
*
33242 TTATAAACAAGTTACTTATATA
1 TTATAAACAAGTTACTAATATA
33264 ATTGAAGGAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.48, C:0.09, G:0.05, T:0.39
Consensus pattern (22 bp):
TTATAAACAAGTTACTAATATA
Found at i:41150 original size:15 final size:15
Alignment explanation
Indices: 41130--41158 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
41120 ATTTTCAAAC
41130 AAAAAAATAAAAATA
1 AAAAAAATAAAAATA
41145 AAAAAAATAAAAAT
1 AAAAAAATAAAAAT
41159 TTTTAAAATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.86, C:0.00, G:0.00, T:0.14
Consensus pattern (15 bp):
AAAAAAATAAAAATA
Found at i:41234 original size:26 final size:25
Alignment explanation
Indices: 41196--41254 Score: 68
Period size: 26 Copynumber: 2.4 Consensus size: 25
41186 AAATAAGGAT
* *
41196 GAAA-TTCTTAGAAATTTC-AAATG
1 GAAATTTCTTAGAAATCTCTAAATA
41219 GTAAATTTCTTAAGAAATCTCTAAATA
1 G-AAATTTCTT-AGAAATCTCTAAATA
41246 GAAATTTCT
1 GAAATTTCT
41255 CTAAATTTGT
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
23 1 0.03
24 3 0.10
25 5 0.17
26 16 0.53
27 5 0.17
ACGTcount: A:0.42, C:0.10, G:0.10, T:0.37
Consensus pattern (25 bp):
GAAATTTCTTAGAAATCTCTAAATA
Done.