Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168384.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_601, 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: 21776
ACGTcount: A:0.35, C:0.17, G:0.14, T:0.35
Found at i:4521 original size:33 final size:33
Alignment explanation
Indices: 4479--4553 Score: 150
Period size: 33 Copynumber: 2.3 Consensus size: 33
4469 TAGGCCTGAA
4479 GCAATAAACACAATAATGCAAAAGCAATATATC
1 GCAATAAACACAATAATGCAAAAGCAATATATC
4512 GCAATAAACACAATAATGCAAAAGCAATATATC
1 GCAATAAACACAATAATGCAAAAGCAATATATC
4545 GCAATAAAC
1 GCAATAAAC
4554 CCATAGCAAT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 42 1.00
ACGTcount: A:0.55, C:0.19, G:0.09, T:0.17
Consensus pattern (33 bp):
GCAATAAACACAATAATGCAAAAGCAATATATC
Found at i:7788 original size:25 final size:24
Alignment explanation
Indices: 7759--7806 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
7749 ATTTTCTTTT
*
7759 CTCTAAGAATTCTTACAAAAAAAAA
1 CTCTAAG-ATACTTACAAAAAAAAA
* *
7784 CTCTATGATACTTACCAAAAAAA
1 CTCTAAGATACTTACAAAAAAAA
7807 TAATGATCAC
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
24 14 0.70
25 6 0.30
ACGTcount: A:0.52, C:0.19, G:0.04, T:0.25
Consensus pattern (24 bp):
CTCTAAGATACTTACAAAAAAAAA
Found at i:11597 original size:2 final size:2
Alignment explanation
Indices: 11592--11620 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
11582 TGAGTGTGTC
11592 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
11621 ATTTCTCTTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:12470 original size:17 final size:17
Alignment explanation
Indices: 12448--12480 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
12438 TTCTAAATTA
12448 AAAT-AATAATAATAAAT
1 AAATAAATAA-AATAAAT
12465 AAATAAATAAAATAAA
1 AAATAAATAAAATAAA
12481 CCTTGAATCG
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (17 bp):
AAATAAATAAAATAAAT
Found at i:13262 original size:18 final size:18
Alignment explanation
Indices: 13239--13293 Score: 51
Period size: 18 Copynumber: 3.0 Consensus size: 18
13229 TCAAGAAAAA
13239 GATAAAATAAAAATAATT
1 GATAAAATAAAAATAATT
13257 GAT-AAATAATAAATATATT
1 GATAAAATAA-AAATA-ATT
* *
13276 AATAGATATAAAAA-AATT
1 GATA-AAATAAAAATAATT
13294 AATAGGTAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 8
0.76 0.05 0.20
Matches are distributed among these distances:
17 6 0.19
18 11 0.35
19 6 0.19
20 3 0.10
21 5 0.16
ACGTcount: A:0.64, C:0.00, G:0.05, T:0.31
Consensus pattern (18 bp):
GATAAAATAAAAATAATT
Found at i:13294 original size:18 final size:18
Alignment explanation
Indices: 13245--13322 Score: 66
Period size: 20 Copynumber: 4.1 Consensus size: 18
13235 AAAAGATAAA
* *
13245 ATAAAAATAATTGATAAAT
1 ATAAAAA-AATTAATAGAT
* *
13264 AATAAATATATTAATAGAT
1 -ATAAAAAAATTAATAGAT
*
13283 ATAAAAAAATTAATAGGTAA
1 ATAAAAAAATTAATA-G-AT
13303 ATAAAAAATATTAATAGAT
1 ATAAAAAA-ATTAATAGAT
13322 A
1 A
13323 AATAATATAA
Statistics
Matches: 47, Mismatches: 8, Indels: 7
0.76 0.13 0.11
Matches are distributed among these distances:
18 13 0.28
19 11 0.23
20 16 0.34
21 7 0.15
ACGTcount: A:0.63, C:0.00, G:0.06, T:0.31
Consensus pattern (18 bp):
ATAAAAAAATTAATAGAT
Found at i:13315 original size:21 final size:21
Alignment explanation
Indices: 13259--13327 Score: 81
Period size: 21 Copynumber: 3.3 Consensus size: 21
13249 AAATAATTGA
13259 TAAATAATAAATATATTAATA-G
1 TAAATAA-AAA-ATATTAATAGG
*
13281 -ATATAAAAAA-ATTAATAGG
1 TAAATAAAAAATATTAATAGG
*
13300 TAAATAAAAAATATTAATAGA
1 TAAATAAAAAATATTAATAGG
13321 TAAATAA
1 TAAATAA
13328 TATAATAATC
Statistics
Matches: 41, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
18 7 0.17
19 2 0.05
20 12 0.29
21 20 0.49
ACGTcount: A:0.64, C:0.00, G:0.06, T:0.30
Consensus pattern (21 bp):
TAAATAAAAAATATTAATAGG
Found at i:13820 original size:21 final size:21
Alignment explanation
Indices: 13796--13928 Score: 87
Period size: 21 Copynumber: 6.1 Consensus size: 21
13786 TAACTTTTAG
13796 GTAA-TAACTGATAATTTAATA
1 GTAATTAA-TGATAATTTAATA
13817 GTAATTAATGATAATTTAATA
1 GTAATTAATGATAATTTAATA
* *
13838 GTAAATTAGT-TTCAATTTAATA
1 GT-AATTAATGAT-AATTTAATA
13860 GTAATTAAT--TAA-TTAATTTA
1 GTAATTAATGATAATTTAA--TA
* *
13880 GTAAGTTACTCATAAATAGCTTAATA
1 GTAA-TTAATGAT-AAT---TTAATA
* *
13906 GTAATCAATGATAATTTAGTA
1 GTAATTAATGATAATTTAATA
13927 GT
1 GT
13929 TAATCATTGA
Statistics
Matches: 91, Mismatches: 8, Indels: 26
0.73 0.06 0.21
Matches are distributed among these distances:
18 4 0.04
19 2 0.02
20 7 0.08
21 37 0.41
22 20 0.22
23 1 0.01
24 5 0.05
25 5 0.05
26 6 0.07
28 4 0.04
ACGTcount: A:0.44, C:0.05, G:0.11, T:0.41
Consensus pattern (21 bp):
GTAATTAATGATAATTTAATA
Found at i:14022 original size:44 final size:45
Alignment explanation
Indices: 13899--14050 Score: 163
Period size: 44 Copynumber: 3.5 Consensus size: 45
13889 TCATAAATAG
*
13899 CTTAATAGT-AATCAATGATAATTT-AGTAGTTAATCATTGAAAA
1 CTTAATAGTAAATCAATGATAATTTAAGTAGTTAATCATCGAAAA
* * * *
13942 CTTAA-AGTAAATCAA-CATGACTTATAGTAGTTAATCATCAAAAA
1 CTTAATAGTAAATCAATGATAATTTA-AGTAGTTAATCATCGAAAA
* * * *
13986 CTTAATAGTTAATCAATGATAATTTAAG-AGTAAATCATGGATAA
1 CTTAATAGTAAATCAATGATAATTTAAGTAGTTAATCATCGAAAA
*
14030 TTTAATA-TAAATCAATGATAA
1 CTTAATAGTAAATCAATGATAA
14051 CTTGATAACG
Statistics
Matches: 89, Mismatches: 15, Indels: 10
0.78 0.13 0.09
Matches are distributed among these distances:
42 8 0.09
43 24 0.27
44 40 0.45
45 11 0.12
46 6 0.07
ACGTcount: A:0.47, C:0.09, G:0.11, T:0.34
Consensus pattern (45 bp):
CTTAATAGTAAATCAATGATAATTTAAGTAGTTAATCATCGAAAA
Found at i:14049 original size:21 final size:22
Alignment explanation
Indices: 13752--14050 Score: 110
Period size: 22 Copynumber: 13.8 Consensus size: 22
13742 TAACACATAT
**
13752 TAGTAAATCAATGATACGTTAA
1 TAGTAAATCAATGATAATTTAA
13774 TA--AAAT-AAGTGATAACTTT--
1 TAGTAAATCAA-TGATAA-TTTAA
13793 TAGGT-AAT-AACTGATAATTTAA
1 TA-GTAAATCAA-TGATAATTTAA
*
13815 TAGT-AATTAATGATAATTTAA
1 TAGTAAATCAATGATAATTTAA
* * *
13836 TAGTAAATTAGT-TTCAATTTAA
1 TAGTAAATCAATGAT-AATTTAA
* * *
13858 TAGT-AATTAATTAATTAATTTAG
1 TAGTAAATCAA-TGA-TAATTTAA
* * * **
13881 TAAGTTACTC-ATAAATAGCTTAA
1 T-AGTAAATCAAT-GATAATTTAA
*
13904 TAGT-AATCAATGATAATTTAG
1 TAGTAAATCAATGATAATTTAA
* * * *
13925 TAGTTAATCATTGAAAACTTAA
1 TAGTAAATCAATGATAATTTAA
* * *
13947 -AGTAAATCAA-CATGACTTATAG
1 TAGTAAATCAATGAT-AATT-TAA
* * * *
13969 TAGTTAATC-ATCAAAAACTTAA
1 TAGTAAATCAAT-GATAATTTAA
*
13991 TAGTTAATCAATGATAATTTAA
1 TAGTAAATCAATGATAATTTAA
*
14013 GAGTAAATC-ATGGATAATTTAA
1 TAGTAAATCAAT-GATAATTTAA
14035 TA-TAAATCAATGATAA
1 TAGTAAATCAATGATAA
14051 CTTGATAACG
Statistics
Matches: 210, Mismatches: 41, Indels: 53
0.69 0.13 0.17
Matches are distributed among these distances:
19 4 0.02
20 13 0.06
21 75 0.36
22 83 0.40
23 25 0.12
24 8 0.04
25 2 0.01
ACGTcount: A:0.46, C:0.07, G:0.11, T:0.37
Consensus pattern (22 bp):
TAGTAAATCAATGATAATTTAA
Found at i:14182 original size:44 final size:45
Alignment explanation
Indices: 14134--14231 Score: 114
Period size: 44 Copynumber: 2.2 Consensus size: 45
14124 GTAAATCATG
*
14134 ATAATATAGTA-GTAAATGTA-TAATAACATA-CAGTAAATTAATGA
1 ATAATTTAGTATGTAAAT-TATTAATAACATAGCAGTAAATTAAT-A
* * *
14178 ATAATTTAG-ATGTAAATTATTAATAACTTAGTAGTAAATTACTA
1 ATAATTTAGTATGTAAATTATTAATAACATAGCAGTAAATTAATA
14222 ATAATTTAGT
1 ATAATTTAGT
14232 GATAAATAAG
Statistics
Matches: 46, Mismatches: 4, Indels: 7
0.81 0.07 0.12
Matches are distributed among these distances:
43 3 0.07
44 33 0.72
45 10 0.22
ACGTcount: A:0.48, C:0.04, G:0.10, T:0.38
Consensus pattern (45 bp):
ATAATTTAGTATGTAAATTATTAATAACATAGCAGTAAATTAATA
Found at i:14202 original size:22 final size:21
Alignment explanation
Indices: 14166--14253 Score: 86
Period size: 22 Copynumber: 4.0 Consensus size: 21
14156 ATAACATACA
*
14166 GTAAATTAATGAATAATTTAGAT
1 GTAAATT-ATTAATAATTTAG-T
*
14189 GTAAATTATTAATAACTTAGT
1 GTAAATTATTAATAATTTAGT
*
14210 AGTAAATTACTAATAATTTAGT
1 -GTAAATTATTAATAATTTAGT
* * *
14232 GATAAATAAGTGATAATTTAGT
1 G-TAAATTATTAATAATTTAGT
14254 AGCTAATTAG
Statistics
Matches: 56, Mismatches: 7, Indels: 5
0.82 0.10 0.07
Matches are distributed among these distances:
21 2 0.04
22 47 0.84
23 7 0.12
ACGTcount: A:0.45, C:0.02, G:0.12, T:0.40
Consensus pattern (21 bp):
GTAAATTATTAATAATTTAGT
Found at i:14253 original size:44 final size:45
Alignment explanation
Indices: 14165--14255 Score: 114
Period size: 44 Copynumber: 2.0 Consensus size: 45
14155 AATAACATAC
* *
14165 AGTAAATTAATGAATAATTTAGATGTAAATTATTAATAACTTAGT
1 AGTAAATTAATGAATAATTTAGATGTAAATAAGTAATAACTTAGT
* * *
14210 AGTAAATTACT-AATAATTTAG-TGATAAATAAGTGATAATTTAGT
1 AGTAAATTAATGAATAATTTAGATG-TAAATAAGTAATAACTTAGT
14254 AG
1 AG
14256 CTAATTAGTT
Statistics
Matches: 40, Mismatches: 5, Indels: 3
0.83 0.10 0.06
Matches are distributed among these distances:
43 2 0.05
44 28 0.70
45 10 0.25
ACGTcount: A:0.46, C:0.02, G:0.13, T:0.38
Consensus pattern (45 bp):
AGTAAATTAATGAATAATTTAGATGTAAATAAGTAATAACTTAGT
Found at i:14452 original size:22 final size:22
Alignment explanation
Indices: 14333--14495 Score: 155
Period size: 22 Copynumber: 7.4 Consensus size: 22
14323 TATAATCAAC
* *
14333 CATTAGTAACTTAGTAGTAAAT
1 CATTAATAATTTAGTAGTAAAT
* *
14355 CATCAACAATTTAGTAGTAAAT
1 CATTAATAATTTAGTAGTAAAT
*
14377 CAGTAATAATTTAGTAGTAAAT
1 CATTAATAATTTAGTAGTAAAT
* * * *
14399 CATTTACAAATTAGTATTAAAT
1 CATTAATAATTTAGTAGTAAAT
* *
14421 CAATAGTAATTTAGTAGTAAAT
1 CATTAATAATTTAGTAGTAAAT
* * * *
14443 TATTAATAATTTATTAATATAT
1 CATTAATAATTTAGTAGTAAAT
* * **
14465 CATTGATAGTTTAGTAACAAAT
1 CATTAATAATTTAGTAGTAAAT
14487 CATTAATAA
1 CATTAATAA
14496 CATAATAATA
Statistics
Matches: 109, Mismatches: 32, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
22 109 1.00
ACGTcount: A:0.45, C:0.07, G:0.09, T:0.39
Consensus pattern (22 bp):
CATTAATAATTTAGTAGTAAAT
Found at i:14505 original size:44 final size:44
Alignment explanation
Indices: 14416--14516 Score: 105
Period size: 44 Copynumber: 2.3 Consensus size: 44
14406 AAATTAGTAT
* ** * ** *
14416 TAAATCAAT-AGTAATTTAGTAGTAAATTATTAATAATTTATTAA
1 TAAATCAATGA-TAGTTTAGTAACAAATCATTAATAACATAATAA
* *
14460 TATATCATTGATAGTTTAGTAACAAATCATTAATAACATAATAA
1 TAAATCAATGATAGTTTAGTAACAAATCATTAATAACATAATAA
14504 TAAATCAATGATA
1 TAAATCAATGATA
14517 ACTAAATTGT
Statistics
Matches: 45, Mismatches: 11, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
44 44 0.98
45 1 0.02
ACGTcount: A:0.49, C:0.06, G:0.07, T:0.39
Consensus pattern (44 bp):
TAAATCAATGATAGTTTAGTAACAAATCATTAATAACATAATAA
Found at i:14622 original size:19 final size:20
Alignment explanation
Indices: 14581--14622 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
14571 CTAAATTTGA
*
14581 ATAAAATAATAATGTATTAT
1 ATAAAATAAAAATGTATTAT
*
14601 ATAAAATAAAAAT-TATTTT
1 ATAAAATAAAAATGTATTAT
14620 ATA
1 ATA
14623 TTAGAACTGA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 8 0.40
20 12 0.60
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.40
Consensus pattern (20 bp):
ATAAAATAAAAATGTATTAT
Found at i:15043 original size:4 final size:4
Alignment explanation
Indices: 15034--15069 Score: 54
Period size: 4 Copynumber: 9.0 Consensus size: 4
15024 CCAAAAACTA
* *
15034 GTAT GTAT GTAT GTAT GTGT GTGT GTAT GTAT GTAT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
15070 ATATATATAT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
4 30 1.00
ACGTcount: A:0.19, C:0.00, G:0.31, T:0.50
Consensus pattern (4 bp):
GTAT
Found at i:15726 original size:2 final size:2
Alignment explanation
Indices: 15719--15754 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
15709 TTTATACCCC
15719 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
15755 GATGACTACC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:17549 original size:40 final size:40
Alignment explanation
Indices: 17438--17551 Score: 192
Period size: 40 Copynumber: 2.9 Consensus size: 40
17428 TTAATAGTAG
* *
17438 AATAAAAGCCTTGAGAACCAGTCTCGTGATTAGCTAAGAA
1 AATAAAAGCCTTGAGAACCAGTCTCATGATTGGCTAAGAA
* *
17478 AATAAAAGCCTTGAGAGCCAGTCTCATGATTGGCTAAGGA
1 AATAAAAGCCTTGAGAACCAGTCTCATGATTGGCTAAGAA
17518 AATAAAAGCCTTGAGAACCAGTCTCATGATTGGC
1 AATAAAAGCCTTGAGAACCAGTCTCATGATTGGC
17552 CAAGTCCTAA
Statistics
Matches: 69, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
40 69 1.00
ACGTcount: A:0.37, C:0.18, G:0.22, T:0.23
Consensus pattern (40 bp):
AATAAAAGCCTTGAGAACCAGTCTCATGATTGGCTAAGAA
Done.