Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168404.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_62, 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: 141830
ACGTcount: A:0.43, C:0.06, G:0.07, T:0.44
File 5 of 5
Found at i:135062 original size:11 final size:12
Alignment explanation
Indices: 135022--135064 Score: 52
Period size: 12 Copynumber: 3.4 Consensus size: 12
135012 TTTAATTCTA
135022 ATTAATTAAAAT
1 ATTAATTAAAAT
135034 ATTAATTAATAATTT
1 ATTAATTAA-AA--T
135049 ATTAA-TAAAAT
1 ATTAATTAAAAT
135060 ATTAA
1 ATTAA
135065 ACCTATTGTT
Statistics
Matches: 28, Mismatches: 0, Indels: 7
0.80 0.00 0.20
Matches are distributed among these distances:
11 6 0.21
12 9 0.32
13 4 0.14
14 3 0.11
15 6 0.21
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (12 bp):
ATTAATTAAAAT
Found at i:135652 original size:23 final size:23
Alignment explanation
Indices: 135622--135667 Score: 58
Period size: 26 Copynumber: 1.9 Consensus size: 23
135612 TATAACTATT
135622 AATATATTT-TAAGTATATAATA
1 AATATATTTATAAGTATATAATA
135644 AATAGTATTTGAATAAGTATATAA
1 AATA-TATTT--ATAAGTATATAA
135668 ATTATAAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
22 4 0.20
23 5 0.25
26 11 0.55
ACGTcount: A:0.50, C:0.00, G:0.09, T:0.41
Consensus pattern (23 bp):
AATATATTTATAAGTATATAATA
Found at i:136189 original size:180 final size:176
Alignment explanation
Indices: 135823--136233 Score: 432
Period size: 180 Copynumber: 2.3 Consensus size: 176
135813 ATAAGTAGAA
* * *
135823 TTATTTTCTAAATCTCTTATAAAATTTT-GAAATATTAATAAATTAATT-TTATTCTATTCCAAA
1 TTATTTTTTAAATCTCTTAT-TAATTTTCAAAATATTAATAAATT-ATTATTATT-TATTCCAAA
* * ** *
135886 CAAGCTTCTATGAGCTTAAATAATTGTTTCATGACAAAACAAAAGGTTATAACAAGTTGAAATAA
63 CAAACTTCTATGAACAGAAACAATTGTTTCATGACAAAACAAAAGGTTATAACAAGTTGAAATAA
* * * * ** * *
135951 ATAATTTTTCATATAGTCTTAACTATTTGAACTGGTTTGATAAACATAT
128 ATAATTGTTCAAATAGTCATAACTATTTGAACTGGATCAACAAACAGAT
* *
136000 TTATTTTTTAAATCTCATAGTTATTCATTTTCAAAATATTACTAAATTATTATTACTTTATTCCA
1 TTATTTTTTAAATCTC----TTATTAATTTTCAAAATATTAATAAATTATTATTA-TTTATTCCA
* * * * * * * *
136065 AATAAACTTGTATGAACAGAAACAATTGTTTTATGATAGAGC-AAAGGTTATAATAATTTGAAAT
61 AACAAACTTCTATGAACAGAAACAATTGTTTCATGACAAAACAAAAGGTTATAACAAGTTGAAAT
* * * *
136129 AGATAATTGTTCAAATATTCATAACTATTTGAATTGGATCAACAAATAGAT
126 AAATAATTGTTCAAATAGTCATAACTATTTGAACTGGATCAACAAACAGAT
* * *
136180 TTCTTTTTTAAATCTCTTATTAATTTTTAAAATATTAATAAATTAGTATTATTT
1 TTATTTTTTAAATCTCTTATTAATTTTCAAAATATTAATAAATTATTATTATTT
136234 TATTTAGAAA
Statistics
Matches: 192, Mismatches: 35, Indels: 16
0.79 0.14 0.07
Matches are distributed among these distances:
175 3 0.02
176 31 0.16
177 15 0.08
180 82 0.43
181 59 0.31
182 2 0.01
ACGTcount: A:0.40, C:0.09, G:0.08, T:0.43
Consensus pattern (176 bp):
TTATTTTTTAAATCTCTTATTAATTTTCAAAATATTAATAAATTATTATTATTTATTCCAAACAA
ACTTCTATGAACAGAAACAATTGTTTCATGACAAAACAAAAGGTTATAACAAGTTGAAATAAATA
ATTGTTCAAATAGTCATAACTATTTGAACTGGATCAACAAACAGAT
Found at i:136370 original size:177 final size:178
Alignment explanation
Indices: 135998--136491 Score: 437
Period size: 181 Copynumber: 2.8 Consensus size: 178
135988 TGATAAACAT
* * * * *
135998 ATTTATTTTTTAAATCTCATAGTTATTCATTTTCAAAATATTACTAAATTATTATTACTTTAT-T
1 ATTTATTTTTTAAATCTC-T--TTATTAATTTTTAAAATATTAATAAAGTAGTATTA-TTTATAT
** * * * * * * * *
136062 CCAAATAAACTT-GTATGAAC-AGAAACAATTGTTTTATGATAGAGC-AAAGGTTATAATAATTT
62 TTAGATAAA-TTCTTATGAACTA-AAACAATTATTTTATGACAAAACAAAAGGTAATAATGATTT
* * * *** * * *
136124 GAAATAGATAATTGTTCAAATATTCATAACTATTTGAATTGGATCAACAAATAG
125 AAAATAGATAGTTGTTTAAATGGCCTTGATTATTTGAATTGGATCAACAAATAG
* *
136178 ATTTCTTTTTTAAATCTC-TTATTAATTTTTAAAATATTAATAAATTAGTATTATTT-TATTTAG
1 ATTTATTTTTTAAATCTCTTTATTAATTTTTAAAATATTAATAAAGTAGTATTATTTATATTTAG
****
136241 A-AAATTCTTATTTGTTGAAGAACAATTATTTTATGACAAAACAAAAGGTAATAATGATTTAAAA
66 ATAAATTCTTATGAACT-AA-AACAATTATTTTATGACAAAACAAAAGGTAATAATGATTTAAAA
** *
136305 TAGATAGTTGTTTAAATGGCCTTGATTATTTGAATT-GATTCAGTAAATTG
129 TAGATAGTTGTTTAAATGGCCTTGATTATTTGAATTGGA-TCAACAAATAG
* *
136355 ATTTATTTTTTAAATCTCTTGTTTATTAATTTTTGAAATATTAATAAAGTAGTATTATTTATTTT
1 ATTTATTTTTTAAATCTC---TTTATTAATTTTTAAAATATTAATAAAGTAGTATTATTTATATT
* * * * ** * *
136420 TGGATAAGTTTTTATGAACTAAAACAATTGTTTTATGACAAAACAATTGGTCATAATGATTTTAA
63 TAGATAAATTCTTATGAACTAAAACAATTATTTTATGACAAAACAAAAGGTAATAATGATTTAAA
136485 ATAGATA
128 ATAGATA
136492 ATTATTGAAA
Statistics
Matches: 254, Mismatches: 47, Indels: 25
0.78 0.14 0.08
Matches are distributed among these distances:
173 2 0.01
174 7 0.03
175 7 0.03
176 52 0.20
177 71 0.28
180 17 0.07
181 81 0.32
182 8 0.03
183 9 0.04
ACGTcount: A:0.39, C:0.07, G:0.10, T:0.44
Consensus pattern (178 bp):
ATTTATTTTTTAAATCTCTTTATTAATTTTTAAAATATTAATAAAGTAGTATTATTTATATTTAG
ATAAATTCTTATGAACTAAAACAATTATTTTATGACAAAACAAAAGGTAATAATGATTTAAAATA
GATAGTTGTTTAAATGGCCTTGATTATTTGAATTGGATCAACAAATAG
Found at i:136464 original size:19 final size:21
Alignment explanation
Indices: 136429--136468 Score: 66
Period size: 19 Copynumber: 2.0 Consensus size: 21
136419 TTGGATAAGT
136429 TTTTATGAACTAAAACAATTG
1 TTTTATGAACTAAAACAATTG
136450 TTTTATG-AC-AAAACAATTG
1 TTTTATGAACTAAAACAATTG
136469 GTCATAATGA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 10 0.53
20 2 0.11
21 7 0.37
ACGTcount: A:0.42, C:0.10, G:0.10, T:0.38
Consensus pattern (21 bp):
TTTTATGAACTAAAACAATTG
Found at i:137162 original size:13 final size:14
Alignment explanation
Indices: 137117--137160 Score: 54
Period size: 14 Copynumber: 3.1 Consensus size: 14
137107 GAATGTTAAT
137117 AATTAAAA-ATTTTA
1 AATTAAAATA-TTTA
*
137131 AATTTTAAATATTTA
1 AA-TTAAAATATTTA
137146 AATTAAAATATTTA
1 AATTAAAATATTTA
137160 A
1 A
137161 TTTTTATTAT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
14 14 0.54
15 11 0.42
16 1 0.04
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (14 bp):
AATTAAAATATTTA
Found at i:137162 original size:28 final size:29
Alignment explanation
Indices: 137117--137174 Score: 75
Period size: 28 Copynumber: 2.0 Consensus size: 29
137107 GAATGTTAAT
137117 AATTAAAAATTTTAAATTTTAAATATTTA
1 AATTAAAAATTTTAAATTTTAAATATTTA
* *
137146 AATT-AAAATATTT-AATTTTTATTATTTA
1 AATTAAAAAT-TTTAAATTTTAAATATTTA
137174 A
1 A
137175 TTATCGATAT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
28 19 0.73
29 7 0.27
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (29 bp):
AATTAAAAATTTTAAATTTTAAATATTTA
Found at i:138536 original size:16 final size:16
Alignment explanation
Indices: 138515--138578 Score: 69
Period size: 16 Copynumber: 4.0 Consensus size: 16
138505 TGAAAATTAA
*
138515 TATATTATTAACTATT
1 TATATTATTAAATATT
138531 TATATTATTAAATA-T
1 TATATTATTAAATATT
* *
138546 TACATTAATAACATATT
1 TATATTATTAA-ATATT
138563 TAATATT-TTAAATATT
1 T-ATATTATTAAATATT
138579 AAAATAATTT
Statistics
Matches: 40, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
15 10 0.25
16 21 0.52
17 5 0.12
18 4 0.10
ACGTcount: A:0.44, C:0.05, G:0.00, T:0.52
Consensus pattern (16 bp):
TATATTATTAAATATT
Found at i:138574 original size:32 final size:31
Alignment explanation
Indices: 138518--138579 Score: 90
Period size: 32 Copynumber: 2.0 Consensus size: 31
138508 AAATTAATAT
*
138518 ATTATTAACTATTTATATTATTAAATATTAC
1 ATTAATAACTATTTATATTATTAAATATTAC
138549 ATTAATAACATATTTAATATT-TTAAATATTA
1 ATTAATAAC-TATTT-ATATTATTAAATATTA
138580 AAATAATTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
31 8 0.29
32 15 0.54
33 5 0.18
ACGTcount: A:0.45, C:0.05, G:0.00, T:0.50
Consensus pattern (31 bp):
ATTAATAACTATTTATATTATTAAATATTAC
Found at i:138801 original size:31 final size:34
Alignment explanation
Indices: 138732--138801 Score: 83
Period size: 31 Copynumber: 2.1 Consensus size: 34
138722 TTTTTAATTA
* *
138732 ATTAATAATTAAATATATATTAAATTATTTAATG
1 ATTATTAATTAAATATATATTAAATTAATTAATG
* *
138766 ATTATTAATT-AATA-A-ATTAAATTAATTGATT
1 ATTATTAATTAAATATATATTAAATTAATTAATG
138797 ATTAT
1 ATTAT
138802 ATACTTAACA
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
31 18 0.56
32 1 0.03
33 4 0.12
34 9 0.28
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (34 bp):
ATTATTAATTAAATATATATTAAATTAATTAATG
Found at i:139608 original size:27 final size:27
Alignment explanation
Indices: 139578--139647 Score: 81
Period size: 25 Copynumber: 2.6 Consensus size: 27
139568 GAATTAAAAC
139578 AATTATAGTAATAATATATATTAT-TTT
1 AATTATA-TAATAATATATATTATATTT
* *
139605 AATTATA-ATTAAAATATATTATATTT
1 AATTATATAATAATATATATTATATTT
* *
139631 AAATATATTATAATATA
1 AATTATATAATAATATA
139648 CATGTCAAAT
Statistics
Matches: 35, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
25 13 0.37
26 9 0.26
27 13 0.37
ACGTcount: A:0.50, C:0.00, G:0.01, T:0.49
Consensus pattern (27 bp):
AATTATATAATAATATATATTATATTT
Found at i:139625 original size:16 final size:16
Alignment explanation
Indices: 139606--139644 Score: 62
Period size: 15 Copynumber: 2.5 Consensus size: 16
139596 TATTATTTTA
139606 ATTATAATTAAAATAT
1 ATTATAATTAAAATAT
*
139622 ATTAT-ATTTAAATAT
1 ATTATAATTAAAATAT
139637 ATTATAAT
1 ATTATAAT
139645 ATACATGTCA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 14 0.67
16 7 0.33
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (16 bp):
ATTATAATTAAAATAT
Found at i:139780 original size:15 final size:15
Alignment explanation
Indices: 139760--139799 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
139750 ATAATAATAT
139760 TAATTATTTATATTA
1 TAATTATTTATATTA
*
139775 TAATTATATAATATTA
1 TAATTAT-TTATATTA
139791 TAA-TATTTA
1 TAATTATTTA
139800 CTATATTAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
14 2 0.09
15 10 0.45
16 10 0.45
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (15 bp):
TAATTATTTATATTA
Found at i:139790 original size:16 final size:16
Alignment explanation
Indices: 139741--139794 Score: 60
Period size: 16 Copynumber: 3.5 Consensus size: 16
139731 TTATCTAACA
139741 ATTAT-ATTA-ATAAT
1 ATTATAATTATATAAT
* *
139755 AATATTAATTAT-TTAT
1 ATTA-TAATTATATAAT
139771 ATTATAATTATATAAT
1 ATTATAATTATATAAT
139787 ATTATAAT
1 ATTATAAT
139795 ATTTACTATA
Statistics
Matches: 32, Mismatches: 4, Indels: 6
0.76 0.10 0.14
Matches are distributed among these distances:
14 3 0.09
15 8 0.25
16 21 0.66
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (16 bp):
ATTATAATTATATAAT
Found at i:139790 original size:25 final size:25
Alignment explanation
Indices: 139742--139791 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
139732 TATCTAACAA
*
139742 TTATATTAATAATAATATTAATTAT
1 TTATATTAATAATAATATAAATTAT
*
139767 TTATATT-ATAATTATATAATATTAT
1 TTATATTAATAATAATATAA-ATTAT
139792 AATATTTACT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
24 10 0.45
25 12 0.55
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (25 bp):
TTATATTAATAATAATATAAATTAT
Found at i:139897 original size:21 final size:22
Alignment explanation
Indices: 139866--139907 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
139856 AATAATTTAA
139866 TTATTATATTTAATAAT-AATTG
1 TTATTATATTTAA-AATGAATTG
139888 TTATTA-ATTTAAAATGAATT
1 TTATTATATTTAAAATGAATT
139908 AGATTAATAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 3 0.16
21 10 0.53
22 6 0.32
ACGTcount: A:0.43, C:0.00, G:0.05, T:0.52
Consensus pattern (22 bp):
TTATTATATTTAAAATGAATTG
Found at i:139977 original size:14 final size:13
Alignment explanation
Indices: 139944--140008 Score: 51
Period size: 14 Copynumber: 4.7 Consensus size: 13
139934 AAATTTAATC
*
139944 TATTAACAATTATT
1 TATTAATAATTA-T
139958 TATTAATAATTAT
1 TATTAATAATTAT
139971 TAGTTAATAAGTTAT
1 TA-TTAATAA-TTAT
* *
139986 AATAACACTAATTAT
1 TATTA-A-TAATTAT
140001 TA-TAATAA
1 TATTAATAA
140009 CTAATTGAAA
Statistics
Matches: 42, Mismatches: 5, Indels: 10
0.74 0.09 0.18
Matches are distributed among these distances:
12 3 0.07
13 4 0.10
14 21 0.50
15 11 0.26
16 3 0.07
ACGTcount: A:0.48, C:0.05, G:0.03, T:0.45
Consensus pattern (13 bp):
TATTAATAATTAT
Found at i:141113 original size:21 final size:21
Alignment explanation
Indices: 141079--141124 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
141069 AATAATAATT
* *
141079 AAATAATTATTATTATTTTAA
1 AAATAATTACTATTATTATAA
141100 CAAAT-ATTACTATTATTATAA
1 -AAATAATTACTATTATTATAA
141121 AAAT
1 AAAT
141125 TTATAATAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 4 0.18
21 14 0.64
22 4 0.18
ACGTcount: A:0.50, C:0.04, G:0.00, T:0.46
Consensus pattern (21 bp):
AAATAATTACTATTATTATAA
Found at i:141487 original size:14 final size:14
Alignment explanation
Indices: 141428--141487 Score: 56
Period size: 14 Copynumber: 4.4 Consensus size: 14
141418 AACCAGTTTA
141428 TATAATTATAATTA-
1 TATAATTA-AATTAT
*
141442 TATAA-TAACTTAT
1 TATAATTAAATTAT
141455 TAGTAATTAAA-TAT
1 TA-TAATTAAATTAT
*
141469 T-TAATTAAATTCT
1 TATAATTAAATTAT
141482 TATAAT
1 TATAAT
141488 AATAATCGAT
Statistics
Matches: 38, Mismatches: 3, Indels: 10
0.75 0.06 0.20
Matches are distributed among these distances:
12 12 0.32
13 7 0.18
14 16 0.42
15 3 0.08
ACGTcount: A:0.47, C:0.03, G:0.02, T:0.48
Consensus pattern (14 bp):
TATAATTAAATTAT
Found at i:141612 original size:25 final size:24
Alignment explanation
Indices: 141539--141615 Score: 77
Period size: 25 Copynumber: 3.1 Consensus size: 24
141529 TTATCTAATA
141539 AATTAAATATTTATTTAATTAATATAT
1 AATT-AATA-TTA-TTAATTAATATAT
*
141566 -ATTAATAATATT-ATATAATATAT
1 AATTAATATTATTAAT-TAATATAT
*
141589 AATTGAATATTATTAATTATTATAT
1 AATT-AATATTATTAATTAATATAT
141614 AA
1 AA
141616 ACTAATCTAT
Statistics
Matches: 43, Mismatches: 3, Indels: 10
0.77 0.05 0.18
Matches are distributed among these distances:
22 2 0.05
23 10 0.23
24 5 0.12
25 21 0.49
26 5 0.12
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.49
Consensus pattern (24 bp):
AATTAATATTATTAATTAATATAT
Found at i:141743 original size:28 final size:29
Alignment explanation
Indices: 141692--141749 Score: 75
Period size: 28 Copynumber: 2.0 Consensus size: 29
141682 TAATAGCTTA
*
141692 TATAGTTTAAGTTATAAATATTAAT-ATT
1 TATAATTTAAGTTATAAATATTAATCATT
*
141720 TATAATTTAAGTTAT-TATATTTAATCATT
1 TATAATTTAAGTTATAAATA-TTAATCATT
141749 T
1 T
141750 GTATTAATAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
27 3 0.12
28 19 0.73
29 4 0.15
ACGTcount: A:0.40, C:0.02, G:0.05, T:0.53
Consensus pattern (29 bp):
TATAATTTAAGTTATAAATATTAATCATT
Done.