Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168412.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_627, 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: 21242
ACGTcount: A:0.31, C:0.16, G:0.17, T:0.36
Found at i:203 original size:13 final size:13
Alignment explanation
Indices: 187--256 Score: 85
Period size: 13 Copynumber: 5.5 Consensus size: 13
177 AAAAAAAAAG
187 AAATATTAAAATT
1 AAATATTAAAATT
200 AAATATTAAAATATT
1 AAATATT-AAA-ATT
215 AAA-ATTAAATATT
1 AAATATTAAA-ATT
228 AAA-A--AAAATT
1 AAATATTAAAATT
238 AAATATTAAAATT
1 AAATATTAAAATT
251 AAATAT
1 AAATAT
257 ATATTGTGAT
Statistics
Matches: 52, Mismatches: 0, Indels: 10
0.84 0.00 0.16
Matches are distributed among these distances:
10 6 0.12
11 4 0.08
13 30 0.58
14 6 0.12
15 6 0.12
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (13 bp):
AAATATTAAAATT
Found at i:211 original size:21 final size:21
Alignment explanation
Indices: 187--249 Score: 98
Period size: 21 Copynumber: 3.2 Consensus size: 21
177 AAAAAAAAAG
187 AAATATTAAAATTAAATATTA
1 AAATATTAAAATTAAATATTA
208 AAATATTAAAATTAAATATT-
1 AAATATTAAAATTAAATATTA
228 AAA-A--AAAATTAAATATTA
1 AAATATTAAAATTAAATATTA
246 AAAT
1 AAAT
250 TAAATATATA
Statistics
Matches: 40, Mismatches: 0, Indels: 6
0.87 0.00 0.13
Matches are distributed among these distances:
17 13 0.32
18 3 0.08
19 1 0.03
20 3 0.08
21 20 0.50
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (21 bp):
AAATATTAAAATTAAATATTA
Found at i:3707 original size:22 final size:22
Alignment explanation
Indices: 3676--3726 Score: 86
Period size: 22 Copynumber: 2.4 Consensus size: 22
3666 TTGTTTTTTA
*
3676 GAATTATAATTATATAAGAAAT
1 GAATTCTAATTATATAAGAAAT
3698 GAATTCTAATTATATAAGAAAT
1 GAATTCTAATTATATAAGAAAT
3720 -AATTCTA
1 GAATTCTA
3727 TTTAGTTTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
21 7 0.25
22 21 0.75
ACGTcount: A:0.51, C:0.04, G:0.08, T:0.37
Consensus pattern (22 bp):
GAATTCTAATTATATAAGAAAT
Found at i:4717 original size:17 final size:15
Alignment explanation
Indices: 4680--4720 Score: 57
Period size: 14 Copynumber: 2.7 Consensus size: 15
4670 CAATATTCTT
4680 TTATTTTTTTTATTC
1 TTATTTTTTTTATTC
4695 -TATTTTTATTTAGTTC
1 TTATTTTT-TTTA-TTC
4711 TTATTTTTTT
1 TTATTTTTTT
4721 AATAATTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
14 7 0.30
15 4 0.17
16 5 0.22
17 7 0.30
ACGTcount: A:0.15, C:0.05, G:0.02, T:0.78
Consensus pattern (15 bp):
TTATTTTTTTTATTC
Found at i:4792 original size:25 final size:25
Alignment explanation
Indices: 4759--4810 Score: 95
Period size: 25 Copynumber: 2.1 Consensus size: 25
4749 ATTATTTATT
*
4759 TTTTTAGTTTACCGTCTTCGAATGA
1 TTTTTAGTTTACAGTCTTCGAATGA
4784 TTTTTAGTTTACAGTCTTCGAATGA
1 TTTTTAGTTTACAGTCTTCGAATGA
4809 TT
1 TT
4811 AGGAGTTGGA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.21, C:0.13, G:0.15, T:0.50
Consensus pattern (25 bp):
TTTTTAGTTTACAGTCTTCGAATGA
Found at i:4817 original size:25 final size:25
Alignment explanation
Indices: 4764--4817 Score: 72
Period size: 25 Copynumber: 2.2 Consensus size: 25
4754 TTATTTTTTT
* ***
4764 AGTTTACCGTCTTCGAATGATTTTT
1 AGTTTACAGTCTTCGAATGATTAGG
4789 AGTTTACAGTCTTCGAATGATTAGG
1 AGTTTACAGTCTTCGAATGATTAGG
4814 AGTT
1 AGTT
4818 GGATTTTCAT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.24, C:0.13, G:0.20, T:0.43
Consensus pattern (25 bp):
AGTTTACAGTCTTCGAATGATTAGG
Found at i:4916 original size:15 final size:15
Alignment explanation
Indices: 4896--4945 Score: 73
Period size: 15 Copynumber: 3.1 Consensus size: 15
4886 CATAATGATT
4896 ATTTTAATATTGTTA
1 ATTTTAATATTGTTA
4911 ATTTTAATATTGTTGTTA
1 ATTTTAATA---TTGTTA
4929 ATTTTAATATTGTTA
1 ATTTTAATATTGTTA
4944 AT
1 AT
4946 ATTGTATTAT
Statistics
Matches: 32, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
15 17 0.53
18 15 0.47
ACGTcount: A:0.32, C:0.00, G:0.08, T:0.60
Consensus pattern (15 bp):
ATTTTAATATTGTTA
Found at i:4928 original size:18 final size:18
Alignment explanation
Indices: 4905--4942 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
4895 TATTTTAATA
4905 TTGTTAATTTTAATATTG
1 TTGTTAATTTTAATATTG
4923 TTGTTAATTTTAATATTG
1 TTGTTAATTTTAATATTG
4941 TT
1 TT
4943 AATATTGTAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.26, C:0.00, G:0.11, T:0.63
Consensus pattern (18 bp):
TTGTTAATTTTAATATTG
Found at i:4964 original size:17 final size:17
Alignment explanation
Indices: 4944--4977 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
4934 AATATTGTTA
*
4944 ATATTGTATTATTTATT
1 ATATTGTATGATTTATT
4961 ATATTGTATGATTTATT
1 ATATTGTATGATTTATT
4978 CATTACTATA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.29, C:0.00, G:0.09, T:0.62
Consensus pattern (17 bp):
ATATTGTATGATTTATT
Found at i:5001 original size:19 final size:19
Alignment explanation
Indices: 4979--5028 Score: 82
Period size: 19 Copynumber: 2.6 Consensus size: 19
4969 TGATTTATTC
*
4979 ATTACTATATTTTTTAGTT
1 ATTACTATATTTTGTAGTT
*
4998 ATTACTATATTTTGTATTT
1 ATTACTATATTTTGTAGTT
5017 ATTACTATATTT
1 ATTACTATATTT
5029 CATTATTTAT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.28, C:0.06, G:0.04, T:0.62
Consensus pattern (19 bp):
ATTACTATATTTTGTAGTT
Found at i:5046 original size:19 final size:19
Alignment explanation
Indices: 5012--5066 Score: 65
Period size: 19 Copynumber: 2.8 Consensus size: 19
5002 CTATATTTTG
*
5012 TATTTATTACTATATTTCAT
1 TATTTATTTCT-TATTTCAT
*
5032 TATTTATTTCTTATTTTAT
1 TATTTATTTCTTATTTCAT
* *
5051 TAATTATTTATTATTT
1 TATTTATTTCTTATTT
5067 TCGTGTCGGT
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
19 21 0.68
20 10 0.32
ACGTcount: A:0.27, C:0.05, G:0.00, T:0.67
Consensus pattern (19 bp):
TATTTATTTCTTATTTCAT
Found at i:5047 original size:38 final size:38
Alignment explanation
Indices: 4974--5048 Score: 98
Period size: 38 Copynumber: 2.0 Consensus size: 38
4964 TTGTATGATT
*
4974 TATTCATTACTATATTTTTTAGTTATTACTATATTTTG
1 TATTCATTACTATATTTATTAGTTATTACTATATTTTG
* * *
5012 TATTTATTACTATATTTCATTATTTATTTCT-TATTTT
1 TATTCATTACTATATTT-ATTAGTTATTACTATATTTT
5049 ATTAATTATT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
38 22 0.69
39 10 0.31
ACGTcount: A:0.25, C:0.08, G:0.03, T:0.64
Consensus pattern (38 bp):
TATTCATTACTATATTTATTAGTTATTACTATATTTTG
Found at i:5162 original size:52 final size:52
Alignment explanation
Indices: 5079--5314 Score: 197
Period size: 50 Copynumber: 4.7 Consensus size: 52
5069 GTGTCGGTTC
*
5079 TATATATATTTA--TAAATTATATTTATTTATTATTTATGTATTATCACAGT
1 TATATATATTTATTTAAATTATATTTATATATTATTTATGTATTATCACAGT
* * * ** *
5129 TATAGATATTTATTTAAATTATATTTATATATTA--AATATATTAAAATA-T
1 TATATATATTTATTTAAATTATATTTATATATTATTTATGTATTATCACAGT
* ** * ** * *
5178 TAAATTATATTTATATTTTA-TATATTAAATATATTAAAATATGAAATTAT---ATT
1 TATA-TATATTTAT-TTAAATTATATT-TATATATT-ATTTATG-TATTATCACAGT
*
5231 TATATATATTTA--TAAATTATATTTATTTATTATTTATGTATTATCACAGT
1 TATATATATTTATTTAAATTATATTTATATATTATTTATGTATTATCACAGT
*
5281 TATAGATATTTATTTAAATTATATTTATATATTA
1 TATATATATTTATTTAAATTATATTTATATATTA
5315 AATATATTAA
Statistics
Matches: 143, Mismatches: 27, Indels: 30
0.71 0.14 0.15
Matches are distributed among these distances:
47 5 0.03
48 5 0.03
49 12 0.08
50 53 0.37
51 10 0.07
52 48 0.34
53 4 0.03
54 2 0.01
55 4 0.03
ACGTcount: A:0.42, C:0.02, G:0.03, T:0.54
Consensus pattern (52 bp):
TATATATATTTATTTAAATTATATTTATATATTATTTATGTATTATCACAGT
Found at i:5181 original size:35 final size:35
Alignment explanation
Indices: 5142--5524 Score: 360
Period size: 35 Copynumber: 11.4 Consensus size: 35
5132 AGATATTTAT
5142 TTAAATTATATTTATATATTAAATATATTAAAATA
1 TTAAATTATATTTATATATTAAATATATTAAAATA
*
5177 TTAAATTATATTTATAT-TT-TATATATTAAATATA
1 TTAAATTATATTTATATATTAAATATATTAAA-ATA
* * * *
5211 TTAAAATATGAAATTATAT-TTATATATATTTATAA-A
1 TTAAATTAT--ATTTATATATTAAATATA-TTAAAATA
* * * ** *
5247 TTATATT-TATTTAT-TATT-TATGTATTATCACA
1 TTAAATTATATTTATATATTAAATATATTAAAATA
* * * *
5279 GTTATA-GATA-TT-TAT-TTAAATTATATTTATATA
1 -TTAAATTATATTTATATATTAAA-TATATTAAAATA
* *
5312 TTAAA-TATATTAAAATATTAAAT-TA-T---AT-
1 TTAAATTATATTTATATATTAAATATATTAAAATA
5340 TT--A-TAT-TTTATATATTAAATATATTAAAATA
1 TTAAATTATATTTATATATTAAATATATTAAAATA
*
5371 TGAAATTATATTTATATATTAAATATATTAAAATA
1 TTAAATTATATTTATATATTAAATATATTAAAATA
*
5406 TGAAATTATATTTATATATTAAATATATTAAAATA
1 TTAAATTATATTTATATATTAAATATATTAAAATA
*
5441 TGAAATTATATTTATATATTAAATATATTAAAATA
1 TTAAATTATATTTATATATTAAATATATTAAAATA
*
5476 TGAAATTATATTTATATATTAAATATATTAAAATA
1 TTAAATTATATTTATATATTAAATATATTAAAATA
*
5511 TGAAATTATATTTA
1 TTAAATTATATTTA
5525 AATAAATATC
Statistics
Matches: 300, Mismatches: 23, Indels: 50
0.80 0.06 0.13
Matches are distributed among these distances:
25 12 0.04
26 6 0.02
27 1 0.00
28 2 0.01
29 2 0.01
30 2 0.01
31 9 0.03
32 19 0.06
33 35 0.12
34 19 0.06
35 167 0.56
36 15 0.05
37 7 0.02
38 4 0.01
ACGTcount: A:0.48, C:0.01, G:0.02, T:0.50
Consensus pattern (35 bp):
TTAAATTATATTTATATATTAAATATATTAAAATA
Found at i:5247 original size:152 final size:152
Alignment explanation
Indices: 5079--5524 Score: 640
Period size: 152 Copynumber: 3.0 Consensus size: 152
5069 GTGTCGGTTC
5079 TATATATATTTATAAATTATATTTATTTATTATTTATGTATTATCACAGTTATAGATATTTATTT
1 TATATATATTTATAAATTATATTTATTTATTATTTATGTATTATCACAGTTATAGATATTTATTT
5144 AAATTATATTTATATATTAAATATATTAAAATATTAAATTATATTTATATTTTATATATTAAATA
66 AAATTATATTTATATATTAAATATATTAAAATATTAAATTATATTTATATTTTATATATTAAATA
5209 TATTAAAATATGAAATTATATT
131 TATTAAAATATGAAATTATATT
5231 TATATATATTTATAAATTATATTTATTTATTATTTATGTATTATCACAGTTATAGATATTTATTT
1 TATATATATTTATAAATTATATTTATTTATTATTTATGTATTATCACAGTTATAGATATTTATTT
5296 AAATTATATTTATATATTAAATATATTAAAATATTAAATTATATTTATATTTTATATATTAAATA
66 AAATTATATTTATATATTAAATATATTAAAATATTAAATTATATTTATATTTTATATATTAAATA
5361 TATTAAAATATGAAATTATATT
131 TATTAAAATATGAAATTATATT
* ** * *
5383 TATATATTAAATATATTAAA--ATATGAAATTA-TATTTATATATTA--A-A-TATATTA-A-A-
1 TATATA-T--ATTTA-TAAATTATATTTATTTATTATTTATGTATTATCACAGT-TA-TAGATAT
* * *
5438 ATA-TGAAATTATATTTATATATTAAATATATTAAAATA-T-GA--A-A-TTATA-TTTATATAT
60 TTATTTAAATTATATTTATATATTAAATATATTAAAATATTAAATTATATTTATATTTTATATAT
5495 TAAATATATTAAAATATGAAATTATATT
125 TAAATATATTAAAATATGAAATTATATT
5523 TA
1 TA
5525 AATAAATATC
Statistics
Matches: 280, Mismatches: 8, Indels: 24
0.90 0.03 0.08
Matches are distributed among these distances:
140 39 0.14
141 5 0.02
142 1 0.00
143 1 0.00
145 1 0.00
146 1 0.00
147 34 0.12
148 2 0.01
149 2 0.01
150 4 0.01
151 3 0.01
152 158 0.56
153 13 0.05
154 8 0.03
155 4 0.01
156 4 0.01
ACGTcount: A:0.46, C:0.01, G:0.03, T:0.50
Consensus pattern (152 bp):
TATATATATTTATAAATTATATTTATTTATTATTTATGTATTATCACAGTTATAGATATTTATTT
AAATTATATTTATATATTAAATATATTAAAATATTAAATTATATTTATATTTTATATATTAAATA
TATTAAAATATGAAATTATATT
Found at i:5334 original size:7 final size:8
Alignment explanation
Indices: 5309--5511 Score: 111
Period size: 8 Copynumber: 23.5 Consensus size: 8
5299 TTATATTTAT
5309 ATATTAAA
1 ATATTAAA
5317 TATATTAAA
1 -ATATTAAA
5326 ATATTAAA
1 ATATTAAA
* *
5334 TTATATTTAT
1 --ATATTAAA
* *
5344 AT-TTTAT
1 ATATTAAA
5351 ATATTAAA
1 ATATTAAA
5359 TATATTAAA
1 -ATATTAAA
*
5368 ATATGAAA
1 ATATTAAA
* *
5376 TTATATTTAT
1 --ATATTAAA
5386 ATATTAAA
1 ATATTAAA
5394 TATATTAAA
1 -ATATTAAA
*
5403 ATATGAAA
1 ATATTAAA
* *
5411 TTATATTTAT
1 --ATATTAAA
5421 ATATTAAA
1 ATATTAAA
5429 TATATTAAA
1 -ATATTAAA
*
5438 ATATGAAA
1 ATATTAAA
* *
5446 TTATATTTAT
1 --ATATTAAA
5456 ATATTAAA
1 ATATTAAA
5464 TATATTAAA
1 -ATATTAAA
*
5473 ATATGAAA
1 ATATTAAA
* *
5481 TTATATTTAT
1 --ATATTAAA
5491 ATATTAAA
1 ATATTAAA
5499 TATATTAAA
1 -ATATTAAA
5508 ATAT
1 ATAT
5512 GAAATTATAT
Statistics
Matches: 150, Mismatches: 28, Indels: 33
0.71 0.13 0.16
Matches are distributed among these distances:
7 7 0.05
8 69 0.46
9 48 0.32
10 26 0.17
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (8 bp):
ATATTAAA
Found at i:5543 original size:4 final size:4
Alignment explanation
Indices: 5536--5661 Score: 90
Period size: 4 Copynumber: 32.2 Consensus size: 4
5526 ATAAATATCT
* *
5536 ATAA AT-A ATATA AT-A ATAAA ATAA CT-A ATAA ATAA ACAA ATAA AT-A
1 ATAA ATAA ATA-A ATAA AT-AA ATAA ATAA ATAA ATAA ATAA ATAA ATAA
* * *
5582 ATAA ATAA ATAA TTAAA ATAA ACT-A ATAAA ATAA ACAA ATAA AT-A AGAA
1 ATAA ATAA ATAA AT-AA ATAA A-TAA AT-AA ATAA ATAA ATAA ATAA ATAA
5631 ATAA AT-A ATAA ATAA AT-A ATACA AT-A ATAA A
1 ATAA ATAA ATAA ATAA ATAA ATA-A ATAA ATAA A
5662 AAACACAAAG
Statistics
Matches: 97, Mismatches: 10, Indels: 30
0.71 0.07 0.22
Matches are distributed among these distances:
3 23 0.24
4 58 0.60
5 16 0.16
ACGTcount: A:0.71, C:0.04, G:0.01, T:0.25
Consensus pattern (4 bp):
ATAA
Found at i:5546 original size:35 final size:35
Alignment explanation
Indices: 5316--5524 Score: 370
Period size: 35 Copynumber: 6.0 Consensus size: 35
5306 TATATATTAA
* *
5316 ATATATTAAA-ATATTAAATTAT--ATTTATATTTT
1 ATATATTAAATATATTAAAATATGAAATTATA-TTT
5349 ATATATTAAATATATTAAAATATGAAATTATATTT
1 ATATATTAAATATATTAAAATATGAAATTATATTT
5384 ATATATTAAATATATTAAAATATGAAATTATATTT
1 ATATATTAAATATATTAAAATATGAAATTATATTT
5419 ATATATTAAATATATTAAAATATGAAATTATATTT
1 ATATATTAAATATATTAAAATATGAAATTATATTT
5454 ATATATTAAATATATTAAAATATGAAATTATATTT
1 ATATATTAAATATATTAAAATATGAAATTATATTT
5489 ATATATTAAATATATTAAAATATGAAATTATATTT
1 ATATATTAAATATATTAAAATATGAAATTATATTT
5524 A
1 A
5525 AATAAATATC
Statistics
Matches: 171, Mismatches: 2, Indels: 4
0.97 0.01 0.02
Matches are distributed among these distances:
33 10 0.06
34 11 0.06
35 144 0.84
36 6 0.04
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (35 bp):
ATATATTAAATATATTAAAATATGAAATTATATTT
Found at i:5577 original size:45 final size:45
Alignment explanation
Indices: 5536--5657 Score: 164
Period size: 45 Copynumber: 2.8 Consensus size: 45
5526 ATAAATATCT
5536 ATAAATAATATAATAATAAAAT-AACTAAT-AAATAAACAAATAAATA
1 ATAAATAA-ATAAT--TAAAATAAACTAATAAAATAAACAAATAAATA
5582 ATAAATAAATAATTAAAATAAACTAATAAAATAAACAAATAAATA
1 ATAAATAAATAATTAAAATAAACTAATAAAATAAACAAATAAATA
* *
5627 AGAAATAAATAA-T-AAATAAA-TAATACAATAA
1 ATAAATAAATAATTAAAATAAACTAATAAAATAA
5658 TAAAAAACAC
Statistics
Matches: 72, Mismatches: 2, Indels: 8
0.88 0.02 0.10
Matches are distributed among these distances:
42 10 0.14
43 13 0.18
44 8 0.11
45 33 0.46
46 8 0.11
ACGTcount: A:0.70, C:0.04, G:0.01, T:0.25
Consensus pattern (45 bp):
ATAAATAAATAATTAAAATAAACTAATAAAATAAACAAATAAATA
Found at i:5587 original size:56 final size:56
Alignment explanation
Indices: 5542--5661 Score: 110
Period size: 56 Copynumber: 2.2 Consensus size: 56
5532 ATCTATAAAT
*
5542 AATATAAT-AATAAAAT-AACTAAT-AAATAAACAAATAAATAATAAATAAATAATTAA
1 AATA-AATAAATAAAATAAACTAATAAAATAAACAAATAAATAACAAATAAATAA-T-A
* * *
5598 AATAAACT-AATAAAATAAACAAAT-AAAT-AAGAAATAAATAATAAATAAATAATA
1 AATAAA-TAAATAAAATAAACTAATAAAATAAACAAATAAATAACAAATAAATAATA
5652 CAAT-AATAAA
1 -AATAAATAAA
5662 AAACACAAAG
Statistics
Matches: 58, Mismatches: 2, Indels: 10
0.83 0.03 0.14
Matches are distributed among these distances:
53 1 0.02
54 5 0.09
55 6 0.10
56 36 0.62
57 10 0.17
ACGTcount: A:0.71, C:0.04, G:0.01, T:0.24
Consensus pattern (56 bp):
AATAAATAAATAAAATAAACTAATAAAATAAACAAATAAATAACAAATAAATAATA
Found at i:5660 original size:11 final size:11
Alignment explanation
Indices: 5536--5657 Score: 108
Period size: 11 Copynumber: 10.7 Consensus size: 11
5526 ATAAATATCT
5536 ATAAATAATATA
1 ATAAATAA-ATA
5548 AT-AATAAAATA
1 ATAAAT-AAATA
5559 ACT-AATAAATAA
1 A-TAAATAAAT-A
*
5571 ACAAATAAATA
1 ATAAATAAATA
5582 ATAAATAAATA
1 ATAAATAAATA
5593 ATTAAAATAAACTA
1 A-T-AAATAAA-TA
*
5607 ATAAA-ATA-A
1 ATAAATAAATA
*
5616 ACAAATAAATA
1 ATAAATAAATA
*
5627 AGAAATAAATA
1 ATAAATAAATA
5638 ATAAATAAATA
1 ATAAATAAATA
5649 ATACAATAA
1 ATA-AATAA
5658 TAAAAAACAC
Statistics
Matches: 93, Mismatches: 7, Indels: 20
0.77 0.06 0.17
Matches are distributed among these distances:
9 5 0.05
10 2 0.02
11 49 0.53
12 26 0.28
13 8 0.09
14 3 0.03
ACGTcount: A:0.70, C:0.04, G:0.01, T:0.25
Consensus pattern (11 bp):
ATAAATAAATA
Found at i:5660 original size:45 final size:44
Alignment explanation
Indices: 5558--5670 Score: 136
Period size: 45 Copynumber: 2.4 Consensus size: 44
5548 ATAATAAAAT
* * *
5558 AACTAATAAATAAACAAATAAATAATAAATAAATAATTAAAATA
1 AACTAATAAAAAAACAAATAAATAAGAAATAAATAATAAAAATA
5602 AACTAATAAAATAAACAAATAAATAAGAAATAAATAATAAATAAATA
1 AACTAATAAAA-AAACAAATAAATAAGAAATAAATAAT-AA-AAATA
5649 ATACAATAATAAAAAACACAAA
1 A-AC--TAATAAAAAA-ACAAA
5671 GCAAATCGTA
Statistics
Matches: 59, Mismatches: 3, Indels: 8
0.84 0.04 0.11
Matches are distributed among these distances:
44 10 0.17
45 25 0.42
46 1 0.02
47 6 0.10
48 2 0.03
49 2 0.03
50 13 0.22
ACGTcount: A:0.72, C:0.06, G:0.01, T:0.21
Consensus pattern (44 bp):
AACTAATAAAAAAACAAATAAATAAGAAATAAATAATAAAAATA
Found at i:7780 original size:30 final size:30
Alignment explanation
Indices: 7746--8025 Score: 560
Period size: 30 Copynumber: 9.3 Consensus size: 30
7736 AAATGGTGTT
7746 CCATTGTCGTCAAATGGTGGTCTTCCATTG
1 CCATTGTCGTCAAATGGTGGTCTTCCATTG
7776 CCATTGTCGTCAAATGGTGGTCTTCCATTG
1 CCATTGTCGTCAAATGGTGGTCTTCCATTG
7806 CCATTGTCGTCAAATGGTGGTCTTCCATTG
1 CCATTGTCGTCAAATGGTGGTCTTCCATTG
7836 CCATTGTCGTCAAATGGTGGTCTTCCATTG
1 CCATTGTCGTCAAATGGTGGTCTTCCATTG
7866 CCATTGTCGTCAAATGGTGGTCTTCCATTG
1 CCATTGTCGTCAAATGGTGGTCTTCCATTG
7896 CCATTGTCGTCAAATGGTGGTCTTCCATTG
1 CCATTGTCGTCAAATGGTGGTCTTCCATTG
7926 CCATTGTCGTCAAATGGTGGTCTTCCATTG
1 CCATTGTCGTCAAATGGTGGTCTTCCATTG
7956 CCATTGTCGTCAAATGGTGGTCTTCCATTG
1 CCATTGTCGTCAAATGGTGGTCTTCCATTG
7986 CCATTGTCGTCAAATGGTGGTCTTCCATTG
1 CCATTGTCGTCAAATGGTGGTCTTCCATTG
8016 CCATTGTCGT
1 CCATTGTCGT
8026 TAACTAGTCT
Statistics
Matches: 250, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 250 1.00
ACGTcount: A:0.16, C:0.24, G:0.23, T:0.37
Consensus pattern (30 bp):
CCATTGTCGTCAAATGGTGGTCTTCCATTG
Found at i:8066 original size:18 final size:18
Alignment explanation
Indices: 8039--8273 Score: 397
Period size: 18 Copynumber: 13.1 Consensus size: 18
8029 CTAGTCTCCA
*
8039 TTTTTTATTCACTATAGG
1 TTTTTCATTCACTATAGG
8057 TTTGTT-ATTCACTATAGG
1 TTT-TTCATTCACTATAGG
8075 TTTGTT-ATTCACTATAGG
1 TTT-TTCATTCACTATAGG
8093 TTTGTT-ATTCACTATAGG
1 TTT-TTCATTCACTATAGG
8111 TTTTTCATTCACTATAGG
1 TTTTTCATTCACTATAGG
8129 TTTTTCATTCACTATAGG
1 TTTTTCATTCACTATAGG
8147 TTTTTCATTCACTATAGG
1 TTTTTCATTCACTATAGG
8165 TTTTTCATTCACTATAGG
1 TTTTTCATTCACTATAGG
8183 TTTGTT-ATTCACTATAGG
1 TTT-TTCATTCACTATAGG
8201 TTTTTCATTCACTATAGG
1 TTTTTCATTCACTATAGG
8219 TTTTTCATTCACTATAGG
1 TTTTTCATTCACTATAGG
8237 TTTTTCATTCACTATAGG
1 TTTTTCATTCACTATAGG
8255 TTTTTCATTCACTATAGG
1 TTTTTCATTCACTATAGG
8273 T
1 T
8274 CTCGATTCTG
Statistics
Matches: 213, Mismatches: 0, Indels: 8
0.96 0.00 0.04
Matches are distributed among these distances:
17 4 0.02
18 205 0.96
19 4 0.02
ACGTcount: A:0.22, C:0.14, G:0.13, T:0.51
Consensus pattern (18 bp):
TTTTTCATTCACTATAGG
Found at i:8614 original size:18 final size:18
Alignment explanation
Indices: 8591--8628 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
8581 TTTTTTGCGC
8591 ATTGCATACGGCTTTACA
1 ATTGCATACGGCTTTACA
8609 ATTGCATACGGCTTTACA
1 ATTGCATACGGCTTTACA
8627 AT
1 AT
8629 GGAATTCTCT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.29, C:0.21, G:0.16, T:0.34
Consensus pattern (18 bp):
ATTGCATACGGCTTTACA
Found at i:10564 original size:78 final size:78
Alignment explanation
Indices: 10435--10603 Score: 320
Period size: 78 Copynumber: 2.2 Consensus size: 78
10425 AGTAAAAAGA
* *
10435 ATGTAAAATTATATTTCGCTTTGATTGTGGAAGCGTAATACGTAATGTAATACGTAATAATGGTC
1 ATGTAATATTATATTTCACTTTGATTGTGGAAGCGTAATACGTAATGTAATACGTAATAATGGTC
10500 TTATCTTAATAAT
66 TTATCTTAATAAT
10513 ATGTAATATTATATTTCACTTTGATTGTGGAAGCGTAATACGTAATGTAATACGTAATAATGGTC
1 ATGTAATATTATATTTCACTTTGATTGTGGAAGCGTAATACGTAATGTAATACGTAATAATGGTC
10578 TTATCTTAATAAT
66 TTATCTTAATAAT
10591 ATGTAATATTATA
1 ATGTAATATTATA
10604 ATATGTAATA
Statistics
Matches: 89, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
78 89 1.00
ACGTcount: A:0.36, C:0.08, G:0.15, T:0.41
Consensus pattern (78 bp):
ATGTAATATTATATTTCACTTTGATTGTGGAAGCGTAATACGTAATGTAATACGTAATAATGGTC
TTATCTTAATAAT
Found at i:10606 original size:15 final size:15
Alignment explanation
Indices: 10586--10618 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
10576 TCTTATCTTA
10586 ATAATATGTAATATT
1 ATAATATGTAATATT
10601 ATAATATGTAATATT
1 ATAATATGTAATATT
10616 ATA
1 ATA
10619 TTTCACTTTG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.48, C:0.00, G:0.06, T:0.45
Consensus pattern (15 bp):
ATAATATGTAATATT
Found at i:10699 original size:15 final size:15
Alignment explanation
Indices: 10679--10711 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
10669 TCTTATCTTA
10679 ATAATATGTAATATT
1 ATAATATGTAATATT
10694 ATAATATGTAATATT
1 ATAATATGTAATATT
10709 ATA
1 ATA
10712 TTTCACTTTG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.48, C:0.00, G:0.06, T:0.45
Consensus pattern (15 bp):
ATAATATGTAATATT
Found at i:10800 original size:93 final size:93
Alignment explanation
Indices: 10508--10784 Score: 554
Period size: 93 Copynumber: 3.0 Consensus size: 93
10498 TCTTATCTTA
10508 ATAATATGTAATATTATATTTCACTTTGATTGTGGAAGCGTAATACGTAATGTAATACGTAATAA
1 ATAATATGTAATATTATATTTCACTTTGATTGTGGAAGCGTAATACGTAATGTAATACGTAATAA
10573 TGGTCTTATCTTAATAATATGTAATATT
66 TGGTCTTATCTTAATAATATGTAATATT
10601 ATAATATGTAATATTATATTTCACTTTGATTGTGGAAGCGTAATACGTAATGTAATACGTAATAA
1 ATAATATGTAATATTATATTTCACTTTGATTGTGGAAGCGTAATACGTAATGTAATACGTAATAA
10666 TGGTCTTATCTTAATAATATGTAATATT
66 TGGTCTTATCTTAATAATATGTAATATT
10694 ATAATATGTAATATTATATTTCACTTTGATTGTGGAAGCGTAATACGTAATGTAATACGTAATAA
1 ATAATATGTAATATTATATTTCACTTTGATTGTGGAAGCGTAATACGTAATGTAATACGTAATAA
10759 TGGTCTTATCTTAATAATATGTAATA
66 TGGTCTTATCTTAATAATATGTAATA
10785 ATGGTCTTAA
Statistics
Matches: 184, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
93 184 1.00
ACGTcount: A:0.37, C:0.08, G:0.14, T:0.42
Consensus pattern (93 bp):
ATAATATGTAATATTATATTTCACTTTGATTGTGGAAGCGTAATACGTAATGTAATACGTAATAA
TGGTCTTATCTTAATAATATGTAATATT
Found at i:13189 original size:21 final size:20
Alignment explanation
Indices: 13172--13223 Score: 79
Period size: 21 Copynumber: 2.6 Consensus size: 20
13162 TTATATAATT
*
13172 ATATAAATA-ATATATATAA
1 ATATAAATATAAATATATAA
13191 ATATAAATATAAATAATATAA
1 ATATAAATATAAAT-ATATAA
13212 ATATAAATATAA
1 ATATAAATATAA
13224 TTTCAAGATC
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 9 0.30
20 3 0.10
21 18 0.60
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (20 bp):
ATATAAATATAAATATATAA
Found at i:13196 original size:6 final size:6
Alignment explanation
Indices: 13172--13223 Score: 65
Period size: 6 Copynumber: 9.0 Consensus size: 6
13162 TTATATAATT
*
13172 ATATAA ATAATAT ATATAA ATATAA ATAT-A A-AT-A ATATAA ATATAA
1 ATATAA AT-ATAA ATATAA ATATAA ATATAA ATATAA ATATAA ATATAA
13218 ATATAA
1 ATATAA
13224 TTTCAAGATC
Statistics
Matches: 41, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
4 4 0.10
5 4 0.10
6 28 0.68
7 5 0.12
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (6 bp):
ATATAA
Found at i:15193 original size:23 final size:23
Alignment explanation
Indices: 15167--15212 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
15157 TATATTGTAA
15167 CCAATCATTTATCTTATTACTTG
1 CCAATCATTTATCTTATTACTTG
15190 CCAATCATTTATCTTATTACTTG
1 CCAATCATTTATCTTATTACTTG
15213 GGGGAGGAAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.26, C:0.22, G:0.04, T:0.48
Consensus pattern (23 bp):
CCAATCATTTATCTTATTACTTG
Found at i:20723 original size:21 final size:21
Alignment explanation
Indices: 20699--20742 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
20689 GATTCTTTGC
20699 TTTGAGATTTTATCTGATCTA
1 TTTGAGATTTTATCTGATCTA
20720 TTTGAGATTTTATCTGATCTA
1 TTTGAGATTTTATCTGATCTA
20741 TT
1 TT
20743 ATAAATTTGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.23, C:0.09, G:0.14, T:0.55
Consensus pattern (21 bp):
TTTGAGATTTTATCTGATCTA
Found at i:20750 original size:21 final size:21
Alignment explanation
Indices: 20699--20750 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
20689 GATTCTTTGC
*
20699 TTTGAGATTTTATCTGATCTA
1 TTTGAAATTTTATCTGATCTA
*
20720 TTTGAGATTTTATCTGATCTA
1 TTTGAAATTTTATCTGATCTA
20741 TTAT-AAATTT
1 TT-TGAAATTT
20751 GTATATCTTG
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
21 28 0.97
22 1 0.03
ACGTcount: A:0.27, C:0.08, G:0.12, T:0.54
Consensus pattern (21 bp):
TTTGAAATTTTATCTGATCTA
Found at i:20992 original size:37 final size:39
Alignment explanation
Indices: 20924--20996 Score: 132
Period size: 37 Copynumber: 1.9 Consensus size: 39
20914 ACAATCAAAT
20924 AAAATGAAAATAAAATTGTTTAAAATGAAAATAAAAAAA
1 AAAATGAAAATAAAATTGTTTAAAATGAAAATAAAAAAA
20963 AAAATGAAAAT-AAATT-TTTAAAATGAAAATAAAA
1 AAAATGAAAATAAAATTGTTTAAAATGAAAATAAAA
20997 TTTTCCGCGG
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
37 18 0.53
38 5 0.15
39 11 0.32
ACGTcount: A:0.68, C:0.00, G:0.07, T:0.25
Consensus pattern (39 bp):
AAAATGAAAATAAAATTGTTTAAAATGAAAATAAAAAAA
Done.