Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168232.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_465, 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: 25980
ACGTcount: A:0.31, C:0.17, G:0.16, T:0.36
Found at i:25 original size:19 final size:19
Alignment explanation
Indices: 1--105 Score: 81
Period size: 19 Copynumber: 5.2 Consensus size: 19
1 AATAAGTAATATAATAAGT
1 AATAAGTAATATAATAAGT
20 AATAAG-ATATATAATAAGT
1 AATAAGTA-ATATAATAAGT
*
39 -ATAAATAAGTATAATAAGTAT
1 AATAAGTAA-TATAATAAG--T
60 AAATAAGTATAAGTATAAATAAGT
1 -AATAAG--TAA-TAT-AATAAGT
*
84 -ATAATATAATATAATAAGT
1 AATAA-GTAATATAATAAGT
103 AAT
1 AAT
106 GGACAACCAA
Statistics
Matches: 71, Mismatches: 3, Indels: 23
0.73 0.03 0.24
Matches are distributed among these distances:
18 6 0.08
19 34 0.48
20 5 0.07
21 4 0.06
22 4 0.06
23 4 0.06
24 1 0.01
25 7 0.10
26 6 0.08
ACGTcount: A:0.58, C:0.00, G:0.10, T:0.32
Consensus pattern (19 bp):
AATAAGTAATATAATAAGT
Found at i:47 original size:10 final size:10
Alignment explanation
Indices: 20--103 Score: 92
Period size: 10 Copynumber: 8.8 Consensus size: 10
10 TATAATAAGT
20 AATAAGATATA
1 AATAAG-TATA
31 TAATAAGTATA
1 -AATAAGTATA
42 AATAAGTAT-
1 AATAAGTATA
51 AATAAGTATA
1 AATAAGTATA
61 AATAAG--T-
1 AATAAGTATA
68 -ATAAGTATA
1 AATAAGTATA
77 AATAAGTATA
1 AATAAGTATA
87 ATATAA-TAT-
1 A-ATAAGTATA
96 AATAAGTA
1 AATAAGTA
104 ATGGACAACC
Statistics
Matches: 65, Mismatches: 0, Indels: 17
0.79 0.00 0.21
Matches are distributed among these distances:
6 5 0.08
8 6 0.09
9 12 0.18
10 28 0.43
11 8 0.12
12 6 0.09
ACGTcount: A:0.58, C:0.00, G:0.10, T:0.32
Consensus pattern (10 bp):
AATAAGTATA
Found at i:52 original size:16 final size:16
Alignment explanation
Indices: 33--97 Score: 87
Period size: 16 Copynumber: 3.9 Consensus size: 16
23 AAGATATATA
33 ATAAGTATAAATAAGTAT
1 ATAAGTATAAATAAG--T
51 AATAAGTATAAATAAGT
1 -ATAAGTATAAATAAGT
68 ATAAGTATAAATAAGT
1 ATAAGTATAAATAAGT
84 ATAA-TATAATATAA
1 ATAAGTATAA-ATAA
98 TAAGTAATGG
Statistics
Matches: 45, Mismatches: 0, Indels: 5
0.90 0.00 0.10
Matches are distributed among these distances:
15 5 0.11
16 24 0.53
17 1 0.02
19 15 0.33
ACGTcount: A:0.58, C:0.00, G:0.09, T:0.32
Consensus pattern (16 bp):
ATAAGTATAAATAAGT
Found at i:79 original size:35 final size:35
Alignment explanation
Indices: 2--103 Score: 120
Period size: 35 Copynumber: 2.9 Consensus size: 35
1 A
*
2 ATAAGTAA-TATAATAAGTAATAAGATATA-TAATAAGT
1 ATAAATAAGTATAATAAGT-ATAA-ATA-AGT-ATAAGT
39 ATAAATAAGTATAATAAGTATAAATAAGTATAAGT
1 ATAAATAAGTATAATAAGTATAAATAAGTATAAGT
*
74 ATAAATAAGTATAATATAATAT-AATAAGTA
1 ATAAATAAGTATAATA-AGTATAAATAAGTA
104 ATGGACAACC
Statistics
Matches: 60, Mismatches: 2, Indels: 8
0.86 0.03 0.11
Matches are distributed among these distances:
35 31 0.52
36 8 0.13
37 11 0.18
38 10 0.17
ACGTcount: A:0.58, C:0.00, G:0.10, T:0.32
Consensus pattern (35 bp):
ATAAATAAGTATAATAAGTATAAATAAGTATAAGT
Found at i:292 original size:13 final size:13
Alignment explanation
Indices: 276--345 Score: 85
Period size: 13 Copynumber: 5.5 Consensus size: 13
266 AAAAAAAAAG
276 AAATATTAAAATT
1 AAATATTAAAATT
289 AAATATTAAAATATT
1 AAATATT-AAA-ATT
304 AAA-ATTAAATATT
1 AAATATTAAA-ATT
317 AAA-A--AAAATT
1 AAATATTAAAATT
327 AAATATTAAAATT
1 AAATATTAAAATT
340 AAATAT
1 AAATAT
346 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:302 original size:21 final size:21
Alignment explanation
Indices: 276--338 Score: 98
Period size: 21 Copynumber: 3.2 Consensus size: 21
266 AAAAAAAAAG
276 AAATATTAAAATTAAATATTA
1 AAATATTAAAATTAAATATTA
297 AAATATTAAAATTAAATATT-
1 AAATATTAAAATTAAATATTA
317 AAA-A--AAAATTAAATATTA
1 AAATATTAAAATTAAATATTA
335 AAAT
1 AAAT
339 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:3797 original size:22 final size:22
Alignment explanation
Indices: 3766--3816 Score: 86
Period size: 22 Copynumber: 2.4 Consensus size: 22
3756 GTTGTTTTTA
*
3766 GAATTATAATTATATAAGAAAT
1 GAATTCTAATTATATAAGAAAT
3788 GAATTCTAATTATATAAGAAAT
1 GAATTCTAATTATATAAGAAAT
3810 -AATTCTA
1 GAATTCTA
3817 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:4884 original size:25 final size:25
Alignment explanation
Indices: 4851--4902 Score: 95
Period size: 25 Copynumber: 2.1 Consensus size: 25
4841 ATTATTTATT
*
4851 TTTTTAGTTTACCGTCTTCGAATGA
1 TTTTTAGTTTACAGTCTTCGAATGA
4876 TTTTTAGTTTACAGTCTTCGAATGA
1 TTTTTAGTTTACAGTCTTCGAATGA
4901 TT
1 TT
4903 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:4909 original size:25 final size:25
Alignment explanation
Indices: 4856--4909 Score: 72
Period size: 25 Copynumber: 2.2 Consensus size: 25
4846 TTATTTTTTT
* ***
4856 AGTTTACCGTCTTCGAATGATTTTT
1 AGTTTACAGTCTTCGAATGATTAGG
4881 AGTTTACAGTCTTCGAATGATTAGG
1 AGTTTACAGTCTTCGAATGATTAGG
4906 AGTT
1 AGTT
4910 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:5008 original size:15 final size:15
Alignment explanation
Indices: 4988--5037 Score: 73
Period size: 15 Copynumber: 3.1 Consensus size: 15
4978 CATAATGATT
4988 ATTTTAATATTGTTA
1 ATTTTAATATTGTTA
5003 ATTTTAATATTGTTGTTA
1 ATTTTAATA---TTGTTA
5021 ATTTTAATATTGTTA
1 ATTTTAATATTGTTA
5036 AT
1 AT
5038 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:5020 original size:18 final size:18
Alignment explanation
Indices: 4997--5034 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
4987 TATTTTAATA
4997 TTGTTAATTTTAATATTG
1 TTGTTAATTTTAATATTG
5015 TTGTTAATTTTAATATTG
1 TTGTTAATTTTAATATTG
5033 TT
1 TT
5035 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:5056 original size:17 final size:17
Alignment explanation
Indices: 5036--5069 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
5026 AATATTGTTA
*
5036 ATATTGTATTATTTATT
1 ATATTGTATGATTTATT
5053 ATATTGTATGATTTATT
1 ATATTGTATGATTTATT
5070 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:5093 original size:19 final size:19
Alignment explanation
Indices: 5071--5120 Score: 82
Period size: 19 Copynumber: 2.6 Consensus size: 19
5061 TGATTTATTC
*
5071 ATTACTATATTTTTTAGTT
1 ATTACTATATTTTGTAGTT
*
5090 ATTACTATATTTTGTATTT
1 ATTACTATATTTTGTAGTT
5109 ATTACTATATTT
1 ATTACTATATTT
5121 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:5138 original size:19 final size:19
Alignment explanation
Indices: 5104--5158 Score: 65
Period size: 19 Copynumber: 2.8 Consensus size: 19
5094 CTATATTTTG
*
5104 TATTTATTACTATATTTCAT
1 TATTTATTTCT-TATTTCAT
*
5124 TATTTATTTCTTATTTTAT
1 TATTTATTTCTTATTTCAT
* *
5143 TAATTATTTATTATTT
1 TATTTATTTCTTATTT
5159 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:5139 original size:38 final size:38
Alignment explanation
Indices: 5066--5140 Score: 98
Period size: 38 Copynumber: 2.0 Consensus size: 38
5056 TTGTATGATT
*
5066 TATTCATTACTATATTTTTTAGTTATTACTATATTTTG
1 TATTCATTACTATATTTATTAGTTATTACTATATTTTG
* * *
5104 TATTTATTACTATATTTCATTATTTATTTCT-TATTTT
1 TATTCATTACTATATTT-ATTAGTTATTACTATATTTT
5141 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:5197 original size:17 final size:18
Alignment explanation
Indices: 5171--5359 Score: 79
Period size: 17 Copynumber: 10.4 Consensus size: 18
5161 GTGTCGGTTC
*
5171 TATATATATTTA-TAAAT
1 TATATTTATTTATTAAAT
5188 TATATTTATTTATT--AT
1 TATATTTATTTATTAAAT
* * *
5204 T-TATGTA-TTATCACAGT
1 TATATTTATTTATTA-AAT
**
5221 TATAGATATTTATTTAAAT
1 TATATTTATTTA-TTAAAT
*
5240 TATATTTATATATTAAA-
1 TATATTTATTTATTAAAT
* **
5257 TATATTAAAATATTAAAT
1 TATATTTATTTATTAAAT
5275 TATATTTATATT-TTATATAT
1 TATATTTAT-TTATTA-A-AT
** *
5295 TAAATATATTAAAATATGAAAT
1 T--ATAT-TT-ATTTATTAAAT
*
5317 TATATTTATATATTAAA-
1 TATATTTATTTATTAAAT
* ** *
5334 TATATTAAAATATGAAAT
1 TATATTTATTTATTAAAT
5352 TATATTTA
1 TATATTTA
5360 AATAAATATC
Statistics
Matches: 130, Mismatches: 25, Indels: 33
0.69 0.13 0.18
Matches are distributed among these distances:
14 4 0.03
15 5 0.04
16 3 0.02
17 42 0.32
18 35 0.27
19 18 0.14
20 9 0.07
22 7 0.05
23 4 0.03
24 3 0.02
ACGTcount: A:0.45, C:0.01, G:0.03, T:0.51
Consensus pattern (18 bp):
TATATTTATTTATTAAAT
Found at i:5253 original size:8 final size:8
Alignment explanation
Indices: 5240--5346 Score: 72
Period size: 8 Copynumber: 12.6 Consensus size: 8
5230 TTATTTAAAT
*
5240 TATATTTA
1 TATATTAA
5248 TATATTAAA
1 TATATT-AA
5257 TATATTAA
1 TATATTAA
*
5265 AATATTAAA
1 TATATT-AA
*
5274 TTATATTTA
1 -TATATTAA
*
5283 TAT-TTTA
1 TATATTAA
5290 TATATTAAA
1 TATATT-AA
5299 TATATTAA
1 TATATTAA
* *
5307 AATATGAAA
1 TATAT-TAA
*
5316 TTATATTTA
1 -TATATTAA
5325 TATATTAAA
1 TATATT-AA
5334 TATATTAA
1 TATATTAA
*
5342 AATAT
1 TATAT
5347 GAAATTATAT
Statistics
Matches: 79, Mismatches: 12, Indels: 16
0.74 0.11 0.15
Matches are distributed among these distances:
7 7 0.09
8 36 0.46
9 27 0.34
10 9 0.11
ACGTcount: A:0.50, C:0.00, G:0.01, T:0.50
Consensus pattern (8 bp):
TATATTAA
Found at i:5270 original size:77 final size:76
Alignment explanation
Indices: 5201--5359 Score: 205
Period size: 77 Copynumber: 2.1 Consensus size: 76
5191 ATTTATTTAT
* * * *
5201 TATTTATGTATTATCACAGTTATAGATATT-TAT-TTAAATTATATTTATATATTAAATATATTA
1 TATTTATATATTAT-ACA-TTAAAGATATTAAATATGAAATTATATTTATATATTAAATATATTA
5264 AAATATTAAATTA
64 AAATATTAAATTA
* * *
5277 TATTTATATTTTATATATTAAATATATTAAAATATGAAATTATATTTATATATTAAATATATTAA
1 TATTTATATATTATACATTAAAGATATT-AAATATGAAATTATATTTATATATTAAATATATTAA
*
5342 AATATGAAATTA
65 AATATTAAATTA
5354 TATTTA
1 TATTTA
5360 AATAAATATC
Statistics
Matches: 72, Mismatches: 8, Indels: 5
0.85 0.09 0.06
Matches are distributed among these distances:
74 9 0.12
75 2 0.03
76 14 0.19
77 47 0.65
ACGTcount: A:0.46, C:0.01, G:0.03, T:0.50
Consensus pattern (76 bp):
TATTTATATATTATACATTAAAGATATTAAATATGAAATTATATTTATATATTAAATATATTAAA
ATATTAAATTA
Found at i:5273 original size:35 final size:35
Alignment explanation
Indices: 5236--5359 Score: 176
Period size: 35 Copynumber: 3.3 Consensus size: 35
5226 ATATTTATTT
*
5236 AAATTATATTTATATATTAAATATATTAAAATATTAA
1 AAATTATATTTATATATTAAATATATTAAAATA-T-G
5273 ATTATATTTATATTTTATATATTAAATATATTAAAATATG
1 A--A-A-TTATA-TTTATATATTAAATATATTAAAATATG
5313 AAATTATATTTATATATTAAATATATTAAAATATG
1 AAATTATATTTATATATTAAATATATTAAAATATG
5348 AAATTATATTTA
1 AAATTATATTTA
5360 AATAAATATC
Statistics
Matches: 81, Mismatches: 1, Indels: 12
0.86 0.01 0.13
Matches are distributed among these distances:
35 39 0.48
36 5 0.06
37 2 0.02
38 1 0.01
39 1 0.01
40 2 0.02
41 6 0.07
42 25 0.31
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (35 bp):
AAATTATATTTATATATTAAATATATTAAAATATG
Found at i:5378 original size:4 final size:4
Alignment explanation
Indices: 5371--5498 Score: 85
Period size: 4 Copynumber: 32.2 Consensus size: 4
5361 ATAAATATCT
*
5371 ATAA AT-A ATATA AT-A ATAAA ATAA ACT-A ATAAA ATAA ACAA ATAA
1 ATAA ATAA ATA-A ATAA AT-AA ATAA A-TAA AT-AA ATAA ATAA ATAA
* *
5416 AT-A ATAA ATAA ATAA TTAAA ATAA ACT-A ATAAA ATAA ACAA ATAA AT-A
1 ATAA ATAA ATAA ATAA AT-AA ATAA A-TAA AT-AA ATAA ATAA ATAA ATAA
*
5464 AGAA ATAA AT-A ATAA ATAA AT-A ATACA AT-A ATAA A
1 ATAA ATAA ATAA ATAA ATAA ATAA ATA-A ATAA ATAA A
5499 AAAACAAAGC
Statistics
Matches: 99, Mismatches: 8, Indels: 34
0.70 0.06 0.24
Matches are distributed among these distances:
3 22 0.22
4 57 0.58
5 20 0.20
ACGTcount: A:0.71, C:0.04, G:0.01, T:0.24
Consensus pattern (4 bp):
ATAA
Found at i:5393 original size:13 final size:13
Alignment explanation
Indices: 5384--5461 Score: 82
Period size: 13 Copynumber: 6.5 Consensus size: 13
5374 AATAATATAA
5384 TAATAAAATAAAC
1 TAATAAAATAAAC
5397 TAATAAAATAAAC
1 TAATAAAATAAAC
5410 -----AAATAAA-
1 TAATAAAATAAAC
5417 TAAT-AAATAAA-
1 TAATAAAATAAAC
5428 TAATTAAAATAAAC
1 TAA-TAAAATAAAC
5442 TAATAAAATAAAC
1 TAATAAAATAAAC
*
5455 AAATAAA
1 TAATAAA
5462 TAAGAAATAA
Statistics
Matches: 57, Mismatches: 1, Indels: 14
0.79 0.01 0.19
Matches are distributed among these distances:
8 7 0.12
11 10 0.18
12 1 0.02
13 36 0.63
14 3 0.05
ACGTcount: A:0.72, C:0.05, G:0.00, T:0.23
Consensus pattern (13 bp):
TAATAAAATAAAC
Found at i:5498 original size:45 final size:44
Alignment explanation
Indices: 5377--5494 Score: 186
Period size: 45 Copynumber: 2.7 Consensus size: 44
5367 ATCTATAAAT
*
5377 AATATAATAATAAAATAAACTAATAAAATAAACAAATAAATAATA
1 AATA-AATAATAAAATAAACTAATAAAATAAACAAATAAATAAGA
5422 AATAAATAATTAAAATAAACTAATAAAATAAACAAATAAATAAGA
1 AATAAATAA-TAAAATAAACTAATAAAATAAACAAATAAATAAGA
*
5467 AATAAATAAT-AAATAAA-TAATACAATAA
1 AATAAATAATAAAATAAACTAATAAAATAA
5495 TAAAAAAACA
Statistics
Matches: 70, Mismatches: 2, Indels: 5
0.91 0.03 0.06
Matches are distributed among these distances:
42 10 0.14
43 7 0.10
44 6 0.09
45 47 0.67
ACGTcount: A:0.71, C:0.04, G:0.01, T:0.24
Consensus pattern (44 bp):
AATAAATAATAAAATAAACTAATAAAATAAACAAATAAATAAGA
Found at i:7616 original size:30 final size:30
Alignment explanation
Indices: 7582--7921 Score: 680
Period size: 30 Copynumber: 11.3 Consensus size: 30
7572 AAATGGTGTT
7582 CCATTGTCGTCAAATGGTGGTCTTCCATTG
1 CCATTGTCGTCAAATGGTGGTCTTCCATTG
7612 CCATTGTCGTCAAATGGTGGTCTTCCATTG
1 CCATTGTCGTCAAATGGTGGTCTTCCATTG
7642 CCATTGTCGTCAAATGGTGGTCTTCCATTG
1 CCATTGTCGTCAAATGGTGGTCTTCCATTG
7672 CCATTGTCGTCAAATGGTGGTCTTCCATTG
1 CCATTGTCGTCAAATGGTGGTCTTCCATTG
7702 CCATTGTCGTCAAATGGTGGTCTTCCATTG
1 CCATTGTCGTCAAATGGTGGTCTTCCATTG
7732 CCATTGTCGTCAAATGGTGGTCTTCCATTG
1 CCATTGTCGTCAAATGGTGGTCTTCCATTG
7762 CCATTGTCGTCAAATGGTGGTCTTCCATTG
1 CCATTGTCGTCAAATGGTGGTCTTCCATTG
7792 CCATTGTCGTCAAATGGTGGTCTTCCATTG
1 CCATTGTCGTCAAATGGTGGTCTTCCATTG
7822 CCATTGTCGTCAAATGGTGGTCTTCCATTG
1 CCATTGTCGTCAAATGGTGGTCTTCCATTG
7852 CCATTGTCGTCAAATGGTGGTCTTCCATTG
1 CCATTGTCGTCAAATGGTGGTCTTCCATTG
7882 CCATTGTCGTCAAATGGTGGTCTTCCATTG
1 CCATTGTCGTCAAATGGTGGTCTTCCATTG
7912 CCATTGTCGT
1 CCATTGTCGT
7922 TAACTAGTCT
Statistics
Matches: 310, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 310 1.00
ACGTcount: A:0.16, C:0.24, G:0.23, T:0.37
Consensus pattern (30 bp):
CCATTGTCGTCAAATGGTGGTCTTCCATTG
Found at i:7962 original size:18 final size:18
Alignment explanation
Indices: 7935--8169 Score: 397
Period size: 18 Copynumber: 13.1 Consensus size: 18
7925 CTAGTCTCCA
*
7935 TTTTTTATTCACTATAGG
1 TTTTTCATTCACTATAGG
7953 TTTGTT-ATTCACTATAGG
1 TTT-TTCATTCACTATAGG
7971 TTTGTT-ATTCACTATAGG
1 TTT-TTCATTCACTATAGG
7989 TTTGTT-ATTCACTATAGG
1 TTT-TTCATTCACTATAGG
8007 TTTTTCATTCACTATAGG
1 TTTTTCATTCACTATAGG
8025 TTTTTCATTCACTATAGG
1 TTTTTCATTCACTATAGG
8043 TTTTTCATTCACTATAGG
1 TTTTTCATTCACTATAGG
8061 TTTTTCATTCACTATAGG
1 TTTTTCATTCACTATAGG
8079 TTTGTT-ATTCACTATAGG
1 TTT-TTCATTCACTATAGG
8097 TTTTTCATTCACTATAGG
1 TTTTTCATTCACTATAGG
8115 TTTTTCATTCACTATAGG
1 TTTTTCATTCACTATAGG
8133 TTTTTCATTCACTATAGG
1 TTTTTCATTCACTATAGG
8151 TTTTTCATTCACTATAGG
1 TTTTTCATTCACTATAGG
8169 T
1 T
8170 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:8510 original size:18 final size:18
Alignment explanation
Indices: 8487--8524 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
8477 TTTTTTGCGC
8487 ATTGCATACGGCTTTACA
1 ATTGCATACGGCTTTACA
8505 ATTGCATACGGCTTTACA
1 ATTGCATACGGCTTTACA
8523 AT
1 AT
8525 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:10461 original size:78 final size:78
Alignment explanation
Indices: 10332--10500 Score: 320
Period size: 78 Copynumber: 2.2 Consensus size: 78
10322 AGTAAAAAGA
* *
10332 ATGTAAAATTATATTTCGCTTTGATTGTGGAAGCGTAATACGTAATGTAATACGTAATAATGGTC
1 ATGTAATATTATATTTCACTTTGATTGTGGAAGCGTAATACGTAATGTAATACGTAATAATGGTC
10397 TTATCTTAATAAT
66 TTATCTTAATAAT
10410 ATGTAATATTATATTTCACTTTGATTGTGGAAGCGTAATACGTAATGTAATACGTAATAATGGTC
1 ATGTAATATTATATTTCACTTTGATTGTGGAAGCGTAATACGTAATGTAATACGTAATAATGGTC
10475 TTATCTTAATAAT
66 TTATCTTAATAAT
10488 ATGTAATATTATA
1 ATGTAATATTATA
10501 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:10503 original size:15 final size:15
Alignment explanation
Indices: 10483--10515 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
10473 TCTTATCTTA
10483 ATAATATGTAATATT
1 ATAATATGTAATATT
10498 ATAATATGTAATATT
1 ATAATATGTAATATT
10513 ATA
1 ATA
10516 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:10596 original size:15 final size:15
Alignment explanation
Indices: 10576--10608 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
10566 TCTTATCTTA
10576 ATAATATGTAATATT
1 ATAATATGTAATATT
10591 ATAATATGTAATATT
1 ATAATATGTAATATT
10606 ATA
1 ATA
10609 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:10697 original size:93 final size:93
Alignment explanation
Indices: 10405--10681 Score: 554
Period size: 93 Copynumber: 3.0 Consensus size: 93
10395 TCTTATCTTA
10405 ATAATATGTAATATTATATTTCACTTTGATTGTGGAAGCGTAATACGTAATGTAATACGTAATAA
1 ATAATATGTAATATTATATTTCACTTTGATTGTGGAAGCGTAATACGTAATGTAATACGTAATAA
10470 TGGTCTTATCTTAATAATATGTAATATT
66 TGGTCTTATCTTAATAATATGTAATATT
10498 ATAATATGTAATATTATATTTCACTTTGATTGTGGAAGCGTAATACGTAATGTAATACGTAATAA
1 ATAATATGTAATATTATATTTCACTTTGATTGTGGAAGCGTAATACGTAATGTAATACGTAATAA
10563 TGGTCTTATCTTAATAATATGTAATATT
66 TGGTCTTATCTTAATAATATGTAATATT
10591 ATAATATGTAATATTATATTTCACTTTGATTGTGGAAGCGTAATACGTAATGTAATACGTAATAA
1 ATAATATGTAATATTATATTTCACTTTGATTGTGGAAGCGTAATACGTAATGTAATACGTAATAA
10656 TGGTCTTATCTTAATAATATGTAATA
66 TGGTCTTATCTTAATAATATGTAATA
10682 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:13086 original size:21 final size:20
Alignment explanation
Indices: 13061--13128 Score: 86
Period size: 21 Copynumber: 3.4 Consensus size: 20
13051 TTCCATTATT
*
13061 ATATAATTATATAAATAATAT
1 ATATAATTATATAAAT-ATAA
13082 ATATAA--ATATAAATATAA
1 ATATAATTATATAAATATAA
*
13100 ATATAAATAATATAAATATAA
1 ATAT-AATTATATAAATATAA
13121 ATATAATT
1 ATATAATT
13129 TCAAGATCAC
Statistics
Matches: 42, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
18 7 0.17
19 10 0.24
20 3 0.07
21 22 0.52
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (20 bp):
ATATAATTATATAAATATAA
Found at i:13093 original size:6 final size:6
Alignment explanation
Indices: 13069--13126 Score: 77
Period size: 6 Copynumber: 10.0 Consensus size: 6
13059 TTATATAATT
*
13069 ATATAA ATAATAT ATATAA ATATAA ATATAA ATAT-A A-AT-A ATATAA
1 ATATAA AT-ATAA ATATAA ATATAA ATATAA ATATAA ATATAA ATATAA
13115 ATATAA ATATAA
1 ATATAA ATATAA
13127 TTTCAAGATC
Statistics
Matches: 47, Mismatches: 2, Indels: 6
0.85 0.04 0.11
Matches are distributed among these distances:
4 4 0.09
5 4 0.09
6 34 0.72
7 5 0.11
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (6 bp):
ATATAA
Found at i:13105 original size:27 final size:26
Alignment explanation
Indices: 13061--13126 Score: 89
Period size: 27 Copynumber: 2.5 Consensus size: 26
13051 TTCCATTATT
*
13061 ATATAATTATATAAAT-AATATATATAA
1 ATATAAATATA-AAATAAATA-ATATAA
13088 ATATAAATATAAATATAAATAATATAA
1 ATATAAATATAAA-ATAAATAATATAA
13115 ATATAAATATAA
1 ATATAAATATAA
13127 TTTCAAGATC
Statistics
Matches: 36, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
26 2 0.06
27 30 0.83
28 4 0.11
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (26 bp):
ATATAAATATAAAATAAATAATATAA
Found at i:15094 original size:23 final size:23
Alignment explanation
Indices: 15068--15113 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
15058 TATATTGTAA
15068 CCAATCATTTATCTTATTACTTG
1 CCAATCATTTATCTTATTACTTG
15091 CCAATCATTTATCTTATTACTTG
1 CCAATCATTTATCTTATTACTTG
15114 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:20621 original size:21 final size:21
Alignment explanation
Indices: 20597--20640 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
20587 GATTCTTTGC
20597 TTTGAGATTTTATCTGATCTA
1 TTTGAGATTTTATCTGATCTA
20618 TTTGAGATTTTATCTGATCTA
1 TTTGAGATTTTATCTGATCTA
20639 TT
1 TT
20641 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:20648 original size:21 final size:21
Alignment explanation
Indices: 20597--20648 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
20587 GATTCTTTGC
*
20597 TTTGAGATTTTATCTGATCTA
1 TTTGAAATTTTATCTGATCTA
*
20618 TTTGAGATTTTATCTGATCTA
1 TTTGAAATTTTATCTGATCTA
20639 TTAT-AAATTT
1 TT-TGAAATTT
20649 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:20844 original size:20 final size:20
Alignment explanation
Indices: 20819--20896 Score: 115
Period size: 20 Copynumber: 4.0 Consensus size: 20
20809 AACAATCAAA
20819 TAAAATGAAAATAAAATTTT
1 TAAAATGAAAATAAAATTTT
**
20839 TAAAATGAAAATAAAA--AA
1 TAAAATGAAAATAAAATTTT
*
20857 AAAAATGAAAATAAAATTTT
1 TAAAATGAAAATAAAATTTT
20877 TAAAATGAAAATAAAATTTT
1 TAAAATGAAAATAAAATTTT
20897 CGCGGGCGAA
Statistics
Matches: 50, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
18 15 0.30
20 35 0.70
ACGTcount: A:0.65, C:0.00, G:0.05, T:0.29
Consensus pattern (20 bp):
TAAAATGAAAATAAAATTTT
Found at i:20862 original size:38 final size:38
Alignment explanation
Indices: 20820--20892 Score: 146
Period size: 38 Copynumber: 1.9 Consensus size: 38
20810 ACAATCAAAT
20820 AAAATGAAAATAAAATTTTTAAAATGAAAATAAAAAAA
1 AAAATGAAAATAAAATTTTTAAAATGAAAATAAAAAAA
20858 AAAATGAAAATAAAATTTTTAAAATGAAAATAAAA
1 AAAATGAAAATAAAATTTTTAAAATGAAAATAAAA
20893 TTTTCGCGGG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 35 1.00
ACGTcount: A:0.70, C:0.00, G:0.05, T:0.25
Consensus pattern (38 bp):
AAAATGAAAATAAAATTTTTAAAATGAAAATAAAAAAA
Found at i:21171 original size:24 final size:25
Alignment explanation
Indices: 21128--21191 Score: 103
Period size: 24 Copynumber: 2.6 Consensus size: 25
21118 TGGAGCCTTA
**
21128 ATTTAATATTTAATAAAAATTTAAT
1 ATTTAATAAATAATAAAAATTTAAT
21153 ATTTAATAAA-AATAAAAATTTAAT
1 ATTTAATAAATAATAAAAATTTAAT
21177 ATTTAATAAATAATA
1 ATTTAATAAATAATA
21192 TTTAATAAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
24 24 0.67
25 12 0.33
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (25 bp):
ATTTAATAAATAATAAAAATTTAAT
Found at i:21186 original size:18 final size:18
Alignment explanation
Indices: 21127--21165 Score: 78
Period size: 18 Copynumber: 2.2 Consensus size: 18
21117 ATGGAGCCTT
21127 AATTTAATATTTAATAAA
1 AATTTAATATTTAATAAA
21145 AATTTAATATTTAATAAA
1 AATTTAATATTTAATAAA
21163 AAT
1 AAT
21166 AAAAATTTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (18 bp):
AATTTAATATTTAATAAA
Found at i:21192 original size:14 final size:14
Alignment explanation
Indices: 21173--21200 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
21163 AATAAAAATT
21173 TAATATTTAATAAA
1 TAATATTTAATAAA
21187 TAATATTTAATAAA
1 TAATATTTAATAAA
21201 AAAATTTGTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (14 bp):
TAATATTTAATAAA
Found at i:21205 original size:18 final size:18
Alignment explanation
Indices: 21131--21205 Score: 73
Period size: 18 Copynumber: 4.1 Consensus size: 18
21121 AGCCTTAATT
**
21131 TAATATTTAATAAAAATT
1 TAATATTTAATAAAAAAA
21149 TAATATTTAATAAAAATAA
1 TAATATTTAATAAAAA-AA
*
21168 -AA-ATTTAATATTTAATAAA
1 TAATATTTAATA---AAAAAA
21187 TAATATTTAATAAAAAAA
1 TAATATTTAATAAAAAAA
21205 T
1 T
21206 TTGTTAATTT
Statistics
Matches: 47, Mismatches: 4, Indels: 12
0.75 0.06 0.19
Matches are distributed among these distances:
17 8 0.17
18 24 0.51
19 2 0.04
20 5 0.11
21 8 0.17
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (18 bp):
TAATATTTAATAAAAAAA
Found at i:23377 original size:15 final size:15
Alignment explanation
Indices: 23357--23386 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
23347 TTTTTTAGTG
23357 AACGTGTCATTTTTT
1 AACGTGTCATTTTTT
23372 AACGTGTCATTTTTT
1 AACGTGTCATTTTTT
23387 TTTTTGTAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.20, C:0.13, G:0.13, T:0.53
Consensus pattern (15 bp):
AACGTGTCATTTTTT
Found at i:23985 original size:14 final size:14
Alignment explanation
Indices: 23968--23998 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
23958 GATGGATATA
23968 TATCGTATAATTCT
1 TATCGTATAATTCT
23982 TATCGTATAATTCT
1 TATCGTATAATTCT
23996 TAT
1 TAT
23999 ATATATTGTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.29, C:0.13, G:0.06, T:0.52
Consensus pattern (14 bp):
TATCGTATAATTCT
Found at i:25310 original size:18 final size:18
Alignment explanation
Indices: 25284--25324 Score: 73
Period size: 18 Copynumber: 2.3 Consensus size: 18
25274 TAATGTTCAT
*
25284 ATATTATCATATAATAGA
1 ATATAATCATATAATAGA
25302 ATATAATCATATAATAGA
1 ATATAATCATATAATAGA
25320 ATATA
1 ATATA
25325 CAACAACAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.54, C:0.05, G:0.05, T:0.37
Consensus pattern (18 bp):
ATATAATCATATAATAGA
Found at i:25872 original size:181 final size:182
Alignment explanation
Indices: 25519--25980 Score: 855
Period size: 181 Copynumber: 2.6 Consensus size: 182
25509 ATGAATAATC
*
25519 ATAT-ATAA-ATCATATAATAAGGAGTATTGATTATCGAACCAATTCGCCGGTATGTAGAAATTG
1 ATATAATAATATCATATAATAAGGAGTATTGATTATCGAACCGATTCGCCGGTATGTAGAAATTG
25582 ATGGACAATTTATTCTATATCAAACTATAAGTA-TTCATTGGTTCATAAAAATAAACATGAAATT
66 ATGGACAATTTATTCTATATCAAACTATAAGTATTTCATTGGTTCATAAAAATAAACATGAAATT
25646 AAATCAAAGACGGCAAAAAAAAAAACTATATTGACAAAATGAATAATCATAT
131 AAATCAAAGACGGCAAAAAAAAAAACTATATTGACAAAATGAATAATCATAT
25698 ATATAATAATATCATATAATAAGGAGGTATTGATTATCGAACCGATTCGCCGGTATGTAGAAATT
1 ATATAATAATATCATATAATAAGGA-GTATTGATTATCGAACCGATTCGCCGGTATGTAGAAATT
25763 GATGGACAA-TTATTCCTATATCAAACTATAAGTATTTCATTGGTTCATAAAAATAAACATGAAA
65 GATGGACAATTTATT-CTATATCAAACTATAAGTATTTCATTGGTTCATAAAAATAAACATGAAA
25827 TT-AATCAAAGAC-GCAAAAAAAAAAACTATATTGACAAAATGAATAATCATAT
129 TTAAATCAAAGACGGCAAAAAAAAAAACTATATTGACAAAATGAATAATCATAT
25879 ATATAATAATATCATATAATAAGGAGTATTGATTATCGAACCGATTCGCCGGTATGTAGAAATTG
1 ATATAATAATATCATATAATAAGGAGTATTGATTATCGAACCGATTCGCCGGTATGTAGAAATTG
25944 ATGGACAATTTATTCTATATCAAACTATAAGTATTTC
66 ATGGACAATTTATTCTATATCAAACTATAAGTATTTC
Statistics
Matches: 276, Mismatches: 1, Indels: 11
0.96 0.00 0.04
Matches are distributed among these distances:
179 4 0.01
180 75 0.27
181 90 0.33
182 76 0.28
183 31 0.11
ACGTcount: A:0.45, C:0.11, G:0.13, T:0.31
Consensus pattern (182 bp):
ATATAATAATATCATATAATAAGGAGTATTGATTATCGAACCGATTCGCCGGTATGTAGAAATTG
ATGGACAATTTATTCTATATCAAACTATAAGTATTTCATTGGTTCATAAAAATAAACATGAAATT
AAATCAAAGACGGCAAAAAAAAAAACTATATTGACAAAATGAATAATCATAT
Done.