Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168323.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_547, 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: 23359
ACGTcount: A:0.31, C:0.17, G:0.16, T:0.36
Found at i:186 original size:13 final size:13
Alignment explanation
Indices: 170--237 Score: 65
Period size: 13 Copynumber: 5.5 Consensus size: 13
160 AAAAAAAAAG
170 AAATATTAAAATT
1 AAATATTAAAATT
*
183 AAATATAAAATATT
1 AAATATTAAA-ATT
197 AAA-ATTAAATATT
1 AAATATTAAA-ATT
*
210 TAA-A--AAAATT
1 AAATATTAAAATT
220 AAATATT-AAATT
1 AAATATTAAAATT
232 AAATAT
1 AAATAT
238 ATATTGTGAT
Statistics
Matches: 47, Mismatches: 4, Indels: 9
0.78 0.07 0.15
Matches are distributed among these distances:
10 5 0.11
11 4 0.09
12 11 0.23
13 21 0.45
14 6 0.13
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (13 bp):
AAATATTAAAATT
Found at i:195 original size:20 final size:20
Alignment explanation
Indices: 170--239 Score: 79
Period size: 20 Copynumber: 3.3 Consensus size: 20
160 AAAAAAAAAG
170 AAATATTAAAATTAAATATA
1 AAATATTAAAATTAAATATA
190 AAATATTAAAATTAAATATTTAA
1 AAATATTAAAATTAAATA--T-A
*
213 AAAAATTAAATATTAAAT-TA
1 AAATATTAAA-ATTAAATATA
233 AATATAT
1 AA-ATAT
240 ATTGTGATTG
Statistics
Matches: 43, Mismatches: 2, Indels: 9
0.80 0.04 0.17
Matches are distributed among these distances:
20 21 0.49
21 4 0.09
22 1 0.02
23 10 0.23
24 7 0.16
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (20 bp):
AAATATTAAAATTAAATATA
Found at i:229 original size:7 final size:7
Alignment explanation
Indices: 170--230 Score: 63
Period size: 7 Copynumber: 8.6 Consensus size: 7
160 AAAAAAAAAG
170 AAATATT
1 AAATATT
177 AAA-ATT
1 AAATATT
*
183 AAATATA
1 AAATATT
190 AAATATT
1 AAATATT
197 AAA-ATT
1 AAATATT
203 AAATATTT
1 AAATA-TT
*
211 AAAAAAATT
1 --AAATATT
220 AAATATT
1 AAATATT
227 AAAT
1 AAAT
231 TAAATATATA
Statistics
Matches: 45, Mismatches: 4, Indels: 10
0.76 0.07 0.17
Matches are distributed among these distances:
6 12 0.27
7 25 0.56
8 2 0.04
9 2 0.04
10 4 0.09
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (7 bp):
AAATATT
Found at i:235 original size:17 final size:17
Alignment explanation
Indices: 178--235 Score: 55
Period size: 17 Copynumber: 3.2 Consensus size: 17
168 AGAAATATTA
*
178 AAATTAAATATAAAATATT
1 AAATTAAATAT-TAA-ATT
*
197 AAAATTAAATATTTAAA-A
1 -AAATTAAATA-TTAAATT
215 AAATTAAATATTAAATT
1 AAATTAAATATTAAATT
232 AAAT
1 AAAT
236 ATATATTGTG
Statistics
Matches: 33, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
16 5 0.15
17 14 0.42
19 1 0.03
20 12 0.36
21 1 0.03
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (17 bp):
AAATTAAATATTAAATT
Found at i:3689 original size:22 final size:22
Alignment explanation
Indices: 3658--3708 Score: 86
Period size: 22 Copynumber: 2.4 Consensus size: 22
3648 GTTGTTTTTA
*
3658 GAATTATAATTATATAAGAAAT
1 GAATTCTAATTATATAAGAAAT
3680 GAATTCTAATTATATAAGAAAT
1 GAATTCTAATTATATAAGAAAT
3702 -AATTCTA
1 GAATTCTA
3709 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:4775 original size:25 final size:25
Alignment explanation
Indices: 4742--4793 Score: 95
Period size: 25 Copynumber: 2.1 Consensus size: 25
4732 ATTATTTATT
*
4742 TTTTTAGTTTACCGTCTTCGAATGA
1 TTTTTAGTTTACAGTCTTCGAATGA
4767 TTTTTAGTTTACAGTCTTCGAATGA
1 TTTTTAGTTTACAGTCTTCGAATGA
4792 TT
1 TT
4794 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:4800 original size:25 final size:25
Alignment explanation
Indices: 4747--4800 Score: 72
Period size: 25 Copynumber: 2.2 Consensus size: 25
4737 TTATTTTTTT
* ***
4747 AGTTTACCGTCTTCGAATGATTTTT
1 AGTTTACAGTCTTCGAATGATTAGG
4772 AGTTTACAGTCTTCGAATGATTAGG
1 AGTTTACAGTCTTCGAATGATTAGG
4797 AGTT
1 AGTT
4801 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:4900 original size:15 final size:15
Alignment explanation
Indices: 4880--4929 Score: 73
Period size: 15 Copynumber: 3.1 Consensus size: 15
4870 CATAATGATT
4880 ATTTTAATATTGTTA
1 ATTTTAATATTGTTA
4895 ATTTTAATATTGTTGTTA
1 ATTTTAATA---TTGTTA
4913 ATTTTAATATTGTTA
1 ATTTTAATATTGTTA
4928 AT
1 AT
4930 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:4912 original size:18 final size:18
Alignment explanation
Indices: 4889--4926 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
4879 TATTTTAATA
4889 TTGTTAATTTTAATATTG
1 TTGTTAATTTTAATATTG
4907 TTGTTAATTTTAATATTG
1 TTGTTAATTTTAATATTG
4925 TT
1 TT
4927 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:4948 original size:17 final size:17
Alignment explanation
Indices: 4928--4961 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
4918 AATATTGTTA
*
4928 ATATTGTATTATTTATT
1 ATATTGTATGATTTATT
4945 ATATTGTATGATTTATT
1 ATATTGTATGATTTATT
4962 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:4985 original size:19 final size:19
Alignment explanation
Indices: 4963--5012 Score: 82
Period size: 19 Copynumber: 2.6 Consensus size: 19
4953 TGATTTATTC
*
4963 ATTACTATATTTTTTAGTT
1 ATTACTATATTTTGTAGTT
*
4982 ATTACTATATTTTGTATTT
1 ATTACTATATTTTGTAGTT
5001 ATTACTATATTT
1 ATTACTATATTT
5013 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:5030 original size:19 final size:19
Alignment explanation
Indices: 4996--5050 Score: 65
Period size: 19 Copynumber: 2.8 Consensus size: 19
4986 CTATATTTTG
*
4996 TATTTATTACTATATTTCAT
1 TATTTATTTCT-TATTTCAT
*
5016 TATTTATTTCTTATTTTAT
1 TATTTATTTCTTATTTCAT
* *
5035 TAATTATTTATTATTT
1 TATTTATTTCTTATTT
5051 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:5031 original size:38 final size:38
Alignment explanation
Indices: 4958--5032 Score: 98
Period size: 38 Copynumber: 2.0 Consensus size: 38
4948 TTGTATGATT
*
4958 TATTCATTACTATATTTTTTAGTTATTACTATATTTTG
1 TATTCATTACTATATTTATTAGTTATTACTATATTTTG
* * *
4996 TATTTATTACTATATTTCATTATTTATTTCT-TATTTT
1 TATTCATTACTATATTT-ATTAGTTATTACTATATTTT
5033 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:5089 original size:17 final size:18
Alignment explanation
Indices: 5063--5251 Score: 79
Period size: 17 Copynumber: 10.4 Consensus size: 18
5053 GTGTCGGTTC
*
5063 TATATATATTTA-TAAAT
1 TATATTTATTTATTAAAT
5080 TATATTTATTTATT--AT
1 TATATTTATTTATTAAAT
* * *
5096 T-TATGTA-TTATCACAGT
1 TATATTTATTTATTA-AAT
**
5113 TATAGATATTTATTTAAAT
1 TATATTTATTTA-TTAAAT
*
5132 TATATTTATATATTAAA-
1 TATATTTATTTATTAAAT
* **
5149 TATATTAAAATATTAAAT
1 TATATTTATTTATTAAAT
5167 TATATTTATATT-TTATATAT
1 TATATTTAT-TTATTA-A-AT
** *
5187 TAAATATATTAAAATATGAAAT
1 T--ATAT-TT-ATTTATTAAAT
*
5209 TATATTTATATATTAAA-
1 TATATTTATTTATTAAAT
* ** *
5226 TATATTAAAATATGAAAT
1 TATATTTATTTATTAAAT
5244 TATATTTA
1 TATATTTA
5252 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:5145 original size:8 final size:8
Alignment explanation
Indices: 5132--5238 Score: 72
Period size: 8 Copynumber: 12.6 Consensus size: 8
5122 TTATTTAAAT
*
5132 TATATTTA
1 TATATTAA
5140 TATATTAAA
1 TATATT-AA
5149 TATATTAA
1 TATATTAA
*
5157 AATATTAAA
1 TATATT-AA
*
5166 TTATATTTA
1 -TATATTAA
*
5175 TAT-TTTA
1 TATATTAA
5182 TATATTAAA
1 TATATT-AA
5191 TATATTAA
1 TATATTAA
* *
5199 AATATGAAA
1 TATAT-TAA
*
5208 TTATATTTA
1 -TATATTAA
5217 TATATTAAA
1 TATATT-AA
5226 TATATTAA
1 TATATTAA
*
5234 AATAT
1 TATAT
5239 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:5162 original size:77 final size:76
Alignment explanation
Indices: 5093--5251 Score: 205
Period size: 77 Copynumber: 2.1 Consensus size: 76
5083 ATTTATTTAT
* * * *
5093 TATTTATGTATTATCACAGTTATAGATATT-TAT-TTAAATTATATTTATATATTAAATATATTA
1 TATTTATATATTAT-ACA-TTAAAGATATTAAATATGAAATTATATTTATATATTAAATATATTA
5156 AAATATTAAATTA
64 AAATATTAAATTA
* * *
5169 TATTTATATTTTATATATTAAATATATTAAAATATGAAATTATATTTATATATTAAATATATTAA
1 TATTTATATATTATACATTAAAGATATT-AAATATGAAATTATATTTATATATTAAATATATTAA
*
5234 AATATGAAATTA
65 AATATTAAATTA
5246 TATTTA
1 TATTTA
5252 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:5165 original size:35 final size:35
Alignment explanation
Indices: 5128--5251 Score: 176
Period size: 35 Copynumber: 3.3 Consensus size: 35
5118 ATATTTATTT
*
5128 AAATTATATTTATATATTAAATATATTAAAATATTAA
1 AAATTATATTTATATATTAAATATATTAAAATA-T-G
5165 ATTATATTTATATTTTATATATTAAATATATTAAAATATG
1 A--A-A-TTATA-TTTATATATTAAATATATTAAAATATG
5205 AAATTATATTTATATATTAAATATATTAAAATATG
1 AAATTATATTTATATATTAAATATATTAAAATATG
5240 AAATTATATTTA
1 AAATTATATTTA
5252 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:5270 original size:4 final size:4
Alignment explanation
Indices: 5263--5390 Score: 85
Period size: 4 Copynumber: 32.2 Consensus size: 4
5253 ATAAATATCT
*
5263 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
* *
5308 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
*
5356 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
5391 AAAAACAAAG
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:5285 original size:13 final size:13
Alignment explanation
Indices: 5276--5353 Score: 82
Period size: 13 Copynumber: 6.5 Consensus size: 13
5266 AATAATATAA
5276 TAATAAAATAAAC
1 TAATAAAATAAAC
5289 TAATAAAATAAAC
1 TAATAAAATAAAC
5302 -----AAATAAA-
1 TAATAAAATAAAC
5309 TAAT-AAATAAA-
1 TAATAAAATAAAC
5320 TAATTAAAATAAAC
1 TAA-TAAAATAAAC
5334 TAATAAAATAAAC
1 TAATAAAATAAAC
*
5347 AAATAAA
1 TAATAAA
5354 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:5390 original size:45 final size:44
Alignment explanation
Indices: 5269--5386 Score: 186
Period size: 45 Copynumber: 2.7 Consensus size: 44
5259 ATCTATAAAT
*
5269 AATATAATAATAAAATAAACTAATAAAATAAACAAATAAATAATA
1 AATA-AATAATAAAATAAACTAATAAAATAAACAAATAAATAAGA
5314 AATAAATAATTAAAATAAACTAATAAAATAAACAAATAAATAAGA
1 AATAAATAA-TAAAATAAACTAATAAAATAAACAAATAAATAAGA
*
5359 AATAAATAAT-AAATAAA-TAATACAATAA
1 AATAAATAATAAAATAAACTAATAAAATAA
5387 TAAAAAAAAC
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:7509 original size:30 final size:30
Alignment explanation
Indices: 7475--7814 Score: 680
Period size: 30 Copynumber: 11.3 Consensus size: 30
7465 AAATGGTGTT
7475 CCATTGTCGTCAAATGGTGGTCTTCCATTG
1 CCATTGTCGTCAAATGGTGGTCTTCCATTG
7505 CCATTGTCGTCAAATGGTGGTCTTCCATTG
1 CCATTGTCGTCAAATGGTGGTCTTCCATTG
7535 CCATTGTCGTCAAATGGTGGTCTTCCATTG
1 CCATTGTCGTCAAATGGTGGTCTTCCATTG
7565 CCATTGTCGTCAAATGGTGGTCTTCCATTG
1 CCATTGTCGTCAAATGGTGGTCTTCCATTG
7595 CCATTGTCGTCAAATGGTGGTCTTCCATTG
1 CCATTGTCGTCAAATGGTGGTCTTCCATTG
7625 CCATTGTCGTCAAATGGTGGTCTTCCATTG
1 CCATTGTCGTCAAATGGTGGTCTTCCATTG
7655 CCATTGTCGTCAAATGGTGGTCTTCCATTG
1 CCATTGTCGTCAAATGGTGGTCTTCCATTG
7685 CCATTGTCGTCAAATGGTGGTCTTCCATTG
1 CCATTGTCGTCAAATGGTGGTCTTCCATTG
7715 CCATTGTCGTCAAATGGTGGTCTTCCATTG
1 CCATTGTCGTCAAATGGTGGTCTTCCATTG
7745 CCATTGTCGTCAAATGGTGGTCTTCCATTG
1 CCATTGTCGTCAAATGGTGGTCTTCCATTG
7775 CCATTGTCGTCAAATGGTGGTCTTCCATTG
1 CCATTGTCGTCAAATGGTGGTCTTCCATTG
7805 CCATTGTCGT
1 CCATTGTCGT
7815 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:7855 original size:18 final size:18
Alignment explanation
Indices: 7828--8062 Score: 397
Period size: 18 Copynumber: 13.1 Consensus size: 18
7818 CTAGTCTCCA
*
7828 TTTTTTATTCACTATAGG
1 TTTTTCATTCACTATAGG
7846 TTTGTT-ATTCACTATAGG
1 TTT-TTCATTCACTATAGG
7864 TTTGTT-ATTCACTATAGG
1 TTT-TTCATTCACTATAGG
7882 TTTGTT-ATTCACTATAGG
1 TTT-TTCATTCACTATAGG
7900 TTTTTCATTCACTATAGG
1 TTTTTCATTCACTATAGG
7918 TTTTTCATTCACTATAGG
1 TTTTTCATTCACTATAGG
7936 TTTTTCATTCACTATAGG
1 TTTTTCATTCACTATAGG
7954 TTTTTCATTCACTATAGG
1 TTTTTCATTCACTATAGG
7972 TTTGTT-ATTCACTATAGG
1 TTT-TTCATTCACTATAGG
7990 TTTTTCATTCACTATAGG
1 TTTTTCATTCACTATAGG
8008 TTTTTCATTCACTATAGG
1 TTTTTCATTCACTATAGG
8026 TTTTTCATTCACTATAGG
1 TTTTTCATTCACTATAGG
8044 TTTTTCATTCACTATAGG
1 TTTTTCATTCACTATAGG
8062 T
1 T
8063 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:8403 original size:18 final size:18
Alignment explanation
Indices: 8380--8417 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
8370 TTTTTTGCGC
8380 ATTGCATACGGCTTTACA
1 ATTGCATACGGCTTTACA
8398 ATTGCATACGGCTTTACA
1 ATTGCATACGGCTTTACA
8416 AT
1 AT
8418 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:10354 original size:78 final size:78
Alignment explanation
Indices: 10225--10393 Score: 320
Period size: 78 Copynumber: 2.2 Consensus size: 78
10215 AGTAAAAAGA
* *
10225 ATGTAAAATTATATTTCGCTTTGATTGTGGAAGCGTAATACGTAATGTAATACGTAATAATGGTC
1 ATGTAATATTATATTTCACTTTGATTGTGGAAGCGTAATACGTAATGTAATACGTAATAATGGTC
10290 TTATCTTAATAAT
66 TTATCTTAATAAT
10303 ATGTAATATTATATTTCACTTTGATTGTGGAAGCGTAATACGTAATGTAATACGTAATAATGGTC
1 ATGTAATATTATATTTCACTTTGATTGTGGAAGCGTAATACGTAATGTAATACGTAATAATGGTC
10368 TTATCTTAATAAT
66 TTATCTTAATAAT
10381 ATGTAATATTATA
1 ATGTAATATTATA
10394 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:10396 original size:15 final size:15
Alignment explanation
Indices: 10376--10408 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
10366 TCTTATCTTA
10376 ATAATATGTAATATT
1 ATAATATGTAATATT
10391 ATAATATGTAATATT
1 ATAATATGTAATATT
10406 ATA
1 ATA
10409 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:10489 original size:15 final size:15
Alignment explanation
Indices: 10469--10501 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
10459 TCTTATCTTA
10469 ATAATATGTAATATT
1 ATAATATGTAATATT
10484 ATAATATGTAATATT
1 ATAATATGTAATATT
10499 ATA
1 ATA
10502 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:10590 original size:93 final size:93
Alignment explanation
Indices: 10298--10574 Score: 554
Period size: 93 Copynumber: 3.0 Consensus size: 93
10288 TCTTATCTTA
10298 ATAATATGTAATATTATATTTCACTTTGATTGTGGAAGCGTAATACGTAATGTAATACGTAATAA
1 ATAATATGTAATATTATATTTCACTTTGATTGTGGAAGCGTAATACGTAATGTAATACGTAATAA
10363 TGGTCTTATCTTAATAATATGTAATATT
66 TGGTCTTATCTTAATAATATGTAATATT
10391 ATAATATGTAATATTATATTTCACTTTGATTGTGGAAGCGTAATACGTAATGTAATACGTAATAA
1 ATAATATGTAATATTATATTTCACTTTGATTGTGGAAGCGTAATACGTAATGTAATACGTAATAA
10456 TGGTCTTATCTTAATAATATGTAATATT
66 TGGTCTTATCTTAATAATATGTAATATT
10484 ATAATATGTAATATTATATTTCACTTTGATTGTGGAAGCGTAATACGTAATGTAATACGTAATAA
1 ATAATATGTAATATTATATTTCACTTTGATTGTGGAAGCGTAATACGTAATGTAATACGTAATAA
10549 TGGTCTTATCTTAATAATATGTAATA
66 TGGTCTTATCTTAATAATATGTAATA
10575 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:12980 original size:21 final size:20
Alignment explanation
Indices: 12955--13022 Score: 86
Period size: 21 Copynumber: 3.4 Consensus size: 20
12945 TTCCATTATT
*
12955 ATATAATTATATAAATAATAT
1 ATATAATTATATAAAT-ATAA
12976 ATATAA--ATATAAATATAA
1 ATATAATTATATAAATATAA
*
12994 ATATAAATAATATAAATATAA
1 ATAT-AATTATATAAATATAA
13015 ATATAATT
1 ATATAATT
13023 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:12987 original size:6 final size:6
Alignment explanation
Indices: 12963--13020 Score: 77
Period size: 6 Copynumber: 10.0 Consensus size: 6
12953 TTATATAATT
*
12963 ATATAA ATAATAT ATATAA ATATAA ATATAA ATAT-A A-AT-A ATATAA
1 ATATAA AT-ATAA ATATAA ATATAA ATATAA ATATAA ATATAA ATATAA
13009 ATATAA ATATAA
1 ATATAA ATATAA
13021 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:12999 original size:27 final size:26
Alignment explanation
Indices: 12955--13020 Score: 89
Period size: 27 Copynumber: 2.5 Consensus size: 26
12945 TTCCATTATT
*
12955 ATATAATTATATAAAT-AATATATATAA
1 ATATAAATATA-AAATAAATA-ATATAA
12982 ATATAAATATAAATATAAATAATATAA
1 ATATAAATATAAA-ATAAATAATATAA
13009 ATATAAATATAA
1 ATATAAATATAA
13021 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:14991 original size:23 final size:23
Alignment explanation
Indices: 14965--15010 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
14955 TATATTGTAA
14965 CCAATCATTTATCTTATTACTTG
1 CCAATCATTTATCTTATTACTTG
14988 CCAATCATTTATCTTATTACTTG
1 CCAATCATTTATCTTATTACTTG
15011 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:20513 original size:21 final size:21
Alignment explanation
Indices: 20489--20532 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
20479 GATTCTTTGC
20489 TTTGAGATTTTATCTGATCTA
1 TTTGAGATTTTATCTGATCTA
20510 TTTGAGATTTTATCTGATCTA
1 TTTGAGATTTTATCTGATCTA
20531 TT
1 TT
20533 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:20540 original size:21 final size:21
Alignment explanation
Indices: 20489--20540 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
20479 GATTCTTTGC
*
20489 TTTGAGATTTTATCTGATCTA
1 TTTGAAATTTTATCTGATCTA
*
20510 TTTGAGATTTTATCTGATCTA
1 TTTGAAATTTTATCTGATCTA
20531 TTAT-AAATTT
1 TT-TGAAATTT
20541 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:20736 original size:20 final size:20
Alignment explanation
Indices: 20711--20788 Score: 115
Period size: 20 Copynumber: 4.0 Consensus size: 20
20701 AACAATCAAA
20711 TAAAATGAAAATAAAATTTT
1 TAAAATGAAAATAAAATTTT
**
20731 TAAAATGAAAATAAAA--AA
1 TAAAATGAAAATAAAATTTT
*
20749 AAAAATGAAAATAAAATTTT
1 TAAAATGAAAATAAAATTTT
20769 TAAAATGAAAATAAAATTTT
1 TAAAATGAAAATAAAATTTT
20789 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:20754 original size:38 final size:38
Alignment explanation
Indices: 20712--20784 Score: 146
Period size: 38 Copynumber: 1.9 Consensus size: 38
20702 ACAATCAAAT
20712 AAAATGAAAATAAAATTTTTAAAATGAAAATAAAAAAA
1 AAAATGAAAATAAAATTTTTAAAATGAAAATAAAAAAA
20750 AAAATGAAAATAAAATTTTTAAAATGAAAATAAAA
1 AAAATGAAAATAAAATTTTTAAAATGAAAATAAAA
20785 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:21063 original size:24 final size:25
Alignment explanation
Indices: 21020--21083 Score: 103
Period size: 24 Copynumber: 2.6 Consensus size: 25
21010 TGGAGCCTTA
**
21020 ATTTAATATTTAATAAAAATTTAAT
1 ATTTAATAAATAATAAAAATTTAAT
21045 ATTTAATAAA-AATAAAAATTTAAT
1 ATTTAATAAATAATAAAAATTTAAT
21069 ATTTAATAAATAATA
1 ATTTAATAAATAATA
21084 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:21078 original size:18 final size:18
Alignment explanation
Indices: 21019--21057 Score: 78
Period size: 18 Copynumber: 2.2 Consensus size: 18
21009 ATGGAGCCTT
21019 AATTTAATATTTAATAAA
1 AATTTAATATTTAATAAA
21037 AATTTAATATTTAATAAA
1 AATTTAATATTTAATAAA
21055 AAT
1 AAT
21058 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:21084 original size:14 final size:14
Alignment explanation
Indices: 21065--21092 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
21055 AATAAAAATT
21065 TAATATTTAATAAA
1 TAATATTTAATAAA
21079 TAATATTTAATAAA
1 TAATATTTAATAAA
21093 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:21097 original size:18 final size:18
Alignment explanation
Indices: 21023--21097 Score: 73
Period size: 18 Copynumber: 4.1 Consensus size: 18
21013 AGCCTTAATT
**
21023 TAATATTTAATAAAAATT
1 TAATATTTAATAAAAAAA
21041 TAATATTTAATAAAAATAA
1 TAATATTTAATAAAAA-AA
*
21060 -AA-ATTTAATATTTAATAAA
1 TAATATTTAATA---AAAAAA
21079 TAATATTTAATAAAAAAA
1 TAATATTTAATAAAAAAA
21097 T
1 T
21098 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:23263 original size:15 final size:15
Alignment explanation
Indices: 23243--23272 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
23233 TTTTTTAGTG
23243 AACGTGTCATTTTTT
1 AACGTGTCATTTTTT
23258 AACGTGTCATTTTTT
1 AACGTGTCATTTTTT
23273 TTTTTTGTAA
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
Done.