Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032251.1 Gossypioides kirkii chromosome KI_09
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: 38743931
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 2800 characters in sequence are not A, C, G, or T
File 20 of 144
Found at i:4973606 original size:25 final size:23
Alignment explanation
Indices: 4973539--4973611 Score: 85
Period size: 23 Copynumber: 3.2 Consensus size: 23
4973529 ACACTAGCGC
* *
4973539 GCTCTCTGTTTAGCAC-GTCTCGT
1 GCTCTCTGATTAGCACTGTGT-GT
*
4973562 GCTCTCTTATTAGCACTGTGTGT
1 GCTCTCTGATTAGCACTGTGTGT
* *
4973585 GCTCTCTGATTAGCGCTTTGTGT
1 GCTCTCTGATTAGCACTGTGTGT
4973608 GCTC
1 GCTC
4973612 AGTACTTTGT
Statistics
Matches: 43, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
23 40 0.93
24 3 0.07
ACGTcount: A:0.10, C:0.26, G:0.23, T:0.41
Consensus pattern (23 bp):
GCTCTCTGATTAGCACTGTGTGT
Found at i:4993513 original size:23 final size:24
Alignment explanation
Indices: 4993482--4993545 Score: 80
Period size: 23 Copynumber: 2.8 Consensus size: 24
4993472 TCTAATGTTC
**
4993482 ACGAACATGTTCATTTAAC-TTAA
1 ACGAACATGTTCATCGAACATTAA
*
4993505 TCGAACATGTTCA-CGAACATTAA
1 ACGAACATGTTCATCGAACATTAA
4993528 ACGAACATGTTCAT-GAAC
1 ACGAACATGTTCATCGAAC
4993546 GTATAATTGA
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
22 3 0.09
23 32 0.91
ACGTcount: A:0.39, C:0.20, G:0.12, T:0.28
Consensus pattern (24 bp):
ACGAACATGTTCATCGAACATTAA
Found at i:5001251 original size:196 final size:196
Alignment explanation
Indices: 5000917--5001309 Score: 786
Period size: 196 Copynumber: 2.0 Consensus size: 196
5000907 GAACCTTGAG
5000917 CTCCAACCATTAATTTTAATTCCATTTGGTCTTTAATATTTTGAAAAGAGACTTTCTTTCTTCGA
1 CTCCAACCATTAATTTTAATTCCATTTGGTCTTTAATATTTTGAAAAGAGACTTTCTTTCTTCGA
5000982 CCAACCAAATTCGGAAGCCCTAAGTACTTTTCTATGTCATTAGAGCATTTCACCTCAAGTAGATT
66 CCAACCAAATTCGGAAGCCCTAAGTACTTTTCTATGTCATTAGAGCATTTCACCTCAAGTAGATT
5001047 TGAAAAAGCATCTTTATTGTCCCTTGATGAATTAGTACTAAAGCAGCCTATAGATTTCTCGTAAT
131 TGAAAAAGCATCTTTATTGTCCCTTGATGAATTAGTACTAAAGCAGCCTATAGATTTCTCGTAAT
5001112 T
196 T
5001113 CTCCAACCATTAATTTTAATTCCATTTGGTCTTTAATATTTTGAAAAGAGACTTTCTTTCTTCGA
1 CTCCAACCATTAATTTTAATTCCATTTGGTCTTTAATATTTTGAAAAGAGACTTTCTTTCTTCGA
5001178 CCAACCAAATTCGGAAGCCCTAAGTACTTTTCTATGTCATTAGAGCATTTCACCTCAAGTAGATT
66 CCAACCAAATTCGGAAGCCCTAAGTACTTTTCTATGTCATTAGAGCATTTCACCTCAAGTAGATT
5001243 TGAAAAAGCATCTTTATTGTCCCTTGATGAATTAGTACTAAAGCAGCCTATAGATTTCTCGTAAT
131 TGAAAAAGCATCTTTATTGTCCCTTGATGAATTAGTACTAAAGCAGCCTATAGATTTCTCGTAAT
5001308 T
196 T
5001309 C
1 C
5001310 ACACTTTGAC
Statistics
Matches: 197, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
196 197 1.00
ACGTcount: A:0.30, C:0.20, G:0.13, T:0.37
Consensus pattern (196 bp):
CTCCAACCATTAATTTTAATTCCATTTGGTCTTTAATATTTTGAAAAGAGACTTTCTTTCTTCGA
CCAACCAAATTCGGAAGCCCTAAGTACTTTTCTATGTCATTAGAGCATTTCACCTCAAGTAGATT
TGAAAAAGCATCTTTATTGTCCCTTGATGAATTAGTACTAAAGCAGCCTATAGATTTCTCGTAAT
T
Found at i:5003814 original size:23 final size:23
Alignment explanation
Indices: 5003788--5003953 Score: 150
Period size: 23 Copynumber: 7.4 Consensus size: 23
5003778 TGTGCTGGGC
5003788 AACAGAGAGCACACAAAGTGCTA
1 AACAGAGAGCACACAAAGTGCTA
*
5003811 AACAGAGAGTACACAAA--G-T-
1 AACAGAGAGCACACAAAGTGCTA
*
5003830 -AC--TGAGCACACAAAGTGCTA
1 AACAGAGAGCACACAAAGTGCTA
* *
5003850 ATCAGAGAGCACACGAAGTGCTA
1 AACAGAGAGCACACAAAGTGCTA
* * *
5003873 ATCGGAGAGCACACACAGTGCTAA
1 AACAGAGAGCACACAAAGTGCT-A
* *
5003897 TAACAGAGAGCACGA-GACGTGCTA
1 -AACAGAGAGCAC-ACAAAGTGCTA
*
5003921 AACAGAGAGCACACACAGTGCTA
1 AACAGAGAGCACACAAAGTGCTA
*
5003944 ATCAGAGAGC
1 AACAGAGAGC
5003954 GCGCTAGTGT
Statistics
Matches: 114, Mismatches: 18, Indels: 22
0.74 0.12 0.14
Matches are distributed among these distances:
16 10 0.09
18 3 0.03
19 1 0.01
20 1 0.01
21 2 0.02
22 1 0.01
23 78 0.68
24 2 0.02
25 15 0.13
26 1 0.01
ACGTcount: A:0.42, C:0.22, G:0.24, T:0.11
Consensus pattern (23 bp):
AACAGAGAGCACACAAAGTGCTA
Found at i:5003848 original size:39 final size:39
Alignment explanation
Indices: 5003794--5003868 Score: 123
Period size: 39 Copynumber: 1.9 Consensus size: 39
5003784 GGGCAACAGA
*
5003794 GAGCACACAAAGTGCTAAACAGAGAGTACACAAAGTACT
1 GAGCACACAAAGTGCTAAACAGAGAGCACACAAAGTACT
* *
5003833 GAGCACACAAAGTGCTAATCAGAGAGCACACGAAGT
1 GAGCACACAAAGTGCTAAACAGAGAGCACACAAAGT
5003869 GCTAATCGGA
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
39 33 1.00
ACGTcount: A:0.44, C:0.21, G:0.23, T:0.12
Consensus pattern (39 bp):
GAGCACACAAAGTGCTAAACAGAGAGCACACAAAGTACT
Found at i:5003907 original size:48 final size:46
Alignment explanation
Indices: 5003833--5003953 Score: 172
Period size: 48 Copynumber: 2.6 Consensus size: 46
5003823 ACAAAGTACT
* * *
5003833 GAGCACACAAAGTGCTAATCAGAGAGCAC-ACGAAGTGCTAATCGGA
1 GAGCACACACAGTGCTAATCAGAGAGCACGA-GAAGTGCTAAACAGA
*
5003879 GAGCACACACAGTGCTAATAACAGAGAGCACGAGACGTGCTAAACAGA
1 GAGCACACACAGTGCTAAT--CAGAGAGCACGAGAAGTGCTAAACAGA
5003927 GAGCACACACAGTGCTAATCAGAGAGC
1 GAGCACACACAGTGCTAATCAGAGAGC
5003954 GCGCTAGTGT
Statistics
Matches: 68, Mismatches: 4, Indels: 6
0.87 0.05 0.08
Matches are distributed among these distances:
46 26 0.38
48 41 0.60
49 1 0.01
ACGTcount: A:0.40, C:0.23, G:0.26, T:0.12
Consensus pattern (46 bp):
GAGCACACACAGTGCTAATCAGAGAGCACGAGAAGTGCTAAACAGA
Found at i:5010839 original size:36 final size:36
Alignment explanation
Indices: 5010771--5010844 Score: 105
Period size: 36 Copynumber: 2.1 Consensus size: 36
5010761 AATAATATAG
* *
5010771 TTTGTTTAACTTGACTTGCAAGCAATTCTTTAATAT
1 TTTGTTTAACTTAACTTGCAAGCAATTCTTTAAAAT
*
5010807 TTTGTTTAACTTAACTTGCAAGTAA-TCTTTTAAAAT
1 TTTGTTTAACTTAACTTGCAAGCAATTC-TTTAAAAT
5010843 TT
1 TT
5010845 AAGTCACACA
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
35 2 0.06
36 32 0.94
ACGTcount: A:0.30, C:0.12, G:0.09, T:0.49
Consensus pattern (36 bp):
TTTGTTTAACTTAACTTGCAAGCAATTCTTTAAAAT
Found at i:5012058 original size:18 final size:17
Alignment explanation
Indices: 5012024--5012059 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
5012014 AATTTAAAAA
*
5012024 TAAAAATAAAAATATTT
1 TAAAAATAAAAAAATTT
5012041 TAAAAATAAATAAAATTT
1 TAAAAATAAA-AAAATTT
5012059 T
1 T
5012060 TCAAAAGTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 10 0.59
18 7 0.41
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (17 bp):
TAAAAATAAAAAAATTT
Found at i:5017218 original size:23 final size:23
Alignment explanation
Indices: 5017192--5017339 Score: 183
Period size: 23 Copynumber: 6.3 Consensus size: 23
5017182 ACACTAGAGC
5017192 GCTCTCTGATTAGCACTGTGTGT
1 GCTCTCTGATTAGCACTGTGTGT
5017215 GCTCTCTGATTAGCACTGTGTGT
1 GCTCTCTGATTAGCACTGTGTGT
* *
5017238 GCTCTCTGTTTAGCAC-GTCTCGT
1 GCTCTCTGATTAGCACTGTGT-GT
* *
5017261 GCTTTATGTTATTAGCACTGTGTGT
1 GCTCTCTG--ATTAGCACTGTGTGT
*
5017286 GGTCTCTGATTAGCACT-TCGTGT
1 GCTCTCTGATTAGCACTGT-GTGT
* *
5017309 GCTATCTGATTAGCACTTTGTGT
1 GCTCTCTGATTAGCACTGTGTGT
5017332 GCTCTCTG
1 GCTCTCTG
5017340 TTGCCCAGCA
Statistics
Matches: 107, Mismatches: 12, Indels: 12
0.82 0.09 0.09
Matches are distributed among these distances:
22 4 0.04
23 85 0.79
24 1 0.01
25 14 0.13
26 3 0.03
ACGTcount: A:0.13, C:0.22, G:0.24, T:0.41
Consensus pattern (23 bp):
GCTCTCTGATTAGCACTGTGTGT
Found at i:5021924 original size:23 final size:21
Alignment explanation
Indices: 5021864--5021931 Score: 64
Period size: 23 Copynumber: 3.0 Consensus size: 21
5021854 TCACAAATAA
*
5021864 AAAAAATAACCAAAAATAAAAT
1 AAAAAATAA-CTAAAATAAAAT
*
5021886 AAAAGTATAACTTAAAATAAAAT
1 AAAA-AATAAC-TAAAATAAAAT
5021909 AAATAAAGTAACTAAAATGAAAA
1 AAA-AAA-TAACTAAAAT-AAAA
5021932 CATATCGAGG
Statistics
Matches: 38, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
22 5 0.13
23 24 0.63
24 9 0.24
ACGTcount: A:0.71, C:0.06, G:0.04, T:0.19
Consensus pattern (21 bp):
AAAAAATAACTAAAATAAAAT
Found at i:5023310 original size:6 final size:6
Alignment explanation
Indices: 5023270--5023355 Score: 54
Period size: 6 Copynumber: 14.5 Consensus size: 6
5023260 GTCTTTTAAC
*
5023270 ATTTTT ATTTATT -TATTTT A-TTTT ATTTTC A--TTT ATTTTT ATTTTT
1 ATTTTT ATTT-TT AT-TTTT ATTTTT ATTTTT ATTTTT ATTTTT ATTTTT
* * * * * *
5023316 ATTATT ATGTTTT ATTATT ACTATT ATTATT ATTATT ATT
1 ATTTTT AT-TTTT ATTTTT ATTTTT ATTTTT ATTTTT ATT
5023356 ACTACTACTA
Statistics
Matches: 66, Mismatches: 7, Indels: 14
0.76 0.08 0.16
Matches are distributed among these distances:
4 3 0.05
5 5 0.08
6 49 0.74
7 9 0.14
ACGTcount: A:0.24, C:0.02, G:0.01, T:0.72
Consensus pattern (6 bp):
ATTTTT
Found at i:5023322 original size:3 final size:3
Alignment explanation
Indices: 5023282--5023356 Score: 66
Period size: 3 Copynumber: 25.0 Consensus size: 3
5023272 TTTTATTTAT
* * *
5023282 TTA TT- TTA TT- TTA TT- TTCA TTTA TTT TTA TTT TTA TTA TTA TGTT
1 TTA TTA TTA TTA TTA TTA TT-A -TTA TTA TTA TTA TTA TTA TTA T-TA
*
5023327 TTA TTA TTA CTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
5023357 CTACTACTAC
Statistics
Matches: 58, Mismatches: 8, Indels: 12
0.74 0.10 0.15
Matches are distributed among these distances:
2 6 0.10
3 47 0.81
4 3 0.05
5 2 0.03
ACGTcount: A:0.25, C:0.03, G:0.01, T:0.71
Consensus pattern (3 bp):
TTA
Found at i:5023329 original size:25 final size:25
Alignment explanation
Indices: 5023314--5023362 Score: 73
Period size: 24 Copynumber: 2.0 Consensus size: 25
5023304 ATTTTTATTT
5023314 TTATTATTATGTTTTATTATTACTA
1 TTATTATTATGTTTTATTATTACTA
* *
5023339 TTATTATTAT-TATTATTACTACTA
1 TTATTATTATGTTTTATTATTACTA
5023363 CTACTCTATT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 12 0.55
25 10 0.45
ACGTcount: A:0.31, C:0.06, G:0.02, T:0.61
Consensus pattern (25 bp):
TTATTATTATGTTTTATTATTACTA
Found at i:5023333 original size:28 final size:27
Alignment explanation
Indices: 5023270--5023352 Score: 82
Period size: 28 Copynumber: 3.1 Consensus size: 27
5023260 GTCTTTTAAC
*
5023270 ATTTTTATT-TATTTA-TTTTATT-TT
1 ATTTTTATTATTTTTATTTTTATTATT
*
5023294 ATTTTCATTTATTTTTATTTTTATTATT
1 ATTTTTA-TTATTTTTATTTTTATTATT
** *
5023322 ATGTTTTATTATTACTATTATTATTATT
1 AT-TTTTATTATTTTTATTTTTATTATT
5023350 ATT
1 ATT
5023353 ATTACTACTA
Statistics
Matches: 48, Mismatches: 6, Indels: 7
0.79 0.10 0.11
Matches are distributed among these distances:
24 6 0.12
25 2 0.04
26 5 0.10
27 8 0.17
28 23 0.48
29 4 0.08
ACGTcount: A:0.24, C:0.02, G:0.01, T:0.72
Consensus pattern (27 bp):
ATTTTTATTATTTTTATTTTTATTATT
Found at i:5024947 original size:21 final size:23
Alignment explanation
Indices: 5024923--5024976 Score: 67
Period size: 21 Copynumber: 2.4 Consensus size: 23
5024913 ACTGCAACTT
*
5024923 CTACCGATACAAGTAT-TC-GAA
1 CTACCGATACAACTATATCAGAA
*
5024944 CTACCGATACTACTATATCAGAA
1 CTACCGATACAACTATATCAGAA
*
5024967 CTATCGATAC
1 CTACCGATAC
5024977 TTCATTATTT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
21 14 0.50
22 2 0.07
23 12 0.43
ACGTcount: A:0.37, C:0.26, G:0.11, T:0.26
Consensus pattern (23 bp):
CTACCGATACAACTATATCAGAA
Found at i:5025621 original size:26 final size:26
Alignment explanation
Indices: 5025565--5025622 Score: 73
Period size: 26 Copynumber: 2.2 Consensus size: 26
5025555 CTTCCAAAAA
* *
5025565 TTTAGCTCATTACGAGCCTAGATAGG
1 TTTAGCTCATTACGAGCCCAGATAAG
*
5025591 GTTAGCTC-TTACGAGCCCAGATAAAG
1 TTTAGCTCATTACGAGCCCAGAT-AAG
5025617 TTTAGC
1 TTTAGC
5025623 CAGTATACAA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
25 13 0.48
26 14 0.52
ACGTcount: A:0.28, C:0.21, G:0.22, T:0.29
Consensus pattern (26 bp):
TTTAGCTCATTACGAGCCCAGATAAG
Found at i:5037254 original size:14 final size:14
Alignment explanation
Indices: 5037229--5037282 Score: 72
Period size: 14 Copynumber: 3.9 Consensus size: 14
5037219 AGTCGTAATG
* *
5037229 AAATTAAAATTTGA
1 AAATTTAAATTTTA
*
5037243 AAACTTAAATTTTA
1 AAATTTAAATTTTA
*
5037257 AAATTTGAATTTTA
1 AAATTTAAATTTTA
5037271 AAATTTAAATTT
1 AAATTTAAATTT
5037283 AATTTTGAAA
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 34 1.00
ACGTcount: A:0.50, C:0.02, G:0.04, T:0.44
Consensus pattern (14 bp):
AAATTTAAATTTTA
Found at i:5037280 original size:6 final size:7
Alignment explanation
Indices: 5037232--5037284 Score: 54
Period size: 7 Copynumber: 7.6 Consensus size: 7
5037222 CGTAATGAAA
5037232 TTAAAAT
1 TTAAAAT
*
5037239 TTGAAAAC
1 TT-AAAAT
*
5037247 TTAAATT
1 TTAAAAT
5037254 TTAAAAT
1 TTAAAAT
* *
5037261 TTGAATT
1 TTAAAAT
5037268 TTAAAAT
1 TTAAAAT
5037275 TT-AAAT
1 TTAAAAT
5037281 TTAA
1 TTAA
5037285 TTTTGAAAGC
Statistics
Matches: 36, Mismatches: 8, Indels: 4
0.75 0.17 0.08
Matches are distributed among these distances:
6 6 0.17
7 24 0.67
8 6 0.17
ACGTcount: A:0.49, C:0.02, G:0.04, T:0.45
Consensus pattern (7 bp):
TTAAAAT
Found at i:5037298 original size:19 final size:20
Alignment explanation
Indices: 5037257--5037298 Score: 50
Period size: 19 Copynumber: 2.1 Consensus size: 20
5037247 TTAAATTTTA
**
5037257 AAATTTGAATTTTAAAATTT
1 AAATTTGAATTTTAAAAGCT
*
5037277 AAATTT-AATTTTGAAAGCT
1 AAATTTGAATTTTAAAAGCT
5037296 AAA
1 AAA
5037299 ACTTTAAAGA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
19 13 0.68
20 6 0.32
ACGTcount: A:0.48, C:0.02, G:0.07, T:0.43
Consensus pattern (20 bp):
AAATTTGAATTTTAAAAGCT
Found at i:5041986 original size:146 final size:146
Alignment explanation
Indices: 5041832--5042136 Score: 418
Period size: 146 Copynumber: 2.1 Consensus size: 146
5041822 ACCTAGAGAC
* *
5041832 AAAATGGTAATTTTAGACTCTCGAGGGCAAAATGGTGATTTTGGG-AAAATTTAGGGTTAGAAAT
1 AAAATGGTAATTTTAGACTCTCGAGGGCAAAATGGTAATTTTGGGAAAAATTTAGGGTTAAAAAT
** * *
5041896 GACATTTTAAAT-GTTCGAGGGTAAAACGGTAATTTTCA-AAAGAATCGGGATAAAAAATGAGAC
66 GACATTTT-AATCAATCGAGAGTAAAACGGTAATTTTCAGAAA-AATCGAGATAAAAAATGAGA-
*
5041959 TTTTTGGATGCCCGAGGGT
128 TTTTTGGATACCCGAGGGT
* * *
5041978 AAAATGGTAATTTTGGACTTTCGAGGGCAAAATGGTAATTTTGGGAAAAATTTATGGTTAAAAAT
1 AAAATGGTAATTTTAGACTCTCGAGGGCAAAATGGTAATTTTGGGAAAAATTTAGGGTTAAAAAT
* * * *
5042043 GACATTTTAGTCAATCGAGAGTAAAACGGTAATTTTTAGAAAAATCGAGATCAAAAATGGGATTT
66 GACATTTTAATCAATCGAGAGTAAAACGGTAATTTTCAGAAAAATCGAGATAAAAAATGAGATTT
* *
5042108 TTGGATATCCGGGGGT
131 TTGGATACCCGAGGGT
5042124 AAAATGGTAATTT
1 AAAATGGTAATTT
5042137 CAAGAGTTTC
Statistics
Matches: 140, Mismatches: 16, Indels: 6
0.86 0.10 0.04
Matches are distributed among these distances:
146 73 0.52
147 64 0.46
148 3 0.02
ACGTcount: A:0.37, C:0.08, G:0.25, T:0.31
Consensus pattern (146 bp):
AAAATGGTAATTTTAGACTCTCGAGGGCAAAATGGTAATTTTGGGAAAAATTTAGGGTTAAAAAT
GACATTTTAATCAATCGAGAGTAAAACGGTAATTTTCAGAAAAATCGAGATAAAAAATGAGATTT
TTGGATACCCGAGGGT
Found at i:5041991 original size:29 final size:29
Alignment explanation
Indices: 5041959--5042019 Score: 72
Period size: 28 Copynumber: 2.1 Consensus size: 29
5041949 AAAATGAGAC
*
5041959 TTTTTGGA-TGCCCGAGGGTAAAATGGTAA
1 TTTTTGGACT-CCCGAGGGCAAAATGGTAA
**
5041988 -TTTTGGACTTTCGAGGGCAAAATGGTAA
1 TTTTTGGACTCCCGAGGGCAAAATGGTAA
5042016 TTTT
1 TTTT
5042020 GGGAAAAATT
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
28 23 0.85
29 4 0.15
ACGTcount: A:0.26, C:0.10, G:0.28, T:0.36
Consensus pattern (29 bp):
TTTTTGGACTCCCGAGGGCAAAATGGTAA
Found at i:5042147 original size:147 final size:146
Alignment explanation
Indices: 5041832--5042156 Score: 422
Period size: 147 Copynumber: 2.2 Consensus size: 146
5041822 ACCTAGAGAC
* * *
5041832 AAAATGGTAATTTTAGACTCTCGAGGGCAAAATGGTGATTTTGGGAAAATTTAGGGTTAGAAATG
1 AAAATGGTAATTTTAGACTTTCGAGGGCAAAATGGTAATTTTGGGAAAATTTAGGGTTAAAAATG
** * *
5041897 ACATTTTAAATGTTCGAGGGTAAAACGGTAATTTTCAAAAGAATCGGGATAAAAAATGAGACTTT
66 ACATTTTAAATAATCGAGAGTAAAACGGTAATTTTCAAAAGAATCGAGATAAAAAATGAGACTTT
*
5041962 TTGGATGCCCGAGGGT
131 TTGGATACCCGAGGGT
* *
5041978 AAAATGGTAATTTTGGACTTTCGAGGGCAAAATGGTAATTTTGGGAAAAATTTATGGTTAAAAAT
1 AAAATGGTAATTTTAGACTTTCGAGGGCAAAATGGTAATTTTGGG-AAAATTTAGGGTTAAAAAT
* * * *
5042043 GACATTTT-AGTCAATCGAGAGTAAAACGGTAATTTTTAGAAA-AATCGAGATCAAAAATGGGA-
65 GACATTTTAAAT-AATCGAGAGTAAAACGGTAATTTTCA-AAAGAATCGAGATAAAAAATGAGAC
* *
5042105 TTTTTGGATATCCGGGGGT
128 TTTTTGGATACCCGAGGGT
* * *
5042124 AAAATGGTAATTTCAAGAGTTTCGAGGTCAAAA
1 AAAATGGTAATTT-TAGACTTTCGAGGGCAAAA
5042157 ATGAAATTTT
Statistics
Matches: 155, Mismatches: 20, Indels: 7
0.85 0.11 0.04
Matches are distributed among these distances:
146 73 0.47
147 79 0.51
148 3 0.02
ACGTcount: A:0.37, C:0.08, G:0.25, T:0.30
Consensus pattern (146 bp):
AAAATGGTAATTTTAGACTTTCGAGGGCAAAATGGTAATTTTGGGAAAATTTAGGGTTAAAAATG
ACATTTTAAATAATCGAGAGTAAAACGGTAATTTTCAAAAGAATCGAGATAAAAAATGAGACTTT
TTGGATACCCGAGGGT
Found at i:5042180 original size:58 final size:58
Alignment explanation
Indices: 5042087--5042233 Score: 172
Period size: 58 Copynumber: 2.5 Consensus size: 58
5042077 TTTAGAAAAA
* ** ** *
5042087 TCGAGATCAAAAATGGGATTTTTGGATA-TCCGGGGGTAAAATGGTAATTTCAAG-AGTT
1 TCGAGGTCAAAAATGAAATTTTTGGA-AGTTTGGGGGAAAAAT-GTAATTTCAAGAAGTT
***
5042145 TCGAGGTCAAAAATGAAATTTTTGGAAGTTTGGGGGAAAAATGTAATTTTTGGAAGTT
1 TCGAGGTCAAAAATGAAATTTTTGGAAGTTTGGGGGAAAAATGTAATTTCAAGAAGTT
*
5042203 TTGAGGTCAAAAATGAAATTTTTGGAAGTTT
1 TCGAGGTCAAAAATGAAATTTTTGGAAGTTT
5042234 CGAGTTCAAA
Statistics
Matches: 77, Mismatches: 10, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
57 9 0.12
58 68 0.88
ACGTcount: A:0.34, C:0.05, G:0.27, T:0.34
Consensus pattern (58 bp):
TCGAGGTCAAAAATGAAATTTTTGGAAGTTTGGGGGAAAAATGTAATTTCAAGAAGTT
Found at i:5042271 original size:60 final size:58
Alignment explanation
Indices: 5042141--5042274 Score: 196
Period size: 58 Copynumber: 2.3 Consensus size: 58
5042131 TAATTTCAAG
* * *
5042141 AGTTTCGAGGTCAAAAATGAAATTTTTGGAAGTTTGGGGGAAAAATGTAATTTTTGGA
1 AGTTTTGAGGTCAAAAATGAAATTTTTGGAAGTTTGGGGCAAAAATGTAATTTTTGAA
**
5042199 AGTTTTGAGGTCAAAAATGAAATTTTTGGAAGTTTCGAGTTCAAAAATGTAATTTTTGAA
1 AGTTTTGAGGTCAAAAATGAAATTTTTGGAAGTTT-G-GGGCAAAAATGTAATTTTTGAA
*
5042259 AGTTTTGGGGTCAAAA
1 AGTTTTGAGGTCAAAA
5042275 TGTATGTTCT
Statistics
Matches: 68, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
58 34 0.50
59 1 0.01
60 33 0.49
ACGTcount: A:0.35, C:0.04, G:0.25, T:0.36
Consensus pattern (58 bp):
AGTTTTGAGGTCAAAAATGAAATTTTTGGAAGTTTGGGGCAAAAATGTAATTTTTGAA
Found at i:5042275 original size:29 final size:30
Alignment explanation
Indices: 5042141--5042278 Score: 174
Period size: 30 Copynumber: 4.7 Consensus size: 30
5042131 TAATTTCAAG
* *
5042141 AGTTTCGAGGTCAAAAATGAAATTTTTGGA
1 AGTTTTGAGGTCAAAAATGTAATTTTTGGA
**
5042171 AG-TTTG-GGGGAAAAATGTAATTTTTGGA
1 AGTTTTGAGGTCAAAAATGTAATTTTTGGA
*
5042199 AGTTTTGAGGTCAAAAATGAAATTTTTGGA
1 AGTTTTGAGGTCAAAAATGTAATTTTTGGA
* * *
5042229 AGTTTCGAGTTCAAAAATGTAATTTTTGAA
1 AGTTTTGAGGTCAAAAATGTAATTTTTGGA
*
5042259 AGTTTTGGGGTC-AAAATGTA
1 AGTTTTGAGGTCAAAAATGTA
5042279 TGTTCTGGAT
Statistics
Matches: 92, Mismatches: 14, Indels: 5
0.83 0.13 0.05
Matches are distributed among these distances:
28 21 0.23
29 15 0.16
30 56 0.61
ACGTcount: A:0.35, C:0.04, G:0.25, T:0.36
Consensus pattern (30 bp):
AGTTTTGAGGTCAAAAATGTAATTTTTGGA
Found at i:5043449 original size:17 final size:17
Alignment explanation
Indices: 5043421--5043462 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
5043411 CCTTTTTTTT
* *
5043421 TTATTCTTTTAT-TATA
1 TTATTATTTTATAAATA
5043437 TTAATTATTTTATAAATA
1 TT-ATTATTTTATAAATA
5043455 TTATTATT
1 TTATTATT
5043463 AATAAAAGCA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
16 2 0.09
17 15 0.68
18 5 0.23
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.64
Consensus pattern (17 bp):
TTATTATTTTATAAATA
Found at i:5044226 original size:6 final size:6
Alignment explanation
Indices: 5044217--5044345 Score: 98
Period size: 6 Copynumber: 22.8 Consensus size: 6
5044207 ACTTGGGCAT
* * *
5044217 TTTAAA TTTACAA -ATAATA TT-AAA TTTGAA -TTAAA TTTGAA -TTAAA
1 TTTAAA TTTA-AA TTTAA-A TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
* **
5044263 TTTAAA CTTAAA -TTAAA TTTAAA TTTAAA CATAAA -TTAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
* *
5044309 --TAAA TTTAAA TTT-AA TTAAAA TTTAAA -ATAAA TTTAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAA
5044346 TTTCAAAGTA
Statistics
Matches: 97, Mismatches: 14, Indels: 24
0.72 0.10 0.18
Matches are distributed among these distances:
4 4 0.04
5 29 0.30
6 62 0.64
7 2 0.02
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.43
Consensus pattern (6 bp):
TTTAAA
Found at i:5044267 original size:17 final size:16
Alignment explanation
Indices: 5044247--5044335 Score: 99
Period size: 17 Copynumber: 5.3 Consensus size: 16
5044237 TAAATTTGAA
5044247 TTAAATTTGAATTAAAT
1 TTAAATTT-AATTAAAT
*
5044264 TTAAACTTAAATTAAAT
1 TTAAA-TTTAATTAAAT
*
5044281 TTAAATTTAAACATAAA-
1 TTAAATTT-AA-TTAAAT
*
5044298 TTAAATTTAAATAAAT
1 TTAAATTTAATTAAAT
5044314 TTAAATTTAATTAAAAT
1 TTAAATTTAATT-AAAT
5044331 TTAAA
1 TTAAA
5044336 ATAAATTTAA
Statistics
Matches: 63, Mismatches: 4, Indels: 10
0.82 0.05 0.13
Matches are distributed among these distances:
15 5 0.08
16 15 0.24
17 37 0.59
18 6 0.10
ACGTcount: A:0.54, C:0.02, G:0.01, T:0.43
Consensus pattern (16 bp):
TTAAATTTAATTAAAT
Found at i:5044325 original size:11 final size:11
Alignment explanation
Indices: 5044231--5044348 Score: 89
Period size: 11 Copynumber: 10.5 Consensus size: 11
5044221 AATTTACAAA
5044231 TAATATTAAATT
1 TAAT-TTAAATT
5044243 TGAA-TTAAATT
1 T-AATTTAAATT
5044254 TGAA-TTAAATT
1 T-AATTTAAATT
*
5044265 TAAACTTAAATT
1 T-AATTTAAATT
*
5044277 AAATTTAAATT
1 TAATTTAAATT
**
5044288 TAAACATAAATT
1 T-AATTTAAATT
*
5044300 AAATTTAAA-T
1 TAATTTAAATT
*
5044310 AAATTTAAATT
1 TAATTTAAATT
*
5044321 TAATTAAAATT
1 TAATTTAAATT
**
5044332 TAAAATAAATT
1 TAATTTAAATT
5044343 TAATTT
1 TAATTT
5044349 CAAAGTAAAT
Statistics
Matches: 86, Mismatches: 16, Indels: 9
0.77 0.14 0.08
Matches are distributed among these distances:
10 10 0.12
11 58 0.67
12 16 0.19
13 2 0.02
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.44
Consensus pattern (11 bp):
TAATTTAAATT
Found at i:5044357 original size:17 final size:16
Alignment explanation
Indices: 5044245--5044360 Score: 73
Period size: 17 Copynumber: 7.3 Consensus size: 16
5044235 ATTAAATTTG
* * *
5044245 AATTAAATTTGAATTA
1 AATTTAATTTAAAATA
* *
5044261 AATTTAAACTTAAATTA
1 AATTT-AATTTAAAATA
5044278 AATTTAAATTTAAACATA
1 AATTT-AATTTAAA-ATA
*
5044296 AATTAAATTT-AAATA
1 AATTTAATTTAAAATA
*
5044311 AATTTAAATTT--AATT
1 AATTT-AATTTAAAATA
5044326 AA---AATTTAAAATA
1 AATTTAATTTAAAATA
*
5044339 AATTTAATTTCAAAGTA
1 AATTTAATTT-AAAATA
5044356 AATTT
1 AATTT
5044361 TAAAATGGTT
Statistics
Matches: 81, Mismatches: 10, Indels: 17
0.75 0.09 0.16
Matches are distributed among these distances:
11 5 0.06
13 5 0.06
15 12 0.15
16 16 0.20
17 37 0.46
18 6 0.07
ACGTcount: A:0.53, C:0.03, G:0.02, T:0.42
Consensus pattern (16 bp):
AATTTAATTTAAAATA
Found at i:5044360 original size:28 final size:27
Alignment explanation
Indices: 5044282--5044345 Score: 58
Period size: 27 Copynumber: 2.3 Consensus size: 27
5044272 AAATTAAATT
*
5044282 TAAATTTAAACATAAA-TTAAATTTAAA
1 TAAATTTAAA-ATAAATTTAAATTTAAG
* * * *
5044309 TAAATTTAAATTTAATTAAAATTTAAAA
1 TAAATTTAAAATAAATTTAAATTT-AAG
5044337 TAAATTTAA
1 TAAATTTAA
5044346 TTTCAAAGTA
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
26 3 0.09
27 17 0.53
28 12 0.38
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.41
Consensus pattern (27 bp):
TAAATTTAAAATAAATTTAAATTTAAG
Found at i:5044904 original size:39 final size:39
Alignment explanation
Indices: 5044871--5045004 Score: 144
Period size: 39 Copynumber: 3.4 Consensus size: 39
5044861 ATCTGCTTCG
5044871 GGCTCGAGGTAAAAGATCAAATGGCTGTAATCTGCCCCA
1 GGCTCGAGGTAAAAGATCAAATGGCTGTAATCTGCCCCA
* * **** * *
5044910 GGCTTGAGGTAAGAGATTGGTTAG-TGATGATCTGCCCCA
1 GGCTCGAGGTAAAAGATCAAATGGCTG-TAATCTGCCCCA
* *
5044949 GGCTCGAGGTAAAAGATCAAATGGCTGCAATCTGCCCGA
1 GGCTCGAGGTAAAAGATCAAATGGCTGTAATCTGCCCCA
* *
5044988 GGCTCGGGGTAAGAGAT
1 GGCTCGAGGTAAAAGAT
5045005 TGGTTGGTGA
Statistics
Matches: 73, Mismatches: 20, Indels: 4
0.75 0.21 0.04
Matches are distributed among these distances:
38 2 0.03
39 69 0.95
40 2 0.03
ACGTcount: A:0.28, C:0.19, G:0.31, T:0.22
Consensus pattern (39 bp):
GGCTCGAGGTAAAAGATCAAATGGCTGTAATCTGCCCCA
Found at i:5044953 original size:78 final size:77
Alignment explanation
Indices: 5044822--5045047 Score: 299
Period size: 78 Copynumber: 2.9 Consensus size: 77
5044812 GATAACTACC
* * * * ** *
5044822 ATCTGGCCCAAGCTCGGGGTAAGAGATTGGTTGATGGTGATCTGCTTCGGGCTCGAGGTAAAAGA
1 ATCTGCCCCAGGCTCGAGGTAAGAGATTGGTTG-TGATGATCTGCCCCAGGCTCGAGGTAAAAGA
*
5044887 TCAAATGGCTGTA
65 TCAAATGGCTGCA
*
5044900 ATCTGCCCCAGGCTTGAGGTAAGAGATTGGTTAGTGATGATCTGCCCCAGGCTCGAGGTAAAAGA
1 ATCTGCCCCAGGCTCGAGGTAAGAGATTGGTT-GTGATGATCTGCCCCAGGCTCGAGGTAAAAGA
5044965 TCAAATGGCTGCA
65 TCAAATGGCTGCA
* * * * *
5044978 ATCTGCCCGAGGCTCGGGGTAAGAGATTGGTTGGTGATGATCTACCCCAAGTTCGAGGTAAAAGA
1 ATCTGCCCCAGGCTCGAGGTAAGAGATTGGTT-GTGATGATCTGCCCCAGGCTCGAGGTAAAAGA
5045043 TCAAA
65 TCAAA
5045048 ATCTTCATTT
Statistics
Matches: 131, Mismatches: 16, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
78 130 0.99
79 1 0.01
ACGTcount: A:0.27, C:0.19, G:0.31, T:0.24
Consensus pattern (77 bp):
ATCTGCCCCAGGCTCGAGGTAAGAGATTGGTTGTGATGATCTGCCCCAGGCTCGAGGTAAAAGAT
CAAATGGCTGCA
Found at i:5045241 original size:92 final size:92
Alignment explanation
Indices: 5045144--5045827 Score: 1099
Period size: 92 Copynumber: 7.5 Consensus size: 92
5045134 TGGTATCGAA
5045144 GCTTCATCTTGCTCTTACTACAACTTCAGAGAGATAAAGACTTGCTATCCAACTTTACTACAACT
1 GCTTCATCTTGCTCTTACTACAACTTCAGAGAGATAAAGACTTGCTATCCAACTTTACTACAACT
5045209 TCAAGAGGATAGGAATTGATGTTTGAT
66 TCAAGAGGATAGGAATTGATGTTTGAT
*
5045236 GCTTCATCTTGCTCTTACTACAACTTCAGAGAGATAAAGACTTGCTATCCAACTTTACTACAATT
1 GCTTCATCTTGCTCTTACTACAACTTCAGAGAGATAAAGACTTGCTATCCAACTTTACTACAACT
* *
5045301 TTAAGAGGATAGAAATTGATGTTTGAT
66 TCAAGAGGATAGGAATTGATGTTTGAT
*
5045328 GCTTCATCTTGCTCTTACTACAACTTCAGAGAGATAAAGACTTACTATCCAACTTTACTACAACT
1 GCTTCATCTTGCTCTTACTACAACTTCAGAGAGATAAAGACTTGCTATCCAACTTTACTACAACT
*
5045393 TCAAGAGGATAGGAATTGATGTTTTAT
66 TCAAGAGGATAGGAATTGATGTTTGAT
* *
5045420 GCTTCACCTTGCTCTTACTACAACTTCAGAGAGATAAAGACTTACTATCCAACTTTACTACAACT
1 GCTTCATCTTGCTCTTACTACAACTTCAGAGAGATAAAGACTTGCTATCCAACTTTACTACAACT
*
5045485 TCAAGAGGATAGGAATTGATGTTTTAT
66 TCAAGAGGATAGGAATTGATGTTTGAT
*
5045512 GCTTCACCTTGCTCTTACTACAACTTCAGAGAGATAAAGACTTGCTATCCAACTTTACTACAACT
1 GCTTCATCTTGCTCTTACTACAACTTCAGAGAGATAAAGACTTGCTATCCAACTTTACTACAACT
*
5045577 TCAAGAGGATAGGATTTGATGTTTGAT
66 TCAAGAGGATAGGAATTGATGTTTGAT
* * *
5045604 GTTTTATCTTGCTCTTACTACAGCTTCAGAGAGATAAAGACTTGCTATCCAACTTTACTACAACT
1 GCTTCATCTTGCTCTTACTACAACTTCAGAGAGATAAAGACTTGCTATCCAACTTTACTACAACT
*
5045669 T-TA-A--A-AGGAATTGATGTTTGAT
66 TCAAGAGGATAGGAATTGATGTTTGAT
* * *
5045691 GCTTTATCTTGTTCTTACTACATCTTCAGAGAGATAAAGACTTGCTATCCAACTTTACTACAACT
1 GCTTCATCTTGCTCTTACTACAACTTCAGAGAGATAAAGACTTGCTATCCAACTTTACTACAACT
* * *
5045756 TTAAGAGGATAGGAATTGATGTTTAAA
66 TCAAGAGGATAGGAATTGATGTTTGAT
* * * * *
5045783 ACTTTATCTAGCTCTTACTACAAACTTTAGAGAGATGAAGACTTG
1 GCTTCATCTTGCTCTTACTAC-AACTTCAGAGAGATAAAGACTTG
5045828 GTATTTTGAT
Statistics
Matches: 556, Mismatches: 30, Indels: 11
0.93 0.05 0.02
Matches are distributed among these distances:
87 79 0.14
88 2 0.00
89 1 0.00
90 1 0.00
91 2 0.00
92 451 0.81
93 20 0.04
ACGTcount: A:0.32, C:0.19, G:0.15, T:0.34
Consensus pattern (92 bp):
GCTTCATCTTGCTCTTACTACAACTTCAGAGAGATAAAGACTTGCTATCCAACTTTACTACAACT
TCAAGAGGATAGGAATTGATGTTTGAT
Found at i:5046003 original size:48 final size:48
Alignment explanation
Indices: 5045951--5046101 Score: 146
Period size: 49 Copynumber: 3.1 Consensus size: 48
5045941 GAATCTTCGT
5045951 GGTACTGGATGCCATTGCGGTCTTAGATCTTTCTCTTCATGCTTTTGA
1 GGTACTGGATGCCATTGCGGTCTTAGATCTTTCTCTTCATGCTTTTGA
* * * * * * * *
5045999 GGTACACGG-TCCGCAGTTGC-GACTTAGACCTTTCCCTTTTAT-ATCTTTGC
1 GGTAC-TGGATGC-CA-TTGCGGTCTTAGATCTTTCTC-TTCATGCT-TTTGA
* *
5046049 GGTACTGTATGCCATTGCGGTCTTAGATCTTTCTCTTCATGCTTCTGA
1 GGTACTGGATGCCATTGCGGTCTTAGATCTTTCTCTTCATGCTTTTGA
5046097 GGTAC
1 GGTAC
5046102 ACGGTCTACC
Statistics
Matches: 77, Mismatches: 18, Indels: 16
0.69 0.16 0.14
Matches are distributed among these distances:
48 23 0.30
49 35 0.45
50 19 0.25
ACGTcount: A:0.15, C:0.24, G:0.22, T:0.39
Consensus pattern (48 bp):
GGTACTGGATGCCATTGCGGTCTTAGATCTTTCTCTTCATGCTTTTGA
Found at i:5046032 original size:49 final size:49
Alignment explanation
Indices: 5045972--5046130 Score: 128
Period size: 49 Copynumber: 3.2 Consensus size: 49
5045962 CCATTGCGGT
* *
5045972 CTTAGATCTTTCTCTTCATGCTTTTGAGGTACACGGTCCGCAGTTGCGA
1 CTTAGACCTTTCTCTTCATGCTTTTGAGGTACACGGTCTGCAGTTGCGA
* * * * * * *
5046021 CTTAGACCTTTCCCTTTTAT-ATCTTTGCGGT--ACTGTATGCCA-TTGCGGT
1 CTTAGACCTTTCTC-TTCATGCT-TTTGAGGTACACGGTCTG-CAGTTGC-GA
* * * *
5046070 CTTAGATCTTTCTCTTCATGCTTCTGAGGTACACGGTCTACCGTTGCGA
1 CTTAGACCTTTCTCTTCATGCTTTTGAGGTACACGGTCTGCAGTTGCGA
*
5046119 CTTAAACCTTTC
1 CTTAGACCTTTC
5046131 CCTTTTGTAT
Statistics
Matches: 80, Mismatches: 22, Indels: 16
0.68 0.19 0.14
Matches are distributed among these distances:
48 19 0.24
49 41 0.51
50 20 0.25
ACGTcount: A:0.16, C:0.26, G:0.19, T:0.39
Consensus pattern (49 bp):
CTTAGACCTTTCTCTTCATGCTTTTGAGGTACACGGTCTGCAGTTGCGA
Found at i:5046077 original size:98 final size:98
Alignment explanation
Indices: 5045922--5046180 Score: 376
Period size: 98 Copynumber: 2.6 Consensus size: 98
5045912 TTGTCATTGT
* * * *
5045922 GACTTAAACCTTTCCCTTTGA-ATCTTCGTGGTACTGGATGCCATTGCGGTCTTAGATCTTTCTC
1 GACTTAAACCTTTCCCTTTTATATCTTTGCGGTACTGTATGCCATTGCGGTCTTAGATCTTTCTC
* *
5045986 TTCATGCTTTTGAGGTACACGGTCCGCAGTTGC
66 TTCATGCTTCTGAGGTACACGGTCCACAGTTGC
*
5046019 GACTTAGACCTTTCCCTTTTATATCTTTGCGGTACTGTATGCCATTGCGGTCTTAGATCTTTCTC
1 GACTTAAACCTTTCCCTTTTATATCTTTGCGGTACTGTATGCCATTGCGGTCTTAGATCTTTCTC
* *
5046084 TTCATGCTTCTGAGGTACACGGTCTACCGTTGC
66 TTCATGCTTCTGAGGTACACGGTCCACAGTTGC
* * * *
5046117 GACTTAAACCTTTCCCTTTTGTATCTTTGCGGTACTGGATCTGCCGTTGCGGTCTTAAATCTTT
1 GACTTAAACCTTTCCCTTTTATATCTTTGCGGTACT-G-TATGCCATTGCGGTCTTAGATCTTT
5046181 TTCCGTCGTG
Statistics
Matches: 145, Mismatches: 14, Indels: 3
0.90 0.09 0.02
Matches are distributed among these distances:
97 19 0.13
98 103 0.71
99 1 0.01
100 22 0.15
ACGTcount: A:0.16, C:0.25, G:0.20, T:0.39
Consensus pattern (98 bp):
GACTTAAACCTTTCCCTTTTATATCTTTGCGGTACTGTATGCCATTGCGGTCTTAGATCTTTCTC
TTCATGCTTCTGAGGTACACGGTCCACAGTTGC
Found at i:5046151 original size:50 final size:49
Alignment explanation
Indices: 5045994--5046167 Score: 133
Period size: 50 Copynumber: 3.5 Consensus size: 49
5045984 TCTTCATGCT
* *
5045994 TTTGAGGTACACGGTCCGCAGTTGCGACTTAGACCTTTCCCTTTTATATC
1 TTTGAGGTACACGGTCTGCCGTTGCGACTTAGACCTTTCCCTTTT-TATC
* * * * * * * *
5046044 TTTGCGGT--ACTGTATGCCATTGCGGTCTTAGATCTTT--CTCTTCATGC
1 TTTGAGGTACACGGTCTGCCGTTGC-GACTTAGACCTTTCCCTTTTTAT-C
* *
5046091 TTCTGAGGTACACGGTCTACCGTTGCGACTTAAACCTTTCCCTTTTGTATC
1 TT-TGAGGTACACGGTCTGCCGTTGCGACTTAGACCTTTCCCTTTT-TATC
* *
5046142 TTTGCGGTAC-TGGATCTGCCGTTGCG
1 TTTGAGGTACACGG-TCTGCCGTTGCG
5046168 GTCTTAAATC
Statistics
Matches: 92, Mismatches: 23, Indels: 18
0.69 0.17 0.14
Matches are distributed among these distances:
46 2 0.02
47 7 0.08
48 15 0.16
49 23 0.25
50 36 0.39
51 7 0.08
52 2 0.02
ACGTcount: A:0.15, C:0.25, G:0.22, T:0.38
Consensus pattern (49 bp):
TTTGAGGTACACGGTCTGCCGTTGCGACTTAGACCTTTCCCTTTTTATC
Found at i:5046289 original size:152 final size:150
Alignment explanation
Indices: 5046058--5046417 Score: 472
Period size: 151 Copynumber: 2.4 Consensus size: 150
5046048 CGGTACTGTA
* * ** * ** *
5046058 TGCCATTGCGGTCTTAGATCTTTCTCTTCATG-CTTCTGAGGTACACGGTCTACCGTTGCGACTT
1 TGCCATTGTGGTCTTAGATCTTTCCCTTCGCGTCTTTTGAGGTACAC-GTCCGCCGTTCCGACTT
* * *
5046122 AAACCTTTCCCTTTTGTATCTTTGCGGTACTGGATCTGCCGTTGCGGTCTTAAATCTTTTTCCGT
65 AAACCTTACCCTTTTGTATCTTTGCGGTACTGGATCTGCCGTTGCGGTCTTAAATC-TTTCCCAT
*
5046187 CGTGTTTTTGTGATATTGGATC
129 CGTGTTTTTATGATATTGGATC
5046209 TGCCATTGTGGTCTTAGATCTTTCCCTTCGCGTCTTTTGAGGTACACAGTCCGCCGTTACCG-CT
1 TGCCATTGTGGTCTTAGATCTTTCCCTTCGCGTCTTTTGAGGTACAC-GTCCGCCGTT-CCGACT
* *
5046273 TAGACCTTACCCTTTTGTATCTTTGCGGTACTGGATCTGCCGTTGCGGTCTTAGATCTTTCCCAT
64 TAAACCTTACCCTTTTGTATCTTTGCGGTACTGGATCTGCCGTTGCGGTCTTAAATCTTTCCCAT
*
5046338 CGTGTTTTTATGGTATTGGATC
129 CGTGTTTTTATGATATTGGATC
** * * * *
5046360 CACCGTTGTGGTCTTAAATATTTCCCTTCGCATCTTTTGAGGTACACGATCCGCCGTT
1 TGCCATTGTGGTCTTAGATCTTTCCCTTCGCGTCTTTTGAGGTACACG-TCCGCCGTT
5046418 GCGGTCTTAG
Statistics
Matches: 184, Mismatches: 22, Indels: 6
0.87 0.10 0.03
Matches are distributed among these distances:
150 1 0.01
151 104 0.57
152 77 0.42
153 2 0.01
ACGTcount: A:0.14, C:0.25, G:0.21, T:0.40
Consensus pattern (150 bp):
TGCCATTGTGGTCTTAGATCTTTCCCTTCGCGTCTTTTGAGGTACACGTCCGCCGTTCCGACTTA
AACCTTACCCTTTTGTATCTTTGCGGTACTGGATCTGCCGTTGCGGTCTTAAATCTTTCCCATCG
TGTTTTTATGATATTGGATC
Found at i:5053591 original size:30 final size:30
Alignment explanation
Indices: 5053555--5053816 Score: 261
Period size: 29 Copynumber: 8.9 Consensus size: 30
5053545 ATCCGAGGGT
*
5053555 AAAATGGTAA-TTTTGGGAGTTTCGGGGTCA
1 AAAAT-GTAATTTTTGGAAGTTTCGGGGTCA
*
5053585 AAAATGGAA-TTTTGGAAG-TTCGGGGTCA
1 AAAATGTAATTTTTGGAAGTTTCGGGGTCA
** **
5053613 AAAATCAAATTTTTGGAAGTTT-GGGGGAA
1 AAAATGTAATTTTTGGAAGTTTCGGGGTCA
* *
5053642 AAAATGTAATTTTTGGAAGTTTCGAGGTTA
1 AAAATGTAATTTTTGGAAGTTTCGGGGTCA
* *
5053672 AAAATGGAATTTTTGGAAATTT-GAGGGT-A
1 AAAATGTAATTTTTGGAAGTTTCG-GGGTCA
* * **
5053701 AAAATGTAATATTAGGAAGTTTTAGGGTCA
1 AAAATGTAATTTTTGGAAGTTTCGGGGTCA
* * * *
5053731 AAAATGGAATTTTTGAAAGTTTAGGAGT-A
1 AAAATGTAATTTTTGGAAGTTTCGGGGTCA
* *
5053760 AAAACGTAATTTTTGGAAATTTCGGGGTC-
1 AAAATGTAATTTTTGGAAGTTTCGGGGTCA
5053789 AAAATGTAATTTTTGGATAGTTTCGGGG
1 AAAATGTAATTTTTGGA-AGTTTCGGGG
5053817 AGCAAAATAA
Statistics
Matches: 190, Mismatches: 34, Indels: 16
0.79 0.14 0.07
Matches are distributed among these distances:
28 17 0.09
29 108 0.57
30 65 0.34
ACGTcount: A:0.34, C:0.04, G:0.27, T:0.34
Consensus pattern (30 bp):
AAAATGTAATTTTTGGAAGTTTCGGGGTCA
Found at i:5053688 original size:59 final size:59
Alignment explanation
Indices: 5053555--5053817 Score: 248
Period size: 59 Copynumber: 4.5 Consensus size: 59
5053545 ATCCGAGGGT
* ** * *
5053555 AAAATGGTAA-TTTTGGGAGTTTCGGGGTCAAAAATGGAA-TTTTGGAAG-TTCGGGGTCA
1 AAAATGG-AATTTTTGGAAGTTT-GGGGGAAAAAATGTAATTTTTGGAAGTTTCGAGGTCA
** *
5053613 AAAATCAAATTTTTGGAAGTTTGGGGGAAAAAATGTAATTTTTGGAAGTTTCGAGGTTA
1 AAAATGGAATTTTTGGAAGTTTGGGGGAAAAAATGTAATTTTTGGAAGTTTCGAGGTCA
* * * * * *
5053672 AAAATGGAATTTTTGGAAATTTGAGGGTAAAAATGTAATATTAGGAAGTTT-TAGGGTCA
1 AAAATGGAATTTTTGGAAGTTTGGGGGAAAAAATGTAATTTTTGGAAGTTTCGA-GGTCA
* * * * * * *
5053731 AAAATGGAATTTTTGAAAGTTTAGGAGTAAAAACGTAATTTTTGGAAATTTCGGGGTC-
1 AAAATGGAATTTTTGGAAGTTTGGGGGAAAAAATGTAATTTTTGGAAGTTTCGAGGTCA
* *
5053789 AAAATGTAATTTTTGGATAGTTTCGGGGA
1 AAAATGGAATTTTTGGA-AGTTTGGGGGA
5053818 GCAAAATAAA
Statistics
Matches: 166, Mismatches: 33, Indels: 11
0.79 0.16 0.05
Matches are distributed among these distances:
57 15 0.09
58 41 0.25
59 110 0.66
ACGTcount: A:0.35, C:0.04, G:0.27, T:0.34
Consensus pattern (59 bp):
AAAATGGAATTTTTGGAAGTTTGGGGGAAAAAATGTAATTTTTGGAAGTTTCGAGGTCA
Found at i:5053762 original size:88 final size:86
Alignment explanation
Indices: 5053555--5053817 Score: 235
Period size: 88 Copynumber: 3.0 Consensus size: 86
5053545 ATCCGAGGGT
** * * *
5053555 AAAATGGTAA-TTTTGGGAGTTTCGGGGTCAAAAATGGAA-TTTTGGAAGTTCGGGGTCAAAAAT
1 AAAATGG-AATTTTTGAAAGTTTCAGGGT-AAAAATGGAATTTTTGGAAATTTGGGGT-AAAAAT
** * * *
5053618 CAAATTTTTGGAAGTTTGGGGGAA
63 GTAATATTAGGAAGTTTAGGGGAA
* * *
5053642 AAAATGTAATTTTTGGAAGTTTCGAGGTTAAAAATGGAATTTTTGGAAATTTGAGGGTAAAAATG
1 AAAATGGAATTTTTGAAAGTTTC-AGGGTAAAAATGGAATTTTTGGAAATTTG-GGGTAAAAATG
**
5053707 TAATATTAGGAAGTTTTAGGGTCA
64 TAATATTAGGAAG-TTTAGGGGAA
* * *
5053731 AAAATGGAATTTTTGAAAGTTT-AGGAGTAAAAACGTAATTTTTGGAAATTTCGGGGTCAAAATG
1 AAAATGGAATTTTTGAAAGTTTCAGG-GTAAAAATGGAATTTTTGGAAATTT-GGGGTAAAAATG
* * *
5053795 TAATTTTTGGATAGTTTCGGGGA
64 TAATATTAGGA-AGTTTAGGGGA
5053818 GCAAAATAAA
Statistics
Matches: 144, Mismatches: 24, Indels: 15
0.79 0.13 0.08
Matches are distributed among these distances:
86 2 0.01
87 31 0.22
88 77 0.53
89 34 0.24
ACGTcount: A:0.35, C:0.04, G:0.27, T:0.34
Consensus pattern (86 bp):
AAAATGGAATTTTTGAAAGTTTCAGGGTAAAAATGGAATTTTTGGAAATTTGGGGTAAAAATGTA
ATATTAGGAAGTTTAGGGGAA
Found at i:5061202 original size:21 final size:20
Alignment explanation
Indices: 5061176--5061232 Score: 62
Period size: 21 Copynumber: 2.8 Consensus size: 20
5061166 CAGGGCAACA
5061176 TCTTCTTCTTTTTCTTCCTTC
1 TCTTCTTCTTTTTCTT-CTTC
*
5061197 TCTTC-TCTTTATTCTTCTTT
1 TCTTCTTCTTT-TTCTTCTTC
*
5061217 TCTTTCTTCTTATTCT
1 TC-TTCTTCTTTTTCT
5061233 ACCTCAGTAC
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
20 10 0.32
21 17 0.55
22 4 0.13
ACGTcount: A:0.04, C:0.28, G:0.00, T:0.68
Consensus pattern (20 bp):
TCTTCTTCTTTTTCTTCTTC
Found at i:5079323 original size:35 final size:35
Alignment explanation
Indices: 5079277--5079345 Score: 111
Period size: 35 Copynumber: 2.0 Consensus size: 35
5079267 AAGATAATAT
* *
5079277 ATTTTGTTTAACTTGACTTGCAAGCAATTTCTTAG
1 ATTTTGTTTAACATGACTTGCAAGCAATATCTTAG
*
5079312 ATTTTGTTTAACATGACTTGCAAGTAATATCTTA
1 ATTTTGTTTAACATGACTTGCAAGCAATATCTTA
5079346 TTTGACTGAA
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
35 31 1.00
ACGTcount: A:0.29, C:0.13, G:0.13, T:0.45
Consensus pattern (35 bp):
ATTTTGTTTAACATGACTTGCAAGCAATATCTTAG
Found at i:5080253 original size:11 final size:11
Alignment explanation
Indices: 5080237--5080262 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
5080227 GTTTTAATTG
5080237 TCTCTTTTGTA
1 TCTCTTTTGTA
5080248 TCTCTTTTGTA
1 TCTCTTTTGTA
5080259 TCTC
1 TCTC
5080263 AGTTCAGAAG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.08, C:0.23, G:0.08, T:0.62
Consensus pattern (11 bp):
TCTCTTTTGTA
Found at i:5094961 original size:10 final size:9
Alignment explanation
Indices: 5094908--5094942 Score: 61
Period size: 9 Copynumber: 3.9 Consensus size: 9
5094898 ACTAAGTTAT
*
5094908 TTTTAAAAT
1 TTTTAAAAA
5094917 TTTTAAAAA
1 TTTTAAAAA
5094926 TTTTAAAAA
1 TTTTAAAAA
5094935 TTTTAAAA
1 TTTTAAAA
5094943 TCTTATAAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
9 25 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (9 bp):
TTTTAAAAA
Found at i:5111654 original size:11 final size:10
Alignment explanation
Indices: 5111638--5111675 Score: 51
Period size: 10 Copynumber: 3.7 Consensus size: 10
5111628 ACCCACGAAA
5111638 TATTTTTTATT
1 TATTTTTT-TT
5111649 TATTTTTTTT
1 TATTTTTTTT
5111659 GTA-TTTTTTT
1 -TATTTTTTTT
5111669 TATTTTT
1 TATTTTT
5111676 GCTCTTTTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
9 2 0.08
10 13 0.52
11 10 0.40
ACGTcount: A:0.13, C:0.00, G:0.03, T:0.84
Consensus pattern (10 bp):
TATTTTTTTT
Found at i:5112640 original size:17 final size:17
Alignment explanation
Indices: 5112600--5112641 Score: 59
Period size: 17 Copynumber: 2.5 Consensus size: 17
5112590 TCTTTATAAT
5112600 TAAAAAA-TAAAAAAAA
1 TAAAAAATTAAAAAAAA
* *
5112616 TAAAAAATTTAAAAATA
1 TAAAAAATTAAAAAAAA
5112633 TAAAAAATT
1 TAAAAAATT
5112642 CCAAAATTCA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
16 7 0.30
17 16 0.70
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (17 bp):
TAAAAAATTAAAAAAAA
Found at i:5112647 original size:17 final size:17
Alignment explanation
Indices: 5112600--5112648 Score: 55
Period size: 17 Copynumber: 2.9 Consensus size: 17
5112590 TCTTTATAAT
* *
5112600 TAAAAAA-TAAAAAAAA
1 TAAAAAATTCAAAAATA
*
5112616 TAAAAAATTTAAAAATA
1 TAAAAAATTCAAAAATA
*
5112633 TAAAAAATTCCAAAAT
1 TAAAAAATTCAAAAAT
5112649 TCATTGTTAT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
16 7 0.25
17 21 0.75
ACGTcount: A:0.73, C:0.04, G:0.00, T:0.22
Consensus pattern (17 bp):
TAAAAAATTCAAAAATA
Found at i:5116345 original size:31 final size:30
Alignment explanation
Indices: 5116307--5116443 Score: 122
Period size: 31 Copynumber: 4.5 Consensus size: 30
5116297 TAATTATAAT
*
5116307 ATTTGGTACTTCAACTTGACACTTTTTTCTA
1 ATTTGGTAC-TAAACTTGACACTTTTTTCTA
* *
5116338 ATTTGGTACCTAAACATT-----TTTTATCCA
1 ATTTGGTA-CTAAAC-TTGACACTTTTTTCTA
5116365 ATTTGGTACTCAAACTTGACACTTTTTTCTA
1 ATTTGGTACT-AAACTTGACACTTTTTTCTA
* * *
5116396 ATTTGATACTAAACTTCACACTTTTTTTATA
1 ATTTGGTACTAAACTTGACAC-TTTTTTCTA
*
5116427 AGTTGGTACTTAAACTT
1 ATTTGGTAC-TAAACTT
5116444 TTTGGGGTCC
Statistics
Matches: 86, Mismatches: 10, Indels: 19
0.75 0.09 0.17
Matches are distributed among these distances:
26 4 0.05
27 19 0.22
30 10 0.12
31 43 0.50
32 10 0.12
ACGTcount: A:0.28, C:0.18, G:0.09, T:0.46
Consensus pattern (30 bp):
ATTTGGTACTAAACTTGACACTTTTTTCTA
Found at i:5116471 original size:90 final size:88
Alignment explanation
Indices: 5116319--5116495 Score: 205
Period size: 90 Copynumber: 2.0 Consensus size: 88
5116309 TTGGTACTTC
* * * *
5116319 AACTTGACACTTTTTTCTAATTTGGTACCTAAACATTTTTTATCCAATTTGGTACTCAAACTTGA
1 AACTTCACACTTTTTTATAAGTTGGTACCTAAACATTTTTGATCCAATTTGGTACTCAAACTTGA
*
5116384 CACTTTTTTCTAATTTGATACTA
66 CACTTTTTCCTAATTTGATACTA
* * *
5116407 AACTTCACACTTTTTTTATAAGTTGGTACTTAAAC-TTTTTGGGGTCCAATTTGGTACAT-GAAC
1 AACTTCACAC-TTTTTTATAAGTTGGTACCTAAACATTTTT--GATCCAATTTGGTAC-TCAAAC
* * *
5116470 TTTACTCTTTTTCCTAATTTGGTACT
62 TTGACACTTTTTCCTAATTTGATACT
5116496 TAATCTTTTT
Statistics
Matches: 74, Mismatches: 11, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
88 14 0.19
89 21 0.28
90 38 0.51
91 1 0.01
ACGTcount: A:0.26, C:0.18, G:0.11, T:0.46
Consensus pattern (88 bp):
AACTTCACACTTTTTTATAAGTTGGTACCTAAACATTTTTGATCCAATTTGGTACTCAAACTTGA
CACTTTTTCCTAATTTGATACTA
Found at i:5116740 original size:28 final size:28
Alignment explanation
Indices: 5116709--5116805 Score: 74
Period size: 28 Copynumber: 3.4 Consensus size: 28
5116699 TCAAGTTCAA
*
5116709 GTACCAAATTGGGTCCAAAAAAGTTTAG
1 GTACCAAATTGGGTCAAAAAAAGTTTAG
* * *
5116737 GTA-CAGAATTAGG--AAAAAGTGTCAAGTTCAA
1 GTACCA-AATTGGGTCAAAAA-----AAGTTTAG
*
5116768 GTACCAAATTGGGTCAAAAAAAATTTAG
1 GTACCAAATTGGGTCAAAAAAAGTTTAG
5116796 GTACCAAATT
1 GTACCAAATT
5116806 AGAAAAAAAT
Statistics
Matches: 52, Mismatches: 8, Indels: 18
0.67 0.10 0.23
Matches are distributed among these distances:
26 4 0.08
27 2 0.04
28 24 0.46
31 15 0.29
32 2 0.04
33 5 0.10
ACGTcount: A:0.43, C:0.12, G:0.20, T:0.25
Consensus pattern (28 bp):
GTACCAAATTGGGTCAAAAAAAGTTTAG
Found at i:5116750 original size:59 final size:59
Alignment explanation
Indices: 5116665--5116835 Score: 254
Period size: 59 Copynumber: 2.9 Consensus size: 59
5116655 ATTGAATCTA
* *
5116665 AAAAAAAGCTTAGGTACCAAAATAGGAAAAAATGTCAAGTTCAAGTACCAAATTGGGTC
1 AAAAAAAGTTTAGGTACCAAATTAGGAAAAAATGTCAAGTTCAAGTACCAAATTGGGTC
* *
5116724 CAAAAAAGTTTAGGTA-CAGAATTAGGAAAAAGTGTCAAGTTCAAGTACCAAATTGGGTC
1 AAAAAAAGTTTAGGTACCA-AATTAGGAAAAAATGTCAAGTTCAAGTACCAAATTGGGTC
* * * *
5116783 AAAAAAAATTTAGGTACCAAATTAGAAAAAAATGCCAAGTTCAGGTACCAAAT
1 AAAAAAAGTTTAGGTACCAAATTAGGAAAAAATGTCAAGTTCAAGTACCAAAT
5116836 GTTATATTAA
Statistics
Matches: 100, Mismatches: 10, Indels: 4
0.88 0.09 0.04
Matches are distributed among these distances:
58 2 0.02
59 96 0.96
60 2 0.02
ACGTcount: A:0.47, C:0.13, G:0.18, T:0.22
Consensus pattern (59 bp):
AAAAAAAGTTTAGGTACCAAATTAGGAAAAAATGTCAAGTTCAAGTACCAAATTGGGTC
Found at i:5117549 original size:37 final size:37
Alignment explanation
Indices: 5117484--5117757 Score: 226
Period size: 37 Copynumber: 7.4 Consensus size: 37
5117474 AATCCTGATT
* * *
5117484 ACACAGGCATGAAGTCTGCTAGGCACATAGCCCGATA
1 ACACCGGCACGAAGCCTGCTAGGCACATAGCCCGATA
*
5117521 ACACCGGCACGAAGCCTGCTAGGCACATAACCCGATA
1 ACACCGGCACGAAGCCTGCTAGGCACATAGCCCGATA
** * *
5117558 ACACCAACATGAAGGCCTGATAGGCACATAGCCCGATA
1 ACACCGGCACGAA-GCCTGCTAGGCACATAGCCCGATA
** * * * *
5117596 ACACTAGCACGAGGGCCTGCTAGGCATAAAGTCCGATA
1 ACACCGGCACGA-AGCCTGCTAGGCACATAGCCCGATA
* * *
5117634 ACATCAGCACGAAGTCTGCTAGGCACATAGCCCGATA
1 ACACCGGCACGAAGCCTGCTAGGCACATAGCCCGATA
* * * * * *
5117671 ACACTGACATGAAGCTTGCTAGGCATGA-AGCCTGATA
1 ACACCGGCACGAAGCCTGCTAGGCA-CATAGCCCGATA
* * * * ** ***
5117708 ACACTGACATGAAGCCTACTAGATACATAGCTTAATA
1 ACACCGGCACGAAGCCTGCTAGGCACATAGCCCGATA
5117745 ACACCGGCACGAA
1 ACACCGGCACGAA
5117758 ACTTGCTAAA
Statistics
Matches: 190, Mismatches: 43, Indels: 8
0.79 0.18 0.03
Matches are distributed among these distances:
36 1 0.01
37 127 0.67
38 62 0.33
ACGTcount: A:0.34, C:0.28, G:0.22, T:0.16
Consensus pattern (37 bp):
ACACCGGCACGAAGCCTGCTAGGCACATAGCCCGATA
Found at i:5117585 original size:38 final size:38
Alignment explanation
Indices: 5117499--5117674 Score: 230
Period size: 38 Copynumber: 4.7 Consensus size: 38
5117489 GGCATGAAGT
*
5117499 CTGCTAGGCACATAGCCCGATAACACCGGCACGAA-GC
1 CTGCTAGGCACATAGCCCGATAACACCAGCACGAAGGC
* * *
5117536 CTGCTAGGCACATAACCCGATAACACCAACATGAAGGC
1 CTGCTAGGCACATAGCCCGATAACACCAGCACGAAGGC
* * *
5117574 CTGATAGGCACATAGCCCGATAACACTAGCACGAGGGC
1 CTGCTAGGCACATAGCCCGATAACACCAGCACGAAGGC
* * * * *
5117612 CTGCTAGGCATAAAGTCCGATAACATCAGCACGAA-GT
1 CTGCTAGGCACATAGCCCGATAACACCAGCACGAAGGC
5117649 CTGCTAGGCACATAGCCCGATAACAC
1 CTGCTAGGCACATAGCCCGATAACAC
5117675 TGACATGAAG
Statistics
Matches: 116, Mismatches: 22, Indels: 2
0.83 0.16 0.01
Matches are distributed among these distances:
37 54 0.47
38 62 0.53
ACGTcount: A:0.33, C:0.31, G:0.22, T:0.14
Consensus pattern (38 bp):
CTGCTAGGCACATAGCCCGATAACACCAGCACGAAGGC
Found at i:5117657 original size:75 final size:74
Alignment explanation
Indices: 5117494--5117695 Score: 246
Period size: 75 Copynumber: 2.7 Consensus size: 74
5117484 ACACAGGCAT
**
5117494 GAAGTCTGCTAGGCACATAGCCCGATAACACCGGCACGAAGCCTGCTAGGCACATAACCCGATAA
1 GAAGTCTGCTAGGCACATAGCCCGATAACACTAGCACGAAGCCTGCTAGGCACATAACCCGATAA
*
5117559 CACCAACAT
66 CACCAACAC
* * * * *
5117568 GAAGGCCTGATAGGCACATAGCCCGATAACACTAGCACGAGGGCCTGCTAGGCATA-AAGTCCGA
1 GAA-GTCTGCTAGGCACATAGCCCGATAACACTAGCACGA-AGCCTGCTAGGCACATAA-CCCGA
* *
5117632 TAACATCAGCAC
63 TAACACCAACAC
* *
5117644 GAAGTCTGCTAGGCACATAGCCCGATAACACT-GACATGAAGCTTGCTAGGCA
1 GAAGTCTGCTAGGCACATAGCCCGATAACACTAG-CACGAAGCCTGCTAGGCA
5117696 TGAAGCCTGA
Statistics
Matches: 109, Mismatches: 15, Indels: 8
0.83 0.11 0.06
Matches are distributed among these distances:
74 15 0.14
75 65 0.60
76 29 0.27
ACGTcount: A:0.33, C:0.29, G:0.23, T:0.15
Consensus pattern (74 bp):
GAAGTCTGCTAGGCACATAGCCCGATAACACTAGCACGAAGCCTGCTAGGCACATAACCCGATAA
CACCAACAC
Found at i:5120069 original size:40 final size:40
Alignment explanation
Indices: 5120025--5120109 Score: 102
Period size: 40 Copynumber: 2.1 Consensus size: 40
5120015 GAAGTATAAA
* * *
5120025 CAGGGGTACA-AATGTGTAAACAG-GAGCACCGAAATGCAAT
1 CAGGGGCACATAA-GTGAAAACAGAG-GCACCGAAATGCAAG
*
5120065 CAGGGGCACATAAGTGAAAACAGAGGCACCGAAGTGCAAG
1 CAGGGGCACATAAGTGAAAACAGAGGCACCGAAATGCAAG
5120105 CAGGG
1 CAGGG
5120110 ATACCGAAAT
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
40 36 0.92
41 3 0.08
ACGTcount: A:0.39, C:0.19, G:0.32, T:0.11
Consensus pattern (40 bp):
CAGGGGCACATAAGTGAAAACAGAGGCACCGAAATGCAAG
Found at i:5120073 original size:20 final size:20
Alignment explanation
Indices: 5120042--5120163 Score: 64
Period size: 20 Copynumber: 6.1 Consensus size: 20
5120032 ACAAATGTGT
*
5120042 AAACAGGAGCACCGAAATGC
1 AAACAGGGGCACCGAAATGC
* ** * *
5120062 AATCAGGGGCACATAAGTGA
1 AAACAGGGGCACCGAAATGC
* *
5120082 AAACAGAGGCACCGAAGTGC
1 AAACAGGGGCACCGAAATGC
* ** *
5120102 AAGCAGGGATACCGAAATGT
1 AAACAGGGGCACCGAAATGC
* * * ***
5120122 ATACGGGGGCACAGTTGTGC
1 AAACAGGGGCACCGAAATGC
* *
5120142 AAACAAGGGCACCGAAGTGC
1 AAACAGGGGCACCGAAATGC
5120162 AA
1 AA
5120164 TTAGAGACAC
Statistics
Matches: 69, Mismatches: 33, Indels: 0
0.68 0.32 0.00
Matches are distributed among these distances:
20 69 1.00
ACGTcount: A:0.39, C:0.20, G:0.30, T:0.11
Consensus pattern (20 bp):
AAACAGGGGCACCGAAATGC
Found at i:5123198 original size:25 final size:25
Alignment explanation
Indices: 5123170--5123220 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
5123160 TGGGTTAAAC
*
5123170 TAATTAAATTAAATCAATTAATTAA
1 TAATTAAATTAAACCAATTAATTAA
* * *
5123195 TAATTTAATTAACCCAATTTATTAA
1 TAATTAAATTAAACCAATTAATTAA
5123220 T
1 T
5123221 GAAATAGTTC
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.49, C:0.08, G:0.00, T:0.43
Consensus pattern (25 bp):
TAATTAAATTAAACCAATTAATTAA
Found at i:5124577 original size:12 final size:12
Alignment explanation
Indices: 5124560--5124592 Score: 57
Period size: 12 Copynumber: 2.8 Consensus size: 12
5124550 CGAATCTTGC
5124560 TTTTATTTTCCT
1 TTTTATTTTCCT
*
5124572 TTTTATTTTCTT
1 TTTTATTTTCCT
5124584 TTTTATTTT
1 TTTTATTTT
5124593 ATGCTCTTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.09, C:0.09, G:0.00, T:0.82
Consensus pattern (12 bp):
TTTTATTTTCCT
Found at i:5125042 original size:12 final size:12
Alignment explanation
Indices: 5125025--5125049 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
5125015 CAAATGAAAT
5125025 TTATAACGATGA
1 TTATAACGATGA
5125037 TTATAACGATGA
1 TTATAACGATGA
5125049 T
1 T
5125050 ATTTATGAAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.40, C:0.08, G:0.16, T:0.36
Consensus pattern (12 bp):
TTATAACGATGA
Found at i:5129638 original size:21 final size:23
Alignment explanation
Indices: 5129588--5129638 Score: 61
Period size: 24 Copynumber: 2.3 Consensus size: 23
5129578 TCTCTTAAAA
*
5129588 ATGGAGAAATAAGGAAGGTGAGAG
1 ATGGAGAAATAAAGAAGGT-AGAG
*
5129612 AAGGAGAAATAAAG-AGGT-GAG
1 ATGGAGAAATAAAGAAGGTAGAG
5129633 ATGGAG
1 ATGGAG
5129639 TGGGACATAA
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
21 8 0.33
23 4 0.17
24 12 0.50
ACGTcount: A:0.47, C:0.00, G:0.41, T:0.12
Consensus pattern (23 bp):
ATGGAGAAATAAAGAAGGTAGAG
Found at i:5134594 original size:9 final size:9
Alignment explanation
Indices: 5134573--5134611 Score: 71
Period size: 9 Copynumber: 4.4 Consensus size: 9
5134563 ATTTAAAAAT
5134573 AAAATAT-A
1 AAAATATAA
5134581 AAAATATAA
1 AAAATATAA
5134590 AAAATATAA
1 AAAATATAA
5134599 AAAATATAA
1 AAAATATAA
5134608 AAAA
1 AAAA
5134612 ATTCCAAAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
8 7 0.23
9 23 0.77
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (9 bp):
AAAATATAA
Found at i:5134803 original size:14 final size:15
Alignment explanation
Indices: 5134784--5134817 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
5134774 ATATTTTTAA
*
5134784 TATTTTTTAA-ATTT
1 TATTTTTTAATAATT
5134798 TATTTTTTAATAATT
1 TATTTTTTAATAATT
5134813 TATTT
1 TATTT
5134818 GCTTTGAACC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 10 0.56
15 8 0.44
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (15 bp):
TATTTTTTAATAATT
Found at i:5135369 original size:28 final size:29
Alignment explanation
Indices: 5135291--5135371 Score: 78
Period size: 28 Copynumber: 2.8 Consensus size: 29
5135281 GGAGAATCAA
* *
5135291 AAATTTTATATAAAAAAATA-CAAGGACT
1 AAATTTTAAATAAAAAAATATAAAGGACT
** *
5135319 AAATATTTCAAA-ACTATAATATAAAGG-CT
1 AAAT-TTT-AAATAAAAAAATATAAAGGACT
5135348 AAATTTTAAATAAAAAAATATAAA
1 AAATTTTAAATAAAAAAATATAAA
5135372 AAACTTTGAA
Statistics
Matches: 41, Mismatches: 8, Indels: 8
0.72 0.14 0.14
Matches are distributed among these distances:
27 3 0.07
28 17 0.41
29 15 0.37
30 6 0.15
ACGTcount: A:0.59, C:0.06, G:0.05, T:0.30
Consensus pattern (29 bp):
AAATTTTAAATAAAAAAATATAAAGGACT
Found at i:5135777 original size:16 final size:16
Alignment explanation
Indices: 5135756--5135793 Score: 67
Period size: 16 Copynumber: 2.4 Consensus size: 16
5135746 TAAATGATGT
5135756 TTCCTTCCCCAAAGAC
1 TTCCTTCCCCAAAGAC
*
5135772 TTCCTTCCCCAAGGAC
1 TTCCTTCCCCAAAGAC
5135788 TTCCTT
1 TTCCTT
5135794 TGCCCTGCAC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.18, C:0.42, G:0.08, T:0.32
Consensus pattern (16 bp):
TTCCTTCCCCAAAGAC
Found at i:5139499 original size:15 final size:15
Alignment explanation
Indices: 5139479--5139515 Score: 74
Period size: 15 Copynumber: 2.5 Consensus size: 15
5139469 ATACGGGGTG
5139479 GAAGCATTCAAAGCC
1 GAAGCATTCAAAGCC
5139494 GAAGCATTCAAAGCC
1 GAAGCATTCAAAGCC
5139509 GAAGCAT
1 GAAGCAT
5139516 CATTACAAAC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.41, C:0.24, G:0.22, T:0.14
Consensus pattern (15 bp):
GAAGCATTCAAAGCC
Found at i:5142708 original size:19 final size:18
Alignment explanation
Indices: 5142660--5142709 Score: 52
Period size: 19 Copynumber: 2.8 Consensus size: 18
5142650 TTACCATAAC
5142660 TTATTTATAAAAAA-TAA
1 TTATTTATAAAAAATTAA
*
5142677 -T-TTTAGAAAAAAATTATA
1 TTATTTA-TAAAAAATTA-A
5142695 TTATTTATAAAAAAT
1 TTATTTATAAAAAAT
5142710 GCTATAGAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 8
0.72 0.06 0.22
Matches are distributed among these distances:
15 4 0.15
16 7 0.27
17 2 0.08
18 1 0.04
19 8 0.31
20 4 0.15
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (18 bp):
TTATTTATAAAAAATTAA
Found at i:5143282 original size:21 final size:21
Alignment explanation
Indices: 5143243--5143283 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
5143233 ATAATTATTT
5143243 TAAATTTTTATGATATAAAAA
1 TAAATTTTTATGATATAAAAA
*
5143264 TAAATATTTTAT-ATTTAAAA
1 TAAAT-TTTTATGATATAAAA
5143284 TAGTGAAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 12 0.67
22 6 0.33
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.46
Consensus pattern (21 bp):
TAAATTTTTATGATATAAAAA
Found at i:5168596 original size:11 final size:11
Alignment explanation
Indices: 5168580--5168610 Score: 55
Period size: 10 Copynumber: 2.9 Consensus size: 11
5168570 TTCTAAATTT
5168580 GAAAAATTATA
1 GAAAAATTATA
5168591 GAAAAA-TATA
1 GAAAAATTATA
5168601 GAAAAATTAT
1 GAAAAATTAT
5168611 TAGAGACTGA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
10 10 0.53
11 9 0.47
ACGTcount: A:0.65, C:0.00, G:0.10, T:0.26
Consensus pattern (11 bp):
GAAAAATTATA
Found at i:5169103 original size:25 final size:25
Alignment explanation
Indices: 5169084--5169211 Score: 160
Period size: 23 Copynumber: 5.4 Consensus size: 25
5169074 AGCACGTCTC
5169084 GTGCTCTCTGTTATTAGCACTGTGT
1 GTGCTCTCTGTTATTAGCACTGTGT
*
5169109 ATGCTCTCTGTTATTAGCACTGTGT
1 GTGCTCTCTGTTATTAGCACTGTGT
*
5169134 GTGCTCTCTG--ATTAGCACTTTGT
1 GTGCTCTCTGTTATTAGCACTGTGT
* * *
5169157 GTGCTTTCTG--ATTAGTACTTTGT
1 GTGCTCTCTGTTATTAGCACTGTGT
*
5169180 GTACTCTCTG-T-TTAGCACTGTGT
1 GTGCTCTCTGTTATTAGCACTGTGT
5169203 GTGCTCTCT
1 GTGCTCTCT
5169212 ATTGCCCAGC
Statistics
Matches: 92, Mismatches: 10, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
23 59 0.64
25 33 0.36
ACGTcount: A:0.12, C:0.20, G:0.22, T:0.45
Consensus pattern (25 bp):
GTGCTCTCTGTTATTAGCACTGTGT
Found at i:5169187 original size:46 final size:47
Alignment explanation
Indices: 5169066--5169211 Score: 154
Period size: 46 Copynumber: 3.1 Consensus size: 47
5169056 CTAGCGCGCG
* * *
5169066 CTCTGT-TTAGCAC-GTCTCGTGCTCTCTGTTATTAGCACTGTGTATGCT
1 CTCTGTATTAGCACTGTGT-GTACTCTCTG--ATTAGCACTGTGTGTGCT
* *
5169114 CTCTGTTATTAGCACTGTGTGTGCTCTCTGATTAGCACTTTGTGTGCT
1 CTCTG-TATTAGCACTGTGTGTACTCTCTGATTAGCACTGTGTGTGCT
* * * *
5169162 TTCTG-ATTAGTACTTTGTGTACTCTCTGTTTAGCACTGTGTGTGCT
1 CTCTGTATTAGCACTGTGTGTACTCTCTGATTAGCACTGTGTGTGCT
5169208 CTCT
1 CTCT
5169212 ATTGCCCAGC
Statistics
Matches: 85, Mismatches: 10, Indels: 8
0.83 0.10 0.08
Matches are distributed among these distances:
46 39 0.46
48 25 0.29
49 1 0.01
50 17 0.20
51 3 0.04
ACGTcount: A:0.12, C:0.22, G:0.21, T:0.45
Consensus pattern (47 bp):
CTCTGTATTAGCACTGTGTGTACTCTCTGATTAGCACTGTGTGTGCT
Found at i:5169253 original size:69 final size:69
Alignment explanation
Indices: 5169084--5169261 Score: 193
Period size: 69 Copynumber: 2.5 Consensus size: 69
5169074 AGCACGTCTC
* * * *
5169084 GTGCTCTCTGTTATTAGCACTGTGTATGCTCTCTGTTATTAGCACTGTGTGTGCTCTCTGATTAG
1 GTGCTCTCTG--ATTAGTACTTTGTGTACTCTCTG-T-TTAGCACTGTGTGTGCTCTCTGATTAG
*
5169149 CACTTTGT
62 CACTTTAT
*
5169157 GTGCTTTCTGATTAGTACTTTGTGTACTCTCTGTTTAGCACTGTGTGTGCTCTCT-ATTGCCCAG
1 GTGCTCTCTGATTAGTACTTTGTGTACTCTCTGTTTAGCACTGTGTGTGCTCTCTGATT----AG
5169221 CAC-TTAT
62 CACTTTAT
*
5169228 GTGCTCTCTG-TTAGTACTTTG-GTACTCTTTGTTT
1 GTGCTCTCTGATTAGTACTTTGTGTACTCTCTGTTT
5169262 GTTCCGTATA
Statistics
Matches: 93, Mismatches: 8, Indels: 12
0.82 0.07 0.11
Matches are distributed among these distances:
68 3 0.03
69 33 0.35
70 12 0.13
71 31 0.33
72 5 0.05
73 9 0.10
ACGTcount: A:0.13, C:0.21, G:0.21, T:0.46
Consensus pattern (69 bp):
GTGCTCTCTGATTAGTACTTTGTGTACTCTCTGTTTAGCACTGTGTGTGCTCTCTGATTAGCACT
TTAT
Found at i:5182407 original size:78 final size:78
Alignment explanation
Indices: 5182263--5182421 Score: 205
Period size: 78 Copynumber: 2.0 Consensus size: 78
5182253 TGAATATTTT
* * *
5182263 AAATACTAAGATTATGTTATTATGCCCCGCAAGAATGATGGTCATGAGAGTAGCAATCTTGAATT
1 AAATACTAAGATTACGTTATTATGCCCCGCAAGAATGATGGTCATGAGAGCAACAATCTTGAATT
**
5182328 GATGATGAC-AAA
66 GACAATGACGAAA
* * * *
5182340 AAATACTAAGATTACGTTATTATGCTCTCGCAAGATTGATGGTC-GGTAGAGCAACAATCTTGGA
1 AAATACTAAGATTACGTTATTATGC-CCCGCAAGAATGATGGTCATG-AGAGCAACAATCTTGAA
5182404 TTGACAATGACGAAA
64 TTGACAATGACGAAA
5182419 AAA
1 AAA
5182422 GCACGAACAG
Statistics
Matches: 70, Mismatches: 9, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
77 25 0.36
78 39 0.56
79 6 0.09
ACGTcount: A:0.38, C:0.14, G:0.21, T:0.28
Consensus pattern (78 bp):
AAATACTAAGATTACGTTATTATGCCCCGCAAGAATGATGGTCATGAGAGCAACAATCTTGAATT
GACAATGACGAAA
Found at i:5194400 original size:29 final size:29
Alignment explanation
Indices: 5194320--5194399 Score: 99
Period size: 29 Copynumber: 2.7 Consensus size: 29
5194310 ATCTTAGAAC
5194320 TATACATGAATTTT-ATCTTAATGTGTAATTT
1 TATACATGAATTTTGAT-TT--TGTGTAATTT
*
5194351 TATACATGTATTTTGATTTTGTGTAATTT
1 TATACATGAATTTTGATTTTGTGTAATTT
*
5194380 TATACGTGAAATTTTGATTT
1 TATACATG-AATTTTGATTT
5194400 GATTCGATTC
Statistics
Matches: 44, Mismatches: 3, Indels: 5
0.85 0.06 0.10
Matches are distributed among these distances:
29 17 0.39
30 10 0.23
31 15 0.34
32 2 0.05
ACGTcount: A:0.29, C:0.05, G:0.12, T:0.54
Consensus pattern (29 bp):
TATACATGAATTTTGATTTTGTGTAATTT
Found at i:5196490 original size:20 final size:20
Alignment explanation
Indices: 5196429--5196507 Score: 70
Period size: 20 Copynumber: 4.0 Consensus size: 20
5196419 AACCAAAATT
* * *
5196429 TCAATATTTCTAAGGAATTA
1 TCAAAATTTCTAAAGATTTA
*
5196449 TAAAAATTTCTAAAG-TTATA
1 TCAAAATTTCTAAAGATT-TA
* * *
5196469 TCAATATTTTTAAGGATTTA
1 TCAAAATTTCTAAAGATTTA
*
5196489 TCAAAATTTTTAAAGATTT
1 TCAAAATTTCTAAAGATTT
5196508 TTCTAGTGTC
Statistics
Matches: 47, Mismatches: 10, Indels: 4
0.77 0.16 0.07
Matches are distributed among these distances:
19 1 0.02
20 44 0.94
21 2 0.04
ACGTcount: A:0.42, C:0.06, G:0.08, T:0.44
Consensus pattern (20 bp):
TCAAAATTTCTAAAGATTTA
Found at i:5203803 original size:19 final size:19
Alignment explanation
Indices: 5203781--5203818 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
5203771 TTTTTAAAAG
5203781 TATAAATTTTTGGAATTTT
1 TATAAATTTTTGGAATTTT
* *
5203800 TATATATTTTTTGAATTTT
1 TATAAATTTTTGGAATTTT
5203819 GAAAATTATT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.29, C:0.00, G:0.08, T:0.63
Consensus pattern (19 bp):
TATAAATTTTTGGAATTTT
Found at i:5203836 original size:11 final size:12
Alignment explanation
Indices: 5203814--5203842 Score: 51
Period size: 11 Copynumber: 2.5 Consensus size: 12
5203804 TATTTTTTGA
5203814 ATTTTGAAAATT
1 ATTTTGAAAATT
5203826 ATTTT-AAAATT
1 ATTTTGAAAATT
5203837 ATTTTG
1 ATTTTG
5203843 TAATTTTTGT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
11 11 0.69
12 5 0.31
ACGTcount: A:0.38, C:0.00, G:0.07, T:0.55
Consensus pattern (12 bp):
ATTTTGAAAATT
Found at i:5204652 original size:26 final size:26
Alignment explanation
Indices: 5204623--5204673 Score: 93
Period size: 26 Copynumber: 2.0 Consensus size: 26
5204613 CATTGGTTTT
5204623 TTTAACTTTCATTACCCTTAACCAAC
1 TTTAACTTTCATTACCCTTAACCAAC
*
5204649 TTTAACTTTTATTACCCTTAACCAA
1 TTTAACTTTCATTACCCTTAACCAA
5204674 ATAATGATGA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.31, C:0.27, G:0.00, T:0.41
Consensus pattern (26 bp):
TTTAACTTTCATTACCCTTAACCAAC
Found at i:5205988 original size:24 final size:24
Alignment explanation
Indices: 5205959--5206010 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
5205949 TTTCTAGAAG
* *
5205959 ATTTAATATTTATTAGTATAATAT
1 ATTTAACATTTATTAGCATAATAT
*
5205983 ATTTAACATTTATTAGCATAATTT
1 ATTTAACATTTATTAGCATAATAT
5206007 ATTT
1 ATTT
5206011 GACCTACAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.38, C:0.04, G:0.04, T:0.54
Consensus pattern (24 bp):
ATTTAACATTTATTAGCATAATAT
Found at i:5207961 original size:24 final size:24
Alignment explanation
Indices: 5207927--5207978 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
5207917 TTTCTAAAAG
*
5207927 ATTTAATATTTATTAATATAATAT
1 ATTTAACATTTATTAATATAATAT
* *
5207951 ATTTAACATTTATTAGTATAATTT
1 ATTTAACATTTATTAATATAATAT
5207975 ATTT
1 ATTT
5207979 GACCTACAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.56
Consensus pattern (24 bp):
ATTTAACATTTATTAATATAATAT
Found at i:5210673 original size:23 final size:24
Alignment explanation
Indices: 5210647--5210698 Score: 63
Period size: 23 Copynumber: 2.2 Consensus size: 24
5210637 AAAAATCTAA
5210647 AAAAACAC-TAAAAC-AAAACCCCT
1 AAAAAC-CTTAAAACTAAAACCCCT
**
5210670 AAAAACCTTAAAACTAAAATTCCT
1 AAAAACCTTAAAACTAAAACCCCT
5210694 AAAAA
1 AAAAA
5210699 AAACCGTAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
22 1 0.04
23 12 0.48
24 12 0.48
ACGTcount: A:0.62, C:0.23, G:0.00, T:0.15
Consensus pattern (24 bp):
AAAAACCTTAAAACTAAAACCCCT
Found at i:5214520 original size:28 final size:27
Alignment explanation
Indices: 5214476--5214531 Score: 67
Period size: 28 Copynumber: 2.0 Consensus size: 27
5214466 CTTGAACTTG
** *
5214476 ATATTTTTTTCTTAATTTAGTACTTAA
1 ATATTTTTTTCCCAATTTAGTACCTAA
*
5214503 ATATTTTTTTACCCAATTTTGTACCTAA
1 ATATTTTTTT-CCCAATTTAGTACCTAA
5214531 A
1 A
5214532 CTTGACACTT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
27 10 0.42
28 14 0.58
ACGTcount: A:0.30, C:0.12, G:0.04, T:0.54
Consensus pattern (27 bp):
ATATTTTTTTCCCAATTTAGTACCTAA
Found at i:5214592 original size:27 final size:26
Alignment explanation
Indices: 5214540--5214592 Score: 61
Period size: 27 Copynumber: 2.0 Consensus size: 26
5214530 AACTTGACAC
* *
5214540 TTTTTCCTAATTTGATACTTAAACTT
1 TTTTTCCCAATTTGATACATAAACTT
* *
5214566 TTTTTACCCAATTTGGTACATACACTT
1 TTTTT-CCCAATTTGATACATAAACTT
5214593 GATATTTTTT
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
26 5 0.23
27 17 0.77
ACGTcount: A:0.26, C:0.19, G:0.06, T:0.49
Consensus pattern (26 bp):
TTTTTCCCAATTTGATACATAAACTT
Found at i:5214626 original size:59 final size:58
Alignment explanation
Indices: 5214458--5214630 Score: 199
Period size: 59 Copynumber: 2.9 Consensus size: 58
5214448 TTAATATAAT
* *
5214458 ATTTGGTACTTGAACTTGATATTTTTTTCTTAATTT-AGTACTTAAATATTTTTTTACCCA
1 ATTTGGTACAT-AACTTGATATTTTTTTCTTAATTTGA-TACTTAAA-CTTTTTTTACCCA
* * * * *
5214518 ATTTTGTACCTAAACTTGACA-CTTTTTCCTAATTTGATACTTAAACTTTTTTTACCCA
1 ATTTGGTACAT-AACTTGATATTTTTTTCTTAATTTGATACTTAAACTTTTTTTACCCA
*
5214576 ATTTGGTACATACACTTGATATTTTTTTCTTAATTTGATA-TCTAAGCTTTTTTTA
1 ATTTGGTACATA-ACTTGATATTTTTTTCTTAATTTGATACT-TAAACTTTTTTTA
5214631 ATATTCAATT
Statistics
Matches: 96, Mismatches: 13, Indels: 9
0.81 0.11 0.08
Matches are distributed among these distances:
57 1 0.01
58 29 0.30
59 48 0.50
60 18 0.19
ACGTcount: A:0.27, C:0.14, G:0.08, T:0.51
Consensus pattern (58 bp):
ATTTGGTACATAACTTGATATTTTTTTCTTAATTTGATACTTAAACTTTTTTTACCCA
Found at i:5214892 original size:31 final size:31
Alignment explanation
Indices: 5214852--5214930 Score: 88
Period size: 31 Copynumber: 2.5 Consensus size: 31
5214842 GGATCTCAAA
* * *
5214852 AAGTATAAGTACTAACTTA-AAAAAAAGTGTC
1 AAGTTTAAGTACCAAATTAGAAAAAAA-TGTC
* *
5214883 AAGTTTAAGTACCAAATTAGGAAAAAATGTT
1 AAGTTTAAGTACCAAATTAGAAAAAAATGTC
*
5214914 AAGTTTGAGTACCAAAT
1 AAGTTTAAGTACCAAAT
5214931 ATAATATTAA
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
31 35 0.85
32 6 0.15
ACGTcount: A:0.48, C:0.09, G:0.15, T:0.28
Consensus pattern (31 bp):
AAGTTTAAGTACCAAATTAGAAAAAAATGTC
Found at i:5216486 original size:96 final size:96
Alignment explanation
Indices: 5216313--5216493 Score: 222
Period size: 96 Copynumber: 1.9 Consensus size: 96
5216303 AGGATGTTCA
** * * * * *
5216313 ATTATCTCGATTTAAAGAAAGGTTGCACCTAGTGAGTTAAGGTGCAAATTTTCAGAATCGGAGAT
1 ATTATCTCGATTTAAAGAAAAATTGCACCTAGTGAGTTAAGGTACAAAATTTCAAAATCGAAAAT
*
5216378 AAGGAAACATTGCCTCGATTAAGGATATTTG
66 AAAGAAACATTGCCTCGATTAAGGATATTTG
* * *
5216409 ATTATTTCGATTTGAAGAAAAATTGTACCTAGTGAGTTAAGGTACAAAATTTCAAAACTC-AAAA
1 ATTATCTCGATTTAAAGAAAAATTGCACCTAGTGAGTTAAGGTACAAAATTTCAAAA-TCGAAAA
*
5216473 TAAA-AGAATATTGCCTCGATT
65 TAAAGA-AACATTGCCTCGATT
5216494 TTAAAGTTTT
Statistics
Matches: 71, Mismatches: 12, Indels: 4
0.82 0.14 0.05
Matches are distributed among these distances:
95 1 0.01
96 68 0.96
97 2 0.03
ACGTcount: A:0.38, C:0.12, G:0.19, T:0.31
Consensus pattern (96 bp):
ATTATCTCGATTTAAAGAAAAATTGCACCTAGTGAGTTAAGGTACAAAATTTCAAAATCGAAAAT
AAAGAAACATTGCCTCGATTAAGGATATTTG
Found at i:5216891 original size:29 final size:29
Alignment explanation
Indices: 5216857--5216950 Score: 86
Period size: 29 Copynumber: 3.3 Consensus size: 29
5216847 TCAAAAACGG
5216857 AATTTTTGGACACTCGGGGGTAAAATGGT
1 AATTTTTGGACACTCGGGGGTAAAATGGT
* *
5216886 AATTTTT-GAAAGCTTC-GGGTTAAAATGG-
1 AATTTTTGGACA-C-TCGGGGGTAAAATGGT
* * * **
5216914 AGTTTTTGGACATTTGGGGGTAAAATCAT
1 AATTTTTGGACACTCGGGGGTAAAATGGT
5216943 AATTTTTG
1 AATTTTTG
5216951 AAAGTTTTGG
Statistics
Matches: 50, Mismatches: 10, Indels: 10
0.71 0.14 0.14
Matches are distributed among these distances:
27 1 0.02
28 18 0.36
29 29 0.58
30 2 0.04
ACGTcount: A:0.29, C:0.07, G:0.27, T:0.37
Consensus pattern (29 bp):
AATTTTTGGACACTCGGGGGTAAAATGGT
Found at i:5216962 original size:29 final size:28
Alignment explanation
Indices: 5216873--5217130 Score: 141
Period size: 30 Copynumber: 8.8 Consensus size: 28
5216863 TGGACACTCG
* * *
5216873 GGGGTAAAATGGTAATTTTTGAAAGCTTC
1 GGGGTAAAAT-ATAATTTTTGAAAGTTTT
* ** * * *
5216902 GGGTTAAAATGGAGTTTTTGGACA-TTTG
1 GGGGTAAAATATAATTTTT-GAAAGTTTT
5216930 GGGGTAAAATCATAATTTTTGAAAGTTTT
1 GGGGTAAAAT-ATAATTTTTGAAAGTTTT
* * *
5216959 GGGGTCAAAAATAGAATTTTTGGAAGTTTG
1 GGGGT--AAAATATAATTTTTGAAAGTTTT
*
5216989 GGGGTAAAA-ATGGAATTTTTGGAAGTTTT
1 GGGGTAAAATAT--AATTTTTGAAAGTTTT
* *
5217018 AGGGTCAAAA-ATGGAATTTTTGGAAG-TTT
1 GGGGT-AAAATAT--AATTTTTGAAAGTTTT
5217047 GAGGGTAAAA-ATGGAATTTTT-AGAAGTTTT
1 G-GGGTAAAATAT--AATTTTTGA-AAGTTTT
* * * *
5217077 GAGGTTAAAAATGTAATTTTGGAGAAGTTTG
1 G-GGGT-AAAATATAATTTTTGA-AAGTTTT
5217108 GGGGTCAAAATATAATTTTTGAA
1 GGGGT-AAAATATAATTTTTGAA
5217131 CAATTTAGGG
Statistics
Matches: 187, Mismatches: 28, Indels: 28
0.77 0.12 0.12
Matches are distributed among these distances:
27 1 0.01
28 25 0.13
29 67 0.36
30 75 0.40
31 18 0.10
32 1 0.01
ACGTcount: A:0.33, C:0.03, G:0.28, T:0.36
Consensus pattern (28 bp):
GGGGTAAAATATAATTTTTGAAAGTTTT
Found at i:5216962 original size:30 final size:29
Alignment explanation
Indices: 5216926--5217130 Score: 155
Period size: 30 Copynumber: 6.9 Consensus size: 29
5216916 TTTTTGGACA
5216926 TTTGGGGGT-AAAATCATAATTTTTGAAAG
1 TTTGGGGGTCAAAAT-ATAATTTTTGAAAG
* * *
5216955 TTTTGGGGTCAAAAATAGAATTTTTGGAAG
1 TTTGGGGGTC-AAAATATAATTTTTGAAAG
* ** *
5216985 TTTGGGGGTAAAAATGGAATTTTTGGAAG
1 TTTGGGGGTCAAAATATAATTTTTGAAAG
** *
5217014 TTTTAGGGTCAAAA-ATGGAATTTTTGGAAG
1 TTTGGGGGTCAAAATAT--AATTTTTGAAAG
* * **
5217044 TTTGAGGGTAAAAATGGAATTTTT-AGAAG
1 TTTGGGGGTCAAAATATAATTTTTGA-AAG
* * * * *
5217073 TTTTGAGGTTAAAAATGTAATTTTGGAGAAG
1 -TTTGGGGGTCAAAATATAATTTTTGA-AAG
5217104 TTTGGGGGTCAAAATATAATTTTTGAA
1 TTTGGGGGTCAAAATATAATTTTTGAA
5217131 CAATTTAGGG
Statistics
Matches: 144, Mismatches: 24, Indels: 16
0.78 0.13 0.09
Matches are distributed among these distances:
29 48 0.33
30 86 0.60
31 10 0.07
ACGTcount: A:0.34, C:0.02, G:0.27, T:0.37
Consensus pattern (29 bp):
TTTGGGGGTCAAAATATAATTTTTGAAAG
Found at i:5216995 original size:59 final size:58
Alignment explanation
Indices: 5216847--5217130 Score: 276
Period size: 59 Copynumber: 4.8 Consensus size: 58
5216837 AAAATCGAGA
* * * * * *
5216847 TCAAAAACGGAATTTTTGGACA-CTCGGGGGTAAAATGGTAATTTTTGAAAG-CTTCGGG
1 TCAAAAATGGAATTTTTGGA-AGTTTGGGGGTAAAAT-ATAATTTTTGAAAGTTTTGGGG
* *
5216905 T-TAAAATGGAGTTTTTGGACA-TTTGGGGGTAAAATCATAATTTTTGAAAGTTTTGGGG
1 TCAAAAATGGAATTTTTGGA-AGTTTGGGGGTAAAAT-ATAATTTTTGAAAGTTTTGGGG
* * *
5216963 TCAAAAATAGAATTTTTGGAAGTTTGGGGGTAAAA-ATGGAATTTTTGGAAGTTTTAGGG
1 TCAAAAATGGAATTTTTGGAAGTTTGGGGGTAAAATAT--AATTTTTGAAAGTTTTGGGG
* *
5217022 TCAAAAATGGAATTTTTGGAAGTTTGAGGGTAAAA-ATGGAATTTTT-AGAAGTTTTGAGG
1 TCAAAAATGGAATTTTTGGAAGTTTGGGGGTAAAATAT--AATTTTTGA-AAGTTTTGGGG
* * *
5217081 TTAAAAATGTAATTTTGGAGAAGTTTGGGGGTCAAAATATAATTTTTGAA
1 TCAAAAATGGAATTTTTG-GAAGTTTGGGGGT-AAAATATAATTTTTGAA
5217131 CAATTTAGGG
Statistics
Matches: 193, Mismatches: 23, Indels: 18
0.82 0.10 0.08
Matches are distributed among these distances:
57 44 0.23
58 8 0.04
59 114 0.59
60 20 0.10
61 5 0.03
62 2 0.01
ACGTcount: A:0.33, C:0.04, G:0.27, T:0.36
Consensus pattern (58 bp):
TCAAAAATGGAATTTTTGGAAGTTTGGGGGTAAAATATAATTTTTGAAAGTTTTGGGG
Found at i:5218185 original size:18 final size:17
Alignment explanation
Indices: 5218162--5218195 Score: 59
Period size: 18 Copynumber: 1.9 Consensus size: 17
5218152 TTTTTTTTTA
5218162 ATTAATATTATTATAATT
1 ATTAATATTATT-TAATT
5218180 ATTAATATTATTTAAT
1 ATTAATATTATTTAAT
5218196 AATAACATTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 4 0.25
18 12 0.75
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (17 bp):
ATTAATATTATTTAATT
Found at i:5218900 original size:14 final size:14
Alignment explanation
Indices: 5218864--5218905 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
5218854 TTCAATGTGT
5218864 AATTTATTTAA--A
1 AATTTATTTAATTA
* *
5218876 ATTTTAATTAATTA
1 AATTTATTTAATTA
5218890 AATTTATTTAATTA
1 AATTTATTTAATTA
5218904 AA
1 AA
5218906 ATCTATTTTC
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
12 9 0.38
14 15 0.62
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (14 bp):
AATTTATTTAATTA
Found at i:5220213 original size:21 final size:21
Alignment explanation
Indices: 5220180--5220220 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
5220170 GAACCATAAC
**
5220180 CTTAAACTTTAAACCCCAAAT
1 CTTAAACCCTAAACCCCAAAT
*
5220201 CTTAAACCCTAAATCCCAAA
1 CTTAAACCCTAAACCCCAAA
5220221 CTTCAAATCC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.44, C:0.32, G:0.00, T:0.24
Consensus pattern (21 bp):
CTTAAACCCTAAACCCCAAAT
Found at i:5221551 original size:7 final size:6
Alignment explanation
Indices: 5221531--5221574 Score: 52
Period size: 6 Copynumber: 7.0 Consensus size: 6
5221521 CAAGATTTAA
* *
5221531 AGTTCG AGTTTG AGATTTG AGGTTTG GGTTTG AGTTTG AGTTTG
1 AGTTTG AGTTTG AG-TTTG A-GTTTG AGTTTG AGTTTG AGTTTG
5221575 GGGTTCAAGA
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
6 23 0.70
7 9 0.27
8 1 0.03
ACGTcount: A:0.16, C:0.02, G:0.36, T:0.45
Consensus pattern (6 bp):
AGTTTG
Found at i:5221579 original size:19 final size:20
Alignment explanation
Indices: 5221538--5221576 Score: 64
Period size: 18 Copynumber: 2.0 Consensus size: 20
5221528 TAAAGTTCGA
5221538 GTTTGAGATTTGAGGTTTGG
1 GTTTGAGATTTGAGGTTTGG
5221558 GTTTGAG-TTTGA-GTTTGG
1 GTTTGAGATTTGAGGTTTGG
5221576 G
1 G
5221577 GTTCAAGATT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 7 0.37
19 5 0.26
20 7 0.37
ACGTcount: A:0.13, C:0.00, G:0.41, T:0.46
Consensus pattern (20 bp):
GTTTGAGATTTGAGGTTTGG
Found at i:5222715 original size:23 final size:23
Alignment explanation
Indices: 5222688--5222734 Score: 85
Period size: 23 Copynumber: 2.0 Consensus size: 23
5222678 GTTCCTCCAA
5222688 GCATCTGATCTGTTGTTGAGTAC
1 GCATCTGATCTGTTGTTGAGTAC
*
5222711 GCATCTGATCTTTTGTTGAGTAC
1 GCATCTGATCTGTTGTTGAGTAC
5222734 G
1 G
5222735 AGATTCTTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.17, C:0.17, G:0.26, T:0.40
Consensus pattern (23 bp):
GCATCTGATCTGTTGTTGAGTAC
Found at i:5223238 original size:20 final size:18
Alignment explanation
Indices: 5223200--5223247 Score: 69
Period size: 20 Copynumber: 2.6 Consensus size: 18
5223190 TTTAAATTGG
5223200 TTTAAATTTATTCTTAAA
1 TTTAAATTTATTCTTAAA
*
5223218 TTTAAATTTATCTTTTTAAA
1 TTTAAATTTA--TTCTTAAA
5223238 TTTAAATTTA
1 TTTAAATTTA
5223248 ATTAAATTTG
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
18 10 0.37
20 17 0.63
ACGTcount: A:0.38, C:0.04, G:0.00, T:0.58
Consensus pattern (18 bp):
TTTAAATTTATTCTTAAA
Found at i:5223268 original size:16 final size:17
Alignment explanation
Indices: 5223200--5223269 Score: 63
Period size: 16 Copynumber: 4.0 Consensus size: 17
5223190 TTTAAATTGG
*
5223200 TTTAAATTTATTCTTAAA
1 TTTAAATTTAAT-TTAAA
*
5223218 TTTAAATTTATCTTTTTAAA
1 TTTAAATTTA---ATTTAAA
5223238 TTTAAATTTAA-TTAAA
1 TTTAAATTTAATTTAAA
*
5223254 TTTGAA-TTAATTTAAA
1 TTTAAATTTAATTTAAA
5223270 ACTTAATATT
Statistics
Matches: 46, Mismatches: 2, Indels: 10
0.79 0.03 0.17
Matches are distributed among these distances:
15 4 0.09
16 15 0.33
18 10 0.22
20 15 0.33
21 2 0.04
ACGTcount: A:0.41, C:0.03, G:0.01, T:0.54
Consensus pattern (17 bp):
TTTAAATTTAATTTAAA
Found at i:5223507 original size:25 final size:25
Alignment explanation
Indices: 5223479--5223531 Score: 61
Period size: 25 Copynumber: 2.1 Consensus size: 25
5223469 GTTGTTGCCT
* *
5223479 ACCAGCTTCAACTTGCTCTGCCACC
1 ACCAACTTCAACCTGCTCTGCCACC
* * *
5223504 ACCAATTTCAACCTGCTTTGCCATC
1 ACCAACTTCAACCTGCTCTGCCACC
5223529 ACC
1 ACC
5223532 GCCACTGCAT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.23, C:0.42, G:0.09, T:0.26
Consensus pattern (25 bp):
ACCAACTTCAACCTGCTCTGCCACC
Found at i:5225212 original size:28 final size:28
Alignment explanation
Indices: 5225115--5225235 Score: 88
Period size: 28 Copynumber: 4.2 Consensus size: 28
5225105 TCAATTTTTC
*
5225115 CCAAAATTACCATTTTACCCCCGAATAT
1 CCAAAATTACCATTTTACCCCCGAGTAT
* ** *
5225143 CTAAAAATT-CCATTTTTGA-CCTTGAACCT-T
1 C-CAAAATTACCA-TTTT-ACCCCCG-A-GTAT
5225173 CCAAGAATTACCATTTT-CCCCTCGAGTAT
1 CCAA-AATTACCATTTTACCCC-CGAGTAT
* *
5225202 CCAAAATTACCGTTTTACCCCCGGGTAT
1 CCAAAATTACCATTTTACCCCCGAGTAT
5225230 CCAAAA
1 CCAAAA
5225236 GTCTCATTTT
Statistics
Matches: 72, Mismatches: 10, Indels: 22
0.69 0.10 0.21
Matches are distributed among these distances:
28 28 0.39
29 27 0.38
30 13 0.18
31 4 0.06
ACGTcount: A:0.31, C:0.30, G:0.08, T:0.31
Consensus pattern (28 bp):
CCAAAATTACCATTTTACCCCCGAGTAT
Found at i:5225245 original size:28 final size:28
Alignment explanation
Indices: 5225172--5225246 Score: 73
Period size: 28 Copynumber: 2.6 Consensus size: 28
5225162 CCTTGAACCT
*
5225172 TCCAAGAATTACCATTTTCCCCTCGAGTA
1 TCCAA-AAGTACCATTTTCCCCTCGAGTA
* * *
5225201 TCCAAAATTACCGTTTTACCCC-CGGGTA
1 TCCAAAAGTACCATTTT-CCCCTCGAGTA
5225229 TCCAAAAGT-CTCATTTTC
1 TCCAAAAGTAC-CATTTTC
5225247 AACTCCGATT
Statistics
Matches: 40, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
27 2 0.05
28 29 0.73
29 9 0.22
ACGTcount: A:0.27, C:0.31, G:0.11, T:0.32
Consensus pattern (28 bp):
TCCAAAAGTACCATTTTCCCCTCGAGTA
Found at i:5226178 original size:5 final size:5
Alignment explanation
Indices: 5226154--5226197 Score: 65
Period size: 5 Copynumber: 9.0 Consensus size: 5
5226144 CGTGACATTT
5226154 TTAAA TTAAA --AAA TTAAAA TTAAA TTAAA TTAAA TTAAA TTAAA
1 TTAAA TTAAA TTAAA TT-AAA TTAAA TTAAA TTAAA TTAAA TTAAA
5226198 ACAATCAAAT
Statistics
Matches: 36, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
3 3 0.08
5 28 0.78
6 5 0.14
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (5 bp):
TTAAA
Found at i:5228870 original size:22 final size:22
Alignment explanation
Indices: 5228845--5228886 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
5228835 TCTATGAATA
*
5228845 TCGAGATCAATTTGACCTGAGT
1 TCGAGATAAATTTGACCTGAGT
*
5228867 TCGAGATAAATTTGAGCTGA
1 TCGAGATAAATTTGACCTGA
5228887 AGCTTGAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.31, C:0.14, G:0.24, T:0.31
Consensus pattern (22 bp):
TCGAGATAAATTTGACCTGAGT
Found at i:5230991 original size:24 final size:23
Alignment explanation
Indices: 5230960--5231007 Score: 78
Period size: 24 Copynumber: 2.0 Consensus size: 23
5230950 TTACGATAGT
5230960 ATAAATATAATTTTATTATTTTA
1 ATAAATATAATTTTATTATTTTA
*
5230983 ATAATATATATTTTTATTATTTTA
1 ATAA-ATATAATTTTATTATTTTA
5231007 A
1 A
5231008 AGAGTTAAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
23 4 0.17
24 19 0.83
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (23 bp):
ATAAATATAATTTTATTATTTTA
Found at i:5234963 original size:30 final size:30
Alignment explanation
Indices: 5234927--5234990 Score: 110
Period size: 30 Copynumber: 2.1 Consensus size: 30
5234917 CAACTTAACA
* *
5234927 AACAAATGTCTCTAAAATAATAATAAAATT
1 AACAAATGCCTCTAAAATAATAACAAAATT
5234957 AACAAATGCCTCTAAAATAATAACAAAATT
1 AACAAATGCCTCTAAAATAATAACAAAATT
5234987 AACA
1 AACA
5234991 TTAAAATAAG
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.58, C:0.14, G:0.03, T:0.25
Consensus pattern (30 bp):
AACAAATGCCTCTAAAATAATAACAAAATT
Found at i:5236227 original size:15 final size:15
Alignment explanation
Indices: 5236207--5236236 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
5236197 TATATATATT
5236207 GAATAAATGGTTGAA
1 GAATAAATGGTTGAA
5236222 GAATAAATGGTTGAA
1 GAATAAATGGTTGAA
5236237 TTGTGAAGTT
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:0.47, C:0.00, G:0.27, T:0.27
Consensus pattern (15 bp):
GAATAAATGGTTGAA
Found at i:5236471 original size:22 final size:22
Alignment explanation
Indices: 5236445--5236496 Score: 86
Period size: 22 Copynumber: 2.4 Consensus size: 22
5236435 AGCTCGTATA
*
5236445 GTGCTCTCCGTTTAGCACGTTT
1 GTGCTCTCCGTTTAGCACCTTT
*
5236467 GTGCTCCCCGTTTAGCACCTTT
1 GTGCTCTCCGTTTAGCACCTTT
5236489 GTGCTCTC
1 GTGCTCTC
5236497 TGTTCATTAG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.08, C:0.33, G:0.21, T:0.38
Consensus pattern (22 bp):
GTGCTCTCCGTTTAGCACCTTT
Found at i:5239055 original size:25 final size:23
Alignment explanation
Indices: 5238984--5239132 Score: 151
Period size: 23 Copynumber: 6.5 Consensus size: 23
5238974 GAACGCTAGC
* *
5238984 GTGCTTACCG-TTCAGCACTGTGT
1 GTGCTTACTGTTTC-GCACTTTGT
5239007 GTGCTTACTGTTTCGCACTTTGT
1 GTGCTTACTGTTTCGCACTTTGT
5239030 GTGCTTACTGTTTCGCACTTTGT
1 GTGCTTACTGTTTCGCACTTTGT
* * *
5239053 GTGCCTACTGTTCCGCACTTCGT
1 GTGCTTACTGTTTCGCACTTTGT
* * *
5239076 GTGCCTACTGATTT-GCGCTATGT
1 GTGCTTACTG-TTTCGCACTTTGT
* * * *
5239099 GCGCCTACTGATT-GCACTGTGT
1 GTGCTTACTGTTTCGCACTTTGT
5239121 GTGCTTACTGTT
1 GTGCTTACTGTT
5239133 AAGTACTTCG
Statistics
Matches: 108, Mismatches: 16, Indels: 5
0.84 0.12 0.04
Matches are distributed among these distances:
22 18 0.17
23 85 0.79
24 5 0.05
ACGTcount: A:0.11, C:0.25, G:0.24, T:0.40
Consensus pattern (23 bp):
GTGCTTACTGTTTCGCACTTTGT
Found at i:5251981 original size:22 final size:22
Alignment explanation
Indices: 5251939--5252004 Score: 87
Period size: 22 Copynumber: 3.0 Consensus size: 22
5251929 TCTGTTTATT
*
5251939 AGCACGTATAGTGCTCTCCGTTG
1 AGCACGT-TTGTGCTCTCCGTTG
* *
5251962 AGCACGTTTGTGATCTCCGTTT
1 AGCACGTTTGTGCTCTCCGTTG
*
5251984 AGCACCTTTGTGCTCTCCGTT
1 AGCACGTTTGTGCTCTCCGTT
5252005 CATTAGTGCA
Statistics
Matches: 38, Mismatches: 5, Indels: 1
0.86 0.11 0.02
Matches are distributed among these distances:
22 31 0.82
23 7 0.18
ACGTcount: A:0.14, C:0.27, G:0.23, T:0.36
Consensus pattern (22 bp):
AGCACGTTTGTGCTCTCCGTTG
Found at i:5260795 original size:39 final size:40
Alignment explanation
Indices: 5260741--5260827 Score: 131
Period size: 39 Copynumber: 2.2 Consensus size: 40
5260731 GGAACACTAT
* *
5260741 AAATATTTGAAAATGTTCTAATAATCTCCCCCCATTTTC-
1 AAATATTTGAAAATGTTCCAACAATCTCCCCCCATTTTCA
* *
5260780 AAATATTTGAAAATGTTCCAACAGTCTTCCCCCATTTTCA
1 AAATATTTGAAAATGTTCCAACAATCTCCCCCCATTTTCA
5260820 AAATATTT
1 AAATATTT
5260828 TAGATTTTGA
Statistics
Matches: 43, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
39 35 0.81
40 8 0.19
ACGTcount: A:0.34, C:0.22, G:0.06, T:0.38
Consensus pattern (40 bp):
AAATATTTGAAAATGTTCCAACAATCTCCCCCCATTTTCA
Found at i:5265484 original size:2 final size:2
Alignment explanation
Indices: 5265477--5265531 Score: 110
Period size: 2 Copynumber: 27.5 Consensus size: 2
5265467 AGTATCTTAA
5265477 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5265519 AT AT AT AT AT AT A
1 AT AT AT AT AT AT A
5265532 ATTATTCATT
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 53 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:5269823 original size:63 final size:63
Alignment explanation
Indices: 5269600--5269839 Score: 214
Period size: 63 Copynumber: 3.8 Consensus size: 63
5269590 ATTGGAAAAA
* * * * ** *
5269600 GTGTTGATGCATGGAATGATTGCACGTGTTGA-GGTGCTTGTGAAAAATAAACCAGTGATGACT
1 GTGTTGGTGCAAGGAATGATTGCACGTGAT-ATGGTGCTTGTGTAAAATAAACTGGTGATGAAT
* * * * *** * * *
5269663 ATGGTGGTGCAAGAAATAATTGTGTGTGCTATGATGCTTGTGTGAAATAAACTGGTGATGAAT
1 GTGTTGGTGCAAGGAATGATTGCACGTGATATGGTGCTTGTGTAAAATAAACTGGTGATGAAT
* * * *
5269726 GTGTCGGTGCAAGGAACGATTGCGCGTGCA-ATGGTGCTTGTGTAAAATAAAGTGGTGATGAAT
1 GTGTTGGTGCAAGGAATGATTGCACGTG-ATATGGTGCTTGTGTAAAATAAACTGGTGATGAAT
* * ** *
5269789 GTGTTGGTGCATGGAATGATTGCACATGATATGGTAATTGTGCAAAATAAA
1 GTGTTGGTGCAAGGAATGATTGCACGTGATATGGTGCTTGTGTAAAATAAA
5269840 TTAGTGTTGT
Statistics
Matches: 138, Mismatches: 36, Indels: 6
0.77 0.20 0.03
Matches are distributed among these distances:
62 2 0.01
63 136 0.99
ACGTcount: A:0.30, C:0.09, G:0.31, T:0.30
Consensus pattern (63 bp):
GTGTTGGTGCAAGGAATGATTGCACGTGATATGGTGCTTGTGTAAAATAAACTGGTGATGAAT
Found at i:5271695 original size:28 final size:28
Alignment explanation
Indices: 5271664--5271717 Score: 72
Period size: 28 Copynumber: 1.9 Consensus size: 28
5271654 AATTGCTTTG
* *
5271664 GAATTGAAAATTTAGAATAAAAAATCGA
1 GAATTGAAAACTGAGAATAAAAAATCGA
* *
5271692 GAATTGACAACTGAGAATAACAAATC
1 GAATTGAAAACTGAGAATAAAAAATC
5271718 AAAAACAATA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 22 1.00
ACGTcount: A:0.54, C:0.09, G:0.15, T:0.22
Consensus pattern (28 bp):
GAATTGAAAACTGAGAATAAAAAATCGA
Found at i:5274271 original size:11 final size:11
Alignment explanation
Indices: 5274255--5274347 Score: 71
Period size: 11 Copynumber: 8.0 Consensus size: 11
5274245 TTTTTTAAAG
5274255 TTTAAATTAAT
1 TTTAAATTAAT
5274266 TTTAAATTAATT
1 TTTAAATTAA-T
*
5274278 TTTAAATTTACTT
1 TTTAAA-TTA-AT
*
5274291 ATTTAAATTTAT
1 -TTTAAATTAAT
*
5274303 TTTAAATTTAAA
1 TTTAAA-TTAAT
*
5274315 TTT-AATTAAA
1 TTTAAATTAAT
*
5274325 TTTAAAATAAT
1 TTTAAATTAAT
*
5274336 ATTAAACTTAAT
1 TTTAAA-TTAAT
5274348 AAATAAAAGT
Statistics
Matches: 66, Mismatches: 9, Indels: 13
0.75 0.10 0.15
Matches are distributed among these distances:
10 8 0.12
11 28 0.42
12 18 0.27
13 6 0.09
14 6 0.09
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (11 bp):
TTTAAATTAAT
Found at i:5274287 original size:6 final size:6
Alignment explanation
Indices: 5274248--5274330 Score: 59
Period size: 6 Copynumber: 14.0 Consensus size: 6
5274238 CTTTTGATTT
* * *
5274248 TTTAAA GTTTAAA -TTAAT TTTAAA -TTAATT TTTAAA TTTACTTA TTTAAA
1 TTTAAA -TTTAAA TTTAAA TTTAAA TTTAA-A TTTAAA TTTA--AA TTTAAA
*
5274298 TTT-AT TTTAAA TTTAAA TTT-AA -TTAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
5274331 ATAATATTAA
Statistics
Matches: 60, Mismatches: 8, Indels: 17
0.71 0.09 0.20
Matches are distributed among these distances:
4 2 0.03
5 16 0.27
6 27 0.45
7 10 0.17
8 5 0.08
ACGTcount: A:0.43, C:0.01, G:0.01, T:0.54
Consensus pattern (6 bp):
TTTAAA
Found at i:5274332 original size:17 final size:16
Alignment explanation
Indices: 5274248--5274330 Score: 70
Period size: 16 Copynumber: 5.4 Consensus size: 16
5274238 CTTTTGATTT
*
5274248 TTTAAAGTTTAAATTAAT
1 TTTAAA-TTT-AATTAAA
5274266 TTTAAA-TTAATT---
1 TTTAAATTTAATTAAA
*
5274278 TTTAAATTTACTT--A
1 TTTAAATTTAATTAAA
*
5274292 TTTAAATTTATTTTAAA
1 TTTAAATTTA-ATTAAA
5274309 TTTAAATTTAATTAAA
1 TTTAAATTTAATTAAA
5274325 TTTAAA
1 TTTAAA
5274331 ATAATATTAA
Statistics
Matches: 57, Mismatches: 3, Indels: 12
0.79 0.04 0.17
Matches are distributed among these distances:
12 6 0.11
13 5 0.09
14 10 0.18
15 6 0.11
16 13 0.23
17 11 0.19
18 6 0.11
ACGTcount: A:0.43, C:0.01, G:0.01, T:0.54
Consensus pattern (16 bp):
TTTAAATTTAATTAAA
Found at i:5274339 original size:17 final size:16
Alignment explanation
Indices: 5274304--5274346 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
5274294 TAAATTTATT
* *
5274304 TTAAATTTAAATTTAA
1 TTAAATTTAAAATAAA
5274320 TTAAATTTAAAATAATA
1 TTAAATTTAAAATAA-A
*
5274337 TTAAACTTAA
1 TTAAATTTAA
5274347 TAAATAAAAG
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
16 13 0.57
17 10 0.43
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.44
Consensus pattern (16 bp):
TTAAATTTAAAATAAA
Found at i:5275120 original size:3 final size:3
Alignment explanation
Indices: 5275105--5275144 Score: 53
Period size: 3 Copynumber: 13.0 Consensus size: 3
5275095 TGAATGTTAT
* *
5275105 TAA TAA TAT TAA TAA TAA TTA TAA TAA TAAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA T-AA TAA TAA TAA
5275145 ATATTTATAA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
3 29 0.91
4 3 0.09
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (3 bp):
TAA
Found at i:5275154 original size:10 final size:10
Alignment explanation
Indices: 5275106--5275147 Score: 52
Period size: 10 Copynumber: 4.4 Consensus size: 10
5275096 GAATGTTATT
*
5275106 AATAAT-ATT
1 AATAATAATA
5275115 AATAATAAT-
1 AATAATAATA
*
5275124 TATAATAATA
1 AATAATAATA
5275134 AATAATAATA
1 AATAATAATA
5275144 AATA
1 AATA
5275148 TTTATAATTA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
9 14 0.48
10 15 0.52
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (10 bp):
AATAATAATA
Done.