Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018397255.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_44.0, 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: 14367614
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 51264 characters in sequence are not A, C, G, or T
File 8 of 31
Found at i:4155720 original size:15 final size:16
Alignment explanation
Indices: 4155691--4155720 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
4155681 TATAAATAAA
4155691 ATATTAATATTTTAAC
1 ATATTAATATTTTAAC
4155707 ATATTAAT-TTTTAA
1 ATATTAATATTTTAA
4155721 ACTATTAAGG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.43, C:0.03, G:0.00, T:0.53
Consensus pattern (16 bp):
ATATTAATATTTTAAC
Found at i:4155726 original size:15 final size:16
Alignment explanation
Indices: 4155687--4155728 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
4155677 AAATTATAAA
*
4155687 TAAAATATTAATATTT
1 TAAACTATTAATATTT
4155703 T-AACATATTAAT-TTT
1 TAAAC-TATTAATATTT
4155718 TAAACTATTAA
1 TAAACTATTAA
4155729 GGGAAAATAT
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
15 12 0.52
16 11 0.48
ACGTcount: A:0.48, C:0.05, G:0.00, T:0.48
Consensus pattern (16 bp):
TAAACTATTAATATTT
Found at i:4155885 original size:17 final size:17
Alignment explanation
Indices: 4155852--4155885 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
4155842 TTAAAAGTAT
*
4155852 TAATATTTTAATCATAA
1 TAATATTTAAATCATAA
*
4155869 TAATATTTAAATTATAA
1 TAATATTTAAATCATAA
4155886 ACTAAATTAC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (17 bp):
TAATATTTAAATCATAA
Found at i:4156057 original size:22 final size:22
Alignment explanation
Indices: 4156024--4156247 Score: 93
Period size: 22 Copynumber: 10.3 Consensus size: 22
4156014 ATTAAATTTT
* * *
4156024 AAATAAAATATTTATACTTAAA
1 AAATAAATTATTAATATTTAAA
*
4156046 TAATAAATTATTAATATTTTAAA
1 AAATAAATTATTAATA-TTTAAA
4156069 AATATAAATTATTAATATTTAAA
1 AA-ATAAATTATTAATATTTAAA
* *
4156092 AGATAAA--AATAA-A--TAAA
1 AAATAAATTATTAATATTTAAA
* *
4156109 CATAATAACA-T-CTAA-A-TT-AT
1 -A-AATAA-ATTATTAATATTTAAA
4156129 AAATAAATTATTAATATTTTAAA
1 AAATAAATTATTAATA-TTTAAA
* *
4156152 AAAGT-AATAATT-A-ATTT-AC
1 AAA-TAAATTATTAATATTTAAA
*
4156171 AAAT-AAGTATTAATATTTAAA
1 AAATAAATTATTAATATTTAAA
**
4156192 TGATAAATTATTAATATCATAAATAAA
1 AAATAAATTATTAATAT--T---TAAA
*
4156219 ATAAAAAATTATTAATATTT-AA
1 A-AATAAATTATTAATATTTAAA
4156241 AAATAAA
1 AAATAAA
4156248 ATAAAATAAA
Statistics
Matches: 154, Mismatches: 24, Indels: 49
0.68 0.11 0.22
Matches are distributed among these distances:
17 5 0.03
18 13 0.08
19 14 0.09
20 18 0.12
21 10 0.06
22 35 0.23
23 24 0.16
24 16 0.10
26 1 0.01
27 4 0.03
28 14 0.09
ACGTcount: A:0.58, C:0.03, G:0.02, T:0.38
Consensus pattern (22 bp):
AAATAAATTATTAATATTTAAA
Found at i:4156079 original size:24 final size:23
Alignment explanation
Indices: 4156043--4156101 Score: 82
Period size: 24 Copynumber: 2.4 Consensus size: 23
4156033 ATTTATACTT
4156043 AAATAATAAATTATTAATATTTTAA
1 AAAT-ATAAATTATTAATA-TTTAA
4156068 AAATATAAATTATTAATATTTAA
1 AAATATAAATTATTAATATTTAA
*
4156091 AAGATAAAAAT
1 AA-ATATAAAT
4156102 AAATAAACAT
Statistics
Matches: 32, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
23 7 0.22
24 21 0.66
25 4 0.12
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (23 bp):
AAATATAAATTATTAATATTTAA
Found at i:4156188 original size:20 final size:18
Alignment explanation
Indices: 4156137--4156191 Score: 56
Period size: 20 Copynumber: 2.8 Consensus size: 18
4156127 ATAAATAAAT
4156137 TATTAATATTTTAAAAAAG
1 TATTAATA-TTTAAAAAAG
*
4156156 TAATAATTAATTTACAAATAAG
1 TATTAA-T-ATTTA-AAA-AAG
4156178 TATTAATATTTAAA
1 TATTAATATTTAAA
4156192 TGATAAATTA
Statistics
Matches: 30, Mismatches: 2, Indels: 8
0.75 0.05 0.20
Matches are distributed among these distances:
19 7 0.23
20 10 0.33
21 5 0.17
22 8 0.27
ACGTcount: A:0.53, C:0.02, G:0.04, T:0.42
Consensus pattern (18 bp):
TATTAATATTTAAAAAAG
Found at i:4156253 original size:28 final size:28
Alignment explanation
Indices: 4156196--4156253 Score: 89
Period size: 29 Copynumber: 2.0 Consensus size: 28
4156186 TTTAAATGAT
*
4156196 AAATTATTAATATCATAAATAAAATAAA
1 AAATTATTAATATCAAAAATAAAATAAA
*
4156224 AAATTATTAATATTTAAAAATAAAATAAA
1 AAATTATTAATA-TCAAAAATAAAATAAA
4156253 A
1 A
4156254 TAAAAATAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
28 12 0.44
29 15 0.56
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.33
Consensus pattern (28 bp):
AAATTATTAATATCAAAAATAAAATAAA
Found at i:4156386 original size:27 final size:28
Alignment explanation
Indices: 4156347--4156405 Score: 66
Period size: 27 Copynumber: 2.1 Consensus size: 28
4156337 TATTAATATT
* * * *
4156347 TAAACTATCAATTTTTAATATTT-TAAA
1 TAAACTATAAATTATTAAAATTTAAAAA
*
4156374 TAAATTATAAATTATTAAAATTTAAAAA
1 TAAACTATAAATTATTAAAATTTAAAAA
4156402 TAAA
1 TAAA
4156406 ATAAAATAAA
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
27 19 0.73
28 7 0.27
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.42
Consensus pattern (28 bp):
TAAACTATAAATTATTAAAATTTAAAAA
Found at i:4156427 original size:158 final size:156
Alignment explanation
Indices: 4155896--4156663 Score: 838
Period size: 158 Copynumber: 5.0 Consensus size: 156
4155886 ACTAAATTAC
* * * *
4155896 CAATTATTGATATTTTAAATCAATTATAAATTATTAATATTT---AA-AAAATAAAATAAAAATA
1 CAATTTTTAATATTTTAAATAAATTAAAAATTATTAATATTTAAAAATAAAATAAAATAAAAATA
* * * * * * *
4155957 AATAATCATAATAACATTTAAATTATAAATAAAATGGTTGTATTTTATATATTAATGATTAAATT
66 AATAATCATAATAACATTTAAATTATAAATAAAGT-ATTATATTTTAAATAATAATAATTAAAGT
* * *
4156022 TTAAATAAAATATTTATACTTAAA-TAAT
130 ATAAAT-AAATATTAATATTTAAACT-AT
* * *
4156050 AAATTATTAATATTTT-AA-AAA-TATAAATTATTAATATTTAAAAGAT---A-AAAAT--AAAT
1 CAATTTTTAATATTTTAAATAAATTAAAAATTATTAATATTTAAAA-ATAAAATAAAATAAAAAT
* * * *
4156106 --A-AA-CATAATAACATCTAAATTATAAATAAATTATTAATATTTTAAAAAAGTAATAATTAAT
65 AAATAATCATAATAACATTTAAATTATAAATAAAGTATT-ATATTTTAAATAA-TAATAATTAAA
* * *
4156167 TTACAAATAAGTATTAATATTTAAA-TGAT
128 GTATAAATAAATATTAATATTTAAACT-AT
* * ** *
4156196 AAATTATTAATATCATAAATAAAATAAAAAATTATTAATATTTAAAAATAAAATAAAATAAAAAT
1 CAATTTTTAATATTTTAAAT-AAATTAAAAATTATTAATATTTAAAAATAAAATAAAATAAAAAT
* * *
4156261 AAATAATCATAAGAACATTTAAATTATAAATTAAGTATTATCATCTTT-AATAATAATGATTAAA
65 AAATAATCATAATAACATTTAAATTATAAATAAAGTATTAT-AT-TTTAAATAATAATAATTAAA
4156325 GTATAAATAAAATATTAATATTTAAACTAT
128 GTATAAAT-AAATATTAATATTTAAACTAT
* *
4156355 CAATTTTTAATATTTTAAATAAATTATAAATTATTAAAATTTAAAAATAAAATAAAATAAAAATA
1 CAATTTTTAATATTTTAAATAAATTAAAAATTATTAATATTTAAAAATAAAATAAAATAAAAATA
* * * * *
4156420 AATAATCATAATAACACTTAAATTATAAATTAAGTATTATTATTTTTAATATTAATGATTAAAGT
66 AATAATCATAATAACATTTAAATTATAAATAAAGTATTA-TATTTTAAATAATAATAATTAAAGT
4156485 ATAAATAAATATTAATATTTAAACTAT
130 ATAAATAAATATTAATATTTAAACTAT
* **
4156512 CAATGTTTAATATTTTAAATAAATTAAAAATTATTAATATTTAAAAATAAAATAATTTAAAAATA
1 CAATTTTTAATATTTTAAATAAATTAAAAATTATTAATATTTAAAAATAAAATAAAATAAAAATA
* * * * *
4156577 AATAATCATAATAACATTTAAATTCTAAATAAAATATTAGTATTTTAAAATATTAATAATTAGAT
66 AATAATCATAATAACATTTAAATTATAAATAAAGTATTA-TATTTT-AAATAATAATAATTAAAG
4156642 TATAAATAAAATATTAATATTT
129 TATAAAT-AAATATTAATATTT
4156664 TAAAAAATAA
Statistics
Matches: 529, Mismatches: 56, Indels: 53
0.83 0.09 0.08
Matches are distributed among these distances:
145 2 0.00
146 67 0.13
147 19 0.04
148 1 0.00
149 5 0.01
150 24 0.05
151 18 0.03
152 8 0.02
153 8 0.02
154 15 0.03
155 5 0.01
157 126 0.24
158 144 0.27
159 83 0.16
160 4 0.01
ACGTcount: A:0.55, C:0.03, G:0.02, T:0.39
Consensus pattern (156 bp):
CAATTTTTAATATTTTAAATAAATTAAAAATTATTAATATTTAAAAATAAAATAAAATAAAAATA
AATAATCATAATAACATTTAAATTATAAATAAAGTATTATATTTTAAATAATAATAATTAAAGTA
TAAATAAATATTAATATTTAAACTAT
Found at i:4156569 original size:16 final size:16
Alignment explanation
Indices: 4156528--4156582 Score: 60
Period size: 16 Copynumber: 3.4 Consensus size: 16
4156518 TTAATATTTT
*
4156528 AAATAAATTAAAAATTA
1 AAATAATTTAAAAA-TA
*
4156545 TTAAT-ATTTAAAAATA
1 -AAATAATTTAAAAATA
4156561 AAATAATTTAAAAAT-
1 AAATAATTTAAAAATA
4156576 AAATAAT
1 AAATAAT
4156583 CATAATAACA
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
15 10 0.30
16 12 0.36
17 8 0.24
18 3 0.09
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (16 bp):
AAATAATTTAAAAATA
Found at i:4156667 original size:20 final size:20
Alignment explanation
Indices: 4156602--4156667 Score: 62
Period size: 20 Copynumber: 3.2 Consensus size: 20
4156592 ATTTAAATTC
*
4156602 TAAATAAAATATTAGTATTT
1 TAAATAAAATATTAATATTT
* * *
4156622 TAAAATATTAATAATT-AGATTA
1 T-AAATA-AAAT-ATTAATATTT
4156644 TAAATAAAATATTAATATTT
1 TAAATAAAATATTAATATTT
4156664 TAAA
1 TAAA
4156668 AAATAAAATA
Statistics
Matches: 35, Mismatches: 7, Indels: 8
0.70 0.14 0.16
Matches are distributed among these distances:
19 3 0.09
20 12 0.34
21 10 0.29
22 7 0.20
23 3 0.09
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.42
Consensus pattern (20 bp):
TAAATAAAATATTAATATTT
Found at i:4156716 original size:24 final size:24
Alignment explanation
Indices: 4156689--4156735 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 24
4156679 AATAACCATA
4156689 TGTATGATAAATTTTTTTTATTTT
1 TGTATGATAAATTTTTTTTATTTT
** **
4156713 TGTATTTTTTATTTTTTTTATTT
1 TGTATGATAAATTTTTTTTATTT
4156736 CAAAATTATT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.19, C:0.00, G:0.06, T:0.74
Consensus pattern (24 bp):
TGTATGATAAATTTTTTTTATTTT
Found at i:4165290 original size:18 final size:18
Alignment explanation
Indices: 4165266--4165316 Score: 57
Period size: 18 Copynumber: 2.8 Consensus size: 18
4165256 GCCAGCAGCC
4165266 CCAACACCTTCCCCATCG
1 CCAACACCTTCCCCATCG
* ** *
4165284 GCAACACCGACCCCATCT
1 CCAACACCTTCCCCATCG
*
4165302 CCAACTCCTTCCCCA
1 CCAACACCTTCCCCA
4165317 ACCCGCAACC
Statistics
Matches: 25, Mismatches: 8, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.24, C:0.55, G:0.06, T:0.16
Consensus pattern (18 bp):
CCAACACCTTCCCCATCG
Found at i:4165333 original size:36 final size:36
Alignment explanation
Indices: 4165266--4165334 Score: 86
Period size: 36 Copynumber: 1.9 Consensus size: 36
4165256 GCCAGCAGCC
* * *
4165266 CCAACACCTTCCCCATCGGCAACACCGACCCCATCT
1 CCAACACCTTCCCCACCCGCAACACCAACCCCATCT
*
4165302 CCAACTCCTTCCCCAACCCGCAAC-CCAACCCCA
1 CCAACACCTTCCCC-ACCCGCAACACCAACCCCA
4165335 ACCCTTCTCC
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
36 21 0.75
37 7 0.25
ACGTcount: A:0.26, C:0.57, G:0.06, T:0.12
Consensus pattern (36 bp):
CCAACACCTTCCCCACCCGCAACACCAACCCCATCT
Found at i:4174552 original size:23 final size:23
Alignment explanation
Indices: 4174532--4174576 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
4174522 ACGTGACTGA
*
4174532 TTAATATGACATTGCATGACTAG
1 TTAATAAGACATTGCATGACTAG
* *
4174555 TTAGTAAGGCATTGCATGACTA
1 TTAATAAGACATTGCATGACTA
4174577 ATTTTTGGGC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.33, C:0.13, G:0.20, T:0.33
Consensus pattern (23 bp):
TTAATAAGACATTGCATGACTAG
Found at i:4174732 original size:22 final size:22
Alignment explanation
Indices: 4174707--4174768 Score: 79
Period size: 22 Copynumber: 2.8 Consensus size: 22
4174697 AAACCAGTTT
4174707 CATAATATTTAAAAACTAGTAA
1 CATAATATTTAAAAACTAGTAA
*
4174729 CATAATATCTAAAAACTAGTAA
1 CATAATATTTAAAAACTAGTAA
** * *
4174751 TGTAATACTTAATAACTA
1 CATAATATTTAAAAACTA
4174769 ATTGATTTGT
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 34 1.00
ACGTcount: A:0.52, C:0.11, G:0.05, T:0.32
Consensus pattern (22 bp):
CATAATATTTAAAAACTAGTAA
Found at i:4180388 original size:7 final size:8
Alignment explanation
Indices: 4180371--4180396 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
4180361 GTTGCAAGGA
4180371 TTTTTATT
1 TTTTTATT
4180379 TTTTTATT
1 TTTTTATT
4180387 TTTTTATT
1 TTTTTATT
4180395 TT
1 TT
4180397 CCAGGCACAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.12, C:0.00, G:0.00, T:0.88
Consensus pattern (8 bp):
TTTTTATT
Found at i:4183099 original size:28 final size:28
Alignment explanation
Indices: 4183052--4183107 Score: 78
Period size: 28 Copynumber: 2.0 Consensus size: 28
4183042 GTTTAGAACC
*
4183052 TTTGAATATTCTGAATTAATCACAAATG
1 TTTGAATATTCTGAATTAATAACAAATG
*
4183080 TTTGAATATTTTG-ATCTAATAACAAATG
1 TTTGAATATTCTGAAT-TAATAACAAATG
4183108 CATGTATCTC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
27 2 0.08
28 23 0.92
ACGTcount: A:0.39, C:0.09, G:0.11, T:0.41
Consensus pattern (28 bp):
TTTGAATATTCTGAATTAATAACAAATG
Found at i:4186051 original size:28 final size:29
Alignment explanation
Indices: 4185990--4186051 Score: 72
Period size: 28 Copynumber: 2.2 Consensus size: 29
4185980 CATTGACTGA
4185990 AAATACAGAAATTAAACTTGTAAAAATTG
1 AAATACAGAAATTAAACTTGTAAAAATTG
* * * * *
4186019 TAATATAGAGATTAAA-TTGTTAATATTG
1 AAATACAGAAATTAAACTTGTAAAAATTG
4186047 AAATA
1 AAATA
4186052 GTATCAAGAT
Statistics
Matches: 27, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
28 14 0.52
29 13 0.48
ACGTcount: A:0.52, C:0.03, G:0.11, T:0.34
Consensus pattern (29 bp):
AAATACAGAAATTAAACTTGTAAAAATTG
Found at i:4186620 original size:22 final size:22
Alignment explanation
Indices: 4186544--4186650 Score: 79
Period size: 22 Copynumber: 4.9 Consensus size: 22
4186534 TTTCAGTGAA
* * *
4186544 TTTTAGATATTGCGTAACTAGT
1 TTTTAGACATTACGTAACTAAT
* * * *
4186566 TTTTAAATATTATGTAACTAGT
1 TTTTAGACATTACGTAACTAAT
* * * *
4186588 TTTTCGGCATTGCGTTACTAAT
1 TTTTAGACATTACGTAACTAAT
** *
4186610 TTTTAGACATTATATGACTAAT
1 TTTTAGACATTACGTAACTAAT
*
4186632 TTTTAGATATTACGTAACT
1 TTTTAGACATTACGTAACT
4186651 GATTGATATG
Statistics
Matches: 64, Mismatches: 21, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
22 64 1.00
ACGTcount: A:0.30, C:0.10, G:0.13, T:0.47
Consensus pattern (22 bp):
TTTTAGACATTACGTAACTAAT
Found at i:4186635 original size:44 final size:44
Alignment explanation
Indices: 4186552--4186635 Score: 105
Period size: 44 Copynumber: 1.9 Consensus size: 44
4186542 AATTTTAGAT
* * * *
4186552 ATTGCGTAACTAGTTTTTAAATATTATGTAACTAGTTTTTCGGC
1 ATTGCGTAACTAATTTTTAAACATTATATAACTAATTTTTCGGC
* * *
4186596 ATTGCGTTACTAATTTTTAGACATTATATGACTAATTTTT
1 ATTGCGTAACTAATTTTTAAACATTATATAACTAATTTTT
4186636 AGATATTACG
Statistics
Matches: 33, Mismatches: 7, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
44 33 1.00
ACGTcount: A:0.29, C:0.11, G:0.13, T:0.48
Consensus pattern (44 bp):
ATTGCGTAACTAATTTTTAAACATTATATAACTAATTTTTCGGC
Found at i:4186686 original size:23 final size:23
Alignment explanation
Indices: 4186639--4186692 Score: 65
Period size: 23 Copynumber: 2.3 Consensus size: 23
4186629 AATTTTTAGA
* *
4186639 TATTACGTAACTGATTGATATGG
1 TATTGCGTAACTGATTGATAAGG
4186662 TATTGCGTAACTGATT-AGTAAGG
1 TATTGCGTAACTGATTGA-TAAGG
*
4186685 TACTGCGT
1 TATTGCGT
4186693 GACTAATTTT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
22 1 0.04
23 26 0.96
ACGTcount: A:0.28, C:0.11, G:0.24, T:0.37
Consensus pattern (23 bp):
TATTGCGTAACTGATTGATAAGG
Found at i:4189742 original size:15 final size:15
Alignment explanation
Indices: 4189722--4189751 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
4189712 TAAAATGTCC
*
4189722 TTTCTTTTTTTTCTT
1 TTTCTTTTTTCTCTT
4189737 TTTCTTTTTTCTCTT
1 TTTCTTTTTTCTCTT
4189752 AAACAATATT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (15 bp):
TTTCTTTTTTCTCTT
Found at i:4191094 original size:16 final size:16
Alignment explanation
Indices: 4191072--4191112 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
4191062 ATATAAATAT
4191072 TTTTATTATTATTAAGA
1 TTTTATTATTATTAA-A
4191089 -TTTATTGA-TATTAAA
1 TTTTATT-ATTATTAAA
4191104 TTTTATTAT
1 TTTTATTAT
4191113 ATTTGTTAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 7
0.75 0.00 0.25
Matches are distributed among these distances:
15 2 0.10
16 18 0.86
17 1 0.05
ACGTcount: A:0.34, C:0.00, G:0.05, T:0.61
Consensus pattern (16 bp):
TTTTATTATTATTAAA
Found at i:4191104 original size:35 final size:35
Alignment explanation
Indices: 4191065--4191145 Score: 80
Period size: 35 Copynumber: 2.3 Consensus size: 35
4191055 TATATAAATA
4191065 TAAATATTTTTAT-TATTATTAAGAT-TTATTGATA-T
1 TAAATATTTTTATAT-TTATTAA-ATGTTA-TGATATT
*
4191100 TAAAT-TTTATTATATTTGTTAAATGTTATGATATT
1 TAAATATTT-TTATATTTATTAAATGTTATGATATT
4191135 TATAATATTTT
1 TA-AATATTTT
4191146 GTTATAAATT
Statistics
Matches: 39, Mismatches: 1, Indels: 11
0.76 0.02 0.22
Matches are distributed among these distances:
34 10 0.26
35 21 0.54
36 5 0.13
37 3 0.08
ACGTcount: A:0.36, C:0.00, G:0.06, T:0.58
Consensus pattern (35 bp):
TAAATATTTTTATATTTATTAAATGTTATGATATT
Found at i:4191121 original size:19 final size:19
Alignment explanation
Indices: 4191099--4191135 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
4191089 TTTATTGATA
* *
4191099 TTAAATTTTATTATATTTG
1 TTAAATGTTATGATATTTG
4191118 TTAAATGTTATGATATTT
1 TTAAATGTTATGATATTT
4191136 ATAATATTTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.32, C:0.00, G:0.08, T:0.59
Consensus pattern (19 bp):
TTAAATGTTATGATATTTG
Found at i:4191227 original size:19 final size:19
Alignment explanation
Indices: 4191203--4191257 Score: 92
Period size: 19 Copynumber: 2.9 Consensus size: 19
4191193 ATTTTGATCA
4191203 TGTTAATCATATTAATTTG
1 TGTTAATCATATTAATTTG
4191222 TGTTAATCATATTAATTTG
1 TGTTAATCATATTAATTTG
* *
4191241 TATTAATCATATCAATT
1 TGTTAATCATATTAATT
4191258 GTATAAATAA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 34 1.00
ACGTcount: A:0.35, C:0.07, G:0.07, T:0.51
Consensus pattern (19 bp):
TGTTAATCATATTAATTTG
Found at i:4191544 original size:18 final size:20
Alignment explanation
Indices: 4191514--4191550 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
4191504 AATTTAGGTG
4191514 CAACTATCACTTC-TATTCA
1 CAACTATCACTTCATATTCA
4191533 CAACTA-CACTTCATATTC
1 CAACTATCACTTCATATTC
4191551 TTCCGAAAAG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 6 0.35
19 11 0.65
ACGTcount: A:0.32, C:0.32, G:0.00, T:0.35
Consensus pattern (20 bp):
CAACTATCACTTCATATTCA
Found at i:4197205 original size:283 final size:283
Alignment explanation
Indices: 4196694--4197236 Score: 731
Period size: 283 Copynumber: 1.9 Consensus size: 283
4196684 CTTATTTATG
* * *
4196694 AATATGTGTAAGTATTTTTAATTGGTAAAGATCACGAAATTATGAGTATTTTAATCATATTTTAT
1 AATATGTGTAACTATCTTTAATTGGTAAAGATCACGAAATTATGAGTATTTTAATCACATTTTAT
* ** *
4196759 TTTTTATACAAATTTTTTTTACTTCCATGAATATTAAACTTTGTTGAATTGTTAATACAAATATA
66 TTTTTATACAAATTTTTTATACTAACATGAATATTAAACTTTATTGAATTGTTAATACAAATATA
4196824 TAATCAATTAATTGAATTAATGAATACTTACCATCATCGTTAAGATTTGATAAAGATGTTAACCG
131 TAATCAATTAATTGAATTAATGAATACTTACCATCATCGTTAAGATTTGATAAAGATGTTAACCG
* * * *
4196889 CAGATGTATAGTAAGTATCATGAACATTAAAAATTTTCATTGGGTTGCCTTTTATAGAACATTTT
196 CAGATGTATAGTAAGTATCATGAACACTAAAAATGTTCATTGGATTACCTTTTATAGAACATTTT
4196954 TTTAACTTTTATAAGGTTAGTAA
261 TTTAACTTTTATAAGGTTAGTAA
* * * *
4196977 AATATGTGTAACTATCTTTAATTGGTAAATATCGC-AGAATTATGAGTGTTTTAATCACGTTTTA
1 AATATGTGTAACTATCTTTAATTGGTAAAGATCACGA-AATTATGAGTATTTTAATCACATTTTA
* * * *
4197041 TTTTTTATATGAAA-TTTTTATACTAACATGAATATTAAGCTTTATTGAGTTGTTAGA-GCAAAT
65 TTTTTTATA-CAAATTTTTTATACTAACATGAATATTAAACTTTATTGAATTGTTA-ATACAAAT
* * *
4197104 AT-TGAAAT-AATTAATTGAATTAATGAATTCTTACTATCATCGTTAAGATTTGATAAATATGTT
128 ATAT--AATCAATTAATTGAATTAATGAATACTTACCATCATCGTTAAGATTTGATAAAGATGTT
* * * *
4197167 AACCG-TG-TGCGTATAGTAAGTATCATGGACACTAAAAATGTTCATTGTATTACTTTTTATAGA
191 AACCGCAGAT--GTATAGTAAGTATCATGAACACTAAAAATGTTCATTGGATTACCTTTTATAGA
*
4197230 GCATTTT
254 ACATTTT
4197237 AAAAGGTAAC
Statistics
Matches: 226, Mismatches: 27, Indels: 14
0.85 0.10 0.05
Matches are distributed among these distances:
281 1 0.00
282 3 0.01
283 215 0.95
284 7 0.03
ACGTcount: A:0.36, C:0.09, G:0.13, T:0.43
Consensus pattern (283 bp):
AATATGTGTAACTATCTTTAATTGGTAAAGATCACGAAATTATGAGTATTTTAATCACATTTTAT
TTTTTATACAAATTTTTTATACTAACATGAATATTAAACTTTATTGAATTGTTAATACAAATATA
TAATCAATTAATTGAATTAATGAATACTTACCATCATCGTTAAGATTTGATAAAGATGTTAACCG
CAGATGTATAGTAAGTATCATGAACACTAAAAATGTTCATTGGATTACCTTTTATAGAACATTTT
TTTAACTTTTATAAGGTTAGTAA
Found at i:4206838 original size:2 final size:2
Alignment explanation
Indices: 4206831--4206867 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
4206821 CTTTTGACCT
4206831 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
4206868 TCAATAAAAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:4207209 original size:2 final size:2
Alignment explanation
Indices: 4207197--4207231 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
4207187 CAAATTGATA
* *
4207197 AT AT GT AT AT AT AT AA AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
4207232 ATGTAAGCAA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (2 bp):
AT
Found at i:4208622 original size:16 final size:16
Alignment explanation
Indices: 4208592--4208641 Score: 59
Period size: 16 Copynumber: 3.2 Consensus size: 16
4208582 ATCTTAATTG
*
4208592 ATATATAAATTAATAA
1 ATATATTAATTAATAA
4208608 AT-TATTAATTAA-ATA
1 ATATATTAATTAATA-A
*
4208623 ATATCTTAATTAATAA
1 ATATATTAATTAATAA
4208639 ATA
1 ATA
4208642 AGTTTTTATG
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
14 1 0.03
15 12 0.41
16 15 0.52
17 1 0.03
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (16 bp):
ATATATTAATTAATAA
Found at i:4211576 original size:16 final size:16
Alignment explanation
Indices: 4211557--4211590 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
4211547 AAAATTCCAC
4211557 ATGCTTCAAATCATAT
1 ATGCTTCAAATCATAT
* *
4211573 ATGCTTCCAATTATAT
1 ATGCTTCAAATCATAT
4211589 AT
1 AT
4211591 TTATTTTAAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.35, C:0.18, G:0.06, T:0.41
Consensus pattern (16 bp):
ATGCTTCAAATCATAT
Found at i:4230201 original size:2 final size:2
Alignment explanation
Indices: 4230151--4230181 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
4230141 GAGTTGGAAG
4230151 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
4230182 NNNNNNNNNN
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:4230202 original size:2 final size:2
Alignment explanation
Indices: 4230192--4230218 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
4230182 NNNNNNNNNN
4230192 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
4230219 GAGAGAGAGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:4230223 original size:2 final size:2
Alignment explanation
Indices: 4230218--4230271 Score: 81
Period size: 2 Copynumber: 27.0 Consensus size: 2
4230208 ATATATATAT
* *
4230218 AG AG AG AG AG AG AG AG AG AC AG AG AG AG AG AG AG AG AG AG AC
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
*
4230260 AG AG AC AG AG AG
1 AG AG AG AG AG AG
4230272 TGTATCATAT
Statistics
Matches: 46, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.06, G:0.44, T:0.00
Consensus pattern (2 bp):
AG
Found at i:4234655 original size:25 final size:23
Alignment explanation
Indices: 4234616--4234663 Score: 60
Period size: 25 Copynumber: 2.0 Consensus size: 23
4234606 AAATTCAATA
4234616 TTTAAAAAAACAAAATTATAAAATT
1 TTTAAAAAAACAAAA--ATAAAATT
**
4234641 TTTAAAAAATTAAAAATAAAATT
1 TTTAAAAAAACAAAAATAAAATT
4234664 ATAGATATTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
23 8 0.38
25 13 0.62
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (23 bp):
TTTAAAAAAACAAAAATAAAATT
Found at i:4234662 original size:31 final size:30
Alignment explanation
Indices: 4234621--4234680 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 30
4234611 CAATATTTAA
*
4234621 AAAAACAAAATTATAAAATTTTTAAAAAATT
1 AAAAACAAAATTAT-AAATATTTAAAAAATT
* *
4234652 AAAAATAAAATTATAGATATTTAAAAAAT
1 AAAAACAAAATTATAAATATTTAAAAAAT
4234681 ATATGAATTT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 13 0.50
31 13 0.50
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.32
Consensus pattern (30 bp):
AAAAACAAAATTATAAATATTTAAAAAATT
Found at i:4263804 original size:2 final size:2
Alignment explanation
Indices: 4263797--4263833 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
4263787 AACACCTGAC
4263797 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
4263834 AACAAAATCA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:4266423 original size:14 final size:14
Alignment explanation
Indices: 4266404--4266432 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
4266394 TACTGTAAAG
4266404 TCAATTAATAAAAA
1 TCAATTAATAAAAA
4266418 TCAATTAATAAAAA
1 TCAATTAATAAAAA
4266432 T
1 T
4266433 TATTAAATTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.62, C:0.07, G:0.00, T:0.31
Consensus pattern (14 bp):
TCAATTAATAAAAA
Found at i:4285361 original size:20 final size:20
Alignment explanation
Indices: 4285322--4285361 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
4285312 TTTTATTTTT
**
4285322 TGATTTTTTGTAAAGTAAAA
1 TGATTTTTTGTAAAAAAAAA
*
4285342 TGATTTTTTTTAAAAAAAAA
1 TGATTTTTTGTAAAAAAAAA
4285362 GCTCATATAT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.45, C:0.00, G:0.10, T:0.45
Consensus pattern (20 bp):
TGATTTTTTGTAAAAAAAAA
Found at i:4289485 original size:20 final size:21
Alignment explanation
Indices: 4289448--4289487 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
4289438 TTATTCTGAA
**
4289448 AAATTGTTAAAATGTAAAACC
1 AAATTGTTAAAAAATAAAACC
4289469 AAATTG-TAAAAAATAAAAC
1 AAATTGTTAAAAAATAAAAC
4289488 AATGAGTAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 11 0.65
21 6 0.35
ACGTcount: A:0.60, C:0.07, G:0.07, T:0.25
Consensus pattern (21 bp):
AAATTGTTAAAAAATAAAACC
Found at i:4291029 original size:1 final size:1
Alignment explanation
Indices: 4291023--4291050 Score: 56
Period size: 1 Copynumber: 28.0 Consensus size: 1
4291013 CAAAAGTGAT
4291023 CCCCCCCCCCCCCCCCCCCCCCCCCCCC
1 CCCCCCCCCCCCCCCCCCCCCCCCCCCC
4291051 AAAAAAAAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 27 1.00
ACGTcount: A:0.00, C:1.00, G:0.00, T:0.00
Consensus pattern (1 bp):
C
Found at i:4298365 original size:18 final size:18
Alignment explanation
Indices: 4298344--4298381 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
4298334 ATCAGTATTT
4298344 TTTAAAAAATAAAAAAAA
1 TTTAAAAAATAAAAAAAA
*
4298362 TTTAAAAAATAATAAAAA
1 TTTAAAAAATAAAAAAAA
4298380 TT
1 TT
4298382 ATATTATAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (18 bp):
TTTAAAAAATAAAAAAAA
Found at i:4298548 original size:13 final size:13
Alignment explanation
Indices: 4298532--4298558 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
4298522 AATTAATAAA
4298532 TTTATTTAAAATT
1 TTTATTTAAAATT
4298545 TTTATTTAAAATT
1 TTTATTTAAAATT
4298558 T
1 T
4298559 AAAACAGTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (13 bp):
TTTATTTAAAATT
Found at i:4303560 original size:24 final size:23
Alignment explanation
Indices: 4303506--4303567 Score: 70
Period size: 23 Copynumber: 2.7 Consensus size: 23
4303496 TCTTCCTAAT
* * *
4303506 AAATATAACTGTTTATTTTTAAT
1 AAATATAATTATTTATTTTTAAC
* *
4303529 AGACATAATTATTTATTTTTCAAC
1 AAATATAATTATTTATTTTT-AAC
4303553 AAATATAATTATTTA
1 AAATATAATTATTTA
4303568 AATAAATTTA
Statistics
Matches: 31, Mismatches: 7, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
23 16 0.52
24 15 0.48
ACGTcount: A:0.42, C:0.06, G:0.03, T:0.48
Consensus pattern (23 bp):
AAATATAATTATTTATTTTTAAC
Found at i:4303579 original size:18 final size:18
Alignment explanation
Indices: 4303553--4303596 Score: 70
Period size: 18 Copynumber: 2.4 Consensus size: 18
4303543 ATTTTTCAAC
*
4303553 AAATATAATTATTTAAAT
1 AAATATAATAATTTAAAT
*
4303571 AAATTTAATAATTTAAAT
1 AAATATAATAATTTAAAT
4303589 AAATATAA
1 AAATATAA
4303597 CTCGAACAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (18 bp):
AAATATAATAATTTAAAT
Found at i:4306873 original size:7 final size:7
Alignment explanation
Indices: 4306861--4306886 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
4306851 GCCTGCCTAG
4306861 ATGTTCC
1 ATGTTCC
4306868 ATGTTCC
1 ATGTTCC
4306875 ATGTTCC
1 ATGTTCC
4306882 ATGTT
1 ATGTT
4306887 ACGATTCAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.15, C:0.23, G:0.15, T:0.46
Consensus pattern (7 bp):
ATGTTCC
Found at i:4310481 original size:2 final size:2
Alignment explanation
Indices: 4310474--4310504 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
4310464 NNNNNNNNNN
4310474 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
4310505 TCAATCACTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:4316768 original size:22 final size:23
Alignment explanation
Indices: 4316743--4316789 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 23
4316733 AATATTGTTA
*
4316743 AAATCATGTGTATTTA-TTTTTT
1 AAATCATGTGTATTTAGTTTATT
* *
4316765 AAATCATTTTTATTTAGTTTATT
1 AAATCATGTGTATTTAGTTTATT
4316788 AA
1 AA
4316790 TAAAATAATA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
22 14 0.67
23 7 0.33
ACGTcount: A:0.32, C:0.04, G:0.06, T:0.57
Consensus pattern (23 bp):
AAATCATGTGTATTTAGTTTATT
Found at i:4320228 original size:4 final size:4
Alignment explanation
Indices: 4320219--4320243 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
4320209 CGATTGTGAT
4320219 AGAA AGAA AGAA AGAA AGAA AGAA A
1 AGAA AGAA AGAA AGAA AGAA AGAA A
4320244 TAAATAAAGG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (4 bp):
AGAA
Found at i:4326096 original size:2 final size:2
Alignment explanation
Indices: 4326089--4326133 Score: 72
Period size: 2 Copynumber: 22.5 Consensus size: 2
4326079 TGTATGTATG
* *
4326089 TA TA TA TA TA TA TA TA TG TA TG TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
4326131 TA T
1 TA T
4326134 TCTTTTGTGC
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.44, C:0.00, G:0.04, T:0.51
Consensus pattern (2 bp):
TA
Found at i:4326106 original size:22 final size:22
Alignment explanation
Indices: 4326076--4326127 Score: 95
Period size: 22 Copynumber: 2.4 Consensus size: 22
4326066 CTGCTTTTCA
*
4326076 ATATGTATGTATGTATATATAT
1 ATATATATGTATGTATATATAT
4326098 ATATATATGTATGTATATATAT
1 ATATATATGTATGTATATATAT
4326120 ATATATAT
1 ATATATAT
4326128 ATATATTCTT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.40, C:0.00, G:0.10, T:0.50
Consensus pattern (22 bp):
ATATATATGTATGTATATATAT
Found at i:4327450 original size:230 final size:229
Alignment explanation
Indices: 4327040--4327494 Score: 820
Period size: 230 Copynumber: 2.0 Consensus size: 229
4327030 GCTATGTGAT
4327040 TACCTATGGCATTCATGACATGGAGTTGGATTAAAAAGATGAAAAAAGCAATGTGAAGATTTGAA
1 TACCTATGGCATTCATGACATGGAGTTGGATTAAAAAGATGAAAAAAGCAATGTGAAGATTTGAA
* *
4327105 AAGATACATAAAACCTCCAGACTGGTCTGGGATAATGCAGTAGATTGCTCTTACTGCAACTTGCC
66 AAGATACATAAAACCTCCAGACTGATCTGGGATAATGAAGTAGATTGCTCTTACTGCAACTTGCC
*
4327170 AAAAACGTTAAATTCATTGCGATGCCTTTGGGGATGAAAATGATGGATAGTCAACTCAACAGAAG
131 AAAAACGTTAAATTCATTGCGATGCCTTTGGGGATGAAAATGAGGGATAGTCAACTCAACAGAAG
*
4327235 TAATGATATTTACCCAGAGTATGATTAAAAAGAG
196 AAATGATATTTACCCAGAGTATGATTAAAAAGAG
4327269 TACCTATTGGCATTCATGACATGGAGTTGGATTAAAAAGATGAAAAAAGCAATGTGAAGATTTGA
1 TACCTA-TGGCATTCATGACATGGAGTTGGATTAAAAAGATGAAAAAAGCAATGTGAAGATTTGA
*
4327334 AAAGATACATAAAACCTCCAGACTGATCTGTGATAATGAAGTAGATTGCTCTTACTGCAACTTGC
65 AAAGATACATAAAACCTCCAGACTGATCTGGGATAATGAAGTAGATTGCTCTTACTGCAACTTGC
* * *
4327399 GAATAACGTTAAATTCATTGCGATGCCTTTTGGGATGAAAATGAGGGATAGTCAACTCAACAGAA
130 CAAAAACGTTAAATTCATTGCGATGCCTTTGGGGATGAAAATGAGGGATAGTCAACTCAACAGAA
*
4327464 GAAATGGTATTTACCCAGAGTATGATTAAAA
195 GAAATGATATTTACCCAGAGTATGATTAAAA
4327495 TGAGGTAAAA
Statistics
Matches: 216, Mismatches: 9, Indels: 1
0.96 0.04 0.00
Matches are distributed among these distances:
229 6 0.03
230 210 0.97
ACGTcount: A:0.38, C:0.14, G:0.21, T:0.27
Consensus pattern (229 bp):
TACCTATGGCATTCATGACATGGAGTTGGATTAAAAAGATGAAAAAAGCAATGTGAAGATTTGAA
AAGATACATAAAACCTCCAGACTGATCTGGGATAATGAAGTAGATTGCTCTTACTGCAACTTGCC
AAAAACGTTAAATTCATTGCGATGCCTTTGGGGATGAAAATGAGGGATAGTCAACTCAACAGAAG
AAATGATATTTACCCAGAGTATGATTAAAAAGAG
Found at i:4342375 original size:6 final size:6
Alignment explanation
Indices: 4342366--4342399 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
4342356 AAATGTGGCA
* *
4342366 TAAAAC TAAAGC TAAAAC CAAAAC TAAAAC TAAA
1 TAAAAC TAAAAC TAAAAC TAAAAC TAAAAC TAAA
4342400 CTGACGAAGA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.65, C:0.18, G:0.03, T:0.15
Consensus pattern (6 bp):
TAAAAC
Found at i:4349971 original size:33 final size:33
Alignment explanation
Indices: 4349934--4350047 Score: 140
Period size: 33 Copynumber: 3.5 Consensus size: 33
4349924 AAAGGTCGTG
* * *
4349934 GAAGTAGCTTCAGAGGCAGATGGAAAGATTTCA
1 GAAGTGGCTTCAGAGGCTGATGAAAAGATTTCA
*
4349967 GAAGTGGCTTCAGAGGCTGATGAAAAGATCTCCA
1 GAAGTGGCTTCAGAGGCTGATGAAAAGAT-TTCA
* * *
4350001 -AAGTGACTTCAGAGGCTGAAGAAAAGATCTCA
1 GAAGTGGCTTCAGAGGCTGATGAAAAGATTTCA
*
4350033 GAAGTGGCTTTAGAG
1 GAAGTGGCTTCAGAG
4350048 ACCAAGTTGG
Statistics
Matches: 69, Mismatches: 10, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
32 2 0.03
33 64 0.93
34 3 0.04
ACGTcount: A:0.35, C:0.14, G:0.30, T:0.21
Consensus pattern (33 bp):
GAAGTGGCTTCAGAGGCTGATGAAAAGATTTCA
Found at i:4353128 original size:60 final size:60
Alignment explanation
Indices: 4353035--4353154 Score: 240
Period size: 60 Copynumber: 2.0 Consensus size: 60
4353025 CCCCATAACC
4353035 AAATAACAAGTGCCTTGGACAGAATCAGCAGGTCAGATTGTACCTTGTTAAACATCAACT
1 AAATAACAAGTGCCTTGGACAGAATCAGCAGGTCAGATTGTACCTTGTTAAACATCAACT
4353095 AAATAACAAGTGCCTTGGACAGAATCAGCAGGTCAGATTGTACCTTGTTAAACATCAACT
1 AAATAACAAGTGCCTTGGACAGAATCAGCAGGTCAGATTGTACCTTGTTAAACATCAACT
4353155 GTCAAGGGTT
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
60 60 1.00
ACGTcount: A:0.37, C:0.20, G:0.18, T:0.25
Consensus pattern (60 bp):
AAATAACAAGTGCCTTGGACAGAATCAGCAGGTCAGATTGTACCTTGTTAAACATCAACT
Found at i:4359791 original size:66 final size:63
Alignment explanation
Indices: 4359713--4359915 Score: 155
Period size: 66 Copynumber: 3.1 Consensus size: 63
4359703 TAATAAAGTC
*
4359713 TTATATTATATATAAATATATTTGATTTATACATAAGCATTATTATAACTTATAATAGACTTTAT
1 TTATA-TATATATAAATATATTTGATATATACATAAGCATTATTATAACTTATAATA-ACTTTAT
* * * * * *
4359778 TTATATAATTATATAAA-ACATTTTAACATATA-ATTTGTATCACTAATTAT-A-TATATAATAA
1 TTATAT-A-TATATAAATATA-TTTGATATATACA--T-AAGCA-TTATTATAACT-TATAATAA
*
4359839 -TGTAAT
58 CT-TTAT
* * *
4359845 ATTATATATATATACATATATTTGATATATACATAAGTATTACTATAACTTATAATAAACTTTAT
1 -TTATATATATATAAATATATTTGATATATACATAAGCATTATTATAACTTATAAT-AACTTTAT
4359910 TTATAT
1 TTATAT
4359916 GATTATAGTT
Statistics
Matches: 104, Mismatches: 18, Indels: 33
0.67 0.12 0.21
Matches are distributed among these distances:
63 5 0.05
64 16 0.15
65 16 0.15
66 34 0.33
67 10 0.10
68 17 0.16
69 6 0.06
ACGTcount: A:0.44, C:0.06, G:0.03, T:0.46
Consensus pattern (63 bp):
TTATATATATATAAATATATTTGATATATACATAAGCATTATTATAACTTATAATAACTTTAT
Found at i:4359794 original size:128 final size:132
Alignment explanation
Indices: 4359662--4359922 Score: 341
Period size: 132 Copynumber: 2.0 Consensus size: 132
4359652 AAACTTTGAC
* * * * **
4359662 ATAAAATATTATAATATATAAGTTATGCCATTAA-T-TATATATAATAAAGTCTTA-TAT-TATA
1 ATAAAACATTATAACATATAAGTTATACCACTAATTATATATATAATAAAGTAATATTATATATA
* * *
4359723 TATAAATATATTTGATTTATACATAAGCATTATTATAACTTATAATAGACTTTATTTATATAATT
66 TATAAATATATTTGATATATACATAAGCATTACTATAACTTATAATAAACTTTATTTATATAATT
4359788 AT
131 AT
* * * * *
4359790 ATAAAACATTTTAACATATAATTTGTATCACTAATTATATATATAATAATGTAATATTATATATA
1 ATAAAACATTATAACATATAAGTTATACCACTAATTATATATATAATAAAGTAATATTATATATA
* * *
4359855 TATACATATATTTGATATATACATAAGTATTACTATAACTTATAATAAACTTTATTTATATGATT
66 TATAAATATATTTGATATATACATAAGCATTACTATAACTTATAATAAACTTTATTTATATAATT
4359920 AT
131 AT
4359922 A
1 A
4359923 GTTAATAAGT
Statistics
Matches: 112, Mismatches: 17, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
128 26 0.23
129 1 0.01
130 16 0.14
131 3 0.03
132 66 0.59
ACGTcount: A:0.45, C:0.06, G:0.04, T:0.45
Consensus pattern (132 bp):
ATAAAACATTATAACATATAAGTTATACCACTAATTATATATATAATAAAGTAATATTATATATA
TATAAATATATTTGATATATACATAAGCATTACTATAACTTATAATAAACTTTATTTATATAATT
AT
Found at i:4359863 original size:17 final size:17
Alignment explanation
Indices: 4359847--4359879 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
4359837 AATGTAATAT
4359847 TATAT-ATATATACATA
1 TATATGATATATACATA
*
4359863 TATTTGATATATACATA
1 TATATGATATATACATA
4359880 AGTATTACTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.45, C:0.06, G:0.03, T:0.45
Consensus pattern (17 bp):
TATATGATATATACATA
Found at i:4361928 original size:21 final size:20
Alignment explanation
Indices: 4361904--4361982 Score: 63
Period size: 21 Copynumber: 3.8 Consensus size: 20
4361894 ATTTATAATT
4361904 TATTTAAAATATTAATTTTGA
1 TATTTAAAATATTAATTTT-A
* *
4361925 TATTTTAAATATTAATACTT-
1 TATTTAAAATATTAAT-TTTA
*
4361945 TATTTATAAT-TTAATTATTAA
1 TATTTAAAATATTAATT-TT-A
*
4361966 AATTTTAAAATATTAAT
1 TA-TTTAAAATATTAAT
4361983 ATATTATTTA
Statistics
Matches: 45, Mismatches: 7, Indels: 10
0.73 0.11 0.16
Matches are distributed among these distances:
19 7 0.16
20 8 0.18
21 16 0.36
22 9 0.20
23 5 0.11
ACGTcount: A:0.44, C:0.01, G:0.01, T:0.53
Consensus pattern (20 bp):
TATTTAAAATATTAATTTTA
Found at i:4361963 original size:26 final size:25
Alignment explanation
Indices: 4361892--4361965 Score: 69
Period size: 26 Copynumber: 2.9 Consensus size: 25
4361882 TTAATATTAA
* *
4361892 TAATTTATAATTTATTTA-AAATAT
1 TAATTTATAATTTAATTATTAATAT
* *
4361916 TAATTTTGATATTTTAAATATTAATACT
1 TAA-TTT-ATAATTTAATTATTAATA-T
*
4361944 TTATTTATAATTTAATTATTAA
1 TAATTTATAATTTAATTATTAA
4361966 AATTTTAAAA
Statistics
Matches: 39, Mismatches: 7, Indels: 6
0.75 0.13 0.12
Matches are distributed among these distances:
24 3 0.08
25 3 0.08
26 23 0.59
27 7 0.18
28 3 0.08
ACGTcount: A:0.42, C:0.01, G:0.01, T:0.55
Consensus pattern (25 bp):
TAATTTATAATTTAATTATTAATAT
Found at i:4371066 original size:24 final size:22
Alignment explanation
Indices: 4371024--4371068 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
4371014 GGAAAAGTTA
4371024 AAAAAAAAGAAGAAAAAATATG
1 AAAAAAAAGAAGAAAAAATATG
*
4371046 AAAAAAAGGAAAGAGAAAAATAT
1 AAAAAAAAG-AAGA-AAAAATAT
4371069 CAATATGAGG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 8 0.40
23 4 0.20
24 8 0.40
ACGTcount: A:0.76, C:0.00, G:0.16, T:0.09
Consensus pattern (22 bp):
AAAAAAAAGAAGAAAAAATATG
Found at i:4379114 original size:19 final size:18
Alignment explanation
Indices: 4379092--4379148 Score: 51
Period size: 19 Copynumber: 2.8 Consensus size: 18
4379082 ATAAACATTA
4379092 TATATATATATATTTAACT
1 TATA-ATATATATTTAACT
4379111 TATACATAAGTATTATTATAACT
1 TATA-AT-A-TA-TATT-TAACT
*
4379134 TATAATATTTATTTA
1 TATAATATATATTTA
4379149 TATGATTATA
Statistics
Matches: 32, Mismatches: 2, Indels: 9
0.74 0.05 0.21
Matches are distributed among these distances:
18 2 0.06
19 10 0.31
20 2 0.06
21 3 0.09
22 6 0.19
23 9 0.28
ACGTcount: A:0.42, C:0.05, G:0.02, T:0.51
Consensus pattern (18 bp):
TATAATATATATTTAACT
Found at i:4379348 original size:213 final size:217
Alignment explanation
Indices: 4379088--4379550 Score: 588
Period size: 216 Copynumber: 2.1 Consensus size: 217
4379078 TTGTATAAAC
* *
4379088 ATTATATATATA-TATATTTAA--CTTATACATAAGTATTATTATAACTTATAAT-A-TTTATTT
1 ATTATATATATACTATATTTAATTTTTATACATAAGTATTACTATAACTTATAATAACTTTATTT
* * * * *
4379148 ATATGATTATATTTAATAACCTTATTAATTATCAC-TTAAGTTTTTATAATATATTTTTTATAAT
66 ACATGATTATACTTAATAACCTTATTAATTATCACTTTAA-ATTTTATAACATATTGTTTATAAT
4379212 TAGTTATTATTTATACAAACTTTG-AT-A-TAAAATATTATAACATAAAAGTTGTGACATTAATT
130 TAGTTATTATTTATACAAACTTTGAATAATTAAAATATTATAACATAAAAGTTGTGACATTAATT
*
4379274 TCATATATACATAATAAAAT-A-AT
195 TCATATAT--ATAAGAAAATAATAT
*
4379297 ATTATATATATACGTATATTTAATTTTTATACATAAGTATTACTGTAACTTATAATAGACTTTAT
1 ATTATATATATAC-TATATTTAATTTTTATACATAAGTATTACTATAACTTATAATA-ACTTTAT
** * *
4379362 TTACATGATTATACTTAATAATTTTATTAGTTATCTCTTTAAATTTTATAACATATTGTTTATAA
64 TTACATGATTATACTTAATAACCTTATTAATTATCACTTTAAATTTTATAACATATTGTTTATAA
* * *
4379427 TTAGTTATTATTTATACAAACTTTGATATAAAAATTAAAATATTATGACATATAAGTTGTGCCAT
129 TTAGTTATTATTTATACAAACTTTGA-AT---AATTAAAATATTATAACATAAAAGTTGTGACAT
* *
4379492 TATTTTCATATATATAAGAAGATAATAT
190 TAATTTCATATATATAAGAAAATAATAT
*
4379520 ATTATATATATACATATATTTAATTTATATA
1 ATTATATATATAC-TATATTTAATTTTTATA
4379551 TAATTTTTAT
Statistics
Matches: 217, Mismatches: 20, Indels: 20
0.84 0.08 0.08
Matches are distributed among these distances:
209 12 0.06
211 9 0.04
213 28 0.13
215 1 0.00
216 81 0.37
217 4 0.02
218 2 0.01
221 8 0.04
222 2 0.01
223 70 0.32
ACGTcount: A:0.41, C:0.06, G:0.05, T:0.47
Consensus pattern (217 bp):
ATTATATATATACTATATTTAATTTTTATACATAAGTATTACTATAACTTATAATAACTTTATTT
ACATGATTATACTTAATAACCTTATTAATTATCACTTTAAATTTTATAACATATTGTTTATAATT
AGTTATTATTTATACAAACTTTGAATAATTAAAATATTATAACATAAAAGTTGTGACATTAATTT
CATATATATAAGAAAATAATAT
Found at i:4385914 original size:25 final size:28
Alignment explanation
Indices: 4385857--4385916 Score: 81
Period size: 25 Copynumber: 2.2 Consensus size: 28
4385847 AAATTAAACA
*
4385857 AAACAAATAAAATACAATGATCAATGAG
1 AAACAAATAAAATACAATCATCAATGAG
4385885 AAACAAAT-AAA-ACAATCA-CAATGAG
1 AAACAAATAAAATACAATCATCAATGAG
*
4385910 GAACAAA
1 AAACAAA
4385917 AGCAAAAGTC
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
25 13 0.43
26 6 0.20
27 3 0.10
28 8 0.27
ACGTcount: A:0.63, C:0.13, G:0.10, T:0.13
Consensus pattern (28 bp):
AAACAAATAAAATACAATCATCAATGAG
Found at i:4400201 original size:6 final size:6
Alignment explanation
Indices: 4400190--4400215 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
4400180 GCAAAGAATG
4400190 GAGAGT GAGAGT GAGAGT GAGAGT GA
1 GAGAGT GAGAGT GAGAGT GAGAGT GA
4400216 AAGAAACGTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.35, C:0.00, G:0.50, T:0.15
Consensus pattern (6 bp):
GAGAGT
Found at i:4407849 original size:2 final size:2
Alignment explanation
Indices: 4407842--4407867 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
4407832 TAAAGTTAAG
4407842 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
4407868 TACAAATTTG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:4408291 original size:19 final size:18
Alignment explanation
Indices: 4408249--4408292 Score: 52
Period size: 19 Copynumber: 2.4 Consensus size: 18
4408239 TTTAAAAAAT
*
4408249 ATTTTTAAATTATTTTAA
1 ATTTTTAAATAATTTTAA
*
4408267 AATTTTAAATAAATTTTAA
1 ATTTTTAAAT-AATTTTAA
*
4408286 TTTTTTA
1 ATTTTTA
4408293 TTTTATATTC
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
18 9 0.43
19 12 0.57
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (18 bp):
ATTTTTAAATAATTTTAA
Found at i:4408457 original size:17 final size:17
Alignment explanation
Indices: 4408435--4408472 Score: 76
Period size: 17 Copynumber: 2.2 Consensus size: 17
4408425 TTTACTCTTC
4408435 ATGTTATTATTATGTCA
1 ATGTTATTATTATGTCA
4408452 ATGTTATTATTATGTCA
1 ATGTTATTATTATGTCA
4408469 ATGT
1 ATGT
4408473 GATATAAACA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.29, C:0.05, G:0.13, T:0.53
Consensus pattern (17 bp):
ATGTTATTATTATGTCA
Found at i:4408565 original size:29 final size:27
Alignment explanation
Indices: 4408533--4408605 Score: 74
Period size: 27 Copynumber: 2.6 Consensus size: 27
4408523 AAAATTAGTG
* * *
4408533 ATAAAAATTTATTTGATTAAAAATAAAA
1 ATAAAAAATTATTTAAAT-AAAATAAAA
* * *
4408561 TATAAAAACTTAATTAAATATAATAAAA
1 -ATAAAAAATTATTTAAATAAAATAAAA
4408589 ATAAAAAATTATTTAAA
1 ATAAAAAATTATTTAAA
4408606 ATTTTTTAAA
Statistics
Matches: 37, Mismatches: 7, Indels: 2
0.80 0.15 0.04
Matches are distributed among these distances:
27 15 0.41
28 8 0.22
29 14 0.38
ACGTcount: A:0.63, C:0.01, G:0.01, T:0.34
Consensus pattern (27 bp):
ATAAAAAATTATTTAAATAAAATAAAA
Found at i:4416015 original size:20 final size:23
Alignment explanation
Indices: 4415982--4416037 Score: 64
Period size: 20 Copynumber: 2.6 Consensus size: 23
4415972 TGAAGCTCTG
* *
4415982 ATAAAAAATAATAATT-TTTAA-
1 ATAATAAATTATAATTATTTAAC
*
4416003 A-ATTAAATTATAATTATTTAAC
1 ATAATAAATTATAATTATTTAAC
4416025 ATAATAAATTATA
1 ATAATAAATTATA
4416038 TAAGTTCTAA
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
20 11 0.39
21 6 0.21
22 1 0.04
23 10 0.36
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (23 bp):
ATAATAAATTATAATTATTTAAC
Found at i:4420528 original size:47 final size:47
Alignment explanation
Indices: 4420459--4420552 Score: 188
Period size: 47 Copynumber: 2.0 Consensus size: 47
4420449 ATTTGGGAGG
4420459 TTCTAGAAGTTCGGTTGGGAGGGAAAATTTGAATTTTCCAGCAGCCC
1 TTCTAGAAGTTCGGTTGGGAGGGAAAATTTGAATTTTCCAGCAGCCC
4420506 TTCTAGAAGTTCGGTTGGGAGGGAAAATTTGAATTTTCCAGCAGCCC
1 TTCTAGAAGTTCGGTTGGGAGGGAAAATTTGAATTTTCCAGCAGCCC
4420553 CCCTTACATG
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
47 47 1.00
ACGTcount: A:0.26, C:0.17, G:0.28, T:0.30
Consensus pattern (47 bp):
TTCTAGAAGTTCGGTTGGGAGGGAAAATTTGAATTTTCCAGCAGCCC
Found at i:4420621 original size:35 final size:35
Alignment explanation
Indices: 4420581--4420647 Score: 125
Period size: 35 Copynumber: 1.9 Consensus size: 35
4420571 GGGCTGGCAC
4420581 CCTCTTGGGCCTCCTGGCGGGTCTGGACTGTGTCA
1 CCTCTTGGGCCTCCTGGCGGGTCTGGACTGTGTCA
*
4420616 CCTCTTGGGCCTCCTGGTGGGTCTGGACTGTG
1 CCTCTTGGGCCTCCTGGCGGGTCTGGACTGTG
4420648 GCCCGTGACA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 31 1.00
ACGTcount: A:0.04, C:0.30, G:0.36, T:0.30
Consensus pattern (35 bp):
CCTCTTGGGCCTCCTGGCGGGTCTGGACTGTGTCA
Found at i:4427194 original size:17 final size:17
Alignment explanation
Indices: 4427166--4427199 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
4427156 TTAATTTGCT
4427166 AATTTAATATAATATATA
1 AATTTAATATAAT-TATA
4427184 AATTT-ATATAATTATA
1 AATTTAATATAATTATA
4427200 CAACAAACAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 4 0.25
17 7 0.44
18 5 0.31
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (17 bp):
AATTTAATATAATTATA
Found at i:4430845 original size:2 final size:2
Alignment explanation
Indices: 4430838--4430885 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
4430828 TCTTTTAAAA
4430838 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
4430880 AT AT AT
1 AT AT AT
4430886 GAATGTCGTC
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:4431836 original size:2 final size:2
Alignment explanation
Indices: 4431829--4431856 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
4431819 TCAAGCATCA
4431829 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
4431857 TTGGAGATGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:4441959 original size:2 final size:2
Alignment explanation
Indices: 4441952--4441976 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
4441942 GGCGTTATGT
4441952 AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC A
4441977 TTGGATCTAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:4449049 original size:2 final size:2
Alignment explanation
Indices: 4449044--4449082 Score: 53
Period size: 2 Copynumber: 20.0 Consensus size: 2
4449034 ATATATTTTG
* *
4449044 TA TA TA -A TG TA TA AA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
4449083 AGAATTTTGC
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (2 bp):
TA
Found at i:4469157 original size:10 final size:10
Alignment explanation
Indices: 4469142--4469173 Score: 55
Period size: 10 Copynumber: 3.2 Consensus size: 10
4469132 GAAAGTGAGT
*
4469142 AGCTTAATAA
1 AGCTTAACAA
4469152 AGCTTAACAA
1 AGCTTAACAA
4469162 AGCTTAACAA
1 AGCTTAACAA
4469172 AG
1 AG
4469174 AATATTGATC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 21 1.00
ACGTcount: A:0.50, C:0.16, G:0.12, T:0.22
Consensus pattern (10 bp):
AGCTTAACAA
Found at i:4473040 original size:2 final size:2
Alignment explanation
Indices: 4473033--4473059 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
4473023 GCACCTCCGA
4473033 TG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG T
4473060 ATTGTCTCAG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:4474703 original size:29 final size:31
Alignment explanation
Indices: 4474671--4474742 Score: 87
Period size: 31 Copynumber: 2.4 Consensus size: 31
4474661 AATTTTCGTC
4474671 AATTTAGTTTCT--ATACTT-AAAATTAAAAT
1 AATTTAGTTTCTCAAT-CTTAAAAATTAAAAT
* *
4474700 AATTTAGTTTTTCAATTTTAAAAATTAAAAT
1 AATTTAGTTTCTCAATCTTAAAAATTAAAAT
*
4474731 AATTTAATTTCT
1 AATTTAGTTTCT
4474743 TCTCTTAATG
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
29 11 0.31
30 2 0.06
31 23 0.64
ACGTcount: A:0.43, C:0.06, G:0.03, T:0.49
Consensus pattern (31 bp):
AATTTAGTTTCTCAATCTTAAAAATTAAAAT
Found at i:4478442 original size:33 final size:33
Alignment explanation
Indices: 4478405--4478472 Score: 82
Period size: 33 Copynumber: 2.1 Consensus size: 33
4478395 TTGACATAAT
* * *
4478405 ATGTTAACATACCATAATTGCTGATTATTTGAC
1 ATGTTAACATACCATAATTGATGATGATATGAC
* **
4478438 ATGTTAATATATTATAATTGATGATGATATGAC
1 ATGTTAACATACCATAATTGATGATGATATGAC
4478471 AT
1 AT
4478473 ATAAATTAGG
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.37, C:0.09, G:0.13, T:0.41
Consensus pattern (33 bp):
ATGTTAACATACCATAATTGATGATGATATGAC
Found at i:4478674 original size:29 final size:29
Alignment explanation
Indices: 4478599--4478675 Score: 70
Period size: 29 Copynumber: 2.6 Consensus size: 29
4478589 AATCATTAGT
* *
4478599 TATAAGAGCTTATTTGATCCAAAATAAAAG
1 TATAAGGGCTTATTTGAACC-AAATAAAAG
*
4478629 TATAATGGG-TTGA-TTGAACGC-AATATAAG
1 TATAA-GGGCTT-ATTTGAAC-CAAATAAAAG
4478658 TATAAGGGCTTATTTGAA
1 TATAAGGGCTTATTTGAA
4478676 TTTTCTTGAA
Statistics
Matches: 39, Mismatches: 3, Indels: 11
0.74 0.06 0.21
Matches are distributed among these distances:
28 4 0.10
29 19 0.49
30 12 0.31
31 4 0.10
ACGTcount: A:0.40, C:0.08, G:0.19, T:0.32
Consensus pattern (29 bp):
TATAAGGGCTTATTTGAACCAAATAAAAG
Found at i:4478772 original size:11 final size:11
Alignment explanation
Indices: 4478717--4478778 Score: 54
Period size: 13 Copynumber: 5.3 Consensus size: 11
4478707 CATTATGCTA
4478717 AAATAAAAAA-
1 AAATAAAAAAT
*
4478727 AATTAAAAAAT
1 AAATAAAAAAT
4478738 ACTAATAAAAAATT
1 A--AATAAAAAA-T
*
4478752 AAGAAAAAAAAGT
1 AA-ATAAAAAA-T
4478765 AAATAAAAAAT
1 AAATAAAAAAT
4478776 AAA
1 AAA
4478779 AGTTAGAAAA
Statistics
Matches: 42, Mismatches: 5, Indels: 9
0.75 0.09 0.16
Matches are distributed among these distances:
10 9 0.21
11 5 0.12
12 8 0.19
13 18 0.43
14 2 0.05
ACGTcount: A:0.77, C:0.02, G:0.03, T:0.18
Consensus pattern (11 bp):
AAATAAAAAAT
Found at i:4504413 original size:17 final size:18
Alignment explanation
Indices: 4504383--4504416 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
4504373 AAAATTTTAA
4504383 ATTTTTTAACATATTTTT
1 ATTTTTTAACATATTTTT
*
4504401 ATTTTTTTA-ATATTTT
1 ATTTTTTAACATATTTT
4504417 ATAATTTTAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.26, C:0.03, G:0.00, T:0.71
Consensus pattern (18 bp):
ATTTTTTAACATATTTTT
Found at i:4504423 original size:19 final size:20
Alignment explanation
Indices: 4504376--4504424 Score: 61
Period size: 19 Copynumber: 2.6 Consensus size: 20
4504366 ACCTACGAAA
4504376 ATTTTA-AATTTTTTAACAT
1 ATTTTATAATTTTTTAACAT
*
4504395 ATTTT-T-ATTTTTTTA-AT
1 ATTTTATAATTTTTTAACAT
4504412 ATTTTATAATTTT
1 ATTTTATAATTTT
4504425 ATTTGTAAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
17 7 0.27
18 9 0.35
19 10 0.38
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.67
Consensus pattern (20 bp):
ATTTTATAATTTTTTAACAT
Found at i:4505170 original size:18 final size:18
Alignment explanation
Indices: 4505134--4505171 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
4505124 TTATCTTTGA
*
4505134 ATTAAGATTATTTTTATT
1 ATTAAGATTATTTTGATT
4505152 ATTAA-ATTATTTATGATT
1 ATTAAGATTATTT-TGATT
4505170 AT
1 AT
4505172 AGTAGTTAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 7 0.39
18 11 0.61
ACGTcount: A:0.37, C:0.00, G:0.05, T:0.58
Consensus pattern (18 bp):
ATTAAGATTATTTTGATT
Found at i:4524440 original size:2 final size:2
Alignment explanation
Indices: 4524433--4524463 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
4524423 AGCTTGAAAG
*
4524433 TA TA TA TA TA TA TA TA CA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
4524464 GTGTGTGTGT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:4559471 original size:20 final size:21
Alignment explanation
Indices: 4559446--4559484 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
4559436 AAAAAAACTA
4559446 ATTGTTTC-AAACTGATTATC
1 ATTGTTTCTAAACTGATTATC
*
4559466 ATTGTTTCTTAACTGATTA
1 ATTGTTTCTAAACTGATTA
4559485 CCATCTTTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.28, C:0.13, G:0.10, T:0.49
Consensus pattern (21 bp):
ATTGTTTCTAAACTGATTATC
Found at i:4566981 original size:7 final size:8
Alignment explanation
Indices: 4566965--4566992 Score: 56
Period size: 8 Copynumber: 3.5 Consensus size: 8
4566955 CTTCATATTG
4566965 AAAAGAAA
1 AAAAGAAA
4566973 AAAAGAAA
1 AAAAGAAA
4566981 AAAAGAAA
1 AAAAGAAA
4566989 AAAA
1 AAAA
4566993 ATTCATCATC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.89, C:0.00, G:0.11, T:0.00
Consensus pattern (8 bp):
AAAAGAAA
Found at i:4575254 original size:6 final size:6
Alignment explanation
Indices: 4575246--4575278 Score: 57
Period size: 6 Copynumber: 5.5 Consensus size: 6
4575236 TATTATTTTG
*
4575246 ATGGAG ATGGAA ATGGAA ATGGAA ATGGAA ATG
1 ATGGAA ATGGAA ATGGAA ATGGAA ATGGAA ATG
4575279 AGGGAGAAGA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.45, C:0.00, G:0.36, T:0.18
Consensus pattern (6 bp):
ATGGAA
Found at i:4585442 original size:15 final size:15
Alignment explanation
Indices: 4585422--4585451 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
4585412 AATCAAAAGG
*
4585422 CAGAATTTGAGTAAA
1 CAGAATTTAAGTAAA
4585437 CAGAATTTAAGTAAA
1 CAGAATTTAAGTAAA
4585452 TTAAAATTTG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.50, C:0.07, G:0.17, T:0.27
Consensus pattern (15 bp):
CAGAATTTAAGTAAA
Found at i:4600514 original size:2 final size:2
Alignment explanation
Indices: 4600509--4600545 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
4600499 GAGGGGGGGG
4600509 GA GA GA GA GA GA GA GA GA GA GA GA G- GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
4600546 CTTACAGGAG
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 33 0.97
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (2 bp):
GA
Found at i:4602601 original size:26 final size:26
Alignment explanation
Indices: 4602519--4602604 Score: 79
Period size: 26 Copynumber: 3.4 Consensus size: 26
4602509 TATTTTAATT
* * * *
4602519 ATAATTTTACTACCAGAGGTGGATGG
1 ATAATTTTACTACTAGAAGTGGTTAG
* * *
4602545 ATAATTTTATTATTAGAA-T--TTAAA
1 ATAATTTTACTACTAGAAGTGGTT-AG
4602569 ATAATTTTACTACTAGAAGTGGTTAG
1 ATAATTTTACTACTAGAAGTGGTTAG
4602595 ATAATTTTAC
1 ATAATTTTAC
4602605 CATCGAAAGT
Statistics
Matches: 46, Mismatches: 10, Indels: 8
0.72 0.16 0.12
Matches are distributed among these distances:
23 1 0.02
24 16 0.35
25 2 0.04
26 25 0.54
27 2 0.04
ACGTcount: A:0.37, C:0.07, G:0.15, T:0.41
Consensus pattern (26 bp):
ATAATTTTACTACTAGAAGTGGTTAG
Found at i:4607107 original size:13 final size:13
Alignment explanation
Indices: 4607089--4607119 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
4607079 TCTATTTTTA
4607089 TATTTTTTATAAT
1 TATTTTTTATAAT
*
4607102 TATTTTTTATATT
1 TATTTTTTATAAT
4607115 TATTT
1 TATTT
4607120 CATAACATAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (13 bp):
TATTTTTTATAAT
Found at i:4611352 original size:50 final size:49
Alignment explanation
Indices: 4611277--4611429 Score: 153
Period size: 50 Copynumber: 3.2 Consensus size: 49
4611267 TAACCTTATA
*
4611277 TATTTT-ATTTTTGTTTCTT-TA--ATATAATTTTTTGTGTTATATATTT
1 TATTTTAATTTTTGATTCTTATATTATATAATTTTTT-TGTTATATATTT
* **
4611323 TATTTTAATTTTT-TTTACTTATATTATATAAATTTTAATGTCT-TATATTT
1 TATTTTAATTTTTGATT-CTTATATTATAT-AATTTTTTTGT-TATATATTT
*
4611373 TATTTTAATTTTTGATTCTTATATTATAT-ATTTTCTT-TTA-ATATTTT
1 TATTTTAATTTTTGATTCTTATATTATATAATTTTTTTGTTATATA-TTT
4611420 TATTTTAATT
1 TATTTTAATT
4611430 ATAATATTTT
Statistics
Matches: 92, Mismatches: 5, Indels: 19
0.79 0.04 0.16
Matches are distributed among these distances:
46 13 0.14
47 23 0.25
48 8 0.09
50 39 0.42
51 9 0.10
ACGTcount: A:0.26, C:0.03, G:0.03, T:0.67
Consensus pattern (49 bp):
TATTTTAATTTTTGATTCTTATATTATATAATTTTTTTGTTATATATTT
Found at i:4611392 original size:26 final size:25
Alignment explanation
Indices: 4611316--4611406 Score: 87
Period size: 26 Copynumber: 3.5 Consensus size: 25
4611306 TTTTGTGTTA
*
4611316 TATATTTTATTTTAATTTTTTTTACT
1 TATATTTTATTTTAATTTTTATT-CT
* * *
4611342 TATA--TTATATAAATTTTAATGTCT
1 TATATTTTATTTTAATTTTTAT-TCT
4611366 TATATTTTATTTTAATTTTTGATTCT
1 TATATTTTATTTTAATTTTT-ATTCT
4611392 TATATTATATATTTT
1 TATATT-T-TATTTT
4611407 CTTTTAATAT
Statistics
Matches: 52, Mismatches: 7, Indels: 10
0.75 0.10 0.14
Matches are distributed among these distances:
24 18 0.35
25 1 0.02
26 24 0.46
27 3 0.06
28 6 0.12
ACGTcount: A:0.29, C:0.03, G:0.02, T:0.66
Consensus pattern (25 bp):
TATATTTTATTTTAATTTTTATTCT
Found at i:4611404 original size:33 final size:32
Alignment explanation
Indices: 4611366--4611440 Score: 98
Period size: 33 Copynumber: 2.3 Consensus size: 32
4611356 TTTAATGTCT
4611366 TATATTTTATTTTAAT-TTTTGATTCTTATATTA
1 TATATTTTATTTTAATATTTTGATT-TTA-ATTA
* *
4611399 TATATTTTCTTTTAATATTTTTATTTTAATTA
1 TATATTTTATTTTAATATTTTGATTTTAATTA
4611431 TAATATTTTA
1 T-ATATTTTA
4611441 AAATATTTTT
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
32 5 0.14
33 25 0.68
34 7 0.19
ACGTcount: A:0.29, C:0.03, G:0.01, T:0.67
Consensus pattern (32 bp):
TATATTTTATTTTAATATTTTGATTTTAATTA
Found at i:4611425 original size:14 final size:15
Alignment explanation
Indices: 4611366--4611449 Score: 57
Period size: 14 Copynumber: 5.5 Consensus size: 15
4611356 TTTAATGTCT
4611366 TATATTTTATTTTAA
1 TATATTTTATTTTAA
* *
4611381 TTTTTGATTCTTATATT-A
1 --TAT-ATT-TTATTTTAA
*
4611399 TATATTTTCTTTTAA
1 TATATTTTATTTTAA
4611414 TAT-TTTTATTTTAA
1 TATATTTTATTTTAA
**
4611428 T-TATAATATTTTAA
1 TATATTTTATTTTAA
*
4611442 AATATTTT
1 TATATTTT
4611450 TAATAAGGTG
Statistics
Matches: 51, Mismatches: 11, Indels: 12
0.69 0.15 0.16
Matches are distributed among these distances:
13 1 0.02
14 25 0.49
15 11 0.22
16 2 0.04
17 2 0.04
18 4 0.08
19 6 0.12
ACGTcount: A:0.31, C:0.02, G:0.01, T:0.65
Consensus pattern (15 bp):
TATATTTTATTTTAA
Found at i:4612247 original size:2 final size:2
Alignment explanation
Indices: 4612240--4612268 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
4612230 AGATAGGCAC
4612240 AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
4612269 CAATGGCAAC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:4625678 original size:3 final size:3
Alignment explanation
Indices: 4625670--4625698 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
4625660 ATAAAACAGA
4625670 GAG GAG GAG GAG GAG GAG GAG GAG GAG GA
1 GAG GAG GAG GAG GAG GAG GAG GAG GAG GA
4625699 TAAAATATGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.34, C:0.00, G:0.66, T:0.00
Consensus pattern (3 bp):
GAG
Found at i:4635782 original size:18 final size:18
Alignment explanation
Indices: 4635745--4635795 Score: 57
Period size: 18 Copynumber: 2.8 Consensus size: 18
4635735 TAAAAGAAAC
** *
4635745 ATATTAGCTGAACCAGAA
1 ATATTAGCTGAATAAAAA
4635763 ATATTAGCTGAATAAAAA
1 ATATTAGCTGAATAAAAA
*
4635781 ATATATATCTGAATA
1 ATAT-TAGCTGAATA
4635796 TTAGCAGAAC
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
18 19 0.68
19 9 0.32
ACGTcount: A:0.49, C:0.10, G:0.12, T:0.29
Consensus pattern (18 bp):
ATATTAGCTGAATAAAAA
Found at i:4635826 original size:31 final size:30
Alignment explanation
Indices: 4635762--4635826 Score: 78
Period size: 31 Copynumber: 2.1 Consensus size: 30
4635752 CTGAACCAGA
* **
4635762 AATATTAGCTGAATAAAAAATATATATCTG
1 AATATTAGCAGAATAAAAAATATATATAAG
4635792 AATATTAGCAGAACTAAAAGAA-ATATATAAG
1 AATATTAGCAGAA-TAAAA-AATATATATAAG
4635823 AATA
1 AATA
4635827 AAACTTAATA
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
30 12 0.40
31 16 0.53
32 2 0.07
ACGTcount: A:0.55, C:0.06, G:0.11, T:0.28
Consensus pattern (30 bp):
AATATTAGCAGAATAAAAAATATATATAAG
Found at i:4646666 original size:20 final size:19
Alignment explanation
Indices: 4646620--4646686 Score: 66
Period size: 19 Copynumber: 3.5 Consensus size: 19
4646610 ACGTATGAAC
*
4646620 AAATAGATTATAAATGAAAA
1 AAATA-ATTATAAATTAAAA
4646640 AAATAATTATAAATTAAAA
1 AAATAATTATAAATTAAAA
* *
4646659 TTAATAA-TACAAATTAAAA
1 -AAATAATTATAAATTAAAA
4646678 GAAA-AATTA
1 -AAATAATTA
4646687 AAAAAAACTA
Statistics
Matches: 40, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
18 2 0.05
19 28 0.70
20 10 0.25
ACGTcount: A:0.66, C:0.01, G:0.04, T:0.28
Consensus pattern (19 bp):
AAATAATTATAAATTAAAA
Found at i:4647216 original size:15 final size:15
Alignment explanation
Indices: 4647184--4647249 Score: 51
Period size: 15 Copynumber: 4.1 Consensus size: 15
4647174 CATCCATTAA
* *
4647184 ATATAATTTTAATGTC
1 ATAT-ATTTTATTTTC
4647200 ATATATTTTATTTTC
1 ATATATTTTATTTTC
* * *
4647215 ATTTCTTATTATAATCTC
1 ATATATT-TTAT--TTTC
4647233 ATATATTTTATTTTC
1 ATATATTTTATTTTC
4647248 AT
1 AT
4647250 TTTTAATATA
Statistics
Matches: 39, Mismatches: 8, Indels: 7
0.72 0.15 0.13
Matches are distributed among these distances:
15 19 0.49
16 8 0.21
17 4 0.10
18 8 0.21
ACGTcount: A:0.30, C:0.09, G:0.02, T:0.59
Consensus pattern (15 bp):
ATATATTTTATTTTC
Found at i:4647271 original size:32 final size:32
Alignment explanation
Indices: 4647193--4647261 Score: 111
Period size: 33 Copynumber: 2.1 Consensus size: 32
4647183 AATATAATTT
* *
4647193 TAATGTCATATATTTTATTTTCATTTCTTATTA
1 TAATCTCATATATTTTATTTTCATTT-TTAATA
4647226 TAATCTCATATATTTTATTTTCATTTTTAATA
1 TAATCTCATATATTTTATTTTCATTTTTAATA
4647258 TAAT
1 TAAT
4647262 TTTTTATATT
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
32 9 0.26
33 25 0.74
ACGTcount: A:0.30, C:0.09, G:0.01, T:0.59
Consensus pattern (32 bp):
TAATCTCATATATTTTATTTTCATTTTTAATA
Found at i:4647309 original size:50 final size:49
Alignment explanation
Indices: 4647255--4647387 Score: 125
Period size: 50 Copynumber: 2.7 Consensus size: 49
4647245 TTCATTTTTA
*
4647255 ATATAATTTTTTATATTATGTATTTTATTTTAATTTTT-TTTACCTATATT
1 ATATAATTTTTTATATTAT-TATTTTATTTTAATTTTTGATT-CCTATATT
* *
4647305 ATATAAATTTTAATT-TCTTA-TATTTTATTTTAATTTTTGATTCTTATATT
1 ATAT-AATTTT--TTATATTATTATTTTATTTTAATTTTTGATTCCTATATT
*
4647355 ATAT-ATTATATTT-TAATATT-TTTTATTTTAATT
1 ATATAATT-T-TTTATATTATTATTTTATTTTAATT
4647388 ATAATATTAT
Statistics
Matches: 71, Mismatches: 5, Indels: 16
0.77 0.05 0.17
Matches are distributed among these distances:
48 21 0.30
49 2 0.03
50 34 0.48
51 8 0.11
52 4 0.06
53 2 0.03
ACGTcount: A:0.30, C:0.03, G:0.02, T:0.65
Consensus pattern (49 bp):
ATATAATTTTTTATATTATTATTTTATTTTAATTTTTGATTCCTATATT
Found at i:4647383 original size:48 final size:49
Alignment explanation
Indices: 4647275--4647387 Score: 131
Period size: 50 Copynumber: 2.3 Consensus size: 49
4647265 TTATATTATG
* * **
4647275 TATTTTATTTTAATTTTTTTTACCTATATTATATAAATTTTAATTTCTTA
1 TATTTTATTTTAATTTTTATTACCTATATTATAT-AATTATAATTTAATA
* *
4647325 TATTTTATTTTAATTTTTGATT-CTTATATTATAT-ATTATATTTTAATA
1 TATTTTATTTTAATTTTT-ATTACCTATATTATATAATTATAATTTAATA
*
4647373 TTTTTTATTTTAATT
1 TATTTTATTTTAATT
4647388 ATAATATTAT
Statistics
Matches: 55, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
48 24 0.44
50 29 0.53
51 2 0.04
ACGTcount: A:0.29, C:0.04, G:0.01, T:0.66
Consensus pattern (49 bp):
TATTTTATTTTAATTTTTATTACCTATATTATATAATTATAATTTAATA
Found at i:4647389 original size:33 final size:33
Alignment explanation
Indices: 4647323--4647398 Score: 93
Period size: 33 Copynumber: 2.3 Consensus size: 33
4647313 TTTAATTTCT
*
4647323 TATATTTTATTTTAATTTTTGATTCTTATATTA
1 TATATTATATTTTAATTTTTGATTCTTATATTA
*
4647356 TATATTATATTTTAATATTTTTTATT-TTA-ATTA
1 TATATTATATTTT-A-ATTTTTGATTCTTATATTA
4647389 TAATATTATA
1 T-ATATTATA
4647399 AAATATTTTT
Statistics
Matches: 38, Mismatches: 2, Indels: 5
0.84 0.04 0.11
Matches are distributed among these distances:
33 17 0.45
34 12 0.32
35 9 0.24
ACGTcount: A:0.33, C:0.01, G:0.01, T:0.64
Consensus pattern (33 bp):
TATATTATATTTTAATTTTTGATTCTTATATTA
Found at i:4656164 original size:2 final size:2
Alignment explanation
Indices: 4656157--4656185 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
4656147 GAAGCAAGGC
4656157 AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
4656186 TTATTGTAGC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:4657413 original size:24 final size:24
Alignment explanation
Indices: 4657386--4657439 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 24
4657376 CTAATTCATT
*
4657386 TTCTTCCTTCTTGTCTTCATCTCC
1 TTCTTCCTTCTTGCCTTCATCTCC
* **
4657410 TTCTTTCTTCTTGCCTTTTTCTCC
1 TTCTTCCTTCTTGCCTTCATCTCC
4657434 TTCTTC
1 TTCTTC
4657440 TCACCTTGCT
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.02, C:0.35, G:0.04, T:0.59
Consensus pattern (24 bp):
TTCTTCCTTCTTGCCTTCATCTCC
Found at i:4657451 original size:24 final size:26
Alignment explanation
Indices: 4657405--4657465 Score: 74
Period size: 25 Copynumber: 2.5 Consensus size: 26
4657395 CTTGTCTTCA
**
4657405 TCTCCTTCTT-TCTTCTTGCCTTT-T
1 TCTCCTTCTTCTCACCTTGCCTTTAT
4657429 TCTCCTTCTTCTCACCTTG-CTTTAT
1 TCTCCTTCTTCTCACCTTGCCTTTAT
*
4657454 TCTCTTTCTTCT
1 TCTCCTTCTTCT
4657466 TACTGTTCGT
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
24 14 0.44
25 18 0.56
ACGTcount: A:0.03, C:0.34, G:0.03, T:0.59
Consensus pattern (26 bp):
TCTCCTTCTTCTCACCTTGCCTTTAT
Found at i:4657810 original size:20 final size:20
Alignment explanation
Indices: 4657785--4657837 Score: 61
Period size: 20 Copynumber: 2.6 Consensus size: 20
4657775 ATTATTACTT
* *
4657785 ATCTATTGATAAATAGTATA
1 ATCTATCGATAAATAATATA
* *
4657805 ATCTATCGATAGATAATATG
1 ATCTATCGATAAATAATATA
*
4657825 ATCTATCGTTAAA
1 ATCTATCGATAAA
4657838 ATTATCTATT
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.42, C:0.09, G:0.11, T:0.38
Consensus pattern (20 bp):
ATCTATCGATAAATAATATA
Found at i:4657985 original size:13 final size:14
Alignment explanation
Indices: 4657967--4657995 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
4657957 TAAAAATATT
4657967 ATGTTATT-TTTTA
1 ATGTTATTATTTTA
4657980 ATGTTATTATTTTA
1 ATGTTATTATTTTA
4657994 AT
1 AT
4657996 TATTTAAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 8 0.53
14 7 0.47
ACGTcount: A:0.28, C:0.00, G:0.07, T:0.66
Consensus pattern (14 bp):
ATGTTATTATTTTA
Found at i:4661026 original size:27 final size:28
Alignment explanation
Indices: 4660973--4661026 Score: 67
Period size: 27 Copynumber: 2.0 Consensus size: 28
4660963 TTATTCCATT
* *
4660973 TAGTTACTAATTTTATTTTCAAAAGAAA
1 TAGTTACTAATTTTAGTTTAAAAAGAAA
4661001 TAGTTACT-ATTTT-GTTTAAAAGAGAA
1 TAGTTACTAATTTTAGTTTAAAA-AGAA
4661027 CGCAGAAAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
26 6 0.26
27 9 0.39
28 8 0.35
ACGTcount: A:0.41, C:0.06, G:0.11, T:0.43
Consensus pattern (28 bp):
TAGTTACTAATTTTAGTTTAAAAAGAAA
Found at i:4663696 original size:6 final size:6
Alignment explanation
Indices: 4663685--4663712 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
4663675 ACAAGTGTGA
4663685 AAAAAG AAAAAG AAAAAG AAAAAG AAAA
1 AAAAAG AAAAAG AAAAAG AAAAAG AAAA
4663713 CAACTTTTAG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (6 bp):
AAAAAG
Found at i:4667373 original size:2 final size:2
Alignment explanation
Indices: 4667366--4667403 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
4667356 GAAGCAGACA
4667366 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
4667404 GGAGGGAATT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:4669841 original size:12 final size:12
Alignment explanation
Indices: 4669823--4669852 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
4669813 GTTAATCTCA
4669823 AGAGGGAGGGAG
1 AGAGGGAGGGAG
*
4669835 GGAGGGAGGGAG
1 AGAGGGAGGGAG
4669847 AGAGGG
1 AGAGGG
4669853 GGCGGGGGGA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.30, C:0.00, G:0.70, T:0.00
Consensus pattern (12 bp):
AGAGGGAGGGAG
Found at i:4684372 original size:60 final size:59
Alignment explanation
Indices: 4684299--4684693 Score: 283
Period size: 56 Copynumber: 6.7 Consensus size: 59
4684289 CTAATTATTA
**
4684299 AAATATAAGTTTAATATATTTATATTTTTTATTATTAATTTTTATATAATATCATTTCTT
1 AAATATATTTTTAATATATTTATA-TTTTTATTATTAATTTTTATATAATATCATTTCTT
* *
4684359 AAATATATTTTTAATATCA--TATA-TTTTATT-TTTATTTATTATTATAATAT--TTT-AT
1 AAATATATTTTTAATAT-ATTTATATTTTTATTATTAATTT-TTA-TATAATATCATTTCTT
* * * *
4684414 -ATTTTATTTTTAATATATTTATATTTTTATTATTAATTTTTATATAACATCATATCTT
1 AAATATATTTTTAATATATTTATATTTTTATTATTAATTTTTATATAATATCATTTCTT
* * *
4684472 AAATATATTTTTAATGTCA--TATA-TTTTATT-TTTATTTATTATTATAATAT--TTT-AT
1 AAATATATTTTTAATAT-ATTTATATTTTTATTATTAATTT-TTA-TATAATATCATTTCTT
** * *
4684527 ATTTA-ATATTTAATATATTTATATTTATATTATTAATTTTTATATAATATCATATT-TT
1 AAATATATTTTTAATATATTTATATTTTTATTATTAATTTTTATATAATATCAT-TTCTT
* *
4684585 AAATATATTTTTAATGTCATATATTTTATTTTTATTTATTATTATAATTTTATATATTTATTTTC
1 AAATATATTTTTAA--T-ATAT-TTATATTTTTA-TTATTA--AT--TTTTATATA---A-TATC
4684650 ATTTCTT
53 ATTTCTT
*
4684657 TAATATATTTTT--TATA-TTATATATTTTATT-TTAATTT
1 AAATATATTTTTAATATATTTATAT-TTTTATTATTAATTT
4684694 GTTTTATCTA
Statistics
Matches: 266, Mismatches: 32, Indels: 74
0.72 0.09 0.20
Matches are distributed among these distances:
53 2 0.01
54 23 0.09
55 28 0.11
56 36 0.14
57 35 0.13
58 26 0.10
59 24 0.09
60 18 0.07
61 2 0.01
62 6 0.02
63 9 0.03
64 9 0.03
65 7 0.03
66 7 0.03
67 3 0.01
68 10 0.04
71 3 0.01
72 18 0.07
ACGTcount: A:0.34, C:0.03, G:0.01, T:0.62
Consensus pattern (59 bp):
AAATATATTTTTAATATATTTATATTTTTATTATTAATTTTTATATAATATCATTTCTT
Done.