Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr13 124041150
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: 124041150
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 335 characters in sequence are not A, C, G, or T
File 71 of 410
Found at i:19899375 original size:47 final size:48
Alignment explanation
Indices: 19899305--19899570 Score: 193
Period size: 47 Copynumber: 5.7 Consensus size: 48
19899295 GTAAGGTGCA
* **
19899305 GATGCCATGTCCCAGACACGGTCTTACACTAGCTCAT-ATCTCATGTT
1 GATGCCATGTCCCAGACATGGTCTTACACTAGCTCATCATCTCATGCC
*
19899352 GATGCCATGTCCCAGACATGGTCTTACACT-GACT-ATCATCTCGTAGCC
1 GATGCCATGTCCCAGACATGGTCTTACACTAG-CTCATCATCTCAT-GCC
* * * * *
19899400 GATG-CATGTCCCAGACAT-GTCTTACACTGGTTTA-CGTTTCGA-GACC
1 GATGCCATGTCCCAGACATGGTCTTACACTAGCTCATCATCTC-ATG-CC
* * * * *
19899446 AATG-CATGTCCCAGACAT-GTCTTACACTAGCAC-TCGTCTTGATGCT
1 GATGCCATGTCCCAGACATGGTCTTACACTAGCTCATCATC-TCATGCC
* * *
19899492 GATGCCATGTCCCAGACATGGTCTTACACT-GACTC-TCATAAT-GTGGCT
1 GATGCCATGTCCCAGACATGGTCTTACACTAG-CTCATCAT-CTCAT-GCC
*
19899540 AATG-CATGTCCCAGACAT-GTCTTACACTAGC
1 GATGCCATGTCCCAGACATGGTCTTACACTAGC
19899571 CCACAATAAC
Statistics
Matches: 181, Mismatches: 22, Indels: 33
0.77 0.09 0.14
Matches are distributed among these distances:
45 1 0.01
46 67 0.37
47 86 0.48
48 27 0.15
ACGTcount: A:0.24, C:0.29, G:0.19, T:0.29
Consensus pattern (48 bp):
GATGCCATGTCCCAGACATGGTCTTACACTAGCTCATCATCTCATGCC
Found at i:19899451 original size:46 final size:46
Alignment explanation
Indices: 19899357--19899567 Score: 182
Period size: 46 Copynumber: 4.5 Consensus size: 46
19899347 ATGTTGATGC
*
19899357 CATGTCCCAGACATGGTCTTACACTGACTATCATCTCGTAGCCGATG
1 CATGTCCCAGACAT-GTCTTACACTGACTATCATCTCGTAGCCAATG
* * * *
19899404 CATGTCCCAGACATGTCTTACACTG-GTTTACGTTTCG-AGACCAATG
1 CATGTCCCAGACATGTCTTACACTGACTAT-CATCTCGTAG-CCAATG
* * **
19899450 CATGTCCCAGACATGTCTTACACT-AGC-ACTCGTCTTG-ATGCTGATG
1 CATGTCCCAGACATGTCTTACACTGA-CTA-TCATCTCGTA-GCCAATG
* * * *
19899496 CCATGTCCCAGACATGGTCTTACACTGACTCTCATAAT-GTGGCTAATG
1 -CATGTCCCAGACAT-GTCTTACACTGACTATCAT-CTCGTAGCCAATG
19899544 CATGTCCCAGACATGTCTTACACT
1 CATGTCCCAGACATGTCTTACACT
19899568 AGCCCACAAT
Statistics
Matches: 136, Mismatches: 16, Indels: 25
0.77 0.09 0.14
Matches are distributed among these distances:
45 4 0.03
46 65 0.48
47 44 0.32
48 21 0.15
49 2 0.01
ACGTcount: A:0.24, C:0.28, G:0.18, T:0.29
Consensus pattern (46 bp):
CATGTCCCAGACATGTCTTACACTGACTATCATCTCGTAGCCAATG
Found at i:19899562 original size:140 final size:140
Alignment explanation
Indices: 19899310--19899567 Score: 378
Period size: 140 Copynumber: 1.8 Consensus size: 140
19899300 GTGCAGATGC
*
19899310 CATGTCCCAGACACGGTCTTACACTAGCTCATATCTCATGTTGATGCCATGTCCCAGACATGGTC
1 CATGTCCCAGACACGGTCTTACACTAGCTCATATCTCATGCTGATGCCATGTCCCAGACATGGTC
* *
19899375 TTACACTGACTATCATCTCGTAGCCGATGCATGTCCCAGACATGTCTTACACTGGTTTACGTTTC
66 TTACACTGACTATCATATCGTAGCCAATGCATGTCCCAGACATGTCTTACACTGGTTTACGTTTC
19899440 GAGACCAATG
131 GAGACCAATG
* * * *
19899450 CATGTCCCAGACA-TGTCTTACACTAGCAC-TCGTCTTGATGCTGATGCCATGTCCCAGACATGG
1 CATGTCCCAGACACGGTCTTACACTAGCTCAT-ATC-TCATGCTGATGCCATGTCCCAGACATGG
* * *
19899513 TCTTACACTGACTCTCATAAT-GTGGCTAATGCATGTCCCAGACATGTCTTACACT
64 TCTTACACTGACTATCAT-ATCGTAGCCAATGCATGTCCCAGACATGTCTTACACT
19899568 AGCCCACAAT
Statistics
Matches: 105, Mismatches: 10, Indels: 6
0.87 0.08 0.05
Matches are distributed among these distances:
138 1 0.01
139 16 0.15
140 87 0.83
141 1 0.01
ACGTcount: A:0.24, C:0.29, G:0.18, T:0.29
Consensus pattern (140 bp):
CATGTCCCAGACACGGTCTTACACTAGCTCATATCTCATGCTGATGCCATGTCCCAGACATGGTC
TTACACTGACTATCATATCGTAGCCAATGCATGTCCCAGACATGTCTTACACTGGTTTACGTTTC
GAGACCAATG
Found at i:19905863 original size:43 final size:43
Alignment explanation
Indices: 19905801--19905961 Score: 162
Period size: 43 Copynumber: 3.8 Consensus size: 43
19905791 GTACAACGGC
* * *
19905801 ATATCCCAGATATGGTCTTACATGTTATCACATATCAATGCCA
1 ATATCCCAGACATGGTCTTACACGTAATCACATATCAATGCCA
* * * * * * *
19905844 CTATCCCAGACAAGGTCTTACACGAAATTATATAACGATGCCA
1 ATATCCCAGACATGGTCTTACACGTAATCACATATCAATGCCA
* * * *
19905887 ATGTCCTAGACATGGTCTTACACATAATCACAAAT-AATGCCA
1 ATATCCCAGACATGGTCTTACACGTAATCACATATCAATGCCA
* * *
19905929 ATGTCCTAGACATGGTCTTACATGTAATCACAT
1 ATATCCCAGACATGGTCTTACACGTAATCACAT
19905962 CTCGGTAACC
Statistics
Matches: 94, Mismatches: 24, Indels: 1
0.79 0.20 0.01
Matches are distributed among these distances:
42 36 0.38
43 58 0.62
ACGTcount: A:0.35, C:0.24, G:0.13, T:0.29
Consensus pattern (43 bp):
ATATCCCAGACATGGTCTTACACGTAATCACATATCAATGCCA
Found at i:19905937 original size:42 final size:42
Alignment explanation
Indices: 19905881--19905960 Score: 142
Period size: 42 Copynumber: 1.9 Consensus size: 42
19905871 TTATATAACG
19905881 ATGCCAATGTCCTAGACATGGTCTTACACATAATCACAAATA
1 ATGCCAATGTCCTAGACATGGTCTTACACATAATCACAAATA
**
19905923 ATGCCAATGTCCTAGACATGGTCTTACATGTAATCACA
1 ATGCCAATGTCCTAGACATGGTCTTACACATAATCACA
19905961 TCTCGGTAAC
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 36 1.00
ACGTcount: A:0.35, C:0.24, G:0.14, T:0.28
Consensus pattern (42 bp):
ATGCCAATGTCCTAGACATGGTCTTACACATAATCACAAATA
Found at i:19910727 original size:23 final size:21
Alignment explanation
Indices: 19910697--19910743 Score: 67
Period size: 23 Copynumber: 2.1 Consensus size: 21
19910687 AGCCCACATC
19910697 AAAAAATAAAAATAAAAATTTCA
1 AAAAAATAAAAA-AAAAATTT-A
*
19910720 AAAAAATAAAAAAAATATTTA
1 AAAAAATAAAAAAAAAATTTA
19910741 AAA
1 AAA
19910744 TTATTTTTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 4 0.17
22 7 0.30
23 12 0.52
ACGTcount: A:0.77, C:0.02, G:0.00, T:0.21
Consensus pattern (21 bp):
AAAAAATAAAAAAAAAATTTA
Found at i:19910873 original size:19 final size:17
Alignment explanation
Indices: 19910832--19910918 Score: 68
Period size: 18 Copynumber: 4.6 Consensus size: 17
19910822 TCTATTCTAG
19910832 AATTATAAAAAT-ATAAGA
1 AATTATAAAAATAAT-A-A
19910850 AATTATAAAAATAATTAA
1 AATTATAAAAATAA-TAA
*
19910868 ACATTATAAAAATTATTAGA
1 A-ATTATAAAAA-TAATA-A
19910888 AATTAATTAAAAATAATAA
1 AATT-A-TAAAAATAATAA
*
19910907 ATTTTATAAAAA
1 A-ATTATAAAAA
19910919 ATATTATATT
Statistics
Matches: 58, Mismatches: 3, Indels: 16
0.75 0.04 0.21
Matches are distributed among these distances:
18 20 0.34
19 20 0.34
20 12 0.21
21 6 0.10
ACGTcount: A:0.63, C:0.01, G:0.02, T:0.33
Consensus pattern (17 bp):
AATTATAAAAATAATAA
Found at i:19910916 original size:18 final size:18
Alignment explanation
Indices: 19910832--19910918 Score: 77
Period size: 19 Copynumber: 4.6 Consensus size: 18
19910822 TCTATTCTAG
19910832 AATTATAAAAAT-ATAAGA
1 AATTATAAAAATAATAA-A
19910850 AATTATAAAAATAATTAAA
1 AATTATAAAAATAA-TAAA
* * *
19910869 CATTATAAAAATTATTAGA
1 AATTATAAAAA-TAATAAA
19910888 AATTAATTAAAAATAATAAA
1 AATT-A-TAAAAATAATAAA
**
19910908 TTTTATAAAAA
1 AATTATAAAAA
19910919 ATATTATATT
Statistics
Matches: 56, Mismatches: 8, Indels: 10
0.76 0.11 0.14
Matches are distributed among these distances:
18 18 0.32
19 19 0.34
20 13 0.23
21 6 0.11
ACGTcount: A:0.63, C:0.01, G:0.02, T:0.33
Consensus pattern (18 bp):
AATTATAAAAATAATAAA
Found at i:19910920 original size:19 final size:18
Alignment explanation
Indices: 19910834--19910932 Score: 58
Period size: 19 Copynumber: 5.3 Consensus size: 18
19910824 TATTCTAGAA
*
19910834 TTATAAAAATATAAGAAA-
1 TTATAAAAA-ATAATAAAT
*
19910852 TTAT-AAAAATAATTAAACA
1 TTATAAAAAATAA-TAAA-T
* *
19910871 TTATAAAAATTATTAGAAAT
1 TTATAAAAA--ATAATAAAT
* *
19910891 TAATTAAAAATAATAAATT
1 TTATAAAAAATAATAAA-T
* *
19910910 TTATAAAAAATATTATAT
1 TTATAAAAAATAATAAAT
19910928 TTATA
1 TTATA
19910933 TTTTAACTCA
Statistics
Matches: 62, Mismatches: 12, Indels: 14
0.70 0.14 0.16
Matches are distributed among these distances:
16 4 0.06
17 7 0.11
18 16 0.26
19 18 0.29
20 11 0.18
21 3 0.05
22 3 0.05
ACGTcount: A:0.60, C:0.01, G:0.02, T:0.37
Consensus pattern (18 bp):
TTATAAAAAATAATAAAT
Found at i:19911111 original size:19 final size:19
Alignment explanation
Indices: 19911087--19911145 Score: 64
Period size: 19 Copynumber: 3.1 Consensus size: 19
19911077 AATTAATTTC
*
19911087 TAATAATTTTTATAAATAT
1 TAATAATTTTTATAATTAT
* * *
19911106 TAATAAATTTTAATGATTTT
1 TAAT-AATTTTTATAATTAT
*
19911126 TAATTATTTTTATAATTAT
1 TAATAATTTTTATAATTAT
19911145 T
1 T
19911146 TTATGTTTTT
Statistics
Matches: 31, Mismatches: 8, Indels: 2
0.76 0.20 0.05
Matches are distributed among these distances:
19 16 0.52
20 15 0.48
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.58
Consensus pattern (19 bp):
TAATAATTTTTATAATTAT
Found at i:19911246 original size:6 final size:7
Alignment explanation
Indices: 19911228--19911252 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
19911218 TTTTTTTAAT
19911228 ATTTTTA
1 ATTTTTA
19911235 ATTTTTA
1 ATTTTTA
19911242 ATTTTTA
1 ATTTTTA
19911249 ATTT
1 ATTT
19911253 ATGTTGATAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (7 bp):
ATTTTTA
Found at i:19911281 original size:74 final size:74
Alignment explanation
Indices: 19911203--19911352 Score: 282
Period size: 74 Copynumber: 2.0 Consensus size: 74
19911193 TAATTTGTCC
*
19911203 AGATTCATTGTATATTTTTTTTAATATTTTTAATTTTTAATTTTTAATTTATGTTGATATGGCAC
1 AGATTCATTGTATATTTTTTTAAATATTTTTAATTTTTAATTTTTAATTTATGTTGATATGGCAC
19911268 TGTCACCAT
66 TGTCACCAT
*
19911277 AGATTCATTGTATATTTTTTTAAATATTTTTAATTTTTAATTTTTAATTTATGTTGATGTGGCAC
1 AGATTCATTGTATATTTTTTTAAATATTTTTAATTTTTAATTTTTAATTTATGTTGATATGGCAC
19911342 TGTCACCAT
66 TGTCACCAT
19911351 AG
1 AG
19911353 CAATTAGCGC
Statistics
Matches: 74, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
74 74 1.00
ACGTcount: A:0.27, C:0.08, G:0.11, T:0.54
Consensus pattern (74 bp):
AGATTCATTGTATATTTTTTTAAATATTTTTAATTTTTAATTTTTAATTTATGTTGATATGGCAC
TGTCACCAT
Found at i:19911320 original size:6 final size:7
Alignment explanation
Indices: 19911302--19911326 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
19911292 TTTTTTAAAT
19911302 ATTTTTA
1 ATTTTTA
19911309 ATTTTTA
1 ATTTTTA
19911316 ATTTTTA
1 ATTTTTA
19911323 ATTT
1 ATTT
19911327 ATGTTGATGT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (7 bp):
ATTTTTA
Found at i:19912683 original size:30 final size:30
Alignment explanation
Indices: 19912649--19912711 Score: 108
Period size: 30 Copynumber: 2.1 Consensus size: 30
19912639 CTTTATTTTA
*
19912649 TTGTTAATTTTCTTATTATTTTAAAGGCAT
1 TTGTTAATTTTCTTATTATTTTAAAAGCAT
*
19912679 TTGTTAATTTTTTTATTATTTTAAAAGCAT
1 TTGTTAATTTTCTTATTATTTTAAAAGCAT
19912709 TTG
1 TTG
19912712 CTTGTTAAGT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.27, C:0.05, G:0.10, T:0.59
Consensus pattern (30 bp):
TTGTTAATTTTCTTATTATTTTAAAAGCAT
Found at i:19913268 original size:12 final size:12
Alignment explanation
Indices: 19913251--19913276 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
19913241 AAAATAGGGC
19913251 TTTAGCGGCGTT
1 TTTAGCGGCGTT
19913263 TTTAGCGGCGTT
1 TTTAGCGGCGTT
19913275 TT
1 TT
19913277 ATCAAAAAAC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.08, C:0.15, G:0.31, T:0.46
Consensus pattern (12 bp):
TTTAGCGGCGTT
Found at i:19913406 original size:41 final size:41
Alignment explanation
Indices: 19913330--19913590 Score: 382
Period size: 41 Copynumber: 6.4 Consensus size: 41
19913320 CGTTTTATCA
* * *
19913330 AAAACGCCGCTAAAA-ACTGAGCAATAGCGGTGCTTTTGGT
1 AAAACGCCGCTAAAAGACAGAGCATTAGCGGCGCTTTTGGT
*
19913370 AAAGCGCCGCTAAAAGACAGAG-ATTTAGCGGCGCTTTTGGT
1 AAAACGCCGCTAAAAGACAGAGCA-TTAGCGGCGCTTTTGGT
*
19913411 AAAACGCCGCTAAAAGACAGAGCTTTAGCGGCGCTTTTGGT
1 AAAACGCCGCTAAAAGACAGAGCATTAGCGGCGCTTTTGGT
* *
19913452 AAAATGCCGCTAAAAGACAGAGCAGTAGCGGCGCTTTTGGT
1 AAAACGCCGCTAAAAGACAGAGCATTAGCGGCGCTTTTGGT
* * * *
19913493 AAAACGTCACGAAAAGACAAAGCATTAGCGGCGCTTTTGGT
1 AAAACGCCGCTAAAAGACAGAGCATTAGCGGCGCTTTTGGT
* *
19913534 AAAACGCCGCTAAAAGACAGAGCAGTATCGGCGCTTTTGGT
1 AAAACGCCGCTAAAAGACAGAGCATTAGCGGCGCTTTTGGT
19913575 AAAACGCCGCTAAAAG
1 AAAACGCCGCTAAAAG
19913591 TCATATAACT
Statistics
Matches: 197, Mismatches: 21, Indels: 5
0.88 0.09 0.02
Matches are distributed among these distances:
40 15 0.08
41 182 0.92
ACGTcount: A:0.33, C:0.21, G:0.26, T:0.20
Consensus pattern (41 bp):
AAAACGCCGCTAAAAGACAGAGCATTAGCGGCGCTTTTGGT
Found at i:19914229 original size:24 final size:24
Alignment explanation
Indices: 19914202--19914250 Score: 89
Period size: 24 Copynumber: 2.0 Consensus size: 24
19914192 CGTATATTTA
*
19914202 TTAAAAGTTTATATAAAAATTAAT
1 TTAAAAGTCTATATAAAAATTAAT
19914226 TTAAAAGTCTATATAAAAATTAAT
1 TTAAAAGTCTATATAAAAATTAAT
19914250 T
1 T
19914251 GTTATTTTAA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.53, C:0.02, G:0.04, T:0.41
Consensus pattern (24 bp):
TTAAAAGTCTATATAAAAATTAAT
Found at i:19914563 original size:15 final size:14
Alignment explanation
Indices: 19914543--19914574 Score: 55
Period size: 15 Copynumber: 2.2 Consensus size: 14
19914533 GGTTTACGGA
19914543 TTATGGATTATGGGT
1 TTATGGATTAT-GGT
19914558 TTATGGATTATGGT
1 TTATGGATTATGGT
19914572 TTA
1 TTA
19914575 CAATTTATGG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 6 0.35
15 11 0.65
ACGTcount: A:0.22, C:0.00, G:0.28, T:0.50
Consensus pattern (14 bp):
TTATGGATTATGGT
Found at i:19914602 original size:21 final size:22
Alignment explanation
Indices: 19914578--19914643 Score: 59
Period size: 21 Copynumber: 3.1 Consensus size: 22
19914568 TGGTTTACAA
*
19914578 TTTATGGTTTAAGG-GTT-GGGG
1 TTTAAGGTTT-AGGTGTTAGGGG
19914599 TTTAAGGTTTAGGTGTTAGGGG
1 TTTAAGGTTTAGGTGTTAGGGG
* *
19914621 -TTAGGGGTTATGG-GTTAGGGG
1 TTTAAGGTTTA-GGTGTTAGGGG
19914642 TT
1 TT
19914644 AGGGGTTATG
Statistics
Matches: 38, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
20 3 0.08
21 28 0.74
22 7 0.18
ACGTcount: A:0.15, C:0.00, G:0.44, T:0.41
Consensus pattern (22 bp):
TTTAAGGTTTAGGTGTTAGGGG
Found at i:19914617 original size:7 final size:7
Alignment explanation
Indices: 19914607--19914651 Score: 72
Period size: 7 Copynumber: 6.4 Consensus size: 7
19914597 GGTTTAAGGT
*
19914607 TTAGGTG
1 TTAGGGG
19914614 TTAGGGG
1 TTAGGGG
19914621 TTAGGGG
1 TTAGGGG
*
19914628 TTATGGG
1 TTAGGGG
19914635 TTAGGGG
1 TTAGGGG
19914642 TTAGGGG
1 TTAGGGG
19914649 TTA
1 TTA
19914652 TGGATTTAAG
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
7 35 1.00
ACGTcount: A:0.16, C:0.00, G:0.49, T:0.36
Consensus pattern (7 bp):
TTAGGGG
Found at i:19914644 original size:21 final size:21
Alignment explanation
Indices: 19914613--19914654 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
19914603 AGGTTTAGGT
19914613 GTTAGGGGTTAGGGGTTATGG
1 GTTAGGGGTTAGGGGTTATGG
19914634 GTTAGGGGTTAGGGGTTATGG
1 GTTAGGGGTTAGGGGTTATGG
19914655 ATTTAAGGGT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.14, C:0.00, G:0.52, T:0.33
Consensus pattern (21 bp):
GTTAGGGGTTAGGGGTTATGG
Found at i:19915041 original size:22 final size:23
Alignment explanation
Indices: 19915016--19915079 Score: 71
Period size: 22 Copynumber: 2.9 Consensus size: 23
19915006 AAATTTTTAA
*
19915016 AAAAATTATTTAAAATT-AATAT
1 AAAAATTATTAAAAATTCAATAT
19915038 AAAAGA-TA-TAAAAATTCAATAT
1 AAAA-ATTATTAAAAATTCAATAT
* *
19915060 AAAAATTATAAAAAAGTCAA
1 AAAAATTATTAAAAATTCAA
19915080 AAATTAGCGG
Statistics
Matches: 35, Mismatches: 3, Indels: 7
0.78 0.07 0.16
Matches are distributed among these distances:
21 8 0.23
22 17 0.49
23 10 0.29
ACGTcount: A:0.64, C:0.03, G:0.03, T:0.30
Consensus pattern (23 bp):
AAAAATTATTAAAAATTCAATAT
Found at i:19915152 original size:38 final size:40
Alignment explanation
Indices: 19915084--19915192 Score: 186
Period size: 38 Copynumber: 2.8 Consensus size: 40
19915074 AGTCAAAAAT
19915084 TAGCGGCGTTTATGATAAAAACGCCGCAAAAGACAAGCAA
1 TAGCGGCGTTTATGATAAAAACGCCGCAAAAGACAAGCAA
* *
19915124 TAGCGGCGTTTAT-AT-AAAACGCCGCAAAAGGCAATCAA
1 TAGCGGCGTTTATGATAAAAACGCCGCAAAAGACAAGCAA
19915162 TAGCGGCGTTTATGATAAAAACGCCGCAAAA
1 TAGCGGCGTTTATGATAAAAACGCCGCAAAA
19915193 AGTAATTTAT
Statistics
Matches: 65, Mismatches: 2, Indels: 4
0.92 0.03 0.06
Matches are distributed among these distances:
38 34 0.52
39 4 0.06
40 27 0.42
ACGTcount: A:0.40, C:0.20, G:0.22, T:0.17
Consensus pattern (40 bp):
TAGCGGCGTTTATGATAAAAACGCCGCAAAAGACAAGCAA
Found at i:19915500 original size:35 final size:34
Alignment explanation
Indices: 19915418--19915501 Score: 98
Period size: 35 Copynumber: 2.4 Consensus size: 34
19915408 AGACTAAGCC
* *
19915418 ATTTGCCTAAATCATAGTTCCCCCGAAACCCTCA
1 ATTTCCCTAAATCATAGTTCCCCCAAAACCCTCA
* *
19915452 TTTTCCCCCAAATCATAGTTCCCCCAAAACCC-CAAA
1 ATTT-CCCTAAATCATAGTTCCCCCAAAACCCTC--A
19915488 ATTTCCCTAAATCA
1 ATTTCCCTAAATCA
19915502 AACCCATTTG
Statistics
Matches: 41, Mismatches: 6, Indels: 5
0.79 0.12 0.10
Matches are distributed among these distances:
34 4 0.10
35 33 0.80
36 4 0.10
ACGTcount: A:0.32, C:0.37, G:0.05, T:0.26
Consensus pattern (34 bp):
ATTTCCCTAAATCATAGTTCCCCCAAAACCCTCA
Found at i:19919448 original size:241 final size:241
Alignment explanation
Indices: 19919025--19919699 Score: 1278
Period size: 241 Copynumber: 2.8 Consensus size: 241
19919015 ATGAATTAAT
*
19919025 TTTATTACCATGTAGCTTGCTTGTCCATTAAAATTACAACAATAGCTCACCTTCTCTCCAACCTT
1 TTTATTACCATGTAGCTTGCTTGTCCATTAAAATTACAACAATAGCTGACCTTCTCTCCAACCTT
*
19919090 TTTTTAAATATTTTAAAGATTCAAAGTACATAGGCTGGAAACCTGACGGGTTGCCTTATATCGAG
66 TTTTTAAATATTTTAAAGATTCAAAGTATATAGGCTGGAAACCTGACGGGTTGCCTTATATCGAG
*
19919155 CTGTAAGATATAATGGATCCTCCCTAGGTGTAACAACGTCACGTATGATGAATCTTAAAAAATTC
131 CTGTAAGATATAATGGATCCTCCCTAGGTGTAACAACGCCACGTATGATGAATCTTAAAAAATTC
* *
19919220 AAAAAGACTTGAAAAAAGTTTTATCGAGCTCATTTACTATTGAATA
196 AAAAAGACTTGAAAAAAGTTCTATCAAGCTCATTTACTATTGAATA
19919266 TTTATTACCATGTAGCTTGCTTGTCCATTAAAATTACAACAATAGCTGACCTTCTCTCCAACCTT
1 TTTATTACCATGTAGCTTGCTTGTCCATTAAAATTACAACAATAGCTGACCTTCTCTCCAACCTT
*
19919331 TTTTTAAATATTTTAAAGATTCAAAGTATATAGGCTGGAAACCTGACGGGTTGCCTTATATCAAG
66 TTTTTAAATATTTTAAAGATTCAAAGTATATAGGCTGGAAACCTGACGGGTTGCCTTATATCGAG
19919396 CTGTAAGATATAATGGATCCTCCCTAGGTGTAACAACGCCACGTATGATGAATCTTAAAAAATTC
131 CTGTAAGATATAATGGATCCTCCCTAGGTGTAACAACGCCACGTATGATGAATCTTAAAAAATTC
19919461 AAAAAGACTTGAAAAAAGTTCTATCAAGCTCATTTACTATTGAATA
196 AAAAAGACTTGAAAAAAGTTCTATCAAGCTCATTTACTATTGAATA
*
19919507 TTTATTACCATGTAGCTTGCTTATCCATTAAAATTACAACAATAGCTGACCTTCTCTCCAACCTT
1 TTTATTACCATGTAGCTTGCTTGTCCATTAAAATTACAACAATAGCTGACCTTCTCTCCAACCTT
19919572 TTTTTAAATATTTTAAAGATTCAAAGTATATAGGCTGGAAACCTGACGGGTTGCCTTATATCGAG
66 TTTTTAAATATTTTAAAGATTCAAAGTATATAGGCTGGAAACCTGACGGGTTGCCTTATATCGAG
*
19919637 CTGTAAGATATAATGGATCTTCCCTAGGTGTAACAACGCCACGTATGATGAATCTTAAAAAAT
131 CTGTAAGATATAATGGATCCTCCCTAGGTGTAACAACGCCACGTATGATGAATCTTAAAAAAT
19919700 AACTTACATA
Statistics
Matches: 425, Mismatches: 9, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
241 425 1.00
ACGTcount: A:0.34, C:0.18, G:0.15, T:0.33
Consensus pattern (241 bp):
TTTATTACCATGTAGCTTGCTTGTCCATTAAAATTACAACAATAGCTGACCTTCTCTCCAACCTT
TTTTTAAATATTTTAAAGATTCAAAGTATATAGGCTGGAAACCTGACGGGTTGCCTTATATCGAG
CTGTAAGATATAATGGATCCTCCCTAGGTGTAACAACGCCACGTATGATGAATCTTAAAAAATTC
AAAAAGACTTGAAAAAAGTTCTATCAAGCTCATTTACTATTGAATA
Found at i:19919736 original size:27 final size:27
Alignment explanation
Indices: 19919698--19919756 Score: 91
Period size: 27 Copynumber: 2.2 Consensus size: 27
19919688 ATCTTAAAAA
* *
19919698 ATAACTTACATAATTCACATAACTTAC
1 ATAACTTACATAACTCACATAACGTAC
*
19919725 ATAATTTACATAACTCACATAACGTAC
1 ATAACTTACATAACTCACATAACGTAC
19919752 ATAAC
1 ATAAC
19919757 AACTTACGGA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.46, C:0.22, G:0.02, T:0.31
Consensus pattern (27 bp):
ATAACTTACATAACTCACATAACGTAC
Found at i:19919747 original size:9 final size:9
Alignment explanation
Indices: 19919698--19919756 Score: 75
Period size: 9 Copynumber: 6.6 Consensus size: 9
19919688 ATCTTAAAAA
19919698 ATAACTTAC
1 ATAACTTAC
19919707 ATAA-TTCAC
1 ATAACTT-AC
19919716 ATAACTTAC
1 ATAACTTAC
*
19919725 ATAATTTAC
1 ATAACTTAC
*
19919734 ATAACTCAC
1 ATAACTTAC
*
19919743 ATAACGTAC
1 ATAACTTAC
19919752 ATAAC
1 ATAAC
19919757 AACTTACGGA
Statistics
Matches: 43, Mismatches: 5, Indels: 4
0.83 0.10 0.08
Matches are distributed among these distances:
8 2 0.05
9 39 0.91
10 2 0.05
ACGTcount: A:0.46, C:0.22, G:0.02, T:0.31
Consensus pattern (9 bp):
ATAACTTAC
Found at i:19924951 original size:46 final size:46
Alignment explanation
Indices: 19924882--19924976 Score: 163
Period size: 46 Copynumber: 2.1 Consensus size: 46
19924872 ACTTAATAAT
*
19924882 ATTTGATTTATTCTAAATATTTATAATCTTTAATGATAATTTTTTA
1 ATTTGATTTATTCTAAATATTTATAATCTTTAATGATAATTGTTTA
* *
19924928 ATTTGATTTATTCTAAATCTTTATAATCTTTAATTATAATTGTTTA
1 ATTTGATTTATTCTAAATATTTATAATCTTTAATGATAATTGTTTA
19924974 ATT
1 ATT
19924977 CAATTTATCA
Statistics
Matches: 46, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
46 46 1.00
ACGTcount: A:0.34, C:0.05, G:0.04, T:0.57
Consensus pattern (46 bp):
ATTTGATTTATTCTAAATATTTATAATCTTTAATGATAATTGTTTA
Found at i:19930665 original size:22 final size:21
Alignment explanation
Indices: 19930640--19930681 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
19930630 AAATTTAATA
* *
19930640 TTGAAAGTGCAAAAAGAAAAAG
1 TTGAAAATG-AAAAAAAAAAAG
19930662 TTGAAAATGAAAAAAAAAAA
1 TTGAAAATGAAAAAAAAAAA
19930682 CGTAAAAGAG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 10 0.56
22 8 0.44
ACGTcount: A:0.67, C:0.02, G:0.17, T:0.14
Consensus pattern (21 bp):
TTGAAAATGAAAAAAAAAAAG
Found at i:19933631 original size:13 final size:15
Alignment explanation
Indices: 19933598--19933631 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
19933588 TAAAAAATTG
19933598 ATATATCTTTTTTAA
1 ATATATCTTTTTTAA
*
19933613 ATATATCTTTTTTTA
1 ATATATCTTTTTTAA
19933628 ATAT
1 ATAT
19933632 TTTACTATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.32, C:0.06, G:0.00, T:0.62
Consensus pattern (15 bp):
ATATATCTTTTTTAA
Found at i:19934624 original size:83 final size:84
Alignment explanation
Indices: 19934537--19934727 Score: 284
Period size: 83 Copynumber: 2.3 Consensus size: 84
19934527 TTTTCTTACA
* *
19934537 TATAATTA-TATTTATTTAAATAA-A-AAAAATTATATTTTTATTATTTCTAATTTATCCAATTA
1 TATAATTATTA-TTAGTT-AATAATATAAAAAGTATATTTTTATTATTTCTAATTTATCCAATTA
19934599 TATTTAATGAATTGTTAGATT
64 TATTTAATGAATTGTTAGATT
** *
19934620 TATAA-TATTATTAGTTAATAATATAGTAGGTATATTTTTATTATTTCTAATTTATCCAATTATA
1 TATAATTATTATTAGTTAATAATATAAAAAGTATATTTTTATTATTTCTAATTTATCCAATTATA
19934684 TTTAATGAATTGTTAGATT
66 TTTAATGAATTGTTAGATT
19934703 TATAA-TATTATTAGTTAATAATATA
1 TATAATTATTATTAGTTAATAATATA
19934728 GTAGGTAGAA
Statistics
Matches: 100, Mismatches: 5, Indels: 6
0.90 0.05 0.05
Matches are distributed among these distances:
81 5 0.05
82 8 0.08
83 87 0.87
ACGTcount: A:0.40, C:0.03, G:0.06, T:0.51
Consensus pattern (84 bp):
TATAATTATTATTAGTTAATAATATAAAAAGTATATTTTTATTATTTCTAATTTATCCAATTATA
TTTAATGAATTGTTAGATT
Found at i:19934728 original size:83 final size:83
Alignment explanation
Indices: 19934567--19934734 Score: 336
Period size: 83 Copynumber: 2.0 Consensus size: 83
19934557 TAAAAAAAAT
19934567 TATATTTTTATTATTTCTAATTTATCCAATTATATTTAATGAATTGTTAGATTTATAATATTATT
1 TATATTTTTATTATTTCTAATTTATCCAATTATATTTAATGAATTGTTAGATTTATAATATTATT
19934632 AGTTAATAATATAGTAGG
66 AGTTAATAATATAGTAGG
19934650 TATATTTTTATTATTTCTAATTTATCCAATTATATTTAATGAATTGTTAGATTTATAATATTATT
1 TATATTTTTATTATTTCTAATTTATCCAATTATATTTAATGAATTGTTAGATTTATAATATTATT
19934715 AGTTAATAATATAGTAGG
66 AGTTAATAATATAGTAGG
19934733 TA
1 TA
19934735 GAAGGAAGAA
Statistics
Matches: 85, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
83 85 1.00
ACGTcount: A:0.36, C:0.04, G:0.08, T:0.52
Consensus pattern (83 bp):
TATATTTTTATTATTTCTAATTTATCCAATTATATTTAATGAATTGTTAGATTTATAATATTATT
AGTTAATAATATAGTAGG
Found at i:19935464 original size:16 final size:16
Alignment explanation
Indices: 19935423--19935464 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
19935413 AAATCTATCT
* **
19935423 AATTTATTTAAATTTA
1 AATTTATTTGAATCCA
19935439 AATTTATTTGAATCCA
1 AATTTATTTGAATCCA
19935455 AATTTATTTG
1 AATTTATTTG
19935465 GACATATAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.38, C:0.05, G:0.05, T:0.52
Consensus pattern (16 bp):
AATTTATTTGAATCCA
Found at i:19942238 original size:30 final size:31
Alignment explanation
Indices: 19942195--19942259 Score: 82
Period size: 30 Copynumber: 2.1 Consensus size: 31
19942185 TATTAGTATT
19942195 ACTAATACATAAAATAATATT-ATA-ATATATA
1 ACTAATACAT-AAA-AATATTAATACATATATA
*
19942226 ACTATTAC-TAAAAATATTAATACATATATA
1 ACTAATACATAAAAATATTAATACATATATA
19942256 ACTA
1 ACTA
19942260 CAATTATAAT
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
28 6 0.19
29 6 0.19
30 12 0.39
31 7 0.23
ACGTcount: A:0.55, C:0.09, G:0.00, T:0.35
Consensus pattern (31 bp):
ACTAATACATAAAAATATTAATACATATATA
Found at i:19949478 original size:7 final size:7
Alignment explanation
Indices: 19949468--19949500 Score: 57
Period size: 7 Copynumber: 4.7 Consensus size: 7
19949458 GAAAAAAGAA
19949468 AAAATTG
1 AAAATTG
19949475 AAAATTG
1 AAAATTG
19949482 AAAATTG
1 AAAATTG
*
19949489 AAAAATG
1 AAAATTG
19949496 AAAAT
1 AAAAT
19949501 AAAATTGTTC
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.64, C:0.00, G:0.12, T:0.24
Consensus pattern (7 bp):
AAAATTG
Found at i:19949492 original size:21 final size:19
Alignment explanation
Indices: 19949467--19949507 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 19
19949457 TGAAAAAAGA
19949467 AAAAATTGAAAATTGAAAATTG
1 AAAAA-TGAAAA-T-AAAATTG
19949489 AAAAATGAAAATAAAATTG
1 AAAAATGAAAATAAAATTG
19949508 TTCTCTTTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 7 0.37
20 1 0.05
21 6 0.32
22 5 0.26
ACGTcount: A:0.63, C:0.00, G:0.12, T:0.24
Consensus pattern (19 bp):
AAAAATGAAAATAAAATTG
Found at i:19954137 original size:46 final size:44
Alignment explanation
Indices: 19954086--19954257 Score: 175
Period size: 46 Copynumber: 3.7 Consensus size: 44
19954076 ATTCGTGTAT
* * *
19954086 GAGCTAGTGTAAGACATGTCTGGGACATGCATTGGCTACATTATGA
1 GAGCTAGTGTAAGACATGTCTGGGACATGCATCGGCT-CA-GACGA
* * *
19954132 GAGCTAGTGTAAGACCAAGTCTGGGACATGCCATCGGCATTGAGACAA
1 GAGCTAGTGTAAGA-CATGTCTGGGACATG-CATCGGC--TCAGACGA
* *
19954180 GGGCTAGTGTAAGACATGTCTGGGACATGCATCGACCTCGAGACGTA
1 GAGCTAGTGTAAGACATGTCTGGGACATGCATCG-GCTC-AGACG-A
*
19954227 -AGCCAGTGTAAGACATGTCTGGGACATGCAT
1 GAGCTAGTGTAAGACATGTCTGGGACATGCAT
19954258 TGACTATGAG
Statistics
Matches: 106, Mismatches: 13, Indels: 14
0.80 0.10 0.11
Matches are distributed among these distances:
45 1 0.01
46 52 0.49
47 30 0.28
48 21 0.20
49 1 0.01
50 1 0.01
ACGTcount: A:0.28, C:0.19, G:0.30, T:0.23
Consensus pattern (44 bp):
GAGCTAGTGTAAGACATGTCTGGGACATGCATCGGCTCAGACGA
Found at i:19954194 original size:48 final size:46
Alignment explanation
Indices: 19954087--19954309 Score: 167
Period size: 46 Copynumber: 4.8 Consensus size: 46
19954077 TTCGTGTATG
* *
19954087 AGCTAGTGTAAGACATGTCTGGGACATG-CATTGGCTACAT-TATGA-G-
1 AGCTAGTGTAAGACATGTCTGGGACATGCCA-T--CGACATCGA-GACGA
* * *
19954133 AGCTAGTGTAAGACCAAGTCTGGGACATGCCATCGGCATTGAGAC-A
1 AGCTAGTGTAAGA-CATGTCTGGGACATGCCATCGACATCGAGACGA
*
19954179 AGGGCTAGTGTAAGACATGTCTGGGACATG-CATCGACCTCGAGACGTA
1 A--GCTAGTGTAAGACATGTCTGGGACATGCCATCGACATCGAGACG-A
* * *
19954227 AGCCAGTGTAAGACATGTCTGGGACATG-CATTGACTAT-GAGATGA
1 AGCTAGTGTAAGACATGTCTGGGACATGCCATCGAC-ATCGAGACGA
* * *
19954272 TA-ATCAATGTAAGACCATGTCTGGGACATGGCATCGAC
1 -AGCT-AGTGTAAGA-CATGTCTGGGACATGCCATCGAC
19954310 TTGAGATAAG
Statistics
Matches: 147, Mismatches: 16, Indels: 26
0.78 0.08 0.14
Matches are distributed among these distances:
45 7 0.05
46 73 0.50
47 45 0.31
48 22 0.15
ACGTcount: A:0.30, C:0.19, G:0.28, T:0.23
Consensus pattern (46 bp):
AGCTAGTGTAAGACATGTCTGGGACATGCCATCGACATCGAGACGA
Found at i:19954340 original size:140 final size:140
Alignment explanation
Indices: 19954091--19954348 Score: 342
Period size: 140 Copynumber: 1.8 Consensus size: 140
19954081 TGTATGAGCT
* * * *
19954091 AGTGTAAGACATGTCTGGGACATGCATTGGCTACATTATGAGAGCTAGTGTAAGACCAAGTCTGG
1 AGTGTAAGACATGTCTGGGACATGCATTGACTACATGATGAAAGCTAATGTAAGACCAAGTCTGG
* * * *
19954156 GACATGCCATCGGCATTGAGACAAGGGCTAGTGTAAGACATGTCTGGGACATGCATCGACCTCGA
66 GACATGCCATCGACATTGAGACAAGAGCCAGTGTAAGACATGTCTAGGACATGCATCGACCTCGA
19954221 GACGTAAGCC
131 GACGTAAGCC
* * *
19954231 AGTGTAAGACATGTCTGGGACATGCATTGACTATGA-GATGATAATC-AATGTAAGACCATGTCT
1 AGTGTAAGACATGTCTGGGACATGCATTGACTA-CATGATGA-AAGCTAATGTAAGACCAAGTCT
* * *
19954294 GGGACATGGCATCGAC-TTGAGATAAGAGCCAGTGTAAGACCGTGTCTAGGACATG
64 GGGACATGCCATCGACATTGAGACAAGAGCCAGTGTAAGA-CATGTCTAGGACATG
19954349 GCATTGGCAC
Statistics
Matches: 101, Mismatches: 14, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
139 20 0.20
140 78 0.77
141 3 0.03
ACGTcount: A:0.30, C:0.18, G:0.29, T:0.23
Consensus pattern (140 bp):
AGTGTAAGACATGTCTGGGACATGCATTGACTACATGATGAAAGCTAATGTAAGACCAAGTCTGG
GACATGCCATCGACATTGAGACAAGAGCCAGTGTAAGACATGTCTAGGACATGCATCGACCTCGA
GACGTAAGCC
Found at i:19954349 original size:47 final size:47
Alignment explanation
Indices: 19954086--19954352 Score: 217
Period size: 47 Copynumber: 5.7 Consensus size: 47
19954076 ATTCGTGTAT
* * * ** * *
19954086 GAGCTAGTGTAAGA-CATGTCTGGGACAT-GCATTGGCTACATTATGA
1 GAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGACTTGA-GATAA
* * * * *
19954132 GAGCTAGTGTAAGACCAAGTCTGGGACATGCCATCGGCATTGAGACAA
1 GAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGAC-TTGAGATAA
* * *
19954180 GGGCTAGTGTAAGA-CATGTCTGGGACAT-GCATCGACCTCGAGACGT-A
1 GAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGA-CTTGAGA--TAA
* *
19954227 -AGCCAGTGTAAGA-CATGTCTGGGACAT-GCATTGACTATGAGATGA
1 GAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGACT-TGAGATAA
* ** *
19954272 TAATCAATGTAAGACCATGTCTGGGACATGGCATCGACTTGAGATAA
1 GAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGACTTGAGATAA
* *
19954319 GAGCCAGTGTAAGACCGTGTCTAGGACATGGCAT
1 GAGCCAGTGTAAGACCATGTCTGGGACATGGCAT
19954353 TGGCACCTTA
Statistics
Matches: 181, Mismatches: 29, Indels: 21
0.78 0.13 0.09
Matches are distributed among these distances:
44 1 0.01
45 3 0.02
46 69 0.38
47 77 0.43
48 29 0.16
49 2 0.01
ACGTcount: A:0.30, C:0.18, G:0.29, T:0.23
Consensus pattern (47 bp):
GAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGACTTGAGATAA
Found at i:19956664 original size:82 final size:82
Alignment explanation
Indices: 19956525--19956691 Score: 280
Period size: 82 Copynumber: 2.0 Consensus size: 82
19956515 AAGAAGAGAC
** * *
19956525 AGATGGGGAAATCACATCAGTTTTCTTCAAAAAGATCAAGAGAGTTTACTACTCGATCGAATGCT
1 AGATGGGGAAATCACATCAGTCCTCATCAAAAAGATCAAGAGAGTTTACTACCCGATCGAATGCT
19956590 TCGGTAGGTTTTCTAAT
66 TCGGTAGGTTTTCTAAT
*
19956607 AGATGGGGAAATCACATCAGTCCTCATCTAAAAGATCAAGAGAGTTTACTACCCGATCGAATGCT
1 AGATGGGGAAATCACATCAGTCCTCATCAAAAAGATCAAGAGAGTTTACTACCCGATCGAATGCT
*
19956672 TCGGTGGGTTTTCTAAT
66 TCGGTAGGTTTTCTAAT
19956689 AGA
1 AGA
19956692 AACAAGAACT
Statistics
Matches: 79, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
82 79 1.00
ACGTcount: A:0.32, C:0.17, G:0.22, T:0.29
Consensus pattern (82 bp):
AGATGGGGAAATCACATCAGTCCTCATCAAAAAGATCAAGAGAGTTTACTACCCGATCGAATGCT
TCGGTAGGTTTTCTAAT
Found at i:19959113 original size:47 final size:47
Alignment explanation
Indices: 19959044--19959137 Score: 188
Period size: 47 Copynumber: 2.0 Consensus size: 47
19959034 CATAAGGTAA
19959044 GTTCATATGATTTTTAATAATGCAATGTGTAATTTAATGTTATTGCC
1 GTTCATATGATTTTTAATAATGCAATGTGTAATTTAATGTTATTGCC
19959091 GTTCATATGATTTTTAATAATGCAATGTGTAATTTAATGTTATTGCC
1 GTTCATATGATTTTTAATAATGCAATGTGTAATTTAATGTTATTGCC
19959138 TTGATATTAA
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:0.30, C:0.09, G:0.15, T:0.47
Consensus pattern (47 bp):
GTTCATATGATTTTTAATAATGCAATGTGTAATTTAATGTTATTGCC
Found at i:19961864 original size:36 final size:36
Alignment explanation
Indices: 19961821--19961894 Score: 139
Period size: 36 Copynumber: 2.1 Consensus size: 36
19961811 GCCTGAAATG
*
19961821 AATGACATGATTTTGACGATGTTGCTATGATGATGA
1 AATGACATCATTTTGACGATGTTGCTATGATGATGA
19961857 AATGACATCATTTTGACGATGTTGCTATGATGATGA
1 AATGACATCATTTTGACGATGTTGCTATGATGATGA
19961893 AA
1 AA
19961895 GTTGTGTCAT
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 37 1.00
ACGTcount: A:0.32, C:0.09, G:0.23, T:0.35
Consensus pattern (36 bp):
AATGACATCATTTTGACGATGTTGCTATGATGATGA
Found at i:19970837 original size:46 final size:47
Alignment explanation
Indices: 19970779--19971003 Score: 190
Period size: 47 Copynumber: 4.8 Consensus size: 47
19970769 ATTCGTGTGT
* *
19970779 GAGCTAGTGTAAGA-CATGTCTGGGACAT-GCATCGGCTACATTATGA
1 GAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCTACA-GATGA
* * ** **
19970825 GAGCCAGTGTAAGACCAAGTCTGGGACATGGCATTGGCATTGAGACAA
1 GAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGC-TACAGATGA
* *
19970873 GGGCTAGTGTAAGA-CATGTCTGGGACAT-GCATCGGCTACAAGATGA
1 GAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCTAC-AGATGA
* ** * * **
19970919 TAATCAGTGTGAGACCATGTCTGGGACATGGCATCGACTTGAGAT-A
1 GAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCTACAGATGA
* * * *
19970965 TGAGCCAGTGTAAGATCGTGTTTAGGACATGGCATCGGC
1 -GAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGC
19971004 ACCTTATCCT
Statistics
Matches: 138, Mismatches: 34, Indels: 13
0.75 0.18 0.07
Matches are distributed among these distances:
45 1 0.01
46 33 0.24
47 73 0.53
48 29 0.21
49 2 0.01
ACGTcount: A:0.28, C:0.18, G:0.31, T:0.24
Consensus pattern (47 bp):
GAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCTACAGATGA
Found at i:19970993 original size:94 final size:94
Alignment explanation
Indices: 19970778--19971003 Score: 283
Period size: 94 Copynumber: 2.4 Consensus size: 94
19970768 CATTCGTGTG
** *
19970778 TGAGCTAGTGTAAGACATGTCTGGGACATGCATCGGCTACATTATGAGAGCCAGTGTAAGACCAA
1 TGAGCTAGTGTAAGACATGTCTGGGACATGCATCGGCTACAAGATGAGAACCAGTGTAAGACCAA
* *
19970843 GTCTGGGACATGGCATTGGCATTGAGACA
66 GTCTGGGACATGGCATCGACATTGAGACA
* * * * * *
19970872 AGGGCTAGTGTAAGACATGTCTGGGACATGCATCGGCTACAAGATGATAATCAGTGTGAGACCAT
1 TGAGCTAGTGTAAGACATGTCTGGGACATGCATCGGCTACAAGATGAGAACCAGTGTAAGACCAA
*
19970937 GTCTGGGACATGGCATCGAC-TTGAGATA
66 GTCTGGGACATGGCATCGACATTGAGACA
* * * *
19970965 TGAGCCAGTGTAAGATCGTGTTTAGGACATGGCATCGGC
1 TGAGCTAGTGTAAGA-CATGTCTGGGACAT-GCATCGGC
19971004 ACCTTATCCT
Statistics
Matches: 112, Mismatches: 18, Indels: 3
0.84 0.14 0.02
Matches are distributed among these distances:
93 19 0.17
94 85 0.76
95 8 0.07
ACGTcount: A:0.28, C:0.18, G:0.31, T:0.24
Consensus pattern (94 bp):
TGAGCTAGTGTAAGACATGTCTGGGACATGCATCGGCTACAAGATGAGAACCAGTGTAAGACCAA
GTCTGGGACATGGCATCGACATTGAGACA
Found at i:19974915 original size:47 final size:45
Alignment explanation
Indices: 19974758--19975120 Score: 286
Period size: 47 Copynumber: 7.8 Consensus size: 45
19974748 GGGATATATT
* *
19974758 GCCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCTCATATACGAG
1 GCCGATG-CATGTCCCAGACAT-GTCTTACACTGGCTATCATGT--GAG
** * * *
19974807 TGCTAATGCATGTCCCAGACATGTCTTACACTAGC-A-CAACTTTTA-
1 -GCCGATGCATGTCCCAGACATGTCTTACACTGGCTATC-A-TGTGAG
* *
19974852 GCCGATGCGTGTCCCAGACACGTCTTACACTGGCTATCACTGTCGAG
1 GCCGATGCATGTCCCAGACATGTCTTACACTGGCTATCA-TGT-GAG
* * **
19974899 GCTGATGCATGTCCCAGACATGTCTTACACTGGC-ACTCATCTCTG
1 GCCGATGCATGTCCCAGACATGTCTTACACTGGCTA-TCATGTGAG
*
19974944 TGCCGATGCCATGTCCCAGACATGGTTTTACACTGGCTATCATAGT-ATG
1 -GCCGATG-CATGTCCCAGACAT-GTCTTACACTGGCTATCAT-GTGA-G
* * ** * * *
19974993 GCTGATGCATGTCCCAGACATGTCTTACACTAGCCCTCGTCTGGAT
1 GCCGATGCATGTCCCAGACATGTCTTACACTGGCTATCATGT-GAG
* * *
19975039 GCCGATGCTATGTCCCAGACATGCTCTTACACTGGCTCTCATAATGTG
1 GCCGATGC-ATGTCCCAGACATG-TCTTACACTGGCTATCAT-GTGAG
* *
19975087 GCCGAAGCATGTCCCAGACACGTCTTACACTGGC
1 GCCGATGCATGTCCCAGACATGTCTTACACTGGC
19975121 GCACAAAACC
Statistics
Matches: 255, Mismatches: 40, Indels: 40
0.76 0.12 0.12
Matches are distributed among these distances:
44 29 0.11
45 7 0.03
46 46 0.18
47 91 0.36
48 59 0.23
49 18 0.07
50 5 0.02
ACGTcount: A:0.22, C:0.30, G:0.21, T:0.27
Consensus pattern (45 bp):
GCCGATGCATGTCCCAGACATGTCTTACACTGGCTATCATGTGAG
Found at i:19975007 original size:94 final size:93
Alignment explanation
Indices: 19974757--19975117 Score: 412
Period size: 94 Copynumber: 3.9 Consensus size: 93
19974747 TGGGATATAT
* * *
19974757 TGCCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCTCATA-TACGAGTGCTAATGCATGTC
1 TGCCGATGCCATGTCCCAGACATGGTCTTACACTGGCTATCATAGTA--TG-GCTGATGCATGTC
* *
19974821 CCAGACATGTCTTACACTAGCA--CAACTTT
63 CCAGACATGTCTTACACTAGCACTCATCTTG
* *
19974850 TAGCCGATG-CGTGTCCCAGACA-CGTCTTACACTGGCTATCACT-GTCGA-GGCTGATGCATGT
1 T-GCCGATGCCATGTCCCAGACATGGTCTTACACTGGCTATCA-TAGT--ATGGCTGATGCATGT
*
19974911 CCCAGACATGTCTTACACTGGCACTCATCTCTG
62 CCCAGACATGTCTTACACTAGCACTCATCT-TG
*
19974944 TGCCGATGCCATGTCCCAGACATGGTTTTACACTGGCTATCATAGTATGGCTGATGCATGTCCCA
1 TGCCGATGCCATGTCCCAGACATGGTCTTACACTGGCTATCATAGTATGGCTGATGCATGTCCCA
* * *
19975009 GACATGTCTTACACTAGCCCTCGTCTGG
66 GACATGTCTTACACTAGCACTCATCTTG
* * * * * * *
19975037 ATGCCGATGCTATGTCCCAGACATGCTCTTACACTGGCTCTCATAATGTGGCCGAAGCATGTCCC
1 -TGCCGATGCCATGTCCCAGACATGGTCTTACACTGGCTATCATAGTATGGCTGATGCATGTCCC
*
19975102 AGACACGTCTTACACT
65 AGACATGTCTTACACT
19975118 GGCGCACAAA
Statistics
Matches: 232, Mismatches: 23, Indels: 25
0.83 0.08 0.09
Matches are distributed among these distances:
91 33 0.14
92 18 0.08
93 28 0.12
94 133 0.57
95 20 0.09
ACGTcount: A:0.22, C:0.30, G:0.21, T:0.27
Consensus pattern (93 bp):
TGCCGATGCCATGTCCCAGACATGGTCTTACACTGGCTATCATAGTATGGCTGATGCATGTCCCA
GACATGTCTTACACTAGCACTCATCTTG
Found at i:19975018 original size:141 final size:135
Alignment explanation
Indices: 19974758--19975120 Score: 370
Period size: 141 Copynumber: 2.6 Consensus size: 135
19974748 GGGATATATT
* **
19974758 GCCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCTCATATACGAGTGCTAATGCATGTCCC
1 GCCGATG-CATGTCCCAGACAT-GTCTTACACTGGCTCTCAT-T-C-TGTGCCGATGCATGTCCC
* * * * * *
19974823 AGACATGTCTTACACTAGCACAACTTTTAGCCGATGCGTGTCCCAGACACGTCTTACACTGGCTA
61 AGACATGTCTTACACTGGCACAACGTATAGCCGATGCATGTCCCAGACACGTCTTACACTAGCCA
19974888 TC-ACTGTCGAG
126 TCGACTG--GAG
* *
19974899 GCTGATGCATGTCCCAGACATGTCTTACACTGGCACTCATCTCTGTGCCGATGCCATGTCCCAGA
1 GCCGATGCATGTCCCAGACATGTCTTACACTGGCTCTCAT-TCTGTGCCGATG-CATGTCCCAGA
* * * *
19974964 CATGGTTTTACACTGGCTATCATA-GTATGGCTGATGCATGTCCCAGACATGTCTTACACTAGCC
64 CAT-GTCTTACACTGGC-A-CA-ACGTATAGCCGATGCATGTCCCAGACACGTCTTACACTAGCC
* * *
19975028 CTCGTCTGGAT
125 ATCGACTGGAG
** *
19975039 GCCGATGCTATGTCCCAGACATGCTCTTACACTGGCTCTCATAATGTGGCCGAAGCATGTCCCAG
1 GCCGATGC-ATGTCCCAGACATG-TCTTACACTGGCTCTCATTCTGT-GCCGATGCATGTCCCAG
*
19975104 ACACGTCTTACACTGGC
63 ACATGTCTTACACTGGC
19975121 GCACAAAACC
Statistics
Matches: 187, Mismatches: 26, Indels: 19
0.81 0.11 0.08
Matches are distributed among these distances:
137 7 0.04
138 15 0.08
139 30 0.16
140 36 0.19
141 72 0.39
142 27 0.14
ACGTcount: A:0.22, C:0.30, G:0.21, T:0.27
Consensus pattern (135 bp):
GCCGATGCATGTCCCAGACATGTCTTACACTGGCTCTCATTCTGTGCCGATGCATGTCCCAGACA
TGTCTTACACTGGCACAACGTATAGCCGATGCATGTCCCAGACACGTCTTACACTAGCCATCGAC
TGGAG
Found at i:19982524 original size:27 final size:27
Alignment explanation
Indices: 19982494--19982634 Score: 173
Period size: 27 Copynumber: 5.2 Consensus size: 27
19982484 GTGACGAAGT
*
19982494 CACCAGATATAGATATTGTGGCAGAGC
1 CACCAGATACAGATATTGTGGCAGAGC
19982521 CACCAGA-ACAGATATATGTGGCAGAGC
1 CACCAGATACAGATAT-TGTGGCAGAGC
* *
19982548 CACCAGAT-CAGATAATCGTGGCATAGC
1 CACCAGATACAGAT-ATTGTGGCAGAGC
19982575 CACCAGA-ACAGATATATGTGGCAGAGC
1 CACCAGATACAGATAT-TGTGGCAGAGC
* *
19982602 CACCAGAT-CAGATAATTGTGACATAGC
1 CACCAGATACAGAT-ATTGTGGCAGAGC
19982629 CACCAG
1 CACCAG
19982635 GACGCTTCCT
Statistics
Matches: 100, Mismatches: 7, Indels: 14
0.83 0.06 0.12
Matches are distributed among these distances:
26 9 0.09
27 87 0.87
28 4 0.04
ACGTcount: A:0.35, C:0.23, G:0.23, T:0.18
Consensus pattern (27 bp):
CACCAGATACAGATATTGTGGCAGAGC
Found at i:19982576 original size:54 final size:54
Alignment explanation
Indices: 19982494--19982634 Score: 230
Period size: 54 Copynumber: 2.6 Consensus size: 54
19982484 GTGACGAAGT
* *
19982494 CACCAGATATAGAT-ATTGTGGCAGAGCCACCAGAACAGATATATGTGGCAGAGC
1 CACCAGAT-CAGATAATTGTGGCATAGCCACCAGAACAGATATATGTGGCAGAGC
*
19982548 CACCAGATCAGATAATCGTGGCATAGCCACCAGAACAGATATATGTGGCAGAGC
1 CACCAGATCAGATAATTGTGGCATAGCCACCAGAACAGATATATGTGGCAGAGC
*
19982602 CACCAGATCAGATAATTGTGACATAGCCACCAG
1 CACCAGATCAGATAATTGTGGCATAGCCACCAG
19982635 GACGCTTCCT
Statistics
Matches: 81, Mismatches: 5, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
53 4 0.05
54 77 0.95
ACGTcount: A:0.35, C:0.23, G:0.23, T:0.18
Consensus pattern (54 bp):
CACCAGATCAGATAATTGTGGCATAGCCACCAGAACAGATATATGTGGCAGAGC
Found at i:19984287 original size:26 final size:26
Alignment explanation
Indices: 19984256--19984363 Score: 171
Period size: 26 Copynumber: 4.2 Consensus size: 26
19984246 TGAAATGCCC
* *
19984256 ATCATGGAACATTTATCTAAACCATT
1 ATCATGGAACATTTACCTAACCCATT
19984282 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
* *
19984308 ATCATGGAATATTTACCTAATCCATT
1 ATCATGGAACATTTACCTAACCCATT
*
19984334 ATCATGGAATATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
19984360 ATCA
1 ATCA
19984364 ATTTGTACCA
Statistics
Matches: 77, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 77 1.00
ACGTcount: A:0.36, C:0.22, G:0.07, T:0.34
Consensus pattern (26 bp):
ATCATGGAACATTTACCTAACCCATT
Found at i:19985676 original size:41 final size:41
Alignment explanation
Indices: 19985493--19985936 Score: 446
Period size: 41 Copynumber: 10.9 Consensus size: 41
19985483 GTTTTGAATA
* * * * * *
19985493 AAACACCACTAAAAACTGAGCAATAGCGACATTTTTGGTCA
1 AAACGCCACTAAAAACCGAGCAATAGCGGCGTTTCTGGTCC
* * * * * *
19985534 AAATGCCACTAAGAACCGAGCAATAACGGCATTT-TGAAT-A
1 AAACGCCACTAAAAACCGAGCAATAGCGGCGTTTCTG-GTCC
* * ** *
19985574 AAACGCCACTAAGAACCGAGCATTAGCATCGTTTCTGATCC
1 AAACGCCACTAAAAACCGAGCAATAGCGGCGTTTCTGGTCC
* * * **
19985615 TAA-GCCACTAAAAACCGAGCAATAGTGGTGTTTCTAATCC
1 AAACGCCACTAAAAACCGAGCAATAGCGGCGTTTCTGGTCC
* * *
19985655 AAACGCCACTAAAAACAGAGCAATAGCAGTGTTTCTGGTCC
1 AAACGCCACTAAAAACCGAGCAATAGCGGCGTTTCTGGTCC
* * * * *
19985696 AAATGCCACTAAAAACCAAGCATTAGCGGCATTTCTGAT-C
1 AAACGCCACTAAAAACCGAGCAATAGCGGCGTTTCTGGTCC
* * * *
19985736 ATAACGCCATTAAAAACCTAGCAATAGCGGTGTTTCTAGTCC
1 A-AACGCCACTAAAAACCGAGCAATAGCGGCGTTTCTGGTCC
* *
19985778 AAACGCCACTAAAAACTGAGCAATAGCGGCGTTTCTAGTCC
1 AAACGCCACTAAAAACCGAGCAATAGCGGCGTTTCTGGTCC
*
19985819 AAACGCCACTAAAAACCTAGCAATAGCGGCGTTTCTGGTCC
1 AAACGCCACTAAAAACCGAGCAATAGCGGCGTTTCTGGTCC
** * *
19985860 AAACGCCACTAAAAACCGAGCAATAGCATCATTTTTGGTCC
1 AAACGCCACTAAAAACCGAGCAATAGCGGCGTTTCTGGTCC
* * *
19985901 AAACACCACTAAAAATCGAGCAATAACGGCGTTTCT
1 AAACGCCACTAAAAACCGAGCAATAGCGGCGTTTCT
19985937 ACTCAAAACG
Statistics
Matches: 334, Mismatches: 63, Indels: 12
0.82 0.15 0.03
Matches are distributed among these distances:
40 67 0.20
41 265 0.79
42 2 0.01
ACGTcount: A:0.36, C:0.25, G:0.17, T:0.22
Consensus pattern (41 bp):
AAACGCCACTAAAAACCGAGCAATAGCGGCGTTTCTGGTCC
Found at i:19986004 original size:123 final size:123
Alignment explanation
Indices: 19985493--19985989 Score: 386
Period size: 123 Copynumber: 4.1 Consensus size: 123
19985483 GTTTTGAATA
* * ** * *
19985493 AAACACCACTAAAAACTGAGCAATAGCGA-CATTTTTGGTCAAAATGCCACTAAGAACCGAGCAA
1 AAACACCACTAAAAACCGAGCAATAGC-ATCATTTTTGGTCCAAACACCACTAAAAACTGAGCAA
* * * * * ** *
19985557 TAACGGCATTT-TGAAT-AAAACGCCACTAAGAACCGAGCATTAGCATCGTTTCTGATCC
65 TAACGGCGTTTCT-ACTCAAAACGCCACTAAAAACCTAGCAATAGCGGCGTTTCTGGTCC
* * ** ** * *
19985615 TAA-GCCACTAAAAACCGAGCAATAG--TGGTGTTTCTAATCCAAACGCCACTAAAAACAGAGCA
1 AAACACCACTAAAAACCGAGCAATAGCATCAT-TTT-TGGTCCAAACACCACTAAAAACTGAGCA
* * * ** * * * * * *
19985677 ATAGCAGTGTTTCTGGTCCAAATGCCACTAAAAACCAAGCATTAGCGGCATTTCTGAT-C
64 ATAACGGCGTTTCTACTCAAAACGCCACTAAAAACCTAGCAATAGCGGCGTTTCTGGTCC
* * * * * * * *
19985736 ATAACGCCATTAAAAACCTAGCAATAGCGGT-GTTTCTAGTCCAAACGCCACTAAAAACTGAGCA
1 A-AACACCACTAAAAACCGAGCAATAGC-ATCATTTTTGGTCCAAACACCACTAAAAACTGAGCA
* * *
19985800 ATAGCGGCGTTTCTAGTCCAAACGCCACTAAAAACCTAGCAATAGCGGCGTTTCTGGTCC
64 ATAACGGCGTTTCTACTCAAAACGCCACTAAAAACCTAGCAATAGCGGCGTTTCTGGTCC
*
19985860 AAACGCCACTAAAAACCGAGCAATAGCATCATTTTTGGTCCAAACACCACTAAAAA-TCGAGCAA
1 AAACACCACTAAAAACCGAGCAATAGCATCATTTTTGGTCCAAACACCACTAAAAACT-GAGCAA
* ** * *
19985924 TAACGGCGTTTCTACTCAAAACGCC-GTAAAAAGTTTA-TATATAGCGGCGTTTTTGGTCC
65 TAACGGCGTTTCTACTCAAAACGCCACTAAAAA-CCTAGCA-ATAGCGGCGTTTCTGGTCC
19985983 AAACACC
1 AAACACC
19985990 GCAAAAAGTT
Statistics
Matches: 306, Mismatches: 54, Indels: 29
0.79 0.14 0.07
Matches are distributed among these distances:
119 1 0.00
120 3 0.01
121 52 0.17
122 47 0.15
123 196 0.64
124 4 0.01
125 2 0.01
126 1 0.00
ACGTcount: A:0.36, C:0.25, G:0.17, T:0.22
Consensus pattern (123 bp):
AAACACCACTAAAAACCGAGCAATAGCATCATTTTTGGTCCAAACACCACTAAAAACTGAGCAAT
AACGGCGTTTCTACTCAAAACGCCACTAAAAACCTAGCAATAGCGGCGTTTCTGGTCC
Found at i:19986873 original size:21 final size:21
Alignment explanation
Indices: 19986821--19986874 Score: 81
Period size: 21 Copynumber: 2.6 Consensus size: 21
19986811 TTTAAGTTAT
19986821 GGTTTAAGGTTTGTTATTTTG
1 GGTTTAAGGTTTGTTATTTTG
* **
19986842 GGCTTGGGGTTTGTTATTTTG
1 GGTTTAAGGTTTGTTATTTTG
19986863 GGTTTAAGGTTT
1 GGTTTAAGGTTT
19986875 AGGGTATATA
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.11, C:0.02, G:0.33, T:0.54
Consensus pattern (21 bp):
GGTTTAAGGTTTGTTATTTTG
Found at i:19987294 original size:21 final size:21
Alignment explanation
Indices: 19987250--19987294 Score: 65
Period size: 20 Copynumber: 2.1 Consensus size: 21
19987240 AATTAATTTT
*
19987250 ATTTTATTTAAAAGTTTAATA
1 ATTTTATTTAAAAGTTTAAAA
19987271 ATTTTA-TTAAAAGTTTATAAA
1 ATTTTATTTAAAAGTTTA-AAA
19987292 ATT
1 ATT
19987295 ATACAAATTA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 11 0.50
21 11 0.50
ACGTcount: A:0.44, C:0.00, G:0.04, T:0.51
Consensus pattern (21 bp):
ATTTTATTTAAAAGTTTAAAA
Found at i:19987322 original size:30 final size:29
Alignment explanation
Indices: 19987239--19987328 Score: 87
Period size: 26 Copynumber: 3.0 Consensus size: 29
19987229 AAAATCTTAC
19987239 AAATTAATTTTATTTTATTTAAAAGTTT-
1 AAATTAATTTTATTTTATTTAAAAGTTTA
** *
19987267 -AA-TAATTTTATTAAAAGTTTATAAAATTATA
1 AAATTAATTTTATT-TTA-TTTA-AAAGTT-TA
19987298 CAAATTAATTTTATTTTATTTAAAAGTTTA
1 -AAATTAATTTTATTTTATTTAAAAGTTTA
19987328 A
1 A
19987329 TAAAATTAAT
Statistics
Matches: 48, Mismatches: 6, Indels: 15
0.70 0.09 0.22
Matches are distributed among these distances:
26 10 0.21
27 3 0.06
28 4 0.08
29 6 0.12
30 3 0.06
31 5 0.10
32 4 0.08
33 3 0.06
34 10 0.21
ACGTcount: A:0.44, C:0.01, G:0.03, T:0.51
Consensus pattern (29 bp):
AAATTAATTTTATTTTATTTAAAAGTTTA
Found at i:19987340 original size:32 final size:32
Alignment explanation
Indices: 19987239--19987340 Score: 99
Period size: 32 Copynumber: 3.3 Consensus size: 32
19987229 AAAATCTTAC
19987239 AAATTAATTTTATTTTATTTAAAAGTTTAAT-
1 AAATTAATTTTATTTTATTTAAAAGTTTAATA
* * ** *
19987270 AATTTTATTAAAAGTTTA--TAAAA--TT-ATA
1 AAATTAATT-TTATTTTATTTAAAAGTTTAATA
19987298 CAAATTAATTTTATTTTATTTAAAAGTTTAATA
1 -AAATTAATTTTATTTTATTTAAAAGTTTAATA
19987331 AAATTAATTT
1 AAATTAATTT
19987341 ACTTTAGGCT
Statistics
Matches: 53, Mismatches: 10, Indels: 15
0.68 0.13 0.19
Matches are distributed among these distances:
27 2 0.04
28 7 0.13
29 7 0.13
30 10 0.19
31 7 0.13
32 17 0.32
33 3 0.06
ACGTcount: A:0.45, C:0.01, G:0.03, T:0.51
Consensus pattern (32 bp):
AAATTAATTTTATTTTATTTAAAAGTTTAATA
Found at i:19988320 original size:9 final size:9
Alignment explanation
Indices: 19988308--19988345 Score: 53
Period size: 9 Copynumber: 4.4 Consensus size: 9
19988298 CATTTGAAAA
19988308 TTAATGTTT
1 TTAATGTTT
*
19988317 TTAATG-AT
1 TTAATGTTT
19988325 TTAAT-TTT
1 TTAATGTTT
19988333 TTAATGTTT
1 TTAATGTTT
19988342 TTAA
1 TTAA
19988346 CGATTTAAAC
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
8 12 0.48
9 13 0.52
ACGTcount: A:0.29, C:0.00, G:0.08, T:0.63
Consensus pattern (9 bp):
TTAATGTTT
Found at i:19991145 original size:2 final size:2
Alignment explanation
Indices: 19991138--19991176 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
19991128 GGATCAAATT
19991138 TA 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 TA T
19991177 GATTCATTCA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:19991975 original size:104 final size:104
Alignment explanation
Indices: 19991719--19992119 Score: 678
Period size: 104 Copynumber: 3.9 Consensus size: 104
19991709 TTGAATATGT
* *
19991719 TATTTTATTTTATTTTATTTTAATCACGAAAAATATTTTGTCAACTTTTATTTTATTTTTAAATT
1 TATTTTATTTTATTTTATTTTAATCACAAAAAATATTTTGTCTACTTTTATTTTATTTTTAAATT
19991784 ACCTAATTAAATTAAATTGTATTTAAA-GTTTTTTTAAA
66 ACCTAATTAAATTAAATTGTATTTAAAGGTTTTTTTAAA
19991822 TATTTTATTTTATTTTATTTTAATCACAAAAAATATTTTGTCTACTTTTATTTTATTTTTAAATT
1 TATTTTATTTTATTTTATTTTAATCACAAAAAATATTTTGTCTACTTTTATTTTATTTTTAAATT
19991887 ACCTAATTAAATTAAATTGTATTTAAAGGTTTTTTTAAA
66 ACCTAATTAAATTAAATTGTATTTAAAGGTTTTTTTAAA
19991926 TATTTTATTTTATTTTATTTTAATCACAAAAAATATTTTGTCTACTTTTATTTTATTTTTAAATT
1 TATTTTATTTTATTTTATTTTAATCACAAAAAATATTTTGTCTACTTTTATTTTATTTTTAAATT
*
19991991 ACCTAATTAAATTAAATTGTATTTAAAGTTTTATTTTAAA
66 ACCTAATTAAATTAAATTGTATTTAAAGGTTT-TTTTAAA
* ** * * * *
19992031 TATTTTATTTTATTTTAATTTAATCATGAAAAATATTTTATTTACTTTTATTTTATTGTTAAATA
1 TATTTTATTTTATTTTATTTTAATCACAAAAAATATTTTGTCTACTTTTATTTTATTTTTAAATT
* *
19992096 ACTTAATTAAATTAAATTTTATTT
66 ACCTAATTAAATTAAATTGTATTT
19992120 TTAAATATTG
Statistics
Matches: 284, Mismatches: 12, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
103 90 0.32
104 107 0.38
105 87 0.31
ACGTcount: A:0.35, C:0.05, G:0.03, T:0.56
Consensus pattern (104 bp):
TATTTTATTTTATTTTATTTTAATCACAAAAAATATTTTGTCTACTTTTATTTTATTTTTAAATT
ACCTAATTAAATTAAATTGTATTTAAAGGTTTTTTTAAA
Found at i:19992418 original size:9 final size:9
Alignment explanation
Indices: 19992393--19992632 Score: 106
Period size: 9 Copynumber: 26.0 Consensus size: 9
19992383 ATATCATATC
19992393 TTACATAAT
1 TTACATAAT
19992402 TTACATAAT
1 TTACATAAT
*
19992411 TTACATAAC
1 TTACATAAT
19992420 TTACATAA-
1 TTACATAAT
19992428 -TACATAAAT
1 TTACAT-AAT
19992437 ATATATCAT-AT
1 -T-TA-CATAAT
*
19992448 CGTACATAAT
1 -TTACATAAT
*
19992458 TTACATAAG
1 TTACATAAT
* * * *
19992467 ATAAACAAC
1 TTACATAAT
19992476 TTACATAA-
1 TTACATAAT
19992484 -TACATAAAT
1 TTACAT-AAT
19992493 ATATATCAT-AT
1 -T-TA-CATAAT
19992504 CTTACATAAT
1 -TTACATAAT
*
19992514 TTACATAAG
1 TTACATAAT
* * *
19992523 ATAAACAACT
1 TTACATAA-T
19992533 TT-CATAAT
1 TTACATAAT
*
19992541 TTACATAAC
1 TTACATAAT
*
19992550 TTACATGA-
1 TTACATAAT
19992558 -TACATAAAT
1 TTACAT-AAT
19992567 ATATATCAT-AT
1 -T-TA-CATAAT
19992578 CTTACATAAT
1 -TTACATAAT
19992588 TTACATAAT
1 TTACATAAT
* *
19992597 TCGA-ATAAC
1 T-TACATAAT
19992606 TTACATAAT
1 TTACATAAT
*
19992615 TTACATAAC
1 TTACATAAT
19992624 TTACATAAT
1 TTACATAAT
19992633 ACATAAATAT
Statistics
Matches: 175, Mismatches: 31, Indels: 50
0.68 0.12 0.20
Matches are distributed among these distances:
7 15 0.09
8 9 0.05
9 114 0.65
10 14 0.08
11 8 0.05
12 6 0.03
13 9 0.05
ACGTcount: A:0.47, C:0.15, G:0.02, T:0.37
Consensus pattern (9 bp):
TTACATAAT
Found at i:19992459 original size:56 final size:56
Alignment explanation
Indices: 19992373--19992540 Score: 282
Period size: 56 Copynumber: 3.0 Consensus size: 56
19992363 AATCTCATCA
** * *
19992373 ACATAAATATATATCATATCTTACATAATTTACATAATTTACATAACTTACATAAT
1 ACATAAATATATATCATATCTTACATAATTTACATAAGATAAACAACTTACATAAT
*
19992429 ACATAAATATATATCATATCGTACATAATTTACATAAGATAAACAACTTACATAAT
1 ACATAAATATATATCATATCTTACATAATTTACATAAGATAAACAACTTACATAAT
*
19992485 ACATAAATATATATCATATCTTACATAATTTACATAAGATAAACAACTTTCATAAT
1 ACATAAATATATATCATATCTTACATAATTTACATAAGATAAACAACTTACATAAT
19992541 TTACATAACT
Statistics
Matches: 105, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
56 105 1.00
ACGTcount: A:0.48, C:0.14, G:0.02, T:0.36
Consensus pattern (56 bp):
ACATAAATATATATCATATCTTACATAATTTACATAAGATAAACAACTTACATAAT
Found at i:19992539 original size:74 final size:74
Alignment explanation
Indices: 19992473--19992652 Score: 299
Period size: 74 Copynumber: 2.4 Consensus size: 74
19992463 TAAGATAAAC
*
19992473 AACTTACATAATACATAAATATATATCATATCTTACATAATTTACATAAGAT-AAACAACTTTCA
1 AACTTACATAATACATAAATATATATCATATCTTACATAATTTACATAA-ATCAAACAACTTACA
19992537 TAATTTACAT
65 TAATTTACAT
* * * *
19992547 AACTTACATGATACATAAATATATATCATATCTTACATAATTTACATAATTCGAATAACTTACAT
1 AACTTACATAATACATAAATATATATCATATCTTACATAATTTACATAAATCAAACAACTTACAT
19992612 AATTTACAT
66 AATTTACAT
19992621 AACTTACATAATACATAAATATATATCATATC
1 AACTTACATAATACATAAATATATATCATATC
19992653 ATAACTTACA
Statistics
Matches: 99, Mismatches: 6, Indels: 2
0.93 0.06 0.02
Matches are distributed among these distances:
73 1 0.01
74 98 0.99
ACGTcount: A:0.47, C:0.15, G:0.02, T:0.37
Consensus pattern (74 bp):
AACTTACATAATACATAAATATATATCATATCTTACATAATTTACATAAATCAAACAACTTACAT
AATTTACAT
Found at i:19992631 original size:27 final size:27
Alignment explanation
Indices: 19992573--19992665 Score: 79
Period size: 27 Copynumber: 3.5 Consensus size: 27
19992563 AAATATATAT
*
19992573 CATATCTTACATAATTTACATAA-TT-
1 CATAACTTACATAATTTACATAACTTA
19992598 CGAATAACTTACATAATTTACATAACTTA
1 C--ATAACTTACATAATTTACATAACTTA
* * * *
19992627 CATAA--TACATAA-ATATATATCATA
1 CATAACTTACATAATTTACATAACTTA
19992651 TCATAACTTACATAA
1 -CATAACTTACATAA
19992666 CTTAATTATA
Statistics
Matches: 56, Mismatches: 5, Indels: 12
0.77 0.07 0.16
Matches are distributed among these distances:
24 8 0.14
25 13 0.23
27 32 0.57
28 2 0.04
29 1 0.02
ACGTcount: A:0.46, C:0.16, G:0.01, T:0.37
Consensus pattern (27 bp):
CATAACTTACATAATTTACATAACTTA
Found at i:19998470 original size:31 final size:31
Alignment explanation
Indices: 19998434--19998499 Score: 105
Period size: 31 Copynumber: 2.1 Consensus size: 31
19998424 TGTATTTTTT
19998434 ATGCTACATTTGCTATTTTTGGTTGGATTCA
1 ATGCTACATTTGCTATTTTTGGTTGGATTCA
* * *
19998465 ATGCTATATTTTCTATTTTTGGTTGGATTTA
1 ATGCTACATTTGCTATTTTTGGTTGGATTCA
19998496 ATGC
1 ATGC
19998500 AGGAAGGGTT
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.20, C:0.11, G:0.18, T:0.52
Consensus pattern (31 bp):
ATGCTACATTTGCTATTTTTGGTTGGATTCA
Found at i:19998597 original size:43 final size:42
Alignment explanation
Indices: 19998549--19998760 Score: 203
Period size: 43 Copynumber: 4.9 Consensus size: 42
19998539 TATGCCAAAA
* *
19998549 TTAGCGGCATTTGTAACA-AAAGCGCCGCTAAAAACCATGACTT
1 TTAGCGGCATTT-TACCACAAA-CGCCGCTAAAAGCCATGACTT
* * * *
19998592 TTAGCGGCGTTTCACCCAAAAACGCCACTAAAAGCCATGACTT
1 TTAGCGGCATTTTA-CCACAAACGCCGCTAAAAGCCATGACTT
* * *
19998635 TTAGCAACGC-TTTTCCCACAAATGCCGCTAAAAGCCATGACTT
1 TTAGC--GGCATTTTACCACAAACGCCGCTAAAAGCCATGACTT
* * * *
19998678 TTAGTGGCACTTTTCCCACAAATGCAGCTAAAAGCCATGACTT
1 TTAGCGGCA-TTTTACCACAAACGCCGCTAAAAGCCATGACTT
* * *
19998721 TTAGCGGCACTTTTCCCACAAACGCCACTAAAAGTCATGA
1 TTAGCGGCA-TTTTACCACAAACGCCGCTAAAAGCCATGA
19998761 TCTGTTGCGG
Statistics
Matches: 144, Mismatches: 19, Indels: 12
0.82 0.11 0.07
Matches are distributed among these distances:
41 2 0.01
42 1 0.01
43 133 0.92
44 6 0.04
45 2 0.01
ACGTcount: A:0.32, C:0.28, G:0.16, T:0.24
Consensus pattern (42 bp):
TTAGCGGCATTTTACCACAAACGCCGCTAAAAGCCATGACTT
Found at i:19998771 original size:43 final size:43
Alignment explanation
Indices: 19998571--19998760 Score: 231
Period size: 43 Copynumber: 4.4 Consensus size: 43
19998561 GTAACAAAAG
* * * * *
19998571 CGCCGCTAAAAACCATGACTTTTAGCGGC-GTTTCACCCAAAAA
1 CGCCACTAAAAGCCATGACTTTTAGCGGCACTTT-TCCCACAAA
** *
19998614 CGCCACTAAAAGCCATGACTTTTAGCAACGCTTTTCCCACAAA
1 CGCCACTAAAAGCCATGACTTTTAGCGGCACTTTTCCCACAAA
* * *
19998657 TGCCGCTAAAAGCCATGACTTTTAGTGGCACTTTTCCCACAAA
1 CGCCACTAAAAGCCATGACTTTTAGCGGCACTTTTCCCACAAA
*
19998700 TG-CAGCTAAAAGCCATGACTTTTAGCGGCACTTTTCCCACAAA
1 CGCCA-CTAAAAGCCATGACTTTTAGCGGCACTTTTCCCACAAA
*
19998743 CGCCACTAAAAGTCATGA
1 CGCCACTAAAAGCCATGA
19998761 TCTGTTGCGG
Statistics
Matches: 127, Mismatches: 17, Indels: 6
0.85 0.11 0.04
Matches are distributed among these distances:
42 1 0.01
43 121 0.95
44 5 0.04
ACGTcount: A:0.32, C:0.29, G:0.15, T:0.24
Consensus pattern (43 bp):
CGCCACTAAAAGCCATGACTTTTAGCGGCACTTTTCCCACAAA
Found at i:20001392 original size:40 final size:40
Alignment explanation
Indices: 20001348--20001426 Score: 122
Period size: 40 Copynumber: 2.0 Consensus size: 40
20001338 TTACAGTACC
* *
20001348 ACTTGGTGTGTAGGACTGGATGGGTCGATTTTGTCCCCAT
1 ACTTGGTGTGTAGGACTGGATGGGTCAATTTTATCCCCAT
* *
20001388 ACTTGGTGTGTAGGGCTGGGTGGGTCAATTTTATCCCCA
1 ACTTGGTGTGTAGGACTGGATGGGTCAATTTTATCCCCA
20001427 CATGGTGTGT
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
40 35 1.00
ACGTcount: A:0.15, C:0.18, G:0.33, T:0.34
Consensus pattern (40 bp):
ACTTGGTGTGTAGGACTGGATGGGTCAATTTTATCCCCAT
Found at i:20012248 original size:11 final size:11
Alignment explanation
Indices: 20012234--20012290 Score: 55
Period size: 11 Copynumber: 5.2 Consensus size: 11
20012224 ATTGAATTAA
*
20012234 TAAAATACTAT
1 TAAAATAATAT
20012245 TAAAATAAGTAT
1 TAAAATAA-TAT
*
20012257 TAAATTTAATAT
1 TAAA-ATAATAT
*
20012269 T-AAAT-TTAT
1 TAAAATAATAT
20012278 TAAAATAATAT
1 TAAAATAATAT
20012289 TA
1 TA
20012291 TTTTTGAAAT
Statistics
Matches: 37, Mismatches: 5, Indels: 8
0.74 0.10 0.16
Matches are distributed among these distances:
9 4 0.11
10 5 0.14
11 14 0.38
12 11 0.30
13 3 0.08
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.42
Consensus pattern (11 bp):
TAAAATAATAT
Found at i:20029413 original size:330 final size:330
Alignment explanation
Indices: 20028798--20029454 Score: 1145
Period size: 330 Copynumber: 2.0 Consensus size: 330
20028788 AACCCATATG
* * *
20028798 ACATCTTTCTTTTTCGGAGTCATAGGTAGTCTTGTCACAAAGTCCATGGTAATTCTGTCCCACTT
1 ACATCTATCTTTTTCGGAGTCATAGGTAGTCCTCTCACAAAGTCCATGGTAATTCTGTCCCACTT
*
20028863 CCATTCGGGGACCATTACAGGTTGTAACAAACTTGAAGGAACTTGATATTCAGCTTTAACTTGCT
66 CCATTCGGGGACCATTACAGGTTGTAACAAACCTGAAGGAACTTGATATTCAGCTTTAACTTGCT
* *
20028928 AACATACCAGGCATTTCGATACAAATTTAGAAACATCTCTTTTCATGTCGCTCCACCAGTACATC
131 AACATACCAGGCATTTCGATACAAATTCAGAAACATCTCTTTTCATGCCGCTCCACCAGTACATC
*
20028993 TTCTTTAAATTGTTGTACATCTTGGTACTTCCTGGGTGAACTAACAAACGACTATTATATGCTTC
196 TTCTTTAAATCGTTGTACATCTTGGTACTTCCTGGGTGAACTAACAAACGACTATTATATGCTTC
* *
20029058 TTGCAAAATCTTCCGAATCAGTTCATTATCTTTGGGTACACAAACCCTATCTCTAAACATTAAAC
261 TTGCAAAATATTCCGAATAAGTTCATTATCTTTGGGTACACAAACCCTATCTCTAAACATTAAAC
20029123 ATTAA
326 ATTAA
20029128 ACATCTATCTTTTTCGGAGTCATAGGTAGTCCTCTCACAAAGTCCATGGTAATTCTGTCCCACTT
1 ACATCTATCTTTTTCGGAGTCATAGGTAGTCCTCTCACAAAGTCCATGGTAATTCTGTCCCACTT
* * * *
20029193 CCATTTGGGGACCATTACAGGTTGTAATAAACCTGAAGGCACTTGATGTTCAGCTTTAACTTGCT
66 CCATTCGGGGACCATTACAGGTTGTAACAAACCTGAAGGAACTTGATATTCAGCTTTAACTTGCT
*
20029258 AACATACCAGGCATTTTGATACAAATTCAGAAACATCTCTTTTCATGCCGCTCCACCAGTACATC
131 AACATACCAGGCATTTCGATACAAATTCAGAAACATCTCTTTTCATGCCGCTCCACCAGTACATC
* *
20029323 TTCTTTAAATCGTTGTACATCTTGGTACTTCCCT-GGTGAACTAATAAACGACTATTATGTGCTT
196 TTCTTTAAATCGTTGTACATCTTGGTACTT-CCTGGGTGAACTAACAAACGACTATTATATGCTT
*
20029387 CTTGCAAAATATTCTGAATAAGTTCATTATCTTTGGGTACACAAACCCTATCTCTAAACATTAAA
260 CTTGCAAAATATTCCGAATAAGTTCATTATCTTTGGGTACACAAACCCTATCTCTAAACATTAAA
20029452 CAT
325 CAT
20029455 CCCTTAGGAC
Statistics
Matches: 309, Mismatches: 17, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
330 306 0.99
331 3 0.01
ACGTcount: A:0.29, C:0.23, G:0.14, T:0.34
Consensus pattern (330 bp):
ACATCTATCTTTTTCGGAGTCATAGGTAGTCCTCTCACAAAGTCCATGGTAATTCTGTCCCACTT
CCATTCGGGGACCATTACAGGTTGTAACAAACCTGAAGGAACTTGATATTCAGCTTTAACTTGCT
AACATACCAGGCATTTCGATACAAATTCAGAAACATCTCTTTTCATGCCGCTCCACCAGTACATC
TTCTTTAAATCGTTGTACATCTTGGTACTTCCTGGGTGAACTAACAAACGACTATTATATGCTTC
TTGCAAAATATTCCGAATAAGTTCATTATCTTTGGGTACACAAACCCTATCTCTAAACATTAAAC
ATTAA
Found at i:20044737 original size:16 final size:17
Alignment explanation
Indices: 20044706--20044738 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
20044696 TATGTAGCTA
*
20044706 GATTTTTTGTATAAATT
1 GATTTTTTGGATAAATT
20044723 GATTTTTTGGA-AAATT
1 GATTTTTTGGATAAATT
20044739 ATATTTGCTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.30, C:0.00, G:0.15, T:0.55
Consensus pattern (17 bp):
GATTTTTTGGATAAATT
Found at i:20044940 original size:8 final size:8
Alignment explanation
Indices: 20044925--20044963 Score: 51
Period size: 8 Copynumber: 4.8 Consensus size: 8
20044915 CTTCACACAC
20044925 AAAAATAA
1 AAAAATAA
*
20044933 ATAAATAA
1 AAAAATAA
*
20044941 ATAAATAA
1 AAAAATAA
20044949 TAAAAATAA
1 -AAAAATAA
20044958 AAAAAT
1 AAAAAT
20044964 TATTAAAAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
8 21 0.75
9 7 0.25
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (8 bp):
AAAAATAA
Found at i:20044972 original size:18 final size:17
Alignment explanation
Indices: 20044925--20044963 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
20044915 CTTCACACAC
*
20044925 AAAAATAA-ATAAATAA
1 AAAAATAATAAAAATAA
*
20044941 ATAAATAATAAAAATAA
1 AAAAATAATAAAAATAA
20044958 AAAAAT
1 AAAAAT
20044964 TATTAAAAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
16 7 0.37
17 12 0.63
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (17 bp):
AAAAATAATAAAAATAA
Found at i:20052087 original size:21 final size:20
Alignment explanation
Indices: 20052054--20052093 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
20052044 GAATTAATGG
20052054 CTACACGGCCGTGTTGCCCTT
1 CTACACGGCCGTG-TGCCCTT
* *
20052075 CTACATGGGCGTGTGCCCT
1 CTACACGGCCGTGTGCCCT
20052094 GTTCTAGAGC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 6 0.35
21 11 0.65
ACGTcount: A:0.10, C:0.35, G:0.28, T:0.28
Consensus pattern (20 bp):
CTACACGGCCGTGTGCCCTT
Found at i:20056106 original size:24 final size:24
Alignment explanation
Indices: 20056079--20056169 Score: 164
Period size: 24 Copynumber: 3.8 Consensus size: 24
20056069 CTTATTATGT
**
20056079 TCGCACACATAGTGCCATAGCGAA
1 TCGCACACATAGTGCCATAGTAAA
20056103 TCGCACACATAGTGCCATAGTAAA
1 TCGCACACATAGTGCCATAGTAAA
20056127 TCGCACACATAGTGCCATAGTAAA
1 TCGCACACATAGTGCCATAGTAAA
20056151 TCGCACACATAGTGCCATA
1 TCGCACACATAGTGCCATA
20056170 TATTTCCAGC
Statistics
Matches: 65, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 65 1.00
ACGTcount: A:0.35, C:0.27, G:0.18, T:0.20
Consensus pattern (24 bp):
TCGCACACATAGTGCCATAGTAAA
Found at i:20059674 original size:4 final size:4
Alignment explanation
Indices: 20059665--20059713 Score: 64
Period size: 4 Copynumber: 12.2 Consensus size: 4
20059655 TTGCTTGTAC
* *
20059665 ATAA ATAA ATAA ATAA ATAAA ATGA A-AA TTAA ATAA ATAA ATAA ATAA
1 ATAA ATAA ATAA ATAA AT-AA ATAA ATAA ATAA ATAA ATAA ATAA ATAA
20059713 A
1 A
20059714 GGCTCAAGTT
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
3 1 0.03
4 34 0.87
5 4 0.10
ACGTcount: A:0.73, C:0.00, G:0.02, T:0.24
Consensus pattern (4 bp):
ATAA
Found at i:20061207 original size:18 final size:18
Alignment explanation
Indices: 20061184--20061218 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
20061174 AATCTGAATG
20061184 TATTTCCCAAT-TTAATTT
1 TATTT-CCAATATTAATTT
20061202 TATTTCCAATATTAATT
1 TATTTCCAATATTAATT
20061219 AATTGTTTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.31, C:0.14, G:0.00, T:0.54
Consensus pattern (18 bp):
TATTTCCAATATTAATTT
Found at i:20064975 original size:49 final size:49
Alignment explanation
Indices: 20064917--20065149 Score: 288
Period size: 49 Copynumber: 4.7 Consensus size: 49
20064907 ATCTCGTATG
* *
20064917 CATAGTAGCCTGCACTTAGTACTACACATGCGACCAATTATCCAGTACA
1 CATAGTAGCCTGCACTTAGTACTACACACGCGACCAATTATCCGGTACA
* * ** * *
20064966 CGTAGTAGCCTGCACTTAGTACTACAC-CGTGACCTAACCATCTGATACA
1 CATAGTAGCCTGCACTTAGTACTACACACGCGACC-AATTATCCGGTACA
* * * * *
20065015 CGTAGTAGCCTGCACTTAGTACTACACACGTGATCAAAGTTATCGGGTACG
1 CATAGTAGCCTGCACTTAGTACTACACACGCGA-CCAA-TTATCCGGTACA
* *
20065066 CATAGTAGCCTGCACTTAGTACTACACATGCTACCAATTATCCGGTACA
1 CATAGTAGCCTGCACTTAGTACTACACACGCGACCAATTATCCGGTACA
*
20065115 CATAGTAGCCTGCACTTAGTACTACACACGTGACC
1 CATAGTAGCCTGCACTTAGTACTACACACGCGACC
20065150 TCACAATAGA
Statistics
Matches: 156, Mismatches: 24, Indels: 8
0.83 0.13 0.04
Matches are distributed among these distances:
48 5 0.03
49 104 0.67
50 10 0.06
51 37 0.24
ACGTcount: A:0.30, C:0.28, G:0.17, T:0.25
Consensus pattern (49 bp):
CATAGTAGCCTGCACTTAGTACTACACACGCGACCAATTATCCGGTACA
Found at i:20065090 original size:100 final size:97
Alignment explanation
Indices: 20064917--20065148 Score: 295
Period size: 100 Copynumber: 2.4 Consensus size: 97
20064907 ATCTCGTATG
* * * *
20064917 CATAGTAGCCTGCACTTAGTACTACACATGCGACCAATTATCCAGTACACGTAGTAGCCTGCACT
1 CATAGTAGCCTGCACTTAGTACTACACACGTGACAAATTATCCAGTACACATAGTAGCCTGCACT
* *
20064982 TAGTACTACACCGTG-ACCTAACCATCTGATACA
66 TAGTACTACA-CATGCACC-AACCATCCGATACA
* ** *
20065015 CGTAGTAGCCTGCACTTAGTACTACACACGTGATCAAAGTTATCGGGTACGCATAGTAGCCTGCA
1 CATAGTAGCCTGCACTTAGTACTACACACGTGA-CAAA-TTATCCAGTACACATAGTAGCCTGCA
** *
20065080 CTTAGTACTACACATGCTACCAATTATCCGGTACA
64 CTTAGTACTACACATGC-ACCAACCATCCGATACA
20065115 CATAGTAGCCTGCACTTAGTACTACACACGTGAC
1 CATAGTAGCCTGCACTTAGTACTACACACGTGAC
20065149 CTCACAATAG
Statistics
Matches: 116, Mismatches: 14, Indels: 7
0.85 0.10 0.05
Matches are distributed among these distances:
98 30 0.26
99 7 0.06
100 76 0.66
101 3 0.03
ACGTcount: A:0.30, C:0.28, G:0.17, T:0.25
Consensus pattern (97 bp):
CATAGTAGCCTGCACTTAGTACTACACACGTGACAAATTATCCAGTACACATAGTAGCCTGCACT
TAGTACTACACATGCACCAACCATCCGATACA
Found at i:20075598 original size:11 final size:11
Alignment explanation
Indices: 20075582--20075606 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
20075572 TTATTATCTC
20075582 TTATTATTTTA
1 TTATTATTTTA
20075593 TTATTATTTTA
1 TTATTATTTTA
20075604 TTA
1 TTA
20075607 CGAATTTTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (11 bp):
TTATTATTTTA
Found at i:20076997 original size:22 final size:22
Alignment explanation
Indices: 20076969--20077013 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
20076959 GAAAGATAAA
20076969 TCTGTGATGTTTAAGGATGGAC
1 TCTGTGATGTTTAAGGATGGAC
20076991 TCTGTGATGTTTAAGGATGGAC
1 TCTGTGATGTTTAAGGATGGAC
20077013 T
1 T
20077014 GCATTAGGAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.22, C:0.09, G:0.31, T:0.38
Consensus pattern (22 bp):
TCTGTGATGTTTAAGGATGGAC
Found at i:20088350 original size:40 final size:40
Alignment explanation
Indices: 20088305--20088442 Score: 138
Period size: 40 Copynumber: 3.5 Consensus size: 40
20088295 GGATATAACG
*
20088305 ACTCGCTCAAATGCCTTCGAGAC-AAAGCCC-GGTTATAGTA
1 ACTCGCACAAATGCCTTCGAGACTAAA-CCCGGGTT-TAGTA
* * *
20088345 ACTCGCACGAATGCCTTCGGGACTTAACCCGGGTTTAGTA
1 ACTCGCACAAATGCCTTCGAGACTAAACCCGGGTTTAGTA
* * * * *
20088385 ACTCGCACAAATGCCTTCG-GGCTTAGCCCGGATTTATTA
1 ACTCGCACAAATGCCTTCGAGACTAAACCCGGGTTTAGTA
* *
20088424 ACTCGCACGAACGCCTTCG
1 ACTCGCACAAATGCCTTCG
20088443 GATCTTAGTC
Statistics
Matches: 85, Mismatches: 11, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
39 33 0.39
40 46 0.54
41 6 0.07
ACGTcount: A:0.25, C:0.30, G:0.22, T:0.24
Consensus pattern (40 bp):
ACTCGCACAAATGCCTTCGAGACTAAACCCGGGTTTAGTA
Found at i:20088413 original size:79 final size:79
Alignment explanation
Indices: 20088279--20088496 Score: 212
Period size: 79 Copynumber: 2.7 Consensus size: 79
20088269 GAATCACGTA
*** * * **
20088279 CCTTCGGAAT-TTAA-CCGGATATAACGACTCGCTCAAATGCCTTCGAGACAAAGCCCGG-TTAT
1 CCTTCGG-ATCTTAACCCGGATATAGTAACTCGCACAAATGCCTTCG-GGCTTAGCCCGGATT-T
*
20088341 AGTAACTCGCACGAATG
63 AGTAACTCGCACGAACG
* * *
20088358 CCTTCGGGA-CTTAACCCGGGTTTAGTAACTCGCACAAATGCCTTCGGGCTTAGCCCGGATTTAT
1 CCTTC-GGATCTTAACCCGGATATAGTAACTCGCACAAATGCCTTCGGGCTTAGCCCGGATTTAG
20088422 TAACTCGCACGAACG
65 TAACTCGCACGAACG
** * *
20088437 CCTTCGGATCTTAGTCCGGATATAGTCACTTAGCACAAA-GCCTTCGGGACTTAGCCCGGA
1 CCTTCGGATCTTAACCCGGATATAGTAAC-TCGCACAAATGCCTTCGGG-CTTAGCCCGGA
20088497 CATCATTCAA
Statistics
Matches: 115, Mismatches: 17, Indels: 13
0.79 0.12 0.09
Matches are distributed among these distances:
78 3 0.03
79 64 0.56
80 48 0.42
ACGTcount: A:0.26, C:0.28, G:0.22, T:0.24
Consensus pattern (79 bp):
CCTTCGGATCTTAACCCGGATATAGTAACTCGCACAAATGCCTTCGGGCTTAGCCCGGATTTAGT
AACTCGCACGAACG
Found at i:20093076 original size:26 final size:26
Alignment explanation
Indices: 20093040--20093093 Score: 99
Period size: 26 Copynumber: 2.1 Consensus size: 26
20093030 GTTTGATGTG
20093040 TTAGCAAGTAAAAGTAGAACACCAAT
1 TTAGCAAGTAAAAGTAGAACACCAAT
*
20093066 TTAGCAAGTAAAAGTAGAAGACCAAT
1 TTAGCAAGTAAAAGTAGAACACCAAT
20093092 TT
1 TT
20093094 CCTTCTGGGT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.48, C:0.13, G:0.17, T:0.22
Consensus pattern (26 bp):
TTAGCAAGTAAAAGTAGAACACCAAT
Found at i:20098364 original size:13 final size:13
Alignment explanation
Indices: 20098346--20098374 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
20098336 CGTAAACAAT
20098346 TTTTTGTGTCATG
1 TTTTTGTGTCATG
20098359 TTTTTGTGTCATG
1 TTTTTGTGTCATG
20098372 TTT
1 TTT
20098375 ATCATAGTGC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.07, C:0.07, G:0.21, T:0.66
Consensus pattern (13 bp):
TTTTTGTGTCATG
Found at i:20100775 original size:89 final size:91
Alignment explanation
Indices: 20100555--20100786 Score: 281
Period size: 92 Copynumber: 2.6 Consensus size: 91
20100545 CTCTTTTTTT
* * *
20100555 TTTTTTTTGCACTCAATTGGGTACTTCAACTTTCAAAATGCATCAAAAATGCCCTCAAACTTGAG
1 TTTTTTTTGCACTCAATTGGATACTTGAACTTTCAAAATGCATCAAAAAGGCCCTCAAACTTGAG
* * **
20100620 AAAAGAAGAAGCAATTAAGCTATTGT
66 AAAAGAAGAAGAAATTAAGCCATTAC
*
20100646 TTGTTTTTTGCACTCAATT-GAGTACTTGAACTTTCAAAATGCATCAAAAAGGCCCTCAAACTTT
1 TT-TTTTTTGCACTCAATTGGA-TACTTGAACTTTCAAAATGCATCAAAAAGGCCCTCAAACTTG
*** * *
20100710 TTCAAA-AA-AAGAAATTAGGCCCTTAC
64 AGAAAAGAAGAAGAAATTAAGCCATTAC
** *
20100736 TTTTTTTTGCACTCAATTGGATACTTGAACTGCCAAAATGCATAAAAAAGG
1 TTTTTTTTGCACTCAATTGGATACTTGAACTTTCAAAATGCATCAAAAAGG
20100787 TTCTTTGACT
Statistics
Matches: 122, Mismatches: 16, Indels: 8
0.84 0.11 0.05
Matches are distributed among these distances:
89 43 0.35
90 16 0.13
91 5 0.04
92 58 0.48
ACGTcount: A:0.36, C:0.18, G:0.14, T:0.32
Consensus pattern (91 bp):
TTTTTTTTGCACTCAATTGGATACTTGAACTTTCAAAATGCATCAAAAAGGCCCTCAAACTTGAG
AAAAGAAGAAGAAATTAAGCCATTAC
Found at i:20100966 original size:19 final size:18
Alignment explanation
Indices: 20100942--20101025 Score: 51
Period size: 19 Copynumber: 4.4 Consensus size: 18
20100932 TTAAATTTTA
*
20100942 ATTAAAATTATTAAAAATT
1 ATTAAAATT-TTAAAAAAT
* *
20100961 ATTAAAATCATAAAAAAAT
1 ATTAAAAT-TTTAAAAAAT
* ***
20100980 ATAGAAAATTTTAAATTTT
1 AT-TAAAATTTTAAAAAAT
* *
20100999 ATAAAAATTGTAAAAAAT
1 ATTAAAATTTTAAAAAAT
20101017 ATATAAAAT
1 AT-TAAAAT
20101026 ATATAGAAAT
Statistics
Matches: 47, Mismatches: 15, Indels: 6
0.69 0.22 0.09
Matches are distributed among these distances:
18 13 0.28
19 29 0.62
20 5 0.11
ACGTcount: A:0.61, C:0.01, G:0.02, T:0.36
Consensus pattern (18 bp):
ATTAAAATTTTAAAAAAT
Found at i:20101097 original size:67 final size:66
Alignment explanation
Indices: 20100972--20101121 Score: 153
Period size: 67 Copynumber: 2.2 Consensus size: 66
20100962 TTAAAATCAT
* * * * *
20100972 AAAAAAATATAGAAAATTTTAAATTTTATAAAAATTGTAAAAAATATATAAAATATATAGAAATA
1 AAAAAAAT-TATAAAATTTTAAATTATATAAAAATTATAAAAAATATACAAAAAATATA-AAAT-
20101037 TAG-
63 TAGA
* *
20101040 AAAAAAATTATAAAATTTTATATTATA-AGAAAATTATAAAAAA-ATGCAAAGAAATATAAAATT
1 AAAAAAATTATAAAATTTTAAATTATATA-AAAATTATAAAAAATATACAAA-AAATATAAAATT
*
20101103 TGTA
64 AG-A
20101107 AAAAAAATTATAAAA
1 AAAAAAATTATAAAA
20101122 ATTATTTTAC
Statistics
Matches: 70, Mismatches: 8, Indels: 9
0.80 0.09 0.10
Matches are distributed among these distances:
65 2 0.03
66 10 0.14
67 50 0.71
68 8 0.11
ACGTcount: A:0.63, C:0.01, G:0.05, T:0.31
Consensus pattern (66 bp):
AAAAAAATTATAAAATTTTAAATTATATAAAAATTATAAAAAATATACAAAAAATATAAAATTAG
A
Found at i:20101325 original size:14 final size:14
Alignment explanation
Indices: 20101306--20101335 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
20101296 TTTTTATGCA
20101306 TTTTATAATTTTAT
1 TTTTATAATTTTAT
*
20101320 TTTTATGATTTTAT
1 TTTTATAATTTTAT
20101334 TT
1 TT
20101336 AAAATTTTAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.23, C:0.00, G:0.03, T:0.73
Consensus pattern (14 bp):
TTTTATAATTTTAT
Found at i:20101380 original size:18 final size:17
Alignment explanation
Indices: 20101333--20101382 Score: 57
Period size: 19 Copynumber: 2.8 Consensus size: 17
20101323 TATGATTTTA
20101333 TTTAAA-ATTTTATAAT
1 TTTAAATATTTTATAAT
*
20101349 TTAATAATATTTTTATGAAT
1 TTTA-AATA-TTTTAT-AAT
20101369 TTTAAATATTTTAT
1 TTTAAATATTTTAT
20101383 TTAAAATTTA
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
16 3 0.11
17 2 0.07
18 7 0.25
19 10 0.36
20 6 0.21
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (17 bp):
TTTAAATATTTTATAAT
Found at i:20101761 original size:89 final size:89
Alignment explanation
Indices: 20101595--20101763 Score: 200
Period size: 89 Copynumber: 1.9 Consensus size: 89
20101585 AAGCAAGAGA
* * * ** * *
20101595 TTAATTGCTTTTTTTGAAAAAGTTTGGGGGCCTTTTTGATACATTTTGAAAGTTCAAGTGCTCAA
1 TTAATTGCATTTTGTAAAAAAGTTTGAAGGCCTTTTTGATACATTTTAAAAGTTCAAGTACTCAA
*
20101660 CTGAGTGCAAAAAAAAAGTAGGGC
66 CTGAATGCAAAAAAAAAGTAGGGC
*
20101684 TTAATTGCATTTTGTAAAAAAGTTTGAAGGCCTTTTTTTG-TACATTTTAAAAGTTTAAGTAC-C
1 TTAATTGCATTTTGTAAAAAAGTTTGAAGGCC--TTTTTGATACATTTTAAAAGTTCAAGTACTC
*
20101747 AAATTGAATG-AAAAAAA
64 -AACTGAATGCAAAAAAA
20101764 TAGACTTAAT
Statistics
Matches: 67, Mismatches: 10, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
89 35 0.52
90 26 0.39
91 6 0.09
ACGTcount: A:0.36, C:0.09, G:0.18, T:0.37
Consensus pattern (89 bp):
TTAATTGCATTTTGTAAAAAAGTTTGAAGGCCTTTTTGATACATTTTAAAAGTTCAAGTACTCAA
CTGAATGCAAAAAAAAAGTAGGGC
Found at i:20101762 original size:90 final size:90
Alignment explanation
Indices: 20101577--20101763 Score: 200
Period size: 90 Copynumber: 2.1 Consensus size: 90
20101567 TTGAGTGCAA
* * * **
20101577 AAAAAAAAAAGCAAGAGATTAATTGCTTTTTTTGAAAAAGTTTGGGGGCCTTTTTGATACATTTT
1 AAAAAAAAAAGCAAGAGATTAATTGCATTTTGTAAAAAAGTTTGAAGGCCTTTTTGATACATTTT
* * *
20101642 GAAAGTTCAAGTGCTCAACTGAGTG
66 AAAAGTTCAAGTACTCAACTGAATG
* * * *
20101667 CAAAAAAAAAG-TAGGGCTTAATTGCATTTTGTAAAAAAGTTTGAAGGCCTTTTTTTG-TACATT
1 AAAAAAAAAAGCAAGAGATTAATTGCATTTTGTAAAAAAGTTTGAAGGCC--TTTTTGATACATT
* *
20101730 TTAAAAGTTTAAGTAC-CAAATTGAATG
64 TTAAAAGTTCAAGTACTC-AACTGAATG
20101757 AAAAAAA
1 AAAAAAA
20101764 TAGACTTAAT
Statistics
Matches: 79, Mismatches: 15, Indels: 6
0.79 0.15 0.06
Matches are distributed among these distances:
89 31 0.39
90 42 0.53
91 6 0.08
ACGTcount: A:0.40, C:0.09, G:0.18, T:0.33
Consensus pattern (90 bp):
AAAAAAAAAAGCAAGAGATTAATTGCATTTTGTAAAAAAGTTTGAAGGCCTTTTTGATACATTTT
AAAAGTTCAAGTACTCAACTGAATG
Found at i:20102063 original size:12 final size:12
Alignment explanation
Indices: 20102042--20102071 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
20102032 TTTGTTGCTA
20102042 AAACGAAAACGT
1 AAACGAAAACGT
*
20102054 AAACGTAAACGT
1 AAACGAAAACGT
20102066 AAACGA
1 AAACGA
20102072 GAGGATTTAG
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:0.57, C:0.17, G:0.17, T:0.10
Consensus pattern (12 bp):
AAACGAAAACGT
Found at i:20107713 original size:29 final size:29
Alignment explanation
Indices: 20107650--20107713 Score: 110
Period size: 29 Copynumber: 2.2 Consensus size: 29
20107640 TGACGAGATT
*
20107650 GGCACTAAGTGTGCATGCTGGAAATATAT
1 GGCACTAAGTGTGCATGCTGGAAATATAC
*
20107679 GACACTAAGTGTGCATGCTGGAAATATAC
1 GGCACTAAGTGTGCATGCTGGAAATATAC
20107708 GGCACT
1 GGCACT
20107714 GGGTGTGCGA
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
29 32 1.00
ACGTcount: A:0.31, C:0.17, G:0.27, T:0.25
Consensus pattern (29 bp):
GGCACTAAGTGTGCATGCTGGAAATATAC
Found at i:20107807 original size:28 final size:28
Alignment explanation
Indices: 20107738--20107834 Score: 106
Period size: 28 Copynumber: 3.4 Consensus size: 28
20107728 GAAGGGTATG
* * * *
20107738 GCACTAAGTGTGCGGGTTTAAAATTGTACA
1 GCACTAAGTGTGCGAGTTT--GATTATATA
20107768 GCACTAAGTGTGCGAGTTTGATTATATA
1 GCACTAAGTGTGCGAGTTTGATTATATA
*
20107796 GCACTAAGTGTGCGAG-TTGAATACATATA
1 GCACTAAGTGTGCGAGTTTG-AT-TATATA
20107825 GCACTAAGTG
1 GCACTAAGTG
20107835 CGCGGATTCA
Statistics
Matches: 60, Mismatches: 5, Indels: 5
0.86 0.07 0.07
Matches are distributed among these distances:
27 3 0.05
28 24 0.40
29 15 0.25
30 18 0.30
ACGTcount: A:0.31, C:0.13, G:0.26, T:0.30
Consensus pattern (28 bp):
GCACTAAGTGTGCGAGTTTGATTATATA
Found at i:20109426 original size:32 final size:32
Alignment explanation
Indices: 20109387--20109450 Score: 110
Period size: 32 Copynumber: 2.0 Consensus size: 32
20109377 AGATACTTTC
20109387 AAAAATACTTTATCACCGACTTGATACTCAAT
1 AAAAATACTTTATCACCGACTTGATACTCAAT
* *
20109419 AAAAATACTTTATTACTGACTTGATACTCAAT
1 AAAAATACTTTATCACCGACTTGATACTCAAT
20109451 TTCTTTTCTT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.41, C:0.19, G:0.06, T:0.34
Consensus pattern (32 bp):
AAAAATACTTTATCACCGACTTGATACTCAAT
Found at i:20112857 original size:224 final size:224
Alignment explanation
Indices: 20112467--20112912 Score: 813
Period size: 224 Copynumber: 2.0 Consensus size: 224
20112457 GCTACTAGCT
20112467 CTATTACCGGCATTTCTCAGGGGTCTCCCTTTTGTAGCCGTACTATTCGATCTCGCACTCTGAAA
1 CTATTACCGGCATTTCTCAGGGGTCTCCCTTTTGTAGCCGTACTATTCGATCTCGCACTCTGAAA
* **
20112532 TTTTTCTTTCTCGATCATCTCAGGACAGTCATTAATATAGTGGCCTTGAGAACCACATTGGAAAC
66 ATTTTCTTTCTCGATCATCTCAGGACAGTCATTAATATAGTGGCCTTGAGAACCACATCAGAAAC
20112597 AAGATCCATCATTCGTCCTACACATACCAAAATGGCTTCTACCACATTGTTGGCACTCGGATTTA
131 AAGATCCATCATTCGTCCTACACATACCAAAATGGCTTCTACCACATTGTTGGCACTCGGATTTA
20112662 GAAGGCCGAGCATTACCCACACTAGCCCC
196 GAAGGCCGAGCATTACCCACACTAGCCCC
*
20112691 CTATTACCGGTATTTCTCAGGGGTCTCCCTTTTGTAGCCGTACTATTC-AGTCTCGCACTCTGAA
1 CTATTACCGGCATTTCTCAGGGGTCTCCCTTTTGTAGCCGTACTATTCGA-TCTCGCACTCTGAA
*
20112755 AATTTTCTTTCTCGATCATCTCAGGACAGTTATTAATATAGTGGCCTTGAGAACCACATCAGAAA
65 AATTTTCTTTCTCGATCATCTCAGGACAGTCATTAATATAGTGGCCTTGAGAACCACATCAGAAA
* *
20112820 CAAGATCCATCATTCGTCCTACACATACCAAAATGGCTTCTACCATATTGTTGGCACTCGGGTTT
130 CAAGATCCATCATTCGTCCTACACATACCAAAATGGCTTCTACCACATTGTTGGCACTCGGATTT
20112885 AGAAGGCCGAGCATTACCCACACTAGCC
195 AGAAGGCCGAGCATTACCCACACTAGCC
20112913 ACAGATGTAC
Statistics
Matches: 214, Mismatches: 7, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
223 1 0.00
224 213 1.00
ACGTcount: A:0.26, C:0.27, G:0.17, T:0.30
Consensus pattern (224 bp):
CTATTACCGGCATTTCTCAGGGGTCTCCCTTTTGTAGCCGTACTATTCGATCTCGCACTCTGAAA
ATTTTCTTTCTCGATCATCTCAGGACAGTCATTAATATAGTGGCCTTGAGAACCACATCAGAAAC
AAGATCCATCATTCGTCCTACACATACCAAAATGGCTTCTACCACATTGTTGGCACTCGGATTTA
GAAGGCCGAGCATTACCCACACTAGCCCC
Found at i:20116294 original size:18 final size:19
Alignment explanation
Indices: 20116271--20116314 Score: 56
Period size: 18 Copynumber: 2.4 Consensus size: 19
20116261 TGTTATTTAC
*
20116271 ATTTGTGGAAGA-AATCAA
1 ATTTGTGGAACATAATCAA
20116289 ATTTGT-GAACATAATCAA
1 ATTTGTGGAACATAATCAA
20116307 ACTTTGTG
1 A-TTTGTG
20116315 AGGGTTCTGC
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
17 4 0.18
18 13 0.59
19 5 0.23
ACGTcount: A:0.39, C:0.09, G:0.18, T:0.34
Consensus pattern (19 bp):
ATTTGTGGAACATAATCAA
Found at i:20116566 original size:15 final size:15
Alignment explanation
Indices: 20116529--20116567 Score: 60
Period size: 15 Copynumber: 2.6 Consensus size: 15
20116519 GAATAACCTA
* *
20116529 AACCCTAAGCTTAAC
1 AACCCTAGGCCTAAC
20116544 AACCCTAGGCCTAAC
1 AACCCTAGGCCTAAC
20116559 AACCCTAGG
1 AACCCTAGG
20116568 AAGTCAAATT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.36, C:0.36, G:0.13, T:0.15
Consensus pattern (15 bp):
AACCCTAGGCCTAAC
Found at i:20119582 original size:42 final size:42
Alignment explanation
Indices: 20119472--20119625 Score: 148
Period size: 42 Copynumber: 3.6 Consensus size: 42
20119462 TACCACACCA
* * * ** ** *
20119472 ATGCCATATCCCAGATGTGGTCTTATATGGGATCTTGTTTTG
1 ATGCCATATCCCAGATATGGTCTTACAAGAAATCTCATATTG
* * *
20119514 ATGCCAATAGCCCAGCTATGGTCTTACAAGAAATCTCATGTTG
1 ATGCC-ATATCCCAGATATGGTCTTACAAGAAATCTCATATTG
* *
20119557 ATGCCATATCCTAGATGTGGTCTTACACA-AAATCTCATATTG
1 ATGCCATATCCCAGATATGGTCTTACA-AGAAATCTCATATTG
* *
20119599 ATGTCATATCCTAGATATGGTCTTACA
1 ATGCCATATCCCAGATATGGTCTTACA
20119626 CATAGTCTCG
Statistics
Matches: 93, Mismatches: 17, Indels: 4
0.82 0.15 0.04
Matches are distributed among these distances:
42 60 0.65
43 33 0.35
ACGTcount: A:0.27, C:0.20, G:0.18, T:0.34
Consensus pattern (42 bp):
ATGCCATATCCCAGATATGGTCTTACAAGAAATCTCATATTG
Found at i:20119626 original size:42 final size:43
Alignment explanation
Indices: 20119511--20119627 Score: 157
Period size: 42 Copynumber: 2.7 Consensus size: 43
20119501 GGATCTTGTT
* * * *
20119511 TTGATGCCAATAGCCCAGCTATGGTCTTACA-AGAAATCTCATG
1 TTGATGCC-ATATCCTAGATATGGTCTTACACAGAAATCTCATA
*
20119554 TTGATGCCATATCCTAGATGTGGTCTTACACA-AAATCTCATA
1 TTGATGCCATATCCTAGATATGGTCTTACACAGAAATCTCATA
*
20119596 TTGATGTCATATCCTAGATATGGTCTTACACA
1 TTGATGCCATATCCTAGATATGGTCTTACACA
20119628 TAGTCTCGGT
Statistics
Matches: 66, Mismatches: 7, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
42 57 0.86
43 9 0.14
ACGTcount: A:0.30, C:0.21, G:0.16, T:0.32
Consensus pattern (43 bp):
TTGATGCCATATCCTAGATATGGTCTTACACAGAAATCTCATA
Found at i:20121499 original size:40 final size:40
Alignment explanation
Indices: 20121430--20121673 Score: 292
Period size: 40 Copynumber: 6.1 Consensus size: 40
20121420 TGAATGATAC
* * * * **
20121430 CCGGGCTAAGTCCCGAAGACATTTATGCTAGTAATTATAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCAAGTTGTTATAT
* * * * *
20121470 CTGGGTTAAGACCCGAAGGCAATTGTGCTAG-TGACTATAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCAAGTTG-TTATAT
*
20121510 CCGGGCTAATACCCGAAGGCATTTGTGCAAGTTGTTATAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCAAGTTGTTATAT
*
20121550 CCGGGCTAATACCCGAAGGCATTTGTGCAAGTTGTTATAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCAAGTTGTTATAT
* *
20121590 CCGGGCTAATACCCGAAGGCATTTGTGCAAGTCGTTATAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCAAGTTGTTATAT
* * ** *
20121630 CCGGGCTAAGACCCGAGGGCATTCGTGCGTGTGGTTATAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCAAGTTGTTATAT
20121670 CCGG
1 CCGG
20121674 TTGTATTCCG
Statistics
Matches: 180, Mismatches: 22, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
40 178 0.99
41 2 0.01
ACGTcount: A:0.25, C:0.21, G:0.27, T:0.28
Consensus pattern (40 bp):
CCGGGCTAAGACCCGAAGGCATTTGTGCAAGTTGTTATAT
Found at i:20122219 original size:64 final size:64
Alignment explanation
Indices: 20122118--20122246 Score: 258
Period size: 64 Copynumber: 2.0 Consensus size: 64
20122108 TTAGTTGAAT
20122118 TTTGGATATGGCATGTATAGGACTACCCTTGGTTGTTTTCAAGTATCTTTGTGATGTATATGTG
1 TTTGGATATGGCATGTATAGGACTACCCTTGGTTGTTTTCAAGTATCTTTGTGATGTATATGTG
20122182 TTTGGATATGGCATGTATAGGACTACCCTTGGTTGTTTTCAAGTATCTTTGTGATGTATATGTG
1 TTTGGATATGGCATGTATAGGACTACCCTTGGTTGTTTTCAAGTATCTTTGTGATGTATATGTG
20122246 T
1 T
20122247 ACGGCCATGC
Statistics
Matches: 65, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
64 65 1.00
ACGTcount: A:0.20, C:0.11, G:0.25, T:0.44
Consensus pattern (64 bp):
TTTGGATATGGCATGTATAGGACTACCCTTGGTTGTTTTCAAGTATCTTTGTGATGTATATGTG
Found at i:20126292 original size:15 final size:15
Alignment explanation
Indices: 20126272--20126304 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
20126262 TTTACTAAAT
20126272 TTAGCAAACAACTGC
1 TTAGCAAACAACTGC
20126287 TTAGCAAACAACTGC
1 TTAGCAAACAACTGC
20126302 TTA
1 TTA
20126305 TCTCTTAAAG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.39, C:0.24, G:0.12, T:0.24
Consensus pattern (15 bp):
TTAGCAAACAACTGC
Found at i:20129512 original size:42 final size:42
Alignment explanation
Indices: 20129462--20129542 Score: 153
Period size: 42 Copynumber: 1.9 Consensus size: 42
20129452 AGCCCAGCTA
20129462 TGGTCTTACAAGAAATCTCATATCGATGCCATATCCTAGATG
1 TGGTCTTACAAGAAATCTCATATCGATGCCATATCCTAGATG
*
20129504 TGGTCTTACACGAAATCTCATATCGATGCCATATCCTAG
1 TGGTCTTACAAGAAATCTCATATCGATGCCATATCCTAG
20129543 TCTCGGTAAC
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
42 38 1.00
ACGTcount: A:0.30, C:0.23, G:0.16, T:0.31
Consensus pattern (42 bp):
TGGTCTTACAAGAAATCTCATATCGATGCCATATCCTAGATG
Found at i:20135134 original size:37 final size:37
Alignment explanation
Indices: 20135084--20135157 Score: 139
Period size: 37 Copynumber: 2.0 Consensus size: 37
20135074 ACTGCTGCCA
*
20135084 AGGTTTTCCAATCTGGCTTTTATTGGCAGAGTCTGTT
1 AGGTTTTCCAATCTAGCTTTTATTGGCAGAGTCTGTT
20135121 AGGTTTTCCAATCTAGCTTTTATTGGCAGAGTCTGTT
1 AGGTTTTCCAATCTAGCTTTTATTGGCAGAGTCTGTT
20135158 CAAAGATGCT
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 36 1.00
ACGTcount: A:0.18, C:0.16, G:0.23, T:0.43
Consensus pattern (37 bp):
AGGTTTTCCAATCTAGCTTTTATTGGCAGAGTCTGTT
Found at i:20142546 original size:22 final size:22
Alignment explanation
Indices: 20142515--20142625 Score: 105
Period size: 22 Copynumber: 5.0 Consensus size: 22
20142505 ACTCTGCATA
*
20142515 ACATGCGAGCCTATATGTTAGT
1 ACATGTGAGCCTATATGTTAGT
* * * *
20142537 CCATGTGAGCTTGTACGTTAGT
1 ACATGTGAGCCTATATGTTAGT
* ** *
20142559 ATATGCAAGCCTATACGTTAGT
1 ACATGTGAGCCTATATGTTAGT
* * *
20142581 TCATGTAAACCTATATGTTAGT
1 ACATGTGAGCCTATATGTTAGT
*
20142603 ACATGTGAGCTTATATGTTAGT
1 ACATGTGAGCCTATATGTTAGT
20142625 A
1 A
20142626 TGTGCAAACC
Statistics
Matches: 69, Mismatches: 20, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
22 69 1.00
ACGTcount: A:0.28, C:0.15, G:0.21, T:0.36
Consensus pattern (22 bp):
ACATGTGAGCCTATATGTTAGT
Found at i:20142623 original size:44 final size:44
Alignment explanation
Indices: 20142515--20142624 Score: 121
Period size: 44 Copynumber: 2.5 Consensus size: 44
20142505 ACTCTGCATA
* * * *
20142515 ACATGCGAGCCTATATGTTAGTCCATGTGAGCTTGTACGTTAGT
1 ACATGCGAGCCTATATGTTAGTCCATGTAAACCTATACGTTAGT
* * * * *
20142559 ATATGCAAGCCTATACGTTAGTTCATGTAAACCTATATGTTAGT
1 ACATGCGAGCCTATATGTTAGTCCATGTAAACCTATACGTTAGT
* *
20142603 ACATGTGAGCTTATATGTTAGT
1 ACATGCGAGCCTATATGTTAGT
20142625 ATGTGCAAAC
Statistics
Matches: 52, Mismatches: 14, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
44 52 1.00
ACGTcount: A:0.27, C:0.15, G:0.21, T:0.36
Consensus pattern (44 bp):
ACATGCGAGCCTATATGTTAGTCCATGTAAACCTATACGTTAGT
Found at i:20145905 original size:40 final size:40
Alignment explanation
Indices: 20145820--20145970 Score: 134
Period size: 40 Copynumber: 3.8 Consensus size: 40
20145810 AATTGAATGA
* * *
20145820 TATCCGGGCTAA-ATCCCGAAGACAATTATGCTG-GAAATTA-
1 TATCCGGGCTAAGA-CCCGAAGGCAATTGTGC-GAGACA-TAC
* * *
20145860 TATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGGC-TAC
1 TATCCGGGCTAAGACCCGAAGGCAATTGTGC--GAGACATAC
*
20145901 -ATCCGGGCTAAGACCCGAAGGC-ATTCGTGCGAGACATTC
1 TATCCGGGCTAAGACCCGAAGGCAATT-GTGCGAGACATAC
*
20145940 TATCCGGGCTAAGACCCGAAGGCATTTGTGC
1 TATCCGGGCTAAGACCCGAAGGCAATTGTGC
20145971 ACATGGTTAT
Statistics
Matches: 92, Mismatches: 11, Indels: 16
0.77 0.09 0.13
Matches are distributed among these distances:
38 3 0.03
39 5 0.05
40 79 0.86
41 4 0.04
42 1 0.01
ACGTcount: A:0.27, C:0.24, G:0.26, T:0.23
Consensus pattern (40 bp):
TATCCGGGCTAAGACCCGAAGGCAATTGTGCGAGACATAC
Found at i:20145984 original size:40 final size:40
Alignment explanation
Indices: 20145857--20145986 Score: 138
Period size: 40 Copynumber: 3.2 Consensus size: 40
20145847 ATGCTGGAAA
* * * *
20145857 TTATATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGG
1 TTATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAATGG
* * * **
20145897 CTACATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGA-CA
1 TTATATCCGGGCTAAGACCCGAAGGCATTTGTGCGA-ATGG
*
20145937 TTCTATCCGGGCTAAGACCCGAAGGCATTTGTGC-ACATGG
1 TTATATCCGGGCTAAGACCCGAAGGCATTTGTGCGA-ATGG
20145977 TTATATCCGG
1 TTATATCCGG
20145987 TTATGTTCCG
Statistics
Matches: 71, Mismatches: 17, Indels: 4
0.77 0.18 0.04
Matches are distributed among these distances:
39 2 0.03
40 69 0.97
ACGTcount: A:0.25, C:0.24, G:0.28, T:0.24
Consensus pattern (40 bp):
TTATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAATGG
Found at i:20153917 original size:40 final size:40
Alignment explanation
Indices: 20153832--20153982 Score: 134
Period size: 40 Copynumber: 3.8 Consensus size: 40
20153822 AATTGAATGA
* * *
20153832 TATCCGGGCTAA-ATCCCGAAGACAATTATGCTG-GAAATTA-
1 TATCCGGGCTAAGA-CCCGAAGGCAATTGTGC-GAGACA-TAC
* * *
20153872 TATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGGC-TAC
1 TATCCGGGCTAAGACCCGAAGGCAATTGTGC--GAGACATAC
*
20153913 -ATCCGGGCTAAGACCCGAAGGC-ATTCGTGCGAGACATTC
1 TATCCGGGCTAAGACCCGAAGGCAATT-GTGCGAGACATAC
*
20153952 TATCCGGGCTAAGACCCGAAGGCATTTGTGC
1 TATCCGGGCTAAGACCCGAAGGCAATTGTGC
20153983 ACATGGTTAT
Statistics
Matches: 92, Mismatches: 11, Indels: 16
0.77 0.09 0.13
Matches are distributed among these distances:
38 3 0.03
39 5 0.05
40 79 0.86
41 4 0.04
42 1 0.01
ACGTcount: A:0.27, C:0.24, G:0.26, T:0.23
Consensus pattern (40 bp):
TATCCGGGCTAAGACCCGAAGGCAATTGTGCGAGACATAC
Found at i:20153996 original size:40 final size:40
Alignment explanation
Indices: 20153869--20153998 Score: 138
Period size: 40 Copynumber: 3.2 Consensus size: 40
20153859 ATGCTGGAAA
* * * *
20153869 TTATATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGG
1 TTATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAATGG
* * * **
20153909 CTACATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGA-CA
1 TTATATCCGGGCTAAGACCCGAAGGCATTTGTGCGA-ATGG
*
20153949 TTCTATCCGGGCTAAGACCCGAAGGCATTTGTGC-ACATGG
1 TTATATCCGGGCTAAGACCCGAAGGCATTTGTGCGA-ATGG
20153989 TTATATCCGG
1 TTATATCCGG
20153999 TTATATTCCG
Statistics
Matches: 71, Mismatches: 17, Indels: 4
0.77 0.18 0.04
Matches are distributed among these distances:
39 2 0.03
40 69 0.97
ACGTcount: A:0.25, C:0.24, G:0.28, T:0.24
Consensus pattern (40 bp):
TTATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAATGG
Found at i:20158032 original size:24 final size:26
Alignment explanation
Indices: 20157972--20158035 Score: 71
Period size: 24 Copynumber: 2.5 Consensus size: 26
20157962 AAAATATACT
*
20157972 TATAATAAAAAATATGATATTTAATA
1 TATAATATAAAATATGATATTTAATA
* *
20157998 -AGAATTTTAAAATA-G-TATTTAATA
1 TATAA-TATAAAATATGATATTTAATA
20158022 TATAATATAAAATA
1 TATAATATAAAATA
20158036 AGAAAAAAAA
Statistics
Matches: 31, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
24 17 0.55
25 7 0.23
26 7 0.23
ACGTcount: A:0.56, C:0.00, G:0.05, T:0.39
Consensus pattern (26 bp):
TATAATATAAAATATGATATTTAATA
Found at i:20158418 original size:7 final size:7
Alignment explanation
Indices: 20158406--20158460 Score: 55
Period size: 7 Copynumber: 8.1 Consensus size: 7
20158396 ATATGTAAGA
20158406 ATAATAT
1 ATAATAT
20158413 ATAATAT
1 ATAATAT
20158420 AT-ATA-
1 ATAATAT
20158425 AGTAATAT
1 A-TAATAT
20158433 ATAA-A-
1 ATAATAT
20158438 ATAATTAT
1 ATAA-TAT
*
20158446 ATGATAT
1 ATAATAT
20158453 ATAATAT
1 ATAATAT
20158460 A
1 A
20158461 AAAATAAGAT
Statistics
Matches: 40, Mismatches: 2, Indels: 12
0.74 0.04 0.22
Matches are distributed among these distances:
5 5 0.12
6 5 0.12
7 26 0.65
8 4 0.10
ACGTcount: A:0.56, C:0.00, G:0.04, T:0.40
Consensus pattern (7 bp):
ATAATAT
Found at i:20158432 original size:11 final size:10
Alignment explanation
Indices: 20158405--20158458 Score: 51
Period size: 9 Copynumber: 5.4 Consensus size: 10
20158395 TATATGTAAG
20158405 AATAATATAT
1 AATAATATAT
20158415 AAT-ATATAT
1 AATAATATAT
20158424 AAGTAATATAT
1 AA-TAATATAT
20158435 AA-AATA-ATT
1 AATAATATA-T
*
20158444 ATATGATATAT
1 A-ATAATATAT
20158455 AATA
1 AATA
20158459 TAAAAATAAG
Statistics
Matches: 36, Mismatches: 2, Indels: 12
0.72 0.04 0.24
Matches are distributed among these distances:
8 1 0.03
9 14 0.39
10 7 0.19
11 13 0.36
12 1 0.03
ACGTcount: A:0.57, C:0.00, G:0.04, T:0.39
Consensus pattern (10 bp):
AATAATATAT
Found at i:20158440 original size:22 final size:22
Alignment explanation
Indices: 20158380--20158463 Score: 62
Period size: 22 Copynumber: 3.5 Consensus size: 22
20158370 AATATGACAT
*
20158380 AATAATATGAAAGTATATATGTAAG
1 AATAATAT-AAA--ATATATATAAG
*
20158405 AATAATATATAATATATATAAG
1 AATAATATAAAATATATATAAG
* *
20158427 TAAT-ATATAAAATAATTATATGAT
1 -AATAATATAAAAT-A-TATATAAG
20158451 ATATAATATAAAA
1 A-ATAATATAAAA
20158464 ATAAGATTAA
Statistics
Matches: 49, Mismatches: 5, Indels: 10
0.77 0.08 0.16
Matches are distributed among these distances:
22 18 0.37
23 5 0.10
24 10 0.20
25 16 0.33
ACGTcount: A:0.57, C:0.00, G:0.07, T:0.36
Consensus pattern (22 bp):
AATAATATAAAATATATATAAG
Found at i:20162121 original size:46 final size:46
Alignment explanation
Indices: 20162068--20162194 Score: 200
Period size: 46 Copynumber: 2.8 Consensus size: 46
20162058 GTTGAGCATT
* *
20162068 CGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATACGAATGTC
1 CGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATACGAACGCC
*
20162114 CGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCC
1 CGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATACGAACGCC
* * *
20162160 CGAGCTTGTTGAGTTGAGTCCGAGTTCGCTTATGG
1 CGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
20162195 GCGGGTTAGA
Statistics
Matches: 75, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
46 75 1.00
ACGTcount: A:0.20, C:0.20, G:0.29, T:0.30
Consensus pattern (46 bp):
CGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATACGAACGCC
Found at i:20169601 original size:46 final size:46
Alignment explanation
Indices: 20169551--20169679 Score: 222
Period size: 46 Copynumber: 2.8 Consensus size: 46
20169541 TGGTTGAGCA
*
20169551 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
20169597 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
* * *
20169643 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCGCTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
20169680 CGGGTTACAT
Statistics
Matches: 79, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
46 79 1.00
ACGTcount: A:0.19, C:0.22, G:0.29, T:0.29
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
Found at i:20172962 original size:29 final size:29
Alignment explanation
Indices: 20172934--20173035 Score: 150
Period size: 29 Copynumber: 3.5 Consensus size: 29
20172924 CCTCCGAGCT
** * * *
20172934 CGCACACCCAGTGCCGTATTTTTCCAGCT
1 CGCACACTTAGTGCCATATATTTCCAGCA
*
20172963 TGCACACTTAGTGCCATATATTTCCAGCA
1 CGCACACTTAGTGCCATATATTTCCAGCA
20172992 CGCACACTTAGTGCCATATATTTCCAGCA
1 CGCACACTTAGTGCCATATATTTCCAGCA
20173021 CGCACACTTAGTGCC
1 CGCACACTTAGTGCC
20173036 GATCTCGTCA
Statistics
Matches: 66, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 66 1.00
ACGTcount: A:0.24, C:0.33, G:0.16, T:0.27
Consensus pattern (29 bp):
CGCACACTTAGTGCCATATATTTCCAGCA
Found at i:20180812 original size:29 final size:29
Alignment explanation
Indices: 20180784--20180885 Score: 150
Period size: 29 Copynumber: 3.5 Consensus size: 29
20180774 CCTCCGAGCT
** * * *
20180784 CGCACACCCAGTGCCGTATTTTTCCAGCT
1 CGCACACTTAGTGCCATATATTTCCAGCA
*
20180813 TGCACACTTAGTGCCATATATTTCCAGCA
1 CGCACACTTAGTGCCATATATTTCCAGCA
20180842 CGCACACTTAGTGCCATATATTTCCAGCA
1 CGCACACTTAGTGCCATATATTTCCAGCA
20180871 CGCACACTTAGTGCC
1 CGCACACTTAGTGCC
20180886 GATCTCGTCA
Statistics
Matches: 66, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 66 1.00
ACGTcount: A:0.24, C:0.33, G:0.16, T:0.27
Consensus pattern (29 bp):
CGCACACTTAGTGCCATATATTTCCAGCA
Done.