Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D13
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: 60343961
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 596159 characters in sequence are not A, C, G, or T
File 42 of 204
Found at i:12245616 original size:15 final size:15
Alignment explanation
Indices: 12245595--12245634 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
12245585 AGTATGTGCG
12245595 AACCCCTAAGG-TAA
1 AACCCCTAAGGTTAA
*
12245609 ACACCCCTAAGGTTCA
1 A-ACCCCTAAGGTTAA
12245625 AACCCCTAAG
1 AACCCCTAAG
12245635 TTTGAGAAAC
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
14 1 0.04
15 19 0.83
16 3 0.13
ACGTcount: A:0.38, C:0.35, G:0.12, T:0.15
Consensus pattern (15 bp):
AACCCCTAAGGTTAA
Found at i:12251094 original size:22 final size:22
Alignment explanation
Indices: 12251068--12251123 Score: 58
Period size: 28 Copynumber: 2.3 Consensus size: 22
12251058 TCAGAAATAG
12251068 TACAGTGTGGGCCTTAGCCCAA
1 TACAGTGTGGGCCTTAGCCCAA
12251090 TACAGTAACAATGTGGGCCTTAGCCCAA
1 TACAG------TGTGGGCCTTAGCCCAA
12251118 TACAGT
1 TACAGT
12251124 ATCGATACAG
Statistics
Matches: 28, Mismatches: 0, Indels: 12
0.70 0.00 0.30
Matches are distributed among these distances:
22 6 0.21
28 22 0.79
ACGTcount: A:0.29, C:0.25, G:0.23, T:0.23
Consensus pattern (22 bp):
TACAGTGTGGGCCTTAGCCCAA
Found at i:12251261 original size:26 final size:26
Alignment explanation
Indices: 12251232--12251286 Score: 83
Period size: 26 Copynumber: 2.1 Consensus size: 26
12251222 AAGACACCAA
*
12251232 TATCGCAGCAAAGCTACCAATAATAG
1 TATCGCAGCAAAGCTACCAATAACAG
* *
12251258 TATCGCAGCAAAGCTGCCAGTAACAG
1 TATCGCAGCAAAGCTACCAATAACAG
12251284 TAT
1 TAT
12251287 ACTTCCTCCA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.38, C:0.24, G:0.18, T:0.20
Consensus pattern (26 bp):
TATCGCAGCAAAGCTACCAATAACAG
Found at i:12254080 original size:10 final size:10
Alignment explanation
Indices: 12254065--12254089 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
12254055 ATGCCATCAC
12254065 ACATATATAT
1 ACATATATAT
12254075 ACATATATAT
1 ACATATATAT
12254085 ACATA
1 ACATA
12254090 AGATTTCTCA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.52, C:0.12, G:0.00, T:0.36
Consensus pattern (10 bp):
ACATATATAT
Found at i:12256474 original size:20 final size:20
Alignment explanation
Indices: 12256432--12256472 Score: 57
Period size: 19 Copynumber: 2.1 Consensus size: 20
12256422 TGTTTAGTTA
12256432 TTATTTTAAATATTTATTAT
1 TTATTTTAAATATTTATTAT
* *
12256452 TTATTTTTAA-ATTTCTTAT
1 TTATTTTAAATATTTATTAT
12256471 TT
1 TT
12256473 TAGTTATTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 10 0.53
20 9 0.47
ACGTcount: A:0.29, C:0.02, G:0.00, T:0.68
Consensus pattern (20 bp):
TTATTTTAAATATTTATTAT
Found at i:12257039 original size:18 final size:18
Alignment explanation
Indices: 12257016--12257053 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
12257006 TGGAACTTAC
12257016 TTCCTTTGGAGTCGAGTT
1 TTCCTTTGGAGTCGAGTT
12257034 TTCCTTTGGAGTCGAGTT
1 TTCCTTTGGAGTCGAGTT
12257052 TT
1 TT
12257054 GTTAAAGAGT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.11, C:0.16, G:0.26, T:0.47
Consensus pattern (18 bp):
TTCCTTTGGAGTCGAGTT
Found at i:12266225 original size:7 final size:7
Alignment explanation
Indices: 12266213--12266290 Score: 156
Period size: 7 Copynumber: 11.1 Consensus size: 7
12266203 ATTATTCTAA
12266213 TCTCTTT
1 TCTCTTT
12266220 TCTCTTT
1 TCTCTTT
12266227 TCTCTTT
1 TCTCTTT
12266234 TCTCTTT
1 TCTCTTT
12266241 TCTCTTT
1 TCTCTTT
12266248 TCTCTTT
1 TCTCTTT
12266255 TCTCTTT
1 TCTCTTT
12266262 TCTCTTT
1 TCTCTTT
12266269 TCTCTTT
1 TCTCTTT
12266276 TCTCTTT
1 TCTCTTT
12266283 TCTCTTT
1 TCTCTTT
12266290 T
1 T
12266291 GACTCAATCA
Statistics
Matches: 71, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 71 1.00
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (7 bp):
TCTCTTT
Found at i:12266732 original size:16 final size:15
Alignment explanation
Indices: 12266708--12266741 Score: 50
Period size: 16 Copynumber: 2.2 Consensus size: 15
12266698 GGTTTAATTG
12266708 ATTTCATTGTTTGTTT
1 ATTTCATTGTTT-TTT
*
12266724 ATTTTATTGTTTTTT
1 ATTTCATTGTTTTTT
12266739 ATT
1 ATT
12266742 ATTTATTTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 6 0.35
16 11 0.65
ACGTcount: A:0.15, C:0.03, G:0.09, T:0.74
Consensus pattern (15 bp):
ATTTCATTGTTTTTT
Found at i:12270408 original size:40 final size:41
Alignment explanation
Indices: 12270364--12270479 Score: 157
Period size: 40 Copynumber: 2.9 Consensus size: 41
12270354 GTTTGGACAA
*
12270364 AAAACGCCGCTAAAAATTGAGCATTAGCGGCGCTTCTCA-T
1 AAAACGCCGCTAAAAATTGAGCATTAGCGGCGCTTCTCAGG
**
12270404 AAAACGCCGCTAAAAATCAAGCATTAGCGGCGCTT-TCAGG
1 AAAACGCCGCTAAAAATTGAGCATTAGCGGCGCTTCTCAGG
* * *
12270444 AAAGCGCCACTAAAAA-TGAGCATTAGCGGCGTTTCT
1 AAAACGCCGCTAAAAATTGAGCATTAGCGGCGCTTCT
12270480 TGGAAAAACG
Statistics
Matches: 66, Mismatches: 8, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
39 18 0.27
40 48 0.73
ACGTcount: A:0.34, C:0.24, G:0.22, T:0.21
Consensus pattern (41 bp):
AAAACGCCGCTAAAAATTGAGCATTAGCGGCGCTTCTCAGG
Found at i:12270499 original size:40 final size:39
Alignment explanation
Indices: 12270375--12270500 Score: 105
Period size: 40 Copynumber: 3.2 Consensus size: 39
12270365 AAACGCCGCT
* * *
12270375 AAAAATTGAGCATTAGCGGCGCTTCT-CATAAAACGCC-G
1 AAAAAATGAGCATTAGCGGCGTTTCTGGA-AAAACGCCAG
* * * * *
12270413 CTAAAAATCAAGCATTAGCGGCGCTTTCAGG-AAAGCGCCAC
1 -AAAAAAT-GAGCATTAGCGGCG-TTTCTGGAAAAACGCCAG
*
12270454 TAAAAATGAGCATTAGCGGCGTTTCTTGGAAAAACGCCAG
1 AAAAAATGAGCATTAGCGGCGTTTC-TGGAAAAACGCCAG
12270494 AAAAAAT
1 AAAAAAT
12270501 CTAAACCCAA
Statistics
Matches: 68, Mismatches: 13, Indels: 11
0.74 0.14 0.12
Matches are distributed among these distances:
38 4 0.06
39 20 0.29
40 41 0.60
41 3 0.04
ACGTcount: A:0.37, C:0.21, G:0.21, T:0.20
Consensus pattern (39 bp):
AAAAAATGAGCATTAGCGGCGTTTCTGGAAAAACGCCAG
Found at i:12270602 original size:41 final size:41
Alignment explanation
Indices: 12270536--12270647 Score: 143
Period size: 41 Copynumber: 2.7 Consensus size: 41
12270526 ACCTTCTAGG
* *
12270536 GCTTTAGCGGCGTTTTTAAAAAAGCGTCGCTAATGCTCAGA
1 GCTTTAGCGGCGTTTTCAAAAAAGCGCCGCTAATGCTCAGA
* * * * *
12270577 GCTTTAGCGGCATTTTCCAAGAAGCGCCGCTAATGCTCGGG
1 GCTTTAGCGGCGTTTTCAAAAAAGCGCCGCTAATGCTCAGA
* *
12270618 GCTTTAGCGGCGTTTTTAAAAAAGTGCCGC
1 GCTTTAGCGGCGTTTTCAAAAAAGCGCCGC
12270648 AAAAACATTT
Statistics
Matches: 59, Mismatches: 12, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
41 59 1.00
ACGTcount: A:0.23, C:0.22, G:0.27, T:0.28
Consensus pattern (41 bp):
GCTTTAGCGGCGTTTTCAAAAAAGCGCCGCTAATGCTCAGA
Found at i:12271082 original size:22 final size:21
Alignment explanation
Indices: 12271057--12271101 Score: 72
Period size: 22 Copynumber: 2.1 Consensus size: 21
12271047 ATTTTGAGGT
12271057 TTATAGATTATGGAATTAGGGA
1 TTATAGATTATGG-ATTAGGGA
*
12271079 TTATGGATTATGGATTAGGGA
1 TTATAGATTATGGATTAGGGA
12271100 TT
1 TT
12271102 CTGGTTTAAG
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 10 0.45
22 12 0.55
ACGTcount: A:0.31, C:0.00, G:0.29, T:0.40
Consensus pattern (21 bp):
TTATAGATTATGGATTAGGGA
Found at i:12271093 original size:14 final size:14
Alignment explanation
Indices: 12271057--12271101 Score: 54
Period size: 14 Copynumber: 3.1 Consensus size: 14
12271047 ATTTTGAGGT
*
12271057 TTATAGATTATGGAA
1 TTATGGATTATGG-A
*
12271072 TTAGGGATTATGGA
1 TTATGGATTATGGA
*
12271086 TTATGGATTAGGGA
1 TTATGGATTATGGA
12271100 TT
1 TT
12271102 CTGGTTTAAG
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
14 15 0.58
15 11 0.42
ACGTcount: A:0.31, C:0.00, G:0.29, T:0.40
Consensus pattern (14 bp):
TTATGGATTATGGA
Found at i:12271269 original size:47 final size:48
Alignment explanation
Indices: 12271194--12271300 Score: 135
Period size: 47 Copynumber: 2.2 Consensus size: 48
12271184 AAGTTAGGGC
* * *
12271194 TTAGGGTTTAGGTTAATTAGTATGTTTTAA-TCTATATTAAATAAGAT
1 TTAGGGGTTAGATTAATTAGTATGTTTTAATTATATATTAAATAAGAT
* * *
12271241 TTAGGGGTTAGATTAATTAGTGTTTTTTAATTTATATATTAAATAAGGT
1 TTAGGGGTTAGATTAATTAGTATGTTTTAA-TTATATATTAAATAAGAT
*
12271290 TTATGGGTTAG
1 TTAGGGGTTAG
12271301 TAGTTAAGGG
Statistics
Matches: 51, Mismatches: 7, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
47 26 0.51
49 25 0.49
ACGTcount: A:0.32, C:0.01, G:0.20, T:0.48
Consensus pattern (48 bp):
TTAGGGGTTAGATTAATTAGTATGTTTTAATTATATATTAAATAAGAT
Found at i:12271475 original size:13 final size:14
Alignment explanation
Indices: 12271457--12271494 Score: 51
Period size: 15 Copynumber: 2.7 Consensus size: 14
12271447 TAAAAGAGGG
12271457 GTTAGGG-TTAAGA
1 GTTAGGGATTAAGA
12271470 GTTAGGGATTTAAGA
1 GTTAGGGA-TTAAGA
*
12271485 TTTAGGGATT
1 GTTAGGGATT
12271495 TTAGGGTCGA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
13 7 0.32
14 2 0.09
15 13 0.59
ACGTcount: A:0.29, C:0.00, G:0.34, T:0.37
Consensus pattern (14 bp):
GTTAGGGATTAAGA
Found at i:12271484 original size:15 final size:15
Alignment explanation
Indices: 12271464--12271495 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
12271454 GGGGTTAGGG
12271464 TTAAGAGTTAGGGAT
1 TTAAGAGTTAGGGAT
*
12271479 TTAAGATTTAGGGAT
1 TTAAGAGTTAGGGAT
12271494 TT
1 TT
12271496 TAGGGTCGAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.31, C:0.00, G:0.28, T:0.41
Consensus pattern (15 bp):
TTAAGAGTTAGGGAT
Found at i:12272158 original size:11 final size:11
Alignment explanation
Indices: 12272142--12272166 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
12272132 AGTTCTTCGA
12272142 TCCTTTCCGTC
1 TCCTTTCCGTC
12272153 TCCTTTCCGTC
1 TCCTTTCCGTC
12272164 TCC
1 TCC
12272167 AAAGCTCTCC
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:0.00, C:0.48, G:0.08, T:0.44
Consensus pattern (11 bp):
TCCTTTCCGTC
Found at i:12275740 original size:43 final size:43
Alignment explanation
Indices: 12275673--12275877 Score: 270
Period size: 43 Copynumber: 4.8 Consensus size: 43
12275663 TTTGCAAAAA
* * * * *
12275673 CGTCGCGAAAGGTCATGGTTTTTAGCAGCGTTTGTTG-GAAAAG
1 CGTCGCTAAAGGTCTTGGTCTTTAGCGGCGTTTG-TGAGAGAAG
* *
12275716 TG-CTGCTAAAAGTCTTGGTCTTTAGCGGCGTTTGTGAGAGAAG
1 CGTC-GCTAAAGGTCTTGGTCTTTAGCGGCGTTTGTGAGAGAAG
*
12275759 CGTCGCTAAAGGTCTTGGTCTTTAGCGGCGTTTGTGGGAGAAG
1 CGTCGCTAAAGGTCTTGGTCTTTAGCGGCGTTTGTGAGAGAAG
* * *
12275802 CGCCGCTAAAGGTCTTGGACTTAAGCGGCGTTTGTGAGAGAAG
1 CGTCGCTAAAGGTCTTGGTCTTTAGCGGCGTTTGTGAGAGAAG
*
12275845 TGTCGCTAAAGGTCTTGGTCTTTAGCGGCGTTT
1 CGTCGCTAAAGGTCTTGGTCTTTAGCGGCGTTT
12275878 TTTTCTAAAA
Statistics
Matches: 141, Mismatches: 18, Indels: 6
0.85 0.11 0.04
Matches are distributed among these distances:
42 3 0.02
43 137 0.97
44 1 0.01
ACGTcount: A:0.20, C:0.16, G:0.34, T:0.31
Consensus pattern (43 bp):
CGTCGCTAAAGGTCTTGGTCTTTAGCGGCGTTTGTGAGAGAAG
Found at i:12275783 original size:86 final size:86
Alignment explanation
Indices: 12275673--12275877 Score: 302
Period size: 86 Copynumber: 2.4 Consensus size: 86
12275663 TTTGCAAAAA
* * * * * * * *
12275673 CGTCGCGAAAGGTCATGGTTTTTAGCAGCGTTTGTTGGAAAAGTGCTGCTAAAAGTCTTGGTCTT
1 CGTCGCTAAAGGTCTTGGTCTTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAAGTCTTGGACTT
*
12275738 TAGCGGCGTTTGTGAGAGAAG
66 AAGCGGCGTTTGTGAGAGAAG
* *
12275759 CGTCGCTAAAGGTCTTGGTCTTTAGCGGCGTTTGTGGGAGAAGCGCCGCTAAAGGTCTTGGACTT
1 CGTCGCTAAAGGTCTTGGTCTTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAAGTCTTGGACTT
12275824 AAGCGGCGTTTGTGAGAGAAG
66 AAGCGGCGTTTGTGAGAGAAG
*
12275845 TGTCGCTAAAGGTCTTGGTCTTTAGCGGCGTTT
1 CGTCGCTAAAGGTCTTGGTCTTTAGCGGCGTTT
12275878 TTTTCTAAAA
Statistics
Matches: 107, Mismatches: 12, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
86 107 1.00
ACGTcount: A:0.20, C:0.16, G:0.34, T:0.31
Consensus pattern (86 bp):
CGTCGCTAAAGGTCTTGGTCTTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAAGTCTTGGACTT
AAGCGGCGTTTGTGAGAGAAG
Found at i:12277007 original size:15 final size:15
Alignment explanation
Indices: 12276998--12277031 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
12276988 CAAATGCTAT
12276998 AATAATAAATACAAC
1 AATAATAAATACAAC
*
12277013 AATAATAAATACATC
1 AATAATAAATACAAC
12277028 AATA
1 AATA
12277032 GCATAAAAAT
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:0.65, C:0.12, G:0.00, T:0.24
Consensus pattern (15 bp):
AATAATAAATACAAC
Found at i:12277056 original size:13 final size:14
Alignment explanation
Indices: 12277038--12277074 Score: 51
Period size: 13 Copynumber: 2.7 Consensus size: 14
12277028 AATAGCATAA
12277038 AAATAATATAAAC-
1 AAATAATATAAACG
12277051 AAATAA-ATAAACG
1 AAATAATATAAACG
12277064 AAATGAATATA
1 AAAT-AATATA
12277075 TATGAAAGCA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
12 6 0.29
13 10 0.48
14 2 0.10
15 3 0.14
ACGTcount: A:0.68, C:0.05, G:0.05, T:0.22
Consensus pattern (14 bp):
AAATAATATAAACG
Found at i:12277658 original size:3 final size:3
Alignment explanation
Indices: 12277652--12277680 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
12277642 TTACAATACC
12277652 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
12277681 GGAGAAAATA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:12279729 original size:17 final size:16
Alignment explanation
Indices: 12279700--12279736 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 16
12279690 GTTTTAGGTG
*
12279700 ATATAAATTATATAAT
1 ATATAAATAATATAAT
12279716 ATATAAAATAATATAAT
1 ATAT-AAATAATATAAT
12279733 ATAT
1 ATAT
12279737 TATAAATTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 4 0.21
17 15 0.79
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (16 bp):
ATATAAATAATATAAT
Found at i:12281222 original size:20 final size:20
Alignment explanation
Indices: 12281182--12281222 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
12281172 CTTCTAATTG
*
12281182 TATTTATATATATTATTATA
1 TATTTATATATAATATTATA
12281202 TATTTATATA-AATATTGATA
1 TATTTATATATAATATT-ATA
12281222 T
1 T
12281223 GCTAATCTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 5 0.26
20 14 0.74
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.56
Consensus pattern (20 bp):
TATTTATATATAATATTATA
Found at i:12282160 original size:4 final size:4
Alignment explanation
Indices: 12282151--12282185 Score: 52
Period size: 4 Copynumber: 8.2 Consensus size: 4
12282141 TATTAATATG
12282151 ATAA ATAA ATCAA ATAA ATAA ATAA ATAAA ATAA A
1 ATAA ATAA AT-AA ATAA ATAA ATAA AT-AA ATAA A
12282186 AATGCTATGC
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
4 21 0.72
5 8 0.28
ACGTcount: A:0.74, C:0.03, G:0.00, T:0.23
Consensus pattern (4 bp):
ATAA
Found at i:12282169 original size:13 final size:12
Alignment explanation
Indices: 12282151--12282185 Score: 52
Period size: 13 Copynumber: 2.8 Consensus size: 12
12282141 TATTAATATG
12282151 ATAAATAAATCAA
1 ATAAATAAAT-AA
12282164 ATAAATAAATAA
1 ATAAATAAATAA
12282176 ATAAAATAAA
1 AT-AAATAAA
12282186 AATGCTATGC
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
12 4 0.19
13 17 0.81
ACGTcount: A:0.74, C:0.03, G:0.00, T:0.23
Consensus pattern (12 bp):
ATAAATAAATAA
Found at i:12282173 original size:17 final size:17
Alignment explanation
Indices: 12282151--12282185 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
12282141 TATTAATATG
*
12282151 ATAAATAAATCAAATAA
1 ATAAATAAATAAAATAA
12282168 ATAAATAAATAAAATAA
1 ATAAATAAATAAAATAA
12282185 A
1 A
12282186 AATGCTATGC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.74, C:0.03, G:0.00, T:0.23
Consensus pattern (17 bp):
ATAAATAAATAAAATAA
Found at i:12284268 original size:44 final size:44
Alignment explanation
Indices: 12284196--12284318 Score: 102
Period size: 44 Copynumber: 2.8 Consensus size: 44
12284186 ATTCCAACCC
* * * * * ***
12284196 ACTACAACTTCAGGGGTATAGGAATTGTAGCTTTAATTTGATCA
1 ACTACAAATTTAGGGATATAAGATTTGTAGCTTTAACCCGATCA
* * * *
12284240 ACTATAAATTTAGGGATATAAGATTTGTAACTTCAACCCGATCC
1 ACTACAAATTTAGGGATATAAGATTTGTAGCTTTAACCCGATCA
* * * *
12284284 ACTACCACTTTAGGGATATAGGATTCGTAGCTTTA
1 ACTACAAATTTAGGGATATAAGATTTGTAGCTTTA
12284319 TCTTCTTCCA
Statistics
Matches: 60, Mismatches: 19, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
44 60 1.00
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.33
Consensus pattern (44 bp):
ACTACAAATTTAGGGATATAAGATTTGTAGCTTTAACCCGATCA
Found at i:12284354 original size:44 final size:44
Alignment explanation
Indices: 12284305--12284448 Score: 112
Period size: 44 Copynumber: 3.1 Consensus size: 44
12284295 AGGGATATAG
*
12284305 GATTCGTAGCTTTATCTTCTTCCACTGCAACTTCAAGGAGATAA
1 GATTCGTAGCTTTATCTTCCTCCACTGCAACTTCAAGGAGATAA
* * * *
12284349 GATTCGCTATCATTGTTTCATTCCAATCAACTGCAACTTCAAGG-GTATAG
1 GATTCG-TAGC-TT-TATC-TTCC--TCCACTGCAACTTCAAGGAG-ATAA
* * * * *
12284399 GATTTGTAGCTTCATATTGCTCCACTGCAACTTC-AGAGAGATTA
1 GATTCGTAGCTTTATCTTCCTCCACTGCAACTTCAAG-GAGATAA
12284443 GATTCG
1 GATTCG
12284449 CCATTGTAAT
Statistics
Matches: 76, Mismatches: 15, Indels: 18
0.70 0.14 0.17
Matches are distributed among these distances:
43 2 0.03
44 27 0.36
45 4 0.05
46 5 0.07
47 4 0.05
48 5 0.07
49 4 0.05
50 25 0.33
ACGTcount: A:0.27, C:0.22, G:0.17, T:0.34
Consensus pattern (44 bp):
GATTCGTAGCTTTATCTTCCTCCACTGCAACTTCAAGGAGATAA
Found at i:12284425 original size:94 final size:94
Alignment explanation
Indices: 12284295--12284546 Score: 301
Period size: 94 Copynumber: 2.7 Consensus size: 94
12284285 CTACCACTTT
* *
12284295 AGGGATATAGGATTCGTAGCTTTATCTT-CTTCCACTGCAACTTCAAGGAGATAAGATTCGCTAT
1 AGGG-TATAGGATTTGTAGCTTCATCTTGC-TCCACTGCAACTTCAAGGAGATAAGATTCGCTAT
** *
12284359 CATTGTTTCATTCCAATCAACTGCAACTTCA
64 CATAATTTCATTCCAACCAACTGCAACTTCA
* * * *
12284390 AGGGTATAGGATTTGTAGCTTCATATTGCTCCACTGCAACTTC-AGAGAGATTAGATTCGCCATT
1 AGGGTATAGGATTTGTAGCTTCATCTTGCTCCACTGCAACTTCAAG-GAGATAAGATTCGCTATC
* * *
12284454 GTAATTTCATTCCAACCCACTGCAACTTTA
65 ATAATTTCATTCCAACCAACTGCAACTTCA
* * * * * *
12284484 AGAGTATAGCAATTGTAGCTTCATCTTGCTCCACTGTAACTTCAGGGAGATAAGATCCGCTAT
1 AGGGTATAGGATTTGTAGCTTCATCTTGCTCCACTGCAACTTCAAGGAGATAAGATTCGCTAT
12284547 GGCAGATTCA
Statistics
Matches: 133, Mismatches: 21, Indels: 7
0.83 0.13 0.04
Matches are distributed among these distances:
93 2 0.02
94 125 0.94
95 6 0.05
ACGTcount: A:0.28, C:0.22, G:0.17, T:0.33
Consensus pattern (94 bp):
AGGGTATAGGATTTGTAGCTTCATCTTGCTCCACTGCAACTTCAAGGAGATAAGATTCGCTATCA
TAATTTCATTCCAACCAACTGCAACTTCA
Found at i:12284576 original size:94 final size:93
Alignment explanation
Indices: 12284282--12284590 Score: 245
Period size: 94 Copynumber: 3.3 Consensus size: 93
12284272 TCAACCCGAT
* * * *
12284282 CCACTACCACTTT-AGGGATATAGGATTCGTAGCTTTATCTT-CTTCCACTGCAACTTCA-AGGA
1 CCACTACAACTTTAAGGG-TATAGAATT-GTAGCTTCATATTGC-TCCACTGCAACTTCAGA-GA
* * * * *
12284344 GATAAGATTCGCTAT--CATTGTTTCATTCCAAT
62 GATAAGATCCGCCATGGCA--ATTTCAATCCAAC
* * * *
12284376 CAACTGCAACTTCAAGGGTATAGGATTTGTAGCTTCATATTGCTCCACTGCAACTTCAGAGAGAT
1 CCACTACAACTTTAAGGGTATA-GAATTGTAGCTTCATATTGCTCCACTGCAACTTCAGAGAGAT
* * * * *
12284441 TAGATTCGCCATTGTAATTTCATTCCAAC
65 AAGATCCGCCATGGCAATTTCAATCCAAC
* * * * *
12284470 CCACTGCAACTTTAAGAGTATAGCAATTGTAGCTTCATCTTGCTCCACTGTAACTTCAGGGAGAT
1 CCACTACAACTTTAAGGGTATAG-AATTGTAGCTTCATATTGCTCCACTGCAACTTCAGAGAGAT
* *
12284535 AAGATCCGCTATGGCAGA-TTCAATCCGAC
65 AAGATCCGCCATGGCA-ATTTCAATCCAAC
*
12284564 CCACTA-ACACTTTAGGGGTATAGAATT
1 CCACTACA-ACTTTAAGGGTATAGAATT
12284591 TGTGGTTTCA
Statistics
Matches: 176, Mismatches: 30, Indels: 19
0.78 0.13 0.08
Matches are distributed among these distances:
93 6 0.03
94 159 0.90
95 10 0.06
96 1 0.01
ACGTcount: A:0.28, C:0.23, G:0.17, T:0.31
Consensus pattern (93 bp):
CCACTACAACTTTAAGGGTATAGAATTGTAGCTTCATATTGCTCCACTGCAACTTCAGAGAGATA
AGATCCGCCATGGCAATTTCAATCCAAC
Found at i:12291092 original size:28 final size:28
Alignment explanation
Indices: 12291059--12291157 Score: 110
Period size: 28 Copynumber: 3.5 Consensus size: 28
12291049 TAATGAGATT
*
12291059 AGCACTAAGTGTGCGAGTTTAATCG-AA
1 AGCACTAAGTGTGCGAGTTTAAGCGTAA
* *
12291086 ATGCACTAAGTGTGCGAGTATAAGGGTAA
1 A-GCACTAAGTGTGCGAGTTTAAGCGTAA
* *** *
12291115 AGCACTAAGTGTGCGAGTTTGATTATTA
1 AGCACTAAGTGTGCGAGTTTAAGCGTAA
12291143 AGCACTAAGTGTGCG
1 AGCACTAAGTGTGCG
12291158 TACTTGTTAA
Statistics
Matches: 61, Mismatches: 9, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
27 1 0.02
28 57 0.93
29 3 0.05
ACGTcount: A:0.31, C:0.13, G:0.28, T:0.27
Consensus pattern (28 bp):
AGCACTAAGTGTGCGAGTTTAAGCGTAA
Found at i:12292163 original size:47 final size:47
Alignment explanation
Indices: 12292094--12292349 Score: 397
Period size: 47 Copynumber: 5.4 Consensus size: 47
12292084 GTGTTATAAA
*
12292094 TTTAACGTATAATGCTGTCCAATTTTGAGTATATTGATGTTGTCCAT
1 TTTAATGTATAATGCTGTCCAATTTTGAGTATATTGATGTTGTCCAT
*
12292141 TTTAATGTATAATGCTGTCCAATTTTAAGTATATTGATGTTGTCCAT
1 TTTAATGTATAATGCTGTCCAATTTTGAGTATATTGATGTTGTCCAT
*
12292188 TTTAATGTATAATGCTGTCCAATTTTAAGTATATTGATGTTGTCCAT
1 TTTAATGTATAATGCTGTCCAATTTTGAGTATATTGATGTTGTCCAT
*
12292235 TTTAATGTATAATGCTGTCCAATTTTGAGTATATTGATGCTGTCCAT
1 TTTAATGTATAATGCTGTCCAATTTTGAGTATATTGATGTTGTCCAT
* * * * * *
12292282 TTTAATATATAATGTTGTCCAATTTTGAGTATATTTAAT-CTGTCTAA
1 TTTAATGTATAATGCTGTCCAATTTTGAGTATA-TTGATGTTGTCCAT
*
12292329 TTTGATGTATAATGCTGTCCA
1 TTTAATGTATAATGCTGTCCA
12292350 TTTAGAGCAT
Statistics
Matches: 196, Mismatches: 12, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
47 192 0.98
48 4 0.02
ACGTcount: A:0.27, C:0.11, G:0.15, T:0.46
Consensus pattern (47 bp):
TTTAATGTATAATGCTGTCCAATTTTGAGTATATTGATGTTGTCCAT
Found at i:12292392 original size:141 final size:141
Alignment explanation
Indices: 12292092--12292397 Score: 386
Period size: 141 Copynumber: 2.2 Consensus size: 141
12292082 TTGTGTTATA
* * * *
12292092 AATTTAACGTATAATGCTGTCCAATTTTGAGTATATTGATGTTGTCCATTTTAATGTATAATGCT
1 AATTTAATGAATAATGCTGTCCAATTTTGAGTATATTGATGCTGTCCATTTTAATATATAATGCT
* * * * *
12292157 GTCCAATTTTAAGTATATTGATGTTGTCCATTTTAATGTATAATGCTGTCCAATTTTAAGTATAT
66 GTCCAATTTTAAGTATATTAATGCTGTCCAATTTAATGTATAATGCTGTCCAATTTTAAGCATAG
*
12292222 TGATGTTGTCC
131 TGATGCTGTCC
* * *
12292233 ATTTTAATGTATAATGCTGTCCAATTTTGAGTATATTGATGCTGTCCATTTTAATATATAATGTT
1 AATTTAATGAATAATGCTGTCCAATTTTGAGTATATTGATGCTGTCCATTTTAATATATAATGCT
* * *
12292298 GTCCAATTTTGAGTATATTTAAT-CTGTCTAATTTGATGTATAATGCTGTCC-A-TTTAGAGCAT
66 GTCCAATTTTAAGTATA-TTAATGCTGTCCAATTTAATGTATAATGCTGTCCAATTTTA-AGCAT
*
12292360 AGT-ATTGCTGTTC
129 AGTGA-TGCTGTCC
*
12292373 AATTTGATGAATAATTGCTGTCCAA
1 AATTTAATGAATAA-TGCTGTCCAA
12292398 AATAGGGTTG
Statistics
Matches: 143, Mismatches: 18, Indels: 8
0.85 0.11 0.05
Matches are distributed among these distances:
139 5 0.03
140 24 0.17
141 110 0.77
142 4 0.03
ACGTcount: A:0.28, C:0.11, G:0.16, T:0.45
Consensus pattern (141 bp):
AATTTAATGAATAATGCTGTCCAATTTTGAGTATATTGATGCTGTCCATTTTAATATATAATGCT
GTCCAATTTTAAGTATATTAATGCTGTCCAATTTAATGTATAATGCTGTCCAATTTTAAGCATAG
TGATGCTGTCC
Found at i:12292395 original size:94 final size:94
Alignment explanation
Indices: 12292102--12292397 Score: 377
Period size: 94 Copynumber: 3.1 Consensus size: 94
12292092 AATTTAACGT
12292102 ATAATGCTGTCCAATTTTGAGTATATTGATGTTGTCCATTTTAATGTATAATGCTGTCCAATTTT
1 ATAATGCTGTCCAATTTTGAGTATATTGATGTTGTCCATTTTAATGTATAATGCTGTCCAA-TTT
* *
12292167 A-AGTATATTGATGTTGTCCATTTTAATGT
65 AGAGTATATTGATGCTGTCCATTTTAATGA
* *
12292196 ATAATGCTGTCCAATTTTAAGTATATTGATGTTGTCCATTTTAATGTATAATGCTGTCCAATTTT
1 ATAATGCTGTCCAATTTTGAGTATATTGATGTTGTCCATTTTAATGTATAATGCTGTCCAATTTA
12292261 GAGTATATTGATGCTGTCCATTTTAAT-A
66 GAGTATATTGATGCTGTCCATTTTAATGA
* * * * * *
12292289 TATAATGTTGTCCAATTTTGAGTATATTTAAT-CTGTCTAATTTGATGTATAATGCTGTCC-ATT
1 -ATAATGCTGTCCAATTTTGAGTATA-TTGATGTTGTCCATTTTAATGTATAATGCTGTCCAATT
* * * * *
12292352 TAGAGCATAGT-ATTGCTGTTCAATTTGATGA
64 TAGAGTATATTGA-TGCTGTCCATTTTAATGA
12292383 ATAATTGCTGTCCAA
1 ATAA-TGCTGTCCAA
12292398 AATAGGGTTG
Statistics
Matches: 178, Mismatches: 18, Indels: 12
0.86 0.09 0.06
Matches are distributed among these distances:
92 1 0.01
93 31 0.17
94 142 0.80
95 4 0.02
ACGTcount: A:0.28, C:0.11, G:0.16, T:0.45
Consensus pattern (94 bp):
ATAATGCTGTCCAATTTTGAGTATATTGATGTTGTCCATTTTAATGTATAATGCTGTCCAATTTA
GAGTATATTGATGCTGTCCATTTTAATGA
Found at i:12298794 original size:28 final size:27
Alignment explanation
Indices: 12298761--12298857 Score: 115
Period size: 28 Copynumber: 3.5 Consensus size: 27
12298751 TAATGAGATT
12298761 AGCACTAAGTGTGCGAGTTTAATTGAA
1 AGCACTAAGTGTGCGAGTTTAATTGAA
* **
12298788 ATGCACTAAGTGTGCGAGTATAAGGGTAA
1 A-GCACTAAGTGTGCGAGTTTAATTG-AA
*
12298817 AGCACTAAGTGTGCGAGTTTGATT-ATTA
1 AGCACTAAGTGTGCGAGTTTAATTGA--A
12298845 AGCACTAAGTGTG
1 AGCACTAAGTGTG
12298858 TGTACTTGTT
Statistics
Matches: 59, Mismatches: 7, Indels: 7
0.81 0.10 0.10
Matches are distributed among these distances:
26 1 0.02
27 1 0.02
28 54 0.92
29 3 0.05
ACGTcount: A:0.32, C:0.11, G:0.28, T:0.29
Consensus pattern (27 bp):
AGCACTAAGTGTGCGAGTTTAATTGAA
Found at i:12299852 original size:25 final size:25
Alignment explanation
Indices: 12299807--12299985 Score: 134
Period size: 25 Copynumber: 7.6 Consensus size: 25
12299797 TTAACGTATA
*
12299807 ATGCTGTCCAATTTTGAGTATATTG
1 ATGCTGTCCAATTTTAAGTATATTG
*
12299832 ATGTTGTCC-ATTTTAATGTATA---
1 ATGCTGTCCAATTTTAA-GTATATTG
12299854 ATGCTGTCCAATTTTAAGTATATTG
1 ATGCTGTCCAATTTTAAGTATATTG
*
12299879 ATGCTGT-CTATTTTAATGTATA---
1 ATGCTGTCCAATTTTAA-GTATATTG
* *
12299901 ATGCTGTCCAATTTTGAGTATATTT
1 ATGCTGTCCAATTTTAAGTATATTG
* * * *
12299926 AAGCTGTCTAATTTGATGTATA---
1 ATGCTGTCCAATTTTAAGTATATTG
12299948 ATGCTGTCC-A-TTTAGAGTATATT-
1 ATGCTGTCCAATTTTA-AGTATATTG
*
12299971 ATTGCTATCCAATTT
1 A-TGCTGTCCAATTT
12299986 GATGAATAAT
Statistics
Matches: 122, Mismatches: 16, Indels: 31
0.72 0.09 0.18
Matches are distributed among these distances:
20 3 0.02
21 6 0.05
22 32 0.26
23 15 0.12
24 21 0.17
25 43 0.35
26 2 0.02
ACGTcount: A:0.27, C:0.12, G:0.16, T:0.46
Consensus pattern (25 bp):
ATGCTGTCCAATTTTAAGTATATTG
Found at i:12299865 original size:47 final size:47
Alignment explanation
Indices: 12299794--12300005 Score: 266
Period size: 47 Copynumber: 4.5 Consensus size: 47
12299784 TTGTGTTATA
* *
12299794 AATTTAACGTATAATGCTGTCCAATTTTGAGTATATTGATGTTGTCC
1 AATTTAATGTATAATGCTGTCCAATTTTGAGTATATTGATGCTGTCC
* * *
12299841 ATTTTAATGTATAATGCTGTCCAATTTTAAGTATATTGATGCTGTCT
1 AATTTAATGTATAATGCTGTCCAATTTTGAGTATATTGATGCTGTCC
* * * *
12299888 ATTTTAATGTATAATGCTGTCCAATTTTGAGTATATTTAAGCTGTCT
1 AATTTAATGTATAATGCTGTCCAATTTTGAGTATATTGATGCTGTCC
* * *
12299935 AATTTGATGTATAATGCTGTCC-ATTTAGAGTATATT-ATTGCTATCC
1 AATTTAATGTATAATGCTGTCCAATTTTGAGTATATTGA-TGCTGTCC
* *
12299981 AATTTGATGAATAATTGCTGTCCAA
1 AATTTAATGTATAA-TGCTGTCCAA
12300006 AACAGGGTTG
Statistics
Matches: 147, Mismatches: 15, Indels: 5
0.88 0.09 0.03
Matches are distributed among these distances:
45 1 0.01
46 31 0.21
47 114 0.78
48 1 0.01
ACGTcount: A:0.29, C:0.12, G:0.16, T:0.44
Consensus pattern (47 bp):
AATTTAATGTATAATGCTGTCCAATTTTGAGTATATTGATGCTGTCC
Found at i:12305178 original size:21 final size:21
Alignment explanation
Indices: 12305154--12305218 Score: 94
Period size: 21 Copynumber: 3.0 Consensus size: 21
12305144 TTTTTTGGTC
12305154 AAATTTTATATTTTTGTATAT
1 AAATTTTATATTTTTGTATAT
* *
12305175 AAATTTTATACTTTGGTATAT
1 AAATTTTATATTTTTGTATAT
12305196 AAATTTTATATATTTTCGTATAT
1 AAATTTTATAT-TTTT-GTATAT
12305219 TAGTTTTTTT
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
21 29 0.76
22 3 0.08
23 6 0.16
ACGTcount: A:0.34, C:0.03, G:0.06, T:0.57
Consensus pattern (21 bp):
AAATTTTATATTTTTGTATAT
Found at i:12305266 original size:47 final size:45
Alignment explanation
Indices: 12305201--12305289 Score: 108
Period size: 46 Copynumber: 1.9 Consensus size: 45
12305191 TATATAAATT
* *
12305201 TTATATATTTTCGTATATTAGTTTTTTTAAATGTACATATTTTTATA
1 TTATATATTTGCGTATATTA-TTTGTTTAAAT-TACATATTTTTATA
* *
12305248 TTAT-TATTTGCGTAATATTATTTGTTTGAATTATATATTTTT
1 TTATATATTTGCGT-ATATTATTTGTTTAAATTACATATTTTT
12305290 GACTTAATAT
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
45 10 0.27
46 17 0.46
47 10 0.27
ACGTcount: A:0.28, C:0.03, G:0.08, T:0.61
Consensus pattern (45 bp):
TTATATATTTGCGTATATTATTTGTTTAAATTACATATTTTTATA
Found at i:12315636 original size:7 final size:7
Alignment explanation
Indices: 12315626--12315700 Score: 141
Period size: 7 Copynumber: 10.7 Consensus size: 7
12315616 TTAAATTTTA
12315626 AAAATTC
1 AAAATTC
*
12315633 AAAATTA
1 AAAATTC
12315640 AAAATTC
1 AAAATTC
12315647 AAAATTC
1 AAAATTC
12315654 AAAATTC
1 AAAATTC
12315661 AAAATTC
1 AAAATTC
12315668 AAAATTC
1 AAAATTC
12315675 AAAATTC
1 AAAATTC
12315682 AAAATTC
1 AAAATTC
12315689 AAAATTC
1 AAAATTC
12315696 AAAAT
1 AAAAT
12315701 AATATATAAA
Statistics
Matches: 66, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
7 66 1.00
ACGTcount: A:0.60, C:0.12, G:0.00, T:0.28
Consensus pattern (7 bp):
AAAATTC
Found at i:12315906 original size:15 final size:14
Alignment explanation
Indices: 12315880--12315916 Score: 56
Period size: 15 Copynumber: 2.6 Consensus size: 14
12315870 ATTGTCGTAC
*
12315880 TTTTTTTGTAAATT
1 TTTTTTTATAAATT
12315894 TTATTTTTATAAATT
1 TT-TTTTTATAAATT
12315909 TTTTTTTA
1 TTTTTTTA
12315917 GATTAAGAAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 8 0.38
15 13 0.62
ACGTcount: A:0.24, C:0.00, G:0.03, T:0.73
Consensus pattern (14 bp):
TTTTTTTATAAATT
Found at i:12316621 original size:11 final size:11
Alignment explanation
Indices: 12316605--12316646 Score: 57
Period size: 11 Copynumber: 3.7 Consensus size: 11
12316595 GTCCATGAAC
12316605 ATGTTCGTTTA
1 ATGTTCGTTTA
**
12316616 ATGTTCGTGAA
1 ATGTTCGTTTA
12316627 CATGTTCGTTTA
1 -ATGTTCGTTTA
12316639 ATGTTCGT
1 ATGTTCGT
12316647 GAACATGTTC
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
11 17 0.65
12 9 0.35
ACGTcount: A:0.19, C:0.12, G:0.21, T:0.48
Consensus pattern (11 bp):
ATGTTCGTTTA
Found at i:12316626 original size:23 final size:23
Alignment explanation
Indices: 12316576--12316658 Score: 121
Period size: 23 Copynumber: 3.6 Consensus size: 23
12316566 ACATTGTTGT
** * *
12316576 TGAACATGTTCAATTATATGTCCA
1 TGAACATGTTCGTTTA-ATGTTCG
12316600 TGAACATGTTCGTTTAATGTTCG
1 TGAACATGTTCGTTTAATGTTCG
12316623 TGAACATGTTCGTTTAATGTTCG
1 TGAACATGTTCGTTTAATGTTCG
12316646 TGAACATGTTCGT
1 TGAACATGTTCGT
12316659 GACCATTTAA
Statistics
Matches: 55, Mismatches: 4, Indels: 1
0.92 0.07 0.02
Matches are distributed among these distances:
23 41 0.75
24 14 0.25
ACGTcount: A:0.25, C:0.14, G:0.19, T:0.41
Consensus pattern (23 bp):
TGAACATGTTCGTTTAATGTTCG
Found at i:12316633 original size:12 final size:12
Alignment explanation
Indices: 12316600--12316660 Score: 72
Period size: 12 Copynumber: 5.2 Consensus size: 12
12316590 TATATGTCCA
12316600 TGAACATGTTCG
1 TGAACATGTTCG
**
12316612 TTTA-ATGTTCG
1 TGAACATGTTCG
12316623 TGAACATGTTCG
1 TGAACATGTTCG
**
12316635 TTTA-ATGTTCG
1 TGAACATGTTCG
12316646 TGAACATGTTCG
1 TGAACATGTTCG
12316658 TGA
1 TGA
12316661 CCATTTAACA
Statistics
Matches: 39, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
11 18 0.46
12 21 0.54
ACGTcount: A:0.23, C:0.13, G:0.23, T:0.41
Consensus pattern (12 bp):
TGAACATGTTCG
Found at i:12323505 original size:7 final size:7
Alignment explanation
Indices: 12323493--12323532 Score: 80
Period size: 7 Copynumber: 5.7 Consensus size: 7
12323483 TCTTTATTAT
12323493 AATGAGA
1 AATGAGA
12323500 AATGAGA
1 AATGAGA
12323507 AATGAGA
1 AATGAGA
12323514 AATGAGA
1 AATGAGA
12323521 AATGAGA
1 AATGAGA
12323528 AATGA
1 AATGA
12323533 ATATGATAAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 33 1.00
ACGTcount: A:0.57, C:0.00, G:0.28, T:0.15
Consensus pattern (7 bp):
AATGAGA
Found at i:12326840 original size:18 final size:18
Alignment explanation
Indices: 12326817--12326851 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
12326807 TAAATAATTT
12326817 TAAATAT-TGTATAAAAAA
1 TAAATATAT-TATAAAAAA
12326835 TAAATATATTATAAAAA
1 TAAATATATTATAAAAA
12326852 TACATTGTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 15 0.94
19 1 0.06
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.34
Consensus pattern (18 bp):
TAAATATATTATAAAAAA
Found at i:12331057 original size:23 final size:23
Alignment explanation
Indices: 12331013--12331057 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 23
12331003 TAAATAATTC
* ***
12331013 TTTCAAATTTGAAATTTCAAAAT
1 TTTCAAATGTGAAATAAAAAAAT
12331036 TTTCAAATGTGAAATAAAAAAA
1 TTTCAAATGTGAAATAAAAAAA
12331058 AACTTGATTA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.51, C:0.07, G:0.07, T:0.36
Consensus pattern (23 bp):
TTTCAAATGTGAAATAAAAAAAT
Found at i:12332804 original size:22 final size:22
Alignment explanation
Indices: 12332773--12332823 Score: 93
Period size: 22 Copynumber: 2.3 Consensus size: 22
12332763 TTTATCTACT
12332773 AATTAATGAGATGATATTAATGA
1 AATT-ATGAGATGATATTAATGA
12332796 AATTATGAGATGATATTAATGA
1 AATTATGAGATGATATTAATGA
12332818 AATTAT
1 AATTAT
12332824 AAACAGATCT
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
22 24 0.86
23 4 0.14
ACGTcount: A:0.47, C:0.00, G:0.16, T:0.37
Consensus pattern (22 bp):
AATTATGAGATGATATTAATGA
Found at i:12337430 original size:11 final size:11
Alignment explanation
Indices: 12337414--12337465 Score: 54
Period size: 11 Copynumber: 4.9 Consensus size: 11
12337404 ATAATTCAAA
12337414 ATTATAAAAAT
1 ATTATAAAAAT
12337425 ATTAT-AAAAT
1 ATTATAAAAAT
* * *
12337435 ACTGTAGAAAT
1 ATTATAAAAAT
12337446 -TTATAAAAAT
1 ATTATAAAAAT
*
12337456 AATATAAAAA
1 ATTATAAAAA
12337466 AATCTATAAC
Statistics
Matches: 32, Mismatches: 7, Indels: 4
0.74 0.16 0.09
Matches are distributed among these distances:
10 15 0.47
11 17 0.53
ACGTcount: A:0.62, C:0.02, G:0.04, T:0.33
Consensus pattern (11 bp):
ATTATAAAAAT
Found at i:12342093 original size:13 final size:13
Alignment explanation
Indices: 12342075--12342100 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
12342065 TCATATTGAT
12342075 GTTACTAACAAAA
1 GTTACTAACAAAA
12342088 GTTACTAACAAAA
1 GTTACTAACAAAA
12342101 ATCCAATAGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.54, C:0.15, G:0.08, T:0.23
Consensus pattern (13 bp):
GTTACTAACAAAA
Found at i:12346887 original size:5 final size:5
Alignment explanation
Indices: 12346877--12346909 Score: 66
Period size: 5 Copynumber: 6.6 Consensus size: 5
12346867 TTATTTTCAA
12346877 AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAA
1 AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAA
12346910 GATGAGTTAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 28 1.00
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (5 bp):
AAAAG
Found at i:12347705 original size:35 final size:35
Alignment explanation
Indices: 12347659--12347731 Score: 146
Period size: 35 Copynumber: 2.1 Consensus size: 35
12347649 TGTACACACA
12347659 TTTGGACTTAGTACCCATACTTTACCCAGTGGTTC
1 TTTGGACTTAGTACCCATACTTTACCCAGTGGTTC
12347694 TTTGGACTTAGTACCCATACTTTACCCAGTGGTTC
1 TTTGGACTTAGTACCCATACTTTACCCAGTGGTTC
12347729 TTT
1 TTT
12347732 AGTGGTCATT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 38 1.00
ACGTcount: A:0.19, C:0.25, G:0.16, T:0.40
Consensus pattern (35 bp):
TTTGGACTTAGTACCCATACTTTACCCAGTGGTTC
Found at i:12356384 original size:3 final size:3
Alignment explanation
Indices: 12356378--12356412 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
12356368 CGACGACGAC
12356378 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GA
12356413 CAATGAGCTT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:12357049 original size:28 final size:27
Alignment explanation
Indices: 12356983--12357050 Score: 77
Period size: 28 Copynumber: 2.4 Consensus size: 27
12356973 TTTTGTACAG
12356983 TTTTTAGATTTTTTACATTTACATTTA
1 TTTTTAGATTTTTTACATTTACATTTA
*
12357010 TATTTT-GAATTTTTTGA-ATTTATATTTA
1 T-TTTTAG-ATTTTTT-ACATTTACATTTA
12357038 TTTTTAAGATTTT
1 TTTTT-AGATTTT
12357051 AAAAAATAGA
Statistics
Matches: 35, Mismatches: 1, Indels: 9
0.78 0.02 0.20
Matches are distributed among these distances:
27 6 0.17
28 27 0.77
29 2 0.06
ACGTcount: A:0.26, C:0.03, G:0.06, T:0.65
Consensus pattern (27 bp):
TTTTTAGATTTTTTACATTTACATTTA
Found at i:12357565 original size:23 final size:24
Alignment explanation
Indices: 12357535--12357602 Score: 77
Period size: 23 Copynumber: 2.9 Consensus size: 24
12357525 CTTGATTGTT
* *
12357535 AGAATATGTCACACAGGCTTT-CC
1 AGAATATGCCACAAAGGCTTTACC
* *
12357558 AGAATATGCCACATAGACTTTACC
1 AGAATATGCCACAAAGGCTTTACC
*
12357582 -GAATACGCCACAAAGGCTTTA
1 AGAATATGCCACAAAGGCTTTA
12357603 TAGGACATTA
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
23 36 0.95
24 2 0.05
ACGTcount: A:0.35, C:0.25, G:0.16, T:0.24
Consensus pattern (24 bp):
AGAATATGCCACAAAGGCTTTACC
Found at i:12361540 original size:54 final size:54
Alignment explanation
Indices: 12361430--12361540 Score: 134
Period size: 54 Copynumber: 2.1 Consensus size: 54
12361420 TGAGTTGGGT
** * * **
12361430 CACACGACCGTGTCGCAGGCCATGTGACAGACCGTGTAACTCTTTGAGTTGCAA
1 CACACGACCGTGTCGCAGGCCATGTGACAGACCGTGTAACTCACTAACTTAAAA
* *
12361484 CACACGACCGTGTCGCAGGCCGTGTG-CTAGGCCGTGTAACTCACTAACTTAAAA
1 CACACGACCGTGTCGCAGGCCATGTGAC-AGACCGTGTAACTCACTAACTTAAAA
12361538 CAC
1 CAC
12361541 TAGGAATTCA
Statistics
Matches: 48, Mismatches: 8, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
53 1 0.02
54 47 0.98
ACGTcount: A:0.25, C:0.30, G:0.24, T:0.21
Consensus pattern (54 bp):
CACACGACCGTGTCGCAGGCCATGTGACAGACCGTGTAACTCACTAACTTAAAA
Found at i:12365195 original size:27 final size:27
Alignment explanation
Indices: 12365123--12365179 Score: 114
Period size: 27 Copynumber: 2.1 Consensus size: 27
12365113 ATCCATTCAC
12365123 TCAATACAATTTTATTTTATCTCAATG
1 TCAATACAATTTTATTTTATCTCAATG
12365150 TCAATACAATTTTATTTTATCTCAATG
1 TCAATACAATTTTATTTTATCTCAATG
12365177 TCA
1 TCA
12365180 CCATTTTGTA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.33, C:0.16, G:0.04, T:0.47
Consensus pattern (27 bp):
TCAATACAATTTTATTTTATCTCAATG
Found at i:12371363 original size:22 final size:22
Alignment explanation
Indices: 12371335--12371377 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
12371325 CTTATATATA
*
12371335 GATATTGTAGACCTTTTGTTTG
1 GATATTGTAGAACTTTTGTTTG
*
12371357 GATATTGTTGAACTTTTGTTT
1 GATATTGTAGAACTTTTGTTT
12371378 AAAAGCTTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.19, C:0.07, G:0.21, T:0.53
Consensus pattern (22 bp):
GATATTGTAGAACTTTTGTTTG
Found at i:12391647 original size:14 final size:15
Alignment explanation
Indices: 12391622--12391657 Score: 51
Period size: 14 Copynumber: 2.6 Consensus size: 15
12391612 TCCCACCATT
12391622 AATATT-TTAAAA-C
1 AATATTCTTAAAAGC
12391635 AATATTCTTAAAAGC
1 AATATTCTTAAAAGC
12391650 AAT-TTCTT
1 AATATTCTT
12391658 TAAGAGGTCA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 6 0.29
14 11 0.52
15 4 0.19
ACGTcount: A:0.44, C:0.11, G:0.03, T:0.42
Consensus pattern (15 bp):
AATATTCTTAAAAGC
Found at i:12391833 original size:17 final size:17
Alignment explanation
Indices: 12391813--12391852 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
12391803 AATTTTTTAA
12391813 TTATTTTTCTTTTA-GTT
1 TTATTTTT-TTTTATGTT
*
12391830 TTATTTTTTTTTATTTT
1 TTATTTTTTTTTATGTT
12391847 TTATTT
1 TTATTT
12391853 AATTTTAAAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 5 0.24
17 16 0.76
ACGTcount: A:0.12, C:0.03, G:0.03, T:0.82
Consensus pattern (17 bp):
TTATTTTTTTTTATGTT
Found at i:12391853 original size:27 final size:28
Alignment explanation
Indices: 12391799--12391859 Score: 72
Period size: 27 Copynumber: 2.2 Consensus size: 28
12391789 CCAAATTTTC
*
12391799 TTTTAATTTTTTAATTATTTTTCTTTTAG
1 TTTT-ATTTTTTAATTATTTTTCTTTTAA
*
12391828 TTTTATTTTTT-TTTATTTTT-TATTTAA
1 TTTTATTTTTTAATTATTTTTCT-TTTAA
12391855 TTTTA
1 TTTTA
12391860 AAGTTATTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
26 1 0.03
27 17 0.59
28 7 0.24
29 4 0.14
ACGTcount: A:0.20, C:0.02, G:0.02, T:0.77
Consensus pattern (28 bp):
TTTTATTTTTTAATTATTTTTCTTTTAA
Found at i:12392595 original size:1 final size:1
Alignment explanation
Indices: 12392589--12392617 Score: 58
Period size: 1 Copynumber: 29.0 Consensus size: 1
12392579 ACAATATATG
12392589 TTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTT
12392618 GCGGTGATTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 28 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:12393889 original size:2 final size:2
Alignment explanation
Indices: 12393882--12393910 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
12393872 ATTAATTCAT
12393882 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 T
12393911 CTATCTTTCA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:12404152 original size:37 final size:35
Alignment explanation
Indices: 12404095--12404166 Score: 92
Period size: 37 Copynumber: 2.0 Consensus size: 35
12404085 TCTCTATAAT
*
12404095 ATTAAATTAATAAAATACTATTAAGATAAGTATTAA
1 ATTAAATTAATAAAATACTATTAAAATAA-TATTAA
*
12404131 ATTAAATTTAATATTAA-ACTATTAAAATAATATTAA
1 ATTAAA-TTAATA-AAATACTATTAAAATAATATTAA
12404167 TTTTAGAATA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
36 12 0.38
37 18 0.56
38 2 0.06
ACGTcount: A:0.56, C:0.03, G:0.03, T:0.39
Consensus pattern (35 bp):
ATTAAATTAATAAAATACTATTAAAATAATATTAA
Found at i:12408703 original size:24 final size:24
Alignment explanation
Indices: 12408669--12408734 Score: 78
Period size: 24 Copynumber: 2.8 Consensus size: 24
12408659 TCGCATATAT
* * *
12408669 TGACTCTCATGTAATAACAACAGG
1 TGACTCACATGGAATAACAACAAG
* *
12408693 TGACTCGCATGGCATAACAACAAG
1 TGACTCACATGGAATAACAACAAG
*
12408717 TGACTCACATGGTATAAC
1 TGACTCACATGGAATAAC
12408735 CTAGGGTTCG
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 36 1.00
ACGTcount: A:0.36, C:0.23, G:0.18, T:0.23
Consensus pattern (24 bp):
TGACTCACATGGAATAACAACAAG
Found at i:12408912 original size:53 final size:52
Alignment explanation
Indices: 12408845--12408955 Score: 143
Period size: 53 Copynumber: 2.1 Consensus size: 52
12408835 AAGGGCTCGT
* * *
12408845 GCACATATGTTCACACACAT-GCTCACACACGGGCTCGCACCTATAGAGGGTTC
1 GCACATAGGCTCACACAC-TGGCTCACACACGGACTCGCACCTATAG-GGGTTC
* * *
12408898 GCACATAGGCTCACACACTGGCTCGCACACGGACTCGCACTTATAGGGGTTT
1 GCACATAGGCTCACACACTGGCTCACACACGGACTCGCACCTATAGGGGTTC
12408950 GCACAT
1 GCACAT
12408956 GCTAGTTCTC
Statistics
Matches: 51, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
52 12 0.24
53 39 0.76
ACGTcount: A:0.25, C:0.32, G:0.23, T:0.21
Consensus pattern (52 bp):
GCACATAGGCTCACACACTGGCTCACACACGGACTCGCACCTATAGGGGTTC
Found at i:12411040 original size:19 final size:18
Alignment explanation
Indices: 12410986--12411046 Score: 54
Period size: 18 Copynumber: 3.3 Consensus size: 18
12410976 TAAATATAAA
*
12410986 AAATTATATATTTAAATTT
1 AAATTATATA-TTAAAATT
12411005 ATAA-TAGTA-ATTAAAATAT
1 A-AATTA-TATATTAAAAT-T
*
12411024 AAATTATATATTCAAATT
1 AAATTATATATTAAAATT
12411042 AAATT
1 AAATT
12411047 TTAAAAATAA
Statistics
Matches: 35, Mismatches: 2, Indels: 11
0.73 0.04 0.23
Matches are distributed among these distances:
18 16 0.46
19 15 0.43
20 4 0.11
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.44
Consensus pattern (18 bp):
AAATTATATATTAAAATT
Found at i:12416008 original size:2 final size:2
Alignment explanation
Indices: 12416003--12416028 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
12415993 CTCCACAAAT
12416003 CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA
12416029 AGGGCATTGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:12426141 original size:14 final size:14
Alignment explanation
Indices: 12426118--12426151 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 14
12426108 AGTTTTTTTT
12426118 AAAAAAAAAAAAAG
1 AAAAAAAAAAAAAG
12426132 AAAAAGAAAAAAAACG
1 AAAAA-AAAAAAAA-G
12426148 AAAA
1 AAAA
12426152 TGAAAATGAC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 5 0.28
15 8 0.44
16 5 0.28
ACGTcount: A:0.88, C:0.03, G:0.09, T:0.00
Consensus pattern (14 bp):
AAAAAAAAAAAAAG
Found at i:12426143 original size:16 final size:16
Alignment explanation
Indices: 12426118--12426157 Score: 55
Period size: 16 Copynumber: 2.6 Consensus size: 16
12426108 AGTTTTTTTT
12426118 AAAA-AAAAAAAAAGA
1 AAAAGAAAAAAAAAGA
*
12426133 AAAAGAAAAAAAACGA
1 AAAAGAAAAAAAAAGA
*
12426149 AAATGAAAA
1 AAAAGAAAA
12426158 TGACAATTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 4 0.18
16 18 0.82
ACGTcount: A:0.85, C:0.03, G:0.10, T:0.03
Consensus pattern (16 bp):
AAAAGAAAAAAAAAGA
Found at i:12427231 original size:31 final size:31
Alignment explanation
Indices: 12427196--12427255 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 31
12427186 TAATTTACAT
12427196 TTTATGTATCATTATATTAAATTATTTAAGC
1 TTTATGTATCATTATATTAAATTATTTAAGC
* * * *
12427227 TTTATTTATTATTATATTTAATTTTTTAA
1 TTTATGTATCATTATATTAAATTATTTAA
12427256 AATATTTTAT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.33, C:0.03, G:0.03, T:0.60
Consensus pattern (31 bp):
TTTATGTATCATTATATTAAATTATTTAAGC
Found at i:12446744 original size:15 final size:15
Alignment explanation
Indices: 12446724--12446753 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
12446714 TAATCAAACC
12446724 CTCAAGAATGTCTAA
1 CTCAAGAATGTCTAA
12446739 CTCAAGAATGTCTAA
1 CTCAAGAATGTCTAA
12446754 GGGTACCTCT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.40, C:0.20, G:0.13, T:0.27
Consensus pattern (15 bp):
CTCAAGAATGTCTAA
Found at i:12449987 original size:46 final size:45
Alignment explanation
Indices: 12449920--12450153 Score: 229
Period size: 46 Copynumber: 5.6 Consensus size: 45
12449910 TTTGAGTACT
* *
12449920 TCTGATCAAGAGATAAAGTGATAAGTGGTAGCTTTAGCTACACTTA
1 TCTGATCAAGTGACAAAGTGATAAGTGGTAGC-TTAGCTACACTTA
*
12449966 TCTGATCAAGAGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTA
1 TCTGATCAAGTGACAAAGTGATAAGTGGTAGC-TTAGCTACACTTA
*
12450012 TCTGATCAAGTGAAAAAGTGATAA---GT-G-TTA--T--ACTTA
1 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTAGCTACACTTA
*
12450048 TCTGATCAAGTGAAAAAGTGATAA---GT-GC-TA--T--ACTTA
1 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTAGCTACACTTA
* *
12450084 TTTGATCAAGTGACAAAGTGATAAGTGGCAGCTTAGCTACACTTA
1 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTAGCTACACTTA
* *
12450129 TCTGA-CCAGGGACAAA-TGATAAGTG
1 TCTGATCAAGTGACAAAGTGATAAGTG
12450154 ATCATACGTA
Statistics
Matches: 169, Mismatches: 9, Indels: 23
0.84 0.04 0.11
Matches are distributed among these distances:
36 62 0.37
38 1 0.01
39 1 0.01
40 5 0.03
41 2 0.01
42 1 0.01
43 12 0.07
44 9 0.05
45 9 0.05
46 67 0.40
ACGTcount: A:0.36, C:0.13, G:0.22, T:0.29
Consensus pattern (45 bp):
TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTAGCTACACTTA
Found at i:12450048 original size:36 final size:36
Alignment explanation
Indices: 12450002--12450110 Score: 182
Period size: 36 Copynumber: 3.0 Consensus size: 36
12449992 GGTAGCTTTA
*
12450002 GCTACACTTATCTGATCAAGTGAAAAAGTGATAAGT
1 GCTATACTTATCTGATCAAGTGAAAAAGTGATAAGT
*
12450038 GTTATACTTATCTGATCAAGTGAAAAAGTGATAAGT
1 GCTATACTTATCTGATCAAGTGAAAAAGTGATAAGT
* *
12450074 GCTATACTTATTTGATCAAGTGACAAAGTGATAAGT
1 GCTATACTTATCTGATCAAGTGAAAAAGTGATAAGT
12450110 G
1 G
12450111 GCAGCTTAGC
Statistics
Matches: 68, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
36 68 1.00
ACGTcount: A:0.38, C:0.11, G:0.20, T:0.31
Consensus pattern (36 bp):
GCTATACTTATCTGATCAAGTGAAAAAGTGATAAGT
Found at i:12452426 original size:21 final size:21
Alignment explanation
Indices: 12452381--12452427 Score: 53
Period size: 21 Copynumber: 2.3 Consensus size: 21
12452371 AAATAATAAA
*
12452381 ATAG-ATTATATAGTATTTTT
1 ATAGTATTATATAGTATATTT
*
12452401 ATAGTATTATATATTATGATTT
1 ATAGTATTATATAGTAT-ATTT
12452423 -TAGTA
1 ATAGTA
12452428 AATTTATATA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
20 4 0.17
21 16 0.70
22 3 0.13
ACGTcount: A:0.36, C:0.00, G:0.11, T:0.53
Consensus pattern (21 bp):
ATAGTATTATATAGTATATTT
Found at i:12452475 original size:35 final size:35
Alignment explanation
Indices: 12452406--12452477 Score: 101
Period size: 35 Copynumber: 2.1 Consensus size: 35
12452396 TTTTTATAGT
12452406 ATTATATATTATGATTTTAGTAAATTTATATAATA
1 ATTATATATTATGATTTTAGTAAATTTATATAATA
* * *
12452441 ATTATATA-TATTATTTTATTAAATTATATTTAATA
1 ATTATATATTATGATTTTAGTAAATT-TATATAATA
12452476 AT
1 AT
12452478 AATTATGTTA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
34 15 0.45
35 18 0.55
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.54
Consensus pattern (35 bp):
ATTATATATTATGATTTTAGTAAATTTATATAATA
Found at i:12454758 original size:164 final size:164
Alignment explanation
Indices: 12454548--12455039 Score: 653
Period size: 164 Copynumber: 3.0 Consensus size: 164
12454538 CTCACGAAGA
* * * * * * * *
12454548 GCCATATAACGGGACGCTTATAAAAGTTGCGGTGTGTCCACAACACATGTAGGATCACAATCGAT
1 GCCATATAACGAGATGCTCATAAGAGCTACGGTGTGTCCACAACACATGCAGGATCACAACCGAT
* * ** ** *
12454613 CGGGATGCTGCAAAGAGAAATTAACGGTAAGCTCGCAAGAATTATATAACGAGAAGCTTGAGTGG
66 CGGGATGCTCCGAAGAGCTATTAACGGTAAGCTCGCAAGAACCATATAACGAGAAGCTTGAGAGG
*
12454678 GCCAAATATCGGGATGCTCATTAGAGATAATAAC
131 GCCAAATATCGGGATGCTCATGAGAGATAATAAC
*
12454712 GCCATATAACGAGATGCTCATAAGAGCTACGGTGTGTCTACAACACATGCAGGATCACAACCGAT
1 GCCATATAACGAGATGCTCATAAGAGCTACGGTGTGTCCACAACACATGCAGGATCACAACCGAT
** * *
12454777 CGGGATGCTTTGAAGAGCTATTAACGGTAAGCTCGCAAGAACCATATAACGGGAAG-TTCGAGAA
66 CGGGATGCTCCGAAGAGCTATTAACGGTAAGCTCGCAAGAACCATATAACGAGAAGCTT-GAGAG
* *
12454841 GGCCAGATATCGGGATGCTCATGAGAGATAATAAT
130 GGCCAAATATCGGGATGCTCATGAGAGATAATAAC
* * * * *
12454876 GTCATATAATGAGATGCTCATAAGAGCTATGGTGTGTCCACAACACATGCAGAATCACAACCAAT
1 GCCATATAACGAGATGCTCATAAGAGCTACGGTGTGTCCACAACACATGCAGGATCACAACCGAT
* * * * *
12454941 CAGGATGCTCCGAAGAGCTATTAACGGTAAGCTTGCAATAACCATATAATGAGAAGCTCGAGAGG
66 CGGGATGCTCCGAAGAGCTATTAACGGTAAGCTCGCAAGAACCATATAACGAGAAGCTTGAGAGG
**
12455006 GCCAAATATCGATATGCTCATGAGAGATAATAAC
131 GCCAAATATCGGGATGCTCATGAGAGATAATAAC
12455040 AGGATGCTCT
Statistics
Matches: 285, Mismatches: 41, Indels: 4
0.86 0.12 0.01
Matches are distributed among these distances:
163 2 0.01
164 282 0.99
165 1 0.00
ACGTcount: A:0.36, C:0.19, G:0.24, T:0.22
Consensus pattern (164 bp):
GCCATATAACGAGATGCTCATAAGAGCTACGGTGTGTCCACAACACATGCAGGATCACAACCGAT
CGGGATGCTCCGAAGAGCTATTAACGGTAAGCTCGCAAGAACCATATAACGAGAAGCTTGAGAGG
GCCAAATATCGGGATGCTCATGAGAGATAATAAC
Found at i:12457674 original size:54 final size:54
Alignment explanation
Indices: 12457616--12457720 Score: 138
Period size: 54 Copynumber: 1.9 Consensus size: 54
12457606 CGACACAGCC
* *
12457616 ATGTGACCCAAGTCAGTGAGTTACACAAGTAGAGACACGAGCTGGGACACGAGT
1 ATGTGACCCAAGTCAGTGAGTTACACAAGCAAAGACACGAGCTGGGACACGAGT
*** ** *
12457670 ATGTGTTTCAAGTCAGTGAGTTACACGGGCAAAGACACGGGCTGGGACACG
1 ATGTGACCCAAGTCAGTGAGTTACACAAGCAAAGACACGAGCTGGGACACG
12457721 GTCGTGTGTC
Statistics
Matches: 43, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
54 43 1.00
ACGTcount: A:0.30, C:0.20, G:0.31, T:0.18
Consensus pattern (54 bp):
ATGTGACCCAAGTCAGTGAGTTACACAAGCAAAGACACGAGCTGGGACACGAGT
Found at i:12459231 original size:50 final size:50
Alignment explanation
Indices: 12459164--12459406 Score: 247
Period size: 50 Copynumber: 4.7 Consensus size: 50
12459154 TTTCTTGTAC
* * * **
12459164 TGCCAATGCCATATCCCAGATATGGTCTTATATGGGAGTTCTCATATAGG
1 TGCCACTGCCATGTCCCAGACATGGTCTTATATGGGACCTCTCATATAGG
* * * * *
12459214 TGCCCCTGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
1 TGCCACTGCCATGTCCCAGACATGGTCTTATATGGGACCTCTCATATAGG
* * * *
12459264 TGCTAAC-GCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
1 TGC-CACTGCCATGTCCCAGACATGGTCTTATATGGGACCTCTCATATAGG
* *
12459314 TGCCAAC-GCCATGTCCTAGACATGGTCTTATATGGGACCTCTCATAATCTCAATGA
1 TGCC-ACTGCCATGTCCCAGACATGGTCTTATATGGGACCTCTCAT-A--T--A-GG
*
12459370 TGCCAATGCCATGTCCCAGACATGGTCTTATATGGGA
1 TGCCACTGCCATGTCCCAGACATGGTCTTATATGGGA
12459407 TCTCATCCTC
Statistics
Matches: 163, Mismatches: 21, Indels: 12
0.83 0.11 0.06
Matches are distributed among these distances:
50 126 0.77
51 1 0.01
53 1 0.01
55 1 0.01
56 34 0.21
ACGTcount: A:0.23, C:0.28, G:0.22, T:0.28
Consensus pattern (50 bp):
TGCCACTGCCATGTCCCAGACATGGTCTTATATGGGACCTCTCATATAGG
Found at i:12459289 original size:100 final size:102
Alignment explanation
Indices: 12459164--12459406 Score: 285
Period size: 100 Copynumber: 2.4 Consensus size: 102
12459154 TTTCTTGTAC
* * * ** *
12459164 TGCCAATGCCATATCCCAGATATGGTCTTATATGGGAGTTCTCATATAGGTGCC-CCTGCCATGT
1 TGCCAACGCCATGTCCCAGACATGGTCTTATATGGGACCTCTCATATAGGTGCCAAC-GCCATGT
*
12459228 CCCAGACATGGTCTTACAGGGGACCTCTC-ATCTC-GG
65 CCCAGACATGGTCTTACAGGGGACCTCTCAATCTCAGA
* * * *
12459264 TGCTAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGGTGCCAACGCCATGTC
1 TGCCAACGCCATGTCCCAGACATGGTCTTATATGGGACCTCTCATATAGGTGCCAACGCCATGTC
* * *
12459329 CTAGACATGGTCTTATATGGGACCTCTCATAATCTCAATGA
66 CCAGACATGGTCTTACAGGGGACCTCTC--AATCTC-A-GA
*
12459370 TGCCAATGCCATGTCCCAGACATGGTCTTATATGGGA
1 TGCCAACGCCATGTCCCAGACATGGTCTTATATGGGA
12459407 TCTCATCCTC
Statistics
Matches: 119, Mismatches: 17, Indels: 8
0.83 0.12 0.06
Matches are distributed among these distances:
100 78 0.66
101 1 0.01
103 5 0.04
106 35 0.29
ACGTcount: A:0.23, C:0.28, G:0.22, T:0.28
Consensus pattern (102 bp):
TGCCAACGCCATGTCCCAGACATGGTCTTATATGGGACCTCTCATATAGGTGCCAACGCCATGTC
CCAGACATGGTCTTACAGGGGACCTCTCAATCTCAGA
Found at i:12465056 original size:21 final size:21
Alignment explanation
Indices: 12465030--12465134 Score: 156
Period size: 21 Copynumber: 5.0 Consensus size: 21
12465020 CGAACATGCC
12465030 AACAGAAGCTCATAAGAGCTG
1 AACAGAAGCTCATAAGAGCTG
*
12465051 AACAGAAGCTCAAAAGAGCTG
1 AACAGAAGCTCATAAGAGCTG
* *
12465072 AATAGAAGCTCGTAAGAGCTG
1 AACAGAAGCTCATAAGAGCTG
* *
12465093 AATAGAAGCTCGTAAGAGCTG
1 AACAGAAGCTCATAAGAGCTG
*
12465114 AACAGAAGCTCAAAAGAGCTG
1 AACAGAAGCTCATAAGAGCTG
12465135 GTTCACCCGA
Statistics
Matches: 77, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 77 1.00
ACGTcount: A:0.43, C:0.17, G:0.26, T:0.14
Consensus pattern (21 bp):
AACAGAAGCTCATAAGAGCTG
Found at i:12471234 original size:12 final size:12
Alignment explanation
Indices: 12471217--12471241 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
12471207 AACAATAAAT
12471217 TCCATCTCAAGA
1 TCCATCTCAAGA
12471229 TCCATCTCAAGA
1 TCCATCTCAAGA
12471241 T
1 T
12471242 ACCAAACACA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.32, C:0.32, G:0.08, T:0.28
Consensus pattern (12 bp):
TCCATCTCAAGA
Found at i:12479645 original size:34 final size:35
Alignment explanation
Indices: 12479601--12479668 Score: 93
Period size: 34 Copynumber: 2.0 Consensus size: 35
12479591 GCACAGTTGA
* **
12479601 ACAGTCTTGGGCCTAAGCCCTTTTCAGTATCAGTG
1 ACAGTCTTGGGCCTAAGCCCATCACAGTATCAGTG
*
12479636 ACAGT-TTGGGCCTTAGCCCATCACAGTATCAGT
1 ACAGTCTTGGGCCTAAGCCCATCACAGTATCAGT
12479669 AGCAGTAACA
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
34 24 0.83
35 5 0.17
ACGTcount: A:0.22, C:0.26, G:0.22, T:0.29
Consensus pattern (35 bp):
ACAGTCTTGGGCCTAAGCCCATCACAGTATCAGTG
Found at i:12480935 original size:22 final size:23
Alignment explanation
Indices: 12480882--12480935 Score: 67
Period size: 23 Copynumber: 2.4 Consensus size: 23
12480872 CCCAATTTTA
*
12480882 ATTAAAATTAAAATTATATTTGT
1 ATTAAAATTAAAACTATATTTGT
*
12480905 AATAAAATTAAAACTA-A-TTGTT
1 ATTAAAATTAAAACTATATTTG-T
12480927 ATTAAAATT
1 ATTAAAATT
12480936 GTATCAAATT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
21 3 0.11
22 10 0.37
23 14 0.52
ACGTcount: A:0.52, C:0.02, G:0.04, T:0.43
Consensus pattern (23 bp):
ATTAAAATTAAAACTATATTTGT
Found at i:12480999 original size:16 final size:16
Alignment explanation
Indices: 12480978--12481019 Score: 84
Period size: 16 Copynumber: 2.6 Consensus size: 16
12480968 AATAAAATTT
12480978 TTAATTGTTAATTATA
1 TTAATTGTTAATTATA
12480994 TTAATTGTTAATTATA
1 TTAATTGTTAATTATA
12481010 TTAATTGTTA
1 TTAATTGTTA
12481020 CTAAAAAAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 26 1.00
ACGTcount: A:0.36, C:0.00, G:0.07, T:0.57
Consensus pattern (16 bp):
TTAATTGTTAATTATA
Found at i:12481177 original size:52 final size:52
Alignment explanation
Indices: 12481114--12481213 Score: 191
Period size: 52 Copynumber: 1.9 Consensus size: 52
12481104 CATGTTCACC
*
12481114 ATCCTGTTCACTGGACATTGAATCACTTGGGTCTCTTTCTATTAAACACACT
1 ATCCTATTCACTGGACATTGAATCACTTGGGTCTCTTTCTATTAAACACACT
12481166 ATCCTATTCACTGGACATTGAATCACTTGGGTCTCTTTCTATTAAACA
1 ATCCTATTCACTGGACATTGAATCACTTGGGTCTCTTTCTATTAAACA
12481214 ATTAAAAGGA
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
52 47 1.00
ACGTcount: A:0.26, C:0.24, G:0.13, T:0.37
Consensus pattern (52 bp):
ATCCTATTCACTGGACATTGAATCACTTGGGTCTCTTTCTATTAAACACACT
Found at i:12481620 original size:9 final size:9
Alignment explanation
Indices: 12481608--12481645 Score: 58
Period size: 9 Copynumber: 4.2 Consensus size: 9
12481598 ATCATCCTCA
*
12481608 TCGTCGTCG
1 TCGTCATCG
12481617 TCGTCATCG
1 TCGTCATCG
12481626 TCGTCATCG
1 TCGTCATCG
*
12481635 TCTTCATCG
1 TCGTCATCG
12481644 TC
1 TC
12481646 CCTTTTGCAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 27 1.00
ACGTcount: A:0.08, C:0.34, G:0.21, T:0.37
Consensus pattern (9 bp):
TCGTCATCG
Found at i:12483927 original size:45 final size:45
Alignment explanation
Indices: 12483863--12483958 Score: 165
Period size: 45 Copynumber: 2.1 Consensus size: 45
12483853 AGCAAGGCAA
*
12483863 TAATGTGAAATTTTTAGCTAATGTTCCATTATATAAACAATAGGC
1 TAATGTGAAATTTTGAGCTAATGTTCCATTATATAAACAATAGGC
* *
12483908 TAATGTGAAATTTTGAGCTAATTTTCCATTATATAAACAATCGGC
1 TAATGTGAAATTTTGAGCTAATGTTCCATTATATAAACAATAGGC
12483953 TAATGT
1 TAATGT
12483959 TCCATTTATA
Statistics
Matches: 48, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
45 48 1.00
ACGTcount: A:0.36, C:0.11, G:0.14, T:0.39
Consensus pattern (45 bp):
TAATGTGAAATTTTGAGCTAATGTTCCATTATATAAACAATAGGC
Found at i:12485412 original size:10 final size:10
Alignment explanation
Indices: 12485399--12485428 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
12485389 TGTCAAAATT
12485399 ATATATAATG
1 ATATATAATG
*
12485409 ATATATAATA
1 ATATATAATG
12485419 ATATATAATG
1 ATATATAATG
12485429 GTGGCTCATG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.53, C:0.00, G:0.07, T:0.40
Consensus pattern (10 bp):
ATATATAATG
Found at i:12490363 original size:12 final size:12
Alignment explanation
Indices: 12490346--12490410 Score: 51
Period size: 12 Copynumber: 5.2 Consensus size: 12
12490336 ATTTATCCAA
12490346 TTTTTATTTTAT
1 TTTTTATTTTAT
12490358 TTTTTATTTT-T
1 TTTTTATTTTAT
* *
12490369 GTCTTTAGTTTAAT
1 -TTTTTA-TTTTAT
* *
12490383 TTTTATATTCTAA
1 TTTT-TATTTTAT
*
12490396 TTTTTCTTTTAT
1 TTTTTATTTTAT
12490408 TTT
1 TTT
12490411 CTACTGGCAG
Statistics
Matches: 40, Mismatches: 9, Indels: 8
0.70 0.16 0.14
Matches are distributed among these distances:
11 1 0.03
12 23 0.57
13 13 0.32
14 3 0.08
ACGTcount: A:0.17, C:0.05, G:0.03, T:0.75
Consensus pattern (12 bp):
TTTTTATTTTAT
Found at i:12494305 original size:33 final size:35
Alignment explanation
Indices: 12494268--12494335 Score: 86
Period size: 34 Copynumber: 2.0 Consensus size: 35
12494258 GTATTTTTGA
* *
12494268 CACTG-TACTGAGATGGGCTAAGGCCCAA-ACTGT
1 CACTGATACTGAAAAGGGCTAAGGCCCAAGACTGT
**
12494301 CACTGATACTGAAAAGGGCTTTGGCCCAAGACTGT
1 CACTGATACTGAAAAGGGCTAAGGCCCAAGACTGT
12494336 TCAACTGTGC
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
33 5 0.17
34 19 0.66
35 5 0.17
ACGTcount: A:0.28, C:0.24, G:0.26, T:0.22
Consensus pattern (35 bp):
CACTGATACTGAAAAGGGCTAAGGCCCAAGACTGT
Found at i:12495106 original size:26 final size:26
Alignment explanation
Indices: 12495039--12495100 Score: 106
Period size: 26 Copynumber: 2.4 Consensus size: 26
12495029 CCTGTAAGTG
*
12495039 TTCTGAAACTGATAGATGCTATGATA
1 TTCTGAAACTGATATATGCTATGATA
*
12495065 TTCTGAAACTGATATATGTTATGATA
1 TTCTGAAACTGATATATGCTATGATA
12495091 TTCTGAAACT
1 TTCTGAAACT
12495101 ACTATAGGTA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 34 1.00
ACGTcount: A:0.34, C:0.11, G:0.16, T:0.39
Consensus pattern (26 bp):
TTCTGAAACTGATATATGCTATGATA
Found at i:12503628 original size:42 final size:42
Alignment explanation
Indices: 12503498--12503627 Score: 206
Period size: 42 Copynumber: 3.1 Consensus size: 42
12503488 CCTGGCGACA
**
12503498 TGGCAATGTGACCCACACAGCCTAGACACACGAATGTGTCCT
1 TGGCAATGTGACCCACACAGCCTAGACACACGGGTGTGTCCT
*
12503540 TGGCAATGTGACCCACACAGCCTAGACACACTGGTGTGTCCT
1 TGGCAATGTGACCCACACAGCCTAGACACACGGGTGTGTCCT
* * *
12503582 TGGCCATGTGACCCATACGGCCTAGACACACGGGTGTGTCCT
1 TGGCAATGTGACCCACACAGCCTAGACACACGGGTGTGTCCT
12503624 TGGC
1 TGGC
12503628 CGTGTGAGTT
Statistics
Matches: 81, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
42 81 1.00
ACGTcount: A:0.23, C:0.31, G:0.25, T:0.21
Consensus pattern (42 bp):
TGGCAATGTGACCCACACAGCCTAGACACACGGGTGTGTCCT
Found at i:12510259 original size:2 final size:2
Alignment explanation
Indices: 12510252--12510286 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
12510242 TCACCACCAC
12510252 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
12510287 AATTTTTTTA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:12534039 original size:23 final size:23
Alignment explanation
Indices: 12533978--12534378 Score: 371
Period size: 23 Copynumber: 17.3 Consensus size: 23
12533968 TGAGCAGCAT
12533978 ATATATATACAAAATTGGACAGC
1 ATATATATACAAAATTGGACAGC
* * *
12534001 ATTTATACACCAAAATTTGACAGC
1 ATATATATA-CAAAATTGGACAGC
*
12534025 ATATATATACAAAATTGGAGAGC
1 ATATATATACAAAATTGGACAGC
* * * *
12534048 ATTTATACT-CTAAAACTGGGCAAC
1 ATATATA-TAC-AAAATTGGACAGC
* * *
12534072 ATATATATACCAATTTGGACAAC
1 ATATATATACAAAATTGGACAGC
* *
12534095 ACT-TATACACAAAATTTGACAGC
1 A-TATATATACAAAATTGGACAGC
*
12534118 ATGTATATACAAAATTGGACAGC
1 ATATATATACAAAATTGGACAGC
* * *
12534141 ATTTATACACAAAATTTGACAGC
1 ATATATATACAAAATTGGACAGC
*
12534164 ATGTATATACAAAATTGGACAGC
1 ATATATATACAAAATTGGACAGC
* * *
12534187 ATTTATACACTAAAATTGGGCAGC
1 ATATATATAC-AAAATTGGACAGC
* * *
12534211 GTATATATACCAATTTGGACAGC
1 ATATATATACAAAATTGGACAGC
* *
12534234 ACT-TATACACAAAATTTGACAGC
1 A-TATATATACAAAATTGGACAGC
* *
12534257 ATGTATATACAAAATTGGATAGC
1 ATATATATACAAAATTGGACAGC
* * *
12534280 ATTTATACACTAAAATTGGGCAGC
1 ATATATATAC-AAAATTGGACAGC
* *
12534304 ATATATATACCAATTTGG-CAGC
1 ATATATATACAAAATTGGACAGC
12534326 ATATATATACAAAATTGGACAGC
1 ATATATATACAAAATTGGACAGC
* *
12534349 ATTTATACACCAAAATTAGG-CAGC
1 ATATATATA-CAAAATT-GGACAGC
12534373 ATATAT
1 ATATAT
12534379 TCGATTTTTG
Statistics
Matches: 305, Mismatches: 60, Indels: 25
0.78 0.15 0.06
Matches are distributed among these distances:
22 22 0.07
23 188 0.62
24 93 0.30
25 2 0.01
ACGTcount: A:0.42, C:0.16, G:0.13, T:0.28
Consensus pattern (23 bp):
ATATATATACAAAATTGGACAGC
Found at i:12534129 original size:93 final size:93
Alignment explanation
Indices: 12533943--12534374 Score: 487
Period size: 93 Copynumber: 4.6 Consensus size: 93
12533933 TCTACCCTGT
12533943 TTGGACAGC-TCTTATACATCAAAA-TTGAGCAGCATATATATATACAAAATTGGACAGCATTTA
1 TTGGACAGCAT-TTATACA-CAAAATTTGA-CAGC--ATATATATACAAAATTGGACAGCATTTA
* *
12534006 TACACCAAAATTTGACAGCATATATATACAAAA
61 TACACTAAAATTGGACAGCATATATATACAAAA
* * * * * * * * * *
12534039 TTGGAGAGCATTTATACTCTAAAACTGGGCAACATATATATACCAATTTGGACAACACTTATACA
1 TTGGACAGCATTTATACAC-AAAATTTGACAGCATATATATACAAAATTGGACAGCATTTATACA
* *
12534104 C-AAAATTTGACAGCATGTATATACAAAA
65 CTAAAATTGGACAGCATATATATACAAAA
*
12534132 TTGGACAGCATTTATACACAAAATTTGACAGCATGTATATACAAAATTGGACAGCATTTATACAC
1 TTGGACAGCATTTATACACAAAATTTGACAGCATATATATACAAAATTGGACAGCATTTATACAC
* * * *
12534197 TAAAATTGGGCAGCGTATATATACCAAT
66 TAAAATTGGACAGCATATATATACAAAA
* * *
12534225 TTGGACAGCACTTATACACAAAATTTGACAGCATGTATATACAAAATTGGATAGCATTTATACAC
1 TTGGACAGCATTTATACACAAAATTTGACAGCATATATATACAAAATTGGACAGCATTTATACAC
* * *
12534290 TAAAATTGGGCAGCATATATATACCAAT
66 TAAAATTGGACAGCATATATATACAAAA
* * * * *
12534318 TTGG-CAGCATATATATACAAAATTGGACAGCATTTATACACCAAAATTAGG-CAGCAT
1 TTGGACAGCATTTATACACAAAATTTGACAGCATATATATA-CAAAATT-GGACAGCAT
12534375 ATATTCGATT
Statistics
Matches: 293, Mismatches: 37, Indels: 15
0.85 0.11 0.04
Matches are distributed among these distances:
92 67 0.23
93 170 0.58
94 31 0.11
95 1 0.00
96 21 0.07
97 3 0.01
ACGTcount: A:0.41, C:0.17, G:0.14, T:0.28
Consensus pattern (93 bp):
TTGGACAGCATTTATACACAAAATTTGACAGCATATATATACAAAATTGGACAGCATTTATACAC
TAAAATTGGACAGCATATATATACAAAA
Found at i:12534373 original size:139 final size:139
Alignment explanation
Indices: 12533942--12534361 Score: 587
Period size: 139 Copynumber: 3.0 Consensus size: 139
12533932 ATCTACCCTG
* *
12533942 TTTGGACAGCTCTTATACATCAAAA-TTGAGCAGCATATATATATACAAAATTGGACAGCATTTA
1 TTTGGACAGCACTTATACA-CAAAATTTGA-CAGC--ATGTATATACAAAATTGGACAGCATTTA
* *
12534006 TACACCAAAATTTGACAGCATATATATACAAAATTGGAGAGCATTTATACT-CTAAAACTGGGCA
62 TACA-CAAAATTTGACAGCATATATATACAAAATTGGACAGCATTTATA-TACTAAAATTGGGCA
*
12534070 ACATATATATACCAA
125 GCATATATATACCAA
*
12534085 TTTGGACAACACTTATACACAAAATTTGACAGCATGTATATACAAAATTGGACAGCATTTATACA
1 TTTGGACAGCACTTATACACAAAATTTGACAGCATGTATATACAAAATTGGACAGCATTTATACA
* * *
12534150 CAAAATTTGACAGCATGTATATACAAAATTGGACAGCATTTATACACTAAAATTGGGCAGCGTAT
66 CAAAATTTGACAGCATATATATACAAAATTGGACAGCATTTATATACTAAAATTGGGCAGCATAT
12534215 ATATACCAA
131 ATATACCAA
*
12534224 TTTGGACAGCACTTATACACAAAATTTGACAGCATGTATATACAAAATTGGATAGCATTTATACA
1 TTTGGACAGCACTTATACACAAAATTTGACAGCATGTATATACAAAATTGGACAGCATTTATACA
* * * * * * *
12534289 CTAAAATTGGGCAGCATATATATACCAATTTGG-CAGCATATATATAC-AAAATTGGACAGCATT
66 C-AAAATTTGACAGCATATATATACAAAATTGGACAGCATTTATATACTAAAATTGGGCAGCATA
*
12534352 TATACACCAA
130 TATATACCAA
12534362 AATTAGGCAG
Statistics
Matches: 252, Mismatches: 22, Indels: 11
0.88 0.08 0.04
Matches are distributed among these distances:
138 22 0.09
139 143 0.57
140 57 0.23
142 9 0.04
143 21 0.08
ACGTcount: A:0.41, C:0.17, G:0.13, T:0.29
Consensus pattern (139 bp):
TTTGGACAGCACTTATACACAAAATTTGACAGCATGTATATACAAAATTGGACAGCATTTATACA
CAAAATTTGACAGCATATATATACAAAATTGGACAGCATTTATATACTAAAATTGGGCAGCATAT
ATATACCAA
Found at i:12535340 original size:43 final size:43
Alignment explanation
Indices: 12535275--12535384 Score: 154
Period size: 43 Copynumber: 2.6 Consensus size: 43
12535265 CGTACAATGA
*
12535275 CAACGTCCCAGACGTGGTCTTACATGTAATCACATA-TAGATGC
1 CAACGTCCCAGACGTGGTCTTACATGTAAACACA-AGTAGATGC
*
12535318 C-ACTGTCCCAGACAG-GGTCTTACATGTAAACACAAGTCGATGC
1 CAAC-GTCCCAGAC-GTGGTCTTACATGTAAACACAAGTAGATGC
12535361 CAACGTCCCAGACGTGGTCTTACA
1 CAACGTCCCAGACGTGGTCTTACA
12535385 CGATAGTACA
Statistics
Matches: 60, Mismatches: 2, Indels: 10
0.83 0.03 0.14
Matches are distributed among these distances:
42 4 0.07
43 53 0.88
44 3 0.05
ACGTcount: A:0.29, C:0.28, G:0.20, T:0.23
Consensus pattern (43 bp):
CAACGTCCCAGACGTGGTCTTACATGTAAACACAAGTAGATGC
Found at i:12541891 original size:23 final size:23
Alignment explanation
Indices: 12541821--12542245 Score: 401
Period size: 23 Copynumber: 18.3 Consensus size: 23
12541811 AGCAGCATAT
*
12541821 ATATATATACAAAATTGGACAGC
1 ATATATACACAAAATTGGACAGC
* * *
12541844 ATTTATCCACCAAAATTTGACAGC
1 ATATATACA-CAAAATTGGACAGC
* *
12541868 ATATATATACAAAATTGGAGAGC
1 ATATATACACAAAATTGGACAGC
* * *
12541891 ATTTATACCCTAAAATTGGGCAGC
1 ATATATACAC-AAAATTGGACAGC
* * *
12541915 ATATATATACCAATTTGGACAGC
1 ATATATACACAAAATTGGACAGC
*
12541938 ACT-TATACACAAAATTTGACAGC
1 A-TATATACACAAAATTGGACAGC
* * *
12541961 ATGTATATACAAAATTGAACAGC
1 ATATATACACAAAATTGGACAGC
*
12541984 ACT-TATACACAAAATTTGACAGC
1 A-TATATACACAAAATTGGACAGC
* *
12542007 ATGTATATACAAAATTGGACAGC
1 ATATATACACAAAATTGGACAGC
* *
12542030 ATTTATACACTAAAATTGGGCAGC
1 ATATATACAC-AAAATTGGACAGC
* * *
12542054 ATATATATACCAATTTGGACAGC
1 ATATATACACAAAATTGGACAGC
*
12542077 ACT-TATACACAAAATTTGACAGC
1 A-TATATACACAAAATTGGACAGC
* *
12542100 ATGTATATACAAAATTGGACAGC
1 ATATATACACAAAATTGGACAGC
* *
12542123 ATTTATACACTAAAATTGGGCAGC
1 ATATATACAC-AAAATTGGACAGC
* * *
12542147 ATATATATACCAATTTGGACAGC
1 ATATATACACAAAATTGGACAGC
12542170 ACT-TATACACAAAATTTGG-CAGC
1 A-TATATACACAAAA-TTGGACAGC
* *
12542193 ATATATATACAAAATTAGACAGC
1 ATATATACACAAAATTGGACAGC
* *
12542216 ATTTATACACCAAAATTGGGCAGC
1 ATATATACA-CAAAATTGGACAGC
12542240 ATATAT
1 ATATAT
12542246 TCGATTTTGG
Statistics
Matches: 323, Mismatches: 64, Indels: 29
0.78 0.15 0.07
Matches are distributed among these distances:
22 7 0.02
23 214 0.66
24 102 0.32
ACGTcount: A:0.42, C:0.17, G:0.13, T:0.28
Consensus pattern (23 bp):
ATATATACACAAAATTGGACAGC
Found at i:12541990 original size:93 final size:92
Alignment explanation
Indices: 12541784--12542245 Score: 602
Period size: 93 Copynumber: 4.9 Consensus size: 92
12541774 TCTATCCTGT
*
12541784 TTGGACAGCTCTTATACATCAAAA-TTGAGCAGCATATATATATATACAAAATTGGACAGCATTT
1 TTGGACAGCACTTATACA-CAAAATTTGA-CAGC----ATATATATACAAAATTGGACAGCATTT
* * *
12541848 ATCCACCAAAATTTGACAGCATATATATACAAAA
60 ATACA-CAAAATTGGGCAGCATATATATACAAAA
* * * * * * * *
12541882 TTGGAGAGCATTTATACCCTAAAATTGGGCAGCATATATATACCAATTTGGACAGCACTTATACA
1 TTGGACAGCACTTATACAC-AAAATTTGACAGCATATATATACAAAATTGGACAGCATTTATACA
* * *
12541947 CAAAATTTGACAGCATGTATATACAAAA
65 CAAAATTGGGCAGCATATATATACAAAA
* *
12541975 TTGAACAGCACTTATACACAAAATTTGACAGCATGTATATACAAAATTGGACAGCATTTATACAC
1 TTGGACAGCACTTATACACAAAATTTGACAGCATATATATACAAAATTGGACAGCATTTATACAC
* *
12542040 TAAAATTGGGCAGCATATATATACCAAT
66 -AAAATTGGGCAGCATATATATACAAAA
*
12542068 TTGGACAGCACTTATACACAAAATTTGACAGCATGTATATACAAAATTGGACAGCATTTATACAC
1 TTGGACAGCACTTATACACAAAATTTGACAGCATATATATACAAAATTGGACAGCATTTATACAC
* *
12542133 TAAAATTGGGCAGCATATATATACCAAT
66 -AAAATTGGGCAGCATATATATACAAAA
* *
12542161 TTGGACAGCACTTATACACAAAATTTGGCAGCATATATATACAAAATTAGACAGCATTTATACAC
1 TTGGACAGCACTTATACACAAAATTTGACAGCATATATATACAAAATTGGACAGCATTTATACA-
12542226 CAAAATTGGGCAGCATATAT
65 CAAAATTGGGCAGCATATAT
12542246 TCGATTTTGG
Statistics
Matches: 330, Mismatches: 30, Indels: 13
0.88 0.08 0.03
Matches are distributed among these distances:
92 40 0.12
93 236 0.72
94 29 0.09
97 1 0.00
98 22 0.07
99 2 0.01
ACGTcount: A:0.41, C:0.17, G:0.13, T:0.28
Consensus pattern (92 bp):
TTGGACAGCACTTATACACAAAATTTGACAGCATATATATACAAAATTGGACAGCATTTATACAC
AAAATTGGGCAGCATATATATACAAAA
Found at i:12542043 original size:139 final size:140
Alignment explanation
Indices: 12541783--12542241 Score: 638
Period size: 139 Copynumber: 3.3 Consensus size: 140
12541773 ATCTATCCTG
* * *
12541783 TTTGGACAGCTCTTATACATCAAAA-TTGAGCAGCATATATATATATACAAAATTGGACAGCATT
1 TTTGGACAGCACTTATACACCAAAATTTGA-CAGC----ATGTATATACAAAATTGGACAGCATT
* * *
12541847 TATCCACCAAAATTTGACAGCATATATATACAAAATTGGAGAGCATTTATACCCTAAAATTGGGC
61 TATACA-CAAAATTTGACAGCATATATATACAAAATTGGACAGCATTTATACACTAAAATTGGGC
12541912 AGCATATATATACCAA
125 AGCATATATATACCAA
* *
12541928 TTTGGACAGCACTTATACA-CAAAATTTGACAGCATGTATATACAAAATTGAACAGCACTTATAC
1 TTTGGACAGCACTTATACACCAAAATTTGACAGCATGTATATACAAAATTGGACAGCATTTATAC
*
12541992 ACAAAATTTGACAGCATGTATATACAAAATTGGACAGCATTTATACACTAAAATTGGGCAGCATA
66 ACAAAATTTGACAGCATATATATACAAAATTGGACAGCATTTATACACTAAAATTGGGCAGCATA
12542057 TATATACCAA
131 TATATACCAA
12542067 TTTGGACAGCACTTATACA-CAAAATTTGACAGCATGTATATACAAAATTGGACAGCATTTATAC
1 TTTGGACAGCACTTATACACCAAAATTTGACAGCATGTATATACAAAATTGGACAGCATTTATAC
* * * * * *
12542131 ACTAAAATTGGGCAGCATATATATACCAATTTGGACAGCACTTATACAC-AAAATTTGGCAGCAT
66 AC-AAAATTTGACAGCATATATATACAAAATTGGACAGCATTTATACACTAAAATTGGGCAGCAT
*
12542195 ATATATACAAA
130 ATATATACCAA
* * * * *
12542206 ATTAGACAGCATTTATACACCAAAATTGGGCAGCAT
1 TTTGGACAGCACTTATACACCAAAATTTGACAGCAT
12542242 ATATTCGATT
Statistics
Matches: 288, Mismatches: 23, Indels: 11
0.89 0.07 0.03
Matches are distributed among these distances:
139 175 0.61
140 82 0.28
144 9 0.03
145 22 0.08
ACGTcount: A:0.41, C:0.17, G:0.14, T:0.28
Consensus pattern (140 bp):
TTTGGACAGCACTTATACACCAAAATTTGACAGCATGTATATACAAAATTGGACAGCATTTATAC
ACAAAATTTGACAGCATATATATACAAAATTGGACAGCATTTATACACTAAAATTGGGCAGCATA
TATATACCAA
Found at i:12543204 original size:43 final size:43
Alignment explanation
Indices: 12543139--12543250 Score: 140
Period size: 43 Copynumber: 2.6 Consensus size: 43
12543129 CGTACAATGA
* *
12543139 CAACGTCCCAGACGTGGTCTTACATGTAATCACATA-TAGATGC
1 CAACGTCCCAGACGTGGTCTTACACGTAAACACA-AGTAGATGC
*
12543182 C-ACTGTCCCAGACAG-GGTCTTACACGTAAACACAAGTCGATGC
1 CAAC-GTCCCAGAC-GTGGTCTTACACGTAAACACAAGTAGATGC
*
12543225 CAACATCCCAGACGTGGTCTTACACG
1 CAACGTCCCAGACGTGGTCTTACACG
12543251 ATAGTACATA
Statistics
Matches: 60, Mismatches: 4, Indels: 10
0.81 0.05 0.14
Matches are distributed among these distances:
42 4 0.07
43 53 0.88
44 3 0.05
ACGTcount: A:0.29, C:0.29, G:0.20, T:0.21
Consensus pattern (43 bp):
CAACGTCCCAGACGTGGTCTTACACGTAAACACAAGTAGATGC
Found at i:12544477 original size:10 final size:9
Alignment explanation
Indices: 12544457--12544481 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
12544447 TAAATATATA
12544457 TTTTTTATT
1 TTTTTTATT
12544466 TTTTTTATT
1 TTTTTTATT
12544475 TTTTTTA
1 TTTTTTA
12544482 GACTCAGATT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.12, C:0.00, G:0.00, T:0.88
Consensus pattern (9 bp):
TTTTTTATT
Found at i:12544978 original size:50 final size:50
Alignment explanation
Indices: 12544812--12545004 Score: 181
Period size: 50 Copynumber: 3.7 Consensus size: 50
12544802 GGGAATGAGA
* *
12544812 TCCCATGTAAGACCATATCTCGGACATGGCATTGGCATCATTGAGATTATGAGAGG
1 TCCCATGTAAGACCATATCTGGGACATGGCATTGGCATC-----GA-TATGAGAAG
* * * * * *
12544868 TCCCATGTAAGACAATGTCTGGGACATGGCGTTGGCACCTAGATGA-AAGG
1 TCCCATGTAAGACCATATCTGGGACATGGCATTGGCATCGATATGAGAA-G
** * * * *
12544918 TCCCCCGTAAGACCATGTTTGGGACATGGCATGGGCATCGATATGAGAAC
1 TCCCATGTAAGACCATATCTGGGACATGGCATTGGCATCGATATGAGAAG
*
12544968 TCCCATGTAAGACCATATCTGGGATATGGCATTGGCA
1 TCCCATGTAAGACCATATCTGGGACATGGCATTGGCA
12545005 GTAAAGAAAA
Statistics
Matches: 111, Mismatches: 24, Indels: 10
0.77 0.17 0.07
Matches are distributed among these distances:
49 1 0.01
50 73 0.66
51 3 0.03
56 34 0.31
ACGTcount: A:0.27, C:0.21, G:0.27, T:0.24
Consensus pattern (50 bp):
TCCCATGTAAGACCATATCTGGGACATGGCATTGGCATCGATATGAGAAG
Found at i:12547108 original size:17 final size:17
Alignment explanation
Indices: 12547088--12547120 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
12547078 ACAAATTTCT
12547088 AAAAAGTTC-ATAATTAA
1 AAAAAG-TCAATAATTAA
12547105 AAAAAGTCAATAATTA
1 AAAAAGTCAATAATTA
12547121 TACTGTCATG
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 2 0.13
17 13 0.87
ACGTcount: A:0.61, C:0.06, G:0.06, T:0.27
Consensus pattern (17 bp):
AAAAAGTCAATAATTAA
Found at i:12550558 original size:13 final size:11
Alignment explanation
Indices: 12550522--12550552 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
12550512 CTGCTCGTAT
12550522 TAATTTTTATA
1 TAATTTTTATA
*
12550533 TTATTTTTATA
1 TAATTTTTATA
12550544 TAATTTTTA
1 TAATTTTTA
12550553 AATATATAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (11 bp):
TAATTTTTATA
Found at i:12550706 original size:30 final size:30
Alignment explanation
Indices: 12550672--12550734 Score: 108
Period size: 30 Copynumber: 2.1 Consensus size: 30
12550662 ACTTAATAAG
12550672 CAAATACCTCTAAAATAATAACAAAATTAA
1 CAAATACCTCTAAAATAATAACAAAATTAA
* *
12550702 CAAATGCCTTTAAAATAATAACAAAATTAA
1 CAAATACCTCTAAAATAATAACAAAATTAA
12550732 CAA
1 CAA
12550735 TAAAATAAGT
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:0.59, C:0.16, G:0.02, T:0.24
Consensus pattern (30 bp):
CAAATACCTCTAAAATAATAACAAAATTAA
Found at i:12551765 original size:66 final size:65
Alignment explanation
Indices: 12551648--12551784 Score: 170
Period size: 66 Copynumber: 2.1 Consensus size: 65
12551638 TGAGCAAATT
* * * *
12551648 GCTA-AACTTAAAGCGGAGGTAGCATCGAGAGAAGTAGAGGCTCAAGGAAAATATGAAGAACTCC
1 GCTACAACTTAAAGCGGAGGCAGCAGCGAGAGAAGCAGAGGC-CAAGAAAAATATGAAGAACTCC
12551712 A
65 A
* *
12551713 GCTACAACTTAAAGCGGAGGCAGCAGCGAGGGAAGCAGAGG-CAAGCAAAAAATATGATGAACTC
1 GCTACAACTTAAAGCGGAGGCAGCAGCGAGAGAAGCAGAGGCCAAG--AAAAATATGAAGAACTC
12551777 CA
64 CA
*
12551779 ACTACA
1 GCTACA
12551785 GCTTCAAAAT
Statistics
Matches: 62, Mismatches: 7, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
64 4 0.06
65 4 0.06
66 54 0.87
ACGTcount: A:0.42, C:0.18, G:0.27, T:0.13
Consensus pattern (65 bp):
GCTACAACTTAAAGCGGAGGCAGCAGCGAGAGAAGCAGAGGCCAAGAAAAATATGAAGAACTCCA
Found at i:12552255 original size:43 final size:43
Alignment explanation
Indices: 12552129--12552264 Score: 130
Period size: 43 Copynumber: 3.2 Consensus size: 43
12552119 AGAACATGAC
* * **
12552129 CTTTAGCGGCGTTTTTAGGGAAAGCACCACTAATTGTCATGTT
1 CTTTAGCGGCGTTTGTAGGGAAAGCGCCACTAAAAGTCATGTT
** * * * *
12552172 CTTTAAAGGCGTTTGTGGGGAAATCGCCATTAAAAATCATGTT
1 CTTTAGCGGCGTTTGTAGGGAAAGCGCCACTAAAAGTCATGTT
* * *
12552215 CTTTAGCGGCGTTTGT-GGGATAAGCGCCGCTAAAGGTCATGCT
1 CTTTAGCGGCGTTTGTAGGGA-AAGCGCCACTAAAAGTCATGTT
*
12552258 CTATAGC
1 CTTTAGC
12552265 AGCATTTTTC
Statistics
Matches: 73, Mismatches: 19, Indels: 2
0.78 0.20 0.02
Matches are distributed among these distances:
42 4 0.05
43 69 0.95
ACGTcount: A:0.24, C:0.18, G:0.26, T:0.32
Consensus pattern (43 bp):
CTTTAGCGGCGTTTGTAGGGAAAGCGCCACTAAAAGTCATGTT
Found at i:12558632 original size:20 final size:20
Alignment explanation
Indices: 12558609--12558646 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
12558599 TGTTATTGGA
* *
12558609 TTATGAAATGTGATATTAAG
1 TTATGAAAAGTAATATTAAG
12558629 TTATGAAAAGTAATATTA
1 TTATGAAAAGTAATATTA
12558647 TGGACTTGTA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.45, C:0.00, G:0.16, T:0.39
Consensus pattern (20 bp):
TTATGAAAAGTAATATTAAG
Found at i:12558810 original size:75 final size:76
Alignment explanation
Indices: 12558684--12558961 Score: 260
Period size: 75 Copynumber: 3.7 Consensus size: 76
12558674 TCGATTCATT
* ** *
12558684 CGACTAGC-ACTGGGTGCAACTTCTGTCAGTTTATC-TGACTAGTGCTAGGCACATTATTATAAT
1 CGACTAGCGA-TGGGCGCAACTTCTACCAGTTTATCTTGACTAGTGCTGGGCACATTATTATAAT
* * *
12558747 TGTTGTTATATC
65 CGTCGGTATATC
* * * *
12558759 CGACTGGCGATGGGCGCATCTTTTGCCAGTTTATCTTG-CTAGTGCTGGGCACATTATTATAATC
1 CGACTAGCGATGGGCGCAACTTCTACCAGTTTATCTTGACTAGTGCTGGGCACATTATTATAATC
*
12558823 ATCGGTATATC
66 GTCGGTATATC
* * * * * * *
12558834 CGACTAGTGCTGGGTGCAACTTCTATCAGTTTAT-TTGACTAATGTTGGGCACATAATTATAATC
1 CGACTAGCGATGGGCGCAACTTCTACCAGTTTATCTTGACTAGTGCTGGGCACATTATTATAATC
12558898 GTCGGTATATC
66 GTCGGTATATC
* * * * *** * *
12558909 CGACTAGTGCTGGGCCCAACCTCTGTTAGTTTGTC-TGACTAGTGCTCGGCACA
1 CGACTAGCGATGGGCGCAACTTCTACCAGTTTATCTTGACTAGTGCTGGGCACA
12558962 CTCTCTATAT
Statistics
Matches: 168, Mismatches: 31, Indels: 8
0.81 0.15 0.04
Matches are distributed among these distances:
74 3 0.02
75 162 0.96
76 3 0.02
ACGTcount: A:0.22, C:0.21, G:0.23, T:0.35
Consensus pattern (76 bp):
CGACTAGCGATGGGCGCAACTTCTACCAGTTTATCTTGACTAGTGCTGGGCACATTATTATAATC
GTCGGTATATC
Found at i:12558960 original size:150 final size:150
Alignment explanation
Indices: 12558684--12558961 Score: 342
Period size: 150 Copynumber: 1.9 Consensus size: 150
12558674 TCGATTCATT
* * * *
12558684 CGACTAGCACTGGGTGCAACTTCTGTCAGTTTATCTGACTAGTGCTAGGCACATTATTATAATTG
1 CGACTAGCACTGGGTGCAACTTCTATCAGTTTATCTGACTAATGCTAGGCACATAATTATAATCG
* * * * * * * *
12558749 TTGTTATATCCGACTGGCGATGGGCGCATCTTTTGCCAGTTTATCTTGCTAGTGCTGGGCACATT
66 TCGGTATATCCGACTAGCGATGGGCCCAACCTCTGCCAGTTTATCTTGCTAGTGCTCGGCACATT
12558814 ATTATAATCATCGGTATATC
131 ATTATAATCATCGGTATATC
** * * *
12558834 CGACTAGTGCTGGGTGCAACTTCTATCAGTTTATTTGACTAATGTTGGGCACATAATTATAATCG
1 CGACTAGCACTGGGTGCAACTTCTATCAGTTTATCTGACTAATGCTAGGCACATAATTATAATCG
* * ** *
12558899 TCGGTATATCCGACTAGTGCTGGGCCCAACCTCTGTTAGTTTGTC-TGACTAGTGCTCGGCACA
66 TCGGTATATCCGACTAGCGATGGGCCCAACCTCTGCCAGTTTATCTTG-CTAGTGCTCGGCACA
12558962 CTCTCTATAT
Statistics
Matches: 105, Mismatches: 22, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
149 2 0.02
150 103 0.98
ACGTcount: A:0.22, C:0.21, G:0.23, T:0.35
Consensus pattern (150 bp):
CGACTAGCACTGGGTGCAACTTCTATCAGTTTATCTGACTAATGCTAGGCACATAATTATAATCG
TCGGTATATCCGACTAGCGATGGGCCCAACCTCTGCCAGTTTATCTTGCTAGTGCTCGGCACATT
ATTATAATCATCGGTATATC
Found at i:12561727 original size:20 final size:20
Alignment explanation
Indices: 12561702--12561740 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
12561692 CTAACCATCA
12561702 ACCACGCATG-CCTCCGTACC
1 ACCACG-ATGACCTCCGTACC
*
12561722 ACCACGTTGACCTCCGTAC
1 ACCACGATGACCTCCGTAC
12561741 GGCCTCCGTA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 2 0.12
20 15 0.88
ACGTcount: A:0.21, C:0.46, G:0.15, T:0.18
Consensus pattern (20 bp):
ACCACGATGACCTCCGTACC
Found at i:12562765 original size:18 final size:17
Alignment explanation
Indices: 12562742--12562777 Score: 63
Period size: 18 Copynumber: 2.1 Consensus size: 17
12562732 TTTTACTTTA
12562742 TTTATATTTTATGTTTTT
1 TTTATATTTTAT-TTTTT
12562760 TTTATATTTTATTTTTT
1 TTTATATTTTATTTTTT
12562777 T
1 T
12562778 GGATAAAACT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 6 0.33
18 12 0.67
ACGTcount: A:0.17, C:0.00, G:0.03, T:0.81
Consensus pattern (17 bp):
TTTATATTTTATTTTTT
Found at i:12562776 original size:16 final size:16
Alignment explanation
Indices: 12562732--12562777 Score: 56
Period size: 18 Copynumber: 2.8 Consensus size: 16
12562722 TTTGTTATCT
* *
12562732 TTTTACTTTATTTATA
1 TTTTATTTTTTTTATA
12562748 TTTTATGTTTTTTTTATA
1 TTTTA--TTTTTTTTATA
12562766 TTTTATTTTTTT
1 TTTTATTTTTTT
12562778 GGATAAAACT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
16 12 0.46
18 14 0.54
ACGTcount: A:0.17, C:0.02, G:0.02, T:0.78
Consensus pattern (16 bp):
TTTTATTTTTTTTATA
Found at i:12564351 original size:53 final size:54
Alignment explanation
Indices: 12564290--12564403 Score: 212
Period size: 53 Copynumber: 2.1 Consensus size: 54
12564280 GGTGTCATTA
*
12564290 GGTATGTTGATTCTGATTTTGCTGGAGACCTTAATAAAAGAAGATCTTTCACAT
1 GGTATGTTGATTCTGATTTTGCTGAAGACCTTAATAAAAGAAGATCTTTCACAT
12564344 GG-ATGTTGATTCTGATTTTGCTGAAGACCTTAATAAAAGAAGATCTTTCACAT
1 GGTATGTTGATTCTGATTTTGCTGAAGACCTTAATAAAAGAAGATCTTTCACAT
12564397 GGTATGT
1 GGTATGT
12564404 CTTTACTATT
Statistics
Matches: 58, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
53 52 0.90
54 6 0.10
ACGTcount: A:0.30, C:0.12, G:0.21, T:0.37
Consensus pattern (54 bp):
GGTATGTTGATTCTGATTTTGCTGAAGACCTTAATAAAAGAAGATCTTTCACAT
Found at i:12564873 original size:29 final size:29
Alignment explanation
Indices: 12564831--12564887 Score: 87
Period size: 29 Copynumber: 2.0 Consensus size: 29
12564821 GTGGAAGAGA
* *
12564831 TGAAGAATTTGTTCATTGAGAGTTCGTGG
1 TGAAGAACTTGTTCATTGAGAATTCGTGG
*
12564860 TGAAGAACTTGTTCGTTGAGAATTCGTG
1 TGAAGAACTTGTTCATTGAGAATTCGTG
12564888 TCAAGGTGGA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.25, C:0.09, G:0.30, T:0.37
Consensus pattern (29 bp):
TGAAGAACTTGTTCATTGAGAATTCGTGG
Found at i:12566127 original size:16 final size:16
Alignment explanation
Indices: 12566106--12566163 Score: 62
Period size: 16 Copynumber: 3.5 Consensus size: 16
12566096 CCCTTCAAGA
12566106 ATTTTATTAATAAATG
1 ATTTTATTAATAAATG
* ***
12566122 ATTTTATTTTATTTTTTG
1 ATTTTA--TTAATAAATG
12566140 ATTTTATTAATAAATG
1 ATTTTATTAATAAATG
12566156 ATTTTATT
1 ATTTTATT
12566164 TGTATGACAT
Statistics
Matches: 32, Mismatches: 8, Indels: 4
0.73 0.18 0.09
Matches are distributed among these distances:
16 20 0.62
18 12 0.38
ACGTcount: A:0.33, C:0.00, G:0.05, T:0.62
Consensus pattern (16 bp):
ATTTTATTAATAAATG
Found at i:12566535 original size:25 final size:23
Alignment explanation
Indices: 12566500--12566549 Score: 64
Period size: 25 Copynumber: 2.1 Consensus size: 23
12566490 AGATCGTTAA
* *
12566500 AAAAAATTTATATATTTTATTTT
1 AAAAAATTTATAAATTTAATTTT
12566523 AAAAAATCATTATAAATTTAATTTT
1 AAAAAAT--TTATAAATTTAATTTT
12566548 AA
1 AA
12566550 TAATTATATT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
23 7 0.30
25 16 0.70
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (23 bp):
AAAAAATTTATAAATTTAATTTT
Done.