Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr11
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: 61124829
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1263459 characters in sequence are not A, C, G, or T
File 159 of 205
Found at i:47532141 original size:21 final size:21
Alignment explanation
Indices: 47532117--47532158 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
47532107 TTTTTTTTAA
*
47532117 TTAAGTTGAGTAAAATGAAAT
1 TTAAGTTGAGTAAAATCAAAT
*
47532138 TTAAGTTGAGTAGAATCAAAT
1 TTAAGTTGAGTAAAATCAAAT
47532159 AAATTTGTTC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.45, C:0.02, G:0.19, T:0.33
Consensus pattern (21 bp):
TTAAGTTGAGTAAAATCAAAT
Found at i:47532418 original size:23 final size:23
Alignment explanation
Indices: 47532392--47532452 Score: 70
Period size: 23 Copynumber: 2.6 Consensus size: 23
47532382 TATATTAAAA
* *
47532392 ATAATTTTTTGAATATATGTTTT
1 ATAATTTTTTGAATAAATATTTT
47532415 ATAATTTTTTAGAA-AAATATTTT
1 ATAATTTTTT-GAATAAATATTTT
*
47532438 ATAAATATTTTGAAT
1 AT-AATTTTTTGAAT
47532453 TTTACAATAT
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
23 22 0.69
24 10 0.31
ACGTcount: A:0.39, C:0.00, G:0.07, T:0.54
Consensus pattern (23 bp):
ATAATTTTTTGAATAAATATTTT
Found at i:47532630 original size:23 final size:24
Alignment explanation
Indices: 47532584--47532632 Score: 64
Period size: 24 Copynumber: 2.1 Consensus size: 24
47532574 CAAACTCAAA
* *
47532584 AAAAAAACCGAATTACTTTGATTC
1 AAAAAAACCGAATAACTTTAATTC
*
47532608 AAAAGAACCGAATAAC-TTAATTC
1 AAAAAAACCGAATAACTTTAATTC
47532631 AA
1 AA
47532633 TTAACTCGAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
23 8 0.36
24 14 0.64
ACGTcount: A:0.51, C:0.16, G:0.08, T:0.24
Consensus pattern (24 bp):
AAAAAAACCGAATAACTTTAATTC
Found at i:47532894 original size:19 final size:18
Alignment explanation
Indices: 47532872--47532905 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
47532862 ACAGTTATTT
47532872 TTTTTTA-AATATCAAAC
1 TTTTTTATAATATCAAAC
47532889 TTTTTTATAATATCAAA
1 TTTTTTATAATATCAAA
47532906 TAACAAATGA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 7 0.44
18 9 0.56
ACGTcount: A:0.41, C:0.09, G:0.00, T:0.50
Consensus pattern (18 bp):
TTTTTTATAATATCAAAC
Found at i:47541899 original size:11 final size:11
Alignment explanation
Indices: 47541883--47541980 Score: 55
Period size: 11 Copynumber: 9.3 Consensus size: 11
47541873 TCAATTATTT
47541883 TCTCAATTTCC
1 TCTCAATTTCC
47541894 TCTCAATTTCC
1 TCTCAATTTCC
* * *
47541905 TCTTAAATTGC
1 TCTCAATTTCC
*
47541916 TCTCATTTTCC
1 TCTCAATTTCC
47541927 T-TCCAAATTT-C
1 TCT-C-AATTTCC
*
47541938 TCTCAA-ATCC
1 TCTCAATTTCC
* **
47541948 -AT--ATTTAA
1 TCTCAATTTCC
*
47541956 TCTCAATTTGC
1 TCTCAATTTCC
47541967 TCTCAATTTCC
1 TCTCAATTTCC
47541978 TCT
1 TCT
47541981 TAAATTTCTC
Statistics
Matches: 62, Mismatches: 17, Indels: 16
0.65 0.18 0.17
Matches are distributed among these distances:
7 1 0.02
8 1 0.02
9 3 0.05
10 4 0.06
11 48 0.77
12 5 0.08
ACGTcount: A:0.22, C:0.30, G:0.02, T:0.46
Consensus pattern (11 bp):
TCTCAATTTCC
Found at i:47543174 original size:39 final size:39
Alignment explanation
Indices: 47543120--47543196 Score: 154
Period size: 39 Copynumber: 2.0 Consensus size: 39
47543110 TAGCGTGAGA
47543120 CAAAAAGTAAGCTAAACGTACCGCACCGCACCCAATCGT
1 CAAAAAGTAAGCTAAACGTACCGCACCGCACCCAATCGT
47543159 CAAAAAGTAAGCTAAACGTACCGCACCGCACCCAATCG
1 CAAAAAGTAAGCTAAACGTACCGCACCGCACCCAATCG
47543197 CCCATCTAAA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 38 1.00
ACGTcount: A:0.39, C:0.34, G:0.16, T:0.12
Consensus pattern (39 bp):
CAAAAAGTAAGCTAAACGTACCGCACCGCACCCAATCGT
Found at i:47552998 original size:2 final size:2
Alignment explanation
Indices: 47552991--47553029 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
47552981 TGCAAACAGA
47552991 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
47553030 CTTACTGGAA
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:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:47554874 original size:68 final size:66
Alignment explanation
Indices: 47554814--47554946 Score: 149
Period size: 72 Copynumber: 1.9 Consensus size: 66
47554804 TATTAAATCT
*
47554814 TATTAAATTAATAGAATATTTATCTACAAGATAAATATTAAATTTAATTTAATATTAATATAATC
1 TATTAAATTAATAAAATATTT-T-T--AAGATAAATATTAAATTTAATTTAATATTAATATAA-C
*
47554879 ACTTTAA
61 ACTCT-A
* *
47554886 TATTAAATTAATAAAATATTTTTAAGATAAGTATTAAATTAAATATTAAATATTAAATATA
1 TATTAAATTAATAAAATATTTTTAAGATAAATATTAAATTTAAT-TT-AATATT-AATATA
47554947 TGAAAATAAT
Statistics
Matches: 55, Mismatches: 3, Indels: 7
0.85 0.05 0.11
Matches are distributed among these distances:
68 19 0.35
69 2 0.04
70 7 0.13
71 7 0.13
72 20 0.36
ACGTcount: A:0.51, C:0.03, G:0.03, T:0.43
Consensus pattern (66 bp):
TATTAAATTAATAAAATATTTTTAAGATAAATATTAAATTTAATTTAATATTAATATAACACTCT
A
Found at i:47556066 original size:9 final size:9
Alignment explanation
Indices: 47556048--47556096 Score: 62
Period size: 9 Copynumber: 5.4 Consensus size: 9
47556038 TTTGGTTAAA
47556048 AATTAACCG
1 AATTAACCG
*
47556057 AATTATCCG
1 AATTAACCG
47556066 AATTAACCG
1 AATTAACCG
* *
47556075 GATTACCCG
1 AATTAACCG
*
47556084 AATTAACCA
1 AATTAACCG
47556093 AATT
1 AATT
47556097 GAATCACTAC
Statistics
Matches: 33, Mismatches: 7, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
9 33 1.00
ACGTcount: A:0.41, C:0.22, G:0.10, T:0.27
Consensus pattern (9 bp):
AATTAACCG
Found at i:47556071 original size:18 final size:18
Alignment explanation
Indices: 47556048--47556096 Score: 71
Period size: 18 Copynumber: 2.7 Consensus size: 18
47556038 TTTGGTTAAA
*
47556048 AATTAACCGAATTATCCG
1 AATTAACCGAATTACCCG
*
47556066 AATTAACCGGATTACCCG
1 AATTAACCGAATTACCCG
*
47556084 AATTAACCAAATT
1 AATTAACCGAATT
47556097 GAATCACTAC
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.41, C:0.22, G:0.10, T:0.27
Consensus pattern (18 bp):
AATTAACCGAATTACCCG
Found at i:47556186 original size:6 final size:6
Alignment explanation
Indices: 47556136--47556170 Score: 70
Period size: 6 Copynumber: 5.8 Consensus size: 6
47556126 ACTTTTAGAC
47556136 TTTAGT TTTAGT TTTAGT TTTAGT TTTAGT TTTAG
1 TTTAGT TTTAGT TTTAGT TTTAGT TTTAGT TTTAG
47556171 AATTTTATTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.17, C:0.00, G:0.17, T:0.66
Consensus pattern (6 bp):
TTTAGT
Found at i:47556194 original size:20 final size:20
Alignment explanation
Indices: 47556136--47556183 Score: 73
Period size: 18 Copynumber: 2.5 Consensus size: 20
47556126 ACTTTTAGAC
47556136 TTTAGTTTTAGTTTTAG--T
1 TTTAGTTTTAGTTTTAGAAT
47556154 TTTAGTTTTAGTTTTAGAAT
1 TTTAGTTTTAGTTTTAGAAT
*
47556174 TTTATTTTTA
1 TTTAGTTTTA
47556184 TTTATTAAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
18 17 0.63
20 10 0.37
ACGTcount: A:0.21, C:0.00, G:0.12, T:0.67
Consensus pattern (20 bp):
TTTAGTTTTAGTTTTAGAAT
Found at i:47556585 original size:117 final size:118
Alignment explanation
Indices: 47556447--47556676 Score: 399
Period size: 118 Copynumber: 2.0 Consensus size: 118
47556437 ACCGAATTCA
* *
47556447 GTCGGTTAACCAAATTTTTTCGGTTTTACCCGAATTTTGCACA-CCCTACTTATGGCTGTAGATA
1 GTCGGTTAACCAAATTTTTTCGGTTTTACCCAAATTTTACACACCCCTACTTATGGCTGTAGATA
*
47556511 TTGAAGAATCATTTTATACATTTATGTTTTAATAAATAATATATTATTAATCG
66 TTGAAGAACCATTTTATACATTTATGTTTTAATAAATAATATATTATTAATCG
* * *
47556564 GTCGGTTAATCGAATTTTTTCGGTTTTACCCAAATTTTACACACCCCTACTTATGGTTGTAGATA
1 GTCGGTTAACCAAATTTTTTCGGTTTTACCCAAATTTTACACACCCCTACTTATGGCTGTAGATA
47556629 TTGAAGAACCATTTTATACATTTATGTTTTAATAAATAATATATTATT
66 TTGAAGAACCATTTTATACATTTATGTTTTAATAAATAATATATTATT
47556677 GGTTAAAAAG
Statistics
Matches: 106, Mismatches: 6, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
117 39 0.37
118 67 0.63
ACGTcount: A:0.31, C:0.14, G:0.12, T:0.43
Consensus pattern (118 bp):
GTCGGTTAACCAAATTTTTTCGGTTTTACCCAAATTTTACACACCCCTACTTATGGCTGTAGATA
TTGAAGAACCATTTTATACATTTATGTTTTAATAAATAATATATTATTAATCG
Found at i:47565274 original size:29 final size:28
Alignment explanation
Indices: 47565233--47565290 Score: 75
Period size: 29 Copynumber: 2.0 Consensus size: 28
47565223 CTTTTATAAA
47565233 AGATTAAGAGCTAAACTT-AGCTAAAAAAT
1 AGATTAAGAGCTAAA-TTGA-CTAAAAAAT
47565262 AGATTAA-AGGCTAAATTGACTAAAAAAT
1 AGATTAAGA-GCTAAATTGACTAAAAAAT
47565290 A
1 A
47565291 TGTAAACATT
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
28 13 0.48
29 14 0.52
ACGTcount: A:0.53, C:0.09, G:0.14, T:0.24
Consensus pattern (28 bp):
AGATTAAGAGCTAAATTGACTAAAAAAT
Found at i:47568300 original size:24 final size:23
Alignment explanation
Indices: 47568273--47568338 Score: 57
Period size: 21 Copynumber: 2.9 Consensus size: 23
47568263 AATTTAAAGG
47568273 ATGTATAATGCTTTCCTTTAAATA
1 ATGTATAATGC-TTCCTTTAAATA
* *
47568297 ATGTA-ACA-GC-TCCTTTGAATG
1 ATGTATA-ATGCTTCCTTTAAATA
*
47568318 ATGTATAATGCTCTCATTTAA
1 ATGTATAATGCT-TCCTTTAA
47568339 TTGATGTAAC
Statistics
Matches: 33, Mismatches: 4, Indels: 10
0.70 0.09 0.21
Matches are distributed among these distances:
21 15 0.45
22 3 0.09
23 3 0.09
24 12 0.36
ACGTcount: A:0.32, C:0.15, G:0.12, T:0.41
Consensus pattern (23 bp):
ATGTATAATGCTTCCTTTAAATA
Found at i:47568489 original size:21 final size:20
Alignment explanation
Indices: 47568453--47568494 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 20
47568443 ACAATCAAAG
47568453 CACATTAAAAACATATTAAA
1 CACATTAAAAACATATTAAA
*
47568473 CACATTAAACCACATATTAAA
1 CACATTAAA-AACATATTAAA
47568494 C
1 C
47568495 TTAATAAGCT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
20 9 0.45
21 11 0.55
ACGTcount: A:0.55, C:0.21, G:0.00, T:0.24
Consensus pattern (20 bp):
CACATTAAAAACATATTAAA
Found at i:47568675 original size:40 final size:40
Alignment explanation
Indices: 47568621--47568706 Score: 136
Period size: 40 Copynumber: 2.1 Consensus size: 40
47568611 GTTTAATGAA
*
47568621 AATAAAGTCAAACAACTCAATTATTAACTAAGATGAGTTT
1 AATAAAGTCAAACAACTCAATTATTAACTAAAATGAGTTT
* *
47568661 AATATAGTCCAACAACTCAATTATTAACTAAAATGAGTTT
1 AATAAAGTCAAACAACTCAATTATTAACTAAAATGAGTTT
*
47568701 ATTAAA
1 AATAAA
47568707 ATTAAAGTTC
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
40 41 1.00
ACGTcount: A:0.48, C:0.13, G:0.08, T:0.31
Consensus pattern (40 bp):
AATAAAGTCAAACAACTCAATTATTAACTAAAATGAGTTT
Found at i:47571194 original size:33 final size:33
Alignment explanation
Indices: 47571156--47571218 Score: 108
Period size: 33 Copynumber: 1.9 Consensus size: 33
47571146 ATATATTTTG
*
47571156 TTTAACTTGACTTGCAAGCAATCTTTTAGATTT
1 TTTAACTTGACATGCAAGCAATCTTTTAGATTT
*
47571189 TTTAACTTGACATGCAAGTAATCTTTTAGA
1 TTTAACTTGACATGCAAGCAATCTTTTAGA
47571219 ATTCGGGTCA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 28 1.00
ACGTcount: A:0.30, C:0.14, G:0.13, T:0.43
Consensus pattern (33 bp):
TTTAACTTGACATGCAAGCAATCTTTTAGATTT
Found at i:47576240 original size:211 final size:211
Alignment explanation
Indices: 47575876--47576933 Score: 2021
Period size: 211 Copynumber: 5.0 Consensus size: 211
47575866 GAAACCCTAG
47575876 TAGTGTTGCCCCCCTTAATTGTAACCTAGGTATAAATGTTAAAATTTTCTACTCAGCCTCTTCTT
1 TAGTGTTGCCCCCCTTAATTGTAACCTAGGTATAAATGTTAAAATTTTCTACTCAGCCTCTTCTT
47575941 TTCTCATTTTCTTTTCCTATTGTTGTCCCCCTCCATTCTTCCTCTCCGTTTCCTTCAATTTTCTC
66 TTCTCATTTTCTTTTCCTATTGTTGTCCCCCTCCATTCTTCCTCTCCGTTTCCTTCAATTTTCTC
47576006 TATTTTCTTCCCCTCTATACTGCCCATAATACCCCAAAACTCTACTATTGTGCCACCTCATTGAT
131 TATTTTCTTCCCCTCTATACTGCCCATAATACCCCAAAACTCTACTATTGTGCCACCTCATTGAT
47576071 CATCAACTCCTATTGT
196 CATCAACTCCTATTGT
47576087 TAGTGTTGCCCCCCTTAATTGTAACCTAGGTATAAATGTTAAAATTTTCTACTCAGCCTCTTCTT
1 TAGTGTTGCCCCCCTTAATTGTAACCTAGGTATAAATGTTAAAATTTTCTACTCAGCCTCTTCTT
47576152 TTCTCATTTTCTTTTCCTATTGTTGTCCCCCTCCATTCTTCCTCTCCGTTTCCTTCAATTTTCTC
66 TTCTCATTTTCTTTTCCTATTGTTGTCCCCCTCCATTCTTCCTCTCCGTTTCCTTCAATTTTCTC
47576217 TATTTTCTTCCCCTCTATACTGCCCATAATACCCCAAAACTCTACTATTGTGCCACCTCATTGAT
131 TATTTTCTTCCCCTCTATACTGCCCATAATACCCCAAAACTCTACTATTGTGCCACCTCATTGAT
47576282 CATCAACTCCTATTGT
196 CATCAACTCCTATTGT
47576298 TAGTGTTGCCCCCCTTAATTGTAACCTAGGTATAAATGTTAAAATTTTCTACTCAGCCTCTTCTT
1 TAGTGTTGCCCCCCTTAATTGTAACCTAGGTATAAATGTTAAAATTTTCTACTCAGCCTCTTCTT
47576363 TTCTCATTTTCTTTTCCTATTGTTGTCCCCCTCCATTCTTCCTCTCCGTTTCCTTCAATTTTCTC
66 TTCTCATTTTCTTTTCCTATTGTTGTCCCCCTCCATTCTTCCTCTCCGTTTCCTTCAATTTTCTC
47576428 TATTTTCTTCCCCTCTATACTGCCCATAATACCCCAAAACTCTACTATTGTGCCACCTCATTGAT
131 TATTTTCTTCCCCTCTATACTGCCCATAATACCCCAAAACTCTACTATTGTGCCACCTCATTGAT
47576493 CATCAACTCCTATTGT
196 CATCAACTCCTATTGT
47576509 TAGTGTTGCCCCCCTTAATTGTAACCTAGGTATAAATGTTAAAATTTTCTACTCAGCCTCTTCTT
1 TAGTGTTGCCCCCCTTAATTGTAACCTAGGTATAAATGTTAAAATTTTCTACTCAGCCTCTTCTT
47576574 TTCTCATTTTCTTTTCCTATTGTTGTCCCCCTCCATTCTTCCTCTCCGTTTCCTTCAATTTTCTC
66 TTCTCATTTTCTTTTCCTATTGTTGTCCCCCTCCATTCTTCCTCTCCGTTTCCTTCAATTTTCTC
47576639 TATTTTCTTCCCCTCTATACTGCCCATAATACCCCAAAACTCTACTATTGTGCCACCTCATTGAT
131 TATTTTCTTCCCCTCTATACTGCCCATAATACCCCAAAACTCTACTATTGTGCCACCTCATTGAT
47576704 CATCAACTCCTATTGT
196 CATCAACTCCTATTGT
47576720 TAGTGTTGCCCCCCTTAATTGTAACCTAGGTATAAATGTTAAAATTTTCTACTCAGCCTCTTCTT
1 TAGTGTTGCCCCCCTTAATTGTAACCTAGGTATAAATGTTAAAATTTTCTACTCAGCCTCTTCTT
* *
47576785 TTCTCATTTTTTCTTTTCCTATTGTTGTCCCCCTCCCTTCTTCCTCTCTGTTT-CTCTCAATTTT
66 TTCTCA--TTTTCTTTTCCTATTGTTGTCCCCCTCCATTCTTCCTCTCCGTTTCCT-TCAATTTT
*
47576849 CTCTATTTTCTTCCCCTCTATACTGCCCATAATACCCCAAAACTCTACTATTAG-GCCACATCAT
128 CTCTATTTTCTTCCCCTCTATACTGCCCATAATACCCCAAAACTCTACTATT-GTGCCACCTCAT
**
47576913 TGATCATCAACTTATATTGT
192 TGATCATCAACTCCTATTGT
47576933 T
1 T
47576934 TCCTATTTTA
Statistics
Matches: 838, Mismatches: 5, Indels: 6
0.99 0.01 0.01
Matches are distributed among these distances:
211 704 0.84
212 2 0.00
213 131 0.16
214 1 0.00
ACGTcount: A:0.20, C:0.30, G:0.08, T:0.42
Consensus pattern (211 bp):
TAGTGTTGCCCCCCTTAATTGTAACCTAGGTATAAATGTTAAAATTTTCTACTCAGCCTCTTCTT
TTCTCATTTTCTTTTCCTATTGTTGTCCCCCTCCATTCTTCCTCTCCGTTTCCTTCAATTTTCTC
TATTTTCTTCCCCTCTATACTGCCCATAATACCCCAAAACTCTACTATTGTGCCACCTCATTGAT
CATCAACTCCTATTGT
Found at i:47577209 original size:233 final size:233
Alignment explanation
Indices: 47576802--47577266 Score: 912
Period size: 233 Copynumber: 2.0 Consensus size: 233
47576792 TTTTTCTTTT
* *
47576802 CCTATTGTTGTCCCCCTCCCTTCTTCCTCTCTGTTTCTCTCAATTTTCTCTATTTTCTTCCCCTC
1 CCTATTGTTGTCCCCCTCCCTTATTCCTCTCTATTTCTCTCAATTTTCTCTATTTTCTTCCCCTC
47576867 TATACTGCCCATAATACCCCAAAACTCTACTATTAGGCCACATCATTGATCATCAACTTATATTG
66 TATACTGCCCATAATACCCCAAAACTCTACTATTAGGCCACATCATTGATCATCAACTTATATTG
47576932 TTTCCTATTTTATTTTCTTCTCATCTCATCTTTTACCCTTATAGCCAAATTTTTGCTGTTATTTT
131 TTTCCTATTTTATTTTCTTCTCATCTCATCTTTTACCCTTATAGCCAAATTTTTGCTGTTATTTT
47576997 TTTTGTCATTGCTGTTGCCCTTTTGTTTCACTTCTTCC
196 TTTTGTCATTGCTGTTGCCCTTTTGTTTCACTTCTTCC
47577035 CCTATTGTTGTCCCCCTCCCTTATTCCTCTCTATTTCTCTCAATTTTCTCTATTTTCTTCCCCTC
1 CCTATTGTTGTCCCCCTCCCTTATTCCTCTCTATTTCTCTCAATTTTCTCTATTTTCTTCCCCTC
47577100 TATACTGCCCATAATACCCCAAAACTCTACTATTAGGCCACATCATTGATCATCAACTTATATTG
66 TATACTGCCCATAATACCCCAAAACTCTACTATTAGGCCACATCATTGATCATCAACTTATATTG
47577165 TTTCCTATTTTATTTTCTTCTCATCTCATCTTTTACCCTTATAGCCAAATTTTTGCTGTTATTTT
131 TTTCCTATTTTATTTTCTTCTCATCTCATCTTTTACCCTTATAGCCAAATTTTTGCTGTTATTTT
47577230 TTTTGTCATTGCTGTTGCCCTTTTGTTTCACTTCTTC
196 TTTTGTCATTGCTGTTGCCCTTTTGTTTCACTTCTTC
47577267 TACTCTTTGT
Statistics
Matches: 230, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
233 230 1.00
ACGTcount: A:0.17, C:0.29, G:0.07, T:0.47
Consensus pattern (233 bp):
CCTATTGTTGTCCCCCTCCCTTATTCCTCTCTATTTCTCTCAATTTTCTCTATTTTCTTCCCCTC
TATACTGCCCATAATACCCCAAAACTCTACTATTAGGCCACATCATTGATCATCAACTTATATTG
TTTCCTATTTTATTTTCTTCTCATCTCATCTTTTACCCTTATAGCCAAATTTTTGCTGTTATTTT
TTTTGTCATTGCTGTTGCCCTTTTGTTTCACTTCTTCC
Found at i:47579812 original size:21 final size:21
Alignment explanation
Indices: 47579788--47579933 Score: 157
Period size: 21 Copynumber: 7.0 Consensus size: 21
47579778 GTACATCGTT
*
47579788 AACAGAAGCTTGTAAGAGCTG
1 AACAGAAGCTCGTAAGAGCTG
*
47579809 AACAAAAGCTCGTAAGAGCTG
1 AACAGAAGCTCGTAAGAGCTG
* ** * *
47579830 AACAGAAACTCACAAGAGTTA
1 AACAGAAGCTCGTAAGAGCTG
*
47579851 AATAGAAGCTCGTAAGAGCTG
1 AACAGAAGCTCGTAAGAGCTG
* * * *
47579872 AACGGAAACTCATAAGAGTTG
1 AACAGAAGCTCGTAAGAGCTG
*
47579893 AACAGAAGCTCGTAAGAGCTA
1 AACAGAAGCTCGTAAGAGCTG
**
47579914 AACAGAAGCTCACAAGAGCT
1 AACAGAAGCTCGTAAGAGCT
47579934 AAAGAGAAAG
Statistics
Matches: 99, Mismatches: 26, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
21 99 1.00
ACGTcount: A:0.43, C:0.18, G:0.23, T:0.16
Consensus pattern (21 bp):
AACAGAAGCTCGTAAGAGCTG
Found at i:47579847 original size:42 final size:42
Alignment explanation
Indices: 47579801--47579933 Score: 185
Period size: 42 Copynumber: 3.2 Consensus size: 42
47579791 AGAAGCTTGT
*
47579801 AAGAGCTGAACAAAAGCTCGTAAGAGCTGAACAGAAACTCAC
1 AAGAGCTGAACAGAAGCTCGTAAGAGCTGAACAGAAACTCAC
* * * * *
47579843 AAGAGTTAAATAGAAGCTCGTAAGAGCTGAACGGAAACTCAT
1 AAGAGCTGAACAGAAGCTCGTAAGAGCTGAACAGAAACTCAC
* * *
47579885 AAGAGTTGAACAGAAGCTCGTAAGAGCTAAACAGAAGCTCAC
1 AAGAGCTGAACAGAAGCTCGTAAGAGCTGAACAGAAACTCAC
47579927 AAGAGCT
1 AAGAGCT
47579934 AAAGAGAAAG
Statistics
Matches: 78, Mismatches: 13, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
42 78 1.00
ACGTcount: A:0.44, C:0.18, G:0.23, T:0.15
Consensus pattern (42 bp):
AAGAGCTGAACAGAAGCTCGTAAGAGCTGAACAGAAACTCAC
Found at i:47579867 original size:63 final size:63
Alignment explanation
Indices: 47579788--47579933 Score: 177
Period size: 63 Copynumber: 2.3 Consensus size: 63
47579778 GTACATCGTT
* * *
47579788 AACAGAAGCTTGTAAGAGCTGAAC-AAAAGCTCGTAAGAGCTGAACAGAAACTCACAAGAGTTA
1 AACAGAAGCTCGTAAGAGCTGAACGAAAA-CTCATAAGAGCTGAACAGAAACTCACAAGAGCTA
* * * * **
47579851 AATAGAAGCTCGTAAGAGCTGAACGGAAACTCATAAGAGTTGAACAGAAGCTCGTAAGAGCTA
1 AACAGAAGCTCGTAAGAGCTGAACGAAAACTCATAAGAGCTGAACAGAAACTCACAAGAGCTA
**
47579914 AACAGAAGCTCACAAGAGCT
1 AACAGAAGCTCGTAAGAGCT
47579934 AAAGAGAAAG
Statistics
Matches: 70, Mismatches: 12, Indels: 2
0.83 0.14 0.02
Matches are distributed among these distances:
63 67 0.96
64 3 0.04
ACGTcount: A:0.43, C:0.18, G:0.23, T:0.16
Consensus pattern (63 bp):
AACAGAAGCTCGTAAGAGCTGAACGAAAACTCATAAGAGCTGAACAGAAACTCACAAGAGCTA
Found at i:47584497 original size:31 final size:31
Alignment explanation
Indices: 47584462--47584558 Score: 93
Period size: 31 Copynumber: 3.4 Consensus size: 31
47584452 AATTTACCCT
47584462 ATATTTAATATATATAATGATTGTATTAAAA
1 ATATTTAATATATATAATGATTGTATTAAAA
* **
47584493 ATATTT--TATAT-TCAT-A----ATTAACCT
1 ATATTTAATATATATAATGATTGTATTAA-AA
47584517 ATATTTAATATATATAATGATTGTATTAAAA
1 ATATTTAATATATATAATGATTGTATTAAAA
*
47584548 ATATTTTATAT
1 ATATTTAATAT
47584559 TCATAATTAA
Statistics
Matches: 50, Mismatches: 7, Indels: 18
0.67 0.09 0.24
Matches are distributed among these distances:
23 5 0.10
24 6 0.12
26 5 0.10
27 4 0.08
28 4 0.08
29 5 0.10
31 16 0.32
32 5 0.10
ACGTcount: A:0.44, C:0.03, G:0.04, T:0.48
Consensus pattern (31 bp):
ATATTTAATATATATAATGATTGTATTAAAA
Found at i:47584524 original size:55 final size:55
Alignment explanation
Indices: 47584450--47584568 Score: 220
Period size: 55 Copynumber: 2.1 Consensus size: 55
47584440 TAACATTTTA
*
47584450 ATAATTTACCCTATATTTAATATATATAATGATTGTATTAAAAATATTTTATATTC
1 ATAA-TTAACCTATATTTAATATATATAATGATTGTATTAAAAATATTTTATATTC
47584506 ATAATTAACCTATATTTAATATATATAATGATTGTATTAAAAATATTTTATATTC
1 ATAATTAACCTATATTTAATATATATAATGATTGTATTAAAAATATTTTATATTC
47584561 ATAATTAA
1 ATAATTAA
47584569 TCTTTTTTTT
Statistics
Matches: 62, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
55 58 0.94
56 4 0.06
ACGTcount: A:0.44, C:0.06, G:0.03, T:0.47
Consensus pattern (55 bp):
ATAATTAACCTATATTTAATATATATAATGATTGTATTAAAAATATTTTATATTC
Found at i:47588231 original size:14 final size:15
Alignment explanation
Indices: 47588207--47588235 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
47588197 ACAGATATGG
47588207 CTTTCCAGCAATTTT
1 CTTTCCAGCAATTTT
47588222 CTTT-CAGCAATTTT
1 CTTTCCAGCAATTTT
47588236 GGCATATTAC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 10 0.71
15 4 0.29
ACGTcount: A:0.21, C:0.24, G:0.07, T:0.48
Consensus pattern (15 bp):
CTTTCCAGCAATTTT
Found at i:47589283 original size:35 final size:35
Alignment explanation
Indices: 47589237--47589306 Score: 140
Period size: 35 Copynumber: 2.0 Consensus size: 35
47589227 GAATCGGCCT
47589237 CTGAAGCCGTCGTCGTCGTCGGCCCTTCTCCGTCG
1 CTGAAGCCGTCGTCGTCGTCGGCCCTTCTCCGTCG
47589272 CTGAAGCCGTCGTCGTCGTCGGCCCTTCTCCGTCG
1 CTGAAGCCGTCGTCGTCGTCGGCCCTTCTCCGTCG
47589307 TCGGACGCGA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.06, C:0.40, G:0.29, T:0.26
Consensus pattern (35 bp):
CTGAAGCCGTCGTCGTCGTCGGCCCTTCTCCGTCG
Found at i:47589307 original size:17 final size:17
Alignment explanation
Indices: 47589250--47589310 Score: 56
Period size: 17 Copynumber: 3.5 Consensus size: 17
47589240 AAGCCGTCGT
47589250 CGTCGTCGGCCCTTCTC
1 CGTCGTCGGCCCTTCTC
*
47589267 CGTCG-CTGAAG-CCGTCGT-
1 CGTCGTC-G--GCCCTTC-TC
47589285 CGTCGTCGGCCCTTCTC
1 CGTCGTCGGCCCTTCTC
47589302 CGTCGTCGG
1 CGTCGTCGG
47589311 ACGCGAGTTT
Statistics
Matches: 35, Mismatches: 2, Indels: 14
0.69 0.04 0.27
Matches are distributed among these distances:
16 3 0.09
17 19 0.54
18 10 0.29
19 3 0.09
ACGTcount: A:0.03, C:0.41, G:0.30, T:0.26
Consensus pattern (17 bp):
CGTCGTCGGCCCTTCTC
Found at i:47589708 original size:128 final size:129
Alignment explanation
Indices: 47589479--47589737 Score: 502
Period size: 128 Copynumber: 2.0 Consensus size: 129
47589469 GCCTTGGAAC
47589479 CCTAGCACAGAAAGGAGAACCCCCATTTTTATTTTTTTTAGATTCTTTGCAAAAGAAAAATGAAA
1 CCTAGCACAGAAAGGAGAACCCCCATTTTTATTTTTTTTAGATTCTTTGCAAAAGAAAAATGAAA
*
47589544 CTGTAGGAGGCAGATTTTTTTTAAGCTTTTATTGATTAAAACGGCGCCGTTTGAGGGAGGGTGA
66 CTGCAGGAGGCAGATTTTTTTTAAGCTTTTATTGATTAAAACGGCGCCGTTTGAGGGAGGGTGA
47589608 CCTAGCACAGAAAGGAGAACCCCCATTTTTA-TTTTTTTAGATTCTTTGCAAAAGAAAAATGAAA
1 CCTAGCACAGAAAGGAGAACCCCCATTTTTATTTTTTTTAGATTCTTTGCAAAAGAAAAATGAAA
47589672 CTGCAGGAGGCAGATTTTTTTTAAGCTTTTATTGATTAAAACGGCGCCGTTTGAGGGAGGGTGA
66 CTGCAGGAGGCAGATTTTTTTTAAGCTTTTATTGATTAAAACGGCGCCGTTTGAGGGAGGGTGA
47589736 CC
1 CC
47589738 AGCCCATTAT
Statistics
Matches: 129, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
128 98 0.76
129 31 0.24
ACGTcount: A:0.31, C:0.15, G:0.22, T:0.32
Consensus pattern (129 bp):
CCTAGCACAGAAAGGAGAACCCCCATTTTTATTTTTTTTAGATTCTTTGCAAAAGAAAAATGAAA
CTGCAGGAGGCAGATTTTTTTTAAGCTTTTATTGATTAAAACGGCGCCGTTTGAGGGAGGGTGA
Found at i:47602288 original size:132 final size:132
Alignment explanation
Indices: 47602048--47602345 Score: 488
Period size: 132 Copynumber: 2.3 Consensus size: 132
47602038 AGGCGTAAAT
* *
47602048 AGGTCCTATCTTCCTATATTGGTAGGAAGTGGATCAAAGATGCAGATCTTGTCTTCCCATATTGG
1 AGGTCCTATCTTCCTATATTGGTAGGAAGTGGATCAAAGATACAGATCTTGTCTTCCCATACTGG
* *
47602113 TGGCGAAGTAGATCGAAGAAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATA
66 TGGCGAAGTAGATCGAAGAAAGCAGATCTTGTATTCATATATTGGCGTGAAGTAGATCGAAGATA
47602178 GC
131 GC
* * * *
47602180 AGGTCCTATCTTCCTGTATTGATAGAAAGTGGATCCAAGATACAGATCTTGTCTTCCCATACTGG
1 AGGTCCTATCTTCCTATATTGGTAGGAAGTGGATCAAAGATACAGATCTTGTCTTCCCATACTGG
* *
47602245 TGGTGAAGTAGATCGAAGAAAGCAGATCTTGTATTCATATATTGGTGTGAAGTAGATCGAAGATA
66 TGGCGAAGTAGATCGAAGAAAGCAGATCTTGTATTCATATATTGGCGTGAAGTAGATCGAAGATA
47602310 GC
131 GC
* *
47602312 AGATCCTGTCTTCCTATATTGGTAGGAAGTGGAT
1 AGGTCCTATCTTCCTATATTGGTAGGAAGTGGAT
47602346 TGAAAAATAG
Statistics
Matches: 151, Mismatches: 15, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
132 151 1.00
ACGTcount: A:0.29, C:0.15, G:0.26, T:0.31
Consensus pattern (132 bp):
AGGTCCTATCTTCCTATATTGGTAGGAAGTGGATCAAAGATACAGATCTTGTCTTCCCATACTGG
TGGCGAAGTAGATCGAAGAAAGCAGATCTTGTATTCATATATTGGCGTGAAGTAGATCGAAGATA
GC
Found at i:47602334 original size:44 final size:45
Alignment explanation
Indices: 47602056--47602341 Score: 307
Period size: 44 Copynumber: 6.5 Consensus size: 45
47602046 ATAGGTCCTA
* *
47602056 TCTTCCTATATTGGTAG-GAAGTGGATCAAAGAT-GCAGATCTTG
1 TCTTCCTATATTGGTAGTGAAGTAGATCGAAGATAGCAGATCTTG
* * * *
47602099 TCTTCCCATATTGGTGGCGAAGTAGATCGAAGAAAGCAGATCTTG
1 TCTTCCTATATTGGTAGTGAAGTAGATCGAAGATAGCAGATCTTG
* * * * * *
47602144 TCTTCATGTATTGG-CGTGAAGTAGATCGAAGATAGCAGGTCCTA
1 TCTTCCTATATTGGTAGTGAAGTAGATCGAAGATAGCAGATCTTG
* * * * *
47602188 TCTTCCTGTATTGATAG-AAAGTGGATCCAAGATA-CAGATCTTG
1 TCTTCCTATATTGGTAGTGAAGTAGATCGAAGATAGCAGATCTTG
* * * *
47602231 TCTTCCCATACTGGTGGTGAAGTAGATCGAAGAAAGCAGATCTTG
1 TCTTCCTATATTGGTAGTGAAGTAGATCGAAGATAGCAGATCTTG
* * *
47602276 TATTCATATATTGGT-GTGAAGTAGATCGAAGATAGCAGATCCTG
1 TCTTCCTATATTGGTAGTGAAGTAGATCGAAGATAGCAGATCTTG
47602320 TCTTCCTATATTGGTAG-GAAGT
1 TCTTCCTATATTGGTAGTGAAGT
47602342 GGATTGAAAA
Statistics
Matches: 197, Mismatches: 40, Indels: 11
0.79 0.16 0.04
Matches are distributed among these distances:
43 33 0.17
44 121 0.61
45 43 0.22
ACGTcount: A:0.29, C:0.15, G:0.25, T:0.31
Consensus pattern (45 bp):
TCTTCCTATATTGGTAGTGAAGTAGATCGAAGATAGCAGATCTTG
Found at i:47609978 original size:18 final size:18
Alignment explanation
Indices: 47609955--47609990 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
47609945 TAAAGAACCC
47609955 GAAGTTTCTTTAATTTAA
1 GAAGTTTCTTTAATTTAA
47609973 GAAGTTTCTTTAATTTAA
1 GAAGTTTCTTTAATTTAA
47609991 AGAATTCTCA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.33, C:0.06, G:0.11, T:0.50
Consensus pattern (18 bp):
GAAGTTTCTTTAATTTAA
Found at i:47611092 original size:9 final size:9
Alignment explanation
Indices: 47611078--47611106 Score: 58
Period size: 9 Copynumber: 3.2 Consensus size: 9
47611068 TAGAAGTGAA
47611078 AATGAAAAT
1 AATGAAAAT
47611087 AATGAAAAT
1 AATGAAAAT
47611096 AATGAAAAT
1 AATGAAAAT
47611105 AA
1 AA
47611107 AGAGATCTTG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.69, C:0.00, G:0.10, T:0.21
Consensus pattern (9 bp):
AATGAAAAT
Found at i:47612668 original size:33 final size:33
Alignment explanation
Indices: 47612631--47612698 Score: 118
Period size: 33 Copynumber: 2.1 Consensus size: 33
47612621 AAAGACAAGT
47612631 ATACAAGATTGAAAGCGTCACCTTAAAGATGTA
1 ATACAAGATTGAAAGCGTCACCTTAAAGATGTA
* *
47612664 ATACAAGATTGAAAGCGTCATCTTAGAGATGTA
1 ATACAAGATTGAAAGCGTCACCTTAAAGATGTA
47612697 AT
1 AT
47612699 GTGATATTGC
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.41, C:0.13, G:0.19, T:0.26
Consensus pattern (33 bp):
ATACAAGATTGAAAGCGTCACCTTAAAGATGTA
Found at i:47614152 original size:17 final size:18
Alignment explanation
Indices: 47614130--47614163 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
47614120 GACAATTTCT
47614130 TTTTTATATT-TGTAATG
1 TTTTTATATTATGTAATG
47614147 TTTTTATATTATGTAAT
1 TTTTTATATTATGTAAT
47614164 TTATAACACA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 10 0.62
18 6 0.38
ACGTcount: A:0.26, C:0.00, G:0.09, T:0.65
Consensus pattern (18 bp):
TTTTTATATTATGTAATG
Found at i:47614276 original size:14 final size:14
Alignment explanation
Indices: 47614257--47614309 Score: 56
Period size: 14 Copynumber: 3.8 Consensus size: 14
47614247 TATAATTTGA
47614257 ATAAA-TAAAAATAT
1 ATAAATTAAAAAT-T
*
47614271 ATAAATTATTAAATT
1 ATAAATTA-AAAATT
*
47614286 ATAAATTATAAATT
1 ATAAATTAAAAATT
47614300 ATAAA-TAAAA
1 ATAAATTAAAA
47614310 TAAGTATTAT
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
13 4 0.11
14 16 0.46
15 11 0.31
16 4 0.11
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (14 bp):
ATAAATTAAAAATT
Found at i:47614292 original size:7 final size:7
Alignment explanation
Indices: 47614265--47614305 Score: 64
Period size: 7 Copynumber: 5.6 Consensus size: 7
47614255 GAATAAATAA
47614265 AAATATAT
1 AAAT-TAT
47614273 AAATTATT
1 AAATTA-T
47614281 AAATTAT
1 AAATTAT
47614288 AAATTAT
1 AAATTAT
47614295 AAATTAT
1 AAATTAT
47614302 AAAT
1 AAAT
47614306 AAAATAAGTA
Statistics
Matches: 32, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
7 21 0.66
8 11 0.34
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (7 bp):
AAATTAT
Found at i:47625320 original size:17 final size:17
Alignment explanation
Indices: 47625287--47625320 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
47625277 GTATATGCAA
*
47625287 AACAATTTAAAGCAAAT
1 AACAATTTAAAACAAAT
*
47625304 AACAATTTAAAATAAAT
1 AACAATTTAAAACAAAT
47625321 GATTTACAAG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.62, C:0.09, G:0.03, T:0.26
Consensus pattern (17 bp):
AACAATTTAAAACAAAT
Found at i:47625567 original size:25 final size:26
Alignment explanation
Indices: 47625529--47625603 Score: 75
Period size: 27 Copynumber: 2.8 Consensus size: 26
47625519 ATGCAAAAAT
* *
47625529 AGTTTATAATAAATGATAAATAA-G-A
1 AGTTTA-AAAAAATAATAAATAAGGAA
47625554 AGTTTAAAACAAATAAT-AATAAAGGAA
1 AGTTTAAAA-AAATAATAAAT-AAGGAA
47625581 AGTTTAAAAAAATAAATAAATAA
1 AGTTTAAAAAAAT-AATAAATAA
47625604 AGATCTTAAA
Statistics
Matches: 42, Mismatches: 2, Indels: 10
0.78 0.04 0.19
Matches are distributed among these distances:
24 5 0.12
25 14 0.33
26 5 0.12
27 15 0.36
28 3 0.07
ACGTcount: A:0.63, C:0.01, G:0.09, T:0.27
Consensus pattern (26 bp):
AGTTTAAAAAAATAATAAATAAGGAA
Found at i:47625587 original size:27 final size:28
Alignment explanation
Indices: 47625553--47625605 Score: 83
Period size: 27 Copynumber: 1.9 Consensus size: 28
47625543 GATAAATAAG
47625553 AAGTTTAAAACAAAT-AAT-AATAAAGGA
1 AAGTTTAAAA-AAATAAATAAATAAAGGA
47625580 AAGTTTAAAAAAATAAATAAATAAAG
1 AAGTTTAAAAAAATAAATAAATAAAG
47625606 ATCTTAAAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
26 4 0.17
27 13 0.54
28 7 0.29
ACGTcount: A:0.66, C:0.02, G:0.09, T:0.23
Consensus pattern (28 bp):
AAGTTTAAAAAAATAAATAAATAAAGGA
Found at i:47636846 original size:24 final size:24
Alignment explanation
Indices: 47636802--47636847 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
47636792 TTTAAAAGGG
*
47636802 AAAAAAATATATTTAGTTGATTTA
1 AAAAAAATATATTTAGGTGATTTA
47636826 AAAAAAATTATATTT-GGTGATT
1 AAAAAAA-TATATTTAGGTGATT
47636848 GAGTCTTAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
24 13 0.65
25 7 0.35
ACGTcount: A:0.48, C:0.00, G:0.11, T:0.41
Consensus pattern (24 bp):
AAAAAAATATATTTAGGTGATTTA
Found at i:47653087 original size:13 final size:13
Alignment explanation
Indices: 47653069--47653093 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
47653059 TAAGTTATAT
47653069 GTGTGAAAATTTC
1 GTGTGAAAATTTC
47653082 GTGTGAAAATTT
1 GTGTGAAAATTT
47653094 GATAGTTTGA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.04, G:0.24, T:0.40
Consensus pattern (13 bp):
GTGTGAAAATTTC
Found at i:47656127 original size:62 final size:62
Alignment explanation
Indices: 47656035--47656167 Score: 146
Period size: 62 Copynumber: 2.1 Consensus size: 62
47656025 CAAAAAAATG
* *
47656035 GGAAATTTTGAATTCTCCATTGAAAATTTTAGAAA-ATTTTAATTAAG-TCCGTCAAAATTTTT
1 GGAAATTTTCAATTCTCCATTGAAAATTTTAGAAATA-TTTAATTAAGCCCCGTC-AAATTTTT
* ** * *
47656097 GGAAATTTTCATTTCTCTC-TTGAAGTTTTTAGAAATATTTAATTAGGCCCCTTCAAATTTTT
1 GGAAATTTTCAATTCTC-CATTGAAAATTTTAGAAATATTTAATTAAGCCCCGTCAAATTTTT
*
47656159 GAAAATTTT
1 GGAAATTTT
47656168 AATCAAGCTC
Statistics
Matches: 60, Mismatches: 8, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
62 54 0.90
63 6 0.10
ACGTcount: A:0.33, C:0.11, G:0.11, T:0.44
Consensus pattern (62 bp):
GGAAATTTTCAATTCTCCATTGAAAATTTTAGAAATATTTAATTAAGCCCCGTCAAATTTTT
Found at i:47672846 original size:23 final size:24
Alignment explanation
Indices: 47672803--47672853 Score: 61
Period size: 23 Copynumber: 2.2 Consensus size: 24
47672793 TTTAAAATTT
*
47672803 AAAAACTTTAAAAGACTTAAAT-G
1 AAAAACTTTAAAAGACCTAAATAG
*
47672826 AAAAA-TTTAAATGGACCTAAATAG
1 AAAAACTTTAAA-AGACCTAAATAG
47672850 AAAA
1 AAAA
47672854 TTTTCCATTA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
22 6 0.25
23 13 0.54
24 5 0.21
ACGTcount: A:0.59, C:0.08, G:0.10, T:0.24
Consensus pattern (24 bp):
AAAAACTTTAAAAGACCTAAATAG
Found at i:47673465 original size:19 final size:17
Alignment explanation
Indices: 47673441--47673484 Score: 54
Period size: 19 Copynumber: 2.5 Consensus size: 17
47673431 TAAATACCAA
47673441 GTTTTTTAGTTAAAAAAAT
1 GTTTTTTAG-T-AAAAAAT
*
47673460 GTTTTTGAGTAAAAAAT
1 GTTTTTTAGTAAAAAAT
47673477 -TTTTTTAG
1 GTTTTTTAG
47673485 GAGGGCCGAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
16 7 0.30
17 7 0.30
18 1 0.04
19 8 0.35
ACGTcount: A:0.36, C:0.00, G:0.14, T:0.50
Consensus pattern (17 bp):
GTTTTTTAGTAAAAAAT
Found at i:47673482 original size:18 final size:18
Alignment explanation
Indices: 47673442--47673484 Score: 54
Period size: 16 Copynumber: 2.4 Consensus size: 18
47673432 AAATACCAAG
47673442 TTTTTTAGTTAAAAAAAT
1 TTTTTTAGTTAAAAAAAT
*
47673460 GTTTTTGAG-T-AAAAAAT
1 -TTTTTTAGTTAAAAAAAT
47673477 TTTTTTAG
1 TTTTTTAG
47673485 GAGGGCCGAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
16 7 0.32
17 7 0.32
18 1 0.05
19 7 0.32
ACGTcount: A:0.37, C:0.00, G:0.12, T:0.51
Consensus pattern (18 bp):
TTTTTTAGTTAAAAAAAT
Found at i:47683756 original size:26 final size:26
Alignment explanation
Indices: 47683722--47683799 Score: 111
Period size: 26 Copynumber: 2.8 Consensus size: 26
47683712 ATAATAAATA
47683722 TTTTTATTTTTTATTTTTAAAATACT
1 TTTTTATTTTTTATTTTTAAAATACT
47683748 TTTTTATTTTTTATTTTTAAAATACT
1 TTTTTATTTTTTATTTTTAAAATACT
*
47683774 TTTAAAATACTTTTTTATTTTTAAAA
1 TTT---TTA-TTTTTTATTTTTAAAA
47683800 AAATATTTTT
Statistics
Matches: 47, Mismatches: 1, Indels: 4
0.90 0.02 0.08
Matches are distributed among these distances:
26 29 0.62
29 2 0.04
30 16 0.34
ACGTcount: A:0.31, C:0.04, G:0.00, T:0.65
Consensus pattern (26 bp):
TTTTTATTTTTTATTTTTAAAATACT
Found at i:47683778 original size:11 final size:11
Alignment explanation
Indices: 47683762--47683787 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
47683752 TATTTTTTAT
47683762 TTTTAAAATAC
1 TTTTAAAATAC
47683773 TTTTAAAATAC
1 TTTTAAAATAC
47683784 TTTT
1 TTTT
47683788 TTATTTTTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.38, C:0.08, G:0.00, T:0.54
Consensus pattern (11 bp):
TTTTAAAATAC
Found at i:47683817 original size:21 final size:22
Alignment explanation
Indices: 47683777--47683817 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
47683767 AAATACTTTT
* *
47683777 AAAATACTTTTTTATTTTTAAA
1 AAAATACTTTTTGATGTTTAAA
47683799 AAAATA-TTTTTGATGTTTA
1 AAAATACTTTTTGATGTTTA
47683818 TTTAAAAAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 11 0.65
22 6 0.35
ACGTcount: A:0.39, C:0.02, G:0.05, T:0.54
Consensus pattern (22 bp):
AAAATACTTTTTGATGTTTAAA
Found at i:47684294 original size:107 final size:107
Alignment explanation
Indices: 47683975--47684383 Score: 554
Period size: 107 Copynumber: 3.8 Consensus size: 107
47683965 CACCTCTAGT
* *
47683975 CGGCACCACCTTTTTTGGGGAAATTTTTTTTCACTTTTTTCGTGTCAATAGCAGATATCAGTATA
1 CGGCACCACCTTTTTTGGGG-AATTTTTTTTTACTTTTTTCGTGTCAATAGCAGGTATCAGTATA
** * *
47684040 TAAAAAAAGTAAAAAAAAAATTTTGGTGGTGGCTTGCCAATGGC
65 CGAAAAAAGTAAAAAAAAAA-ATTGGTGGTGGCCTGCCAATGGC
* * * *
47684084 CGGCACCATCTTTTTGGGGGGAGAAATTTTTTTTTACTTTTTTCGTGTCAATAGCTGGTATCAAT
1 CGGCACCACCTTTTT--TGGG-G-AATTTTTTTTTACTTTTTTCGTGTCAATAGCAGGTATCAGT
47684149 ATACGAAAAAAAGT-AAAAAAAAAATTGGTGGTGGCCTGCCAATGGC
62 ATACG-AAAAAAGTAAAAAAAAAAATTGGTGGTGGCCTGCCAATGGC
*
47684195 CGGCACCACCTTTTATGGGGAATTTTTTTTTCACTTTTTTCGTGTCAATAGCAGGTA-CTAGTAT
1 CGGCACCACCTTTTTTGGGGAATTTTTTTTT-ACTTTTTTCGTGTCAATAGCAGGTATC-AGTAT
* *
47684259 ACGAAAAAAGTAAAAAAAAAAATT-GTGGTGGCCTGCCAACGGT
64 ACGAAAAAAGTAAAAAAAAAAATTGGTGGTGGCCTGCCAATGGC
* *
47684302 CGGCACCACCTTTTTTGTGAGAATTTTTTTTTACTTTTTTCGTGTCAATAACAGGTATCAGTATA
1 CGGCACCACCTTTTTTG-GGGAATTTTTTTTTACTTTTTTCGTGTCAATAGCAGGTATCAGTATA
* *
47684367 CGAGAAAAGTTAAAAAA
65 CGAAAAAAGTAAAAAAA
47684384 TTTCCCCCAA
Statistics
Matches: 269, Mismatches: 22, Indels: 20
0.86 0.07 0.06
Matches are distributed among these distances:
107 98 0.36
108 58 0.22
109 17 0.06
111 37 0.14
112 51 0.19
113 8 0.03
ACGTcount: A:0.31, C:0.15, G:0.20, T:0.34
Consensus pattern (107 bp):
CGGCACCACCTTTTTTGGGGAATTTTTTTTTACTTTTTTCGTGTCAATAGCAGGTATCAGTATAC
GAAAAAAGTAAAAAAAAAAATTGGTGGTGGCCTGCCAATGGC
Found at i:47684631 original size:17 final size:17
Alignment explanation
Indices: 47684595--47684639 Score: 56
Period size: 17 Copynumber: 2.7 Consensus size: 17
47684585 TCGATATAAT
* *
47684595 AAATATATTT-ATTTTT
1 AAATATTTTTAATTTTA
*
47684611 AAATTTTTTTAATTTTA
1 AAATATTTTTAATTTTA
47684628 AAATATTTTTAA
1 AAATATTTTTAA
47684640 AATACTTTTT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
16 8 0.33
17 16 0.67
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (17 bp):
AAATATTTTTAATTTTA
Found at i:47684637 original size:11 final size:11
Alignment explanation
Indices: 47684623--47684701 Score: 67
Period size: 11 Copynumber: 7.4 Consensus size: 11
47684613 ATTTTTTTAA
47684623 TTTTAAAATAT
1 TTTTAAAATAT
47684634 TTTTAAAATACT
1 TTTTAAAATA-T
**
47684646 TTTTTTAA-A-
1 TTTTAAAATAT
*
47684655 TTTAAAAATAT
1 TTTTAAAATAT
47684666 TTTTAAAATACT
1 TTTTAAAATA-T
**
47684678 TTTT--TTTAT
1 TTTTAAAATAT
47684687 TTTTAAAATAT
1 TTTTAAAATAT
47684698 TTTT
1 TTTT
47684702 TGGTATTTTA
Statistics
Matches: 52, Mismatches: 10, Indels: 12
0.70 0.14 0.16
Matches are distributed among these distances:
9 10 0.19
10 3 0.06
11 27 0.52
12 12 0.23
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.59
Consensus pattern (11 bp):
TTTTAAAATAT
Found at i:47684649 original size:31 final size:32
Alignment explanation
Indices: 47684614--47684701 Score: 149
Period size: 32 Copynumber: 2.8 Consensus size: 32
47684604 TATTTTTAAA
47684614 TTTTTTTAATTTTAAAATATTTTTAAAATACT
1 TTTTTTTAATTTTAAAATATTTTTAAAATACT
* *
47684646 TTTTTTAAATTTAAAAATATTTTTAAAATACT
1 TTTTTTTAATTTTAAAATATTTTTAAAATACT
*
47684678 TTTTTTTATTTTTAAAATATTTTT
1 TTTTTTTAATTTTAAAATATTTTT
47684702 TGGTATTTTA
Statistics
Matches: 51, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
32 51 1.00
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.61
Consensus pattern (32 bp):
TTTTTTTAATTTTAAAATATTTTTAAAATACT
Found at i:47684700 original size:20 final size:21
Alignment explanation
Indices: 47684663--47684702 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
47684653 AATTTAAAAA
47684663 TATTTTTAAAATACTTTTTTT
1 TATTTTTAAAATACTTTTTTT
47684684 TATTTTTAAAATA-TTTTTT
1 TATTTTTAAAATACTTTTTT
47684703 GGTATTTTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 6 0.32
21 13 0.68
ACGTcount: A:0.30, C:0.03, G:0.00, T:0.68
Consensus pattern (21 bp):
TATTTTTAAAATACTTTTTTT
Found at i:47684711 original size:20 final size:21
Alignment explanation
Indices: 47684663--47684710 Score: 71
Period size: 21 Copynumber: 2.3 Consensus size: 21
47684653 AATTTAAAAA
*
47684663 TATTTTTAAAATACTTTTTTT
1 TATTTTTAAAATACTTTTTTG
47684684 TATTTTTAAAATA-TTTTTTGG
1 TATTTTTAAAATACTTTTTT-G
47684705 TATTTT
1 TATTTT
47684711 ATTAAAAAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
20 6 0.24
21 19 0.76
ACGTcount: A:0.27, C:0.02, G:0.04, T:0.67
Consensus pattern (21 bp):
TATTTTTAAAATACTTTTTTG
Found at i:47687159 original size:6 final size:6
Alignment explanation
Indices: 47687149--47687182 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
47687139 AGGTTTCAAG
* *
47687149 AAATGG AAATGA AAATGA AAATGA AAATGG AAAT
1 AAATGA AAATGA AAATGA AAATGA AAATGA AAAT
47687183 TTGCAATCAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.62, C:0.00, G:0.21, T:0.18
Consensus pattern (6 bp):
AAATGA
Found at i:47687170 original size:12 final size:12
Alignment explanation
Indices: 47687149--47687182 Score: 59
Period size: 12 Copynumber: 2.8 Consensus size: 12
47687139 AGGTTTCAAG
47687149 AAATGGAAATGA
1 AAATGGAAATGA
*
47687161 AAATGAAAATGA
1 AAATGGAAATGA
47687173 AAATGGAAAT
1 AAATGGAAAT
47687183 TTGCAATCAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.62, C:0.00, G:0.21, T:0.18
Consensus pattern (12 bp):
AAATGGAAATGA
Found at i:47688079 original size:23 final size:22
Alignment explanation
Indices: 47688040--47688095 Score: 85
Period size: 22 Copynumber: 2.5 Consensus size: 22
47688030 ATTTAAATTT
*
47688040 TAAAAACTTTAAAAGACTTAAA
1 TAAAAATTTTAAAAGACTTAAA
47688062 TAAAAATTTTAAATAGACTTAAA
1 TAAAAATTTTAAA-AGACTTAAA
47688085 TAGAAAATTTT
1 TA-AAAATTTT
47688096 CCATTATCAT
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
22 12 0.39
23 11 0.35
24 8 0.26
ACGTcount: A:0.55, C:0.05, G:0.05, T:0.34
Consensus pattern (22 bp):
TAAAAATTTTAAAAGACTTAAA
Found at i:47689568 original size:6 final size:6
Alignment explanation
Indices: 47689557--47689588 Score: 64
Period size: 6 Copynumber: 5.3 Consensus size: 6
47689547 CTAAGGAAAA
47689557 GAAATT GAAATT GAAATT GAAATT GAAATT GA
1 GAAATT GAAATT GAAATT GAAATT GAAATT GA
47689589 TTTTCAATTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.19, T:0.31
Consensus pattern (6 bp):
GAAATT
Found at i:47695446 original size:42 final size:42
Alignment explanation
Indices: 47695399--47695484 Score: 172
Period size: 42 Copynumber: 2.0 Consensus size: 42
47695389 GGCAGCAATG
47695399 TCAATTTCAAGCAGCGGGCAAGGACCCACAGAAAGTTCTCTT
1 TCAATTTCAAGCAGCGGGCAAGGACCCACAGAAAGTTCTCTT
47695441 TCAATTTCAAGCAGCGGGCAAGGACCCACAGAAAGTTCTCTT
1 TCAATTTCAAGCAGCGGGCAAGGACCCACAGAAAGTTCTCTT
47695483 TC
1 TC
47695485 GTTCATAAAA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 44 1.00
ACGTcount: A:0.30, C:0.27, G:0.21, T:0.22
Consensus pattern (42 bp):
TCAATTTCAAGCAGCGGGCAAGGACCCACAGAAAGTTCTCTT
Found at i:47697673 original size:85 final size:85
Alignment explanation
Indices: 47697578--47697746 Score: 277
Period size: 85 Copynumber: 2.0 Consensus size: 85
47697568 TTTTTTTGAC
*
47697578 TTATCCCTAAGACTATTTTTACAAACGAATATGAAAAAGAGGACTCTCC-TTTACATAACAAACA
1 TTATCCCTAAGACTATTTTTACAAACGAATATGAAAAAGAGGAATCTCCGTTT-CATAACAAACA
47697642 AACAACCTTTTTGACTCATAT
65 AACAACCTTTTTGACTCATAT
** * *
47697663 TTATCCCTAAGACTATTTTTACAGGCGAATATGATAAGGAGGAATCTCCGTTTCATAACAAACAA
1 TTATCCCTAAGACTATTTTTACAAACGAATATGAAAAAGAGGAATCTCCGTTTCATAACAAACAA
47697728 ACAACCTTTTTGACTCATA
66 ACAACCTTTTTGACTCATA
47697747 CTTTTATGAC
Statistics
Matches: 78, Mismatches: 5, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
85 75 0.96
86 3 0.04
ACGTcount: A:0.38, C:0.21, G:0.11, T:0.31
Consensus pattern (85 bp):
TTATCCCTAAGACTATTTTTACAAACGAATATGAAAAAGAGGAATCTCCGTTTCATAACAAACAA
ACAACCTTTTTGACTCATAT
Found at i:47698995 original size:19 final size:20
Alignment explanation
Indices: 47698952--47698997 Score: 60
Period size: 19 Copynumber: 2.4 Consensus size: 20
47698942 CTCTTAAATG
* *
47698952 ACTTTTTTATAATTTTTATT
1 ACTTTTTTATAATATTTATA
47698972 A-TTTTTTATAA-ATTTATA
1 ACTTTTTTATAATATTTATA
47698990 ACTTTTTT
1 ACTTTTTT
47698998 TTTAAAATTT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
18 6 0.26
19 16 0.70
20 1 0.04
ACGTcount: A:0.28, C:0.04, G:0.00, T:0.67
Consensus pattern (20 bp):
ACTTTTTTATAATATTTATA
Found at i:47701259 original size:28 final size:28
Alignment explanation
Indices: 47701210--47701298 Score: 106
Period size: 28 Copynumber: 3.1 Consensus size: 28
47701200 TATTTTTGAC
* *
47701210 CCCTAAATTTTTCCAAAATTACATTTTAA
1 CCCTAAA-CTTTCTAAAATTACATTTTAA
*
47701239 CCCTTAACTTTCTAAAATTACATTTTAA
1 CCCTAAACTTTCTAAAATTACATTTTAA
* * *
47701267 CCCTAAACGTTCTCAAAATTATACTTTAA
1 CCCTAAACTTTCT-AAAATTACATTTTAA
47701296 CCC
1 CCC
47701299 CAAAAGTTTT
Statistics
Matches: 52, Mismatches: 7, Indels: 2
0.85 0.11 0.03
Matches are distributed among these distances:
28 30 0.58
29 22 0.42
ACGTcount: A:0.36, C:0.25, G:0.01, T:0.38
Consensus pattern (28 bp):
CCCTAAACTTTCTAAAATTACATTTTAA
Found at i:47701294 original size:29 final size:29
Alignment explanation
Indices: 47701223--47701298 Score: 109
Period size: 28 Copynumber: 2.7 Consensus size: 29
47701213 TAAATTTTTC
* *
47701223 CAAAATTACATTTTAACCCTTAACTTTCT
1 CAAAATTACATTTTAACCCTAAACGTTCT
47701252 -AAAATTACATTTTAACCCTAAACGTTCT
1 CAAAATTACATTTTAACCCTAAACGTTCT
* *
47701280 CAAAATTATACTTTAACCC
1 CAAAATTACATTTTAACCC
47701299 CAAAAGTTTT
Statistics
Matches: 42, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
28 26 0.62
29 16 0.38
ACGTcount: A:0.38, C:0.24, G:0.01, T:0.37
Consensus pattern (29 bp):
CAAAATTACATTTTAACCCTAAACGTTCT
Found at i:47701819 original size:10 final size:10
Alignment explanation
Indices: 47701794--47701827 Score: 50
Period size: 10 Copynumber: 3.3 Consensus size: 10
47701784 CTGCCGAAGG
47701794 AGAAGAAAAA
1 AGAAGAAAAA
47701804 ATGAAGAAAAA
1 A-GAAGAAAAA
*
47701815 AGAAGAAGAA
1 AGAAGAAAAA
47701825 AGA
1 AGA
47701828 GGAAGAAGAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
10 12 0.55
11 10 0.45
ACGTcount: A:0.74, C:0.00, G:0.24, T:0.03
Consensus pattern (10 bp):
AGAAGAAAAA
Found at i:47702011 original size:5 final size:5
Alignment explanation
Indices: 47702001--47702033 Score: 66
Period size: 5 Copynumber: 6.6 Consensus size: 5
47701991 TATTTATATT
47702001 TTTAA TTTAA TTTAA TTTAA TTTAA TTTAA TTT
1 TTTAA TTTAA TTTAA TTTAA TTTAA TTTAA TTT
47702034 TAAGTAATTT
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:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (5 bp):
TTTAA
Found at i:47702041 original size:15 final size:15
Alignment explanation
Indices: 47702001--47702043 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
47701991 TATTTATATT
*
47702001 TTTAATTTAATTTAA
1 TTTAATGTAATTTAA
*
47702016 TTTAATTTAATTTAA
1 TTTAATGTAATTTAA
47702031 TTTTAA-GTAATTT
1 -TTTAATGTAATTT
47702044 CAATAAATAG
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
15 21 0.81
16 5 0.19
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.60
Consensus pattern (15 bp):
TTTAATGTAATTTAA
Found at i:47702342 original size:17 final size:17
Alignment explanation
Indices: 47702320--47702405 Score: 66
Period size: 18 Copynumber: 5.0 Consensus size: 17
47702310 AAGAAGAAAA
*
47702320 TCAAAAAATTCGTTTTT
1 TCAAAAAATTCGTGTTT
* ***
47702337 TCAAAATATTCCCCTATT
1 TCAAAAAATTCGTGT-TT
*
47702355 TCAAAAATTTCCGTGTTT
1 TCAAAAAATT-CGTGTTT
** *
47702373 TCAAAATTTTCATGTTT
1 TCAAAAAATTCGTGTTT
47702390 TC-AAAAATTCGTGTTT
1 TCAAAAAATTCGTGTTT
47702406 AAAATTTTTT
Statistics
Matches: 53, Mismatches: 14, Indels: 5
0.74 0.19 0.07
Matches are distributed among these distances:
16 11 0.21
17 19 0.36
18 21 0.40
19 2 0.04
ACGTcount: A:0.31, C:0.16, G:0.07, T:0.45
Consensus pattern (17 bp):
TCAAAAAATTCGTGTTT
Found at i:47702374 original size:18 final size:18
Alignment explanation
Indices: 47702353--47702398 Score: 67
Period size: 17 Copynumber: 2.6 Consensus size: 18
47702343 TATTCCCCTA
*
47702353 TTTCAAAAATTTCCGTGT
1 TTTCAAAAATTTCCATGT
*
47702371 TTTC-AAAATTTTCATGT
1 TTTCAAAAATTTCCATGT
47702388 TTTCAAAAATT
1 TTTCAAAAATT
47702399 CGTGTTTAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
17 15 0.60
18 10 0.40
ACGTcount: A:0.33, C:0.13, G:0.07, T:0.48
Consensus pattern (18 bp):
TTTCAAAAATTTCCATGT
Found at i:47702444 original size:18 final size:17
Alignment explanation
Indices: 47702353--47702413 Score: 65
Period size: 17 Copynumber: 3.7 Consensus size: 17
47702343 TATTCCCCTA
*
47702353 TTTCAAAAATTTCCGTGT
1 TTTC-AAAATTTTCGTGT
*
47702371 TTTCAAAATTTTCATGT
1 TTTCAAAATTTTCGTGT
*
47702388 TTTCAAAA-ATTCGTG-
1 TTTCAAAATTTTCGTGT
47702403 TTT-AAAATTTT
1 TTTCAAAATTTT
47702414 TTTTCCATGT
Statistics
Matches: 37, Mismatches: 5, Indels: 5
0.79 0.11 0.11
Matches are distributed among these distances:
14 4 0.11
15 5 0.14
16 5 0.14
17 19 0.51
18 4 0.11
ACGTcount: A:0.31, C:0.11, G:0.08, T:0.49
Consensus pattern (17 bp):
TTTCAAAATTTTCGTGT
Found at i:47702572 original size:18 final size:18
Alignment explanation
Indices: 47702487--47702575 Score: 67
Period size: 18 Copynumber: 4.9 Consensus size: 18
47702477 TTTAAAAAAT
47702487 TTTGTG-TTCAAAAA-TC
1 TTTGTGTTTCAAAAATTC
*
47702503 TTCGTGCTTTCAAAAATTC
1 TTTGTG-TTTCAAAAATTC
** * *
47702522 -CGGTGTGTCAAAAATTTT
1 TTTGTGTTTCAAAAA-TTC
* *
47702540 TTTGTTTTTGAAAAAATTC
1 TTTGTGTTT-CAAAAATTC
47702559 TTTGTGTTTCAAAAATT
1 TTTGTGTTTCAAAAATT
47702576 TCCGTGTTTT
Statistics
Matches: 54, Mismatches: 13, Indels: 10
0.70 0.17 0.13
Matches are distributed among these distances:
16 5 0.09
17 8 0.15
18 20 0.37
19 16 0.30
20 5 0.09
ACGTcount: A:0.29, C:0.11, G:0.13, T:0.46
Consensus pattern (18 bp):
TTTGTGTTTCAAAAATTC
Found at i:47702573 original size:20 final size:20
Alignment explanation
Indices: 47702550--47702724 Score: 61
Period size: 19 Copynumber: 9.2 Consensus size: 20
47702540 TTTGTTTTTG
47702550 AAAAAATTCTTTGTGTTTC-
1 AAAAAATTCTTTGTGTTTCA
* ** *
47702569 AAAAATTTCCGTGT-TTTAAA
1 AAAAAATTCTTTGTGTTT-CA
**
47702589 AAAAAATTTCCATGT-TTTCA
1 AAAAAA-TTCTTTGTGTTTCA
* **
47702609 AAAAACTT-TCCGTGTTTTCAA
1 AAAAAATTCTTTGTG-TTTC-A
*
47702630 AAAAAATTC-TCGTGTTTC-
1 AAAAAATTCTTTGTGTTTCA
* * *
47702648 ACAAATTTCTGTGT-TTTCA
1 AAAAAATTCTTTGTGTTTCA
*
47702667 AAAAAA---ATTGTGTTTCA
1 AAAAAATTCTTTGTGTTTCA
*
47702684 AAAAAA--ATTTGTGTTTTCA
1 AAAAAATTCTTTGTG-TTTCA
* *
47702703 AAAAATTTC-TCGTGTTTCA
1 AAAAAATTCTTTGTGTTTCA
47702722 AAA
1 AAA
47702725 TTGTCGTGTT
Statistics
Matches: 117, Mismatches: 25, Indels: 28
0.69 0.15 0.16
Matches are distributed among these distances:
16 3 0.03
17 11 0.09
18 21 0.18
19 37 0.32
20 23 0.20
21 22 0.19
ACGTcount: A:0.37, C:0.13, G:0.10, T:0.41
Consensus pattern (20 bp):
AAAAAATTCTTTGTGTTTCA
Found at i:47702582 original size:17 final size:17
Alignment explanation
Indices: 47702562--47702796 Score: 106
Period size: 17 Copynumber: 12.9 Consensus size: 17
47702552 AAAATTCTTT
47702562 GTGTTTCAAAAATTTCC
1 GTGTTTCAAAAATTTCC
*
47702579 GTGTTTTAAAAAAAAATTTCC
1 GTG-TTT---CAAAAATTTCC
*
47702600 ATGTTTTCAAAAAACTTTCC
1 GTG-TTTC-AAAAA-TTTCC
*
47702620 GTGTTTTCAAAAAAAATTCTC
1 GTG-TTTC--AAAAATTTC-C
* *
47702641 GTGTTTCACAAATTTCT
1 GTGTTTCAAAAATTTCC
*
47702658 GTGTTTTCAAAAAAAATT--
1 GTG-TTTC--AAAAATTTCC
47702676 GTGTTTCAAAAAAAATTT--
1 GTGTTTC---AAAAATTTCC
47702694 GTGTTTTCAAAAAATTTCTC
1 GTG-TTTC-AAAAATTTC-C
47702714 GTGTTTC-AAAATTGT-C
1 GTGTTTCAAAAATT-TCC
*
47702730 GTGTTTTCAAAAATTTTC
1 GTG-TTTCAAAAATTTCC
* * *
47702748 GTGTTTTAAGAATTTTC
1 GTGTTTCAAAAATTTCC
*
47702765 GTGTTTCTAAAA-TTCTC
1 GTGTTTCAAAAATTTC-C
*
47702782 GTGTTTTAAAAATTT
1 GTGTTTCAAAAATTT
47702797 TTCATGTTTT
Statistics
Matches: 177, Mismatches: 19, Indels: 43
0.74 0.08 0.18
Matches are distributed among these distances:
16 6 0.03
17 62 0.35
18 42 0.24
19 13 0.07
20 28 0.16
21 26 0.15
ACGTcount: A:0.33, C:0.12, G:0.11, T:0.44
Consensus pattern (17 bp):
GTGTTTCAAAAATTTCC
Found at i:47702590 original size:18 final size:18
Alignment explanation
Indices: 47702569--47702813 Score: 109
Period size: 18 Copynumber: 13.3 Consensus size: 18
47702559 TTTGTGTTTC
47702569 AAAAATTTCCGTGTTTTAAAA
1 AAAAATTTCCGTGTTTT---A
*
47702590 AAAAATTTCCATGTTTTCA
1 AAAAATTTCCGTGTTTT-A
47702609 AAAAACTTTCCGTGTTTTCAA
1 AAAAA-TTTCCGTGTTTT--A
* *
47702630 AAAAAATTCTCGTG-TTTC
1 AAAAATTTC-CGTGTTTTA
* *
47702648 ACAAATTTCTGTGTTTTCAA
1 AAAAATTTCCGTGTTTT--A
* *
47702668 AAAAAATT--GTGTTTCAAA
1 AAAAATTTCCGTGTTT--TA
47702686 AAAAATTT--GTGTTTTCA
1 AAAAATTTCCGTGTTTT-A
47702703 AAAAATTTCTCGTG-TTT-
1 AAAAATTTC-CGTGTTTTA
* *
47702720 CAAAATTGT-CGTGTTTTC
1 AAAAATT-TCCGTGTTTTA
*
47702738 AAAAATTTTCGTGTTTT-
1 AAAAATTTCCGTGTTTTA
* *
47702755 AAGAATTTTCGTGTTTCT-
1 AAAAATTTCCGTGTTT-TA
47702773 -AAAA-TTCTCGTGTTTTA
1 AAAAATTTC-CGTGTTTTA
* * *
47702790 AAAATTTTTCATGTTTTCA
1 AAAAATTTCCGTGTTTT-A
47702809 AAAAA
1 AAAAA
47702814 AATTGTTTCA
Statistics
Matches: 178, Mismatches: 24, Indels: 46
0.72 0.10 0.19
Matches are distributed among these distances:
16 7 0.04
17 47 0.26
18 56 0.31
19 16 0.09
20 26 0.15
21 26 0.15
ACGTcount: A:0.34, C:0.12, G:0.11, T:0.43
Consensus pattern (18 bp):
AAAAATTTCCGTGTTTTA
Found at i:47702665 original size:38 final size:38
Alignment explanation
Indices: 47702550--47702817 Score: 208
Period size: 34 Copynumber: 7.2 Consensus size: 38
47702540 TTTGTTTTTG
* *
47702550 AAAAAATTCTTTGTGTTTCAAAAATTTCCGTGTTTTAAA
1 AAAAAATTC-TCGTGTTTCAAAAATTTCCGTGTTTTCAA
*
47702589 AAAAAATT-TCCATGTTTTCAAAAAACTTTCCGTGTTTTCAA
1 AAAAAATTCT-CGTG-TTTC-AAAAA-TTTCCGTGTTTTCAA
* *
47702630 AAAAAATTCTCGTGTTTCACAAATTTCTGTGTTTTCAA
1 AAAAAATTCTCGTGTTTCAAAAATTTCCGTGTTTTCAA
47702668 AAAAAA-T-T-GTGTTTCAAAAAAAATTT--GTGTTTTC-A
1 AAAAAATTCTCGTGTTTC---AAAAATTTCCGTGTTTTCAA
*
47702703 AAAAATTTCTCGTGTTTC-AAAATTGT-CGTGTTTTC--
1 AAAAAATTCTCGTGTTTCAAAAATT-TCCGTGTTTTCAA
* * * *
47702738 -AAAAATTTTCGTGTTTTAAGAATTTTCGTG-TTTC--
1 AAAAAATTCTCGTGTTTCAAAAATTTCCGTGTTTTCAA
* * * *
47702772 -TAAAATTCTCGTGTTTTAAAAATTTTTCATGTTTTCAA
1 AAAAAATTCTCGTGTTTCAAAAA-TTTCCGTGTTTTCAA
47702810 AAAAAATT
1 AAAAAATT
47702818 GTTTCAAAAT
Statistics
Matches: 192, Mismatches: 17, Indels: 40
0.77 0.07 0.16
Matches are distributed among these distances:
34 44 0.23
35 30 0.16
36 22 0.11
37 3 0.02
38 36 0.19
39 22 0.11
40 9 0.05
41 25 0.13
42 1 0.01
ACGTcount: A:0.34, C:0.12, G:0.10, T:0.44
Consensus pattern (38 bp):
AAAAAATTCTCGTGTTTCAAAAATTTCCGTGTTTTCAA
Found at i:47702777 original size:52 final size:52
Alignment explanation
Indices: 47702706--47702806 Score: 152
Period size: 52 Copynumber: 1.9 Consensus size: 52
47702696 GTTTTCAAAA
* *
47702706 AATTTCTCGTGTTTCAAAATTGTCGTGTTTTCAAAAA-TTTTCGTGTTTTAAG
1 AATTTCTCGTGTTTCAAAATTCTCGTGTTTT-AAAAATTTTTCATGTTTTAAG
47702758 AATTT-TCGTGTTTCTAAAATTCTCGTGTTTTAAAAATTTTTCATGTTTT
1 AATTTCTCGTGTTTC-AAAATTCTCGTGTTTTAAAAATTTTTCATGTTTT
47702807 CAAAAAAAAT
Statistics
Matches: 45, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
51 14 0.31
52 31 0.69
ACGTcount: A:0.25, C:0.11, G:0.13, T:0.51
Consensus pattern (52 bp):
AATTTCTCGTGTTTCAAAATTCTCGTGTTTTAAAAATTTTTCATGTTTTAAG
Found at i:47702796 original size:34 final size:35
Alignment explanation
Indices: 47702496--47702812 Score: 169
Period size: 35 Copynumber: 8.7 Consensus size: 35
47702486 TTTTGTGTTC
* * * *
47702496 AAAAATCTTCGTGCTTTCAAAAATTC-CGGTGTGTC
1 AAAAATTTTCGTGTTTTCAAAAATTCTC-GTGTTTT
** * * *
47702531 AAAAATTTTTTTGTTTTTGAAAAAATTCTTTGTGTTTC
1 AAAAATTTTCGTG-TTTT-CAAAAATTC-TCGTGTTTT
* * *
47702569 AAAAATTTCCGTGTTTTAAAAAAAAATT-TCCATGTTTT
1 AAAAATTTTCGTGTTTT---CAAAAATTCT-CGTGTTTT
* *
47702607 CAAAAAACTTTCCGTGTTTTCAAAAAAAATTCTCGTGTTTC
1 --AAAAA-TTTTCGTGTTTTC---AAAAATTCTCGTGTTTT
* *** * *
47702648 ACAAA-TTTCTGTGTTTTCAAAAAAAATTGTGTTTCAA
1 AAAAATTTTC-GTGTTTTCAAAAATTCTCGTGTTT--T
*
47702685 AAAAAATTT-GTGTTTTCAAAAAATTTCTCGTG-TTT
1 AAAAATTTTCGTGTTTTC-AAAAA-TTCTCGTGTTTT
* * *
47702720 CAAAATTGTCGTGTTTTCAAAAATTTTCGTGTTTT
1 AAAAATTTTCGTGTTTTCAAAAATTCTCGTGTTTT
* *
47702755 AAGAATTTTCGTG-TTTCTAAAATTCTCGTGTTTT
1 AAAAATTTTCGTGTTTTCAAAAATTCTCGTGTTTT
*
47702789 AAAAATTTTTCATGTTTTCAAAAA
1 AAAAA-TTTTCGTGTTTTCAAAAA
47702813 AAATTGTTTC
Statistics
Matches: 216, Mismatches: 42, Indels: 47
0.71 0.14 0.15
Matches are distributed among these distances:
34 30 0.14
35 53 0.25
36 27 0.12
37 27 0.12
38 36 0.17
39 12 0.06
40 5 0.02
41 25 0.12
42 1 0.00
ACGTcount: A:0.33, C:0.12, G:0.11, T:0.44
Consensus pattern (35 bp):
AAAAATTTTCGTGTTTTCAAAAATTCTCGTGTTTT
Found at i:47702841 original size:17 final size:17
Alignment explanation
Indices: 47702694--47702843 Score: 105
Period size: 17 Copynumber: 8.7 Consensus size: 17
47702684 AAAAAAATTT
47702694 GTGTTTTCAAAAAATTTCTC
1 GTGTTTTC--AAAA-TTCTC
*
47702714 GTG-TTTCAAAATTGTC
1 GTGTTTTCAAAATTCTC
*
47702730 GTGTTTTCAAAAATTTTC
1 GTGTTTTC-AAAATTCTC
*
47702748 GTGTTTT-AAGAATTTTC
1 GTGTTTTCAA-AATTCTC
47702765 GTG-TTTCTAAAATTCTC
1 GTGTTTTC-AAAATTCTC
* *
47702782 GTGTTTTAAAAATTTTTC
1 GTGTTTTCAAAA-TTCTC
* ***
47702800 ATGTTTTCAAAAAAAAT-
1 GTGTTTTC-AAAATTCTC
47702817 -TG-TTTCAAAATTCTC
1 GTGTTTTCAAAATTCTC
47702832 GTGTTTTCAAAA
1 GTGTTTTCAAAA
47702844 CAAAATTTTT
Statistics
Matches: 106, Mismatches: 13, Indels: 25
0.74 0.09 0.17
Matches are distributed among these distances:
14 5 0.05
15 4 0.04
16 16 0.15
17 39 0.37
18 31 0.29
19 8 0.08
20 3 0.03
ACGTcount: A:0.30, C:0.11, G:0.12, T:0.47
Consensus pattern (17 bp):
GTGTTTTCAAAATTCTC
Found at i:47703938 original size:9 final size:9
Alignment explanation
Indices: 47703920--47703968 Score: 71
Period size: 9 Copynumber: 5.4 Consensus size: 9
47703910 TTTGGTTAAA
47703920 AATTAACCG
1 AATTAACCG
*
47703929 AATTATCCG
1 AATTAACCG
*
47703938 AATTAACTG
1 AATTAACCG
*
47703947 AATTACCCG
1 AATTAACCG
47703956 AATTAACCG
1 AATTAACCG
47703965 AATT
1 AATT
47703969 GAATCACTAC
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
9 34 1.00
ACGTcount: A:0.41, C:0.20, G:0.10, T:0.29
Consensus pattern (9 bp):
AATTAACCG
Found at i:47703943 original size:18 final size:18
Alignment explanation
Indices: 47703920--47703968 Score: 80
Period size: 18 Copynumber: 2.7 Consensus size: 18
47703910 TTTGGTTAAA
*
47703920 AATTAACCGAATTATCCG
1 AATTAACCGAATTACCCG
*
47703938 AATTAACTGAATTACCCG
1 AATTAACCGAATTACCCG
47703956 AATTAACCGAATT
1 AATTAACCGAATT
47703969 GAATCACTAC
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.41, C:0.20, G:0.10, T:0.29
Consensus pattern (18 bp):
AATTAACCGAATTACCCG
Found at i:47706858 original size:18 final size:20
Alignment explanation
Indices: 47706827--47706864 Score: 53
Period size: 18 Copynumber: 2.0 Consensus size: 20
47706817 GAACAATAAT
*
47706827 TTTTAATATTTTTTA-AAAA
1 TTTTAATATATTTTAGAAAA
47706846 TTTT-ATATATTTTAGAAAA
1 TTTTAATATATTTTAGAAAA
47706865 ATCATCCTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 9 0.53
19 8 0.47
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (20 bp):
TTTTAATATATTTTAGAAAA
Found at i:47706864 original size:20 final size:19
Alignment explanation
Indices: 47706827--47706866 Score: 53
Period size: 20 Copynumber: 2.1 Consensus size: 19
47706817 GAACAATAAT
**
47706827 TTTTAATATTTTTTAAAAA
1 TTTTAATATTTTAGAAAAA
47706846 TTTTATATATTTTAGAAAAA
1 TTTTA-ATATTTTAGAAAAA
47706866 T
1 T
47706867 CATCCTAAAC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 5 0.28
20 13 0.72
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (19 bp):
TTTTAATATTTTAGAAAAA
Found at i:47721180 original size:28 final size:30
Alignment explanation
Indices: 47721130--47721196 Score: 111
Period size: 29 Copynumber: 2.3 Consensus size: 30
47721120 AATGTGTTTA
*
47721130 AATAAAATAATGTTAAGTTTTTTTATATTT
1 AATAAAATAATGTTAAGCTTTTTTATATTT
47721160 AA-AAAATAATGTTAA-CTTTTTTATATTT
1 AATAAAATAATGTTAAGCTTTTTTATATTT
47721188 AATAAAATA
1 AATAAAATA
47721197 TATATAAGAA
Statistics
Matches: 35, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
28 14 0.40
29 19 0.54
30 2 0.06
ACGTcount: A:0.46, C:0.01, G:0.04, T:0.48
Consensus pattern (30 bp):
AATAAAATAATGTTAAGCTTTTTTATATTT
Found at i:47724701 original size:21 final size:22
Alignment explanation
Indices: 47724653--47724702 Score: 61
Period size: 21 Copynumber: 2.4 Consensus size: 22
47724643 TGAAATTATT
*
47724653 GAAA-TAAAACACTATTATCAA
1 GAAATTAAAACACCATTATCAA
47724674 GAAATTAAAACATCCATTA-CAA
1 GAAATTAAAACA-CCATTATCAA
47724696 -AAATTAA
1 GAAATTAA
47724703 TTAGTGAATA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
21 11 0.42
22 10 0.38
23 5 0.19
ACGTcount: A:0.58, C:0.14, G:0.04, T:0.24
Consensus pattern (22 bp):
GAAATTAAAACACCATTATCAA
Found at i:47728284 original size:44 final size:46
Alignment explanation
Indices: 47728197--47728289 Score: 154
Period size: 44 Copynumber: 2.1 Consensus size: 46
47728187 GGTTCGTTGT
*
47728197 AATGGAATAGAGGCGTAATAAGTAATTCTTTTGTTTGGTTGAATGG
1 AATGGAATAGAGGCGTAATAAGTAATTCTTGTGTTTGGTTGAATGG
*
47728243 AATGGAATAGAGGCGTAAT-GGT-ATTCTTGTGTTTGGTTGAATGG
1 AATGGAATAGAGGCGTAATAAGTAATTCTTGTGTTTGGTTGAATGG
47728287 AAT
1 AAT
47728290 AGAGGTGTAA
Statistics
Matches: 45, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
44 24 0.53
45 2 0.04
46 19 0.42
ACGTcount: A:0.29, C:0.04, G:0.30, T:0.37
Consensus pattern (46 bp):
AATGGAATAGAGGCGTAATAAGTAATTCTTGTGTTTGGTTGAATGG
Found at i:47728285 original size:39 final size:41
Alignment explanation
Indices: 47728192--47728301 Score: 125
Period size: 46 Copynumber: 2.6 Consensus size: 41
47728182 CGTTTGGTTC
*
47728192 GTTGTAATGGAATAGAGGCGTAATAAGTAATTCTTTTGTTTG
1 GTTG-AATGGAATAGAGGCGTAATAAGTAATTCTTGTGTTTG
*
47728234 GTTGAATGGAATGGAATAGAGGCGTAAT-GGT-ATTCTTGTGTTTG
1 G-T---T-GAATGGAATAGAGGCGTAATAAGTAATTCTTGTGTTTG
*
47728278 GTTGAATGGAATAGAGGTGTAATA
1 GTTGAATGGAATAGAGGCGTAATA
47728302 GCATAAGGAA
Statistics
Matches: 59, Mismatches: 3, Indels: 14
0.78 0.04 0.18
Matches are distributed among these distances:
39 19 0.32
40 1 0.02
42 1 0.02
43 2 0.03
44 13 0.22
45 2 0.03
46 20 0.34
47 1 0.02
ACGTcount: A:0.29, C:0.04, G:0.31, T:0.36
Consensus pattern (41 bp):
GTTGAATGGAATAGAGGCGTAATAAGTAATTCTTGTGTTTG
Found at i:47728494 original size:39 final size:41
Alignment explanation
Indices: 47728446--47728546 Score: 109
Period size: 41 Copynumber: 2.4 Consensus size: 41
47728436 AATTGTTATT
*
47728446 AAATATAATTTAATAAAAATCA-TAATATATAA-TACT-ATA
1 AAATATAATTTAATAAAAATCATTAA-ATATAATTAATAATA
* *
47728485 AAATATAATTTAAAATAATAATTATTAAATATAATTTAATAATA
1 AAATATAATTT--AATAAAAATCATTAAATATAA-TTAATAATA
*
47728529 ATATATAATTTAATAAAA
1 AAATATAATTTAATAAAA
47728547 TTCTTATTCT
Statistics
Matches: 51, Mismatches: 5, Indels: 9
0.78 0.08 0.14
Matches are distributed among these distances:
39 11 0.22
41 15 0.29
42 9 0.18
43 3 0.06
44 13 0.25
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (41 bp):
AAATATAATTTAATAAAAATCATTAAATATAATTAATAATA
Found at i:47728519 original size:109 final size:107
Alignment explanation
Indices: 47728406--47728628 Score: 290
Period size: 110 Copynumber: 2.0 Consensus size: 107
47728396 ATTAATATAA
* *
47728406 ATAATAAATAATTTAATCATAT-TTTAACATAATTGTTATT-AAATAT-AATTTAATAAAAATCA
1 ATAATAAATAA--TAAT-ATATATTTAACAAAATTCTTATTCAAATATGAATTTAAT-AAAATCA
47728468 TAATATATAATACTATAAAATATAATTTAAAATAATAATTATTAAAT
62 TAATATATAATACTATAAAATATAATTT-AAATAATAATTATTAAAT
* * ** *
47728515 ATAATTTAATAATAATATATAATTTAATAAAATTCTTATTCTTATATGAATTTACTAAAATCATA
1 ATAA-TAAATAATAATATAT-ATTTAACAAAATTCTTATTCAAATATGAATTTAATAAAATCATA
*
47728580 ATATATAATACTATAAAATATAATTTAAATAATTATTATTAAAT
64 ATATATAATACTATAAAATATAATTTAAATAATAATTATTAAAT
47728624 ATAAT
1 ATAAT
47728629 TTATAATCTA
Statistics
Matches: 101, Mismatches: 8, Indels: 11
0.84 0.07 0.09
Matches are distributed among these distances:
107 4 0.04
108 5 0.05
109 40 0.40
110 45 0.45
111 7 0.07
ACGTcount: A:0.52, C:0.04, G:0.01, T:0.43
Consensus pattern (107 bp):
ATAATAAATAATAATATATATTTAACAAAATTCTTATTCAAATATGAATTTAATAAAATCATAAT
ATATAATACTATAAAATATAATTTAAATAATAATTATTAAAT
Found at i:47728533 original size:59 final size:58
Alignment explanation
Indices: 47728428--47728635 Score: 166
Period size: 65 Copynumber: 3.6 Consensus size: 58
47728418 TTAATCATAT
*
47728428 TTTAACATAATTGTTATTAAATATAATTTAATAAAAATCATAATATATAATACTATAAAATATAA
1 TTTAA-ATAATTATTATTAAATATAATTTAAT----A--ATAATATATAATACTATAAAATATAA
* *
47728493 TTTAAAATAATAATTATTAAATATAATTTAATAATAATATATAAT--T-T--AATAAAA
1 TTT-AAATAATTATTATTAAATATAATTTAATAATAATATATAATACTATAAAATATAA
* * * * ** *
47728547 TTCT---T-ATTCTTATATGAATTTACTAAAATCATAATATATAATACTATAAAATATAA
1 TT-TAAATAATTATTAT-TAAATATAATTTAATAATAATATATAATACTATAAAATATAA
47728603 TTTAAATAATTATTATTAAATATAATTT-ATAAT
1 TTTAAATAATTATTATTAAATATAATTTAATAAT
47728636 CTACTTTATT
Statistics
Matches: 112, Mismatches: 19, Indels: 32
0.69 0.12 0.20
Matches are distributed among these distances:
50 6 0.05
51 23 0.21
53 1 0.01
54 9 0.08
55 2 0.02
56 9 0.08
57 5 0.04
58 8 0.07
59 19 0.17
61 1 0.01
65 27 0.24
66 2 0.02
ACGTcount: A:0.52, C:0.04, G:0.01, T:0.43
Consensus pattern (58 bp):
TTTAAATAATTATTATTAAATATAATTTAATAATAATATATAATACTATAAAATATAA
Found at i:47728537 original size:13 final size:13
Alignment explanation
Indices: 47728448--47728537 Score: 57
Period size: 13 Copynumber: 7.0 Consensus size: 13
47728438 TTGTTATTAA
47728448 ATATAATT-TAAT
1 ATATAATTATAAT
* *
47728460 A-AAAATCATAAT
1 ATATAATTATAAT
*
47728472 ATATAATACTATAAA
1 ATATAAT--TATAAT
*
47728487 ATATAATT-TAAA
1 ATATAATTATAAT
47728499 ATAATAATTATTAA-
1 AT-ATAATTA-TAAT
47728513 ATATAATT-TAAT
1 ATATAATTATAAT
47728525 A-ATAATATATAAT
1 ATATAAT-TATAAT
47728538 TTAATAAAAT
Statistics
Matches: 63, Mismatches: 5, Indels: 19
0.72 0.06 0.22
Matches are distributed among these distances:
11 12 0.19
12 14 0.22
13 21 0.33
14 2 0.03
15 14 0.22
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (13 bp):
ATATAATTATAAT
Found at i:47730210 original size:25 final size:25
Alignment explanation
Indices: 47730176--47730237 Score: 115
Period size: 25 Copynumber: 2.5 Consensus size: 25
47730166 CAATTTACTG
47730176 GAATTGCAACTATAAAATACCTCTT
1 GAATTGCAACTATAAAATACCTCTT
47730201 GAATTGCAACTATAAAATACCTCTT
1 GAATTGCAACTATAAAATACCTCTT
*
47730226 GAAATGCAACTA
1 GAATTGCAACTA
47730238 GAGCTTCAGC
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 36 1.00
ACGTcount: A:0.42, C:0.19, G:0.10, T:0.29
Consensus pattern (25 bp):
GAATTGCAACTATAAAATACCTCTT
Found at i:47733787 original size:19 final size:19
Alignment explanation
Indices: 47733744--47733787 Score: 54
Period size: 19 Copynumber: 2.3 Consensus size: 19
47733734 ATCATTTTTA
* *
47733744 TTTACAAAAAACCTTAGTT
1 TTTAGAAAAAACCGTAGTT
47733763 TTTAGAAAAAACCGT-GTT
1 TTTAGAAAAAACCGTAGTT
47733781 TTGTAGA
1 TT-TAGA
47733788 GTTGCAGTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
18 5 0.23
19 17 0.77
ACGTcount: A:0.39, C:0.11, G:0.14, T:0.36
Consensus pattern (19 bp):
TTTAGAAAAAACCGTAGTT
Found at i:47736504 original size:4 final size:4
Alignment explanation
Indices: 47736497--47736554 Score: 50
Period size: 4 Copynumber: 14.8 Consensus size: 4
47736487 CCCTCCTTTC
* * *
47736497 TTTA TTTA TTTC TCTA TTTA TTTA -TTA TTTA -TTA -TTA GTTA TTTTA
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA -TTTA
47736543 TTTTA TTTA TTT
1 -TTTA TTTA TTT
47736555 CTTGTTTATT
Statistics
Matches: 46, Mismatches: 5, Indels: 6
0.81 0.09 0.11
Matches are distributed among these distances:
3 9 0.20
4 29 0.63
5 8 0.17
ACGTcount: A:0.22, C:0.03, G:0.02, T:0.72
Consensus pattern (4 bp):
TTTA
Found at i:47738971 original size:14 final size:14
Alignment explanation
Indices: 47738948--47738978 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
47738938 TGTCGCGTTC
*
47738948 TTAGTTAATTTAGA
1 TTAGTAAATTTAGA
47738962 TTAGTAAATTTAGA
1 TTAGTAAATTTAGA
47738976 TTA
1 TTA
47738979 AAACAATTCC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.39, C:0.00, G:0.13, T:0.48
Consensus pattern (14 bp):
TTAGTAAATTTAGA
Found at i:47741126 original size:29 final size:30
Alignment explanation
Indices: 47741079--47741145 Score: 91
Period size: 29 Copynumber: 2.2 Consensus size: 30
47741069 CTAAGATGAC
* *
47741079 TATATAAAAATTTTCAATAATAAAA-AATA
1 TATATAAAAATATTAAATAATAAAATAATA
*
47741108 TATATAAAAATATTAAATATTAAAATAATA
1 TATATAAAAATATTAAATAATAAAATAATA
47741138 TAATATAA
1 T-ATATAA
47741146 TATAAGTATT
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
29 22 0.67
30 5 0.15
31 6 0.18
ACGTcount: A:0.63, C:0.01, G:0.00, T:0.36
Consensus pattern (30 bp):
TATATAAAAATATTAAATAATAAAATAATA
Found at i:47741496 original size:17 final size:17
Alignment explanation
Indices: 47741454--47741497 Score: 63
Period size: 17 Copynumber: 2.6 Consensus size: 17
47741444 AAATTTTCAT
47741454 TTAATTAAAAGTTAAAA
1 TTAATTAAAAGTTAAAA
47741471 -TAACTTAAAAGTTAAAA
1 TTAA-TTAAAAGTTAAAA
*
47741488 TTAAATAAAA
1 TTAATTAAAA
47741498 TATTGTTGTC
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
16 3 0.12
17 18 0.75
18 3 0.12
ACGTcount: A:0.61, C:0.02, G:0.05, T:0.32
Consensus pattern (17 bp):
TTAATTAAAAGTTAAAA
Found at i:47742493 original size:3 final size:3
Alignment explanation
Indices: 47742485--47742572 Score: 158
Period size: 3 Copynumber: 29.3 Consensus size: 3
47742475 TGAGCAACTC
*
47742485 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTA TTG TTG TTG TTG TTG TTG
1 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG
*
47742533 TTG TTG TTG TTA TTG TTG TTG TTG TTG TTG TTG TTG TTG T
1 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG T
47742573 CATCATTATT
Statistics
Matches: 81, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 81 1.00
ACGTcount: A:0.02, C:0.00, G:0.31, T:0.67
Consensus pattern (3 bp):
TTG
Found at i:47744016 original size:31 final size:31
Alignment explanation
Indices: 47743981--47744046 Score: 96
Period size: 31 Copynumber: 2.1 Consensus size: 31
47743971 ACAAAATGGT
*
47743981 CACTGAACTATTCAAAACTTTTCATTTAAGC
1 CACTGAACAATTCAAAACTTTTCATTTAAGC
* * *
47744012 CACTGAACAATTCAAAAGTTTTTATTTAAGT
1 CACTGAACAATTCAAAACTTTTCATTTAAGC
47744043 CACT
1 CACT
47744047 AGGCTATTAA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.36, C:0.20, G:0.08, T:0.36
Consensus pattern (31 bp):
CACTGAACAATTCAAAACTTTTCATTTAAGC
Found at i:47749849 original size:62 final size:57
Alignment explanation
Indices: 47749751--47749883 Score: 167
Period size: 62 Copynumber: 2.2 Consensus size: 57
47749741 ATCATTTTAA
* * * *
47749751 TATTAAATTAATATAATATTTATCAAGATAAATATTAGATTAAATTAAATTTTAAATTT
1 TATTAAAATAATATAATATTTATCAAGATAAATATTAAATTAAATTAAATATTAAA--C
* *
47749810 TATTAAAATAATATAATGTTTATCTGCAAGATAAATATTAAATTAAATTTAATATTAAAC
1 TATTAAAATAATATAATATTTA--T-CAAGATAAATATTAAATTAAATTAAATATTAAAC
47749870 TATTAAAATAATAT
1 TATTAAAATAATAT
47749884 TATTTTTGGA
Statistics
Matches: 65, Mismatches: 6, Indels: 5
0.86 0.08 0.07
Matches are distributed among these distances:
59 20 0.31
60 14 0.22
61 1 0.02
62 30 0.46
ACGTcount: A:0.50, C:0.03, G:0.04, T:0.43
Consensus pattern (57 bp):
TATTAAAATAATATAATATTTATCAAGATAAATATTAAATTAAATTAAATATTAAAC
Found at i:47750012 original size:23 final size:22
Alignment explanation
Indices: 47749986--47750030 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 22
47749976 CGTAGCCGGC
*
47749986 CACTGGGA-CGCCGTCGTCGCAGT
1 CACTGGCACCGCCGT-GTC-CAGT
47750009 CACTGGCACCGCCGTGTCCAGT
1 CACTGGCACCGCCGTGTCCAGT
47750031 GATGTAGGTG
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
22 4 0.20
23 10 0.50
24 6 0.30
ACGTcount: A:0.13, C:0.38, G:0.31, T:0.18
Consensus pattern (22 bp):
CACTGGCACCGCCGTGTCCAGT
Found at i:47755247 original size:14 final size:15
Alignment explanation
Indices: 47755219--47755255 Score: 58
Period size: 14 Copynumber: 2.5 Consensus size: 15
47755209 CAATGTAGAT
47755219 AAAATGAAACAAATAA
1 AAAAT-AAACAAATAA
47755235 AAAATAAAC-AATAA
1 AAAATAAACAAATAA
47755249 AAAATAA
1 AAAATAA
47755256 TCATACGGGC
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
14 12 0.57
15 4 0.19
16 5 0.24
ACGTcount: A:0.78, C:0.05, G:0.03, T:0.14
Consensus pattern (15 bp):
AAAATAAACAAATAA
Found at i:47758628 original size:77 final size:77
Alignment explanation
Indices: 47758501--47758658 Score: 282
Period size: 77 Copynumber: 2.1 Consensus size: 77
47758491 CCACCAATTG
*
47758501 ACAATCACTAAGAACCTCTCTAAAAGCTTTCATTCGTCTTTCCTCTCTAGGTAGCCCTCATTTCT
1 ACAATCACTAAGAACCTCTCTAAAAGCTTTCATTCGTCTTTCCTCTCTAGGTAGCCCTAATTTCT
*
47758566 TTTTAAAGGTAT
66 TTTTAAAGGCAT
47758578 ACAATCACTAAGAACCTCTCTAAAAGC-TTCTATTCGTCTTTCCTCTCTAGGTAGCCCTAATTTC
1 ACAATCACTAAGAACCTCTCTAAAAGCTTTC-ATTCGTCTTTCCTCTCTAGGTAGCCCTAATTTC
47758642 TTTTTAAAGGCAT
65 TTTTTAAAGGCAT
47758655 ACAA
1 ACAA
47758659 AATCTCATTA
Statistics
Matches: 78, Mismatches: 2, Indels: 2
0.95 0.02 0.02
Matches are distributed among these distances:
76 3 0.04
77 75 0.96
ACGTcount: A:0.28, C:0.26, G:0.10, T:0.36
Consensus pattern (77 bp):
ACAATCACTAAGAACCTCTCTAAAAGCTTTCATTCGTCTTTCCTCTCTAGGTAGCCCTAATTTCT
TTTTAAAGGCAT
Found at i:47763262 original size:16 final size:16
Alignment explanation
Indices: 47763241--47763272 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
47763231 GTACCACCCA
47763241 TGTGACCATTGTCATC
1 TGTGACCATTGTCATC
47763257 TGTGACCATTGTCATC
1 TGTGACCATTGTCATC
47763273 CGATACATGC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.19, C:0.25, G:0.19, T:0.38
Consensus pattern (16 bp):
TGTGACCATTGTCATC
Found at i:47763403 original size:51 final size:50
Alignment explanation
Indices: 47763269--47763463 Score: 193
Period size: 51 Copynumber: 3.9 Consensus size: 50
47763259 TGACCATTGT
47763269 CATCCGATACATGCA-A-TAGCCTACACATAGTACTACACACGTGATC-AAG-
1 CATCCGATACA--CATAGTAGCCTACACATAGTACTACACACGTGA-CAAAGC
* * * * * *
47763318 CTTTCTAGTTCACGTAGTAGCCTGCACATAGTACTACACACGTGACCAAAGC
1 CATCCGA-TACACATAGTAGCCTACACATAGTACTACACACGTGA-CAAAGC
* * *
47763370 CATCCGATACACATAGTAGCCTGCACATAGTACTACACATGTGACAATCATC
1 CATCCGATACACATAGTAGCCTACACATAGTACTACACACGTGACAA--AGC
* *
47763422 TAT-CGATACACATAGTAGCCTACACTTAGTACTACACACGTG
1 CATCCGATACACATAGTAGCCTACACATAGTACTACACACGTG
47763464 TTCATAAGTA
Statistics
Matches: 121, Mismatches: 18, Indels: 12
0.80 0.12 0.08
Matches are distributed among these distances:
48 1 0.01
49 5 0.04
50 34 0.28
51 73 0.60
52 8 0.07
ACGTcount: A:0.33, C:0.28, G:0.15, T:0.24
Consensus pattern (50 bp):
CATCCGATACACATAGTAGCCTACACATAGTACTACACACGTGACAAAGC
Found at i:47767686 original size:14 final size:13
Alignment explanation
Indices: 47767669--47767705 Score: 56
Period size: 14 Copynumber: 2.7 Consensus size: 13
47767659 GTTTCTCTCA
47767669 TTTTTCTTCTTTC
1 TTTTTCTTCTTTC
47767682 TTTTTCATTCTTTC
1 TTTTTC-TTCTTTC
47767696 TTTTTTCTTC
1 -TTTTTCTTC
47767706 AATTTATTTG
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 6 0.27
14 10 0.45
15 6 0.27
ACGTcount: A:0.03, C:0.22, G:0.00, T:0.76
Consensus pattern (13 bp):
TTTTTCTTCTTTC
Found at i:47769455 original size:18 final size:20
Alignment explanation
Indices: 47769422--47769507 Score: 74
Period size: 19 Copynumber: 4.5 Consensus size: 20
47769412 ACAAAAAATT
*
47769422 AAATTCAAAATAATTT-TTA
1 AAATTCAAAATAATTTATAA
47769441 AAATTCAAAAT-ATTTATAA
1 AAATTCAAAATAATTTATAA
*
47769460 AAATTC-CAA-AATTTAT-A
1 AAATTCAAAATAATTTATAA
* * * *
47769477 TATTTAAAAAAAATTTATAA
1 AAATTCAAAATAATTTATAA
47769497 AAATTTCAAAA
1 AAA-TTCAAAA
47769508 AAAATCTATA
Statistics
Matches: 52, Mismatches: 9, Indels: 10
0.73 0.13 0.14
Matches are distributed among these distances:
17 4 0.08
18 14 0.27
19 26 0.50
20 2 0.04
21 6 0.12
ACGTcount: A:0.57, C:0.06, G:0.00, T:0.37
Consensus pattern (20 bp):
AAATTCAAAATAATTTATAA
Found at i:47769510 original size:22 final size:21
Alignment explanation
Indices: 47769478--47769520 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 21
47769468 AAATTTATAT
*
47769478 ATTTAAAAAAAATTTATAAAA
1 ATTTAAAAAAAATCTATAAAA
47769499 ATTTCAAAAAAAATCTATAAAA
1 ATTT-AAAAAAAATCTATAAAA
47769521 TATATAAAGA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 4 0.20
22 16 0.80
ACGTcount: A:0.65, C:0.05, G:0.00, T:0.30
Consensus pattern (21 bp):
ATTTAAAAAAAATCTATAAAA
Found at i:47769668 original size:16 final size:16
Alignment explanation
Indices: 47769649--47769679 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
47769639 TTGAAAAAGT
47769649 TTTCAAATATATATGG
1 TTTCAAATATATATGG
*
47769665 TTTCAAATTTATATG
1 TTTCAAATATATATG
47769680 CTCCGACATG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.35, C:0.06, G:0.10, T:0.48
Consensus pattern (16 bp):
TTTCAAATATATATGG
Found at i:47771181 original size:21 final size:21
Alignment explanation
Indices: 47771157--47771199 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
47771147 AAAAGTTAAC
47771157 ATTTGTTACAT-TATAAATAAA
1 ATTTGTTA-ATCTATAAATAAA
* *
47771178 ATTTTTTAATCTATAAGTAAA
1 ATTTGTTAATCTATAAATAAA
47771199 A
1 A
47771200 AAAATTATAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 2 0.11
21 17 0.89
ACGTcount: A:0.47, C:0.05, G:0.05, T:0.44
Consensus pattern (21 bp):
ATTTGTTAATCTATAAATAAA
Found at i:47771254 original size:15 final size:15
Alignment explanation
Indices: 47771230--47771259 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
47771220 GAGTATGGTA
47771230 AAATAATAAAAAAAT
1 AAATAATAAAAAAAT
*
47771245 AAATATTAAAAAAAT
1 AAATAATAAAAAAAT
47771260 TACTAATAGT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (15 bp):
AAATAATAAAAAAAT
Found at i:47776013 original size:23 final size:24
Alignment explanation
Indices: 47775972--47776019 Score: 80
Period size: 24 Copynumber: 2.0 Consensus size: 24
47775962 CAGTACAAAT
47775972 AACAAAAACAATAGCAAAAATAAC
1 AACAAAAACAATAGCAAAAATAAC
*
47775996 AACAAAAACAGTAG-AAAAATAAC
1 AACAAAAACAATAGCAAAAATAAC
47776019 A
1 A
47776020 GCACCAAAAC
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
23 10 0.43
24 13 0.57
ACGTcount: A:0.71, C:0.15, G:0.06, T:0.08
Consensus pattern (24 bp):
AACAAAAACAATAGCAAAAATAAC
Found at i:47776546 original size:24 final size:24
Alignment explanation
Indices: 47776503--47776552 Score: 75
Period size: 25 Copynumber: 2.0 Consensus size: 24
47776493 TTTTTGACCA
47776503 TTTAAAAATTTGACTCTAATTTTTT
1 TTTAAAAATTT-ACTCTAATTTTTT
47776528 TTTAAAAATTT-CTCTTAATTTTTT
1 TTTAAAAATTTACTC-TAATTTTTT
47776552 T
1 T
47776553 GAACTTTATT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
23 3 0.12
24 10 0.42
25 11 0.46
ACGTcount: A:0.30, C:0.08, G:0.02, T:0.60
Consensus pattern (24 bp):
TTTAAAAATTTACTCTAATTTTTT
Found at i:47776663 original size:11 final size:11
Alignment explanation
Indices: 47776643--47776686 Score: 70
Period size: 11 Copynumber: 3.9 Consensus size: 11
47776633 CTCAACACTA
47776643 AAATTGAGAGG
1 AAATTGAGAGG
*
47776654 AAATTTAGAGG
1 AAATTGAGAGG
47776665 AAATTGAGAGG
1 AAATTGAGAGG
47776676 AAATTTGAGAG
1 AAA-TTGAGAG
47776687 AGGATTAGTT
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
11 23 0.77
12 7 0.23
ACGTcount: A:0.45, C:0.00, G:0.32, T:0.23
Consensus pattern (11 bp):
AAATTGAGAGG
Found at i:47776671 original size:22 final size:23
Alignment explanation
Indices: 47776643--47776686 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 23
47776633 CTCAACACTA
47776643 AAATTGAGAGGAAATTT-AGAGG
1 AAATTGAGAGGAAATTTGAGAGG
47776665 AAATTGAGAGGAAATTTGAGAG
1 AAATTGAGAGGAAATTTGAGAG
47776687 AGGATTAGTT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
22 17 0.81
23 4 0.19
ACGTcount: A:0.45, C:0.00, G:0.32, T:0.23
Consensus pattern (23 bp):
AAATTGAGAGGAAATTTGAGAGG
Found at i:47776811 original size:20 final size:20
Alignment explanation
Indices: 47776782--47776820 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
47776772 CGCTTTGCTG
*
47776782 ACGTGGCAACAAATCGCGTT
1 ACGTGACAACAAATCGCGTT
47776802 ACGTGACAACAAATCGCGT
1 ACGTGACAACAAATCGCGT
47776821 CCACGTCAGC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.33, C:0.26, G:0.23, T:0.18
Consensus pattern (20 bp):
ACGTGACAACAAATCGCGTT
Found at i:47776845 original size:60 final size:60
Alignment explanation
Indices: 47776752--47776875 Score: 221
Period size: 60 Copynumber: 2.1 Consensus size: 60
47776742 TTGAGGGGAG
47776752 AAATCGCGGCCACGTCAACACGCTTTGCTGACGTGGCAACAAATCGCGTTACGTGACAAC
1 AAATCGCGGCCACGTCAACACGCTTTGCTGACGTGGCAACAAATCGCGTTACGTGACAAC
* * *
47776812 AAATCGCGTCCACGTCAGCACGCTTTGCTGACGTGGCAACAAATCGCGTTACGTGGCAAC
1 AAATCGCGGCCACGTCAACACGCTTTGCTGACGTGGCAACAAATCGCGTTACGTGACAAC
47776872 AAAT
1 AAAT
47776876 TGCCCCCTCA
Statistics
Matches: 61, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
60 61 1.00
ACGTcount: A:0.28, C:0.29, G:0.23, T:0.19
Consensus pattern (60 bp):
AAATCGCGGCCACGTCAACACGCTTTGCTGACGTGGCAACAAATCGCGTTACGTGACAAC
Found at i:47780841 original size:22 final size:24
Alignment explanation
Indices: 47780805--47780851 Score: 64
Period size: 22 Copynumber: 2.0 Consensus size: 24
47780795 GTCCTCAAGA
47780805 TCGAAGATCTTTATTTAA-TTTCTT
1 TCGAAGATCTTTA-TTAAGTTTCTT
47780829 TCGAAG-T-TTTATTAAGTTTCTT
1 TCGAAGATCTTTATTAAGTTTCTT
47780851 T
1 T
47780852 ATATCTTGTG
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
21 4 0.18
22 11 0.50
23 1 0.05
24 6 0.27
ACGTcount: A:0.23, C:0.11, G:0.11, T:0.55
Consensus pattern (24 bp):
TCGAAGATCTTTATTAAGTTTCTT
Found at i:47781778 original size:33 final size:33
Alignment explanation
Indices: 47781684--47781784 Score: 103
Period size: 33 Copynumber: 3.0 Consensus size: 33
47781674 TCAACTTGCA
* *
47781684 TTGTGTTTACTGTCCCGATAGACTTCATCTCTATT
1 TTGTGTTTACTGTCCCAATAGACTT-A-CTCTTTT
** * ** *
47781719 CCGTGTTTACTGTCCTAGCAGGCTTACTCTTTT
1 TTGTGTTTACTGTCCCAATAGACTTACTCTTTT
*
47781752 TTGTGTTTACTATCCCAATAGACTTACTCTTTT
1 TTGTGTTTACTGTCCCAATAGACTTACTCTTTT
47781785 AATGCCATAG
Statistics
Matches: 51, Mismatches: 15, Indels: 2
0.75 0.22 0.03
Matches are distributed among these distances:
33 32 0.63
34 1 0.02
35 18 0.35
ACGTcount: A:0.17, C:0.24, G:0.14, T:0.46
Consensus pattern (33 bp):
TTGTGTTTACTGTCCCAATAGACTTACTCTTTT
Found at i:47783370 original size:17 final size:18
Alignment explanation
Indices: 47783333--47783375 Score: 61
Period size: 17 Copynumber: 2.4 Consensus size: 18
47783323 TTTATATTTT
* *
47783333 TAAAAATATTAATTATTA
1 TAAAAATATTAAGTATGA
47783351 TAAAAATATT-AGTATGA
1 TAAAAATATTAAGTATGA
47783368 TAAAAATA
1 TAAAAATA
47783376 ATTTCTAAAC
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 13 0.57
18 10 0.43
ACGTcount: A:0.58, C:0.00, G:0.05, T:0.37
Consensus pattern (18 bp):
TAAAAATATTAAGTATGA
Found at i:47786304 original size:12 final size:12
Alignment explanation
Indices: 47786264--47786304 Score: 57
Period size: 12 Copynumber: 3.4 Consensus size: 12
47786254 GACAATTCCT
*
47786264 AAACCAGAGGCC
1 AAACCAGAGACC
47786276 AAA-CAGGAGACC
1 AAACCA-GAGACC
47786288 AAACCAGAGACC
1 AAACCAGAGACC
47786300 AAACC
1 AAACC
47786305 GGAAACTGAA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
11 2 0.08
12 22 0.85
13 2 0.08
ACGTcount: A:0.49, C:0.32, G:0.20, T:0.00
Consensus pattern (12 bp):
AAACCAGAGACC
Done.