Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr03 135709677
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: 135709677
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 350 characters in sequence are not A, C, G, or T
File 109 of 438
Found at i:31538497 original size:54 final size:53
Alignment explanation
Indices: 31538414--31538523 Score: 166
Period size: 54 Copynumber: 2.1 Consensus size: 53
31538404 GGAAACCTTA
* *
31538414 TTCCAGAAAAAACCATTGTTCAAAAGGAAGCTACTATTTAGGGGGAGACTATTG
1 TTCCAGAAAAAACCATAGTTCAAAAGGAAGCTACTACTTA-GGGGAGACTATTG
* **
31538468 TTCCAGAAAACACCATAGTTCAATGGGAAGCTACTACTTAGGGGAGACTATTG
1 TTCCAGAAAAAACCATAGTTCAAAAGGAAGCTACTACTTAGGGGAGACTATTG
31538521 TTC
1 TTC
31538524 AAAAGAAGAT
Statistics
Matches: 51, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
53 16 0.31
54 35 0.69
ACGTcount: A:0.35, C:0.17, G:0.22, T:0.26
Consensus pattern (53 bp):
TTCCAGAAAAAACCATAGTTCAAAAGGAAGCTACTACTTAGGGGAGACTATTG
Found at i:31539162 original size:16 final size:16
Alignment explanation
Indices: 31539143--31539175 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
31539133 TTACATGGTG
31539143 ACTTGATAACATTTAA
1 ACTTGATAACATTTAA
31539159 ACTTGATAACATTTAA
1 ACTTGATAACATTTAA
31539175 A
1 A
31539176 TTAATAATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.45, C:0.12, G:0.06, T:0.36
Consensus pattern (16 bp):
ACTTGATAACATTTAA
Found at i:31541554 original size:24 final size:24
Alignment explanation
Indices: 31541522--31541568 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
31541512 CTGTTAGGAG
**
31541522 AGGATTTAGGAGTTGATAAGGGAT
1 AGGATTTAGGAGCAGATAAGGGAT
31541546 AGGATTTAGGAGCAGATAAGGGA
1 AGGATTTAGGAGCAGATAAGGGA
31541569 GGAAATCTAG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.36, C:0.02, G:0.38, T:0.23
Consensus pattern (24 bp):
AGGATTTAGGAGCAGATAAGGGAT
Found at i:31542012 original size:27 final size:27
Alignment explanation
Indices: 31541982--31542035 Score: 99
Period size: 27 Copynumber: 2.0 Consensus size: 27
31541972 CTACACTTTT
*
31541982 GCAAAAAGCCGAAACTCTCACACTATC
1 GCAAAAAGCCGAAACTCCCACACTATC
31542009 GCAAAAAGCCGAAACTCCCACACTATC
1 GCAAAAAGCCGAAACTCCCACACTATC
31542036 CTAAGGACAT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.41, C:0.35, G:0.11, T:0.13
Consensus pattern (27 bp):
GCAAAAAGCCGAAACTCCCACACTATC
Found at i:31543034 original size:27 final size:26
Alignment explanation
Indices: 31542994--31543105 Score: 100
Period size: 27 Copynumber: 4.2 Consensus size: 26
31542984 AGGAAGCGTC
*
31542994 CTGGTGGCTATGCCACAATTATCTGAT
1 CTGGTGGCTTTGCCAC-ATTATCTGAT
*
31543021 CTGGTGGCTTTGCCACATATATCTGTT
1 CTGGTGGCTTTGCCACAT-TATCTGAT
* *
31543048 CTGGTGG-TTCTACCACGATTATTTGTAT
1 CTGGTGGCTT-TGCCAC-ATTATCTG-AT
* * * *
31543076 CTGGTGACTCTGTCACATTATCTGTT
1 CTGGTGGCTTTGCCACATTATCTGAT
31543102 CTGG
1 CTGG
31543106 CAGCCATGCT
Statistics
Matches: 69, Mismatches: 11, Indels: 11
0.76 0.12 0.12
Matches are distributed among these distances:
26 9 0.13
27 46 0.67
28 13 0.19
29 1 0.01
ACGTcount: A:0.17, C:0.21, G:0.22, T:0.39
Consensus pattern (26 bp):
CTGGTGGCTTTGCCACATTATCTGAT
Found at i:31545069 original size:40 final size:40
Alignment explanation
Indices: 31544984--31545134 Score: 134
Period size: 40 Copynumber: 3.8 Consensus size: 40
31544974 AATTGAATGA
* * *
31544984 TATCCGGGCTAA-ATCCCGAAGACAATTATGCTG-GAAATTA-
1 TATCCGGGCTAAGA-CCCGAAGGCAATTGTGC-GAGACA-TAC
* * *
31545024 TATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGGC-TAC
1 TATCCGGGCTAAGACCCGAAGGCAATTGTGC--GAGACATAC
*
31545065 -ATCCGGGCTAAGACCCGAAGGC-ATTCGTGCGAGACATTC
1 TATCCGGGCTAAGACCCGAAGGCAATT-GTGCGAGACATAC
*
31545104 TATCCGGGCTAAGACCCGAAGGCATTTGTGC
1 TATCCGGGCTAAGACCCGAAGGCAATTGTGC
31545135 ACATGGTTAT
Statistics
Matches: 92, Mismatches: 11, Indels: 16
0.77 0.09 0.13
Matches are distributed among these distances:
38 3 0.03
39 5 0.05
40 79 0.86
41 4 0.04
42 1 0.01
ACGTcount: A:0.27, C:0.24, G:0.26, T:0.23
Consensus pattern (40 bp):
TATCCGGGCTAAGACCCGAAGGCAATTGTGCGAGACATAC
Found at i:31545148 original size:40 final size:40
Alignment explanation
Indices: 31545021--31545150 Score: 138
Period size: 40 Copynumber: 3.2 Consensus size: 40
31545011 ATGCTGGAAA
* * * *
31545021 TTATATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGG
1 TTATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAATGG
* * * **
31545061 CTACATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGA-CA
1 TTATATCCGGGCTAAGACCCGAAGGCATTTGTGCGA-ATGG
*
31545101 TTCTATCCGGGCTAAGACCCGAAGGCATTTGTGC-ACATGG
1 TTATATCCGGGCTAAGACCCGAAGGCATTTGTGCGA-ATGG
31545141 TTATATCCGG
1 TTATATCCGG
31545151 TTATATTCCG
Statistics
Matches: 71, Mismatches: 17, Indels: 4
0.77 0.18 0.04
Matches are distributed among these distances:
39 2 0.03
40 69 0.97
ACGTcount: A:0.25, C:0.24, G:0.28, T:0.24
Consensus pattern (40 bp):
TTATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAATGG
Found at i:31553119 original size:40 final size:40
Alignment explanation
Indices: 31552953--31553137 Score: 189
Period size: 40 Copynumber: 4.6 Consensus size: 40
31552943 TTCGAATGAT
* * *
31552953 ATCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACTAA
1 ATCCGGGCTAAGTCCCGAAGGCATTCGTGC-GAGTTACTAA
* * *
31552993 ATCCGGACTAAGAT-CCGACGGCATACGTGCGAGTTACTAA
1 ATCCGGGCTAAG-TCCCGAAGGCATTCGTGCGAGTTACTAA
* * * *
31553033 ATCCGGACTAAGAT-CCGAAGGCTTTCGAGCGAGCTACTAA
1 ATCCGGGCTAAG-TCCCGAAGGCATTCGTGCGAGTTACTAA
* *
31553073 ATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTGTA
1 ATCCGGGCTAAGTCCCGAAGGCATTCGTGCGAGTTACT-AA
*
31553114 A-CCGGGCTATGTCCCGAAGGCATT
1 ATCCGGGCTAAGTCCCGAAGGCATT
31553138 TGAATGTGTA
Statistics
Matches: 122, Mismatches: 19, Indels: 8
0.82 0.13 0.05
Matches are distributed among these distances:
39 1 0.01
40 113 0.93
41 8 0.07
ACGTcount: A:0.26, C:0.24, G:0.27, T:0.23
Consensus pattern (40 bp):
ATCCGGGCTAAGTCCCGAAGGCATTCGTGCGAGTTACTAA
Found at i:31561088 original size:40 final size:40
Alignment explanation
Indices: 31561009--31561166 Score: 160
Period size: 40 Copynumber: 4.0 Consensus size: 40
31560999 TTCGAATGAT
* * * *
31561009 ATCCGGGCTAAG-TCCCGAAGGC-TTTGTGCTAAGTGACTAA
1 ATCCGGACTAAGAT-CCGAAGGCATTCGTGC-GAGTTACTAA
* * *
31561049 ATCCGGACTAAGATCCGACGGCATACGTTCGAGTTACTAA
1 ATCCGGACTAAGATCCGAAGGCATTCGTGCGAGTTACTAA
* * *
31561089 ATCCGGACTAAGATCCGAAGGCTTTCGAGCGAGCTACTAA
1 ATCCGGACTAAGATCCGAAGGCATTCGTGCGAGTTACTAA
**
31561129 ATCCGGGTTAAG-TCCCGAAGGCATTCGTGCGAGTTACT
1 ATCCGGACTAAGAT-CCGAAGGCATTCGTGCGAGTTACT
31561167 GTAACCGGGC
Statistics
Matches: 97, Mismatches: 18, Indels: 6
0.80 0.15 0.05
Matches are distributed among these distances:
39 1 0.01
40 91 0.94
41 5 0.05
ACGTcount: A:0.27, C:0.24, G:0.26, T:0.23
Consensus pattern (40 bp):
ATCCGGACTAAGATCCGAAGGCATTCGTGCGAGTTACTAA
Found at i:31561175 original size:40 final size:40
Alignment explanation
Indices: 31561009--31561193 Score: 137
Period size: 40 Copynumber: 4.6 Consensus size: 40
31560999 TTCGAATGAT
* * *
31561009 ATCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAG-TGACTAA
1 ATCCGGGCTAAGTCCCGAAGGCATTCGAGC-GAGCT-ACTAA
* * * ** *
31561049 ATCCGGACTAAGAT-CCGACGGCATACGTTCGAGTTACTAA
1 ATCCGGGCTAAG-TCCCGAAGGCATTCGAGCGAGCTACTAA
* *
31561089 ATCCGGACTAAGAT-CCGAAGGCTTTCGAGCGAGCTACTAA
1 ATCCGGGCTAAG-TCCCGAAGGCATTCGAGCGAGCTACTAA
* * * *
31561129 ATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTGTA
1 ATCCGGGCTAAGTCCCGAAGGCATTCGAGCGAGCTACT-AA
* *
31561170 A-CCGGGCTATGTCCCAAAGGCATT
1 ATCCGGGCTAAGTCCCGAAGGCATT
31561194 TGAATGTGTA
Statistics
Matches: 119, Mismatches: 21, Indels: 10
0.79 0.14 0.07
Matches are distributed among these distances:
39 1 0.01
40 110 0.92
41 8 0.07
ACGTcount: A:0.26, C:0.24, G:0.26, T:0.23
Consensus pattern (40 bp):
ATCCGGGCTAAGTCCCGAAGGCATTCGAGCGAGCTACTAA
Found at i:31564896 original size:259 final size:259
Alignment explanation
Indices: 31564437--31564955 Score: 1020
Period size: 259 Copynumber: 2.0 Consensus size: 259
31564427 CTTCTTAATA
31564437 TGGAAATTTTACCATTTTCGCCATACAAATTATTGTTTGAGATGTTCATATCATGTTGTATTTTA
1 TGGAAATTTTACCATTTTCGCCATACAAATTATTGTTTGAGATGTTCATATCATGTTGTATTTTA
31564502 ATCATTTTTCTTATATATCGTATCCAAAATTATCAAATATAATTTTTACTACAATGTTAAATTAG
66 ATCATTTTTCTTATATATCGTATCCAAAATTATCAAATATAATTTTTACTACAATGTTAAATTAG
31564567 ACTGCCTATAATATTAACTCTGAAATTCATGATGACTATAAAATTCTGCTTCGCGGTCCAGAACT
131 ACTGCCTATAATATTAACTCTGAAATTCATGATGACTATAAAATTCTGCTTCGCGGTCCAGAACT
*
31564632 GACAGAACATGTTGCAGAGCACTGAACAGTGGAAAAGAAAGACGGAAAGAAATACGTTTTCTAC
196 GACAGAACATGTTGCAGAGCACTAAACAGTGGAAAAGAAAGACGGAAAGAAATACGTTTTCTAC
31564696 TGGAAATTTTACCATTTTCGCCATACAAATTATTGTTTGAGATGTTCATATCATGTTGTATTTTA
1 TGGAAATTTTACCATTTTCGCCATACAAATTATTGTTTGAGATGTTCATATCATGTTGTATTTTA
31564761 ATCATTTTTCTTATATATCGTATCCAAAATTATCAAATATAATTTTTACTACAATGTTAAATTAG
66 ATCATTTTTCTTATATATCGTATCCAAAATTATCAAATATAATTTTTACTACAATGTTAAATTAG
*
31564826 ACTGCCTATAATATTAACTCTGAAATTCATGATGACTATAAAATTCTTCTTCGCGGTCCAGAACT
131 ACTGCCTATAATATTAACTCTGAAATTCATGATGACTATAAAATTCTGCTTCGCGGTCCAGAACT
31564891 GACAGAACATGTTGCAGAGCACTAAACAGTGGAAAAGAAAGACGGAAAGAAATACGTTTTCTAC
196 GACAGAACATGTTGCAGAGCACTAAACAGTGGAAAAGAAAGACGGAAAGAAATACGTTTTCTAC
31564955 T
1 T
31564956 AATTTTCTTC
Statistics
Matches: 258, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
259 258 1.00
ACGTcount: A:0.35, C:0.15, G:0.14, T:0.35
Consensus pattern (259 bp):
TGGAAATTTTACCATTTTCGCCATACAAATTATTGTTTGAGATGTTCATATCATGTTGTATTTTA
ATCATTTTTCTTATATATCGTATCCAAAATTATCAAATATAATTTTTACTACAATGTTAAATTAG
ACTGCCTATAATATTAACTCTGAAATTCATGATGACTATAAAATTCTGCTTCGCGGTCCAGAACT
GACAGAACATGTTGCAGAGCACTAAACAGTGGAAAAGAAAGACGGAAAGAAATACGTTTTCTAC
Found at i:31565931 original size:22 final size:21
Alignment explanation
Indices: 31565906--31565946 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
31565896 AATTGACTTC
*
31565906 AATATTTTAATTAAAATAATTA
1 AATATATTAATT-AAATAATTA
*
31565928 AATATATTAGTTAAATAAT
1 AATATATTAATTAAATAAT
31565947 ATTATGTAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 7 0.41
22 10 0.59
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (21 bp):
AATATATTAATTAAATAATTA
Found at i:31565986 original size:13 final size:13
Alignment explanation
Indices: 31565968--31566000 Score: 50
Period size: 14 Copynumber: 2.5 Consensus size: 13
31565958 GAATTAAATT
31565968 ATATTAATTTTAA
1 ATATTAATTTTAA
31565981 ATATTAAATTTTAA
1 ATATT-AATTTTAA
31565995 AT-TTAA
1 ATATTAA
31566001 ATATTGTAGA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
12 2 0.11
13 7 0.37
14 10 0.53
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (13 bp):
ATATTAATTTTAA
Found at i:31566001 original size:13 final size:14
Alignment explanation
Indices: 31565968--31566002 Score: 56
Period size: 13 Copynumber: 2.6 Consensus size: 14
31565958 GAATTAAATT
31565968 ATATT-AATTTTAA
1 ATATTAAATTTTAA
31565981 ATATTAAATTTTAA
1 ATATTAAATTTTAA
31565995 AT-TTAAAT
1 ATATTAAAT
31566003 ATTGTAGATA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
13 11 0.52
14 10 0.48
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (14 bp):
ATATTAAATTTTAA
Found at i:31566264 original size:8 final size:8
Alignment explanation
Indices: 31566251--31566275 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
31566241 ATATGGTGGA
31566251 ATCCATTT
1 ATCCATTT
31566259 ATCCATTT
1 ATCCATTT
31566267 ATCCATTT
1 ATCCATTT
31566275 A
1 A
31566276 AGGGGTAACA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.28, C:0.24, G:0.00, T:0.48
Consensus pattern (8 bp):
ATCCATTT
Found at i:31567114 original size:24 final size:24
Alignment explanation
Indices: 31567087--31567149 Score: 78
Period size: 21 Copynumber: 2.8 Consensus size: 24
31567077 TTTAGAGTTT
31567087 AGAGACCGTAAACTCCAAAGAGGC
1 AGAGACCGTAAACTCCAAAGAGGC
*
31567111 AGAGACC--AAA-TCGAAAGAGGC
1 AGAGACCGTAAACTCCAAAGAGGC
* *
31567132 AAAGACTGTAAACTCCAA
1 AGAGACCGTAAACTCCAA
31567150 GTAAGTACCT
Statistics
Matches: 32, Mismatches: 4, Indels: 6
0.76 0.10 0.14
Matches are distributed among these distances:
21 15 0.47
22 3 0.09
23 3 0.09
24 11 0.34
ACGTcount: A:0.46, C:0.22, G:0.22, T:0.10
Consensus pattern (24 bp):
AGAGACCGTAAACTCCAAAGAGGC
Found at i:31569443 original size:46 final size:46
Alignment explanation
Indices: 31569384--31569556 Score: 181
Period size: 46 Copynumber: 3.7 Consensus size: 46
31569374 TGGTTGAGCA
* *
31569384 TCCGAACTAGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACG
* * * * *
31569430 TCCAAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATGTAACTAGGCA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAA--A--CG
* *
31569477 TCCGAACTCGTTGAGTTGAGTCCGAGTTCATTTATGGATGCGAACG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACG
* * *
31569523 CCCGAGCTCATTGAGTTGAGTCCGAGTTCACTTA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTA
31569557 GGGGCGGGTT
Statistics
Matches: 103, Mismatches: 17, Indels: 14
0.77 0.13 0.10
Matches are distributed among these distances:
43 6 0.06
45 3 0.03
46 58 0.56
47 28 0.27
48 3 0.03
50 5 0.05
ACGTcount: A:0.24, C:0.20, G:0.27, T:0.29
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACG
Found at i:31569540 original size:93 final size:93
Alignment explanation
Indices: 31569381--31569551 Score: 270
Period size: 93 Copynumber: 1.8 Consensus size: 93
31569371 GGATGGTTGA
* * *
31569381 GCATCCGAACTAGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATGTCCAAACTCGTTGAGT
1 GCATCCGAACTAGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACGCCCAAACTCATTGAGT
31569446 TGAGTCCGAGTTCGTGAGATGTAACTAG
66 TGAGTCCGAGTTCGTGAGATGTAACTAG
* * * * *
31569474 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCATTTATGGATGCGAACGCCCGAGCTCATTGAGT
1 GCATCCGAACTAGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACGCCCAAACTCATTGAGT
31569539 TGAGTCCGAGTTC
66 TGAGTCCGAGTTC
31569552 ACTTAGGGGC
Statistics
Matches: 70, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
93 70 1.00
ACGTcount: A:0.23, C:0.20, G:0.27, T:0.29
Consensus pattern (93 bp):
GCATCCGAACTAGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACGCCCAAACTCATTGAGT
TGAGTCCGAGTTCGTGAGATGTAACTAG
Found at i:31569818 original size:19 final size:20
Alignment explanation
Indices: 31569781--31569818 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
31569771 ATAAGGTGGT
31569781 AAGATGATGAATGATGTTTA
1 AAGATGATGAATGATGTTTA
31569801 AAGATG-TGATAT-ATGTTT
1 AAGATGATGA-ATGATGTTT
31569819 TGGTGGTACC
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.37, C:0.00, G:0.24, T:0.39
Consensus pattern (20 bp):
AAGATGATGAATGATGTTTA
Found at i:31571031 original size:6 final size:6
Alignment explanation
Indices: 31571022--31571070 Score: 89
Period size: 6 Copynumber: 8.2 Consensus size: 6
31571012 TTTCAAAACC
*
31571022 AAAGGG AAAGGG AAAGGG AAAGGG AAAGGG AAAGGG AAAGGG GAAGGG
1 AAAGGG AAAGGG AAAGGG AAAGGG AAAGGG AAAGGG AAAGGG AAAGGG
31571070 A
1 A
31571071 TCGTATAGGT
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
6 41 1.00
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (6 bp):
AAAGGG
Found at i:31571317 original size:20 final size:20
Alignment explanation
Indices: 31571294--31571341 Score: 82
Period size: 19 Copynumber: 2.5 Consensus size: 20
31571284 TTATATTTCA
31571294 TTTTTATTTA-TTATCAATG
1 TTTTTATTTATTTATCAATG
31571313 TTTTTATTTATTTATCAATG
1 TTTTTATTTATTTATCAATG
31571333 TTTTT-TTTA
1 TTTTTATTTA
31571342 AATCTAATAT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
19 14 0.50
20 14 0.50
ACGTcount: A:0.23, C:0.04, G:0.04, T:0.69
Consensus pattern (20 bp):
TTTTTATTTATTTATCAATG
Found at i:31571964 original size:40 final size:39
Alignment explanation
Indices: 31571885--31571974 Score: 103
Period size: 40 Copynumber: 2.3 Consensus size: 39
31571875 TTTTTTGGGA
* * *
31571885 TTTA-GGGTTTAGGGGTTATAGATTAGTGTTTAGG-GTT
1 TTTAGGGGTTTAGGGGTTATAGACTAGTGTCTAGGATTT
* *
31571922 TTTCGGGGTTTAGGGGTTATATAGACTAGTGTCTATGATTT
1 TTTAGGGGTTTAGGGG-T-TATAGACTAGTGTCTAGGATTT
31571963 TTTAGGGGTTTA
1 TTTAGGGGTTTA
31571975 AGGTTTTAAG
Statistics
Matches: 43, Mismatches: 6, Indels: 4
0.81 0.11 0.08
Matches are distributed among these distances:
37 3 0.07
38 11 0.26
39 1 0.02
40 15 0.35
41 13 0.30
ACGTcount: A:0.19, C:0.03, G:0.32, T:0.46
Consensus pattern (39 bp):
TTTAGGGGTTTAGGGGTTATAGACTAGTGTCTAGGATTT
Found at i:31572242 original size:7 final size:7
Alignment explanation
Indices: 31572230--31572372 Score: 63
Period size: 7 Copynumber: 20.1 Consensus size: 7
31572220 CACTAATTAA
31572230 CTAAACC
1 CTAAACC
31572237 CTAAACTC
1 CTAAAC-C
* *
31572245 TTAATCC
1 CTAAACC
* *
31572252 TTAATCC
1 CTAAACC
31572259 CTAAACC
1 CTAAACC
*
31572266 ATAAACC
1 CTAAACC
*
31572273 CTAAATC
1 CTAAACC
*
31572280 CTAAAAC
1 CTAAACC
* *
31572287 ATAAAAC
1 CTAAACC
* *
31572294 ATAAACT
1 CTAAACC
* *
31572301 CTTAATC
1 CTAAACC
*
31572308 CTAGACC
1 CTAAACC
*
31572315 CTTAACCC
1 C-TAAACC
*
31572323 CTAACCC
1 CTAAACC
31572330 CTAAACC
1 CTAAACC
*
31572337 TTAAACC
1 CTAAACC
*
31572344 C-CAACC
1 CTAAACC
31572350 CTTAAACC
1 C-TAAACC
* **
31572358 ATAATTC
1 CTAAACC
31572365 CTAAACC
1 CTAAACC
31572372 C
1 C
31572373 ATAATCCATA
Statistics
Matches: 101, Mismatches: 31, Indels: 8
0.72 0.22 0.06
Matches are distributed among these distances:
6 5 0.05
7 82 0.81
8 14 0.14
ACGTcount: A:0.41, C:0.36, G:0.01, T:0.23
Consensus pattern (7 bp):
CTAAACC
Found at i:31572276 original size:14 final size:14
Alignment explanation
Indices: 31572257--31572454 Score: 55
Period size: 14 Copynumber: 13.9 Consensus size: 14
31572247 AATCCTTAAT
31572257 CCCTAAACCATAAA
1 CCCTAAACCATAAA
31572271 CCCTAAATCC-TAAA
1 CCCTAAA-CCATAAA
* * *
31572285 ACATAAAACATAAA
1 CCCTAAACCATAAA
* * *
31572299 CTCTTAATCC-TAGA
1 C-CCTAAACCATAAA
* * *
31572313 CCCTTAACCCCTAAC
1 CCC-TAAACCATAAA
*
31572328 CCCTAAACCTTAAA
1 CCCTAAACCATAAA
* * *
31572342 CCCCAACCCTTAAA
1 CCCTAAACCATAAA
* *
31572356 CCATAATTCC-TAAA
1 CCCTAA-ACCATAAA
*
31572370 CCCATAATCCATAAA
1 CCC-TAAACCATAAA
* *
31572385 ACTTAAA--ATAGTAA
1 CCCTAAACCATA--AA
* *
31572399 CTCATAAACCTTAAA
1 C-CCTAAACCATAAA
* **
31572414 CCCTTAACCATATG
1 CCCTAAACCATAAA
* *
31572428 CCCTAAATCGTAAA
1 CCCTAAACCATAAA
*
31572442 CCCTAAACTATAA
1 CCCTAAACCATAA
31572455 TGATAATTCA
Statistics
Matches: 131, Mismatches: 40, Indels: 26
0.66 0.20 0.13
Matches are distributed among these distances:
12 3 0.02
13 2 0.02
14 94 0.72
15 30 0.23
17 2 0.02
ACGTcount: A:0.43, C:0.32, G:0.02, T:0.23
Consensus pattern (14 bp):
CCCTAAACCATAAA
Found at i:31572625 original size:23 final size:22
Alignment explanation
Indices: 31572595--31572642 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 22
31572585 ATTTAGGGGT
* *
31572595 TTTTAGGGTTTACAGGTTTAGTG
1 TTTTAGGGGTTACA-GATTAGTG
*
31572618 TTTTAGGGGTTATAGATTAGTG
1 TTTTAGGGGTTACAGATTAGTG
31572640 TTT
1 TTT
31572643 ATGATTTTTT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
22 10 0.45
23 12 0.55
ACGTcount: A:0.19, C:0.02, G:0.29, T:0.50
Consensus pattern (22 bp):
TTTTAGGGGTTACAGATTAGTG
Found at i:31572652 original size:54 final size:54
Alignment explanation
Indices: 31572555--31572672 Score: 130
Period size: 54 Copynumber: 2.2 Consensus size: 54
31572545 TATTTTTTTG
* *
31572555 GGTTTAGGGTTTTAAGGGTTATAGTTTAATATTTAGGGGTTTTTAG-GGTTTACA
1 GGTTTAGGGTTTTAAGGGTTATAGATTAATATTTAGGAGTTTTTAGAGGTTTA-A
* * * * * * *
31572609 GGTTTAGTGTTTTAGGGGTTATAGATTAGTGTTTATGATTTTTTTGAGGTTTAA
1 GGTTTAGGGTTTTAAGGGTTATAGATTAATATTTAGGAGTTTTTAGAGGTTTAA
31572663 GGTTTTAGGG
1 GG-TTTAGGG
31572673 GTTATATGAC
Statistics
Matches: 52, Mismatches: 10, Indels: 3
0.80 0.15 0.05
Matches are distributed among these distances:
54 40 0.77
55 12 0.23
ACGTcount: A:0.20, C:0.01, G:0.31, T:0.48
Consensus pattern (54 bp):
GGTTTAGGGTTTTAAGGGTTATAGATTAATATTTAGGAGTTTTTAGAGGTTTAA
Found at i:31572782 original size:41 final size:41
Alignment explanation
Indices: 31572683--31572782 Score: 164
Period size: 41 Copynumber: 2.4 Consensus size: 41
31572673 GTTATATGAC
* * *
31572683 TTTTAGCGGCGTTTTACAGAAAGCGCTGTTAATGCTCTGGT
1 TTTTAGCGGCGTTTTACCGAAAGCGCCGCTAATGCTCTGGT
*
31572724 TTTTAGCGGCGTTTTACCGGAAGCGCCGCTAATGCTCTGGT
1 TTTTAGCGGCGTTTTACCGAAAGCGCCGCTAATGCTCTGGT
31572765 TTTTAGCGGCGTTTTACC
1 TTTTAGCGGCGTTTTACC
31572783 AAAAACGTCG
Statistics
Matches: 55, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
41 55 1.00
ACGTcount: A:0.16, C:0.21, G:0.27, T:0.36
Consensus pattern (41 bp):
TTTTAGCGGCGTTTTACCGAAAGCGCCGCTAATGCTCTGGT
Found at i:31572810 original size:41 final size:40
Alignment explanation
Indices: 31572683--31572802 Score: 152
Period size: 41 Copynumber: 2.9 Consensus size: 40
31572673 GTTATATGAC
31572683 TTTTAGCGGCGTTTTA-CAGAAAGCGCTGTTAATGCTCTGGT
1 TTTTAGCGGCGTTTTACCA-AAAGCGC-GTTAATGCTCTGGT
** *
31572724 TTTTAGCGGCGTTTTACCGGAAGCGCCGCTAATGCTCTGGT
1 TTTTAGCGGCGTTTTACCAAAAGCG-CGTTAATGCTCTGGT
* *
31572765 TTTTAGCGGCGTTTTACCAAAAACGTCGTTATTGCTCT
1 TTTTAGCGGCGTTTTACCAAAAGCG-CGTTAATGCTCT
31572803 TTGTTTTACA
Statistics
Matches: 68, Mismatches: 9, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
41 66 0.97
42 2 0.03
ACGTcount: A:0.18, C:0.21, G:0.25, T:0.36
Consensus pattern (40 bp):
TTTTAGCGGCGTTTTACCAAAAGCGCGTTAATGCTCTGGT
Found at i:31578954 original size:29 final size:29
Alignment explanation
Indices: 31578921--31579081 Score: 207
Period size: 29 Copynumber: 5.6 Consensus size: 29
31578911 GTGACGAGAT
31578921 TGGCACTAAGTGTGCGTGCTGGAAATATA
1 TGGCACTAAGTGTGCGTGCTGGAAATATA
31578950 TGGCACTAAGTGTGCGTGCTGGAAATATA
1 TGGCACTAAGTGTGCGTGCTGGAAATATA
*
31578979 TGGCACTAAGTGTGCATGCTGGAAATATA
1 TGGCACTAAGTGTGCGTGCTGGAAATATA
* * ***
31579008 TGGCACTAAGTGTGCGAGCTCGAAGGGTA
1 TGGCACTAAGTGTGCGTGCTGGAAATATA
* * * **
31579037 TGGCACTATGTGTGCGGGCT-TAAATCGCA
1 TGGCACTAAGTGTGCGTGCTGGAAAT-ATA
31579066 TGGCACTAAGTGTGCG
1 TGGCACTAAGTGTGCG
31579082 AAATCGAGTA
Statistics
Matches: 117, Mismatches: 14, Indels: 2
0.88 0.11 0.02
Matches are distributed among these distances:
28 2 0.02
29 115 0.98
ACGTcount: A:0.25, C:0.16, G:0.32, T:0.26
Consensus pattern (29 bp):
TGGCACTAAGTGTGCGTGCTGGAAATATA
Found at i:31586896 original size:29 final size:29
Alignment explanation
Indices: 31586863--31587023 Score: 207
Period size: 29 Copynumber: 5.6 Consensus size: 29
31586853 GTGACGAGAT
31586863 TGGCACTAAGTGTGCGTGCTGGAAATATA
1 TGGCACTAAGTGTGCGTGCTGGAAATATA
31586892 TGGCACTAAGTGTGCGTGCTGGAAATATA
1 TGGCACTAAGTGTGCGTGCTGGAAATATA
*
31586921 TGGCACTAAGTGTGCATGCTGGAAATATA
1 TGGCACTAAGTGTGCGTGCTGGAAATATA
* * ***
31586950 TGGCACTAAGTGTGCGAGCTCGAAGGGTA
1 TGGCACTAAGTGTGCGTGCTGGAAATATA
* * * **
31586979 TGGCACTATGTGTGCGGGCT-TAAATCGCA
1 TGGCACTAAGTGTGCGTGCTGGAAAT-ATA
31587008 TGGCACTAAGTGTGCG
1 TGGCACTAAGTGTGCG
31587024 AAATCGAGTA
Statistics
Matches: 117, Mismatches: 14, Indels: 2
0.88 0.11 0.02
Matches are distributed among these distances:
28 2 0.02
29 115 0.98
ACGTcount: A:0.25, C:0.16, G:0.32, T:0.26
Consensus pattern (29 bp):
TGGCACTAAGTGTGCGTGCTGGAAATATA
Found at i:31590093 original size:29 final size:29
Alignment explanation
Indices: 31590060--31590192 Score: 167
Period size: 29 Copynumber: 4.6 Consensus size: 29
31590050 CGGTGACGAG
*
31590060 ATGGCACTAAGTGTGCGTGCTGGAAATAT
1 ATGGCACTAAGTGTGCGTGCTGGAAAAAT
*
31590089 ATGGCACTAAGTGTGCGTGCTGGAAATAT
1 ATGGCACTAAGTGTGCGTGCTGGAAAAAT
* *
31590118 AAGGCACTAAGTGTGCATGCTGGAAAAAT
1 ATGGCACTAAGTGTGCGTGCTGGAAAAAT
* * **
31590147 ATGACACTATGTGTGCAAGCTGGAAAAAT
1 ATGGCACTAAGTGTGCGTGCTGGAAAAAT
* **
31590176 ACGGCACTGGGTGTGCG
1 ATGGCACTAAGTGTGCG
31590193 AGCTCGGAGG
Statistics
Matches: 92, Mismatches: 12, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
29 92 1.00
ACGTcount: A:0.30, C:0.15, G:0.31, T:0.24
Consensus pattern (29 bp):
ATGGCACTAAGTGTGCGTGCTGGAAAAAT
Found at i:31598168 original size:29 final size:29
Alignment explanation
Indices: 31598135--31598265 Score: 163
Period size: 29 Copynumber: 4.5 Consensus size: 29
31598125 TGACGAGATC
*
31598135 GGCACTAAGTGTGCGTGCTGGAAATATAT
1 GGCACTAAGTGTGCGTGCTGGAAAAATAT
* *
31598164 GGCACTAAGTGTGCGTGCTGGAAATATAA
1 GGCACTAAGTGTGCGTGCTGGAAAAATAT
*
31598193 GGCACTAAGTGTGCATGCTGGAAAAATAT
1 GGCACTAAGTGTGCGTGCTGGAAAAATAT
* * ** *
31598222 GACACTATGTGTGCAAGCTGGAAAAATAC
1 GGCACTAAGTGTGCGTGCTGGAAAAATAT
**
31598251 GGCACTGGGTGTGCG
1 GGCACTAAGTGTGCG
31598266 AGCTCGGAGG
Statistics
Matches: 90, Mismatches: 12, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
29 90 1.00
ACGTcount: A:0.30, C:0.15, G:0.31, T:0.24
Consensus pattern (29 bp):
GGCACTAAGTGTGCGTGCTGGAAAAATAT
Found at i:31603646 original size:42 final size:42
Alignment explanation
Indices: 31603599--31603705 Score: 196
Period size: 42 Copynumber: 2.5 Consensus size: 42
31603589 TATTGGTCTC
31603599 GGCACTAAGTGTGCGGGTATAAATGGACACGGTGACAAGATT
1 GGCACTAAGTGTGCGGGTATAAATGGACACGGTGACAAGATT
31603641 GGCACTAAGTGTGCGGGTATAAATGGACACGGTGACAAGATT
1 GGCACTAAGTGTGCGGGTATAAATGGACACGGTGACAAGATT
* *
31603683 GGCACTACGTGTGCGGGTTTAAA
1 GGCACTAAGTGTGCGGGTATAAA
31603706 ATTGTACAGC
Statistics
Matches: 63, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
42 63 1.00
ACGTcount: A:0.29, C:0.15, G:0.34, T:0.22
Consensus pattern (42 bp):
GGCACTAAGTGTGCGGGTATAAATGGACACGGTGACAAGATT
Found at i:31603770 original size:27 final size:28
Alignment explanation
Indices: 31603713--31603782 Score: 97
Period size: 27 Copynumber: 2.5 Consensus size: 28
31603703 AAAATTGTAC
**
31603713 AGCACTAAGTGTGCGAATTTGATTATAT
1 AGCACTAAGTGTGCGAAGCTGATTATAT
* *
31603741 AGCACTATGTGTGCG-AGCTGATTTTAT
1 AGCACTAAGTGTGCGAAGCTGATTATAT
31603768 AGCACTAAGTGTGCG
1 AGCACTAAGTGTGCG
31603783 GATTCACTAT
Statistics
Matches: 37, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
27 23 0.62
28 14 0.38
ACGTcount: A:0.27, C:0.14, G:0.26, T:0.33
Consensus pattern (28 bp):
AGCACTAAGTGTGCGAAGCTGATTATAT
Found at i:31605913 original size:28 final size:28
Alignment explanation
Indices: 31605880--31605938 Score: 109
Period size: 28 Copynumber: 2.1 Consensus size: 28
31605870 AACCTAAACC
31605880 ATTTAGCTCGATTTCACATTCGATCTTA
1 ATTTAGCTCGATTTCACATTCGATCTTA
*
31605908 ATTTAGCTCGATTTCACATTTGATCTTA
1 ATTTAGCTCGATTTCACATTCGATCTTA
31605936 ATT
1 ATT
31605939 CAACATTGCC
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.25, C:0.19, G:0.10, T:0.46
Consensus pattern (28 bp):
ATTTAGCTCGATTTCACATTCGATCTTA
Found at i:31607563 original size:17 final size:17
Alignment explanation
Indices: 31607543--31607575 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
31607533 ATAAGCACAA
31607543 TTAAACAAGTTAAATGT
1 TTAAACAAGTTAAATGT
31607560 TTAAACAAGTTAAATG
1 TTAAACAAGTTAAATG
31607576 GCTATAGCAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.48, C:0.06, G:0.12, T:0.33
Consensus pattern (17 bp):
TTAAACAAGTTAAATGT
Found at i:31625390 original size:46 final size:47
Alignment explanation
Indices: 31625289--31625509 Score: 163
Period size: 46 Copynumber: 4.8 Consensus size: 47
31625279 ATATATGTGT
* * * *
31625289 CGATGTCA-GTCCCAGACATGGTCTTACACTA--ACACATCTCGTA-GC
1 CGATGCCATGTCCCAGACAT-GTCTTACACTAGCTCACGTCTC-AAGGC
* * * * *
31625334 CGAT-ACATGTCCCACACATGTCTTACACTGGCTCACGTCTCGAGGT
1 CGATGCCATGTCCCAGACATGTCTTACACTAGCTCACGTCTCAAGGC
* * * *
31625380 TGATG-CATGTCCTAGACATGTCTTACACTAGCAT-TCGTCTCAATGC
1 CGATGCCATGTCCCAGACATGTCTTACACTAGC-TCACGTCTCAAGGC
* * * * *
31625426 CGATGCCATGTCCCAGACATGGTCTTACACTTGCTCTCATAAT-ATGGC
1 CGATGCCATGTCCCAGACAT-GTCTTACACTAGCTCACGT-CTCAAGGC
*
31625474 CAATG-CATGTCCCAGACATGTCTTACACTAGCTCAC
1 CGATGCCATGTCCCAGACATGTCTTACACTAGCTCAC
31625510 ACAAGTGACC
Statistics
Matches: 141, Mismatches: 25, Indels: 19
0.76 0.14 0.10
Matches are distributed among these distances:
44 12 0.09
45 15 0.11
46 62 0.44
47 29 0.21
48 22 0.16
49 1 0.01
ACGTcount: A:0.24, C:0.30, G:0.18, T:0.28
Consensus pattern (47 bp):
CGATGCCATGTCCCAGACATGTCTTACACTAGCTCACGTCTCAAGGC
Found at i:31625483 original size:47 final size:44
Alignment explanation
Indices: 31625382--31625507 Score: 146
Period size: 47 Copynumber: 2.7 Consensus size: 44
31625372 CTCGAGGTTG
* * *
31625382 ATGCATGTCCTAGACATGTCTTACACTAGCATTCGTCTCAATGCCG
1 ATGCATGTCCCAGACATGTCTTACACTAGC--TCGTCTAAATGCCA
*
31625428 ATGCCATGTCCCAGACATGGTCTTACACTTGCTC-TCATAATATGGCCA
1 ATG-CATGTCCCAGACAT-GTCTTACACTAGCTCGTC-TAA-AT-GCCA
31625476 ATGCATGTCCCAGACATGTCTTACACTAGCTC
1 ATGCATGTCCCAGACATGTCTTACACTAGCTC
31625508 ACACAAGTGA
Statistics
Matches: 70, Mismatches: 5, Indels: 10
0.82 0.06 0.12
Matches are distributed among these distances:
45 2 0.03
46 21 0.30
47 29 0.41
48 18 0.26
ACGTcount: A:0.25, C:0.29, G:0.17, T:0.29
Consensus pattern (44 bp):
ATGCATGTCCCAGACATGTCTTACACTAGCTCGTCTAAATGCCA
Found at i:31628805 original size:40 final size:40
Alignment explanation
Indices: 31628746--31628953 Score: 236
Period size: 40 Copynumber: 5.2 Consensus size: 40
31628736 CAATTGAATG
* * *
31628746 ATATCCGGGCTAAGTCCCGAAGACATTTGTGCTAGTAATT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGTAATT
* * * * *
31628786 ATATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGACT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGTAATT
* * **
31628826 ACATCCGGGCTAAGACCCGAAGGCATTCGTGCAAGTTGTT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGTAATT
* * **
31628866 AAATCCGGGCTAATACCCGAAGGCATTTGTGCAAGTCGTT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGTAATT
* * **
31628906 ATATCCGGGCTAAGACCCGAAGGCATTCGTGCATGTGGTT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGTAATT
31628946 ATATCCGG
1 ATATCCGG
31628954 TTGTAATCCG
Statistics
Matches: 145, Mismatches: 23, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
40 145 1.00
ACGTcount: A:0.26, C:0.22, G:0.26, T:0.25
Consensus pattern (40 bp):
ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGTAATT
Found at i:31628884 original size:80 final size:80
Alignment explanation
Indices: 31628748--31628953 Score: 261
Period size: 80 Copynumber: 2.6 Consensus size: 80
31628738 ATTGAATGAT
* * * * * *
31628748 ATCCGGGCTAAGTCCCGAAGACATTTGTGCTAGTAATTATATCCGGGTTAAGACCCGAAGGCAAT
1 ATCCGGGCTAAGACCCGAAGGCATTCGTGCAAGTAGTTATATCCGGGCTAAGACCCGAAGGCAAT
*
31628813 TGTGCTAGT-GACTAC
66 TGTGCAAGTCG-CTAC
* * * *
31628828 ATCCGGGCTAAGACCCGAAGGCATTCGTGCAAGTTGTTAAATCCGGGCTAATACCCGAAGGCATT
1 ATCCGGGCTAAGACCCGAAGGCATTCGTGCAAGTAGTTATATCCGGGCTAAGACCCGAAGGCAAT
* *
31628893 TGTGCAAGTCGTTAT
66 TGTGCAAGTCGCTAC
* *
31628908 ATCCGGGCTAAGACCCGAAGGCATTCGTGCATGTGGTTATATCCGG
1 ATCCGGGCTAAGACCCGAAGGCATTCGTGCAAGTAGTTATATCCGG
31628954 TTGTAATCCG
Statistics
Matches: 109, Mismatches: 16, Indels: 2
0.86 0.13 0.02
Matches are distributed among these distances:
80 108 0.99
81 1 0.01
ACGTcount: A:0.26, C:0.22, G:0.27, T:0.25
Consensus pattern (80 bp):
ATCCGGGCTAAGACCCGAAGGCATTCGTGCAAGTAGTTATATCCGGGCTAAGACCCGAAGGCAAT
TGTGCAAGTCGCTAC
Found at i:31636819 original size:40 final size:40
Alignment explanation
Indices: 31636760--31636967 Score: 236
Period size: 40 Copynumber: 5.2 Consensus size: 40
31636750 CAATTGAATG
* * *
31636760 ATATCCGGGCTAAGTCCCGAAGACATTTGTGCTAGTAATT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGTAATT
* * * * *
31636800 ATATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGACT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGTAATT
* * **
31636840 ACATCCGGGCTAAGACCCGAAGGCATTCGTGCAAGTTGTT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGTAATT
* * **
31636880 AAATCCGGGCTAATACCCGAAGGCATTTGTGCAAGTCGTT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGTAATT
* * **
31636920 ATATCCGGGCTAAGACCCGAAGGCATTCGTGCATGTGGTT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGTAATT
31636960 ATATCCGG
1 ATATCCGG
31636968 TTGTAATCCG
Statistics
Matches: 145, Mismatches: 23, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
40 145 1.00
ACGTcount: A:0.26, C:0.22, G:0.26, T:0.25
Consensus pattern (40 bp):
ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGTAATT
Found at i:31636898 original size:80 final size:80
Alignment explanation
Indices: 31636762--31636967 Score: 261
Period size: 80 Copynumber: 2.6 Consensus size: 80
31636752 ATTGAATGAT
* * * * * *
31636762 ATCCGGGCTAAGTCCCGAAGACATTTGTGCTAGTAATTATATCCGGGTTAAGACCCGAAGGCAAT
1 ATCCGGGCTAAGACCCGAAGGCATTCGTGCAAGTAGTTATATCCGGGCTAAGACCCGAAGGCAAT
*
31636827 TGTGCTAGT-GACTAC
66 TGTGCAAGTCG-CTAC
* * * *
31636842 ATCCGGGCTAAGACCCGAAGGCATTCGTGCAAGTTGTTAAATCCGGGCTAATACCCGAAGGCATT
1 ATCCGGGCTAAGACCCGAAGGCATTCGTGCAAGTAGTTATATCCGGGCTAAGACCCGAAGGCAAT
* *
31636907 TGTGCAAGTCGTTAT
66 TGTGCAAGTCGCTAC
* *
31636922 ATCCGGGCTAAGACCCGAAGGCATTCGTGCATGTGGTTATATCCGG
1 ATCCGGGCTAAGACCCGAAGGCATTCGTGCAAGTAGTTATATCCGG
31636968 TTGTAATCCG
Statistics
Matches: 109, Mismatches: 16, Indels: 2
0.86 0.13 0.02
Matches are distributed among these distances:
80 108 0.99
81 1 0.01
ACGTcount: A:0.26, C:0.22, G:0.27, T:0.25
Consensus pattern (80 bp):
ATCCGGGCTAAGACCCGAAGGCATTCGTGCAAGTAGTTATATCCGGGCTAAGACCCGAAGGCAAT
TGTGCAAGTCGCTAC
Found at i:31640892 original size:26 final size:24
Alignment explanation
Indices: 31640862--31640911 Score: 73
Period size: 26 Copynumber: 2.0 Consensus size: 24
31640852 AAATAAAAAA
*
31640862 ATTTAAAAATATAATAAATCAAATAT
1 ATTTAAAAACATAA-AAA-CAAATAT
31640888 ATTTAAAAACATAAAAACAAATAT
1 ATTTAAAAACATAAAAACAAATAT
31640912 TAAAACAAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 7 0.30
25 3 0.13
26 13 0.57
ACGTcount: A:0.64, C:0.06, G:0.00, T:0.30
Consensus pattern (24 bp):
ATTTAAAAACATAAAAACAAATAT
Found at i:31640931 original size:21 final size:21
Alignment explanation
Indices: 31640882--31640940 Score: 59
Period size: 21 Copynumber: 2.8 Consensus size: 21
31640872 ATAATAAATC
*
31640882 AAAT-ATATTTAAAA-ACATAA
1 AAATAATA-TTAAAACAAATAA
*
31640902 AAACAAATATTAAAACAAATAA
1 AAA-TAATATTAAAACAAATAA
*
31640924 AAATAATACTAAAACAA
1 AAATAATATTAAAACAA
31640941 TTCTTAAAAC
Statistics
Matches: 32, Mismatches: 4, Indels: 5
0.78 0.10 0.12
Matches are distributed among these distances:
20 3 0.09
21 18 0.56
22 11 0.34
ACGTcount: A:0.69, C:0.08, G:0.00, T:0.22
Consensus pattern (21 bp):
AAATAATATTAAAACAAATAA
Found at i:31642114 original size:38 final size:38
Alignment explanation
Indices: 31642045--31642117 Score: 103
Period size: 38 Copynumber: 1.9 Consensus size: 38
31642035 CTCAACCTTC
* *
31642045 AGATTCTGATTTTGTCAAACTGTAATAGTTTAAAAGCT
1 AGATTCTAATTTTGTCAAACTGTAACAGTTTAAAAGCT
*
31642083 AGATTCTAATTTTGTCAAA-TCGTAACCGTTTAAAA
1 AGATTCTAATTTTGTCAAACT-GTAACAGTTTAAAA
31642118 ATATATTTTT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
37 1 0.03
38 30 0.97
ACGTcount: A:0.36, C:0.12, G:0.14, T:0.38
Consensus pattern (38 bp):
AGATTCTAATTTTGTCAAACTGTAACAGTTTAAAAGCT
Found at i:31648189 original size:27 final size:28
Alignment explanation
Indices: 31648133--31648202 Score: 124
Period size: 27 Copynumber: 2.5 Consensus size: 28
31648123 AAACTTGTAC
31648133 AGCACTAAGTGTGCGAGTTTGATCATAT
1 AGCACTAAGTGTGCGAGTTTGATCATAT
*
31648161 AGCACTAAGTGTGCGAG-TTGATTATAT
1 AGCACTAAGTGTGCGAGTTTGATCATAT
31648188 AGCACTAAGTGTGCG
1 AGCACTAAGTGTGCG
31648203 GACTCACTAT
Statistics
Matches: 41, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
27 24 0.59
28 17 0.41
ACGTcount: A:0.29, C:0.14, G:0.27, T:0.30
Consensus pattern (28 bp):
AGCACTAAGTGTGCGAGTTTGATCATAT
Found at i:31648213 original size:27 final size:27
Alignment explanation
Indices: 31648133--31648214 Score: 78
Period size: 27 Copynumber: 3.0 Consensus size: 27
31648123 AAACTTGTAC
* *
31648133 AGCACTAAGTGTGCGAGTTTGA-TCATAT
1 AGCACTAAGTGTGCGAG-CTCACT-ATAT
* * *
31648161 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGAGCTCACTATAT
31648188 AGCACTAAGTGTGCG-GACTCACTATAT
1 AGCACTAAGTGTGCGAG-CTCACTATAT
31648215 GCTTTTGAAT
Statistics
Matches: 49, Mismatches: 3, Indels: 5
0.86 0.05 0.09
Matches are distributed among these distances:
26 1 0.02
27 30 0.61
28 18 0.37
ACGTcount: A:0.29, C:0.16, G:0.24, T:0.30
Consensus pattern (27 bp):
AGCACTAAGTGTGCGAGCTCACTATAT
Found at i:31656216 original size:27 final size:28
Alignment explanation
Indices: 31656160--31656229 Score: 124
Period size: 27 Copynumber: 2.5 Consensus size: 28
31656150 AAACTTGTAC
31656160 AGCACTAAGTGTGCGAGTTTGATCATAT
1 AGCACTAAGTGTGCGAGTTTGATCATAT
*
31656188 AGCACTAAGTGTGCGAG-TTGATTATAT
1 AGCACTAAGTGTGCGAGTTTGATCATAT
31656215 AGCACTAAGTGTGCG
1 AGCACTAAGTGTGCG
31656230 GACTCACTAT
Statistics
Matches: 41, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
27 24 0.59
28 17 0.41
ACGTcount: A:0.29, C:0.14, G:0.27, T:0.30
Consensus pattern (28 bp):
AGCACTAAGTGTGCGAGTTTGATCATAT
Found at i:31656240 original size:27 final size:27
Alignment explanation
Indices: 31656160--31656241 Score: 78
Period size: 27 Copynumber: 3.0 Consensus size: 27
31656150 AAACTTGTAC
* *
31656160 AGCACTAAGTGTGCGAGTTTGA-TCATAT
1 AGCACTAAGTGTGCGAG-CTCACT-ATAT
* * *
31656188 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGAGCTCACTATAT
31656215 AGCACTAAGTGTGCG-GACTCACTATAT
1 AGCACTAAGTGTGCGAG-CTCACTATAT
31656242 GCTTTTGAAT
Statistics
Matches: 49, Mismatches: 3, Indels: 5
0.86 0.05 0.09
Matches are distributed among these distances:
26 1 0.02
27 30 0.61
28 18 0.37
ACGTcount: A:0.29, C:0.16, G:0.24, T:0.30
Consensus pattern (27 bp):
AGCACTAAGTGTGCGAGCTCACTATAT
Found at i:31660327 original size:17 final size:17
Alignment explanation
Indices: 31660305--31660337 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
31660295 TTTTTATCAT
*
31660305 TTATTATTTATCGGGCA
1 TTATTATTAATCGGGCA
31660322 TTATTATTAATCGGGC
1 TTATTATTAATCGGGC
31660338 TTTGTCAGAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.24, C:0.12, G:0.18, T:0.45
Consensus pattern (17 bp):
TTATTATTAATCGGGCA
Found at i:31661507 original size:26 final size:26
Alignment explanation
Indices: 31661470--31661587 Score: 119
Period size: 26 Copynumber: 4.5 Consensus size: 26
31661460 GGGCCATCTG
* * *
31661470 ACCAACTTAAACTCTAGGGTTCTCCA
1 ACCAACTAAAACTCAAGGGTCCTCCA
* * *
31661496 ACCCACTAAAACTCAAGTGTCCTCTA
1 ACCAACTAAAACTCAAGGGTCCTCCA
* **
31661522 ACCAACTCAAACTCAAGGGTCCTCTG
1 ACCAACTAAAACTCAAGGGTCCTCCA
* * *
31661548 ACCAACTCAAACTCAAAGGTCCTCCG
1 ACCAACTAAAACTCAAGGGTCCTCCA
*
31661574 ACCAACTCAAACTC
1 ACCAACTAAAACTC
31661588 CCAAGACCTT
Statistics
Matches: 80, Mismatches: 12, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
26 80 1.00
ACGTcount: A:0.34, C:0.36, G:0.10, T:0.20
Consensus pattern (26 bp):
ACCAACTAAAACTCAAGGGTCCTCCA
Found at i:31661560 original size:52 final size:52
Alignment explanation
Indices: 31661470--31661587 Score: 139
Period size: 52 Copynumber: 2.3 Consensus size: 52
31661460 GGGCCATCTG
* * * * *
31661470 ACCAACTTAAACTCTAGGGTTCTCCAACCCACTAAAACTC-AAGTGTCCTCTA
1 ACCAACTCAAACTCAAGGGTCCTCCAACCAACTAAAACTCAAAG-GTCCTCCA
** * *
31661522 ACCAACTCAAACTCAAGGGTCCTCTGACCAACTCAAACTCAAAGGTCCTCCG
1 ACCAACTCAAACTCAAGGGTCCTCCAACCAACTAAAACTCAAAGGTCCTCCA
31661574 ACCAACTCAAACTC
1 ACCAACTCAAACTC
31661588 CCAAGACCTT
Statistics
Matches: 56, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
52 53 0.95
53 3 0.05
ACGTcount: A:0.34, C:0.36, G:0.10, T:0.20
Consensus pattern (52 bp):
ACCAACTCAAACTCAAGGGTCCTCCAACCAACTAAAACTCAAAGGTCCTCCA
Found at i:31672250 original size:11 final size:11
Alignment explanation
Indices: 31672234--31672263 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
31672224 TATCTTATAT
*
31672234 TAAAATAATAG
1 TAAAATAATAA
31672245 TAAAATAATAA
1 TAAAATAATAA
31672256 TAAAATAA
1 TAAAATAA
31672264 ACCTAACCAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.70, C:0.00, G:0.03, T:0.27
Consensus pattern (11 bp):
TAAAATAATAA
Found at i:31673526 original size:16 final size:16
Alignment explanation
Indices: 31673505--31673552 Score: 53
Period size: 16 Copynumber: 2.9 Consensus size: 16
31673495 ACCAACTATT
31673505 TATTTTAATATTTAAA
1 TATTTTAATATTTAAA
*
31673521 TATTTTAAATATTTTTAA
1 TATTTT-AATA-TTTAAA
31673539 T-TTTTAATAATTTA
1 TATTTTAAT-ATTTA
31673553 TTTGATAGAA
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
16 12 0.44
17 9 0.33
18 6 0.22
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (16 bp):
TATTTTAATATTTAAA
Found at i:31673543 original size:8 final size:9
Alignment explanation
Indices: 31673505--31673545 Score: 52
Period size: 9 Copynumber: 4.9 Consensus size: 9
31673495 ACCAACTATT
31673505 TATTTT-AA
1 TATTTTAAA
31673513 TA-TTTAAA
1 TATTTTAAA
31673521 TATTTTAAA
1 TATTTTAAA
*
31673530 TATTTTTAA
1 TATTTTAAA
31673539 T-TTTTAA
1 TATTTTAA
31673546 TAATTTATTT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
7 3 0.10
8 11 0.38
9 15 0.52
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (9 bp):
TATTTTAAA
Found at i:31676366 original size:17 final size:17
Alignment explanation
Indices: 31676344--31676377 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
31676334 TCCGTTCAAG
31676344 CAAATAACATGAGAGGT
1 CAAATAACATGAGAGGT
31676361 CAAATAACATGAGAGGT
1 CAAATAACATGAGAGGT
31676378 TTTATATTTG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.47, C:0.12, G:0.24, T:0.18
Consensus pattern (17 bp):
CAAATAACATGAGAGGT
Found at i:31681678 original size:6 final size:6
Alignment explanation
Indices: 31681667--31681717 Score: 52
Period size: 6 Copynumber: 8.8 Consensus size: 6
31681657 CAGGCCCAGA
* * * *
31681667 AAAAAG AAAAAG AAAAAG --AAAG AAAAAG GAAAAC AAAAAC AAAAAC
1 AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG
31681713 AAAAA
1 AAAAA
31681718 AAAGGGTACA
Statistics
Matches: 40, Mismatches: 3, Indels: 4
0.85 0.06 0.09
Matches are distributed among these distances:
4 4 0.10
6 36 0.90
ACGTcount: A:0.82, C:0.06, G:0.12, T:0.00
Consensus pattern (6 bp):
AAAAAG
Found at i:31681690 original size:16 final size:15
Alignment explanation
Indices: 31681666--31681721 Score: 58
Period size: 16 Copynumber: 3.5 Consensus size: 15
31681656 GCAGGCCCAG
31681666 AAAAAAGAAAAAGAA
1 AAAAAAGAAAAAGAA
31681681 AAAGAAAGAAAAAGGAAA
1 AAA-AAAGAAAAA-G-AA
* *
31681699 ACAAAAACAAAAACAA
1 A-AAAAAGAAAAAGAA
31681715 AAAAAAG
1 AAAAAAG
31681722 GGTACAAGAG
Statistics
Matches: 34, Mismatches: 3, Indels: 8
0.76 0.07 0.18
Matches are distributed among these distances:
15 8 0.24
16 12 0.35
17 1 0.03
18 11 0.32
19 2 0.06
ACGTcount: A:0.82, C:0.05, G:0.12, T:0.00
Consensus pattern (15 bp):
AAAAAAGAAAAAGAA
Found at i:31681704 original size:28 final size:27
Alignment explanation
Indices: 31681668--31681722 Score: 74
Period size: 28 Copynumber: 2.0 Consensus size: 27
31681658 AGGCCCAGAA
* * *
31681668 AAAAGAAAAAGAAAAAGAAAGAAAAAGG
1 AAAACAAAAACAAAAACAAA-AAAAAGG
31681696 AAAACAAAAACAAAAACAAAAAAAAGG
1 AAAACAAAAACAAAAACAAAAAAAAGG
31681723 GTACAAGAGG
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
27 7 0.29
28 17 0.71
ACGTcount: A:0.80, C:0.05, G:0.15, T:0.00
Consensus pattern (27 bp):
AAAACAAAAACAAAAACAAAAAAAAGG
Found at i:31695814 original size:24 final size:24
Alignment explanation
Indices: 31695787--31695850 Score: 92
Period size: 24 Copynumber: 2.7 Consensus size: 24
31695777 AAACCTAATT
* * *
31695787 CTAATCAATGTTAAATATATTATG
1 CTAATAAATGCTAAATATATTATA
31695811 CTAATAAATGCTAAATATATTATA
1 CTAATAAATGCTAAATATATTATA
*
31695835 CTAATAAATACTAAAT
1 CTAATAAATGCTAAAT
31695851 CTTCTAGAAA
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 36 1.00
ACGTcount: A:0.48, C:0.09, G:0.05, T:0.38
Consensus pattern (24 bp):
CTAATAAATGCTAAATATATTATA
Found at i:31695975 original size:29 final size:29
Alignment explanation
Indices: 31695942--31696000 Score: 100
Period size: 29 Copynumber: 2.0 Consensus size: 29
31695932 TTTGCTTTGA
* *
31695942 CACGAATTCTCAACGAACAAGTTCTTCAC
1 CACGAACTCTCAACAAACAAGTTCTTCAC
31695971 CACGAACTCTCAACAAACAAGTTCTTCAC
1 CACGAACTCTCAACAAACAAGTTCTTCAC
31696000 C
1 C
31696001 TCTTCCAAGA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.36, C:0.34, G:0.08, T:0.22
Consensus pattern (29 bp):
CACGAACTCTCAACAAACAAGTTCTTCAC
Found at i:31698486 original size:18 final size:18
Alignment explanation
Indices: 31698447--31698487 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
31698437 CCATAACACG
* * *
31698447 GCCCATGTGGGCCTATAC
1 GCCCATGTGGCCCAATAA
31698465 GCCCATGTGGCCCAATAA
1 GCCCATGTGGCCCAATAA
31698483 GCCCA
1 GCCCA
31698488 AAAATAGCCT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.22, C:0.37, G:0.24, T:0.17
Consensus pattern (18 bp):
GCCCATGTGGCCCAATAA
Found at i:31702491 original size:37 final size:36
Alignment explanation
Indices: 31702441--31702527 Score: 147
Period size: 37 Copynumber: 2.3 Consensus size: 36
31702431 TACGAAGTCT
31702441 TACCCGGACATAATCTCCACACGTAGTCATCGGGTC
1 TACCCGGACATAATCTCCACACGTAGTCATCGGGTC
31702477 GTACCCGGACATAATCTCCACACGTAGTCATCGGGTC
1 -TACCCGGACATAATCTCCACACGTAGTCATCGGGTC
31702514 TCACCCGGAACATA
1 T-ACCCGG-ACATA
31702528 TTTCTAAGTT
Statistics
Matches: 48, Mismatches: 0, Indels: 3
0.94 0.00 0.06
Matches are distributed among these distances:
36 1 0.02
37 42 0.88
38 5 0.10
ACGTcount: A:0.26, C:0.33, G:0.20, T:0.21
Consensus pattern (36 bp):
TACCCGGACATAATCTCCACACGTAGTCATCGGGTC
Found at i:31702663 original size:49 final size:49
Alignment explanation
Indices: 31702596--31702944 Score: 599
Period size: 49 Copynumber: 7.1 Consensus size: 49
31702586 TTTACCACAT
*
31702596 ATATATATACACTTTCACATTCATCACGTCGGCCATTAGGCCTTATCAC
1 ATATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCAC
*
31702645 ATATATATACATTTTCACATTCATCACATCGGCCATTAGGCCTTATCAC
1 ATATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCAC
*
31702694 ATATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTGTCAC
1 ATATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCAC
* * *
31702743 ATATGTATACAGTTTCACATTCATCACGTCGGCCATTAGGCCTTATCAC
1 ATATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCAC
*
31702792 ATATGTATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCAC
1 ATATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCAC
*
31702841 ATATGTATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCAC
1 ATATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCAC
* * *
31702890 ATATGTATACATTTTCACATTCATCACGTCGGCCATTAGGCCTTATCAC
1 ATATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCAC
31702939 ATATAT
1 ATATAT
31702945 TATTATGTAC
Statistics
Matches: 287, Mismatches: 13, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
49 287 1.00
ACGTcount: A:0.29, C:0.27, G:0.11, T:0.34
Consensus pattern (49 bp):
ATATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCAC
Found at i:31705939 original size:40 final size:40
Alignment explanation
Indices: 31705841--31706060 Score: 278
Period size: 40 Copynumber: 5.5 Consensus size: 40
31705831 CGAATGGTAT
* * * * * *
31705841 CCGGGCTAAGTCCCGAAGGCTTTTGTGCTAAGTGACTAAAT
1 CCGGGTTAAGTCCCGAAGGCATTTGTGC-GAGTTACCAAAA
* * *
31705882 CCGGGTCAATTCTCGAAGGCATTTGTGCGAGTTACCAAAA
1 CCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACCAAAA
*
31705922 CCGGGTTAAGTCCCGAAGGCATTTGTACGAGTTACCAAAA
1 CCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACCAAAA
*
31705962 CCGGGTTAAGTCCCAAAGGCATTTGTGCGAGTTACCAAAA
1 CCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACCAAAA
* * * *
31706002 CCGGGTTAAGTCCTGAAGGCATTTGTACGAGTTACTAAAT
1 CCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACCAAAA
* *
31706042 CCGGGCTAATTCCCGAAGG
1 CCGGGTTAAGTCCCGAAGG
31706061 TAATTGTGTG
Statistics
Matches: 156, Mismatches: 23, Indels: 1
0.87 0.13 0.01
Matches are distributed among these distances:
40 133 0.85
41 23 0.15
ACGTcount: A:0.27, C:0.22, G:0.26, T:0.25
Consensus pattern (40 bp):
CCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACCAAAA
Found at i:31705994 original size:80 final size:80
Alignment explanation
Indices: 31705841--31706060 Score: 314
Period size: 80 Copynumber: 2.7 Consensus size: 80
31705831 CGAATGGTAT
* * * * * * *
31705841 CCGGGCTAAGTCCCGAAGGCTTTTGTGCTAAGTGACTAAATCCGGGTCAATTCTCGAAGGCATTT
1 CCGGGTTAAGTCCCGAAGGCATTTGTAC-GAGTTACTAAATCCGGGTTAATTCCCGAAGGCATTT
31705906 GTGCGAGTTACCAAAA
65 GTGCGAGTTACCAAAA
* * * *
31705922 CCGGGTTAAGTCCCGAAGGCATTTGTACGAGTTACCAAAACCGGGTTAAGTCCCAAAGGCATTTG
1 CCGGGTTAAGTCCCGAAGGCATTTGTACGAGTTACTAAATCCGGGTTAATTCCCGAAGGCATTTG
31705987 TGCGAGTTACCAAAA
66 TGCGAGTTACCAAAA
* *
31706002 CCGGGTTAAGTCCTGAAGGCATTTGTACGAGTTACTAAATCCGGGCTAATTCCCGAAGG
1 CCGGGTTAAGTCCCGAAGGCATTTGTACGAGTTACTAAATCCGGGTTAATTCCCGAAGG
31706061 TAATTGTGTG
Statistics
Matches: 122, Mismatches: 17, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
80 97 0.80
81 25 0.20
ACGTcount: A:0.27, C:0.22, G:0.26, T:0.25
Consensus pattern (80 bp):
CCGGGTTAAGTCCCGAAGGCATTTGTACGAGTTACTAAATCCGGGTTAATTCCCGAAGGCATTTG
TGCGAGTTACCAAAA
Found at i:31706084 original size:120 final size:121
Alignment explanation
Indices: 31705841--31706095 Score: 280
Period size: 120 Copynumber: 2.1 Consensus size: 121
31705831 CGAATGGTAT
* * * * *
31705841 CCGGGCTAAGTCCCGAAGGCTTTTGTGCTAAGTGACTAAATCCGGGTCAATTCTCGAAGGCATTT
1 CCGGGCTAAGTCCCAAAGGCATTTGTGCTAAGTGACCAAAACCGGGTCAATCCTCGAAGGCATTT
* * * * *
31705906 GTGCGAGTTACCAAAACCGGGTTAAGTCCCGAAGGCATTTGTACGAGTTACCAAAA
66 GTACGAGTTACCAAAACCGGGCTAAGTCCCGAAGGCAATTGTACGAATCACCAAAA
* * * *
31705962 CCGGGTTAAGTCCCAAAGGCATTTGTGC-GAGTTACCAAAACCGGGTTAAGTCCT-GAAGGCATT
1 CCGGGCTAAGTCCCAAAGGCATTTGTGCTAAGTGACCAAAACCGGGTCAA-TCCTCGAAGGCATT
* * * * ** * *
31706025 TGTACGAGTTACTAAATCCGGGCTAATTCCCGAAGGTAATTGTGTGAATCACTATAA
65 TGTACGAGTTACCAAAACCGGGCTAAGTCCCGAAGGCAATTGTACGAATCACCAAAA
*
31706082 CCGGGCTATGTCCC
1 CCGGGCTAAGTCCC
31706096 GAAGACAATC
Statistics
Matches: 109, Mismatches: 24, Indels: 3
0.80 0.18 0.02
Matches are distributed among these distances:
120 81 0.74
121 28 0.26
ACGTcount: A:0.27, C:0.22, G:0.25, T:0.25
Consensus pattern (121 bp):
CCGGGCTAAGTCCCAAAGGCATTTGTGCTAAGTGACCAAAACCGGGTCAATCCTCGAAGGCATTT
GTACGAGTTACCAAAACCGGGCTAAGTCCCGAAGGCAATTGTACGAATCACCAAAA
Found at i:31715376 original size:40 final size:40
Alignment explanation
Indices: 31715280--31715538 Score: 320
Period size: 40 Copynumber: 6.5 Consensus size: 40
31715270 CGAATGGTAT
* * * * * *
31715280 CCGGGCTAAGTCCCGAAGGCTTTTGTGCTAAGTGACTAAAT
1 CCGGGTTAAGTCCCGAAGGCATTTGTGC-GAGTTACCAAAA
* *
31715321 CCGGGTCAATTCCCGAAGGCATTTGTGCGAGTTACCAAAA
1 CCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACCAAAA
*
31715361 CCGGGTTAAGTCCCGAAGGCATTTGTACGAGTTACCAAAA
1 CCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACCAAAA
31715401 CCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACCAAAA
1 CCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACCAAAA
* *
31715441 CCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAAT
1 CCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACCAAAA
* * * * * * * *
31715481 CCGGGCTAATTCCCGAAGGTAATTGTGCGAATCACTATAA
1 CCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACCAAAA
* *
31715521 CCGGGCTATGTCCCGAAG
1 CCGGGTTAAGTCCCGAAG
31715539 ACAATCGAGC
Statistics
Matches: 194, Mismatches: 24, Indels: 1
0.89 0.11 0.00
Matches are distributed among these distances:
40 170 0.88
41 24 0.12
ACGTcount: A:0.27, C:0.23, G:0.26, T:0.24
Consensus pattern (40 bp):
CCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACCAAAA
Found at i:31715563 original size:80 final size:80
Alignment explanation
Indices: 31715314--31715564 Score: 218
Period size: 80 Copynumber: 3.1 Consensus size: 80
31715304 GTGCTAAGTG
* * * * *
31715314 ACTAAATCCGGG-TCAATTCCCGAAGGCATTTGTGCGAGTTACCAAAACCGGGTTAAGTCCCGAA
1 ACTAAATCCGGGCT-AAGTCCCGAAGGCAATTGTGCGAATCACCAAAACCGGGCTAAGTCCCGAA
* * * *
31715378 GGCATTTGTA-CGAGTT
65 GACAATCG-AGCGAGTC
* * * * * * *
31715394 ACCAAAACCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACCAAAACCGGGTTAAGTCCCGAAG
1 ACTAAATCCGGGCTAAGTCCCGAAGGCAATTGTGCGAATCACCAAAACCGGGCTAAGTCCCGAAG
* * * * *
31715459 GCATTTGTGCGAGTT
66 ACAATCGAGCGAGTC
* * * * *
31715474 ACTAAATCCGGGCTAATTCCCGAAGGTAATTGTGCGAATCACTATAACCGGGCTATGTCCCGAAG
1 ACTAAATCCGGGCTAAGTCCCGAAGGCAATTGTGCGAATCACCAAAACCGGGCTAAGTCCCGAAG
31715539 ACAATCGAGCGAGTC
66 ACAATCGAGCGAGTC
* *
31715554 GCTATATCCGG
1 ACTAAATCCGG
31715565 TTAAATTCGA
Statistics
Matches: 146, Mismatches: 23, Indels: 4
0.84 0.13 0.02
Matches are distributed among these distances:
80 145 0.99
81 1 0.01
ACGTcount: A:0.28, C:0.24, G:0.25, T:0.23
Consensus pattern (80 bp):
ACTAAATCCGGGCTAAGTCCCGAAGGCAATTGTGCGAATCACCAAAACCGGGCTAAGTCCCGAAG
ACAATCGAGCGAGTC
Found at i:31723946 original size:42 final size:42
Alignment explanation
Indices: 31723841--31723949 Score: 128
Period size: 42 Copynumber: 2.6 Consensus size: 42
31723831 TCACGTCGAT
* * * * * *
31723841 GCCATATCCCAGATATGGTCTCATACGAATTCTCATTTCGAC
1 GCCATATCCCAAATATGGTCTTACACGAAATCTCATATCAAC
* * *
31723883 GCCATGTCCTAAACATGGTCTTACACGAAATCTCATATCAAC
1 GCCATATCCCAAATATGGTCTTACACGAAATCTCATATCAAC
*
31723925 GCCTTATCCCAAATATGGTCTTACA
1 GCCATATCCCAAATATGGTCTTACA
31723950 TGATGACTCA
Statistics
Matches: 54, Mismatches: 13, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
42 54 1.00
ACGTcount: A:0.29, C:0.28, G:0.13, T:0.29
Consensus pattern (42 bp):
GCCATATCCCAAATATGGTCTTACACGAAATCTCATATCAAC
Found at i:31740890 original size:9 final size:9
Alignment explanation
Indices: 31740871--31740899 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
31740861 TAGCACCCAG
31740871 ATCAC-ATA
1 ATCACAATA
31740879 ATCACAATA
1 ATCACAATA
31740888 ATCACAATA
1 ATCACAATA
31740897 ATC
1 ATC
31740900 CCCTAATGAC
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
8 5 0.25
9 15 0.75
ACGTcount: A:0.52, C:0.24, G:0.00, T:0.24
Consensus pattern (9 bp):
ATCACAATA
Found at i:31748622 original size:20 final size:21
Alignment explanation
Indices: 31748580--31748622 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
31748570 ATTTCGATGA
*
31748580 TTGATGATAGATTATGAATGT
1 TTGATGATAGATTATGAAAGT
31748601 TTGATGATAG-TTAT-ACAAGT
1 TTGATGATAGATTATGA-AAGT
31748621 TT
1 TT
31748623 TGTTTAGTGA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
19 1 0.05
20 9 0.45
21 10 0.50
ACGTcount: A:0.33, C:0.02, G:0.21, T:0.44
Consensus pattern (21 bp):
TTGATGATAGATTATGAAAGT
Found at i:31749249 original size:48 final size:48
Alignment explanation
Indices: 31749176--31749356 Score: 285
Period size: 48 Copynumber: 3.8 Consensus size: 48
31749166 CATTAGGGAA
31749176 TACATTGATTTGGCTTCGGGCCATGATATCGGCACTTCGAGTGCGAGCT
1 TACATTGATTTGGCTTCGGGCCATGATATCGGCACTTCGAGTGCGAG-T
* *
31749225 T-CATTGATTTGGCTTCGGGACATGATATCGGCACTTC-AGGTGTGAGT
1 TACATTGATTTGGCTTCGGGCCATGATATCGGCACTTCGA-GTGCGAGT
* *
31749272 TACATTGATTTGGCTTCAGGCCATGATATCGGCACTTCGGGTGCGAGT
1 TACATTGATTTGGCTTCGGGCCATGATATCGGCACTTCGAGTGCGAGT
*
31749320 TACATTGATTTGGCTTCGGGCCATGATATTGGCACTT
1 TACATTGATTTGGCTTCGGGCCATGATATCGGCACTT
31749357 AAGGTACGAG
Statistics
Matches: 121, Mismatches: 8, Indels: 7
0.89 0.06 0.05
Matches are distributed among these distances:
47 3 0.02
48 117 0.97
49 1 0.01
ACGTcount: A:0.19, C:0.20, G:0.28, T:0.33
Consensus pattern (48 bp):
TACATTGATTTGGCTTCGGGCCATGATATCGGCACTTCGAGTGCGAGT
Found at i:31757568 original size:58 final size:61
Alignment explanation
Indices: 31757518--31757634 Score: 177
Period size: 61 Copynumber: 2.0 Consensus size: 61
31757508 AATCACTTTA
* *
31757518 CTATTAAATTAATATAAT-ATT-TGT-CAAGATAAATATTAGATTAAATTTAATATTAAAT
1 CTATTAAATTAATAGAATAATTGTCTACAAGATAAATATTAGATTAAATTTAATATTAAAT
* *
31757576 CTATTAAATTAATAGAATAATTGTCTACAATATAAATATTAAATTAAATTTAATATTAA
1 CTATTAAATTAATAGAATAATTGTCTACAAGATAAATATTAGATTAAATTTAATATTAA
31757635 GATAATCACT
Statistics
Matches: 52, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
58 17 0.33
59 3 0.06
60 2 0.04
61 30 0.58
ACGTcount: A:0.50, C:0.04, G:0.04, T:0.42
Consensus pattern (61 bp):
CTATTAAATTAATAGAATAATTGTCTACAAGATAAATATTAGATTAAATTTAATATTAAAT
Found at i:31757660 original size:20 final size:18
Alignment explanation
Indices: 31757610--31757661 Score: 63
Period size: 20 Copynumber: 2.8 Consensus size: 18
31757600 CTACAATATA
31757610 AATATTAAATTAA-ATTT
1 AATATTAAATTAATATTT
31757627 AATATTAAGA-TAATCACTTT
1 AATATTAA-ATTAAT-A-TTT
31757647 AATATTAAATTAATA
1 AATATTAAATTAATA
31757662 ATATACTATC
Statistics
Matches: 30, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
17 11 0.37
18 1 0.03
19 3 0.10
20 15 0.50
ACGTcount: A:0.52, C:0.04, G:0.02, T:0.42
Consensus pattern (18 bp):
AATATTAAATTAATATTT
Found at i:31767311 original size:24 final size:24
Alignment explanation
Indices: 31767282--31767329 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
31767272 TGAACATTTA
31767282 TTCCAGCAACTAATTAACTAAAAG
1 TTCCAGCAACTAATTAACTAAAAG
31767306 TTCCAGCAACTAATTAACTAAAAG
1 TTCCAGCAACTAATTAACTAAAAG
31767330 GAGTGTAATA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.46, C:0.21, G:0.08, T:0.25
Consensus pattern (24 bp):
TTCCAGCAACTAATTAACTAAAAG
Found at i:31768935 original size:12 final size:12
Alignment explanation
Indices: 31768918--31768942 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
31768908 TCACTATCTT
31768918 TTTCTTTTTCAC
1 TTTCTTTTTCAC
31768930 TTTCTTTTTCAC
1 TTTCTTTTTCAC
31768942 T
1 T
31768943 CTCAATCTCT
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:0.08, C:0.24, G:0.00, T:0.68
Consensus pattern (12 bp):
TTTCTTTTTCAC
Found at i:31768935 original size:18 final size:20
Alignment explanation
Indices: 31768893--31768940 Score: 64
Period size: 18 Copynumber: 2.5 Consensus size: 20
31768883 ATTCTTTATC
31768893 TCTTTTTGCATTTTCTCACTA
1 TCTTTTT-CATTTTCTCACTA
*
31768914 TCTTTTTC-TTTT-TCACTT
1 TCTTTTTCATTTTCTCACTA
31768932 TCTTTTTCA
1 TCTTTTTCA
31768941 CTCTCAATCT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
18 13 0.52
19 4 0.16
20 1 0.04
21 7 0.28
ACGTcount: A:0.10, C:0.23, G:0.02, T:0.65
Consensus pattern (20 bp):
TCTTTTTCATTTTCTCACTA
Found at i:31771451 original size:40 final size:40
Alignment explanation
Indices: 31771400--31771546 Score: 231
Period size: 40 Copynumber: 3.7 Consensus size: 40
31771390 ATGTAATAAA
* *
31771400 AATAAAGTCCAGAAAATCAATAACTAACTAAGATGAGTTT
1 AATAAAGTCCAGCAAATCAATAATTAACTAAGATGAGTTT
*
31771440 AATAAAGTCCAGCACATCAATAATTAACTAAGATGAGTTT
1 AATAAAGTCCAGCAAATCAATAATTAACTAAGATGAGTTT
*
31771480 AATAAAGTCCAGCAAATCAATAATTAAATAAGATGAGTTT
1 AATAAAGTCCAGCAAATCAATAATTAACTAAGATGAGTTT
* * *
31771520 AATAAAGTCTAGCAACTCAATTATTAA
1 AATAAAGTCCAGCAAATCAATAATTAA
31771547 ACCAAAATTA
Statistics
Matches: 99, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
40 99 1.00
ACGTcount: A:0.48, C:0.13, G:0.12, T:0.27
Consensus pattern (40 bp):
AATAAAGTCCAGCAAATCAATAATTAACTAAGATGAGTTT
Found at i:31785859 original size:44 final size:43
Alignment explanation
Indices: 31785796--31785936 Score: 148
Period size: 42 Copynumber: 3.3 Consensus size: 43
31785786 TATGTGTTTT
* *
31785796 CGTGTAAGACCACGTCTGGGATGTTGGCATCGACT-TATGATTTA
1 CGTGTAAGACCATGTCTGGGAAGTTGGCATCGA-TATATGA-TTA
*
31785840 CGTGTAAGACCATGTCTGGGACA-TCGGCATCG-TATATGAGTT-
1 CGTGTAAGACCATGTCTGGGA-AGTTGGCATCGATATATGA-TTA
* *
31785882 CGTGTAAGACCCTGTCTGGGACAG-TGGCATCGATATTTGATTA
1 CGTGTAAGACCATGTCTGGGA-AGTTGGCATCGATATATGATTA
*
31785925 CATGTAAGACCA
1 CGTGTAAGACCA
31785937 CATGTGGGAC
Statistics
Matches: 83, Mismatches: 9, Indels: 11
0.81 0.09 0.11
Matches are distributed among these distances:
42 32 0.39
43 23 0.28
44 28 0.34
ACGTcount: A:0.25, C:0.19, G:0.27, T:0.29
Consensus pattern (43 bp):
CGTGTAAGACCATGTCTGGGAAGTTGGCATCGATATATGATTA
Found at i:31789297 original size:35 final size:36
Alignment explanation
Indices: 31789243--31789314 Score: 110
Period size: 35 Copynumber: 2.0 Consensus size: 36
31789233 GATGCCTTCT
*
31789243 TTCTGTGTATAGTCTTTCCCTACAATTCTAGCTTTA
1 TTCTGTATATAGTCTTTCCCTACAATTCTAGCTTTA
* *
31789279 TTCTGTATATA-TTTTTCCCTACAATTTTAGCTTTA
1 TTCTGTATATAGTCTTTCCCTACAATTCTAGCTTTA
31789314 T
1 T
31789315 GTGTTTCCAC
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
35 23 0.70
36 10 0.30
ACGTcount: A:0.21, C:0.19, G:0.08, T:0.51
Consensus pattern (36 bp):
TTCTGTATATAGTCTTTCCCTACAATTCTAGCTTTA
Found at i:31790429 original size:26 final size:26
Alignment explanation
Indices: 31790399--31790461 Score: 72
Period size: 27 Copynumber: 2.4 Consensus size: 26
31790389 TTCTACTGCC
** *
31790399 AGTAAAATTTTGATGATTTTACCCTT
1 AGTAAAATTTTGACAATTTTACCCCT
* *
31790425 GGTAAATTTTTTGACAATTTTACCCCT
1 AGTAAA-ATTTTGACAATTTTACCCCT
31790452 AGTAAAATTT
1 AGTAAAATTT
31790462 CGAGAAAATA
Statistics
Matches: 29, Mismatches: 7, Indels: 2
0.76 0.18 0.05
Matches are distributed among these distances:
26 8 0.28
27 21 0.72
ACGTcount: A:0.32, C:0.13, G:0.11, T:0.44
Consensus pattern (26 bp):
AGTAAAATTTTGACAATTTTACCCCT
Found at i:31793899 original size:82 final size:82
Alignment explanation
Indices: 31793762--31793922 Score: 277
Period size: 82 Copynumber: 2.0 Consensus size: 82
31793752 TACTAATTAT
* * *
31793762 ATCTATAAATGTCGAAGTTAGAATTAGTTTAGTTTCGTCTCCCTTGGGAACAATCCTCGAACTAC
1 ATCTATAAACGTCGAAGTTAGAATTAGTTTAGTTTCATCTCCCTTAGGAACAATCCTCGAACTAC
31793827 TCCAATACTTCATTTAG
66 TCCAATACTTCATTTAG
* *
31793844 ATCTATTAACGTCGAAGTTAGAATTAGTTTAGTTTCATCTCCCTTAGGAACAATCCTCGGACTAC
1 ATCTATAAACGTCGAAGTTAGAATTAGTTTAGTTTCATCTCCCTTAGGAACAATCCTCGAACTAC
31793909 TCCAATACTTCATT
66 TCCAATACTTCATT
31793923 GTATAAATCT
Statistics
Matches: 74, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
82 74 1.00
ACGTcount: A:0.29, C:0.22, G:0.14, T:0.35
Consensus pattern (82 bp):
ATCTATAAACGTCGAAGTTAGAATTAGTTTAGTTTCATCTCCCTTAGGAACAATCCTCGAACTAC
TCCAATACTTCATTTAG
Found at i:31795469 original size:26 final size:25
Alignment explanation
Indices: 31795440--31795496 Score: 69
Period size: 26 Copynumber: 2.2 Consensus size: 25
31795430 TACCTCCAGC
*
31795440 AAAATTTTAACGATTTTACCCATGGT
1 AAAATTTTAACAATTTTACCC-TGGT
* * *
31795466 AAAATTTTCATAATTTTTCCCTGGT
1 AAAATTTTAACAATTTTACCCTGGT
31795491 AAAATT
1 AAAATT
31795497 GCAAGAATAG
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
25 10 0.37
26 17 0.63
ACGTcount: A:0.35, C:0.14, G:0.09, T:0.42
Consensus pattern (25 bp):
AAAATTTTAACAATTTTACCCTGGT
Found at i:31815370 original size:22 final size:23
Alignment explanation
Indices: 31815344--31815421 Score: 85
Period size: 22 Copynumber: 3.6 Consensus size: 23
31815334 TAGTGCTTGT
31815344 TAATT-TATTAAATTATATGTTA
1 TAATTATATTAAATTATATGTTA
*
31815366 TAATTATGTTATAA-T-TATGTTA
1 TAATTATATTA-AATTATATGTTA
*
31815388 TAATTATGTTAAATTATA-GTTA
1 TAATTATATTAAATTATATGTTA
*
31815410 -AAATATATTAAA
1 TAATTATATTAAA
31815422 ACATAAAAAC
Statistics
Matches: 49, Mismatches: 3, Indels: 9
0.80 0.05 0.15
Matches are distributed among these distances:
21 12 0.24
22 28 0.57
23 7 0.14
24 2 0.04
ACGTcount: A:0.44, C:0.00, G:0.06, T:0.50
Consensus pattern (23 bp):
TAATTATATTAAATTATATGTTA
Found at i:31815375 original size:11 final size:11
Alignment explanation
Indices: 31815359--31815409 Score: 86
Period size: 11 Copynumber: 4.6 Consensus size: 11
31815349 TATTAAATTA
31815359 TATGTTATAAT
1 TATGTTATAAT
31815370 TATGTTATAAT
1 TATGTTATAAT
31815381 TATGTTATAAT
1 TATGTTATAAT
31815392 TATGTTA-AAT
1 TATGTTATAAT
31815402 TATAGTTA
1 TAT-GTTA
31815410 AAATATATTA
Statistics
Matches: 39, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
10 6 0.15
11 33 0.85
ACGTcount: A:0.37, C:0.00, G:0.10, T:0.53
Consensus pattern (11 bp):
TATGTTATAAT
Found at i:31815410 original size:11 final size:10
Alignment explanation
Indices: 31815359--31815421 Score: 72
Period size: 11 Copynumber: 5.9 Consensus size: 10
31815349 TATTAAATTA
31815359 TATGTTATAAT
1 TATGTTA-AAT
31815370 TATGTTATAAT
1 TATGTTA-AAT
31815381 TATGTTATAAT
1 TATGTTA-AAT
31815392 TATGTTAAAT
1 TATGTTAAAT
*
31815402 TATAGTTAAAA
1 TAT-GTTAAAT
*
31815413 TATATTAAA
1 TATGTTAAA
31815422 ACATAAAAAC
Statistics
Matches: 49, Mismatches: 2, Indels: 3
0.91 0.04 0.06
Matches are distributed among these distances:
10 11 0.22
11 38 0.78
ACGTcount: A:0.43, C:0.00, G:0.08, T:0.49
Consensus pattern (10 bp):
TATGTTAAAT
Found at i:31818514 original size:50 final size:49
Alignment explanation
Indices: 31818453--31818607 Score: 188
Period size: 50 Copynumber: 3.1 Consensus size: 49
31818443 ACAAGTTGTG
* *
31818453 AATCGGTATGCTCATT-TGAGT-TGAAGATCGGTATGCTCTCACGAGTTATA
1 AATCGGTATGCTC-TTATGAGTAT-AA-ATCGGTATGCTCTTACGAGCTATA
* * *
31818503 AATCAGTATGCTCTTATGATCTATAAATCAGTATGCTCTTACGAGCTATA
1 AATCGGTATGCTCTTATGA-GTATAAATCGGTATGCTCTTACGAGCTATA
* *
31818553 AATCGGTATGCTCTTCTGAGCTATAAATTGGTATGCTCTTACGAGCTATA
1 AATCGGTATGCTCTTATGAG-TATAAATCGGTATGCTCTTACGAGCTATA
31818603 AATCG
1 AATCG
31818608 ATAACCCTAA
Statistics
Matches: 91, Mismatches: 10, Indels: 8
0.83 0.09 0.07
Matches are distributed among these distances:
49 2 0.02
50 85 0.93
51 3 0.03
52 1 0.01
ACGTcount: A:0.28, C:0.17, G:0.19, T:0.35
Consensus pattern (49 bp):
AATCGGTATGCTCTTATGAGTATAAATCGGTATGCTCTTACGAGCTATA
Found at i:31818527 original size:25 final size:25
Alignment explanation
Indices: 31818483--31818606 Score: 169
Period size: 25 Copynumber: 5.0 Consensus size: 25
31818473 TTGAAGATCG
* *
31818483 GTATGCTCTCACGAGTTATAAATCA
1 GTATGCTCTTACGAGCTATAAATCA
* *
31818508 GTATGCTCTTATGATCTATAAATCA
1 GTATGCTCTTACGAGCTATAAATCA
*
31818533 GTATGCTCTTACGAGCTATAAATCG
1 GTATGCTCTTACGAGCTATAAATCA
**
31818558 GTATGCTCTT-CTGAGCTATAAATTG
1 GTATGCTCTTAC-GAGCTATAAATCA
31818583 GTATGCTCTTACGAGCTATAAATC
1 GTATGCTCTTACGAGCTATAAATC
31818607 GATAACCCTA
Statistics
Matches: 88, Mismatches: 9, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
24 1 0.01
25 86 0.98
26 1 0.01
ACGTcount: A:0.29, C:0.19, G:0.17, T:0.35
Consensus pattern (25 bp):
GTATGCTCTTACGAGCTATAAATCA
Found at i:31820169 original size:68 final size:68
Alignment explanation
Indices: 31820044--31820174 Score: 165
Period size: 68 Copynumber: 1.9 Consensus size: 68
31820034 TATACATATA
* * * *
31820044 TGTGTTTATATGCAAACTATGTCAATGTGTGAACCATGTAAATATGTGAAATGTGACAATGTGCA
1 TGTGTTTATAAGCAAACTATGCCAATGTGTGAACCATGTAAATATGCGAAATATGACAATGTGCA
31820109 TGT
66 TGT
* * ***
31820112 TGTGTTTATAAGCAAACTGTGCCAATGTGT-AGACCGTGTAAATATGCGGCCTATGACAATGTG
1 TGTGTTTATAAGCAAACTATGCCAATGTGTGA-ACCATGTAAATATGCGAAATATGACAATGTG
31820175 TGGGCTGTGT
Statistics
Matches: 53, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
67 1 0.02
68 52 0.98
ACGTcount: A:0.31, C:0.13, G:0.24, T:0.33
Consensus pattern (68 bp):
TGTGTTTATAAGCAAACTATGCCAATGTGTGAACCATGTAAATATGCGAAATATGACAATGTGCA
TGT
Found at i:31820317 original size:34 final size:33
Alignment explanation
Indices: 31820274--31820357 Score: 114
Period size: 34 Copynumber: 2.5 Consensus size: 33
31820264 TGACAATGTG
* *
31820274 CGAGTTGTGTTTATATGCTAGCTATTTTTATAT
1 CGAGTTGTGTTTATATGCAAGCTATGTTTATAT
*
31820307 CCGAGTTGTGTTTACATGCAAGCTATGTTTATAT
1 -CGAGTTGTGTTTATATGCAAGCTATGTTTATAT
**
31820341 ATAGTTGTGTTTATATG
1 CGAGTTGTGTTTATATG
31820358 TGAGCTAGCT
Statistics
Matches: 44, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
33 14 0.32
34 30 0.68
ACGTcount: A:0.23, C:0.10, G:0.20, T:0.48
Consensus pattern (33 bp):
CGAGTTGTGTTTATATGCAAGCTATGTTTATAT
Found at i:31820320 original size:17 final size:17
Alignment explanation
Indices: 31820272--31820357 Score: 66
Period size: 17 Copynumber: 5.1 Consensus size: 17
31820262 TATGACAATG
31820272 TGCGAGTTGTGTTTATA
1 TGCGAGTTGTGTTTATA
* * * *
31820289 TGCTAGCTATTTTTATA
1 TGCGAGTTGTGTTTATA
* *
31820306 TCCGAGTTGTGTTTACA
1 TGCGAGTTGTGTTTATA
* * *
31820323 TGCAAGCTATGTTTATA
1 TGCGAGTTGTGTTTATA
**
31820340 T-ATAGTTGTGTTTATA
1 TGCGAGTTGTGTTTATA
31820356 TG
1 TG
31820358 TGAGCTAGCT
Statistics
Matches: 49, Mismatches: 19, Indels: 2
0.70 0.27 0.03
Matches are distributed among these distances:
16 12 0.24
17 37 0.76
ACGTcount: A:0.22, C:0.09, G:0.21, T:0.48
Consensus pattern (17 bp):
TGCGAGTTGTGTTTATA
Found at i:31822361 original size:19 final size:20
Alignment explanation
Indices: 31822327--31822364 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
31822317 ATCTTGGTGG
31822327 TGCAAAAATGCATATTGATT
1 TGCAAAAATGCATATTGATT
*
31822347 TGCAAGAAT-CATATTGAT
1 TGCAAAAATGCATATTGAT
31822365 GGTCAGGTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.39, C:0.11, G:0.16, T:0.34
Consensus pattern (20 bp):
TGCAAAAATGCATATTGATT
Found at i:31824292 original size:27 final size:29
Alignment explanation
Indices: 31824253--31824316 Score: 78
Period size: 29 Copynumber: 2.2 Consensus size: 29
31824243 GAATCAATTG
*
31824253 TTATATATTTATAT-TTTTG-TATTTTTAT
1 TTATA-ATATATATGTTTTGATATTTTTAT
* *
31824281 TTTTAATATATATGTTTTGATTTTTTTAT
1 TTATAATATATATGTTTTGATATTTTTAT
31824310 TTATAAT
1 TTATAAT
31824317 TTATGTATGC
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
27 7 0.23
28 9 0.30
29 14 0.47
ACGTcount: A:0.27, C:0.00, G:0.05, T:0.69
Consensus pattern (29 bp):
TTATAATATATATGTTTTGATATTTTTAT
Found at i:31831476 original size:58 final size:58
Alignment explanation
Indices: 31831414--31831555 Score: 171
Period size: 58 Copynumber: 2.4 Consensus size: 58
31831404 TTTTTAATTC
* *
31831414 ATTTAATAATAATTATATTAAGAATTTTATTAAATCATATATTA-TTTTATTAAATTAT
1 ATTTAATAATAATTATATTAA-AATTTGATTAAATCATATATTATTTTTATTAAAATAT
* * * * * *
31831472 ATTTAGTAATAATCATGTTAAAATATGATTAAATTATTTATTATTTTTATTAAAATAT
1 ATTTAATAATAATTATATTAAAATTTGATTAAATCATATATTATTTTTATTAAAATAT
*
31831530 TTTTAATAATAATCT-TATTAAAATTT
1 ATTTAATAATAAT-TATATTAAAATTT
31831556 AATAATAATA
Statistics
Matches: 69, Mismatches: 13, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
57 18 0.26
58 51 0.74
ACGTcount: A:0.44, C:0.02, G:0.03, T:0.51
Consensus pattern (58 bp):
ATTTAATAATAATTATATTAAAATTTGATTAAATCATATATTATTTTTATTAAAATAT
Found at i:31831725 original size:24 final size:24
Alignment explanation
Indices: 31831690--31831792 Score: 71
Period size: 24 Copynumber: 4.4 Consensus size: 24
31831680 AATAATTTTA
31831690 TATTAAAATTATTATTTA-AATAT
1 TATTAAAATTATTATTTATAATAT
* *
31831713 TATTAATAATTA-TATTAATAATGT
1 TATTAA-AATTATTATTTATAATAT
31831737 TATTAAAA-TA-TATATTAT--T-T
1 TATTAAAATTATTAT-TTATAATAT
31831757 TATT-AAATTA-TATTTAATAATAAT
1 TATTAAAATTATTATTT-ATAAT-AT
31831781 TATGTTAAAATT
1 TA--TTAAAATT
31831793 TGATTAAATT
Statistics
Matches: 65, Mismatches: 3, Indels: 20
0.74 0.03 0.23
Matches are distributed among these distances:
19 5 0.08
20 12 0.18
21 1 0.02
22 6 0.09
23 16 0.25
24 18 0.28
26 2 0.03
27 5 0.08
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (24 bp):
TATTAAAATTATTATTTATAATAT
Found at i:31831728 original size:12 final size:12
Alignment explanation
Indices: 31831687--31831753 Score: 54
Period size: 12 Copynumber: 5.7 Consensus size: 12
31831677 AATAATAATT
31831687 TTATATTAA-AA
1 TTATATTAATAA
31831698 TTATTATT--TAA
1 TTA-TATTAATAA
*
31831709 ATATTATTAATAA
1 TTA-TATTAATAA
31831722 TTATATTAATAA
1 TTATATTAATAA
31831734 TGT-TATTAA-AA
1 T-TATATTAATAA
31831745 TATATATTA
1 T-TATATTA
31831754 TTTTATTAAA
Statistics
Matches: 47, Mismatches: 3, Indels: 11
0.77 0.05 0.18
Matches are distributed among these distances:
11 16 0.34
12 25 0.53
13 6 0.13
ACGTcount: A:0.48, C:0.00, G:0.01, T:0.51
Consensus pattern (12 bp):
TTATATTAATAA
Found at i:31831760 original size:55 final size:54
Alignment explanation
Indices: 31831701--31831816 Score: 123
Period size: 55 Copynumber: 2.1 Consensus size: 54
31831691 ATTAAAATTA
*
31831701 TTATTTAA-ATA-TTATTAATAATTATATTAATAATGTT-ATTAAAATATATATTA-TT
1 TTATTTAATATATTTAATAATAATTATATTAA-AAT-TTGATT-AAAT-TAT-TTATTT
* *
31831756 TTATTAAATTATATTTAATAATAATTATGTTAAAATTTGATTAAATTATTTATTT
1 TTATTTAA-TATATTTAATAATAATTATATTAAAATTTGATTAAATTATTTATTT
31831811 TTATTT
1 TTATTT
31831817 TTATTAAAAT
Statistics
Matches: 52, Mismatches: 4, Indels: 10
0.79 0.06 0.15
Matches are distributed among these distances:
54 3 0.06
55 17 0.33
56 6 0.12
57 9 0.17
58 17 0.33
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (54 bp):
TTATTTAATATATTTAATAATAATTATATTAAAATTTGATTAAATTATTTATTT
Found at i:31832048 original size:16 final size:15
Alignment explanation
Indices: 31832013--31832066 Score: 56
Period size: 16 Copynumber: 3.4 Consensus size: 15
31832003 TTAATTACTG
*
31832013 ATTACAGCTCTATTTC
1 ATTACAACTCTA-TTC
31832029 ATTACAACTCTATTC
1 ATTACAACTCTATTC
31832044 AATTACAA-TCCTATTCC
1 -ATTACAACT-CTATT-C
31832061 ATTACA
1 ATTACA
31832067 GTGAACCAAA
Statistics
Matches: 34, Mismatches: 1, Indels: 6
0.83 0.02 0.15
Matches are distributed among these distances:
15 4 0.12
16 29 0.85
17 1 0.03
ACGTcount: A:0.33, C:0.26, G:0.02, T:0.39
Consensus pattern (15 bp):
ATTACAACTCTATTC
Found at i:31836407 original size:33 final size:33
Alignment explanation
Indices: 31836369--31836467 Score: 153
Period size: 33 Copynumber: 3.0 Consensus size: 33
31836359 GACTGAGTGG
* * *
31836369 GAGTGTTTGGTTGTTGGACAGGAGTTGGAATGT
1 GAGTGTTTTGTTGCTGGACAGGAGCTGGAATGT
*
31836402 GAGTGTTTTGCTGCTGGACAGGAGCTGGAATGT
1 GAGTGTTTTGTTGCTGGACAGGAGCTGGAATGT
*
31836435 GGGTGTTTTGTTGCTGGACAGGAGCTGGAATGT
1 GAGTGTTTTGTTGCTGGACAGGAGCTGGAATGT
31836468 CAAGAAGAAA
Statistics
Matches: 60, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 60 1.00
ACGTcount: A:0.17, C:0.08, G:0.41, T:0.33
Consensus pattern (33 bp):
GAGTGTTTTGTTGCTGGACAGGAGCTGGAATGT
Found at i:31845460 original size:21 final size:21
Alignment explanation
Indices: 31845434--31845502 Score: 86
Period size: 21 Copynumber: 3.3 Consensus size: 21
31845424 TCACTTGGTT
*
31845434 TCTTTTTGTCCAAGTTATTTC
1 TCTTTTTGTCCAAGTTACTTC
*
31845455 TCTTTTTGTCCAAGTTGCTTC
1 TCTTTTTGTCCAAGTTACTTC
* * *
31845476 TCTTTTTGTCTAACTCACTTC
1 TCTTTTTGTCCAAGTTACTTC
31845497 -CTTTTT
1 TCTTTTT
31845503 TCTTTGTGAG
Statistics
Matches: 42, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
20 6 0.14
21 36 0.86
ACGTcount: A:0.12, C:0.23, G:0.09, T:0.57
Consensus pattern (21 bp):
TCTTTTTGTCCAAGTTACTTC
Found at i:31847187 original size:16 final size:16
Alignment explanation
Indices: 31847168--31847198 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
31847158 TAATAAGGAT
31847168 AATATAATAAGTATAA
1 AATATAATAAGTATAA
*
31847184 AATATATTAAGTATA
1 AATATAATAAGTATA
31847199 TAATTAGTTA
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:0.58, C:0.00, G:0.06, T:0.35
Consensus pattern (16 bp):
AATATAATAAGTATAA
Found at i:31847231 original size:12 final size:12
Alignment explanation
Indices: 31847216--31847246 Score: 53
Period size: 12 Copynumber: 2.5 Consensus size: 12
31847206 TTATATAACA
31847216 CATATTTTCTTT
1 CATATTTTCTTT
31847228 CATATTTTCTTT
1 CATATTTTCTTT
31847240 CTATATT
1 C-ATATT
31847247 ATTATATTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 13 0.72
13 5 0.28
ACGTcount: A:0.19, C:0.16, G:0.00, T:0.65
Consensus pattern (12 bp):
CATATTTTCTTT
Found at i:31847252 original size:8 final size:8
Alignment explanation
Indices: 31847241--31847296 Score: 66
Period size: 8 Copynumber: 7.2 Consensus size: 8
31847231 ATTTTCTTTC
31847241 TATATTAT
1 TATATTAT
31847249 TATATTAT
1 TATATTAT
31847257 TATATTAT
1 TATATTAT
31847265 TA-A-TAT
1 TATATTAT
31847271 TAT-TTA-
1 TATATTAT
31847277 TATATTAT
1 TATATTAT
31847285 TAAATATTAT
1 T--ATATTAT
31847295 TA
1 TA
31847297 ATATATTTAA
Statistics
Matches: 42, Mismatches: 0, Indels: 12
0.78 0.00 0.22
Matches are distributed among these distances:
6 8 0.19
7 6 0.14
8 20 0.48
10 8 0.19
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (8 bp):
TATATTAT
Found at i:31847290 original size:21 final size:19
Alignment explanation
Indices: 31847242--31847300 Score: 72
Period size: 20 Copynumber: 3.2 Consensus size: 19
31847232 TTTTCTTTCT
31847242 ATATTATT--ATATTATT-
1 ATATTATTAAATATTATTA
31847258 ATATTATT-AATATTATTTA
1 ATATTATTAAATATTA-TTA
31847277 TATATTATTAAATATTATTA
1 -ATATTATTAAATATTATTA
31847297 ATAT
1 ATAT
31847301 ATTTAAATTT
Statistics
Matches: 38, Mismatches: 0, Indels: 7
0.84 0.00 0.16
Matches are distributed among these distances:
16 8 0.21
17 6 0.16
18 2 0.05
19 4 0.11
20 11 0.29
21 7 0.18
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (19 bp):
ATATTATTAAATATTATTA
Found at i:31847294 original size:30 final size:27
Alignment explanation
Indices: 31847241--31847305 Score: 87
Period size: 30 Copynumber: 2.3 Consensus size: 27
31847231 ATTTTCTTTC
31847241 TATA-TTATTATATTATTATATTATTAA
1 TATATTTA-TATATTATTATATTATTAA
31847268 TATTATTTATATATTATTAAATATTATTAA
1 TA-TATTTATATATTATT--ATATTATTAA
31847298 TATATTTA
1 TATATTTA
31847306 AATTTCTATA
Statistics
Matches: 34, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
27 2 0.06
28 11 0.32
29 9 0.26
30 12 0.35
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (27 bp):
TATATTTATATATTATTATATTATTAA
Found at i:31847301 original size:21 final size:20
Alignment explanation
Indices: 31847241--31847303 Score: 80
Period size: 21 Copynumber: 3.3 Consensus size: 20
31847231 ATTTTCTTTC
31847241 TATATTATT-ATATTA-T--
1 TATATTATTAATATTATTAA
*
31847257 TATATTATTAATATTATTTA
1 TATATTATTAATATTATTAA
31847277 TATATTATTAAATATTATTAA
1 TATATTATT-AATATTATTAA
31847298 TATATT
1 TATATT
31847304 TAAATTTCTA
Statistics
Matches: 41, Mismatches: 1, Indels: 5
0.87 0.02 0.11
Matches are distributed among these distances:
16 9 0.22
17 6 0.15
18 1 0.02
20 9 0.22
21 16 0.39
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (20 bp):
TATATTATTAATATTATTAA
Found at i:31849264 original size:13 final size:13
Alignment explanation
Indices: 31849246--31849271 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
31849236 AGTTGCATAG
31849246 TATTCACGTATTA
1 TATTCACGTATTA
31849259 TATTCACGTATTA
1 TATTCACGTATTA
31849272 AAATTACACA
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:0.31, C:0.15, G:0.08, T:0.46
Consensus pattern (13 bp):
TATTCACGTATTA
Found at i:31849698 original size:247 final size:247
Alignment explanation
Indices: 31849263--31850004 Score: 1398
Period size: 247 Copynumber: 3.0 Consensus size: 247
31849253 GTATTATATT
31849263 CACGTATTAAAATTACACAACTGAGACGCTTGTTTTTA-TTTTTTTAACAAAAACAAATTTGGAT
1 CACGTATTAAAATTACACAACTGAGACGCTTGTTTTTATTTTTTTTAACAAAAACAAATTTGGAT
* *
31849327 TTTATTTTATTTTTTACATTTTAGTTTATATTTATCTCTTTTTTTAAATATGACATTATTTAGCT
66 TTTATTTTATTTTTTACATTTTAGCTTATATTTATCTTTTTTTTTAAATATGACATTATTTAGCT
*
31849392 TTTAACATTTTTACTTTCAATAGTTATTAAATTATTTTTTTGAAGTGATTAAACCATCTAGATGA
131 TTTAACATTTTTACTTTCAATAGTTATTAAATTATTTTTTTGAAGTGGTTAAACCATCTAGATGA
31849457 TCCAATTGAACTATAACTCCAATCGATTCAACCTTAGCCTTACATTGCAAAA
196 TCCAATTGAACTATAACTCCAATCGATTCAACCTTAGCCTTACATTGCAAAA
* *
31849509 CACGTATTAAAATTACACAATTGAGACGCTTGTTTTTATTTTTTTTATCAAAAACAAATTTGGAT
1 CACGTATTAAAATTACACAACTGAGACGCTTGTTTTTATTTTTTTTAACAAAAACAAATTTGGAT
31849574 TTTATTTTATTTTTTACATTTTAGCTTATATTTATCTTTTTTTTTAAATATGACATTATTTAGCT
66 TTTATTTTATTTTTTACATTTTAGCTTATATTTATCTTTTTTTTTAAATATGACATTATTTAGCT
31849639 TTTAACATTTTTACTTTCAATAGTTATTAAATTATTTTTTTGAAGTGGTTAAACCATCTAGATGA
131 TTTAACATTTTTACTTTCAATAGTTATTAAATTATTTTTTTGAAGTGGTTAAACCATCTAGATGA
* *
31849704 TCCAATTAAACTATAACTCCAATCGATTCAACCTTAGTCTTACATTGCAAAA
196 TCCAATTGAACTATAACTCCAATCGATTCAACCTTAGCCTTACATTGCAAAA
31849756 CACGTATTAAAATTACACAACTGAGACGCTTGTTTTTATTTTTTTTAACAAAAACAAATTTGGAT
1 CACGTATTAAAATTACACAACTGAGACGCTTGTTTTTATTTTTTTTAACAAAAACAAATTTGGAT
31849821 TTTATTTTATTTTTTACATTTTAGCTTATATTTATC-TTTTTTTTAAATATGACATTATTTAGCT
66 TTTATTTTATTTTTTACATTTTAGCTTATATTTATCTTTTTTTTTAAATATGACATTATTTAGCT
31849885 TTTAACATTTTTACTTTCAATAGTTATTAAATTATTTTTTTGAAGTGGTTAAACCATCTAGATGA
131 TTTAACATTTTTACTTTCAATAGTTATTAAATTATTTTTTTGAAGTGGTTAAACCATCTAGATGA
*
31849950 TCCAATTGAACTATAACTCCAATCGATTCAACCTTAGCATTACATTGCAAAA
196 TCCAATTGAACTATAACTCCAATCGATTCAACCTTAGCCTTACATTGCAAAA
31850002 CAC
1 CAC
31850005 CACAGATTCT
Statistics
Matches: 483, Mismatches: 12, Indels: 2
0.97 0.02 0.00
Matches are distributed among these distances:
246 182 0.38
247 301 0.62
ACGTcount: A:0.33, C:0.14, G:0.08, T:0.45
Consensus pattern (247 bp):
CACGTATTAAAATTACACAACTGAGACGCTTGTTTTTATTTTTTTTAACAAAAACAAATTTGGAT
TTTATTTTATTTTTTACATTTTAGCTTATATTTATCTTTTTTTTTAAATATGACATTATTTAGCT
TTTAACATTTTTACTTTCAATAGTTATTAAATTATTTTTTTGAAGTGGTTAAACCATCTAGATGA
TCCAATTGAACTATAACTCCAATCGATTCAACCTTAGCCTTACATTGCAAAA
Found at i:31854898 original size:33 final size:33
Alignment explanation
Indices: 31854854--31854919 Score: 123
Period size: 33 Copynumber: 2.0 Consensus size: 33
31854844 TTTCTTCTTG
31854854 ACATTCCAGCTCCTGTCCAGCAACCAAACACTC
1 ACATTCCAGCTCCTGTCCAGCAACCAAACACTC
*
31854887 ACATTCTAGCTCCTGTCCAGCAACCAAACACTC
1 ACATTCCAGCTCCTGTCCAGCAACCAAACACTC
31854920 CCACTCAGTC
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.30, C:0.41, G:0.09, T:0.20
Consensus pattern (33 bp):
ACATTCCAGCTCCTGTCCAGCAACCAAACACTC
Found at i:31859121 original size:12 final size:12
Alignment explanation
Indices: 31859104--31859128 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
31859094 TCCTGAAGTG
31859104 ACAAATAAATAA
1 ACAAATAAATAA
31859116 ACAAATAAATAA
1 ACAAATAAATAA
31859128 A
1 A
31859129 AGAGACTTGG
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:0.76, C:0.08, G:0.00, T:0.16
Consensus pattern (12 bp):
ACAAATAAATAA
Found at i:31860411 original size:14 final size:14
Alignment explanation
Indices: 31860392--31860419 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
31860382 CTAAACTAGT
31860392 AAAAAATAGTCAAA
1 AAAAAATAGTCAAA
31860406 AAAAAATAGTCAAA
1 AAAAAATAGTCAAA
31860420 CTTTTAATTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.71, C:0.07, G:0.07, T:0.14
Consensus pattern (14 bp):
AAAAAATAGTCAAA
Found at i:31863558 original size:12 final size:12
Alignment explanation
Indices: 31863541--31863580 Score: 52
Period size: 12 Copynumber: 3.7 Consensus size: 12
31863531 CCACTGTTTT
31863541 CCTGTTTTGGAA
1 CCTGTTTTGGAA
31863553 CCTGTTTT----
1 CCTGTTTTGGAA
31863561 CCTGTTTTGGAA
1 CCTGTTTTGGAA
31863573 CCTGTTTT
1 CCTGTTTT
31863581 TCCTATCTCC
Statistics
Matches: 24, Mismatches: 0, Indels: 8
0.75 0.00 0.25
Matches are distributed among these distances:
8 8 0.33
12 16 0.67
ACGTcount: A:0.10, C:0.20, G:0.20, T:0.50
Consensus pattern (12 bp):
CCTGTTTTGGAA
Found at i:31863584 original size:21 final size:20
Alignment explanation
Indices: 31863534--31863580 Score: 94
Period size: 20 Copynumber: 2.4 Consensus size: 20
31863524 CCTACAGCCA
31863534 CTGTTTTCCTGTTTTGGAAC
1 CTGTTTTCCTGTTTTGGAAC
31863554 CTGTTTTCCTGTTTTGGAAC
1 CTGTTTTCCTGTTTTGGAAC
31863574 CTGTTTT
1 CTGTTTT
31863581 TCCTATCTCC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.09, C:0.19, G:0.19, T:0.53
Consensus pattern (20 bp):
CTGTTTTCCTGTTTTGGAAC
Found at i:31876489 original size:135 final size:133
Alignment explanation
Indices: 31876314--31876564 Score: 346
Period size: 135 Copynumber: 1.9 Consensus size: 133
31876304 TGTAATTATA
* *
31876314 TAATGGAAATATTTTTTATATATATTATTATATTAAATATATTTTATCTTTTAAAAACAT-AATT
1 TAATGAAAATATATTTTATATATATTATTATATTAAATATATTTTAT-TTTTAAAAACATCAA--
* * * * *
31876378 TTTATTTTTTTATATTTTTCTTTATATATAATTTTTTATGTAAAATATTT-TTTTTCACTTACAT
63 ATAACTTTTTTATATTTTT-TATATATA-AATTTTATATGTAAAATATTTATTTTTCACTTACAT
31876442 TGCGGAAG
126 TGCGGAAG
* *
31876450 TAATGAAAATATATTTT-TATATGTTATTATGTTAAATATATTTTATTTTTAAAAACATCAAATA
1 TAATGAAAATATATTTTATATATATTATTATATTAAATATATTTTATTTTTAAAAACATCAAATA
*
31876514 ACTTTTTTATATTTTTTATATATAAATTTTATGTGTAAAATATTTATTTTT
66 ACTTTTTTATATTTTTTATATATAAATTTTATATGTAAAATATTTATTTTT
31876565 TCATATACAT
Statistics
Matches: 103, Mismatches: 10, Indels: 8
0.85 0.08 0.07
Matches are distributed among these distances:
131 19 0.18
132 12 0.12
133 16 0.16
134 12 0.12
135 29 0.28
136 15 0.15
ACGTcount: A:0.36, C:0.04, G:0.05, T:0.55
Consensus pattern (133 bp):
TAATGAAAATATATTTTATATATATTATTATATTAAATATATTTTATTTTTAAAAACATCAAATA
ACTTTTTTATATTTTTTATATATAAATTTTATATGTAAAATATTTATTTTTCACTTACATTGCGG
AAG
Found at i:31882373 original size:19 final size:19
Alignment explanation
Indices: 31882349--31882389 Score: 82
Period size: 19 Copynumber: 2.2 Consensus size: 19
31882339 TATTTTAAAG
31882349 TTATTTAGGTAGATAAATC
1 TTATTTAGGTAGATAAATC
31882368 TTATTTAGGTAGATAAATC
1 TTATTTAGGTAGATAAATC
31882387 TTA
1 TTA
31882390 GAATAAATCA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.37, C:0.05, G:0.15, T:0.44
Consensus pattern (19 bp):
TTATTTAGGTAGATAAATC
Found at i:31882917 original size:18 final size:17
Alignment explanation
Indices: 31882892--31882944 Score: 52
Period size: 20 Copynumber: 2.9 Consensus size: 17
31882882 TTGAATCTTA
31882892 AAATGGTATCGATACAT
1 AAATGGTATCGATACAT
*
31882909 AAATAGGTATCTATACCAT
1 AAAT-GGTATCGATA-CAT
*
31882928 ATAACCGGTATCGATAC
1 A-AA-TGGTATCGATAC
31882945 CAGTGAATTA
Statistics
Matches: 29, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
17 4 0.14
18 9 0.31
19 5 0.17
20 11 0.38
ACGTcount: A:0.40, C:0.17, G:0.15, T:0.28
Consensus pattern (17 bp):
AAATGGTATCGATACAT
Found at i:31883115 original size:22 final size:22
Alignment explanation
Indices: 31883088--31883131 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
31883078 CTTTCATAAG
31883088 CTCGATTAAAGCTCAGTTTCAA
1 CTCGATTAAAGCTCAGTTTCAA
*
31883110 CTCGATTAAAGCTTAGTTTCAA
1 CTCGATTAAAGCTCAGTTTCAA
31883132 TTATATATCA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.32, C:0.20, G:0.14, T:0.34
Consensus pattern (22 bp):
CTCGATTAAAGCTCAGTTTCAA
Found at i:31883432 original size:48 final size:46
Alignment explanation
Indices: 31883361--31883484 Score: 180
Period size: 45 Copynumber: 2.7 Consensus size: 46
31883351 TATTATAAAA
*
31883361 TCAAATAATTATTTCAAATATCATAATTATTTTTACATGTGAAATATT
1 TCAAATAATTATTTCAAATATC--AATTATTTTTACATGTAAAATATT
* *
31883409 TCAAAAAATTATTTCAAATATC-ATTATTTTTATATGTAAAATATT
1 TCAAATAATTATTTCAAATATCAATTATTTTTACATGTAAAATATT
*
31883454 TCAAATAATTAATTCAAATATCAA-TATTTTT
1 TCAAATAATTATTTCAAATATCAATTATTTTT
31883485 TCACCTGCAT
Statistics
Matches: 70, Mismatches: 5, Indels: 5
0.88 0.06 0.06
Matches are distributed among these distances:
45 48 0.69
46 1 0.01
48 21 0.30
ACGTcount: A:0.44, C:0.08, G:0.02, T:0.46
Consensus pattern (46 bp):
TCAAATAATTATTTCAAATATCAATTATTTTTACATGTAAAATATT
Found at i:31883717 original size:70 final size:67
Alignment explanation
Indices: 31883630--31883762 Score: 162
Period size: 68 Copynumber: 1.9 Consensus size: 67
31883620 TATATTTACT
* *
31883630 AAAAATAATTATATTTGAAATAGTTAATTGATTT-TATATATTAG-ATTTACCATACCCACAATG
1 AAAAATAATGATATTTGAAATAATT-ATT--TTTATA-ATATTAGAATTTACCATACCCACAATG
31883693 TAGGTA
62 TAGGTA
* * *
31883699 AAAAGATAATGATATTTGAGATAATTATTTTTATAATATTAGAATTTACGATACTCACAATGTA
1 AAAA-ATAATGATATTTGAAATAATTATTTTTATAATATTAGAATTTACCATACCCACAATGTA
31883763 CATGAAGAAA
Statistics
Matches: 56, Mismatches: 5, Indels: 7
0.82 0.07 0.10
Matches are distributed among these distances:
67 10 0.18
68 21 0.38
69 7 0.12
70 18 0.32
ACGTcount: A:0.43, C:0.08, G:0.11, T:0.39
Consensus pattern (67 bp):
AAAAATAATGATATTTGAAATAATTATTTTTATAATATTAGAATTTACCATACCCACAATGTAGG
TA
Done.