Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr02 ID=Chr02-JGI_221_v2.0
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: 62769430
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1067035 characters in sequence are not A, C, G, or T
File 107 of 206
Found at i:31688492 original size:9 final size:9
Alignment explanation
Indices: 31688478--31688504 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
31688468 ACACATATTT
31688478 TTCGGTTAA
1 TTCGGTTAA
31688487 TTCGGTTAA
1 TTCGGTTAA
31688496 TTCGGTTAA
1 TTCGGTTAA
31688505 CTACCTTATT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 18 1.00
ACGTcount: A:0.22, C:0.11, G:0.22, T:0.44
Consensus pattern (9 bp):
TTCGGTTAA
Found at i:31693056 original size:21 final size:21
Alignment explanation
Indices: 31692903--31693059 Score: 138
Period size: 21 Copynumber: 7.5 Consensus size: 21
31692893 AAGCCTGAAG
* *
31692903 GCTGAACAG-AGCACATAAGT
1 GCTGAACAGAAGCTCATAAGA
* * * * *
31692923 GCTAAACAAAAACCCATAAGG
1 GCTGAACAGAAGCTCATAAGA
* *
31692944 GTTGAACGGAAGCTCATAAGA
1 GCTGAACAGAAGCTCATAAGA
*
31692965 GCTAAAC-GAAAGCTCATAAGA
1 GCTGAACAG-AAGCTCATAAGA
*
31692986 GCTGAACGGAAGCTCATAAGA
1 GCTGAACAGAAGCTCATAAGA
* * *
31693007 GCTGAACAGAAACCCATAAGG
1 GCTGAACAGAAGCTCATAAGA
* * *
31693028 GTTAAACAGAAGCTCGTAAGA
1 GCTGAACAGAAGCTCATAAGA
31693049 GCTGAACAGAA
1 GCTGAACAGAA
31693060 ACCCATCAGG
Statistics
Matches: 107, Mismatches: 27, Indels: 5
0.77 0.19 0.04
Matches are distributed among these distances:
20 8 0.07
21 98 0.92
22 1 0.01
ACGTcount: A:0.43, C:0.19, G:0.24, T:0.14
Consensus pattern (21 bp):
GCTGAACAGAAGCTCATAAGA
Found at i:31693073 original size:42 final size:42
Alignment explanation
Indices: 31692907--31693125 Score: 212
Period size: 42 Copynumber: 5.2 Consensus size: 42
31692897 CTGAAGGCTG
* * * * *
31692907 AACAG-AGCACATAAGTGCTAAACAAAAACCCATAAGGGTTG
1 AACAGAAGCTCATAAGAGCTGAACAGAAACCCATAAGGGTTA
* * * * * *
31692948 AACGGAAGCTCATAAGAGCTAAAC-GAAAGCTCATAAGAGCTG
1 AACAGAAGCTCATAAGAGCTGAACAGAAA-CCCATAAGGGTTA
*
31692990 AACGGAAGCTCATAAGAGCTGAACAGAAACCCATAAGGGTTA
1 AACAGAAGCTCATAAGAGCTGAACAGAAACCCATAAGGGTTA
* *
31693032 AACAGAAGCTCGTAAGAGCTGAACAGAAACCCATCAGGGTTA
1 AACAGAAGCTCATAAGAGCTGAACAGAAACCCATAAGGGTTA
* ** * *
31693074 AATAGAAGCTCA-ATAGAGCTGAA-AGAAAACTAATATGAGTTA
1 AACAGAAGCTCATA-AGAGCTGAACAG-AAACCCATAAGGGTTA
31693116 AACAGAAGCT
1 AACAGAAGCT
31693126 TGTGAGAGCT
Statistics
Matches: 150, Mismatches: 23, Indels: 9
0.82 0.13 0.05
Matches are distributed among these distances:
41 10 0.07
42 136 0.91
43 4 0.03
ACGTcount: A:0.45, C:0.18, G:0.22, T:0.16
Consensus pattern (42 bp):
AACAGAAGCTCATAAGAGCTGAACAGAAACCCATAAGGGTTA
Found at i:31693134 original size:42 final size:41
Alignment explanation
Indices: 31693004--31693144 Score: 101
Period size: 42 Copynumber: 3.4 Consensus size: 41
31692994 GAAGCTCATA
* * * *
31693004 AGAGCTGAACAG-AAACCCATAAGGGTTAAACAGAAGCTCGT
1 AGAGCTGAA-AGAAAACCAATCAGAGTTAAACAGAAGCTAGT
* * * *
31693045 AAGAGCTGAACAG-AAACCCATCAGGGTTAAATAGAAGCTCAAT
1 -AGAGCTGAA-AGAAAACCAATCAGAGTTAAACAGAAGCT-AGT
* *
31693088 AGAGCTGAAAGAAAACTAAT-ATGAGTTAAACAGAAGCTTGT
1 AGAGCTGAAAGAAAACCAATCA-GAGTTAAACAGAAGCTAGT
31693129 GAGAGCT-AAACGAAAA
1 -AGAGCTGAAA-GAAAA
31693145 GTAAACATGA
Statistics
Matches: 84, Mismatches: 10, Indels: 10
0.81 0.10 0.10
Matches are distributed among these distances:
41 7 0.08
42 76 0.90
43 1 0.01
ACGTcount: A:0.45, C:0.16, G:0.23, T:0.16
Consensus pattern (41 bp):
AGAGCTGAAAGAAAACCAATCAGAGTTAAACAGAAGCTAGT
Found at i:31695274 original size:24 final size:25
Alignment explanation
Indices: 31695220--31695276 Score: 73
Period size: 24 Copynumber: 2.4 Consensus size: 25
31695210 ATAAATTATT
* *
31695220 AATATTAATTACTTAGAAATATTTA
1 AATATTAATTACTTACAAATATTAA
*
31695245 AA-ATTAATTACTT-CATATATTAA
1 AATATTAATTACTTACAAATATTAA
31695268 AATATTAAT
1 AATATTAAT
31695277 AATAAGTTAT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
23 9 0.32
24 17 0.61
25 2 0.07
ACGTcount: A:0.49, C:0.05, G:0.02, T:0.44
Consensus pattern (25 bp):
AATATTAATTACTTACAAATATTAA
Found at i:31700317 original size:41 final size:41
Alignment explanation
Indices: 31700251--31700342 Score: 112
Period size: 41 Copynumber: 2.2 Consensus size: 41
31700241 CTTACCTTTT
* * *
31700251 GGGGCTTTAGCGGCGATTTCAAAAAAGTGCCGCTAATGCTC
1 GGGGCTTTAACGGCGATTTCAAAAAAGCGCCGCTAATACTC
* ** *
31700292 GGGGCTTTAACGGCGTTTTTGAAAAAGCGCCGCTAATACTG
1 GGGGCTTTAACGGCGATTTCAAAAAAGCGCCGCTAATACTC
*
31700333 GGGGATTTAA
1 GGGGCTTTAA
31700343 AAGCGCCGCT
Statistics
Matches: 43, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
41 43 1.00
ACGTcount: A:0.25, C:0.18, G:0.30, T:0.26
Consensus pattern (41 bp):
GGGGCTTTAACGGCGATTTCAAAAAAGCGCCGCTAATACTC
Found at i:31700776 original size:14 final size:14
Alignment explanation
Indices: 31700757--31700790 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
31700747 GGTTATGGGT
* *
31700757 TTAGGGGTTAGACG
1 TTAGGGGTTAAAAG
31700771 TTAGGGGTTAAAAG
1 TTAGGGGTTAAAAG
31700785 TTAGGG
1 TTAGGG
31700791 ATTTAAGGTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.26, C:0.03, G:0.41, T:0.29
Consensus pattern (14 bp):
TTAGGGGTTAAAAG
Found at i:31700914 original size:18 final size:18
Alignment explanation
Indices: 31700893--31700929 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
31700883 TGTAAAAGAG
31700893 ATAATAATAAATTTGTTA
1 ATAATAATAAATTTGTTA
31700911 ATAATAATAAATTTGTTA
1 ATAATAATAAATTTGTTA
31700929 A
1 A
31700930 GGGTTTTTGG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.51, C:0.00, G:0.05, T:0.43
Consensus pattern (18 bp):
ATAATAATAAATTTGTTA
Found at i:31701014 original size:15 final size:14
Alignment explanation
Indices: 31700996--31701044 Score: 71
Period size: 14 Copynumber: 3.4 Consensus size: 14
31700986 CATATTTTAA
*
31700996 GGTTTAGGGAGTAT
1 GGTTTAGGGATTAT
31701010 GGGTTTAGGGATTAT
1 -GGTTTAGGGATTAT
*
31701025 GGATTAGGGATTAT
1 GGTTTAGGGATTAT
31701039 GGTTTA
1 GGTTTA
31701045 ATAGTTGAGA
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
14 18 0.58
15 13 0.42
ACGTcount: A:0.22, C:0.00, G:0.39, T:0.39
Consensus pattern (14 bp):
GGTTTAGGGATTAT
Found at i:31701308 original size:14 final size:15
Alignment explanation
Indices: 31701282--31701315 Score: 61
Period size: 14 Copynumber: 2.3 Consensus size: 15
31701272 GTTTAAGGAG
31701282 TATGGATTTAGGGAT
1 TATGGATTTAGGGAT
31701297 TATGGA-TTAGGGAT
1 TATGGATTTAGGGAT
31701311 TATGG
1 TATGG
31701316 TTCAAGGGTT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 13 0.68
15 6 0.32
ACGTcount: A:0.26, C:0.00, G:0.35, T:0.38
Consensus pattern (15 bp):
TATGGATTTAGGGAT
Found at i:31701363 original size:14 final size:14
Alignment explanation
Indices: 31701346--31701378 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
31701336 GTTTAGGGGC
31701346 TAGGGGTT-AGACGT
1 TAGGGGTTAAGA-GT
31701360 TAGGGGTTAAGAGT
1 TAGGGGTTAAGAGT
31701374 TAGGG
1 TAGGG
31701379 ATTTAAAGTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 15 0.83
15 3 0.17
ACGTcount: A:0.24, C:0.03, G:0.45, T:0.27
Consensus pattern (14 bp):
TAGGGGTTAAGAGT
Found at i:31705654 original size:43 final size:43
Alignment explanation
Indices: 31705594--31705684 Score: 121
Period size: 43 Copynumber: 2.1 Consensus size: 43
31705584 CTTTGAGTTC
* * * *
31705594 ATTA-CAAGATTTCCTTGATTAAGTAAGTGTATTATATCTTTT
1 ATTACCAAGATTTACTTGATTAAGAAAATGCATTATATCTTTT
* *
31705636 ATTACCAAGATTTACTTGATTAAGAAAATGCATTGTATTTTTT
1 ATTACCAAGATTTACTTGATTAAGAAAATGCATTATATCTTTT
31705679 ATTACC
1 ATTACC
31705685 TTGCAATGTG
Statistics
Matches: 42, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
42 4 0.10
43 38 0.90
ACGTcount: A:0.33, C:0.11, G:0.11, T:0.45
Consensus pattern (43 bp):
ATTACCAAGATTTACTTGATTAAGAAAATGCATTATATCTTTT
Found at i:31706132 original size:43 final size:43
Alignment explanation
Indices: 31706085--31706337 Score: 305
Period size: 43 Copynumber: 5.9 Consensus size: 43
31706075 TAAATGCCAC
*
31706085 GATCTTTAGCGGCGTTTGTGATAAAAGCACCGCTAAAGGTCAA
1 GATCTTTAGCGGCGTTTGTGATAAAAGCGCCGCTAAAGGTCAA
* * *
31706128 GATCTTTAGCGGCGTTTGTGATAAAAGTGCTGCGAAAGGTCAAA
1 GATCTTTAGCGGCGTTTGTGATAAAAGCGCCGCTAAAGGTC-AA
*
31706172 GATATTTAGCGGCGTTTGTGATAAAAGCGCCGCTAAAGGTCATA
1 GATCTTTAGCGGCGTTTGTGATAAAAGCGCCGCTAAAGGTCA-A
* * * *
31706216 -ATCTTTAGCGGTGTTCGTGAGAAAAGCGCCGCTAAAGGTCAT
1 GATCTTTAGCGGCGTTTGTGATAAAAGCGCCGCTAAAGGTCAA
* * * ** * *
31706258 GTTCTTTAGCAGCGTTCGTGGGAAAAGCACCGCTAAAGGTCAT
1 GATCTTTAGCGGCGTTTGTGATAAAAGCGCCGCTAAAGGTCAA
*
31706301 GTTCTTTAGCGGCGTTT-TCGA-AAAAGCGCCGCTAAAG
1 GATCTTTAGCGGCGTTTGT-GATAAAAGCGCCGCTAAAG
31706338 ATCATATTCT
Statistics
Matches: 184, Mismatches: 22, Indels: 9
0.86 0.10 0.04
Matches are distributed among these distances:
42 16 0.09
43 128 0.70
44 40 0.22
ACGTcount: A:0.28, C:0.18, G:0.28, T:0.26
Consensus pattern (43 bp):
GATCTTTAGCGGCGTTTGTGATAAAAGCGCCGCTAAAGGTCAA
Found at i:31706188 original size:87 final size:86
Alignment explanation
Indices: 31706089--31706337 Score: 297
Period size: 87 Copynumber: 2.9 Consensus size: 86
31706079 TGCCACGATC
*
31706089 TTTAGCGGCGTTTGTGATAAAAGCACCGCTAAAGGTCAAGATCTTTAGCGGCGTTTGTGATAAAA
1 TTTAGCGGCGTTTGTGATAAAAGCACCGCTAAAGGTCAAGATCTTTAGCGGCGTTTGTGAGAAAA
* *
31706154 GTGCTGCGAAAGGTCAAAGATA
66 GCGCCGCGAAAGGTC-AAGATA
* * *
31706176 TTTAGCGGCGTTTGTGATAAAAGCGCCGCTAAAGGTCATA-ATCTTTAGCGGTGTTCGTGAGAAA
1 TTTAGCGGCGTTTGTGATAAAAGCACCGCTAAAGGTCA-AGATCTTTAGCGGCGTTTGTGAGAAA
* * * *
31706240 AGCGCCGCTAAAGGTCATGTTC
65 AGCGCCGCGAAAGGTCAAGATA
* * ** * *
31706262 TTTAGCAGCGTTCGTGGGAAAAGCACCGCTAAAGGTCATGTTCTTTAGCGGCGTTT-TCGA-AAA
1 TTTAGCGGCGTTTGTGATAAAAGCACCGCTAAAGGTCAAGATCTTTAGCGGCGTTTGT-GAGAAA
*
31706325 AGCGCCGCTAAAG
65 AGCGCCGCGAAAG
31706338 ATCATATTCT
Statistics
Matches: 140, Mismatches: 19, Indels: 8
0.84 0.11 0.05
Matches are distributed among these distances:
85 17 0.12
86 51 0.36
87 71 0.51
88 1 0.01
ACGTcount: A:0.28, C:0.18, G:0.28, T:0.27
Consensus pattern (86 bp):
TTTAGCGGCGTTTGTGATAAAAGCACCGCTAAAGGTCAAGATCTTTAGCGGCGTTTGTGAGAAAA
GCGCCGCGAAAGGTCAAGATA
Found at i:31706284 original size:130 final size:128
Alignment explanation
Indices: 31706086--31706358 Score: 323
Period size: 130 Copynumber: 2.1 Consensus size: 128
31706076 AAATGCCACG
* * * * *
31706086 ATCTTTAGCGGCGTTTGTGATAAAAGCACCGCTAAAGGTCAAGATCTTTAGCGGCGTTTGTGATA
1 ATCTTTAGCGGCGTTCGTGAGAAAAGCACCGCTAAAGGTCAAGATCTTTAGCAGCGTTCGTGAGA
** * *
31706151 AAAGTGCTGCGAAAGGTCAAAGATATTTAGCGGCGTTTGT-GATAAAAGCGCCGCTAAAGGTCAT
66 AAAGCACCGCGAAAGGTC-AAGATATTTAGCGGCGTTT-TCGA-AAAAGCGCCGCTAAAGATCAT
31706215 A
128 A
* * * * *
31706216 ATCTTTAGCGGTGTTCGTGAGAAAAGCGCCGCTAAAGGTCATGTTCTTTAGCAGCGTTCGTGGGA
1 ATCTTTAGCGGCGTTCGTGAGAAAAGCACCGCTAAAGGTCAAGATCTTTAGCAGCGTTCGTGAGA
* * * *
31706281 AAAGCACCGCTAAAGGTCATGTTCTTTAGCGGCGTTTTCGAAAAAGCGCCGCTAAAGATCATA
66 AAAGCACCGCGAAAGGTCAAGATATTTAGCGGCGTTTTCGAAAAAGCGCCGCTAAAGATCATA
* * *
31706344 TTCTATAGTGGCGTT
1 ATCTTTAGCGGCGTT
31706359 TTTTCACATA
Statistics
Matches: 120, Mismatches: 22, Indels: 4
0.82 0.15 0.03
Matches are distributed among these distances:
128 33 0.28
129 18 0.15
130 69 0.57
ACGTcount: A:0.27, C:0.18, G:0.27, T:0.28
Consensus pattern (128 bp):
ATCTTTAGCGGCGTTCGTGAGAAAAGCACCGCTAAAGGTCAAGATCTTTAGCAGCGTTCGTGAGA
AAAGCACCGCGAAAGGTCAAGATATTTAGCGGCGTTTTCGAAAAAGCGCCGCTAAAGATCATA
Found at i:31718972 original size:16 final size:15
Alignment explanation
Indices: 31718947--31718976 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
31718937 GTACGATGTA
31718947 TCCCCCCATTATGCC
1 TCCCCCCATTATGCC
31718962 TCCCACCCATTATGC
1 TCCC-CCCATTATGC
31718977 ATCTTCTCCA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 4 0.29
16 10 0.71
ACGTcount: A:0.17, C:0.50, G:0.07, T:0.27
Consensus pattern (15 bp):
TCCCCCCATTATGCC
Found at i:31723369 original size:20 final size:20
Alignment explanation
Indices: 31723335--31723402 Score: 84
Period size: 21 Copynumber: 3.3 Consensus size: 20
31723325 AACTTTACCT
31723335 CTAAAAAATATTATAAAAAAA
1 CTAAAAAATA-TATAAAAAAA
* *
31723356 CTAAAAAAGATAT-AATAAA
1 CTAAAAAATATATAAAAAAA
31723375 CTTAAAAAATATATAAAAAAA
1 C-TAAAAAATATATAAAAAAA
31723396 CTCAAAA
1 CT-AAAA
31723403 CCTTACAAAA
Statistics
Matches: 40, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
19 6 0.15
20 15 0.38
21 19 0.47
ACGTcount: A:0.69, C:0.07, G:0.01, T:0.22
Consensus pattern (20 bp):
CTAAAAAATATATAAAAAAA
Found at i:31723375 original size:19 final size:20
Alignment explanation
Indices: 31723353--31723390 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
31723343 TATTATAAAA
31723353 AAAC-TAAAAAAGATATAAT
1 AAACTTAAAAAAGATATAAT
*
31723372 AAACTTAAAAAATATATAA
1 AAACTTAAAAAAGATATAA
31723391 AAAAACTCAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 4 0.24
20 13 0.76
ACGTcount: A:0.68, C:0.05, G:0.03, T:0.24
Consensus pattern (20 bp):
AAACTTAAAAAAGATATAAT
Found at i:31723386 original size:18 final size:18
Alignment explanation
Indices: 31723353--31723391 Score: 53
Period size: 19 Copynumber: 2.2 Consensus size: 18
31723343 TATTATAAAA
31723353 AAACTAAAAAAGATATAAT
1 AAACTAAAAAAGATAT-AT
*
31723372 AAACTTAAAAA-ATATAT
1 AAACTAAAAAAGATATAT
31723389 AAA
1 AAA
31723392 AAAACTCAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 5 0.26
18 4 0.21
19 10 0.53
ACGTcount: A:0.69, C:0.05, G:0.03, T:0.23
Consensus pattern (18 bp):
AAACTAAAAAAGATATAT
Found at i:31724064 original size:10 final size:9
Alignment explanation
Indices: 31723991--31724169 Score: 87
Period size: 9 Copynumber: 18.8 Consensus size: 9
31723981 GATTTAAGCC
31723991 TAAAAATTA
1 TAAAAATTA
31724000 TTAAAATATTTA
1 -TAAAA-A-TTA
31724012 TAAAAATT-
1 TAAAAATTA
*
31724020 TAGAAAATCA
1 TA-AAAATTA
*
31724030 TAAAAAATA
1 TAAAAATTA
* *
31724039 TATAATTTA
1 TAAAAATTA
31724048 TTAAAATATTA
1 -TAAAA-ATTA
*
31724059 T-AAAATGA
1 TAAAAATTA
*
31724067 TTAAATATTA
1 -TAAAAATTA
31724077 TAAAAATT-
1 TAAAAATTA
*
31724085 TAGAAATTA
1 TAAAAATTA
31724094 TAAAAAAGCATT-
1 T--AAAA--ATTA
*
31724106 TAAAAATTT
1 TAAAAATTA
*
31724115 TAAACAGTTA
1 TAAA-AATTA
*
31724125 TTGAAAATTA
1 -TAAAAATTA
31724135 TATAAAATTA
1 TA-AAAATTA
* *
31724145 TTAAAATGA
1 TAAAAATTA
*
31724154 TAAAAAATA
1 TAAAAATTA
31724163 TAAAAAT
1 TAAAAAT
31724170 GATTATAATA
Statistics
Matches: 127, Mismatches: 25, Indels: 35
0.68 0.13 0.19
Matches are distributed among these distances:
8 15 0.12
9 53 0.42
10 37 0.29
11 15 0.12
12 4 0.03
13 3 0.02
ACGTcount: A:0.59, C:0.02, G:0.04, T:0.36
Consensus pattern (9 bp):
TAAAAATTA
Found at i:31724168 original size:18 final size:19
Alignment explanation
Indices: 31724128--31724177 Score: 57
Period size: 18 Copynumber: 2.6 Consensus size: 19
31724118 ACAGTTATTG
* * *
31724128 AAAATTATATAAAATTATT
1 AAAATGATATAAAAATATA
31724147 AAAATGATA-AAAAATATA
1 AAAATGATATAAAAATATA
31724165 AAAATGATTATAA
1 AAAATGA-TATAA
31724178 TATTAGTAAC
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
18 14 0.54
19 10 0.38
20 2 0.08
ACGTcount: A:0.64, C:0.00, G:0.04, T:0.32
Consensus pattern (19 bp):
AAAATGATATAAAAATATA
Found at i:31737915 original size:81 final size:81
Alignment explanation
Indices: 31737814--31738084 Score: 271
Period size: 81 Copynumber: 3.3 Consensus size: 81
31737804 TCCTTGGCGA
* * ** *
31737814 CAGTTTT-CAAAGCTTGTTCACTATCTTTCTTTACTGGTTCAACTTCTTGTGATGGTGGCTTTGC
1 CAGTTTTGC-AAGCTTCTTCACTATCTTTCTTTAATGGTGGAACTTCTTGTGAAGGTGGCTTTGC
*
31737878 TTCAGAATCTTCTATTT
65 TTCAGAATCTTCGATTT
* * * *
31737895 CAGTTTTGCAAGCTTCTTCACTATCTTTCTTCAATGGTGGAACTTCTTGTGAAGCTGGGTTGGCT
1 CAGTTTTGCAAGCTTCTTCACTATCTTTCTTTAATGGTGGAACTTCTTGTGAAGGTGGCTTTGCT
*
31737960 TCAGGAA-CTTCGACTT
66 TCA-GAATCTTCGATTT
* * * * *
31737976 CATTTTTGGAAGCTTCTTCACTCTCTTTCTTTAAAGGTGGGGAC-TCTTGTGACA-GTGGCTTTG
1 CAGTTTTGCAAGCTTCTTCACTATCTTTCTTTAATGGT-GGAACTTCTTGTGA-AGGTGGCTTTG
** * *
31738039 CTTTGGAATTTTCGGTTT
64 CTTCAGAATCTTCGATTT
***
31738057 CAGTTTTTTTAGCTTCTTCACTATCTTT
1 CAGTTTTGCAAGCTTCTTCACTATCTTT
31738085 GCTTGATGGA
Statistics
Matches: 155, Mismatches: 30, Indels: 10
0.79 0.15 0.05
Matches are distributed among these distances:
80 3 0.02
81 143 0.92
82 9 0.06
ACGTcount: A:0.17, C:0.20, G:0.19, T:0.45
Consensus pattern (81 bp):
CAGTTTTGCAAGCTTCTTCACTATCTTTCTTTAATGGTGGAACTTCTTGTGAAGGTGGCTTTGCT
TCAGAATCTTCGATTT
Found at i:31739900 original size:18 final size:18
Alignment explanation
Indices: 31739845--31739950 Score: 86
Period size: 18 Copynumber: 5.9 Consensus size: 18
31739835 CTACATCACC
* * *
31739845 TGCAGGTGGCTCTGTACT
1 TGCAGGTGGATCCGTAGT
* * * *
31739863 TGTAGGCGGATCAGTTGT
1 TGCAGGTGGATCCGTAGT
*
31739881 TGTAGGTGGATCCGTAGT
1 TGCAGGTGGATCCGTAGT
*
31739899 TGCAGGTGGATCCATAGT
1 TGCAGGTGGATCCGTAGT
* * *
31739917 TGCAGGTGCATCTGTACT
1 TGCAGGTGGATCCGTAGT
* *
31739935 TGCAGGAGGACCCGTA
1 TGCAGGTGGATCCGTA
31739951 CTTGGCGATG
Statistics
Matches: 69, Mismatches: 19, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
18 69 1.00
ACGTcount: A:0.18, C:0.18, G:0.35, T:0.29
Consensus pattern (18 bp):
TGCAGGTGGATCCGTAGT
Found at i:31742652 original size:64 final size:64
Alignment explanation
Indices: 31742546--31742678 Score: 248
Period size: 64 Copynumber: 2.1 Consensus size: 64
31742536 ATCGAACCCT
* *
31742546 ACTTGAGAGATGCGAGATTTTTGAACGTGGCCCTTATGGGTGAGGGGTGTAAATTGAACCCCAC
1 ACTTGAGAGATGCGAGATTTTTGAACGTGGCCCTTATAGGTGAGGGGTGTAAATTGAACCACAC
31742610 ACTTGAGAGATGCGAGATTTTTGAACGTGGCCCTTATAGGTGAGGGGTGTAAATTGAACCACAC
1 ACTTGAGAGATGCGAGATTTTTGAACGTGGCCCTTATAGGTGAGGGGTGTAAATTGAACCACAC
31742674 ACTTG
1 ACTTG
31742679 TAAGCGCGTT
Statistics
Matches: 67, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
64 67 1.00
ACGTcount: A:0.26, C:0.17, G:0.30, T:0.27
Consensus pattern (64 bp):
ACTTGAGAGATGCGAGATTTTTGAACGTGGCCCTTATAGGTGAGGGGTGTAAATTGAACCACAC
Found at i:31743463 original size:24 final size:24
Alignment explanation
Indices: 31743436--31743482 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
31743426 TTTTTTAAAT
*
31743436 TTGAATTATATAA-TATTAGTATAG
1 TTGAATTATA-AATTAATAGTATAG
*
31743460 TTGACTTATAAATTAATAGTATA
1 TTGAATTATAAATTAATAGTATA
31743483 TATAACTAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 2 0.10
24 18 0.90
ACGTcount: A:0.43, C:0.02, G:0.11, T:0.45
Consensus pattern (24 bp):
TTGAATTATAAATTAATAGTATAG
Found at i:31744838 original size:18 final size:18
Alignment explanation
Indices: 31744815--31744851 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
31744805 TAAAAGTTCG
*
31744815 AAAATAATGCATTGAAAA
1 AAAATAATGCACTGAAAA
31744833 AAAATAATGCACTGAAAA
1 AAAATAATGCACTGAAAA
31744851 A
1 A
31744852 TCTAATTGAC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.62, C:0.08, G:0.11, T:0.19
Consensus pattern (18 bp):
AAAATAATGCACTGAAAA
Found at i:31745115 original size:23 final size:22
Alignment explanation
Indices: 31745076--31745129 Score: 72
Period size: 23 Copynumber: 2.4 Consensus size: 22
31745066 CTCAAAAAAG
* *
31745076 TATAAAAAAAAACTAAAGAGTA
1 TATAAAAAAAAACTAAAAAATA
*
31745098 TATAAAAATAAACTTAAAAAATA
1 TATAAAAAAAAAC-TAAAAAATA
31745121 TATAAAAAA
1 TATAAAAAA
31745130 CCCTTTTACA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
22 12 0.44
23 15 0.56
ACGTcount: A:0.70, C:0.04, G:0.04, T:0.22
Consensus pattern (22 bp):
TATAAAAAAAAACTAAAAAATA
Found at i:31747697 original size:16 final size:16
Alignment explanation
Indices: 31747664--31747708 Score: 54
Period size: 16 Copynumber: 2.8 Consensus size: 16
31747654 GGGATCACTA
**
31747664 ACTAATATTAATCTAAT
1 ACTAATA-TAATAGAAT
31747681 ACTAATATAATAGAAT
1 ACTAATATAATAGAAT
*
31747697 ACTAATCTAATA
1 ACTAATATAATA
31747709 CCAATAGAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
16 18 0.72
17 7 0.28
ACGTcount: A:0.51, C:0.11, G:0.02, T:0.36
Consensus pattern (16 bp):
ACTAATATAATAGAAT
Found at i:31747697 original size:27 final size:27
Alignment explanation
Indices: 31747667--31747731 Score: 85
Period size: 27 Copynumber: 2.3 Consensus size: 27
31747657 ATCACTAACT
* * *
31747667 AATATTAATCTAATACTAATATAATAG
1 AATACTAATCTAATACCAATAGAATAG
31747694 AATACTAATCTAATACCAATAGAATAG
1 AATACTAATCTAATACCAATAGAATAG
31747721 AAAATACTAAT
1 --AATACTAAT
31747732 AGAATAGAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
27 24 0.73
29 9 0.27
ACGTcount: A:0.54, C:0.11, G:0.05, T:0.31
Consensus pattern (27 bp):
AATACTAATCTAATACCAATAGAATAG
Found at i:31747732 original size:18 final size:18
Alignment explanation
Indices: 31747705--31747741 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
31747695 ATACTAATCT
31747705 AATACCAATAGAATAGAA
1 AATACCAATAGAATAGAA
*
31747723 AATACTAATAGAATAGAA
1 AATACCAATAGAATAGAA
31747741 A
1 A
31747742 GAAAGAACTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.62, C:0.08, G:0.11, T:0.19
Consensus pattern (18 bp):
AATACCAATAGAATAGAA
Found at i:31753779 original size:25 final size:25
Alignment explanation
Indices: 31753731--31753779 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 25
31753721 TCAATTTATT
* *
31753731 TCATAAACAATAAATATCCCTTAAC
1 TCATAAACAATAAATAGCCATTAAC
* *
31753756 TCATAATCACTAAATAGCCATTAA
1 TCATAAACAATAAATAGCCATTAA
31753780 TATGACTCAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.47, C:0.22, G:0.02, T:0.29
Consensus pattern (25 bp):
TCATAAACAATAAATAGCCATTAAC
Found at i:31754946 original size:22 final size:22
Alignment explanation
Indices: 31754921--31754963 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
31754911 TATATATTAA
31754921 CTTTTAGTTGAATCTTTTCTTC
1 CTTTTAGTTGAATCTTTTCTTC
* **
31754943 CTTTTATTTTTATCTTTTCTT
1 CTTTTAGTTGAATCTTTTCTT
31754964 ATTTTAATAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.12, C:0.16, G:0.05, T:0.67
Consensus pattern (22 bp):
CTTTTAGTTGAATCTTTTCTTC
Found at i:31755040 original size:25 final size:24
Alignment explanation
Indices: 31754998--31755059 Score: 61
Period size: 24 Copynumber: 2.5 Consensus size: 24
31754988 ATTAAAATTT
* *
31754998 TCTAAAAATGATAATTAATTAATTTCA
1 TCTAAAAAT--TATTTAATGAA-TTCA
*
31755025 TTTAAAAATTATTTAATGAATTCA
1 TCTAAAAATTATTTAATGAATTCA
*
31755049 TCTCAAAATTA
1 TCTAAAAATTA
31755060 ATATATAATT
Statistics
Matches: 30, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
24 13 0.43
25 9 0.30
27 8 0.27
ACGTcount: A:0.47, C:0.08, G:0.03, T:0.42
Consensus pattern (24 bp):
TCTAAAAATTATTTAATGAATTCA
Found at i:31755668 original size:20 final size:18
Alignment explanation
Indices: 31755621--31755668 Score: 51
Period size: 21 Copynumber: 2.5 Consensus size: 18
31755611 TCATTTTTCG
*
31755621 ATAAAAATACATCAAATT
1 ATAAAAATACATAAAATT
*
31755639 TTATAAAATACATATAAAATT
1 ATA-AAAATAC--ATAAAATT
31755660 ATAAAAATA
1 ATAAAAATA
31755669 TTTATAAATA
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
18 2 0.08
19 7 0.29
20 6 0.25
21 9 0.38
ACGTcount: A:0.62, C:0.06, G:0.00, T:0.31
Consensus pattern (18 bp):
ATAAAAATACATAAAATT
Found at i:31756404 original size:7 final size:7
Alignment explanation
Indices: 31756392--31756422 Score: 62
Period size: 7 Copynumber: 4.4 Consensus size: 7
31756382 TTTAAAATTT
31756392 TTTTAAA
1 TTTTAAA
31756399 TTTTAAA
1 TTTTAAA
31756406 TTTTAAA
1 TTTTAAA
31756413 TTTTAAA
1 TTTTAAA
31756420 TTT
1 TTT
31756423 AATTTTTTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (7 bp):
TTTTAAA
Found at i:31757982 original size:13 final size:13
Alignment explanation
Indices: 31757964--31758006 Score: 56
Period size: 13 Copynumber: 3.5 Consensus size: 13
31757954 TAGATTTTTC
31757964 CTAAATATTATCA
1 CTAAATATTATCA
*
31757977 CTAAATA--AT-T
1 CTAAATATTATCA
31757987 CTAAATATTATCA
1 CTAAATATTATCA
31758000 CTAAATA
1 CTAAATA
31758007 ATTCAAAATT
Statistics
Matches: 25, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
10 7 0.28
11 2 0.08
12 2 0.08
13 14 0.56
ACGTcount: A:0.49, C:0.14, G:0.00, T:0.37
Consensus pattern (13 bp):
CTAAATATTATCA
Found at i:31757994 original size:23 final size:23
Alignment explanation
Indices: 31757964--31758015 Score: 95
Period size: 23 Copynumber: 2.3 Consensus size: 23
31757954 TAGATTTTTC
31757964 CTAAATATTATCACTAAATAATT
1 CTAAATATTATCACTAAATAATT
31757987 CTAAATATTATCACTAAATAATT
1 CTAAATATTATCACTAAATAATT
*
31758010 CAAAAT
1 CTAAAT
31758016 TTAAAAATCA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.50, C:0.13, G:0.00, T:0.37
Consensus pattern (23 bp):
CTAAATATTATCACTAAATAATT
Found at i:31762462 original size:17 final size:17
Alignment explanation
Indices: 31762442--31762476 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
31762432 ACAAATTCAA
31762442 AAATGCAAAAATAAAAT
1 AAATGCAAAAATAAAAT
* *
31762459 AAATGGATAAATAAAAT
1 AAATGCAAAAATAAAAT
31762476 A
1 A
31762477 TTTTTTAAGC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.69, C:0.03, G:0.09, T:0.20
Consensus pattern (17 bp):
AAATGCAAAAATAAAAT
Found at i:31763322 original size:13 final size:13
Alignment explanation
Indices: 31763304--31763346 Score: 56
Period size: 13 Copynumber: 3.5 Consensus size: 13
31763294 TAGGATTTTC
31763304 CTAAATATTATCA
1 CTAAATATTATCA
*
31763317 CTAAATA--AT-T
1 CTAAATATTATCA
31763327 CTAAATATTATCA
1 CTAAATATTATCA
31763340 CTAAATA
1 CTAAATA
31763347 ATTCAAAATT
Statistics
Matches: 25, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
10 7 0.28
11 2 0.08
12 2 0.08
13 14 0.56
ACGTcount: A:0.49, C:0.14, G:0.00, T:0.37
Consensus pattern (13 bp):
CTAAATATTATCA
Found at i:31763334 original size:23 final size:23
Alignment explanation
Indices: 31763304--31763355 Score: 95
Period size: 23 Copynumber: 2.3 Consensus size: 23
31763294 TAGGATTTTC
31763304 CTAAATATTATCACTAAATAATT
1 CTAAATATTATCACTAAATAATT
31763327 CTAAATATTATCACTAAATAATT
1 CTAAATATTATCACTAAATAATT
*
31763350 CAAAAT
1 CTAAAT
31763356 TTAGAAATCA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.50, C:0.13, G:0.00, T:0.37
Consensus pattern (23 bp):
CTAAATATTATCACTAAATAATT
Found at i:31765130 original size:23 final size:25
Alignment explanation
Indices: 31765077--31765131 Score: 60
Period size: 25 Copynumber: 2.2 Consensus size: 25
31765067 ATCTTCAGAA
*
31765077 AAAATAATAACACGTAGAAATAATT
1 AAAATAATAACACATAGAAATAATT
* *
31765102 AGAAATAA-AACACATGGAAA-ATTT
1 A-AAATAATAACACATAGAAATAATT
31765126 AAAATA
1 AAAATA
31765132 CTATTATTTA
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
23 5 0.19
24 4 0.15
25 11 0.42
26 6 0.23
ACGTcount: A:0.62, C:0.07, G:0.09, T:0.22
Consensus pattern (25 bp):
AAAATAATAACACATAGAAATAATT
Found at i:31765362 original size:15 final size:15
Alignment explanation
Indices: 31765342--31765373 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
31765332 TATTTTAAGG
31765342 TTTAGGGAGTATGGA
1 TTTAGGGAGTATGGA
*
31765357 TTTAGGGATTATGGA
1 TTTAGGGAGTATGGA
31765372 TT
1 TT
31765374 AAGGATTATG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.25, C:0.00, G:0.34, T:0.41
Consensus pattern (15 bp):
TTTAGGGAGTATGGA
Found at i:31765381 original size:14 final size:15
Alignment explanation
Indices: 31765351--31765388 Score: 53
Period size: 14 Copynumber: 2.7 Consensus size: 15
31765341 GTTTAGGGAG
*
31765351 TATGGATTTAGGGAT
1 TATGGATTTAAGGAT
31765366 TATGGA-TTAAGGAT
1 TATGGATTTAAGGAT
31765380 TATGG-TTTA
1 TATGGATTTA
31765389 TGGGTTGGGA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
14 15 0.71
15 6 0.29
ACGTcount: A:0.29, C:0.00, G:0.29, T:0.42
Consensus pattern (15 bp):
TATGGATTTAAGGAT
Found at i:31765407 original size:21 final size:20
Alignment explanation
Indices: 31765335--31765409 Score: 53
Period size: 21 Copynumber: 3.5 Consensus size: 20
31765325 GAGCTACTAT
*
31765335 TTTAAGGTTTAGGGAGTATGGA
1 TTTAAGGTTTATGG-GT-TGGA
* * *
31765357 TTTAGGGATTATGGATTAAGGA
1 TTTAAGGTTTATGGGTT--GGA
*
31765379 -TTATGGTTTATGGGTTGGGA
1 TTTAAGGTTTATGGGTT-GGA
31765399 TTTAAGGTTTA
1 TTTAAGGTTTA
31765410 GTGGTTAGGA
Statistics
Matches: 41, Mismatches: 9, Indels: 7
0.72 0.16 0.12
Matches are distributed among these distances:
20 4 0.10
21 23 0.56
22 14 0.34
ACGTcount: A:0.25, C:0.00, G:0.33, T:0.41
Consensus pattern (20 bp):
TTTAAGGTTTATGGGTTGGA
Found at i:31765430 original size:22 final size:21
Alignment explanation
Indices: 31765404--31765455 Score: 59
Period size: 22 Copynumber: 2.4 Consensus size: 21
31765394 TGGGATTTAA
*
31765404 GGTTTAGTGGTTAGGAATTAGG
1 GGTTTAG-GGTTAAGAATTAGG
*
31765426 GGTTTAAGGGTTAAGAGTTAGG
1 GGTTT-AGGGTTAAGAATTAGG
*
31765448 GATTTAGG
1 GGTTTAGG
31765456 ATTTAAGGAT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
21 3 0.12
22 21 0.81
23 2 0.08
ACGTcount: A:0.25, C:0.00, G:0.40, T:0.35
Consensus pattern (21 bp):
GGTTTAGGGTTAAGAATTAGG
Found at i:31765707 original size:14 final size:15
Alignment explanation
Indices: 31765680--31765718 Score: 64
Period size: 14 Copynumber: 2.7 Consensus size: 15
31765670 TGGGGATTAT
31765680 TTATGGATTTAGGGA
1 TTATGGATTTAGGGA
31765695 TTATGGA-TTAGGGA
1 TTATGGATTTAGGGA
31765709 TTATGG-TTTA
1 TTATGGATTTA
31765719 AGGGTTAGGA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
14 16 0.70
15 7 0.30
ACGTcount: A:0.26, C:0.00, G:0.31, T:0.44
Consensus pattern (15 bp):
TTATGGATTTAGGGA
Found at i:31765727 original size:21 final size:21
Alignment explanation
Indices: 31765709--31765753 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
31765699 GGATTAGGGA
*
31765709 TTATGGTTTAAGGGTTAGGAG
1 TTATGGGTTAAGGGTTAGGAG
* *
31765730 TTATGGGTTAGGGGTTAAGAG
1 TTATGGGTTAAGGGTTAGGAG
31765751 TTA
1 TTA
31765754 GAGATTTAGG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.24, C:0.00, G:0.38, T:0.38
Consensus pattern (21 bp):
TTATGGGTTAAGGGTTAGGAG
Found at i:31765753 original size:14 final size:14
Alignment explanation
Indices: 31765716--31765754 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
31765706 GGATTATGGT
31765716 TTAAGGGTTAGGAG
1 TTAAGGGTTAGGAG
* *
31765730 TTATGGGTTAGGGG
1 TTAAGGGTTAGGAG
*
31765744 TTAAGAGTTAG
1 TTAAGGGTTAG
31765755 AGATTTAGGG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.26, C:0.00, G:0.41, T:0.33
Consensus pattern (14 bp):
TTAAGGGTTAGGAG
Found at i:31765899 original size:25 final size:24
Alignment explanation
Indices: 31765863--31765912 Score: 57
Period size: 25 Copynumber: 2.0 Consensus size: 24
31765853 ATAATAATAA
*
31765863 ATTTAATATATTGC-ATACATAAAT
1 ATTTAATATATT-CAATACAAAAAT
*
31765887 ATTTATATTTATTCAATACAAAAAT
1 ATTTA-ATATATTCAATACAAAAAT
31765912 A
1 A
31765913 GATTGATGGA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
24 6 0.27
25 16 0.73
ACGTcount: A:0.48, C:0.08, G:0.02, T:0.42
Consensus pattern (24 bp):
ATTTAATATATTCAATACAAAAAT
Found at i:31766458 original size:73 final size:73
Alignment explanation
Indices: 31766334--31766488 Score: 172
Period size: 73 Copynumber: 2.1 Consensus size: 73
31766324 TTCTTTGCTT
*
31766334 TTAGTGGCGCTTTACATAAACGCCGCAAAAATGTATTAGGAGTTAAGGAAAC-TGTGCCGTTTT-
1 TTAGTGGCGCTTTACATAAACGCCGCAAAAATGTATTAAGAGTTAAGGAAACGT-TGCCGTTTTG
31766397 CC-ATTGTTA
65 CCTA-TGTTA
* * * * * * **
31766406 TTAGTGGCGCTTTCCTTAAAATGCCGCAAAAATGTTTTAATATTTATTGAAACGTTGCCGTTTTG
1 TTAGTGGCGCTTTACAT-AAACGCCGCAAAAATGTATTAAGAGTTAAGGAAACGTTGCCGTTTTG
*
31766471 TCTATGTTA
65 CCTATGTTA
31766480 TTAGTGGCG
1 TTAGTGGCG
31766489 TTTTTTCAAA
Statistics
Matches: 69, Mismatches: 10, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
72 15 0.22
73 37 0.54
74 16 0.23
75 1 0.01
ACGTcount: A:0.26, C:0.15, G:0.21, T:0.37
Consensus pattern (73 bp):
TTAGTGGCGCTTTACATAAACGCCGCAAAAATGTATTAAGAGTTAAGGAAACGTTGCCGTTTTGC
CTATGTTA
Found at i:31768407 original size:23 final size:21
Alignment explanation
Indices: 31768375--31768416 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 21
31768365 TATTTTAACC
31768375 CTATTTATAAAATCTAAAAACT
1 CTATTTAT-AAATCTAAAAACT
*
31768397 CTATTATATAAATCTGAAAA
1 CTATT-TATAAATCTAAAAA
31768417 TGCTTCTCCC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 15 0.83
23 3 0.17
ACGTcount: A:0.50, C:0.12, G:0.02, T:0.36
Consensus pattern (21 bp):
CTATTTATAAATCTAAAAACT
Found at i:31770543 original size:43 final size:42
Alignment explanation
Indices: 31770495--31770719 Score: 227
Period size: 43 Copynumber: 5.3 Consensus size: 42
31770485 ATGGCACTTT
* *
31770495 TAGCGGCATTTGTGATAAAAGCGCCGCTAAAAGTCATGATCTA
1 TAGCGGCGTTTGTGA-AAAAGCGCCGCTAAAGGTCATGATCTA
* * * * *
31770538 TAGCGGCGTTTGGGCAAAAAGTGCTGCTAAAGGT-TTGGAGCTA
1 TAGCGGCGTTTGTG-AAAAAGCGCCGCTAAAGGTCAT-GATCTA
* * * *
31770581 TAACGGCGTTTGTGTAAAAGCGCCACTAAAGGTCCTGATCTA
1 TAGCGGCGTTTGTGAAAAAGCGCCGCTAAAGGTCATGATCTA
* * ** *
31770623 TAGCAGCGTTTGTAGAAAAAACGTAGCTAAAGGTCCTGATCTA
1 TAGCGGCGTTTGT-GAAAAAGCGCCGCTAAAGGTCATGATCTA
* * *
31770666 TAGCGACGTTTGTGGGAAAAGCGCCGCTAAAGGTCATGACCTA
1 TAGCGGCGTTTGT-GAAAAAGCGCCGCTAAAGGTCATGATCTA
31770709 TAGCGGCGTTT
1 TAGCGGCGTTT
31770720 ATTTCTAAAA
Statistics
Matches: 146, Mismatches: 32, Indels: 8
0.78 0.17 0.04
Matches are distributed among these distances:
42 32 0.22
43 113 0.77
44 1 0.01
ACGTcount: A:0.29, C:0.18, G:0.28, T:0.25
Consensus pattern (42 bp):
TAGCGGCGTTTGTGAAAAAGCGCCGCTAAAGGTCATGATCTA
Found at i:31770652 original size:85 final size:84
Alignment explanation
Indices: 31770498--31770719 Score: 250
Period size: 85 Copynumber: 2.6 Consensus size: 84
31770488 GCACTTTTAG
* * * * *
31770498 CGGCATTTGTGATAAAAGCGCCGCTAAAAGTCATGATCTATAGCGGCGTTTGGGCAAAAAGTGCT
1 CGGCGTTTGTG-TAAAAGCGCCGCTAAAGGTCATGATCTATAGCGGCGTTTGAGAAAAAAGT-CA
*
31770563 GCTAAAGGT-TTGGAGCTATAA
64 GCTAAAGGTCCT-GAGCTATAA
* * *
31770584 CGGCGTTTGTGTAAAAGCGCCACTAAAGGTCCTGATCTATAGCAGCGTTTGTAGAAAAAACGT-A
1 CGGCGTTTGTGTAAAAGCGCCGCTAAAGGTCATGATCTATAGCGGCGTTTG-AGAAAAAA-GTCA
* *
31770648 GCTAAAGGTCCTGATCTATAG
64 GCTAAAGGTCCTGAGCTATAA
* * *
31770669 CGACGTTTGTGGGAAAAGCGCCGCTAAAGGTCATGACCTATAGCGGCGTTT
1 CGGCGTTTGT-GTAAAAGCGCCGCTAAAGGTCATGATCTATAGCGGCGTTT
31770720 ATTTCTAAAA
Statistics
Matches: 115, Mismatches: 17, Indels: 8
0.82 0.12 0.06
Matches are distributed among these distances:
85 61 0.53
86 52 0.45
87 2 0.02
ACGTcount: A:0.29, C:0.18, G:0.27, T:0.25
Consensus pattern (84 bp):
CGGCGTTTGTGTAAAAGCGCCGCTAAAGGTCATGATCTATAGCGGCGTTTGAGAAAAAAGTCAGC
TAAAGGTCCTGAGCTATAA
Found at i:31771958 original size:144 final size:144
Alignment explanation
Indices: 31771698--31772072 Score: 705
Period size: 144 Copynumber: 2.6 Consensus size: 144
31771688 AAGAGACTTG
31771698 TATAGGTTTATGTACAAAAAATTGAGAGCACTTAATCTGTTCAAGTGATGAACAATATTTGTGTG
1 TATAGGTTTATGTACAAAAAATTGAGAGCACTTAATCTGTTCAAGTGATGAACAATATTTGTGTG
31771763 AGTGCATTTGATTGTAAAACCTTTTTGTTGTGGTTTTACAAGCTAAGTTTTCAGGGGAGAAGAGT
66 AGTGCATTTGATTGTAAAACCTTTTTGTTGTGGTTTTACAAGCTAAGTTTTCAGGGGAGAAGAGT
31771828 TTTTCGATACTTAT
131 TTTTCGATACTTAT
* * *
31771842 TATAGGTTTATGTACTAAGAATTGAGAGCACTTAATCTGTTCAAGTGATGAACAATATTTATGTG
1 TATAGGTTTATGTACAAAAAATTGAGAGCACTTAATCTGTTCAAGTGATGAACAATATTTGTGTG
31771907 AGTGCATTTGATTGTAAAACCTTTTTGTTGTGGTTTTACAAGCTAAGTTTTCAGGGGAGAAGAGT
66 AGTGCATTTGATTGTAAAACCTTTTTGTTGTGGTTTTACAAGCTAAGTTTTCAGGGGAGAAGAGT
31771972 TTTTCGATACTTAT
131 TTTTCGATACTTAT
* *
31771986 TATAGGTTTATGTACCAAAAATTGAGAGCACTTAATCTGTTCAAGTGAGGAACAATATTTGTGTG
1 TATAGGTTTATGTACAAAAAATTGAGAGCACTTAATCTGTTCAAGTGATGAACAATATTTGTGTG
31772051 AGTGCATTTGATTGTAAAACCT
66 AGTGCATTTGATTGTAAAACCT
31772073 ATGTAGTTTT
Statistics
Matches: 224, Mismatches: 7, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
144 224 1.00
ACGTcount: A:0.30, C:0.10, G:0.21, T:0.38
Consensus pattern (144 bp):
TATAGGTTTATGTACAAAAAATTGAGAGCACTTAATCTGTTCAAGTGATGAACAATATTTGTGTG
AGTGCATTTGATTGTAAAACCTTTTTGTTGTGGTTTTACAAGCTAAGTTTTCAGGGGAGAAGAGT
TTTTCGATACTTAT
Found at i:31773540 original size:27 final size:27
Alignment explanation
Indices: 31773510--31773621 Score: 170
Period size: 27 Copynumber: 4.1 Consensus size: 27
31773500 CATCATAGAA
* * *
31773510 AGTCTGATGAGACATTAAATATGGGAT
1 AGTCTGATGGGACATTAAACACGGGAT
*
31773537 AGTCTGATGGGACATTAAACACAGGAT
1 AGTCTGATGGGACATTAAACACGGGAT
*
31773564 AGTCTAATGGGACATTAAACACGGGAT
1 AGTCTGATGGGACATTAAACACGGGAT
*
31773591 AGTCTGATGGGACATCAAACACGGGAT
1 AGTCTGATGGGACATTAAACACGGGAT
31773618 AGTC
1 AGTC
31773622 CATTACGACA
Statistics
Matches: 77, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
27 77 1.00
ACGTcount: A:0.36, C:0.14, G:0.27, T:0.23
Consensus pattern (27 bp):
AGTCTGATGGGACATTAAACACGGGAT
Found at i:31773579 original size:54 final size:54
Alignment explanation
Indices: 31773510--31773638 Score: 170
Period size: 54 Copynumber: 2.4 Consensus size: 54
31773500 CATCATAGAA
* * * *
31773510 AGTCTGATGAGACATTAAATATGGGATAGTCTGATGGGACATTAAACACAGGAT
1 AGTCTAATGAGACATTAAACACGGGATAGTCTGATGGGACATCAAACACAGGAT
* *
31773564 AGTCTAATGGGACATTAAACACGGGATAGTCTGATGGGACATCAAACACGGGAT
1 AGTCTAATGAGACATTAAACACGGGATAGTCTGATGGGACATCAAACACAGGAT
* *
31773618 AGTC-CATTACGACATTAAACA
1 AGTCTAATGA-GACATTAAACA
31773639 TGGGGATCCC
Statistics
Matches: 65, Mismatches: 9, Indels: 2
0.86 0.12 0.03
Matches are distributed among these distances:
53 2 0.03
54 63 0.97
ACGTcount: A:0.37, C:0.16, G:0.24, T:0.23
Consensus pattern (54 bp):
AGTCTAATGAGACATTAAACACGGGATAGTCTGATGGGACATCAAACACAGGAT
Found at i:31773631 original size:27 final size:26
Alignment explanation
Indices: 31773520--31773638 Score: 121
Period size: 27 Copynumber: 4.4 Consensus size: 26
31773510 AGTCTGATGA
* * *
31773520 GACATTAAATATGGGATAGTCTGATGG
1 GACATTAAACACGGGATAGTC-CATGG
* *
31773547 GACATTAAACACAGGATAGTCTAATGG
1 GACATTAAACACGGGATAGTC-CATGG
*
31773574 GACATTAAACACGGGATAGTCTGATGG
1 GACATTAAACACGGGATAGTC-CATGG
* **
31773601 GACATCAAACACGGGATAGTCCATTAC
1 GACATTAAACACGGGATAGTCCA-TGG
31773628 GACATTAAACA
1 GACATTAAACA
31773639 TGGGGATCCC
Statistics
Matches: 80, Mismatches: 11, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
26 1 0.01
27 79 0.99
ACGTcount: A:0.38, C:0.16, G:0.24, T:0.23
Consensus pattern (26 bp):
GACATTAAACACGGGATAGTCCATGG
Found at i:31782186 original size:17 final size:17
Alignment explanation
Indices: 31782172--31782209 Score: 60
Period size: 16 Copynumber: 2.3 Consensus size: 17
31782162 TTTATTTTTT
31782172 AATTAAAAATATTTTAA
1 AATTAAAAATATTTTAA
*
31782189 AATT-AAAATTTTTTAA
1 AATTAAAAATATTTTAA
31782205 AATTA
1 AATTA
31782210 TATAAATCTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 15 0.79
17 4 0.21
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (17 bp):
AATTAAAAATATTTTAA
Found at i:31785118 original size:25 final size:25
Alignment explanation
Indices: 31785090--31785146 Score: 114
Period size: 25 Copynumber: 2.3 Consensus size: 25
31785080 TCATTAGGGT
31785090 TACCGATTTATAGCTCATGAGAGCA
1 TACCGATTTATAGCTCATGAGAGCA
31785115 TACCGATTTATAGCTCATGAGAGCA
1 TACCGATTTATAGCTCATGAGAGCA
31785140 TACCGAT
1 TACCGAT
31785147 CTTCAGCTAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 32 1.00
ACGTcount: A:0.32, C:0.21, G:0.19, T:0.28
Consensus pattern (25 bp):
TACCGATTTATAGCTCATGAGAGCA
Found at i:31785154 original size:25 final size:25
Alignment explanation
Indices: 31785090--31785179 Score: 103
Period size: 25 Copynumber: 3.6 Consensus size: 25
31785080 TCATTAGGGT
*
31785090 TACCGATTTATAGCTCATGAGAGCA
1 TACCGATTTACAGCTCATGAGAGCA
*
31785115 TACCGATTTATAGCTCATGAGAGCA
1 TACCGATTTACAGCTCATGAGAGCA
**
31785140 TACCGATCTT-CAGCT-AAAATGAGCA
1 TACCGAT-TTACAGCTCATGA-GAGCA
*
31785165 TACCGATTCACAGCT
1 TACCGATTTACAGCT
31785180 TGTATGAGCA
Statistics
Matches: 58, Mismatches: 4, Indels: 6
0.85 0.06 0.09
Matches are distributed among these distances:
24 3 0.05
25 53 0.91
26 2 0.03
ACGTcount: A:0.32, C:0.23, G:0.18, T:0.27
Consensus pattern (25 bp):
TACCGATTTACAGCTCATGAGAGCA
Found at i:31785889 original size:27 final size:28
Alignment explanation
Indices: 31785858--31785917 Score: 77
Period size: 28 Copynumber: 2.2 Consensus size: 28
31785848 CTATTTAGTG
*
31785858 ACAGTA-CAATGAGGGCCTTAGCCCAAT
1 ACAGTAGCAATGAGGGCCTTAACCCAAT
* * *
31785885 TCAGTAGCACTGTGGGCCTTAACCCAAT
1 ACAGTAGCAATGAGGGCCTTAACCCAAT
31785913 ACAGT
1 ACAGT
31785918 GTCATTATAG
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
27 5 0.19
28 22 0.81
ACGTcount: A:0.30, C:0.27, G:0.22, T:0.22
Consensus pattern (28 bp):
ACAGTAGCAATGAGGGCCTTAACCCAAT
Found at i:31786302 original size:27 final size:27
Alignment explanation
Indices: 31786270--31786519 Score: 353
Period size: 27 Copynumber: 9.3 Consensus size: 27
31786260 TATAAAGATC
*
31786270 ATTTTACCCTTAG-GGGATATTTCGATA
1 ATTTTACCCTTCGAGGG-TATTTCGATA
* *
31786297 ATTTTACCCTTTGAGGGTATTTCGGTA
1 ATTTTACCCTTCGAGGGTATTTCGATA
*
31786324 ATTTTACCCTTTGAGGGTATTTCGATA
1 ATTTTACCCTTCGAGGGTATTTCGATA
31786351 ATTTTACCCTTCGAGGGTATTTCGATA
1 ATTTTACCCTTCGAGGGTATTTCGATA
* * *
31786378 ATTTAACCCTTCGAGCGTATTT-TAGTA
1 ATTTTACCCTTCGAGGGTATTTCGA-TA
31786405 ATTTTACCCTTCGAGGGTATTTCGATA
1 ATTTTACCCTTCGAGGGTATTTCGATA
* * *
31786432 AATTCACCCTTCGAGGGTATTTCGGTA
1 ATTTTACCCTTCGAGGGTATTTCGATA
31786459 ATTTTACCCTTCGAGGGTATTTC-AGTA
1 ATTTTACCCTTCGAGGGTATTTCGA-TA
*
31786486 ATTTTACCCTTCAAGGGTATTTCGATA
1 ATTTTACCCTTCGAGGGTATTTCGATA
31786513 ATTTTAC
1 ATTTTAC
31786520 TCATGAATCG
Statistics
Matches: 201, Mismatches: 17, Indels: 10
0.88 0.07 0.04
Matches are distributed among these distances:
26 1 0.00
27 195 0.97
28 5 0.02
ACGTcount: A:0.23, C:0.18, G:0.18, T:0.41
Consensus pattern (27 bp):
ATTTTACCCTTCGAGGGTATTTCGATA
Found at i:31790383 original size:18 final size:18
Alignment explanation
Indices: 31790360--31790395 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
31790350 TAAGTTCGTA
31790360 AATATTTTTATTTAATAT
1 AATATTTTTATTTAATAT
31790378 AATATTTTTATTTAATAT
1 AATATTTTTATTTAATAT
31790396 TTACGAGTCA
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:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (18 bp):
AATATTTTTATTTAATAT
Found at i:31791709 original size:25 final size:25
Alignment explanation
Indices: 31791681--31791738 Score: 71
Period size: 25 Copynumber: 2.3 Consensus size: 25
31791671 CAGCTCTCTT
* **
31791681 GAGCTTCTCGATATTTGGCTCACAA
1 GAGCTTCCCGATATACGGCTCACAA
*
31791706 GAGCTTCCCGATATACGGCTCACAT
1 GAGCTTCCCGATATACGGCTCACAA
*
31791731 GGGCTTCC
1 GAGCTTCC
31791739 AATTCTATGG
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
25 28 1.00
ACGTcount: A:0.21, C:0.29, G:0.22, T:0.28
Consensus pattern (25 bp):
GAGCTTCCCGATATACGGCTCACAA
Found at i:31797933 original size:25 final size:25
Alignment explanation
Indices: 31797905--31797961 Score: 87
Period size: 25 Copynumber: 2.3 Consensus size: 25
31797895 TCATTAGGGT
31797905 TACCGATTAATAGCTCATGAGAGCA
1 TACCGATTAATAGCTCATGAGAGCA
* * *
31797930 TACCAATTTATAGCTCGTGAGAGCA
1 TACCGATTAATAGCTCATGAGAGCA
31797955 TACCGAT
1 TACCGAT
31797962 CTTCTAATCA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 28 1.00
ACGTcount: A:0.33, C:0.21, G:0.19, T:0.26
Consensus pattern (25 bp):
TACCGATTAATAGCTCATGAGAGCA
Found at i:31803660 original size:25 final size:25
Alignment explanation
Indices: 31803632--31803688 Score: 87
Period size: 25 Copynumber: 2.2 Consensus size: 25
31803622 TTTGTGCTGG
31803632 TGTTATCTATCAGGCCTTGAGCCGA
1 TGTTATCTATCAGGCCTTGAGCCGA
* *
31803657 TGTTTTCTATTAGGCCTTGAGCCGA
1 TGTTATCTATCAGGCCTTGAGCCGA
31803682 TGATTAT
1 TG-TTAT
31803689 TTAGTAGGTA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
25 25 0.89
26 3 0.11
ACGTcount: A:0.19, C:0.19, G:0.23, T:0.39
Consensus pattern (25 bp):
TGTTATCTATCAGGCCTTGAGCCGA
Found at i:31813539 original size:101 final size:101
Alignment explanation
Indices: 31813418--31813602 Score: 293
Period size: 101 Copynumber: 1.8 Consensus size: 101
31813408 AAAGTGATGG
***
31813418 TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTATCGGAAT-G-ATGGTTTGTATGTGTAGT
1 TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTATCGG-ATGGAATGG-TCACATGTGTAGT
*
31813481 ACTATGTGCAGGCTACTATGCGTACCGAATAGCTTCGA
64 ACTATATGCAGGCTACTATGCGTACCGAATAGCTTCGA
31813519 TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTATCGGATGGAAATGGTCACATGTGTAGTA
1 TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTATCGGATGG-AATGGTCACATGTGTAGTA
31813584 CTATATGCAGGCTACTATG
65 CTATATGCAGGCTACTATG
31813603 TGAACCGGGT
Statistics
Matches: 77, Mismatches: 4, Indels: 5
0.90 0.05 0.06
Matches are distributed among these distances:
100 2 0.03
101 42 0.55
102 29 0.38
103 4 0.05
ACGTcount: A:0.24, C:0.17, G:0.28, T:0.32
Consensus pattern (101 bp):
TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTATCGGATGGAATGGTCACATGTGTAGTAC
TATATGCAGGCTACTATGCGTACCGAATAGCTTCGA
Found at i:31813549 original size:51 final size:49
Alignment explanation
Indices: 31813417--31813609 Score: 176
Period size: 51 Copynumber: 3.8 Consensus size: 49
31813407 GAAAGTGATG
* *
31813417 GTCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTATCGGAATGATGGTTT
1 GTCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTA-CCGAAT-A--GATT
* * *
31813470 GT-A--TGTGTAGTACTATGTGCAGGCTACTATGCGTACCGAATAGCTT
1 GTCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCGAATAGATT
* * * *
31813516 CGATCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTATCGGATGGAAATG
1 -G-TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCGAAT--AGATT
* * * *
31813569 GTCACATGTGTAGTACTATATGCAGGCTACTATGTGAACCG
1 GTCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCG
31813610 GGTACCATTG
Statistics
Matches: 117, Mismatches: 16, Indels: 16
0.79 0.11 0.11
Matches are distributed among these distances:
46 3 0.03
47 1 0.01
48 2 0.02
49 6 0.05
50 30 0.26
51 69 0.59
52 2 0.02
53 4 0.03
ACGTcount: A:0.24, C:0.17, G:0.28, T:0.31
Consensus pattern (49 bp):
GTCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCGAATAGATT
Found at i:31819733 original size:50 final size:49
Alignment explanation
Indices: 31819674--31819805 Score: 158
Period size: 50 Copynumber: 2.7 Consensus size: 49
31819664 CATTGAGATT
* *
31819674 ATGAGAGGTCTCATGTAAGACCATGTCTGGGACATGGC-GGTTGCACCGAG
1 ATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCAGG--GAACCGAG
** *
31819724 ATGAGAGGTCCCCCGTAAGACCATGTCTGGGACATGGCATGGGAACCGAT
1 ATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCA-GGGAACCGAG
** *
31819774 ATGAGAACTCCCATGTAAGACCATATCTGGGA
1 ATGAGAGGTCCCATGTAAGACCATGTCTGGGA
31819806 TATGTTATTG
Statistics
Matches: 70, Mismatches: 10, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
50 68 0.97
52 2 0.03
ACGTcount: A:0.27, C:0.22, G:0.30, T:0.20
Consensus pattern (49 bp):
ATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCAGGGAACCGAG
Found at i:31825317 original size:15 final size:14
Alignment explanation
Indices: 31825290--31825333 Score: 54
Period size: 15 Copynumber: 3.1 Consensus size: 14
31825280 TTTTAGTGAA
31825290 TATTA-TTTTTATT
1 TATTATTTTTTATT
*
31825303 TTTTATTTTTATATT
1 TATTATTTTT-TATT
*
31825318 CATTATTTTTTATT
1 TATTATTTTTTATT
31825332 TA
1 TA
31825334 AGATTTATTT
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
13 4 0.16
14 9 0.36
15 12 0.48
ACGTcount: A:0.23, C:0.02, G:0.00, T:0.75
Consensus pattern (14 bp):
TATTATTTTTTATT
Found at i:31825345 original size:22 final size:22
Alignment explanation
Indices: 31825297--31825357 Score: 61
Period size: 22 Copynumber: 2.7 Consensus size: 22
31825287 GAATATTATT
* *
31825297 TTTATTTTTTATTTTTATATTCA
1 TTTATTTTTTA-TTTAAGATTCA
*
31825320 -TTATTTTTTATTTAAGATTTA
1 TTTATTTTTTATTTAAGATTCA
*
31825341 TTTATTAATTTATTTAA
1 TTTATT-TTTTATTTAA
31825358 CTATTTTGTT
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
21 8 0.25
22 15 0.47
23 9 0.28
ACGTcount: A:0.28, C:0.02, G:0.02, T:0.69
Consensus pattern (22 bp):
TTTATTTTTTATTTAAGATTCA
Found at i:31837905 original size:89 final size:89
Alignment explanation
Indices: 31837761--31838182 Score: 261
Period size: 89 Copynumber: 4.8 Consensus size: 89
31837751 TCGAAGAAAG
* * * * * * *
31837761 CAAGTCTTATCCCCCTTGAAGTTGCAGTGGGGCAGAGTGAAGATGACGAATCTTATTTCCCTGAA
1 CAAGTCTTAACTCCC-TGAAGTTGCAGTGGAGCAGACTGAAGATGACAAACCTTATCTCCCTGAA
*
31837826 GTTGTAGTGGAACAGATTAAAGCCA-A
65 GTTGCAGTGGAACAGATTAAAG--ATA
* * *
31837852 TAA-TCTTAACTCCCTGAAGTTGCAGTGGAGTAGACTGAGGATAGA-AAACCTTATCTCCCTGAA
1 CAAGTCTTAACTCCCTGAAGTTGCAGTGGAGCAGACTGAAGAT-GACAAACCTTATCTCCCTGAA
* * *
31837915 GTTGCAGTGGAGCAGGTTGAAGATA
65 GTTGCAGTGGAACAGATTAAAGATA
* * * ** *
31837940 CAAGTCTTATCTCCCTGAAGTTGCAGTGGAGCATA-TTAA-ACCACAAACCTTATCTCTCTGAAG
1 CAAGTCTTAACTCCCTGAAGTTGCAGTGGAGCAGACTGAAGATGACAAACCTTATCTCCCTGAAG
* * * * *
31838003 TTGCAATAGAGCAGGTTGAAATAATA
66 TTGCAGTGGAACAGATT-AAA-GATA
* * * * ** * ** *
31838029 -AA-CCTTATC-CTCCTGAAGTTGCAGTGGGGTAGGTTGAGGATG-CAAGTCTTATCTCCCTGAC
1 CAAGTCTTAACTC-CCTGAAGTTGCAGTGGAGCAGACTGAAGATGACAAACCTTATCTCCCTGAA
*** * * * *
31838090 GTTGCAGTGGGGTAGGTTGAGGATG
65 GTTGCAGTGGAACAGATTAAAGATA
* * * ** * * *
31838115 CAAGTCTTATCTCCCTGACGTTGCAGTGGAGCAGACT-AAAACCACAAATCTCATCCCCCTGAAG
1 CAAGTCTTAACTCCCTGAAGTTGCAGTGGAGCAGACTGAAGATGACAAACCTTATCTCCCTGAAG
31838179 TTGC
66 TTGC
31838183 GGCAGAGTAG
Statistics
Matches: 256, Mismatches: 62, Indels: 29
0.74 0.18 0.08
Matches are distributed among these distances:
86 4 0.02
87 64 0.25
88 85 0.33
89 90 0.35
90 11 0.04
91 2 0.01
ACGTcount: A:0.28, C:0.20, G:0.24, T:0.27
Consensus pattern (89 bp):
CAAGTCTTAACTCCCTGAAGTTGCAGTGGAGCAGACTGAAGATGACAAACCTTATCTCCCTGAAG
TTGCAGTGGAACAGATTAAAGATA
Found at i:31837964 original size:44 final size:44
Alignment explanation
Indices: 31837761--31838148 Score: 297
Period size: 44 Copynumber: 8.8 Consensus size: 44
31837751 TCGAAGAAAG
* *
31837761 CAAGTCTTATCCCCCTTGAAGTTGCAGTGGGGCAGAG-TGAAGATGA
1 CAAGTCTTATCTCCC-TGAAGTTGCAGTGGAGCAG-GTTGAAGAT-A
* * * * *
31837807 CGAA-TCTTATTTCCCTGAAGTTGTAGTGGAACAGATTAAAGCCA-A
1 C-AAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGGTTGAAG--ATA
* * * ** *
31837852 TAA-TCTTAACTCCCTGAAGTTGCAGTGGAGTAGACTGAGGATA
1 CAAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGGTTGAAGATA
* **
31837895 GAAAACCTTATCTCCCTGAAGTTGCAGTGGAGCAGGTTGAAGATA
1 -CAAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGGTTGAAGATA
** *
31837940 CAAGTCTTATCTCCCTGAAGTTGCAGTGGAGCATATT-AA-ACCA
1 CAAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGGTTGAAGA-TA
** * * *
31837983 CAAACCTTATCTCTCTGAAGTTGCAATAGAGCAGGTTGAA-ATAA
1 CAAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGGTTGAAGAT-A
* ** * * * *
31838027 TAAACCTTATC-CTCCTGAAGTTGCAGTGGGGTAGGTTGAGGATG
1 CAAGTCTTATCTC-CCTGAAGTTGCAGTGGAGCAGGTTGAAGATA
* * * * *
31838071 CAAGTCTTATCTCCCTGACGTTGCAGTGGGGTAGGTTGAGGATG
1 CAAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGGTTGAAGATA
*
31838115 CAAGTCTTATCTCCCTGACGTTGCAGTGGAGCAG
1 CAAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAG
31838149 ACTAAAACCA
Statistics
Matches: 278, Mismatches: 51, Indels: 28
0.78 0.14 0.08
Matches are distributed among these distances:
42 2 0.01
43 35 0.13
44 170 0.61
45 58 0.21
46 10 0.04
47 3 0.01
ACGTcount: A:0.28, C:0.19, G:0.26, T:0.27
Consensus pattern (44 bp):
CAAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGGTTGAAGATA
Found at i:31838063 original size:131 final size:133
Alignment explanation
Indices: 31837766--31838099 Score: 385
Period size: 131 Copynumber: 2.5 Consensus size: 133
31837756 GAAAGCAAGT
* *
31837766 CTTATCCCCCTTGAAGTTGCAGTGGGGCAGAG-TGAAGATGACGAA-TCTTATTTCCCTGAAGTT
1 CTTATCCTCC-TGAAGTTGCAGTGGGGCAG-GTTGAAGAT-AC-AAGTCTTATCTCCCTGAAGTT
* * * * * *
31837829 GTAGTGGAACAGATTAAAGCCAATAATCTTAACTCCCTGAAGTTGCAGTGGAGTAGACTGAGGAT
62 GCAGTGGAACAGATTAAAGCCAATAACCTTAACTCCCTGAAGTTGCAATAGAGCAGACTGAGAAT
31837894 AGAAAAC
127 AGAAAAC
*
31837901 CTTAT-CTCCCTGAAGTTGCAGTGGAGCAGGTTGAAGATACAAGTCTTATCTCCCTGAAGTTGCA
1 CTTATCCT-CCTGAAGTTGCAGTGGGGCAGGTTGAAGATACAAGTCTTATCTCCCTGAAGTTGCA
* * * * **
31837965 GTGGAGCATATTAAA-CCACA-AACCTTATCTCTCTGAAGTTGCAATAGAGCAGGTTGA-AATA-
65 GTGGAACAGATTAAAGCCA-ATAACCTTAACTCCCTGAAGTTGCAATAGAGCAGACTGAGAATAG
31838026 ATAAAC
129 A-AAAC
* * * *
31838032 CTTATCCTCCTGAAGTTGCAGTGGGGTAGGTTGAGGATGCAAGTCTTATCTCCCTGACGTTGCAG
1 CTTATCCTCCTGAAGTTGCAGTGGGGCAGGTTGAAGATACAAGTCTTATCTCCCTGAAGTTGCAG
31838097 TGG
66 TGG
31838100 GGTAGGTTGA
Statistics
Matches: 173, Mismatches: 20, Indels: 16
0.83 0.10 0.08
Matches are distributed among these distances:
130 1 0.01
131 67 0.39
132 36 0.21
133 36 0.21
134 26 0.15
135 7 0.04
ACGTcount: A:0.29, C:0.19, G:0.25, T:0.28
Consensus pattern (133 bp):
CTTATCCTCCTGAAGTTGCAGTGGGGCAGGTTGAAGATACAAGTCTTATCTCCCTGAAGTTGCAG
TGGAACAGATTAAAGCCAATAACCTTAACTCCCTGAAGTTGCAATAGAGCAGACTGAGAATAGAA
AAC
Found at i:31838121 original size:175 final size:177
Alignment explanation
Indices: 31837864--31838182 Score: 462
Period size: 175 Copynumber: 1.8 Consensus size: 177
31837854 ATCTTAACTC
31837864 CCTGAAGTTGCAGTGGAGTAGACTGAGGATAGAAAACCTTATCTCCCTGAAGTTGCAGTGGAGCA
1 CCTGAAGTTGCAGTGGAGTAGACTGAGGATAGAAAACCTTATCTCCCTGAAGTTGCAGTGGAGCA
* * *
31837929 GGTTGAAGATACAAGTCTTATCTCCCTGAAGTTGCAGTGGAGCATA-TTAAACCACAAACCTTAT
66 GGTTGAAGATACAAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAAACCACAAACCTCAT
* *
31837993 CTCTCTGAAGTTGCAATAGAGCAGGTTGAAATAATAAACCTTATCCT
131 CCCCCTGAAGTTGCAATAGAGCAGGTTGAAATAATAAACCTTATCCT
* ** * ** * * *
31838040 CCTGAAGTTGCAGTGGGGTAGGTTGAGGAT-GCAAGTCTTATCTCCCTGACGTTGCAGTGGGGTA
1 CCTGAAGTTGCAGTGGAGTAGACTGAGGATAGAAAACCTTATCTCCCTGAAGTTGCAGTGGAGCA
* * * *
31838104 GGTTGAGGATGCAAGTCTTATCTCCCTGACGTTGCAGTGGAGCAGACTAAAACCACAAATCTCAT
66 GGTTGAAGATACAAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAAACCACAAACCTCAT
31838169 CCCCCTGAAGTTGC
131 CCCCCTGAAGTTGC
31838183 GGCAGAGTAG
Statistics
Matches: 124, Mismatches: 18, Indels: 2
0.86 0.12 0.01
Matches are distributed among these distances:
175 70 0.56
176 54 0.44
ACGTcount: A:0.28, C:0.21, G:0.25, T:0.26
Consensus pattern (177 bp):
CCTGAAGTTGCAGTGGAGTAGACTGAGGATAGAAAACCTTATCTCCCTGAAGTTGCAGTGGAGCA
GGTTGAAGATACAAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAAACCACAAACCTCAT
CCCCCTGAAGTTGCAATAGAGCAGGTTGAAATAATAAACCTTATCCT
Found at i:31842087 original size:27 final size:26
Alignment explanation
Indices: 31842049--31842099 Score: 75
Period size: 27 Copynumber: 1.9 Consensus size: 26
31842039 TCATTATTTA
*
31842049 TTTTTTATTTTTGCAATTAATGTTTC
1 TTTTTTATTTTTGAAATTAATGTTTC
*
31842075 TTTTATTATTTTTTAAATTAATGTT
1 TTTT-TTATTTTTGAAATTAATGTT
31842100 GCTTGTAATT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 4 0.18
27 18 0.82
ACGTcount: A:0.24, C:0.04, G:0.06, T:0.67
Consensus pattern (26 bp):
TTTTTTATTTTTGAAATTAATGTTTC
Found at i:31842265 original size:20 final size:20
Alignment explanation
Indices: 31842217--31842265 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 20
31842207 AGTTGGAATT
*
31842217 ATATAAAAAATATTTTATTA
1 ATATATAAAATATTTTATTA
* *
31842237 ACATTTAAAATA-TTTATTTA
1 ATATATAAAATATTTTA-TTA
31842257 ATATATAAA
1 ATATATAAA
31842266 TTTATATTTA
Statistics
Matches: 23, Mismatches: 5, Indels: 2
0.77 0.17 0.07
Matches are distributed among these distances:
19 4 0.17
20 19 0.83
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (20 bp):
ATATATAAAATATTTTATTA
Found at i:31844953 original size:21 final size:21
Alignment explanation
Indices: 31844929--31844986 Score: 73
Period size: 21 Copynumber: 2.8 Consensus size: 21
31844919 TTGATAATTT
*
31844929 CAATAAAGTATCGGTACCAAA
1 CAATAAAGTATCGATACCAAA
* *
31844950 CAATCAAGTATCAATACCAAA
1 CAATAAAGTATCGATACCAAA
31844971 CAATCAAA-TATCGATA
1 CAAT-AAAGTATCGATA
31844987 TTAAACCCTT
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
21 29 0.94
22 2 0.06
ACGTcount: A:0.50, C:0.21, G:0.09, T:0.21
Consensus pattern (21 bp):
CAATAAAGTATCGATACCAAA
Found at i:31848881 original size:16 final size:15
Alignment explanation
Indices: 31848862--31848917 Score: 58
Period size: 16 Copynumber: 3.5 Consensus size: 15
31848852 TCGTCAGCCT
31848862 CTCCCTCCGTCGACCG
1 CTCCCTCCGTCGA-CG
*
31848878 CTCCCTCTGTCGACG
1 CTCCCTCCGTCGACG
* *
31848893 TTTCCTTCCGTCGAACG
1 -CTCCCTCCGTCG-ACG
31848910 CTCCCTCC
1 CTCCCTCC
31848918 ATTGCTCACT
Statistics
Matches: 32, Mismatches: 6, Indels: 4
0.76 0.14 0.10
Matches are distributed among these distances:
15 2 0.06
16 27 0.84
17 3 0.09
ACGTcount: A:0.07, C:0.50, G:0.16, T:0.27
Consensus pattern (15 bp):
CTCCCTCCGTCGACG
Found at i:31851901 original size:30 final size:29
Alignment explanation
Indices: 31851865--31852022 Score: 135
Period size: 30 Copynumber: 5.3 Consensus size: 29
31851855 ATTTAAAATT
31851865 TAAAATTTACATTTTGACTTCTTAATTTTTC
1 TAAAA-TTACATTTTGAC-TCTTAATTTTTC
* * *
31851896 TAAATTTATATTTTGACCCTTTAA-TTTTC
1 TAAAATTACATTTTGACTC-TTAATTTTTC
* * *
31851925 TTAATATTACATTTTGACCTCTAAACTTTTC
1 -TAAAATTACATTTTGA-CTCTTAATTTTTC
*
31851956 TAAAATTACATTTGGAACT-TTAACTTTTT-
1 TAAAATTACATTTTG-ACTCTTAA-TTTTTC
* *
31851985 TAAAATTATATTTTGAC-CTTAAATTTTCC
1 TAAAATTACATTTTGACTCTT-AATTTTTC
31852014 TAAAATTAC
1 TAAAATTAC
31852023 TCTCTGACCT
Statistics
Matches: 102, Mismatches: 16, Indels: 20
0.74 0.12 0.14
Matches are distributed among these distances:
28 8 0.08
29 32 0.31
30 50 0.49
31 12 0.12
ACGTcount: A:0.32, C:0.14, G:0.04, T:0.50
Consensus pattern (29 bp):
TAAAATTACATTTTGACTCTTAATTTTTC
Found at i:31852002 original size:59 final size:58
Alignment explanation
Indices: 31851863--31852022 Score: 180
Period size: 60 Copynumber: 2.7 Consensus size: 58
31851853 AAATTTAAAA
* * * * * *
31851863 TTTAAAATTTACATTTTGACTTCTTAATTTTTCTAAATTTATATTTTGACCCTTTAATTT
1 TTTAAAA-TTACATTTTGACCTC-TAAATTTTCTAAAATTACATTTGGACACTTTAATTT
*
31851923 TCTTAATATTACATTTTGACCTCTAAACTTTTCTAAAATTACATTTGGA-ACTTTAACTTT
1 T-TTAAAATTACATTTTGACCTCTAAA-TTTTCTAAAATTACATTTGGACACTTTAA-TTT
*
31851983 TTTAAAATTATATTTTGACCT-TAAATTTTCCTAAAATTAC
1 TTTAAAATTACATTTTGACCTCTAAATTTT-CTAAAATTAC
31852023 TCTCTGACCT
Statistics
Matches: 87, Mismatches: 9, Indels: 10
0.82 0.08 0.09
Matches are distributed among these distances:
57 4 0.05
58 14 0.16
59 27 0.31
60 37 0.43
61 5 0.06
ACGTcount: A:0.32, C:0.14, G:0.04, T:0.51
Consensus pattern (58 bp):
TTTAAAATTACATTTTGACCTCTAAATTTTCTAAAATTACATTTGGACACTTTAATTT
Found at i:31858220 original size:30 final size:30
Alignment explanation
Indices: 31858179--31858336 Score: 149
Period size: 30 Copynumber: 5.2 Consensus size: 30
31858169 ACGATGAGGT
* *
31858179 ATTTTAGGAAAGTTTTGAGGTTAAAATATA
1 ATTTTAAGAAAGTTTAGAGGTTAAAATATA
31858209 ATTTTAAGAAAGTTTAG-GGTTTAAAATATA
1 ATTTTAAGAAAGTTTAGAGG-TTAAAATATA
* * *
31858239 ATTTTAAAAAACTTAAGAGGTTAAAATATA
1 ATTTTAAGAAAGTTTAGAGGTTAAAATATA
* * * *
31858269 AATTTAGGAAAATTTAGAGGTCAAAATATA
1 ATTTTAAGAAAGTTTAGAGGTTAAAATATA
* * * * *
31858299 AATTT-AGAAAAATTAAGAGGTCAAAATGTAA
1 ATTTTAAG-AAAGTTTAGAGGTTAAAATAT-A
31858330 ATTTTAA
1 ATTTTAA
31858337 ATTTTATATT
Statistics
Matches: 108, Mismatches: 15, Indels: 8
0.82 0.11 0.06
Matches are distributed among these distances:
29 3 0.03
30 97 0.90
31 7 0.06
32 1 0.01
ACGTcount: A:0.48, C:0.02, G:0.15, T:0.35
Consensus pattern (30 bp):
ATTTTAAGAAAGTTTAGAGGTTAAAATATA
Found at i:31858285 original size:60 final size:60
Alignment explanation
Indices: 31858195--31858333 Score: 183
Period size: 60 Copynumber: 2.3 Consensus size: 60
31858185 GGAAAGTTTT
* * * *
31858195 GAGGTTAAAATATAATTTTAAGAAAGTTTAG-GGTTTAAAATATAATTTTA-AAAAACTTAA
1 GAGGTTAAAATATAAATTTAAGAAAATTTAGAGG-TCAAAATATAAATTTAGAAAAA-TTAA
*
31858255 GAGGTTAAAATATAAATTTAGGAAAATTTAGAGGTCAAAATATAAATTTAGAAAAATTAA
1 GAGGTTAAAATATAAATTTAAGAAAATTTAGAGGTCAAAATATAAATTTAGAAAAATTAA
* *
31858315 GAGGTCAAAATGTAAATTT
1 GAGGTTAAAATATAAATTT
31858334 TAAATTTTAT
Statistics
Matches: 70, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
60 63 0.90
61 7 0.10
ACGTcount: A:0.50, C:0.02, G:0.15, T:0.33
Consensus pattern (60 bp):
GAGGTTAAAATATAAATTTAAGAAAATTTAGAGGTCAAAATATAAATTTAGAAAAATTAA
Found at i:31866667 original size:28 final size:28
Alignment explanation
Indices: 31866635--31866696 Score: 88
Period size: 28 Copynumber: 2.2 Consensus size: 28
31866625 GCTGGCAGAA
* *
31866635 CGTGCGGCGCTGGGGCATTGGGTAGAGG
1 CGTGCGGCGCTGAGGCATTGGGCAGAGG
* *
31866663 TGTGCGGTGCTGAGGCATTGGGCAGAGG
1 CGTGCGGCGCTGAGGCATTGGGCAGAGG
31866691 CGTGCG
1 CGTGCG
31866697 ACACTTTAGG
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.11, C:0.18, G:0.52, T:0.19
Consensus pattern (28 bp):
CGTGCGGCGCTGAGGCATTGGGCAGAGG
Found at i:31866785 original size:18 final size:19
Alignment explanation
Indices: 31866743--31866787 Score: 58
Period size: 18 Copynumber: 2.5 Consensus size: 19
31866733 GCTGCTGTTG
31866743 GTTTGGGCTGGGGTTATTA
1 GTTTGGGCTGGGGTTATTA
* *
31866762 G-ATGGGCTTGGGTTATT-
1 GTTTGGGCTGGGGTTATTA
31866779 GTTTGGGCT
1 GTTTGGGCT
31866788 AGAGTAACAA
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
17 1 0.05
18 20 0.91
19 1 0.05
ACGTcount: A:0.09, C:0.07, G:0.42, T:0.42
Consensus pattern (19 bp):
GTTTGGGCTGGGGTTATTA
Found at i:31867249 original size:41 final size:41
Alignment explanation
Indices: 31867215--31867334 Score: 222
Period size: 41 Copynumber: 2.9 Consensus size: 41
31867205 ATAAGGTTCA
*
31867215 ATATGATCTGCTCTACTGCGACTTTAGAGAGATAAGATTTG
1 ATATGATCTGCTCTACTGCGACTTCAGAGAGATAAGATTTG
*
31867256 ATATGATCTGCTCTACTGCGACTTCAGAGAAATAAGATTTG
1 ATATGATCTGCTCTACTGCGACTTCAGAGAGATAAGATTTG
31867297 ATATGATCTGCTCTACTGCGACTTCAGAGAGATAAGAT
1 ATATGATCTGCTCTACTGCGACTTCAGAGAGATAAGAT
31867335 CTGTTATGGT
Statistics
Matches: 76, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
41 76 1.00
ACGTcount: A:0.31, C:0.17, G:0.21, T:0.32
Consensus pattern (41 bp):
ATATGATCTGCTCTACTGCGACTTCAGAGAGATAAGATTTG
Found at i:31867555 original size:44 final size:45
Alignment explanation
Indices: 31867503--31867611 Score: 123
Period size: 44 Copynumber: 2.5 Consensus size: 45
31867493 CGACCGACTG
* * *
31867503 CAACTTCAGAGATATAAGATTTA-TAGTTTTAATCCGCTCCACTA
1 CAACTTCAGGGAAATAAGATTTAGTAGTTTCAATCCGCTCCACTA
* * * * *
31867547 CAATTTCAGGGAAATAGGA-TTAGTGGTTTCAATCTGCTCCACTG
1 CAACTTCAGGGAAATAAGATTTAGTAGTTTCAATCCGCTCCACTA
*
31867591 CAACTTCAGGGAGATAAGATT
1 CAACTTCAGGGAAATAAGATT
31867612 CACCATGATG
Statistics
Matches: 52, Mismatches: 11, Indels: 3
0.79 0.17 0.05
Matches are distributed among these distances:
43 3 0.06
44 48 0.92
45 1 0.02
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.31
Consensus pattern (45 bp):
CAACTTCAGGGAAATAAGATTTAGTAGTTTCAATCCGCTCCACTA
Found at i:31867555 original size:138 final size:138
Alignment explanation
Indices: 31867302--31867610 Score: 413
Period size: 138 Copynumber: 2.2 Consensus size: 138
31867292 ATTTGATATG
* * * *
31867302 ATCTGCTCTACTGCGACTTCAGAGAGATAAGATCTGTTATGGTAAATTTAATCCGACCTACTGCA
1 ATCTGCTCCACTGCAACTTCAGGGAGATAAGATCTGTTATGGTAAATTTAATCCGACCGACTGCA
* * * ** * *
31867367 ACTTCAGAGGTATAGGATTCATTGTTTTAATCCGCTCCACTGTAACTTCAGGTAGATAGGATTAG
66 ACTTCAGAGATATAAGATTCATAGTTTTAATCCGCTCCACTACAACTTCAGGGAAATAGGATTAG
31867432 TAGCTTCA
131 TAGCTTCA
* * * * * *
31867440 GTTTGCTCCACTGCAATTTTAGGGAGATAAGA-CTTGTTATGGTAGATTTGATCCGACCGACTGC
1 ATCTGCTCCACTGCAACTTCAGGGAGATAAGATC-TGTTATGGTAAATTTAATCCGACCGACTGC
* *
31867504 AACTTCAGAGATATAAGATTTATAGTTTTAATCCGCTCCACTACAATTTCAGGGAAATAGGATTA
65 AACTTCAGAGATATAAGATTCATAGTTTTAATCCGCTCCACTACAACTTCAGGGAAATAGGATTA
* *
31867569 GTGGTTTCA
130 GTAGCTTCA
31867578 ATCTGCTCCACTGCAACTTCAGGGAGATAAGAT
1 ATCTGCTCCACTGCAACTTCAGGGAGATAAGAT
31867611 TCACCATGAT
Statistics
Matches: 144, Mismatches: 25, Indels: 3
0.84 0.15 0.02
Matches are distributed among these distances:
137 1 0.01
138 143 0.99
ACGTcount: A:0.29, C:0.19, G:0.20, T:0.32
Consensus pattern (138 bp):
ATCTGCTCCACTGCAACTTCAGGGAGATAAGATCTGTTATGGTAAATTTAATCCGACCGACTGCA
ACTTCAGAGATATAAGATTCATAGTTTTAATCCGCTCCACTACAACTTCAGGGAAATAGGATTAG
TAGCTTCA
Found at i:31867662 original size:138 final size:138
Alignment explanation
Indices: 31867302--31867662 Score: 343
Period size: 138 Copynumber: 2.6 Consensus size: 138
31867292 ATTTGATATG
* * * * * * * * *
31867302 ATCTGCTCTACTGCGACTTCAGAGAGATAAGATCTGT--TATGGTAAATTTAATCCGACCTACTG
1 ATCTGCTCCACTGCAACTTCAGGGAGATAAGA-CT-TACCATGATAGATTTAATCCCACCCACTA
* * ** * *
31867365 CAACTTCAGAGGTATAGGATTCATTGTTTTAATCCGCTCCACTGTAACTTCAGGTAGATAGGATT
64 CAACTTCAGAGGTATAGGATTTATAGTTTTAATCCGCTCCACTACAACTTCAGGGAAATAGGATT
31867430 AGTAGCTTCA
129 AGTAGCTTCA
* * * * *** * * * * *
31867440 GTTTGCTCCACTGCAATTTTAGGGAGATAAGACTTGTTATGGTAGATTTGATCCGACCGACTGCA
1 ATCTGCTCCACTGCAACTTCAGGGAGATAAGACTTACCATGATAGATTTAATCCCACCCACTACA
* * *
31867505 ACTTCAGAGATATAAGATTTATAGTTTTAATCCGCTCCACTACAATTTCAGGGAAATAGGATTAG
66 ACTTCAGAGGTATAGGATTTATAGTTTTAATCCGCTCCACTACAACTTCAGGGAAATAGGATTAG
* *
31867570 TGGTTTCA
131 TAGCTTCA
*
31867578 ATCTGCTCCACTGCAACTTCAGGGAGATAAGA-TTCACCATGAT-GACTTTAATCCCTCCCACTA
1 ATCTGCTCCACTGCAACTTCAGGGAGATAAGACTT-ACCATGATAGA-TTTAATCCCACCCACTA
* *
31867641 TAACTTCAGGGGTATAGGATTT
64 CAACTTCAGAGGTATAGGATTT
31867663 GTGGTTTCAC
Statistics
Matches: 181, Mismatches: 38, Indels: 8
0.80 0.17 0.04
Matches are distributed among these distances:
136 1 0.01
137 6 0.03
138 174 0.96
ACGTcount: A:0.29, C:0.20, G:0.20, T:0.32
Consensus pattern (138 bp):
ATCTGCTCCACTGCAACTTCAGGGAGATAAGACTTACCATGATAGATTTAATCCCACCCACTACA
ACTTCAGAGGTATAGGATTTATAGTTTTAATCCGCTCCACTACAACTTCAGGGAAATAGGATTAG
TAGCTTCA
Found at i:31883534 original size:28 final size:28
Alignment explanation
Indices: 31883500--31883560 Score: 86
Period size: 28 Copynumber: 2.2 Consensus size: 28
31883490 GCTGGCAGAA
* *
31883500 CGTGCAGCGCTGGGGAATTGGGCAGAGG
1 CGTGCAGCACTGAGGAATTGGGCAGAGG
* *
31883528 TGTGCAGCACTGAGGCATTGGGCAGAGG
1 CGTGCAGCACTGAGGAATTGGGCAGAGG
31883556 CGTGC
1 CGTGC
31883561 GACGCCTTAG
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.18, C:0.20, G:0.46, T:0.16
Consensus pattern (28 bp):
CGTGCAGCACTGAGGAATTGGGCAGAGG
Found at i:31883616 original size:16 final size:17
Alignment explanation
Indices: 31883582--31883617 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
31883572 GTTTGCTTCT
*
31883582 CTGCTGTTTGTTGTGGG
1 CTGCTGTTGGTTGTGGG
31883599 CTGCTGTTGGTT-TGGG
1 CTGCTGTTGGTTGTGGG
31883615 CTG
1 CTG
31883618 GGGTTATTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 7 0.39
17 11 0.61
ACGTcount: A:0.00, C:0.14, G:0.42, T:0.44
Consensus pattern (17 bp):
CTGCTGTTGGTTGTGGG
Found at i:31892415 original size:15 final size:14
Alignment explanation
Indices: 31892395--31892432 Score: 58
Period size: 15 Copynumber: 2.6 Consensus size: 14
31892385 TTTGTTGAAA
31892395 TTTCACTTCTAGTCC
1 TTTCACTTCTAGT-C
31892410 TTTCACTTCTAGTC
1 TTTCACTTCTAGTC
31892424 TTTCCACTT
1 TTT-CACTT
31892433 TTTCGTCCTA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
14 4 0.18
15 18 0.82
ACGTcount: A:0.13, C:0.32, G:0.05, T:0.50
Consensus pattern (14 bp):
TTTCACTTCTAGTC
Found at i:31896036 original size:128 final size:128
Alignment explanation
Indices: 31894992--31896024 Score: 1591
Period size: 128 Copynumber: 8.1 Consensus size: 128
31894982 CGCAACGTCG
* * * * * * * * * *
31894992 GGGAGATAGGATTTGTGGCTTCAACCTACTTCCCTACTCCTAAAGATAAGATTTGTCGTCTTCGG
1 GGGAGATAGGACTTGTGGCTTAAATCTGCTTCCTTACTCTTGAAGATAAGATTCGCCGTCTTCGA
* * * *
31895057 TATGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATTTCCAACCTATTCCACTGCTGACAA
66 TCTGCTCCGCTACTGCTTAGGGAGACAAGATCTGTAATTTCCAACCTATTCCACTGCTGACCA
* * * * * *
31895120 GGCAGATAGAACTTGTGGCTTAAATTTGCTTCCCTACTCTTGAAGATAAGATTTGCCGTCTTTGA
1 GGGAGATAGGACTTGTGGCTTAAATCTGCTTCCTTACTCTTGAAGATAAGATTCGCCGTCTTCGA
* * *
31895185 TCTGCTCCACTACTGCTTCGGGAGATAAGATCTGTAATTTCCAACCTATTCCACTGCTGACCA
66 TCTGCTCCGCTACTGCTTAGGGAGACAAGATCTGTAATTTCCAACCTATTCCACTGCTGACCA
31895248 GGGAGATAGGACTTGTGGCTTAAATCTGCTTCCTTACTCTTGAAGATAAGATTCGCCGTCTTCGA
1 GGGAGATAGGACTTGTGGCTTAAATCTGCTTCCTTACTCTTGAAGATAAGATTCGCCGTCTTCGA
* * **
31895313 TCTGCTTCGTTACTGCTTAGGGAGACAAGATCTGTAATTTCCAACCTATTCCACTATTGACCA
66 TCTGCTCCGCTACTGCTTAGGGAGACAAGATCTGTAATTTCCAACCTATTCCACTGCTGACCA
* **
31895376 GGGAGATAGGACTTGTGGCTTAAATCTGCTTCCTTACTCATGAAGATAAGATTCATCGTCTTCGA
1 GGGAGATAGGACTTGTGGCTTAAATCTGCTTCCTTACTCTTGAAGATAAGATTCGCCGTCTTCGA
* *
31895441 TCTGCTCTGCTACTGCTTACGGAGACAAGATCTGTAATTTCCAACCTATTCCACTGCTGACCA
66 TCTGCTCCGCTACTGCTTAGGGAGACAAGATCTGTAATTTCCAACCTATTCCACTGCTGACCA
* * *
31895504 GGGAGATAGGACTTGTGGCTTAAATCTGATTCCTTACTCTTGAAGATAAGATTCACCGTCTTTGA
1 GGGAGATAGGACTTGTGGCTTAAATCTGCTTCCTTACTCTTGAAGATAAGATTCGCCGTCTTCGA
31895569 TCTGCTCCGCTACTGCTTAGGGAGACAAGATCTGTAATTTCCAACCTATTCCACTGCTGACCA
66 TCTGCTCCGCTACTGCTTAGGGAGACAAGATCTGTAATTTCCAACCTATTCCACTGCTGACCA
*
31895632 GGGAGATAGGCCTTGTGGCTTAAATCTGCTTCCTTACTCTTGAAGATAAGATTCGCCGTCTTCGA
1 GGGAGATAGGACTTGTGGCTTAAATCTGCTTCCTTACTCTTGAAGATAAGATTCGCCGTCTTCGA
* * * *
31895697 TCTGCTCCGCTACTGCTTAGGGAGACAAGATTTGTAATTTCTAACATATTCCACTACTGACCA
66 TCTGCTCCGCTACTGCTTAGGGAGACAAGATCTGTAATTTCCAACCTATTCCACTGCTGACCA
* * * *
31895760 GGGAGATAGGACTTATGGCTTAAATCTGCTTCCTTACTCTTGAAGATAAGATTCACCATCTTCGG
1 GGGAGATAGGACTTGTGGCTTAAATCTGCTTCCTTACTCTTGAAGATAAGATTCGCCGTCTTCGA
*
31895825 TCTGCTCCGCTACTGCTTAGGGAGACAAGATCTGTAATTTCCAACCTATTCCATTGCTGACCA
66 TCTGCTCCGCTACTGCTTAGGGAGACAAGATCTGTAATTTCCAACCTATTCCACTGCTGACCA
*
31895888 GGGAGATAGGACTTGTGGCTTAAATCTGCTTCCTTACTCTTGAAGATAAGATTCGCCGTCTTTGA
1 GGGAGATAGGACTTGTGGCTTAAATCTGCTTCCTTACTCTTGAAGATAAGATTCGCCGTCTTCGA
* * ** *
31895953 TCTGCTCCGCTACTGCTTAGGGAGACAAGATTTGTAATCTT-CAATCTATTCCACTGCCAACTA
66 TCTGCTCCGCTACTGCTTAGGGAGACAAGATCTGTAAT-TTCCAACCTATTCCACTGCTGACCA
31896016 GGGAGATAG
1 GGGAGATAG
31896025 AATTACTGGC
Statistics
Matches: 832, Mismatches: 72, Indels: 2
0.92 0.08 0.00
Matches are distributed among these distances:
128 830 1.00
129 2 0.00
ACGTcount: A:0.25, C:0.23, G:0.20, T:0.32
Consensus pattern (128 bp):
GGGAGATAGGACTTGTGGCTTAAATCTGCTTCCTTACTCTTGAAGATAAGATTCGCCGTCTTCGA
TCTGCTCCGCTACTGCTTAGGGAGACAAGATCTGTAATTTCCAACCTATTCCACTGCTGACCA
Found at i:31897513 original size:12 final size:13
Alignment explanation
Indices: 31897490--31897527 Score: 51
Period size: 12 Copynumber: 2.8 Consensus size: 13
31897480 CTTTTCCATT
31897490 TTTTCATTTTTCA
1 TTTTCATTTTTCA
31897503 TTTTC-TTTTTCA
1 TTTTCATTTTTCA
31897515 TTTATCACTTTTT
1 TTT-TCA-TTTTT
31897528 TTTATTTTTG
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
12 10 0.45
13 7 0.32
15 5 0.23
ACGTcount: A:0.13, C:0.16, G:0.00, T:0.71
Consensus pattern (13 bp):
TTTTCATTTTTCA
Found at i:31897513 original size:19 final size:18
Alignment explanation
Indices: 31897488--31897536 Score: 64
Period size: 19 Copynumber: 2.7 Consensus size: 18
31897478 TCCTTTTCCA
*
31897488 TTTTTTCATTTTTCATTT
1 TTTTTTCATTTTTCACTT
*
31897506 TCTTTTTCATTTATCACTT
1 T-TTTTTCATTTTTCACTT
31897525 TTTTTT-ATTTTT
1 TTTTTTCATTTTT
31897537 GACTCAAAGT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
17 5 0.19
18 6 0.22
19 16 0.59
ACGTcount: A:0.12, C:0.12, G:0.00, T:0.76
Consensus pattern (18 bp):
TTTTTTCATTTTTCACTT
Found at i:31898495 original size:26 final size:25
Alignment explanation
Indices: 31898426--31898495 Score: 70
Period size: 26 Copynumber: 2.7 Consensus size: 25
31898416 TTTTCCCCTC
*
31898426 CTTTTCATTTTCATTTTTTGACTTTG
1 CTTTTGATTTT-ATTTTTTGACTTTG
* *
31898452 ATTTTGATTTTTTCTTTTTG-CTTTTG
1 CTTTTGATTTTAT-TTTTTGAC-TTTG
31898478 CTTTTGATTTTGATTTTT
1 CTTTTGATTTT-ATTTTT
31898496 CTTCCCCCCC
Statistics
Matches: 36, Mismatches: 5, Indels: 6
0.77 0.11 0.13
Matches are distributed among these distances:
25 2 0.06
26 33 0.92
27 1 0.03
ACGTcount: A:0.10, C:0.10, G:0.10, T:0.70
Consensus pattern (25 bp):
CTTTTGATTTTATTTTTTGACTTTG
Found at i:31911191 original size:16 final size:16
Alignment explanation
Indices: 31911170--31911239 Score: 95
Period size: 16 Copynumber: 4.4 Consensus size: 16
31911160 TTTGGTTCGC
* * *
31911170 TGTATTGGATTAGATG
1 TGTAATGGAATAGAGG
* *
31911186 TGTATTGGATTAGAGG
1 TGTAATGGAATAGAGG
31911202 TGTAATGGAATAGAGG
1 TGTAATGGAATAGAGG
31911218 TGTAATGGAATAGAGG
1 TGTAATGGAATAGAGG
31911234 TGTAAT
1 TGTAAT
31911240 AGCAAATCAA
Statistics
Matches: 51, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 51 1.00
ACGTcount: A:0.31, C:0.00, G:0.34, T:0.34
Consensus pattern (16 bp):
TGTAATGGAATAGAGG
Found at i:31911323 original size:39 final size:43
Alignment explanation
Indices: 31911218--31911327 Score: 129
Period size: 45 Copynumber: 2.6 Consensus size: 43
31911208 GGAATAGAGG
31911218 TGTAATGGAATAGAGGTGTAATAGCAAATCAACTGTTTGGTTGAA
1 TGTAATGGAATAGAGGTGTAATAGCAAATCAACTGTTTGGTT--A
* * ***
31911263 TGTAATGGAATAGAGGCGTAATAG-TAATCTTGTGTTTGG-T-
1 TGTAATGGAATAGAGGTGTAATAGCAAATCAACTGTTTGGTTA
31911303 TG-AATGGAATAGAGGTGTAATAGCA
1 TGTAATGGAATAGAGGTGTAATAGCA
31911328 TAATGGAAAA
Statistics
Matches: 57, Mismatches: 7, Indels: 7
0.80 0.10 0.10
Matches are distributed among these distances:
39 20 0.35
40 2 0.04
43 1 0.02
44 11 0.19
45 23 0.40
ACGTcount: A:0.34, C:0.05, G:0.29, T:0.32
Consensus pattern (43 bp):
TGTAATGGAATAGAGGTGTAATAGCAAATCAACTGTTTGGTTA
Found at i:31911481 original size:25 final size:25
Alignment explanation
Indices: 31911449--31911503 Score: 69
Period size: 25 Copynumber: 2.2 Consensus size: 25
31911439 TAATTTAATC
*
31911449 ATAT-TTAAACATAATTATTATT-AA
1 ATATATTAAACAT-ATTATAATTAAA
*
31911473 ATATATTAAATATATTATAATTAAA
1 ATATATTAAACATATTATAATTAAA
31911498 ATATAT
1 ATATAT
31911504 AATTTAATAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
24 12 0.44
25 15 0.56
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (25 bp):
ATATATTAAACATATTATAATTAAA
Found at i:31911707 original size:26 final size:28
Alignment explanation
Indices: 31911678--31911738 Score: 81
Period size: 28 Copynumber: 2.2 Consensus size: 28
31911668 TATGAATTTG
*
31911678 TATAATTTAA-AATAAT-TATTATTACA
1 TATAATTTAATAATAATATATAATTACA
*
31911704 TATAATTTAATAATAATATATAATTTCA
1 TATAATTTAATAATAATATATAATTACA
*
31911732 TAAAATT
1 TATAATT
31911739 ATTGATAATA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
26 10 0.33
27 6 0.20
28 14 0.47
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (28 bp):
TATAATTTAATAATAATATATAATTACA
Found at i:31911740 original size:91 final size:89
Alignment explanation
Indices: 31911644--31911860 Score: 299
Period size: 91 Copynumber: 2.4 Consensus size: 89
31911634 AATTTAAAAT
* * * *
31911644 AATTATAACTAATAAATTATCTTATATGAATTTGTATAATTTAAAATAATTATTATTACATATAA
1 AATTATAA-TAATAAATT-TCTTATATGAATTTATACAATTTAAAATAATTAATATTAAATATAA
31911709 TTTAATAATAATATATAATTTCATAA
64 TTTAATAATAATATATAATTTCATAA
* *
31911735 AATTATTGATAATAATTTTTCTTATATGAATTTATACAATTTAAAATAATTAATATTAAATATAA
1 AATTA-TAATAATAA-ATTTCTTATATGAATTTATACAATTTAAAATAATTAATATTAAATATAA
*
31911800 TTTAATAATGATATATAATTTCATAA
64 TTTAATAATAATATATAATTTCATAA
*
31911826 AATTCTTAATAATAAAATGTTCTTATATGAATTTA
1 AATT-ATAATAAT-AAAT-TTCTTATATGAATTTA
31911861 CTAAAATCAA
Statistics
Matches: 111, Mismatches: 10, Indels: 9
0.85 0.08 0.07
Matches are distributed among these distances:
91 89 0.80
92 22 0.20
ACGTcount: A:0.47, C:0.04, G:0.03, T:0.46
Consensus pattern (89 bp):
AATTATAATAATAAATTTCTTATATGAATTTATACAATTTAAAATAATTAATATTAAATATAATT
TAATAATAATATATAATTTCATAA
Found at i:31911741 original size:44 final size:42
Alignment explanation
Indices: 31911678--31911820 Score: 119
Period size: 44 Copynumber: 3.2 Consensus size: 42
31911668 TATGAATTTG
31911678 TATAATTTAAAATAATTATTATTACATATAATTTAATAATAATA
1 TATAATTTAAAATAATTATTATTA-ATATAATTTAATAAT-ATA
* ** *
31911722 TATAATTTCATAA-AATTATTGA-TAATAATTTTTCTTATATGAATTTA
1 TATAATTT-AAAATAATTATT-ATTAAT-A-TAAT-TTA-AT-AATATA
* *
31911769 TACAATTTAAAATAATTAATATTAAATATAATTTAATAATGATA
1 TATAATTTAAAATAATTATTATT-AATATAATTTAATAAT-ATA
31911813 TATAATTT
1 TATAATTT
31911821 CATAAAATTC
Statistics
Matches: 77, Mismatches: 11, Indels: 22
0.70 0.10 0.20
Matches are distributed among these distances:
43 5 0.06
44 29 0.38
45 9 0.12
46 9 0.12
47 19 0.25
48 6 0.08
ACGTcount: A:0.48, C:0.03, G:0.02, T:0.47
Consensus pattern (42 bp):
TATAATTTAAAATAATTATTATTAATATAATTTAATAATATA
Found at i:31911835 original size:47 final size:47
Alignment explanation
Indices: 31911685--31911841 Score: 128
Period size: 47 Copynumber: 3.4 Consensus size: 47
31911675 TTGTATAATT
* * * * *
31911685 TAAAATAATTATTATTACATATAATTTAATAATAATATATAATTTCA
1 TAAAATTATTAATAATAAATATAATTTAATAATGATATATAATTTCA
* ** * *
31911732 TAAAATTATTGATAAT-AAT-T--TTTCTTATATGAATTTATACAATT--
1 TAAAATTATTAATAATAAATATAATTTAATA-ATG-ATATATA-ATTTCA
* *
31911776 TAAAATAATTAATATTAAATATAATTTAATAATGATATATAATTTCA
1 TAAAATTATTAATAATAAATATAATTTAATAATGATATATAATTTCA
*
31911823 TAAAATTCTTAATAATAAA
1 TAAAATTATTAATAATAAA
31911842 ATGTTCTTAT
Statistics
Matches: 81, Mismatches: 20, Indels: 18
0.68 0.17 0.15
Matches are distributed among these distances:
43 5 0.06
44 15 0.19
45 13 0.16
46 12 0.15
47 31 0.38
48 5 0.06
ACGTcount: A:0.50, C:0.04, G:0.02, T:0.45
Consensus pattern (47 bp):
TAAAATTATTAATAATAAATATAATTTAATAATGATATATAATTTCA
Found at i:31919653 original size:30 final size:30
Alignment explanation
Indices: 31919608--31919809 Score: 214
Period size: 30 Copynumber: 6.8 Consensus size: 30
31919598 TAGCAAAACT
* *
31919608 TTTAA-GGCTAAAATGTAATTTCATGAAAA-
1 TTTAAGGGTTAAAATGTAATTTTA-GAAAAG
* *
31919637 TTTAAGGGTCAAAATGTAATTTTAGAAAAT
1 TTTAAGGGTTAAAATGTAATTTTAGAAAAG
31919667 TTTAAGGGTTAAAATGTAATTTTAGGAAAA-
1 TTTAAGGGTTAAAATGTAATTTTA-GAAAAG
* * * * *
31919697 TTTAGGGGTTGAAATATAATTTTAGGAAAC
1 TTTAAGGGTTAAAATGTAATTTTAGAAAAG
* *
31919727 TTT-AGGATTTGAAATGTAATTTTAGAAAAG
1 TTTAAGG-GTTAAAATGTAATTTTAGAAAAG
* * *
31919757 TTTAGGGGTTAAAATGTAATTTCAAAAAAG
1 TTTAAGGGTTAAAATGTAATTTTAGAAAAG
*
31919787 TTTAGGGGTTAAAATGTAATTTT
1 TTTAAGGGTTAAAATGTAATTTT
31919810 TAAAGAAAAT
Statistics
Matches: 148, Mismatches: 19, Indels: 11
0.83 0.11 0.06
Matches are distributed among these distances:
29 16 0.11
30 125 0.84
31 7 0.05
ACGTcount: A:0.41, C:0.02, G:0.19, T:0.38
Consensus pattern (30 bp):
TTTAAGGGTTAAAATGTAATTTTAGAAAAG
Found at i:31919827 original size:90 final size:90
Alignment explanation
Indices: 31919648--31919828 Score: 224
Period size: 90 Copynumber: 2.0 Consensus size: 90
31919638 TTAAGGGTCA
* * * *
31919648 AAATGTAATTTTAGAAAATTTTAAGGGTTAAAATGTAATTTTAGGAAAATTTAGGGGTTGAAATA
1 AAATGTAATTTTAGAAAAGTTTAAGGGTTAAAATGTAATTTCAGAAAAATTTAGGGGTTAAAATA
* * * *
31919713 TAATTTTAGGAAACTTTAGGATTTG
66 TAATTTTAAGAAACATGAGAATTTG
*
31919738 AAATGTAATTTTAGAAAAGTTTAGGGGTTAAAATGTAATTTCA-AAAAAGTTTAGGGGTTAAAAT
1 AAATGTAATTTTAGAAAAGTTTAAGGGTTAAAATGTAATTTCAGAAAAA-TTTAGGGGTTAAAAT
*
31919802 GTAATTTTTAAAGAAA-ATGA-AATTTG
65 ATAA-TTTT-AAGAAACATGAGAATTTG
31919828 A
1 A
31919829 TCCAAAAAAT
Statistics
Matches: 78, Mismatches: 10, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
89 4 0.05
90 63 0.81
91 6 0.08
92 5 0.06
ACGTcount: A:0.43, C:0.01, G:0.19, T:0.37
Consensus pattern (90 bp):
AAATGTAATTTTAGAAAAGTTTAAGGGTTAAAATGTAATTTCAGAAAAATTTAGGGGTTAAAATA
TAATTTTAAGAAACATGAGAATTTG
Found at i:31920584 original size:16 final size:16
Alignment explanation
Indices: 31920563--31920632 Score: 104
Period size: 16 Copynumber: 4.4 Consensus size: 16
31920553 TTTGGTTCGC
* *
31920563 TGTATTGGATTAGAGG
1 TGTAATGGAATAGAGG
* *
31920579 TGTATTGGATTAGAGG
1 TGTAATGGAATAGAGG
31920595 TGTAATGGAATAGAGG
1 TGTAATGGAATAGAGG
31920611 TGTAATGGAATAGAGG
1 TGTAATGGAATAGAGG
31920627 TGTAAT
1 TGTAAT
31920633 AGCAAATCAA
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 52 1.00
ACGTcount: A:0.31, C:0.00, G:0.36, T:0.33
Consensus pattern (16 bp):
TGTAATGGAATAGAGG
Found at i:31921223 original size:47 final size:47
Alignment explanation
Indices: 31921091--31921229 Score: 128
Period size: 47 Copynumber: 3.0 Consensus size: 47
31921081 TACGATTTAC
* *
31921091 ATATAATTTAATAATAATATATAATTTCATAAAATTATTGATAAT-A
1 ATATAATTTAATAATGATATATAATTTCATAAAATTATTAATAATAA
** * * * *
31921137 AT-T--TTTCTTATATGAATTTATACAATT--TAAAATAATTAATATTAA
1 ATATAATTTAATA-ATG-ATATATA-ATTTCATAAAATTATTAATAATAA
*
31921182 ATATAATTTAATAATGATATATAATTTCATAAAATTCTTAATAATAA
1 ATATAATTTAATAATGATATATAATTTCATAAAATTATTAATAATAA
31921229 A
1 A
31921230 ATGTTCTTAT
Statistics
Matches: 69, Mismatches: 15, Indels: 17
0.68 0.15 0.17
Matches are distributed among these distances:
43 5 0.07
44 15 0.22
45 13 0.19
46 12 0.17
47 19 0.28
48 5 0.07
ACGTcount: A:0.50, C:0.04, G:0.02, T:0.45
Consensus pattern (47 bp):
ATATAATTTAATAATGATATATAATTTCATAAAATTATTAATAATAA
Found at i:31924393 original size:36 final size:37
Alignment explanation
Indices: 31924350--31924435 Score: 129
Period size: 36 Copynumber: 2.4 Consensus size: 37
31924340 AAGAAACGGG
* *
31924350 GGGAGCAAATCGGCAGAAAAGAAAAGAAAATAAAC-T
1 GGGAGCAAATCGGCAGAAAAGAAAAGAAAAGAAACAA
*
31924386 GGGAGCAAATCGGCAGAAAAGAAAAGCAAAGAAACAA
1 GGGAGCAAATCGGCAGAAAAGAAAAGAAAAGAAACAA
*
31924423 GGAAGCAAATCGG
1 GGGAGCAAATCGG
31924436 ATGAAGGTAG
Statistics
Matches: 45, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
36 33 0.73
37 12 0.27
ACGTcount: A:0.53, C:0.13, G:0.28, T:0.06
Consensus pattern (37 bp):
GGGAGCAAATCGGCAGAAAAGAAAAGAAAAGAAACAA
Found at i:31930369 original size:43 final size:43
Alignment explanation
Indices: 31930295--31930382 Score: 106
Period size: 43 Copynumber: 2.0 Consensus size: 43
31930285 AAAATCTGAA
* * *
31930295 TATGCAATGCAATTTACTATTACATTTAAATAAT-TTAATTTTT
1 TATGCAATGCAATTTACAATTACACTAAAATAATCTT-ATTTTT
* * *
31930338 TATGGAATGTAATTTACAATTATACTAAAATAATCTTATTTTT
1 TATGCAATGCAATTTACAATTACACTAAAATAATCTTATTTTT
31930381 TA
1 TA
31930383 ATTAATATTA
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
43 36 0.95
44 2 0.05
ACGTcount: A:0.39, C:0.08, G:0.06, T:0.48
Consensus pattern (43 bp):
TATGCAATGCAATTTACAATTACACTAAAATAATCTTATTTTT
Found at i:31931622 original size:17 final size:16
Alignment explanation
Indices: 31931588--31931618 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
31931578 CCCCCTTACT
*
31931588 TTCCCTCAAACTTTTA
1 TTCCCTAAAACTTTTA
31931604 TTCCCTAAAACTTTT
1 TTCCCTAAAACTTTT
31931619 TATTTTTCCT
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:0.26, C:0.29, G:0.00, T:0.45
Consensus pattern (16 bp):
TTCCCTAAAACTTTTA
Found at i:31932895 original size:14 final size:14
Alignment explanation
Indices: 31932876--31932902 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
31932866 ATTATACTTC
31932876 TTTTATATTTTATG
1 TTTTATATTTTATG
31932890 TTTTATATTTTAT
1 TTTTATATTTTAT
31932903 ACATATATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.22, C:0.00, G:0.04, T:0.74
Consensus pattern (14 bp):
TTTTATATTTTATG
Found at i:31934057 original size:16 final size:16
Alignment explanation
Indices: 31934036--31934072 Score: 74
Period size: 16 Copynumber: 2.3 Consensus size: 16
31934026 TTGGTTCGCT
31934036 GTAATGGAATAGAGGC
1 GTAATGGAATAGAGGC
31934052 GTAATGGAATAGAGGC
1 GTAATGGAATAGAGGC
31934068 GTAAT
1 GTAAT
31934073 AGGTAATTCT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.38, C:0.05, G:0.35, T:0.22
Consensus pattern (16 bp):
GTAATGGAATAGAGGC
Found at i:31934141 original size:44 final size:46
Alignment explanation
Indices: 31934052--31934142 Score: 159
Period size: 46 Copynumber: 2.0 Consensus size: 46
31934042 GAATAGAGGC
*
31934052 GTAATGGAATAGAGGCGTAATAGGTAATTCTTTTGTTTGGTTGAAT
1 GTAATGGAATAGAGGCGTAATAGGTAATTCTTGTGTTTGGTTGAAT
31934098 GTAATGGAATAGAGGCGTAAT-GGT-ATTCTTGTGTTTGGTTGAAT
1 GTAATGGAATAGAGGCGTAATAGGTAATTCTTGTGTTTGGTTGAAT
31934142 G
1 G
31934143 GAATAGAGGT
Statistics
Matches: 44, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
44 20 0.45
45 3 0.07
46 21 0.48
ACGTcount: A:0.26, C:0.04, G:0.31, T:0.38
Consensus pattern (46 bp):
GTAATGGAATAGAGGCGTAATAGGTAATTCTTGTGTTTGGTTGAAT
Found at i:31934143 original size:39 final size:44
Alignment explanation
Indices: 31934052--31934159 Score: 145
Period size: 46 Copynumber: 2.5 Consensus size: 44
31934042 GAATAGAGGC
*
31934052 GTAATGGAATAGAGGCGTAATAGGTAATTCTTTTGTTTGGTTGAAT
1 GTAATGGAATAGAGGCGTAATAGGTAATTCTTGTGTTTGGTT--AT
31934098 GTAATGGAATAGAGGCGTAAT-GGT-ATTCTTGTGTTTGG-T-T
1 GTAATGGAATAGAGGCGTAATAGGTAATTCTTGTGTTTGGTTAT
*
31934138 G-AATGGAATAGAGGTGTAATAG
1 GTAATGGAATAGAGGCGTAATAG
31934160 CATAAGGAAA
Statistics
Matches: 59, Mismatches: 2, Indels: 8
0.86 0.03 0.12
Matches are distributed among these distances:
39 18 0.31
40 3 0.05
43 1 0.02
44 13 0.22
45 3 0.05
46 21 0.36
ACGTcount: A:0.29, C:0.04, G:0.31, T:0.36
Consensus pattern (44 bp):
GTAATGGAATAGAGGCGTAATAGGTAATTCTTGTGTTTGGTTAT
Found at i:31934321 original size:15 final size:15
Alignment explanation
Indices: 31934301--31934339 Score: 60
Period size: 17 Copynumber: 2.5 Consensus size: 15
31934291 CATAATTGTT
31934301 ATAAAATATAATTTA
1 ATAAAATATAATTTA
31934316 ATAAAATATATAATTTA
1 AT-AAA-ATATAATTTA
31934333 ATAAAAT
1 ATAAAAT
31934340 TGTTAATAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
15 4 0.18
16 6 0.27
17 12 0.55
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (15 bp):
ATAAAATATAATTTA
Found at i:31934346 original size:17 final size:17
Alignment explanation
Indices: 31934306--31934339 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
31934296 TTGTTATAAA
31934306 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
31934323 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
31934340 TGTTAATAAA
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:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:31934411 original size:20 final size:21
Alignment explanation
Indices: 31934372--31934411 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
31934362 AATTTACTAA
*
31934372 TAAAATCATAATATATAATAC
1 TAAAATCATAATATAAAATAC
*
31934393 TAAAAT-ATAATTTAAAATA
1 TAAAATCATAATATAAAATA
31934412 ATTATTATTA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 11 0.65
21 6 0.35
ACGTcount: A:0.60, C:0.05, G:0.00, T:0.35
Consensus pattern (21 bp):
TAAAATCATAATATAAAATAC
Found at i:31934424 original size:26 final size:28
Alignment explanation
Indices: 31934395--31934458 Score: 96
Period size: 26 Copynumber: 2.4 Consensus size: 28
31934385 TATAATACTA
*
31934395 AAATATAATTTAA-AATAATTATT-ATT
1 AAATATAATTTAATAATAATAATTAATT
31934421 AAATATAATTTAATAATAATAATTAATT
1 AAATATAATTTAATAATAATAATTAATT
*
31934449 AAATAAAATT
1 AAATATAATT
31934459 CTTATTCTTA
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
26 13 0.38
27 9 0.26
28 12 0.35
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (28 bp):
AAATATAATTTAATAATAATAATTAATT
Found at i:31934427 original size:117 final size:109
Alignment explanation
Indices: 31934286--31934542 Score: 306
Period size: 117 Copynumber: 2.3 Consensus size: 109
31934276 TTAATCATAT
* * * *
31934286 TTTAACATAATTGTTATAAAATATAATTTAATAA-AAT-ATATAATTTAATAAAATTGTTAATAA
1 TTTAAAATAATTATTATTAAATATAATTTAATAATAATAAT-TAATTAAATAAAA---TT-AT--
31934349 ATATTCTTATATAAATTTACTAATAAAATCATAATATATAATAC-TAAAATATAA
59 -TATTCTTATATAAATTTAC---TAAAATCATAATATATAATACATAAAATATAA
*
31934403 TTTAAAATAATTATTATTAAATATAATTTAATAATAATAATTAATTAAATAAAATTCTTATTCTT
1 TTTAAAATAATTATTATTAAATATAATTTAATAATAATAATTAATTAAATAAAATTATTATTCTT
*
31934468 ATATGAATTTACTAAAATCATAATATATAATACTATAAAATATAA
66 ATATAAATTTACTAAAATCATAATATATAATAC-ATAAAATATAA
*
31934513 TTT-AAATAATTATTATTATAATATACTTTA
1 TTTAAAATAATTATTATTA-AATATAATTTA
31934543 TTATTATTAA
Statistics
Matches: 128, Mismatches: 7, Indels: 17
0.84 0.05 0.11
Matches are distributed among these distances:
108 21 0.16
109 15 0.12
110 23 0.18
111 18 0.14
114 1 0.01
115 2 0.02
117 31 0.24
118 15 0.12
119 2 0.02
ACGTcount: A:0.51, C:0.04, G:0.01, T:0.43
Consensus pattern (109 bp):
TTTAAAATAATTATTATTAAATATAATTTAATAATAATAATTAATTAAATAAAATTATTATTCTT
ATATAAATTTACTAAAATCATAATATATAATACATAAAATATAA
Found at i:31935965 original size:49 final size:49
Alignment explanation
Indices: 31935893--31935996 Score: 145
Period size: 49 Copynumber: 2.1 Consensus size: 49
31935883 AGAAAAAAAC
* * ** * *
31935893 AAATTAAAATTAAGTTTAATATCATGAATCAAAAGGTGAACACTTTATA
1 AAATTAAAATTAAGTTCAATATCATGAATAAAAAACTCAACACTGTATA
*
31935942 AAATTAAAATTGAGTTCAATATCATGAATAAAAAACTCAACACTGTATA
1 AAATTAAAATTAAGTTCAATATCATGAATAAAAAACTCAACACTGTATA
31935991 AAATTA
1 AAATTA
31935997 TAACATATGA
Statistics
Matches: 48, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
49 48 1.00
ACGTcount: A:0.51, C:0.10, G:0.09, T:0.31
Consensus pattern (49 bp):
AAATTAAAATTAAGTTCAATATCATGAATAAAAAACTCAACACTGTATA
Done.