Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007763.1 Hibiscus syriacus cultivar Beakdansim tig00110034_pilon, whole genome shotgun sequence
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: 397934
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 2
Found at i:254163 original size:31 final size:29
Alignment explanation
Indices: 254126--254187 Score: 81
Period size: 31 Copynumber: 2.1 Consensus size: 29
254116 TTTTTACTAC
254126 ATATAATTA-AATTAAAATAAAAATATTATGT
1 ATATAATTACAA-T-AAATAAAAAT-TTATGT
*
254157 ATATAATTACAATAAATTAAAATTTATGT
1 ATATAATTACAATAAATAAAAATTTATGT
254186 AT
1 AT
254188 TACACCAAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
29 8 0.28
30 9 0.31
31 10 0.34
32 2 0.07
ACGTcount: A:0.55, C:0.02, G:0.03, T:0.40
Consensus pattern (29 bp):
ATATAATTACAATAAATAAAAATTTATGT
Found at i:258289 original size:24 final size:24
Alignment explanation
Indices: 258247--258305 Score: 66
Period size: 24 Copynumber: 2.5 Consensus size: 24
258237 CAACCCAATT
* *
258247 TGACTGACCCGACCTGGTCTGACCC
1 TGACTG-CCTGACCCGGTCTGACCC
*
258272 TGACTGCCTGACCCGGTCTTACCC
1 TGACTGCCTGACCCGGTCTGACCC
*
258296 -GACTCCCTGA
1 TGACTGCCTGA
258306 TCCGATCCAA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
23 9 0.30
24 15 0.50
25 6 0.20
ACGTcount: A:0.15, C:0.41, G:0.22, T:0.22
Consensus pattern (24 bp):
TGACTGCCTGACCCGGTCTGACCC
Found at i:263393 original size:2 final size:2
Alignment explanation
Indices: 263386--263427 Score: 75
Period size: 2 Copynumber: 21.0 Consensus size: 2
263376 AACTGGTTTG
*
263386 AT AT AT AT GT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
263428 GTGGAATTTA
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (2 bp):
AT
Found at i:267905 original size:69 final size:69
Alignment explanation
Indices: 267750--267975 Score: 184
Period size: 69 Copynumber: 3.3 Consensus size: 69
267740 TGTTCCCTTG
* * * * *
267750 TGAGTCACTCTAATCCTTCGGAGCTCCCGTGCAAGTGAACCGAAGTAATTATGATTAGGTGCTCC
1 TGAGTCACTCTAATCCTTCGGGGCTCCCGTACAAGTCAACCGAAATAATAATGATTAGGTGCTCC
*
267815 CGTG
66 CGTA
** * * * * * *
267819 CAAGTTACCCTAATCCTTCGGGGCTCCTGTACAAGTCACCCTAAATAATAATGATTAGGTTCTCC
1 TGAGTCACTCTAATCCTTCGGGGCTCCCGTACAAGTCAACCGAAATAATAATGATTAGGTGCTCC
*
267884 TGTA
66 CGTA
* * ** * * * * * *
267888 TGAGTCACTCTATTCCTTAGGGGCTTTCATGCGAGT-AACCAAGAATAATCACGATTAGGTGCTC
1 TGAGTCACTCTAATCCTTCGGGGCTCCCGTACAAGTCAACCGA-AATAATAATGATTAGGTGCTC
* *
267952 CCTTG
65 CCGTA
*
267957 CGAGTCACTCTAATCCTTC
1 TGAGTCACTCTAATCCTTC
267976 AAGGCTCATG
Statistics
Matches: 118, Mismatches: 38, Indels: 2
0.75 0.24 0.01
Matches are distributed among these distances:
68 4 0.03
69 114 0.97
ACGTcount: A:0.25, C:0.26, G:0.20, T:0.30
Consensus pattern (69 bp):
TGAGTCACTCTAATCCTTCGGGGCTCCCGTACAAGTCAACCGAAATAATAATGATTAGGTGCTCC
CGTA
Found at i:279905 original size:13 final size:13
Alignment explanation
Indices: 279889--279913 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
279879 CCGTTGACGT
279889 TTGACTTTGACCG
1 TTGACTTTGACCG
279902 TTGACTTTGACC
1 TTGACTTTGACC
279914 AAAAAGTAAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.16, C:0.24, G:0.20, T:0.40
Consensus pattern (13 bp):
TTGACTTTGACCG
Found at i:281626 original size:24 final size:24
Alignment explanation
Indices: 281561--281630 Score: 77
Period size: 24 Copynumber: 2.9 Consensus size: 24
281551 CTTGACCTGG
* * * *
281561 ATTCTATTTTGATTTCTAATCTGG
1 ATTCTGTTTTGATTTCTGATATGA
* * *
281585 ATTATGTTCTGATATCTGATATGA
1 ATTCTGTTTTGATTTCTGATATGA
281609 ATTCTGTTTTGATTTCTGATAT
1 ATTCTGTTTTGATTTCTGATAT
281631 CTACGTTTAT
Statistics
Matches: 36, Mismatches: 10, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
24 36 1.00
ACGTcount: A:0.23, C:0.10, G:0.14, T:0.53
Consensus pattern (24 bp):
ATTCTGTTTTGATTTCTGATATGA
Found at i:283755 original size:14 final size:15
Alignment explanation
Indices: 283723--283762 Score: 64
Period size: 14 Copynumber: 2.7 Consensus size: 15
283713 TGTACCCGAT
283723 TGAGTCAACTCGTGC
1 TGAGTCAACTCGTGC
*
283738 TGAGTTAACTCG-GC
1 TGAGTCAACTCGTGC
283752 TGAGTCAACTC
1 TGAGTCAACTC
283763 ACTAGGTCAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
14 12 0.52
15 11 0.48
ACGTcount: A:0.23, C:0.25, G:0.25, T:0.28
Consensus pattern (15 bp):
TGAGTCAACTCGTGC
Found at i:285925 original size:24 final size:24
Alignment explanation
Indices: 285887--285974 Score: 95
Period size: 24 Copynumber: 3.7 Consensus size: 24
285877 ATTAAATTTT
* *
285887 TGTTCTGATACCTGACCTGAATTC
1 TGTTCTGATATCTGATCTGAATTC
* * *
285911 TATTCTGATTTCTGATCTGGATTC
1 TGTTCTGATATCTGATCTGAATTC
* *
285935 TGTTATGATATCTGATATGAATTC
1 TGTTCTGATATCTGATCTGAATTC
* *
285959 TGTTTTGATTTCTGAT
1 TGTTCTGATATCTGAT
285975 ATCTCTATTT
Statistics
Matches: 52, Mismatches: 12, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
24 52 1.00
ACGTcount: A:0.20, C:0.15, G:0.17, T:0.48
Consensus pattern (24 bp):
TGTTCTGATATCTGATCTGAATTC
Found at i:285929 original size:12 final size:12
Alignment explanation
Indices: 285916--285976 Score: 52
Period size: 12 Copynumber: 5.1 Consensus size: 12
285906 AATTCTATTC
*
285916 TGATTTCTGATC
1 TGATTTCTGATA
*
285928 TGGA-TTCTGTTA
1 T-GATTTCTGATA
*
285940 TGATATCTGATA
1 TGATTTCTGATA
* * *
285952 TGAATTCTGTTT
1 TGATTTCTGATA
285964 TGATTTCTGATA
1 TGATTTCTGATA
285976 T
1 T
285977 CTCTATTTAT
Statistics
Matches: 36, Mismatches: 11, Indels: 4
0.71 0.22 0.08
Matches are distributed among these distances:
11 2 0.06
12 32 0.89
13 2 0.06
ACGTcount: A:0.21, C:0.10, G:0.18, T:0.51
Consensus pattern (12 bp):
TGATTTCTGATA
Found at i:292608 original size:69 final size:69
Alignment explanation
Indices: 292454--292667 Score: 214
Period size: 69 Copynumber: 3.1 Consensus size: 69
292444 TACGATAATA
* * * *
292454 TGCTCCCTTGTGAGTCACTCTAATCCTTCAGAACTCCCGTGCGAGTCAATCGAAATAATTTCGAT
1 TGCTCCCATGTGAGTCACTCTAATCCTTCAGAACTCCCGTGCAAGTCAACCGAAATAATTACGAT
292519 TAGG
66 TAGG
* ** * * * *
292523 TGGTCCCATGCAAGTCACTCTAATCCTTCGGAGCTCCTGTGCAAGTCACCCGAAATAATTACGAT
1 TGCTCCCATGTGAGTCACTCTAATCCTTCAGAACTCCCGTGCAAGTCAACCGAAATAATTACGAT
292588 TAGG
66 TAGG
* * * ** * ** * * *
292592 TGCTTCCGTGTGAGTCACTCTATTCCTTTGGGACTTTCGTGCGAGT-AACCAAGAATAATCACGA
1 TGCTCCCATGTGAGTCACTCTAATCCTTCAGAACTCCCGTGCAAGTCAACCGA-AATAATTACGA
292656 TTAGG
65 TTAGG
292661 TGCTCCC
1 TGCTCCC
292668 TTGCAAGTGA
Statistics
Matches: 116, Mismatches: 28, Indels: 2
0.79 0.19 0.01
Matches are distributed among these distances:
68 4 0.03
69 112 0.97
ACGTcount: A:0.24, C:0.26, G:0.21, T:0.29
Consensus pattern (69 bp):
TGCTCCCATGTGAGTCACTCTAATCCTTCAGAACTCCCGTGCAAGTCAACCGAAATAATTACGAT
TAGG
Found at i:292999 original size:76 final size:76
Alignment explanation
Indices: 292819--293233 Score: 484
Period size: 76 Copynumber: 5.5 Consensus size: 76
292809 TCTAGCAGAA
* * * * *
292819 AAACTTAACATCGACTTATACCAGTGAAATGAATACATAATTCTAGCACTAAACTTAT--GAT--
1 AAACTTAACATTGACTTACACCAGTGAAATGAATACGTAATTCAAGCACTAAACTTATCACATAA
**
292880 TT-CAGGAGTG
66 TTCCAACAGTG
* ** *
292890 AAACTTAACATTGACTTACACCAGTGAAATGAATACATAATTCAATAACTAAACTTATCACATCA
1 AAACTTAACATTGACTTACACCAGTGAAATGAATACGTAATTCAAGCACTAAACTTATCACATAA
* * *
292955 TTTCAGCAATG
66 TTCCAACAGTG
* * * **
292966 -AACTCTAACATTGACTTACACCAGTAAAATGAATACGTAATTCCAGCGCTAAACTTAAAACATA
1 AAACT-TAACATTGACTTACACCAGTGAAATGAATACGTAATTCAAGCACTAAACTTATCACATA
293030 ATTCCAACAGTG
65 ATTCCAACAGTG
* * *
293042 AAACTTAACATTGACTTACACCAGTGAAATTAATACGTAATTCCAGCACTAGACTTATCACATAA
1 AAACTTAACATTGACTTACACCAGTGAAATGAATACGTAATTCAAGCACTAAACTTATCACATAA
* *
293107 TTCCATCAATG
66 TTCCAACAGTG
* * * *
293118 AAATTTAACATTGACTTAAACCAGTAAAATGAATACGTAATTCCAA-CACTAAACTTATCATATA
1 AAACTTAACATTGACTTACACCAGTGAAATGAATACGTAATT-CAAGCACTAAACTTATCACATA
293182 ATTCCAACAGTG
65 ATTCCAACAGTG
* **
293194 AAACTTAACATTGGCTTACATTAGTGAAATGAATACGTAA
1 AAACTTAACATTGACTTACACCAGTGAAATGAATACGTAA
293234 CTCGAGTTAC
Statistics
Matches: 293, Mismatches: 43, Indels: 11
0.84 0.12 0.03
Matches are distributed among these distances:
71 53 0.18
73 2 0.01
75 6 0.02
76 226 0.77
77 6 0.02
ACGTcount: A:0.42, C:0.19, G:0.10, T:0.28
Consensus pattern (76 bp):
AAACTTAACATTGACTTACACCAGTGAAATGAATACGTAATTCAAGCACTAAACTTATCACATAA
TTCCAACAGTG
Found at i:293226 original size:228 final size:223
Alignment explanation
Indices: 292819--293233 Score: 537
Period size: 228 Copynumber: 1.8 Consensus size: 223
292809 TCTAGCAGAA
* * *
292819 AAACTTAACATCGACTTATACCAGTGAAATGAATACATAATTCTAGCACTAAACTTATGATTTCA
1 AAACTTAACATCGACTTACACCAGTGAAATGAATACATAATTCCAGCACTAAACTTATCATTTCA
* * * *
292884 GGAGTGAAACTTAACATTGACTTACACCAGTGAAATGAATACATAATTCAATAACTAAACTTATC
66 GCAATGAAACTTAACATTGACTTAAACCAGTAAAATGAATACATAATTCAATAACTAAACTTATC
* * *
292949 ACATCATTTCAGCAATGAACTCTAACATTGACTTACACCAGTAAAATGAATACGTAATTCCAGCG
131 ACATAATTCCAACAATGAACTCTAACATTGACTTACACCAGTAAAATGAATACGTAATTCCAGCG
293014 CTAAACTTAAAACATAATTCCAACAGTG
196 CTAAACTTAAAACATAATTCCAACAGTG
* * * *
293042 AAACTTAACATTGACTTACACCAGTGAAATTAATACGTAATTCCAGCACTAGACTTATCACATAA
1 AAACTTAACATCGACTTACACCAGTGAAATGAATACATAATTCCAGCACTAAACTTAT--CAT--
* * * *
293107 TTCCATCAATGAAATTTAACATTGACTTAAACCAGTAAAATGAATACGTAATTCCAA-CACTAAA
62 TT-CAGCAATGAAACTTAACATTGACTTAAACCAGTAAAATGAATACATAATT-CAATAACTAAA
* * * ** *
293171 CTTATCATATAATTCCAACAGTGAAACT-TAACATTGGCTTACATTAGTGAAATGAATACGTAA
125 CTTATCACATAATTCCAACAATG-AACTCTAACATTGACTTACACCAGTAAAATGAATACGTAA
293234 CTCGAGTTAC
Statistics
Matches: 161, Mismatches: 24, Indels: 9
0.83 0.12 0.05
Matches are distributed among these distances:
223 52 0.32
225 2 0.01
227 2 0.01
228 98 0.61
229 7 0.04
ACGTcount: A:0.42, C:0.19, G:0.10, T:0.28
Consensus pattern (223 bp):
AAACTTAACATCGACTTACACCAGTGAAATGAATACATAATTCCAGCACTAAACTTATCATTTCA
GCAATGAAACTTAACATTGACTTAAACCAGTAAAATGAATACATAATTCAATAACTAAACTTATC
ACATAATTCCAACAATGAACTCTAACATTGACTTACACCAGTAAAATGAATACGTAATTCCAGCG
CTAAACTTAAAACATAATTCCAACAGTG
Found at i:293265 original size:183 final size:183
Alignment explanation
Indices: 293057--293412 Score: 516
Period size: 183 Copynumber: 1.9 Consensus size: 183
293047 TAACATTGAC
* * * *
293057 TTACACCAGTGAAATTAATACGTAATTCCAGCACTAGACTTATCACATAATTC-CATCAATGAAA
1 TTACACCAGTGAAATGAATACGTAATTACAGCACTAAACTTATCACATAATTCTC-GCAATGAAA
* *
293121 TTTAACATTGACTTAAACCAGTAAAATGAATACGTAATTCCAACACTAAACTTATCATATAATTC
65 TTTAACATTGACTTAAACCAGTAAAACGAATACGTAATTCCAACACTAAACTTATCACATAATTC
* * *
293186 CAACAGTGAAACTTAACATTGGCTTACATTAGTGAAATGAATACGTAACTCGAG
130 CAACAGTGAAACTTAACATTGACTTACATCAGCGAAATGAATACGTAACTCGAG
* * * *
293240 TTACATCAGTGAAATGAATACGTAATTATAGCACTAAACTTATCACATAATTCTCGCAGTGTAAT
1 TTACACCAGTGAAATGAATACGTAATTACAGCACTAAACTTATCACATAATTCTCGCAATGAAAT
* * * *
293305 TTAACATTGACTTACACCAGTGAAACGAATACGTAATTTCAGCACTAAACTTATCACATAATTCC
66 TTAACATTGACTTAAACCAGTAAAACGAATACGTAATTCCAACACTAAACTTATCACATAATTCC
***
293370 TGTAGTGAAACTTAACATTGACTTACATCAGCGAAATGAATAC
131 AACAGTGAAACTTAACATTGACTTACATCAGCGAAATGAATAC
293413 ATAATTCCAG
Statistics
Matches: 152, Mismatches: 20, Indels: 2
0.87 0.11 0.01
Matches are distributed among these distances:
183 151 0.99
184 1 0.01
ACGTcount: A:0.40, C:0.19, G:0.12, T:0.29
Consensus pattern (183 bp):
TTACACCAGTGAAATGAATACGTAATTACAGCACTAAACTTATCACATAATTCTCGCAATGAAAT
TTAACATTGACTTAAACCAGTAAAACGAATACGTAATTCCAACACTAAACTTATCACATAATTCC
AACAGTGAAACTTAACATTGACTTACATCAGCGAAATGAATACGTAACTCGAG
Found at i:293275 original size:107 final size:107
Alignment explanation
Indices: 293139--293340 Score: 280
Period size: 107 Copynumber: 1.9 Consensus size: 107
293129 TGACTTAAAC
* *
293139 CAGTAAAATGAATACGTAATTCCAACACTAAACTTATCATATAATTC-CAACAGTGAAACTTAAC
1 CAGTAAAATGAATACGTAATTACAACACTAAACTTATCACATAATTCTC-ACAGTGAAACTTAAC
* ** *
293203 ATTGGCTTACATTAGTGAAATGAATACGTAACTCGAGTTACAT
65 ATTGACTTACACCAGTGAAACGAATACGTAACTCGAGTTACAT
* * * * * *
293246 CAGTGAAATGAATACGTAATTATAGCACTAAACTTATCACATAATTCTCGCAGTGTAATTTAACA
1 CAGTAAAATGAATACGTAATTACAACACTAAACTTATCACATAATTCTCACAGTGAAACTTAACA
293311 TTGACTTACACCAGTGAAACGAATACGTAA
66 TTGACTTACACCAGTGAAACGAATACGTAA
293341 TTTCAGCACT
Statistics
Matches: 82, Mismatches: 12, Indels: 2
0.85 0.12 0.02
Matches are distributed among these distances:
107 81 0.99
108 1 0.01
ACGTcount: A:0.41, C:0.18, G:0.13, T:0.29
Consensus pattern (107 bp):
CAGTAAAATGAATACGTAATTACAACACTAAACTTATCACATAATTCTCACAGTGAAACTTAACA
TTGACTTACACCAGTGAAACGAATACGTAACTCGAGTTACAT
Found at i:293335 original size:76 final size:76
Alignment explanation
Indices: 293240--293582 Score: 420
Period size: 76 Copynumber: 4.5 Consensus size: 76
293230 GTAACTCGAG
* ** * *
293240 TTACATCAGTGAAATGAATACGTAATTATAGCACTAAACTTATCACATAATTCTC-GCAGTGTAA
1 TTACACCAGTGAAATGAATACGTAATTCCAGCACTAAACTTATCACATAATTC-CAGTAGTGAAA
*
293304 TTTAACATTGAC
65 CTTAACATTGAC
* * *
293316 TTACACCAGTGAAACGAATACGTAATTTCAGCACTAAACTTATCACATAATTCCTGTAGTGAAAC
1 TTACACCAGTGAAATGAATACGTAATTCCAGCACTAAACTTATCACATAATTCCAGTAGTGAAAC
293381 TTAACATTGAC
66 TTAACATTGAC
* * * * **
293392 TTACATCAGCGAAATGAATACATAATTCCAGCATTAAAAATAT-ATCATAATTCCAGTAGTGAAA
1 TTACACCAGTGAAATGAATACGTAATTCCAGCACTAAACTTATCA-CATAATTCCAGTAGTGAAA
*
293456 CTTAACATCGAC
65 CTTAACATTGAC
* * * * * *
293468 TTAAACCAGTGAAATGAATACGTAATTCCAGCACTACACTTTTCACATAAGTCAAGGAGTGAAAC
1 TTACACCAGTGAAATGAATACGTAATTCCAGCACTAAACTTATCACATAATTCCAGTAGTGAAAC
*
293533 TGAACATTGAC
66 TTAACATTGAC
* * *
293544 TTAGACTAGTGAAATGAATACGTAATTCCAGCATTAAAC
1 TTACACCAGTGAAATGAATACGTAATTCCAGCACTAAAC
293583 ATATGATTTC
Statistics
Matches: 229, Mismatches: 35, Indels: 6
0.85 0.13 0.02
Matches are distributed among these distances:
75 2 0.01
76 226 0.99
77 1 0.00
ACGTcount: A:0.40, C:0.19, G:0.13, T:0.29
Consensus pattern (76 bp):
TTACACCAGTGAAATGAATACGTAATTCCAGCACTAAACTTATCACATAATTCCAGTAGTGAAAC
TTAACATTGAC
Found at i:293455 original size:259 final size:259
Alignment explanation
Indices: 292981--293492 Score: 679
Period size: 259 Copynumber: 2.0 Consensus size: 259
292971 TAACATTGAC
* *
292981 TTACACCAGTAAAATGAATACGTAATTCCAGCGCTAAACTTAAAACATAATTCCAACAGTGAAAC
1 TTACACCAGTAAAATGAATACGTAATTACAGCACTAAACTTAAAACATAATTCCAACAGTGAAAC
** *
293046 TTAACATTGACTTACACCAGTGAAATTAATACGTAATTCCAGCACTAGACTTATCACATAATTCC
66 TTAACATTGACTTACACCAGTGAAACGAATACGTAATTCCAGCACTAAACTTATCACATAATTCC
* * * **
293111 ATCAATGAAATTTAACATTGACTTAAACCAGTAAAATGAATACGTAATTCCAACACTAAACTTAT
131 ATCAATGAAACTTAACATTGACTTAAACCAGCAAAATGAATACATAATTCCAACACTAAAAATAT
* * * **
293176 CATATAATTCCAACAGTGAAACTTAACATTGGCTTACATTAGTGAAATGAATACGTAACTCGAG
196 CATATAATTCCAACAGTGAAACTTAACATCGACTTAAACCAGTGAAATGAATACGTAACTCGAG
* * * ** * *
293240 TTACATCAGTGAAATGAATACGTAATTATAGCACTAAACTTATCACATAATTCTC-GCAGTGTAA
1 TTACACCAGTAAAATGAATACGTAATTACAGCACTAAACTTAAAACATAATTC-CAACAGTGAAA
* *
293304 TTTAACATTGACTTACACCAGTGAAACGAATACGTAATTTCAGCACTAAACTTATCACATAATTC
65 CTTAACATTGACTTACACCAGTGAAACGAATACGTAATTCCAGCACTAAACTTATCACATAATTC
* * * * * * *
293369 C-TGTAGTGAAACTTAACATTGACTTACATCAGCGAAATGAATACATAATTCCAGCATTAAAAAT
130 CAT-CAATGAAACTTAACATTGACTTAAACCAGCAAAATGAATACATAATTCCAACACTAAAAAT
**
293433 AT-ATCATAATTCCAGTAGTGAAACTTAACATCGACTTAAACCAGTGAAATGAATACGTAA
194 ATCAT-ATAATTCCAACAGTGAAACTTAACATCGACTTAAACCAGTGAAATGAATACGTAA
293493 TTCCAGCACT
Statistics
Matches: 217, Mismatches: 33, Indels: 6
0.85 0.13 0.02
Matches are distributed among these distances:
258 3 0.01
259 213 0.98
260 1 0.00
ACGTcount: A:0.41, C:0.19, G:0.11, T:0.29
Consensus pattern (259 bp):
TTACACCAGTAAAATGAATACGTAATTACAGCACTAAACTTAAAACATAATTCCAACAGTGAAAC
TTAACATTGACTTACACCAGTGAAACGAATACGTAATTCCAGCACTAAACTTATCACATAATTCC
ATCAATGAAACTTAACATTGACTTAAACCAGCAAAATGAATACATAATTCCAACACTAAAAATAT
CATATAATTCCAACAGTGAAACTTAACATCGACTTAAACCAGTGAAATGAATACGTAACTCGAG
Found at i:293531 original size:335 final size:334
Alignment explanation
Indices: 292905--293568 Score: 890
Period size: 335 Copynumber: 2.0 Consensus size: 334
292895 TAACATTGAC
*
292905 TTACACCAGTGAAATGAATACATAATTCAATAACTAAACTTATCACATCATTTCAGCAATGAACT
1 TTACACCAGTGAAATGAATACATAATT-AATAACTAAACTTATCACATAATTTCAGCAATGAACT
* *
292970 CTAACATTGACTTACACCAGTAAAATGAATACGTAATTCCAGCGCTAAACTTAAAACATAATTCC
65 CTAACATTGACTTACACCAGTAAAACGAATACGTAATTCCAGCACTAAACTTAAAACATAATTCC
* * * * **
293035 AACAGTGAAACTTAACATTGACTTACACCAGTGAAATTAATACGTAATTCCAGCACTAGACTTAT
130 AACAGTGAAACTTAACATTGACTTACACCAGCGAAATGAATACATAATTCCAGCACTAAAAATAT
* *
293100 CACATAATTCCATCAATGAAATTTAACATTGACTTAAACCAGTAAAATGAATACGTAATTCCAAC
195 CACATAATTCCATCAATGAAACTTAACATCGACTTAAACCAGTAAAATGAATACGTAATTCCAAC
* * * * *
293165 ACTAAACTTATCATATAATTCCAACAGTGAAACTTAACATTGGCTTACATTAGTGAAATGAATAC
260 ACTAAACTTATCACATAAGTCCAACAGTGAAACTGAACATTGACTTACACTAGTGAAATGAATAC
293230 GTAACTCGAG
325 GTAACTCGAG
* * *
293240 TTACATCAGTGAAATGAATACGTAATT-ATAGCACTAAACTTATCACATAATTCTC-GCAGTGTA
1 TTACACCAGTGAAATGAATACATAATTAATA--ACTAAACTTATCACATAATT-TCAGCAATG-A
* * * **
293303 A-TTTAACATTGACTTACACCAGTGAAACGAATACGTAATTTCAGCACTAAACTTATCACATAAT
62 ACTCTAACATTGACTTACACCAGTAAAACGAATACGTAATTCCAGCACTAAACTTAAAACATAAT
*** * *
293367 TCCTGTAGTGAAACTTAACATTGACTTACATCAGCGAAATGAATACATAATTCCAGCATTAAAAA
127 TCCAACAGTGAAACTTAACATTGACTTACACCAGCGAAATGAATACATAATTCCAGCACTAAAAA
* *
293432 TAT-ATCATAATTCCAGT-AGTGAAACTTAACATCGACTTAAACCAGTGAAATGAATACGTAATT
192 TATCA-CATAATTCCA-TCAATGAAACTTAACATCGACTTAAACCAGTAAAATGAATACGTAATT
* * * * *
293495 CCAGCACTACACTTTTCACATAAGT-CAAGGAGTGAAACTGAACATTGACTTAGACTAGTGAAAT
255 CCAACACTAAACTTATCACATAAGTCCAA-CAGTGAAACTGAACATTGACTTACACTAGTGAAAT
293559 GAATACGTAA
319 GAATACGTAA
293569 TTCCAGCATT
Statistics
Matches: 286, Mismatches: 36, Indels: 14
0.85 0.11 0.04
Matches are distributed among these distances:
333 3 0.01
334 4 0.01
335 274 0.96
336 5 0.02
ACGTcount: A:0.41, C:0.19, G:0.12, T:0.28
Consensus pattern (334 bp):
TTACACCAGTGAAATGAATACATAATTAATAACTAAACTTATCACATAATTTCAGCAATGAACTC
TAACATTGACTTACACCAGTAAAACGAATACGTAATTCCAGCACTAAACTTAAAACATAATTCCA
ACAGTGAAACTTAACATTGACTTACACCAGCGAAATGAATACATAATTCCAGCACTAAAAATATC
ACATAATTCCATCAATGAAACTTAACATCGACTTAAACCAGTAAAATGAATACGTAATTCCAACA
CTAAACTTATCACATAAGTCCAACAGTGAAACTGAACATTGACTTACACTAGTGAAATGAATACG
TAACTCGAG
Found at i:296613 original size:28 final size:28
Alignment explanation
Indices: 296573--296635 Score: 81
Period size: 28 Copynumber: 2.2 Consensus size: 28
296563 AGTTTACAAA
*
296573 ATTTGAAGTTTATGATACAATTCATAGG
1 ATTTGGAGTTTATGATACAATTCATAGG
** *
296601 ATTTGGAGTTTATGATGTAATTTATAGG
1 ATTTGGAGTTTATGATACAATTCATAGG
*
296629 GTTTGGA
1 ATTTGGA
296636 TTAAATTTAA
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.30, C:0.03, G:0.24, T:0.43
Consensus pattern (28 bp):
ATTTGGAGTTTATGATACAATTCATAGG
Found at i:299076 original size:76 final size:76
Alignment explanation
Indices: 298970--299253 Score: 367
Period size: 76 Copynumber: 3.8 Consensus size: 76
298960 ATTCTAGCAG
* * * * * *
298970 TGAAACTTAACATTGATTTACGCCAATGAAATGAATACGTAATTCTAGCACTAAACTTATGACAT
1 TGAAACTTAACATTGACTTACACCAGTGAAATGAATACGTAATTCCAACACTAAACTTATCACAT
* * *
299035 GATTTCAACAG
66 AATTCCAACAA
* *
299046 TGAAACTTAACGTT-AGCTTACACCAGTGAAATGAATATGTAATTCCAACACTAAACTTATCACA
1 TGAAACTTAACATTGA-CTTACACCAGTGAAATGAATACGTAATTCCAACACTAAACTTATCACA
299110 TAATTCCAACAA
65 TAATTCCAACAA
* * *
299122 TGAAATTTAATATTGACTT--ACCAGTAAAATGAATACGTAATTCCAACACTAAACTTATCACAT
1 TGAAACTTAACATTGACTTACACCAGTGAAATGAATACGTAATTCCAACACTAAACTTATCACAT
*
299185 AATTCCAATAA
66 AATTCCAACAA
* * * *
299196 CGAAACTTAACATTGACTTACATCAGTGAAATGAATACGTGACTCCAACACTAAACTT
1 TGAAACTTAACATTGACTTACACCAGTGAAATGAATACGTAATTCCAACACTAAACTT
299254 TGAAGCTTAA
Statistics
Matches: 180, Mismatches: 24, Indels: 8
0.85 0.11 0.04
Matches are distributed among these distances:
74 68 0.38
75 1 0.01
76 110 0.61
77 1 0.01
ACGTcount: A:0.42, C:0.19, G:0.10, T:0.29
Consensus pattern (76 bp):
TGAAACTTAACATTGACTTACACCAGTGAAATGAATACGTAATTCCAACACTAAACTTATCACAT
AATTCCAACAA
Found at i:299386 original size:77 final size:76
Alignment explanation
Indices: 299254--299439 Score: 255
Period size: 77 Copynumber: 2.4 Consensus size: 76
299244 CACTAAACTT
* * * **
299254 TGAAGCTTAACATTGACTTACATCAGTGAAATGGATACGTAATTGTAGCACTAAACTTATCACAT
1 TGAAACTTAACATTGACTTACACCAGTGAAATGCATACGTAATTCCAGCACTAAACTTATCACAT
*
299319 AATTCCCACAG
66 AATTCACACAG
*
299330 TGAAATTTAACATTGACTTACACCAGTGTAAATGCATACGTAATTCCAGCACTAAACTTATCACA
1 TGAAACTTAACATTGACTTACACCAGTG-AAATGCATACGTAATTCCAGCACTAAACTTATCACA
**
299395 TAATTCATGCAG
65 TAATTCACACAG
* * *
299407 TGAAACTTAACATTAACTTACAACAGCGAAATG
1 TGAAACTTAACATTGACTTACACCAGTGAAATG
299440 AAAACAGAAT
Statistics
Matches: 96, Mismatches: 13, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
76 30 0.31
77 66 0.69
ACGTcount: A:0.39, C:0.20, G:0.13, T:0.28
Consensus pattern (76 bp):
TGAAACTTAACATTGACTTACACCAGTGAAATGCATACGTAATTCCAGCACTAAACTTATCACAT
AATTCACACAG
Found at i:299440 original size:211 final size:208
Alignment explanation
Indices: 299062--299441 Score: 548
Period size: 211 Copynumber: 1.8 Consensus size: 208
299052 TTAACGTTAG
*
299062 CTTACACCAGTGAAATGAATATGTAATTCCAACACTAAACTTATCACATAATTCCAACAATGAAA
1 CTTACACCAGTGAAATGAATACGTAATTCCAACACTAAACTTATCACATAATTCCAACAATGAAA
*
299127 TTTAATATTGACTTACCAGTAAAATGAATACGTAATTCCAACACTAAACTTATCACATAATTCCA
66 TTTAACATTGACTTACCAGTAAAATGAATACGTAATTCCAACACTAAACTTATCACATAATTCCA
* * *
299192 ATAACGAAACTTAACATTGACTTACATCAGTGAAATGAATACGTGACTCCAACACTAAACTTTGA
131 ATAACGAAACTTAACATTAACTTACAACAGCGAAATGAATACGTGACTCCAACACTAAACTTTGA
299257 AGCTTAACATTGA
196 AGCTTAACATTGA
* * ** * * *
299270 CTTACATCAGTGAAATGGATACGTAATTGTAGCACTAAACTTATCACATAATTCCCACAGTGAAA
1 CTTACACCAGTGAAATGAATACGTAATTCCAACACTAAACTTATCACATAATTCCAACAATGAAA
* * *
299335 TTTAACATTGACTTACACCAGTGTAAATGCATACGTAATTCCAGCACTAAACTTATCACATAATT
66 TTTAACATTGACTT--ACCAGT-AAAATGAATACGTAATTCCAACACTAAACTTATCACATAATT
**
299400 -C-ATGCAGTGAAACTTAACATTAACTTACAACAGCGAAATGAA
128 CCAAT--AACGAAACTTAACATTAACTTACAACAGCGAAATGAA
299442 AACAGAATTC
Statistics
Matches: 150, Mismatches: 17, Indels: 7
0.86 0.10 0.04
Matches are distributed among these distances:
208 70 0.47
209 2 0.01
210 7 0.05
211 71 0.47
ACGTcount: A:0.41, C:0.20, G:0.11, T:0.28
Consensus pattern (208 bp):
CTTACACCAGTGAAATGAATACGTAATTCCAACACTAAACTTATCACATAATTCCAACAATGAAA
TTTAACATTGACTTACCAGTAAAATGAATACGTAATTCCAACACTAAACTTATCACATAATTCCA
ATAACGAAACTTAACATTAACTTACAACAGCGAAATGAATACGTGACTCCAACACTAAACTTTGA
AGCTTAACATTGA
Found at i:299485 original size:76 final size:77
Alignment explanation
Indices: 299254--299489 Score: 221
Period size: 77 Copynumber: 3.1 Consensus size: 77
299244 CACTAAACTT
* * * * * * **
299254 TGAAGCTTAACATTGACTTACATCAGTG-AAATGGATACGTAATTGTAGCACTAAACTTATCACA
1 TGAAACTTAACATTAACTTACAACAGCGTAAATGAAAACGTAATTCCAGCACTAAACTTATCACA
***
299318 TAATTCCCACAG
66 TAATTCATGCAG
* * * * * *
299330 TGAAATTTAACATTGACTTACACCAGTGTAAATGCATACGTAATTCCAGCACTAAACTTATCACA
1 TGAAACTTAACATTAACTTACAACAGCGTAAATGAAAACGTAATTCCAGCACTAAACTTATCACA
299395 TAATTCATGCAG
66 TAATTCATGCAG
* * *
299407 TGAAACTTAACATTAACTTACAACAGCG-AAATGAAAACAG-AATTCCAGGATTAAATTTATCA-
1 TGAAACTTAACATTAACTTACAACAGCGTAAATGAAAAC-GTAATTCCAGCACTAAACTTATCAC
*
299469 ACTAATTCCA-GTAG
65 A-TAATT-CATGCAG
299483 TGAAACT
1 TGAAACT
299490 AATGTACGCG
Statistics
Matches: 137, Mismatches: 19, Indels: 8
0.84 0.12 0.05
Matches are distributed among these distances:
75 1 0.01
76 67 0.49
77 69 0.50
ACGTcount: A:0.40, C:0.19, G:0.13, T:0.28
Consensus pattern (77 bp):
TGAAACTTAACATTAACTTACAACAGCGTAAATGAAAACGTAATTCCAGCACTAAACTTATCACA
TAATTCATGCAG
Found at i:300800 original size:83 final size:83
Alignment explanation
Indices: 300539--300846 Score: 280
Period size: 83 Copynumber: 3.7 Consensus size: 83
300529 TAAAAGCACT
* * * * * * * * *
300539 TAAAGTACTATTTTGTTGCGGAGTTTGTTG-AAAAATGGCACCATAGATGAACCCTATTACAACA
1 TAAAGTACTACTCTGTTGCGGCGTTTGTTGAAAAAATGCCACTATAAATGAACCCTATTATAGCG
* *
300603 TCTGTATAAAAATGCTGC
66 TTTGTATAAAAATGCCGC
* * * * * * *
300621 TAAAGTACTCCACTGTTGCGACGTTTGGTGGAAAAAATGCAACTATAAATGAACTCT-TTATTGT
1 TAAAGTACTACTCTGTTGCGGCGTTT-GTTGAAAAAATGCCACTATAAATGAACCCTATTATAG-
*
300685 CGTTTGTATAAAAATGCCAC
64 CGTTTGTATAAAAATGCCGC
* * * * *
300705 TAACA-TAATACTCTATTGCGGCGTTTGTTGAAAAAATACCATTATATATGAACCCTATTATAGC
1 TAA-AGTACTACTCTGTTGCGGCGTTTGTTGAAAAAATGCCACTATAAATGAACCCTATTATAGC
* **
300769 GTTTATATAAAAACACCGC
65 GTTTGTATAAAAATGCCGC
* * * * *
300788 TAAAGTACTACTCTTTTGCGGCATTTGTTGAAAAAATGGCACTATAGATGAACCTTATT
1 TAAAGTACTACTCTGTTGCGGCGTTTGTTGAAAAAATGCCACTATAAATGAACCCTATT
300847 GCGGTATTTT
Statistics
Matches: 177, Mismatches: 43, Indels: 11
0.77 0.19 0.05
Matches are distributed among these distances:
82 21 0.12
83 95 0.54
84 60 0.34
85 1 0.01
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Consensus pattern (83 bp):
TAAAGTACTACTCTGTTGCGGCGTTTGTTGAAAAAATGCCACTATAAATGAACCCTATTATAGCG
TTTGTATAAAAATGCCGC
Found at i:301811 original size:44 final size:44
Alignment explanation
Indices: 301744--301832 Score: 117
Period size: 44 Copynumber: 2.0 Consensus size: 44
301734 ATAAGTTCTA
301744 TTTTAGTTGAATCTTCATATTTCTAGACA-ACAGGGGAGTTGATG
1 TTTTAGTTGAATCTTCATATTTCTAGACAGACA-GGGAGTTGATG
* * * * *
301788 TTTTAGTTGCATCTTCGTGTTTCTGGACAGTCAGGGAGTTGATG
1 TTTTAGTTGAATCTTCATATTTCTAGACAGACAGGGAGTTGATG
301832 T
1 T
301833 AAGGAGATTT
Statistics
Matches: 39, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
44 37 0.95
45 2 0.05
ACGTcount: A:0.21, C:0.12, G:0.26, T:0.40
Consensus pattern (44 bp):
TTTTAGTTGAATCTTCATATTTCTAGACAGACAGGGAGTTGATG
Found at i:306873 original size:23 final size:23
Alignment explanation
Indices: 306843--306913 Score: 92
Period size: 23 Copynumber: 3.1 Consensus size: 23
306833 ATAACATGAT
*
306843 ATATTAATAAATGAATTAAATAA
1 ATATTAATAAATAAATTAAATAA
306866 ATATTAATAAATAAATTAAATAA
1 ATATTAATAAATAAATTAAATAA
* *
306889 ATATGAATCACA-AAA-TAAATAA
1 ATATTAAT-AAATAAATTAAATAA
306911 ATA
1 ATA
306914 CAAATACTCA
Statistics
Matches: 44, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
22 10 0.23
23 32 0.73
24 2 0.05
ACGTcount: A:0.63, C:0.03, G:0.03, T:0.31
Consensus pattern (23 bp):
ATATTAATAAATAAATTAAATAA
Found at i:306878 original size:14 final size:13
Alignment explanation
Indices: 306848--306891 Score: 58
Period size: 13 Copynumber: 3.6 Consensus size: 13
306838 ATGATATATT
*
306848 AATAAATGAATTA
1 AATAAATAAATTA
306861 AATAAAT--ATT-
1 AATAAATAAATTA
306871 AATAAATAAATTA
1 AATAAATAAATTA
306884 AATAAATA
1 AATAAATA
306892 TGAATCACAA
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
10 7 0.25
11 3 0.11
12 3 0.11
13 15 0.54
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.32
Consensus pattern (13 bp):
AATAAATAAATTA
Found at i:308458 original size:2 final size:2
Alignment explanation
Indices: 308451--308479 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
308441 TAAAGTATTC
308451 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
308480 GTTTAGGAGG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:309120 original size:27 final size:26
Alignment explanation
Indices: 309068--309156 Score: 90
Period size: 27 Copynumber: 3.3 Consensus size: 26
309058 TCAGAGCTTG
* **
309068 GGGTATTTTGATCAGGTT-GAAGTTCA
1 GGGTATTTTGATAATTTTGGAA-TTCA
309094 TGGGTATTTTGATAATTTTGGAATTCA
1 -GGGTATTTTGATAATTTTGGAATTCA
* *
309121 GGGGTGTTTTGGTAATTTTGGAATTCA
1 -GGGTATTTTGATAATTTTGGAATTCA
*
309148 AGGTATTTT
1 GGGTATTTT
309157 TGATTTGGGG
Statistics
Matches: 53, Mismatches: 8, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
26 7 0.13
27 43 0.81
28 3 0.06
ACGTcount: A:0.22, C:0.04, G:0.28, T:0.45
Consensus pattern (26 bp):
GGGTATTTTGATAATTTTGGAATTCA
Found at i:310057 original size:2 final size:2
Alignment explanation
Indices: 310050--310078 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
310040 TAAAGTATTC
310050 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
310079 GTTTAGGAGG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:310621 original size:90 final size:90
Alignment explanation
Indices: 310463--310645 Score: 276
Period size: 90 Copynumber: 2.0 Consensus size: 90
310453 AGCTCTAATC
* * * *
310463 TTAACAGTATCAAGCATTGTTGATATGATTAGGTCGTGATTCAACCTTTAGGAGCGATACAACCT
1 TTAACAGTATCAAGCATTATCGATATGATTAGGTCATGATTCAACCGTTAGGAGCGATACAACCT
310528 TTAATTTTATCAATATCTAAAGAAT
66 TTAATTTTATCAATATCTAAAGAAT
* * **
310553 TTAATAGTATCAAGCATTATCGATATGATTAGGTCATGCTTCAACCGTTAGGAGTTATACAACCT
1 TTAACAGTATCAAGCATTATCGATATGATTAGGTCATGATTCAACCGTTAGGAGCGATACAACCT
* *
310618 TTAATTTTATCAATATCTATAGATT
66 TTAATTTTATCAATATCTAAAGAAT
310643 TTA
1 TTA
310646 TCCAAATGTC
Statistics
Matches: 83, Mismatches: 10, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
90 83 1.00
ACGTcount: A:0.34, C:0.14, G:0.14, T:0.38
Consensus pattern (90 bp):
TTAACAGTATCAAGCATTATCGATATGATTAGGTCATGATTCAACCGTTAGGAGCGATACAACCT
TTAATTTTATCAATATCTAAAGAAT
Found at i:310809 original size:27 final size:26
Alignment explanation
Indices: 310757--310846 Score: 117
Period size: 27 Copynumber: 3.3 Consensus size: 26
310747 TCAGATCTCG
* ** *
310757 GGGTATTTTGATAAGGTTGAAGTTCAT
1 GGGTATTTTGGTAATTTTGAA-TTCAA
310784 GGGTATTTTGGTAATTTTGGAATTCAA
1 GGGTATTTTGGTAATTTT-GAATTCAA
310811 GGGTATTTTGGTAATTTTTGAATTCAA
1 GGGTATTTTGGTAA-TTTTGAATTCAA
310838 GGGTATTTT
1 GGGTATTTT
310847 TGATTTGGGG
Statistics
Matches: 57, Mismatches: 4, Indels: 4
0.88 0.06 0.06
Matches are distributed among these distances:
27 50 0.88
28 7 0.12
ACGTcount: A:0.24, C:0.03, G:0.27, T:0.46
Consensus pattern (26 bp):
GGGTATTTTGGTAATTTTGAATTCAA
Found at i:314989 original size:17 final size:18
Alignment explanation
Indices: 314951--314993 Score: 70
Period size: 18 Copynumber: 2.4 Consensus size: 18
314941 TTCAAATGAG
*
314951 AATGTAAAGGTAAAACAA
1 AATGTAAAGGCAAAACAA
314969 AATGTAAAGGCAAAA-AA
1 AATGTAAAGGCAAAACAA
314986 AATGTAAA
1 AATGTAAA
314994 CACTGGATTT
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 10 0.42
18 14 0.58
ACGTcount: A:0.63, C:0.05, G:0.16, T:0.16
Consensus pattern (18 bp):
AATGTAAAGGCAAAACAA
Found at i:317098 original size:16 final size:17
Alignment explanation
Indices: 317067--317101 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
317057 ATCAAAACTT
*
317067 TGGAACAAGAGATTGAG
1 TGGAAAAAGAGATTGAG
317084 TGGAAAAAG-GATTGAG
1 TGGAAAAAGAGATTGAG
317100 TG
1 TG
317102 TAAGAGATCA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 9 0.53
17 8 0.47
ACGTcount: A:0.40, C:0.03, G:0.37, T:0.20
Consensus pattern (17 bp):
TGGAAAAAGAGATTGAG
Found at i:322825 original size:21 final size:21
Alignment explanation
Indices: 322801--322840 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
322791 CTTTTCCTCA
* *
322801 GACGTAACCAGCTTTTCTTAG
1 GACGTAACAAACTTTTCTTAG
322822 GACGTAACAAACTTTTCTT
1 GACGTAACAAACTTTTCTT
322841 GTGAAATTGC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.28, C:0.23, G:0.15, T:0.35
Consensus pattern (21 bp):
GACGTAACAAACTTTTCTTAG
Found at i:324357 original size:26 final size:26
Alignment explanation
Indices: 324326--324395 Score: 122
Period size: 26 Copynumber: 2.7 Consensus size: 26
324316 ATTATTATTT
324326 AAAGAAATAAAAAAGATAAAGATTAA
1 AAAGAAATAAAAAAGATAAAGATTAA
324352 AAAGAAATAAAAAAGATAAAGATTAA
1 AAAGAAATAAAAAAGATAAAGATTAA
* *
324378 AAATAAATAAAAGAGATA
1 AAAGAAATAAAAAAGATA
324396 GGGATAATGA
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
26 42 1.00
ACGTcount: A:0.73, C:0.00, G:0.11, T:0.16
Consensus pattern (26 bp):
AAAGAAATAAAAAAGATAAAGATTAA
Found at i:327162 original size:69 final size:69
Alignment explanation
Indices: 327000--327162 Score: 209
Period size: 69 Copynumber: 2.4 Consensus size: 69
326990 GATAATATGT
*
327000 TCCCATGTGAGTCACTTTAATCCTTCGGAGCTCCCGTGCAAGTCAACCGAAATAATTACGATTAG
1 TCCCATGTGAGTCACTCTAATCCTTCGGAGCTCCCGTGCAAGTCAACCGAAATAATTACGATTAG
327065 GTGC
66 GTGC
* ** * * * * * * *
327069 TTCCATGCAAGTTAATGTAATCCTTTGGGGCTCCTGTGCAAGTCACCCGAAATAATTACGATTAG
1 TCCCATGTGAGTCACTCTAATCCTTCGGAGCTCCCGTGCAAGTCAACCGAAATAATTACGATTAG
327134 GTGC
66 GTGC
* *
327138 TCCCGTGTGAGTCACTCTATTCCTT
1 TCCCATGTGAGTCACTCTAATCCTT
327163 AATGGCTTTC
Statistics
Matches: 76, Mismatches: 18, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
69 76 1.00
ACGTcount: A:0.24, C:0.25, G:0.20, T:0.31
Consensus pattern (69 bp):
TCCCATGTGAGTCACTCTAATCCTTCGGAGCTCCCGTGCAAGTCAACCGAAATAATTACGATTAG
GTGC
Found at i:327314 original size:25 final size:24
Alignment explanation
Indices: 327204--327318 Score: 72
Period size: 25 Copynumber: 4.6 Consensus size: 24
327194 CACGAAATGA
*
327204 ATACGTAATTCCAGCACTAAACTT
1 ATACATAATTCCAGCACTAAACTT
* *
327228 ATCACATAATTCCAACAGTGAAACTT
1 AT-ACATAATTCCAGCACT-AAACTT
* * * * *
327254 A-ACATTGACTTACACCAGCGAAA-TGA
1 ATACA-T-AATTCCAGCA-CTAAACT-T
*
327280 ATACGTAATTCCAGCACTAAACTT
1 ATACATAATTCCAGCACTAAACTT
327304 ATCACATAATTCCAG
1 AT-ACATAATTCCAG
327319 TAATGAAATT
Statistics
Matches: 66, Mismatches: 16, Indels: 17
0.67 0.16 0.17
Matches are distributed among these distances:
24 11 0.17
25 34 0.52
26 19 0.29
27 2 0.03
ACGTcount: A:0.40, C:0.24, G:0.10, T:0.26
Consensus pattern (24 bp):
ATACATAATTCCAGCACTAAACTT
Found at i:327326 original size:76 final size:76
Alignment explanation
Indices: 327196--327455 Score: 387
Period size: 76 Copynumber: 3.4 Consensus size: 76
327186 AAAATAATCA
* * *
327196 CGAAATGAATACGTAATTCCAGCACTAAACTTATCACATAATTCCAACAGTGAAACTTAACATTG
1 CGAAATGAATACGTAATTCCAACACTAAACTTATCACATAATTCCAGCAATGAAACTTAACATTG
327261 ACTTACACCAG
66 ACTTACACCAG
* * *
327272 CGAAATGAATACGTAATTCCAGCACTAAACTTATCACATAATTCCAGTAATGAAATTTAACATTG
1 CGAAATGAATACGTAATTCCAACACTAAACTTATCACATAATTCCAGCAATGAAACTTAACATTG
327337 ACTTACACCAG
66 ACTTACACCAG
* * * *
327348 TC-AAATGAGTATGTAATTCCAACACTAAACTTATCACACAATTCCAGCAACGAAACTTAACATT
1 -CGAAATGAATACGTAATTCCAACACTAAACTTATCACATAATTCCAGCAATGAAACTTAACATT
*
327412 GACTTACATCAG
65 GACTTACACCAG
* *
327424 TGAAATGAATACGTAACTCCAACACTAAACTT
1 CGAAATGAATACGTAATTCCAACACTAAACTT
327456 TGAAGCTTAA
Statistics
Matches: 166, Mismatches: 16, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
76 165 0.99
77 1 0.01
ACGTcount: A:0.41, C:0.23, G:0.10, T:0.26
Consensus pattern (76 bp):
CGAAATGAATACGTAATTCCAACACTAAACTTATCACATAATTCCAGCAATGAAACTTAACATTG
ACTTACACCAG
Found at i:327508 original size:58 final size:58
Alignment explanation
Indices: 327403--327513 Score: 168
Period size: 58 Copynumber: 1.9 Consensus size: 58
327393 AGCAACGAAA
*
327403 CTTAACATTGACTTACATCAGTGAAATGAATACGTAACTCCAACACTAAACTTTGAAG
1 CTTAACATTGACTTACATCAGTGAAATGAATACGTAACTACAACACTAAACTTTGAAG
* * * * *
327461 CTTAATATTGACTTACATCAGTGAAATGAATATGTAATTATAGCACTAAACTT
1 CTTAACATTGACTTACATCAGTGAAATGAATACGTAACTACAACACTAAACTT
327514 ATCACATAAT
Statistics
Matches: 47, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
58 47 1.00
ACGTcount: A:0.40, C:0.17, G:0.12, T:0.32
Consensus pattern (58 bp):
CTTAACATTGACTTACATCAGTGAAATGAATACGTAACTACAACACTAAACTTTGAAG
Found at i:327573 original size:134 final size:134
Alignment explanation
Indices: 327328--327573 Score: 359
Period size: 134 Copynumber: 1.8 Consensus size: 134
327318 GTAATGAAAT
* *
327328 TTAACATTGACTTACACCAGTCAAATGAGTATGTAATTCCAACACTAAACTTATCACACAATTCC
1 TTAACATTGACTTACACCAGTCAAATGAATATGTAATTACAACACTAAACTTATCACACAATTCC
*
327393 AGCAACGAAACTTAACATTGACTTACATCAGTGAAATGAATACGTAACTCCAACACTAAACTTTG
66 AGCAACGAAACTTAACATTGACTTACACCAGTGAAATGAATACGTAACTCCAACACTAAACTTTG
327458 AAGC
131 AAGC
* * * * * *
327462 TTAATATTGACTTACATCAGTGAAATGAATATGTAATTATAGCACTAAACTTATCACATAATTCC
1 TTAACATTGACTTACACCAGTCAAATGAATATGTAATTACAACACTAAACTTATCACACAATT-C
** * *
327527 CA-CAGTGAAATTTATCATTGACTTACACCAGTGAAATGAATACGTAA
65 CAGCAACGAAACTTAACATTGACTTACACCAGTGAAATGAATACGTAA
327574 TTCAAGCACT
Statistics
Matches: 98, Mismatches: 13, Indels: 2
0.87 0.12 0.02
Matches are distributed among these distances:
134 95 0.97
135 3 0.03
ACGTcount: A:0.40, C:0.20, G:0.11, T:0.29
Consensus pattern (134 bp):
TTAACATTGACTTACACCAGTCAAATGAATATGTAATTACAACACTAAACTTATCACACAATTCC
AGCAACGAAACTTAACATTGACTTACACCAGTGAAATGAATACGTAACTCCAACACTAAACTTTG
AAGC
Found at i:327890 original size:76 final size:76
Alignment explanation
Indices: 327758--328108 Score: 416
Period size: 76 Copynumber: 4.6 Consensus size: 76
327748 TTCAAAAAAA
* * * *
327758 AAACTTATCACATCATTTCAGTAGTGAAATTTAACATTGACTTACACCAGTA-AAATGAATACGT
1 AAACTTATCACATAATTCCAGTAATGAAACTTAACATTGACTTACACCAG-AGAAATGAATACGT
* *
327822 AATTCCAACGCT
65 AATTCCAGCACT
* * * * *
327834 AAACTTATCACATAATTCCAGTAATGAAACTTAAAATTAACTTATACAAGAGAAATGAATATGTA
1 AAACTTATCACATAATTCCAGTAATGAAACTTAACATTGACTTACACCAGAGAAATGAATACGTA
327899 ATTCCAGCACT
66 ATTCCAGCACT
* * ** *
327910 AAACTTATCACATAATTCCTGCAATGAAACTTAACATTGACTTACACCATCGAAATGAATACATA
1 AAACTTATCACATAATTCCAGTAATGAAACTTAACATTGACTTACACCAGAGAAATGAATACGTA
* * *
327975 ATTCTATCATT
66 ATTCCAGCACT
* * * * *
327986 AAATTTATCACCTAATTCCAGTAGTGAAACTTAACATTGACTTAAACCAGTGAAATGAATACGTA
1 AAACTTATCACATAATTCCAGTAATGAAACTTAACATTGACTTACACCAGAGAAATGAATACGTA
328051 ATTCCAGCACT
66 ATTCCAGCACT
* * * * * *
328062 AAACTTTTCACATAAGTCAAGGAGTGAAACTGAACATTGACTTACAC
1 AAACTTATCACATAATTCCAGTAATGAAACTTAACATTGACTTACAC
328109 TAGTATATTG
Statistics
Matches: 230, Mismatches: 44, Indels: 2
0.83 0.16 0.01
Matches are distributed among these distances:
75 1 0.00
76 229 1.00
ACGTcount: A:0.41, C:0.19, G:0.10, T:0.29
Consensus pattern (76 bp):
AAACTTATCACATAATTCCAGTAATGAAACTTAACATTGACTTACACCAGAGAAATGAATACGTA
ATTCCAGCACT
Found at i:329214 original size:69 final size:69
Alignment explanation
Indices: 329053--329278 Score: 233
Period size: 69 Copynumber: 3.3 Consensus size: 69
329043 TGTTCCCTTG
* * *
329053 TGAGTCACTCTAATCCTTCGGAGATCCTGTGCAAGTCAACCGAAGTAATTATGATTAGGTGCTCC
1 TGAGTCACTCTAATCCTTCGGGGCTCCTGTGCAAGTCAACCGAAATAATTATGATTAGGTGCTCC
*
329118 CGTG
66 CGTA
** * * *
329122 CAAGTTACTCTAATCCTTCGGGGCTCCTGTGCAAGTCACCCGAAATAATTATGATTAGGTTCTCC
1 TGAGTCACTCTAATCCTTCGGGGCTCCTGTGCAAGTCAACCGAAATAATTATGATTAGGTGCTCC
329187 CGTA
66 CGTA
* * * * * * *
329191 TGAGTCACTCTATTCATTAGGGGCTTTCGTGTG--AGT-AACCAAGAATAATCACGATTAGGTGC
1 TGAGTCACTCTAATCCTTCGGGGC--TCCTGTGCAAGTCAACCGA-AATAATTATGATTAGGTGC
* *
329253 TCCCTTG
63 TCCCGTA
*
329260 CGAGTCACTCTAATCCTTC
1 TGAGTCACTCTAATCCTTC
329279 AAGGCTCATG
Statistics
Matches: 127, Mismatches: 27, Indels: 6
0.79 0.17 0.04
Matches are distributed among these distances:
68 4 0.03
69 117 0.92
71 6 0.05
ACGTcount: A:0.24, C:0.24, G:0.21, T:0.31
Consensus pattern (69 bp):
TGAGTCACTCTAATCCTTCGGGGCTCCTGTGCAAGTCAACCGAAATAATTATGATTAGGTGCTCC
CGTA
Found at i:336005 original size:21 final size:20
Alignment explanation
Indices: 335968--336006 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
335958 GACTGTGGTG
*
335968 TTTCTGATTTAATAAAAATC
1 TTTCTGATTTAAGAAAAATC
*
335988 TTTCTTGATTTTAGAAAAA
1 TTTC-TGATTTAAGAAAAA
336007 GATAGAATTC
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 4 0.25
21 12 0.75
ACGTcount: A:0.38, C:0.08, G:0.08, T:0.46
Consensus pattern (20 bp):
TTTCTGATTTAAGAAAAATC
Found at i:336141 original size:19 final size:18
Alignment explanation
Indices: 336122--336169 Score: 64
Period size: 16 Copynumber: 2.7 Consensus size: 18
336112 GTTATGGTTA
336122 AAATAAAAAATAAGAATT
1 AAATAAAAAATAAGAATT
*
336140 AAAT-AAAAA-AATAATT
1 AAATAAAAAATAAGAATT
336156 AAATAAACAAATAA
1 AAATAAA-AAATAA
336170 AAGAGATTAA
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
16 10 0.38
17 7 0.27
18 7 0.27
19 2 0.08
ACGTcount: A:0.75, C:0.02, G:0.02, T:0.21
Consensus pattern (18 bp):
AAATAAAAAATAAGAATT
Found at i:336771 original size:74 final size:75
Alignment explanation
Indices: 336685--336847 Score: 233
Period size: 74 Copynumber: 2.2 Consensus size: 75
336675 TAAAAAAAAT
*
336685 ATAATATTCTAAATCCTAATTAAAATACT-AAAACCTATTTAAACTAAAATACAAAGATAAAGAT
1 ATAATATCCTAAATCCTAATTAAAATA-TAAAAACCTATTTAAACTAAAATACAAAGATAAA-AT
336749 A-AA-ATATAAA
64 ATAATATATAAA
* *
336759 ATAATATCCTAAAACTTAATTAAAATATAAAAACCTATTTAAACTAAAATACAAAGATAAAATAT
1 ATAATATCCTAAATCCTAATTAAAATATAAAAACCTATTTAAACTAAAATACAAAGATAAAATAT
* *
336824 AATTTTTAAA
66 AATATATAAA
*
336834 ATATTATCCTAAAT
1 ATAATATCCTAAAT
336848 TTGAGTTTAA
Statistics
Matches: 79, Mismatches: 7, Indels: 5
0.87 0.08 0.05
Matches are distributed among these distances:
73 4 0.05
74 58 0.73
75 17 0.22
ACGTcount: A:0.56, C:0.10, G:0.02, T:0.31
Consensus pattern (75 bp):
ATAATATCCTAAATCCTAATTAAAATATAAAAACCTATTTAAACTAAAATACAAAGATAAAATAT
AATATATAAA
Found at i:346038 original size:40 final size:40
Alignment explanation
Indices: 345983--346104 Score: 235
Period size: 40 Copynumber: 3.0 Consensus size: 40
345973 TGCAGGTTTA
*
345983 TAATACACTTTGGTGTATATGGTGGGCACGACCTTATGTG
1 TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
346023 TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
1 TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
346063 TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
1 TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
346103 TA
1 TA
346105 GCACTACGGT
Statistics
Matches: 81, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
40 81 1.00
ACGTcount: A:0.23, C:0.16, G:0.27, T:0.34
Consensus pattern (40 bp):
TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
Found at i:346303 original size:47 final size:45
Alignment explanation
Indices: 346209--346334 Score: 155
Period size: 47 Copynumber: 2.8 Consensus size: 45
346199 GTAACCATGC
* * *
346209 AAATAAGCTTATGAGCTTACGGAAT-AATGGCAAGTATATAGGAA
1 AAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATAGGAA
* * *
346253 AAATAAGCTTACGAGCTTATGGAATTTAAATGGTAAGTATTTTGGTA
1 AAATAAGCTTACGAGCTTATGGAA--TAAATGGTAAGTATATAGGAA
* *
346300 AAATAAGCTTACAAGCTTATGGGATAAATGGTAAG
1 AAATAAGCTTACGAGCTTATGGAATAAATGGTAAG
346335 AGATTTTATA
Statistics
Matches: 71, Mismatches: 8, Indels: 5
0.85 0.10 0.06
Matches are distributed among these distances:
44 22 0.31
45 11 0.15
46 1 0.01
47 37 0.52
ACGTcount: A:0.40, C:0.08, G:0.22, T:0.29
Consensus pattern (45 bp):
AAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATAGGAA
Found at i:348276 original size:15 final size:16
Alignment explanation
Indices: 348246--348286 Score: 57
Period size: 15 Copynumber: 2.5 Consensus size: 16
348236 TGGTTAAAAT
348246 TAAAAATATGAATTAAA
1 TAAAAA-ATGAATTAAA
348263 TAAAAAAT-AATTAAA
1 TAAAAAATGAATTAAA
348278 TAAACAAAT
1 TAAA-AAAT
348287 TAAAGAGATT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 11 0.48
16 6 0.26
17 6 0.26
ACGTcount: A:0.68, C:0.02, G:0.02, T:0.27
Consensus pattern (16 bp):
TAAAAAATGAATTAAA
Found at i:348835 original size:19 final size:19
Alignment explanation
Indices: 348811--348848 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
348801 ATAATATAAT
*
348811 ATTCTAAATCCTAATTAAA
1 ATTCTAAAACCTAATTAAA
*
348830 ATTCTAAAACCTATTTAAA
1 ATTCTAAAACCTAATTAAA
348849 CTAAAATACA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.47, C:0.16, G:0.00, T:0.37
Consensus pattern (19 bp):
ATTCTAAAACCTAATTAAA
Found at i:348893 original size:75 final size:76
Alignment explanation
Indices: 348806--348970 Score: 226
Period size: 76 Copynumber: 2.2 Consensus size: 76
348796 AAAAAATAAT
* **
348806 ATAATATTCTAAATCCTAATTAAAATTCT-AAAACCTATTTAAACTAAAATACAAAGATAAAGAT
1 ATAATATCCTAAATCCTAATTAAAAAACTAAAAACCTATTTAAACTAAAATACAAAGATAAA-AT
348870 AAAAT-ATAAAA
65 AAAATGATAAAA
* *
348881 ATAATATCCTAAAACTTAATTAAAAAACTAAAAACCTATTTAAACTAAAATACAAAGATAAAATA
1 ATAATATCCTAAATCCTAATTAAAAAACTAAAAACCTATTTAAACTAAAATACAAAGATAAAATA
* * *
348946 TAATGTTTAAA
66 AAATGATAAAA
*
348957 ATATTATCCTAAAT
1 ATAATATCCTAAAT
348971 TTGAGTTTAA
Statistics
Matches: 78, Mismatches: 10, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
75 30 0.38
76 48 0.62
ACGTcount: A:0.56, C:0.11, G:0.02, T:0.30
Consensus pattern (76 bp):
ATAATATCCTAAATCCTAATTAAAAAACTAAAAACCTATTTAAACTAAAATACAAAGATAAAATA
AAATGATAAAA
Found at i:351817 original size:24 final size:24
Alignment explanation
Indices: 351781--351860 Score: 88
Period size: 24 Copynumber: 3.3 Consensus size: 24
351771 CAAAAATAAA
* *
351781 AACATAATTCAGGTCAGATATCAT
1 AACATAATCCAGGTCAGGTATCAT
* * *
351805 AACAGAATCCAGGTCAGGTATTAG
1 AACATAATCCAGGTCAGGTATCAT
* *
351829 AACATAATCCATGTTAGGTATCAT
1 AACATAATCCAGGTCAGGTATCAT
*
351853 AATATAAT
1 AACATAAT
351861 TCAAATAAGA
Statistics
Matches: 45, Mismatches: 11, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
24 45 1.00
ACGTcount: A:0.41, C:0.15, G:0.15, T:0.29
Consensus pattern (24 bp):
AACATAATCCAGGTCAGGTATCAT
Found at i:354327 original size:17 final size:17
Alignment explanation
Indices: 354292--354328 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
354282 TAAAATGGTC
*
354292 GACTGTTGACCTGCATT
1 GACTGTTGACCGGCATT
*
354309 GACTGTTGACCGGCGTT
1 GACTGTTGACCGGCATT
354326 GAC
1 GAC
354329 CACTATTGAC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.16, C:0.24, G:0.30, T:0.30
Consensus pattern (17 bp):
GACTGTTGACCGGCATT
Found at i:354957 original size:353 final size:353
Alignment explanation
Indices: 354311--355023 Score: 1034
Period size: 353 Copynumber: 2.0 Consensus size: 353
354301 CCTGCATTGA
* * *
354311 CTGTTGACCGGCGTTGACCACTATTGACAAGAACTTTGACCGGTGTTGACCGGGAATTAAACGAC
1 CTGTTGACCGGCGTTGACCACTATTGACAAGAACTTTGACCGGCGTTGACCAGGAATTAAAAGAC
** * *
354376 CATTGACTTTGACCGATTATACCTATCCTGATGTTTTTCGATGTTCTAAGTCTGATTCCGTAATC
66 CATTGACTTTGACCGATTATACCTATCCTGACATTTTTCGATCTTCTAAGTCTGATTCCGCAATC
* * * ** *
354441 TGTTTTTCGAATTTAGGACCCGAAGGCCTTGAAATTGCTAGTCAAACTTGTTGACTTTGACCAAA
131 TGTTTTTCGAAATTAGGACCCGAAGGCCTCGAAATTGCCAGTCAAACCCGTTGACTTTGACAAAA
* * *
354506 AATTCAAAAATTTTGAAATTCATATTTAATGTTTTCGACGTTCTGAATCTGTTTTTGGGGTCTGT
196 AATTCAAAAATTTTGAAAGTCATATTTAATGTTTTCGACGTCCTGAATCTGTTTTTGGGGTCCGT
354571 TTCACCAAACTCAAACCGATAAGTTATTTTTGACTGATTTATCACCCGATTCTATCCATTTTTCA
261 TTCACCAAACTCAAACCGATAAGTTATTTTTGACTGATTTATCACCCGATTCTATCCATTTTTCA
*
354636 GAATTAAGCTCCATTTTTTATGTAATAT
326 GAATTAAGCTCCATTATTTATGTAATAT
* * *
354664 CTGTTGACCGGCTTTGACCACTATTGACCAGAACTTTGACCGGCGTTGACCAGGCATTAAAAGAC
1 CTGTTGACCGGCGTTGACCACTATTGACAAGAACTTTGACCGGCGTTGACCAGGAATTAAAAGAC
* * * *
354729 CTTTGGCTTTGACCGATTATACCTATCCTGACATTTTTCGATACTT-TGAGTCTGATTCCGCAGT
66 CATTGACTTTGACCGATTATACCTATCCTGACATTTTTCGAT-CTTCTAAGTCTGATTCCGCAAT
*
354793 CTGTTTTTCGAAATTCGGACCCGAAGGCCTCGAAATTGCCAGTCAAACCCGTTGA-TTTGACAAA
130 CTGTTTTTCGAAATTAGGACCCGAAGGCCTCGAAATTGCCAGTCAAACCCGTTGACTTTGACAAA
* * * *
354857 AAATTCAAAATTTTTGAAAAGTCATATTTTATGTTTTCTATGTCCTGAATCTGTTTTTGGGGTCC
195 AAATTCAAAAATTTTG-AAAGTCATATTTAATGTTTTCGACGTCCTGAATCTGTTTTTGGGGTCC
* * * * *
354922 GTTTCGCCAAACTCAAATCGGTAAGTTGTTTTTGACTGATTTATCACCCGATTCTATCCGTTTTT
259 GTTTCACCAAACTCAAACCGATAAGTTATTTTTGACTGATTTATCACCCGATTCTATCCATTTTT
** ** *
354987 TGGAATTAAGCTCTGTTATTTATGTAATTT
324 CAGAATTAAGCTCCATTATTTATGTAATAT
*
355017 ATGTTGA
1 CTGTTGA
355024 TATGCATCTG
Statistics
Matches: 318, Mismatches: 40, Indels: 4
0.88 0.11 0.01
Matches are distributed among these distances:
352 23 0.07
353 293 0.92
354 2 0.01
ACGTcount: A:0.26, C:0.19, G:0.18, T:0.37
Consensus pattern (353 bp):
CTGTTGACCGGCGTTGACCACTATTGACAAGAACTTTGACCGGCGTTGACCAGGAATTAAAAGAC
CATTGACTTTGACCGATTATACCTATCCTGACATTTTTCGATCTTCTAAGTCTGATTCCGCAATC
TGTTTTTCGAAATTAGGACCCGAAGGCCTCGAAATTGCCAGTCAAACCCGTTGACTTTGACAAAA
AATTCAAAAATTTTGAAAGTCATATTTAATGTTTTCGACGTCCTGAATCTGTTTTTGGGGTCCGT
TTCACCAAACTCAAACCGATAAGTTATTTTTGACTGATTTATCACCCGATTCTATCCATTTTTCA
GAATTAAGCTCCATTATTTATGTAATAT
Found at i:363014 original size:69 final size:69
Alignment explanation
Indices: 362941--363176 Score: 258
Period size: 69 Copynumber: 3.4 Consensus size: 69
362931 TACGATAATA
* * *
362941 TGCTCCCTTGTGAGTCACTCTAATCCTTCGGAGCTCCCGTGCGAGTCAACTGAAATAATTACGAT
1 TGCTCCCTTATGAGTCACTCTAATCCTTCGGGGCTCCCGTGCGAGTCAACCGAAATAATTACGAT
363006 TAGG
66 TAGG
** ** * * * * *
363010 TGCTCCCAAACAAGTCACTCTAATCCTTCGGGGCTCCTGTGCAAGTCACCCGAAATAATTATGAC
1 TGCTCCCTTATGAGTCACTCTAATCCTTCGGGGCTCCCGTGCGAGTCAACCGAAATAATTACGAT
*
363075 TAGA
66 TAGG
* * * * ** * *
363079 TGCTCCCGTGTGAGTCACTCTATTCCTTAGGGGCTTTCGTGCGAGT-AACCAAGAATAATCACGA
1 TGCTCCCTTATGAGTCACTCTAATCCTTCGGGGCTCCCGTGCGAGTCAACCGA-AATAATTACGA
363143 TTAGG
65 TTAGG
*
363148 TGCTCTCTTATGAGTCACTCTAATCCTTC
1 TGCTCCCTTATGAGTCACTCTAATCCTTC
363177 AAAGCTCATG
Statistics
Matches: 131, Mismatches: 35, Indels: 2
0.78 0.21 0.01
Matches are distributed among these distances:
68 4 0.03
69 127 0.97
ACGTcount: A:0.24, C:0.27, G:0.20, T:0.29
Consensus pattern (69 bp):
TGCTCCCTTATGAGTCACTCTAATCCTTCGGGGCTCCCGTGCGAGTCAACCGAAATAATTACGAT
TAGG
Found at i:363189 original size:138 final size:138
Alignment explanation
Indices: 362940--363189 Score: 322
Period size: 138 Copynumber: 1.8 Consensus size: 138
362930 ATACGATAAT
* * ** *
362940 ATGCTCCCTTGTGAGTCACTCTAATCCTTCGGAGCTCCCGTGCGAGTCAACTGAAATAATTACGA
1 ATGCTCCCGTGTGAGTCACTCTAATCCTTAGGAGCTCCCGTGCGAGTCAACCAAAATAATCACGA
*** *
363005 TTAGGTGCTCCCAAACAAGTCACTCTAATCCTTCGGGGCTCCTGTGCAAGTCACCCGAAATAATT
66 TTAGGTGCTCCCAAACAAGTCACTCTAATCCTTCAAAGCTCATGTGCAAGTCACCCGAAATAATT
363070 ATGACTAG
131 ATGACTAG
* * **
363078 ATGCTCCCGTGTGAGTCACTCTATTCCTTAGGGGCTTTCGTGCGAGT-AACCAAGAATAATCACG
1 ATGCTCCCGTGTGAGTCACTCTAATCCTTAGGAGCTCCCGTGCGAGTCAACCAA-AATAATCACG
* ** **
363142 ATTAGGTGCTCTCTTATGAGTCACTCTAATCCTTCAAAGCTCATGTGC
65 ATTAGGTGCTCCCAAACAAGTCACTCTAATCCTTCAAAGCTCATGTGC
363190 GACTTGTAAC
Statistics
Matches: 93, Mismatches: 18, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
137 4 0.04
138 89 0.96
ACGTcount: A:0.25, C:0.26, G:0.20, T:0.29
Consensus pattern (138 bp):
ATGCTCCCGTGTGAGTCACTCTAATCCTTAGGAGCTCCCGTGCGAGTCAACCAAAATAATCACGA
TTAGGTGCTCCCAAACAAGTCACTCTAATCCTTCAAAGCTCATGTGCAAGTCACCCGAAATAATT
ATGACTAG
Found at i:363981 original size:20 final size:20
Alignment explanation
Indices: 363952--364002 Score: 68
Period size: 20 Copynumber: 2.6 Consensus size: 20
363942 TTGACCGCCA
* *
363952 TTGACCATTGACTTTAATTG
1 TTGACTATTGACTTTAATCG
*
363972 TTGACTATTGACTTTGATCG
1 TTGACTATTGACTTTAATCG
363992 TTGACT-TTGAC
1 TTGACTATTGAC
364003 AAAAAAGTCA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 5 0.18
20 23 0.82
ACGTcount: A:0.22, C:0.16, G:0.18, T:0.45
Consensus pattern (20 bp):
TTGACTATTGACTTTAATCG
Found at i:366438 original size:43 final size:43
Alignment explanation
Indices: 366372--366838 Score: 551
Period size: 43 Copynumber: 10.8 Consensus size: 43
366362 CCGTTACCAG
* * * * *
366372 AGGCTCCTCTGTTATGTGCAAGGGTAAGTCCTTACCATTACCC
1 AGGCTCCTTTGCTATGTGCAAGGATAAGACCTTACCATTTCCC
* * * * * *
366415 AGGCTCCTTTGCTATGTGTAAGGGTAAGTCATAACCATTTCCT
1 AGGCTCCTTTGCTATGTGCAAGGATAAGACCTTACCATTTCCC
* * * *
366458 AGGCTCCTCTACTATGTGCAATGG-TAAGTCCTTACCGTTTTCCC
1 AGGCTCCTTTGCTATGTGCAA-GGATAAGACCTTACC-ATTTCCC
* *
366502 AGGCTCCTTTGCTATGTGCAAGGATAAGACCTTACCGTTTCTC
1 AGGCTCCTTTGCTATGTGCAAGGATAAGACCTTACCATTTCCC
* * *
366545 AAGCTCCTTTGCTATGTGCAAGGATAAGACCTTACTATTTCTC
1 AGGCTCCTTTGCTATGTGCAAGGATAAGACCTTACCATTTCCC
* * *
366588 AGGCTCCTTTCCTATGTACAAGGATAAGACCTTACCGTTTCCC
1 AGGCTCCTTTGCTATGTGCAAGGATAAGACCTTACCATTTCCC
* * *
366631 AGGCTCCTTTGCTATGTGCAAGGATAAGACATTACCGTTTCTC
1 AGGCTCCTTTGCTATGTGCAAGGATAAGACCTTACCATTTCCC
* * * *
366674 AGGCTCATTTGCAATGTGCAAGGATAAGACCTTACCGTTTCTC
1 AGGCTCCTTTGCTATGTGCAAGGATAAGACCTTACCATTTCCC
* *
366717 AGGCTCCTTTGTTATGTGCAAGGATAAGACCTTACCATTTCCA
1 AGGCTCCTTTGCTATGTGCAAGGATAAGACCTTACCATTTCCC
* *
366760 AGGCTCCTTTGCTATGTGTAAGGATAAGACCTTATCATTTCCC
1 AGGCTCCTTTGCTATGTGCAAGGATAAGACCTTACCATTTCCC
* * * *
366803 AAGCTCTTTTTCTATGTGCAAAGG-TAAGTCCTTACC
1 AGGCTCCTTTGCTATGTGC-AAGGATAAGACCTTACC
366839 GTTTTTGCAT
Statistics
Matches: 369, Mismatches: 51, Indels: 8
0.86 0.12 0.02
Matches are distributed among these distances:
43 328 0.89
44 41 0.11
ACGTcount: A:0.23, C:0.25, G:0.19, T:0.33
Consensus pattern (43 bp):
AGGCTCCTTTGCTATGTGCAAGGATAAGACCTTACCATTTCCC
Found at i:367992 original size:76 final size:76
Alignment explanation
Indices: 367885--368401 Score: 624
Period size: 76 Copynumber: 6.8 Consensus size: 76
367875 ACAATTCTAT
* * * * * *
367885 CAGTGAAACTTAACATTGACTTACACTAGTGAAATGAATACGTAGTTCTAGCACTAAACCTATGA
1 CAGTGAAACTTAACATTGACTTACACCAGTGAAATGAATACGTAATTCCAACACTAAACTTATCA
* *
367950 CATGATTTCAG
66 CATAATTCCAG
*
367961 TAGTGAAACTTAACATTGACTTACACCAGTGAAATGAATACGTAATT-CAAGCACTAAACTTATC
1 CAGTGAAACTTAACATTGACTTACACCAGTGAAATGAATACGTAATTCCAA-CACTAAACTTATC
* *
368025 ACATCATTTCAG
65 ACATAATTCCAG
* * * * * * *
368037 TAGTGAAATTTAACATTGACTTACACCAATAAAATGAATACGGAATTCTAGCACTAAACTTATCA
1 CAGTGAAACTTAACATTGACTTACACCAGTGAAATGAATACGTAATTCCAACACTAAACTTATCA
*
368102 AATAATTCCA-
66 CATAATTCCAG
* * ** * *
368112 CTAATGAAACTTAACATTAACTTACACCAACGAAATAAATACATAATTCCAACACTAAACTTATC
1 C-AGTGAAACTTAACATTGACTTACACCAGTGAAATGAATACGTAATTCCAACACTAAACTTATC
*
368177 ACATAATTCCAA
65 ACATAATTCCAG
*
368189 CAGTGAAACTTAACATTGACTTACACCAGTGAAATGAATATGTAATTCCAACACTAAACTTATCA
1 CAGTGAAACTTAACATTGACTTACACCAGTGAAATGAATACGTAATTCCAACACTAAACTTATCA
**
368254 CATAATTCTTG
66 CATAATTCCAG
* * * *
368265 CAATGAAATTTAACATTGACTTACACTAGTAAAATGAATACGTAATTCCAACACTAAACTTATCA
1 CAGTGAAACTTAACATTGACTTACACCAGTGAAATGAATACGTAATTCCAACACTAAACTTATCA
*
368330 CATAATTCCAA
66 CATAATTCCAG
* * ** ** * *
368341 CAATGAAACTTAACATTGACTAACAGTAGTGAAATGAATAAATGACTCCAACACTAAACTT
1 CAGTGAAACTTAACATTGACTTACACCAGTGAAATGAATACGTAATTCCAACACTAAACTT
368402 TGAAGCTTAA
Statistics
Matches: 382, Mismatches: 55, Indels: 8
0.86 0.12 0.02
Matches are distributed among these distances:
75 1 0.00
76 379 0.99
77 2 0.01
ACGTcount: A:0.43, C:0.20, G:0.10, T:0.28
Consensus pattern (76 bp):
CAGTGAAACTTAACATTGACTTACACCAGTGAAATGAATACGTAATTCCAACACTAAACTTATCA
CATAATTCCAG
Found at i:368181 original size:25 final size:26
Alignment explanation
Indices: 368152--368200 Score: 82
Period size: 25 Copynumber: 1.9 Consensus size: 26
368142 CGAAATAAAT
368152 ACATAATTCCAACACT-AAACTTATC
1 ACATAATTCCAACACTGAAACTTATC
*
368177 ACATAATTCCAACAGTGAAACTTA
1 ACATAATTCCAACACTGAAACTTA
368201 ACATTGACTT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
25 15 0.68
26 7 0.32
ACGTcount: A:0.45, C:0.24, G:0.04, T:0.27
Consensus pattern (26 bp):
ACATAATTCCAACACTGAAACTTATC
Found at i:368393 original size:228 final size:227
Alignment explanation
Indices: 367888--368401 Score: 692
Period size: 228 Copynumber: 2.3 Consensus size: 227
367878 ATTCTATCAG
* * * * *
367888 TGAAACTTAACATTGACTTACACTAGTGAAATGAATACGTAGTTCTAGCACTAAACCTATGACAT
1 TGAAACTTAACATTGACTTACACTAGTGAAATGAATACATA-TTCCAACACTAAACTTATCACAT
* * **
367953 GATTTCAGTAGTGAAACTTAACATTGACTTACACCAGTGAAATGAATACGTAATTCAAGCACTAA
65 AATTCCAACAGTGAAACTTAACATTGACTTACACCAGTGAAATGAATACGTAATTCAAGCACTAA
* * *
368018 ACTTATCACATCATTTCAGTAGTGAAATTTAACATTGACTTACACCAATAAAATGAATACGGAAT
130 ACTTATCACATAATTTCAGCAATGAAATTTAACATTGACTTACACCAATAAAATGAATACGGAAT
* *
368083 TCTAGCACTAAACTTATCAAATAATTCCACTAA
195 TCCAACACTAAACTTATCAAATAATTCCACTAA
* * ** *
368116 TGAAACTTAACATTAACTTACACCAACGAAATAAATACATAATTCCAACACTAAACTTATCACAT
1 TGAAACTTAACATTGACTTACACTAGTGAAATGAATACAT-ATTCCAACACTAAACTTATCACAT
*
368181 AATTCCAACAGTGAAACTTAACATTGACTTACACCAGTGAAATGAATATGTAATTCCAA-CACTA
65 AATTCCAACAGTGAAACTTAACATTGACTTACACCAGTGAAATGAATACGTAATT-CAAGCACTA
* * * *
368245 AACTTATCACATAA-TTCTTGCAATGAAATTTAACATTGACTTACACTAGTAAAATGAATACGTA
129 AACTTATCACATAATTTC-AGCAATGAAATTTAACATTGACTTACACCAATAAAATGAATACGGA
*
368309 ATTCCAACACTAAACTTATCACATAATTCCAAC-AA
193 ATTCCAACACTAAACTTATCAAATAATTCC-ACTAA
* * * *
368344 TGAAACTTAACATTGACTAACAGTAGTGAAATGAATAAATGACTCCAACACTAAACTT
1 TGAAACTTAACATTGACTTACACTAGTGAAATGAATACAT-ATTCCAACACTAAACTT
368402 TGAAGCTTAA
Statistics
Matches: 247, Mismatches: 35, Indels: 8
0.85 0.12 0.03
Matches are distributed among these distances:
227 3 0.01
228 238 0.96
229 6 0.02
ACGTcount: A:0.43, C:0.19, G:0.10, T:0.28
Consensus pattern (227 bp):
TGAAACTTAACATTGACTTACACTAGTGAAATGAATACATATTCCAACACTAAACTTATCACATA
ATTCCAACAGTGAAACTTAACATTGACTTACACCAGTGAAATGAATACGTAATTCAAGCACTAAA
CTTATCACATAATTTCAGCAATGAAATTTAACATTGACTTACACCAATAAAATGAATACGGAATT
CCAACACTAAACTTATCAAATAATTCCACTAA
Found at i:368530 original size:134 final size:134
Alignment explanation
Indices: 368274--368535 Score: 346
Period size: 134 Copynumber: 2.0 Consensus size: 134
368264 GCAATGAAAT
*
368274 TTAACATTGACTTACACTAGTAAAATGAATACGTAATTCCAACACTAAACTTATCACATAATTCC
1 TTAACATTGACTTACACTAGTAAAATGAATACGTAATTACAACACTAAACTTATCACATAATTCC
** *
368339 AACAATGAAACTTAACATTGACTAACAGTAGTGAAATGAATAAATGACTCCAACACTAAACTTTG
66 AACAATGAAACTTAACATTGACTAACACCAGTGAAATGAATAAATAACTCCAACACTAAACTTTG
368404 AAGC
131 AAGC
* * * * *
368408 TTAATATTGACTTGCA-TCAGTGAAATGAATACGTAATTATAGCACTAAACTTATCACATAATTC
1 TTAACATTGACTTACACT-AGTAAAATGAATACGTAATTACAACACTAAACTTATCACATAATTC
*** * * * * * *
368472 CCGTAGTGAAATTTAACATTGACTTACACCAGTGAAATGAATACATAATTCCAGCACTAAACTT
65 CAACAATGAAACTTAACATTGACTAACACCAGTGAAATGAATAAATAACTCCAACACTAAACTT
368536 ATCACATAAT
Statistics
Matches: 109, Mismatches: 18, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
133 1 0.01
134 108 0.99
ACGTcount: A:0.42, C:0.19, G:0.11, T:0.29
Consensus pattern (134 bp):
TTAACATTGACTTACACTAGTAAAATGAATACGTAATTACAACACTAAACTTATCACATAATTCC
AACAATGAAACTTAACATTGACTAACACCAGTGAAATGAATAAATAACTCCAACACTAAACTTTG
AAGC
Found at i:368539 original size:76 final size:76
Alignment explanation
Indices: 368402--368575 Score: 240
Period size: 76 Copynumber: 2.3 Consensus size: 76
368392 CACTAAACTT
* * * * * *
368402 TGAAGCTTAATATTGACTTGCATCAGTGAAATGAATACGTAATTATAGCACTAAACTTATCACAT
1 TGAAACTTAACATTGACTTACACCAGTGAAATGAATACATAATTACAGCACTAAACTTATCACAT
*
368467 AATTCCCGTAG
66 AATTCCCGCAG
* *
368478 TGAAATTTAACATTGACTTACACCAGTGAAATGAATACATAATTCCAGCACTAAACTTATCACAT
1 TGAAACTTAACATTGACTTACACCAGTGAAATGAATACATAATTACAGCACTAAACTTATCACAT
* *
368543 AATTCCTGCCG
66 AATTCCCGCAG
*
368554 TGAAACTTAACATTAACTTACA
1 TGAAACTTAACATTGACTTACA
368576 ACAACAAAAT
Statistics
Matches: 85, Mismatches: 13, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
76 85 1.00
ACGTcount: A:0.39, C:0.20, G:0.11, T:0.30
Consensus pattern (76 bp):
TGAAACTTAACATTGACTTACACCAGTGAAATGAATACATAATTACAGCACTAAACTTATCACAT
AATTCCCGCAG
Found at i:368586 original size:76 final size:76
Alignment explanation
Indices: 368430--368600 Score: 216
Period size: 76 Copynumber: 2.2 Consensus size: 76
368420 TGCATCAGTG
* ** * * *
368430 AAATGAATACGTAATTATAGCACTAAACTTATCACATAATTCCCGTAGTGAAATTTAACATTGAC
1 AAATGAATACATAATTCCAGCACTAAACTTATCACATAATTCCCGCAGTGAAACTTAACATTAAC
* ***
368495 TTACACCAGTG
66 TTACAACAACA
* *
368506 AAATGAATACATAATTCCAGCACTAAACTTATCACATAATTCCTGCCGTGAAACTTAACATTAAC
1 AAATGAATACATAATTCCAGCACTAAACTTATCACATAATTCCCGCAGTGAAACTTAACATTAAC
368571 TTACAACAACA
66 TTACAACAACA
* *
368582 AAATGAATTCAGAATTCCA
1 AAATGAATACATAATTCCA
368601 TCATTTTTAA
Statistics
Matches: 81, Mismatches: 14, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
76 81 1.00
ACGTcount: A:0.42, C:0.20, G:0.09, T:0.28
Consensus pattern (76 bp):
AAATGAATACATAATTCCAGCACTAAACTTATCACATAATTCCCGCAGTGAAACTTAACATTAAC
TTACAACAACA
Found at i:368588 original size:210 final size:210
Alignment explanation
Indices: 368192--368589 Score: 553
Period size: 210 Copynumber: 1.9 Consensus size: 210
368182 ATTCCAACAG
* *
368192 TGAAACTTAACATTGACTTACACCAGTGAAATGAATATGTAATTCCAACACTAAACTTATCACAT
1 TGAAACTTAACATTGACTTACACCAGTGAAATGAATACGTAATTACAACACTAAACTTATCACAT
** * *
368257 AATTCTTGCAATGAAATTTAACATTGACTTACACTAGTAAAATGAATACGTAATTCCAACACTAA
66 AATTCCCGCAATGAAATTTAACATTGACTTACACCAGTAAAATGAATACATAATTCCAACACTAA
* ** ***
368322 ACTTATCACATAATTCCAACAATGAAACTTAACATTGACTAACAGTAGTGAAATGAATAAATGAC
131 ACTTATCACATAATTCCAACAATGAAACTTAACATTAACTAACAACAACAAAATGAATAAATGAC
368387 TCCAACACTAAACTT
196 TCCAACACTAAACTT
* * * * * *
368402 TGAAGCTTAATATTGACTTGCATCAGTGAAATGAATACGTAATTATAGCACTAAACTTATCACAT
1 TGAAACTTAACATTGACTTACACCAGTGAAATGAATACGTAATTACAACACTAAACTTATCACAT
* * * *
368467 AATTCCCGTAGTGAAATTTAACATTGACTTACACCAGTGAAATGAATACATAATTCCAGCACTAA
66 AATTCCCGCAATGAAATTTAACATTGACTTACACCAGTAAAATGAATACATAATTCCAACACTAA
** ** *
368532 ACTTATCACATAATTCCTGCCGTGAAACTTAACATTAACTTACAACAACAAAATGAAT
131 ACTTATCACATAATTCCAACAATGAAACTTAACATTAACTAACAACAACAAAATGAAT
368590 TCAGAATTCC
Statistics
Matches: 161, Mismatches: 27, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
210 161 1.00
ACGTcount: A:0.42, C:0.19, G:0.10, T:0.29
Consensus pattern (210 bp):
TGAAACTTAACATTGACTTACACCAGTGAAATGAATACGTAATTACAACACTAAACTTATCACAT
AATTCCCGCAATGAAATTTAACATTGACTTACACCAGTAAAATGAATACATAATTCCAACACTAA
ACTTATCACATAATTCCAACAATGAAACTTAACATTAACTAACAACAACAAAATGAATAAATGAC
TCCAACACTAAACTT
Found at i:378871 original size:22 final size:23
Alignment explanation
Indices: 378843--378897 Score: 67
Period size: 23 Copynumber: 2.4 Consensus size: 23
378833 ATACATGAAT
**
378843 TAAATAAATAGGAAT-CACAAAA
1 TAAATAAATACAAATACACAAAA
* *
378865 TAAATAAATACAAATACTCATAA
1 TAAATAAATACAAATACACAAAA
378888 TAAATAAATA
1 TAAATAAATA
378898 AATAAATGTA
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
22 13 0.46
23 15 0.54
ACGTcount: A:0.64, C:0.09, G:0.04, T:0.24
Consensus pattern (23 bp):
TAAATAAATACAAATACACAAAA
Found at i:382401 original size:86 final size:84
Alignment explanation
Indices: 382237--382574 Score: 258
Period size: 85 Copynumber: 4.0 Consensus size: 84
382227 CGAAGTCATT
* * * ** *
382237 ATCAATGGTTGATCTGCTCCTTTCTTTGAAGAACGCAAAATCAAAGAACAATCTT-CTTATTTTC
1 ATCAATGGTTGATCTGCTCCTTTCTCTGAAG-ACGCCAAATCAGAGAATGATCTTGCTCA-TTTC
*
382301 TCTAAAGGACGCCAAGTCGTA
64 TCTAAAGGAAGCCAAGTCGTA
* * *
382322 ATCAATGGTTGATCTGCTTCTTTCTCCTGAATGATGCCAAATCAGAGAATGATCTTGCACATTTC
1 ATCAATGGTTGATCTGCTCCTTTCT-CTGAA-GACGCCAAATCAGAGAATGATCTTGCTCATTTC
**
382387 TCTAAAGGAAGCCAAGTAATA
64 TCTAAAGGAAGCCAAGTCGTA
* * ** * *
382408 ATCAAAGGTTGATATGCTCCTTTCTCAAAAGGACGCCAAATCGGGTAGCAATG---TTGCTCCTT
1 ATCAATGGTTGATCTGCTCCTTTCTCTGAA-GACGCCAAATC-AG-AG-AATGATCTTGCTCATT
382470 TCTCTAAAGGACA-CCAAGTCGTA
62 TCTCTAAAGGA-AGCCAAGTCGTA
* * * * * * *
382493 ATCAATGATTGATTTGCTTCATTATCTGAAGGACACCAAAT-ATCG-GAATGATCTTGCTCCTTT
1 ATCAATGGTTGATCTGCTCCTTTCTCTGAA-GACGCCAAATCA--GAGAATGATCTTGCTCATTT
* * * *
382556 ATCTGAAGGATGCTAAGTC
63 CTCTAAAGGAAGCCAAGTC
382575 ACGATTAATG
Statistics
Matches: 202, Mismatches: 38, Indels: 26
0.76 0.14 0.10
Matches are distributed among these distances:
82 4 0.02
83 1 0.00
85 120 0.59
86 68 0.34
87 5 0.02
88 4 0.02
ACGTcount: A:0.30, C:0.21, G:0.18, T:0.31
Consensus pattern (84 bp):
ATCAATGGTTGATCTGCTCCTTTCTCTGAAGACGCCAAATCAGAGAATGATCTTGCTCATTTCTC
TAAAGGAAGCCAAGTCGTA
Found at i:382495 original size:85 final size:84
Alignment explanation
Indices: 382297--382497 Score: 210
Period size: 86 Copynumber: 2.4 Consensus size: 84
382287 ATCTTCTTAT
* * * * ** * *
382297 TTTCTCTAAAGGACGCCAAGTCGTAATCAATGGTTGATCTGCTTCTTTCTCCTGAATGATGCCAA
1 TTTCTCTAAAGGACACCAAGTCGTAATCAAAGGTTGATATGCTCCTTTCTCCAAAAGGACGCCAA
382362 ATCAGAGAATGATCTTGCACA
66 ATCAGAGAATGA--TTGCACA
**
382383 TTTCTCTAAAGGA-AGCCAAGTAATAATCAAAGGTTGATATGCTCCTTTCT-CAAAAGGACGCCA
1 TTTCTCTAAAGGACA-CCAAGTCGTAATCAAAGGTTGATATGCTCCTTTCTCCAAAAGGACGCCA
* * *
382446 AATCGGGTAGCAATG-TTGCTCC
65 AATC-AG-AG-AATGATTGCACA
382468 TTTCTCTAAAGGACACCAAGTCGTAATCAA
1 TTTCTCTAAAGGACACCAAGTCGTAATCAA
382498 TGATTGATTT
Statistics
Matches: 95, Mismatches: 15, Indels: 11
0.79 0.12 0.09
Matches are distributed among these distances:
85 44 0.46
86 45 0.47
87 2 0.02
88 4 0.04
ACGTcount: A:0.31, C:0.22, G:0.18, T:0.29
Consensus pattern (84 bp):
TTTCTCTAAAGGACACCAAGTCGTAATCAAAGGTTGATATGCTCCTTTCTCCAAAAGGACGCCAA
ATCAGAGAATGATTGCACA
Found at i:384969 original size:20 final size:20
Alignment explanation
Indices: 384944--384983 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
384934 TTAGGAGATT
*
384944 GCTTAGTGTTCTAGAGAATA
1 GCTTAGTGTTCGAGAGAATA
384964 GCTTAGTGTTCGAGAGAATA
1 GCTTAGTGTTCGAGAGAATA
384984 ACTAAGTAGC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.30, C:0.10, G:0.28, T:0.33
Consensus pattern (20 bp):
GCTTAGTGTTCGAGAGAATA
Found at i:393650 original size:21 final size:21
Alignment explanation
Indices: 393602--393651 Score: 73
Period size: 21 Copynumber: 2.4 Consensus size: 21
393592 GGGTAATTAG
* **
393602 CTTTTCCTGGGATGTAACCAA
1 CTTTTCTTGGGACATAACCAA
393623 CTTTTCTTGGGACATAACCAA
1 CTTTTCTTGGGACATAACCAA
393644 CTTTTCTT
1 CTTTTCTT
393652 ATGAAATTGC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.22, C:0.24, G:0.14, T:0.40
Consensus pattern (21 bp):
CTTTTCTTGGGACATAACCAA
Found at i:393859 original size:26 final size:26
Alignment explanation
Indices: 393823--393875 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
393813 TGGACCTGGA
393823 AAGTTTCCTACGACATTGATTTTTGC
1 AAGTTTCCTACGACATTGATTTTTGC
393849 AAGTTTCCTACGACATTGATTTTTGC
1 AAGTTTCCTACGACATTGATTTTTGC
393875 A
1 A
393876 TTGCATTCTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.25, C:0.19, G:0.15, T:0.42
Consensus pattern (26 bp):
AAGTTTCCTACGACATTGATTTTTGC
Found at i:394781 original size:76 final size:76
Alignment explanation
Indices: 394685--395171 Score: 343
Period size: 76 Copynumber: 6.5 Consensus size: 76
394675 TGTCCAACTC
* * **
394685 CACCAGTGAAATGAATACGTAATTCAATAACTAAACTTATCATATAATTCCCGCAGTT-AAATTT
1 CACCAGTGAAATGAATACGTAATTCAAGAACTAAACTTATCACATAATTCCAACA-TTGAAATTT
*
394749 ATCATTGACTTA
65 AACATTGACTTA
* * * * *
394761 CATCAGTGTAATGAATACGTAATTCAAGCACTAAACTTATCACATCATTTCAACATTGAAATTTA
1 CACCAGTGAAATGAATACGTAATTCAAGAACTAAACTTATCACATAATTCCAACATTGAAATTTA
394826 ACATTGACTTA
66 ACATTGACTTA
* * ** * * * *
394837 CACCAGTAAAATGAATACGTAATTCCAGCGCTAAACTTATCACATGATTCCAATAATGAAACTTA
1 CACCAGTGAAATGAATACGTAATTCAAGAACTAAACTTATCACATAATTCCAACATTGAAATTTA
* * *
394902 TCATTAATTTA
66 ACATTGACTTA
** * * * * *
394913 CACCAGTGATTTGAATACGTAATTC--CAAC---ACTAATCACATAATTCCTACAGTGAAACTTA
1 CACCAGTGAAATGAATACGTAATTCAAGAACTAAACTTATCACATAATTCCAACATTGAAATTTA
**
394973 ACATTTTCTTA
66 ACATTGACTTA
** * * ** * * * * ** * *
394984 CACCAACGAAAT-AATA-ATAATTCCATCATTAAATTTATCACCTAATTCTAGTAGTGAAACTTA
1 CACCAGTGAAATGAATACGTAATTCAAGAACTAAACTTATCACATAATTCCAACATTGAAATTTA
395047 ACA-TGACTTA
66 ACATTGACTTA
* * * * ** * *
395057 AACCAGTGAAATGAATACGTAATTCTAA-CACTAAACTTTTCACATAA--GCATGGAGTGAAACT
1 CACCAGTGAAATGAATACGTAATTC-AAGAACTAAACTTATCACATAATTCCA-ACATTGAAATT
*
395119 GAACATTGACTTA
64 TAACATTGACTTA
* * *
395132 CACTAGCGAAATGAATACGTAATTCCAGCAA-TAAACTTAT
1 CACCAGTGAAATGAATACGTAATTCAAG-AACTAAACTTAT
395172 GATTTCACAT
Statistics
Matches: 324, Mismatches: 74, Indels: 27
0.76 0.17 0.06
Matches are distributed among these distances:
69 6 0.02
70 4 0.01
71 42 0.13
73 15 0.05
74 47 0.15
75 60 0.19
76 150 0.46
ACGTcount: A:0.40, C:0.19, G:0.10, T:0.31
Consensus pattern (76 bp):
CACCAGTGAAATGAATACGTAATTCAAGAACTAAACTTATCACATAATTCCAACATTGAAATTTA
ACATTGACTTA
Found at i:394905 original size:152 final size:149
Alignment explanation
Indices: 394685--395171 Score: 452
Period size: 152 Copynumber: 3.3 Consensus size: 149
394675 TGTCCAACTC
* * ** * * * * *
394685 CACCAGTGAAATGAATACGTAATTCAATAACTAAACTTATCATATAATTCCCGCAGTTAAATTTA
1 CACCAGCGAAATGAATACGTAATTCCAGCACTAAACTTATCACATAATTCCAGTAGTGAAACTTA
* *
394750 TCATTGACTTACATCAGTGTAATGAATACGTAATTCAAGCACTAAACTTATCACATCATTTCAAC
66 TCATTGACTTACACCAGTG-AATGAATACGTAATTCAA-CACTAAACTTATCACAT-ATTCCAAC
* *
394815 ATTGAAATTTAACATTGACTTA
128 AGTGAAACTTAACATTGACTTA
** * * * *
394837 CACCAGTAAAATGAATACGTAATTCCAGCGCTAAACTTATCACATGATTCCAATAATGAAACTTA
1 CACCAGCGAAATGAATACGTAATTCCAGCACTAAACTTATCACATAATTCCAGTAGTGAAACTTA
* * * *
394902 TCATTAATTTACACCAGTGATTTGAATACGTAATTCCAACACT--A---ATCACATAATTCCTAC
66 TCATTGACTTACACCAGTGA-ATGAATACGTAATT-CAACACTAAACTTATCACAT-ATTCCAAC
**
394962 AGTGAAACTTAACATTTTCTTA
128 AGTGAAACTTAACATTGACTTA
* * * * * * *
394984 CACCAACGAAAT-AATA-ATAATTCCATCATTAAATTTATCACCTAATTCTAGTAGTGAAACTTA
1 CACCAGCGAAATGAATACGTAATTCCAGCACTAAACTTATCACATAATTCCAGTAGTGAAACTTA
* * * ** **
395047 ACA-TGACTTAAACCAGTGAAATGAATACGTAATTCTAACACTAAACTTTTCACATA-AGCATGG
66 TCATTGACTTACACCAGTG-AATGAATACGTAATTC-AACACTAAACTTATCACATATTCCA-AC
*
395110 AGTGAAACTGAACATTGACTTA
128 AGTGAAACTTAACATTGACTTA
* *
395132 CACTAGCGAAATGAATACGTAATTCCAGCAATAAACTTAT
1 CACCAGCGAAATGAATACGTAATTCCAGCACTAAACTTAT
395172 GATTTCACAT
Statistics
Matches: 266, Mismatches: 57, Indels: 26
0.76 0.16 0.07
Matches are distributed among these distances:
143 1 0.00
144 31 0.12
145 40 0.15
146 5 0.02
147 41 0.15
148 30 0.11
149 10 0.04
150 19 0.07
151 1 0.00
152 85 0.32
153 3 0.01
ACGTcount: A:0.40, C:0.19, G:0.10, T:0.31
Consensus pattern (149 bp):
CACCAGCGAAATGAATACGTAATTCCAGCACTAAACTTATCACATAATTCCAGTAGTGAAACTTA
TCATTGACTTACACCAGTGAATGAATACGTAATTCAACACTAAACTTATCACATATTCCAACAGT
GAAACTTAACATTGACTTA
Found at i:395543 original size:19 final size:21
Alignment explanation
Indices: 395512--395553 Score: 54
Period size: 19 Copynumber: 2.1 Consensus size: 21
395502 CTTCCCGTCC
395512 ATTTGTGATTCTT-A-CCTTA
1 ATTTGTGATTCTTCACCCTTA
395531 ATTTGT-ATGTCTTCACCCTTA
1 ATTTGTGAT-TCTTCACCCTTA
395552 AT
1 AT
395554 CACCTTTATG
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
18 2 0.10
19 10 0.50
20 1 0.05
21 7 0.35
ACGTcount: A:0.21, C:0.19, G:0.10, T:0.50
Consensus pattern (21 bp):
ATTTGTGATTCTTCACCCTTA
Done.