Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr10 ID=Chr10-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: 62175169
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 981721 characters in sequence are not A, C, G, or T
File 178 of 202
Found at i:55170421 original size:27 final size:26
Alignment explanation
Indices: 55170363--55170548 Score: 158
Period size: 27 Copynumber: 6.8 Consensus size: 26
55170353 TCATCTCCTA
* *
55170363 AGGGTATAATAGTCATTTTATCCTGT-G
1 AGGGTAT-TTAGTCATTTTACCCT-TCG
*
55170390 GGGGTATTATAGTCATTTTACCCTTCG
1 AGGGTATT-TAGTCATTTTACCCTTCG
* * * *
55170417 AGGGTATTTTGGTTATTTTACCATTCA
1 AGGGTA-TTTAGTCATTTTACCCTTCG
* * *
55170444 AGGTTATTTCGGTCATTTTACCATTCG
1 AGGGTATTT-AGTCATTTTACCCTTCG
* *
55170471 AGGGTATTTTGGTCATTTTACCCTTCA
1 AGGGTA-TTTAGTCATTTTACCCTTCG
* *
55170498 ATGGGCATTTCAGTCATTTTACCCTTTG
1 A-GGGTATTT-AGTCATTTTACCCTTCG
55170526 AGGGTATTTCAGTCATTTTACCC
1 AGGGTATTT-AGTCATTTTACCC
55170549 ATTTTCGCCG
Statistics
Matches: 133, Mismatches: 19, Indels: 14
0.80 0.11 0.08
Matches are distributed among these distances:
26 4 0.03
27 105 0.79
28 24 0.18
ACGTcount: A:0.20, C:0.17, G:0.19, T:0.43
Consensus pattern (26 bp):
AGGGTATTTAGTCATTTTACCCTTCG
Found at i:55170435 original size:54 final size:53
Alignment explanation
Indices: 55170391--55170547 Score: 199
Period size: 54 Copynumber: 2.9 Consensus size: 53
55170381 TATCCTGTGG
*
55170391 GGGTATTAT-AGTCATTTTACCCTTCGAGGGTATTTTGGTTATTTTACCATTCAA
1 GGGTATT-TCAGTCATTTTACCCTTCGAGGGTATTTTGGTCATTTTACC-TTCAA
* * *
55170445 GGTTATTTCGGTCATTTTACCATTCGAGGGTATTTTGGTCATTTTACCCTTCAA
1 GGGTATTTCAGTCATTTTACCCTTCGAGGGTATTTTGGTCATTTTA-CCTTCAA
* * **
55170499 TGGGCATTTCAGTCATTTTACCCTTTGAGGGTATTTCAGTCATTTTACC
1 -GGGTATTTCAGTCATTTTACCCTTCGAGGGTATTTTGGTCATTTTACC
55170548 CATTTTCGCC
Statistics
Matches: 89, Mismatches: 11, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
53 1 0.01
54 47 0.53
55 41 0.46
ACGTcount: A:0.20, C:0.18, G:0.18, T:0.44
Consensus pattern (53 bp):
GGGTATTTCAGTCATTTTACCCTTCGAGGGTATTTTGGTCATTTTACCTTCAA
Found at i:55170533 original size:55 final size:54
Alignment explanation
Indices: 55170400--55170548 Score: 208
Period size: 55 Copynumber: 2.7 Consensus size: 54
55170390 GGGGTATTAT
* * **
55170400 AGTCATTTTACCCTTCGAGGGTATTTTGGTTATTTTACCATTCAAGGTTATTTC
1 AGTCATTTTACCCTTCGAGGGTATTTTGGTCATTTTACCCTTCAAGGGCATTTC
* *
55170454 GGTCATTTTACCATTCGAGGGTATTTTGGTCATTTTACCCTTCAATGGGCATTTC
1 AGTCATTTTACCCTTCGAGGGTATTTTGGTCATTTTACCCTTCAA-GGGCATTTC
* **
55170509 AGTCATTTTACCCTTTGAGGGTATTTCAGTCATTTTACCC
1 AGTCATTTTACCCTTCGAGGGTATTTTGGTCATTTTACCC
55170549 ATTTTCGCCG
Statistics
Matches: 83, Mismatches: 11, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
54 41 0.49
55 42 0.51
ACGTcount: A:0.19, C:0.19, G:0.17, T:0.44
Consensus pattern (54 bp):
AGTCATTTTACCCTTCGAGGGTATTTTGGTCATTTTACCCTTCAAGGGCATTTC
Found at i:55171341 original size:18 final size:19
Alignment explanation
Indices: 55171305--55171347 Score: 52
Period size: 18 Copynumber: 2.3 Consensus size: 19
55171295 GCAAAAACGC
*
55171305 AAAACTGACCGAAACAAAA
1 AAAACTGACCAAAACAAAA
*
55171324 AAAACTGA-CAAAAGAAAA
1 AAAACTGACCAAAACAAAA
*
55171342 ACAACT
1 AAAACT
55171348 TCAAAAACCG
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
18 13 0.62
19 8 0.38
ACGTcount: A:0.65, C:0.19, G:0.09, T:0.07
Consensus pattern (19 bp):
AAAACTGACCAAAACAAAA
Found at i:55173331 original size:238 final size:238
Alignment explanation
Indices: 55172906--55173381 Score: 907
Period size: 238 Copynumber: 2.0 Consensus size: 238
55172896 CAGAACGAAG
* *
55172906 ATCAATATTCGAGAACACTGTGGCACCTTTCAACTAATCAAAAAAATCATTAATGCGAGGTAGCG
1 ATCAATATTCGAGAACACTGTGACACCTTTCAACTAATCAAAAAAATCATCAATGCGAGGTAGCG
55172971 GATATTTATTCTTGATTGTAACTTTGTTGAGCTGATGGTAGTCAATGCATAATCTCATCGATTCG
66 GATATTTATTCTTGATTGTAACTTTGTTGAGCTGATGGTAGTCAATGCATAATCTCATCGATTCG
55173036 TCTTTTTTCTTAATAAACAGAATCGGTGCACCCAAGGTGAAAAACTAGGTCGAGCAAAACCCCTA
131 TCTTTTTTCTTAATAAACAGAATCGGTGCACCCAAGGTGAAAAACTAGGTCGAGCAAAACCCCTA
55173101 TCAATCAACTCTTGCAATTGTGCTTTCAACTCTTTTAACTCTC
196 TCAATCAACTCTTGCAATTGTGCTTTCAACTCTTTTAACTCTC
* * *
55173144 ATCAATCTTCGAGAACACTGTGACACCTTTCAACTGATCAAACAAATCATCAATGCGAGGTAGCG
1 ATCAATATTCGAGAACACTGTGACACCTTTCAACTAATCAAAAAAATCATCAATGCGAGGTAGCG
55173209 GATATTTATTCTTGATTGTAACTTTGTTGAGCTGATGGTAGTCAATGCATAATCTCATCGATTCG
66 GATATTTATTCTTGATTGTAACTTTGTTGAGCTGATGGTAGTCAATGCATAATCTCATCGATTCG
55173274 TCTTTTTTCTTAATAAACAGAATCGGTGCACCCAAGGTGAAAAACTAGGTCGAGCAAAACCCCTA
131 TCTTTTTTCTTAATAAACAGAATCGGTGCACCCAAGGTGAAAAACTAGGTCGAGCAAAACCCCTA
55173339 TCAATCAACTCTTGCAATTGTGCTTTCAACTCTTTTAACTCTC
196 TCAATCAACTCTTGCAATTGTGCTTTCAACTCTTTTAACTCTC
55173382 TAGGAGCCAT
Statistics
Matches: 233, Mismatches: 5, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
238 233 1.00
ACGTcount: A:0.31, C:0.21, G:0.16, T:0.32
Consensus pattern (238 bp):
ATCAATATTCGAGAACACTGTGACACCTTTCAACTAATCAAAAAAATCATCAATGCGAGGTAGCG
GATATTTATTCTTGATTGTAACTTTGTTGAGCTGATGGTAGTCAATGCATAATCTCATCGATTCG
TCTTTTTTCTTAATAAACAGAATCGGTGCACCCAAGGTGAAAAACTAGGTCGAGCAAAACCCCTA
TCAATCAACTCTTGCAATTGTGCTTTCAACTCTTTTAACTCTC
Found at i:55176820 original size:25 final size:25
Alignment explanation
Indices: 55176792--55176849 Score: 73
Period size: 25 Copynumber: 2.3 Consensus size: 25
55176782 TGTAAACAGT
* *
55176792 AAGCTCTTCCGAA-CTGAATAACGGG
1 AAGCTCATCC-AAGCTGAATAACGGA
*
55176817 AAGCTCATGCAAGCTGAATAACGGA
1 AAGCTCATCCAAGCTGAATAACGGA
55176842 AAGCTCAT
1 AAGCTCAT
55176850 ACGAGCTAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
24 2 0.07
25 27 0.93
ACGTcount: A:0.36, C:0.22, G:0.22, T:0.19
Consensus pattern (25 bp):
AAGCTCATCCAAGCTGAATAACGGA
Found at i:55176856 original size:25 final size:25
Alignment explanation
Indices: 55176805--55176900 Score: 104
Period size: 25 Copynumber: 3.8 Consensus size: 25
55176795 CTCTTCCGAA
* *
55176805 CTGAATAACGGGAAGCTCATGCAAG
1 CTGAATAACGGGAAGCTCATACGAG
*
55176830 CTGAATAACGGAAAGCTCATACGAG
1 CTGAATAACGGGAAGCTCATACGAG
* * * *
55176855 CTAAATAATGGGAAGGTCATGCGAG
1 CTGAATAACGGGAAGCTCATACGAG
*
55176880 CT-AAGTATCGGGAAGCTCATA
1 CTGAA-TAACGGGAAGCTCATA
55176901 AAAGCCGTGG
Statistics
Matches: 58, Mismatches: 12, Indels: 2
0.81 0.17 0.03
Matches are distributed among these distances:
24 2 0.03
25 56 0.97
ACGTcount: A:0.36, C:0.18, G:0.27, T:0.19
Consensus pattern (25 bp):
CTGAATAACGGGAAGCTCATACGAG
Found at i:55177561 original size:24 final size:24
Alignment explanation
Indices: 55177529--55177609 Score: 135
Period size: 24 Copynumber: 3.4 Consensus size: 24
55177519 AAATTGAAGC
*
55177529 ATACTCATCAAAGGCAAAACCCTA
1 ATACTCATCAATGGCAAAACCCTA
*
55177553 ATACCCATCAATGGCAAAACCCTA
1 ATACTCATCAATGGCAAAACCCTA
*
55177577 ATACTCATCAATGGAAAAACCCTA
1 ATACTCATCAATGGCAAAACCCTA
55177601 ATACTCATC
1 ATACTCATC
55177610 CCCGAGTTGG
Statistics
Matches: 53, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 53 1.00
ACGTcount: A:0.43, C:0.30, G:0.07, T:0.20
Consensus pattern (24 bp):
ATACTCATCAATGGCAAAACCCTA
Found at i:55190597 original size:22 final size:22
Alignment explanation
Indices: 55190567--55190609 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
55190557 ACAGCAGAAC
* *
55190567 AGGTTTTTAGCGGCGTTTTTTT
1 AGGTCTTTAGCGGCGCTTTTTT
55190589 AGGTCTTTAGCGGCGCTTTTT
1 AGGTCTTTAGCGGCGCTTTTT
55190610 AACGCCACTA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.09, C:0.14, G:0.28, T:0.49
Consensus pattern (22 bp):
AGGTCTTTAGCGGCGCTTTTTT
Found at i:55190788 original size:42 final size:42
Alignment explanation
Indices: 55190688--55190877 Score: 245
Period size: 42 Copynumber: 4.5 Consensus size: 42
55190678 TAACTTTTGT
55190688 GGCGCTTACATAAAAAAACGCCGCTAAAGATCATGTTCTTTAGC
1 GGCGCTT--ATAAAAAAACGCCGCTAAAGATCATGTTCTTTAGC
*
55190732 GGCGCTTAGAAAAAAAACGCCGCTAAAGATCATGTTCTTTAGC
1 GGCGCTTA-TAAAAAAACGCCGCTAAAGATCATGTTCTTTAGC
* ** *
55190775 GGCGGTTATAAAAATGCGCCGCTAAAGATCATGTTCTTTAGT
1 GGCGCTTATAAAAAAACGCCGCTAAAGATCATGTTCTTTAGC
* * * **
55190817 GGCGCTTACAAATAAACGCCGCTAAAGAACATAATCTTTAGC
1 GGCGCTTATAAAAAAACGCCGCTAAAGATCATGTTCTTTAGC
* *
55190859 GGCGCTTAGAAATAAACGC
1 GGCGCTTATAAAAAAACGC
55190878 NNNNNNNNNN
Statistics
Matches: 129, Mismatches: 16, Indels: 4
0.87 0.11 0.03
Matches are distributed among these distances:
42 82 0.64
43 40 0.31
44 7 0.05
ACGTcount: A:0.34, C:0.21, G:0.21, T:0.24
Consensus pattern (42 bp):
GGCGCTTATAAAAAAACGCCGCTAAAGATCATGTTCTTTAGC
Found at i:55191110 original size:42 final size:42
Alignment explanation
Indices: 55190983--55191129 Score: 163
Period size: 43 Copynumber: 3.5 Consensus size: 42
55190973 NNNNNATATC
* ** *
55190983 ATGTTCTCTAGCGGCGCTTAGGAAAAAAACGCCGCT-AAAGTTC
1 ATGTTCTTTAGCGGCGCTT-GTTAAAAAACGCCGCTAAAAG-TA
* *
55191026 ATGTTCTTTAGCGGCGCTT-TTGAGGAAAACGCCTCTAAAAGTA
1 ATGTTCTTTAGCGGCGCTTGTT-A-AAAAACGCCGCTAAAAGTA
* *
55191069 ATGTTCTATAGCGGCGCTTGTTCAAAAACGCCGCTAAAAGTA
1 ATGTTCTTTAGCGGCGCTTGTTAAAAAACGCCGCTAAAAGTA
*
55191111 GTGTTCTTTAGCGGCGCTT
1 ATGTTCTTTAGCGGCGCTT
55191130 ATTTCACAAA
Statistics
Matches: 88, Mismatches: 12, Indels: 9
0.81 0.11 0.08
Matches are distributed among these distances:
42 35 0.40
43 47 0.53
44 6 0.07
ACGTcount: A:0.27, C:0.21, G:0.24, T:0.29
Consensus pattern (42 bp):
ATGTTCTTTAGCGGCGCTTGTTAAAAAACGCCGCTAAAAGTA
Found at i:55191594 original size:10 final size:12
Alignment explanation
Indices: 55191550--55191601 Score: 77
Period size: 12 Copynumber: 4.3 Consensus size: 12
55191540 TTTTGAACCT
* *
55191550 CTGCTTCTATTG
1 CTGCTTCTCTCG
55191562 CTGCTTCTCTCG
1 CTGCTTCTCTCG
55191574 CTGCTTCTCTCG
1 CTGCTTCTCTCG
*
55191586 CTGCTTCTCTTG
1 CTGCTTCTCTCG
55191598 CTGC
1 CTGC
55191602 GGCCTCTGCT
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
12 37 1.00
ACGTcount: A:0.02, C:0.37, G:0.17, T:0.44
Consensus pattern (12 bp):
CTGCTTCTCTCG
Found at i:55191610 original size:21 final size:21
Alignment explanation
Indices: 55191586--55191664 Score: 95
Period size: 21 Copynumber: 3.8 Consensus size: 21
55191576 GCTTCTCTCG
**
55191586 CTGCTTCTCTTGCTGCGGCCT
1 CTGCTTCTCTCACTGCGGCCT
55191607 CTGCTTCTCTCACTGCGGCCT
1 CTGCTTCTCTCACTGCGGCCT
* ** *
55191628 TTGCTTCTCTCACTGTAGCCG
1 CTGCTTCTCTCACTGCGGCCT
*
55191649 CTGCTTCCCTCACTGC
1 CTGCTTCTCTCACTGC
55191665 CGTATCTGCT
Statistics
Matches: 49, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 49 1.00
ACGTcount: A:0.05, C:0.41, G:0.19, T:0.35
Consensus pattern (21 bp):
CTGCTTCTCTCACTGCGGCCT
Found at i:55197157 original size:9 final size:9
Alignment explanation
Indices: 55197143--55197335 Score: 149
Period size: 9 Copynumber: 22.8 Consensus size: 9
55197133 AACTTATTTA
55197143 TTATGTAAG
1 TTATGTAAG
55197152 TTATGTAAG
1 TTATGTAAG
*
55197161 TTGTGTAAG
1 TTATGTAAG
55197170 TTATGTAAG
1 TTATGTAAG
*
55197179 CTATGTAAG
1 TTATGTAAG
*
55197188 TTGTGT-A-
1 TTATGTAAG
* *
55197195 TTATGAAAC
1 TTATGTAAG
55197204 TTATGTAAG
1 TTATGTAAG
*
55197213 TTATGT--C
1 TTATGTAAG
55197220 TTATGTAAG
1 TTATGTAAG
* *
55197229 TGATGTAAA
1 TTATGTAAG
*
55197238 ATATGT-A-
1 TTATGTAAG
55197245 TTATGTAAG
1 TTATGTAAG
*
55197254 TTATGTCAG
1 TTATGTAAG
*
55197263 TTGTGT-A-
1 TTATGTAAG
*
55197270 TTATGTAAA
1 TTATGTAAG
55197279 TTATGT-A-
1 TTATGTAAG
55197286 TTATGTAAG
1 TTATGTAAG
*
55197295 TTATGTAAT
1 TTATGTAAG
*
55197304 TTGTGT-A-
1 TTATGTAAG
*
55197311 TTATGTAAC
1 TTATGTAAG
* *
55197320 TTATTTAAT
1 TTATGTAAG
55197329 TTATGTA
1 TTATGTA
55197336 CGGTATGTGT
Statistics
Matches: 147, Mismatches: 25, Indels: 24
0.75 0.13 0.12
Matches are distributed among these distances:
7 31 0.21
8 10 0.07
9 106 0.72
ACGTcount: A:0.31, C:0.03, G:0.19, T:0.47
Consensus pattern (9 bp):
TTATGTAAG
Found at i:55197208 original size:25 final size:25
Alignment explanation
Indices: 55197141--55197285 Score: 139
Period size: 25 Copynumber: 5.7 Consensus size: 25
55197131 ATAACTTATT
*
55197141 TATTATGTAAGTTATGTAAGTTGTG
1 TATTATGAAAGTTATGTAAGTTGTG
* *
55197166 TAAGTTATGTAAGCTATGTAAGTTGTG
1 T-A-TTATGAAAGTTATGTAAGTTGTG
* *
55197193 TATTATGAAACTTATGTAAGTTATG
1 TATTATGAAAGTTATGTAAGTTGTG
* * * ** *
55197218 TCTTATGTAAGTGATGTAAAATATG
1 TATTATGAAAGTTATGTAAGTTGTG
* *
55197243 TATTATGTAAGTTATGTCAGTTGTG
1 TATTATGAAAGTTATGTAAGTTGTG
55197268 TATTATGTAAA-TTATGTA
1 TATTATG-AAAGTTATGTA
55197286 TTATGTAAGT
Statistics
Matches: 98, Mismatches: 19, Indels: 6
0.80 0.15 0.05
Matches are distributed among these distances:
25 71 0.72
26 4 0.04
27 23 0.23
ACGTcount: A:0.32, C:0.03, G:0.21, T:0.45
Consensus pattern (25 bp):
TATTATGAAAGTTATGTAAGTTGTG
Found at i:55197222 original size:16 final size:16
Alignment explanation
Indices: 55197136--55197301 Score: 98
Period size: 16 Copynumber: 10.4 Consensus size: 16
55197126 TAGGAATAAC
*
55197136 TTATTTATTATGTAAG
1 TTATGTATTATGTAAG
*
55197152 TTATGTAAGTTGTGTAAG
1 TTATGT-A-TTATGTAAG
*
55197170 TTATGTAAGCTATGTAAG
1 TTATGT-A-TTATGTAAG
*
55197188 TTGTGTATTATG-AA-
1 TTATGTATTATGTAAG
*
55197202 --A---CTTATGTAAG
1 TTATGTATTATGTAAG
*
55197213 TTATGTCTTATGTAAG
1 TTATGTATTATGTAAG
* *
55197229 TGATGTAAAATATGT-A-
1 TTATGT--ATTATGTAAG
*
55197245 TTATGTAAGTTATGTCAG
1 TTATGT-A-TTATGTAAG
* *
55197263 TTGTGTATTATGTAAA
1 TTATGTATTATGTAAG
55197279 TTATGTATTATGTAAG
1 TTATGTATTATGTAAG
55197295 TTATGTA
1 TTATGTA
55197302 ATTTGTGTAT
Statistics
Matches: 118, Mismatches: 18, Indels: 28
0.72 0.11 0.17
Matches are distributed among these distances:
9 5 0.04
10 2 0.02
13 1 0.01
15 4 0.03
16 62 0.53
17 5 0.04
18 39 0.33
ACGTcount: A:0.31, C:0.02, G:0.20, T:0.46
Consensus pattern (16 bp):
TTATGTATTATGTAAG
Found at i:55197249 original size:41 final size:40
Alignment explanation
Indices: 55197204--55197318 Score: 133
Period size: 41 Copynumber: 2.8 Consensus size: 40
55197194 ATTATGAAAC
55197204 TTATGTAAGTTATGTC-TTATGTAAGTGATGTAAAATATGTA
1 TTATGTAAGTTATGTCATTATGT-A-TGATGTAAAATATGTA
* * *
55197245 TTATGTAAGTTATGTCAGTTGTGTATTATGTAAATTATGTA
1 TTATGTAAGTTATGTCA-TTATGTATGATGTAAAATATGTA
* * *
55197286 TTATGTAAGTTATGTAATTTGTGTATTATGTAA
1 TTATGTAAGTTATGTCA-TTATGTATGATGTAA
55197319 CTTATTTAAT
Statistics
Matches: 67, Mismatches: 5, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
41 61 0.91
42 1 0.01
43 5 0.07
ACGTcount: A:0.31, C:0.02, G:0.19, T:0.48
Consensus pattern (40 bp):
TTATGTAAGTTATGTCATTATGTATGATGTAAAATATGTA
Found at i:55197298 original size:25 final size:24
Alignment explanation
Indices: 55197142--55197335 Score: 99
Period size: 25 Copynumber: 7.7 Consensus size: 24
55197132 TAACTTATTT
* *
55197142 ATTATGTAAGTTATGTAAGTTGTGTA
1 ATTATGTAATTTATGT-A-TTATGTA
** *
55197168 AGTTATGTAAGCTATGTAAGTTGTGT-
1 A-TTATGTAATTTATGT-A-TTATGTA
* *
55197194 ATTATGAAACTTATGTAAGTTATGT-
1 ATTATGTAATTTATGT-A-TTATGTA
* * * *
55197219 CTTATGTAAGTGATGTAAAATATGT-
1 ATTATGTAATTTATGT--ATTATGTA
* *
55197244 ATTATGTAAGTTATGTCAGTTGTGT-
1 ATTATGTAATTTATGT-A-TTATGTA
*
55197269 ATTATGTAAATTATGTATTATGTA
1 ATTATGTAATTTATGTATTATGTA
*
55197293 AGTTATGTAATTTGTGTATTATGTA
1 A-TTATGTAATTTATGTATTATGTA
*
55197318 ACTTATTTAATTTATGTA
1 A-TTATGTAATTTATGTA
55197336 CGGTATGTGT
Statistics
Matches: 141, Mismatches: 22, Indels: 11
0.81 0.13 0.06
Matches are distributed among these distances:
23 5 0.04
24 3 0.02
25 106 0.75
26 4 0.03
27 23 0.16
ACGTcount: A:0.31, C:0.03, G:0.19, T:0.47
Consensus pattern (24 bp):
ATTATGTAATTTATGTATTATGTA
Found at i:55197536 original size:87 final size:87
Alignment explanation
Indices: 55197438--55197647 Score: 365
Period size: 87 Copynumber: 2.4 Consensus size: 87
55197428 CTTAAAAATT
* *
55197438 TAATACTAATAAATTTAATATTTAAACAATATTTATAATTATTTAGAAAACTTTTAAATTTTATA
1 TAATACTAATAAATTTAATATTAAAACAATATTTATAATTATTTAGAAAACATTTAAATTTTATA
55197503 GGTTATATTAAAACAATATTTA
66 GGTTATATTAAAACAATATTTA
55197525 TAATACTAATAAATTTAATATTAAAACAATATTTATAATTATTTAGAAAACATTTAAATTTTATA
1 TAATACTAATAAATTTAATATTAAAACAATATTTATAATTATTTAGAAAACATTTAAATTTTATA
55197590 GGTTATATTAAAACAATATTTA
66 GGTTATATTAAAACAATATTTA
55197612 TAATACTAAT--A--TAGATATTAAAACAATATTTATAAT
1 TAATACTAATAAATTTA-ATATTAAAACAATATTTATAAT
55197648 ACTAATATAG
Statistics
Matches: 120, Mismatches: 2, Indels: 5
0.94 0.02 0.04
Matches are distributed among these distances:
83 2 0.02
84 22 0.18
85 1 0.01
87 95 0.79
ACGTcount: A:0.49, C:0.05, G:0.03, T:0.43
Consensus pattern (87 bp):
TAATACTAATAAATTTAATATTAAAACAATATTTATAATTATTTAGAAAACATTTAAATTTTATA
GGTTATATTAAAACAATATTTA
Found at i:55197565 original size:18 final size:18
Alignment explanation
Indices: 55197505--55197565 Score: 58
Period size: 17 Copynumber: 3.5 Consensus size: 18
55197495 ATTTTATAGG
55197505 TTAT-ATTAAAACAATAT
1 TTATAATTAAAACAATAT
* *
55197522 TTATAA-TACTAATAA-AT
1 TTATAATTA-AAACAATAT
55197539 TTA-ATATTAAAACAATAT
1 TTATA-ATTAAAACAATAT
55197557 TTATAATTA
1 TTATAATTA
55197566 TTTAGAAAAC
Statistics
Matches: 34, Mismatches: 4, Indels: 11
0.69 0.08 0.22
Matches are distributed among these distances:
16 1 0.03
17 16 0.47
18 16 0.47
19 1 0.03
ACGTcount: A:0.52, C:0.05, G:0.00, T:0.43
Consensus pattern (18 bp):
TTATAATTAAAACAATAT
Found at i:55197632 original size:32 final size:32
Alignment explanation
Indices: 55197594--55197675 Score: 164
Period size: 32 Copynumber: 2.6 Consensus size: 32
55197584 TTTATAGGTT
55197594 ATATTAAAACAATATTTATAATACTAATATAG
1 ATATTAAAACAATATTTATAATACTAATATAG
55197626 ATATTAAAACAATATTTATAATACTAATATAG
1 ATATTAAAACAATATTTATAATACTAATATAG
55197658 ATATTAAAACAATATTTA
1 ATATTAAAACAATATTTA
55197676 GAATTATTTA
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 50 1.00
ACGTcount: A:0.54, C:0.06, G:0.02, T:0.38
Consensus pattern (32 bp):
ATATTAAAACAATATTTATAATACTAATATAG
Found at i:55197705 original size:15 final size:15
Alignment explanation
Indices: 55197685--55197717 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
55197675 AGAATTATTT
*
55197685 ATAAATTTAATAGTA
1 ATAAATTTAATACTA
55197700 ATAAATTTAATACTA
1 ATAAATTTAATACTA
55197715 ATA
1 ATA
55197718 TAGAAACCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.55, C:0.03, G:0.03, T:0.39
Consensus pattern (15 bp):
ATAAATTTAATACTA
Found at i:55197783 original size:42 final size:46
Alignment explanation
Indices: 55197732--55197876 Score: 145
Period size: 52 Copynumber: 3.0 Consensus size: 46
55197722 AACCTTATAA
55197732 ATTTAGAAAACTT-A-TATA-G-ATATTAAAACAATATTTATAATT
1 ATTTAGAAAACTTAATTATAGGTATATTAAAACAATATTTATAATT
55197774 ATTTAGAAAACTTTTAAATTTTATAGGTTATATTAAAACAATATTTATAATT
1 ATTTAGAAAAC--TT-AA--TTATAGG-TATATTAAAACAATATTTATAATT
*
55197826 ATTTAAAAAACTTTTAAATTTTATAGGTTATATTAAAACAATATTTATAAT
1 ATTTAGAAAAC--TT-AA--TTATAGG-TATATTAAAACAATATTTATAAT
55197877 ACTAATATAG
Statistics
Matches: 92, Mismatches: 1, Indels: 10
0.89 0.01 0.10
Matches are distributed among these distances:
42 11 0.12
44 2 0.02
46 1 0.01
49 4 0.04
50 1 0.01
52 73 0.79
ACGTcount: A:0.47, C:0.04, G:0.05, T:0.44
Consensus pattern (46 bp):
ATTTAGAAAACTTAATTATAGGTATATTAAAACAATATTTATAATT
Found at i:55197789 original size:21 final size:21
Alignment explanation
Indices: 55197732--55197793 Score: 51
Period size: 21 Copynumber: 3.0 Consensus size: 21
55197722 AACCTTATAA
*
55197732 ATTTAGAAAACTTATATAGA-T
1 ATTTAGAAAACTTTTATA-ATT
*
55197753 A-TTA-AAACAATATTTATAATT
1 ATTTAGAAA-ACT-TTTATAATT
55197774 ATTTAGAAAACTTTTA-AATT
1 ATTTAGAAAACTTTTATAATT
55197794 TTATAGGTTA
Statistics
Matches: 33, Mismatches: 3, Indels: 11
0.70 0.06 0.23
Matches are distributed among these distances:
19 3 0.09
20 10 0.30
21 12 0.36
22 5 0.15
23 3 0.09
ACGTcount: A:0.48, C:0.05, G:0.05, T:0.42
Consensus pattern (21 bp):
ATTTAGAAAACTTTTATAATT
Found at i:55197807 original size:52 final size:52
Alignment explanation
Indices: 55197751--55197876 Score: 243
Period size: 52 Copynumber: 2.4 Consensus size: 52
55197741 ACTTATATAG
*
55197751 ATATTAAAACAATATTTATAATTATTTAGAAAACTTTTAAATTTTATAGGTT
1 ATATTAAAACAATATTTATAATTATTTAAAAAACTTTTAAATTTTATAGGTT
55197803 ATATTAAAACAATATTTATAATTATTTAAAAAACTTTTAAATTTTATAGGTT
1 ATATTAAAACAATATTTATAATTATTTAAAAAACTTTTAAATTTTATAGGTT
55197855 ATATTAAAACAATATTTATAAT
1 ATATTAAAACAATATTTATAAT
55197877 ACTAATATAG
Statistics
Matches: 73, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
52 73 1.00
ACGTcount: A:0.47, C:0.04, G:0.04, T:0.45
Consensus pattern (52 bp):
ATATTAAAACAATATTTATAATTATTTAAAAAACTTTTAAATTTTATAGGTT
Found at i:55197820 original size:24 final size:24
Alignment explanation
Indices: 55197793--55197874 Score: 71
Period size: 24 Copynumber: 3.2 Consensus size: 24
55197783 ACTTTTAAAT
55197793 TTTATAGGTTATATTAAAACAATA
1 TTTATAGGTTATATTAAAACAATA
*
55197817 TTTATA-ATTAT-TTAAAA-AACTTTTAAA
1 TTTATAGGTTATATTAAAACAA----T--A
55197844 TTTTATAGGTTATATTAAAACAATA
1 -TTTATAGGTTATATTAAAACAATA
55197869 TTTATA
1 TTTATA
55197875 ATACTAATAT
Statistics
Matches: 46, Mismatches: 2, Indels: 20
0.68 0.03 0.29
Matches are distributed among these distances:
21 2 0.04
22 6 0.13
23 4 0.09
24 12 0.26
25 2 0.04
27 2 0.04
28 6 0.13
29 4 0.09
30 6 0.13
31 2 0.04
ACGTcount: A:0.45, C:0.04, G:0.05, T:0.46
Consensus pattern (24 bp):
TTTATAGGTTATATTAAAACAATA
Found at i:55197934 original size:15 final size:15
Alignment explanation
Indices: 55197914--55197946 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
55197904 AGAATTTTTT
*
55197914 ATAAATTTAATAGTA
1 ATAAATTTAATACTA
55197929 ATAAATTTAATACTA
1 ATAAATTTAATACTA
55197944 ATA
1 ATA
55197947 TAGAAACCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.55, C:0.03, G:0.03, T:0.39
Consensus pattern (15 bp):
ATAAATTTAATACTA
Found at i:55199170 original size:24 final size:25
Alignment explanation
Indices: 55199141--55199195 Score: 78
Period size: 25 Copynumber: 2.2 Consensus size: 25
55199131 TGGGGGAATA
55199141 GGAATT-GGGGGGAA-ATGAAATCGG
1 GGAATTGGGGGGGAATATGAAAT-GG
55199165 GGAATTGGGGGGGAATATGAAATGG
1 GGAATTGGGGGGGAATATGAAATGG
*
55199190 GAAATT
1 GGAATT
55199196 AGGGAATGAA
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
24 6 0.21
25 15 0.54
26 7 0.25
ACGTcount: A:0.35, C:0.02, G:0.44, T:0.20
Consensus pattern (25 bp):
GGAATTGGGGGGGAATATGAAATGG
Found at i:55199761 original size:22 final size:22
Alignment explanation
Indices: 55199735--55199783 Score: 89
Period size: 22 Copynumber: 2.2 Consensus size: 22
55199725 CCCTAAGTTT
*
55199735 AACCCGTAACCTTTATACTTTA
1 AACCCGTAACCTTTAAACTTTA
55199757 AACCCGTAACCTTTAAACTTTA
1 AACCCGTAACCTTTAAACTTTA
55199779 AACCC
1 AACCC
55199784 TAAACTACAA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.35, C:0.31, G:0.04, T:0.31
Consensus pattern (22 bp):
AACCCGTAACCTTTAAACTTTA
Found at i:55200708 original size:189 final size:189
Alignment explanation
Indices: 55200378--55200770 Score: 603
Period size: 189 Copynumber: 2.1 Consensus size: 189
55200368 GTGTTTGAAC
*
55200378 GTAAGCGCCACTAATTAAAGTATACATCGAGACCAAAACGGTGCGTTTTGGTTCAGATATTTTGC
1 GTAAGCGCCACTAATTAAAGTATACATCGAGACCAAAACGGTGCGTTTTGGTTCAGATAGTTTGC
*
55200443 GGCGTTTTCATATAAGCGCCACTAAATGTAACATAGCTTAAGACAAACCACTGCGTTTTGTTAAG
66 GGCGTTTTCATATAAGCGCCACTAAATGTAACATAACTTAAGACAAACCACTGCGTTTTGTTAAG
* * *
55200508 ATACGTTGCGGCGCTTTACCCAAAGCGCCGCTAAAT-ATATTCTTTAACGGCGTTTTCTA
131 ATACGTTGCGGCGCTTCACCCAAAGCACCGCT-AATGATATTCTATAACGGCGTTTTCTA
* *
55200567 GTAAGCGCCACTAATTGAAGTATACATCGAGACCAAAATGGTGCGTTTTGGTTCAGATAGTTTGC
1 GTAAGCGCCACTAATTAAAGTATACATCGAGACCAAAACGGTGCGTTTTGGTTCAGATAGTTTGC
*
55200632 GGCGTTTTGC-TATAAGCGCCACTAAATGTAACATAACTTCAGACGAAA-CACTGCGTTTTGTTA
66 GGCGTTTT-CATATAAGCGCCACTAAATGTAACATAACTTAAGAC-AAACCACTGCGTTTTGTTA
* * ** * * *
55200695 AGGTACTTTGCGGCGCTTCGGCTAAAGCACTGCTAATGCTATTCTATAACGGCGTTTTCTA
129 AGATACGTTGCGGCGCTTCACCCAAAGCACCGCTAATGATATTCTATAACGGCGTTTTCTA
55200756 GTAAGCGCCACTAAT
1 GTAAGCGCCACTAAT
55200771 ATAATCAAAA
Statistics
Matches: 186, Mismatches: 15, Indels: 6
0.90 0.07 0.03
Matches are distributed among these distances:
188 3 0.02
189 179 0.96
190 4 0.02
ACGTcount: A:0.28, C:0.21, G:0.21, T:0.30
Consensus pattern (189 bp):
GTAAGCGCCACTAATTAAAGTATACATCGAGACCAAAACGGTGCGTTTTGGTTCAGATAGTTTGC
GGCGTTTTCATATAAGCGCCACTAAATGTAACATAACTTAAGACAAACCACTGCGTTTTGTTAAG
ATACGTTGCGGCGCTTCACCCAAAGCACCGCTAATGATATTCTATAACGGCGTTTTCTA
Found at i:55228068 original size:27 final size:27
Alignment explanation
Indices: 55227965--55228066 Score: 136
Period size: 27 Copynumber: 3.8 Consensus size: 27
55227955 CCCTAAAATA
55227965 GGTAAAATGA-TCGAAATACCCCCATAG
1 GGTAAAATGACT-GAAATACCCCCATAG
*
55227992 GATAAAATGACTGAAATACCCCCATAG
1 GGTAAAATGACTGAAATACCCCCATAG
* *
55228019 GGT-AAATGACTAAAATACCCCTATAG
1 GGTAAAATGACTGAAATACCCCCATAG
**
55228045 GGTAAAATGACTGTTATACCCC
1 GGTAAAATGACTGAAATACCCC
55228067 TAGGAGATGA
Statistics
Matches: 66, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
26 24 0.36
27 41 0.62
28 1 0.02
ACGTcount: A:0.40, C:0.22, G:0.17, T:0.22
Consensus pattern (27 bp):
GGTAAAATGACTGAAATACCCCCATAG
Found at i:55229587 original size:42 final size:42
Alignment explanation
Indices: 55229541--55229641 Score: 98
Period size: 42 Copynumber: 2.4 Consensus size: 42
55229531 CCGTGTGTAT
* * *
55229541 TAAGTCAATGAGTTACATAGTCTA-GTACACGGTCGTGTGACA
1 TAAGTCAATGAGTTACATAGCCTATG-ACACAGCCGTGTGACA
* * *
55229583 TAAGTTAGA-GAGTTACATGGCCTATGACACAGCCGTGTGACC
1 TAAGTCA-ATGAGTTACATAGCCTATGACACAGCCGTGTGACA
* *
55229625 TAAATCAGTGAGTTACA
1 TAAGTCAATGAGTTACA
55229642 CGGTTTAAGA
Statistics
Matches: 47, Mismatches: 9, Indels: 6
0.76 0.15 0.10
Matches are distributed among these distances:
42 45 0.96
43 2 0.04
ACGTcount: A:0.32, C:0.18, G:0.24, T:0.27
Consensus pattern (42 bp):
TAAGTCAATGAGTTACATAGCCTATGACACAGCCGTGTGACA
Found at i:55233927 original size:29 final size:29
Alignment explanation
Indices: 55233894--55233961 Score: 91
Period size: 29 Copynumber: 2.3 Consensus size: 29
55233884 ATCGACAAAT
* *
55233894 GAAAAAGGATAGCTTCAGTTATCGAATAC
1 GAAAAGGGATAGCTTCAGCTATCGAATAC
* * *
55233923 GAAAAGGGATAGCTTCCGCTATCGATTAT
1 GAAAAGGGATAGCTTCAGCTATCGAATAC
55233952 GAAAAGGGAT
1 GAAAAGGGAT
55233962 GGTGATGACC
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
29 34 1.00
ACGTcount: A:0.38, C:0.13, G:0.25, T:0.24
Consensus pattern (29 bp):
GAAAAGGGATAGCTTCAGCTATCGAATAC
Found at i:55233982 original size:29 final size:30
Alignment explanation
Indices: 55233950--55234022 Score: 103
Period size: 29 Copynumber: 2.5 Consensus size: 30
55233940 GCTATCGATT
* * *
55233950 ATGAAAAGGGATGGTGATGACCAT-TAACA
1 ATGAAAAGGGATAGTGACGACCATCGAACA
*
55233979 ATGAAAAGGGATAGTGACGACCATCGAACT
1 ATGAAAAGGGATAGTGACGACCATCGAACA
55234009 ATGAAAAGGGATAG
1 ATGAAAAGGGATAG
55234023 CTTCGACTAG
Statistics
Matches: 39, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
29 22 0.56
30 17 0.44
ACGTcount: A:0.42, C:0.11, G:0.29, T:0.18
Consensus pattern (30 bp):
ATGAAAAGGGATAGTGACGACCATCGAACA
Found at i:55234039 original size:30 final size:30
Alignment explanation
Indices: 55233892--55234229 Score: 132
Period size: 30 Copynumber: 11.4 Consensus size: 30
55233882 TCATCGACAA
* *
55233892 ATGAAAAAGGATAGCTTC-AGTTATCGAA-T
1 ATGAAAAGGGATAGCTTCGA-CTATCGAACT
* *
55233921 ACGAAAAGGGATAGCTTCCG-CTATCG-ATT
1 ATGAAAAGGGATAGCTT-CGACTATCGAACT
* * * *
55233950 ATGAAAAGGGAT-GGTGAT-GACCAT-TAACA
1 ATGAAAAGGGATAGCT--TCGACTATCGAACT
* *
55233979 ATGAAAAGGGATAG-TGACGACCATCGAACT
1 ATGAAAAGGGATAGCT-TCGACTATCGAACT
* *
55234009 ATGAAAAGGGATAGCTTCGACTAGCAAACT
1 ATGAAAAGGGATAGCTTCGACTATCGAACT
* *
55234039 ATGGAAAA-GGAT-GACTTTGGCTATCGAACT
1 AT-GAAAAGGGATAG-CTTCGACTATCGAACT
* *
55234069 ATGAAAAGGGATAGCTTC-AGCTATCAAATT
1 ATGAAAAGGGATAGCTTCGA-CTATCGAACT
* * * * * **
55234099 ATGAGAAGAGAT-GGTGACGACCATCGAAAA
1 ATGAAAAGGGATAGCT-TCGACTATCGAACT
* * * * *
55234129 ATGAAAAGGCAT-G-TTGATGACAAT-TAATTT
1 ATGAAAAGGGATAGCTT--CGACTATCGAA-CT
* * *
55234159 ATGAAAAGGGATAGTTTCAACTATTGAACT
1 ATGAAAAGGGATAGCTTCGACTATCGAACT
* ** *
55234189 ATGAAAAGGGATAACTTCGGTTATCGAATT
1 ATGAAAAGGGATAGCTTCGACTATCGAACT
*
55234219 ACG-AAAGGGAT
1 ATGAAAAGGGAT
55234230 GTGTCAACCA
Statistics
Matches: 229, Mismatches: 56, Indels: 48
0.69 0.17 0.14
Matches are distributed among these distances:
28 4 0.02
29 74 0.32
30 138 0.60
31 11 0.05
32 2 0.01
ACGTcount: A:0.39, C:0.13, G:0.24, T:0.24
Consensus pattern (30 bp):
ATGAAAAGGGATAGCTTCGACTATCGAACT
Found at i:55234125 original size:60 final size:56
Alignment explanation
Indices: 55233992--55234137 Score: 150
Period size: 60 Copynumber: 2.5 Consensus size: 56
55233982 AAAAGGGATA
55233992 GTGACGACCATCGAACTATGAAAAGGGATAGCTTCGACTAGCAAACTATGGAAAAG
1 GTGACGACCATCGAACTATGAAAAGGGATAGCTTCGACTAGCAAACTATGGAAAAG
* * * *
55234048 GATGACTTTGGCTATCGAACTATGAAAAGGGATAGCTTC-AGCTATCAAATTATGAGAAGAGATG
1 G-TGAC---GACCATCGAACTATGAAAAGGGATAGCTTCGA-CTAGCAAACTATG-GAA-A-A-G
**
55234112 GTGACGACCATCGAAAAATGAAAAGG
1 GTGACGACCATCGAACTATGAAAAGG
55234138 CATGTTGATG
Statistics
Matches: 73, Mismatches: 8, Indels: 14
0.77 0.08 0.15
Matches are distributed among these distances:
56 1 0.01
57 4 0.05
59 1 0.01
60 56 0.77
61 3 0.04
62 1 0.01
63 5 0.07
64 2 0.03
ACGTcount: A:0.39, C:0.15, G:0.25, T:0.21
Consensus pattern (56 bp):
GTGACGACCATCGAACTATGAAAAGGGATAGCTTCGACTAGCAAACTATGGAAAAG
Found at i:55235408 original size:21 final size:21
Alignment explanation
Indices: 55235384--55235424 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
55235374 TGCAGTGTTG
*
55235384 AAAATTTTCATGA-TTTTTTAA
1 AAAATTCTC-TGAGTTTTTTAA
55235405 AAAATTCTCTGAGTTTTTTA
1 AAAATTCTCTGAGTTTTTTA
55235425 TTTAGTCTCG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 3 0.17
21 15 0.83
ACGTcount: A:0.34, C:0.07, G:0.07, T:0.51
Consensus pattern (21 bp):
AAAATTCTCTGAGTTTTTTAA
Found at i:55235421 original size:20 final size:21
Alignment explanation
Indices: 55235384--55235422 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 21
55235374 TGCAGTGTTG
* *
55235384 AAAATTTTCATGATTTTTTAA
1 AAAATTCTCATGAGTTTTTAA
55235405 AAAATTCTC-TGAGTTTTT
1 AAAATTCTCATGAGTTTTT
55235423 TATTTAGTCT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 8 0.50
21 8 0.50
ACGTcount: A:0.33, C:0.08, G:0.08, T:0.51
Consensus pattern (21 bp):
AAAATTCTCATGAGTTTTTAA
Found at i:55242607 original size:3 final size:3
Alignment explanation
Indices: 55242601--55242683 Score: 50
Period size: 3 Copynumber: 27.7 Consensus size: 3
55242591 TCCTTTACTT
*
55242601 TTA TTA TT- TCTA TTA -TA TTTA TTA TTT TTA TTA TTA TT- TCGTA TTA
1 TTA TTA TTA T-TA TTA TTA -TTA TTA TTA TTA TTA TTA TTA T--TA TTA
* * *
55242647 TTA -TA CCTA TTA TTA TCA TTA CTA TTA TTA TT- TTA TT
1 TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
55242684 TATTTAGTTT
Statistics
Matches: 63, Mismatches: 7, Indels: 20
0.70 0.08 0.22
Matches are distributed among these distances:
2 8 0.13
3 48 0.76
4 6 0.10
5 1 0.02
ACGTcount: A:0.28, C:0.07, G:0.01, T:0.64
Consensus pattern (3 bp):
TTA
Found at i:55242623 original size:18 final size:19
Alignment explanation
Indices: 55242600--55242639 Score: 64
Period size: 18 Copynumber: 2.2 Consensus size: 19
55242590 CTCCTTTACT
55242600 TTTATTATTTCTATTA-TA
1 TTTATTATTTCTATTATTA
*
55242618 TTTATTATTTTTATTATTA
1 TTTATTATTTCTATTATTA
55242637 TTT
1 TTT
55242640 CGTATTATTA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
18 15 0.75
19 5 0.25
ACGTcount: A:0.25, C:0.03, G:0.00, T:0.72
Consensus pattern (19 bp):
TTTATTATTTCTATTATTA
Found at i:55242662 original size:15 final size:15
Alignment explanation
Indices: 55242601--55242678 Score: 56
Period size: 15 Copynumber: 5.3 Consensus size: 15
55242591 TCCTTTACTT
*
55242601 TTATTATTTCTATTA
1 TTATTATTACTATTA
* *
55242616 -TATTTATTATTTTTA
1 TTA-TTATTACTATTA
*
55242631 TTATTATTTCGTATTA
1 TTATTATTAC-TATTA
*
55242647 TTA-TA--CCTATTA
1 TTATTATTACTATTA
*
55242659 TTATCATTACTATTA
1 TTATTATTACTATTA
55242674 TTATT
1 TTATT
55242679 TTATTTATTT
Statistics
Matches: 47, Mismatches: 10, Indels: 12
0.68 0.14 0.17
Matches are distributed among these distances:
12 8 0.17
13 2 0.04
14 2 0.04
15 26 0.55
16 9 0.19
ACGTcount: A:0.28, C:0.08, G:0.01, T:0.63
Consensus pattern (15 bp):
TTATTATTACTATTA
Found at i:55242790 original size:18 final size:18
Alignment explanation
Indices: 55242757--55242791 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
55242747 TTCAAATTTT
55242757 TTTTATTTTTAGTATTAG
1 TTTTATTTTTAGTATTAG
55242775 TTTTAGTTTTTA-TATTA
1 TTTTA-TTTTTAGTATTA
55242792 AGAATAGATA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 10 0.62
19 6 0.38
ACGTcount: A:0.23, C:0.00, G:0.09, T:0.69
Consensus pattern (18 bp):
TTTTATTTTTAGTATTAG
Found at i:55252656 original size:19 final size:19
Alignment explanation
Indices: 55252619--55252658 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
55252609 AGATTTAGAG
*
55252619 TTTAAGAGGGTCTGAGGGA
1 TTTAAGAGAGTCTGAGGGA
* *
55252638 TTTAAGAGAGTTTGGGGGA
1 TTTAAGAGAGTCTGAGGGA
55252657 TT
1 TT
55252659 AAGGGTTAAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.25, C:0.03, G:0.40, T:0.33
Consensus pattern (19 bp):
TTTAAGAGAGTCTGAGGGA
Found at i:55255939 original size:50 final size:50
Alignment explanation
Indices: 55255828--55256126 Score: 391
Period size: 50 Copynumber: 5.8 Consensus size: 50
55255818 ATTTGGGTAA
* * *
55255828 AGAGATCCTATGTAAGACCATGTCTGGGACATGGCATTGGCATCCTTGAGATCATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCA-CC--GAG---ATG
55255884 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATG
* *
55255934 AGAGGTCCCATGTAAGACCATGTCTAGGACATGGCGTTGGCACCAAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATG
* *
55255984 AGAGGTCCCATGTAAGACCATGTTTGGGACATGGCGTTGGCATCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATG
* * * * * *
55256034 AAAGGTCCCCTATAAGACCATGTCTGGGACATAGCATGGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATG
** *
55256084 AGAACATCCCATGTAAGACCATGTCTGGGACATGGCTTTGGCA
1 AG-AGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCA
55256127 TGTTATTATC
Statistics
Matches: 217, Mismatches: 25, Indels: 7
0.87 0.10 0.03
Matches are distributed among these distances:
50 140 0.65
51 33 0.15
53 3 0.01
55 2 0.01
56 39 0.18
ACGTcount: A:0.27, C:0.21, G:0.30, T:0.22
Consensus pattern (50 bp):
AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATG
Found at i:55272769 original size:2 final size:2
Alignment explanation
Indices: 55272762--55272799 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
55272752 TATTAGAAAG
55272762 AT AT AT 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
55272800 CAAAAGAAAG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:55272895 original size:10 final size:11
Alignment explanation
Indices: 55272863--55272897 Score: 54
Period size: 12 Copynumber: 3.2 Consensus size: 11
55272853 ATTTGCAGAC
55272863 AATGAAAGGAA
1 AATGAAAGGAA
55272874 AATGACAAGGAA
1 AATGA-AAGGAA
55272886 AATG-AAGGAA
1 AATGAAAGGAA
55272896 AA
1 AA
55272898 CTTGTTGAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
10 8 0.35
11 5 0.22
12 10 0.43
ACGTcount: A:0.63, C:0.03, G:0.26, T:0.09
Consensus pattern (11 bp):
AATGAAAGGAA
Found at i:55280072 original size:9 final size:9
Alignment explanation
Indices: 55280035--55280064 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
55280025 AAACTAATAA
*
55280035 ATTATTATT
1 ATTAATATT
55280044 ATTAATATT
1 ATTAATATT
55280053 ATTAATATT
1 ATTAATATT
55280062 ATT
1 ATT
55280065 GTTATTATCA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (9 bp):
ATTAATATT
Found at i:55283644 original size:42 final size:43
Alignment explanation
Indices: 55283579--55283734 Score: 148
Period size: 42 Copynumber: 3.7 Consensus size: 43
55283569 AACTCCTACA
* *
55283579 ATGCCAAC-ATCCCAGACGTGGTCTTACATGTAATCAATATCG
1 ATGCCAACTGTCCCAGACGTGGTCTTACATGAAATCAATATCG
* *
55283621 ATGCC-ACTGTCCCAGACAG-GGTCTTACACGAAATCAAATAT-A
1 ATGCCAACTGTCCCAGAC-GTGGTCTTACATGAAATC-AATATCG
* *
55283663 ATGCCGA-TGTCCCAGACATGGTCTTATACAT-AAATCTCAA-ATCG
1 ATGCCAACTGTCCCAGACGTGGTC-T-TACATGAAA--TCAATATCG
55283707 ATGCCAAC-GTCCCAGACGTGGTCTTACA
1 ATGCCAACTGTCCCAGACGTGGTCTTACA
55283735 CGATAACACA
Statistics
Matches: 94, Mismatches: 9, Indels: 22
0.75 0.07 0.18
Matches are distributed among these distances:
41 2 0.02
42 50 0.53
43 14 0.15
44 26 0.28
45 2 0.02
ACGTcount: A:0.31, C:0.27, G:0.17, T:0.24
Consensus pattern (43 bp):
ATGCCAACTGTCCCAGACGTGGTCTTACATGAAATCAATATCG
Found at i:55285623 original size:31 final size:30
Alignment explanation
Indices: 55285557--55285624 Score: 82
Period size: 30 Copynumber: 2.2 Consensus size: 30
55285547 TTGCCCAAGA
** ***
55285557 GTAAATACTCAAAATTTGAAGGGTTAAAGT
1 GTAAATACAAAAAATTTGAAGGACCAAAGT
55285587 GTAAATACAAAAAATTTGAAGGACCAAAGGT
1 GTAAATACAAAAAATTTGAAGGACCAAA-GT
55285618 GTAAATA
1 GTAAATA
55285625 TTTTAAGGGT
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
30 23 0.72
31 9 0.28
ACGTcount: A:0.49, C:0.07, G:0.19, T:0.25
Consensus pattern (30 bp):
GTAAATACAAAAAATTTGAAGGACCAAAGT
Found at i:55287025 original size:29 final size:28
Alignment explanation
Indices: 55286972--55287026 Score: 83
Period size: 28 Copynumber: 1.9 Consensus size: 28
55286962 TATTTTAAAA
*
55286972 TATTTTTAAAATAAATTTTTTTATTTTT
1 TATTTTTAAAATAAATTTTTGTATTTTT
*
55287000 TATTTTTTAAATAAATTTTTGGTATTT
1 TATTTTTAAAATAAATTTTT-GTATTT
55287027 ATTAAAAAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
28 19 0.79
29 5 0.21
ACGTcount: A:0.31, C:0.00, G:0.04, T:0.65
Consensus pattern (28 bp):
TATTTTTAAAATAAATTTTTGTATTTTT
Found at i:55294001 original size:24 final size:24
Alignment explanation
Indices: 55293955--55294001 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
55293945 CCATCTGCTT
* *
55293955 CTGATATGTATGATATGATATGAA
1 CTGATATGAATGATATGAGATGAA
55293979 CTGATATGAAGTGATA-GAGATGA
1 CTGATATGAA-TGATATGAGATGA
55294002 GGAGATATGT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 15 0.75
25 5 0.25
ACGTcount: A:0.38, C:0.04, G:0.26, T:0.32
Consensus pattern (24 bp):
CTGATATGAATGATATGAGATGAA
Found at i:55301109 original size:23 final size:23
Alignment explanation
Indices: 55301082--55301180 Score: 180
Period size: 23 Copynumber: 4.3 Consensus size: 23
55301072 AGTGTTATTG
55301082 ATCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
*
55301105 TTCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
55301128 ATCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
*
55301151 TTCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
55301174 ATCAGTG
1 ATCAGTG
55301181 TGGCACTTAT
Statistics
Matches: 72, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 72 1.00
ACGTcount: A:0.20, C:0.21, G:0.26, T:0.32
Consensus pattern (23 bp):
ATCAGTGGTAGCTTCGGCTACAT
Found at i:55301352 original size:38 final size:37
Alignment explanation
Indices: 55301310--55301382 Score: 103
Period size: 38 Copynumber: 1.9 Consensus size: 37
55301300 ATGTGCGGAA
* *
55301310 TTGAATTGAATATTGACTTGAAAA-TGGAAAAGTGAATT
1 TTGAATTGAATAGTGA-TT-AAAAGTGAAAAAGTGAATT
55301348 TTGAATTGAATAGTGATTAAAAGTGAAAAAGTGAA
1 TTGAATTGAATAGTGATTAAAAGTGAAAAAGTGAA
55301383 ATTATGAAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
36 4 0.12
37 13 0.41
38 15 0.47
ACGTcount: A:0.45, C:0.01, G:0.22, T:0.32
Consensus pattern (37 bp):
TTGAATTGAATAGTGATTAAAAGTGAAAAAGTGAATT
Found at i:55307252 original size:27 final size:27
Alignment explanation
Indices: 55307214--55307342 Score: 138
Period size: 27 Copynumber: 4.7 Consensus size: 27
55307204 GTGAGGTCAA
* *
55307214 TAAAATAATCGAAGTACCCCTATAGGG
1 TAAAATGATCGAAATACCCCTATAGGG
*
55307241 TAAAATGATCGAAATACCCTTATAGGG
1 TAAAATGATCGAAATACCCCTATAGGG
* * *
55307268 TAAAATAACCGAAATACCCCCATAGGG
1 TAAAATGATCGAAATACCCCTATAGGG
*
55307295 TAAAATGAGT-GAAATA-CCCTGATATGG
1 TAAAATGA-TCGAAATACCCCT-ATAGGG
55307322 TAAAATGA-CTGAAATATCCCC
1 TAAAATGATC-GAAATA-CCCC
55307343 ATAAGTTAAA
Statistics
Matches: 85, Mismatches: 11, Indels: 10
0.80 0.10 0.09
Matches are distributed among these distances:
26 3 0.04
27 79 0.93
29 3 0.04
ACGTcount: A:0.42, C:0.19, G:0.17, T:0.22
Consensus pattern (27 bp):
TAAAATGATCGAAATACCCCTATAGGG
Found at i:55307296 original size:54 final size:54
Alignment explanation
Indices: 55307214--55307354 Score: 176
Period size: 54 Copynumber: 2.6 Consensus size: 54
55307204 GTGAGGTCAA
* * * *
55307214 TAAAATAATCGAAGTACCCCTATAGGGTAAAATGA-TCGAAATACCCTTATAGGG
1 TAAAATAACCGAAATACCCCCATAGGGTAAAATGAGT-GAAATACCCTGATAGGG
*
55307268 TAAAATAACCGAAATACCCCCATAGGGTAAAATGAGTGAAATACCCTGATATGG
1 TAAAATAACCGAAATACCCCCATAGGGTAAAATGAGTGAAATACCCTGATAGGG
* * * * *
55307322 TAAAATGACTGAAATATCCCCATAAGTTAAAAT
1 TAAAATAACCGAAATACCCCCATAGGGTAAAAT
55307355 AACTGTTATA
Statistics
Matches: 76, Mismatches: 10, Indels: 2
0.86 0.11 0.02
Matches are distributed among these distances:
54 75 0.99
55 1 0.01
ACGTcount: A:0.43, C:0.17, G:0.16, T:0.23
Consensus pattern (54 bp):
TAAAATAACCGAAATACCCCCATAGGGTAAAATGAGTGAAATACCCTGATAGGG
Found at i:55307352 original size:27 final size:26
Alignment explanation
Indices: 55307214--55307368 Score: 98
Period size: 27 Copynumber: 5.8 Consensus size: 26
55307204 GTGAGGTCAA
* *
55307214 TAAAATAA-TCGAAGTACCCCTATAGGG
1 TAAAATAACT-GAAATACCCC-ATAAGG
* * *
55307241 TAAAATGA-TCGAAATACCCTTATAGGG
1 TAAAATAACT-GAAATACCC-CATAAGG
* *
55307268 TAAAATAACCGAAATACCCCCATAGGG
1 TAAAATAACTGAAATA-CCCCATAAGG
* * * *
55307295 TAAAATGAGTGAAATACCCTGATATGG
1 TAAAATAACTGAAATACCC-CATAAGG
* *
55307322 TAAAATGACTGAAATATCCCCATAAGT
1 TAAAATAACTGAAATA-CCCCATAAGG
**
55307349 TAAAATAACTGTTATACCCC
1 TAAAATAACTGAAATACCCC
55307369 TAGGAGATTA
Statistics
Matches: 105, Mismatches: 18, Indels: 11
0.78 0.13 0.08
Matches are distributed among these distances:
26 7 0.07
27 92 0.88
28 6 0.06
ACGTcount: A:0.42, C:0.19, G:0.15, T:0.24
Consensus pattern (26 bp):
TAAAATAACTGAAATACCCCATAAGG
Found at i:55307584 original size:26 final size:26
Alignment explanation
Indices: 55307531--55307585 Score: 83
Period size: 26 Copynumber: 2.1 Consensus size: 26
55307521 TCTGGCACAT
* *
55307531 ATACTGTTACTGGCAGCTTTGTTACG
1 ATACTGATACTGGCAGCTTTGCTACG
*
55307557 ATACTGATACTGGCAGCTTTGCTGCG
1 ATACTGATACTGGCAGCTTTGCTACG
55307583 ATA
1 ATA
55307586 TTGGTGTGTT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.22, C:0.20, G:0.24, T:0.35
Consensus pattern (26 bp):
ATACTGATACTGGCAGCTTTGCTACG
Found at i:55314708 original size:27 final size:27
Alignment explanation
Indices: 55314670--55314745 Score: 100
Period size: 27 Copynumber: 2.8 Consensus size: 27
55314660 TGAGGTTAAT
*
55314670 AAAATGACTGAAATACCCCTATAGGGC
1 AAAATGATTGAAATACCCCTATAGGGC
*
55314697 AAAATGATTGAAATA-CCCTCATAGGGT
1 AAAATGATTGAAATACCCCT-ATAGGGC
**
55314724 AAAATGATTGTTATACCCCTAT
1 AAAATGATTGAAATACCCCTAT
55314746 GAGATTAAAT
Statistics
Matches: 43, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
26 4 0.09
27 35 0.81
28 4 0.09
ACGTcount: A:0.39, C:0.18, G:0.16, T:0.26
Consensus pattern (27 bp):
AAAATGATTGAAATACCCCTATAGGGC
Found at i:55315108 original size:33 final size:34
Alignment explanation
Indices: 55315057--55315127 Score: 90
Period size: 33 Copynumber: 2.1 Consensus size: 34
55315047 GCATTATTAC
* * *
55315057 ACTGTTACTGTATTGGGCTAAGGCCCACACTG-T
1 ACTGATACTGAATAGGGCTAAGGCCCACACTGTT
* *
55315090 ACTGATACTGAATAGGGCTCAGGCCCAGACTGTT
1 ACTGATACTGAATAGGGCTAAGGCCCACACTGTT
55315124 ACTG
1 ACTG
55315128 CATGTTGTAT
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
33 27 0.84
34 5 0.16
ACGTcount: A:0.24, C:0.24, G:0.25, T:0.27
Consensus pattern (34 bp):
ACTGATACTGAATAGGGCTAAGGCCCACACTGTT
Found at i:55323881 original size:12 final size:12
Alignment explanation
Indices: 55323847--55323875 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
55323837 AATTTGAATT
55323847 TTATTAGGATTA
1 TTATTAGGATTA
55323859 TTATTAGGATTA
1 TTATTAGGATTA
55323871 TTATT
1 TTATT
55323876 TAGATTTAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.31, C:0.00, G:0.14, T:0.55
Consensus pattern (12 bp):
TTATTAGGATTA
Found at i:55324630 original size:19 final size:20
Alignment explanation
Indices: 55324608--55324646 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
55324598 TCTCAATTTT
*
55324608 ATTTC-TTTTTACAATTTCG
1 ATTTCATTTATACAATTTCG
55324627 ATTTCAATTTATACAATTTC
1 ATTTC-ATTTATACAATTTC
55324647 AACCCCTCCA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 5 0.29
21 12 0.71
ACGTcount: A:0.28, C:0.15, G:0.03, T:0.54
Consensus pattern (20 bp):
ATTTCATTTATACAATTTCG
Found at i:55327382 original size:13 final size:12
Alignment explanation
Indices: 55327346--55327383 Score: 51
Period size: 12 Copynumber: 3.1 Consensus size: 12
55327336 ATATGGATTA
55327346 TTGTTT-TTTAT
1 TTGTTTATTTAT
55327357 CTTGTTTATTTAT
1 -TTGTTTATTTAT
55327370 TTGTTTATATTAT
1 TTGTTTAT-TTAT
55327383 T
1 T
55327384 CTTATGCGAT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
12 14 0.58
13 10 0.42
ACGTcount: A:0.16, C:0.03, G:0.08, T:0.74
Consensus pattern (12 bp):
TTGTTTATTTAT
Found at i:55339430 original size:132 final size:132
Alignment explanation
Indices: 55339193--55339540 Score: 588
Period size: 132 Copynumber: 2.6 Consensus size: 132
55339183 ATAGGTGAAA
*
55339193 CACCAAGCCTTGTCTCCCTAAGCAGCAGTGGAGAAGGTTGAAGATTGTAGATCTTATCTCCCTAA
1 CACCAAGCCTTGTCTCCCTGAGCAGCAGTGGAGAAGGTTGAAGATTGTAGATCTTATCTCCCTAA
* * *
55339258 GCAGTAGTGGAGTAGATCAAAGATGGCGAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTGA
66 GCAGTAGTGGAGTAGATCGAAGACGGCGAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAA
55339323 GC
131 GC
* *
55339325 CACCAAGCCTTGTCTCCCTGAGCAGCAGTGGAGAAGGTTGAAGATTGTAGATCTTATCTGCTTAA
1 CACCAAGCCTTGTCTCCCTGAGCAGCAGTGGAGAAGGTTGAAGATTGTAGATCTTATCTCCCTAA
*
55339390 GCAGTAGTGGAGTAGATCGAAGACGGCGAATCTTATCTTTCCAGGATAGTGGGAAGCAGATTTAA
66 GCAGTAGTGGAGTAGATCGAAGACGGCGAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAA
55339455 GC
131 GC
* * * *
55339457 CACCAAGCCTTGTCTCCCTGAGTAGCAGCGGAGAAAGTTGAAGATTGTAGATCTTATTTCCCTAA
1 CACCAAGCCTTGTCTCCCTGAGCAGCAGTGGAGAAGGTTGAAGATTGTAGATCTTATCTCCCTAA
*
55339522 GCAGTAGTGGAGCAGATCG
66 GCAGTAGTGGAGTAGATCG
55339541 CATCCAATCT
Statistics
Matches: 202, Mismatches: 14, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
132 202 1.00
ACGTcount: A:0.28, C:0.19, G:0.27, T:0.26
Consensus pattern (132 bp):
CACCAAGCCTTGTCTCCCTGAGCAGCAGTGGAGAAGGTTGAAGATTGTAGATCTTATCTCCCTAA
GCAGTAGTGGAGTAGATCGAAGACGGCGAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAA
GC
Found at i:55341137 original size:2 final size:2
Alignment explanation
Indices: 55341099--55341123 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
55341089 TCATATAACC
55341099 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
55341124 TTTGGTGCAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:55344435 original size:9 final size:9
Alignment explanation
Indices: 55344421--55344460 Score: 53
Period size: 9 Copynumber: 4.4 Consensus size: 9
55344411 ATATTATTTT
55344421 ATTTAATTA
1 ATTTAATTA
55344430 ATTTAATTA
1 ATTTAATTA
**
55344439 ATCAAATTA
1 ATTTAATTA
*
55344448 AATTAATTA
1 ATTTAATTA
55344457 ATTT
1 ATTT
55344461 TCCAATTAAA
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
9 25 1.00
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (9 bp):
ATTTAATTA
Found at i:55346511 original size:28 final size:28
Alignment explanation
Indices: 55346462--55346519 Score: 68
Period size: 28 Copynumber: 2.1 Consensus size: 28
55346452 CACAATGACT
55346462 AATTAATTTAATTTAATTTTAA-AACTTC
1 AATTAATTTAATTTAATTTTAATAA-TTC
55346490 AATTAA-TTAA-TTAATTAATTAATAATTC
1 AATTAATTTAATTTAATT--TTAATAATTC
55346518 AA
1 AA
55346520 AAAATCATAA
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
26 6 0.22
27 4 0.15
28 15 0.56
29 2 0.07
ACGTcount: A:0.48, C:0.05, G:0.00, T:0.47
Consensus pattern (28 bp):
AATTAATTTAATTTAATTTTAATAATTC
Found at i:55350923 original size:11 final size:12
Alignment explanation
Indices: 55350893--55350925 Score: 52
Period size: 11 Copynumber: 2.9 Consensus size: 12
55350883 TGATTTGTAA
55350893 TAATAAATATAT
1 TAATAAATATAT
55350905 T-ATAAATATAT
1 TAATAAATATAT
55350916 TAAT-AATATA
1 TAATAAATATA
55350926 AAAAAAGAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
11 17 0.85
12 3 0.15
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (12 bp):
TAATAAATATAT
Found at i:55351891 original size:30 final size:29
Alignment explanation
Indices: 55351856--55351912 Score: 87
Period size: 30 Copynumber: 1.9 Consensus size: 29
55351846 TTTTATATAT
*
55351856 ATATACATACTTACACTGTTTTATTTTACG
1 ATATACATACTTACA-TCTTTTATTTTACG
*
55351886 ATATACATACTTATATCTTTTATTTTA
1 ATATACATACTTACATCTTTTATTTTA
55351913 TGTAATATAT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
29 11 0.44
30 14 0.56
ACGTcount: A:0.32, C:0.14, G:0.04, T:0.51
Consensus pattern (29 bp):
ATATACATACTTACATCTTTTATTTTACG
Found at i:55356148 original size:10 final size:10
Alignment explanation
Indices: 55356110--55356168 Score: 57
Period size: 10 Copynumber: 5.7 Consensus size: 10
55356100 ACAATGGAGG
55356110 CAAAATAAAAA
1 CAAAA-AAAAA
55356121 CAAAAACAAAAA
1 C-AAAA-AAAAA
* *
55356133 CAAAAAAGAG
1 CAAAAAAAAA
55356143 CAAAAAAAAA
1 CAAAAAAAAA
*
55356153 CAAAAAACAA
1 CAAAAAAAAA
55356163 -AAAAAA
1 CAAAAAA
55356169 CTCTACCGGG
Statistics
Matches: 41, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
9 6 0.15
10 20 0.49
11 5 0.12
12 10 0.24
ACGTcount: A:0.83, C:0.12, G:0.03, T:0.02
Consensus pattern (10 bp):
CAAAAAAAAA
Found at i:55357172 original size:108 final size:108
Alignment explanation
Indices: 55356983--55357179 Score: 299
Period size: 108 Copynumber: 1.8 Consensus size: 108
55356973 TCTCATTTTG
*
55356983 TAGCAAAATTTACTATCTTGATTAATTTTTTCATTTAGAGCTTTGCTCTCAATAAATTTCCATCT
1 TAGCAAAATTTACTATCTTGATTAATTTTTTCATTTAGAGCTTTGCTCTCAAAAAATTTCCATCT
55357048 TATCCATTGTGATAATCTTTTTCATCTTATTCATCTCGTATCT
66 TATCCATTGTGATAATCTTTTTCATCTTATTCATCTCGTATCT
** * *
55357091 TAGCAAAATTTGTTATCTTGATTGATTTATTT-GTTTAGAGCTTTGCTCTCAACAAAATTT-CAT
1 TAGCAAAATTTACTATCTTGATTAATTT-TTTCATTTAGAGCTTTGCTCTCAA-AAAATTTCCAT
* *
55357154 CTTGTCCATTTTGATAATCTTTTTCA
64 CTTATCCATTGTGATAATCTTTTTCA
55357180 AGCATTTTTT
Statistics
Matches: 80, Mismatches: 7, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
108 71 0.89
109 9 0.11
ACGTcount: A:0.26, C:0.17, G:0.09, T:0.48
Consensus pattern (108 bp):
TAGCAAAATTTACTATCTTGATTAATTTTTTCATTTAGAGCTTTGCTCTCAAAAAATTTCCATCT
TATCCATTGTGATAATCTTTTTCATCTTATTCATCTCGTATCT
Found at i:55358139 original size:46 final size:46
Alignment explanation
Indices: 55358071--55358905 Score: 1121
Period size: 46 Copynumber: 18.2 Consensus size: 46
55358061 GACTAGAAGC
55358071 AGCAGATCTTGTCTTCCTGTATTTGGCAGCGAAGTAGATCGAAGAT
1 AGCAGATCTTGTCTTCCTGTATTTGGCAGCGAAGTAGATCGAAGAT
* * *
55358117 TGCAGATCTTGTCTTCCTGTATTTGGCAGCGGAGTAGATCGAAAAT
1 AGCAGATCTTGTCTTCCTGTATTTGGCAGCGAAGTAGATCGAAGAT
* * * *
55358163 TGTAGAACTTGTCTTCCTATATTTGGCAGCGAAGTAGATCGAAGAT
1 AGCAGATCTTGTCTTCCTGTATTTGGCAGCGAAGTAGATCGAAGAT
*
55358209 TGCAGATCTTGTCTTCCTGTATTTGGCAGC-AGAGTAGATCGAAGAT
1 AGCAGATCTTGTCTTCCTGTATTTGGCAGCGA-AGTAGATCGAAGAT
* * *
55358255 AGTAGATCTTGTCTTCCTGTATTTGGCAGTGGAGTAGATCGAAGATT
1 AGCAGATCTTGTCTTCCTGTATTTGGCAGCGAAGTAGATCGAAGA-T
*
55358302 A-TAGATCTTGTCTTCCTGTATTTGGCAGC-AGAGTAGATCGAAGAT
1 AGCAGATCTTGTCTTCCTGTATTTGGCAGCGA-AGTAGATCGAAGAT
* * * * *
55358347 AGTAGATCTTGTCTTTCTGTATTTGGTAGTGGAGTAGATCGAAGAT
1 AGCAGATCTTGTCTTCCTGTATTTGGCAGCGAAGTAGATCGAAGAT
** * *
55358393 AATAGATCTTGTCTTCCTGTATTTGGCAGCGAAGTAGGTCAAAGATT
1 AGCAGATCTTGTCTTCCTGTATTTGGCAGCGAAGTAGATCGAAGA-T
*
55358440 A-CAGATCTTGTCTTCCTGTATTTGGCAGCGGAGTAGATCGAAGAT
1 AGCAGATCTTGTCTTCCTGTATTTGGCAGCGAAGTAGATCGAAGAT
* *
55358485 AGCAGATCTTGTCTTCCTGTATTTGGCAGTGGAGTAGATCGAAGAT
1 AGCAGATCTTGTCTTCCTGTATTTGGCAGCGAAGTAGATCGAAGAT
*
55358531 AGCAGATCTTGTCTTCCTGTATTTGGCAGTGGAA-TAGATCGAAGAT
1 AGCAGATCTTGTCTTCCTGTATTTGGCAG-CGAAGTAGATCGAAGAT
**
55358577 AATAGATCTTGTCTTCCTGTATTTGGCAGCGAAGTA-AGTCGAAGATT
1 AGCAGATCTTGTCTTCCTGTATTTGGCAGCGAAGTAGA-TCGAAGA-T
*
55358624 A-CAGATCTTGTCTTCCTATATTTGGCAGC-AGAGTAGATCGAAGAT
1 AGCAGATCTTGTCTTCCTGTATTTGGCAGCGA-AGTAGATCGAAGAT
* * *
55358669 AGCAGATCTTGTCTTCTTGTATTTGGCAGTGGAGTAGATCGAAGAT
1 AGCAGATCTTGTCTTCCTGTATTTGGCAGCGAAGTAGATCGAAGAT
* * * *
55358715 AGTAGATCTTGTCTTCCTGTATTTGGCAGCGAAGTAGGTCAAAAATT
1 AGCAGATCTTGTCTTCCTGTATTTGGCAGCGAAGTAGATCGAAGA-T
* *
55358762 A-CAGATCTTGTCTTCCTGTATTTGGCAGCGGAGTAGATCAAAGAT
1 AGCAGATCTTGTCTTCCTGTATTTGGCAGCGAAGTAGATCGAAGAT
* * * * *
55358807 AGTAGATCTTGTCTTCCTATATTTAGCAGCGGAGCAGATCGAAGAT
1 AGCAGATCTTGTCTTCCTGTATTTGGCAGCGAAGTAGATCGAAGAT
* *
55358853 AGCAGGTCTTATCTTCCTGTATTTGGCAGCGAAGTAGATCGAAGAT
1 AGCAGATCTTGTCTTCCTGTATTTGGCAGCGAAGTAGATCGAAGAT
*
55358899 TGCAGAT
1 AGCAGAT
55358906 TCTGTCACCC
Statistics
Matches: 702, Mismatches: 69, Indels: 36
0.87 0.09 0.04
Matches are distributed among these distances:
45 14 0.02
46 677 0.96
47 11 0.02
ACGTcount: A:0.26, C:0.16, G:0.26, T:0.33
Consensus pattern (46 bp):
AGCAGATCTTGTCTTCCTGTATTTGGCAGCGAAGTAGATCGAAGAT
Found at i:55359259 original size:128 final size:128
Alignment explanation
Indices: 55359119--55359805 Score: 1088
Period size: 128 Copynumber: 5.4 Consensus size: 128
55359109 TATTTAAGCC
* * * *
55359119 ATCAGTCCTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAACCCCAGATCTTATCTCTCTGAAG
1 ATCAATCCTATCTCCCTGAAGTTACAGTGGAGCGGATTAAAACCACAGATCTTATCTCTCTAAAG
* *
55359184 TTGCAGTAGAGCAGATCGCATCTAGTCTTATCTCCCTAAGCAGTAGTGGAGCAGACGAAAGAA
66 TTGCAGTAGAGCAGATCGCATCAAGTCTTATCTCCCTAAGCAGTAGTGGAGTAGACGAAAGAA
* * *
55359247 ATCAATCCTATCTTCCTGAAGTTGCAGTGGAGCGGATTAAAACCACAGATCTTATCTCTCTGAAG
1 ATCAATCCTATCTCCCTGAAGTTACAGTGGAGCGGATTAAAACCACAGATCTTATCTCTCTAAAG
*
55359312 TTGCAGTAGAGCAGATCGCATCAAGTCTTATCTCCCTAAGCAGTAGTGGAGTAGACGAAAAAA
66 TTGCAGTAGAGCAGATCGCATCAAGTCTTATCTCCCTAAGCAGTAGTGGAGTAGACGAAAGAA
* * *
55359375 ATCAATCCTATCTCTCTGAAGTTACAATAGAGCGGATTAAAACCACAGATCTTATCTCTCTAAAG
1 ATCAATCCTATCTCCCTGAAGTTACAGTGGAGCGGATTAAAACCACAGATCTTATCTCTCTAAAG
*
55359440 TTGCAGTAGAGCAGATCGCATCAAGTCTTATCTCCCTAAACAGTAGTGGAGTAGACGAAAGAA
66 TTGCAGTAGAGCAGATCGCATCAAGTCTTATCTCCCTAAGCAGTAGTGGAGTAGACGAAAGAA
* *
55359503 ATCAATCCTATCTCCCTGAAGTTACAGTGGGGCGGATTAAAACCCCAGATCTTATCTCTCTAAAG
1 ATCAATCCTATCTCCCTGAAGTTACAGTGGAGCGGATTAAAACCACAGATCTTATCTCTCTAAAG
* *
55359568 TTGCAGTAGAGTAGATCGCATCCAGTCTTATCTCCCTAAGCAGTAGTGGAGTAGACGAAAGAA
66 TTGCAGTAGAGCAGATCGCATCAAGTCTTATCTCCCTAAGCAGTAGTGGAGTAGACGAAAGAA
* *
55359631 ATCAATCATATCTCCCTGAAGTTACAGTGGAGCGGATTAAAACCACAGATCTTATCTCTCTTAAG
1 ATCAATCCTATCTCCCTGAAGTTACAGTGGAGCGGATTAAAACCACAGATCTTATCTCTCTAAAG
* * * ** * *
55359696 TTACAGTAGAGCAGATCACATCTAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGAC-AGAAGAA
66 TTGCAGTAGAGCAGATCGCATCAAGTCTTATCTCCCT-AAGCAGTAGTGGAGTAGACGA-AAGAA
* *
55359760 ACCAATCCTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAACCAC
1 ATCAATCCTATCTCCCTGAAGTTACAGTGGAGCGGATTAAAACCAC
55359806 GAATCTCGTC
Statistics
Matches: 520, Mismatches: 37, Indels: 3
0.93 0.07 0.01
Matches are distributed among these distances:
128 457 0.88
129 63 0.12
ACGTcount: A:0.32, C:0.22, G:0.20, T:0.25
Consensus pattern (128 bp):
ATCAATCCTATCTCCCTGAAGTTACAGTGGAGCGGATTAAAACCACAGATCTTATCTCTCTAAAG
TTGCAGTAGAGCAGATCGCATCAAGTCTTATCTCCCTAAGCAGTAGTGGAGTAGACGAAAGAA
Found at i:55359360 original size:84 final size:85
Alignment explanation
Indices: 55359270--55359618 Score: 187
Period size: 84 Copynumber: 4.1 Consensus size: 85
55359260 TCCTGAAGTT
* * * *
55359270 GCAGTGGAGCGGATTAAAACCACAGATCTTATCTCTCTGAAGTTGCAGTAGAGCAGATCGCATCA
1 GCAGTGGAGCAGATTAAAACCACAGATCTTATCTCTCTAAAGTTGCAGTAGAGCAGATAGAATCA
55359335 AGTCTTATCTCCCT-AAGCA
66 AGTCTTATCTCCCTAAAGCA
* * ** ** * * * * * * *
55359354 GTAGTGGAGTAGACGAAAAAAATCA-ATCCTATCTCTCTGAAGTTACAATAGAGCGGATTAAAAC
1 GCAGTGGAGCAGATTAAAACCA-CAGATCTTATCTCTCTAAAGTTGCAGTAGAGCAGA-TAGAAT
* **
55359418 CACAGATCTTATCTCTCTAAAGTT
64 CA-AG-TCTTATCTCCCTAAAGCA
* *** * * * *
55359442 GCAGTAGAGCAGA-TCGCATCA-AG-TCTTATCTCCCTAAACAGTAGTGGAGTAGA-C-GAAAGA
1 GCAGTGGAGCAGATTAAAACCACAGATCTTATCTCTCT-AA-AGT--TGCAGTAGAGCAGATAG-
* * *
55359502 AATCAA-TCCTATCTCCCTGAAGTTA
61 AATCAAGTCTTATCTCCCTAAAG-CA
* * * * * * *
55359527 -CAGTGGGGCGGATTAAAACCCCAGATCTTATCTCTCTAAAGTTGCAGTAGAGTAGATCGCATCC
1 GCAGTGGAGCAGATTAAAACCACAGATCTTATCTCTCTAAAGTTGCAGTAGAGCAGATAGAATCA
55359591 AGTCTTATCTCCCT-AAGCA
66 AGTCTTATCTCCCTAAAGCA
*
55359610 GTAGTGGAG
1 GCAGTGGAG
55359619 TAGACGAAAG
Statistics
Matches: 187, Mismatches: 59, Indels: 38
0.66 0.21 0.13
Matches are distributed among these distances:
83 9 0.05
84 78 0.42
85 38 0.20
86 9 0.05
87 33 0.18
88 14 0.07
89 6 0.03
ACGTcount: A:0.32, C:0.22, G:0.21, T:0.26
Consensus pattern (85 bp):
GCAGTGGAGCAGATTAAAACCACAGATCTTATCTCTCTAAAGTTGCAGTAGAGCAGATAGAATCA
AGTCTTATCTCCCTAAAGCA
Found at i:55359738 original size:41 final size:44
Alignment explanation
Indices: 55359127--55359805 Score: 218
Period size: 44 Copynumber: 15.9 Consensus size: 44
55359117 CCATCAGTCC
* * *
55359127 TATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAACCCCAGATCT
1 TATCTCCCTGAAGTTACAGTGGAGCAGATTAAAACCACAGATCT
* * * *** * *
55359171 TATCTCTCTGAAGTTGCAGTAGAGCAGA-TCGCATC-TAG-TCT
1 TATCTCCCTGAAGTTACAGTGGAGCAGATTAAAACCACAGATCT
* * ** * *
55359212 TATCTCCCT-AAG-CAGTAGTGGAGCAGACGAAAGA-AATCA-ATCC
1 TATCTCCCTGAAGTTA-CAGTGGAGCAGATTAAA-ACCA-CAGATCT
* * *
55359255 TATCTTCCTGAAGTTGCAGTGGAGCGGATTAAAACCACAGATCT
1 TATCTCCCTGAAGTTACAGTGGAGCAGATTAAAACCACAGATCT
* * * *** *
55359299 TATCTCTCTGAAGTTGCAGTAGAGCAGA-TCGCATCA-AG-TCT
1 TATCTCCCTGAAGTTACAGTGGAGCAGATTAAAACCACAGATCT
* * * ** ** *
55359340 TATCTCCCT-AAG-CAGTAGTGGAGTAGACGAAAAAAATCA-ATCC
1 TATCTCCCTGAAGTTA-CAGTGGAGCAGATTAAAACCA-CAGATCT
* * * *
55359383 TATCTCTCTGAAGTTACAATAGAGCGGATTAAAACCACAGATCT
1 TATCTCCCTGAAGTTACAGTGGAGCAGATTAAAACCACAGATCT
* * * * *** *
55359427 TATCTCTCTAAAGTTGCAGTAGAGCAGA-TCGCATCA-AG-TCT
1 TATCTCCCTGAAGTTACAGTGGAGCAGATTAAAACCACAGATCT
* * ** * *
55359468 TATCTCCCTAAACAG-T--AGTGGAGTAGACGAAAGA-AATCA-ATCC
1 TATCTCCCT-GA-AGTTACAGTGGAGCAGATTAAA-ACCA-CAGATCT
* * *
55359511 TATCTCCCTGAAGTTACAGTGGGGCGGATTAAAACCCCAGATCT
1 TATCTCCCTGAAGTTACAGTGGAGCAGATTAAAACCACAGATCT
* * * * * *** *
55359555 TATCTCTCTAAAGTTGCAGTAGAGTAGA-TCGCATC-CAG-TCT
1 TATCTCCCTGAAGTTACAGTGGAGCAGATTAAAACCACAGATCT
* * * ** * *
55359596 TATCTCCCT-AAG-CAGTAGTGGAGTAGACGAAAGA-AATCA-ATCA
1 TATCTCCCTGAAGTTA-CAGTGGAGCAGATTAAA-ACCA-CAGATCT
*
55359639 TATCTCCCTGAAGTTACAGTGGAGCGGATTAAAACCACAGATCT
1 TATCTCCCTGAAGTTACAGTGGAGCAGATTAAAACCACAGATCT
* * * * * * *
55359683 TATCTCTCTTAAGTTACAGTAGAGCAGA-TCACATC-TAG-TCT
1 TATCTCCCTGAAGTTACAGTGGAGCAGATTAAAACCACAGATCT
* ** * *
55359724 TATCTCCCTGAAGTTGCAGTGGAGCAGACAGAAGAAAC-CA-ATCC
1 TATCTCCCTGAAGTTACAGTGGAGCAGA-TTAA-AACCACAGATCT
* *
55359768 TATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAACCAC
1 TATCTCCCTGAAGTTACAGTGGAGCAGATTAAAACCAC
55359806 GAATCTCGTC
Statistics
Matches: 450, Mismatches: 140, Indels: 91
0.66 0.21 0.13
Matches are distributed among these distances:
40 47 0.10
41 76 0.17
42 22 0.05
43 82 0.18
44 221 0.49
45 2 0.00
ACGTcount: A:0.32, C:0.22, G:0.20, T:0.25
Consensus pattern (44 bp):
TATCTCCCTGAAGTTACAGTGGAGCAGATTAAAACCACAGATCT
Found at i:55361326 original size:18 final size:18
Alignment explanation
Indices: 55361305--55361353 Score: 66
Period size: 18 Copynumber: 2.8 Consensus size: 18
55361295 CTATTATAAC
55361305 TATTTATATATATCATCT
1 TATTTATATATATCATCT
*
55361323 TATTATATATTTAT-ATCT
1 TATT-TATATATATCATCT
55361341 TA-TTATATATATC
1 TATTTATATATATC
55361354 TATATATCTC
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
16 8 0.30
17 1 0.04
18 10 0.37
19 8 0.30
ACGTcount: A:0.35, C:0.08, G:0.00, T:0.57
Consensus pattern (18 bp):
TATTTATATATATCATCT
Found at i:55361523 original size:30 final size:29
Alignment explanation
Indices: 55361489--55361545 Score: 87
Period size: 30 Copynumber: 1.9 Consensus size: 29
55361479 TTATATATAT
*
55361489 ATATACATACTTACACTGTTTTATTTTACG
1 ATATACATACTTACA-TCTTTTATTTTACG
*
55361519 ATATACATACTTATATCTTTTATTTTA
1 ATATACATACTTACATCTTTTATTTTA
55361546 TGTAATATAT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
29 11 0.44
30 14 0.56
ACGTcount: A:0.32, C:0.14, G:0.04, T:0.51
Consensus pattern (29 bp):
ATATACATACTTACATCTTTTATTTTACG
Found at i:55368403 original size:23 final size:22
Alignment explanation
Indices: 55368360--55368403 Score: 52
Period size: 23 Copynumber: 2.0 Consensus size: 22
55368350 CAATTTAATC
* *
55368360 TATATTTTTCATTTTAATATTG
1 TATATTTTTAATATTAATATTG
*
55368382 TATATATTTTAATATTATTATT
1 TATAT-TTTTAATATTAATATT
55368404 AATTAATTTC
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
22 5 0.28
23 13 0.72
ACGTcount: A:0.32, C:0.02, G:0.02, T:0.64
Consensus pattern (22 bp):
TATATTTTTAATATTAATATTG
Found at i:55376866 original size:33 final size:35
Alignment explanation
Indices: 55376824--55376889 Score: 100
Period size: 33 Copynumber: 1.9 Consensus size: 35
55376814 TGTCTCCTGC
55376824 GGTTAGGGTTTTGG-GTTATT-GGATTAGGGTTAG
1 GGTTAGGGTTTTGGTGTTATTAGGATTAGGGTTAG
* *
55376857 GGTTAGGGTTTTGGTGTTTTTAGGTTTAGGGTT
1 GGTTAGGGTTTTGGTGTTATTAGGATTAGGGTT
55376890 TTAGAGAAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
33 14 0.48
34 5 0.17
35 10 0.34
ACGTcount: A:0.12, C:0.00, G:0.41, T:0.47
Consensus pattern (35 bp):
GGTTAGGGTTTTGGTGTTATTAGGATTAGGGTTAG
Found at i:55377205 original size:97 final size:94
Alignment explanation
Indices: 55376990--55377219 Score: 257
Period size: 95 Copynumber: 2.4 Consensus size: 94
55376980 TGTTTATTAT
* * * * *
55376990 TTTTTAAGAAAAAATCAATTAAATTAAGGTTTATGGTTTCTTGAGTAATTTAATTAAAAAAATTT
1 TTTTTAAG-AAAAATCAAATAAATTAGGGTTTAGGGTTACTTGAGTAAATTAATTAAAAAAATTT
55377055 AAAAATCAAATTAGGGTTTAGAGTTAAGGG
65 AAAAATCAAATTAGGGTTTAGAGTTAAGGG
* * * **
55377085 TTTTTATGGAAAAATCAAATAAATTAGGGTTCAGGGTTACTTGAGTAAATTAATTATAAATTTTT
1 TTTTTA-AGAAAAATCAAATAAATTAGGGTTTAGGGTTACTTGAGTAAATTAATTAAAAAAATTT
* * *
55377150 AAAAATTTTAGATTAGGGTTTA-AGGTTTAGGG
65 AAAAA--TCAAATTAGGGTTTAGA-GTTAAGGG
*
55377182 -TTTTAAGTAAAAACTTAAATAAATTAGGGTTTAGGGTT
1 TTTTTAAG-AAAAA-TCAAATAAATTAGGGTTTAGGGTT
55377220 TACGGTTACT
Statistics
Matches: 113, Mismatches: 16, Indels: 10
0.81 0.12 0.07
Matches are distributed among these distances:
95 59 0.52
96 12 0.11
97 42 0.37
ACGTcount: A:0.40, C:0.03, G:0.18, T:0.39
Consensus pattern (94 bp):
TTTTTAAGAAAAATCAAATAAATTAGGGTTTAGGGTTACTTGAGTAAATTAATTAAAAAAATTTA
AAAATCAAATTAGGGTTTAGAGTTAAGGG
Found at i:55377663 original size:125 final size:125
Alignment explanation
Indices: 55377252--55377668 Score: 613
Period size: 126 Copynumber: 3.3 Consensus size: 125
55377242 TTGTTAATTT
* * * *
55377252 AAAGAATCTCTCACGTGGACGCGCTTTTGCTACAGTAGCTCCTGAAAAAAATAATTTCGAGTAGA
1 AAAGAAGCTCCCACGTGGACGCGCTTTTGCTACAATAGCTCCTG-AAAAAATAATTTCGAGTTGA
*
55377317 CGTTTCTGAGCAAATAGTGTCAAAAACGCTTTAAGTAGGATGCTTTGTCAGCAGTAGTACTG
65 CGTTTCTGAGCAAATAGTGTCAAAAACGCTTTAAGTA-GATGCTTTGTCAGCAGAAGTACTG
* * * *
55377379 AAAGAAGCTCCCACGTGGTCGCGCTTTTGCTATAGTAGCTCCTGAAAAAATAATTTTGAGTTGAC
1 AAAGAAGCTCCCACGTGGACGCGCTTTTGCTACAATAGCTCCTGAAAAAATAATTTCGAGTTGAC
* * * * *
55377444 GTTTCTGAGCAAATATTGTCAAAAACGTTTTAAGCAG-GGCACTTTGTCAGCA-ATAGTACTA
66 GTTTCTGAGCAAATAGTGTCAAAAACGCTTTAAGTAGATG--CTTTGTCAGCAGA-AGTACTG
*
55377505 AAAGAAGCTCCCACGTGGACGCGCTTTTGCTACAATAGCTCTTGAAAAAATAATTTCGAGTTGAC
1 AAAGAAGCTCCCACGTGGACGCGCTTTTGCTACAATAGCTCCTGAAAAAATAATTTCGAGTTGAC
* * *
55377570 GTTTCTAAGAAAATAGTGTCAAAAACGCTTTAAGTAGATGCTTTGTTAGCAGAAGTACTG
66 GTTTCTGAGCAAATAGTGTCAAAAACGCTTTAAGTAGATGCTTTGTCAGCAGAAGTACTG
55377630 AAAGAAGCTCCCACGTGGACGCGCTTTTGCTACAATAGC
1 AAAGAAGCTCCCACGTGGACGCGCTTTTGCTACAATAGC
55377669 GCATGTTTGG
Statistics
Matches: 260, Mismatches: 25, Indels: 12
0.88 0.08 0.04
Matches are distributed among these distances:
124 1 0.00
125 56 0.22
126 162 0.62
127 41 0.16
ACGTcount: A:0.32, C:0.19, G:0.21, T:0.28
Consensus pattern (125 bp):
AAAGAAGCTCCCACGTGGACGCGCTTTTGCTACAATAGCTCCTGAAAAAATAATTTCGAGTTGAC
GTTTCTGAGCAAATAGTGTCAAAAACGCTTTAAGTAGATGCTTTGTCAGCAGAAGTACTG
Found at i:55390903 original size:54 final size:55
Alignment explanation
Indices: 55390787--55391004 Score: 258
Period size: 55 Copynumber: 4.0 Consensus size: 55
55390777 GGAACAATTA
* * ** * ** *
55390787 ATTTAAATATATAAACAATCAATTTAAAAGAAGTAGTATTCCAACACAACAATTG
1 ATTTAAACATATAAACAATCAATTCAAAAGAAACAATATTCCAACATGACAATCG
* * *
55390842 ATTTAAACATGTAAACAATCTATTCAAAAG-AACAATATTCCAACATGATAATCG
1 ATTTAAACATATAAACAATCAATTCAAAAGAAACAATATTCCAACATGACAATCG
* *
55390896 ATTTAAACATATAAACAATCAATTCAAAAGAAACAGTATTCTAACATGACAATCG
1 ATTTAAACATATAAACAATCAATTCAAAAGAAACAATATTCCAACATGACAATCG
* * * * * *
55390951 GTTTAAACATAAAAATAATCGATTCAAAAGAAATAATATTCCAGCATGACAATC
1 ATTTAAACATATAAACAATCAATTCAAAAGAAACAATATTCCAACATGACAATC
55391005 AATTAAGTGC
Statistics
Matches: 138, Mismatches: 24, Indels: 2
0.84 0.15 0.01
Matches are distributed among these distances:
54 45 0.33
55 93 0.67
ACGTcount: A:0.50, C:0.15, G:0.08, T:0.27
Consensus pattern (55 bp):
ATTTAAACATATAAACAATCAATTCAAAAGAAACAATATTCCAACATGACAATCG
Found at i:55390978 original size:109 final size:110
Alignment explanation
Indices: 55390787--55391004 Score: 285
Period size: 109 Copynumber: 2.0 Consensus size: 110
55390777 GGAACAATTA
* * ** *
55390787 ATTTAAATATATAAACAATCAATTTAAAAGAAGTAGTATTCCAACACAACAATTGATTTAAACAT
1 ATTTAAACATATAAACAATCAATTCAAAAGAAACAGTATTCCAACACAACAATCGATTTAAACAT
** * *
55390852 GTAAACAATCTATTCAAAAG-AACAATATTCCAACATGATAATCG
66 AAAAACAATCGATTCAAAAGAAACAATATTCCAACATGACAATCG
* ** *
55390896 ATTTAAACATATAAACAATCAATTCAAAAGAAACAGTATTCTAACATGACAATCGGTTTAAACAT
1 ATTTAAACATATAAACAATCAATTCAAAAGAAACAGTATTCCAACACAACAATCGATTTAAACAT
* * *
55390961 AAAAATAATCGATTCAAAAGAAATAATATTCCAGCATGACAATC
66 AAAAACAATCGATTCAAAAGAAACAATATTCCAACATGACAATC
55391005 AATTAAGTGC
Statistics
Matches: 92, Mismatches: 16, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
109 72 0.78
110 20 0.22
ACGTcount: A:0.50, C:0.15, G:0.08, T:0.27
Consensus pattern (110 bp):
ATTTAAACATATAAACAATCAATTCAAAAGAAACAGTATTCCAACACAACAATCGATTTAAACAT
AAAAACAATCGATTCAAAAGAAACAATATTCCAACATGACAATCG
Found at i:55405981 original size:28 final size:26
Alignment explanation
Indices: 55405947--55406006 Score: 68
Period size: 28 Copynumber: 2.2 Consensus size: 26
55405937 ATCATTACTT
*
55405947 TTTCAAT-ACAGAAATTTTAATCCAATCA
1 TTTCAATGA-AGAAAGTTTAAT-CAA-CA
*
55405975 TTTCAATGAAGACAGTTTAATCAACA
1 TTTCAATGAAGAAAGTTTAATCAACA
55406001 TTTCAA
1 TTTCAA
55406007 ATATATGTTG
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
26 8 0.28
27 3 0.10
28 17 0.59
29 1 0.03
ACGTcount: A:0.42, C:0.17, G:0.07, T:0.35
Consensus pattern (26 bp):
TTTCAATGAAGAAAGTTTAATCAACA
Found at i:55406860 original size:12 final size:11
Alignment explanation
Indices: 55406836--55406870 Score: 54
Period size: 12 Copynumber: 3.2 Consensus size: 11
55406826 TTTCAACAAG
55406836 TTTTCC-TTCA
1 TTTTCCTTTCA
55406846 TTTTCCTTGTCA
1 TTTTCCTT-TCA
55406858 TTTTCCTTTCA
1 TTTTCCTTTCA
55406869 TT
1 TT
55406871 GTCTGCAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
10 6 0.26
11 6 0.26
12 11 0.48
ACGTcount: A:0.09, C:0.26, G:0.03, T:0.63
Consensus pattern (11 bp):
TTTTCCTTTCA
Found at i:55409470 original size:15 final size:15
Alignment explanation
Indices: 55409423--55409470 Score: 53
Period size: 15 Copynumber: 3.3 Consensus size: 15
55409413 AGGAGTTAAA
55409423 AAAAAACATAAAATG
1 AAAAAACATAAAATG
*** *
55409438 AAAAATTTTAAAA-A
1 AAAAAACATAAAATG
55409452 AAAAAACATAAAATG
1 AAAAAACATAAAATG
55409467 AAAA
1 AAAA
55409471 GTATAGATTC
Statistics
Matches: 24, Mismatches: 8, Indels: 2
0.71 0.24 0.06
Matches are distributed among these distances:
14 10 0.42
15 14 0.58
ACGTcount: A:0.75, C:0.04, G:0.04, T:0.17
Consensus pattern (15 bp):
AAAAAACATAAAATG
Found at i:55426750 original size:15 final size:15
Alignment explanation
Indices: 55426730--55426771 Score: 50
Period size: 15 Copynumber: 2.8 Consensus size: 15
55426720 TGTAGGTATA
*
55426730 ATAATAATATATAAT-
1 ATAATAATA-AAAATG
55426745 ATAATAATAAAAATG
1 ATAATAATAAAAATG
*
55426760 ATAATAACAAAA
1 ATAATAATAAAA
55426772 TTAATAAAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
14 4 0.17
15 20 0.83
ACGTcount: A:0.67, C:0.02, G:0.02, T:0.29
Consensus pattern (15 bp):
ATAATAATAAAAATG
Found at i:55427026 original size:19 final size:21
Alignment explanation
Indices: 55426988--55427026 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 21
55426978 CCTTTTTTAA
*
55426988 AATCGTAAATAAGTAAAAAAT
1 AATCGTAAATAAGAAAAAAAT
55427009 AATCG-AAA-AAGAAAAAAA
1 AATCGTAAATAAGAAAAAAA
55427027 AAAGAAAACA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 9 0.53
20 3 0.18
21 5 0.29
ACGTcount: A:0.69, C:0.05, G:0.10, T:0.15
Consensus pattern (21 bp):
AATCGTAAATAAGAAAAAAAT
Found at i:55427248 original size:24 final size:23
Alignment explanation
Indices: 55427201--55427269 Score: 76
Period size: 21 Copynumber: 3.2 Consensus size: 23
55427191 TACAAATTAA
* *
55427201 ATCTT-TAAGATTACAAAATCAT
1 ATCTTCTAAGATTGCAATATCAT
55427223 ATCTTCTAAGATTGCATATATCAT
1 ATCTTCTAAGATTGCA-ATATCAT
55427247 A---TCTAAGATTGC-ATATCAT
1 ATCTTCTAAGATTGCAATATCAT
55427266 ATCT
1 ATCT
55427270 AAGATTGTAT
Statistics
Matches: 40, Mismatches: 2, Indels: 10
0.77 0.04 0.19
Matches are distributed among these distances:
19 8 0.20
21 11 0.28
22 5 0.12
23 9 0.22
24 7 0.17
ACGTcount: A:0.38, C:0.16, G:0.07, T:0.39
Consensus pattern (23 bp):
ATCTTCTAAGATTGCAATATCAT
Found at i:55427253 original size:21 final size:21
Alignment explanation
Indices: 55427227--55427281 Score: 87
Period size: 19 Copynumber: 2.7 Consensus size: 21
55427217 AATCATATCT
55427227 TCTAAGATTGCATATATCATA
1 TCTAAGATTGCATATATCATA
55427248 TCTAAGATTGC--ATATCATA
1 TCTAAGATTGCATATATCATA
*
55427267 TCTAAGATTGTATAT
1 TCTAAGATTGCATAT
55427282 CCTCGAAAAT
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
19 18 0.58
21 13 0.42
ACGTcount: A:0.36, C:0.13, G:0.11, T:0.40
Consensus pattern (21 bp):
TCTAAGATTGCATATATCATA
Found at i:55427538 original size:44 final size:44
Alignment explanation
Indices: 55427485--55427569 Score: 136
Period size: 44 Copynumber: 1.9 Consensus size: 44
55427475 AGGAATTCGT
55427485 GCTTCAATCTACTCCACTGCAACTTC-AGAGAGATAAGACTTATA
1 GCTTCAATCTACTCCACTGCAACTTCAAGAG-GATAAGACTTATA
* *
55427529 GCTTTAATCTGCTCCACTGCAACTTCAAGAGGATAAGACTT
1 GCTTCAATCTACTCCACTGCAACTTCAAGAGGATAAGACTT
55427570 GCTGGCTTAA
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
44 34 0.89
45 4 0.11
ACGTcount: A:0.32, C:0.25, G:0.15, T:0.28
Consensus pattern (44 bp):
GCTTCAATCTACTCCACTGCAACTTCAAGAGGATAAGACTTATA
Found at i:55427739 original size:132 final size:132
Alignment explanation
Indices: 55427567--55428493 Score: 1521
Period size: 132 Copynumber: 7.0 Consensus size: 132
55427557 GAGGATAAGA
* * * *
55427567 CTTGCTGGCTTAAATCTGCTTCCCACTATCTTGGGAAGATAAGATTTGCTGTCTTCGATCTACTC
1 CTTGGTGGCTTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTTGCCGTCTTCGATCTGCTC
* *
55427632 CACTATTGCTTAGGGAGAAAAGATCTACAATCTTCAGCCTACTCCGCTGCTGCTCAGGGAGACAA
66 CACTACTGCTTAGGGAGATAAGATCTACAATCTTCAGCCTACTCCGCTGCTGCTCAGGGAGACAA
55427697 GG
131 GG
* * *
55427699 CTTGGTGGCTTAAATATGCTTTCCACTATCTTGGAAAGATAAGATTTGCCGTCTTTGATCTGCTC
1 CTTGGTGGCTTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTTGCCGTCTTCGATCTGCTC
55427764 CACTACTGCTTAGGGAGATAAGATCTACAATCTTCAGCCTACTCCGCTGCTGCTCAGGGAGACAA
66 CACTACTGCTTAGGGAGATAAGATCTACAATCTTCAGCCTACTCCGCTGCTGCTCAGGGAGACAA
55427829 GG
131 GG
* *
55427831 CTTGGTGGCTTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTTGTCGTCTTTGATCTGCTC
1 CTTGGTGGCTTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTTGCCGTCTTCGATCTGCTC
55427896 CACTACTGCTTAGGGAGATAAGATCTACAATCTTCAGCCTACTCCGCTGCTGCTCAGGGAGACAA
66 CACTACTGCTTAGGGAGATAAGATCTACAATCTTCAGCCTACTCCGCTGCTGCTCAGGGAGACAA
55427961 GG
131 GG
* * * *
55427963 CTTGGTGGCTTAAATATGCTTTCCACTATCTTGGAAAGATAAGATTTACCGTCTTTGATCTGCTC
1 CTTGGTGGCTTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTTGCCGTCTTCGATCTGCTC
55428028 CACTACTGCTTAGGGAGATAAGATCTACAATCTTCAGCCTACTCCGCTGCTGCTCAGGGAGACAA
66 CACTACTGCTTAGGGAGATAAGATCTACAATCTTCAGCCTACTCCGCTGCTGCTCAGGGAGACAA
55428093 GG
131 GG
* * *
55428095 CTTGGTAGCTTAAATCTGCTTCCCACTATCTTAGAAAGATAAGATTTGCCGTCTTCGATCTTCTC
1 CTTGGTGGCTTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTTGCCGTCTTCGATCTGCTC
* * * * *
55428160 CACTATTGCTTAGGGAGATAAGATCTACAATTTTCAACCTACTCCACTGCTACTCAGGGAGACAA
66 CACTACTGCTTAGGGAGATAAGATCTACAATCTTCAGCCTACTCCGCTGCTGCTCAGGGAGACAA
55428225 GG
131 GG
* * *
55428227 CTTGGTGGCTTAAATCTGCTTCCCACTATCTTAGAAAGATAAGATTTGCCGTCTTCAATCTTCTC
1 CTTGGTGGCTTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTTGCCGTCTTCGATCTGCTC
* *
55428292 CACTACTGCTTAGGGAGATAAGATCTATAATCTTCAACCTACTCCGCTGCTGCTCAGGGAGACAA
66 CACTACTGCTTAGGGAGATAAGATCTACAATCTTCAGCCTACTCCGCTGCTGCTCAGGGAGACAA
55428357 GG
131 GG
* * * * *
55428359 CTTGGTGGCTTAAATCTGCTTCTCACTATCTTGGAAAGATAAGATTTGTCGTCCTCGATCTACTT
1 CTTGGTGGCTTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTTGCCGTCTTCGATCTGCTC
* * * *
55428424 CACTACTGCTTAGGGAGATAAGATCTACGATCCTCAACCTACTCCGCTGTTGCTCAGGGAGACAA
66 CACTACTGCTTAGGGAGATAAGATCTACAATCTTCAGCCTACTCCGCTGCTGCTCAGGGAGACAA
55428489 GG
131 GG
55428491 CTT
1 CTT
55428494 AGTGTTTCAC
Statistics
Matches: 749, Mismatches: 46, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
132 749 1.00
ACGTcount: A:0.25, C:0.24, G:0.20, T:0.30
Consensus pattern (132 bp):
CTTGGTGGCTTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTTGCCGTCTTCGATCTGCTC
CACTACTGCTTAGGGAGATAAGATCTACAATCTTCAGCCTACTCCGCTGCTGCTCAGGGAGACAA
GG
Found at i:55427785 original size:44 final size:44
Alignment explanation
Indices: 55427735--55428315 Score: 189
Period size: 44 Copynumber: 13.2 Consensus size: 44
55427725 TATCTTGGAA
*
55427735 AGATAAGATTTGCCGTCTTTGATCTGCTCCACTACTGCTTAGGG
1 AGATAAGATTTGCCGTCTTTAATCTGCTCCACTACTGCTTAGGG
* * ** * ** * * * *
55427779 AGATAAGATCTACAATCTTCAGCCTACTCCGCTGCTGCTCAGGG
1 AGATAAGATTTGCCGTCTTTAATCTGCTCCACTACTGCTTAGGG
* ** ** * * *
55427823 AGACAAGGCTTGGTGGCTTAAATCTGCTTCCCACTA-T-CTT-GGAA
1 AGATAAGATTTGCCGTCTTTAATCTGC-T-CCACTACTGCTTAGG-G
* *
55427867 AGATAAGATTTGTCGTCTTTGATCTGCTCCACTACTGCTTAGGG
1 AGATAAGATTTGCCGTCTTTAATCTGCTCCACTACTGCTTAGGG
* * ** * ** * * * *
55427911 AGATAAGATCTACAATCTTCAGCCTACTCCGCTGCTGCTCAGGG
1 AGATAAGATTTGCCGTCTTTAATCTGCTCCACTACTGCTTAGGG
* ** ** * * * *
55427955 AGACAAGGCTTGGTGGCTTAAATATGCTTTCCACTA-T-CTT-GGAA
1 AGATAAGATTTGCCGTCTTTAATCTGC--TCCACTACTGCTTAGG-G
* *
55427999 AGATAAGATTTACCGTCTTTGATCTGCTCCACTACTGCTTAGGG
1 AGATAAGATTTGCCGTCTTTAATCTGCTCCACTACTGCTTAGGG
* * ** * ** * * * *
55428043 AGATAAGATCTACAATCTTCAGCCTACTCCGCTGCTGCTCAGGG
1 AGATAAGATTTGCCGTCTTTAATCTGCTCCACTACTGCTTAGGG
* ** * **
55428087 AGACAAGGCTTG--GTAGCTTAAATCTGCTTCCCACTA-T-CTTAGAA
1 AGATAAGATTTGCCGT--CTTTAATCTGC-T-CCACTACTGCTTAGGG
** * *
55428131 AGATAAGATTTGCCGTCTTCGATCTTCTCCACTATTGCTTAGGG
1 AGATAAGATTTGCCGTCTTTAATCTGCTCCACTACTGCTTAGGG
* * ** * * * * *
55428175 AGATAAGATCTACAAT-TTTCAACCTACTCCACTGCTACTCAGGG
1 AGATAAGATTTGCCGTCTTT-AATCTGCTCCACTACTGCTTAGGG
* ** ** * * **
55428219 AGACAAGGCTTGGTGGCTTAAATCTGCTTCCCACTA-T-CTTAGAA
1 AGATAAGATTTGCCGTCTTTAATCTGC-T-CCACTACTGCTTAGGG
* *
55428263 AGATAAGATTTGCCGTCTTCAATCTTCTCCACTACTGCTTAGGG
1 AGATAAGATTTGCCGTCTTTAATCTGCTCCACTACTGCTTAGGG
55428307 AGATAAGAT
1 AGATAAGAT
55428316 CTATAATCTT
Statistics
Matches: 359, Mismatches: 152, Indels: 52
0.64 0.27 0.09
Matches are distributed among these distances:
42 26 0.07
43 13 0.04
44 287 0.80
45 13 0.04
46 20 0.06
ACGTcount: A:0.25, C:0.24, G:0.20, T:0.30
Consensus pattern (44 bp):
AGATAAGATTTGCCGTCTTTAATCTGCTCCACTACTGCTTAGGG
Found at i:55436033 original size:21 final size:21
Alignment explanation
Indices: 55436009--55436054 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
55435999 TACAAGTGAA
*
55436009 AAATAT-TATGCATAAAATAAT
1 AAATATATATACATAAAA-AAT
55436030 AAAT-TATATACATAAAAAAT
1 AAATATATATACATAAAAAAT
55436050 AAATA
1 AAATA
55436055 ATTGATAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
20 8 0.36
21 14 0.64
ACGTcount: A:0.63, C:0.04, G:0.02, T:0.30
Consensus pattern (21 bp):
AAATATATATACATAAAAAAT
Found at i:55436064 original size:18 final size:18
Alignment explanation
Indices: 55436041--55436081 Score: 59
Period size: 18 Copynumber: 2.3 Consensus size: 18
55436031 AATTATATAC
55436041 ATAAAAAATAA-ATAATTG
1 ATAAAAAA-AAGATAATTG
55436059 ATAAAAAAAAGATAATTG
1 ATAAAAAAAAGATAATTG
55436077 -TAAAA
1 ATAAAA
55436082 TTTATATAAC
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 7 0.32
18 15 0.68
ACGTcount: A:0.68, C:0.00, G:0.07, T:0.24
Consensus pattern (18 bp):
ATAAAAAAAAGATAATTG
Found at i:55437144 original size:18 final size:17
Alignment explanation
Indices: 55437117--55437150 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
55437107 TTATTTGTAT
55437117 TTTTAAATTAAATTTAAA
1 TTTTAAATT-AATTTAAA
*
55437135 TTTTATATTAATTTAA
1 TTTTAAATTAATTTAA
55437151 TATAATGATA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (17 bp):
TTTTAAATTAATTTAAA
Found at i:55440331 original size:17 final size:16
Alignment explanation
Indices: 55440301--55440339 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 16
55440291 TCTAAAAATT
55440301 ATAA-TAAAAATATAA
1 ATAATTAAAAATATAA
*
55440316 ATCATTAAAAACTATAA
1 ATAATTAAAAA-TATAA
55440333 ATAATTA
1 ATAATTA
55440340 TTTAAAAATT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
15 3 0.15
16 6 0.30
17 11 0.55
ACGTcount: A:0.64, C:0.05, G:0.00, T:0.31
Consensus pattern (16 bp):
ATAATTAAAAATATAA
Found at i:55440354 original size:21 final size:20
Alignment explanation
Indices: 55440320--55440358 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
55440310 ATATAAATCA
55440320 TTAAAAACTATAAATAATTAT
1 TTAAAAACTATAAA-AATTAT
* *
55440341 TTAAAAATTCTAAAAATT
1 TTAAAAACTATAAAAATT
55440359 CTAAAAAATA
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:0.56, C:0.05, G:0.00, T:0.38
Consensus pattern (20 bp):
TTAAAAACTATAAAAATTAT
Found at i:55440404 original size:16 final size:16
Alignment explanation
Indices: 55440362--55440404 Score: 54
Period size: 16 Copynumber: 2.8 Consensus size: 16
55440352 AAAAATTCTA
55440362 AAAAATATT-AATAAT
1 AAAAATATTAAATAAT
*
55440377 AGAAAA-ATTAAATTAT
1 A-AAAATATTAAATAAT
55440393 AAAAATATTAAA
1 AAAAATATTAAA
55440405 AAGTATAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
15 8 0.33
16 16 0.67
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.30
Consensus pattern (16 bp):
AAAAATATTAAATAAT
Found at i:55440587 original size:9 final size:8
Alignment explanation
Indices: 55440575--55440625 Score: 50
Period size: 9 Copynumber: 5.9 Consensus size: 8
55440565 TTTTTCTTGG
55440575 AATTTTAAT
1 AATTTT-AT
55440584 AATTTTTAT
1 AA-TTTTAT
55440593 AATTTTAT
1 AATTTTAT
55440601 AATTATT-T
1 AATT-TTAT
55440609 GAATTTCTAT
1 -AATTT-TAT
55440619 AATTTTA
1 AATTTTA
55440626 AAAACATTTT
Statistics
Matches: 37, Mismatches: 0, Indels: 11
0.77 0.00 0.23
Matches are distributed among these distances:
8 14 0.38
9 18 0.49
10 5 0.14
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.59
Consensus pattern (8 bp):
AATTTTAT
Found at i:55440634 original size:26 final size:26
Alignment explanation
Indices: 55440584--55440634 Score: 66
Period size: 26 Copynumber: 2.0 Consensus size: 26
55440574 GAATTTTAAT
* * **
55440584 AATTTTTATAATTTTATAATTATTTG
1 AATTTCTATAATTTTAAAAACATTTG
55440610 AATTTCTATAATTTTAAAAACATTT
1 AATTTCTATAATTTTAAAAACATTT
55440635 TATGATTTTC
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.39, C:0.04, G:0.02, T:0.55
Consensus pattern (26 bp):
AATTTCTATAATTTTAAAAACATTTG
Found at i:55450737 original size:32 final size:32
Alignment explanation
Indices: 55450699--55450794 Score: 90
Period size: 31 Copynumber: 3.0 Consensus size: 32
55450689 TATCTAATTA
*
55450699 AGTTAATATCCGTTTAACTCATGACACAAGTG
1 AGTTAATATCCGTTTAACTCATCACACAAGTG
** * * *
55450731 AGTTAATAAT-ATTTTTA-TCATTATC-CAATTG
1 AGTTAAT-ATCCGTTTAACTCATCA-CACAAGTG
*
55450762 AGTTAATATCCGTTTAACTCATCACACAGGTG
1 AGTTAATATCCGTTTAACTCATCACACAAGTG
55450794 A
1 A
55450795 TTATCTCCCA
Statistics
Matches: 48, Mismatches: 11, Indels: 10
0.70 0.16 0.14
Matches are distributed among these distances:
30 2 0.04
31 22 0.46
32 22 0.46
33 2 0.04
ACGTcount: A:0.34, C:0.17, G:0.12, T:0.36
Consensus pattern (32 bp):
AGTTAATATCCGTTTAACTCATCACACAAGTG
Found at i:55450739 original size:63 final size:63
Alignment explanation
Indices: 55450665--55450794 Score: 215
Period size: 63 Copynumber: 2.1 Consensus size: 63
55450655 CTTAAAACAG
* *
55450665 GTGAGTTAATAATATTTTCATCATTATCTAATTAAGTTAATATCCGTTTAACTCATGACACAA
1 GTGAGTTAATAATATTTTCATCATTATCCAATTAAGTTAATATCCGTTTAACTCATCACACAA
* * *
55450728 GTGAGTTAATAATATTTTTATCATTATCCAATTGAGTTAATATCCGTTTAACTCATCACACAG
1 GTGAGTTAATAATATTTTCATCATTATCCAATTAAGTTAATATCCGTTTAACTCATCACACAA
55450791 GTGA
1 GTGA
55450795 TTATCTCCCA
Statistics
Matches: 62, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
63 62 1.00
ACGTcount: A:0.35, C:0.15, G:0.12, T:0.39
Consensus pattern (63 bp):
GTGAGTTAATAATATTTTCATCATTATCCAATTAAGTTAATATCCGTTTAACTCATCACACAA
Found at i:55450767 original size:31 final size:31
Alignment explanation
Indices: 55450666--55450769 Score: 95
Period size: 31 Copynumber: 3.3 Consensus size: 31
55450656 TTAAAACAGG
* *
55450666 TGAGTTAATAATATTTTCATCATTATCTAAT
1 TGAGTTAATAATATTTTAATCATTATCCAAT
* ** * *
55450697 TAAGTTAAT-ATCCGTTTAACTCATGA-CACAAG
1 TGAGTTAATAAT-ATTTTAA-TCATTATC-CAAT
*
55450729 TGAGTTAATAATATTTTTATCATTATCCAAT
1 TGAGTTAATAATATTTTAATCATTATCCAAT
55450760 TGAGTTAATA
1 TGAGTTAATA
55450770 TCCGTTTAAC
Statistics
Matches: 55, Mismatches: 13, Indels: 10
0.71 0.17 0.13
Matches are distributed among these distances:
30 2 0.04
31 31 0.56
32 20 0.36
33 2 0.04
ACGTcount: A:0.37, C:0.12, G:0.10, T:0.42
Consensus pattern (31 bp):
TGAGTTAATAATATTTTAATCATTATCCAAT
Found at i:55453578 original size:15 final size:15
Alignment explanation
Indices: 55453560--55453590 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
55453550 ATTTGTCTTA
55453560 ATATGTTCATTAATT
1 ATATGTTCATTAATT
*
55453575 ATATTTTCATTAATT
1 ATATGTTCATTAATT
55453590 A
1 A
55453591 CTTACAAATG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.35, C:0.06, G:0.03, T:0.55
Consensus pattern (15 bp):
ATATGTTCATTAATT
Found at i:55455707 original size:16 final size:16
Alignment explanation
Indices: 55455688--55455720 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
55455678 TAAAATTTTG
55455688 AAAAAATAAAAAATAC
1 AAAAAATAAAAAATAC
*
55455704 AAAAAATAAAAATTAC
1 AAAAAATAAAAAATAC
55455720 A
1 A
55455721 TTTTGACCCT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.79, C:0.06, G:0.00, T:0.15
Consensus pattern (16 bp):
AAAAAATAAAAAATAC
Found at i:55455849 original size:29 final size:29
Alignment explanation
Indices: 55455817--55455877 Score: 70
Period size: 29 Copynumber: 2.1 Consensus size: 29
55455807 ACAGTCAGGC
*
55455817 CCCTAAACTTTCC-AGAAATTACATTTTTG
1 CCCTAAACTTTCCTAG-AATCACATTTTTG
* * *
55455846 CCCTATATTTTCCTAGAATCGCATTTTTG
1 CCCTAAACTTTCCTAGAATCACATTTTTG
55455875 CCC
1 CCC
55455878 CAGAAATTTT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
29 25 0.93
30 2 0.07
ACGTcount: A:0.25, C:0.28, G:0.08, T:0.39
Consensus pattern (29 bp):
CCCTAAACTTTCCTAGAATCACATTTTTG
Found at i:55456512 original size:11 final size:11
Alignment explanation
Indices: 55456496--55456532 Score: 65
Period size: 11 Copynumber: 3.4 Consensus size: 11
55456486 CCCATTTTTG
55456496 GCAGTCCAGCA
1 GCAGTCCAGCA
55456507 GCAGTCCAGCA
1 GCAGTCCAGCA
*
55456518 GCAGTCCACCA
1 GCAGTCCAGCA
55456529 GCAG
1 GCAG
55456533 CAGCCCACCA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
11 25 1.00
ACGTcount: A:0.27, C:0.38, G:0.27, T:0.08
Consensus pattern (11 bp):
GCAGTCCAGCA
Found at i:55456521 original size:14 final size:14
Alignment explanation
Indices: 55456501--55456546 Score: 62
Period size: 14 Copynumber: 3.5 Consensus size: 14
55456491 TTTTGGCAGT
55456501 CCAGCAGCAGT---
1 CCAGCAGCAGTCCA
55456512 CCAGCAGCAGTCCA
1 CCAGCAGCAGTCCA
*
55456526 CCAGCAGCAGCCCA
1 CCAGCAGCAGTCCA
55456540 CCAGCAG
1 CCAGCAG
55456547 TGGCCCACCC
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
11 11 0.35
14 20 0.65
ACGTcount: A:0.28, C:0.43, G:0.24, T:0.04
Consensus pattern (14 bp):
CCAGCAGCAGTCCA
Found at i:55456672 original size:15 final size:15
Alignment explanation
Indices: 55456652--55456680 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
55456642 CCAACAGCAG
55456652 CAGGCCACTGCCCAA
1 CAGGCCACTGCCCAA
55456667 CAGGCCACTGCCCA
1 CAGGCCACTGCCCA
55456681 GCCCAACGCC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.24, C:0.48, G:0.21, T:0.07
Consensus pattern (15 bp):
CAGGCCACTGCCCAA
Found at i:55457256 original size:17 final size:17
Alignment explanation
Indices: 55457229--55457274 Score: 58
Period size: 17 Copynumber: 2.6 Consensus size: 17
55457219 AAAAAAATCG
55457229 TGTTTCAAAAATTT-TCA
1 TGTTTC-AAAATTTCTCA
*
55457246 TGTCTTCAAAATTTCTCG
1 TGT-TTCAAAATTTCTCA
55457264 TGTTTCAAAAT
1 TGTTTCAAAAT
55457275 AATAATAATA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
17 18 0.69
18 8 0.31
ACGTcount: A:0.30, C:0.15, G:0.09, T:0.46
Consensus pattern (17 bp):
TGTTTCAAAATTTCTCA
Found at i:55457355 original size:18 final size:18
Alignment explanation
Indices: 55457332--55457384 Score: 56
Period size: 18 Copynumber: 3.0 Consensus size: 18
55457322 TTTTCAAAAA
55457332 AAAAATTTCCGTGTTTTC
1 AAAAATTTCCGTGTTTTC
* * *
55457350 AAAAATTCCCTTG-TTTG
1 AAAAATTTCCGTGTTTTC
55457367 AAAAATGTT-CGTGTTTTC
1 AAAAAT-TTCCGTGTTTTC
55457385 GTGTTTTCAA
Statistics
Matches: 27, Mismatches: 6, Indels: 4
0.73 0.16 0.11
Matches are distributed among these distances:
17 12 0.44
18 15 0.56
ACGTcount: A:0.28, C:0.15, G:0.13, T:0.43
Consensus pattern (18 bp):
AAAAATTTCCGTGTTTTC
Found at i:55457577 original size:18 final size:16
Alignment explanation
Indices: 55457507--55457745 Score: 75
Period size: 17 Copynumber: 13.3 Consensus size: 16
55457497 CGTGTTTAAA
*
55457507 AAAAATTTTCGCGTTTC
1 AAAAA-TTTCGTGTTTC
*
55457524 AAAAATCTTCGTATTTTC
1 AAAAAT-TTCGT-GTTTC
*
55457542 -AAAATTCCAGTGTTTC
1 AAAAATTTC-GTGTTTC
55457558 AAAAATTGTCGTGTTTTC
1 AAAAATT-TCGTG-TTTC
*
55457576 AAAAAAAAATTTCCTTGTTTTC
1 ----AAAAATTT-CGTG-TTTC
* ** *
55457598 AAAAGTCCCGTATTTC
1 AAAAATTTCGTGTTTC
** *
55457614 GAAACTTTTCTTGTCTTC
1 -AAAAATTTCGTGT-TTC
*
55457632 AAAAAAATTCTGTGTTTC
1 -AAAAATTTC-GTGTTTC
*
55457650 ATAAATTTCCGTGTTTTC
1 AAAAATTT-CGTG-TTTC
* *
55457668 AAAAAAATCTCGTCTTTC
1 --AAAAATTTCGTGTTTC
55457686 AAAAATTTTCGTGTTTTC
1 AAAAA-TTTCGTG-TTTC
*
55457704 AAAAAAATTGACCGTGTTTC
1 --AAAAATT--TCGTGTTTC
*
55457724 ATAAATTTTCGTGTTTC
1 A-AAAATTTCGTGTTTC
55457741 AAAAA
1 AAAAA
55457746 AAATCCTCGT
Statistics
Matches: 164, Mismatches: 33, Indels: 51
0.66 0.13 0.21
Matches are distributed among these distances:
16 19 0.12
17 57 0.35
18 40 0.24
19 13 0.08
20 15 0.09
21 5 0.03
22 15 0.09
ACGTcount: A:0.33, C:0.16, G:0.10, T:0.41
Consensus pattern (16 bp):
AAAAATTTCGTGTTTC
Found at i:55457584 original size:22 final size:22
Alignment explanation
Indices: 55457558--55457601 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
55457548 CCAGTGTTTC
55457558 AAAAATTGT-CGTGTTTTCAAAA
1 AAAAATT-TCCGTGTTTTCAAAA
*
55457580 AAAAATTTCCTTGTTTTCAAAA
1 AAAAATTTCCGTGTTTTCAAAA
55457602 GTCCCGTATT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 1 0.05
22 19 0.95
ACGTcount: A:0.41, C:0.11, G:0.09, T:0.39
Consensus pattern (22 bp):
AAAAATTTCCGTGTTTTCAAAA
Found at i:55457709 original size:37 final size:38
Alignment explanation
Indices: 55457610--55457760 Score: 152
Period size: 36 Copynumber: 4.1 Consensus size: 38
55457600 AAGTCCCGTA
* * * * *
55457610 TTTCGAAACTTTTCTTGTCTTC-AAAAAAATTCT-GTG
1 TTTCAAAAATTTTCGTGTTTTCAAAAAAAATACTCGTG
* * *
55457646 TTTCATAAATTTCCGTGTTTTC-AAAAAAAT-CTCGTC
1 TTTCAAAAATTTTCGTGTTTTCAAAAAAAATACTCGTG
*
55457682 TTTCAAAAATTTTCGTGTTTTCAAAAAAATTGAC-CGTG
1 TTTCAAAAATTTTCGTGTTTTCAAAAAAAAT-ACTCGTG
* *
55457720 TTTCATAAATTTTCGTG-TTTCAAAAAAAATCCTCGTG
1 TTTCAAAAATTTTCGTGTTTTCAAAAAAAATACTCGTG
55457757 TTTC
1 TTTC
55457761 GTATTTTATC
Statistics
Matches: 96, Mismatches: 14, Indels: 9
0.81 0.12 0.08
Matches are distributed among these distances:
35 2 0.02
36 47 0.49
37 27 0.28
38 19 0.20
39 1 0.01
ACGTcount: A:0.30, C:0.17, G:0.11, T:0.42
Consensus pattern (38 bp):
TTTCAAAAATTTTCGTGTTTTCAAAAAAAATACTCGTG
Found at i:55457749 original size:38 final size:36
Alignment explanation
Indices: 55457619--55457747 Score: 163
Period size: 36 Copynumber: 3.6 Consensus size: 36
55457609 ATTTCGAAAC
* * *
55457619 TTTTCTTGTCTTCAAAAAAATTCTGTGTTTCATAAA
1 TTTTCGTGTTTTCAAAAAAATTCCGTGTTTCATAAA
* * *
55457655 TTTCCGTGTTTTCAAAAAAA-TCTCGTCTTTCAAAAA
1 TTTTCGTGTTTTCAAAAAAATTC-CGTGTTTCATAAA
55457691 TTTTCGTGTTTTCAAAAAAATTGACCGTGTTTCATAAA
1 TTTTCGTGTTTTCAAAAAAATT--CCGTGTTTCATAAA
55457729 TTTTCGTG-TTTCAAAAAAA
1 TTTTCGTGTTTTCAAAAAAA
55457748 ATCCTCGTGT
Statistics
Matches: 80, Mismatches: 9, Indels: 7
0.83 0.09 0.07
Matches are distributed among these distances:
35 2 0.03
36 46 0.57
37 12 0.15
38 19 0.24
39 1 0.01
ACGTcount: A:0.33, C:0.15, G:0.10, T:0.43
Consensus pattern (36 bp):
TTTTCGTGTTTTCAAAAAAATTCCGTGTTTCATAAA
Found at i:55457802 original size:18 final size:17
Alignment explanation
Indices: 55457771--55457809 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 17
55457761 GTATTTTATC
*
55457771 AAAAATATTATGTTTTCA
1 AAAAAAATTATGTTTT-A
*
55457789 AAAAAAATTGTGTTTTA
1 AAAAAAATTATGTTTTA
55457806 AAAA
1 AAAA
55457810 TTTTCCTGTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 5 0.26
18 14 0.74
ACGTcount: A:0.51, C:0.03, G:0.08, T:0.38
Consensus pattern (17 bp):
AAAAAAATTATGTTTTA
Found at i:55457848 original size:39 final size:35
Alignment explanation
Indices: 55457784--55457864 Score: 92
Period size: 39 Copynumber: 2.2 Consensus size: 35
55457774 AATATTATGT
* *
55457784 TTTC-AAAAAAAATTGTGTTTTAAAAATTTTCCTG
1 TTTCAAAAAAAAATTGTGTTTTAAAAAATCTCCTG
*
55457818 TTTCAAAAAGAAAATTCGTGTTTCCTAAAAAATCTCGTG
1 TTTCAAAAA-AAAATT-GTGTTT--TAAAAAATCTCCTG
55457857 TTTCAAAA
1 TTTCAAAA
55457865 TTTTCGTTTT
Statistics
Matches: 39, Mismatches: 3, Indels: 5
0.83 0.06 0.11
Matches are distributed among these distances:
34 4 0.10
35 4 0.10
36 6 0.15
37 6 0.15
39 19 0.49
ACGTcount: A:0.40, C:0.12, G:0.10, T:0.38
Consensus pattern (35 bp):
TTTCAAAAAAAAATTGTGTTTTAAAAAATCTCCTG
Found at i:55459657 original size:4 final size:4
Alignment explanation
Indices: 55459648--55459672 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
55459638 CATCCATTGG
55459648 TCAT TCAT TCAT TCAT TCAT TCAT T
1 TCAT TCAT TCAT TCAT TCAT TCAT T
55459673 GCGTATACAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.24, C:0.24, G:0.00, T:0.52
Consensus pattern (4 bp):
TCAT
Found at i:55463619 original size:1 final size:1
Alignment explanation
Indices: 55463613--55463670 Score: 53
Period size: 1 Copynumber: 58.0 Consensus size: 1
55463603 TATTATGCCT
* * * * * * *
55463613 AAAAAAAACAAAAACAAAAAAACAAAAAAAACAAAACAAAAAAACAAACAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
55463671 TCAAGATGAA
Statistics
Matches: 43, Mismatches: 14, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
1 43 1.00
ACGTcount: A:0.88, C:0.12, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:55463633 original size:8 final size:8
Alignment explanation
Indices: 55463613--55463668 Score: 62
Period size: 8 Copynumber: 6.9 Consensus size: 8
55463603 TATTATGCCT
55463613 AAAAAAA-
1 AAAAAAAC
*
55463620 ACAAAAAC
1 AAAAAAAC
55463628 AAAAAAAC
1 AAAAAAAC
55463636 AAAAAAAAC
1 -AAAAAAAC
55463645 AAAACAAA-
1 AAAA-AAAC
55463653 AAAACAAAC
1 AAAA-AAAC
55463662 AAAAAAA
1 AAAAAAA
55463669 AATCAAGATG
Statistics
Matches: 43, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
7 6 0.14
8 22 0.51
9 15 0.35
ACGTcount: A:0.88, C:0.12, G:0.00, T:0.00
Consensus pattern (8 bp):
AAAAAAAC
Done.