Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.04
Sequence: scaffold433
Parameters: 2 7 7 80 10 50 500
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 500
Length: 1285081
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.29
Warning! 132229 characters in sequence are not A, C, G, or T
File 4 of 4
Found at i:682279 original size:38 final size:38
Alignment explanation
Indices: 682204--682341 Score: 231
Period size: 38 Copynumber: 3.6 Consensus size: 38
682194 TAGACAGGTT
* *
682204 AGCTGTTACAATGGTTACTAGTGTAGACAGGTACATGTATA
1 AGCTGTTACAATGGTTA--A-AGAAGACAGGTACATGTATA
682245 AGCTGTTACAATGGTTAAAGAAGACAGGTACATGTATA
1 AGCTGTTACAATGGTTAAAGAAGACAGGTACATGTATA
682283 AGCTGTTACAATGGTTAAAGAAGACAGGTACATGTATA
1 AGCTGTTACAATGGTTAAAGAAGACAGGTACATGTATA
682321 AGCTGTTACAATGGTTAAAGA
1 AGCTGTTACAATGGTTAAAGA
682342 CAGGTAAGCT
Statistics
Matches: 95, Mismatches: 2, Indels: 3
0.95 0.02 0.03
Matches are distributed among these distances:
38 77 0.81
39 1 0.01
41 17 0.18
ACGTcount: A:0.37, C:0.11, G:0.24, T:0.28
Consensus pattern (38 bp):
AGCTGTTACAATGGTTAAAGAAGACAGGTACATGTATA
Found at i:682573 original size:35 final size:35
Alignment explanation
Indices: 682532--682630 Score: 162
Period size: 35 Copynumber: 2.8 Consensus size: 35
682522 TATAGACAGG
*
682532 TAAGCTGTTAGAATGGTTAAAGACAGGTACATGTA
1 TAAGCTGTTACAATGGTTAAAGACAGGTACATGTA
* *
682567 TTAGCTGTTACATTGGTTAAAGACAGGTACATGTA
1 TAAGCTGTTACAATGGTTAAAGACAGGTACATGTA
*
682602 TAAGCTGTTACAATGGTTATAGACAGGTA
1 TAAGCTGTTACAATGGTTAAAGACAGGTA
682631 AGCTGTTACA
Statistics
Matches: 58, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
35 58 1.00
ACGTcount: A:0.34, C:0.10, G:0.24, T:0.31
Consensus pattern (35 bp):
TAAGCTGTTACAATGGTTAAAGACAGGTACATGTA
Found at i:688417 original size:2 final size:2
Alignment explanation
Indices: 688410--688453 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
688400 TTTAAAGCCT
688410 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
688452 GA
1 GA
688454 TGAATATCAC
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:689379 original size:74 final size:75
Alignment explanation
Indices: 689279--689426 Score: 253
Period size: 74 Copynumber: 2.0 Consensus size: 75
689269 ATTTTAGTTT
*
689279 GTTTTATTCGAGAGCTTTTTTTATCATCAAAATAGTCATATTGTCGGAATTTACAATCAATACAA
1 GTTTTATTCGAAAGC-TTTTTTATCATCAAAATAGTCATATTGTCGGAATTTACAATCAATACAA
689344 TGCACAATTTA
65 TGCACAATTTA
**
689355 GTTTTATTCGAAAG-TTTTTTATCATCAAAATAGTTTTATTGTCGGAATTTACAATCAATACAAT
1 GTTTTATTCGAAAGCTTTTTTATCATCAAAATAGTCATATTGTCGGAATTTACAATCAATACAAT
689419 GCACAATT
66 GCACAATT
689427 CATTTTTAAA
Statistics
Matches: 69, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
74 56 0.81
76 13 0.19
ACGTcount: A:0.34, C:0.14, G:0.11, T:0.41
Consensus pattern (75 bp):
GTTTTATTCGAAAGCTTTTTTATCATCAAAATAGTCATATTGTCGGAATTTACAATCAATACAAT
GCACAATTTA
Found at i:692889 original size:2 final size:2
Alignment explanation
Indices: 692882--692934 Score: 106
Period size: 2 Copynumber: 26.5 Consensus size: 2
692872 CTAGAATCCC
692882 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
692924 CT CT CT CT CT C
1 CT CT CT CT CT C
692935 CGAAAACAAT
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 51 1.00
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
CT
Found at i:698633 original size:101 final size:102
Alignment explanation
Indices: 698457--699496 Score: 1855
Period size: 101 Copynumber: 10.3 Consensus size: 102
698447 GAACATGACA
*
698457 GTTATGTTGGAGACCCCATCAGTCTCCCTCTCTTTTATTGGGAGGGGG-CGGTTATGTTGGAGAC
1 GTTATGTTGGAGACCCCATCAGTCTCCTTCTCTTTTATTGGGAGGGGGACGGTTATGTTGGAGAC
* *
698521 CCCATCCGTCTCCCTCTCTTTTATTGGGAGGGGGACG
66 CCCATCAGTCTCCCTCTCTTTTATTGGGAGGGGGGCG
*
698558 GTTATGTTGGAGACCCCATCAGTCTCCTTCTCTTTTATTGGGAGGGGGGCGGTTATGTT-GAGAC
1 GTTATGTTGGAGACCCCATCAGTCTCCTTCTCTTTTATTGGGAGGGGGACGGTTATGTTGGAGAC
*
698622 CCCATCAGTCTCCTTCTCTTTTATTGGGAGGGGGGCG
66 CCCATCAGTCTCCCTCTCTTTTATTGGGAGGGGGGCG
*
698659 GTTATGTTGGAGACCCCATCAGTCTCCTTCTCTTTTATTGGGAGGGGGACAGTTATGTTGGAGAC
1 GTTATGTTGGAGACCCCATCAGTCTCCTTCTCTTTTATTGGGAGGGGGACGGTTATGTTGGAGAC
698724 CCCATCAGTCTCCCTCTCTTTTATTGGGAGGGGGGCG
66 CCCATCAGTCTCCCTCTCTTTTATTGGGAGGGGGGCG
*
698761 GTTATGTT-GAGACCCCATCAGTCTCCTTCTCTTTTATTGGGAGGGGGACGGATATGTTGGAGAC
1 GTTATGTTGGAGACCCCATCAGTCTCCTTCTCTTTTATTGGGAGGGGGACGGTTATGTTGGAGAC
698825 CCCATCAGTCTCCCTCTCTTTTATTGGGAGGGGGGCG
66 CCCATCAGTCTCCCTCTCTTTTATTGGGAGGGGGGCG
698862 GTTATGTTGGAGACCCCATCAGTCTCCTTCTCTTTTATTGGGAGGGGGACGGTTATGTT-GAGAC
1 GTTATGTTGGAGACCCCATCAGTCTCCTTCTCTTTTATTGGGAGGGGGACGGTTATGTTGGAGAC
* *
698926 CCCATCAGTCTCCTTCTCTTTTATTGGGAGGGGGACG
66 CCCATCAGTCTCCCTCTCTTTTATTGGGAGGGGGGCG
* *
698963 GATATGTTGGAGACCCCATCAGTCTCCCTCTCTTTTATTGGGAGGGGGACGGTTATGTTGGAGAC
1 GTTATGTTGGAGACCCCATCAGTCTCCTTCTCTTTTATTGGGAGGGGGACGGTTATGTTGGAGAC
699028 CCCATCAGTCTCCCTCTCTTTTATTGGGAGGGGGGCG
66 CCCATCAGTCTCCCTCTCTTTTATTGGGAGGGGGGCG
699065 GTTATGTT-GAGACCCCATCAGTCTCCTTCTCTTTTATTGGGAGGGGGACGGTTATGTTGGAGAC
1 GTTATGTTGGAGACCCCATCAGTCTCCTTCTCTTTTATTGGGAGGGGGACGGTTATGTTGGAGAC
699129 CCCATCAGTCTCCCTCTCTTTTATTGGGAGGGGGGCG
66 CCCATCAGTCTCCCTCTCTTTTATTGGGAGGGGGGCG
*
699166 GTTATGTT-GAGACCCCATCAGTCTCCTTCTCTTTTATTGGGAGGGGGACGGATATGTTGGAGAC
1 GTTATGTTGGAGACCCCATCAGTCTCCTTCTCTTTTATTGGGAGGGGGACGGTTATGTTGGAGAC
*
699230 CCCATCAGTCTCCCTCTCTTTTATTGGGAGGGGGACG
66 CCCATCAGTCTCCCTCTCTTTTATTGGGAGGGGGGCG
699267 GTTATGTTGGAGACCCCATCAGTCTCCTTCTCTTTTATTGGGAGGGGGACGGTTATGTT-GAGAC
1 GTTATGTTGGAGACCCCATCAGTCTCCTTCTCTTTTATTGGGAGGGGGACGGTTATGTTGGAGAC
* *
699331 CCCATCAGTCTCCTTCTCTTTTATTGGGAGGGGGACG
66 CCCATCAGTCTCCCTCTCTTTTATTGGGAGGGGGGCG
*
699368 GTTATGTTGGAGACCCCATCCGTCTCCTTCTCTTTTATTGGGAGGGGGACGGTTATGTT-GAGAC
1 GTTATGTTGGAGACCCCATCAGTCTCCTTCTCTTTTATTGGGAGGGGGACGGTTATGTTGGAGAC
* *
699432 CCCATCAGCCTCCTTCTCTTTTATTGGGA-GGGGGCG
66 CCCATCAGTCTCCCTCTCTTTTATTGGGAGGGGGGCG
699468 GTTATGTTGGAGACCCCATCAGTCTCCTT
1 GTTATGTTGGAGACCCCATCAGTCTCCTT
699497 TTCTCATTTT
Statistics
Matches: 908, Mismatches: 26, Indels: 11
0.96 0.03 0.01
Matches are distributed among these distances:
100 34 0.04
101 670 0.74
102 204 0.22
ACGTcount: A:0.15, C:0.23, G:0.29, T:0.33
Consensus pattern (102 bp):
GTTATGTTGGAGACCCCATCAGTCTCCTTCTCTTTTATTGGGAGGGGGACGGTTATGTTGGAGAC
CCCATCAGTCTCCCTCTCTTTTATTGGGAGGGGGGCG
Found at i:698733 original size:152 final size:152
Alignment explanation
Indices: 698457--699496 Score: 1838
Period size: 152 Copynumber: 6.9 Consensus size: 152
698447 GAACATGACA
*
698457 GTTATGTTGGAGACCCCATCAGTCTCCCTCTCTTTTATTGGGAGGGGG-CGGTTATGTTGGAGAC
1 GTTATGTT-GAGACCCCATCAGTCTCCTTCTCTTTTATTGGGAGGGGGACGGTTATGTTGGAGAC
*
698521 CCCATCCGTCTCCCTCTCTTTTATTGGGAGGGGGACGGTTATGTTGGAGACCCCATCAGTCTCCT
65 CCCATCAGTCTCCCTCTCTTTTATTGGGAGGGGGACGGTTATGTTGGAGACCCCATCAGTCTCCT
*
698586 TCTCTTTTATTGGGAGGGGGGCG
130 TCTCTTTTATTGGGAGGGGGACG
*
698609 GTTATGTTGAGACCCCATCAGTCTCCTTCTCTTTTATTGGGAGGGGGGCGGTTATGTTGGAGACC
1 GTTATGTTGAGACCCCATCAGTCTCCTTCTCTTTTATTGGGAGGGGGACGGTTATGTTGGAGACC
* * *
698674 CCATCAGTCTCCTTCTCTTTTATTGGGAGGGGGACAGTTATGTTGGAGACCCCATCAGTCTCCCT
66 CCATCAGTCTCCCTCTCTTTTATTGGGAGGGGGACGGTTATGTTGGAGACCCCATCAGTCTCCTT
*
698739 CTCTTTTATTGGGAGGGGGGCG
131 CTCTTTTATTGGGAGGGGGACG
*
698761 GTTATGTTGAGACCCCATCAGTCTCCTTCTCTTTTATTGGGAGGGGGACGGATATGTTGGAGACC
1 GTTATGTTGAGACCCCATCAGTCTCCTTCTCTTTTATTGGGAGGGGGACGGTTATGTTGGAGACC
*
698826 CCATCAGTCTCCCTCTCTTTTATTGGGAGGGGGGCGGTTATGTTGGAGACCCCATCAGTCTCCTT
66 CCATCAGTCTCCCTCTCTTTTATTGGGAGGGGGACGGTTATGTTGGAGACCCCATCAGTCTCCTT
698891 CTCTTTTATTGGGAGGGGGACG
131 CTCTTTTATTGGGAGGGGGACG
*
698913 GTTATGTTGAGACCCCATCAGTCTCCTTCTCTTTTATTGGGAGGGGGACGGATATGTTGGAGACC
1 GTTATGTTGAGACCCCATCAGTCTCCTTCTCTTTTATTGGGAGGGGGACGGTTATGTTGGAGACC
*
698978 CCATCAGTCTCCCTCTCTTTTATTGGGAGGGGGACGGTTATGTTGGAGACCCCATCAGTCTCCCT
66 CCATCAGTCTCCCTCTCTTTTATTGGGAGGGGGACGGTTATGTTGGAGACCCCATCAGTCTCCTT
*
699043 CTCTTTTATTGGGAGGGGGGCG
131 CTCTTTTATTGGGAGGGGGACG
699065 GTTATGTTGAGACCCCATCAGTCTCCTTCTCTTTTATTGGGAGGGGGACGGTTATGTTGGAGACC
1 GTTATGTTGAGACCCCATCAGTCTCCTTCTCTTTTATTGGGAGGGGGACGGTTATGTTGGAGACC
*
699130 CCATCAGTCTCCCTCTCTTTTATTGGGAGGGGGGCGGTTATGTT-GAGACCCCATCAGTCTCCTT
66 CCATCAGTCTCCCTCTCTTTTATTGGGAGGGGGACGGTTATGTTGGAGACCCCATCAGTCTCCTT
699194 CTCTTTTATTGGGAGGGGGACG
131 CTCTTTTATTGGGAGGGGGACG
* *
699216 GATATGTTGGAGACCCCATCAGTCTCCCTCTCTTTTATTGGGAGGGGGACGGTTATGTTGGAGAC
1 GTTATGTT-GAGACCCCATCAGTCTCCTTCTCTTTTATTGGGAGGGGGACGGTTATGTTGGAGAC
*
699281 CCCATCAGTCTCCTTCTCTTTTATTGGGAGGGGGACGGTTATGTT-GAGACCCCATCAGTCTCCT
65 CCCATCAGTCTCCCTCTCTTTTATTGGGAGGGGGACGGTTATGTTGGAGACCCCATCAGTCTCCT
699345 TCTCTTTTATTGGGAGGGGGACG
130 TCTCTTTTATTGGGAGGGGGACG
*
699368 GTTATGTTGGAGACCCCATCCGTCTCCTTCTCTTTTATTGGGAGGGGGACGGTTATGTT-GAGAC
1 GTTATGTT-GAGACCCCATCAGTCTCCTTCTCTTTTATTGGGAGGGGGACGGTTATGTTGGAGAC
* *
699432 CCCATCAGCCTCCTTCTCTTTTATTGGGAGGGGG-CGGTTATGTTGGAGACCCCATCAGTCTCCT
65 CCCATCAGTCTCCCTCTCTTTTATTGGGAGGGGGACGGTTATGTTGGAGACCCCATCAGTCTCCT
699496 T
130 T
699497 TTCTCATTTT
Statistics
Matches: 858, Mismatches: 27, Indels: 7
0.96 0.03 0.01
Matches are distributed among these distances:
150 10 0.01
151 143 0.17
152 705 0.82
ACGTcount: A:0.15, C:0.23, G:0.29, T:0.33
Consensus pattern (152 bp):
GTTATGTTGAGACCCCATCAGTCTCCTTCTCTTTTATTGGGAGGGGGACGGTTATGTTGGAGACC
CCATCAGTCTCCCTCTCTTTTATTGGGAGGGGGACGGTTATGTTGGAGACCCCATCAGTCTCCTT
CTCTTTTATTGGGAGGGGGACG
Found at i:698927 original size:253 final size:253
Alignment explanation
Indices: 698457--699494 Score: 1868
Period size: 253 Copynumber: 4.1 Consensus size: 253
698447 GAACATGACA
698457 GTTATGTTGGAGACCCCATCAGTCTCCCTCTCTTTTATTGGGAGGGGG-CGGTTATGTTGGAGAC
1 GTTATGTTGGAGACCCCATCAGTCTCCCTCTCTTTTATTGGGAGGGGGACGGTTATGTTGGAGAC
*
698521 CCCATCCGTCTCCCTCTCTTTTATTGGGAGGGGGACGGTTATGTTGGAGACCCCATCAGTCTCCT
66 CCCATCAGTCTCCCTCTCTTTTATTGGGAGGGGGACGGTTATGTT-GAGACCCCATCAGTCTCCT
*
698586 TCTCTTTTATTGGGAGGGGGGCGGTTATGTT-GAGACCCCATCAGTCTCCTTCTCTTTTATTGGG
130 TCTCTTTTATTGGGAGGGGGACGGTTATGTTGGAGACCCCATCAGTCTCCTTCTCTTTTATTGGG
* *
698650 AGGGGGGCGGTTATGTTGGAGACCCCATCAGTCTCCTTCTCTTTTATTGGGAGGGGGACA
195 AGGGGGACGGTTATGTT-GAGACCCCATCAGTCTCCTTCTCTTTTATTGGGAGGGGGACG
*
698710 GTTATGTTGGAGACCCCATCAGTCTCCCTCTCTTTTATTGGGAGGGGGGCGGTTATGTT-GAGAC
1 GTTATGTTGGAGACCCCATCAGTCTCCCTCTCTTTTATTGGGAGGGGGACGGTTATGTTGGAGAC
* * *
698774 CCCATCAGTCTCCTTCTCTTTTATTGGGAGGGGGACGGATATGTTGGAGACCCCATCAGTCTCCC
66 CCCATCAGTCTCCCTCTCTTTTATTGGGAGGGGGACGGTTATGTT-GAGACCCCATCAGTCTCCT
*
698839 TCTCTTTTATTGGGAGGGGGGCGGTTATGTTGGAGACCCCATCAGTCTCCTTCTCTTTTATTGGG
130 TCTCTTTTATTGGGAGGGGGACGGTTATGTTGGAGACCCCATCAGTCTCCTTCTCTTTTATTGGG
698904 AGGGGGACGGTTATGTTGAGACCCCATCAGTCTCCTTCTCTTTTATTGGGAGGGGGACG
195 AGGGGGACGGTTATGTTGAGACCCCATCAGTCTCCTTCTCTTTTATTGGGAGGGGGACG
*
698963 GATATGTTGGAGACCCCATCAGTCTCCCTCTCTTTTATTGGGAGGGGGACGGTTATGTTGGAGAC
1 GTTATGTTGGAGACCCCATCAGTCTCCCTCTCTTTTATTGGGAGGGGGACGGTTATGTTGGAGAC
*
699028 CCCATCAGTCTCCCTCTCTTTTATTGGGAGGGGGGCGGTTATGTTGAGACCCCATCAGTCTCCTT
66 CCCATCAGTCTCCCTCTCTTTTATTGGGAGGGGGACGGTTATGTTGAGACCCCATCAGTCTCCTT
*
699093 CTCTTTTATTGGGAGGGGGACGGTTATGTTGGAGACCCCATCAGTCTCCCTCTCTTTTATTGGGA
131 CTCTTTTATTGGGAGGGGGACGGTTATGTTGGAGACCCCATCAGTCTCCTTCTCTTTTATTGGGA
*
699158 GGGGGGCGGTTATGTTGAGACCCCATCAGTCTCCTTCTCTTTTATTGGGAGGGGGACG
196 GGGGGACGGTTATGTTGAGACCCCATCAGTCTCCTTCTCTTTTATTGGGAGGGGGACG
*
699216 GATATGTTGGAGACCCCATCAGTCTCCCTCTCTTTTATTGGGAGGGGGACGGTTATGTTGGAGAC
1 GTTATGTTGGAGACCCCATCAGTCTCCCTCTCTTTTATTGGGAGGGGGACGGTTATGTTGGAGAC
*
699281 CCCATCAGTCTCCTTCTCTTTTATTGGGAGGGGGACGGTTATGTTGAGACCCCATCAGTCTCCTT
66 CCCATCAGTCTCCCTCTCTTTTATTGGGAGGGGGACGGTTATGTTGAGACCCCATCAGTCTCCTT
*
699346 CTCTTTTATTGGGAGGGGGACGGTTATGTTGGAGACCCCATCCGTCTCCTTCTCTTTTATTGGGA
131 CTCTTTTATTGGGAGGGGGACGGTTATGTTGGAGACCCCATCAGTCTCCTTCTCTTTTATTGGGA
*
699411 GGGGGACGGTTATGTTGAGACCCCATCAGCCTCCTTCTCTTTTATTGGGAGGGGG-CG
196 GGGGGACGGTTATGTTGAGACCCCATCAGTCTCCTTCTCTTTTATTGGGAGGGGGACG
699468 GTTATGTTGGAGACCCCATCAGTCTCC
1 GTTATGTTGGAGACCCCATCAGTCTCC
699495 TTTTCTCATT
Statistics
Matches: 760, Mismatches: 22, Indels: 7
0.96 0.03 0.01
Matches are distributed among these distances:
252 28 0.04
253 626 0.82
254 106 0.14
ACGTcount: A:0.15, C:0.23, G:0.29, T:0.32
Consensus pattern (253 bp):
GTTATGTTGGAGACCCCATCAGTCTCCCTCTCTTTTATTGGGAGGGGGACGGTTATGTTGGAGAC
CCCATCAGTCTCCCTCTCTTTTATTGGGAGGGGGACGGTTATGTTGAGACCCCATCAGTCTCCTT
CTCTTTTATTGGGAGGGGGACGGTTATGTTGGAGACCCCATCAGTCTCCTTCTCTTTTATTGGGA
GGGGGACGGTTATGTTGAGACCCCATCAGTCTCCTTCTCTTTTATTGGGAGGGGGACG
Found at i:702156 original size:48 final size:48
Alignment explanation
Indices: 702084--702178 Score: 172
Period size: 48 Copynumber: 2.0 Consensus size: 48
702074 ATGACCTTGG
702084 ATGGATTAACTATAATTATCAAATGGAATGTCTCAATGGAATTATAGT
1 ATGGATTAACTATAATTATCAAATGGAATGTCTCAATGGAATTATAGT
* *
702132 ATGGATTAACTATAATTATTAAATGGAATGTCTCTATGGAATTATAG
1 ATGGATTAACTATAATTATCAAATGGAATGTCTCAATGGAATTATAG
702179 GAGAAAATAA
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
48 45 1.00
ACGTcount: A:0.39, C:0.07, G:0.17, T:0.37
Consensus pattern (48 bp):
ATGGATTAACTATAATTATCAAATGGAATGTCTCAATGGAATTATAGT
Found at i:704716 original size:16 final size:16
Alignment explanation
Indices: 704697--704729 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
704687 AAATGTAGAA
704697 GGGCGAAAATAACACG
1 GGGCGAAAATAACACG
704713 GGGCGAAAATAACACG
1 GGGCGAAAATAACACG
704729 G
1 G
704730 TATACAGTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.42, C:0.18, G:0.33, T:0.06
Consensus pattern (16 bp):
GGGCGAAAATAACACG
Found at i:704949 original size:35 final size:35
Alignment explanation
Indices: 704903--705037 Score: 227
Period size: 35 Copynumber: 3.9 Consensus size: 35
704893 GATGACACTA
* * *
704903 TCCATAATCTAAAATACAGGTACAGGTAATCACAG
1 TCCATACTCTAAAATACAGGTACAGGTAATCGCTG
704938 TCCATACTCTAAAATACAGGTACAGGTAAAT-GCTG
1 TCCATACTCTAAAATACAGGTACAGGT-AATCGCTG
704973 TCCATACTCTAAAATACAGGTACAGGTAATCGCTG
1 TCCATACTCTAAAATACAGGTACAGGTAATCGCTG
705008 TCCATACTCTAAAATACAGGTACAGGTAAT
1 TCCATACTCTAAAATACAGGTACAGGTAAT
705038 TCAAAAACAA
Statistics
Matches: 95, Mismatches: 3, Indels: 4
0.93 0.03 0.04
Matches are distributed among these distances:
34 3 0.03
35 89 0.94
36 3 0.03
ACGTcount: A:0.39, C:0.21, G:0.16, T:0.25
Consensus pattern (35 bp):
TCCATACTCTAAAATACAGGTACAGGTAATCGCTG
Found at i:709392 original size:30 final size:31
Alignment explanation
Indices: 709333--709405 Score: 103
Period size: 30 Copynumber: 2.3 Consensus size: 31
709323 ATATAAATAA
*
709333 TTCCTTTATACAAGAAACGTAAATTAAGATTAT
1 TTCCTTTATACAAGAAACCT--ATTAAGATTAT
*
709366 TTCCTATATACAAGAAACCT-TTAAGATTAT
1 TTCCTTTATACAAGAAACCTATTAAGATTAT
709396 TTCCTTTATA
1 TTCCTTTATA
709406 TGATGAGCAT
Statistics
Matches: 37, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
30 19 0.51
33 18 0.49
ACGTcount: A:0.38, C:0.15, G:0.07, T:0.40
Consensus pattern (31 bp):
TTCCTTTATACAAGAAACCTATTAAGATTAT
Found at i:717510 original size:48 final size:48
Alignment explanation
Indices: 717439--717539 Score: 184
Period size: 48 Copynumber: 2.1 Consensus size: 48
717429 NNNNNNNNNN
*
717439 GCAAACAGTTTGCCAGAAGCTAATTTGCATACGAATTCTGAATTTGCC
1 GCAAACAGTTTGCCAGAAGCTAATTTGCATACGAATTCTGAACTTGCC
*
717487 GCAAACAGTTTGCCAGAAGCTAATTTGCATACGAATTCTGAACTTGCG
1 GCAAACAGTTTGCCAGAAGCTAATTTGCATACGAATTCTGAACTTGCC
717535 GCAAA
1 GCAAA
717540 TTTGCCGCAA
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
48 51 1.00
ACGTcount: A:0.33, C:0.21, G:0.20, T:0.27
Consensus pattern (48 bp):
GCAAACAGTTTGCCAGAAGCTAATTTGCATACGAATTCTGAACTTGCC
Found at i:717551 original size:59 final size:59
Alignment explanation
Indices: 717479--717667 Score: 315
Period size: 59 Copynumber: 3.2 Consensus size: 59
717469 ACGAATTCTG
*
717479 AATTTGCCGCAAACAGTTTGCCAGAAGCTAATTTGCATACGAATTCTGAACTTGCGGCA
1 AATTTGCCGCAAACAGTTTGCCAGAAGCTAATTTGCATACGAATTCTGAACTTGCCGCA
* *
717538 AATTTGCCGCAAACAGTTTCCCAGAAGCTAATTTGCATACGAATTCTGAACTTGCTGCA
1 AATTTGCCGCAAACAGTTTGCCAGAAGCTAATTTGCATACGAATTCTGAACTTGCCGCA
* * *
717597 ACTTTGCCGCAAACAGTTTGCCAGAAGCTAATTTGCAAACGAATTCTGAACCTGCCGCA
1 AATTTGCCGCAAACAGTTTGCCAGAAGCTAATTTGCATACGAATTCTGAACTTGCCGCA
*
717656 AATTTGCGGCAA
1 AATTTGCCGCAA
717668 CTGTTTGTCG
Statistics
Matches: 121, Mismatches: 9, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
59 121 1.00
ACGTcount: A:0.31, C:0.24, G:0.19, T:0.26
Consensus pattern (59 bp):
AATTTGCCGCAAACAGTTTGCCAGAAGCTAATTTGCATACGAATTCTGAACTTGCCGCA
Found at i:717684 original size:24 final size:24
Alignment explanation
Indices: 717652--717720 Score: 81
Period size: 24 Copynumber: 3.0 Consensus size: 24
717642 CTGAACCTGC
717652 CGCAAATTTGCGGCAACTGTTTGT
1 CGCAAATTTGCGGCAACTGTTTGT
* * *
717676 CGCAAATTTGCAGCAAAC--TCTCT
1 CGCAAATTTGCGGC-AACTGTTTGT
717699 -GCAAATTTGCGGCAACTGTTTG
1 CGCAAATTTGCGGCAACTGTTTG
717721 CCAGAGGCCT
Statistics
Matches: 36, Mismatches: 6, Indels: 7
0.73 0.12 0.14
Matches are distributed among these distances:
21 3 0.08
22 12 0.33
23 5 0.14
24 13 0.36
25 3 0.08
ACGTcount: A:0.25, C:0.23, G:0.22, T:0.30
Consensus pattern (24 bp):
CGCAAATTTGCGGCAACTGTTTGT
Found at i:727483 original size:2 final size:2
Alignment explanation
Indices: 727476--727527 Score: 104
Period size: 2 Copynumber: 26.0 Consensus size: 2
727466 AAGGCACAAC
727476 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
727518 CT CT CT CT CT
1 CT CT CT CT CT
727528 GAAAGGAAAG
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 50 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:730278 original size:20 final size:20
Alignment explanation
Indices: 729931--730623 Score: 625
Period size: 20 Copynumber: 34.6 Consensus size: 20
729921 CCATGATCCG
*
729931 CCACGCTCCACAACGACCCA
1 CCACGCTCCACAATGACCCA
* * * **
729951 CCATGCTTCACAACGAATCA
1 CCACGCTCCACAATGACCCA
* * *
729971 CCACGATTCACAATGATCCA
1 CCACGCTCCACAATGACCCA
**
729991 CCACGCTCCACAATGAATCA
1 CCACGCTCCACAATGACCCA
*
730011 CCACGCTCCACAACGACCCA
1 CCACGCTCCACAATGACCCA
* * * **
730031 CCATGCTTCACAACGAATCA
1 CCACGCTCCACAATGACCCA
* * **
730051 CCACGATTCACAATGATTCA
1 CCACGCTCCACAATGACCCA
* **
730071 CCACGCTCCATAATGAATCA
1 CCACGCTCCACAATGACCCA
*
730091 CCACGCTCCACAATGATCCA
1 CCACGCTCCACAATGACCCA
730111 CCTA-GCTCCACAATGACCCA
1 CC-ACGCTCCACAATGACCCA
* *
730131 CAACGCTCCACAATGATCCA
1 CCACGCTCCACAATGACCCA
* * *
730151 CCACCCTCCACAATTATCCA
1 CCACGCTCCACAATGACCCA
730171 CCACGCTCCACAATGACCCA
1 CCACGCTCCACAATGACCCA
* * *
730191 CTACGCTCCACAATTATCCA
1 CCACGCTCCACAATGACCCA
730211 CCACGCTCCACAATGACCCA
1 CCACGCTCCACAATGACCCA
730231 CCACGCTCCACAATGACCCA
1 CCACGCTCCACAATGACCCA
730251 CCACGCTCCACAATGACCCA
1 CCACGCTCCACAATGACCCA
*
730271 TCACG-----C--T---CCA
1 CCACGCTCCACAATGACCCA
* * *
730281 CCATGCTCCACTATAACCCA
1 CCACGCTCCACAATGACCCA
*
730301 TCACGCTCCACAATGACCCA
1 CCACGCTCCACAATGACCCA
* * *
730321 CCACGCCCCAAAATAACCCA
1 CCACGCTCCACAATGACCCA
**
730341 CCACGCTCCACAATGAATCA
1 CCACGCTCCACAATGACCCA
*
730361 CCACGCTCCACAATGATCCA
1 CCACGCTCCACAATGACCCA
730381 CCACGCTCCACAATGACCCATAA
1 CCACGCTCCACAATGACCC---A
* *
730404 CGCTCCACCATGCTCCACAATAACCTA
1 ----CCA-C--GCTCCACAATGACCCA
*
730431 TCACGCTCCACAATGACCCA
1 CCACGCTCCACAATGACCCA
**
730451 CCACGCTCCACAATGAATCA
1 CCACGCTCCACAATGACCCA
* * *
730471 CCACCCTCCACAATTATCCA
1 CCACGCTCCACAATGACCCA
730491 CCACGCTCCACAATGACCCA
1 CCACGCTCCACAATGACCCA
*
730511 CTACGCTCCACAATGACCCA
1 CCACGCTCCACAATGACCCA
* *
730531 CCACGATCCACAATAACCCA
1 CCACGCTCCACAATGACCCA
*
730551 CCACGCTCCACAATGATCCA
1 CCACGCTCCACAATGACCCA
* ** *
730571 CCATGCTCCACAATGATGCG
1 CCACGCTCCACAATGACCCA
* * * **
730591 TCACGCTTCACAATAAATCA
1 CCACGCTCCACAATGACCCA
730611 CCACGCTCCACAA
1 CCACGCTCCACAA
730624 AGATCCAGTA
Statistics
Matches: 552, Mismatches: 99, Indels: 44
0.79 0.14 0.06
Matches are distributed among these distances:
10 6 0.01
13 1 0.00
15 2 0.00
17 1 0.00
19 1 0.00
20 518 0.94
21 1 0.00
22 1 0.00
23 3 0.01
27 4 0.01
28 1 0.00
30 13 0.02
ACGTcount: A:0.32, C:0.44, G:0.09, T:0.15
Consensus pattern (20 bp):
CCACGCTCCACAATGACCCA
Found at i:730289 original size:30 final size:30
Alignment explanation
Indices: 730248--730441 Score: 113
Period size: 30 Copynumber: 6.1 Consensus size: 30
730238 CCACAATGAC
730248 CCACCACGCTCCACAATGACCCATCACGCT
1 CCACCACGCTCCACAATGACCCATCACGCT
* * *
730278 CCACCATGCTCCACTATAACCCATCACGCT
1 CCACCACGCTCCACAATGACCCATCACGCT
* * * * * ** **
730308 CCACAATGAC-CCACCACGCCCCAAAATAAC-
1 CCACCACG-CTCCACAATGACCCATCA-CGCT
*
730338 CCACCACGCTCCACAATGAATCACCACGCTCCACAATGAT
1 CCACCACGCTCCACAATG-A-C-CCA---T-CAC---GCT
*
730378 CCACCACGCTCCACAATGACCCATAACGCT
1 CCACCACGCTCCACAATGACCCATCACGCT
* * *
730408 CCACCATGCTCCACAATAACCTATCACGCT
1 CCACCACGCTCCACAATGACCCATCACGCT
730438 CCAC
1 CCAC
730442 AATGACCCAC
Statistics
Matches: 122, Mismatches: 28, Indels: 28
0.69 0.16 0.16
Matches are distributed among these distances:
29 1 0.01
30 88 0.72
31 2 0.02
32 1 0.01
33 5 0.04
34 1 0.01
37 4 0.03
38 1 0.01
39 1 0.01
40 18 0.15
ACGTcount: A:0.31, C:0.46, G:0.08, T:0.14
Consensus pattern (30 bp):
CCACCACGCTCCACAATGACCCATCACGCT
Found at i:730342 original size:130 final size:129
Alignment explanation
Indices: 730156--730623 Score: 569
Period size: 130 Copynumber: 3.7 Consensus size: 129
730146 ATCCACCACC
* * * * *
730156 CTCCACAATTATCCACCACGCTCCACAATGACCCACTACGCTCCACAATTATCCACCACGCTCCA
1 CTCCACAATAACCCATCACGCTCCACAATGACCCACCACGCTCCACAA-TAACCACCACGCTCCA
*
730221 CAATGACCCACCACGCTCCACAATGACCCACCACGCTCCACAATGACCCATCACGCTCCACCATG
65 CAATGAACCACCACGCTCCACAATGACCCACCACGCTCCACAATGACCCATCACGCTCCACCATG
* * *
730286 CTCCACTATAACCCATCACGCTCCACAATGACCCACCACGCCCCAAAATAACCCACCACGCTCCA
1 CTCCACAATAACCCATCACGCTCCACAATGACCCACCACGCTCCACAATAA-CCACCACGCTCCA
* * *
730351 CAATGAATCACCACGCTCCACAATGATCCACCACGCTCCACAATGACCCATAACGCTCCACCATG
65 CAATGAACCACCACGCTCCACAATGACCCACCACGCTCCACAATGACCCATCACGCTCCACCATG
* * *
730416 CTCCACAATAACCTATCACGCTCCACAATGACCCACCACGCTCCACAATGAATCACCACCCTCCA
1 CTCCACAATAACCCATCACGCTCCACAATGACCCACCACGCTCCACAAT-AACCACCACGCTCCA
* * *
730481 CAATTATCCACCACGCTCCACAATGACCCACTACGCTCCACAATGA-CC--CA----CCA-C--G
65 CAATGAACCACCACGCTCCACAATGACCCACCACGCTCCACAATGACCCATCACGCTCCACCATG
* * * * ** ** *
730536 ATCCACAATAACCCACCACGCTCCACAATGATCCACCATGCTCCACAATGATGCGTCACGCTTCA
1 CTCCACAATAACCCATCACGCTCCACAATGACCCACCACGCTCCACAAT-AACCACCACGCTCCA
* *
730601 CAATAAATCACCACGCTCCACAA
65 CAATGAACCACCACGCTCCACAA
730624 AGATCCAGTA
Statistics
Matches: 298, Mismatches: 38, Indels: 14
0.85 0.11 0.04
Matches are distributed among these distances:
120 75 0.25
122 1 0.00
123 3 0.01
127 1 0.00
129 4 0.01
130 212 0.71
131 2 0.01
ACGTcount: A:0.32, C:0.45, G:0.08, T:0.15
Consensus pattern (129 bp):
CTCCACAATAACCCATCACGCTCCACAATGACCCACCACGCTCCACAATAACCACCACGCTCCAC
AATGAACCACCACGCTCCACAATGACCCACCACGCTCCACAATGACCCATCACGCTCCACCATG
Found at i:741462 original size:2 final size:2
Alignment explanation
Indices: 741455--741517 Score: 126
Period size: 2 Copynumber: 31.5 Consensus size: 2
741445 TTACATTGTG
741455 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
741497 TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA T
741518 GATNNNNNNN
Statistics
Matches: 61, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 61 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:743185 original size:2 final size:2
Alignment explanation
Indices: 743178--743209 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
743168 GAATAGAACG
743178 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
743210 NNNNNNNNNN
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:746459 original size:12 final size:12
Alignment explanation
Indices: 746442--746468 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
746432 TCACACCCCG
746442 ACCAAAATTATC
1 ACCAAAATTATC
746454 ACCAAAATTATC
1 ACCAAAATTATC
746466 ACC
1 ACC
746469 TCCTAATACT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.48, C:0.30, G:0.00, T:0.22
Consensus pattern (12 bp):
ACCAAAATTATC
Found at i:775901 original size:17 final size:17
Alignment explanation
Indices: 775879--775915 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
775869 CATTCGCTAT
*
775879 ATGAAATTGGGTATAAA
1 ATGAAATCGGGTATAAA
*
775896 ATGAAATCGGGTATATA
1 ATGAAATCGGGTATAAA
775913 ATG
1 ATG
775916 TCATTTTACA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.43, C:0.03, G:0.24, T:0.30
Consensus pattern (17 bp):
ATGAAATCGGGTATAAA
Found at i:781173 original size:15 final size:15
Alignment explanation
Indices: 781153--781183 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
781143 CGTGTTGTTA
781153 TAATTATACATGTAT
1 TAATTATACATGTAT
781168 TAATTATACATGTAT
1 TAATTATACATGTAT
781183 T
1 T
781184 TTGAACAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.39, C:0.06, G:0.06, T:0.48
Consensus pattern (15 bp):
TAATTATACATGTAT
Found at i:784530 original size:15 final size:15
Alignment explanation
Indices: 784512--784542 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
784502 TTCCCCGGGG
784512 TGTTTTTGTTGTTGT
1 TGTTTTTGTTGTTGT
784527 TGTTTTTGTTGTTGT
1 TGTTTTTGTTGTTGT
784542 T
1 T
784543 TTGGGGTTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.00, C:0.00, G:0.26, T:0.74
Consensus pattern (15 bp):
TGTTTTTGTTGTTGT
Found at i:784535 original size:12 final size:12
Alignment explanation
Indices: 784520--784544 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
784510 GGTGTTTTTG
784520 TTGTTGTTGTTT
1 TTGTTGTTGTTT
784532 TTGTTGTTGTTT
1 TTGTTGTTGTTT
784544 T
1 T
784545 GGGGTTTTTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.00, G:0.24, T:0.76
Consensus pattern (12 bp):
TTGTTGTTGTTT
Found at i:794371 original size:45 final size:45
Alignment explanation
Indices: 794320--794409 Score: 180
Period size: 45 Copynumber: 2.0 Consensus size: 45
794310 GATAACTGGA
794320 GGACTATACACAGGTGGTCTAACTGACTGGTTAGGTATAGGCCGC
1 GGACTATACACAGGTGGTCTAACTGACTGGTTAGGTATAGGCCGC
794365 GGACTATACACAGGTGGTCTAACTGACTGGTTAGGTATAGGCCGC
1 GGACTATACACAGGTGGTCTAACTGACTGGTTAGGTATAGGCCGC
794410 TTTGGAGCTT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 45 1.00
ACGTcount: A:0.24, C:0.20, G:0.31, T:0.24
Consensus pattern (45 bp):
GGACTATACACAGGTGGTCTAACTGACTGGTTAGGTATAGGCCGC
Found at i:794999 original size:49 final size:49
Alignment explanation
Indices: 794927--795026 Score: 200
Period size: 49 Copynumber: 2.0 Consensus size: 49
794917 AACATGCCTG
794927 GAAACAACAAATATACATTTATGTTTAACATTAACTTTTATTCAGAATA
1 GAAACAACAAATATACATTTATGTTTAACATTAACTTTTATTCAGAATA
794976 GAAACAACAAATATACATTTATGTTTAACATTAACTTTTATTCAGAATA
1 GAAACAACAAATATACATTTATGTTTAACATTAACTTTTATTCAGAATA
795025 GA
1 GA
795027 CTCATGTACA
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
49 51 1.00
ACGTcount: A:0.45, C:0.12, G:0.07, T:0.36
Consensus pattern (49 bp):
GAAACAACAAATATACATTTATGTTTAACATTAACTTTTATTCAGAATA
Found at i:798123 original size:14 final size:14
Alignment explanation
Indices: 798077--798130 Score: 56
Period size: 14 Copynumber: 3.9 Consensus size: 14
798067 GAACGAGCAA
*
798077 GAGAGAGACAGACG
1 GAGAGAGACAGAGG
* *
798091 GACG-GACAAAGAGG
1 GA-GAGAGACAGAGG
*
798105 AAGAGAGACAGAGG
1 GAGAGAGACAGAGG
798119 GAGAGAGACAGA
1 GAGAGAGACAGA
798131 TTTTCGACCT
Statistics
Matches: 31, Mismatches: 7, Indels: 4
0.74 0.17 0.10
Matches are distributed among these distances:
13 1 0.03
14 29 0.94
15 1 0.03
ACGTcount: A:0.46, C:0.11, G:0.43, T:0.00
Consensus pattern (14 bp):
GAGAGAGACAGAGG
Found at i:799169 original size:10 final size:10
Alignment explanation
Indices: 799154--799309 Score: 66
Period size: 10 Copynumber: 16.1 Consensus size: 10
799144 ATATTGTTTG
799154 TATTGTATAT
1 TATTGTATAT
*
799164 TTTTGTATGA-
1 TATTGTAT-AT
799174 TATTGT-T-T
1 TATTGTATAT
799182 GTATTGTATAT
1 -TATTGTATAT
*
799193 TTTTGTATGA-
1 TATTGTAT-AT
**
799203 TATTGT-TCG
1 TATTGTATAT
799212 TATTGTATAT
1 TATTGTATAT
*
799222 TTTTGTATGA-
1 TATTGTAT-AT
**
799232 TATTGT-TCG
1 TATTGTATAT
799241 TATTGTATAT
1 TATTGTATAT
*
799251 TTTTGTATGA-
1 TATTGTAT-AT
799261 TATTGT-TCA-
1 TATTGTAT-AT
799270 TATTGTATAT
1 TATTGTATAT
*
799280 TTTTGTATGA-
1 TATTGTAT-AT
**
799290 TATTGT-TCG
1 TATTGTATAT
799299 TATTGTATAT
1 TATTGTATAT
799309 T
1 T
799310 TTCTCTGTGA
Statistics
Matches: 109, Mismatches: 20, Indels: 34
0.67 0.12 0.21
Matches are distributed among these distances:
9 37 0.34
10 66 0.61
11 6 0.06
ACGTcount: A:0.22, C:0.03, G:0.16, T:0.60
Consensus pattern (10 bp):
TATTGTATAT
Found at i:799175 original size:29 final size:29
Alignment explanation
Indices: 799133--799311 Score: 331
Period size: 29 Copynumber: 6.2 Consensus size: 29
799123 AACACTCTTG
*
799133 ATTTTTGTATGATATTGTTTGTATTGTAT
1 ATTTTTGTATGATATTGTTCGTATTGTAT
*
799162 ATTTTTGTATGATATTGTTTGTATTGTAT
1 ATTTTTGTATGATATTGTTCGTATTGTAT
799191 ATTTTTGTATGATATTGTTCGTATTGTAT
1 ATTTTTGTATGATATTGTTCGTATTGTAT
799220 ATTTTTGTATGATATTGTTCGTATTGTAT
1 ATTTTTGTATGATATTGTTCGTATTGTAT
*
799249 ATTTTTGTATGATATTGTTCATATTGTAT
1 ATTTTTGTATGATATTGTTCGTATTGTAT
799278 ATTTTTGTATGATATTGTTCGTATTGTAT
1 ATTTTTGTATGATATTGTTCGTATTGTAT
799307 ATTTT
1 ATTTT
799312 CTCTGTGATG
Statistics
Matches: 147, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
29 147 1.00
ACGTcount: A:0.21, C:0.02, G:0.16, T:0.60
Consensus pattern (29 bp):
ATTTTTGTATGATATTGTTCGTATTGTAT
Found at i:801295 original size:34 final size:34
Alignment explanation
Indices: 801208--801331 Score: 160
Period size: 34 Copynumber: 3.6 Consensus size: 34
801198 GAATAACAGT
*
801208 TAATAAACATACTGACTAAAACTTACAGACTAGC
1 TAATAAGCATACTGACTAAAACTTACAGACTAGC
* * *
801242 TAATTAGCATATACTGACTAAAATTTACGGACTAGC
1 TAATAAGC--ATACTGACTAAAACTTACAGACTAGC
*
801278 TAATAAGCATACTGACTAAAACTTACAGTCTAGC
1 TAATAAGCATACTGACTAAAACTTACAGACTAGC
*
801312 TAA-CAGCCATACTGACTAAA
1 TAATAAG-CATACTGACTAAA
801332 GAATTATGGA
Statistics
Matches: 78, Mismatches: 9, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
33 2 0.03
34 45 0.58
36 31 0.40
ACGTcount: A:0.43, C:0.20, G:0.11, T:0.26
Consensus pattern (34 bp):
TAATAAGCATACTGACTAAAACTTACAGACTAGC
Found at i:804184 original size:2 final size:2
Alignment explanation
Indices: 804177--804291 Score: 216
Period size: 2 Copynumber: 58.5 Consensus size: 2
804167 TTCATAAATA
804177 CT CT CT CT CT C- CT CT CT CT CT -T CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
804217 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
804259 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
804292 CAGGAAAGTT
Statistics
Matches: 111, Mismatches: 0, Indels: 4
0.97 0.00 0.03
Matches are distributed among these distances:
1 2 0.02
2 109 0.98
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:805426 original size:3 final size:3
Alignment explanation
Indices: 805420--805457 Score: 58
Period size: 3 Copynumber: 12.7 Consensus size: 3
805410 TGACAACAAA
* *
805420 GAT GAT GAT GAT GAT GAT GAT GAT GAT GGT GAT TAT GA
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GA
805458 CTCGGCATTT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.32, C:0.00, G:0.34, T:0.34
Consensus pattern (3 bp):
GAT
Found at i:809457 original size:37 final size:38
Alignment explanation
Indices: 809416--809995 Score: 677
Period size: 37 Copynumber: 15.7 Consensus size: 38
809406 ACTCAAATTG
*
809416 CAATGACAAATCTTACTTTCTGTTCATG-AATAGACAC
1 CAATGACAATTCTTACTTTCTGTTCATGTAATAGACAC
** * *
809453 CAATGGA-AGGTATTA-TTTCTGTTCATGTAATAGAAAC
1 CAAT-GACAATTCTTACTTTCTGTTCATGTAATAGACAC
* **
809490 CAATGGCAATTC-TAAATTCTGTTCATGTAATAGACAC
1 CAATGACAATTCTTACTTTCTGTTCATGTAATAGACAC
*
809527 CAATGACAAGTCTTACTTTCTGTTCATG-AATAGACAC
1 CAATGACAATTCTTACTTTCTGTTCATGTAATAGACAC
* * *
809564 CAATGGA-AGGTATATATTA-TTCCTGTTCATGTAATAGAAAC
1 CAAT-GACA---AT-TCTTACTTTCTGTTCATGTAATAGACAC
*
809605 CAATGGCAATTCTTAC-TTCTGTTCATGTAATAGACAC
1 CAATGACAATTCTTACTTTCTGTTCATGTAATAGACAC
809642 CAATGACAATTCTTA-TTTCTGTTCATG-AATAGACAC
1 CAATGACAATTCTTACTTTCTGTTCATGTAATAGACAC
* * *
809678 CAATGGCAAGTATTA-TTTCTGTTCATG-AATAGACAC
1 CAATGACAATTCTTACTTTCTGTTCATGTAATAGACAC
* * * * *
809714 CAATGGCAAGTCTT-CTTTCTGTTCACGAAAAAGACAC
1 CAATGACAATTCTTACTTTCTGTTCATGTAATAGACAC
* * *
809751 CAATGGCAAGTATTA-TTTCTGTTCATGTAATAGACAC
1 CAATGACAATTCTTACTTTCTGTTCATGTAATAGACAC
*
809788 CAATGACAATTCTTAC-TTCTGTTTATGTAAT---CAC
1 CAATGACAATTCTTACTTTCTGTTCATGTAATAGACAC
*
809822 CAATGGCAATTCTTAC-TTCTGTTCATG-AATAGACAC
1 CAATGACAATTCTTACTTTCTGTTCATGTAATAGACAC
*
809858 CAATGACAAGTCTTAC-TTCTGTTCATGTAATAGACAC
1 CAATGACAATTCTTACTTTCTGTTCATGTAATAGACAC
809895 CAATGACAATTCTTAC-TTCTGTTCATGTAATAGACAC
1 CAATGACAATTCTTACTTTCTGTTCATGTAATAGACAC
*
809932 CAATGGCAATTCTTAC-TTCTGTTCATGTAATAGACAC
1 CAATGACAATTCTTACTTTCTGTTCATGTAATAGACAC
*
809969 CAATGGCAATTCTTAC-TTCTGTTCATG
1 CAATGACAATTCTTACTTTCTGTTCATG
809996 AAAAAACAAT
Statistics
Matches: 478, Mismatches: 43, Indels: 44
0.85 0.08 0.08
Matches are distributed among these distances:
33 3 0.01
34 28 0.06
36 109 0.23
37 289 0.60
38 19 0.04
40 13 0.03
41 17 0.04
ACGTcount: A:0.32, C:0.19, G:0.14, T:0.34
Consensus pattern (38 bp):
CAATGACAATTCTTACTTTCTGTTCATGTAATAGACAC
Found at i:816209 original size:16 final size:17
Alignment explanation
Indices: 816170--816212 Score: 52
Period size: 18 Copynumber: 2.5 Consensus size: 17
816160 ATTTTTTCAT
816170 TGAAACTAAAAAAAAACCA
1 TGAAA-TAAAAAAAAA-CA
*
816189 CGAAATAAAAAAAAA-A
1 TGAAATAAAAAAAAACA
816205 TGAAATAA
1 TGAAATAA
816213 TTATGACGTC
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
16 8 0.36
18 10 0.45
19 4 0.18
ACGTcount: A:0.72, C:0.09, G:0.07, T:0.12
Consensus pattern (17 bp):
TGAAATAAAAAAAAACA
Found at i:823063 original size:25 final size:25
Alignment explanation
Indices: 823021--823112 Score: 89
Period size: 25 Copynumber: 3.7 Consensus size: 25
823011 TGTACCAAAG
** *
823021 GTGCTATGTTTAAATGTCTGTTAAT
1 GTGCTATGTTGCACTGTCTGTTAAT
*
823046 GTGCTATGTTGCACTGTCTGCTAAT
1 GTGCTATGTTGCACTGTCTGTTAAT
* *
823071 G-G-TGATATTGCACTGACTGTTAAT
1 GTGCT-ATGTTGCACTGTCTGTTAAT
*
823095 GATGCTATGTTGCTCTGT
1 G-TGCTATGTTGCACTGT
823113 TAGTTTATGG
Statistics
Matches: 53, Mismatches: 10, Indels: 7
0.76 0.14 0.10
Matches are distributed among these distances:
23 1 0.02
24 19 0.36
25 22 0.42
26 10 0.19
27 1 0.02
ACGTcount: A:0.20, C:0.14, G:0.24, T:0.42
Consensus pattern (25 bp):
GTGCTATGTTGCACTGTCTGTTAAT
Found at i:834300 original size:16 final size:16
Alignment explanation
Indices: 834279--834309 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
834269 ATTAAATTTT
*
834279 GAGAGATCAAGAGTTC
1 GAGAGATCAAAAGTTC
834295 GAGAGATCAAAAGTT
1 GAGAGATCAAAAGTT
834310 AAAAAACAAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.42, C:0.10, G:0.29, T:0.19
Consensus pattern (16 bp):
GAGAGATCAAAAGTTC
Found at i:837758 original size:23 final size:23
Alignment explanation
Indices: 837726--837773 Score: 71
Period size: 23 Copynumber: 2.1 Consensus size: 23
837716 GGGACCAAAT
837726 TTGGCCCTTA-CCTTACCTTGTTC
1 TTGGCCCTTATCC-TACCTTGTTC
*
837749 TTGGCTCTTATCCTACCTTGTTC
1 TTGGCCCTTATCCTACCTTGTTC
837772 TT
1 TT
837774 TAATGATAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 21 0.91
24 2 0.09
ACGTcount: A:0.08, C:0.31, G:0.12, T:0.48
Consensus pattern (23 bp):
TTGGCCCTTATCCTACCTTGTTC
Found at i:843769 original size:14 final size:14
Alignment explanation
Indices: 843750--843777 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
843740 TTTTAATGTC
843750 TGTATATGTGCAGA
1 TGTATATGTGCAGA
843764 TGTATATGTGCAGA
1 TGTATATGTGCAGA
843778 GAACCCAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.29, C:0.07, G:0.29, T:0.36
Consensus pattern (14 bp):
TGTATATGTGCAGA
Found at i:847486 original size:2 final size:2
Alignment explanation
Indices: 847479--847520 Score: 77
Period size: 2 Copynumber: 21.5 Consensus size: 2
847469 GAAAGTGATT
847479 GA GA GA GA GA GA GA GA GA GA G- GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
847520 G
1 G
847521 TGTTTCAGAG
Statistics
Matches: 39, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 38 0.97
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:860950 original size:20 final size:20
Alignment explanation
Indices: 860925--860962 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
860915 TTATTTAATC
860925 ATATGGTATGGTACAAAATT
1 ATATGGTATGGTACAAAATT
860945 ATATGGTATGGTACAAAA
1 ATATGGTATGGTACAAAA
860963 ACTGGCATTG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.42, C:0.05, G:0.21, T:0.32
Consensus pattern (20 bp):
ATATGGTATGGTACAAAATT
Found at i:870199 original size:34 final size:34
Alignment explanation
Indices: 870158--871022 Score: 639
Period size: 34 Copynumber: 25.0 Consensus size: 34
870148 TCATAGTGTT
*
870158 CGTAAATACTAAAGGACCATAGTGGCACCACGTA
1 CGTAAATACTAAAGTACCATAGTGGCACCACGTA
*
870192 CGTAAATAATGAAA-TACCATAGTGGCACCACGTA
1 CGTAAATACT-AAAGTACCATAGTGGCACCACGTA
* *
870226 CGTAAATAATAAAATACCATAGTGGCACCACGTA
1 CGTAAATACTAAAGTACCATAGTGGCACCACGTA
* *
870260 CGTAAATAATAAAATACCATAGTGGCACCACGTA
1 CGTAAATACTAAAGTACCATAGTGGCACCACGTA
* * ** *
870294 CATAAATACTAAAGTATCATAGTAACACGACGTA
1 CGTAAATACTAAAGTACCATAGTGGCACCACGTA
* *
870328 CGTAAATACTAAAGGACCATAGTGGCACTAC-TCA
1 CGTAAATACTAAAGTACCATAGTGGCACCACGT-A
* * * * * *
870362 TGTAAATGCTAAGGTACTATAGTAGCACCAGGTA
1 CGTAAATACTAAAGTACCATAGTGGCACCACGTA
* * * *
870396 CGTAAATAATAAAGGACCACAGTGGCACCTC-TCA
1 CGTAAATACTAAAGTACCATAGTGGCACCACGT-A
** * *
870430 TTTAAATACTAAAGTACCATAGTAGTACCACGTA
1 CGTAAATACTAAAGTACCATAGTGGCACCACGTA
* *
870464 CGTAAATACTAAAGTACC--AGTGACATCACGTA
1 CGTAAATACTAAAGTACCATAGTGGCACCACGTA
* * *
870496 CCTAAATATTAAAGTACCATAGTGGCACAACGTA
1 CGTAAATACTAAAGTACCATAGTGGCACCACGTA
* * * * * *
870530 CGTAAATATTAAAGAAACACAGTAGTACCACGTA
1 CGTAAATACTAAAGTACCATAGTGGCACCACGTA
* *
870564 CGTAAATAATAAAATACCATAGTGGCACCACGTA
1 CGTAAATACTAAAGTACCATAGTGGCACCACGTA
* * * *
870598 CCTAAATATTAAAGTACCATAGTGCCACTACGTA
1 CGTAAATACTAAAGTACCATAGTGGCACCACGTA
* * * *
870632 CGTAAATACTAAAGTAACACAGTAGTACCACGTA
1 CGTAAATACTAAAGTACCATAGTGGCACCACGTA
* * * *
870666 CGTGAATAATAAAATACCATAGTGGAACCACGTA
1 CGTAAATACTAAAGTACCATAGTGGCACCACGTA
* * * * *
870700 CGTAAATACTAAAGTACCATAATCGTACAACCTA
1 CGTAAATACTAAAGTACCATAGTGGCACCACGTA
* * * **
870734 AGTAAATAGTAAAGTACCATAGTGGAACCACCCA
1 CGTAAATACTAAAGTACCATAGTGGCACCACGTA
* * * * * * *
870768 CGTTAATTCTAAAGTACGTAAATATTAAAGTACTACAGTA
1 CGTAAATACTAAAGTAC---CATAGT--GGCACCAC-GTA
* * *
870808 -GTACCACGTACTTAAATGATAAAGTACTATAGTGGCACCACGTT
1 CGTA--A-ATAC-T--A-----AAGTACCATAGTGGCACCACGTA
* * * *
870852 CGTAAATAATAAAGAACCATGGTGGCACCATGTA
1 CGTAAATACTAAAGTACCATAGTGGCACCACGTA
* ** *
870886 CGTAAATACTGAAGTACCATTTTGGTACCACGTA
1 CGTAAATACTAAAGTACCATAGTGGCACCACGTA
* * * *
870920 AGTAAATACTTAAGTACCAT-GATGGTACCATGTA
1 CGTAAATACTAAAGTACCATAG-TGGCACCACGTA
* * * * *
870954 CGTTAATACTAAAATATCATAGTGGTACCATGTA
1 CGTAAATACTAAAGTACCATAGTGGCACCACGTA
* * * *
870988 CATAAATA-TCAAAGAACCATAATGTCACCACGTA
1 CGTAAATACT-AAAGTACCATAGTGGCACCACGTA
871022 C
1 C
871023 ACTCCCGATA
Statistics
Matches: 649, Mismatches: 153, Indels: 58
0.75 0.18 0.07
Matches are distributed among these distances:
32 26 0.04
33 6 0.01
34 569 0.88
35 6 0.01
37 4 0.01
39 8 0.01
40 1 0.00
41 2 0.00
42 4 0.01
43 2 0.00
44 2 0.00
45 9 0.01
47 4 0.01
50 6 0.01
ACGTcount: A:0.41, C:0.20, G:0.16, T:0.23
Consensus pattern (34 bp):
CGTAAATACTAAAGTACCATAGTGGCACCACGTA
Found at i:870935 original size:152 final size:152
Alignment explanation
Indices: 870629--870936 Score: 339
Period size: 152 Copynumber: 2.0 Consensus size: 152
870619 GTGCCACTAC
*
870629 GTACGTAAATACTAAAGTAACACAGTAGTACCACGTACGTGAATAATAAAATACCATAGTGGAAC
1 GTACGTAAATACTAAAGTAACACAGTAGTACCACGTACGTAAATAATAAAATACCATAGTGGAAC
* * * *
870694 CACGTACGTAAATACTAAAGTACCATAATCGTACAACCTAAGTAAATAGTAAAGTACCATAGTGG
66 CACGTACGTAAATAATAAAGAACCATAATCGCACAACCTAAGTAAATACTAAAGTACCATAGTGG
* * *
870759 AACCACCCACGTTAATTCTAAA
131 AACCACCCAAGTAAATACTAAA
* * * * * *
870781 GTACGTAAATATTAAAGT-ACTACAGTAGTACCACGTACTTAAATGATAAAGTACTATAGTGGCA
1 GTACGTAAATACTAAAGTAAC-ACAGTAGTACCACGTACGTAAATAATAAAATACCATAGTGGAA
* ** * * ** * * **
870845 CCACGTTCGTAAATAATAAAGAACCATGGTGGCACCATGTACGTAAATACTGAAGTACCATTTTG
65 CCACGTACGTAAATAATAAAGAACCATAATCGCACAACCTAAGTAAATACTAAAGTACCATAGTG
* ** *
870910 GTACCACGTAAGTAAATACTTAA
130 GAACCACCCAAGTAAATACTAAA
870933 GTAC
1 GTAC
870937 CATGATGGTA
Statistics
Matches: 126, Mismatches: 29, Indels: 2
0.80 0.18 0.01
Matches are distributed among these distances:
151 2 0.02
152 124 0.98
ACGTcount: A:0.41, C:0.19, G:0.16, T:0.25
Consensus pattern (152 bp):
GTACGTAAATACTAAAGTAACACAGTAGTACCACGTACGTAAATAATAAAATACCATAGTGGAAC
CACGTACGTAAATAATAAAGAACCATAATCGCACAACCTAAGTAAATACTAAAGTACCATAGTGG
AACCACCCAAGTAAATACTAAA
Found at i:873616 original size:21 final size:21
Alignment explanation
Indices: 873590--873630 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
873580 ATCTTTTTTC
873590 GCATGTCAACAT-ATATAAGTT
1 GCATGTCAACATGA-ATAAGTT
*
873611 GCATGTCGACATGAATAAGT
1 GCATGTCAACATGAATAAGT
873631 AGAATGCAGC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 17 0.94
22 1 0.06
ACGTcount: A:0.37, C:0.15, G:0.20, T:0.29
Consensus pattern (21 bp):
GCATGTCAACATGAATAAGTT
Found at i:873739 original size:21 final size:21
Alignment explanation
Indices: 873712--873791 Score: 115
Period size: 21 Copynumber: 3.8 Consensus size: 21
873702 ACCGCAATTT
873712 TCTTGCATGTCAACATAACTA
1 TCTTGCATGTCAACATAACTA
* *
873733 TGTTGCATGTTAACATAACTA
1 TCTTGCATGTCAACATAACTA
**
873754 TCTTGCATGTCAACATATTTA
1 TCTTGCATGTCAACATAACTA
*
873775 TCTTGCATGTCGACATA
1 TCTTGCATGTCAACATA
873792 TTCTATAGGA
Statistics
Matches: 52, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 52 1.00
ACGTcount: A:0.30, C:0.20, G:0.12, T:0.38
Consensus pattern (21 bp):
TCTTGCATGTCAACATAACTA
Found at i:876951 original size:31 final size:31
Alignment explanation
Indices: 876145--876940 Score: 1402
Period size: 31 Copynumber: 25.7 Consensus size: 31
876135 GCGATCTTGA
*
876145 TTATATGACTCTATCAACTACACATTATGAT
1 TTATATGACTCTATCAACTACACATTATGTT
876176 TTATATGACTCTATCAACTACACATTATGTT
1 TTATATGACTCTATCAACTACACATTATGTT
*
876207 TTATATGA--CTATCAAATACACATTATGTT
1 TTATATGACTCTATCAACTACACATTATGTT
876236 TTATATGACTCTATCAACTACACATTATGTTT
1 TTATATGACTCTATCAACTACACATTATG-TT
876268 GTANTATATGACTCTATCAACTACACATTATGTT
1 -T--TATATGACTCTATCAACTACACATTATGTT
876302 TTATATGACTCTATCAACTACACATTATGTT
1 TTATATGACTCTATCAACTACACATTATGTT
876333 TTATATGACTCTATCAACTACACATTATGTT
1 TTATATGACTCTATCAACTACACATTATGTT
876364 TTATATGACTCTATCAACTACACATTATGTT
1 TTATATGACTCTATCAACTACACATTATGTT
*
876395 TTATGTGACTCTATCAACTACACATTATGTT
1 TTATATGACTCTATCAACTACACATTATGTT
876426 TTATATGACTCTATCAACTACACATTATGTT
1 TTATATGACTCTATCAACTACACATTATGTT
876457 TTATATGACTCTATCAACTACACATTATGTT
1 TTATATGACTCTATCAACTACACATTATGTT
876488 TTATATGACTCTATCAACTACACATTATGTT
1 TTATATGACTCTATCAACTACACATTATGTT
876519 TTATATGACTCTATCAACTACACATTATGTT
1 TTATATGACTCTATCAACTACACATTATGTT
876550 TTATATGACTCTATCAACTACACATTATGTT
1 TTATATGACTCTATCAACTACACATTATGTT
*
876581 TTATGTGACTCTATCAACTACACATTATGTT
1 TTATATGACTCTATCAACTACACATTATGTT
* * *
876612 TTATGTAAATCTATCAACTACACATTATGTT
1 TTATATGACTCTATCAACTACACATTATGTT
* *
876643 TTATGTGACTCTATCAACTACACATTATGAT
1 TTATATGACTCTATCAACTACACATTATGTT
876674 TTATATGACTCTATCAACTACACATTATGTT
1 TTATATGACTCTATCAACTACACATTATGTT
876705 TTATATGA--CTATCAACTACACATTATGTT
1 TTATATGACTCTATCAACTACACATTATGTT
*
876734 TTATATGTCTCTATCAACTACACATTATGTT
1 TTATATGACTCTATCAACTACACATTATGTT
876765 TTATATGACTCTATCAACTACACATTATGTT
1 TTATATGACTCTATCAACTACACATTATGTT
*
876796 TTATGTGACTCTATCAACTACACATTATGTT
1 TTATATGACTCTATCAACTACACATTATGTT
*
876827 TTATATGTCTCTATCAACTACACATTATGTT
1 TTATATGACTCTATCAACTACACATTATGTT
*
876858 TTATATGACTCTATCAACTACACAGTATGTT
1 TTATATGACTCTATCAACTACACATTATGTT
*
876889 TTATATGACTCTATCAACTACACAGTATGTT
1 TTATATGACTCTATCAACTACACATTATGTT
876920 TTATATGACTCTATCAACTAC
1 TTATATGACTCTATCAACTAC
876941 TCGTTTTGTT
Statistics
Matches: 737, Mismatches: 20, Indels: 16
0.95 0.03 0.02
Matches are distributed among these distances:
29 56 0.08
31 647 0.88
32 2 0.00
33 2 0.00
34 2 0.00
35 28 0.04
ACGTcount: A:0.32, C:0.19, G:0.07, T:0.41
Consensus pattern (31 bp):
TTATATGACTCTATCAACTACACATTATGTT
Found at i:877696 original size:30 final size:30
Alignment explanation
Indices: 877660--877760 Score: 166
Period size: 30 Copynumber: 3.4 Consensus size: 30
877650 TTAGGTATTT
*
877660 AGTGATGGAAATATTGTGTAATGGGTTATG
1 AGTGATGAAAATATTGTGTAATGGGTTATG
*
877690 AGTGATGAAAATATTATGTAATGGGTTATG
1 AGTGATGAAAATATTGTGTAATGGGTTATG
*
877720 AGTGATGAAAATATTGTGTAATGGGTTGTG
1 AGTGATGAAAATATTGTGTAATGGGTTATG
*
877750 AGTGAAGAAAA
1 AGTGATGAAAA
877761 AATGATGTAT
Statistics
Matches: 66, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 66 1.00
ACGTcount: A:0.36, C:0.00, G:0.31, T:0.34
Consensus pattern (30 bp):
AGTGATGAAAATATTGTGTAATGGGTTATG
Found at i:877709 original size:60 final size:60
Alignment explanation
Indices: 877645--877791 Score: 179
Period size: 60 Copynumber: 2.5 Consensus size: 60
877635 TGAACAAAGC
* * * * *
877645 ATGTATTAGG-TATTTAGTGATGGAAATATTGTGTAATGGGTTATGAGTGATGAAAATATT
1 ATGTATTAGGTTA-TGAGTGATGAAAATATTGTGTAATGGGTTATGAGTGAAGAAAAAATG
* * *
877705 ATGTAATGGGTTATGAGTGATGAAAATATTGTGTAATGGGTTGTGAGTGAAGAAAAAATG
1 ATGTATTAGGTTATGAGTGATGAAAATATTGTGTAATGGGTTATGAGTGAAGAAAAAATG
** *
877765 ATGTATTAAATAATGAGTGATGAAAAT
1 ATGTATTAGGTTATGAGTGATGAAAAT
877792 CATTCAGGTT
Statistics
Matches: 73, Mismatches: 13, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
60 71 0.97
61 2 0.03
ACGTcount: A:0.37, C:0.00, G:0.27, T:0.35
Consensus pattern (60 bp):
ATGTATTAGGTTATGAGTGATGAAAATATTGTGTAATGGGTTATGAGTGAAGAAAAAATG
Found at i:878160 original size:32 final size:32
Alignment explanation
Indices: 878119--879457 Score: 1799
Period size: 32 Copynumber: 41.7 Consensus size: 32
878109 AAAACTCTTT
* *
878119 CTTAGTAATACCAGTACATTATATCCTAGGTC
1 CTTAGTAATATCAGTACATTATATCCTCGGTC
878151 CTTAGTAATATCAGTACATTATATCCTCGGTC
1 CTTAGTAATATCAGTACATTATATCCTCGGTC
878183 CTTAGTAATATCAGTACATTATATCCTCGGTC
1 CTTAGTAATATCAGTACATTATATCCTCGGTC
878215 CTTAGTAATATCAGTACATTATATCCTCGGTC
1 CTTAGTAATATCAGTACATTATATCCTCGGTC
*
878247 CTTAGTAATATCAGTACATTATATCCTCGGCC
1 CTTAGTAATATCAGTACATTATATCCTCGGTC
*
878279 CCTAG-ATATATCAGTACATTATATCCTCGGTC
1 CTTAGTA-ATATCAGTACATTATATCCTCGGTC
* *
878311 CTTAGTCATATCAGTACATTATATCCTCGGCC
1 CTTAGTAATATCAGTACATTATATCCTCGGTC
* * * * *
878343 CCTAGTAATATCAGAAGTCCCTGGTA-AT-ATCAGTAC
1 CTTAGTAATATC---AGTACAT--TATATCCTCGGT-C
* * * ** * * *
878379 ATTA-T-ATCCTCGGCCCCTAGTAATATCAGT-AGTC
1 CTTAGTAAT-ATCAG-TAC-A-TTATATC-CTCGGTC
* * * *
878413 CCTGGTGATATCAGTACATTATATCCTCGGCC
1 CTTAGTAATATCAGTACATTATATCCTCGGTC
*
878445 CTTAGTAATATCAGTACATTATATCCTCGGCC
1 CTTAGTAATATCAGTACATTATATCCTCGGTC
878477 CTTAGTAATATCAGTACATTATATCCTCGGTC
1 CTTAGTAATATCAGTACATTATATCCTCGGTC
*
878509 CTTAGTAATATCAGTACATTATATCCTCGGCC
1 CTTAGTAATATCAGTACATTATATCCTCGGTC
878541 CTTAGTAATATCAGTACATTATATCCTCGGTC
1 CTTAGTAATATCAGTACATTATATCCTCGGTC
* *
878573 CTTAGTAATATCAGTACACTATATCCTCGGCC
1 CTTAGTAATATCAGTACATTATATCCTCGGTC
*
878605 CTTAGTAATATCAGTACATTATATCCTCGGCC
1 CTTAGTAATATCAGTACATTATATCCTCGGTC
*
878637 CCTAGTAATATCAGTACATTATATCCTCGGTC
1 CTTAGTAATATCAGTACATTATATCCTCGGTC
*
878669 CTTAGTAATATCAGTACATTATATCCTCGGCC
1 CTTAGTAATATCAGTACATTATATCCTCGGTC
* * *
878701 CCTAGTAATATTAGTACATTATATCCTCGGCC
1 CTTAGTAATATCAGTACATTATATCCTCGGTC
* * * *
878733 CCTGGTAATATCAATACATTATATCCTCGGCC
1 CTTAGTAATATCAGTACATTATATCCTCGGTC
* * *
878765 CCTAGTACTATCAGTACATTATATCCTCGGCC
1 CTTAGTAATATCAGTACATTATATCCTCGGTC
* *
878797 CCTGGTAATATCAGTACATTATATCCTCGGTC
1 CTTAGTAATATCAGTACATTATATCCTCGGTC
*
878829 CTTAGTAATATTAGTACATTATATCCTCGGTC
1 CTTAGTAATATCAGTACATTATATCCTCGGTC
* *
878861 CCTAGTAATATCAGTACATTATATCCTCGGCC
1 CTTAGTAATATCAGTACATTATATCCTCGGTC
* *
878893 CCTGGTAATATCAGTACATTATATCCTCGGTC
1 CTTAGTAATATCAGTACATTATATCCTCGGTC
* *
878925 CTTAGTAATTTCAGTACATTATATCCTCGGCC
1 CTTAGTAATATCAGTACATTATATCCTCGGTC
* *
878957 CCTAGTAATATCAGTATATTATATCCTCGGTC
1 CTTAGTAATATCAGTACATTATATCCTCGGTC
* *
878989 CTTAGTAATTTCAGTACATTATATCCTCGGCC
1 CTTAGTAATATCAGTACATTATATCCTCGGTC
* * *
879021 CCTAGTAATATCAGTACATTATATCCTCAGCC
1 CTTAGTAATATCAGTACATTATATCCTCGGTC
* *
879053 CTTAGTAATATCAGTATATTGTATCCTCGGTC
1 CTTAGTAATATCAGTACATTATATCCTCGGTC
879085 CTTAGTAATATCAGTACATTATATCCTCGGTC
1 CTTAGTAATATCAGTACATTATATCCTCGGTC
*
879117 CTTAGTAATATCAGTACATTATATCCTCGGCC
1 CTTAGTAATATCAGTACATTATATCCTCGGTC
* * * *
879149 CCTAGTGATATCAGTACATTGTATCTTCGGTC
1 CTTAGTAATATCAGTACATTATATCCTCGGTC
* * *
879181 CCTGGTAATATCAGTTCATTATATCCTCGGTC
1 CTTAGTAATATCAGTACATTATATCCTCGGTC
*
879213 CTTAGTAATATCAGTACATTGTATCCTCGGTC
1 CTTAGTAATATCAGTACATTATATCCTCGGTC
879245 CTTAGTAATATCAGTACATTATATCCTCGGTC
1 CTTAGTAATATCAGTACATTATATCCTCGGTC
*
879277 CTTAGTAATATCAGTACATTATATCCTCGGCC
1 CTTAGTAATATCAGTACATTATATCCTCGGTC
* * * *
879309 CCTAGTGATATCAGTACATTGTATCTTCGGTC
1 CTTAGTAATATCAGTACATTATATCCTCGGTC
* * *
879341 CCTGGTAATATCAGTTCATTATATCCTCGGTC
1 CTTAGTAATATCAGTACATTATATCCTCGGTC
879373 CTTAGTAATATCAGTACATTATATCCTCGGTC
1 CTTAGTAATATCAGTACATTATATCCTCGGTC
* * *
879405 CTTAGTAATATCAGTACATTGTATCTTCGGCC
1 CTTAGTAATATCAGTACATTATATCCTCGGTC
* * *
879437 CCTACTAATATTAGTACATTA
1 CTTAGTAATATCAGTACATTA
879458 GAAGTTCTAT
Statistics
Matches: 1164, Mismatches: 125, Indels: 36
0.88 0.09 0.03
Matches are distributed among these distances:
31 2 0.00
32 1122 0.96
33 4 0.00
34 7 0.01
35 19 0.02
36 8 0.01
37 2 0.00
ACGTcount: A:0.27, C:0.24, G:0.13, T:0.35
Consensus pattern (32 bp):
CTTAGTAATATCAGTACATTATATCCTCGGTC
Found at i:878459 original size:51 final size:51
Alignment explanation
Indices: 878318--878460 Score: 259
Period size: 51 Copynumber: 2.8 Consensus size: 51
878308 GTCCTTAGTC
*
878318 ATATCAGTACATTATATCCTCGGCCCCTAGTAATATCAGAAGTCCCTGGTA
1 ATATCAGTACATTATATCCTCGGCCCCTAGTAATATCAGTAGTCCCTGGTA
*
878369 ATATCAGTACATTATATCCTCGGCCCCTAGTAATATCAGTAGTCCCTGGTG
1 ATATCAGTACATTATATCCTCGGCCCCTAGTAATATCAGTAGTCCCTGGTA
*
878420 ATATCAGTACATTATATCCTCGGCCCTTAGTAATATCAGTA
1 ATATCAGTACATTATATCCTCGGCCCCTAGTAATATCAGTA
878461 CATTATATCC
Statistics
Matches: 89, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
51 89 1.00
ACGTcount: A:0.29, C:0.24, G:0.15, T:0.31
Consensus pattern (51 bp):
ATATCAGTACATTATATCCTCGGCCCCTAGTAATATCAGTAGTCCCTGGTA
Found at i:878520 original size:83 final size:81
Alignment explanation
Indices: 878267--878520 Score: 246
Period size: 83 Copynumber: 3.1 Consensus size: 81
878257 TCAGTACATT
* *
878267 ATATCCTCGGCCCCTAG-ATATATCAGTACATTATATCCTCGGTCCTTAGTCATATCAGTACATT
1 ATATCCTCGG-CCCTAGTA-ATATCAGTACATTATATCCTCGGCCCTTAGTAATATCAGTACATT
*
878331 ATATCCTCGGCCCCTAGTA
64 ATATCCTCGG-TCCTAGTA
*** * * * *
878350 ATATCAGAAGTCCCTGGTAATATCAGTACATTATATCCTCGGCCCCTAGTAATATCAGTAGTCCC
1 ATATC-CTCGGCCCTAGTAATATCAGTACATTATATCCTCGGCCCTTAGTAATATCAGTA---CA
** * * * *
878415 TGGTGAT-ATCAGTAC-A-TT
62 TTAT-ATCCTCGGTCCTAGTA
878433 ATATCCTCGGCCCTTAGTAATATCAGTACATTATATCCTCGGCCCTTAGTAATATCAGTACATTA
1 ATATCCTCGGCCC-TAGTAATATCAGTACATTATATCCTCGGCCCTTAGTAATATCAGTACATTA
878498 TATCCTCGGTCCTTAGTA
65 TATCCTCGGTCC-TAGTA
878516 ATATC
1 ATATC
878521 AGTACATTAT
Statistics
Matches: 131, Mismatches: 29, Indels: 22
0.72 0.16 0.12
Matches are distributed among these distances:
79 2 0.02
80 8 0.06
82 5 0.04
83 104 0.79
84 3 0.02
85 1 0.01
86 6 0.05
87 2 0.02
ACGTcount: A:0.27, C:0.26, G:0.14, T:0.33
Consensus pattern (81 bp):
ATATCCTCGGCCCTAGTAATATCAGTACATTATATCCTCGGCCCTTAGTAATATCAGTACATTAT
ATCCTCGGTCCTAGTA
Found at i:881548 original size:18 final size:18
Alignment explanation
Indices: 881525--881560 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
881515 TATAAGTTTG
881525 AATTAATCAAAGAGTCTT
1 AATTAATCAAAGAGTCTT
* *
881543 AATTAATTAAGGAGTCTT
1 AATTAATCAAAGAGTCTT
881561 CTCGTTTTCA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.42, C:0.08, G:0.14, T:0.36
Consensus pattern (18 bp):
AATTAATCAAAGAGTCTT
Found at i:889631 original size:41 final size:41
Alignment explanation
Indices: 889579--889660 Score: 155
Period size: 41 Copynumber: 2.0 Consensus size: 41
889569 ACCAGAGATC
889579 ATCCCCAAGACATAGAGGGAGTGAAGTATCAGCAAACAGAG
1 ATCCCCAAGACATAGAGGGAGTGAAGTATCAGCAAACAGAG
*
889620 ATCCCCAAGACATAGATGGAGTGAAGTATCAGCAAACAGAG
1 ATCCCCAAGACATAGAGGGAGTGAAGTATCAGCAAACAGAG
889661 GATGATAGAC
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 40 1.00
ACGTcount: A:0.41, C:0.20, G:0.26, T:0.13
Consensus pattern (41 bp):
ATCCCCAAGACATAGAGGGAGTGAAGTATCAGCAAACAGAG
Found at i:893163 original size:62 final size:62
Alignment explanation
Indices: 893093--893224 Score: 219
Period size: 62 Copynumber: 2.1 Consensus size: 62
893083 TATTAAATGA
** *
893093 TTTTATTATACTTTTTTGTTAAATACTGAAATCTGATTGGTTTAGACGCAGTTGGTAATTCG
1 TTTTATTATACTTTCATGTTAAATACTGAAATCTGATTGGTTTAGACGCAGTTGGTAATCCG
*
893155 TTTTATTATACTTTCATGTTCAATACTGAAATCTGATTGGTTTAGACGCAGTTGGTAATCCG
1 TTTTATTATACTTTCATGTTAAATACTGAAATCTGATTGGTTTAGACGCAGTTGGTAATCCG
*
893217 TTCTATTA
1 TTTTATTA
893225 CCCTCAGCGT
Statistics
Matches: 65, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
62 65 1.00
ACGTcount: A:0.26, C:0.12, G:0.17, T:0.45
Consensus pattern (62 bp):
TTTTATTATACTTTCATGTTAAATACTGAAATCTGATTGGTTTAGACGCAGTTGGTAATCCG
Found at i:893462 original size:43 final size:43
Alignment explanation
Indices: 893401--893485 Score: 143
Period size: 43 Copynumber: 2.0 Consensus size: 43
893391 GTTTGAGAGG
*
893401 GTAACTGTTGAAATTGACACCCCGAGAAAACCATTGTCAACCA
1 GTAACTGTTGAAACTGACACCCCGAGAAAACCATTGTCAACCA
**
893444 GTAACTGTTGAAACTGACACCCCTCGAAAACCATTGTCAACC
1 GTAACTGTTGAAACTGACACCCCGAGAAAACCATTGTCAACC
893486 TCCGCTTTGC
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
43 39 1.00
ACGTcount: A:0.35, C:0.28, G:0.15, T:0.21
Consensus pattern (43 bp):
GTAACTGTTGAAACTGACACCCCGAGAAAACCATTGTCAACCA
Found at i:894175 original size:21 final size:21
Alignment explanation
Indices: 894149--894276 Score: 179
Period size: 21 Copynumber: 6.1 Consensus size: 21
894139 ATAATATTTT
*
894149 TTTCGCGAATAAACGCGTAAC
1 TTTCGCGAATAAACGCGAAAC
894170 TTTCGCGAATAAACGCGAAAC
1 TTTCGCGAATAAACGCGAAAC
* ** *
894191 TTTTGCG-ATATAACGCGTTAG
1 TTTCGCGAATA-AACGCGAAAC
894212 TTTCGCGAATAAACGCGAAAC
1 TTTCGCGAATAAACGCGAAAC
894233 TTTCGCGAATAAACGCGAAAC
1 TTTCGCGAATAAACGCGAAAC
894254 TTTCGC-AATTAAACGCGAAAC
1 TTTCGCGAA-TAAACGCGAAAC
894275 TT
1 TT
894277 AAAAATAAAT
Statistics
Matches: 95, Mismatches: 9, Indels: 6
0.86 0.08 0.05
Matches are distributed among these distances:
20 5 0.05
21 87 0.92
22 3 0.03
ACGTcount: A:0.34, C:0.22, G:0.19, T:0.25
Consensus pattern (21 bp):
TTTCGCGAATAAACGCGAAAC
Found at i:894269 original size:63 final size:63
Alignment explanation
Indices: 894149--894270 Score: 201
Period size: 63 Copynumber: 1.9 Consensus size: 63
894139 ATAATATTTT
* * *
894149 TTTCGCGAATAAACGCGTAACTTTCGCGAATAAACGCGAAACTTTTGCGATATAACGCGTTAG
1 TTTCGCGAATAAACGCGAAACTTTCGCGAATAAACGCGAAACTTTCGCAATATAACGCGTTAG
894212 TTTCGCGAATAAACGCGAAACTTTCGCGAATAAACGCGAAACTTTCGCAAT-TAAACGCG
1 TTTCGCGAATAAACGCGAAACTTTCGCGAATAAACGCGAAACTTTCGCAATAT-AACGCG
894271 AAACTTAAAA
Statistics
Matches: 55, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
62 1 0.02
63 54 0.98
ACGTcount: A:0.34, C:0.22, G:0.20, T:0.25
Consensus pattern (63 bp):
TTTCGCGAATAAACGCGAAACTTTCGCGAATAAACGCGAAACTTTCGCAATATAACGCGTTAG
Found at i:895162 original size:21 final size:21
Alignment explanation
Indices: 895132--895262 Score: 192
Period size: 21 Copynumber: 6.2 Consensus size: 21
895122 TAATAGTTTT
* * *
895132 GCGTTAATTCGCGAAACTTAC
1 GCGTTTATTCGCGAAAGTAAC
895153 GCGTTTATTCGCGAAAGTAAC
1 GCGTTTATTCGCGAAAGTAAC
895174 GCGTTTATTCGCGAAAGTAAC
1 GCGTTTATTCGCGAAAGTAAC
895195 GCGTTTATTCGCGAAAGTAAC
1 GCGTTTATTCGCGAAAGTAAC
**
895216 GCGTTTATTCGCGAAAGTTTC
1 GCGTTTATTCGCGAAAGTAAC
*
895237 GCG-TTATATCGCGAAAGTTAC
1 GCGTTTAT-TCGCGAAAGTAAC
895258 GCGTT
1 GCGTT
895263 NNNNNNNNNN
Statistics
Matches: 102, Mismatches: 6, Indels: 3
0.92 0.05 0.03
Matches are distributed among these distances:
20 4 0.04
21 97 0.95
22 1 0.01
ACGTcount: A:0.26, C:0.20, G:0.24, T:0.31
Consensus pattern (21 bp):
GCGTTTATTCGCGAAAGTAAC
Found at i:897248 original size:13 final size:12
Alignment explanation
Indices: 897227--897258 Score: 55
Period size: 13 Copynumber: 2.6 Consensus size: 12
897217 ATGCTTATAG
897227 TCTTATACATAA
1 TCTTATACATAA
897239 TCTGTATACATAA
1 TCT-TATACATAA
897252 TCTTATA
1 TCTTATA
897259 TCTAAATACC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 7 0.37
13 12 0.63
ACGTcount: A:0.38, C:0.16, G:0.03, T:0.44
Consensus pattern (12 bp):
TCTTATACATAA
Found at i:898694 original size:2 final size:2
Alignment explanation
Indices: 898687--898713 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
898677 CTGTAATGCA
898687 TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC T
898714 GTAAAAAAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:903142 original size:41 final size:41
Alignment explanation
Indices: 903085--903169 Score: 161
Period size: 41 Copynumber: 2.1 Consensus size: 41
903075 CTTTAGTATA
903085 GGTTTAGGCTTTTACAAGGTAGATTATACTGAGGTAGAGGT
1 GGTTTAGGCTTTTACAAGGTAGATTATACTGAGGTAGAGGT
*
903126 GGTTTAGGCTTTTACAAGGTAGATTATACTGAGGTTGAGGT
1 GGTTTAGGCTTTTACAAGGTAGATTATACTGAGGTAGAGGT
903167 GGT
1 GGT
903170 GATTTGGTAG
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 43 1.00
ACGTcount: A:0.25, C:0.07, G:0.33, T:0.35
Consensus pattern (41 bp):
GGTTTAGGCTTTTACAAGGTAGATTATACTGAGGTAGAGGT
Found at i:903999 original size:60 final size:60
Alignment explanation
Indices: 903906--904028 Score: 210
Period size: 60 Copynumber: 2.0 Consensus size: 60
903896 GAATTTATCA
* * *
903906 TCACATTTTCGCGTTTGTAGAAGTTGAAATCTACTTGTTCATTTAATCAAAATGGTTTAT
1 TCACATTTTCGCCTTTGTAGAACTTGAAATCTACTTGTTCATTTAATCAAAATGGCTTAT
*
903966 TCACATTTTCGCCTTTGTAGAACTTGAAATCTACTTGTTCTTTTAATCAAAATGGCTTAT
1 TCACATTTTCGCCTTTGTAGAACTTGAAATCTACTTGTTCATTTAATCAAAATGGCTTAT
904026 TCA
1 TCA
904029 TTCTATGTAC
Statistics
Matches: 59, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
60 59 1.00
ACGTcount: A:0.28, C:0.16, G:0.13, T:0.43
Consensus pattern (60 bp):
TCACATTTTCGCCTTTGTAGAACTTGAAATCTACTTGTTCATTTAATCAAAATGGCTTAT
Found at i:910432 original size:41 final size:41
Alignment explanation
Indices: 910372--910451 Score: 133
Period size: 41 Copynumber: 2.0 Consensus size: 41
910362 GTATAAGTTA
*
910372 AGGCTTTTACAAGGTAGATTATACTGAGGTAGAGGTGGTTT
1 AGGCTTTTACAAGGAAGATTATACTGAGGTAGAGGTGGTTT
* *
910413 AGGCTTTTACAAGGAAGATTATACTGAGTTTGAGGTGGT
1 AGGCTTTTACAAGGAAGATTATACTGAGGTAGAGGTGGT
910452 GATTTGGTAG
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
41 36 1.00
ACGTcount: A:0.28, C:0.07, G:0.31, T:0.34
Consensus pattern (41 bp):
AGGCTTTTACAAGGAAGATTATACTGAGGTAGAGGTGGTTT
Found at i:911082 original size:2 final size:2
Alignment explanation
Indices: 911075--911147 Score: 146
Period size: 2 Copynumber: 36.5 Consensus size: 2
911065 CGTCATTGAT
911075 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
911117 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
911148 TTTATAAATC
Statistics
Matches: 71, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 71 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:914296 original size:20 final size:20
Alignment explanation
Indices: 914271--914328 Score: 80
Period size: 20 Copynumber: 2.9 Consensus size: 20
914261 TTTACGATAT
914271 CATATGATACAATATCATAA
1 CATATGATACAATATCATAA
* *
914291 CATATGATACATTATCATAT
1 CATATGATACAATATCATAA
**
914311 CATATGATTTAATATCAT
1 CATATGATACAATATCAT
914329 GGGAATAGGA
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.43, C:0.14, G:0.05, T:0.38
Consensus pattern (20 bp):
CATATGATACAATATCATAA
Found at i:915408 original size:19 final size:19
Alignment explanation
Indices: 915374--915410 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
915364 AAGGGCACCT
*
915374 GCTCCAAAAACTTTAACCA
1 GCTCCAAAAACCTTAACCA
*
915393 GCTCCAAAAGCCTTAACC
1 GCTCCAAAAACCTTAACC
915411 TCATCCAGCA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.38, C:0.35, G:0.08, T:0.19
Consensus pattern (19 bp):
GCTCCAAAAACCTTAACCA
Found at i:917788 original size:12 final size:12
Alignment explanation
Indices: 917771--917797 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
917761 ACTGATTTGA
917771 CACCTATTACGT
1 CACCTATTACGT
917783 CACCTATTACGT
1 CACCTATTACGT
917795 CAC
1 CAC
917798 AGCAATGGCA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.26, C:0.37, G:0.07, T:0.30
Consensus pattern (12 bp):
CACCTATTACGT
Found at i:925948 original size:4 final size:4
Alignment explanation
Indices: 925947--926004 Score: 62
Period size: 4 Copynumber: 14.5 Consensus size: 4
925937 GGGACAGACA
* * * * *
925947 GACG GACG GACG GACG GACG GACA GACA GACG GACG GACA GACA GAAG
1 GACG GACG GACG GACG GACG GACG GACG GACG GACG GACG GACG GACG
*
925995 GACT GACG GA
1 GACG GACG GA
926005 TGCAGAGGAA
Statistics
Matches: 46, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
4 46 1.00
ACGTcount: A:0.34, C:0.22, G:0.41, T:0.02
Consensus pattern (4 bp):
GACG
Found at i:925966 original size:16 final size:16
Alignment explanation
Indices: 925938--925997 Score: 83
Period size: 16 Copynumber: 4.0 Consensus size: 16
925928 AATTGAAGTG
925938 GGACAGACAGACGGAC
1 GGACAGACAGACGGAC
925954 GGAC-G---GACGGAC
1 GGACAGACAGACGGAC
925966 GGACAGACAGACGGAC
1 GGACAGACAGACGGAC
*
925982 GGACAGACAGAAGGAC
1 GGACAGACAGACGGAC
925998 TGACGGATGC
Statistics
Matches: 39, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
12 11 0.28
13 1 0.03
15 1 0.03
16 26 0.67
ACGTcount: A:0.37, C:0.23, G:0.40, T:0.00
Consensus pattern (16 bp):
GGACAGACAGACGGAC
Found at i:926551 original size:12 final size:11
Alignment explanation
Indices: 926534--926587 Score: 63
Period size: 12 Copynumber: 4.5 Consensus size: 11
926524 CCCCCCCCAA
926534 AAAAAAAAAACC
1 AAAAAAAAAA-C
926546 AAAAAAACAAAAC
1 -AAAAAA-AAAAC
926559 AAAACAAAAAAC
1 AAAA-AAAAAAC
926571 AAAACAAAAAAC
1 AAAA-AAAAAAC
926583 AAAAA
1 AAAAA
926588 CAAAGTATCC
Statistics
Matches: 39, Mismatches: 0, Indels: 6
0.87 0.00 0.13
Matches are distributed among these distances:
11 1 0.03
12 25 0.64
13 9 0.23
14 4 0.10
ACGTcount: A:0.85, C:0.15, G:0.00, T:0.00
Consensus pattern (11 bp):
AAAAAAAAAAC
Found at i:926557 original size:17 final size:17
Alignment explanation
Indices: 926547--926591 Score: 72
Period size: 17 Copynumber: 2.6 Consensus size: 17
926537 AAAAAAACCA
926547 AAAAAACAAAACAAAAC
1 AAAAAACAAAACAAAAC
*
926564 AAAAAACAAAACAAAAA
1 AAAAAACAAAACAAAAC
926581 ACAAAAACAAA
1 A-AAAAACAAA
926592 GTATCCCCCA
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
17 17 0.65
18 9 0.35
ACGTcount: A:0.84, C:0.16, G:0.00, T:0.00
Consensus pattern (17 bp):
AAAAAACAAAACAAAAC
Found at i:926579 original size:30 final size:31
Alignment explanation
Indices: 926533--926591 Score: 86
Period size: 30 Copynumber: 1.9 Consensus size: 31
926523 CCCCCCCCCA
926533 AAAAAAAAAAACCAAAAAA-ACAAAACAAAAC
1 AAAAAAAAAAACCAAAAAACA-AAAACAAAAC
*
926564 AAAAAACAAAA-CAAAAAACAAAAACAAA
1 AAAAAAAAAAACCAAAAAACAAAAACAAA
926592 GTATCCCCCA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
30 15 0.58
31 11 0.42
ACGTcount: A:0.85, C:0.15, G:0.00, T:0.00
Consensus pattern (31 bp):
AAAAAAAAAAACCAAAAAACAAAAACAAAAC
Found at i:927582 original size:18 final size:18
Alignment explanation
Indices: 927559--927594 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
927549 AAAAATTGAT
927559 AGTGAAAGTTGAAATGTC
1 AGTGAAAGTTGAAATGTC
927577 AGTGAAAGTTGAAATGTC
1 AGTGAAAGTTGAAATGTC
927595 GTATTCATCG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.39, C:0.06, G:0.28, T:0.28
Consensus pattern (18 bp):
AGTGAAAGTTGAAATGTC
Found at i:935426 original size:3 final size:3
Alignment explanation
Indices: 935418--935452 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
935408 AACTTGCCAA
935418 AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AA
1 AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AA
935453 TAACCCAACC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.69, C:0.31, G:0.00, T:0.00
Consensus pattern (3 bp):
AAC
Found at i:944886 original size:66 final size:66
Alignment explanation
Indices: 944810--944942 Score: 230
Period size: 66 Copynumber: 2.0 Consensus size: 66
944800 AAGATACAAG
* * *
944810 TATTTACATTTGCAAATATGTTTTCTGATATGAACCTATAGAATAGCGAAAACGTTCAATTCTGT
1 TATTTACATTTGCAAATATGTTTCCTGATATGAACCTAGAGAATAGCAAAAACGTTCAATTCTGT
944875 A
66 A
*
944876 TATTTACATTTGCAAATATGTTTCCTTATATGAACCTAGAGAATAGCAAAAACGTTCAATTCTGT
1 TATTTACATTTGCAAATATGTTTCCTGATATGAACCTAGAGAATAGCAAAAACGTTCAATTCTGT
944941 A
66 A
944942 T
1 T
944943 GAACTTTTTC
Statistics
Matches: 63, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
66 63 1.00
ACGTcount: A:0.35, C:0.14, G:0.13, T:0.38
Consensus pattern (66 bp):
TATTTACATTTGCAAATATGTTTCCTGATATGAACCTAGAGAATAGCAAAAACGTTCAATTCTGT
A
Found at i:946889 original size:66 final size:66
Alignment explanation
Indices: 946812--946945 Score: 205
Period size: 66 Copynumber: 2.0 Consensus size: 66
946802 ACTGATACAA
* * * * *
946812 ATATTAACATTTGCAAATATGTTTTCTTATATGAACCTATAGAATAGCGAAAACGTTCAGTTCTG
1 ATATTAACATTTGCAAAAATGTTTCCTTACATGAACCTATAGAATAGCAAAAACGTTCAATTCTG
946877 T
66 T
* *
946878 ATATTCACATTTGCAAAAATGTTTCCTTGCATGAACCTATAGAATAGCAAAAACGTTCAATTCTG
1 ATATTAACATTTGCAAAAATGTTTCCTTACATGAACCTATAGAATAGCAAAAACGTTCAATTCTG
946943 T
66 T
946944 AT
1 AT
946946 GAACTTTTTC
Statistics
Matches: 61, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
66 61 1.00
ACGTcount: A:0.36, C:0.16, G:0.13, T:0.36
Consensus pattern (66 bp):
ATATTAACATTTGCAAAAATGTTTCCTTACATGAACCTATAGAATAGCAAAAACGTTCAATTCTG
T
Found at i:950295 original size:11 final size:11
Alignment explanation
Indices: 950279--950303 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
950269 GCGATAGTTT
950279 TTCCTGTATCA
1 TTCCTGTATCA
950290 TTCCTGTATCA
1 TTCCTGTATCA
950301 TTC
1 TTC
950304 ATAAACTAAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.16, C:0.28, G:0.08, T:0.48
Consensus pattern (11 bp):
TTCCTGTATCA
Found at i:950519 original size:2 final size:2
Alignment explanation
Indices: 950512--950570 Score: 118
Period size: 2 Copynumber: 29.5 Consensus size: 2
950502 TATGTACACA
950512 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
950554 TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC T
950571 ACAACATTGA
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 57 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:972512 original size:2 final size:2
Alignment explanation
Indices: 972505--972566 Score: 124
Period size: 2 Copynumber: 31.0 Consensus size: 2
972495 NNNNNNNNNN
972505 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
972547 TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA
972567 AATCACAATC
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 60 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:973081 original size:22 final size:22
Alignment explanation
Indices: 973053--973177 Score: 178
Period size: 22 Copynumber: 5.7 Consensus size: 22
973043 GTAAAATATC
973053 ATTGTAAAGCCTGTTAAACATT
1 ATTGTAAAGCCTGTTAAACATT
* *
973075 ATTGTAAAGCCTGGTACACATT
1 ATTGTAAAGCCTGTTAAACATT
* *
973097 ACTGTAAGGCCTGTTAAACATT
1 ATTGTAAAGCCTGTTAAACATT
* *
973119 ATTGTAAAGCCTGGTACACATT
1 ATTGTAAAGCCTGTTAAACATT
* *
973141 ACTGTAAGGCCTGTTAAACATT
1 ATTGTAAAGCCTGTTAAACATT
973163 ATTGTAAAGCCTGTT
1 ATTGTAAAGCCTGTT
973178 TAAAAAATTA
Statistics
Matches: 87, Mismatches: 16, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
22 87 1.00
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.34
Consensus pattern (22 bp):
ATTGTAAAGCCTGTTAAACATT
Found at i:973109 original size:44 final size:44
Alignment explanation
Indices: 973055--973175 Score: 233
Period size: 44 Copynumber: 2.8 Consensus size: 44
973045 AAAATATCAT
*
973055 TGTAAAGCCTGTTAAACATTATTGTAAAGCCTGGTACACATTAC
1 TGTAAGGCCTGTTAAACATTATTGTAAAGCCTGGTACACATTAC
973099 TGTAAGGCCTGTTAAACATTATTGTAAAGCCTGGTACACATTAC
1 TGTAAGGCCTGTTAAACATTATTGTAAAGCCTGGTACACATTAC
973143 TGTAAGGCCTGTTAAACATTATTGTAAAGCCTG
1 TGTAAGGCCTGTTAAACATTATTGTAAAGCCTG
973176 TTTAAAAAAT
Statistics
Matches: 76, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
44 76 1.00
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.32
Consensus pattern (44 bp):
TGTAAGGCCTGTTAAACATTATTGTAAAGCCTGGTACACATTAC
Found at i:973162 original size:66 final size:66
Alignment explanation
Indices: 973053--973205 Score: 180
Period size: 66 Copynumber: 2.3 Consensus size: 66
973043 GTAAAATATC
* * * *
973053 ATTGTAAAGCCTGTTAAACATTATTGTAAAGCCTGGTACACATTACTGTAAGGCCTGTTAAACAT
1 ATTGTAAAGCCTGGTAAACATTACTGTAAAGCCTGGTAAACATTACTGTAAAGCCTGTTAAACAT
973118 T
66 T
* * * * *
973119 ATTGTAAAGCCTGGTACACATTACTGTAAGGCCTGTTAAACATTATTGTAAAGCCTGTTTAAAAA
1 ATTGTAAAGCCTGGTAAACATTACTGTAAAGCCTGGTAAACATTACTGTAAAGCCTG-TT-AAAC
973184 ATT
64 ATT
**
973187 ATAACTAAAGCCTGGTAAA
1 AT-TGTAAAGCCTGGTAAA
973206 GTATTTAATG
Statistics
Matches: 72, Mismatches: 12, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
66 49 0.68
67 2 0.03
68 8 0.11
69 13 0.18
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (66 bp):
ATTGTAAAGCCTGGTAAACATTACTGTAAAGCCTGGTAAACATTACTGTAAAGCCTGTTAAACAT
T
Found at i:974733 original size:165 final size:166
Alignment explanation
Indices: 974362--974812 Score: 510
Period size: 165 Copynumber: 2.7 Consensus size: 166
974352 AGCTGATCAC
* * * * *
974362 AAAAATCATCTTCTCGGAAACTAATCAGCCAGGAAAGATGAAAGTTGTGTGGAAGCATCCTCACG
1 AAAAATCTTCTTCTCAGAAACTAATCAGCCAGGAAAGCTGAAACTTGTGTGGAAGCATCCTCAGG
* * * * * *
974427 TACTGTAGATTCAAAGTTGTAAAAATCATGACCCCCTCGGTGTAGGGTTGGCCACAGGGGGGGGG
66 TAGTGTAGATTCAAAGTTGTGAAAATCATGACCCCC-AGGGGTAGGGTGGGCCACA-------GA
* * *
974492 GGGGGGGGCGAAGTTTTACATAGGAATATATTCAGTAAATCTTT
123 GGGAGGGGCGAAGTTTTACATACGAATATATACAGTAAATCTTT
* * * *
974536 AAAAATATTCTTCTTAGAAACTAATTAGCCAGGAAAGCTGAAACTTGTGTGGATGCATCCTCAGG
1 AAAAATCTTCTTCTCAGAAACTAATCAGCCAGGAAAGCTGAAACTTGTGTGGAAGCATCCTCAGG
* * * *
974601 TAGTCTAGATTTAAA-TTGATGAAAATCATGACCCCCAGGGGTAGGGTGGGGCACA-ATGGAGGG
66 TAGTGTAGATTCAAAGTTG-TGAAAATCATGACCCCCAGGGGTAGGGTGGGCCACAGAGGGAGGG
* * *
974664 TCGAAGTTTTACATTCGAATATATAGAGTAAATCTTT
130 GCGAAGTTTTACATACGAATATATACAGTAAATCTTT
* ** * *
974701 AAAAATCTTCTTCGCAGAAACTAATCAGCCAGGAACTCTGAAACTTCTTTGGAAGCATCCTCAGG
1 AAAAATCTTCTTCTCAGAAACTAATCAGCCAGGAAAGCTGAAACTTGTGTGGAAGCATCCTCAGG
* **
974766 TAGTGTAGATTCAAAGTTGTGAAAATCATGATCCCTGGGGGTAGGGT
66 TAGTGTAGATTCAAAGTTGTGAAAATCATGACCCCCAGGGGTAGGGT
974813 AGGGTAGGGC
Statistics
Matches: 236, Mismatches: 39, Indels: 13
0.82 0.14 0.05
Matches are distributed among these distances:
165 131 0.56
166 3 0.01
173 18 0.08
174 84 0.36
ACGTcount: A:0.32, C:0.16, G:0.25, T:0.27
Consensus pattern (166 bp):
AAAAATCTTCTTCTCAGAAACTAATCAGCCAGGAAAGCTGAAACTTGTGTGGAAGCATCCTCAGG
TAGTGTAGATTCAAAGTTGTGAAAATCATGACCCCCAGGGGTAGGGTGGGCCACAGAGGGAGGGG
CGAAGTTTTACATACGAATATATACAGTAAATCTTT
Found at i:976347 original size:15 final size:16
Alignment explanation
Indices: 976322--976353 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
976312 CCCATGGGCC
976322 TCTTGTATTATCTTTA
1 TCTTGTATTATCTTTA
976338 TCTT-TATTATCTTTA
1 TCTTGTATTATCTTTA
976353 T
1 T
976354 TTACCTTAAC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 12 0.75
16 4 0.25
ACGTcount: A:0.19, C:0.12, G:0.03, T:0.66
Consensus pattern (16 bp):
TCTTGTATTATCTTTA
Found at i:981483 original size:88 final size:88
Alignment explanation
Indices: 981334--981544 Score: 334
Period size: 88 Copynumber: 2.4 Consensus size: 88
981324 AAAATATAAA
* * **
981334 AAGTTTCAGTAAGTTT-CAGTTGCGGAAACCCTTTGTAAACAATATGTTTCCCAATTGTATATGG
1 AAGTTTCAGTAAGTTTCCA-TTGCGGAAACCATTTGTAAACAATATGTATCCCAAACGTATATGG
* *
981398 AGGTTGAAACTATGCAGAAACTTC
65 AGATTGAAACCATGCAGAAACTTC
*
981422 AAGTTTCAGTAAGTTTCCATCGCGGAAACCATTTGTAAACAATATGTATCCCAAACGTATATGGA
1 AAGTTTCAGTAAGTTTCCATTGCGGAAACCATTTGTAAACAATATGTATCCCAAACGTATATGGA
981487 GATTGAAACCATGCAGAAACTTC
66 GATTGAAACCATGCAGAAACTTC
*
981510 AAGTTTCAGCAAGTTTCCATTGCGGAAACCATTTG
1 AAGTTTCAGTAAGTTTCCATTGCGGAAACCATTTG
981545 GATTCATGGA
Statistics
Matches: 113, Mismatches: 9, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
88 111 0.98
89 2 0.02
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.30
Consensus pattern (88 bp):
AAGTTTCAGTAAGTTTCCATTGCGGAAACCATTTGTAAACAATATGTATCCCAAACGTATATGGA
GATTGAAACCATGCAGAAACTTC
Found at i:981949 original size:22 final size:23
Alignment explanation
Indices: 981924--981969 Score: 76
Period size: 22 Copynumber: 2.0 Consensus size: 23
981914 TCATGAATTT
981924 GTGAGTTTGATATGATTT-TTAA
1 GTGAGTTTGATATGATTTCTTAA
*
981946 GTGATTTTGATATGATTTCTTAA
1 GTGAGTTTGATATGATTTCTTAA
981969 G
1 G
981970 AAAAGTTTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
22 17 0.77
23 5 0.23
ACGTcount: A:0.26, C:0.02, G:0.22, T:0.50
Consensus pattern (23 bp):
GTGAGTTTGATATGATTTCTTAA
Found at i:994441 original size:21 final size:21
Alignment explanation
Indices: 994409--994515 Score: 142
Period size: 21 Copynumber: 5.1 Consensus size: 21
994399 GCTGCACGCT
* * *
994409 CGCTAAACGGTTCACATGAAA
1 CGCTGAACGGTTTACACGAAA
*
994430 CGCTGAATGGTTTACACGAAA
1 CGCTGAACGGTTTACACGAAA
994451 CGCTGAACGGTTTACACGAAA
1 CGCTGAACGGTTTACACGAAA
** * *
994472 CGCCAAACGATTTACACAAAA
1 CGCTGAACGGTTTACACGAAA
994493 CGCTGAACGGTTTACACGAAA
1 CGCTGAACGGTTTACACGAAA
994514 CG
1 CG
994516 ATTCTCGCAC
Statistics
Matches: 73, Mismatches: 13, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 73 1.00
ACGTcount: A:0.36, C:0.24, G:0.21, T:0.19
Consensus pattern (21 bp):
CGCTGAACGGTTTACACGAAA
Found at i:996037 original size:23 final size:21
Alignment explanation
Indices: 996007--996087 Score: 81
Period size: 21 Copynumber: 3.8 Consensus size: 21
995997 TTCTCGCACG
*
996007 CTTTGCCCGAAACGATTTACACA
1 CTTTGCCCGAAACG--CTACACA
* *
996030 CTTTGCCCGAAACGCTGCACG
1 CTTTGCCCGAAACGCTACACA
*
996051 CTTTGCCCGAAACGCTAAACA
1 CTTTGCCCGAAACGCTACACA
* * *
996072 GTTTACACGAAACGCT
1 CTTTGCCCGAAACGCT
996088 TCACGATTCA
Statistics
Matches: 49, Mismatches: 9, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
21 35 0.71
23 14 0.29
ACGTcount: A:0.28, C:0.32, G:0.17, T:0.22
Consensus pattern (21 bp):
CTTTGCCCGAAACGCTACACA
Found at i:996056 original size:21 final size:21
Alignment explanation
Indices: 996002--996066 Score: 85
Period size: 21 Copynumber: 3.0 Consensus size: 21
995992 CACGGTTCTC
*
996002 GCACGCTTTGCCCGAAACGATTT
1 GCACGCTTTGCCCGAAACG--CT
* *
996025 ACACACTTTGCCCGAAACGCT
1 GCACGCTTTGCCCGAAACGCT
996046 GCACGCTTTGCCCGAAACGCT
1 GCACGCTTTGCCCGAAACGCT
996067 AAACAGTTTA
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
21 20 0.54
23 17 0.46
ACGTcount: A:0.23, C:0.35, G:0.20, T:0.22
Consensus pattern (21 bp):
GCACGCTTTGCCCGAAACGCT
Found at i:996082 original size:21 final size:21
Alignment explanation
Indices: 996058--996148 Score: 137
Period size: 21 Copynumber: 4.3 Consensus size: 21
996048 ACGCTTTGCC
*
996058 CGAAACGCTAAACAGTTTACA
1 CGAAACGCTAAACGGTTTACA
** * *
996079 CGAAACGCTTCACGATTCACA
1 CGAAACGCTAAACGGTTTACA
996100 CGAAACGCTAAACGGTTTACA
1 CGAAACGCTAAACGGTTTACA
996121 CGAAACGCTAAACGGTTTACA
1 CGAAACGCTAAACGGTTTACA
996142 CGAAACG
1 CGAAACG
996149 TTTCTCGCAC
Statistics
Matches: 61, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 61 1.00
ACGTcount: A:0.38, C:0.26, G:0.18, T:0.18
Consensus pattern (21 bp):
CGAAACGCTAAACGGTTTACA
Found at i:997191 original size:54 final size:54
Alignment explanation
Indices: 997126--997400 Score: 487
Period size: 54 Copynumber: 5.1 Consensus size: 54
997116 ACATTGCTTT
* *
997126 CAGTCGGGCAGGAGGTGGAAGAGATATGTTTGCTAGTGTCGGTATGTAACTTGA
1 CAGTCCGGCAGGGGGTGGAAGAGATATGTTTGCTAGTGTCGGTATGTAACTTGA
*
997180 CAGTCCTGCAGGGGGTGGAAGAGATATGTTTGCTAGTGTCGGTATGTAACTTGA
1 CAGTCCGGCAGGGGGTGGAAGAGATATGTTTGCTAGTGTCGGTATGTAACTTGA
*
997234 CAGTCCTGCAGGGGGTGGAAGAGATATGTTTGCTAGTGTCGGTATGTAACTTGA
1 CAGTCCGGCAGGGGGTGGAAGAGATATGTTTGCTAGTGTCGGTATGTAACTTGA
*
997288 CAGTCGGGCAGGGGGTGGAAGAGATATGTTTGCTAGTGTCGGTATGTAACTTGA
1 CAGTCCGGCAGGGGGTGGAAGAGATATGTTTGCTAGTGTCGGTATGTAACTTGA
* *
997342 CAGTCGGGCAGGGGGTGGAAGAGATATGTTTGCTAGTGTCGGTACGTAACTTGA
1 CAGTCCGGCAGGGGGTGGAAGAGATATGTTTGCTAGTGTCGGTATGTAACTTGA
997396 CAGTC
1 CAGTC
997401 AGTTAGACAA
Statistics
Matches: 215, Mismatches: 6, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
54 215 1.00
ACGTcount: A:0.23, C:0.13, G:0.37, T:0.28
Consensus pattern (54 bp):
CAGTCCGGCAGGGGGTGGAAGAGATATGTTTGCTAGTGTCGGTATGTAACTTGA
Found at i:1000476 original size:31 final size:31
Alignment explanation
Indices: 1000441--1000508 Score: 136
Period size: 31 Copynumber: 2.2 Consensus size: 31
1000431 ACTATGCATA
1000441 AGAATGAATGGGCAAAGAGAGATAACTGCTG
1 AGAATGAATGGGCAAAGAGAGATAACTGCTG
1000472 AGAATGAATGGGCAAAGAGAGATAACTGCTG
1 AGAATGAATGGGCAAAGAGAGATAACTGCTG
1000503 AGAATG
1 AGAATG
1000509 TTACCATTGT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 37 1.00
ACGTcount: A:0.43, C:0.09, G:0.32, T:0.16
Consensus pattern (31 bp):
AGAATGAATGGGCAAAGAGAGATAACTGCTG
Found at i:1015692 original size:63 final size:63
Alignment explanation
Indices: 1015593--1016106 Score: 949
Period size: 63 Copynumber: 8.2 Consensus size: 63
1015583 NNNNNNNNNN
1015593 CGTCCCTACAACACAAATCATATCTCTATAGCAACCACAGAGCACTCAATGTGCCAGCCAGGT
1 CGTCCCTACAACACAAATCATATCTCTATAGCAACCACAGAGCACTCAATGTGCCAGCCAGGT
1015656 CGTCCCTACAACACAAATCATATCTCTATAGCAACCACAGAGCACTCAATGTGCCAGCCAGGT
1 CGTCCCTACAACACAAATCATATCTCTATAGCAACCACAGAGCACTCAATGTGCCAGCCAGGT
1015719 CGTCCCTACAACACAAATCATATCTCTATAGCAACCACAGAGCACTCAATGTGCCAGCCAGGT
1 CGTCCCTACAACACAAATCATATCTCTATAGCAACCACAGAGCACTCAATGTGCCAGCCAGGT
1015782 CGTCCCTACAACACAAATCATATCTCTATAGCAACCACAGAGCACTCAATGTGCCAGCCAGGT
1 CGTCCCTACAACACAAATCATATCTCTATAGCAACCACAGAGCACTCAATGTGCCAGCCAGGT
1015845 CGTCCCTACAACACAAATCATATCTCTATAGCAACCACAGAGCACTCAATGTGCCAGCCAGGT
1 CGTCCCTACAACACAAATCATATCTCTATAGCAACCACAGAGCACTCAATGTGCCAGCCAGGT
1015908 CGTCCCTACAACACAAATCATATCTCTATAGCAACCACAGAGCACTCAATGTGCCAGCCAGGT
1 CGTCCCTACAACACAAATCATATCTCTATAGCAACCACAGAGCACTCAATGTGCCAGCCAGGT
* * **
1015971 CGTCCCTACAACTCAAATAATATCTCTATAGCAACCACAGAGCACTTGATGTGCCAGCCAGGT
1 CGTCCCTACAACACAAATCATATCTCTATAGCAACCACAGAGCACTCAATGTGCCAGCCAGGT
* * *
1016034 CGTCCCTATAACACAAATAATATCTCTATAGCAACCACAGAGCACTCAATGTGCCAACCAGGAT
1 CGTCCCTACAACACAAATCATATCTCTATAGCAACCACAGAGCACTCAATGTGCCAGCCAGG-T
1016098 -GTCCCTACA
1 CGTCCCTACA
1016107 CAAATATCTT
Statistics
Matches: 440, Mismatches: 10, Indels: 2
0.97 0.02 0.00
Matches are distributed among these distances:
63 439 1.00
64 1 0.00
ACGTcount: A:0.33, C:0.33, G:0.14, T:0.20
Consensus pattern (63 bp):
CGTCCCTACAACACAAATCATATCTCTATAGCAACCACAGAGCACTCAATGTGCCAGCCAGGT
Found at i:1020679 original size:166 final size:165
Alignment explanation
Indices: 1020388--1020729 Score: 492
Period size: 166 Copynumber: 2.0 Consensus size: 165
1020378 AAAGAATCAG
* *
1020388 CTGGCTGATTAGTTTCTGAGAAGATTTTAAAAGATTTACTCTATATATTTCTATGTAAAACTTTA
1 CTGGCTGATTAGTTTCTGAGAAGATTTTAAAAGATTTACTCTATAAATTCCTATGTAAAACTTT-
*
1020453 ACACCCCCCCCCCCAATGTGGCCCAACCCTACCCCCAGGGATCATGATTTTCACAACTTTGAATC
65 ACA----CCCCCCCAATGTGGCCCAACCCTACCCCCAGGGATCATGAATTTCACAACTTTGAATC
1020518 TACACTACCTGAGGATACTTCCACACAAGTTTCAGCTTTC
126 TACACTACCTGAGGATACTTCCACACAAGTTTCAGCTTTC
* *
1020558 CTGGCTGATTAGTTTTTGAGAAGAAGATTTTTAAAGATTTACTCTATAAATTCCTATGTAAAAC-
1 CTGGCTGATTAGTTTCT--G-AGAAGATTTTAAAAGATTTACTCTATAAATTCCTATGTAAAACT
* * * *
1020622 TT-CGA-CCCCCCATTGTGGCCCCACCCTACCCCCGGGGGTCATGAATTTCACAACTTTGAATCT
63 TTAC-ACCCCCCCAATGTGGCCCAACCCTACCCCCAGGGATCATGAATTTCACAACTTTGAATCT
*
1020685 ACACTACCTGAGGATGCTTCCACACAAGTTTCAGCTTTC
127 ACACTACCTGAGGATACTTCCACACAAGTTTCAGCTTTC
1020724 CTGGCT
1 CTGGCT
1020730 TTATGGATCT
Statistics
Matches: 158, Mismatches: 10, Indels: 12
0.88 0.06 0.07
Matches are distributed among these distances:
166 97 0.61
170 17 0.11
171 1 0.01
172 3 0.02
173 40 0.25
ACGTcount: A:0.27, C:0.27, G:0.15, T:0.31
Consensus pattern (165 bp):
CTGGCTGATTAGTTTCTGAGAAGATTTTAAAAGATTTACTCTATAAATTCCTATGTAAAACTTTA
CACCCCCCCAATGTGGCCCAACCCTACCCCCAGGGATCATGAATTTCACAACTTTGAATCTACAC
TACCTGAGGATACTTCCACACAAGTTTCAGCTTTC
Found at i:1042752 original size:2 final size:2
Alignment explanation
Indices: 1042745--1042771 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1042735 ATTACTTCTG
1042745 CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT C
1042772 AAAAAGCTGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:1046834 original size:46 final size:45
Alignment explanation
Indices: 1046782--1047149 Score: 335
Period size: 46 Copynumber: 8.9 Consensus size: 45
1046772 TGTAATAACT
*
1046782 GCTGGCTCAAACCAATCTATACCCCTGTACTGATTTCTGGCTTATA
1 GCTGGCTCACACCAATCTATACCCCTGTACTGATTTCTGGCTT-TA
*
1046828 GCTGGCTCACACCGATCTATACCCCTGTACTGATTTCT-G-----
1 GCTGGCTCACACCAATCTATACCCCTGTACTGATTTCTGGCTTTA
* * *
1046867 GCT--CACACATCAATCTATACCCCTATACTGATTTCTGGCTTATA
1 GCTGGCTCACACCAATCTATACCCCTGTACTGATTTCTGGCTT-TA
1046911 GCTGGCTCACACCAATCTATACCCCTGTACTGATTTCTGGC-TTA
1 GCTGGCTCACACCAATCTATACCCCTGTACTGATTTCTGGCTTTA
*
1046955 ------T---ACCAATCTATACCCCTATACTGATTTCTGGC--T-
1 GCTGGCTCACACCAATCTATACCCCTGTACTGATTTCTGGCTTTA
*
1046988 --T--CT---ACCAATCTATACCCCTATACTGATTTCTGGC--T-
1 GCTGGCTCACACCAATCTATACCCCTGTACTGATTTCTGGCTTTA
* **
1047023 --T--CT---ACCAATCTACACCAATGTACTGATTTCTGGCTTATA
1 GCTGGCTCACACCAATCTATACCCCTGTACTGATTTCTGGCTT-TA
1047062 GCTGGCTCACACCAATCTATACCCCTGTACTGATTTCTGGCTTATA
1 GCTGGCTCACACCAATCTATACCCCTGTACTGATTTCTGGCTT-TA
*
1047108 GCTGGCTCACACCAATCTACACCCCTGTACTGATTTCTGGCT
1 GCTGGCTCACACCAATCTATACCCCTGTACTGATTTCTGGCT
1047150 CACACCAATC
Statistics
Matches: 282, Mismatches: 18, Indels: 44
0.82 0.05 0.13
Matches are distributed among these distances:
34 1 0.00
35 93 0.33
37 29 0.10
38 3 0.01
39 3 0.01
41 1 0.00
43 2 0.01
44 5 0.02
45 2 0.01
46 143 0.51
ACGTcount: A:0.23, C:0.31, G:0.13, T:0.33
Consensus pattern (45 bp):
GCTGGCTCACACCAATCTATACCCCTGTACTGATTTCTGGCTTTA
Found at i:1046952 original size:35 final size:35
Alignment explanation
Indices: 1046912--1047431 Score: 553
Period size: 35 Copynumber: 14.2 Consensus size: 35
1046902 TGGCTTATAG
1046912 CTGGCTCACACCAATCTATACCCCTGTACTGATTT
1 CTGGCTCACACCAATCTATACCCCTGTACTGATTT
* * *
1046947 CTGGCTTATACCAATCTATACCCCTATACTGATTT
1 CTGGCTCACACCAATCTATACCCCTGTACTGATTT
* *
1046982 CTGGCTTC-TACCAATCTATACCCCTATACTGATTT
1 CTGGC-TCACACCAATCTATACCCCTGTACTGATTT
* * **
1047017 CTGGCTTC-TACCAATCTACACCAATGTACTGATTTCTGGCTTAT
1 CTGGC-TCACACCAATCTATACCCCTGTACTGA--------TT-T
1047061 AGCTGGCTCACACCAATCTATACCCCTGTACTGATTTCTGGCTTAT
1 --CTGGCTCACACCAATCTATACCCCTGTACTGA--------TT-T
*
1047107 AGCTGGCTCACACCAATCTACACCCCTGTACTGATTT
1 --CTGGCTCACACCAATCTATACCCCTGTACTGATTT
*
1047144 CTGGCTCACACCAATCTATACCCCTGTATTGATTT
1 CTGGCTCACACCAATCTATACCCCTGTACTGATTT
**
1047179 CTGGCTCACACCAATCTATACCCCAATACTGATTT
1 CTGGCTCACACCAATCTATACCCCTGTACTGATTT
* *
1047214 CTGGCTTC-TACCAATCTATACCCCTATACTGATTT
1 CTGGC-TCACACCAATCTATACCCCTGTACTGATTT
* * *
1047249 CTGTCTTATACCAATCTATACCCCTGTACTGATTT
1 CTGGCTCACACCAATCTATACCCCTGTACTGATTT
*
1047284 CTGGCTCACACCAATCTATACCCCTATACTGATTT
1 CTGGCTCACACCAATCTATACCCCTGTACTGATTT
*
1047319 CTGGCTCACACCAATCTATACCCCTGTATTGATTT
1 CTGGCTCACACCAATCTATACCCCTGTACTGATTT
* **
1047354 CTGGCTCACACAAATCTATACCCCAATACTGATTT
1 CTGGCTCACACCAATCTATACCCCTGTACTGATTT
* *
1047389 CTGGCTTC-TACCAATCTATACCCCTGTATTGATTT
1 CTGGC-TCACACCAATCTATACCCCTGTACTGATTT
1047424 CTGGCTCA
1 CTGGCTCA
1047432 TACCTACTGA
Statistics
Matches: 430, Mismatches: 38, Indels: 34
0.86 0.08 0.07
Matches are distributed among these distances:
34 3 0.01
35 344 0.80
36 5 0.01
37 1 0.00
38 2 0.00
43 2 0.00
44 1 0.00
45 2 0.00
46 70 0.16
ACGTcount: A:0.24, C:0.31, G:0.11, T:0.34
Consensus pattern (35 bp):
CTGGCTCACACCAATCTATACCCCTGTACTGATTT
Found at i:1071486 original size:63 final size:63
Alignment explanation
Indices: 1071387--1071513 Score: 254
Period size: 63 Copynumber: 2.0 Consensus size: 63
1071377 TCATGGCCAT
1071387 TTGCCTAGTGGTTATCAAACCATAAGGTGAATGGTTCAAATTCAGTTGCAATAGATTCACCAA
1 TTGCCTAGTGGTTATCAAACCATAAGGTGAATGGTTCAAATTCAGTTGCAATAGATTCACCAA
1071450 TTGCCTAGTGGTTATCAAACCATAAGGTGAATGGTTCAAATTCAGTTGCAATAGATTCACCAA
1 TTGCCTAGTGGTTATCAAACCATAAGGTGAATGGTTCAAATTCAGTTGCAATAGATTCACCAA
1071513 T
1 T
1071514 AAGTAACCTT
Statistics
Matches: 64, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
63 64 1.00
ACGTcount: A:0.33, C:0.17, G:0.19, T:0.31
Consensus pattern (63 bp):
TTGCCTAGTGGTTATCAAACCATAAGGTGAATGGTTCAAATTCAGTTGCAATAGATTCACCAA
Found at i:1072935 original size:13 final size:13
Alignment explanation
Indices: 1072917--1072942 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1072907 ATCCAAATTA
1072917 TTATTTTTTAAAT
1 TTATTTTTTAAAT
1072930 TTATTTTTTAAAT
1 TTATTTTTTAAAT
1072943 GATAAATGTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (13 bp):
TTATTTTTTAAAT
Found at i:1076323 original size:18 final size:18
Alignment explanation
Indices: 1076279--1076326 Score: 53
Period size: 18 Copynumber: 2.7 Consensus size: 18
1076269 CTACACCATT
*
1076279 ACAGGTAGACAGTTCTAG
1 ACAGGTAGACAATTCTAG
**
1076297 ACACATAGACAATTAC-AG
1 ACAGGTAGACAATT-CTAG
1076315 ACAGGTAGACAA
1 ACAGGTAGACAA
1076327 AATTCAATTG
Statistics
Matches: 24, Mismatches: 5, Indels: 2
0.77 0.16 0.06
Matches are distributed among these distances:
18 23 0.96
19 1 0.04
ACGTcount: A:0.44, C:0.19, G:0.21, T:0.17
Consensus pattern (18 bp):
ACAGGTAGACAATTCTAG
Found at i:1077414 original size:26 final size:27
Alignment explanation
Indices: 1077365--1077423 Score: 109
Period size: 27 Copynumber: 2.2 Consensus size: 27
1077355 AGTGCCAGGT
1077365 AAAATCCACAGCGATAAAGAAAAACAA
1 AAAATCCACAGCGATAAAGAAAAACAA
*
1077392 AAAATCCACGGCGATAAAGAAAAACAA
1 AAAATCCACAGCGATAAAGAAAAACAA
1077419 AAAAT
1 AAAAT
1077424 TTTCTGAATC
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 31 1.00
ACGTcount: A:0.63, C:0.17, G:0.12, T:0.08
Consensus pattern (27 bp):
AAAATCCACAGCGATAAAGAAAAACAA
Found at i:1081224 original size:389 final size:388
Alignment explanation
Indices: 1080507--1081279 Score: 1519
Period size: 389 Copynumber: 2.0 Consensus size: 388
1080497 TTTACTCTTT
*
1080507 TTTTTTTATATCCTGTATTATGTTCCATATAACCTTCATTTTAAGAATACTTATTAGTGAATATT
1 TTTTTTTATATCCTGTATTATGTTCCATATAACCTTCATTTTAAGAATACATATTAGTGAATATT
1080572 TTTTAAAACAAAGGTGTCAGTTTCTATCATATTAAATGAAAAGGACACACCAAACATTTTAAAAA
66 TTTTAAAACAAAGGTGTCAGTTTCTATCATATTAAATGAAAAGGACACACCAAACATTTTAAAAA
1080637 ATAGTGATGCATTTCTTTGCAAATTCATTCACATTTTTGCAATTCATTCAACATGCATTTGTAAG
131 ATAGTGATGCATTTCTTTGCAAATTCATTCACATTTTTGCAATTCATTCAACATGCATTTGTAAG
1080702 TTTATTACATGTATTATATTTCACATTGTTTATATGCTTTAAGTTTGAATTACAAAGTTACATGT
196 TTTATTACATGTATTATATTTCACATTGTTTATATGCTTTAAGTTTGAATTACAAAGTTACATGT
1080767 ATTTCTAAGCTATTTTCATACATTAATGAATGATTTTGTTTTGTATTGTATTCAATGTATCATGA
261 ATTTCTAAGCTATTTTCATACATTAATGAATGATTTTGTTTTGTATTGTATTCAATGTATCATGA
1080832 ACTACCTATGCTGTGATATTAGTTGGCAGAGTTTTTGTATGAAGTAGATTAGAACATANTTAAC
326 ACTACCTATGCTGTGATATTAGTTGGCAGAGTTTTTGTATGAAGTAGATTAGAACATA-TTAAC
1080896 TTTTTTTATATCCTGTATTATGTTCCATATAACCTTCATTTTAAGAATACATATTAGTGAATATT
1 TTTTTTTATATCCTGTATTATGTTCCATATAACCTTCATTTTAAGAATACATATTAGTGAATATT
*
1080961 TTTTAAAACAAAGGTGTCAGTTTCTATCGTATTAAATGAAAAGGACACACCAAACATTTTAAAAA
66 TTTTAAAACAAAGGTGTCAGTTTCTATCATATTAAATGAAAAGGACACACCAAACATTTTAAAAA
1081026 ATAGTGATGCATTTCTTTGCAAATTCATTCACATTTTTGCAATTCATTCAACATGCATTTGTAAG
131 ATAGTGATGCATTTCTTTGCAAATTCATTCACATTTTTGCAATTCATTCAACATGCATTTGTAAG
1081091 TTTATTACATGTATTATATTTCACATTGTTTATATGCTTTAAGTTTGAATTACAAAGTTACATGT
196 TTTATTACATGTATTATATTTCACATTGTTTATATGCTTTAAGTTTGAATTACAAAGTTACATGT
1081156 ATTTCTAAGCTATTTTCATACATTAATGAATGATTTTGTTTTGTATTGTATTCAATGTATCATGA
261 ATTTCTAAGCTATTTTCATACATTAATGAATGATTTTGTTTTGTATTGTATTCAATGTATCATGA
1081221 ACTACCTATGCTGTGATATTAGTTGGCAGAGTTTTTGTATGAAGTAGATTAGAACATAT
326 ACTACCTATGCTGTGATATTAGTTGGCAGAGTTTTTGTATGAAGTAGATTAGAACATAT
1081280 AACATTCAAC
Statistics
Matches: 382, Mismatches: 2, Indels: 1
0.99 0.01 0.00
Matches are distributed among these distances:
388 1 0.00
389 381 1.00
ACGTcount: A:0.33, C:0.12, G:0.13, T:0.43
Consensus pattern (388 bp):
TTTTTTTATATCCTGTATTATGTTCCATATAACCTTCATTTTAAGAATACATATTAGTGAATATT
TTTTAAAACAAAGGTGTCAGTTTCTATCATATTAAATGAAAAGGACACACCAAACATTTTAAAAA
ATAGTGATGCATTTCTTTGCAAATTCATTCACATTTTTGCAATTCATTCAACATGCATTTGTAAG
TTTATTACATGTATTATATTTCACATTGTTTATATGCTTTAAGTTTGAATTACAAAGTTACATGT
ATTTCTAAGCTATTTTCATACATTAATGAATGATTTTGTTTTGTATTGTATTCAATGTATCATGA
ACTACCTATGCTGTGATATTAGTTGGCAGAGTTTTTGTATGAAGTAGATTAGAACATATTAAC
Found at i:1082676 original size:31 final size:31
Alignment explanation
Indices: 1082638--1082704 Score: 125
Period size: 31 Copynumber: 2.2 Consensus size: 31
1082628 CATTTCAATG
*
1082638 TAAATAAGTCATCAGCATTTTACTTTCGCTT
1 TAAATAAGTCATCAGCATTTTACTTTCACTT
1082669 TAAATAAGTCATCAGCATTTTACTTTCACTT
1 TAAATAAGTCATCAGCATTTTACTTTCACTT
1082700 TAAAT
1 TAAAT
1082705 GCAATTGTTC
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 35 1.00
ACGTcount: A:0.33, C:0.18, G:0.07, T:0.42
Consensus pattern (31 bp):
TAAATAAGTCATCAGCATTTTACTTTCACTT
Found at i:1085484 original size:16 final size:16
Alignment explanation
Indices: 1085465--1085499 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
1085455 TCACCGAGAC
*
1085465 GAGGCATCACCTTTAT
1 GAGGAATCACCTTTAT
1085481 GAGGAATCACCTTTAT
1 GAGGAATCACCTTTAT
1085497 GAG
1 GAG
1085500 ACCACCTTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.29, C:0.20, G:0.23, T:0.29
Consensus pattern (16 bp):
GAGGAATCACCTTTAT
Found at i:1085507 original size:14 final size:16
Alignment explanation
Indices: 1085472--1085510 Score: 55
Period size: 16 Copynumber: 2.6 Consensus size: 16
1085462 GACGAGGCAT
*
1085472 CACCTTTATGAGGAAT
1 CACCTTTATGAGGAAC
1085488 CACCTTTATGA-G-AC
1 CACCTTTATGAGGAAC
1085502 CACCTTTAT
1 CACCTTTAT
1085511 CATTTTATTT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 10 0.45
15 1 0.05
16 11 0.50
ACGTcount: A:0.28, C:0.26, G:0.13, T:0.33
Consensus pattern (16 bp):
CACCTTTATGAGGAAC
Found at i:1085857 original size:10 final size:10
Alignment explanation
Indices: 1085851--1085888 Score: 51
Period size: 10 Copynumber: 3.8 Consensus size: 10
1085841 TATTGATATT
1085851 ATATGATACA
1 ATATGATACA
*
1085861 ATATAATA-A
1 ATATGATACA
1085870 TATATGATACA
1 -ATATGATACA
1085881 ATATGATA
1 ATATGATA
1085889 TCACATAATA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
9 1 0.04
10 22 0.92
11 1 0.04
ACGTcount: A:0.53, C:0.05, G:0.08, T:0.34
Consensus pattern (10 bp):
ATATGATACA
Found at i:1086019 original size:35 final size:35
Alignment explanation
Indices: 1085980--1086060 Score: 101
Period size: 35 Copynumber: 2.3 Consensus size: 35
1085970 ATAAAATTAG
*
1085980 ATACAATATCATGTGATA-TAGTACTATATTATATC
1 ATACAATATCATATGATACTA-TACTATATTATATC
* * * *
1086015 ATACAATATCATATTATACTATATTGTATTATATG
1 ATACAATATCATATGATACTATACTATATTATATC
1086050 ATACAATATCA
1 ATACAATATCA
1086061 CATCATACAA
Statistics
Matches: 40, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
35 38 0.95
36 2 0.05
ACGTcount: A:0.42, C:0.11, G:0.06, T:0.41
Consensus pattern (35 bp):
ATACAATATCATATGATACTATACTATATTATATC
Found at i:1086044 original size:15 final size:15
Alignment explanation
Indices: 1086001--1086047 Score: 58
Period size: 15 Copynumber: 3.1 Consensus size: 15
1085991 TGTGATATAG
*
1086001 TACTATATTATATCA
1 TACTATATTATATTA
* *
1086016 TACAATATCATATTA
1 TACTATATTATATTA
*
1086031 TACTATATTGTATTA
1 TACTATATTATATTA
1086046 TA
1 TA
1086048 TGATACAATA
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
15 26 1.00
ACGTcount: A:0.40, C:0.11, G:0.02, T:0.47
Consensus pattern (15 bp):
TACTATATTATATTA
Found at i:1086083 original size:15 final size:15
Alignment explanation
Indices: 1085995--1086084 Score: 54
Period size: 15 Copynumber: 5.7 Consensus size: 15
1085985 ATATCATGTG
* * *
1085995 ATATAGTACTATATT
1 ATATAATACAATATC
*
1086010 ATATCATACAATATC
1 ATATAATACAATATC
* *
1086025 ATATTATACTATATTGTATT
1 ATATAATAC-A-A---TATC
*
1086045 ATATGATACAATATC
1 ATATAATACAATATC
* *
1086060 ACATCATACAATATC
1 ATATAATACAATATC
1086075 ATATAATACA
1 ATATAATACA
1086085 TTTTCGTATG
Statistics
Matches: 58, Mismatches: 12, Indels: 10
0.73 0.15 0.12
Matches are distributed among these distances:
15 43 0.74
16 1 0.02
17 1 0.02
18 1 0.02
19 1 0.02
20 11 0.19
ACGTcount: A:0.44, C:0.13, G:0.03, T:0.39
Consensus pattern (15 bp):
ATATAATACAATATC
Found at i:1086143 original size:20 final size:20
Alignment explanation
Indices: 1086120--1086163 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
1086110 ATATAAACCA
**
1086120 ATATCATATTTTACAATATC
1 ATATCATATGATACAATATC
*
1086140 ATATCATATGATACAATATT
1 ATATCATATGATACAATATC
1086160 ATAT
1 ATAT
1086164 GTTGCAATAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.43, C:0.11, G:0.02, T:0.43
Consensus pattern (20 bp):
ATATCATATGATACAATATC
Found at i:1086158 original size:15 final size:15
Alignment explanation
Indices: 1086140--1086180 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
1086130 TTACAATATC
1086140 ATATCATATGATACA
1 ATATCATATGATACA
* * *
1086155 ATATTATATGTTGCA
1 ATATCATATGATACA
1086170 ATATCATATGA
1 ATATCATATGA
1086181 AATAGCATGT
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.41, C:0.10, G:0.10, T:0.39
Consensus pattern (15 bp):
ATATCATATGATACA
Found at i:1086160 original size:50 final size:50
Alignment explanation
Indices: 1085980--1086178 Score: 170
Period size: 50 Copynumber: 4.0 Consensus size: 50
1085970 ATAAAATTAG
* *
1085980 ATACAATATCATGTGATAT-AGTACTATATTATATCATACAATATCATATT
1 ATACAATATCATATGATATGA-TACAATATTATATCATACAATATCATATT
* ** * * * *
1086030 ATACTATATTGTATTATATGATACAATATCACATCATACAATATCATATA
1 ATACAATATCATATGATATGATACAATATTATATCATACAATATCATATT
* * * * * *
1086080 ATACATTTTCGTATGATATAATA-ATTTATTATAT-AAACCAATATCATATT
1 ATACAATATCATATGATATGATACA-ATATTATATCATA-CAATATCATATT
* * ** *
1086130 TTACAATATCATATCATATGATACAATATTATATGTTGCAATATCATAT
1 ATACAATATCATATGATATGATACAATATTATATCATACAATATCATAT
1086179 GAAATAGCAT
Statistics
Matches: 114, Mismatches: 30, Indels: 10
0.74 0.19 0.06
Matches are distributed among these distances:
49 3 0.03
50 109 0.96
51 2 0.02
ACGTcount: A:0.42, C:0.12, G:0.05, T:0.41
Consensus pattern (50 bp):
ATACAATATCATATGATATGATACAATATTATATCATACAATATCATATT
Found at i:1086338 original size:15 final size:15
Alignment explanation
Indices: 1086318--1086379 Score: 53
Period size: 15 Copynumber: 4.3 Consensus size: 15
1086308 AATTGATACA
1086318 ATATAATATTGTATC
1 ATATAATATTGTATC
*
1086333 ATATAACT-TTTTA-C
1 ATATAA-TATTGTATC
*
1086347 AATATAATA---TATG
1 -ATATAATATTGTATC
1086360 ATATAATATTGTATC
1 ATATAATATTGTATC
1086375 ATATA
1 ATATA
1086380 GAACAATAGT
Statistics
Matches: 37, Mismatches: 3, Indels: 14
0.69 0.06 0.26
Matches are distributed among these distances:
12 10 0.27
14 2 0.05
15 24 0.65
16 1 0.03
ACGTcount: A:0.44, C:0.06, G:0.05, T:0.45
Consensus pattern (15 bp):
ATATAATATTGTATC
Found at i:1086405 original size:20 final size:20
Alignment explanation
Indices: 1086364--1086417 Score: 56
Period size: 20 Copynumber: 2.7 Consensus size: 20
1086354 TATATGATAT
*
1086364 AATATTGTATCATATAGAAC
1 AATACTGTATCATATAGAAC
* *
1086384 AATAGTGTATCATATCA-TAC
1 AATACTGTATCATAT-AGAAC
*
1086404 AATACTATATCATA
1 AATACTGTATCATA
1086418 GGAATCATAT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
20 28 0.97
21 1 0.03
ACGTcount: A:0.44, C:0.13, G:0.07, T:0.35
Consensus pattern (20 bp):
AATACTGTATCATATAGAAC
Found at i:1087341 original size:19 final size:19
Alignment explanation
Indices: 1087314--1087350 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
1087304 AAGTGCACCT
*
1087314 GCTCCAAAAACTTTAACCA
1 GCTCCAAAAACCTTAACCA
*
1087333 GCTCTAAAAACCTTAACC
1 GCTCCAAAAACCTTAACC
1087351 TCATCCAGCA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.41, C:0.32, G:0.05, T:0.22
Consensus pattern (19 bp):
GCTCCAAAAACCTTAACCA
Found at i:1087385 original size:177 final size:174
Alignment explanation
Indices: 1087089--1087811 Score: 909
Period size: 177 Copynumber: 4.2 Consensus size: 174
1087079 AGATTCAGCA
* *
1087089 TGAAGTTAGGACCAGTAATAACTAAGATATAATCATCAGAGGGCACCTGCTCCAAAAGCTTTAAC
1 TGAAGTTAGGACCAGTAATAACT-AG--ATAATCATCAAAGGGCACCTGCTCCAAAAACTTTAAC
* * *
1087154 AAGCTCTTAAAACCTTAACCTCATCCAGCATCTGAAACCTATGGCTCAGATTCAGCATTCATGCC
63 CAGCTCTAAAAACCTTAACCTCATCCAGCATCTGAAACCTATGGCTCAGATTCAGCATTCAAGCC
* *
1087219 TGTCAGGTACATCAGTATCATAAGACGCACCATCTATGCAAGTTCGT
128 TGTCAGGTACATCAGTATCATAAGACGCACCATCCATGCAAGTTCGG
*
1087266 TGAAGTTAGGACCAGTAATAACTAAGTTATAATCATCAAAGTGCACCTGCTCCAAAAACTTTAAC
1 TGAAGTTAGGACCAGTAATAACT-AG--ATAATCATCAAAGGGCACCTGCTCCAAAAACTTTAAC
* **
1087331 CAGCTCTAAAAACCTTAACCTCATCCAGCATCAGAAACCTATGGCTCAGATTCAGCATTCCTGCC
63 CAGCTCTAAAAACCTTAACCTCATCCAGCATCTGAAACCTATGGCTCAGATTCAGCATTCAAGCC
* *
1087396 TGCCAGGTACATCAGTATCATAAGACGCACCATCTATGCAAGTTCGG
128 TGTCAGGTACATCAGTATCATAAGACGCACCATCCATGCAAGTTCGG
1087443 TGAAGTTAGGA-C--------C-AG-TAATCATCAAAGGGCACCTGCTCCAAAAACTTTAACCAG
1 TGAAGTTAGGACCAGTAATAACTAGATAATCATCAAAGGGCACCTGCTCCAAAAACTTTAACCAG
* *
1087497 CTCTAAAAACCTTAACCTCATCCAGCATCTGAAACCTATGGCTCAGATTCAGCATTAAAGCATGT
66 CTCTAAAAACCTTAACCTCATCCAGCATCTGAAACCTATGGCTCAGATTCAGCATTCAAGCCTGT
* * * *
1087562 CTGGTGCATCAGTATCATAAGATGCACCATCCATGCAAGTTTGG
131 CAGGTACATCAGTATCATAAGACGCACCATCCATGCAAGTTCGG
* *
1087606 TGAAGTTAGGACCAGTAGTAACCTAGA-AATTGCTATCAAAGGGCACCTGCACCAAAAACTTTAA
1 TGAAGTTAGGACCAGTAATAA-CTAGATAA-T-C-ATCAAAGGGCACCTGCTCCAAAAACTTTAA
* * * *
1087670 CCTGCTCTAAAAACCTTAACCTCCTCCAGCATCTGAAA-CTCATGGCCCTGATTCAGCATTCAAG
62 CCAGCTCTAAAAACCTTAACCTCATCCAGCATCTGAAACCT-ATGGCTCAGATTCAGCATTCAAG
* * * * * * *
1087734 TCTTTCAAGTCCATGAGTAGGTC--AAGATGCACCATCCATGCAAGTTTGG
126 CCTGTCAGGTACATCAGTA--TCATAAGACGCACCATCCATGCAAGTTCGG
* *
1087783 TGAAGATAGGACAAGTAATAACTTAGATA
1 TGAAGTTAGGACCAGTAATAAC-TAGATA
1087812 CAGGACCTGC
Statistics
Matches: 488, Mismatches: 38, Indels: 39
0.86 0.07 0.07
Matches are distributed among these distances:
163 147 0.30
164 1 0.00
166 2 0.00
168 1 0.00
173 1 0.00
174 4 0.01
175 1 0.00
176 5 0.01
177 323 0.66
178 1 0.00
179 2 0.00
ACGTcount: A:0.34, C:0.25, G:0.17, T:0.25
Consensus pattern (174 bp):
TGAAGTTAGGACCAGTAATAACTAGATAATCATCAAAGGGCACCTGCTCCAAAAACTTTAACCAG
CTCTAAAAACCTTAACCTCATCCAGCATCTGAAACCTATGGCTCAGATTCAGCATTCAAGCCTGT
CAGGTACATCAGTATCATAAGACGCACCATCCATGCAAGTTCGG
Found at i:1087480 original size:163 final size:165
Alignment explanation
Indices: 1087294--1087801 Score: 591
Period size: 163 Copynumber: 3.0 Consensus size: 165
1087284 TAACTAAGTT
*
1087294 ATAATCATCAAAGTGCACCTGCTCCAAAAACTTTAACCAGCTCTAAAAACCTTAACCTCATCCAG
1 ATAATCATCAAAGGGCACCTGCTCCAAAAACTTTAACCAGCTCTAAAAACCTTAACCTCATCCAG
* ** *
1087359 CATCAGAAACCTATGGCTCAGATTCAGCATTCCTGCCTGCCAGGTACATCAGTATCATAAGACGC
66 CATCTGAAACCTATGGCTCAGATTCAGCATTCAAGCATGCCAGGTACATCAGTATCATAAGACGC
*
1087424 ACCATCTATGCAAGTTCGGTGAAGTTAGGACC-AG
131 ACCATCCATGCAAGTTCGGTGAAGTTAGGACCAAG
1087458 -TAATCATCAAAGGGCACCTGCTCCAAAAACTTTAACCAGCTCTAAAAACCTTAACCTCATCCAG
1 ATAATCATCAAAGGGCACCTGCTCCAAAAACTTTAACCAGCTCTAAAAACCTTAACCTCATCCAG
* * * * *
1087522 CATCTGAAACCTATGGCTCAGATTCAGCATTAAAGCATGTCTGGTGCATCAGTATCATAAGATGC
66 CATCTGAAACCTATGGCTCAGATTCAGCATTCAAGCATGCCAGGTACATCAGTATCATAAGACGC
*
1087587 ACCATCCATGCAAGTTTGGTGAAGTTAGGACCAGTAG
131 ACCATCCATGCAAGTTCGGTGAAGTTAGGACCA--AG
* *
1087624 TAACCTAGAAATTGCTATCAAAGGGCACCTGCACCAAAAACTTTAACCTGCTCTAAAAACCTTAA
1 --A--T---AA-T-C-ATCAAAGGGCACCTGCTCCAAAAACTTTAACCAGCTCTAAAAACCTTAA
* * * ** * * *
1087689 CCTCCTCCAGCATCTGAAA-CTCATGGCCCTGATTCAGCATTCAAGTC-TTTCAAGTCCATGAGT
56 CCTCATCCAGCATCTGAAACCT-ATGGCTCAGATTCAGCATTCAAG-CATGCCAGGTACATCAGT
* * *
1087752 AGGTC--AAGATGCACCATCCATGCAAGTTTGGTGAAGATAGGA-CAAG
119 A--TCATAAGACGCACCATCCATGCAAGTTCGGTGAAGTTAGGACCAAG
1087798 -TAAT
1 ATAAT
1087802 AACTTAGATA
Statistics
Matches: 302, Mismatches: 24, Indels: 35
0.84 0.07 0.10
Matches are distributed among these distances:
163 149 0.49
165 1 0.00
166 4 0.01
169 1 0.00
171 1 0.00
174 4 0.01
175 1 0.00
176 5 0.02
177 133 0.44
178 1 0.00
179 2 0.01
ACGTcount: A:0.33, C:0.26, G:0.17, T:0.24
Consensus pattern (165 bp):
ATAATCATCAAAGGGCACCTGCTCCAAAAACTTTAACCAGCTCTAAAAACCTTAACCTCATCCAG
CATCTGAAACCTATGGCTCAGATTCAGCATTCAAGCATGCCAGGTACATCAGTATCATAAGACGC
ACCATCCATGCAAGTTCGGTGAAGTTAGGACCAAG
Found at i:1087504 original size:19 final size:19
Alignment explanation
Indices: 1087477--1087513 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
1087467 AAGGGCACCT
*
1087477 GCTCCAAAAACTTTAACCA
1 GCTCCAAAAACCTTAACCA
*
1087496 GCTCTAAAAACCTTAACC
1 GCTCCAAAAACCTTAACC
1087514 TCATCCAGCA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.41, C:0.32, G:0.05, T:0.22
Consensus pattern (19 bp):
GCTCCAAAAACCTTAACCA
Found at i:1087674 original size:19 final size:19
Alignment explanation
Indices: 1087650--1087691 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
1087640 ATCAAAGGGC
*
1087650 ACCTGCACCAAAAACTTTA
1 ACCTGCACCAAAAACCTTA
* *
1087669 ACCTGCTCTAAAAACCTTA
1 ACCTGCACCAAAAACCTTA
1087688 ACCT
1 ACCT
1087692 CCTCCAGCAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.38, C:0.33, G:0.05, T:0.24
Consensus pattern (19 bp):
ACCTGCACCAAAAACCTTA
Done.