Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: chr9
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 38630433
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 2298367 characters in sequence are not A, C, G, or T
File 66 of 97
Found at i:26680323 original size:24 final size:24
Alignment explanation
Indices: 26680296--26680341 Score: 83
Period size: 24 Copynumber: 1.9 Consensus size: 24
26680286 GGTTCTCTAG
26680296 AACTATACAAATAAAAAATTCTGA
1 AACTATACAAATAAAAAATTCTGA
*
26680320 AACTATACAGATAAAAAATTCT
1 AACTATACAAATAAAAAATTCT
26680342 TGATTTGTGG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.57, C:0.13, G:0.04, T:0.26
Consensus pattern (24 bp):
AACTATACAAATAAAAAATTCTGA
Found at i:26684124 original size:21 final size:20
Alignment explanation
Indices: 26684094--26684142 Score: 89
Period size: 20 Copynumber: 2.5 Consensus size: 20
26684084 CAACTTATTT
*
26684094 TTTATTTTTTTAAAAAAAAA
1 TTTATTTTTTTTAAAAAAAA
26684114 TTTATTTTTTTTAAAAAAAA
1 TTTATTTTTTTTAAAAAAAA
26684134 TTTATTTTT
1 TTTATTTTT
26684143 ATAATTTTAT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (20 bp):
TTTATTTTTTTTAAAAAAAA
Found at i:26684209 original size:21 final size:22
Alignment explanation
Indices: 26684172--26684214 Score: 54
Period size: 21 Copynumber: 2.0 Consensus size: 22
26684162 ATTGTATGAT
*
26684172 TTAATTTATAAATTAAA-ATTA
1 TTAATTTATAAAGTAAAGATTA
26684193 TTAATTTGAT-AAGTAAAGATTA
1 TTAATTT-ATAAAGTAAAGATTA
26684215 AACTCATTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
21 13 0.68
22 6 0.32
ACGTcount: A:0.49, C:0.00, G:0.07, T:0.44
Consensus pattern (22 bp):
TTAATTTATAAAGTAAAGATTA
Found at i:26688089 original size:42 final size:42
Alignment explanation
Indices: 26688030--26688171 Score: 203
Period size: 42 Copynumber: 3.4 Consensus size: 42
26688020 TGTTGATTTG
* *
26688030 GACCCGACTATGTGCGAGTAGGAGTGCACATAAGCCGTTGTT
1 GACCCGGCTATGTGCGAGTAGGAGTGCACATAAGCCGTTGCT
* *
26688072 GACCCGGCTATGTGCGAGTAGGGGTGCACATAAACCGTTGCT
1 GACCCGGCTATGTGCGAGTAGGAGTGCACATAAGCCGTTGCT
* * * *
26688114 AACTCGGCTATGTGTGAGTGGGAGTGCACATAAGCCGTTGCT
1 GACCCGGCTATGTGCGAGTAGGAGTGCACATAAGCCGTTGCT
*
26688156 GACCCGGCTATATGCG
1 GACCCGGCTATGTGCG
26688172 TATAAGCCGT
Statistics
Matches: 86, Mismatches: 14, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
42 86 1.00
ACGTcount: A:0.22, C:0.23, G:0.32, T:0.23
Consensus pattern (42 bp):
GACCCGGCTATGTGCGAGTAGGAGTGCACATAAGCCGTTGCT
Found at i:26688227 original size:26 final size:26
Alignment explanation
Indices: 26688191--26688252 Score: 115
Period size: 26 Copynumber: 2.4 Consensus size: 26
26688181 TTGCATATGA
26688191 GATGATGATGATGGGATGGTGTGCAT
1 GATGATGATGATGGGATGGTGTGCAT
26688217 GATGATGATGATGGGATGGTGTGCAT
1 GATGATGATGATGGGATGGTGTGCAT
*
26688243 GTTGATGATG
1 GATGATGATG
26688253 GGTATATGGT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 35 1.00
ACGTcount: A:0.23, C:0.03, G:0.42, T:0.32
Consensus pattern (26 bp):
GATGATGATGATGGGATGGTGTGCAT
Found at i:26696747 original size:17 final size:19
Alignment explanation
Indices: 26696723--26696762 Score: 53
Period size: 20 Copynumber: 2.1 Consensus size: 19
26696713 AATCTTAGTT
* *
26696723 TTTTTTTATTTTTTTGTTC
1 TTTTTATATTTTTCTGTTC
26696742 TTTTTATACTTTTTCTGTTC
1 TTTTTATA-TTTTTCTGTTC
26696762 T
1 T
26696763 ATGTTGAAGG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 7 0.39
20 11 0.61
ACGTcount: A:0.07, C:0.10, G:0.05, T:0.78
Consensus pattern (19 bp):
TTTTTATATTTTTCTGTTC
Found at i:26697799 original size:16 final size:16
Alignment explanation
Indices: 26697769--26697798 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
26697759 CCAAAATTTA
26697769 GATTTTGATTCTTTTG
1 GATTTTGATTCTTTTG
26697785 GATTTTGATT-TTTT
1 GATTTTGATTCTTTT
26697799 TAATATATTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 4 0.29
16 10 0.71
ACGTcount: A:0.13, C:0.03, G:0.17, T:0.67
Consensus pattern (16 bp):
GATTTTGATTCTTTTG
Found at i:26701227 original size:73 final size:74
Alignment explanation
Indices: 26701107--26701349 Score: 235
Period size: 73 Copynumber: 3.3 Consensus size: 74
26701097 AGAAAATACA
** * * ***
26701107 TAATCGACTAAGAAGTATGGTTAGCCAACTAAAAGCTCGC-GATCAAAAATTTGA-TTGTGAGAC
1 TAATCGACTAAGAAGTATGGTTAGCCAACTAAAAGCTTACTGACCAAAAA-TCGAGTTCAAAGAC
*
26701170 AGAGAAGATT
65 AGAGAAAATT
* * *
26701180 TAGTCGACTAAGAAGTATTGTTAGCCAACTAAGAGCTTACTG-CCAAAAATCGAGTTCAAAGACA
1 TAATCGACTAAGAAGTATGGTTAGCCAACTAAAAGCTTACTGACCAAAAATCGAGTTCAAAGACA
26701244 GAGAAAATT
66 GAGAAAATT
* * * * * *
26701253 TAATCGACTAAAAAGCATGGTTAGTCGACTAAAAGCTTACT-ACCAGAAA-CTGAGTTCAAAGGC
1 TAATCGACTAAGAAGTATGGTTAGCCAACTAAAAGCTTACTGACCAAAAATC-GAGTTCAAAGAC
* * *
26701316 AAAGACAACT
65 AGAGAAAATT
* *
26701326 TAATCGACTAAGAAGCATAGTTAG
1 TAATCGACTAAGAAGTATGGTTAG
26701350 TCGACTAAGA
Statistics
Matches: 141, Mismatches: 25, Indels: 8
0.81 0.14 0.05
Matches are distributed among these distances:
72 4 0.03
73 136 0.96
74 1 0.01
ACGTcount: A:0.41, C:0.16, G:0.20, T:0.23
Consensus pattern (74 bp):
TAATCGACTAAGAAGTATGGTTAGCCAACTAAAAGCTTACTGACCAAAAATCGAGTTCAAAGACA
GAGAAAATT
Found at i:26701786 original size:35 final size:34
Alignment explanation
Indices: 26701747--26701848 Score: 80
Period size: 33 Copynumber: 3.0 Consensus size: 34
26701737 TTTGGGTTTT
26701747 GGTTGATCCCATGAAAAACCATTGTTAAAGGTTGA
1 GGTTGATCCCATGAAAAACCATT-TTAAAGGTTGA
* *** * * ** **
26701782 GGTTGAGCATTTGAGAAGCCATTTT-TGGGTTTT
1 GGTTGATCCCATGAAAAACCATTTTAAAGGTTGA
*
26701815 GGTTGATCCCGTGAAAAACCATTATTAAAGGTTG
1 GGTTGATCCCATGAAAAACCATT-TTAAAGGTTG
26701849 TGGCTGAGCC
Statistics
Matches: 46, Mismatches: 19, Indels: 4
0.67 0.28 0.06
Matches are distributed among these distances:
33 21 0.46
34 4 0.09
35 21 0.46
ACGTcount: A:0.28, C:0.13, G:0.25, T:0.33
Consensus pattern (34 bp):
GGTTGATCCCATGAAAAACCATTTTAAAGGTTGA
Found at i:26701816 original size:68 final size:67
Alignment explanation
Indices: 26701736--26701871 Score: 209
Period size: 68 Copynumber: 2.0 Consensus size: 67
26701726 GAAAAGTTAG
* * * *
26701736 TTTTGGGTTTTGGTTGATCCCATGAAAAACCATTGTTAAAGGTTGAGGTTGAGCATTTGAGAAGC
1 TTTTGGGTTTTGGTTGATCCCATGAAAAACCATTATTAAAGGTTGAGGCTGAGC-CTTGAAAAGC
26701801 CAT
65 CAT
* *
26701804 TTTTGGGTTTTGGTTGATCCCGTGAAAAACCATTATTAAAGGTTGTGGCTGAGCCTTGAAAAGCC
1 TTTTGGGTTTTGGTTGATCCCATGAAAAACCATTATTAAAGGTTGAGGCTGAGCCTTGAAAAGCC
26701869 AT
66 AT
26701871 T
1 T
26701872 GTAAAAGTGT
Statistics
Matches: 62, Mismatches: 6, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
67 12 0.19
68 50 0.81
ACGTcount: A:0.26, C:0.13, G:0.26, T:0.35
Consensus pattern (67 bp):
TTTTGGGTTTTGGTTGATCCCATGAAAAACCATTATTAAAGGTTGAGGCTGAGCCTTGAAAAGCC
AT
Found at i:26701837 original size:33 final size:33
Alignment explanation
Indices: 26701736--26701837 Score: 87
Period size: 33 Copynumber: 3.0 Consensus size: 33
26701726 GAAAAGTTAG
26701736 TTTTGGGTTTTGGTTGATCCCATGAAAAACCAT
1 TTTTGGGTTTTGGTTGATCCCATGAAAAACCAT
** ** * *** * *
26701769 TGTTAAAGGTTGAGGTTGAGCATTTGAGAAGCCAT
1 T-TT-TGGGTTTTGGTTGATCCCATGAAAAACCAT
*
26701804 TTTTGGGTTTTGGTTGATCCCGTGAAAAACCAT
1 TTTTGGGTTTTGGTTGATCCCATGAAAAACCAT
26701837 T
1 T
26701838 ATTAAAGGTT
Statistics
Matches: 47, Mismatches: 20, Indels: 4
0.66 0.28 0.06
Matches are distributed among these distances:
33 22 0.47
34 4 0.09
35 21 0.45
ACGTcount: A:0.25, C:0.13, G:0.25, T:0.37
Consensus pattern (33 bp):
TTTTGGGTTTTGGTTGATCCCATGAAAAACCAT
Found at i:26703180 original size:43 final size:42
Alignment explanation
Indices: 26703133--26703241 Score: 130
Period size: 42 Copynumber: 2.6 Consensus size: 42
26703123 TAGCTCATGT
* *
26703133 GCACTCCCCACT-AGCACATGGCTGGGTCATCATCGACTTATGC
1 GCACT-CCCACTCA-CACATAGCCGGGTCATCATCGACTTATGC
* * *
26703176 GCACTCCTACTCACACATAGCCGGGTCATCATCGGCTTATGT
1 GCACTCCCACTCACACATAGCCGGGTCATCATCGACTTATGC
* *
26703218 ACACTCCTACTCACACATAGCCGG
1 GCACTCCCACTCACACATAGCCGG
26703242 ATCCACAACA
Statistics
Matches: 59, Mismatches: 6, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
42 53 0.90
43 6 0.10
ACGTcount: A:0.23, C:0.36, G:0.18, T:0.23
Consensus pattern (42 bp):
GCACTCCCACTCACACATAGCCGGGTCATCATCGACTTATGC
Found at i:26703202 original size:42 final size:42
Alignment explanation
Indices: 26703147--26703241 Score: 145
Period size: 42 Copynumber: 2.3 Consensus size: 42
26703137 TCCCCACTAG
* * *
26703147 CACATGGCTGGGTCATCATCGACTTATGCGCACTCCTACTCA
1 CACATAGCCGGGTCATCATCGACTTATGCACACTCCTACTCA
* *
26703189 CACATAGCCGGGTCATCATCGGCTTATGTACACTCCTACTCA
1 CACATAGCCGGGTCATCATCGACTTATGCACACTCCTACTCA
26703231 CACATAGCCGG
1 CACATAGCCGG
26703242 ATCCACAACA
Statistics
Matches: 48, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
42 48 1.00
ACGTcount: A:0.23, C:0.34, G:0.19, T:0.24
Consensus pattern (42 bp):
CACATAGCCGGGTCATCATCGACTTATGCACACTCCTACTCA
Found at i:26711634 original size:72 final size:73
Alignment explanation
Indices: 26711515--26711667 Score: 202
Period size: 72 Copynumber: 2.1 Consensus size: 73
26711505 TGTTAGCCAG
* *
26711515 CTAAGAGCTTACTACCAAAAACTGGGTTCAGAGGCAAAGAAGACTTAATCCACTAAAAAGCATGG
1 CTAAGAGCTTACTACCAAAAACTGAGTTCAGAGGCAAAGAAGACTTAATCCACTAAAAAGCATAG
26711580 TTAGTCGA
66 TTAGTCGA
* * * ** * *
26711588 CTAAGAGCTTA-TGCCAGAAACTGAGTTCAGAGGTAGTGACA-ACTTAATCGACTAAAAGGCATA
1 CTAAGAGCTTACTACCAAAAACTGAGTTCAGAGGCAAAGA-AGACTTAATCCACTAAAAAGCATA
26711651 GTTAGTCGA
65 GTTAGTCGA
26711660 CTAAGAGC
1 CTAAGAGC
26711668 ATTTTGTAAA
Statistics
Matches: 70, Mismatches: 9, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
72 58 0.83
73 12 0.17
ACGTcount: A:0.38, C:0.18, G:0.22, T:0.22
Consensus pattern (73 bp):
CTAAGAGCTTACTACCAAAAACTGAGTTCAGAGGCAAAGAAGACTTAATCCACTAAAAAGCATAG
TTAGTCGA
Found at i:26712129 original size:67 final size:67
Alignment explanation
Indices: 26712052--26712187 Score: 191
Period size: 67 Copynumber: 2.0 Consensus size: 67
26712042 CAAAAGTTTG
* * *
26712052 TTTTGGGTTTTGGTTGATCCCATGAAAAACCATTGTTAAAGGTTATGGTCGAGCCTTTGAAAAGC
1 TTTTGGGTTTTGGTTGATCCCAGGAAAAACCATTGTTAAAGGTTATGGTCGAACCATTGAAAAGC
26712117 CA
66 CA
* * * * * *
26712119 TTTTGGGTTTTGGTTGATCCCGGGAAAAATCATTGTTTAAGGTTGTGGTTGAACCATTGAAAAGG
1 TTTTGGGTTTTGGTTGATCCCAGGAAAAACCATTGTTAAAGGTTATGGTCGAACCATTGAAAAGC
26712184 CA
66 CA
26712186 TT
1 TT
26712188 GTAAAAGCTT
Statistics
Matches: 60, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
67 60 1.00
ACGTcount: A:0.26, C:0.12, G:0.26, T:0.36
Consensus pattern (67 bp):
TTTTGGGTTTTGGTTGATCCCAGGAAAAACCATTGTTAAAGGTTATGGTCGAACCATTGAAAAGC
CA
Found at i:26712765 original size:29 final size:29
Alignment explanation
Indices: 26712732--26712890 Score: 189
Period size: 29 Copynumber: 5.5 Consensus size: 29
26712722 CAACTTTAAC
26712732 ATGTTTTGTCTTAACTTAGACAAGAAAAT
1 ATGTTTTGTCTTAACTTAGACAAGAAAAT
*
26712761 ATGTTTTGTCTTAATTTAGACAAGAAAAT
1 ATGTTTTGTCTTAACTTAGACAAGAAAAT
26712790 ATGTTTT-TCTTAACTTAAGACAAGAAAAAT
1 ATGTTTTGTCTTAACTT-AGACAAG-AAAAT
* *
26712820 ATGTTTTGCCTTAA-TCTAGACAAGAAAAC
1 ATGTTTTGTCTTAACT-TAGACAAGAAAAT
* * * * * *
26712849 AT-ATTTGTCTCAATTTAGATAAGATAAC
1 ATGTTTTGTCTTAACTTAGACAAGAAAAT
26712877 ATGTTTTGTCTTAA
1 ATGTTTTGTCTTAA
26712891 TTAAAGACAA
Statistics
Matches: 113, Mismatches: 11, Indels: 12
0.83 0.08 0.09
Matches are distributed among these distances:
28 29 0.26
29 58 0.51
30 20 0.18
31 6 0.05
ACGTcount: A:0.38, C:0.11, G:0.13, T:0.39
Consensus pattern (29 bp):
ATGTTTTGTCTTAACTTAGACAAGAAAAT
Found at i:26712827 original size:59 final size:57
Alignment explanation
Indices: 26712729--26712902 Score: 213
Period size: 59 Copynumber: 3.0 Consensus size: 57
26712719 TGACAACTTT
26712729 AACATGTTTTGTCTTAACTTAGACAAGAAAATATGTTTTGTCTTAATTTAGACAAGAA
1 AACATGTTTT-TCTTAACTTAGACAAGAAAATATGTTTTGTCTTAATTTAGACAAGAA
* * *
26712787 AATATGTTTTTCTTAACTTAAGACAAGAAAAATATGTTTTGCCTTAATCTAGACAAGAA
1 AACATGTTTTTCTTAACTT-AGACAAG-AAAATATGTTTTGTCTTAATTTAGACAAGAA
* * * * * * * *
26712846 AACATATTTGTCTCAATTTAGATAAGATAACATGTTTTGTCTTAATTAAAGACAAGA
1 AACATGTTTTTCTTAACTTAGACAAGAAAATATGTTTTGTCTTAATT-TAGACAAGA
26712903 GTTATCTTAA
Statistics
Matches: 99, Mismatches: 14, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
57 26 0.26
58 30 0.30
59 43 0.43
ACGTcount: A:0.40, C:0.11, G:0.13, T:0.37
Consensus pattern (57 bp):
AACATGTTTTTCTTAACTTAGACAAGAAAATATGTTTTGTCTTAATTTAGACAAGAA
Found at i:26712889 original size:88 final size:88
Alignment explanation
Indices: 26712732--26712902 Score: 231
Period size: 88 Copynumber: 1.9 Consensus size: 88
26712722 CAACTTTAAC
* * * * *
26712732 ATGTTTTGTCTTAACTTAGACAAGAAAATATGTTTTGTCTTAATTTAGACAAGAAAATATGTTTT
1 ATGTTTTGCCTTAACTTAGACAAGAAAACATGATTTGTCTCAATTTAGACAAGAAAACATGTTTT
26712797 TCTTAACTT-AAGACAAGAAAAAT
66 TCTTAA-TTAAAGACAAGAAAAAT
* *
26712820 ATGTTTTGCCTTAA-TCTAGACAAGAAAACAT-ATTTGTCTCAATTTAGATAAGATAACATGTTT
1 ATGTTTTGCCTTAACT-TAGACAAGAAAACATGATTTGTCTCAATTTAGACAAGAAAACATGTTT
26712883 TGTCTTAATTAAAGACAAGA
65 T-TCTTAATTAAAGACAAGA
26712903 GTTATCTTAA
Statistics
Matches: 73, Mismatches: 7, Indels: 6
0.85 0.08 0.07
Matches are distributed among these distances:
87 31 0.42
88 42 0.58
ACGTcount: A:0.39, C:0.11, G:0.13, T:0.37
Consensus pattern (88 bp):
ATGTTTTGCCTTAACTTAGACAAGAAAACATGATTTGTCTCAATTTAGACAAGAAAACATGTTTT
TCTTAATTAAAGACAAGAAAAAT
Found at i:26717963 original size:28 final size:27
Alignment explanation
Indices: 26717912--26717965 Score: 72
Period size: 28 Copynumber: 2.0 Consensus size: 27
26717902 ATGTCCTGGT
* *
26717912 GGTGGAAAATTACAATTTTGCCCCTAG
1 GGTGGAAAATTACAATGTTACCCCTAG
*
26717939 GGTGGCAAAATTACCATGTTACCCCTA
1 GGTGG-AAAATTACAATGTTACCCCTA
26717966 TACTACAAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
27 5 0.22
28 18 0.78
ACGTcount: A:0.30, C:0.22, G:0.20, T:0.28
Consensus pattern (27 bp):
GGTGGAAAATTACAATGTTACCCCTAG
Found at i:26736007 original size:28 final size:28
Alignment explanation
Indices: 26735972--26736026 Score: 92
Period size: 28 Copynumber: 2.0 Consensus size: 28
26735962 GATTGAAATT
26735972 TTATTTATGTTTAATGTAATTTATTTGC
1 TTATTTATGTTTAATGTAATTTATTTGC
**
26736000 TTATTTATGTTTGGTGTAATTTATTTG
1 TTATTTATGTTTAATGTAATTTATTTG
26736027 TTTGTAACAT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.22, C:0.02, G:0.15, T:0.62
Consensus pattern (28 bp):
TTATTTATGTTTAATGTAATTTATTTGC
Found at i:26737850 original size:17 final size:15
Alignment explanation
Indices: 26737814--26737844 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
26737804 TTGCAAAGTT
*
26737814 ATATTTCCAACAATC
1 ATATTCCCAACAATC
26737829 ATATTCCCAACAATC
1 ATATTCCCAACAATC
26737844 A
1 A
26737845 CATATTTAGC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.42, C:0.29, G:0.00, T:0.29
Consensus pattern (15 bp):
ATATTCCCAACAATC
Found at i:26741112 original size:31 final size:31
Alignment explanation
Indices: 26741071--26741134 Score: 83
Period size: 31 Copynumber: 2.1 Consensus size: 31
26741061 AATTTTGAAC
* *
26741071 TTTTACTTTGTTATATTTGATGTTATTATTA
1 TTTTACTTTGTTATAATTGATGTTATAATTA
* * *
26741102 TTTTATTTTGTTATAATTGTTTTTATAATTA
1 TTTTACTTTGTTATAATTGATGTTATAATTA
26741133 TT
1 TT
26741135 GATTTTAAAT
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.23, C:0.02, G:0.08, T:0.67
Consensus pattern (31 bp):
TTTTACTTTGTTATAATTGATGTTATAATTA
Found at i:26745794 original size:49 final size:49
Alignment explanation
Indices: 26745685--26745831 Score: 244
Period size: 49 Copynumber: 3.0 Consensus size: 49
26745675 ATATATGAGT
**
26745685 TAACATGTAAATCCGCATAAATCA-AGAATATTTTTGTG-CATGAACAAG
1 TAACATGTAAATCCATATAAATCACA-AATATTTTTGTGCCATGAACAAG
*
26745733 TAACATGTAAATCCATATAAACCACAAATATTTTTGTGCCATGAACAAG
1 TAACATGTAAATCCATATAAATCACAAATATTTTTGTGCCATGAACAAG
26745782 TAACATGTAAATCCATATAAATCACAAATATTTTTGTGCCATGAACAAG
1 TAACATGTAAATCCATATAAATCACAAATATTTTTGTGCCATGAACAAG
26745831 T
1 T
26745832 TGACATTATT
Statistics
Matches: 93, Mismatches: 4, Indels: 3
0.93 0.04 0.03
Matches are distributed among these distances:
48 33 0.35
49 60 0.65
ACGTcount: A:0.42, C:0.16, G:0.12, T:0.30
Consensus pattern (49 bp):
TAACATGTAAATCCATATAAATCACAAATATTTTTGTGCCATGAACAAG
Found at i:26747505 original size:6 final size:6
Alignment explanation
Indices: 26747494--26747521 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
26747484 AAAACAGATC
26747494 AAAATA AAAATA AAAATA AAAATA AAAA
1 AAAATA AAAATA AAAATA AAAATA AAAA
26747522 CCCTAGTTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.86, C:0.00, G:0.00, T:0.14
Consensus pattern (6 bp):
AAAATA
Found at i:26752263 original size:6 final size:6
Alignment explanation
Indices: 26752252--26752277 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
26752242 TTACTTAACT
26752252 AGAGGG AGAGGG AGAGGG AGAGGG AG
1 AGAGGG AGAGGG AGAGGG AGAGGG AG
26752278 GAATTAAAAG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.35, C:0.00, G:0.65, T:0.00
Consensus pattern (6 bp):
AGAGGG
Found at i:26764186 original size:37 final size:37
Alignment explanation
Indices: 26764145--26764220 Score: 143
Period size: 37 Copynumber: 2.1 Consensus size: 37
26764135 GAATTCATTG
26764145 TTACATTGGTTGGCTGTCACTATTTAAGTAAAAATTT
1 TTACATTGGTTGGCTGTCACTATTTAAGTAAAAATTT
*
26764182 TTACATTGGTTGGCTGTCACTGTTTAAGTAAAAATTT
1 TTACATTGGTTGGCTGTCACTATTTAAGTAAAAATTT
26764219 TT
1 TT
26764221 TTGAGTCTGG
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.28, C:0.11, G:0.17, T:0.45
Consensus pattern (37 bp):
TTACATTGGTTGGCTGTCACTATTTAAGTAAAAATTT
Found at i:26770606 original size:33 final size:34
Alignment explanation
Indices: 26770564--26770628 Score: 98
Period size: 34 Copynumber: 1.9 Consensus size: 34
26770554 TATTGGAGAG
*
26770564 GATCAAGCATAA-CC-TTCTACTACCTTTTCACAA
1 GATCAAGCATAACCCATGC-ACTACCTTTTCACAA
26770597 GATCAAGCATAACCCATGCACTACCTTTTCAC
1 GATCAAGCATAACCCATGCACTACCTTTTCAC
26770629 GTGAGTAAGG
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
33 12 0.41
34 15 0.52
35 2 0.07
ACGTcount: A:0.32, C:0.32, G:0.08, T:0.28
Consensus pattern (34 bp):
GATCAAGCATAACCCATGCACTACCTTTTCACAA
Found at i:26770706 original size:27 final size:27
Alignment explanation
Indices: 26770676--26770728 Score: 79
Period size: 27 Copynumber: 2.0 Consensus size: 27
26770666 TAGATATAAT
* *
26770676 CTTAGTCTTTTCAAGGATCAAACAAAC
1 CTTAGCCTTCTCAAGGATCAAACAAAC
*
26770703 CTTAGCCTTCTCAAGGATCAAGCAAA
1 CTTAGCCTTCTCAAGGATCAAACAAA
26770729 ACTTTTACAT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.36, C:0.25, G:0.13, T:0.26
Consensus pattern (27 bp):
CTTAGCCTTCTCAAGGATCAAACAAAC
Found at i:26771302 original size:21 final size:21
Alignment explanation
Indices: 26771277--26771371 Score: 100
Period size: 21 Copynumber: 4.5 Consensus size: 21
26771267 ACATTGTGAT
* **
26771277 AGGTATCAAGATTTTTAAATT
1 AGGTATCAAGATTTTGAAACC
*
26771298 AGGTATCAAGACTTTGAAACC
1 AGGTATCAAGATTTTGAAACC
* *
26771319 AAGTATCAGGATTTTGAAACC
1 AGGTATCAAGATTTTGAAACC
* * * *
26771340 AAGTATTAGGATTTTGAAATC
1 AGGTATCAAGATTTTGAAACC
26771361 AGGTATCAAGA
1 AGGTATCAAGA
26771372 CTCTGTGAAA
Statistics
Matches: 62, Mismatches: 12, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 62 1.00
ACGTcount: A:0.39, C:0.11, G:0.19, T:0.32
Consensus pattern (21 bp):
AGGTATCAAGATTTTGAAACC
Found at i:26772426 original size:49 final size:50
Alignment explanation
Indices: 26772338--26772435 Score: 128
Period size: 49 Copynumber: 2.0 Consensus size: 50
26772328 TATCTTTAAT
*
26772338 TAACACATATACTATTGTCTAATTTAAGACAACTCTTGTCTTAATTAAGA
1 TAACACATATACTATTGTCTAATTTAAGACAACACTTGTCTTAATTAAGA
* * * *
26772388 TAACATATATAC-CTTGTCTTAA-TTAAGACAAGAGTTGTCTTAATTAAG
1 TAACACATATACTATTGTC-TAATTTAAGACAACACTTGTCTTAATTAAG
26772436 GCAATAGGTA
Statistics
Matches: 42, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
49 28 0.67
50 14 0.33
ACGTcount: A:0.38, C:0.14, G:0.10, T:0.38
Consensus pattern (50 bp):
TAACACATATACTATTGTCTAATTTAAGACAACACTTGTCTTAATTAAGA
Found at i:26773349 original size:45 final size:44
Alignment explanation
Indices: 26773269--26773373 Score: 120
Period size: 45 Copynumber: 2.4 Consensus size: 44
26773259 GACTAATTTT
* ** *
26773269 TAGGTATTGCGTGACTAATTTTTAGGTATTACGTGAATAGTTGA
1 TAGGCATTGCGTGACTAATTGATAGGCATTACGTGAATAGTTGA
* * **
26773313 TATGGCATTGCGTGACTAATTGATAGGCATTGCGTGACTAGTTTT
1 TA-GGCATTGCGTGACTAATTGATAGGCATTACGTGAATAGTTGA
*
26773358 TAGGCATTGTGTGACT
1 TAGGCATTGCGTGACT
26773374 TAGGCAATGC
Statistics
Matches: 51, Mismatches: 9, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
44 15 0.29
45 36 0.71
ACGTcount: A:0.24, C:0.10, G:0.27, T:0.39
Consensus pattern (44 bp):
TAGGCATTGCGTGACTAATTGATAGGCATTACGTGAATAGTTGA
Found at i:26773351 original size:67 final size:66
Alignment explanation
Indices: 26773221--26773361 Score: 174
Period size: 67 Copynumber: 2.1 Consensus size: 66
26773211 ATGTAATCGG
* * ** * ** *
26773221 TTTTTGGGTATTACGTGACTAGTTTTTAAGTATTACGTGACTAATTTTTAGGTATTGCGTGACTA
1 TTTTTAGGTATTACGTGAATAGTTGATAAGCATTACGTGACTAATTGATAGGCATTGCGTGACTA
26773286 A
66 A
* *
26773287 TTTTTAGGTATTACGTGAATAGTTGATATGGCATTGCGTGACTAATTGATAGGCATTGCGTGACT
1 TTTTTAGGTATTACGTGAATAGTTGATA-AGCATTACGTGACTAATTGATAGGCATTGCGTGACT
*
26773352 AG
65 AA
26773354 TTTTTAGG
1 TTTTTAGG
26773362 CATTGTGTGA
Statistics
Matches: 63, Mismatches: 11, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
66 24 0.38
67 39 0.62
ACGTcount: A:0.24, C:0.09, G:0.24, T:0.43
Consensus pattern (66 bp):
TTTTTAGGTATTACGTGAATAGTTGATAAGCATTACGTGACTAATTGATAGGCATTGCGTGACTA
A
Found at i:26773362 original size:22 final size:22
Alignment explanation
Indices: 26773220--26773373 Score: 146
Period size: 22 Copynumber: 7.0 Consensus size: 22
26773210 TATGTAATCG
* *
26773220 GTTTTTGGGTATTACGTGACTA
1 GTTTTTAGGTATTGCGTGACTA
* *
26773242 GTTTTTAAGTATTACGTGACTA
1 GTTTTTAGGTATTGCGTGACTA
*
26773264 ATTTTTAGGTATTGCGTGACTA
1 GTTTTTAGGTATTGCGTGACTA
* * *
26773286 ATTTTTAGGTATTACGTGAATA
1 GTTTTTAGGTATTGCGTGACTA
** *
26773308 GTTGATATGGCATTGCGTGACTA
1 GTTTTTA-GGTATTGCGTGACTA
* ** *
26773331 ATTGATAGGCATTGCGTGACTA
1 GTTTTTAGGTATTGCGTGACTA
* *
26773353 GTTTTTAGGCATTGTGTGACT
1 GTTTTTAGGTATTGCGTGACT
26773374 TAGGCAATGC
Statistics
Matches: 113, Mismatches: 18, Indels: 2
0.85 0.14 0.02
Matches are distributed among these distances:
22 95 0.84
23 18 0.16
ACGTcount: A:0.23, C:0.10, G:0.25, T:0.42
Consensus pattern (22 bp):
GTTTTTAGGTATTGCGTGACTA
Found at i:26773408 original size:22 final size:22
Alignment explanation
Indices: 26773377--26773419 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
26773367 TGTGACTTAG
* *
26773377 GCAATGCCTACAACTTAGTCAC
1 GCAATACCTACAACCTAGTCAC
26773399 GCAATACCTACAACCTAGTCA
1 GCAATACCTACAACCTAGTCA
26773420 AGTAATGCTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.35, C:0.33, G:0.12, T:0.21
Consensus pattern (22 bp):
GCAATACCTACAACCTAGTCAC
Found at i:26773438 original size:22 final size:22
Alignment explanation
Indices: 26773413--26773457 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
26773403 TACCTACAAC
**
26773413 CTAGTCAAGTAATGCTTAAAAA
1 CTAGTCAAACAATGCTTAAAAA
*
26773435 CTAGTTAAACAATGCTTAAAAA
1 CTAGTCAAACAATGCTTAAAAA
26773457 C
1 C
26773458 CAAAGACACA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.47, C:0.16, G:0.11, T:0.27
Consensus pattern (22 bp):
CTAGTCAAACAATGCTTAAAAA
Found at i:26774841 original size:21 final size:19
Alignment explanation
Indices: 26774802--26774846 Score: 63
Period size: 21 Copynumber: 2.3 Consensus size: 19
26774792 ACAAAAAAAA
*
26774802 AAATTGTTTAAAATTTTTT
1 AAATAGTTTAAAATTTTTT
26774821 AAATAGTTTAGAAACTTTTTT
1 AAATAGTTTA-AAA-TTTTTT
26774842 AAATA
1 AAATA
26774847 TTATACTTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 9 0.39
20 3 0.13
21 11 0.48
ACGTcount: A:0.42, C:0.02, G:0.07, T:0.49
Consensus pattern (19 bp):
AAATAGTTTAAAATTTTTT
Found at i:26775367 original size:17 final size:17
Alignment explanation
Indices: 26775341--26775374 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
26775331 CATCCAAATA
*
26775341 AATATATTAATTTTAAT
1 AATATATTAAATTTAAT
*
26775358 AATATCTTAAATTTAAT
1 AATATATTAAATTTAAT
26775375 TTAAATTACT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (17 bp):
AATATATTAAATTTAAT
Found at i:26786595 original size:6 final size:6
Alignment explanation
Indices: 26786584--26786610 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
26786574 TGGACTCTCC
26786584 CTCCCT CTCCCT CTCCCT CTCCCT CTC
1 CTCCCT CTCCCT CTCCCT CTCCCT CTC
26786611 TCTCACACGC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.00, C:0.67, G:0.00, T:0.33
Consensus pattern (6 bp):
CTCCCT
Found at i:26788117 original size:35 final size:35
Alignment explanation
Indices: 26788078--26788156 Score: 106
Period size: 35 Copynumber: 2.3 Consensus size: 35
26788068 AATAATCATT
*
26788078 ACAAGTGAAGCATTACTTT-ACACAGAACAATTAAA
1 ACAAGTGAAGCACTA-TTTCACACAGAACAATTAAA
* * *
26788113 ACAAGTGAAGTACTATTTCACGCAGAACAATTAGA
1 ACAAGTGAAGCACTATTTCACACAGAACAATTAAA
26788148 ACAAGTGAA
1 ACAAGTGAA
26788157 ATGCTACTTC
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
34 3 0.08
35 36 0.92
ACGTcount: A:0.47, C:0.16, G:0.15, T:0.22
Consensus pattern (35 bp):
ACAAGTGAAGCACTATTTCACACAGAACAATTAAA
Found at i:26788173 original size:35 final size:35
Alignment explanation
Indices: 26788091--26788183 Score: 114
Period size: 35 Copynumber: 2.7 Consensus size: 35
26788081 AGTGAAGCAT
* * * *
26788091 TACTTTACACAGAACAATTAAAACAAGTGAAGTAC
1 TACTTCACGCAGAACAATTAGAACAAGTGAAATAC
* *
26788126 TATTTCACGCAGAACAATTAGAACAAGTGAAATGC
1 TACTTCACGCAGAACAATTAGAACAAGTGAAATAC
* *
26788161 TACTTCATGCAGAACAACTAGAA
1 TACTTCACGCAGAACAATTAGAA
26788184 TAAGAGTAAC
Statistics
Matches: 49, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
35 49 1.00
ACGTcount: A:0.45, C:0.18, G:0.14, T:0.23
Consensus pattern (35 bp):
TACTTCACGCAGAACAATTAGAACAAGTGAAATAC
Found at i:26788199 original size:35 final size:35
Alignment explanation
Indices: 26788100--26788204 Score: 84
Period size: 35 Copynumber: 3.0 Consensus size: 35
26788090 TTACTTTACA
* * * ** * *
26788100 CAGAACAATTAAAACAAGTGAAGTACTATTTCACG
1 CAGAACAACTAGAACAAGAGAAACACTACTTCATG
* * **
26788135 CAGAACAATTAGAACAAGTGAAATGCTACTTCATG
1 CAGAACAACTAGAACAAGAGAAACACTACTTCATG
* * *
26788170 CAGAACAACTAGAATAAGAGTAACACTACTCCATG
1 CAGAACAACTAGAACAAGAGAAACACTACTTCATG
26788205 TGTAACAACT
Statistics
Matches: 58, Mismatches: 12, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
35 58 1.00
ACGTcount: A:0.45, C:0.19, G:0.15, T:0.21
Consensus pattern (35 bp):
CAGAACAACTAGAACAAGAGAAACACTACTTCATG
Found at i:26788430 original size:29 final size:29
Alignment explanation
Indices: 26788397--26788477 Score: 126
Period size: 29 Copynumber: 2.8 Consensus size: 29
26788387 TTCACCCTCC
*
26788397 TACCTTGTTCTCGTATACCTGTTTACATA
1 TACCTTGTTCTCGTATACCTATTTACATA
26788426 TACCTTGTTCTCGTATACCTATTTACATA
1 TACCTTGTTCTCGTATACCTATTTACATA
* * *
26788455 TACCTTCTTCTCTTGTACCTATT
1 TACCTTGTTCTCGTATACCTATT
26788478 CATGTACAGC
Statistics
Matches: 48, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
29 48 1.00
ACGTcount: A:0.20, C:0.26, G:0.07, T:0.47
Consensus pattern (29 bp):
TACCTTGTTCTCGTATACCTATTTACATA
Found at i:26788434 original size:15 final size:15
Alignment explanation
Indices: 26788397--26788466 Score: 58
Period size: 14 Copynumber: 4.8 Consensus size: 15
26788387 TTCACCCTCC
*
26788397 TACCTTGTTCTCGTA
1 TACCTTGTTCTCATA
26788412 TACC-TGTT-TACATA
1 TACCTTGTTCT-CATA
*
26788426 TACCTTGTTCTCGTA
1 TACCTTGTTCTCATA
*
26788441 TACCTAT-TT-ACATA
1 TACCT-TGTTCTCATA
*
26788455 TACCTTCTTCTC
1 TACCTTGTTCTC
26788467 TTGTACCTAT
Statistics
Matches: 44, Mismatches: 5, Indels: 12
0.72 0.08 0.20
Matches are distributed among these distances:
13 2 0.05
14 21 0.48
15 19 0.43
16 2 0.05
ACGTcount: A:0.20, C:0.27, G:0.07, T:0.46
Consensus pattern (15 bp):
TACCTTGTTCTCATA
Found at i:26792016 original size:3 final size:3
Alignment explanation
Indices: 26792003--26792035 Score: 57
Period size: 3 Copynumber: 10.7 Consensus size: 3
26791993 GTTAATTAAA
26792003 AAT ATAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT A-AT AAT AAT AAT AAT AAT AAT AAT AAT AA
26792036 CAACAACAAC
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 26 0.90
4 3 0.10
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:26793495 original size:35 final size:35
Alignment explanation
Indices: 26793456--26793528 Score: 101
Period size: 35 Copynumber: 2.1 Consensus size: 35
26793446 CAACTAAAAC
* *
26793456 AAGTGAAGTACTATTTCACGCAGAATAATTAGAAT
1 AAGTGAAATACTATTTCACGCAGAACAATTAGAAT
* * *
26793491 AAGTGAAATATTATTTCATGCAGAACGATTAGAAT
1 AAGTGAAATACTATTTCACGCAGAACAATTAGAAT
26793526 AAG
1 AAG
26793529 CGTAGCACTA
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
35 33 1.00
ACGTcount: A:0.44, C:0.10, G:0.18, T:0.29
Consensus pattern (35 bp):
AAGTGAAATACTATTTCACGCAGAACAATTAGAAT
Found at i:26793786 original size:29 final size:29
Alignment explanation
Indices: 26793754--26793816 Score: 74
Period size: 29 Copynumber: 2.2 Consensus size: 29
26793744 TGTTCTCGTA
*
26793754 TACCTGTTCACATACA-CATTCTTCTCTTG
1 TACCTATTCACATACAGC-TTCTTCTCTTG
** *
26793783 TACCTATTCATGTACAGCTTTTTCTCTTG
1 TACCTATTCACATACAGCTTCTTCTCTTG
26793812 TACCT
1 TACCT
26793817 TTTTACGTAT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
29 28 0.97
30 1 0.03
ACGTcount: A:0.19, C:0.29, G:0.08, T:0.44
Consensus pattern (29 bp):
TACCTATTCACATACAGCTTCTTCTCTTG
Found at i:26795928 original size:2 final size:2
Alignment explanation
Indices: 26795921--26796008 Score: 153
Period size: 2 Copynumber: 45.0 Consensus size: 2
26795911 GAGCAAGGGA
*
26795921 AC AC AC AC AC AC AC AC A- AC AC AC AC AC GC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
26795962 AC AC AC AC AC AC AC AC AC AC AC AC AC A- AC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
26796003 AC AC AC
1 AC AC AC
26796009 TATATAGTGA
Statistics
Matches: 82, Mismatches: 2, Indels: 4
0.93 0.02 0.05
Matches are distributed among these distances:
1 2 0.02
2 80 0.98
ACGTcount: A:0.50, C:0.49, G:0.01, T:0.00
Consensus pattern (2 bp):
AC
Found at i:26796952 original size:12 final size:12
Alignment explanation
Indices: 26796935--26796963 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
26796925 GTCTAGCATA
26796935 TTTCAATGCAAT
1 TTTCAATGCAAT
26796947 TTTCAATGCAAT
1 TTTCAATGCAAT
26796959 TTTCA
1 TTTCA
26796964 CCTTAATCTG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.31, C:0.17, G:0.07, T:0.45
Consensus pattern (12 bp):
TTTCAATGCAAT
Found at i:26798184 original size:21 final size:22
Alignment explanation
Indices: 26798142--26798184 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 22
26798132 ATGTGTTTAA
* * *
26798142 CTAAAGAAAAGGTTATATTAAG
1 CTAAAGAAAAGGATAAACTAAG
26798164 CTAAA-AAAAGGATAAACTAAG
1 CTAAAGAAAAGGATAAACTAAG
26798185 GATAAATATA
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
21 13 0.72
22 5 0.28
ACGTcount: A:0.56, C:0.07, G:0.16, T:0.21
Consensus pattern (22 bp):
CTAAAGAAAAGGATAAACTAAG
Found at i:26799673 original size:2 final size:2
Alignment explanation
Indices: 26799668--26799692 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
26799658 GTGTTTATAT
26799668 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 T
26799693 TTCTATATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:26818906 original size:15 final size:15
Alignment explanation
Indices: 26818865--26818908 Score: 58
Period size: 15 Copynumber: 3.1 Consensus size: 15
26818855 TACCCATTAT
26818865 TTTACTTTTTAA-TTA
1 TTTA-TTTTTAATTTA
26818880 TTTA--TTTAATTTA
1 TTTATTTTTAATTTA
26818893 TTTATTTTTAATTTA
1 TTTATTTTTAATTTA
26818908 T
1 T
26818909 CCATTAATTC
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
12 5 0.19
13 7 0.27
15 14 0.54
ACGTcount: A:0.27, C:0.02, G:0.00, T:0.70
Consensus pattern (15 bp):
TTTATTTTTAATTTA
Found at i:26819009 original size:15 final size:16
Alignment explanation
Indices: 26818989--26819027 Score: 55
Period size: 15 Copynumber: 2.6 Consensus size: 16
26818979 TAATTTTATT
26818989 TTTTTATTTATTTA-A
1 TTTTTATTTATTTAGA
*
26819004 TTTTTA-TTATTTAGG
1 TTTTTATTTATTTAGA
26819019 TTTTTATTT
1 TTTTTATTT
26819028 TGCGTTTTTC
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
14 7 0.33
15 12 0.57
16 2 0.10
ACGTcount: A:0.21, C:0.00, G:0.05, T:0.74
Consensus pattern (16 bp):
TTTTTATTTATTTAGA
Found at i:26819013 original size:18 final size:17
Alignment explanation
Indices: 26818981--26819016 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
26818971 TGAATAATTA
*
26818981 ATTTTATTTTTTTATTT
1 ATTTAATTTTTTTATTT
26818998 ATTTAATTTTTATTATTT
1 ATTTAATTTTT-TTATTT
26819016 A
1 A
26819017 GGTTTTTATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 10 0.59
18 7 0.41
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (17 bp):
ATTTAATTTTTTTATTT
Found at i:26823760 original size:33 final size:34
Alignment explanation
Indices: 26823662--26823789 Score: 143
Period size: 34 Copynumber: 3.8 Consensus size: 34
26823652 ACCAATGTTA
* ** *
26823662 AAGGGTTTCCCTTGATCTTGTGAAAAAACATTAT
1 AAGGGTTTCGCTTGATCCCGTGAAAAAGCATTAT
* **
26823696 AAGGGTTTCACTTGATCATGTGAAAAAGCATTAT
1 AAGGGTTTCGCTTGATCCCGTGAAAAAGCATTAT
* *
26823730 GAGGGTTTCGCTTGATCCCGT-AAAAAGCATTGT
1 AAGGGTTTCGCTTGATCCCGTGAAAAAGCATTAT
* *
26823763 AAGGGTTTTGTTTGATCCCGT-AAAAAG
1 AAGGGTTTCGCTTGATCCCGTGAAAAAG
26823790 GTTATTTCCT
Statistics
Matches: 83, Mismatches: 11, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
33 35 0.42
34 48 0.58
ACGTcount: A:0.30, C:0.14, G:0.23, T:0.33
Consensus pattern (34 bp):
AAGGGTTTCGCTTGATCCCGTGAAAAAGCATTAT
Found at i:26824057 original size:15 final size:16
Alignment explanation
Indices: 26824027--26824057 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
26824017 ACACAAGAAG
26824027 AAATCTTTAGTTTTAA
1 AAATCTTTAGTTTTAA
26824043 AAATCTTTA-TTTTAA
1 AAATCTTTAGTTTTAA
26824058 TATTTAGTCT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 6 0.40
16 9 0.60
ACGTcount: A:0.39, C:0.06, G:0.03, T:0.52
Consensus pattern (16 bp):
AAATCTTTAGTTTTAA
Found at i:26830156 original size:2 final size:2
Alignment explanation
Indices: 26830114--26830144 Score: 53
Period size: 2 Copynumber: 15.0 Consensus size: 2
26830104 CCAAAACTTC
26830114 TA TA TA TA TA TA TA TA TA TA TA TCA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA T-A TA TA TA
26830145 AACAAATATA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 26 0.93
3 2 0.07
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:26830231 original size:42 final size:42
Alignment explanation
Indices: 26830185--26830307 Score: 151
Period size: 42 Copynumber: 2.9 Consensus size: 42
26830175 AACTTTGTCT
* * *
26830185 CAGCTTATGTGCACTACC-ACACCGCACATA-ATCCGGTTAGCA
1 CAGCTCATGTGCACT-CCTACACCGCACATAGCT-CGGTCAGCA
* *
26830227 CAGCTCATGTGCACTCCTACACCGCACATGGCTGGGTCAGCA
1 CAGCTCATGTGCACTCCTACACCGCACATAGCTCGGTCAGCA
* *
26830269 CAGCTCATGTGCACTCCTACACCGCACATGGCTGGGTCA
1 CAGCTCATGTGCACTCCTACACCGCACATAGCTCGGTCA
26830308 TAATTATCAC
Statistics
Matches: 74, Mismatches: 5, Indels: 4
0.89 0.06 0.05
Matches are distributed among these distances:
41 2 0.03
42 71 0.96
43 1 0.01
ACGTcount: A:0.24, C:0.35, G:0.21, T:0.20
Consensus pattern (42 bp):
CAGCTCATGTGCACTCCTACACCGCACATAGCTCGGTCAGCA
Found at i:26836058 original size:19 final size:19
Alignment explanation
Indices: 26836034--26836071 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
26836024 CCATTTAACT
*
26836034 TATTGGAGTATGATTTGAG
1 TATTGGAGTATAATTTGAG
26836053 TATTGGAGTATAATTTGAG
1 TATTGGAGTATAATTTGAG
26836072 GGTTTGGCAG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.29, C:0.00, G:0.29, T:0.42
Consensus pattern (19 bp):
TATTGGAGTATAATTTGAG
Found at i:26836289 original size:28 final size:29
Alignment explanation
Indices: 26836235--26836295 Score: 72
Period size: 28 Copynumber: 2.1 Consensus size: 29
26836225 ATGTCTATGG
*
26836235 GTAATTTTTCAGTTTTTGGGGCAAAAA-T
1 GTAATTTTTCACTTTTTGGGGCAAAAAGT
**
26836263 GTAATTTTT-ACTTTTATGGGGGTAAAAGT
1 GTAATTTTTCACTTTT-TGGGGCAAAAAGT
26836292 GTAA
1 GTAA
26836296 ATTTCAAAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
27 5 0.18
28 18 0.64
29 5 0.18
ACGTcount: A:0.30, C:0.05, G:0.23, T:0.43
Consensus pattern (29 bp):
GTAATTTTTCACTTTTTGGGGCAAAAAGT
Found at i:26843241 original size:2 final size:2
Alignment explanation
Indices: 26843234--26843268 Score: 52
Period size: 2 Copynumber: 17.0 Consensus size: 2
26843224 CCAAAACCCC
*
26843234 TA TA TA TA TA TA TA TCA TA TA TA AA TA TA TA TA TA
1 TA TA TA TA TA TA TA T-A TA TA TA TA TA TA TA TA TA
26843269 ACCACCGACC
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
2 28 0.93
3 2 0.07
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (2 bp):
TA
Found at i:26845857 original size:35 final size:34
Alignment explanation
Indices: 26845817--26845893 Score: 113
Period size: 35 Copynumber: 2.3 Consensus size: 34
26845807 CTTGATCCTA
26845817 TGAAAAAGCATTGTAAGGGTTTCGA-TTCGATCTCG
1 TGAAAAAGCATTGTAAGGGTTTC-ACTT-GATCTCG
*
26845852 TGAAAAAGCATTGTGAGGGTTTCACTTGATCTCG
1 TGAAAAAGCATTGTAAGGGTTTCACTTGATCTCG
26845886 T-AAAAAGC
1 TGAAAAAGC
26845894 TAATTTCCCT
Statistics
Matches: 40, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
33 7 0.17
34 9 0.22
35 24 0.60
ACGTcount: A:0.31, C:0.14, G:0.25, T:0.30
Consensus pattern (34 bp):
TGAAAAAGCATTGTAAGGGTTTCACTTGATCTCG
Found at i:26846077 original size:52 final size:52
Alignment explanation
Indices: 26846021--26846122 Score: 143
Period size: 52 Copynumber: 2.0 Consensus size: 52
26846011 GATTTATTGC
*
26846021 TTGCATTT-AACTTAAGAAAATATTTTACCTTGATTGATTATTTATTCTTTGA
1 TTGCATTTGAA-TTAAGAAAATATTTTACCTTAATTGATTATTTATTCTTTGA
* * * *
26846073 TTGCATTTGGATTAGGAAAATATTTTACCTTAATTTATTATTTGTTCTTT
1 TTGCATTTGAATTAAGAAAATATTTTACCTTAATTGATTATTTATTCTTT
26846123 TCAATTTATT
Statistics
Matches: 44, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
52 43 0.98
53 1 0.02
ACGTcount: A:0.28, C:0.09, G:0.11, T:0.52
Consensus pattern (52 bp):
TTGCATTTGAATTAAGAAAATATTTTACCTTAATTGATTATTTATTCTTTGA
Found at i:26847890 original size:30 final size:28
Alignment explanation
Indices: 26847832--26847890 Score: 66
Period size: 30 Copynumber: 2.0 Consensus size: 28
26847822 AAATATGTAG
* *
26847832 ATATTTTATTAATTATCTTAATTTTTAT
1 ATATTTTATTAATTATATTAATTATTAT
26847860 ATATTTTAATATAATTA-ATTATATTATTAT
1 ATATTTT-AT-TAATTATATTA-ATTATTAT
26847890 A
1 A
26847891 AAATTATGAG
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
28 7 0.27
29 5 0.19
30 14 0.54
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (28 bp):
ATATTTTATTAATTATATTAATTATTAT
Found at i:26847895 original size:20 final size:20
Alignment explanation
Indices: 26847859--26847896 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
26847849 TTAATTTTTA
*
26847859 TATATTTTAATATAATTAAT
1 TATATTTTAATAAAATTAAT
26847879 TATATTATT-ATAAAATTA
1 TATATT-TTAATAAAATTA
26847897 TGAGATGTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
20 14 0.88
21 2 0.12
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (20 bp):
TATATTTTAATAAAATTAAT
Found at i:26851886 original size:29 final size:28
Alignment explanation
Indices: 26851819--26851901 Score: 76
Period size: 29 Copynumber: 2.9 Consensus size: 28
26851809 AGATAAGAGG
* *
26851819 TATACGTGAAAAGGTATAAGAAAAGAAGT
1 TATACGTGAAAA-GTACAAGAGAAGAAGT
* *
26851848 TGTATGTGAACAAGTACAAGAGAAGAAGT
1 TATACGTGAA-AAGTACAAGAGAAGAAGT
* * *
26851877 TATACATGAATAGGTAGAAGAGAAG
1 TATACGTGAA-AAGTACAAGAGAAG
26851902 GTGTATGTGA
Statistics
Matches: 43, Mismatches: 10, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
29 41 0.95
30 2 0.05
ACGTcount: A:0.48, C:0.05, G:0.27, T:0.20
Consensus pattern (28 bp):
TATACGTGAAAAGTACAAGAGAAGAAGT
Found at i:26852201 original size:35 final size:35
Alignment explanation
Indices: 26852161--26852257 Score: 151
Period size: 35 Copynumber: 2.8 Consensus size: 35
26852151 GTAGTGCTCA
*
26852161 CTTATTCTAGCTGTTCTGCATGAAGTAACGC-TTC
1 CTTATTCTAGTTGTTCTGCATGAAGTAACGCTTTC
*
26852195 TTTTATTCTAGTTGTTCTGCATGAAGTAACGCTTTC
1 -CTTATTCTAGTTGTTCTGCATGAAGTAACGCTTTC
*
26852231 CTTATTCTAGTTGTTCTGCACGAAGTA
1 CTTATTCTAGTTGTTCTGCATGAAGTA
26852258 GCACTTCATT
Statistics
Matches: 57, Mismatches: 4, Indels: 2
0.90 0.06 0.03
Matches are distributed among these distances:
35 54 0.95
36 3 0.05
ACGTcount: A:0.21, C:0.20, G:0.18, T:0.42
Consensus pattern (35 bp):
CTTATTCTAGTTGTTCTGCATGAAGTAACGCTTTC
Found at i:26852239 original size:70 final size:70
Alignment explanation
Indices: 26852161--26852292 Score: 176
Period size: 70 Copynumber: 1.9 Consensus size: 70
26852151 GTAGTGCTCA
* * *
26852161 CTTATTCTAGCTGTTCTGCATGAAGTAACGCTTCTTTTATTCT-AGTTGTTCTGCATGAAGTAAC
1 CTTATTCTAGCTGTTCTGCACGAAGTAACACTTCATTTATT-TAAGTTGTTCTGCATGAAGTAAC
26852225 GCTTTC
65 GCTTTC
* * * **
26852231 CTTATTCTAGTTGTTCTGCACGAAGTAGCACTTCATTTGTTTAAGTTGTTCTGTGTGAAGTA
1 CTTATTCTAGCTGTTCTGCACGAAGTAACACTTCATTTATTTAAGTTGTTCTGCATGAAGTA
26852293 GTGCTTCACT
Statistics
Matches: 53, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
69 1 0.02
70 52 0.98
ACGTcount: A:0.20, C:0.17, G:0.19, T:0.43
Consensus pattern (70 bp):
CTTATTCTAGCTGTTCTGCACGAAGTAACACTTCATTTATTTAAGTTGTTCTGCATGAAGTAACG
CTTTC
Found at i:26852761 original size:4 final size:4
Alignment explanation
Indices: 26852752--26852804 Score: 88
Period size: 4 Copynumber: 13.2 Consensus size: 4
26852742 AGGCATCTCA
* *
26852752 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ATAT ATAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
26852800 ACAT A
1 ACAT A
26852805 TATATATATA
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
4 47 1.00
ACGTcount: A:0.51, C:0.21, G:0.00, T:0.28
Consensus pattern (4 bp):
ACAT
Found at i:26852809 original size:4 final size:4
Alignment explanation
Indices: 26852782--26852866 Score: 98
Period size: 4 Copynumber: 21.2 Consensus size: 4
26852772 ACATACATAC
* * * *
26852782 ATAT ATAT ATAC ATAC ATAC ATAT ATAT ATAT ATAT AAAT ATAT ATAT
1 ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT
* * * *
26852830 ACAT ATAT ATAT ATAT GTAT GTAT GTAT ATAT ATAT A
1 ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT A
26852867 AACCAAATGT
Statistics
Matches: 73, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
4 73 1.00
ACGTcount: A:0.48, C:0.05, G:0.04, T:0.44
Consensus pattern (4 bp):
ATAT
Found at i:26857102 original size:10 final size:10
Alignment explanation
Indices: 26857070--26857113 Score: 56
Period size: 10 Copynumber: 4.5 Consensus size: 10
26857060 ATTAAATTAG
26857070 TAAATTAAAAA
1 TAAA-TAAAAA
26857081 TAAAT--AAA
1 TAAATAAAAA
*
26857089 TAAATAAAAG
1 TAAATAAAAA
26857099 TAAATAAAAA
1 TAAATAAAAA
26857109 TAAAT
1 TAAAT
26857114 TGAGTTTAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
8 8 0.28
10 17 0.59
11 4 0.14
ACGTcount: A:0.73, C:0.00, G:0.02, T:0.25
Consensus pattern (10 bp):
TAAATAAAAA
Found at i:26857102 original size:18 final size:19
Alignment explanation
Indices: 26857070--26857106 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
26857060 ATTAAATTAG
26857070 TAAATTAAAAATAAATAAA
1 TAAATTAAAAATAAATAAA
*
26857089 TAAA-TAAAAGTAAATAAA
1 TAAATTAAAAATAAATAAA
26857107 AATAAATTGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 13 0.76
19 4 0.24
ACGTcount: A:0.73, C:0.00, G:0.03, T:0.24
Consensus pattern (19 bp):
TAAATTAAAAATAAATAAA
Found at i:26866838 original size:15 final size:16
Alignment explanation
Indices: 26866818--26866847 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
26866808 ACCATTAGTT
26866818 TTTTTCTC-TATTTTG
1 TTTTTCTCTTATTTTG
26866833 TTTTTCTCTTATTTT
1 TTTTTCTCTTATTTT
26866848 CTTTGACTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.07, C:0.13, G:0.03, T:0.77
Consensus pattern (16 bp):
TTTTTCTCTTATTTTG
Found at i:26878097 original size:10 final size:10
Alignment explanation
Indices: 26878079--26878112 Score: 50
Period size: 10 Copynumber: 3.3 Consensus size: 10
26878069 AAGTAGTTAA
26878079 TTTAATTTAT
1 TTTAATTTAT
*
26878089 TTTAGTTTAAT
1 TTTAATTT-AT
26878100 TTTAATTTAT
1 TTTAATTTAT
26878110 TTT
1 TTT
26878113 GCTTTAATTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
10 12 0.57
11 9 0.43
ACGTcount: A:0.26, C:0.00, G:0.03, T:0.71
Consensus pattern (10 bp):
TTTAATTTAT
Found at i:26878103 original size:21 final size:21
Alignment explanation
Indices: 26878075--26878122 Score: 73
Period size: 21 Copynumber: 2.3 Consensus size: 21
26878065 TATTAAGTAG
26878075 TTAA-TTTAATTTATTTTAG-T
1 TTAATTTTAATTTATTTT-GCT
26878095 TTAATTTTAATTTATTTTGCT
1 TTAATTTTAATTTATTTTGCT
26878116 TTAATTT
1 TTAATTT
26878123 ACTTTAAAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
20 5 0.19
21 21 0.81
ACGTcount: A:0.27, C:0.02, G:0.04, T:0.67
Consensus pattern (21 bp):
TTAATTTTAATTTATTTTGCT
Found at i:26882291 original size:39 final size:39
Alignment explanation
Indices: 26882248--26882417 Score: 195
Period size: 39 Copynumber: 4.4 Consensus size: 39
26882238 TAGTGTGTGA
* * *
26882248 TGTGGGAAAGTACACGCTGATGATATATGCCATGTGCGG
1 TGTGGGAAAGCACATGATGATGATATATGCCATGTGCGG
*
26882287 TGTGGGAGAA-CACATGATAATGATATATGCCATGTGCGG
1 TGTGGGA-AAGCACATGATGATGATATATGCCATGTGCGG
* **
26882326 TGTGGGAGAGCACATGATGATGATATATGCCATGTGCAA
1 TGTGGGAAAGCACATGATGATGATATATGCCATGTGCGG
** * *
26882365 TGTGGGAGTGCACATGAGGAT-AT-TA-GCTATGTGCGG
1 TGTGGGAAAGCACATGATGATGATATATGCCATGTGCGG
*
26882401 TGTGGGAGAGCACATGA
1 TGTGGGAAAGCACATGA
26882418 GCTAAATTGA
Statistics
Matches: 115, Mismatches: 14, Indels: 7
0.85 0.10 0.05
Matches are distributed among these distances:
36 24 0.21
37 2 0.02
38 3 0.03
39 84 0.73
40 2 0.02
ACGTcount: A:0.28, C:0.13, G:0.34, T:0.25
Consensus pattern (39 bp):
TGTGGGAAAGCACATGATGATGATATATGCCATGTGCGG
Found at i:26882415 original size:75 final size:78
Alignment explanation
Indices: 26882265--26882417 Score: 222
Period size: 78 Copynumber: 2.0 Consensus size: 78
26882255 AAGTACACGC
** *
26882265 TGATGATATATGCCATGTGCGGTGTGGGAGAACACATGATAATGATATATGCCATGTGCGGTGTG
1 TGATGATATATGCCATGTGCAATGTGGGAGAACACATGAGAATGATATATGCCATGTGCGGTGTG
26882330 GGAGAGCACATGA
66 GGAGAGCACATGA
** * *
26882343 TGATGATATATGCCATGTGCAATGTGGGAGTGCACATGAGGAT-AT-TA-GCTATGTGCGGTGTG
1 TGATGATATATGCCATGTGCAATGTGGGAGAACACATGAGAATGATATATGCCATGTGCGGTGTG
26882405 GGAGAGCACATGA
66 GGAGAGCACATGA
26882418 GCTAAATTGA
Statistics
Matches: 68, Mismatches: 7, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
75 27 0.40
76 2 0.03
77 2 0.03
78 37 0.54
ACGTcount: A:0.27, C:0.12, G:0.34, T:0.26
Consensus pattern (78 bp):
TGATGATATATGCCATGTGCAATGTGGGAGAACACATGAGAATGATATATGCCATGTGCGGTGTG
GGAGAGCACATGA
Found at i:26891641 original size:39 final size:39
Alignment explanation
Indices: 26891591--26891719 Score: 131
Period size: 39 Copynumber: 3.4 Consensus size: 39
26891581 GTGCCGGTAG
*
26891591 TGTGCGATGTGGGAGAGCACA-CACCGATGATATATGCCA
1 TGTGCGGTGTGGGAGAGCACATCA-CGATGATATATGCCA
* * *
26891630 TGTGCGGTGTGGGAGAGCACATGATGATGATTTATGCCA
1 TGTGCGGTGTGGGAGAGCACATCACGATGATATATGCCA
* * * * **
26891669 TGTGCAGTGTGGGAGTGCACATGAGGAT-AT-TA-GTTA
1 TGTGCGGTGTGGGAGAGCACATCACGATGATATATGCCA
26891705 TGTGCGGTGTGGGAG
1 TGTGCGGTGTGGGAG
26891720 TGCTCATGTG
Statistics
Matches: 79, Mismatches: 10, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
36 16 0.20
37 2 0.03
38 2 0.03
39 58 0.73
40 1 0.01
ACGTcount: A:0.23, C:0.13, G:0.37, T:0.26
Consensus pattern (39 bp):
TGTGCGGTGTGGGAGAGCACATCACGATGATATATGCCA
Found at i:26891715 original size:36 final size:39
Alignment explanation
Indices: 26891616--26891727 Score: 140
Period size: 39 Copynumber: 2.9 Consensus size: 39
26891606 AGCACACACC
* * *
26891616 GATGATATATGCCATGTGCGGTGTGGGAGAGCACATGAT
1 GATGATTTATGCCATGTGCGGTGTGGGAGTGCACATGAG
*
26891655 GATGATTTATGCCATGTGCAGTGTGGGAGTGCACATGAG
1 GATGATTTATGCCATGTGCGGTGTGGGAGTGCACATGAG
** *
26891694 GAT-A-TTA-GTTATGTGCGGTGTGGGAGTGCTCATG
1 GATGATTTATGCCATGTGCGGTGTGGGAGTGCACATG
26891728 TGCTGAGTTG
Statistics
Matches: 65, Mismatches: 8, Indels: 3
0.86 0.11 0.04
Matches are distributed among these distances:
36 23 0.35
37 3 0.05
38 1 0.02
39 38 0.58
ACGTcount: A:0.22, C:0.12, G:0.37, T:0.29
Consensus pattern (39 bp):
GATGATTTATGCCATGTGCGGTGTGGGAGTGCACATGAG
Found at i:26895747 original size:137 final size:133
Alignment explanation
Indices: 26895505--26895761 Score: 433
Period size: 137 Copynumber: 1.9 Consensus size: 133
26895495 TGATCCGATC
**
26895505 TAAATCTTGAAACTCTTATTTCAGCCAGTGTGAGGCTTTGTATGTTCACAAGCCATGATCATTAT
1 TAAATCTTGAAACTCTTATTTCAGCCAGTGTGAGGCTTTGTAAATTCACAAGCCATGATCATTAT
*
26895570 GAAAATTAAGTCTATCATAATGTTAAAAAAGCCCTTAAACTATTTAAAAAAATTTCACTAATCTG
66 GAAAATTAAGTCTATCATAATGTTAAAAAAGCCCTTAAACTATTCAAAAAAATTTCACTAATCTG
26895635 ATT
131 ATT
*
26895638 TAAATCTTGAAACTCTTATTTTAGCCAGTGTGAGGCTTCCTTTGTAAATTCACAAGCCATGATCA
1 TAAATCTTGAAACTCTTATTTCAGCCAGTGTGAGG----CTTTGTAAATTCACAAGCCATGATCA
*
26895703 TTATGAAAATTAAGTTTATCATAATGTTAAAAAAGCCCTTAAACTATTCAAAAAAATTT
62 TTATGAAAATTAAGTCTATCATAATGTTAAAAAAGCCCTTAAACTATTCAAAAAAATTT
26895762 GATATAAACC
Statistics
Matches: 115, Mismatches: 5, Indels: 4
0.93 0.04 0.03
Matches are distributed among these distances:
133 34 0.30
137 81 0.70
ACGTcount: A:0.37, C:0.16, G:0.12, T:0.35
Consensus pattern (133 bp):
TAAATCTTGAAACTCTTATTTCAGCCAGTGTGAGGCTTTGTAAATTCACAAGCCATGATCATTAT
GAAAATTAAGTCTATCATAATGTTAAAAAAGCCCTTAAACTATTCAAAAAAATTTCACTAATCTG
ATT
Found at i:26896112 original size:30 final size:30
Alignment explanation
Indices: 26896065--26896122 Score: 73
Period size: 30 Copynumber: 1.9 Consensus size: 30
26896055 AGTTATATAT
* *
26896065 GCTTATTTGGCTTAAAATACAAGCATAAGG
1 GCTTATTTAGCTTAAAATAAAAGCATAAGG
*
26896095 GCTTATTTAG-TTCAAAATAAAAGTATAA
1 GCTTATTTAGCTT-AAAATAAAAGCATAA
26896123 AGGTTTGATG
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 2 0.08
30 22 0.92
ACGTcount: A:0.41, C:0.10, G:0.16, T:0.33
Consensus pattern (30 bp):
GCTTATTTAGCTTAAAATAAAAGCATAAGG
Found at i:26896645 original size:26 final size:25
Alignment explanation
Indices: 26896608--26896714 Score: 117
Period size: 26 Copynumber: 4.1 Consensus size: 25
26896598 TTAATATAAT
*
26896608 TTTTTGTATTATATTTTTATTTTAA
1 TTTTTATATTATATTTTTATTTTAA
* *
26896633 TTTTTTTACTTATATTATATAAATTTTAA
1 TTTTTATA-TTATATT-T-T-TATTTTAA
*
26896662 TTTCTTATATTTTA-TTTTATTTTAA
1 TTT-TTATATTATATTTTTATTTTAA
26896687 TTTTTATATTATATATTTTATTTTAA
1 TTTTTATATTATAT-TTTTATTTTAA
26896713 TT
1 TT
26896715 ATAACGTTAC
Statistics
Matches: 69, Mismatches: 6, Indels: 13
0.78 0.07 0.15
Matches are distributed among these distances:
24 9 0.13
25 17 0.25
26 21 0.30
27 2 0.03
28 2 0.03
29 14 0.20
30 4 0.06
ACGTcount: A:0.28, C:0.02, G:0.01, T:0.69
Consensus pattern (25 bp):
TTTTTATATTATATTTTTATTTTAA
Found at i:26896648 original size:20 final size:20
Alignment explanation
Indices: 26896625--26896685 Score: 52
Period size: 24 Copynumber: 2.8 Consensus size: 20
26896615 ATTATATTTT
26896625 TATTTTAATTTTTTTACTTA
1 TATTTTAATTTTTTTACTTA
26896645 TATTATATAAATTTTAATTT-CTTA
1 TATT-T-T-AATTTT--TTTACTTA
*
26896669 TATTTTATTTTATTTTA
1 TATTTTAATTT-TTTTA
26896686 ATTTTTATAT
Statistics
Matches: 33, Mismatches: 1, Indels: 13
0.70 0.02 0.28
Matches are distributed among these distances:
20 7 0.21
21 5 0.15
22 3 0.09
23 7 0.21
24 8 0.24
25 3 0.09
ACGTcount: A:0.30, C:0.03, G:0.00, T:0.67
Consensus pattern (20 bp):
TATTTTAATTTTTTTACTTA
Found at i:26896653 original size:48 final size:45
Alignment explanation
Indices: 26896580--26896709 Score: 119
Period size: 48 Copynumber: 2.8 Consensus size: 45
26896570 TAATGTCATA
26896580 TATTTTATTTTTATTTCTT-TA--ATATAATTTT-TTGTATTATATTTT
1 TATTTTA-TTTTATTT-TTATATTATATAATTTTATT-TATTATA-TTT
*
26896625 TATTTTAATTTT-TTTACTTATATTATATAAATTTTAATTTCTTATATTT
1 TATTTT-ATTTTATTT--TTATATTATAT-AATTTT-ATTTATTATATTT
26896674 TATTTTATTTTAATTTTTATATTATAT-ATTTTATTT
1 TATTTTATTTT-ATTTTTATATTATATAATTTTATTT
26896710 TAATTATAAC
Statistics
Matches: 74, Mismatches: 1, Indels: 20
0.78 0.01 0.21
Matches are distributed among these distances:
44 3 0.04
45 17 0.23
46 8 0.11
48 20 0.27
49 15 0.20
50 9 0.12
51 2 0.03
ACGTcount: A:0.28, C:0.02, G:0.01, T:0.69
Consensus pattern (45 bp):
TATTTTATTTTATTTTTATATTATATAATTTTATTTATTATATTT
Found at i:26897526 original size:14 final size:14
Alignment explanation
Indices: 26897507--26897546 Score: 66
Period size: 12 Copynumber: 3.0 Consensus size: 14
26897497 AGTTTCATTC
26897507 CATATATATACATA
1 CATATATATACATA
26897521 C--ATATATACATA
1 CATATATATACATA
26897533 CATATATATACATA
1 CATATATATACATA
26897547 TTTGTGTGTA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
12 12 0.50
14 12 0.50
ACGTcount: A:0.50, C:0.15, G:0.00, T:0.35
Consensus pattern (14 bp):
CATATATATACATA
Found at i:26898824 original size:18 final size:18
Alignment explanation
Indices: 26898795--26898831 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
26898785 GGGTTTAATT
26898795 AATTTAATAATTATTATAA
1 AATTTAATAATTATT-TAA
26898814 AATTT-ATAATTATTTAA
1 AATTTAATAATTATTTAA
26898831 A
1 A
26898832 TTAATTAAGA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 4 0.22
18 9 0.50
19 5 0.28
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (18 bp):
AATTTAATAATTATTTAA
Found at i:26903616 original size:77 final size:77
Alignment explanation
Indices: 26903441--26903655 Score: 295
Period size: 77 Copynumber: 2.7 Consensus size: 77
26903431 AATATGTTAA
* * * *
26903441 ATTTACATATTGGCACCATTATACCTTCATGTATAGTAGGAATGCCACATGCCTCTCACTTATCA
1 ATTTACATATTGGCATCATTATACCTTAATGTATAATAGGAATGCCACATG--TC-CAC-CATCA
*
26903506 CGTGGACCTTGATGGT
62 CATGGACCTTGATGGT
* *
26903522 ATTTACATATTAGCATCATTATACCTTAATGTATAATAAGAATGCCACATGTCCACCATCACATG
1 ATTTACATATTGGCATCATTATACCTTAATGTATAATAGGAATGCCACATGTCCACCATCACATG
26903587 GACCTTGATGGT
66 GACCTTGATGGT
* * * *
26903599 ATTTATATTTTGGCATCATTATACCTTAATGTATAACAGGAATGCCATATGTCCACC
1 ATTTACATATTGGCATCATTATACCTTAATGTATAATAGGAATGCCACATGTCCACC
26903656 TTTTGTAAAG
Statistics
Matches: 121, Mismatches: 13, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
77 70 0.58
78 3 0.02
79 2 0.02
81 46 0.38
ACGTcount: A:0.30, C:0.21, G:0.14, T:0.34
Consensus pattern (77 bp):
ATTTACATATTGGCATCATTATACCTTAATGTATAATAGGAATGCCACATGTCCACCATCACATG
GACCTTGATGGT
Found at i:26926849 original size:52 final size:52
Alignment explanation
Indices: 26926783--26926913 Score: 201
Period size: 52 Copynumber: 2.5 Consensus size: 52
26926773 AGGATTTGCT
*
26926783 GCTGGAGCGAGGGAAAGAAGAGCTGAGCGGAGGAATAGAGAGAGGAGCGGCA
1 GCTGGCGCGAGGGAAAGAAGAGCTGAGCGGAGGAATAGAGAGAGGAGCGGCA
* * *
26926835 GCTGGCGCAAGGGAAAGAAAAGCTGAGCGGAGGAATAGAGAGAGGAGCGGCG
1 GCTGGCGCGAGGGAAAGAAGAGCTGAGCGGAGGAATAGAGAGAGGAGCGGCA
* *
26926887 GCTGACGCGAGGGAAGGAAGAG-TGAGC
1 GCTGGCGCGAGGGAAAGAAGAGCTGAGC
26926914 ATAGTGTCAC
Statistics
Matches: 71, Mismatches: 8, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
51 5 0.07
52 66 0.93
ACGTcount: A:0.34, C:0.13, G:0.47, T:0.06
Consensus pattern (52 bp):
GCTGGCGCGAGGGAAAGAAGAGCTGAGCGGAGGAATAGAGAGAGGAGCGGCA
Found at i:26927464 original size:2 final size:2
Alignment explanation
Indices: 26927457--26927486 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
26927447 GAATATAGGA
26927457 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
26927487 NNNNNNNNNN
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:26940263 original size:12 final size:12
Alignment explanation
Indices: 26940246--26940292 Score: 60
Period size: 12 Copynumber: 3.8 Consensus size: 12
26940236 CTATTTTTTT
26940246 AAATTAATAAAA
1 AAATTAATAAAA
*
26940258 AAATTAAT-TAA
1 AAATTAATAAAA
26940269 AAATTAATAAAA
1 AAATTAATAAAA
26940281 AATATATAATAA
1 AA-AT-TAATAA
26940293 TAATTTTTAA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
11 10 0.33
12 12 0.40
13 2 0.07
14 6 0.20
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (12 bp):
AAATTAATAAAA
Found at i:26940272 original size:11 final size:11
Alignment explanation
Indices: 26940246--26940283 Score: 58
Period size: 11 Copynumber: 3.4 Consensus size: 11
26940236 CTATTTTTTT
26940246 AAATTAATAAAA
1 AAATTAAT-AAA
*
26940258 AAATTAATTAA
1 AAATTAATAAA
26940269 AAATTAATAAA
1 AAATTAATAAA
26940280 AAAT
1 AAAT
26940284 ATATAATAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
11 16 0.67
12 8 0.33
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (11 bp):
AAATTAATAAA
Found at i:26946565 original size:15 final size:15
Alignment explanation
Indices: 26946545--26946577 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
26946535 CAATAAGACT
*
26946545 TTAGACATTAATGCC
1 TTAGACAATAATGCC
26946560 TTAGACAATAATGCC
1 TTAGACAATAATGCC
26946575 TTA
1 TTA
26946578 AATAGTAACG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.36, C:0.18, G:0.12, T:0.33
Consensus pattern (15 bp):
TTAGACAATAATGCC
Found at i:26947569 original size:20 final size:20
Alignment explanation
Indices: 26947532--26947569 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
26947522 CTTTTTTTTA
*
26947532 ATTTATTTTATTGTTTATTT
1 ATTTATTTTATTGATTATTT
26947552 ATTTATTATTATT-ATTAT
1 ATTTATT-TTATTGATTAT
26947570 CGATGCATGA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
20 11 0.69
21 5 0.31
ACGTcount: A:0.26, C:0.00, G:0.03, T:0.71
Consensus pattern (20 bp):
ATTTATTTTATTGATTATTT
Found at i:26948759 original size:20 final size:20
Alignment explanation
Indices: 26948734--26948773 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
26948724 TTCTAGATCA
*
26948734 AATGTATCGATACATTTTGG
1 AATGTATCCATACATTTTGG
26948754 AATGTATCCATACATTTTGG
1 AATGTATCCATACATTTTGG
26948774 GCAAAACCAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.30, C:0.12, G:0.17, T:0.40
Consensus pattern (20 bp):
AATGTATCCATACATTTTGG
Found at i:26948937 original size:21 final size:20
Alignment explanation
Indices: 26948913--26948962 Score: 64
Period size: 21 Copynumber: 2.4 Consensus size: 20
26948903 TGCAAGGGAG
26948913 GTTTAAAACTAATTTAAACAA
1 GTTTAAAACT-ATTTAAACAA
*
26948934 GTTTAAATGCTATTTAAACAA
1 GTTTAAA-ACTATTTAAACAA
*
26948955 GTTCAAAA
1 GTTTAAAA
26948963 ATTATTAAAG
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
21 23 0.92
22 2 0.08
ACGTcount: A:0.48, C:0.10, G:0.08, T:0.34
Consensus pattern (20 bp):
GTTTAAAACTATTTAAACAA
Found at i:26948968 original size:21 final size:21
Alignment explanation
Indices: 26948917--26948968 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 21
26948907 AGGGAGGTTT
*
26948917 AAAACTAATTTAAACAAGTTTA
1 AAAACT-ATTTAAACAAGTTCA
**
26948939 AATGCTATTTAAACAAGTTCA
1 AAAACTATTTAAACAAGTTCA
*
26948960 AAAATTATT
1 AAAACTATT
26948969 AAAGCAATTT
Statistics
Matches: 24, Mismatches: 6, Indels: 1
0.77 0.19 0.03
Matches are distributed among these distances:
21 20 0.83
22 4 0.17
ACGTcount: A:0.50, C:0.10, G:0.06, T:0.35
Consensus pattern (21 bp):
AAAACTATTTAAACAAGTTCA
Found at i:26949074 original size:21 final size:21
Alignment explanation
Indices: 26949050--26949112 Score: 81
Period size: 21 Copynumber: 3.0 Consensus size: 21
26949040 TTATTTAGAA
26949050 AAGTTTAAAAACTATTCAAAC
1 AAGTTTAAAAACTATTCAAAC
**
26949071 AAGTGCAAAAACTCATTCAAAC
1 AAGTTTAAAAACT-ATTCAAAC
* *
26949093 AAATTTAAAAATTATTCAAA
1 AAGTTTAAAAACTATTCAAA
26949113 TAAGCTCAAA
Statistics
Matches: 35, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
21 18 0.51
22 17 0.49
ACGTcount: A:0.54, C:0.14, G:0.05, T:0.27
Consensus pattern (21 bp):
AAGTTTAAAAACTATTCAAAC
Found at i:26949102 original size:22 final size:21
Alignment explanation
Indices: 26949053--26949112 Score: 75
Period size: 22 Copynumber: 2.8 Consensus size: 21
26949043 TTTAGAAAAG
*
26949053 TTTAAAAACTATTCAAACAAG
1 TTTAAAAACTATTCAAACAAA
**
26949074 TGCAAAAACTCATTCAAACAAA
1 TTTAAAAACT-ATTCAAACAAA
*
26949096 TTTAAAAATTATTCAAA
1 TTTAAAAACTATTCAAA
26949113 TAAGCTCAAA
Statistics
Matches: 32, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
21 15 0.47
22 17 0.53
ACGTcount: A:0.53, C:0.15, G:0.03, T:0.28
Consensus pattern (21 bp):
TTTAAAAACTATTCAAACAAA
Found at i:26949252 original size:21 final size:21
Alignment explanation
Indices: 26949228--26949292 Score: 76
Period size: 21 Copynumber: 3.1 Consensus size: 21
26949218 CAAAAACATT
* *
26949228 TTCAAACAACTTCAAAAATCA
1 TTCAAACAAGTTCAAAGATCA
* *
26949249 TTCAAATAAGTTCAAGGATCA
1 TTCAAACAAGTTCAAAGATCA
* *
26949270 CTCAAAGAAGTTCAAAGATCA
1 TTCAAACAAGTTCAAAGATCA
26949291 TT
1 TT
26949293 GAAGCAATTT
Statistics
Matches: 36, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 36 1.00
ACGTcount: A:0.46, C:0.18, G:0.09, T:0.26
Consensus pattern (21 bp):
TTCAAACAAGTTCAAAGATCA
Found at i:26953375 original size:20 final size:20
Alignment explanation
Indices: 26953342--26953383 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
26953332 GGAAGAAGAA
*
26953342 GAAGAAGCTACTGGAGAAAT
1 GAAGAAGCTACTGGAAAAAT
* *
26953362 GAAGATGCTGCTGGAAAAAT
1 GAAGAAGCTACTGGAAAAAT
26953382 GA
1 GA
26953384 TATTTATAGC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.43, C:0.10, G:0.31, T:0.17
Consensus pattern (20 bp):
GAAGAAGCTACTGGAAAAAT
Found at i:26955526 original size:140 final size:137
Alignment explanation
Indices: 26955266--26955543 Score: 497
Period size: 140 Copynumber: 2.0 Consensus size: 137
26955256 AATTAACCGA
26955266 GTAAATGTCCCATTTTTGACCGAATTTTCCAAGGAGGAAAGTGAGCTGATTTTGGTGATTTTATA
1 GTAAATGTCCCATTTTTGACCGAATTTTCCAAGGAGGAAAGTGAGCTGATTTTGGTGATTTTATA
26955331 AGGTTATTGGCTGATATTAATGGTAGAAATGTTGTGGAGAAAAATGGGACAAATTTAGAAGCTAA
66 AGGTTATTGGCTGATATTAATGGTAGAAATGTTGTGGAGAAAAATGGGACAAATTTAG-AGCT-A
26955396 AAATGGAGC
129 AAATGGAGC
26955405 GNTAAATGTCCCATTTTTGACCGAATTTTCCAAGGAGGAAAGTGAGCTGATTTTGGTGATTTTAT
1 G-TAAATGTCCCATTTTTGACCGAATTTTCCAAGGAGGAAAGTGAGCTGATTTTGGTGATTTTAT
26955470 AAGGTTATTGGCTGATATTTAATGGTTAGAAATGTTGTGGAG-AAAATGGGAC-AATTTAGAGCT
65 AAGGTTATTGGCTGATA-TTAATGG-TAGAAATGTTGTGGAGAAAAATGGGACAAATTTAGAGCT
26955533 AAAATGGAGC
128 AAAATGGAGC
26955543 G
1 G
26955544 CATTAGTAAT
Statistics
Matches: 136, Mismatches: 0, Indels: 7
0.95 0.00 0.05
Matches are distributed among these distances:
138 11 0.08
139 5 0.04
140 87 0.64
141 17 0.12
142 16 0.12
ACGTcount: A:0.32, C:0.09, G:0.26, T:0.32
Consensus pattern (137 bp):
GTAAATGTCCCATTTTTGACCGAATTTTCCAAGGAGGAAAGTGAGCTGATTTTGGTGATTTTATA
AGGTTATTGGCTGATATTAATGGTAGAAATGTTGTGGAGAAAAATGGGACAAATTTAGAGCTAAA
ATGGAGC
Found at i:26965771 original size:20 final size:20
Alignment explanation
Indices: 26965746--26965785 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
26965736 TGAAAAATGG
26965746 CATCAATGTCAAATTTTCAT
1 CATCAATGTCAAATTTTCAT
26965766 CATCAATGTCAAATTTTCAT
1 CATCAATGTCAAATTTTCAT
26965786 ACTGAATATC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.35, C:0.20, G:0.05, T:0.40
Consensus pattern (20 bp):
CATCAATGTCAAATTTTCAT
Found at i:26972006 original size:43 final size:43
Alignment explanation
Indices: 26971936--26972097 Score: 193
Period size: 43 Copynumber: 3.8 Consensus size: 43
26971926 GTAATTATGT
* * * * *
26971936 TGACTCAGCTATGTGTGAGTAGAGAGTGTGCATAAGCCGAGGA
1 TGACCCAGCTATGTGCGAGTAGGGAGTGCGCATAACCCGAGGA
*
26971979 TGACCCAGTTATGTGCGAGTAGGGAGTGCGCATAACCCG-GTGA
1 TGACCCAGCTATGTGCGAGTAGGGAGTGCGCATAACCCGAG-GA
* * * *
26972022 TGACCC-GATTACGTGAGAGTAGGGAGTGCGCATAACCCGATGA
1 TGACCCAG-CTATGTGCGAGTAGGGAGTGCGCATAACCCGAGGA
*
26972065 TGACCCAGCTATGTGCGAGTAAGGAGTGCGCAT
1 TGACCCAGCTATGTGCGAGTAGGGAGTGCGCAT
26972098 GAGCTGGCGA
Statistics
Matches: 102, Mismatches: 13, Indels: 8
0.83 0.11 0.07
Matches are distributed among these distances:
42 2 0.02
43 99 0.97
44 1 0.01
ACGTcount: A:0.26, C:0.19, G:0.34, T:0.21
Consensus pattern (43 bp):
TGACCCAGCTATGTGCGAGTAGGGAGTGCGCATAACCCGAGGA
Found at i:26981979 original size:19 final size:19
Alignment explanation
Indices: 26981955--26981992 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
26981945 CCTATGCCTA
26981955 AGTTAATTATCTTCTTCCT
1 AGTTAATTATCTTCTTCCT
26981974 AGTTAATTATCTTCTTCCT
1 AGTTAATTATCTTCTTCCT
26981993 TTCTAGCCAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.21, C:0.21, G:0.05, T:0.53
Consensus pattern (19 bp):
AGTTAATTATCTTCTTCCT
Found at i:26984183 original size:2 final size:2
Alignment explanation
Indices: 26984178--26984203 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
26984168 TAATGTGTGC
26984178 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
26984204 TTCATAAAAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:26988182 original size:16 final size:16
Alignment explanation
Indices: 26988143--26988188 Score: 56
Period size: 16 Copynumber: 2.9 Consensus size: 16
26988133 AAACCAAAAA
26988143 TTAGATTTTGATTGTT
1 TTAGATTTTGATTGTT
* *
26988159 TTGGATTTTGATTTTT
1 TTAGATTTTGATTGTT
* *
26988175 TTATATTTTTATTG
1 TTAGATTTTGATTG
26988189 AATCCAAATG
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.17, C:0.00, G:0.15, T:0.67
Consensus pattern (16 bp):
TTAGATTTTGATTGTT
Found at i:27001579 original size:46 final size:46
Alignment explanation
Indices: 27001508--27001596 Score: 169
Period size: 46 Copynumber: 1.9 Consensus size: 46
27001498 AATTTTTACT
27001508 AAGTACTAAAATCTTATAACAAATCAATCTTATTTAAGTAATCGAG
1 AAGTACTAAAATCTTATAACAAATCAATCTTATTTAAGTAATCGAG
*
27001554 AAGTACTAAAATCTTATAACCAATCAATCTTATTTAAGTAATC
1 AAGTACTAAAATCTTATAACAAATCAATCTTATTTAAGTAATC
27001597 AAGATTTGTA
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
46 42 1.00
ACGTcount: A:0.45, C:0.15, G:0.07, T:0.34
Consensus pattern (46 bp):
AAGTACTAAAATCTTATAACAAATCAATCTTATTTAAGTAATCGAG
Found at i:27019696 original size:22 final size:20
Alignment explanation
Indices: 27019671--27019722 Score: 54
Period size: 22 Copynumber: 2.6 Consensus size: 20
27019661 GAAAAATTAG
*
27019671 ATATTATATATTGTAAAAAATT
1 ATATTATAAATT-T-AAAAATT
*
27019693 ATATTTTAAATTTAAAAATT
1 ATATTATAAATTTAAAAATT
27019713 A-ATTA-AAATT
1 ATATTATAAATT
27019723 ATTAATATTT
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
18 5 0.19
19 3 0.11
20 8 0.30
21 1 0.04
22 10 0.37
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (20 bp):
ATATTATAAATTTAAAAATT
Found at i:27019777 original size:20 final size:20
Alignment explanation
Indices: 27019752--27019815 Score: 67
Period size: 20 Copynumber: 3.1 Consensus size: 20
27019742 TTATATTAAA
27019752 ATTTTAAATAAAATAATAAT
1 ATTTTAAATAAAATAATAAT
*
27019772 ATTTTAAAATATTAATGAATAA-
1 ATTTT-AAATA-AAAT-AATAAT
* *
27019794 ATTATAAATAAAATATTAAT
1 ATTTTAAATAAAATAATAAT
27019814 AT
1 AT
27019816 CGAAATTGAA
Statistics
Matches: 36, Mismatches: 4, Indels: 8
0.75 0.08 0.17
Matches are distributed among these distances:
19 4 0.11
20 10 0.28
21 10 0.28
22 7 0.19
23 5 0.14
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.41
Consensus pattern (20 bp):
ATTTTAAATAAAATAATAAT
Found at i:27019995 original size:15 final size:15
Alignment explanation
Indices: 27019960--27020003 Score: 54
Period size: 15 Copynumber: 2.9 Consensus size: 15
27019950 AAATTATAAA
27019960 TAAAATATTAATATTT
1 TAAAATATTAATA-TT
27019976 TAAAATATTAATGA-T
1 TAAAATATTAAT-ATT
*
27019991 TAAAATATAAATA
1 TAAAATATTAATA
27020004 AAATATTAAC
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
14 1 0.04
15 12 0.46
16 12 0.46
17 1 0.04
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (15 bp):
TAAAATATTAATATT
Found at i:27020032 original size:41 final size:42
Alignment explanation
Indices: 27019948--27020049 Score: 127
Period size: 42 Copynumber: 2.4 Consensus size: 42
27019938 CATAATACAT
* * *
27019948 TTAAATTATAAATAAAATATTAATATTTTAAAATATTAATGA
1 TTAAATTATAAATAAAATATTAACATCTTAAAATATCAATGA
*
27019990 TTAAAATATAAATAAAATATTAACA-CTT-AAATAATCAATGA
1 TTAAATTATAAATAAAATATTAACATCTTAAAAT-ATCAATGA
*
27020031 TTAATATTTTAAATAAAAT
1 TTAA-ATTATAAATAAAAT
27020050 TATAAAATAT
Statistics
Matches: 52, Mismatches: 6, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
40 4 0.08
41 13 0.25
42 35 0.67
ACGTcount: A:0.56, C:0.03, G:0.02, T:0.39
Consensus pattern (42 bp):
TTAAATTATAAATAAAATATTAACATCTTAAAATATCAATGA
Found at i:27031044 original size:20 final size:20
Alignment explanation
Indices: 27031021--27031068 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 20
27031011 AAATAATAAT
*
27031021 TAAAATAAGATAAATTAACA
1 TAAAATAAAATAAATTAACA
* *
27031041 TAAAATAAAATAACTTAATA
1 TAAAATAAAATAAATTAACA
27031061 -AAAATAAA
1 TAAAATAAA
27031069 CTAATTAGAA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
19 8 0.32
20 17 0.68
ACGTcount: A:0.69, C:0.04, G:0.02, T:0.25
Consensus pattern (20 bp):
TAAAATAAAATAAATTAACA
Found at i:27031066 original size:14 final size:13
Alignment explanation
Indices: 27031047--27031098 Score: 52
Period size: 14 Copynumber: 3.8 Consensus size: 13
27031037 AACATAAAAT
27031047 AAAATAACTTAATA
1 AAAATAAC-TAATA
*
27031061 AAAATAAACTAATT
1 AAAAT-AACTAATA
*
27031075 AGAATAA-TAACTA
1 AAAATAACTAA-TA
27031088 AAAATAACTAA
1 AAAATAACTAA
27031099 ATCCTAACCT
Statistics
Matches: 31, Mismatches: 4, Indels: 6
0.76 0.10 0.15
Matches are distributed among these distances:
12 3 0.10
13 9 0.29
14 16 0.52
15 3 0.10
ACGTcount: A:0.65, C:0.08, G:0.02, T:0.25
Consensus pattern (13 bp):
AAAATAACTAATA
Found at i:27031669 original size:8 final size:8
Alignment explanation
Indices: 27031653--27031688 Score: 54
Period size: 8 Copynumber: 4.5 Consensus size: 8
27031643 TTATCCAAAG
*
27031653 TTTTATAA
1 TTTTTTAA
27031661 TTTTTTAA
1 TTTTTTAA
*
27031669 TTTTGTAA
1 TTTTTTAA
27031677 TTTTTTAA
1 TTTTTTAA
27031685 TTTT
1 TTTT
27031689 ATGTTGGTTA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
8 25 1.00
ACGTcount: A:0.25, C:0.00, G:0.03, T:0.72
Consensus pattern (8 bp):
TTTTTTAA
Found at i:27031677 original size:16 final size:16
Alignment explanation
Indices: 27031653--27031690 Score: 67
Period size: 16 Copynumber: 2.4 Consensus size: 16
27031643 TTATCCAAAG
27031653 TTTTATAATTTTTTAA
1 TTTTATAATTTTTTAA
*
27031669 TTTTGTAATTTTTTAA
1 TTTTATAATTTTTTAA
27031685 TTTTAT
1 TTTTAT
27031691 GTTGGTTATT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.26, C:0.00, G:0.03, T:0.71
Consensus pattern (16 bp):
TTTTATAATTTTTTAA
Found at i:27033706 original size:34 final size:34
Alignment explanation
Indices: 27033663--27033817 Score: 103
Period size: 34 Copynumber: 4.3 Consensus size: 34
27033653 ACCAAAGCTT
27033663 CAGATGTTACATGCCAAGACCAAAGCCTAAGCAC
1 CAGATGTTACATGCCAAGACCAAAGCCTAAGCAC
** * * *
27033697 CAGATGTTACACGCTAAAGCCAAAGCACCAAAATCAAAGTAG
1 CAGATGTTACA---T---GCC-AAG-ACCAAAGCCTAAGCAC
* * ** * * *
27033739 AAGATGTTACATGCTAAGGTCAAAGCTTTAGTAC
1 CAGATGTTACATGCCAAGACCAAAGCCTAAGCAC
* * *
27033773 TAGATGTTACATGCCAAGACCAAAGCTTCAGCAC
1 CAGATGTTACATGCCAAGACCAAAGCCTAAGCAC
27033807 CAGATGTTACA
1 CAGATGTTACA
27033818 CACCAAAGCT
Statistics
Matches: 91, Mismatches: 22, Indels: 16
0.71 0.17 0.12
Matches are distributed among these distances:
34 57 0.63
35 3 0.03
36 2 0.02
37 1 0.01
39 1 0.01
40 3 0.03
41 3 0.03
42 21 0.23
ACGTcount: A:0.39, C:0.23, G:0.18, T:0.20
Consensus pattern (34 bp):
CAGATGTTACATGCCAAGACCAAAGCCTAAGCAC
Found at i:27040600 original size:15 final size:15
Alignment explanation
Indices: 27040580--27040615 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
27040570 GAGATTTTGG
27040580 TTTTAAAGCTTTAGA
1 TTTTAAAGCTTTAGA
* *
27040595 TTTTAAAGTTTTTGA
1 TTTTAAAGCTTTAGA
27040610 TTTTAA
1 TTTTAA
27040616 GGTTGTTTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.31, C:0.03, G:0.11, T:0.56
Consensus pattern (15 bp):
TTTTAAAGCTTTAGA
Found at i:27047383 original size:22 final size:22
Alignment explanation
Indices: 27047358--27047426 Score: 111
Period size: 22 Copynumber: 3.1 Consensus size: 22
27047348 TAGGCATTAA
*
27047358 GTGAATGGATATTATGTATTGT
1 GTGAATGGATATTATGCATTGT
27047380 GTGAATGGATATTATGCATTGT
1 GTGAATGGATATTATGCATTGT
* *
27047402 ATGAATGGATATTAGGCATTGT
1 GTGAATGGATATTATGCATTGT
27047424 GTG
1 GTG
27047427 TCTGGTTGTT
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 43 1.00
ACGTcount: A:0.28, C:0.03, G:0.29, T:0.41
Consensus pattern (22 bp):
GTGAATGGATATTATGCATTGT
Found at i:27047793 original size:211 final size:209
Alignment explanation
Indices: 27047413--27048064 Score: 705
Period size: 211 Copynumber: 3.1 Consensus size: 209
27047403 TGAATGGATA
* * * * * * * *
27047413 TTAGGCATTGTGTGTCTGGTTGTTATGTATTCCGTGACTGATTTTTATGTATTACGTGAC-GTAG
1 TTAGGCATTGCGTGACTGGTTTTTATGTATTCCGTGACTTATTGTTATGAATTATGTGACATTA-
** * * * ** * * *
27047477 GGCCAATGCATA-ACTGGGTATTTTTTCATAACTTGAGTGGATGTTAGGCATT-ACGTGACTTAT
65 GGCCAAAACA-AGAATGGTTATGTTGGCATAACGTGAGTGGATATTAAGCATTGA-GTGACTTAT
** *
27047540 TATTAGGTATTGCGAGACTGGCTTAAAGGCACTGCATGAATTGTGCAATGCATATCTTGTTTTGA
128 TATTAGGTATTGCGAGACTGGCTT-AAGGTGCT-CGTGAATTGTGCAATGCATATCTTGTTTTGA
27047605 GACATTTCTTGACTACTTTT
191 GACATTTCTTGACTAC-TTT
* * *
27047625 TTAGGCATTACGTGACTGGTTTTTATGTATTCCG-GTCTTATTGTTATGAATTGTGTGACATTAG
1 TTAGGCATTGCGTGACTGGTTTTTATGTATTCCGTGACTTATTGTTATGAATTATGTGACATTAG
** * *
27047689 GCCAAAACGTGATTGGTTATGTTGGCATAATGTGAGTGGATATTAAGCATTGAGTGACTTATTAT
66 GCCAAAACAAGAATGGTTATGTTGGCATAACGTGAGTGGATATTAAGCATTGAGTGACTTATTAT
* * * * *
27047754 TAGATATTGCAAGACTGGCTTATAGGTGCTACGTGAATTGTGTAATGCATATCTTGTTTTAAGAT
131 TAGGTATTGCGAGACTGGCTTA-AGGTGCT-CGTGAATTGTGCAATGCATATCTTGTTTTGAGAC
27047819 ATTTCTTGACTACTTT
194 ATTTCTTGACTACTTT
* * * * * *
27047835 TTAGGCATTGCGTGACTGGTTCTTATGTGTTTCGTGACTTGTTGTTATGTATTATGTGACATTGG
1 TTAGGCATTGCGTGACTGGTTTTTATGTATTCCGTGACTTATTGTTATGAATTATGTGACATTAG
*
27047900 GCCAATACAAGAATGGTTATGTTGGCATAACGTGAGTGGATATTAAGCATTGAGTGACTTATTAT
66 GCCAAAACAAGAATGGTTATGTTGGCATAACGTGAGTGGATATTAAGCATTGAGTGACTTATTAT
* * * *
27047965 TAGGTATTGTGAGACTGGC----GATG-T-GTGACTTGTGCAATGCATCTCTTGTTTTGA-AGCA
131 TAGGTATTGCGAGACTGGCTTAAGGTGCTCGTGAATTGTGCAATGCATATCTTGTTTTGAGA-CA
* *
27048023 TTTCTTCACTAGTTT
195 TTTCTTGACTACTTT
* * *
27048038 TTAGGCATTGCATAAGTGGTTTTTATG
1 TTAGGCATTGCGTGACTGGTTTTTATG
27048065 CATTGAGGGG
Statistics
Matches: 372, Mismatches: 62, Indels: 21
0.82 0.14 0.05
Matches are distributed among these distances:
202 1 0.00
203 63 0.17
205 1 0.00
206 3 0.01
210 34 0.09
211 237 0.64
212 33 0.09
ACGTcount: A:0.23, C:0.12, G:0.24, T:0.40
Consensus pattern (209 bp):
TTAGGCATTGCGTGACTGGTTTTTATGTATTCCGTGACTTATTGTTATGAATTATGTGACATTAG
GCCAAAACAAGAATGGTTATGTTGGCATAACGTGAGTGGATATTAAGCATTGAGTGACTTATTAT
TAGGTATTGCGAGACTGGCTTAAGGTGCTCGTGAATTGTGCAATGCATATCTTGTTTTGAGACAT
TTCTTGACTACTTT
Found at i:27047894 original size:22 final size:22
Alignment explanation
Indices: 27047845--27047887 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
27047835 TTAGGCATTG
*
27047845 CGTGACTGGTTCTTATGTGTTT
1 CGTGACTGGTTCTTATGTATTT
* *
27047867 CGTGACTTGTTGTTATGTATT
1 CGTGACTGGTTCTTATGTATT
27047888 ATGTGACATT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.12, C:0.12, G:0.26, T:0.51
Consensus pattern (22 bp):
CGTGACTGGTTCTTATGTATTT
Found at i:27052493 original size:17 final size:18
Alignment explanation
Indices: 27052468--27052507 Score: 55
Period size: 17 Copynumber: 2.3 Consensus size: 18
27052458 AATTTCGACT
* *
27052468 TTTACATTTGTTTTT-AA
1 TTTAAATTTCTTTTTAAA
27052485 TTTAAATTTCTTTTTAAA
1 TTTAAATTTCTTTTTAAA
27052503 TTTAA
1 TTTAA
27052508 TTAAGGAACT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 13 0.65
18 7 0.35
ACGTcount: A:0.30, C:0.05, G:0.03, T:0.62
Consensus pattern (18 bp):
TTTAAATTTCTTTTTAAA
Done.