Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr05 97880472
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: 97880472
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 192 characters in sequence are not A, C, G, or T
File 158 of 335
Found at i:46417183 original size:119 final size:119
Alignment explanation
Indices: 46416972--46417570 Score: 1038
Period size: 119 Copynumber: 5.0 Consensus size: 119
46416962 CTTGAGTCTG
* * * * * * *
46416972 TTTGAGAACATTTGAGAGTCATATCTGCAATGTCCTCGATTTGTTCCTTGTAAGCACAAGGATGC
1 TTTGAGAACGTCTGAGAGTCAAATCTGCTATGTCCTCGATTTGTTCCTTGTAAACACAAGAATAC
46417037 CAAATCATCTTGGATCTGCTTCAGTATAAACATCTGAAGGTTAGATCTGCTATA
66 CAAATCATCTTGGATCTGCTTCAGTATAAACATCTGAAGGTTAGATCTGCTATA
* *
46417091 TTTGAGAATGTCTGAGAGTCAAATCTGCTATGTCCTCGATTTGTTTCTTGTAAACACAAGAATAC
1 TTTGAGAACGTCTGAGAGTCAAATCTGCTATGTCCTCGATTTGTTCCTTGTAAACACAAGAATAC
** * *
46417156 CAAATCATCTTGGATCTATTTCAGTATAAACATCTGAATGTTAGATCTGTTATA
66 CAAATCATCTTGGATCTGCTTCAGTATAAACATCTGAAGGTTAGATCTGCTATA
46417210 TTTGAGAACGTCTGAGAGTCAAATCTGCTATGTCCTCGATTTGTTCCTTGTAAACACAAGAATAC
1 TTTGAGAACGTCTGAGAGTCAAATCTGCTATGTCCTCGATTTGTTCCTTGTAAACACAAGAATAC
* *
46417275 CAAATCATCTTGGATCTGCTTCAGTATAAACATCTAAAGGTTAGATCTGTTATA
66 CAAATCATCTTGGATCTGCTTCAGTATAAACATCTGAAGGTTAGATCTGCTATA
46417329 TTTGAGAACGTCTGAGAGTCAAATCTGCTATGTCCTC-ATTTGTTCCTTGTAAACACAAGAATAC
1 TTTGAGAACGTCTGAGAGTCAAATCTGCTATGTCCTCGATTTGTTCCTTGTAAACACAAGAATAC
46417393 CAAATCATCTTGGATCTGCTTCAGTATAAACATCTGAAGGTTAGATCTGCTATA
66 CAAATCATCTTGGATCTGCTTCAGTATAAACATCTGAAGGTTAGATCTGCTATA
*
46417447 TTTGAGAACGTCTGAGAGTCAAATCTGCTATGTCCTCGATTTGTTCCTTGTAAACACAAGAATGC
1 TTTGAGAACGTCTGAGAGTCAAATCTGCTATGTCCTCGATTTGTTCCTTGTAAACACAAGAATAC
*
46417512 CAAATCATCTTGGATCTGCTTCAGTATAAACATCTGAAGGTTAGATCTGCTATC
66 CAAATCATCTTGGATCTGCTTCAGTATAAACATCTGAAGGTTAGATCTGCTATA
46417566 TTTGA
1 TTTGA
46417571 TCTGTTCCCT
Statistics
Matches: 456, Mismatches: 23, Indels: 2
0.95 0.05 0.00
Matches are distributed among these distances:
118 116 0.25
119 340 0.75
ACGTcount: A:0.30, C:0.18, G:0.18, T:0.34
Consensus pattern (119 bp):
TTTGAGAACGTCTGAGAGTCAAATCTGCTATGTCCTCGATTTGTTCCTTGTAAACACAAGAATAC
CAAATCATCTTGGATCTGCTTCAGTATAAACATCTGAAGGTTAGATCTGCTATA
Found at i:46417483 original size:237 final size:238
Alignment explanation
Indices: 46416972--46417570 Score: 1047
Period size: 237 Copynumber: 2.5 Consensus size: 238
46416962 CTTGAGTCTG
* * * * * *
46416972 TTTGAGAACATTTGAGAGTCATATCTGCAATGTCCTCGATTTGTTCCTTGTAAGCACAAGGATGC
1 TTTGAGAACGTCTGAGAGTCAAATCTGCTATGTCCTCGATTTGTTCCTTGTAAACACAAGAATGC
*
46417037 CAAATCATCTTGGATCTGCTTCAGTATAAACATCTGAAGGTTAGATCTGCTATATTTGAGAATGT
66 CAAATCATCTTGGATCTGCTTCAGTATAAACATCTGAAGGTTAGATCTGCTATATTTGAGAACGT
*
46417102 CTGAGAGTCAAATCTGCTATGTCCTCGATTTGTTTCTTGTAAACACAAGAATACCAAATCATCTT
131 CTGAGAGTCAAATCTGCTATGTCCTCGATTTGTTCCTTGTAAACACAAGAATACCAAATCATCTT
* * *
46417167 GGATCTATTTCAGTATAAACATCTGAATGTTAGATCTGTTATA
196 GGATCTACTTCAGTATAAACATCTGAAGGTTAGATCTGCTATA
*
46417210 TTTGAGAACGTCTGAGAGTCAAATCTGCTATGTCCTCGATTTGTTCCTTGTAAACACAAGAATAC
1 TTTGAGAACGTCTGAGAGTCAAATCTGCTATGTCCTCGATTTGTTCCTTGTAAACACAAGAATGC
* *
46417275 CAAATCATCTTGGATCTGCTTCAGTATAAACATCTAAAGGTTAGATCTGTTATATTTGAGAACGT
66 CAAATCATCTTGGATCTGCTTCAGTATAAACATCTGAAGGTTAGATCTGCTATATTTGAGAACGT
46417340 CTGAGAGTCAAATCTGCTATGTCCTC-ATTTGTTCCTTGTAAACACAAGAATACCAAATCATCTT
131 CTGAGAGTCAAATCTGCTATGTCCTCGATTTGTTCCTTGTAAACACAAGAATACCAAATCATCTT
*
46417404 GGATCTGCTTCAGTATAAACATCTGAAGGTTAGATCTGCTATA
196 GGATCTACTTCAGTATAAACATCTGAAGGTTAGATCTGCTATA
46417447 TTTGAGAACGTCTGAGAGTCAAATCTGCTATGTCCTCGATTTGTTCCTTGTAAACACAAGAATGC
1 TTTGAGAACGTCTGAGAGTCAAATCTGCTATGTCCTCGATTTGTTCCTTGTAAACACAAGAATGC
*
46417512 CAAATCATCTTGGATCTGCTTCAGTATAAACATCTGAAGGTTAGATCTGCTATCTTTGA
66 CAAATCATCTTGGATCTGCTTCAGTATAAACATCTGAAGGTTAGATCTGCTATATTTGA
46417571 TCTGTTCCCT
Statistics
Matches: 342, Mismatches: 19, Indels: 1
0.94 0.05 0.00
Matches are distributed among these distances:
237 196 0.57
238 146 0.43
ACGTcount: A:0.30, C:0.18, G:0.18, T:0.34
Consensus pattern (238 bp):
TTTGAGAACGTCTGAGAGTCAAATCTGCTATGTCCTCGATTTGTTCCTTGTAAACACAAGAATGC
CAAATCATCTTGGATCTGCTTCAGTATAAACATCTGAAGGTTAGATCTGCTATATTTGAGAACGT
CTGAGAGTCAAATCTGCTATGTCCTCGATTTGTTCCTTGTAAACACAAGAATACCAAATCATCTT
GGATCTACTTCAGTATAAACATCTGAAGGTTAGATCTGCTATA
Found at i:46417609 original size:44 final size:44
Alignment explanation
Indices: 46417556--46417749 Score: 139
Period size: 44 Copynumber: 4.4 Consensus size: 44
46417546 TGAAGGTTAG
*
46417556 ATCTGCTATCTTTGATCTGTTCCCTATAAACACAGGGATGCCAA
1 ATCTACTATCTTTGATCTGTTCCCTATAAACACAGGGATGCCAA
* * *
46417600 ATCTACTATC-TTCAACTTGTTCCCTATAAACACAGGGATTCC--
1 ATCTACTATCTTTGATC-TGTTCCCTATAAACACAGGGATGCCAA
* ** * * * * * *
46417642 ATGCTGA-AATCTTCAATCTGCTTCGC-AGAGAGCACAGGAATGTCAG
1 AT-CT-ACTATCTTTGATCTG-TTCCCTATA-AACACAGGGATGCCAA
* *
46417688 ATCTACTATCTTCGATCTGTT-CCTATAAACATAGGGATGCCAA
1 ATCTACTATCTTTGATCTGTTCCCTATAAACACAGGGATGCCAA
** *
46417731 ATCTTGTTTCTTTGATCTG
1 ATCTACTATCTTTGATCTG
46417750 CATTGTCCCA
Statistics
Matches: 113, Mismatches: 27, Indels: 21
0.70 0.17 0.13
Matches are distributed among these distances:
42 2 0.02
43 40 0.35
44 56 0.50
45 13 0.12
46 2 0.02
ACGTcount: A:0.27, C:0.24, G:0.16, T:0.33
Consensus pattern (44 bp):
ATCTACTATCTTTGATCTGTTCCCTATAAACACAGGGATGCCAA
Found at i:46418627 original size:21 final size:21
Alignment explanation
Indices: 46418603--46418662 Score: 75
Period size: 22 Copynumber: 2.8 Consensus size: 21
46418593 TCACCTTGGC
*
46418603 CTCTCCATTTTTTTCTTTTTT
1 CTCTTCATTTTTTTCTTTTTT
*
46418624 CTCTTTATTTTTTTCTCTTTTT
1 CTCTTCATTTTTTTCT-TTTTT
* *
46418646 CTTTTCTTTTTTTTCTT
1 CTCTTCATTTTTTTCTT
46418663 CTCTTTTTTT
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
21 15 0.45
22 18 0.55
ACGTcount: A:0.03, C:0.20, G:0.00, T:0.77
Consensus pattern (21 bp):
CTCTTCATTTTTTTCTTTTTT
Found at i:46418635 original size:22 final size:20
Alignment explanation
Indices: 46418609--46418658 Score: 73
Period size: 21 Copynumber: 2.4 Consensus size: 20
46418599 TGGCCTCTCC
46418609 ATTTTTTTCTTTTTTCTCTTT
1 ATTTTTTTCTTTTTTCT-TTT
46418630 ATTTTTTTCTCTTTTTCTTTT
1 ATTTTTTTCT-TTTTTCTTTT
*
46418651 CTTTTTTT
1 ATTTTTTT
46418659 TCTTCTCTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
21 20 0.74
22 7 0.26
ACGTcount: A:0.04, C:0.14, G:0.00, T:0.82
Consensus pattern (20 bp):
ATTTTTTTCTTTTTTCTTTT
Found at i:46418637 original size:14 final size:13
Alignment explanation
Indices: 46418613--46418674 Score: 81
Period size: 13 Copynumber: 4.7 Consensus size: 13
46418603 CTCTCCATTT
46418613 TTTTCTTTTTTCTC
1 TTTT-TTTTTTCTC
46418627 TTTATTTTTTTCTC
1 TTT-TTTTTTTCTC
*
46418641 TTTTTCTTTTCT-
1 TTTTTTTTTTCTC
*
46418653 TTTTTTTCTTCTC
1 TTTTTTTTTTCTC
46418666 TTTTTTTTT
1 TTTTTTTTT
46418675 GAAATAGAAG
Statistics
Matches: 42, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
12 10 0.24
13 16 0.38
14 15 0.36
15 1 0.02
ACGTcount: A:0.02, C:0.16, G:0.00, T:0.82
Consensus pattern (13 bp):
TTTTTTTTTTCTC
Found at i:46418659 original size:22 final size:21
Alignment explanation
Indices: 46418609--46418674 Score: 77
Period size: 19 Copynumber: 3.3 Consensus size: 21
46418599 TGGCCTCTCC
46418609 ATTTTTTTCTTTTTTCTCTTT
1 ATTTTTTTCTTTTTTCTCTTT
*
46418630 ATTTTTTTCTCTTTT-TCTTT
1 ATTTTTTTCTTTTTTCTCTTT
* *
46418650 -TCTTTTT-TTTCTTCTCTTT
1 ATTTTTTTCTTTTTTCTCTTT
46418669 -TTTTTT
1 ATTTTTT
46418675 GAAATAGAAG
Statistics
Matches: 39, Mismatches: 5, Indels: 4
0.81 0.10 0.08
Matches are distributed among these distances:
18 4 0.10
19 16 0.41
20 5 0.13
21 14 0.36
ACGTcount: A:0.03, C:0.15, G:0.00, T:0.82
Consensus pattern (21 bp):
ATTTTTTTCTTTTTTCTCTTT
Found at i:46418665 original size:25 final size:24
Alignment explanation
Indices: 46418610--46418674 Score: 82
Period size: 25 Copynumber: 2.8 Consensus size: 24
46418600 GGCCTCTCCA
*
46418610 TTTTTT-TC-TTTTTTCTCTTTAT
1 TTTTTTCTCTTTTTTTTTCTTTAT
46418632 TTTTTTCTCTTTTTCTTTTCTTT-T
1 TTTTTTCTCTTTTT-TTTTCTTTAT
46418656 TTTTCTTCTCTTTTTTTTT
1 TTTT-TTCTCTTTTTTTTT
46418675 GAAATAGAAG
Statistics
Matches: 38, Mismatches: 1, Indels: 6
0.84 0.02 0.13
Matches are distributed among these distances:
22 6 0.16
23 2 0.05
24 13 0.34
25 17 0.45
ACGTcount: A:0.02, C:0.15, G:0.00, T:0.83
Consensus pattern (24 bp):
TTTTTTCTCTTTTTTTTTCTTTAT
Found at i:46423182 original size:39 final size:39
Alignment explanation
Indices: 46423128--46423280 Score: 236
Period size: 39 Copynumber: 3.9 Consensus size: 39
46423118 GAATGTTCGA
46423128 ATGATATCCGGGCTAAGCCCGAAGGCAATTGTGCGAGCT
1 ATGATATCCGGGCTAAGCCCGAAGGCAATTGTGCGAGCT
46423167 ATGATATCCGGGCTAAGCCCGAAGGCAATTGTGCGAGCT
1 ATGATATCCGGGCTAAGCCCGAAGGCAATTGTGCGAGCT
* *
46423206 ATGATA-CTCGAGCTAAGCCCGAAGGCAATTGTGCGAGTT
1 ATGATATC-CGGGCTAAGCCCGAAGGCAATTGTGCGAGCT
* * *
46423245 GTGATATCCGGGTTAAGTCCCGAAGGCATTTGTGCG
1 ATGATATCCGGGCTAAG-CCCGAAGGCAATTGTGCG
46423281 GGTTACCATA
Statistics
Matches: 105, Mismatches: 6, Indels: 5
0.91 0.05 0.04
Matches are distributed among these distances:
38 1 0.01
39 86 0.82
40 18 0.17
ACGTcount: A:0.25, C:0.22, G:0.31, T:0.23
Consensus pattern (39 bp):
ATGATATCCGGGCTAAGCCCGAAGGCAATTGTGCGAGCT
Found at i:46423296 original size:40 final size:39
Alignment explanation
Indices: 46423128--46423310 Score: 215
Period size: 39 Copynumber: 4.6 Consensus size: 39
46423118 GAATGTTCGA
*
46423128 ATGATATCCGGGCTAAGCCCGAAGGCAATTGTGCGAGCT
1 ATGATAACCGGGCTAAGCCCGAAGGCAATTGTGCGAGCT
*
46423167 ATGATATCCGGGCTAAGCCCGAAGGCAATTGTGCGAGCT
1 ATGATAACCGGGCTAAGCCCGAAGGCAATTGTGCGAGCT
* *
46423206 ATGAT-ACTCGAGCTAAGCCCGAAGGCAATTGTGCGAGTT
1 ATGATAAC-CGGGCTAAGCCCGAAGGCAATTGTGCGAGCT
* * * * * *
46423245 GTGATATCCGGGTTAAGTCCCGAAGGCATTTGTGCGGGTT
1 ATGATAACCGGGCTAAG-CCCGAAGGCAATTGTGCGAGCT
** *
46423285 ACCATAACCGGGCTATGTCCCGAAGG
1 ATGATAACCGGGCTAAG-CCCGAAGG
46423311 TGTTTTGAAC
Statistics
Matches: 126, Mismatches: 15, Indels: 5
0.86 0.10 0.03
Matches are distributed among these distances:
38 1 0.01
39 84 0.67
40 41 0.33
ACGTcount: A:0.25, C:0.22, G:0.31, T:0.22
Consensus pattern (39 bp):
ATGATAACCGGGCTAAGCCCGAAGGCAATTGTGCGAGCT
Found at i:46428176 original size:18 final size:18
Alignment explanation
Indices: 46428140--46428264 Score: 182
Period size: 18 Copynumber: 6.9 Consensus size: 18
46428130 AATCATATCT
*
46428140 TCTAAGATTGTATATCATA
1 TCTAAGATTGCA-ATCATA
46428159 TCTAAGATTGCAATCATA
1 TCTAAGATTGCAATCATA
*
46428177 TCTAAGATTG-TATCATA
1 TCTAAGATTGCAATCATA
46428194 TCTAAGATTGCAATCATA
1 TCTAAGATTGCAATCATA
46428212 TCTAAGATTGCAATCATA
1 TCTAAGATTGCAATCATA
* *
46428230 TATAAGATTG-TATCATA
1 TCTAAGATTGCAATCATA
46428247 TCTAAGATTGCATATCAT
1 TCTAAGATTGCA-ATCAT
46428265 TGAAGATTAT
Statistics
Matches: 96, Mismatches: 7, Indels: 6
0.88 0.06 0.06
Matches are distributed among these distances:
17 31 0.32
18 49 0.51
19 16 0.17
ACGTcount: A:0.38, C:0.14, G:0.11, T:0.38
Consensus pattern (18 bp):
TCTAAGATTGCAATCATA
Found at i:46428198 original size:35 final size:36
Alignment explanation
Indices: 46428140--46428264 Score: 184
Period size: 35 Copynumber: 3.5 Consensus size: 36
46428130 AATCATATCT
46428140 TCTAAGATTGTATATCATATCTAAGATTGCAATCATA
1 TCTAAGATTG-ATATCATATCTAAGATTGCAATCATA
46428177 TCTAAGATTG-TATCATATCTAAGATTGCAATCATA
1 TCTAAGATTGATATCATATCTAAGATTGCAATCATA
* *
46428212 TCTAAGATTGCA-ATCATATATAAGATTG-TATCATA
1 TCTAAGATTG-ATATCATATCTAAGATTGCAATCATA
46428247 TCTAAGATTGCATATCAT
1 TCTAAGATTG-ATATCAT
46428265 TGAAGATTAT
Statistics
Matches: 83, Mismatches: 2, Indels: 7
0.90 0.02 0.08
Matches are distributed among these distances:
35 53 0.64
36 20 0.24
37 10 0.12
ACGTcount: A:0.38, C:0.14, G:0.11, T:0.38
Consensus pattern (36 bp):
TCTAAGATTGATATCATATCTAAGATTGCAATCATA
Found at i:46428215 original size:53 final size:54
Alignment explanation
Indices: 46428140--46428264 Score: 225
Period size: 53 Copynumber: 2.3 Consensus size: 54
46428130 AATCATATCT
* *
46428140 TCTAAGATTGTATATCATATCTAAGATTGCAATCATATCTAAGATTGTATCATA
1 TCTAAGATTGCATATCATATCTAAGATTGCAATCATATATAAGATTGTATCATA
46428194 TCTAAGATTGCA-ATCATATCTAAGATTGCAATCATATATAAGATTGTATCATA
1 TCTAAGATTGCATATCATATCTAAGATTGCAATCATATATAAGATTGTATCATA
46428247 TCTAAGATTGCATATCAT
1 TCTAAGATTGCATATCAT
46428265 TGAAGATTAT
Statistics
Matches: 68, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
53 52 0.76
54 16 0.24
ACGTcount: A:0.38, C:0.14, G:0.11, T:0.38
Consensus pattern (54 bp):
TCTAAGATTGCATATCATATCTAAGATTGCAATCATATATAAGATTGTATCATA
Found at i:46436740 original size:5 final size:5
Alignment explanation
Indices: 46436730--46436773 Score: 79
Period size: 5 Copynumber: 8.6 Consensus size: 5
46436720 CTGTGTGTTC
46436730 TTTAT TTTAT TTTATT TTTAT TTTAT TTTAT TTTAT TTTAT TTT
1 TTTAT TTTAT TTTA-T TTTAT TTTAT TTTAT TTTAT TTTAT TTT
46436774 CACAACTACC
Statistics
Matches: 38, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
5 33 0.87
6 5 0.13
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (5 bp):
TTTAT
Found at i:46436916 original size:5 final size:5
Alignment explanation
Indices: 46436906--46436943 Score: 60
Period size: 5 Copynumber: 7.6 Consensus size: 5
46436896 CTGTGTGTTC
46436906 TTTAT TTTAT TTT-T TATTAT TTTAT TTTAT TTTAT TTT
1 TTTAT TTTAT TTTAT T-TTAT TTTAT TTTAT TTTAT TTT
46436944 CACAACTACC
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
4 2 0.06
5 27 0.87
6 2 0.06
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (5 bp):
TTTAT
Found at i:46436976 original size:170 final size:173
Alignment explanation
Indices: 46436688--46437022 Score: 543
Period size: 170 Copynumber: 1.9 Consensus size: 173
46436678 CTTCCCATAG
* * *
46436688 TTTTTTTCCCTAAAGGGTTTCCACGTTAAAATCTGTGTGTTCTTTATTTTATTTTATTTTTATTT
1 TTTTTTTCCCGAAAGGGTTTCCACATAAAAATCTGTGTGTTCTTTATTTTA--TTATTTTTA-TT
46436753 TATTTTATTTTATTTTATTTTCACAACTACCATGATCAAAAAGTTCTCCAAGTGGACTAGACGAG
63 TATTTTATTTTATTTTATTTTCACAACTACCATGATCAAAAAGTTCTCCAAGTGGACTAGACGAG
46436818 TTTGTTCTGCAGGCTTGTTTCCCAT-TGATGGCATCTCTGCCCTTTA
128 TTTGTTCTGCAGGCTTGTTTCCCATCT-ATGGCATCTCTGCCCTTTA
*
46436864 TTTTTTTCCCGAAAGGGTTTTCACATAAAAATCTGTGTGTTCTTTATTTTA-T-TTTTTA-TTAT
1 TTTTTTTCCCGAAAGGGTTTCCACATAAAAATCTGTGTGTTCTTTATTTTATTATTTTTATTTAT
*
46436926 TTTATTTTATTTTATTTTCACAACTACCATGATCAAAAAGTTCTCCAAGTGGACTAGAGGAGTTT
66 TTTATTTTATTTTATTTTCACAACTACCATGATCAAAAAGTTCTCCAAGTGGACTAGACGAGTTT
* *
46436991 GTTCTTCGGGCTTGTTTCCCATCTATGGCATC
131 GTTCTGCAGGCTTGTTTCCCATCTATGGCATC
46437023 AAATGTCTAG
Statistics
Matches: 151, Mismatches: 7, Indels: 8
0.91 0.04 0.05
Matches are distributed among these distances:
170 96 0.64
171 1 0.01
172 6 0.04
173 1 0.01
176 47 0.31
ACGTcount: A:0.22, C:0.17, G:0.14, T:0.47
Consensus pattern (173 bp):
TTTTTTTCCCGAAAGGGTTTCCACATAAAAATCTGTGTGTTCTTTATTTTATTATTTTTATTTAT
TTTATTTTATTTTATTTTCACAACTACCATGATCAAAAAGTTCTCCAAGTGGACTAGACGAGTTT
GTTCTGCAGGCTTGTTTCCCATCTATGGCATCTCTGCCCTTTA
Found at i:46438767 original size:22 final size:23
Alignment explanation
Indices: 46438742--46438797 Score: 71
Period size: 23 Copynumber: 2.4 Consensus size: 23
46438732 TATTTATATA
46438742 TTTAGAATTTAA-TTTTTTTA-TT
1 TTTA-AATTTAATTTTTTTTACTT
*
46438764 TTTAATTTTTAATTTTTTTTACTT
1 TTTAA-ATTTAATTTTTTTTACTT
46438788 TTTAAATTTA
1 TTTAAATTTA
46438798 TAAAATTATG
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
21 1 0.03
22 9 0.31
23 12 0.41
24 7 0.24
ACGTcount: A:0.27, C:0.02, G:0.02, T:0.70
Consensus pattern (23 bp):
TTTAAATTTAATTTTTTTTACTT
Found at i:46439746 original size:30 final size:30
Alignment explanation
Indices: 46439712--46439774 Score: 108
Period size: 30 Copynumber: 2.1 Consensus size: 30
46439702 ACTTAACAAT
46439712 CAAATATCTCTAAAATAATAACAAAATTAA
1 CAAATATCTCTAAAATAATAACAAAATTAA
* *
46439742 CAAATGTCTTTAAAATAATAACAAAATTAA
1 CAAATATCTCTAAAATAATAACAAAATTAA
46439772 CAA
1 CAA
46439775 TAAAATAGAT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.59, C:0.13, G:0.02, T:0.27
Consensus pattern (30 bp):
CAAATATCTCTAAAATAATAACAAAATTAA
Found at i:46442923 original size:2 final size:2
Alignment explanation
Indices: 46442916--46442941 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
46442906 AAGAAACTAG
46442916 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
46442942 CTCAAATTCA
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):
TA
Found at i:46443808 original size:16 final size:16
Alignment explanation
Indices: 46443787--46443825 Score: 78
Period size: 16 Copynumber: 2.4 Consensus size: 16
46443777 GTTAAGTTTG
46443787 CTGTAATGAAATAGAA
1 CTGTAATGAAATAGAA
46443803 CTGTAATGAAATAGAA
1 CTGTAATGAAATAGAA
46443819 CTGTAAT
1 CTGTAAT
46443826 CAGTAATTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.46, C:0.08, G:0.18, T:0.28
Consensus pattern (16 bp):
CTGTAATGAAATAGAA
Found at i:46459193 original size:11 final size:11
Alignment explanation
Indices: 46459179--46459224 Score: 51
Period size: 11 Copynumber: 4.4 Consensus size: 11
46459169 GTCCTCTTAC
46459179 AATTCTCTCTA
1 AATTCTCTCTA
* *
46459190 AATTTTCTCCA
1 AATTCTCTCTA
46459201 AATTCTCTC-A
1 AATTCTCTCTA
*
46459211 AATT-TCTCTC
1 AATTCTCTCTA
46459221 AATT
1 AATT
46459225 TTTGTCAAAG
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
9 4 0.13
10 9 0.30
11 17 0.57
ACGTcount: A:0.28, C:0.26, G:0.00, T:0.46
Consensus pattern (11 bp):
AATTCTCTCTA
Found at i:46459216 original size:20 final size:22
Alignment explanation
Indices: 46459179--46459220 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
46459169 GTCCTCTTAC
46459179 AATTCTCTCTAAATTTTCTCCA
1 AATTCTCTCTAAATTTTCTCCA
46459201 AATTCTCTC-AAATTTCTCTC
1 AATTCTCTCTAAATTT-TCTC
46459221 AATTTTTGTC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 6 0.32
22 13 0.68
ACGTcount: A:0.26, C:0.29, G:0.00, T:0.45
Consensus pattern (22 bp):
AATTCTCTCTAAATTTTCTCCA
Found at i:46459224 original size:20 final size:21
Alignment explanation
Indices: 46459178--46459224 Score: 62
Period size: 20 Copynumber: 2.2 Consensus size: 21
46459168 AGTCCTCTTA
46459178 CAATTCTCTCTAAATTTTCTC
1 CAATTCTCTCTAAATTTTCTC
46459199 CAAATTCTCTC-AAA-TTTCTC
1 C-AATTCTCTCTAAATTTTCTC
46459219 TCAATT
1 -CAATT
46459225 TTTGTCAAAG
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
20 10 0.42
21 5 0.21
22 9 0.38
ACGTcount: A:0.28, C:0.28, G:0.00, T:0.45
Consensus pattern (21 bp):
CAATTCTCTCTAAATTTTCTC
Found at i:46459239 original size:21 final size:21
Alignment explanation
Indices: 46459215--46459254 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
46459205 CTCTCAAATT
46459215 TCTC-TCAATTTTTGTCAAAGC
1 TCTCTTCAATTTTTG-CAAAGC
*
46459236 TCTCTTTAATTTTTGCAAA
1 TCTCTTCAATTTTTGCAAA
46459255 AAAGATCTGT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 8 0.47
22 9 0.53
ACGTcount: A:0.25, C:0.20, G:0.07, T:0.47
Consensus pattern (21 bp):
TCTCTTCAATTTTTGCAAAGC
Found at i:46460417 original size:7 final size:7
Alignment explanation
Indices: 46460402--46460447 Score: 83
Period size: 7 Copynumber: 6.6 Consensus size: 7
46460392 AATCGTTTCA
46460402 TATTTAG
1 TATTTAG
*
46460409 TAGTTAG
1 TATTTAG
46460416 TATTTAG
1 TATTTAG
46460423 TATTTAG
1 TATTTAG
46460430 TATTTAG
1 TATTTAG
46460437 TATTTAG
1 TATTTAG
46460444 TATT
1 TATT
46460448 ACGTATATAA
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
7 37 1.00
ACGTcount: A:0.28, C:0.00, G:0.15, T:0.57
Consensus pattern (7 bp):
TATTTAG
Found at i:46461061 original size:18 final size:18
Alignment explanation
Indices: 46461038--46461078 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
46461028 TCAGGTGCGC
*
46461038 ATCCTAGCCCTTATATGT
1 ATCCTAACCCTTATATGT
*
46461056 ATCCTAACCCTTTTATGT
1 ATCCTAACCCTTATATGT
*
46461074 TTCCT
1 ATCCT
46461079 TTTCCCAGTC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.20, C:0.29, G:0.07, T:0.44
Consensus pattern (18 bp):
ATCCTAACCCTTATATGT
Found at i:46461351 original size:22 final size:21
Alignment explanation
Indices: 46461326--46461380 Score: 74
Period size: 21 Copynumber: 2.6 Consensus size: 21
46461316 CCACAACCAG
* *
46461326 ATCCCCTGCCGGAGGAATCACA
1 ATCCCC-GCCGGAGCAACCACA
*
46461348 ATCCCCACCGGAGCAACCACA
1 ATCCCCGCCGGAGCAACCACA
46461369 ATCCCCGCCGGA
1 ATCCCCGCCGGA
46461381 AGCTGAACCA
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
21 23 0.79
22 6 0.21
ACGTcount: A:0.27, C:0.44, G:0.20, T:0.09
Consensus pattern (21 bp):
ATCCCCGCCGGAGCAACCACA
Found at i:46461727 original size:130 final size:130
Alignment explanation
Indices: 46461485--46461858 Score: 603
Period size: 129 Copynumber: 2.9 Consensus size: 130
46461475 TGTAGAAACT
*
46461485 TTTTTTATATAGTTTC-ATATAATAAAATAAAAGTTGTTTTTAATATTTTAATTGTACTTTAC--
1 TTTTTTATATAGTTTCAAT-TAATAAAATAAAATTTGTTTTTAATATTTTAATTGTACTTTACTT
* **
46461547 TTTTTAATTTTATTAAAACAAATGTTCTTTTAAATTAGGTAATATTTTTTTATCATTTTTATATT
65 TTTTTAATTTTATTAAAATAAATGTTCTTTTAAATTAGCCAATA--TTTTTATCATTTTTATATT
46461612 TAA
128 TAA
*
46461615 TTTTTTATATAGTTTCAATTAATAAAATAAAATTTGTTTTTAATATTTTAATTGTACGTTACTTT
1 TTTTTTATATAGTTTCAATTAATAAAATAAAATTTGTTTTTAATATTTTAATTGTACTTTACTTT
*
46461680 TTTTAATTTTATTAAAATAAATGTTCTTTTAAATTAGCCAATATTTTTATTATTTTTATATTTAA
66 TTTTAATTTTATTAAAATAAATGTTCTTTTAAATTAGCCAATATTTTTATCATTTTTATATTTAA
* *
46461745 -TTTTTATATATTTTTAATTAATAAAATAAAATTTGTTTTTAATATTTTAATTGTACTTTACTTT
1 TTTTTTATATAGTTTCAATTAATAAAATAAAATTTGTTTTTAATATTTTAATTGTACTTTACTTT
* *
46461809 TTTTAATTTTAATACAATAAATGTTCTTTTAAATTAGCCAATATTTTTAT
66 TTTTAATTTTATTAAAATAAATGTTCTTTTAAATTAGCCAATATTTTTAT
46461859 TAAAAAAATG
Statistics
Matches: 230, Mismatches: 11, Indels: 7
0.93 0.04 0.03
Matches are distributed among these distances:
129 109 0.47
130 78 0.34
131 2 0.01
132 41 0.18
ACGTcount: A:0.35, C:0.05, G:0.05, T:0.56
Consensus pattern (130 bp):
TTTTTTATATAGTTTCAATTAATAAAATAAAATTTGTTTTTAATATTTTAATTGTACTTTACTTT
TTTTAATTTTATTAAAATAAATGTTCTTTTAAATTAGCCAATATTTTTATCATTTTTATATTTAA
Found at i:46461761 original size:17 final size:17
Alignment explanation
Indices: 46461720--46461764 Score: 51
Period size: 17 Copynumber: 2.8 Consensus size: 17
46461710 AAATTAGCCA
46461720 ATATTTTT-ATTATTTT
1 ATATTTTTAATTATTTT
*
46461736 -TATATTTAATT-TTTAT
1 ATATTTTTAATTATTT-T
46461752 ATATTTTTAATTA
1 ATATTTTTAATTA
46461765 ATAAAATAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 6
0.74 0.06 0.19
Matches are distributed among these distances:
15 9 0.39
16 4 0.17
17 10 0.43
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (17 bp):
ATATTTTTAATTATTTT
Found at i:46469768 original size:17 final size:17
Alignment explanation
Indices: 46469746--46469780 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
46469736 CACGGCCTAG
46469746 GCTCTGTCACACAGCCT
1 GCTCTGTCACACAGCCT
46469763 GCTCTGTCACACAGCCT
1 GCTCTGTCACACAGCCT
46469780 G
1 G
46469781 ACCACATGAC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.17, C:0.40, G:0.20, T:0.23
Consensus pattern (17 bp):
GCTCTGTCACACAGCCT
Found at i:46470296 original size:60 final size:60
Alignment explanation
Indices: 46470180--46470330 Score: 167
Period size: 60 Copynumber: 2.5 Consensus size: 60
46470170 TCCTTTTAAG
* * * * *
46470180 TTTTTAAGAAGTAAAACTAAATCGATAGAATATGTAAAGTTGAGGGCTAAAGTTATTGAGT
1 TTTTTAA-AATTAAAACTAAATTGATAGAATATGTAAAGTTGAGGACTAAAGTTATTAAAT
** * * * * *
46470241 TTTTTAAAATTAAGGCTAAATTGATAGAATGTGTAAAGTTGATGATTGAATTTATTAAAT
1 TTTTTAAAATTAAAACTAAATTGATAGAATATGTAAAGTTGAGGACTAAAGTTATTAAAT
* *
46470301 TTTTTAGAATTAAAACTAAATTAATAGAAT
1 TTTTTAAAATTAAAACTAAATTGATAGAAT
46470331 TTATAAATAT
Statistics
Matches: 74, Mismatches: 16, Indels: 1
0.81 0.18 0.01
Matches are distributed among these distances:
60 67 0.91
61 7 0.09
ACGTcount: A:0.42, C:0.03, G:0.17, T:0.38
Consensus pattern (60 bp):
TTTTTAAAATTAAAACTAAATTGATAGAATATGTAAAGTTGAGGACTAAAGTTATTAAAT
Found at i:46471596 original size:16 final size:16
Alignment explanation
Indices: 46471558--46471589 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
46471548 AGCTACTTTT
46471558 AAGTTGAGCTTTACAG
1 AAGTTGAGCTTTACAG
46471574 AAGTTGAGCTTTACAG
1 AAGTTGAGCTTTACAG
46471590 GGTTTGACAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.31, C:0.12, G:0.25, T:0.31
Consensus pattern (16 bp):
AAGTTGAGCTTTACAG
Found at i:46478701 original size:1 final size:1
Alignment explanation
Indices: 46478695--46478723 Score: 58
Period size: 1 Copynumber: 29.0 Consensus size: 1
46478685 AGGATTTTCC
46478695 AAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAA
46478724 GAAGAAAACC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 28 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:46484035 original size:31 final size:31
Alignment explanation
Indices: 46483997--46484145 Score: 244
Period size: 31 Copynumber: 4.8 Consensus size: 31
46483987 ACAAATGACA
46483997 AGTGAAAAGTGGTAGCTTCGGCTACCTGATC
1 AGTGAAAAGTGGTAGCTTCGGCTACCTGATC
**
46484028 AGTGAAAAGTGGTAGCTTCTACTACCTGATC
1 AGTGAAAAGTGGTAGCTTCGGCTACCTGATC
*
46484059 AGTGAAAAGTGGTAGCTCCGGCTACCTGATC
1 AGTGAAAAGTGGTAGCTTCGGCTACCTGATC
* *
46484090 AGTGAAAAATGGTAGCTCCGGCTACCTGATC
1 AGTGAAAAGTGGTAGCTTCGGCTACCTGATC
*
46484121 AGTGAATAGTGGTAGCTTCGGCTAC
1 AGTGAAAAGTGGTAGCTTCGGCTAC
46484146 AAGTGACAAG
Statistics
Matches: 109, Mismatches: 9, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
31 109 1.00
ACGTcount: A:0.27, C:0.20, G:0.28, T:0.26
Consensus pattern (31 bp):
AGTGAAAAGTGGTAGCTTCGGCTACCTGATC
Found at i:46484268 original size:49 final size:47
Alignment explanation
Indices: 46484167--46484338 Score: 205
Period size: 49 Copynumber: 3.7 Consensus size: 47
46484157 GATTTCCGTA
* * * *
46484167 TAAGACCATATCTGGGATATGGCATCA-GTGAGATATGTGATTCGTG
1 TAAGACCATAGCTGGGCTATGGCATCATATGTGATATGTGATTCGTG
*
46484213 TAAGACCATAGCTGAGCTATGGCATCGATATGTGATATGTGATTACGTG
1 TAAGACCATAGCTGGGCTATGGCATC-ATATGTGATATGTGATT-CGTG
*
46484262 TAAGACCATAGCTGGGCTATGGCATCGATATATGA-A--T-A-T-GTG
1 TAAGACCATAGCTGGGCTATGGCATC-ATATGTGATATGTGATTCGTG
46484304 TAAGACCATAGCTGGGCTATGGCATCATTATGTGA
1 TAAGACCATAGCTGGGCTATGGCATCA-TATGTGA
46484339 AGATGTGTAA
Statistics
Matches: 114, Mismatches: 8, Indels: 12
0.85 0.06 0.09
Matches are distributed among these distances:
41 1 0.01
42 35 0.31
44 1 0.01
45 1 0.01
46 24 0.21
47 1 0.01
48 14 0.12
49 37 0.32
ACGTcount: A:0.29, C:0.15, G:0.27, T:0.30
Consensus pattern (47 bp):
TAAGACCATAGCTGGGCTATGGCATCATATGTGATATGTGATTCGTG
Found at i:46484305 original size:42 final size:43
Alignment explanation
Indices: 46484210--46484373 Score: 172
Period size: 42 Copynumber: 3.7 Consensus size: 43
46484200 TATGTGATTC
* *
46484210 GTGTAAGACCATAGCTGAGCTATGGCATCGATATGTGATATG-TGATT
1 GTGTAAGACCATAGCTGGGCTATGGCATCG--AT-T-ATATGAAGA-T
*
46484257 ACGTGTAAGACCATAGCTGGGCTATGGCATCGA-TATATGAATAT
1 --GTGTAAGACCATAGCTGGGCTATGGCATCGATTATATGAAGAT
*
46484301 GTGTAAGACCATAGCTGGGCTATGGCATC-ATTATGTGAAGAT
1 GTGTAAGACCATAGCTGGGCTATGGCATCGATTATATGAAGAT
* * **
46484343 GTGTAAAACCATAGTTGAACTATGGCATCGA
1 GTGTAAGACCATAGCTGGGCTATGGCATCGA
46484374 GAAAACGAAG
Statistics
Matches: 103, Mismatches: 9, Indels: 12
0.83 0.07 0.10
Matches are distributed among these distances:
41 1 0.01
42 63 0.61
43 1 0.01
44 6 0.06
45 2 0.02
47 1 0.01
49 29 0.28
ACGTcount: A:0.30, C:0.15, G:0.26, T:0.29
Consensus pattern (43 bp):
GTGTAAGACCATAGCTGGGCTATGGCATCGATTATATGAAGAT
Found at i:46485466 original size:3 final size:3
Alignment explanation
Indices: 46485458--46485494 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
46485448 AAATTGAGTA
46485458 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
46485495 TATATTATTA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:46485503 original size:3 final size:3
Alignment explanation
Indices: 46485497--46485528 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
46485487 TAATAATATA
*
46485497 TAT TAT TAT TAT CAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
46485529 AGCCCGAAGA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.62
Consensus pattern (3 bp):
TAT
Found at i:46494134 original size:19 final size:19
Alignment explanation
Indices: 46494110--46494153 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
46494100 TAATATATAT
*
46494110 TAATATTTTTTTATCAAAA
1 TAATATTTATTTATCAAAA
*
46494129 TAATATTTATTTATTAAAA
1 TAATATTTATTTATCAAAA
*
46494148 TGATAT
1 TAATAT
46494154 GTTTACTAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.52
Consensus pattern (19 bp):
TAATATTTATTTATCAAAA
Found at i:46497272 original size:16 final size:15
Alignment explanation
Indices: 46497247--46497276 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
46497237 CTAAAGATTC
46497247 CTTTTTTTTTTTTCT
1 CTTTTTTTTTTTTCT
46497262 CTTTTTGTTTTTTTC
1 CTTTTT-TTTTTTTC
46497277 GCCCTTTTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.00, C:0.13, G:0.03, T:0.83
Consensus pattern (15 bp):
CTTTTTTTTTTTTCT
Found at i:46505707 original size:19 final size:19
Alignment explanation
Indices: 46505683--46505729 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 19
46505673 TTTTTATAAA
46505683 TATTTTGAAGTTTAAAAAT
1 TATTTTGAAGTTTAAAAAT
* * *
46505702 TATTTTAAAATTTTAAAATT
1 TATTTT-GAAGTTTAAAAAT
46505722 TATTTTGA
1 TATTTTGA
46505730 TTTATTTTGT
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
19 7 0.30
20 16 0.70
ACGTcount: A:0.40, C:0.00, G:0.06, T:0.53
Consensus pattern (19 bp):
TATTTTGAAGTTTAAAAAT
Found at i:46516417 original size:16 final size:15
Alignment explanation
Indices: 46516392--46516480 Score: 58
Period size: 16 Copynumber: 5.7 Consensus size: 15
46516382 ATTATTCTAC
46516392 AAAAATAAAATAAAT
1 AAAAATAAAATAAAT
46516407 AAAATATAAAATAAACTT
1 AAAA-ATAAAATAAA--T
* *
46516425 GAACA-AAAA-AAAT
1 AAAAATAAAATAAAT
46516438 -AAAATAAAATAACAT
1 AAAAATAAAATAA-AT
** *
46516453 AATGATAAATTCAAAT
1 AAAAATAAAAT-AAAT
46516469 AAAAATTAAAAT
1 AAAAA-TAAAAT
46516481 TTTTCGACCA
Statistics
Matches: 56, Mismatches: 9, Indels: 16
0.69 0.11 0.20
Matches are distributed among these distances:
12 3 0.05
13 5 0.09
14 2 0.04
15 9 0.16
16 26 0.46
17 8 0.14
18 3 0.05
ACGTcount: A:0.71, C:0.04, G:0.02, T:0.22
Consensus pattern (15 bp):
AAAAATAAAATAAAT
Found at i:46519175 original size:16 final size:16
Alignment explanation
Indices: 46519156--46519186 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
46519146 CTTCTTCACT
46519156 TACTCACTTACTTAAA
1 TACTCACTTACTTAAA
*
46519172 TACTTACTTACTTAA
1 TACTCACTTACTTAA
46519187 TCAAATTTAT
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:0.35, C:0.23, G:0.00, T:0.42
Consensus pattern (16 bp):
TACTCACTTACTTAAA
Found at i:46519192 original size:20 final size:20
Alignment explanation
Indices: 46519153--46519192 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
46519143 AAACTTCTTC
* *
46519153 ACTTACTCACTTACTTAAAT
1 ACTTACTCACTTAATCAAAT
*
46519173 ACTTACTTACTTAATCAAAT
1 ACTTACTCACTTAATCAAAT
46519193 TTATTAATAC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.38, C:0.23, G:0.00, T:0.40
Consensus pattern (20 bp):
ACTTACTCACTTAATCAAAT
Found at i:46519573 original size:55 final size:53
Alignment explanation
Indices: 46519383--46519637 Score: 236
Period size: 55 Copynumber: 4.8 Consensus size: 53
46519373 ACACGGGTAC
* * * * *
46519383 CTTACCATTGCCATGACTTGTCATGGTCTTACGTGGTATCC-T---TT-TGAAA
1 CTTACCAATGCCATGTCTTGACATGGTCTTACATGGGATCCTTGCCTTATG-AA
* *
46519432 CTTACCATTGCCATGTCTTGACATGGTCTTACATGGTATCCTTGCCTTATGAA
1 CTTACCAATGCCATGTCTTGACATGGTCTTACATGGGATCCTTGCCTTATGAA
* * *
46519485 CTCACCAATGCCATGCCTTGGCATGGTCTTACATGGGA-CCTTTGCCTTATAGTAA
1 CTTACCAATGCCATGTCTTGACATGGTCTTACATGGGATCC-TTGCCTTAT-G-AA
* ***
46519540 CTTATCAATGCCATGTCTTGACATGGTCTTACATGATTTCCTTGCCTTA-GAAA
1 CTTACCAATGCCATGTCTTGACATGGTCTTACATGGGATCCTTGCCTTATG-AA
* * * *
46519593 CCTTACCAATTGCCATGCCTTGGCATGGTCTTACACGGTATCCTT
1 -CTTACCAA-TGCCATGTCTTGACATGGTCTTACATGGGATCCTT
46519638 AAACCCTAAT
Statistics
Matches: 173, Mismatches: 22, Indels: 16
0.82 0.10 0.08
Matches are distributed among these distances:
49 38 0.22
50 1 0.01
52 2 0.01
53 49 0.28
54 10 0.06
55 71 0.41
56 2 0.01
ACGTcount: A:0.21, C:0.25, G:0.18, T:0.36
Consensus pattern (53 bp):
CTTACCAATGCCATGTCTTGACATGGTCTTACATGGGATCCTTGCCTTATGAA
Found at i:46519574 original size:108 final size:110
Alignment explanation
Indices: 46519430--46519627 Score: 321
Period size: 108 Copynumber: 1.8 Consensus size: 110
46519420 ATCCTTTTGA
* *
46519430 AACTTACCATTGCCATGTCTTGACATGGTCTTACATGGTATCCTTGCCTTATG-AA-CTCACCAA
1 AACTTACCAATGCCATGTCTTGACATGGTCTTACATGATATCCTTGCCTTA-GAAACCTCACCAA
46519493 -TGCCATGCCTTGGCATGGTCTTACATGGGACCTTTGCCTTATAGT
65 TTGCCATGCCTTGGCATGGTCTTACATGGGACCTTTGCCTTATAGT
* * *
46519538 AACTTATCAATGCCATGTCTTGACATGGTCTTACATGATTTCCTTGCCTTAGAAACCTTACCAAT
1 AACTTACCAATGCCATGTCTTGACATGGTCTTACATGATATCCTTGCCTTAGAAACCTCACCAAT
46519603 TGCCATGCCTTGGCATGGTCTTACA
66 TGCCATGCCTTGGCATGGTCTTACA
46519628 CGGTATCCTT
Statistics
Matches: 82, Mismatches: 5, Indels: 4
0.90 0.05 0.04
Matches are distributed among these distances:
107 1 0.01
108 49 0.60
109 7 0.09
110 25 0.30
ACGTcount: A:0.23, C:0.26, G:0.17, T:0.34
Consensus pattern (110 bp):
AACTTACCAATGCCATGTCTTGACATGGTCTTACATGATATCCTTGCCTTAGAAACCTCACCAAT
TGCCATGCCTTGGCATGGTCTTACATGGGACCTTTGCCTTATAGT
Found at i:46526681 original size:9 final size:9
Alignment explanation
Indices: 46526667--46526691 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
46526657 AGAACTATCT
46526667 TATTGTGTG
1 TATTGTGTG
46526676 TATTGTGTG
1 TATTGTGTG
46526685 TATTGTG
1 TATTGTG
46526692 ATTAATGGTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.12, C:0.00, G:0.32, T:0.56
Consensus pattern (9 bp):
TATTGTGTG
Found at i:46532023 original size:40 final size:39
Alignment explanation
Indices: 46531939--46532123 Score: 162
Period size: 40 Copynumber: 4.6 Consensus size: 39
46531929 TCGAATGATG
* * **
46531939 TCCGGGCTAAGTCCCGAAAGC-TTTGTGCTAAGTGGCT-AT
1 TCCGGGCTAAGT-CCGAAGGCATTTGTGC-GAGTTACTAAT
*
46531978 ATCCGGACTAAGATCCGAAGGCATTTGTGCGAGTTACTAAT
1 -TCCGGGCTAAG-TCCGAAGGCATTTGTGCGAGTTACTAAT
* * *
46532019 TCCGGGCTAAGCCCGAAGGCATTTGCGCGAGGTACTAAAT
1 TCCGGGCTAAGTCCGAAGGCATTTGTGCGAGTTACT-AAT
* *
46532059 T-CGGGTTAAGTCTCGAAGGCATTTATGCGAGTTACT-AT
1 TCCGGGCTAAGTC-CGAAGGCATTTGTGCGAGTTACTAAT
* *
46532097 AACCGGGCTATGTCCCGAAGGCATTTG
1 -TCCGGGCTAAGT-CCGAAGGCATTTG
46532124 AACGAGTAGC
Statistics
Matches: 119, Mismatches: 18, Indels: 16
0.78 0.12 0.10
Matches are distributed among these distances:
38 2 0.02
39 31 0.26
40 75 0.63
41 11 0.09
ACGTcount: A:0.24, C:0.22, G:0.28, T:0.26
Consensus pattern (39 bp):
TCCGGGCTAAGTCCGAAGGCATTTGTGCGAGTTACTAAT
Found at i:46532145 original size:79 final size:79
Alignment explanation
Indices: 46531973--46532156 Score: 207
Period size: 79 Copynumber: 2.3 Consensus size: 79
46531963 GTGCTAAGTG
* * *
46531973 GCTATATCCGGACTAAGATCCGAAGGCATTTGTGCGAGTTACTAATTCCGGGCTAAGCCCGAAGG
1 GCTATATCCGG-TTAAGATCCGAAGGCATTTATGCGAGTTACTAATACCGGGCTAAGCCCGAAGG
**
46532038 CATTTGCGCGAGGTA
65 CATTTGAACGAGGTA
* * *
46532053 -CTAAATTCGGGTTAAG-TCTCGAAGGCATTTATGCGAGTTACT-ATAACCGGGCTATGTCCCGA
1 GCTATA-TCCGGTTAAGATC-CGAAGGCATTTATGCGAGTTACTAAT-ACCGGGCTAAG-CCCGA
46532115 AGGCATTTGAACGA-GTA
62 AGGCATTTGAACGAGGTA
46532132 GCTATATCCGGTTAA-ATTCCGAAGG
1 GCTATATCCGGTTAAGA-TCCGAAGG
46532157 TACGTGATTC
Statistics
Matches: 87, Mismatches: 10, Indels: 15
0.78 0.09 0.13
Matches are distributed among these distances:
78 4 0.05
79 56 0.64
80 27 0.31
ACGTcount: A:0.27, C:0.21, G:0.27, T:0.26
Consensus pattern (79 bp):
GCTATATCCGGTTAAGATCCGAAGGCATTTATGCGAGTTACTAATACCGGGCTAAGCCCGAAGGC
ATTTGAACGAGGTA
Found at i:46533945 original size:23 final size:25
Alignment explanation
Indices: 46533918--46533972 Score: 64
Period size: 25 Copynumber: 2.3 Consensus size: 25
46533908 AATATTTACG
*
46533918 AAGTTAAGTG-AGTG-ATTAATTTA
1 AAGTTAAGTGAAGTGAATTAACTTA
46533941 AAGTTTAA-TGAAGTGAATTAACTTA
1 AAG-TTAAGTGAAGTGAATTAACTTA
46533966 AA-TTAAG
1 AAGTTAAG
46533973 GATAATTAGA
Statistics
Matches: 27, Mismatches: 1, Indels: 7
0.77 0.03 0.20
Matches are distributed among these distances:
23 9 0.33
24 8 0.30
25 10 0.37
ACGTcount: A:0.44, C:0.02, G:0.18, T:0.36
Consensus pattern (25 bp):
AAGTTAAGTGAAGTGAATTAACTTA
Found at i:46534430 original size:17 final size:17
Alignment explanation
Indices: 46534410--46534445 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 17
46534400 CAGGGGAAGG
46534410 AAGAAAGAA-AAAGAGAA
1 AAGAAAGAAGAAA-AGAA
46534427 AAGAAAGAAGAAAAGAA
1 AAGAAAGAAGAAAAGAA
46534444 AA
1 AA
46534446 AATTAAAGGT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 15 0.83
18 3 0.17
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (17 bp):
AAGAAAGAAGAAAAGAA
Found at i:46536012 original size:53 final size:53
Alignment explanation
Indices: 46535829--46536036 Score: 258
Period size: 55 Copynumber: 3.8 Consensus size: 53
46535819 ATTAGGGTTT
*
46535829 AAGGATACCATGTAAGACCATGCCAAGGCATGGCAGTTGGTAAGGTTTC-TAAGGC
1 AAGGATACCATGTAAGACCATGCCAAGACATGGCA-TTGGTAA-G-TTCATAAGGC
* * * *
46535884 AAGGAAATCATGTAAGACCATGTCAAGACATGGCATTGATAAGTTACTATAAGGC
1 AAGGATACCATGTAAGACCATGCCAAGACATGGCATTGGTAAGTT-C-ATAAGGC
* * *
46535939 AAAGG-TCCCATGTAAGACCATGCCAAGGCATGGCATTGGTGAGTTCATAAGGC
1 -AAGGATACCATGTAAGACCATGCCAAGACATGGCATTGGTAAGTTCATAAGGC
* *
46535992 AAGGATACCATGTAAGACCATGTCAAGACATGGCAATGGTAAGTT
1 AAGGATACCATGTAAGACCATGCCAAGACATGGCATTGGTAAGTT
46536037 TCAAAAGGAT
Statistics
Matches: 131, Mismatches: 17, Indels: 12
0.82 0.11 0.08
Matches are distributed among these distances:
52 6 0.05
53 44 0.34
54 7 0.05
55 70 0.53
56 4 0.03
ACGTcount: A:0.35, C:0.17, G:0.26, T:0.22
Consensus pattern (53 bp):
AAGGATACCATGTAAGACCATGCCAAGACATGGCATTGGTAAGTTCATAAGGC
Found at i:46536035 original size:108 final size:110
Alignment explanation
Indices: 46535836--46536036 Score: 327
Period size: 108 Copynumber: 1.8 Consensus size: 110
46535826 TTTAAGGATA
*
46535836 CCATGTAAGACCATGCCAAGGCATGGCAGTTGGTAAGGTTTCTAAGGCAAGGAAATCATGTAAGA
1 CCATGTAAGACCATGCCAAGGCATGGCAGTTGGTAAGGTTTCTAAGGCAAGGAAACCATGTAAGA
*
46535901 CCATGTCAAGACATGGCATTGATAAGTTACTATAAGGCAAAGGTC
66 CCATGTCAAGACATGGCAATGATAAGTTACTATAAGGCAAAGGTC
* *
46535946 CCATGTAAGACCATGCCAAGGCATGGCA-TTGGTGA-G-TTCATAAGGCAAGGATACCATGTAAG
1 CCATGTAAGACCATGCCAAGGCATGGCAGTTGGTAAGGTTTC-TAAGGCAAGGAAACCATGTAAG
*
46536008 ACCATGTCAAGACATGGCAATGGTAAGTT
65 ACCATGTCAAGACATGGCAATGATAAGTT
46536037 TCAAAAGGAT
Statistics
Matches: 85, Mismatches: 5, Indels: 4
0.90 0.05 0.04
Matches are distributed among these distances:
107 3 0.04
108 48 0.56
109 6 0.07
110 28 0.33
ACGTcount: A:0.34, C:0.18, G:0.26, T:0.22
Consensus pattern (110 bp):
CCATGTAAGACCATGCCAAGGCATGGCAGTTGGTAAGGTTTCTAAGGCAAGGAAACCATGTAAGA
CCATGTCAAGACATGGCAATGATAAGTTACTATAAGGCAAAGGTC
Found at i:46537845 original size:3 final size:3
Alignment explanation
Indices: 46537837--46537873 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
46537827 GAATGGTAAG
46537837 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
46537874 GAATTGAATA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:46538254 original size:6 final size:6
Alignment explanation
Indices: 46538239--46538271 Score: 57
Period size: 6 Copynumber: 5.5 Consensus size: 6
46538229 GTACTTTATG
*
46538239 TACTGC TACTGT TACTGT TACTGT TACTGT TAC
1 TACTGT TACTGT TACTGT TACTGT TACTGT TAC
46538272 CCTTACAGTG
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.18, C:0.21, G:0.15, T:0.45
Consensus pattern (6 bp):
TACTGT
Found at i:46538277 original size:18 final size:18
Alignment explanation
Indices: 46538239--46538277 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
46538229 GTACTTTATG
**
46538239 TACTGCTACTGTTACTGT
1 TACTGCTACTGTTACCCT
*
46538257 TACTGTTACTGTTACCCT
1 TACTGCTACTGTTACCCT
46538275 TAC
1 TAC
46538278 AGTGTATTTC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.18, C:0.26, G:0.13, T:0.44
Consensus pattern (18 bp):
TACTGCTACTGTTACCCT
Found at i:46538436 original size:18 final size:18
Alignment explanation
Indices: 46538415--46538449 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
46538405 TTGAATAATT
*
46538415 GACTGTTACAGAATAAAC
1 GACTGATACAGAATAAAC
*
46538433 GACTGATACTGAATAAA
1 GACTGATACAGAATAAA
46538450 TGAATATTAT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.46, C:0.14, G:0.17, T:0.23
Consensus pattern (18 bp):
GACTGATACAGAATAAAC
Found at i:46541054 original size:21 final size:22
Alignment explanation
Indices: 46541028--46541077 Score: 75
Period size: 22 Copynumber: 2.3 Consensus size: 22
46541018 TTGCAGCATT
*
46541028 GGCGTGT-CCTCAGACCACACG
1 GGCGTGTCCCTCAGACCACACA
*
46541049 GGCGTGTCCCTCGGACCACACA
1 GGCGTGTCCCTCAGACCACACA
46541071 GGCGTGT
1 GGCGTGT
46541078 GAGCCCTGTA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
21 7 0.27
22 19 0.73
ACGTcount: A:0.16, C:0.36, G:0.32, T:0.16
Consensus pattern (22 bp):
GGCGTGTCCCTCAGACCACACA
Found at i:46546847 original size:46 final size:44
Alignment explanation
Indices: 46546712--46546917 Score: 168
Period size: 46 Copynumber: 4.5 Consensus size: 44
46546702 GTTGATGCTG
* *
46546712 TGTCCCAGACAGGTCTTACACTGACACATATC-AAGCCGATGCCA
1 TGTCCCAGACAAGTCTTACACTGACACATATCGTAGCCGATG-CA
* * * * *
46546756 TGTCCCAGGCATGGTCTTACACT-AGCTTTCACGAT-GTAGCTGATGCA
1 TGTCCCAGACA-AGTCTTACACTGA-C--ACA-TATCGTAGCCGATGCA
*
46546803 TGTCCCAGACAAGTCTTACACTAGCACATATATCCGT-GCCGATGCCA
1 TGTCCCAGACAAGTCTTACACT-G-ACACATAT-CGTAGCCGATG-CA
* *
46546850 TGTCCCAGACATGGTCTTACACTGACACATCTCGTAGCCGATGCA
1 TGTCCCAGACA-AGTCTTACACTGACACATATCGTAGCCGATGCA
* * *
46546895 TGTCCTAGACATGTTTTACACTG
1 TGTCCCAGACAAGTCTTACACTG
46546918 GCTTACGTCC
Statistics
Matches: 131, Mismatches: 17, Indels: 28
0.74 0.10 0.16
Matches are distributed among these distances:
44 21 0.16
45 29 0.22
46 30 0.23
47 30 0.23
48 20 0.15
49 1 0.01
ACGTcount: A:0.25, C:0.29, G:0.19, T:0.26
Consensus pattern (44 bp):
TGTCCCAGACAAGTCTTACACTGACACATATCGTAGCCGATGCA
Found at i:46546957 original size:138 final size:137
Alignment explanation
Indices: 46546712--46546974 Score: 345
Period size: 138 Copynumber: 1.9 Consensus size: 137
46546702 GTTGATGCTG
*
46546712 TGTCCCAGACAGGTCTTACACTGACACATATCAAGCCGATGCCATGTCCCAGGCATGGTCTTACA
1 TGTCCCAGACAGGTCTTACACTGACACATATCAAGCCGATGCCATGTCCCAGACATGGTCTTACA
*
46546777 CTAGCTTTCACGATGTAGCTGATGCATGTCCCAGACAAGTCTTACACTAGCACATATATCCGTGC
66 CTAGCTTTCACGATG-AGCTGATGCATGTCCCAGACAAGTCTTACACTAGCACACATATCCGTGC
46546842 CGATGCCA
130 CGATGCCA
* * * *
46546850 TGTCCCAGACATGGTCTTACACTGACACATCTCGTAGCCGATG-CATGTCCTAGACAT-GTTTTA
1 TGTCCCAGACA-GGTCTTACACTGACACATATC-AAGCCGATGCCATGTCCCAGACATGGTCTTA
* * * * *
46546913 CACTGGCTTACGTCCCGA-G-GTTGATGCATGTCCCAGACATGTCTTACACTGGCACACATATC
64 CACTAGCTT---TCACGATGAGCTGATGCATGTCCCAGACAAGTCTTACACTAGCACACATATC
46546975 ACTTGCACTG
Statistics
Matches: 109, Mismatches: 11, Indels: 10
0.84 0.08 0.08
Matches are distributed among these distances:
138 63 0.58
139 32 0.29
140 9 0.08
141 5 0.05
ACGTcount: A:0.25, C:0.29, G:0.20, T:0.26
Consensus pattern (137 bp):
TGTCCCAGACAGGTCTTACACTGACACATATCAAGCCGATGCCATGTCCCAGACATGGTCTTACA
CTAGCTTTCACGATGAGCTGATGCATGTCCCAGACAAGTCTTACACTAGCACACATATCCGTGCC
GATGCCA
Found at i:46555558 original size:17 final size:17
Alignment explanation
Indices: 46555536--46555568 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
46555526 TCTCTTCACT
46555536 TTAGTTTAATTAATTAA
1 TTAGTTTAATTAATTAA
*
46555553 TTAGTTTAGTTAATTA
1 TTAGTTTAATTAATTA
46555569 GTTTAATAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.36, C:0.00, G:0.09, T:0.55
Consensus pattern (17 bp):
TTAGTTTAATTAATTAA
Found at i:46555567 original size:13 final size:13
Alignment explanation
Indices: 46555549--46555573 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
46555539 GTTTAATTAA
46555549 TTAATTAGTTTAG
1 TTAATTAGTTTAG
46555562 TTAATTAGTTTA
1 TTAATTAGTTTA
46555574 ATAAACAACC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.00, G:0.12, T:0.56
Consensus pattern (13 bp):
TTAATTAGTTTAG
Found at i:46561044 original size:6 final size:6
Alignment explanation
Indices: 46561033--46561086 Score: 53
Period size: 6 Copynumber: 9.7 Consensus size: 6
46561023 TCCTCTTATC
* **
46561033 TTTTTA TTTTTA TTTTTA -TTTT- TTTTTA TTTTCA TTTCAA TTTTT-
1 TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA
46561078 TTTTT- TTTT
1 TTTTTA TTTT
46561087 GAAAGACAAT
Statistics
Matches: 41, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
5 17 0.41
6 24 0.59
ACGTcount: A:0.13, C:0.04, G:0.00, T:0.83
Consensus pattern (6 bp):
TTTTTA
Found at i:46561060 original size:16 final size:17
Alignment explanation
Indices: 46561034--46561069 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 17
46561024 CCTCTTATCT
*
46561034 TTTTATTTTTATTTTTA
1 TTTTATTTTTATTTTCA
46561051 TTTT-TTTTTATTTTCA
1 TTTTATTTTTATTTTCA
46561067 TTT
1 TTT
46561070 CAATTTTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 14 0.78
17 4 0.22
ACGTcount: A:0.14, C:0.03, G:0.00, T:0.83
Consensus pattern (17 bp):
TTTTATTTTTATTTTCA
Found at i:46561061 original size:22 final size:22
Alignment explanation
Indices: 46561033--46561086 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
46561023 TCCTCTTATC
**
46561033 TTTTTATTTTTATTTTTATTTT
1 TTTTTATTTTTATTTCAATTTT
*
46561055 TTTTTATTTTCATTTCAATTTT
1 TTTTTATTTTTATTTCAATTTT
46561077 TTTTT-TTTTT
1 TTTTTATTTTT
46561087 GAAAGACAAT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
21 4 0.14
22 24 0.86
ACGTcount: A:0.13, C:0.04, G:0.00, T:0.83
Consensus pattern (22 bp):
TTTTTATTTTTATTTCAATTTT
Found at i:46563941 original size:22 final size:22
Alignment explanation
Indices: 46563916--46563958 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
46563906 TTCTCTTCAC
46563916 TTTAGTTTAATTAG-TTAATAAG
1 TTTAG-TTAATTAGTTTAATAAG
46563938 TTTAGTTAATTAGTTTAATAA
1 TTTAGTTAATTAGTTTAATAA
46563959 ACAACCCCTC
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
21 8 0.40
22 12 0.60
ACGTcount: A:0.37, C:0.00, G:0.12, T:0.51
Consensus pattern (22 bp):
TTTAGTTAATTAGTTTAATAAG
Found at i:46567331 original size:40 final size:40
Alignment explanation
Indices: 46567262--46567426 Score: 296
Period size: 40 Copynumber: 4.2 Consensus size: 40
46567252 AACCCAAGTA
* *
46567262 CCTTCGGGATTTAG-CCGGATATAGCAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
46567301 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
46567341 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
*
46567381 CCTTCGGAACTTAGCCCGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
46567421 CCTTCG
1 CCTTCG
46567427 AATCTTAGTC
Statistics
Matches: 122, Mismatches: 3, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
39 13 0.11
40 109 0.89
ACGTcount: A:0.27, C:0.28, G:0.22, T:0.23
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
Found at i:46567965 original size:2 final size:2
Alignment explanation
Indices: 46567958--46567987 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
46567948 CACCATACGC
46567958 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
46567988 TTCTCTAGTC
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:46570743 original size:37 final size:36
Alignment explanation
Indices: 46570690--46570779 Score: 144
Period size: 37 Copynumber: 2.4 Consensus size: 36
46570680 TATAAAAGAA
46570690 GTCTTACCCGGACATAATCTCCACACGTAGTCATCGG
1 GTCTTACCCGGACATAATCTCCACACGTAGTCATC-G
*
46570727 GTCTTACCCGGTCATAATCTCCACACGTAGTCATCG
1 GTCTTACCCGGACATAATCTCCACACGTAGTCATCG
*
46570763 GTCTCACCCGGAACATA
1 GTCTTACCCGG-ACATA
46570780 TTCCAAGTTT
Statistics
Matches: 49, Mismatches: 3, Indels: 2
0.91 0.06 0.04
Matches are distributed among these distances:
36 11 0.22
37 38 0.78
ACGTcount: A:0.24, C:0.33, G:0.18, T:0.24
Consensus pattern (36 bp):
GTCTTACCCGGACATAATCTCCACACGTAGTCATCG
Found at i:46570930 original size:49 final size:49
Alignment explanation
Indices: 46570875--46571089 Score: 367
Period size: 49 Copynumber: 4.4 Consensus size: 49
46570865 TTTTACATTA
46570875 GCCATTAGGCCTTATCACATATACATACACTTTCACATTCACCACATCG
1 GCCATTAGGCCTTATCACATATACATACACTTTCACATTCACCACATCG
*
46570924 GCCATTAGGCCTCATCACATATACATACACTTTCACATTCACCACATCG
1 GCCATTAGGCCTTATCACATATACATACACTTTCACATTCACCACATCG
* *
46570973 GCCATTAGGCCTCATCACATATACATACACTTTCACATTCATCACATCG
1 GCCATTAGGCCTTATCACATATACATACACTTTCACATTCACCACATCG
* * *
46571022 GCCATTAGGCCTTATCACATATACATACACTTTCACATTCATCGCATTG
1 GCCATTAGGCCTTATCACATATACATACACTTTCACATTCACCACATCG
*
46571071 GCCATTCGGCCTTATCACA
1 GCCATTAGGCCTTATCACA
46571090 CATATATGTA
Statistics
Matches: 160, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
49 160 1.00
ACGTcount: A:0.29, C:0.33, G:0.09, T:0.29
Consensus pattern (49 bp):
GCCATTAGGCCTTATCACATATACATACACTTTCACATTCACCACATCG
Found at i:46574142 original size:16 final size:17
Alignment explanation
Indices: 46574123--46574156 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
46574113 AAATATTATG
*
46574123 AAATAATAAT-AAACAA
1 AAATAAAAATCAAACAA
46574139 AAATAAAAATCAAACAA
1 AAATAAAAATCAAACAA
46574156 A
1 A
46574157 CATTATCCCC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 9 0.56
17 7 0.44
ACGTcount: A:0.76, C:0.09, G:0.00, T:0.15
Consensus pattern (17 bp):
AAATAAAAATCAAACAA
Found at i:46584559 original size:29 final size:29
Alignment explanation
Indices: 46584492--46584559 Score: 75
Period size: 29 Copynumber: 2.2 Consensus size: 29
46584482 ACCATAGCAT
46584492 CCTACAATTTTCATTTATTTCACAATTTAAC
1 CCTA-AATTTTCA-TTATTTCACAATTTAAC
* *
46584523 CATAAAATTTTCA-TATTTCTCAATTTAATC
1 CCT-AAATTTTCATTATTTCACAATTTAA-C
46584553 CCTAAAT
1 CCTAAAT
46584560 GACAATTTTG
Statistics
Matches: 32, Mismatches: 3, Indels: 6
0.78 0.07 0.15
Matches are distributed among these distances:
29 18 0.56
30 3 0.09
31 10 0.31
32 1 0.03
ACGTcount: A:0.35, C:0.21, G:0.00, T:0.44
Consensus pattern (29 bp):
CCTAAATTTTCATTATTTCACAATTTAAC
Found at i:46596035 original size:29 final size:30
Alignment explanation
Indices: 46596002--46596059 Score: 91
Period size: 29 Copynumber: 2.0 Consensus size: 30
46595992 AATTATTCAT
46596002 ATTTAATAATATAATAAATTA-TTAATATA
1 ATTTAATAATATAATAAATTATTTAATATA
* *
46596031 ATTTAATATTTTAATAAATTATTTAATAT
1 ATTTAATAATATAATAAATTATTTAATAT
46596060 TATAATTTTA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
29 19 0.73
30 7 0.27
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (30 bp):
ATTTAATAATATAATAAATTATTTAATATA
Found at i:46599190 original size:18 final size:18
Alignment explanation
Indices: 46599148--46599192 Score: 76
Period size: 17 Copynumber: 2.6 Consensus size: 18
46599138 GAAAAATGAG
46599148 AATTTTT-AAAACACGAA
1 AATTTTTGAAAACACGAA
46599165 AA-TTTTGAAAACACGAA
1 AATTTTTGAAAACACGAA
46599182 AATTTTTGAAA
1 AATTTTTGAAA
46599193 CCTGAATTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
16 4 0.15
17 14 0.54
18 8 0.31
ACGTcount: A:0.51, C:0.09, G:0.09, T:0.31
Consensus pattern (18 bp):
AATTTTTGAAAACACGAA
Found at i:46606436 original size:22 final size:21
Alignment explanation
Indices: 46606385--46606438 Score: 56
Period size: 22 Copynumber: 2.5 Consensus size: 21
46606375 ATTTTTTTTC
46606385 TATTTTTTGAATGTTTGAATTA
1 TATTTTTT-AATGTTTGAATTA
* *
46606407 T-TATTTTTAATTTTTAGATTTA
1 TAT-TTTTTAATGTTT-GAATTA
46606429 TATTTTTTAA
1 TATTTTTTAA
46606439 AAAAATTAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
21 7 0.26
22 19 0.70
23 1 0.04
ACGTcount: A:0.28, C:0.00, G:0.07, T:0.65
Consensus pattern (21 bp):
TATTTTTTAATGTTTGAATTA
Found at i:46606593 original size:29 final size:30
Alignment explanation
Indices: 46606558--46606618 Score: 90
Period size: 29 Copynumber: 2.1 Consensus size: 30
46606548 TTTTCAATTT
*
46606558 TTATATTTAT-TATTTTGAAATTTTA-AAAA
1 TTATATTTATATA-TTTAAAATTTTATAAAA
46606587 TTATATTTATATATTTAAAATTTTATAAAA
1 TTATATTTATATATTTAAAATTTTATAAAA
46606617 TT
1 TT
46606619 TTAAAAATAA
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
29 21 0.72
30 8 0.28
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.56
Consensus pattern (30 bp):
TTATATTTATATATTTAAAATTTTATAAAA
Found at i:46607822 original size:33 final size:33
Alignment explanation
Indices: 46607785--46607852 Score: 109
Period size: 33 Copynumber: 2.1 Consensus size: 33
46607775 AGATTACTTT
*
46607785 ATATTTTACATATCATTATATTAAATTATTTAA
1 ATATTTAACATATCATTATATTAAATTATTTAA
**
46607818 ATATTTAATTTATCATTATATTAAATTATTTAA
1 ATATTTAACATATCATTATATTAAATTATTTAA
46607851 AT
1 AT
46607853 CTTATTTATT
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.43, C:0.04, G:0.00, T:0.53
Consensus pattern (33 bp):
ATATTTAACATATCATTATATTAAATTATTTAA
Found at i:46607825 original size:17 final size:16
Alignment explanation
Indices: 46607802--46607852 Score: 52
Period size: 16 Copynumber: 3.1 Consensus size: 16
46607792 ACATATCATT
46607802 ATATTAAATTATTTAA
1 ATATTAAATTATTTAA
*
46607818 ATATTTAATTTATCATT--
1 ATA-TTAAATTAT--TTAA
46607835 ATATTAAATTATTTAA
1 ATATTAAATTATTTAA
46607851 AT
1 AT
46607853 CTTATTTATT
Statistics
Matches: 28, Mismatches: 2, Indels: 10
0.70 0.05 0.25
Matches are distributed among these distances:
14 2 0.07
16 13 0.46
17 11 0.39
19 2 0.07
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (16 bp):
ATATTAAATTATTTAA
Found at i:46607839 original size:25 final size:29
Alignment explanation
Indices: 46607811--46607868 Score: 72
Period size: 25 Copynumber: 2.2 Consensus size: 29
46607801 TATATTAAAT
46607811 TATTTAAA-TATTT-AAT-TTA-TCATTA
1 TATTTAAATTATTTAAATCTTATTCATTA
*
46607836 TA-TTAAATTATTTAAATCTTATTTATTA
1 TATTTAAATTATTTAAATCTTATTCATTA
46607864 TATTT
1 TATTT
46607869 GATTTTTTAA
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
24 5 0.19
25 7 0.26
26 3 0.11
27 3 0.11
28 7 0.26
29 2 0.07
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.59
Consensus pattern (29 bp):
TATTTAAATTATTTAAATCTTATTCATTA
Found at i:46607841 original size:16 final size:16
Alignment explanation
Indices: 46607795--46607846 Score: 54
Period size: 16 Copynumber: 3.2 Consensus size: 16
46607785 ATATTTTACA
46607795 TATCATTATATTAAAT
1 TATCATTATATTAAAT
*
46607811 TAT--TTAAATATTTAATT
1 TATCATT--ATA-TTAAAT
46607828 TATCATTATATTAAAT
1 TATCATTATATTAAAT
46607844 TAT
1 TAT
46607847 TTAAATCTTA
Statistics
Matches: 29, Mismatches: 2, Indels: 10
0.71 0.05 0.24
Matches are distributed among these distances:
14 2 0.07
16 14 0.48
17 11 0.38
19 2 0.07
ACGTcount: A:0.42, C:0.04, G:0.00, T:0.54
Consensus pattern (16 bp):
TATCATTATATTAAAT
Found at i:46611320 original size:61 final size:62
Alignment explanation
Indices: 46611213--46611339 Score: 148
Period size: 61 Copynumber: 2.1 Consensus size: 62
46611203 TTCTTCATCT
* * * * ** * * * *
46611213 TTTTTTAAATACTTAATATTTAATTTCGAATCTTGTATGATAAGTAATATATTAGTTTGGTA
1 TTTTTTAAAGACTTAATACTCAATTTCGAATCTTCTACAATAAGTAAGATAATAATTTGATA
*
46611275 TTTTTTAAGGACTTAATACTCAATTT-GAATCTTCTACAATAAGTAAGATAATAATTTGATA
1 TTTTTTAAAGACTTAATACTCAATTTCGAATCTTCTACAATAAGTAAGATAATAATTTGATA
46611336 TTTT
1 TTTT
46611340 GAATTTTTTT
Statistics
Matches: 54, Mismatches: 11, Indels: 1
0.82 0.17 0.02
Matches are distributed among these distances:
61 32 0.59
62 22 0.41
ACGTcount: A:0.35, C:0.07, G:0.10, T:0.47
Consensus pattern (62 bp):
TTTTTTAAAGACTTAATACTCAATTTCGAATCTTCTACAATAAGTAAGATAATAATTTGATA
Found at i:46611534 original size:20 final size:22
Alignment explanation
Indices: 46611497--46611537 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 22
46611487 AATAAAAGAA
46611497 AAAATAAAAAGATATAAAAATG
1 AAAATAAAAAGATATAAAAATG
*
46611519 AAAA-AAAAA-ATTTAAAAAT
1 AAAATAAAAAGATATAAAAAT
46611538 TTAAAAAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 9 0.50
21 5 0.28
22 4 0.22
ACGTcount: A:0.76, C:0.00, G:0.05, T:0.20
Consensus pattern (22 bp):
AAAATAAAAAGATATAAAAATG
Found at i:46616885 original size:3 final size:3
Alignment explanation
Indices: 46616879--46616905 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
46616869 TAACGGGTGT
46616879 TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA
46616906 CTTTGTATAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:46619939 original size:49 final size:50
Alignment explanation
Indices: 46619814--46619996 Score: 168
Period size: 49 Copynumber: 3.7 Consensus size: 50
46619804 TATGAGATGT
*
46619814 GTCAGTGTAAGACCATGTCTGGGACATGGCATCGGCACGGAAATGTGAGA
1 GTCAGTGTAAGACCATGTCTGGGACATGGCATCGGCACCGAAATGTGAGA
* * * * * *
46619864 G-CTAGTGTAAGACTATGTTTGGGACATGGCGTCGGC-CTCG-ATTTTGATA
1 GTC-AGTGTAAGACCATGTCTGGGACATGGCATCGGCAC-CGAAATGTGAGA
* * *
46619913 GTCAGTGTAGGACCATGTCTGGGACATGGCATC--AACTTG--ATG-GATGA
1 GTCAGTGTAAGACCATGTCTGGGACATGGCATCGGCAC-CGAAATGTGA-GA
46619960 G-CTAGTGTAAGACCATGTCTGGGACATGGCATCGGCA
1 GTC-AGTGTAAGACCATGTCTGGGACATGGCATCGGCA
46619997 TTATACCCTA
Statistics
Matches: 107, Mismatches: 18, Indels: 17
0.75 0.13 0.12
Matches are distributed among these distances:
46 3 0.03
47 32 0.30
48 3 0.03
49 36 0.34
50 33 0.31
ACGTcount: A:0.25, C:0.18, G:0.32, T:0.25
Consensus pattern (50 bp):
GTCAGTGTAAGACCATGTCTGGGACATGGCATCGGCACCGAAATGTGAGA
Found at i:46623216 original size:79 final size:82
Alignment explanation
Indices: 46623073--46623257 Score: 220
Period size: 79 Copynumber: 2.3 Consensus size: 82
46623063 TCGAATGATG
* * *
46623073 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACTATATCCGGACTAGGATCCGAAGACATT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACTAAACCCGGACTAAGATCCGAAGACATT
*
46623137 CGTGCGAGTTAATA-AA
66 CGTGCGAGTCAATATAA
* ** *
46623153 TCCGGGCTAAG-CCCGAAGGCATTTGTGC-AAGTTACTAAACCCGGGTTAAG-TCCCGAAGGCAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACTAAACCCGGACTAAGAT-CCGAAGACAT
*
46623215 TCGTGCGAGTCACTATAA
65 TCGTGCGAGTCAATATAA
**
46623233 -CCGGGCTTCGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
46623258 AGCGAGTCGT
Statistics
Matches: 90, Mismatches: 11, Indels: 8
0.83 0.10 0.07
Matches are distributed among these distances:
78 1 0.01
79 55 0.61
80 34 0.38
ACGTcount: A:0.25, C:0.24, G:0.27, T:0.24
Consensus pattern (82 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACTAAACCCGGACTAAGATCCGAAGACATT
CGTGCGAGTCAATATAA
Found at i:46623265 original size:40 final size:40
Alignment explanation
Indices: 46623074--46623265 Score: 142
Period size: 40 Copynumber: 4.8 Consensus size: 40
46623064 CGAATGATGT
* * * * *
46623074 CCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACTATAT
1 CCGGGTTAAGTCCCGAAGGCATTTGTGC-GAGTCACTAAAC
** * * * * * *
46623114 CCGGACTAGGAT-CCGAAGACATTCGTGCGAGTTAATAAAT
1 CCGGGTTAAG-TCCCGAAGGCATTTGTGCGAGTCACTAAAC
* * *
46623154 CCGGGCTAAG-CCCGAAGGCATTTGTGCAAGTTACTAAAC
1 CCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTCACTAAAC
*
46623193 CCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTCACTATAA-
1 CCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTCACTA-AAC
* *
46623233 CCGGGCTT-CGTCCCGAAGGCATTTGAGCGAGTC
1 CCGGG-TTAAGTCCCGAAGGCATTTGTGCGAGTC
46623266 GTTATATCCG
Statistics
Matches: 124, Mismatches: 22, Indels: 12
0.78 0.14 0.08
Matches are distributed among these distances:
39 32 0.26
40 81 0.65
41 11 0.09
ACGTcount: A:0.25, C:0.24, G:0.28, T:0.23
Consensus pattern (40 bp):
CCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTCACTAAAC
Found at i:46627657 original size:40 final size:39
Alignment explanation
Indices: 46627612--46627741 Score: 163
Period size: 40 Copynumber: 3.3 Consensus size: 39
46627602 CGGAATACAA
46627612 CCGGATATAACCACGTGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATAACCAC-TGCACGAATGCCTTCGGGTCTTAGC
* *
46627652 CCGGATAGAACGACTTGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATAACCAC-TGCACGAATGCCTTCGGGTCTTAGC
* * * *
46627692 CCGGATGTAGCCGCTAGCAC-AATTGCCTTCGGGTCTTAAC
1 CCGGATATAACCACT-GCACGAA-TGCCTTCGGGTCTTAGC
46627732 CCGGATATAA
1 CCGGATATAA
46627742 TTTCCAGCAT
Statistics
Matches: 77, Mismatches: 11, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
39 3 0.04
40 74 0.96
ACGTcount: A:0.23, C:0.28, G:0.25, T:0.23
Consensus pattern (39 bp):
CCGGATATAACCACTGCACGAATGCCTTCGGGTCTTAGC
Found at i:46635577 original size:40 final size:40
Alignment explanation
Indices: 46635503--46635721 Score: 363
Period size: 40 Copynumber: 5.5 Consensus size: 40
46635493 AACCCAAGTA
* *
46635503 CCTTCGGGATTTAG-CCGGATATAG-CAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTC-ACTAGCACAAATG
46635542 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
*
46635582 CCTTCGGGACTTAGCCCGGATATAGTCAATAGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
*
46635622 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAACTG
1 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
*
46635662 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCAC-CATG
1 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
46635701 CCTTCGGGACTTAGCCCGGAT
1 CCTTCGGGACTTAGCCCGGAT
46635722 GTCATCCGAA
Statistics
Matches: 171, Mismatches: 7, Indels: 4
0.94 0.04 0.02
Matches are distributed among these distances:
39 36 0.21
40 134 0.78
41 1 0.01
ACGTcount: A:0.26, C:0.28, G:0.23, T:0.23
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
Found at i:46644063 original size:40 final size:40
Alignment explanation
Indices: 46643989--46644167 Score: 292
Period size: 40 Copynumber: 4.5 Consensus size: 40
46643979 AACCCAAGTA
* *
46643989 CCTTCGGGATTTAG-CCGGATATAG-CAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTC-ACTAGCACAAATG
46644028 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
*
46644068 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAACTG
1 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
*
46644108 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCAC-CATG
1 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
46644147 CCTTCGGGACTTAGCCCGGAT
1 CCTTCGGGACTTAGCCCGGAT
46644168 GTCATCGAAT
Statistics
Matches: 133, Mismatches: 5, Indels: 4
0.94 0.04 0.03
Matches are distributed among these distances:
39 36 0.27
40 96 0.72
41 1 0.01
ACGTcount: A:0.25, C:0.29, G:0.23, T:0.23
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
Found at i:46649090 original size:16 final size:15
Alignment explanation
Indices: 46649069--46649098 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
46649059 TCATTTTAAA
46649069 ATTTATTTTACATTTT
1 ATTTATTTTA-ATTTT
46649085 ATTTATTTTAATTT
1 ATTTATTTTAATTT
46649099 GCTTTTTATA
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:0.27, C:0.03, G:0.00, T:0.70
Consensus pattern (15 bp):
ATTTATTTTAATTTT
Found at i:46649610 original size:103 final size:103
Alignment explanation
Indices: 46649431--46649728 Score: 526
Period size: 103 Copynumber: 2.9 Consensus size: 103
46649421 AAAAAGAGAA
** *
46649431 CTTTCTAAATAAGATAATATTTTGCGTTTTAGGAAATTCGAGGAATCGTGCCCTAACTTAC-GAG
1 CTTTCTAAATAAGGCAATATTTCGCGTTTTAGGAAATTCGAGGAATCGTGCCCTAACTTACAG-G
46649495 GCTTCGATTTTTCTCGTTAAACCTAAATAGCCAAGTATC
65 GCTTCGATTTTTCTCGTTAAACCTAAATAGCCAAGTATC
*
46649534 CTTTCTAAATAAGGCAATATTTCGCGTTTTAGGAAATTCGAGGAATCGTGTCCTAACTTACAGGG
1 CTTTCTAAATAAGGCAATATTTCGCGTTTTAGGAAATTCGAGGAATCGTGCCCTAACTTACAGGG
46649599 CTTCGATTTTTCTCGTTAAACCTAAATAGCCAAGTATC
66 CTTCGATTTTTCTCGTTAAACCTAAATAGCCAAGTATC
*
46649637 CTTTCTAAATAAGGCAATATTACGCGTTTTAGGAAATTCGAGGAATCGTGCCCTAACTTACAGGG
1 CTTTCTAAATAAGGCAATATTTCGCGTTTTAGGAAATTCGAGGAATCGTGCCCTAACTTACAGGG
46649702 CTTCGATTTTTCTCGATTAAACCTAAA
66 CTTCGATTTTTCTCG-TTAAACCTAAA
46649729 GTATCCTTTT
Statistics
Matches: 187, Mismatches: 6, Indels: 3
0.95 0.03 0.02
Matches are distributed among these distances:
103 175 0.94
104 12 0.06
ACGTcount: A:0.30, C:0.19, G:0.17, T:0.34
Consensus pattern (103 bp):
CTTTCTAAATAAGGCAATATTTCGCGTTTTAGGAAATTCGAGGAATCGTGCCCTAACTTACAGGG
CTTCGATTTTTCTCGTTAAACCTAAATAGCCAAGTATC
Found at i:46651618 original size:19 final size:19
Alignment explanation
Indices: 46651586--46651623 Score: 51
Period size: 18 Copynumber: 2.0 Consensus size: 19
46651576 GCATGCTAAA
*
46651586 GTTTTTTTTCCTTT-TTTT
1 GTTTTTTTCCCTTTATTTT
46651604 GTTTTTTTCCTCTTTATTTT
1 GTTTTTTTCC-CTTTATTTT
46651624 CCTTTCTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 9 0.53
19 4 0.24
20 4 0.24
ACGTcount: A:0.03, C:0.13, G:0.05, T:0.79
Consensus pattern (19 bp):
GTTTTTTTCCCTTTATTTT
Found at i:46652348 original size:3 final size:3
Alignment explanation
Indices: 46652342--46652400 Score: 57
Period size: 3 Copynumber: 18.3 Consensus size: 3
46652332 TTACTACTTG
*
46652342 TTA TTA TTA TTA -TA TTA TTGAA TTAA TTAA CTTA GTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TT--A TT-A TT-A -TTA TTA TTA TTA TTA
46652388 TTA TTA TTA TTA T
1 TTA TTA TTA TTA T
46652401 AGTTCTTTCT
Statistics
Matches: 50, Mismatches: 2, Indels: 8
0.83 0.03 0.13
Matches are distributed among these distances:
2 2 0.04
3 36 0.72
4 7 0.14
5 5 0.10
ACGTcount: A:0.36, C:0.02, G:0.03, T:0.59
Consensus pattern (3 bp):
TTA
Found at i:46652556 original size:3 final size:3
Alignment explanation
Indices: 46652550--46652590 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
46652540 TACATAATAT
46652550 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
46652591 TTAGACGGTT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:46653214 original size:2 final size:2
Alignment explanation
Indices: 46653201--46653265 Score: 112
Period size: 2 Copynumber: 32.5 Consensus size: 2
46653191 TACTTTAGGT
* *
46653201 TA TA TT TA TA TA TA TA CA 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
46653243 TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA T
46653266 TTATTTAAAC
Statistics
Matches: 59, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 59 1.00
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:46653296 original size:26 final size:26
Alignment explanation
Indices: 46653255--46653315 Score: 81
Period size: 26 Copynumber: 2.3 Consensus size: 26
46653245 TATATATATA
46653255 TATATATATATTTA-TTTAAACTGTCTT-
1 TATATAT-TATTTATTTTAAAC--TCTTG
46653282 TATATATTATTTATTTTAAACTCTTG
1 TATATATTATTTATTTTAAACTCTTG
46653308 TATATATT
1 TATATATT
46653316 TCCTTTTTTA
Statistics
Matches: 32, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
25 4 0.12
26 14 0.44
27 14 0.44
ACGTcount: A:0.33, C:0.07, G:0.03, T:0.57
Consensus pattern (26 bp):
TATATATTATTTATTTTAAACTCTTG
Found at i:46659444 original size:9 final size:9
Alignment explanation
Indices: 46659421--46659504 Score: 68
Period size: 9 Copynumber: 9.4 Consensus size: 9
46659411 TAATATATTT
46659421 TAAAAAGTTA
1 TAAAAA-TTA
46659431 T-AAAATTA
1 TAAAAATTA
*
46659439 TAAAAA-AA
1 TAAAAATTA
*
46659447 TTAAAATTA
1 TAAAAATTA
46659456 TAAAAATGT-
1 TAAAAAT-TA
*
46659465 TAAAATTTA
1 TAAAAATTA
46659474 T-AAAATTA
1 TAAAAATTA
*
46659482 TTAAAAATCA
1 -TAAAAATTA
*
46659492 TAAAAAATA
1 TAAAAATTA
46659501 TAAA
1 TAAA
46659505 TTTATATAAA
Statistics
Matches: 59, Mismatches: 9, Indels: 13
0.73 0.11 0.16
Matches are distributed among these distances:
8 17 0.29
9 34 0.58
10 8 0.14
ACGTcount: A:0.64, C:0.01, G:0.02, T:0.32
Consensus pattern (9 bp):
TAAAAATTA
Found at i:46659451 original size:17 final size:17
Alignment explanation
Indices: 46659431--46659518 Score: 79
Period size: 17 Copynumber: 5.0 Consensus size: 17
46659421 TAAAAAGTTA
46659431 TAAAATTATAAAAAAAT
1 TAAAATTATAAAAAAAT
**
46659448 TAAAATTATAAAAATGT
1 TAAAATTATAAAAAAAT
**
46659465 TAAAATTTATAAAATTAT
1 TAAAA-TTATAAAAAAAT
*
46659483 TAAAAATCAT-AAAAAAT
1 T-AAAATTATAAAAAAAT
*
46659500 ATAAATTTATATAAAAAAT
1 -TAAAATTATA-AAAAAAT
46659519 ATTATTTTTT
Statistics
Matches: 57, Mismatches: 9, Indels: 8
0.77 0.12 0.11
Matches are distributed among these distances:
17 31 0.54
18 15 0.26
19 11 0.19
ACGTcount: A:0.64, C:0.01, G:0.01, T:0.34
Consensus pattern (17 bp):
TAAAATTATAAAAAAAT
Found at i:46659475 original size:35 final size:35
Alignment explanation
Indices: 46659407--46659518 Score: 111
Period size: 35 Copynumber: 3.1 Consensus size: 35
46659397 ATGTTTTTTT
* *
46659407 AAATTAATATATTTTAAAAAGTTATAAAATTATAAAA
1 AAATTAA-A-ATTATAAAAAGTTATAAATTTATAAAA
46659444 AAATTAAAATTATAAAAATGTTA-AAATTTATAAAA
1 AAATTAAAATTATAAAAA-GTTATAAATTTATAAAA
** * *
46659479 TTATTAAAAATCATAAAAA-ATATAAATTTATATAAA
1 AAATT-AAAATTATAAAAAGTTATAAATTTATA-AAA
46659515 AAAT
1 AAAT
46659519 ATTATTTTTT
Statistics
Matches: 63, Mismatches: 8, Indels: 9
0.79 0.10 0.11
Matches are distributed among these distances:
34 2 0.03
35 32 0.51
36 22 0.35
37 7 0.11
ACGTcount: A:0.62, C:0.01, G:0.02, T:0.36
Consensus pattern (35 bp):
AAATTAAAATTATAAAAAGTTATAAATTTATAAAA
Found at i:46659494 original size:18 final size:18
Alignment explanation
Indices: 46659432--46659497 Score: 80
Period size: 18 Copynumber: 3.7 Consensus size: 18
46659422 AAAAAGTTAT
*
46659432 AAAATTATAAAAAAATT-
1 AAAATTATAAAAATATTA
*
46659449 AAAATTATAAAAATGTTA
1 AAAATTATAAAAATATTA
* *
46659467 AAATTTATAAAATTATTA
1 AAAATTATAAAAATATTA
*
46659485 AAAATCATAAAAA
1 AAAATTATAAAAA
46659498 ATATAAATTT
Statistics
Matches: 40, Mismatches: 8, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
17 15 0.38
18 25 0.62
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.32
Consensus pattern (18 bp):
AAAATTATAAAAATATTA
Found at i:46659495 original size:27 final size:27
Alignment explanation
Indices: 46659432--46659516 Score: 84
Period size: 27 Copynumber: 3.1 Consensus size: 27
46659422 AAAAAGTTAT
*
46659432 AAAATTATAAAAAA-ATTAAAATTA-TA
1 AAAATCATAAAAAATA-TAAAATTATTA
** **
46659458 AAAATGTTAAAATTTATAAAATTATTA
1 AAAATCATAAAAAATATAAAATTATTA
*
46659485 AAAATCATAAAAAATATAAATTTATATA
1 AAAATCATAAAAAATATAAAATTAT-TA
46659513 AAAA
1 AAAA
46659517 ATATTATTTT
Statistics
Matches: 47, Mismatches: 9, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
26 18 0.38
27 23 0.49
28 6 0.13
ACGTcount: A:0.65, C:0.01, G:0.01, T:0.33
Consensus pattern (27 bp):
AAAATCATAAAAAATATAAAATTATTA
Found at i:46666973 original size:15 final size:16
Alignment explanation
Indices: 46666953--46666984 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
46666943 CTTTCAGTTC
46666953 TAAATTTGGTT-ATGT
1 TAAATTTGGTTCATGT
46666968 TAAATTTGGTTCATGT
1 TAAATTTGGTTCATGT
46666984 T
1 T
46666985 GATTTCGGTC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 11 0.69
16 5 0.31
ACGTcount: A:0.25, C:0.03, G:0.19, T:0.53
Consensus pattern (16 bp):
TAAATTTGGTTCATGT
Found at i:46668991 original size:321 final size:321
Alignment explanation
Indices: 46668409--46669050 Score: 1011
Period size: 321 Copynumber: 2.0 Consensus size: 321
46668399 TTTTCTCGGC
* * *
46668409 TCGGGTTGCACTGAAACTGGAGCTTCTGTTAGCAATGCCCTTAATTTCTCGAAACTCTCCTGACA
1 TCGGGTTGCACTAAAACTAGAGCTTCTGTTAGCAATGCCCTTAATTTCTCGAAACTCTCCTGAAA
**
46668474 TTTTTTTGACCAGTCAAACTTAACATCTTTTTGCAGCAACCTCGTCAAGGGAGTTGCAATCATAG
66 TTTTTCCGACCAGTCAAACTTAACATCTTTTTGCAGCAACCTCGTCAAGGGAGTTGCAATCATAG
* *
46668539 AAACTCCCTTTACAAAGCGTTGGTAGTAACTGACTAAGTCCAAGAAGCTTCTAACCTCAGTTACA
131 AAAATCCCTTTACAAAGCGTTGGTAGTAACCGACTAAGTCCAAGAAGCTTCTAACCTCAGTTACA
*
46668604 TTATCTGGCGGCTTCCACTCGACAATAGCAGAAATCTTATTTGGATCAACTCGAATGCCATCACC
196 TTATCTAGCGGCTTCCACTCGACAATAGCAGAAATCTTATTTGGATCAACTCGAATGCCATCACC
**
46668669 CGACACCATGTGACCCAAGAACCTGACCTCTCAAAGCCAAAATTCACTT-TGGCTGAACTTA
261 CGACACCATGTGACCCAAGAACCCAACCTCTCAAAGCCAAAATTCACTTCT-GCTGAACTTA
* * * * * *
46668730 TCGGGTTGCACTAAAATTAGAGCTTCTGTTGGGAATGTCCTTAATTTCTCGAAACTTTGCTGAAA
1 TCGGGTTGCACTAAAACTAGAGCTTCTGTTAGCAATGCCCTTAATTTCTCGAAACTCTCCTGAAA
*
46668795 TTTTTCCGACCAG-CAAAACTTAACATCTTTTTGCAGCAACCTCGTCAAGGGAGTTGCTATCATA
66 TTTTTCCGACCAGTC-AAACTTAACATCTTTTTGCAGCAACCTCGTCAAGGGAGTTGCAATCATA
*
46668859 GAAAATCCCTTTACAAAGCGTTGGTAGTAACCGTCTAAGTCCAAGAAGCTTCTAACCTCAGTTAC
130 GAAAATCCCTTTACAAAGCGTTGGTAGTAACCGACTAAGTCCAAGAAGCTTCTAACCTCAGTTAC
* *
46668924 ATTATTTAGCGGCTTCCACTCGACAATAGTAGAAATCTTATTTGGATCAACTC-AGATGCCATCA
195 ATTATCTAGCGGCTTCCACTCGACAATAGCAGAAATCTTATTTGGATCAACTCGA-ATGCCATCA
* * * * *
46668988 CCCGGCACTATGTGACCTAATAACCCAACCTCTCGAAGCCAAAATTCACTTCTGCTGAACTTA
259 CCCGACACCATGTGACCCAAGAACCCAACCTCTCAAAGCCAAAATTCACTTCTGCTGAACTTA
46669051 GCATATAATT
Statistics
Matches: 293, Mismatches: 25, Indels: 6
0.90 0.08 0.02
Matches are distributed among these distances:
320 2 0.01
321 290 0.99
322 1 0.00
ACGTcount: A:0.29, C:0.25, G:0.17, T:0.29
Consensus pattern (321 bp):
TCGGGTTGCACTAAAACTAGAGCTTCTGTTAGCAATGCCCTTAATTTCTCGAAACTCTCCTGAAA
TTTTTCCGACCAGTCAAACTTAACATCTTTTTGCAGCAACCTCGTCAAGGGAGTTGCAATCATAG
AAAATCCCTTTACAAAGCGTTGGTAGTAACCGACTAAGTCCAAGAAGCTTCTAACCTCAGTTACA
TTATCTAGCGGCTTCCACTCGACAATAGCAGAAATCTTATTTGGATCAACTCGAATGCCATCACC
CGACACCATGTGACCCAAGAACCCAACCTCTCAAAGCCAAAATTCACTTCTGCTGAACTTA
Found at i:46683017 original size:108 final size:108
Alignment explanation
Indices: 46682828--46683045 Score: 418
Period size: 108 Copynumber: 2.0 Consensus size: 108
46682818 ACCACTGATA
*
46682828 AGCTGTGTCCCTCAGAAGTGATACGACACATTTTAAACATTCAGTCAGTGTGCAAGAAAGCTCAT
1 AGCTGTGTCCCTCAGAAGTGATACGACACATTTTAAACACTCAGTCAGTGTGCAAGAAAGCTCAT
46682893 CAAATACCCGAATCATATTTTCAAGCCAAAATTTGGCTTTCTC
66 CAAATACCCGAATCATATTTTCAAGCCAAAATTTGGCTTTCTC
*
46682936 AGCTGTGTCCCTCAGAAGTGATACGACACATTTTAAACACTCAGTCGGTGTGCAAGAAAGCTCAT
1 AGCTGTGTCCCTCAGAAGTGATACGACACATTTTAAACACTCAGTCAGTGTGCAAGAAAGCTCAT
46683001 CAAATACCCGAATCATATTTTCAAGCCAAAATTTGGCTTTCTC
66 CAAATACCCGAATCATATTTTCAAGCCAAAATTTGGCTTTCTC
46683044 AG
1 AG
46683046 GATTGTCGTC
Statistics
Matches: 108, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
108 108 1.00
ACGTcount: A:0.32, C:0.23, G:0.17, T:0.28
Consensus pattern (108 bp):
AGCTGTGTCCCTCAGAAGTGATACGACACATTTTAAACACTCAGTCAGTGTGCAAGAAAGCTCAT
CAAATACCCGAATCATATTTTCAAGCCAAAATTTGGCTTTCTC
Found at i:46684721 original size:29 final size:28
Alignment explanation
Indices: 46684687--46684789 Score: 116
Period size: 29 Copynumber: 3.6 Consensus size: 28
46684677 TACTCAATCA
*
46684687 CGCACACTTAGTGCCATATGATTCAAGCC
1 CGCACACTTAGTGCCATAT-ATTCAAGCT
* * *
46684716 CGCACACATAGTGCCATATAGTCCAAACT
1 CGCACACTTAGTGCCATATA-TTCAAGCT
* *
46684745 CGCACACTTAGTGCCGTACATTACAAGCT
1 CGCACACTTAGTGCCATATATT-CAAGCT
*
46684774 CGCACACTCAGTGCCA
1 CGCACACTTAGTGCCA
46684790 ATCTCGTCAC
Statistics
Matches: 61, Mismatches: 11, Indels: 4
0.80 0.14 0.05
Matches are distributed among these distances:
28 2 0.03
29 59 0.97
ACGTcount: A:0.29, C:0.33, G:0.17, T:0.21
Consensus pattern (28 bp):
CGCACACTTAGTGCCATATATTCAAGCT
Found at i:46695942 original size:21 final size:21
Alignment explanation
Indices: 46695918--46695970 Score: 63
Period size: 21 Copynumber: 2.5 Consensus size: 21
46695908 ATTTATTTCT
46695918 TTAGTTAGTT-AGTTTAAAATC
1 TTAGTT-GTTAAGTTTAAAATC
* *
46695939 TTAGTTTTTAATTTTAAAATC
1 TTAGTTGTTAAGTTTAAAATC
*
46695960 TTAGTTTTTAA
1 TTAGTTGTTAA
46695971 TCACCCTCTT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
20 2 0.07
21 27 0.93
ACGTcount: A:0.32, C:0.04, G:0.09, T:0.55
Consensus pattern (21 bp):
TTAGTTGTTAAGTTTAAAATC
Found at i:46695971 original size:21 final size:21
Alignment explanation
Indices: 46695930--46695971 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
46695920 AGTTAGTTAG
46695930 TTTAAAATCTTAGTTTTTAAT
1 TTTAAAATCTTAGTTTTTAAT
46695951 TTTAAAATCTTAGTTTTTAAT
1 TTTAAAATCTTAGTTTTTAAT
46695972 CACCCTCTTC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.33, C:0.05, G:0.05, T:0.57
Consensus pattern (21 bp):
TTTAAAATCTTAGTTTTTAAT
Found at i:46701289 original size:30 final size:29
Alignment explanation
Indices: 46701234--46701364 Score: 149
Period size: 30 Copynumber: 4.5 Consensus size: 29
46701224 ATAGTGAATC
*
46701234 CGCACACTTAGTGCTATATATTTTCAGCT
1 CGCACACTTAGTGCTATATATTTTCAACT
*
46701263 CGCACACTTAGTGCTATATAATTTTCAGCT
1 CGCACACTTAGTGCTATAT-ATTTTCAACT
*
46701293 CGCACACTTAGTGCTATATA--GTCAAACT
1 CGCACACTTAGTGCTATATATTTTC-AACT
* * * * *
46701321 CGCACACCTAGTGCTGTACAATTTTAAACC
1 CGCACACTTAGTGCTATA-TATTTTCAACT
46701351 CGCACACTTAGTGC
1 CGCACACTTAGTGC
46701365 CAATCTTGTC
Statistics
Matches: 88, Mismatches: 9, Indels: 9
0.83 0.08 0.08
Matches are distributed among these distances:
27 2 0.02
28 19 0.22
29 21 0.24
30 45 0.51
31 1 0.01
ACGTcount: A:0.27, C:0.27, G:0.15, T:0.31
Consensus pattern (29 bp):
CGCACACTTAGTGCTATATATTTTCAACT
Found at i:46701344 original size:58 final size:58
Alignment explanation
Indices: 46701233--46701364 Score: 167
Period size: 58 Copynumber: 2.3 Consensus size: 58
46701223 TATAGTGAAT
* * * * * *
46701233 CCGCACACTTAGTGCTATATATTTTCAGCTCGCACACTTAGTGCTATATAATTTTCAGC
1 CCGCACACTTAGTGCTATATA-TGTCAACTCGCACACCTAGTGCTATACAATTTTAAAC
* *
46701292 TCGCACACTTAGTGCTATATA-GTCAAACTCGCACACCTAGTGCTGTACAATTTTAAAC
1 CCGCACACTTAGTGCTATATATGTC-AACTCGCACACCTAGTGCTATACAATTTTAAAC
46701350 CCGCACACTTAGTGC
1 CCGCACACTTAGTGC
46701365 CAATCTTGTC
Statistics
Matches: 63, Mismatches: 9, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
57 2 0.03
58 41 0.65
59 20 0.32
ACGTcount: A:0.27, C:0.27, G:0.14, T:0.31
Consensus pattern (58 bp):
CCGCACACTTAGTGCTATATATGTCAACTCGCACACCTAGTGCTATACAATTTTAAAC
Found at i:46704252 original size:20 final size:20
Alignment explanation
Indices: 46704221--46704274 Score: 81
Period size: 20 Copynumber: 2.7 Consensus size: 20
46704211 CACAGCCTGC
46704221 CCACACGGGCGTGTCCCAAA
1 CCACACGGGCGTGTCCCAAA
* * *
46704241 CCATATGGGCGTGTTCCAAA
1 CCACACGGGCGTGTCCCAAA
46704261 CCACACGGGCGTGT
1 CCACACGGGCGTGT
46704275 GACTCCTTTT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.22, C:0.33, G:0.28, T:0.17
Consensus pattern (20 bp):
CCACACGGGCGTGTCCCAAA
Found at i:46708899 original size:134 final size:136
Alignment explanation
Indices: 46708616--46708906 Score: 318
Period size: 134 Copynumber: 2.1 Consensus size: 136
46708606 ACCCAACATG
* * * **
46708616 AACTATTCATGATCGTAAATCAATGAAATTAGGTTGTGATCGTAAATCAGTAAGCTTTAATATTA
1 AACTGTTCATGATCGTAAATCAATGAAATTAAGTTGTGATCATAAATCAACAAGCTTTAATA-TA
* * ** **
46708681 TTATCAGTTGTGATCGTAAATCAACGAACTATTTGAATGAAGTTGTGATTTTAAATCTGCAAACT
65 TTACCAGTTGTGATCGTAAATCAACGAACTATTTGAATGAAGTAGTGATCATAAATCAACAAACT
*
46708746 TAAAACA
130 CAAAACA
* ** * *
46708753 AACTGTTGATGATCGTAAATCAATGAGCTTAAGTTGTGATCATACATCAACAAGTTTTAATA-A-
1 AACTGTTCATGATCGTAAATCAATGAAATTAAGTTGTGATCATAAATCAACAAGCTTTAATATAT
* * * * *
46708816 TGCCAGTCT-TGATTGTAAATCAATGAACTATTTGAATGGAGTAGTGATCATAAATCAACGAACT
66 TACCAGT-TGTGATCGTAAATCAACGAACTATTTGAATGAAGTAGTGATCATAAATCAACAAACT
*
46708880 CAAAATA
130 CAAAACA
* *
46708887 AATTGTTCATGATCATAAAT
1 AACTGTTCATGATCGTAAAT
46708907 AAGCAAACTT
Statistics
Matches: 127, Mismatches: 26, Indels: 5
0.80 0.16 0.03
Matches are distributed among these distances:
134 73 0.57
135 2 0.02
137 52 0.41
ACGTcount: A:0.38, C:0.12, G:0.15, T:0.34
Consensus pattern (136 bp):
AACTGTTCATGATCGTAAATCAATGAAATTAAGTTGTGATCATAAATCAACAAGCTTTAATATAT
TACCAGTTGTGATCGTAAATCAACGAACTATTTGAATGAAGTAGTGATCATAAATCAACAAACTC
AAAACA
Found at i:46709298 original size:134 final size:134
Alignment explanation
Indices: 46708938--46709298 Score: 415
Period size: 134 Copynumber: 2.7 Consensus size: 134
46708928 GTCATGATCA
* * * * * * *
46708938 GAACTCAAAATGAACTATTCATGATCT-TAAATCAATTAACTTAAGATGTGACCGTAAATCAACA
1 GAACTCAAAATGAACTGTTCATGAT-TGTAAATTAGTGAACTTAAGCTATGATCGTAAATCAACA
* ** * * * *
46709002 AGCTTTAGTAATACTAGTCGTGATTGTAAATCAGCGAATTGTTTGGATGGAGTTACGATCATAAA
65 AGCTTTAATAATACTAGTCGTGATCATAAATCAACGAAATGTTTGAATGGAATTACGATCATAAA
* *
46709067 TTAGT
130 TCAAT
* * * * * *
46709072 AAAATCAAAATGAATTGTTCATGATCGTAATTTAGTGAACTTAAGCTATGATTGTAAATCAACAA
1 GAACTCAAAATGAACTGTTCATGATTGTAAATTAGTGAACTTAAGCTATGATCGTAAATCAACAA
* * * *
46709137 GCTTTAATAATACCAGT-GATAACCATAAATCAACGAACAT-TTTGAAT-GAATTAGTGATCATA
66 GCTTTAATAATACTAGTCG-TGATCATAAATCAACGAA-ATGTTTGAATGGAATTA-CGATCATA
46709199 AATCAAT
128 AATCAAT
*
46709206 GAACTCAAAATGAACTGTTCATGATTGTAAATTAGTGAACTTAAGCTATGATCGTAAATCAGCAA
1 GAACTCAAAATGAACTGTTCATGATTGTAAATTAGTGAACTTAAGCTATGATCGTAAATCAACAA
46709271 GCTTTAATAATACTAGTCGTGATCATAA
66 GCTTTAATAATACTAGTCGTGATCATAA
46709299 TTAGCGAATT
Statistics
Matches: 186, Mismatches: 36, Indels: 10
0.80 0.16 0.04
Matches are distributed among these distances:
133 6 0.03
134 178 0.96
135 2 0.01
ACGTcount: A:0.40, C:0.13, G:0.15, T:0.32
Consensus pattern (134 bp):
GAACTCAAAATGAACTGTTCATGATTGTAAATTAGTGAACTTAAGCTATGATCGTAAATCAACAA
GCTTTAATAATACTAGTCGTGATCATAAATCAACGAAATGTTTGAATGGAATTACGATCATAAAT
CAAT
Found at i:46718006 original size:13 final size:13
Alignment explanation
Indices: 46717988--46718012 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
46717978 AGGAGAAGAC
46717988 ACAGTCGTGCGAG
1 ACAGTCGTGCGAG
46718001 ACAGTCGTGCGA
1 ACAGTCGTGCGA
46718013 AAACAGGGCA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.24, C:0.24, G:0.36, T:0.16
Consensus pattern (13 bp):
ACAGTCGTGCGAG
Found at i:46724472 original size:30 final size:31
Alignment explanation
Indices: 46724401--46724477 Score: 138
Period size: 31 Copynumber: 2.5 Consensus size: 31
46724391 TTTAATGGTT
46724401 ACTGGGCCGAAGCCTTTTCATAAATCATATC
1 ACTGGGCCGAAGCCTTTTCATAAATCATATC
*
46724432 ACTGGGCCGAAGCCTTTTCATAAATCATTTC
1 ACTGGGCCGAAGCCTTTTCATAAATCATATC
46724463 ACT-GGCCGAAGCCTT
1 ACTGGGCCGAAGCCTT
46724478 ACTGTAAACG
Statistics
Matches: 45, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
30 12 0.27
31 33 0.73
ACGTcount: A:0.26, C:0.27, G:0.18, T:0.29
Consensus pattern (31 bp):
ACTGGGCCGAAGCCTTTTCATAAATCATATC
Found at i:46724548 original size:42 final size:42
Alignment explanation
Indices: 46724501--46724592 Score: 139
Period size: 42 Copynumber: 2.2 Consensus size: 42
46724491 TGGCCCATAG
* ** *
46724501 GCCCATTTCAATATCACATGTAATGTCAATGGATGTATGCAA
1 GCCCATTTCAATATCACATGAAATACCAATGAATGTATGCAA
*
46724543 GCCCATTTCAATATCATATGAAATACCAATGAATGTATGCAA
1 GCCCATTTCAATATCACATGAAATACCAATGAATGTATGCAA
46724585 GCCCATTT
1 GCCCATTT
46724593 GGGGAGACTA
Statistics
Matches: 45, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
42 45 1.00
ACGTcount: A:0.35, C:0.21, G:0.14, T:0.30
Consensus pattern (42 bp):
GCCCATTTCAATATCACATGAAATACCAATGAATGTATGCAA
Found at i:46724780 original size:26 final size:26
Alignment explanation
Indices: 46724725--46724835 Score: 156
Period size: 26 Copynumber: 4.3 Consensus size: 26
46724715 CTGAAGGCCT
46724725 AGCCTCTTTT-AAT-AACTGGGGCA-A
1 AGCC-CTTTTCAATAAACTGGGGCATA
*
46724749 AGCCCTTTTCAATAAATTGGGGCATA
1 AGCCCTTTTCAATAAACTGGGGCATA
** *
46724775 AGCCCTTTTCGGTAAACTAGGGCATA
1 AGCCCTTTTCAATAAACTGGGGCATA
46724801 AGCCCTTTTCAATAAACTGGGGCATA
1 AGCCCTTTTCAATAAACTGGGGCATA
46724827 AGCCCTTTT
1 AGCCCTTTT
46724836 GCACTTCCTC
Statistics
Matches: 76, Mismatches: 8, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
23 5 0.07
24 7 0.09
25 9 0.12
26 55 0.72
ACGTcount: A:0.28, C:0.23, G:0.20, T:0.30
Consensus pattern (26 bp):
AGCCCTTTTCAATAAACTGGGGCATA
Found at i:46725728 original size:27 final size:27
Alignment explanation
Indices: 46725637--46725720 Score: 143
Period size: 27 Copynumber: 3.1 Consensus size: 27
46725627 GGGCATATTC
*
46725637 GTCATTTTACCCTACAGGGG-TATTACG
1 GTCACTTTACCCTACAGGGGCT-TTACG
46725664 GTCACTTTACCCTACAGGGGCTTTACG
1 GTCACTTTACCCTACAGGGGCTTTACG
46725691 GTCACTTTACCCTACAGGGGCTTTACG
1 GTCACTTTACCCTACAGGGGCTTTACG
46725718 GTC
1 GTC
46725721 TTTTTACCTA
Statistics
Matches: 55, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
27 54 0.98
28 1 0.02
ACGTcount: A:0.19, C:0.27, G:0.23, T:0.31
Consensus pattern (27 bp):
GTCACTTTACCCTACAGGGGCTTTACG
Found at i:46725812 original size:27 final size:27
Alignment explanation
Indices: 46725782--46726056 Score: 139
Period size: 27 Copynumber: 10.1 Consensus size: 27
46725772 GTAAATCTAC
46725782 AAACCAAGGGTATTTTAGTAATTTTGT
1 AAACCAAGGGTATTTTAGTAATTTTGT
*
46725809 AAACCAATGGTATTTCTA-TAATTTT-T
1 AAACCAAGGGTATTT-TAGTAATTTTGT
* *
46725835 AGGAAGTCAAGGGTATTTCT-GTAACTTTGT
1 A--AA-CCAAGGGTATTT-TAGTAATTTTGT
* * **
46725865 AAATC-AGGGATATTTTGGTAATTTTAC
1 AAACCAAGGG-TATTTTAGTAATTTTGT
*** ***
46725892 AAATTGAGGGTATTTT-GATAATTTCAC
1 AAACCAAGGGTATTTTAG-TAATTTTGT
* **
46725919 AAACC-AGTGGTATTTTGGTAATTTTAC
1 AAACCAAG-GGTATTTTAGTAATTTTGT
* * * **
46725946 AAACTAGGGGTATTTTTGTAATTTTAC
1 AAACCAAGGGTATTTTAGTAATTTTGT
46725973 AAACCAAGGGTATTTTAGTAATTTTGT
1 AAACCAAGGGTATTTTAGTAATTTTGT
*** *** *
46726000 AAATTGAGGGTAAAATAGTAATTCTGT
1 AAACCAAGGGTATTTTAGTAATTTTGT
* *** *
46726027 AAATCAAGGGTAAAATAGTAATTCTGT
1 AAACCAAGGGTATTTTAGTAATTTTGT
46726054 AAA
1 AAA
46726057 TTGAGGGTAA
Statistics
Matches: 206, Mismatches: 29, Indels: 26
0.79 0.11 0.10
Matches are distributed among these distances:
26 10 0.05
27 164 0.80
28 12 0.06
29 18 0.09
30 2 0.01
ACGTcount: A:0.35, C:0.08, G:0.19, T:0.39
Consensus pattern (27 bp):
AAACCAAGGGTATTTTAGTAATTTTGT
Found at i:46725933 original size:54 final size:54
Alignment explanation
Indices: 46725870--46726011 Score: 182
Period size: 54 Copynumber: 2.6 Consensus size: 54
46725860 TTTGTAAATC
46725870 AGGGATATTTTGGTAATTTTACAAATTGAGGGTA-TTTTGATAATTTCACAAACC-
1 AGGG-TATTTTGGTAATTTTACAAATTGAGGGTATTTTTG-TAATTTCACAAACCA
* *
46725924 AGTGGTATTTTGGTAATTTTACAAACT-AGGGGTATTTTTGTAATTTTACAAACCA
1 AG-GGTATTTTGGTAATTTTACAAATTGA-GGGTATTTTTGTAATTTCACAAACCA
* **
46725979 AGGGTATTTTAGTAATTTTGTAAATTGAGGGTA
1 AGGGTATTTTGGTAATTTTACAAATTGAGGGTA
46726012 AAATAGTAAT
Statistics
Matches: 77, Mismatches: 6, Indels: 10
0.83 0.06 0.11
Matches are distributed among these distances:
53 1 0.01
54 66 0.86
55 10 0.13
ACGTcount: A:0.32, C:0.07, G:0.20, T:0.41
Consensus pattern (54 bp):
AGGGTATTTTGGTAATTTTACAAATTGAGGGTATTTTTGTAATTTCACAAACCA
Found at i:46726021 original size:54 final size:54
Alignment explanation
Indices: 46725963--46726185 Score: 160
Period size: 54 Copynumber: 4.1 Consensus size: 54
46725953 GGGTATTTTT
* *** *
46725963 GTAATTTTACAAACCAAGGGTATTTTAGTAATTTTGTAAATTGAGGGTAAAATA
1 GTAATTCTACAAACCAAGGGTAAAATAGTAATTCTGTAAATTGAGGGTAAAATA
** * **
46726017 GTAATTCTGTAAATCAAGGGTAAAATAGTAATTCTGTAAATTGAGGGTAAAACG
1 GTAATTCTACAAACCAAGGGTAAAATAGTAATTCTGTAAATTGAGGGTAAAATA
** * * ** * * * **
46726071 GTAATTCTGTAAATCGAGGGTAAAACGGTAATTCTATAAGTCGAGGGTAAAACG
1 GTAATTCTACAAACCAAGGGTAAAATAGTAATTCTGTAAATTGAGGGTAAAATA
* ** *** * * * *
46726125 GTAATTATGTAAA-TTGGGGTAAAATTGTAATTATGTAAATTGGGGGTAAAATG
1 GTAATTCTACAAACCAAGGGTAAAATAGTAATTCTGTAAATTGAGGGTAAAATA
46726178 GTAATTCT
1 GTAATTCT
46726186 GTAAATCGGG
Statistics
Matches: 140, Mismatches: 29, Indels: 1
0.82 0.17 0.01
Matches are distributed among these distances:
53 36 0.26
54 104 0.74
ACGTcount: A:0.38, C:0.06, G:0.23, T:0.33
Consensus pattern (54 bp):
GTAATTCTACAAACCAAGGGTAAAATAGTAATTCTGTAAATTGAGGGTAAAATA
Done.