Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032253.1 Gossypioides kirkii chromosome KI_11
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: 55708359
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 2600 characters in sequence are not A, C, G, or T
File 126 of 182
Found at i:40172609 original size:34 final size:34
Alignment explanation
Indices: 40172560--40172693 Score: 144
Period size: 34 Copynumber: 3.9 Consensus size: 34
40172550 GATTTTGATG
* * *
40172560 AGAAGAAGAAGTGGTGTTAGATGGAAGAATGGTGA
1 AGAAGGAGAAATGGTGTTAAATGGAAGAATGGT-A
* *
40172595 A-AAGGAGAAGTGGTGTTAAATGGAAGAGTGGTA
1 AGAAGGAGAAATGGTGTTAAATGGAAGAATGGTA
* * * *
40172628 AGAAGAAGAAATGATGTGAAAGGGAAGAATGGTA
1 AGAAGGAGAAATGGTGTTAAATGGAAGAATGGTA
* * *
40172662 AGAAGGAGAAATGGTATTAGATGGAAAAATGG
1 AGAAGGAGAAATGGTGTTAAATGGAAGAATGG
40172694 GGAAGAAGAT
Statistics
Matches: 82, Mismatches: 16, Indels: 3
0.81 0.16 0.03
Matches are distributed among these distances:
33 2 0.02
34 79 0.96
35 1 0.01
ACGTcount: A:0.44, C:0.00, G:0.37, T:0.19
Consensus pattern (34 bp):
AGAAGGAGAAATGGTGTTAAATGGAAGAATGGTA
Found at i:40172626 original size:18 final size:19
Alignment explanation
Indices: 40172564--40172626 Score: 73
Period size: 18 Copynumber: 3.6 Consensus size: 19
40172554 TTGATGAGAA
*
40172564 GAAGAAGTGGTGTTAGATG
1 GAAGAAGTGGTGTTAAATG
*
40172583 GAAGAA-TGGTG--AAAAG
1 GAAGAAGTGGTGTTAAATG
40172599 G-AGAAGTGGTGTTAAATG
1 GAAGAAGTGGTGTTAAATG
40172617 GAAG-AGTGGT
1 GAAGAAGTGGT
40172627 AAGAAGAAGA
Statistics
Matches: 37, Mismatches: 3, Indels: 9
0.76 0.06 0.18
Matches are distributed among these distances:
15 4 0.11
16 9 0.24
18 16 0.43
19 8 0.22
ACGTcount: A:0.37, C:0.00, G:0.41, T:0.22
Consensus pattern (19 bp):
GAAGAAGTGGTGTTAAATG
Found at i:40172752 original size:16 final size:15
Alignment explanation
Indices: 40172729--40172776 Score: 53
Period size: 15 Copynumber: 3.2 Consensus size: 15
40172719 AATTATTTAA
40172729 TAATTTTAATAAATT
1 TAATTTTAATAAATT
**
40172744 TATATTTTAA-AAAAA
1 TA-ATTTTAATAAATT
*
40172759 TAATTTTAATAATTT
1 TAATTTTAATAAATT
40172774 TAA
1 TAA
40172777 AATCATTTAC
Statistics
Matches: 26, Mismatches: 5, Indels: 4
0.74 0.14 0.11
Matches are distributed among these distances:
14 7 0.27
15 12 0.46
16 7 0.27
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (15 bp):
TAATTTTAATAAATT
Found at i:40172760 original size:21 final size:23
Alignment explanation
Indices: 40172736--40172778 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
40172726 TAATAATTTT
40172736 AATAAATTT-AT-ATTTTAAAAA
1 AATAAATTTAATAATTTTAAAAA
*
40172757 AATAATTTTAATAATTTTAAAA
1 AATAAATTTAATAATTTTAAAA
40172779 TCATTTACCG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 8 0.42
22 2 0.11
23 9 0.47
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (23 bp):
AATAAATTTAATAATTTTAAAAA
Found at i:40173154 original size:7 final size:6
Alignment explanation
Indices: 40173132--40173195 Score: 51
Period size: 6 Copynumber: 10.5 Consensus size: 6
40173122 AACCCAAATA
* **
40173132 AAATTT AAATTT AAATTT AAAATGTT CAAATAT ATTTTT AAATTT AAATTT
1 AAATTT AAATTT AAATTT -AAAT-TT -AAATTT AAATTT AAATTT AAATTT
*
40173183 --GTTT AAATTT AAA
1 AAATTT AAATTT AAA
40173196 AGGCCCAAAT
Statistics
Matches: 45, Mismatches: 9, Indels: 8
0.73 0.15 0.13
Matches are distributed among these distances:
4 3 0.07
6 31 0.69
7 5 0.11
8 6 0.13
ACGTcount: A:0.47, C:0.02, G:0.03, T:0.48
Consensus pattern (6 bp):
AAATTT
Found at i:40174856 original size:30 final size:29
Alignment explanation
Indices: 40174823--40175059 Score: 179
Period size: 30 Copynumber: 7.9 Consensus size: 29
40174813 TAGGTCCCTG
* * *
40174823 AACTTTTCCAAAATCATATTTTAACCTCCG
1 AACTTTTCCAAAATTACATTTTAACC-CCA
* * *
40174853 AACTTCTCCAAAATTATATTTTAACCCTTA
1 AACTTTTCCAAAATTACATTTTAACCC-CA
* *
40174883 AACTTTTTCCAAAATTGCATTTTGACCCCCTA
1 AAC-TTTTCCAAAATTACATTTT-AACCCC-A
* * * *
40174915 AACTTCTT-AAAAATTATATTTTGACCCTTA
1 AACTT-TTCCAAAATTACATTTTAACCC-CA
*
40174945 AACTTTTCCAAAATCACATTTTAACCCCA
1 AACTTTTCCAAAATTACATTTTAACCCCA
* * * * *
40174974 AACATCTCTAAAATCACACTTTAACCCCA
1 AACTTTTCCAAAATTACATTTTAACCCCA
* * * *
40175003 AAATTTCCCAAAATTACATTTTTACCTCCT
1 AACTTTTCCAAAATTACATTTTAACC-CCA
* *
40175033 AACTTTTCCAAAATTACGTTTCAACCC
1 AACTTTTCCAAAATTACATTTTAACCC
40175060 GAATTCTCTG
Statistics
Matches: 161, Mismatches: 38, Indels: 17
0.75 0.18 0.08
Matches are distributed among these distances:
29 48 0.30
30 74 0.46
31 29 0.18
32 10 0.06
ACGTcount: A:0.35, C:0.27, G:0.02, T:0.36
Consensus pattern (29 bp):
AACTTTTCCAAAATTACATTTTAACCCCA
Found at i:40174932 original size:62 final size:61
Alignment explanation
Indices: 40174823--40175048 Score: 210
Period size: 61 Copynumber: 3.8 Consensus size: 61
40174813 TAGGTCCCTG
* * * *
40174823 AACTTTTCCAAAATCATATTTTAACCTCC-GAACTTCTCCAAAATTATATTTTAACCCTTA
1 AACTTTTCCAAAATCACATTTTAACCCCCTAAACTTCTCAAAAATTATATTTTAACCCTTA
** * * *
40174883 AACTTTTTCCAAAATTGCATTTTGACCCCCTAAACTTCTTAAAAATTATATTTTGACCCTTA
1 AAC-TTTTCCAAAATCACATTTTAACCCCCTAAACTTCTCAAAAATTATATTTTAACCCTTA
* * * * * *
40174945 AACTTTTCCAAAATCACATTTTAA-CCCC-AAACATCTCTAAAATCACACTTTAACCC-CA
1 AACTTTTCCAAAATCACATTTTAACCCCCTAAACTTCTCAAAAATTATATTTTAACCCTTA
* * * * * * *
40175003 AAATTTCCCAAAATTACATTTTTACCTCCT-AACTTTTCCAAAATTA
1 AACTTTTCCAAAATCACATTTTAACCCCCTAAACTTCTCAAAAATTA
40175049 CGTTTCAACC
Statistics
Matches: 133, Mismatches: 29, Indels: 9
0.78 0.17 0.05
Matches are distributed among these distances:
58 21 0.16
59 36 0.27
60 7 0.05
61 39 0.29
62 30 0.23
ACGTcount: A:0.36, C:0.26, G:0.02, T:0.36
Consensus pattern (61 bp):
AACTTTTCCAAAATCACATTTTAACCCCCTAAACTTCTCAAAAATTATATTTTAACCCTTA
Found at i:40178703 original size:161 final size:158
Alignment explanation
Indices: 40178401--40178766 Score: 455
Period size: 161 Copynumber: 2.3 Consensus size: 158
40178391 ATGAGGCGAT
* * * *
40178401 CATCTTCCTGATGCGATATAGAGAAGTAAACTGAATCAATAAAGCAAAGCTCAATATGAGGGAAA
1 CATCTTCCTGATGAGATACAGAGAAGTAGACT-AATCAATGAAGCAAAGCTCAATATGAGGGAAA
* * *
40178466 ATTCAAACCCCATCTCCTAATGAGATACTGAGAAGTAGGATGAAGCAATAAATTATTCATCTTCC
65 ATTCAAACCCCATCTCCTAATGAGATACGGAGAACTAGGATGAAGCAATAAAGTATTCATCTTCC
*
40178531 TGACGAGATGCAGAGAAGTAAACCAAATC
130 TGACGAGATGCAGAGAAATAAACCAAATC
* * * *
40178560 TATCTTCTTGATGAGATACAGAGAAGTAGACTAATTCAATGAAGCAAAGCTCAATGTGAGTGAAA
1 CATCTTCCTGATGAGATACAGAGAAGTAGACTAA-TCAATGAAGCAAAGCTCAATATGAGGGAAA
* * * * * *
40178625 CTTCCAAACCCCATCTTCTTGATGAGATACGGAGAACT-GGGTCGACGCAATAAAGTGTTCATCT
65 ATT-CAAACCCCATC-TCCTAATGAGATACGGAGAACTAGGAT-GAAGCAATAAAGTATTCATCT
*
40178689 TCCTGACGAGATGCAGAGAAATGAACCAAATC
127 TCCTGACGAGATGCAGAGAAATAAACCAAATC
* * * * *
40178721 CATCTTCCTGATGAAATACAGAAAAGTGGATTAAAACAATGAAGCA
1 CATCTTCCTGATGAGATACAGAGAAGTAGACT-AATCAATGAAGCA
40178767 GTCATCTTCC
Statistics
Matches: 176, Mismatches: 26, Indels: 8
0.84 0.12 0.04
Matches are distributed among these distances:
158 2 0.01
159 56 0.32
160 14 0.08
161 102 0.58
162 2 0.01
ACGTcount: A:0.39, C:0.18, G:0.19, T:0.23
Consensus pattern (158 bp):
CATCTTCCTGATGAGATACAGAGAAGTAGACTAATCAATGAAGCAAAGCTCAATATGAGGGAAAA
TTCAAACCCCATCTCCTAATGAGATACGGAGAACTAGGATGAAGCAATAAAGTATTCATCTTCCT
GACGAGATGCAGAGAAATAAACCAAATC
Found at i:40178788 original size:48 final size:48
Alignment explanation
Indices: 40178721--40178831 Score: 134
Period size: 48 Copynumber: 2.3 Consensus size: 48
40178711 GAACCAAATC
*
40178721 CATCTTCCTGATGAAATACAGAAAAGTGGATTAAAACAATGAAGCAGT
1 CATCTTCCTGATGAAATACAGAAAAGTGGATCAAAACAATGAAGCAGT
* * * * *
40178769 CATCTTCCTGAT-AAGATACAGAGAAGTGGGTCGAAGCAATGAAGCGGT
1 CATCTTCCTGATGAA-ATACAGAAAAGTGGATCAAAACAATGAAGCAGT
* *
40178817 AATCTTCCTAATGAA
1 CATCTTCCTGATGAA
40178832 TTATAGAGAA
Statistics
Matches: 53, Mismatches: 8, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
47 2 0.04
48 49 0.92
49 2 0.04
ACGTcount: A:0.39, C:0.16, G:0.22, T:0.23
Consensus pattern (48 bp):
CATCTTCCTGATGAAATACAGAAAAGTGGATCAAAACAATGAAGCAGT
Found at i:40179246 original size:12 final size:13
Alignment explanation
Indices: 40179224--40179252 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
40179214 GGAACCCAAA
40179224 TAAATTTTAAATT
1 TAAATTTTAAATT
40179237 TAAA-TTTAAATT
1 TAAATTTTAAATT
40179249 TAAA
1 TAAA
40179253 ATATCCAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 12 0.75
13 4 0.25
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (13 bp):
TAAATTTTAAATT
Found at i:40179287 original size:27 final size:28
Alignment explanation
Indices: 40179241--40179294 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 28
40179231 TAAATTTAAA
* *
40179241 TTTAAATTTAAAATATCCAAA-TACATT
1 TTTAAATTTAAAAGACCCAAATTACATT
*
40179268 TTTAAATTTAAAAGGCCCAAATTACAT
1 TTTAAATTTAAAAGACCCAAATTACAT
40179295 GTCCCTAAAG
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
27 18 0.78
28 5 0.22
ACGTcount: A:0.46, C:0.13, G:0.04, T:0.37
Consensus pattern (28 bp):
TTTAAATTTAAAAGACCCAAATTACATT
Found at i:40180966 original size:61 final size:62
Alignment explanation
Indices: 40180886--40181268 Score: 198
Period size: 59 Copynumber: 6.4 Consensus size: 62
40180876 AGTCCATGAA
* * *
40180886 TTTTCCAAAAATTATATTTTGACCCTCGAACTTCT-TCAAAATCATATTTTGA-CCCTCAAACT
1 TTTTCCAAAAATTACATTTTGACCCTCGAACTTCTCT-AAAATCACATTTTAACCCCT-AAACT
* ** *
40180948 TTTTCC-AAAATTGCATTTTGACCCTTTAACTTCTCTAAAATTACATTTTAACCCCTAAAC-
1 TTTTCCAAAAATTACATTTTGACCCTCGAACTTCTCTAAAATCACATTTTAACCCCTAAACT
* * * * * * * * *
40181008 TTTT-CTAAAATCACATTTTAACCC-CTAAACTTTTCCAAAA-CTTCATTTCAACCCCTAAGC-
1 TTTTCCAAAAATTACATTTTGACCCTC-GAACTTCTCTAAAATC-ACATTTTAACCCCTAAACT
** * * * *
40181068 TTTTCC-AAAATTATGTTTTGACCC-CTAAACTT-TCCAAAATTACATGTTAACCCCTAAAC-
1 TTTTCCAAAAATTACATTTTGACCCTC-GAACTTCTCTAAAATCACATTTTAACCCCTAAACT
* * * * *
40181127 TTTTCC-AAAATCACATTTTAACCGC-CAAACTTTTTTAAAATCACATTTTAACCCC-AAAC-
1 TTTTCCAAAAATTACATTTTGACC-CTCGAACTTCTCTAAAATCACATTTTAACCCCTAAACT
* * * ** * * * *
40181186 ATCTCC-AAAATCATTTTTTGACCCT-AAACTT-TTTCAAAATTACATTTTTACCTCCT-AAC-
1 TTTTCCAAAAATTACATTTTGACCCTCGAACTTCTCT-AAAATCACATTTTAACC-CCTAAACT
* *
40181245 TTTTCC-AAAATTACGTTTTAACCC
1 TTTTCCAAAAATTACATTTTGACCC
40181269 AGATTCTTTG
Statistics
Matches: 260, Mismatches: 48, Indels: 29
0.77 0.14 0.09
Matches are distributed among these distances:
57 3 0.01
58 22 0.08
59 92 0.35
60 91 0.35
61 41 0.16
62 11 0.04
ACGTcount: A:0.33, C:0.26, G:0.03, T:0.38
Consensus pattern (62 bp):
TTTTCCAAAAATTACATTTTGACCCTCGAACTTCTCTAAAATCACATTTTAACCCCTAAACT
Found at i:40181144 original size:89 final size:90
Alignment explanation
Indices: 40180922--40181268 Score: 330
Period size: 89 Copynumber: 3.9 Consensus size: 90
40180912 CGAACTTCTT
* * ** * * * *
40180922 CAAAATCATATTTTGA-CCCTCAAACTTTTTCCAAAATTGCATTTTGACC-CTTTAACTTCTCTA
1 CAAAATCACATTTTAACCCCT-AAAC-TTTTCCAAAATCACATTTTAACCGC-CTAACTTTTCCA
*
40180985 AAATTACATTTTAACCCCTAAACTTTTC
63 AAATTACATTTTAACCCCTAAACATTTC
* * *
40181013 TAAAATCACATTTTAACCCCTAAACTTTTCCAAAA-CTTCATTTCAACC-CCTAAGCTTTTCCAA
1 CAAAATCACATTTTAACCCCTAAACTTTTCCAAAATC-ACATTTTAACCGCCTAA-CTTTTCCAA
** *
40181076 AATTATGTTTTGACCCCTAAAC-TTTC
64 AATTACATTTTAACCCCTAAACATTTC
* * * **
40181102 CAAAATTACATGTTAACCCCTAAACTTTTCCAAAATCACATTTTAACCGCCAAACTTTTTTAAAA
1 CAAAATCACATTTTAACCCCTAAACTTTTCCAAAATCACATTTTAACCGCCTAACTTTTCCAAAA
* *
40181167 TCACATTTTAACCCC-AAACATCTC
66 TTACATTTTAACCCCTAAACATTTC
** * * * * *
40181191 CAAAATCATTTTTTGA-CCCTAAACTTTTTCAAAATTACATTTTTACCTCCTAACTTTTCCAAAA
1 CAAAATCACATTTTAACCCCTAAACTTTTCCAAAATCACATTTTAACCGCCTAACTTTTCCAAAA
*
40181255 TTACGTTTTAACCC
66 TTACATTTTAACCC
40181269 AGATTCTTTG
Statistics
Matches: 210, Mismatches: 40, Indels: 15
0.79 0.15 0.06
Matches are distributed among these distances:
88 57 0.27
89 82 0.39
90 50 0.24
91 17 0.08
92 4 0.02
ACGTcount: A:0.34, C:0.27, G:0.03, T:0.37
Consensus pattern (90 bp):
CAAAATCACATTTTAACCCCTAAACTTTTCCAAAATCACATTTTAACCGCCTAACTTTTCCAAAA
TTACATTTTAACCCCTAAACATTTC
Found at i:40181258 original size:30 final size:30
Alignment explanation
Indices: 40180886--40181268 Score: 334
Period size: 30 Copynumber: 12.8 Consensus size: 30
40180876 AGTCCATGAA
* * *
40180886 TTTTCCAAAAATTATATTTTGA-CCCTCGAAC
1 TTTTCC-AAAATTACATTTTAACCCCT-AAAC
* * *
40180917 TTCTT-CAAAATCATATTTTGA-CCCTCAAAC
1 TT-TTCCAAAATTACATTTTAACCCCT-AAAC
* * * *
40180947 TTTTTCCAAAATTGCATTTTGACCCTTTAAC
1 -TTTTCCAAAATTACATTTTAACCCCTAAAC
* *
40180978 TTCTCTAAAATTACATTTTAACCCCTAAAC
1 TTTTCCAAAATTACATTTTAACCCCTAAAC
* *
40181008 TTTTCTAAAATCACATTTTAACCCCTAAAC
1 TTTTCCAAAATTACATTTTAACCCCTAAAC
* *
40181038 TTTTCCAAAACTT-CATTTCAACCCCTAAGC
1 TTTTCCAAAA-TTACATTTTAACCCCTAAAC
** *
40181068 TTTTCCAAAATTATGTTTTGACCCCTAAAC
1 TTTTCCAAAATTACATTTTAACCCCTAAAC
*
40181098 -TTTCCAAAATTACATGTTAACCCCTAAAC
1 TTTTCCAAAATTACATTTTAACCCCTAAAC
*
40181127 TTTTCCAAAATCACATTTTAACCGCC-AAAC
1 TTTTCCAAAATTACATTTTAACC-CCTAAAC
** *
40181157 TTTTTTAAAATCACATTTTAACCCC-AAAC
1 TTTTCCAAAATTACATTTTAACCCCTAAAC
* * * ** *
40181186 ATCTCCAAAATCATTTTTTGA-CCCTAAAC
1 TTTTCCAAAATTACATTTTAACCCCTAAAC
* *
40181215 TTTTTCAAAATTACATTTTTACCTCCT-AAC
1 TTTTCCAAAATTACATTTTAACC-CCTAAAC
*
40181245 TTTTCCAAAATTACGTTTTAACCC
1 TTTTCCAAAATTACATTTTAACCC
40181269 AGATTCTTTG
Statistics
Matches: 292, Mismatches: 49, Indels: 24
0.80 0.13 0.07
Matches are distributed among these distances:
28 3 0.01
29 66 0.23
30 191 0.65
31 27 0.09
32 5 0.02
ACGTcount: A:0.33, C:0.26, G:0.03, T:0.38
Consensus pattern (30 bp):
TTTTCCAAAATTACATTTTAACCCCTAAAC
Found at i:40181805 original size:18 final size:18
Alignment explanation
Indices: 40181762--40181797 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
40181752 GAAAAATTTC
*
40181762 TCTTTAAAACTTTTACTT
1 TCTTTAAAAATTTTACTT
*
40181780 TCTATAAAAATTTTACTT
1 TCTTTAAAAATTTTACTT
40181798 ATTTTAAACT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.33, C:0.14, G:0.00, T:0.53
Consensus pattern (18 bp):
TCTTTAAAAATTTTACTT
Found at i:40183519 original size:41 final size:41
Alignment explanation
Indices: 40183474--40183609 Score: 123
Period size: 41 Copynumber: 3.2 Consensus size: 41
40183464 AAAATTAAAC
*
40183474 AAATTCAAAGTGCTAAATTTATTTTATTAACAAAATCATGA
1 AAATTCAAAGTGATAAATTTATTTTATTAACAAAATCATGA
* * * *** * *
40183515 AAATTCAAATTTAATAATATTAAAGACATATTTAAC-AAATTA-AA
1 AAATTCAAA-GTGATAA-ATT-TA-TTTTA-TTAACAAAATCATGA
40183559 CAAATTCAAAGTGATAAATTTATTTTATTAACAAAATCATGA
1 -AAATTCAAAGTGATAAATTTATTTTATTAACAAAATCATGA
40183601 AAATTCAAA
1 AAATTCAAA
40183610 TTTAATAATA
Statistics
Matches: 70, Mismatches: 17, Indels: 16
0.68 0.17 0.16
Matches are distributed among these distances:
40 5 0.07
41 25 0.36
42 6 0.09
43 6 0.09
44 7 0.10
45 16 0.23
46 5 0.07
ACGTcount: A:0.51, C:0.09, G:0.05, T:0.35
Consensus pattern (41 bp):
AAATTCAAAGTGATAAATTTATTTTATTAACAAAATCATGA
Found at i:40183567 original size:86 final size:86
Alignment explanation
Indices: 40183465--40183624 Score: 311
Period size: 86 Copynumber: 1.9 Consensus size: 86
40183455 ATTAAACATA
*
40183465 AAATTAAACAAATTCAAAGTGCTAAATTTATTTTATTAACAAAATCATGAAAATTCAAATTTAAT
1 AAATTAAACAAATTCAAAGTGATAAATTTATTTTATTAACAAAATCATGAAAATTCAAATTTAAT
40183530 AATATTAAAGACATATTTAAC
66 AATATTAAAGACATATTTAAC
40183551 AAATTAAACAAATTCAAAGTGATAAATTTATTTTATTAACAAAATCATGAAAATTCAAATTTAAT
1 AAATTAAACAAATTCAAAGTGATAAATTTATTTTATTAACAAAATCATGAAAATTCAAATTTAAT
40183616 AATATTAAA
66 AATATTAAA
40183625 AATTAACATT
Statistics
Matches: 73, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
86 73 1.00
ACGTcount: A:0.53, C:0.08, G:0.04, T:0.35
Consensus pattern (86 bp):
AAATTAAACAAATTCAAAGTGATAAATTTATTTTATTAACAAAATCATGAAAATTCAAATTTAAT
AATATTAAAGACATATTTAAC
Found at i:40183630 original size:41 final size:41
Alignment explanation
Indices: 40183499--40183632 Score: 105
Period size: 41 Copynumber: 3.2 Consensus size: 41
40183489 AATTTATTTT
40183499 ATTAACAAAATCATGAAAATTCAAATTTAATAATATTAAAGACA
1 ATTAACAAAATCATGAAAATTCAAATTTAATAATATT-AA-A-A
* * * * ***
40183543 TATTTAAC-AAATTA-AACAAATTCAAA-GTGATAA-ATTTATTTT
1 -A-TTAACAAAATCATGA-AAATTCAAATTTAATAATA-TTA-AAA
40183585 ATTAACAAAATCATGAAAATTCAAATTTAATAATATTAAAA
1 ATTAACAAAATCATGAAAATTCAAATTTAATAATATTAAAA
40183626 ATTAACA
1 ATTAACA
40183633 TTCATCGGAT
Statistics
Matches: 67, Mismatches: 14, Indels: 20
0.66 0.14 0.20
Matches are distributed among these distances:
40 5 0.07
41 22 0.33
42 9 0.13
43 3 0.04
44 8 0.12
45 15 0.22
46 5 0.07
ACGTcount: A:0.54, C:0.08, G:0.04, T:0.34
Consensus pattern (41 bp):
ATTAACAAAATCATGAAAATTCAAATTTAATAATATTAAAA
Found at i:40183952 original size:20 final size:19
Alignment explanation
Indices: 40183914--40183953 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
40183904 ATAAAAATTA
* *
40183914 TCTTGTTGTTTTTTGTTGT
1 TCTTGGTGTTTTGTGTTGT
40183933 TCTTGGTGTTTTGGTGTTGT
1 TCTTGGTGTTTT-GTGTTGT
40183953 T
1 T
40183954 TTGCTACTAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 11 0.61
20 7 0.39
ACGTcount: A:0.00, C:0.05, G:0.28, T:0.68
Consensus pattern (19 bp):
TCTTGGTGTTTTGTGTTGT
Found at i:40183985 original size:12 final size:12
Alignment explanation
Indices: 40183961--40184030 Score: 59
Period size: 12 Copynumber: 5.8 Consensus size: 12
40183951 GTTTTGCTAC
*
40183961 TATTTTTGCTGT
1 TATTTTTGTTGT
40183973 TATTTTTGTTGT
1 TATTTTTGTTGT
* * *
40183985 TGTTTTAGTTTT
1 TATTTTTGTTGT
** *
40183997 TATTTTTGCGGC
1 TATTTTTGTTGT
**
40184009 TATTTTTGTTAC
1 TATTTTTGTTGT
40184021 TATTTTTGTT
1 TATTTTTGTT
40184031 ATTTTTACTA
Statistics
Matches: 45, Mismatches: 13, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
12 45 1.00
ACGTcount: A:0.10, C:0.06, G:0.16, T:0.69
Consensus pattern (12 bp):
TATTTTTGTTGT
Found at i:40184106 original size:23 final size:23
Alignment explanation
Indices: 40184075--40184130 Score: 69
Period size: 23 Copynumber: 2.4 Consensus size: 23
40184065 TTTTTGTGCA
*
40184075 TTTTTATATTGTTTCA-TTACAGC
1 TTTTAATATTGTTTCACTTAC-GC
* *
40184098 TTTTAATATTGTTTCACTTTCGT
1 TTTTAATATTGTTTCACTTACGC
40184121 TTTTAATATT
1 TTTTAATATT
40184131 ATTTGTATAT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
23 26 0.90
24 3 0.10
ACGTcount: A:0.21, C:0.11, G:0.07, T:0.61
Consensus pattern (23 bp):
TTTTAATATTGTTTCACTTACGC
Found at i:40190329 original size:23 final size:24
Alignment explanation
Indices: 40190298--40190348 Score: 59
Period size: 23 Copynumber: 2.2 Consensus size: 24
40190288 TAACATTGTT
*
40190298 CATATTTCAATTTCAT-TCTCAAG
1 CATAATTCAATTTCATATCTCAAG
* * *
40190321 CATAATTCATTTTCGTATCTCAAT
1 CATAATTCAATTTCATATCTCAAG
40190345 CATA
1 CATA
40190349 TAACACTTTG
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
23 13 0.57
24 10 0.43
ACGTcount: A:0.31, C:0.22, G:0.04, T:0.43
Consensus pattern (24 bp):
CATAATTCAATTTCATATCTCAAG
Found at i:40192246 original size:35 final size:35
Alignment explanation
Indices: 40192200--40192268 Score: 120
Period size: 35 Copynumber: 2.0 Consensus size: 35
40192190 AAGATAATAT
*
40192200 ATTTTGTTTAACTTGACTTGCAAGCAATCTCTTAG
1 ATTTTGTTTAACCTGACTTGCAAGCAATCTCTTAG
*
40192235 ATTTTGTTTAACCTGACTTGCAAGCTATCTCTTA
1 ATTTTGTTTAACCTGACTTGCAAGCAATCTCTTA
40192269 TTTGATTGAA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
35 32 1.00
ACGTcount: A:0.25, C:0.19, G:0.13, T:0.43
Consensus pattern (35 bp):
ATTTTGTTTAACCTGACTTGCAAGCAATCTCTTAG
Found at i:40196607 original size:24 final size:24
Alignment explanation
Indices: 40196571--40196624 Score: 83
Period size: 24 Copynumber: 2.2 Consensus size: 24
40196561 TTTTTCTAGA
40196571 ATATTTATTATTTATTAGTATAAT
1 ATATTTATTATTTATTAGTATAAT
40196595 ATATTT-TTCATTTATTAGTATAAT
1 ATATTTATT-ATTTATTAGTATAAT
*
40196619 TTATTT
1 ATATTT
40196625 GACTTATGAA
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
23 2 0.07
24 26 0.93
ACGTcount: A:0.33, C:0.02, G:0.04, T:0.61
Consensus pattern (24 bp):
ATATTTATTATTTATTAGTATAAT
Found at i:40198897 original size:3 final size:3
Alignment explanation
Indices: 40198889--40198931 Score: 86
Period size: 3 Copynumber: 14.3 Consensus size: 3
40198879 TTTGTTTTTT
40198889 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
40198932 AAGCAAAATA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:40200220 original size:9 final size:9
Alignment explanation
Indices: 40200186--40200295 Score: 75
Period size: 9 Copynumber: 12.1 Consensus size: 9
40200176 TGTGGCAAAT
40200186 AAATTATAA
1 AAATTATAA
*
40200195 GAA--ATAA
1 AAATTATAA
*
40200202 AAATCAATAA
1 AAAT-TATAA
*
40200212 AAGTTATAA
1 AAATTATAA
40200221 AAATTATTAA
1 AAATTA-TAA
**
40200231 ATTTTAATAA
1 AAATT-ATAA
40200241 AAA-TATAA
1 AAATTATAA
*
40200249 AAAATAGTAA
1 AAATTA-TAA
40200259 AAATTATAA
1 AAATTATAA
40200268 AAATGTA-AA
1 AAAT-TATAA
**
40200277 ATTTTATAA
1 AAATTATAA
40200286 AAATTATAA
1 AAATTATAA
40200295 A
1 A
40200296 GGGTGAAGAT
Statistics
Matches: 78, Mismatches: 14, Indels: 18
0.71 0.13 0.16
Matches are distributed among these distances:
7 6 0.08
8 9 0.12
9 35 0.45
10 27 0.35
11 1 0.01
ACGTcount: A:0.64, C:0.01, G:0.04, T:0.32
Consensus pattern (9 bp):
AAATTATAA
Found at i:40200680 original size:18 final size:18
Alignment explanation
Indices: 40200657--40200697 Score: 82
Period size: 18 Copynumber: 2.3 Consensus size: 18
40200647 ATTGCTTTTC
40200657 AAAAATATTTTTGAGATA
1 AAAAATATTTTTGAGATA
40200675 AAAAATATTTTTGAGATA
1 AAAAATATTTTTGAGATA
40200693 AAAAA
1 AAAAA
40200698 ACTACTAAAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.56, C:0.00, G:0.10, T:0.34
Consensus pattern (18 bp):
AAAAATATTTTTGAGATA
Found at i:40208957 original size:30 final size:30
Alignment explanation
Indices: 40208919--40209004 Score: 121
Period size: 25 Copynumber: 3.1 Consensus size: 30
40208909 ACTTTTGTTT
40208919 AAAA-AAACTTAAGTATTTTATAGTGATCC
1 AAAATAAACTTAAGTATTTTATAGTGATCC
40208948 AAAATAAACTTAAGTA---T-T-GTGATCC
1 AAAATAAACTTAAGTATTTTATAGTGATCC
*
40208973 AAAATAAACTTAAGTATTTTACAGTGATCC
1 AAAATAAACTTAAGTATTTTATAGTGATCC
40209003 AA
1 AA
40209005 TCACACTAAA
Statistics
Matches: 50, Mismatches: 1, Indels: 11
0.81 0.02 0.18
Matches are distributed among these distances:
25 23 0.46
26 1 0.02
27 1 0.02
28 1 0.02
29 4 0.08
30 20 0.40
ACGTcount: A:0.45, C:0.12, G:0.10, T:0.33
Consensus pattern (30 bp):
AAAATAAACTTAAGTATTTTATAGTGATCC
Found at i:40212371 original size:12 final size:12
Alignment explanation
Indices: 40212354--40212387 Score: 68
Period size: 12 Copynumber: 2.8 Consensus size: 12
40212344 GTATACAAGG
40212354 TGATTGCGAAGA
1 TGATTGCGAAGA
40212366 TGATTGCGAAGA
1 TGATTGCGAAGA
40212378 TGATTGCGAA
1 TGATTGCGAA
40212388 TTAGTTTAGA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.32, C:0.09, G:0.32, T:0.26
Consensus pattern (12 bp):
TGATTGCGAAGA
Found at i:40220617 original size:12 final size:10
Alignment explanation
Indices: 40220591--40220629 Score: 51
Period size: 10 Copynumber: 3.6 Consensus size: 10
40220581 AAAATTTTAT
40220591 TTAATTGAAAA
1 TTAATT-AAAA
40220602 TTAATTAATTAA
1 TTAATTAA--AA
40220614 TTAATTAAAA
1 TTAATTAAAA
40220624 TTAATT
1 TTAATT
40220630 TAATAATATT
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
10 10 0.38
11 6 0.23
12 10 0.38
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (10 bp):
TTAATTAAAA
Found at i:40223018 original size:11 final size:11
Alignment explanation
Indices: 40222998--40223135 Score: 76
Period size: 12 Copynumber: 12.8 Consensus size: 11
40222988 GCTGGTTTGG
40222998 TTGTTGTTTTT
1 TTGTTGTTTTT
40223009 TTGTTG--TTT
1 TTGTTGTTTTT
40223018 TTG-TGTTTTT
1 TTGTTGTTTTT
*
40223028 TTATTG---TT
1 TTGTTGTTTTT
*
40223036 TTGGTGTTTTT
1 TTGTTGTTTTT
* *
40223047 TTATTGTTTTGA
1 TTGTTGTTTT-T
* *
40223059 TTGTTATTTTC
1 TTGTTGTTTTT
*
40223070 GTGTTG--TTT
1 TTGTTGTTTTT
* *
40223079 TTGCTATTATTT
1 TTGTTGTT-TTT
*
40223091 TTGTTGCTATTT
1 TTGTTG-TTTTT
40223103 TTGTTGTTATTT
1 TTGTTGTT-TTT
40223115 TTGTTGTTTTT
1 TTGTTGTTTTT
*
40223126 AATGTTGTTT
1 -TTGTTGTTT
40223136 GTTGTTATTT
Statistics
Matches: 94, Mismatches: 20, Indels: 25
0.68 0.14 0.18
Matches are distributed among these distances:
8 8 0.09
9 11 0.12
10 5 0.05
11 26 0.28
12 43 0.46
13 1 0.01
ACGTcount: A:0.07, C:0.02, G:0.18, T:0.72
Consensus pattern (11 bp):
TTGTTGTTTTT
Found at i:40223026 original size:19 final size:21
Alignment explanation
Indices: 40222998--40223148 Score: 116
Period size: 19 Copynumber: 7.1 Consensus size: 21
40222988 GCTGGTTTGG
40222998 TTGTTGTT-TTTTTGTTGTTT
1 TTGTTGTTATTTTTGTTGTTT
*
40223018 TTG-TGTT-TTTTTATTG-TT
1 TTGTTGTTATTTTTGTTGTTT
* *
40223036 TTGGTGTT-TTTTTATTG-TT
1 TTGTTGTTATTTTTGTTGTTT
40223055 TTGATTGTTATTTTCGTGTTGTTT
1 TTG-TTGTTATTTT--TGTTGTTT
* *
40223079 TTGCTATTATTTTTGTTGCTATTT
1 TTGTTGTTATTTTTGTTG---TTT
40223103 TTGTTGTTATTTTTGTTGTTT
1 TTGTTGTTATTTTTGTTGTTT
** * *
40223124 TTAATGTTGTTTGTTGTTATTT
1 TTGTTGTTATTT-TTGTTGTTT
40223146 TTG
1 TTG
40223149 CTACTATTTT
Statistics
Matches: 109, Mismatches: 12, Indels: 18
0.78 0.09 0.13
Matches are distributed among these distances:
18 5 0.05
19 30 0.28
20 7 0.06
21 21 0.19
22 10 0.09
23 12 0.11
24 24 0.22
ACGTcount: A:0.07, C:0.02, G:0.19, T:0.72
Consensus pattern (21 bp):
TTGTTGTTATTTTTGTTGTTT
Found at i:40223091 original size:12 final size:12
Alignment explanation
Indices: 40223053--40223177 Score: 84
Period size: 12 Copynumber: 10.8 Consensus size: 12
40223043 TTTTTTATTG
40223053 TTTTGATTGTTAT
1 TTTTG-TTGTTAT
* *
40223066 TTTCG-TGTTGT
1 TTTTGTTGTTAT
* *
40223077 TTTTGCTATTAT
1 TTTTGTTGTTAT
*
40223089 TTTTGTTGCTAT
1 TTTTGTTGTTAT
40223101 TTTTGTTGTTAT
1 TTTTGTTGTTAT
40223113 TTTTGTTGTT-T
1 TTTTGTTGTTAT
*
40223124 TTAATGTTG----
1 TT-TTGTTGTTAT
40223133 -TTTGTTGTTAT
1 TTTTGTTGTTAT
* **
40223144 TTTTGCTACTAT
1 TTTTGTTGTTAT
*
40223156 TTTGGTTGTTAT
1 TTTTGTTGTTAT
*
40223168 TTTTGCTGTT
1 TTTTGTTGTT
40223178 TGGATGTTAT
Statistics
Matches: 85, Mismatches: 20, Indels: 15
0.71 0.17 0.12
Matches are distributed among these distances:
7 5 0.06
8 1 0.01
11 12 0.14
12 63 0.74
13 4 0.05
ACGTcount: A:0.10, C:0.05, G:0.18, T:0.68
Consensus pattern (12 bp):
TTTTGTTGTTAT
Found at i:40223099 original size:15 final size:15
Alignment explanation
Indices: 40223073--40223122 Score: 54
Period size: 15 Copynumber: 3.5 Consensus size: 15
40223063 TATTTTCGTG
*
40223073 TTGTTTTTGCTATTAT
1 TTGTTGTTGCTATT-T
40223089 TT-TTGTTGCTATTT
1 TTGTTGTTGCTATTT
40223103 TTGTTG-T--TATTT
1 TTGTTGTTGCTATTT
40223115 TTGTTGTT
1 TTGTTGTT
40223123 TTTAATGTTG
Statistics
Matches: 31, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
12 11 0.35
13 1 0.03
14 4 0.13
15 13 0.42
16 2 0.06
ACGTcount: A:0.08, C:0.04, G:0.16, T:0.72
Consensus pattern (15 bp):
TTGTTGTTGCTATTT
Found at i:40223157 original size:43 final size:43
Alignment explanation
Indices: 40223090--40223191 Score: 107
Period size: 43 Copynumber: 2.3 Consensus size: 43
40223080 TGCTATTATT
* * ** * *
40223090 TTTGTTGCTATTTTTGTTGTTATTTTTGTTGTT-TTTAATGTTG
1 TTTGTTGTTATTTTTGCTACTATTTTGGTTGTTATTT-ATGCTG
*
40223133 TTTGTTGTTATTTTTGCTACTATTTTGGTTGTTATTTTTGCTG
1 TTTGTTGTTATTTTTGCTACTATTTTGGTTGTTATTTATGCTG
*
40223176 TTTGGATGTTATTTTT
1 TTT-GTTGTTATTTTT
40223192 TATGCGTTTT
Statistics
Matches: 49, Mismatches: 8, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
43 35 0.71
44 14 0.29
ACGTcount: A:0.10, C:0.04, G:0.19, T:0.68
Consensus pattern (43 bp):
TTTGTTGTTATTTTTGCTACTATTTTGGTTGTTATTTATGCTG
Found at i:40223391 original size:38 final size:38
Alignment explanation
Indices: 40223305--40223389 Score: 100
Period size: 39 Copynumber: 2.2 Consensus size: 38
40223295 TTAATATAAA
* * *
40223305 ATTTTTTTAATGTATTTTAAATTTATTTATTTTTTAAT
1 ATTTTTTTAATGTATTTTAAATGTATTTATATATTAAT
*
40223343 ATTTGTTTTAATGT-TTTTAAGTGTATTTGATATATTATAT
1 ATTT-TTTTAATGTATTTTAAATGTATTT-ATATATTA-AT
40223383 ATTTTTT
1 ATTTTTT
40223390 AAATTTGTTG
Statistics
Matches: 40, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
38 16 0.40
39 18 0.45
40 6 0.15
ACGTcount: A:0.27, C:0.00, G:0.07, T:0.66
Consensus pattern (38 bp):
ATTTTTTTAATGTATTTTAAATGTATTTATATATTAAT
Found at i:40229701 original size:15 final size:15
Alignment explanation
Indices: 40229666--40229711 Score: 51
Period size: 15 Copynumber: 3.2 Consensus size: 15
40229656 TTTTAAATAA
40229666 AAATATT-AAAT-TT
1 AAATATTAAAATATT
* * *
40229679 ATATATTATATTATT
1 AAATATTAAAATATT
40229694 AAATATTAAAATATT
1 AAATATTAAAATATT
40229709 AAA
1 AAA
40229712 AAATCTATTG
Statistics
Matches: 25, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
13 6 0.24
14 2 0.08
15 17 0.68
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (15 bp):
AAATATTAAAATATT
Found at i:40230141 original size:21 final size:21
Alignment explanation
Indices: 40230111--40230155 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
40230101 TTTTCTAGAT
* *
40230111 TATATATATTCTGATTTTTTA
1 TATATATATTCTCATTTTTCA
* *
40230132 TATATTTATTTTCATTTTTCA
1 TATATATATTCTCATTTTTCA
40230153 TAT
1 TAT
40230156 TTGTAATGTG
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.27, C:0.07, G:0.02, T:0.64
Consensus pattern (21 bp):
TATATATATTCTCATTTTTCA
Found at i:40230821 original size:31 final size:29
Alignment explanation
Indices: 40230754--40230823 Score: 79
Period size: 29 Copynumber: 2.3 Consensus size: 29
40230744 GTTAATGTAC
* * *
40230754 AAATTTGTCACTATACTTTATAGAAATTG
1 AAATTTATCACTATACTTTATAAAAATGG
40230783 AAATTTATCACTATACTTT-TAAATTAATGG
1 AAATTTATCACTATACTTTATAAA--AATGG
40230813 TAAATTTATCA
1 -AAATTTATCA
40230824 TTCTATTTCA
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
28 3 0.09
29 18 0.51
30 4 0.11
31 10 0.29
ACGTcount: A:0.40, C:0.10, G:0.07, T:0.43
Consensus pattern (29 bp):
AAATTTATCACTATACTTTATAAAAATGG
Found at i:40246685 original size:84 final size:82
Alignment explanation
Indices: 40246532--40246686 Score: 217
Period size: 84 Copynumber: 1.9 Consensus size: 82
40246522 ATGGTGTGTG
* *
40246532 TGGCACACGAGGGTGTGTCAGGGTGTGTGTATACTGTTTGGAGGCACACGAGCGTGTGTCAAGGT
1 TGGCACACGAGGGTGTGTCAGGGTGTGTGTATACTATTTGGAGGCACACGAGCGTGTGTCAAGGC
40246597 GTGTATGGCACACGGGC
66 GTGTATGGCACACGGGC
*
40246614 TGGCACAC-AGGGGTGTGTCAAGGTGTGTGTGTATACTATTTGGAGGCACACGGGC-TG-GCTCA
1 TGGCACACGA-GGGTGTGTC-AGG-GTGTGTGTATACTATTTGGAGGCACACGAGCGTGTG-TCA
40246676 TAGGCGTGTAT
62 -AGGCGTGTAT
40246687 CAGAGTGTGT
Statistics
Matches: 65, Mismatches: 3, Indels: 8
0.86 0.04 0.11
Matches are distributed among these distances:
81 1 0.02
82 18 0.28
83 8 0.12
84 38 0.58
ACGTcount: A:0.19, C:0.17, G:0.39, T:0.26
Consensus pattern (82 bp):
TGGCACACGAGGGTGTGTCAGGGTGTGTGTATACTATTTGGAGGCACACGAGCGTGTGTCAAGGC
GTGTATGGCACACGGGC
Found at i:40247379 original size:29 final size:29
Alignment explanation
Indices: 40247314--40247373 Score: 84
Period size: 29 Copynumber: 2.1 Consensus size: 29
40247304 ACGGATGGGG
* * * *
40247314 GTATCATGTCTACATTTGTAATTGTATTT
1 GTATCATGTCTACATTCGTAACTATATAT
40247343 GTATCATGTCTACATTCGTAACTATATAT
1 GTATCATGTCTACATTCGTAACTATATAT
40247372 GT
1 GT
40247374 GACATGACTG
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.27, C:0.13, G:0.13, T:0.47
Consensus pattern (29 bp):
GTATCATGTCTACATTCGTAACTATATAT
Found at i:40251689 original size:18 final size:18
Alignment explanation
Indices: 40251658--40251692 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
40251648 TAATAATTAA
* *
40251658 ATAAATAATTAAAAATTC
1 ATAAAAAATAAAAAATTC
40251676 ATAAAAAATAAAAAATT
1 ATAAAAAATAAAAAATT
40251693 ATTAAACCGT
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:0.69, C:0.03, G:0.00, T:0.29
Consensus pattern (18 bp):
ATAAAAAATAAAAAATTC
Found at i:40252646 original size:22 final size:23
Alignment explanation
Indices: 40252621--40252664 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
40252611 ATATTCTTAT
40252621 TTTTTTATAATAT-TTAATTAAA
1 TTTTTTATAATATATTAATTAAA
* *
40252643 TTTTTTATTATATATTATTTAA
1 TTTTTTATAATATATTAATTAA
40252665 TAATAGTTAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 12 0.63
23 7 0.37
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (23 bp):
TTTTTTATAATATATTAATTAAA
Found at i:40256016 original size:6 final size:6
Alignment explanation
Indices: 40255998--40256096 Score: 80
Period size: 6 Copynumber: 16.8 Consensus size: 6
40255988 TTAAATTGAT
* * * *
40255998 TTTAAA TTT--A TTTAAA TTTAGA TTT-AT TTTAAA TTAAAA TTAAATA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAA-A
* ** *
40256044 TTTAAA TTT-AA TTTGAA TTTAAA TTTAAA TAAAAA TTAAAA TATTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA T-TTAAA
40256092 TTTAA
1 TTTAA
40256097 CATTAAAAGT
Statistics
Matches: 76, Mismatches: 11, Indels: 12
0.77 0.11 0.12
Matches are distributed among these distances:
4 4 0.05
5 8 0.11
6 54 0.71
7 10 0.13
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.48
Consensus pattern (6 bp):
TTTAAA
Found at i:40256053 original size:36 final size:34
Alignment explanation
Indices: 40256006--40256096 Score: 101
Period size: 36 Copynumber: 2.5 Consensus size: 34
40255996 ATTTTAAATT
*
40256006 TATTTAAATTTAGATTTATTTTAAATTAAAATTAAA
1 TATTTAAATTTA-ATTTAATTTAAATTAAAA-TAAA
*
40256042 TATTTAAATTTAATTTGAATTTAAATTTAAATAAA
1 TATTTAAATTTAATTT-AATTTAAATTAAAATAAA
* *
40256077 AATTAAAATATTAAATTTAA
1 TATTTAAAT-TT-AATTTAA
40256097 CATTAAAAGT
Statistics
Matches: 48, Mismatches: 4, Indels: 6
0.83 0.07 0.10
Matches are distributed among these distances:
35 15 0.31
36 28 0.58
37 5 0.10
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (34 bp):
TATTTAAATTTAATTTAATTTAAATTAAAATAAA
Found at i:40256057 original size:11 final size:11
Alignment explanation
Indices: 40255988--40256073 Score: 59
Period size: 11 Copynumber: 7.5 Consensus size: 11
40255978 GACTCTTGAG
* *
40255988 TTAAATTGATT
1 TTAAATTTAAT
40255999 TTAAATTT-AT
1 TTAAATTTAAT
40256009 TTAAATTTAGAT
1 TTAAATTTA-AT
*
40256021 TT-ATTTTAAAT
1 TTAAATTT-AAT
* *
40256032 TAAAATTAAATAT
1 TTAAATT-TA-AT
40256045 TTAAATTTAAT
1 TTAAATTTAAT
*
40256056 TTGAATTTAAAT
1 TTAAATTT-AAT
40256068 TTAAAT
1 TTAAAT
40256074 AAAAATTAAA
Statistics
Matches: 58, Mismatches: 10, Indels: 13
0.72 0.12 0.16
Matches are distributed among these distances:
10 9 0.16
11 23 0.40
12 18 0.31
13 8 0.14
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.52
Consensus pattern (11 bp):
TTAAATTTAAT
Found at i:40256071 original size:17 final size:17
Alignment explanation
Indices: 40255988--40256071 Score: 61
Period size: 16 Copynumber: 5.2 Consensus size: 17
40255978 GACTCTTGAG
* *
40255988 TTAAATTGATTTTAAAT
1 TTAATTTGAATTTAAAT
* *
40256005 TT-ATTTAAATTTAGAT
1 TTAATTTGAATTTAAAT
* * *
40256021 TT-ATTTTAAATTAAAA
1 TTAATTTGAATTTAAAT
*
40256037 TTAA-AT--ATTTAAAT
1 TTAATTTGAATTTAAAT
40256051 TTAATTTGAATTTAAAT
1 TTAATTTGAATTTAAAT
40256068 TTAA
1 TTAA
40256072 ATAAAAATTA
Statistics
Matches: 51, Mismatches: 12, Indels: 8
0.72 0.17 0.11
Matches are distributed among these distances:
14 10 0.20
15 1 0.02
16 25 0.49
17 15 0.29
ACGTcount: A:0.44, C:0.00, G:0.04, T:0.52
Consensus pattern (17 bp):
TTAATTTGAATTTAAAT
Found at i:40256151 original size:14 final size:14
Alignment explanation
Indices: 40256132--40256185 Score: 85
Period size: 14 Copynumber: 4.0 Consensus size: 14
40256122 CATGGCCCAC
40256132 GGCCCAATTACAAT
1 GGCCCAATTACAAT
40256146 GGCCCAATTACAAT
1 GGCCCAATTACAAT
*
40256160 GGCCCAATT--AAG
1 GGCCCAATTACAAT
40256172 GGCCCAATTACAAT
1 GGCCCAATTACAAT
40256186 AGTCCAAATC
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
12 11 0.31
14 25 0.69
ACGTcount: A:0.35, C:0.28, G:0.17, T:0.20
Consensus pattern (14 bp):
GGCCCAATTACAAT
Found at i:40256181 original size:26 final size:27
Alignment explanation
Indices: 40256132--40256185 Score: 83
Period size: 26 Copynumber: 2.0 Consensus size: 27
40256122 CATGGCCCAC
*
40256132 GGCCCAATTACAATGGCCCAATTACAAT
1 GGCCCAATTA-AAGGGCCCAATTACAAT
40256160 GGCCCAATT-AAGGGCCCAATTACAAT
1 GGCCCAATTAAAGGGCCCAATTACAAT
40256186 AGTCCAAATC
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
26 16 0.64
28 9 0.36
ACGTcount: A:0.35, C:0.28, G:0.17, T:0.20
Consensus pattern (27 bp):
GGCCCAATTAAAGGGCCCAATTACAAT
Found at i:40256252 original size:20 final size:20
Alignment explanation
Indices: 40256227--40256267 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
40256217 GTGCCTACTG
* *
40256227 CTGCTGGCCACCGGCTCCAT
1 CTGCTGACCACCAGCTCCAT
40256247 CTGCTGACCACCAGCTCCAT
1 CTGCTGACCACCAGCTCCAT
40256267 C
1 C
40256268 CACCAGCTCT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.15, C:0.46, G:0.20, T:0.20
Consensus pattern (20 bp):
CTGCTGACCACCAGCTCCAT
Found at i:40256801 original size:3 final size:3
Alignment explanation
Indices: 40256793--40256824 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
40256783 TTATAACATC
40256793 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
40256825 ATATTTAATA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:40258054 original size:29 final size:30
Alignment explanation
Indices: 40257914--40258088 Score: 221
Period size: 30 Copynumber: 5.8 Consensus size: 30
40257904 CCCCAAACAA
* *
40257914 TCTAGAAATTGCATTTTAACCCCAAAACTTT
1 TCTA-AAATTACATTTTGACCCCAAAACTTT
*
40257945 TCCAAAATTACATTTTGACCCCAAAACTTT
1 TCTAAAATTACATTTTGACCCCAAAACTTT
*
40257975 TCTAGAATTACATTTTGACCCCAAAACTTT
1 TCTAAAATTACATTTTGACCCCAAAACTTT
40258005 TCTAAAATTACATTTTGACCCCAAAAC-TT
1 TCTAAAATTACATTTTGACCCCAAAACTTT
* *
40258034 TCGAAAATTATCATTTT-ACCCCCAAACTTCT
1 TCTAAAATTA-CATTTTGACCCCAAAACTT-T
* *
40258065 T-TAAAATTCCATTTTTAACCCCAA
1 TCTAAAATTACA-TTTTGACCCCAA
40258089 TTTCATCAAA
Statistics
Matches: 128, Mismatches: 11, Indels: 10
0.86 0.07 0.07
Matches are distributed among these distances:
29 22 0.17
30 95 0.74
31 11 0.09
ACGTcount: A:0.35, C:0.25, G:0.04, T:0.35
Consensus pattern (30 bp):
TCTAAAATTACATTTTGACCCCAAAACTTT
Found at i:40258130 original size:59 final size:58
Alignment explanation
Indices: 40258037--40258287 Score: 333
Period size: 59 Copynumber: 4.2 Consensus size: 58
40258027 AAAACTTTCG
* * * *
40258037 AAAATTATCATTTTACCCCC-AAACTTCTTTAAAATTCCATTTTTAACCCCAATTTCATCA
1 AAAATTACCATTTTACCCCCGAAGC--CTCTAAAATTCCATTTTTAACCCCGATTTCA-CA
*
40258097 AAAATTACCATTTTACCCCCGAAGCCTCTAAAATTCCATTTTTAACCTCGATTTCACAA
1 AAAATTACCATTTTACCCCCGAAGCCTCTAAAATTCCATTTTTAACCCCGATTTCAC-A
*
40258156 AAAATTACCATTTTACCCCCGAAGCTTCTAAAATTCCATTTTTAACCCCGATTTCACCA
1 AAAATTACCATTTTACCCCCGAAGCCTCTAAAATTCCATTTTTAACCCCGATTTCA-CA
* * * * * *
40258215 AAAATTACCATTTTACCCCCGAATCTTTTAAAATTCCATTTTTTTACCCCGATTACACC
1 AAAATTACCATTTTACCCCCGAAGCCTCTAAAATTCCA-TTTTTAACCCCGATTTCACA
40258274 AAAATTACCATTTT
1 AAAATTACCATTTT
40258288 GCCCTCGGGT
Statistics
Matches: 175, Mismatches: 12, Indels: 9
0.89 0.06 0.05
Matches are distributed among these distances:
58 1 0.01
59 135 0.77
60 36 0.21
61 3 0.02
ACGTcount: A:0.33, C:0.28, G:0.03, T:0.35
Consensus pattern (58 bp):
AAAATTACCATTTTACCCCCGAAGCCTCTAAAATTCCATTTTTAACCCCGATTTCACA
Found at i:40258229 original size:30 final size:30
Alignment explanation
Indices: 40258067--40258287 Score: 134
Period size: 30 Copynumber: 7.4 Consensus size: 30
40258057 AAACTTCTTT
* *
40258067 AAAATTCCATTTTTAACCCCAATTTCATCA
1 AAAATTCCATTTTTAACCCCGATTTCACCA
* ** *
40258097 AAAATTACCA-TTTTACCCCCGA-AGC-CTCT
1 AAAATT-CCATTTTTAACCCCGATTTCAC-CA
* *
40258126 AAAATTCCATTTTTAACCTCGATTTCACAA
1 AAAATTCCATTTTTAACCCCGATTTCACCA
* ** ** *
40258156 AAAATTACCA-TTTTACCCCCGA-AGCTTCT
1 AAAATT-CCATTTTTAACCCCGATTTCACCA
40258185 AAAATTCCATTTTTAACCCCGATTTCACCA
1 AAAATTCCATTTTTAACCCCGATTTCACCA
* * ****
40258215 AAAATTACCA-TTTTACCCCCGA-ATCTTTT
1 AAAATT-CCATTTTTAACCCCGATTTCACCA
* *
40258244 AAAATTCCATTTTTTTACCCCGATTACACC-
1 AAAATTCCA-TTTTTAACCCCGATTTCACCA
40258274 AAAATTACCATTTT
1 AAAATT-CCATTTT
40258288 GCCCTCGGGT
Statistics
Matches: 139, Mismatches: 39, Indels: 26
0.68 0.19 0.13
Matches are distributed among these distances:
28 9 0.06
29 44 0.32
30 72 0.52
31 14 0.10
ACGTcount: A:0.33, C:0.28, G:0.04, T:0.35
Consensus pattern (30 bp):
AAAATTCCATTTTTAACCCCGATTTCACCA
Found at i:40270303 original size:23 final size:23
Alignment explanation
Indices: 40270247--40270334 Score: 97
Period size: 23 Copynumber: 3.8 Consensus size: 23
40270237 TCATTAACAT
* *
40270247 TGTTCTTGAACATGTTCAATTATA
1 TGTTCATGAACATGTTCGATTA-A
* * *
40270271 TGTTCTTGAACATGTTTGTTTAA
1 TGTTCATGAACATGTTCGATTAA
40270294 TGTTCATGAACATGTTCGATTAA
1 TGTTCATGAACATGTTCGATTAA
*
40270317 -GTTAAATGAACATGTTCG
1 TGTT-CATGAACATGTTCG
40270335 TGAACATTAA
Statistics
Matches: 56, Mismatches: 7, Indels: 3
0.85 0.11 0.05
Matches are distributed among these distances:
22 3 0.05
23 34 0.61
24 19 0.34
ACGTcount: A:0.28, C:0.11, G:0.17, T:0.43
Consensus pattern (23 bp):
TGTTCATGAACATGTTCGATTAA
Found at i:40270344 original size:23 final size:23
Alignment explanation
Indices: 40270299--40270346 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
40270289 TTTAATGTTC
* *
40270299 ATGAACATGTTCGATTAAGTTAA
1 ATGAACATGTTCGATGAAATTAA
40270322 ATGAACATGTTCG-TGAACATTAA
1 ATGAACATGTTCGATGAA-ATTAA
40270345 AT
1 AT
40270347 AAACGAACAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
22 3 0.14
23 19 0.86
ACGTcount: A:0.40, C:0.10, G:0.17, T:0.33
Consensus pattern (23 bp):
ATGAACATGTTCGATGAAATTAA
Found at i:40275090 original size:17 final size:17
Alignment explanation
Indices: 40275060--40275093 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
40275050 TACTCGATAT
*
40275060 TTAATTAAATAAAAATA
1 TTAATTAAAGAAAAATA
*
40275077 TTAATTAAGGAAAAATA
1 TTAATTAAAGAAAAATA
40275094 ATTTAATAAT
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:0.62, C:0.00, G:0.06, T:0.32
Consensus pattern (17 bp):
TTAATTAAAGAAAAATA
Found at i:40282590 original size:24 final size:23
Alignment explanation
Indices: 40282528--40282590 Score: 63
Period size: 24 Copynumber: 2.7 Consensus size: 23
40282518 ATACAACTTA
* **
40282528 AAAAAAATCAGAGAAGGAAGGGT
1 AAAAAAATCAGAAAAGGAAAAGT
* *
40282551 AAAAAAAACAAAAAAAGGAAAAGT
1 AAAAAAATC-AGAAAAGGAAAAGT
40282575 AAAAAATATCAGAAAA
1 AAAAAA-ATCAGAAAA
40282591 AAAAAAGCTG
Statistics
Matches: 31, Mismatches: 7, Indels: 3
0.76 0.17 0.07
Matches are distributed among these distances:
23 8 0.26
24 21 0.68
25 2 0.06
ACGTcount: A:0.70, C:0.05, G:0.17, T:0.08
Consensus pattern (23 bp):
AAAAAAATCAGAAAAGGAAAAGT
Found at i:40283959 original size:30 final size:29
Alignment explanation
Indices: 40283892--40284063 Score: 145
Period size: 30 Copynumber: 5.8 Consensus size: 29
40283882 ATTGAGGTTA
* *
40283892 AAAATGGAA-TTTGGAAA-ATTTAGGGGT-
1 AAAATGTAATTTTGGAAAGTTTTA-GGGTC
40283919 AAAATGGTAATTTTAGGAAAGTTTTAGGGTC
1 AAAAT-GTAATTTT-GGAAAGTTTTAGGGTC
* *
40283950 AAAATGTAATATTGGAAAAGTTTTAGGGTT
1 AAAATGTAATTTTGG-AAAGTTTTAGGGTC
* * *
40283980 AAAATATAATTTTGGAAAAGTTTTGGGGTT
1 AAAATGTAATTTTGG-AAAGTTTTAGGGTC
**
40284010 AAAATGTAATTTTCAAAAAGTTTT-GAGGTC
1 AAAATGTAATTTT-GGAAAGTTTTAG-GGTC
* *
40284040 AAAATATAATTTTTGGACAGTTTT
1 AAAATGTAA-TTTTGGAAAGTTTT
40284064 GGGACGTACA
Statistics
Matches: 121, Mismatches: 15, Indels: 15
0.80 0.10 0.10
Matches are distributed among these distances:
27 5 0.04
28 3 0.02
29 6 0.05
30 94 0.78
31 13 0.11
ACGTcount: A:0.38, C:0.02, G:0.22, T:0.37
Consensus pattern (29 bp):
AAAATGTAATTTTGGAAAGTTTTAGGGTC
Found at i:40284001 original size:60 final size:59
Alignment explanation
Indices: 40283892--40284063 Score: 181
Period size: 60 Copynumber: 2.9 Consensus size: 59
40283882 ATTGAGGTTA
* * *
40283892 AAAATGGAATTTGGAAAA--TTTAGGGGTAAAATGGTAATTTTAGGAAAGTTTTAGGGTC
1 AAAATGTAATTTGGAAAAGTTTTAGGGTTAAAAT-ATAATTTTAGGAAAGTTTTAGGGTC
* *
40283950 AAAATGTAATATTGGAAAAGTTTTAGGGTTAAAATATAATTTT-GGAAAAGTTTTGGGGTT
1 AAAATGTAAT-TTGGAAAAGTTTTAGGGTTAAAATATAATTTTAGG-AAAGTTTTAGGGTC
** * * *
40284010 AAAATGTAATTTTCAAAAAGTTTT-GAGGTCAAAATATAATTTTTGGACAGTTTT
1 AAAATGTAA-TTTGGAAAAGTTTTAG-GGTTAAAATATAATTTTAGGAAAGTTTT
40284064 GGGACGTACA
Statistics
Matches: 98, Mismatches: 9, Indels: 12
0.82 0.08 0.10
Matches are distributed among these distances:
58 9 0.09
59 11 0.11
60 62 0.63
61 16 0.16
ACGTcount: A:0.38, C:0.02, G:0.22, T:0.37
Consensus pattern (59 bp):
AAAATGTAATTTGGAAAAGTTTTAGGGTTAAAATATAATTTTAGGAAAGTTTTAGGGTC
Found at i:40285211 original size:22 final size:21
Alignment explanation
Indices: 40285173--40285216 Score: 54
Period size: 21 Copynumber: 2.0 Consensus size: 21
40285163 AGTCATTAAA
40285173 ATTAATACTAATATTATTTATT
1 ATTAATACTAATATTA-TTATT
*
40285195 ATTAATA-TTATACTTATTATT
1 ATTAATACTAATA-TTATTATT
40285216 A
1 A
40285217 ATATTATCAT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
21 10 0.50
22 10 0.50
ACGTcount: A:0.41, C:0.05, G:0.00, T:0.55
Consensus pattern (21 bp):
ATTAATACTAATATTATTATT
Found at i:40285213 original size:18 final size:16
Alignment explanation
Indices: 40285181--40285223 Score: 68
Period size: 18 Copynumber: 2.6 Consensus size: 16
40285171 AAATTAATAC
40285181 TAATATTATTTATTAT
1 TAATATTATTTATTAT
40285197 TAATATTATACTTATTAT
1 TAATATTAT--TTATTAT
40285215 TAATATTAT
1 TAATATTAT
40285224 CATTAATGCT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
16 9 0.36
18 16 0.64
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (16 bp):
TAATATTATTTATTAT
Found at i:40285953 original size:6 final size:6
Alignment explanation
Indices: 40285944--40286034 Score: 63
Period size: 6 Copynumber: 16.2 Consensus size: 6
40285934 GGACATTTTT
* *
40285944 AATTTA AATTTA CAA--T- AATATTA AATTTA AA-TTA AATTCA AATTCA
1 AATTTA AATTTA -AATTTA AAT-TTA AATTTA AATTTA AATTTA AATTTA
* * *
40285990 AA-TTA AA-TTA AATTTA AA-ATA AATTTA AAATTA AA-ATA AATTTA
1 AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA
40286034 A
1 A
40286035 TTTCAAAATG
Statistics
Matches: 69, Mismatches: 7, Indels: 18
0.73 0.07 0.19
Matches are distributed among these distances:
3 2 0.03
5 23 0.33
6 39 0.57
7 5 0.07
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.40
Consensus pattern (6 bp):
AATTTA
Found at i:40285969 original size:17 final size:15
Alignment explanation
Indices: 40285947--40286037 Score: 83
Period size: 17 Copynumber: 5.5 Consensus size: 15
40285937 CATTTTTAAT
40285947 TTAAATTTACAATAATA
1 TTAAATTTA-AATAA-A
40285964 TTAAATTTAAATTAAA
1 TTAAATTTAAA-TAAA
*
40285980 TTCAAATTCAAATTAAA
1 TT-AAATTTAAA-TAAA
40285997 TTAAATTTAAAATAAA
1 TTAAATTT-AAATAAA
*
40286013 TTTAAAATTAAAATAAA
1 -TT-AAATTTAAATAAA
*
40286030 TTTAATTT
1 TTAAATTT
40286038 CAAAATGGTT
Statistics
Matches: 64, Mismatches: 5, Indels: 12
0.79 0.06 0.15
Matches are distributed among these distances:
15 4 0.06
16 16 0.25
17 39 0.61
18 5 0.08
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (15 bp):
TTAAATTTAAATAAA
Found at i:40285979 original size:11 final size:11
Alignment explanation
Indices: 40285963--40286037 Score: 82
Period size: 11 Copynumber: 6.8 Consensus size: 11
40285953 TTACAATAAT
40285963 ATTAAATTTAA
1 ATTAAATTTAA
*
40285974 ATTAAATTCAA
1 ATTAAATTTAA
40285985 ATTCAAA-TTAA
1 ATT-AAATTTAA
40285996 ATTAAATTTAA
1 ATTAAATTTAA
*
40286007 AATAAATTTAAA
1 ATTAAATTT-AA
*
40286019 ATTAAA-ATAA
1 ATTAAATTTAA
*
40286029 ATTTAATTT
1 ATTAAATTT
40286038 CAAAATGGTT
Statistics
Matches: 53, Mismatches: 7, Indels: 8
0.78 0.10 0.12
Matches are distributed among these distances:
10 10 0.19
11 33 0.62
12 10 0.19
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.41
Consensus pattern (11 bp):
ATTAAATTTAA
Found at i:40286442 original size:43 final size:48
Alignment explanation
Indices: 40286350--40286879 Score: 186
Period size: 49 Copynumber: 11.3 Consensus size: 48
40286340 CAGCTCTACT
*
40286350 TCAATTTCAAGAGGATAGGAAATGATGTTGGTGCTTCATCTTACTCTTAC
1 TCAATTTCAAGAGGATAGAAAATGATGTTGGTGCTT-ATC-TACTCTTAC
40286400 TCAATTTC-AGAGGA-ACGAAAATGATGTTGGTGCTTCATCTTACTCTTAC
1 TCAATTTCAAGAGGATA-GAAAATGATGTTGGTGCTT-ATC-TACTCTTAC
* * *
40286449 TTCAATTTC-AGAGG---GACGAA-G--GCT--TG-TTATCCAGCT-TTAC
1 -TCAATTTCAAGAGGATAGA-AAATGATGTTGGTGCTTATCTA-CTCTTAC
* * *
40286489 TTCAATTTCAAGAGGATAGGAAAATGATGTTGGTCCTTCTTCTTACCCTTAC
1 -TCAATTTCAAGAGGATA-GAAAATGATGTTGGTGCTT-ATC-TACTCTTAC
* *
40286541 TTCAATTTC-AGAGG---GACAAA-G--GCT--TG-TTATCCAGCT-TTAC
1 -TCAATTTCAAGAGGATAGA-AAATGATGTTGGTGCTTATCTA-CTCTTAC
* *
40286581 TTCAATTTCAAGGGGATAGGAAAATGATATTGGTGCTTCATCTTACTCTTAC
1 -TCAATTTCAAGAGGATA-GAAAATGATGTTGGTGCTT-ATC-TACTCTTAC
* *
40286633 TCAATTTC-AGAGGGA-CGAAAATGACGTTGGTGCTTCATCTTACTCTTAC
1 TCAATTTCAAGA-GGATAGAAAATGATGTTGGTGCTT-ATC-TACTCTTAC
* * *
40286682 TTCAATTTC-AGAGG---GACGAA--A-GCT--TG-TTATCCAGCT-TTAC
1 -TCAATTTCAAGAGGATAGA-AAATGATGTTGGTGCTTATCTA-CTCTTAC
* * *
40286722 TTCAATTTCAAGAGAATAGGAAAATGATGTTGGTCCTTCTTCTTACTCTTAC
1 -TCAATTTCAAGAGGATA-GAAAATGATGTTGGTGCTT-ATC-TACTCTTAC
* * *
40286774 TTCAATTTC-AGAGG---GACGAA-G--GCT--TG-TTATCCAGCT-TTAC
1 -TCAATTTCAAGAGGATAGA-AAATGATGTTGGTGCTTATCTA-CTCTTAC
40286814 TTCAATTTCAAGAGGATAGGAAAATGATGTTGGTGCTTCATCTTACTCTTAC
1 -TCAATTTCAAGAGGATA-GAAAATGATGTTGGTGCTT-ATC-TACTCTTAC
40286866 TTCAATTTC-AGAGG
1 -TCAATTTCAAGAGG
40286880 GACGAAGGCT
Statistics
Matches: 371, Mismatches: 41, Indels: 135
0.68 0.07 0.25
Matches are distributed among these distances:
40 56 0.15
41 35 0.09
42 8 0.02
43 6 0.02
44 9 0.02
45 19 0.05
46 2 0.01
47 18 0.05
48 10 0.03
49 77 0.21
50 42 0.11
51 42 0.11
52 47 0.13
ACGTcount: A:0.28, C:0.18, G:0.19, T:0.35
Consensus pattern (48 bp):
TCAATTTCAAGAGGATAGAAAATGATGTTGGTGCTTATCTACTCTTAC
Found at i:40286516 original size:92 final size:92
Alignment explanation
Indices: 40286396--40286651 Score: 421
Period size: 92 Copynumber: 2.8 Consensus size: 92
40286386 CATCTTACTC
*
40286396 TTAC-TCAATTTC-AGAGGA-ACGAAAATGATGTTGGTGCTTCATCTTACTCTTACTTCAATTTC
1 TTACTTCAATTTCAAGAGGATAGGAAAATGATGTTGGTGCTTCATCTTACTCTTACTTCAATTTC
40286458 AGAGGGACGAAGGCTTGTTATCCAGCT
66 AGAGGGACGAAGGCTTGTTATCCAGCT
* * *
40286485 TTACTTCAATTTCAAGAGGATAGGAAAATGATGTTGGTCCTTCTTCTTACCCTTACTTCAATTTC
1 TTACTTCAATTTCAAGAGGATAGGAAAATGATGTTGGTGCTTCATCTTACTCTTACTTCAATTTC
*
40286550 AGAGGGACAAAGGCTTGTTATCCAGCT
66 AGAGGGACGAAGGCTTGTTATCCAGCT
* *
40286577 TTACTTCAATTTCAAGGGGATAGGAAAATGATATTGGTGCTTCATCTTACTCTTAC-TCAATTTC
1 TTACTTCAATTTCAAGAGGATAGGAAAATGATGTTGGTGCTTCATCTTACTCTTACTTCAATTTC
40286641 AGAGGGACGAA
66 AGAGGGACGAA
40286652 AATGACGTTG
Statistics
Matches: 153, Mismatches: 11, Indels: 4
0.91 0.07 0.02
Matches are distributed among these distances:
89 4 0.03
90 8 0.05
91 24 0.16
92 117 0.76
ACGTcount: A:0.28, C:0.18, G:0.20, T:0.34
Consensus pattern (92 bp):
TTACTTCAATTTCAAGAGGATAGGAAAATGATGTTGGTGCTTCATCTTACTCTTACTTCAATTTC
AGAGGGACGAAGGCTTGTTATCCAGCT
Found at i:40286653 original size:141 final size:142
Alignment explanation
Indices: 40286485--40286793 Score: 478
Period size: 141 Copynumber: 2.2 Consensus size: 142
40286475 TTATCCAGCT
* * * *
40286485 TTACTTCAATTTCAAGAGGATAGGAAAATGATGTTGGTCCTTCTTCTTACCCTTACTTCAATTTC
1 TTACTTCAATTTC-AGAGG-GACGAAAATGACGTTGGTCCTTCATCTTACCCTTACTTCAATTTC
* *
40286550 AGAGGGAC-AAAGGCTTGTTATCCAGCTTTACTTCAATTTCAAGGGGATAGGAAAATGATATTGG
64 AGAGGGACGAAA-GCTTGTTATCCAGCTTTACTTCAATTTCAAGAGAATAGGAAAATGATATTGG
*
40286614 TGCTTCATCTTACTC
128 TCCTTCATCTTACTC
* *
40286629 TTAC-TCAATTTCAGAGGGACGAAAATGACGTTGGTGCTTCATCTTACTCTTACTTCAATTTCAG
1 TTACTTCAATTTCAGAGGGACGAAAATGACGTTGGTCCTTCATCTTACCCTTACTTCAATTTCAG
*
40286693 AGGGACGAAAGCTTGTTATCCAGCTTTACTTCAATTTCAAGAGAATAGGAAAATGATGTTGGTCC
66 AGGGACGAAAGCTTGTTATCCAGCTTTACTTCAATTTCAAGAGAATAGGAAAATGATATTGGTCC
*
40286758 TTCTTCTTACTC
131 TTCATCTTACTC
40286770 TTACTTCAATTTCAGAGGGACGAA
1 TTACTTCAATTTCAGAGGGACGAA
40286794 GGCTTGTTAT
Statistics
Matches: 152, Mismatches: 11, Indels: 6
0.90 0.07 0.04
Matches are distributed among these distances:
141 113 0.74
142 27 0.18
143 8 0.05
144 4 0.03
ACGTcount: A:0.28, C:0.18, G:0.19, T:0.35
Consensus pattern (142 bp):
TTACTTCAATTTCAGAGGGACGAAAATGACGTTGGTCCTTCATCTTACCCTTACTTCAATTTCAG
AGGGACGAAAGCTTGTTATCCAGCTTTACTTCAATTTCAAGAGAATAGGAAAATGATATTGGTCC
TTCATCTTACTC
Found at i:40286743 original size:233 final size:232
Alignment explanation
Indices: 40286315--40286885 Score: 1004
Period size: 233 Copynumber: 2.5 Consensus size: 232
40286305 CTCTTATTTT
* * *
40286315 AATTTCAGAGGGAC--GACTTGATATCCAGCTCTACTTCAATTTCAAGAGGATAGG-AAATGATG
1 AATTTCAGAGGGACAAGGCTTGTTATCCAGCTTTACTTCAATTTCAAGAGGATAGGAAAATGATG
* *
40286377 TTGGTGCTTCATCTTACTCTTACTCAATTTCAGAGGAACGAAAATGATGTTGGTGCTTCATCTTA
66 TTGGTGCTTCATCTTACTCTTACTCAATTTCAGAGGGACGAAAATGACGTTGGTGCTTCATCTTA
* *
40286442 CTCTTACTTCAATTTCAGAGGGACGAAGGCTTGTTATCCAGCTTTACTTCAATTTCAAGAGGATA
131 CTCTTACTTCAATTTCAGAGGGACGAAAGCTTGTTATCCAGCTTTACTTCAATTTCAAGAGAATA
40286507 GGAAAATGATGTTGGTCCTTCTTCTTACCCTTACTTC
196 GGAAAATGATGTTGGTCCTTCTTCTTACCCTTACTTC
*
40286544 AATTTCAGAGGGACAAAGGCTTGTTATCCAGCTTTACTTCAATTTCAAGGGGATAGGAAAATGAT
1 AATTTCAGAGGGAC-AAGGCTTGTTATCCAGCTTTACTTCAATTTCAAGAGGATAGGAAAATGAT
*
40286609 ATTGGTGCTTCATCTTACTCTTACTCAATTTCAGAGGGACGAAAATGACGTTGGTGCTTCATCTT
65 GTTGGTGCTTCATCTTACTCTTACTCAATTTCAGAGGGACGAAAATGACGTTGGTGCTTCATCTT
40286674 ACTCTTACTTCAATTTCAGAGGGACGAAAGCTTGTTATCCAGCTTTACTTCAATTTCAAGAGAAT
130 ACTCTTACTTCAATTTCAGAGGGACGAAAGCTTGTTATCCAGCTTTACTTCAATTTCAAGAGAAT
*
40286739 AGGAAAATGATGTTGGTCCTTCTTCTTACTCTTACTTC
195 AGGAAAATGATGTTGGTCCTTCTTCTTACCCTTACTTC
40286777 AATTTCAGAGGGACGAAGGCTTGTTATCCAGCTTTACTTCAATTTCAAGAGGATAGGAAAATGAT
1 AATTTCAGAGGGAC-AAGGCTTGTTATCCAGCTTTACTTCAATTTCAAGAGGATAGGAAAATGAT
40286842 GTTGGTGCTTCATCTTACTCTTACTTCAATTTCAGAGGGACGAA
65 GTTGGTGCTTCATCTTACTCTTAC-TCAATTTCAGAGGGACGAA
40286886 GGCTTGTTAT
Statistics
Matches: 324, Mismatches: 13, Indels: 5
0.95 0.04 0.01
Matches are distributed among these distances:
229 14 0.04
232 36 0.11
233 255 0.79
234 19 0.06
ACGTcount: A:0.28, C:0.18, G:0.20, T:0.34
Consensus pattern (232 bp):
AATTTCAGAGGGACAAGGCTTGTTATCCAGCTTTACTTCAATTTCAAGAGGATAGGAAAATGATG
TTGGTGCTTCATCTTACTCTTACTCAATTTCAGAGGGACGAAAATGACGTTGGTGCTTCATCTTA
CTCTTACTTCAATTTCAGAGGGACGAAAGCTTGTTATCCAGCTTTACTTCAATTTCAAGAGAATA
GGAAAATGATGTTGGTCCTTCTTCTTACCCTTACTTC
Found at i:40286766 original size:92 final size:92
Alignment explanation
Indices: 40286629--40286937 Score: 509
Period size: 92 Copynumber: 3.4 Consensus size: 92
40286619 CATCTTACTC
* * *
40286629 TTAC-TCAATTTC-AGAGG-GACGAAAATGACGTTGGTGCTTCATCTTACTCTTACTTCAATTTC
1 TTACTTCAATTTCAAGAGGATAGGAAAATGATGTTGGTGCTTCATCTTACTCTTACTTCAATTTC
*
40286691 AGAGGGACGAAAGCTTGTTATCCAGCT
66 AGAGGGACGAAGGCTTGTTATCCAGCT
* * *
40286718 TTACTTCAATTTCAAGAGAATAGGAAAATGATGTTGGTCCTTCTTCTTACTCTTACTTCAATTTC
1 TTACTTCAATTTCAAGAGGATAGGAAAATGATGTTGGTGCTTCATCTTACTCTTACTTCAATTTC
40286783 AGAGGGACGAAGGCTTGTTATCCAGCT
66 AGAGGGACGAAGGCTTGTTATCCAGCT
40286810 TTACTTCAATTTCAAGAGGATAGGAAAATGATGTTGGTGCTTCATCTTACTCTTACTTCAATTTC
1 TTACTTCAATTTCAAGAGGATAGGAAAATGATGTTGGTGCTTCATCTTACTCTTACTTCAATTTC
40286875 AGAGGGACGAAGGCTTGTTATCCAGCT
66 AGAGGGACGAAGGCTTGTTATCCAGCT
40286902 ACTTACTTCAATTTCAAGAGGATAGG-AAATGATGTT
1 --TTACTTCAATTTCAAGAGGATAGGAAAATGATGTT
40286938 TGATTGATCT
Statistics
Matches: 205, Mismatches: 10, Indels: 6
0.93 0.05 0.03
Matches are distributed among these distances:
89 4 0.02
90 8 0.04
91 4 0.02
92 155 0.76
93 10 0.05
94 24 0.12
ACGTcount: A:0.28, C:0.18, G:0.20, T:0.34
Consensus pattern (92 bp):
TTACTTCAATTTCAAGAGGATAGGAAAATGATGTTGGTGCTTCATCTTACTCTTACTTCAATTTC
AGAGGGACGAAGGCTTGTTATCCAGCT
Found at i:40289011 original size:22 final size:22
Alignment explanation
Indices: 40288986--40289029 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
40288976 ATCTAGGACG
40288986 TACTCGTTCACGAGCCTTCTCA
1 TACTCGTTCACGAGCCTTCTCA
*
40289008 TACTCGTTCGCGAGCCTTCTCA
1 TACTCGTTCACGAGCCTTCTCA
40289030 ATGTCCTTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.16, C:0.36, G:0.16, T:0.32
Consensus pattern (22 bp):
TACTCGTTCACGAGCCTTCTCA
Found at i:40299059 original size:29 final size:29
Alignment explanation
Indices: 40299016--40299129 Score: 112
Period size: 29 Copynumber: 3.9 Consensus size: 29
40299006 TTTTGTATGC
*
40299016 CGGGGGTAAAAATGGTAATTTTGGAAGGTT
1 CGGGGGTAAAAATGGTAATTTTGGAA-ATT
*
40299046 CGGGGGT-AAAATGGTAAATTTTGGCAAAAT
1 CGGGGGTAAAAATGGT-AATTTTGG-AAATT
*
40299076 C-GAGGTCAAAAATGG-AATTTTGGAAAATT
1 CGGGGGT-AAAAATGGTAATTTTGG-AAATT
*
40299105 CGAGGGT-AAAAT-GTAATTTTGGAAA
1 CGGGGGTAAAAATGGTAATTTTGGAAA
40299130 AGTTTTAGGG
Statistics
Matches: 71, Mismatches: 7, Indels: 15
0.76 0.08 0.16
Matches are distributed among these distances:
27 4 0.06
28 13 0.18
29 25 0.35
30 20 0.28
31 9 0.13
ACGTcount: A:0.37, C:0.05, G:0.30, T:0.28
Consensus pattern (29 bp):
CGGGGGTAAAAATGGTAATTTTGGAAATT
Found at i:40299142 original size:59 final size:60
Alignment explanation
Indices: 40299019--40299160 Score: 161
Period size: 59 Copynumber: 2.4 Consensus size: 60
40299009 TGTATGCCGG
** *
40299019 GGGT-AAAAATGGTAATTTTGGAAGGTTCGGGGGTAAAATGGTAAATTTTGGCAAAATCGA
1 GGGTCAAAAATGG-AATTTTGGAAAATTCGAGGGTAAAATGGTAAATTTTGGCAAAATCGA
**
40299079 -GGTCAAAAATGGAATTTTGGAAAATTCGAGGGTAAAAT-GT-AATTTTGG-AAAAGTTTTA
1 GGGTCAAAAATGGAATTTTGGAAAATTCGAGGGTAAAATGGTAAATTTTGGCAAAA--TCGA
*
40299137 GGGTC-AAAATGTAATTTTGGAAAA
1 GGGTCAAAAATGGAATTTTGGAAAA
40299161 GTTTTGGGGT
Statistics
Matches: 72, Mismatches: 6, Indels: 10
0.82 0.07 0.11
Matches are distributed among these distances:
56 4 0.06
57 8 0.11
58 22 0.31
59 30 0.42
60 8 0.11
ACGTcount: A:0.38, C:0.04, G:0.27, T:0.30
Consensus pattern (60 bp):
GGGTCAAAAATGGAATTTTGGAAAATTCGAGGGTAAAATGGTAAATTTTGGCAAAATCGA
Found at i:40299148 original size:30 final size:30
Alignment explanation
Indices: 40299079--40299170 Score: 125
Period size: 30 Copynumber: 3.1 Consensus size: 30
40299069 GCAAAATCGA
* **
40299079 GGTCAAAAATGGAATTTTGGAAAA-TTCGAG
1 GGTC-AAAATGTAATTTTGGAAAAGTTTTAG
40299109 GGT-AAAATGTAATTTTGGAAAAGTTTTAG
1 GGTCAAAATGTAATTTTGGAAAAGTTTTAG
*
40299138 GGTCAAAATGTAATTTTGGAAAAGTTTTGG
1 GGTCAAAATGTAATTTTGGAAAAGTTTTAG
40299168 GGT
1 GGT
40299171 TATGTAAAAT
Statistics
Matches: 56, Mismatches: 4, Indels: 4
0.88 0.06 0.06
Matches are distributed among these distances:
28 18 0.32
29 7 0.12
30 31 0.55
ACGTcount: A:0.36, C:0.03, G:0.27, T:0.34
Consensus pattern (30 bp):
GGTCAAAATGTAATTTTGGAAAAGTTTTAG
Found at i:40299215 original size:30 final size:30
Alignment explanation
Indices: 40299091--40299214 Score: 103
Period size: 30 Copynumber: 4.2 Consensus size: 30
40299081 TCAAAAATGG
* * *
40299091 AATTTTGGAAAA--TTCGAGGGTAAAATGT
1 AATTTTGGAAAAGTTTTGAGGTTAAAATAT
* *
40299119 AATTTTGGAAAAGTTTT-AGGGTCAAAATGT
1 AATTTTGGAAAAGTTTTGA-GGTTAAAATAT
* ** *
40299149 AATTTTGGAAAAGTTTTGGGGTT-ATGTAA
1 AATTTTGGAAAAGTTTTGAGGTTAAAATAT
**
40299178 AATTTTTTAAAAAGTTTTGAGGTTAAAATAT
1 AA-TTTTGGAAAAGTTTTGAGGTTAAAATAT
40299209 AATTTT
1 AATTTT
40299215 TGGATAGTTT
Statistics
Matches: 75, Mismatches: 15, Indels: 10
0.75 0.15 0.10
Matches are distributed among these distances:
28 12 0.16
29 5 0.07
30 53 0.71
31 5 0.07
ACGTcount: A:0.37, C:0.02, G:0.21, T:0.40
Consensus pattern (30 bp):
AATTTTGGAAAAGTTTTGAGGTTAAAATAT
Found at i:40300362 original size:22 final size:21
Alignment explanation
Indices: 40300324--40300367 Score: 54
Period size: 21 Copynumber: 2.0 Consensus size: 21
40300314 AACAGTCAAA
40300324 ATTAATACTAATATTATTTATT
1 ATTAATACTAATATTA-TTATT
*
40300346 ATTAATA-TTATACTTATTATT
1 ATTAATACTAATA-TTATTATT
40300367 A
1 A
40300368 ATATTATCAT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
21 10 0.50
22 10 0.50
ACGTcount: A:0.41, C:0.05, G:0.00, T:0.55
Consensus pattern (21 bp):
ATTAATACTAATATTATTATT
Found at i:40300364 original size:18 final size:16
Alignment explanation
Indices: 40300332--40300374 Score: 68
Period size: 18 Copynumber: 2.6 Consensus size: 16
40300322 AAATTAATAC
40300332 TAATATTATTTATTAT
1 TAATATTATTTATTAT
40300348 TAATATTATACTTATTAT
1 TAATATTAT--TTATTAT
40300366 TAATATTAT
1 TAATATTAT
40300375 CATTAATGCT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
16 9 0.36
18 16 0.64
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (16 bp):
TAATATTATTTATTAT
Found at i:40301105 original size:6 final size:6
Alignment explanation
Indices: 40301096--40301186 Score: 54
Period size: 6 Copynumber: 16.2 Consensus size: 6
40301086 GGATATTTTT
* *
40301096 AATTTA AATTTA CAA--T- AATATTA AATTTA AA-TTA AATTCA AATTCA
1 AATTTA AATTTA -AATTTA AAT-TTA AATTTA AATTTA AATTTA AATTTA
* * * *
40301142 AA-TTA AA-TTG AATTTA AA-ATA AATTTA AAATTA AA-ATA AATTTA
1 AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA
40301186 A
1 A
40301187 TTTCAAAATG
Statistics
Matches: 67, Mismatches: 9, Indels: 18
0.71 0.10 0.19
Matches are distributed among these distances:
3 2 0.03
5 22 0.33
6 38 0.57
7 5 0.07
ACGTcount: A:0.56, C:0.03, G:0.01, T:0.40
Consensus pattern (6 bp):
AATTTA
Found at i:40301131 original size:11 final size:11
Alignment explanation
Indices: 40301115--40301189 Score: 73
Period size: 11 Copynumber: 6.8 Consensus size: 11
40301105 TTACAATAAT
40301115 ATTAAATTTAA
1 ATTAAATTTAA
*
40301126 ATTAAATTCAA
1 ATTAAATTTAA
40301137 ATTCAAA-TTAA
1 ATT-AAATTTAA
*
40301148 ATTGAATTTAA
1 ATTAAATTTAA
*
40301159 AATAAATTTAAA
1 ATTAAATTT-AA
*
40301171 ATTAAA-ATAA
1 ATTAAATTTAA
*
40301181 ATTTAATTT
1 ATTAAATTT
40301190 CAAAATGGTT
Statistics
Matches: 51, Mismatches: 9, Indels: 8
0.75 0.13 0.12
Matches are distributed among these distances:
10 9 0.18
11 32 0.63
12 10 0.20
ACGTcount: A:0.55, C:0.03, G:0.01, T:0.41
Consensus pattern (11 bp):
ATTAAATTTAA
Found at i:40301138 original size:17 final size:16
Alignment explanation
Indices: 40301099--40301195 Score: 95
Period size: 17 Copynumber: 5.8 Consensus size: 16
40301089 TATTTTTAAT
*
40301099 TTAAATTTACAATAATA
1 TTAAATTTAAAATAA-A
*
40301116 TTAAATTTAAATTAAA
1 TTAAATTTAAAATAAA
* *
40301132 TTCAAATTCAAATTAAA
1 TT-AAATTTAAAATAAA
*
40301149 TTGAATTTAAAATAAA
1 TTAAATTTAAAATAAA
*
40301165 TTTAAAATTAAAATAAA
1 -TTAAATTTAAAATAAA
*
40301182 TTTAATTTCAAAAT
1 TTAAATTT-AAAAT
40301196 GGTTTGGATC
Statistics
Matches: 67, Mismatches: 10, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
16 20 0.30
17 47 0.70
ACGTcount: A:0.55, C:0.04, G:0.01, T:0.40
Consensus pattern (16 bp):
TTAAATTTAAAATAAA
Found at i:40307304 original size:29 final size:28
Alignment explanation
Indices: 40307264--40307324 Score: 97
Period size: 29 Copynumber: 2.1 Consensus size: 28
40307254 GTTTCAATCT
40307264 TATAATTTACATACTG-TATTATATGTATA
1 TATAATTTACATACTGTTATT-TATG-ATA
40307293 TATAATTTACATACTGTTATTTATGATA
1 TATAATTTACATACTGTTATTTATGATA
40307321 TATA
1 TATA
40307325 GATATTGACA
Statistics
Matches: 31, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
28 7 0.23
29 20 0.65
30 4 0.13
ACGTcount: A:0.38, C:0.07, G:0.07, T:0.49
Consensus pattern (28 bp):
TATAATTTACATACTGTTATTTATGATA
Found at i:40319921 original size:126 final size:127
Alignment explanation
Indices: 40319695--40319946 Score: 350
Period size: 126 Copynumber: 2.0 Consensus size: 127
40319685 CACTTTTGGT
* *
40319695 ACGACACTTTCTTAAGTGTTGGCATAGATTTACCGACATAAGCTTTTGCCAACTCTTTTGTATAA
1 ACGACACTTTCTTAAGTGTTGGCATAGACTTACCGACATAAGCCTTTGCCAACTCTTTTGTATAA
* * *
40319760 GGGTTGAGATATGTATGCCTAAGGCAACTCTTAAATAAGAGTCGACTTTGTCCAACACTATA
66 GGGTTGAGATATGCATGCCTAAGGCAACTCTTAAATAAAAGTCGACTTTATCCAACACTATA
* **
40319822 ACGACACTTTCTTAAGTGTTGGGATAGACTTGTCGACA-AA-CACTTTGACCAACT-TTTTGTAT
1 ACGACACTTTCTTAAGTGTTGGCATAGACTTACCGACATAAGC-CTTTG-CCAACTCTTTTGTAT
* * *
40319884 AAGGGTTGAGATATGCATGGCTAAGGCAA-TGCTTAAATAAAAGTTGGCTTTATCCAACACTAT
64 AAGGGTTGAGATATGCATGCCTAAGGCAACT-CTTAAATAAAAGTCGACTTTATCCAACACTAT
40319947 GTCAACCTTT
Statistics
Matches: 111, Mismatches: 11, Indels: 7
0.86 0.09 0.05
Matches are distributed among these distances:
125 2 0.02
126 69 0.62
127 40 0.36
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.33
Consensus pattern (127 bp):
ACGACACTTTCTTAAGTGTTGGCATAGACTTACCGACATAAGCCTTTGCCAACTCTTTTGTATAA
GGGTTGAGATATGCATGCCTAAGGCAACTCTTAAATAAAAGTCGACTTTATCCAACACTATA
Found at i:40320042 original size:30 final size:30
Alignment explanation
Indices: 40320001--40320058 Score: 98
Period size: 30 Copynumber: 1.9 Consensus size: 30
40319991 TTTTAAAAGG
*
40320001 TTGCCTTAGACAAGGTCTATCTCAACCTGT
1 TTGCCTCAGACAAGGTCTATCTCAACCTGT
*
40320031 TTGCCTCAGACAAGGTCTATCTCGACCT
1 TTGCCTCAGACAAGGTCTATCTCAACCT
40320059 TCTTTAAAGG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.22, C:0.29, G:0.17, T:0.31
Consensus pattern (30 bp):
TTGCCTCAGACAAGGTCTATCTCAACCTGT
Found at i:40320084 original size:68 final size:68
Alignment explanation
Indices: 40319970--40320096 Score: 166
Period size: 68 Copynumber: 1.9 Consensus size: 68
40319960 AGGTTGTCTT
* * * *
40319970 AGACAATGTCTATCCCAACCTTTTTAAAAGGTTGCCTTAGACAAGGTCTATCTCAACCTGTTTGC
1 AGACAAGGTCTATCCCAACCTTTTTAAAAGGTTGCCTCAAACAAGGTCTATCCCAACCTGTTTGC
40320035 CTC
66 CTC
* * * *
40320038 AGACAAGGTCTATCTCGACCTTCTTT-AAAGGTTGCCTCAAATAAGGTTTATCCCAACCT
1 AGACAAGGTCTATCCCAACCTT-TTTAAAAGGTTGCCTCAAACAAGGTCTATCCCAACCT
40320097 TTTTTAAAGG
Statistics
Matches: 50, Mismatches: 8, Indels: 2
0.83 0.13 0.03
Matches are distributed among these distances:
68 47 0.94
69 3 0.06
ACGTcount: A:0.28, C:0.26, G:0.15, T:0.31
Consensus pattern (68 bp):
AGACAAGGTCTATCCCAACCTTTTTAAAAGGTTGCCTCAAACAAGGTCTATCCCAACCTGTTTGC
CTC
Found at i:40320147 original size:37 final size:37
Alignment explanation
Indices: 40320031--40320185 Score: 154
Period size: 38 Copynumber: 4.2 Consensus size: 37
40320021 CTCAACCTGT
* * * *
40320031 TTGCCTCAGACAAGGTCTATCTCGACCTTCTTTAAAGG
1 TTGCCTCAAACAAGGTCTATC-CCAACTTTTTTAAAGG
* *
40320069 TTGCCTCAAATAAGGTTTATCCCAACCTTTTTTAAAGG
1 TTGCCTCAAACAAGGTCTATCCCAA-CTTTTTTAAAGG
* *
40320107 TTGCCTCAAACACGGTCTATCCCAACTTTTTTAAAAG
1 TTGCCTCAAACAAGGTCTATCCCAACTTTTTTAAAGG
** *
40320144 TTGCCT-AAGACAAGACCTACCCCAA-TCTTTTTAAA-G
1 TTGCCTCAA-ACAAGGTCTATCCCAACT-TTTTTAAAGG
40320180 TTGCCT
1 TTGCCT
40320186 TAGATGAGTA
Statistics
Matches: 100, Mismatches: 14, Indels: 8
0.82 0.11 0.07
Matches are distributed among these distances:
36 10 0.10
37 39 0.39
38 51 0.51
ACGTcount: A:0.28, C:0.26, G:0.14, T:0.33
Consensus pattern (37 bp):
TTGCCTCAAACAAGGTCTATCCCAACTTTTTTAAAGG
Found at i:40320174 original size:38 final size:37
Alignment explanation
Indices: 40320061--40320185 Score: 103
Period size: 37 Copynumber: 3.4 Consensus size: 37
40320051 CTCGACCTTC
* * *** *
40320061 TTTAAAGGTTGCCTCAAATAAGGTTTATCCCAACCTTT
1 TTTAAAAGTTGCCTCAAACAAGACCTACCCCAA-CTTT
* * ** *
40320099 TTTAAAGGTTGCCTCAAACACGGTCTATCCCAACTTT
1 TTTAAAAGTTGCCTCAAACAAGACCTACCCCAACTTT
40320136 TTTAAAAGTTGCCT-AAGACAAGACCTACCCCAA-TCTT
1 TTTAAAAGTTGCCTCAA-ACAAGACCTACCCCAACT-TT
40320173 TTT-AAAGTTGCCT
1 TTTAAAAGTTGCCT
40320186 TAGATGAGTA
Statistics
Matches: 77, Mismatches: 8, Indels: 6
0.85 0.09 0.07
Matches are distributed among these distances:
36 13 0.17
37 34 0.44
38 30 0.39
ACGTcount: A:0.30, C:0.24, G:0.13, T:0.34
Consensus pattern (37 bp):
TTTAAAAGTTGCCTCAAACAAGACCTACCCCAACTTT
Found at i:40320575 original size:45 final size:43
Alignment explanation
Indices: 40320491--40320576 Score: 102
Period size: 45 Copynumber: 2.0 Consensus size: 43
40320481 ATGTATTAGC
* *
40320491 ATCAAATATTTAGGCATTTTAGTTCAATTAAAAGATAAAAACA
1 ATCAAATATTTAGACATTTTAGTTCAACTAAAAGATAAAAACA
* *
40320534 ATCAAATATATATAGACATTTTAGTT-AACCTAGAAGCTAAAAA
1 ATCAAATAT-T-TAGACATTTTAGTTCAA-CTAAAAGATAAAAA
40320577 GTGATCTTTA
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
43 9 0.25
44 3 0.08
45 24 0.67
ACGTcount: A:0.49, C:0.10, G:0.09, T:0.31
Consensus pattern (43 bp):
ATCAAATATTTAGACATTTTAGTTCAACTAAAAGATAAAAACA
Found at i:40321076 original size:14 final size:14
Alignment explanation
Indices: 40321031--40321113 Score: 64
Period size: 14 Copynumber: 6.1 Consensus size: 14
40321021 CATAACTCAT
40321031 AACCTTAAATTCTTG
1 AACCTTAAA-TCTTG
* *
40321046 AACCATAAA-CATG
1 AACCTTAAATCTTG
40321059 AACCTTAAATCTTG
1 AACCTTAAATCTTG
* * *
40321073 AACCTCAAACCTTA
1 AACCTTAAATCTTG
** *
40321087 AACCTTGCATCTCG
1 AACCTTAAATCTTG
40321101 AA-C-TAAATCTTG
1 AACCTTAAATCTTG
40321113 A
1 A
40321114 GAGGTTCGAG
Statistics
Matches: 51, Mismatches: 16, Indels: 5
0.71 0.22 0.07
Matches are distributed among these distances:
12 7 0.14
13 12 0.24
14 24 0.47
15 8 0.16
ACGTcount: A:0.39, C:0.25, G:0.07, T:0.29
Consensus pattern (14 bp):
AACCTTAAATCTTG
Found at i:40324618 original size:17 final size:18
Alignment explanation
Indices: 40324596--40324629 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
40324586 TGTCGTGTAT
40324596 ATTTAATTTT-TATTTTA
1 ATTTAATTTTATATTTTA
40324613 ATTTAATTTTATATTTT
1 ATTTAATTTTATATTTT
40324630 TAGTTGTTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 10 0.62
18 6 0.38
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (18 bp):
ATTTAATTTTATATTTTA
Found at i:40324874 original size:75 final size:72
Alignment explanation
Indices: 40324765--40324945 Score: 179
Period size: 73 Copynumber: 2.4 Consensus size: 72
40324755 CTTTAGACGT
* * *
40324765 GTTTATCTTAGTCTTTTTTAAAGGTTG-TCGTAGACAATG-TTTATTTCAAATTTTTTAAAAGAT
1 GTTTATC-TAATCTTTTTTAAAGGTTGCT-TTAGACAA-GATTTA-TTCAAATTATTT-AAAGAT
40324828 TGTTGTAGGTA-AA
61 TGTTGTA-G-ACAA
* * * *
40324841 GTTTATCTAATCTTTTTAAAAGGTTGCTTTAGACAAGATTTATTCCAATTATTTAAAGGTTGTTT
1 GTTTATCTAATCTTTTTTAAAGGTTGCTTTAGACAAGATTTATTCAAATTATTTAAAGATTGTTG
*
40324906 TAGACAT
66 TAGACAA
* *
40324913 GTTTATCCTAATCTTTTTTAAAGATTGCATTAG
1 GTTTAT-CTAATCTTTTTTAAAGGTTGCTTTAG
40324946 TTAAGACATA
Statistics
Matches: 90, Mismatches: 11, Indels: 11
0.80 0.10 0.10
Matches are distributed among these distances:
71 1 0.01
72 8 0.09
73 34 0.38
74 11 0.12
75 28 0.31
76 8 0.09
ACGTcount: A:0.29, C:0.09, G:0.15, T:0.47
Consensus pattern (72 bp):
GTTTATCTAATCTTTTTTAAAGGTTGCTTTAGACAAGATTTATTCAAATTATTTAAAGATTGTTG
TAGACAA
Found at i:40324933 original size:37 final size:36
Alignment explanation
Indices: 40324733--40324935 Score: 137
Period size: 37 Copynumber: 5.5 Consensus size: 36
40324723 TACACGTGTC
* * *
40324733 TATCCCAATTTTTTT-AAGGTTGCTTTAGACGTGTT
1 TATCCTAATTTTTTTAAAGGTTGTTTTAGACATGTT
* * **
40324768 TATCTTAGTCTTTTTTAAAGGTTGTCGTAGACAATGTT
1 TATCCTAAT-TTTTTTAAAGGTTGTTTTAGAC-ATGTT
* * * * * *
40324806 TATTTCAAATTTTTTAAAAGATTGTTGTAGGTA-AAGTT
1 TA-TCCTAATTTTTTTAAAGGTTGTTTTA-G-ACATGTT
* * *
40324844 TAT-CTAATCTTTTTAAAAGGTTGCTTTAGACAAGATT
1 TATCCTAAT-TTTTTTAAAGGTTGTTTTAGACATG-TT
*
40324881 TATTCC-AA-TTATTTAAAGGTTGTTTTAGACATGTT
1 TA-TCCTAATTTTTTTAAAGGTTGTTTTAGACATGTT
40324916 TATCCTAATCTTTTTTAAAG
1 TATCCTAAT-TTTTTTAAAG
40324936 ATTGCATTAG
Statistics
Matches: 130, Mismatches: 24, Indels: 26
0.72 0.13 0.14
Matches are distributed among these distances:
34 3 0.02
35 13 0.10
36 35 0.27
37 42 0.32
38 31 0.24
39 5 0.04
40 1 0.01
ACGTcount: A:0.28, C:0.10, G:0.15, T:0.47
Consensus pattern (36 bp):
TATCCTAATTTTTTTAAAGGTTGTTTTAGACATGTT
Found at i:40325515 original size:5 final size:5
Alignment explanation
Indices: 40325505--40325532 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
40325495 TAATACATAC
40325505 ATAAA ATAAA ATAAA ATAAA ATAAA ATA
1 ATAAA ATAAA ATAAA ATAAA ATAAA ATA
40325533 TTATACATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (5 bp):
ATAAA
Found at i:40325649 original size:30 final size:31
Alignment explanation
Indices: 40325585--40325726 Score: 120
Period size: 31 Copynumber: 4.8 Consensus size: 31
40325575 CATTAAAATC
40325585 GGGTCAAATTTGAA---TT-GAAAACTTT-A
1 GGGTCAAATTTGAATTTTTAGAAAACTTTAA
* *
40325611 GGGATCAAATTGGAATTTTTGGAAAA-TTTAA
1 GGG-TCAAATTTGAATTTTTAGAAAACTTTAA
* * * *
40325642 GGGTCAAATTT-AAATTTT-GGAAAGTTTAGG
1 GGGTCAAATTTGAATTTTTAGAAAACTTTA-A
* * *
40325672 GGGTTAAATTTTAATTTTTAGAAAATTTTAA
1 GGGTCAAATTTGAATTTTTAGAAAACTTTAA
*
40325703 GGGTTAAATTTGAATTTTTAGAAA
1 GGGTCAAATTTGAATTTTTAGAAA
40325727 GTTTGGGAGT
Statistics
Matches: 95, Mismatches: 11, Indels: 15
0.79 0.09 0.12
Matches are distributed among these distances:
26 3 0.03
27 10 0.11
28 4 0.04
29 10 0.11
30 22 0.23
31 38 0.40
32 8 0.08
ACGTcount: A:0.37, C:0.03, G:0.20, T:0.39
Consensus pattern (31 bp):
GGGTCAAATTTGAATTTTTAGAAAACTTTAA
Found at i:40325719 original size:61 final size:59
Alignment explanation
Indices: 40325611--40325770 Score: 166
Period size: 60 Copynumber: 2.7 Consensus size: 59
40325601 GAAAACTTTA
* * * *
40325611 GGGA-TCAAATTGGAATTTTTGGAAAATTTAAGGGTCAAATTTAAA-TTTTGGAAAGTTT
1 GGGAGTCAAATT-TAATTTTTAGAAAATTTAAGGGTTAAATTTAAATTTTTAGAAAGTTT
* * *
40325669 AGGGGGTTAAATTTTAATTTTTAGAAAATTTTAAGGGTTAAATTTGAATTTTTAGAAAGTTT
1 -GGGAGTCAAA-TTTAATTTTTAGAAAA-TTTAAGGGTTAAATTTAAATTTTTAGAAAGTTT
40325731 GGGAGTCAAATTTAGATTTTTA-AAAAGTTT-AGAGGTTAAA
1 GGGAGTCAAATTTA-ATTTTTAGAAAA-TTTAAG-GGTTAAA
40325771 AAATAATTTT
Statistics
Matches: 85, Mismatches: 10, Indels: 11
0.80 0.09 0.10
Matches are distributed among these distances:
59 5 0.06
60 34 0.40
61 34 0.40
62 12 0.14
ACGTcount: A:0.37, C:0.02, G:0.21, T:0.40
Consensus pattern (59 bp):
GGGAGTCAAATTTAATTTTTAGAAAATTTAAGGGTTAAATTTAAATTTTTAGAAAGTTT
Found at i:40325750 original size:30 final size:29
Alignment explanation
Indices: 40325607--40325762 Score: 134
Period size: 30 Copynumber: 5.2 Consensus size: 29
40325597 AATTGAAAAC
* * * *
40325607 TTTAGGGATCAAATTGGAATTTTTGGAAAA
1 TTTAGGGGTCAAATT-TAATTTTTAGAAAG
* * *
40325637 TTTAAGGGTCAAATTTAAATTTTGGAAAG
1 TTTAGGGGTCAAATTTAATTTTTAGAAAG
* *
40325666 TTTAGGGGGTTAAATTTTAATTTTTAGAAAAT
1 TTTA-GGGGTCAAA-TTTAATTTTTAG-AAAG
* *
40325698 TTTAAGGGTTAAATTTGAATTTTTAGAAAG
1 TTTAGGGGTCAAATTT-AATTTTTAGAAAG
*
40325728 TTT-GGGAGTCAAATTTAGATTTTTAAAAAG
1 TTTAGGG-GTCAAATTTA-ATTTTTAGAAAG
40325758 TTTAG
1 TTTAG
40325763 AGGTTAAAAA
Statistics
Matches: 104, Mismatches: 15, Indels: 13
0.79 0.11 0.10
Matches are distributed among these distances:
29 18 0.17
30 51 0.49
31 28 0.27
32 7 0.07
ACGTcount: A:0.36, C:0.02, G:0.21, T:0.42
Consensus pattern (29 bp):
TTTAGGGGTCAAATTTAATTTTTAGAAAG
Found at i:40326881 original size:19 final size:17
Alignment explanation
Indices: 40326848--40326883 Score: 54
Period size: 19 Copynumber: 2.0 Consensus size: 17
40326838 TTATTTATAT
40326848 TTATAAAATAATAAATA
1 TTATAAAATAATAAATA
40326865 TTATAAATATAAATAAATA
1 TTATAAA-AT-AATAAATA
40326884 AAAATAAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 7 0.41
18 2 0.12
19 8 0.47
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (17 bp):
TTATAAAATAATAAATA
Found at i:40327108 original size:16 final size:16
Alignment explanation
Indices: 40327087--40327118 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
40327077 TTTGTCAACC
40327087 CTTCAATAAAAGTTGA
1 CTTCAATAAAAGTTGA
40327103 CTTCAATAAAAGTTGA
1 CTTCAATAAAAGTTGA
40327119 TTGATGCCAA
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:0.44, C:0.12, G:0.12, T:0.31
Consensus pattern (16 bp):
CTTCAATAAAAGTTGA
Found at i:40330216 original size:40 final size:40
Alignment explanation
Indices: 40330183--40330346 Score: 168
Period size: 40 Copynumber: 4.1 Consensus size: 40
40330173 TGTCACAGCT
**
40330183 AGTTCAGTAATAATATTATAGTGTTTACAGTGTCACTGTC
1 AGTTCAGTAATAATATTGCAGTGTTTACAGTGTCACTGTC
* * * * * *
40330223 AATTTAGTAGTAATGTCGCAGTGTTTACAGTGTCACTGCC
1 AGTTCAGTAATAATATTGCAGTGTTTACAGTGTCACTGTC
** * *
40330263 AGTTCAGTAATAGCATTGTAGTGTTTACAGTATCA-TCGTC
1 AGTTCAGTAATAATATTGCAGTGTTTACAGTGTCACT-GTC
* * * *
40330303 AGTTTAGTAATATTATGGCAGTGTTTACAGTGTCACTGCC
1 AGTTCAGTAATAATATTGCAGTGTTTACAGTGTCACTGTC
40330343 AGTT
1 AGTT
40330347 ATAAACGTTT
Statistics
Matches: 97, Mismatches: 25, Indels: 4
0.77 0.20 0.03
Matches are distributed among these distances:
39 1 0.01
40 95 0.98
41 1 0.01
ACGTcount: A:0.27, C:0.15, G:0.21, T:0.38
Consensus pattern (40 bp):
AGTTCAGTAATAATATTGCAGTGTTTACAGTGTCACTGTC
Found at i:40330309 original size:80 final size:80
Alignment explanation
Indices: 40330172--40330346 Score: 235
Period size: 80 Copynumber: 2.2 Consensus size: 80
40330162 GGTGCTCACT
* * * * *
40330172 GTGTCACAGCTAGTTCAGTAATAATATTATAGTGTTTACAGTGTCACTGTCAATTTAGTAGTAAT
1 GTGTCACTGCCAGTTCAGTAATAACATTATAGTGTTTACAGTATCACTGTCAATTTAGTAATAAT
*
40330237 GTCGCAGTGTTTACA
66 ATCGCAGTGTTTACA
* * * *
40330252 GTGTCACTGCCAGTTCAGTAATAGCATTGTAGTGTTTACAGTATCA-TCGTCAGTTTAGTAATAT
1 GTGTCACTGCCAGTTCAGTAATAACATTATAGTGTTTACAGTATCACT-GTCAATTTAGTAATAA
*
40330316 TATGGCAGTGTTTACA
65 TATCGCAGTGTTTACA
40330332 GTGTCACTGCCAGTT
1 GTGTCACTGCCAGTT
40330347 ATAAACGTTT
Statistics
Matches: 83, Mismatches: 11, Indels: 2
0.86 0.11 0.02
Matches are distributed among these distances:
79 1 0.01
80 82 0.99
ACGTcount: A:0.26, C:0.15, G:0.21, T:0.37
Consensus pattern (80 bp):
GTGTCACTGCCAGTTCAGTAATAACATTATAGTGTTTACAGTATCACTGTCAATTTAGTAATAAT
ATCGCAGTGTTTACA
Found at i:40338287 original size:25 final size:23
Alignment explanation
Indices: 40338246--40338291 Score: 65
Period size: 25 Copynumber: 1.9 Consensus size: 23
40338236 CCAATTAGGG
40338246 AATTATTATTTAGATTTAATTCA
1 AATTATTATTTAGATTTAATTCA
*
40338269 AATTATCTTTTTAGAATTTAATT
1 AATTAT-TATTTAG-ATTTAATT
40338292 TGAATCCAAC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 6 0.30
24 6 0.30
25 8 0.40
ACGTcount: A:0.37, C:0.04, G:0.04, T:0.54
Consensus pattern (23 bp):
AATTATTATTTAGATTTAATTCA
Found at i:40339373 original size:10 final size:11
Alignment explanation
Indices: 40339356--40339387 Score: 57
Period size: 10 Copynumber: 3.0 Consensus size: 11
40339346 TACTTTAGCC
40339356 ATTTTATTATT
1 ATTTTATTATT
40339367 A-TTTATTATT
1 ATTTTATTATT
40339377 ATTTTATTATT
1 ATTTTATTATT
40339388 TTCATTTTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
10 10 0.50
11 10 0.50
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (11 bp):
ATTTTATTATT
Found at i:40344913 original size:12 final size:12
Alignment explanation
Indices: 40344896--40344930 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
40344886 AAAAAATTAG
40344896 CATATTTATTTT
1 CATATTTATTTT
40344908 CATATTTATTTT
1 CATATTTATTTT
*
40344920 TAT-TTTATTTT
1 CATATTTATTTT
40344931 ATTTTAATTA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
11 8 0.36
12 14 0.64
ACGTcount: A:0.23, C:0.06, G:0.00, T:0.71
Consensus pattern (12 bp):
CATATTTATTTT
Found at i:40345930 original size:13 final size:13
Alignment explanation
Indices: 40345880--40345936 Score: 55
Period size: 13 Copynumber: 4.4 Consensus size: 13
40345870 AAAAAAGTCG
40345880 AAAAGAAAAA-AA
1 AAAAGAAAAAGAA
*
40345892 AGAATTGAAAAA-AA
1 A-AA-AGAAAAAGAA
40345906 AAAAGAAAAAGAA
1 AAAAGAAAAAGAA
* *
40345919 AAAAGAAGAAGAC
1 AAAAGAAAAAGAA
40345932 AAAAG
1 AAAAG
40345937 TGTGTTTGAG
Statistics
Matches: 38, Mismatches: 4, Indels: 5
0.81 0.09 0.11
Matches are distributed among these distances:
12 7 0.18
13 22 0.58
14 9 0.24
ACGTcount: A:0.79, C:0.02, G:0.16, T:0.04
Consensus pattern (13 bp):
AAAAGAAAAAGAA
Found at i:40346994 original size:25 final size:23
Alignment explanation
Indices: 40346953--40346998 Score: 65
Period size: 25 Copynumber: 1.9 Consensus size: 23
40346943 TCAATTAGGG
40346953 AATTATTGTTTAGATTTAATTCA
1 AATTATTGTTTAGATTTAATTCA
*
40346976 AATTATCTTTTTAGAATTTAATT
1 AATTAT-TGTTTAG-ATTTAATT
40346999 TGGATCCAAC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 6 0.30
24 6 0.30
25 8 0.40
ACGTcount: A:0.35, C:0.04, G:0.07, T:0.54
Consensus pattern (23 bp):
AATTATTGTTTAGATTTAATTCA
Found at i:40349873 original size:21 final size:21
Alignment explanation
Indices: 40349848--40349906 Score: 93
Period size: 21 Copynumber: 2.8 Consensus size: 21
40349838 GAATAACATG
*
40349848 GAAGAAGAGTCTGAGAATTTT
1 GAAGAAGAATCTGAGAATTTT
40349869 GAAGAAGAATCTGAGAATTTT
1 GAAGAAGAATCTGAGAATTTT
40349890 -AAGGAAGAATCTGAGAA
1 GAA-GAAGAATCTGAGAA
40349907 GTCTGAGGAA
Statistics
Matches: 36, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
20 2 0.06
21 34 0.94
ACGTcount: A:0.44, C:0.05, G:0.27, T:0.24
Consensus pattern (21 bp):
GAAGAAGAATCTGAGAATTTT
Found at i:40349915 original size:21 final size:21
Alignment explanation
Indices: 40349851--40349918 Score: 91
Period size: 21 Copynumber: 3.2 Consensus size: 21
40349841 TAACATGGAA
* *
40349851 GAAGAGTCTGAGAATTTTGAA
1 GAAGAATCTGAGAATTTTGAG
*
40349872 GAAGAATCTGAGAATTTTAAG
1 GAAGAATCTGAGAATTTTGAG
* *
40349893 GAAGAATCTGAGAAGTCTGAG
1 GAAGAATCTGAGAATTTTGAG
40349914 GAAGA
1 GAAGA
40349919 TCATAGCAAT
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 41 1.00
ACGTcount: A:0.41, C:0.06, G:0.29, T:0.24
Consensus pattern (21 bp):
GAAGAATCTGAGAATTTTGAG
Found at i:40350193 original size:19 final size:20
Alignment explanation
Indices: 40350156--40350193 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 20
40350146 TGGGTCTTTG
**
40350156 GAATTGTGAGATGTTCATAT
1 GAATTGTGAGATGGGCATAT
40350176 GAATTG-GAGATGGGCATA
1 GAATTGTGAGATGGGCATA
40350194 GTCAAATACT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 10 0.62
20 6 0.38
ACGTcount: A:0.32, C:0.05, G:0.32, T:0.32
Consensus pattern (20 bp):
GAATTGTGAGATGGGCATAT
Found at i:40357218 original size:21 final size:21
Alignment explanation
Indices: 40357193--40357238 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
40357183 AGGTTGGACT
* *
40357193 AATATTGGACTTTGGATGTTG
1 AATATTGAACTTTAGATGTTG
* *
40357214 AATATTGAATTTTAGATTTTG
1 AATATTGAACTTTAGATGTTG
40357235 AATA
1 AATA
40357239 ATGTGATTAA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.33, C:0.02, G:0.20, T:0.46
Consensus pattern (21 bp):
AATATTGAACTTTAGATGTTG
Found at i:40369572 original size:22 final size:22
Alignment explanation
Indices: 40369532--40369591 Score: 79
Period size: 22 Copynumber: 2.8 Consensus size: 22
40369522 CGATCTAAGA
*
40369532 AAAAATAAAAG-AAACAGAATT
1 AAAAATAAAAGAAAATAGAATT
40369553 AAAAATAAAAGAAAATAGAATT
1 AAAAATAAAAGAAAATAGAATT
*
40369575 AAAAGA-AATAGAAAATA
1 AAAA-ATAAAAGAAAATA
40369592 AGGAAGTCGA
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
21 11 0.31
22 23 0.66
23 1 0.03
ACGTcount: A:0.73, C:0.02, G:0.10, T:0.15
Consensus pattern (22 bp):
AAAAATAAAAGAAAATAGAATT
Found at i:40369583 original size:15 final size:16
Alignment explanation
Indices: 40369558--40369587 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
40369548 GAATTAAAAA
40369558 TAAAAGAAAATAGAAT
1 TAAAAGAAAATAGAAT
40369574 TAAAAG-AAATAGAA
1 TAAAAGAAAATAGAA
40369588 AATAAGGAAG
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:0.70, C:0.00, G:0.13, T:0.17
Consensus pattern (16 bp):
TAAAAGAAAATAGAAT
Found at i:40370417 original size:19 final size:19
Alignment explanation
Indices: 40370393--40370435 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
40370383 AAACATAAAT
40370393 TAAATACAAAT-TTAAATAA
1 TAAATA-AAATCTTAAATAA
* *
40370412 TAAATAATATCTTAAATAT
1 TAAATAAAATCTTAAATAA
40370431 TAAAT
1 TAAAT
40370436 CCTAATATAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 3 0.14
19 18 0.86
ACGTcount: A:0.58, C:0.05, G:0.00, T:0.37
Consensus pattern (19 bp):
TAAATAAAATCTTAAATAA
Found at i:40372008 original size:8 final size:9
Alignment explanation
Indices: 40371988--40372035 Score: 64
Period size: 8 Copynumber: 5.3 Consensus size: 9
40371978 TCGAGTTTCC
40371988 TAAATAAAAA
1 TAAAT-AAAA
40371998 TAAAT-AAA
1 TAAATAAAA
40372006 TAAATAAAA
1 TAAATAAAA
40372015 TAAAATAAAA
1 T-AAATAAAA
40372025 TAAA-AAAA
1 TAAATAAAA
40372033 TAA
1 TAA
40372036 TTGGGTTGCC
Statistics
Matches: 36, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
8 15 0.42
9 7 0.19
10 14 0.39
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (9 bp):
TAAATAAAA
Found at i:40372009 original size:18 final size:20
Alignment explanation
Indices: 40371988--40372032 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 20
40371978 TCGAGTTTCC
40371988 TAAATAAAAAT-AAAT-AAA
1 TAAATAAAAATAAAATAAAA
40372006 TAAAT-AAAATAAAATAAAA
1 TAAATAAAAATAAAATAAAA
40372025 TAAA-AAAA
1 TAAATAAAA
40372033 TAATTGGGTT
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
17 5 0.21
18 9 0.38
19 10 0.42
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (20 bp):
TAAATAAAAATAAAATAAAA
Found at i:40372017 original size:5 final size:5
Alignment explanation
Indices: 40371989--40372029 Score: 52
Period size: 5 Copynumber: 8.6 Consensus size: 5
40371979 CGAGTTTCCT
40371989 AAATA AAA-A TAAAT- AAAT- AAATA AAATA AAATA AAATA AAA
1 AAATA AAATA -AAATA AAATA AAATA AAATA AAATA AAATA AAA
40372030 AAATAATTGG
Statistics
Matches: 33, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
4 9 0.27
5 24 0.73
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (5 bp):
AAATA
Found at i:40372017 original size:23 final size:23
Alignment explanation
Indices: 40371989--40372035 Score: 69
Period size: 23 Copynumber: 2.0 Consensus size: 23
40371979 CGAGTTTCCT
*
40371989 AAATAAAA-ATAAATAAATAAATA
1 AAATAAAATA-AAATAAAAAAATA
40372012 AAATAAAATAAAATAAAAAAATA
1 AAATAAAATAAAATAAAAAAATA
40372035 A
1 A
40372036 TTGGGTTGCC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 21 0.95
24 1 0.05
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (23 bp):
AAATAAAATAAAATAAAAAAATA
Found at i:40372033 original size:18 final size:17
Alignment explanation
Indices: 40371993--40372035 Score: 61
Period size: 18 Copynumber: 2.5 Consensus size: 17
40371983 TTTCCTAAAT
40371993 AAAAAT-AAATAAATAA
1 AAAAATAAAATAAATAA
40372009 ATAAAATAAAATAAAATAA
1 A-AAAATAAAAT-AAATAA
40372028 AAAAATAA
1 AAAAATAA
40372036 TTGGGTTGCC
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
16 1 0.04
17 5 0.21
18 11 0.46
19 7 0.29
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (17 bp):
AAAAATAAAATAAATAA
Found at i:40374829 original size:22 final size:22
Alignment explanation
Indices: 40374793--40374852 Score: 97
Period size: 21 Copynumber: 2.8 Consensus size: 22
40374783 CGATCTAAGG
40374793 AAAAATAAAAG-AAATAGAATT
1 AAAAATAAAAGAAAATAGAATT
40374814 AAAAATAAAAGAAAATAGAATT
1 AAAAATAAAAGAAAATAGAATT
40374836 -AAAATAAATAGAAAATA
1 AAAAATAAA-AGAAAATA
40374853 AGGAAGTCGA
Statistics
Matches: 37, Mismatches: 0, Indels: 3
0.93 0.00 0.08
Matches are distributed among these distances:
21 19 0.51
22 18 0.49
ACGTcount: A:0.73, C:0.00, G:0.08, T:0.18
Consensus pattern (22 bp):
AAAAATAAAAGAAAATAGAATT
Found at i:40384926 original size:37 final size:38
Alignment explanation
Indices: 40384884--40385027 Score: 173
Period size: 39 Copynumber: 3.8 Consensus size: 38
40384874 ATTGAAGATG
* * *
40384884 TACTGAACTAGCAATGACACTGTAAACACTATAATGT-
1 TACTGAACTAACAGTGACACTGTAAACACTACAATGTA
** * *
40384921 TACTGAACCGACAGTGACATTGTAAACACTGCAATGTTA
1 TACTGAACTAACAGTGACACTGTAAACACTACAATG-TA
* *
40384960 TACTGAACTAACGGTGACACTGTAAACACTACAATATAA
1 TACTGAACTAACAGTGACACTGTAAACACTACAATGT-A
*
40384999 TACTAAACTAACAGTGACACTGTAAACAC
1 TACTGAACTAACAGTGACACTGTAAACAC
40385028 CGCAACATTA
Statistics
Matches: 89, Mismatches: 15, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
37 29 0.33
38 2 0.02
39 58 0.65
ACGTcount: A:0.41, C:0.21, G:0.14, T:0.24
Consensus pattern (38 bp):
TACTGAACTAACAGTGACACTGTAAACACTACAATGTA
Found at i:40385058 original size:78 final size:76
Alignment explanation
Indices: 40384884--40385042 Score: 192
Period size: 78 Copynumber: 2.1 Consensus size: 76
40384874 ATTGAAGATG
* * * * * * *
40384884 TACTGAACTAGCAATGACACTGTAAACACTATAATGTTACTGAACCGACAGTGACATTGTAAACA
1 TACTGAACTAACAGTGACACTGTAAACACTACAATATTACTAAACCAACAGTGACACTGTAAACA
* **
40384949 CTGCAATGTTA
66 CCGCAACATTA
* *
40384960 TACTGAACTAACGGTGACACTGTAAACACTACAATATAATACTAAACTAACAGTGACACTGTAAA
1 TACTGAACTAACAGTGACACTGTAAACACTACAATAT--TACTAAACCAACAGTGACACTGTAAA
40385025 CACCGCAACATTA
64 CACCGCAACATTA
40385038 TACTG
1 TACTG
40385043 TGCTGGTAGT
Statistics
Matches: 69, Mismatches: 12, Indels: 2
0.83 0.14 0.02
Matches are distributed among these distances:
76 32 0.46
78 37 0.54
ACGTcount: A:0.40, C:0.21, G:0.14, T:0.25
Consensus pattern (76 bp):
TACTGAACTAACAGTGACACTGTAAACACTACAATATTACTAAACCAACAGTGACACTGTAAACA
CCGCAACATTA
Found at i:40388059 original size:389 final size:389
Alignment explanation
Indices: 40387338--40388119 Score: 1305
Period size: 389 Copynumber: 2.0 Consensus size: 389
40387328 AGACTATCTG
*
40387338 ACCAATGTCATCTTTACCCTCGTAGTTGAAAAACTTGTAAGGAAAGGGAGTAACTTGTGAGGTGT
1 ACCAATGTCATCTTTACCCTCGTAGCTGAAAAACTTGTAAGGAAAGGGAGTAACTTGTGAGGTGT
* * * * * *
40387403 ACCTCTCCTTTATCACTGATATTGTACCGGTCAAATTAACTTTTCGTGACATTCGTGCCGTCAAG
66 ACCTCGCCTTTATCACTGATACTGTACAGGTCAAATTAACTTTCCGCGACATTCGTACCGTCAAG
*
40387468 GATTTTTTGAATGTCTTTCCTGATAAGCTATCGGGTGTAGCGCCAACCCGAAAAGTTGAGTTTGG
131 GATTTTTTGAATGTCTTTCCTGATAAGATATCGGGTGTAGCGCCAACCCGAAAAGTTGAGTTTGG
* *
40387533 TATTGAATTTTTACCAGGTACTTCACCAGTGTCAATTGCTCCTTATTGCATAGCAACAAAGGAAC
196 TACTGAATTTTTACCAGGTACTTCACCAATGTCAATTGCTCCTTATTGCATAGCAACAAAGGAAC
* * **
40387598 TTATTAAATTAAAGGCTCAATTGCAAGAACTTCTTGACTGAGGGCTCATTTGGTCGATTGTGTCT
261 TTATTAAATTAAAGGCTCAATTGCAAGAAATTCTTAACTGAGGGCTCATTTGGTCGATCATGTCT
*
40387663 CCATGAGGAGCACCTGTATTGTTTGTTAAGAGGAAGGAAAAAACGATGAGAATGTGTATAAACT
326 CCATGAGGAGCACCTGTACTGTTTGTTAAGAGGAAGGAAAAAACGATGAGAATGTGTATAAACT
*
40387727 ACCAATGTCATCTTTACCCTCGTAGCTGAAAAACTTGTAAGGAAAGGGTGTAACTTGTGAGGTGT
1 ACCAATGTCATCTTTACCCTCGTAGCTGAAAAACTTGTAAGGAAAGGGAGTAACTTGTGAGGTGT
* *
40387792 ACCTCGCCTTTATCACTGATACTGTACAGGTCAAATTAACTTTCCGCGACATTCGTACCGTTAGG
66 ACCTCGCCTTTATCACTGATACTGTACAGGTCAAATTAACTTTCCGCGACATTCGTACCGTCAAG
*
40387857 GATTTTTTGAATGTCTTTCCTGATAAGATATCGGGTGTAGCGTCAACCCGAAAAGTTGAGTTTGG
131 GATTTTTTGAATGTCTTTCCTGATAAGATATCGGGTGTAGCGCCAACCCGAAAAGTTGAGTTTGG
* *
40387922 TACTGAATTTTTACCAGGTACTTCACCAATGTCAATTGCTCCTTATTAG-ATGGCAACTAAGGAA
196 TACTGAATTTTTACCAGGTACTTCACCAATGTCAATTGCTCCTTATT-GCATAGCAACAAAGGAA
*
40387986 CTTATTAAATTGAAGGCTCAATTGCAAGAAATTCTTAACTGAGGGCTCATTTGGTCGATCATGTC
260 CTTATTAAATTAAAGGCTCAATTGCAAGAAATTCTTAACTGAGGGCTCATTTGGTCGATCATGTC
* * ** *
40388051 TTCATGAGGAGCACTTGTACTGTTTGTTAAGAGGAAGGAAAAATTGATGATAATGTGTATAAACT
325 TCCATGAGGAGCACCTGTACTGTTTGTTAAGAGGAAGGAAAAAACGATGAGAATGTGTATAAACT
40388116 ACCA
1 ACCA
40388120 TAATTAAACA
Statistics
Matches: 365, Mismatches: 27, Indels: 2
0.93 0.07 0.01
Matches are distributed among these distances:
389 364 1.00
390 1 0.00
ACGTcount: A:0.29, C:0.18, G:0.21, T:0.32
Consensus pattern (389 bp):
ACCAATGTCATCTTTACCCTCGTAGCTGAAAAACTTGTAAGGAAAGGGAGTAACTTGTGAGGTGT
ACCTCGCCTTTATCACTGATACTGTACAGGTCAAATTAACTTTCCGCGACATTCGTACCGTCAAG
GATTTTTTGAATGTCTTTCCTGATAAGATATCGGGTGTAGCGCCAACCCGAAAAGTTGAGTTTGG
TACTGAATTTTTACCAGGTACTTCACCAATGTCAATTGCTCCTTATTGCATAGCAACAAAGGAAC
TTATTAAATTAAAGGCTCAATTGCAAGAAATTCTTAACTGAGGGCTCATTTGGTCGATCATGTCT
CCATGAGGAGCACCTGTACTGTTTGTTAAGAGGAAGGAAAAAACGATGAGAATGTGTATAAACT
Done.