Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr13
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: 46006518
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 2011935 characters in sequence are not A, C, G, or T
File 63 of 141
Found at i:20555118 original size:36 final size:36
Alignment explanation
Indices: 20555078--20555150 Score: 137
Period size: 36 Copynumber: 2.0 Consensus size: 36
20555068 AGATGATTAA
20555078 GAGTAAAATAGTAATAGTTAAATAAGATATTTATGG
1 GAGTAAAATAGTAATAGTTAAATAAGATATTTATGG
*
20555114 GAGTAAAATAGTAATAGTTAAATAAGATATTTCTGG
1 GAGTAAAATAGTAATAGTTAAATAAGATATTTATGG
20555150 G
1 G
20555151 TGTAGTCTAA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.45, C:0.01, G:0.21, T:0.33
Consensus pattern (36 bp):
GAGTAAAATAGTAATAGTTAAATAAGATATTTATGG
Found at i:20555506 original size:25 final size:25
Alignment explanation
Indices: 20555457--20555511 Score: 94
Period size: 26 Copynumber: 2.2 Consensus size: 25
20555447 GAGAAAAGAG
20555457 AAAGTTAGGGATTTAGTGGTGATAT
1 AAAGTTAGGGATTTAGTGGTGATAT
20555482 CAAAGTTAGGGATTT-GTGGTGATAT
1 -AAAGTTAGGGATTTAGTGGTGATAT
20555507 AAAGT
1 AAAGT
20555512 AATAAGGTAA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
24 5 0.17
25 10 0.34
26 14 0.48
ACGTcount: A:0.33, C:0.02, G:0.31, T:0.35
Consensus pattern (25 bp):
AAAGTTAGGGATTTAGTGGTGATAT
Found at i:20567124 original size:36 final size:36
Alignment explanation
Indices: 20567074--20567146 Score: 128
Period size: 36 Copynumber: 2.0 Consensus size: 36
20567064 TTATGTATGC
20567074 ATGCATTCAAACTTACTTAAAAAGATTTAAGAACTT
1 ATGCATTCAAACTTACTTAAAAAGATTTAAGAACTT
* *
20567110 ATGCATTCAGACTTACTTAAAAATATTTAAGAACTT
1 ATGCATTCAAACTTACTTAAAAAGATTTAAGAACTT
20567146 A
1 A
20567147 GTCCAAGGTT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
36 35 1.00
ACGTcount: A:0.44, C:0.14, G:0.08, T:0.34
Consensus pattern (36 bp):
ATGCATTCAAACTTACTTAAAAAGATTTAAGAACTT
Found at i:20572730 original size:10 final size:10
Alignment explanation
Indices: 20572715--20572743 Score: 58
Period size: 10 Copynumber: 2.9 Consensus size: 10
20572705 TTAAATTCTA
20572715 AAAGATAAAT
1 AAAGATAAAT
20572725 AAAGATAAAT
1 AAAGATAAAT
20572735 AAAGATAAA
1 AAAGATAAA
20572744 AACTAAAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.72, C:0.00, G:0.10, T:0.17
Consensus pattern (10 bp):
AAAGATAAAT
Found at i:20577499 original size:17 final size:17
Alignment explanation
Indices: 20577479--20577511 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
20577469 TTTAACCATC
20577479 AAATTAAATTAATTCAA
1 AAATTAAATTAATTCAA
*
20577496 AAATTAATTTAATTCA
1 AAATTAAATTAATTCA
20577512 TGTGACAACT
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:0.55, C:0.06, G:0.00, T:0.39
Consensus pattern (17 bp):
AAATTAAATTAATTCAA
Found at i:20580158 original size:27 final size:27
Alignment explanation
Indices: 20580117--20580179 Score: 92
Period size: 27 Copynumber: 2.4 Consensus size: 27
20580107 ATAGGTTAAT
*
20580117 TTTAAAAT-AAGTAATATGTAAAATAA
1 TTTAAAATAAAATAATATGTAAAATAA
*
20580143 TTTAAAATAAAATAATATGTAAAGTAA
1 TTTAAAATAAAATAATATGTAAAATAA
*
20580170 CTTAAAATAA
1 TTTAAAATAA
20580180 TTAGACTTAT
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
26 8 0.24
27 25 0.76
ACGTcount: A:0.59, C:0.02, G:0.06, T:0.33
Consensus pattern (27 bp):
TTTAAAATAAAATAATATGTAAAATAA
Found at i:20580227 original size:21 final size:21
Alignment explanation
Indices: 20580198--20580237 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
20580188 ATAAGTTAGG
20580198 TTAAGATAATAAATAAAAGGT
1 TTAAGATAATAAATAAAAGGT
* **
20580219 TTAATATAATCTATAAAAG
1 TTAAGATAATAAATAAAAG
20580238 AGAAAATTGG
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.55, C:0.03, G:0.10, T:0.33
Consensus pattern (21 bp):
TTAAGATAATAAATAAAAGGT
Found at i:20582615 original size:94 final size:95
Alignment explanation
Indices: 20582397--20582877 Score: 371
Period size: 100 Copynumber: 5.0 Consensus size: 95
20582387 ACTCTTTTTA
* * * * *
20582397 ATTGCAATGTCAGGGAAATAAGATTCGCCATCGTAGCTTTAATCTATTCCACTGCACT-CTCAGG
1 ATTGCAATGTCAGGGAAACAAGATTCGCCGTCGTAGCTTCAATCTGTTCCACTGCACTGCTAAGG
* * *
20582461 AAAGTAAGATTCGCTGTCGTAGCTTCAATCT
66 -AAGTAAGATTCGCCGTTGTGGCTTCAATCT
* * * * * * *
20582492 A---CAATGTCGGGGAAACAATATTCGCCGTCGTAACTTCAATCTGTTCCTCTACACTGTTAAAG
1 ATTGCAATGTCAGGGAAACAAGATTCGCCGTCGTAGCTTCAATCTGTTCCACTGCACTGCTAAGG
20582554 AAGTAAGATTCGCCGTTG-GGCTTCAATCT
66 AAGTAAGATTCGCCGTTGTGGCTTCAATCT
* * * *
20582583 ATTGCAATGTCAGGGAAACGAGATTCACCGTCGTAGCTTCAATCTGTTCCACTGCACTGCCAGGG
1 ATTGCAATGTCAGGGAAACAAGATTCGCCGTCGTAGCTTCAATCTGTTCCACTGCACTGCTAAGG
* *
20582648 AAGTAAGATTCACCGTTGTGGCTTAAATCTTTTT
66 AAGTAAGATTCGCCGTTGTGGCTTCAATC----T
* ** * * * * * * * *
20582682 AACTGCAATGTTGGGGAAGCAAGATTCGCCGTTGTGGCTTTAATCTATTCCACTACA-TCGCCAG
1 -ATTGCAATGTCAGGGAAACAAGATTCGCCGTCGTAGCTTCAATCTGTTCCACTGCACT-GCTAA
*
20582746 GGAAGTAAGATTCGCCGTTGTGGCTTTAATCTTTTT
64 GGAAGTAAGATTCGCCGTTGTGGCTTCAATC----T
* * ** ** * * * * * * **
20582782 AACTGCAATTTTGGGGAAGTAAGATTCGCCGTTGTGGCTTTAACCTGTTCCACTACACCGCTTGG
1 -ATTGCAATGTCAGGGAAACAAGATTCGCCGTCGTAGCTTCAATCTGTTCCACTGCACTGCTAAG
* *
20582847 GAAGTAATATTCGCCGTTGTGGCTTTAATCT
65 GAAGTAAGATTCGCCGTTGTGGCTTCAATCT
20582878 GTTCCATTGC
Statistics
Matches: 325, Mismatches: 49, Indels: 23
0.82 0.12 0.06
Matches are distributed among these distances:
91 11 0.03
92 61 0.19
93 3 0.01
94 67 0.21
95 10 0.03
96 1 0.00
99 2 0.01
100 170 0.52
ACGTcount: A:0.25, C:0.22, G:0.22, T:0.31
Consensus pattern (95 bp):
ATTGCAATGTCAGGGAAACAAGATTCGCCGTCGTAGCTTCAATCTGTTCCACTGCACTGCTAAGG
AAGTAAGATTCGCCGTTGTGGCTTCAATCT
Found at i:20582657 original size:50 final size:50
Alignment explanation
Indices: 20582603--20582999 Score: 364
Period size: 50 Copynumber: 7.9 Consensus size: 50
20582593 CAGGGAAACG
* * * * * * *
20582603 AGATTCACCGTCGTAGCTTCAATCTGTTCCACTGCACTGCCAGGGAAGTA
1 AGATTCGCCGTTGTGGCTTTAATCTGTTCAACTGCAATGCCGGGGAAGTA
* * * * ** *
20582653 AGATTCACCGTTGTGGCTTAAATCTTTTTAACTGCAATGTTGGGGAAGCA
1 AGATTCGCCGTTGTGGCTTTAATCTGTTCAACTGCAATGCCGGGGAAGTA
* * * *
20582703 AGATTCGCCGTTGTGGCTTTAATCTATTCCACTAC-ATCGCCAGGGAAGTA
1 AGATTCGCCGTTGTGGCTTTAATCTGTTCAACTGCAAT-GCCGGGGAAGTA
* * ***
20582753 AGATTCGCCGTTGTGGCTTTAATCTTTTTAACTGCAATTTTGGGGAAGTA
1 AGATTCGCCGTTGTGGCTTTAATCTGTTCAACTGCAATGCCGGGGAAGTA
* * * ** **
20582803 AGATTCGCCGTTGTGGCTTTAACCTGTTCCACTACACCGCTTGGGAAGTA
1 AGATTCGCCGTTGTGGCTTTAATCTGTTCAACTGCAATGCCGGGGAAGTA
* * * ** **
20582853 ATATTCGCCGTTGTGGCTTTAATCTGTTCCATTGCACCGCTTGGGAAGTA
1 AGATTCGCCGTTGTGGCTTTAATCTGTTCAACTGCAATGCCGGGGAAGTA
* * * * *
20582903 AGATTCACCGTTGTGGCTTTAATCTTTTTAACTGCAATGTCGGGGAAGCA
1 AGATTCGCCGTTGTGGCTTTAATCTGTTCAACTGCAATGCCGGGGAAGTA
* * * *
20582953 AGATTCGCCATTGTGGCTTTAATTTGTTCAACTGCATTGCCTGGGAA
1 AGATTCGCCGTTGTGGCTTTAATCTGTTCAACTGCAATGCCGGGGAA
20583000 AACTGGTTTC
Statistics
Matches: 282, Mismatches: 63, Indels: 4
0.81 0.18 0.01
Matches are distributed among these distances:
49 2 0.01
50 278 0.99
51 2 0.01
ACGTcount: A:0.22, C:0.21, G:0.23, T:0.33
Consensus pattern (50 bp):
AGATTCGCCGTTGTGGCTTTAATCTGTTCAACTGCAATGCCGGGGAAGTA
Found at i:20582727 original size:100 final size:100
Alignment explanation
Indices: 20582585--20582988 Score: 427
Period size: 100 Copynumber: 4.0 Consensus size: 100
20582575 TTCAATCTAT
** * * * * * *
20582585 TGCAATGTCAGGGAAACGAGATTCACCGTCGTAGCTTCAATCTGTTCCACTGCACTGCCAGGGAA
1 TGCAATGTTGGGGAAGCAAGATTCACCGTTGTGGCTTTAATCTGTTCCACTACACTGCCAGGGAA
* * *
20582650 GTAAGATTCACCGTTGTGGCTTAAATCTTTTTAAC
66 GTAAGATTCGCCGTTGTGGCTTTAATCTTTTCAAC
* *
20582685 TGCAATGTTGGGGAAGCAAGATTCGCCGTTGTGGCTTTAATCTATTCCACTACA-TCGCCAGGGA
1 TGCAATGTTGGGGAAGCAAGATTCACCGTTGTGGCTTTAATCTGTTCCACTACACT-GCCAGGGA
*
20582749 AGTAAGATTCGCCGTTGTGGCTTTAATCTTTTTAAC
65 AGTAAGATTCGCCGTTGTGGCTTTAATCTTTTCAAC
* * * * * **
20582785 TGCAATTTTGGGGAAGTAAGATTCGCCGTTGTGGCTTTAACCTGTTCCACTACACCGCTTGGGAA
1 TGCAATGTTGGGGAAGCAAGATTCACCGTTGTGGCTTTAATCTGTTCCACTACACTGCCAGGGAA
* * * *
20582850 GTAATATTCGCCGTTGTGGCTTTAATCTGTTCCAT
66 GTAAGATTCGCCGTTGTGGCTTTAATCTTTTCAAC
** * * ** * * * *
20582885 TGCACCGCTT-GGGAAGTAAGATTCACCGTTGTGGCTTTAATCTTTTTAACTGCAATGTCGGGGA
1 TGCAATG-TTGGGGAAGCAAGATTCACCGTTGTGGCTTTAATCTGTTCCACTACACTGCCAGGGA
* *
20582949 AGCAAGATTCGCCATTGTGGCTTTAAT-TTGTTCAAC
65 AGTAAGATTCGCCGTTGTGGCTTTAATCTT-TTCAAC
20582985 TGCA
1 TGCA
20582989 TTGCCTGGGA
Statistics
Matches: 256, Mismatches: 44, Indels: 8
0.83 0.14 0.03
Matches are distributed among these distances:
99 2 0.01
100 252 0.98
101 2 0.01
ACGTcount: A:0.23, C:0.21, G:0.24, T:0.33
Consensus pattern (100 bp):
TGCAATGTTGGGGAAGCAAGATTCACCGTTGTGGCTTTAATCTGTTCCACTACACTGCCAGGGAA
GTAAGATTCGCCGTTGTGGCTTTAATCTTTTCAAC
Found at i:20582998 original size:150 final size:150
Alignment explanation
Indices: 20582603--20582999 Score: 465
Period size: 150 Copynumber: 2.6 Consensus size: 150
20582593 CAGGGAAACG
* * * * ** * * * *
20582603 AGATTCACCGTCGTAGCTTCAATCTGTTCCACTGCACTGCCAGGGAAGTAAGATTCACCGTTGTG
1 AGATTCACCGTTGTGGCTTTAATCTTTTTAACTGCAATGTCGGGGAAGTAAGATTCGCCGTTGTG
* *
20582668 GCTTAAATCTT-TTTAACTGCAATG-TTGGGGAAGCAAGATTCGCCGTTGTGGCTTTAATCTATT
66 GCTTTAAT-TTGTTCAACTGCAATGCTT-GGGAAGCAAGATTCGCCGTTGTGGCTTTAATCTATT
*
20582731 CCACTACATCGCCAGGGAAGTA
129 CCACTACACCGCCAGGGAAGTA
* * *
20582753 AGATTCGCCGTTGTGGCTTTAATCTTTTTAACTGCAATTTTGGGGAAGTAAGATTCGCCGTTGTG
1 AGATTCACCGTTGTGGCTTTAATCTTTTTAACTGCAATGTCGGGGAAGTAAGATTCGCCGTTGTG
** * * ** * * *
20582818 GCTTTAACCTGTTCCACTACACCGCTTGGGAAGTAATATTCGCCGTTGTGGCTTTAATCTGTTCC
66 GCTTTAATTTGTTCAACTGCAATGCTTGGGAAGCAAGATTCGCCGTTGTGGCTTTAATCTATTCC
* * **
20582883 ATTGCACCGCTTGGGAAGTA
131 ACTACACCGCCAGGGAAGTA
* *
20582903 AGATTCACCGTTGTGGCTTTAATCTTTTTAACTGCAATGTCGGGGAAGCAAGATTCGCCATTGTG
1 AGATTCACCGTTGTGGCTTTAATCTTTTTAACTGCAATGTCGGGGAAGTAAGATTCGCCGTTGTG
* *
20582968 GCTTTAATTTGTTCAACTGCATTGCCTGGGAA
66 GCTTTAATTTGTTCAACTGCAATGCTTGGGAA
20583000 AACTGGTTTC
Statistics
Matches: 204, Mismatches: 41, Indels: 4
0.82 0.16 0.02
Matches are distributed among these distances:
149 1 0.00
150 201 0.99
151 2 0.01
ACGTcount: A:0.22, C:0.21, G:0.23, T:0.33
Consensus pattern (150 bp):
AGATTCACCGTTGTGGCTTTAATCTTTTTAACTGCAATGTCGGGGAAGTAAGATTCGCCGTTGTG
GCTTTAATTTGTTCAACTGCAATGCTTGGGAAGCAAGATTCGCCGTTGTGGCTTTAATCTATTCC
ACTACACCGCCAGGGAAGTA
Found at i:20583169 original size:44 final size:45
Alignment explanation
Indices: 20583121--20583217 Score: 117
Period size: 44 Copynumber: 2.2 Consensus size: 45
20583111 CTCCTGGGGA
* * * * *
20583121 AGATAAGATTC-GCCATCTTCGATCTGCTCCACTACTGCTTAGGG
1 AGATAAGATTCTGCAATCTTCAACCTACTCCACTACTGCTAAGGG
* *
20583165 AGATAAGA-TCTGTAATCTTCAACCTACTCCACTGCTGCTAAGGG
1 AGATAAGATTCTGCAATCTTCAACCTACTCCACTACTGCTAAGGG
20583209 AGATAAGAT
1 AGATAAGAT
20583218 CTGGGTCTTC
Statistics
Matches: 44, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
43 2 0.05
44 42 0.95
ACGTcount: A:0.29, C:0.24, G:0.20, T:0.28
Consensus pattern (45 bp):
AGATAAGATTCTGCAATCTTCAACCTACTCCACTACTGCTAAGGG
Found at i:20590373 original size:27 final size:27
Alignment explanation
Indices: 20590332--20590394 Score: 92
Period size: 27 Copynumber: 2.4 Consensus size: 27
20590322 ATAGGTTAAT
*
20590332 TTTAAAAT-AAGTAATATGTAAAATAA
1 TTTAAAATAAAATAATATGTAAAATAA
*
20590358 TTTAAAATAAAATAATATGTAAAGTAA
1 TTTAAAATAAAATAATATGTAAAATAA
*
20590385 CTTAAAATAA
1 TTTAAAATAA
20590395 TTAGACTTAT
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
26 8 0.24
27 25 0.76
ACGTcount: A:0.59, C:0.02, G:0.06, T:0.33
Consensus pattern (27 bp):
TTTAAAATAAAATAATATGTAAAATAA
Found at i:20590442 original size:21 final size:21
Alignment explanation
Indices: 20590413--20590452 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
20590403 ATAAGTTAGG
20590413 TTAAGATAATAAATAAAAGGT
1 TTAAGATAATAAATAAAAGGT
* **
20590434 TTAATATAATCTATAAAAG
1 TTAAGATAATAAATAAAAG
20590453 AGAAAATTGG
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.55, C:0.03, G:0.10, T:0.33
Consensus pattern (21 bp):
TTAAGATAATAAATAAAAGGT
Found at i:20606334 original size:16 final size:17
Alignment explanation
Indices: 20606295--20606331 Score: 74
Period size: 17 Copynumber: 2.2 Consensus size: 17
20606285 GTAGAGACTG
20606295 TAAATAAACTATTTTTA
1 TAAATAAACTATTTTTA
20606312 TAAATAAACTATTTTTA
1 TAAATAAACTATTTTTA
20606329 TAA
1 TAA
20606332 TAATATCCTG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.49, C:0.05, G:0.00, T:0.46
Consensus pattern (17 bp):
TAAATAAACTATTTTTA
Found at i:20615373 original size:18 final size:18
Alignment explanation
Indices: 20615340--20615374 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
20615330 AAAATCGGGA
*
20615340 AAAAATATTCTCGAAAAT
1 AAAAATATTCTAGAAAAT
*
20615358 AAAAATATTGTAGAAAA
1 AAAAATATTCTAGAAAA
20615375 ATTAAATTAA
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:0.60, C:0.06, G:0.09, T:0.26
Consensus pattern (18 bp):
AAAAATATTCTAGAAAAT
Found at i:20623741 original size:5 final size:6
Alignment explanation
Indices: 20623722--20623779 Score: 53
Period size: 6 Copynumber: 9.2 Consensus size: 6
20623712 TTTGGAATTC
* * *
20623722 AAATAA AAATAA AAATAA AACATTAC AAATAG AAATAA AAAGGAA AAATAA
1 AAATAA AAATAA AAATAA AA-A-TAA AAATAA AAATAA AAA-TAA AAATAA
*
20623773 AGATAA A
1 AAATAA A
20623780 CTAAATTTGT
Statistics
Matches: 43, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
6 32 0.74
7 7 0.16
8 4 0.09
ACGTcount: A:0.74, C:0.03, G:0.07, T:0.16
Consensus pattern (6 bp):
AAATAA
Found at i:20626580 original size:47 final size:47
Alignment explanation
Indices: 20626507--20626605 Score: 162
Period size: 47 Copynumber: 2.1 Consensus size: 47
20626497 CTTCTAAGAT
* * *
20626507 ACTCTCATATGGTTATTCCAGTAACTTTTACCAATGGGAAGTTTTAG
1 ACTCTCATATGGTTATTCCAGCAACTTTTACAAATGGGAAGTTTCAG
*
20626554 ACTCTCATATGGTTATTCCCGCAACTTTTACAAATGGGAAGTTTCAG
1 ACTCTCATATGGTTATTCCAGCAACTTTTACAAATGGGAAGTTTCAG
20626601 ACTCT
1 ACTCT
20626606 GGGACCCTCT
Statistics
Matches: 48, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
47 48 1.00
ACGTcount: A:0.27, C:0.20, G:0.16, T:0.36
Consensus pattern (47 bp):
ACTCTCATATGGTTATTCCAGCAACTTTTACAAATGGGAAGTTTCAG
Found at i:20627552 original size:21 final size:20
Alignment explanation
Indices: 20627523--20627562 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
20627513 CTTTTTCAAT
*
20627523 CTCAATCTCTCTTTTCTTTTC
1 CTCAATCTC-ATTTTCTTTTC
*
20627544 CTCACTCTCATTTTCTTTT
1 CTCAATCTCATTTTCTTTT
20627563 TCGATTTCTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.10, C:0.33, G:0.00, T:0.57
Consensus pattern (20 bp):
CTCAATCTCATTTTCTTTTC
Found at i:20630158 original size:10 final size:10
Alignment explanation
Indices: 20630143--20630193 Score: 59
Period size: 10 Copynumber: 5.1 Consensus size: 10
20630133 TTGGGTTAAG
20630143 ATTGAGCTGA
1 ATTGAGCTGA
20630153 ATTGAGCTCGA
1 ATTGAGCT-GA
20630164 A-TGAGCTGA
1 ATTGAGCTGA
* *
20630173 CTTGAGCTCA
1 ATTGAGCTGA
*
20630183 AGTGAGCTGA
1 ATTGAGCTGA
20630193 A
1 A
20630194 CTAAGTTGCA
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
9 2 0.06
10 29 0.85
11 3 0.09
ACGTcount: A:0.29, C:0.16, G:0.29, T:0.25
Consensus pattern (10 bp):
ATTGAGCTGA
Found at i:20630168 original size:20 final size:20
Alignment explanation
Indices: 20630145--20630193 Score: 73
Period size: 20 Copynumber: 2.5 Consensus size: 20
20630135 GGGTTAAGAT
20630145 TGAGCTGAATTGAGCTCGAA-
1 TGAGCTGAATTGAGCTC-AAG
*
20630165 TGAGCTGACTTGAGCTCAAG
1 TGAGCTGAATTGAGCTCAAG
20630185 TGAGCTGAA
1 TGAGCTGAA
20630194 CTAAGTTGCA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
19 2 0.08
20 24 0.92
ACGTcount: A:0.29, C:0.16, G:0.31, T:0.24
Consensus pattern (20 bp):
TGAGCTGAATTGAGCTCAAG
Found at i:20632619 original size:24 final size:25
Alignment explanation
Indices: 20632592--20632638 Score: 69
Period size: 24 Copynumber: 1.9 Consensus size: 25
20632582 CTGTGGTTAA
* *
20632592 ATGACTGGTTTGTTTGTG-TTTGGT
1 ATGACTGATTTGTCTGTGATTTGGT
20632616 ATGACTGATTTGTCTGTGATTTG
1 ATGACTGATTTGTCTGTGATTTG
20632639 AGTGACTGAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 16 0.80
25 4 0.20
ACGTcount: A:0.13, C:0.06, G:0.30, T:0.51
Consensus pattern (25 bp):
ATGACTGATTTGTCTGTGATTTGGT
Found at i:20632869 original size:32 final size:32
Alignment explanation
Indices: 20632824--20633010 Score: 232
Period size: 32 Copynumber: 5.8 Consensus size: 32
20632814 ACGATGCTAT
*
20632824 TGATGGCTTTGTACCGATCATATTACCATTAC
1 TGATGGCTTTGTACCGATCATATTACTATTAC
* * *
20632856 TAATGGCTATGTACCGATCATATTACCATTAC
1 TGATGGCTTTGTACCGATCATATTACTATTAC
* * *
20632888 TGATGG-TTGTGTGCCGATCATATTACTACTAT
1 TGATGGCTT-TGTACCGATCATATTACTATTAC
*
20632920 TGATGGCTTTGTACCGATCATACTACTATTAC
1 TGATGGCTTTGTACCGATCATATTACTATTAC
* * *
20632952 TGATGGCTGTGTGCCGATCATATTACTACTAC
1 TGATGGCTTTGTACCGATCATATTACTATTAC
** *
20632984 TGATGGCTTTGTGTCAATCATATTACT
1 TGATGGCTTTGTACCGATCATATTACT
20633011 GTACTTGTGG
Statistics
Matches: 134, Mismatches: 19, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
31 1 0.01
32 131 0.98
33 2 0.01
ACGTcount: A:0.25, C:0.20, G:0.18, T:0.38
Consensus pattern (32 bp):
TGATGGCTTTGTACCGATCATATTACTATTAC
Found at i:20632928 original size:96 final size:96
Alignment explanation
Indices: 20632820--20633010 Score: 285
Period size: 96 Copynumber: 2.0 Consensus size: 96
20632810 TACTACGATG
* *
20632820 CTATTGATGGCTTTGTACCGATCATATTACCATTACTAATGGCTATGTACCGATCATATTACCAT
1 CTATTGATGGCTTTGTACCGATCATACTACCATTACTAATGGCTATGTACCGATCATATTACCAC
*
20632885 TACTGATGG-TTGTGTGCCGATCATATTACTA
66 TACTGATGGCTT-TGTGCCAATCATATTACTA
* * * * *
20632916 CTATTGATGGCTTTGTACCGATCATACTACTATTACTGATGGCTGTGTGCCGATCATATTACTAC
1 CTATTGATGGCTTTGTACCGATCATACTACCATTACTAATGGCTATGTACCGATCATATTACCAC
*
20632981 TACTGATGGCTTTGTGTCAATCATATTACT
66 TACTGATGGCTTTGTGCCAATCATATTACT
20633011 GTACTTGTGG
Statistics
Matches: 85, Mismatches: 9, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
96 83 0.98
97 2 0.02
ACGTcount: A:0.25, C:0.20, G:0.17, T:0.38
Consensus pattern (96 bp):
CTATTGATGGCTTTGTACCGATCATACTACCATTACTAATGGCTATGTACCGATCATATTACCAC
TACTGATGGCTTTGTGCCAATCATATTACTA
Found at i:20641526 original size:17 final size:18
Alignment explanation
Indices: 20641493--20641526 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
20641483 ATGATATGCC
*
20641493 AAACTATTTTTATGCTTG
1 AAACTATTTTGATGCTTG
20641511 AAACTA-TTTGATGCTT
1 AAACTATTTTGATGCTT
20641527 ACTATTCTTG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.29, C:0.12, G:0.12, T:0.47
Consensus pattern (18 bp):
AAACTATTTTGATGCTTG
Found at i:20648560 original size:25 final size:25
Alignment explanation
Indices: 20648526--20648582 Score: 96
Period size: 25 Copynumber: 2.3 Consensus size: 25
20648516 GGGTCAGACG
20648526 GCCGTGTCACACGCCCATGTGCCAA
1 GCCGTGTCACACGCCCATGTGCCAA
* *
20648551 GCCGTGTCACACGCCCGTGTGCCAG
1 GCCGTGTCACACGCCCATGTGCCAA
20648576 GCCGTGT
1 GCCGTGT
20648583 AACTCTCTGA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
25 30 1.00
ACGTcount: A:0.14, C:0.39, G:0.30, T:0.18
Consensus pattern (25 bp):
GCCGTGTCACACGCCCATGTGCCAA
Found at i:20660160 original size:51 final size:50
Alignment explanation
Indices: 20660028--20660230 Score: 243
Period size: 51 Copynumber: 4.0 Consensus size: 50
20660018 ACTATTATCA
*
20660028 TTCGATACACGTAGTAGCCTTCACATAGTACTACACACGTGATC-AAGTT
1 TTCGATACACATAGTAGCCTTCACATAGTACTACACACGTGATCAAAGTT
* * * *
20660077 TTATGGTTCACATAGTAGCCTTCACATGGTACTACACACGTGA-CAAAAGCTT
1 TT-CGATACACATAGTAGCCTTCACATAGTACTACACACGTGATC-AAAG-TT
* * * *
20660129 TTCGGTACACATAGTAGCCTTCACTTAGTACTACACATGTGATCATTA-TT
1 TTCGATACACATAGTAGCCTTCACATAGTACTACACACGTGATCA-AAGTT
*
20660179 TATCGATACACGTAGTAGCCTTCACATAGTACTACACACGTGATC-AAGTT
1 T-TCGATACACATAGTAGCCTTCACATAGTACTACACACGTGATCAAAGTT
20660229 TT
1 TT
20660231 ANNNNNNNNN
Statistics
Matches: 130, Mismatches: 16, Indels: 16
0.80 0.10 0.10
Matches are distributed among these distances:
49 5 0.04
50 41 0.32
51 78 0.60
52 6 0.05
ACGTcount: A:0.30, C:0.23, G:0.16, T:0.31
Consensus pattern (50 bp):
TTCGATACACATAGTAGCCTTCACATAGTACTACACACGTGATCAAAGTT
Found at i:20660166 original size:26 final size:26
Alignment explanation
Indices: 20660134--20660216 Score: 66
Period size: 26 Copynumber: 3.2 Consensus size: 26
20660124 AGCTTTTCGG
20660134 TACACATAGTAGCCTTCACTTAGTAC
1 TACACATAGTAGCCTTCACTTAGTAC
* * *
20660160 TACACAT-GTGATCATT-ATTTA-T-C
1 TACACATAGT-AGCCTTCACTTAGTAC
* *
20660183 GATACACGTAGTAGCCTTCACATAGTAC
1 --TACACATAGTAGCCTTCACTTAGTAC
20660211 TACACA
1 TACACA
20660217 CGTGATCAAG
Statistics
Matches: 41, Mismatches: 9, Indels: 14
0.64 0.14 0.22
Matches are distributed among these distances:
23 1 0.02
24 1 0.02
25 16 0.39
26 21 0.51
27 1 0.02
28 1 0.02
ACGTcount: A:0.33, C:0.24, G:0.12, T:0.31
Consensus pattern (26 bp):
TACACATAGTAGCCTTCACTTAGTAC
Found at i:20660171 original size:101 final size:102
Alignment explanation
Indices: 20660028--20660221 Score: 284
Period size: 101 Copynumber: 1.9 Consensus size: 102
20660018 ACTATTATCA
* * *
20660028 TTCGATACACGTAGTAGCCTTCACATAGTACTACACACGTGATCAAGT-TTTAT-GGTTCACATA
1 TTCGATACACATAGTAGCCTTCACATAGTACTACACACGTGATC-AGTATTTATCGATACACATA
*
20660091 GTAGCCTTCACATGGTACTACACACGTGACAAAAGCTT
65 GTAGCCTTCACATAGTACTACACACGTGACAAAAGCTT
* * * * *
20660129 TTCGGTACACATAGTAGCCTTCACTTAGTACTACACATGTGATCATTATTTATCGATACACGTAG
1 TTCGATACACATAGTAGCCTTCACATAGTACTACACACGTGATCAGTATTTATCGATACACATAG
20660194 TAGCCTTCACATAGTACTACACACGTGA
66 TAGCCTTCACATAGTACTACACACGTGA
20660222 TCAAGTTTTA
Statistics
Matches: 82, Mismatches: 9, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
100 2 0.02
101 45 0.55
102 35 0.43
ACGTcount: A:0.30, C:0.24, G:0.16, T:0.30
Consensus pattern (102 bp):
TTCGATACACATAGTAGCCTTCACATAGTACTACACACGTGATCAGTATTTATCGATACACATAG
TAGCCTTCACATAGTACTACACACGTGACAAAAGCTT
Found at i:20661689 original size:27 final size:27
Alignment explanation
Indices: 20661651--20661821 Score: 252
Period size: 27 Copynumber: 6.3 Consensus size: 27
20661641 TAGATTAGGT
20661651 ATTCCTTTCATATATTGCCACAAAGGC
1 ATTCCTTTCATATATTGCCACAAAGGC
* *
20661678 ATTCCTTTCATATATTACCACAAAGGA
1 ATTCCTTTCATATATTGCCACAAAGGC
**
20661705 ATTCCTTTCATATATTGTGACAAAGGC
1 ATTCCTTTCATATATTGCCACAAAGGC
*
20661732 ATACCTTTCATATATTGCCACAAAGGC
1 ATTCCTTTCATATATTGCCACAAAGGC
* *
20661759 GTTCCTTTCATATATTGCCACAAAGCC
1 ATTCCTTTCATATATTGCCACAAAGGC
* * *
20661786 AATCCTTTCATATATTGCCAAAAAGCC
1 ATTCCTTTCATATATTGCCACAAAGGC
20661813 ATTCCTTTC
1 ATTCCTTTC
20661822 CTAGCGTGTT
Statistics
Matches: 128, Mismatches: 16, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 128 1.00
ACGTcount: A:0.31, C:0.25, G:0.10, T:0.34
Consensus pattern (27 bp):
ATTCCTTTCATATATTGCCACAAAGGC
Found at i:20669763 original size:13 final size:13
Alignment explanation
Indices: 20669745--20669772 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
20669735 AGGTACACTG
20669745 TTGCATTTTAGTA
1 TTGCATTTTAGTA
20669758 TTGCATTTTAGTA
1 TTGCATTTTAGTA
20669771 TT
1 TT
20669773 ACAGGAAGCT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.21, C:0.07, G:0.14, T:0.57
Consensus pattern (13 bp):
TTGCATTTTAGTA
Found at i:20671921 original size:29 final size:30
Alignment explanation
Indices: 20671886--20671956 Score: 117
Period size: 29 Copynumber: 2.4 Consensus size: 30
20671876 CTATCAAATT
20671886 ATGAAAAGGGATGGTGACGACCATC-AACA
1 ATGAAAAGGGATGGTGACGACCATCAAACA
* *
20671915 ATGAAAAGGGATGGTGACGACTATCAAATA
1 ATGAAAAGGGATGGTGACGACCATCAAACA
20671945 ATGAAAAGGGAT
1 ATGAAAAGGGAT
20671957 AGCTTCGGTT
Statistics
Matches: 39, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
29 24 0.62
30 15 0.38
ACGTcount: A:0.44, C:0.11, G:0.28, T:0.17
Consensus pattern (30 bp):
ATGAAAAGGGATGGTGACGACCATCAAACA
Found at i:20671950 original size:30 final size:30
Alignment explanation
Indices: 20671761--20671956 Score: 150
Period size: 30 Copynumber: 6.6 Consensus size: 30
20671751 GGAGGTTATT
* * *
20671761 AAATTATGAAAAGGGATGGTAACGACCATT
1 AAATAATGAAAAGGGATGGTGACGACCATC
*
20671791 AAATAATGAAAAGGGATGGTGATGACCATC
1 AAATAATGAAAAGGGATGGTGACGACCATC
* * * * *
20671821 GAACAATGAAAAGGGATGGCT-TCGGCTATCC
1 AAATAATGAAAAGGGATGG-TGACGACCAT-C
* * * * * * *
20671852 AACT-GTAAAAATGGAGA-GCT-TCGGCTATC
1 AAATAATGAAAA-GG-GATGGTGACGACCATC
*
20671881 AAATTATGAAAAGGGATGGTGACGACCATC
1 AAATAATGAAAAGGGATGGTGACGACCATC
* *
20671911 -AACAATGAAAAGGGATGGTGACGACTATC
1 AAATAATGAAAAGGGATGGTGACGACCATC
20671940 AAATAATGAAAAGGGAT
1 AAATAATGAAAAGGGAT
20671957 AGCTTCGGTT
Statistics
Matches: 131, Mismatches: 27, Indels: 16
0.75 0.16 0.09
Matches are distributed among these distances:
28 2 0.02
29 34 0.26
30 87 0.66
31 6 0.05
32 2 0.02
ACGTcount: A:0.41, C:0.13, G:0.26, T:0.20
Consensus pattern (30 bp):
AAATAATGAAAAGGGATGGTGACGACCATC
Found at i:20671961 original size:89 final size:90
Alignment explanation
Indices: 20671791--20671999 Score: 237
Period size: 89 Copynumber: 2.3 Consensus size: 90
20671781 AACGACCATT
* * * * *
20671791 AAATAATGAAAAGGGATGGTGATGACCATCGAACAATGAAAAGGGATGGCTTCGGCTATCCAACT
1 AAATTATGAAAAGGGATGGTGACGACCATCGAACAATGAAAAGGGATGGCTACGACTATCCAAAT
* *
20671856 GTAAAAATGGAGAGCTTCGGCTATC
66 ATAAAAAGGGAGAGCTTCGGCTATC
20671881 AAATTATGAAAAGGGATGGTGACGACCATC-AACAATGAAAAGGGATGG-TGACGACTAT-CAAA
1 AAATTATGAAAAGGGATGGTGACGACCATCGAACAATGAAAAGGGATGGCT-ACGACTATCCAAA
* * *
20671943 TAATGAAAAGGGATAGCTTCGGTTATC
65 T-ATAAAAAGGGAGAGCTTCGGCTATC
* ** * *
20671970 GAGCTATGAAAAGGGTTGG-GACAACCATCG
1 AAATTATGAAAAGGGATGGTGACGACCATCG
20672000 TGATTTTATT
Statistics
Matches: 101, Mismatches: 15, Indels: 7
0.82 0.12 0.06
Matches are distributed among these distances:
88 14 0.14
89 59 0.58
90 28 0.28
ACGTcount: A:0.38, C:0.14, G:0.27, T:0.21
Consensus pattern (90 bp):
AAATTATGAAAAGGGATGGTGACGACCATCGAACAATGAAAAGGGATGGCTACGACTATCCAAAT
ATAAAAAGGGAGAGCTTCGGCTATC
Found at i:20678630 original size:75 final size:75
Alignment explanation
Indices: 20678544--20678691 Score: 260
Period size: 75 Copynumber: 2.0 Consensus size: 75
20678534 AGAAAACCAT
* * *
20678544 GATTATTCCCTTATTAATAGAGAAGGCAAATGGAAAGTTAGAAAAATGAATTATATTCTTTTCAA
1 GATTATTCCCTTATTAATAGAGAAGACAAATGAAAAGTTAGAAAAATGAATTATATTCTTTCCAA
20678609 AAGAATATAA
66 AAGAATATAA
*
20678619 GATTATTCCCTTATTAATAGAGAAGACAAATGAAAAGTTAGAAAAATGAATTTTATTCTTTCCAA
1 GATTATTCCCTTATTAATAGAGAAGACAAATGAAAAGTTAGAAAAATGAATTATATTCTTTCCAA
20678684 AAGAATAT
66 AAGAATAT
20678692 TAATTATCAT
Statistics
Matches: 69, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
75 69 1.00
ACGTcount: A:0.45, C:0.09, G:0.14, T:0.32
Consensus pattern (75 bp):
GATTATTCCCTTATTAATAGAGAAGACAAATGAAAAGTTAGAAAAATGAATTATATTCTTTCCAA
AAGAATATAA
Found at i:20679111 original size:13 final size:13
Alignment explanation
Indices: 20679093--20679119 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
20679083 TTTCCAAAAG
20679093 AATATTAATTTTC
1 AATATTAATTTTC
20679106 AATATTAATTTTC
1 AATATTAATTTTC
20679119 A
1 A
20679120 TGTCTTTTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.41, C:0.07, G:0.00, T:0.52
Consensus pattern (13 bp):
AATATTAATTTTC
Found at i:20681572 original size:20 final size:20
Alignment explanation
Indices: 20681547--20681584 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
20681537 CTTAATCGAG
**
20681547 GATAATTATTTATTTAATTA
1 GATAATTAAATATTTAATTA
20681567 GATAATTAAATATTTAAT
1 GATAATTAAATATTTAAT
20681585 CGATCATACG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.45, C:0.00, G:0.05, T:0.50
Consensus pattern (20 bp):
GATAATTAAATATTTAATTA
Found at i:20686066 original size:43 final size:43
Alignment explanation
Indices: 20686018--20686105 Score: 167
Period size: 43 Copynumber: 2.0 Consensus size: 43
20686008 AGTAATTATT
20686018 TTATGTAATTAATTTAATATTAATTTCTCAAATCTACAATCCC
1 TTATGTAATTAATTTAATATTAATTTCTCAAATCTACAATCCC
*
20686061 TTATGTAATTAATTTAATATTAATTTTTCAAATCTACAATCCC
1 TTATGTAATTAATTTAATATTAATTTCTCAAATCTACAATCCC
20686104 TT
1 TT
20686106 GGGTACGATC
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
43 44 1.00
ACGTcount: A:0.36, C:0.15, G:0.02, T:0.47
Consensus pattern (43 bp):
TTATGTAATTAATTTAATATTAATTTCTCAAATCTACAATCCC
Found at i:20687375 original size:9 final size:9
Alignment explanation
Indices: 20687361--20687436 Score: 84
Period size: 9 Copynumber: 8.4 Consensus size: 9
20687351 TTTGGTTAAA
20687361 AATTAACCG
1 AATTAACCG
*
20687370 AATTAACTG
1 AATTAACCG
* *
20687379 AATTATCTG
1 AATTAACCG
20687388 AATTAACCG
1 AATTAACCG
20687397 AATT-ACCTG
1 AATTAACC-G
20687406 AATT-ACCTG
1 AATTAACC-G
20687415 AATTAACCG
1 AATTAACCG
*
20687424 AATTAACCT
1 AATTAACCG
20687433 AATT
1 AATT
20687437 GAATCATACA
Statistics
Matches: 60, Mismatches: 5, Indels: 4
0.87 0.07 0.06
Matches are distributed among these distances:
8 3 0.05
9 54 0.90
10 3 0.05
ACGTcount: A:0.41, C:0.18, G:0.09, T:0.32
Consensus pattern (9 bp):
AATTAACCG
Found at i:20687436 original size:27 final size:28
Alignment explanation
Indices: 20687361--20687436 Score: 122
Period size: 27 Copynumber: 2.8 Consensus size: 28
20687351 TTTGGTTAAA
*
20687361 AATTAACCGAATTAA-CTGAATTATCTG
1 AATTAACCGAATTAACCTGAATTACCTG
20687388 AATTAACCGAATT-ACCTGAATTACCTG
1 AATTAACCGAATTAACCTGAATTACCTG
20687415 AATTAACCGAATTAACCT-AATT
1 AATTAACCGAATTAACCTGAATT
20687437 GAATCATACA
Statistics
Matches: 46, Mismatches: 1, Indels: 4
0.90 0.02 0.08
Matches are distributed among these distances:
26 1 0.02
27 41 0.89
28 4 0.09
ACGTcount: A:0.41, C:0.18, G:0.09, T:0.32
Consensus pattern (28 bp):
AATTAACCGAATTAACCTGAATTACCTG
Found at i:20690279 original size:40 final size:40
Alignment explanation
Indices: 20690219--20690399 Score: 238
Period size: 40 Copynumber: 4.5 Consensus size: 40
20690209 TGTAAACAGA
*
20690219 GGCAAGTATGTGCAATCAGGGGTACCAAAGTACAAAAAAG
1 GGCACGTATGTGCAATCAGGGGTACCAAAGTACAAAAAAG
** * * *
20690259 GGCGTGTATGTGCAATCAGGGGTAACGAAGTACAAACAAG
1 GGCACGTATGTGCAATCAGGGGTACCAAAGTACAAAAAAG
* *
20690299 GGCACGTATGTGCAATCAGGGGTACCGAAGTAC-AAACAG
1 GGCACGTATGTGCAATCAGGGGTACCAAAGTACAAAAAAG
* * *
20690338 TGGCACGTATGTGCAATCAGGGATACCAAAGTACAAATAGG
1 -GGCACGTATGTGCAATCAGGGGTACCAAAGTACAAAAAAG
20690379 GGCACGTATGTGCAATTCAGG
1 GGCACGTATGTGCAA-TCAGG
20690400 TATAATTAAC
Statistics
Matches: 123, Mismatches: 15, Indels: 5
0.86 0.10 0.03
Matches are distributed among these distances:
39 4 0.03
40 111 0.90
41 8 0.07
ACGTcount: A:0.35, C:0.17, G:0.30, T:0.18
Consensus pattern (40 bp):
GGCACGTATGTGCAATCAGGGGTACCAAAGTACAAAAAAG
Found at i:20697696 original size:40 final size:40
Alignment explanation
Indices: 20697652--20697789 Score: 179
Period size: 40 Copynumber: 3.4 Consensus size: 40
20697642 AATCAGCGGT
* *
20697652 ACGTATTTGCAATCAGGGGTACTGAAGTAAAAATAGGGGC
1 ACGTATGTGCAATCAGGGGTACTGAAGTACAAATAGGGGC
** *
20697692 ACGTATGTGCAATCAGGGGTACCAAAGTACAAACAGGGGC
1 ACGTATGTGCAATCAGGGGTACTGAAGTACAAATAGGGGC
* * *
20697732 ATGTATGTGTAATTAGGGGTA-TCGAAGTACAAATAGGGGC
1 ACGTATGTGCAATCAGGGGTACT-GAAGTACAAATAGGGGC
20697772 ACGTATGTGCAATTCAGG
1 ACGTATGTGCAA-TCAGG
20697790 TATAATTAAC
Statistics
Matches: 82, Mismatches: 14, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
40 78 0.95
41 4 0.05
ACGTcount: A:0.33, C:0.14, G:0.30, T:0.22
Consensus pattern (40 bp):
ACGTATGTGCAATCAGGGGTACTGAAGTACAAATAGGGGC
Found at i:20697709 original size:20 final size:20
Alignment explanation
Indices: 20697686--20697789 Score: 59
Period size: 20 Copynumber: 5.2 Consensus size: 20
20697676 AAGTAAAAAT
20697686 AGGGGCACGTATGTGCAATC
1 AGGGGCACGTATGTGCAATC
* ** * * *
20697706 AGGGGTACCAAAGTACAAAC
1 AGGGGCACGTATGTGCAATC
* * *
20697726 AGGGGCATGTATGTGTAATT
1 AGGGGCACGTATGTGCAATC
* * *
20697746 AGGGGTATCG-AAGTACAAAT-
1 AGGGGCA-CGTATGTGC-AATC
20697766 AGGGGCACGTATGTGCAATTC
1 AGGGGCACGTATGTGCAA-TC
20697787 AGG
1 AGG
20697790 TATAATTAAC
Statistics
Matches: 56, Mismatches: 23, Indels: 9
0.64 0.26 0.10
Matches are distributed among these distances:
19 4 0.07
20 45 0.80
21 7 0.12
ACGTcount: A:0.32, C:0.14, G:0.33, T:0.21
Consensus pattern (20 bp):
AGGGGCACGTATGTGCAATC
Found at i:20698621 original size:24 final size:23
Alignment explanation
Indices: 20698592--20698661 Score: 81
Period size: 24 Copynumber: 3.0 Consensus size: 23
20698582 AGGTAGGCAA
20698592 CTTCTTTTTTTGCACTTTTTGCTT
1 CTTCTTTTTTTGC-CTTTTTGCTT
* *
20698616 CTTCTTTTTGTG-CTTTTTACTTT
1 CTTCTTTTTTTGCCTTTTTGC-TT
20698639 CTT-TTTTTTTGCTCTTTTTGCTT
1 CTTCTTTTTTTGC-CTTTTTGCTT
20698662 TTTTTCTATT
Statistics
Matches: 39, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
22 14 0.36
23 7 0.18
24 18 0.46
ACGTcount: A:0.03, C:0.19, G:0.09, T:0.70
Consensus pattern (23 bp):
CTTCTTTTTTTGCCTTTTTGCTT
Found at i:20698665 original size:22 final size:22
Alignment explanation
Indices: 20698596--20698666 Score: 72
Period size: 22 Copynumber: 3.1 Consensus size: 22
20698586 AGGCAACTTC
* *
20698596 TTTTTTTGCACTTTTTGCTTCT
1 TTTTTTTGCTCTTTTTGCTTTT
* *
20698618 TCTTTTTG-TGCTTTTTACTTTCTT
1 TTTTTTTGCT-CTTTTTGC-TT-TT
20698642 TTTTTTTGCTCTTTTTGCTTTT
1 TTTTTTTGCTCTTTTTGCTTTT
20698664 TTT
1 TTT
20698667 CTATTTTTTT
Statistics
Matches: 39, Mismatches: 6, Indels: 8
0.74 0.11 0.15
Matches are distributed among these distances:
22 19 0.49
23 4 0.10
24 15 0.38
25 1 0.03
ACGTcount: A:0.03, C:0.15, G:0.08, T:0.73
Consensus pattern (22 bp):
TTTTTTTGCTCTTTTTGCTTTT
Found at i:20699297 original size:31 final size:32
Alignment explanation
Indices: 20699221--20699285 Score: 123
Period size: 32 Copynumber: 2.1 Consensus size: 32
20699211 GGCAAATTAC
20699221 AAGAGTAATTGAATCCTAATAAAAACTCTTTA
1 AAGAGTAATTGAATCCTAATAAAAACTCTTTA
20699253 AAGAGTAATTGAATCCTAAT-AAAACTCTTTA
1 AAGAGTAATTGAATCCTAATAAAAACTCTTTA
20699284 AA
1 AA
20699286 ATTATGATGA
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
31 13 0.39
32 20 0.61
ACGTcount: A:0.48, C:0.12, G:0.09, T:0.31
Consensus pattern (32 bp):
AAGAGTAATTGAATCCTAATAAAAACTCTTTA
Found at i:20706197 original size:33 final size:33
Alignment explanation
Indices: 20706160--20706231 Score: 92
Period size: 33 Copynumber: 2.2 Consensus size: 33
20706150 CCCTTTCTAG
* *
20706160 ATCACTTTCACCATCAGA-TTCTACCCCATCATC
1 ATCACCTTCACCATCA-ACTTCTACCCCATCAAC
* *
20706193 ATCACCTTCCCCATCAACTTCTACCCCTTCAAC
1 ATCACCTTCACCATCAACTTCTACCCCATCAAC
20706226 ATCACC
1 ATCACC
20706232 CTCCCCAGTA
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
32 1 0.03
33 33 0.97
ACGTcount: A:0.26, C:0.44, G:0.01, T:0.28
Consensus pattern (33 bp):
ATCACCTTCACCATCAACTTCTACCCCATCAAC
Found at i:20706237 original size:33 final size:33
Alignment explanation
Indices: 20706170--20706238 Score: 95
Period size: 33 Copynumber: 2.1 Consensus size: 33
20706160 ATCACTTTCA
* *
20706170 CCATCAGATTCTACCCCATCATCATCACCTTCC
1 CCATCAGATTCTACCCCATCAACATCACCCTCC
*
20706203 CCATCA-ACTTCTACCCCTTCAACATCACCCTCC
1 CCATCAGA-TTCTACCCCATCAACATCACCCTCC
20706236 CCA
1 CCA
20706239 GTAGTCAACA
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
32 1 0.03
33 31 0.97
ACGTcount: A:0.25, C:0.49, G:0.01, T:0.25
Consensus pattern (33 bp):
CCATCAGATTCTACCCCATCAACATCACCCTCC
Found at i:20706924 original size:117 final size:116
Alignment explanation
Indices: 20706718--20707042 Score: 506
Period size: 117 Copynumber: 2.8 Consensus size: 116
20706708 GGTAACAAAA
* *
20706718 ATCAACAGCATCGGGACCACTGTCACATCACAAATCGACAAAACAAAACCTACATTGTGGCACTA
1 ATCAACAACATCGGGACCACTGTCACATCACAAATCGACAAAAC-AAACCTACATTGTGGCACTG
* *
20706783 AAATTGCAATAATAAATCACAAATAACCATCTACAATTTTAACAACAGCTTT
65 AAATTGCAATAATAAATCACAAATAACCATCTACAAGTTTAACAACAACTTT
* * * *
20706835 ATCAACAACATCGAGACCATTGTCGCATCACAAATTGACAAAACAAACCTTACATTGTGGCACTG
1 ATCAACAACATCGGGACCACTGTCACATCACAAATCGACAAAACAAACC-TACATTGTGGCACTG
*
20706900 AAATTGCAATAATAAATCAAAAATAACCATCTACAAGTTTAACAACAACTTT
65 AAATTGCAATAATAAATCACAAATAACCATCTACAAGTTTAACAACAACTTT
* * *
20706952 ATCAACAACATTGGGACCACTGTCACATCACAAATCGACAAAACTAACCCTACATTGTGGCATTG
1 ATCAACAACATCGGGACCACTGTCACATCACAAATCGACAAAAC-AAACCTACATTGTGGCACTG
*
20707017 AAATTACAATAATAAATCACAAATAA
65 AAATTGCAATAATAAATCACAAATAA
20707043 TCAACAAACT
Statistics
Matches: 188, Mismatches: 18, Indels: 4
0.90 0.09 0.02
Matches are distributed among these distances:
116 5 0.03
117 179 0.95
118 4 0.02
ACGTcount: A:0.44, C:0.23, G:0.10, T:0.23
Consensus pattern (116 bp):
ATCAACAACATCGGGACCACTGTCACATCACAAATCGACAAAACAAACCTACATTGTGGCACTGA
AATTGCAATAATAAATCACAAATAACCATCTACAAGTTTAACAACAACTTT
Found at i:20707309 original size:17 final size:17
Alignment explanation
Indices: 20707285--20707331 Score: 53
Period size: 17 Copynumber: 2.9 Consensus size: 17
20707275 AATGTTATGG
20707285 ATTT-GGGAATTTTACC
1 ATTTGGGGAATTTTACC
* *
20707301 ATTTGGGGAATTTAACG
1 ATTTGGGGAATTTTACC
*
20707318 AGTTGGGG-ATTTTA
1 ATTTGGGGAATTTTA
20707332 GAACTTGTGA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
16 9 0.35
17 17 0.65
ACGTcount: A:0.26, C:0.06, G:0.28, T:0.40
Consensus pattern (17 bp):
ATTTGGGGAATTTTACC
Found at i:20709717 original size:36 final size:37
Alignment explanation
Indices: 20709670--20709744 Score: 134
Period size: 36 Copynumber: 2.1 Consensus size: 37
20709660 ATATAGATGG
*
20709670 ATACTATTGTAATATCAGTACAT-CCAATTTAATGAA
1 ATACTATTGTAATATCAGTACATCCCAATTAAATGAA
20709706 ATACTATTGTAATATCAGTACATCCCAATTAAATGAA
1 ATACTATTGTAATATCAGTACATCCCAATTAAATGAA
20709743 AT
1 AT
20709745 TATTCAATTA
Statistics
Matches: 37, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
36 23 0.62
37 14 0.38
ACGTcount: A:0.43, C:0.15, G:0.08, T:0.35
Consensus pattern (37 bp):
ATACTATTGTAATATCAGTACATCCCAATTAAATGAA
Found at i:20711686 original size:32 final size:32
Alignment explanation
Indices: 20711645--20711711 Score: 134
Period size: 32 Copynumber: 2.1 Consensus size: 32
20711635 TCTAAACAAG
20711645 ATTTGGGAAAACTATTTCCTATGATGTATAAT
1 ATTTGGGAAAACTATTTCCTATGATGTATAAT
20711677 ATTTGGGAAAACTATTTCCTATGATGTATAAT
1 ATTTGGGAAAACTATTTCCTATGATGTATAAT
20711709 ATT
1 ATT
20711712 CTCTTTATTC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 35 1.00
ACGTcount: A:0.34, C:0.09, G:0.15, T:0.42
Consensus pattern (32 bp):
ATTTGGGAAAACTATTTCCTATGATGTATAAT
Found at i:20717478 original size:21 final size:22
Alignment explanation
Indices: 20717454--20717494 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
20717444 CAACACAACC
*
20717454 ATATAAAATTTTAA-AATATAT
1 ATATAAAATATTAACAATATAT
*
20717475 ATATACAATATTAACAATAT
1 ATATAAAATATTAACAATAT
20717495 TTGATAAAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 12 0.71
22 5 0.29
ACGTcount: A:0.56, C:0.05, G:0.00, T:0.39
Consensus pattern (22 bp):
ATATAAAATATTAACAATATAT
Found at i:20718016 original size:19 final size:18
Alignment explanation
Indices: 20717979--20718021 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 18
20717969 TAGGGGTTTA
* *
20717979 TTTAACTAAATAAATTAC
1 TTTAAATAAATAAAGTAC
20717997 TTTAAATAAAGTAAAGTAC
1 TTTAAATAAA-TAAAGTAC
20718016 TTTAAA
1 TTTAAA
20718022 GGGTTTTTTC
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 9 0.41
19 13 0.59
ACGTcount: A:0.51, C:0.07, G:0.05, T:0.37
Consensus pattern (18 bp):
TTTAAATAAATAAAGTAC
Found at i:20724959 original size:2 final size:2
Alignment explanation
Indices: 20724952--20724977 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
20724942 NNNNNNNNNN
20724952 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
20724978 AAATACTAAC
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:20727812 original size:26 final size:24
Alignment explanation
Indices: 20727769--20727859 Score: 85
Period size: 26 Copynumber: 3.5 Consensus size: 24
20727759 CTGTTAAATG
*
20727769 AACACTGACTCAAGGCCTGATAATTA
1 AACACCGACTCAA-GCCTGATAA-TA
*
20727795 AACACCGACTCACAGCCTGCTAGATA
1 AACACCGACTCA-AGCCTGATA-ATA
*
20727821 AATCACCGGCTCAAAGCCT-ACTAATA
1 AA-CACCGACTC-AAGCCTGA-TAATA
20727847 AACACCGACTCAA
1 AACACCGACTCAA
20727860 ATCCTACAAA
Statistics
Matches: 55, Mismatches: 5, Indels: 12
0.76 0.07 0.17
Matches are distributed among these distances:
24 2 0.04
25 8 0.15
26 27 0.49
27 17 0.31
28 1 0.02
ACGTcount: A:0.38, C:0.31, G:0.13, T:0.18
Consensus pattern (24 bp):
AACACCGACTCAAGCCTGATAATA
Found at i:20727858 original size:25 final size:25
Alignment explanation
Indices: 20727769--20727889 Score: 109
Period size: 25 Copynumber: 4.7 Consensus size: 25
20727759 CTGTTAAATG
* *
20727769 AACACTGACTCAAGGCCTGA-TAATTA
1 AACACCGACTCAAAGCCT-ACTAA-TA
* *
20727795 AACACCGACTCACAGCCTGCTAGATA
1 AACACCGACTCAAAGCCTACTA-ATA
*
20727821 AATCACCGGCTCAAAGCCTACTAATA
1 AA-CACCGACTCAAAGCCTACTAATA
* *
20727847 AACACCGACTCAAATCCTACAAATA
1 AACACCGACTCAAAGCCTACTAATA
* * *
20727872 AACATCGGCTTAAAGCCT
1 AACACCGACTCAAAGCCT
20727890 GCTAGGCAAT
Statistics
Matches: 78, Mismatches: 14, Indels: 7
0.79 0.14 0.07
Matches are distributed among these distances:
25 34 0.44
26 26 0.33
27 18 0.23
ACGTcount: A:0.39, C:0.30, G:0.12, T:0.19
Consensus pattern (25 bp):
AACACCGACTCAAAGCCTACTAATA
Found at i:20733153 original size:28 final size:28
Alignment explanation
Indices: 20733087--20733420 Score: 359
Period size: 28 Copynumber: 12.0 Consensus size: 28
20733077 TGCTCTGTAA
* * * *
20733087 CATAGACCGCCATAAAGGCTT-TCATTT
1 CATAGATCGCCACAAAGGCTTCCCTTTT
* *
20733114 CATAAATCGCCATAAAGGCTTCCCTTTT
1 CATAGATCGCCACAAAGGCTTCCCTTTT
* *
20733142 CATAGATTGCCATAAAGGCTTCCCTTTT
1 CATAGATCGCCACAAAGGCTTCCCTTTT
* * * **
20733170 TATAGTTCGCCACAAAGGTTTCTTTTTT
1 CATAGATCGCCACAAAGGCTTCCCTTTT
20733198 CATAGATCGCCACAAAGGCTTCCCTTTT
1 CATAGATCGCCACAAAGGCTTCCCTTTT
** *
20733226 CATAGATCGATACAAAGGCTTCCCTCTT
1 CATAGATCGCCACAAAGGCTTCCCTTTT
* * * *
20733254 -ATTGTTCACCACAAAGGCTTCTCTTTT
1 CATAGATCGCCACAAAGGCTTCCCTTTT
* *
20733281 CATATATCACCACAAAGGCTTCCCTTTT
1 CATAGATCGCCACAAAGGCTTCCCTTTT
* * *
20733309 CATAGATCGCCGCAAAGGCTTTCTTTTT
1 CATAGATCGCCACAAAGGCTTCCCTTTT
* * *
20733337 TATA-ATTCGCCACAAAGACTTCCCTTGT
1 CATAGA-TCGCCACAAAGGCTTCCCTTTT
*
20733365 CATAAATCGCCACAAAGGCTTCCCTTTT
1 CATAGATCGCCACAAAGGCTTCCCTTTT
* *
20733393 TATAGTTCGCCACAAAGGCTTCCCTTTT
1 CATAGATCGCCACAAAGGCTTCCCTTTT
20733421 TCTGACGTGT
Statistics
Matches: 254, Mismatches: 49, Indels: 7
0.82 0.16 0.02
Matches are distributed among these distances:
27 40 0.16
28 213 0.84
29 1 0.00
ACGTcount: A:0.26, C:0.28, G:0.13, T:0.34
Consensus pattern (28 bp):
CATAGATCGCCACAAAGGCTTCCCTTTT
Found at i:20733243 original size:84 final size:84
Alignment explanation
Indices: 20733094--20733421 Score: 426
Period size: 84 Copynumber: 3.9 Consensus size: 84
20733084 TAACATAGAC
* * * * *
20733094 CGCCATAAAGGCTT-TCATTTCATAAATCGCCATAAAGGCTTCCCTTTTCATAGATTGCCATAAA
1 CGCCACAAAGGCTTCTCTTTTCATAAATCGCCACAAAGGCTTCCCTTTTCATAGATCGCCACAAA
20733158 GGCTTCCCTTTTTATAGTT
66 GGCTTCCCTTTTTATAGTT
* * * **
20733177 CGCCACAAAGGTTTCTTTTTTCATAGATCGCCACAAAGGCTTCCCTTTTCATAGATCGATACAAA
1 CGCCACAAAGGCTTCTCTTTTCATAAATCGCCACAAAGGCTTCCCTTTTCATAGATCGCCACAAA
* *
20733242 GGCTTCCC-TCTTATTGTT
66 GGCTTCCCTTTTTATAGTT
* * * *
20733260 CACCACAAAGGCTTCTCTTTTCATATATCACCACAAAGGCTTCCCTTTTCATAGATCGCCGCAAA
1 CGCCACAAAGGCTTCTCTTTTCATAAATCGCCACAAAGGCTTCCCTTTTCATAGATCGCCACAAA
* * *
20733325 GGCTTTCTTTTTTATAATT
66 GGCTTCCCTTTTTATAGTT
* * * * *
20733344 CGCCACAAAGACTTCCCTTGTCATAAATCGCCACAAAGGCTTCCCTTTTTATAGTTCGCCACAAA
1 CGCCACAAAGGCTTCTCTTTTCATAAATCGCCACAAAGGCTTCCCTTTTCATAGATCGCCACAAA
20733409 GGCTTCCCTTTTT
66 GGCTTCCCTTTTT
20733422 CTGACGTGTT
Statistics
Matches: 207, Mismatches: 36, Indels: 3
0.84 0.15 0.01
Matches are distributed among these distances:
83 83 0.40
84 124 0.60
ACGTcount: A:0.25, C:0.27, G:0.13, T:0.34
Consensus pattern (84 bp):
CGCCACAAAGGCTTCTCTTTTCATAAATCGCCACAAAGGCTTCCCTTTTCATAGATCGCCACAAA
GGCTTCCCTTTTTATAGTT
Found at i:20736311 original size:10 final size:10
Alignment explanation
Indices: 20736292--20736338 Score: 51
Period size: 10 Copynumber: 4.6 Consensus size: 10
20736282 AAATCTATCG
20736292 AAAA-TAATC
1 AAAATTAATC
20736301 AAAATTAATC
1 AAAATTAATC
*
20736311 AAAATTAATTAT
1 AAAATTAA-T-C
*
20736323 AAAATTAATT
1 AAAATTAATC
20736333 AAAATT
1 AAAATT
20736339 CAACATGTTA
Statistics
Matches: 34, Mismatches: 1, Indels: 5
0.85 0.03 0.12
Matches are distributed among these distances:
9 4 0.12
10 20 0.59
11 2 0.06
12 8 0.24
ACGTcount: A:0.62, C:0.04, G:0.00, T:0.34
Consensus pattern (10 bp):
AAAATTAATC
Found at i:20736488 original size:69 final size:69
Alignment explanation
Indices: 20736415--20736625 Score: 164
Period size: 69 Copynumber: 3.1 Consensus size: 69
20736405 TTATCGAAAC
20736415 TGCATGAATTTGAGTTAAAAAGGGGCATGGAAAAGTGTGTATATTTTCGTGTTTCCAAAGATCAA
1 TGCATGAATTTGAGTTAAAAAGGGGCATGGAAAAGTGTGTATATTTTCGTGTTTCCAAAGATCAA
20736480 AAAA
66 AAAA
* * ****** ** * *** * **
20736484 TGCAT-AATTTAAGTAAAATAATTATTTTATAATAA-T-TATATATTTTTCG-ACAT-GAATTTT
1 TGCATGAATTTGAGTTAAA-AAGGGGCATGGAA-AAGTGTGTATA-TTTTCGTGTTTCCAA--AG
* *
20736544 ATC-GAAAC
61 ATCAAAAAA
20736552 TGCATGAATTTGAGTTAAAAAGGGGCATGGAAAAGTGTGTATATTTTCGTGTTTCCAAAGATCAA
1 TGCATGAATTTGAGTTAAAAAGGGGCATGGAAAAGTGTGTATATTTTCGTGTTTCCAAAGATCAA
20736617 AAAA
66 AAAA
20736621 TGCAT
1 TGCAT
20736626 ATCGGGCATA
Statistics
Matches: 93, Mismatches: 38, Indels: 22
0.61 0.25 0.14
Matches are distributed among these distances:
67 4 0.04
68 40 0.43
69 45 0.48
70 4 0.04
ACGTcount: A:0.38, C:0.09, G:0.18, T:0.35
Consensus pattern (69 bp):
TGCATGAATTTGAGTTAAAAAGGGGCATGGAAAAGTGTGTATATTTTCGTGTTTCCAAAGATCAA
AAAA
Found at i:20736607 original size:137 final size:138
Alignment explanation
Indices: 20736349--20736626 Score: 549
Period size: 137 Copynumber: 2.0 Consensus size: 138
20736339 CAACATGTTA
20736349 ATAATTTAAGTAAAAATAATTATTTTATAATAATTATATATTTTTCGACATGAATTTTATCGAAA
1 ATAATTTAAGTAAAAATAATTATTTTATAATAATTATATATTTTTCGACATGAATTTTATCGAAA
20736414 CTGCATGAATTTGAGTTAAAAAGGGGCATGGAAAAGTGTGTATATTTTCGTGTTTCCAAAGATCA
66 CTGCATGAATTTGAGTTAAAAAGGGGCATGGAAAAGTGTGTATATTTTCGTGTTTCCAAAGATCA
20736479 AAAAATGC
131 AAAAATGC
20736487 ATAATTTAAGT-AAAATAATTATTTTATAATAATTATATATTTTTCGACATGAATTTTATCGAAA
1 ATAATTTAAGTAAAAATAATTATTTTATAATAATTATATATTTTTCGACATGAATTTTATCGAAA
20736551 CTGCATGAATTTGAGTTAAAAAGGGGCATGGAAAAGTGTGTATATTTTCGTGTTTCCAAAGATCA
66 CTGCATGAATTTGAGTTAAAAAGGGGCATGGAAAAGTGTGTATATTTTCGTGTTTCCAAAGATCA
20736616 AAAAATGC
131 AAAAATGC
20736624 ATA
1 ATA
20736627 TCGGGCATAA
Statistics
Matches: 140, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
137 129 0.92
138 11 0.08
ACGTcount: A:0.40, C:0.08, G:0.15, T:0.37
Consensus pattern (138 bp):
ATAATTTAAGTAAAAATAATTATTTTATAATAATTATATATTTTTCGACATGAATTTTATCGAAA
CTGCATGAATTTGAGTTAAAAAGGGGCATGGAAAAGTGTGTATATTTTCGTGTTTCCAAAGATCA
AAAAATGC
Found at i:20737639 original size:10 final size:11
Alignment explanation
Indices: 20737619--20737654 Score: 56
Period size: 11 Copynumber: 3.4 Consensus size: 11
20737609 ATTTTTTTCT
20737619 TTTTCAAAAAA
1 TTTTCAAAAAA
20737630 TTTT-AAAAAA
1 TTTTCAAAAAA
*
20737640 TTTTCAAAATA
1 TTTTCAAAAAA
20737651 TTTT
1 TTTT
20737655 TCAGTTTTTA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
10 10 0.43
11 13 0.57
ACGTcount: A:0.47, C:0.06, G:0.00, T:0.47
Consensus pattern (11 bp):
TTTTCAAAAAA
Found at i:20743445 original size:16 final size:17
Alignment explanation
Indices: 20743426--20743457 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
20743416 TTTTTAAATA
20743426 TTTTTATTTTT-CTCTC
1 TTTTTATTTTTACTCTC
20743442 TTTTTATTTTTACTCT
1 TTTTTATTTTTACTCT
20743458 GCCAAGCAAC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.09, C:0.16, G:0.00, T:0.75
Consensus pattern (17 bp):
TTTTTATTTTTACTCTC
Found at i:20743549 original size:13 final size:13
Alignment explanation
Indices: 20743533--20743557 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
20743523 TGATTAAAAC
20743533 TTTTGAAAATAAT
1 TTTTGAAAATAAT
20743546 TTTTGAAAATAA
1 TTTTGAAAATAA
20743558 AAATATGTTA
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:0.48, C:0.00, G:0.08, T:0.44
Consensus pattern (13 bp):
TTTTGAAAATAAT
Found at i:20746357 original size:252 final size:252
Alignment explanation
Indices: 20745907--20746387 Score: 944
Period size: 252 Copynumber: 1.9 Consensus size: 252
20745897 GTCAAACGTC
*
20745907 AAAACTTTGAAAAGATTGGAAACGATTCCCCTTTTATTAATGCCATATTTTAAAACAATGCTTGG
1 AAAAATTTGAAAAGATTGGAAACGATTCCCCTTTTATTAATGCCATATTTTAAAACAATGCTTGG
*
20745972 ATAGATTTGAACGAATGTGAAAGGGTTTCTCATCCCGAGGCAACAAGATGTCGTATCCTGTAAGT
66 ATAGATTTGAACGAATGTGAAAGGGTTTCTCATCCCGAGGCAACAAGATGCCGTATCCTGTAAGT
20746037 TAAGATGCAACGTTTGGATTCCCGAGCATAAGCTAACCTTTTAAAAATCTTTATTGAAACTTTGT
131 TAAGATGCAACGTTTGGATTCCCGAGCATAAGCTAACCTTTTAAAAATCTTTATTGAAACTTTGT
20746102 GCATTTGAAAACTAAAAAGTTTAGTCGTTTTAGTAATGCTTTGTGCATTTGAAAACT
196 GCATTTGAAAACTAAAAAGTTTAGTCGTTTTAGTAATGCTTTGTGCATTTGAAAACT
20746159 AAAAATTTGAAAAGATTGGAAACGATTCCCCTTTTATTAATGCCATATTTTAAAACAATGCTTGG
1 AAAAATTTGAAAAGATTGGAAACGATTCCCCTTTTATTAATGCCATATTTTAAAACAATGCTTGG
20746224 ATAGATTTGAACGAATGTGAAAGGGTTTCTCATCCCGAGGCAACAAGATGCCGTATCCTGTAAGT
66 ATAGATTTGAACGAATGTGAAAGGGTTTCTCATCCCGAGGCAACAAGATGCCGTATCCTGTAAGT
20746289 TAAGATGCAACGTTTGGATTCCCGAGCATAAGCTAACCTTTTAAAAATCTTTATTGAAACTTTGT
131 TAAGATGCAACGTTTGGATTCCCGAGCATAAGCTAACCTTTTAAAAATCTTTATTGAAACTTTGT
20746354 GCATTTGAAAACTAAAAAGTTTAGTCGTTTTAGT
196 GCATTTGAAAACTAAAAAGTTTAGTCGTTTTAGT
20746388 TCGATGAGAA
Statistics
Matches: 227, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
252 227 1.00
ACGTcount: A:0.34, C:0.15, G:0.18, T:0.33
Consensus pattern (252 bp):
AAAAATTTGAAAAGATTGGAAACGATTCCCCTTTTATTAATGCCATATTTTAAAACAATGCTTGG
ATAGATTTGAACGAATGTGAAAGGGTTTCTCATCCCGAGGCAACAAGATGCCGTATCCTGTAAGT
TAAGATGCAACGTTTGGATTCCCGAGCATAAGCTAACCTTTTAAAAATCTTTATTGAAACTTTGT
GCATTTGAAAACTAAAAAGTTTAGTCGTTTTAGTAATGCTTTGTGCATTTGAAAACT
Found at i:20746762 original size:43 final size:43
Alignment explanation
Indices: 20746714--20746805 Score: 166
Period size: 43 Copynumber: 2.1 Consensus size: 43
20746704 ATCGAACTCG
* *
20746714 AAATAATATATAAAACAAATTTAATTTCAAAGAAAGGGTACAT
1 AAATAATATATAAAACAAACTTAATTCCAAAGAAAGGGTACAT
20746757 AAATAATATATAAAACAAACTTAATTCCAAAGAAAGGGTACAT
1 AAATAATATATAAAACAAACTTAATTCCAAAGAAAGGGTACAT
20746800 AAATAA
1 AAATAA
20746806 AACAACATGA
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
43 47 1.00
ACGTcount: A:0.58, C:0.09, G:0.09, T:0.25
Consensus pattern (43 bp):
AAATAATATATAAAACAAACTTAATTCCAAAGAAAGGGTACAT
Found at i:20747025 original size:25 final size:26
Alignment explanation
Indices: 20746997--20747045 Score: 64
Period size: 25 Copynumber: 1.9 Consensus size: 26
20746987 TATAGAAAAA
20746997 TAATAAAAATAATT-AAAAAAATAAG
1 TAATAAAAATAATTCAAAAAAATAAG
***
20747022 TAATATGTATAATTCAAAAAAATA
1 TAATAAAAATAATTCAAAAAAATA
20747046 GTATGTATAT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
25 11 0.55
26 9 0.45
ACGTcount: A:0.65, C:0.02, G:0.04, T:0.29
Consensus pattern (26 bp):
TAATAAAAATAATTCAAAAAAATAAG
Found at i:20747190 original size:24 final size:23
Alignment explanation
Indices: 20747152--20747327 Score: 96
Period size: 24 Copynumber: 7.5 Consensus size: 23
20747142 TGAATTGGAT
* *
20747152 AATTTACAATAAATAATATATAATA
1 AATTTA-AAT-AATAATACATGATA
20747177 AATTTGAAATAATAATACAT-ATAA
1 AATTT-AAATAATAATACATGAT-A
* **
20747201 AATTTAAA-AAT-TTTGATGAT-
1 AATTTAAATAATAATACATGATA
* *
20747221 AATTCTAGAATAATCATACGTGATA
1 AATT-TA-AATAATAATACATGATA
** * * *
20747246 AATCCAAAATAATAGTATATAATA
1 AAT-TTAAATAATAATACATGATA
*
20747270 AATTTAAA-AATATTA-ATGATA
1 AATTTAAATAATAATACATGATA
20747291 AATTTGAAATAGAT-ATACATGATA
1 AATTT-AAATA-ATAATACATGATA
20747315 AATTTAAAATAAT
1 AATTT-AAATAAT
20747328 GTTAAAGATG
Statistics
Matches: 117, Mismatches: 21, Indels: 28
0.70 0.13 0.17
Matches are distributed among these distances:
20 4 0.03
21 15 0.13
22 16 0.14
23 16 0.14
24 53 0.45
25 12 0.10
26 1 0.01
ACGTcount: A:0.54, C:0.05, G:0.06, T:0.35
Consensus pattern (23 bp):
AATTTAAATAATAATACATGATA
Found at i:20747248 original size:69 final size:69
Alignment explanation
Indices: 20747174--20747327 Score: 172
Period size: 69 Copynumber: 2.2 Consensus size: 69
20747164 ATAATATATA
* * *
20747174 ATAAATTTGAAATAATAATACAT-ATAAAATTTAAAAATTTTGATGAT-AATTCT-AGAATA-AT
1 ATAAATTTAAAATAATAATACATAAT-AAATTTAAAAATATTAATGATAAATT-TGA-AATAGAT
*
20747235 CATACGTG
63 -ATACATG
** * *
20747243 ATAAATCCAAAATAATAGTATATAATAAATTTAAAAATATTAATGATAAATTTGAAATAGATATA
1 ATAAATTTAAAATAATAATACATAATAAATTTAAAAATATTAATGATAAATTTGAAATAGATATA
20747308 CATG
66 CATG
20747312 ATAAATTTAAAATAAT
1 ATAAATTTAAAATAAT
20747328 GTTAAAGATG
Statistics
Matches: 71, Mismatches: 10, Indels: 8
0.80 0.11 0.09
Matches are distributed among these distances:
69 62 0.87
70 9 0.13
ACGTcount: A:0.53, C:0.05, G:0.07, T:0.35
Consensus pattern (69 bp):
ATAAATTTAAAATAATAATACATAATAAATTTAAAAATATTAATGATAAATTTGAAATAGATATA
CATG
Found at i:20748078 original size:20 final size:20
Alignment explanation
Indices: 20748045--20748107 Score: 83
Period size: 19 Copynumber: 3.1 Consensus size: 20
20748035 TTTGATTTCT
20748045 TTTTTCCTCCCTTTACACTGA
1 TTTTTCC-CCCTTTACACTGA
** *
20748066 TTTTTTTCTCTTTACACTGA
1 TTTTTCCCCCTTTACACTGA
20748086 -TTTTCCCCCTTTACACTGA
1 TTTTTCCCCCTTTACACTGA
20748105 TTT
1 TTT
20748108 CCTCCCTTTT
Statistics
Matches: 35, Mismatches: 6, Indels: 3
0.80 0.14 0.07
Matches are distributed among these distances:
19 16 0.46
20 14 0.40
21 5 0.14
ACGTcount: A:0.14, C:0.29, G:0.05, T:0.52
Consensus pattern (20 bp):
TTTTTCCCCCTTTACACTGA
Found at i:20748097 original size:19 final size:20
Alignment explanation
Indices: 20748046--20748116 Score: 101
Period size: 20 Copynumber: 3.6 Consensus size: 20
20748036 TTGATTTCTT
20748046 TTTTCCTCCCTTTACACTGA
1 TTTTCCTCCCTTTACACTGA
** *
20748066 TTTTTTTCTCTTTACACTGA
1 TTTTCCTCCCTTTACACTGA
20748086 TTTTCC-CCCTTTACACTGA
1 TTTTCCTCCCTTTACACTGA
20748105 -TTTCCTCCCTTT
1 TTTTCCTCCCTTT
20748117 TTTATGAATA
Statistics
Matches: 44, Mismatches: 6, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
18 5 0.11
19 18 0.41
20 21 0.48
ACGTcount: A:0.13, C:0.32, G:0.04, T:0.51
Consensus pattern (20 bp):
TTTTCCTCCCTTTACACTGA
Found at i:20750380 original size:21 final size:21
Alignment explanation
Indices: 20750354--20750393 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
20750344 TACATTTATG
20750354 GGCATTAAAACAAGCCTACGA
1 GGCATTAAAACAAGCCTACGA
* *
20750375 GGCATTCAAACGAGCCTAC
1 GGCATTAAAACAAGCCTAC
20750394 AATGCCTTAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.38, C:0.28, G:0.20, T:0.15
Consensus pattern (21 bp):
GGCATTAAAACAAGCCTACGA
Found at i:20751249 original size:38 final size:37
Alignment explanation
Indices: 20751202--20751343 Score: 153
Period size: 38 Copynumber: 3.7 Consensus size: 37
20751192 CACTGGCACG
20751202 AAGCCTGCTAGGCATC-AAGCCTGATAAACTCTGGCATA
1 AAGCCTGCTAGGC-TCAAAGCCTGATAAACTC-GGCATA
* * * *
20751240 AAGCTTGCTACGCATC-AAGCCTGATAAACATCGGAACA
1 AAGCCTGCTAGGC-TCAAAGCCTGATAAAC-TCGGCATA
* * *
20751278 AAGCCTGCTAGGCTCAAAGCCCGATAAGTCTCCGGCATG
1 AAGCCTGCTAGGCTCAAAGCCTGATAA-ACT-CGGCATA
20751317 AAGCCTGCTAGGCTCAAAGCCTGATAA
1 AAGCCTGCTAGGCTCAAAGCCTGATAA
20751344 GTCACTAGCA
Statistics
Matches: 88, Mismatches: 12, Indels: 7
0.82 0.11 0.07
Matches are distributed among these distances:
37 2 0.02
38 53 0.60
39 33 0.38
ACGTcount: A:0.32, C:0.27, G:0.22, T:0.19
Consensus pattern (37 bp):
AAGCCTGCTAGGCTCAAAGCCTGATAAACTCGGCATA
Found at i:20751326 original size:39 final size:39
Alignment explanation
Indices: 20751275--20751461 Score: 169
Period size: 39 Copynumber: 4.7 Consensus size: 39
20751265 AAACATCGGA
* *
20751275 ACAAAGCCTGCTAGGCTCAAAGCCCGATAAGTCTCCGGC
1 ACAAAGCCTGCTAGGCTCAAAGCCCGATAAGTCACCAGC
** * *
20751314 ATGAAGCCTGCTAGGCTCAAAGCCTGATAAGTCACTAGC
1 ACAAAGCCTGCTAGGCTCAAAGCCCGATAAGTCACCAGC
* * * *
20751353 ACAAAGCTTGTTGGGCTCAAAGCCCGATAAGTCACTAGC
1 ACAAAGCCTGCTAGGCTCAAAGCCCGATAAGTCACCAGC
* * * * *
20751392 ACGAGGCCTGCTAGGCTCAAGGCTCGATACAATACACC-GAC
1 ACAAAGCCTGCTAGGCTCAAAGCCCGATA-AGT-CACCAG-C
* * * *
20751433 ATAAAGCCTGCTAGACCCAAGGCCCGATA
1 ACAAAGCCTGCTAGGCTCAAAGCCCGATA
20751462 CAATGCACCG
Statistics
Matches: 118, Mismatches: 27, Indels: 4
0.79 0.18 0.03
Matches are distributed among these distances:
39 88 0.75
40 3 0.03
41 27 0.23
ACGTcount: A:0.30, C:0.29, G:0.23, T:0.17
Consensus pattern (39 bp):
ACAAAGCCTGCTAGGCTCAAAGCCCGATAAGTCACCAGC
Found at i:20751454 original size:41 final size:41
Alignment explanation
Indices: 20751397--20751477 Score: 117
Period size: 41 Copynumber: 2.0 Consensus size: 41
20751387 CTAGCACGAG
* * *
20751397 GCCTGCTAGGCTCAAGGCTCGATACAATACACCGACATAAA
1 GCCTGCTAGACCCAAGGCCCGATACAATACACCGACATAAA
* *
20751438 GCCTGCTAGACCCAAGGCCCGATACAATGCACCGCCATAA
1 GCCTGCTAGACCCAAGGCCCGATACAATACACCGACATAA
20751478 CAACTCAATT
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
41 35 1.00
ACGTcount: A:0.32, C:0.33, G:0.20, T:0.15
Consensus pattern (41 bp):
GCCTGCTAGACCCAAGGCCCGATACAATACACCGACATAAA
Found at i:20752100 original size:43 final size:41
Alignment explanation
Indices: 20752047--20752322 Score: 241
Period size: 42 Copynumber: 6.6 Consensus size: 41
20752037 CAAACAAAAA
* *
20752047 CGCCACTAAAGAACATGATCTTTAGCGGCGTTTTTTTTCTAAG
1 CGCCGCTAAAGAACATGATCTTTAGCGGCG--TTTTTTATAAG
*
20752090 CGCCGCTAAAGAAAATGATCTTTAGCGGCGTTTTTT-TAAG
1 CGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTATAAG
* *
20752130 CGCCGCTAAAGAACATGATCTTTAGTGGCGATTTTTATTAAG
1 CGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTA-TAAG
* * * ** *
20752172 TGCCGCTGAAA-ATCATGTTCTTTAGCGGCGTTTGTGAATATG
1 CGCCGCT-AAAGAACATGATCTTTAGCGGCGTTT-TTTATAAG
* * * * * *
20752214 CGCCGCTAAAGAACATGTTCTTTAACGGCGCTTTGTAAAAAA
1 CGCCGCTAAAGAACATGATCTTTAGCGGCG-TTTTTTATAAG
* * * * * *
20752256 CGTCGCTAGAGATCATGATATTTAGCGGCGCTTTTTTTACAAA
1 CGCCGCTAAAGAACATGATCTTTAGCGGCG--TTTTTTATAAG
**
20752299 CATCGCTAAAGAACATGATCTTTA
1 CGCCGCTAAAGAACATGATCTTTA
20752323 CCGACGCTTT
Statistics
Matches: 191, Mismatches: 35, Indels: 14
0.80 0.15 0.06
Matches are distributed among these distances:
40 37 0.19
41 9 0.05
42 81 0.42
43 64 0.34
ACGTcount: A:0.28, C:0.19, G:0.21, T:0.33
Consensus pattern (41 bp):
CGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTATAAG
Found at i:20752331 original size:43 final size:43
Alignment explanation
Indices: 20752217--20752343 Score: 130
Period size: 43 Copynumber: 3.0 Consensus size: 43
20752207 GAATATGCGC
* *
20752217 CGCTAAAGAACATGTTCTTTAACGGCGC-TTTGTAAAAAACGT
1 CGCTAAAGAACATGATCTTTAACGGCGCTTTTGTAAAAAACAT
* * * * * * *
20752259 CGCTAGAGATCATGATATTTAGCGGCGCTTTTTTTACAAACAT
1 CGCTAAAGAACATGATCTTTAACGGCGCTTTTGTAAAAAACAT
* * *
20752302 CGCTAAAGAACATGATCTTTACCGACGCTTTTATACAAAAAC
1 CGCTAAAGAACATGATCTTTAACGGCGCTTTTGTA-AAAAAC
20752344 GCCACTATTT
Statistics
Matches: 66, Mismatches: 17, Indels: 2
0.78 0.20 0.02
Matches are distributed among these distances:
42 23 0.35
43 38 0.58
44 5 0.08
ACGTcount: A:0.33, C:0.20, G:0.17, T:0.30
Consensus pattern (43 bp):
CGCTAAAGAACATGATCTTTAACGGCGCTTTTGTAAAAAACAT
Found at i:20758343 original size:16 final size:15
Alignment explanation
Indices: 20758321--20758363 Score: 59
Period size: 16 Copynumber: 2.7 Consensus size: 15
20758311 GTTGTTCACT
*
20758321 TTTTTATGTAAGTTG
1 TTTTTATGTAAGTTA
20758336 TATTTTATGTAAGTTA
1 T-TTTTATGTAAGTTA
20758352 TTTATTATGTAA
1 TTT-TTATGTAA
20758364 ACTACGTAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
15 3 0.12
16 22 0.88
ACGTcount: A:0.28, C:0.00, G:0.14, T:0.58
Consensus pattern (15 bp):
TTTTTATGTAAGTTA
Found at i:20758399 original size:66 final size:66
Alignment explanation
Indices: 20758325--20758521 Score: 245
Period size: 66 Copynumber: 3.0 Consensus size: 66
20758315 TTCACTTTTT
* * *
20758325 TATGTAAGTTGTATTTTATGTAAGTTATTTATTATGTAAACTACGTAAATTGTGTAGAATGTAAG
1 TATGTAAGTTGTATTTTATGTAAGTTATTTATTATGTAAGCTAAGTAAGTTGTGTAGAATGTAAG
20758390 C
66 C
* **
20758391 TATGTAAGTTGTATTTTATGTAAGTTATTTATTATGTAAGCTAAGTAAGTTGAGTATTATGTAAG
1 TATGTAAGTTGTATTTTATGTAAGTTATTTATTATGTAAGCTAAGTAAGTTGTGTAGAATGTAAG
20758456 C
66 C
* * * * * * *
20758457 TATGT-A-TTATATTAGTTATGTAAATTATGTATTATGTATGTTATGTAAGTTCTGTAGAATGTA
1 TATGTAAGTTGTATT--TTATGTAAGTTATTTATTATGTAAGCTAAGTAAGTTGTGTAGAATGTA
20758520 AG
64 AG
20758522 TTATCTTAAT
Statistics
Matches: 113, Mismatches: 16, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
64 6 0.05
65 1 0.01
66 106 0.94
ACGTcount: A:0.32, C:0.03, G:0.19, T:0.46
Consensus pattern (66 bp):
TATGTAAGTTGTATTTTATGTAAGTTATTTATTATGTAAGCTAAGTAAGTTGTGTAGAATGTAAG
C
Found at i:20758410 original size:16 final size:16
Alignment explanation
Indices: 20758391--20758430 Score: 55
Period size: 16 Copynumber: 2.5 Consensus size: 16
20758381 GAATGTAAGC
*
20758391 TATGTAAGTTGTATT-T
1 TATGTAAGTTAT-TTAT
20758407 TATGTAAGTTATTTAT
1 TATGTAAGTTATTTAT
20758423 TATGTAAG
1 TATGTAAG
20758431 CTAAGTAAGT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 2 0.09
16 20 0.91
ACGTcount: A:0.30, C:0.00, G:0.17, T:0.53
Consensus pattern (16 bp):
TATGTAAGTTATTTAT
Found at i:20758428 original size:41 final size:41
Alignment explanation
Indices: 20758383--20758466 Score: 116
Period size: 41 Copynumber: 2.0 Consensus size: 41
20758373 ATTGTGTAGA
* * * *
20758383 ATGTAAGCTATGTAAGTTGTA-TTTTATGTAAGTTATTTATT
1 ATGTAAGCTAAGTAAGTTG-AGTATTATGTAAGCTATGTATT
20758424 ATGTAAGCTAAGTAAGTTGAGTATTATGTAAGCTATGTATT
1 ATGTAAGCTAAGTAAGTTGAGTATTATGTAAGCTATGTATT
20758465 AT
1 AT
20758467 ATTAGTTATG
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
40 1 0.03
41 37 0.97
ACGTcount: A:0.32, C:0.04, G:0.19, T:0.45
Consensus pattern (41 bp):
ATGTAAGCTAAGTAAGTTGAGTATTATGTAAGCTATGTATT
Found at i:20758438 original size:25 final size:25
Alignment explanation
Indices: 20758410--20758479 Score: 74
Period size: 25 Copynumber: 2.8 Consensus size: 25
20758400 TGTATTTTAT
20758410 GTAAGTTATTTATTATGTAAGCTAA
1 GTAAGTTATTTATTATGTAAGCTAA
* *
20758435 GTAAGTTGA-GTATTATGTAAGCTAT
1 GTAAGTT-ATTTATTATGTAAGCTAA
20758460 GT-A-TTATATTAGTTATGTAA
1 GTAAGTTAT-TTA-TTATGTAA
20758480 ATTATGTATT
Statistics
Matches: 38, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
22 1 0.03
23 2 0.05
24 3 0.08
25 31 0.82
26 1 0.03
ACGTcount: A:0.34, C:0.03, G:0.19, T:0.44
Consensus pattern (25 bp):
GTAAGTTATTTATTATGTAAGCTAA
Found at i:20758512 original size:25 final size:25
Alignment explanation
Indices: 20758447--20758512 Score: 80
Period size: 25 Copynumber: 2.6 Consensus size: 25
20758437 AAGTTGAGTA
*
20758447 TTATGTAAGCTATGTATTATATTAG
1 TTATGTAAGTTATGTATTATATTAG
* *
20758472 TTATGTAAATTATGTATTAT-GTATG
1 TTATGTAAGTTATGTATTATATTA-G
*
20758497 TTATGTAAGTTCTGTA
1 TTATGTAAGTTATGTA
20758513 GAATGTAAGT
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
24 2 0.06
25 33 0.94
ACGTcount: A:0.30, C:0.03, G:0.17, T:0.50
Consensus pattern (25 bp):
TTATGTAAGTTATGTATTATATTAG
Found at i:20758518 original size:25 final size:25
Alignment explanation
Indices: 20758470--20758525 Score: 67
Period size: 25 Copynumber: 2.2 Consensus size: 25
20758460 GTATTATATT
**
20758470 AGTTATGTAAATTATGTATTATGTA
1 AGTTATGTAAATTATGTAGAATGTA
* * *
20758495 TGTTATGTAAGTTCTGTAGAATGTA
1 AGTTATGTAAATTATGTAGAATGTA
20758520 AGTTAT
1 AGTTAT
20758526 CTTAATTTTA
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.32, C:0.02, G:0.20, T:0.46
Consensus pattern (25 bp):
AGTTATGTAAATTATGTAGAATGTA
Found at i:20758584 original size:40 final size:40
Alignment explanation
Indices: 20758534--20758610 Score: 145
Period size: 40 Copynumber: 1.9 Consensus size: 40
20758524 ATCTTAATTT
20758534 TATGTAGGTTATGCAAGTTATGTAATGTATCAATTTTATG
1 TATGTAGGTTATGCAAGTTATGTAATGTATCAATTTTATG
*
20758574 TATGTAGGTTATGCAAGTTATGTATTGTATCAATTTT
1 TATGTAGGTTATGCAAGTTATGTAATGTATCAATTTT
20758611 TAAAAATATA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
40 36 1.00
ACGTcount: A:0.29, C:0.05, G:0.19, T:0.47
Consensus pattern (40 bp):
TATGTAGGTTATGCAAGTTATGTAATGTATCAATTTTATG
Found at i:20760156 original size:27 final size:29
Alignment explanation
Indices: 20760102--20760156 Score: 78
Period size: 30 Copynumber: 1.9 Consensus size: 29
20760092 TAATTATCAC
*
20760102 AACAATCAACTTAATAATAATTGATAAAGT
1 AACAATCAACTTAATAATAAAT-ATAAAGT
20760132 AACAATCAACTTAAT-ATAAAT-TAAA
1 AACAATCAACTTAATAATAAATATAAA
20760157 TTAGAAACTT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
27 4 0.17
29 5 0.21
30 15 0.62
ACGTcount: A:0.56, C:0.11, G:0.04, T:0.29
Consensus pattern (29 bp):
AACAATCAACTTAATAATAAATATAAAGT
Found at i:20761942 original size:8 final size:7
Alignment explanation
Indices: 20761927--20761989 Score: 56
Period size: 7 Copynumber: 8.9 Consensus size: 7
20761917 ATTAACTATA
20761927 AACCCCT
1 AACCCCT
20761934 AAGCCCCT
1 AA-CCCCT
20761942 AACCCC-
1 AACCCCT
* *
20761948 AGCCCTT
1 AACCCCT
*
20761955 AACCCTT
1 AACCCCT
20761962 AACCCCT
1 AACCCCT
*
20761969 AAACCCTT
1 -AACCCCT
*
20761977 AACCCTT
1 AACCCCT
20761984 AACCCC
1 AACCCC
20761990 AATCCTTAAA
Statistics
Matches: 47, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
6 4 0.09
7 30 0.64
8 13 0.28
ACGTcount: A:0.29, C:0.51, G:0.03, T:0.17
Consensus pattern (7 bp):
AACCCCT
Found at i:20761947 original size:15 final size:14
Alignment explanation
Indices: 20761927--20761989 Score: 56
Period size: 15 Copynumber: 4.4 Consensus size: 14
20761917 ATTAACTATA
20761927 AACCCCTAAGCCCCT
1 AACCCCTAA-CCCCT
* *
20761942 AACCCC-AGCCCTT
1 AACCCCTAACCCCT
*
20761955 AACCCTTAACCCCT
1 AACCCCTAACCCCT
* *
20761969 AAACCCTTAACCCTT
1 -AACCCCTAACCCCT
20761984 AACCCC
1 AACCCC
20761990 AATCCTTAAA
Statistics
Matches: 39, Mismatches: 7, Indels: 5
0.76 0.14 0.10
Matches are distributed among these distances:
13 9 0.23
14 11 0.28
15 19 0.49
ACGTcount: A:0.29, C:0.51, G:0.03, T:0.17
Consensus pattern (14 bp):
AACCCCTAACCCCT
Found at i:20761960 original size:7 final size:7
Alignment explanation
Indices: 20761950--20761988 Score: 60
Period size: 7 Copynumber: 5.4 Consensus size: 7
20761940 CTAACCCCAG
20761950 CCCTTAA
1 CCCTTAA
20761957 CCCTTAA
1 CCCTTAA
*
20761964 CCCCTAAA
1 -CCCTTAA
20761972 CCCTTAA
1 CCCTTAA
20761979 CCCTTAA
1 CCCTTAA
20761986 CCC
1 CCC
20761989 CAATCCTTAA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
7 23 0.79
8 6 0.21
ACGTcount: A:0.28, C:0.49, G:0.00, T:0.23
Consensus pattern (7 bp):
CCCTTAA
Found at i:20762893 original size:114 final size:114
Alignment explanation
Indices: 20762641--20762993 Score: 333
Period size: 114 Copynumber: 3.1 Consensus size: 114
20762631 TCCTATATTT
* * * * *
20762641 TGCGGCGTTTTT-AGACAAGCGCCACTAAAGTCTCTAAAACCTAAATTAAAAATGACATCGTTTT
1 TGCGGCGTTTTTCAGAAAAGCGCCACTAAAGTCTCCAAAACCTAAATGAAAAATGGCAACGTTTT
* * * * * **
20762705 CTTAACAGTTTTGCAGCACTTGTGATAAAGCACCACTAAAGCTTCGCTAA
66 CTTAACAGTTTTGCGGCGCTTATGATAAAGCGCCGCTAATTCTT-GCTAA
* ** * **
20762755 TGCGGCG-TTTTCTGAAAATTGCCACTAACA-TCTCGAAAAGATAAATGAAAAATGGCAACGTTT
1 TGCGGCGTTTTTCAGAAAAGCGCCACTAA-AGTCTCCAAAACCTAAATGAAAAATGGCAACGTTT
20762818 TCTTAACAGTTTTGCGGCGCTTATGATAAAGCGCCGCTAATTCTTGACT-A
65 TCTTAACAGTTTTGCGGCGCTTATGATAAAGCGCCGCTAATTCTTG-CTAA
* * * * *
20762868 TAGCGGCGTTTTTCAG-TAAGCGCCACTAAAGTCCCCAAAACCTAAACTG-AAAACGGCAGCATT
1 T-GCGGCGTTTTTCAGAAAAGCGCCACTAAAGTCTCCAAAACCTAAA-TGAAAAATGGCAACGTT
* * * *
20762931 TTCTTAACAGTTTTTGCGGCGTTTATGACCAAA-CGCCGGTAATTCTTGCATAT
64 TTCTTAACAG-TTTTGCGGCGCTTATGA-TAAAGCGCCGCTAATTCTTGC-TAA
*
20762984 TGCGGTGTTT
1 TGCGGCGTTT
20762994 CTAAGAAAGG
Statistics
Matches: 195, Mismatches: 33, Indels: 21
0.78 0.13 0.08
Matches are distributed among these distances:
113 8 0.04
114 135 0.69
115 48 0.25
116 4 0.02
ACGTcount: A:0.30, C:0.22, G:0.19, T:0.30
Consensus pattern (114 bp):
TGCGGCGTTTTTCAGAAAAGCGCCACTAAAGTCTCCAAAACCTAAATGAAAAATGGCAACGTTTT
CTTAACAGTTTTGCGGCGCTTATGATAAAGCGCCGCTAATTCTTGCTAA
Found at i:20763850 original size:22 final size:22
Alignment explanation
Indices: 20763825--20763891 Score: 98
Period size: 26 Copynumber: 2.9 Consensus size: 22
20763815 CATAATTAAC
20763825 TATTTTATGCAATTAACACCCT
1 TATTTTATGCAATTAACACCCT
20763847 TATTTTTATGTTGCAATTAACACCCT
1 TA-TTTTA---TGCAATTAACACCCT
20763873 TATTTTATGCAATTAACAC
1 TATTTTATGCAATTAACAC
20763892 TCAATTATCA
Statistics
Matches: 41, Mismatches: 0, Indels: 8
0.84 0.00 0.16
Matches are distributed among these distances:
22 14 0.34
23 5 0.12
25 5 0.12
26 17 0.41
ACGTcount: A:0.31, C:0.19, G:0.06, T:0.43
Consensus pattern (22 bp):
TATTTTATGCAATTAACACCCT
Found at i:20773145 original size:17 final size:19
Alignment explanation
Indices: 20773099--20773134 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
20773089 ATATATAAAA
20773099 AATC-AGAAAAATATATAT
1 AATCTAGAAAAATATATAT
*
20773117 TATCTAGAAAAATATATA
1 AATCTAGAAAAATATATA
20773135 AATTATAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 3 0.19
19 13 0.81
ACGTcount: A:0.58, C:0.06, G:0.06, T:0.31
Consensus pattern (19 bp):
AATCTAGAAAAATATATAT
Found at i:20773495 original size:31 final size:32
Alignment explanation
Indices: 20773437--20773498 Score: 81
Period size: 31 Copynumber: 2.0 Consensus size: 32
20773427 ACCACTATTG
* *
20773437 GTCAATATTCGATCAACGCTTGGTCAACAACA
1 GTCAATATTCGATCAACGCTCGATCAACAACA
* *
20773469 GTCAATATT-GATCAATGGTCGATCAACAAC
1 GTCAATATTCGATCAACGCTCGATCAACAAC
20773499 CGATCAAAGT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
31 17 0.65
32 9 0.35
ACGTcount: A:0.35, C:0.23, G:0.16, T:0.26
Consensus pattern (32 bp):
GTCAATATTCGATCAACGCTCGATCAACAACA
Found at i:20777369 original size:12 final size:12
Alignment explanation
Indices: 20777352--20777404 Score: 52
Period size: 12 Copynumber: 4.2 Consensus size: 12
20777342 ATCAACTTGC
20777352 CCTTGTGAGTAA
1 CCTTGTGAGTAA
***
20777364 CCTTGTTTTTTAA
1 CCTTG-TGAGTAA
20777377 CAACTTGTGAGTAA
1 C--CTTGTGAGTAA
20777391 CCTTGTGAGTAA
1 CCTTGTGAGTAA
20777403 CC
1 CC
20777405 ATTCAAACCA
Statistics
Matches: 32, Mismatches: 6, Indels: 6
0.73 0.14 0.14
Matches are distributed among these distances:
12 18 0.56
13 5 0.16
14 5 0.16
15 4 0.12
ACGTcount: A:0.25, C:0.19, G:0.19, T:0.38
Consensus pattern (12 bp):
CCTTGTGAGTAA
Found at i:20778824 original size:29 final size:29
Alignment explanation
Indices: 20778782--20778843 Score: 124
Period size: 29 Copynumber: 2.1 Consensus size: 29
20778772 TGGATAGTAT
20778782 GTTCGATACGTGCTCGCAATAATCCGATA
1 GTTCGATACGTGCTCGCAATAATCCGATA
20778811 GTTCGATACGTGCTCGCAATAATCCGATA
1 GTTCGATACGTGCTCGCAATAATCCGATA
20778840 GTTC
1 GTTC
20778844 CCAAGTAAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 33 1.00
ACGTcount: A:0.26, C:0.24, G:0.21, T:0.29
Consensus pattern (29 bp):
GTTCGATACGTGCTCGCAATAATCCGATA
Found at i:20783385 original size:45 final size:45
Alignment explanation
Indices: 20783334--20783440 Score: 162
Period size: 45 Copynumber: 2.4 Consensus size: 45
20783324 TGTTCAATTA
20783334 GTTTGACTCTCTTCTTGA-TTGGTTAGTTGGGAGTCAACCAGATTG
1 GTTTGACTCTCTTCTTGACTT-GTTAGTTGGGAGTCAACCAGATTG
*
20783379 GTTTGACTCTCTTCTTGACTTGTTAGTTGGGAGTTAACCAGATTG
1 GTTTGACTCTCTTCTTGACTTGTTAGTTGGGAGTCAACCAGATTG
* * *
20783424 ATTTGGCTCTATTCTTG
1 GTTTGACTCTCTTCTTG
20783441 GCTGGTCTAC
Statistics
Matches: 57, Mismatches: 4, Indels: 2
0.90 0.06 0.03
Matches are distributed among these distances:
45 55 0.96
46 2 0.04
ACGTcount: A:0.17, C:0.16, G:0.24, T:0.43
Consensus pattern (45 bp):
GTTTGACTCTCTTCTTGACTTGTTAGTTGGGAGTCAACCAGATTG
Found at i:20800549 original size:14 final size:14
Alignment explanation
Indices: 20800530--20800558 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
20800520 GAGATAATAG
20800530 ACATGATTTAGTAA
1 ACATGATTTAGTAA
20800544 ACATGATTTAGTAA
1 ACATGATTTAGTAA
20800558 A
1 A
20800559 GTATGCAATT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.45, C:0.07, G:0.14, T:0.34
Consensus pattern (14 bp):
ACATGATTTAGTAA
Found at i:20802068 original size:16 final size:17
Alignment explanation
Indices: 20802043--20802075 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
20802033 TTCATCACAC
*
20802043 TTAGGTTAA-TTTGCAT
1 TTAGGATAATTTTGCAT
20802059 TTAGGATAATTTTGCAT
1 TTAGGATAATTTTGCAT
20802076 CTAGTTATTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.27, C:0.06, G:0.18, T:0.48
Consensus pattern (17 bp):
TTAGGATAATTTTGCAT
Found at i:20803763 original size:39 final size:40
Alignment explanation
Indices: 20803696--20803838 Score: 150
Period size: 39 Copynumber: 3.6 Consensus size: 40
20803686 ATTGTATGAT
*
20803696 TGCACAT-CGTGCCCCTGTTTGTACTTCGGTACCCCTGAA
1 TGCACATACATGCCCCTGTTTGTACTTCGGTACCCCTGAA
* * * *
20803735 TGTATATACATGCCCC-GTTTGTATTTCGGTACCCCTGAT
1 TGCACATACATGCCCCTGTTTGTACTTCGGTACCCCTGAA
* * *
20803774 TGCACATACGTGCCCCTGTTTGTAC-TCTGGTACCCTTGAT
1 TGCACATACATGCCCCTGTTTGTACTTC-GGTACCCCTGAA
* * *
20803814 TGCAC-TACGTGCTCCTGTTTATACT
1 TGCACATACATGCCCCTGTTTGTACT
20803839 ATATTAACTT
Statistics
Matches: 88, Mismatches: 12, Indels: 7
0.82 0.11 0.07
Matches are distributed among these distances:
39 58 0.66
40 30 0.34
ACGTcount: A:0.16, C:0.29, G:0.19, T:0.36
Consensus pattern (40 bp):
TGCACATACATGCCCCTGTTTGTACTTCGGTACCCCTGAA
Found at i:20804837 original size:73 final size:73
Alignment explanation
Indices: 20804718--20804860 Score: 268
Period size: 73 Copynumber: 2.0 Consensus size: 73
20804708 ACGATTTGCT
*
20804718 TTTAAGTTATTTTCAAGGCCTCAAAGGCTAGTTTTAGGGATAATATGCATGTATATGAATGGTTT
1 TTTAAGTTATTTTCAAGGCCTCAAAGGCTAGTTTTAGGGACAATATGCATGTATATGAATGGTTT
20804783 ATGATATA
66 ATGATATA
*
20804791 TTTAAGTTATTTTCAAGGCCTCAAAGGCTCGTTTTAGGGACAATATGCATGTATATGAATGGTTT
1 TTTAAGTTATTTTCAAGGCCTCAAAGGCTAGTTTTAGGGACAATATGCATGTATATGAATGGTTT
20804856 ATGAT
66 ATGAT
20804861 TGTAAGGTGT
Statistics
Matches: 68, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
73 68 1.00
ACGTcount: A:0.30, C:0.10, G:0.21, T:0.39
Consensus pattern (73 bp):
TTTAAGTTATTTTCAAGGCCTCAAAGGCTAGTTTTAGGGACAATATGCATGTATATGAATGGTTT
ATGATATA
Found at i:20818832 original size:23 final size:24
Alignment explanation
Indices: 20818784--20818832 Score: 64
Period size: 26 Copynumber: 2.0 Consensus size: 24
20818774 TGACCCACAA
*
20818784 CTCGTGTGAGCAGGCCTATTTCAAAG
1 CTCGTGTGAGCA-G-CTATTTAAAAG
20818810 CTCGTGTGAGCA-CTATTTAAAAG
1 CTCGTGTGAGCAGCTATTTAAAAG
20818833 GAAAGGTTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
23 10 0.45
26 12 0.55
ACGTcount: A:0.27, C:0.20, G:0.24, T:0.29
Consensus pattern (24 bp):
CTCGTGTGAGCAGCTATTTAAAAG
Found at i:20823936 original size:19 final size:19
Alignment explanation
Indices: 20823903--20823942 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
20823893 AAAATATAAT
*
20823903 ATTAATTTTAATTTATTTG
1 ATTAATTTTAATTTACTTG
20823922 ATTAA-TTTAATTTTACTTG
1 ATTAATTTTAA-TTTACTTG
20823941 AT
1 AT
20823943 CAAAATTAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 5 0.26
19 14 0.74
ACGTcount: A:0.33, C:0.03, G:0.05, T:0.60
Consensus pattern (19 bp):
ATTAATTTTAATTTACTTG
Found at i:20830293 original size:31 final size:31
Alignment explanation
Indices: 20830250--20830319 Score: 113
Period size: 31 Copynumber: 2.3 Consensus size: 31
20830240 CCGTGTCTAA
*
20830250 GGCCATGTGGACATTCGAAATAGGGATACAC
1 GGCCGTGTGGACATTCGAAATAGGGATACAC
*
20830281 GGCCGTGTGGACATTCGAAATAGGTATACAC
1 GGCCGTGTGGACATTCGAAATAGGGATACAC
*
20830312 GACCGTGT
1 GGCCGTGT
20830320 CTAAACATGT
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
31 36 1.00
ACGTcount: A:0.29, C:0.20, G:0.30, T:0.21
Consensus pattern (31 bp):
GGCCGTGTGGACATTCGAAATAGGGATACAC
Found at i:20832545 original size:26 final size:26
Alignment explanation
Indices: 20832509--20832568 Score: 95
Period size: 26 Copynumber: 2.3 Consensus size: 26
20832499 AAAGCTCTGG
20832509 AGAGCCATTAATCAGGAAGCTCAC-A
1 AGAGCCATTAATCAGGAAGCTCACGA
*
20832534 ATGAGCCTTTAATCAGGAAGCTCACGA
1 A-GAGCCATTAATCAGGAAGCTCACGA
20832561 AGAGCCAT
1 AGAGCCAT
20832569 ATATCGGGAT
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
25 1 0.03
26 28 0.90
27 2 0.06
ACGTcount: A:0.37, C:0.23, G:0.22, T:0.18
Consensus pattern (26 bp):
AGAGCCATTAATCAGGAAGCTCACGA
Found at i:20835668 original size:34 final size:34
Alignment explanation
Indices: 20835625--20835692 Score: 136
Period size: 34 Copynumber: 2.0 Consensus size: 34
20835615 TTTCACACTT
20835625 GTGAACTTAATCAATATAAATCTTATGAATTCCA
1 GTGAACTTAATCAATATAAATCTTATGAATTCCA
20835659 GTGAACTTAATCAATATAAATCTTATGAATTCCA
1 GTGAACTTAATCAATATAAATCTTATGAATTCCA
20835693 TTGTATAAGA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.41, C:0.15, G:0.09, T:0.35
Consensus pattern (34 bp):
GTGAACTTAATCAATATAAATCTTATGAATTCCA
Found at i:20842319 original size:17 final size:18
Alignment explanation
Indices: 20842290--20842324 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
20842280 TTCTCCTAAA
*
20842290 TTTCAATTTTATTTAATT
1 TTTCAATTTTATTAAATT
20842308 TTTCAA-TTTATTAAATT
1 TTTCAATTTTATTAAATT
20842325 ATTAATATTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 10 0.62
18 6 0.38
ACGTcount: A:0.31, C:0.06, G:0.00, T:0.63
Consensus pattern (18 bp):
TTTCAATTTTATTAAATT
Found at i:20844550 original size:13 final size:13
Alignment explanation
Indices: 20844534--20844558 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
20844524 AAAATACAAG
20844534 AAAAAAAGAGAGA
1 AAAAAAAGAGAGA
20844547 AAAAAAAGAGAG
1 AAAAAAAGAGAG
20844559 CATATGTACT
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:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (13 bp):
AAAAAAAGAGAGA
Found at i:20847866 original size:3 final size:3
Alignment explanation
Indices: 20847858--20847923 Score: 114
Period size: 3 Copynumber: 22.0 Consensus size: 3
20847848 TGTTATTAAG
*
20847858 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TCA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
*
20847906 TTA TCA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA
20847924 CTATATATAC
Statistics
Matches: 59, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 59 1.00
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.64
Consensus pattern (3 bp):
TTA
Found at i:20848067 original size:102 final size:103
Alignment explanation
Indices: 20847890--20848094 Score: 403
Period size: 102 Copynumber: 2.0 Consensus size: 103
20847880 TATTATTATT
20847890 ATTATTATTATTATCATTATCATTATTATTATTACTATATATACATACGCATATTTTTTTTACAA
1 ATTATTATTATTATCATTATCATTATTATTATTACTATATATACATACGCATATTTTTTTTACAA
20847955 TAATATATATACATACATTTGTTTAAAACATTTCATTA
66 TAATATATATACATACATTTGTTTAAAACATTTCATTA
20847993 ATTATTATTA-TATCATTATCATTATTATTATTACTATATATACATACGCATATTTTTTTTACAA
1 ATTATTATTATTATCATTATCATTATTATTATTACTATATATACATACGCATATTTTTTTTACAA
20848057 TAATATATATACATACATTTGTTTAAAACATTTCATTA
66 TAATATATATACATACATTTGTTTAAAACATTTCATTA
20848095 CAAATATGAA
Statistics
Matches: 102, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
102 92 0.90
103 10 0.10
ACGTcount: A:0.38, C:0.11, G:0.02, T:0.49
Consensus pattern (103 bp):
ATTATTATTATTATCATTATCATTATTATTATTACTATATATACATACGCATATTTTTTTTACAA
TAATATATATACATACATTTGTTTAAAACATTTCATTA
Found at i:20850859 original size:20 final size:19
Alignment explanation
Indices: 20850836--20850892 Score: 62
Period size: 20 Copynumber: 2.9 Consensus size: 19
20850826 GGGAGCACCG
20850836 ATGTGCTAAGCAGGGCACAA
1 ATGTGC-AAGCAGGGCACAA
* *
20850856 ATGTGCATAGAAGAGCACCAA
1 ATGTGCA-AGCAGGGCA-CAA
20850877 A-GTGCAAGCAGGGCAC
1 ATGTGCAAGCAGGGCAC
20850893 CAGAGTGCAT
Statistics
Matches: 31, Mismatches: 4, Indels: 6
0.76 0.10 0.15
Matches are distributed among these distances:
18 1 0.03
19 8 0.26
20 18 0.58
21 4 0.13
ACGTcount: A:0.37, C:0.21, G:0.30, T:0.12
Consensus pattern (19 bp):
ATGTGCAAGCAGGGCACAA
Found at i:20850894 original size:19 final size:19
Alignment explanation
Indices: 20850838--20850901 Score: 67
Period size: 19 Copynumber: 3.3 Consensus size: 19
20850828 GAGCACCGAT
20850838 GTGCTAAGCAGGGCA-CAAA
1 GTGC-AAGCAGGGCACCAAA
* *
20850857 TGTGCATAGAAGAGCACCAAA
1 -GTGCA-AGCAGGGCACCAAA
*
20850878 GTGCAAGCAGGGCACCAGA
1 GTGCAAGCAGGGCACCAAA
20850897 GTGCA
1 GTGCA
20850902 TAACAAGGAA
Statistics
Matches: 37, Mismatches: 5, Indels: 5
0.79 0.11 0.11
Matches are distributed among these distances:
19 17 0.46
20 16 0.43
21 4 0.11
ACGTcount: A:0.36, C:0.22, G:0.31, T:0.11
Consensus pattern (19 bp):
GTGCAAGCAGGGCACCAAA
Found at i:20850959 original size:19 final size:19
Alignment explanation
Indices: 20850897--20850961 Score: 78
Period size: 20 Copynumber: 3.3 Consensus size: 19
20850887 GGGCACCAGA
*
20850897 GTGCATAACAAGGAACATAT
1 GTGCA-AACAAGGCACATAT
*
20850917 GTGCAATCAGAGGCATCATA-
1 GTGCAAACA-AGGCA-CATAT
20850937 GTGCAAACAAGGCACATAT
1 GTGCAAACAAGGCACATAT
20850956 GTGCAA
1 GTGCAA
20850962 TCAAAAGTAA
Statistics
Matches: 39, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
18 4 0.10
19 14 0.36
20 17 0.44
21 4 0.10
ACGTcount: A:0.40, C:0.18, G:0.23, T:0.18
Consensus pattern (19 bp):
GTGCAAACAAGGCACATAT
Found at i:20850962 original size:39 final size:39
Alignment explanation
Indices: 20850878--20850964 Score: 122
Period size: 39 Copynumber: 2.2 Consensus size: 39
20850868 GAGCACCAAA
*
20850878 GTGCAAGCAGGGCACCAGAGTGCATAACAAGGAACATAT
1 GTGCAATCAGGGCACCAGAGTGCATAACAAGGAACATAT
* * *
20850917 GTGCAATCAGAGGCATCATAGTGCA-AACAAGGCACATAT
1 GTGCAATCAG-GGCACCAGAGTGCATAACAAGGAACATAT
20850956 GTGCAATCA
1 GTGCAATCA
20850965 AAAGTAATGT
Statistics
Matches: 43, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
39 31 0.72
40 12 0.28
ACGTcount: A:0.38, C:0.21, G:0.25, T:0.16
Consensus pattern (39 bp):
GTGCAATCAGGGCACCAGAGTGCATAACAAGGAACATAT
Found at i:20854782 original size:15 final size:16
Alignment explanation
Indices: 20854737--20854792 Score: 51
Period size: 16 Copynumber: 3.4 Consensus size: 16
20854727 AATAAGATTT
* *
20854737 AATATTAAATTTAATCT
1 AATATTATA-TTAATCA
*
20854754 AATATTTATCTTAA-CA
1 AATA-TTATATTAATCA
*
20854770 AATATTATATTAATTA
1 AATATTATATTAATCA
20854786 AATATTA
1 AATATTA
20854793 AAGTGATTAA
Statistics
Matches: 32, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
15 8 0.25
16 13 0.41
17 8 0.25
18 3 0.09
ACGTcount: A:0.48, C:0.05, G:0.00, T:0.46
Consensus pattern (16 bp):
AATATTATATTAATCA
Found at i:20863223 original size:24 final size:24
Alignment explanation
Indices: 20863191--20863237 Score: 94
Period size: 24 Copynumber: 2.0 Consensus size: 24
20863181 TAGTCGTTAG
20863191 GTGTACAAGCCAACTCATCAAACT
1 GTGTACAAGCCAACTCATCAAACT
20863215 GTGTACAAGCCAACTCATCAAAC
1 GTGTACAAGCCAACTCATCAAAC
20863238 ACCCTCTGAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.38, C:0.30, G:0.13, T:0.19
Consensus pattern (24 bp):
GTGTACAAGCCAACTCATCAAACT
Found at i:20865092 original size:19 final size:20
Alignment explanation
Indices: 20865068--20865109 Score: 77
Period size: 19 Copynumber: 2.1 Consensus size: 20
20865058 GTATTAAGGA
20865068 GCACCAAAGTGCA-AACAGG
1 GCACCAAAGTGCATAACAGG
20865087 GCACCAAAGTGCATAACAGG
1 GCACCAAAGTGCATAACAGG
20865107 GCA
1 GCA
20865110 TAGATTAGGG
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
19 13 0.59
20 9 0.41
ACGTcount: A:0.40, C:0.26, G:0.26, T:0.07
Consensus pattern (20 bp):
GCACCAAAGTGCATAACAGG
Found at i:20867116 original size:10 final size:10
Alignment explanation
Indices: 20867103--20867153 Score: 54
Period size: 10 Copynumber: 5.4 Consensus size: 10
20867093 TTTATACATA
*
20867103 TTTAATTAAT
1 TTTAATTATT
20867113 TTT-A-TATT
1 TTTAATTATT
**
20867121 TTTAACAATT
1 TTTAATTATT
20867131 TTT-ATTATT
1 TTTAATTATT
20867140 TTTAATTATT
1 TTTAATTATT
20867150 TTTA
1 TTTA
20867154 TAAATTTCCT
Statistics
Matches: 34, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
8 6 0.18
9 9 0.26
10 19 0.56
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.67
Consensus pattern (10 bp):
TTTAATTATT
Found at i:20867141 original size:19 final size:19
Alignment explanation
Indices: 20867112--20867154 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
20867102 ATTTAATTAA
20867112 TTTTA-TATTTTTAACAAT
1 TTTTATTATTTTTAACAAT
**
20867130 TTTTATTATTTTTAATTAT
1 TTTTATTATTTTTAACAAT
20867149 TTTTAT
1 TTTTAT
20867155 AAATTTCCTA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 5 0.23
19 17 0.77
ACGTcount: A:0.28, C:0.02, G:0.00, T:0.70
Consensus pattern (19 bp):
TTTTATTATTTTTAACAAT
Found at i:20872251 original size:16 final size:16
Alignment explanation
Indices: 20872232--20872274 Score: 54
Period size: 16 Copynumber: 2.7 Consensus size: 16
20872222 ATAGCTCTTA
20872232 TTCAAGACAT-ATGTTG
1 TTCAAGA-ATAATGTTG
20872248 TTCAAGAATAGATGTTG
1 TTCAAGAATA-ATGTTG
20872265 TTC-AGAATAA
1 TTCAAGAATAA
20872275 CCTCTACCAA
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
15 3 0.12
16 13 0.52
17 9 0.36
ACGTcount: A:0.37, C:0.09, G:0.19, T:0.35
Consensus pattern (16 bp):
TTCAAGAATAATGTTG
Done.