Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: chr3
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: 36364294
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 2168405 characters in sequence are not A, C, G, or T
File 57 of 91
Found at i:20398241 original size:22 final size:22
Alignment explanation
Indices: 20398214--20398294 Score: 63
Period size: 22 Copynumber: 3.5 Consensus size: 22
20398204 ATTTTTATTT
20398214 TAATTTATTTTTTAAATATTAA
1 TAATTTATTTTTTAAATATTAA
*
20398236 TAATTTATAATTAATTTAAAATACTAA
1 TAATTTAT--TT--TTT-AAATATTAA
* ** *
20398263 TAATTGATCATTCAAATATTAA
1 TAATTTATTTTTTAAATATTAA
*
20398285 TATTTTATTT
1 TAATTTATTT
20398295 ATAATTTAAA
Statistics
Matches: 44, Mismatches: 10, Indels: 10
0.69 0.16 0.16
Matches are distributed among these distances:
22 22 0.50
23 2 0.05
24 2 0.05
26 3 0.07
27 15 0.34
ACGTcount: A:0.43, C:0.04, G:0.01, T:0.52
Consensus pattern (22 bp):
TAATTTATTTTTTAAATATTAA
Found at i:20398282 original size:118 final size:118
Alignment explanation
Indices: 20397951--20398318 Score: 334
Period size: 118 Copynumber: 3.1 Consensus size: 118
20397941 TTATTATATA
* * * * *
20397951 TATGATTAATT-TTTTTATTTT-ATATTATTTTTTAAATGTTAATAATTTAAAATTTATTTTAAA
1 TATGATTATTTATTTTTATTTTAAT-TTATTTTTTAAATATTAATAATTTATAATTAATTTAAAA
* * * *
20398014 TATTAATACTTAATAATTTAAATATTAATC-TTTTATTAATATTTTAATAT-TAATT
65 TATTAATAATTAATAATTTAAATATTAA-CATTTTATTTATAATTTAA-ATGTTA-T
* * * * * * * * *
20398069 TATAAAATATTAATATTTTATTTATAATTTAGGTGTTATTATGACTATTTAT-TTTTAT-TTTAT
1 TAT-GATTATTTAT-TTTTATTT-TAATTTA--T-TT-TT-TAAATATTAATAATTTATAATTAA
* * *
20398132 TTTAAAATATTAATATTTTATAATTTAAATATTAACATTTAATTTATAATTTAAATGTTAT
58 TTTAAAATATTAATAATTAATAATTTAAATATTAACATTTTATTTATAATTTAAATGTTAT
20398193 TATGATTATTTATTTTTATTTTAATTTATTTTTTAAATATTAATAATTTATAATTAATTTAAAAT
1 TATGATTATTTATTTTTATTTTAATTTATTTTTTAAATATTAATAATTTATAATTAATTTAAAAT
* * * * * * *
20398258 ACTAATAATTGATCATTCAAATATTAATATTTTATTTATAATTTAAATGATAG
66 ATTAATAATTAATAATTTAAATATTAACATTTTATTTATAATTTAAATGTTAT
20398311 TATGATTA
1 TATGATTA
20398319 AAATATTAAT
Statistics
Matches: 198, Mismatches: 38, Indels: 28
0.75 0.14 0.11
Matches are distributed among these distances:
116 8 0.04
117 7 0.04
118 68 0.34
119 5 0.03
120 1 0.01
121 15 0.08
122 12 0.06
123 9 0.05
124 8 0.04
125 52 0.26
126 6 0.03
127 7 0.04
ACGTcount: A:0.39, C:0.02, G:0.03, T:0.55
Consensus pattern (118 bp):
TATGATTATTTATTTTTATTTTAATTTATTTTTTAAATATTAATAATTTATAATTAATTTAAAAT
ATTAATAATTAATAATTTAAATATTAACATTTTATTTATAATTTAAATGTTAT
Found at i:20398438 original size:41 final size:40
Alignment explanation
Indices: 20398393--20398480 Score: 108
Period size: 41 Copynumber: 2.1 Consensus size: 40
20398383 GTTTTTTCTT
20398393 TTTTATAATAATATTAATAATTGATA-ATTT-AAATATTAATA
1 TTTTATAATAAT-TTAATAATT-A-ACATTTAAAATATTAATA
* *
20398434 TTTTATTTATAATTTAATCATTAACATTTAAAATATTAATA
1 TTTTA-TAATAATTTAATAATTAACATTTAAAATATTAATA
20398475 TTTTAT
1 TTTTAT
20398481 TTATAATTGA
Statistics
Matches: 42, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
39 1 0.02
40 6 0.14
41 29 0.69
42 6 0.14
ACGTcount: A:0.44, C:0.02, G:0.01, T:0.52
Consensus pattern (40 bp):
TTTTATAATAATTTAATAATTAACATTTAAAATATTAATA
Found at i:20399519 original size:15 final size:17
Alignment explanation
Indices: 20399499--20399530 Score: 50
Period size: 15 Copynumber: 2.0 Consensus size: 17
20399489 ACAAAGAAAT
20399499 AAACA-TGAAC-ATAAA
1 AAACATTGAACTATAAA
20399514 AAACATTGAACTATAAA
1 AAACATTGAACTATAAA
20399531 TCGGTTGTAC
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 5 0.33
16 5 0.33
17 5 0.33
ACGTcount: A:0.62, C:0.12, G:0.06, T:0.19
Consensus pattern (17 bp):
AAACATTGAACTATAAA
Found at i:20403746 original size:64 final size:64
Alignment explanation
Indices: 20403587--20403747 Score: 241
Period size: 64 Copynumber: 2.5 Consensus size: 64
20403577 CCGGAGCTTT
* * ** ***
20403587 CACATGGTGTGAGGTAACATTTCACATGAGGTGAATTGCATTTAGTATGATGATGATAGTGCTC
1 CACATGGTGTGAGGTAACATTCCACATGTGGTGAATTGCATCGAGTATGATGATGATAACACTC
*
20403651 CACATGGTGTGAGGTAACATTCCACATGTGGTGAATTGCATCGAGTATGATGATGATAACATTC
1 CACATGGTGTGAGGTAACATTCCACATGTGGTGAATTGCATCGAGTATGATGATGATAACACTC
*
20403715 CACATGGTGTGAGGTAACATTCCACACGTGGTG
1 CACATGGTGTGAGGTAACATTCCACATGTGGTG
20403748 CCAATGCACA
Statistics
Matches: 88, Mismatches: 9, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
64 88 1.00
ACGTcount: A:0.28, C:0.16, G:0.27, T:0.30
Consensus pattern (64 bp):
CACATGGTGTGAGGTAACATTCCACATGTGGTGAATTGCATCGAGTATGATGATGATAACACTC
Found at i:20405137 original size:21 final size:21
Alignment explanation
Indices: 20405111--20405152 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
20405101 AAACAGAAGG
* *
20405111 TTTCTCGCTGCAGCGAAATTC
1 TTTCTCACTGCAGCAAAATTC
*
20405132 TTTCTCACTGTAGCAAAATTC
1 TTTCTCACTGCAGCAAAATTC
20405153 AGCTGATGAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.24, C:0.26, G:0.14, T:0.36
Consensus pattern (21 bp):
TTTCTCACTGCAGCAAAATTC
Found at i:20405164 original size:60 final size:60
Alignment explanation
Indices: 20405041--20405186 Score: 161
Period size: 60 Copynumber: 2.4 Consensus size: 60
20405031 TAGGAGACCA
* * * * * *
20405041 AAACAGAAGGTTTTTCGCTACAGCGAGATTTTTTCTCGCTGCAGCGAAATTGTAACCCAG
1 AAACAGAAGGTTTTTCGCTGCAGCGAAATTCTTTCTCACTGCAGCAAAATTGCAACCCAG
* * * **
20405101 AAACAGAAGGTTTCTCGCTGCAGCGAAATTCTTTCTCACTGTAGCAAAATT-CAGCTGATG
1 AAACAGAAGGTTTTTCGCTGCAGCGAAATTCTTTCTCACTGCAGCAAAATTGCAACCCA-G
20405161 AAACAG-AGAGTTTTTCGCTGCAGCGA
1 AAACAGAAG-GTTTTTCGCTGCAGCGA
20405187 GGTTCCTTTT
Statistics
Matches: 72, Mismatches: 12, Indels: 4
0.82 0.14 0.05
Matches are distributed among these distances:
59 5 0.07
60 67 0.93
ACGTcount: A:0.29, C:0.21, G:0.22, T:0.27
Consensus pattern (60 bp):
AAACAGAAGGTTTTTCGCTGCAGCGAAATTCTTTCTCACTGCAGCAAAATTGCAACCCAG
Found at i:20405622 original size:43 final size:43
Alignment explanation
Indices: 20405549--20405660 Score: 127
Period size: 43 Copynumber: 2.6 Consensus size: 43
20405539 TCACCAGCTC
* * ** *
20405549 ATGCGCACTCCTTACTTGCACATGGCTGGGTCATCAC-CGGGTT
1 ATGCGCACTCCCTACTCGCACATAACTGGGTCATC-CTCGGCTT
*
20405592 ATGCGCACTCCCTACTCGCACATAATTGGGTCATCCTCGGCTT
1 ATGCGCACTCCCTACTCGCACATAACTGGGTCATCCTCGGCTT
* * *
20405635 ATACGTACTCTCTACTCGCACATAAC
1 ATGCGCACTCCCTACTCGCACATAAC
20405661 CGAGTCAATA
Statistics
Matches: 58, Mismatches: 10, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
42 1 0.02
43 57 0.98
ACGTcount: A:0.21, C:0.33, G:0.19, T:0.28
Consensus pattern (43 bp):
ATGCGCACTCCCTACTCGCACATAACTGGGTCATCCTCGGCTT
Found at i:20408562 original size:439 final size:437
Alignment explanation
Indices: 20407738--20408613 Score: 1504
Period size: 439 Copynumber: 2.0 Consensus size: 437
20407728 TTTAATTAAG
*
20407738 TAATGGGCCTAATATTATAATGTATTATAATATTGAGGGCTTAATTACAAAATTGAAGTTATTTT
1 TAATAGGCCTAATATTATAATGTATTATAATATTGAGGGCTTAATTACAAAATTGAAGTTATTTT
*
20407803 AACCTAACTATATAAGTCACCTTTTAACTATTTTCTATATGAGCGTTTTTCACAATTGAAAAAAC
66 AACCTAACTATATAAGTCACCTTTTAACTATTTTCTATATGAGAGTTTTTCACAATTGAAAAAAC
20407868 GTAGTTTTTGTCAGAAAAAGAAAAAACGTTTTTTTTTGCCACCCCTCCTTTTGTGTGAAAGAGAA
131 GTAGTTTTTGTCAGAAAAAGAAAAAACGTTTTTTTTTGCCACCCCTCCTTTTGTGTGAAAGAGAA
*
20407933 AATTGCTTATGAAGCAATTTTCAAGAGAGGTTTGGCTAAGATTGTGAAAAAGAAGAAAAGGGAAA
196 AATTGCTTATGAAGCAATTTTCAAGAGAGGTTTGGCTAAGATTGTGAAAAAGAAGAAAAGGAAAA
* * * * * *
20407998 TTGTTGTTCTCTTTGCTAGCACAAAGTATAGTTAAAAACTCCTTCCTTTGTTGAAGGTTCAAGTG
261 TTATTGTCCTCTTTGCTAGCAAAAAGTATAGTTAAAAACTCCCTACTTTATTGAAGGTTCAAGTG
20408063 CAATCGTGTGTACTACCATTGGAGGCCAAGCACTTGATTGGCTAGGGTTTTTGTTCCTTGTGGTG
326 CAATCGTGTGTACTACCATTGGAGGCCAAGCACTTGATTGGCTAGGGTTTTTGTTCCTTGTGGTG
*
20408128 TTCGCGGGATTGCTTTAGAAAGTGCCATTGTGGTTACGAAATTACAT
391 TTCGCGGGATTGCTTTAGAAAGTGCCATTGTGATTACGAAATTACAT
* * *
20408175 NTAATAGGCCTAATATTATAATGTTTTATAATATTGAGGGCTTAATTGCCAAATTGAAGTTATTT
1 -TAATAGGCCTAATATTATAATGTATTATAATATTGAGGGCTTAATTACAAAATTGAAGTTATTT
* *
20408240 TAACCTAACTATATAAGTCACCTTTTAAGTATTTT-TCATATGAGAGTTTTTCATAATTGAACAA
65 TAACCTAACTATATAAGTCACCTTTTAACTATTTTCT-ATATGAGAGTTTTTCACAATTGAA-AA
20408304 AACGTAGTTTTTGTCAGAAAAAGAAAAAACGTTTTTTTTTGCCACCCCTCCTTTTGTGTGAAAGA
128 AACGTAGTTTTTGTCAGAAAAAGAAAAAACGTTTTTTTTTGCCACCCCTCCTTTTGTGTGAAAGA
20408369 GAAAATTGCTTATGAAGCAATTTTCAAGAGAGGTTTGGCTAAGATTGTGAAAAAGAAGAAAAGGA
193 GAAAATTGCTTATGAAGCAATTTTCAAGAGAGGTTTGGCTAAGATTGTGAAAAAGAAGAAAAGGA
* *
20408434 AAATTATTGTCCTCTTTGCTAGCAAAAAGTATAGTTAAAAACTCCCTATTTTATTGAAGGTTCAG
258 AAATTATTGTCCTCTTTGCTAGCAAAAAGTATAGTTAAAAACTCCCTACTTTATTGAAGGTTCAA
*
20408499 GTGCAATCGTGTGTACTACCATTGGAGGCCCAGCACTTGATTGGCTAGGGTTTTT-TCTCCTTGT
323 GTGCAATCGTGTGTACTACCATTGGAGGCCAAGCACTTGATTGGCTAGGGTTTTTGT-TCCTTGT
* * * *
20408563 GGTGTTCGTGGGATTGCTTTGGGAAGTGCCATTGTGATTATGAAATTACAT
387 GGTGTTCGCGGGATTGCTTTAGAAAGTGCCATTGTGATTACGAAATTACAT
20408614 GGCACGGTAA
Statistics
Matches: 413, Mismatches: 22, Indels: 5
0.94 0.05 0.01
Matches are distributed among these distances:
437 1 0.00
438 117 0.28
439 295 0.71
ACGTcount: A:0.31, C:0.13, G:0.20, T:0.36
Consensus pattern (437 bp):
TAATAGGCCTAATATTATAATGTATTATAATATTGAGGGCTTAATTACAAAATTGAAGTTATTTT
AACCTAACTATATAAGTCACCTTTTAACTATTTTCTATATGAGAGTTTTTCACAATTGAAAAAAC
GTAGTTTTTGTCAGAAAAAGAAAAAACGTTTTTTTTTGCCACCCCTCCTTTTGTGTGAAAGAGAA
AATTGCTTATGAAGCAATTTTCAAGAGAGGTTTGGCTAAGATTGTGAAAAAGAAGAAAAGGAAAA
TTATTGTCCTCTTTGCTAGCAAAAAGTATAGTTAAAAACTCCCTACTTTATTGAAGGTTCAAGTG
CAATCGTGTGTACTACCATTGGAGGCCAAGCACTTGATTGGCTAGGGTTTTTGTTCCTTGTGGTG
TTCGCGGGATTGCTTTAGAAAGTGCCATTGTGATTACGAAATTACAT
Found at i:20410463 original size:17 final size:19
Alignment explanation
Indices: 20410422--20410463 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 19
20410412 ATATATATAT
20410422 ATGAATATATGTTGTGCATTG
1 ATGAATATATGTTGTG-A-TG
20410443 ATGAATA-ATGTTGTG-TG
1 ATGAATATATGTTGTGATG
20410460 ATGA
1 ATGA
20410464 TATTGACCCA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
17 6 0.29
20 8 0.38
21 7 0.33
ACGTcount: A:0.31, C:0.02, G:0.26, T:0.40
Consensus pattern (19 bp):
ATGAATATATGTTGTGATG
Found at i:20410512 original size:49 final size:48
Alignment explanation
Indices: 20410458--20410646 Score: 172
Period size: 42 Copynumber: 4.1 Consensus size: 48
20410448 TAATGTTGTG
* *
20410458 TGATGATATTGACCCAGTTATGTGCGAGTAGGGAGTGCGGATAAGCCGA
1 TGATGATATTGACCC-GCTATGTGCGAGTAGGGAGTGCGCATAAGCCGA
* *
20410507 TGATGATATTGACCTGGCTATGCGCGAGTA-GGAGTGCGCATAAGCC--
1 TGATGATATTGACC-CGCTATGTGCGAGTAGGGAGTGCGCATAAGCCGA
20410553 -GATG---TTGACCCGACTATGTGCGAGT-GGGAGTGCGCATAAGCC--
1 TGATGATATTGACCCG-CTATGTGCGAGTAGGGAGTGCGCATAAGCCGA
* * **
20410595 -GATG---CTGACCCGGCTATGTGAGAGTAGGGAGTGCGCATAAGTTGA
1 TGATGATATTGACCC-GCTATGTGCGAGTAGGGAGTGCGCATAAGCCGA
20410640 TGATGAT
1 TGATGAT
20410647 GATGACCTGG
Statistics
Matches: 120, Mismatches: 10, Indels: 21
0.79 0.07 0.14
Matches are distributed among these distances:
41 1 0.01
42 54 0.45
43 16 0.13
45 4 0.03
46 4 0.03
48 15 0.12
49 26 0.22
ACGTcount: A:0.24, C:0.17, G:0.35, T:0.24
Consensus pattern (48 bp):
TGATGATATTGACCCGCTATGTGCGAGTAGGGAGTGCGCATAAGCCGA
Found at i:20410576 original size:42 final size:43
Alignment explanation
Indices: 20410466--20410635 Score: 200
Period size: 42 Copynumber: 3.9 Consensus size: 43
20410456 TGTGATGATA
* * *
20410466 TTGACCCAGTTATGTGCGAGTAGGGAGTGCGGATAAGCCGATGATG
1 TTGACCCGGCTATGTGCGAGTAGGGAGTGCGCATAAGCC---GATG
* *
20410512 ATATTGACCTGGCTATGCGCGAGTA-GGAGTGCGCATAAGCCGATG
1 ---TTGACCCGGCTATGTGCGAGTAGGGAGTGCGCATAAGCCGATG
*
20410557 TTGACCCGACTATGTGCGAGT-GGGAGTGCGCATAAGCCGATG
1 TTGACCCGGCTATGTGCGAGTAGGGAGTGCGCATAAGCCGATG
* *
20410599 CTGACCCGGCTATGTGAGAGTAGGGAGTGCGCATAAG
1 TTGACCCGGCTATGTGCGAGTAGGGAGTGCGCATAAG
20410636 TTGATGATGA
Statistics
Matches: 108, Mismatches: 11, Indels: 10
0.84 0.09 0.08
Matches are distributed among these distances:
42 56 0.52
43 15 0.14
45 4 0.04
48 15 0.14
49 18 0.17
ACGTcount: A:0.24, C:0.19, G:0.36, T:0.22
Consensus pattern (43 bp):
TTGACCCGGCTATGTGCGAGTAGGGAGTGCGCATAAGCCGATG
Found at i:20418924 original size:21 final size:21
Alignment explanation
Indices: 20418884--20418924 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
20418874 TATAATATTA
* * *
20418884 TTTTATTCATTTTTTTAATTT
1 TTTTATTAATTTCTTAAATTT
20418905 TTTTATTAATTTCTTAAATT
1 TTTTATTAATTTCTTAAATT
20418925 CTAGCCATCC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.24, C:0.05, G:0.00, T:0.71
Consensus pattern (21 bp):
TTTTATTAATTTCTTAAATTT
Found at i:20428189 original size:24 final size:26
Alignment explanation
Indices: 20428145--20428193 Score: 84
Period size: 24 Copynumber: 2.0 Consensus size: 26
20428135 TCGGCCGAAC
20428145 TTCCTTCTCTCTTTTTCTTTCCTTTG
1 TTCCTTCTCTCTTTTTCTTTCCTTTG
20428171 TTCCTTCT-TCTTTTT-TTTCCTTT
1 TTCCTTCTCTCTTTTTCTTTCCTTT
20428194 CTTTTCTTCC
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
24 8 0.35
25 7 0.30
26 8 0.35
ACGTcount: A:0.00, C:0.29, G:0.02, T:0.69
Consensus pattern (26 bp):
TTCCTTCTCTCTTTTTCTTTCCTTTG
Found at i:20428527 original size:3 final size:3
Alignment explanation
Indices: 20428514--20428544 Score: 53
Period size: 3 Copynumber: 10.0 Consensus size: 3
20428504 AATTTTTTTA
20428514 ATT ATT CATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT -ATT ATT ATT ATT ATT ATT ATT ATT
20428545 TATCTTATTT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 24 0.89
4 3 0.11
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:20439114 original size:22 final size:24
Alignment explanation
Indices: 20439079--20439125 Score: 64
Period size: 22 Copynumber: 2.0 Consensus size: 24
20439069 CAAACCCTAG
20439079 GTGAAGAATTTCAAGAGAAA-AAGT
1 GTGAAGAATTTCAAG-GAAACAAGT
20439103 GTGAA-AA-TTCAAGGAAACAAGT
1 GTGAAGAATTTCAAGGAAACAAGT
20439125 G
1 G
20439126 ACAAAAGGTA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
21 4 0.18
22 11 0.50
23 2 0.09
24 5 0.23
ACGTcount: A:0.49, C:0.06, G:0.26, T:0.19
Consensus pattern (24 bp):
GTGAAGAATTTCAAGGAAACAAGT
Found at i:20439131 original size:22 final size:22
Alignment explanation
Indices: 20439088--20439131 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
20439078 GGTGAAGAAT
**
20439088 TTCAAGAGAAAAAGTGTGAAAA
1 TTCAAGAGAAAAAGTGACAAAA
20439110 TTCAAG-GAAACAAGTGACAAAA
1 TTCAAGAGAAA-AAGTGACAAAA
20439132 GGTAAAATTT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 4 0.21
22 15 0.79
ACGTcount: A:0.55, C:0.09, G:0.20, T:0.16
Consensus pattern (22 bp):
TTCAAGAGAAAAAGTGACAAAA
Found at i:20441851 original size:42 final size:42
Alignment explanation
Indices: 20441656--20441839 Score: 242
Period size: 42 Copynumber: 4.4 Consensus size: 42
20441646 GTAATGATAT
* * * *
20441656 TGACCCAACTATGTGCGAGTAGGAGTGTGCATGAGCCAATGC
1 TGACCCAGCTATGTGCGAGTAGGAGTGCGCATAAGCCGATGC
* ** **
20441698 TGACTCAGCTATGTGCGAGGGGGAGTGCGCATAAATCGATGC
1 TGACCCAGCTATGTGCGAGTAGGAGTGCGCATAAGCCGATGC
** *
20441740 TGACCTGGCTATGTGCGAGTAAGAGTGCGCATAAGCCGATGC
1 TGACCCAGCTATGTGCGAGTAGGAGTGCGCATAAGCCGATGC
*
20441782 TGACCCGGCTATGTGCGAGTAGGAGTGCGCATAAGCCGATGC
1 TGACCCAGCTATGTGCGAGTAGGAGTGCGCATAAGCCGATGC
*
20441824 TGACCCAGCAATGTGC
1 TGACCCAGCTATGTGC
20441840 TGGTGGGAGT
Statistics
Matches: 121, Mismatches: 21, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
42 121 1.00
ACGTcount: A:0.24, C:0.22, G:0.33, T:0.21
Consensus pattern (42 bp):
TGACCCAGCTATGTGCGAGTAGGAGTGCGCATAAGCCGATGC
Found at i:20441897 original size:2 final size:2
Alignment explanation
Indices: 20441892--20441929 Score: 58
Period size: 2 Copynumber: 19.0 Consensus size: 2
20441882 ATGGTGATGG
* *
20441892 AT AT AT AT AT AT AT AT AT AT AT AT AC AT AT AT AG AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
20441930 GTGTGTTATA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.03, G:0.03, T:0.45
Consensus pattern (2 bp):
AT
Found at i:20443261 original size:46 final size:46
Alignment explanation
Indices: 20443185--20443277 Score: 159
Period size: 46 Copynumber: 2.0 Consensus size: 46
20443175 ATTATGTGCA
* * *
20443185 AGCAAGTATATATGTATATATATGTGTGTGTGTGTGTGTAAACGAT
1 AGCAAGTATATATGTATACATATATATGTGTGTGTGTGTAAACGAT
20443231 AGCAAGTATATATGTATACATATATATGTGTGTGTGTGTAAACGAT
1 AGCAAGTATATATGTATACATATATATGTGTGTGTGTGTAAACGAT
20443277 A
1 A
20443278 TGTGTTAAGG
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
46 44 1.00
ACGTcount: A:0.33, C:0.05, G:0.24, T:0.38
Consensus pattern (46 bp):
AGCAAGTATATATGTATACATATATATGTGTGTGTGTGTAAACGAT
Found at i:20445371 original size:22 final size:20
Alignment explanation
Indices: 20445324--20445361 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
20445314 AAATATCTTT
*
20445324 TTCTTCCAGCAACTTCTTCA
1 TTCTTCTAGCAACTTCTTCA
20445344 TT-TTCTAGCAACTTCTTC
1 TTCTTCTAGCAACTTCTTC
20445362 TCCTTCTTCT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 15 0.88
20 2 0.12
ACGTcount: A:0.18, C:0.32, G:0.05, T:0.45
Consensus pattern (20 bp):
TTCTTCTAGCAACTTCTTCA
Found at i:20446224 original size:1 final size:1
Alignment explanation
Indices: 20446218--20446248 Score: 62
Period size: 1 Copynumber: 31.0 Consensus size: 1
20446208 NNNNNNNNNN
20446218 GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG
1 GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG
20446249 AGGGATGTAC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 30 1.00
ACGTcount: A:0.00, C:0.00, G:1.00, T:0.00
Consensus pattern (1 bp):
G
Found at i:20446300 original size:38 final size:39
Alignment explanation
Indices: 20446252--20446336 Score: 127
Period size: 39 Copynumber: 2.2 Consensus size: 39
20446242 GGGGGGGAGG
*
20446252 GATGTACACGATGGCACTGAT-TGTGCACGATGTGGGGA
1 GATGCACACGATGGCACTGATATGTGCACGATGTGGGGA
* * *
20446290 GATGCACACGATGGCGCTGCTATGTGCACGATGTGGGGG
1 GATGCACACGATGGCACTGATATGTGCACGATGTGGGGA
20446329 GATGCACA
1 GATGCACA
20446337 TGAGCCGAGT
Statistics
Matches: 42, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
38 18 0.43
39 24 0.57
ACGTcount: A:0.22, C:0.19, G:0.38, T:0.21
Consensus pattern (39 bp):
GATGCACACGATGGCACTGATATGTGCACGATGTGGGGA
Found at i:20448510 original size:20 final size:21
Alignment explanation
Indices: 20448476--20448519 Score: 63
Period size: 20 Copynumber: 2.1 Consensus size: 21
20448466 GCAATAAATA
*
20448476 TCTAAGTTTCTAGCAACTTCT
1 TCTAAGTTTCCAGCAACTTCT
*
20448497 TCTAA-TTTCCAGCAACTTTT
1 TCTAAGTTTCCAGCAACTTCT
20448517 TCT
1 TCT
20448520 TCTTCCTCTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 16 0.76
21 5 0.24
ACGTcount: A:0.23, C:0.25, G:0.07, T:0.45
Consensus pattern (21 bp):
TCTAAGTTTCCAGCAACTTCT
Found at i:20449301 original size:2 final size:2
Alignment explanation
Indices: 20449294--20449334 Score: 57
Period size: 2 Copynumber: 20.0 Consensus size: 2
20449284 CATTATGTTG
20449294 AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT GAT AT AT GAT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT AT -AT AT
20449335 GTATTGATAA
Statistics
Matches: 36, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
1 1 0.03
2 31 0.86
3 4 0.11
ACGTcount: A:0.49, C:0.00, G:0.05, T:0.46
Consensus pattern (2 bp):
AT
Found at i:20449461 original size:29 final size:29
Alignment explanation
Indices: 20449428--20449508 Score: 77
Period size: 23 Copynumber: 3.0 Consensus size: 29
20449418 CAGCTATGTG
20449428 CGGTGTGGGAGTGCACATGAGCTGATGAC
1 CGGTGTGGGAGTGCACATGAGCTGATGAC
* * *
20449457 CGGTGGGGGA-TTC-CA--ACCTTG-TG--
1 CGGTGTGGGAGTGCACATGAGC-TGATGAC
20449480 CGGTGTGGGAGTGCACATGAGCTGATGAC
1 CGGTGTGGGAGTGCACATGAGCTGATGAC
20449509 TAGTGGTGCT
Statistics
Matches: 38, Mismatches: 6, Indels: 16
0.63 0.10 0.27
Matches are distributed among these distances:
23 9 0.24
24 2 0.05
25 6 0.16
26 4 0.11
27 6 0.16
28 2 0.05
29 9 0.24
ACGTcount: A:0.19, C:0.19, G:0.41, T:0.22
Consensus pattern (29 bp):
CGGTGTGGGAGTGCACATGAGCTGATGAC
Found at i:20453111 original size:56 final size:52
Alignment explanation
Indices: 20452972--20453130 Score: 140
Period size: 52 Copynumber: 3.0 Consensus size: 52
20452962 AATGACGGGT
* * **
20452972 GATTCCAGCTATGTTCGATGTGGGAATGCACATGAGCTGATGACCGGTGGGG
1 GATTCCAGCTATGTGCGATGTGGGAGTGCACACAAGCTGATGACCGGTGGGG
** * *
20453024 GATTCCAGCCGTGTG-TAGTGTGGGAGTGCACACAAGCTGATGACTGGTGGTGG
1 GATTCCAGCTATGTGCGA-TGTGGGAGTGCACACAAGCTGATGACCGGTGG-GG
* * ** * *
20453077 TCTATATCCAGCTATGTGCGATGTGGGAGGGCACATGAGCTGAGGACCGTTGGG
1 --GAT-TCCAGCTATGTGCGATGTGGGAGTGCACACAAGCTGATGACCGGTGGG
20453131 CATATACATG
Statistics
Matches: 83, Mismatches: 18, Indels: 9
0.75 0.16 0.08
Matches are distributed among these distances:
51 1 0.01
52 40 0.48
53 2 0.02
55 3 0.04
56 36 0.43
57 1 0.01
ACGTcount: A:0.20, C:0.18, G:0.38, T:0.25
Consensus pattern (52 bp):
GATTCCAGCTATGTGCGATGTGGGAGTGCACACAAGCTGATGACCGGTGGGG
Found at i:20453152 original size:2 final size:2
Alignment explanation
Indices: 20453145--20453173 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
20453135 TACATGCTTG
20453145 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
20453174 GCCATAGAGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:20455135 original size:18 final size:18
Alignment explanation
Indices: 20455095--20455133 Score: 53
Period size: 19 Copynumber: 2.2 Consensus size: 18
20455085 ATTTAGTTAC
20455095 TTTTA-TAATTAGTTTAT
1 TTTTATTAATTAGTTTAT
*
20455112 TTTTATTAAGTTATTTTAT
1 TTTTATTAA-TTAGTTTAT
20455131 TTT
1 TTT
20455134 ATGTTTATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 5 0.26
18 3 0.16
19 11 0.58
ACGTcount: A:0.26, C:0.00, G:0.05, T:0.69
Consensus pattern (18 bp):
TTTTATTAATTAGTTTAT
Found at i:20456216 original size:7 final size:7
Alignment explanation
Indices: 20456204--20456256 Score: 54
Period size: 7 Copynumber: 7.6 Consensus size: 7
20456194 CATTATAATT
20456204 AAAATAA
1 AAAATAA
*
20456211 AAAATATT
1 AAAATA-A
20456219 AAAATAA
1 AAAATAA
* *
20456226 AATATAT
1 AAAATAA
*
20456233 AATAT-A
1 AAAATAA
20456239 AAAATAA
1 AAAATAA
20456246 AAAATAA
1 AAAATAA
20456253 AAAA
1 AAAA
20456257 ATATAAGAAA
Statistics
Matches: 38, Mismatches: 6, Indels: 4
0.79 0.12 0.08
Matches are distributed among these distances:
6 4 0.11
7 28 0.74
8 6 0.16
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (7 bp):
AAAATAA
Found at i:20456221 original size:15 final size:14
Alignment explanation
Indices: 20456203--20456262 Score: 68
Period size: 15 Copynumber: 4.2 Consensus size: 14
20456193 ACATTATAAT
20456203 TAAAATAAAAAATA
1 TAAAATAAAAAATA
*
20456217 TTAAAATAAAATATA
1 -TAAAATAAAAAATA
*
20456232 TAATAT-AAAAATA
1 TAAAATAAAAAATA
*
20456245 AAAAATAAAAAAATA
1 TAAAAT-AAAAAATA
20456260 TAA
1 TAA
20456263 GAAATTAAAA
Statistics
Matches: 37, Mismatches: 6, Indels: 4
0.79 0.13 0.09
Matches are distributed among these distances:
13 10 0.27
14 5 0.14
15 22 0.59
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (14 bp):
TAAAATAAAAAATA
Found at i:20456228 original size:20 final size:20
Alignment explanation
Indices: 20456203--20456272 Score: 68
Period size: 20 Copynumber: 3.2 Consensus size: 20
20456193 ACATTATAAT
*
20456203 TAAAATAAAAAATATTAAAA
1 TAAAATAAAAAATATAAAAA
* *
20456223 TAAAATATATAATATAAAAA
1 TAAAATAAAAAATATAAAAA
20456243 TAAAAAATAAAAAAATATAAGAAA
1 T--AAAAT-AAAAAATATAA-AAA
20456267 TTAAAA
1 -TAAAA
20456273 NTTTTCTTGT
Statistics
Matches: 40, Mismatches: 5, Indels: 7
0.77 0.10 0.13
Matches are distributed among these distances:
20 18 0.45
22 5 0.12
23 13 0.32
24 3 0.08
25 1 0.03
ACGTcount: A:0.74, C:0.00, G:0.01, T:0.24
Consensus pattern (20 bp):
TAAAATAAAAAATATAAAAA
Found at i:20456333 original size:20 final size:18
Alignment explanation
Indices: 20456308--20456387 Score: 70
Period size: 20 Copynumber: 4.1 Consensus size: 18
20456298 AGGTAATAAT
20456308 TAAAATAAAAAACATTAAAA
1 TAAAATAAAAAA-A-TAAAA
* *
20456328 TAAAATATATAATATAAAA
1 TAAAATA-AAAAAATAAAA
*
20456347 TATAAATAATTAAAATAAAA
1 TA-AAATAA-AAAAATAAAA
20456367 TAAAATATAAAAAATTAAAA
1 TAAAATA-AAAAAA-TAAAA
20456387 T
1 T
20456388 TTATATAATA
Statistics
Matches: 51, Mismatches: 4, Indels: 10
0.78 0.06 0.15
Matches are distributed among these distances:
19 17 0.33
20 31 0.61
21 3 0.06
ACGTcount: A:0.71, C:0.01, G:0.00, T:0.28
Consensus pattern (18 bp):
TAAAATAAAAAAATAAAA
Found at i:20456354 original size:40 final size:40
Alignment explanation
Indices: 20456310--20456468 Score: 117
Period size: 40 Copynumber: 3.8 Consensus size: 40
20456300 GTAATAATTA
20456310 AAATAA-AAAACATTAAAATAAAATATATAATATAAAATAT
1 AAATAAGAAAA-ATTAAAATAAAATATATAATATAAAATAT
** * *
20456350 AAATAATTAAAA-TAAAATAAAATATAAAAAATTAAAATTTAT
1 AAATAAGAAAAATTAAAATAAAATATATAATA-TAAAA--TAT
*
20456392 ATAATATAGGTAAAAGCAATTAAAATAAAATATATAATATAAAAAATT
1 A-AATA-A-G--AAA--AATTAAAATAAAATATATAATATAAAATA-T
* * *
20456440 ATATTA-AAAAATGAAAATAAAATATATAA
1 AAATAAGAAAAATTAAAATAAAATATATAA
20456469 GATTATAATA
Statistics
Matches: 95, Mismatches: 11, Indels: 26
0.72 0.08 0.20
Matches are distributed among these distances:
39 17 0.18
40 31 0.33
41 3 0.03
42 7 0.07
43 4 0.04
44 1 0.01
46 1 0.01
47 5 0.05
48 2 0.02
49 7 0.07
50 17 0.18
ACGTcount: A:0.67, C:0.01, G:0.03, T:0.29
Consensus pattern (40 bp):
AAATAAGAAAAATTAAAATAAAATATATAATATAAAATAT
Found at i:20456359 original size:34 final size:33
Alignment explanation
Indices: 20456301--20456378 Score: 108
Period size: 34 Copynumber: 2.4 Consensus size: 33
20456291 TTTTGTAAGG
20456301 TAATAAT-TAAAATAAAAAACATTAAAATAAAA
1 TAATAATATAAAATAAAAAACATTAAAATAAAA
*
20456333 TATATAATATAAAATATAAATA-ATTAAAATAAAA
1 TA-ATAATATAAAATA-AAAAACATTAAAATAAAA
20456367 TAA-AATATAAAA
1 TAATAATATAAAA
20456379 AATTAAAATT
Statistics
Matches: 42, Mismatches: 1, Indels: 6
0.86 0.02 0.12
Matches are distributed among these distances:
32 11 0.26
33 6 0.14
34 21 0.50
35 4 0.10
ACGTcount: A:0.71, C:0.01, G:0.00, T:0.28
Consensus pattern (33 bp):
TAATAATATAAAATAAAAAACATTAAAATAAAA
Found at i:20456364 original size:25 final size:25
Alignment explanation
Indices: 20456336--20456440 Score: 102
Period size: 25 Copynumber: 3.9 Consensus size: 25
20456326 AATAAAATAT
* *
20456336 ATAATATAAAATATAAATAATTAAA
1 ATAAAATAAAATATAAAAAATTAAA
20456361 ATAAAATAAAATATAAAAAATTAAA
1 ATAAAATAAAATATAAAAAATTAAA
* * *
20456386 ATTTATATAATATAGGTAAAAGCAATTAAA
1 A-TAAAATAAAATA--TAAAA--AATTAAA
20456416 ATAAAATATATAATATAAAAAATTA
1 ATAAAATA-A-AATATAAAAAATTA
20456441 TATTAAAAAA
Statistics
Matches: 65, Mismatches: 8, Indels: 12
0.76 0.09 0.14
Matches are distributed among these distances:
25 24 0.37
26 9 0.14
27 5 0.08
28 5 0.08
29 10 0.15
30 9 0.14
31 3 0.05
ACGTcount: A:0.66, C:0.01, G:0.03, T:0.30
Consensus pattern (25 bp):
ATAAAATAAAATATAAAAAATTAAA
Found at i:20456378 original size:7 final size:7
Alignment explanation
Indices: 20456308--20456378 Score: 53
Period size: 7 Copynumber: 10.7 Consensus size: 7
20456298 AGGTAATAAT
20456308 TAAAATA
1 TAAAATA
* *
20456315 AAAAACA
1 TAAAATA
*
20456322 TTAAA-A
1 TAAAATA
20456328 TAAAATA
1 TAAAATA
*
20456335 TATAATA
1 TAAAATA
20456342 TAAAATA
1 TAAAATA
20456349 T-AAATAA
1 TAAAAT-A
*
20456356 TTAAA-A
1 TAAAATA
20456362 T-AAA-A
1 TAAAATA
20456367 TAAAATA
1 TAAAATA
20456374 TAAAA
1 TAAAA
20456379 AATTAAAATT
Statistics
Matches: 52, Mismatches: 7, Indels: 10
0.75 0.10 0.14
Matches are distributed among these distances:
5 5 0.10
6 14 0.27
7 30 0.58
8 3 0.06
ACGTcount: A:0.72, C:0.01, G:0.00, T:0.27
Consensus pattern (7 bp):
TAAAATA
Found at i:20456398 original size:49 final size:52
Alignment explanation
Indices: 20456302--20456440 Score: 119
Period size: 49 Copynumber: 2.7 Consensus size: 52
20456292 TTTGTAAGGT
* * *
20456302 AATAATTAAAATAAAA-AACATTAAAATAAAATATATAATAT-AAA-ATA-T-A
1 AATAATTAAAATAAAATAACAATATAA-AAAAT-TAAAATATAAAATATAGTAA
*
20456351 AATAATTAAAATAAAATAA-AATATAAAAAATTAAAATTTATATAATATAGGTAA
1 AATAATTAAAATAAAATAACAATATAAAAAATTAAAA--TATAAAATATA-GTAA
* *
20456405 AAGCAATTAAAATAAAATATATAATATAAAAAATTA
1 AA-TAATTAAAATAAAATA-ACAATATAAAAAATTA
20456441 TATTAAAAAA
Statistics
Matches: 74, Mismatches: 5, Indels: 14
0.80 0.05 0.15
Matches are distributed among these distances:
47 4 0.05
48 5 0.07
49 24 0.32
50 4 0.05
51 3 0.04
53 1 0.01
54 3 0.04
55 15 0.20
56 1 0.01
57 14 0.19
ACGTcount: A:0.67, C:0.01, G:0.02, T:0.29
Consensus pattern (52 bp):
AATAATTAAAATAAAATAACAATATAAAAAATTAAAATATAAAATATAGTAA
Found at i:20456461 original size:55 final size:55
Alignment explanation
Indices: 20456354--20456461 Score: 123
Period size: 55 Copynumber: 2.0 Consensus size: 55
20456344 AAATATAAAT
* * **
20456354 AATTAAAATAAAATAAAATATAAAAAATTAAAATTTATATAATATAGGTAAAAGC
1 AATTAAAATAAAATAAAATATAAAAAATTAAAATTTAAAAAATATAAATAAAAGC
*
20456409 AATTAAAATAAAATATATAATATAAAAAATT-ATA-TTAAAAAATGA-AAATAAAA
1 AATTAAAATAAAATA-A-AATATAAAAAATTAAAATTTAAAAAAT-ATAAATAAAA
20456462 TATATAAGAT
Statistics
Matches: 45, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
55 28 0.62
56 4 0.09
57 13 0.29
ACGTcount: A:0.67, C:0.01, G:0.04, T:0.29
Consensus pattern (55 bp):
AATTAAAATAAAATAAAATATAAAAAATTAAAATTTAAAAAATATAAATAAAAGC
Found at i:20456473 original size:28 final size:28
Alignment explanation
Indices: 20456442--20456510 Score: 66
Period size: 33 Copynumber: 2.3 Consensus size: 28
20456432 AAAAAATTAT
* *
20456442 ATTAAAAAATGAAAATAAAATATATAAG
1 ATTAAAAAATAAAAATAAAATATATAAC
*
20456470 ATTATAATAAGAAATAAAAATAAAATATATGAC
1 A-T-T-A-AA-AAATAAAAATAAAATATATAAC
20456503 ATTAAAAA
1 ATTAAAAA
20456511 TATATTTAAG
Statistics
Matches: 33, Mismatches: 3, Indels: 10
0.72 0.07 0.22
Matches are distributed among these distances:
28 3 0.09
29 3 0.09
30 2 0.06
31 2 0.06
32 3 0.09
33 20 0.61
ACGTcount: A:0.67, C:0.01, G:0.06, T:0.26
Consensus pattern (28 bp):
ATTAAAAAATAAAAATAAAATATATAAC
Found at i:20456499 original size:33 final size:33
Alignment explanation
Indices: 20456413--20456499 Score: 111
Period size: 33 Copynumber: 2.6 Consensus size: 33
20456403 AAAAGCAATT
* * *
20456413 AAAATAAAATATATAATATAAAAAATTATATTAA
1 AAAATAAAA-ATAAAATATATAAAATTATAATAA
* *
20456447 AAAATGAAAATAAAATATATAAGATTATAATAA
1 AAAATAAAAATAAAATATATAAAATTATAATAA
*
20456480 GAAATAAAAATAAAATATAT
1 AAAATAAAAATAAAATATAT
20456500 GACATTAAAA
Statistics
Matches: 46, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
33 38 0.83
34 8 0.17
ACGTcount: A:0.68, C:0.00, G:0.03, T:0.29
Consensus pattern (33 bp):
AAAATAAAAATAAAATATATAAAATTATAATAA
Found at i:20456733 original size:15 final size:15
Alignment explanation
Indices: 20456713--20456752 Score: 62
Period size: 15 Copynumber: 2.7 Consensus size: 15
20456703 ATTTTCCCTA
*
20456713 CAATCACATTTCTTG
1 CAATCACATTTCCTG
20456728 CAATCACATTTCCTG
1 CAATCACATTTCCTG
*
20456743 TAATCACATT
1 CAATCACATT
20456753 GCATTGTAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.30, C:0.28, G:0.05, T:0.38
Consensus pattern (15 bp):
CAATCACATTTCCTG
Found at i:20467895 original size:25 final size:25
Alignment explanation
Indices: 20467862--20467921 Score: 84
Period size: 25 Copynumber: 2.4 Consensus size: 25
20467852 GTGGTTGCAA
**
20467862 CCACGTATATCAACTTGTGGCCTAG
1 CCACGTATATCAACCCGTGGCCTAG
* *
20467887 CCATGTATATCAACCCGTGGCCTTG
1 CCACGTATATCAACCCGTGGCCTAG
20467912 CCACGTATAT
1 CCACGTATAT
20467922 ATATCACAGA
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
25 30 1.00
ACGTcount: A:0.23, C:0.30, G:0.18, T:0.28
Consensus pattern (25 bp):
CCACGTATATCAACCCGTGGCCTAG
Found at i:20477341 original size:27 final size:28
Alignment explanation
Indices: 20477281--20477343 Score: 74
Period size: 29 Copynumber: 2.2 Consensus size: 28
20477271 AGAGTAATTT
* *
20477281 TTGAAATTTACACTTTTGCCCCTATAAAA
1 TTGAAAATTACACTTTTG-CCCTAAAAAA
* *
20477310 GTGAAAATTACATTTTTG-CCTAAAAAA
1 TTGAAAATTACACTTTTGCCCTAAAAAA
20477337 TTGAAAA
1 TTGAAAA
20477344 ATTGCCCATA
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
27 14 0.48
29 15 0.52
ACGTcount: A:0.41, C:0.14, G:0.10, T:0.35
Consensus pattern (28 bp):
TTGAAAATTACACTTTTGCCCTAAAAAA
Found at i:20488926 original size:21 final size:19
Alignment explanation
Indices: 20488897--20488939 Score: 59
Period size: 21 Copynumber: 2.2 Consensus size: 19
20488887 GGAATAACAT
*
20488897 AAAATTAAACTAACTTACTAA
1 AAAAATAAACTAA-TTAC-AA
20488918 AAAAATAAACTAATTACAA
1 AAAAATAAACTAATTACAA
20488937 AAA
1 AAA
20488940 CAACTAGAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 5 0.24
20 4 0.19
21 12 0.57
ACGTcount: A:0.65, C:0.12, G:0.00, T:0.23
Consensus pattern (19 bp):
AAAAATAAACTAATTACAA
Found at i:20495466 original size:52 final size:48
Alignment explanation
Indices: 20495388--20495487 Score: 164
Period size: 52 Copynumber: 2.0 Consensus size: 48
20495378 CTCACTAGGT
20495388 GGACGTTTAAAAGAGAGAGAGAGAGAGAGGAGGTCTTTACCAAATAGCTTG
1 GGACGTTTAAAAGAGAGAGAGAGAGAGA-GAGG-CTTT-CCAAATAGCTTG
20495439 NGGACGTTTAAAAGAGAGAGAGAGAGAGAGAGGCTTTCCAAATAGCTTG
1 -GGACGTTTAAAAGAGAGAGAGAGAGAGAGAGGCTTTCCAAATAGCTTG
20495488 AGGAAAACTC
Statistics
Matches: 48, Mismatches: 0, Indels: 3
0.94 0.00 0.06
Matches are distributed among these distances:
49 12 0.25
50 4 0.08
51 4 0.08
52 28 0.58
ACGTcount: A:0.37, C:0.10, G:0.33, T:0.19
Consensus pattern (48 bp):
GGACGTTTAAAAGAGAGAGAGAGAGAGAGAGGCTTTCCAAATAGCTTG
Found at i:20500754 original size:43 final size:42
Alignment explanation
Indices: 20500635--20500757 Score: 131
Period size: 43 Copynumber: 2.9 Consensus size: 42
20500625 TGACTTGACT
****
20500635 ATGTGCGAGTAGGGAGTGCGCATAGGC-TGATGATGACCCGGTT
1 ATGTGCGAGTAGGGAGTGCGCATA-GCATG-TGATGACCCAACC
* * *
20500678 ATGTGCGAGTAGGGAGTGCGTATAACACGGTGATGACCCAACC
1 ATGTGCGAGTAGGGAGTGCGCATAGCA-TGTGATGACCCAACC
*
20500721 ATGTGCAAGTAGGGAGTGCGCATGAGCATGTGATGAC
1 ATGTGCGAGTAGGGAGTGCGCAT-AGCATGTGATGAC
20500758 GAGACGATGT
Statistics
Matches: 66, Mismatches: 11, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
42 1 0.02
43 61 0.92
44 4 0.06
ACGTcount: A:0.25, C:0.17, G:0.37, T:0.21
Consensus pattern (42 bp):
ATGTGCGAGTAGGGAGTGCGCATAGCATGTGATGACCCAACC
Found at i:20502611 original size:2 final size:2
Alignment explanation
Indices: 20502604--20502631 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
20502594 TTTGGAAAGC
20502604 CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT
20502632 AAAACATCCA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:20510344 original size:21 final size:21
Alignment explanation
Indices: 20510303--20510344 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
20510293 AAACAGAATG
* *
20510303 TTTCTCACTACAGTGAGATTC
1 TTTCTCACTACAGCGAAATTC
*
20510324 TTTCTCACTGCAGCGAAATTC
1 TTTCTCACTACAGCGAAATTC
20510345 AGCTGATGAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.24, C:0.26, G:0.14, T:0.36
Consensus pattern (21 bp):
TTTCTCACTACAGCGAAATTC
Found at i:20510729 original size:23 final size:23
Alignment explanation
Indices: 20510699--20510758 Score: 84
Period size: 23 Copynumber: 2.6 Consensus size: 23
20510689 TATACGTATA
* * *
20510699 CCCATCATTATCATGCACATCAT
1 CCCATCATCATCATACACACCAT
20510722 CCCATCATCATCATACACACCAT
1 CCCATCATCATCATACACACCAT
*
20510745 CACATCATCATCAT
1 CCCATCATCATCAT
20510759 CACCAGCTCA
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.33, C:0.38, G:0.02, T:0.27
Consensus pattern (23 bp):
CCCATCATCATCATACACACCAT
Found at i:20516722 original size:21 final size:20
Alignment explanation
Indices: 20516698--20516745 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 20
20516688 ATCTTACCTT
*
20516698 TTTTTCACTTGTTTCCTTGAA
1 TTTTTCACTT-TTCCCTTGAA
*
20516719 TTTTCACACTTTTCCCTTGAA
1 TTTT-TCACTTTTCCCTTGAA
20516740 TTTTTC
1 TTTTTC
20516746 CACCTAGGGT
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
20 1 0.04
21 17 0.74
22 5 0.22
ACGTcount: A:0.15, C:0.23, G:0.06, T:0.56
Consensus pattern (20 bp):
TTTTTCACTTTTCCCTTGAA
Found at i:20516745 original size:22 final size:22
Alignment explanation
Indices: 20516703--20516743 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
20516693 ACCTTTTTTT
*
20516703 CACTTGTTTCCTTGAATTTTCA
1 CACTTGTTCCCTTGAATTTTCA
20516725 CACTT-TTCCCTTGAATTTT
1 CACTTGTTCCCTTGAATTTT
20516744 TCCACCTAGG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 13 0.72
22 5 0.28
ACGTcount: A:0.17, C:0.24, G:0.07, T:0.51
Consensus pattern (22 bp):
CACTTGTTCCCTTGAATTTTCA
Found at i:20533598 original size:10 final size:9
Alignment explanation
Indices: 20533573--20533601 Score: 58
Period size: 9 Copynumber: 3.2 Consensus size: 9
20533563 TTTGCAGAAA
20533573 ACTAAAAAG
1 ACTAAAAAG
20533582 ACTAAAAAG
1 ACTAAAAAG
20533591 ACTAAAAAG
1 ACTAAAAAG
20533600 AC
1 AC
20533602 ACTATGCTGT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.66, C:0.14, G:0.10, T:0.10
Consensus pattern (9 bp):
ACTAAAAAG
Found at i:20541092 original size:55 final size:55
Alignment explanation
Indices: 20541006--20541270 Score: 354
Period size: 55 Copynumber: 4.8 Consensus size: 55
20540996 GTAACCGCGC
* * *
20541006 GTGTGCGGTGTGGGAGTGCACATGAGCTGATGACCT-GTGGATGATGATTTTTGTT
1 GTGTGCGGTGTGGGAGTGCACATGAGCTGATGA-CTAGTGGATGATGATTCTAGCT
* * * *
20541061 GTGTGCGGTGTGGGAGTGCACATGAGTTGATGACCT-GTGGATGATGATTTTTGTT
1 GTGTGCGGTGTGGGAGTGCACATGAGCTGATGA-CTAGTGGATGATGATTCTAGCT
*
20541116 GTGTGCGGTGTGGGAGTGCACATGAGCTAATGACTAGTGGATGATGATTCTAGCT
1 GTGTGCGGTGTGGGAGTGCACATGAGCTGATGACTAGTGGATGATGATTCTAGCT
* * * *
20541171 ATGTGTGGTGTGGGAGTGCACATGAGCTGATGATTGGTGGATGATGATTCTAGCT
1 GTGTGCGGTGTGGGAGTGCACATGAGCTGATGACTAGTGGATGATGATTCTAGCT
* * * *
20541226 ATGTCCGGTGTGGGAGTGCACATGAGCTGATGATTGGTGGATGAT
1 GTGTGCGGTGTGGGAGTGCACATGAGCTGATGACTAGTGGATGAT
20541271 TACATGTTTA
Statistics
Matches: 196, Mismatches: 13, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
54 2 0.01
55 194 0.99
ACGTcount: A:0.19, C:0.11, G:0.38, T:0.32
Consensus pattern (55 bp):
GTGTGCGGTGTGGGAGTGCACATGAGCTGATGACTAGTGGATGATGATTCTAGCT
Found at i:20542608 original size:15 final size:15
Alignment explanation
Indices: 20542590--20542618 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
20542580 CTAATTAGTC
20542590 TAAGTTAGATTAGAT
1 TAAGTTAGATTAGAT
20542605 TAAGTTAGATTAGA
1 TAAGTTAGATTAGA
20542619 CTTAGGATTG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.41, C:0.00, G:0.21, T:0.38
Consensus pattern (15 bp):
TAAGTTAGATTAGAT
Found at i:20542677 original size:24 final size:23
Alignment explanation
Indices: 20542646--20542691 Score: 56
Period size: 24 Copynumber: 2.0 Consensus size: 23
20542636 GTGTTTTTAC
**
20542646 TTATTTTATTTGTTTAGTTTAAT
1 TTATTTTAAATGTTTAGTTTAAT
*
20542669 TTATGTTTAAATGTTTATTTTAA
1 TTAT-TTTAAATGTTTAGTTTAA
20542692 GTTAATAATG
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
23 4 0.21
24 15 0.79
ACGTcount: A:0.26, C:0.00, G:0.09, T:0.65
Consensus pattern (23 bp):
TTATTTTAAATGTTTAGTTTAAT
Found at i:20544318 original size:75 final size:75
Alignment explanation
Indices: 20544232--20544408 Score: 318
Period size: 75 Copynumber: 2.4 Consensus size: 75
20544222 TTGCCTAGCA
* *
20544232 TTTCTACCAACTCATGCTTTCCACAATAATAGTTTATAAAACTTTCACAAATAGGTACTTAAAAC
1 TTTCTAGCAACTCATGCTTTCCACAATAATAGTTTATAAAACTTTCACAAATAAGTACTTAAAAC
20544297 CACCTATCAT
66 CACCTATCAT
*
20544307 TTTCTAGCAACTCATGCTTTCCACAATAATAGTTTATAAAACTTTCACGAATAAGTACTTAAAAC
1 TTTCTAGCAACTCATGCTTTCCACAATAATAGTTTATAAAACTTTCACAAATAAGTACTTAAAAC
*
20544372 CACCTATCGT
66 CACCTATCAT
20544382 TTTCTAGCAACTCATGCTTTCCACAAT
1 TTTCTAGCAACTCATGCTTTCCACAAT
20544409 GACATTGAAT
Statistics
Matches: 98, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
75 98 1.00
ACGTcount: A:0.35, C:0.24, G:0.07, T:0.34
Consensus pattern (75 bp):
TTTCTAGCAACTCATGCTTTCCACAATAATAGTTTATAAAACTTTCACAAATAAGTACTTAAAAC
CACCTATCAT
Found at i:20546058 original size:42 final size:42
Alignment explanation
Indices: 20546005--20546135 Score: 190
Period size: 42 Copynumber: 3.1 Consensus size: 42
20545995 GTACATGGCT
* * * *
20546005 GGGTCATCATCGGCTTATGTGCACTCCCACTCACACATAGTC
1 GGGTCATCATCGGCTTATGTACACTCCTACTCGCACATAATC
* *
20546047 GGGTCATCATCGGCTTATGCACACTCTTACTCGCACATAATC
1 GGGTCATCATCGGCTTATGTACACTCCTACTCGCACATAATC
* *
20546089 GGGTCATCATTGGCTTATGTACACTCCTACTCGCACATAACC
1 GGGTCATCATCGGCTTATGTACACTCCTACTCGCACATAATC
20546131 GGGTC
1 GGGTC
20546136 CACATCAACA
Statistics
Matches: 79, Mismatches: 10, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
42 79 1.00
ACGTcount: A:0.22, C:0.31, G:0.19, T:0.27
Consensus pattern (42 bp):
GGGTCATCATCGGCTTATGTACACTCCTACTCGCACATAATC
Found at i:20548329 original size:55 final size:55
Alignment explanation
Indices: 20548260--20548469 Score: 314
Period size: 55 Copynumber: 3.8 Consensus size: 55
20548250 TCATCTACCG
* *
20548260 GTCATCAGCTCATGTGCACTCCCACACCTCACATAGCTAGAATCATCAACCACTA
1 GTCATCAGCTCATGTGCACTCCCACACCTCACATAGCTGGAATCATCAACCACCA
* * *
20548315 GTCATCAGCTCATGTGCACTCTCACA-CTGCACATAGCTGGAATCATCATCCACCG
1 GTCATCAGCTCATGTGCACTCCCACACCT-CACATAGCTGGAATCATCAACCACCA
* * *
20548370 GTCATCAACTCATGTGCACTCCCACACCACACATAGCTGGAATCATCACCCACCA
1 GTCATCAGCTCATGTGCACTCCCACACCTCACATAGCTGGAATCATCAACCACCA
* *
20548425 ATCATCAGCTCATGTGCACTCCCACACCGCACATAGCTGGAATCA
1 GTCATCAGCTCATGTGCACTCCCACACCTCACATAGCTGGAATCA
20548470 CCTGTCATCA
Statistics
Matches: 140, Mismatches: 13, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
54 2 0.01
55 137 0.98
56 1 0.01
ACGTcount: A:0.29, C:0.37, G:0.13, T:0.21
Consensus pattern (55 bp):
GTCATCAGCTCATGTGCACTCCCACACCTCACATAGCTGGAATCATCAACCACCA
Found at i:20548442 original size:110 final size:110
Alignment explanation
Indices: 20548249--20548469 Score: 361
Period size: 110 Copynumber: 2.0 Consensus size: 110
20548239 TAAACATGTA
* * * *
20548249 ATCATCTACCGGTCATCAGCTCATGTGCACTCCCACACCTCACATAGCTAGAATCATCAACCACT
1 ATCATCCACCGGTCATCAACTCATGTGCACTCCCACACCACACATAGCTAGAATCATCAACCACC
* * *
20548314 AGTCATCAGCTCATGTGCACTCTCACACTGCACATAGCTGGAATC
66 AATCATCAGCTCATGTGCACTCCCACACCGCACATAGCTGGAATC
* *
20548359 ATCATCCACCGGTCATCAACTCATGTGCACTCCCACACCACACATAGCTGGAATCATCACCCACC
1 ATCATCCACCGGTCATCAACTCATGTGCACTCCCACACCACACATAGCTAGAATCATCAACCACC
20548424 AATCATCAGCTCATGTGCACTCCCACACCGCACATAGCTGGAATC
66 AATCATCAGCTCATGTGCACTCCCACACCGCACATAGCTGGAATC
20548469 A
1 A
20548470 CCTGTCATCA
Statistics
Matches: 102, Mismatches: 9, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
110 102 1.00
ACGTcount: A:0.29, C:0.37, G:0.13, T:0.21
Consensus pattern (110 bp):
ATCATCCACCGGTCATCAACTCATGTGCACTCCCACACCACACATAGCTAGAATCATCAACCACC
AATCATCAGCTCATGTGCACTCCCACACCGCACATAGCTGGAATC
Found at i:20549293 original size:14 final size:14
Alignment explanation
Indices: 20549258--20549284 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
20549248 AAAGAAAGGA
20549258 AAGGAAAAGAAAAC
1 AAGGAAAAGAAAAC
20549272 AAGGAAAAGAAAA
1 AAGGAAAAGAAAA
20549285 TGAAGAAAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.74, C:0.04, G:0.22, T:0.00
Consensus pattern (14 bp):
AAGGAAAAGAAAAC
Found at i:20554128 original size:42 final size:41
Alignment explanation
Indices: 20554073--20554204 Score: 156
Period size: 42 Copynumber: 3.1 Consensus size: 41
20554063 GTAATGATAT
*
20554073 TGACCCGGCTATGTGCGAGTAAGAGTGCGCATACGTCGATGA
1 TGACCC-GCTATGTGCGAGTAGGAGTGCGCATACGTCGATGA
* * * *
20554115 TGACCCAGCTATGTGCTAGGAGGAATGTGCATACGTCGATGA
1 TGACCC-GCTATGTGCGAGTAGGAGTGCGCATACGTCGATGA
* * *
20554157 TTGACCCGACTATGTGCGAGTGGGAGTGCGCATAAGCCGATGA
1 -TGACCCG-CTATGTGCGAGTAGGAGTGCGCATACGTCGATGA
20554200 TGACC
1 TGACC
20554205 TAGCCATCTG
Statistics
Matches: 75, Mismatches: 13, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
42 42 0.56
43 33 0.44
ACGTcount: A:0.24, C:0.21, G:0.33, T:0.22
Consensus pattern (41 bp):
TGACCCGCTATGTGCGAGTAGGAGTGCGCATACGTCGATGA
Found at i:20554226 original size:43 final size:42
Alignment explanation
Indices: 20554080--20554245 Score: 131
Period size: 43 Copynumber: 3.9 Consensus size: 42
20554070 TATTGACCCG
* * * *
20554080 GCTATGTGCGAGT-AAGAGTGCGCATACGTCGATGATGACCCA
1 GCTATGTGCTAGTGAGGAGTGCGCATAAGCCGATGATGA-CCA
* * * * *
20554122 GCTATGTGCTAG-GAGGAATGTGCATACGTCGATGATTGACCC
1 GCTATGTGCTAGTGAGGAGTGCGCATAAGCCGATGA-TGACCA
*
20554164 GACTATGTGCGAGTG-GGAGTGCGCATAAGCCGATGATGACCTA
1 G-CTATGTGCTAGTGAGGAGTGCGCATAAGCCGATGATGACC-A
* * * * * *
20554207 GCCATCTGCTAGTGAGGAGTACACATGAGCTGATGATGA
1 GCTATGTGCTAGTGAGGAGTGCGCATAAGCCGATGATGA
20554246 TGGTAGAGTG
Statistics
Matches: 100, Mismatches: 18, Indels: 11
0.78 0.14 0.09
Matches are distributed among these distances:
42 48 0.48
43 51 0.51
44 1 0.01
ACGTcount: A:0.26, C:0.19, G:0.32, T:0.23
Consensus pattern (42 bp):
GCTATGTGCTAGTGAGGAGTGCGCATAAGCCGATGATGACCA
Found at i:20554279 original size:2 final size:2
Alignment explanation
Indices: 20554272--20554350 Score: 133
Period size: 2 Copynumber: 40.0 Consensus size: 2
20554262 ATGATGATGG
20554272 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* *
20554313 NT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AC AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
20554351 GTAAATATGT
Statistics
Matches: 72, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
1 1 0.01
2 71 0.99
ACGTcount: A:0.49, C:0.01, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:20555617 original size:66 final size:66
Alignment explanation
Indices: 20555524--20555716 Score: 217
Period size: 66 Copynumber: 2.9 Consensus size: 66
20555514 AAGTTGGTTG
* * * ***
20555524 TTGGGTTTTGGTTGATCCCG-GTAAAAACCATTGTTGTAGGTTGTGGTTGAGCCTTGAAAAACCA
1 TTGGGTTTTAGTTGAGCCCGTG-AAAAACCAGTGTAAAAGGTTGTGGTTGAGCCTTGAAAAACCA
20555588 CC
65 CC
* * * *
20555590 TTGGGTTTTAGTTTAGCTCGTGAAAAACTAGTGTAAAAGGTTGTGGTTGAGCCTTGGAAAACCAC
1 TTGGGTTTTAGTTGAGCCCGTGAAAAACCAGTGTAAAAGGTTGTGGTTGAGCCTTGAAAAACCAC
*
20555655 T
66 C
** * * *
20555656 TTGGGTTTTAGTTGAGCCCGTGAAAAAATAGTGTGAAAGGTTTTGGCTGAGCCTGTGAAAA
1 TTGGGTTTTAGTTGAGCCCGTGAAAAACCAGTGTAAAAGGTTGTGGTTGAGCCT-TGAAAA
20555717 GCCATTGTAA
Statistics
Matches: 107, Mismatches: 18, Indels: 3
0.84 0.14 0.02
Matches are distributed among these distances:
66 101 0.94
67 6 0.06
ACGTcount: A:0.26, C:0.13, G:0.28, T:0.33
Consensus pattern (66 bp):
TTGGGTTTTAGTTGAGCCCGTGAAAAACCAGTGTAAAAGGTTGTGGTTGAGCCTTGAAAAACCAC
C
Found at i:20559495 original size:38 final size:37
Alignment explanation
Indices: 20559438--20559530 Score: 91
Period size: 38 Copynumber: 2.4 Consensus size: 37
20559428 CATGTGTATC
*
20559438 CCCCCAA-ATCGTGCACATAGCCGAAGT-CATTGTGTGCAT
1 CCCCCAACATCGTG--CATAGCC--AGTCCATTGTGTACAT
*
20559477 CCCCCAACATCGTGCATAGTCAGTGCCATTGTGTACAT
1 CCCCCAACATCGTGCATAGCCAGT-CCATTGTGTACAT
* *
20559515 CCCCCCACATCATGCA
1 CCCCCAACATCGTGCA
20559531 CACGGGCATT
Statistics
Matches: 47, Mismatches: 4, Indels: 7
0.81 0.07 0.12
Matches are distributed among these distances:
36 3 0.06
38 31 0.66
39 7 0.15
40 6 0.13
ACGTcount: A:0.25, C:0.35, G:0.17, T:0.23
Consensus pattern (37 bp):
CCCCCAACATCGTGCATAGCCAGTCCATTGTGTACAT
Found at i:20561682 original size:35 final size:34
Alignment explanation
Indices: 20561632--20561802 Score: 149
Period size: 35 Copynumber: 5.1 Consensus size: 34
20561622 CCACCAAGCT
* *
20561632 TTTACAATGGCTTTTCGCAGGCTCAACCACAACC
1 TTTACAATGGTTTTTCACAGGCTCAACCACAACC
* * *
20561666 TTTAGCAATGGTTTTTCACAAGATCAACCAAAACC
1 TTTA-CAATGGTTTTTCACAGGCTCAACCACAACC
*
20561701 --TA-AAGTGGTTTTTCAAAGGCTCAACCACAACC
1 TTTACAA-TGGTTTTTCACAGGCTCAACCACAACC
** * *
20561733 TTTCACAATGGTTTTTCATGGGCTCAACAAAAACC
1 TTT-ACAATGGTTTTTCACAGGCTCAACCACAACC
* *
20561768 --CA-AAGTGGTTTTCCA-AGGCTCAACCACAACC
1 TTTACAA-TGGTTTTTCACAGGCTCAACCACAACC
20561799 TTTA
1 TTTA
20561803 ATAATCAAGC
Statistics
Matches: 109, Mismatches: 19, Indels: 19
0.74 0.13 0.13
Matches are distributed among these distances:
31 17 0.16
32 33 0.30
33 3 0.03
34 5 0.05
35 49 0.45
36 2 0.02
ACGTcount: A:0.32, C:0.26, G:0.14, T:0.27
Consensus pattern (34 bp):
TTTACAATGGTTTTTCACAGGCTCAACCACAACC
Found at i:20561800 original size:66 final size:67
Alignment explanation
Indices: 20561650--20561802 Score: 220
Period size: 67 Copynumber: 2.3 Consensus size: 67
20561640 GGCTTTTCGC
* *
20561650 AGGCTCAACCACAACCTTTAGCAATGGTTTTTCACAAGATCAACCAAAACCTAAAGTGGTTTTTC
1 AGGCTCAACCACAACCTTTAGCAATGGTTTTTCACAAGATCAACAAAAACCCAAAGTGGTTTTTC
20561715 AA
66 AA
*** *
20561717 AGGCTCAACCACAACCTTTCA-CAATGGTTTTTCATGGGCTCAACAAAAACCCAAAGTGG-TTTT
1 AGGCTCAACCACAACCTTT-AGCAATGGTTTTTCACAAGATCAACAAAAACCCAAAGTGGTTTTT
*
20561780 CCA
65 CAA
20561783 AGGCTCAACCACAACCTTTA
1 AGGCTCAACCACAACCTTTA
20561803 ATAATCAAGC
Statistics
Matches: 78, Mismatches: 7, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
65 1 0.01
66 25 0.32
67 51 0.65
68 1 0.01
ACGTcount: A:0.34, C:0.27, G:0.14, T:0.25
Consensus pattern (67 bp):
AGGCTCAACCACAACCTTTAGCAATGGTTTTTCACAAGATCAACAAAAACCCAAAGTGGTTTTTC
AA
Found at i:20570798 original size:2 final size:2
Alignment explanation
Indices: 20570791--20570828 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
20570781 ATTGCACAAC
20570791 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
20570829 CAACATAATG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:20575440 original size:37 final size:37
Alignment explanation
Indices: 20575397--20575468 Score: 126
Period size: 37 Copynumber: 1.9 Consensus size: 37
20575387 GTGATCGTCA
*
20575397 TGTGCACTCCTTACTCACACACTTCAACATCATCATG
1 TGTGCACTCCCTACTCACACACTTCAACATCATCATG
*
20575434 TGTGCACTCCCTACTCGCACACTTCAACATCATCA
1 TGTGCACTCCCTACTCACACACTTCAACATCATCA
20575469 CATAACATTA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
37 33 1.00
ACGTcount: A:0.26, C:0.38, G:0.08, T:0.28
Consensus pattern (37 bp):
TGTGCACTCCCTACTCACACACTTCAACATCATCATG
Found at i:20576069 original size:19 final size:20
Alignment explanation
Indices: 20576045--20576083 Score: 62
Period size: 19 Copynumber: 2.0 Consensus size: 20
20576035 AGAAGAACAA
*
20576045 GAAGCTGTTGGA-AAATGAG
1 GAAGCTGTTAGAGAAATGAG
20576064 GAAGCTGTTAGAGAAATGAG
1 GAAGCTGTTAGAGAAATGAG
20576084 ATATTTATAG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 11 0.61
20 7 0.39
ACGTcount: A:0.38, C:0.05, G:0.36, T:0.21
Consensus pattern (20 bp):
GAAGCTGTTAGAGAAATGAG
Found at i:20579667 original size:28 final size:27
Alignment explanation
Indices: 20579628--20579681 Score: 81
Period size: 28 Copynumber: 2.0 Consensus size: 27
20579618 GTGTCTTGGT
**
20579628 GGTGGAAAATTACTGTTTTGCCCCTAA
1 GGTGGAAAATTACCATTTTGCCCCTAA
20579655 GGTGGCAAAATTACCATTTTGCCCCTA
1 GGTGG-AAAATTACCATTTTGCCCCTA
20579682 TGCTCTAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
27 5 0.21
28 19 0.79
ACGTcount: A:0.26, C:0.22, G:0.20, T:0.31
Consensus pattern (27 bp):
GGTGGAAAATTACCATTTTGCCCCTAA
Found at i:20584038 original size:25 final size:24
Alignment explanation
Indices: 20584006--20584053 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 24
20583996 ACTTCTCAAC
20584006 ATATTAGTGTA-AATGCAACATTTT
1 ATATTAGT-TAGAATGCAACATTTT
*
20584030 ATATATAGTTAGAATGCCACATTT
1 ATAT-TAGTTAGAATGCAACATTT
20584054 CTAGGGCAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
24 6 0.29
25 15 0.71
ACGTcount: A:0.38, C:0.10, G:0.12, T:0.40
Consensus pattern (24 bp):
ATATTAGTTAGAATGCAACATTTT
Found at i:20585400 original size:41 final size:41
Alignment explanation
Indices: 20585337--20585429 Score: 123
Period size: 41 Copynumber: 2.3 Consensus size: 41
20585327 CTACAACAAT
* *
20585337 TCTATCGATACACTCTGGAATGTATCAATACATGCAAGGAG
1 TCTATCGATACACTATGAAATGTATCAATACATGCAAGGAG
* * *
20585378 TCTATCGATACATTATGAAATGTATCGATGCATGCAAGGAG
1 TCTATCGATACACTATGAAATGTATCAATACATGCAAGGAG
* *
20585419 TTTATCAATAC
1 TCTATCGATAC
20585430 CTTTGGGAAA
Statistics
Matches: 45, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
41 45 1.00
ACGTcount: A:0.34, C:0.17, G:0.18, T:0.30
Consensus pattern (41 bp):
TCTATCGATACACTATGAAATGTATCAATACATGCAAGGAG
Found at i:20585444 original size:41 final size:41
Alignment explanation
Indices: 20585337--20585451 Score: 117
Period size: 41 Copynumber: 2.8 Consensus size: 41
20585327 CTACAACAAT
* * * * *
20585337 TCTATCGATACACTCTGGAATGTATCAATACATGCAAGGAG
1 TCTATCAATACATTATGGAAAGTATCGATACATGCAAGGAG
* *
20585378 TCTATCGATACATTAT-GAAATGTATCGATGCATGCAAGGAG
1 TCTATCAATACATTATGGAAA-GTATCGATACATGCAAGGAG
* *
20585419 TTTATCAATACCTT-TGGGAAAGTATCGATACAT
1 TCTATCAATACATTAT-GGAAAGTATCGATACAT
20585452 TTCACACAAT
Statistics
Matches: 62, Mismatches: 9, Indels: 6
0.81 0.12 0.08
Matches are distributed among these distances:
40 4 0.06
41 54 0.87
42 4 0.06
ACGTcount: A:0.34, C:0.17, G:0.19, T:0.30
Consensus pattern (41 bp):
TCTATCAATACATTATGGAAAGTATCGATACATGCAAGGAG
Found at i:20587223 original size:12 final size:12
Alignment explanation
Indices: 20587187--20587223 Score: 53
Period size: 12 Copynumber: 3.3 Consensus size: 12
20587177 TTTTGGGAAA
20587187 ATGTATCGATAC
1 ATGTATCGATAC
20587199 AT-TAT-GA-AC
1 ATGTATCGATAC
20587208 ATGTATCGATAC
1 ATGTATCGATAC
20587220 ATGT
1 ATGT
20587224 TCATCAGAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
9 4 0.18
10 5 0.23
11 5 0.23
12 8 0.36
ACGTcount: A:0.35, C:0.14, G:0.16, T:0.35
Consensus pattern (12 bp):
ATGTATCGATAC
Found at i:20590031 original size:56 final size:55
Alignment explanation
Indices: 20589942--20590090 Score: 178
Period size: 55 Copynumber: 2.7 Consensus size: 55
20589932 AACGGTCCTT
* * * *
20589942 AGCTCATGTGCCCTCCCACACCGTACATAGCTGGATAT-AGAC-CACCACCAGTCATC
1 AGCTCATGTGCACTCTCACACCGCACATAGCTGGA-ATCA-ACAC-CCACCAATCATC
*
20589998 AGCTCATGTGCACTCTCACACCGCACATGGCTGGAATCAACACCCACCAATCATC
1 AGCTCATGTGCACTCTCACACCGCACATAGCTGGAATCAACACCCACCAATCATC
* *
20590053 AACTCATGTGCACT-TCAACACTGCACATAGCTGGAATC
1 AGCTCATGTGCACTCTC-ACACCGCACATAGCTGGAATC
20590091 TCCCGTCCTT
Statistics
Matches: 82, Mismatches: 8, Indels: 7
0.85 0.08 0.07
Matches are distributed among these distances:
54 2 0.02
55 47 0.57
56 33 0.40
ACGTcount: A:0.29, C:0.36, G:0.15, T:0.20
Consensus pattern (55 bp):
AGCTCATGTGCACTCTCACACCGCACATAGCTGGAATCAACACCCACCAATCATC
Found at i:20594999 original size:2 final size:2
Alignment explanation
Indices: 20594992--20595018 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
20594982 GGTATATGCG
20594992 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
20595019 GTAAATATCT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:20599678 original size:66 final size:65
Alignment explanation
Indices: 20599572--20599702 Score: 244
Period size: 66 Copynumber: 2.0 Consensus size: 65
20599562 AAGTAAGCAA
*
20599572 TCGTTCTCATAGGTTGAAGTATAAATATACTTGGAACTAGCATGTGGGTGTTTGCCATGGGAGAG
1 TCGTTCTCATAGGTTGAAGTATAAAGATACTTGGAACTAGCATGTGGGTGTTTGCCATGGGAGAG
20599637 NTCGTTCTCATAGGTTGAAGTATAAAGATACTTGGAACTAGCATGTGGGTGTTTGCCATGGGAGA
1 -TCGTTCTCATAGGTTGAAGTATAAAGATACTTGGAACTAGCATGTGGGTGTTTGCCATGGGAGA
20599702 G
65 G
20599703 CGAGTTCACT
Statistics
Matches: 64, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
66 64 1.00
ACGTcount: A:0.26, C:0.12, G:0.30, T:0.31
Consensus pattern (65 bp):
TCGTTCTCATAGGTTGAAGTATAAAGATACTTGGAACTAGCATGTGGGTGTTTGCCATGGGAGAG
Found at i:20600293 original size:20 final size:19
Alignment explanation
Indices: 20600268--20600322 Score: 60
Period size: 20 Copynumber: 2.8 Consensus size: 19
20600258 TGGTCTATGG
20600268 AATTGAATTAGTTAATTTAA
1 AATTGAATTAGTTAATTT-A
*
20600288 AATTGAA-TATGATTCATTTA
1 AATTGAATTA-G-TTAATTTA
20600308 AATT-AATTAGTTAAT
1 AATTGAATTAGTTAAT
20600323 AATATTATAA
Statistics
Matches: 30, Mismatches: 2, Indels: 8
0.75 0.05 0.20
Matches are distributed among these distances:
18 4 0.13
19 5 0.17
20 15 0.50
21 6 0.20
ACGTcount: A:0.44, C:0.02, G:0.09, T:0.45
Consensus pattern (19 bp):
AATTGAATTAGTTAATTTA
Found at i:20601222 original size:35 final size:35
Alignment explanation
Indices: 20601183--20601291 Score: 139
Period size: 35 Copynumber: 3.1 Consensus size: 35
20601173 GGGAATGCGT
20601183 ATGATGATATTGAAATGTGCGAGTAAGGAGTGCAC
1 ATGATGATATTGAAATGTGCGAGTAAGGAGTGCAC
* * *
20601218 ATGATGATAGTGAAATGTGTGAAT-AGGAAGTGCAC
1 ATGATGATATTGAAATGTGCGAGTAAGG-AGTGCAC
** * *
20601253 ATGATGATATTGAAATGTGCTTGTAGGGAGTGTAC
1 ATGATGATATTGAAATGTGCGAGTAAGGAGTGCAC
20601288 ATGA
1 ATGA
20601292 GCTGAGTGAA
Statistics
Matches: 62, Mismatches: 10, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
34 3 0.05
35 57 0.92
36 2 0.03
ACGTcount: A:0.34, C:0.06, G:0.31, T:0.28
Consensus pattern (35 bp):
ATGATGATATTGAAATGTGCGAGTAAGGAGTGCAC
Found at i:20603906 original size:25 final size:25
Alignment explanation
Indices: 20603877--20603960 Score: 127
Period size: 25 Copynumber: 3.4 Consensus size: 25
20603867 GGTCTGTGAT
*
20603877 TATACGTGGCA-AGGCCAC-AGGTTGT
1 TATACGTGGCAGA-GCCACGA-GTTGA
20603902 TATACGTGGCAGAGCCACGAGTTGA
1 TATACGTGGCAGAGCCACGAGTTGA
20603927 TATACGTGGCAGAGCCACGAGTTGA
1 TATACGTGGCAGAGCCACGAGTTGA
20603952 TATACGTGG
1 TATACGTGG
20603961 TTACGACCAC
Statistics
Matches: 56, Mismatches: 1, Indels: 4
0.92 0.02 0.07
Matches are distributed among these distances:
25 54 0.96
26 2 0.04
ACGTcount: A:0.26, C:0.19, G:0.32, T:0.23
Consensus pattern (25 bp):
TATACGTGGCAGAGCCACGAGTTGA
Found at i:20606897 original size:39 final size:39
Alignment explanation
Indices: 20606810--20606898 Score: 117
Period size: 39 Copynumber: 2.3 Consensus size: 39
20606800 CGAGATTGAA
*
20606810 TCTTGCTGTAGTGAAAATATGACCCAGAAACAAAATGTT
1 TCTTGCTGTAGTGAAAATATAACCCAGAAACAAAATGTT
** * *
20606849 TCTCACTGTAGTGAAATTGTAACCCAGAAACAGAAA-GTT
1 TCTTGCTGTAGTGAAAATATAACCCAGAAACA-AAATGTT
20606888 TCTTGCTGTAG
1 TCTTGCTGTAG
20606899 CGAGAATGAA
Statistics
Matches: 42, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
39 39 0.93
40 3 0.07
ACGTcount: A:0.35, C:0.17, G:0.19, T:0.29
Consensus pattern (39 bp):
TCTTGCTGTAGTGAAAATATAACCCAGAAACAAAATGTT
Found at i:20607192 original size:2 final size:2
Alignment explanation
Indices: 20607180--20607213 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
20607170 ACCATATACC
*
20607180 AT AT AT GT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
20607214 CAATCATCAT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:20607306 original size:42 final size:42
Alignment explanation
Indices: 20607254--20607371 Score: 164
Period size: 42 Copynumber: 2.8 Consensus size: 42
20607244 CATCTCATAT
* * * *
20607254 GCAACAGCTTATGCGCACTCCCACTTGCACATAGTCGGGTTA
1 GCAACGGCTTATGTGCACTCCCACTCGCACATAGTCGGGTCA
20607296 GCAACGGCTTATGTGCACTCCCACTCGCACATAGTCGGGTCA
1 GCAACGGCTTATGTGCACTCCCACTCGCACATAGTCGGGTCA
* * **
20607338 GCAATGGCTTATATGCACTCCTTCTCGCACATAG
1 GCAACGGCTTATGTGCACTCCCACTCGCACATAG
20607372 CCGAGTCCAA
Statistics
Matches: 68, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
42 68 1.00
ACGTcount: A:0.23, C:0.31, G:0.21, T:0.25
Consensus pattern (42 bp):
GCAACGGCTTATGTGCACTCCCACTCGCACATAGTCGGGTCA
Found at i:20609504 original size:71 final size:71
Alignment explanation
Indices: 20609397--20609634 Score: 212
Period size: 71 Copynumber: 3.4 Consensus size: 71
20609387 GGAAAGTCAT
* * ** * * *
20609397 GCATTCTAGTCCAGGATAGACTATAGGCCTTTTATAGTTGATCCTATGAAGAGAAAATGGAAGAA
1 GCATTCTAGTCCAAGATCGACTATAAACCTTCTATAGTTGATCCTGTGAA-AGAAAATGGATGAA
*
20609462 ATGC-AA
65 AAGCAAA
* * *
20609468 GCATTCTAGTCCAAGATCGACTATAAACCCTCTATAGTCGATCTTGTGAAAGAAAAT-GAGTGAA
1 GCATTCTAGTCCAAGATCGACTATAAACCTTCTATAGTTGATCCTGTGAAAGAAAATGGA-TGAA
*
20609532 AAGCGAA
65 AAGCAAA
* * * * * * *
20609539 -CATTTTAGGCCAATATCGACTACAAACCTTGTACAGTTGATCCTGTGAAAGGGAAATGGATGAA
1 GCATTCTAGTCCAAGATCGACTATAAACCTTCTATAGTTGATCCTGTGAAA-GAAAATGGATGAA
*
20609603 ACGCAAA
65 AAGCAAA
* * * *
20609610 ACCTTCTGGTCCAAGATTGACTATA
1 GCATTCTAGTCCAAGATCGACTATA
20609635 GCCCCTCCAT
Statistics
Matches: 132, Mismatches: 30, Indels: 9
0.77 0.18 0.05
Matches are distributed among these distances:
69 2 0.02
70 54 0.41
71 57 0.43
72 19 0.14
ACGTcount: A:0.36, C:0.18, G:0.21, T:0.26
Consensus pattern (71 bp):
GCATTCTAGTCCAAGATCGACTATAAACCTTCTATAGTTGATCCTGTGAAAGAAAATGGATGAAA
AGCAAA
Found at i:20613941 original size:55 final size:55
Alignment explanation
Indices: 20613854--20614034 Score: 278
Period size: 55 Copynumber: 3.3 Consensus size: 55
20613844 GCTGACCTTG
* * * *
20613854 CCGCACATAGTTGGAATCATCACCCACTGGTCATTAGCTCATGTGCACTCCCACA
1 CCGCACATAGCTGGAATCATCACCCACCGGTCACTAGCTCAAGTGCACTCCCACA
20613909 CCGCACATAGCTGGAATCATCACCCACCGGTCACTAGCTCAAGTGCACTCCCACA
1 CCGCACATAGCTGGAATCATCACCCACCGGTCACTAGCTCAAGTGCACTCCCACA
* * *
20613964 CCGCACATAGTTGG-A--ATCACCCACCGCTCACCAGCTCAAGTGCACTCCCACA
1 CCGCACATAGCTGGAATCATCACCCACCGGTCACTAGCTCAAGTGCACTCCCACA
20614016 CCGCACATAGCTGGAATCA
1 CCGCACATAGCTGGAATCA
20614035 CCCATCGTCA
Statistics
Matches: 115, Mismatches: 8, Indels: 6
0.89 0.06 0.05
Matches are distributed among these distances:
52 48 0.42
53 1 0.01
54 1 0.01
55 65 0.57
ACGTcount: A:0.27, C:0.38, G:0.17, T:0.18
Consensus pattern (55 bp):
CCGCACATAGCTGGAATCATCACCCACCGGTCACTAGCTCAAGTGCACTCCCACA
Found at i:20614005 original size:52 final size:54
Alignment explanation
Indices: 20613854--20614065 Score: 267
Period size: 55 Copynumber: 4.0 Consensus size: 54
20613844 GCTGACCTTG
* * ** *
20613854 CCGCACATAGTTGGAATCATCACCCACTGGTCATTAGCTCATGTGCACTCCCACA
1 CCGCACATAGCTGGAA-CATCACCCACCGGTCACCAGCTCAAGTGCACTCCCACA
*
20613909 CCGCACATAGCTGGAATCATCACCCACCGGTCACTAGCTCAAGTGCACTCCCACA
1 CCGCACATAGCTGGAA-CATCACCCACCGGTCACCAGCTCAAGTGCACTCCCACA
* *
20613964 CCGCACATAGTTGG-A-ATCACCCACCGCTCACCAGCTCAAGTGCACTCCCACA
1 CCGCACATAGCTGGAACATCACCCACCGGTCACCAGCTCAAGTGCACTCCCACA
* *
20614016 CCGCACATAGCTGG-A-ATCACCCATC-GTCACCAG--CATGTGCACTCCCACA
1 CCGCACATAGCTGGAACATCACCCACCGGTCACCAGCTCAAGTGCACTCCCACA
20614065 C
1 C
20614066 TTCACACGCG
Statistics
Matches: 146, Mismatches: 11, Indels: 6
0.90 0.07 0.04
Matches are distributed among these distances:
49 16 0.11
51 7 0.05
52 58 0.40
54 1 0.01
55 64 0.44
ACGTcount: A:0.26, C:0.40, G:0.16, T:0.18
Consensus pattern (54 bp):
CCGCACATAGCTGGAACATCACCCACCGGTCACCAGCTCAAGTGCACTCCCACA
Found at i:20617064 original size:42 final size:42
Alignment explanation
Indices: 20616951--20617106 Score: 215
Period size: 42 Copynumber: 3.7 Consensus size: 42
20616941 CAGCTCATGT
*
20616951 GCACTCTCTACTCGCACATAGCTGGGTCAGCATCGGCTTATGC
1 GCACTC-CCACTCGCACATAGCTGGGTCAGCATCGGCTTATGC
*
20616994 GCACTCCCTACTCGCACATAG-TCGGGTCAGCATCGGCTTATGT
1 GCACTCCC-ACTCGCACATAGCT-GGGTCAGCATCGGCTTATGC
* * *
20617037 GCACACCCACTCGTACATAGCTAGGTCAGCATCGGCTTATGC
1 GCACTCCCACTCGCACATAGCTGGGTCAGCATCGGCTTATGC
* *
20617079 GCACTCCCACTAGCACATAGCCGGGTCA
1 GCACTCCCACTCGCACATAGCTGGGTCA
20617107 ATATCATTAC
Statistics
Matches: 99, Mismatches: 11, Indels: 7
0.85 0.09 0.06
Matches are distributed among these distances:
42 54 0.55
43 45 0.45
ACGTcount: A:0.21, C:0.34, G:0.22, T:0.22
Consensus pattern (42 bp):
GCACTCCCACTCGCACATAGCTGGGTCAGCATCGGCTTATGC
Found at i:20618589 original size:43 final size:43
Alignment explanation
Indices: 20618492--20618600 Score: 128
Period size: 43 Copynumber: 2.5 Consensus size: 43
20618482 TGACTCGGCT
** * * * **
20618492 ATGTGCGAGTAAAGAGTGCGCATAAGCCGATGATGACCCGATT
1 ATGTGCGAGTAGGGAGTGCGCATAACCCGATGATAACCCAACC
* *
20618535 ATGTGCTAGTAGGGAGTGCGCATAACCCGGTGATAACCCAACC
1 ATGTGCGAGTAGGGAGTGCGCATAACCCGATGATAACCCAACC
*
20618578 ATGTGCGAGTAGGGAGTACGCAT
1 ATGTGCGAGTAGGGAGTGCGCAT
20618601 GAACTGATGA
Statistics
Matches: 55, Mismatches: 11, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
43 55 1.00
ACGTcount: A:0.28, C:0.20, G:0.31, T:0.20
Consensus pattern (43 bp):
ATGTGCGAGTAGGGAGTGCGCATAACCCGATGATAACCCAACC
Found at i:20624151 original size:2 final size:2
Alignment explanation
Indices: 20624144--20624177 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
20624134 TGGCAACCGA
20624144 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
20624178 TATTCACAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:20630664 original size:20 final size:21
Alignment explanation
Indices: 20630621--20630665 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 21
20630611 ATGTCTAAAG
* *
20630621 TAATTATTTGAAATGAAATTA
1 TAATTATTTGAAATAAAATAA
*
20630642 TAATTGTTTG-AATAAAATAA
1 TAATTATTTGAAATAAAATAA
20630662 TAAT
1 TAAT
20630666 ATTCAATAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
20 12 0.57
21 9 0.43
ACGTcount: A:0.49, C:0.00, G:0.09, T:0.42
Consensus pattern (21 bp):
TAATTATTTGAAATAAAATAA
Found at i:20638437 original size:15 final size:14
Alignment explanation
Indices: 20638417--20638467 Score: 57
Period size: 15 Copynumber: 3.4 Consensus size: 14
20638407 TTCTTAAAAC
20638417 AACTTTAAAATCGAA
1 AACTTTAAAATC-AA
20638432 AACTTTAAAATCTAA
1 AACTTTAAAATC-AA
**
20638447 CGCTTTAAAATCAA
1 AACTTTAAAATCAA
20638461 AATCTTT
1 AA-CTTT
20638468 GATCTTTAAA
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
14 2 0.07
15 28 0.93
ACGTcount: A:0.47, C:0.16, G:0.04, T:0.33
Consensus pattern (14 bp):
AACTTTAAAATCAA
Found at i:20638921 original size:28 final size:29
Alignment explanation
Indices: 20638864--20638921 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 29
20638854 ATAATAATAT
** *
20638864 TAAATAAAATATTCTATTTTCTAAATAAA
1 TAAATAAAATATAATATTTTCTAAAGAAA
*
20638893 TAAATAAAATATAATA-TTTCTAGAGAAA
1 TAAATAAAATATAATATTTTCTAAAGAAA
20638921 T
1 T
20638922 CCGTAATTTA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
28 11 0.44
29 14 0.56
ACGTcount: A:0.53, C:0.05, G:0.03, T:0.38
Consensus pattern (29 bp):
TAAATAAAATATAATATTTTCTAAAGAAA
Found at i:20642179 original size:55 final size:55
Alignment explanation
Indices: 20642087--20642232 Score: 220
Period size: 55 Copynumber: 2.7 Consensus size: 55
20642077 GGTCGTGACA
* * *
20642087 TCATGTGCACTCCCACACCGCACATAGCTAGAATCATCACCCACCGGTCATCGGC
1 TCATGTGCACTCCCACACCGCACATAGCTGGAATCATCACCCACCGATCATCAGC
* * * *
20642142 TCATGTGCACTCCCACACCACACATAGCTGGATTCATCACCCATCGATCATTAGC
1 TCATGTGCACTCCCACACCGCACATAGCTGGAATCATCACCCACCGATCATCAGC
*
20642197 TCATGTGCACTCCCACACCGCACATAGTTGGAATCA
1 TCATGTGCACTCCCACACCGCACATAGCTGGAATCA
20642233 CTCGTCATCA
Statistics
Matches: 81, Mismatches: 10, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
55 81 1.00
ACGTcount: A:0.27, C:0.37, G:0.15, T:0.21
Consensus pattern (55 bp):
TCATGTGCACTCCCACACCGCACATAGCTGGAATCATCACCCACCGATCATCAGC
Found at i:20642252 original size:49 final size:52
Alignment explanation
Indices: 20642088--20642265 Score: 182
Period size: 55 Copynumber: 3.4 Consensus size: 52
20642078 GTCGTGACAT
* * * * *
20642088 CATGTGCACTCCCACACCGCACATAGCTAGAATCATCACCCACCGGTCATCGGC
1 CATGTGCACTCCCACACCGCACATAGCT-GGAT-ATCACCCATCGATCACCAGC
* **
20642142 TCATGTGCACTCCCACACCACACATAGCTGGATTCATCACCCATCGATCATTAGC
1 -CATGTGCACTCCCACACCGCACATAGCTGGA-T-ATCACCCATCGATCACCAGC
* * *
20642197 TCATGTGCACTCCCACACCGCACATAGTTGGA-ATCACTCGTC-ATCACCAG-
1 -CATGTGCACTCCCACACCGCACATAGCTGGATATCACCCATCGATCACCAGC
20642247 CATGTGCACTCCCACACCG
1 CATGTGCACTCCCACACCG
20642266 AACACACACG
Statistics
Matches: 110, Mismatches: 12, Indels: 8
0.85 0.09 0.06
Matches are distributed among these distances:
49 19 0.17
51 6 0.05
52 8 0.07
54 2 0.02
55 75 0.68
ACGTcount: A:0.26, C:0.39, G:0.15, T:0.20
Consensus pattern (52 bp):
CATGTGCACTCCCACACCGCACATAGCTGGATATCACCCATCGATCACCAGC
Found at i:20646020 original size:20 final size:20
Alignment explanation
Indices: 20645997--20646034 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
20645987 AAGGAAGAAG
* *
20645997 TAAGAAAATAAAGGAAAGGA
1 TAAGAAAACAAAGAAAAGGA
20646017 TAAGAAAACAAAGAAAAG
1 TAAGAAAACAAAGAAAAG
20646035 AAAATGAAGC
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:0.68, C:0.03, G:0.21, T:0.08
Consensus pattern (20 bp):
TAAGAAAACAAAGAAAAGGA
Found at i:20655036 original size:17 final size:17
Alignment explanation
Indices: 20654995--20655040 Score: 51
Period size: 17 Copynumber: 2.7 Consensus size: 17
20654985 AATAAAGTCT
*
20654995 ATTATATGT-TACAATA
1 ATTATATGTATAAAATA
20655011 A-TACTTATGTATAAAATA
1 ATTA--TATGTATAAAATA
20655029 ATTATATGTATA
1 ATTATATGTATA
20655041 TATATAGTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
15 2 0.08
16 1 0.04
17 13 0.52
18 7 0.28
19 2 0.08
ACGTcount: A:0.46, C:0.04, G:0.07, T:0.43
Consensus pattern (17 bp):
ATTATATGTATAAAATA
Found at i:20655483 original size:20 final size:20
Alignment explanation
Indices: 20655460--20655497 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
20655450 CCCATTTGAC
20655460 TTATTGGAGTATAATTTGGA
1 TTATTGGAGTATAATTTGGA
*
20655480 TTATTGGAGTATGATTTG
1 TTATTGGAGTATAATTTG
20655498 AGGTTTAGAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.26, C:0.00, G:0.26, T:0.47
Consensus pattern (20 bp):
TTATTGGAGTATAATTTGGA
Found at i:20655685 original size:28 final size:28
Alignment explanation
Indices: 20655543--20655678 Score: 238
Period size: 28 Copynumber: 4.9 Consensus size: 28
20655533 TTTGGAGTAT
20655543 AGGGGCAAAATGGTAATTTTGCCACTAG
1 AGGGGCAAAATGGTAATTTTGCCACTAG
20655571 AGGGGCAAAATGGTAATTTTGCCACTAG
1 AGGGGCAAAATGGTAATTTTGCCACTAG
20655599 AGGGGCAAAATGGTAATTTTGCCACTAG
1 AGGGGCAAAATGGTAATTTTGCCACTAG
* *
20655627 AGGGGCAAAATTGTAATTTTGCCACTAT
1 AGGGGCAAAATGGTAATTTTGCCACTAG
*
20655655 AGGGGCAAAATTGTAATTTT-CCAC
1 AGGGGCAAAATGGTAATTTTGCCAC
20655679 CACTAGGATA
Statistics
Matches: 106, Mismatches: 2, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
27 4 0.04
28 102 0.96
ACGTcount: A:0.32, C:0.15, G:0.26, T:0.27
Consensus pattern (28 bp):
AGGGGCAAAATGGTAATTTTGCCACTAG
Found at i:20665492 original size:18 final size:20
Alignment explanation
Indices: 20665453--20665492 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
20665443 GGGTATTTTC
*
20665453 ATAATTTGCTACCGAGACTG
1 ATAATTTGCTACCGACACTG
20665473 ATAATTTGC-ACC-ACACTG
1 ATAATTTGCTACCGACACTG
20665491 AT
1 AT
20665493 GGACATTAAG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 7 0.37
19 3 0.16
20 9 0.47
ACGTcount: A:0.33, C:0.23, G:0.15, T:0.30
Consensus pattern (20 bp):
ATAATTTGCTACCGACACTG
Found at i:20682784 original size:20 final size:20
Alignment explanation
Indices: 20682759--20682799 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
20682749 TGACTTTTTT
20682759 TCATTCCCATCCAAACCACA
1 TCATTCCCATCCAAACCACA
*
20682779 TCATTCCCATTCAAACCACA
1 TCATTCCCATCCAAACCACA
20682799 T
1 T
20682800 TCACACCATT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.34, C:0.41, G:0.00, T:0.24
Consensus pattern (20 bp):
TCATTCCCATCCAAACCACA
Found at i:20688751 original size:22 final size:22
Alignment explanation
Indices: 20688723--20688766 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
20688713 CCGTCGCTCC
20688723 CTTCACCACCGTGGCTTCCTCT
1 CTTCACCACCGTGGCTTCCTCT
20688745 CTTCACCACCGTGGCTTCCTCT
1 CTTCACCACCGTGGCTTCCTCT
20688767 ATTCCTTTCC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.09, C:0.45, G:0.14, T:0.32
Consensus pattern (22 bp):
CTTCACCACCGTGGCTTCCTCT
Found at i:20689024 original size:23 final size:22
Alignment explanation
Indices: 20688998--20689051 Score: 56
Period size: 23 Copynumber: 2.3 Consensus size: 22
20688988 CTTCAATGGT
20688998 AGCAAAAACCTCCAAAAATTT-CC
1 AGCAAAAACCT-C-AAAATTTACC
*
20689021 AGCAACAAAACCTCAAAATTTAGC
1 AGC-A-AAAACCTCAAAATTTACC
20689045 AGCAAAA
1 AGCAAAA
20689052 TCTTTGAATT
Statistics
Matches: 27, Mismatches: 1, Indels: 7
0.77 0.03 0.20
Matches are distributed among these distances:
22 3 0.11
23 11 0.41
24 6 0.22
25 7 0.26
ACGTcount: A:0.52, C:0.26, G:0.07, T:0.15
Consensus pattern (22 bp):
AGCAAAAACCTCAAAATTTACC
Found at i:20703188 original size:68 final size:68
Alignment explanation
Indices: 20703079--20703325 Score: 341
Period size: 68 Copynumber: 3.6 Consensus size: 68
20703069 ATCTGATAAG
* * * *
20703079 GTATATGGAAAATACATCATATACATAATCTTATGGCATTCATCATGCTTCCTCAAGCATCTCAT
1 GTATATGGAATATACATCATATACATAATCTCATGGCATTCATCATGCTTACTCAATCATCTCAT
20703144 GTA
66 GTA
*
20703147 GTATATGGAATATACATCATATACATAATCTCATGGCATTCATCATGCTTTCTCAATCATCTCAT
1 GTATATGGAATATACATCATATACATAATCTCATGGCATTCATCATGCTTACTCAATCATCTCAT
20703212 GTA
66 GTA
* * * * * * *
20703215 GCATATAGAATATACATCATATACATAATCTCATGGCATTTATCATGCATACTTAATCACCTGAT
1 GTATATGGAATATACATCATATACATAATCTCATGGCATTCATCATGCTTACTCAATCATCTCAT
* *
20703280 ATG
66 GTA
* * *
20703283 GTATATGGAATTTACATCATATATATAATCTTATGGCATTCAT
1 GTATATGGAATATACATCATATACATAATCTCATGGCATTCAT
20703326 TATACCAATT
Statistics
Matches: 159, Mismatches: 20, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
68 159 1.00
ACGTcount: A:0.34, C:0.19, G:0.11, T:0.36
Consensus pattern (68 bp):
GTATATGGAATATACATCATATACATAATCTCATGGCATTCATCATGCTTACTCAATCATCTCAT
GTA
Found at i:20704590 original size:16 final size:16
Alignment explanation
Indices: 20704566--20704596 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
20704556 TATAAATATA
20704566 AAAAAAATCAAAATCT
1 AAAAAAATCAAAATCT
*
20704582 AAAAGAATCAAAATC
1 AAAAAAATCAAAATC
20704597 AAATTTTTGG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.68, C:0.13, G:0.03, T:0.16
Consensus pattern (16 bp):
AAAAAAATCAAAATCT
Found at i:20708523 original size:63 final size:63
Alignment explanation
Indices: 20708437--20708574 Score: 188
Period size: 63 Copynumber: 2.2 Consensus size: 63
20708427 TATCGGCATG
* **
20708437 TGCACTGCCCACTCCGCACATGCACAGTTGTAAG-TGTCACAACATCATCATTTGACCGACATA
1 TGCACTGCCCACTCAGCACATGCACAGTTGT-AGTTGTCACAACATCATCATTCAACCGACATA
* * * * *
20708500 TGCACTGCCCACTCAGCATATGCACGGTTGTAGTTGTCACTACATCGTCATTCAACCGGCATA
1 TGCACTGCCCACTCAGCACATGCACAGTTGTAGTTGTCACAACATCATCATTCAACCGACATA
20708563 TGCACTGCCCAC
1 TGCACTGCCCAC
20708575 AAACACATGC
Statistics
Matches: 66, Mismatches: 8, Indels: 2
0.87 0.11 0.03
Matches are distributed among these distances:
62 2 0.03
63 64 0.97
ACGTcount: A:0.25, C:0.33, G:0.17, T:0.25
Consensus pattern (63 bp):
TGCACTGCCCACTCAGCACATGCACAGTTGTAGTTGTCACAACATCATCATTCAACCGACATA
Found at i:20712848 original size:34 final size:34
Alignment explanation
Indices: 20712742--20712852 Score: 150
Period size: 34 Copynumber: 3.3 Consensus size: 34
20712732 TTGGCTGTTG
* *
20712742 AAAATTTGAGCTGTTTGCTGCCAATTTGTGCAAA
1 AAAATTGGAGCTGTTTGCTGCCAATTTGTGCAGA
**
20712776 AAAATTGGAATTGTTTGCTGCCAATTTGTGCAGA
1 AAAATTGGAGCTGTTTGCTGCCAATTTGTGCAGA
* * * *
20712810 AAAATTGGAGCTGTTTGTTACCAATTTGTGTAGG
1 AAAATTGGAGCTGTTTGCTGCCAATTTGTGCAGA
20712844 AAAATTGGA
1 AAAATTGGA
20712853 CAGCATAGTG
Statistics
Matches: 67, Mismatches: 10, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
34 67 1.00
ACGTcount: A:0.31, C:0.11, G:0.23, T:0.35
Consensus pattern (34 bp):
AAAATTGGAGCTGTTTGCTGCCAATTTGTGCAGA
Found at i:20712986 original size:15 final size:16
Alignment explanation
Indices: 20712966--20712998 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
20712956 AGCCAAGGAG
20712966 AAGAAAA-AAAAAGAA
1 AAGAAAAGAAAAAGAA
*
20712981 AAGAAAAGAAATAGAA
1 AAGAAAAGAAAAAGAA
20712997 AA
1 AA
20712999 TAAATGGGCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 7 0.44
16 9 0.56
ACGTcount: A:0.82, C:0.00, G:0.15, T:0.03
Consensus pattern (16 bp):
AAGAAAAGAAAAAGAA
Found at i:20713018 original size:25 final size:25
Alignment explanation
Indices: 20712990--20713052 Score: 90
Period size: 25 Copynumber: 2.5 Consensus size: 25
20712980 AAAGAAAAGA
20712990 AATAGAAAATAAATGGGCATGACCC
1 AATAGAAAATAAATGGGCATGACCC
* * *
20713015 AATATAAAATAAGTGGGCATGGCCC
1 AATAGAAAATAAATGGGCATGACCC
*
20713040 AATAGGAAATAAA
1 AATAGAAAATAAA
20713053 AATAAATGGG
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
25 32 1.00
ACGTcount: A:0.49, C:0.13, G:0.21, T:0.17
Consensus pattern (25 bp):
AATAGAAAATAAATGGGCATGACCC
Found at i:20713056 original size:31 final size:33
Alignment explanation
Indices: 20713015--20713080 Score: 91
Period size: 31 Copynumber: 2.1 Consensus size: 33
20713005 GGCATGACCC
* *
20713015 AATATAAAATAAGTGGGCATGGCCC-AATAGGA
1 AATATAAAATAAATGGGCATAGCCCAAATAGGA
*
20713047 AATA-AAAATAAATGGGCTTAGCCCAAATAGGA
1 AATATAAAATAAATGGGCATAGCCCAAATAGGA
20713079 AA
1 AA
20713081 AATGAAGAAG
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
31 17 0.57
32 13 0.43
ACGTcount: A:0.48, C:0.12, G:0.21, T:0.18
Consensus pattern (33 bp):
AATATAAAATAAATGGGCATAGCCCAAATAGGA
Found at i:20722302 original size:42 final size:42
Alignment explanation
Indices: 20722250--20722457 Score: 256
Period size: 42 Copynumber: 5.0 Consensus size: 42
20722240 CATCTCATAT
* * * * * *
20722250 GCAACGGCTTATGCGTACTCCCACTCGTATATAACCAGGTCA
1 GCAACGGCTTATGTGCACTCCCACTCGCACATAGCCGGGTCA
* * *
20722292 GCAATGGCTTATGTGCACTTCTACTCGCACATAGCCGGGTCA
1 GCAACGGCTTATGTGCACTCCCACTCGCACATAGCCGGGTCA
*
20722334 GCAACGACTTATGTGCACTCCCACTCGCACATAGCCGGGTCA
1 GCAACGGCTTATGTGCACTCCCACTCGCACATAGCCGGGTCA
* * * * *
20722376 GCAA-TGCATATGTGCACTCCTACTCGCACATAGTCGAGTCA
1 GCAACGGCTTATGTGCACTCCCACTCGCACATAGCCGGGTCA
* *
20722417 GCAACGGCTTATGTGCACTCCTACTCGTACATAGCCGGGTC
1 GCAACGGCTTATGTGCACTCCCACTCGCACATAGCCGGGTC
20722458 CACATCAACA
Statistics
Matches: 141, Mismatches: 24, Indels: 2
0.84 0.14 0.01
Matches are distributed among these distances:
41 35 0.25
42 106 0.75
ACGTcount: A:0.24, C:0.31, G:0.22, T:0.24
Consensus pattern (42 bp):
GCAACGGCTTATGTGCACTCCCACTCGCACATAGCCGGGTCA
Found at i:20722422 original size:83 final size:84
Alignment explanation
Indices: 20722250--20722457 Score: 301
Period size: 83 Copynumber: 2.5 Consensus size: 84
20722240 CATCTCATAT
* * * * * * *
20722250 GCAACGGCTTATGCGTACTCCCACTCGTATATAACCAGGTCAGCAATGGCTTATGTGCACTTCTA
1 GCAACGGCTTATGTGCACTCCCACTCGTACATAGCCGGGTCAGCAATGGCATATGTGCACTCCTA
*
20722315 CTCGCACATAGCCGGGTCA
66 CTCGCACATAGCCGAGTCA
* *
20722334 GCAACGACTTATGTGCACTCCCACTCGCACATAGCCGGGTCAGCAAT-GCATATGTGCACTCCTA
1 GCAACGGCTTATGTGCACTCCCACTCGTACATAGCCGGGTCAGCAATGGCATATGTGCACTCCTA
*
20722398 CTCGCACATAGTCGAGTCA
66 CTCGCACATAGCCGAGTCA
*
20722417 GCAACGGCTTATGTGCACTCCTACTCGTACATAGCCGGGTC
1 GCAACGGCTTATGTGCACTCCCACTCGTACATAGCCGGGTC
20722458 CACATCAACA
Statistics
Matches: 110, Mismatches: 14, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
83 70 0.64
84 40 0.36
ACGTcount: A:0.24, C:0.31, G:0.22, T:0.24
Consensus pattern (84 bp):
GCAACGGCTTATGTGCACTCCCACTCGTACATAGCCGGGTCAGCAATGGCATATGTGCACTCCTA
CTCGCACATAGCCGAGTCA
Found at i:20726811 original size:39 final size:39
Alignment explanation
Indices: 20726757--20726836 Score: 135
Period size: 39 Copynumber: 2.1 Consensus size: 39
20726747 TCACTGTAGT
*
20726757 GAAATTGTAACCCAGAAACAGAATGTTTCTCGCTGCAGC
1 GAAATTGTAACCCAGAAACAGAAAGTTTCTCGCTGCAGC
20726796 GAAATTGCT-ACCCAGAAACAGAAAGTTTCTCGCTGCAGC
1 GAAATTG-TAACCCAGAAACAGAAAGTTTCTCGCTGCAGC
20726835 GA
1 GA
20726837 GAATGTATTT
Statistics
Matches: 39, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
39 38 0.97
40 1 0.03
ACGTcount: A:0.34, C:0.24, G:0.21, T:0.21
Consensus pattern (39 bp):
GAAATTGTAACCCAGAAACAGAAAGTTTCTCGCTGCAGC
Found at i:20727274 original size:43 final size:43
Alignment explanation
Indices: 20727213--20727335 Score: 158
Period size: 43 Copynumber: 2.9 Consensus size: 43
20727203 CCCATCATCA
* * **
20727213 TCATCACCAGCTCATGCGCACTCCCTACTCGCACAT-GGCTGGG
1 TCATCACCGGCTTATGCGCACTCCCTACTCGCACATAATC-GGG
* *
20727256 TCATCACCGGGTTATGCGCACTCCCTACTCGTACATAATCGGG
1 TCATCACCGGCTTATGCGCACTCCCTACTCGCACATAATCGGG
**
20727299 TCATCTTCGGCTTATGCGCACTCCCTACTCGCACATA
1 TCATCACCGGCTTATGCGCACTCCCTACTCGCACATA
20727336 GCCGAGTCAA
Statistics
Matches: 69, Mismatches: 10, Indels: 2
0.85 0.12 0.02
Matches are distributed among these distances:
43 68 0.99
44 1 0.01
ACGTcount: A:0.20, C:0.37, G:0.19, T:0.25
Consensus pattern (43 bp):
TCATCACCGGCTTATGCGCACTCCCTACTCGCACATAATCGGG
Found at i:20729678 original size:74 final size:74
Alignment explanation
Indices: 20729529--20729671 Score: 182
Period size: 74 Copynumber: 1.9 Consensus size: 74
20729519 AAATTCAAAT
* * * * * *
20729529 TCAAATTCTTAGACAGTGTGCTTTTAGTTGGATACCCATACTTGTTAGTCGATTAAGTCTTCTTT
1 TCAAATTCTTAGACAATGAGCTTTTAGCTGGATAACCATACTTCTTAGTCGATTAAGTCTTCTCT
*
20729594 GTCTCGCAA
66 ATCTCGCAA
*
20729603 TCAAATTCTCTA-ACAATGAGCTTTTAGCT-GACTAACCATACTTCTTAGTCGATTGAGTCTTCT
1 TCAAATTCT-TAGACAATGAGCTTTTAGCTGGA-TAACCATACTTCTTAGTCGATTAAGTCTTCT
20729666 CTATCT
64 CTATCT
20729672 TCCAATCTGG
Statistics
Matches: 59, Mismatches: 8, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
73 2 0.03
74 55 0.93
75 2 0.03
ACGTcount: A:0.24, C:0.21, G:0.15, T:0.40
Consensus pattern (74 bp):
TCAAATTCTTAGACAATGAGCTTTTAGCTGGATAACCATACTTCTTAGTCGATTAAGTCTTCTCT
ATCTCGCAA
Found at i:20732104 original size:35 final size:35
Alignment explanation
Indices: 20732058--20732188 Score: 145
Period size: 35 Copynumber: 3.7 Consensus size: 35
20732048 TCCTTAAGAA
*** *
20732058 GCCCAATTAACTTAATTGTTTAATTTAATCAATTAG
1 GCCCAA-TAACTTAATTAAATAATTTAATTAATTAG
*
20732094 GCCCAATAACTTAATTAAACAATTTAATTAATTAG
1 GCCCAATAACTTAATTAAATAATTTAATTAATTAG
* * * *
20732129 GCTCAATGACTTAGTTAAATAATTTAATTAATTAA
1 GCCCAATAACTTAATTAAATAATTTAATTAATTAG
* * *
20732164 GCTCAATAACTCAATTAAACAATTT
1 GCCCAATAACTTAATTAAATAATTT
20732189 TAATCAAGCC
Statistics
Matches: 81, Mismatches: 14, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
35 75 0.93
36 6 0.07
ACGTcount: A:0.42, C:0.14, G:0.07, T:0.37
Consensus pattern (35 bp):
GCCCAATAACTTAATTAAATAATTTAATTAATTAG
Found at i:20736052 original size:17 final size:17
Alignment explanation
Indices: 20736022--20736054 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
20736012 TTCTTGATAA
20736022 AATAAAACTCCTTATTG
1 AATAAAACTCCTTATTG
20736039 AATAATAACT-CTTATT
1 AATAA-AACTCCTTATT
20736055 TTATTATTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.42, C:0.15, G:0.03, T:0.39
Consensus pattern (17 bp):
AATAAAACTCCTTATTG
Found at i:20736321 original size:60 final size:57
Alignment explanation
Indices: 20736219--20736366 Score: 163
Period size: 60 Copynumber: 2.5 Consensus size: 57
20736209 TAAGACAAAC
* ** * *
20736219 ATATTTTATCTTGTCTAAATTGAGACAATTATGTTTTATTGTCTAGATTAAGATAAAAAA
1 ATATTTT-TCTTGTCTAAATTAAGACAAACATATTTTATTGTCTAAATT-A-ATAAAAAA
* * * *
20736279 ATATTTTTCTTGTCTTAAATTAAGAAAAACATATTTTTTTGTCTAAATTAATACAAAC
1 ATATTTTTCTTGTC-TAAATTAAGACAAACATATTTTATTGTCTAAATTAATAAAAAA
*
20736337 AT-GTTTTCTTGTCTAAATTAAGACAAACAT
1 ATATTTTTCTTGTCTAAATTAAGACAAACAT
20736367 GTTGAAGCTG
Statistics
Matches: 76, Mismatches: 11, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
56 16 0.21
57 10 0.13
58 8 0.11
59 8 0.11
60 34 0.45
ACGTcount: A:0.39, C:0.09, G:0.09, T:0.43
Consensus pattern (57 bp):
ATATTTTTCTTGTCTAAATTAAGACAAACATATTTTATTGTCTAAATTAATAAAAAA
Found at i:20736325 original size:28 final size:28
Alignment explanation
Indices: 20736206--20736366 Score: 160
Period size: 28 Copynumber: 5.5 Consensus size: 28
20736196 TCTTGTCTTT
20736206 AATTAAGACAAACATATTTTATCTTGTCTA
1 AATTAAGACAAACATATTTT-T-TTGTCTA
* ** * *
20736236 AATTGAGACAATTATGTTTTATTGTCTA
1 AATTAAGACAAACATATTTTTTTGTCTA
* * *
20736264 GATTAAGATAAAAAAATATTTTTCTTGTCTTA
1 AATTAAG--ACAAACATATTTTT-TTGTC-TA
*
20736296 AATTAAGAAAAACATATTTTTTTGTCTA
1 AATTAAGACAAACATATTTTTTTGTCTA
* * *
20736324 AATTAATACAAACATGTTTTCTTGTCTA
1 AATTAAGACAAACATATTTTTTTGTCTA
20736352 AATTAAGACAAACAT
1 AATTAAGACAAACAT
20736367 GTTGAAGCTG
Statistics
Matches: 108, Mismatches: 19, Indels: 10
0.79 0.14 0.07
Matches are distributed among these distances:
28 52 0.48
29 5 0.05
30 38 0.35
31 5 0.05
32 8 0.07
ACGTcount: A:0.40, C:0.10, G:0.09, T:0.41
Consensus pattern (28 bp):
AATTAAGACAAACATATTTTTTTGTCTA
Done.