Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr14
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: 244914714
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.31
Warning! 4503000 characters in sequence are not A, C, G, or T
File 71 of 770
Found at i:20928271 original size:34 final size:34
Alignment explanation
Indices: 20928233--20928304 Score: 110
Period size: 34 Copynumber: 2.1 Consensus size: 34
20928223 AAATATAAAA
20928233 AACCTTAAACCCT-ATTTTAAATAAACAAAACCCT
1 AACCTTAAACCCTAATTTT-AATAAACAAAACCCT
* *
20928267 AACCTTAAATCCTAATTTTAATAAATAAAACCCT
1 AACCTTAAACCCTAATTTTAATAAACAAAACCCT
20928301 AACC
1 AACC
20928305 CTATTAAAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
34 30 0.86
35 5 0.14
ACGTcount: A:0.47, C:0.25, G:0.00, T:0.28
Consensus pattern (34 bp):
AACCTTAAACCCTAATTTTAATAAACAAAACCCT
Found at i:20931485 original size:43 final size:43
Alignment explanation
Indices: 20931428--20931527 Score: 114
Period size: 43 Copynumber: 2.3 Consensus size: 43
20931418 GTTTGTTTGA
* * * *
20931428 AAAAAACGCCGCTAAAGATCAGGATTTTTAGCGGC-ATTATTTT
1 AAAAAACGACGCTAAAGACCAAGACTTTTAGCGGCGATT-TTTT
* *
20931471 AAAAAACGATGCTAAAGACCAAGACTTTTAGCGGCGCTTTTTT
1 AAAAAACGACGCTAAAGACCAAGACTTTTAGCGGCGATTTTTT
*
20931514 -AAAAACGCCGCTAA
1 AAAAAACGACGCTAA
20931528 TTTGCCCAGT
Statistics
Matches: 48, Mismatches: 8, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
42 12 0.25
43 34 0.71
44 2 0.04
ACGTcount: A:0.37, C:0.19, G:0.18, T:0.26
Consensus pattern (43 bp):
AAAAAACGACGCTAAAGACCAAGACTTTTAGCGGCGATTTTTT
Found at i:20931844 original size:21 final size:21
Alignment explanation
Indices: 20931820--20931867 Score: 87
Period size: 21 Copynumber: 2.3 Consensus size: 21
20931810 TTCTGTTCTG
*
20931820 CTCCGCCTCCCTCGCTGCTGC
1 CTCCGCCTCCCGCGCTGCTGC
20931841 CTCCGCCTCCCGCGCTGCTGC
1 CTCCGCCTCCCGCGCTGCTGC
20931862 CTCCGC
1 CTCCGC
20931868 TCTAAGTTGA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.00, C:0.58, G:0.21, T:0.21
Consensus pattern (21 bp):
CTCCGCCTCCCGCGCTGCTGC
Found at i:20935245 original size:35 final size:35
Alignment explanation
Indices: 20935199--20935268 Score: 140
Period size: 35 Copynumber: 2.0 Consensus size: 35
20935189 CATCCGGAAC
20935199 CTTTATATCCTTCAACACCGTGCAGAACATTTCTT
1 CTTTATATCCTTCAACACCGTGCAGAACATTTCTT
20935234 CTTTATATCCTTCAACACCGTGCAGAACATTTCTT
1 CTTTATATCCTTCAACACCGTGCAGAACATTTCTT
20935269 TCTCTTCCTT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.26, C:0.29, G:0.09, T:0.37
Consensus pattern (35 bp):
CTTTATATCCTTCAACACCGTGCAGAACATTTCTT
Found at i:20937426 original size:9 final size:9
Alignment explanation
Indices: 20937412--20937539 Score: 121
Period size: 9 Copynumber: 13.6 Consensus size: 9
20937402 ATGTATTAGT
20937412 TAAGTTATG
1 TAAGTTATG
20937421 TAAGTTGTTATG
1 TAA---GTTATG
*
20937433 TACGTTATG
1 TAAGTTATG
*
20937442 TGAGTTATG
1 TAAGTTATG
*
20937451 TAAATTATG
1 TAAGTTATG
20937460 TAAGTTATG
1 TAAGTTATG
*
20937469 TGAGTTATG
1 TAAGTTATG
20937478 TAAGTTGTTATG
1 TAA---GTTATG
*
20937490 TAAATTATG
1 TAAGTTATG
*
20937499 TAAGTTATA
1 TAAGTTATG
20937508 TAAGTTATG
1 TAAGTTATG
*
20937517 TAAGTTGTG
1 TAAGTTATG
* *
20937526 TAATTTATT
1 TAAGTTATG
20937535 TAAGT
1 TAAGT
20937540 AATGATCAAT
Statistics
Matches: 96, Mismatches: 17, Indels: 12
0.77 0.14 0.10
Matches are distributed among these distances:
9 79 0.82
12 17 0.18
ACGTcount: A:0.31, C:0.01, G:0.21, T:0.47
Consensus pattern (9 bp):
TAAGTTATG
Found at i:20937459 original size:39 final size:41
Alignment explanation
Indices: 20937416--20937504 Score: 109
Period size: 39 Copynumber: 2.3 Consensus size: 41
20937406 ATTAGTTAAG
20937416 TTATGTAAGTTGTTATGT-ACGTTATGT-G-AGTTATGTAAA
1 TTATGTAAGTTGTTATGTGA-GTTATGTAGTAGTTATGTAAA
*
20937455 TTATGTAA---GTTATGTGAGTTATGTAAGTTGTTATGTAAA
1 TTATGTAAGTTGTTATGTGAGTTATGT-AGTAGTTATGTAAA
20937494 TTATGTAAGTT
1 TTATGTAAGTT
20937505 ATATAAGTTA
Statistics
Matches: 42, Mismatches: 1, Indels: 11
0.78 0.02 0.20
Matches are distributed among these distances:
36 14 0.33
37 1 0.02
38 1 0.02
39 26 0.62
ACGTcount: A:0.29, C:0.01, G:0.22, T:0.47
Consensus pattern (41 bp):
TTATGTAAGTTGTTATGTGAGTTATGTAGTAGTTATGTAAA
Found at i:20937505 original size:39 final size:39
Alignment explanation
Indices: 20937445--20937524 Score: 142
Period size: 39 Copynumber: 2.1 Consensus size: 39
20937435 CGTTATGTGA
* *
20937445 GTTATGTAAATTATGTAAGTTATGTGAGTTATGTAAGTT
1 GTTATGTAAATTATGTAAGTTATATAAGTTATGTAAGTT
20937484 GTTATGTAAATTATGTAAGTTATATAAGTTATGTAAGTT
1 GTTATGTAAATTATGTAAGTTATATAAGTTATGTAAGTT
20937523 GT
1 GT
20937525 GTAATTTATT
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
39 39 1.00
ACGTcount: A:0.33, C:0.00, G:0.21, T:0.46
Consensus pattern (39 bp):
GTTATGTAAATTATGTAAGTTATATAAGTTATGTAAGTT
Found at i:20937539 original size:57 final size:57
Alignment explanation
Indices: 20937412--20937539 Score: 175
Period size: 57 Copynumber: 2.2 Consensus size: 57
20937402 ATGTATTAGT
** * *
20937412 TAAGTTATGTAAGTTGTTATGTACGTTATGTGAGTTATGTAAATTATGTAAGTTATG
1 TAAGTTATGTAAGTTGTTATGTAAATTATGTAAGTTATATAAATTATGTAAGTTATG
* * *
20937469 TGAGTTATGTAAGTTGTTATGTAAATTATGTAAGTTATATAAGTTATGTAAGTTGTG
1 TAAGTTATGTAAGTTGTTATGTAAATTATGTAAGTTATATAAATTATGTAAGTTATG
* *
20937526 TAATTTATTTAAGT
1 TAAGTTATGTAAGT
20937540 AATGATCAAT
Statistics
Matches: 61, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
57 61 1.00
ACGTcount: A:0.31, C:0.01, G:0.21, T:0.47
Consensus pattern (57 bp):
TAAGTTATGTAAGTTGTTATGTAAATTATGTAAGTTATATAAATTATGTAAGTTATG
Found at i:20938395 original size:241 final size:239
Alignment explanation
Indices: 20937974--20938458 Score: 907
Period size: 241 Copynumber: 2.0 Consensus size: 239
20937964 TTAAGGTTAT
20937974 ATAAATATTCAATAGTAAATGAGCTCGATAGAACATTTTTCAAGTCTTTTTGAATTTTTTAAATT
1 ATAAATATTCAATAGTAAATGAGCTCGATAGAACATTTTTCAAGTCTTTTTGAATTTTTTAAATT
*
20938039 CATCATACGTGGCATTGTTACACCTAGGAGGATCCATTATATCTTACAGCTCGATATAAGGCAAC
66 CATCATACGTGACATTGTTACACCTAGGAGGATCCATTATATCTTACAGCTCGATATAAGGCAAC
20938104 CCGTCAGGTTTCCAGCCTATATACTTTGAATCTTTAAAATATTTAAAATAAGGTTGGAGAGAAGG
131 CCGTCAGGTTTCCAGCCTATATACTTTGAATCTTTAAAATATTTAAAATAAGGTTGGAGAGAAGG
*
20938169 TCAGCTATTGTTGTAATTTTAATGGACAAGCAAGCTACATGGTA
196 TCAGCTATTGTTGTAATTTTAATGGACAAGCAAGCTACATGATA
*
20938213 ATAAATATTCAATAGTAAATGAGCTCGATAGAACTTTTTTCAAGTCTTTTTGAATTTTTTAAGAT
1 ATAAATATTCAATAGTAAATGAGCTCGATAGAACATTTTTCAAGTCTTTTTGAATTTTTTAA-AT
*
20938278 TCATCATACGTGACGTTGTTACACCTATGGAGGATCCATTATATCTTACAGCTCGATATAAGGCA
65 TCATCATACGTGACATTGTTACACCTA-GGAGGATCCATTATATCTTACAGCTCGATATAAGGCA
*
20938343 ACCCGTTAGGTTTCCAGCCTATATACTTTGAATCTTTAAAATATTTAAAATAAGGTTGGAGAGAA
129 ACCCGTCAGGTTTCCAGCCTATATACTTTGAATCTTTAAAATATTTAAAATAAGGTTGGAGAGAA
20938408 GGTCAGCTATTGTTGTAATTTTAATGGACAAGCAAGCTACATGATA
194 GGTCAGCTATTGTTGTAATTTTAATGGACAAGCAAGCTACATGATA
20938454 ATAAA
1 ATAAA
20938459 ATTAATTCAT
Statistics
Matches: 239, Mismatches: 5, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
239 61 0.26
240 27 0.11
241 151 0.63
ACGTcount: A:0.34, C:0.15, G:0.17, T:0.35
Consensus pattern (239 bp):
ATAAATATTCAATAGTAAATGAGCTCGATAGAACATTTTTCAAGTCTTTTTGAATTTTTTAAATT
CATCATACGTGACATTGTTACACCTAGGAGGATCCATTATATCTTACAGCTCGATATAAGGCAAC
CCGTCAGGTTTCCAGCCTATATACTTTGAATCTTTAAAATATTTAAAATAAGGTTGGAGAGAAGG
TCAGCTATTGTTGTAATTTTAATGGACAAGCAAGCTACATGATA
Found at i:20938617 original size:23 final size:23
Alignment explanation
Indices: 20938591--20938640 Score: 100
Period size: 23 Copynumber: 2.2 Consensus size: 23
20938581 GTTCAAGTTT
20938591 ATTTAAAGGGCTGCAATTCATAC
1 ATTTAAAGGGCTGCAATTCATAC
20938614 ATTTAAAGGGCTGCAATTCATAC
1 ATTTAAAGGGCTGCAATTCATAC
20938637 ATTT
1 ATTT
20938641 GATTAATGTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Consensus pattern (23 bp):
ATTTAAAGGGCTGCAATTCATAC
Found at i:20942131 original size:42 final size:40
Alignment explanation
Indices: 20942062--20942152 Score: 96
Period size: 42 Copynumber: 2.2 Consensus size: 40
20942052 AAATATTTGC
** *
20942062 GGCG-TTTTTATTTAAAACGCCGGTATAGGTCAACTTTTAGT
1 GGCGTTTTTTATTTAAAACGCCACTATAGCTC-A-TTTTAGT
*
20942103 GGCGTTTTTTA-TTACAAACGCCACTATAGCTCATTTTTGT
1 GGCGTTTTTTATTTA-AAACGCCACTATAGCTCATTTTAGT
*
20942143 GGCTTTTTTT
1 GGCGTTTTTT
20942153 CAAAAACACC
Statistics
Matches: 43, Mismatches: 5, Indels: 5
0.81 0.09 0.09
Matches are distributed among these distances:
40 15 0.35
41 8 0.19
42 20 0.47
ACGTcount: A:0.21, C:0.16, G:0.19, T:0.44
Consensus pattern (40 bp):
GGCGTTTTTTATTTAAAACGCCACTATAGCTCATTTTAGT
Found at i:20942363 original size:28 final size:28
Alignment explanation
Indices: 20942324--20942386 Score: 74
Period size: 28 Copynumber: 2.2 Consensus size: 28
20942314 ATTCCAAAAT
* *
20942324 TAAACCCTAAACC-CTAAATTACAAACTC
1 TAAACCCCAAACCTC-AAATTACAAACAC
*
20942352 TAAACCCCAAACCTCAAATTCCAAACAC
1 TAAACCCCAAACCTCAAATTACAAACAC
*
20942380 CAAACCC
1 TAAACCC
20942387 TAAGCCATAA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
28 29 0.97
29 1 0.03
ACGTcount: A:0.46, C:0.38, G:0.00, T:0.16
Consensus pattern (28 bp):
TAAACCCCAAACCTCAAATTACAAACAC
Found at i:20942369 original size:21 final size:21
Alignment explanation
Indices: 20942345--20942385 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
20942335 CCCTAAATTA
* *
20942345 CAAACTCTAAACCCCAAACCT
1 CAAACTCCAAACACCAAACCT
*
20942366 CAAATTCCAAACACCAAACC
1 CAAACTCCAAACACCAAACC
20942386 CTAAGCCATA
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:0.46, C:0.41, G:0.00, T:0.12
Consensus pattern (21 bp):
CAAACTCCAAACACCAAACCT
Found at i:20942401 original size:7 final size:7
Alignment explanation
Indices: 20942381--20942414 Score: 50
Period size: 7 Copynumber: 4.9 Consensus size: 7
20942371 TCCAAACACC
*
20942381 AAACCCT
1 AAACCAT
*
20942388 AAGCCAT
1 AAACCAT
20942395 AAACCAT
1 AAACCAT
20942402 AAACCAT
1 AAACCAT
20942409 AAACCA
1 AAACCA
20942415 CAAAACTCAA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.53, C:0.32, G:0.03, T:0.12
Consensus pattern (7 bp):
AAACCAT
Found at i:20942686 original size:7 final size:7
Alignment explanation
Indices: 20942663--20942718 Score: 58
Period size: 7 Copynumber: 8.0 Consensus size: 7
20942653 TAAGACCCTG
*
20942663 ACCCTAT
1 ACCCTAA
*
20942670 ACCATAA
1 ACCCTAA
20942677 ACCCTAA
1 ACCCTAA
*
20942684 ACCATAA
1 ACCCTAA
*
20942691 ACCCCAA
1 ACCCTAA
* *
20942698 ACACTAG
1 ACCCTAA
20942705 ACCCTAA
1 ACCCTAA
20942712 ACCCTAA
1 ACCCTAA
20942719 TTAACCCCTA
Statistics
Matches: 38, Mismatches: 11, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
7 38 1.00
ACGTcount: A:0.45, C:0.39, G:0.02, T:0.14
Consensus pattern (7 bp):
ACCCTAA
Found at i:20943059 original size:8 final size:7
Alignment explanation
Indices: 20943013--20943060 Score: 51
Period size: 7 Copynumber: 6.7 Consensus size: 7
20943003 ATCCCTTAAT
20943013 CCTAACC
1 CCTAACC
*
20943020 ACTAACC
1 CCTAACC
*
20943027 ACTAACC
1 CCTAACC
* *
20943034 CTTAAAC
1 CCTAACC
20943041 CCTAACC
1 CCTAACC
20943048 CCTAACC
1 CCTAACC
20943055 TCCTAA
1 -CCTAA
20943061 ATTATAAACC
Statistics
Matches: 34, Mismatches: 6, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
7 29 0.85
8 5 0.15
ACGTcount: A:0.35, C:0.46, G:0.00, T:0.19
Consensus pattern (7 bp):
CCTAACC
Found at i:20943124 original size:14 final size:13
Alignment explanation
Indices: 20943074--20943139 Score: 51
Period size: 14 Copynumber: 4.7 Consensus size: 13
20943064 ATAAACCTCA
20943074 AACCCTAAATCAT
1 AACCCTAAATCAT
* * *
20943087 AAAACATAAATTAT
1 -AACCCTAAATCAT
20943101 CAACCCTAAATCAT
1 -AACCCTAAATCAT
*
20943115 AACCCTTAAACCCAT
1 AACCC-TAAA-TCAT
20943130 AACCCCTAAA
1 AA-CCCTAAA
20943140 CCTATAAAAA
Statistics
Matches: 41, Mismatches: 8, Indels: 5
0.76 0.15 0.09
Matches are distributed among these distances:
13 5 0.12
14 24 0.59
15 9 0.22
16 3 0.07
ACGTcount: A:0.48, C:0.30, G:0.00, T:0.21
Consensus pattern (13 bp):
AACCCTAAATCAT
Found at i:20943132 original size:15 final size:15
Alignment explanation
Indices: 20943112--20943146 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
20943102 AACCCTAAAT
*
20943112 CATAACCCTTAAACC
1 CATAACCCCTAAACC
20943127 CATAACCCCTAAACC
1 CATAACCCCTAAACC
*
20943142 TATAA
1 CATAA
20943147 AAATATTAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.43, C:0.37, G:0.00, T:0.20
Consensus pattern (15 bp):
CATAACCCCTAAACC
Found at i:20943199 original size:24 final size:25
Alignment explanation
Indices: 20943154--20943200 Score: 60
Period size: 25 Copynumber: 1.9 Consensus size: 25
20943144 TAAAAATATT
*
20943154 AAATTTAAAAATCAGTTTAAAAAGA
1 AAATTTAAAAATCAGTTAAAAAAGA
* *
20943179 AAATTTTAAATTCA-TTAAAAAA
1 AAATTTAAAAATCAGTTAAAAAA
20943201 AAGTTAGACT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
24 7 0.37
25 12 0.63
ACGTcount: A:0.60, C:0.04, G:0.04, T:0.32
Consensus pattern (25 bp):
AAATTTAAAAATCAGTTAAAAAAGA
Found at i:20945604 original size:25 final size:25
Alignment explanation
Indices: 20945566--20945624 Score: 66
Period size: 25 Copynumber: 2.3 Consensus size: 25
20945556 AAAAAAATTG
20945566 TAAAAATTACAAATTGATGTAAAAA-A
1 TAAAAA-TACAAATTGAT-TAAAAATA
* *
20945592 TAAAAATAGAAATTTATTAAAAATA
1 TAAAAATACAAATTGATTAAAAATA
*
20945617 GAAAAATA
1 TAAAAATA
20945625 TATATAATTA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
24 6 0.21
25 17 0.59
26 6 0.21
ACGTcount: A:0.64, C:0.02, G:0.07, T:0.27
Consensus pattern (25 bp):
TAAAAATACAAATTGATTAAAAATA
Found at i:20946115 original size:19 final size:19
Alignment explanation
Indices: 20946065--20946119 Score: 56
Period size: 21 Copynumber: 2.7 Consensus size: 19
20946055 TATTTAGTAC
20946065 TTTTTATATTTTAAATTTTT
1 TTTTTATATTTTAAA-TTTT
*
20946085 TTTTGTAAATTTATAAATTTT
1 TTTT-TATATTT-TAAATTTT
*
20946106 TTTTCTATTTTTTA
1 TTTT-TATATTTTA
20946120 GTAATATTAA
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
20 6 0.21
21 19 0.66
22 4 0.14
ACGTcount: A:0.25, C:0.02, G:0.02, T:0.71
Consensus pattern (19 bp):
TTTTTATATTTTAAATTTT
Found at i:20947286 original size:24 final size:24
Alignment explanation
Indices: 20947242--20947293 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
20947232 TTTCTAAAAA
* **
20947242 ATTTAGTATTTATTAGTATAATAT
1 ATTTAGCATTTATTAACATAATAT
*
20947266 ATTTAGCATTTATTAACATAATTT
1 ATTTAGCATTTATTAACATAATAT
20947290 ATTT
1 ATTT
20947294 GACCTAAGAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.37, C:0.04, G:0.06, T:0.54
Consensus pattern (24 bp):
ATTTAGCATTTATTAACATAATAT
Found at i:20949249 original size:24 final size:24
Alignment explanation
Indices: 20949220--20949271 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
20949210 TTTTTAAAAG
* *
20949220 ATTTAGTATTTATTAGTATAATAT
1 ATTTAGCATTTATTAGCATAATAT
*
20949244 ATTTAGCATTTATTAGCATAATTT
1 ATTTAGCATTTATTAGCATAATAT
20949268 ATTT
1 ATTT
20949272 GACCTACGAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.35, C:0.04, G:0.08, T:0.54
Consensus pattern (24 bp):
ATTTAGCATTTATTAGCATAATAT
Found at i:20953254 original size:24 final size:24
Alignment explanation
Indices: 20953208--20953256 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
20953198 TAGTGATATT
* *
20953208 AAAAAATAATAGCTATAAAAATAA
1 AAAAAATAATAACCATAAAAATAA
* *
20953232 AAAAAATAATAACCATGACAATAA
1 AAAAAATAATAACCATAAAAATAA
20953256 A
1 A
20953257 GAATAATAGT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.69, C:0.08, G:0.04, T:0.18
Consensus pattern (24 bp):
AAAAAATAATAACCATAAAAATAA
Found at i:20953462 original size:3 final size:3
Alignment explanation
Indices: 20953454--20953683 Score: 148
Period size: 3 Copynumber: 76.0 Consensus size: 3
20953444 TTAATTAGTT
* * * *
20953454 TAA TAA TAA TAG TAA TAA TAA TAA TAA TAA TGAA -AA CAA AAA TAT
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T-AA TAA TAA TAA TAA
* * * * * * *
20953499 TAA GTTA CAA TAG TAA -AA TAA TAA TAG TGA TAA TAA TAG T-A TAT
1 TAA -TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
*
20953543 TAGA TAA CAA TAA TAA -AA TAA TAA GTAA TAA TAA TAGA GT-A TAAA
1 TA-A TAA TAA TAA TAA TAA TAA TAA -TAA TAA TAA TA-A -TAA T-AA
* * *
20953588 TAG TAG TTA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* * ** * * *
20953636 TAA TAA TAG TGA CGA TAG TAG TAA TAA T-A TAT TAA TAA TACA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA-A TAA
20953681 TAA
1 TAA
20953684 AAGGAACAAT
Statistics
Matches: 177, Mismatches: 36, Indels: 28
0.73 0.15 0.12
Matches are distributed among these distances:
2 10 0.06
3 151 0.85
4 15 0.08
5 1 0.01
ACGTcount: A:0.58, C:0.02, G:0.08, T:0.32
Consensus pattern (3 bp):
TAA
Found at i:20953584 original size:44 final size:46
Alignment explanation
Indices: 20953505--20953626 Score: 128
Period size: 47 Copynumber: 2.7 Consensus size: 46
20953495 ATATTAAGTT
* * *
20953505 ACAATAGTAAAATAATAATAGTGATAATAAT-AGTAT-ATTAG-A-TA
1 ACAATAATAAAATAAT-A-AGTAATAATAATAAGTATAAATAGTAGTA
*
20953549 ACAATAATAAAATAATAAGTAATAATAATAGAGTATAAATAGTAGTT
1 ACAATAATAAAATAATAAGTAATAATAATA-AGTATAAATAGTAGTA
*
20953596 ATAATAATAATAATAATAA-TAATAATAATAA
1 ACAATAATAA-AATAATAAGTAATAATAATAA
20953627 TAATAATAAT
Statistics
Matches: 67, Mismatches: 5, Indels: 10
0.82 0.06 0.12
Matches are distributed among these distances:
42 11 0.16
43 1 0.01
44 20 0.30
45 4 0.06
46 2 0.03
47 21 0.31
48 8 0.12
ACGTcount: A:0.59, C:0.02, G:0.08, T:0.31
Consensus pattern (46 bp):
ACAATAATAAAATAATAAGTAATAATAATAAGTATAAATAGTAGTA
Found at i:20955935 original size:20 final size:21
Alignment explanation
Indices: 20955907--20955966 Score: 68
Period size: 20 Copynumber: 2.9 Consensus size: 21
20955897 AACCGTGAAT
*
20955907 CTCAAACCCCGAACTCAAACC
1 CTCAAACCCCGAACTCAAAAC
** *
20955928 CT-AAACCCTAAACCCAAAAC
1 CTCAAACCCCGAACTCAAAAC
20955948 CTCAAACCCCGAACCTCAA
1 CTCAAACCCCGAA-CTCAA
20955967 TGTTGGGAAA
Statistics
Matches: 30, Mismatches: 7, Indels: 3
0.75 0.17 0.08
Matches are distributed among these distances:
20 16 0.53
21 10 0.33
22 4 0.13
ACGTcount: A:0.42, C:0.45, G:0.03, T:0.10
Consensus pattern (21 bp):
CTCAAACCCCGAACTCAAAAC
Found at i:20955954 original size:14 final size:14
Alignment explanation
Indices: 20955907--20955966 Score: 61
Period size: 14 Copynumber: 4.4 Consensus size: 14
20955897 AACCGTGAAT
*
20955907 CTCAAACCCCGAA-
1 CTCAAACCCCAAAC
*
20955920 CTCAAACCCTAAAC
1 CTCAAACCCCAAAC
*
20955934 C-CTAAACCCAAAAC
1 CTC-AAACCCCAAAC
*
20955948 CTCAAACCCCGAAC
1 CTCAAACCCCAAAC
20955962 CTCAA
1 CTCAA
20955967 TGTTGGGAAA
Statistics
Matches: 39, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
13 12 0.31
14 26 0.67
15 1 0.03
ACGTcount: A:0.42, C:0.45, G:0.03, T:0.10
Consensus pattern (14 bp):
CTCAAACCCCAAAC
Found at i:20958830 original size:17 final size:16
Alignment explanation
Indices: 20958810--20958856 Score: 58
Period size: 17 Copynumber: 2.9 Consensus size: 16
20958800 TATCATTTTG
20958810 AAAAATATATAAAATAT
1 AAAAATATATAAAAT-T
* *
20958827 AAAATTATATACAATT
1 AAAAATATATAAAATT
*
20958843 AAAAATATGTAAAA
1 AAAAATATATAAAA
20958857 CACTTATAAT
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
16 12 0.48
17 13 0.52
ACGTcount: A:0.66, C:0.02, G:0.02, T:0.30
Consensus pattern (16 bp):
AAAAATATATAAAATT
Found at i:20958957 original size:44 final size:43
Alignment explanation
Indices: 20958873--20958972 Score: 121
Period size: 44 Copynumber: 2.3 Consensus size: 43
20958863 TAATATCTTG
* *
20958873 AAAATATATAAAAAAAATAAACACATAACTTTTTAAAAATAAA
1 AAAATATATAAAAAAAATAAACACATAAATTTATAAAAATAAA
* * *
20958916 AAAAT-TATAAAAATATATATACACTATAAATTTATAAAAATATA
1 AAAATATATAAAAA-AAATAAACAC-ATAAATTTATAAAAATAAA
*
20958960 TAAATATATAAAA
1 AAAATATATAAAA
20958973 TTATTAAAAA
Statistics
Matches: 48, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
42 8 0.17
43 13 0.27
44 20 0.42
45 7 0.15
ACGTcount: A:0.65, C:0.05, G:0.00, T:0.30
Consensus pattern (43 bp):
AAAATATATAAAAAAAATAAACACATAAATTTATAAAAATAAA
Found at i:20958973 original size:27 final size:26
Alignment explanation
Indices: 20958906--20958982 Score: 82
Period size: 27 Copynumber: 2.8 Consensus size: 26
20958896 CATAACTTTT
*
20958906 TAAAAATAAAAAAATTATAAAAATATA
1 TAAAAAT-ATAAAATTATAAAAATATA
* * *
20958933 TATACACTATAAATTTATAAAAATATA
1 TA-AAAATATAAAATTATAAAAATATA
*
20958960 TAAATATATAAAATTATTAAAAA
1 TAAAAATATAAAATTA-TAAAAA
20958983 GTATGTCTAG
Statistics
Matches: 40, Mismatches: 8, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
26 10 0.25
27 27 0.68
28 3 0.08
ACGTcount: A:0.65, C:0.03, G:0.00, T:0.32
Consensus pattern (26 bp):
TAAAAATATAAAATTATAAAAATATA
Found at i:20959056 original size:16 final size:17
Alignment explanation
Indices: 20959037--20959083 Score: 60
Period size: 17 Copynumber: 2.8 Consensus size: 17
20959027 CCTAATGTGA
20959037 ATTATTTTATAT-TTTT
1 ATTATTTTATATATTTT
*
20959053 ATTACTTTATATATTTT
1 ATTATTTTATATATTTT
**
20959070 AAAATTTTATATAT
1 ATTATTTTATATAT
20959084 ATTTTTAAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
16 11 0.42
17 15 0.58
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (17 bp):
ATTATTTTATATATTTT
Found at i:20959102 original size:19 final size:21
Alignment explanation
Indices: 20959060--20959103 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 21
20959050 TTTATTACTT
**
20959060 TATATATTTTAAAATTTTATA
1 TATATATTTTAAAATAGTATA
20959081 TATAT-TTTTAAAATAGTA-A
1 TATATATTTTAAAATAGTATA
20959100 TATA
1 TATA
20959104 AATAACATGA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 5 0.24
20 11 0.52
21 5 0.24
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.52
Consensus pattern (21 bp):
TATATATTTTAAAATAGTATA
Found at i:20961381 original size:17 final size:16
Alignment explanation
Indices: 20961338--20961392 Score: 58
Period size: 17 Copynumber: 3.4 Consensus size: 16
20961328 TTCAATAAAT
*
20961338 AAAAAATAAA-AATAA
1 AAAAAATAAATATTAA
* *
20961353 AAATATTAAATATTAA
1 AAAAAATAAATATTAA
*
20961369 AATAAAATAAATATTTA
1 AA-AAAATAAATATTAA
20961386 AAAAAAT
1 AAAAAAT
20961393 TTAAAAATAA
Statistics
Matches: 32, Mismatches: 6, Indels: 3
0.78 0.15 0.07
Matches are distributed among these distances:
15 8 0.25
16 11 0.34
17 13 0.41
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (16 bp):
AAAAAATAAATATTAA
Found at i:20961397 original size:18 final size:17
Alignment explanation
Indices: 20961351--20961397 Score: 51
Period size: 18 Copynumber: 2.6 Consensus size: 17
20961341 AAATAAAAAT
20961351 AAAAATATTAAATATTAA
1 AAAAAT-TTAAATATTAA
*
20961369 AATAAA-ATAAATATTTAA
1 AA-AAATTTAAATA-TTAA
20961387 AAAAATTTAAA
1 AAAAATTTAAA
20961398 AATAATATGG
Statistics
Matches: 24, Mismatches: 2, Indels: 6
0.75 0.06 0.19
Matches are distributed among these distances:
17 9 0.38
18 12 0.50
19 3 0.12
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (17 bp):
AAAAATTTAAATATTAA
Found at i:20962911 original size:4 final size:4
Alignment explanation
Indices: 20962902--20962928 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
20962892 TTCTAAAGCA
20962902 TATT TATT TATT TATT TATT TATT TAT
1 TATT TATT TATT TATT TATT TATT TAT
20962929 ATTAGTGTAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (4 bp):
TATT
Found at i:20964477 original size:7 final size:7
Alignment explanation
Indices: 20964465--20964494 Score: 51
Period size: 7 Copynumber: 4.3 Consensus size: 7
20964455 ATTATTTTTA
20964465 ATTCAAT
1 ATTCAAT
20964472 ATTCAAT
1 ATTCAAT
20964479 ATTCAAT
1 ATTCAAT
*
20964486 ATTTAAT
1 ATTCAAT
20964493 AT
1 AT
20964495 ATCTTTATTT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.43, C:0.10, G:0.00, T:0.47
Consensus pattern (7 bp):
ATTCAAT
Found at i:20973297 original size:133 final size:134
Alignment explanation
Indices: 20973075--20973541 Score: 336
Period size: 133 Copynumber: 3.5 Consensus size: 134
20973065 CGAAGGGATC
* * * * * *
20973075 TTCGATCGTTTTGAACAAATGAAAAAGCACAACCCAGCACGATAGGGCACGATTCTCGAATTACC
1 TTCGATTGTTTTGAACAAACGAGAAATCACAACCCAGCACGATAGGGCACGATTCCCAAATTACC
* * *
20973140 AAACATCGAACATCACCTTTGTTTTAAAGG-GTTTTCTTAAAAAACATGAGTGAAAACCTAAAGG
66 AAACACCGAACATCACCTTCGTTTTAAAGGAGTTTTCTTAAAAAACATGACTGAAAACCTAAAGG
20973204 AATA
131 AATA
* **
20973208 TTCGATTGTTTTGAACAAACGAGAAATCACAACCCAGCACGATAGGGCATGATTCCCAAATTGTC
1 TTCGATTGTTTTGAACAAACGAGAAATCACAACCCAGCACGATAGGGCACGATTCCCAAATTACC
* ** ** * * * * *** *
20973273 GAACACCGAGTATTGCCTTCGTTTTAAAGGATTTTTTTTAGAAGACATGACTGAAATTTTGAAGG
66 AAACACCGAACATCACCTTCGTTTTAAAGGAGTTTTCTTAAAAAACATGACTGAAAACCTAAAGG
*
20973338 GATA
131 AATA
* * *** * * * *
20973342 TTTGATTATTTT-AAGCAAACGAGAAATTGTAATCCAGCACGTTAGGGCACGATTCCGCTAACTA
1 TTCGATTGTTTTGAA-CAAACGAGAAATCACAACCCAGCACGATAGGGCACGATTCC-CAAATTA
* * * * * * * * ** **
20973406 CCAAATATCGCACATCGCATTCG-TTT-AAGGA-ATTT-TTAAAAGATATGGGTGAAATTCTAAA
64 CCAAACACCGAACATCACCTTCGTTTTAAAGGAGTTTTCTTAAAAAACATGACTGAAAACCTAAA
**
20973467 GGAACC
129 GGAATA
** ** * * * *
20973473 TTCGATTACTTT-AAGCAAACGAGAAATTGCAACCCAACAGGTTAGGGCACGATTCCGAGAATTA
1 TTCGATTGTTTTGAA-CAAACGAGAAATCACAACCCAGCACGATAGGGCACGATTCCCA-AATTA
20973537 CCAAA
64 CCAAA
20973542 TATCAAATGT
Statistics
Matches: 265, Mismatches: 65, Indels: 10
0.78 0.19 0.03
Matches are distributed among these distances:
131 82 0.31
132 3 0.01
133 86 0.32
134 76 0.29
135 18 0.07
ACGTcount: A:0.36, C:0.19, G:0.18, T:0.27
Consensus pattern (134 bp):
TTCGATTGTTTTGAACAAACGAGAAATCACAACCCAGCACGATAGGGCACGATTCCCAAATTACC
AAACACCGAACATCACCTTCGTTTTAAAGGAGTTTTCTTAAAAAACATGACTGAAAACCTAAAGG
AATA
Found at i:20974562 original size:2 final size:2
Alignment explanation
Indices: 20974555--20974581 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
20974545 AAGGTTAACA
20974555 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
20974582 ATAATAGCTT
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:20975878 original size:23 final size:23
Alignment explanation
Indices: 20975852--20975896 Score: 90
Period size: 23 Copynumber: 2.0 Consensus size: 23
20975842 CTGTTGCTGT
20975852 GTTTGTCTTGTTCACAGGTACGA
1 GTTTGTCTTGTTCACAGGTACGA
20975875 GTTTGTCTTGTTCACAGGTACG
1 GTTTGTCTTGTTCACAGGTACG
20975897 GAGCAGAGGA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.16, C:0.18, G:0.27, T:0.40
Consensus pattern (23 bp):
GTTTGTCTTGTTCACAGGTACGA
Found at i:20976214 original size:17 final size:17
Alignment explanation
Indices: 20976188--20976226 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
20976178 GTTTGGTTTA
*
20976188 ATTTTTTATTTTTAT-T
1 ATTTTTTATTTGTATAT
20976204 ATTTATTTATTTGTATAT
1 ATTT-TTTATTTGTATAT
20976222 ATTTT
1 ATTTT
20976227 GGTTTCTAGT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
16 4 0.20
17 11 0.55
18 5 0.25
ACGTcount: A:0.23, C:0.00, G:0.03, T:0.74
Consensus pattern (17 bp):
ATTTTTTATTTGTATAT
Found at i:20980551 original size:25 final size:25
Alignment explanation
Indices: 20980523--20980573 Score: 93
Period size: 25 Copynumber: 2.0 Consensus size: 25
20980513 TTTAATTAAG
20980523 GAGTTAGGCCAATTACCTTGCCCCT
1 GAGTTAGGCCAATTACCTTGCCCCT
*
20980548 GAGTTAGGCCAATTGCCTTGCCCCT
1 GAGTTAGGCCAATTACCTTGCCCCT
20980573 G
1 G
20980574 CAAGGGATCC
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.18, C:0.31, G:0.24, T:0.27
Consensus pattern (25 bp):
GAGTTAGGCCAATTACCTTGCCCCT
Found at i:20981667 original size:33 final size:34
Alignment explanation
Indices: 20981625--20981711 Score: 108
Period size: 33 Copynumber: 2.6 Consensus size: 34
20981615 TTGCGTACTG
*
20981625 TACTGTTACT-ATGATGGGCTTAGGCCC-CATTGA
1 TACTGTTACTAAT-ATGGGCTCAGGCCCGCATTGA
* *
20981658 TACTGTTACTGAA-ATGGGCTCAGGCCCGGATTGT
1 TACTGTTACT-AATATGGGCTCAGGCCCGCATTGA
20981692 TACTGTTACTAATATGGGCT
1 TACTGTTACTAATATGGGCT
20981712 AAAACCCTAA
Statistics
Matches: 47, Mismatches: 3, Indels: 7
0.82 0.05 0.12
Matches are distributed among these distances:
33 25 0.53
34 21 0.45
35 1 0.02
ACGTcount: A:0.22, C:0.20, G:0.25, T:0.33
Consensus pattern (34 bp):
TACTGTTACTAATATGGGCTCAGGCCCGCATTGA
Found at i:20995981 original size:44 final size:45
Alignment explanation
Indices: 20995914--20996021 Score: 137
Period size: 44 Copynumber: 2.4 Consensus size: 45
20995904 TGTCTTTGAC
** * * *
20995914 ATGGACTTACATGAATTATTCCTGTCTCCAATGCCATA-TATAAT
1 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATTATAAT
* *
20995958 ATGGACTTATATGGCTCAATCCTGTCTCCAAAGCCATATTTCTAAT
1 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATA-TTATAAT
20996004 ATGGACTTACATGGCTCA
1 ATGGACTTACATGGCTCA
20996022 TTTCGTTCTG
Statistics
Matches: 54, Mismatches: 8, Indels: 2
0.84 0.12 0.03
Matches are distributed among these distances:
44 32 0.59
46 22 0.41
ACGTcount: A:0.30, C:0.22, G:0.14, T:0.34
Consensus pattern (45 bp):
ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATTATAAT
Found at i:20999787 original size:12 final size:12
Alignment explanation
Indices: 20999770--20999812 Score: 61
Period size: 12 Copynumber: 3.6 Consensus size: 12
20999760 TGTTGATGAT
20999770 TATTATCATTTA
1 TATTATCATTTA
*
20999782 TATTATCATTTC
1 TATTATCATTTA
20999794 TATTATCA-TTA
1 TATTATCATTTA
20999805 TTATTATC
1 -TATTATC
20999813 CATGCATGTT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
11 2 0.07
12 26 0.93
ACGTcount: A:0.30, C:0.12, G:0.00, T:0.58
Consensus pattern (12 bp):
TATTATCATTTA
Found at i:21002858 original size:27 final size:27
Alignment explanation
Indices: 21002823--21002877 Score: 110
Period size: 27 Copynumber: 2.0 Consensus size: 27
21002813 ATTAAAGAAG
21002823 AAAAGACTAAAGCCGATCATTGAGAGA
1 AAAAGACTAAAGCCGATCATTGAGAGA
21002850 AAAAGACTAAAGCCGATCATTGAGAGA
1 AAAAGACTAAAGCCGATCATTGAGAGA
21002877 A
1 A
21002878 GAAGTTTCAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.49, C:0.15, G:0.22, T:0.15
Consensus pattern (27 bp):
AAAAGACTAAAGCCGATCATTGAGAGA
Found at i:21005117 original size:19 final size:19
Alignment explanation
Indices: 21005093--21005134 Score: 84
Period size: 19 Copynumber: 2.2 Consensus size: 19
21005083 ATGGATAAAC
21005093 GCAATAGTTGAGAGCGGGA
1 GCAATAGTTGAGAGCGGGA
21005112 GCAATAGTTGAGAGCGGGA
1 GCAATAGTTGAGAGCGGGA
21005131 GCAA
1 GCAA
21005135 AAGAATCAAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.33, C:0.12, G:0.40, T:0.14
Consensus pattern (19 bp):
GCAATAGTTGAGAGCGGGA
Found at i:21011655 original size:44 final size:44
Alignment explanation
Indices: 21011592--21011760 Score: 155
Period size: 44 Copynumber: 3.8 Consensus size: 44
21011582 ATCATGGCGA
21011592 ATCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGCCATAT
1 ATCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGCCATAT
* * * * * *
21011636 ATCTTATCTCACTGAAGTTGCAATAGAGAAGATTAAAGCCATGA-
1 ATCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGCCAT-AT
* * * ** *
21011680 ACCTTATGTCCCTGAAGTTCCAGTGGAGCAGGTTGAAG--TTACT
1 ATCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGCCATA-T
* * *
21011723 AGTCTCATCTCCCTAAAGTTGCAGTGGAGCTGACTGAA
1 A-TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAA
21011761 AAGAGCGAAT
Statistics
Matches: 97, Mismatches: 24, Indels: 8
0.75 0.19 0.06
Matches are distributed among these distances:
41 1 0.01
42 1 0.01
43 1 0.01
44 93 0.96
45 1 0.01
ACGTcount: A:0.29, C:0.21, G:0.22, T:0.28
Consensus pattern (44 bp):
ATCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGCCATAT
Found at i:21011983 original size:43 final size:43
Alignment explanation
Indices: 21011910--21012017 Score: 105
Period size: 45 Copynumber: 2.5 Consensus size: 43
21011900 ACTAGCCTTG
* * * *
21011910 TCTCCC-AAAGTAGTAGTGGAGCAAGTTGAAGTTA-AAGTCTTA
1 TCTCCCTAAAGTTGCAGTGGAGCAAGCTGAAGATAGAA-TCTTA
21011952 TCTCCCTAAAGTTGCAGTGGAGC-AGACTGAAGATAGCGAATCTTA
1 TCTCCCTAAAGTTGCAGTGGAGCAAG-CTGAAGATA--GAATCTTA
* *
21011997 TTTCCCTGAAGTTGCAGTGGA
1 TCTCCCTAAAGTTGCAGTGGA
21012018 ATAGATTAAA
Statistics
Matches: 55, Mismatches: 6, Indels: 7
0.81 0.09 0.10
Matches are distributed among these distances:
42 8 0.15
43 21 0.38
45 24 0.44
46 2 0.04
ACGTcount: A:0.30, C:0.18, G:0.25, T:0.28
Consensus pattern (43 bp):
TCTCCCTAAAGTTGCAGTGGAGCAAGCTGAAGATAGAATCTTA
Found at i:21016792 original size:46 final size:45
Alignment explanation
Indices: 21016740--21016953 Score: 284
Period size: 46 Copynumber: 4.6 Consensus size: 45
21016730 TTTCTGAAAT
*
21016740 GAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGATA
1 GAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAACATGATA
*
21016785 CGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGATA
1 -GAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAACATGATA
* *
21016831 TGAAATGAATAAGACCATGGTTGAAAGATATACCATGGCAACATGATGGG
1 -GAAATGAGTAAGACCATGGTTGAAAG--ATACCATGGCAACATGAT--A
* * *
21016881 GAAATGAATAAGACCATGGTTGAAAGATACCATAGCAACATGACA
1 GAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAACATGATA
* *
21016926 GTAAATGAGTAAGACCATAGTTCAAAGA
1 G-AAATGAGTAAGACCATGGTTGAAAGA
21016954 CATTATGGCA
Statistics
Matches: 153, Mismatches: 10, Indels: 10
0.88 0.06 0.06
Matches are distributed among these distances:
45 1 0.01
46 92 0.60
47 16 0.10
48 18 0.12
49 26 0.17
ACGTcount: A:0.42, C:0.14, G:0.23, T:0.21
Consensus pattern (45 bp):
GAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAACATGATA
Found at i:21016911 original size:95 final size:93
Alignment explanation
Indices: 21016738--21016953 Score: 301
Period size: 95 Copynumber: 2.3 Consensus size: 93
21016728 GCTTTCTGAA
* **
21016738 ATGAAATGTGTAAGACCATGGTTGAAAG-ATACCATGGCAACATGATACGAAATGTGTAAGACCA
1 ATGAAATGAGTAAGACCATGGTTGAAAGAATACCATGGCAACATGATACGAAATGAATAAGACCA
* *
21016802 TGGTTGAAAGATACCATGGCAACATGAT
66 TGGTTGAAAGATACCATAGCAACATGAC
* **
21016830 ATGAAATGAATAAGACCATGGTTGAAAGATATACCATGGCAACATGATGGGGAAATGAATAAGAC
1 ATGAAATGAGTAAGACCATGGTTGAAAGA-ATACCATGGCAACATGAT-ACGAAATGAATAAGAC
21016895 CATGGTTGAAAGATACCATAGCAACATGAC
64 CATGGTTGAAAGATACCATAGCAACATGAC
* *
21016925 A-GTAAATGAGTAAGACCATAGTTCAAAGA
1 ATG-AAATGAGTAAGACCATGGTTGAAAGA
21016954 CATTATGGCA
Statistics
Matches: 109, Mismatches: 11, Indels: 5
0.87 0.09 0.04
Matches are distributed among these distances:
92 26 0.24
94 19 0.17
95 64 0.59
ACGTcount: A:0.42, C:0.13, G:0.23, T:0.21
Consensus pattern (93 bp):
ATGAAATGAGTAAGACCATGGTTGAAAGAATACCATGGCAACATGATACGAAATGAATAAGACCA
TGGTTGAAAGATACCATAGCAACATGAC
Found at i:21017958 original size:3 final size:3
Alignment explanation
Indices: 21017950--21018002 Score: 106
Period size: 3 Copynumber: 17.7 Consensus size: 3
21017940 ATTCGTACAC
21017950 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
21017998 TTA TT
1 TTA TT
21018003 TCTATTGTTG
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 50 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:21023490 original size:21 final size:21
Alignment explanation
Indices: 21023451--21023490 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
21023441 AAATCTGACT
* * *
21023451 AAGATTGAAGAGTTGAAGGGA
1 AAGATAGAAGAGCTCAAGGGA
21023472 AAGATAGAAGAGCTCAAGG
1 AAGATAGAAGAGCTCAAGG
21023491 CAGCATTGTA
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:0.45, C:0.05, G:0.35, T:0.15
Consensus pattern (21 bp):
AAGATAGAAGAGCTCAAGGGA
Found at i:21032040 original size:22 final size:22
Alignment explanation
Indices: 21032008--21032053 Score: 83
Period size: 22 Copynumber: 2.1 Consensus size: 22
21031998 CTACACCCCT
*
21032008 AAAGTCGTAGTGGGATGGATTG
1 AAAGTCATAGTGGGATGGATTG
21032030 AAAGTCATAGTGGGATGGATTG
1 AAAGTCATAGTGGGATGGATTG
21032052 AA
1 AA
21032054 TCTACCATAG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.33, C:0.04, G:0.37, T:0.26
Consensus pattern (22 bp):
AAAGTCATAGTGGGATGGATTG
Found at i:21032261 original size:44 final size:44
Alignment explanation
Indices: 21032064--21032251 Score: 236
Period size: 44 Copynumber: 4.3 Consensus size: 44
21032054 TCTACCATAG
* *
21032064 CAAATCTTATCT-CACTGAAGA-TGTAATGGAGCAAATTAAAGCTA
1 CAAATCTTATCTCCA-TGAA-ATTGCAGTGGAGCAAATTAAAGCTA
* * *
21032108 CAAATCATATCTCCCTGAAATTGCAGTGAAGCAAATTAAAGCTA
1 CAAATCTTATCTCCATGAAATTGCAGTGGAGCAAATTAAAGCTA
* * * *
21032152 CAAAACTTATCTCCTTGAAATTGCAGTGGAGCGAATTGAAGCTA
1 CAAATCTTATCTCCATGAAATTGCAGTGGAGCAAATTAAAGCTA
* * *
21032196 CAAATCTTATCTCCATGAAGTTGCAGTGGAGCAGAGTAAAGCTA
1 CAAATCTTATCTCCATGAAATTGCAGTGGAGCAAATTAAAGCTA
21032240 CAAATCTTATCT
1 CAAATCTTATCT
21032252 TGCTAAAGTT
Statistics
Matches: 124, Mismatches: 18, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
43 1 0.01
44 122 0.98
45 1 0.01
ACGTcount: A:0.37, C:0.19, G:0.17, T:0.27
Consensus pattern (44 bp):
CAAATCTTATCTCCATGAAATTGCAGTGGAGCAAATTAAAGCTA
Found at i:21033681 original size:13 final size:13
Alignment explanation
Indices: 21033663--21033690 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
21033653 TCTATCTTAT
21033663 TTAGATTTAATCC
1 TTAGATTTAATCC
21033676 TTAGATTTAATCC
1 TTAGATTTAATCC
21033689 TT
1 TT
21033691 TATATTTTGT
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:0.29, C:0.14, G:0.07, T:0.50
Consensus pattern (13 bp):
TTAGATTTAATCC
Found at i:21034027 original size:21 final size:21
Alignment explanation
Indices: 21034003--21034043 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
21033993 TTAAACATGA
21034003 CATTAGTTA-AATCATTATCAT
1 CATTA-TTATAATCATTATCAT
*
21034024 CATTATTATTATCATTATCA
1 CATTATTATAATCATTATCA
21034044 ATTTATTATT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 3 0.17
21 15 0.83
ACGTcount: A:0.37, C:0.15, G:0.02, T:0.46
Consensus pattern (21 bp):
CATTATTATAATCATTATCAT
Found at i:21037945 original size:60 final size:60
Alignment explanation
Indices: 21037852--21037971 Score: 240
Period size: 60 Copynumber: 2.0 Consensus size: 60
21037842 TGCTTGCTTG
21037852 TAGCAGCTTTAATGTTCAAGGTTGTTTCTTTCCTGAATAGGGGCCTAATGGTAATGCATC
1 TAGCAGCTTTAATGTTCAAGGTTGTTTCTTTCCTGAATAGGGGCCTAATGGTAATGCATC
21037912 TAGCAGCTTTAATGTTCAAGGTTGTTTCTTTCCTGAATAGGGGCCTAATGGTAATGCATC
1 TAGCAGCTTTAATGTTCAAGGTTGTTTCTTTCCTGAATAGGGGCCTAATGGTAATGCATC
21037972 GATGACAAAT
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
60 60 1.00
ACGTcount: A:0.23, C:0.17, G:0.23, T:0.37
Consensus pattern (60 bp):
TAGCAGCTTTAATGTTCAAGGTTGTTTCTTTCCTGAATAGGGGCCTAATGGTAATGCATC
Found at i:21038664 original size:20 final size:20
Alignment explanation
Indices: 21038639--21038676 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
21038629 GCTGACAAAA
* *
21038639 CAGTCATTCAAGTTTCAATT
1 CAGTCACTCAACTTTCAATT
21038659 CAGTCACTCAACTTTCAA
1 CAGTCACTCAACTTTCAA
21038677 AAAATAACAA
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:0.32, C:0.26, G:0.08, T:0.34
Consensus pattern (20 bp):
CAGTCACTCAACTTTCAATT
Found at i:21038825 original size:23 final size:23
Alignment explanation
Indices: 21038793--21038854 Score: 70
Period size: 23 Copynumber: 2.7 Consensus size: 23
21038783 AATAAAAGAA
* * *
21038793 AAAAAAAAGAAGAAGCATACGAG
1 AAAAAGAAGAAGAAGAAGACGAG
*
21038816 AAAAAGAAGAAGAAGAAGAGGAG
1 AAAAAGAAGAAGAAGAAGACGAG
* *
21038839 GAAGAGAAGAAGAAGA
1 AAAAAGAAGAAGAAGA
21038855 GAAAATTTCC
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.65, C:0.03, G:0.31, T:0.02
Consensus pattern (23 bp):
AAAAAGAAGAAGAAGAAGACGAG
Found at i:21039617 original size:29 final size:31
Alignment explanation
Indices: 21039561--21039631 Score: 85
Period size: 31 Copynumber: 2.3 Consensus size: 31
21039551 GGAGAAGAAG
* *
21039561 AAGTATAAACATATTGGGCCATTTATG-TAAA
1 AAGTAAAAAAATATTGGGCCA-TTATGTTAAA
21039592 AAGTAAAAAAATATTGGGCCA-TATGTTAAA
1 AAGTAAAAAAATATTGGGCCATTATGTTAAA
21039622 AACG-AAAAAA
1 AA-GTAAAAAA
21039632 GAAGGACGAA
Statistics
Matches: 36, Mismatches: 2, Indels: 5
0.84 0.05 0.12
Matches are distributed among these distances:
29 4 0.11
30 12 0.33
31 20 0.56
ACGTcount: A:0.51, C:0.08, G:0.15, T:0.25
Consensus pattern (31 bp):
AAGTAAAAAAATATTGGGCCATTATGTTAAA
Found at i:21041498 original size:27 final size:27
Alignment explanation
Indices: 21041409--21041498 Score: 63
Period size: 27 Copynumber: 3.2 Consensus size: 27
21041399 AATTGAACTT
*
21041409 AAAAAAAATCTTAGGTATCAAATTAGAA
1 AAAAAAAAT-TTAGGTACCAAATTAGAA
* * * * * **
21041437 AAAATGCCAAGTTCAGGTACTAAATTGGCC
1 AAAA---AAAATTTAGGTACCAAATTAGAA
*
21041467 CAAAAAAATTTAGGTACCAAATTAGAA
1 AAAAAAAATTTAGGTACCAAATTAGAA
21041494 AAAAA
1 AAAAA
21041499 GTGTCAAGTT
Statistics
Matches: 42, Mismatches: 17, Indels: 7
0.64 0.26 0.11
Matches are distributed among these distances:
27 20 0.48
28 4 0.10
30 15 0.36
31 3 0.07
ACGTcount: A:0.52, C:0.12, G:0.13, T:0.22
Consensus pattern (27 bp):
AAAAAAAATTTAGGTACCAAATTAGAA
Found at i:21041531 original size:58 final size:58
Alignment explanation
Indices: 21041410--21041553 Score: 163
Period size: 59 Copynumber: 2.5 Consensus size: 58
21041400 ATTGAACTTA
* * *
21041410 AAAAAAATCTTAGGTATCAAATTAG-AAAAAATGCCAAGTTCAGGTACTAAATTGGCCC
1 AAAAAAAT-TTAGGTAACAAATTAGAAAAAAATGCCAAGTTCAGATACTAAATTGGCAC
* *
21041468 AAAAAAATTTAGGTACCAAATTAGAAAAAAAGTGTCAAGTTCAGATA-TCAAATTGAG-AC
1 AAAAAAATTTAGGTAACAAATTAGAAAAAAA-TGCCAAGTTCAGATACT-AAATTG-GCAC
*
21041527 AAAAAAATTTA-ATAACAAATTA-AAAAA
1 AAAAAAATTTAGGTAACAAATTAGAAAAA
21041554 TACTAAATTT
Statistics
Matches: 76, Mismatches: 6, Indels: 9
0.84 0.07 0.10
Matches are distributed among these distances:
57 20 0.26
58 24 0.32
59 31 0.41
60 1 0.01
ACGTcount: A:0.53, C:0.11, G:0.12, T:0.24
Consensus pattern (58 bp):
AAAAAAATTTAGGTAACAAATTAGAAAAAAATGCCAAGTTCAGATACTAAATTGGCAC
Found at i:21043125 original size:3 final size:3
Alignment explanation
Indices: 21043119--21043161 Score: 86
Period size: 3 Copynumber: 14.3 Consensus size: 3
21043109 TAACAAAAGC
21043119 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
21043162 AATCTAAAGT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:21043346 original size:9 final size:8
Alignment explanation
Indices: 21043320--21043349 Score: 51
Period size: 8 Copynumber: 3.8 Consensus size: 8
21043310 AATTGAAGCT
*
21043320 AAATAAAT
1 AAATAAAA
21043328 AAATAAAA
1 AAATAAAA
21043336 AAATAAAA
1 AAATAAAA
21043344 AAATAA
1 AAATAA
21043350 CAAATGACAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (8 bp):
AAATAAAA
Found at i:21049810 original size:5 final size:5
Alignment explanation
Indices: 21049800--21049834 Score: 52
Period size: 5 Copynumber: 6.6 Consensus size: 5
21049790 ATCTGTGTTC
21049800 TTTAT TTTAT TTTATTT TTTAT TTTAT TTTAT TTT
1 TTTAT TTTAT TTTA--T TTTAT TTTAT TTTAT TTT
21049835 CACAAATTAG
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
5 23 0.82
7 5 0.18
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (5 bp):
TTTAT
Found at i:21049821 original size:12 final size:12
Alignment explanation
Indices: 21049804--21049829 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
21049794 GTGTTCTTTA
21049804 TTTTATTTTATT
1 TTTTATTTTATT
21049816 TTTTATTTTATT
1 TTTTATTTTATT
21049828 TT
1 TT
21049830 ATTTTCACAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (12 bp):
TTTTATTTTATT
Found at i:21049822 original size:17 final size:17
Alignment explanation
Indices: 21049800--21049834 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
21049790 ATCTGTGTTC
21049800 TTTATTTTATTTTATTT
1 TTTATTTTATTTTATTT
21049817 TTTATTTTATTTTATTT
1 TTTATTTTATTTTATTT
21049834 T
1 T
21049835 CACAAATTAG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (17 bp):
TTTATTTTATTTTATTT
Found at i:21055093 original size:2 final size:2
Alignment explanation
Indices: 21055086--21055127 Score: 75
Period size: 2 Copynumber: 21.0 Consensus size: 2
21055076 GAATATTGGA
*
21055086 AT AT AT AT AT AA 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 AT AT
21055128 TTGTTGAAGG
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:21055930 original size:20 final size:21
Alignment explanation
Indices: 21055885--21055936 Score: 65
Period size: 19 Copynumber: 2.6 Consensus size: 21
21055875 CAAAAGATAA
* *
21055885 ATAATAAAATTATATTATTTT
1 ATAATAAAATTATATTATGTG
21055906 A-AATAAAATTA-ATTATGTG
1 ATAATAAAATTATATTATGTG
21055925 ATAAT-AAATTAT
1 ATAATAAAATTAT
21055937 TATTTTATTC
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
19 13 0.48
20 13 0.48
21 1 0.04
ACGTcount: A:0.52, C:0.00, G:0.04, T:0.44
Consensus pattern (21 bp):
ATAATAAAATTATATTATGTG
Found at i:21057878 original size:22 final size:22
Alignment explanation
Indices: 21057852--21057899 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 22
21057842 ACACTAGTAT
* *
21057852 ATGAAAGCCCTTTACAGGTAGC
1 ATGAAAACCCTTTAAAGGTAGC
* *
21057874 ATGAAAACTCTTTAAAGGTAGT
1 ATGAAAACCCTTTAAAGGTAGC
21057896 ATGA
1 ATGA
21057900 GACTCTACGA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.38, C:0.15, G:0.21, T:0.27
Consensus pattern (22 bp):
ATGAAAACCCTTTAAAGGTAGC
Found at i:21061268 original size:5 final size:6
Alignment explanation
Indices: 21061249--21061285 Score: 60
Period size: 6 Copynumber: 6.5 Consensus size: 6
21061239 TTGTGTGTTC
21061249 TTTATT TTTATT TTTATT TTTA-T TTTA-T TTTATT TTT
1 TTTATT TTTATT TTTATT TTTATT TTTATT TTTATT TTT
21061286 CTTAAACTGG
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
5 10 0.33
6 20 0.67
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (6 bp):
TTTATT
Found at i:21065677 original size:6 final size:6
Alignment explanation
Indices: 21065666--21065708 Score: 63
Period size: 6 Copynumber: 7.5 Consensus size: 6
21065656 TTGTGTGTTC
*
21065666 TTTATT TTTATT TTTATC TTTATT TTTA-T TTTA-T TTTATT TTT
1 TTTATT TTTATT TTTATT TTTATT TTTATT TTTATT TTTATT TTT
21065709 CTCACCCATC
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
5 10 0.29
6 24 0.71
ACGTcount: A:0.16, C:0.02, G:0.00, T:0.81
Consensus pattern (6 bp):
TTTATT
Found at i:21065687 original size:18 final size:17
Alignment explanation
Indices: 21065664--21065708 Score: 74
Period size: 18 Copynumber: 2.6 Consensus size: 17
21065654 ATTTGTGTGT
21065664 TCTTTATTTTTATTTTTA
1 TCTTTATTTTTA-TTTTA
21065682 TCTTTATTTTTATTTTA
1 TCTTTATTTTTATTTTA
21065699 T-TTTATTTTT
1 TCTTTATTTTT
21065709 CTCACCCATC
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
16 9 0.33
17 6 0.22
18 12 0.44
ACGTcount: A:0.16, C:0.04, G:0.00, T:0.80
Consensus pattern (17 bp):
TCTTTATTTTTATTTTA
Found at i:21066551 original size:18 final size:18
Alignment explanation
Indices: 21066528--21066569 Score: 75
Period size: 18 Copynumber: 2.3 Consensus size: 18
21066518 ACAATTACAT
21066528 AGAATATCTCATATATTA
1 AGAATATCTCATATATTA
21066546 AGAATATCTCATATATTA
1 AGAATATCTCATATATTA
*
21066564 ATAATA
1 AGAATA
21066570 GTTTAATTCT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.48, C:0.10, G:0.05, T:0.38
Consensus pattern (18 bp):
AGAATATCTCATATATTA
Found at i:21067495 original size:80 final size:82
Alignment explanation
Indices: 21067362--21067519 Score: 239
Period size: 80 Copynumber: 2.0 Consensus size: 82
21067352 ATAAGGTAAT
* * *
21067362 ATTTAACTTAAAGGGACCATGAATATCTTATGAGGGTAATACACATATGACAAGTTCATTGGAT-
1 ATTTAACCTAAAGGGACCATGAATATCCTATGAGGATAATACACATATGACAAGTTCATTGGATA
21067426 AAA-TTTAATTAAGTAG
66 AAAGTTTAATTAAGTAG
* * * *
21067442 ATTTAACCTAAATGGATCATGAATATCCTATGAGGATAATACATATATGACAAGTTTATTGGATA
1 ATTTAACCTAAAGGGACCATGAATATCCTATGAGGATAATACACATATGACAAGTTCATTGGATA
21067507 AAAGTTTAATTAA
66 AAAGTTTAATTAA
21067520 TCAAGATATA
Statistics
Matches: 69, Mismatches: 7, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
80 57 0.83
81 3 0.04
82 9 0.13
ACGTcount: A:0.41, C:0.09, G:0.16, T:0.34
Consensus pattern (82 bp):
ATTTAACCTAAAGGGACCATGAATATCCTATGAGGATAATACACATATGACAAGTTCATTGGATA
AAAGTTTAATTAAGTAG
Found at i:21069499 original size:21 final size:21
Alignment explanation
Indices: 21069470--21069510 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
21069460 AATTAAGTAA
*
21069470 AATAAGATTAATTAGAATTAG
1 AATAAGATTAATTAAAATTAG
*
21069491 AATATGATTAATTAAAATTA
1 AATAAGATTAATTAAAATTA
21069511 ATTTAATGTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.54, C:0.00, G:0.10, T:0.37
Consensus pattern (21 bp):
AATAAGATTAATTAAAATTAG
Found at i:21073957 original size:25 final size:25
Alignment explanation
Indices: 21073929--21073976 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
21073919 TTATACCATG
* * *
21073929 AAAATGACCGTTTTGCCCCTAGGTA
1 AAAATGACCATTATACCCCTAGGTA
21073954 AAAATGACCATTATACCCCTAGG
1 AAAATGACCATTATACCCCTAGG
21073977 GTTTATGTAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.33, C:0.25, G:0.17, T:0.25
Consensus pattern (25 bp):
AAAATGACCATTATACCCCTAGGTA
Found at i:21074079 original size:20 final size:20
Alignment explanation
Indices: 21074019--21074079 Score: 104
Period size: 20 Copynumber: 3.0 Consensus size: 20
21074009 ATAAATATGG
*
21074019 TATGTATGAGATGCACATGA
1 TATGTATGATATGCACATGA
*
21074039 CATGTATGATATGCACATGA
1 TATGTATGATATGCACATGA
21074059 TATGTATGATATGCACATGA
1 TATGTATGATATGCACATGA
21074079 T
1 T
21074080 GTAATCATAA
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 38 1.00
ACGTcount: A:0.34, C:0.11, G:0.21, T:0.33
Consensus pattern (20 bp):
TATGTATGATATGCACATGA
Found at i:21074156 original size:24 final size:24
Alignment explanation
Indices: 21074129--21074271 Score: 209
Period size: 24 Copynumber: 6.0 Consensus size: 24
21074119 GAGGAAGTGA
21074129 AAAAGGGCTTATGCCCCAGTTATC
1 AAAAGGGCTTATGCCCCAGTTATC
21074153 AAAAGGGCTTATGCCCCAGTTATC
1 AAAAGGGCTTATGCCCCAGTTATC
21074177 AAAAGGGCTTATGCCCCAGTTAT-
1 AAAAGGGCTTATGCCCCAGTTATC
*
21074200 AAAAGGGCTTATGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATC
* * *
21074224 GAAAGGGCTTTTGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATC
*
21074248 AAAAGAGGC-TAGGCCTCCAGTTAT
1 AAAAG-GGCTTATGCC-CCAGTTAT
21074272 ATGATAAAGC
Statistics
Matches: 111, Mismatches: 5, Indels: 5
0.92 0.04 0.04
Matches are distributed among these distances:
23 23 0.21
24 77 0.69
25 11 0.10
ACGTcount: A:0.29, C:0.22, G:0.22, T:0.27
Consensus pattern (24 bp):
AAAAGGGCTTATGCCCCAGTTATC
Found at i:21074222 original size:47 final size:47
Alignment explanation
Indices: 21074129--21074271 Score: 207
Period size: 47 Copynumber: 3.0 Consensus size: 47
21074119 GAGGAAGTGA
21074129 AAAAGGGCTTATGCCCCAGTTATCAAAAGGGCTTATGCCCCAGTTATC
1 AAAAGGGCTTATGCCCCAGTTAT-AAAAGGGCTTATGCCCCAGTTATC
*
21074177 AAAAGGGCTTATGCCCCAGTTATAAAAGGGCTTATGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATAAAAGGGCTTATGCCCCAGTTATC
* * *
21074224 GAAAGGGCTTTTGCCCCAGTTATTAAAAGAGGC-TAGGCCTCCAGTTAT
1 AAAAGGGCTTATGCCCCAGTTA-TAAAAG-GGCTTATGCC-CCAGTTAT
21074272 ATGATAAAGC
Statistics
Matches: 88, Mismatches: 4, Indels: 5
0.91 0.04 0.05
Matches are distributed among these distances:
47 43 0.49
48 34 0.39
49 11 0.12
ACGTcount: A:0.29, C:0.22, G:0.22, T:0.27
Consensus pattern (47 bp):
AAAAGGGCTTATGCCCCAGTTATAAAAGGGCTTATGCCCCAGTTATC
Found at i:21074245 original size:71 final size:72
Alignment explanation
Indices: 21074129--21074272 Score: 220
Period size: 71 Copynumber: 2.0 Consensus size: 72
21074119 GAGGAAGTGA
*
21074129 AAAAGGGCTTATGCCCCAGTTATCAAAAGGGCTTATGCCCCAGTTATCAAAAG-GGCTTATGCC-
1 AAAAGGGCTTATGCCCCAGTTATCAAAAGGGCTTATGCCCCAGTTATCAAAAGAGGC-TAGGCCT
21074192 CCAGTTAT
65 CCAGTTAT
** * *
21074200 AAAAGGGCTTATGCCCCAGTTATTGAAAGGGCTTTTGCCCCAGTTATTAAAAGAGGCTAGGCCTC
1 AAAAGGGCTTATGCCCCAGTTATCAAAAGGGCTTATGCCCCAGTTATCAAAAGAGGCTAGGCCTC
21074265 CAGTTAT
66 CAGTTAT
21074272 A
1 A
21074273 TGATAAAGCA
Statistics
Matches: 66, Mismatches: 5, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
71 54 0.82
72 12 0.18
ACGTcount: A:0.29, C:0.22, G:0.22, T:0.26
Consensus pattern (72 bp):
AAAAGGGCTTATGCCCCAGTTATCAAAAGGGCTTATGCCCCAGTTATCAAAAGAGGCTAGGCCTC
CAGTTAT
Found at i:21074523 original size:30 final size:31
Alignment explanation
Indices: 21074463--21074525 Score: 101
Period size: 31 Copynumber: 2.1 Consensus size: 31
21074453 CGTTTACAGT
21074463 AAAGGCTTCGGCCCAGTAATATGAAATATGA
1 AAAGGCTTCGGCCCAGTAATATGAAATATGA
**
21074494 AAAGGCTTCGGCCCAGTGTTATG-AATATGA
1 AAAGGCTTCGGCCCAGTAATATGAAATATGA
21074524 AA
1 AA
21074526 CATGAAAAGG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
30 9 0.30
31 21 0.70
ACGTcount: A:0.37, C:0.16, G:0.24, T:0.24
Consensus pattern (31 bp):
AAAGGCTTCGGCCCAGTAATATGAAATATGA
Found at i:21084586 original size:15 final size:16
Alignment explanation
Indices: 21084556--21084589 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
21084546 ACATGACAAA
21084556 ATAACAAAATCAATAT
1 ATAACAAAATCAATAT
*
21084572 ATAATAAAA-CAATAT
1 ATAACAAAATCAATAT
21084587 ATA
1 ATA
21084590 CATGAAATAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 9 0.53
16 8 0.47
ACGTcount: A:0.65, C:0.09, G:0.00, T:0.26
Consensus pattern (16 bp):
ATAACAAAATCAATAT
Found at i:21097972 original size:40 final size:40
Alignment explanation
Indices: 21097914--21098054 Score: 122
Period size: 40 Copynumber: 3.5 Consensus size: 40
21097904 GAAATTGAAT
* * *
21097914 TATCCGGGCTAAGCCCCGAAGACAATTATGCTGGAAATTA
1 TATCCGGGCTAAGACCCGAAGACAATTATGCTAGAAACTA
* * * ***
21097954 TATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGGCTA
1 TATCCGGGCTAAGACCCGAAGACAATTATGCTAGAAACTA
* * * ** * *
21097994 TATCCGGGCTAAGACCCGAAGGC-ATTCGTGCGAGTCATTC
1 TATCCGGGCTAAGACCCGAAGACAATT-ATGCTAGAAACTA
21098034 TATCCGGGCTAAGACCCGAAG
1 TATCCGGGCTAAGACCCGAAG
21098055 GCATTTGTGC
Statistics
Matches: 85, Mismatches: 15, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
39 3 0.04
40 82 0.96
ACGTcount: A:0.27, C:0.24, G:0.27, T:0.22
Consensus pattern (40 bp):
TATCCGGGCTAAGACCCGAAGACAATTATGCTAGAAACTA
Found at i:21098013 original size:80 final size:80
Alignment explanation
Indices: 21097914--21098064 Score: 198
Period size: 80 Copynumber: 1.9 Consensus size: 80
21097904 GAAATTGAAT
* *
21097914 TATCCGGGCTAAGCCCCGAAGACAATT-ATGCTG-GAAATTATATCCGGGTTAAGACCCGAAGGC
1 TATCCGGGCTAAGACCCGAAGAC-ATTCATGC-GAGAAATTATATCCGGGCTAAGACCCGAAGGC
21097977 AATTGTGCTAGTGGCTA
64 AATTGTGCTAGTGGCTA
* * ** * *
21097994 TATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTCATTCTATCCGGGCTAAGACCCGAAGGCAT
1 TATCCGGGCTAAGACCCGAAGACATTCATGCGAGAAATTATATCCGGGCTAAGACCCGAAGGCAA
21098059 TTGTGC
66 TTGTGC
21098065 ACATGCTTAT
Statistics
Matches: 61, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
79 4 0.07
80 57 0.93
ACGTcount: A:0.26, C:0.24, G:0.27, T:0.23
Consensus pattern (80 bp):
TATCCGGGCTAAGACCCGAAGACATTCATGCGAGAAATTATATCCGGGCTAAGACCCGAAGGCAA
TTGTGCTAGTGGCTA
Found at i:21098078 original size:40 final size:39
Alignment explanation
Indices: 21097951--21098080 Score: 147
Period size: 40 Copynumber: 3.3 Consensus size: 39
21097941 ATGCTGGAAA
* * *
21097951 TTATATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGGC
1 TTATATCCGGGCTAAGACCCGAAGGCATTTGTGC-AAT-GC
* *
21097992 -TATATCCGGGCTAAGACCCGAAGGCATTCGTGCGA-GTC
1 TTATATCCGGGCTAAGACCCGAAGGCATTTGTGCAATG-C
*
21098030 ATTCTATCCGGGCTAAGACCCGAAGGCATTTGTGCACATGC
1 -TTATATCCGGGCTAAGACCCGAAGGCATTTGTGCA-ATGC
21098071 TTATATCCGG
1 TTATATCCGG
21098081 TTATATTCCG
Statistics
Matches: 75, Mismatches: 9, Indels: 11
0.79 0.09 0.12
Matches are distributed among these distances:
37 1 0.01
38 1 0.01
40 70 0.93
41 2 0.03
42 1 0.01
ACGTcount: A:0.24, C:0.24, G:0.27, T:0.25
Consensus pattern (39 bp):
TTATATCCGGGCTAAGACCCGAAGGCATTTGTGCAATGC
Found at i:21100543 original size:20 final size:19
Alignment explanation
Indices: 21100494--21100543 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 19
21100484 GGGCACACAC
*
21100494 CCGTGTGGCCTGGGACATG
1 CCGTGTGGCCTAGGACATG
21100513 CCAGTGTGGCCTAGGACATGG
1 CC-GTGTGGCCTAGGACAT-G
*
21100534 CCGTGGGGCC
1 CCGTGTGGCC
21100544 AGGCCGTGGG
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
19 2 0.07
20 22 0.81
21 3 0.11
ACGTcount: A:0.12, C:0.28, G:0.42, T:0.18
Consensus pattern (19 bp):
CCGTGTGGCCTAGGACATG
Found at i:21102327 original size:12 final size:12
Alignment explanation
Indices: 21102287--21102320 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
21102277 AAAACCCTAT
*
21102287 TTTTTCCTT-TC
1 TTTTTCTTTCTC
21102298 TTTTTCTTTCTC
1 TTTTTCTTTCTC
21102310 TTTTTCTTTCT
1 TTTTTCTTTCT
21102321 TTCTTTCCCT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
11 8 0.38
12 13 0.62
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (12 bp):
TTTTTCTTTCTC
Found at i:21111027 original size:75 final size:75
Alignment explanation
Indices: 21110908--21111079 Score: 205
Period size: 75 Copynumber: 2.4 Consensus size: 75
21110898 CATGGCAAAG
** *
21110908 TGTGAAATGTAGGTATGG---TATC--ATCCATACTGAGTTGTGAAATGTAGGTATGGTATTAT-
1 TGTGAAATGTAGGTATGGTATTATCAAATCCATACTGAGTTAAGAAATGTAGGTATGGCATT-TC
*
21110967 CCATACTGAGC
65 CCATACCGAGC
21110978 TGTGAAATGTAGGTATGGTATTATCAAATCCATACTGAGTTAAGAAATGTAGGTATGGCATTTCC
1 TGTGAAATGTAGGTATGGTATTATCAAATCCATACTGAGTTAAGAAATGTAGGTATGGCATTTCC
*
21111043 CATACCGAGT
66 CATACCGAGC
***
21111053 TAAAAAAATGTAGGTATGGTATT-TCAA
1 T-GTGAAATGTAGGTATGGTATTATCAA
21111080 TGAGGAAAAC
Statistics
Matches: 87, Mismatches: 8, Indels: 9
0.84 0.08 0.09
Matches are distributed among these distances:
70 18 0.21
73 4 0.05
74 1 0.01
75 46 0.53
76 18 0.21
ACGTcount: A:0.33, C:0.11, G:0.23, T:0.33
Consensus pattern (75 bp):
TGTGAAATGTAGGTATGGTATTATCAAATCCATACTGAGTTAAGAAATGTAGGTATGGCATTTCC
CATACCGAGC
Found at i:21111046 original size:35 final size:35
Alignment explanation
Indices: 21110911--21111077 Score: 167
Period size: 35 Copynumber: 4.6 Consensus size: 35
21110901 GGCAAAGTGT
* **
21110911 GAAATGTAGGTATGGTATCAT-CCATACTGAGTTGT
1 GAAATGTAGGTATGGTAT-TTCCCATACTGAGTTAA
* **
21110946 GAAATGTAGGTATGGTATTAT-CCATACTGAGCTGT
1 GAAATGTAGGTATGGTATT-TCCCATACTGAGTTAA
21110981 GAAATGTAGGTATGGTATTATCAAATCCATACTGAGTTAA
1 GAAATGTAGGTATGGTATT-TC----CCATACTGAGTTAA
* *
21111021 GAAATGTAGGTATGGCATTTCCCATACCGAGTTAAA
1 GAAATGTAGGTATGGTATTTCCCATACTGAGTT-AA
*
21111057 AAAATGTAGGTATGGTATTTC
1 GAAATGTAGGTATGGTATTTC
21111078 AATGAGGAAA
Statistics
Matches: 116, Mismatches: 9, Indels: 13
0.84 0.07 0.09
Matches are distributed among these distances:
35 64 0.55
36 21 0.18
39 2 0.02
40 29 0.25
ACGTcount: A:0.32, C:0.11, G:0.23, T:0.33
Consensus pattern (35 bp):
GAAATGTAGGTATGGTATTTCCCATACTGAGTTAA
Found at i:21111069 original size:36 final size:35
Alignment explanation
Indices: 21111007--21111077 Score: 106
Period size: 36 Copynumber: 2.0 Consensus size: 35
21110997 ATTATCAAAT
* *
21111007 CCATACTGAGTTAAGAAATGTAGGTATGGCATTTC
1 CCATACCGAGTTAAAAAATGTAGGTATGGCATTTC
*
21111042 CCATACCGAGTTAAAAAAATGTAGGTATGGTATTTC
1 CCATACCGAGTT-AAAAAATGTAGGTATGGCATTTC
21111078 AATGAGGAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
35 11 0.34
36 21 0.66
ACGTcount: A:0.34, C:0.14, G:0.21, T:0.31
Consensus pattern (35 bp):
CCATACCGAGTTAAAAAATGTAGGTATGGCATTTC
Found at i:21129444 original size:12 final size:12
Alignment explanation
Indices: 21129427--21129451 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
21129417 TTCTCTGTGT
21129427 GTGTGGTGGGGG
1 GTGTGGTGGGGG
21129439 GTGTGGTGGGGG
1 GTGTGGTGGGGG
21129451 G
1 G
21129452 GGGGGGGAGG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.00, G:0.76, T:0.24
Consensus pattern (12 bp):
GTGTGGTGGGGG
Found at i:21136357 original size:33 final size:33
Alignment explanation
Indices: 21136315--21136382 Score: 136
Period size: 33 Copynumber: 2.1 Consensus size: 33
21136305 ACATAGAGTG
21136315 GAATCGGGGAATCTCGCCGGCGGGTAATAAAAC
1 GAATCGGGGAATCTCGCCGGCGGGTAATAAAAC
21136348 GAATCGGGGAATCTCGCCGGCGGGTAATAAAAC
1 GAATCGGGGAATCTCGCCGGCGGGTAATAAAAC
21136381 GA
1 GA
21136383 TCTTTTAAAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.31, C:0.21, G:0.34, T:0.15
Consensus pattern (33 bp):
GAATCGGGGAATCTCGCCGGCGGGTAATAAAAC
Found at i:21136856 original size:41 final size:40
Alignment explanation
Indices: 21136769--21136855 Score: 140
Period size: 40 Copynumber: 2.2 Consensus size: 40
21136759 ATACAAATAA
*
21136769 GAAAAAGGAAAACTCAAAAATTAGCTACGAATTTAAGCTT
1 GAAAAAAGAAAACTCAAAAATTAGCTACGAATTTAAGCTT
*
21136809 GAAAAAAGAAAAC-CTAAAAATTAGCTATGAATTTAAGCTT
1 GAAAAAAGAAAACTC-AAAAATTAGCTACGAATTTAAGCTT
21136849 GAAAAAA
1 GAAAAAA
21136856 ACTGAAATCA
Statistics
Matches: 44, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
39 1 0.02
40 43 0.98
ACGTcount: A:0.54, C:0.10, G:0.14, T:0.22
Consensus pattern (40 bp):
GAAAAAAGAAAACTCAAAAATTAGCTACGAATTTAAGCTT
Found at i:21137985 original size:22 final size:23
Alignment explanation
Indices: 21137928--21137986 Score: 59
Period size: 25 Copynumber: 2.5 Consensus size: 23
21137918 TACTTTTTTT
21137928 ATAAAATAAA-AAACTTTAAAAA
1 ATAAAATAAATAAACTTTAAAAA
* *
21137950 ATAATAATTCAAATACA-TTTAAAAC
1 ATAA-AA-T-AAATAAACTTTAAAAA
21137975 ATAAAATAAATA
1 ATAAAATAAATA
21137987 TTAAAACAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 8
0.76 0.05 0.20
Matches are distributed among these distances:
22 9 0.29
23 3 0.10
24 3 0.10
25 14 0.45
26 2 0.06
ACGTcount: A:0.66, C:0.07, G:0.00, T:0.27
Consensus pattern (23 bp):
ATAAAATAAATAAACTTTAAAAA
Found at i:21138225 original size:11 final size:11
Alignment explanation
Indices: 21138211--21138317 Score: 74
Period size: 11 Copynumber: 9.8 Consensus size: 11
21138201 AAGTAGCAGT
*
21138211 AAAATAGCACC
1 AAAACAGCACC
*
21138222 AAAACAGCATC
1 AAAACAGCACC
*
21138233 AAAACAACACC
1 AAAACAGCACC
* * *
21138244 AAAATACCATC
1 AAAACAGCACC
*
21138255 -AAA-AGCACA
1 AAAACAGCACC
* * *
21138264 AAAATACCATC
1 AAAACAGCACC
21138275 AAAACAGCACC
1 AAAACAGCACC
* *
21138286 CAAACAGCAAC
1 AAAACAGCACC
*
21138297 AAAACAGCACAA
1 AAAACAGCAC-C
21138309 AAAACAGCA
1 AAAACAGCA
21138318 TCACCAACAA
Statistics
Matches: 72, Mismatches: 21, Indels: 5
0.73 0.21 0.05
Matches are distributed among these distances:
9 3 0.04
10 6 0.08
11 54 0.75
12 9 0.12
ACGTcount: A:0.59, C:0.29, G:0.07, T:0.06
Consensus pattern (11 bp):
AAAACAGCACC
Found at i:21138236 original size:22 final size:22
Alignment explanation
Indices: 21138211--21138335 Score: 110
Period size: 22 Copynumber: 5.7 Consensus size: 22
21138201 AAGTAGCAGT
*
21138211 AAAATAGCACCAAAACAGCATC
1 AAAACAGCACCAAAACAGCATC
* * *
21138233 AAAACAACACCAAAATACCATC
1 AAAACAGCACCAAAACAGCATC
* * *
21138255 -AAA-AGCACAAAAATACCATC
1 AAAACAGCACCAAAACAGCATC
* *
21138275 AAAACAGCACCCAAACAGCAAC
1 AAAACAGCACCAAAACAGCATC
*
21138297 AAAACAGCACAAAAAACAGCATC
1 AAAACAGCAC-CAAAACAGCATC
* *
21138320 ACCAACAACACCAAAA
1 A-AAACAGCACCAAAA
21138336 ACCTACAAAA
Statistics
Matches: 82, Mismatches: 17, Indels: 7
0.77 0.16 0.07
Matches are distributed among these distances:
20 15 0.18
21 6 0.07
22 40 0.49
23 14 0.17
24 7 0.09
ACGTcount: A:0.58, C:0.30, G:0.06, T:0.06
Consensus pattern (22 bp):
AAAACAGCACCAAAACAGCATC
Found at i:21138275 original size:42 final size:44
Alignment explanation
Indices: 21138222--21138345 Score: 121
Period size: 42 Copynumber: 2.8 Consensus size: 44
21138212 AAATAGCACC
* *
21138222 AAAACAGCATCAAAACAACACCAAAATACCATC-AAA-AGCACAA
1 AAAACA-CATCAAAACAACACCAAAACACCAACAAAACAGCACAA
* * *
21138265 AAATAC-CATCAAAACAGCACCCAAACAGCAACAAAACAGCACAA
1 AAA-ACACATCAAAACAACACCAAAACACCAACAAAACAGCACAA
* *
21138309 AAAACAGCATCACCAACAACACCAAAA-ACCTACAAAA
1 AAAACA-CATCA-AAACAACACCAAAACACCAACAAAA
21138346 TATAATCAAC
Statistics
Matches: 65, Mismatches: 10, Indels: 10
0.76 0.12 0.12
Matches are distributed among these distances:
42 21 0.32
43 8 0.12
44 12 0.18
45 13 0.20
46 11 0.17
ACGTcount: A:0.59, C:0.31, G:0.05, T:0.06
Consensus pattern (44 bp):
AAAACACATCAAAACAACACCAAAACACCAACAAAACAGCACAA
Found at i:21138492 original size:9 final size:9
Alignment explanation
Indices: 21138478--21138519 Score: 66
Period size: 9 Copynumber: 4.7 Consensus size: 9
21138468 ATCGAAGAAA
21138478 CATCGTCCT
1 CATCGTCCT
21138487 CATCGTCCT
1 CATCGTCCT
*
21138496 CGTCGTCCT
1 CATCGTCCT
*
21138505 CATCATCCT
1 CATCGTCCT
21138514 CATCGT
1 CATCGT
21138520 TCTTGCAACC
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
9 29 1.00
ACGTcount: A:0.12, C:0.43, G:0.12, T:0.33
Consensus pattern (9 bp):
CATCGTCCT
Found at i:21143721 original size:5 final size:5
Alignment explanation
Indices: 21143711--21143749 Score: 51
Period size: 5 Copynumber: 7.6 Consensus size: 5
21143701 CAAAATGATG
* *
21143711 TGAAT TGAAT TGAAT TGAAT ATGAAT TGTAT TAAAT TGA
1 TGAAT TGAAT TGAAT TGAAT -TGAAT TGAAT TGAAT TGA
21143750 GCTAAATTTG
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
5 24 0.83
6 5 0.17
ACGTcount: A:0.41, C:0.00, G:0.18, T:0.41
Consensus pattern (5 bp):
TGAAT
Found at i:21144730 original size:25 final size:25
Alignment explanation
Indices: 21144702--21144754 Score: 79
Period size: 25 Copynumber: 2.1 Consensus size: 25
21144692 GAGCTTTCTG
* *
21144702 TTATATGGTTCTTGTGAGTTTCCCA
1 TTATATGGTTCTTATGAGCTTCCCA
*
21144727 TTATATGGTTCTTATGAGCTTCCTA
1 TTATATGGTTCTTATGAGCTTCCCA
21144752 TTA
1 TTA
21144755 ATAGCTCTTC
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.19, C:0.15, G:0.17, T:0.49
Consensus pattern (25 bp):
TTATATGGTTCTTATGAGCTTCCCA
Found at i:21144888 original size:26 final size:26
Alignment explanation
Indices: 21144842--21144908 Score: 73
Period size: 26 Copynumber: 2.6 Consensus size: 26
21144832 GTTATATAAT
* **
21144842 TCTTCGTGAGCTTCCCGATTAAAGAC
1 TCTTTGTGAGCTTCCTAATTAAAGAC
* *
21144868 TCTTTGTGAGCTTCCTAATTAATGGC
1 TCTTTGTGAGCTTCCTAATTAAAGAC
*
21144894 TCTCTG-GAGCTTCCT
1 TCTTTGTGAGCTTCCT
21144909 GATATGGCTC
Statistics
Matches: 35, Mismatches: 6, Indels: 1
0.83 0.14 0.02
Matches are distributed among these distances:
25 9 0.26
26 26 0.74
ACGTcount: A:0.18, C:0.25, G:0.19, T:0.37
Consensus pattern (26 bp):
TCTTTGTGAGCTTCCTAATTAAAGAC
Found at i:21148155 original size:20 final size:20
Alignment explanation
Indices: 21148130--21148199 Score: 59
Period size: 20 Copynumber: 3.3 Consensus size: 20
21148120 CTTTTGGACA
21148130 TAATTGCAATTACTATAGTC
1 TAATTGCAATTACTATAGTC
* * * * *
21148150 TAATTGGAACGATACTTTTGGAC
1 TAATTGCAA--TTAC-TATAGTC
21148173 TTAATTGCAATTACTATAGTC
1 -TAATTGCAATTACTATAGTC
21148194 TAATTG
1 TAATTG
21148200 TATATGTTCA
Statistics
Matches: 36, Mismatches: 10, Indels: 8
0.67 0.19 0.15
Matches are distributed among these distances:
20 14 0.39
21 4 0.11
22 6 0.17
23 4 0.11
24 8 0.22
ACGTcount: A:0.33, C:0.13, G:0.14, T:0.40
Consensus pattern (20 bp):
TAATTGCAATTACTATAGTC
Found at i:21148178 original size:44 final size:44
Alignment explanation
Indices: 21148111--21148199 Score: 169
Period size: 44 Copynumber: 2.0 Consensus size: 44
21148101 GCGAATTATC
21148111 GGAACGATACTTTTGGACATAATTGCAATTACTATAGTCTAATT
1 GGAACGATACTTTTGGACATAATTGCAATTACTATAGTCTAATT
*
21148155 GGAACGATACTTTTGGACTTAATTGCAATTACTATAGTCTAATT
1 GGAACGATACTTTTGGACATAATTGCAATTACTATAGTCTAATT
21148199 G
1 G
21148200 TATATGTTCA
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
44 44 1.00
ACGTcount: A:0.33, C:0.13, G:0.17, T:0.37
Consensus pattern (44 bp):
GGAACGATACTTTTGGACATAATTGCAATTACTATAGTCTAATT
Found at i:21155706 original size:31 final size:31
Alignment explanation
Indices: 21155642--21155725 Score: 89
Period size: 31 Copynumber: 2.7 Consensus size: 31
21155632 TTGATTCAAA
* ** *
21155642 TAAGTATTAATTTGGATTAAAAAATTAAGTT
1 TAAGTATTAATTTGAATTAAAAAACAAAATT
* *
21155673 TAAGTAGTAATTTGAATTAATAAACAAAATT
1 TAAGTATTAATTTGAATTAAAAAACAAAATT
*
21155704 TAAATAATTAATTT-AATTAAAA
1 TAAGT-ATTAATTTGAATTAAAA
21155726 TAGAATTAAA
Statistics
Matches: 43, Mismatches: 9, Indels: 2
0.80 0.17 0.04
Matches are distributed among these distances:
31 36 0.84
32 7 0.16
ACGTcount: A:0.51, C:0.01, G:0.08, T:0.39
Consensus pattern (31 bp):
TAAGTATTAATTTGAATTAAAAAACAAAATT
Found at i:21157422 original size:87 final size:87
Alignment explanation
Indices: 21157273--21157433 Score: 295
Period size: 87 Copynumber: 1.9 Consensus size: 87
21157263 TTATCCTTTG
21157273 GGTTGATTTAGTTTGCTGTTAAACACATGTAAAGGTGACGACTTTTCATGATCTTTGCATAGTCA
1 GGTTGATTTAGTTTGCTGTTAAACACATGTAAAGGTGACGACTTTTCATGATCTTTGCATAGTCA
21157338 TTTCTAGAATTTTTCTTTTTTT
66 TTTCTAGAATTTTTCTTTTTTT
* * *
21157360 GGTTGATTTAGTTTGCTGTTAGAGACATGTAAAGGTGACGACTTTTCATGATCTTTGGATAGTCA
1 GGTTGATTTAGTTTGCTGTTAAACACATGTAAAGGTGACGACTTTTCATGATCTTTGCATAGTCA
21157425 TTTCTAGAA
66 TTTCTAGAA
21157434 AATTTTTGGG
Statistics
Matches: 71, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
87 71 1.00
ACGTcount: A:0.24, C:0.12, G:0.20, T:0.43
Consensus pattern (87 bp):
GGTTGATTTAGTTTGCTGTTAAACACATGTAAAGGTGACGACTTTTCATGATCTTTGCATAGTCA
TTTCTAGAATTTTTCTTTTTTT
Found at i:21161486 original size:30 final size:30
Alignment explanation
Indices: 21161454--21161513 Score: 75
Period size: 32 Copynumber: 1.9 Consensus size: 30
21161444 TGACATCCTT
*
21161454 AAACTATGATTCAGATTTTTAAATTGGTTTAA
1 AAACTATGATTCAGA-TTCTAAATTGGTTT-A
* *
21161486 AAATTATGATTGAGATTCTAAATTGGTT
1 AAACTATGATTCAGATTCTAAATTGGTT
21161514 CAGAGAGTAT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
31 12 0.48
32 13 0.52
ACGTcount: A:0.37, C:0.05, G:0.15, T:0.43
Consensus pattern (30 bp):
AAACTATGATTCAGATTCTAAATTGGTTTA
Found at i:21165778 original size:18 final size:18
Alignment explanation
Indices: 21165731--21165792 Score: 70
Period size: 18 Copynumber: 3.4 Consensus size: 18
21165721 AGTCACTCTT
* *
21165731 TAACAGTCAGTTATTCAG
1 TAACAATCAATTATTCAG
** * *
21165749 TAATGATAAATTATTTAG
1 TAACAATCAATTATTCAG
21165767 TAACAATCAATTATTCAG
1 TAACAATCAATTATTCAG
21165785 TAACAATC
1 TAACAATC
21165793 TTTTTACGCA
Statistics
Matches: 34, Mismatches: 10, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
18 34 1.00
ACGTcount: A:0.42, C:0.13, G:0.10, T:0.35
Consensus pattern (18 bp):
TAACAATCAATTATTCAG
Found at i:21165982 original size:6 final size:6
Alignment explanation
Indices: 21165967--21165996 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
21165957 GGAATACGCT
*
21165967 GTAACG GTAACA GTAACA GTAACA GTAACA
1 GTAACA GTAACA GTAACA GTAACA GTAACA
21165997 ATAGTGGTAC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.47, C:0.17, G:0.20, T:0.17
Consensus pattern (6 bp):
GTAACA
Found at i:21166083 original size:51 final size:54
Alignment explanation
Indices: 21165981--21166099 Score: 154
Period size: 51 Copynumber: 2.3 Consensus size: 54
21165971 CGGTAACAGT
* *
21165981 AACAGTAACAGTAACAATAGTGGTACACAGAGTACCTCATCGGAACAAATCCGG
1 AACAGTAACAGTAACAATAGAGGTACACAGAGTACCTCATCAGAACAAATCCGG
* * * **
21166035 AATAGTAACAGTAACAGTA-AGGTACA-A-AGTACCTCTTCAGAATGAATCCGG
1 AACAGTAACAGTAACAATAGAGGTACACAGAGTACCTCATCAGAACAAATCCGG
21166086 AACAGTAACAGTAA
1 AACAGTAACAGTAA
21166100 GGCGACACTT
Statistics
Matches: 57, Mismatches: 8, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
51 33 0.58
52 1 0.02
53 6 0.11
54 17 0.30
ACGTcount: A:0.43, C:0.19, G:0.19, T:0.18
Consensus pattern (54 bp):
AACAGTAACAGTAACAATAGAGGTACACAGAGTACCTCATCAGAACAAATCCGG
Found at i:21167117 original size:27 final size:27
Alignment explanation
Indices: 21167087--21167144 Score: 89
Period size: 27 Copynumber: 2.1 Consensus size: 27
21167077 TGACTTACCT
21167087 ATTTAAACTTCAAGCTTCAAACCCTCA
1 ATTTAAACTTCAAGCTTCAAACCCTCA
***
21167114 ATTTCCCCTTCAAGCTTCAAACCCTCA
1 ATTTAAACTTCAAGCTTCAAACCCTCA
21167141 ATTT
1 ATTT
21167145 CCCTTTTCTT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.31, C:0.33, G:0.03, T:0.33
Consensus pattern (27 bp):
ATTTAAACTTCAAGCTTCAAACCCTCA
Found at i:21167145 original size:27 final size:27
Alignment explanation
Indices: 21167094--21167147 Score: 108
Period size: 27 Copynumber: 2.0 Consensus size: 27
21167084 CCTATTTAAA
21167094 CTTCAAGCTTCAAACCCTCAATTTCCC
1 CTTCAAGCTTCAAACCCTCAATTTCCC
21167121 CTTCAAGCTTCAAACCCTCAATTTCCC
1 CTTCAAGCTTCAAACCCTCAATTTCCC
21167148 TTTTCTTCTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.26, C:0.41, G:0.04, T:0.30
Consensus pattern (27 bp):
CTTCAAGCTTCAAACCCTCAATTTCCC
Found at i:21167164 original size:12 final size:12
Alignment explanation
Indices: 21167147--21167182 Score: 54
Period size: 12 Copynumber: 2.9 Consensus size: 12
21167137 CTCAATTTCC
21167147 CTTTTCTTCTTT
1 CTTTTCTTCTTT
21167159 CTTTTCTTTCTTT
1 CTTTTC-TTCTTT
*
21167172 CTTTCCTTCTT
1 CTTTTCTTCTT
21167183 CTCTGTTTCG
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
12 11 0.50
13 11 0.50
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTCTTCTTT
Found at i:21167191 original size:19 final size:19
Alignment explanation
Indices: 21167169--21167214 Score: 60
Period size: 19 Copynumber: 2.4 Consensus size: 19
21167159 CTTTTCTTTC
21167169 TTTCTTTCCTTCT-TCTCTG
1 TTTCTTTCCTTCTAT-TCTG
21167188 TTTCGTTT-CTTCTATTCTG
1 TTTC-TTTCCTTCTATTCTG
21167207 TTTCTTTC
1 TTTCTTTC
21167215 TTTTATTTTC
Statistics
Matches: 24, Mismatches: 0, Indels: 6
0.80 0.00 0.20
Matches are distributed among these distances:
18 3 0.12
19 17 0.71
20 4 0.17
ACGTcount: A:0.02, C:0.26, G:0.07, T:0.65
Consensus pattern (19 bp):
TTTCTTTCCTTCTATTCTG
Found at i:21167402 original size:18 final size:19
Alignment explanation
Indices: 21167374--21167427 Score: 67
Period size: 18 Copynumber: 2.9 Consensus size: 19
21167364 ATAATATAAT
21167374 TATTTAATTAATAAATATC
1 TATTTAATTAATAAATATC
* *
21167393 T-TTTACTTAATAATTATC
1 TATTTAATTAATAAATATC
21167411 TATTTAA-TAACTAAATA
1 TATTTAATTAA-TAAATA
21167428 CAAGTATTAC
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
18 19 0.66
19 10 0.34
ACGTcount: A:0.44, C:0.07, G:0.00, T:0.48
Consensus pattern (19 bp):
TATTTAATTAATAAATATC
Found at i:21167643 original size:20 final size:20
Alignment explanation
Indices: 21167603--21167639 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 20
21167593 TTACAAATAT
21167603 ATGTATAATATTTATTACAC
1 ATGTATAATATTTATTACAC
*
21167623 ATGTAT-ATTTTTATTAC
1 ATGTATAATATTTATTAC
21167640 CACACATTTG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
19 10 0.62
20 6 0.38
ACGTcount: A:0.35, C:0.08, G:0.05, T:0.51
Consensus pattern (20 bp):
ATGTATAATATTTATTACAC
Found at i:21168504 original size:2 final size:2
Alignment explanation
Indices: 21168497--21168524 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
21168487 TTTAAGTTTA
21168497 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
21168525 TTATTAGTAA
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:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:21178662 original size:17 final size:17
Alignment explanation
Indices: 21178640--21178673 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
21178630 CAATTCAGAG
21178640 TAAAATTTACTATTATA
1 TAAAATTTACTATTATA
*
21178657 TAAAATTTACTCTTATA
1 TAAAATTTACTATTATA
21178674 ATCCTTAATA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.44, C:0.09, G:0.00, T:0.47
Consensus pattern (17 bp):
TAAAATTTACTATTATA
Found at i:21184363 original size:16 final size:16
Alignment explanation
Indices: 21184324--21184363 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 16
21184314 TTTATATCGA
* *
21184324 AAAAATAAAATATTTT
1 AAAATTAAAAAATTTT
21184340 AAAATTAAAAAATTTT
1 AAAATTAAAAAATTTT
*
21184356 AAATTTAA
1 AAAATTAA
21184364 CTTAATTAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (16 bp):
AAAATTAAAAAATTTT
Done.