Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_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: 100348136
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.31
Warning! 3062571 characters in sequence are not A, C, G, or T
File 39 of 290
Found at i:13195383 original size:63 final size:63
Alignment explanation
Indices: 13195307--13195429 Score: 201
Period size: 63 Copynumber: 2.0 Consensus size: 63
13195297 GCCCGATGAC
* * * *
13195307 GCTTCTTACAGTGCTCATCAAACTGAATGCTCGTACCACTACTGGCACCCTCTGAAAAACGAT
1 GCTTCTTACAGTGCTCATAAAACGGAACGCTCGTACCACTACTGGCACCCTCCGAAAAACGAT
*
13195370 GCTTCTTATAGTGCTCATAAAACGGAACGCTCGTACCACTACTGGCACCCTCCGAAAAAC
1 GCTTCTTACAGTGCTCATAAAACGGAACGCTCGTACCACTACTGGCACCCTCCGAAAAAC
13195430 TACTATTGCC
Statistics
Matches: 55, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
63 55 1.00
ACGTcount: A:0.29, C:0.31, G:0.16, T:0.24
Consensus pattern (63 bp):
GCTTCTTACAGTGCTCATAAAACGGAACGCTCGTACCACTACTGGCACCCTCCGAAAAACGAT
Found at i:13196710 original size:43 final size:44
Alignment explanation
Indices: 13196643--13196768 Score: 159
Period size: 46 Copynumber: 2.9 Consensus size: 44
13196633 CCTAAATTCA
*
13196643 TTCACCGGCATT-TCGCCTGCTAGGCTCGAA-GCCCGATA-TCAT
1 TTCACCGGCATTATAGCCTGCTAGGCTCGAAGGCCCGATAGT-AT
* *
13196685 TTCACTGGCATTATAGCCTGCTAGGCTCGACAGGCCCAAATAGTAT
1 TTCACCGGCATTATAGCCTGCTAGGCTCGA-AGGCCC-GATAGTAT
* *
13196731 CTCACCGGCATTATAGCCTGCTAGGCTCAAAGGCCCGA
1 TTCACCGGCATTATAGCCTGCTAGGCTCGAAGGCCCGA
13196769 ATAATACTGT
Statistics
Matches: 72, Mismatches: 7, Indels: 8
0.83 0.08 0.09
Matches are distributed among these distances:
42 11 0.15
43 16 0.22
44 2 0.03
45 10 0.14
46 32 0.44
47 1 0.01
ACGTcount: A:0.23, C:0.31, G:0.22, T:0.24
Consensus pattern (44 bp):
TTCACCGGCATTATAGCCTGCTAGGCTCGAAGGCCCGATAGTAT
Found at i:13197642 original size:47 final size:47
Alignment explanation
Indices: 13197581--13197678 Score: 160
Period size: 47 Copynumber: 2.1 Consensus size: 47
13197571 AAAATTTTCT
* * *
13197581 TTAACTAAGCAACTTATCTGGAAATATTAAGGGCAAATTTAACAAGC
1 TTAACCAAGCAACTTATCTGAAAATATTAAGGGAAAATTTAACAAGC
*
13197628 TTAACCAAGTAACTTATCTGAAAATATTAAGGGAAAATTTAACAAGC
1 TTAACCAAGCAACTTATCTGAAAATATTAAGGGAAAATTTAACAAGC
13197675 TTAA
1 TTAA
13197679 ATTCAACTTA
Statistics
Matches: 47, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
47 47 1.00
ACGTcount: A:0.45, C:0.13, G:0.13, T:0.29
Consensus pattern (47 bp):
TTAACCAAGCAACTTATCTGAAAATATTAAGGGAAAATTTAACAAGC
Found at i:13202469 original size:17 final size:18
Alignment explanation
Indices: 13202437--13202470 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
13202427 ATTGGGCCAA
*
13202437 AATGGGCTGGGTGGGCCT
1 AATGGGCTGCGTGGGCCT
13202455 AATGGGCT-CGTGGGCC
1 AATGGGCTGCGTGGGCC
13202471 CTGCACAGAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.12, C:0.21, G:0.47, T:0.21
Consensus pattern (18 bp):
AATGGGCTGCGTGGGCCT
Found at i:13213262 original size:53 final size:53
Alignment explanation
Indices: 13213196--13213446 Score: 353
Period size: 53 Copynumber: 4.7 Consensus size: 53
13213186 CCCCAAAATA
* * * *
13213196 GGTAAAATAACCGTAATGCCCCTAT-AGG-ATAAATGACCGTTATGCCCCTGTAG
1 GGTAAAATGACCGTAATGCCCCTGTAAGGTA-AAATGACCATAATG-CCCTGTAG
13213249 GGTAAAATGACCGTAATGCCCCTGTAAGGTAAAATGACCATAATGCCCTGTAG
1 GGTAAAATGACCGTAATGCCCCTGTAAGGTAAAATGACCATAATGCCCTGTAG
13213302 GGTAAAATGACCGTAATGCCCCTGTAAGGTAAAATGACCATAATGCCCTGTAG
1 GGTAAAATGACCGTAATGCCCCTGTAAGGTAAAATGACCATAATGCCCTGTAG
* *** *
13213355 GGTAAAATGACCGTAATGCCCCTGTAGGGTAAAATGATTGTAATACCCCTGTAG
1 GGTAAAATGACCGTAATGCCCCTGTAAGGTAAAATGACCATAAT-GCCCTGTAG
* * *
13213409 GGTAAAATGACCGTAATTCCACTGTATGGTAAAATGAC
1 GGTAAAATGACCGTAATGCCCCTGTAAGGTAAAATGAC
13213447 GATTACGCCA
Statistics
Matches: 182, Mismatches: 13, Indels: 5
0.91 0.06 0.03
Matches are distributed among these distances:
53 124 0.68
54 57 0.31
55 1 0.01
ACGTcount: A:0.33, C:0.20, G:0.22, T:0.24
Consensus pattern (53 bp):
GGTAAAATGACCGTAATGCCCCTGTAAGGTAAAATGACCATAATGCCCTGTAG
Found at i:13213267 original size:27 final size:27
Alignment explanation
Indices: 13213196--13213446 Score: 355
Period size: 27 Copynumber: 9.4 Consensus size: 27
13213186 CCCCAAAATA
* *
13213196 GGTAAAATAACCGTAATGCCCCTATAG
1 GGTAAAATGACCGTAATGCCCCTGTAG
* *
13213223 GAT-AAATGACCGTTATGCCCCTGTAG
1 GGTAAAATGACCGTAATGCCCCTGTAG
*
13213249 GGTAAAATGACCGTAATGCCCCTGTAA
1 GGTAAAATGACCGTAATGCCCCTGTAG
*
13213276 GGTAAAATGACCATAATG-CCCTGTAG
1 GGTAAAATGACCGTAATGCCCCTGTAG
*
13213302 GGTAAAATGACCGTAATGCCCCTGTAA
1 GGTAAAATGACCGTAATGCCCCTGTAG
*
13213329 GGTAAAATGACCATAATG-CCCTGTAG
1 GGTAAAATGACCGTAATGCCCCTGTAG
13213355 GGTAAAATGACCGTAATGCCCCTGTAG
1 GGTAAAATGACCGTAATGCCCCTGTAG
** *
13213382 GGTAAAATGATTGTAATACCCCTGTAG
1 GGTAAAATGACCGTAATGCCCCTGTAG
* * *
13213409 GGTAAAATGACCGTAATTCCACTGTAT
1 GGTAAAATGACCGTAATGCCCCTGTAG
13213436 GGTAAAATGAC
1 GGTAAAATGAC
13213447 GATTACGCCA
Statistics
Matches: 199, Mismatches: 22, Indels: 6
0.88 0.10 0.03
Matches are distributed among these distances:
26 70 0.35
27 129 0.65
ACGTcount: A:0.33, C:0.20, G:0.22, T:0.24
Consensus pattern (27 bp):
GGTAAAATGACCGTAATGCCCCTGTAG
Found at i:13213333 original size:80 final size:81
Alignment explanation
Indices: 13213195--13213446 Score: 357
Period size: 80 Copynumber: 3.1 Consensus size: 81
13213185 ACCCCAAAAT
* * * *
13213195 AGGTAAAATAACCGTAATGCCCCTATAGGAT-AAATGACCGTTATGCCCCTGTAGGGTAAAATGA
1 AGGTAAAATGACCGTAATGCCCCTGTAGGGTAAAATGACCGTAATGCCCCTGTAGGGTAAAATGA
13213259 CCGTAATGCCCCTGTA
66 CCGTAATGCCCCTGTA
* *
13213275 AGGTAAAATGACCATAATG-CCCTGTAGGGTAAAATGACCGTAATGCCCCTGTAAGGTAAAATGA
1 AGGTAAAATGACCGTAATGCCCCTGTAGGGTAAAATGACCGTAATGCCCCTGTAGGGTAAAATGA
*
13213339 CCATAATG-CCCTGTA
66 CCGTAATGCCCCTGTA
* ** *
13213354 GGGTAAAATGACCGTAATGCCCCTGTAGGGTAAAATGATTGTAATACCCCTGTAGGGTAAAATGA
1 AGGTAAAATGACCGTAATGCCCCTGTAGGGTAAAATGACCGTAATGCCCCTGTAGGGTAAAATGA
* *
13213419 CCGTAATTCCACTGTA
66 CCGTAATGCCCCTGTA
*
13213435 TGGTAAAATGAC
1 AGGTAAAATGAC
13213447 GATTACGCCA
Statistics
Matches: 152, Mismatches: 17, Indels: 5
0.87 0.10 0.03
Matches are distributed among these distances:
79 33 0.22
80 102 0.67
81 17 0.11
ACGTcount: A:0.34, C:0.20, G:0.22, T:0.24
Consensus pattern (81 bp):
AGGTAAAATGACCGTAATGCCCCTGTAGGGTAAAATGACCGTAATGCCCCTGTAGGGTAAAATGA
CCGTAATGCCCCTGTA
Found at i:13213824 original size:28 final size:28
Alignment explanation
Indices: 13213770--13213824 Score: 65
Period size: 28 Copynumber: 2.0 Consensus size: 28
13213760 ATTACACTGT
** * *
13213770 ACTAATACTGTATTGGGCTTAGGCCCAC
1 ACTAATACTGTATAAGGCTAAGCCCCAC
*
13213798 ACTATTACTGTATAAGGCTAAGCCCCA
1 ACTAATACTGTATAAGGCTAAGCCCCA
13213825 GACTGTACTG
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
28 22 1.00
ACGTcount: A:0.29, C:0.25, G:0.18, T:0.27
Consensus pattern (28 bp):
ACTAATACTGTATAAGGCTAAGCCCCAC
Found at i:13213858 original size:33 final size:34
Alignment explanation
Indices: 13213803--13213868 Score: 89
Period size: 33 Copynumber: 2.0 Consensus size: 34
13213793 CCCACACTAT
*
13213803 TACTGTATAAGGCTAAGCCCCAGACTG-TACTGA
1 TACTGAATAAGGCTAAGCCCCAGACTGTTACTGA
* * *
13213836 TACTGAATAGGGCTCAGGCCCAGACTGTTACTG
1 TACTGAATAAGGCTAAGCCCCAGACTGTTACTG
13213869 CATGCACTAT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
33 23 0.82
34 5 0.18
ACGTcount: A:0.27, C:0.24, G:0.24, T:0.24
Consensus pattern (34 bp):
TACTGAATAAGGCTAAGCCCCAGACTGTTACTGA
Found at i:13217674 original size:40 final size:40
Alignment explanation
Indices: 13217630--13217821 Score: 194
Period size: 40 Copynumber: 4.8 Consensus size: 40
13217620 GGATATAGCT
* * *
13217630 ACTCGTTCAAATGTCTTCGGGACATAGCCCGG-TTATAGTA
1 ACTCGTACAAATGCCTTCGGGACTTAGCCCGGATT-TAGTA
* * *
13217670 ACTCGCACAATTGCCTTCGGGACTTAACCCGGATTTAGTA
1 ACTCGTACAAATGCCTTCGGGACTTAGCCCGGATTTAGTA
*
13217710 ACTCGTACAAATGCCTTCGGG-CTTAGCCCGGAATTAGTA
1 ACTCGTACAAATGCCTTCGGGACTTAGCCCGGATTTAGTA
* * * * * *
13217749 TCTCGCACAAATGCCTTC-GGATCTTAGTCCGGATATGGTC
1 ACTCGTACAAATGCCTTCGGGA-CTTAGCCCGGATTTAGTA
* *
13217789 ACTTAGCACAAA-GCCTTCGGGACTTAGCCCGGA
1 AC-TCGTACAAATGCCTTCGGGACTTAGCCCGGA
13217822 CATCATTCAA
Statistics
Matches: 127, Mismatches: 20, Indels: 10
0.81 0.13 0.06
Matches are distributed among these distances:
38 2 0.02
39 32 0.25
40 80 0.63
41 13 0.10
ACGTcount: A:0.24, C:0.27, G:0.22, T:0.27
Consensus pattern (40 bp):
ACTCGTACAAATGCCTTCGGGACTTAGCCCGGATTTAGTA
Found at i:13217748 original size:79 final size:79
Alignment explanation
Indices: 13217604--13217821 Score: 221
Period size: 79 Copynumber: 2.7 Consensus size: 79
13217594 AAATCACGTA
* * * * * *
13217604 CCTTCGGAATTTAACCGGATATAGCTACTCGTTCAAATGTCTTCGGGACATAGCCCGG-TTATAG
1 CCTTCGGGACTTAACCGGATATAG-TACTCGTACAAATGCCTTCGGGACTTAGCCCGGAATATAG
*
13217668 TAACTCGCACAATTG
65 TAACTCGCACAAATG
*
13217683 CCTTCGGGACTTAACCCGGATTTAGTAACTCGTACAAATGCCTTCGGG-CTTAGCCCGGAAT-TA
1 CCTTCGGGACTTAA-CCGGATATAGT-ACTCGTACAAATGCCTTCGGGACTTAGCCCGGAATATA
*
13217746 GTATCTCGCACAAATG
64 GTAACTCGCACAAATG
* * * *
13217762 CCTTC-GGATCTTAGTCCGGATATGGTCACTTAGCACAAA-GCCTTCGGGACTTAGCCCGGA
1 CCTTCGGGA-CTTA-ACCGGATATAGT-AC-TCGTACAAATGCCTTCGGGACTTAGCCCGGA
13217822 CATCATTCAA
Statistics
Matches: 117, Mismatches: 15, Indels: 13
0.81 0.10 0.09
Matches are distributed among these distances:
78 3 0.03
79 67 0.57
80 47 0.40
ACGTcount: A:0.25, C:0.26, G:0.22, T:0.27
Consensus pattern (79 bp):
CCTTCGGGACTTAACCGGATATAGTACTCGTACAAATGCCTTCGGGACTTAGCCCGGAATATAGT
AACTCGCACAAATG
Found at i:13224634 original size:58 final size:58
Alignment explanation
Indices: 13224544--13224659 Score: 205
Period size: 58 Copynumber: 2.0 Consensus size: 58
13224534 TAGACAAAGT
*
13224544 CTCCCATGTTACAGGGATCGACTACACTGACCTTTGCTCATTACGACTTGGATATCTC
1 CTCCCATGTTACAGGGATCGACTACACTGACCTTTGCCCATTACGACTTGGATATCTC
* *
13224602 CTCCCATGTTACAGGGGTCGACTACACTGACCTTTTCCCATTACGACTTGGATATCTC
1 CTCCCATGTTACAGGGATCGACTACACTGACCTTTGCCCATTACGACTTGGATATCTC
13224660 TCCTCACAGA
Statistics
Matches: 55, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
58 55 1.00
ACGTcount: A:0.22, C:0.30, G:0.17, T:0.31
Consensus pattern (58 bp):
CTCCCATGTTACAGGGATCGACTACACTGACCTTTGCCCATTACGACTTGGATATCTC
Found at i:13225788 original size:39 final size:40
Alignment explanation
Indices: 13225745--13225844 Score: 148
Period size: 39 Copynumber: 2.5 Consensus size: 40
13225735 TCCTCGTTCA
* **
13225745 AATGCCTTCGGGACATAGCCCGGATTTAGTAACTCACAC-
1 AATGCCTTCGGGACATAACCCGGATTTAACAACTCACACG
*
13225784 AATGCCTTCGGGACATAACCCGGATTTAACAACTCGCACG
1 AATGCCTTCGGGACATAACCCGGATTTAACAACTCACACG
*
13225824 AATGCCTTCGGGACTTAACCC
1 AATGCCTTCGGGACATAACCC
13225845 AATGCCGTCG
Statistics
Matches: 55, Mismatches: 5, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
39 35 0.64
40 20 0.36
ACGTcount: A:0.28, C:0.30, G:0.20, T:0.22
Consensus pattern (40 bp):
AATGCCTTCGGGACATAACCCGGATTTAACAACTCACACG
Found at i:13225879 original size:61 final size:60
Alignment explanation
Indices: 13225783--13225905 Score: 183
Period size: 61 Copynumber: 2.0 Consensus size: 60
13225773 GTAACTCACA
* *
13225783 CAATGCCTTCGGGACATAACCCGGATTTAACAACTCGCACGAATGCCTTCGGGACTTAACC
1 CAATGCCGTCGGGACATAACCCGGATTTAACAACTCACAC-AATGCCTTCGGGACTTAACC
* * **
13225844 CAATGCCGTCGGGACATAGCCCGGTTTTAGTAACTCACACAATGCCTTCGGGACTTAACC
1 CAATGCCGTCGGGACATAACCCGGATTTAACAACTCACACAATGCCTTCGGGACTTAACC
13225904 CA
1 CA
13225906 GATTTAATAA
Statistics
Matches: 56, Mismatches: 6, Indels: 1
0.89 0.10 0.02
Matches are distributed among these distances:
60 22 0.39
61 34 0.61
ACGTcount: A:0.27, C:0.31, G:0.20, T:0.22
Consensus pattern (60 bp):
CAATGCCGTCGGGACATAACCCGGATTTAACAACTCACACAATGCCTTCGGGACTTAACC
Found at i:13225918 original size:100 final size:100
Alignment explanation
Indices: 13225745--13225944 Score: 355
Period size: 100 Copynumber: 2.0 Consensus size: 100
13225735 TCCTCGTTCA
* *
13225745 AATGCCTTCGGGACATAGCCCGGATTTAGTAACTCACACAATGCCTTCGGGACATAACCCGGATT
1 AATGCCGTCGGGACATAGCCCGGATTTAGTAACTCACACAATGCCTTCGGGACATAACCCAGATT
13225810 TAACAACTCGCACGAATGCCTTCGGGACTTAACCC
66 TAACAACTCGCACGAATGCCTTCGGGACTTAACCC
* *
13225845 AATGCCGTCGGGACATAGCCCGGTTTTAGTAACTCACACAATGCCTTCGGGACTTAACCCAGATT
1 AATGCCGTCGGGACATAGCCCGGATTTAGTAACTCACACAATGCCTTCGGGACATAACCCAGATT
*
13225910 TAATAACTCGCACGAATGCCTTCGGGACTTAACCC
66 TAACAACTCGCACGAATGCCTTCGGGACTTAACCC
13225945 GGATTTAGTA
Statistics
Matches: 95, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
100 95 1.00
ACGTcount: A:0.28, C:0.29, G:0.20, T:0.23
Consensus pattern (100 bp):
AATGCCGTCGGGACATAGCCCGGATTTAGTAACTCACACAATGCCTTCGGGACATAACCCAGATT
TAACAACTCGCACGAATGCCTTCGGGACTTAACCC
Found at i:13225936 original size:40 final size:39
Alignment explanation
Indices: 13225844--13226027 Score: 181
Period size: 40 Copynumber: 4.6 Consensus size: 39
13225834 GGACTTAACC
* * * * *
13225844 CAATGCCGTCGGGACATAGCCCGGTTTTAGTAACTCACA
1 CAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
* *
13225883 CAATGCCTTCGGGACTTAACCCAGATTTAATAACTCGCA
1 CAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
*
13225922 CGAATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCA
1 C-AATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
* * * * * *
13225962 CAAAGGCCTTC-GGATCTTAATCCGGATGTATTCACTTAGCA
1 C-AATGCCTTCGGGA-CTTAACCCGGATTTAGTAAC-TCGCA
* *
13226003 CAAAGCCTTCGGGACTTAGCCCGGA
1 CAATGCCTTCGGGACTTAACCCGGA
13226028 CAGCATTCAA
Statistics
Matches: 120, Mismatches: 21, Indels: 7
0.81 0.14 0.05
Matches are distributed among these distances:
39 36 0.30
40 76 0.63
41 8 0.07
ACGTcount: A:0.26, C:0.28, G:0.21, T:0.25
Consensus pattern (39 bp):
CAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
Found at i:13229022 original size:11 final size:12
Alignment explanation
Indices: 13228993--13229035 Score: 52
Period size: 12 Copynumber: 3.6 Consensus size: 12
13228983 AAAACAGTGG
13228993 AGAAAAAGAGAA
1 AGAAAAAGAGAA
*
13229005 AGAAAAAGGGAA
1 AGAAAAAGAGAA
*
13229017 AG-AAAAGAAAA
1 AGAAAAAGAGAA
13229028 AGGAAAAA
1 A-GAAAAA
13229036 CTAGATATTT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
11 8 0.31
12 14 0.54
13 4 0.15
ACGTcount: A:0.74, C:0.00, G:0.26, T:0.00
Consensus pattern (12 bp):
AGAAAAAGAGAA
Found at i:13229025 original size:17 final size:18
Alignment explanation
Indices: 13228997--13229030 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
13228987 CAGTGGAGAA
13228997 AAAGAGAAAGAAAAAGGG
1 AAAGAGAAAGAAAAAGGG
13229015 AAAGA-AAAGAAAAAGG
1 AAAGAGAAAGAAAAAGG
13229031 AAAAACTAGA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 11 0.69
18 5 0.31
ACGTcount: A:0.71, C:0.00, G:0.29, T:0.00
Consensus pattern (18 bp):
AAAGAGAAAGAAAAAGGG
Found at i:13230083 original size:6 final size:6
Alignment explanation
Indices: 13230072--13230115 Score: 61
Period size: 6 Copynumber: 7.2 Consensus size: 6
13230062 GTGTGTTCAA
* *
13230072 TACTGT TACTGT TACTGT TACTGC TACCGT TACTGAT TACTGT T
1 TACTGT TACTGT TACTGT TACTGT TACTGT TACTG-T TACTGT T
13230116 TAGGTACTGT
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
6 27 0.82
7 6 0.18
ACGTcount: A:0.18, C:0.20, G:0.16, T:0.45
Consensus pattern (6 bp):
TACTGT
Found at i:13232269 original size:39 final size:39
Alignment explanation
Indices: 13232199--13232382 Score: 237
Period size: 39 Copynumber: 4.7 Consensus size: 39
13232189 ACAAAGCATG
* * * *
13232199 CGGGACTTTAAGCCCGGATATAATACCAGCAC-AAAGCCTG
1 CGGGAC-TT-AGCCCGGATATAACACCAACACGAATGCCTT
* *
13232239 CGGGACTTTAGCCCGGATATAACACTAGCACGAATGCCTT
1 CGGGAC-TTAGCCCGGATATAACACCAACACGAATGCCTT
* *
13232279 CGGGGCTTAGCCCGGATATAACGCCAACACGAATGCCTT
1 CGGGACTTAGCCCGGATATAACACCAACACGAATGCCTT
*
13232318 CAGGACTTAGCCCGGATATAACACCAACACGAATGCCTT
1 CGGGACTTAGCCCGGATATAACACCAACACGAATGCCTT
13232357 CGGGACTTAGCCC-GATTATAACACCA
1 CGGGACTTAGCCCGGA-TATAACACCA
13232383 TTATAAAGTC
Statistics
Matches: 130, Mismatches: 12, Indels: 5
0.88 0.08 0.03
Matches are distributed among these distances:
38 2 0.02
39 108 0.83
40 20 0.15
ACGTcount: A:0.30, C:0.29, G:0.22, T:0.19
Consensus pattern (39 bp):
CGGGACTTAGCCCGGATATAACACCAACACGAATGCCTT
Found at i:13232496 original size:28 final size:28
Alignment explanation
Indices: 13232455--13232519 Score: 96
Period size: 28 Copynumber: 2.3 Consensus size: 28
13232445 ATTTAATCAT
13232455 TCAATATTCTGCACACTAAGTGACATTC
1 TCAATATTCTGCACACTAAGTGACATTC
* *
13232483 TCAATA-TCTCGCACATTAAGTGCCATTC
1 TCAATATTCT-GCACACTAAGTGACATTC
13232511 TCAATATTC
1 TCAATATTC
13232520 CGTACACTGA
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
27 3 0.09
28 28 0.85
29 2 0.06
ACGTcount: A:0.31, C:0.26, G:0.09, T:0.34
Consensus pattern (28 bp):
TCAATATTCTGCACACTAAGTGACATTC
Found at i:13232536 original size:28 final size:28
Alignment explanation
Indices: 13232455--13232536 Score: 87
Period size: 28 Copynumber: 2.9 Consensus size: 28
13232445 ATTTAATCAT
*
13232455 TCAATATTCTGCACACTAAGTGA-CATTC
1 TCAATATTCCGCACACTAAGT-ACCATTC
* *
13232483 TCAATA-TCTCGCACATTAAGTGCCATTC
1 TCAATATTC-CGCACACTAAGTACCATTC
* *
13232511 TCAATATTCCGTACACTGAGTACCAT
1 TCAATATTCCGCACACTAAGTACCAT
13232537 ATTTGATCGC
Statistics
Matches: 44, Mismatches: 7, Indels: 6
0.77 0.12 0.11
Matches are distributed among these distances:
27 2 0.05
28 40 0.91
29 2 0.05
ACGTcount: A:0.30, C:0.27, G:0.11, T:0.32
Consensus pattern (28 bp):
TCAATATTCCGCACACTAAGTACCATTC
Found at i:13238188 original size:22 final size:23
Alignment explanation
Indices: 13238155--13238198 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 23
13238145 AATATTTAAG
*
13238155 TATTAATATATAATATATTATAT
1 TATTAATATATAATATAATATAT
13238178 TATT-ATATATAATATAATATA
1 TATTAATATATAATATAATATA
13238199 ATATATAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
22 16 0.80
23 4 0.20
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (23 bp):
TATTAATATATAATATAATATAT
Found at i:13238192 original size:20 final size:20
Alignment explanation
Indices: 13238144--13238206 Score: 67
Period size: 20 Copynumber: 3.1 Consensus size: 20
13238134 TATATTAACT
*
13238144 TAATATTTAAGTATTAATATA
1 TAATATATAA-TATTAATATA
* *
13238165 TAATATATTATATTATTATA
1 TAATATATAATATTAATATA
13238185 T-ATAATATAATA-TAATATA
1 TAAT-ATATAATATTAATATA
13238204 TAA
1 TAA
13238207 AACATAAGTA
Statistics
Matches: 35, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
19 9 0.26
20 18 0.51
21 8 0.23
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.48
Consensus pattern (20 bp):
TAATATATAATATTAATATA
Found at i:13238193 original size:17 final size:17
Alignment explanation
Indices: 13238162--13238206 Score: 58
Period size: 17 Copynumber: 2.8 Consensus size: 17
13238152 AAGTATTAAT
13238162 ATATAATATAT--TATA
1 ATATAATATATAATATA
* *
13238177 TTATTATATATAATATA
1 ATATAATATATAATATA
13238194 ATATAATATATAA
1 ATATAATATATAA
13238207 AACATAAGTA
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
15 9 0.38
17 15 0.62
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (17 bp):
ATATAATATATAATATA
Found at i:13239372 original size:29 final size:30
Alignment explanation
Indices: 13239340--13239396 Score: 98
Period size: 29 Copynumber: 1.9 Consensus size: 30
13239330 GCGCTCTCTG
13239340 ATTATTAGCACATT-AGTGCTCTCTGTTCT
1 ATTATTAGCACATTAAGTGCTCTCTGTTCT
*
13239369 ATTATTAGCACGTTAAGTGCTCTCTGTT
1 ATTATTAGCACATTAAGTGCTCTCTGTT
13239397 TAGCACATCT
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
29 13 0.50
30 13 0.50
ACGTcount: A:0.21, C:0.19, G:0.16, T:0.44
Consensus pattern (30 bp):
ATTATTAGCACATTAAGTGCTCTCTGTTCT
Found at i:13239413 original size:22 final size:22
Alignment explanation
Indices: 13239384--13239440 Score: 80
Period size: 22 Copynumber: 2.6 Consensus size: 22
13239374 TAGCACGTTA
13239384 AGTGCTCTCTGTTTAGCACATCT
1 AGTGCTCTCTGTTTAGCAC-TCT
* *
13239407 -GTGCTCTCTGTATAGCACTTT
1 AGTGCTCTCTGTTTAGCACTCT
13239428 AGTGCTCTCTGTT
1 AGTGCTCTCTGTT
13239441 CATTTGTGCA
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
21 2 0.07
22 28 0.93
ACGTcount: A:0.14, C:0.25, G:0.19, T:0.42
Consensus pattern (22 bp):
AGTGCTCTCTGTTTAGCACTCT
Found at i:13241453 original size:16 final size:16
Alignment explanation
Indices: 13241399--13241461 Score: 72
Period size: 16 Copynumber: 3.9 Consensus size: 16
13241389 CACTGTAACA
* *
13241399 GAATAGGGCTATAATT
1 GAATAGAGCTGTAATT
* * *
13241415 GAATAGGGTTGTAAAT
1 GAATAGAGCTGTAATT
13241431 GAATAGAGCTGTAATT
1 GAATAGAGCTGTAATT
*
13241447 GAATAGAACTGTAAT
1 GAATAGAGCTGTAAT
13241462 CAGTAATTCA
Statistics
Matches: 40, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
16 40 1.00
ACGTcount: A:0.40, C:0.05, G:0.25, T:0.30
Consensus pattern (16 bp):
GAATAGAGCTGTAATT
Found at i:13241460 original size:32 final size:32
Alignment explanation
Indices: 13241390--13241460 Score: 81
Period size: 32 Copynumber: 2.2 Consensus size: 32
13241380 CGTTTGATTC
* *
13241390 ACTGTAACAGAATAGGGCTATAATTGAATAGG
1 ACTGTAACAGAATAGAGCTATAATTGAATAGA
** *
13241422 GTTGTAA-ATGAATAGAGCTGTAATTGAATAGA
1 ACTGTAACA-GAATAGAGCTATAATTGAATAGA
13241454 ACTGTAA
1 ACTGTAA
13241461 TCAGTAATTC
Statistics
Matches: 31, Mismatches: 7, Indels: 2
0.77 0.17 0.05
Matches are distributed among these distances:
31 1 0.03
32 30 0.97
ACGTcount: A:0.41, C:0.07, G:0.24, T:0.28
Consensus pattern (32 bp):
ACTGTAACAGAATAGAGCTATAATTGAATAGA
Found at i:13241531 original size:43 final size:45
Alignment explanation
Indices: 13241447--13241535 Score: 128
Period size: 43 Copynumber: 2.0 Consensus size: 45
13241437 AGCTGTAATT
13241447 GAATAGAACTGTAATCAGTAATTCAACTGTTTGGTTGAATGGAATG
1 GAATAGAACTGTAATCAG-AATTCAACTGTTTGGTTGAATGGAATG
***
13241493 GAATAGAACTGTAAT-AG-ATTCTTGTGTTTGGTTGAATGGAATG
1 GAATAGAACTGTAATCAGAATTCAACTGTTTGGTTGAATGGAATG
13241536 ATGTTGTAAT
Statistics
Matches: 40, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
43 23 0.57
45 2 0.05
46 15 0.38
ACGTcount: A:0.33, C:0.07, G:0.26, T:0.35
Consensus pattern (45 bp):
GAATAGAACTGTAATCAGAATTCAACTGTTTGGTTGAATGGAATG
Found at i:13245214 original size:72 final size:73
Alignment explanation
Indices: 13245124--13245279 Score: 233
Period size: 72 Copynumber: 2.2 Consensus size: 73
13245114 GGATAAAAGC
* *
13245124 ATGAAAAAGAGGGAGAAGGTTTGAAGAAAATGGGAAGAAGAATG-AAAAAAAGAAGATGCTTCAG
1 ATGAAAAAGAGAGAGAAGGTTGGAAGAAAATGGGAAGAAGAATGAAAAAAAAGAAGATGCTTCAG
*
13245188 ACGTGAAA
66 ACATGAAA
* * **
13245196 ATGAAAAAGAGAGTGAAGGTTGGAAGGACTTGGGAAGAAGAATGAAAAAAAAGAAGATGCTTCAG
1 ATGAAAAAGAGAGAGAAGGTTGGAAGAAAATGGGAAGAAGAATGAAAAAAAAGAAGATGCTTCAG
*
13245261 ACATGAGA
66 ACATGAAA
13245269 ATGAAAAAGAG
1 ATGAAAAAGAG
13245280 GGACAAGGGT
Statistics
Matches: 75, Mismatches: 8, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
72 38 0.51
73 37 0.49
ACGTcount: A:0.51, C:0.04, G:0.31, T:0.14
Consensus pattern (73 bp):
ATGAAAAAGAGAGAGAAGGTTGGAAGAAAATGGGAAGAAGAATGAAAAAAAAGAAGATGCTTCAG
ACATGAAA
Found at i:13248719 original size:55 final size:55
Alignment explanation
Indices: 13248650--13248772 Score: 160
Period size: 55 Copynumber: 2.2 Consensus size: 55
13248640 AGGTAGTATT
* * * *
13248650 CACACGGCCATGTAACACGCTCGTGTCCA-AGGCCGTGTCAACCACACGACTAAGA
1 CACACGACCATGTAACACACCCGTGTCCACA-GCCGTGTCAACCACACAACTAAGA
*
13248705 CACACGACCGTGTAACACACCCGTGTCCACAGCCGTGTCAACCACACAACTAAGA
1 CACACGACCATGTAACACACCCGTGTCCACAGCCGTGTCAACCACACAACTAAGA
*
13248760 AACAC-ACCCATGT
1 CACACGA-CCATGT
13248773 CTCTGCCCGT
Statistics
Matches: 59, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
54 1 0.02
55 57 0.97
56 1 0.02
ACGTcount: A:0.32, C:0.37, G:0.18, T:0.14
Consensus pattern (55 bp):
CACACGACCATGTAACACACCCGTGTCCACAGCCGTGTCAACCACACAACTAAGA
Found at i:13249886 original size:18 final size:18
Alignment explanation
Indices: 13249863--13249898 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
13249853 ATATATCATC
13249863 TCACACAAATCAACTCAA
1 TCACACAAATCAACTCAA
* *
13249881 TCACACAATTCAATTCAA
1 TCACACAAATCAACTCAA
13249899 GCATAATAAC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.47, C:0.31, G:0.00, T:0.22
Consensus pattern (18 bp):
TCACACAAATCAACTCAA
Found at i:13250995 original size:14 final size:14
Alignment explanation
Indices: 13250976--13251002 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
13250966 CAAAATCGAT
13250976 AAAATTTTCATATC
1 AAAATTTTCATATC
13250990 AAAATTTTCATAT
1 AAAATTTTCATAT
13251003 GACCTTCCTA
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:0.44, C:0.11, G:0.00, T:0.44
Consensus pattern (14 bp):
AAAATTTTCATATC
Found at i:13254705 original size:29 final size:30
Alignment explanation
Indices: 13254650--13254729 Score: 83
Period size: 29 Copynumber: 2.7 Consensus size: 30
13254640 AATCTCAACA
* ***
13254650 TATACTGGGCTGAAGCCTTTTGTTAAA-CAG
1 TATACTGGGCCGAAGCCTTTCCATAAATC-G
13254680 T-TACTGGGCCGAAGCCTTTCCATAAATCG
1 TATACTGGGCCGAAGCCTTTCCATAAATCG
*
13254709 TATCACTGGGTCGAAGCCTTT
1 TAT-ACTGGGCCGAAGCCTTT
13254730 ACTGTAAACG
Statistics
Matches: 42, Mismatches: 5, Indels: 5
0.81 0.10 0.10
Matches are distributed among these distances:
29 23 0.55
30 3 0.07
31 16 0.38
ACGTcount: A:0.24, C:0.23, G:0.23, T:0.31
Consensus pattern (30 bp):
TATACTGGGCCGAAGCCTTTCCATAAATCG
Found at i:13254970 original size:24 final size:23
Alignment explanation
Indices: 13254943--13254992 Score: 66
Period size: 23 Copynumber: 2.1 Consensus size: 23
13254933 GCCTAGCCTC
13254943 TTTTAAT-AACTGGGGCAAAGCCCT
1 TTTTAATAAACT--GGCAAAGCCCT
*
13254967 TTTTGATAAACTGGCAAAGCCCT
1 TTTTAATAAACTGGCAAAGCCCT
13254990 TTT
1 TTT
13254993 GCACTTCCTC
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
23 14 0.58
24 6 0.25
25 4 0.17
ACGTcount: A:0.28, C:0.20, G:0.18, T:0.34
Consensus pattern (23 bp):
TTTTAATAAACTGGCAAAGCCCT
Found at i:13255062 original size:21 final size:21
Alignment explanation
Indices: 13255038--13255098 Score: 68
Period size: 21 Copynumber: 2.9 Consensus size: 21
13255028 TATAATGAGT
*
13255038 ATATCATGGCATATCATGTGA
1 ATATCATGACATATCATGTGA
** * *
13255059 ATATCAAAACGTATCATGTGC
1 ATATCATGACATATCATGTGA
*
13255080 ATATCATGTCATATCATGT
1 ATATCATGACATATCATGT
13255099 ATAATAACAA
Statistics
Matches: 31, Mismatches: 9, Indels: 0
0.77 0.22 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.34, C:0.16, G:0.15, T:0.34
Consensus pattern (21 bp):
ATATCATGACATATCATGTGA
Found at i:13255098 original size:10 final size:10
Alignment explanation
Indices: 13255038--13255098 Score: 50
Period size: 10 Copynumber: 5.9 Consensus size: 10
13255028 TATAATGAGT
*
13255038 ATATCATGGC
1 ATATCATGTC
*
13255048 ATATCATGTGA
1 ATATCATGT-C
***
13255059 ATATCAAAAC
1 ATATCATGTC
*
13255069 GTATCATGTGC
1 ATATCATGT-C
13255080 ATATCATGTC
1 ATATCATGTC
13255090 ATATCATGT
1 ATATCATGT
13255099 ATAATAACAA
Statistics
Matches: 38, Mismatches: 11, Indels: 4
0.72 0.21 0.08
Matches are distributed among these distances:
10 23 0.61
11 15 0.39
ACGTcount: A:0.34, C:0.16, G:0.15, T:0.34
Consensus pattern (10 bp):
ATATCATGTC
Found at i:13255166 original size:25 final size:25
Alignment explanation
Indices: 13255138--13255185 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
13255128 ATAATTAAAC
* * *
13255138 CCTAGGGGTATAATGGTCATTTTTA
1 CCTAGGGGCAAAATAGTCATTTTTA
13255163 CCTAGGGGCAAAATAGTCATTTT
1 CCTAGGGGCAAAATAGTCATTTT
13255186 CATATTATAA
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:0.27, C:0.15, G:0.23, T:0.35
Consensus pattern (25 bp):
CCTAGGGGCAAAATAGTCATTTTTA
Found at i:13274125 original size:18 final size:18
Alignment explanation
Indices: 13274104--13274213 Score: 105
Period size: 18 Copynumber: 6.1 Consensus size: 18
13274094 AGTCACTCTT
13274104 TAACAGTCAGTTATTCAG
1 TAACAGTCAGTTATTCAG
* * *
13274122 TAACTA-TAAATTATTCAA
1 TAAC-AGTCAGTTATTCAG
* *
13274140 TAACAGTCAATTTTTCAG
1 TAACAGTCAGTTATTCAG
** *
13274158 TAGTAGTCAGTTATCCAG
1 TAACAGTCAGTTATTCAG
* *
13274176 TAACAATTAGTTATTCAG
1 TAACAGTCAGTTATTCAG
*
13274194 TAGCAGTCAGTTATTCAG
1 TAACAGTCAGTTATTCAG
13274212 TA
1 TA
13274214 CCTTTATTTA
Statistics
Matches: 71, Mismatches: 19, Indels: 4
0.76 0.20 0.04
Matches are distributed among these distances:
17 1 0.01
18 69 0.97
19 1 0.01
ACGTcount: A:0.35, C:0.15, G:0.14, T:0.36
Consensus pattern (18 bp):
TAACAGTCAGTTATTCAG
Found at i:13274166 original size:54 final size:54
Alignment explanation
Indices: 13274108--13274213 Score: 140
Period size: 54 Copynumber: 2.0 Consensus size: 54
13274098 ACTCTTTAAC
* * *
13274108 AGTCAGTTATTCAGTAACTATAAATTATTCAATAACAGTCAATTTTTCAGTAGT
1 AGTCAGTTATCCAGTAACAATAAATTATTCAATAACAGTCAATTATTCAGTAGT
* * * * *
13274162 AGTCAGTTATCCAGTAACAATTAGTTATTCAGTAGCAGTCAGTTATTCAGTA
1 AGTCAGTTATCCAGTAACAATAAATTATTCAATAACAGTCAATTATTCAGTA
13274214 CCTTTATTTA
Statistics
Matches: 44, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
54 44 1.00
ACGTcount: A:0.35, C:0.14, G:0.14, T:0.37
Consensus pattern (54 bp):
AGTCAGTTATCCAGTAACAATAAATTATTCAATAACAGTCAATTATTCAGTAGT
Found at i:13276107 original size:47 final size:47
Alignment explanation
Indices: 13276048--13276166 Score: 193
Period size: 47 Copynumber: 2.5 Consensus size: 47
13276038 TTGGCACTAG
*
13276048 GACAAGGATACCATGTAAGACCATGTTTGGAACGTGGCATTTGGTAA
1 GACAAGGATACCATGTAAGACCATGTTTGGAACATGGCATTTGGTAA
13276095 GACAAGGATACCATGTAAGACCATGTTTGGAACATGGCATTTGGTAA
1 GACAAGGATACCATGTAAGACCATGTTTGGAACATGGCATTTGGTAA
* * * *
13276142 GATAAGGACATCATGTAAAACCATG
1 GACAAGGATACCATGTAAGACCATG
13276167 CCAAGGCATG
Statistics
Matches: 67, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
47 67 1.00
ACGTcount: A:0.35, C:0.15, G:0.25, T:0.24
Consensus pattern (47 bp):
GACAAGGATACCATGTAAGACCATGTTTGGAACATGGCATTTGGTAA
Found at i:13276272 original size:55 final size:54
Alignment explanation
Indices: 13276154--13276341 Score: 186
Period size: 55 Copynumber: 3.5 Consensus size: 54
13276144 TAAGGACATC
* * * ***
13276154 ATGTAAAACCATGCCAAGGCATGGCATTGATAAGTTCTATAAGG-AAAGGAAAT
1 ATGTAAGACCATGCCAAGACATGGCATTGATGAGTTCTATAAGGCAAAGGTCCT
** *
13276207 CATGTAAGACCATGTAAAGACATGGCATTGATGACTTACTATAAGGCAAAGGTCCT
1 -ATGTAAGACCATGCCAAGACATGGCATTGATGAGTT-CTATAAGGCAAAGGTCCT
* *
13276263 ATGTAAGACCATGCCAAGGCATGGCATTGGTGAGTTC-ATAAGGC-AAGGATACC-
1 ATGTAAGACCATGCCAAGACATGGCATTGATGAGTTCTATAAGGCAAAGG-T-CCT
* **
13276316 AAGTAAGACCATATCAAGACATGGCA
1 ATGTAAGACCATGCCAAGACATGGCA
13276342 ATGGTAAGTT
Statistics
Matches: 112, Mismatches: 18, Indels: 9
0.81 0.13 0.06
Matches are distributed among these distances:
52 4 0.04
53 30 0.27
54 33 0.29
55 39 0.35
56 6 0.05
ACGTcount: A:0.38, C:0.17, G:0.23, T:0.22
Consensus pattern (54 bp):
ATGTAAGACCATGCCAAGACATGGCATTGATGAGTTCTATAAGGCAAAGGTCCT
Found at i:13276353 original size:53 final size:54
Alignment explanation
Indices: 13276153--13276352 Score: 199
Period size: 53 Copynumber: 3.7 Consensus size: 54
13276143 ATAAGGACAT
* * * * * *
13276153 CATGTAAAACCATGCCAAGGCATGGCATTGATAAGTTCTATAAGGAAAGGAAAT
1 CATGTAAGACCATGTCAAGACATGGCATTGATAAGTTCTATAAGGCAAGGATAC
* * *
13276207 CATGTAAGACCATGTAAAGACATGGCATTGATGACTTACTATAAGGCAAAGG-T-C
1 CATGTAAGACCATGTCAAGACATGGCATTGATAAGTT-CTATAAGGC-AAGGATAC
* * * *
13276261 CTATGTAAGACCATGCCAAGGCATGGCATTGGTGAGTTC-ATAAGGCAAGGATAC
1 C-ATGTAAGACCATGTCAAGACATGGCATTGATAAGTTCTATAAGGCAAGGATAC
* * * *
13276315 CAAGTAAGACCATATCAAGACATGGCAATGGTAAGTTC
1 CATGTAAGACCATGTCAAGACATGGCATTGATAAGTTC
13276353 AAAAAGGAAA
Statistics
Matches: 121, Mismatches: 20, Indels: 11
0.80 0.13 0.07
Matches are distributed among these distances:
52 4 0.03
53 39 0.32
54 35 0.29
55 39 0.32
56 4 0.03
ACGTcount: A:0.37, C:0.17, G:0.23, T:0.23
Consensus pattern (54 bp):
CATGTAAGACCATGTCAAGACATGGCATTGATAAGTTCTATAAGGCAAGGATAC
Found at i:13276367 original size:108 final size:109
Alignment explanation
Indices: 13276154--13276363 Score: 262
Period size: 108 Copynumber: 1.9 Consensus size: 109
13276144 TAAGGACATC
* *
13276154 ATGTAAAACCATGCCAAGGCATGGCATTGATAAGTTCTATAAGGAAAGGAAATCATGTAAGACCA
1 ATGTAAAACCATGCCAAGGCATGGCATTGATAAGTTCTATAAGGAAAGGAAACCAAGTAAGACCA
* * * * * *
13276219 TGTAAAGACATGGCATTGATGACTTACTATAAGGCAAAGGTCCT
66 TATAAAGACATGGCAATGATAACTTACAAAAAGGAAAAGGTCCT
* * * * *
13276263 ATGTAAGACCATGCCAAGGCATGGCATTGGTGAGTTC-ATAAGGCAAGGATACCAAGTAAGACCA
1 ATGTAAAACCATGCCAAGGCATGGCATTGATAAGTTCTATAAGGAAAGGAAACCAAGTAAGACCA
* * *
13276327 TATCAAGACATGGCAATGGTAAGTT-CAAAAAGGAAAA
66 TATAAAGACATGGCAATGATAACTTACAAAAAGGAAAA
13276364 AGGTTCCCGA
Statistics
Matches: 85, Mismatches: 16, Indels: 2
0.83 0.16 0.02
Matches are distributed among these distances:
107 9 0.11
108 42 0.49
109 34 0.40
ACGTcount: A:0.40, C:0.16, G:0.23, T:0.21
Consensus pattern (109 bp):
ATGTAAAACCATGCCAAGGCATGGCATTGATAAGTTCTATAAGGAAAGGAAACCAAGTAAGACCA
TATAAAGACATGGCAATGATAACTTACAAAAAGGAAAAGGTCCT
Found at i:13278666 original size:24 final size:24
Alignment explanation
Indices: 13278639--13278689 Score: 59
Period size: 24 Copynumber: 2.1 Consensus size: 24
13278629 GTATTACAAA
*
13278639 TGTATGTATT-TTTATCCATACATT
1 TGTATATATTATTTA-CCATACATT
* *
13278663 TGTATATTTTATTTACTATACATT
1 TGTATATATTATTTACCATACATT
13278687 TGT
1 TGT
13278690 CTTTGTACTA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
24 19 0.83
25 4 0.17
ACGTcount: A:0.25, C:0.10, G:0.08, T:0.57
Consensus pattern (24 bp):
TGTATATATTATTTACCATACATT
Found at i:13283823 original size:68 final size:64
Alignment explanation
Indices: 13283714--13283944 Score: 189
Period size: 68 Copynumber: 3.5 Consensus size: 64
13283704 TACAGATGGT
* * * * * *
13283714 ATGTAGCTAGGTCACATGTATTATGCTAAGTGTACATCATGT-GTATAAGAGAGCTACGAGATAC
1 ATGTAGCTAGGTCACATGTGTGATACGAAGTGTACACCATGTAG-ACAAGAGAGCTACGAGATA-
13283778 A
64 A
* *
13283779 ATGCGGTAGCTAGGTCACATGTGTGATACG-AGATGTATACCATGTAGACAAGAGAGCTACGGGA
1 AT---GTAGCTAGGTCACATGTGTGATACGAAG-TGTACACCATGTAGACAAGAGAGCTACGAGA
13283843 TAA
62 TAA
* * * * * * *
13283846 ATGTAGCTAGGTCGCATGTGTGGTTCCAGGTGAAGGACACCATGTAGATAAGAGAGCTACGAGAT
1 ATGTAGCTAGGTCACATGTGTGATACGAAGT---GTACACCATGTAGACAAGAGAGCTACGAGAT
13283911 AA
63 AA
* * * *
13283913 A-GTGGCTAGGTCACATGGGTGGTACTAAGTGT
1 ATGTAGCTAGGTCACATGTGTGATACGAAGTGT
13283945 TCATGTTCAC
Statistics
Matches: 133, Mismatches: 24, Indels: 20
0.75 0.14 0.11
Matches are distributed among these distances:
63 1 0.01
64 22 0.17
65 3 0.02
66 23 0.17
67 35 0.26
68 48 0.36
69 1 0.01
ACGTcount: A:0.31, C:0.14, G:0.29, T:0.25
Consensus pattern (64 bp):
ATGTAGCTAGGTCACATGTGTGATACGAAGTGTACACCATGTAGACAAGAGAGCTACGAGATAA
Found at i:13287954 original size:40 final size:40
Alignment explanation
Indices: 13287051--13287940 Score: 1633
Period size: 40 Copynumber: 22.3 Consensus size: 40
13287041 TCCTCGTTCA
* * * *
13287051 AATGCCTTCGGGACATAGCCCGG-TTTTAGTAACTCACAC-
1 AATGCCTTCGGGACTTAACCCGGATTTAAG-AACTCGCACG
* *
13287090 AATGCCTTCGGGACTTAACCCGGATTTGATAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAAGAACTCGCACG
13287130 AATGCCTTCGGGACTTAACCCGGATTTAAGAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAAGAACTCGCACG
13287170 AATGCCTTCGGGACTTAACCCGGATTTAAGAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAAGAACTCGCACG
13287210 AATGCCTTCGGGACTTAACCCGGATTTAAGAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAAGAACTCGCACG
13287250 AATGCCTTCGGGACTTAACCCGGATTTAAGAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAAGAACTCGCACG
13287290 AATGCCTTCGGGACTTAACCCGGATTTAAGAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAAGAACTCGCACG
13287330 AATGCCTTCGGGACTTAACCCGGATTTAAGAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAAGAACTCGCACG
13287370 AATGCCTTCGGGACTTAACCCGGATTTAAGAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAAGAACTCGCACG
13287410 AATGCCTTCGGGACTTAACCCGGATTTAAGAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAAGAACTCGCACG
13287450 AATGCCTTCGGGACTTAACCCGGATTTAAGAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAAGAACTCGCACG
13287490 AATGCCTTCGGGACTTAACCCGGATTTAAGAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAAGAACTCGCACG
13287530 AATGCCTTCGGGACTTAACCCGGATTTAAGAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAAGAACTCGCACG
13287570 AATGCCTTCGGGACTTAACCCGGATTTAAGAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAAGAACTCGCACG
13287610 AATGCCTTCGGGACTTAACCCGGATTTAAGAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAAGAACTCGCACG
13287650 AATGCCTTCGGGACTTAACCCGGATTTAAGAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAAGAACTCGCACG
13287690 AATGCCTTCGGGACTTAACCCGGATTTAAGAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAAGAACTCGCACG
13287730 AATGCCTTCGGGACTTAACCCGGATTTAAGAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAAGAACTCGCACG
13287770 AATGCCTTCGGGACTTAACCCGGATTTAAGAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAAGAACTCGCACG
* *
13287810 AATGCCTTCGGGACTTAACCCGGATTTGATAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAAGAACTCGCACG
*
13287850 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAAGAACTCGCACG
* *
13287890 AATGCCTTCGGGACTTAACCCGGATTT-AGTATCTCGCACA
1 AATGCCTTCGGGACTTAACCCGGATTTAAG-AACTCGCACG
*
13287930 AAGGCCTTCGG
1 AATGCCTTCGG
13287941 ATCTTAGTCC
Statistics
Matches: 834, Mismatches: 14, Indels: 5
0.98 0.02 0.01
Matches are distributed among these distances:
39 30 0.04
40 804 0.96
ACGTcount: A:0.27, C:0.28, G:0.22, T:0.23
Consensus pattern (40 bp):
AATGCCTTCGGGACTTAACCCGGATTTAAGAACTCGCACG
Found at i:13288002 original size:41 final size:41
Alignment explanation
Indices: 13287925--13288002 Score: 104
Period size: 40 Copynumber: 1.9 Consensus size: 41
13287915 TTAGTATCTC
* * * *
13287925 GCACAAAGGCCTTCGGATCTTAGTCCGGATATATTCACTTA
1 GCACAAAGGCCTTCGGAACTTAGCCCGGACACATTCACTTA
13287966 GCACAAA-GCCTTCGGAACTTAGCCCGGACAGCATTCA
1 GCACAAAGGCCTTCGGAACTTAGCCCGGACA-CATTCA
13288003 ATTAATCATG
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
40 20 0.62
41 12 0.38
ACGTcount: A:0.28, C:0.28, G:0.21, T:0.23
Consensus pattern (41 bp):
GCACAAAGGCCTTCGGAACTTAGCCCGGACACATTCACTTA
Found at i:13289951 original size:100 final size:100
Alignment explanation
Indices: 13289773--13289975 Score: 334
Period size: 100 Copynumber: 2.0 Consensus size: 100
13289763 TTCAATCAAA
* * **
13289773 GGTAAATACCGTTCCCATGAACTACTGAACTCGGGGATGCAACATCTCAACATATCCTCAAGTAT
1 GGTAAATACCGTTCCCATGAACCACTAAACTCAAGGATGCAACATCTCAACATATCCTCAAGTAT
13289838 CTGAATTATCCGCTCGGATTGACCATCGGTTTGGG
66 CTGAATTATCCGCTCGGATTGACCATCGGTTTGGG
* * * *
13289873 GGTACATACCGTTCCCATGAACCACTAAACTCAAGGATGCAGCATCTCACCATATCCTCGAGTAT
1 GGTAAATACCGTTCCCATGAACCACTAAACTCAAGGATGCAACATCTCAACATATCCTCAAGTAT
13289938 CTGAATTATCCGCTCGGATTGACCATCGGTTTGGG
66 CTGAATTATCCGCTCGGATTGACCATCGGTTTGGG
13289973 GGT
1 GGT
13289976 GAAAAGCAGT
Statistics
Matches: 95, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
100 95 1.00
ACGTcount: A:0.26, C:0.26, G:0.21, T:0.27
Consensus pattern (100 bp):
GGTAAATACCGTTCCCATGAACCACTAAACTCAAGGATGCAACATCTCAACATATCCTCAAGTAT
CTGAATTATCCGCTCGGATTGACCATCGGTTTGGG
Found at i:13291163 original size:93 final size:93
Alignment explanation
Indices: 13290999--13291185 Score: 329
Period size: 93 Copynumber: 2.0 Consensus size: 93
13290989 GACGCATAGG
*
13290999 CCACGACTCGACCTTCTTGCATCAATACGCAACCCAACCCAAATAGGGATGCGTCACTATAAATG
1 CCACAACTCGACCTTCTTGCATCAATACGCAACCCAACCCAAATAGGGATGCGTCACTATAAATG
*
13291064 ACAAACTTTTTACCTGATTCGGGTTGCA
66 ACAAACTCTTTACCTGATTCGGGTTGCA
* *
13291092 CCACAACTCGACCTTCTTGCATCAATACGCAACCCAACCCGAGTAGGGATGCGTCACTATAAATG
1 CCACAACTCGACCTTCTTGCATCAATACGCAACCCAACCCAAATAGGGATGCGTCACTATAAATG
*
13291157 ACAAACTCTTTGCCTGATTCGGGTTGCA
66 ACAAACTCTTTACCTGATTCGGGTTGCA
13291185 C
1 C
13291186 TAAAATTGGA
Statistics
Matches: 89, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
93 89 1.00
ACGTcount: A:0.29, C:0.30, G:0.17, T:0.24
Consensus pattern (93 bp):
CCACAACTCGACCTTCTTGCATCAATACGCAACCCAACCCAAATAGGGATGCGTCACTATAAATG
ACAAACTCTTTACCTGATTCGGGTTGCA
Found at i:13291470 original size:105 final size:105
Alignment explanation
Indices: 13291288--13291498 Score: 377
Period size: 105 Copynumber: 2.0 Consensus size: 105
13291278 GCTTCGTCAT
*
13291288 TGGTGTGGCTATCATCGAGAAACCTTTCACAAATCGTCGGTAATAACCGGCGAGCCCCAAAAAGC
1 TGGTGTGGCTATCATCAAGAAACCTTTCACAAATCGTCGGTAATAACCGGCGAGCCCCAAAAAGC
*
13291353 TCCGAACTTCAGTAATATTTCTCGGAGGTTTCCAGTCAAG
66 TCCGAACCTCAGTAATATTTCTCGGAGGTTTCCAGTCAAG
* *
13291393 TGGTGTGGCTATCATCAAGAAACCTTTGACAAATCGTCGGTAATAACCGGCGAGTCCCAAAAAGC
1 TGGTGTGGCTATCATCAAGAAACCTTTCACAAATCGTCGGTAATAACCGGCGAGCCCCAAAAAGC
*
13291458 TCCGAACCTCAGTAATATTTCTCGGAGGTTTCCAGTTAAG
66 TCCGAACCTCAGTAATATTTCTCGGAGGTTTCCAGTCAAG
13291498 T
1 T
13291499 ATGGCTGAGA
Statistics
Matches: 101, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
105 101 1.00
ACGTcount: A:0.29, C:0.24, G:0.22, T:0.26
Consensus pattern (105 bp):
TGGTGTGGCTATCATCAAGAAACCTTTCACAAATCGTCGGTAATAACCGGCGAGCCCCAAAAAGC
TCCGAACCTCAGTAATATTTCTCGGAGGTTTCCAGTCAAG
Found at i:13294074 original size:78 final size:78
Alignment explanation
Indices: 13293941--13294096 Score: 231
Period size: 78 Copynumber: 2.0 Consensus size: 78
13293931 TTTCCATATA
* * * * ***
13293941 TGGTATGACTCCTACTTGTCTCTGGTTAATTTATAATGAATTTCCAAATTTGGAACAGGGAATCC
1 TGGTATGACCCCTAATTATCTCTGGTCAATTTATAATGAATTTCCAAAGGCGGAACAGGGAATCC
13294006 AGAAACCGTTCTG
66 AGAAACCGTTCTG
*
13294019 TGGTATGACCCCTAATTATCTCTGGTCAATTTATAGTGAATTTCCAAAGGCGGAACAGGGAATCC
1 TGGTATGACCCCTAATTATCTCTGGTCAATTTATAATGAATTTCCAAAGGCGGAACAGGGAATCC
*
13294084 AGAAACTGTTCTG
66 AGAAACCGTTCTG
13294097 GCCCTGTTCC
Statistics
Matches: 69, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
78 69 1.00
ACGTcount: A:0.29, C:0.19, G:0.21, T:0.32
Consensus pattern (78 bp):
TGGTATGACCCCTAATTATCTCTGGTCAATTTATAATGAATTTCCAAAGGCGGAACAGGGAATCC
AGAAACCGTTCTG
Found at i:13295130 original size:40 final size:39
Alignment explanation
Indices: 13295032--13295313 Score: 249
Period size: 40 Copynumber: 7.3 Consensus size: 39
13295022 TCCTCGTTCA
* * *
13295032 AATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACAC
1 AATGCCTTCGGGACATAACCCGGATTTAGTAACTCGCAC
**
13295071 AATGCCTTCGGGACATAACCCGGATTTAACAACTCGCAC
1 AATGCCTTCGGGACATAACCCGGATTTAGTAACTCGCAC
* *
13295110 GAATGCCTTCGGGACGTAACCCGGATTTAGTATCTCGCAC
1 -AATGCCTTCGGGACATAACCCGGATTTAGTAACTCGCAC
* * ** * * * *
13295150 AAAGGCCTTC-GGATCTTAGTCCGGATATATTCACTTAGCAC
1 -AATGCCTTCGGGA-CATAACCCGGATTTAGTAAC-TCGCAC
*
13295191 AAAGCCTTC-GG----AA---GGATTTAGTAACTCGCAC
1 AATGCCTTCGGGACATAACCCGGATTTAGTAACTCGCAC
* *
13295222 GAATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCAC
1 -AATGCCTTCGGGACATAACCCGGATTTAGTAACTCGCAC
* *
13295262 GAATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCAC
1 -AATGCCTTCGGGACATAACCCGGATTTAGTAACTCGCAC
*
13295302 AAAGGCCTTCGG
1 -AATGCCTTCGG
13295314 ATCTTAGTCC
Statistics
Matches: 200, Mismatches: 31, Indels: 23
0.79 0.12 0.09
Matches are distributed among these distances:
31 5 0.03
32 17 0.09
33 2 0.01
35 1 0.00
37 2 0.01
39 37 0.19
40 131 0.65
41 5 0.03
ACGTcount: A:0.27, C:0.27, G:0.22, T:0.25
Consensus pattern (39 bp):
AATGCCTTCGGGACATAACCCGGATTTAGTAACTCGCAC
Found at i:13295270 original size:72 final size:72
Alignment explanation
Indices: 13295132--13295355 Score: 209
Period size: 72 Copynumber: 3.0 Consensus size: 72
13295122 GACGTAACCC
* ** * *
13295132 GGATTTAGTATCTCGCACAAAGGCCTTCGGATCTTAGTCCGGATATATTCACTTAGCACAAAGCC
1 GGATTTAGTAACTCGCACAAAGGCCTTCGGATCTTAACCCGGATATAATAACTTAGCACAAAGCC
13295197 TTCGGAA
66 TTCGGAA
* * * * *
13295204 GGATTTAGTAACTCGCACGAATGCCTTCGGGA-CTTAACCCGGATTTAATAAC-TCGCACGAATG
1 GGATTTAGTAACTCGCACAAAGGCCTTC-GGATCTTAACCCGGATATAATAACTTAGCAC-AAAG
13295267 CCTTCGGGACTTAA
64 CCTTC-GG----AA
* ** * *
13295281 CCCGGATTTAGTATCTCGCACAAAGGCCTTCGGATCTTAGTCCGGATATATTCACTTAGCACAAA
1 ---GGATTTAGTAACTCGCACAAAGGCCTTCGGATCTTAACCCGGATATAATAACTTAGCACAAA
13295346 GCCTTCGGAA
63 GCCTTCGGAA
13295356 CTTAGCCCGG
Statistics
Matches: 120, Mismatches: 20, Indels: 21
0.75 0.12 0.13
Matches are distributed among these distances:
71 5 0.04
72 48 0.40
73 5 0.04
75 2 0.02
77 2 0.02
79 5 0.04
80 48 0.40
81 5 0.04
ACGTcount: A:0.27, C:0.25, G:0.21, T:0.27
Consensus pattern (72 bp):
GGATTTAGTAACTCGCACAAAGGCCTTCGGATCTTAACCCGGATATAATAACTTAGCACAAAGCC
TTCGGAA
Found at i:13295310 original size:112 final size:112
Alignment explanation
Indices: 13295092--13295314 Score: 290
Period size: 112 Copynumber: 2.0 Consensus size: 112
13295082 GACATAACCC
* *
13295092 GGATTTAACAACTCGCACGAATGCCTTCGGGACGTAACCCGGATTTAGTATCTCGCACAAAGGCC
1 GGATTTAACAACTCGCACGAATGCCTTCGGGACGTAACCCGGATTTAATAACTCGCACAAAGGCC
** *
13295157 TTCGGATCTTAGTCCGGATATATTCACTTAGCACAAAGCCTTCGGAA
66 TTCGGATCTTAACCCGGATATAGTCACTTAGCACAAAGCCTTCGGAA
** * * *
13295204 GGATTTAGTAACTCGCACGAATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACGAATGCC
1 GGATTTAACAACTCGCACGAATGCCTTCGGGACGTAACCCGGATTTAATAACTCGCACAAAGGCC
* *
13295269 TTCGGGA-CTTAACCCGGATTTAGT-A-TCTCGCACAAAGGCCTTCGGA
66 TTC-GGATCTTAACCCGGATATAGTCACT-TAGCACAAA-GCCTTCGGA
13295315 TCTTAGTCCG
Statistics
Matches: 96, Mismatches: 12, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
110 1 0.01
111 9 0.09
112 83 0.86
113 3 0.03
ACGTcount: A:0.27, C:0.26, G:0.22, T:0.25
Consensus pattern (112 bp):
GGATTTAACAACTCGCACGAATGCCTTCGGGACGTAACCCGGATTTAATAACTCGCACAAAGGCC
TTCGGATCTTAACCCGGATATAGTCACTTAGCACAAAGCCTTCGGAA
Found at i:13295326 original size:40 final size:40
Alignment explanation
Indices: 13295204--13295366 Score: 177
Period size: 40 Copynumber: 4.1 Consensus size: 40
13295194 GCCTTCGGAA
*
13295204 GGATTTAGTAACTCGCACGAATGCCTTCGGGACTTAACCC
1 GGATTTAGTAACTCGCACAAATGCCTTCGGGACTTAACCC
* *
13295244 GGATTTAATAACTCGCACGAATGCCTTCGGGACTTAACCC
1 GGATTTAGTAACTCGCACAAATGCCTTCGGGACTTAACCC
* * **
13295284 GGATTTAGTATCTCGCACAAAGGCCTTC-GGATCTTAGTCC
1 GGATTTAGTAACTCGCACAAATGCCTTCGGGA-CTTAACCC
* * * * * *
13295324 GGATATATTCACTTAGCACAAA-GCCTTCGGAACTTAGCCC
1 GGATTTAGTAAC-TCGCACAAATGCCTTCGGGACTTAACCC
13295364 GGA
1 GGA
13295367 CAGCATTCAA
Statistics
Matches: 106, Mismatches: 14, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
39 3 0.03
40 93 0.88
41 10 0.09
ACGTcount: A:0.26, C:0.26, G:0.21, T:0.26
Consensus pattern (40 bp):
GGATTTAGTAACTCGCACAAATGCCTTCGGGACTTAACCC
Found at i:13295347 original size:152 final size:151
Alignment explanation
Indices: 13295056--13295355 Score: 555
Period size: 152 Copynumber: 2.0 Consensus size: 151
13295046 ATAGCCCGGT
13295056 TTTAGTAACTCACACAATGCCTTCGGGACATAACCCGGATTTAACAACTCGCACGAATGCCTTCG
1 TTTAGTAACTCACACAATGCCTTCGGGACATAACCCGGATTTAACAACTCGCACGAATGCCTTCG
13295121 GGACGTAACCCGGATTTAGTATCTCGCACAAAGGCCTTCGGATCTTAGTCCGGATATATTCACTT
66 GGACGTAACCCGGATTTAGTATCTCGCACAAAGGCCTTCGGATCTTAGTCCGGATATATTCACTT
13295186 AGCACAAAGCCTTCGGAAGGA
131 AGCACAAAGCCTTCGGAAGGA
* * *
13295207 TTTAGTAACTCGCACGAATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACGAATGCCTTC
1 TTTAGTAACTCACAC-AATGCCTTCGGGACATAACCCGGATTTAACAACTCGCACGAATGCCTTC
*
13295272 GGGACTTAACCCGGATTTAGTATCTCGCACAAAGGCCTTCGGATCTTAGTCCGGATATATTCACT
65 GGGACGTAACCCGGATTTAGTATCTCGCACAAAGGCCTTCGGATCTTAGTCCGGATATATTCACT
13295337 TAGCACAAAGCCTTCGGAA
130 TAGCACAAAGCCTTCGGAA
13295356 CTTAGCCCGG
Statistics
Matches: 144, Mismatches: 4, Indels: 1
0.97 0.03 0.01
Matches are distributed among these distances:
151 14 0.10
152 130 0.90
ACGTcount: A:0.28, C:0.26, G:0.20, T:0.26
Consensus pattern (151 bp):
TTTAGTAACTCACACAATGCCTTCGGGACATAACCCGGATTTAACAACTCGCACGAATGCCTTCG
GGACGTAACCCGGATTTAGTATCTCGCACAAAGGCCTTCGGATCTTAGTCCGGATATATTCACTT
AGCACAAAGCCTTCGGAAGGA
Found at i:13295375 original size:41 final size:41
Alignment explanation
Indices: 13295298--13295375 Score: 104
Period size: 40 Copynumber: 1.9 Consensus size: 41
13295288 TTAGTATCTC
* * * *
13295298 GCACAAAGGCCTTCGGATCTTAGTCCGGATATATTCACTTA
1 GCACAAAGGCCTTCGGAACTTAGCCCGGACACATTCACTTA
13295339 GCACAAA-GCCTTCGGAACTTAGCCCGGACAGCATTCA
1 GCACAAAGGCCTTCGGAACTTAGCCCGGACA-CATTCA
13295376 ATTAATCATG
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
40 20 0.62
41 12 0.38
ACGTcount: A:0.28, C:0.28, G:0.21, T:0.23
Consensus pattern (41 bp):
GCACAAAGGCCTTCGGAACTTAGCCCGGACACATTCACTTA
Found at i:13302662 original size:81 final size:81
Alignment explanation
Indices: 13302542--13302729 Score: 286
Period size: 81 Copynumber: 2.3 Consensus size: 81
13302532 AATGCTCTCG
* * *
13302542 ATTTGTAGAATTACCATTTTACCCTCGATTTATATAATTACCGTTTCACCCTCGATTTACAAAAT
1 ATTTATAGAATTACCATTTTACCCTCGATTTACAGAATTACCGTTTCACCCTCGATTTACAAAAT
* *
13302607 TACCGTTTTACCGTCA
66 TACCATTTTACCCTCA
* *
13302623 ATTTATAGAATTACCGTTTTACCCTCGATTTACAGAATTACCGTTTTACCCTCGATTTACAAAAT
1 ATTTATAGAATTACCATTTTACCCTCGATTTACAGAATTACCGTTTCACCCTCGATTTACAAAAT
13302688 TACCATTTTACCCTCA
66 TACCATTTTACCCTCA
* * *
13302704 GTTTACAAAATTACCATTTTACCCTC
1 ATTTATAGAATTACCATTTTACCCTC
13302730 AATTGTGAAA
Statistics
Matches: 96, Mismatches: 11, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
81 96 1.00
ACGTcount: A:0.29, C:0.24, G:0.07, T:0.39
Consensus pattern (81 bp):
ATTTATAGAATTACCATTTTACCCTCGATTTACAGAATTACCGTTTCACCCTCGATTTACAAAAT
TACCATTTTACCCTCA
Found at i:13302730 original size:27 final size:27
Alignment explanation
Indices: 13302550--13302729 Score: 245
Period size: 27 Copynumber: 6.7 Consensus size: 27
13302540 CGATTTGTAG
* * *
13302550 AATTACCATTTTACCCTCGATTTATAT
1 AATTACCGTTTTACCCTCGATTTACAA
*
13302577 AATTACCGTTTCACCCTCGATTTACAA
1 AATTACCGTTTTACCCTCGATTTACAA
* * * *
13302604 AATTACCGTTTTACCGTCAATTTATAG
1 AATTACCGTTTTACCCTCGATTTACAA
*
13302631 AATTACCGTTTTACCCTCGATTTACAG
1 AATTACCGTTTTACCCTCGATTTACAA
13302658 AATTACCGTTTTACCCTCGATTTACAA
1 AATTACCGTTTTACCCTCGATTTACAA
*
13302685 AATTACCATTTTACCCTC-AGTTTACAA
1 AATTACCGTTTTACCCTCGA-TTTACAA
*
13302712 AATTACCATTTTACCCTC
1 AATTACCGTTTTACCCTC
13302730 AATTGTGAAA
Statistics
Matches: 138, Mismatches: 14, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
26 1 0.01
27 137 0.99
ACGTcount: A:0.29, C:0.26, G:0.07, T:0.38
Consensus pattern (27 bp):
AATTACCGTTTTACCCTCGATTTACAA
Found at i:13302795 original size:27 final size:27
Alignment explanation
Indices: 13302765--13302915 Score: 157
Period size: 27 Copynumber: 5.6 Consensus size: 27
13302755 TGTAGGATAG
13302765 AATTACCAAAATACCCCTAGTTTGTAA
1 AATTACCAAAATACCCCTAGTTTGTAA
*
13302792 AATTACCAAAATACCCCTAATTTGTAA
1 AATTACCAAAATACCCCTAGTTTGTAA
* ** * *
13302819 AATTACCGAAATACTACTGGTTTGTGA
1 AATTACCAAAATACCCCTAGTTTGTAA
* *
13302846 AATTACCGAAATA-CCCTCAATTTGTAA
1 AATTACCAAAATACCCCT-AGTTTGTAA
*
13302873 AATTACCAAAAATACCCCT-GATTAG-AA
1 AATTACC-AAAATACCCCTAG-TTTGTAA
13302900 AATTA-CAGAAATACCC
1 AATTACCA-AAATACCC
13302916 TTGACTTTCT
Statistics
Matches: 104, Mismatches: 15, Indels: 11
0.80 0.12 0.08
Matches are distributed among these distances:
25 1 0.01
26 11 0.11
27 80 0.77
28 8 0.08
29 4 0.04
ACGTcount: A:0.42, C:0.21, G:0.09, T:0.28
Consensus pattern (27 bp):
AATTACCAAAATACCCCTAGTTTGTAA
Found at i:13302858 original size:81 final size:81
Alignment explanation
Indices: 13302765--13302913 Score: 221
Period size: 81 Copynumber: 1.8 Consensus size: 81
13302755 TGTAGGATAG
* * *
13302765 AATTACCAAAATACCC-CTAGTTTGTAAAATTACC-AAAATACCCCTAATTTGTAAAATTACCGA
1 AATTACCAAAATACCCTC-AATTTGTAAAATTACCAAAAATACCCCTAATTAG-AAAATTACAGA
13302828 AATACTACTGGTTTGTGA
64 AATACTACTGGTTTGTGA
* *
13302846 AATTACCGAAATACCCTCAATTTGTAAAATTACCAAAAATACCCCTGATTAGAAAATTACAGAAA
1 AATTACCAAAATACCCTCAATTTGTAAAATTACCAAAAATACCCCTAATTAGAAAATTACAGAAA
13302911 TAC
66 TAC
13302914 CCTTGACTTT
Statistics
Matches: 61, Mismatches: 5, Indels: 4
0.87 0.07 0.06
Matches are distributed among these distances:
81 45 0.74
82 16 0.26
ACGTcount: A:0.43, C:0.20, G:0.09, T:0.28
Consensus pattern (81 bp):
AATTACCAAAATACCCTCAATTTGTAAAATTACCAAAAATACCCCTAATTAGAAAATTACAGAAA
TACTACTGGTTTGTGA
Found at i:13302916 original size:54 final size:55
Alignment explanation
Indices: 13302765--13302916 Score: 179
Period size: 54 Copynumber: 2.8 Consensus size: 55
13302755 TGTAGGATAG
13302765 AATTACCAAAATACCCCT-AGTTTGTAAAATTACCA-AAATACCC-CTAATTTGTAA
1 AATTACCAAAATACCCCTGA-TTTGTAAAATTA-CAGAAATACCCTCTAATTTGTAA
* ** * * *
13302819 AATTACCGAAATACTACTGGTTTGTGAAATTACCGAAATACCCTC-AATTTGTAA
1 AATTACCAAAATACCCCTGATTTGTAAAATTACAGAAATACCCTCTAATTTGTAA
*
13302873 AATTACCAAAAATACCCCTGATTAG-AAAATTACAGAAATACCCT
1 AATTACC-AAAATACCCCTGATTTGTAAAATTACAGAAATACCCT
13302917 TGACTTTCTA
Statistics
Matches: 81, Mismatches: 13, Indels: 8
0.79 0.13 0.08
Matches are distributed among these distances:
53 1 0.01
54 67 0.83
55 13 0.16
ACGTcount: A:0.42, C:0.21, G:0.09, T:0.28
Consensus pattern (55 bp):
AATTACCAAAATACCCCTGATTTGTAAAATTACAGAAATACCCTCTAATTTGTAA
Found at i:13302966 original size:27 final size:27
Alignment explanation
Indices: 13302927--13302978 Score: 79
Period size: 27 Copynumber: 1.9 Consensus size: 27
13302917 TGACTTTCTA
13302927 AAAATTATAGAAATACCATTGGTTTAC
1 AAAATTATAGAAATACCATTGGTTTAC
*
13302954 AAAATTACT-GAAATACCCTTGGTTT
1 AAAATTA-TAGAAATACCATTGGTTT
13302979 GTAGATTTAC
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
27 22 0.96
28 1 0.04
ACGTcount: A:0.40, C:0.13, G:0.12, T:0.35
Consensus pattern (27 bp):
AAAATTATAGAAATACCATTGGTTTAC
Found at i:13303074 original size:27 final size:27
Alignment explanation
Indices: 13303033--13303096 Score: 67
Period size: 27 Copynumber: 2.4 Consensus size: 27
13303023 CCCATAATAA
* *
13303033 GTAAAAAGACCGTAA-AGCCCCTGTAGG
1 GTAAAATGACTGTAATA-CCCCTGTAGG
* * *
13303060 GTAAAGTGACTGTAATACCCTTGTATG
1 GTAAAATGACTGTAATACCCCTGTAGG
13303087 GTAAAATGAC
1 GTAAAATGAC
13303097 AAATATGCCC
Statistics
Matches: 30, Mismatches: 6, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
27 29 0.97
28 1 0.03
ACGTcount: A:0.36, C:0.17, G:0.23, T:0.23
Consensus pattern (27 bp):
GTAAAATGACTGTAATACCCCTGTAGG
Found at i:13303944 original size:25 final size:24
Alignment explanation
Indices: 13303906--13303975 Score: 95
Period size: 25 Copynumber: 2.8 Consensus size: 24
13303896 AGGAAGTGCT
* *
13303906 AAAAGGGCTCTGCCTCAGTTTACC
1 AAAAGGGCTTTGCCCCAGTTTACC
*
13303930 GAAAAGGGCTTTGCCCCAGTTTATC
1 -AAAAGGGCTTTGCCCCAGTTTACC
13303955 AGAAAGGGCTTTGCCCCAGTT
1 A-AAAGGGCTTTGCCCCAGTT
13303976 ATTAAAAGAG
Statistics
Matches: 41, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
24 1 0.02
25 40 0.98
ACGTcount: A:0.24, C:0.26, G:0.24, T:0.26
Consensus pattern (24 bp):
AAAAGGGCTTTGCCCCAGTTTACC
Found at i:13303988 original size:24 final size:23
Alignment explanation
Indices: 13303906--13304002 Score: 86
Period size: 25 Copynumber: 4.0 Consensus size: 23
13303896 AGGAAGTGCT
* * *
13303906 AAAAGGGCTCTGCCTCAGTTTACC
1 AAAAGGGCTTTGCCCCAG-TTATC
13303930 GAAAAGGGCTTTGCCCCAGTTTATC
1 -AAAAGGGCTTTGCCCCAG-TTATC
*
13303955 AGAAAGGGCTTTGCCCCAGTTATT
1 A-AAAGGGCTTTGCCCCAGTTATC
**
13303979 AAAAGAGGCTAGGCCTCCAGTTAT
1 AAAAG-GGCTTTGCC-CCAGTTAT
13304003 ATGATAAAGC
Statistics
Matches: 63, Mismatches: 6, Indels: 6
0.84 0.08 0.08
Matches are distributed among these distances:
23 4 0.06
24 13 0.21
25 46 0.73
ACGTcount: A:0.27, C:0.24, G:0.24, T:0.26
Consensus pattern (23 bp):
AAAAGGGCTTTGCCCCAGTTATC
Found at i:13304182 original size:42 final size:42
Alignment explanation
Indices: 13304123--13304256 Score: 250
Period size: 42 Copynumber: 3.2 Consensus size: 42
13304113 TAGTCTCCCC
13304123 AAATGGGCTTGCATACATTCATTGACATTACATGTGATATTG
1 AAATGGGCTTGCATACATTCATTGACATTACATGTGATATTG
*
13304165 AAATGGGCATGCATACATTCATTGACATTACATGTGATATTG
1 AAATGGGCTTGCATACATTCATTGACATTACATGTGATATTG
*
13304207 AAATGGGCTTGCATACATCCATTGACATTACATGTGATATTG
1 AAATGGGCTTGCATACATTCATTGACATTACATGTGATATTG
13304249 AAATGGGC
1 AAATGGGC
13304257 CTAAAGGCCA
Statistics
Matches: 89, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
42 89 1.00
ACGTcount: A:0.32, C:0.15, G:0.20, T:0.33
Consensus pattern (42 bp):
AAATGGGCTTGCATACATTCATTGACATTACATGTGATATTG
Found at i:13304315 original size:31 final size:31
Alignment explanation
Indices: 13304280--13304425 Score: 249
Period size: 31 Copynumber: 4.7 Consensus size: 31
13304270 CGTTTACAGT
13304280 AAAGGCTTCGGCCCAGTGATATGATTTATGA
1 AAAGGCTTCGGCCCAGTGATATGATTTATGA
* *
13304311 AAAGGCTTTGACCCAGTGATATGATTTATGA
1 AAAGGCTTCGGCCCAGTGATATGATTTATGA
*
13304342 GAAGGCTTCGGCCCAGTGATATGATTTATGA
1 AAAGGCTTCGGCCCAGTGATATGATTTATGA
13304373 AAAGGCTTCGGCCCAGTGATATGATTTATGA
1 AAAGGCTTCGGCCCAGTGATATGATTTATGA
*
13304404 AAAGGCTTCGACCCAGT-ATATG
1 AAAGGCTTCGGCCCAGTGATATG
13304426 TCAAGACTAA
Statistics
Matches: 108, Mismatches: 7, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
30 5 0.05
31 103 0.95
ACGTcount: A:0.29, C:0.16, G:0.25, T:0.29
Consensus pattern (31 bp):
AAAGGCTTCGGCCCAGTGATATGATTTATGA
Found at i:13308162 original size:23 final size:23
Alignment explanation
Indices: 13308132--13308178 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
13308122 ATACACCATT
13308132 TAGCATCAATTTGATAATGGCTA
1 TAGCATCAATTTGATAATGGCTA
13308155 TAGCATCAATTTGATAATGGCTA
1 TAGCATCAATTTGATAATGGCTA
13308178 T
1 T
13308179 GTAGCGATAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.34, C:0.13, G:0.17, T:0.36
Consensus pattern (23 bp):
TAGCATCAATTTGATAATGGCTA
Found at i:13313255 original size:24 final size:23
Alignment explanation
Indices: 13313212--13313256 Score: 56
Period size: 24 Copynumber: 1.9 Consensus size: 23
13313202 CACCTCAAAC
*
13313212 ACATACAAACAATACTTAATTGA
1 ACATACAAACAATACATAATTGA
13313235 ACATATCAAA-AATACCATAATT
1 ACATA-CAAACAATA-CATAATT
13313257 CATGCATAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
23 9 0.47
24 10 0.53
ACGTcount: A:0.53, C:0.18, G:0.02, T:0.27
Consensus pattern (23 bp):
ACATACAAACAATACATAATTGA
Found at i:13319411 original size:26 final size:26
Alignment explanation
Indices: 13319382--13319431 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
13319372 CTGGATATTC
*
13319382 TATGTGGAC-ATTTATTTTCAGAAGTA
1 TATGT-GACTATTTAATTTCAGAAGTA
*
13319408 TATGTGACTGTTTAATTTCAGAAG
1 TATGTGACTATTTAATTTCAGAAG
13319432 AATTCTTATC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 3 0.14
26 18 0.86
ACGTcount: A:0.30, C:0.08, G:0.20, T:0.42
Consensus pattern (26 bp):
TATGTGACTATTTAATTTCAGAAGTA
Found at i:13323196 original size:43 final size:43
Alignment explanation
Indices: 13323071--13323229 Score: 191
Period size: 43 Copynumber: 3.7 Consensus size: 43
13323061 TGTGTTATCG
* * *
13323071 TGTAAGACCACGTCTGGGACATTGGCATCGAT-TTGTGATTTACT
1 TGTAAGACCACGTCTGGGACAGTGGCATTGATATT-TGATTT-CA
* * *
13323115 TGTAAGACCATGTCTGGGACATTGGCATT-ATATATGATTTCA
1 TGTAAGACCACGTCTGGGACAGTGGCATTGATATTTGATTTCA
*
13323157 TGTAAGACC-CTGTCTGGGACAGTGGCATTGATATTTGATTACA
1 TGTAAGACCAC-GTCTGGGACAGTGGCATTGATATTTGATTTCA
13323200 TGTAAGACCACGTCTGGGAC-GTTGGCATTG
1 TGTAAGACCACGTCTGGGACAG-TGGCATTG
13323230 TACGAGCTAT
Statistics
Matches: 102, Mismatches: 8, Indels: 11
0.84 0.07 0.09
Matches are distributed among these distances:
42 28 0.27
43 45 0.44
44 29 0.28
ACGTcount: A:0.25, C:0.17, G:0.26, T:0.33
Consensus pattern (43 bp):
TGTAAGACCACGTCTGGGACAGTGGCATTGATATTTGATTTCA
Found at i:13323196 original size:86 final size:85
Alignment explanation
Indices: 13323071--13323228 Score: 230
Period size: 85 Copynumber: 1.8 Consensus size: 85
13323061 TGTGTTATCG
* * *
13323071 TGTAAGACCACGTCTGGGACATTGGCATCGATTTGTGATTTACTTGTAAGACCATGTCTGGGACA
1 TGTAAGACCACGTCTGGGACAGTGGCATCGATTTGTGA-TTACATGTAAGACCACGTCTGGGACA
13323136 TTGGCATTATATATGATTTCA
65 TTGGCATTATATATGATTTCA
*
13323157 TGTAAGACC-CTGTCTGGGACAGTGGCATTGATATT-TGATTACATGTAAGACCACGTCTGGGAC
1 TGTAAGACCAC-GTCTGGGACAGTGGCATCGAT-TTGTGATTACATGTAAGACCACGTCTGGGAC
*
13323220 GTTGGCATT
64 ATTGGCATT
13323229 GTACGAGCTA
Statistics
Matches: 65, Mismatches: 5, Indels: 5
0.87 0.07 0.07
Matches are distributed among these distances:
85 32 0.49
86 31 0.48
87 2 0.03
ACGTcount: A:0.25, C:0.17, G:0.25, T:0.33
Consensus pattern (85 bp):
TGTAAGACCACGTCTGGGACAGTGGCATCGATTTGTGATTACATGTAAGACCACGTCTGGGACAT
TGGCATTATATATGATTTCA
Found at i:13324805 original size:55 final size:55
Alignment explanation
Indices: 13324689--13324806 Score: 134
Period size: 55 Copynumber: 2.1 Consensus size: 55
13324679 TCCTAAAATT
*
13324689 TTAAGTCAGTCTCGAACACGGCCAAGGCACACGGGCGTGTGGCTAGCCGTGTGAC
1 TTAAGTCAGTCTCGAACACGGCCAAGGCACACGGGCGTCTGGCTAGCCGTGTGAC
** * * *
13324744 CCAAGTCAGTTTCG-ACTACGGCCAAGGCACACGGGCATGTCTTG-TGGCCGTGTGA-
1 TTAAGTCAGTCTCGAAC-ACGGCCAAGGCACACGGGC--GTCTGGCTAGCCGTGTGAC
13324799 TTAAGTCA
1 TTAAGTCA
13324807 ATATGTATGC
Statistics
Matches: 52, Mismatches: 8, Indels: 6
0.79 0.12 0.09
Matches are distributed among these distances:
54 2 0.04
55 36 0.69
56 10 0.19
57 4 0.08
ACGTcount: A:0.22, C:0.26, G:0.31, T:0.21
Consensus pattern (55 bp):
TTAAGTCAGTCTCGAACACGGCCAAGGCACACGGGCGTCTGGCTAGCCGTGTGAC
Found at i:13330349 original size:27 final size:27
Alignment explanation
Indices: 13330319--13330381 Score: 108
Period size: 27 Copynumber: 2.3 Consensus size: 27
13330309 GACACGGCAA
* *
13330319 GCCACACGCCCATGTGTCAGACCGTGT
1 GCCACACACCCATGTGCCAGACCGTGT
13330346 GCCACACACCCATGTGCCAGACCGTGT
1 GCCACACACCCATGTGCCAGACCGTGT
13330373 GCCACACAC
1 GCCACACAC
13330382 GACCAATACT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
27 34 1.00
ACGTcount: A:0.22, C:0.41, G:0.22, T:0.14
Consensus pattern (27 bp):
GCCACACACCCATGTGCCAGACCGTGT
Found at i:13335146 original size:12 final size:12
Alignment explanation
Indices: 13335129--13335156 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
13335119 CGAGCACCTT
13335129 CACGGCCTCTTC
1 CACGGCCTCTTC
13335141 CACGGCCTCTTC
1 CACGGCCTCTTC
13335153 CACG
1 CACG
13335157 AGTACTTCTG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.11, C:0.50, G:0.18, T:0.21
Consensus pattern (12 bp):
CACGGCCTCTTC
Found at i:13338122 original size:12 final size:12
Alignment explanation
Indices: 13338107--13338145 Score: 60
Period size: 12 Copynumber: 3.2 Consensus size: 12
13338097 CCTTGATCCA
13338107 CTCCTCAAATCT
1 CTCCTCAAATCT
*
13338119 CTCCCCAAATCT
1 CTCCTCAAATCT
*
13338131 CTCCTCTAATCT
1 CTCCTCAAATCT
13338143 CTC
1 CTC
13338146 TTTTAACCAA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.21, C:0.46, G:0.00, T:0.33
Consensus pattern (12 bp):
CTCCTCAAATCT
Found at i:13338817 original size:47 final size:47
Alignment explanation
Indices: 13338764--13338874 Score: 141
Period size: 47 Copynumber: 2.4 Consensus size: 47
13338754 TCTCTTGATA
* * * *
13338764 AGTACCTATACCATGGCCCGTAACTAAATCAAGGTAACTTATCCTTG
1 AGTACCTATACCATGGCCCATAACCAAATAAAGGTAACTCATCCTTG
* * *
13338811 AGTACCTATACCATGGCCCATAGCCAAATAAAGGTAACTCCTCTTTG
1 AGTACCTATACCATGGCCCATAACCAAATAAAGGTAACTCATCCTTG
* *
13338858 AATTCCTATACCATGGC
1 AGTACCTATACCATGGC
13338875 ATAACAAAAG
Statistics
Matches: 55, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
47 55 1.00
ACGTcount: A:0.32, C:0.27, G:0.14, T:0.27
Consensus pattern (47 bp):
AGTACCTATACCATGGCCCATAACCAAATAAAGGTAACTCATCCTTG
Found at i:13340829 original size:43 final size:43
Alignment explanation
Indices: 13340751--13340907 Score: 122
Period size: 43 Copynumber: 3.7 Consensus size: 43
13340741 AGCTCGTACA
* * *
13340751 ATGCCAATATCCCAGACGTGGTCTTACATGTAATCAAATATCG
1 ATGCCAATATCCCAAACGTGGTCTTACACGAAATCAAATATCG
* *
13340794 ATGCCACTATCCCAAACAG-GGTCTTACACGAAATCATATAT-G
1 ATGCCAATATCCCAAAC-GTGGTCTTACACGAAATCAAATATCG
* * * * * * *
13340836 ATACCAATGTTCCAGACATGGTTTTACACGTAAATCACAA-ATTG
1 ATGCCAATATCCCAAACGTGGTCTTACACG-AAATCA-AATATCG
* * * *
13340880 ATGCCAACATTCCAGACGTGGTCATACA
1 ATGCCAATATCCCAAACGTGGTCTTACA
13340908 TATTAAACTT
Statistics
Matches: 90, Mismatches: 19, Indels: 9
0.76 0.16 0.08
Matches are distributed among these distances:
42 23 0.26
43 42 0.47
44 25 0.28
ACGTcount: A:0.34, C:0.24, G:0.15, T:0.26
Consensus pattern (43 bp):
ATGCCAATATCCCAAACGTGGTCTTACACGAAATCAAATATCG
Found at i:13346427 original size:37 final size:37
Alignment explanation
Indices: 13346368--13346476 Score: 173
Period size: 37 Copynumber: 2.9 Consensus size: 37
13346358 AGCTCAGATG
* *
13346368 AAATCTCCACACGAAGTTATCGGGTCTTACCCGGACA
1 AAATCTCCACACGTAGTCATCGGGTCTTACCCGGACA
* *
13346405 AAATCTCTAAACGTAGTCATCGGGTCTTACCCGGACA
1 AAATCTCCACACGTAGTCATCGGGTCTTACCCGGACA
*
13346442 TAATCTCCACACGTAGTCATCGGGTCTTACCCGGA
1 AAATCTCCACACGTAGTCATCGGGTCTTACCCGGA
13346477 ATATATTTCC
Statistics
Matches: 65, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
37 65 1.00
ACGTcount: A:0.28, C:0.29, G:0.19, T:0.24
Consensus pattern (37 bp):
AAATCTCCACACGTAGTCATCGGGTCTTACCCGGACA
Found at i:13346678 original size:48 final size:48
Alignment explanation
Indices: 13346623--13348786 Score: 3710
Period size: 48 Copynumber: 45.0 Consensus size: 48
13346613 ACACATCGCC
13346623 TACATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCTCA
1 TACATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCTCA
*
13346671 TACATATTTCACACTAGCCATTCGGCTTTACCACATATACATATCTCATA
1 TACATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCTC--A
* * *
13346721 TATATATTTCACATT-GACCATTCGGCTTTCCCACATATGCATATCTCA
1 TACATATTTCACATTAG-CCATTCGGCTTTACCACATATACATATCTCA
13346769 TACATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCTCA
1 TACATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCTCA
*
13346817 TACATATTTCACACTAGCCATTCGGCTTTACCACATATACATATCTCA
1 TACATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCTCA
*
13346865 TACATATTTCACACTAGCCATTCGGCTTTACCACATATACATATCTCA
1 TACATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCTCA
*
13346913 TACATATTTCACACTAGCCATTCGGCTTTACCACATATACATATCTCA
1 TACATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCTCA
*
13346961 TACATATTTCACACTAGCCATTCGGCTTTACCACATATACATATCTCA
1 TACATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCTCA
*
13347009 TACATATTTCACACTAGCCATTCGGCTTTACCACATATACATATCTCA
1 TACATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCTCA
*
13347057 TACATATTTCACACTAGCCATTCGGCTTTACCACATATACATATCTCA
1 TACATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCTCA
* *
13347105 TACATATTTCACACTAGCCATTCGGCTTTACCGCATAT-C---TCAT-A
1 TACATATTTCACATTAGCCATTCGGCTTTACCACATATACATATC-TCA
* * *
13347149 TATATATATCACATTAGCCATTCGGCTTTACCACATATGCATATCTCA
1 TACATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCTCA
*
13347197 TACATATTTCACACTAGCCATTCGGCTTTACCACATATACATATCTCA
1 TACATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCTCA
*
13347245 TACATATTTCACACTAGCCATTCGGCTTTACCACATATACATATCTCA
1 TACATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCTCA
*
13347293 TACATATTTCACACTAGCCATTCGGCTTTACCACATATACATATCTCA
1 TACATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCTCA
*
13347341 TACATATTTCACACTAGCCATTCGGCTTTACCACATATACATATCTCA
1 TACATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCTCA
*
13347389 TACATATTTCACACTAGCCATTCGGCTTTACCACATATACATATCTCA
1 TACATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCTCA
*
13347437 TACATATTTCACACTAGCCATTCGGCTTTACCACATATACATATCTCA
1 TACATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCTCA
*
13347485 TACATATTTCACACTAGCCATTCGGCTTTACCACATATACATATCTCA
1 TACATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCTCA
*
13347533 TACATATTTCACACTAGCCATTCGGCTTTACCACATATACATATCTCA
1 TACATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCTCA
*
13347581 TACATATTTCACACTAGCCATTCGGCTTTACCACATATACATATCTCA
1 TACATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCTCA
*
13347629 TACATATTTCACACTAGCCATTCGGCTTTACCACATATACATATCTCA
1 TACATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCTCA
*
13347677 TACATATTTCACATTAGCCATTCGGCTTTACCACATATGCATATCTCA
1 TACATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCTCA
* *
13347725 TACATATTTCACATTAGCCATTCGACTTTACCACATACACATATCTCATATA
1 TACATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCTC----A
* * *
13347777 TATATATTTCACATTAACCATTCAGCTTTACCACATATACATATCTCA
1 TACATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCTCA
*
13347825 TACATATTTCACATTAGCTATTCGGCTTTACCACATATACATATCTCA
1 TACATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCTCA
*
13347873 TACATATTTCACATTAGCTATTCGGCTTTACCACATATACATATCTCA
1 TACATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCTCA
* *
13347921 TACATATTTCACATTAGCCATTCGGCTTTACCATATATGCATATCTCA
1 TACATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCTCA
*
13347969 TACATATTTCACATTAGCCACTCGGCTTTACCACATATACATATCTCA
1 TACATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCTCA
* *
13348017 TATATATATCACATTAGCCATTCGGCCAGCTTTACCACATATACATATCTCA
1 TACATATTTCACATTAGCCATTC-G---GCTTTACCACATATACATATCTCA
*
13348069 TACATATTTCACATTAGCCATTCGGCTTTACCACATATGCATATCTCA
1 TACATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCTCA
*
13348117 TACATATTTCACATTAGCCATTCGGCTTTACCACATATGCATATCTCA
1 TACATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCTCA
*
13348165 TACATATTTCACATTAGCCATTCGGCTTTACCACATATGCATATCTCA
1 TACATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCTCA
*
13348213 TACATATTTCACATTAGCCATTCGGCTTTACCACATATGCATATCTCA
1 TACATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCTCA
*
13348261 TACATATTTCACATTAGCCATTCGGCTTTACCACATATGCATATCTCA
1 TACATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCTCA
*
13348309 TACATATTTCACATTAGCCATTCGGCTTTACCACATATGCATATCTCA
1 TACATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCTCA
*
13348357 TACATATTTCACATTAGCCATTCGGCTTTACCACATATGCATATCTCA
1 TACATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCTCA
*
13348405 TACATATTTCACATTAGCCATTCGGCTTTACCACATATGCATATCTCA
1 TACATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCTCA
*
13348453 TACATATTTCACATTAGCCATTCGGCTTTACCACATATGCATATCTCA
1 TACATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCTCA
*
13348501 TACATATTTCACATTAGCCATTCGGCTTTACCACATATGCATATCTCA
1 TACATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCTCA
*
13348549 TACATATTTCACATTAGCCATTCGGCTTTACCACATATGCATATCTCA
1 TACATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCTCA
*
13348597 TACATATTTCACATTAGCCATTCGGCTTTACCACATATGCATATCTCA
1 TACATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCTCA
*
13348645 TACATATTTCACATTAGCCATTCGGCTTTACCACATATGCATATCTCA
1 TACATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCTCA
*
13348693 TACATATTTCACATTAGCCATTCGGCTTTACCACATATGCATATCTCA
1 TACATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCTCA
13348741 TACATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCT
1 TACATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCT
13348787 TGTGGATGAA
Statistics
Matches: 2053, Mismatches: 45, Indels: 36
0.96 0.02 0.02
Matches are distributed among these distances:
44 37 0.02
45 2 0.00
47 2 0.00
48 1878 0.91
49 3 0.00
50 42 0.02
51 1 0.00
52 88 0.04
ACGTcount: A:0.31, C:0.28, G:0.07, T:0.35
Consensus pattern (48 bp):
TACATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCTCA
Found at i:13350073 original size:40 final size:39
Alignment explanation
Indices: 13349989--13350173 Score: 185
Period size: 40 Copynumber: 4.6 Consensus size: 39
13349979 TTGAATGATG
* * * *
13349989 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATA
1 TCCGGGCTAAGT-CCGAAGGCATTTGTGC-GAGTTACTAAA
* * *
13350029 TCCGGACTAAGATCCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGCTAAG-TCCGAAGGCATTTGTGCGAGTTACTAAA
* * *
13350069 TCCGGGCTAAGCCCGAAGGCATTTGTGAGGGTTACTAAA
1 TCCGGGCTAAGTCCGAAGGCATTTGTGCGAGTTACTAAA
* *
13350108 TCCGGGTTAAGTCCGGAAGGCAATTGTGCGAGTTACTATAA
1 TCCGGGCTAAGTCC-GAAGGCATTTGTGCGAGTTACTA-AA
*
13350149 -CCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGT-CCGAAGGCATTTG
13350174 AACGAGTAGC
Statistics
Matches: 119, Mismatches: 21, Indels: 10
0.79 0.14 0.07
Matches are distributed among these distances:
39 35 0.29
40 72 0.61
41 12 0.10
ACGTcount: A:0.25, C:0.22, G:0.29, T:0.25
Consensus pattern (39 bp):
TCCGGGCTAAGTCCGAAGGCATTTGTGCGAGTTACTAAA
Found at i:13350195 original size:79 final size:78
Alignment explanation
Indices: 13349990--13350196 Score: 183
Period size: 79 Copynumber: 2.6 Consensus size: 78
13349980 TGAATGATGT
* * * * *
13349990 CCGGGCTAAGTCCCGAAGGC-TTTGTGCTA-AGTGACCATATCCGGACTAAGATCCGAAGGCATT
1 CCGGGCTAAG-CCCGAAGGCATTTGT--AAGAGTTACTATATCCGG-TTAAGATCCGAAGGCAAT
*
13350053 TGTGCGAGATACTAATT
62 TGTGCGAGATACTAATA
* * *
13350070 CCGGGCTAAGCCCGAAGGCATTTGTGAGGGTTACTAAATCCGGGTTAAG-TCCGGAAGGCAATTG
1 CCGGGCTAAGCCCGAAGGCATTTGTAAGAGTTACTATATCC-GGTTAAGATCC-GAAGGCAATTG
*
13350134 TGCGAGTTACT-ATAA
64 TGCGAGATACTAAT-A
*
13350149 CCGGGCTATGTCCCGAAGGCATTTG-AACGAG-TAGCTATATCCGGTTAA
1 CCGGGCTAAG-CCCGAAGGCATTTGTAA-GAGTTA-CTATATCCGGTTAA
13350197 ATTCTGAAGG
Statistics
Matches: 106, Mismatches: 13, Indels: 17
0.78 0.10 0.12
Matches are distributed among these distances:
78 6 0.06
79 60 0.57
80 40 0.38
ACGTcount: A:0.26, C:0.21, G:0.28, T:0.25
Consensus pattern (78 bp):
CCGGGCTAAGCCCGAAGGCATTTGTAAGAGTTACTATATCCGGTTAAGATCCGAAGGCAATTGTG
CGAGATACTAATA
Found at i:13357440 original size:49 final size:49
Alignment explanation
Indices: 13357319--13357879 Score: 945
Period size: 49 Copynumber: 11.6 Consensus size: 49
13357309 CCCTTCGGGA
* * * **
13357319 CTTATCACAT-T-TATGCACTTTCACATCCATCACATCGGCCACTCGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAAGC
* *
13357366 CCTGTCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAAGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAAGC
**
13357413 CTTATCACGCATATATACACTTTCACATTCATCACATCGGCCATTAAGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAAGC
* *
13357462 CTTATCACATATATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAAGC
* *
13357511 CTTATCGC--ACATATACACTTTCACATTCATCACATCGGCCATTAAGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAAGC
* *
13357558 CTTATCGCATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAAGC
13357607 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAAGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAAGC
13357656 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAAGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAAGC
13357705 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAAGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAAGC
13357754 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAAGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAAGC
13357803 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAAGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAAGC
13357852 CTTATCACATATATATACACTTTCACAT
1 CTTATCACATATATATACACTTTCACAT
13357880 ATTTAGAATT
Statistics
Matches: 487, Mismatches: 21, Indels: 10
0.94 0.04 0.02
Matches are distributed among these distances:
46 1 0.00
47 87 0.18
49 399 0.82
ACGTcount: A:0.31, C:0.30, G:0.07, T:0.32
Consensus pattern (49 bp):
CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAAGC
Found at i:13362606 original size:39 final size:40
Alignment explanation
Indices: 13362506--13362690 Score: 191
Period size: 40 Copynumber: 4.7 Consensus size: 40
13362496 TTGAATGATG
* * * *
13362506 TCCGGGCTAAGTCCCAAAGGC-TTTGTGCTAAGTGAC-CAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAT
* *
13362545 ATCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTAAT
1 -TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAT
* *
13362586 TCCGGGCTACG-CCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAT
* *
13362625 TCCGGGTTAAGTCCCGAAGGCAATTGTGCGAGTTACT-AT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAT
* *
13362664 AACCGGGCTATGTCCCGAAGGCATTTG
1 -TCCGGGCTAAGTCCCGAAGGCATTTG
13362691 AACGAGTAGC
Statistics
Matches: 121, Mismatches: 18, Indels: 12
0.80 0.12 0.08
Matches are distributed among these distances:
39 35 0.29
40 76 0.63
41 10 0.08
ACGTcount: A:0.25, C:0.23, G:0.27, T:0.25
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAT
Found at i:13362712 original size:79 final size:79
Alignment explanation
Indices: 13362559--13362723 Score: 201
Period size: 79 Copynumber: 2.1 Consensus size: 79
13362549 GGACTAAGAT
* * **
13362559 CCGAAGGCATTTGTGCGAGATACTAATTCCGGGCTACGCCCGAAGGCATTTGTGCGAGTTACTAA
1 CCGAAGGCAATTGTGCGAGATACTAATACCGGGCTACGCCCGAAGGCATTTGAACGAGTTACTAA
*
13362624 ATCCGGGTTAAGTC
66 ATCCGGGTTAAATC
* *
13362638 CCGAAGGCAATTGTGCGAGTTACT-ATAACCGGGCTATGTCCCGAAGGCATTTGAACGAG-TAGC
1 CCGAAGGCAATTGTGCGAGATACTAAT-ACCGGGCTACG-CCCGAAGGCATTTGAACGAGTTA-C
* *
13362701 TATATCC-GGTTAAATT
63 TAAATCCGGGTTAAATC
13362717 CCGAAGG
1 CCGAAGG
13362724 TACGTGATTT
Statistics
Matches: 74, Mismatches: 9, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
78 2 0.03
79 47 0.64
80 25 0.34
ACGTcount: A:0.26, C:0.22, G:0.27, T:0.25
Consensus pattern (79 bp):
CCGAAGGCAATTGTGCGAGATACTAATACCGGGCTACGCCCGAAGGCATTTGAACGAGTTACTAA
ATCCGGGTTAAATC
Found at i:13364212 original size:48 final size:48
Alignment explanation
Indices: 13364033--13365461 Score: 2500
Period size: 48 Copynumber: 29.7 Consensus size: 48
13364023 TCCGGGGTGT
13364033 TACATATCTCATACATATTTCACATTAGCCATTCGGCTTTACCACATA
1 TACATATCTCATACATATTTCACATTAGCCATTCGGCTTTACCACATA
13364081 TACATATCTCATAC--ATTTCACATTAGCCATTCGGCTTTACCACATA
1 TACATATCTCATACATATTTCACATTAGCCATTCGGCTTTACCACATA
*
13364127 TACATATCTCATAC--ATTTCACATTAGCCATTCGGCTTTACCATATA
1 TACATATCTCATACATATTTCACATTAGCCATTCGGCTTTACCACATA
*
13364173 TGCATATCTCATACATATTTCACATTAGCCATTCGGCTTTACCACATA
1 TACATATCTCATACATATTTCACATTAGCCATTCGGCTTTACCACATA
*
13364221 TACATATCTCATAC--ATTTCACATTAGCCATTCGGCTTTACCATATA
1 TACATATCTCATACATATTTCACATTAGCCATTCGGCTTTACCACATA
*
13364267 TGCATATCTCATACATATTTCACATTAGCCATTCGGCTTTACCACATA
1 TACATATCTCATACATATTTCACATTAGCCATTCGGCTTTACCACATA
*
13364315 TACATATCTCATAC--ATTTCACATTAGCCATTCGGCTTTACCATATA
1 TACATATCTCATACATATTTCACATTAGCCATTCGGCTTTACCACATA
*
13364361 TGCATATCTCATACATATTTCACATTAGCCATTCGGCTTTACCACATA
1 TACATATCTCATACATATTTCACATTAGCCATTCGGCTTTACCACATA
*
13364409 TACATATCTCATAC--ATTTCACATTAGCCATTCGGCTTTACCATATA
1 TACATATCTCATACATATTTCACATTAGCCATTCGGCTTTACCACATA
*
13364455 TGCATATCTCATACATATTTCACATTAGCCATTCGGCTTTACCACATA
1 TACATATCTCATACATATTTCACATTAGCCATTCGGCTTTACCACATA
* * * *
13364503 TACATATCTAATATATATATATATTTCACATTAACCATTCAGCTTTACCACATA
1 TACATATC-----T-CATACATATTTCACATTAGCCATTCGGCTTTACCACATA
* * * *
13364557 TACATATCTCATATATATATATTTCACATTAACCATTCAGCTTTACAACATA
1 TACATATCTC----ATACATATTTCACATTAGCCATTCGGCTTTACCACATA
* *
13364609 TACATATCTCATATATATATATTTCGCATTAGCCATTCGGCTTTACCACATA
1 TACATATCTC----ATACATATTTCACATTAGCCATTCGGCTTTACCACATA
13364661 TACATATCTCATACATATTTCACATTAGCCATTCGGCTTTACCACATA
1 TACATATCTCATACATATTTCACATTAGCCATTCGGCTTTACCACATA
13364709 TACATATCTCATACATATTTCACATTAGCCATTCGGCTTTACCACATA
1 TACATATCTCATACATATTTCACATTAGCCATTCGGCTTTACCACATA
13364757 TACATATCTCATACATATTTCACATTAGCCATTCGGCTTTACCACATA
1 TACATATCTCATACATATTTCACATTAGCCATTCGGCTTTACCACATA
13364805 TACATATCTCATACATATTTCACATTAGCCATTCGGCTTTACCACATA
1 TACATATCTCATACATATTTCACATTAGCCATTCGGCTTTACCACATA
13364853 TACATATCTCATACATATTTCACATTAGCCATTCGGCTTTACCACATA
1 TACATATCTCATACATATTTCACATTAGCCATTCGGCTTTACCACATA
13364901 TACATATCTCATACATATTTCACATTAGCCATTCGGCTTTACCACATA
1 TACATATCTCATACATATTTCACATTAGCCATTCGGCTTTACCACATA
13364949 TACATATCTCATACATATTTCACATTAGCCATTCGGCTTTACCACATA
1 TACATATCTCATACATATTTCACATTAGCCATTCGGCTTTACCACATA
13364997 TACATATCTCATACATATTTCACATTAGCCATTCGGCTTTACCACATA
1 TACATATCTCATACATATTTCACATTAGCCATTCGGCTTTACCACATA
13365045 TACATATCTCATACATATTTCACATTAGCCATTCGGCTTTACCACATA
1 TACATATCTCATACATATTTCACATTAGCCATTCGGCTTTACCACATA
13365093 TACATATCTCATACATATTTCACATTAGCCATTCGGCTTTACCACATA
1 TACATATCTCATACATATTTCACATTAGCCATTCGGCTTTACCACATA
13365141 TACATATCTCATACATATTTCACATTAGCCATTCGGCTTTACCACATA
1 TACATATCTCATACATATTTCACATTAGCCATTCGGCTTTACCACATA
13365189 TACATATCTCATACATATTTCACATTAGCCATTCGGCTTTACCACATA
1 TACATATCTCATACATATTTCACATTAGCCATTCGGCTTTACCACATA
13365237 TACATATCTCATACATATTTCACATTAGCCATTCGGCTTTACCACATA
1 TACATATCTCATACATATTTCACATTAGCCATTCGGCTTTACCACATA
13365285 TACATATCTCATACATATTTCACATTAGCCATTCGGCTTTACCACATA
1 TACATATCTCATACATATTTCACATTAGCCATTCGGCTTTACCACATA
13365333 TACATATCTCATACATATTTCACATTAGCCATTCGGCTTTACCACATA
1 TACATATCTCATACATATTTCACATTAGCCATTCGGCTTTACCACATA
13365381 TACATATCTCATACATATTTCACATTAGCCATTCGGCTTTACCACATA
1 TACATATCTCATACATATTTCACATTAGCCATTCGGCTTTACCACATA
13365429 TACATATCTCATACATATTTCACATTAGCCATT
1 TACATATCTCATACATATTTCACATTAGCCATT
13365462 TTTGTACAAA
Statistics
Matches: 1335, Mismatches: 28, Indels: 36
0.95 0.02 0.03
Matches are distributed among these distances:
46 222 0.17
48 973 0.73
49 1 0.00
52 95 0.07
53 1 0.00
54 43 0.03
ACGTcount: A:0.31, C:0.26, G:0.06, T:0.36
Consensus pattern (48 bp):
TACATATCTCATACATATTTCACATTAGCCATTCGGCTTTACCACATA
Found at i:13369540 original size:46 final size:46
Alignment explanation
Indices: 13369483--13369649 Score: 146
Period size: 46 Copynumber: 3.6 Consensus size: 46
13369473 TTGAGCATCT
*
13369483 GAACTCATTGAGTTGAGTCTGAGTTCACCTATGGATGCGAATGTCC
1 GAACTCATTGAGTTGAGTCCGAGTTCACCTATGGATGCGAATGTCC
* * *
13369529 GAACTCGTTGAGTTGAGTCCGAGTT--CGTGA-GG-TG-TAACTAGGCATCC
1 GAACTCATTGAGTTGAGTCCGAGTTCACCT-ATGGATGCGAA-T--G--TCC
* ** * *
13369576 GAACTCGTTGAGTTGAGTCCGAGTTCATTTATGGATGCGAACGCCC
1 GAACTCATTGAGTTGAGTCCGAGTTCACCTATGGATGCGAATGTCC
* *
13369622 GAGCTCATTGAGTTGAGTTCGAGTTCAC
1 GAACTCATTGAGTTGAGTCCGAGTTCAC
13369650 TTAGGGGCGG
Statistics
Matches: 97, Mismatches: 13, Indels: 22
0.73 0.10 0.17
Matches are distributed among these distances:
42 2 0.02
43 3 0.03
44 4 0.04
45 2 0.02
46 49 0.51
47 28 0.29
48 2 0.02
49 3 0.03
50 2 0.02
51 2 0.02
ACGTcount: A:0.22, C:0.20, G:0.29, T:0.29
Consensus pattern (46 bp):
GAACTCATTGAGTTGAGTCCGAGTTCACCTATGGATGCGAATGTCC
Found at i:13369636 original size:93 final size:93
Alignment explanation
Indices: 13369477--13369647 Score: 252
Period size: 93 Copynumber: 1.8 Consensus size: 93
13369467 GGATGGTTGA
* * * * *
13369477 GCATCTGAACTCATTGAGTTGAGTCTGAGTTCACCTATGGATGCGAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCATTGAGTTGAGTCCGAGTTCACCTATGGATGCGAACGCCCGAACTCATTGAGT
13369542 TGAGTCCGAGTTCGTGAGGTGTAACTAG
66 TGAGTCCGAGTTCGTGAGGTGTAACTAG
* ** *
13369570 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCATTTATGGATGCGAACGCCCGAGCTCATTGAGT
1 GCATCCGAACTCATTGAGTTGAGTCCGAGTTCACCTATGGATGCGAACGCCCGAACTCATTGAGT
*
13369635 TGAGTTCGAGTTC
66 TGAGTCCGAGTTC
13369648 ACTTAGGGGC
Statistics
Matches: 68, Mismatches: 10, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
93 68 1.00
ACGTcount: A:0.22, C:0.20, G:0.29, T:0.30
Consensus pattern (93 bp):
GCATCCGAACTCATTGAGTTGAGTCCGAGTTCACCTATGGATGCGAACGCCCGAACTCATTGAGT
TGAGTCCGAGTTCGTGAGGTGTAACTAG
Found at i:13369913 original size:19 final size:20
Alignment explanation
Indices: 13369876--13369913 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
13369866 ATAAGGTGGT
13369876 AAGATGATGAATGATGTTTA
1 AAGATGATGAATGATGTTTA
13369896 AAGATG-TGATAT-ATGTTT
1 AAGATGATGA-ATGATGTTT
13369914 TGGTGGTACC
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.37, C:0.00, G:0.24, T:0.39
Consensus pattern (20 bp):
AAGATGATGAATGATGTTTA
Found at i:13371061 original size:42 final size:43
Alignment explanation
Indices: 13370968--13371110 Score: 148
Period size: 42 Copynumber: 3.3 Consensus size: 43
13370958 TGGGGGCGTT
* * * *
13370968 ACATGGTCTTATATGTAATCAAATATCGATGCCATTGTCCCAA
1 ACATGGTCTTACACGAAATCAAATATCGATGCCAATGTCCCAA
* * * * *
13371011 ATAAGGTCTTACACGAAATCATATA-CGATACCAATGTCCCAG
1 ACATGGTCTTACACGAAATCAAATATCGATGCCAATGTCCCAA
13371053 ACATGGTCTTACACGTAAATCACGAAT-T-GATGCCAATGTCCCAA
1 ACATGGTCTTACACG-AAATCA--AATATCGATGCCAATGTCCCAA
*
13371097 ACGTGGTCTTACAC
1 ACATGGTCTTACAC
13371111 AATAACACAT
Statistics
Matches: 81, Mismatches: 15, Indels: 7
0.79 0.15 0.07
Matches are distributed among these distances:
42 27 0.33
43 25 0.31
44 27 0.33
45 2 0.02
ACGTcount: A:0.34, C:0.24, G:0.15, T:0.27
Consensus pattern (43 bp):
ACATGGTCTTACACGAAATCAAATATCGATGCCAATGTCCCAA
Found at i:13374159 original size:56 final size:56
Alignment explanation
Indices: 13374099--13374288 Score: 308
Period size: 56 Copynumber: 3.4 Consensus size: 56
13374089 CTAGACAGGT
* *
13374099 TCTTACTCGTAAACACATATCGGAATCACATATCGATGCCAACATATTAAACATGG
1 TCTTACTCGCAAACACATATCGGAATCACATATCGATGCCAACATATTAAACGTGG
*
13374155 TCTTACTCGCACACACATATCGGAATCACATATCGATGCCAACATATTAAACGTGG
1 TCTTACTCGCAAACACATATCGGAATCACATATCGATGCCAACATATTAAACGTGG
* * *
13374211 TCTTAGTCGCACACACATATCGGAATCACATATCGATGCCAACGTATTAAACGTGG
1 TCTTACTCGCAAACACATATCGGAATCACATATCGATGCCAACATATTAAACGTGG
* *
13374267 TCTTACTCGTAATCACATATCG
1 TCTTACTCGCAAACACATATCG
13374289 ATGCTAATGT
Statistics
Matches: 125, Mismatches: 9, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
56 125 1.00
ACGTcount: A:0.34, C:0.25, G:0.14, T:0.27
Consensus pattern (56 bp):
TCTTACTCGCAAACACATATCGGAATCACATATCGATGCCAACATATTAAACGTGG
Found at i:13374201 original size:27 final size:27
Alignment explanation
Indices: 13374113--13374201 Score: 69
Period size: 27 Copynumber: 3.2 Consensus size: 27
13374103 ACTCGTAAAC
13374113 ACATATCGGAATCACATATCGATGCCA
1 ACATATCGGAATCACATATCGATGCCA
* * *
13374140 ACATAT--TAA--ACATGGTCTTACTCGCACA
1 ACATATCGGAATCACAT-ATC-GA-T-GC-CA
13374168 CACATATCGGAATCACATATCGATGCCA
1 -ACATATCGGAATCACATATCGATGCCA
13374196 ACATAT
1 ACATAT
13374202 TAAACGTGGT
Statistics
Matches: 46, Mismatches: 6, Indels: 20
0.64 0.08 0.28
Matches are distributed among these distances:
23 4 0.09
24 2 0.04
25 3 0.07
26 1 0.02
27 14 0.30
28 4 0.09
29 8 0.17
30 1 0.02
31 3 0.07
32 2 0.04
33 4 0.09
ACGTcount: A:0.37, C:0.26, G:0.12, T:0.25
Consensus pattern (27 bp):
ACATATCGGAATCACATATCGATGCCA
Found at i:13374282 original size:43 final size:43
Alignment explanation
Indices: 13374234--13374418 Score: 217
Period size: 43 Copynumber: 4.3 Consensus size: 43
13374224 CACATATCGG
** *
13374234 AATCACATATCGATGCCAACGTATTAAACGTGGTCTTACTCGT
1 AATCACATATCGATGCCAACGTCCTAAACGTGGTCTTACACGT
* * * * *
13374277 AATCACATATCGATGCTAATGTCTTAGACATGGTCTTACACGT
1 AATCACATATCGATGCCAACGTCCTAAACGTGGTCTTACACGT
** * * *
13374320 AATCACATATCGATTTCAACATCCCAAATGTGGTCTTACACGT
1 AATCACATATCGATGCCAACGTCCTAAACGTGGTCTTACACGT
** * *
13374363 AATCACCGATCGATGCCAACGTCCTAGACGTGGTCTTACACAT
1 AATCACATATCGATGCCAACGTCCTAAACGTGGTCTTACACGT
13374406 AATCACATATCGA
1 AATCACATATCGA
13374419 AAATCCTATG
Statistics
Matches: 115, Mismatches: 27, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
43 115 1.00
ACGTcount: A:0.31, C:0.25, G:0.15, T:0.29
Consensus pattern (43 bp):
AATCACATATCGATGCCAACGTCCTAAACGTGGTCTTACACGT
Found at i:13377791 original size:34 final size:34
Alignment explanation
Indices: 13377748--13377816 Score: 120
Period size: 34 Copynumber: 2.0 Consensus size: 34
13377738 ATTCTTTTAT
* *
13377748 TGTTATTGTAATGGGCTAAGGCTCACGCTGATAC
1 TGTTATTGTAATGGGCTAAGGCCCACGCTAATAC
13377782 TGTTATTGTAATGGGCTAAGGCCCACGCTAATAC
1 TGTTATTGTAATGGGCTAAGGCCCACGCTAATAC
13377816 T
1 T
13377817 AGACTGTTAC
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 33 1.00
ACGTcount: A:0.25, C:0.19, G:0.25, T:0.32
Consensus pattern (34 bp):
TGTTATTGTAATGGGCTAAGGCCCACGCTAATAC
Found at i:13383874 original size:41 final size:41
Alignment explanation
Indices: 13383817--13383898 Score: 128
Period size: 41 Copynumber: 2.0 Consensus size: 41
13383807 GGTAAACAAC
* * *
13383817 ACCCGATTAGAACCTTATTTTGATGAGATTGATAGCAGGAA
1 ACCCGATTAAAACCTTATTTTGATGAGATTAACAGCAGGAA
*
13383858 ACCCGTTTAAAACCTTATTTTGATGAGATTAACAGCAGGAA
1 ACCCGATTAAAACCTTATTTTGATGAGATTAACAGCAGGAA
13383899 TGAGAAGTAT
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
41 37 1.00
ACGTcount: A:0.35, C:0.16, G:0.20, T:0.29
Consensus pattern (41 bp):
ACCCGATTAAAACCTTATTTTGATGAGATTAACAGCAGGAA
Found at i:13384731 original size:21 final size:21
Alignment explanation
Indices: 13384707--13384779 Score: 110
Period size: 21 Copynumber: 3.5 Consensus size: 21
13384697 GGGTACTGTT
13384707 TAGCCACCGATAGGTTTTCTG
1 TAGCCACCGATAGGTTTTCTG
13384728 TAGCCACCGATAGGTTTTCTG
1 TAGCCACCGATAGGTTTTCTG
* * *
13384749 TAGCCACCGAGAGGTGTTCAG
1 TAGCCACCGATAGGTTTTCTG
*
13384770 CAGCCACCGA
1 TAGCCACCGA
13384780 GAGGCCATGG
Statistics
Matches: 48, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 48 1.00
ACGTcount: A:0.22, C:0.27, G:0.26, T:0.25
Consensus pattern (21 bp):
TAGCCACCGATAGGTTTTCTG
Found at i:13387191 original size:27 final size:28
Alignment explanation
Indices: 13387025--13387178 Score: 247
Period size: 28 Copynumber: 5.5 Consensus size: 28
13387015 CATGAGATTG
* * * *
13387025 GCACTAAGTGTGCGGGTTTAAATTGTACA
1 GCACTAAGTGTGCGAGTTT-GATTATATA
13387054 GCACTAAGTGTGCGAGTTTGATTATATA
1 GCACTAAGTGTGCGAGTTTGATTATATA
13387082 GCACTAAGTGTGCGAGTTTGATTATATA
1 GCACTAAGTGTGCGAGTTTGATTATATA
13387110 GCACTAAGTGTGCGAGTTTGATTATATA
1 GCACTAAGTGTGCGAGTTTGATTATATA
13387138 GCACTAAGTGTGCGAG-TTGATTATATA
1 GCACTAAGTGTGCGAGTTTGATTATATA
*
13387165 GCACTGAGTGTGCG
1 GCACTAAGTGTGCG
13387179 GACTTAATAT
Statistics
Matches: 120, Mismatches: 5, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
27 24 0.20
28 78 0.65
29 18 0.15
ACGTcount: A:0.27, C:0.12, G:0.27, T:0.33
Consensus pattern (28 bp):
GCACTAAGTGTGCGAGTTTGATTATATA
Found at i:13387499 original size:27 final size:28
Alignment explanation
Indices: 13387415--13387512 Score: 171
Period size: 28 Copynumber: 3.5 Consensus size: 28
13387405 TAAATTGTAC
*
13387415 AGCACTAGGTGTGCGAGTTTGATTATAT
1 AGCACTAAGTGTGCGAGTTTGATTATAT
13387443 AGCACTAAGTGTGCGAGTTTGATTATAT
1 AGCACTAAGTGTGCGAGTTTGATTATAT
13387471 AGCACTAAGTGTGCGAG-TTGATTATAT
1 AGCACTAAGTGTGCGAGTTTGATTATAT
*
13387498 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
13387513 GACTTAATAT
Statistics
Matches: 68, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
27 24 0.35
28 44 0.65
ACGTcount: A:0.27, C:0.12, G:0.29, T:0.33
Consensus pattern (28 bp):
AGCACTAAGTGTGCGAGTTTGATTATAT
Found at i:13387523 original size:27 final size:27
Alignment explanation
Indices: 13387415--13387525 Score: 134
Period size: 28 Copynumber: 4.0 Consensus size: 27
13387405 TAAATTGTAC
* *
13387415 AGCACTAGGTGTGCGAGTTTGATTATAT
1 AGCACTAAGTGTGCGA-CTTGATTATAT
*
13387443 AGCACTAAGTGTGCGAGTTTGATTATAT
1 AGCACTAAGTGTGCGA-CTTGATTATAT
*
13387471 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGACTTGATTATAT
* *
13387498 AGCACTGAGTGTGCGGACTT-AATATAT
1 AGCACTAAGTGTGC-GACTTGATTATAT
13387525 A
1 A
13387526 CTTTTGAATC
Statistics
Matches: 77, Mismatches: 5, Indels: 3
0.91 0.06 0.04
Matches are distributed among these distances:
27 30 0.39
28 47 0.61
ACGTcount: A:0.29, C:0.12, G:0.26, T:0.33
Consensus pattern (27 bp):
AGCACTAAGTGTGCGACTTGATTATAT
Found at i:13387690 original size:334 final size:334
Alignment explanation
Indices: 13387081--13387741 Score: 1313
Period size: 334 Copynumber: 2.0 Consensus size: 334
13387071 TTGATTATAT
13387081 AGCACTAAGTGTGCGAGTTTGATTATATAGCACTAAGTGTGCGAGTTTGATTATATAGCACTAAG
1 AGCACTAAGTGTGCGAGTTTGATTATATAGCACTAAGTGTGCGAGTTTGATTATATAGCACTAAG
13387146 TGTGCGAGTTGATTATATAGCACTGAGTGTGCGGACTTAATATATACTTTTGAATCACTATGGAC
66 TGTGCGAGTTGATTATATAGCACTGAGTGTGCGGACTTAATATATACTTTTGAATCACTATGGAC
13387211 ACTAAGTGTGCGACATTATTGAGTTGATATCGGACAGCGGATCGGGTAAGTACCTTGAGTTCATG
131 ACTAAGTGTGCGACATTATTGAGTTGATATCGGACAGCGGATCGGGTAAGTACCTTGAGTTCATG
13387276 GCTAATAGGCGCTATGTTTATATTTGGAGTTGAGCTTGGTAAGTTTGAACCTATGTGACAATCAT
196 GCTAATAGGCGCTATGTTTATATTTGGAGTTGAGCTTGGTAAGTTTGAACCTATGTGACAATCAT
13387341 AATTGAAGTCACGTACATAAGATTTATTGTGGAATAGGTGAAAGGTCGTTTAGTTGTATGATTGT
261 AATTGAAGTCACGTACATAAGATTTATTGTGGAATAGGTGAAAGGTCGTTTAGTTGTATGATTGT
13387406 AAATTGTAC
326 AAATTGTAC
*
13387415 AGCACTAGGTGTGCGAGTTTGATTATATAGCACTAAGTGTGCGAGTTTGATTATATAGCACTAAG
1 AGCACTAAGTGTGCGAGTTTGATTATATAGCACTAAGTGTGCGAGTTTGATTATATAGCACTAAG
13387480 TGTGCGAGTTGATTATATAGCACTGAGTGTGCGGACTTAATATATACTTTTGAATCACTATGGAC
66 TGTGCGAGTTGATTATATAGCACTGAGTGTGCGGACTTAATATATACTTTTGAATCACTATGGAC
13387545 ACTAAGTGTGCGACATTATTGAGTTGATATCGGACAGCGGATCGGGTAAGTACCTTGAGTTCATG
131 ACTAAGTGTGCGACATTATTGAGTTGATATCGGACAGCGGATCGGGTAAGTACCTTGAGTTCATG
13387610 GCTAATAGGCGCTATGTTTATATTTGGAGTTGAGCTTGGTAAGTTTGAACCTATGTGACAATCAT
196 GCTAATAGGCGCTATGTTTATATTTGGAGTTGAGCTTGGTAAGTTTGAACCTATGTGACAATCAT
13387675 AATTGAAGTCACGTACATAAGATTTATTGTGGAATAGGTGAAAGGTCGTTTAGTTGTATGATTGT
261 AATTGAAGTCACGTACATAAGATTTATTGTGGAATAGGTGAAAGGTCGTTTAGTTGTATGATTGT
13387740 AA
326 AA
13387742 CGAAAATACA
Statistics
Matches: 326, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
334 326 1.00
ACGTcount: A:0.29, C:0.12, G:0.25, T:0.34
Consensus pattern (334 bp):
AGCACTAAGTGTGCGAGTTTGATTATATAGCACTAAGTGTGCGAGTTTGATTATATAGCACTAAG
TGTGCGAGTTGATTATATAGCACTGAGTGTGCGGACTTAATATATACTTTTGAATCACTATGGAC
ACTAAGTGTGCGACATTATTGAGTTGATATCGGACAGCGGATCGGGTAAGTACCTTGAGTTCATG
GCTAATAGGCGCTATGTTTATATTTGGAGTTGAGCTTGGTAAGTTTGAACCTATGTGACAATCAT
AATTGAAGTCACGTACATAAGATTTATTGTGGAATAGGTGAAAGGTCGTTTAGTTGTATGATTGT
AAATTGTAC
Found at i:13395421 original size:56 final size:56
Alignment explanation
Indices: 13395324--13395449 Score: 182
Period size: 55 Copynumber: 2.2 Consensus size: 56
13395314 CATGAGATTG
* * *
13395324 GCACTAAGTGTGCGGGTTTAAATTGTACAGCACTAAGTGTGCGAGTTTGATTATGTA
1 GCACTAAGTGTGCGAGTTTAAATTATACAGCACTAAGTGTGCGAG-TTGATTATATA
* *
13395381 GCACTAAGTGTGCGAGTTT-GATTATATAGCACTAAGTGTGCGAGTTGATTATATA
1 GCACTAAGTGTGCGAGTTTAAATTATACAGCACTAAGTGTGCGAGTTGATTATATA
*
13395436 GCACTGAGTGTGCG
1 GCACTAAGTGTGCG
13395450 GACTTAATAT
Statistics
Matches: 63, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
55 23 0.37
56 22 0.35
57 18 0.29
ACGTcount: A:0.26, C:0.13, G:0.29, T:0.33
Consensus pattern (56 bp):
GCACTAAGTGTGCGAGTTTAAATTATACAGCACTAAGTGTGCGAGTTGATTATATA
Found at i:13395436 original size:27 final size:28
Alignment explanation
Indices: 13395324--13395449 Score: 182
Period size: 28 Copynumber: 4.5 Consensus size: 28
13395314 CATGAGATTG
* * * *
13395324 GCACTAAGTGTGCGGGTTTAAATTGTACA
1 GCACTAAGTGTGCGAGTTT-GATTATATA
*
13395353 GCACTAAGTGTGCGAGTTTGATTATGTA
1 GCACTAAGTGTGCGAGTTTGATTATATA
13395381 GCACTAAGTGTGCGAGTTTGATTATATA
1 GCACTAAGTGTGCGAGTTTGATTATATA
13395409 GCACTAAGTGTGCGAG-TTGATTATATA
1 GCACTAAGTGTGCGAGTTTGATTATATA
*
13395436 GCACTGAGTGTGCG
1 GCACTAAGTGTGCG
13395450 GACTTAATAT
Statistics
Matches: 90, Mismatches: 7, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
27 24 0.27
28 48 0.53
29 18 0.20
ACGTcount: A:0.26, C:0.13, G:0.29, T:0.33
Consensus pattern (28 bp):
GCACTAAGTGTGCGAGTTTGATTATATA
Found at i:13395460 original size:27 final size:27
Alignment explanation
Indices: 13395352--13395462 Score: 116
Period size: 28 Copynumber: 4.0 Consensus size: 27
13395342 TAAATTGTAC
* * *
13395352 AGCACTAAGTGTGCGAGTTTGATTATGT
1 AGCACTAAGTGTGCGA-CTTGAATATAT
* *
13395380 AGCACTAAGTGTGCGAGTTTGATTATAT
1 AGCACTAAGTGTGCGA-CTTGAATATAT
* *
13395408 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGACTTGAATATAT
*
13395435 AGCACTGAGTGTGCGGACTT-AATATAT
1 AGCACTAAGTGTGC-GACTTGAATATAT
13395462 A
1 A
13395463 CTTTTGAATC
Statistics
Matches: 77, Mismatches: 5, Indels: 3
0.91 0.06 0.04
Matches are distributed among these distances:
27 30 0.39
28 47 0.61
ACGTcount: A:0.29, C:0.12, G:0.26, T:0.33
Consensus pattern (27 bp):
AGCACTAAGTGTGCGACTTGAATATAT
Found at i:13406022 original size:13 final size:13
Alignment explanation
Indices: 13406006--13406048 Score: 56
Period size: 13 Copynumber: 3.5 Consensus size: 13
13405996 ACCGTGTGTC
13406006 ACACACGGTCGAG
1 ACACACGGTCGAG
*
13406019 ACACAC-G-C-CG
1 ACACACGGTCGAG
13406029 ACACACGGTCGAG
1 ACACACGGTCGAG
13406042 ACACACG
1 ACACACG
13406049 CCAGTGTCTC
Statistics
Matches: 25, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
10 7 0.28
11 2 0.08
12 2 0.08
13 14 0.56
ACGTcount: A:0.33, C:0.37, G:0.26, T:0.05
Consensus pattern (13 bp):
ACACACGGTCGAG
Found at i:13406032 original size:23 final size:23
Alignment explanation
Indices: 13406006--13406050 Score: 90
Period size: 23 Copynumber: 2.0 Consensus size: 23
13405996 ACCGTGTGTC
13406006 ACACACGGTCGAGACACACGCCG
1 ACACACGGTCGAGACACACGCCG
13406029 ACACACGGTCGAGACACACGCC
1 ACACACGGTCGAGACACACGCC
13406051 AGTGTCTCTA
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:0.31, C:0.40, G:0.24, T:0.04
Consensus pattern (23 bp):
ACACACGGTCGAGACACACGCCG
Found at i:13408170 original size:50 final size:50
Alignment explanation
Indices: 13408111--13408220 Score: 132
Period size: 50 Copynumber: 2.2 Consensus size: 50
13408101 CCCTCGTAGT
* * *
13408111 CAAAGCTATCTTCTT-CACAAAGTGGCCTTCACATAGTACCACACTTTGAC
1 CAAAGCTATCTT-TTACACAAAGTGGCCTGCACATAGCACCACACTGTGAC
* * * *
13408161 CAAAGCTATCTTTTACACATAGTGGCCTGCACTTAGCATCACACTGTGAT
1 CAAAGCTATCTTTTACACAAAGTGGCCTGCACATAGCACCACACTGTGAC
*
13408211 CGAAGCTATC
1 CAAAGCTATC
13408221 GAGTACACAT
Statistics
Matches: 51, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
49 2 0.04
50 49 0.96
ACGTcount: A:0.29, C:0.28, G:0.15, T:0.28
Consensus pattern (50 bp):
CAAAGCTATCTTTTACACAAAGTGGCCTGCACATAGCACCACACTGTGAC
Found at i:13408299 original size:50 final size:52
Alignment explanation
Indices: 13408222--13408358 Score: 174
Period size: 52 Copynumber: 2.7 Consensus size: 52
13408212 GAAGCTATCG
13408222 AGTACACATAGTAG-CTGCACTTAGTACTACACATGCGACCT-AACCA-TCT
1 AGTACACATAGTAGCCTGCACTTAGTACTACACATGCGACCTAAACCATTCT
* * * *
13408271 AGTACACGTAGTAGCCTGCACTTAGTACTACACACGTGACCTAAAACCATTTT
1 AGTACACATAGTAGCCTGCACTTAGTACTACACATGCGACCT-AAACCATTCT
* * *
13408324 AAT-CACATAGTAGCCTACACATAGTACTACACATG
1 AGTACACATAGTAGCCTGCACTTAGTACTACACATG
13408359 TGTTCTCACA
Statistics
Matches: 75, Mismatches: 9, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
49 13 0.17
50 25 0.33
52 33 0.44
53 4 0.05
ACGTcount: A:0.34, C:0.27, G:0.14, T:0.25
Consensus pattern (52 bp):
AGTACACATAGTAGCCTGCACTTAGTACTACACATGCGACCTAAACCATTCT
Found at i:13409531 original size:20 final size:20
Alignment explanation
Indices: 13409508--13409548 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
13409498 AAACTGTAGC
13409508 TCATCCATATAAACAATATT
1 TCATCCATATAAACAATATT
13409528 TCATCCATATAAACAATATT
1 TCATCCATATAAACAATATT
13409548 T
1 T
13409549 ATACCTGTTG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.44, C:0.20, G:0.00, T:0.37
Consensus pattern (20 bp):
TCATCCATATAAACAATATT
Found at i:13409759 original size:47 final size:47
Alignment explanation
Indices: 13409698--13409812 Score: 113
Period size: 47 Copynumber: 2.4 Consensus size: 47
13409688 AGCTCTATTG
* * ** * * * *
13409698 AGCTTAAACGGTAAGCTCTGACGAGCTGAAAATAGTAAGCTTTTACA
1 AGCTAAAACAGTAAGCTCCAACGACCTGAAAACAATAAGCTCTTACA
**
13409745 AGCTAAAACAGTAAGCTCCAACGACCTGAAAACAATAAGCTCTTATG
1 AGCTAAAACAGTAAGCTCCAACGACCTGAAAACAATAAGCTCTTACA
13409792 AGCTGAAATATCAGTAAGCTC
1 AGCT-AAA-A-CAGTAAGCTC
13409813 ATTCGAGCTG
Statistics
Matches: 55, Mismatches: 10, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
47 41 0.75
48 3 0.05
49 1 0.02
50 10 0.18
ACGTcount: A:0.39, C:0.20, G:0.18, T:0.23
Consensus pattern (47 bp):
AGCTAAAACAGTAAGCTCCAACGACCTGAAAACAATAAGCTCTTACA
Found at i:13409797 original size:24 final size:24
Alignment explanation
Indices: 13409673--13409822 Score: 110
Period size: 24 Copynumber: 6.2 Consensus size: 24
13409663 AGCTCCCCCT
** *
13409673 GAGCTGATGACAGTAAGCTC-TATT
1 GAGCTGAAAACAGTAAGCTCTTA-C
* * *
13409697 GAGCT-TAAACGGTAAGCTCTGAC
1 GAGCTGAAAACAGTAAGCTCTTAC
* *
13409720 GAGCTGAAAATAGTAAGCTTTTAC
1 GAGCTGAAAACAGTAAGCTCTTAC
* **
13409744 AAGCT-AAAACAGTAAGCTCCAAC
1 GAGCTGAAAACAGTAAGCTCTTAC
* * *
13409767 GACCTGAAAACAATAAGCTCTTAT
1 GAGCTGAAAACAGTAAGCTCTTAC
13409791 GAGCTGAAATATCAGTAAGCTCATT-C
1 GAGCTGAAA-A-CAGTAAGCTC-TTAC
13409817 GAGCTG
1 GAGCTG
13409823 TGGTGAGTCC
Statistics
Matches: 95, Mismatches: 25, Indels: 10
0.73 0.19 0.08
Matches are distributed among these distances:
23 32 0.34
24 45 0.47
25 1 0.01
26 15 0.16
27 2 0.02
ACGTcount: A:0.36, C:0.19, G:0.21, T:0.24
Consensus pattern (24 bp):
GAGCTGAAAACAGTAAGCTCTTAC
Found at i:13410340 original size:37 final size:37
Alignment explanation
Indices: 13410299--13410374 Score: 125
Period size: 37 Copynumber: 2.1 Consensus size: 37
13410289 TTAGCCGAAT
* * *
13410299 TTTCATGGAGTCCTTAGCAGCCCATGTCTTTTATTTA
1 TTTCATGGAGTCCCTAGCAGCCCATATCTTTAATTTA
13410336 TTTCATGGAGTCCCTAGCAGCCCATATCTTTAATTTA
1 TTTCATGGAGTCCCTAGCAGCCCATATCTTTAATTTA
13410373 TT
1 TT
13410375 CACACCTTTA
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
37 36 1.00
ACGTcount: A:0.21, C:0.22, G:0.14, T:0.42
Consensus pattern (37 bp):
TTTCATGGAGTCCCTAGCAGCCCATATCTTTAATTTA
Found at i:13416439 original size:85 final size:85
Alignment explanation
Indices: 13416287--13416790 Score: 983
Period size: 85 Copynumber: 5.9 Consensus size: 85
13416277 TTAACATGTA
13416287 TAACCGTGG-ATATCCACTTAGCACCACGTTAATGAATCAATATATGTAACCGTGGCATATCCAC
1 TAACCGTGGTATATCCACTTAGCACCACGTTAATGAATCAATATATGTAACCGTGGCATATCCAC
13416351 TTAGCACCACGTTACGTGCT
66 TTAGCACCACGTTACGTGCT
13416371 TAACCGTGGTATATCCACTTAGCACCACGTTAATGAATCAATATATGTAACCGTGGCATATCCAC
1 TAACCGTGGTATATCCACTTAGCACCACGTTAATGAATCAATATATGTAACCGTGGCATATCCAC
13416436 TTAGCACCACGTTACGTGCT
66 TTAGCACCACGTTACGTGCT
13416456 TAACCGTGGTATATCCACTTAGCACCACGTTAATGAATCAATATATGTAACCGTGGCATATCCAC
1 TAACCGTGGTATATCCACTTAGCACCACGTTAATGAATCAATATATGTAACCGTGGCATATCCAC
13416521 TTAGCACCACGTTACGTGCT
66 TTAGCACCACGTTACGTGCT
13416541 TAACCGTGGTATATCCACTTAGCACCACGTTAATGAATCAATATATGTAACCGTGGCATATCCAC
1 TAACCGTGGTATATCCACTTAGCACCACGTTAATGAATCAATATATGTAACCGTGGCATATCCAC
13416606 TTAGCACCACGTTACGTGCT
66 TTAGCACCACGTTACGTGCT
13416626 TAACCGTGGTATATCCACTTAGCACCACGTTAATGAATCAATATATGTAACCGTGGCATATCCAC
1 TAACCGTGGTATATCCACTTAGCACCACGTTAATGAATCAATATATGTAACCGTGGCATATCCAC
13416691 TTAGCACCACGTTACGTGCT
66 TTAGCACCACGTTACGTGCT
*
13416711 TAACCGTGGTATATCCACTTAGCACCACGTTAATGAATCAATATATGTAACCGTGCCATATCCAC
1 TAACCGTGGTATATCCACTTAGCACCACGTTAATGAATCAATATATGTAACCGTGGCATATCCAC
*
13416776 CTAGCACCACGTTAC
66 TTAGCACCACGTTAC
13416791 ATGTATCAAT
Statistics
Matches: 417, Mismatches: 2, Indels: 1
0.99 0.00 0.00
Matches are distributed among these distances:
84 9 0.02
85 408 0.98
ACGTcount: A:0.30, C:0.26, G:0.16, T:0.28
Consensus pattern (85 bp):
TAACCGTGGTATATCCACTTAGCACCACGTTAATGAATCAATATATGTAACCGTGGCATATCCAC
TTAGCACCACGTTACGTGCT
Found at i:13416821 original size:48 final size:48
Alignment explanation
Indices: 13416711--13416839 Score: 188
Period size: 48 Copynumber: 2.7 Consensus size: 48
13416701 GTTACGTGCT
13416711 TAACCGTGGTATATCCACTTAGCACCACGTTA-ATGAATCAATATATG
1 TAACCGTGGTATATCCACTTAGCACCACGTTACATGAATCAATATATG
** * * *
13416758 TAACCGTGCCATATCCACCTAGCACCACGTTACATGTATCAATATGTG
1 TAACCGTGGTATATCCACTTAGCACCACGTTACATGAATCAATATATG
* *
13416806 TAATCGTGGTGTATCCACTTAGCACCACGTTACA
1 TAACCGTGGTATATCCACTTAGCACCACGTTACA
13416840 CATATAACCA
Statistics
Matches: 71, Mismatches: 10, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
47 29 0.41
48 42 0.59
ACGTcount: A:0.30, C:0.26, G:0.16, T:0.29
Consensus pattern (48 bp):
TAACCGTGGTATATCCACTTAGCACCACGTTACATGAATCAATATATG
Found at i:13416863 original size:133 final size:131
Alignment explanation
Indices: 13416626--13416871 Score: 359
Period size: 133 Copynumber: 1.9 Consensus size: 131
13416616 GTTACGTGCT
** *
13416626 TAACCGTGGTATATCCACTTAGCACCACGTTAATGAATCAATATATGTAACCGTGGCATATCCAC
1 TAACCGTGCCATATCCACCTAGCACCACGTTAATGAATCAATATATGTAACCGTGGCATATCCAC
* *
13416691 TTAGCACCACGTTACGTGCTTAACCGTGGTATATCCACTTAGCACCACGTTAATGAATCAATATA
66 TTAGCACCACGTTACG-ACTTAACCATGGTATATCCACTTAGCACCACGTTAATGAATCAATATA
13416756 TG
130 TG
* * * **
13416758 TAACCGTGCCATATCCACCTAGCACCACGTTACATGTATCAATATGTGTAATCGTGGTGTATCCA
1 TAACCGTGCCATATCCACCTAGCACCACGTTA-ATGAATCAATATATGTAACCGTGGCATATCCA
13416823 CTTAGCACCACGTTAC-ACATATAACCATGGTATATCCACTTAGCACCAC
65 CTTAGCACCACGTTACGAC-T-TAACCATGGTATATCCACTTAGCACCAC
13416872 TTTTTTTTAT
Statistics
Matches: 101, Mismatches: 10, Indels: 5
0.87 0.09 0.04
Matches are distributed among these distances:
131 1 0.01
132 30 0.30
133 70 0.69
ACGTcount: A:0.30, C:0.26, G:0.15, T:0.28
Consensus pattern (131 bp):
TAACCGTGCCATATCCACCTAGCACCACGTTAATGAATCAATATATGTAACCGTGGCATATCCAC
TTAGCACCACGTTACGACTTAACCATGGTATATCCACTTAGCACCACGTTAATGAATCAATATAT
G
Found at i:13418598 original size:22 final size:22
Alignment explanation
Indices: 13418570--13418613 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
13418560 ATAGTAAAAC
13418570 TAGCCAGTTCATCTCAACCTCA
1 TAGCCAGTTCATCTCAACCTCA
13418592 TAGCCAGTTCATCTCAACCTCA
1 TAGCCAGTTCATCTCAACCTCA
13418614 CACTCTTTAT
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:0.27, C:0.36, G:0.09, T:0.27
Consensus pattern (22 bp):
TAGCCAGTTCATCTCAACCTCA
Found at i:13418920 original size:51 final size:50
Alignment explanation
Indices: 13418839--13418939 Score: 157
Period size: 51 Copynumber: 2.0 Consensus size: 50
13418829 TGCACATCTC
* **
13418839 ATAATGTTTAACAACGCTGTATATCACTTTCCTCTTTCAAGAGCAGGAAT
1 ATAACGTTTAACAACGCTACATATCACTTTCCTCTTTCAAGAGCAGGAAT
*
13418889 NATAACGTTTAACAACGCTACATATCACTTTCCTCTTTCAAGGGCAGGAAT
1 -ATAACGTTTAACAACGCTACATATCACTTTCCTCTTTCAAGAGCAGGAAT
13418940 GATCCAGACA
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
51 46 1.00
ACGTcount: A:0.32, C:0.22, G:0.14, T:0.32
Consensus pattern (50 bp):
ATAACGTTTAACAACGCTACATATCACTTTCCTCTTTCAAGAGCAGGAAT
Found at i:13419702 original size:15 final size:15
Alignment explanation
Indices: 13419663--13419704 Score: 57
Period size: 15 Copynumber: 2.8 Consensus size: 15
13419653 GAAGCCCAGA
*
13419663 ATAAGGAAAGCCAAG
1 ATAAGGAAATCCAAG
* *
13419678 ATAAAGAAATCCATG
1 ATAAGGAAATCCAAG
13419693 ATAAGGAAATCC
1 ATAAGGAAATCC
13419705 CATTTACAGT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.52, C:0.14, G:0.19, T:0.14
Consensus pattern (15 bp):
ATAAGGAAATCCAAG
Done.