Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr02 ID=Chr02-JGI_221_v2.0
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: 62769430
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1067035 characters in sequence are not A, C, G, or T
File 99 of 206
Found at i:28918569 original size:27 final size:25
Alignment explanation
Indices: 28918539--28918611 Score: 65
Period size: 27 Copynumber: 2.7 Consensus size: 25
28918529 AATTTCGAGG
*
28918539 TTTATAATTTTTAATTTTTATTAATT
1 TTTAT-ATTTTTAACTTTTATTAATT
* *
28918565 ATTTATGTTTTCTCACTTTTATTAATT
1 -TTTATATTTT-TAACTTTTATTAATT
28918592 TTTATTATTATTTAAACTTT
1 TTTA-TATT-TTT-AACTTT
28918612 CTTTATTTGC
Statistics
Matches: 37, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
26 8 0.22
27 22 0.59
28 7 0.19
ACGTcount: A:0.27, C:0.05, G:0.01, T:0.66
Consensus pattern (25 bp):
TTTATATTTTTAACTTTTATTAATT
Found at i:28918847 original size:43 final size:43
Alignment explanation
Indices: 28918783--28918878 Score: 138
Period size: 43 Copynumber: 2.2 Consensus size: 43
28918773 ATGATATGTT
* * *
28918783 TTTAGCGGCGTTTTTGCGAGAAGCGTCGCTAAAGATCATGGTC
1 TTTAGCGGCGCTTGTGCGAGAAGCGCCGCTAAAGATCATGGTC
* *
28918826 TTTAGCGGCGCTTGTGGGAGAAGCGCCGCTAAAGGTCATGGTC
1 TTTAGCGGCGCTTGTGCGAGAAGCGCCGCTAAAGATCATGGTC
*
28918869 TTTAGTGGCG
1 TTTAGCGGCG
28918879 TTTATTTCCA
Statistics
Matches: 47, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
43 47 1.00
ACGTcount: A:0.19, C:0.19, G:0.34, T:0.28
Consensus pattern (43 bp):
TTTAGCGGCGCTTGTGCGAGAAGCGCCGCTAAAGATCATGGTC
Found at i:28919003 original size:22 final size:22
Alignment explanation
Indices: 28918975--28919017 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
28918965 TAGTGGCGCT
*
28918975 AAAAAGCACCGCTAAAGGCCTA
1 AAAAAGCACCGCTAAAAGCCTA
*
28918997 AAAAAGCGCCGCTAAAAGCCT
1 AAAAAGCACCGCTAAAAGCCT
28919018 GCTTTGGTGT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.44, C:0.28, G:0.19, T:0.09
Consensus pattern (22 bp):
AAAAAGCACCGCTAAAAGCCTA
Found at i:28921939 original size:26 final size:26
Alignment explanation
Indices: 28921903--28921957 Score: 101
Period size: 26 Copynumber: 2.1 Consensus size: 26
28921893 ATCCTATTGT
28921903 CATGATTTTTTAAATGGTGTTAAAAA
1 CATGATTTTTTAAATGGTGTTAAAAA
*
28921929 CATGATTTTTTAAATGGTGTTAAAGA
1 CATGATTTTTTAAATGGTGTTAAAAA
28921955 CAT
1 CAT
28921958 TTCTTGTATA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.36, C:0.05, G:0.16, T:0.42
Consensus pattern (26 bp):
CATGATTTTTTAAATGGTGTTAAAAA
Found at i:28922337 original size:41 final size:41
Alignment explanation
Indices: 28922280--28922520 Score: 342
Period size: 41 Copynumber: 5.9 Consensus size: 41
28922270 GAGTTTTTGG
* * *
28922280 GGCCTTTAGCGACGTTTTTGAAAAATCGCCGCTAATGCTCG
1 GGCCTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTCT
* * *
28922321 GGCCTTTAACGGCGTTTTTGAAAAAGCGTCGCTAGTGCTCT
1 GGCCTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTCT
*
28922362 GGCCTTTAGCGGCGTTTTTCAAAAAGCGCCGCTAATGCTCT
1 GGCCTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTCT
*
28922403 GGCCTTTAGCGGCGTTTTTGAAAAAGTGCCGCTAATGCTCT
1 GGCCTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTCT
**
28922444 TTCCTTTAGCGGCGTTTTT-AAAGAAGCGCCGCTAATGCTC-
1 GGCCTTTAGCGGCGTTTTTGAAA-AAGCGCCGCTAATGCTCT
* *
28922484 GACCTTTAGTGGCGTTTTTTGAAAAAGCGCCGCTAAT
1 GGCCTTTAGCGGCG-TTTTTGAAAAAGCGCCGCTAAT
28922521 AATAATAAAA
Statistics
Matches: 179, Mismatches: 18, Indels: 6
0.88 0.09 0.03
Matches are distributed among these distances:
40 14 0.08
41 162 0.91
42 3 0.02
ACGTcount: A:0.21, C:0.23, G:0.25, T:0.31
Consensus pattern (41 bp):
GGCCTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTCT
Found at i:28927674 original size:21 final size:21
Alignment explanation
Indices: 28927659--28927713 Score: 110
Period size: 21 Copynumber: 2.6 Consensus size: 21
28927649 CAGATGCTAC
28927659 TGTAGTTACTCAAGATTGCCA
1 TGTAGTTACTCAAGATTGCCA
28927680 TGTAGTTACTCAAGATTGCCA
1 TGTAGTTACTCAAGATTGCCA
28927701 TGTAGTTACTCAA
1 TGTAGTTACTCAA
28927714 AGAAGGCAGA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.29, C:0.18, G:0.18, T:0.35
Consensus pattern (21 bp):
TGTAGTTACTCAAGATTGCCA
Found at i:28928054 original size:23 final size:22
Alignment explanation
Indices: 28928024--28928067 Score: 61
Period size: 23 Copynumber: 2.0 Consensus size: 22
28928014 CCCGTATAAT
*
28928024 GAAATTTATTTATTTATTGTTAG
1 GAAATTTAATTATTTA-TGTTAG
*
28928047 GAAATTTAATTGTTTATGTTA
1 GAAATTTAATTATTTATGTTA
28928068 ATTTATTTAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 5 0.26
23 14 0.74
ACGTcount: A:0.32, C:0.00, G:0.14, T:0.55
Consensus pattern (22 bp):
GAAATTTAATTATTTATGTTAG
Found at i:28928112 original size:13 final size:13
Alignment explanation
Indices: 28928094--28928140 Score: 51
Period size: 13 Copynumber: 3.6 Consensus size: 13
28928084 TGAATGTTGA
28928094 AATTTATTACTAT
1 AATTTATTACTAT
* **
28928107 AATTTAATGTTGA-
1 AATTTATTACT-AT
28928120 AATTTATTACTAT
1 AATTTATTACTAT
28928133 AATTTATT
1 AATTTATT
28928141 TTACTTTTAT
Statistics
Matches: 26, Mismatches: 6, Indels: 4
0.72 0.17 0.11
Matches are distributed among these distances:
12 1 0.04
13 24 0.92
14 1 0.04
ACGTcount: A:0.38, C:0.04, G:0.04, T:0.53
Consensus pattern (13 bp):
AATTTATTACTAT
Found at i:28928115 original size:26 final size:26
Alignment explanation
Indices: 28928086--28928138 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
28928076 ATTATAGGTG
28928086 AATGTTGAAATTTATTACTATAATTT
1 AATGTTGAAATTTATTACTATAATTT
28928112 AATGTTGAAATTTATTACTATAATTT
1 AATGTTGAAATTTATTACTATAATTT
28928138 A
1 A
28928139 TTTTACTTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.40, C:0.04, G:0.08, T:0.49
Consensus pattern (26 bp):
AATGTTGAAATTTATTACTATAATTT
Found at i:28928313 original size:43 final size:43
Alignment explanation
Indices: 28928242--28928551 Score: 489
Period size: 43 Copynumber: 7.3 Consensus size: 43
28928232 ATGGCACTTT
** * *
28928242 TAGCGGCGTTTGTGAAAAAAACGTCGCTAAAGGTCCTGATCTA
1 TAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCCTGATCTA
*
28928285 TAGCGGTGTTTGTGGGAAAAGCGCCGCTAAAGGTCCTGATCTA
1 TAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCCTGATCTA
*
28928328 TAGCGGTGTTTGTGGGAAAAGCGCCGCTAAAGGTCC-GATCTA
1 TAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCCTGATCTA
*
28928370 TAGCGGCGTTTGTGGGAAAAGCGCAGCTAAAGGTCCTGATCTA
1 TAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCCTGATCTA
* * *
28928413 TAGCGGTGTTTGTGGAAAAAGTGCCGCTAAAGGTCCTGATCTA
1 TAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCCTGATCTA
28928456 TAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCCTGATCTA
1 TAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCCTGATCTA
* * *
28928499 TAGCGGCGTTTTTGGG-AAAGCGCCGCTAAAGATCCTGATCTT
1 TAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCCTGATCTA
28928541 TAGCGGCGTTT
1 TAGCGGCGTTT
28928552 ATTTCTAAAA
Statistics
Matches: 249, Mismatches: 17, Indels: 3
0.93 0.06 0.01
Matches are distributed among these distances:
42 75 0.30
43 174 0.70
ACGTcount: A:0.24, C:0.19, G:0.31, T:0.26
Consensus pattern (43 bp):
TAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCCTGATCTA
Found at i:28928389 original size:85 final size:86
Alignment explanation
Indices: 28928242--28928551 Score: 489
Period size: 85 Copynumber: 3.6 Consensus size: 86
28928232 ATGGCACTTT
* * * *
28928242 TAGCGGCGTTTGTGAAAAAAACGTCGCTAAAGGTCCTGATCTATAGCGGTGTTTGTGGGAAAAGC
1 TAGCGGCGTTTGTGGAAAAAGCGCCGCTAAAGGTCCTGATCTATAGCGGCGTTTGTGGGAAAAGC
28928307 GCCGCTAAAGGTCCTGATCTA
66 GCCGCTAAAGGTCCTGATCTA
* *
28928328 TAGCGGTGTTTGTGGGAAAAGCGCCGCTAAAGGTCC-GATCTATAGCGGCGTTTGTGGGAAAAGC
1 TAGCGGCGTTTGTGGAAAAAGCGCCGCTAAAGGTCCTGATCTATAGCGGCGTTTGTGGGAAAAGC
*
28928392 GCAGCTAAAGGTCCTGATCTA
66 GCCGCTAAAGGTCCTGATCTA
* *
28928413 TAGCGGTGTTTGTGGAAAAAGTGCCGCTAAAGGTCCTGATCTATAGCGGCGTTTGTGGGAAAAGC
1 TAGCGGCGTTTGTGGAAAAAGCGCCGCTAAAGGTCCTGATCTATAGCGGCGTTTGTGGGAAAAGC
28928478 GCCGCTAAAGGTCCTGATCTA
66 GCCGCTAAAGGTCCTGATCTA
* * * *
28928499 TAGCGGCGTTTTTGG-GAAAGCGCCGCTAAAGATCCTGATCTTTAGCGGCGTTT
1 TAGCGGCGTTTGTGGAAAAAGCGCCGCTAAAGGTCCTGATCTATAGCGGCGTTT
28928552 ATTTCTAAAA
Statistics
Matches: 207, Mismatches: 16, Indels: 3
0.92 0.07 0.01
Matches are distributed among these distances:
85 115 0.56
86 92 0.44
ACGTcount: A:0.24, C:0.19, G:0.31, T:0.26
Consensus pattern (86 bp):
TAGCGGCGTTTGTGGAAAAAGCGCCGCTAAAGGTCCTGATCTATAGCGGCGTTTGTGGGAAAAGC
GCCGCTAAAGGTCCTGATCTA
Found at i:28928470 original size:128 final size:128
Alignment explanation
Indices: 28928242--28928551 Score: 489
Period size: 128 Copynumber: 2.4 Consensus size: 128
28928232 ATGGCACTTT
** * *
28928242 TAGCGGCGTTTGTGAAAAAAACGTCGCTAAAGGTCCTGATCTATAGCGGTGTTTGTGGGAAAAGC
1 TAGCGGCGTTTGTGGGAAAAGCG-CGCTAAAGGTCCTGATCTATAGCGGTGTTTGTGGAAAAAGC
*
28928307 GCCGCTAAAGGTCCTGATCTATAGCGGTGTTTGTGGGAAAAGCGCCGCTAAAGGTCC-GATCTA
65 GCCGCTAAAGGTCCTGATCTATAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCCTGATCTA
*
28928370 TAGCGGCGTTTGTGGGAAAAGCGCAGCTAAAGGTCCTGATCTATAGCGGTGTTTGTGGAAAAAGT
1 TAGCGGCGTTTGTGGGAAAAGCGC-GCTAAAGGTCCTGATCTATAGCGGTGTTTGTGGAAAAAGC
28928435 GCCGCTAAAGGTCCTGATCTATAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCCTGATCTA
65 GCCGCTAAAGGTCCTGATCTATAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCCTGATCTA
* * * *
28928499 TAGCGGCGTTTTTGGG-AAAGCGCCGCTAAAGATCCTGATCTTTAGCGGCGTTT
1 TAGCGGCGTTTGTGGGAAAAGCG-CGCTAAAGGTCCTGATCTATAGCGGTGTTT
28928552 ATTTCTAAAA
Statistics
Matches: 169, Mismatches: 10, Indels: 6
0.91 0.05 0.03
Matches are distributed among these distances:
127 1 0.01
128 146 0.86
129 22 0.13
ACGTcount: A:0.24, C:0.19, G:0.31, T:0.26
Consensus pattern (128 bp):
TAGCGGCGTTTGTGGGAAAAGCGCGCTAAAGGTCCTGATCTATAGCGGTGTTTGTGGAAAAAGCG
CCGCTAAAGGTCCTGATCTATAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCCTGATCTA
Found at i:28931662 original size:27 final size:26
Alignment explanation
Indices: 28931618--28931672 Score: 65
Period size: 27 Copynumber: 2.1 Consensus size: 26
28931608 ATAAGGGTGG
* *
28931618 TCCTTAAGAGTGTGCCACGAAGGCAT
1 TCCTTAAGAGTGTGCCACCAAGGAAT
* *
28931644 TCCTTACAGAGTTTTCCACCAAGGAAT
1 TCCTTA-AGAGTGTGCCACCAAGGAAT
28931671 TC
1 TC
28931673 TTTCATGTTA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
26 6 0.25
27 18 0.75
ACGTcount: A:0.27, C:0.25, G:0.20, T:0.27
Consensus pattern (26 bp):
TCCTTAAGAGTGTGCCACCAAGGAAT
Found at i:28934099 original size:54 final size:54
Alignment explanation
Indices: 28934039--28934306 Score: 297
Period size: 54 Copynumber: 5.0 Consensus size: 54
28934029 TACCGAACCG
* * *
28934039 TGTGTCAAACTATGTAACTCACTGACTTGGTCCACACGCCCGTGTCTTAACCCA
1 TGTGTCAGACTGTGTAACTCACTGACTTGGTCCACACGCCCGTGTCTCAACCCA
* * *
28934093 TGTGTCATACCGTGTAACTCACTGACTTGGTCGACACGCCCGTGTCTCAACCCA
1 TGTGTCAGACTGTGTAACTCACTGACTTGGTCCACACGCCCGTGTCTCAACCCA
* * * *
28934147 TGTGCCAGA-TCGTGCAACTCACTGACTTGGTCCACATGCCTGTGTCTCAACCCA
1 TGTGTCAGACT-GTGTAACTCACTGACTTGGTCCACACGCCCGTGTCTCAACCCA
* * * * * * * * **
28934201 TGTGCCAGACCGTGTAACTCATTGAATTGGTCAATACGCCTGTGTCCCAACCTG
1 TGTGTCAGACTGTGTAACTCACTGACTTGGTCCACACGCCCGTGTCTCAACCCA
* **
28934255 TGTGTCAGA-TCGTGTAACTCACTGACTTGGTCTACACGCTTGTGTCTCAACC
1 TGTGTCAGACT-GTGTAACTCACTGACTTGGTCCACACGCCCGTGTCTCAACC
28934307 AGTTTGAGAC
Statistics
Matches: 181, Mismatches: 30, Indels: 6
0.83 0.14 0.03
Matches are distributed among these distances:
54 181 1.00
ACGTcount: A:0.21, C:0.31, G:0.20, T:0.28
Consensus pattern (54 bp):
TGTGTCAGACTGTGTAACTCACTGACTTGGTCCACACGCCCGTGTCTCAACCCA
Found at i:28934246 original size:108 final size:108
Alignment explanation
Indices: 28934054--28934306 Score: 353
Period size: 108 Copynumber: 2.3 Consensus size: 108
28934044 CAAACTATGT
* * * * *
28934054 AACTCACTGACTTGGTCCACACGCCCGTGTCTTAACCCATGTGTCATACCGTGTAACTCACTGAC
1 AACTCACTGACTTGGTCCACACGCCTGTGTCTCAACCCATGTGCCAGACCGTGTAACTCACTGAA
* *
28934119 TTGGTCGACACGCCCGTGTCTCAACCCATGTGCCAGATCGTGC
66 TTGGTCAACACGCCCGTGTCCCAACCCATGTGCCAGATCGTGC
* *
28934162 AACTCACTGACTTGGTCCACATGCCTGTGTCTCAACCCATGTGCCAGACCGTGTAACTCATTGAA
1 AACTCACTGACTTGGTCCACACGCCTGTGTCTCAACCCATGTGCCAGACCGTGTAACTCACTGAA
* * ** * *
28934227 TTGGTCAATACGCCTGTGTCCCAACCTGTGTGTCAGATCGTGT
66 TTGGTCAACACGCCCGTGTCCCAACCCATGTGCCAGATCGTGC
* *
28934270 AACTCACTGACTTGGTCTACACGCTTGTGTCTCAACC
1 AACTCACTGACTTGGTCCACACGCCTGTGTCTCAACC
28934307 AGTTTGAGAC
Statistics
Matches: 127, Mismatches: 18, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
108 127 1.00
ACGTcount: A:0.21, C:0.32, G:0.20, T:0.27
Consensus pattern (108 bp):
AACTCACTGACTTGGTCCACACGCCTGTGTCTCAACCCATGTGCCAGACCGTGTAACTCACTGAA
TTGGTCAACACGCCCGTGTCCCAACCCATGTGCCAGATCGTGC
Found at i:28935530 original size:11 final size:12
Alignment explanation
Indices: 28935504--28935536 Score: 50
Period size: 11 Copynumber: 2.8 Consensus size: 12
28935494 AAGTATCATC
*
28935504 TTTTTCTTTAAT
1 TTTTTATTTAAT
28935516 TTTTTATTTAA-
1 TTTTTATTTAAT
28935527 TTTTTATTTA
1 TTTTTATTTA
28935537 TATACCTAGG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
11 10 0.50
12 10 0.50
ACGTcount: A:0.21, C:0.03, G:0.00, T:0.76
Consensus pattern (12 bp):
TTTTTATTTAAT
Found at i:28940174 original size:2 final size:2
Alignment explanation
Indices: 28940167--28940199 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
28940157 AATTGGAATT
28940167 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
28940200 CATACATTAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:28940970 original size:41 final size:41
Alignment explanation
Indices: 28940828--28940964 Score: 256
Period size: 41 Copynumber: 3.3 Consensus size: 41
28940818 GCTCTGTGCT
28940828 TAGCAGGCTTAATGCCAGTGAAATAATTCAGACTTTACGTC
1 TAGCAGGCTTAATGCCAGTGAAATAATTCAGACTTTACGTC
28940869 TAGCAGGCTTAATGCCAGTGAAATAATTCAGACTTTACGTC
1 TAGCAGGCTTAATGCCAGTGAAATAATTCAGACTTTACGTC
* *
28940910 TAGCAGGCTTAATGCCGGTGAAATATTTCAGACTTTACGTC
1 TAGCAGGCTTAATGCCAGTGAAATAATTCAGACTTTACGTC
28940951 TAGCAGGCTTAATG
1 TAGCAGGCTTAATG
28940965 TCGGTGTTCT
Statistics
Matches: 94, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 94 1.00
ACGTcount: A:0.30, C:0.19, G:0.21, T:0.30
Consensus pattern (41 bp):
TAGCAGGCTTAATGCCAGTGAAATAATTCAGACTTTACGTC
Found at i:28940987 original size:41 final size:40
Alignment explanation
Indices: 28940828--28941013 Score: 230
Period size: 41 Copynumber: 4.5 Consensus size: 40
28940818 GCTCTGTGCT
*
28940828 TAGCAGGCTTAATGCCAGTGAAATAATTCAGACTTTACGTC
1 TAGCAGGCTTAATGCCGGTGAAATAA-TCAGACTTTACGTC
*
28940869 TAGCAGGCTTAATGCCAGTGAAATAATTCAGACTTTACGTC
1 TAGCAGGCTTAATGCCGGTGAAATAA-TCAGACTTTACGTC
*
28940910 TAGCAGGCTTAATGCCGGTGAAATATTTCAGACTTTACGTC
1 TAGCAGGCTTAATGCCGGTGAAATA-ATCAGACTTTACGTC
* *** * * *
28940951 TAGCAGGCTTAATGTCGGTGTTCTGAATCAGGCTTTAAGCC
1 TAGCAGGCTTAATGCCGGTGAAAT-AATCAGACTTTACGTC
28940992 TAGCAGGC-TATATGCCGGTGAA
1 TAGCAGGCTTA-ATGCCGGTGAA
28941014 TCATTTTAAA
Statistics
Matches: 129, Mismatches: 13, Indels: 6
0.87 0.09 0.04
Matches are distributed among these distances:
40 2 0.02
41 126 0.98
42 1 0.01
ACGTcount: A:0.28, C:0.19, G:0.23, T:0.30
Consensus pattern (40 bp):
TAGCAGGCTTAATGCCGGTGAAATAATCAGACTTTACGTC
Found at i:28947013 original size:21 final size:23
Alignment explanation
Indices: 28946967--28947014 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 23
28946957 GAACGAATCC
28946967 AAAATGAAATTGAGAAAAGAAAA
1 AAAATGAAATTGAGAAAAGAAAA
*
28946990 AAAAT-AAATGAGAGAAAAAGAAAA
1 AAAATGAAAT-TGAG-AAAAGAAAA
28947014 A
1 A
28947015 GAGATCGAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
22 4 0.18
23 8 0.36
24 10 0.45
ACGTcount: A:0.73, C:0.00, G:0.17, T:0.10
Consensus pattern (23 bp):
AAAATGAAATTGAGAAAAGAAAA
Found at i:28955705 original size:57 final size:57
Alignment explanation
Indices: 28955631--28955742 Score: 147
Period size: 57 Copynumber: 2.0 Consensus size: 57
28955621 TTCATTTCTT
*
28955631 ATTTTTATTTTGAAGAAAAC-AAAATTCATTTCCAAATGATTTCAT-TTCTCCATTTTC
1 ATTTTCATTTTGAAGAAAACTAAAA-TCATTTCCAAATG-TTTCATATTCTCCATTTTC
* ** *
28955688 ATTTTCATTTTGGAGAAAACTTTAATCATTTCCAAATGTTTCCTATTCTCCATTT
1 ATTTTCATTTTGAAGAAAACTAAAATCATTTCCAAATGTTTCATATTCTCCATTT
28955743 CACCATTTCT
Statistics
Matches: 48, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
56 5 0.10
57 41 0.85
58 2 0.04
ACGTcount: A:0.30, C:0.17, G:0.06, T:0.46
Consensus pattern (57 bp):
ATTTTCATTTTGAAGAAAACTAAAATCATTTCCAAATGTTTCATATTCTCCATTTTC
Found at i:28959515 original size:5 final size:5
Alignment explanation
Indices: 28959489--28959548 Score: 93
Period size: 5 Copynumber: 11.4 Consensus size: 5
28959479 TCTAAATAGT
28959489 TTTTA CTTTTA CTTTTA TTTTTA TTTTA TTTTA TTTTA TTTTA TTTTA
1 TTTTA -TTTTA -TTTTA -TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA
28959537 TTTTA TTTTA TT
1 TTTTA TTTTA TT
28959549 ATTGTGTTGA
Statistics
Matches: 53, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
5 37 0.70
6 16 0.30
ACGTcount: A:0.18, C:0.03, G:0.00, T:0.78
Consensus pattern (5 bp):
TTTTA
Found at i:28965806 original size:566 final size:563
Alignment explanation
Indices: 28964728--28965857 Score: 1947
Period size: 566 Copynumber: 2.0 Consensus size: 563
28964718 GAGTACTGTG
* *
28964728 ATGAAGAAGCAACTCTATTTTGAATTTCTGTACTAGCTTGAGGAGTTGACTTTGTTGTAGATTCT
1 ATGAAGAAGCAACTCTATTCTGAATTTCTGTACTAGCTTGAGGAGTCGACTTTGTTGTAGATTCT
*
28964793 GGATTAATTTGATGCTCCACCTACTTTTGTTGTTCTTTATTGAAAGAGTCTTTAAGAGATAAGTT
66 GGATTAATTTGATGCTCCACCTACTTTTGTTGTTCTTTATTGAAAGAGTCTGTAAGAGATAAGTT
* * *
28964858 AGGTAGCATAATAGTTTCATAAAAAACATCTATTCTAATCACAACTTTTTTATTTTTAAGACACC
131 AGGTAGCATAATAGTTTCATAAAAAACATCTATGCTAATCACAACTTTTCTATTTTCAAGACACC
28964923 ATAACTTATACCCTTTTACACTAGCTTTATAACAAAAAAAAACACATTTAATGGATCTCGGTTCT
196 ATAACTTATACCCTTTTACACTAGCTTTATAACAAAAAAAAACACATTTAATGGATCTCGGTTCT
28964988 AATTTTCCATTATCAACATGAGCATACGCAGGACACCCAAAGATATTTAAATAAGAATAATTAGC
261 AATTTTCCATTATCAACATGAGCATACGCAGGACACCCAAAGATATTTAAATAAGAATAATTAGC
* * * * *
28965053 AGGATTACCAGACCATACCTCTTGTGGAGTCTTTTTGTCAATGGCAACTAATGGAGATTGGTTGA
326 AAGATTACCAGACCATACCTCTTATGGAGTCTTTTTGTCAATGGCAACGAATGAAGATCGGTTGA
28965118 TGAAAAAGCATGCAGTAGAGGTTGCTTTGGCCCAAAACGACTTTGGTAAGTTGACATTTGACAAC
391 TGAAAAAGCATGCAGTAGAGGTTGCTTTGGCCCAAAACGACTTTGGTAAGTTGACATTTGACAAC
* *
28965183 ATACATTGAACCTTCTCCATGATCATTTTGCTCATTCGTTCTAGAACAACATTTTGCTGTGGAGT
456 ATACATTGAACCTTCTCCATGATCATTTTGCTCATTCGTTCTAGAAAAACATTTTGCTGTGAAGT
*
28965248 ATGACGAACTGTCAAGTGTCTCACGATCCCTTCTGACTTGCAC
521 ATGACGAACTGTCAAGTGTCTCACGATCCCTTCTAACTTGCAC
* *
28965291 ATGAAGAAGCAACTCTATTCTGAATTTTTGTACTGGCTTGAGGAGTCGACTTTGTTGTAGATTCT
1 ATGAAGAAGCAACTCTATTCTGAATTTCTGTACTAGCTTGAGGAGTCGACTTTGTTGTAGATTCT
28965356 GGATTAATTTGATGCTCCACCTACTTTTGTTGTTCTTTATTGAAAGAGTCTGTAAGAGATAAGTT
66 GGATTAATTTGATGCTCCACCTACTTTTGTTGTTCTTTATTGAAAGAGTCTGTAAGAGATAAGTT
* * *
28965421 AGGTAGTATAATAGTTTCATTAAAAACAATATCTCTGCTAATCACAACTTTTCTATTTTCAAGAC
131 AGGTAGCATAATAGTTTCA-T-AAAA-AACATCTATGCTAATCACAACTTTTCTATTTTCAAGAC
* * * *
28965486 TCTATAACTTATACCCTTTTACACTAGCTTTATAACCAAGAAAAACACATTTAATGGATCTCGGT
193 ACCATAACTTATACCCTTTTACACTAGCTTTATAACAAAAAAAAACACATTTAATGGATCTCGGT
* * *
28965551 TCTAATTTTCCATTATCAACATGAGCATACGTAGGACGCCCAAAGATTTTTAAATAAGAATAATT
258 TCTAATTTTCCATTATCAACATGAGCATACGCAGGACACCCAAAGATATTTAAATAAGAATAATT
*
28965616 AGCAAGATTACCAGACCATACCTCTTATGGAGTCTTTTTGTCAATGGCAACGGATGAAGATCGGT
323 AGCAAGATTACCAGACCATACCTCTTATGGAGTCTTTTTGTCAATGGCAACGAATGAAGATCGGT
28965681 TGATGAAAAAGCATGCAGTAGAGGCTT-CTTTGGCCCAAAACGACTTTGGTAAGTTGACATTTGA
388 TGATGAAAAAGCATGCAGTAGAGG-TTGCTTTGGCCCAAAACGACTTTGGTAAGTTGACATTTGA
* **
28965745 CAACATACATTGAACCTTCTCTATGATCATTTTGCTCATTCGTTCTAGAAAAATGTTTTGCTGTG
452 CAACATACATTGAACCTTCTCCATGATCATTTTGCTCATTCGTTCTAGAAAAACATTTTGCTGTG
28965810 AAGTATGACGAACTGTCAAGTGTCTCACGATCCCTTCTAACTTGCAC
517 AAGTATGACGAACTGTCAAGTGTCTCACGATCCCTTCTAACTTGCAC
28965857 A
1 A
28965858 GTTCATTAAA
Statistics
Matches: 533, Mismatches: 30, Indels: 5
0.94 0.05 0.01
Matches are distributed among these distances:
563 143 0.27
564 1 0.00
565 4 0.01
566 383 0.72
567 2 0.00
ACGTcount: A:0.31, C:0.18, G:0.17, T:0.34
Consensus pattern (563 bp):
ATGAAGAAGCAACTCTATTCTGAATTTCTGTACTAGCTTGAGGAGTCGACTTTGTTGTAGATTCT
GGATTAATTTGATGCTCCACCTACTTTTGTTGTTCTTTATTGAAAGAGTCTGTAAGAGATAAGTT
AGGTAGCATAATAGTTTCATAAAAAACATCTATGCTAATCACAACTTTTCTATTTTCAAGACACC
ATAACTTATACCCTTTTACACTAGCTTTATAACAAAAAAAAACACATTTAATGGATCTCGGTTCT
AATTTTCCATTATCAACATGAGCATACGCAGGACACCCAAAGATATTTAAATAAGAATAATTAGC
AAGATTACCAGACCATACCTCTTATGGAGTCTTTTTGTCAATGGCAACGAATGAAGATCGGTTGA
TGAAAAAGCATGCAGTAGAGGTTGCTTTGGCCCAAAACGACTTTGGTAAGTTGACATTTGACAAC
ATACATTGAACCTTCTCCATGATCATTTTGCTCATTCGTTCTAGAAAAACATTTTGCTGTGAAGT
ATGACGAACTGTCAAGTGTCTCACGATCCCTTCTAACTTGCAC
Found at i:28969634 original size:20 final size:20
Alignment explanation
Indices: 28969611--28969651 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
28969601 AATAATCTTT
*
28969611 AAAATTACAAAAAAATATAA
1 AAAATCACAAAAAAATATAA
*
28969631 AAAATCACAAAAAAATGTAA
1 AAAATCACAAAAAAATATAA
28969651 A
1 A
28969652 TAAAATTATA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.73, C:0.07, G:0.02, T:0.17
Consensus pattern (20 bp):
AAAATCACAAAAAAATATAA
Found at i:28969726 original size:22 final size:21
Alignment explanation
Indices: 28969679--28969723 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
28969669 ATGAATTTTT
*
28969679 AAATTTTTTAAAAATATGTTA
1 AAATTTTTTAAAAATATGTAA
*
28969700 TAATTTTTTAAGAAAT-TGTAA
1 AAATTTTTTAA-AAATATGTAA
28969721 AAA
1 AAA
28969724 ATTATAAAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 2
0.80 0.12 0.08
Matches are distributed among these distances:
21 16 0.80
22 4 0.20
ACGTcount: A:0.49, C:0.00, G:0.07, T:0.44
Consensus pattern (21 bp):
AAATTTTTTAAAAATATGTAA
Found at i:28969746 original size:41 final size:40
Alignment explanation
Indices: 28969687--28969789 Score: 95
Period size: 40 Copynumber: 2.6 Consensus size: 40
28969677 TTAAATTTTT
* * * *
28969687 TAAAAATATGTTATAATTTTTTAAGAAATTGTAAAAAATTA
1 TAAAAATATATTATAATTTATT-ACAAATTCTAAAAAATTA
* *
28969728 TAAAAATACTATTA-AATTTATTACAAATTCTAAAATATTG
1 TAAAAATA-TATTATAATTTATTACAAATTCTAAAAAATTA
*
28969768 TAAAAA-AT-TATAAAATTTATTA
1 TAAAAATATAT-TATAATTTATTA
28969790 GAATTCATAA
Statistics
Matches: 53, Mismatches: 6, Indels: 8
0.79 0.09 0.12
Matches are distributed among these distances:
37 1 0.02
38 3 0.06
39 10 0.19
40 20 0.38
41 15 0.28
42 4 0.08
ACGTcount: A:0.52, C:0.03, G:0.04, T:0.41
Consensus pattern (40 bp):
TAAAAATATATTATAATTTATTACAAATTCTAAAAAATTA
Found at i:28969801 original size:39 final size:39
Alignment explanation
Indices: 28969712--28969817 Score: 106
Period size: 39 Copynumber: 2.7 Consensus size: 39
28969702 ATTTTTTAAG
* * * *
28969712 AAATTGTAAAAAATTATAAAAATACTATTAAATTTATTAC
1 AAATTCTAAAAAATTGTAAAAA-ATTATAAAATTTATTAC
*
28969752 AAATTCTAAAATATTGTAAAAAATTATAAAATTTATTA-
1 AAATTCTAAAAAATTGTAAAAAATTATAAAATTTATTAC
* * * *
28969790 GAATTCATAAAAGATGGTATAAAATTAT
1 AAATTC-TAAAAAATTGTAAAAAATTAT
28969818 TGAAAGTTCT
Statistics
Matches: 56, Mismatches: 9, Indels: 3
0.82 0.13 0.04
Matches are distributed among these distances:
38 5 0.09
39 32 0.57
40 19 0.34
ACGTcount: A:0.54, C:0.04, G:0.06, T:0.37
Consensus pattern (39 bp):
AAATTCTAAAAAATTGTAAAAAATTATAAAATTTATTAC
Found at i:28970418 original size:12 final size:12
Alignment explanation
Indices: 28970401--28970425 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
28970391 GGAATAATTA
28970401 AAATTATTATTT
1 AAATTATTATTT
28970413 AAATTATTATTT
1 AAATTATTATTT
28970425 A
1 A
28970426 TTAAAATAAC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (12 bp):
AAATTATTATTT
Found at i:28987321 original size:30 final size:31
Alignment explanation
Indices: 28987270--28987330 Score: 97
Period size: 30 Copynumber: 2.0 Consensus size: 31
28987260 AAAAAGGTTA
28987270 AGAACATTCAAGGACCAAATCGAAACAAATC
1 AGAACATTCAAGGACCAAATCGAAACAAATC
* *
28987301 AGAACATTTAGGGA-CAAATCGAAACAAATC
1 AGAACATTCAAGGACCAAATCGAAACAAATC
28987331 GGACAAAAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
30 16 0.57
31 12 0.43
ACGTcount: A:0.51, C:0.20, G:0.15, T:0.15
Consensus pattern (31 bp):
AGAACATTCAAGGACCAAATCGAAACAAATC
Found at i:28988270 original size:34 final size:34
Alignment explanation
Indices: 28988223--28988309 Score: 104
Period size: 34 Copynumber: 2.6 Consensus size: 34
28988213 ACACGGTTAA
* * *
28988223 CCATCCAGCACACCAGATGA-TCGTATGAGCTAAT
1 CCATCCAGCACACCAAAT-ACTCGTATAAGCCAAT
* *
28988257 TCATCCAGTACACCAAATACTCGTATAAGCCAAT
1 CCATCCAGCACACCAAATACTCGTATAAGCCAAT
*
28988291 CCATCCAACACACCAAATA
1 CCATCCAGCACACCAAATA
28988310 AAACTATAAA
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
33 1 0.02
34 43 0.98
ACGTcount: A:0.38, C:0.32, G:0.10, T:0.20
Consensus pattern (34 bp):
CCATCCAGCACACCAAATACTCGTATAAGCCAAT
Found at i:28993938 original size:18 final size:18
Alignment explanation
Indices: 28993912--28993948 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
28993902 AGTTCGTGGG
*
28993912 TGGTGTCTAATGGATCAA
1 TGGTATCTAATGGATCAA
28993930 TGGTATCTAATGGATCAA
1 TGGTATCTAATGGATCAA
28993948 T
1 T
28993949 CCCTGCCACC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.30, C:0.11, G:0.24, T:0.35
Consensus pattern (18 bp):
TGGTATCTAATGGATCAA
Found at i:29000647 original size:15 final size:15
Alignment explanation
Indices: 29000627--29000660 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
29000617 GCTTTCAATA
*
29000627 TTTATTTTTTATTAT
1 TTTATTTTTAATTAT
*
29000642 TTTATTTTTAATTTT
1 TTTATTTTTAATTAT
29000657 TTTA
1 TTTA
29000661 AAGATTATTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (15 bp):
TTTATTTTTAATTAT
Found at i:29001136 original size:29 final size:30
Alignment explanation
Indices: 29001104--29001161 Score: 73
Period size: 30 Copynumber: 2.0 Consensus size: 30
29001094 AATTTAATTC
29001104 AAAATT-TAAAAAATAAATTTGGAAATAAA
1 AAAATTATAAAAAATAAATTTGGAAATAAA
* * * *
29001133 AAAATTATAATAACTTATTTTGGAAATAA
1 AAAATTATAAAAAATAAATTTGGAAATAA
29001162 TTTTTCATTT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
29 6 0.25
30 18 0.75
ACGTcount: A:0.59, C:0.02, G:0.07, T:0.33
Consensus pattern (30 bp):
AAAATTATAAAAAATAAATTTGGAAATAAA
Found at i:29001331 original size:26 final size:26
Alignment explanation
Indices: 29001302--29001351 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
29001292 AATTAATTTA
*
29001302 TTAAAATTTAAAAATTA-TAAAAATGT
1 TTAAAAATT-AAAATTATTAAAAATGT
*
29001328 TTAAAAATTAGAATTATTAAAAAT
1 TTAAAAATTAAAATTATTAAAAAT
29001352 ATAAAGTAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 6 0.29
26 15 0.71
ACGTcount: A:0.58, C:0.00, G:0.04, T:0.38
Consensus pattern (26 bp):
TTAAAAATTAAAATTATTAAAAATGT
Found at i:29001623 original size:13 final size:13
Alignment explanation
Indices: 29001558--29001623 Score: 53
Period size: 13 Copynumber: 5.1 Consensus size: 13
29001548 AGTTCTTCAT
29001558 TGCTTTTGAAAAG
1 TGCTTTTGAAAAG
*
29001571 TGC-TGTGAAAAAG
1 TGCTTTTG-AAAAG
* * *
29001584 TACTGTGGAAAAG
1 TGCTTTTGAAAAG
* *
29001597 TGATTTTGAGAAG
1 TGCTTTTGAAAAG
*
29001610 TGCTTTTAAAAAG
1 TGCTTTTGAAAAG
29001623 T
1 T
29001624 TTAGTTTAAA
Statistics
Matches: 38, Mismatches: 13, Indels: 4
0.69 0.24 0.07
Matches are distributed among these distances:
12 3 0.08
13 34 0.89
14 1 0.03
ACGTcount: A:0.35, C:0.06, G:0.26, T:0.33
Consensus pattern (13 bp):
TGCTTTTGAAAAG
Found at i:29001831 original size:30 final size:30
Alignment explanation
Indices: 29001792--29001853 Score: 90
Period size: 30 Copynumber: 2.1 Consensus size: 30
29001782 TTATAACTTG
* *
29001792 TTGTTAATA-TTTTAATATATAAAATATAAA
1 TTGTAAATATTTTTAAT-TAAAAAATATAAA
29001822 TTGTAAATATTTTTAATTAAAAAATATAAA
1 TTGTAAATATTTTTAATTAAAAAATATAAA
29001852 TT
1 TT
29001854 ATTTATAAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
30 22 0.76
31 7 0.24
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (30 bp):
TTGTAAATATTTTTAATTAAAAAATATAAA
Found at i:29001868 original size:31 final size:33
Alignment explanation
Indices: 29001833--29001901 Score: 90
Period size: 31 Copynumber: 2.2 Consensus size: 33
29001823 TGTAAATATT
29001833 TTTAATTAAAAAATATAAA-T-TATTTATAAA-A
1 TTTAATTAAAAAATATAAACTATATTT-TAAATA
* *
29001864 TTTAATTAGAATATATAAACTATATTTTAAATA
1 TTTAATTAAAAAATATAAACTATATTTTAAATA
29001897 TTTAA
1 TTTAA
29001902 ATATAACCAT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
31 17 0.52
32 5 0.15
33 11 0.33
ACGTcount: A:0.52, C:0.01, G:0.01, T:0.45
Consensus pattern (33 bp):
TTTAATTAAAAAATATAAACTATATTTTAAATA
Found at i:29004272 original size:14 final size:13
Alignment explanation
Indices: 29004240--29004277 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 13
29004230 AAATGTTCCC
29004240 ATTTCTTTTTTTT
1 ATTTCTTTTTTTT
29004253 ATTTCTTTTATTTT
1 ATTTCTTTT-TTTT
29004267 -TCTTCTTTTTT
1 AT-TTCTTTTTT
29004278 CATCTTCTCC
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
13 12 0.52
14 11 0.48
ACGTcount: A:0.08, C:0.11, G:0.00, T:0.82
Consensus pattern (13 bp):
ATTTCTTTTTTTT
Found at i:29004797 original size:13 final size:13
Alignment explanation
Indices: 29004778--29004810 Score: 59
Period size: 12 Copynumber: 2.6 Consensus size: 13
29004768 AGAGGAGATA
29004778 GAAAAAAATAA-G
1 GAAAAAAATAAGG
29004790 GAAAAAAATAAGG
1 GAAAAAAATAAGG
29004803 GAAAAAAA
1 GAAAAAAA
29004811 AGAAGAATTA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 11 0.55
13 9 0.45
ACGTcount: A:0.76, C:0.00, G:0.18, T:0.06
Consensus pattern (13 bp):
GAAAAAAATAAGG
Found at i:29011190 original size:46 final size:46
Alignment explanation
Indices: 29011123--29011218 Score: 167
Period size: 46 Copynumber: 2.1 Consensus size: 46
29011113 TATTAATAAG
29011123 TTAAGTCATTTAATTTGTCTAAATT-TCTACAGCAATTTAAGTTGTC
1 TTAAGTCATTTAATTTGTCTAAATTAT-TACAGCAATTTAAGTTGTC
*
29011169 TTAAGTCATTTAATTTGTCTAAATTATTACAGGAATTTAAGTTGTC
1 TTAAGTCATTTAATTTGTCTAAATTATTACAGCAATTTAAGTTGTC
29011215 TTAA
1 TTAA
29011219 ACTAATTTAT
Statistics
Matches: 48, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
46 47 0.98
47 1 0.02
ACGTcount: A:0.32, C:0.10, G:0.11, T:0.46
Consensus pattern (46 bp):
TTAAGTCATTTAATTTGTCTAAATTATTACAGCAATTTAAGTTGTC
Found at i:29019357 original size:13 final size:14
Alignment explanation
Indices: 29019339--29019367 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
29019329 AAAGCGTAAG
29019339 AATGAGG-AGAAAA
1 AATGAGGAAGAAAA
29019352 AATGAGGAAGAAAA
1 AATGAGGAAGAAAA
29019366 AA
1 AA
29019368 CATAATGCAG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 7 0.47
14 8 0.53
ACGTcount: A:0.66, C:0.00, G:0.28, T:0.07
Consensus pattern (14 bp):
AATGAGGAAGAAAA
Found at i:29021014 original size:34 final size:34
Alignment explanation
Indices: 29020975--29021043 Score: 111
Period size: 34 Copynumber: 2.0 Consensus size: 34
29020965 TCAATCTTAC
*
29020975 TTGGGTTTTAATGTTTTTAGCATGAAAGTGTTAT
1 TTGGGTTTGAATGTTTTTAGCATGAAAGTGTTAT
* *
29021009 TTGGGTTTGAATGTTTTTAGCGTGGAAGTGTTAT
1 TTGGGTTTGAATGTTTTTAGCATGAAAGTGTTAT
29021043 T
1 T
29021044 GCGGTCACTT
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
34 32 1.00
ACGTcount: A:0.20, C:0.03, G:0.28, T:0.49
Consensus pattern (34 bp):
TTGGGTTTGAATGTTTTTAGCATGAAAGTGTTAT
Found at i:29026364 original size:24 final size:24
Alignment explanation
Indices: 29026304--29026364 Score: 63
Period size: 24 Copynumber: 2.6 Consensus size: 24
29026294 TTACATATTC
29026304 AAATTAA-ATTTTAAAAATAATTA
1 AAATTAATATTTTAAAAATAATTA
* * *
29026327 ATATTAAT-TGTTTAACAATATTTA
1 AAATTAATAT-TTTAAAAATAATTA
*
29026351 AAATTTATATTTTA
1 AAATTAATATTTTA
29026365 TATAAAAATA
Statistics
Matches: 30, Mismatches: 5, Indels: 5
0.75 0.12 0.12
Matches are distributed among these distances:
23 7 0.23
24 22 0.73
25 1 0.03
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.48
Consensus pattern (24 bp):
AAATTAATATTTTAAAAATAATTA
Found at i:29028819 original size:21 final size:19
Alignment explanation
Indices: 29028779--29028822 Score: 52
Period size: 19 Copynumber: 2.2 Consensus size: 19
29028769 TTTCATCTTA
* *
29028779 TTTTTTATACTTATCGTAT
1 TTTTTTATACTTAACCTAT
29028798 TTTTTTATACTTCAACACTAT
1 TTTTTTATACTT-AAC-CTAT
29028819 TTTT
1 TTTT
29028823 ACTATTTCGA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 12 0.57
20 2 0.10
21 7 0.33
ACGTcount: A:0.23, C:0.14, G:0.02, T:0.61
Consensus pattern (19 bp):
TTTTTTATACTTAACCTAT
Found at i:29033211 original size:16 final size:18
Alignment explanation
Indices: 29033181--29033213 Score: 52
Period size: 16 Copynumber: 1.9 Consensus size: 18
29033171 GAAATTTAAG
29033181 AAAAACATAATTAATTTT
1 AAAAACATAATTAATTTT
29033199 AAAAA-ATAA-TAATTT
1 AAAAACATAATTAATTT
29033214 ATCAAAGATA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 6 0.40
17 4 0.27
18 5 0.33
ACGTcount: A:0.61, C:0.03, G:0.00, T:0.36
Consensus pattern (18 bp):
AAAAACATAATTAATTTT
Found at i:29041569 original size:26 final size:26
Alignment explanation
Indices: 29041538--29041594 Score: 69
Period size: 26 Copynumber: 2.2 Consensus size: 26
29041528 TCTTATACCT
* * *
29041538 ATTTTACCTCTAACAAAATTTTGACG
1 ATTTTACCCCTAACAAAATCTTAACG
**
29041564 ATTTTACCCCTAGTAAAATCTTAACG
1 ATTTTACCCCTAACAAAATCTTAACG
29041590 ATTTT
1 ATTTT
29041595 TCCATTGGTA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.33, C:0.19, G:0.07, T:0.40
Consensus pattern (26 bp):
ATTTTACCCCTAACAAAATCTTAACG
Found at i:29043911 original size:15 final size:15
Alignment explanation
Indices: 29043891--29043919 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
29043881 TGTATGTTGC
29043891 TTGATAACACGGTGA
1 TTGATAACACGGTGA
29043906 TTGATAACACGGTG
1 TTGATAACACGGTG
29043920 TGTGAGGCAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.31, C:0.14, G:0.28, T:0.28
Consensus pattern (15 bp):
TTGATAACACGGTGA
Found at i:29058834 original size:8 final size:8
Alignment explanation
Indices: 29058815--29058849 Score: 54
Period size: 8 Copynumber: 4.5 Consensus size: 8
29058805 AAGTTTTATA
29058815 TTTA-TTT
1 TTTATTTT
*
29058822 TTTATTCT
1 TTTATTTT
29058830 TTTATTTT
1 TTTATTTT
29058838 TTTATTTT
1 TTTATTTT
29058846 TTTA
1 TTTA
29058850 CTTAGTTTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
7 4 0.16
8 21 0.84
ACGTcount: A:0.14, C:0.03, G:0.00, T:0.83
Consensus pattern (8 bp):
TTTATTTT
Found at i:29067088 original size:18 final size:18
Alignment explanation
Indices: 29067061--29067101 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
29067051 AATCAAGATG
29067061 AAAC-TGATAAAATACGT
1 AAACATGATAAAATACGT
*
29067078 AAACATGATAAAATATGT
1 AAACATGATAAAATACGT
29067096 AAACAT
1 AAACAT
29067102 CAAGGTCAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 4 0.18
18 18 0.82
ACGTcount: A:0.56, C:0.10, G:0.10, T:0.24
Consensus pattern (18 bp):
AAACATGATAAAATACGT
Found at i:29068206 original size:45 final size:45
Alignment explanation
Indices: 29068142--29069193 Score: 1392
Period size: 45 Copynumber: 23.4 Consensus size: 45
29068132 CGAAAGAGTT
*
29068142 GGAAGACAAGATATGTTATCTTTGATCTACTTCGCTGCCAATACA
1 GGAAGACAAGATCTGTTATCTTTGATCTACTTCGCTGCCAATACA
* * * *
29068187 GGAAGACAAGATATGTTATCTTCGATCTACTTCGCTACCAATATA
1 GGAAGACAAGATCTGTTATCTTTGATCTACTTCGCTGCCAATACA
* *
29068232 GGAAGACAAGATCTGCTATCTTTGATCTACTTCGCTGCCGATACA
1 GGAAGACAAGATCTGTTATCTTTGATCTACTTCGCTGCCAATACA
* * *
29068277 GGAAGACAAGATCTGTTAT-TTTCGATATACTTCGCTACCAATATA
1 GGAAGACAAGATCTGTTATCTTT-GATCTACTTCGCTGCCAATACA
* * *
29068322 GGAAGATAAGATCTGCTATCTTTGATCTACTTCGCTGCTAGA-ACA
1 GGAAGACAAGATCTGTTATCTTTGATCTACTTCGCTGCCA-ATACA
* *
29068367 GGAAGACAAGATCTGTTATCTTTGATCTACTTCACTGCCACTACA
1 GGAAGACAAGATCTGTTATCTTTGATCTACTTCGCTGCCAATACA
* * *
29068412 GGAAGACAAGATCTGTTATCTTCGATCTACTTCGCTACCAATATA
1 GGAAGACAAGATCTGTTATCTTTGATCTACTTCGCTGCCAATACA
*
29068457 GGAAGACAAGATCTGCTATCTTTGATCTACTTCGCTGCCAATACA
1 GGAAGACAAGATCTGTTATCTTTGATCTACTTCGCTGCCAATACA
* * * * * *
29068502 GAAAGACAAAATCTGTTATCTTCGATCTACTTTGCTACCAATATA
1 GGAAGACAAGATCTGTTATCTTTGATCTACTTCGCTGCCAATACA
* * **
29068547 GGAAGACAAGATCTGCTATCTTTGATCTACTTCGCTGTCGGTACA
1 GGAAGACAAGATCTGTTATCTTTGATCTACTTCGCTGCCAATACA
* *
29068592 GGAAGACAAGATTTGTTATCTTTGATCTACTTCACTGCCAATACA
1 GGAAGACAAGATCTGTTATCTTTGATCTACTTCGCTGCCAATACA
* * **
29068637 GGAAGACAATATCTGTTATCTTCGATCTACTTCGCTGCCGGTACA
1 GGAAGACAAGATCTGTTATCTTTGATCTACTTCGCTGCCAATACA
* *
29068682 GGAAGACAAGATCTGTTATCTTTGATCTACTTCACTACCAATACA
1 GGAAGACAAGATCTGTTATCTTTGATCTACTTCGCTGCCAATACA
* * *
29068727 GGAAGACAAGATCTGTTATCTTCGATCTACTTCGCTACCAATATA
1 GGAAGACAAGATCTGTTATCTTTGATCTACTTCGCTGCCAATACA
*
29068772 GGAAGACAAGATCTGCTATCTTTGATCTACTTCGCTGCCAATACA
1 GGAAGACAAGATCTGTTATCTTTGATCTACTTCGCTGCCAATACA
* * * * * * *
29068817 GGAAGATAAGATCTATTATCTTCGATCTACTTTGCTACTAATATA
1 GGAAGACAAGATCTGTTATCTTTGATCTACTTCGCTGCCAATACA
* *
29068862 GGAAGACAAGATCTGTTATCTTTGATCTACTACGCTACCAATACA
1 GGAAGACAAGATCTGTTATCTTTGATCTACTTCGCTGCCAATACA
* * * *
29068907 AGAAGACAAAATCTGTTAT-TTTCGATCTACTTCGCTACCAATATA
1 GGAAGACAAGATCTGTTATCTTT-GATCTACTTCGCTGCCAATACA
* * * * * *
29068952 GGAAGATAAGATCTGTTATCTTCGATCTATTTTGCTACCAATATA
1 GGAAGACAAGATCTGTTATCTTTGATCTACTTCGCTGCCAATACA
*
29068997 GGAAGACAAGATCTGCTATCTTTGATCTACTTCGCTGCCAATACA
1 GGAAGACAAGATCTGTTATCTTTGATCTACTTCGCTGCCAATACA
* * * *
29069042 AGAAGACAAGATCTGTTATCTTCGATCTACTTCGCTACCAATATA
1 GGAAGACAAGATCTGTTATCTTTGATCTACTTCGCTGCCAATACA
* * *
29069087 GGAAGACAATATCTGTTAT-TTTCGATCTGCTTCACTGCCAATACA
1 GGAAGACAAGATCTGTTATCTTT-GATCTACTTCGCTGCCAATACA
* * * *
29069132 GGAAGACAATATCTGCTATTTTTGATCTACTTCGCTGCCAATATA
1 GGAAGACAAGATCTGTTATCTTTGATCTACTTCGCTGCCAATACA
29069177 GGAAGACAAGATCTGTT
1 GGAAGACAAGATCTGTT
29069194 GTTTTCACTG
Statistics
Matches: 873, Mismatches: 126, Indels: 16
0.86 0.12 0.02
Matches are distributed among these distances:
44 8 0.01
45 856 0.98
46 9 0.01
ACGTcount: A:0.31, C:0.21, G:0.16, T:0.32
Consensus pattern (45 bp):
GGAAGACAAGATCTGTTATCTTTGATCTACTTCGCTGCCAATACA
Found at i:29071603 original size:25 final size:25
Alignment explanation
Indices: 29071550--29071615 Score: 71
Period size: 25 Copynumber: 2.6 Consensus size: 25
29071540 AAGAAAATCC
* *
29071550 AAAAGAATGAAAGAATAATTATTCG
1 AAAAGAATGAAAGAATAATTACTCA
*
29071575 AAAAGAATGAAAGAAT-ATTGGCTCA
1 AAAAGAATGAAAGAATAATT-ACTCA
29071600 AAAATGAATGCAAAGA
1 AAAA-GAATG-AAAGA
29071616 TGTATTTTAT
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
24 3 0.09
25 22 0.63
26 5 0.14
27 5 0.14
ACGTcount: A:0.56, C:0.06, G:0.18, T:0.20
Consensus pattern (25 bp):
AAAAGAATGAAAGAATAATTACTCA
Found at i:29075743 original size:25 final size:24
Alignment explanation
Indices: 29075698--29075760 Score: 63
Period size: 25 Copynumber: 2.5 Consensus size: 24
29075688 TGTTATTATT
*
29075698 TATTTTAAAATTTTTCATATATAA
1 TATTTTTAAATTTTTCATATATAA
** *
29075722 TATTTTTAAATTGTTTTGTATATAG
1 TATTTTTAAATT-TTTCATATATAA
*
29075747 TTTATTTTAAATTT
1 TAT-TTTTAAATTT
29075761 CGTTTTTACA
Statistics
Matches: 32, Mismatches: 5, Indels: 3
0.80 0.12 0.08
Matches are distributed among these distances:
24 11 0.34
25 12 0.38
26 9 0.28
ACGTcount: A:0.33, C:0.02, G:0.05, T:0.60
Consensus pattern (24 bp):
TATTTTTAAATTTTTCATATATAA
Found at i:29077292 original size:11 final size:11
Alignment explanation
Indices: 29077276--29077300 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
29077266 ATGCGGAGGT
29077276 GAAAACCTCAC
1 GAAAACCTCAC
29077287 GAAAACCTCAC
1 GAAAACCTCAC
29077298 GAA
1 GAA
29077301 GGCGTAGTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.48, C:0.32, G:0.12, T:0.08
Consensus pattern (11 bp):
GAAAACCTCAC
Found at i:29078912 original size:44 final size:40
Alignment explanation
Indices: 29078823--29078912 Score: 101
Period size: 40 Copynumber: 2.1 Consensus size: 40
29078813 TTTAATATGT
* *
29078823 AAAAATATATATAAGTATGTATATAAAATTATGAAACATA
1 AAAAATATATAAAAGTATGTATATAAAATTATGAAAAATA
*
29078863 GAAAATATATAAAAGTATGTGTATATATATAATTAT-AAAAATTA
1 AAAAATATATAAAAGTA--TGTATATA-A-AATTATGAAAAA-TA
29078907 AAAAAT
1 AAAAAT
29078913 GTGTACGTAT
Statistics
Matches: 41, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
40 15 0.37
42 8 0.20
43 5 0.12
44 13 0.32
ACGTcount: A:0.58, C:0.01, G:0.08, T:0.33
Consensus pattern (40 bp):
AAAAATATATAAAAGTATGTATATAAAATTATGAAAAATA
Found at i:29079534 original size:21 final size:21
Alignment explanation
Indices: 29079508--29079562 Score: 96
Period size: 19 Copynumber: 2.7 Consensus size: 21
29079498 AATCATATCT
29079508 TCTAAGATTGCATATATCATA
1 TCTAAGATTGCATATATCATA
29079529 TCTAAGATTGC--ATATCATA
1 TCTAAGATTGCATATATCATA
29079548 TCTAAGATTGCATAT
1 TCTAAGATTGCATAT
29079563 CCTTGAAGAT
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
19 19 0.59
21 13 0.41
ACGTcount: A:0.36, C:0.15, G:0.11, T:0.38
Consensus pattern (21 bp):
TCTAAGATTGCATATATCATA
Found at i:29094064 original size:19 final size:19
Alignment explanation
Indices: 29094040--29094083 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
29094030 TAAAAGTAAC
29094040 ACAACATCAACCCAAATAA
1 ACAACATCAACCCAAATAA
* **
29094059 ACAACATGATTCCAAATAA
1 ACAACATCAACCCAAATAA
29094078 ACAACA
1 ACAACA
29094084 AAAATAATAC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.57, C:0.27, G:0.02, T:0.14
Consensus pattern (19 bp):
ACAACATCAACCCAAATAA
Found at i:29095533 original size:27 final size:29
Alignment explanation
Indices: 29095476--29095534 Score: 109
Period size: 29 Copynumber: 2.0 Consensus size: 29
29095466 TTTGTTTTAA
*
29095476 ATGTAGTGTATTTTAAAAATAAAAAATAT
1 ATGTAGTATATTTTAAAAATAAAAAATAT
29095505 ATGTAGTATATTTTAAAAATAAAAAATAT
1 ATGTAGTATATTTTAAAAATAAAAAATAT
29095534 A
1 A
29095535 GTTTTTATTC
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.54, C:0.00, G:0.08, T:0.37
Consensus pattern (29 bp):
ATGTAGTATATTTTAAAAATAAAAAATAT
Found at i:29095553 original size:9 final size:9
Alignment explanation
Indices: 29095539--29095576 Score: 58
Period size: 9 Copynumber: 4.2 Consensus size: 9
29095529 AATATAGTTT
*
29095539 TTATTCAAA
1 TTATTCGAA
29095548 TTATTCGAA
1 TTATTCGAA
*
29095557 TTATTCGAG
1 TTATTCGAA
29095566 TTATTCGAA
1 TTATTCGAA
29095575 TT
1 TT
29095577 CGAAAATTCA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.32, C:0.11, G:0.11, T:0.47
Consensus pattern (9 bp):
TTATTCGAA
Found at i:29099964 original size:14 final size:14
Alignment explanation
Indices: 29099941--29099979 Score: 60
Period size: 14 Copynumber: 2.8 Consensus size: 14
29099931 TATTCAGTAA
*
29099941 TATTAATATTAATC
1 TATTATTATTAATC
*
29099955 TATTATTATTAATT
1 TATTATTATTAATC
29099969 TATTATTATTA
1 TATTATTATTA
29099980 TCACCATTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.59
Consensus pattern (14 bp):
TATTATTATTAATC
Found at i:29106633 original size:24 final size:24
Alignment explanation
Indices: 29106589--29106634 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
29106579 AAAGATTGAA
* *
29106589 GCAAAAACTGAATAAAGAACTTTG
1 GCAAAAAATAAATAAAGAACTTTG
29106613 GCAAAAAATAAATGAAA-AACTT
1 GCAAAAAATAAAT-AAAGAACTT
29106635 CACGCTATTT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
24 16 0.84
25 3 0.16
ACGTcount: A:0.57, C:0.11, G:0.13, T:0.20
Consensus pattern (24 bp):
GCAAAAAATAAATAAAGAACTTTG
Found at i:29119087 original size:41 final size:41
Alignment explanation
Indices: 29118986--29119089 Score: 145
Period size: 41 Copynumber: 2.5 Consensus size: 41
29118976 AATTATTGTA
* *
29118986 TGAATTGCACATGTGTGCCCCTGTTTGTACTTTAGTACCCC
1 TGAATTGCACATGTGTGCCCCTGTTCGTACTTCAGTACCCC
* * *
29119027 TAAATTGCACATGTATGCCCCTGTTCGTACTTCGGTACCCC
1 TGAATTGCACATGTGTGCCCCTGTTCGTACTTCAGTACCCC
**
29119068 TGAATTGCACATACGTGCCCCT
1 TGAATTGCACATGTGTGCCCCT
29119090 ATACAAACAA
Statistics
Matches: 54, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
41 54 1.00
ACGTcount: A:0.19, C:0.30, G:0.18, T:0.33
Consensus pattern (41 bp):
TGAATTGCACATGTGTGCCCCTGTTCGTACTTCAGTACCCC
Found at i:29121289 original size:32 final size:32
Alignment explanation
Indices: 29121248--29121317 Score: 131
Period size: 32 Copynumber: 2.2 Consensus size: 32
29121238 GGCCAACAAA
29121248 GAACATGCATGGTTATTACTATACAGGAAAAT
1 GAACATGCATGGTTATTACTATACAGGAAAAT
*
29121280 GAACATGCATGGTTATTACTATACAGGATAAT
1 GAACATGCATGGTTATTACTATACAGGAAAAT
29121312 GAACAT
1 GAACAT
29121318 AAAAGCTCAA
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 37 1.00
ACGTcount: A:0.40, C:0.13, G:0.19, T:0.29
Consensus pattern (32 bp):
GAACATGCATGGTTATTACTATACAGGAAAAT
Found at i:29124898 original size:75 final size:75
Alignment explanation
Indices: 29124676--29124886 Score: 332
Period size: 75 Copynumber: 2.8 Consensus size: 75
29124666 AATTTCACGT
* * * * * *
29124676 TCCCTCTCTTGATCGCGTTCACTCTCGTGTCTCCTCAACCTACTACTGCTTCTCTCTCTCCTATC
1 TCCCTCTCTAGCTCACGATCACTCTCGTGCCTCCTCGACCTACTACTGCTTCTCTCTCTCCTATC
29124741 TCTCTCCCGC
66 TCTCTCCCGC
*
29124751 TCCCTCTCTAGCTCACGATCACTCTCGTGCCTCCTCGACCTACTACTGCTCCTCTCTCTCCTATC
1 TCCCTCTCTAGCTCACGATCACTCTCGTGCCTCCTCGACCTACTACTGCTTCTCTCTCTCCTATC
*
29124816 TCTCTCCCGT
66 TCTCTCCCGC
* *
29124826 TCCCTCTCTATCTCACGATCACTTTCGTGCCTCCTCGACCTACTACTGCTTCTCTCTCTCC
1 TCCCTCTCTAGCTCACGATCACTCTCGTGCCTCCTCGACCTACTACTGCTTCTCTCTCTCC
29124887 GGTCTATCTC
Statistics
Matches: 125, Mismatches: 11, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
75 125 1.00
ACGTcount: A:0.10, C:0.45, G:0.09, T:0.36
Consensus pattern (75 bp):
TCCCTCTCTAGCTCACGATCACTCTCGTGCCTCCTCGACCTACTACTGCTTCTCTCTCTCCTATC
TCTCTCCCGC
Found at i:29124923 original size:20 final size:20
Alignment explanation
Indices: 29124898--29124956 Score: 69
Period size: 20 Copynumber: 3.3 Consensus size: 20
29124888 GTCTATCTCC
29124898 CTCTCTTTCTCCTTTTCCTT
1 CTCTCTTTCTCCTTTTCCTT
29124918 CTCTCTTTC-CC---TCC-T
1 CTCTCTTTCTCCTTTTCCTT
29124933 CTCTC--TCTCCTTTTCCTT
1 CTCTCTTTCTCCTTTTCCTT
29124951 CTCTCT
1 CTCTCT
29124957 CCTATCCCTC
Statistics
Matches: 33, Mismatches: 0, Indels: 13
0.72 0.00 0.28
Matches are distributed among these distances:
13 2 0.06
14 2 0.06
15 6 0.18
16 3 0.09
17 3 0.09
18 6 0.18
19 2 0.06
20 9 0.27
ACGTcount: A:0.00, C:0.46, G:0.00, T:0.54
Consensus pattern (20 bp):
CTCTCTTTCTCCTTTTCCTT
Found at i:29124935 original size:33 final size:33
Alignment explanation
Indices: 29124895--29125035 Score: 128
Period size: 33 Copynumber: 4.3 Consensus size: 33
29124885 CCGGTCTATC
29124895 TCCCTCTCTTTCTCCTTTTCCTTCTCTCT--T-
1 TCCCTCTCTTTCTCCTTTTCCTTCTCTCTCCTA
29124925 TCCCTCCTCTCTCTCTCCTTTTCCTTCTCTCTCCTA
1 TCCCT-CTCT-T-TCTCCTTTTCCTTCTCTCTCCTA
* * * * *
29124961 TCCCTCTCTTTCTCCTTATCTTTTTCTCTTCTT
1 TCCCTCTCTTTCTCCTTTTCCTTCTCTCTCCTA
* * * * *
29124994 TCTCTCTCCCTT-TCCTTCTCCCTCTCTCTGCTA
1 TCCCTCT-CTTTCTCCTTTTCCTTCTCTCTCCTA
29125027 TCCCTCTCT
1 TCCCTCTCT
29125036 CTGCTACCCC
Statistics
Matches: 89, Mismatches: 15, Indels: 12
0.77 0.13 0.10
Matches are distributed among these distances:
30 5 0.06
31 4 0.04
32 2 0.02
33 64 0.72
34 4 0.04
35 5 0.06
36 5 0.06
ACGTcount: A:0.02, C:0.45, G:0.01, T:0.52
Consensus pattern (33 bp):
TCCCTCTCTTTCTCCTTTTCCTTCTCTCTCCTA
Found at i:29124969 original size:66 final size:66
Alignment explanation
Indices: 29124895--29125035 Score: 176
Period size: 66 Copynumber: 2.1 Consensus size: 66
29124885 CCGGTCTATC
* * * *
29124895 TCCCTCTCTTTCTCCTTTTCCTTCTCTCTTTCCCTC-CTCTCTCTCTCCTTTTCCTTCTCTCTCC
1 TCCCTCTCTTTCTCCTTATCCTTCTCTC-TTCCCTCTCTCTCCCTCTCCTTCTCCCTCTCTCTCC
29124959 TA
65 TA
* * ** * *
29124961 TCCCTCTCTTTCTCCTTATCTTTTTCTCTTCTTTCTCTCTCCCTTTCCTTCTCCCTCTCTCTGCT
1 TCCCTCTCTTTCTCCTTATCCTTCTCTCTTCCCTCTCTCTCCCTCTCCTTCTCCCTCTCTCTCCT
29125026 A
66 A
29125027 TCCCTCTCT
1 TCCCTCTCT
29125036 CTGCTACCCC
Statistics
Matches: 64, Mismatches: 10, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
65 5 0.08
66 59 0.92
ACGTcount: A:0.02, C:0.45, G:0.01, T:0.52
Consensus pattern (66 bp):
TCCCTCTCTTTCTCCTTATCCTTCTCTCTTCCCTCTCTCTCCCTCTCCTTCTCCCTCTCTCTCCT
A
Found at i:29125032 original size:15 final size:15
Alignment explanation
Indices: 29125012--29125053 Score: 66
Period size: 15 Copynumber: 2.7 Consensus size: 15
29125002 CCTTTCCTTC
29125012 TCCCTCTCTCTGCTA
1 TCCCTCTCTCTGCTA
29125027 TCCCTCTCTCTGCTA
1 TCCCTCTCTCTGCTA
*
29125042 CCCCTCCTCTCT
1 TCCCT-CTCTCT
29125054 AAATCCTTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
15 19 0.76
16 6 0.24
ACGTcount: A:0.05, C:0.52, G:0.05, T:0.38
Consensus pattern (15 bp):
TCCCTCTCTCTGCTA
Found at i:29130147 original size:23 final size:23
Alignment explanation
Indices: 29130118--29130179 Score: 81
Period size: 23 Copynumber: 2.7 Consensus size: 23
29130108 GCCCGGCCCG
* *
29130118 TTTTTAATTAAAATTAAAATTAT
1 TTTTTAATTAAAATTAAAACTAA
*
29130141 TTTTTAAATAAAATTAAAACTAA
1 TTTTTAATTAAAATTAAAACTAA
*
29130164 TTGTT-ATTAAAATTAA
1 TTTTTAATTAAAATTAA
29130180 TTGTTAGTAA
Statistics
Matches: 34, Mismatches: 5, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
22 10 0.29
23 24 0.71
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.47
Consensus pattern (23 bp):
TTTTTAATTAAAATTAAAACTAA
Found at i:29130192 original size:16 final size:16
Alignment explanation
Indices: 29130155--29130194 Score: 62
Period size: 16 Copynumber: 2.5 Consensus size: 16
29130145 TAAATAAAAT
* *
29130155 TAAAACTAATTGTTAT
1 TAAAATTAATTGTTAG
29130171 TAAAATTAATTGTTAG
1 TAAAATTAATTGTTAG
29130187 TAAAATTA
1 TAAAATTA
29130195 TCAAATTATT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.47, C:0.03, G:0.07, T:0.42
Consensus pattern (16 bp):
TAAAATTAATTGTTAG
Found at i:29130273 original size:59 final size:63
Alignment explanation
Indices: 29130210--29130451 Score: 357
Period size: 68 Copynumber: 3.7 Consensus size: 63
29130200 TTATTAATTG
29130210 TTAATTGTATTAATTGTTGTAATAAAATCTAACATTTGATTAGTAAATTTATCAAATTATTAATT
1 TTAATTGTATTAATTGTTGTAATAAAATCTAACATTTGATTAGTAAATTTATC--A--A-TAATT
29130275 GTA
61 GTA
29130278 TTAATTGTATTAATTGTTGTAATAAAATCTAACATTTGATTAGTAAATTTATCAAATTATTAATT
1 TTAATTGTATTAATTGTTGTAATAAAATCTAACATTTGATTAGTAAATTTATC--A--A-TAATT
29130343 GTA
61 GTA
29130346 TTAATTGTATTAATTGTTGTAATAAAATCTAACATTTGATTAGTAAATTTATC-A-AA-T-TA
1 TTAATTGTATTAATTGTTGTAATAAAATCTAACATTTGATTAGTAAATTTATCAATAATTGTA
*
29130405 TTAATTGTATTAATTGTTGTAACAAAATCTAACATTTGATTAGTAAA
1 TTAATTGTATTAATTGTTGTAATAAAATCTAACATTTGATTAGTAAA
29130452 ACAAACTTGA
Statistics
Matches: 173, Mismatches: 1, Indels: 9
0.95 0.01 0.05
Matches are distributed among these distances:
59 48 0.28
60 1 0.01
61 2 0.01
63 1 0.01
68 121 0.70
ACGTcount: A:0.40, C:0.05, G:0.09, T:0.46
Consensus pattern (63 bp):
TTAATTGTATTAATTGTTGTAATAAAATCTAACATTTGATTAGTAAATTTATCAATAATTGTA
Found at i:29130300 original size:9 final size:9
Alignment explanation
Indices: 29130267--29130294 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
29130257 TTTATCAAAT
29130267 TATTAATTG
1 TATTAATTG
29130276 TATTAATTG
1 TATTAATTG
29130285 TATTAATTG
1 TATTAATTG
29130294 T
1 T
29130295 TGTAATAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.32, C:0.00, G:0.11, T:0.57
Consensus pattern (9 bp):
TATTAATTG
Found at i:29130304 original size:68 final size:68
Alignment explanation
Indices: 29130183--29130421 Score: 455
Period size: 68 Copynumber: 3.5 Consensus size: 68
29130173 AAATTAATTG
*
29130183 TTAGTAAAATTATCAAATTATTAATTG--TTAATTGTATTAATTGTTGTAATAAAATCTAACATT
1 TTAGTAAATTTATCAAATTATTAATTGTATTAATTGTATTAATTGTTGTAATAAAATCTAACATT
29130246 TGA
66 TGA
29130249 TTAGTAAATTTATCAAATTATTAATTGTATTAATTGTATTAATTGTTGTAATAAAATCTAACATT
1 TTAGTAAATTTATCAAATTATTAATTGTATTAATTGTATTAATTGTTGTAATAAAATCTAACATT
29130314 TGA
66 TGA
29130317 TTAGTAAATTTATCAAATTATTAATTGTATTAATTGTATTAATTGTTGTAATAAAATCTAACATT
1 TTAGTAAATTTATCAAATTATTAATTGTATTAATTGTATTAATTGTTGTAATAAAATCTAACATT
29130382 TGA
66 TGA
29130385 TTAGTAAATTTATCAAATTATTAATTGTATTAATTGT
1 TTAGTAAATTTATCAAATTATTAATTGTATTAATTGT
29130422 TGTAACAAAA
Statistics
Matches: 170, Mismatches: 1, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
66 26 0.15
68 144 0.85
ACGTcount: A:0.40, C:0.04, G:0.09, T:0.47
Consensus pattern (68 bp):
TTAGTAAATTTATCAAATTATTAATTGTATTAATTGTATTAATTGTTGTAATAAAATCTAACATT
TGA
Found at i:29130368 original size:9 final size:9
Alignment explanation
Indices: 29130335--29130362 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
29130325 TTTATCAAAT
29130335 TATTAATTG
1 TATTAATTG
29130344 TATTAATTG
1 TATTAATTG
29130353 TATTAATTG
1 TATTAATTG
29130362 T
1 T
29130363 TGTAATAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.32, C:0.00, G:0.11, T:0.57
Consensus pattern (9 bp):
TATTAATTG
Found at i:29132782 original size:7 final size:7
Alignment explanation
Indices: 29132770--29132853 Score: 109
Period size: 7 Copynumber: 12.0 Consensus size: 7
29132760 AAATAATTTT
29132770 AAAAATA
1 AAAAATA
29132777 AAAAAT-
1 AAAAATA
29132783 AAAAAT-
1 AAAAATA
29132789 AAAAATA
1 AAAAATA
* *
29132796 AAAGTATTT
1 AAA--AATA
*
29132805 TAAAATA
1 AAAAATA
29132812 AAAAATA
1 AAAAATA
29132819 AAAAATA
1 AAAAATA
29132826 AAAAATA
1 AAAAATA
29132833 AAAAATA
1 AAAAATA
29132840 AAAAATA
1 AAAAATA
29132847 AAAAATA
1 AAAAATA
29132854 TATTTTTATT
Statistics
Matches: 68, Mismatches: 6, Indels: 6
0.85 0.08 0.08
Matches are distributed among these distances:
6 12 0.18
7 52 0.76
9 4 0.06
ACGTcount: A:0.80, C:0.00, G:0.01, T:0.19
Consensus pattern (7 bp):
AAAAATA
Found at i:29138543 original size:18 final size:17
Alignment explanation
Indices: 29138495--29138544 Score: 57
Period size: 16 Copynumber: 2.9 Consensus size: 17
29138485 TTAAAATAAA
*
29138495 TATTTTATATTTAAAAT
1 TATTATATATTTAAAAT
* *
29138512 GATGATA-ATTTAAAAT
1 TATTATATATTTAAAAT
29138528 TATTATATACTTTAAAA
1 TATTATATA-TTTAAAA
29138545 ACAAAGTTGA
Statistics
Matches: 26, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
16 14 0.54
17 5 0.19
18 7 0.27
ACGTcount: A:0.46, C:0.02, G:0.04, T:0.48
Consensus pattern (17 bp):
TATTATATATTTAAAAT
Found at i:29139975 original size:40 final size:40
Alignment explanation
Indices: 29139920--29139999 Score: 160
Period size: 40 Copynumber: 2.0 Consensus size: 40
29139910 GTGTTGGCTG
29139920 AACCTTGGAAGCTTTAAAAATGGCTTCTCATGCTATGGTT
1 AACCTTGGAAGCTTTAAAAATGGCTTCTCATGCTATGGTT
29139960 AACCTTGGAAGCTTTAAAAATGGCTTCTCATGCTATGGTT
1 AACCTTGGAAGCTTTAAAAATGGCTTCTCATGCTATGGTT
29140000 TTCTAATTTT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 40 1.00
ACGTcount: A:0.28, C:0.17, G:0.20, T:0.35
Consensus pattern (40 bp):
AACCTTGGAAGCTTTAAAAATGGCTTCTCATGCTATGGTT
Found at i:29145771 original size:8 final size:8
Alignment explanation
Indices: 29145758--29145784 Score: 54
Period size: 8 Copynumber: 3.4 Consensus size: 8
29145748 GAGAGGTATG
29145758 AAACCTCT
1 AAACCTCT
29145766 AAACCTCT
1 AAACCTCT
29145774 AAACCTCT
1 AAACCTCT
29145782 AAA
1 AAA
29145785 TGGTGGAGGG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 19 1.00
ACGTcount: A:0.44, C:0.33, G:0.00, T:0.22
Consensus pattern (8 bp):
AAACCTCT
Found at i:29149095 original size:15 final size:16
Alignment explanation
Indices: 29149075--29149104 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
29149065 TTTAAATAGC
29149075 ATTTTAATG-TATTTG
1 ATTTTAATGCTATTTG
29149090 ATTTTAATGCTATTT
1 ATTTTAATGCTATTT
29149105 TGTCATATTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.27, C:0.03, G:0.10, T:0.60
Consensus pattern (16 bp):
ATTTTAATGCTATTTG
Found at i:29149870 original size:12 final size:12
Alignment explanation
Indices: 29149853--29149884 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
29149843 CTTGTCGGAG
29149853 ATCCATCACACT
1 ATCCATCACACT
*
29149865 ATCCATCATACT
1 ATCCATCACACT
29149877 ATCCATCA
1 ATCCATCA
29149885 GCTATATCGG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.34, C:0.38, G:0.00, T:0.28
Consensus pattern (12 bp):
ATCCATCACACT
Found at i:29152630 original size:138 final size:136
Alignment explanation
Indices: 29152232--29152655 Score: 650
Period size: 138 Copynumber: 3.1 Consensus size: 136
29152222 AGAGAACATA
* *
29152232 AATATAATGAATATATGAATTTGATTCATACAAAATATTAATTGTATATATTTTACAAAATTTAT
1 AATATAATTAATATATGAATTTGATTCATACAAAATATTAATTGTATATATTTTACCAAATTTAT
* * * * *
29152297 TAATATAAACATTTATATTAATTATTTATGTCAAAATGTAAAAGACATGGAAATAAATATTATTT
66 TAATATAAACAATTATATTAATAATTTA-GTCAAAATATAAAAGACATGGAAATTAATATTCTTT
29152362 TGGAAAG
130 TGGAAAG
* * *
29152369 AATATAATCAATATATTAATTTGATTCATACAAAATATTAATTGTATATATATTTTATCAAATTT
1 AATATAATTAATATATGAATTTGATTCATACAAAATATTAATTG--TATATATTTTACCAAATTT
29152434 ATTAATATAAACAATTATATTAATTAATTTCAGTCAAAATATAAAAGACATGGAAATTAATATTC
64 ATTAATATAAACAATTATATTAA-TAATTT-AGTCAAAATATAAAAGACATGGAAATTAATATTC
29152499 TTTTGGAAAG
127 TTTTGGAAAG
*
29152509 AATATAATTAATATATGAATTTGATTCAAACAAAATATTAATTGTATATATTTTACCAAATTTAT
1 AATATAATTAATATATGAATTTGATTCATACAAAATATTAATTGTATATATTTTACCAAATTTAT
* *
29152574 TAATATAAACAGTTATATTAATGAAGTTTAGTCAAAATATAAAAGACATAGAAATTAATATTCTT
66 TAATATAAACAATTATATTAAT-AA-TTTAGTCAAAATATAAAAGACATGGAAATTAATATTCTT
* *
29152639 TTAGAAAT
129 TTGGAAAG
29152647 AATATAATT
1 AATATAATT
29152656 CATTTTTCTA
Statistics
Matches: 264, Mismatches: 17, Indels: 11
0.90 0.06 0.04
Matches are distributed among these distances:
137 43 0.16
138 92 0.35
139 42 0.16
140 86 0.33
141 1 0.00
ACGTcount: A:0.47, C:0.05, G:0.07, T:0.40
Consensus pattern (136 bp):
AATATAATTAATATATGAATTTGATTCATACAAAATATTAATTGTATATATTTTACCAAATTTAT
TAATATAAACAATTATATTAATAATTTAGTCAAAATATAAAAGACATGGAAATTAATATTCTTTT
GGAAAG
Found at i:29156519 original size:21 final size:21
Alignment explanation
Indices: 29156493--29156539 Score: 76
Period size: 21 Copynumber: 2.2 Consensus size: 21
29156483 AGCAACGTGT
* *
29156493 ACATAACTTACAAATATGATC
1 ACATAACGTACAAATATAATC
29156514 ACATAACGTACAAATATAATC
1 ACATAACGTACAAATATAATC
29156535 ACATA
1 ACATA
29156540 TCACATAACG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.51, C:0.19, G:0.04, T:0.26
Consensus pattern (21 bp):
ACATAACGTACAAATATAATC
Found at i:29156644 original size:26 final size:26
Alignment explanation
Indices: 29156608--29156676 Score: 129
Period size: 26 Copynumber: 2.7 Consensus size: 26
29156598 TTTACATCAA
29156608 TGCTCACACGAGCTGTGAAATGGGCT
1 TGCTCACACGAGCTGTGAAATGGGCT
29156634 TGCTCACACGAGCTGTGAAATGGGCT
1 TGCTCACACGAGCTGTGAAATGGGCT
*
29156660 TGCTCACACGAGTTGTG
1 TGCTCACACGAGCTGTG
29156677 GGTCGGAATA
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
26 42 1.00
ACGTcount: A:0.22, C:0.23, G:0.30, T:0.25
Consensus pattern (26 bp):
TGCTCACACGAGCTGTGAAATGGGCT
Found at i:29158455 original size:58 final size:58
Alignment explanation
Indices: 29158393--29158715 Score: 280
Period size: 58 Copynumber: 5.6 Consensus size: 58
29158383 GAGACGGCCG
* * *
29158393 CAAAGACATCCTTTTAACATAGATAGCCATAAAGACATTCATTTAATTGAGATAGCCA
1 CAAAGGCATCCTTTTAACAGAGATAGCCATAAAGACATTCATTTAACTGAGATAGCCA
* * * * * *
29158451 CAAAGGCATCCTTTTAACAAAGATCGCCAGAAA-ATCATTCATTTAATTTAGATCA-CTA
1 CAAAGGCATCCTTTTAACAGAGATAGCCATAAAGA-CATTCATTTAACTGAGAT-AGCCA
* * * * * *
29158509 CAAAGGCATCCTTTCAACAGAGATCGACAAAAAGGCATTCATTTAACTAAGATAGCCA
1 CAAAGGCATCCTTTTAACAGAGATAGCCATAAAGACATTCATTTAACTGAGATAGCCA
* * *
29158567 CAAAGGCTTCCTTATAACAGAGATCA-CCATAAAGGCATTCATTTAACTGAGATAGCCA
1 CAAAGGCATCCTTTTAACAGAGAT-AGCCATAAAGACATTCATTTAACTGAGATAGCCA
* * * * * * *
29158625 CAAAGGCATTCATTTAACTA-AGACT-GCCACAAAGGC-TTCGTTATAACTAAGATCGCCA
1 CAAAGGCATCCTTTTAAC-AGAGA-TAGCCATAAAGACATTCATT-TAACTGAGATAGCCA
* * * * *
29158683 CAAATGCTTTCTTATAACAGAGATAGCCGTAAA
1 CAAAGGCATCCTTTTAACAGAGATAGCCATAAA
29158716 TGTGTCCATT
Statistics
Matches: 219, Mismatches: 35, Indels: 22
0.79 0.13 0.08
Matches are distributed among these distances:
57 9 0.04
58 207 0.95
59 3 0.01
ACGTcount: A:0.39, C:0.21, G:0.14, T:0.25
Consensus pattern (58 bp):
CAAAGGCATCCTTTTAACAGAGATAGCCATAAAGACATTCATTTAACTGAGATAGCCA
Found at i:29158628 original size:116 final size:114
Alignment explanation
Indices: 29158393--29158706 Score: 319
Period size: 116 Copynumber: 2.7 Consensus size: 114
29158383 GAGACGGCCG
* * * * * *
29158393 CAAAGACATCCTTTTAACATAGATAGCCATAAAGACATTCATTTAATTGAGATAGCCACAAAGGC
1 CAAAGGCATCC-TTTAACA-AGATCGCCAAAAAGGCATTCATTTAACTAAGATAGCCACAAAGGC
* * * * * * * *
29158458 ATCCTTTTAACAAAGATCGCCAGAAAATCATTCATTTAATTTAGATCACTA
64 TTCCTTATAACAGAGATCACCAGAAAAGCATTCATTTAACTGAGATCACCA
*
29158509 CAAAGGCATCCTTTCAACAGAGATCGACAAAAAGGCATTCATTTAACTAAGATAGCCACAAAGGC
1 CAAAGGCATCCTTT-AACA-AGATCGCCAAAAAGGCATTCATTTAACTAAGATAGCCACAAAGGC
* *
29158574 TTCCTTATAACAGAGATCACCATAAAGGCATTCATTTAACTGAGAT-AGCCA
64 TTCCTTATAACAGAGATCACCAGAAAAGCATTCATTTAACTGAGATCA-CCA
* * * * *
29158625 CAAAGGCATTCATTTAACTAAGA-CTGCCACAAAGGC-TTCGTTATAACTAAGATCGCCACAAAT
1 CAAAGGCA-TCCTTTAAC-AAGATC-GCCAAAAAGGCATTCATT-TAACTAAGATAGCCACAAAG
*
29158688 GCTTTCTTATAACAGAGAT
62 GCTTCCTTATAACAGAGAT
29158707 AGCCGTAAAT
Statistics
Matches: 167, Mismatches: 25, Indels: 12
0.82 0.12 0.06
Matches are distributed among these distances:
115 10 0.06
116 151 0.90
117 6 0.04
ACGTcount: A:0.39, C:0.21, G:0.14, T:0.26
Consensus pattern (114 bp):
CAAAGGCATCCTTTAACAAGATCGCCAAAAAGGCATTCATTTAACTAAGATAGCCACAAAGGCTT
CCTTATAACAGAGATCACCAGAAAAGCATTCATTTAACTGAGATCACCA
Found at i:29158630 original size:29 final size:29
Alignment explanation
Indices: 29158405--29158773 Score: 247
Period size: 29 Copynumber: 12.8 Consensus size: 29
29158395 AAGACATCCT
* *
29158405 TTTAACAT-AGATAGCCATAAAGACATTCA
1 TTTAAC-TGAGATAGCCACAAAGGCATTCA
* * *
29158434 TTTAATTGAGATAGCCACAAAGGCATCCT
1 TTTAACTGAGATAGCCACAAAGGCATTCA
** * * **
29158463 TTTAACAAAGATCGCCAGAAAATCATTCA
1 TTTAACTGAGATAGCCACAAAGGCATTCA
* * * *
29158492 TTTAATTTAGATCA-CTACAAAGGCA-TCC
1 TTTAACTGAGAT-AGCCACAAAGGCATTCA
* * * *
29158520 TTTCAACAGAGATCGACAAAAAGGCATTCA
1 TTT-AACTGAGATAGCCACAAAGGCATTCA
* *
29158550 TTTAACTAAGATAGCCACAAAGGC-TTCC
1 TTTAACTGAGATAGCCACAAAGGCATTCA
* *
29158578 TTATAACAGAGATCA-CCATAAAGGCATTCA
1 TT-TAACTGAGAT-AGCCACAAAGGCATTCA
29158608 TTTAACTGAGATAGCCACAAAGGCATTCA
1 TTTAACTGAGATAGCCACAAAGGCATTCA
* *
29158637 TTTAACTAAGACT-GCCACAAAGGC-TTCG
1 TTTAACTGAGA-TAGCCACAAAGGCATTCA
* * * *
29158665 TTATAACTAAGATCGCCACAAATGCTTTC-
1 TT-TAACTGAGATAGCCACAAAGGCATTCA
* ** * ** *
29158694 TTATAACAGAGATAGCCGTAAATGTGTCCA
1 TT-TAACTGAGATAGCCACAAAGGCATTCA
* *
29158724 -TTAA--GAGATAGCGAAAAAGGCATTCA
1 TTTAACTGAGATAGCCACAAAGGCATTCA
29158750 TTTAACTGAGATAGCCACAAAGGC
1 TTTAACTGAGATAGCCACAAAGGC
29158774 TTACGTATAC
Statistics
Matches: 260, Mismatches: 63, Indels: 34
0.73 0.18 0.10
Matches are distributed among these distances:
26 15 0.06
27 4 0.02
28 21 0.08
29 205 0.79
30 15 0.06
ACGTcount: A:0.39, C:0.20, G:0.15, T:0.25
Consensus pattern (29 bp):
TTTAACTGAGATAGCCACAAAGGCATTCA
Found at i:29164180 original size:25 final size:25
Alignment explanation
Indices: 29164110--29164194 Score: 93
Period size: 25 Copynumber: 3.4 Consensus size: 25
29164100 CCTGTACATG
*
29164110 TATGCTCATACGAGCTATGAATCGA
1 TATGCTCATACAAGCTATGAATCGA
* * *
29164135 TATGCTC-T-CATGAGTTGTGAATCGG
1 TATGCTCATACA--AGCTATGAATCGA
*
29164160 TAAGCTCATACAAGCTATGAATCGA
1 TATGCTCATACAAGCTATGAATCGA
29164185 TATGCTCATA
1 TATGCTCATA
29164195 AGAGTCGTAG
Statistics
Matches: 47, Mismatches: 9, Indels: 8
0.73 0.14 0.12
Matches are distributed among these distances:
23 1 0.02
24 1 0.02
25 42 0.89
26 1 0.02
27 2 0.04
ACGTcount: A:0.31, C:0.19, G:0.20, T:0.31
Consensus pattern (25 bp):
TATGCTCATACAAGCTATGAATCGA
Found at i:29168708 original size:20 final size:20
Alignment explanation
Indices: 29168668--29168715 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 20
29168658 CATGCTTTCT
*
29168668 ATTCAC-ATTTTCATATTTA
1 ATTCACAATTTTCAAATTTA
29168687 ATTCACAATTTT-AAATTATA
1 ATTCACAATTTTCAAATT-TA
*
29168707 ATCCACAAT
1 ATTCACAAT
29168716 CACGTTTCTT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 10 0.40
20 15 0.60
ACGTcount: A:0.40, C:0.17, G:0.00, T:0.44
Consensus pattern (20 bp):
ATTCACAATTTTCAAATTTA
Found at i:29168910 original size:38 final size:39
Alignment explanation
Indices: 29168868--29168971 Score: 104
Period size: 41 Copynumber: 2.7 Consensus size: 39
29168858 AGTTCAAAGC
*
29168868 AAAGTTGACACCTAGTGTCTCATCG-GCCTAGCCGAAGT
1 AAAGTTGACACCTAGTGTCTCATCGAACCTAGCCGAAGT
* * * * * *
29168906 AAAG-TGATACCCAGTATCTCATCGAATCTATCTGAAGT
1 AAAGTTGACACCTAGTGTCTCATCGAACCTAGCCGAAGT
*
29168944 AAAATAGTGACACCTAGTGTCTCATCGA
1 AAAGT--TGACACCTAGTGTCTCATCGA
29168972 CTCGAGGTCG
Statistics
Matches: 51, Mismatches: 11, Indels: 5
0.76 0.16 0.07
Matches are distributed among these distances:
37 17 0.33
38 16 0.31
41 18 0.35
ACGTcount: A:0.32, C:0.23, G:0.19, T:0.26
Consensus pattern (39 bp):
AAAGTTGACACCTAGTGTCTCATCGAACCTAGCCGAAGT
Found at i:29169109 original size:18 final size:17
Alignment explanation
Indices: 29169063--29169116 Score: 72
Period size: 18 Copynumber: 3.1 Consensus size: 17
29169053 TTTCCAATTC
29169063 TCAATTCAAATTCACTT
1 TCAATTCAAATTCACTT
* *
29169080 TCATTTCAAAATTTACTT
1 TCAATTC-AAATTCACTT
29169098 TCAATATCAAATTCACTT
1 TCAAT-TCAAATTCACTT
29169116 T
1 T
29169117 TTCATTCACT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
17 6 0.19
18 23 0.74
19 2 0.06
ACGTcount: A:0.35, C:0.20, G:0.00, T:0.44
Consensus pattern (17 bp):
TCAATTCAAATTCACTT
Found at i:29170111 original size:18 final size:19
Alignment explanation
Indices: 29170085--29170120 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
29170075 AAATAATAAT
*
29170085 TATTATAATAATAAATATC
1 TATTATAATAACAAATATC
29170104 TATT-TAATAACAAATAT
1 TATTATAATAACAAATAT
29170121 AAATATTACA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 12 0.75
19 4 0.25
ACGTcount: A:0.53, C:0.06, G:0.00, T:0.42
Consensus pattern (19 bp):
TATTATAATAACAAATATC
Found at i:29170254 original size:33 final size:32
Alignment explanation
Indices: 29170206--29170277 Score: 103
Period size: 33 Copynumber: 2.2 Consensus size: 32
29170196 TATTTATCCT
29170206 ATAAAA-ATCTTTTACTAATTAGTA-ATAAATA
1 ATAAAATATCTTTTACTAATTA-TATATAAATA
29170237 ATAAAATATCTTTTTACTAATTATATATAAATA
1 ATAAAATATC-TTTTACTAATTATATATAAATA
29170270 ATACAAAT
1 ATA-AAAT
29170278 GTACTCATTT
Statistics
Matches: 37, Mismatches: 0, Indels: 5
0.88 0.00 0.12
Matches are distributed among these distances:
31 6 0.16
32 5 0.14
33 22 0.59
34 4 0.11
ACGTcount: A:0.51, C:0.07, G:0.01, T:0.40
Consensus pattern (32 bp):
ATAAAATATCTTTTACTAATTATATATAAATA
Found at i:29179527 original size:14 final size:14
Alignment explanation
Indices: 29179510--29179546 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
29179500 ATAATTCAAT
29179510 AAATTAAAAAAATA
1 AAATTAAAAAAATA
**
29179524 AAATTATTAAAATA
1 AAATTAAAAAAATA
29179538 AAATTAAAA
1 AAATTAAAA
29179547 TTTAGGAGAA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (14 bp):
AAATTAAAAAAATA
Found at i:29193442 original size:20 final size:20
Alignment explanation
Indices: 29193417--29193454 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
29193407 TTGGTATATG
29193417 TATGTTTA-TGATCATTTGGT
1 TATGTTTAGTG-TCATTTGGT
29193437 TATGTTTAGTGTCATTTG
1 TATGTTTAGTGTCATTTG
29193455 ATATATGAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
20 15 0.88
21 2 0.12
ACGTcount: A:0.18, C:0.05, G:0.21, T:0.55
Consensus pattern (20 bp):
TATGTTTAGTGTCATTTGGT
Found at i:29199560 original size:16 final size:18
Alignment explanation
Indices: 29199533--29199567 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
29199523 CATTTAGTGT
29199533 ATTATATTTTAAA-AAAA
1 ATTATATTTTAAATAAAA
29199550 ATTAT-TTTTAAATAAAA
1 ATTATATTTTAAATAAAA
29199567 A
1 A
29199568 ACTAATCTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.41
17 10 0.59
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (18 bp):
ATTATATTTTAAATAAAA
Found at i:29200094 original size:5 final size:5
Alignment explanation
Indices: 29200084--29200122 Score: 78
Period size: 5 Copynumber: 7.8 Consensus size: 5
29200074 CTTACTGATT
29200084 ATATC ATATC ATATC ATATC ATATC ATATC ATATC ATAT
1 ATATC ATATC ATATC ATATC ATATC ATATC ATATC ATAT
29200123 ATTAATAGTT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 34 1.00
ACGTcount: A:0.41, C:0.18, G:0.00, T:0.41
Consensus pattern (5 bp):
ATATC
Found at i:29200200 original size:256 final size:253
Alignment explanation
Indices: 29199726--29200222 Score: 655
Period size: 253 Copynumber: 1.9 Consensus size: 253
29199716 TGAGCACCTC
* ** *
29199726 TATATGTTAATTATTATAATATATTATTGTTTATTATTATACTGGTTAAAATATGCTCTAAGTCC
1 TATATATTAATTATTATAATATATTACCGTTTATTATTATACTAGTTAAAATATGCTCTAAGT-C
* * **
29199791 CTATATTTTTCTTACATTTGAAAGTTAGCCCTCCTACTATAATGTTTTATCATATCATATAGTAT
65 CTATATTTTTCTTACATTTAAAAGTTAGCCCTCCTACTATAATATCATATCATATCATATAGTAT
** * *
29199856 ATAATATGTTAATAGTTTATATATATATATATGCATCAATGATTAAGCATTATAATATCATGTAA
130 ATAATATCATAATAGTTAATATATATATATATGCATCAATGATTAAACATTATAATATCATGTAA
*
29199921 TACTATATCTTTTATTGTAATCTATATTATAATAATAGTTATATATAATAGCAATACAT
195 TACTATATCTTTTATTATAATCTATATTATAATAATAGTTATATATAATAGCAATACAT
* *
29199980 TATATATTACTTATTAT-ATATATTACCGTTTATTATTATACTAGTTGAAATATGCTCTAAGT-C
1 TATATATTAATTATTATAATATATTACCGTTTATTATTATACTAGTTAAAATATGCTCTAAGTCC
* * *
29200043 TATATTTTTCTTACATTTAAAAGTTAGCTCTCTTACTGATTATATCATATCATATCATATCA-TA
66 TATATTTTTCTTACATTTAAAAGTTAGCCCTCCTACT-ATAATATCATATCATATCATAT-AGTA
* *
29200107 TCATATCATATCAT-ATA-TTAATAGTTTATATATATGCA-CTGATGATTAAACATTATAATATC
129 T-ATA--ATATCATAATAGTTAATA-TATATATATATGCATC-AATGATTAAACATTATAATAT-
* * *
29200169 ACATGTAATATTTTATCTTTTATTATAATCTATATTATAATAATATTTATATAT
188 -CATGTAATACTATATCTTTTATTATAATCTATATTATAATAATAGTTATATAT
29200223 GTATTAATAT
Statistics
Matches: 211, Mismatches: 23, Indels: 16
0.84 0.09 0.06
Matches are distributed among these distances:
251 35 0.17
252 21 0.10
253 51 0.24
254 50 0.24
255 5 0.02
256 49 0.23
ACGTcount: A:0.36, C:0.10, G:0.07, T:0.46
Consensus pattern (253 bp):
TATATATTAATTATTATAATATATTACCGTTTATTATTATACTAGTTAAAATATGCTCTAAGTCC
TATATTTTTCTTACATTTAAAAGTTAGCCCTCCTACTATAATATCATATCATATCATATAGTATA
TAATATCATAATAGTTAATATATATATATATGCATCAATGATTAAACATTATAATATCATGTAAT
ACTATATCTTTTATTATAATCTATATTATAATAATAGTTATATATAATAGCAATACAT
Found at i:29200243 original size:30 final size:31
Alignment explanation
Indices: 29200209--29200266 Score: 82
Period size: 30 Copynumber: 1.9 Consensus size: 31
29200199 TATATTATAA
* *
29200209 TAATATTTATATA-TGTATTAATATTTTTAG
1 TAATAGTTATATATTATATTAATATTTTTAG
*
29200239 TAATAGTTATATATTATATTATTATTTT
1 TAATAGTTATATATTATATTAATATTTT
29200267 ATGTATTAGT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
30 12 0.50
31 12 0.50
ACGTcount: A:0.36, C:0.00, G:0.05, T:0.59
Consensus pattern (31 bp):
TAATAGTTATATATTATATTAATATTTTTAG
Found at i:29200282 original size:31 final size:31
Alignment explanation
Indices: 29200224--29200282 Score: 75
Period size: 31 Copynumber: 1.9 Consensus size: 31
29200214 TTTATATATG
*
29200224 TATTAATATTTTTAGTAATAGTTATATATTA
1 TATTAATATTTTTAGTAATAGTAATATATTA
* *
29200255 TATTATTA-TTTTATGTATTAGTAATATA
1 TATTAATATTTTTA-GTAATAGTAATATA
29200283 CTAATTTAGT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
30 5 0.21
31 19 0.79
ACGTcount: A:0.37, C:0.00, G:0.07, T:0.56
Consensus pattern (31 bp):
TATTAATATTTTTAGTAATAGTAATATATTA
Found at i:29204929 original size:2 final size:2
Alignment explanation
Indices: 29204922--29204960 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
29204912 CTTAAAGAAA
29204922 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
29204961 TGCATAAGAA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:29207365 original size:4 final size:4
Alignment explanation
Indices: 29207356--29207383 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
29207346 TATGCTGCTG
29207356 TTTC TTTC TTTC TTTC TTTC TTTC TTTC
1 TTTC TTTC TTTC TTTC TTTC TTTC TTTC
29207384 AAAATTCTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.00, C:0.25, G:0.00, T:0.75
Consensus pattern (4 bp):
TTTC
Found at i:29213837 original size:16 final size:14
Alignment explanation
Indices: 29213818--29213851 Score: 50
Period size: 16 Copynumber: 2.3 Consensus size: 14
29213808 TTTATAAACA
29213818 TTAATTATTATTATAT
1 TTAATTATT-TT-TAT
29213834 TTAATTATTTTTAT
1 TTAATTATTTTTAT
29213848 TTAA
1 TTAA
29213852 AGTGTATATA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 7 0.39
15 2 0.11
16 9 0.50
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (14 bp):
TTAATTATTTTTAT
Found at i:29223622 original size:25 final size:25
Alignment explanation
Indices: 29223588--29223637 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
29223578 TTTGGCTAAA
29223588 ATGAGTTTTTAGTCAATTCAACACT
1 ATGAGTTTTTAGTCAATTCAACACT
29223613 ATGAGTTTTTAGTCAATTCAACACT
1 ATGAGTTTTTAGTCAATTCAACACT
29223638 TTCCCAAATA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.32, C:0.16, G:0.12, T:0.40
Consensus pattern (25 bp):
ATGAGTTTTTAGTCAATTCAACACT
Found at i:29227850 original size:16 final size:15
Alignment explanation
Indices: 29227814--29227853 Score: 80
Period size: 15 Copynumber: 2.7 Consensus size: 15
29227804 ATGTCCTCAC
29227814 AATTTTTATTCTAGA
1 AATTTTTATTCTAGA
29227829 AATTTTTATTCTAGA
1 AATTTTTATTCTAGA
29227844 AATTTTTATT
1 AATTTTTATT
29227854 TTTTAACTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 25 1.00
ACGTcount: A:0.33, C:0.05, G:0.05, T:0.57
Consensus pattern (15 bp):
AATTTTTATTCTAGA
Found at i:29237180 original size:31 final size:31
Alignment explanation
Indices: 29237142--29237206 Score: 130
Period size: 31 Copynumber: 2.1 Consensus size: 31
29237132 TTTTCACCTT
29237142 AGGGGTGCACCTATTCTGTTCGTTAAGAAAA
1 AGGGGTGCACCTATTCTGTTCGTTAAGAAAA
29237173 AGGGGTGCACCTATTCTGTTCGTTAAGAAAA
1 AGGGGTGCACCTATTCTGTTCGTTAAGAAAA
29237204 AGG
1 AGG
29237207 ACAGATCAAT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 34 1.00
ACGTcount: A:0.29, C:0.15, G:0.28, T:0.28
Consensus pattern (31 bp):
AGGGGTGCACCTATTCTGTTCGTTAAGAAAA
Found at i:29242901 original size:27 final size:27
Alignment explanation
Indices: 29242878--29242944 Score: 116
Period size: 27 Copynumber: 2.5 Consensus size: 27
29242868 ACATACTCTA
29242878 AATGGATTGCCTTTTTGGTGTACTATG
1 AATGGATTGCCTTTTTGGTGTACTATG
* *
29242905 AATGGATTGCCTTTTTTGTGTAGTATG
1 AATGGATTGCCTTTTTGGTGTACTATG
29242932 AATGGATTGCCTT
1 AATGGATTGCCTT
29242945 ATGGCGAATT
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
27 38 1.00
ACGTcount: A:0.19, C:0.10, G:0.25, T:0.45
Consensus pattern (27 bp):
AATGGATTGCCTTTTTGGTGTACTATG
Found at i:29257461 original size:20 final size:20
Alignment explanation
Indices: 29257436--29257477 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
29257426 ACTATTATTA
*
29257436 TAATATTCAACATTATTGCT
1 TAATATCCAACATTATTGCT
*
29257456 TAATATCCAATATTATTGCT
1 TAATATCCAACATTATTGCT
29257476 TA
1 TA
29257478 GCATAATAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.36, C:0.14, G:0.05, T:0.45
Consensus pattern (20 bp):
TAATATCCAACATTATTGCT
Found at i:29258589 original size:20 final size:20
Alignment explanation
Indices: 29258551--29258588 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
29258541 AGAGGTCTTT
29258551 TACCAATAAATACTTTTTTC
1 TACCAATAAATACTTTTTTC
29258571 TACCAA-AAAGTA-TTTTTT
1 TACCAATAAA-TACTTTTTT
29258589 TTCTTTCGTA
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:0.16, G:0.03, T:0.45
Consensus pattern (20 bp):
TACCAATAAATACTTTTTTC
Found at i:29267862 original size:15 final size:16
Alignment explanation
Indices: 29267842--29267873 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
29267832 AAATATTTTT
29267842 AAAAATAA-TTTAATA
1 AAAAATAATTTTAATA
29267857 AAAAATAATTTTAATA
1 AAAAATAATTTTAATA
29267873 A
1 A
29267874 TATGCTTATA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 8 0.50
16 8 0.50
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (16 bp):
AAAAATAATTTTAATA
Found at i:29268111 original size:9 final size:9
Alignment explanation
Indices: 29268097--29268127 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
29268087 GTTAAATGAA
29268097 TCGAGTTAT
1 TCGAGTTAT
*
29268106 TCGAGTTAA
1 TCGAGTTAT
29268115 TCGAGTTAT
1 TCGAGTTAT
29268124 TCGA
1 TCGA
29268128 ATCAACTCGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.26, C:0.13, G:0.23, T:0.39
Consensus pattern (9 bp):
TCGAGTTAT
Found at i:29268197 original size:9 final size:9
Alignment explanation
Indices: 29268180--29268216 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
29268170 TGAGTTTTCG
29268180 AATTCGAAT
1 AATTCGAAT
*
29268189 AACTCGAAT
1 AATTCGAAT
29268198 AATTCGAAT
1 AATTCGAAT
29268207 AATTCGAAT
1 AATTCGAAT
29268216 A
1 A
29268217 TCAAACTATA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.46, C:0.14, G:0.11, T:0.30
Consensus pattern (9 bp):
AATTCGAAT
Found at i:29269235 original size:5 final size:5
Alignment explanation
Indices: 29269225--29269250 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
29269215 CTTGAAAATT
29269225 TTCGA TTCGA TTCGA TTCGA TTCGA T
1 TTCGA TTCGA TTCGA TTCGA TTCGA T
29269251 CGAATGCTCA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.19, C:0.19, G:0.19, T:0.42
Consensus pattern (5 bp):
TTCGA
Found at i:29269765 original size:235 final size:243
Alignment explanation
Indices: 29269550--29270028 Score: 609
Period size: 252 Copynumber: 1.9 Consensus size: 243
29269540 AATGTAGTAC
* *
29269550 TATTATATTATTAATATAATAAAAGATATAATATTACATGATACTATAATATTTAATCATTGATG
1 TATTATATTA-TAATATAATAAAATATATAGTATTACATGATACTATAATATTTAATCATTGATG
* * *
29269615 CATATATATAAATTATTAATATCTTATATATTATATGATATGATATAGCATTATATAAAGTTGTA
65 CATATATATAAACTATTAATATATTATATATTATATGATAT-ATATAGCATTATATAAA-TAGTA
* * * *
29269680 GGAGAACTAACTTTCAAATTTACAAAAAGTATAGAGACTTAGAGCACATTTCAGCCAATATAATA
128 GGA-AACTAACTTTCAAATGTATAAAAAGTATAGAGACTTAGAGCATATTTCAACCAATATAATA
29269745 ATAAACAATAGTATATAATAATTAATATATAATGTACTACTATTATCTATAATAAT
192 ATAAACAATA-TATATAATAATTAATATATAATGTACTAC--TTA-CTATAATAAT
* *
29269801 TATTATATTATAAATTATAATAAAATATATAGTATTACATGATATTATAATCTTTAATCATTGAT
1 TATTATATTAT-AA-TATAATAAAATATATAGTATTACATGATACTATAATATTTAATCATTGAT
* * * *
29269866 GCATATATATTAACTATTAATATATTATATACTATATAATATTATATAGCATTATATTATATAGT
64 GCATATATATAAACTATTAATATATTATATATTATATGATA-TATATAGCATTATA-TAAATAGT
* * * * * *
29269931 AGAAAAACTAATTTTCAAATGTATTAAAAGTTACAGAGACTTAGAGCATATTGCAATCAATATAA
127 AG-GAAACTAACTTTCAAATGTATAAAAAG-TATAGAGACTTAGAGCATATTTCAACCAATATAA
*
29269996 TAATAAACAATAATATATGATAA-TAATTATATA
190 TAATAAACAAT-ATATATAATAATTAA-TATATA
29270029 TTATGTATTG
Statistics
Matches: 198, Mismatches: 22, Indels: 14
0.85 0.09 0.06
Matches are distributed among these distances:
250 1 0.01
251 12 0.06
252 124 0.63
253 60 0.30
254 1 0.01
ACGTcount: A:0.46, C:0.07, G:0.07, T:0.39
Consensus pattern (243 bp):
TATTATATTATAATATAATAAAATATATAGTATTACATGATACTATAATATTTAATCATTGATGC
ATATATATAAACTATTAATATATTATATATTATATGATATATATAGCATTATATAAATAGTAGGA
AACTAACTTTCAAATGTATAAAAAGTATAGAGACTTAGAGCATATTTCAACCAATATAATAATAA
ACAATATATATAATAATTAATATATAATGTACTACTTACTATAATAAT
Found at i:29269890 original size:17 final size:20
Alignment explanation
Indices: 29269868--29269913 Score: 57
Period size: 19 Copynumber: 2.5 Consensus size: 20
29269858 TCATTGATGC
29269868 ATATATAT-TA-ACTAT-TA
1 ATATATATATATACTATATA
29269885 ATATAT-TATATACTATATA
1 ATATATATATATACTATATA
29269904 ATAT-TATATA
1 ATATATATATA
29269914 GCATTATATT
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
16 1 0.04
17 8 0.32
18 6 0.24
19 10 0.40
ACGTcount: A:0.48, C:0.04, G:0.00, T:0.48
Consensus pattern (20 bp):
ATATATATATATACTATATA
Found at i:29269922 original size:15 final size:17
Alignment explanation
Indices: 29269885--29269929 Score: 60
Period size: 17 Copynumber: 2.8 Consensus size: 17
29269875 TTAACTATTA
29269885 ATATATTATATA-CTAT
1 ATATATTATATAGCTAT
29269901 ATAATATTATATAGC-AT
1 AT-ATATTATATAGCTAT
29269918 -TATATTATATAG
1 ATATATTATATAG
29269930 TAGAAAAACT
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
15 11 0.41
16 3 0.11
17 12 0.44
18 1 0.04
ACGTcount: A:0.44, C:0.04, G:0.04, T:0.47
Consensus pattern (17 bp):
ATATATTATATAGCTAT
Found at i:29270338 original size:17 final size:17
Alignment explanation
Indices: 29270298--29270330 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
29270288 TACAAACAGT
29270298 ATAA-TAATAAATAATA
1 ATAATTAATAAATAATA
*
29270314 ATAATTAATAATTAATA
1 ATAATTAATAAATAATA
29270331 CTAGTTAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (17 bp):
ATAATTAATAAATAATA
Found at i:29284185 original size:52 final size:52
Alignment explanation
Indices: 29284043--29284178 Score: 200
Period size: 52 Copynumber: 2.6 Consensus size: 52
29284033 GGCTATTATA
** * * *
29284043 GAATGTATATGCGAGTTGTCATTGTATCGAATGCATGAATTATTTTGTGATG
1 GAATGTATATGCGAACTGTCATTGCATCGAATGCATGAACTAGTTTGTGATG
29284095 GAATGTATATGCGAACTGTCATTGCATCGAATGCATGAACTAGTTTGTGATG
1 GAATGTATATGCGAACTGTCATTGCATCGAATGCATGAACTAGTTTGTGATG
* * *
29284147 GAATATATATGCGACCTATCATTGCATCGAAT
1 GAATGTATATGCGAACTGTCATTGCATCGAAT
29284179 ATATGAAATG
Statistics
Matches: 76, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
52 76 1.00
ACGTcount: A:0.29, C:0.12, G:0.23, T:0.35
Consensus pattern (52 bp):
GAATGTATATGCGAACTGTCATTGCATCGAATGCATGAACTAGTTTGTGATG
Found at i:29284647 original size:17 final size:17
Alignment explanation
Indices: 29284627--29284666 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
29284617 CAAATGTGCC
* *
29284627 AGTTGTGCCCATGTGTG
1 AGTTGTGACCATGTGTA
*
29284644 AGTTGTGATCATGTGTA
1 AGTTGTGACCATGTGTA
29284661 AGTTGT
1 AGTTGT
29284667 AACAAAAGAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.17, C:0.10, G:0.33, T:0.40
Consensus pattern (17 bp):
AGTTGTGACCATGTGTA
Found at i:29288877 original size:20 final size:20
Alignment explanation
Indices: 29288835--29288957 Score: 84
Period size: 22 Copynumber: 5.8 Consensus size: 20
29288825 CATACATAAT
** *
29288835 ATGCCACAAAGGCTAGTAGA
1 ATGCCACAAAGGCTAAAAAA
*
29288855 ATGCCACAAAGACTAAAAAA
1 ATGCCACAAAGGCTAAAAAA
29288875 ATGTGCCACAAAGGCTAACAAAA
1 A--TGCCACAAAGGCTAA-AAAA
* * *
29288898 TACGCCAAAAAGGCTAACAAA
1 -ATGCCACAAAGGCTAAAAAA
* *
29288919 ATGCATTACAAAGGCTAATAGAAT
1 ATGC--CACAAAGGCTAA-A-AAA
*
29288943 ATGCCATAAAGGCTA
1 ATGCCACAAAGGCTA
29288958 TCGGAATGCC
Statistics
Matches: 80, Mismatches: 15, Indels: 14
0.73 0.14 0.13
Matches are distributed among these distances:
20 20 0.25
21 3 0.04
22 46 0.57
23 4 0.05
24 7 0.09
ACGTcount: A:0.48, C:0.20, G:0.17, T:0.15
Consensus pattern (20 bp):
ATGCCACAAAGGCTAAAAAA
Found at i:29288884 original size:22 final size:22
Alignment explanation
Indices: 29288856--29288957 Score: 87
Period size: 22 Copynumber: 4.6 Consensus size: 22
29288846 GCTAGTAGAA
* *
29288856 TGCCACAAAGACTAAAAAAATG
1 TGCCACAAAGGCTAACAAAATG
*
29288878 TGCCACAAAGGCTAACAAAATA
1 TGCCACAAAGGCTAACAAAATG
* *
29288900 CGCCAAAAAGGCTAACAAAATG
1 TGCCACAAAGGCTAACAAAATG
**** * * *
29288922 CATTACAAAGGCTAATAGAATA
1 TGCCACAAAGGCTAACAAAATG
*
29288944 TGCCATAAAGGCTA
1 TGCCACAAAGGCTA
29288958 TCGGAATGCC
Statistics
Matches: 62, Mismatches: 18, Indels: 0
0.77 0.22 0.00
Matches are distributed among these distances:
22 62 1.00
ACGTcount: A:0.49, C:0.20, G:0.16, T:0.16
Consensus pattern (22 bp):
TGCCACAAAGGCTAACAAAATG
Found at i:29291374 original size:16 final size:16
Alignment explanation
Indices: 29291350--29291382 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
29291340 TCTTCTCCCT
29291350 ATAAATATTTTTTTAC
1 ATAAATATTTTTTTAC
*
29291366 ATAATTATTTTTTTAC
1 ATAAATATTTTTTTAC
29291382 A
1 A
29291383 ATTTTTAGAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.36, C:0.06, G:0.00, T:0.58
Consensus pattern (16 bp):
ATAAATATTTTTTTAC
Done.