Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr2
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: 50190067
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.32
Warning! 915496 characters in sequence are not A, C, G, or T
File 152 of 161
Found at i:47313249 original size:152 final size:153
Alignment explanation
Indices: 47312973--47313332 Score: 528
Period size: 152 Copynumber: 2.4 Consensus size: 153
47312963 CAAAAGTTAG
*
47312973 AAAATAATATATTGTTTTAAAGTAATAAAATCCGGGAAAAAATACGAACAAAAGGCCGAAATAAG
1 AAAATAATATATTTTTTTAAAGTAATAAAATCCGGGAAAAAATACGAACAAAAGGCCGAAATAAG
* * * * *
47313038 AGTTTTTTTTAAATTTATTTTAAAAAACACAGTAAATTAATACATTTCAAACATAATGTACTAAA
66 AGGTTTTTTTAAATTTATTTTAAAAAACAAACTAAATGAATACATTTCAAAAATAATGTACTAAA
47313103 ATAATGTAAAATAATAAAATGAA
131 ATAATGTAAAATAATAAAATGAA
* * *
47313126 AAAATAATATATTTTTATTGAAAGAAATAAAATTC-GGAAAAAATACGAACAAAGGGCCGAAATA
1 AAAATAATATATTTTT-TT-AAAGTAATAAAATCCGGGAAAAAATACGAACAAAAGGCCGAAATA
*
47313190 AG-GGTTTTTTTAAATTTA-TTTAAAAATCAAACTAAATGAATACATTTCAAAAATAATGTACTA
64 AGAGGTTTTTTTAAATTTATTTTAAAAAACAAACTAAATGAATACATTTCAAAAATAATGTACTA
* *
47313253 AAATAATGTAAAATAATAAAATTAG
129 AAATAATGTAAAATAATAAAATGAA
**** *
47313278 AAAATAATATATTTTTTTAAAGTAATAAAATCTAAAAAAAAATACGAATAAAAGG
1 AAAATAATATATTTTTTTAAAGTAATAAAATCCGGGAAAAAATACGAACAAAAGG
47313333 TCAAAATACA
Statistics
Matches: 185, Mismatches: 19, Indels: 8
0.87 0.09 0.04
Matches are distributed among these distances:
150 12 0.06
151 19 0.10
152 79 0.43
153 30 0.16
154 32 0.17
155 13 0.07
ACGTcount: A:0.54, C:0.07, G:0.10, T:0.30
Consensus pattern (153 bp):
AAAATAATATATTTTTTTAAAGTAATAAAATCCGGGAAAAAATACGAACAAAAGGCCGAAATAAG
AGGTTTTTTTAAATTTATTTTAAAAAACAAACTAAATGAATACATTTCAAAAATAATGTACTAAA
ATAATGTAAAATAATAAAATGAA
Found at i:47313421 original size:373 final size:371
Alignment explanation
Indices: 47312628--47313344 Score: 1115
Period size: 373 Copynumber: 1.9 Consensus size: 371
47312618 TTAAAGTAAT
* *
47312628 AAAATCCGGAGAAAAAAATACGAACAAATGGCAGAAATA-AG-GTTTTTTT-AATTTATTTAAAA
1 AAAATCCGG-G-AAAAAATACGAACAAAAGGCCGAAATAGAGTGTTTTTTTAAATTTATTTAAAA
*
47312690 AACACATTAAATTAATACATTTCAAACATAATGTACTAAAATAATGTAAAATAATAAAATGAAAA
64 AACACAGTAAATTAATACATTTCAAACATAATGTACTAAAATAATGTAAAATAATAAAATGAAAA
47312755 AATAATATATTTTTATTGAAAGAAATAAAATTCGGAAAAAATACGAACAAAGGGCCGAAATAAGG
129 AATAATATATTTTTATTGAAAGAAATAAAATTCGGAAAAAATACGAACAAAGGGCCGAAATAAGG
* *
47312820 GTTTTTTTTAAATATAAATAAAAAACACACTAAATGAATACATTTCAAACATAATGTACTAAAAT
194 GTTTTTTTTAAATATAAATAAAAAACAAACTAAATGAATACATTTCAAAAATAATGTACTAAAAT
* * *** *
47312885 AATGTAAAATAATAAAATTAGAAAGTAGTATATTTTTTTAAAGTAATAAAATCTGGGGACAAAAT
259 AATGTAAAATAATAAAATTAGAAAATAATATATTTTTTTAAAGTAATAAAATCTGAAAAAAAAAT
* * * * * * * *
47312950 ACGAACAAATGGCCAAAAGTTAGAAAATAATATATTGTTTTAAAGTAAT
324 ACGAACAAAAGGCCAAAAG-TACAAAATAATATAGTCTCTGAAAGCAAG
47312999 AAAATCCGGGAAAAAATACGAACAAAAGGCCGAAATAAGAGT-TTTTTTTAAATTTATTTTAAAA
1 AAAATCCGGGAAAAAATACGAACAAAAGGCCGAAAT-AGAGTGTTTTTTTAAATTTA-TTTAAAA
47313063 AACACAGTAAATTAATACATTTCAAACATAATGTACTAAAATAATGTAAAATAATAAAATGAAAA
64 AACACAGTAAATTAATACATTTCAAACATAATGTACTAAAATAATGTAAAATAATAAAATGAAAA
47313128 AATAATATATTTTTATTGAAAGAAATAAAATTCGGAAAAAATACGAACAAAGGGCCGAAATAAGG
129 AATAATATATTTTTATTGAAAGAAATAAAATTCGGAAAAAATACGAACAAAGGGCCGAAATAAGG
* ** *
47313193 G-TTTTTTTAAATTTATTTAAAAATCAAACTAAATGAATACATTTCAAAAATAATGTACTAAAAT
194 GTTTTTTTTAAATATAAATAAAAAACAAACTAAATGAATACATTTCAAAAATAATGTACTAAAAT
47313257 AATGTAAAATAATAAAATTAGAAAATAATATATTTTTTTAAAGTAATAAAATCT-AAAAAAAAAT
259 AATGTAAAATAATAAAATTAGAAAATAATATATTTTTTTAAAGTAATAAAATCTGAAAAAAAAAT
* *
47313321 ACGAATAAAAGGTCAAAA-TACAAA
324 ACGAACAAAAGGCCAAAAGTACAAA
47313345 CATGTTGGTG
Statistics
Matches: 322, Mismatches: 19, Indels: 12
0.91 0.05 0.03
Matches are distributed among these distances:
369 29 0.09
370 2 0.01
371 39 0.12
372 115 0.36
373 137 0.43
ACGTcount: A:0.53, C:0.08, G:0.10, T:0.29
Consensus pattern (371 bp):
AAAATCCGGGAAAAAATACGAACAAAAGGCCGAAATAGAGTGTTTTTTTAAATTTATTTAAAAAA
CACAGTAAATTAATACATTTCAAACATAATGTACTAAAATAATGTAAAATAATAAAATGAAAAAA
TAATATATTTTTATTGAAAGAAATAAAATTCGGAAAAAATACGAACAAAGGGCCGAAATAAGGGT
TTTTTTTAAATATAAATAAAAAACAAACTAAATGAATACATTTCAAAAATAATGTACTAAAATAA
TGTAAAATAATAAAATTAGAAAATAATATATTTTTTTAAAGTAATAAAATCTGAAAAAAAAATAC
GAACAAAAGGCCAAAAGTACAAAATAATATAGTCTCTGAAAGCAAG
Found at i:47326036 original size:18 final size:17
Alignment explanation
Indices: 47326000--47326038 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
47325990 TGTCATCCTT
*
47326000 TATTGAACTGTCGTTTG
1 TATTGAACTGTAGTTTG
*
47326017 TATTGAACTGATATTTTG
1 TATTGAACTG-TAGTTTG
47326035 TATT
1 TATT
47326039 TATTTGAAAG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 10 0.53
18 9 0.47
ACGTcount: A:0.23, C:0.08, G:0.18, T:0.51
Consensus pattern (17 bp):
TATTGAACTGTAGTTTG
Found at i:47340692 original size:18 final size:17
Alignment explanation
Indices: 47340656--47340694 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
47340646 TGTCATCCTT
*
47340656 TATTGAACTGTCGTTTG
1 TATTGAACTGTAGTTTG
*
47340673 TATTGAACTGATATTTTG
1 TATTGAACTG-TAGTTTG
47340691 TATT
1 TATT
47340695 TATTTGAAAG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 10 0.53
18 9 0.47
ACGTcount: A:0.23, C:0.08, G:0.18, T:0.51
Consensus pattern (17 bp):
TATTGAACTGTAGTTTG
Found at i:47353468 original size:82 final size:81
Alignment explanation
Indices: 47353371--47353527 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
47353361 ATTTACAAAT
*
47353371 ATAATTCTATTTATTAAAGATTATTTTCATTTAATAAAATACAATTAATCTTTTTTATATAAAAT
1 ATAATGCTATTTATTAAAGATTATTTTCATTTAATAAAATACAATTAAT-TTTTTTATATAAAAT
47353436 TTAAACATTTTGTTGAA
65 TTAAACATTTTGTTGAA
* * *** *
47353453 ATAATGCTTTTTATTAAAGATTATTTTTATTTAATAAAATTTTATTACTTTTTTTATATAAAATT
1 ATAATGCTATTTATTAAAGATTATTTTCATTTAATAAAATACAATTAATTTTTTTATATAAAATT
*
47353518 TAAATATTTT
66 TAAACATTTT
47353528 ATTAAAATTT
Statistics
Matches: 67, Mismatches: 8, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
81 25 0.37
82 42 0.63
ACGTcount: A:0.39, C:0.04, G:0.03, T:0.53
Consensus pattern (81 bp):
ATAATGCTATTTATTAAAGATTATTTTCATTTAATAAAATACAATTAATTTTTTTATATAAAATT
TAAACATTTTGTTGAA
Found at i:47353519 original size:23 final size:24
Alignment explanation
Indices: 47353472--47353518 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
47353462 TTTATTAAAG
*
47353472 ATTATTTTTATTTAATAAAATTTT
1 ATTACTTTTATTTAATAAAATTTT
47353496 ATTACTTTT-TTTATATAAAATTT
1 ATTACTTTTATTTA-ATAAAATTT
47353519 AAATATTTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 4 0.19
24 17 0.81
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (24 bp):
ATTACTTTTATTTAATAAAATTTT
Found at i:47353525 original size:27 final size:27
Alignment explanation
Indices: 47353466--47353525 Score: 65
Period size: 24 Copynumber: 2.3 Consensus size: 27
47353456 ATGCTTTTTA
* *
47353466 TTAAAGATTATTTTTATTTAATAAAAT
1 TTAAATATTACTTTTATTTAATAAAAT
47353493 TT---TATTACTTTT-TTTATATAAAAT
1 TTAAATATTACTTTTATTTA-ATAAAAT
47353517 TTAAATATT
1 TTAAATATT
47353526 TTATTAAAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 8
0.73 0.05 0.22
Matches are distributed among these distances:
23 4 0.15
24 17 0.63
27 6 0.22
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.57
Consensus pattern (27 bp):
TTAAATATTACTTTTATTTAATAAAAT
Found at i:47353527 original size:23 final size:24
Alignment explanation
Indices: 47353477--47353530 Score: 67
Period size: 24 Copynumber: 2.3 Consensus size: 24
47353467 TAAAGATTAT
* *
47353477 TTTTATTTAATAAAATTTTATTAC
1 TTTTATTTAATAAAATTTAAATAC
47353501 TTTT-TTTATATAAAATTTAAATA-
1 TTTTATTTA-ATAAAATTTAAATAC
47353524 TTTTATT
1 TTTTATT
47353531 AAAATTTAAG
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
23 8 0.31
24 18 0.69
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (24 bp):
TTTTATTTAATAAAATTTAAATAC
Found at i:47353546 original size:18 final size:20
Alignment explanation
Indices: 47353504--47353548 Score: 67
Period size: 18 Copynumber: 2.4 Consensus size: 20
47353494 TTATTACTTT
*
47353504 TTTTATATAAAATTTAAATA
1 TTTTATATAAAATTTAAAGA
47353524 TTTTAT-TAAAATTT-AAGA
1 TTTTATATAAAATTTAAAGA
47353542 TTTTATA
1 TTTTATA
47353549 GATGAAAAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
18 9 0.39
19 8 0.35
20 6 0.26
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.53
Consensus pattern (20 bp):
TTTTATATAAAATTTAAAGA
Found at i:47354069 original size:66 final size:66
Alignment explanation
Indices: 47353957--47354088 Score: 219
Period size: 66 Copynumber: 2.0 Consensus size: 66
47353947 GTTTATCCTA
* * * *
47353957 TCTTAATTCTAGCCTTGTTGTTTGCCATGAGATTCTTTTTAGCCATTGGTAATCAAGTTCATCTT
1 TCTTAATTCTAGCATTGTTGTTTGCCATGAGATTCTTCTTAACCATTGATAATCAAGTTCATCTT
47354022 G
66 G
*
47354023 TCTTGATTCTAGCATTGTTGTTTGCCATGAGATTCTTCTTAACCATTGATAATCAAGTTCATCTT
1 TCTTAATTCTAGCATTGTTGTTTGCCATGAGATTCTTCTTAACCATTGATAATCAAGTTCATCTT
47354088 G
66 G
47354089 CGAATTCAAT
Statistics
Matches: 61, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
66 61 1.00
ACGTcount: A:0.21, C:0.18, G:0.16, T:0.45
Consensus pattern (66 bp):
TCTTAATTCTAGCATTGTTGTTTGCCATGAGATTCTTCTTAACCATTGATAATCAAGTTCATCTT
G
Found at i:47359193 original size:15 final size:15
Alignment explanation
Indices: 47359173--47359203 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
47359163 AAGATCAGCA
47359173 ATATAATATATATAT
1 ATATAATATATATAT
47359188 ATATAATATATATAT
1 ATATAATATATATAT
47359203 A
1 A
47359204 AAGAAATTGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (15 bp):
ATATAATATATATAT
Found at i:47359196 original size:11 final size:11
Alignment explanation
Indices: 47359172--47359204 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
47359162 AAAGATCAGC
47359172 AATATA-ATAT
1 AATATATATAT
47359182 -ATATATATAT
1 AATATATATAT
47359192 AATATATATAT
1 AATATATATAT
47359203 AA
1 AA
47359205 AGAAATTGAG
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
9 5 0.24
10 4 0.19
11 12 0.57
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (11 bp):
AATATATATAT
Found at i:47371827 original size:13 final size:13
Alignment explanation
Indices: 47371809--47371839 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
47371799 ATGATGTAAA
47371809 AATTAAAACACAT
1 AATTAAAACACAT
47371822 AATTAAAACACAT
1 AATTAAAACACAT
47371835 -ATTAA
1 AATTAA
47371840 TGATATTCAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 5 0.28
13 13 0.72
ACGTcount: A:0.61, C:0.13, G:0.00, T:0.26
Consensus pattern (13 bp):
AATTAAAACACAT
Found at i:47376284 original size:22 final size:23
Alignment explanation
Indices: 47376259--47376321 Score: 67
Period size: 22 Copynumber: 2.7 Consensus size: 23
47376249 TCATTTTAAA
47376259 TTCTTTTTTCCTTTCTTTT-TTT
1 TTCTTTTTTCCTTTCTTTTCTTT
** *
47376281 TTCTGATTTCTTTTCTTTTTCTTT
1 TTCTTTTTTCCTTTC-TTTTCTTT
47376305 TTCATTTTTT-CTTTCTT
1 TTC-TTTTTTCCTTTCTT
47376322 GACCACTTAC
Statistics
Matches: 32, Mismatches: 6, Indels: 5
0.74 0.14 0.12
Matches are distributed among these distances:
22 12 0.38
23 6 0.19
24 10 0.31
25 4 0.12
ACGTcount: A:0.03, C:0.17, G:0.02, T:0.78
Consensus pattern (23 bp):
TTCTTTTTTCCTTTCTTTTCTTT
Found at i:47376312 original size:18 final size:16
Alignment explanation
Indices: 47376270--47376321 Score: 59
Period size: 18 Copynumber: 3.0 Consensus size: 16
47376260 TCTTTTTTCC
*
47376270 TTTCTTTTTTTTTCTGA
1 TTTCTTTTTTTTTCT-T
47376287 TTTCTTTTCTTTTTCTT
1 TTTCTTTT-TTTTTCTT
47376304 TTTCATTTTTTCTTTCTT
1 TTTC-TTTTTT-TTTCTT
47376322 GACCACTTAC
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
17 14 0.45
18 17 0.55
ACGTcount: A:0.04, C:0.15, G:0.02, T:0.79
Consensus pattern (16 bp):
TTTCTTTTTTTTTCTT
Found at i:47383736 original size:368 final size:368
Alignment explanation
Indices: 47383056--47383791 Score: 1305
Period size: 368 Copynumber: 2.0 Consensus size: 368
47383046 ACACATAAAA
**
47383056 GTGCTGGGTACGTTAGTTAAGCCGAATGGCATAACCAACCACTTGTACAAACCGTGCTTTGTCTT
1 GTGCTGGGTACGTTAGTTAAGCCGAATGGCATAACCAACCACTCATACAAACCGTGCTTTGTCTT
47383121 AAACACCGTTCTCCACTCATCTAGTTCTCGCATTCGGATTTGCTGATATCCACTCTTGAGATATA
66 AAACACCGTTCTCCACTCATCTAGTTCTCGCATTCGGATTTGCTGATATCCACTCTTGAGATATA
47383186 TTTTGGAGAAAAGTTAGGCTCCGTTTAGTTCATCAAACATGTCATCAAGGCGTGGAATTGGATGC
131 TTTTGGAGAAAAGTTAGGCTCCGTTTAGTTCATCAAACATGTCATCAAGGCGTGGAATTGGATGC
*
47383251 CTATACTTGATTATGATCTTGTTAATTGTTTGGTAGTCGACAAATATGAGCCAAGTTCCATCCTT
196 CTATACTTGATTATGATCTTGTTAATTGTTTGGTAGTCCACAAATATGAGCCAAGTTCCATCCTT
*
47383316 TTGAGCACGAAGAGCACGGGCACGACGCAAGGACTTAAGCTCTCTTGAATGTACCCCTTTTCCAT
261 TTGAGCACGAAGAGCACGGGCACGACGCAAGGACTTAAGCTCTCTCGAATGTACCCCTTTTCCAT
47383381 CAACGTAGCTACTCGCCTTTAAAGTTCCTTAGTTTCTTTAGGG
326 CAACGTAGCTACTCGCCTTTAAAGTTCCTTAGTTTCTTTAGGG
*
47383424 GTGCTGGGTGCGTTAGTTAAGCCGAATGGCATAACCAACCACTCATAC-AACCTGTGCTTTGTCT
1 GTGCTGGGTACGTTAGTTAAGCCGAATGGCATAACCAACCACTCATACAAACC-GTGCTTTGTCT
** * * *
47383488 TAAACGTCGTTTTCCACTCATCTGGTTCTCGCATTCGGATTTGCTGATATCCACTCTTGAGATCT
65 TAAACACCGTTCTCCACTCATCTAGTTCTCGCATTCGGATTTGCTGATATCCACTCTTGAGATAT
*
47383553 ATTTTGGAGAAAAGTTAGGCTCCGTTTAGTTCATCAAACATGTCATCAAGGCGTGGAATTGGGTG
130 ATTTTGGAGAAAAGTTAGGCTCCGTTTAGTTCATCAAACATGTCATCAAGGCGTGGAATTGGATG
*
47383618 CCTATACTTGATTATGATCTTGTTAATTTTTTGGTAGTCCACAAATAT-ATGCCAAGTTCCATCC
195 CCTATACTTGATTATGATCTTGTTAATTGTTTGGTAGTCCACAAATATGA-GCCAAGTTCCATCC
47383682 TTTTGAGCACGAAGAGCACGGGCACGACGCAAGGACTTAAGCTCTCTCGAATGTACCCCTTTTCC
259 TTTTGAGCACGAAGAGCACGGGCACGACGCAAGGACTTAAGCTCTCTCGAATGTACCCCTTTTCC
* * *
47383747 ATCAACTTAGCTACTTGCCTTTGAAGTTCCTTAGTTTCTTTAGGG
324 ATCAACGTAGCTACTCGCCTTTAAAGTTCCTTAGTTTCTTTAGGG
47383792 TTACTTCAAT
Statistics
Matches: 351, Mismatches: 15, Indels: 4
0.95 0.04 0.01
Matches are distributed among these distances:
367 5 0.01
368 346 0.99
ACGTcount: A:0.24, C:0.22, G:0.20, T:0.33
Consensus pattern (368 bp):
GTGCTGGGTACGTTAGTTAAGCCGAATGGCATAACCAACCACTCATACAAACCGTGCTTTGTCTT
AAACACCGTTCTCCACTCATCTAGTTCTCGCATTCGGATTTGCTGATATCCACTCTTGAGATATA
TTTTGGAGAAAAGTTAGGCTCCGTTTAGTTCATCAAACATGTCATCAAGGCGTGGAATTGGATGC
CTATACTTGATTATGATCTTGTTAATTGTTTGGTAGTCCACAAATATGAGCCAAGTTCCATCCTT
TTGAGCACGAAGAGCACGGGCACGACGCAAGGACTTAAGCTCTCTCGAATGTACCCCTTTTCCAT
CAACGTAGCTACTCGCCTTTAAAGTTCCTTAGTTTCTTTAGGG
Found at i:47398324 original size:15 final size:15
Alignment explanation
Indices: 47398300--47398338 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 15
47398290 ATCCTATTAT
*
47398300 GAAA-GAAGTTGTGG
1 GAAAGGAAGTTGTGA
*
47398314 GAAAGGAAGTTGTTA
1 GAAAGGAAGTTGTGA
47398329 GAAAGGAAGT
1 GAAAGGAAGT
47398339 GATCAAATGG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
14 4 0.18
15 18 0.82
ACGTcount: A:0.41, C:0.00, G:0.38, T:0.21
Consensus pattern (15 bp):
GAAAGGAAGTTGTGA
Found at i:47411526 original size:17 final size:15
Alignment explanation
Indices: 47411506--47411544 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 15
47411496 GCGAGCGAGA
47411506 AAATGAACATGAAAAAG
1 AAATGAA-A-GAAAAAG
47411523 AAATGAAAGAAAAAG
1 AAATGAAAGAAAAAG
47411538 AAGATGA
1 AA-ATGA
47411545 GTGGGACATA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 9 0.43
16 5 0.24
17 7 0.33
ACGTcount: A:0.67, C:0.03, G:0.21, T:0.10
Consensus pattern (15 bp):
AAATGAAAGAAAAAG
Found at i:47417407 original size:23 final size:22
Alignment explanation
Indices: 47417355--47417407 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 22
47417345 TCCACGTCTT
*
47417355 TTTCTTTTGTTTCTTTTTCTAA
1 TTTCTTTTCTTTCTTTTTCTAA
47417377 -TTCATTTTCTCTTCTTTCTTC-AA
1 TTTC-TTTTCT-TTCTTT-TTCTAA
47417400 TTTCTTTT
1 TTTCTTTT
47417408 TCACTCTCAA
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 3 0.12
22 5 0.19
23 12 0.46
24 6 0.23
ACGTcount: A:0.09, C:0.19, G:0.02, T:0.70
Consensus pattern (22 bp):
TTTCTTTTCTTTCTTTTTCTAA
Found at i:47430366 original size:31 final size:32
Alignment explanation
Indices: 47430298--47430376 Score: 92
Period size: 31 Copynumber: 2.6 Consensus size: 32
47430288 ATATAATATG
*
47430298 GTAATTAAATTAAATT--AATCATTATATAAT
1 GTAATTAAATTAAATTAAAATCATTACATAAT
* * *
47430328 GTGATTAACTTAAATTAAAAT-GTTACATAAT
1 GTAATTAAATTAAATTAAAATCATTACATAAT
*
47430359 GTAATTAAATTAAGTTAA
1 GTAATTAAATTAAATTAA
47430377 TAGGGGGTCC
Statistics
Matches: 40, Mismatches: 7, Indels: 3
0.80 0.14 0.06
Matches are distributed among these distances:
30 14 0.35
31 23 0.57
32 3 0.08
ACGTcount: A:0.48, C:0.04, G:0.08, T:0.41
Consensus pattern (32 bp):
GTAATTAAATTAAATTAAAATCATTACATAAT
Found at i:47434420 original size:107 final size:101
Alignment explanation
Indices: 47434261--47434460 Score: 256
Period size: 107 Copynumber: 1.9 Consensus size: 101
47434251 TACATTTGTA
* * *
47434261 GTGCCATAACCTAGTTATGGTCTTATCATCAGAACGCCATAAACCAGTTATGGTCTTACACATGT
1 GTGCCATAACCCAGTTATGGTCTTATCATCAAAACGCCATAAACCAGCTATGGTCTT--ACAT-T
* *
47434326 ATATATATACTGTCATGGTCCAACCATGGTCTTACGTTCAAT
63 -TA-A-ACACTGCCATGGTCCAACCATGGTCTTACGTTCAAT
* * * **
47434368 GTGCCATAACCCAGTTATGGTCTTTTCATTAAAATGCCATAGCCCAGCTATGGTCTTACATTTAA
1 GTGCCATAACCCAGTTATGGTCTTATCATCAAAACGCCATAAACCAGCTATGGTCTTACATTTAA
47434433 ACACTGCCATGGTCCAACCATGGTCTTA
66 ACACTGCCATGGTCCAACCATGGTCTTA
47434461 TCCGTAAATT
Statistics
Matches: 83, Mismatches: 10, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
101 26 0.31
102 1 0.01
103 2 0.02
104 1 0.01
105 4 0.05
107 49 0.59
ACGTcount: A:0.28, C:0.24, G:0.16, T:0.32
Consensus pattern (101 bp):
GTGCCATAACCCAGTTATGGTCTTATCATCAAAACGCCATAAACCAGCTATGGTCTTACATTTAA
ACACTGCCATGGTCCAACCATGGTCTTACGTTCAAT
Found at i:47434433 original size:33 final size:33
Alignment explanation
Indices: 47434351--47434460 Score: 87
Period size: 33 Copynumber: 3.3 Consensus size: 33
47434341 TGGTCCAACC
* * ** * *
47434351 ATGGTCTTACGTTCAATGTGCCATAACCCAGTT
1 ATGGTCTTACATTTAAAATGCCATAGCCCAGCT
*
47434384 ATGGTCTTTTCA-TTAAAATGCCATAGCCCAGCT
1 ATGGTC-TTACATTTAAAATGCCATAGCCCAGCT
* * * *
47434417 ATGGTCTTACATTTAAACACTGCCATGGTCCAACC
1 ATGGTCTTACATTTAAA-A-TGCCATAGCCCAGCT
47434452 ATGGTCTTA
1 ATGGTCTTA
47434461 TCCGTAAATT
Statistics
Matches: 61, Mismatches: 12, Indels: 6
0.77 0.15 0.08
Matches are distributed among these distances:
32 4 0.07
33 33 0.54
34 4 0.07
35 20 0.33
ACGTcount: A:0.26, C:0.25, G:0.16, T:0.33
Consensus pattern (33 bp):
ATGGTCTTACATTTAAAATGCCATAGCCCAGCT
Found at i:47439702 original size:21 final size:21
Alignment explanation
Indices: 47439678--47439746 Score: 68
Period size: 21 Copynumber: 3.2 Consensus size: 21
47439668 GATTTCACAA
47439678 CTCCCTTCAAACAGATCTAAT
1 CTCCCTTCAAACAGATCTAAT
* * * *
47439699 CTCCCCTCCAA-AGATTTCACAA
1 CTCCCTTCAAACAGATCT-A-AT
*
47439721 CTCCCTTCAAACAGCTCTAAT
1 CTCCCTTCAAACAGATCTAAT
47439742 CTCCC
1 CTCCC
47439747 CTCCAATGAA
Statistics
Matches: 36, Mismatches: 9, Indels: 6
0.71 0.18 0.12
Matches are distributed among these distances:
20 5 0.14
21 16 0.44
22 11 0.31
23 4 0.11
ACGTcount: A:0.29, C:0.41, G:0.04, T:0.26
Consensus pattern (21 bp):
CTCCCTTCAAACAGATCTAAT
Found at i:47439710 original size:22 final size:22
Alignment explanation
Indices: 47439680--47439752 Score: 62
Period size: 22 Copynumber: 3.4 Consensus size: 22
47439670 TTTCACAACT
*
47439680 CCCTTCAAACAGATCTAATCTC
1 CCCTCCAAACAGATCTAATCTC
* *
47439702 CCCTCC-AA-AGATTTCACAACT-
1 CCCTCCAAACAGATCT-A-ATCTC
* *
47439723 CCCTTCAAACAGCTCTAATCTC
1 CCCTCCAAACAGATCTAATCTC
47439745 CCCTCCAA
1 CCCTCCAA
47439753 TGAAGAACAA
Statistics
Matches: 38, Mismatches: 8, Indels: 10
0.68 0.14 0.18
Matches are distributed among these distances:
20 5 0.13
21 11 0.29
22 18 0.47
23 4 0.11
ACGTcount: A:0.30, C:0.41, G:0.04, T:0.25
Consensus pattern (22 bp):
CCCTCCAAACAGATCTAATCTC
Found at i:47439726 original size:43 final size:43
Alignment explanation
Indices: 47439665--47439752 Score: 167
Period size: 43 Copynumber: 2.0 Consensus size: 43
47439655 TGAAATCCCG
47439665 AAAGATTTCACAACTCCCTTCAAACAGATCTAATCTCCCCTCC
1 AAAGATTTCACAACTCCCTTCAAACAGATCTAATCTCCCCTCC
*
47439708 AAAGATTTCACAACTCCCTTCAAACAGCTCTAATCTCCCCTCC
1 AAAGATTTCACAACTCCCTTCAAACAGATCTAATCTCCCCTCC
47439751 AA
1 AA
47439753 TGAAGAACAA
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
43 44 1.00
ACGTcount: A:0.33, C:0.38, G:0.05, T:0.25
Consensus pattern (43 bp):
AAAGATTTCACAACTCCCTTCAAACAGATCTAATCTCCCCTCC
Found at i:47444058 original size:37 final size:37
Alignment explanation
Indices: 47444008--47444081 Score: 139
Period size: 37 Copynumber: 2.0 Consensus size: 37
47443998 TCCCGAAAGA
*
47444008 TTTCACAACTCCCTTCAAACAGCTCTAATCTCCCCTC
1 TTTCACAACTCCCTTCAAACAGATCTAATCTCCCCTC
47444045 TTTCACAACTCCCTTCAAACAGATCTAATCTCCCCTC
1 TTTCACAACTCCCTTCAAACAGATCTAATCTCCCCTC
47444082 CAATGAAGAA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 36 1.00
ACGTcount: A:0.26, C:0.42, G:0.03, T:0.30
Consensus pattern (37 bp):
TTTCACAACTCCCTTCAAACAGATCTAATCTCCCCTC
Found at i:47454757 original size:14 final size:14
Alignment explanation
Indices: 47454724--47454773 Score: 55
Period size: 14 Copynumber: 3.4 Consensus size: 14
47454714 ACTTCTCTAA
*
47454724 AAAATATTATAATTT
1 AAAATTTTA-AATTT
47454739 AAAATTTTAAATTT
1 AAAATTTTAAATTT
* *
47454753 TAAATTTTAAAATT
1 AAAATTTTAAATTT
47454767 AAGAATT
1 AA-AATT
47454774 AAAAATTAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
14 18 0.60
15 12 0.40
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (14 bp):
AAAATTTTAAATTT
Found at i:47454766 original size:8 final size:7
Alignment explanation
Indices: 47454734--47454763 Score: 51
Period size: 7 Copynumber: 4.3 Consensus size: 7
47454724 AAAATATTAT
*
47454734 AATTTAA
1 AATTTTA
47454741 AATTTTA
1 AATTTTA
47454748 AATTTTA
1 AATTTTA
47454755 AATTTTA
1 AATTTTA
47454762 AA
1 AA
47454764 ATTAAGAATT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (7 bp):
AATTTTA
Found at i:47459602 original size:35 final size:35
Alignment explanation
Indices: 47459549--47459623 Score: 134
Period size: 35 Copynumber: 2.2 Consensus size: 35
47459539 TTTTTATAAT
47459549 AAAG-TAAATTTTTTTTTGAAATATGGTGATTAAG
1 AAAGATAAATTTTTTTTTGAAATATGGTGATTAAG
*
47459583 AAAGATAATTTTTTTTTTGAAATATGGTGATTAAG
1 AAAGATAAATTTTTTTTTGAAATATGGTGATTAAG
47459618 AAAGAT
1 AAAGAT
47459624 GATATCAACA
Statistics
Matches: 39, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
34 4 0.10
35 35 0.90
ACGTcount: A:0.40, C:0.00, G:0.17, T:0.43
Consensus pattern (35 bp):
AAAGATAAATTTTTTTTTGAAATATGGTGATTAAG
Found at i:47462567 original size:41 final size:39
Alignment explanation
Indices: 47462520--47462689 Score: 170
Period size: 41 Copynumber: 4.2 Consensus size: 39
47462510 GCGTTTGAAA
*
47462520 CAAAACGCCTTTAAAAACTGAGCAATAGTGGCGTTTTTATC
1 CAAAACGCCTCTAAAAACTGAG-AATAGTGGCGTTTTT-TC
* *
47462561 CAAAACGCCGCTAAAAACTGAGTAATAGTGGCGTTTTCATC
1 CAAAACGCCTCTAAAAACTGAG-AATAGTGGCGTTTT-TTC
*
47462602 CAAAACG-CTGCAAAAAACTGAGAAATAGTGGCGTTTTTT-
1 CAAAACGCCT-CTAAAAACTGAG-AATAGTGGCGTTTTTTC
*
47462641 CAAAAC-ACTGC-AAAAACTGAGATATAGTGGCGCTTTATTTC
1 CAAAACGCCT-CTAAAAACTGAGA-ATAGTGGCG-TTT-TTTC
47462682 C-AAACGCC
1 CAAAACGCC
47462690 ACAAAAGGTA
Statistics
Matches: 112, Mismatches: 9, Indels: 16
0.82 0.07 0.12
Matches are distributed among these distances:
37 1 0.01
38 19 0.17
39 13 0.12
40 9 0.08
41 70 0.62
ACGTcount: A:0.36, C:0.21, G:0.18, T:0.25
Consensus pattern (39 bp):
CAAAACGCCTCTAAAAACTGAGAATAGTGGCGTTTTTTC
Found at i:47462695 original size:79 final size:82
Alignment explanation
Indices: 47462532--47462695 Score: 205
Period size: 79 Copynumber: 2.0 Consensus size: 82
47462522 AAACGCCTTT
* *
47462532 AAAAACTGAGCAATAGTGGCGTTTTTATCCAAAACGCCGCTAAAAACTGAGTAATAGTGGCGTTT
1 AAAAACTGAGAAATAGTGGCGTTTTTATCCAAAACACCGCTAAAAACTGAGTAATAGTGGCGTTT
**
47462597 TCATCCAAAACGCTGCA
66 TCATCCAAAACGCCACA
*
47462614 AAAAACTGAGAAATAGTGGCGTTTTT-T-CAAAACACTGC-AAAAACTGAG-ATATAGTGGCGCT
1 AAAAACTGAGAAATAGTGGCGTTTTTATCCAAAACACCGCTAAAAACTGAGTA-ATAGTGGCG-T
*
47462675 TTAT-TTCC-AAACGCCACA
64 TT-TCATCCAAAACGCCACA
47462693 AAA
1 AAA
47462696 GGTAGAGCTA
Statistics
Matches: 73, Mismatches: 6, Indels: 9
0.83 0.07 0.10
Matches are distributed among these distances:
78 1 0.01
79 30 0.41
80 15 0.21
81 2 0.03
82 25 0.34
ACGTcount: A:0.38, C:0.20, G:0.18, T:0.24
Consensus pattern (82 bp):
AAAAACTGAGAAATAGTGGCGTTTTTATCCAAAACACCGCTAAAAACTGAGTAATAGTGGCGTTT
TCATCCAAAACGCCACA
Found at i:47463272 original size:14 final size:14
Alignment explanation
Indices: 47463255--47463305 Score: 59
Period size: 14 Copynumber: 3.6 Consensus size: 14
47463245 ATATGAAGCC
47463255 TAACCCATAAATCA
1 TAACCCATAAATCA
*
47463269 TAACCCAT-GATCGCA
1 TAACCCATAAAT--CA
*
47463284 TAACCCCTAAATCA
1 TAACCCATAAATCA
47463298 TAACCCAT
1 TAACCCAT
47463306 GATCTAAACT
Statistics
Matches: 30, Mismatches: 4, Indels: 6
0.75 0.10 0.15
Matches are distributed among these distances:
13 2 0.07
14 17 0.57
15 9 0.30
16 2 0.07
ACGTcount: A:0.41, C:0.33, G:0.04, T:0.22
Consensus pattern (14 bp):
TAACCCATAAATCA
Found at i:47464570 original size:20 final size:20
Alignment explanation
Indices: 47464525--47464576 Score: 70
Period size: 19 Copynumber: 2.6 Consensus size: 20
47464515 CCCCACCCAA
*
47464525 ATTTCCCCAAATCCCTAACT
1 ATTTCCCCAAATCCCTAAAT
*
47464545 -TTTCCCCTAATCCCTAAAT
1 ATTTCCCCAAATCCCTAAAT
*
47464564 ATTTCCCCGAATC
1 ATTTCCCCAAATC
47464577 AAAATCGAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
19 17 0.61
20 11 0.39
ACGTcount: A:0.27, C:0.38, G:0.02, T:0.33
Consensus pattern (20 bp):
ATTTCCCCAAATCCCTAAAT
Found at i:47467310 original size:64 final size:64
Alignment explanation
Indices: 47467237--47467370 Score: 250
Period size: 64 Copynumber: 2.1 Consensus size: 64
47467227 TAATATTTCT
* *
47467237 ATATTTCTATCACGATTTTTAATAAATTTATTTATTGATATAATATGTCCCATCTAATATACAA
1 ATATTTCTATCACGATGTTTAATAAATTTATTTATTAATATAATATGTCCCATCTAATATACAA
47467301 ATATTTCTATCACGATGTTTAATAAATTTATTTATTAATATAATATGTCCCATCTAATATACAA
1 ATATTTCTATCACGATGTTTAATAAATTTATTTATTAATATAATATGTCCCATCTAATATACAA
47467365 ATATTT
1 ATATTT
47467371 AATAAAATAT
Statistics
Matches: 68, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
64 68 1.00
ACGTcount: A:0.38, C:0.12, G:0.04, T:0.46
Consensus pattern (64 bp):
ATATTTCTATCACGATGTTTAATAAATTTATTTATTAATATAATATGTCCCATCTAATATACAA
Found at i:47467445 original size:24 final size:24
Alignment explanation
Indices: 47467418--47467488 Score: 106
Period size: 24 Copynumber: 3.0 Consensus size: 24
47467408 ATTATTATTG
*
47467418 AAATATTCTCGTCCGTTTTATCAC
1 AAATATTATCGTCCGTTTTATCAC
* *
47467442 AAATATTATTGTTCGTTTTATCAC
1 AAATATTATCGTCCGTTTTATCAC
*
47467466 AAATATTATCGCCCGTTTTATCA
1 AAATATTATCGTCCGTTTTATCA
47467489 TTTAAGTTAA
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 41 1.00
ACGTcount: A:0.28, C:0.20, G:0.08, T:0.44
Consensus pattern (24 bp):
AAATATTATCGTCCGTTTTATCAC
Found at i:47467695 original size:29 final size:29
Alignment explanation
Indices: 47467662--47467735 Score: 112
Period size: 29 Copynumber: 2.6 Consensus size: 29
47467652 ACCGACATGT
* * *
47467662 ATATTATTGAATTAAAATAATTTTTTTCA
1 ATATTATTTAATTAAAATAATTTTTATAA
*
47467691 GTATTATTTAATTAAAATAATTTTTATAA
1 ATATTATTTAATTAAAATAATTTTTATAA
47467720 ATATTATTTAATTAAA
1 ATATTATTTAATTAAA
47467736 TATTATTTAA
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 40 1.00
ACGTcount: A:0.45, C:0.01, G:0.03, T:0.51
Consensus pattern (29 bp):
ATATTATTTAATTAAAATAATTTTTATAA
Found at i:47467735 original size:15 final size:15
Alignment explanation
Indices: 47467692--47467746 Score: 71
Period size: 15 Copynumber: 3.7 Consensus size: 15
47467682 TTTTTTTCAG
47467692 TATTATTTAATTAAAA
1 TATTATTTAATT-AAA
47467708 TAATT-TTT-A-TAAA
1 T-ATTATTTAATTAAA
47467721 TATTATTTAATTAAA
1 TATTATTTAATTAAA
47467736 TATTATTTAAT
1 TATTATTTAAT
47467747 CCGCAGCTTA
Statistics
Matches: 35, Mismatches: 0, Indels: 9
0.80 0.00 0.20
Matches are distributed among these distances:
12 3 0.09
13 7 0.20
14 2 0.06
15 16 0.46
16 4 0.11
17 3 0.09
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (15 bp):
TATTATTTAATTAAA
Found at i:47467875 original size:9 final size:9
Alignment explanation
Indices: 47467857--47468146 Score: 302
Period size: 9 Copynumber: 32.7 Consensus size: 9
47467847 TAAATATTTA
47467857 ACATAACTT
1 ACATAACTT
*
47467866 ACAAAACTT
1 ACATAACTT
47467875 ACATAACTT
1 ACATAACTT
*
47467884 ATATAACTT
1 ACATAACTT
47467893 ACATAACTT
1 ACATAACTT
*
47467902 ATATAACTT
1 ACATAACTT
*
47467911 ATATAACTT
1 ACATAACTT
* *
47467920 AGATAA-AT
1 ACATAACTT
*
47467928 ATATAACTT
1 ACATAACTT
47467937 ACATAACTT
1 ACATAACTT
47467946 ACATAACTT
1 ACATAACTT
*
47467955 ATATAACTT
1 ACATAACTT
* *
47467964 AGATAA-AT
1 ACATAACTT
*
47467972 ATATAACTT
1 ACATAACTT
47467981 ACATAACTT
1 ACATAACTT
47467990 ACATAACTT
1 ACATAACTT
47467999 ACATAACTT
1 ACATAACTT
*
47468008 ATATAACTT
1 ACATAACTT
47468017 ACATAACTT
1 ACATAACTT
*
47468026 AGATAACTT
1 ACATAACTT
*
47468035 ATATAACTT
1 ACATAACTT
* *
47468044 AGATAA-AT
1 ACATAACTT
*
47468052 ATATAACTT
1 ACATAACTT
47468061 ACATAACTT
1 ACATAACTT
47468070 ACATAACTT
1 ACATAACTT
**
47468079 ATGTAACTT
1 ACATAACTT
* *
47468088 AGATAA-AT
1 ACATAACTT
*
47468096 ATATAACTT
1 ACATAACTT
*
47468105 ACATAA-AT
1 ACATAACTT
* * *
47468113 ATATATCAT
1 ACATAACTT
47468122 ATCATAACTT
1 A-CATAACTT
47468132 ACATAACTT
1 ACATAACTT
47468141 ACATAA
1 ACATAA
47468147 TACTTAAATA
Statistics
Matches: 236, Mismatches: 39, Indels: 12
0.82 0.14 0.04
Matches are distributed among these distances:
8 29 0.12
9 201 0.85
10 6 0.03
ACGTcount: A:0.47, C:0.15, G:0.02, T:0.36
Consensus pattern (9 bp):
ACATAACTT
Found at i:47467940 original size:44 final size:44
Alignment explanation
Indices: 47467858--47468146 Score: 181
Period size: 44 Copynumber: 6.5 Consensus size: 44
47467848 AAATATTTAA
* * * * *
47467858 CATAACTTACAAAACTTACATAACTTATATAACTTACATAACTTA
1 CATAACTTACATAACTTATATAACTTAGATAA-ATATATAACTTA
* * * * * * *
47467903 TATAACTTATATAACTTAGATAA-ATATATAACTTACATAACTTA
1 CATAACTTACATAACTTATATAACTTAGATAA-ATATATAACTTA
* * * * * *
47467947 CATAACTTATATAACTTAGATAA-ATATATAACTTACATAACTTA
1 CATAACTTACATAACTTATATAACTTAGATAA-ATATATAACTTA
* * *
47467991 CATAACTTACATAACTTATATAACTTACATAACTTAGATAACTTA
1 CATAACTTACATAACTTATATAACTTAGATAA-ATATATAACTTA
* * * * * *
47468036 TATAACTTAGATAA-ATATATAACTTACATAACTTACATAACTTA
1 CATAACTTACATAACTTATATAACTTAGATAA-ATATATAACTTA
** * * * * *
47468080 TGTAACTTAGATAA-ATATATAACTTACATAAATATATATCATA
1 CATAACTTACATAACTTATATAACTTAGATAAATATATAACTTA
*
47468123 TCATAACTTACATAACTTACATAA
1 -CATAACTTACATAACTTATATAA
47468147 TACTTAAATA
Statistics
Matches: 216, Mismatches: 25, Indels: 6
0.87 0.10 0.02
Matches are distributed among these distances:
43 8 0.04
44 153 0.71
45 55 0.25
ACGTcount: A:0.47, C:0.15, G:0.02, T:0.36
Consensus pattern (44 bp):
CATAACTTACATAACTTATATAACTTAGATAAATATATAACTTA
Found at i:47468077 original size:124 final size:124
Alignment explanation
Indices: 47467857--47468146 Score: 492
Period size: 124 Copynumber: 2.3 Consensus size: 124
47467847 TAAATATTTA
* *
47467857 ACATAACTTACAAAACTTACATAACTTATATAACTTACATAACTTATATAACTTATATAACTTAG
1 ACATAACTTACATAACTTACATAACTTATATAACTTACATAACTTAGATAACTTATATAACTTAG
47467922 ATAAATATATAACTTACATAACTTACATAACTTATATAACTTAGATAAATATATAACTT
66 ATAAATATATAACTTACATAACTTACATAACTTATATAACTTAGATAAATATATAACTT
47467981 ACATAACTTACATAACTTACATAACTTATATAACTTACATAACTTAGATAACTTATATAACTTAG
1 ACATAACTTACATAACTTACATAACTTATATAACTTACATAACTTAGATAACTTATATAACTTAG
*
47468046 ATAAATATATAACTTACATAACTTACATAACTTATGTAACTTAGATAAATATATAACTT
66 ATAAATATATAACTTACATAACTTACATAACTTATATAACTTAGATAAATATATAACTT
* * * * *
47468105 ACATAA-ATATATATCATATCATAACTTACATAACTTACATAA
1 ACATAACTTACATAACTTA-CATAACTTATATAACTTACATAA
47468147 TACTTAAATA
Statistics
Matches: 157, Mismatches: 8, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
123 8 0.05
124 149 0.95
ACGTcount: A:0.47, C:0.15, G:0.02, T:0.36
Consensus pattern (124 bp):
ACATAACTTACATAACTTACATAACTTATATAACTTACATAACTTAGATAACTTATATAACTTAG
ATAAATATATAACTTACATAACTTACATAACTTATATAACTTAGATAAATATATAACTT
Found at i:47470032 original size:12 final size:12
Alignment explanation
Indices: 47470015--47470039 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
47470005 AAGATCGAGG
47470015 GATGAATCTGAT
1 GATGAATCTGAT
47470027 GATGAATCTGAT
1 GATGAATCTGAT
47470039 G
1 G
47470040 GAGAAGATGA
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:0.32, C:0.08, G:0.28, T:0.32
Consensus pattern (12 bp):
GATGAATCTGAT
Found at i:47473300 original size:40 final size:40
Alignment explanation
Indices: 47473256--47473407 Score: 286
Period size: 40 Copynumber: 3.8 Consensus size: 40
47473246 ATAACCACAA
*
47473256 GCACAAATGCCCTCGGGTCTTAGCCCGGATATATCAACTC
1 GCACAAATGCCTTCGGGTCTTAGCCCGGATATATCAACTC
*
47473296 GCACAAATGCCTTCGGGTCTTAGCCCGGATATATCAACTT
1 GCACAAATGCCTTCGGGTCTTAGCCCGGATATATCAACTC
47473336 GCACAAATGCCTTCGGGTCTTAGCCCGGATATATCAACTC
1 GCACAAATGCCTTCGGGTCTTAGCCCGGATATATCAACTC
47473376 GCACAAATGCCTTCGGGTCTTAGCCCGGATAT
1 GCACAAATGCCTTCGGGTCTTAGCCCGGATAT
47473408 CATTCAAATG
Statistics
Matches: 109, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
40 109 1.00
ACGTcount: A:0.24, C:0.30, G:0.21, T:0.25
Consensus pattern (40 bp):
GCACAAATGCCTTCGGGTCTTAGCCCGGATATATCAACTC
Found at i:47477098 original size:13 final size:14
Alignment explanation
Indices: 47477082--47477110 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
47477072 TTCTAAATAT
47477082 TTATAA-TGTTTAA
1 TTATAATTGTTTAA
47477095 TTATAATTGTTTAA
1 TTATAATTGTTTAA
47477109 TT
1 TT
47477111 CAATTCCTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 6 0.40
14 9 0.60
ACGTcount: A:0.34, C:0.00, G:0.07, T:0.59
Consensus pattern (14 bp):
TTATAATTGTTTAA
Found at i:47477610 original size:21 final size:21
Alignment explanation
Indices: 47477537--47477621 Score: 111
Period size: 21 Copynumber: 4.0 Consensus size: 21
47477527 GGCAACAGAA
* *
47477537 AGGGAGGCAGCGACAGCAGCG
1 AGGGAGGCAGAGGCAGCAGCG
47477558 AGGGAGGCAGCA-GCAGCAGCG
1 AGGGAGGCAG-AGGCAGCAGCG
47477579 AGGGAGGCAGAGGCA-CGAGCG
1 AGGGAGGCAGAGGCAGC-AGCG
*
47477600 AGGGAGGCAGAGGTAGCAGCG
1 AGGGAGGCAGAGGCAGCAGCG
47477621 A
1 A
47477622 TGGCAGAAGA
Statistics
Matches: 57, Mismatches: 3, Indels: 8
0.84 0.04 0.12
Matches are distributed among these distances:
20 2 0.04
21 54 0.95
22 1 0.02
ACGTcount: A:0.29, C:0.20, G:0.49, T:0.01
Consensus pattern (21 bp):
AGGGAGGCAGAGGCAGCAGCG
Found at i:47479940 original size:16 final size:15
Alignment explanation
Indices: 47479912--47479964 Score: 56
Period size: 16 Copynumber: 3.5 Consensus size: 15
47479902 AAGTAATTAA
47479912 AAATAGTACTATATAT
1 AAATA-TACTATATAT
47479928 AAATATACATATATAT
1 AAATATAC-TATATAT
* *
47479944 ACATATA-TA-ATAA
1 AAATATACTATATAT
47479957 AAATATAC
1 AAATATAC
47479965 ACTAGTATTA
Statistics
Matches: 32, Mismatches: 3, Indels: 6
0.78 0.07 0.15
Matches are distributed among these distances:
13 9 0.28
14 2 0.06
15 3 0.09
16 18 0.56
ACGTcount: A:0.57, C:0.08, G:0.02, T:0.34
Consensus pattern (15 bp):
AAATATACTATATAT
Found at i:47479962 original size:29 final size:28
Alignment explanation
Indices: 47479928--47479989 Score: 74
Period size: 29 Copynumber: 2.2 Consensus size: 28
47479918 TACTATATAT
47479928 AAATATACA-TA-TATATACATATATAATAA
1 AAATATACACTAGTAT-TA-ATA-ATAATAA
47479957 AAATATACACTAGTATTAATAATAATAA
1 AAATATACACTAGTATTAATAATAATAA
*
47479985 TAATA
1 AAATA
47479990 ATAATAATAA
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
28 11 0.37
29 12 0.40
30 4 0.13
31 3 0.10
ACGTcount: A:0.58, C:0.06, G:0.02, T:0.34
Consensus pattern (28 bp):
AAATATACACTAGTATTAATAATAATAA
Found at i:47479981 original size:3 final size:3
Alignment explanation
Indices: 47479973--47480013 Score: 73
Period size: 3 Copynumber: 13.7 Consensus size: 3
47479963 ACACTAGTAT
*
47479973 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAG TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
47480014 TTGAAATACA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:47480130 original size:3 final size:3
Alignment explanation
Indices: 47480116--47480154 Score: 60
Period size: 3 Copynumber: 12.7 Consensus size: 3
47480106 AAGTATACAC
*
47480116 TAA TATA TAA TAA TAA TAA TAA TAA TAA TAG TAA TAA TA
1 TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
47480155 TTGAAATACA
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
3 30 0.91
4 3 0.09
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:47480167 original size:141 final size:141
Alignment explanation
Indices: 47479827--47480463 Score: 654
Period size: 141 Copynumber: 4.2 Consensus size: 141
47479817 AATAATGATG
* * *
47479827 ATAATGATAATAA-AACTAGCAATAATAATGAAATACAAAAAAAAGCAAATATAAAATAATAATA
1 ATAATAATAATAATAA-TAGTAATAATATTGAAATAC---AAAAAGCAAATAT--AAT-A-AA-A
* * * *
47479891 ATGTTAAAATAAAGTAATTAAAAATAGTACTATATATAAATATACATATATATACATATATAATA
57 ATATTAAAATAAAGTAATAAAAAATAATACTATATATAAATATAC----ATATACGTATATAATA
47479956 -AAAATATACACTAGTATTAATAATAATAATA
118 TAAAATATACAC------TAAT-AT-ATAATA
47479987 ATAATAATAATAATAATAGTAATAATATTGAAATACAAAAAGCAAATATAATAAAAATATTAAAA
1 ATAATAATAATAATAATAGTAATAATATTGAAATACAAAAAGCAAATATAATAAAAATATTAAAA
* * * *
47480052 TAGACTAATAAAAAATAATACTATATATAAATATACATATACGTATATAATATCAAGTATACACT
66 TAAAGTAATAAAAAATAATACTATATATAAATATACATATACGTATATAATATAAAATATACACT
47480117 AATATATAATA
131 AATATATAATA
*
47480128 ATAATAATAATAATAATAGTAATAATATTGAAATACAAAAAGCCAATATAATAAAAATATTAAAA
1 ATAATAATAATAATAATAGTAATAATATTGAAATACAAAAAGCAAATATAATAAAAATATTAAAA
* *
47480193 CAAAGTAATAAAAAATAATACTATATATAAATATATATATATATACGTATACATATATAATAAAA
66 TAAAGTAATAAAAAATAATACTATATAT--A-A-ATATACATATACGTAT--ATA-AT-AT-AAA
*
47480258 AAATACACTAATATATAATA
122 ATATACACTAATATATAATA
*
47480278 AAAAT-ATAATAATAATAGTAATAATATTGAAATACAAAAAGCCAATACAATATAATAAAAATAT
1 ATAATAATAATAATAATAGTAATAATATTGAAATACAAAAAG-C---A-AATATAATAAAAATAT
* *
47480342 TAAAATAAAGTAATTAAAAAATAATACTATGTATAAATATATATACATATACATACATATAATA-
61 TAAAATAAAGTAA-TAAAAAATAATACTA--TAT--ATAAATATACATATACGT--ATATAATAT
47480406 AAAATATACACTAATAT-TAATA
119 AAAATATACACTAATATATAATA
* * * *
47480428 ATGATAATAATGATAATATTAATAATAATAGAAATA
1 ATAATAATAATAATAATAGTAATAAT-ATTGAAATA
47480464 ATAATAATAT
Statistics
Matches: 421, Mismatches: 31, Indels: 58
0.83 0.06 0.11
Matches are distributed among these distances:
141 95 0.23
142 2 0.00
143 5 0.01
144 1 0.00
145 15 0.04
147 3 0.01
148 17 0.04
149 47 0.11
150 33 0.08
151 34 0.08
152 49 0.12
153 3 0.01
154 31 0.07
155 33 0.08
157 19 0.05
159 2 0.00
160 30 0.07
161 2 0.00
ACGTcount: A:0.60, C:0.06, G:0.04, T:0.30
Consensus pattern (141 bp):
ATAATAATAATAATAATAGTAATAATATTGAAATACAAAAAGCAAATATAATAAAAATATTAAAA
TAAAGTAATAAAAAATAATACTATATATAAATATACATATACGTATATAATATAAAATATACACT
AATATATAATA
Found at i:47480233 original size:16 final size:16
Alignment explanation
Indices: 47480205--47480256 Score: 52
Period size: 16 Copynumber: 3.2 Consensus size: 16
47480195 AAGTAATAAA
47480205 AAATA-ATACTATATAT
1 AAATATATA-TATATAT
47480221 AAATATATATATATAT
1 AAATATATATATATAT
** *
47480237 ACGTATACATATATAAT
1 AAATATATATATAT-AT
47480254 AAA
1 AAA
47480257 AAAATACACT
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
16 23 0.79
17 6 0.21
ACGTcount: A:0.56, C:0.06, G:0.02, T:0.37
Consensus pattern (16 bp):
AAATATATATATATAT
Found at i:47480280 original size:21 final size:21
Alignment explanation
Indices: 47480245--47480301 Score: 60
Period size: 23 Copynumber: 2.5 Consensus size: 21
47480235 ATACGTATAC
*
47480245 ATATATAATAAAAAAATACACTA
1 ATATATAAT--AAAAATACAATA
*
47480268 ATATATAATAAAAATATAATA
1 ATATATAATAAAAATACAATA
47480289 ATAATAGTAATAA
1 AT-ATA-TAATAA
47480302 TATTGAAATA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
21 12 0.40
22 3 0.10
23 15 0.50
ACGTcount: A:0.65, C:0.04, G:0.02, T:0.30
Consensus pattern (21 bp):
ATATATAATAAAAATACAATA
Found at i:47480413 original size:21 final size:22
Alignment explanation
Indices: 47480388--47480428 Score: 59
Period size: 21 Copynumber: 1.9 Consensus size: 22
47480378 ATATATATAC
47480388 ATATACA-TACATA-TAATAAAA
1 ATATACACTA-ATATTAATAAAA
47480409 ATATACACTAATATTAATAA
1 ATATACACTAATATTAATAA
47480429 TGATAATAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 10 0.56
22 8 0.44
ACGTcount: A:0.59, C:0.10, G:0.00, T:0.32
Consensus pattern (22 bp):
ATATACACTAATATTAATAAAA
Found at i:47480437 original size:3 final size:3
Alignment explanation
Indices: 47480417--47480472 Score: 60
Period size: 3 Copynumber: 18.7 Consensus size: 3
47480407 AAATATACAC
* * * *
47480417 TAA TAT TAA TAA TGA TAA TAA TGA TAA TAT TAA TAA TAA TAGA -AA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA-A TAA
47480462 TAA TAA TAA TA
1 TAA TAA TAA TA
47480473 TTTAATAAAG
Statistics
Matches: 43, Mismatches: 8, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
2 1 0.02
3 41 0.95
4 1 0.02
ACGTcount: A:0.59, C:0.00, G:0.05, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:47480484 original size:24 final size:24
Alignment explanation
Indices: 47480417--47480494 Score: 79
Period size: 27 Copynumber: 3.1 Consensus size: 24
47480407 AAATATACAC
* *
47480417 TAATA-TTAATAATGATAATAATGA
1 TAATATTTAATAAAGA-AATAATAA
47480441 TAATATTAATAATAATAGAAATAATAA
1 TAATATT--TAATAA-AGAAATAATAA
47480468 TAATATTTAATAAAGAAATGAA-AA
1 TAATATTTAATAAAGAAAT-AATAA
47480492 TAA
1 TAA
47480495 ACAAGAAAGG
Statistics
Matches: 47, Mismatches: 2, Indels: 10
0.80 0.03 0.17
Matches are distributed among these distances:
24 16 0.34
25 9 0.19
27 20 0.43
28 2 0.04
ACGTcount: A:0.60, C:0.00, G:0.06, T:0.33
Consensus pattern (24 bp):
TAATATTTAATAAAGAAATAATAA
Found at i:47482201 original size:133 final size:134
Alignment explanation
Indices: 47481937--47482201 Score: 349
Period size: 133 Copynumber: 2.0 Consensus size: 134
47481927 AAACTGACGT
* * * * * *
47481937 TCAACTCATCTCTCGGATTATGAGTTAATTTTTGAAAAAAGTAAAAAAATTGAAAATACCTTAGT
1 TCAACTCACCTCTCGCAATATGAGTCAATTTTTGAAAAAAGTAAAAAAATTGAAAATA-CTCAGC
* * *
47482002 GTGTGACCTGAGGCTCAACTCACATCTCTCAATATGAGTTGAATTTTTTGAAAAATAGAGATTAA
65 GTGTGACCCGAGGCTCAACTCACATCTCTCAATATGAGTTGAATTTTTTGAAAAATAGAAACTAA
47482067 AAGGC
130 AAGGC
*
47482072 TCAACTCACCTCTCGCAATATGAGTCAATTTTTTG-AAAAAG-AACATAAATTGAAAAT-CTCAG
1 TCAACTCACCTCTCGCAATATGAGTCAA-TTTTTGAAAAAAGTAA-AAAAATTGAAAATACTCAG
* * *
47482134 CGTGTGTCCCGAGGCTCAACTCACCTCTCGT-AATATGAGTTGATTTTTTTGAAAAATAGAAACT
64 CGTGTGACCCGAGGCTCAACTCACATCTC-TCAATATGAGTTGAATTTTTTGAAAAATAGAAACT
47482198 AAAA
128 AAAA
47482202 ATACCTCAGC
Statistics
Matches: 114, Mismatches: 13, Indels: 8
0.84 0.10 0.06
Matches are distributed among these distances:
133 63 0.55
134 3 0.03
135 42 0.37
136 6 0.05
ACGTcount: A:0.37, C:0.17, G:0.15, T:0.31
Consensus pattern (134 bp):
TCAACTCACCTCTCGCAATATGAGTCAATTTTTGAAAAAAGTAAAAAAATTGAAAATACTCAGCG
TGTGACCCGAGGCTCAACTCACATCTCTCAATATGAGTTGAATTTTTTGAAAAATAGAAACTAAA
AGGC
Found at i:47482210 original size:77 final size:77
Alignment explanation
Indices: 47482068--47482430 Score: 402
Period size: 77 Copynumber: 4.8 Consensus size: 77
47482058 AGAGATTAAA
* * * *
47482068 AGGCTCAACTCACCTCTCGCAATATGAG-TCAATTTTTTG-AAAA-AG-AACATAAATTGAAAAT
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAAATAGAAAC-TAAA---AATAC
*
47482129 CTCAGCGTGTGTCCCG
62 CTCAGCGTGTGACCCG
*
47482145 AGGCTCAACTCACCTCTCGTAATATGAGTTGATTTTTTTGAAAAATAGAAACTAAAAATACCTCA
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAAATAGAAACTAAAAATACCTCA
*
47482210 GCATGTGACCCG
66 GCGTGTGACCCG
* * ** * *
47482222 AGGCTCAACTCACTTCTCGCAATTTGAGTTGATTTTTTTGAAACGT--AAATTGAAAATACCTCA
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAAATAGAAACTAAAAATACCTCA
* * ****
47482285 GTGCGTGATTTA
66 GCGTGTGACCCG
* * * *
47482297 AGGCTCAACTCACCTCTCTCAATATGAGTTGATTTTTTTGAAAAATAGGAACTAAAGATGCCTCA
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAAATAGAAACTAAAAATACCTCA
47482362 GCGTGTGACCCG
66 GCGTGTGACCCG
* *
47482374 AGGCTCAACTCACCTCTCGCAATATGAGTTGA--TTTTTGAAAAAAATAAA-TAAAAATA
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAAATAGAAACTAAAAATA
47482431 TCAGGATACC
Statistics
Matches: 237, Mismatches: 43, Indels: 15
0.80 0.15 0.05
Matches are distributed among these distances:
74 6 0.03
75 75 0.32
77 134 0.57
78 9 0.04
79 4 0.02
80 6 0.03
81 3 0.01
ACGTcount: A:0.34, C:0.20, G:0.17, T:0.30
Consensus pattern (77 bp):
AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAAATAGAAACTAAAAATACCTCA
GCGTGTGACCCG
Found at i:47482423 original size:152 final size:150
Alignment explanation
Indices: 47482068--47482423 Score: 464
Period size: 152 Copynumber: 2.3 Consensus size: 150
47482058 AGAGATTAAA
**
47482068 AGGCTCAACTCACCTCTCGCAATATGAGTCAATTTTTTGAAAAAGAACATAAATTGAAAATCTCA
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGA-TTTTTG-AAAA-AA-ATAAATTGAAAATCTCA
* *
47482133 GCGTGTGTCCCGAGGCTCAACTCACCTCTCGTAATATGAGTTGATTTTTTTGAAAAATAGAAACT
62 GCGCGTGTCCCAAGGCTCAACTCACCTCTCGTAATATGAGTTGATTTTTTTGAAAAATAGAAACT
47482198 AAAAATACCTCAGCATGTGACCCG
127 AAAAATACCTCAGCATGTGACCCG
* * *** ** *
47482222 AGGCTCAACTCACTTCTCGCAATTTGAGTTGATTTTTTTGAAACGTAAATTGAAAATACCTCAGT
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAAAATAAATTGAAAAT--CTCAGC
** *
47482287 GCGTGAT-TTAAGGCTCAACTCACCTCTC-TCAATATGAGTTGATTTTTTTGAAAAATAGGAACT
64 GCGTG-TCCCAAGGCTCAACTCACCTCTCGT-AATATGAGTTGATTTTTTTGAAAAATAGAAACT
* * *
47482350 AAAGATGCCTCAGCGTGTGACCCG
127 AAAAATACCTCAGCATGTGACCCG
47482374 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAAAATAAAT
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAAAATAAAT
47482424 AAAAATATCA
Statistics
Matches: 173, Mismatches: 25, Indels: 10
0.83 0.12 0.05
Matches are distributed among these distances:
150 12 0.07
151 2 0.01
152 125 0.72
153 6 0.03
154 28 0.16
ACGTcount: A:0.33, C:0.20, G:0.17, T:0.30
Consensus pattern (150 bp):
AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAAAATAAATTGAAAATCTCAGCGC
GTGTCCCAAGGCTCAACTCACCTCTCGTAATATGAGTTGATTTTTTTGAAAAATAGAAACTAAAA
ATACCTCAGCATGTGACCCG
Found at i:47496226 original size:16 final size:15
Alignment explanation
Indices: 47496198--47496250 Score: 56
Period size: 16 Copynumber: 3.5 Consensus size: 15
47496188 AAGTAATTAA
47496198 AAATAGTACTATATAT
1 AAATA-TACTATATAT
47496214 AAATATACATATATAT
1 AAATATAC-TATATAT
* *
47496230 ACATATA-TA-ATAA
1 AAATATACTATATAT
47496243 AAATATAC
1 AAATATAC
47496251 ACTAGTATTA
Statistics
Matches: 32, Mismatches: 3, Indels: 6
0.78 0.07 0.15
Matches are distributed among these distances:
13 9 0.28
14 2 0.06
15 3 0.09
16 18 0.56
ACGTcount: A:0.57, C:0.08, G:0.02, T:0.34
Consensus pattern (15 bp):
AAATATACTATATAT
Found at i:47496248 original size:29 final size:28
Alignment explanation
Indices: 47496214--47496296 Score: 75
Period size: 27 Copynumber: 3.0 Consensus size: 28
47496204 TACTATATAT
47496214 AAATATACA-TA-TATATACATATATAATAA
1 AAATATACACTAGTAT-TA-ATA-ATAATAA
47496243 AAATATACACTAGTATTAATAATAATAA
1 AAATATACACTAGTATTAATAATAATAA
* * *
47496271 TAATAATA-A-TAATAATAATAATAATA
1 AAAT-ATACACTAGTATTAATAATAATA
47496297 TTGAAATACA
Statistics
Matches: 48, Mismatches: 3, Indels: 8
0.81 0.05 0.14
Matches are distributed among these distances:
27 15 0.31
28 11 0.23
29 15 0.31
30 4 0.08
31 3 0.06
ACGTcount: A:0.60, C:0.05, G:0.01, T:0.34
Consensus pattern (28 bp):
AAATATACACTAGTATTAATAATAATAA
Found at i:47496267 original size:3 final size:3
Alignment explanation
Indices: 47496259--47496296 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
47496249 ACACTAGTAT
47496259 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
47496297 TTGAAATACA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:47496614 original size:144 final size:145
Alignment explanation
Indices: 47496113--47496826 Score: 888
Period size: 144 Copynumber: 4.8 Consensus size: 145
47496103 AATAATGATG
* * *
47496113 ATAATGATAATAA-AACTAGCAATAATAATGAAATACAAAAAAAAGCAAATATAAAATAATAATA
1 ATAATAATAATAATAA-TAGTAATAATATTGAAATAC-AAAAAAAGCAAATAT--AAT-A-AA-A
* * * * *
47496177 ATGTTAAAATAAAGTAATTAAAAATAGTACTATATATAAATATACATATATATACATATATAAT-
59 ATATTAAAATAAAGTAATAAAAAATAATACTATATATAAATATATATACATATACATATATAATA
47496241 AAAAATATACACTAGTATTAATAATAATA
124 AAAAATATACAC------TAAT-ATAATA
* **
47496270 ATAATAATAATAATAATAATAATAATATTGAAATACAAAAAGCAAATATAATATAATAAAAATAT
1 ATAATAATAATAATAATAGTAATAATATTGAAATACAAAAA--AAGCA-AATATAATAAAAATAT
* *
47496335 TAAAATAAAGTAATTAAAAAAATAATACTATGTATAAATATATATACATATACATACATATATAA
63 TAAAATAAAGTAA-T-AAAAAATAATACTATATATAAATATATATACATATACATATATA-AT-A
47496400 TAAAAATATACACTAATAT--TA
124 -AAAAATATACACTAATATAATA
* *
47496421 ATAATAATAATGATAATAGTAATAATATTGAAATAC--AAAAAGCCAATATAATAAAAATATTAA
1 ATAATAATAATAATAATAGTAATAATATTGAAATACAAAAAAAGCAAATATAATAAAAATATTAA
* * *
47496484 AACAAAATAATAAAAAATAATACTATATATAAATATATTTACATATACATATATAATAAAAAATA
66 AATAAAGTAATAAAAAATAATACTATATATAAATATATATACATATACATATATAATAAAAAATA
47496549 TACACTAATAT-ATA
131 TACACTAATATAATA
* * * * *
47496563 ATAATGATAATAATAATAGTAATCATGTTGAAATGCAAAAAAAGCAAATATAATAAAAGTATTAA
1 ATAATAATAATAATAATAGTAATAATATTGAAATACAAAAAAAGCAAATATAATAAAAATATTAA
* *
47496628 AATAAAATAATAAAAAATAATACTATATATAAATATATATACATATACATATACAATAAAAAATA
66 AATAAAGTAATAAAAAATAATACTATATATAAATATATATACATATACATATATAATAAAAAATA
*
47496693 TACATTAATATATAATA
131 TACACT-A-ATATAATA
* *
47496710 ATAATAATAATAATAATAGTGATCATATTGAAATACAAAAAAAAGCAAATATAATAAAAATATTA
1 ATAATAATAATAATAATAGTAATAATATTGAAATAC-AAAAAAAGCAAATATAATAAAAATATTA
47496775 AAATAAAGT-A-AAAAAATAATACTATATATAAATATATATACATATACATATA
65 AAATAAAGTAATAAAAAATAATACTATATATAAATATATATACATATACATATA
47496827 CAAAACTCAA
Statistics
Matches: 500, Mismatches: 40, Indels: 45
0.85 0.07 0.08
Matches are distributed among these distances:
141 18 0.04
142 34 0.07
143 2 0.00
144 133 0.27
145 2 0.00
146 73 0.15
147 38 0.08
148 35 0.07
149 3 0.01
151 36 0.07
153 2 0.00
154 21 0.04
155 3 0.01
156 44 0.09
157 34 0.07
158 5 0.01
159 5 0.01
160 12 0.02
ACGTcount: A:0.61, C:0.06, G:0.04, T:0.30
Consensus pattern (145 bp):
ATAATAATAATAATAATAGTAATAATATTGAAATACAAAAAAAGCAAATATAATAAAAATATTAA
AATAAAGTAATAAAAAATAATACTATATATAAATATATATACATATACATATATAATAAAAAATA
TACACTAATATAATA
Found at i:47496712 original size:3 final size:3
Alignment explanation
Indices: 47496698--47496727 Score: 51
Period size: 3 Copynumber: 9.7 Consensus size: 3
47496688 AAATATACAT
47496698 TAA TATA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TA-A TAA TAA TAA TAA TAA TAA TAA TA
47496728 GTGATCATAT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 23 0.88
4 3 0.12
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (3 bp):
TAA
Found at i:47496718 original size:26 final size:27
Alignment explanation
Indices: 47496658--47496718 Score: 74
Period size: 26 Copynumber: 2.3 Consensus size: 27
47496648 TACTATATAT
47496658 AAATATATATACATATACATATACAATA
1 AAATA-ATATACATATACATATACAATA
*
47496686 AAA-AATATACAT-TA-ATATATAATA
1 AAATAATATACATATACATATACAATA
47496710 ATAATAATA
1 A-AATAATA
47496719 ATAATAATAG
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
24 10 0.33
25 4 0.13
26 12 0.40
27 1 0.03
28 3 0.10
ACGTcount: A:0.61, C:0.07, G:0.00, T:0.33
Consensus pattern (27 bp):
AAATAATATACATATACATATACAATA
Found at i:47497479 original size:39 final size:39
Alignment explanation
Indices: 47497425--47497505 Score: 153
Period size: 39 Copynumber: 2.1 Consensus size: 39
47497415 GCTTTGCTTT
*
47497425 TATAGCTATTTTTACATGCTTTCATTATTATTTCTTTAC
1 TATAGCCATTTTTACATGCTTTCATTATTATTTCTTTAC
47497464 TATAGCCATTTTTACATGCTTTCATTATTATTTCTTTAC
1 TATAGCCATTTTTACATGCTTTCATTATTATTTCTTTAC
47497503 TAT
1 TAT
47497506 CTCTTGTTTC
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
39 41 1.00
ACGTcount: A:0.23, C:0.16, G:0.05, T:0.56
Consensus pattern (39 bp):
TATAGCCATTTTTACATGCTTTCATTATTATTTCTTTAC
Found at i:47502719 original size:18 final size:18
Alignment explanation
Indices: 47502649--47502712 Score: 101
Period size: 18 Copynumber: 3.6 Consensus size: 18
47502639 GGACTTGCAT
*
47502649 ACTGTTTACTGATACTAC
1 ACTGTTTACTGATACTGC
*
47502667 ACTGTTTATTGATACTGC
1 ACTGTTTACTGATACTGC
*
47502685 ACTGTTTACTGTTACTGC
1 ACTGTTTACTGATACTGC
47502703 ACTGTTTACT
1 ACTGTTTACT
47502713 ATTACTGAAT
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 42 1.00
ACGTcount: A:0.22, C:0.20, G:0.14, T:0.44
Consensus pattern (18 bp):
ACTGTTTACTGATACTGC
Found at i:47509522 original size:14 final size:14
Alignment explanation
Indices: 47509503--47509531 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
47509493 TTATTGACCC
47509503 AACATATCCAGAAG
1 AACATATCCAGAAG
47509517 AACATATCCAGAAG
1 AACATATCCAGAAG
47509531 A
1 A
47509532 TATGTAATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.52, C:0.21, G:0.14, T:0.14
Consensus pattern (14 bp):
AACATATCCAGAAG
Found at i:47513945 original size:22 final size:22
Alignment explanation
Indices: 47513911--47513954 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
47513901 TTGTGTTTAG
47513911 GGTTTAAAGGTTAATTAAATTAA
1 GGTTTAAAGGTTAATT-AATTAA
47513934 GGTTT-AAGGTTAATTAATTAA
1 GGTTTAAAGGTTAATTAATTAA
47513955 ATTAACTATT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
21 6 0.29
22 10 0.48
23 5 0.24
ACGTcount: A:0.41, C:0.00, G:0.18, T:0.41
Consensus pattern (22 bp):
GGTTTAAAGGTTAATTAATTAA
Found at i:47514032 original size:8 final size:8
Alignment explanation
Indices: 47514021--47514097 Score: 56
Period size: 8 Copynumber: 10.0 Consensus size: 8
47514011 ATTAATTAAA
47514021 TTAGGGTT
1 TTAGGGTT
47514029 TTA-GGTT
1 TTAGGGTT
47514036 TTA-GGTT
1 TTAGGGTT
47514043 TTAGGG--
1 TTAGGGTT
*
47514049 TTAAGGTT
1 TTAGGGTT
*
47514057 TTAAGAG-T
1 TT-AGGGTT
*
47514065 TTAAGGTT
1 TTAGGGTT
**
47514073 TTATTGTGT
1 TTAGGGT-T
47514082 TTAGGGTT
1 TTAGGGTT
47514090 TTAGGGTT
1 TTAGGGTT
47514098 AATTAAATTA
Statistics
Matches: 54, Mismatches: 9, Indels: 12
0.72 0.12 0.16
Matches are distributed among these distances:
6 5 0.09
7 16 0.30
8 25 0.46
9 8 0.15
ACGTcount: A:0.18, C:0.00, G:0.31, T:0.51
Consensus pattern (8 bp):
TTAGGGTT
Found at i:47514037 original size:7 final size:7
Alignment explanation
Indices: 47514025--47514094 Score: 59
Period size: 7 Copynumber: 9.3 Consensus size: 7
47514015 ATTAAATTAG
47514025 GGTTTTA
1 GGTTTTA
47514032 GGTTTTA
1 GGTTTTA
47514039 GGTTTTA
1 GGTTTTA
* *
47514046 GGGTTAA
1 GGTTTTA
47514053 GGTTTTAA
1 GGTTTT-A
*
47514061 GAGTTTAA
1 G-GTTTTA
47514069 GGTTTTA
1 GGTTTTA
*
47514076 TTGTGTTTA
1 -GGT-TTTA
47514085 GGGTTTTA
1 -GGTTTTA
47514093 GG
1 GG
47514095 GTTAATTAAA
Statistics
Matches: 50, Mismatches: 9, Indels: 8
0.75 0.13 0.12
Matches are distributed among these distances:
7 30 0.60
8 10 0.20
9 10 0.20
ACGTcount: A:0.19, C:0.00, G:0.31, T:0.50
Consensus pattern (7 bp):
GGTTTTA
Found at i:47514044 original size:14 final size:14
Alignment explanation
Indices: 47514025--47514099 Score: 69
Period size: 14 Copynumber: 5.0 Consensus size: 14
47514015 ATTAAATTAG
*
47514025 GGTTTTAGGTTTTA
1 GGTTTTAGGTTTAA
*
47514039 GGTTTTAGGGTTAA
1 GGTTTTAGGTTTAA
47514053 GGTTTTAAGAGTTTAA
1 GGTTTT-AG-GTTTAA
*
47514069 GGTTTTATTGTGTTTAG
1 GGTTTTA--G-GTTTAA
*
47514086 GGTTTTAGGGTTAA
1 GGTTTTAGGTTTAA
47514100 TTAAATTAGG
Statistics
Matches: 50, Mismatches: 7, Indels: 8
0.77 0.11 0.12
Matches are distributed among these distances:
14 22 0.44
15 4 0.08
16 11 0.22
17 13 0.26
ACGTcount: A:0.20, C:0.00, G:0.31, T:0.49
Consensus pattern (14 bp):
GGTTTTAGGTTTAA
Found at i:47514117 original size:22 final size:23
Alignment explanation
Indices: 47514082--47514125 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 23
47514072 TTTATTGTGT
47514082 TTAGGGTTTTAGGGTTAATTAAA
1 TTAGGGTTTTAGGGTTAATTAAA
47514105 TTAGGG-TTTAGGGTTAATTAA
1 TTAGGGTTTTAGGGTTAATTAA
47514126 TTAAATTAAC
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
22 15 0.71
23 6 0.29
ACGTcount: A:0.30, C:0.00, G:0.27, T:0.43
Consensus pattern (23 bp):
TTAGGGTTTTAGGGTTAATTAAA
Found at i:47514274 original size:180 final size:173
Alignment explanation
Indices: 47513859--47514376 Score: 761
Period size: 175 Copynumber: 2.9 Consensus size: 173
47513849 TGATTTGGGA
* * * * *
47513859 TTTTAGGGTTTAGGGTTAGGGTTTTAAGAGTTTAAGAG-TTTGTTGTGTTTAGGGTTTAAAGGTT
1 TTTTAGGTTTTAGGGTTAAGGTTTTAAGAGTTTAAG-GTTTTATTGTGTTTAGGGTTTTAGGGTT
* *
47513923 AATTAAATTAAGGTTTAAGGTTAATTAATTAAATTAACTATTAATTTTAAAAAATCAATTAAATT
65 AATTAAATTAGGGTTTAGGGTTAATTAATTAAATTAACTATTAA-TTTAAAAAATCAATTAAATT
* * *
47513988 AGGGTTTAGAGTTTTTAAGGTTAATTAATTAAATTAGGGTTTTAGG
129 AGGGTTTAG-GTTTTTAAGGTTAATTAATTAAATCAGGGTTTAAAG
47514034 TTTTAGGTTTTAGGGTTAAGGTTTTAAGAGTTTAAGGTTTTATTGTGTTTAGGGTTTTAGGGTTA
1 TTTTAGGTTTTAGGGTTAAGGTTTTAAGAGTTTAAGGTTTTATTGTGTTTAGGGTTTTAGGGTTA
*
47514099 ATTAAATTAGGGTTTAGGGTTAATTAATTAAATTAACTATTAATTTAAAAAA-CAATTAAATTAA
66 ATTAAATTAGGGTTTAGGGTTAATTAATTAAATTAACTATTAATTTAAAAAATCAATTAAATTAG
47514163 GGTTTAAGGTTTTTAAGGTTAATTAATTAAATCAGGGTTTAAAG
131 GGTTT-AGGTTTTTAAGGTTAATTAATTAAATCAGGGTTTAAAG
* * *
47514207 TTTTAAGGTTCAGGATTTAGGGTTAATGTTTTAAGAGTTTAAGGTTTTATTGTGTTTATGATTTT
1 TTTT-AGG-T-----TTTAGGGTTAAGGTTTTAAGAGTTTAAGGTTTTATTGTGTTTAGGGTTTT
*
47514272 AGGGTTAATTAAATTAGGGTTTAGGGTTAATTAATTAAATTAACTATTAATTTAAAAAAATTAAT
59 AGGGTTAATTAAATTAGGGTTTAGGGTTAATTAATTAAATTAACTATTAATTT-AAAAAATCAAT
*
47514337 TAATTTAGGGTTTAGGATTTTTAAGGTTAATTAATTAAAT
123 TAAATTAGGGTTTAGG-TTTTTAAGGTTAATTAATTAAAT
47514377 TAGGATGCAC
Statistics
Matches: 314, Mismatches: 17, Indels: 17
0.90 0.05 0.05
Matches are distributed among these distances:
173 53 0.17
174 15 0.05
175 100 0.32
180 100 0.32
181 9 0.03
182 37 0.12
ACGTcount: A:0.34, C:0.01, G:0.20, T:0.45
Consensus pattern (173 bp):
TTTTAGGTTTTAGGGTTAAGGTTTTAAGAGTTTAAGGTTTTATTGTGTTTAGGGTTTTAGGGTTA
ATTAAATTAGGGTTTAGGGTTAATTAATTAAATTAACTATTAATTTAAAAAATCAATTAAATTAG
GGTTTAGGTTTTTAAGGTTAATTAATTAAATCAGGGTTTAAAG
Found at i:47514294 original size:47 final size:44
Alignment explanation
Indices: 47514185--47514299 Score: 99
Period size: 47 Copynumber: 2.5 Consensus size: 44
47514175 TTAAGGTTAA
* *
47514185 TTAATTAAATCAGGGTTTAAAGTTTTAAGGTTCAGGATTTAGGG
1 TTAATTAAATTAGGGTTTAAGGTTTTAAGGTTCAGGATTTAGGG
* * * * *
47514229 TTAATGT--TTTAAGAGTTTAAGGTTTTATTGTGTTTATGATTTTAGGG
1 TTAAT-TAAATT-AGGGTTTAAGGTTTTA-AG-GTTCAGGA-TTTAGGG
*
47514276 TTAATTAAATTAGGGTTTAGGGTT
1 TTAATTAAATTAGGGTTTAAGGTT
47514300 AATTAATTAA
Statistics
Matches: 54, Mismatches: 10, Indels: 11
0.72 0.13 0.15
Matches are distributed among these distances:
43 1 0.02
44 19 0.35
45 2 0.04
46 7 0.13
47 23 0.43
48 2 0.04
ACGTcount: A:0.28, C:0.02, G:0.24, T:0.46
Consensus pattern (44 bp):
TTAATTAAATTAGGGTTTAAGGTTTTAAGGTTCAGGATTTAGGG
Found at i:47514637 original size:126 final size:125
Alignment explanation
Indices: 47514378--47514638 Score: 391
Period size: 126 Copynumber: 2.1 Consensus size: 125
47514368 TAATTAAATT
*
47514378 AGGATGCACTGTCAGTAAAATTACTGAAAAAAGCTCTAACATAGACGCTCTTTTGCTACAGTAGT
1 AGGATGCACTGTCAGCAAAATTACTGAAAAAAGCTCTAACATAGACGCTCTTTTGCTACAGTAGT
** *
47514443 ATTTGAAAAATAATTTTGAGAAGACATTTCTGAACAAATAATGTCCAAAACGCTTCAAGC
66 ATTAAAAAAATAATTTTGAGAAAACATTTCTGAACAAATAATGTCCAAAACGCTTCAAGC
* * *
47514503 AGGATGCACTGTCAGCAAAATTACT-AAGATAAGCTC-ACACTTGGACGCTCTTTTGCTACAGTA
1 AGGATGCACTGTCAGCAAAATTACTGAA-AAAAGCTCTA-ACATAGACGCTCTTTTGCTACAGTA
* * *
47514566 GTATCTAAAAAAATAATTTTGAGAAAATATTTCTGAATAAATAGTGTCCAAAACGCTTCAAGC
64 GTAT-TAAAAAAATAATTTTGAGAAAACATTTCTGAACAAATAATGTCCAAAACGCTTCAAGC
47514629 AGGATGCACT
1 AGGATGCACT
47514639 ATGTAACACC
Statistics
Matches: 123, Mismatches: 10, Indels: 5
0.89 0.07 0.04
Matches are distributed among these distances:
124 3 0.02
125 58 0.47
126 62 0.50
ACGTcount: A:0.38, C:0.17, G:0.16, T:0.28
Consensus pattern (125 bp):
AGGATGCACTGTCAGCAAAATTACTGAAAAAAGCTCTAACATAGACGCTCTTTTGCTACAGTAGT
ATTAAAAAAATAATTTTGAGAAAACATTTCTGAACAAATAATGTCCAAAACGCTTCAAGC
Found at i:47515519 original size:46 final size:46
Alignment explanation
Indices: 47515470--47515731 Score: 350
Period size: 46 Copynumber: 5.7 Consensus size: 46
47515460 GCCATAGTGT
* * * * *
47515470 CTTTCAACTATGGTCTTACTCATTTTC-TGTCATGTTGCCATGGTAT
1 CTTTCAACCATGGTCTTACACA-TTTCATATCAGGTTGCCATGGTAC
* * * *
47515516 CTTTCAACCATGGTCTTATTA-TTTTCATGTCACGG-TGCCATGGTAT
1 CTTTCAACCATGGTCTTA-CACATTTCATATCA-GGTTGCCATGGTAC
*
47515562 CTTTCAACCATGGTCTTACACATTTCATATCAGGTTGTCATGGTAC
1 CTTTCAACCATGGTCTTACACATTTCATATCAGGTTGCCATGGTAC
* *
47515608 CTTTCAACCATGGTCTTACACATTTCATATCAGGTGGTCATGGTAC
1 CTTTCAACCATGGTCTTACACATTTCATATCAGGTTGCCATGGTAC
* *
47515654 CTTTCAACCATGGTCTTACACATTTCATATCAGGTGGTCATGGTAC
1 CTTTCAACCATGGTCTTACACATTTCATATCAGGTTGCCATGGTAC
47515700 CTTTCAACCATGGTCTTACACATTTCATATCA
1 CTTTCAACCATGGTCTTACACATTTCATATCA
47515732 TAGATCACCC
Statistics
Matches: 200, Mismatches: 11, Indels: 10
0.90 0.05 0.05
Matches are distributed among these distances:
45 7 0.04
46 192 0.96
47 1 0.00
ACGTcount: A:0.23, C:0.24, G:0.15, T:0.39
Consensus pattern (46 bp):
CTTTCAACCATGGTCTTACACATTTCATATCAGGTTGCCATGGTAC
Found at i:47515659 original size:25 final size:25
Alignment explanation
Indices: 47515584--47515705 Score: 97
Period size: 25 Copynumber: 5.2 Consensus size: 25
47515574 GTCTTACACA
*
47515584 TTTCATATCAGGTTGTCATGGTACC
1 TTTCATATCAGGTGGTCATGGTACC
*
47515609 TTTCA-ACCA--TGGTC-T--TACAC
1 TTTCATATCAGGTGGTCATGGTAC-C
47515629 ATTTCATATCAGGTGGTCATGGTACC
1 -TTTCATATCAGGTGGTCATGGTACC
*
47515655 TTTCA-ACCA--TGGTC-T--TACAC
1 TTTCATATCAGGTGGTCATGGTAC-C
47515675 ATTTCATATCAGGTGGTCATGGTACC
1 -TTTCATATCAGGTGGTCATGGTACC
47515701 TTTCA
1 TTTCA
47515706 ACCATGGTCT
Statistics
Matches: 76, Mismatches: 5, Indels: 32
0.67 0.04 0.28
Matches are distributed among these distances:
19 6 0.08
20 2 0.03
21 12 0.16
22 15 0.20
24 16 0.21
25 17 0.22
26 2 0.03
27 6 0.08
ACGTcount: A:0.23, C:0.23, G:0.17, T:0.37
Consensus pattern (25 bp):
TTTCATATCAGGTGGTCATGGTACC
Found at i:47517879 original size:11 final size:11
Alignment explanation
Indices: 47517863--47517915 Score: 54
Period size: 11 Copynumber: 4.7 Consensus size: 11
47517853 TTTACTAAAT
47517863 AAATAATAATA
1 AAATAATAATA
47517874 AAATAATAAT-
1 AAATAATAATA
* *
47517884 AAATATCTCATTA
1 AAATA-AT-AATA
*
47517897 AAATATTAATA
1 AAATAATAATA
47517908 AAATAATA
1 AAATAATA
47517916 TTTATCTAAT
Statistics
Matches: 34, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
10 5 0.15
11 21 0.62
12 3 0.09
13 5 0.15
ACGTcount: A:0.64, C:0.04, G:0.00, T:0.32
Consensus pattern (11 bp):
AAATAATAATA
Found at i:47517922 original size:31 final size:33
Alignment explanation
Indices: 47517863--47517928 Score: 82
Period size: 34 Copynumber: 2.0 Consensus size: 33
47517853 TTTACTAAAT
*
47517863 AAATAATAATAAAATAATAATAAATATCTCATTA
1 AAATAATAATAAAATAATAAT-AATATCTAATTA
* *
47517897 AAATATTAATAAAATAAT-AT-TTATCTAATTA
1 AAATAATAATAAAATAATAATAATATCTAATTA
47517928 A
1 A
47517929 TTAATTAATT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
31 10 0.34
33 2 0.07
34 17 0.59
ACGTcount: A:0.59, C:0.05, G:0.00, T:0.36
Consensus pattern (33 bp):
AAATAATAATAAAATAATAATAATATCTAATTA
Found at i:47521841 original size:24 final size:23
Alignment explanation
Indices: 47521790--47521834 Score: 65
Period size: 24 Copynumber: 2.0 Consensus size: 23
47521780 AATAATAATT
*
47521790 GCGGAGGTGTTTGCATCACCCATG
1 GCGGAGGTGTTTGAAT-ACCCATG
47521814 GCGGAGGTGTTTGAAT-CCCAT
1 GCGGAGGTGTTTGAATACCCAT
47521835 AAGGCGGTGG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 5 0.25
24 15 0.75
ACGTcount: A:0.18, C:0.22, G:0.33, T:0.27
Consensus pattern (23 bp):
GCGGAGGTGTTTGAATACCCATG
Found at i:47522101 original size:30 final size:30
Alignment explanation
Indices: 47522067--47522131 Score: 85
Period size: 30 Copynumber: 2.2 Consensus size: 30
47522057 GTTGAAGTGT
* *
47522067 TGGGCACGGTGACTGTGTGGATGCTGTTAA
1 TGGGCACGGTGACTGTGTGGACGCTATTAA
* * *
47522097 TGGGCCCGGTGATTGTGTGGACGCTATTGA
1 TGGGCACGGTGACTGTGTGGACGCTATTAA
47522127 TGGGC
1 TGGGC
47522132 TCGCGTGATC
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.14, C:0.15, G:0.42, T:0.29
Consensus pattern (30 bp):
TGGGCACGGTGACTGTGTGGACGCTATTAA
Found at i:47523219 original size:13 final size:13
Alignment explanation
Indices: 47523201--47523228 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
47523191 AAAATATTTT
47523201 TTAATTAAAAAAA
1 TTAATTAAAAAAA
47523214 TTAATTAAAAAAA
1 TTAATTAAAAAAA
47523227 TT
1 TT
47523229 TTAAATAGAG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (13 bp):
TTAATTAAAAAAA
Found at i:47527622 original size:19 final size:19
Alignment explanation
Indices: 47527594--47527641 Score: 89
Period size: 19 Copynumber: 2.6 Consensus size: 19
47527584 ATATATATTT
47527594 TAAA-TTTATTTAGGTAGA
1 TAAATTTTATTTAGGTAGA
47527612 TAAATTTTATTTAGGTAGA
1 TAAATTTTATTTAGGTAGA
47527631 TAAATTTTATT
1 TAAATTTTATT
47527642 CTTATTTTAA
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
18 4 0.14
19 25 0.86
ACGTcount: A:0.38, C:0.00, G:0.12, T:0.50
Consensus pattern (19 bp):
TAAATTTTATTTAGGTAGA
Found at i:47527705 original size:39 final size:39
Alignment explanation
Indices: 47527649--47527730 Score: 121
Period size: 39 Copynumber: 2.1 Consensus size: 39
47527639 ATTCTTATTT
* *
47527649 TAAGAATATTATATTTTATCTTTTTGTAGTTTATTAGAA
1 TAAGAATATTATATTTTATATTTTAGTAGTTTATTAGAA
*
47527688 TAAGAGATATT-TTTTTTATATTTTAGTAGTTTATTAGAA
1 TAAGA-ATATTATATTTTATATTTTAGTAGTTTATTAGAA
47527727 TAAG
1 TAAG
47527731 GGAATTATTT
Statistics
Matches: 39, Mismatches: 3, Indels: 2
0.89 0.07 0.05
Matches are distributed among these distances:
39 34 0.87
40 5 0.13
ACGTcount: A:0.34, C:0.01, G:0.12, T:0.52
Consensus pattern (39 bp):
TAAGAATATTATATTTTATATTTTAGTAGTTTATTAGAA
Found at i:47527930 original size:104 final size:105
Alignment explanation
Indices: 47527717--47527930 Score: 333
Period size: 104 Copynumber: 2.1 Consensus size: 105
47527707 ATTTTAGTAG
* * *
47527717 TTTATTAGAATAAGGGAATTATTTTCTCAATTAGGATTAATATTCTTTTCTCTATTTAAGTTCAG
1 TTTATTAGAATAAGAGAATTATTTTCTCAATTAGGATTAAGACTCTTTTCTCTATTTAAGTTCAG
*
47527782 TTCTTTAATTAATAAAAGATATATCACTTTTATTAGAAGC
66 TTCTTTAATTAATAAAAGATATATCACTTTTATTAAAAGC
* * * *
47527822 -TTATTAGAATAAGAGAATTATTTTCTTAATTAGGATTAAGACTCTTTTTTCTATTTAATTTTAG
1 TTTATTAGAATAAGAGAATTATTTTCTCAATTAGGATTAAGACTCTTTTCTCTATTTAAGTTCAG
*
47527886 TTCTTTAATTAATAAGA-ATATATCACTTTTATTAAAAGC
66 TTCTTTAATTAATAAAAGATATATCACTTTTATTAAAAGC
47527925 TTTATT
1 TTTATT
47527931 GAAAACTTTC
Statistics
Matches: 99, Mismatches: 9, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
103 21 0.21
104 78 0.79
ACGTcount: A:0.35, C:0.08, G:0.09, T:0.48
Consensus pattern (105 bp):
TTTATTAGAATAAGAGAATTATTTTCTCAATTAGGATTAAGACTCTTTTCTCTATTTAAGTTCAG
TTCTTTAATTAATAAAAGATATATCACTTTTATTAAAAGC
Found at i:47537107 original size:39 final size:39
Alignment explanation
Indices: 47537064--47537227 Score: 238
Period size: 39 Copynumber: 4.2 Consensus size: 39
47537054 CTATAACCCT
** * *
47537064 GATATTTTTCCAGCACGTAGCCTGCGGACCTTAAGTCCG
1 GATATTTTTCCAGCATATAGCCTGCGGACCTCATGTCCG
* * *
47537103 GATATATTTCTAGCATATAGCCTGCGGATCTCATGTCCG
1 GATATTTTTCCAGCATATAGCCTGCGGACCTCATGTCCG
* *
47537142 GATATTTTTACAGCATATAGCCTGCGGATCTCATGTCCG
1 GATATTTTTCCAGCATATAGCCTGCGGACCTCATGTCCG
*
47537181 GATATTTTTCCTGCATATAGCCTGCGGACCTCATGTCCG
1 GATATTTTTCCAGCATATAGCCTGCGGACCTCATGTCCG
47537220 GATATTTT
1 GATATTTT
47537228 CAATCTCATA
Statistics
Matches: 112, Mismatches: 13, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
39 112 1.00
ACGTcount: A:0.21, C:0.24, G:0.21, T:0.34
Consensus pattern (39 bp):
GATATTTTTCCAGCATATAGCCTGCGGACCTCATGTCCG
Found at i:47537156 original size:78 final size:78
Alignment explanation
Indices: 47537027--47537227 Score: 246
Period size: 78 Copynumber: 2.6 Consensus size: 78
47537017 AGAGCTCGAA
* * ** * * *
47537027 ATATATTACTAGCATA-AGCCTGCGGGTCT-ATAACCCTGATATTTTTCCAGCACGTAGCCTGCG
1 ATATATTTCTAGCATATAGCCTGCGGATCTCAT-GTCCGGATATTTTTACAGCACATAGCCTGCG
*
47537090 GACCTTAAGTCCGG
65 GACCTCAAGTCCGG
*
47537104 ATATATTTCTAGCATATAGCCTGCGGATCTCATGTCCGGATATTTTTACAGCATATAGCCTGCGG
1 ATATATTTCTAGCATATAGCCTGCGGATCTCATGTCCGGATATTTTTACAGCACATAGCCTGCGG
* *
47537169 ATCTCATGTCCGG
66 ACCTCAAGTCCGG
* *
47537182 ATATTTTTCCT-GCATATAGCCTGCGGACCTCATGTCCGGATATTTT
1 ATATATTT-CTAGCATATAGCCTGCGGATCTCATGTCCGGATATTTT
47537228 CAATCTCATA
Statistics
Matches: 108, Mismatches: 13, Indels: 5
0.86 0.10 0.04
Matches are distributed among these distances:
77 15 0.14
78 89 0.82
79 4 0.04
ACGTcount: A:0.23, C:0.24, G:0.20, T:0.33
Consensus pattern (78 bp):
ATATATTTCTAGCATATAGCCTGCGGATCTCATGTCCGGATATTTTTACAGCACATAGCCTGCGG
ACCTCAAGTCCGG
Found at i:47546156 original size:14 final size:14
Alignment explanation
Indices: 47546137--47546163 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
47546127 TTCTCTTGCA
47546137 CACTTGTATTTTAC
1 CACTTGTATTTTAC
47546151 CACTTGTATTTTA
1 CACTTGTATTTTA
47546164 TTTTATCATG
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:0.22, C:0.19, G:0.07, T:0.52
Consensus pattern (14 bp):
CACTTGTATTTTAC
Found at i:47548545 original size:31 final size:31
Alignment explanation
Indices: 47548507--47548575 Score: 113
Period size: 31 Copynumber: 2.3 Consensus size: 31
47548497 TGACTTCTAT
* *
47548507 AGTTCATTAAACTTATCAGAACAGATATTTA
1 AGTTCATTAAACTCATCAGAACAGAAATTTA
47548538 AGTTCATTAAACTCATCAGAACAGAAATTTA
1 AGTTCATTAAACTCATCAGAACAGAAATTTA
47548569 AG-TCATT
1 AGTTCATT
47548576 GTTTGTGCGA
Statistics
Matches: 36, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
30 5 0.14
31 31 0.86
ACGTcount: A:0.42, C:0.14, G:0.10, T:0.33
Consensus pattern (31 bp):
AGTTCATTAAACTCATCAGAACAGAAATTTA
Found at i:47556317 original size:15 final size:15
Alignment explanation
Indices: 47556293--47556333 Score: 55
Period size: 15 Copynumber: 2.6 Consensus size: 15
47556283 AATTTAAGCA
47556293 TATATCACAATTATC
1 TATATCACAATTATC
*
47556308 TATATGACAATTATC
1 TATATCACAATTATC
47556323 TTATAATCACA
1 -TAT-ATCACA
47556334 CAACATTCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
15 14 0.64
16 3 0.14
17 5 0.23
ACGTcount: A:0.41, C:0.17, G:0.02, T:0.39
Consensus pattern (15 bp):
TATATCACAATTATC
Found at i:47556371 original size:23 final size:24
Alignment explanation
Indices: 47556342--47556408 Score: 68
Period size: 23 Copynumber: 2.9 Consensus size: 24
47556332 CACAACATTC
47556342 AAGCATATATAACAATACTCATAT
1 AAGCATATATAACAATACTCATAT
* * *
47556366 AA-CATATA-ATCACATA-ACATTT
1 AAGCATATATAACA-ATACTCATAT
*
47556388 AAGCATATATCACAATACTCA
1 AAGCATATATAACAATACTCA
47556409 AAAACATGTT
Statistics
Matches: 33, Mismatches: 6, Indels: 8
0.70 0.13 0.17
Matches are distributed among these distances:
22 9 0.27
23 18 0.55
24 6 0.18
ACGTcount: A:0.49, C:0.19, G:0.03, T:0.28
Consensus pattern (24 bp):
AAGCATATATAACAATACTCATAT
Found at i:47556401 original size:22 final size:22
Alignment explanation
Indices: 47556328--47556401 Score: 69
Period size: 22 Copynumber: 3.3 Consensus size: 22
47556318 TTATCTTATA
* *
47556328 ATCACACAACATTCAAGCATAT
1 ATCACATAACATTTAAGCATAT
* * *
47556350 ATAACAATACTCATATAA-CATAT
1 ATCAC-ATA-ACATTTAAGCATAT
47556373 AATCACATAACATTTAAGCATAT
1 -ATCACATAACATTTAAGCATAT
47556396 ATCACA
1 ATCACA
47556402 ATACTCAAAA
Statistics
Matches: 40, Mismatches: 8, Indels: 8
0.71 0.14 0.14
Matches are distributed among these distances:
22 16 0.40
23 15 0.38
24 9 0.22
ACGTcount: A:0.49, C:0.22, G:0.03, T:0.27
Consensus pattern (22 bp):
ATCACATAACATTTAAGCATAT
Found at i:47564498 original size:22 final size:22
Alignment explanation
Indices: 47564454--47564498 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
47564444 AGATGTATTA
* *
47564454 TGCCAATATAGTTGATTGATTG
1 TGCCAATATAATTGAATGATTG
*
47564476 TGCCAATATAATTGAATGTTTG
1 TGCCAATATAATTGAATGATTG
47564498 T
1 T
47564499 AACACCCCGA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.29, C:0.09, G:0.20, T:0.42
Consensus pattern (22 bp):
TGCCAATATAATTGAATGATTG
Found at i:47565986 original size:39 final size:40
Alignment explanation
Indices: 47565869--47566053 Score: 198
Period size: 40 Copynumber: 4.7 Consensus size: 40
47565859 GCTACTCGTT
*
47565869 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATT-TAGTAACTCGCA
* * * *
47565909 CAATTGCCTTTGGGACTTAACCCGGATTTAGTAACTCGCG
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
* *
47565949 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
* * * * * *
47565988 CAAATGCC-TCCGGATCTTAGTCCGGATATGGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGATTTAGTAAC-TCGCA
47566029 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
47566054 CATCATTCAA
Statistics
Matches: 119, Mismatches: 21, Indels: 10
0.79 0.14 0.07
Matches are distributed among these distances:
38 4 0.03
39 29 0.24
40 71 0.60
41 15 0.13
ACGTcount: A:0.24, C:0.28, G:0.23, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
Found at i:47566013 original size:79 final size:82
Alignment explanation
Indices: 47565869--47566053 Score: 202
Period size: 79 Copynumber: 2.3 Consensus size: 82
47565859 GCTACTCGTT
* * * **
47565869 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCACAATTGCCTTTGGGACTTAACCCG
1 CAAATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCCGGACTTAACCCG
* * *
47565933 GATTTAGTAAC-TCGCG
66 GATATAGTAACTTAGCA
* **
47565949 CAAATGCCTTCGGG-CTTAGCCCGGAAT-TAGTATCTCGCACAAATGCC-TCCGGATCTTAGTCC
1 CAAATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCCGGA-CTTAACCC
* *
47566011 GGATATGGTCACTTAGCA
65 GGATATAGTAACTTAGCA
47566029 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
47566054 CATCATTCAA
Statistics
Matches: 88, Mismatches: 13, Indels: 8
0.81 0.12 0.07
Matches are distributed among these distances:
78 4 0.05
79 51 0.58
80 33 0.38
ACGTcount: A:0.24, C:0.28, G:0.23, T:0.25
Consensus pattern (82 bp):
CAAATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCCGGACTTAACCCG
GATATAGTAACTTAGCA
Found at i:47569752 original size:27 final size:28
Alignment explanation
Indices: 47569716--47569769 Score: 74
Period size: 28 Copynumber: 2.0 Consensus size: 28
47569706 TGAAAATTCA
*
47569716 CACTTTAATTA-TAAAATAATTAATTTG
1 CACTTAAATTATTAAAATAATTAATTTG
* *
47569743 CACTTAAATTATTAATATATTTAATTT
1 CACTTAAATTATTAAAATAATTAATTT
47569770 TAATTATTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
27 10 0.43
28 13 0.57
ACGTcount: A:0.43, C:0.07, G:0.02, T:0.48
Consensus pattern (28 bp):
CACTTAAATTATTAAAATAATTAATTTG
Found at i:47575965 original size:16 final size:15
Alignment explanation
Indices: 47575944--47575973 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
47575934 TGTCACTGCC
47575944 TTAAAATTGTTATCTT
1 TTAAAATTG-TATCTT
47575960 TTAAAATTGTATCT
1 TTAAAATTGTATCT
47575974 AGTGTAAACC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.33, C:0.07, G:0.07, T:0.53
Consensus pattern (15 bp):
TTAAAATTGTATCTT
Found at i:47577092 original size:14 final size:14
Alignment explanation
Indices: 47577073--47577112 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
47577063 TTGATTGCCA
47577073 GTAAAATGTTTTCC
1 GTAAAATGTTTTCC
* *
47577087 GTAAAATGATTTCT
1 GTAAAATGTTTTCC
*
47577101 GGAAAATGTTTT
1 GTAAAATGTTTT
47577113 ACTTTTCTGT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.33, C:0.07, G:0.17, T:0.42
Consensus pattern (14 bp):
GTAAAATGTTTTCC
Found at i:47577121 original size:20 final size:20
Alignment explanation
Indices: 47577096--47577135 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
47577086 CGTAAAATGA
*
47577096 TTTCTGGAAAATGTTTTACT
1 TTTCTGGAAAATGATTTACT
*
47577116 TTTCTGTAAAATGATTTACT
1 TTTCTGGAAAATGATTTACT
47577136 AGAAAATATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.28, C:0.10, G:0.12, T:0.50
Consensus pattern (20 bp):
TTTCTGGAAAATGATTTACT
Found at i:47577125 original size:34 final size:35
Alignment explanation
Indices: 47577081--47577147 Score: 100
Period size: 34 Copynumber: 1.9 Consensus size: 35
47577071 CAGTAAAATG
* *
47577081 TTTTCCGTAAAATGATTT-CTGGAAAATGTTTTAC
1 TTTTCCGTAAAATGATTTACTAGAAAATATTTTAC
*
47577115 TTTTCTGTAAAATGATTTACTAGAAAATATTTT
1 TTTTCCGTAAAATGATTTACTAGAAAATATTTT
47577148 CTGCTGTTTG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
34 17 0.59
35 12 0.41
ACGTcount: A:0.33, C:0.09, G:0.12, T:0.46
Consensus pattern (35 bp):
TTTTCCGTAAAATGATTTACTAGAAAATATTTTAC
Found at i:47580391 original size:36 final size:36
Alignment explanation
Indices: 47580344--47580413 Score: 122
Period size: 36 Copynumber: 1.9 Consensus size: 36
47580334 ATAAGTAGAA
*
47580344 CGTCACCATGCGTTGTGATGAGAAATCCATATCTAG
1 CGTCACCATGCGTTGTAATGAGAAATCCATATCTAG
*
47580380 CGTCACCATGCGTTGTAATGAGAAATTCATATCT
1 CGTCACCATGCGTTGTAATGAGAAATCCATATCT
47580414 CTCAGGTGCA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 32 1.00
ACGTcount: A:0.29, C:0.21, G:0.20, T:0.30
Consensus pattern (36 bp):
CGTCACCATGCGTTGTAATGAGAAATCCATATCTAG
Found at i:47583391 original size:12 final size:13
Alignment explanation
Indices: 47583374--47583403 Score: 53
Period size: 12 Copynumber: 2.4 Consensus size: 13
47583364 CTCATACATG
47583374 AATAAATAAA-GC
1 AATAAATAAATGC
47583386 AATAAATAAATGC
1 AATAAATAAATGC
47583399 AATAA
1 AATAA
47583404 TTATAGCTCA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 10 0.59
13 7 0.41
ACGTcount: A:0.67, C:0.07, G:0.07, T:0.20
Consensus pattern (13 bp):
AATAAATAAATGC
Found at i:47588532 original size:19 final size:19
Alignment explanation
Indices: 47588494--47588533 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
47588484 ATTGTTTCTA
*
47588494 TTTAGGAAAAACCTTAGTT
1 TTTAGGAAAAACCATAGTT
47588513 TTTAGGAAAAAACCAT-GTT
1 TTTAGG-AAAAACCATAGTT
47588532 TT
1 TT
47588534 GTGGAGTTGC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 11 0.58
20 8 0.42
ACGTcount: A:0.38, C:0.10, G:0.15, T:0.38
Consensus pattern (19 bp):
TTTAGGAAAAACCATAGTT
Found at i:47592288 original size:20 final size:20
Alignment explanation
Indices: 47592265--47592318 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 20
47592255 AGTTTTTCCC
*
47592265 AGCTCGATTTAGCTCACATG
1 AGCTCAATTTAGCTCACATG
* ***
47592285 AGCTTAATTTAGCTCGTTTG
1 AGCTCAATTTAGCTCACATG
47592305 AGCTCAATTTAGCT
1 AGCTCAATTTAGCT
47592319 TACTTTAGCT
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.24, C:0.20, G:0.19, T:0.37
Consensus pattern (20 bp):
AGCTCAATTTAGCTCACATG
Found at i:47592300 original size:30 final size:30
Alignment explanation
Indices: 47592265--47592338 Score: 98
Period size: 30 Copynumber: 2.5 Consensus size: 30
47592255 AGTTTTTCCC
47592265 AGCTCGATTT-AGCTCACA-TGAGCTTAATTT
1 AGCTCG-TTTGAGCTCA-ATTGAGCTTAATTT
* *
47592295 AGCTCGTTTGAGCTCAATTTAGCTTACTTT
1 AGCTCGTTTGAGCTCAATTGAGCTTAATTT
47592325 AGCTCGTTTGAGCT
1 AGCTCGTTTGAGCT
47592339 TGGCTTAAGT
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
29 4 0.10
30 36 0.90
ACGTcount: A:0.22, C:0.20, G:0.19, T:0.39
Consensus pattern (30 bp):
AGCTCGTTTGAGCTCAATTGAGCTTAATTT
Found at i:47592328 original size:20 final size:20
Alignment explanation
Indices: 47592265--47592329 Score: 53
Period size: 20 Copynumber: 3.2 Consensus size: 20
47592255 AGTTTTTCCC
* * * *
47592265 AGCTCGATTTAGCTCACATG
1 AGCTCAATTTAGCTTACTTT
*
47592285 AGCTTAATTTAGC-T-CGTTT
1 AGCTCAATTTAGCTTAC-TTT
47592304 GAGCTCAATTTAGCTTACTTT
1 -AGCTCAATTTAGCTTACTTT
47592325 AGCTC
1 AGCTC
47592330 GTTTGAGCTT
Statistics
Matches: 35, Mismatches: 6, Indels: 8
0.71 0.12 0.16
Matches are distributed among these distances:
18 1 0.03
19 1 0.03
20 28 0.80
21 4 0.11
22 1 0.03
ACGTcount: A:0.23, C:0.22, G:0.17, T:0.38
Consensus pattern (20 bp):
AGCTCAATTTAGCTTACTTT
Found at i:47604074 original size:27 final size:27
Alignment explanation
Indices: 47604044--47604098 Score: 101
Period size: 27 Copynumber: 2.0 Consensus size: 27
47604034 TTGTTATGAA
*
47604044 ACTTTAAATTGGAGGTCCTTATATGGT
1 ACTTCAAATTGGAGGTCCTTATATGGT
47604071 ACTTCAAATTGGAGGTCCTTATATGGT
1 ACTTCAAATTGGAGGTCCTTATATGGT
47604098 A
1 A
47604099 ATTAGACCAT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.27, C:0.13, G:0.22, T:0.38
Consensus pattern (27 bp):
ACTTCAAATTGGAGGTCCTTATATGGT
Found at i:47605174 original size:50 final size:50
Alignment explanation
Indices: 47605049--47605345 Score: 299
Period size: 50 Copynumber: 5.8 Consensus size: 50
47605039 ATTTGGATAA
* * *
47605049 AGAGGTCCCATGTAAGACCATATCTGGGACATGGCATTGGCATCATTGAGATTATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCA-C--CGAG---ATG
*
47605105 AGAGGTCCCATGTAAGACCATGTCTAGGACATGGCGTTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATG
* * *
47605155 AGAGGTCTCATGTAAGACCATGTCTAGGACATGGCGTTGGCACCAAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATG
** * *
47605205 AGAGGTCCCCCGTAAGACCATGTCTGGGACATGGCGTGGGCACCGATATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATG
** * * * * ** * *
47605255 AGAACTCCCATGTAAGACAATATCTGGGATATGGCATTGGCA-ATACAAG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATG
* ** * *
47605304 AAATATCTCATGTAAGACCATGTCTGGGACATGGCTTTGGCA
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCA
47605346 TGTTATTATT
Statistics
Matches: 207, Mismatches: 34, Indels: 7
0.83 0.14 0.03
Matches are distributed among these distances:
49 37 0.18
50 127 0.61
53 3 0.01
55 1 0.00
56 39 0.19
ACGTcount: A:0.28, C:0.21, G:0.28, T:0.23
Consensus pattern (50 bp):
AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATG
Found at i:47622745 original size:26 final size:25
Alignment explanation
Indices: 47622715--47622763 Score: 89
Period size: 26 Copynumber: 1.9 Consensus size: 25
47622705 ATCATTTTAT
47622715 CATCTTCAAGCTTCCACTGCTTCTAC
1 CATCTTCAAGCTTCCACT-CTTCTAC
47622741 CATCTTCAAGCTTCCACTCTTCT
1 CATCTTCAAGCTTCCACTCTTCT
47622764 TCTTTTTTCA
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
25 5 0.22
26 18 0.78
ACGTcount: A:0.18, C:0.39, G:0.06, T:0.37
Consensus pattern (25 bp):
CATCTTCAAGCTTCCACTCTTCTAC
Found at i:47623508 original size:29 final size:28
Alignment explanation
Indices: 47623476--47623531 Score: 76
Period size: 29 Copynumber: 2.0 Consensus size: 28
47623466 GTAACGATTT
*
47623476 AATAATTTAGGTACCAATTCTAACAAAAA
1 AATAATTTAAGTACCAATT-TAACAAAAA
* *
47623505 AATATTTTAAGTACCAATTTAAGAAAA
1 AATAATTTAAGTACCAATTTAACAAAA
47623532 CAAGTATAGT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
28 7 0.29
29 17 0.71
ACGTcount: A:0.52, C:0.11, G:0.07, T:0.30
Consensus pattern (28 bp):
AATAATTTAAGTACCAATTTAACAAAAA
Found at i:47636661 original size:45 final size:45
Alignment explanation
Indices: 47636610--47636698 Score: 160
Period size: 45 Copynumber: 2.0 Consensus size: 45
47636600 CACAAAGTGA
* *
47636610 CCAAGGTTCTGTACTTCCCTTTCACCATGGACAAATGTACTAAGG
1 CCAAGGTTCTCTACTTCCCTTTCACCATAGACAAATGTACTAAGG
47636655 CCAAGGTTCTCTACTTCCCTTTCACCATAGACAAATGTACTAAG
1 CCAAGGTTCTCTACTTCCCTTTCACCATAGACAAATGTACTAAG
47636699 TAGACTTTCC
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
45 42 1.00
ACGTcount: A:0.28, C:0.28, G:0.15, T:0.29
Consensus pattern (45 bp):
CCAAGGTTCTCTACTTCCCTTTCACCATAGACAAATGTACTAAGG
Found at i:47641657 original size:9 final size:9
Alignment explanation
Indices: 47641643--47641797 Score: 63
Period size: 9 Copynumber: 16.8 Consensus size: 9
47641633 GAAAAAGAAT
47641643 ATTTTTATA
1 ATTTTTATA
*
47641652 ATTTTTTTA
1 ATTTTTATA
*
47641661 ATTTTCATA
1 ATTTTTATA
*
47641670 ATTTTTCCAAA
1 ATTTTT--ATA
*
47641681 ATGTTTATA
1 ATTTTTATA
47641690 A-TTTTATA
1 ATTTTTATA
*
47641698 ATTATTTACA
1 ATT-TTTATA
*
47641708 ATATTTAT-
1 ATTTTTATA
*
47641716 -TATTTAT-
1 ATTTTTATA
*
47641723 -TTTTTGT-
1 ATTTTTATA
*
47641730 A-TTTTAAA
1 ATTTTTATA
47641738 ATTTTCTATA
1 ATTTT-TATA
*
47641748 ACTTTTATGTA
1 A-TTTT-TATA
47641759 ATTTTTTATA
1 A-TTTTTATA
*
47641769 CATTTTGTACA
1 -ATTTT-TATA
47641780 ATTATTTATCA
1 ATT-TTTAT-A
47641791 ATTTTTA
1 ATTTTTA
47641798 ATCACTTTTA
Statistics
Matches: 111, Mismatches: 22, Indels: 25
0.70 0.14 0.16
Matches are distributed among these distances:
7 16 0.14
8 8 0.07
9 31 0.28
10 27 0.24
11 29 0.26
ACGTcount: A:0.32, C:0.06, G:0.03, T:0.60
Consensus pattern (9 bp):
ATTTTTATA
Found at i:47642558 original size:30 final size:31
Alignment explanation
Indices: 47642522--47642589 Score: 95
Period size: 31 Copynumber: 2.2 Consensus size: 31
47642512 AATTTCAATC
47642522 CAGTCACTCAA-CTT-TCGAAAAGTAACAAAT
1 CAGTCACT-AATCTTATCGAAAAGTAACAAAT
* *
47642552 CAGTCACTAATGTTATCGAAAAGTGACAAAT
1 CAGTCACTAATCTTATCGAAAAGTAACAAAT
47642583 CAGTCAC
1 CAGTCAC
47642590 CCATTAACAT
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
29 2 0.06
30 10 0.29
31 22 0.65
ACGTcount: A:0.41, C:0.22, G:0.13, T:0.24
Consensus pattern (31 bp):
CAGTCACTAATCTTATCGAAAAGTAACAAAT
Found at i:47651079 original size:14 final size:14
Alignment explanation
Indices: 47651060--47651088 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
47651050 CGAACCATAA
47651060 ACCTTCTCCTTGAG
1 ACCTTCTCCTTGAG
47651074 ACCTTCTCCTTGAG
1 ACCTTCTCCTTGAG
47651088 A
1 A
47651089 GTCGGTTTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.17, C:0.34, G:0.14, T:0.34
Consensus pattern (14 bp):
ACCTTCTCCTTGAG
Found at i:47654406 original size:14 final size:14
Alignment explanation
Indices: 47654387--47654415 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
47654377 CGAACCATAA
47654387 ACCTTCTCCTTGAG
1 ACCTTCTCCTTGAG
47654401 ACCTTCTCCTTGAG
1 ACCTTCTCCTTGAG
47654415 A
1 A
47654416 GTCGGTTTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.17, C:0.34, G:0.14, T:0.34
Consensus pattern (14 bp):
ACCTTCTCCTTGAG
Found at i:47658930 original size:11 final size:10
Alignment explanation
Indices: 47658900--47658947 Score: 51
Period size: 10 Copynumber: 4.6 Consensus size: 10
47658890 GAATCTGTTG
* *
47658900 AAAATAAATC
1 AAAATTAATA
47658910 AAAATTAATA
1 AAAATTAATA
47658920 AAAATTTAATA
1 AAAA-TTAATA
*
47658931 TAAAATTAATT
1 -AAAATTAATA
47658942 AAAATT
1 AAAATT
47658948 CAACATGTTA
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
10 18 0.55
11 11 0.33
12 4 0.12
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (10 bp):
AAAATTAATA
Found at i:47664649 original size:39 final size:39
Alignment explanation
Indices: 47664609--47664735 Score: 173
Period size: 39 Copynumber: 3.3 Consensus size: 39
47664599 ATTCACTTTT
* * * * * *
47664609 AAGCATATATCGCATTACACATATAATCATATAACATTT
1 AAGCATATATCACAATACTCATATAATCACATAATATTC
* *
47664648 AAGCATATATCACAATACTCATATAATTACATAATGTTC
1 AAGCATATATCACAATACTCATATAATCACATAATATTC
*
47664687 AAGCATATATCACAATACTCATATATTCACATAATATTC
1 AAGCATATATCACAATACTCATATAATCACATAATATTC
47664726 AAGCATATAT
1 AAGCATATAT
47664736 ATCGTAATAC
Statistics
Matches: 77, Mismatches: 11, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
39 77 1.00
ACGTcount: A:0.44, C:0.18, G:0.05, T:0.33
Consensus pattern (39 bp):
AAGCATATATCACAATACTCATATAATCACATAATATTC
Found at i:47671498 original size:27 final size:27
Alignment explanation
Indices: 47671468--47671555 Score: 108
Period size: 27 Copynumber: 3.3 Consensus size: 27
47671458 AGAACATGCA
47671468 ACAAAGGCTATTCTTTTCGAGTTCGCC
1 ACAAAGGCTATTCTTTTCGAGTTCGCC
* * *
47671495 ACAAATGCTATTATTTTAGAGTAT-GCC
1 ACAAAGGCTATTCTTTTCGAGT-TCGCC
*
47671522 ACAAAGGCTATTC-TTTCAGAGTACGCC
1 ACAAAGGCTATTCTTTTC-GAGTTCGCC
47671549 ACAAAGG
1 ACAAAGG
47671556 TTGTTTCTTA
Statistics
Matches: 51, Mismatches: 7, Indels: 6
0.80 0.11 0.09
Matches are distributed among these distances:
26 3 0.06
27 47 0.92
28 1 0.02
ACGTcount: A:0.31, C:0.22, G:0.18, T:0.30
Consensus pattern (27 bp):
ACAAAGGCTATTCTTTTCGAGTTCGCC
Found at i:47672891 original size:14 final size:14
Alignment explanation
Indices: 47672869--47672904 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
47672859 TGGTAGATAC
47672869 TATACGCCCACACA
1 TATACGCCCACACA
* *
47672883 TATATGCCCACACG
1 TATACGCCCACACA
47672897 TATACGCC
1 TATACGCC
47672905 AAAACAATCA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.31, C:0.39, G:0.11, T:0.19
Consensus pattern (14 bp):
TATACGCCCACACA
Found at i:47675121 original size:31 final size:31
Alignment explanation
Indices: 47675083--47675163 Score: 112
Period size: 31 Copynumber: 2.6 Consensus size: 31
47675073 CTCAAAATTG
* * *
47675083 TACATGAATTTTGATTTAATGTGTAGTTTTA
1 TACATGAATTTTGATTTAATGTGCAATTTCA
47675114 TACATGAATTTTGATTT--TGTGCAATTTCA
1 TACATGAATTTTGATTTAATGTGCAATTTCA
47675143 TACATGAAATTTTGATTTAAT
1 TACATG-AATTTTGATTTAAT
47675164 CCAACTCTCA
Statistics
Matches: 44, Mismatches: 3, Indels: 5
0.85 0.06 0.10
Matches are distributed among these distances:
29 15 0.34
30 11 0.25
31 17 0.39
32 1 0.02
ACGTcount: A:0.31, C:0.06, G:0.14, T:0.49
Consensus pattern (31 bp):
TACATGAATTTTGATTTAATGTGCAATTTCA
Found at i:47675329 original size:31 final size:31
Alignment explanation
Indices: 47675294--47675370 Score: 102
Period size: 31 Copynumber: 2.5 Consensus size: 31
47675284 AATGTTATGA
*
47675294 TTGAATCAAAATTAAAATTTCATATATACAT
1 TTGAACCAAAATTAAAATTTCATATATACAT
* * *
47675325 TTGAACCACAATTAAAATTTCATATGTACAA
1 TTGAACCAAAATTAAAATTTCATATATACAT
*
47675356 TTGTACC-AAATTAAA
1 TTGAACCAAAATTAAA
47675371 GATTATATGT
Statistics
Matches: 40, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
30 7 0.17
31 33 0.82
ACGTcount: A:0.47, C:0.13, G:0.05, T:0.35
Consensus pattern (31 bp):
TTGAACCAAAATTAAAATTTCATATATACAT
Done.