Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A08
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: 119882356
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 2655529 characters in sequence are not A, C, G, or T
File 139 of 362
Found at i:46425863 original size:54 final size:53
Alignment explanation
Indices: 46425776--46425948 Score: 213
Period size: 54 Copynumber: 3.2 Consensus size: 53
46425766 GGGGCAAAAT
* * * * *
46425776 GGTAATTTTACCCCACAAGGGTATCTCGATAATTCTGCCTTACAGGTGTATTTC
1 GGTAATTCTACCCTACAAGGGTATTTCGGTAATTCTACCTTACAGG-GTATTTC
* * * *
46425830 AGTAATTCTACCTTACAAGGGTATTTCGGTAATTATATCC-TACAGGGGCATTTC
1 GGTAATTCTACCCTACAAGGGTATTTCGGTAATTCTA-CCTTACA-GGGTATTTC
*
46425884 GGTAATTCTACCCTACAGGGGTATTTCGGTAATTCTACCTTACAAGGGTATTTC
1 GGTAATTCTACCCTACAAGGGTATTTCGGTAATTCTACCTTAC-AGGGTATTTC
46425938 GGTAATTCTAC
1 GGTAATTCTAC
46425949 AACTTATCCA
Statistics
Matches: 101, Mismatches: 14, Indels: 8
0.82 0.11 0.07
Matches are distributed among these distances:
53 2 0.02
54 94 0.93
55 5 0.05
ACGTcount: A:0.25, C:0.20, G:0.19, T:0.35
Consensus pattern (53 bp):
GGTAATTCTACCCTACAAGGGTATTTCGGTAATTCTACCTTACAGGGTATTTC
Found at i:46432650 original size:67 final size:70
Alignment explanation
Indices: 46432493--46432652 Score: 227
Period size: 67 Copynumber: 2.3 Consensus size: 70
46432483 CACCACAGAA
* * *
46432493 ATTGCAACGACGCTACCAGATATTGTGACGAAGTCACCAAAACAGATATATATATATGTGGCGAA
1 ATTGCAACGAGGCTGCCAGATATTGTGACGAAGTCACC---ACAGATACATATATATGTGGCGAA
46432558 GCCACCAG
63 GCCACCAG
*
46432566 ATTGCAACGAGGCTGCCAGATATTGTGACGAAGTCA-C-CAGA-ACATATATATGTGGCGAGGCC
1 ATTGCAACGAGGCTGCCAGATATTGTGACGAAGTCACCACAGATACATATATATGTGGCGAAGCC
46432628 ACCAG
66 ACCAG
*
46432633 ATTGCAGCGAGGCTGCCAGA
1 ATTGCAACGAGGCTGCCAGA
46432653 ATGCTTCCTC
Statistics
Matches: 82, Mismatches: 5, Indels: 6
0.88 0.05 0.06
Matches are distributed among these distances:
67 43 0.52
68 4 0.05
72 1 0.01
73 34 0.41
ACGTcount: A:0.33, C:0.23, G:0.25, T:0.19
Consensus pattern (70 bp):
ATTGCAACGAGGCTGCCAGATATTGTGACGAAGTCACCACAGATACATATATATGTGGCGAAGCC
ACCAG
Found at i:46433261 original size:26 final size:27
Alignment explanation
Indices: 46433232--46433293 Score: 81
Period size: 27 Copynumber: 2.3 Consensus size: 27
46433222 TCACACAAGT
*
46433232 TAGTCATTT-ACGCACGAGGGGCAAAA
1 TAGTCATTTAACACACGAGGGGCAAAA
* *
46433258 TAGTCATTTAACACCCTAGGGGCAAAA
1 TAGTCATTTAACACACGAGGGGCAAAA
*
46433285 TAGTAATTT
1 TAGTCATTT
46433294 TACCCCACAA
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
26 9 0.29
27 22 0.71
ACGTcount: A:0.35, C:0.18, G:0.21, T:0.26
Consensus pattern (27 bp):
TAGTCATTTAACACACGAGGGGCAAAA
Found at i:46433364 original size:27 final size:27
Alignment explanation
Indices: 46433287--46433535 Score: 284
Period size: 27 Copynumber: 9.2 Consensus size: 27
46433277 GGGCAAAATA
* * * *
46433287 GTAATTTTACCCCACAAGGGTATCTCA
1 GTAATTCTACCCTACAAGGGTATTTCG
** * *
46433314 AAAATTCTTCCCTACAGGGGTATTTCG
1 GTAATTCTACCCTACAAGGGTATTTCG
* *
46433341 ATAATTCTACCTTACAAGGGTATTTCG
1 GTAATTCTACCCTACAAGGGTATTTCG
* *
46433368 GTAATTCTATCCTAC-AGGTGTATTTCA
1 GTAATTCTACCCTACAAGG-GTATTTCG
*
46433395 GTAATTCTACCCTACAAGGGTGTTTCG
1 GTAATTCTACCCTACAAGGGTATTTCG
* *
46433422 GTAATTCTATCCTACATGGGTATTTCG
1 GTAATTCTACCCTACAAGGGTATTTCG
* *
46433449 GTAATTCTACCCTACAGGGGTATTTCA
1 GTAATTCTACCCTACAAGGGTATTTCG
* * *
46433476 ATAATTCTACCCTATAGGGGTATTTCG
1 GTAATTCTACCCTACAAGGGTATTTCG
* *
46433503 GTAATTCTACCTTACAGGGGTATTTCG
1 GTAATTCTACCCTACAAGGGTATTTCG
46433530 GTAATT
1 GTAATT
46433536 TACAACTTAT
Statistics
Matches: 189, Mismatches: 31, Indels: 4
0.84 0.14 0.02
Matches are distributed among these distances:
26 3 0.02
27 183 0.97
28 3 0.02
ACGTcount: A:0.26, C:0.20, G:0.18, T:0.36
Consensus pattern (27 bp):
GTAATTCTACCCTACAAGGGTATTTCG
Found at i:46433427 original size:81 final size:81
Alignment explanation
Indices: 46433287--46433535 Score: 347
Period size: 81 Copynumber: 3.1 Consensus size: 81
46433277 GGGCAAAATA
* * * * * * *
46433287 GTAATTTTACCCCACAAGGGTATCTCAAAAATTCTTCCCTACAGGGGTATTTCGATAATTCTACC
1 GTAATTCTACCCTACAGGGGTATTTCAATAATTCTACCCTACAGGGGTATTTCGGTAATTCTACC
46433352 TTACAAGGGTATTTCG
66 TTACAAGGGTATTTCG
* * * * *
46433368 GTAATTCTATCCTACAGGTGTATTTCAGTAATTCTACCCTACAAGGGTGTTTCGGTAATTCTATC
1 GTAATTCTACCCTACAGGGGTATTTCAATAATTCTACCCTACAGGGGTATTTCGGTAATTCTA-C
*
46433433 C-TACATGGGTATTTCG
65 CTTACAAGGGTATTTCG
*
46433449 GTAATTCTACCCTACAGGGGTATTTCAATAATTCTACCCTATAGGGGTATTTCGGTAATTCTACC
1 GTAATTCTACCCTACAGGGGTATTTCAATAATTCTACCCTACAGGGGTATTTCGGTAATTCTACC
*
46433514 TTACAGGGGTATTTCG
66 TTACAAGGGTATTTCG
46433530 GTAATT
1 GTAATT
46433536 TACAACTTAT
Statistics
Matches: 146, Mismatches: 20, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
80 2 0.01
81 142 0.97
82 2 0.01
ACGTcount: A:0.26, C:0.20, G:0.18, T:0.36
Consensus pattern (81 bp):
GTAATTCTACCCTACAGGGGTATTTCAATAATTCTACCCTACAGGGGTATTTCGGTAATTCTACC
TTACAAGGGTATTTCG
Found at i:46435440 original size:40 final size:40
Alignment explanation
Indices: 46435371--46435611 Score: 308
Period size: 40 Copynumber: 6.0 Consensus size: 40
46435361 GGATTTAACT
* *
46435371 GGATATAGCT-ACTCGCTC-AATGCCTTCGGGACATAGCCC
1 GGATATAG-TAACTCGCACAAATGCCTTCGGGACTTAGCCC
* *
46435410 GGATATAGTAACTCGTACCAATGCCTTCGGGACTTAGCCC
1 GGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGCCC
* *
46435450 GGATATAGTAGCTCGCACAAATGCCTTCGAGACTTAGCCC
1 GGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGCCC
* *
46435490 GGATGTAATAACTCGCACAAATGCCTTCGGGACTTAGCCC
1 GGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGCCC
* * * *
46435530 AGATGTAATAACTCGCACAAATGCCTTCGGGACTTATCCC
1 GGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGCCC
* * *
46435570 GGA-ACTAGTCACTAGCGCAAATGCCTTCGGGACTTAGCCC
1 GGATA-TAGTAACTCGCACAAATGCCTTCGGGACTTAGCCC
46435610 GG
1 GG
46435612 TTATCATCCA
Statistics
Matches: 179, Mismatches: 20, Indels: 5
0.88 0.10 0.02
Matches are distributed among these distances:
38 1 0.01
39 14 0.08
40 164 0.92
ACGTcount: A:0.26, C:0.28, G:0.23, T:0.23
Consensus pattern (40 bp):
GGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGCCC
Found at i:46436930 original size:52 final size:53
Alignment explanation
Indices: 46436856--46436983 Score: 206
Period size: 52 Copynumber: 2.4 Consensus size: 53
46436846 CTCAAAGCTC
*
46436856 TTTTTCCTTCTTTTTCTTTCTTCTATTCGGCCAAGAACAACATGAGAG-CTTT
1 TTTTTTCTTCTTTTTCTTTCTTCTATTCGGCCAAGAACAACATGAGAGCCTTT
*
46436908 TTTTTTCTTCTTTTTCTTTCTTCTATTCGGTCAAGAACAACATGAGAGCCTTT
1 TTTTTTCTTCTTTTTCTTTCTTCTATTCGGCCAAGAACAACATGAGAGCCTTT
46436961 TTTTTTCTT-TCTTTTCATTTCTT
1 TTTTTTCTTCT-TTTTC-TTTCTT
46436984 TCATCATCAT
Statistics
Matches: 71, Mismatches: 2, Indels: 4
0.92 0.03 0.05
Matches are distributed among these distances:
52 47 0.66
53 18 0.25
54 6 0.08
ACGTcount: A:0.16, C:0.21, G:0.09, T:0.53
Consensus pattern (53 bp):
TTTTTTCTTCTTTTTCTTTCTTCTATTCGGCCAAGAACAACATGAGAGCCTTT
Found at i:46443628 original size:40 final size:40
Alignment explanation
Indices: 46443540--46443801 Score: 257
Period size: 40 Copynumber: 6.6 Consensus size: 40
46443530 ATTCCCAAGC
* * * * *
46443540 CAAATACCTTCGGGATTTA-ACCGGATATAGCT-ACTCGCT
1 CAAATGCCTTCGGGACTTAGCCCGGATATAG-TAACTCACA
*
46443579 C-AATGCCTTCGGGACATAGCCCGGATATAGTAACTCACA
1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCACA
* * *
46443618 CCAATGCCTTCGGGACTTAGCCCGGATATAGTAGCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCACA
* * * * *
46443658 CAAATGCCTTCGAGACTTAACCCGGATGTAATAACT-AGTA
1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCA-CA
* * *
46443698 CAAATGCCTTCGGGACTTAGCCCGGATGTAATAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCACA
* * *
46443738 CAAATGCATTCGGGACTTAGCCCGGA-ACTAGTCACT-AGCG
1 CAAATGCCTTCGGGACTTAGCCCGGATA-TAGTAACTCA-CA
*
46443778 CAAATGCCTTCGGGACTTAACCCG
1 CAAATGCCTTCGGGACTTAGCCCG
46443802 ATTATCATCC
Statistics
Matches: 187, Mismatches: 29, Indels: 13
0.82 0.13 0.06
Matches are distributed among these distances:
38 15 0.08
39 17 0.09
40 155 0.83
ACGTcount: A:0.28, C:0.27, G:0.21, T:0.23
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCACA
Found at i:46443682 original size:80 final size:79
Alignment explanation
Indices: 46443540--46443801 Score: 298
Period size: 80 Copynumber: 3.3 Consensus size: 79
46443530 ATTCCCAAGC
* * * * *
46443540 CAAATACCTTCGGGATTTA-ACCGGATATAGCTACTCGCTC-AATGCCTTCGGGACATAGCCCGG
1 CAAATGCCTTCGGGACTTAGCCCGGATATAG-TACTCGCACAAATGCCTTCGGGACTTAGCCCGG
46443603 ATATAGTAACTCA-CA
65 ATATAGTAACT-AGCA
* * *
46443618 CCAATGCCTTCGGGACTTAGCCCGGATATAGTAGCTCGCACAAATGCCTTCGAGACTTAACCCGG
1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTA-CTCGCACAAATGCCTTCGGGACTTAGCCCGG
* * *
46443683 ATGTAATAACTAGTA
65 ATATAGTAACTAGCA
* * *
46443698 CAAATGCCTTCGGGACTTAGCCCGGATGTAATAACTCGCACAAATGCATTCGGGACTTAGCCCGG
1 CAAATGCCTTCGGGACTTAGCCCGGATATAGT-ACTCGCACAAATGCCTTCGGGACTTAGCCCGG
* *
46443763 A-ACTAGTCACTAGCG
65 ATA-TAGTAACTAGCA
*
46443778 CAAATGCCTTCGGGACTTAACCCG
1 CAAATGCCTTCGGGACTTAGCCCG
46443802 ATTATCATCC
Statistics
Matches: 155, Mismatches: 23, Indels: 10
0.82 0.12 0.05
Matches are distributed among these distances:
78 18 0.12
79 17 0.11
80 119 0.77
81 1 0.01
ACGTcount: A:0.28, C:0.27, G:0.21, T:0.23
Consensus pattern (79 bp):
CAAATGCCTTCGGGACTTAGCCCGGATATAGTACTCGCACAAATGCCTTCGGGACTTAGCCCGGA
TATAGTAACTAGCA
Found at i:46443751 original size:120 final size:120
Alignment explanation
Indices: 46443580--46443801 Score: 331
Period size: 120 Copynumber: 1.9 Consensus size: 120
46443570 CTACTCGCTC
* * *
46443580 AATGCCTTCGGGACATAGCCCGGATATAGTAACTCACACCAATGCCTTCGGGACTTAGCCCGGAT
1 AATGCCTTCGGGACATAGCCCGGATATAATAACTCACACAAATGCATTCGGGACTTAGCCCGGA-
*
46443645 A-TAGT-AGCTCGCACAAATGCCTTCGAGACTTAACCCGGATGTAATAACTAGTACA
65 ACTAGTCA-CTAGCACAAATGCCTTCGAGACTTAACCCGGATGTAATAACTAGTACA
* * *
46443700 AATGCCTTCGGGACTTAGCCCGGATGTAATAACTCGCACAAATGCATTCGGGACTTAGCCCGGAA
1 AATGCCTTCGGGACATAGCCCGGATATAATAACTCACACAAATGCATTCGGGACTTAGCCCGGAA
* *
46443765 CTAGTCACTAGCGCAAATGCCTTCGGGACTTAACCCG
66 CTAGTCACTAGCACAAATGCCTTCGAGACTTAACCCG
46443802 ATTATCATCC
Statistics
Matches: 91, Mismatches: 9, Indels: 4
0.88 0.09 0.04
Matches are distributed among these distances:
119 1 0.01
120 89 0.98
121 1 0.01
ACGTcount: A:0.28, C:0.27, G:0.22, T:0.22
Consensus pattern (120 bp):
AATGCCTTCGGGACATAGCCCGGATATAATAACTCACACAAATGCATTCGGGACTTAGCCCGGAA
CTAGTCACTAGCACAAATGCCTTCGAGACTTAACCCGGATGTAATAACTAGTACA
Found at i:46445151 original size:54 final size:54
Alignment explanation
Indices: 46445045--46445166 Score: 169
Period size: 53 Copynumber: 2.3 Consensus size: 54
46445035 CTCAAAGCTC
*
46445045 TTTTTCGTTCTTTTTCTTTCTTCTATTCGGCCAAGAACAACATGAGAGCTTTTT
1 TTTTTCGTTCGTTTTCTTTCTTCTATTCGGCCAAGAACAACATGAGAGCTTTTT
* * *
46445099 TTTTTC-TTCGTTTTCTTT-TCTCTCTTCGGTCAAGAACAACATGAGAGCCTTTT
1 TTTTTCGTTCGTTTTCTTTCT-TCTATTCGGCCAAGAACAACATGAGAGCTTTTT
*
46445152 TTTTTCTTTC-TTTTC
1 TTTTTCGTTCGTTTTC
46445167 CTTTTTTTCA
Statistics
Matches: 62, Mismatches: 4, Indels: 5
0.87 0.06 0.07
Matches are distributed among these distances:
52 1 0.02
53 52 0.84
54 9 0.15
ACGTcount: A:0.16, C:0.21, G:0.11, T:0.52
Consensus pattern (54 bp):
TTTTTCGTTCGTTTTCTTTCTTCTATTCGGCCAAGAACAACATGAGAGCTTTTT
Found at i:46446588 original size:27 final size:27
Alignment explanation
Indices: 46446545--46446772 Score: 330
Period size: 27 Copynumber: 8.4 Consensus size: 27
46446535 GAATCATTAC
*
46446545 GTGATAAAATGTCGATTTTGCCCTTAT
1 GTGATAAAATGACGATTTTGCCCTTAT
* *
46446572 GCGATAAAATGATGATTTTGCCCTTAT
1 GTGATAAAATGACGATTTTGCCCTTAT
* *
46446599 GTGATAAAATGACGATTTTGCTCTCAT
1 GTGATAAAATGACGATTTTGCCCTTAT
* * *
46446626 GTGATAAAATGAAGATTTTTCTCTTAT
1 GTGATAAAATGACGATTTTGCCCTTAT
* * *
46446653 GTGATAAAATGACAATTTTTCCCATAT
1 GTGATAAAATGACGATTTTGCCCTTAT
*
46446680 GTGATAAAATGACGATTTCGCCCTTAT
1 GTGATAAAATGACGATTTTGCCCTTAT
*
46446707 GTGATAAAATGACGATTTTGCCATTAT
1 GTGATAAAATGACGATTTTGCCCTTAT
*
46446734 GTGATAAAATGACTATTTTGCCCTTAT
1 GTGATAAAATGACGATTTTGCCCTTAT
46446761 GTGATAAAATGA
1 GTGATAAAATGA
46446773 TCGAAATACC
Statistics
Matches: 179, Mismatches: 22, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 179 1.00
ACGTcount: A:0.32, C:0.13, G:0.17, T:0.38
Consensus pattern (27 bp):
GTGATAAAATGACGATTTTGCCCTTAT
Found at i:46446805 original size:26 final size:26
Alignment explanation
Indices: 46446765--46446875 Score: 84
Period size: 27 Copynumber: 4.2 Consensus size: 26
46446755 CCTTATGTGA
*
46446765 TAAAATGATCGAAATACCCTCATAGG
1 TAAAATGACCGAAATACCCTCATAGG
* *
46446791 TAAAATGACCAAAATACCCCTACA-GGG
1 TAAAATGACCGAAATA-CCCT-CATAGG
* *
46446818 TAGAATGACCGAAATACCACT-GTAGAG
1 TAAAATGACCGAAATACC-CTCATAG-G
* *
46446845 TAAAATGACTGTAATA-CCTCAGTAAGG
1 TAAAATGACCGAAATACCCTCA-T-AGG
46446872 TAAA
1 TAAA
46446876 CTAACAGATT
Statistics
Matches: 66, Mismatches: 11, Indels: 15
0.72 0.12 0.16
Matches are distributed among these distances:
25 2 0.03
26 18 0.27
27 42 0.64
28 4 0.06
ACGTcount: A:0.43, C:0.19, G:0.17, T:0.21
Consensus pattern (26 bp):
TAAAATGACCGAAATACCCTCATAGG
Found at i:46447279 original size:18 final size:18
Alignment explanation
Indices: 46447223--46447281 Score: 64
Period size: 18 Copynumber: 3.3 Consensus size: 18
46447213 TCTGCTTACA
*
46447223 TACTGCACTGATTACTGT
1 TACTGCACTGATAACTGT
* * * *
46447241 TTCTGCATTGATCATTGT
1 TACTGCACTGATAACTGT
*
46447259 TACTGCACTGATAACTAT
1 TACTGCACTGATAACTGT
46447277 TACTG
1 TACTG
46447282 AAATGGGCTA
Statistics
Matches: 32, Mismatches: 9, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
18 32 1.00
ACGTcount: A:0.24, C:0.20, G:0.15, T:0.41
Consensus pattern (18 bp):
TACTGCACTGATAACTGT
Found at i:46448365 original size:9 final size:9
Alignment explanation
Indices: 46448351--46448424 Score: 87
Period size: 9 Copynumber: 8.0 Consensus size: 9
46448341 CATATCATAT
46448351 CATAACTTA
1 CATAACTTA
46448360 CATAACTTA
1 CATAACTTA
46448369 CATAACTTA
1 CATAACTTA
*
46448378 TATAACTTA
1 CATAACTTA
46448387 -ATAACTTA
1 CATAACTTA
* *
46448395 TATATATCATA
1 CATA-A-CTTA
46448406 TCATAACTTA
1 -CATAACTTA
46448416 CATAACTTA
1 CATAACTTA
46448425 ATTATACTTA
Statistics
Matches: 57, Mismatches: 4, Indels: 8
0.83 0.06 0.12
Matches are distributed among these distances:
8 8 0.14
9 38 0.67
10 4 0.07
11 4 0.07
12 3 0.05
ACGTcount: A:0.45, C:0.18, G:0.00, T:0.38
Consensus pattern (9 bp):
CATAACTTA
Found at i:46456043 original size:28 final size:28
Alignment explanation
Indices: 46456009--46456190 Score: 213
Period size: 28 Copynumber: 6.5 Consensus size: 28
46455999 ACTTGATATT
**
46456009 TCACACACTAAGTGCCATACCCAATGTC
1 TCACACACTAAGTGCCATAATCAATGTC
** *
46456037 TTGCACACTAAGTGCCATATTCAATGTC
1 TCACACACTAAGTGCCATAATCAATGTC
* * * *
46456065 TCACACGCTAAGTGCCATGATCGATATC
1 TCACACACTAAGTGCCATAATCAATGTC
* * * *
46456093 TCGA-GCACTAAGTGTCACAATAAATGTC
1 TC-ACACACTAAGTGCCATAATCAATGTC
*
46456121 TCACACACTAAGTGTCATAATCAATGTC
1 TCACACACTAAGTGCCATAATCAATGTC
46456149 TCACACACTAAGTGCCATAATCAATGTC
1 TCACACACTAAGTGCCATAATCAATGTC
*
46456177 TCGCACACTAAGTG
1 TCACACACTAAGTG
46456191 TCGTACATAG
Statistics
Matches: 128, Mismatches: 24, Indels: 4
0.82 0.15 0.03
Matches are distributed among these distances:
27 1 0.01
28 126 0.98
29 1 0.01
ACGTcount: A:0.32, C:0.27, G:0.14, T:0.26
Consensus pattern (28 bp):
TCACACACTAAGTGCCATAATCAATGTC
Found at i:46456145 original size:84 final size:84
Alignment explanation
Indices: 46456031--46456192 Score: 236
Period size: 84 Copynumber: 1.9 Consensus size: 84
46456021 TGCCATACCC
** * * * *
46456031 AATGTCTTGCACACTAAGTGCCATATTCAATGTCTCACACGCTAAGTGCCATGATCGATATCTCG
1 AATGTCTCACACACTAAGTGCCATAATCAATGTCTCACACACTAAGTGCCATAATCAATATCTCG
46456096 -AGCACTAAGTGTCACAATA
66 CA-CACTAAGTGTCACAATA
* *
46456115 AATGTCTCACACACTAAGTGTCATAATCAATGTCTCACACACTAAGTGCCATAATCAATGTCTCG
1 AATGTCTCACACACTAAGTGCCATAATCAATGTCTCACACACTAAGTGCCATAATCAATATCTCG
46456180 CACACTAAGTGTC
66 CACACTAAGTGTC
46456193 GTACATAGCC
Statistics
Matches: 69, Mismatches: 8, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
84 68 0.99
85 1 0.01
ACGTcount: A:0.32, C:0.26, G:0.15, T:0.27
Consensus pattern (84 bp):
AATGTCTCACACACTAAGTGCCATAATCAATGTCTCACACACTAAGTGCCATAATCAATATCTCG
CACACTAAGTGTCACAATA
Found at i:46459507 original size:13 final size:13
Alignment explanation
Indices: 46459489--46459515 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
46459479 ATTTTAAAAG
46459489 CTTGAATTTTGAA
1 CTTGAATTTTGAA
46459502 CTTGAATTTTGAA
1 CTTGAATTTTGAA
46459515 C
1 C
46459516 CTATGGCATG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.11, G:0.15, T:0.44
Consensus pattern (13 bp):
CTTGAATTTTGAA
Found at i:46460236 original size:20 final size:21
Alignment explanation
Indices: 46460207--46460255 Score: 57
Period size: 20 Copynumber: 2.4 Consensus size: 21
46460197 ATATTTTATA
*
46460207 ATTA-TTTAATTAGATAA-AT
1 ATTATTTTAATGAGATAATAT
* *
46460226 ATTATTTTAATGATATAATTT
1 ATTATTTTAATGAGATAATAT
46460247 ATTATTTTA
1 ATTATTTTA
46460256 TTATTATTTA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
19 4 0.16
20 11 0.44
21 10 0.40
ACGTcount: A:0.41, C:0.00, G:0.04, T:0.55
Consensus pattern (21 bp):
ATTATTTTAATGAGATAATAT
Found at i:46462142 original size:46 final size:46
Alignment explanation
Indices: 46462090--46462302 Score: 259
Period size: 46 Copynumber: 4.6 Consensus size: 46
46462080 GATTTCTGAA
** * *
46462090 ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGACAACGTGAC
1 ATGAAATGAATAAGACCATGGTTGAAAGATACCGTGGCAACGTGAC
* * * *
46462136 ATGAAATGAACAAGACCATGGATGAAAAATACCGTGGC-AGGATGAC
1 ATGAAATGAATAAGACCATGGTTGAAAGATACCGTGGCAACG-TGAC
* *
46462182 AGGAAATGAATAAGACCATGGTTGAAAGATACTGTGGCAACGTGAC
1 ATGAAATGAATAAGACCATGGTTGAAAGATACCGTGGCAACGTGAC
* *
46462228 ATGAAATGAAAAAGACCATGGTTGAAAGATATCC-TGGCAACATGAC
1 ATGAAATGAATAAGACCATGGTTGAAAGATA-CCGTGGCAACGTGAC
* * *
46462274 AGGAAATGAGTAAGACCATAGTTGAAAGA
1 ATGAAATGAATAAGACCATGGTTGAAAGA
46462303 CACTATGTGT
Statistics
Matches: 142, Mismatches: 22, Indels: 6
0.84 0.13 0.04
Matches are distributed among these distances:
45 2 0.01
46 137 0.96
47 3 0.02
ACGTcount: A:0.42, C:0.14, G:0.25, T:0.19
Consensus pattern (46 bp):
ATGAAATGAATAAGACCATGGTTGAAAGATACCGTGGCAACGTGAC
Found at i:46462254 original size:92 final size:92
Alignment explanation
Indices: 46462100--46462302 Score: 300
Period size: 92 Copynumber: 2.2 Consensus size: 92
46462090 ATGAAATGTG
*
46462100 TAAGACCATGGTTGAAAGATACCATGACAACGTGACATGAAATGAACAAGACCATGGATGAAAAA
1 TAAGACCATGGTTGAAAGATACCATGACAACGTGACATGAAATGAAAAAGACCATGGATGAAAAA
**
46462165 TA-CCGTGGCAGGATGACAGGAAATGAA
66 TATCC-TGGCAACATGACAGGAAATGAA
** * * *
46462192 TAAGACCATGGTTGAAAGATACTGTGGCAACGTGACATGAAATGAAAAAGACCATGGTTGAAAGA
1 TAAGACCATGGTTGAAAGATACCATGACAACGTGACATGAAATGAAAAAGACCATGGATGAAAAA
*
46462257 TATCCTGGCAACATGACAGGAAATGAG
66 TATCCTGGCAACATGACAGGAAATGAA
*
46462284 TAAGACCATAGTTGAAAGA
1 TAAGACCATGGTTGAAAGA
46462303 CACTATGTGT
Statistics
Matches: 100, Mismatches: 10, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
92 98 0.98
93 2 0.02
ACGTcount: A:0.42, C:0.14, G:0.25, T:0.18
Consensus pattern (92 bp):
TAAGACCATGGTTGAAAGATACCATGACAACGTGACATGAAATGAAAAAGACCATGGATGAAAAA
TATCCTGGCAACATGACAGGAAATGAA
Found at i:46463200 original size:20 final size:20
Alignment explanation
Indices: 46463175--46463220 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
46463165 ATTGGGCCTT
46463175 GCCCATATT-AACACAGTTGG
1 GCCCATATTCAACACAGTT-G
*
46463195 GCCCAT-TTCAATACAGTTG
1 GCCCATATTCAACACAGTTG
46463214 GCCCATA
1 GCCCATA
46463221 ACAAAATAGT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
19 9 0.39
20 14 0.61
ACGTcount: A:0.28, C:0.28, G:0.17, T:0.26
Consensus pattern (20 bp):
GCCCATATTCAACACAGTTG
Found at i:46464469 original size:27 final size:27
Alignment explanation
Indices: 46464439--46464646 Score: 240
Period size: 27 Copynumber: 7.7 Consensus size: 27
46464429 TTAGTTTACC
*
46464439 AAATTACCAAAATACCCCTGGTTTGTA
1 AAATTACCAAAATACCCCTAGTTTGTA
* * ** * *
46464466 AAATTACTAAAACACCATTTGTTTATA
1 AAATTACCAAAATACCCCTAGTTTGTA
46464493 AAATTACCAAAATACCCCTAGTTTGTA
1 AAATTACCAAAATACCCCTAGTTTGTA
*
46464520 AAATTACCAAAATACCCCTGGTTTGTA
1 AAATTACCAAAATACCCCTAGTTTGTA
*
46464547 AAATTATCAAAATACCCCTAGTTTGTA
1 AAATTACCAAAATACCCCTAGTTTGTA
*
46464574 AAATTACCAAAATA-CCCTCAATTTGTA
1 AAATTACCAAAATACCCCT-AGTTTGTA
* * **
46464601 AAATTACTAAAATGCCCCTA-TAGGGTA
1 AAATTACCAAAATACCCCTAGT-TTGTA
* *
46464628 GAATTACTAAAATACCCCT
1 AAATTACCAAAATACCCCT
46464647 GTAGGGTAGA
Statistics
Matches: 155, Mismatches: 23, Indels: 6
0.84 0.12 0.03
Matches are distributed among these distances:
26 5 0.03
27 146 0.94
28 4 0.03
ACGTcount: A:0.41, C:0.21, G:0.08, T:0.30
Consensus pattern (27 bp):
AAATTACCAAAATACCCCTAGTTTGTA
Found at i:46464633 original size:54 final size:54
Alignment explanation
Indices: 46464439--46464698 Score: 179
Period size: 54 Copynumber: 4.8 Consensus size: 54
46464429 TTAGTTTACC
* * ** * * ** ** *
46464439 AAATTACCAAAATACCCCTGGTTTGTAAAATTACTAAAACACCATTTGTTTATA
1 AAATTATCAAAATACCCCTAGTGGGTAAAATTACCAAAATACCCCTAATTTGTA
* ** **
46464493 AAATTACCAAAATACCCCTAGTTTGTAAAATTACCAAAATACCCCTGGTTTGTA
1 AAATTATCAAAATACCCCTAGTGGGTAAAATTACCAAAATACCCCTAATTTGTA
**
46464547 AAATTATCAAAATACCCCTAGTTTGTAAAATTACCAAAATA-CCCTCAATTTGTA
1 AAATTATCAAAATACCCCTAGTGGGTAAAATTACCAAAATACCCCT-AATTTGTA
* * * * **
46464601 AAATTA-CTAAAATGCCCCTA-TAGGGTAGAATTACTAAAATACCCCT-GTAGGGTA
1 AAATTATC-AAAATACCCCTAGT-GGGTAAAATTACCAAAATACCCCTAAT-TTGTA
* * * * *
46464655 GAATTATCGAAATACCCCT-GTAGGATAGAATTACCGAAATACCC
1 AAATTATCAAAATACCCCTAGT-GGGTAAAATTACCAAAATACCC
46464699 TGTAGGGTAG
Statistics
Matches: 175, Mismatches: 24, Indels: 14
0.82 0.11 0.07
Matches are distributed among these distances:
53 7 0.04
54 163 0.93
55 5 0.03
ACGTcount: A:0.40, C:0.20, G:0.11, T:0.29
Consensus pattern (54 bp):
AAATTATCAAAATACCCCTAGTGGGTAAAATTACCAAAATACCCCTAATTTGTA
Found at i:46464660 original size:81 final size:80
Alignment explanation
Indices: 46464494--46464876 Score: 355
Period size: 81 Copynumber: 4.7 Consensus size: 80
46464484 TTGTTTATAA
* ** * ** *
46464494 AATTACCAAAATACCCCTAGTTTGTAAAATTACCAAAATACCCCTGGT-TTGTAAAATTA-TCAA
1 AATTACCGAAATACCCC-AGTGGGTAGAATTACCAAAATACCCCT-GTAGGGTAGAATTACT-AA
** *
46464557 AATACCCCTAGT-TTGTAA
63 AATACCCCT-GTAGGGTAG
* * ** * * * *
46464575 AATTACCAAAATACCCTCAATTTGTAAAATTACTAAAATGCCCCTATAGGGTAGAATTACTAAAA
1 AATTACCGAAATACCC-CAGTGGGTAGAATTACCAAAATACCCCTGTAGGGTAGAATTACTAAAA
46464640 TACCCCTGTAGGGTAG
65 TACCCCTGTAGGGTAG
* * * * *
46464656 AATTATCGAAATACCCCTGTAGGATAGAATTACCGAAATA-CCCTGTAGGGTAGAATTACCAAAA
1 AATTACCGAAATACCCCAGT-GGGTAGAATTACCAAAATACCCCTGTAGGGTAGAATTACTAAAA
*
46464720 TACCCCTGTAAGGTAG
65 TACCCCTGTAGGGTAG
* * * *
46464736 AATTTCTGAACTACCCCAGTAGGGTAGAATTACCAAAATACCCTTGTAGGGTAGAATTATCGT--
1 AATTACCGAAATACCCCAGT-GGGTAGAATTACCAAAATACCCCTGTAGGGTAGAATTA-C-TAA
46464799 AATACCCCTGTAGGGTAG
63 AATACCCCTGTAGGGTAG
* * *
46464817 AATTACCGAAATACCCCTGTAGGGTAGAATTACTAAAATACCCCTGTAGGGTGGAATTAC
1 AATTACCGAAATACCCCAGT-GGGTAGAATTACCAAAATACCCCTGTAGGGTAGAATTAC
46464877 CGAGATACCT
Statistics
Matches: 253, Mismatches: 41, Indels: 17
0.81 0.13 0.05
Matches are distributed among these distances:
80 76 0.30
81 174 0.69
82 3 0.01
ACGTcount: A:0.37, C:0.20, G:0.16, T:0.27
Consensus pattern (80 bp):
AATTACCGAAATACCCCAGTGGGTAGAATTACCAAAATACCCCTGTAGGGTAGAATTACTAAAAT
ACCCCTGTAGGGTAG
Found at i:46464884 original size:27 final size:27
Alignment explanation
Indices: 46464610--46464903 Score: 367
Period size: 27 Copynumber: 11.0 Consensus size: 27
46464600 AAAATTACTA
* * **
46464610 AAATGCCCCTATAGGGTAGAATTACTA
1 AAATACCCCTGTAGGGTAGAATTACCG
*
46464637 AAATACCCCTGTAGGGTAGAATTATCG
1 AAATACCCCTGTAGGGTAGAATTACCG
*
46464664 AAATACCCCTGTAGGATAGAATTACCG
1 AAATACCCCTGTAGGGTAGAATTACCG
*
46464691 AAATA-CCCTGTAGGGTAGAATTACCA
1 AAATACCCCTGTAGGGTAGAATTACCG
* * *
46464717 AAATACCCCTGTAAGGTAGAATTTCTG
1 AAATACCCCTGTAGGGTAGAATTACCG
* * *
46464744 AACTACCCCAGTAGGGTAGAATTACCA
1 AAATACCCCTGTAGGGTAGAATTACCG
* *
46464771 AAATACCCTTGTAGGGTAGAATTATCG
1 AAATACCCCTGTAGGGTAGAATTACCG
*
46464798 TAATACCCCTGTAGGGTAGAATTACCG
1 AAATACCCCTGTAGGGTAGAATTACCG
**
46464825 AAATACCCCTGTAGGGTAGAATTACTA
1 AAATACCCCTGTAGGGTAGAATTACCG
*
46464852 AAATACCCCTGTAGGGTGGAATTACCG
1 AAATACCCCTGTAGGGTAGAATTACCG
* * * *
46464879 AGATA-CCTTGTGGGGTAAAATTACC
1 AAATACCCCTGTAGGGTAGAATTACC
46464904 ATTTTGCCCC
Statistics
Matches: 228, Mismatches: 38, Indels: 3
0.85 0.14 0.01
Matches are distributed among these distances:
26 40 0.18
27 188 0.82
ACGTcount: A:0.34, C:0.20, G:0.21, T:0.25
Consensus pattern (27 bp):
AAATACCCCTGTAGGGTAGAATTACCG
Found at i:46465381 original size:22 final size:22
Alignment explanation
Indices: 46465329--46465393 Score: 78
Period size: 22 Copynumber: 3.0 Consensus size: 22
46465319 TTAAAGCCTT
* *
46465329 CTGATTATGGCTTTATGTCAAC
1 CTGATTATGGCTTTGTGCCAAC
*
46465351 CT-ACATATGGCTTTGTGCCAAC
1 CTGA-TTATGGCTTTGTGCCAAC
*
46465373 CTGATTATGGCTGTGTGCCAA
1 CTGATTATGGCTTTGTGCCAA
46465394 ACGTATTTGC
Statistics
Matches: 36, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
21 1 0.03
22 34 0.94
23 1 0.03
ACGTcount: A:0.22, C:0.22, G:0.22, T:0.35
Consensus pattern (22 bp):
CTGATTATGGCTTTGTGCCAAC
Found at i:46465582 original size:27 final size:27
Alignment explanation
Indices: 46465552--46465653 Score: 127
Period size: 27 Copynumber: 3.8 Consensus size: 27
46465542 ATTCTGTTAA
* *
46465552 GTGGCTTTGCCACATTATCTGTTTCTG
1 GTGGCTCTGCCACAATATCTGTTTCTG
*
46465579 GTGGCTATGCCACAAATATCTG-TTCTG
1 GTGGCTCTGCCAC-AATATCTGTTTCTG
46465606 GTGGCTCTGCCACAATATCTGTATT-TG
1 GTGGCTCTGCCACAATATCTGT-TTCTG
* *
46465633 GTGACTCTGTCACAATATCTG
1 GTGGCTCTGCCACAATATCTG
46465654 ATAACTGAGC
Statistics
Matches: 67, Mismatches: 5, Indels: 6
0.86 0.06 0.08
Matches are distributed among these distances:
26 8 0.12
27 50 0.75
28 9 0.13
ACGTcount: A:0.19, C:0.23, G:0.22, T:0.37
Consensus pattern (27 bp):
GTGGCTCTGCCACAATATCTGTTTCTG
Found at i:46465825 original size:6 final size:6
Alignment explanation
Indices: 46465785--46465872 Score: 65
Period size: 6 Copynumber: 14.3 Consensus size: 6
46465775 TTGCATTCAC
* * *
46465785 ATTCTG ATTTTG ATTCTG -TTACCTG ATACTG ATTCTA ATTCTG ATTCT-
1 ATTCTG ATTCTG ATTCTG ATT--CTG ATTCTG ATTCTG ATTCTG ATTCTG
* *
46465833 ATCACCTA ATTCTG ATTCTG ATTCTG ATTCT- AGTTCTG AT
1 AT--TCTG ATTCTG ATTCTG ATTCTG ATTCTG A-TTCTG AT
46465873 AATGTTTCTT
Statistics
Matches: 65, Mismatches: 9, Indels: 16
0.72 0.10 0.18
Matches are distributed among these distances:
5 5 0.08
6 51 0.78
7 6 0.09
8 3 0.05
ACGTcount: A:0.22, C:0.18, G:0.12, T:0.48
Consensus pattern (6 bp):
ATTCTG
Found at i:46465830 original size:31 final size:31
Alignment explanation
Indices: 46465785--46465888 Score: 104
Period size: 31 Copynumber: 3.4 Consensus size: 31
46465775 TTGCATTCAC
*
46465785 ATTCTGATTTTGATTCTGTTACCTGATACTG
1 ATTCTGATTCTGATTCTGTTACCTGATACTG
* * * * *
46465816 ATTCTAATTCTGATTCTATCACCTAATTCTG
1 ATTCTGATTCTGATTCTGTTACCTGATACTG
*
46465847 ATTCTGATTCTGATTCTAGTT--CTGATAATG
1 ATTCTGATTCTGATTCT-GTTACCTGATACTG
* *
46465877 TTTCTTATTCTG
1 ATTCTGATTCTG
46465889 TAATGGATTA
Statistics
Matches: 58, Mismatches: 14, Indels: 3
0.77 0.19 0.04
Matches are distributed among these distances:
30 16 0.28
31 41 0.71
32 1 0.02
ACGTcount: A:0.21, C:0.17, G:0.12, T:0.49
Consensus pattern (31 bp):
ATTCTGATTCTGATTCTGTTACCTGATACTG
Found at i:46466464 original size:27 final size:27
Alignment explanation
Indices: 46466416--46466827 Score: 450
Period size: 27 Copynumber: 15.3 Consensus size: 27
46466406 AGGGCAAAAT
* * *
46466416 GGTAATTTTACCCCAC-GAGGGTATCTC
1 GGTAATTCTACCCTACAG-GGGTATTTC
46466443 GGTAATTCTACCCTACAGGGGTATTTC
1 GGTAATTCTACCCTACAGGGGTATTTC
* * * *
46466470 AGTATTTCTACCCTACAAGGCTATTTC
1 GGTAATTCTACCCTACAGGGGTATTTC
*
46466497 GATAATTCTACCCTACAGGGGTATTTC
1 GGTAATTCTACCCTACAGGGGTATTTC
* * *
46466524 AGTAATCCTACCCTATAGGGGTATTTC
1 GGTAATTCTACCCTACAGGGGTATTTC
* * *
46466551 GATAATTCTACCTTATAGGGGTATTTC
1 GGTAATTCTACCCTACAGGGGTATTTC
*
46466578 AGTAATTCTACCCTACAGGGGTATTTC
1 GGTAATTCTACCCTACAGGGGTATTTC
*
46466605 GGTAATTCTACCTTACAGGGGTATTTC
1 GGTAATTCTACCCTACAGGGGTATTTC
* * * *
46466632 AGTCATTCTACCCTATATGGGTATTTC
1 GGTAATTCTACCCTACAGGGGTATTTC
* * *
46466659 GGTAATTGTACCATACAGGAGTATTTC
1 GGTAATTCTACCCTACAGGGGTATTTC
** *
46466686 AATAATTCTACCCTATAGGGGTATTTC
1 GGTAATTCTACCCTACAGGGGTATTTC
* *
46466713 GGTAATTCTACCTTACAGGAGTATTTC
1 GGTAATTCTACCCTACAGGGGTATTTC
* * *
46466740 AGTAATTCCACCCTACAAGGGTATTTC
1 GGTAATTCTACCCTACAGGGGTATTTC
* *
46466767 GATAATTCTACCTTACAGGGGTATTTC
1 GGTAATTCTACCCTACAGGGGTATTTC
* * ** *
46466794 GATAATTTTA-CAAATCAGGGGTATTTT
1 GGTAATTCTACCCTA-CAGGGGTATTTC
46466821 GGTAATT
1 GGTAATT
46466828 TTGCTAATCG
Statistics
Matches: 319, Mismatches: 64, Indels: 4
0.82 0.17 0.01
Matches are distributed among these distances:
26 2 0.01
27 316 0.99
28 1 0.00
ACGTcount: A:0.26, C:0.20, G:0.18, T:0.36
Consensus pattern (27 bp):
GGTAATTCTACCCTACAGGGGTATTTC
Found at i:46466800 original size:54 final size:54
Alignment explanation
Indices: 46466417--46466793 Score: 511
Period size: 54 Copynumber: 7.0 Consensus size: 54
46466407 GGGCAAAATG
* * * * *
46466417 GTAATTTTACCCCACGAGGGTATCTCGGTAATTCTACCCTACAGGGGTATTTCA
1 GTAATTCTACCCTACAAGGGTATTTCGGTAATTCTACCTTACAGGGGTATTTCA
* * * *
46466471 GTATTTCTACCCTACAAGGCTATTTCGATAATTCTACCCTACAGGGGTATTTCA
1 GTAATTCTACCCTACAAGGGTATTTCGGTAATTCTACCTTACAGGGGTATTTCA
* * * * *
46466525 GTAATCCTACCCTATAGGGGTATTTCGATAATTCTACCTTATAGGGGTATTTCA
1 GTAATTCTACCCTACAAGGGTATTTCGGTAATTCTACCTTACAGGGGTATTTCA
*
46466579 GTAATTCTACCCTACAGGGGTATTTCGGTAATTCTACCTTACAGGGGTATTTCA
1 GTAATTCTACCCTACAAGGGTATTTCGGTAATTCTACCTTACAGGGGTATTTCA
* * * * * *
46466633 GTCATTCTACCCTATATGGGTATTTCGGTAATTGTACCATACAGGAGTATTTCA
1 GTAATTCTACCCTACAAGGGTATTTCGGTAATTCTACCTTACAGGGGTATTTCA
* * * *
46466687 ATAATTCTACCCTATAGGGGTATTTCGGTAATTCTACCTTACAGGAGTATTTCA
1 GTAATTCTACCCTACAAGGGTATTTCGGTAATTCTACCTTACAGGGGTATTTCA
* *
46466741 GTAATTCCACCCTACAAGGGTATTTCGATAATTCTACCTTACAGGGGTATTTC
1 GTAATTCTACCCTACAAGGGTATTTCGGTAATTCTACCTTACAGGGGTATTTC
46466794 GATAATTTTA
Statistics
Matches: 288, Mismatches: 35, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
54 288 1.00
ACGTcount: A:0.26, C:0.21, G:0.18, T:0.35
Consensus pattern (54 bp):
GTAATTCTACCCTACAAGGGTATTTCGGTAATTCTACCTTACAGGGGTATTTCA
Found at i:46466828 original size:27 final size:27
Alignment explanation
Indices: 46466785--46466882 Score: 126
Period size: 27 Copynumber: 3.6 Consensus size: 27
46466775 TACCTTACAG
* * *
46466785 GGGTATTTCGATAATTTTACAAATC-A
1 GGGTATTTTGGTAATTTTACTAATCGA
*
46466811 GGGGTATTTTGGTAATTTTGCTAATCGA
1 -GGGTATTTTGGTAATTTTACTAATCGA
* *
46466839 GGGTATTTTGGAAATTTTTCTAATCGA
1 GGGTATTTTGGTAATTTTACTAATCGA
46466866 GGGTATTTTGGTAATTT
1 GGGTATTTTGGTAATTT
46466883 GGTAAACTAA
Statistics
Matches: 63, Mismatches: 7, Indels: 2
0.88 0.10 0.03
Matches are distributed among these distances:
27 62 0.98
28 1 0.02
ACGTcount: A:0.26, C:0.07, G:0.23, T:0.44
Consensus pattern (27 bp):
GGGTATTTTGGTAATTTTACTAATCGA
Found at i:46468885 original size:6 final size:6
Alignment explanation
Indices: 46468855--46468929 Score: 55
Period size: 6 Copynumber: 12.3 Consensus size: 6
46468845 AAGAAACATT
* * * *
46468855 ATCAGA A-CTAGA ATCAAA ATGAGA ATCAGA ATTAGA ATCAG- GTGACAGA
1 ATCAGA ATC-AGA ATCAGA ATCAGA ATCAGA ATCAGA ATCAGA AT--CAGA
* *
46468904 ATCATA ATCAAA ATCAGA ATCAGA AT
1 ATCAGA ATCAGA ATCAGA ATCAGA AT
46468930 TAGGTGACAA
Statistics
Matches: 53, Mismatches: 11, Indels: 10
0.72 0.15 0.14
Matches are distributed among these distances:
5 2 0.04
6 46 0.87
7 4 0.08
8 1 0.02
ACGTcount: A:0.51, C:0.13, G:0.16, T:0.20
Consensus pattern (6 bp):
ATCAGA
Found at i:46468905 original size:37 final size:37
Alignment explanation
Indices: 46468864--46468938 Score: 105
Period size: 37 Copynumber: 2.0 Consensus size: 37
46468854 TATCAGAACT
* * *
46468864 AGAATCAAAATGAGAATCAGAATTAGAATCAGGTGAC
1 AGAATCAAAATCAAAATCAGAATCAGAATCAGGTGAC
* *
46468901 AGAATCATAATCAAAATCAGAATCAGAATTAGGTGAC
1 AGAATCAAAATCAAAATCAGAATCAGAATCAGGTGAC
46468938 A
1 A
46468939 AAATTAGAAT
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
37 33 1.00
ACGTcount: A:0.49, C:0.12, G:0.19, T:0.20
Consensus pattern (37 bp):
AGAATCAAAATCAAAATCAGAATCAGAATCAGGTGAC
Found at i:46468950 original size:37 final size:37
Alignment explanation
Indices: 46468878--46468950 Score: 101
Period size: 37 Copynumber: 2.0 Consensus size: 37
46468868 TCAAAATGAG
* * *
46468878 AATCAGAATTAGAATCAGGTGACAGAATCATAATCAA
1 AATCAGAATCAGAATCAGGTGACAAAATCAGAATCAA
* *
46468915 AATCAGAATCAGAATTAGGTGACAAAATTAGAATCA
1 AATCAGAATCAGAATCAGGTGACAAAATCAGAATCA
46468951 GAATGTGAAT
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
37 31 1.00
ACGTcount: A:0.49, C:0.12, G:0.16, T:0.22
Consensus pattern (37 bp):
AATCAGAATCAGAATCAGGTGACAAAATCAGAATCAA
Found at i:46469109 original size:27 final size:26
Alignment explanation
Indices: 46469072--46469152 Score: 99
Period size: 27 Copynumber: 3.0 Consensus size: 26
46469062 AGCATGGCTG
*
46469072 CCAGAACAGATATTGTGACAGAGTCA
1 CCAGAACAGATATTGTGACAGAGCCA
*
46469098 CCAGATACAGATATTGTGGCAGAGCCA
1 CCAGA-ACAGATATTGTGACAGAGCCA
* * *
46469125 CCAGAATCAGATAATGTGGCAAAGCCA
1 CCAGAA-CAGATATTGTGACAGAGCCA
46469152 C
1 C
46469153 TTAACAGAAT
Statistics
Matches: 49, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
26 6 0.12
27 43 0.88
ACGTcount: A:0.37, C:0.22, G:0.23, T:0.17
Consensus pattern (26 bp):
CCAGAACAGATATTGTGACAGAGCCA
Found at i:46469358 original size:22 final size:22
Alignment explanation
Indices: 46469310--46469368 Score: 64
Period size: 22 Copynumber: 2.7 Consensus size: 22
46469300 GTAAATACGT
* *
46469310 TTGGCACGAAGCCATAGTCATG
1 TTGGCACAAAGCCATAGTCAGG
* * *
46469332 ATGGCACAAAGCCATATTTAGG
1 TTGGCACAAAGCCATAGTCAGG
*
46469354 TTGGCACAGAGCCAT
1 TTGGCACAAAGCCAT
46469369 CGATAACGGG
Statistics
Matches: 30, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.31, C:0.22, G:0.25, T:0.22
Consensus pattern (22 bp):
TTGGCACAAAGCCATAGTCAGG
Found at i:46469765 original size:27 final size:27
Alignment explanation
Indices: 46469735--46470014 Score: 281
Period size: 27 Copynumber: 10.6 Consensus size: 27
46469725 TACCCCATGA
*
46469735 GGGTATCTCAGTAATTCTACCCTACAG
1 GGGTATTTCAGTAATTCTACCCTACAG
* **
46469762 GGGTA-TTCAGTATTTGAACCCTACCA-
1 GGGTATTTCAGTAATTCTACCCTA-CAG
*
46469788 GGGTATTTCGGTAATTCTACCCTACAG
1 GGGTATTTCAGTAATTCTACCCTACAG
46469815 GGGTATTTCAGTAATTCTACCCTACAG
1 GGGTATTTCAGTAATTCTACCCTACAG
*
46469842 GGGTATTTC-GATAATTCTACCTTACAG
1 GGGTATTTCAG-TAATTCTACCCTACAG
* * *
46469869 GGGTATTTCAGTCATTCTACCTTACAA
1 GGGTATTTCAGTAATTCTACCCTACAG
*
46469896 GGGTATTTCGGTAATTCTA--C-A-A-
1 GGGTATTTCAGTAATTCTACCCTACAG
** *
46469918 GGGTATTTTGGTAATTCTACCATACAG
1 GGGTATTTCAGTAATTCTACCCTACAG
** *
46469945 AAGTATTTCAATAATTCTACCCTACAG
1 GGGTATTTCAGTAATTCTACCCTACAG
* * * *
46469972 GGGTATTT-TGATAATTCTATCTTACAA
1 GGGTATTTCAG-TAATTCTACCCTACAG
*
46469999 GGGTATTTCGGTAATT
1 GGGTATTTCAGTAATT
46470015 TTACAAATCA
Statistics
Matches: 210, Mismatches: 31, Indels: 24
0.79 0.12 0.09
Matches are distributed among these distances:
22 18 0.09
23 1 0.00
24 1 0.00
25 1 0.00
26 23 0.11
27 164 0.78
28 2 0.01
ACGTcount: A:0.27, C:0.19, G:0.19, T:0.36
Consensus pattern (27 bp):
GGGTATTTCAGTAATTCTACCCTACAG
Found at i:46469944 original size:103 final size:103
Alignment explanation
Indices: 46469737--46470020 Score: 333
Period size: 103 Copynumber: 2.7 Consensus size: 103
46469727 CCCCATGAGG
* * * *
46469737 GTATCTCAGTAATTCTACCCTACAGGGGTA-TTCAGTATT-TGAACCCTACCAGGGTATTTCGGT
1 GTATTTCAATAATTCTACCCTACAGGGGTATTTCAGTATTCT--ACCTTACAAGGGTATTTCGGT
* **
46469800 AATTCTACCCTACAGGGGTATTTCAGTAATTCTACCCTACAGGG
64 AATTCTA--C-A-AGGGGTATTTCAGTAATTCTACCATACAGAA
* *
46469844 GTATTTCGATAATTCTACCTTACAGGGGTATTTCAGTCATTCTACCTTACAAGGGTATTTCGGTA
1 GTATTTCAATAATTCTACCCTACAGGGGTATTTCAGT-ATTCTACCTTACAAGGGTATTTCGGTA
**
46469909 ATTCTACAA-GGGTATTTTGGTAATTCTACCATACAGAA
65 ATTCTACAAGGGGTATTTCAGTAATTCTACCATACAGAA
* *
46469947 GTATTTCAATAATTCTACCCTACAGGGGTATTT-TGATAATTCTATCTTACAAGGGTATTTCGGT
1 GTATTTCAATAATTCTACCCTACAGGGGTATTTCAG-T-ATTCTACCTTACAAGGGTATTTCGGT
*
46470011 AATTTTACAA
64 AATTCTACAA
46470021 ATCAGGGGTA
Statistics
Matches: 156, Mismatches: 17, Indels: 12
0.84 0.09 0.06
Matches are distributed among these distances:
102 1 0.01
103 90 0.58
104 1 0.01
105 1 0.01
106 1 0.01
107 26 0.17
108 32 0.21
109 3 0.02
110 1 0.01
ACGTcount: A:0.27, C:0.19, G:0.18, T:0.36
Consensus pattern (103 bp):
GTATTTCAATAATTCTACCCTACAGGGGTATTTCAGTATTCTACCTTACAAGGGTATTTCGGTAA
TTCTACAAGGGGTATTTCAGTAATTCTACCATACAGAA
Found at i:46470029 original size:27 final size:27
Alignment explanation
Indices: 46469998--46470069 Score: 101
Period size: 27 Copynumber: 2.7 Consensus size: 27
46469988 CTATCTTACA
*
46469998 AGGGTATTTCGGTAATTTTACAAATC-
1 AGGGTATTTTGGTAATTTTACAAATCG
* *
46470024 AGGGGTATTTTGGTAATTTTGCTAATCG
1 A-GGGTATTTTGGTAATTTTACAAATCG
46470052 AGGGTATTTTGGTAATTT
1 AGGGTATTTTGGTAATTT
46470070 GGTAAACTAA
Statistics
Matches: 41, Mismatches: 3, Indels: 3
0.87 0.06 0.06
Matches are distributed among these distances:
26 1 0.02
27 39 0.95
28 1 0.02
ACGTcount: A:0.25, C:0.07, G:0.25, T:0.43
Consensus pattern (27 bp):
AGGGTATTTTGGTAATTTTACAAATCG
Found at i:46470030 original size:130 final size:132
Alignment explanation
Indices: 46469734--46470068 Score: 365
Period size: 130 Copynumber: 2.5 Consensus size: 132
46469724 TTACCCCATG
* ** * * * *
46469734 AGGGTATCTCAGTAATTCTACCCTACAGGGGTA-TTCAGT-ATTTGAACCCTACCAGGGTATTTC
1 AGGGTATTTCAGTAATTCTACAATACAAGGGTATTTCGGTAATTTG----CTACAAGGGTATTTT
* ** *
46469797 GGTAATTCTACCCTACAGGGGTATTTCAGTAATTCTACCCTACAGGGGTATTTCGATAATTCTAC
62 GGTAATTCTACCATACAGAAGTATTTCAATAATTCTACCCTACAGGGGTATTTCGATAATTCTAC
46469862 CTTACA
127 CTTACA
* * **
46469868 GGGGTATTTCAGTCATTCTACCTTACAAGGGTATTTCGGTAA-TT-CTACAAGGGTATTTTGGTA
1 AGGGTATTTCAGTAATTCTACAATACAAGGGTATTTCGGTAATTTGCTACAAGGGTATTTTGGTA
* *
46469931 ATTCTACCATACAGAAGTATTTCAATAATTCTACCCTACAGGGGTATTTTGATAATTCTATCTTA
66 ATTCTACCATACAGAAGTATTTCAATAATTCTACCCTACAGGGGTATTTCGATAATTCTACCTTA
46469996 CA
131 CA
* * * * *
46469998 AGGGTATTTCGGTAATTTTACAA-ATCAGGGGTATTTTGGTAATTTTGCTAATCGAGGGTATTTT
1 AGGGTATTTCAGTAATTCTACAATA-CAAGGGTATTTCGGTAA-TTTGCT-A-CAAGGGTATTTT
46470062 GGTAATT
62 GGTAATT
46470069 TGGTAAACTA
Statistics
Matches: 170, Mismatches: 23, Indels: 15
0.82 0.11 0.07
Matches are distributed among these distances:
129 1 0.01
130 110 0.65
132 2 0.01
133 2 0.01
134 29 0.17
135 25 0.15
136 1 0.01
ACGTcount: A:0.27, C:0.17, G:0.19, T:0.37
Consensus pattern (132 bp):
AGGGTATTTCAGTAATTCTACAATACAAGGGTATTTCGGTAATTTGCTACAAGGGTATTTTGGTA
ATTCTACCATACAGAAGTATTTCAATAATTCTACCCTACAGGGGTATTTCGATAATTCTACCTTA
CA
Found at i:46478841 original size:14 final size:14
Alignment explanation
Indices: 46478822--46478849 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
46478812 TTCGACAAGG
46478822 ATTGATAAGGTTTA
1 ATTGATAAGGTTTA
46478836 ATTGATAAGGTTTA
1 ATTGATAAGGTTTA
46478850 CTCATTGATC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.36, C:0.00, G:0.21, T:0.43
Consensus pattern (14 bp):
ATTGATAAGGTTTA
Found at i:46481316 original size:28 final size:28
Alignment explanation
Indices: 46481285--46481519 Score: 258
Period size: 28 Copynumber: 8.4 Consensus size: 28
46481275 CGATATTTTG
**
46481285 CACACTAAGTGCCATACCCAATGTCTCA
1 CACACTAAGTGCCATAATCAATGTCTCA
* *
46481313 CACACTAAGTGCCATATTCAGTGTCTCA
1 CACACTAAGTGCCATAATCAATGTCTCA
** *
46481341 CACACTAAGTGCCATGCT-AGATGTCTCG
1 CACACTAAGTGCCATAATCA-ATGTCTCA
* * **
46481369 CACACTAAGTTCCATATTCAATGTCTTG
1 CACACTAAGTGCCATAATCAATGTCTCA
46481397 CACACTAAGTGCCATAATCAATGTCTCA
1 CACACTAAGTGCCATAATCAATGTCTCA
* * * * *
46481425 TGA-ATTAAATGTCACAATCAATGTCTCA
1 -CACACTAAGTGCCATAATCAATGTCTCA
* *
46481453 CGCACTAAGTGCCATAATCAATGTCGCA
1 CACACTAAGTGCCATAATCAATGTCTCA
*
46481481 CACACTAAGTGCCATAATCAATGTCTCG
1 CACACTAAGTGCCATAATCAATGTCTCA
*
46481509 TACACTAAGTG
1 CACACTAAGTG
46481520 TCGTACATAG
Statistics
Matches: 172, Mismatches: 31, Indels: 8
0.82 0.15 0.04
Matches are distributed among these distances:
27 1 0.01
28 169 0.98
29 2 0.01
ACGTcount: A:0.32, C:0.27, G:0.14, T:0.27
Consensus pattern (28 bp):
CACACTAAGTGCCATAATCAATGTCTCA
Found at i:46484053 original size:29 final size:29
Alignment explanation
Indices: 46484011--46484095 Score: 118
Period size: 29 Copynumber: 3.0 Consensus size: 29
46484001 GCATGTATAT
46484011 GAATGTGATTTGGGCCTAATGGGCCATAC
1 GAATGTGATTTGGGCCTAATGGGCCATAC
* *
46484040 GAATGTGATTTGGGCCTAATAGGCCATAT
1 GAATGTGATTTGGGCCTAATGGGCCATAC
* * *
46484069 GAATGAGA-TTGGGCCTAGTGGGTCATA
1 GAATGTGATTTGGGCCTAATGGGCCATA
46484096 TACATGTATG
Statistics
Matches: 50, Mismatches: 6, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
28 16 0.32
29 34 0.68
ACGTcount: A:0.26, C:0.14, G:0.32, T:0.28
Consensus pattern (29 bp):
GAATGTGATTTGGGCCTAATGGGCCATAC
Found at i:46489302 original size:26 final size:27
Alignment explanation
Indices: 46489251--46489302 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 27
46489241 TTGCCTGGTG
* *
46489251 GCTTTGCCACGTTTACTGTTATTAGCA
1 GCTTTGCCACGTTTACTATTAGTAGCA
*
46489278 GCTTTGCTACG-TTACTATTAGTAGC
1 GCTTTGCCACGTTTACTATTAGTAGC
46489303 TTCACTGCGA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
26 12 0.55
27 10 0.45
ACGTcount: A:0.19, C:0.21, G:0.19, T:0.40
Consensus pattern (27 bp):
GCTTTGCCACGTTTACTATTAGTAGCA
Found at i:46490911 original size:35 final size:35
Alignment explanation
Indices: 46490871--46490943 Score: 146
Period size: 35 Copynumber: 2.1 Consensus size: 35
46490861 GGTATGTGAT
46490871 ATATATATTATTTATGTGAGATTGATCTGACGAGA
1 ATATATATTATTTATGTGAGATTGATCTGACGAGA
46490906 ATATATATTATTTATGTGAGATTGATCTGACGAGA
1 ATATATATTATTTATGTGAGATTGATCTGACGAGA
46490941 ATA
1 ATA
46490944 AAGAATGTGT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 38 1.00
ACGTcount: A:0.36, C:0.05, G:0.19, T:0.40
Consensus pattern (35 bp):
ATATATATTATTTATGTGAGATTGATCTGACGAGA
Found at i:46492352 original size:43 final size:43
Alignment explanation
Indices: 46492303--46492653 Score: 549
Period size: 43 Copynumber: 8.2 Consensus size: 43
46492293 GCATGAAACT
*
46492303 CGGTGATATGTATTGGGGCCTTCGTGCCTAGCAGGCTTCGTGC
1 CGGTGATATGTATTCGGGCCTTCGTGCCTAGCAGGCTTCGTGC
* *
46492346 CGGTGATGTGTATTGGGGCCTTCGTGCCTAGCAGGCTTCGTGC
1 CGGTGATATGTATTCGGGCCTTCGTGCCTAGCAGGCTTCGTGC
* **
46492389 CGATGATATGTATTTAGGCCTTCGTGCCTAGCAGGCTTCGTGC
1 CGGTGATATGTATTCGGGCCTTCGTGCCTAGCAGGCTTCGTGC
** *
46492432 CAATGATGTGTATTCGGGCCTTCGTGCCTAGCAGGCTTCGTGC
1 CGGTGATATGTATTCGGGCCTTCGTGCCTAGCAGGCTTCGTGC
* * *
46492475 CGATGATGTGTATTCGGGCCTTCGTCCCTAGCAGGCTTCGTGC
1 CGGTGATATGTATTCGGGCCTTCGTGCCTAGCAGGCTTCGTGC
46492518 CGGTGATATGTATTCGGGCCTTCGTGCCTAGCAGGCTTCGTGC
1 CGGTGATATGTATTCGGGCCTTCGTGCCTAGCAGGCTTCGTGC
46492561 CGGTGATATGTATTCGGGCCTTCGTGCCTAGCAGGCTTCGTGC
1 CGGTGATATGTATTCGGGCCTTCGTGCCTAGCAGGCTTCGTGC
* * * **
46492604 CGGTGATGTGTATTCGGGTCTTTGTGCCTAGCAGGCTTAATGC
1 CGGTGATATGTATTCGGGCCTTCGTGCCTAGCAGGCTTCGTGC
46492647 CGGTGAT
1 CGGTGAT
46492654 TCGAGCAAGG
Statistics
Matches: 289, Mismatches: 19, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
43 289 1.00
ACGTcount: A:0.13, C:0.24, G:0.32, T:0.31
Consensus pattern (43 bp):
CGGTGATATGTATTCGGGCCTTCGTGCCTAGCAGGCTTCGTGC
Found at i:46492811 original size:25 final size:25
Alignment explanation
Indices: 46492772--46492822 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
46492762 TGTGTAAAAA
* *
46492772 CGAATGAATATAGGCATTATGTGTG
1 CGAATGAATAGAGGCACTATGTGTG
* *
46492797 CGAATGATTAGAGGCACTGTGTGTG
1 CGAATGAATAGAGGCACTATGTGTG
46492822 C
1 C
46492823 AAATTCCTTT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.27, C:0.12, G:0.31, T:0.29
Consensus pattern (25 bp):
CGAATGAATAGAGGCACTATGTGTG
Found at i:46492843 original size:29 final size:29
Alignment explanation
Indices: 46492810--46492909 Score: 78
Period size: 29 Copynumber: 3.4 Consensus size: 29
46492800 ATGATTAGAG
*
46492810 GCACTGTGTGTGCAAATTCCTTTAACCGA
1 GCACTATGTGTGCAAATTCCTTTAACCGA
* ** **
46492839 GCACTATGTGTGCGAGA-T-CAGTAATTGA
1 GCACTATGTGTGC-AAATTCCTTTAACCGA
** * *
46492867 GGCACTGCGTGTACGAATTCCTTTAACCGA
1 -GCACTATGTGTGCAAATTCCTTTAACCGA
46492897 GCACTATGTGTGC
1 GCACTATGTGTGC
46492910 GAGATCGGTA
Statistics
Matches: 49, Mismatches: 18, Indels: 8
0.65 0.24 0.11
Matches are distributed among these distances:
28 7 0.14
29 34 0.69
30 8 0.16
ACGTcount: A:0.24, C:0.22, G:0.25, T:0.29
Consensus pattern (29 bp):
GCACTATGTGTGCAAATTCCTTTAACCGA
Found at i:46492886 original size:58 final size:58
Alignment explanation
Indices: 46492807--46492972 Score: 262
Period size: 58 Copynumber: 2.9 Consensus size: 58
46492797 CGAATGATTA
46492807 GAGGCACTGTGTGTGCAAATTCCTTTAACCGAGCACTATGTGTGCGAGATCAGTAATT
1 GAGGCACTGTGTGTGCAAATTCCTTTAACCGAGCACTATGTGTGCGAGATCAGTAATT
* * * *
46492865 GAGGCACTGCGTGTACGAATTCCTTTAACCGAGCACTATGTGTGCGAGATCGGTAATT
1 GAGGCACTGTGTGTGCAAATTCCTTTAACCGAGCACTATGTGTGCGAGATCAGTAATT
* * *
46492923 GAGGCACTGTGTGTGCCAGTT-CTTCAACCGAGCACTATGTGTGCGAGATC
1 GAGGCACTGTGTGTGCAAATTCCTTTAACCGAGCACTATGTGTGCGAGATC
46492973 GGTCAGTCGG
Statistics
Matches: 99, Mismatches: 9, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
57 28 0.28
58 71 0.72
ACGTcount: A:0.23, C:0.21, G:0.28, T:0.28
Consensus pattern (58 bp):
GAGGCACTGTGTGTGCAAATTCCTTTAACCGAGCACTATGTGTGCGAGATCAGTAATT
Found at i:46492929 original size:29 final size:28
Alignment explanation
Indices: 46492832--46492975 Score: 103
Period size: 29 Copynumber: 5.0 Consensus size: 28
46492822 CAAATTCCTT
*
46492832 TAACCGAGCACTATGTGTGCGAGATCAG
1 TAACCGAGCACTATGTGTGCGAGATCGG
** ** * **
46492860 TAATTGAGGCACTGCGTGTACGA-ATTCCTT
1 TAACCGA-GCACTATGTGTGCGAGA-T-CGG
46492890 TAACCGAGCACTATGTGTGCGAGATCGG
1 TAACCGAGCACTATGTGTGCGAGATCGG
** * * * *
46492918 TAATTGAGGCACTGTGTGTGCCAGTTC-T
1 TAACCGA-GCACTATGTGTGCGAGATCGG
46492946 TCAACCGAGCACTATGTGTGCGAGATCGG
1 T-AACCGAGCACTATGTGTGCGAGATCGG
46492975 T
1 T
46492976 CAGTCGGCAC
Statistics
Matches: 83, Mismatches: 26, Indels: 13
0.68 0.21 0.11
Matches are distributed among these distances:
28 29 0.35
29 47 0.57
30 7 0.08
ACGTcount: A:0.24, C:0.21, G:0.28, T:0.27
Consensus pattern (28 bp):
TAACCGAGCACTATGTGTGCGAGATCGG
Found at i:46492963 original size:28 final size:28
Alignment explanation
Indices: 46492890--46492975 Score: 84
Period size: 28 Copynumber: 3.0 Consensus size: 28
46492880 CGAATTCCTT
*
46492890 TAACCGAGCACTATGTGTGCGAGATCGG
1 TAACCGAGCACTATGTGTGCCAGATCGG
** * * *
46492918 TAATTGAGGCACTGTGTGTGCCAGTTC-T
1 TAACCGA-GCACTATGTGTGCCAGATCGG
*
46492946 TCAACCGAGCACTATGTGTGCGAGATCGG
1 T-AACCGAGCACTATGTGTGCCAGATCGG
46492975 T
1 T
46492976 CAGTCGGCAC
Statistics
Matches: 43, Mismatches: 12, Indels: 5
0.72 0.20 0.08
Matches are distributed among these distances:
28 22 0.51
29 21 0.49
ACGTcount: A:0.22, C:0.21, G:0.30, T:0.27
Consensus pattern (28 bp):
TAACCGAGCACTATGTGTGCCAGATCGG
Found at i:46492985 original size:28 final size:28
Alignment explanation
Indices: 46492897--46492993 Score: 81
Period size: 28 Copynumber: 3.4 Consensus size: 28
46492887 CTTTAACCGA
*
46492897 GCACTATGTGTGCGAGATCGGT-AATTGAG
1 GCACTATGTGTGCGAGATCGGTCAA-T-CG
* * * * *
46492926 GCACTGTGTGTGCCAGTTC-TTCAACCG
1 GCACTATGTGTGCGAGATCGGTCAATCG
*
46492953 AGCACTATGTGTGCGAGATCGGTCAGTCG
1 -GCACTATGTGTGCGAGATCGGTCAATCG
*
46492982 GCACTAAGTGTG
1 GCACTATGTGTG
46492994 TGAAATGAGA
Statistics
Matches: 52, Mismatches: 13, Indels: 7
0.72 0.18 0.10
Matches are distributed among these distances:
27 1 0.02
28 28 0.54
29 23 0.44
ACGTcount: A:0.21, C:0.21, G:0.32, T:0.27
Consensus pattern (28 bp):
GCACTATGTGTGCGAGATCGGTCAATCG
Found at i:46496977 original size:35 final size:35
Alignment explanation
Indices: 46496930--46497002 Score: 137
Period size: 35 Copynumber: 2.1 Consensus size: 35
46496920 GGTATGTGAT
46496930 ATATATAGTATTTATGTGAGATTGATCTGACGAGA
1 ATATATAGTATTTATGTGAGATTGATCTGACGAGA
*
46496965 ATATATATTATTTATGTGAGATTGATCTGACGAGA
1 ATATATAGTATTTATGTGAGATTGATCTGACGAGA
46497000 ATA
1 ATA
46497003 AAGAATGTGT
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 37 1.00
ACGTcount: A:0.36, C:0.05, G:0.21, T:0.38
Consensus pattern (35 bp):
ATATATAGTATTTATGTGAGATTGATCTGACGAGA
Found at i:46500042 original size:34 final size:34
Alignment explanation
Indices: 46499957--46500054 Score: 142
Period size: 34 Copynumber: 2.9 Consensus size: 34
46499947 GCGGATACAT
* * *
46499957 TCTGGGCCTAAGCCCATATCAGTAACGGTAGCAG
1 TCTGGGCCTTAGCCCATTTCAGTAACAGTAGCAG
46499991 TCTGGGCCTTAGCCCATTTCAGTAACAGTAGCAG
1 TCTGGGCCTTAGCCCATTTCAGTAACAGTAGCAG
* * *
46500025 TCTGGGCTTTAGCCCATTTTAGTAATAGTA
1 TCTGGGCCTTAGCCCATTTCAGTAACAGTA
46500055 ATTAGTGCAG
Statistics
Matches: 58, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
34 58 1.00
ACGTcount: A:0.24, C:0.23, G:0.23, T:0.29
Consensus pattern (34 bp):
TCTGGGCCTTAGCCCATTTCAGTAACAGTAGCAG
Found at i:46508541 original size:46 final size:46
Alignment explanation
Indices: 46508488--46508660 Score: 172
Period size: 46 Copynumber: 3.7 Consensus size: 46
46508478 TGGTTGAGCA
*
46508488 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACG
* * * * * * *
46508534 TCTGAACTCGTTTATTTGAGTCCGAGTTC-GTGA--GATGTAACTAGGCA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAA--A--CG
* *
46508581 TCCGAACTCGTTGAGTTGAGTCCGAGTTCATTTATGGATGCGAACG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACG
* * *
46508627 CCCGAGCTCGTTGAGTTGAGTCTGAGTTCACTTA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTA
46508661 GGGGCAGGTT
Statistics
Matches: 100, Mismatches: 20, Indels: 14
0.75 0.15 0.10
Matches are distributed among these distances:
43 6 0.06
45 3 0.03
46 57 0.57
47 26 0.26
48 3 0.03
50 5 0.05
ACGTcount: A:0.22, C:0.20, G:0.27, T:0.32
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACG
Found at i:46508646 original size:93 final size:93
Alignment explanation
Indices: 46508485--46508655 Score: 261
Period size: 93 Copynumber: 1.8 Consensus size: 93
46508475 GGATGGTTGA
* * * * *
46508485 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATGTCTGAACTCGTTTATT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACGCCCGAACTCGTTGAGT
46508550 TGAGTCCGAGTTCGTGAGATGTAACTAG
66 TGAGTCCGAGTTCGTGAGATGTAACTAG
* * *
46508578 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCATTTATGGATGCGAACGCCCGAGCTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACGCCCGAACTCGTTGAGT
*
46508643 TGAGTCTGAGTTC
66 TGAGTCCGAGTTC
46508656 ACTTAGGGGC
Statistics
Matches: 69, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
93 69 1.00
ACGTcount: A:0.22, C:0.20, G:0.27, T:0.31
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACGCCCGAACTCGTTGAGT
TGAGTCCGAGTTCGTGAGATGTAACTAG
Found at i:46508922 original size:19 final size:20
Alignment explanation
Indices: 46508885--46508922 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
46508875 ATAAGGTGGT
46508885 AAGATGATGAATGATGTTTA
1 AAGATGATGAATGATGTTTA
46508905 AAGATG-TGATAT-ATGTTT
1 AAGATGATGA-ATGATGTTT
46508923 TGGTGGTACC
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.37, C:0.00, G:0.24, T:0.39
Consensus pattern (20 bp):
AAGATGATGAATGATGTTTA
Found at i:46515263 original size:47 final size:47
Alignment explanation
Indices: 46515211--46515404 Score: 271
Period size: 47 Copynumber: 4.1 Consensus size: 47
46515201 TTAGGATTTT
** * *
46515211 ATGTGATGAATGTGAATGTACATATATGAGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
*
46515258 ATGTGATGAATGTGAACATGCATATATGTGATAAGTCCGAATGGCCA
1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
* *
46515305 ATGTGATGAATGTGAGCATGCATATGTGTGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
* * * * * *
46515352 ATGTGGTAAATATGAACATGCATATATGTGGTAAAGCCGAATGGCTA
1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
46515399 ATGTGA
1 ATGTGA
46515405 AATATGTATG
Statistics
Matches: 130, Mismatches: 17, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
47 130 1.00
ACGTcount: A:0.34, C:0.11, G:0.28, T:0.27
Consensus pattern (47 bp):
ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
Found at i:46515532 original size:98 final size:96
Alignment explanation
Indices: 46515375--46515558 Score: 289
Period size: 98 Copynumber: 1.9 Consensus size: 96
46515365 GAACATGCAT
*
46515375 ATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAGAAATGTATATGTGGTAAAGCCGA
1 ATATGTGGTAAAGCCGAATGGCTAATGTGAAATATATATGAGAAATGTATATGTGGTAAAGCCGA
46515440 ATGGCTAATGTGAAATATGTATGAGATATGC
66 ATGGCTAATGTGAAATATGTATGAGATATGC
** *
46515471 ATATGTGGTAAAGTTGAATGG-TCAATGTGAAATATATATATGAGATATGTATATGTGGTAAAGC
1 ATATGTGGTAAAGCCGAATGGCT-AATGTG-AA-ATATATATGAGAAATGTATATGTGGTAAAGC
*
46515535 CGAATGGCTAGTGTGAAATATGTA
63 CGAATGGCTAATGTGAAATATGTA
46515559 GGCGATGTGC
Statistics
Matches: 80, Mismatches: 5, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
95 1 0.01
96 25 0.31
97 2 0.03
98 52 0.65
ACGTcount: A:0.36, C:0.06, G:0.27, T:0.31
Consensus pattern (96 bp):
ATATGTGGTAAAGCCGAATGGCTAATGTGAAATATATATGAGAAATGTATATGTGGTAAAGCCGA
ATGGCTAATGTGAAATATGTATGAGATATGC
Found at i:46515574 original size:50 final size:48
Alignment explanation
Indices: 46515374--46515558 Score: 282
Period size: 48 Copynumber: 3.8 Consensus size: 48
46515364 TGAACATGCA
*
46515374 TATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAGAAATG
1 TATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAGATATG
46515422 TATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAGATATG
1 TATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAGATATG
* ** *
46515470 CATATGTGGTAAAGTTGAATGG-TCAATGTGAAATATATATATGAGATATG
1 TATATGTGGTAAAGCCGAATGGCT-AATGTG-AA-ATATGTATGAGATATG
*
46515520 TATATGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTA
1 TATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTA
46515559 GGCGATGTGC
Statistics
Matches: 123, Mismatches: 10, Indels: 8
0.87 0.07 0.06
Matches are distributed among these distances:
47 1 0.01
48 78 0.63
49 4 0.03
50 39 0.32
51 1 0.01
ACGTcount: A:0.36, C:0.06, G:0.26, T:0.31
Consensus pattern (48 bp):
TATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAGATATG
Found at i:46515805 original size:37 final size:37
Alignment explanation
Indices: 46515704--46515812 Score: 164
Period size: 37 Copynumber: 2.9 Consensus size: 37
46515694 GGAAATATAT
* * *
46515704 TCCGGGTAAGACCCGATGACTACCTGAGGAGATTATG
1 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTTTG
46515741 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTTTG
1 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTTTG
* **
46515778 TCCGGGTAAGACCCGATAACTTTGTGTGGAGATTT
1 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTT
46515813 CGTCTGAGCT
Statistics
Matches: 66, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
37 66 1.00
ACGTcount: A:0.24, C:0.19, G:0.30, T:0.27
Consensus pattern (37 bp):
TCCGGGTAAGACCCGATGACTACGTGTGGAGATTTTG
Found at i:46520230 original size:45 final size:46
Alignment explanation
Indices: 46520177--46520346 Score: 172
Period size: 46 Copynumber: 3.7 Consensus size: 46
46520167 TGGTTGAGCA
*
46520177 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACG
* * * *
46520223 TCC-AACTCGTTGAGTTGAGT-C-AGTTC-GTGA--GATGTAACTAGGCA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAA--A--CG
* *
46520267 TCCGAACTCGTTGAGTTGAGTCCGAGTTCATTTATGGATGCGAACG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACG
* * *
46520313 CCCGAGCTCATTGAGTTGAGTCCGAGTTCACTTA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTA
46520347 GGGGCGGGTT
Statistics
Matches: 100, Mismatches: 14, Indels: 20
0.75 0.10 0.15
Matches are distributed among these distances:
40 6 0.06
42 3 0.03
43 5 0.05
44 4 0.04
45 34 0.34
46 35 0.35
47 5 0.05
48 3 0.03
50 5 0.05
ACGTcount: A:0.23, C:0.21, G:0.26, T:0.30
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACG
Found at i:46520608 original size:19 final size:20
Alignment explanation
Indices: 46520571--46520608 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
46520561 ATAAGGTGGT
46520571 AAGATGATGAATGATGTTTA
1 AAGATGATGAATGATGTTTA
46520591 AAGATG-TGATAT-ATGTTT
1 AAGATGATGA-ATGATGTTT
46520609 TGGTGGTACC
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.37, C:0.00, G:0.24, T:0.39
Consensus pattern (20 bp):
AAGATGATGAATGATGTTTA
Found at i:46524240 original size:27 final size:27
Alignment explanation
Indices: 46524194--46524313 Score: 138
Period size: 27 Copynumber: 4.5 Consensus size: 27
46524184 GAACAAATCT
* * * *
46524194 GTCATTTTACCTTACCGGGGTATTACA
1 GTCATTTTACCCTACAGGGGTATTTCG
*
46524221 ATCATTTTACCCTACAGGGGTATTTCG
1 GTCATTTTACCCTACAGGGGTATTTCG
* *
46524248 GTCATTCTACCCTA-TGAGGGTATTTCG
1 GTCATTTTACCCTACAG-GGGTATTTCG
*
46524275 GTCA-TTTACCCTATA-GGGTATTTCG
1 GTCATTTTACCCTACAGGGGTATTTCG
46524300 GTCATTTTACCCTA
1 GTCATTTTACCCTA
46524314 TGAGGTTATT
Statistics
Matches: 80, Mismatches: 10, Indels: 7
0.82 0.10 0.07
Matches are distributed among these distances:
25 14 0.17
26 18 0.22
27 48 0.60
ACGTcount: A:0.21, C:0.23, G:0.18, T:0.38
Consensus pattern (27 bp):
GTCATTTTACCCTACAGGGGTATTTCG
Found at i:46524311 original size:52 final size:53
Alignment explanation
Indices: 46524226--46524333 Score: 164
Period size: 52 Copynumber: 2.1 Consensus size: 53
46524216 TTACAATCAT
46524226 TTTACCCTACAGGGGTATTTCGGTCATTCTACCCTATGAGGGTATTTCGGTCA
1 TTTACCCTACAGGGGTATTTCGGTCATTCTACCCTATGAGGGTATTTCGGTCA
* * * * *
46524279 TTTACCCTATA-GGGTATTTCGGTCATTTTACCCTATGAGGTTATTTTGGTTA
1 TTTACCCTACAGGGGTATTTCGGTCATTCTACCCTATGAGGGTATTTCGGTCA
46524331 TTT
1 TTT
46524334 TATCACATAA
Statistics
Matches: 50, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
52 40 0.80
53 10 0.20
ACGTcount: A:0.19, C:0.19, G:0.20, T:0.43
Consensus pattern (53 bp):
TTTACCCTACAGGGGTATTTCGGTCATTCTACCCTATGAGGGTATTTCGGTCA
Found at i:46524333 original size:27 final size:27
Alignment explanation
Indices: 46524222--46524335 Score: 153
Period size: 27 Copynumber: 4.3 Consensus size: 27
46524212 GGTATTACAA
*
46524222 TCATTTTACCCTA-CAGGGGTATTTCGG
1 TCATTTTACCCTATGA-GGGTATTTCGG
*
46524249 TCATTCTACCCTATGAGGGTATTTCGG
1 TCATTTTACCCTATGAGGGTATTTCGG
46524276 TCA-TTTACCCTAT-AGGGTATTTCGG
1 TCATTTTACCCTATGAGGGTATTTCGG
* *
46524301 TCATTTTACCCTATGAGGTTATTTTGG
1 TCATTTTACCCTATGAGGGTATTTCGG
*
46524328 TTATTTTA
1 TCATTTTA
46524336 TCACATAAGG
Statistics
Matches: 78, Mismatches: 6, Indels: 6
0.87 0.07 0.07
Matches are distributed among these distances:
25 15 0.19
26 19 0.24
27 43 0.55
28 1 0.01
ACGTcount: A:0.19, C:0.18, G:0.19, T:0.43
Consensus pattern (27 bp):
TCATTTTACCCTATGAGGGTATTTCGG
Found at i:46524455 original size:27 final size:27
Alignment explanation
Indices: 46524330--46524455 Score: 171
Period size: 27 Copynumber: 4.7 Consensus size: 27
46524320 TATTTTGGTT
* *
46524330 ATTTTATCACATAAGGGCAAAATCGTC
1 ATTTTATCACATGAGGGTAAAATCGTC
*
46524357 ATTTTATCACATGAGGGAAAAATCGTC
1 ATTTTATCACATGAGGGTAAAATCGTC
* * * * *
46524384 ATTTTATAACCTAAGGCTAAAATCGAC
1 ATTTTATCACATGAGGGTAAAATCGTC
*
46524411 ATTTTATCACATGAGGGTAAAATCGCC
1 ATTTTATCACATGAGGGTAAAATCGTC
46524438 ATTTTATCACATGAGGGT
1 ATTTTATCACATGAGGGT
46524456 TCAAGTATGC
Statistics
Matches: 86, Mismatches: 13, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
27 86 1.00
ACGTcount: A:0.36, C:0.17, G:0.17, T:0.31
Consensus pattern (27 bp):
ATTTTATCACATGAGGGTAAAATCGTC
Found at i:46537841 original size:37 final size:39
Alignment explanation
Indices: 46537788--46537884 Score: 101
Period size: 43 Copynumber: 2.4 Consensus size: 39
46537778 TCCCAAACAG
*
46537788 GGTCTTACAC-TAAATCATATAA-C-AATGTCCTAGACAT
1 GGTCTTACACGT-AATCATACAAGCAAATGTCCTAGACAT
*
46537825 GGTCTTACACGTAATCACAATACAATGCAAATTTCCTAGACAT
1 GGTCTTACACGTAAT--C-ATACAA-GCAAATGTCCTAGACAT
*
46537868 GGTCTTACATGTAATCA
1 GGTCTTACACGTAATCA
46537885 CTTCTCGATA
Statistics
Matches: 50, Mismatches: 3, Indels: 11
0.78 0.05 0.17
Matches are distributed among these distances:
37 13 0.26
38 1 0.02
39 1 0.02
40 6 0.12
41 1 0.02
42 1 0.02
43 27 0.54
ACGTcount: A:0.36, C:0.22, G:0.12, T:0.30
Consensus pattern (39 bp):
GGTCTTACACGTAATCATACAAGCAAATGTCCTAGACAT
Found at i:46550341 original size:52 final size:52
Alignment explanation
Indices: 46550212--46550343 Score: 180
Period size: 50 Copynumber: 2.6 Consensus size: 52
46550202 ATGTGTTATG
* *
46550212 CATTTAATAAAGTCATGCATTATGTAACT-CTCATGTTAGTTAAGTTTGCAT
1 CATTAAATTAAGTCATGCATTATGTAACTCCTCATGTTAGTTAAGTTTGCAT
* *
46550263 CA-TAAATTATGACATGCATTATGTAACTCCT-ATGTTAGTTAAAGTTTGCAT
1 CATTAAATTAAGTCATGCATTATGTAACTCCTCATGTTAGTT-AAGTTTGCAT
* *
46550314 CATTAAATTAAGTCACGCATTAAGTAACTC
1 CATTAAATTAAGTCATGCATTATGTAACTC
46550344 ATTTGTTCAT
Statistics
Matches: 70, Mismatches: 8, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
50 31 0.44
51 16 0.23
52 23 0.33
ACGTcount: A:0.34, C:0.15, G:0.13, T:0.38
Consensus pattern (52 bp):
CATTAAATTAAGTCATGCATTATGTAACTCCTCATGTTAGTTAAGTTTGCAT
Found at i:46550360 original size:51 final size:52
Alignment explanation
Indices: 46550228--46550350 Score: 153
Period size: 52 Copynumber: 2.4 Consensus size: 52
46550218 ATAAAGTCAT
* * *
46550228 GCATTATGTAACTC-TCATGTTAGTT-AAGTTTGCATCA-TAAATTATGACAT
1 GCATTAAGTAACTCAT-ATGTTAGTTAAAGTTTGCATCATTAAATTAAGACAC
* * *
46550278 GCATTATGTAACTCCTATGTTAGTTAAAGTTTGCATCATTAAATTAAGTCAC
1 GCATTAAGTAACTCATATGTTAGTTAAAGTTTGCATCATTAAATTAAGACAC
*
46550330 GCATTAAGTAACTCATTTGTT
1 GCATTAAGTAACTCATATGTT
46550351 CATTTAGTTT
Statistics
Matches: 64, Mismatches: 6, Indels: 4
0.86 0.08 0.05
Matches are distributed among these distances:
50 23 0.36
51 13 0.20
52 28 0.44
ACGTcount: A:0.32, C:0.15, G:0.14, T:0.40
Consensus pattern (52 bp):
GCATTAAGTAACTCATATGTTAGTTAAAGTTTGCATCATTAAATTAAGACAC
Found at i:46551807 original size:29 final size:29
Alignment explanation
Indices: 46551772--46551829 Score: 107
Period size: 29 Copynumber: 2.0 Consensus size: 29
46551762 ATCCTTAAAT
46551772 ATTGAGTGTGACGATCATAAGCAAATGAA
1 ATTGAGTGTGACGATCATAAGCAAATGAA
*
46551801 ATTGAGTGTGACGATCTTAAGCAAATGAA
1 ATTGAGTGTGACGATCATAAGCAAATGAA
46551830 CTCACACCTA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.40, C:0.10, G:0.24, T:0.26
Consensus pattern (29 bp):
ATTGAGTGTGACGATCATAAGCAAATGAA
Found at i:46554435 original size:5 final size:5
Alignment explanation
Indices: 46554425--46554449 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
46554415 ACTAATTATG
46554425 AAAAT AAAAT AAAAT AAAAT AAAAT
1 AAAAT AAAAT AAAAT AAAAT AAAAT
46554450 TACAAAAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (5 bp):
AAAAT
Found at i:46557765 original size:47 final size:47
Alignment explanation
Indices: 46557712--46558382 Score: 1090
Period size: 47 Copynumber: 14.3 Consensus size: 47
46557702 ACAAGATATG
*
46557712 TATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTA
1 TATATGTGATAAGGCCTAATGGCCAATGTGATGAATGTGAAAGTGTA
* *
46557759 TATATGTGACAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTA
1 TATATGTGATAAGGCCTAATGGCCAATGTGATGAATGTGAAAGTGTA
* *
46557806 TATATGTGAGAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTA
1 TATATGTGATAAGGCCTAATGGCCAATGTGATGAATGTGAAAGTGTA
46557853 TATATGTGATAAGGCCTAATGGCCAATGTGATGAATGTGAAAGTGTA
1 TATATGTGATAAGGCCTAATGGCCAATGTGATGAATGTGAAAGTGTA
*
46557900 TATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTA
1 TATATGTGATAAGGCCTAATGGCCAATGTGATGAATGTGAAAGTGTA
*
46557947 TATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTA
1 TATATGTGATAAGGCCTAATGGCCAATGTGATGAATGTGAAAGTGTA
* * *
46557994 TATATGTGACAAGGCCTAATGGCCGATGTGATTAATGTGAAAGTGTA
1 TATATGTGATAAGGCCTAATGGCCAATGTGATGAATGTGAAAGTGTA
*
46558041 TATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTA
1 TATATGTGATAAGGCCTAATGGCCAATGTGATGAATGTGAAAGTGTA
* *
46558088 TATATGTGACAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTA
1 TATATGTGATAAGGCCTAATGGCCAATGTGATGAATGTGAAAGTGTA
**
46558135 TATATGTGATAAGGCAGAATGGCCAATGTGATGAATGTGAAAGTGTA
1 TATATGTGATAAGGCCTAATGGCCAATGTGATGAATGTGAAAGTGTA
* *
46558182 TATATGTGACAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTA
1 TATATGTGATAAGGCCTAATGGCCAATGTGATGAATGTGAAAGTGTA
* * *
46558229 TATTTGTGATAAGGCCGAATGACCAATGTGATGAATGTGAAAGTGTA
1 TATATGTGATAAGGCCTAATGGCCAATGTGATGAATGTGAAAGTGTA
* * * * *
46558276 TATATGAGATAAGACCTAATGGCCGATGTGATGGATGTGAATGTGTA
1 TATATGTGATAAGGCCTAATGGCCAATGTGATGAATGTGAAAGTGTA
* *
46558323 TATATGTGATAAGGCCGAATGGCCAATGTGATGGATGTGAAAGTGTA
1 TATATGTGATAAGGCCTAATGGCCAATGTGATGAATGTGAAAGTGTA
*
46558370 TAAATGTGATAAG
1 TATATGTGATAAG
46558383 TCCCGAAGGG
Statistics
Matches: 579, Mismatches: 45, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
47 579 1.00
ACGTcount: A:0.33, C:0.09, G:0.30, T:0.28
Consensus pattern (47 bp):
TATATGTGATAAGGCCTAATGGCCAATGTGATGAATGTGAAAGTGTA
Found at i:46560381 original size:38 final size:38
Alignment explanation
Indices: 46560330--46560411 Score: 119
Period size: 38 Copynumber: 2.2 Consensus size: 38
46560320 AATCCGGGCT
* * *
46560330 TAAAGACCCGATGACTATAAGTAGAGATTGTGTCTGGG
1 TAAAGACCCGATGACTATAAGTAGAGATTATGCCCGGG
* *
46560368 TAAAGACCCGATGACTATATGTGGAGATTATGCCCGGG
1 TAAAGACCCGATGACTATAAGTAGAGATTATGCCCGGG
46560406 TAAAGA
1 TAAAGA
46560412 TCTGATGGCT
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
38 39 1.00
ACGTcount: A:0.33, C:0.15, G:0.28, T:0.24
Consensus pattern (38 bp):
TAAAGACCCGATGACTATAAGTAGAGATTATGCCCGGG
Found at i:46560555 original size:40 final size:40
Alignment explanation
Indices: 46560500--46560690 Score: 337
Period size: 40 Copynumber: 4.8 Consensus size: 40
46560490 CTTGACGATG
*
46560500 ATCCGGGTTAAGTCCCGAAGAGCATTCGTGCTGGTGTTAC
1 ATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTGGTGTTAC
46560540 ATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTGGTGTTAC
1 ATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTGGTGTTAC
46560580 ATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTGGTGTTAC
1 ATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTGGTGTTAC
* *
46560620 ATCCGGGCTAAGTCCCAAAGAGCATTTGTGCTGGTGTTAC
1 ATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTGGTGTTAC
* *
46560660 ATCCGGGCTAAGTCCTGAAGGGCATTCGTGC
1 ATCCGGGCTAAGTCCCGAAGAGCATTCGTGC
46560691 CGATGATGTG
Statistics
Matches: 144, Mismatches: 7, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 144 1.00
ACGTcount: A:0.20, C:0.24, G:0.30, T:0.26
Consensus pattern (40 bp):
ATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTGGTGTTAC
Found at i:46564056 original size:47 final size:47
Alignment explanation
Indices: 46564003--46564813 Score: 1336
Period size: 47 Copynumber: 17.3 Consensus size: 47
46563993 ACAAGATATG
*
46564003 TATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTA
1 TATATGTGATAAGGCCTAATGGCCAATGTGATGAATGTGAAAGTGTA
* *
46564050 TATATGTGACAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTA
1 TATATGTGATAAGGCCTAATGGCCAATGTGATGAATGTGAAAGTGTA
* *
46564097 TATATGTGAGAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTA
1 TATATGTGATAAGGCCTAATGGCCAATGTGATGAATGTGAAAGTGTA
46564144 TATATGTGATAAGGCCTAATGGCCAATGTGATGAATGTGAAAGTGTA
1 TATATGTGATAAGGCCTAATGGCCAATGTGATGAATGTGAAAGTGTA
* * *
46564191 TATATGTGATAAGGCCGAATGACCAATGTGATGAAGGTGAAAGTGTA
1 TATATGTGATAAGGCCTAATGGCCAATGTGATGAATGTGAAAGTGTA
* * *
46564238 TATATGTGACAAGGCCTAATGGCCGATGTCATGAATGTGAAAGTGTA
1 TATATGTGATAAGGCCTAATGGCCAATGTGATGAATGTGAAAGTGTA
46564285 TATATGTGATAAGGCCTAATGGCCAATGTGATGAATGTGAAAGTGTA
1 TATATGTGATAAGGCCTAATGGCCAATGTGATGAATGTGAAAGTGTA
46564332 TATATGTGATAAGGCCTAATGGCCAATGTGATGAATGTGAAAGTGTA
1 TATATGTGATAAGGCCTAATGGCCAATGTGATGAATGTGAAAGTGTA
* *
46564379 TATATGTGATAAGGCCGAATGGCCAATATGATGAATGTGAAAGTGTA
1 TATATGTGATAAGGCCTAATGGCCAATGTGATGAATGTGAAAGTGTA
* *
46564426 TATATGTGACAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTA
1 TATATGTGATAAGGCCTAATGGCCAATGTGATGAATGTGAAAGTGTA
*
46564473 TATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTA
1 TATATGTGATAAGGCCTAATGGCCAATGTGATGAATGTGAAAGTGTA
* *
46564520 TATATGTGATAAGGCCTAATGACCAATGTGATGAATGTGAGAGTGTA
1 TATATGTGATAAGGCCTAATGGCCAATGTGATGAATGTGAAAGTGTA
*
46564567 TATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTA
1 TATATGTGATAAGGCCTAATGGCCAATGTGATGAATGTGAAAGTGTA
* * *
46564614 TATATGTGACACGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTA
1 TATATGTGATAAGGCCTAATGGCCAATGTGATGAATGTGAAAGTGTA
*
46564661 TATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTA
1 TATATGTGATAAGGCCTAATGGCCAATGTGATGAATGTGAAAGTGTA
* * * * *
46564708 TATATGAGAT-AGACCTAATGGCCGATGTGATGGATGTGAAGGTGTA
1 TATATGTGATAAGGCCTAATGGCCAATGTGATGAATGTGAAAGTGTA
* *
46564754 TATATGTGATAAGGCCGAATGGCCAATGTGATGGATGTGAAAGTGTA
1 TATATGTGATAAGGCCTAATGGCCAATGTGATGAATGTGAAAGTGTA
*
46564801 TAAATGTGATAAG
1 TATATGTGATAAG
46564814 TCCCGAAGGG
Statistics
Matches: 710, Mismatches: 53, Indels: 2
0.93 0.07 0.00
Matches are distributed among these distances:
46 40 0.06
47 670 0.94
ACGTcount: A:0.33, C:0.09, G:0.29, T:0.28
Consensus pattern (47 bp):
TATATGTGATAAGGCCTAATGGCCAATGTGATGAATGTGAAAGTGTA
Found at i:46564313 original size:22 final size:22
Alignment explanation
Indices: 46564288--46564363 Score: 62
Period size: 22 Copynumber: 3.3 Consensus size: 22
46564278 AAGTGTATAT
46564288 ATGTGATAAGGCCTAATGGCCA
1 ATGTGATAAGGCCTAATGGCCA
* *** ***
46564310 ATGTGATGAATGTGAAAGTGTATA
1 ATGTGAT-AAGGCCTAA-TGGCCA
46564334 TATGTGATAAGGCCTAATGGCCA
1 -ATGTGATAAGGCCTAATGGCCA
46564357 ATGTGAT
1 ATGTGAT
46564364 GAATGTGAAA
Statistics
Matches: 37, Mismatches: 14, Indels: 6
0.65 0.25 0.11
Matches are distributed among these distances:
22 14 0.38
23 8 0.22
24 8 0.22
25 7 0.19
ACGTcount: A:0.33, C:0.11, G:0.28, T:0.29
Consensus pattern (22 bp):
ATGTGATAAGGCCTAATGGCCA
Found at i:46567945 original size:40 final size:40
Alignment explanation
Indices: 46567886--46568029 Score: 193
Period size: 40 Copynumber: 3.6 Consensus size: 40
46567876 CATTTGAATG
* *
46567886 ATATCCGGGCTAAGTCCCGAAGGCATTTATGCTAG-TGATT
1 ATATCCGGGCTAAGACCCGAAGGCATTTATGCGAGTTGA-T
* *
46567926 TTATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGAT
1 ATATCCGGGCTAAGACCCGAAGGCATTTATGCGAGTTGAT
* *
46567966 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGCT
1 ATATCCGGGCTAAGACCCGAAGGCATTTATGCGAGTTGAT
* *
46568006 ATACCCGGGTTAAGACCC-AAGGCA
1 ATATCCGGGCTAAGACCCGAAGGCA
46568030 ATTGTGCTTG
Statistics
Matches: 95, Mismatches: 8, Indels: 3
0.90 0.08 0.03
Matches are distributed among these distances:
39 6 0.06
40 86 0.91
41 3 0.03
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.25
Consensus pattern (40 bp):
ATATCCGGGCTAAGACCCGAAGGCATTTATGCGAGTTGAT
Found at i:46570327 original size:18 final size:19
Alignment explanation
Indices: 46570286--46570338 Score: 63
Period size: 19 Copynumber: 2.8 Consensus size: 19
46570276 ACTTTCTAGT
*
46570286 AATTTTTATAATATTTAAC
1 AATTTTTATAATTTTTAAC
* *
46570305 AATTTTTATACTTTTTATC
1 AATTTTTATAATTTTTAAC
*
46570324 -ATTTTAATAATTTTT
1 AATTTTTATAATTTTT
46570339 CTATATATAA
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
18 13 0.45
19 16 0.55
ACGTcount: A:0.34, C:0.06, G:0.00, T:0.60
Consensus pattern (19 bp):
AATTTTTATAATTTTTAAC
Found at i:46570328 original size:9 final size:9
Alignment explanation
Indices: 46570269--46570338 Score: 59
Period size: 9 Copynumber: 7.4 Consensus size: 9
46570259 AAACTTTTAA
46570269 TTTTATAACT
1 TTTTATAA-T
*
46570279 TTCTAGTAAT
1 TTTTA-TAAT
46570289 TTTTATAAT
1 TTTTATAAT
* *
46570298 ATTTAACAAT
1 -TTTTATAAT
*
46570308 TTTTATACT
1 TTTTATAAT
*
46570317 TTTTATCAT
1 TTTTATAAT
*
46570326 TTTAATAAT
1 TTTTATAAT
46570335 TTTT
1 TTTT
46570339 CTATATATAA
Statistics
Matches: 46, Mismatches: 12, Indels: 5
0.73 0.19 0.08
Matches are distributed among these distances:
9 27 0.59
10 16 0.35
11 3 0.07
ACGTcount: A:0.31, C:0.07, G:0.01, T:0.60
Consensus pattern (9 bp):
TTTTATAAT
Found at i:46572008 original size:4 final size:4
Alignment explanation
Indices: 46571999--46572030 Score: 55
Period size: 4 Copynumber: 8.0 Consensus size: 4
46571989 GCTAAATATG
*
46571999 AAAT AAAT AAGT AAAT AAAT AAAT AAAT AAAT
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT
46572031 GCAAGCCGTT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
4 26 1.00
ACGTcount: A:0.72, C:0.00, G:0.03, T:0.25
Consensus pattern (4 bp):
AAAT
Found at i:46574162 original size:6 final size:6
Alignment explanation
Indices: 46574153--46574201 Score: 73
Period size: 6 Copynumber: 8.3 Consensus size: 6
46574143 CACCGATCTT
* *
46574153 CCCTTT CCCTTT CCCTT- CCCTTC CCCTTC CCCTTC CCCTTC CCCTTC
1 CCCTTC CCCTTC CCCTTC CCCTTC CCCTTC CCCTTC CCCTTC CCCTTC
46574200 CC
1 CC
46574202 TTGACACCTG
Statistics
Matches: 42, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
5 5 0.12
6 37 0.88
ACGTcount: A:0.00, C:0.63, G:0.00, T:0.37
Consensus pattern (6 bp):
CCCTTC
Found at i:46574172 original size:17 final size:17
Alignment explanation
Indices: 46574150--46574203 Score: 72
Period size: 17 Copynumber: 3.2 Consensus size: 17
46574140 AGACACCGAT
46574150 CTTCCCTTTCCCTTTCC
1 CTTCCCTTTCCCTTTCC
* *
46574167 CTTCCCTTCCCCTTCCC
1 CTTCCCTTTCCCTTTCC
* *
46574184 CTTCCCCTTCCCCTTCC
1 CTTCCCTTTCCCTTTCC
46574201 CTT
1 CTT
46574204 GACACCTGAT
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
17 31 1.00
ACGTcount: A:0.00, C:0.59, G:0.00, T:0.41
Consensus pattern (17 bp):
CTTCCCTTTCCCTTTCC
Found at i:46577224 original size:22 final size:25
Alignment explanation
Indices: 46577174--46577231 Score: 63
Period size: 22 Copynumber: 2.5 Consensus size: 25
46577164 TTGTAATGTT
46577174 TTTATAT-TTTAATAATTGAGTATTA
1 TTTATATATTTAAT-ATTGAGTATTA
46577199 -TTATATATTTAAT-TTGA-T-TTA
1 TTTATATATTTAATATTGAGTATTA
*
46577220 TTTATTTATTTA
1 TTTATATATTTA
46577232 TAAATAAATC
Statistics
Matches: 30, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
21 3 0.10
22 11 0.37
23 4 0.13
24 6 0.20
25 6 0.20
ACGTcount: A:0.33, C:0.00, G:0.05, T:0.62
Consensus pattern (25 bp):
TTTATATATTTAATATTGAGTATTA
Found at i:46577404 original size:14 final size:15
Alignment explanation
Indices: 46577382--46577458 Score: 52
Period size: 14 Copynumber: 5.0 Consensus size: 15
46577372 CAATCAAACA
46577382 CCAGAAAAT-ATTTT
1 CCAGAAAATCATTTT
*
46577396 CCAGTAAATCATTTT
1 CCAGAAAATCATTTT
*
46577411 ACAGAAAAGTAAAACATTTT
1 CCAGAAAA-T----CATTTT
46577431 CCA-AAAATCATTTT
1 CCAGAAAATCATTTT
* *
46577445 AC-GAAAAACATTTT
1 CCAGAAAATCATTTT
46577459 ACTGGCAATC
Statistics
Matches: 50, Mismatches: 6, Indels: 14
0.71 0.09 0.20
Matches are distributed among these distances:
14 25 0.50
15 11 0.22
16 1 0.02
18 1 0.02
19 4 0.08
20 8 0.16
ACGTcount: A:0.45, C:0.16, G:0.06, T:0.32
Consensus pattern (15 bp):
CCAGAAAATCATTTT
Found at i:46577442 original size:34 final size:34
Alignment explanation
Indices: 46577386--46577451 Score: 98
Period size: 34 Copynumber: 1.9 Consensus size: 34
46577376 CAAACACCAG
* *
46577386 AAAATATTTTCCAGTAAATCATTTTACAGAAAAGT
1 AAAACATTTTCCAGAAAATCATTTTAC-GAAAAGT
46577421 AAAACATTTTCCA-AAAATCATTTTACGAAAA
1 AAAACATTTTCCAGAAAATCATTTTACGAAAA
46577452 ACATTTTACT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
33 5 0.17
34 12 0.41
35 12 0.41
ACGTcount: A:0.48, C:0.14, G:0.06, T:0.32
Consensus pattern (34 bp):
AAAACATTTTCCAGAAAATCATTTTACGAAAAGT
Found at i:46577459 original size:14 final size:14
Alignment explanation
Indices: 46577421--46577460 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
46577411 ACAGAAAAGT
46577421 AAAACATTTT-CCA
1 AAAACATTTTACCA
*
46577434 AAAATCATTTTACGA
1 AAAA-CATTTTACCA
46577449 AAAACATTTTAC
1 AAAACATTTTAC
46577461 TGGCAATCAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
13 4 0.17
14 14 0.58
15 6 0.25
ACGTcount: A:0.47, C:0.17, G:0.03, T:0.33
Consensus pattern (14 bp):
AAAACATTTTACCA
Found at i:46581897 original size:34 final size:34
Alignment explanation
Indices: 46581832--46581897 Score: 114
Period size: 34 Copynumber: 1.9 Consensus size: 34
46581822 AAAAATCGTA
* *
46581832 CCTAATTGAGTCAAAATAGCATGGCCGAAAGAAC
1 CCTAATTGAGTCAAAATAGCATGGACAAAAGAAC
46581866 CCTAATTGAGTCAAAATAGCATGGACAAAAGA
1 CCTAATTGAGTCAAAATAGCATGGACAAAAGA
46581898 TGATAGAAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 30 1.00
ACGTcount: A:0.44, C:0.18, G:0.20, T:0.18
Consensus pattern (34 bp):
CCTAATTGAGTCAAAATAGCATGGACAAAAGAAC
Found at i:46585262 original size:42 final size:42
Alignment explanation
Indices: 46585146--46585307 Score: 175
Period size: 42 Copynumber: 3.8 Consensus size: 42
46585136 CATACAAATT
* * * * * *
46585146 CCATATCCCAAATATGGTCTTCCATGTATTCTCATATCGATG
1 CCATATCCCAGACATGGTCTTACACGTAGTCTCATATCAATG
* *
46585188 CCA-ATGGCCC-GGCTATGGTCTTACACGAAGTCTCATATCAATG
1 CCATAT--CCCAGAC-ATGGTCTTACACGTAGTCTCATATCAATG
* **
46585231 CCATATCCTAGACATGGTCTTACACGTAGTCTCATATTGATG
1 CCATATCCCAGACATGGTCTTACACGTAGTCTCATATCAATG
*
46585273 CCATATCCCAGATATGGTCTTACACGTAGTCTCAT
1 CCATATCCCAGACATGGTCTTACACGTAGTCTCAT
46585308 TAACCCTAAT
Statistics
Matches: 100, Mismatches: 15, Indels: 10
0.80 0.12 0.08
Matches are distributed among these distances:
41 2 0.02
42 64 0.64
43 32 0.32
44 2 0.02
ACGTcount: A:0.26, C:0.27, G:0.16, T:0.31
Consensus pattern (42 bp):
CCATATCCCAGACATGGTCTTACACGTAGTCTCATATCAATG
Found at i:46586709 original size:65 final size:65
Alignment explanation
Indices: 46586617--46586764 Score: 161
Period size: 65 Copynumber: 2.3 Consensus size: 65
46586607 CGAGCCATAT
* * ** * *
46586617 CAGGACGCTCACAAAAACTTGTGTTTGTGTCTACAGCATATACAGGATCACAACCGATCATAAAA
1 CAGGACGCTCACAAAGAGTTGCATTTGTGTCTACAACATATACAGGATCACAACCGATAATAAAA
* * * * ** *
46586682 CAGGACACTCACAAAGAGTTGCATTTGTGTTTGCAATATATGTAGGATCACAACCGATAATATAA
1 CAGGACGCTCACAAAGAGTTGCATTTGTGTCTACAACATATACAGGATCACAACCGATAATAAAA
* *
46586747 TAAGACGCTCACAAAGAG
1 CAGGACGCTCACAAAGAG
46586765 CTACGATAGT
Statistics
Matches: 67, Mismatches: 16, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
65 67 1.00
ACGTcount: A:0.38, C:0.20, G:0.18, T:0.24
Consensus pattern (65 bp):
CAGGACGCTCACAAAGAGTTGCATTTGTGTCTACAACATATACAGGATCACAACCGATAATAAAA
Found at i:46588601 original size:44 final size:43
Alignment explanation
Indices: 46588525--46588688 Score: 147
Period size: 43 Copynumber: 3.8 Consensus size: 43
46588515 TTTAATATGT
* ** *
46588525 GATTTCGTGTAAGACCATGTTTGAAACGTTGGCATCGAT-TTAA
1 GATTTCGTGTAAGACCATGTCTGGGACATTGGCATCGATATT-A
46588568 GATTTACGTGTAAGACCATGTCTGGGACATTGGCATC-ATATTTA
1 GATTT-CGTGTAAGACCATGTCTGGGACATTGGCATCGATA-TTA
* * *
46588612 -ATTTTGTGTAAGACCCTGTCTGGGACAGTT-GCATCGATATTT
1 GATTTCGTGTAAGACCATGTCTGGGACA-TTGGCATCGATATTA
* * * * * *
46588654 GATTACATATAGGACCACGTTTGGGACATTGGCAT
1 GATTTCGTGTAAGACCATGTCTGGGACATTGGCAT
46588689 TGTACGAGCT
Statistics
Matches: 99, Mismatches: 15, Indels: 14
0.77 0.12 0.11
Matches are distributed among these distances:
42 30 0.30
43 39 0.39
44 28 0.28
45 2 0.02
ACGTcount: A:0.26, C:0.16, G:0.24, T:0.34
Consensus pattern (43 bp):
GATTTCGTGTAAGACCATGTCTGGGACATTGGCATCGATATTA
Found at i:46599095 original size:27 final size:27
Alignment explanation
Indices: 46599065--46599682 Score: 851
Period size: 27 Copynumber: 22.9 Consensus size: 27
46599055 GTACTCCCGA
46599065 TTTACAGAATTACCGTTTTACCCTCAG
1 TTTACAGAATTACCGTTTTACCCTCAG
*
46599092 TTTACAGAATTACTGTTTTACCCTC-G
1 TTTACAGAATTACCGTTTTACCCTCAG
46599118 ATTTACAGAATTACCGTTTTACCCTCAG
1 -TTTACAGAATTACCGTTTTACCCTCAG
46599146 TTTACAGAATTACCGTTTTACCCTCAG
1 TTTACAGAATTACCGTTTTACCCTCAG
46599173 TTTACAGAATTACCGTTTTACCCTCAG
1 TTTACAGAATTACCGTTTTACCCTCAG
46599200 TTTACAGAATTACCGTTTTACCCTC-G
1 TTTACAGAATTACCGTTTTACCCTCAG
46599226 ATTTACAGAATTACCGTTTTACCCTCAG
1 -TTTACAGAATTACCGTTTTACCCTCAG
* *
46599254 TTTATAGAATTACTGTTTTACCCTC-G
1 TTTACAGAATTACCGTTTTACCCTCAG
* *
46599280 ATTTATAGAATTACCGTTTTACCCTCAA
1 -TTTACAGAATTACCGTTTTACCCTCAG
*
46599308 TTTATAGAATTACCGTTTTACCCTC-G
1 TTTACAGAATTACCGTTTTACCCTCAG
* *
46599334 ATTTATAGAATTACTGTTTTACCCTCAG
1 -TTTACAGAATTACCGTTTTACCCTCAG
*
46599362 TTTACAGAATTATCGTTTTACCCTCAG
1 TTTACAGAATTACCGTTTTACCCTCAG
46599389 TTTACAGAATTACCGTTTTACCCTCAG
1 TTTACAGAATTACCGTTTTACCCTCAG
*
46599416 TTTACAGAATTATCGTTTTACCCTC-G
1 TTTACAGAATTACCGTTTTACCCTCAG
*
46599442 ATTTACAGAATTATCGTTTTACCCTCAG
1 -TTTACAGAATTACCGTTTTACCCTCAG
*
46599470 TTTACAGAATTACCGTTTTACCCTCAA
1 TTTACAGAATTACCGTTTTACCCTCAG
*
46599497 TTTACAAAATTACCGTTTTACCCTCAG
1 TTTACAGAATTACCGTTTTACCCTCAG
* *
46599524 TTTAAAGAATTACTGTTTTACCCTC-G
1 TTTACAGAATTACCGTTTTACCCTCAG
* * * *
46599550 ATCTATAGAATTACTGTTTTACCCTCGAT
1 -TTTACAGAATTACCGTTTTACCCTC-AG
*
46599579 TTGTA-A-AATTACCGTTTTACCCT-TG
1 TT-TACAGAATTACCGTTTTACCCTCAG
* *
46599604 ATTTACAGAATTACTGGTTTACCCTCAG
1 -TTTACAGAATTACCGTTTTACCCTCAG
* *
46599632 TTTACAAAATTATCGTTTTACCCTC-G
1 TTTACAGAATTACCGTTTTACCCTCAG
*
46599658 ATTTACAGAATTATCGTTTTACCCT
1 -TTTACAGAATTACCGTTTTACCCT
46599683 TGATTGTGAA
Statistics
Matches: 537, Mismatches: 35, Indels: 38
0.88 0.06 0.06
Matches are distributed among these distances:
25 2 0.00
26 9 0.02
27 517 0.96
28 7 0.01
29 2 0.00
ACGTcount: A:0.27, C:0.23, G:0.11, T:0.40
Consensus pattern (27 bp):
TTTACAGAATTACCGTTTTACCCTCAG
Found at i:46599103 original size:54 final size:54
Alignment explanation
Indices: 46599062--46599682 Score: 953
Period size: 54 Copynumber: 11.5 Consensus size: 54
46599052 AAAGTACTCC
*
46599062 CGATTTACAGAATTACCGTTTTACCCTCAGTTTACAGAATTACTGTTTTACCCT
1 CGATTTACAGAATTACCGTTTTACCCTCAGTTTACAGAATTACCGTTTTACCCT
46599116 CGATTTACAGAATTACCGTTTTACCCTCAGTTTACAGAATTACCGTTTTACCCT
1 CGATTTACAGAATTACCGTTTTACCCTCAGTTTACAGAATTACCGTTTTACCCT
46599170 C-AGTTTACAGAATTACCGTTTTACCCTCAGTTTACAGAATTACCGTTTTACCCT
1 CGA-TTTACAGAATTACCGTTTTACCCTCAGTTTACAGAATTACCGTTTTACCCT
* *
46599224 CGATTTACAGAATTACCGTTTTACCCTCAGTTTATAGAATTACTGTTTTACCCT
1 CGATTTACAGAATTACCGTTTTACCCTCAGTTTACAGAATTACCGTTTTACCCT
* * *
46599278 CGATTTATAGAATTACCGTTTTACCCTCAATTTATAGAATTACCGTTTTACCCT
1 CGATTTACAGAATTACCGTTTTACCCTCAGTTTACAGAATTACCGTTTTACCCT
* * *
46599332 CGATTTATAGAATTACTGTTTTACCCTCAGTTTACAGAATTATCGTTTTACCCT
1 CGATTTACAGAATTACCGTTTTACCCTCAGTTTACAGAATTACCGTTTTACCCT
*
46599386 C-AGTTTACAGAATTACCGTTTTACCCTCAGTTTACAGAATTATCGTTTTACCCT
1 CGA-TTTACAGAATTACCGTTTTACCCTCAGTTTACAGAATTACCGTTTTACCCT
*
46599440 CGATTTACAGAATTATCGTTTTACCCTCAGTTTACAGAATTACCGTTTTACCCT
1 CGATTTACAGAATTACCGTTTTACCCTCAGTTTACAGAATTACCGTTTTACCCT
* * * *
46599494 CAATTTACAAAATTACCGTTTTACCCTCAGTTTAAAGAATTACTGTTTTACCCT
1 CGATTTACAGAATTACCGTTTTACCCTCAGTTTACAGAATTACCGTTTTACCCT
* * * *
46599548 CGATCTATAGAATTACTGTTTTACCCTCGATTTGTA-A-AATTACCGTTTTACCCT
1 CGATTTACAGAATTACCGTTTTACCCTC-AGTT-TACAGAATTACCGTTTTACCCT
* * * * *
46599602 TGATTTACAGAATTACTGGTTTACCCTCAGTTTACAAAATTATCGTTTTACCCT
1 CGATTTACAGAATTACCGTTTTACCCTCAGTTTACAGAATTACCGTTTTACCCT
*
46599656 CGATTTACAGAATTATCGTTTTACCCT
1 CGATTTACAGAATTACCGTTTTACCCT
46599683 TGATTGTGAA
Statistics
Matches: 523, Mismatches: 36, Indels: 16
0.91 0.06 0.03
Matches are distributed among these distances:
52 2 0.00
53 6 0.01
54 507 0.97
55 6 0.01
56 2 0.00
ACGTcount: A:0.27, C:0.23, G:0.11, T:0.40
Consensus pattern (54 bp):
CGATTTACAGAATTACCGTTTTACCCTCAGTTTACAGAATTACCGTTTTACCCT
Found at i:46599722 original size:27 final size:27
Alignment explanation
Indices: 46599692--46599885 Score: 212
Period size: 27 Copynumber: 7.2 Consensus size: 27
46599682 TTGATTGTGA
*
46599692 AATTATTGAAATACCCCTGTAGGGTAG
1 AATTATCGAAATACCCCTGTAGGGTAG
* *
46599719 AATTTTCGAAATACCCCTATAGGGTAG
1 AATTATCGAAATACCCCTGTAGGGTAG
* * * *
46599746 AATTA-CTGAAATACACTTATAGGATAG
1 AATTATC-GAAATACCCCTGTAGGGTAG
* * *
46599773 AATTACCAAAATACCCCTGTAGGGGAG
1 AATTATCGAAATACCCCTGTAGGGTAG
*
46599800 AATTATCGAAATACCCTTGTAGGGTAG
1 AATTATCGAAATACCCCTGTAGGGTAG
*
46599827 AAATATCGAAATACCCCTGTAGGGTAG
1 AATTATCGAAATACCCCTGTAGGGTAG
* * * *
46599854 AATTA-CCAAGATACCCTTGTGGGGTAA
1 AATTATCGAA-ATACCCCTGTAGGGTAG
46599881 AATTA
1 AATTA
46599886 CCATTTTGCC
Statistics
Matches: 140, Mismatches: 24, Indels: 6
0.82 0.14 0.04
Matches are distributed among these distances:
26 4 0.03
27 135 0.96
28 1 0.01
ACGTcount: A:0.37, C:0.16, G:0.20, T:0.27
Consensus pattern (27 bp):
AATTATCGAAATACCCCTGTAGGGTAG
Found at i:46599792 original size:81 final size:81
Alignment explanation
Indices: 46599700--46599885 Score: 239
Period size: 81 Copynumber: 2.3 Consensus size: 81
46599690 GAAATTATTG
* * *
46599700 AAATACCCCTGTAGGGTAGAATTTTCGAAATACCCCTATAGGGTAGAATTA-CTGAAATACACTT
1 AAATACCCCTGTAGGGTAGAATTATCGAAATACCCCTATAGGGTAGAAATATC-GAAATACACCT
46599764 ATAGGATAGAATTACCA
65 ATAGGATAGAATTACCA
* * * * *
46599781 AAATACCCCTGTAGGGGAGAATTATCGAAATACCCTTGTAGGGTAGAAATATCGAAATACCCCTG
1 AAATACCCCTGTAGGGTAGAATTATCGAAATACCCCTATAGGGTAGAAATATCGAAATACACCTA
*
46599846 TAGGGTAGAATTACCA
66 TAGGATAGAATTACCA
* * * *
46599862 AGATACCCTTGTGGGGTAAAATTA
1 AAATACCCCTGTAGGGTAGAATTA
46599886 CCATTTTGCC
Statistics
Matches: 90, Mismatches: 14, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
81 89 0.99
82 1 0.01
ACGTcount: A:0.37, C:0.17, G:0.20, T:0.26
Consensus pattern (81 bp):
AAATACCCCTGTAGGGTAGAATTATCGAAATACCCCTATAGGGTAGAAATATCGAAATACACCTA
TAGGATAGAATTACCA
Found at i:46600124 original size:27 final size:26
Alignment explanation
Indices: 46600086--46600168 Score: 94
Period size: 27 Copynumber: 3.1 Consensus size: 26
46600076 CGGAGGAAGC
46600086 GTTCTGGTGGCTATGCCACAAATATCT
1 GTTCTGGTGGCTATGCCAC-AATATCT
*
46600113 GTTCTGGTGGCTCTGCCACAATATCT
1 GTTCTGGTGGCTATGCCACAATATCT
* * * * *
46600139 TTATTTGGTGACTCTGTCACAATATCT
1 GT-TCTGGTGGCTATGCCACAATATCT
46600166 GTT
1 GTT
46600169 GACCAATCAA
Statistics
Matches: 49, Mismatches: 6, Indels: 3
0.84 0.10 0.05
Matches are distributed among these distances:
26 9 0.18
27 40 0.82
ACGTcount: A:0.19, C:0.22, G:0.20, T:0.39
Consensus pattern (26 bp):
GTTCTGGTGGCTATGCCACAATATCT
Found at i:46600288 original size:22 final size:22
Alignment explanation
Indices: 46600256--46600314 Score: 64
Period size: 22 Copynumber: 2.7 Consensus size: 22
46600246 CCCGTTATTA
*
46600256 ATGGCTCTGTGCCAACCTAAAT
1 ATGGCTTTGTGCCAACCTAAAT
* * * *
46600278 ATGGCTTTGTGCCATCTTGACT
1 ATGGCTTTGTGCCAACCTAAAT
*
46600300 ATGGCTTCGTGCCAA
1 ATGGCTTTGTGCCAA
46600315 ACATATTTAC
Statistics
Matches: 30, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.20, C:0.25, G:0.22, T:0.32
Consensus pattern (22 bp):
ATGGCTTTGTGCCAACCTAAAT
Found at i:46600501 original size:27 final size:27
Alignment explanation
Indices: 46600479--46600553 Score: 82
Period size: 27 Copynumber: 2.8 Consensus size: 27
46600469 TAGGTGGGTT
*
46600479 TGCCACATTATCTG-ATTCTGGTGGCTC
1 TGCCACAATATCTGTA-TCTGGTGGCTC
* *
46600506 TGCCACAATATCTGTATCTGGTGACTA
1 TGCCACAATATCTGTATCTGGTGGCTC
* *
46600533 TGTCACGATATCTGT-TCTGGT
1 TGCCACAATATCTGTATCTGGT
46600554 AGCCATGCTG
Statistics
Matches: 42, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
26 6 0.14
27 35 0.83
28 1 0.02
ACGTcount: A:0.19, C:0.23, G:0.21, T:0.37
Consensus pattern (27 bp):
TGCCACAATATCTGTATCTGGTGGCTC
Found at i:46600679 original size:6 final size:6
Alignment explanation
Indices: 46600670--46600789 Score: 122
Period size: 6 Copynumber: 19.8 Consensus size: 6
46600660 TTGCATTCAC
*
46600670 ATTCTG ATTCTG ATTCTG ATTCTG ATTCTG -TTACAG ATTCTG ATTCTG
1 ATTCTG ATTCTG ATTCTG ATTCTG ATTCTG ATT-CTG ATTCTG ATTCTG
* * * *
46600718 ATTC-G GTCACCTA ATTCTG ATTCTG ATTCTG ATTCTG -TTACTA ATAT-TG
1 ATTCTG AT--TCTG ATTCTG ATTCTG ATTCTG ATTCTG ATT-CTG AT-TCTG
46600767 ATTCTG ATTCTG ATTCTG ATTCT
1 ATTCTG ATTCTG ATTCTG ATTCT
46600790 CATTTTGGTT
Statistics
Matches: 95, Mismatches: 10, Indels: 18
0.77 0.08 0.15
Matches are distributed among these distances:
5 7 0.07
6 82 0.86
7 4 0.04
8 2 0.02
ACGTcount: A:0.20, C:0.17, G:0.15, T:0.47
Consensus pattern (6 bp):
ATTCTG
Found at i:46602818 original size:27 final size:27
Alignment explanation
Indices: 46602788--46603431 Score: 761
Period size: 27 Copynumber: 23.9 Consensus size: 27
46602778 GTACTCCCGA
* *
46602788 TTTACAGAATTACCGTTTTACCTTCAC
1 TTTACAGAATTACCGTTTTACCCTCAG
*
46602815 TTTACAGAATTACTGTTTTACCCTC-G
1 TTTACAGAATTACCGTTTTACCCTCAG
* * *
46602841 ATTTACAGAATTACCGTTTTATCCTTAC
1 -TTTACAGAATTACCGTTTTACCCTCAG
46602869 TTTACAGAATTACCGTTTTACCCTC-G
1 TTTACAGAATTACCGTTTTACCCTCAG
* *
46602895 ATTTATAGAATTATCGTTTTACCCTCAG
1 -TTTACAGAATTACCGTTTTACCCTCAG
*
46602923 TTTACAGAATTATCGTTTTACCCTCAG
1 TTTACAGAATTACCGTTTTACCCTCAG
46602950 TTTACAGAATTACCGTTTTACCCTC-G
1 TTTACAGAATTACCGTTTTACCCTCAG
46602976 ATTTACAGAATTACCGTTTTACCCTCAG
1 -TTTACAGAATTACCGTTTTACCCTCAG
* *** *
46603004 TTTACAGAAATATTATTTTACCATC-G
1 TTTACAGAATTACCGTTTTACCCTCAG
46603030 ATTTACAGAATTACCGTTTTACCCTCAG
1 -TTTACAGAATTACCGTTTTACCCTCAG
46603058 TTTACAGAATTACCGTTTTACCCTCCA-
1 TTTACAGAATTACCGTTTTACCCT-CAG
* * *
46603085 TTTACAGAATTACTGTTTTACCCTTAA
1 TTTACAGAATTACCGTTTTACCCTCAG
* * *
46603112 TTTATAGAATTATCGCTTTACCCTCAG
1 TTTACAGAATTACCGTTTTACCCTCAG
*
46603139 TTTACAGAATTACCGTTTTACCCTCTG
1 TTTACAGAATTACCGTTTTACCCTCAG
46603166 TTTACAGAATTACCGTTTTACCCTC-G
1 TTTACAGAATTACCGTTTTACCCTCAG
*
46603192 ATTTACAGAATTATCGTTTTACCCTCAG
1 -TTTACAGAATTACCGTTTTACCCTCAG
* **
46603220 TTTACAAAATTACTATTTTACCCTC-G
1 TTTACAGAATTACCGTTTTACCCTCAG
*
46603246 ATTTATAGAATTACCGTTTTACCCTCAG
1 -TTTACAGAATTACCGTTTTACCCTCAG
* *
46603274 TTTACAGAATTACTGTTTTACCCTCAA
1 TTTACAGAATTACCGTTTTACCCTCAG
* *
46603301 TTTACAAAATTACCGTTTTACCCTCGAT
1 TTTACAGAATTACCGTTTTACCCTC-AG
* *
46603329 TTGTA-A-AATTACCATTTTACCCT-TG
1 TT-TACAGAATTACCGTTTTACCCTCAG
* * * *
46603354 ATTACAAAATTACTGGTTTACCCTCAG
1 TTTACAGAATTACCGTTTTACCCTCAG
* *
46603381 TTTACAAAATTATCGTTTTACCCTC-G
1 TTTACAGAATTACCGTTTTACCCTCAG
* *
46603407 ATTTATAGAATTACCATTTTACCCT
1 -TTTACAGAATTACCGTTTTACCCT
46603432 TGATTGTGAA
Statistics
Matches: 530, Mismatches: 67, Indels: 40
0.83 0.11 0.06
Matches are distributed among these distances:
24 2 0.00
25 2 0.00
26 20 0.04
27 493 0.93
28 11 0.02
29 2 0.00
ACGTcount: A:0.28, C:0.23, G:0.09, T:0.40
Consensus pattern (27 bp):
TTTACAGAATTACCGTTTTACCCTCAG
Found at i:46603472 original size:27 final size:27
Alignment explanation
Indices: 46603441--46603608 Score: 176
Period size: 27 Copynumber: 6.2 Consensus size: 27
46603431 TTGATTGTGA
*
46603441 AATTACTGAAATACCCCGGTAGGGTAG
1 AATTACTGAAATACCCCTGTAGGGTAG
* * * *
46603468 AATTACTAAAATACCCTTATAGGATAG
1 AATTACTGAAATACCCCTGTAGGGTAG
**
46603495 AATTACCAAAATACCCCTGTAGGGTAG
1 AATTACTGAAATACCCCTGTAGGGTAG
* *
46603522 AATTA-TCGAAATACCCTTGTAGGGTAA
1 AATTACT-GAAATACCCCTGTAGGGTAG
* *
46603549 AAATACTGAAATACCCATGTAGGGTAG
1 AATTACTGAAATACCCCTGTAGGGTAG
* * * * *
46603576 AATTACCGAGATACCCTTGTGGGGTAA
1 AATTACTGAAATACCCCTGTAGGGTAG
46603603 AATTAC
1 AATTAC
46603609 CATTTTGCCC
Statistics
Matches: 117, Mismatches: 22, Indels: 4
0.82 0.15 0.03
Matches are distributed among these distances:
27 116 0.99
28 1 0.01
ACGTcount: A:0.38, C:0.17, G:0.20, T:0.26
Consensus pattern (27 bp):
AATTACTGAAATACCCCTGTAGGGTAG
Found at i:46603561 original size:81 final size:81
Alignment explanation
Indices: 46603440--46603607 Score: 203
Period size: 81 Copynumber: 2.1 Consensus size: 81
46603430 CTTGATTGTG
* * *
46603440 AAATTA-CTGAAATACCCCGGTAGGGTAGAATTACTAAAATACCCTTATAGGATAGAATTACCAA
1 AAATTATC-GAAATACCCCGGTAGGGTAAAAATACTAAAATACCCATATAGGATAGAATTACCAA
46603504 AATACCCCTGTAGGGTA
65 AATACCCCTGTAGGGTA
* ** * * * * *
46603521 GAATTATCGAAATACCCTTGTAGGGTAAAAATACTGAAATACCCATGTAGGGTAGAATTACCGAG
1 AAATTATCGAAATACCCCGGTAGGGTAAAAATACTAAAATACCCATATAGGATAGAATTACCAAA
* *
46603586 ATACCCTTGTGGGGTA
66 ATACCCCTGTAGGGTA
46603602 AAATTA
1 AAATTA
46603608 CCATTTTGCC
Statistics
Matches: 72, Mismatches: 14, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
81 71 0.99
82 1 0.01
ACGTcount: A:0.38, C:0.17, G:0.20, T:0.26
Consensus pattern (81 bp):
AAATTATCGAAATACCCCGGTAGGGTAAAAATACTAAAATACCCATATAGGATAGAATTACCAAA
ATACCCCTGTAGGGTA
Found at i:46603590 original size:54 final size:54
Alignment explanation
Indices: 46603444--46603604 Score: 205
Period size: 54 Copynumber: 3.0 Consensus size: 54
46603434 ATTGTGAAAT
* ** * * * *
46603444 TACTGAAATACCCCGGTAGGGTAGAATTACTAAAATACCCTTATAGGATAGAAT
1 TACTGAAATACCCCTGTAGGGTAGAATTACCGAAATACCCTTGTAGGGTAAAAA
** *
46603498 TACCAAAATACCCCTGTAGGGTAGAATTATCGAAATACCCTTGTAGGGTAAAAA
1 TACTGAAATACCCCTGTAGGGTAGAATTACCGAAATACCCTTGTAGGGTAAAAA
* * *
46603552 TACTGAAATACCCATGTAGGGTAGAATTACCGAGATACCCTTGTGGGGTAAAA
1 TACTGAAATACCCCTGTAGGGTAGAATTACCGAAATACCCTTGTAGGGTAAAA
46603605 TTACCATTTT
Statistics
Matches: 91, Mismatches: 16, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
54 91 1.00
ACGTcount: A:0.37, C:0.17, G:0.20, T:0.25
Consensus pattern (54 bp):
TACTGAAATACCCCTGTAGGGTAGAATTACCGAAATACCCTTGTAGGGTAAAAA
Found at i:46603847 original size:27 final size:26
Alignment explanation
Indices: 46603809--46603891 Score: 94
Period size: 27 Copynumber: 3.1 Consensus size: 26
46603799 CGGAGGAAGC
46603809 GTTCTGGTGGCTATGCCACAAATATCT
1 GTTCTGGTGGCTATGCCAC-AATATCT
*
46603836 GTTCTGGTGGCTCTGCCACAATATCT
1 GTTCTGGTGGCTATGCCACAATATCT
* * * * *
46603862 TTATTTGGTGACTCTGTCACAATATCT
1 GT-TCTGGTGGCTATGCCACAATATCT
46603889 GTT
1 GTT
46603892 GACCAATCGA
Statistics
Matches: 49, Mismatches: 6, Indels: 3
0.84 0.10 0.05
Matches are distributed among these distances:
26 9 0.18
27 40 0.82
ACGTcount: A:0.19, C:0.22, G:0.20, T:0.39
Consensus pattern (26 bp):
GTTCTGGTGGCTATGCCACAATATCT
Found at i:46605217 original size:47 final size:47
Alignment explanation
Indices: 46605154--46605547 Score: 608
Period size: 47 Copynumber: 8.4 Consensus size: 47
46605144 CCCTTCGGGA
* * *
46605154 CTTATCACATTTATACACTTTCACATCCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTAGGC
* * * *
46605201 CTTATCACATATATACACCTTCACATCCATCACATCGGCCATTAGGT
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTAGGC
* * *
46605248 CTTATCTCATATATACACTTTCACATTCATCACATTGCCCATTAGGT
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTAGGC
* *
46605295 CTTATCTCATATATACACTTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTAGGC
* * *
46605342 CTTATCACATATATACACTTTCACATTCATCACGTTGGCCACTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTAGGC
*
46605389 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTAGGC
* *
46605436 CTTATCACATATACACACTTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTAGGC
*
46605483 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTAGGC
*
46605530 CTTATCACATATACACAC
1 CTTATCACATATATACAC
46605548 CTTGTACATC
Statistics
Matches: 320, Mismatches: 27, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
47 320 1.00
ACGTcount: A:0.28, C:0.31, G:0.08, T:0.33
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTAGGC
Found at i:46608332 original size:22 final size:22
Alignment explanation
Indices: 46608302--46608358 Score: 60
Period size: 22 Copynumber: 2.6 Consensus size: 22
46608292 GGGTGTCACA
*
46608302 GGCTCTGTGCCAACCTAAATAT
1 GGCTTTGTGCCAACCTAAATAT
* * * *
46608324 GGCTTTGTGCCATCTTGACTAT
1 GGCTTTGTGCCAACCTAAATAT
*
46608346 GGCTTCGTGCCAA
1 GGCTTTGTGCCAA
46608359 ACGTATTTAC
Statistics
Matches: 28, Mismatches: 7, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.19, C:0.26, G:0.23, T:0.32
Consensus pattern (22 bp):
GGCTTTGTGCCAACCTAAATAT
Found at i:46608722 original size:6 final size:6
Alignment explanation
Indices: 46608713--46608911 Score: 205
Period size: 6 Copynumber: 32.8 Consensus size: 6
46608703 TTGCATTCAC
* *
46608713 ATTCTG ATTCTG ATTCTG -TCACGTA ATTCTG ATTCTG ATTCTG ATTCTG
1 ATTCTG ATTCTG ATTCTG AT-TC-TG ATTCTG ATTCTG ATTCTG ATTCTG
* *
46608762 -TTACTA ATACTG ATTCTG ATTCTG ATTCTG ATTCTG -TTACTG ATTCTG
1 ATT-CTG ATTCTG ATTCTG ATTCTG ATTCTG ATTCTG ATT-CTG ATTCTG
*
46608810 ATTCTG ATTCTG ATTCTG -TCACCTG ATTCTG ATTCTG ATTCTG ATTCTG
1 ATTCTG ATTCTG ATTCTG AT--TCTG ATTCTG ATTCTG ATTCTG ATTCTG
* *
46608859 -TTACTA ATAT-TG ATTCTG ATTCTG ATTCTG -TTACTA ATTCTG ATTCTG
1 ATT-CTG AT-TCTG ATTCTG ATTCTG ATTCTG ATT-CTG ATTCTG ATTCTG
46608907 ATTCT
1 ATTCT
46608912 CATTTTGGTT
Statistics
Matches: 163, Mismatches: 14, Indels: 32
0.78 0.07 0.15
Matches are distributed among these distances:
5 11 0.07
6 138 0.85
7 11 0.07
8 3 0.02
ACGTcount: A:0.20, C:0.18, G:0.15, T:0.48
Consensus pattern (6 bp):
ATTCTG
Found at i:46608873 original size:97 final size:97
Alignment explanation
Indices: 46608713--46608911 Score: 330
Period size: 97 Copynumber: 2.1 Consensus size: 97
46608703 TTGCATTCAC
*
46608713 ATTCTGATTCTGATTCTGTCACGTAATTCTGATTCTGATTCTGATTCTGTTACTAATACTGATTC
1 ATTCTGATTCTGATTCTGTCACCTAATTCTGATTCTGATTCTGATTCTGTTACTAATACTGATTC
*
46608778 TGATTCTGATTCTGATT-CT-GTTACTGATTCTG
66 TGATTCTGATTCTG-TTACTAATT-CTGATTCTG
* *
46608810 ATTCTGATTCTGATTCTGTCACCTGATTCTGATTCTGATTCTGATTCTGTTACTAATATTGATTC
1 ATTCTGATTCTGATTCTGTCACCTAATTCTGATTCTGATTCTGATTCTGTTACTAATACTGATTC
46608875 TGATTCTGATTCTGTTACTAATTCTGATTCTG
66 TGATTCTGATTCTGTTACTAATTCTGATTCTG
46608907 ATTCT
1 ATTCT
46608912 CATTTTGGTT
Statistics
Matches: 96, Mismatches: 4, Indels: 4
0.92 0.04 0.04
Matches are distributed among these distances:
96 2 0.02
97 92 0.96
98 2 0.02
ACGTcount: A:0.20, C:0.18, G:0.15, T:0.48
Consensus pattern (97 bp):
ATTCTGATTCTGATTCTGTCACCTAATTCTGATTCTGATTCTGATTCTGTTACTAATACTGATTC
TGATTCTGATTCTGTTACTAATTCTGATTCTG
Found at i:46608932 original size:30 final size:30
Alignment explanation
Indices: 46608713--46608911 Score: 274
Period size: 30 Copynumber: 6.4 Consensus size: 30
46608703 TTGCATTCAC
*
46608713 ATTCTGATTCTGATTCTGTCACGTAATTCTG
1 ATTCTGATTCTGATTCTGTTAC-TAATTCTG
46608744 ATTCTGATTCTGATTCTGTTACTAATACTGATTCTG
1 ATTCTGATTCTGATTCTGTTAC---TA---ATTCTG
*
46608780 ATTCTGATTCTGATTCTGTTACTGATTCTG
1 ATTCTGATTCTGATTCTGTTACTAATTCTG
* *
46608810 ATTCTGATTCTGATTCTGTCACCTGATTCTG
1 ATTCTGATTCTGATTCTGTTA-CTAATTCTG
46608841 ATTCTGATTCTGATTCTGTTACTAATAT-TG
1 ATTCTGATTCTGATTCTGTTACTAAT-TCTG
46608871 ATTCTGATTCTGATTCTGTTACTAATTCTG
1 ATTCTGATTCTGATTCTGTTACTAATTCTG
46608901 ATTCTGATTCT
1 ATTCTGATTCT
46608912 CATTTTGGTT
Statistics
Matches: 154, Mismatches: 6, Indels: 17
0.87 0.03 0.10
Matches are distributed among these distances:
29 1 0.01
30 71 0.46
31 51 0.33
33 3 0.02
36 28 0.18
ACGTcount: A:0.20, C:0.18, G:0.15, T:0.48
Consensus pattern (30 bp):
ATTCTGATTCTGATTCTGTTACTAATTCTG
Found at i:46610169 original size:30 final size:30
Alignment explanation
Indices: 46610133--46610192 Score: 111
Period size: 30 Copynumber: 2.0 Consensus size: 30
46610123 AATAAATGAA
46610133 AAATATGGGCCGCTAAGGACTTAAAGCATG
1 AAATATGGGCCGCTAAGGACTTAAAGCATG
*
46610163 AAATATGGGCTGCTAAGGACTTAAAGCATG
1 AAATATGGGCCGCTAAGGACTTAAAGCATG
46610193 GGTATAGGTT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.37, C:0.15, G:0.27, T:0.22
Consensus pattern (30 bp):
AAATATGGGCCGCTAAGGACTTAAAGCATG
Found at i:46620567 original size:37 final size:37
Alignment explanation
Indices: 46620526--46620599 Score: 148
Period size: 37 Copynumber: 2.0 Consensus size: 37
46620516 TATAGGCTGG
46620526 ATTATATTTTGAATTGTTTAATTTCGGTTTATGTAAC
1 ATTATATTTTGAATTGTTTAATTTCGGTTTATGTAAC
46620563 ATTATATTTTGAATTGTTTAATTTCGGTTTATGTAAC
1 ATTATATTTTGAATTGTTTAATTTCGGTTTATGTAAC
46620600 TATGAGCCAT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.27, C:0.05, G:0.14, T:0.54
Consensus pattern (37 bp):
ATTATATTTTGAATTGTTTAATTTCGGTTTATGTAAC
Found at i:46621838 original size:37 final size:34
Alignment explanation
Indices: 46621788--46621859 Score: 81
Period size: 37 Copynumber: 2.0 Consensus size: 34
46621778 AGTTGTGCCG
* *
46621788 TTTTTCTGACCATCTTTCCTCCTCCTCCTTTCTTTTC
1 TTTTTCTCACCATC-TACCTCCTCCT-C-TTCTTTTC
* *
46621825 TTTTTCTCTCCATCTACCTTCTCCTCTTCTTTTC
1 TTTTTCTCACCATCTACCTCCTCCTCTTCTTTTC
46621859 T
1 T
46621860 CCATAGCCGA
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
34 9 0.29
35 1 0.03
36 9 0.29
37 12 0.39
ACGTcount: A:0.06, C:0.38, G:0.01, T:0.56
Consensus pattern (34 bp):
TTTTTCTCACCATCTACCTCCTCCTCTTCTTTTC
Found at i:46623112 original size:27 final size:26
Alignment explanation
Indices: 46623071--46623182 Score: 109
Period size: 27 Copynumber: 4.2 Consensus size: 26
46623061 AGGAAGGGTC
*
46623071 CTGGTGGCTAC-GCCATAATTATCTGAT
1 CTGGTGGCT-CTGCCA-CATTATCTGAT
*
46623098 CTGGTGGCTCTGCCACATATATCTGTT
1 CTGGTGGCTCTGCCACAT-TATCTGAT
* *
46623125 CTGGTGGGTTTGCCACGATTATCTGTAT
1 CTGGTGGCTCTGCCAC-ATTATCTG-AT
* * *
46623153 CTGGTGACTCTGTCACATTATCTGTT
1 CTGGTGGCTCTGCCACATTATCTGAT
46623179 CTGG
1 CTGG
46623183 CAGCCATGCT
Statistics
Matches: 71, Mismatches: 10, Indels: 9
0.79 0.11 0.10
Matches are distributed among these distances:
26 8 0.11
27 48 0.68
28 15 0.21
ACGTcount: A:0.16, C:0.22, G:0.24, T:0.38
Consensus pattern (26 bp):
CTGGTGGCTCTGCCACATTATCTGAT
Found at i:46630887 original size:27 final size:26
Alignment explanation
Indices: 46630847--46630952 Score: 140
Period size: 27 Copynumber: 3.9 Consensus size: 26
46630837 AGGAAGTGTC
*
46630847 CTGGTGGCTATGCCACAATTATCTGAT
1 CTGGTGGCTCTGCCAC-ATTATCTGAT
*
46630874 CTGGTGGCTCTGCCACATATATCTGTT
1 CTGGTGGCTCTGCCACAT-TATCTGAT
46630901 CTGGTGGCTCTGCCACGATTATCTGTAT
1 CTGGTGGCTCTGCCAC-ATTATCTG-AT
* *
46630929 CTGGTGACTCTGTCACATTATCTG
1 CTGGTGGCTCTGCCACATTATCTG
46630953 TTTTGGCGAT
Statistics
Matches: 71, Mismatches: 5, Indels: 6
0.87 0.06 0.07
Matches are distributed among these distances:
26 2 0.03
27 52 0.73
28 17 0.24
ACGTcount: A:0.17, C:0.25, G:0.23, T:0.36
Consensus pattern (26 bp):
CTGGTGGCTCTGCCACATTATCTGAT
Found at i:46630951 original size:54 final size:54
Alignment explanation
Indices: 46630847--46630954 Score: 164
Period size: 54 Copynumber: 2.0 Consensus size: 54
46630837 AGGAAGTGTC
*
46630847 CTGGTGGCTATGCCACAATTATCTGATCTGGTGGCTCTGCCACATATATCTGTT
1 CTGGTGGCTATGCCACAATTATCTGATCTGGTGACTCTGCCACATATATCTGTT
* * *
46630901 CTGGTGGCTCTGCCACGATTATCTGTATCTGGTGACTCTGTCACAT-TATCTGTT
1 CTGGTGGCTATGCCACAATTATCTG-ATCTGGTGACTCTGCCACATATATCTGTT
46630955 TTGGCGATTA
Statistics
Matches: 49, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
54 31 0.63
55 18 0.37
ACGTcount: A:0.17, C:0.24, G:0.22, T:0.37
Consensus pattern (54 bp):
CTGGTGGCTATGCCACAATTATCTGATCTGGTGACTCTGCCACATATATCTGTT
Found at i:46633660 original size:40 final size:40
Alignment explanation
Indices: 46633616--46633726 Score: 186
Period size: 40 Copynumber: 2.8 Consensus size: 40
46633606 GTACATAGTT
* *
46633616 GAAGCTATCTCAAATCGCACACTAAGTGCCATATATAGCC
1 GAAGCTATGTCGAATCGCACACTAAGTGCCATATATAGCC
*
46633656 GAAGCTATGTCGAATCACACACTAAGTGCCATATATAGCC
1 GAAGCTATGTCGAATCGCACACTAAGTGCCATATATAGCC
*
46633696 GAAGCTATGTCGTATCGCACACTAAGTGCCA
1 GAAGCTATGTCGAATCGCACACTAAGTGCCA
46633727 CAAATAACCG
Statistics
Matches: 66, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
40 66 1.00
ACGTcount: A:0.33, C:0.26, G:0.18, T:0.23
Consensus pattern (40 bp):
GAAGCTATGTCGAATCGCACACTAAGTGCCATATATAGCC
Found at i:46637859 original size:23 final size:23
Alignment explanation
Indices: 46637829--46637874 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
46637819 GTCTACATTA
46637829 TGATAGGAAAGATGTATGAAAAT
1 TGATAGGAAAGATGTATGAAAAT
46637852 TGATAGGAAAGATGTATGAAAAT
1 TGATAGGAAAGATGTATGAAAAT
46637875 GTTGATAAGG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.26, T:0.26
Consensus pattern (23 bp):
TGATAGGAAAGATGTATGAAAAT
Found at i:46640653 original size:93 final size:93
Alignment explanation
Indices: 46640540--46640709 Score: 270
Period size: 93 Copynumber: 1.8 Consensus size: 93
46640530 CCCTTAAGTG
* *
46640540 AACTCCGACTCAACTCAACGAGCTC-AGGCGTTCACATCCATAAGTGAACTCGGACTCAACTCAA
1 AACTCCGACTCAACTCAACGAGCTCGA-ACATTCACATCCATAAGTGAACTCGGACTCAACTCAA
46640604 CGAGTTCGGATGCCTAGTTACATCTCACA
65 CGAGTTCGGATGCCTAGTTACATCTCACA
* * * *
46640633 AACTCGGACTCAACTCAACGAGTTCGAACATTCGCATCCGTAAGTGAACTCGGACTCAACTCAAC
1 AACTCCGACTCAACTCAACGAGCTCGAACATTCACATCCATAAGTGAACTCGGACTCAACTCAAC
46640698 GAGTTCGGATGC
66 GAGTTCGGATGC
46640710 TCAACCATCC
Statistics
Matches: 70, Mismatches: 6, Indels: 2
0.90 0.08 0.03
Matches are distributed among these distances:
93 69 0.99
94 1 0.01
ACGTcount: A:0.30, C:0.30, G:0.19, T:0.21
Consensus pattern (93 bp):
AACTCCGACTCAACTCAACGAGCTCGAACATTCACATCCATAAGTGAACTCGGACTCAACTCAAC
GAGTTCGGATGCCTAGTTACATCTCACA
Done.