Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032248.1 Gossypioides kirkii chromosome KI_06
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: 60359545
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 900 characters in sequence are not A, C, G, or T
File 162 of 193
Found at i:50255389 original size:18 final size:18
Alignment explanation
Indices: 50255353--50255415 Score: 90
Period size: 18 Copynumber: 3.4 Consensus size: 18
50255343 AATTATTCTC
50255353 TAAAAAATTCAAAATATTT
1 TAAAAAATTCAAAAT-TTT
*
50255372 ATAAAAATTTCAAAATTTT
1 -TAAAAAATTCAAAATTTT
*
50255391 TAAAAAATTAAAAATTTT
1 TAAAAAATTCAAAATTTT
50255409 TAAAAAA
1 TAAAAAA
50255416 ATTCTAAAGA
Statistics
Matches: 40, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
18 23 0.57
19 3 0.08
20 14 0.35
ACGTcount: A:0.60, C:0.03, G:0.00, T:0.37
Consensus pattern (18 bp):
TAAAAAATTCAAAATTTT
Found at i:50261478 original size:32 final size:30
Alignment explanation
Indices: 50261440--50261506 Score: 80
Period size: 31 Copynumber: 2.2 Consensus size: 30
50261430 TCATATTTCA
* * *
50261440 AAATTTAGGTTTAATTGTAAAATTATTTTGTT
1 AAATTTAAGTTT-ATTATAAAATCATTTT-TT
*
50261472 AAATTTAAGTTTATTATAACATCATTTTTT
1 AAATTTAAGTTTATTATAAAATCATTTTTT
50261502 AAATT
1 AAATT
50261507 ACATTGCTAT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
30 7 0.23
31 13 0.42
32 11 0.35
ACGTcount: A:0.37, C:0.03, G:0.07, T:0.52
Consensus pattern (30 bp):
AAATTTAAGTTTATTATAAAATCATTTTTT
Found at i:50269828 original size:2 final size:2
Alignment explanation
Indices: 50269821--50269852 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
50269811 TACAAATAAT
*
50269821 TA TA TA TA TA TA TA TA TA TA TA TA TA TG TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
50269853 ATTTTATTAT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
TA
Found at i:50273973 original size:60 final size:60
Alignment explanation
Indices: 50273901--50274020 Score: 213
Period size: 60 Copynumber: 2.0 Consensus size: 60
50273891 ATTTTGTATA
* *
50273901 GATTTGATTCTATATTATAATTGATCCCACATATATTTGTATTTGTGATTATGCCATATT
1 GATTTGATTCTATACTATAATTGATCCCACATATATTTGTATTTGCGATTATGCCATATT
*
50273961 GATTTGATTCTATACTATAATTGATCCCACATATATTTGTATTTGCGATTATGCTATATT
1 GATTTGATTCTATACTATAATTGATCCCACATATATTTGTATTTGCGATTATGCCATATT
50274021 TTTATTAATG
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
60 57 1.00
ACGTcount: A:0.28, C:0.12, G:0.12, T:0.47
Consensus pattern (60 bp):
GATTTGATTCTATACTATAATTGATCCCACATATATTTGTATTTGCGATTATGCCATATT
Found at i:50276366 original size:21 final size:22
Alignment explanation
Indices: 50276341--50276388 Score: 89
Period size: 21 Copynumber: 2.2 Consensus size: 22
50276331 TAAAACAAAA
50276341 TATATAATAATGCAATATCATG
1 TATATAATAATGCAATATCATG
50276363 -ATATAATAATGCAATATCATG
1 TATATAATAATGCAATATCATG
50276384 TATAT
1 TATAT
50276389 TTTAAAAAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
21 21 0.84
22 4 0.16
ACGTcount: A:0.46, C:0.08, G:0.08, T:0.38
Consensus pattern (22 bp):
TATATAATAATGCAATATCATG
Found at i:50276886 original size:12 final size:12
Alignment explanation
Indices: 50276869--50277037 Score: 81
Period size: 12 Copynumber: 14.8 Consensus size: 12
50276859 ATAATAGCAA
50276869 AACAACAAAAAT
1 AACAACAAAAAT
* *
50276881 AGCAACAAAAAC
1 AACAACAAAAAT
50276893 AACAACAAAAAT
1 AACAACAAAAAT
* *
50276905 AACACCAAAAAC
1 AACAACAAAAAT
*
50276917 AACACCAAAACAGT
1 AACAACAAAA-A-T
50276931 -A-AA-AAAAA-
1 AACAACAAAAAT
50276939 AAC--C-AAAAT
1 AACAACAAAAAT
* * *
50276948 AACTACCAAAAC
1 AACAACAAAAAT
** *
50276960 AGTAGCAAAAAT
1 AACAACAAAAAT
* *
50276972 AATAGC---AA-
1 AACAACAAAAAT
50276980 AACAACAAAAAT
1 AACAACAAAAAT
* *
50276992 AGCAACAAAAAC
1 AACAACAAAAAT
50277004 AACAACAAAAAT
1 AACAACAAAAAT
* *
50277016 AACAGCAAAAAC
1 AACAACAAAAAT
*
50277028 AACACCAAAA
1 AACAACAAAA
50277038 CAATAAAAAA
Statistics
Matches: 119, Mismatches: 25, Indels: 26
0.70 0.15 0.15
Matches are distributed among these distances:
8 8 0.07
9 6 0.05
10 1 0.01
11 7 0.06
12 95 0.80
13 2 0.02
ACGTcount: A:0.69, C:0.21, G:0.04, T:0.06
Consensus pattern (12 bp):
AACAACAAAAAT
Found at i:50276892 original size:44 final size:44
Alignment explanation
Indices: 50276813--50277069 Score: 127
Period size: 44 Copynumber: 5.8 Consensus size: 44
50276803 AAAAGCATAT
* * * ** *
50276813 AAATAATATCC-AAACAACCAAAATAACTACCAAAACAGTAGCAA
1 AAATAATA-CCAAAACAACAAAAATAACAACAAAAACAACAACAA
* *
50276857 AAATAATAGCAAAACAACAAAAATAGCAACAAAAACAACAACAA
1 AAATAATACCAAAACAACAAAAATAACAACAAAAACAACAACAA
* ** ** * *
50276901 AAATAACACCAAAAACAACACCAA-AACAGTAAAAA-AAAAACCA
1 AAATAATACC-AAAACAACAAAAATAACAACAAAAACAACAACAA
* *
50276944 AAATAACTACCAAAACAGTAGCAAAAATAATAGC-AAAACAACAA-AA
1 AAATAA-TACCAAAACA--A-CAAAAATAACAACAAAAACAACAACAA
** * ** * *
50276990 ATAGCAACAAAAACAACAACAAAAATAACAGCAAAAACAAC-ACCA
1 A-AATAATACCAA-AACAACAAAAATAACAACAAAAACAACAACAA
* * *
50277035 AAACAATA--AAAAAAATC-AAAATAACAACCAAAACA
1 AAATAATACCAAAACAA-CAAAAATAACAACAAAAACA
50277070 GTAAAAAAAC
Statistics
Matches: 164, Mismatches: 36, Indels: 29
0.72 0.16 0.13
Matches are distributed among these distances:
41 20 0.12
42 3 0.02
43 19 0.12
44 71 0.43
45 23 0.14
46 13 0.08
47 15 0.09
ACGTcount: A:0.67, C:0.21, G:0.04, T:0.08
Consensus pattern (44 bp):
AAATAATACCAAAACAACAAAAATAACAACAAAAACAACAACAA
Found at i:50277012 original size:24 final size:24
Alignment explanation
Indices: 50276869--50277037 Score: 126
Period size: 24 Copynumber: 7.4 Consensus size: 24
50276859 ATAATAGCAA
*
50276869 AACAACAAAAATAGCAACAAAAAC
1 AACAACAAAAATAACAACAAAAAC
*
50276893 AACAACAAAAATAACACCAAAAAC
1 AACAACAAAAATAACAACAAAAAC
*
50276917 AACACCAAAACAGT-A-AA-AAAAA-
1 AACAACAAAA-A-TAACAACAAAAAC
* *
50276939 AAC--C-AAAATAACTACCAAAAC
1 AACAACAAAAATAACAACAAAAAC
** * * *
50276960 AGTAGCAAAAATAATAGC---AA-
1 AACAACAAAAATAACAACAAAAAC
*
50276980 AACAACAAAAATAGCAACAAAAAC
1 AACAACAAAAATAACAACAAAAAC
*
50277004 AACAACAAAAATAACAGCAAAAAC
1 AACAACAAAAATAACAACAAAAAC
*
50277028 AACACCAAAA
1 AACAACAAAA
50277038 CAATAAAAAA
Statistics
Matches: 112, Mismatches: 20, Indels: 26
0.71 0.13 0.16
Matches are distributed among these distances:
17 1 0.01
18 2 0.02
19 4 0.04
20 17 0.15
21 3 0.03
22 3 0.03
23 8 0.07
24 71 0.63
25 2 0.02
26 1 0.01
ACGTcount: A:0.69, C:0.21, G:0.04, T:0.06
Consensus pattern (24 bp):
AACAACAAAAATAACAACAAAAAC
Found at i:50277055 original size:30 final size:30
Alignment explanation
Indices: 50277023--50277086 Score: 87
Period size: 29 Copynumber: 2.2 Consensus size: 30
50277013 AATAACAGCA
50277023 AAAACAAC-ACCAAAACAATAAAAAAAATC
1 AAAACAACAACCAAAACAATAAAAAAAATC
* * *
50277052 AAAATAACAACCAAAACAGT-AAAAAAACC
1 AAAACAACAACCAAAACAATAAAAAAAATC
50277081 AAAACA
1 AAAACA
50277087 GCAAAAAACA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
29 20 0.67
30 10 0.33
ACGTcount: A:0.72, C:0.20, G:0.02, T:0.06
Consensus pattern (30 bp):
AAAACAACAACCAAAACAATAAAAAAAATC
Found at i:50277092 original size:111 final size:110
Alignment explanation
Indices: 50276828--50277072 Score: 438
Period size: 111 Copynumber: 2.2 Consensus size: 110
50276818 ATATCCAAAC
50276828 AACCAAAATAACTACCAAAACAGTAGCAAAAATAATAGCAAAACAACAAAAATAGCAACAAAAAC
1 AACCAAAATAACTACCAAAACAGTAGCAAAAATAATAGCAAAACAACAAAAATAGCAACAAAAAC
50276893 AACAACAAAAATAACACCAAAAACAACACCAAAACAGTAAAAAAAA
66 AACAACAAAAATAACACCAAAAACAACACCAAAACAG-AAAAAAAA
50276939 AACCAAAATAACTACCAAAACAGTAGCAAAAATAATAGCAAAACAACAAAAATAGCAACAAAAAC
1 AACCAAAATAACTACCAAAACAGTAGCAAAAATAATAGCAAAACAACAAAAATAGCAACAAAAAC
* *
50277004 AACAACAAAAATAACAGCAAAAACAACACCAAAACA-ATAAAAAA
66 AACAACAAAAATAACACCAAAAACAACACCAAAACAGAAAAAAAA
* *
50277048 AATCAAAATAACAACCAAAACAGTA
1 AACCAAAATAACTACCAAAACAGTA
50277073 AAAAAACCAA
Statistics
Matches: 130, Mismatches: 4, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
109 30 0.23
111 100 0.77
ACGTcount: A:0.67, C:0.20, G:0.04, T:0.08
Consensus pattern (110 bp):
AACCAAAATAACTACCAAAACAGTAGCAAAAATAATAGCAAAACAACAAAAATAGCAACAAAAAC
AACAACAAAAATAACACCAAAAACAACACCAAAACAGAAAAAAAA
Found at i:50277095 original size:16 final size:17
Alignment explanation
Indices: 50277060--50277094 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
50277050 TCAAAATAAC
50277060 AACCAAAACAGTAAAAA
1 AACCAAAACAGTAAAAA
*
50277077 AACCAAAACAGCAAAAA
1 AACCAAAACAGTAAAAA
50277094 A
1 A
50277095 CAGTAATCAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.71, C:0.20, G:0.06, T:0.03
Consensus pattern (17 bp):
AACCAAAACAGTAAAAA
Found at i:50277106 original size:22 final size:22
Alignment explanation
Indices: 50277080--50277145 Score: 80
Period size: 22 Copynumber: 3.0 Consensus size: 22
50277070 GTAAAAAAAC
*
50277080 CAAAACAGCAAAAAACAGTAAT
1 CAAAACAGTAAAAAACAGTAAT
* *
50277102 CAAAACAGTAAAAAACAATACT
1 CAAAACAGTAAAAAACAGTAAT
50277124 -AAAACAGTAACTAAAACAGTAA
1 CAAAACAGTAA--AAAACAGTAA
50277146 AAAAAGCACC
Statistics
Matches: 37, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
21 10 0.27
22 19 0.51
23 8 0.22
ACGTcount: A:0.64, C:0.17, G:0.08, T:0.12
Consensus pattern (22 bp):
CAAAACAGTAAAAAACAGTAAT
Found at i:50277108 original size:12 final size:10
Alignment explanation
Indices: 50277081--50277149 Score: 66
Period size: 10 Copynumber: 6.4 Consensus size: 10
50277071 TAAAAAAACC
*
50277081 AAAACAGCAA
1 AAAACAGTAA
50277091 AAAACAGTAA
1 AAAACAGTAA
50277101 TCAAAACAGTAA
1 --AAAACAGTAA
* *
50277113 AAAACAATACT
1 AAAACAGTA-A
50277124 AAAACAGTAA
1 AAAACAGTAA
50277134 CTAAAACAGTAA
1 --AAAACAGTAA
50277146 AAAA
1 AAAA
50277150 AGCACCAAAA
Statistics
Matches: 49, Mismatches: 5, Indels: 10
0.77 0.08 0.16
Matches are distributed among these distances:
10 21 0.43
11 8 0.16
12 20 0.41
ACGTcount: A:0.67, C:0.14, G:0.07, T:0.12
Consensus pattern (10 bp):
AAAACAGTAA
Found at i:50277148 original size:21 final size:20
Alignment explanation
Indices: 50277063--50277133 Score: 67
Period size: 22 Copynumber: 3.5 Consensus size: 20
50277053 AAATAACAAC
*
50277063 CAAAACAGT-AAAAA-AA-C
1 CAAAACAGTAAAAAACAATA
* *
50277080 CAAAACAGCAAAAAACAGTAA
1 CAAAACAGTAAAAAACAAT-A
50277101 TCAAAACAGTAAAAAACAATA
1 -CAAAACAGTAAAAAACAATA
50277122 CTAAAACAGTAA
1 C-AAAACAGTAA
50277134 CTAAAACAGT
Statistics
Matches: 43, Mismatches: 5, Indels: 8
0.77 0.09 0.14
Matches are distributed among these distances:
17 8 0.19
18 5 0.12
19 1 0.02
20 1 0.02
21 11 0.26
22 17 0.40
ACGTcount: A:0.66, C:0.17, G:0.07, T:0.10
Consensus pattern (20 bp):
CAAAACAGTAAAAAACAATA
Found at i:50277177 original size:21 final size:22
Alignment explanation
Indices: 50277144--50277196 Score: 63
Period size: 21 Copynumber: 2.4 Consensus size: 22
50277134 CTAAAACAGT
50277144 AAAAAAAGCACCAAAACAACAAC
1 AAAAAAA-CACCAAAACAACAAC
* *
50277167 AAAAAAA-ACCAAAACAGCACC
1 AAAAAAACACCAAAACAACAAC
*
50277188 AAAACAACA
1 AAAAAAACA
50277197 ATATAATTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
21 18 0.69
22 1 0.04
23 7 0.27
ACGTcount: A:0.70, C:0.26, G:0.04, T:0.00
Consensus pattern (22 bp):
AAAAAAACACCAAAACAACAAC
Found at i:50279792 original size:21 final size:20
Alignment explanation
Indices: 50279746--50279795 Score: 64
Period size: 21 Copynumber: 2.4 Consensus size: 20
50279736 AAAAAAAAAT
50279746 TATTATTTTTTATTATTTTA
1 TATTATTTTTTATTATTTTA
* *
50279766 TCATTATTTTTTATTGTTTTGC
1 T-ATTATTTTTTATTATTTT-A
50279788 TATTATTT
1 TATTATTT
50279796 CACTATTATA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
20 1 0.04
21 24 0.92
22 1 0.04
ACGTcount: A:0.20, C:0.04, G:0.04, T:0.72
Consensus pattern (20 bp):
TATTATTTTTTATTATTTTA
Found at i:50302697 original size:27 final size:27
Alignment explanation
Indices: 50302653--50302704 Score: 86
Period size: 27 Copynumber: 1.9 Consensus size: 27
50302643 AAAACAATGG
* *
50302653 CATGAAACATGTTGAAAGACAGTAACC
1 CATGAAACATGCTCAAAGACAGTAACC
50302680 CATGAAACATGCTCAAAGACAGTAA
1 CATGAAACATGCTCAAAGACAGTAA
50302705 GTAAAGGACC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.46, C:0.19, G:0.17, T:0.17
Consensus pattern (27 bp):
CATGAAACATGCTCAAAGACAGTAACC
Found at i:50307261 original size:1 final size:1
Alignment explanation
Indices: 50307255--50307298 Score: 70
Period size: 1 Copynumber: 44.0 Consensus size: 1
50307245 ATCCCTCCCT
* *
50307255 CCCCCCCCCCACCCCCCCCCCCCCCCCCCCCCCCCCCCCACCCC
1 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
50307299 ATAGTAAAAC
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
1 39 1.00
ACGTcount: A:0.05, C:0.95, G:0.00, T:0.00
Consensus pattern (1 bp):
C
Found at i:50307813 original size:30 final size:30
Alignment explanation
Indices: 50307779--50307849 Score: 81
Period size: 30 Copynumber: 2.4 Consensus size: 30
50307769 GCATATTTTA
*
50307779 ACCCAACTA-TTAGTAAATTCCTTTTTGGAC
1 ACCCAACTACTGA-TAAATTCCTTTTTGGAC
* * *
50307809 ACCCAACTACTGATAAATTTCTTTTTTGTC
1 ACCCAACTACTGATAAATTCCTTTTTGGAC
*
50307839 ACCCAATTACT
1 ACCCAACTACT
50307850 TAATTTTGTC
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
30 33 0.94
31 2 0.06
ACGTcount: A:0.30, C:0.25, G:0.07, T:0.38
Consensus pattern (30 bp):
ACCCAACTACTGATAAATTCCTTTTTGGAC
Found at i:50311867 original size:2 final size:2
Alignment explanation
Indices: 50311860--50311885 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
50311850 AAATAAAACA
50311860 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
50311886 CTCAATTTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:50314187 original size:13 final size:14
Alignment explanation
Indices: 50314169--50314197 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
50314159 CCCTTTTTCT
50314169 AATTTTCC-GGGAA
1 AATTTTCCTGGGAA
50314182 AATTTTCCTGGGAA
1 AATTTTCCTGGGAA
50314196 AA
1 AA
50314198 GTAAAAAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 8 0.53
14 7 0.47
ACGTcount: A:0.34, C:0.14, G:0.21, T:0.31
Consensus pattern (14 bp):
AATTTTCCTGGGAA
Found at i:50316215 original size:31 final size:31
Alignment explanation
Indices: 50316156--50316216 Score: 77
Period size: 31 Copynumber: 2.0 Consensus size: 31
50316146 ATAAAAAAAA
* ** *
50316156 CTTTTGAATAGTTCAATAACTTATATGAAAG
1 CTTTCGAATAGTTCAATAACAAAAATGAAAG
*
50316187 CTTTCGAATAGTTCAATGACAAAAATGAAA
1 CTTTCGAATAGTTCAATAACAAAAATGAAA
50316217 ACTTACCCAT
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.43, C:0.11, G:0.13, T:0.33
Consensus pattern (31 bp):
CTTTCGAATAGTTCAATAACAAAAATGAAAG
Found at i:50316959 original size:333 final size:332
Alignment explanation
Indices: 50316331--50317005 Score: 1332
Period size: 333 Copynumber: 2.0 Consensus size: 332
50316321 TTTTAGGGAC
50316331 AATGATTGATTATTTAATATATTTTTTTTAGAGAGAAAACGAATTACAAAAAGAAGACAAAATTA
1 AATGATTGATTATTTAATATATTTTTTTTAGAGAGAAAACGAATTACAAAAAGAAGACAAAATTA
50316396 GACTTGAGCCATTAGTCCACCCTGTTCAATCAAACTTAAAGCCCGTCTTCACGGGTGTTATCAGT
66 GACTTGAGCCATTAGTCCACCCTGTTCAATCAAACTTAAAGCCCGTCTTCACGGGTGTTATCAGT
50316461 AGCATCCAATTGTAGAAAACTCGACAAATAAGATAGGATATCATCATAAACATGAGGGCTTGCTT
131 AGCATCCAATTGTAGAAAACTCGACAAATAAGATAGGATATCATCATAAACATGAGGGCTTGCTT
50316526 GGCACACGGCCCACCCAAACGAGCTGATGATTGATGAGTAACCTTATTAGCATTTTAACGAATCC
196 GGCACACGGCCCACCCAAACGAGCTGATGATTGATGAGTAACCTTATTAGCATTTTAACGAATCC
50316591 AATAAAATATAAATGTTGAAATAACGATCGTAGATATTGACAATAATCAAATAAGGACAACCCAA
261 AATAAAATATAAATGTTGAAATAACGATCGTAGATATTGACAATAATCAAATAAGGACAACCCAA
*
50316656 GCAAACT
326 ACAAACT
50316663 AATGATTGATTATTTAATATATATTTTTTTAGAGAGAAAACGAATTACAAAAAGAAGACAAAATT
1 AATGATTGATTATTTAATATAT-TTTTTTTAGAGAGAAAACGAATTACAAAAAGAAGACAAAATT
50316728 AGACTTGAGCCATTAGTCCACCCTGTTCAATCAAACTTAAAGCCCGTCTTCACGGGTGTTATCAG
65 AGACTTGAGCCATTAGTCCACCCTGTTCAATCAAACTTAAAGCCCGTCTTCACGGGTGTTATCAG
50316793 TAGCATCCAATTGTAGAAAACTCGACAAATAAGATAGGATATCATCATAAACATGAGGGCTTGCT
130 TAGCATCCAATTGTAGAAAACTCGACAAATAAGATAGGATATCATCATAAACATGAGGGCTTGCT
50316858 TGGCACACGGCCCACCCAAACGAGCTGATGATTGATGAGTAACCTTATTAGCATTTTAACGAATC
195 TGGCACACGGCCCACCCAAACGAGCTGATGATTGATGAGTAACCTTATTAGCATTTTAACGAATC
50316923 CAATAAAATATAAATGTTGAAATAACGATCGTAGATATTGACAATAATCAAATAAGGACAACCCA
260 CAATAAAATATAAATGTTGAAATAACGATCGTAGATATTGACAATAATCAAATAAGGACAACCCA
50316988 AACAAACT
325 AACAAACT
50316996 AATGATTGAT
1 AATGATTGAT
50317006 GAGTAACTTT
Statistics
Matches: 341, Mismatches: 1, Indels: 1
0.99 0.00 0.00
Matches are distributed among these distances:
332 22 0.06
333 319 0.94
ACGTcount: A:0.40, C:0.17, G:0.16, T:0.27
Consensus pattern (332 bp):
AATGATTGATTATTTAATATATTTTTTTTAGAGAGAAAACGAATTACAAAAAGAAGACAAAATTA
GACTTGAGCCATTAGTCCACCCTGTTCAATCAAACTTAAAGCCCGTCTTCACGGGTGTTATCAGT
AGCATCCAATTGTAGAAAACTCGACAAATAAGATAGGATATCATCATAAACATGAGGGCTTGCTT
GGCACACGGCCCACCCAAACGAGCTGATGATTGATGAGTAACCTTATTAGCATTTTAACGAATCC
AATAAAATATAAATGTTGAAATAACGATCGTAGATATTGACAATAATCAAATAAGGACAACCCAA
ACAAACT
Found at i:50317100 original size:113 final size:111
Alignment explanation
Indices: 50316867--50317199 Score: 423
Period size: 113 Copynumber: 3.0 Consensus size: 111
50316857 TTGGCACACG
* ** *** *
50316867 GCCCACCCAAACGAGCTGATGATTGATGAGTAACCTTATTAGCATTTTAACGAATCCAATAAAAT
1 GCCCACCCAAACGAGCTGATGATTGATGAGTAACATTATTAATATTCCGATGAATCCAATAAAAT
* *
50316932 ATAAATGTTGAAATAACGATCGTAGATATTGACAATAATCAAATAAG
66 ATAAATGTTGAAATAACGATAGTAGAT-TTGACAATAATCAAATAAA
* * * * * *
50316979 GACAACCCAAACAAACTAATGATTGATGAGTAACTTTATTAATATTCCGATGAATCCAATAAAAT
1 GCCCACCCAAACGAGCTGATGATTGATGAGTAACATTATTAATATTCCGATGAATCCAATAAAAT
* *
50317044 AATAAATGTTGAAATAACGATTGTAGATGTTGACAATAATCCAATAAA
66 -ATAAATGTTGAAATAACGATAGTAGAT-TTGACAATAATCAAATAAA
* *
50317092 GCCCACCCAAACGAGTTGATGATTGATGAGTAACATTATTAATATTGCGATGAATCCAATAAAAC
1 GCCCACCCAAACGAGCTGATGATTGATGAGTAACATTATTAATATTCCGATGAATCCAATAAAA-
* * *
50317157 GATAGATGTTGAAATAACGATAGTAGATTTCGAGAATAATCAA
65 TATAAATGTTGAAATAACGATAGTAGATTT-GACAATAATCAA
50317200 TCAAAAGCCT
Statistics
Matches: 189, Mismatches: 29, Indels: 5
0.85 0.13 0.02
Matches are distributed among these distances:
112 55 0.29
113 134 0.71
ACGTcount: A:0.43, C:0.14, G:0.15, T:0.27
Consensus pattern (111 bp):
GCCCACCCAAACGAGCTGATGATTGATGAGTAACATTATTAATATTCCGATGAATCCAATAAAAT
ATAAATGTTGAAATAACGATAGTAGATTTGACAATAATCAAATAAA
Found at i:50317759 original size:37 final size:37
Alignment explanation
Indices: 50317717--50317825 Score: 92
Period size: 37 Copynumber: 3.2 Consensus size: 37
50317707 GTTGATGTAT
50317717 TTACTAACAATTGGACTAATTTCTCAATTGTTATAAA
1 TTACTAACAATTGGACTAATTTCTCAATTGTTATAAA
* * * *
50317754 TTACT----A-T-GACTAAATT-T-AAGTTGATGT-AT
1 TTACTAACAATTGGACTAATTTCTCAA-TTGTTATAAA
* *
50317783 TTACTAACAATTGGAGTGATTTCTCAATTGTTATAAA
1 TTACTAACAATTGGACTAATTTCTCAATTGTTATAAA
50317820 TTACTA
1 TTACTA
50317826 TGACTAAATT
Statistics
Matches: 52, Mismatches: 10, Indels: 20
0.63 0.12 0.24
Matches are distributed among these distances:
29 8 0.15
30 6 0.12
31 8 0.15
32 1 0.02
33 2 0.04
34 1 0.02
35 6 0.12
36 6 0.12
37 14 0.27
ACGTcount: A:0.36, C:0.11, G:0.11, T:0.42
Consensus pattern (37 bp):
TTACTAACAATTGGACTAATTTCTCAATTGTTATAAA
Found at i:50317783 original size:66 final size:66
Alignment explanation
Indices: 50317702--50317836 Score: 252
Period size: 66 Copynumber: 2.0 Consensus size: 66
50317692 AAATTAATAG
50317702 TTTAAGTTGATGTATTTACTAACAATTGGACTAATTTCTCAATTGTTATAAATTACTATGACTAA
1 TTTAAGTTGATGTATTTACTAACAATTGGACTAATTTCTCAATTGTTATAAATTACTATGACTAA
50317767 A
66 A
* *
50317768 TTTAAGTTGATGTATTTACTAACAATTGGAGTGATTTCTCAATTGTTATAAATTACTATGACTAA
1 TTTAAGTTGATGTATTTACTAACAATTGGACTAATTTCTCAATTGTTATAAATTACTATGACTAA
50317833 A
66 A
50317834 TTT
1 TTT
50317837 TGATAAATTA
Statistics
Matches: 67, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
66 67 1.00
ACGTcount: A:0.35, C:0.10, G:0.12, T:0.44
Consensus pattern (66 bp):
TTTAAGTTGATGTATTTACTAACAATTGGACTAATTTCTCAATTGTTATAAATTACTATGACTAA
A
Found at i:50318253 original size:26 final size:26
Alignment explanation
Indices: 50318218--50318275 Score: 82
Period size: 26 Copynumber: 2.3 Consensus size: 26
50318208 ATTTTCTAAC
* *
50318218 TTTA-CCCCTATCACCATGTGTTAGT
1 TTTATCCCCTATCACCATGTGTGAAT
*
50318243 TTTATCCCCTATCATCATGTGTGAAT
1 TTTATCCCCTATCACCATGTGTGAAT
50318269 TTTATCC
1 TTTATCC
50318276 GATTCTTTTC
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
25 4 0.14
26 25 0.86
ACGTcount: A:0.21, C:0.26, G:0.10, T:0.43
Consensus pattern (26 bp):
TTTATCCCCTATCACCATGTGTGAAT
Found at i:50318577 original size:22 final size:22
Alignment explanation
Indices: 50318550--50318594 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 22
50318540 AAGTCCACTC
50318550 ATATTATTATT-TTTAAATATTT
1 ATATTA-TATTATTTAAATATTT
*
50318572 ATATTATATTATTTTAATATTT
1 ATATTATATTATTTAAATATTT
50318594 A
1 A
50318595 ATAATTTTAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 4 0.19
22 17 0.81
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (22 bp):
ATATTATATTATTTAAATATTT
Found at i:50318581 original size:24 final size:25
Alignment explanation
Indices: 50318566--50318612 Score: 55
Period size: 22 Copynumber: 2.0 Consensus size: 25
50318556 TTATTTTTAA
50318566 ATATTT-AT-ATTATATTA-TTTTA
1 ATATTTAATAATTATATTATTTTTA
*
50318588 ATATTTAATAATTTTATATATTTTT
1 ATATTTAATAATTATAT-TATTTTT
50318613 TATTTATTGA
Statistics
Matches: 20, Mismatches: 1, Indels: 4
0.80 0.04 0.16
Matches are distributed among these distances:
22 6 0.30
23 2 0.10
24 6 0.30
25 2 0.10
26 4 0.20
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (25 bp):
ATATTTAATAATTATATTATTTTTA
Found at i:50328899 original size:3 final size:3
Alignment explanation
Indices: 50328891--50328919 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
50328881 CATGTCTCTG
50328891 TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
50328920 GTTACTGTCC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (3 bp):
TTC
Found at i:50333135 original size:16 final size:17
Alignment explanation
Indices: 50333114--50333153 Score: 57
Period size: 16 Copynumber: 2.5 Consensus size: 17
50333104 GGCTCGAAAC
50333114 CGATCAATCGAC-TGGT
1 CGATCAATCGACATGGT
*
50333130 CGATCAA-CGCCATGGT
1 CGATCAATCGACATGGT
50333146 CGATCAAT
1 CGATCAAT
50333154 GAAGTATCGA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
15 3 0.14
16 18 0.86
ACGTcount: A:0.28, C:0.28, G:0.23, T:0.23
Consensus pattern (17 bp):
CGATCAATCGACATGGT
Found at i:50334310 original size:16 final size:16
Alignment explanation
Indices: 50334289--50334320 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
50334279 TACGAGCATG
50334289 AAATTATTCCTAATGT
1 AAATTATTCCTAATGT
50334305 AAATTATTCCTAATGT
1 AAATTATTCCTAATGT
50334321 TCTCTTGCAC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.38, C:0.12, G:0.06, T:0.44
Consensus pattern (16 bp):
AAATTATTCCTAATGT
Found at i:50340021 original size:162 final size:160
Alignment explanation
Indices: 50339838--50340131 Score: 493
Period size: 162 Copynumber: 1.8 Consensus size: 160
50339828 TTTTTTTTAC
50339838 TCTCTAAATTTGTGGGTTGCTTTTGATTTTAGTTGAAATTTTAGTATTTTAGATTACTCCTGGAA
1 TCTCTAAATTTGTGGGTTGCTTTTGATTTTAGTTGAAATTTTAGTATTTTAGATTACTCCTGGAA
* * * * *
50339903 TTTTTTTTGATATACATATGGAATGATTGTGTTGGAATTTGAGA-TTCTTTGTTGGTTTAACTTA
66 -TTTCTTTGACAT--ATATGGAATGATTGTATTGGAATTTGA-ATTTCTTTCTTGGTATAACTTA
50339967 TTGATGCTTTATGCTCTCTATTTCAATACCCATG
127 TTGATGCTTTATGCTCTCTATTTCAATACCCATG
50340001 TCTC-AAATTTGTGGGTTGCTTTTGATTTTAGTTGAAATTTTAGTATTTTAGATTACTCCTGGAA
1 TCTCTAAATTTGTGGGTTGCTTTTGATTTTAGTTGAAATTTTAGTATTTTAGATTACTCCTGGAA
50340065 TTTCTTTGACATATATGGAATGATTGTATTGGAATTTGAATTTCTTTCTTGGTATAACTTATTGA
66 TTTCTTTGACATATATGGAATGATTGTATTGGAATTTGAATTTCTTTCTTGGTATAACTTATTGA
50340130 TG
131 TG
50340132 TTCCATGATA
Statistics
Matches: 125, Mismatches: 5, Indels: 6
0.92 0.04 0.04
Matches are distributed among these distances:
158 1 0.01
159 50 0.40
161 10 0.08
162 60 0.48
163 4 0.03
ACGTcount: A:0.23, C:0.10, G:0.18, T:0.49
Consensus pattern (160 bp):
TCTCTAAATTTGTGGGTTGCTTTTGATTTTAGTTGAAATTTTAGTATTTTAGATTACTCCTGGAA
TTTCTTTGACATATATGGAATGATTGTATTGGAATTTGAATTTCTTTCTTGGTATAACTTATTGA
TGCTTTATGCTCTCTATTTCAATACCCATG
Found at i:50364106 original size:205 final size:201
Alignment explanation
Indices: 50363580--50364124 Score: 583
Period size: 205 Copynumber: 2.7 Consensus size: 201
50363570 TACAAAATTA
* * * * * * *
50363580 AAAACTACCCATAGCCCCTC-CCAACCCTTAAATAGGAGGTTAATGCGCTTTAGTACACTTGAAC
1 AAAACTACTCATAACTCCTCTCCAACCCTTAAATAGGAGGATAATGCGCTTCAGCACACTCGAAC
* * ** *
50363644 CTACGTCCTCTTGTACTGTCAACAATATCGATACCAATC-AAGT--TCCTCAATCGGCAACTTAA
66 CAACGTCCTCTTGTACTGACAACAATATCGATACCAATCGAAGTAAGACTCAATCGACAACTTAA
* * *
50363706 ACATGTATTATGCA--TTTTTTTTAACATCTCATTATTGGTTCTTATCATCTACTCTTTTTTATG
131 ACATGTATTATGCATTTTTTTTTTAACATCTCATTATAGGTTCTTATCATCTACTC--TTTGATA
*
50363769 CAAAGCCT
194 CAAAACCT
* *
50363777 AAAATTACTCATAACTCCTCTCCAACCCTTAAGTAGGAGGAT-A--CGCTTCAGCACACTCGAAC
1 AAAACTACTCATAACTCCTCTCCAACCCTTAAATAGGAGGATAATGCGCTTCAGCACACTCGAAC
* * * * *
50363839 CAACGTCCTCTTGTACTGGCAACAATGTCGATACCAATCG-AGCTAAGATTAAATTGACAACTTA
66 CAACGTCCTCTTGTACTGACAACAATATCGATACCAATCGAAG-TAAGACTCAATCGACAACTTA
* *
50363903 AACATGTATTATACATTTTTTTTTTAACATTAATCTCATTATAGGTTCTTATCTATCTGCTC-TT
130 AACATGTATTATGCATTTTTTTTTTAAC----ATCTCATTATAGGTTCTTATC-ATCTACTCTTT
50363967 GATACAAAACCT
190 GATACAAAACCT
* ** *
50363979 AAAACTACTTATAGTTCCTCAT-CAACCCTTAAATAGGAGGATAATGCGCTTCAGCGCACTCGAA
1 AAAACTACTCATAACTCCTC-TCCAACCCTTAAATAGGAGGATAATGCGCTTCAGCACACTCGAA
* * * ** * * *
50364043 CCCACGCCCTCCTACACTGACAACAATACCGATACTAATCGAAGTAAGACTCAATCAACAACTTA
65 CCAACGTCCTCTTGTACTGACAACAATATCGATACCAATCGAAGTAAGACTCAATCGACAACTTA
*
50364108 AACATGAATTATGCATT
130 AACATGTATTATGCATT
50364125 GTTGAAATTA
Statistics
Matches: 286, Mismatches: 45, Indels: 26
0.80 0.13 0.07
Matches are distributed among these distances:
195 54 0.19
196 1 0.00
197 17 0.06
198 45 0.16
200 11 0.04
202 46 0.16
203 2 0.01
204 20 0.07
205 88 0.31
206 2 0.01
ACGTcount: A:0.32, C:0.25, G:0.12, T:0.31
Consensus pattern (201 bp):
AAAACTACTCATAACTCCTCTCCAACCCTTAAATAGGAGGATAATGCGCTTCAGCACACTCGAAC
CAACGTCCTCTTGTACTGACAACAATATCGATACCAATCGAAGTAAGACTCAATCGACAACTTAA
ACATGTATTATGCATTTTTTTTTTAACATCTCATTATAGGTTCTTATCATCTACTCTTTGATACA
AAACCT
Found at i:50373355 original size:19 final size:19
Alignment explanation
Indices: 50373314--50373355 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
50373304 TCATACTAAT
* * *
50373314 TTTTTGAATTTATTTTTAT
1 TTTTTGAATATATTTATAA
50373333 TTTTTGAATATATTTATAA
1 TTTTTGAATATATTTATAA
50373352 TTTT
1 TTTT
50373356 CAAATTATTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.26, C:0.00, G:0.05, T:0.69
Consensus pattern (19 bp):
TTTTTGAATATATTTATAA
Found at i:50375837 original size:18 final size:19
Alignment explanation
Indices: 50375809--50375844 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
50375799 TTTTAAGTTA
50375809 CAATGTATAATTATAAATT
1 CAATGTATAATTATAAATT
*
50375828 CAAT-TATAATTGTAAAT
1 CAATGTATAATTATAAAT
50375845 ATAAATAATA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 12 0.75
19 4 0.25
ACGTcount: A:0.47, C:0.06, G:0.06, T:0.42
Consensus pattern (19 bp):
CAATGTATAATTATAAATT
Found at i:50378995 original size:23 final size:23
Alignment explanation
Indices: 50378971--50379069 Score: 162
Period size: 23 Copynumber: 4.3 Consensus size: 23
50378961 TGCTGGGCAA
*
50378971 CAGAGAGCACATAAAGTGCTAAA
1 CAGAGAGCACATAAAGTGCTAAT
*
50378994 CAGAGAGCACACAAAGTGCTAAT
1 CAGAGAGCACATAAAGTGCTAAT
*
50379017 CAGAGAGCACACAAAGTGCTAAT
1 CAGAGAGCACATAAAGTGCTAAT
*
50379040 CAGAGAGCACATACAGTGCTAAT
1 CAGAGAGCACATAAAGTGCTAAT
50379063 CAGAGAG
1 CAGAGAG
50379070 TACGCTAGTG
Statistics
Matches: 72, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 72 1.00
ACGTcount: A:0.43, C:0.20, G:0.23, T:0.13
Consensus pattern (23 bp):
CAGAGAGCACATAAAGTGCTAAT
Found at i:50381001 original size:25 final size:25
Alignment explanation
Indices: 50380973--50381022 Score: 91
Period size: 25 Copynumber: 2.0 Consensus size: 25
50380963 AATTGGGAAG
50380973 ATCTAAATCATCTGATATAAAGACT
1 ATCTAAATCATCTGATATAAAGACT
*
50380998 ATCTAAATCCTCTGATATAAAGACT
1 ATCTAAATCATCTGATATAAAGACT
50381023 CTATGGCATG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.42, C:0.18, G:0.08, T:0.32
Consensus pattern (25 bp):
ATCTAAATCATCTGATATAAAGACT
Found at i:50388284 original size:17 final size:17
Alignment explanation
Indices: 50388262--50388294 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
50388252 TCAAAAGGAA
50388262 TTTGAGGGAAATAAAGC
1 TTTGAGGGAAATAAAGC
50388279 TTTGAGGGAAATAAAG
1 TTTGAGGGAAATAAAG
50388295 AAGGATTAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.42, C:0.03, G:0.30, T:0.24
Consensus pattern (17 bp):
TTTGAGGGAAATAAAGC
Found at i:50389188 original size:19 final size:20
Alignment explanation
Indices: 50389164--50389201 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
50389154 TTTGATAGAC
50389164 TTGGGTAATAA-ATATGGTG
1 TTGGGTAATAATATATGGTG
*
50389183 TTGGGTTATAATATATGGT
1 TTGGGTAATAATATATGGT
50389202 AAATTGGTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.29, C:0.00, G:0.29, T:0.42
Consensus pattern (20 bp):
TTGGGTAATAATATATGGTG
Found at i:50389804 original size:25 final size:24
Alignment explanation
Indices: 50389767--50389814 Score: 60
Period size: 25 Copynumber: 2.0 Consensus size: 24
50389757 TCCATTCATG
*
50389767 TATTTTTATTTTTAGTAAGAGTTT
1 TATTTTTAATTTTAGTAAGAGTTT
* *
50389791 TATTTTTCAATTTTATTGAGAGTT
1 TATTTTT-AATTTTAGTAAGAGTT
50389815 CGAGTGTTTG
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
24 7 0.35
25 13 0.65
ACGTcount: A:0.25, C:0.02, G:0.12, T:0.60
Consensus pattern (24 bp):
TATTTTTAATTTTAGTAAGAGTTT
Found at i:50395990 original size:31 final size:32
Alignment explanation
Indices: 50395951--50396021 Score: 92
Period size: 31 Copynumber: 2.3 Consensus size: 32
50395941 GGGCAAATTA
*
50395951 AGCCTTGAACTTGACAATTGTTCCCACATTGG
1 AGCCTTGAACTAGACAATTGTTCCCACATTGG
* * *
50395983 -GCCTTGAACTAGGCAATTGTTCTCTCATTGG
1 AGCCTTGAACTAGACAATTGTTCCCACATTGG
50396014 AG-CTTGAA
1 AGCCTTGAA
50396022 TTTAATTTTT
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
31 33 0.97
32 1 0.03
ACGTcount: A:0.24, C:0.23, G:0.21, T:0.32
Consensus pattern (32 bp):
AGCCTTGAACTAGACAATTGTTCCCACATTGG
Found at i:50398262 original size:15 final size:15
Alignment explanation
Indices: 50398244--50398275 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
50398234 ATTTTTGAAG
*
50398244 AAAGTTTTTTTTTTA
1 AAAGTATTTTTTTTA
50398259 AAAGTATTTTTTTTA
1 AAAGTATTTTTTTTA
50398274 AA
1 AA
50398276 TAAAGAAATT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.34, C:0.00, G:0.06, T:0.59
Consensus pattern (15 bp):
AAAGTATTTTTTTTA
Found at i:50405507 original size:53 final size:51
Alignment explanation
Indices: 50405417--50405515 Score: 126
Period size: 53 Copynumber: 1.9 Consensus size: 51
50405407 AAATTACTGA
* * * * *
50405417 TACTTATATTTTAAAAATGTTTAATGTAGTACTTGAATTTTTAATATATAG
1 TACTTATATTTCAAAAATGTTCAATATAGTACATGAATTATTAATATATAG
*
50405468 TACTTATACTTTCATAAAATGTTCAATATGGTACATGAATTATTAATA
1 TACTTATA-TTTCA-AAAATGTTCAATATAGTACATGAATTATTAATA
50405516 CGTGATTTAT
Statistics
Matches: 40, Mismatches: 6, Indels: 2
0.83 0.12 0.04
Matches are distributed among these distances:
51 8 0.20
52 4 0.10
53 28 0.70
ACGTcount: A:0.38, C:0.07, G:0.09, T:0.45
Consensus pattern (51 bp):
TACTTATATTTCAAAAATGTTCAATATAGTACATGAATTATTAATATATAG
Found at i:50411454 original size:19 final size:17
Alignment explanation
Indices: 50411427--50411470 Score: 52
Period size: 17 Copynumber: 2.5 Consensus size: 17
50411417 AATATTTACA
*
50411427 TTAAAATAATATTATATAT
1 TTAATATAA-ATT-TATAT
*
50411446 TTAATATAAATTTATTT
1 TTAATATAAATTTATAT
50411463 TTAATATA
1 TTAATATA
50411471 TTTTAAATTA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
17 12 0.52
18 3 0.13
19 8 0.35
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (17 bp):
TTAATATAAATTTATAT
Found at i:50411753 original size:19 final size:19
Alignment explanation
Indices: 50411721--50411763 Score: 54
Period size: 19 Copynumber: 2.3 Consensus size: 19
50411711 AAATAGGAAC
50411721 ATTA-TAAAAGAAAA-AAA
1 ATTATTAAAAGAAAATAAA
*
50411738 TATTATTAAAATAAAATAAA
1 -ATTATTAAAAGAAAATAAA
50411758 ATTATT
1 ATTATT
50411764 GAGTATGCAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
18 4 0.18
19 15 0.68
20 3 0.14
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (19 bp):
ATTATTAAAAGAAAATAAA
Found at i:50415695 original size:173 final size:173
Alignment explanation
Indices: 50415322--50415773 Score: 679
Period size: 173 Copynumber: 2.6 Consensus size: 173
50415312 CTTTTACAGG
* * *
50415322 ATTACACATTAAGTTTTCAAGTTCTATAAGCTCACATACATGGAGTATACTAGTATTAACAAGCT
1 ATTACACATTAAGTTTTCAAGTTCTATGAGCTCACAAACATGGAATATACTAGTATTAACAAGCT
* * * * *
50415387 TACATTCACCATTTTGAAACGATACAATTTCGTTACCATCGAGAAAACAATGACAACGAGGTTAT
66 TACCTTCACCATTTCGAAACGATACAATTTCATT-CCATCAAGAAAACAATGACAACGAGGTAAT
* *
50415452 TGCAACCAAATTTAGTACCGGTTCGAGCACTTAATGAATTAAGG
130 TGCAACCAAATTTAGTACCGATTCGAGCACTTAATGAATTAAGA
* * * * * *
50415496 ATTACACATCAAGTTTTCATGTTCTATGAGCTCATAGACATGGAATATGCTAGTATCAACAAGCT
1 ATTACACATTAAGTTTTCAAGTTCTATGAGCTCACAAACATGGAATATACTAGTATTAACAAGCT
* *
50415561 TACCTTCACCATTTCGAAACAAAACAATTTCATTCCATCAAGAAAACAATGACAACGAGGTAATT
66 TACCTTCACCATTTCGAAACGATACAATTTCATTCCATCAAGAAAACAATGACAACGAGGTAATT
* *
50415626 GCAACCAAATTTAGTACTGATTCGAGCACTTAATGAATTGAGA
131 GCAACCAAATTTAGTACCGATTCGAGCACTTAATGAATTAAGA
* *
50415669 ATTACACATTAAGTTTCCAAGTTCTATGAGCTCCCAAACATGGAATATACTAGTATTAACAAGCT
1 ATTACACATTAAGTTTTCAAGTTCTATGAGCTCACAAACATGGAATATACTAGTATTAACAAGCT
*
50415734 TACCTTCACCATTTCGAATCGATACAATTTCATTTCCATC
66 TACCTTCACCATTTCGAAACGATACAATTTCA-TTCCATC
50415774 TGAAAATAAC
Statistics
Matches: 247, Mismatches: 30, Indels: 2
0.89 0.11 0.01
Matches are distributed among these distances:
173 154 0.62
174 93 0.38
ACGTcount: A:0.37, C:0.20, G:0.13, T:0.30
Consensus pattern (173 bp):
ATTACACATTAAGTTTTCAAGTTCTATGAGCTCACAAACATGGAATATACTAGTATTAACAAGCT
TACCTTCACCATTTCGAAACGATACAATTTCATTCCATCAAGAAAACAATGACAACGAGGTAATT
GCAACCAAATTTAGTACCGATTCGAGCACTTAATGAATTAAGA
Found at i:50420940 original size:52 final size:52
Alignment explanation
Indices: 50420862--50420967 Score: 203
Period size: 52 Copynumber: 2.0 Consensus size: 52
50420852 CCTCGTGATA
*
50420862 TACAAAACACTTGGTAAAAATATCATGGAAGCCCTCATACAAGGAGTCAGAT
1 TACAAAACACTTGGTAAAAATATCATGGAAGCCCACATACAAGGAGTCAGAT
50420914 TACAAAACACTTGGTAAAAATATCATGGAAGCCCACATACAAGGAGTCAGAT
1 TACAAAACACTTGGTAAAAATATCATGGAAGCCCACATACAAGGAGTCAGAT
50420966 TA
1 TA
50420968 TATTTTATCA
Statistics
Matches: 53, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
52 53 1.00
ACGTcount: A:0.43, C:0.19, G:0.17, T:0.21
Consensus pattern (52 bp):
TACAAAACACTTGGTAAAAATATCATGGAAGCCCACATACAAGGAGTCAGAT
Found at i:50426657 original size:41 final size:42
Alignment explanation
Indices: 50426605--50426709 Score: 158
Period size: 41 Copynumber: 2.5 Consensus size: 42
50426595 AATTCGTAAT
* *
50426605 AAATGCAAAATAAGCTAAGAACTAGCTTCA-ATATTAAATAA
1 AAATGCAAAATAAGCTAAGAACTAACTTCAGAAATTAAATAA
* *
50426646 AAATGCAAAATAAGCTAAGGACTAACTTCAGAAATTGAATAA
1 AAATGCAAAATAAGCTAAGAACTAACTTCAGAAATTAAATAA
50426688 AAATGCAAAAATAAGCTAAGAA
1 AAATGC-AAAATAAGCTAAGAA
50426710 AAAACAAGAA
Statistics
Matches: 57, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
41 28 0.49
42 15 0.26
43 14 0.25
ACGTcount: A:0.55, C:0.11, G:0.12, T:0.21
Consensus pattern (42 bp):
AAATGCAAAATAAGCTAAGAACTAACTTCAGAAATTAAATAA
Found at i:50427261 original size:19 final size:19
Alignment explanation
Indices: 50427223--50427261 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
50427213 TTCCTTCTCC
* **
50427223 TTTTTTTTTAATTTGTTTA
1 TTTTTTTTTAAATTCCTTA
50427242 TTTTTTTTTAAATTCCTTA
1 TTTTTTTTTAAATTCCTTA
50427261 T
1 T
50427262 GCTTTGAAAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.18, C:0.05, G:0.03, T:0.74
Consensus pattern (19 bp):
TTTTTTTTTAAATTCCTTA
Found at i:50428444 original size:11 final size:11
Alignment explanation
Indices: 50428428--50428453 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
50428418 CATATTTCAT
50428428 ATTTTATTTAA
1 ATTTTATTTAA
50428439 ATTTTATTTAA
1 ATTTTATTTAA
50428450 ATTT
1 ATTT
50428454 CATCTATTCT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (11 bp):
ATTTTATTTAA
Found at i:50432155 original size:180 final size:180
Alignment explanation
Indices: 50431852--50432710 Score: 1345
Period size: 180 Copynumber: 4.7 Consensus size: 180
50431842 ACATATGGCC
50431852 TATGGGCATAGCTAACTTCTAATTTTATATATGAACTAAAACAACTTCAAATTCTTAAAACAAGA
1 TATGGGCATAGCTAACTTCTAA-TTTATATATGAACTAAAACAACTTCAAATTCTTAAAACAAGA
** *
50431917 GT-AAAATGATTGATGAAATTATCCACAATTATCAAATCAAAATTAATAAACAAAAACAGAAAGA
65 GTAAAAAAAATTGATCAAATTATCCACAATTATCAAATCAAAATTAATAAACAAAAACAGAAAGA
50431981 AAGATACCATTTGTTCTTGGATTTCAGCTAATAGAAAAAAAATGTCTTTACA
130 AAGATACCATTTGTTCTTGGATTTCAGCTAATAGAAAAAAAAT-TCTTTACA
*
50432033 TATGGGCATAGCTAACTTCTAATTTATGTATGAACTAAAACAACTTCAAATTCTTAAAACAAGAG
1 TATGGGCATAGCTAACTTCTAATTTATATATGAACTAAAACAACTTCAAATTCTTAAAACAAGAG
*
50432098 T-AAAAAGATTGATCAAATTATCCACAATTATCAAATCAAAATTAATAAACAAAAACAGAAAGAA
66 TAAAAAAAATTGATCAAATTATCCACAATTATCAAATCAAAATTAATAAACAAAAACAGAAAGAA
50432162 AGATACCATTTGTTCTTGGATTTCAGCTAATAGAAAAAAAAATTCTTTACA
131 AGATACCATTTGTTCTTGGATTTCAGCTAATAG-AAAAAAAATTCTTTACA
* *
50432213 TACGGGCATAGCTAACTTCTAATTTATATATGAACTAAAACAACTCCAAATTCTTAAAACAAGAG
1 TATGGGCATAGCTAACTTCTAATTTATATATGAACTAAAACAACTTCAAATTCTTAAAACAAGAG
* * *
50432278 TAAAAAAAAATGATCAAATTATACACAATTATCAAATCAAAATTAATAAGC---AA-AGAAAGAA
66 TAAAAAAAATTGATCAAATTATCCACAATTATCAAATCAAAATTAATAAACAAAAACAGAAAGAA
* *
50432339 ATATACCATTTGTTCTTGGATTTCAGCTAATAGAAAAACGAAATTCTTTATA
131 AGATACCATTTGTTCTTGGATTTCAGCTAATAGAAAAA--AAATTCTTTACA
*
50432391 TATGGACATAGCTAACTTCTAATTTATATATGAACTAAAACAACTTCAAATTCTTAAAACAAGAG
1 TATGGGCATAGCTAACTTCTAATTTATATATGAACTAAAACAACTTCAAATTCTTAAAACAAGAG
* *
50432456 TAAAAAAAATTGATCAAATAATCCACAATTATCAAATCAAAATTAATAAACAAAAGCAGAAAGAA
66 TAAAAAAAATTGATCAAATTATCCACAATTATCAAATCAAAATTAATAAAC-AAA--A-ACAGAA
* *
50432521 AGAAAGATACCATTTGTTCTTGGATTTCAACTAATAGAAAAAAAAAATC-TTACA
127 AGAAAGATACCATTTGTTCTTGGATTTCAGCTAATAG-AAAAAAAATTCTTTACA
* * * *
50432575 TAAGGGCATAGCTAACTTCTAATTTAGATATATGAACTAAAACAACTTAAAAATCTTAAAAGAAG
1 TATGGGCATAGCTAACTTCTAATTT--ATATATGAACTAAAACAACTTCAAATTCTTAAAACAAG
* *
50432640 AGTAAAAAAAAATTGATCAAATTATCCACAATTATCAAATTAAAATTAATAACCAAAAACAGAAA
64 AGT-AAAAAAAATTGATCAAATTATCCACAATTATCAAATCAAAATTAATAAACAAAAACAGAAA
50432705 GAAAGA
128 GAAAGA
50432711 AAGAAAGATA
Statistics
Matches: 630, Mismatches: 32, Indels: 30
0.91 0.05 0.04
Matches are distributed among these distances:
176 5 0.01
177 40 0.06
178 122 0.19
180 208 0.33
181 76 0.12
183 12 0.02
184 29 0.05
185 6 0.01
186 80 0.13
187 52 0.08
ACGTcount: A:0.49, C:0.13, G:0.10, T:0.28
Consensus pattern (180 bp):
TATGGGCATAGCTAACTTCTAATTTATATATGAACTAAAACAACTTCAAATTCTTAAAACAAGAG
TAAAAAAAATTGATCAAATTATCCACAATTATCAAATCAAAATTAATAAACAAAAACAGAAAGAA
AGATACCATTTGTTCTTGGATTTCAGCTAATAGAAAAAAAATTCTTTACA
Found at i:50433951 original size:90 final size:90
Alignment explanation
Indices: 50433827--50433991 Score: 226
Period size: 90 Copynumber: 1.8 Consensus size: 90
50433817 CGGTGTAGTC
* * * *
50433827 AGGAATAATTGTTAAGTTCAAGCTCTAATATGAGAATAATTGTCTAGTTC-AGAGATTAATTTGG
1 AGGAACAATTGTTAAGTTCAAGCTCTAATATGAGAATAATTATCAAGTTCAAG-GATTAACTTGG
50433891 ACAAAAAAAAATCCAAACCCCAATGT
65 ACAAAAAAAAATCCAAACCCCAATGT
* * *
50433917 AGGAACAATTGTCT-AGTTCAAGTTGTAATGTGAGAATAATTATCAAGTTCAAGGATTAACTTGG
1 AGGAACAATTGT-TAAGTTCAAGCTCTAATATGAGAATAATTATCAAGTTCAAGGATTAACTTGG
*
50433981 ACAATAAAAAA
65 ACAAAAAAAAA
50433992 GTTCAAGCTT
Statistics
Matches: 65, Mismatches: 8, Indels: 4
0.84 0.10 0.05
Matches are distributed among these distances:
90 62 0.95
91 3 0.05
ACGTcount: A:0.42, C:0.12, G:0.17, T:0.29
Consensus pattern (90 bp):
AGGAACAATTGTTAAGTTCAAGCTCTAATATGAGAATAATTATCAAGTTCAAGGATTAACTTGGA
CAAAAAAAAATCCAAACCCCAATGT
Found at i:50435905 original size:29 final size:29
Alignment explanation
Indices: 50435860--50435928 Score: 84
Period size: 29 Copynumber: 2.3 Consensus size: 29
50435850 TGACAGGGAT
* * *
50435860 TAGATCAAATTAGTCCCTCTATTATTAAA
1 TAGATCAAATTAATCCCTATACTATTAAA
*
50435889 TAGATCAATTTAATCCCTATACTATTAAA
1 TAGATCAAATTAATCCCTATACTATTAAA
*
50435918 AAGAATCAAAT
1 TAG-ATCAAAT
50435929 AAGTCCAAAT
Statistics
Matches: 33, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
29 27 0.82
30 6 0.18
ACGTcount: A:0.43, C:0.16, G:0.06, T:0.35
Consensus pattern (29 bp):
TAGATCAAATTAATCCCTATACTATTAAA
Found at i:50440479 original size:31 final size:31
Alignment explanation
Indices: 50440444--50440505 Score: 124
Period size: 31 Copynumber: 2.0 Consensus size: 31
50440434 TGGATGCAAA
50440444 CAAGTGAAAAAGTATATAAGCTACAACTTAT
1 CAAGTGAAAAAGTATATAAGCTACAACTTAT
50440475 CAAGTGAAAAAGTATATAAGCTACAACTTAT
1 CAAGTGAAAAAGTATATAAGCTACAACTTAT
50440506 GTGCAAAAAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.48, C:0.13, G:0.13, T:0.26
Consensus pattern (31 bp):
CAAGTGAAAAAGTATATAAGCTACAACTTAT
Found at i:50440514 original size:29 final size:29
Alignment explanation
Indices: 50440446--50440514 Score: 104
Period size: 31 Copynumber: 2.3 Consensus size: 29
50440436 GATGCAAACA
50440446 AGTGAAAAAGTATATAAGCTACAACTTAT
1 AGTGAAAAAGTATATAAGCTACAACTTAT
50440475 CAAGTGAAAAAGTATATAAGCTACAACTTAT
1 --AGTGAAAAAGTATATAAGCTACAACTTAT
50440506 -GTGCAAAAA
1 AGTG-AAAAA
50440515 TGATATCTAA
Statistics
Matches: 37, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
28 3 0.08
29 5 0.14
31 29 0.78
ACGTcount: A:0.49, C:0.12, G:0.14, T:0.25
Consensus pattern (29 bp):
AGTGAAAAAGTATATAAGCTACAACTTAT
Found at i:50441539 original size:185 final size:182
Alignment explanation
Indices: 50441100--50441563 Score: 546
Period size: 185 Copynumber: 2.5 Consensus size: 182
50441090 CACCGCTTAA
* * *
50441100 TCCATTTGAATCAAT---AA-AACAGTTTCACGCTAGAATCTAGATTGAAATTTAAAAAATCCAC
1 TCCATTTGAATCAATAAAAATAACAGTTTCATGCTAGAATCTAG-TTCAAATTT-AAAAATCCAA
* * * ** *
50441161 CGCAAAATTAACACTTCCCAGATGCCCGAATTAATAGTCCGTTTGAATCATACTAGAATCTACAT
64 AGCAAAATTAACACTTCCCAGATGCCCAAATCACCAGTCCATTTGAATCATACTAGAATCTACAT
* * *
50441226 CCAATTTTCAAAAATCAATGCAAAATTAACACTCCCAGATGCCCAAATCAATAG
129 CCAAATTTCAAAAATCAACGCAAAATTAACACTCCCAGATGCACAAATCAATAG
* * * * *
50441280 TCCATTTGAATCAATAAAAATAACAGTGTCATGTTAGAATCTACATTCAAACATAAAAAATCCAT
1 TCCATTTGAATCAATAAAAATAACAGTTTCATGCTAGAATCTA-GTTCAAA-TTTAAAAATCCA-
*
50441345 CAA--AAAATTAACACTTCCCAGACGCCCAAAATCACCAGTCCATTTGAATCATACTAGAATCTA
63 -AAGCAAAATTAACACTTCCCAGATGCCC-AAATCACCAGTCCATTTGAATCATACTAGAATCTA
**
50441408 CATCCAAATTTCAAAAATCCCCGCAAAATTAACACTACCCAGATGCACAAATCAATAG
126 CATCCAAATTTCAAAAATCAACGCAAAATTAACACT-CCCAGATGCACAAATCAATAG
* * * * *
50441466 TTCATTTGCATCAGTAAAAATTAACAGTTTCATTG-TAGAATCTAGTTCAAATTTCAAAATTCAA
1 TCCATTTGAATCAATAAAAA-TAACAGTTTCA-TGCTAGAATCTAGTTCAAATTTAAAAATCCAA
* *
50441530 AGCAAAATTAATACTACCCAGATGCCCAAATCAC
64 AGCAAAATTAACACTTCCCAGATGCCCAAATCAC
50441564 TAAATCCCCC
Statistics
Matches: 238, Mismatches: 32, Indels: 24
0.81 0.11 0.08
Matches are distributed among these distances:
180 15 0.06
183 4 0.02
184 63 0.26
185 92 0.39
186 43 0.18
187 19 0.08
188 2 0.01
ACGTcount: A:0.42, C:0.23, G:0.09, T:0.26
Consensus pattern (182 bp):
TCCATTTGAATCAATAAAAATAACAGTTTCATGCTAGAATCTAGTTCAAATTTAAAAATCCAAAG
CAAAATTAACACTTCCCAGATGCCCAAATCACCAGTCCATTTGAATCATACTAGAATCTACATCC
AAATTTCAAAAATCAACGCAAAATTAACACTCCCAGATGCACAAATCAATAG
Found at i:50442277 original size:2 final size:2
Alignment explanation
Indices: 50442270--50442313 Score: 79
Period size: 2 Copynumber: 22.0 Consensus size: 2
50442260 ATTGTGAGCT
*
50442270 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GG GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
50442312 GA
1 GA
50442314 AAGGATTTAG
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:50442840 original size:13 final size:13
Alignment explanation
Indices: 50442822--50442846 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
50442812 TGAATTGAAA
50442822 TATTTCGGTTAAC
1 TATTTCGGTTAAC
50442835 TATTTCGGTTAA
1 TATTTCGGTTAA
50442847 TTTAGTTGGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.24, C:0.12, G:0.16, T:0.48
Consensus pattern (13 bp):
TATTTCGGTTAAC
Found at i:50446267 original size:33 final size:33
Alignment explanation
Indices: 50446215--50446289 Score: 89
Period size: 33 Copynumber: 2.3 Consensus size: 33
50446205 AAATCCATTC
*
50446215 ATATTATTTTTAATTTTTAAAAAATATTTATATT
1 ATATTA-TTTTAATATTTAAAAAATATTTATATT
* * *
50446249 ATATTATTTTAATATTTAATAATTTTTTATATT
1 ATATTATTTTAATATTTAAAAAATATTTATATT
*
50446282 -TTTTATTT
1 ATATTATTT
50446290 ATTAAATTTT
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
32 7 0.19
33 23 0.64
34 6 0.17
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (33 bp):
ATATTATTTTAATATTTAAAAAATATTTATATT
Found at i:50446280 original size:28 final size:27
Alignment explanation
Indices: 50446247--50446320 Score: 71
Period size: 27 Copynumber: 2.7 Consensus size: 27
50446237 AATATTTATA
50446247 TTATATTATTTTAATATTTAATAATTTT
1 TTATATTATTTTAATATTTAA-AATTTT
* *
50446275 TTATATT-TTTT-ATTTATTAAATTTTT
1 TTATATTATTTTAATAT-TTAAAATTTT
*
50446301 TATATAATTATCTTAATATT
1 T-TAT-ATTATTTTAATATT
50446321 ATTTTAATGT
Statistics
Matches: 37, Mismatches: 4, Indels: 9
0.74 0.08 0.18
Matches are distributed among these distances:
26 9 0.24
27 11 0.30
28 10 0.27
29 4 0.11
30 3 0.08
ACGTcount: A:0.34, C:0.01, G:0.00, T:0.65
Consensus pattern (27 bp):
TTATATTATTTTAATATTTAAAATTTT
Found at i:50446311 original size:24 final size:24
Alignment explanation
Indices: 50446252--50446326 Score: 66
Period size: 24 Copynumber: 3.1 Consensus size: 24
50446242 TTATATTATA
*
50446252 TTATTTTAA-TATTTAATAATTTT
1 TTATATTAATTATTTAATAATTTT
** *
50446275 TTATATTTTTTATTTATTAAATTTT
1 TTATATTAATTATTTAAT-AATTTT
50446300 TTATA-TAATTATCTTAAT-ATTATT
1 TTATATTAATTAT-TTAATAATT-TT
50446324 TTA
1 TTA
50446327 ATGTTTATAT
Statistics
Matches: 41, Mismatches: 7, Indels: 7
0.75 0.13 0.13
Matches are distributed among these distances:
23 9 0.22
24 17 0.41
25 15 0.37
ACGTcount: A:0.33, C:0.01, G:0.00, T:0.65
Consensus pattern (24 bp):
TTATATTAATTATTTAATAATTTT
Found at i:50446493 original size:18 final size:18
Alignment explanation
Indices: 50446472--50446514 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
50446462 CTAACTCATA
50446472 TTTTAAAT-AAATTTAATT
1 TTTTAAATCAAATTT-ATT
*
50446490 TTTT-ACTCAAATTTATT
1 TTTTAAATCAAATTTATT
50446507 TTTTAAAT
1 TTTTAAAT
50446515 TTAATATTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 4
0.78 0.07 0.15
Matches are distributed among these distances:
17 9 0.43
18 12 0.57
ACGTcount: A:0.37, C:0.05, G:0.00, T:0.58
Consensus pattern (18 bp):
TTTTAAATCAAATTTATT
Found at i:50446517 original size:31 final size:29
Alignment explanation
Indices: 50446479--50446544 Score: 89
Period size: 31 Copynumber: 2.2 Consensus size: 29
50446469 ATATTTTAAA
*
50446479 TAAATTTAAT-TTTTTACTCAAATTTATTTTT
1 TAAATTTAATATTTTTA-TCAAA-AT-TTTTT
50446510 TAAATTTAATATTTTTATCAAAATTTTTT
1 TAAATTTAATATTTTTATCAAAATTTTTT
50446539 TAAATT
1 TAAATT
50446545 CTGAATAAAT
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
29 11 0.33
30 1 0.03
31 15 0.45
32 6 0.18
ACGTcount: A:0.36, C:0.05, G:0.00, T:0.59
Consensus pattern (29 bp):
TAAATTTAATATTTTTATCAAAATTTTTT
Found at i:50447155 original size:94 final size:92
Alignment explanation
Indices: 50446958--50447393 Score: 426
Period size: 94 Copynumber: 4.7 Consensus size: 92
50446948 TCTTTCATGT
* * * *
50446958 TTTTCTTTTAGTAATATTTTTGTCTAAGATGGGAAAACTAGGGGAAAAAATCGAAAATCAACAGA
1 TTTTCTTTTAGTAATATTTTTCTCTAAGACGGGAAAATTAGGGGAAAAAATCGAAAATCAACAAA
*
50447023 TTTCTGGATC----TATTTTTT--ATG
66 TTTCTGGATCTGTGTATTTTTTCCCTG
**
50447044 TTTTCTTTTAGTAATATTTTTCTCTAAGACGGGAAAATTAGGGGGGAAAATCGAAAATCAACAAA
1 TTTTCTTTTAGTAATATTTTTCTCTAAGACGGGAAAATTAGGGGAAAAAATCGAAAATCAACAAA
50447109 TTTCTGGATCTAGTGTATTTTTTCCCTG
66 TTTCTGGATCT-GTGTATTTTTTCCCTG
* * * * * *
50447137 TTTTCCTTTTGGTAATATTTTTTTCTACGAGACGGGAAAAATAGGGG-AAAAATTGAAAATTACC
1 TTTT-CTTTTAGTAATATTTTTCTCTA--AGACGGGAAAATTAGGGGAAAAAATCGAAAATCAAC
*
50447201 AAATTTCTGG--CTTTCG-ATTCTTTTCCCTGTTG
63 AAATTTCTGGATCTGT-GTATT-TTTTCCC---TG
* * * *
50447233 TTTTTCTTTTATTAATATTTTTCTCTGAGACGGGAAAATTAGGGAAAGAAAATCGAGAATCAACA
1 -TTTTCTTTTAGTAATATTTTTCTCTAAGACGGGAAAATTAGGGGAA-AAAATCGAAAATCAACA
* * **
50447298 AATTTCTGGATCTAGGTTTTTTTTTTCGTTG
64 AATTTCTGGATCT--GTGTATTTTTTCCCTG
* * ** *
50447329 TTTTCTTTTAGTAATA-TTTTCTCTGAGACGAGAAAATTAGGAAAAAAAAAACGAAAATCAACAA
1 TTTTCTTTTAGTAATATTTTTCTCTAAGACGGGAAAATTAGG-GGAAAAAATCGAAAATCAACAA
50447393 A
65 A
50447394 GTAATCGATG
Statistics
Matches: 291, Mismatches: 35, Indels: 40
0.80 0.10 0.11
Matches are distributed among these distances:
86 69 0.24
91 8 0.03
92 4 0.01
93 16 0.05
94 77 0.26
95 42 0.14
96 61 0.21
97 4 0.01
98 2 0.01
99 5 0.02
100 3 0.01
ACGTcount: A:0.33, C:0.12, G:0.17, T:0.39
Consensus pattern (92 bp):
TTTTCTTTTAGTAATATTTTTCTCTAAGACGGGAAAATTAGGGGAAAAAATCGAAAATCAACAAA
TTTCTGGATCTGTGTATTTTTTCCCTG
Found at i:50467321 original size:19 final size:18
Alignment explanation
Indices: 50467293--50467330 Score: 58
Period size: 19 Copynumber: 2.1 Consensus size: 18
50467283 TTAAAAATGT
*
50467293 TAAAATATAATTTTATTA
1 TAAAATATAATTTCATTA
50467311 TAAATATATAATTTCATTA
1 TAAA-ATATAATTTCATTA
50467330 T
1 T
50467331 TTTTAAAAGC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 4 0.22
19 14 0.78
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (18 bp):
TAAAATATAATTTCATTA
Found at i:50476388 original size:109 final size:109
Alignment explanation
Indices: 50476197--50476416 Score: 395
Period size: 109 Copynumber: 2.0 Consensus size: 109
50476187 TTTGTGCATG
50476197 TTTGAAGTGATTGTGAAGTGGGAGGAATATAGAATTGAGGTAGGCTTAAGATCAATGTTACTCAA
1 TTTGAAGTGATTGTGAAGTGGGAGGAATATAGAATTGAGGTAGGCTTAAGATCAATGTTACTCAA
50476262 ATTCGGGTGCGAGTGTTGAATAAGAGTCACAACTATGATCAGAT
66 ATTCGGGTGCGAGTGTTGAATAAGAGTCACAACTATGATCAGAT
* * * *
50476306 TTTGAAGTGATTGTGGAGTTGGAGGAATATAGAATTGAGGTAGGCTTGAGATTAATGTTACTCAA
1 TTTGAAGTGATTGTGAAGTGGGAGGAATATAGAATTGAGGTAGGCTTAAGATCAATGTTACTCAA
*
50476371 ATTCGGGTGTGAGTGTTGAATAAGAGTCACAACTATGATCAGAT
66 ATTCGGGTGCGAGTGTTGAATAAGAGTCACAACTATGATCAGAT
50476415 TT
1 TT
50476417 CTTAAGATTT
Statistics
Matches: 106, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
109 106 1.00
ACGTcount: A:0.32, C:0.08, G:0.29, T:0.31
Consensus pattern (109 bp):
TTTGAAGTGATTGTGAAGTGGGAGGAATATAGAATTGAGGTAGGCTTAAGATCAATGTTACTCAA
ATTCGGGTGCGAGTGTTGAATAAGAGTCACAACTATGATCAGAT
Found at i:50480786 original size:18 final size:19
Alignment explanation
Indices: 50480763--50480806 Score: 56
Period size: 18 Copynumber: 2.4 Consensus size: 19
50480753 GAGAAAGCAT
50480763 ATTTTTTT-TTCATTTTTC-
1 ATTTTTTTATT-ATTTTTCA
*
50480781 ATTTTTTTATTTTTTTTCA
1 ATTTTTTTATTATTTTTCA
50480800 ATTTTTT
1 ATTTTTT
50480807 ACTCTACTGA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
18 14 0.61
19 9 0.39
ACGTcount: A:0.14, C:0.07, G:0.00, T:0.80
Consensus pattern (19 bp):
ATTTTTTTATTATTTTTCA
Found at i:50482493 original size:31 final size:28
Alignment explanation
Indices: 50482418--50482494 Score: 73
Period size: 31 Copynumber: 2.6 Consensus size: 28
50482408 GATCCCAAAT
* *
50482418 AATTTAAGTACCAACTTAAAAAAATGTCA
1 AATTT-AGTACCAAATTAAAAAAATATCA
* *
50482447 AGTTTAGGTATCAAATTAAAAAAATATATCA
1 AATTTA-GTACCAAATT-AAAAAA-ATATCA
50482478 AATTTGAGTACCAAATT
1 AATTT-AGTACCAAATT
50482495 GGACAAATAA
Statistics
Matches: 38, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
28 1 0.03
29 12 0.32
30 6 0.16
31 18 0.47
32 1 0.03
ACGTcount: A:0.49, C:0.10, G:0.09, T:0.31
Consensus pattern (28 bp):
AATTTAGTACCAAATTAAAAAAATATCA
Found at i:50482791 original size:16 final size:16
Alignment explanation
Indices: 50482749--50482780 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
50482739 TGACTCGGTC
50482749 TAAATATATTATATTA
1 TAAATATATTATATTA
*
50482765 TAAAAATATTATATTA
1 TAAATATATTATATTA
50482781 ATTATATATT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (16 bp):
TAAATATATTATATTA
Found at i:50482805 original size:29 final size:28
Alignment explanation
Indices: 50482752--50482820 Score: 74
Period size: 29 Copynumber: 2.5 Consensus size: 28
50482742 CTCGGTCTAA
50482752 ATATA-TTATATT--ATAAAAATATTAT
1 ATATATTTATATTAAATAAAAATATTAT
* *
50482777 AT-TAATTATATATTAAATAATAATTTTAT
1 ATAT-ATT-TATATTAAATAAAAATATTAT
50482806 ATATATTTATATTAA
1 ATATATTTATATTAA
50482821 GTTTATTCAA
Statistics
Matches: 36, Mismatches: 2, Indels: 9
0.77 0.04 0.19
Matches are distributed among these distances:
24 1 0.03
25 3 0.08
26 1 0.03
27 6 0.17
28 8 0.22
29 16 0.44
30 1 0.03
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (28 bp):
ATATATTTATATTAAATAAAAATATTAT
Found at i:50483472 original size:12 final size:12
Alignment explanation
Indices: 50483455--50483484 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
50483445 TTTTATGAAA
50483455 TGTTTAATTATT
1 TGTTTAATTATT
50483467 TGTTTAATTATT
1 TGTTTAATTATT
*
50483479 TTTTTA
1 TGTTTA
50483485 TAGGCAATCA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.23, C:0.00, G:0.07, T:0.70
Consensus pattern (12 bp):
TGTTTAATTATT
Found at i:50484479 original size:2 final size:2
Alignment explanation
Indices: 50484472--50484507 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
50484462 GTAAATTAAA
50484472 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
50484508 TGAGCGATAG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:50486759 original size:21 final size:21
Alignment explanation
Indices: 50486735--50486775 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
50486725 AAAAACTATA
*
50486735 TTTAATATTTTATACCTAAAT
1 TTTAAAATTTTATACCTAAAT
* *
50486756 TTTAAAATTTTTTATCTAAA
1 TTTAAAATTTTATACCTAAA
50486776 AATGTTACAT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.39, C:0.07, G:0.00, T:0.54
Consensus pattern (21 bp):
TTTAAAATTTTATACCTAAAT
Found at i:50488554 original size:38 final size:39
Alignment explanation
Indices: 50488498--50488588 Score: 116
Period size: 38 Copynumber: 2.4 Consensus size: 39
50488488 GAAAATTGGA
* *
50488498 AATTAAAATAA-TATAATAATTTTATATT-TCAAAAAAAT
1 AATTATAATAATTTTAATAATTTTATATTCT-AAAAAAAT
*
50488536 AA-TATAATAATTTTAATAATTTTATATTCTTAAAAAAT
1 AATTATAATAATTTTAATAATTTTATATTCTAAAAAAAT
*
50488574 AATTTTAATAATTTT
1 AATTATAATAATTTT
50488589 GAAATCATTT
Statistics
Matches: 46, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
37 7 0.15
38 27 0.59
39 12 0.26
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (39 bp):
AATTATAATAATTTTAATAATTTTATATTCTAAAAAAAT
Found at i:50489091 original size:2 final size:2
Alignment explanation
Indices: 50489084--50489119 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
50489074 ATTCCTCTAC
50489084 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
50489120 AATTCGAGAT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:50490725 original size:32 final size:32
Alignment explanation
Indices: 50490689--50490750 Score: 97
Period size: 32 Copynumber: 1.9 Consensus size: 32
50490679 ATTTAAAATG
*
50490689 AAATAAAAAATTAGACATATTATGTAATTACA
1 AAATAAAAAATAAGACATATTATGTAATTACA
* *
50490721 AAATATAAAATAATACATATTATGTAATTA
1 AAATAAAAAATAAGACATATTATGTAATTA
50490751 TTTAATAGAT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 27 1.00
ACGTcount: A:0.56, C:0.05, G:0.05, T:0.34
Consensus pattern (32 bp):
AAATAAAAAATAAGACATATTATGTAATTACA
Found at i:50491410 original size:30 final size:29
Alignment explanation
Indices: 50491374--50491437 Score: 101
Period size: 30 Copynumber: 2.2 Consensus size: 29
50491364 CCCCCAAACT
*
50491374 TTCTCACTTTCCCCCCAAAATTTTTACTCC
1 TTCTCACTTTCCCCCCAAAACTTTTACT-C
*
50491404 TTCTCACTTTTCCCCCAAAACTTTTACTC
1 TTCTCACTTTCCCCCCAAAACTTTTACTC
50491433 TTCTC
1 TTCTC
50491438 TCGTCCCACC
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
29 6 0.19
30 26 0.81
ACGTcount: A:0.19, C:0.39, G:0.00, T:0.42
Consensus pattern (29 bp):
TTCTCACTTTCCCCCCAAAACTTTTACTC
Found at i:50491584 original size:30 final size:31
Alignment explanation
Indices: 50491550--50491629 Score: 94
Period size: 32 Copynumber: 2.6 Consensus size: 31
50491540 CTCAAAACTT
*
50491550 TTTATTTT-TCCTCAAAATTTTTA-CTCCCCA
1 TTTATTTTCTCCT-AAAACTTTTACCTCCCCA
50491580 TTTATTTTCTCCTAAAACTTTTACTCTCCCCA
1 TTTATTTTCTCCTAAAACTTTTAC-CTCCCCA
*
50491612 TTTACTTTC-CCTTAAAAC
1 TTTATTTTCTCC-TAAAAC
50491630 CCTCAAAACT
Statistics
Matches: 44, Mismatches: 2, Indels: 6
0.85 0.04 0.12
Matches are distributed among these distances:
30 17 0.39
31 6 0.14
32 21 0.48
ACGTcount: A:0.24, C:0.29, G:0.00, T:0.47
Consensus pattern (31 bp):
TTTATTTTCTCCTAAAACTTTTACCTCCCCA
Found at i:50493451 original size:24 final size:24
Alignment explanation
Indices: 50493424--50493497 Score: 62
Period size: 24 Copynumber: 3.1 Consensus size: 24
50493414 TAGAATTAAG
50493424 ATTAAATTGACACAATGAATGAAC
1 ATTAAATTGACACAATGAATGAAC
***** * *
50493448 ATTAAA--GATTTTTTAGAATTAAG
1 ATTAAATTGACACAAT-GAATGAAC
50493471 ATTAAATTGACACAATGAATGAAC
1 ATTAAATTGACACAATGAATGAAC
50493495 ATT
1 ATT
50493498 GAAGGTTAAA
Statistics
Matches: 33, Mismatches: 14, Indels: 6
0.62 0.26 0.11
Matches are distributed among these distances:
22 3 0.09
23 12 0.36
24 15 0.45
25 3 0.09
ACGTcount: A:0.47, C:0.08, G:0.12, T:0.32
Consensus pattern (24 bp):
ATTAAATTGACACAATGAATGAAC
Found at i:50493460 original size:47 final size:47
Alignment explanation
Indices: 50493406--50493497 Score: 184
Period size: 47 Copynumber: 2.0 Consensus size: 47
50493396 GTTAAGAATT
50493406 AGATTTTTTAGAATTAAGATTAAATTGACACAATGAATGAACATTAA
1 AGATTTTTTAGAATTAAGATTAAATTGACACAATGAATGAACATTAA
50493453 AGATTTTTTAGAATTAAGATTAAATTGACACAATGAATGAACATT
1 AGATTTTTTAGAATTAAGATTAAATTGACACAATGAATGAACATT
50493498 GAAGGTTAAA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
47 45 1.00
ACGTcount: A:0.46, C:0.07, G:0.13, T:0.35
Consensus pattern (47 bp):
AGATTTTTTAGAATTAAGATTAAATTGACACAATGAATGAACATTAA
Found at i:50519592 original size:11 final size:11
Alignment explanation
Indices: 50519572--50519646 Score: 62
Period size: 11 Copynumber: 6.5 Consensus size: 11
50519562 AAGCCTCTCA
*
50519572 TCTTTCCTTTC
1 TCTTTTCTTTC
*
50519583 TCTTTTCTTTT
1 TCTTTTCTTTC
*
50519594 TCTCATTCATTTC
1 TCT-TTTC-TTTC
50519607 T-TATTTCTTTC
1 TCT-TTTCTTTC
50519618 TCTTTTCTTTTC
1 TCTTTTC-TTTC
* *
50519630 TATTTTCTTCC
1 TCTTTTCTTTC
50519641 TCTTTT
1 TCTTTT
50519647 AATCACACTT
Statistics
Matches: 51, Mismatches: 9, Indels: 8
0.75 0.13 0.12
Matches are distributed among these distances:
11 29 0.57
12 18 0.35
13 4 0.08
ACGTcount: A:0.05, C:0.25, G:0.00, T:0.69
Consensus pattern (11 bp):
TCTTTTCTTTC
Found at i:50519633 original size:22 final size:22
Alignment explanation
Indices: 50519579--50519643 Score: 58
Period size: 23 Copynumber: 2.8 Consensus size: 22
50519569 TCATCTTTCC
*
50519579 TTTCTCTTTTCTTTTTCTCATTCA
1 TTTCT-TTTTCTTTCTCTC-TTCA
* *
50519603 TTTCTTATTTCTTTCTCTTTTCT
1 TTTCTT-TTTCTTTCTCTCTTCA
*
50519626 TTTCTATTTTCTTCCTCT
1 TTTCT-TTTTCTTTCTCT
50519644 TTTAATCACA
Statistics
Matches: 35, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
23 19 0.54
24 16 0.46
ACGTcount: A:0.06, C:0.25, G:0.00, T:0.69
Consensus pattern (22 bp):
TTTCTTTTTCTTTCTCTCTTCA
Found at i:50520055 original size:21 final size:21
Alignment explanation
Indices: 50520017--50520084 Score: 100
Period size: 21 Copynumber: 3.2 Consensus size: 21
50520007 ACCCATTAAG
*
50520017 CCCAAATTCTATTTAAACCAAA
1 CCCAAATTC-ACTTAAACCAAA
*
50520039 CCCACATTCACTTAAACCAAA
1 CCCAAATTCACTTAAACCAAA
*
50520060 CCCAAATTCATTTAAACCAAA
1 CCCAAATTCACTTAAACCAAA
50520081 CCCA
1 CCCA
50520085 TTTGAACCAA
Statistics
Matches: 42, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
21 34 0.81
22 8 0.19
ACGTcount: A:0.44, C:0.34, G:0.00, T:0.22
Consensus pattern (21 bp):
CCCAAATTCACTTAAACCAAA
Found at i:50520086 original size:15 final size:15
Alignment explanation
Indices: 50520068--50520097 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
50520058 AACCCAAATT
50520068 CATTTAAACCAAACC
1 CATTTAAACCAAACC
*
50520083 CATTTGAACCAAACC
1 CATTTAAACCAAACC
50520098 AAATGAATCA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.43, C:0.33, G:0.03, T:0.20
Consensus pattern (15 bp):
CATTTAAACCAAACC
Found at i:50520175 original size:20 final size:20
Alignment explanation
Indices: 50520152--50520192 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
50520142 CATTGACCAA
*
50520152 TGTTGACCGACTGTTGACCG
1 TGTTGACCGACCGTTGACCG
**
50520172 TGTTGATTGACCGTTGACCG
1 TGTTGACCGACCGTTGACCG
50520192 T
1 T
50520193 TGACTTTTTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.15, C:0.22, G:0.29, T:0.34
Consensus pattern (20 bp):
TGTTGACCGACCGTTGACCG
Found at i:50521257 original size:3 final size:3
Alignment explanation
Indices: 50521245--50521286 Score: 77
Period size: 3 Copynumber: 14.3 Consensus size: 3
50521235 TATTCTATTC
50521245 TAT T-T TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
50521287 TTGGGATGTA
Statistics
Matches: 38, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 2 0.05
3 36 0.95
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TAT
Found at i:50524537 original size:15 final size:16
Alignment explanation
Indices: 50524510--50524539 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
50524500 TAAACAACAT
50524510 ATATTTTTCATATATC
1 ATATTTTTCATATATC
50524526 ATATTTTT-ATATAT
1 ATATTTTTCATATAT
50524540 AATAATCGAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.33, C:0.07, G:0.00, T:0.60
Consensus pattern (16 bp):
ATATTTTTCATATATC
Found at i:50525092 original size:30 final size:30
Alignment explanation
Indices: 50525033--50525092 Score: 95
Period size: 30 Copynumber: 2.0 Consensus size: 30
50525023 ATTTAAACTT
*
50525033 TTTTAAAAATTATAAAAATTTAATGTAATA
1 TTTTAAAAATTATAAAAATTAAATGTAATA
50525063 TTTTAAAAATTATAAAAATATAAAT-TAATA
1 TTTTAAAAATTATAAAAAT-TAAATGTAATA
50525093 AAATAATAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
30 24 0.86
31 4 0.14
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.42
Consensus pattern (30 bp):
TTTTAAAAATTATAAAAATTAAATGTAATA
Found at i:50527371 original size:3 final size:3
Alignment explanation
Indices: 50527363--50527392 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
50527353 ATGAGGACGG
50527363 TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA
1 TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA
50527393 CGACGATGAG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.33, T:0.33
Consensus pattern (3 bp):
TGA
Found at i:50527400 original size:12 final size:12
Alignment explanation
Indices: 50527352--50527401 Score: 55
Period size: 12 Copynumber: 4.2 Consensus size: 12
50527342 TAACGACGGG
* *
50527352 GATGAGGACGGT
1 GATGATGACGAT
*
50527364 GATGATGATGAT
1 GATGATGACGAT
*
50527376 GATGATGATGAT
1 GATGATGACGAT
*
50527388 GATGACGACGAT
1 GATGATGACGAT
50527400 GA
1 GA
50527402 GAGAAAAGAA
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
12 33 1.00
ACGTcount: A:0.32, C:0.06, G:0.38, T:0.24
Consensus pattern (12 bp):
GATGATGACGAT
Found at i:50527873 original size:14 final size:15
Alignment explanation
Indices: 50527850--50527882 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
50527840 TCTCATCACC
*
50527850 AAATGAAAAATTACA
1 AAATGAAAAATTAAA
50527865 AAATG-AAAATTAAA
1 AAATGAAAAATTAAA
50527879 AAAT
1 AAAT
50527883 ATCACTAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 12 0.71
15 5 0.29
ACGTcount: A:0.70, C:0.03, G:0.06, T:0.21
Consensus pattern (15 bp):
AAATGAAAAATTAAA
Found at i:50530233 original size:3 final size:3
Alignment explanation
Indices: 50530225--50530249 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
50530215 AGCTAATGTA
50530225 CAT CAT CAT CAT CAT CAT CAT CAT C
1 CAT CAT CAT CAT CAT CAT CAT CAT C
50530250 TCGTTCTCAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.36, G:0.00, T:0.32
Consensus pattern (3 bp):
CAT
Found at i:50532788 original size:14 final size:14
Alignment explanation
Indices: 50532771--50532797 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
50532761 GAAATTGTAA
50532771 AAAGAAAAAGAAAG
1 AAAGAAAAAGAAAG
50532785 AAAGAAAAAGAAA
1 AAAGAAAAAGAAA
50532798 AGAGAGTTGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (14 bp):
AAAGAAAAAGAAAG
Found at i:50537484 original size:293 final size:294
Alignment explanation
Indices: 50536948--50537511 Score: 923
Period size: 293 Copynumber: 1.9 Consensus size: 294
50536938 GAATTTAAGG
* * * * * *
50536948 TCATGTTGTGCTATATGCTTCTTAATTTGTGAAAGCCATCATAGTCCTTTTCCTCGTTAATGACT
1 TCATGTAGTGCTATATACTTCTTAATTTGTGAAAACCATCATAGTCCTTTTCCCCATTAATAACT
* * *
50537013 GATTTGCAATGAATCAGACGAGTAACCAAATGATGCAAACCGAAGAACATCAACACACAGATGAT
66 GATTTG-AATAAATCAGACGAGAAACCAAATGATGCAAACCGAAGAACATCAAAACACAGATGAT
* *
50537078 ATGCTACAGCAACAGCAGGTAATATGCGATCAGTCATGAGGTTTCTTTACCAAAGATGGAAAATT
130 ATGCTACAGCAACAGCAGGTAATATGAGATCAGTCATGAGGTTTCTTTACCAAAGATAGAAAATT
*
50537143 CCATGTCAGTGGAAAGTGTCATACAGATTTGCATCATAAATGTTGGCTACTTAATGAAATGTTCA
195 CCATGTCAGTGGAAAGTGTCATACAGATTTGCATCATAAATGTTGGCTACTAAATGAAATGTTCA
50537208 TCTGCAGGATTAATGATTGTTTGTGGAGTTTGAGA
260 TCTGCAGGATTAATGATTGTTTGTGGAGTTTGAGA
* *
50537243 TCATGTAGTGCTATATATTTCTTAATTTGTGAAAACCATCATAGTTCTTTTCCCCATTAATAACT
1 TCATGTAGTGCTATATACTTCTTAATTTGTGAAAACCATCATAGTCCTTTTCCCCATTAATAACT
* * *
50537308 GATTTG-TTAAATCAGATGAGAAACCAAATGATGCAAACCGAAGAACATCAAAACATAGATGATA
66 GATTTGAATAAATCAGACGAGAAACCAAATGATGCAAACCGAAGAACATCAAAACACAGATGATA
* * *
50537372 TGCTACAGCAACAGCAGGTAATATGAGATCAGTCATTAGGTTTCTTTGCCAAAGATAGCAAATTC
131 TGCTACAGCAACAGCAGGTAATATGAGATCAGTCATGAGGTTTCTTTACCAAAGATAGAAAATTC
*
50537437 CATGTCAGTGGAAAGTGTCATACAGATTTGCATCATAAATGTTGGCTACTAAATGAAATGTTCGT
196 CATGTCAGTGGAAAGTGTCATACAGATTTGCATCATAAATGTTGGCTACTAAATGAAATGTTCAT
50537502 CTGCAGGATT
261 CTGCAGGATT
50537512 CTGTTGGTAA
Statistics
Matches: 248, Mismatches: 21, Indels: 2
0.92 0.08 0.01
Matches are distributed among these distances:
293 185 0.75
295 63 0.25
ACGTcount: A:0.34, C:0.16, G:0.19, T:0.31
Consensus pattern (294 bp):
TCATGTAGTGCTATATACTTCTTAATTTGTGAAAACCATCATAGTCCTTTTCCCCATTAATAACT
GATTTGAATAAATCAGACGAGAAACCAAATGATGCAAACCGAAGAACATCAAAACACAGATGATA
TGCTACAGCAACAGCAGGTAATATGAGATCAGTCATGAGGTTTCTTTACCAAAGATAGAAAATTC
CATGTCAGTGGAAAGTGTCATACAGATTTGCATCATAAATGTTGGCTACTAAATGAAATGTTCAT
CTGCAGGATTAATGATTGTTTGTGGAGTTTGAGA
Found at i:50549724 original size:230 final size:231
Alignment explanation
Indices: 50549067--50549764 Score: 1175
Period size: 231 Copynumber: 3.0 Consensus size: 231
50549057 ATATGCAATA
* *
50549067 TGTTGACTGGTGGTGGCTCAATTGATCCACTTGGTCCTGAAAAGATAATAAAAAATCCATGACTG
1 TGTTGACTGGTGGTGGCTCAATTGATCCACTTGGTCCTGAAAAGATAATAAAGAATCCATGAATG
* *
50549132 TATGATATACATATACATATAAATAAAGTAAACCAAGGCCAACACTGCATGCATCTCATGCATAT
66 TATGATATACATATAC------ATGAAGTAAACGAAGGCCAACACTGCATGCATCTCATGCATAT
*
50549197 CTTCTCAAATAAAGCAGATACACATTATTCATCTCCTATTTTTTTAACACTGAATGAACCAAAGC
125 CTTCTCAAATAAAGCAGATACACATTATTCATCTCCTATTTTTTTAACACTGAATGAACCAAAAC
50549262 CAGATAAAAGGCCAAGCTAACCTTCACCATGATGTCCAGTGG
190 CAGATAAAAGGCCAAGCTAACCTTCACCATGATGTCCAGTGG
*
50549304 TATTGACTGGTGGTGGCTCAATTGATCCACTTGGTCCTGAAAAGATAATAAAGAATCCATGAATG
1 TGTTGACTGGTGGTGGCTCAATTGATCCACTTGGTCCTGAAAAGATAATAAAGAATCCATGAATG
* *
50549369 TATGATATACATATACATGAAATAAACGAAGGCCAACACTGCATGCATCTCATACATATCTTCTC
66 TATGATATACATATACATGAAGTAAACGAAGGCCAACACTGCATGCATCTCATGCATATCTTCTC
*
50549434 AAATAAAGCAGATACACATTATTCATCTCCTATTTTTTTAAAACTGAATGAACCAAAACCAGATA
131 AAATAAAGCAGATACACATTATTCATCTCCTATTTTTTTAACACTGAATGAACCAAAACCAGATA
50549499 AAAGGCCAAGCTAACCTTCACCATGATGTCCAGTGG
196 AAAGGCCAAGCTAACCTTCACCATGATGTCCAGTGG
*
50549535 TGTTGACTGGTGGTGGCTCAATTGATCCACTTGGTCCTG-AAAGGTAATAAAGAATCCATGAATG
1 TGTTGACTGGTGGTGGCTCAATTGATCCACTTGGTCCTGAAAAGATAATAAAGAATCCATGAATG
50549599 TATGATATACATATACATGAAGTAAACGAAGGCCAACACTGCATGCATCTCATGCATATCTTCTC
66 TATGATATACATATACATGAAGTAAACGAAGGCCAACACTGCATGCATCTCATGCATATCTTCTC
* * *
50549664 AAATAAAGCAGATACACATTATTCATCTCCTGTTCTTTTAACACTG-ATGAACTAAAAACCAGAT
131 AAATAAAGCAGATACACATTATTCATCTCCTATTTTTTTAACACTGAATGAAC-CAAAACCAGAT
* * *
50549728 AAAAGGTCAAGCTAACCTTCACCATGATATCTAGTGG
195 AAAAGGCCAAGCTAACCTTCACCATGATGTCCAGTGG
50549765 CGGCTACTGG
Statistics
Matches: 440, Mismatches: 20, Indels: 9
0.94 0.04 0.02
Matches are distributed among these distances:
229 6 0.01
230 174 0.40
231 182 0.41
237 78 0.18
ACGTcount: A:0.36, C:0.20, G:0.16, T:0.28
Consensus pattern (231 bp):
TGTTGACTGGTGGTGGCTCAATTGATCCACTTGGTCCTGAAAAGATAATAAAGAATCCATGAATG
TATGATATACATATACATGAAGTAAACGAAGGCCAACACTGCATGCATCTCATGCATATCTTCTC
AAATAAAGCAGATACACATTATTCATCTCCTATTTTTTTAACACTGAATGAACCAAAACCAGATA
AAAGGCCAAGCTAACCTTCACCATGATGTCCAGTGG
Found at i:50551180 original size:23 final size:23
Alignment explanation
Indices: 50551150--50551195 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
50551140 CACCTGGTAC
50551150 TGGAGTGATTCCAGGGGGAGCTG
1 TGGAGTGATTCCAGGGGGAGCTG
50551173 TGGAGTGATTCCAGGGGGAGCTG
1 TGGAGTGATTCCAGGGGGAGCTG
50551196 AGTGACAATG
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:0.17, C:0.13, G:0.48, T:0.22
Consensus pattern (23 bp):
TGGAGTGATTCCAGGGGGAGCTG
Found at i:50555154 original size:21 final size:21
Alignment explanation
Indices: 50555128--50555174 Score: 76
Period size: 21 Copynumber: 2.2 Consensus size: 21
50555118 AGGTATACAT
50555128 ATGTTCATGCATCTCATTTTC
1 ATGTTCATGCATCTCATTTTC
*
50555149 ATGTTCATGTATCTCATTTTC
1 ATGTTCATGCATCTCATTTTC
*
50555170 TTGTT
1 ATGTT
50555175 TTTGTTTTGC
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.17, C:0.19, G:0.11, T:0.53
Consensus pattern (21 bp):
ATGTTCATGCATCTCATTTTC
Found at i:50555802 original size:6 final size:6
Alignment explanation
Indices: 50555793--50555819 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
50555783 TGGTTTACTT
50555793 TATGTA TATGTA TATGTA TATGTA TAT
1 TATGTA TATGTA TATGTA TATGTA TAT
50555820 CATAGGATTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.15, T:0.52
Consensus pattern (6 bp):
TATGTA
Found at i:50557313 original size:13 final size:13
Alignment explanation
Indices: 50557297--50557323 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
50557287 TCAGAGCCTT
50557297 GTGTACATATGGA
1 GTGTACATATGGA
50557310 GTGTACATATGGA
1 GTGTACATATGGA
50557323 G
1 G
50557324 CATTTTTGGA
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:0.07, G:0.33, T:0.30
Consensus pattern (13 bp):
GTGTACATATGGA
Found at i:50557463 original size:23 final size:23
Alignment explanation
Indices: 50557433--50557478 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
50557423 CTAGTCGTTT
50557433 GGAATTGGATCCTTTTTCTTTTA
1 GGAATTGGATCCTTTTTCTTTTA
50557456 GGAATTGGATCCTTTTTCTTTTA
1 GGAATTGGATCCTTTTTCTTTTA
50557479 CATGAGAAAT
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:0.17, C:0.13, G:0.17, T:0.52
Consensus pattern (23 bp):
GGAATTGGATCCTTTTTCTTTTA
Found at i:50573714 original size:19 final size:20
Alignment explanation
Indices: 50573677--50573717 Score: 57
Period size: 19 Copynumber: 2.1 Consensus size: 20
50573667 TTCAAAATAA
* *
50573677 TCAAAATAATTTTTTAAAAT
1 TCAAAATAATTTATAAAAAT
50573697 TCAAAAT-ATTTATAAAAAT
1 TCAAAATAATTTATAAAAAT
50573716 TC
1 TC
50573718 TGAAATTTAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 12 0.63
20 7 0.37
ACGTcount: A:0.51, C:0.07, G:0.00, T:0.41
Consensus pattern (20 bp):
TCAAAATAATTTATAAAAAT
Found at i:50573777 original size:9 final size:9
Alignment explanation
Indices: 50573735--50573779 Score: 54
Period size: 9 Copynumber: 4.9 Consensus size: 9
50573725 TATATTTTTA
50573735 AAAAAATAAT
1 AAAAAAT-AT
*
50573745 AAAAAATTT
1 AAAAAATAT
*
50573754 AAAAAATTT
1 AAAAAATAT
50573763 AAAAAATAT
1 AAAAAATAT
*
50573772 ATAAAATA
1 AAAAAATA
50573780 ATAATTTTGA
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
9 25 0.78
10 7 0.22
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (9 bp):
AAAAAATAT
Found at i:50574987 original size:29 final size:32
Alignment explanation
Indices: 50574929--50574995 Score: 95
Period size: 29 Copynumber: 2.2 Consensus size: 32
50574919 TTTGCATATG
* *
50574929 AATTTTGATTTAATATGTAATTTTATACAT-A
1 AATTTTGATTTAATATGTAATTATACACATGA
50574960 AATTTTGATTT-A-ATGTAATTATACACATGA
1 AATTTTGATTTAATATGTAATTATACACATGA
50574990 AATTTT
1 AATTTT
50574996 AATTGAGAAT
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
29 14 0.42
30 8 0.24
31 11 0.33
ACGTcount: A:0.39, C:0.04, G:0.07, T:0.49
Consensus pattern (32 bp):
AATTTTGATTTAATATGTAATTATACACATGA
Found at i:50577667 original size:23 final size:23
Alignment explanation
Indices: 50577619--50577667 Score: 55
Period size: 23 Copynumber: 2.1 Consensus size: 23
50577609 CTAAATTTTG
* *
50577619 AAATTTGAAAAGTAAAATGACTA
1 AAATTTGAAAAATAAAATGACAA
*
50577642 AAATTTTAAAAATAAAA-GTACAA
1 AAATTTGAAAAATAAAATG-ACAA
50577665 AAA
1 AAA
50577668 CTAAATTTCA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
22 1 0.05
23 21 0.95
ACGTcount: A:0.63, C:0.04, G:0.08, T:0.24
Consensus pattern (23 bp):
AAATTTGAAAAATAAAATGACAA
Found at i:50581564 original size:6 final size:6
Alignment explanation
Indices: 50581553--50581794 Score: 65
Period size: 6 Copynumber: 38.7 Consensus size: 6
50581543 GATTGTGCTG
* * **
50581553 ATATGT ATATGT ATATGT ATATGG ATATGGAT ATACGT ATACAT ATATGTAT
1 ATATGT ATATGT ATATGT ATATGT ATAT-G-T ATATGT ATATGT ATATG--T
* * * * * * * ** **
50581605 ATATGCCT ATGTGT CTGTGT ATGTGT ATATGC ATGTAT ATACAT ATACAT
1 ATATG--T ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT
* * * * *
50581655 ATCTGT ATATGT ATGTG- A-ATGT GTATGG ATATGA ATATGGAT ATATGT
1 ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT ATAT-G-T ATATGT
** * * *
50581703 ATACAT ATATGTAT ATATGCCT ATTTGT CTATGT ATATGT ATATGT ACATGT
1 ATATGT ATATG--T ATATG--T ATATGT ATATGT ATATGT ATATGT ATATGT
*** * * * **
50581755 ATGCAT ATATGC ATGTAT ATATGT ATACAT ATATGT ATAT
1 ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT ATAT
50581795 ATGCCTATCT
Statistics
Matches: 169, Mismatches: 57, Indels: 20
0.69 0.23 0.08
Matches are distributed among these distances:
4 2 0.01
5 1 0.01
6 133 0.79
7 4 0.02
8 29 0.17
ACGTcount: A:0.33, C:0.07, G:0.17, T:0.43
Consensus pattern (6 bp):
ATATGT
Found at i:50581739 original size:76 final size:75
Alignment explanation
Indices: 50581658--50581810 Score: 209
Period size: 76 Copynumber: 2.0 Consensus size: 75
50581648 TATACATATC
* ** *
50581658 TGTATATGTATGTGAATGTGTATGGATATGAAT-ATGGATATATGTATACATATATGTATATATG
1 TGTATATGTATATGAACATGTATGCATAT--ATCATGGATATATGTATACATATATGTATATATG
*
50581722 CCTATTTGTCTA
64 CCTATCTGTCTA
* *
50581734 TGTATATGTATATGTACATGTATGCATATATGCATGTATATATGTATACATATATGTATATATGC
1 TGTATATGTATATGAACATGTATGCATATAT-CATGGATATATGTATACATATATGTATATATGC
50581799 CTATCTGTCTA
65 CTATCTGTCTA
50581810 T
1 T
50581811 CTGTCTATGT
Statistics
Matches: 68, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
74 2 0.03
76 66 0.97
ACGTcount: A:0.31, C:0.08, G:0.17, T:0.44
Consensus pattern (75 bp):
TGTATATGTATATGAACATGTATGCATATATCATGGATATATGTATACATATATGTATATATGCC
TATCTGTCTA
Found at i:50581776 original size:112 final size:111
Alignment explanation
Indices: 50581561--50581780 Score: 289
Period size: 112 Copynumber: 2.0 Consensus size: 111
50581551 TGATATGTAT
* * *
50581561 ATGTATATGTATATGGATATGGATATACGTATACATATATGTATATATGCCTATGTGTCTGTGTA
1 ATGTATATGGATATGAATATGGATATACGTATACATATATGTATATATGCCTATGTGTCTATGTA
* * *
50581626 TGTGTATATGCATGTATATACATATACATATCTGTATATGTATGTGA
66 TATGTATATGCATG-ATATACATATACACATCTATATATGTATGTGA
* * *
50581673 ATGTGTATGGATATGAATATGGATATATGTATACATATATGTATATATGCCTATTTGTCTATGTA
1 ATGTATATGGATATGAATATGGATATACGTATACATATATGTATATATGCCTATGTGTCTATGTA
* ** *
50581738 TATGTATATGTACATG-TATGCATATATGCATGTATATATGTAT
66 TATGTATATG--CATGATATACATATACACATCTATATATGTAT
50581781 ACATATATGT
Statistics
Matches: 93, Mismatches: 13, Indels: 4
0.85 0.12 0.04
Matches are distributed among these distances:
112 89 0.96
114 4 0.04
ACGTcount: A:0.32, C:0.07, G:0.18, T:0.43
Consensus pattern (111 bp):
ATGTATATGGATATGAATATGGATATACGTATACATATATGTATATATGCCTATGTGTCTATGTA
TATGTATATGCATGATATACATATACACATCTATATATGTATGTGA
Found at i:50581848 original size:6 final size:6
Alignment explanation
Indices: 50581839--50581875 Score: 60
Period size: 6 Copynumber: 6.5 Consensus size: 6
50581829 ATATGCATTT
50581839 ATATAC ATATAC ATATAC --ATAC ATATAC ATATAC ATA
1 ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC ATA
50581876 ATGTGTATGT
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
4 4 0.14
6 25 0.86
ACGTcount: A:0.51, C:0.16, G:0.00, T:0.32
Consensus pattern (6 bp):
ATATAC
Found at i:50581860 original size:16 final size:16
Alignment explanation
Indices: 50581841--50581875 Score: 70
Period size: 16 Copynumber: 2.2 Consensus size: 16
50581831 ATGCATTTAT
50581841 ATACATATACATATAC
1 ATACATATACATATAC
50581857 ATACATATACATATAC
1 ATACATATACATATAC
50581873 ATA
1 ATA
50581876 ATGTGTATGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.51, C:0.17, G:0.00, T:0.31
Consensus pattern (16 bp):
ATACATATACATATAC
Found at i:50586607 original size:123 final size:125
Alignment explanation
Indices: 50586388--50586636 Score: 385
Period size: 123 Copynumber: 2.0 Consensus size: 125
50586378 TGTTACTGGC
*
50586388 TAGTGCAAGTGTGAATTTGGTTGCGGTGGTAAGACACATTGAGTTTCGAACATAGGTTCCATAAG
1 TAGTGCAAGTGTGAATTTGGATGCGGTGGTAAGACACATTGAGTTTCGAACATAGGTTCCATAAG
* *
50586453 CTCCGAACATGAACTGAAAAACAGAAATGAACAATACGAAATAAAT-TTT-TTTTTTTGT
66 CTCCGAACATGAACTGAAAAACAGAAATGAACAATACCAAATAAATCTTTGTTTCTTTGT
* * * *
50586511 TAGTGCAAGTGTGAGTTTGGATGCGGTGGTAAGGCAGATTGAGTTTCGAACATAGGTTCCATTAG
1 TAGTGCAAGTGTGAATTTGGATGCGGTGGTAAGACACATTGAGTTTCGAACATAGGTTCCATAAG
* * **
50586576 CTTCGAACATGAACTGTAAAATGGAAATGAACAATACCAAATAAATCTTTGTTTCTTTGT
66 CTCCGAACATGAACTGAAAAACAGAAATGAACAATACCAAATAAATCTTTGTTTCTTTGT
50586636 T
1 T
50586637 TTTGTTAGTG
Statistics
Matches: 113, Mismatches: 11, Indels: 2
0.90 0.09 0.02
Matches are distributed among these distances:
123 101 0.89
124 3 0.03
125 9 0.08
ACGTcount: A:0.33, C:0.13, G:0.22, T:0.32
Consensus pattern (125 bp):
TAGTGCAAGTGTGAATTTGGATGCGGTGGTAAGACACATTGAGTTTCGAACATAGGTTCCATAAG
CTCCGAACATGAACTGAAAAACAGAAATGAACAATACCAAATAAATCTTTGTTTCTTTGT
Found at i:50588218 original size:12 final size:11
Alignment explanation
Indices: 50588191--50588215 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
50588181 TGACCATATA
50588191 GAATTTTTTTT
1 GAATTTTTTTT
50588202 GAATTTTTTTT
1 GAATTTTTTTT
50588213 GAA
1 GAA
50588216 ATTAGGCGAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.24, C:0.00, G:0.12, T:0.64
Consensus pattern (11 bp):
GAATTTTTTTT
Found at i:50590045 original size:10 final size:9
Alignment explanation
Indices: 50589978--50590108 Score: 63
Period size: 10 Copynumber: 13.7 Consensus size: 9
50589968 ATCTTGAATT
50589978 TTTTTTATAA
1 TTTTTTA-AA
*
50589988 TTTTTAAATA
1 TTTTTTAA-A
*
50589998 TTTGTTTACA
1 TTT-TTTAAA
50590008 -TTTTT-AA
1 TTTTTTAAA
*
50590015 TTTTTGTCAA
1 TTTTT-TAAA
*
50590025 TTATTTAAA
1 TTTTTTAAA
50590034 TTTTTTATAA
1 TTTTTTA-AA
50590044 --TTTTAAA
1 TTTTTTAAA
*
50590051 TATTTTTACGA
1 T-TTTTTA-AA
*
50590062 TTTTTATAGA
1 TTTTT-TAAA
50590072 TATTTTTAATGA
1 T-TTTTTAA--A
50590084 TTTTTTAACA
1 TTTTTTAA-A
*
50590094 ATTTTTAAA
1 TTTTTTAAA
50590103 TTTTTT
1 TTTTTT
50590109 TGATCTGTGG
Statistics
Matches: 95, Mismatches: 12, Indels: 29
0.70 0.09 0.21
Matches are distributed among these distances:
7 3 0.03
8 12 0.13
9 19 0.20
10 41 0.43
11 18 0.19
12 2 0.02
ACGTcount: A:0.31, C:0.03, G:0.04, T:0.63
Consensus pattern (9 bp):
TTTTTTAAA
Found at i:50590045 original size:19 final size:18
Alignment explanation
Indices: 50589978--50590107 Score: 72
Period size: 18 Copynumber: 6.8 Consensus size: 18
50589968 ATCTTGAATT
50589978 TTTTTTATAATTTTTAAA
1 TTTTTTATAATTTTTAAA
50589996 TATTTGTT-TACATTTTT-AA
1 T-TTT-TTATA-ATTTTTAAA
*
50590015 TTTTTGT-CAATTATTTAAA
1 TTTTT-TATAATT-TTTAAA
50590034 TTTTTTATAA-TTTTAAA
1 TTTTTTATAATTTTTAAA
**
50590051 TATTTTTACGATTTTTATAGA
1 T-TTTTTATAATTTTTA-A-A
*
50590072 TATTTTTAATGATTTTTTAACA
1 T-TTTTT-AT-AATTTTTAA-A
*
50590094 ATTTTTA-AATTTTT
1 TTTTTTATAATTTTT
50590108 TTGATCTGTG
Statistics
Matches: 89, Mismatches: 10, Indels: 26
0.71 0.08 0.21
Matches are distributed among these distances:
17 11 0.12
18 24 0.27
19 22 0.25
20 10 0.11
21 13 0.15
22 3 0.03
23 6 0.07
ACGTcount: A:0.31, C:0.03, G:0.04, T:0.62
Consensus pattern (18 bp):
TTTTTTATAATTTTTAAA
Found at i:50591738 original size:14 final size:15
Alignment explanation
Indices: 50591721--50591753 Score: 59
Period size: 14 Copynumber: 2.3 Consensus size: 15
50591711 TATGAATAAG
50591721 TAAATATAAG-AAAA
1 TAAATATAAGAAAAA
50591735 TAAATATAAGAAAAA
1 TAAATATAAGAAAAA
50591750 TAAA
1 TAAA
50591754 ATACGAATTA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 10 0.56
15 8 0.44
ACGTcount: A:0.73, C:0.00, G:0.06, T:0.21
Consensus pattern (15 bp):
TAAATATAAGAAAAA
Found at i:50591951 original size:48 final size:48
Alignment explanation
Indices: 50591874--50591965 Score: 123
Period size: 48 Copynumber: 1.9 Consensus size: 48
50591864 AGTTTTGGAG
* *
50591874 AGTTTGGGGTTAAAATATAATTTTGGAAAGTTTTACGGGTAAAATGTT
1 AGTTTGGGGTAAAAATATAATTTTGGAAAGTTTAACGGGTAAAATGTT
* * *
50591922 AGTTTGGGGTAAAAATGTGATCTTT-GAAAGTTTAAGGGGTAAAA
1 AGTTTGGGGTAAAAATATAAT-TTTGGAAAGTTTAACGGGTAAAA
50591966 ATGTAATTTT
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
48 35 0.92
49 3 0.08
ACGTcount: A:0.35, C:0.02, G:0.27, T:0.36
Consensus pattern (48 bp):
AGTTTGGGGTAAAAATATAATTTTGGAAAGTTTAACGGGTAAAATGTT
Found at i:50592011 original size:29 final size:29
Alignment explanation
Indices: 50591922--50592383 Score: 311
Period size: 29 Copynumber: 15.9 Consensus size: 29
50591912 GTAAAATGTT
* * *
50591922 AGTTTG-GGGTAAAAATGTGATCTTTGAA
1 AGTTTGAGGGTAAAAATGTAATTTTTGGA
* *
50591950 AGTTTAAGGGGTAAAAATGTAATTTTTAAGA
1 AGTTTGA-GGGTAAAAATGTAATTTTT-GGA
*
50591981 AGTTTGAGGGTAAAAATGTGATTTTTGGA
1 AGTTTGAGGGTAAAAATGTAATTTTTGGA
* * *
50592010 AGTTTAAGGGCAAAAATATAATTTTTGAGA
1 AGTTTGAGGGTAAAAATGTAATTTTTG-GA
* *
50592040 AGTTT-AGGGGTAAAAATGTGATTTTTAGA
1 AGTTTGA-GGGTAAAAATGTAATTTTTGGA
* * * *
50592069 AGTTTGGGGGAAAAAATATAA-TTTTGAA
1 AGTTTGAGGGTAAAAATGTAATTTTTGGA
*
50592097 AGTTT-AGGGGTAAAAATGTGATTTTTGGA
1 AGTTTGA-GGGTAAAAATGTAATTTTTGGA
* * *
50592126 AGTTT-AAGG-ACAAAATATAATTTTTAGA
1 AGTTTGAGGGTA-AAAATGTAATTTTTGGA
* *
50592154 AGTTTGGGGGTAAAAATGTAATTTTTAGA
1 AGTTTGAGGGTAAAAATGTAATTTTTGGA
* * **
50592183 AG-TTCATGGGCAAAAATGTAATTTTTAAA
1 AGTTTGA-GGGTAAAAATGTAATTTTTGGA
* *
50592212 AG-TTCATGGGCAAAAATGTAATTTTTGAGA
1 AGTTTGA-GGGTAAAAATGTAATTTTTG-GA
* * * *
50592242 AGTTTAAGGGTTAAAATGCAATTTTGGAGA
1 AGTTTGAGGGTAAAAATGTAATTTTTG-GA
* * * * *
50592272 AGTTTG-GGGTCAAAATATGATTTTAGAA
1 AGTTTGAGGGTAAAAATGTAATTTTTGGA
* * *
50592300 AGGTTT-AGGGGTCAAAATGCAATTTTGGTGA
1 A-GTTTGA-GGGTAAAAATGTAATTTTTG-GA
* *
50592331 AGTTT-AGAGTCAAAATGTAA-TTTTGAAGA
1 AGTTTGAGGGTAAAAATGTAATTTTTG--GA
* *
50592360 AGTTT-AGGGTCAAAATATAATTTT
1 AGTTTGAGGGTAAAAATGTAATTTT
50592384 GAAAAAATTT
Statistics
Matches: 351, Mismatches: 63, Indels: 38
0.78 0.14 0.08
Matches are distributed among these distances:
27 1 0.00
28 55 0.16
29 173 0.49
30 110 0.31
31 12 0.03
ACGTcount: A:0.37, C:0.03, G:0.24, T:0.35
Consensus pattern (29 bp):
AGTTTGAGGGTAAAAATGTAATTTTTGGA
Found at i:50592034 original size:59 final size:59
Alignment explanation
Indices: 50591922--50592383 Score: 396
Period size: 59 Copynumber: 7.9 Consensus size: 59
50591912 GTAAAATGTT
* * * * *
50591922 AGTTTG-GGGTAAAAATGTGATCTTTGAAAGTTTAAGGGGTAAAAATGTAATTTTTAAGA
1 AGTTTGAGGGTAAAAATGTGATTTTTGGAAGTTTAA-GGGCAAAAATATAATTTTTGAGA
50591981 AGTTTGAGGGTAAAAATGTGATTTTTGGAAGTTTAAGGGCAAAAATATAATTTTTGAGA
1 AGTTTGAGGGTAAAAATGTGATTTTTGGAAGTTTAAGGGCAAAAATATAATTTTTGAGA
* ** *
50592040 AGTTT-AGGGGTAAAAATGTGATTTTTAGAAGTTTGGGGGAAAAAATATAA-TTTTGA-A
1 AGTTTGA-GGGTAAAAATGTGATTTTTGGAAGTTTAAGGGCAAAAATATAATTTTTGAGA
*
50592097 AGTTT-AGGGGTAAAAATGTGATTTTTGGAAGTTTAAGGAC-AAAATATAATTTTT-AGA
1 AGTTTGA-GGGTAAAAATGTGATTTTTGGAAGTTTAAGGGCAAAAATATAATTTTTGAGA
* * * * * * *
50592154 AGTTTGGGGGTAAAAATGTAATTTTTAGAAGTTCATGGGCAAAAATGTAATTTTT-AAA
1 AGTTTGAGGGTAAAAATGTGATTTTTGGAAGTTTAAGGGCAAAAATATAATTTTTGAGA
* * * ** ** *
50592212 AG-TTCATGGGCAAAAATGTAATTTTTGAGAAGTTTAAGGGTTAAAATGCAATTTTGGAGA
1 AGTTTGA-GGGTAAAAATGTGATTTTTG-GAAGTTTAAGGGCAAAAATATAATTTTTGAGA
* * * * * ** * *
50592272 AGTTTG-GGGTCAAAATATGATTTTAGAAAGGTTTAGGGGTC-AAAATGCAATTTTGGTGA
1 AGTTTGAGGGTAAAAATGTGATTTTTGGAA-GTTTAAGGG-CAAAAATATAATTTTTGAGA
* * *
50592331 AGTTT-AGAGTCAAAATGT-AATTTTGAAGAAGTTT-AGGGTC-AAAATATAATTTT
1 AGTTTGAGGGTAAAAATGTGATTTTTG--GAAGTTTAAGGG-CAAAAATATAATTTT
50592384 GAAAAAATTT
Statistics
Matches: 337, Mismatches: 51, Indels: 31
0.80 0.12 0.07
Matches are distributed among these distances:
56 10 0.03
57 76 0.23
58 65 0.19
59 151 0.45
60 33 0.10
61 2 0.01
ACGTcount: A:0.37, C:0.03, G:0.24, T:0.35
Consensus pattern (59 bp):
AGTTTGAGGGTAAAAATGTGATTTTTGGAAGTTTAAGGGCAAAAATATAATTTTTGAGA
Found at i:50592395 original size:88 final size:89
Alignment explanation
Indices: 50592224--50592422 Score: 233
Period size: 88 Copynumber: 2.2 Consensus size: 89
50592214 TTCATGGGCA
* * * * * *
50592224 AAAATGTAATTTTTGAGAAGTTTAAGGGTTAAAATGCAATTTTGGAGAAGTTTGGGGTCAAAATA
1 AAAATGAAATTTTGGAGAAGTTTAAGAGTCAAAATGCAATTTTGAAGAAGTTTAGGGTCAAAATA
* **
50592289 TGATTTTAGAAAGGTTTAGGGG-T
66 TAATTTTAGAAAAATTTAGGGGAT
* * *
50592312 CAAAATGCAATTTTGGTGAAGTTT-AGAGTCAAAATGTAATTTTGAAGAAGTTTAGGGTCAAAAT
1 -AAAATGAAATTTTGGAGAAGTTTAAGAGTCAAAATGCAATTTTGAAGAAGTTTAGGGTCAAAAT
50592376 ATAATTTT-GAAAAAATTTAGGGGAT
65 ATAATTTTAG-AAAAATTTAGGGGAT
* *
50592401 AAAATGAAATTTTAGAAAAGTT
1 AAAATGAAATTTTGGAGAAGTT
50592423 CGAGGACCTA
Statistics
Matches: 93, Mismatches: 15, Indels: 5
0.82 0.13 0.04
Matches are distributed among these distances:
87 1 0.01
88 71 0.76
89 21 0.23
ACGTcount: A:0.40, C:0.03, G:0.23, T:0.34
Consensus pattern (89 bp):
AAAATGAAATTTTGGAGAAGTTTAAGAGTCAAAATGCAATTTTGAAGAAGTTTAGGGTCAAAATA
TAATTTTAGAAAAATTTAGGGGAT
Found at i:50598397 original size:15 final size:15
Alignment explanation
Indices: 50598377--50598426 Score: 73
Period size: 15 Copynumber: 3.3 Consensus size: 15
50598367 TTCAGAGTCT
50598377 TCATCTCTTTCAACA
1 TCATCTCTTTCAACA
* *
50598392 TCATCTCTTTCCACC
1 TCATCTCTTTCAACA
*
50598407 TCATCTCTTTCAACT
1 TCATCTCTTTCAACA
50598422 TCATC
1 TCATC
50598427 AGCATCTTCT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 31 1.00
ACGTcount: A:0.20, C:0.38, G:0.00, T:0.42
Consensus pattern (15 bp):
TCATCTCTTTCAACA
Done.