Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D07
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: 56457815
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1765025 characters in sequence are not A, C, G, or T
File 73 of 189
Found at i:20315123 original size:31 final size:30
Alignment explanation
Indices: 20315088--20315188 Score: 98
Period size: 31 Copynumber: 3.3 Consensus size: 30
20315078 AAAGTAGAAA
*
20315088 ATTATAAAAATTATAGAATAACTATAAAAAT
1 ATTATAAAAATTATAGAA-AAATATAAAAAT
* *
20315119 ATTATACAAAATTACAAAAAAATATAAAAATT
1 ATTATA-AAAATTATAGAAAAATATAAAAA-T
* * **
20315151 ATTA-ATATATTAT-GAAAAATATGCAAAT
1 ATTATAAAAATTATAGAAAAATATAAAAAT
20315179 ATTATAAAAA
1 ATTATAAAAA
20315189 CTAGAATTAT
Statistics
Matches: 56, Mismatches: 11, Indels: 8
0.75 0.15 0.11
Matches are distributed among these distances:
28 5 0.09
29 14 0.25
30 5 0.09
31 17 0.30
32 15 0.27
ACGTcount: A:0.61, C:0.04, G:0.03, T:0.32
Consensus pattern (30 bp):
ATTATAAAAATTATAGAAAAATATAAAAAT
Found at i:20315234 original size:11 final size:11
Alignment explanation
Indices: 20315218--20315250 Score: 52
Period size: 10 Copynumber: 3.2 Consensus size: 11
20315208 TAAAGTATAT
20315218 AAAATTGATAA
1 AAAATTGATAA
20315229 AAAATTG-TAA
1 AAAATTGATAA
20315239 AAAATT-ATAA
1 AAAATTGATAA
20315249 AA
1 AA
20315251 CTATATAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
10 14 0.67
11 7 0.33
ACGTcount: A:0.67, C:0.00, G:0.06, T:0.27
Consensus pattern (11 bp):
AAAATTGATAA
Found at i:20315250 original size:9 final size:10
Alignment explanation
Indices: 20315085--20315188 Score: 61
Period size: 10 Copynumber: 10.3 Consensus size: 10
20315075 ATAAAAGTAG
20315085 AAAATTAT-A
1 AAAATTATAA
20315094 AAAATTATAGA
1 AAAATTATA-A
* *
20315105 ATAACTATAA
1 AAAATTATAA
*
20315115 AAATATTATAC
1 AAA-ATTATAA
*
20315126 AAAATTACAA
1 AAAATTATAA
*
20315136 AAAAATAT-A
1 AAAATTATAA
20315145 AAAATTATTAA
1 AAAATTA-TAA
* * *
20315156 TATATTATGA
1 AAAATTATAA
*
20315166 AAAA-TATGCA
1 AAAATTAT-AA
*
20315176 AATATTATAA
1 AAAATTATAA
20315186 AAA
1 AAA
20315189 CTAGAATTAT
Statistics
Matches: 69, Mismatches: 19, Indels: 13
0.68 0.19 0.13
Matches are distributed among these distances:
9 18 0.26
10 26 0.38
11 25 0.36
ACGTcount: A:0.62, C:0.04, G:0.03, T:0.31
Consensus pattern (10 bp):
AAAATTATAA
Found at i:20315689 original size:20 final size:21
Alignment explanation
Indices: 20315664--20315709 Score: 60
Period size: 20 Copynumber: 2.2 Consensus size: 21
20315654 TGCTTTTATG
20315664 ATTTTA-ATAAATTTTAA-ATA
1 ATTTTATAT-AATTTTAACATA
*
20315684 ATTTTATATCATTTTAACATA
1 ATTTTATATAATTTTAACATA
20315705 ATTTT
1 ATTTT
20315710 CTATGACTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
20 13 0.57
21 10 0.43
ACGTcount: A:0.41, C:0.04, G:0.00, T:0.54
Consensus pattern (21 bp):
ATTTTATATAATTTTAACATA
Found at i:20316212 original size:4 final size:4
Alignment explanation
Indices: 20316203--20316267 Score: 130
Period size: 4 Copynumber: 16.2 Consensus size: 4
20316193 ATCTAACCTC
20316203 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
20316251 GTAT GTAT GTAT GTAT G
1 GTAT GTAT GTAT GTAT G
20316268 AGTTTAGAGA
Statistics
Matches: 61, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 61 1.00
ACGTcount: A:0.25, C:0.00, G:0.26, T:0.49
Consensus pattern (4 bp):
GTAT
Found at i:20325785 original size:15 final size:15
Alignment explanation
Indices: 20325765--20325797 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
20325755 TTCCAAATGT
20325765 TAGTTGTTCTCAACA
1 TAGTTGTTCTCAACA
*
20325780 TAGTTGTTCTCAATA
1 TAGTTGTTCTCAACA
20325795 TAG
1 TAG
20325798 AGATTGTTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.27, C:0.15, G:0.15, T:0.42
Consensus pattern (15 bp):
TAGTTGTTCTCAACA
Found at i:20325903 original size:16 final size:16
Alignment explanation
Indices: 20325881--20325923 Score: 52
Period size: 16 Copynumber: 2.7 Consensus size: 16
20325871 GGGAAAAAAA
20325881 ATTGTTCTAAATACAAG
1 ATTGTTCTAAA-ACAAG
* *
20325898 -TTGTTCCAAAACATG
1 ATTGTTCTAAAACAAG
20325913 ATTGTTCTAAA
1 ATTGTTCTAAA
20325924 CATAGTTATT
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
15 4 0.18
16 18 0.82
ACGTcount: A:0.37, C:0.14, G:0.12, T:0.37
Consensus pattern (16 bp):
ATTGTTCTAAAACAAG
Found at i:20325941 original size:32 final size:30
Alignment explanation
Indices: 20325881--20325958 Score: 84
Period size: 32 Copynumber: 2.5 Consensus size: 30
20325871 GGGAAAAAAA
* *
20325881 ATTGTTCTAAATACAAGTTGTTCCAAAACATG
1 ATTGTTCT-AA-ACAAGTTATTCCAAAACATC
*
20325913 ATTGTTCTAAACATAGTTATTCCTAAAACGTC
1 ATTGTTCTAAACA-AGTTATTCC-AAAACATC
*
20325945 ATTATTCTAAACAA
1 ATTGTTCTAAACAA
20325959 AAGCTATTTC
Statistics
Matches: 40, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
30 3 0.08
31 11 0.28
32 26 0.65
ACGTcount: A:0.38, C:0.17, G:0.09, T:0.36
Consensus pattern (30 bp):
ATTGTTCTAAACAAGTTATTCCAAAACATC
Found at i:20334603 original size:23 final size:22
Alignment explanation
Indices: 20334561--20334603 Score: 52
Period size: 22 Copynumber: 1.9 Consensus size: 22
20334551 TGAGACAAAA
*
20334561 AAAAAATTCAAGTATCAATTTG
1 AAAAAATTCAAGTATAAATTTG
20334583 AAAAAATT-AAGGTACTAAATT
1 AAAAAATTCAA-GTA-TAAATT
20334604 AAATATTGAA
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
21 2 0.11
22 11 0.61
23 5 0.28
ACGTcount: A:0.53, C:0.07, G:0.09, T:0.30
Consensus pattern (22 bp):
AAAAAATTCAAGTATAAATTTG
Found at i:20344730 original size:25 final size:25
Alignment explanation
Indices: 20344696--20344802 Score: 130
Period size: 25 Copynumber: 4.3 Consensus size: 25
20344686 CTATAGCTCT
*
20344696 TATGAGCTTATCGATTCTCAACTCG
1 TATGAGCTTACCGATTCTCAACTCG
20344721 TATGAGCTTACCGATTCTCAACTCG
1 TATGAGCTTACCGATTCTCAACTCG
*
20344746 TATGAGCTTACCGATT-TACAACTCA
1 TATGAGCTTACCGATTCT-CAACTCG
* *
20344771 TGA-GAGCATACCGATTCAT-AGCTCG
1 T-ATGAGCTTACCGATTC-TCAACTCG
20344796 TATGAGC
1 TATGAGC
20344803 ATACATGTAC
Statistics
Matches: 72, Mismatches: 5, Indels: 10
0.83 0.06 0.11
Matches are distributed among these distances:
24 2 0.03
25 68 0.94
26 1 0.01
27 1 0.01
ACGTcount: A:0.27, C:0.24, G:0.18, T:0.31
Consensus pattern (25 bp):
TATGAGCTTACCGATTCTCAACTCG
Found at i:20353261 original size:18 final size:18
Alignment explanation
Indices: 20353238--20353275 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
20353228 TTATTAACCA
20353238 AGCGAGACTCCACAAAGT
1 AGCGAGACTCCACAAAGT
20353256 AGCGAGACTCCACAAAGT
1 AGCGAGACTCCACAAAGT
20353274 AG
1 AG
20353276 GATTTGTGAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.39, C:0.26, G:0.24, T:0.11
Consensus pattern (18 bp):
AGCGAGACTCCACAAAGT
Found at i:20361824 original size:24 final size:24
Alignment explanation
Indices: 20361797--20361842 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
20361787 AATCTGCGTC
* *
20361797 TGCATTTGTATCTAAATTTGAATA
1 TGCATATGTATCTAAATCTGAATA
20361821 TGCATATGTATCTAAATCTGAA
1 TGCATATGTATCTAAATCTGAA
20361843 AATACATCTG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.35, C:0.11, G:0.13, T:0.41
Consensus pattern (24 bp):
TGCATATGTATCTAAATCTGAATA
Found at i:20363298 original size:21 final size:21
Alignment explanation
Indices: 20363254--20363298 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
20363244 TTTGTAGAAA
*
20363254 TTAAAAATATTTGAAATTTCT
1 TTAAAAATATTAGAAATTTCT
*
20363275 TTAAAAACTATTAGAACTTT-T
1 TTAAAAA-TATTAGAAATTTCT
20363296 TTA
1 TTA
20363299 GAACTTTTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 11 0.52
22 10 0.48
ACGTcount: A:0.42, C:0.07, G:0.04, T:0.47
Consensus pattern (21 bp):
TTAAAAATATTAGAAATTTCT
Found at i:20363923 original size:18 final size:19
Alignment explanation
Indices: 20363888--20363926 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
20363878 TTTTAATAAC
**
20363888 TTTTTATATATTTTTAAAA
1 TTTTTATATATTAATAAAA
20363907 TTTTTATA-ATTAATAAAA
1 TTTTTATATATTAATAAAA
20363925 TT
1 TT
20363927 ATATCTCGAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 10 0.56
19 8 0.44
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (19 bp):
TTTTTATATATTAATAAAA
Found at i:20364285 original size:9 final size:9
Alignment explanation
Indices: 20364267--20364306 Score: 62
Period size: 9 Copynumber: 4.4 Consensus size: 9
20364257 TTTGGTTAAA
20364267 AATTAACCG
1 AATTAACCG
*
20364276 AATTACCCG
1 AATTAACCG
*
20364285 AATTAACTG
1 AATTAACCG
20364294 AATTAACCG
1 AATTAACCG
20364303 AATT
1 AATT
20364307 GAATCACTAC
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
9 27 1.00
ACGTcount: A:0.42, C:0.20, G:0.10, T:0.28
Consensus pattern (9 bp):
AATTAACCG
Found at i:20364357 original size:6 final size:6
Alignment explanation
Indices: 20364326--20364374 Score: 62
Period size: 6 Copynumber: 7.7 Consensus size: 6
20364316 CATAATTAAA
*
20364326 TTAGTT TTAGACTT TTAGACT TTAGTT TTAGTT TTAGTT TTAGTT TTAG
1 TTAGTT TTAG--TT TTAG-TT TTAGTT TTAGTT TTAGTT TTAGTT TTAG
20364375 AATTTTATTT
Statistics
Matches: 38, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
6 27 0.71
7 5 0.13
8 6 0.16
ACGTcount: A:0.20, C:0.04, G:0.16, T:0.59
Consensus pattern (6 bp):
TTAGTT
Found at i:20364455 original size:18 final size:18
Alignment explanation
Indices: 20364415--20364458 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
20364405 AATTTTTATG
**
20364415 ATTGGGTTGGGTTGGGTA
1 ATTGGGTTGGGTTGAATA
20364433 ATTGGGTTGGGTTGAATA
1 ATTGGGTTGGGTTGAATA
*
20364451 TTTGGGTT
1 ATTGGGTT
20364459 TGGATTGGGT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.14, C:0.00, G:0.43, T:0.43
Consensus pattern (18 bp):
ATTGGGTTGGGTTGAATA
Found at i:20375338 original size:16 final size:15
Alignment explanation
Indices: 20375297--20375339 Score: 52
Period size: 16 Copynumber: 2.9 Consensus size: 15
20375287 CATTATTTAT
20375297 TTAATTAATTTT-AA
1 TTAATTAATTTTCAA
*
20375311 TTAATTATTTTTCCAA
1 TTAATTAATTTT-CAA
*
20375327 TTAAATAATTTTC
1 TTAATTAATTTTC
20375340 TTAACCCAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
14 11 0.46
15 1 0.04
16 12 0.50
ACGTcount: A:0.37, C:0.07, G:0.00, T:0.56
Consensus pattern (15 bp):
TTAATTAATTTTCAA
Found at i:20399365 original size:44 final size:44
Alignment explanation
Indices: 20399317--20399430 Score: 131
Period size: 44 Copynumber: 2.6 Consensus size: 44
20399307 TCAATCTATT
* * *
20399317 CCACTGCAACCTCAGGGAGATAAGATTTGCTTCT-TCAGTCTGCC
1 CCACTGCAACTTCAGGGAGATAAGACTCG-TTCTCTCAGTCTGCC
** * * *
20399361 CCACTGTGACTTCAGGGGGATAAGACTCGTTTTCTCAGTCTGCT
1 CCACTGCAACTTCAGGGAGATAAGACTCGTTCTCTCAGTCTGCC
*
20399405 CCATTGCAACTTCAGGGAGATAAGAC
1 CCACTGCAACTTCAGGGAGATAAGAC
20399431 CTGATGTGAT
Statistics
Matches: 57, Mismatches: 12, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
43 3 0.05
44 54 0.95
ACGTcount: A:0.24, C:0.26, G:0.23, T:0.27
Consensus pattern (44 bp):
CCACTGCAACTTCAGGGAGATAAGACTCGTTCTCTCAGTCTGCC
Found at i:20399755 original size:87 final size:87
Alignment explanation
Indices: 20399596--20399827 Score: 322
Period size: 87 Copynumber: 2.7 Consensus size: 87
20399586 GTAGGAGGGT
** * * * **
20399596 AAGATCTGCTATCTTTAAATAGCTCCACTGCAACCGATGGAGGCAATGCTTTGTTTTCGATCTGT
1 AAGATCTGCTATCTTTAACCAGCTCCACTGCAACAGATGGAGGCAAGGCTTTGTTTTCAATCTCC
* * *
20399661 TTTGCTGTTAA-CCAATGAAGGC
66 TTCGCTGTCAATCC-AGGAAGGC
*
20399683 AAGATCTGCTATCTTTAACCAGCTCCACTACAACAGATGGAGGCAAGGCTTTGTTTTCAATCTCC
1 AAGATCTGCTATCTTTAACCAGCTCCACTGCAACAGATGGAGGCAAGGCTTTGTTTTCAATCTCC
*
20399748 TTCGCTGTCAATGCAGGAAGGC
66 TTCGCTGTCAATCCAGGAAGGC
* *
20399770 AAGATCTGCTATCTTTAACCAGTTCCACTGCAACTGATGGAGGCAAGGCTTTGTTTTC
1 AAGATCTGCTATCTTTAACCAGCTCCACTGCAACAGATGGAGGCAAGGCTTTGTTTTC
20399828 GATTTTCACT
Statistics
Matches: 129, Mismatches: 15, Indels: 2
0.88 0.10 0.01
Matches are distributed among these distances:
87 128 0.99
88 1 0.01
ACGTcount: A:0.25, C:0.23, G:0.21, T:0.31
Consensus pattern (87 bp):
AAGATCTGCTATCTTTAACCAGCTCCACTGCAACAGATGGAGGCAAGGCTTTGTTTTCAATCTCC
TTCGCTGTCAATCCAGGAAGGC
Found at i:20401071 original size:7 final size:7
Alignment explanation
Indices: 20401059--20401097 Score: 53
Period size: 7 Copynumber: 5.6 Consensus size: 7
20401049 ATAGCCTCTC
20401059 CATTTTT
1 CATTTTT
20401066 CATTTTT
1 CATTTTT
20401073 CA-TTTT
1 CATTTTT
20401079 CATTTTTT
1 CA-TTTTT
*
20401087 AATTTTT
1 CATTTTT
20401094 CATT
1 CATT
20401098 CTCATTCTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
6 6 0.21
7 17 0.61
8 5 0.18
ACGTcount: A:0.18, C:0.13, G:0.00, T:0.69
Consensus pattern (7 bp):
CATTTTT
Found at i:20401114 original size:21 final size:21
Alignment explanation
Indices: 20401061--20401108 Score: 69
Period size: 21 Copynumber: 2.2 Consensus size: 21
20401051 AGCCTCTCCA
* *
20401061 TTTTTCATTTTTCATTTTCAT
1 TTTTTAATTTTTCATTCTCAT
20401082 TTTTTAATTTTTCATTCTCAT
1 TTTTTAATTTTTCATTCTCAT
20401103 TCTTTT
1 T-TTTT
20401109 TTTTTTGACT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
21 20 0.83
22 4 0.17
ACGTcount: A:0.15, C:0.15, G:0.00, T:0.71
Consensus pattern (21 bp):
TTTTTAATTTTTCATTCTCAT
Found at i:20401676 original size:17 final size:17
Alignment explanation
Indices: 20401654--20401688 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
20401644 AACCATGGTG
20401654 TCTGATTTTGAATTGAT
1 TCTGATTTTGAATTGAT
20401671 TCTGATTTTGAATTGAT
1 TCTGATTTTGAATTGAT
20401688 T
1 T
20401689 ACAACCCTCA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.23, C:0.06, G:0.17, T:0.54
Consensus pattern (17 bp):
TCTGATTTTGAATTGAT
Found at i:20410801 original size:17 final size:17
Alignment explanation
Indices: 20410784--20410888 Score: 58
Period size: 17 Copynumber: 6.2 Consensus size: 17
20410774 ATAATATTAT
20410784 TTTAA-TAAATTTAATA
1 TTTAATTAAATTTAATA
*
20410800 TTTAATTTAATTTAATA
1 TTTAATTAAATTTAATA
* *
20410817 CTT-ATCTTAA--TAATA
1 TTTAAT-TAAATTTAATA
*
20410832 TTTTATT-AATTTAATA
1 TTTAATTAAATTTAATA
* * *
20410848 TTAAAGTGATTATCTTAATA
1 TTTAA-TTA-AAT-TTAATA
* *
20410868 TTTAATTTAATTTAATG
1 TTTAATTAAATTTAATA
20410885 TTTA
1 TTTA
20410889 TCTTGTAGAT
Statistics
Matches: 68, Mismatches: 12, Indels: 17
0.70 0.12 0.18
Matches are distributed among these distances:
14 2 0.03
15 8 0.12
16 17 0.25
17 26 0.38
18 2 0.03
19 3 0.04
20 10 0.15
ACGTcount: A:0.40, C:0.03, G:0.03, T:0.54
Consensus pattern (17 bp):
TTTAATTAAATTTAATA
Found at i:20410952 original size:18 final size:17
Alignment explanation
Indices: 20410929--20410962 Score: 59
Period size: 18 Copynumber: 1.9 Consensus size: 17
20410919 AATATTTAAT
20410929 ATTAAATTTAAATATTAG
1 ATTAAATTT-AATATTAG
20410947 ATTAAATTTAATATTA
1 ATTAAATTTAATATTA
20410963 AAGTGATTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 7 0.44
18 9 0.56
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (17 bp):
ATTAAATTTAATATTAG
Found at i:20417555 original size:6 final size:7
Alignment explanation
Indices: 20417522--20417553 Score: 55
Period size: 7 Copynumber: 4.6 Consensus size: 7
20417512 ATAAATATTT
*
20417522 TTTTTTA
1 TTTTTAA
20417529 TTTTTAA
1 TTTTTAA
20417536 TTTTTAA
1 TTTTTAA
20417543 TTTTTAA
1 TTTTTAA
20417550 TTTT
1 TTTT
20417554 AAAATACTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (7 bp):
TTTTTAA
Found at i:20421065 original size:37 final size:36
Alignment explanation
Indices: 20420996--20421070 Score: 91
Period size: 37 Copynumber: 2.1 Consensus size: 36
20420986 AAAGAGTTGT
20420996 ACTCAAAACTTGATGAGTCGTATCTGGAAAGATGTCA
1 ACTCAAAACTTGATGAGTCGTATCTGGAAAGATG-CA
* *
20421033 ACTCAAAACTT-AGTGAGTTGTA-CTTGGGAAGATGCA
1 ACTCAAAACTTGA-TGAGTCGTATC-TGGAAAGATGCA
20421069 AC
1 AC
20421071 CTAAAAATTT
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
36 6 0.18
37 28 0.82
ACGTcount: A:0.35, C:0.16, G:0.23, T:0.27
Consensus pattern (36 bp):
ACTCAAAACTTGATGAGTCGTATCTGGAAAGATGCA
Found at i:20421382 original size:37 final size:37
Alignment explanation
Indices: 20421303--20421404 Score: 100
Period size: 37 Copynumber: 2.8 Consensus size: 37
20421293 AAGGAGCTAT
* * *
20421303 GCTCAAAATTTAGTGAG-TAGAATCTGAGAAGGTATAA
1 GCTCAAAATTTAGTGAGTTATACT-TGAGAAGGTACAA
* *
20421340 ACTCAAAATTTAGTGAGTTATACTTGAGAAGGTACGA
1 GCTCAAAATTTAGTGAGTTATACTTGAGAAGGTACAA
** *
20421377 GCTCAATTTTTAAG-GAGTTGTACTTGAG
1 GCTCAAAATTT-AGTGAGTTATACTTGAG
20421405 GTGTAAACTA
Statistics
Matches: 54, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
37 48 0.89
38 6 0.11
ACGTcount: A:0.35, C:0.10, G:0.24, T:0.31
Consensus pattern (37 bp):
GCTCAAAATTTAGTGAGTTATACTTGAGAAGGTACAA
Found at i:20421426 original size:71 final size:71
Alignment explanation
Indices: 20421332--20421469 Score: 168
Period size: 71 Copynumber: 1.9 Consensus size: 71
20421322 GAATCTGAGA
* * * * * * *
20421332 AGGTATAAACTCAAAATTTAGTGAGTTATACTTGAGAAGGTACGAGCTCAATTTTTAAGGAGTTG
1 AGGTATAAACTAAAAACTTAGTGAGATATACCTGAAAAGGTACGAGCTCAAATTTTAAGGACTTG
20421397 TACTTG
66 TACTTG
* * ** *
20421403 AGGTGTAAACTAAAAACTTAGTGAGATGTACCTGAAAAGGTGTGAGCTCAAATTTTAGGGACTTG
1 AGGTATAAACTAAAAACTTAGTGAGATATACCTGAAAAGGTACGAGCTCAAATTTTAAGGACTTG
20421468 TA
66 TA
20421470 TTTAGGAAGG
Statistics
Matches: 55, Mismatches: 12, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
71 55 1.00
ACGTcount: A:0.35, C:0.10, G:0.24, T:0.31
Consensus pattern (71 bp):
AGGTATAAACTAAAAACTTAGTGAGATATACCTGAAAAGGTACGAGCTCAAATTTTAAGGACTTG
TACTTG
Found at i:20424361 original size:7 final size:7
Alignment explanation
Indices: 20424351--20424381 Score: 62
Period size: 7 Copynumber: 4.4 Consensus size: 7
20424341 AGAGTAGTGA
20424351 GTGGAGG
1 GTGGAGG
20424358 GTGGAGG
1 GTGGAGG
20424365 GTGGAGG
1 GTGGAGG
20424372 GTGGAGG
1 GTGGAGG
20424379 GTG
1 GTG
20424382 ATTTGGTATA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.13, C:0.00, G:0.71, T:0.16
Consensus pattern (7 bp):
GTGGAGG
Found at i:20427356 original size:107 final size:103
Alignment explanation
Indices: 20427093--20427356 Score: 288
Period size: 101 Copynumber: 2.5 Consensus size: 103
20427083 AAAAATTTAC
* * * * *
20427093 TTATTTTTTATGTTTAAATTTTTTAATATTTAAAAATTATTTTTGAAAA-CTTCTAAAACTCTTT
1 TTATTTTATATTTTTAAATTTTTTAACATTT-AAAATTATTTTTGAAAATC-TCTAAAACTCGTG
* * **
20427157 CCCATGTTAGTGGTGTTTTAAGGAGGTATATAAATATTTT
64 CCCATGTTAATGGTCTTTTAAGGAGACATATAAATATTTT
* *
20427197 TTATTTTAT-TTTATT---TTTATTTACCATTTAAAATTATTTTTGAAAATCTCTAAAGCT-GTG
1 TTATTTTATATTT-TTAAATTT-TTTAACATTTAAAATTATTTTTGAAAATCTCTAAAACTCGTG
* *
20427257 CCTCGTGTTAATGGTCTTTTAATGAGACATATAAATATTTTTT
64 CC-CATGTTAATGGTCTTTTAAGGAGACATATAAATA--TTTT
20427300 TATATTTTATATTTTTAAATTCTTTTAACATTTAAAATTATTTTTGAAAATCTCTAA
1 T-TATTTTATATTTTTAAATT-TTTTAACATTTAAAATTATTTTTGAAAATCTCTAA
20427357 CGGTCGCATA
Statistics
Matches: 134, Mismatches: 14, Indels: 21
0.79 0.08 0.12
Matches are distributed among these distances:
100 3 0.02
101 56 0.42
102 9 0.07
103 7 0.05
104 20 0.15
105 3 0.02
107 35 0.26
108 1 0.01
ACGTcount: A:0.32, C:0.08, G:0.08, T:0.52
Consensus pattern (103 bp):
TTATTTTATATTTTTAAATTTTTTAACATTTAAAATTATTTTTGAAAATCTCTAAAACTCGTGCC
CATGTTAATGGTCTTTTAAGGAGACATATAAATATTTT
Found at i:20436500 original size:23 final size:23
Alignment explanation
Indices: 20436473--20436518 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
20436463 AAAAATAAGT
20436473 ATAAAAATACATGGTATTGGATA
1 ATAAAAATACATGGTATTGGATA
20436496 ATAAAAATACATGGTATTGGATA
1 ATAAAAATACATGGTATTGGATA
20436519 TTTACATCAG
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:0.04, G:0.17, T:0.30
Consensus pattern (23 bp):
ATAAAAATACATGGTATTGGATA
Found at i:20440548 original size:12 final size:12
Alignment explanation
Indices: 20440517--20440566 Score: 59
Period size: 12 Copynumber: 4.1 Consensus size: 12
20440507 TCCTTCTGCT
20440517 TCATCACATTCCA
1 TCATC-CATTCCA
20440530 T-ATCCATGT-CA
1 TCATCCAT-TCCA
20440541 TCATCCATTCCA
1 TCATCCATTCCA
20440553 TCATCCATTTCCA
1 TCATCCA-TTCCA
20440566 T
1 T
20440567 ACTCTCATTG
Statistics
Matches: 33, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
11 7 0.21
12 19 0.58
13 7 0.21
ACGTcount: A:0.26, C:0.36, G:0.02, T:0.36
Consensus pattern (12 bp):
TCATCCATTCCA
Found at i:20442279 original size:15 final size:15
Alignment explanation
Indices: 20442259--20442309 Score: 52
Period size: 15 Copynumber: 3.5 Consensus size: 15
20442249 ACAAAACGAT
20442259 AACGTAAGTGACTAA
1 AACGTAAGTGACTAA
*
20442274 AACGTAA-T-ACTTCA
1 AACGTAAGTGAC-TAA
*
20442288 AACATAAGTGACTAA
1 AACGTAAGTGACTAA
*
20442303 AATGTAA
1 AACGTAA
20442310 ATTGAGACAA
Statistics
Matches: 28, Mismatches: 5, Indels: 6
0.72 0.13 0.15
Matches are distributed among these distances:
13 2 0.07
14 9 0.32
15 15 0.54
16 2 0.07
ACGTcount: A:0.49, C:0.14, G:0.14, T:0.24
Consensus pattern (15 bp):
AACGTAAGTGACTAA
Found at i:20444912 original size:9 final size:9
Alignment explanation
Indices: 20444898--20445014 Score: 135
Period size: 9 Copynumber: 12.6 Consensus size: 9
20444888 TTTGGTTAAA
20444898 AATTACCCG
1 AATTACCCG
20444907 AATTACCCG
1 AATTACCCG
*
20444916 ACTTACCCG
1 AATTACCCG
*
20444925 ACTTACCCG
1 AATTACCCG
*
20444934 AATTACCCA
1 AATTACCCG
*
20444943 AATTACTCG
1 AATTACCCG
*
20444952 AATTACCCAAA
1 AATTACCC--G
*
20444963 AATTACCCA
1 AATTACCCG
20444972 AATTACCCG
1 AATTACCCG
*
20444981 AATTACCCACA
1 AATTA-CC-CG
20444992 AATTACCCG
1 AATTACCCG
20445001 AATTACCCG
1 AATTACCCG
20445010 AATTA
1 AATTA
20445015 AATCACTACA
Statistics
Matches: 94, Mismatches: 10, Indels: 8
0.84 0.09 0.07
Matches are distributed among these distances:
9 76 0.81
10 4 0.04
11 14 0.15
ACGTcount: A:0.38, C:0.32, G:0.07, T:0.23
Consensus pattern (9 bp):
AATTACCCG
Found at i:20444972 original size:29 final size:29
Alignment explanation
Indices: 20444959--20445014 Score: 94
Period size: 29 Copynumber: 1.9 Consensus size: 29
20444949 TCGAATTACC
20444959 CAAAAATTACCCAAATTACCCGAATTACC
1 CAAAAATTACCCAAATTACCCGAATTACC
* *
20444988 CACAAATTACCCGAATTACCCGAATTA
1 CAAAAATTACCCAAATTACCCGAATTA
20445015 AATCACTACA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.43, C:0.30, G:0.05, T:0.21
Consensus pattern (29 bp):
CAAAAATTACCCAAATTACCCGAATTACC
Found at i:20445043 original size:17 final size:17
Alignment explanation
Indices: 20445010--20445118 Score: 69
Period size: 17 Copynumber: 6.1 Consensus size: 17
20445000 GAATTACCCG
*
20445010 AATT-AAATCACTACAT
1 AATTAAAATCATTACAT
*
20445026 AATTAAAAGCATTACAT
1 AATTAAAATCATTACAT
* *
20445043 AAATCTTTAAATCACTACAT
1 -AA--TTAAAATCATTACAT
20445063 AATTAAAA-CTATTACAT
1 AATTAAAATC-ATTACAT
** *
20445080 AAGTCTTTGAATCACTACAT
1 AA---TTAAAATCATTACAT
*
20445100 AATTAAAAACATTACAT
1 AATTAAAATCATTACAT
20445117 AA
1 AA
20445119 GTCTTGAATT
Statistics
Matches: 70, Mismatches: 14, Indels: 17
0.69 0.14 0.17
Matches are distributed among these distances:
16 5 0.07
17 36 0.51
18 2 0.03
19 2 0.03
20 24 0.34
21 1 0.01
ACGTcount: A:0.50, C:0.16, G:0.03, T:0.32
Consensus pattern (17 bp):
AATTAAAATCATTACAT
Found at i:20445058 original size:37 final size:36
Alignment explanation
Indices: 20445012--20445123 Score: 179
Period size: 37 Copynumber: 3.0 Consensus size: 36
20445002 ATTACCCGAA
*
20445012 TTAAATCACTACATAATTAAAAGCATTACATAAATCT
1 TTAAATCACTACATAATTAAAA-CATTACATAAGTCT
20445049 TTAAATCACTACATAATTAAAACTATTACATAAGTCT
1 TTAAATCACTACATAATTAAAAC-ATTACATAAGTCT
*
20445086 TTGAATCACTACATAATTAAAAACATTACATAAGTCT
1 TTAAATCACTACATAATT-AAAACATTACATAAGTCT
20445123 T
1 T
20445124 GAATTAACAC
Statistics
Matches: 71, Mismatches: 2, Indels: 4
0.92 0.03 0.05
Matches are distributed among these distances:
36 1 0.01
37 65 0.92
38 5 0.07
ACGTcount: A:0.46, C:0.16, G:0.04, T:0.34
Consensus pattern (36 bp):
TTAAATCACTACATAATTAAAACATTACATAAGTCT
Found at i:20445063 original size:20 final size:18
Alignment explanation
Indices: 20445012--20445064 Score: 54
Period size: 20 Copynumber: 2.9 Consensus size: 18
20445002 ATTACCCGAA
20445012 TTAAATCACTACAT-AAT
1 TTAAATCACTACATAAAT
* * *
20445029 TAAAAGCATTACATAAATCT
1 TTAAATCACTACATAAA--T
20445049 TTAAATCACTACATAA
1 TTAAATCACTACATAA
20445065 TTAAAACTAT
Statistics
Matches: 27, Mismatches: 6, Indels: 3
0.75 0.17 0.08
Matches are distributed among these distances:
17 11 0.41
18 2 0.07
20 14 0.52
ACGTcount: A:0.49, C:0.17, G:0.02, T:0.32
Consensus pattern (18 bp):
TTAAATCACTACATAAAT
Found at i:20447966 original size:15 final size:16
Alignment explanation
Indices: 20447933--20447971 Score: 71
Period size: 16 Copynumber: 2.5 Consensus size: 16
20447923 GGGCCATGAT
20447933 ATTATAATGATGAAAA
1 ATTATAATGATGAAAA
20447949 ATTATAATGATG-AAA
1 ATTATAATGATGAAAA
20447964 ATTATAAT
1 ATTATAAT
20447972 ATTAGTCAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
15 11 0.48
16 12 0.52
ACGTcount: A:0.54, C:0.00, G:0.10, T:0.36
Consensus pattern (16 bp):
ATTATAATGATGAAAA
Found at i:20448222 original size:25 final size:25
Alignment explanation
Indices: 20448189--20448236 Score: 87
Period size: 25 Copynumber: 1.9 Consensus size: 25
20448179 TTTATATATG
*
20448189 CTGGTTGTGTAAAGAAATTTGTACA
1 CTGGATGTGTAAAGAAATTTGTACA
20448214 CTGGATGTGTAAAGAAATTTGTA
1 CTGGATGTGTAAAGAAATTTGTA
20448237 AGTAATAAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.33, C:0.06, G:0.25, T:0.35
Consensus pattern (25 bp):
CTGGATGTGTAAAGAAATTTGTACA
Found at i:20450915 original size:32 final size:32
Alignment explanation
Indices: 20450872--20450986 Score: 137
Period size: 32 Copynumber: 3.6 Consensus size: 32
20450862 TTTTAAAGGA
*
20450872 ATATTT-TTATCATTTAACAAAATTAAAGTTT
1 ATATTTGTTATCATTTCACAAAATTAAAGTTT
*
20450903 ATATTTGTTATCATTTCACAAAATTGAAGTTGT
1 ATATTTGTTATCATTTCACAAAATTAAAGTT-T
* * * *
20450936 -TATTTGGTA-CAATTTCACAAAATGAAAGGTG
1 ATATTTGTTATC-ATTTCACAAAATTAAAGTTT
20450967 ATATTTGTTATCATTTCACA
1 ATATTTGTTATCATTTCACA
20450987 GAACCATGCA
Statistics
Matches: 71, Mismatches: 8, Indels: 9
0.81 0.09 0.10
Matches are distributed among these distances:
31 7 0.10
32 62 0.87
33 2 0.03
ACGTcount: A:0.37, C:0.10, G:0.10, T:0.43
Consensus pattern (32 bp):
ATATTTGTTATCATTTCACAAAATTAAAGTTT
Found at i:20455540 original size:18 final size:18
Alignment explanation
Indices: 20455509--20455547 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
20455499 TCACGTCAAC
20455509 AAATAATTTAAAAATTATA
1 AAATAATTTAAAAATT-TA
*
20455528 AAAT-ATTTTAAAATTTA
1 AAATAATTTAAAAATTTA
20455545 AAA
1 AAA
20455548 ATTCATAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 5 0.26
18 10 0.53
19 4 0.21
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (18 bp):
AAATAATTTAAAAATTTA
Found at i:20455548 original size:18 final size:19
Alignment explanation
Indices: 20455509--20455549 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
20455499 TCACGTCAAC
20455509 AAATAATTTAAAAATTATA
1 AAATAATTTAAAAATTATA
* *
20455528 AAATATTTTAAAATTTA-A
1 AAATAATTTAAAAATTATA
20455546 AAAT
1 AAAT
20455550 TCATAAAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 5 0.25
19 15 0.75
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (19 bp):
AAATAATTTAAAAATTATA
Found at i:20457390 original size:45 final size:47
Alignment explanation
Indices: 20457324--20457415 Score: 161
Period size: 45 Copynumber: 2.0 Consensus size: 47
20457314 AGCGTGGCAC
20457324 TACTACACTTCTCCTATTGATTAGTTGCAGGCAATAATAAATGCCAA
1 TACTACACTTCTCCTATTGATTAGTTGCAGGCAATAATAAATGCCAA
*
20457371 TACTACAC-T-TCCTATTGATTAGTTTCAGGCAATAATAAATGCCAA
1 TACTACACTTCTCCTATTGATTAGTTGCAGGCAATAATAAATGCCAA
20457416 ATACGAAGAT
Statistics
Matches: 44, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
45 35 0.80
46 1 0.02
47 8 0.18
ACGTcount: A:0.35, C:0.21, G:0.12, T:0.33
Consensus pattern (47 bp):
TACTACACTTCTCCTATTGATTAGTTGCAGGCAATAATAAATGCCAA
Found at i:20468969 original size:5 final size:5
Alignment explanation
Indices: 20468959--20468984 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
20468949 GGTTATAATT
20468959 ATAAA ATAAA ATAAA ATAAA ATAAA A
1 ATAAA ATAAA ATAAA ATAAA ATAAA A
20468985 GCTTTCTTCT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (5 bp):
ATAAA
Found at i:20474499 original size:3 final size:3
Alignment explanation
Indices: 20474491--20474520 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
20474481 ATTCCCACTC
*
20474491 ATA ATA ATA ATA ATA ATA ATA ATA TTA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
20474521 CTTACCTCAC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (3 bp):
ATA
Found at i:20475261 original size:20 final size:20
Alignment explanation
Indices: 20475227--20475266 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
20475217 TTCTATTCTG
*
20475227 TTTCTTTTCTGTTTTGTTTC
1 TTTCTTTTCTGTTTTATTTC
20475247 TTTCTTTTTCT-TTTTATTTC
1 TTTC-TTTTCTGTTTTATTTC
20475267 CTTTTATTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 12 0.67
21 6 0.33
ACGTcount: A:0.03, C:0.15, G:0.05, T:0.78
Consensus pattern (20 bp):
TTTCTTTTCTGTTTTATTTC
Found at i:20475433 original size:31 final size:28
Alignment explanation
Indices: 20475397--20475464 Score: 73
Period size: 31 Copynumber: 2.3 Consensus size: 28
20475387 TTGTCTTTAT
**
20475397 TTAATTTATTTCTTAATATAATATTTATAA
1 TTAATTTATTTAATAATAT-A-ATTTATAA
* *
20475427 TGTAATTAATTTAATAATATACTTTATAA
1 T-TAATTTATTTAATAATATAATTTATAA
20475456 TTAATTTAT
1 TTAATTTAT
20475465 ATATTTATAT
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
28 7 0.22
29 8 0.25
30 2 0.06
31 15 0.47
ACGTcount: A:0.41, C:0.03, G:0.01, T:0.54
Consensus pattern (28 bp):
TTAATTTATTTAATAATATAATTTATAA
Found at i:20475481 original size:21 final size:20
Alignment explanation
Indices: 20475443--20475481 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
20475433 TAATTTAATA
*
20475443 ATATACTTTATAATTAATTT
1 ATATACTTTATAAATAATTT
*
20475463 ATATATTTATATAAATAAT
1 ATATACTT-TATAAATAAT
20475482 AATATAAAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 7 0.44
21 9 0.56
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (20 bp):
ATATACTTTATAAATAATTT
Found at i:20475887 original size:12 final size:12
Alignment explanation
Indices: 20475870--20475894 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
20475860 ATGCTTTTCG
20475870 TATCCTAGTCTT
1 TATCCTAGTCTT
20475882 TATCCTAGTCTT
1 TATCCTAGTCTT
20475894 T
1 T
20475895 CGCCTTTGTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.16, C:0.24, G:0.08, T:0.52
Consensus pattern (12 bp):
TATCCTAGTCTT
Found at i:20476000 original size:23 final size:23
Alignment explanation
Indices: 20475951--20476000 Score: 55
Period size: 23 Copynumber: 2.2 Consensus size: 23
20475941 ACTTTTTTTG
* ** *
20475951 AGTTATCTCAAATAAGTGTTTCG
1 AGTTAACTCAAATAAGTAATTCA
*
20475974 AGTTAACTCGAATAAGTAATTCA
1 AGTTAACTCAAATAAGTAATTCA
20475997 AGTT
1 AGTT
20476001 TTGAGTTCGA
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.36, C:0.12, G:0.16, T:0.36
Consensus pattern (23 bp):
AGTTAACTCAAATAAGTAATTCA
Found at i:20476135 original size:9 final size:9
Alignment explanation
Indices: 20476123--20476163 Score: 55
Period size: 9 Copynumber: 4.6 Consensus size: 9
20476113 TTATAAAAAT
20476123 AATTTTTAA
1 AATTTTTAA
*
20476132 AATTTATAA
1 AATTTTTAA
*
20476141 TATTTTTAA
1 AATTTTTAA
*
20476150 AATTTTCAA
1 AATTTTTAA
20476159 AATTT
1 AATTT
20476164 ACATTTTTAA
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
9 27 1.00
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (9 bp):
AATTTTTAA
Found at i:20478516 original size:15 final size:16
Alignment explanation
Indices: 20478500--20478543 Score: 52
Period size: 17 Copynumber: 2.6 Consensus size: 16
20478490 ATAATTAATT
20478500 AATATTTTTATATTTAA
1 AATA-TTTTATATTTAA
*
20478517 AATCATTTTATATTTTTA
1 AAT-ATTTTATA-TTTAA
20478535 AATATTTTA
1 AATATTTTA
20478544 AATATATTAA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
17 16 0.67
18 8 0.33
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (16 bp):
AATATTTTATATTTAA
Found at i:20478541 original size:17 final size:18
Alignment explanation
Indices: 20478500--20478554 Score: 60
Period size: 18 Copynumber: 3.1 Consensus size: 18
20478490 ATAATTAATT
20478500 AATATTTT-TATATTTAA
1 AATATTTTATATATTTAA
*
20478517 AATCATTTTATAT-TTTTA
1 AAT-ATTTTATATATTTAA
*
20478535 AATATTTTAAATATATTAA
1 AATATTTTATATAT-TTAA
20478554 A
1 A
20478555 TGTAGATAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
17 11 0.35
18 13 0.42
19 7 0.23
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.55
Consensus pattern (18 bp):
AATATTTTATATATTTAA
Found at i:20478544 original size:9 final size:9
Alignment explanation
Indices: 20478500--20478555 Score: 53
Period size: 9 Copynumber: 6.3 Consensus size: 9
20478490 ATAATTAATT
20478500 AATATTTT-
1 AATATTTTA
* *
20478508 TATATTTAA
1 AATATTTTA
20478517 AATCATTTTA
1 AAT-ATTTTA
*
20478527 TAT-TTTTA
1 AATATTTTA
20478535 AATATTTTA
1 AATATTTTA
*
20478544 AATATATTA
1 AATATTTTA
20478553 AAT
1 AAT
20478556 GTAGATAAAT
Statistics
Matches: 38, Mismatches: 7, Indels: 5
0.76 0.14 0.10
Matches are distributed among these distances:
8 13 0.34
9 18 0.47
10 7 0.18
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (9 bp):
AATATTTTA
Found at i:20479569 original size:21 final size:21
Alignment explanation
Indices: 20479540--20479594 Score: 60
Period size: 21 Copynumber: 2.7 Consensus size: 21
20479530 AATATATCTG
* * *
20479540 TATTTAAATTTTATTTTATTT
1 TATTCAAATTTTAATCTATTT
20479561 TATTCAAATTTTAATCTATTT
1 TATTCAAATTTTAATCTATTT
*
20479582 TTTTC--ATTTTAAT
1 TATTCAAATTTTAAT
20479595 ATTGTACATA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
19 8 0.27
21 22 0.73
ACGTcount: A:0.29, C:0.05, G:0.00, T:0.65
Consensus pattern (21 bp):
TATTCAAATTTTAATCTATTT
Found at i:20501460 original size:25 final size:24
Alignment explanation
Indices: 20501432--20501489 Score: 71
Period size: 25 Copynumber: 2.3 Consensus size: 24
20501422 GTTTTTCTTA
**
20501432 AATATTTGTATAATTATTTTTAATT
1 AATATTTACATAA-TATTTTTAATT
*
20501457 AATATTAACATAATATTTTTAATT
1 AATATTTACATAATATTTTTAATT
20501481 ATATATTTA
1 A-ATATTTA
20501490 TTTATAAACT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
24 12 0.43
25 16 0.57
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.55
Consensus pattern (24 bp):
AATATTTACATAATATTTTTAATT
Found at i:20501516 original size:19 final size:19
Alignment explanation
Indices: 20501488--20501524 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
20501478 ATTATATATT
*
20501488 TATTTATAAACTTTTTATA
1 TATTTATAAAATTTTTATA
*
20501507 TATTTTTAAAATTTTTAT
1 TATTTATAAAATTTTTAT
20501525 TTCAGTTTAG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.62
Consensus pattern (19 bp):
TATTTATAAAATTTTTATA
Found at i:20504247 original size:28 final size:28
Alignment explanation
Indices: 20504188--20504247 Score: 93
Period size: 28 Copynumber: 2.1 Consensus size: 28
20504178 AATGTTAATC
* * *
20504188 TTTCATAGTTTGCCACAAAGGCTTCTTT
1 TTTCATAGTTTGCCACAAAGGCATATTA
20504216 TTTCATAGTTTGCCACAAAGGCATATTA
1 TTTCATAGTTTGCCACAAAGGCATATTA
20504244 TTTC
1 TTTC
20504248 CTGACATGTT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.25, C:0.20, G:0.13, T:0.42
Consensus pattern (28 bp):
TTTCATAGTTTGCCACAAAGGCATATTA
Found at i:20507420 original size:46 final size:46
Alignment explanation
Indices: 20507350--20507534 Score: 289
Period size: 46 Copynumber: 4.0 Consensus size: 46
20507340 CATGGAAAAG
*
20507350 TGTGAAACGTAGGTATGGTATTTCAGTGAAGAAAACCATACTGAGT
1 TGTGAAAAGTAGGTATGGTATTTCAGTGAAGAAAACCATACTGAGT
* *
20507396 TGTGAAAAGTAGGTATGGTGTTTCAGTGAAGAAAACCATATTGAGT
1 TGTGAAAAGTAGGTATGGTATTTCAGTGAAGAAAACCATACTGAGT
* * * *
20507442 TGTGAAAAGTAGGTATGGTGTTTTAGTGAATAAAACCATACTGAAT
1 TGTGAAAAGTAGGTATGGTATTTCAGTGAAGAAAACCATACTGAGT
* *
20507488 TGTGAAAAATAGGTATGGTATTTCCGTGAAGAAAACCATACTGAGT
1 TGTGAAAAGTAGGTATGGTATTTCAGTGAAGAAAACCATACTGAGT
20507534 T
1 T
20507535 ATAGCAATGT
Statistics
Matches: 126, Mismatches: 13, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
46 126 1.00
ACGTcount: A:0.36, C:0.09, G:0.25, T:0.30
Consensus pattern (46 bp):
TGTGAAAAGTAGGTATGGTATTTCAGTGAAGAAAACCATACTGAGT
Found at i:20509249 original size:38 final size:38
Alignment explanation
Indices: 20509198--20509290 Score: 141
Period size: 38 Copynumber: 2.4 Consensus size: 38
20509188 CTACTGAGTC
* *
20509198 CATGTTAAGCATGTGTACTACTACTATTAAACAAAATA
1 CATGTTAAGCATGTCTACGACTACTATTAAACAAAATA
* **
20509236 CATGTTAAGCATGTCTACGGCTACTATTAAATTAAATA
1 CATGTTAAGCATGTCTACGACTACTATTAAACAAAATA
20509274 CATGTTAAGCATGTCTA
1 CATGTTAAGCATGTCTA
20509291 TTATTTCTGT
Statistics
Matches: 50, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
38 50 1.00
ACGTcount: A:0.38, C:0.16, G:0.13, T:0.33
Consensus pattern (38 bp):
CATGTTAAGCATGTCTACGACTACTATTAAACAAAATA
Found at i:20509512 original size:22 final size:23
Alignment explanation
Indices: 20509450--20509512 Score: 58
Period size: 22 Copynumber: 2.7 Consensus size: 23
20509440 AAAAATAATA
*
20509450 GTGGTTCATCCCCAAATTTTTACTG
1 GTGGTTCATCCTCAAA--TTTACTG
* *
20509475 GTAGTTTAT-CTACAAA-TTACTG
1 GTGGTTCATCCT-CAAATTTACTG
20509497 GTGGTTCATCCTCAAA
1 GTGGTTCATCCTCAAA
20509513 ATGGAATGTT
Statistics
Matches: 31, Mismatches: 5, Indels: 7
0.72 0.12 0.16
Matches are distributed among these distances:
22 17 0.55
23 2 0.06
24 1 0.03
25 11 0.35
ACGTcount: A:0.25, C:0.21, G:0.16, T:0.38
Consensus pattern (23 bp):
GTGGTTCATCCTCAAATTTACTG
Found at i:20511198 original size:48 final size:46
Alignment explanation
Indices: 20511113--20511217 Score: 106
Period size: 46 Copynumber: 2.2 Consensus size: 46
20511103 TGTTATATTC
* *
20511113 ATATATATATATTATGTATATTTTATTATATTTTATTTCATAGCTT
1 ATATATATATATTATGTATATTTTAATATATTTTATTTCATAACTT
* * *
20511159 TTATATATATATT-T-TATAATATTTAATATTTTTCATATTTTATAACTT
1 ATATATATATATTATGTAT-AT-TTTAATATATTT--TATTTCATAACTT
*
20511207 ATACATATATA
1 ATATATATATA
20511218 CACGCATAGG
Statistics
Matches: 48, Mismatches: 7, Indels: 6
0.79 0.11 0.10
Matches are distributed among these distances:
44 3 0.06
45 3 0.06
46 22 0.46
48 20 0.42
ACGTcount: A:0.36, C:0.05, G:0.02, T:0.57
Consensus pattern (46 bp):
ATATATATATATTATGTATATTTTAATATATTTTATTTCATAACTT
Found at i:20517318 original size:3 final size:3
Alignment explanation
Indices: 20517310--20517354 Score: 90
Period size: 3 Copynumber: 15.0 Consensus size: 3
20517300 AATGTTATGG
20517310 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
20517355 AACGCAAGCC
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:20517648 original size:11 final size:11
Alignment explanation
Indices: 20517632--20517675 Score: 54
Period size: 11 Copynumber: 4.0 Consensus size: 11
20517622 AGATTAATTT
20517632 GAATTTTTTTA
1 GAATTTTTTTA
*
20517643 GAATTTTTATA
1 GAATTTTTTTA
20517654 -AGATTTTTTTA
1 GA-ATTTTTTTA
*
20517665 AAATTTTTTTA
1 GAATTTTTTTA
20517676 TAAAATTTTA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
10 1 0.03
11 27 0.93
12 1 0.03
ACGTcount: A:0.32, C:0.00, G:0.07, T:0.61
Consensus pattern (11 bp):
GAATTTTTTTA
Found at i:20517664 original size:13 final size:12
Alignment explanation
Indices: 20517646--20517684 Score: 53
Period size: 13 Copynumber: 3.2 Consensus size: 12
20517636 TTTTTTAGAA
20517646 TTTTTATAAGATT
1 TTTTTATAA-ATT
20517659 TTTTTA-AAATT
1 TTTTTATAAATT
20517670 TTTTTATAAAATT
1 TTTTTAT-AAATT
20517683 TT
1 TT
20517685 AATAATTACT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
11 9 0.38
12 2 0.08
13 13 0.54
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.64
Consensus pattern (12 bp):
TTTTTATAAATT
Found at i:20517684 original size:11 final size:11
Alignment explanation
Indices: 20517633--20517689 Score: 51
Period size: 11 Copynumber: 5.0 Consensus size: 11
20517623 GATTAATTTG
* *
20517633 AATTTTTTTAG
1 AATTTTTATAA
20517644 AATTTTTATAA
1 AATTTTTATAA
* *
20517655 GATTTTTTTAA
1 AATTTTTATAA
20517666 AATTTTTTTATAA
1 AA--TTTTTATAA
*
20517679 AATTTTAATAA
1 AATTTTTATAA
20517690 TTACTAATAA
Statistics
Matches: 37, Mismatches: 7, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
11 27 0.73
13 10 0.27
ACGTcount: A:0.39, C:0.00, G:0.04, T:0.58
Consensus pattern (11 bp):
AATTTTTATAA
Found at i:20518386 original size:18 final size:18
Alignment explanation
Indices: 20518355--20518389 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
20518345 CTATTGAATT
* *
20518355 AATTTTAATTTATATTAG
1 AATTTAAATGTATATTAG
20518373 AATTTAAATGTATATTA
1 AATTTAAATGTATATTA
20518390 AATGTTTAAT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.43, C:0.00, G:0.06, T:0.51
Consensus pattern (18 bp):
AATTTAAATGTATATTAG
Found at i:20522160 original size:41 final size:41
Alignment explanation
Indices: 20522114--20522197 Score: 168
Period size: 41 Copynumber: 2.0 Consensus size: 41
20522104 ATAATTGTTG
20522114 ATTGCCGTCTTGATGATTTAATGTCATTAAATAAGTTATTA
1 ATTGCCGTCTTGATGATTTAATGTCATTAAATAAGTTATTA
20522155 ATTGCCGTCTTGATGATTTAATGTCATTAAATAAGTTATTA
1 ATTGCCGTCTTGATGATTTAATGTCATTAAATAAGTTATTA
20522196 AT
1 AT
20522198 GCTTCAAGAT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 43 1.00
ACGTcount: A:0.32, C:0.10, G:0.14, T:0.44
Consensus pattern (41 bp):
ATTGCCGTCTTGATGATTTAATGTCATTAAATAAGTTATTA
Found at i:20526595 original size:14 final size:14
Alignment explanation
Indices: 20526576--20526618 Score: 59
Period size: 14 Copynumber: 3.0 Consensus size: 14
20526566 AGAAGAGTAA
20526576 TTTTATAATTTTTT
1 TTTTATAATTTTTT
**
20526590 TTTTATAATTTTCC
1 TTTTATAATTTTTT
20526604 TTTTATAATATTTTT
1 TTTTATAAT-TTTTT
20526619 AATTATTTTA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
14 21 0.88
15 3 0.12
ACGTcount: A:0.23, C:0.05, G:0.00, T:0.72
Consensus pattern (14 bp):
TTTTATAATTTTTT
Found at i:20527466 original size:29 final size:29
Alignment explanation
Indices: 20527410--20527477 Score: 84
Period size: 29 Copynumber: 2.3 Consensus size: 29
20527400 CATGATAATG
**
20527410 TAAGTGACTAAAATGTAACATTTCAAACA
1 TAAGTGACTAAAATGTAACAGATCAAACA
*
20527439 TAAGTGACTAAAATGTAACCCGAT-AAACA
1 TAAGTGACTAAAATGTAA-CAGATCAAACA
*
20527468 AAAGTGACTA
1 TAAGTGACTA
20527478 TTTTGGTTGT
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
29 32 0.94
30 2 0.06
ACGTcount: A:0.49, C:0.15, G:0.13, T:0.24
Consensus pattern (29 bp):
TAAGTGACTAAAATGTAACAGATCAAACA
Found at i:20528798 original size:13 final size:13
Alignment explanation
Indices: 20528779--20528821 Score: 52
Period size: 12 Copynumber: 3.3 Consensus size: 13
20528769 TAATTTTATA
20528779 TTATTTATGAATT
1 TTATTTATGAATT
* *
20528792 TTTTTTA-GAATA
1 TTATTTATGAATT
20528804 TTATTTATGAATT
1 TTATTTATGAATT
20528817 CTTAT
1 -TTAT
20528822 GAAAATAAGA
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
12 10 0.42
13 10 0.42
14 4 0.17
ACGTcount: A:0.30, C:0.02, G:0.07, T:0.60
Consensus pattern (13 bp):
TTATTTATGAATT
Found at i:20528810 original size:12 final size:13
Alignment explanation
Indices: 20528776--20528815 Score: 55
Period size: 13 Copynumber: 3.2 Consensus size: 13
20528766 TAGTAATTTT
20528776 ATATTATTTATGA
1 ATATTATTTATGA
* *
20528789 ATTTTTTTTA-GA
1 ATATTATTTATGA
20528801 ATATTATTTATGA
1 ATATTATTTATGA
20528814 AT
1 AT
20528816 TCTTATGAAA
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
12 10 0.45
13 12 0.55
ACGTcount: A:0.35, C:0.00, G:0.07, T:0.57
Consensus pattern (13 bp):
ATATTATTTATGA
Found at i:20528828 original size:25 final size:25
Alignment explanation
Indices: 20528776--20528828 Score: 70
Period size: 25 Copynumber: 2.1 Consensus size: 25
20528766 TAGTAATTTT
* * * *
20528776 ATATTATTTATGAATTTTTTTTAGA
1 ATATTATTTATGAATTCTTATGAAA
20528801 ATATTATTTATGAATTCTTATGAAA
1 ATATTATTTATGAATTCTTATGAAA
20528826 ATA
1 ATA
20528829 AGAAAAAAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.38, C:0.02, G:0.08, T:0.53
Consensus pattern (25 bp):
ATATTATTTATGAATTCTTATGAAA
Found at i:20537103 original size:27 final size:27
Alignment explanation
Indices: 20537086--20537264 Score: 232
Period size: 27 Copynumber: 6.6 Consensus size: 27
20537076 CTGGTGTTCA
*
20537086 AATTGCTGCTGGGTAGGCCGGTGATCG
1 AATTGCTGTTGGGTAGGCCGGTGATCG
* * *
20537113 AATTGCTGCTGGTTAGGCCGGTGCTCG
1 AATTGCTGTTGGGTAGGCCGGTGATCG
* * *
20537140 AATGGCTGTTGGTTAGGCCGGTGTTCG
1 AATTGCTGTTGGGTAGGCCGGTGATCG
* * * *
20537167 AATGGTTGTTGGTTAGGCCGGTGATCA
1 AATTGCTGTTGGGTAGGCCGGTGATCG
*
20537194 AATTGCTGTTGGGTAGGCCGGTGTTCG
1 AATTGCTGTTGGGTAGGCCGGTGATCG
*
20537221 AATGGCTGTTGGGTAGGCCGGTGATCG
1 AATTGCTGTTGGGTAGGCCGGTGATCG
*
20537248 AATTGCTGCTGGGTAGG
1 AATTGCTGTTGGGTAGG
20537265 GCAATAGTCG
Statistics
Matches: 135, Mismatches: 17, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 135 1.00
ACGTcount: A:0.14, C:0.16, G:0.40, T:0.30
Consensus pattern (27 bp):
AATTGCTGTTGGGTAGGCCGGTGATCG
Found at i:20537163 original size:81 final size:81
Alignment explanation
Indices: 20537073--20537264 Score: 276
Period size: 81 Copynumber: 2.4 Consensus size: 81
20537063 GCTGATTGCC
* * * *
20537073 AGGCTGGTGTTCAAATTGCTGCTGGGTAGGCCGGTGATCGAATTGCTGCTGGTTAGGCCGGTGCT
1 AGGCCGGTGTTCGAATTGCTGCTGGGTAGGCCGGTGATCAAATTGCTGCTGGGTAGGCCGGTGCT
*
20537138 CGAATGGCTGTTGGTT
66 CGAATGGCTGTTGGGT
* * * * * *
20537154 AGGCCGGTGTTCGAATGGTTGTTGGTTAGGCCGGTGATCAAATTGCTGTTGGGTAGGCCGGTGTT
1 AGGCCGGTGTTCGAATTGCTGCTGGGTAGGCCGGTGATCAAATTGCTGCTGGGTAGGCCGGTGCT
20537219 CGAATGGCTGTTGGGT
66 CGAATGGCTGTTGGGT
*
20537235 AGGCCGGTGATCGAATTGCTGCTGGGTAGG
1 AGGCCGGTGTTCGAATTGCTGCTGGGTAGG
20537265 GCAATAGTCG
Statistics
Matches: 95, Mismatches: 16, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
81 95 1.00
ACGTcount: A:0.14, C:0.16, G:0.40, T:0.30
Consensus pattern (81 bp):
AGGCCGGTGTTCGAATTGCTGCTGGGTAGGCCGGTGATCAAATTGCTGCTGGGTAGGCCGGTGCT
CGAATGGCTGTTGGGT
Found at i:20537277 original size:54 final size:54
Alignment explanation
Indices: 20537086--20537264 Score: 259
Period size: 54 Copynumber: 3.3 Consensus size: 54
20537076 CTGGTGTTCA
* * * *
20537086 AATTGCTGCTGGGTAGGCCGGTGATCGAATTGCTGCTGGTTAGGCCGGTGCTCG
1 AATTGCTGCTGGGTAGGCCGGTGTTCGAATGGCTGTTGGTTAGGCCGGTGATCG
* * * * *
20537140 AATGGCTGTTGGTTAGGCCGGTGTTCGAATGGTTGTTGGTTAGGCCGGTGATCA
1 AATTGCTGCTGGGTAGGCCGGTGTTCGAATGGCTGTTGGTTAGGCCGGTGATCG
* *
20537194 AATTGCTGTTGGGTAGGCCGGTGTTCGAATGGCTGTTGGGTAGGCCGGTGATCG
1 AATTGCTGCTGGGTAGGCCGGTGTTCGAATGGCTGTTGGTTAGGCCGGTGATCG
20537248 AATTGCTGCTGGGTAGG
1 AATTGCTGCTGGGTAGG
20537265 GCAATAGTCG
Statistics
Matches: 110, Mismatches: 15, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
54 110 1.00
ACGTcount: A:0.14, C:0.16, G:0.40, T:0.30
Consensus pattern (54 bp):
AATTGCTGCTGGGTAGGCCGGTGTTCGAATGGCTGTTGGTTAGGCCGGTGATCG
Found at i:20541937 original size:33 final size:32
Alignment explanation
Indices: 20541821--20541943 Score: 131
Period size: 33 Copynumber: 3.8 Consensus size: 32
20541811 GCAGTAGTCA
* * * *
20541821 CACCCTCCCCATCAGCTTTTACCTTTTCAACAT
1 CACCCTCCCTAGCAGCTTCTACC-CTTCAACAT
* *
20541854 CACCCTCCCTAACAACTTCTATCCCTTCAACAT
1 CACCCTCCCTAGCAGCTTCTA-CCCTTCAACAT
*
20541887 CACCCT-CTTCAGCAGCTTCTACACCTTCAACAT
1 CACCCTCCCT-AGCAGCTTCTAC-CCTTCAACAT
*
20541920 CACCCTCCCTAGTAGCTTCTACCC
1 CACCCTCCCTAGCAGCTTCTACCC
20541944 CCTCCCTAGT
Statistics
Matches: 76, Mismatches: 10, Indels: 9
0.80 0.11 0.09
Matches are distributed among these distances:
32 5 0.07
33 67 0.88
34 4 0.05
ACGTcount: A:0.23, C:0.45, G:0.04, T:0.28
Consensus pattern (32 bp):
CACCCTCCCTAGCAGCTTCTACCCTTCAACAT
Found at i:20541946 original size:21 final size:21
Alignment explanation
Indices: 20541922--20541964 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
20541912 TTCAACATCA
*
20541922 CCCTCCCTAGTAGCTTCTACC
1 CCCTCCCTAGTAACTTCTACC
*
20541943 CCCTCCCTAGTAACTTTTACC
1 CCCTCCCTAGTAACTTCTACC
20541964 C
1 C
20541965 ATTCAACAAC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.16, C:0.47, G:0.07, T:0.30
Consensus pattern (21 bp):
CCCTCCCTAGTAACTTCTACC
Found at i:20541971 original size:54 final size:54
Alignment explanation
Indices: 20541903--20542030 Score: 152
Period size: 54 Copynumber: 2.4 Consensus size: 54
20541893 CTTCAGCAGC
* *
20541903 TTCTACACC-TTCAACATCACCCTCCCTAGTAGCTTCTACCCCCTCCCTAGTAACT
1 TTCTAC-CCATTCAACATCACCCTCCCTAGCAGCTTCTACCCCCTCCCCA-TAACT
* * * * * *
20541958 TT-TACCCATTCAACAACACCCTCCTTAGCAGTTTGTACCCCCTCCCCATCAGT
1 TTCTACCCATTCAACATCACCCTCCCTAGCAGCTTCTACCCCCTCCCCATAACT
20542011 TTCTACCCATTCAACATCAC
1 TTCTACCCATTCAACATCAC
20542031 ACTATCCATC
Statistics
Matches: 62, Mismatches: 9, Indels: 5
0.82 0.12 0.07
Matches are distributed among these distances:
53 7 0.11
54 53 0.85
55 2 0.03
ACGTcount: A:0.23, C:0.42, G:0.05, T:0.29
Consensus pattern (54 bp):
TTCTACCCATTCAACATCACCCTCCCTAGCAGCTTCTACCCCCTCCCCATAACT
Found at i:20548552 original size:134 final size:134
Alignment explanation
Indices: 20548307--20549003 Score: 713
Period size: 134 Copynumber: 5.2 Consensus size: 134
20548297 TAAGTAAAAG
* * * * * *
20548307 GTCGTGATCGTAAATCAGCGAACTGATTAAGTGGAGTCGCGATTGTAAATCAACGAACTGTTTAA
1 GTCGTGATCGTAAATCAGCGAACTGTTTAAGTGGAGTCGCGATCGTAAATCGATGAACTCTTTAT
* * * * * * *
20548372 AAAGTGGTCATGATCGTAAATCGATGAATTGAAGATGTGATCGTAAATTAGCGAGCTTTAAAAAT
66 GAAGTGTTCATGATCGTAAATCAATGAACTGAAGATGTAATCGTAAATCAACGAGCTTTAAAAAT
*
20548437 GATA
131 GACA
* * * *
20548441 GTCGTGATCATAAATCAGCGAACTGTTTAAGTGAAGTCGCGACCGTAAATCGATGAACTCTTTTT
1 GTCGTGATCGTAAATCAGCGAACTGTTTAAGTGGAGTCGCGATCGTAAATCGATGAACTCTTTAT
* * * *
20548506 GAAGTGTTTATGATCGTAAATCAATAAACTGAAGCTGTAATTGTAAATCAACGAGCTTTAAAAAT
66 GAAGTGTTCATGATCGTAAATCAATGAACTGAAGATGTAATCGTAAATCAACGAGCTTTAAAAAT
*
20548571 GATA
131 GACA
* * * *
20548575 GTCGTGATCGTAAATCAGCTAACTGTTTAAGTGGAGTCGCAATCGTAAATCGATGAACTGTTTAA
1 GTCGTGATCGTAAATCAGCGAACTGTTTAAGTGGAGTCGCGATCGTAAATCGATGAACTCTTTAT
* * * * * * *
20548640 GAAGTGATCATGATCGTAAGTCGATGAACTGAAGCTATGATCGTAAATCAACGAACTTTAAAAAT
66 GAAGTGTTCATGATCGTAAATCAATGAACTGAAGATGTAATCGTAAATCAACGAGCTTTAAAAAT
20548705 GACA
131 GACA
* ** * * * * * *
20548709 GTTGTGATTATAAATCGGTGAA-TCGTTTAAGTGGAGTAGCAATCGTAAATTG-TCAAACTCTTT
1 GTCGTGATCGTAAATCAGCGAACT-GTTTAAGTGGAGTCGCGATCGTAAATCGAT-GAACTCTTT
* * * *
20548772 ATAAAGTGTTCATGATCGTAAATCAATGAACT-AAAATCGTAATAGTAAATCATCGAGCTTTAAA
64 ATGAAGTGTTCATGATCGTAAATCAATGAACTGAAGAT-GTAATCGTAAATCAACGAGCTTTAAA
20548836 AATGACA
128 AATGACA
* * * *
20548843 GTCATGATTGTAAATCAGCGAACTGTTTAAGTGGAGT-GTTGATCGTAAATCGACGAACTCTTTA
1 GTCGTGATCGTAAATCAGCGAACTGTTTAAGTGGAGTCG-CGATCGTAAATCGATGAACTCTTTA
* * * * * * * * * * *
20548907 TGAAGTATTTACGATTGTAAATTAACGAACTTAA-ATCGTGATTGTAAATAAACAAGCTTTAAAA
65 TGAAGTGTTCATGATCGTAAATCAATGAACTGAAGAT-GTAATCGTAAATCAACGAGCTTTAAAA
20548971 ATGACA
129 ATGACA
* * *
20548977 ATCAG-GATTGTAAATCAACGAACTGTT
1 GTC-GTGATCGTAAATCAGCGAACTGTT
20549004 AGAAAATCGA
Statistics
Matches: 469, Mismatches: 86, Indels: 16
0.82 0.15 0.03
Matches are distributed among these distances:
133 6 0.01
134 460 0.98
135 3 0.01
ACGTcount: A:0.37, C:0.13, G:0.20, T:0.30
Consensus pattern (134 bp):
GTCGTGATCGTAAATCAGCGAACTGTTTAAGTGGAGTCGCGATCGTAAATCGATGAACTCTTTAT
GAAGTGTTCATGATCGTAAATCAATGAACTGAAGATGTAATCGTAAATCAACGAGCTTTAAAAAT
GACA
Found at i:20548789 original size:268 final size:268
Alignment explanation
Indices: 20548307--20548912 Score: 788
Period size: 268 Copynumber: 2.3 Consensus size: 268
20548297 TAAGTAAAAG
* * *
20548307 GTCGTGATCGTAAATCAGCGAACTGATTAAGTGGAGTCGCGATTGTAAATCAACGAACTGTTTAA
1 GTCGTGATCGTAAATCAGCGAACTGTTTAAGTGGAGTCGCGATCGTAAATCGACGAACTGTTTAA
* * * * * * *
20548372 AAAGTGGTCATGATCGTAAATCGATGAATTGAAGATGTGATCGTAAATTAGCGAGCTTTAAAAAT
66 GAAGTGATCATGATCGTAAATCGATGAACTGAAGATATGATCGTAAATCAACGAACTTTAAAAAT
* * * *
20548437 GATAGTCGTGATCATAAATCAGCGAACTGTTTAAGTGAAGTCGCGACCGTAAATCGATGAACTCT
131 GACAGTCGTGATCATAAATCAGCGAACTGTTTAAGTGAAGTAGCAACCGTAAATCGATAAACTCT
* * * * * *
20548502 TTTTGAAGTGTTTATGATCGTAAATCAATAAACT-GAAGCTGTAATTGTAAATCAACGAGCTTTA
196 TTATAAAGTGTTCATGATCGTAAATCAATAAACTAAAATC-GTAATAGTAAATCAACGAGCTTTA
*
20548566 AAAATGATA
260 AAAATGACA
* * *
20548575 GTCGTGATCGTAAATCAGCTAACTGTTTAAGTGGAGTCGCAATCGTAAATCGATGAACTGTTTAA
1 GTCGTGATCGTAAATCAGCGAACTGTTTAAGTGGAGTCGCGATCGTAAATCGACGAACTGTTTAA
* *
20548640 GAAGTGATCATGATCGTAAGTCGATGAACTGAAGCTATGATCGTAAATCAACGAACTTTAAAAAT
66 GAAGTGATCATGATCGTAAATCGATGAACTGAAGATATGATCGTAAATCAACGAACTTTAAAAAT
* * * * * * *
20548705 GACAGTTGTGATTATAAATCGGTGAA-TCGTTTAAGTGGAGTAGCAATCGTAAATTG-TCAAACT
131 GACAGTCGTGATCATAAATCAGCGAACT-GTTTAAGTGAAGTAGCAACCGTAAATCGAT-AAACT
* *
20548768 CTTTATAAAGTGTTCATGATCGTAAATCAATGAACTAAAATCGTAATAGTAAATCATCGAGCTTT
194 CTTTATAAAGTGTTCATGATCGTAAATCAATAAACTAAAATCGTAATAGTAAATCAACGAGCTTT
20548833 AAAAATGACA
259 AAAAATGACA
* * * *
20548843 GTCATGATTGTAAATCAGCGAACTGTTTAAGTGGAGT-GTTGATCGTAAATCGACGAACTCTTTA
1 GTCGTGATCGTAAATCAGCGAACTGTTTAAGTGGAGTCG-CGATCGTAAATCGACGAACTGTTTA
*
20548907 TGAAGT
65 AGAAGT
20548913 ATTTACGATT
Statistics
Matches: 291, Mismatches: 43, Indels: 8
0.85 0.13 0.02
Matches are distributed among these distances:
267 3 0.01
268 285 0.98
269 3 0.01
ACGTcount: A:0.36, C:0.13, G:0.21, T:0.30
Consensus pattern (268 bp):
GTCGTGATCGTAAATCAGCGAACTGTTTAAGTGGAGTCGCGATCGTAAATCGACGAACTGTTTAA
GAAGTGATCATGATCGTAAATCGATGAACTGAAGATATGATCGTAAATCAACGAACTTTAAAAAT
GACAGTCGTGATCATAAATCAGCGAACTGTTTAAGTGAAGTAGCAACCGTAAATCGATAAACTCT
TTATAAAGTGTTCATGATCGTAAATCAATAAACTAAAATCGTAATAGTAAATCAACGAGCTTTAA
AAATGACA
Found at i:20549029 original size:39 final size:39
Alignment explanation
Indices: 20548986--20549061 Score: 107
Period size: 39 Copynumber: 1.9 Consensus size: 39
20548976 AATCAGGATT
* *
20548986 GTAAATCAACGAACTGTTAGAAAATCGAATGTCGTGATC
1 GTAAATCAACGAACTGTAAGAAAATCGAAGGTCGTGATC
* * *
20549025 GTAAATCAGCGGACTGTAAGAAAGTCGAAGGTCGTGA
1 GTAAATCAACGAACTGTAAGAAAATCGAAGGTCGTGA
20549062 CTGTATTTTC
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
39 32 1.00
ACGTcount: A:0.37, C:0.14, G:0.26, T:0.22
Consensus pattern (39 bp):
GTAAATCAACGAACTGTAAGAAAATCGAAGGTCGTGATC
Found at i:20571315 original size:23 final size:23
Alignment explanation
Indices: 20571245--20571353 Score: 147
Period size: 23 Copynumber: 5.0 Consensus size: 23
20571235 CCTGATCAAT
20571245 ATACGACACAT-AAGTGCCTGA-
1 ATACGACACATAAAGTGCCTGAG
** *
20571266 A-ACGACACACGAGGTGCCT--G
1 ATACGACACATAAAGTGCCTGAG
20571286 ATACGACACATAAAGTGCCTGAG
1 ATACGACACATAAAGTGCCTGAG
20571309 ATACGACACATAAAGTGCCTGAG
1 ATACGACACATAAAGTGCCTGAG
*
20571332 ATACGACACGTAAAGTGCCTGA
1 ATACGACACATAAAGTGCCTGA
20571354 TCGGCAAAGC
Statistics
Matches: 77, Mismatches: 6, Indels: 8
0.85 0.07 0.09
Matches are distributed among these distances:
20 9 0.12
21 23 0.30
23 45 0.58
ACGTcount: A:0.37, C:0.24, G:0.23, T:0.17
Consensus pattern (23 bp):
ATACGACACATAAAGTGCCTGAG
Found at i:20571729 original size:16 final size:17
Alignment explanation
Indices: 20571708--20571739 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
20571698 TAATAATAGT
20571708 ACTTACCTTA-TATTTC
1 ACTTACCTTATTATTTC
20571724 ACTTACCTTATTATTT
1 ACTTACCTTATTATTT
20571740 GCTTGTCATA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.25, C:0.22, G:0.00, T:0.53
Consensus pattern (17 bp):
ACTTACCTTATTATTTC
Found at i:20575436 original size:16 final size:17
Alignment explanation
Indices: 20575408--20575443 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 17
20575398 TTAGAATTGG
*
20575408 ATTGAGAAAATTATTTA
1 ATTGAGAAAATTAATTA
20575425 ATTGAG-AAATTAATTA
1 ATTGAGAAAATTAATTA
20575441 ATT
1 ATT
20575444 TAAATTAACT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 12 0.67
17 6 0.33
ACGTcount: A:0.47, C:0.00, G:0.11, T:0.42
Consensus pattern (17 bp):
ATTGAGAAAATTAATTA
Found at i:20576395 original size:17 final size:17
Alignment explanation
Indices: 20576373--20576439 Score: 62
Period size: 17 Copynumber: 3.6 Consensus size: 17
20576363 AATCTCAGAG
20576373 TTCTAATTGTATACAGC
1 TTCTAATTGTATACAGC
* *
20576390 TTCTAATTGTGTAATCTTAGAG
1 TTCTAATTGTAT-A-C--AG-C
20576412 TTCTAATTGTATACAGC
1 TTCTAATTGTATACAGC
*
20576429 TTTTAATTGTA
1 TTCTAATTGTA
20576440 GCCATTGATA
Statistics
Matches: 40, Mismatches: 5, Indels: 10
0.73 0.09 0.18
Matches are distributed among these distances:
17 21 0.52
18 3 0.08
19 1 0.03
20 1 0.03
21 3 0.08
22 11 0.28
ACGTcount: A:0.28, C:0.12, G:0.13, T:0.46
Consensus pattern (17 bp):
TTCTAATTGTATACAGC
Found at i:20576416 original size:39 final size:39
Alignment explanation
Indices: 20576362--20576438 Score: 136
Period size: 39 Copynumber: 2.0 Consensus size: 39
20576352 TATGATTATA
20576362 TAATCTCAGAGTTCTAATTGTATACAGCTTCTAATTGTG
1 TAATCTCAGAGTTCTAATTGTATACAGCTTCTAATTGTG
* *
20576401 TAATCTTAGAGTTCTAATTGTATACAGCTTTTAATTGT
1 TAATCTCAGAGTTCTAATTGTATACAGCTTCTAATTGT
20576439 AGCCATTGAT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
39 36 1.00
ACGTcount: A:0.29, C:0.13, G:0.14, T:0.44
Consensus pattern (39 bp):
TAATCTCAGAGTTCTAATTGTATACAGCTTCTAATTGTG
Found at i:20582555 original size:24 final size:23
Alignment explanation
Indices: 20582528--20582586 Score: 64
Period size: 24 Copynumber: 2.4 Consensus size: 23
20582518 TCTACTACAA
* *
20582528 GTAGGAGGAGTTGTGTTACTCTTT
1 GTAGGAGCA-TTGTCTTACTCTTT
*
20582552 GTAGGGAGCATTGTCTTACTGTTT
1 GTA-GGAGCATTGTCTTACTCTTT
20582576 GTAGAGAGCAT
1 GTAG-GAGCAT
20582587 CAAAAATCCA
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
23 1 0.03
24 24 0.80
25 5 0.17
ACGTcount: A:0.20, C:0.10, G:0.32, T:0.37
Consensus pattern (23 bp):
GTAGGAGCATTGTCTTACTCTTT
Found at i:20587043 original size:22 final size:24
Alignment explanation
Indices: 20587017--20587060 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
20587007 AAAAAATATT
20587017 AAATAT-ATA-TTTTTTATTTTTA
1 AAATATAATAGTTTTTTATTTTTA
20587039 AAATATAATAGTTTTTTATTTT
1 AAATATAATAGTTTTTTATTTT
20587061 AAGTTTATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 6 0.30
23 3 0.15
24 11 0.55
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.61
Consensus pattern (24 bp):
AAATATAATAGTTTTTTATTTTTA
Found at i:20587192 original size:59 final size:59
Alignment explanation
Indices: 20587126--20587295 Score: 322
Period size: 59 Copynumber: 2.9 Consensus size: 59
20587116 TCAAGTTTGT
*
20587126 TTTACTAATCAAATGTTAGATTTTGTTACAACAATTAATACAATTAATAATTTGATAAA
1 TTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATTAATAATTTGATAAA
20587185 TTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATTAATAATTTGATAAA
1 TTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATTAATAATTTGATAAA
*
20587244 TTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATTAACAATT
1 TTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATTAATAATT
20587296 AATAATTTGA
Statistics
Matches: 109, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
59 109 1.00
ACGTcount: A:0.45, C:0.09, G:0.05, T:0.41
Consensus pattern (59 bp):
TTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATTAATAATTTGATAAA
Found at i:20587327 original size:16 final size:16
Alignment explanation
Indices: 20587306--20587347 Score: 66
Period size: 16 Copynumber: 2.6 Consensus size: 16
20587296 AATAATTTGA
*
20587306 TAATTTTACTAACAAT
1 TAATTTTAATAACAAT
20587322 TAATTTTAATAACAAT
1 TAATTTTAATAACAAT
*
20587338 TAGTTTTAAT
1 TAATTTTAAT
20587348 TTTATTAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.43, C:0.07, G:0.02, T:0.48
Consensus pattern (16 bp):
TAATTTTAATAACAAT
Found at i:20587331 original size:22 final size:23
Alignment explanation
Indices: 20587321--20587376 Score: 69
Period size: 23 Copynumber: 2.5 Consensus size: 23
20587311 TTACTAACAA
* * *
20587321 TTAATTTTAAT-AACAATTAGTT
1 TTAATTTTAATAAAAAAATAATT
*
20587343 TTAATTTTATTAAAAAAATAATT
1 TTAATTTTAATAAAAAAATAATT
20587366 TTAATTTTAAT
1 TTAATTTTAAT
20587377 TTTAATTAAA
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
22 10 0.36
23 18 0.64
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.52
Consensus pattern (23 bp):
TTAATTTTAATAAAAAAATAATT
Found at i:20587634 original size:28 final size:27
Alignment explanation
Indices: 20587603--20587672 Score: 97
Period size: 27 Copynumber: 2.6 Consensus size: 27
20587593 AAATAAAAAA
*
20587603 TTACCAAAATGT-TATAACTTTTTTTTAT
1 TTACCAAAATATATATAA--TTTTTTTAT
*
20587631 TTACCAAAAAATATATAATTTTTTTAT
1 TTACCAAAATATATATAATTTTTTTAT
20587658 TTACCAAAATATATA
1 TTACCAAAATATATA
20587673 AAAAACAAAA
Statistics
Matches: 38, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
27 23 0.61
28 10 0.26
29 5 0.13
ACGTcount: A:0.41, C:0.10, G:0.01, T:0.47
Consensus pattern (27 bp):
TTACCAAAATATATATAATTTTTTTAT
Found at i:20587830 original size:4 final size:4
Alignment explanation
Indices: 20587821--20587951 Score: 94
Period size: 4 Copynumber: 32.0 Consensus size: 4
20587811 GAAGAAGAGG
* *
20587821 GAAA GAAA GAAA GAAA GAAA GGAGAG GAAA GAAA G-AA -AAA GAAG GAAA
1 GAAA GAAA GAAA GAAA GAAA -GA-AA GAAA GAAA GAAA GAAA GAAA GAAA
* *
20587869 GAAAA GGAAA G-GA GAAGA GAAA AAAA GAAA GAAA G-AA -AAA GAAAA
1 G-AAA -GAAA GAAA GAA-A GAAA GAAA GAAA GAAA GAAA GAAA G-AAA
*
20587914 GGAAA GGAGAA GAAA -AAA GAAA GAAA GAAG GAAA GAAA
1 -GAAA -GA-AA GAAA GAAA GAAA GAAA GAAA GAAA GAAA
20587952 AGGAAAGGAG
Statistics
Matches: 103, Mismatches: 10, Indels: 28
0.73 0.07 0.20
Matches are distributed among these distances:
3 13 0.13
4 60 0.58
5 25 0.24
6 5 0.05
ACGTcount: A:0.70, C:0.00, G:0.30, T:0.00
Consensus pattern (4 bp):
GAAA
Found at i:20587850 original size:18 final size:18
Alignment explanation
Indices: 20587829--20587962 Score: 85
Period size: 18 Copynumber: 6.9 Consensus size: 18
20587819 GGGAAAGAAA
20587829 GAAAGAAAGAAAGGAGAG
1 GAAAGAAAGAAAGGAGAG
*
20587847 GAAAGAAAGAAA-AAGAAG
1 GAAAGAAAGAAAGGAG-AG
20587865 GAAAGAAAAGGAAAGGAGAAG
1 GAAAG-AAA-GAAAGGAG-AG
* *
20587886 AGAAAAAAAGAAA-GAAAG
1 -GAAAGAAAGAAAGGAGAG
* *
20587904 AAAAAGAAAAGGAAAGGAGAA
1 -GAAAG-AAA-GAAAGGAGAG
*
20587925 GAAA-AAAGAAAGAAAGAAG
1 GAAAGAAAGAAAG-GAG-AG
20587944 GAAAGAAAAGGAAAGGAGA
1 GAAAG-AAA-GAAAGGAGA
20587963 AGAGAAGAGA
Statistics
Matches: 91, Mismatches: 12, Indels: 24
0.72 0.09 0.19
Matches are distributed among these distances:
17 7 0.08
18 30 0.33
19 13 0.14
20 16 0.18
21 16 0.18
22 9 0.10
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (18 bp):
GAAAGAAAGAAAGGAGAG
Found at i:20587896 original size:40 final size:39
Alignment explanation
Indices: 20587822--20588022 Score: 199
Period size: 39 Copynumber: 5.2 Consensus size: 39
20587812 AAGAAGAGGG
*
20587822 AAAGAAAGAAAG-AAA-GAAAGGAG-AG-GAAAGAAAGAA
1 AAAG-AAGAAAGAAAAGGAAAGGAGAAGAGAAAAAAAGAA
20587858 AAAGAAGGAAAGAAAAGGAAAGGAGAAGAGAAAAAAAGAAA
1 AAAGAA-GAAAGAAAAGGAAAGGAGAAGAGAAAAAAAG-AA
*
20587899 GAAAGAA-AAAGAAAAGGAAAGGAGAAGA-AAAAAGAA-AG
1 -AAAGAAGAAAGAAAAGGAAAGGAGAAGAGAAAAA-AAGAA
20587937 AAAGAAGGAAAGAAAAGGAAAGGAGAAGAGAAGAGAAAA-AA
1 AAAGAA-GAAAGAAAAGGAAAGGAGAAGAGAA-A-AAAAGAA
* * *
20587978 AAAGAAG-AAGAAGAGGGAAGGA-AGGA-AAAAAAAGAA
1 AAAGAAGAAAGAAAAGGAAAGGAGAAGAGAAAAAAAGAA
*
20588014 AAAAAAGAA
1 AAAGAAGAA
20588023 TTTTTTTTTA
Statistics
Matches: 143, Mismatches: 7, Indels: 29
0.80 0.04 0.16
Matches are distributed among these distances:
35 6 0.04
36 18 0.13
37 12 0.08
38 12 0.08
39 41 0.29
40 34 0.24
41 12 0.08
42 8 0.06
ACGTcount: A:0.70, C:0.00, G:0.30, T:0.00
Consensus pattern (39 bp):
AAAGAAGAAAGAAAAGGAAAGGAGAAGAGAAAAAAAGAA
Found at i:20587941 original size:45 final size:45
Alignment explanation
Indices: 20587847--20587983 Score: 139
Period size: 45 Copynumber: 3.2 Consensus size: 45
20587837 GAAAGGAGAG
20587847 GAAAGAAAG-AA-AAAGAAGGAAAGAAAAGGAAAGGAGAAG-----A
1 GAAAGAAAGAAAGAAAGAA--AAAGAAAAGGAAAGGAGAAGAAAAAA
*
20587887 GAAAAAAAGAAAGAAAGAAAAAGAAAAGGAAAGGAGAAGAAAAAA
1 GAAAGAAAGAAAGAAAGAAAAAGAAAAGGAAAGGAGAAGAAAAAA
* *
20587932 GAAAGAAAGAAGGAAAG-AAAAGGAAAGGAGAA-GAGAAGAGAAAAA
1 GAAAGAAAGAAAGAAAGAAAAAGAAAAGGA-AAGGAGAAGA-AAAAA
*
20587977 AAAAGAA
1 GAAAGAA
20587984 GAAGAAGAGG
Statistics
Matches: 83, Mismatches: 5, Indels: 13
0.82 0.05 0.13
Matches are distributed among these distances:
40 28 0.34
41 2 0.02
42 6 0.07
44 18 0.22
45 29 0.35
ACGTcount: A:0.71, C:0.00, G:0.29, T:0.00
Consensus pattern (45 bp):
GAAAGAAAGAAAGAAAGAAAAAGAAAAGGAAAGGAGAAGAAAAAA
Found at i:20587960 original size:79 final size:78
Alignment explanation
Indices: 20587821--20588016 Score: 246
Period size: 79 Copynumber: 2.6 Consensus size: 78
20587811 GAAGAAGAGG
*
20587821 GAAAGAAAG--AAAG-AAA-GAAAGGAGAGGAAAGAAAGAAAAAGAAGGAAAGAAAAGGAAAGGA
1 GAAAGAAAGAAAAAGAAAAGGAAAGGAGAAGAAA-AAAGAAAAAGAAGGAAAGAAAAGGAAAGGA
20587882 GAAGAGAA-AAAAA
65 GAAGAGAAGAAAAA
20587895 GAAAGAAAGAAAAAGAAAAGGAAAGGAGAAGAAAAAAGAAAGAAAGAAGGAAAGAAAAGGAAAGG
1 GAAAGAAAGAAAAAGAAAAGGAAAGGAGAAGAAAAAAG-AA-AAAGAAGGAAAGAAAAGGAAAGG
*
20587960 AGAAGAGAAGAGAAA
64 AGAAGAGAAGAAAAA
* * *
20587975 -AAA-AAAGAAGAAGAAGAGGGAAGGAAGGAA-AAAAAAGAAAAA
1 GAAAGAAAGAAAAAGAAAAGGAAAGG-A-GAAGAAAAAAGAAAAA
20588017 AAAGAATTTT
Statistics
Matches: 108, Mismatches: 5, Indels: 15
0.84 0.04 0.12
Matches are distributed among these distances:
74 9 0.08
76 4 0.04
77 10 0.09
78 35 0.32
79 43 0.40
80 7 0.06
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (78 bp):
GAAAGAAAGAAAAAGAAAAGGAAAGGAGAAGAAAAAAGAAAAAGAAGGAAAGAAAAGGAAAGGAG
AAGAGAAGAAAAA
Found at i:20593358 original size:18 final size:18
Alignment explanation
Indices: 20593335--20593379 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 18
20593325 ATCCCAATGA
20593335 TCGCCACCACATTCTTCT
1 TCGCCACCACATTCTTCT
* *
20593353 TCGCCAGCACCTTCTTCT
1 TCGCCACCACATTCTTCT
*
20593371 TCACCACCA
1 TCGCCACCA
20593380 ACCATGTCAA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.18, C:0.47, G:0.07, T:0.29
Consensus pattern (18 bp):
TCGCCACCACATTCTTCT
Found at i:20594237 original size:3 final size:3
Alignment explanation
Indices: 20594229--20594278 Score: 100
Period size: 3 Copynumber: 16.7 Consensus size: 3
20594219 TCTTAATACT
20594229 AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC
1 AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC
20594277 AA
1 AA
20594279 TAATAATACT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 47 1.00
ACGTcount: A:0.68, C:0.32, G:0.00, T:0.00
Consensus pattern (3 bp):
AAC
Found at i:20594411 original size:10 final size:11
Alignment explanation
Indices: 20594394--20594422 Score: 51
Period size: 10 Copynumber: 2.7 Consensus size: 11
20594384 AAAAAAATAC
20594394 CTTCTTTTTCT
1 CTTCTTTTTCT
20594405 C-TCTTTTTCT
1 CTTCTTTTTCT
20594415 CTTCTTTT
1 CTTCTTTT
20594423 CCGCAGCAAC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
10 10 0.59
11 7 0.41
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (11 bp):
CTTCTTTTTCT
Found at i:20594550 original size:27 final size:27
Alignment explanation
Indices: 20594520--20594604 Score: 134
Period size: 27 Copynumber: 3.1 Consensus size: 27
20594510 CCAATCAGTA
20594520 TGGCACCATTGGTGCCGCCAATGGCAT
1 TGGCACCATTGGTGCCGCCAATGGCAT
**
20594547 TGGCACCATTGGTGCCGCCAATGGTTT
1 TGGCACCATTGGTGCCGCCAATGGCAT
* *
20594574 TGGCACCTTTGGTGCCGCCAATGCCAT
1 TGGCACCATTGGTGCCGCCAATGGCAT
20594601 TGGC
1 TGGC
20594605 GTGACCAAGG
Statistics
Matches: 52, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 52 1.00
ACGTcount: A:0.15, C:0.29, G:0.29, T:0.26
Consensus pattern (27 bp):
TGGCACCATTGGTGCCGCCAATGGCAT
Found at i:20594723 original size:27 final size:27
Alignment explanation
Indices: 20594667--20594735 Score: 86
Period size: 27 Copynumber: 2.5 Consensus size: 27
20594657 TTTGTTTTTG
*
20594667 ATATATTTTGGTAAATAAAAAAATTAT
1 ATATATTTTGGTAAATAAAAAAAGTAT
*
20594694 ATATTTTTTGGTAAATAAAAAAAAGT-T
1 ATATATTTTGGTAAAT-AAAAAAAGTAT
*
20594721 ATAACATTTTGGTAA
1 AT-ATATTTTGGTAA
20594736 TTTTTTTATT
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
27 18 0.50
28 18 0.50
ACGTcount: A:0.48, C:0.01, G:0.10, T:0.41
Consensus pattern (27 bp):
ATATATTTTGGTAAATAAAAAAAGTAT
Found at i:20594730 original size:28 final size:27
Alignment explanation
Indices: 20594671--20594735 Score: 87
Period size: 28 Copynumber: 2.4 Consensus size: 27
20594661 TTTTTGATAT
*
20594671 ATTTTGGTAAATAAAAAAATTATATAT
1 ATTTTGGTAAATAAAAAAATTATATAC
*
20594698 TTTTTGGTAAATAAAAAAAAGTTATA-AC
1 ATTTTGGTAAAT-AAAAAAA-TTATATAC
20594726 ATTTTGGTAA
1 ATTTTGGTAA
20594736 TTTTTTTATT
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
27 11 0.33
28 17 0.52
29 5 0.15
ACGTcount: A:0.48, C:0.02, G:0.11, T:0.40
Consensus pattern (27 bp):
ATTTTGGTAAATAAAAAAATTATATAC
Found at i:20596132 original size:25 final size:25
Alignment explanation
Indices: 20596103--20596167 Score: 116
Period size: 23 Copynumber: 2.7 Consensus size: 25
20596093 TTAAATATAT
20596103 ATAAAAAATATATATTTGATTAAAA
1 ATAAAAAATATATATTTGATTAAAA
20596128 AT--AAAATATATATTTGATTAAAA
1 ATAAAAAATATATATTTGATTAAAA
20596151 ATAAAAAATATATATTT
1 ATAAAAAATATATATTT
20596168 AATATATAAT
Statistics
Matches: 38, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
23 23 0.61
25 15 0.39
ACGTcount: A:0.58, C:0.00, G:0.03, T:0.38
Consensus pattern (25 bp):
ATAAAAAATATATATTTGATTAAAA
Found at i:20598939 original size:18 final size:20
Alignment explanation
Indices: 20598915--20598957 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
20598905 TTTATTTGTT
*
20598915 TTATTATAATAATATAATATA
1 TTATTAT-ATAATAAAATATA
20598936 TTATTATATAATAAAATATA
1 TTATTATATAATAAAATATA
20598956 TT
1 TT
20598958 TACTCAACAT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
20 14 0.67
21 7 0.33
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (20 bp):
TTATTATATAATAAAATATA
Found at i:20604779 original size:34 final size:34
Alignment explanation
Indices: 20604706--20604771 Score: 89
Period size: 34 Copynumber: 2.0 Consensus size: 34
20604696 AATGCCAGTA
* **
20604706 ATCAGTAGGGCCTTTGCCCAATTTCAGTAATAGT
1 ATCAGTAGGGCCTTGGCCCAATAACAGTAATAGT
*
20604740 ATCAGTGGGGCCTTGGCCC-ATAACAGTAATAG
1 ATCAGTAGGGCCTTGGCCCAATAACAGTAATAG
20604772 CTTTCAGTCA
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
33 11 0.39
34 17 0.61
ACGTcount: A:0.27, C:0.21, G:0.24, T:0.27
Consensus pattern (34 bp):
ATCAGTAGGGCCTTGGCCCAATAACAGTAATAGT
Found at i:20605275 original size:27 final size:26
Alignment explanation
Indices: 20605244--20605439 Score: 239
Period size: 27 Copynumber: 7.3 Consensus size: 26
20605234 TATAACAGTT
*
20605244 ATTTTATCCTATGGGGATATTTCGGTC
1 ATTTTACCCTATGGGG-TATTTCGGTC
* * *
20605271 ATTTTACCCTATCAGGGCATTTTGGTC
1 ATTTTACCCTAT-GGGGTATTTCGGTC
*
20605298 ATTTTACCCTATGGGGGTATTTCAGTC
1 ATTTTACCCTAT-GGGGTATTTCGGTC
*
20605325 ATTTTACCCTATGGAGGTATTTCGATC
1 ATTTTACCCTATGG-GGTATTTCGGTC
* *
20605352 ATTTTACCCTATGAGGGTGTTTTGGTC
1 ATTTTACCCTATG-GGGTATTTCGGTC
* *
20605379 ATTTTACCCTATGGGATATTTCGGTT
1 ATTTTACCCTATGGGGTATTTCGGTC
*
20605405 ATTTTACCCTATAGGGGTATTTCGGTT
1 ATTTTACCCTAT-GGGGTATTTCGGTC
20605432 ATTTTACC
1 ATTTTACC
20605440 TTAATTTAGG
Statistics
Matches: 146, Mismatches: 19, Indels: 8
0.84 0.11 0.05
Matches are distributed among these distances:
26 23 0.16
27 119 0.82
28 4 0.03
ACGTcount: A:0.19, C:0.17, G:0.20, T:0.43
Consensus pattern (26 bp):
ATTTTACCCTATGGGGTATTTCGGTC
Found at i:20605354 original size:81 final size:79
Alignment explanation
Indices: 20605226--20605439 Score: 286
Period size: 81 Copynumber: 2.7 Consensus size: 79
20605216 CATTTCATCT
** *
20605226 CCTA-GGGGTATAACAGTTATTTTATCCTATGGGGATATTTCGGTCATTTTACCCTATCAGGGCA
1 CCTATGGGGTATTTCAGTTATTTTACCCTATGGGG-TATTTCGGTCATTTTACCCTATCAGGGCA
20605290 TTTTGGTCATTTTAC
65 TTTTGGTCATTTTAC
* * * *
20605305 CCTATGGGGGTATTTCAGTCATTTTACCCTATGGAGGTATTTCGATCATTTTACCCTATGAGGGT
1 CCTAT-GGGGTATTTCAGTTATTTTACCCTATGG-GGTATTTCGGTCATTTTACCCTATCAGGGC
*
20605370 GTTTTGGTCATTTTAC
64 ATTTTGGTCATTTTAC
* * *
20605386 CCTATGGGATATTTCGGTTATTTTACCCTATAGGGGTATTTCGGTTATTTTACC
1 CCTATGGGGTATTTCAGTTATTTTACCCTAT-GGGGTATTTCGGTCATTTTACC
20605440 TTAATTTAGG
Statistics
Matches: 118, Mismatches: 13, Indels: 7
0.86 0.09 0.05
Matches are distributed among these distances:
79 4 0.03
80 41 0.35
81 71 0.60
82 2 0.02
ACGTcount: A:0.20, C:0.17, G:0.21, T:0.42
Consensus pattern (79 bp):
CCTATGGGGTATTTCAGTTATTTTACCCTATGGGGTATTTCGGTCATTTTACCCTATCAGGGCAT
TTTGGTCATTTTAC
Found at i:20606863 original size:74 final size:74
Alignment explanation
Indices: 20606742--20606894 Score: 297
Period size: 74 Copynumber: 2.1 Consensus size: 74
20606732 CCAGCCAAAT
*
20606742 TCTCTAAACTAGAGTTTTCCCACAAACGGCGCAACACTTTCTGCTCCTTAAAACTCCTTGACTTT
1 TCTCTAAACTAGAGTTTTCCCACAAACGGCGCAACACTTTCTACTCCTTAAAACTCCTTGACTTT
20606807 CTCCTAATA
66 CTCCTAATA
20606816 TCTCTAAACTAGAGTTTTCCCACAAACGGCGCAACACTTTCTACTCCTTAAAACTCCTTGACTTT
1 TCTCTAAACTAGAGTTTTCCCACAAACGGCGCAACACTTTCTACTCCTTAAAACTCCTTGACTTT
20606881 CTCCTAATA
66 CTCCTAATA
20606890 TCTCT
1 TCTCT
20606895 CCCCTTATCC
Statistics
Matches: 78, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
74 78 1.00
ACGTcount: A:0.27, C:0.31, G:0.08, T:0.33
Consensus pattern (74 bp):
TCTCTAAACTAGAGTTTTCCCACAAACGGCGCAACACTTTCTACTCCTTAAAACTCCTTGACTTT
CTCCTAATA
Found at i:20611765 original size:37 final size:37
Alignment explanation
Indices: 20611715--20611881 Score: 107
Period size: 37 Copynumber: 4.5 Consensus size: 37
20611705 TTCAAAGTAA
*
20611715 TAAATTGACACCCAGTGTCTCATCGACTAAATCGAAG
1 TAAATTGGCACCCAGTGTCTCATCGACTAAATCGAAG
* *
20611752 TAAATTGGCACCCAGTGCCTCATTGA--AACA-C-ACCAG
1 TAAATTGGCACCCAGTGTCTCATCGACTAA-ATCGA--AG
* * * *
20611788 T---TTGGCATCCAGTG-CGTCATCGAATAATTCAAAG
1 TAAATTGGCACCCAGTGTC-TCATCGACTAAATCGAAG
* * * *
20611822 TAATAAATTGACACCCAGTGTCTCATTGGCTAAACCGAAG
1 ---TAAATTGGCACCCAGTGTCTCATCGACTAAATCGAAG
*
20611862 TAAATTGGCACCTAGTGTCT
1 TAAATTGGCACCCAGTGTCT
20611882 TATTGAATTA
Statistics
Matches: 99, Mismatches: 16, Indels: 30
0.68 0.11 0.21
Matches are distributed among these distances:
32 1 0.01
33 18 0.18
34 3 0.03
35 6 0.06
36 5 0.05
37 42 0.42
40 23 0.23
41 1 0.01
ACGTcount: A:0.32, C:0.24, G:0.18, T:0.26
Consensus pattern (37 bp):
TAAATTGGCACCCAGTGTCTCATCGACTAAATCGAAG
Found at i:20611861 original size:110 final size:110
Alignment explanation
Indices: 20611667--20611888 Score: 374
Period size: 110 Copynumber: 2.0 Consensus size: 110
20611657 GATCCAACCA
20611667 AAACACACCAGTTTGGCACCTAGTGCGTCATCGAATAATTCAAAGTAATAAATTGACACCCAGTG
1 AAACACACCAGTTTGGCACCTAGTGCGTCATCGAATAATTCAAAGTAATAAATTGACACCCAGTG
*
20611732 TCTCATCGACTAAATCGAAGTAAATTGGCACCCAGTGCCTCATTG
66 TCTCATCGACTAAACCGAAGTAAATTGGCACCCAGTGCCTCATTG
20611777 AAACACACCAGTTTGGCATCC-AGTGCGTCATCGAATAATTCAAAGTAATAAATTGACACCCAGT
1 AAACACACCAGTTTGGCA-CCTAGTGCGTCATCGAATAATTCAAAGTAATAAATTGACACCCAGT
* * * * *
20611841 GTCTCATTGGCTAAACCGAAGTAAATTGGCACCTAGTGTCTTATTG
65 GTCTCATCGACTAAACCGAAGTAAATTGGCACCCAGTGCCTCATTG
20611887 AA
1 AA
20611889 TTAATCCGAA
Statistics
Matches: 105, Mismatches: 6, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
110 103 0.98
111 2 0.02
ACGTcount: A:0.34, C:0.23, G:0.18, T:0.26
Consensus pattern (110 bp):
AAACACACCAGTTTGGCACCTAGTGCGTCATCGAATAATTCAAAGTAATAAATTGACACCCAGTG
TCTCATCGACTAAACCGAAGTAAATTGGCACCCAGTGCCTCATTG
Found at i:20611922 original size:41 final size:39
Alignment explanation
Indices: 20611819--20611924 Score: 108
Period size: 37 Copynumber: 2.7 Consensus size: 39
20611809 GAATAATTCA
*
20611819 AAGTAATAAATTGACACCCAGTGTCTCATTGGCTAAACCG
1 AAGTAA-AAATTGACACCCAGTGTCTCATTGACTAAACCG
* * * * *
20611859 AAGT--AAATTGGCACCTAGTGTCTTATTGAATTAATCCG
1 AAGTAAAAATTGACACCCAGTGTCTCATTG-ACTAAACCG
*
20611897 AAGTAACAAATTGACACCCACTGTCTCA
1 AAGTAA-AAATTGACACCCAGTGTCTCA
20611925 CCGACTCGAA
Statistics
Matches: 52, Mismatches: 10, Indels: 7
0.75 0.14 0.10
Matches are distributed among these distances:
37 21 0.40
38 10 0.19
40 4 0.08
41 17 0.33
ACGTcount: A:0.35, C:0.22, G:0.16, T:0.27
Consensus pattern (39 bp):
AAGTAAAAATTGACACCCAGTGTCTCATTGACTAAACCG
Found at i:20612879 original size:17 final size:16
Alignment explanation
Indices: 20612838--20612880 Score: 52
Period size: 16 Copynumber: 2.6 Consensus size: 16
20612828 TTTCGTTTGG
20612838 CTTTCTCTATT-TCTTT
1 CTTTCTCT-TTCTCTTT
20612854 CTTTCTCTTTCTCTTT
1 CTTTCTCTTTCTCTTT
*
20612870 CCTTTTTCTTT
1 -CTTTCTCTTT
20612881 TTAGTTATTT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
15 2 0.08
16 13 0.54
17 9 0.38
ACGTcount: A:0.02, C:0.28, G:0.00, T:0.70
Consensus pattern (16 bp):
CTTTCTCTTTCTCTTT
Found at i:20622003 original size:15 final size:15
Alignment explanation
Indices: 20621983--20622017 Score: 70
Period size: 15 Copynumber: 2.3 Consensus size: 15
20621973 AGCAGAAAGA
20621983 TTCCTCATGAAGTAT
1 TTCCTCATGAAGTAT
20621998 TTCCTCATGAAGTAT
1 TTCCTCATGAAGTAT
20622013 TTCCT
1 TTCCT
20622018 GCCTAGCAAG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.23, C:0.23, G:0.11, T:0.43
Consensus pattern (15 bp):
TTCCTCATGAAGTAT
Found at i:20630978 original size:18 final size:18
Alignment explanation
Indices: 20630955--20631000 Score: 58
Period size: 18 Copynumber: 2.5 Consensus size: 18
20630945 GGCAACCCAC
20630955 ATTTATTTTCATTTA-GTA
1 ATTTATTTT-ATTTATGTA
*
20630973 ATTTATTTTATTTATTTA
1 ATTTATTTTATTTATGTA
20630991 ATTTAATTTT
1 ATTT-ATTTT
20631001 GAATTCTAGT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
17 5 0.20
18 15 0.60
19 5 0.20
ACGTcount: A:0.28, C:0.02, G:0.02, T:0.67
Consensus pattern (18 bp):
ATTTATTTTATTTATGTA
Found at i:20631347 original size:20 final size:22
Alignment explanation
Indices: 20631301--20631347 Score: 57
Period size: 20 Copynumber: 2.3 Consensus size: 22
20631291 AAATGACCAA
*
20631301 GAAAGAAAAAGAAGGAAAAAAG
1 GAAAGAAAAAGAAAGAAAAAAG
20631323 G--AGAAAAA-AAAG-AAAAAG
1 GAAAGAAAAAGAAAGAAAAAAG
20631341 GAAAGAA
1 GAAAGAA
20631348 GGGCTTGAAG
Statistics
Matches: 22, Mismatches: 1, Indels: 6
0.76 0.03 0.21
Matches are distributed among these distances:
18 7 0.32
19 3 0.14
20 11 0.50
22 1 0.05
ACGTcount: A:0.74, C:0.00, G:0.26, T:0.00
Consensus pattern (22 bp):
GAAAGAAAAAGAAAGAAAAAAG
Found at i:20636527 original size:16 final size:16
Alignment explanation
Indices: 20636502--20636545 Score: 52
Period size: 16 Copynumber: 2.7 Consensus size: 16
20636492 CCGATATAAT
* * *
20636502 AAATTATTTATTTTTA
1 AAATTTTTTAATTTAA
20636518 AAATTTTTTAATTTAA
1 AAATTTTTTAATTTAA
20636534 AAATATTTTTAA
1 AAAT-TTTTTAA
20636546 AATACTTTTT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
16 17 0.71
17 7 0.29
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (16 bp):
AAATTTTTTAATTTAA
Done.