Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D01
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: 62811768
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 736185 characters in sequence are not A, C, G, or T
File 196 of 211
Found at i:57823725 original size:150 final size:156
Alignment explanation
Indices: 57823529--57823839 Score: 481
Period size: 150 Copynumber: 2.0 Consensus size: 156
57823519 TACTTTTATT
* *
57823529 AAAAATTATAAAAAATTAAAATCAATAAAAAATATAAATATGATTAAATTTTAATAAAAAATTTC
1 AAAAATTAT-AAAAATTAAAATCAATAAAAAATATAAATATGATTAAATTTTAATAAAAAAATTA
* * *
57823594 AAATATTAAAAATTAGAAAAATTAAAAATGGT-AAAAATATAAAAAATTGT-AAACTTTTATAAA
65 AAAAATTAAAAATTAGAAAAATTAAAAATCGTAAAAAATATAAAAAACTGTAAAACTTTTATAAA
*
57823657 AATTAT-AAAA-ATTATAAAA-ATACA
130 AATCATAAAAAGATTATAAAATATACA
* *
57823681 AAAAATTAT-AAAATTAAAATCAATAAAAAGTATAAATATTATTAAATTTTAATAAAAAAATTAA
1 AAAAATTATAAAAATTAAAATCAATAAAAAATATAAATATGATTAAATTTTAATAAAAAAATTAA
*
57823745 AAAATTAAAAATTAGAAAAATTAAAAATCGTAAAAAATATAAAAAACTGTAAAATTTTTATAAAA
66 AAAATTAAAAATTAGAAAAATTAAAAATCGTAAAAAATATAAAAAACTGTAAAACTTTTATAAAA
*
57823810 ATCATAAAAAGATTATAAAATATATA
131 ATCATAAAAAGATTATAAAATATACA
57823836 AAAA
1 AAAA
57823840 TACAAAAAAA
Statistics
Matches: 144, Mismatches: 10, Indels: 7
0.89 0.06 0.04
Matches are distributed among these distances:
150 80 0.56
151 17 0.12
152 26 0.18
153 4 0.03
154 9 0.06
155 8 0.06
ACGTcount: A:0.64, C:0.03, G:0.03, T:0.30
Consensus pattern (156 bp):
AAAAATTATAAAAATTAAAATCAATAAAAAATATAAATATGATTAAATTTTAATAAAAAAATTAA
AAAATTAAAAATTAGAAAAATTAAAAATCGTAAAAAATATAAAAAACTGTAAAACTTTTATAAAA
ATCATAAAAAGATTATAAAATATACA
Found at i:57823780 original size:16 final size:16
Alignment explanation
Indices: 57823736--57823772 Score: 67
Period size: 16 Copynumber: 2.4 Consensus size: 16
57823726 ATTTTAATAA
57823736 AAAAATTA-AAAAATT
1 AAAAATTAGAAAAATT
57823751 AAAAATTAGAAAAATT
1 AAAAATTAGAAAAATT
57823767 AAAAAT
1 AAAAAT
57823773 CGTAAAAAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 8 0.38
16 13 0.62
ACGTcount: A:0.73, C:0.00, G:0.03, T:0.24
Consensus pattern (16 bp):
AAAAATTAGAAAAATT
Found at i:57823825 original size:20 final size:20
Alignment explanation
Indices: 57823802--57823839 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
57823792 TGTAAAATTT
57823802 TTATAAAA-ATCATAAAAAGA
1 TTATAAAATAT-ATAAAAAGA
57823822 TTATAAAATATATAAAAA
1 TTATAAAATATATAAAAA
57823840 TACAAAAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
20 15 0.88
21 2 0.12
ACGTcount: A:0.66, C:0.03, G:0.03, T:0.29
Consensus pattern (20 bp):
TTATAAAATATATAAAAAGA
Found at i:57823835 original size:29 final size:27
Alignment explanation
Indices: 57823654--57823885 Score: 119
Period size: 30 Copynumber: 8.4 Consensus size: 27
57823644 AAACTTTTAT
*
57823654 AAAAATTATAAAAATTATAAAAAT-ACA
1 AAAAATTAT-AAAATTATAAAAATCATA
57823681 AAAAATTATAAAA-T-T-AAAATCA-A
1 AAAAATTATAAAATTATAAAAATCATA
* ** *
57823704 TAAAAAGTATAAATATTATTAAATTTTAATAA
1 -AAAAATTATAAA-ATTA-TAAA-AATCAT-A
*
57823736 AAAAATTA-AAAAAT-TAAAAAT--TA
1 AAAAATTATAAAATTATAAAAATCATA
57823759 GAAAAATTA-AAAATCGTA-AAAAAT-ATA
1 -AAAAATTATAAAAT--TATAAAAATCATA
* *
57823786 AAAAACTGTAAAATTTTTATAAAAATCATA
1 AAAAATTATAAAA---TTATAAAAATCATA
*
57823816 AAAAGATTATAAAATATATAAAAATACAAA
1 AAAA-ATTATAAAAT-TATAAAAAT-CATA
* *
57823846 AAAAATTTATAAAATTTTATAAAATCGTA
1 AAAAA-TTATAAAATTATA-AAAATCATA
57823875 AGAAAATTATA
1 A-AAAATTATA
57823886 TATGTAAAGA
Statistics
Matches: 161, Mismatches: 17, Indels: 52
0.70 0.07 0.23
Matches are distributed among these distances:
23 7 0.04
24 26 0.16
25 2 0.01
26 19 0.12
27 19 0.12
28 4 0.02
29 31 0.19
30 38 0.24
31 14 0.09
32 1 0.01
ACGTcount: A:0.64, C:0.03, G:0.03, T:0.30
Consensus pattern (27 bp):
AAAAATTATAAAATTATAAAAATCATA
Found at i:57824090 original size:19 final size:19
Alignment explanation
Indices: 57824068--57824189 Score: 53
Period size: 19 Copynumber: 6.5 Consensus size: 19
57824058 TTTTTTATTA
57824068 TTTTTATAAAATTTTAATT
1 TTTTTATAAAATTTTAATT
**
57824087 TTTTT-T-ATTTTTTACAATT
1 TTTTTATAAAATTTT--AATT
*
57824106 TTTGTATAAAAATTTCTAA--
1 TTTTTAT-AAAATTT-TAATT
* * *
57824125 TTTTTA-ATAATTTTTATA
1 TTTTTATAAAATTTTAATT
*
57824143 TTTTTATTAAAA-TTTAATAA
1 TTTTTA-TAAAATTTTAAT-T
*
57824163 TTTTTCTAAAA-TTT-ATT
1 TTTTTATAAAATTTTAATT
57824180 ATTTTTATAA
1 -TTTTTATAA
57824190 TTTTTTTTCT
Statistics
Matches: 78, Mismatches: 13, Indels: 25
0.67 0.11 0.22
Matches are distributed among these distances:
16 2 0.03
17 11 0.14
18 17 0.22
19 31 0.40
20 10 0.13
21 2 0.03
22 4 0.05
23 1 0.01
ACGTcount: A:0.35, C:0.02, G:0.01, T:0.61
Consensus pattern (19 bp):
TTTTTATAAAATTTTAATT
Found at i:57824137 original size:10 final size:10
Alignment explanation
Indices: 57824122--57824167 Score: 51
Period size: 10 Copynumber: 4.8 Consensus size: 10
57824112 TAAAAATTTC
57824122 TAATTTTTAA
1 TAATTTTTAA
57824132 TAATTTTT-A
1 TAATTTTTAA
*
57824141 T-ATTTTTAT
1 TAATTTTTAA
**
57824150 TAAAATTTAA
1 TAATTTTTAA
57824160 TAATTTTT
1 TAATTTTT
57824168 CTAAAATTTA
Statistics
Matches: 28, Mismatches: 6, Indels: 4
0.74 0.16 0.11
Matches are distributed among these distances:
8 6 0.21
9 3 0.11
10 19 0.68
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (10 bp):
TAATTTTTAA
Found at i:57824139 original size:40 final size:37
Alignment explanation
Indices: 57824068--57824167 Score: 96
Period size: 38 Copynumber: 2.6 Consensus size: 37
57824058 TTTTTTATTA
** *
57824068 TTTTTATAAAATTTTAATTTTTTTTATTTTTTACAAT
1 TTTTTATAAAATTTTAATTTTTAATAATTTTTACAAT
*
57824105 TTTTGTATAAAAATTTCTAATTTTTAATAATTTTTA-TA-
1 TTTT-TAT-AAAATTT-TAATTTTTAATAATTTTTACAAT
57824143 TTTTTATTAAAATTTAATAATTTTT
1 TTTTTA-TAAAATTT--TAATTTTT
57824168 CTAAAATTTA
Statistics
Matches: 53, Mismatches: 5, Indels: 9
0.79 0.07 0.13
Matches are distributed among these distances:
37 13 0.25
38 16 0.30
39 8 0.15
40 16 0.30
ACGTcount: A:0.34, C:0.02, G:0.01, T:0.63
Consensus pattern (37 bp):
TTTTTATAAAATTTTAATTTTTAATAATTTTTACAAT
Found at i:57824154 original size:38 final size:37
Alignment explanation
Indices: 57824059--57824167 Score: 105
Period size: 40 Copynumber: 2.9 Consensus size: 37
57824049 GGTCATTAAT
* ** *
57824059 TTTTTATTATTTTTA-TAAAATTTTAATTTTTTTTAT
1 TTTTTACTATTTTTATTAAAATTTTAATTTTTAATAA
* *
57824095 TTTTTACAATTTTTGTATAAAAATTTCTAATTTTTAATAA
1 TTTTTACTA-TTTT-TATTAAAATTT-TAATTTTTAATAA
57824135 TTTTTA-TATTTTTATTAAAATTTAATAATTTTT
1 TTTTTACTATTTTTATTAAAATTT--TAATTTTT
57824168 CTAAAATTTA
Statistics
Matches: 59, Mismatches: 9, Indels: 8
0.78 0.12 0.11
Matches are distributed among these distances:
36 7 0.12
37 14 0.24
38 14 0.24
39 8 0.14
40 16 0.27
ACGTcount: A:0.33, C:0.02, G:0.01, T:0.64
Consensus pattern (37 bp):
TTTTTACTATTTTTATTAAAATTTTAATTTTTAATAA
Found at i:57824158 original size:18 final size:19
Alignment explanation
Indices: 57824061--57824187 Score: 82
Period size: 18 Copynumber: 6.7 Consensus size: 19
57824051 TCATTAATTT
*
57824061 TTTATTATTTTTA-TAAAA
1 TTTATAATTTTTATTAAAA
* ***
57824079 TTT-TAATTTTTTTTATTT
1 TTTATAATTTTTATTAAAA
* *
57824097 TTTACAATTTTTGTATAAAAA
1 TTTATAA-TTTT-TATTAAAA
* * **
57824118 TTTCTAATTTTTAATAATT
1 TTTATAATTTTTATTAAAA
57824137 TTTAT-ATTTTTATTAAAA
1 TTTATAATTTTTATTAAAA
*
57824155 TTTAATAATTTTT-CTAAAA
1 TTT-ATAATTTTTATTAAAA
*
57824174 TTTATTATTTTTAT
1 TTTATAATTTTTAT
57824188 AATTTTTTTT
Statistics
Matches: 78, Mismatches: 24, Indels: 13
0.68 0.21 0.11
Matches are distributed among these distances:
17 7 0.09
18 29 0.37
19 20 0.26
20 14 0.18
21 8 0.10
ACGTcount: A:0.34, C:0.02, G:0.01, T:0.63
Consensus pattern (19 bp):
TTTATAATTTTTATTAAAA
Found at i:57824192 original size:9 final size:9
Alignment explanation
Indices: 57824059--57824194 Score: 60
Period size: 9 Copynumber: 14.6 Consensus size: 9
57824049 GGTCATTAAT
*
57824059 TTTTTATTA
1 TTTTTATAA
57824068 TTTTTATAAA
1 TTTTTAT-AA
* *
57824078 ATTTTA-AT
1 TTTTTATAA
* *
57824086 TTTTTTTAT
1 TTTTTATAA
*
57824095 TTTTTACAA
1 TTTTTATAA
57824104 TTTTTGTATAAA
1 -TTTT-TAT-AA
** *
57824116 AATTTCTAA
1 TTTTTATAA
57824125 TTTTTAATAA
1 TTTTT-ATAA
57824135 TTTTTAT-A
1 TTTTTATAA
57824143 TTTTTATTAAA
1 TTTTTA-T-AA
* *
57824154 ATTTAATAA
1 TTTTTATAA
*
57824163 TTTTTCTAA
1 TTTTTATAA
** *
57824172 AATTTATTA
1 TTTTTATAA
57824181 TTTTTATAA
1 TTTTTATAA
57824190 TTTTT
1 TTTTT
57824195 TTTCTAATTT
Statistics
Matches: 91, Mismatches: 27, Indels: 18
0.67 0.20 0.13
Matches are distributed among these distances:
8 12 0.13
9 47 0.52
10 21 0.23
11 9 0.10
12 2 0.02
ACGTcount: A:0.33, C:0.02, G:0.01, T:0.64
Consensus pattern (9 bp):
TTTTTATAA
Found at i:57829899 original size:14 final size:14
Alignment explanation
Indices: 57829861--57829903 Score: 54
Period size: 13 Copynumber: 3.1 Consensus size: 14
57829851 CAAAATGTAC
57829861 AATATAATTAAA-T
1 AATATAATTAAATT
57829874 AATATAAATTAAATT
1 AATAT-AATTAAATT
*
57829889 AA-ATAATTTAATT
1 AATATAATTAAATT
57829902 AA
1 AA
57829904 CTGTTTACTC
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
13 15 0.56
14 9 0.33
15 3 0.11
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (14 bp):
AATATAATTAAATT
Found at i:57832332 original size:3 final size:3
Alignment explanation
Indices: 57832324--57832371 Score: 69
Period size: 3 Copynumber: 16.0 Consensus size: 3
57832314 TAAAACAATT
** *
57832324 TAA TAA TAA TAA TAA TAA TAA TGG TAA TAA TAA TAA TAA CAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
57832372 AAATCTTAAA
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.62, C:0.02, G:0.04, T:0.31
Consensus pattern (3 bp):
TAA
Found at i:57832436 original size:17 final size:18
Alignment explanation
Indices: 57832394--57832434 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
57832384 TAAAAATTAT
*
57832394 ATAAAAGGATATAGATAA
1 ATAAAATGATATAGATAA
57832412 ATAAAATGATATA-ATAAA
1 ATAAAATGATATAGAT-AA
57832430 ATAAA
1 ATAAA
57832435 TGTATTTAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 2 0.10
18 19 0.90
ACGTcount: A:0.66, C:0.00, G:0.10, T:0.24
Consensus pattern (18 bp):
ATAAAATGATATAGATAA
Found at i:57836832 original size:57 final size:59
Alignment explanation
Indices: 57836717--57836864 Score: 185
Period size: 57 Copynumber: 2.5 Consensus size: 59
57836707 AATTAACGGT
57836717 AAAAAGGATCTAGCCCGGACGGGTGATCCTATCCTAATATAGCCCTCCCGAAGAATATGTGTG
1 AAAAA-GATCTAGCCCGGACGGGTGATCC-AT-CTAATATAGCCCTCCCGAAGAATATGTG-G
* *
57836780 AAAAAGATCTAGCCCGGACGGGTGAT-C-T-TGATATAGCCCTCCTGAAGAATATGTGG
1 AAAAAGATCTAGCCCGGACGGGTGATCCATCTAATATAGCCCTCCCGAAGAATATGTGG
* * *
57836836 AAAATGAATTTAGCCCGGACGGGTAATCC
1 AAAAAG-ATCTAGCCCGGACGGGTGATCC
57836865 GAATTAGGGT
Statistics
Matches: 78, Mismatches: 5, Indels: 9
0.85 0.05 0.10
Matches are distributed among these distances:
56 6 0.08
57 43 0.55
58 1 0.01
59 1 0.01
61 1 0.01
62 21 0.27
63 5 0.06
ACGTcount: A:0.31, C:0.22, G:0.25, T:0.22
Consensus pattern (59 bp):
AAAAAGATCTAGCCCGGACGGGTGATCCATCTAATATAGCCCTCCCGAAGAATATGTGG
Found at i:57847055 original size:44 final size:47
Alignment explanation
Indices: 57847007--57847125 Score: 154
Period size: 49 Copynumber: 2.6 Consensus size: 47
57846997 TTCAGTTTAT
* *
57847007 TCCACTGTGACTTTAGGGAGATAAGACTAGT-G-G-CTTCAATCTGC
1 TCCACTGTAACTTCAGGGAGATAAGACTAGTAGCGTCTTCAATCTGC
* * *
57847051 TCCACTGCAACTTCAGGGAGATAAGATTTGTAGCCCGTCTTCAATCTGC
1 TCCACTGTAACTTCAGGGAGATAAGACTAGTAG--CGTCTTCAATCTGC
57847100 TCCACTGTAACTTCAGGGAGATAAGA
1 TCCACTGTAACTTCAGGGAGATAAGA
57847126 TTGATTTATT
Statistics
Matches: 64, Mismatches: 6, Indels: 5
0.85 0.08 0.07
Matches are distributed among these distances:
44 26 0.41
45 1 0.02
48 1 0.02
49 36 0.56
ACGTcount: A:0.27, C:0.23, G:0.23, T:0.28
Consensus pattern (47 bp):
TCCACTGTAACTTCAGGGAGATAAGACTAGTAGCGTCTTCAATCTGC
Found at i:57847200 original size:87 final size:87
Alignment explanation
Indices: 57847094--57847537 Score: 306
Period size: 87 Copynumber: 4.9 Consensus size: 87
57847084 CCCGTCTTCA
* * *
57847094 ATCTGCTCCACTGTAACTTCAGGGAGATAAGATTGATTTATTTTTAACCTGTTCCACTGCAACTT
1 ATCTGCTCTACTGCAACTTCAGGGAGATAAGATTGATTTATCTTTAACCTGTTCCACTGCAACTT
*
57847159 CAAGGAGATAAGGTTTGAT-ATG
66 C-AGGAGATAAGATTTGATAATG
* * ** *
57847181 ATCTGCTCTGCTGCAACTTCAGAGAGATAAGATCTGTAATTTATAGCTTTAATATGTTCCATTGC
1 ATCTGCTCTACTGCAACTTCAGGGAGATAAGAT-TG--ATTTAT--CTTTAACCTGTTCCACTGC
* ** *
57847246 AACTTCAGGGAGATAAGATTGGTATCTTCA
61 AACTTCA-GGAGATAAGATTTG-ATAAT-G
* * * * * ** * * *
57847276 ACCTGCTCTATTGTAACTTCAGGGAGATAAGGTT--TGTGGCTTTAATCTGCTCCACTGTAACTT
1 ATCTGCTCTACTGCAACTTCAGGGAGATAAGATTGATTTATCTTTAACCTGTTCCACTGCAACTT
**
57847339 CA-GTTATAAGATTT-ATAACTTG
66 CAGGAGATAAGATTTGATAA--TG
* * * * *
57847361 TCTTCATTTTGCTCCACTGCAACTTCAGGGAGATAAGATTGGTTTATTTTTAACCTGTTCCACTA
1 -----A-TCTGCTCTACTGCAACTTCAGGGAGATAAGATTGATTTATCTTTAACCTGTTCCACTG
*
57847426 CAACTTCAGGAAGATAAGGTTTGAT-ATG
60 CAACTTCAGG-AGATAAGATTTGATAATG
* * *
57847454 ATCTGCTCTACTGCAACTTCAGAGAGATAAGATCTGTAATTTATAGCTTCAATCTGTTCCACTGC
1 ATCTGCTCTACTGCAACTTCAGGGAGATAAGAT-TG--ATTTAT--CTTTAACCTGTTCCACTGC
* * *
57847519 AGCTTTAGGAAATAAGATT
61 AACTTCAGGAGATAAGATT
57847538 CGCTATCTTC
Statistics
Matches: 270, Mismatches: 60, Indels: 50
0.71 0.16 0.13
Matches are distributed among these distances:
84 2 0.01
86 10 0.04
87 58 0.21
88 27 0.10
90 14 0.05
91 36 0.13
92 55 0.20
93 27 0.10
94 3 0.01
95 36 0.13
96 2 0.01
ACGTcount: A:0.28, C:0.18, G:0.18, T:0.35
Consensus pattern (87 bp):
ATCTGCTCTACTGCAACTTCAGGGAGATAAGATTGATTTATCTTTAACCTGTTCCACTGCAACTT
CAGGAGATAAGATTTGATAATG
Found at i:57847208 original size:136 final size:135
Alignment explanation
Indices: 57847045--57847579 Score: 499
Period size: 136 Copynumber: 3.9 Consensus size: 135
57847035 AGTGGCTTCA
* * * ** * *
57847045 ATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGTAGCCCGTCTTCAATCTGCTCCACTGTAA
1 ATCTGCTCCACTGCAACTTCAGAGAGATAAGATCTGTAACTTGTCTTCAATATGCTCCACTGCAA
57847110 CTTCAGGGAGATAAGATTGATTTATTTTTAACCTGTTCCACTGCAACTTCAAGGAGATAAGGTTT
66 CTTCAGGGAGATAAGATTG-TTTATTTTTAACCTGTTCCACTGCAACTTCAAGGAGATAAGGTTT
57847175 GATATG
130 GATATG
** * * * * *
57847181 ATCTGCTCTGCTGCAACTTCAGAGAGATAAGATCTGTAATTTATAGCTTTAATATGTTCCATTGC
1 ATCTGCTCCACTGCAACTTCAGAGAGATAAGATCTGTAACTTGT--CTTCAATATGCTCCACTGC
* * * * * * * *
57847246 AACTTCAGGGAGATAAGATTG-GTATCTTCAACCTGCTCTATTGTAACTTCAGGGAGATAAGGTT
64 AACTTCAGGGAGATAAGATTGTTTATTTTTAACCTGTTCCACTGCAACTTCAAGGAGATAAGG-T
* * *
57847310 TGTGGCTTTA
128 T-T-GATATG
* ** * * * *
57847320 ATCTGCTCCACTGTAACTTC--AGTTATAAGATTTATAACTTGTCTTCATTTTGCTCCACTGCAA
1 ATCTGCTCCACTGCAACTTCAGAGAGATAAGATCTGTAACTTGTCTTCAATATGCTCCACTGCAA
*
57847383 CTTCAGGGAGATAAGATTGGTTTATTTTTAACCTGTTCCACTACAACTTC-AGGAAGATAAGGTT
66 CTTCAGGGAGATAAGATT-GTTTATTTTTAACCTGTTCCACTGCAACTTCAAGG-AGATAAGGTT
57847447 TGATATG
129 TGATATG
* * * * *
57847454 ATCTGCTCTACTGCAACTTCAGAGAGATAAGATCTGTAATTTATAGCTTCAATCTGTTCCACTGC
1 ATCTGCTCCACTGCAACTTCAGAGAGATAAGATCTGTAACTTGT--CTTCAATATGCTCCACTGC
* * * * * * **
57847519 AGCTTTA-GGAAATAAGATTCG-CTATCTTCAGTCTGTTCCACTGCAACTTC-AGGAAGATAAG
64 AACTTCAGGGAGATAAGATT-GTTTATTTTTAACCTGTTCCACTGCAACTTCAAGG-AGATAAG
57847580 ACTAGTAACT
Statistics
Matches: 315, Mismatches: 72, Indels: 24
0.77 0.18 0.06
Matches are distributed among these distances:
134 21 0.07
135 35 0.11
136 123 0.39
137 59 0.19
138 57 0.18
139 20 0.06
ACGTcount: A:0.28, C:0.19, G:0.19, T:0.34
Consensus pattern (135 bp):
ATCTGCTCCACTGCAACTTCAGAGAGATAAGATCTGTAACTTGTCTTCAATATGCTCCACTGCAA
CTTCAGGGAGATAAGATTGTTTATTTTTAACCTGTTCCACTGCAACTTCAAGGAGATAAGGTTTG
ATATG
Found at i:57847326 original size:44 final size:44
Alignment explanation
Indices: 57847007--57847341 Score: 163
Period size: 44 Copynumber: 7.4 Consensus size: 44
57846997 TTCAGTTTAT
* * * * * * *
57847007 TCCACTGTGACTTTAGGGAGATAAGACTAGTGGCTTCAATCTGC
1 TCCATTGTAACTTCAGGGAGATAAGATTGGTAGCTTTAATCTGC
* * *
57847051 TCCACTGCAACTTCAGGGAGATAAGATTTGTAGCCCGTCTTCAATCTGC
1 TCCATTGTAACTTCAGGGAGATAAGATTGGTAG--C-T-TT-AATCTGC
* * ** * *
57847100 TCCACTGTAACTTCAGGGAGATAAGATTGATTTATTTTTAACCTGT
1 TCCATTGTAACTTCAGGGAGATAAGATTG--GTAGCTTTAATCTGC
* * * * * * *
57847146 TCCACTGCAACTTCAAGGAGATAAGGTT--T-GATATGATCTGC
1 TCCATTGTAACTTCAGGGAGATAAGATTGGTAGCTTTAATCTGC
*** * * * * *
57847187 TCTGCTGCAACTTCAGAGAGATAAGATCTGTAATTTATAGCTTTAATATGT
1 TCCATTGTAACTTCAGGGAGATAAGAT-TG------GTAGCTTTAATCTGC
* * * *
57847238 TCCATTGCAACTTCAGGGAGATAAGATTGGTATCTTCAACCTGC
1 TCCATTGTAACTTCAGGGAGATAAGATTGGTAGCTTTAATCTGC
* * * *
57847282 TCTATTGTAACTTCAGGGAGATAAGGTTTGTGGCTTTAATCTGC
1 TCCATTGTAACTTCAGGGAGATAAGATTGGTAGCTTTAATCTGC
*
57847326 TCCACTGTAACTTCAG
1 TCCATTGTAACTTCAG
57847342 TTATAAGATT
Statistics
Matches: 221, Mismatches: 53, Indels: 34
0.72 0.17 0.11
Matches are distributed among these distances:
41 28 0.13
42 2 0.01
44 86 0.39
46 31 0.14
47 3 0.01
48 2 0.01
49 34 0.15
50 3 0.01
51 32 0.14
ACGTcount: A:0.27, C:0.19, G:0.21, T:0.33
Consensus pattern (44 bp):
TCCATTGTAACTTCAGGGAGATAAGATTGGTAGCTTTAATCTGC
Found at i:57847394 original size:273 final size:274
Alignment explanation
Indices: 57847016--57847622 Score: 815
Period size: 273 Copynumber: 2.2 Consensus size: 274
57847006 TTCCACTGTG
* *
57847016 ACTTTAGGGAGATAAGACTAGTGGCTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTG
1 ACTTCAGGGAGATAAGACTAGTGGCTTCAATCTGCTCCACTGCAACTTCA-GGAGATAAGATTTA
* *
57847081 TAGCCCGTCTTCAATCTGCTCCACTGTAACTTCAGGGAGATAAGATTGATTTATTTTTAACCTGT
65 TAACCCGTCTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTGATTTATTTTTAACCTGT
* *
57847146 TCCACTGCAACTTCAAGG-AGATAAGGTTTGATATGATCTGCTCTGCTGCAACTTCAGAGAGATA
130 TCCACTACAACTTC-AGGAAGATAAGGTTTGATATGATCTGCTCTACTGCAACTTCAGAGAGATA
* * * *
57847210 AGATCTGTAATTTATAGCTTTAATATGTTCCATTGCAACTTCAGGGAGATAAGATT-GGTATCTT
194 AGATCTGTAATTTATAGCTTCAATATGTTCCACTGCAACTTCA-GGAAATAAGATTCGCTATCTT
57847274 CAACCTGCTCTATTGTA
258 CAACCTGCTCTATTGTA
** * * * **
57847291 ACTTCAGGGAGATAAGGTTTGTGGCTTTAATCTGCTCCACTGTAACTTCA-GTTATAAGATTTAT
1 ACTTCAGGGAGATAAGACTAGTGGCTTCAATCTGCTCCACTGCAACTTCAGGAGATAAGATTTAT
** * * *
57847355 AACTTGTCTTCATTTTGCTCCACTGCAACTTCAGGGAGATAAGATTGGTTTATTTTTAACCTGTT
66 AACCCGTCTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTGATTTATTTTTAACCTGTT
57847420 CCACTACAACTTCAGGAAGATAAGGTTTGATATGATCTGCTCTACTGCAACTTCAGAGAGATAAG
131 CCACTACAACTTCAGGAAGATAAGGTTTGATATGATCTGCTCTACTGCAACTTCAGAGAGATAAG
* * * *
57847485 ATCTGTAATTTATAGCTTCAATCTGTTCCACTGCAGCTTTAGGAAATAAGATTCGCTATCTTCAG
196 ATCTGTAATTTATAGCTTCAATATGTTCCACTGCAACTTCAGGAAATAAGATTCGCTATCTTCAA
* * * * *
57847550 TCTGTTCCACTGCA
261 CCTGCTCTATTGTA
* ** * * * *
57847564 ACTTCAGGAAGATAAGACTAGTAACTTCAACCTACTTCACTACAACTTCAGGGAGATAA
1 ACTTCAGGGAGATAAGACTAGTGGCTTCAATCTGCTCCACTGCAACTTCA-GGAGATAA
57847623 AGTTTGTTAT
Statistics
Matches: 283, Mismatches: 45, Indels: 8
0.84 0.13 0.02
Matches are distributed among these distances:
272 14 0.05
273 220 0.78
275 49 0.17
ACGTcount: A:0.29, C:0.19, G:0.19, T:0.33
Consensus pattern (274 bp):
ACTTCAGGGAGATAAGACTAGTGGCTTCAATCTGCTCCACTGCAACTTCAGGAGATAAGATTTAT
AACCCGTCTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTGATTTATTTTTAACCTGTT
CCACTACAACTTCAGGAAGATAAGGTTTGATATGATCTGCTCTACTGCAACTTCAGAGAGATAAG
ATCTGTAATTTATAGCTTCAATATGTTCCACTGCAACTTCAGGAAATAAGATTCGCTATCTTCAA
CCTGCTCTATTGTA
Found at i:57847592 original size:44 final size:44
Alignment explanation
Indices: 57847500--57847615 Score: 119
Period size: 44 Copynumber: 2.6 Consensus size: 44
57847490 TAATTTATAG
* * * * *
57847500 CTTCAATCTGTTCCACTGCAGCTTTAGGAAATAAGATTCGCTAT
1 CTTCAATCTGTTCCACTGCAACTTCAGGAAATAAGACTAGCTAA
*
57847544 CTTCAGTCTGTTCCACTGCAACTTCAGGAAGATAAGACTAG-TAA
1 CTTCAATCTGTTCCACTGCAACTTCAGGAA-ATAAGACTAGCTAA
* * *
57847588 CTTCAACCTACTT-CACTACAACTTCAGG
1 CTTCAATCT-GTTCCACTGCAACTTCAGG
57847616 GAGATAAAGT
Statistics
Matches: 60, Mismatches: 10, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
44 50 0.83
45 10 0.17
ACGTcount: A:0.29, C:0.26, G:0.15, T:0.30
Consensus pattern (44 bp):
CTTCAATCTGTTCCACTGCAACTTCAGGAAATAAGACTAGCTAA
Found at i:57848593 original size:14 final size:15
Alignment explanation
Indices: 57848570--57848602 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
57848560 ATCAACACTT
*
57848570 TTCCATATAAGA-CC
1 TTCCACATAAGATCC
57848584 TTCCACATAAGATCC
1 TTCCACATAAGATCC
57848599 TTCC
1 TTCC
57848603 TAGTTTGACA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 11 0.65
15 6 0.35
ACGTcount: A:0.30, C:0.33, G:0.06, T:0.30
Consensus pattern (15 bp):
TTCCACATAAGATCC
Found at i:57859575 original size:16 final size:17
Alignment explanation
Indices: 57859545--57859577 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
57859535 TTTTATAATA
*
57859545 TAAAAATTATATAAAAT
1 TAAAAAATATATAAAAT
57859562 TAAAAAATAT-TAAAAT
1 TAAAAAATATATAAAAT
57859578 ATTAAAGTAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (17 bp):
TAAAAAATATATAAAAT
Found at i:57859590 original size:13 final size:13
Alignment explanation
Indices: 57859572--57859596 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
57859562 TAAAAAATAT
57859572 TAAAATATTAAAG
1 TAAAATATTAAAG
57859585 TAAAATATTAAA
1 TAAAATATTAAA
57859597 CCATGTTTCT
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:0.64, C:0.00, G:0.04, T:0.32
Consensus pattern (13 bp):
TAAAATATTAAAG
Found at i:57867393 original size:23 final size:22
Alignment explanation
Indices: 57867341--57867393 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 22
57867331 TCCACGTCTT
*
57867341 TTTCTTTTGTTTCTTTTTCTAA
1 TTTCTTTTCTTTCTTTTTCTAA
57867363 -TTCATTTTCTCTTCTTTCTTC-AA
1 TTTC-TTTTCT-TTCTTT-TTCTAA
57867386 TTTCTTTT
1 TTTCTTTT
57867394 TCACTCTCAA
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 3 0.12
22 5 0.19
23 12 0.46
24 6 0.23
ACGTcount: A:0.09, C:0.19, G:0.02, T:0.70
Consensus pattern (22 bp):
TTTCTTTTCTTTCTTTTTCTAA
Found at i:57881936 original size:6 final size:6
Alignment explanation
Indices: 57881925--57881963 Score: 53
Period size: 6 Copynumber: 6.5 Consensus size: 6
57881915 TGCACCAACC
*
57881925 AAAAA- AAAAAA AAAGAAG AAAAAG AAAAAG AAAAAG AAA
1 AAAAAG AAAAAG AAA-AAG AAAAAG AAAAAG AAAAAG AAA
57881964 GATGGGGAGG
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
5 5 0.16
6 21 0.68
7 5 0.16
ACGTcount: A:0.87, C:0.00, G:0.13, T:0.00
Consensus pattern (6 bp):
AAAAAG
Found at i:57886178 original size:29 final size:30
Alignment explanation
Indices: 57886116--57886184 Score: 104
Period size: 29 Copynumber: 2.3 Consensus size: 30
57886106 TATCAAAACT
57886116 ATACATAAACTTTGATTTAATGTGTAATGTC
1 ATACATAAACTTTGATTT-ATGTGTAATGTC
* *
57886147 ATACATAAACTTTGATTT-TGTGTGATTTC
1 ATACATAAACTTTGATTTATGTGTAATGTC
57886176 ATACATAAA
1 ATACATAAA
57886185 ATTTTAATTT
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
29 18 0.50
31 18 0.50
ACGTcount: A:0.36, C:0.10, G:0.12, T:0.42
Consensus pattern (30 bp):
ATACATAAACTTTGATTTATGTGTAATGTC
Found at i:57886195 original size:29 final size:29
Alignment explanation
Indices: 57886116--57886195 Score: 79
Period size: 29 Copynumber: 2.7 Consensus size: 29
57886106 TATCAAAACT
* *
57886116 ATACATAAACTTTGATTTAATGTGTAATGTC
1 ATACATAAAATTTGAATT--TGTGTAATGTC
* * * *
57886147 ATACATAAACTTTGATTTTGTGTGATTTC
1 ATACATAAAATTTGAATTTGTGTAATGTC
*
57886176 ATACATAAAATTTTAATTTG
1 ATACATAAAATTTGAATTTG
57886196 ATTCAGTTTT
Statistics
Matches: 44, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
29 26 0.59
31 18 0.41
ACGTcount: A:0.35, C:0.09, G:0.11, T:0.45
Consensus pattern (29 bp):
ATACATAAAATTTGAATTTGTGTAATGTC
Found at i:57886673 original size:12 final size:13
Alignment explanation
Indices: 57886656--57886685 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
57886646 GTTAATAGTA
57886656 TATTTTTA-TTTT
1 TATTTTTATTTTT
57886668 TATTTTTATTTTT
1 TATTTTTATTTTT
57886681 TATTT
1 TATTT
57886686 CAAGTCAATT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 8 0.47
13 9 0.53
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (13 bp):
TATTTTTATTTTT
Found at i:57886674 original size:7 final size:6
Alignment explanation
Indices: 57886656--57886685 Score: 51
Period size: 6 Copynumber: 4.8 Consensus size: 6
57886646 GTTAATAGTA
57886656 TATTTT TATTTT TATTTT TATTTTT TATTT
1 TATTTT TATTTT TATTTT TA-TTTT TATTT
57886686 CAAGTCAATT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
6 17 0.74
7 6 0.26
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (6 bp):
TATTTT
Found at i:57887449 original size:3 final size:3
Alignment explanation
Indices: 57887441--57887488 Score: 96
Period size: 3 Copynumber: 16.0 Consensus size: 3
57887431 CATGTTTTAG
57887441 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA
1 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA
57887489 ATATAGTCTG
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 45 1.00
ACGTcount: A:0.33, C:0.33, G:0.00, T:0.33
Consensus pattern (3 bp):
TCA
Found at i:57888893 original size:17 final size:17
Alignment explanation
Indices: 57888839--57889190 Score: 194
Period size: 17 Copynumber: 19.9 Consensus size: 17
57888829 ATTTTAAAAA
57888839 AAACACGAAAA-TTTTG
1 AAACACGAAAATTTTTG
* *
57888855 AAACACGAGATTTCTTTG
1 AAACACGAAAATT-TTTG
*
57888873 AAACACGAAAATTTATG
1 AAACACGAAAATTTTTG
** *
57888890 AAACACGGTCAATTTCTTA
1 AAACAC-GAAAATTT-TTG
* *
57888909 AAACGCGAAAGTTTTTG
1 AAACACGAAAATTTTTG
* **
57888926 AAAAACGGGAATTTTTTTTTG
1 AAACAC--GAA--AATTTTTG
*
57888947 AAACACGAAAAATTTTG
1 AAACACGAAAATTTTTG
*
57888964 AAACACTG-GAA-TTTTG
1 AAACAC-GAAAATTTTTG
** *
57888980 AAAACACGAGGATTTTTT
1 -AAACACGAAAATTTTTG
* *
57888998 AAATACGAAAA-ATTTG
1 AAACACGAAAATTTTTG
* *
57889014 AAAACAAGAAAATTTTTA
1 -AAACACGAAAATTTTTG
* *
57889032 AAATACGAAAATTTTAG
1 AAACACGAAAATTTTTG
57889049 AAACACGAAAATTTTTG
1 AAACACGAAAATTTTTG
*
57889066 AAACAC-AGAAGTTTTTAG
1 AAACACGA-AAATTTTT-G
*
57889084 AAAACACGAAAAATTTTG
1 -AAACACGAAAATTTTTG
* **
57889102 AAA-ATTGGAATTTTTTTG
1 AAACA--CGAAAATTTTTG
*
57889120 AAAACACGAGAATTTTTG
1 -AAACACGAAAATTTTTG
*
57889138 AAAAACATGAAAATTTTTG
1 --AAACACGAAAATTTTTG
* **
57889157 CAACACGGGAATTTTTG
1 AAACACGAAAATTTTTG
57889174 AAAACACGAAAAATTTT
1 -AAACACG-AAAATTTT
57889191 CCGATTTTTT
Statistics
Matches: 251, Mismatches: 60, Indels: 47
0.70 0.17 0.13
Matches are distributed among these distances:
16 20 0.08
17 111 0.44
18 58 0.23
19 49 0.20
20 2 0.01
21 11 0.04
ACGTcount: A:0.45, C:0.11, G:0.14, T:0.30
Consensus pattern (17 bp):
AAACACGAAAATTTTTG
Found at i:57888928 original size:36 final size:37
Alignment explanation
Indices: 57888838--57888933 Score: 94
Period size: 36 Copynumber: 2.7 Consensus size: 37
57888828 AATTTTAAAA
*
57888838 AAAACACGAAAATTT-TGAAACAC-G--AGATTTCTTT
1 AAAACACGAAAATTTATGAAAAACGGTCA-ATTTCTTT
* *
57888872 GAAACACGAAAATTTATGAAACACGGTCAATTTC-TT
1 AAAACACGAAAATTTATGAAAAACGGTCAATTTCTTT
* * *
57888908 AAAACGCGAAAGTTTTTGAAAAACGG
1 AAAACACGAAAATTTATGAAAAACGG
57888934 GAATTTTTTT
Statistics
Matches: 52, Mismatches: 6, Indels: 6
0.81 0.09 0.09
Matches are distributed among these distances:
34 14 0.27
35 8 0.15
36 24 0.46
37 5 0.10
38 1 0.02
ACGTcount: A:0.44, C:0.15, G:0.16, T:0.26
Consensus pattern (37 bp):
AAAACACGAAAATTTATGAAAAACGGTCAATTTCTTT
Found at i:57888962 original size:21 final size:21
Alignment explanation
Indices: 57888920--57888962 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
57888910 AACGCGAAAG
** *
57888920 TTTTTGAAAAACGGGAATTTT
1 TTTTTGAAAAACGAAAAATTT
*
57888941 TTTTTGAAACACGAAAAATTT
1 TTTTTGAAAAACGAAAAATTT
57888962 T
1 T
57888963 GAAACACTGG
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.37, C:0.07, G:0.14, T:0.42
Consensus pattern (21 bp):
TTTTTGAAAAACGAAAAATTT
Found at i:57889162 original size:36 final size:35
Alignment explanation
Indices: 57889122--57889190 Score: 102
Period size: 35 Copynumber: 1.9 Consensus size: 35
57889112 TTTTTTTGAA
* *
57889122 AACACGAGAATTTTTGAAAAACATGAAAATTTTTGC
1 AACACGAGAATTTTTG-AAAACACGAAAAATTTTGC
*
57889158 AACACGGGAATTTTTGAAAACACGAAAAATTTT
1 AACACGAGAATTTTTGAAAACACGAAAAATTTT
57889191 CCGATTTTTT
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
35 15 0.50
36 15 0.50
ACGTcount: A:0.45, C:0.12, G:0.14, T:0.29
Consensus pattern (35 bp):
AACACGAGAATTTTTGAAAACACGAAAAATTTTGC
Found at i:57889322 original size:21 final size:20
Alignment explanation
Indices: 57889296--57889337 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 20
57889286 TGTTACCTTA
57889296 TTTTTGAAAACACGAGAAATT
1 TTTTTGAAAACACGA-AAATT
*
57889317 TTTTTGAAGACACGAAAATT
1 TTTTTGAAAACACGAAAATT
57889337 T
1 T
57889338 CGAAACCCGA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
20 6 0.30
21 14 0.70
ACGTcount: A:0.40, C:0.10, G:0.14, T:0.36
Consensus pattern (20 bp):
TTTTTGAAAACACGAAAATT
Found at i:57889714 original size:8 final size:8
Alignment explanation
Indices: 57889701--57889786 Score: 104
Period size: 8 Copynumber: 11.0 Consensus size: 8
57889691 TGAAACTCTT
57889701 TTTTTTTC
1 TTTTTTTC
*
57889709 TTTTTTCC
1 TTTTTTTC
*
57889717 TTTTTTCC
1 TTTTTTTC
57889725 TTTTTTTC
1 TTTTTTTC
*
57889733 -TCTTTTC
1 TTTTTTTC
57889740 TTTTTTTC
1 TTTTTTTC
*
57889748 -TTCTTTC
1 TTTTTTTC
57889755 TTTTTTTC
1 TTTTTTTC
57889763 TTTTTTTC
1 TTTTTTTC
* *
57889771 TTTCTCTC
1 TTTTTTTC
57889779 TTTTTTTC
1 TTTTTTTC
57889787 CTGGCCTGCT
Statistics
Matches: 66, Mismatches: 10, Indels: 4
0.82 0.12 0.05
Matches are distributed among these distances:
7 12 0.18
8 54 0.82
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (8 bp):
TTTTTTTC
Found at i:57889782 original size:15 final size:15
Alignment explanation
Indices: 57889702--57889784 Score: 103
Period size: 15 Copynumber: 5.4 Consensus size: 15
57889692 GAAACTCTTT
*
57889702 TTTTTTCTTTTTTCC
1 TTTTTTCTTTTTTTC
57889717 TTTTTTCCTTTTTTTC
1 TTTTTT-CTTTTTTTC
*
57889733 TCTTTTCTTTTTTTC
1 TTTTTTCTTTTTTTC
*
57889748 TTCTTTCTTTTTTTC
1 TTTTTTCTTTTTTTC
* *
57889763 TTTTTTTCTTTCTCTC
1 -TTTTTTCTTTTTTTC
57889779 TTTTTT
1 TTTTTT
57889785 TCCTGGCCTG
Statistics
Matches: 59, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
15 34 0.58
16 25 0.42
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (15 bp):
TTTTTTCTTTTTTTC
Found at i:57889899 original size:15 final size:14
Alignment explanation
Indices: 57889879--57889932 Score: 56
Period size: 15 Copynumber: 3.6 Consensus size: 14
57889869 GGCCTGCTTC
*
57889879 TTTTTTCTGGGCTG
1 TTTTTTTTGGGCTG
57889893 TTTTTTTTTGGGTCT-
1 -TTTTTTTTGGG-CTG
57889908 TTTCTTTTTGGGCTG
1 TTT-TTTTTGGGCTG
57889923 CTTTTTTTTG
1 -TTTTTTTTG
57889933 CTTTGGTTTT
Statistics
Matches: 34, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
14 5 0.15
15 24 0.71
16 5 0.15
ACGTcount: A:0.00, C:0.11, G:0.22, T:0.67
Consensus pattern (14 bp):
TTTTTTTTGGGCTG
Found at i:57889929 original size:32 final size:29
Alignment explanation
Indices: 57889879--57889966 Score: 88
Period size: 32 Copynumber: 2.8 Consensus size: 29
57889869 GGCCTGCTTC
*
57889879 TTTTTTCTGGGCTG-TTTTTTTTTGGGTCT
1 TTTTTTTTGGGCTGTTTTTTTTTTGGGT-T
*
57889908 TTTCTTTTTGGGCTGCTTTTTTTTGCTTTGGTT
1 TTT-TTTTTGGGCTG-TTTTTTTT--TTGGGTT
57889941 TTTTTTTTGGGCTGATTTGTTTTTTT
1 TTTTTTTTGGGCTG-TTT-TTTTTTT
57889967 TTTGTGTTGT
Statistics
Matches: 50, Mismatches: 3, Indels: 10
0.79 0.05 0.16
Matches are distributed among these distances:
29 3 0.06
30 10 0.20
31 2 0.04
32 21 0.42
33 9 0.18
34 5 0.10
ACGTcount: A:0.01, C:0.09, G:0.22, T:0.68
Consensus pattern (29 bp):
TTTTTTTTGGGCTGTTTTTTTTTTGGGTT
Found at i:57889980 original size:32 final size:32
Alignment explanation
Indices: 57889912--57889980 Score: 77
Period size: 32 Copynumber: 2.2 Consensus size: 32
57889902 GGGTCTTTTC
* * *
57889912 TTTTTGGGCTGCTTTTTTTTGCTTTGGTTTTT
1 TTTTTGGGCTGATTTTTTTTGCTTTGGTGTTG
* *
57889944 TTTTTGGGCTGATTTGTTTTT-TTTTTGTGTTG
1 TTTTTGGGCTGATTT-TTTTTGCTTTGGTGTTG
57889976 TTTTT
1 TTTTT
57889981 TTTAATTGTT
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
32 26 0.84
33 5 0.16
ACGTcount: A:0.01, C:0.06, G:0.22, T:0.71
Consensus pattern (32 bp):
TTTTTGGGCTGATTTTTTTTGCTTTGGTGTTG
Found at i:57890103 original size:14 final size:14
Alignment explanation
Indices: 57890080--57890134 Score: 53
Period size: 14 Copynumber: 4.0 Consensus size: 14
57890070 GATTGTTAAA
*
57890080 TTTT-TTTCTTTTT
1 TTTTCTTTCTTCTT
57890093 TTTTCTTTCTTCTT
1 TTTTCTTTCTTCTT
*
57890107 CTTTC-TTCTTCTT
1 TTTTCTTTCTTCTT
57890120 CTTCTTC-TTCTTCTT
1 -TT-TTCTTTCTTCTT
57890135 CTTCTCCTCC
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
13 12 0.33
14 13 0.36
15 11 0.31
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (14 bp):
TTTTCTTTCTTCTT
Found at i:57890105 original size:3 final size:3
Alignment explanation
Indices: 57890099--57890139 Score: 73
Period size: 3 Copynumber: 13.3 Consensus size: 3
57890089 TTTTTTTTCT
57890099 TTC TTC TTC TTTC TTC TTC TTC TTC TTC TTC TTC TTC TTC T
1 TTC TTC TTC -TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC T
57890140 CCTCCTACAC
Statistics
Matches: 37, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
3 34 0.92
4 3 0.08
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TTC
Found at i:57890240 original size:10 final size:10
Alignment explanation
Indices: 57890205--57890254 Score: 59
Period size: 10 Copynumber: 5.2 Consensus size: 10
57890195 ACGCTGATAC
57890205 TCTT-TCTTT
1 TCTTCTCTTT
* *
57890214 TCTTCTCCTC
1 TCTTCTCTTT
57890224 T-TTCTCTTT
1 TCTTCTCTTT
57890233 TCTTCTCTTT
1 TCTTCTCTTT
*
57890243 TCTTCTTTTT
1 TCTTCTCTTT
57890253 TC
1 TC
57890255 CTTCGAAAAA
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
9 11 0.32
10 23 0.68
ACGTcount: A:0.00, C:0.30, G:0.00, T:0.70
Consensus pattern (10 bp):
TCTTCTCTTT
Found at i:57890252 original size:19 final size:19
Alignment explanation
Indices: 57890209--57890251 Score: 63
Period size: 19 Copynumber: 2.3 Consensus size: 19
57890199 TGATACTCTT
57890209 TCTTTTCTTCTCCTCTTTC
1 TCTTTTCTTCTCCTCTTTC
57890228 TCTTTTCTTCT-CT-TTTC
1 TCTTTTCTTCTCCTCTTTC
57890245 TTCTTTT
1 -TCTTTT
57890252 TTCCTTCGAA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 4 0.17
18 8 0.35
19 11 0.48
ACGTcount: A:0.00, C:0.30, G:0.00, T:0.70
Consensus pattern (19 bp):
TCTTTTCTTCTCCTCTTTC
Found at i:57890536 original size:29 final size:29
Alignment explanation
Indices: 57890503--57890619 Score: 94
Period size: 30 Copynumber: 3.9 Consensus size: 29
57890493 TGTAATTTTT
*
57890503 AGAAAATTTAGGATTAAAATGAAATTTAA
1 AGAAAATTTAGGGTTAAAATGAAATTTAA
* * *
57890532 TGAAAGTTTAGGGGTCT-AAGTGAAATTTAA
1 AGAAAATTTA-GGGT-TAAAATGAAATTTAA
* *
57890562 AGAAAGTTTAAGGGTCAAAATGAAATTT-A
1 AGAAAATTT-AGGGTTAAAATGAAATTTAA
* * *
57890591 GGAAAAGTTTAGGGGTCAAAATGTAATTT
1 AGAAAA-TTTA-GGGTTAAAATGAAATTT
57890620 TTATTTTTTA
Statistics
Matches: 72, Mismatches: 10, Indels: 11
0.77 0.11 0.12
Matches are distributed among these distances:
29 14 0.19
30 56 0.78
31 2 0.03
ACGTcount: A:0.44, C:0.03, G:0.22, T:0.31
Consensus pattern (29 bp):
AGAAAATTTAGGGTTAAAATGAAATTTAA
Found at i:57890558 original size:30 final size:30
Alignment explanation
Indices: 57890518--57890619 Score: 134
Period size: 30 Copynumber: 3.4 Consensus size: 30
57890508 ATTTAGGATT
*
57890518 AAAATGAAATTTAATGAAAGTTTAGGGGTC
1 AAAATGAAATTTAAAGAAAGTTTAGGGGTC
* * *
57890548 TAAGTGAAATTTAAAGAAAGTTTAAGGGTC
1 AAAATGAAATTTAAAGAAAGTTTAGGGGTC
*
57890578 AAAATGAAATTT-AGGAAAAGTTTAGGGGTC
1 AAAATGAAATTTAAAG-AAAGTTTAGGGGTC
*
57890608 AAAATGTAATTT
1 AAAATGAAATTT
57890620 TTATTTTTTA
Statistics
Matches: 62, Mismatches: 9, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
29 2 0.03
30 60 0.97
ACGTcount: A:0.44, C:0.03, G:0.23, T:0.30
Consensus pattern (30 bp):
AAAATGAAATTTAAAGAAAGTTTAGGGGTC
Found at i:57890619 original size:60 final size:59
Alignment explanation
Indices: 57890490--57890619 Score: 154
Period size: 60 Copynumber: 2.2 Consensus size: 59
57890480 TTCTGGGGCT
** * * *
57890490 AAATGTAATTTTTAGAAAATTTAGGATTAAAATGAAATTTAATGAAAGTTTAGGGGTCT
1 AAATGTAATTTAAAGAAAATTTAGGATCAAAATGAAATTTAAGGAAAGTTTAGGGGTCA
* * * *
57890549 AAGTGAAATTTAAAGAAAGTTTAAGGGTCAAAATGAAATTT-AGGAAAAGTTTAGGGGTCA
1 AAATGTAATTTAAAGAAAATTT-AGGATCAAAATGAAATTTAAGG-AAAGTTTAGGGGTCA
57890609 AAATGTAATTT
1 AAATGTAATTT
57890620 TTATTTTTTA
Statistics
Matches: 58, Mismatches: 11, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
59 19 0.33
60 39 0.67
ACGTcount: A:0.44, C:0.02, G:0.21, T:0.33
Consensus pattern (59 bp):
AAATGTAATTTAAAGAAAATTTAGGATCAAAATGAAATTTAAGGAAAGTTTAGGGGTCA
Found at i:57890640 original size:14 final size:15
Alignment explanation
Indices: 57890615--57890649 Score: 54
Period size: 14 Copynumber: 2.4 Consensus size: 15
57890605 GTCAAAATGT
*
57890615 AATTTTTATTTTTTA
1 AATTTTTATTTTTGA
57890630 AATTTTT-TTTTTGA
1 AATTTTTATTTTTGA
57890644 AATTTT
1 AATTTT
57890650 GAAAATTAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 12 0.63
15 7 0.37
ACGTcount: A:0.26, C:0.00, G:0.03, T:0.71
Consensus pattern (15 bp):
AATTTTTATTTTTGA
Found at i:57890858 original size:13 final size:13
Alignment explanation
Indices: 57890840--57890875 Score: 54
Period size: 13 Copynumber: 2.8 Consensus size: 13
57890830 AATTGACTCT
* *
57890840 TTAAAACTAGACA
1 TTAAAAATAGAAA
57890853 TTAAAAATAGAAA
1 TTAAAAATAGAAA
57890866 TTAAAAATAG
1 TTAAAAATAG
57890876 CTCAGCACGT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.61, C:0.06, G:0.08, T:0.25
Consensus pattern (13 bp):
TTAAAAATAGAAA
Found at i:57891077 original size:54 final size:54
Alignment explanation
Indices: 57890891--57891162 Score: 428
Period size: 54 Copynumber: 5.1 Consensus size: 54
57890881 CACGTGAGCC
* * *
57890891 AAGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTTG-AAAACAGAATTTGCAA
1 AAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAATAGAAATT--AA
57890946 AAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTGAAAAATAG--A--AA
1 AAGGCTCAACTCACCTCTCGCAATATGAGTTGA-TTTTTGAAAAATAGAAATTAA
*
57890997 AAGGCTCAACTCACCTCTCGCAATATGAGTTGGTTTTTGAAAAATAGAAATTAA
1 AAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAATAGAAATTAA
*
57891051 AAGGCTCAACTCACCTCTCGCAATATGAGTTGGTTTTTGAAAAATAGAAATTAA
1 AAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAATAGAAATTAA
57891105 AAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAATAGAAATTGAA
1 AAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAATAGAAATT-AA
57891160 AAG
1 AAG
57891163 TAGAAATTGA
Statistics
Matches: 205, Mismatches: 5, Indels: 14
0.92 0.02 0.06
Matches are distributed among these distances:
50 14 0.07
51 34 0.17
52 1 0.00
54 107 0.52
55 37 0.18
56 6 0.03
57 6 0.03
ACGTcount: A:0.37, C:0.17, G:0.17, T:0.29
Consensus pattern (54 bp):
AAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAATAGAAATTAA
Found at i:57891160 original size:14 final size:14
Alignment explanation
Indices: 57891141--57891175 Score: 61
Period size: 14 Copynumber: 2.5 Consensus size: 14
57891131 GAGTTGATTT
57891141 TTGAAAAATAGAAA
1 TTGAAAAATAGAAA
*
57891155 TTGAAAAGTAGAAA
1 TTGAAAAATAGAAA
57891169 TTGAAAA
1 TTGAAAA
57891176 TACCTCAGCG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.60, C:0.00, G:0.17, T:0.23
Consensus pattern (14 bp):
TTGAAAAATAGAAA
Found at i:57891410 original size:85 final size:87
Alignment explanation
Indices: 57891266--57891513 Score: 299
Period size: 85 Copynumber: 2.8 Consensus size: 87
57891256 AACAGAAATT
* * *
57891266 AAAAACAGAATTTGAAAAAACCTCAGCGTGTGGCCTGAGACTCAACTCACCTCTTGCAATATGAG
1 AAAAACAGAAATTGAAAATACCTCAGC-TGTGGCCTGAGGCTCAACTCACCTCTTGCAATATGAG
*
57891331 TTGATTTGAAAAG-TAGAATT-AG
65 TTGATTTGAAAAGATAG-ATTGAA
* * * *
57891353 TAAAGCAGAAATTGAAAATACCTCAGC-GT-GCCTTGAGGCTCAACTCACCTCTCGCAATATAAG
1 AAAAACAGAAATTGAAAATACCTCAGCTGTGGCC-TGAGGCTCAACTCACCTCTTGCAATATGAG
57891416 TTGATTTTTGAAAAGCATAGATTGAA
65 TTGA--TTTGAAAAG-ATAGATTGAA
* *
57891442 AAAAACATAAATTGAAAATACCTCAGCATGTGAGCC-AAGGCTCAACTCACCTCTTGCAATATGA
1 AAAAACAGAAATTGAAAATACCTCAGC-TGTG-GCCTGAGGCTCAACTCACCTCTTGCAATATGA
57891506 GTTGATTT
64 GTTGATTT
57891514 TTGAAAAACA
Statistics
Matches: 137, Mismatches: 14, Indels: 18
0.81 0.08 0.11
Matches are distributed among these distances:
84 3 0.02
85 33 0.24
87 32 0.23
88 3 0.02
89 31 0.23
91 32 0.23
93 3 0.02
ACGTcount: A:0.37, C:0.19, G:0.18, T:0.26
Consensus pattern (87 bp):
AAAAACAGAAATTGAAAATACCTCAGCTGTGGCCTGAGGCTCAACTCACCTCTTGCAATATGAGT
TGATTTGAAAAGATAGATTGAA
Found at i:57891459 original size:15 final size:16
Alignment explanation
Indices: 57891426--57891459 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
57891416 TTGATTTTTG
* *
57891426 AAAAGCATAGATTGAA
1 AAAAACATAAATTGAA
57891442 AAAAACATAAATTGAA
1 AAAAACATAAATTGAA
57891458 AA
1 AA
57891460 TACCTCAGCA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.65, C:0.06, G:0.12, T:0.18
Consensus pattern (16 bp):
AAAAACATAAATTGAA
Found at i:57891501 original size:91 final size:88
Alignment explanation
Indices: 57891266--57891520 Score: 315
Period size: 91 Copynumber: 2.9 Consensus size: 88
57891256 AACAGAAATT
* * *
57891266 AAAAACAGAATTTGAAAAAACCTCAGCGTGTGGCCTGAGACTCAACTCACCTCTTGCAATATGAG
1 AAAAACAGAAATTGAAAATACCTCAGC-TGTGGCCTGAGGCTCAACTCACCTCTTGCAATATGAG
*
57891331 TTGA--TTTGAAAAGTAGAATTAG
65 TTGATTTTTGAAAAGTAGAATTAA
* * * *
57891353 TAAAGCAGAAATTGAAAATACCTCAGC-GT-GCCTTGAGGCTCAACTCACCTCTCGCAATATAAG
1 AAAAACAGAAATTGAAAATACCTCAGCTGTGGCC-TGAGGCTCAACTCACCTCTTGCAATATGAG
57891416 TTGATTTTTGAAAAGCATAG-ATTGAA
65 TTGATTTTTGAAAAG--TAGAATT-AA
* *
57891442 AAAAACATAAATTGAAAATACCTCAGCATGTGAGCC-AAGGCTCAACTCACCTCTTGCAATATGA
1 AAAAACAGAAATTGAAAATACCTCAGC-TGTG-GCCTGAGGCTCAACTCACCTCTTGCAATATGA
57891506 GTTGATTTTTGAAAA
64 GTTGATTTTTGAAAA
57891521 ACAAAAATTA
Statistics
Matches: 144, Mismatches: 14, Indels: 16
0.83 0.08 0.09
Matches are distributed among these distances:
84 3 0.02
85 33 0.23
87 32 0.22
88 3 0.02
89 28 0.19
91 42 0.29
93 3 0.02
ACGTcount: A:0.38, C:0.18, G:0.18, T:0.26
Consensus pattern (88 bp):
AAAAACAGAAATTGAAAATACCTCAGCTGTGGCCTGAGGCTCAACTCACCTCTTGCAATATGAGT
TGATTTTTGAAAAGTAGAATTAA
Found at i:57892039 original size:191 final size:192
Alignment explanation
Indices: 57891479--57892280 Score: 1459
Period size: 192 Copynumber: 4.2 Consensus size: 192
57891469 ATGTGAGCCA
** *
57891479 AGGCTCAACTCACCTCTTGCAATATGAGTTGATTTTTGAAAAACAAAAATTAAAAGGCTTAACTC
1 AGGCTCAACTCATTTCTCGCAATATGAGTTGA-TTTTGAAAAACAAAAATTAAAAGGCTTAACTC
57891544 ACCTCTCGCAATATGAGTCAATTTAAAACATAAACTAAAAATACCTCGGCGTGCCCCGAGGCTCA
65 ACCTCTCGCAATATGAGTCAATTTAAAACATAAACTAAAAATACCTCGGCGTGCCCCGAGGCTCA
* **
57891609 ACTCATTTCTCGCAATATGAGTTGATTTTTTT-TTAAATTTAAAAATACCTCAACGTGTCTTG
130 ACTCACTTCTCGCAATATGAGTTGATTTTTTTAAAAAATTTAAAAATACCTCAACGTGTCTTG
57891671 ATGGCTCAACTCATTTCTCGCAATATGAGTTGATTTTGAAAAACAAAAATTAAAAGGCTTAACTC
1 A-GGCTCAACTCATTTCTCGCAATATGAGTTGATTTTGAAAAACAAAAATTAAAAGGCTTAACTC
* *
57891736 ACCTCTCGCAACATGAGTCAATTTAAAACATAAACTAAACATACCTCGGCGTGCCCCGAGGCTCA
65 ACCTCTCGCAATATGAGTCAATTTAAAACATAAACTAAAAATACCTCGGCGTGCCCCGAGGCTCA
57891801 ACTCACTTCTCGCAATATGAGTTGATTTTTTTAAAAAATTT-AAAATACCTCAACGTGTCTTG
130 ACTCACTTCTCGCAATATGAGTTGATTTTTTTAAAAAATTTAAAAATACCTCAACGTGTCTTG
*
57891863 AGGCTCAACTCATTTCTCGCAATATGAGTTGATTTTG-AAAACAAAAATTAAAAGACTTAACTCA
1 AGGCTCAACTCATTTCTCGCAATATGAGTTGATTTTGAAAAACAAAAATTAAAAGGCTTAACTCA
*
57891927 CCTCTCGCAATATGAGTCAATTTAAAACATAAACTAAAAATACCTCTGCGTGCCCCGAGGCTCAA
66 CCTCTCGCAATATGAGTCAATTTAAAACATAAACTAAAAATACCTCGGCGTGCCCCGAGGCTCAA
*
57891992 CTCACTTCTCGCAATATGAGTTGATTTTTTTTAAAAATTTAAAAATACCTCAACGTGTCTTG
131 CTCACTTCTCGCAATATGAGTTGATTTTTTTAAAAAATTTAAAAATACCTCAACGTGTCTTG
57892054 AGGCTCAACTCATTTCTCGCAATATGAGTTGATTTTGAAAAACAAAAATTAAAAGGCTTAACTCA
1 AGGCTCAACTCATTTCTCGCAATATGAGTTGATTTTGAAAAACAAAAATTAAAAGGCTTAACTCA
57892119 CCTCTCGCAATATGAGTCAATTTAAAACATAAACTAAAAATACCTCGGCGTGCCCCGAGGCTCAA
66 CCTCTCGCAATATGAGTCAATTTAAAACATAAACTAAAAATACCTCGGCGTGCCCCGAGGCTCAA
57892184 CTCACTTCTCGCAATATGAGTTGA-TTTTTTAAAAAATTTAAAAATACCTCAACGTGTCTTG
131 CTCACTTCTCGCAATATGAGTTGATTTTTTTAAAAAATTTAAAAATACCTCAACGTGTCTTG
57892245 AGGCTCAACTCATTTCTCGCAATATGAGTTGATTTT
1 AGGCTCAACTCATTTCTCGCAATATGAGTTGATTTT
57892281 CCTTGGAAAG
Statistics
Matches: 590, Mismatches: 16, Indels: 9
0.96 0.03 0.01
Matches are distributed among these distances:
190 127 0.22
191 166 0.28
192 263 0.45
193 34 0.06
ACGTcount: A:0.35, C:0.21, G:0.13, T:0.31
Consensus pattern (192 bp):
AGGCTCAACTCATTTCTCGCAATATGAGTTGATTTTGAAAAACAAAAATTAAAAGGCTTAACTCA
CCTCTCGCAATATGAGTCAATTTAAAACATAAACTAAAAATACCTCGGCGTGCCCCGAGGCTCAA
CTCACTTCTCGCAATATGAGTTGATTTTTTTAAAAAATTTAAAAATACCTCAACGTGTCTTG
Found at i:57892230 original size:382 final size:383
Alignment explanation
Indices: 57891479--57892280 Score: 1475
Period size: 382 Copynumber: 2.1 Consensus size: 383
57891469 ATGTGAGCCA
** * *
57891479 AGGCTCAACTCACCTCTTGCAATATGAGTTGATTTTTGAAAAACAAAAATTAAAAGGCTTAACTC
1 AGGCTCAACTCATTTCTCGCAATATGAGTTGA-TTTTGAAAAACAAAAATTAAAAGACTTAACTC
57891544 ACCTCTCGCAATATGAGTCAATTTAAAACATAAACTAAAAATACCTCGGCGTGCCCCGAGGCTCA
65 ACCTCTCGCAATATGAGTCAATTTAAAACATAAACTAAAAATACCTCGGCGTGCCCCGAGGCTCA
* *
57891609 ACTCATTTCTCGCAATATGAGTTGATTTTTTTTTAAATTTAAAAATACCTCAACGTGTCTTGATG
130 ACTCACTTCTCGCAATATGAGTTGATTTTTTTTAAAATTTAAAAATACCTCAACGTGTCTTGATG
57891674 GCTCAACTCATTTCTCGCAATATGAGTTGATTTTGAAAAACAAAAATTAAAAGGCTTAACTCACC
195 GCTCAACTCATTTCTCGCAATATGAGTTGATTTTGAAAAACAAAAATTAAAAGGCTTAACTCACC
*
57891739 TCTCGCAACATGAGTCAATTTAAAACATAAACTAAACATACCTCGGCGTGCCCCGAGGCTCAACT
260 TCTCGCAACATGAGTCAATTTAAAACATAAACTAAAAATACCTCGGCGTGCCCCGAGGCTCAACT
57891804 CACTTCTCGCAATATGAGTTGATTTTTTTAAAAAATTTAAAATACCTCAACGTGTCTTG
325 CACTTCTCGCAATATGAGTTGATTTTTTTAAAAAATTTAAAATACCTCAACGTGTCTTG
57891863 AGGCTCAACTCATTTCTCGCAATATGAGTTGATTTTG-AAAACAAAAATTAAAAGACTTAACTCA
1 AGGCTCAACTCATTTCTCGCAATATGAGTTGATTTTGAAAAACAAAAATTAAAAGACTTAACTCA
*
57891927 CCTCTCGCAATATGAGTCAATTTAAAACATAAACTAAAAATACCTCTGCGTGCCCCGAGGCTCAA
66 CCTCTCGCAATATGAGTCAATTTAAAACATAAACTAAAAATACCTCGGCGTGCCCCGAGGCTCAA
57891992 CTCACTTCTCGCAATATGAGTTGATTTTTTTTAAAAATTTAAAAATACCTCAACGTGTCTTGA-G
131 CTCACTTCTCGCAATATGAGTTGATTTTTTTT-AAAATTTAAAAATACCTCAACGTGTCTTGATG
57892056 GCTCAACTCATTTCTCGCAATATGAGTTGATTTTGAAAAACAAAAATTAAAAGGCTTAACTCACC
195 GCTCAACTCATTTCTCGCAATATGAGTTGATTTTGAAAAACAAAAATTAAAAGGCTTAACTCACC
*
57892121 TCTCGCAATATGAGTCAATTTAAAACATAAACTAAAAATACCTCGGCGTGCCCCGAGGCTCAACT
260 TCTCGCAACATGAGTCAATTTAAAACATAAACTAAAAATACCTCGGCGTGCCCCGAGGCTCAACT
57892186 CACTTCTCGCAATATGAGTTGA-TTTTTTAAAAAATTTAAAAATACCTCAACGTGTCTTG
325 CACTTCTCGCAATATGAGTTGATTTTTTTAAAAAATTT-AAAATACCTCAACGTGTCTTG
57892245 AGGCTCAACTCATTTCTCGCAATATGAGTTGATTTT
1 AGGCTCAACTCATTTCTCGCAATATGAGTTGATTTT
57892281 CCTTGGAAAG
Statistics
Matches: 407, Mismatches: 9, Indels: 6
0.96 0.02 0.01
Matches are distributed among these distances:
381 15 0.04
382 329 0.81
383 34 0.08
384 29 0.07
ACGTcount: A:0.35, C:0.21, G:0.13, T:0.31
Consensus pattern (383 bp):
AGGCTCAACTCATTTCTCGCAATATGAGTTGATTTTGAAAAACAAAAATTAAAAGACTTAACTCA
CCTCTCGCAATATGAGTCAATTTAAAACATAAACTAAAAATACCTCGGCGTGCCCCGAGGCTCAA
CTCACTTCTCGCAATATGAGTTGATTTTTTTTAAAATTTAAAAATACCTCAACGTGTCTTGATGG
CTCAACTCATTTCTCGCAATATGAGTTGATTTTGAAAAACAAAAATTAAAAGGCTTAACTCACCT
CTCGCAACATGAGTCAATTTAAAACATAAACTAAAAATACCTCGGCGTGCCCCGAGGCTCAACTC
ACTTCTCGCAATATGAGTTGATTTTTTTAAAAAATTTAAAATACCTCAACGTGTCTTG
Found at i:57904001 original size:15 final size:15
Alignment explanation
Indices: 57903981--57904033 Score: 52
Period size: 15 Copynumber: 3.3 Consensus size: 15
57903971 CTTTTTCCTT
57903981 TTTTTTAAACACGAA
1 TTTTTTAAACACGAA
*
57903996 TTTTTTAAAATACAAGAA
1 TTTTTT--AA-ACACGAA
**
57904014 TTTTAGAAACACGAA
1 TTTTTTAAACACGAA
57904029 TTTTT
1 TTTTT
57904034 AAAAAAAACA
Statistics
Matches: 30, Mismatches: 5, Indels: 6
0.73 0.12 0.15
Matches are distributed among these distances:
15 16 0.53
16 2 0.07
17 2 0.07
18 10 0.33
ACGTcount: A:0.42, C:0.09, G:0.08, T:0.42
Consensus pattern (15 bp):
TTTTTTAAACACGAA
Found at i:57904093 original size:17 final size:17
Alignment explanation
Indices: 57904039--57904389 Score: 203
Period size: 17 Copynumber: 19.9 Consensus size: 17
57904029 TTTTTAAAAA
57904039 AAACACGAAAA-TTTTG
1 AAACACGAAAATTTTTG
* *
57904055 AAACACGAGATTTCTTTG
1 AAACACGAAAATT-TTTG
*
57904073 AAACACGAAAATTTATG
1 AAACACGAAAATTTTTG
** *
57904090 AAACACGGTCAATTTCTTA
1 AAACAC-GAAAATTT-TTG
* *
57904109 AAACGCGAAAGTTTTTG
1 AAACACGAAAATTTTTG
* **
57904126 AAAAACGGGAATTTTTTTTTG
1 AAACAC--GAA--AATTTTTG
*
57904147 AAACACGAAAAATTTTG
1 AAACACGAAAATTTTTG
*
57904164 AAACACTG-GAA-TTTTG
1 AAACAC-GAAAATTTTTG
** *
57904180 AAAACACGAGGATTTTTT
1 -AAACACGAAAATTTTTG
* *
57904198 AAATACGAAAA-ATTTG
1 AAACACGAAAATTTTTG
*
57904214 AAAACAAGAAAATTTTTG
1 -AAACACGAAAATTTTTG
* *
57904232 AAATACGAAAATTTTAG
1 AAACACGAAAATTTTTG
57904249 AAACACGAAAATTTTTG
1 AAACACGAAAATTTTTG
*
57904266 AAACAC-AGAAGTTTTTAG
1 AAACACGA-AAATTTTT-G
*
57904284 AAAACACGAAAAATTTTG
1 -AAACACGAAAATTTTTG
* **
57904302 AAA-ATTGGAATTTTTTTG
1 AAACA--CGAAAATTTTTG
*
57904320 AAAACACGAGAATTTTTG
1 -AAACACGAAAATTTTTG
*
57904338 AAAAACATGAAAATTTTTG
1 --AAACACGAAAATTTTTG
* *
57904357 CAACACG-GAATTTTTG
1 AAACACGAAAATTTTTG
57904373 AAAACACGAAAAATTTT
1 -AAACACG-AAAATTTT
57904390 CCGATTTTTT
Statistics
Matches: 253, Mismatches: 56, Indels: 49
0.71 0.16 0.14
Matches are distributed among these distances:
16 28 0.11
17 110 0.43
18 53 0.21
19 49 0.19
20 2 0.01
21 11 0.04
ACGTcount: A:0.45, C:0.11, G:0.14, T:0.30
Consensus pattern (17 bp):
AAACACGAAAATTTTTG
Found at i:57904128 original size:36 final size:37
Alignment explanation
Indices: 57904038--57904133 Score: 94
Period size: 36 Copynumber: 2.7 Consensus size: 37
57904028 ATTTTTAAAA
*
57904038 AAAACACGAAAATTT-TGAAACAC-G--AGATTTCTTT
1 AAAACACGAAAATTTATGAAAAACGGTCA-ATTTCTTT
* *
57904072 GAAACACGAAAATTTATGAAACACGGTCAATTTC-TT
1 AAAACACGAAAATTTATGAAAAACGGTCAATTTCTTT
* * *
57904108 AAAACGCGAAAGTTTTTGAAAAACGG
1 AAAACACGAAAATTTATGAAAAACGG
57904134 GAATTTTTTT
Statistics
Matches: 52, Mismatches: 6, Indels: 6
0.81 0.09 0.09
Matches are distributed among these distances:
34 14 0.27
35 8 0.15
36 24 0.46
37 5 0.10
38 1 0.02
ACGTcount: A:0.44, C:0.15, G:0.16, T:0.26
Consensus pattern (37 bp):
AAAACACGAAAATTTATGAAAAACGGTCAATTTCTTT
Found at i:57904162 original size:21 final size:21
Alignment explanation
Indices: 57904120--57904162 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
57904110 AACGCGAAAG
** *
57904120 TTTTTGAAAAACGGGAATTTT
1 TTTTTGAAAAACGAAAAATTT
*
57904141 TTTTTGAAACACGAAAAATTT
1 TTTTTGAAAAACGAAAAATTT
57904162 T
1 T
57904163 GAAACACTGG
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.37, C:0.07, G:0.14, T:0.42
Consensus pattern (21 bp):
TTTTTGAAAAACGAAAAATTT
Found at i:57904350 original size:55 final size:54
Alignment explanation
Indices: 57904258--57904381 Score: 141
Period size: 55 Copynumber: 2.3 Consensus size: 54
57904248 GAAACACGAA
*
57904258 AATTTTTG-AAACAC-AGAAGTTTTTAGAAAACACGAAAAATTTTG-AAAATTGG
1 AATTTTTGAAAACACGAGAAGTTTTTAGAAAACACGAAAAATTTTGCAAAA-CGG
* * *
57904310 AATTTTTTTGAAAACACGAGAA-TTTTT-GAAAAACATGAAAATTTTTGCAACACGG
1 AA--TTTTTGAAAACACGAGAAGTTTTTAG-AAAACACGAAAAATTTTGCAAAACGG
57904365 AATTTTTGAAAACACGA
1 AATTTTTGAAAACACGA
57904382 AAAATTTTCC
Statistics
Matches: 62, Mismatches: 4, Indels: 11
0.81 0.05 0.14
Matches are distributed among these distances:
52 2 0.03
53 15 0.24
54 7 0.11
55 31 0.50
56 7 0.11
ACGTcount: A:0.44, C:0.10, G:0.15, T:0.31
Consensus pattern (54 bp):
AATTTTTGAAAACACGAGAAGTTTTTAGAAAACACGAAAAATTTTGCAAAACGG
Found at i:57904521 original size:21 final size:20
Alignment explanation
Indices: 57904495--57904536 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 20
57904485 TGTTACCTTA
57904495 TTTTTGAAAACACGAGAAATT
1 TTTTTGAAAACACGA-AAATT
*
57904516 TTTTTGAAGACACGAAAATT
1 TTTTTGAAAACACGAAAATT
57904536 T
1 T
57904537 CGAAACCCGA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
20 6 0.30
21 14 0.70
ACGTcount: A:0.40, C:0.10, G:0.14, T:0.36
Consensus pattern (20 bp):
TTTTTGAAAACACGAAAATT
Found at i:57904912 original size:8 final size:8
Alignment explanation
Indices: 57904899--57904968 Score: 90
Period size: 8 Copynumber: 9.0 Consensus size: 8
57904889 TTGAAACTCT
57904899 TTTTTTTC
1 TTTTTTTC
57904907 TTTTTTTC
1 TTTTTTTC
*
57904915 -TCTTTTC
1 TTTTTTTC
57904922 TTTTTTTC
1 TTTTTTTC
*
57904930 -TTCTTTC
1 TTTTTTTC
57904937 TTTTTTTC
1 TTTTTTTC
57904945 TTTTTTTC
1 TTTTTTTC
* *
57904953 TTTCTCTC
1 TTTTTTTC
57904961 TTTTTTTC
1 TTTTTTTC
57904969 CTGGCCTGCT
Statistics
Matches: 52, Mismatches: 8, Indels: 4
0.81 0.12 0.06
Matches are distributed among these distances:
7 12 0.23
8 40 0.77
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (8 bp):
TTTTTTTC
Found at i:57904929 original size:23 final size:22
Alignment explanation
Indices: 57904901--57904968 Score: 61
Period size: 21 Copynumber: 3.0 Consensus size: 22
57904891 GAAACTCTTT
57904901 TTTTTCTTTTTTTCTCTTTTCTT-
1 TTTTTCTTTTTTTCT-TTTT-TTC
*
57904924 TTTTTC-TTCTTTCTTTTTTTC
1 TTTTTCTTTTTTTCTTTTTTTC
57904945 TTTTT-TTCTTTCTCTCTTTTTTTC
1 TTTTTCTT-TTT-T-TCTTTTTTTC
57904969 CTGGCCTGCT
Statistics
Matches: 38, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
20 2 0.05
21 10 0.26
22 9 0.24
23 7 0.18
24 10 0.26
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (22 bp):
TTTTTCTTTTTTTCTTTTTTTC
Found at i:57904964 original size:15 final size:15
Alignment explanation
Indices: 57904900--57904966 Score: 89
Period size: 15 Copynumber: 4.4 Consensus size: 15
57904890 TGAAACTCTT
57904900 TTTTTTCTTTTTTTC
1 TTTTTTCTTTTTTTC
*
57904915 TCTTTTCTTTTTTTC
1 TTTTTTCTTTTTTTC
*
57904930 TTCTTTCTTTTTTTC
1 TTTTTTCTTTTTTTC
* *
57904945 TTTTTTTCTTTCTCTC
1 -TTTTTTCTTTTTTTC
57904961 TTTTTT
1 TTTTTT
57904967 TCCTGGCCTG
Statistics
Matches: 45, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
15 33 0.73
16 12 0.27
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (15 bp):
TTTTTTCTTTTTTTC
Found at i:57905081 original size:15 final size:14
Alignment explanation
Indices: 57905061--57905113 Score: 54
Period size: 15 Copynumber: 3.6 Consensus size: 14
57905051 GGCCTGCTTC
*
57905061 TTTTTTCTGGGCTG
1 TTTTTTTTGGGCTG
57905075 TTTTTTTTTGGGCCT-
1 -TTTTTTTTGGG-CTG
57905090 TTTCTTTTTGGGCTG
1 TTT-TTTTTGGGCTG
57905105 CTTTTTTTT
1 -TTTTTTTT
57905114 TGCTTTGGTT
Statistics
Matches: 33, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
14 5 0.15
15 23 0.70
16 5 0.15
ACGTcount: A:0.00, C:0.13, G:0.21, T:0.66
Consensus pattern (14 bp):
TTTTTTTTGGGCTG
Found at i:57905131 original size:33 final size:34
Alignment explanation
Indices: 57905089--57905166 Score: 97
Period size: 33 Copynumber: 2.3 Consensus size: 34
57905079 TTTTTGGGCC
* *
57905089 TTTTCTTTTTGGGCTGCTTT-TTTTTTGCTTTG-G
1 TTTTTTTTTTGGGCTGATTTGTTTTTT-CTTTGTG
*
57905122 TTTTTTTTTTGGGCTGATTTGTTTTTTTTTTGTG
1 TTTTTTTTTTGGGCTGATTTGTTTTTTCTTTGTG
57905156 TTGTTTTTTTT
1 TT-TTTTTTTT
57905167 AATTAATTTT
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
33 22 0.56
34 9 0.23
35 8 0.21
ACGTcount: A:0.01, C:0.06, G:0.19, T:0.73
Consensus pattern (34 bp):
TTTTTTTTTTGGGCTGATTTGTTTTTTCTTTGTG
Found at i:57905277 original size:7 final size:7
Alignment explanation
Indices: 57905269--57905318 Score: 54
Period size: 7 Copynumber: 7.6 Consensus size: 7
57905259 TAAATTTTTT
57905269 TTCTTT-
1 TTCTTTC
*
57905275 TTTTTTC
1 TTCTTTC
57905282 TT-TCTTC
1 TTCT-TTC
57905289 TTCTTTC
1 TTCTTTC
57905296 TTCTTTC
1 TTCTTTC
57905303 TTC-TTC
1 TTCTTTC
57905309 TTC-TTC
1 TTCTTTC
57905315 TTCT
1 TTCT
57905319 CCTCCTACAC
Statistics
Matches: 39, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
6 18 0.46
7 20 0.51
8 1 0.03
ACGTcount: A:0.00, C:0.26, G:0.00, T:0.74
Consensus pattern (7 bp):
TTCTTTC
Found at i:57905289 original size:3 final size:3
Alignment explanation
Indices: 57905283--57905318 Score: 54
Period size: 3 Copynumber: 11.3 Consensus size: 3
57905273 TTTTTTTTCT
57905283 TTC TTC TTC TTTC TTC TTTC TTC TTC TTC TTC TTC T
1 TTC TTC TTC -TTC TTC -TTC TTC TTC TTC TTC TTC T
57905319 CCTCCTACAC
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
3 25 0.81
4 6 0.19
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (3 bp):
TTC
Found at i:57905299 original size:17 final size:17
Alignment explanation
Indices: 57905269--57905316 Score: 71
Period size: 17 Copynumber: 2.9 Consensus size: 17
57905259 TAAATTTTTT
* *
57905269 TTCTTTTTTTTTCTTTC
1 TTCTTCTTTCTTCTTTC
57905286 TTCTTCTTTCTTCTTTC
1 TTCTTCTTTCTTCTTTC
57905303 TTCTTC-TTCTTCTT
1 TTCTTCTTTCTTCTT
57905317 CTCCTCCTAC
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
16 8 0.28
17 21 0.72
ACGTcount: A:0.00, C:0.25, G:0.00, T:0.75
Consensus pattern (17 bp):
TTCTTCTTTCTTCTTTC
Found at i:57905306 original size:10 final size:10
Alignment explanation
Indices: 57905269--57905318 Score: 59
Period size: 10 Copynumber: 5.1 Consensus size: 10
57905259 TAAATTTTTT
* *
57905269 TTCTTTTTTT
1 TTCTTTCTTC
57905279 TTCTTTCTTC
1 TTCTTTCTTC
57905289 TTCTTTCTTC
1 TTCTTTCTTC
57905299 TT-TCTTCTTC
1 TTCT-TTCTTC
57905309 TTC-TTCTTC
1 TTCTTTCTTC
57905318 T
1 T
57905319 CCTCCTACAC
Statistics
Matches: 36, Mismatches: 2, Indels: 5
0.84 0.05 0.12
Matches are distributed among these distances:
9 8 0.22
10 28 0.78
ACGTcount: A:0.00, C:0.26, G:0.00, T:0.74
Consensus pattern (10 bp):
TTCTTTCTTC
Found at i:57905419 original size:10 final size:10
Alignment explanation
Indices: 57905384--57905433 Score: 59
Period size: 10 Copynumber: 5.2 Consensus size: 10
57905374 ACGCCGGTAC
57905384 TCTT-TCTTT
1 TCTTCTCTTT
* *
57905393 TCTTCTCCTC
1 TCTTCTCTTT
57905403 T-TTCTCTTT
1 TCTTCTCTTT
57905412 TCTTCTCTTT
1 TCTTCTCTTT
*
57905422 TCTTCTTTTT
1 TCTTCTCTTT
57905432 TC
1 TC
57905434 CTTCAAAAAA
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
9 11 0.32
10 23 0.68
ACGTcount: A:0.00, C:0.30, G:0.00, T:0.70
Consensus pattern (10 bp):
TCTTCTCTTT
Found at i:57905431 original size:19 final size:19
Alignment explanation
Indices: 57905388--57905430 Score: 63
Period size: 19 Copynumber: 2.3 Consensus size: 19
57905378 CGGTACTCTT
57905388 TCTTTTCTTCTCCTCTTTC
1 TCTTTTCTTCTCCTCTTTC
57905407 TCTTTTCTTCT-CT-TTTC
1 TCTTTTCTTCTCCTCTTTC
57905424 TTCTTTT
1 -TCTTTT
57905431 TTCCTTCAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 4 0.17
18 8 0.35
19 11 0.48
ACGTcount: A:0.00, C:0.30, G:0.00, T:0.70
Consensus pattern (19 bp):
TCTTTTCTTCTCCTCTTTC
Found at i:57905737 original size:30 final size:29
Alignment explanation
Indices: 57905697--57905798 Score: 123
Period size: 30 Copynumber: 3.4 Consensus size: 29
57905687 ATTTAGGATT
57905697 AAAATGAAATTTAATGAAAGTTTAGGGGTC
1 AAAATGAAATTTAA-GAAAGTTTAGGGGTC
* * *
57905727 TAAGTGAAATTTAAAGAAAGTTTAAGGGTC
1 AAAATGAAATTT-AAGAAAGTTTAGGGGTC
* *
57905757 AAAATAAAATTTAGAAAAAGTTTAGGGGTC
1 AAAATGAAATTTA-AGAAAGTTTAGGGGTC
*
57905787 AAAATGCAATTT
1 AAAATGAAATTT
57905799 TTATTTTAAA
Statistics
Matches: 60, Mismatches: 10, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
29 1 0.02
30 57 0.95
31 2 0.03
ACGTcount: A:0.46, C:0.04, G:0.21, T:0.29
Consensus pattern (29 bp):
AAAATGAAATTTAAGAAAGTTTAGGGGTC
Found at i:57910182 original size:30 final size:30
Alignment explanation
Indices: 57910119--57910192 Score: 76
Period size: 30 Copynumber: 2.5 Consensus size: 30
57910109 AGTCTATATC
* * * *
57910119 TTTATAATTTTTAAAAGGTTAAATTAAATT
1 TTTATAATTTTTAAAAAGTCAAAATAAACT
* *
57910149 TTTATCATTTTTAAAAAGTCAAAATATACT
1 TTTATAATTTTTAAAAAGTCAAAATAAACT
* *
57910179 TTTATTATTATTAA
1 TTTATAATTTTTAA
57910193 TTTAAATCTT
Statistics
Matches: 36, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
30 36 1.00
ACGTcount: A:0.42, C:0.04, G:0.04, T:0.50
Consensus pattern (30 bp):
TTTATAATTTTTAAAAAGTCAAAATAAACT
Found at i:57910205 original size:82 final size:81
Alignment explanation
Indices: 57910057--57910218 Score: 195
Period size: 82 Copynumber: 2.0 Consensus size: 81
57910047 TGGAAGGCGA
* *
57910057 AAATTAAATTTATATTTTTACAATAGTAAAAATATAATTTCATTATTTTAATAGTCTATATCTTT
1 AAATTAAATTTATATTTTTACAAAAGTAAAAATATAATTTCATTATTTTAATA-TCTAAATCTTT
* *
57910122 ATAATTTTTAAAAGGTT
65 ATAAATTATAAAAGGTT
* * *
57910139 AAATTAAATTTTTATCATTTTTA-AAAAGTCAAAATATACTTTTATTATTATTAAT-T-TAAATC
1 AAATTAAA--TTTAT-ATTTTTACAAAAGTAAAAATATAATTTCATTATT-TTAATATCTAAATC
57910201 TTTATAAATTATAAAAGG
62 TTTATAAATTATAAAAGG
57910219 CCTGAATTAA
Statistics
Matches: 69, Mismatches: 7, Indels: 8
0.82 0.08 0.10
Matches are distributed among these distances:
82 29 0.42
83 1 0.01
84 27 0.39
85 12 0.17
ACGTcount: A:0.43, C:0.05, G:0.04, T:0.48
Consensus pattern (81 bp):
AAATTAAATTTATATTTTTACAAAAGTAAAAATATAATTTCATTATTTTAATATCTAAATCTTTA
TAAATTATAAAAGGTT
Found at i:57915468 original size:47 final size:45
Alignment explanation
Indices: 57915368--57915470 Score: 109
Period size: 47 Copynumber: 2.2 Consensus size: 45
57915358 TGATAAATTT
* * * * * *
57915368 AAATAATATTAATGGTAATTTAAAATAATAGTATATTATATATTA
1 AAATAATACTAATGGAAATTTAAAACAATAGTAGATTAAATACTA
*
57915413 AAACAATACTAATGAGAAATTTAAAACAAT-GTTAAGATTAAATACTA
1 AAATAATACTAATG-GAAATTTAAAACAATAG-T-AGATTAAATACTA
57915460 AAATAATACTA
1 AAATAATACTA
57915471 TATTTAAAAA
Statistics
Matches: 47, Mismatches: 8, Indels: 4
0.80 0.14 0.07
Matches are distributed among these distances:
45 13 0.28
46 14 0.30
47 20 0.43
ACGTcount: A:0.54, C:0.05, G:0.07, T:0.34
Consensus pattern (45 bp):
AAATAATACTAATGGAAATTTAAAACAATAGTAGATTAAATACTA
Found at i:57920816 original size:20 final size:20
Alignment explanation
Indices: 57920778--57920816 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
57920768 CTTCGTCTCC
*
57920778 TTCTTTCTCCTTTTTTTTCT
1 TTCTTTCTCCTTTTGTTTCT
57920798 TTCTTT-TCCTTTGTGTTTC
1 TTCTTTCTCCTTT-TGTTTC
57920817 ATTTTGGTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 6 0.35
20 11 0.65
ACGTcount: A:0.00, C:0.23, G:0.05, T:0.72
Consensus pattern (20 bp):
TTCTTTCTCCTTTTGTTTCT
Found at i:57925524 original size:24 final size:24
Alignment explanation
Indices: 57925479--57925526 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
57925469 TCTTGAGATC
* *
57925479 CATAATCTTAATAATATCTAATAT
1 CATAATATTAATAATATATAATAT
57925503 CATAATATTAATAAT-TAATAATAT
1 CATAATATTAATAATAT-ATAATAT
57925527 AATTTATGAG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.50, C:0.08, G:0.00, T:0.42
Consensus pattern (24 bp):
CATAATATTAATAATATATAATAT
Found at i:57927077 original size:25 final size:25
Alignment explanation
Indices: 57927039--57927087 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 25
57927029 ATGTTCCTGT
57927039 ATTTTTGGACTTTTAATTTATTTTTA
1 ATTTTTGGACTTTT-ATTTATTTTTA
* *
57927065 ATTTTTTGA-TTTTATTTGTTTTT
1 ATTTTTGGACTTTTATTTATTTTT
57927088 GTAAGGGCCG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 9 0.43
25 4 0.19
26 8 0.38
ACGTcount: A:0.18, C:0.02, G:0.08, T:0.71
Consensus pattern (25 bp):
ATTTTTGGACTTTTATTTATTTTTA
Found at i:57932174 original size:29 final size:30
Alignment explanation
Indices: 57932123--57932201 Score: 88
Period size: 29 Copynumber: 2.6 Consensus size: 30
57932113 ATTTTAAATT
* * *
57932123 AATAATGATAAAATTATATTTTAATTTTTTTA
1 AATAAT-A-AAAATTATAATTTAATCTTTATA
57932155 AATAATAAAAATT-TAATTTAATCTTTATA
1 AATAATAAAAATTATAATTTAATCTTTATA
*
57932184 AATTATAAAAATATATAA
1 AATAATAAAAAT-TATAA
57932202 ACTATTAAAA
Statistics
Matches: 41, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
29 24 0.59
30 7 0.17
31 4 0.10
32 6 0.15
ACGTcount: A:0.52, C:0.01, G:0.01, T:0.46
Consensus pattern (30 bp):
AATAATAAAAATTATAATTTAATCTTTATA
Found at i:57932202 original size:17 final size:17
Alignment explanation
Indices: 57932180--57932220 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
57932170 ATTTAATCTT
57932180 TATAAATTATAAAAATA
1 TATAAATTATAAAAATA
* *
57932197 TATAAACTATTAAAATA
1 TATAAATTATAAAAATA
*
57932214 TAAAAAT
1 TATAAAT
57932221 ATTTTTTTAC
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.34
Consensus pattern (17 bp):
TATAAATTATAAAAATA
Found at i:57936791 original size:18 final size:18
Alignment explanation
Indices: 57936770--57936805 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
57936760 CATAAATAAG
57936770 TAAAAATAAATAAAAAAA
1 TAAAAATAAATAAAAAAA
* *
57936788 TAAACATAACTAAAAAAA
1 TAAAAATAAATAAAAAAA
57936806 CATCATAAAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.78, C:0.06, G:0.00, T:0.17
Consensus pattern (18 bp):
TAAAAATAAATAAAAAAA
Found at i:57937094 original size:3 final size:3
Alignment explanation
Indices: 57937080--57937130 Score: 93
Period size: 3 Copynumber: 17.0 Consensus size: 3
57937070 TTTTAAATAT
*
57937080 TTA TTC TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
57937128 TTA
1 TTA
57937131 ACTTTTATGA
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 46 1.00
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:57946736 original size:21 final size:21
Alignment explanation
Indices: 57946711--57946762 Score: 104
Period size: 21 Copynumber: 2.5 Consensus size: 21
57946701 TAGATAATTT
57946711 GACTAAAATTTAAAAGTCGAA
1 GACTAAAATTTAAAAGTCGAA
57946732 GACTAAAATTTAAAAGTCGAA
1 GACTAAAATTTAAAAGTCGAA
57946753 GACTAAAATT
1 GACTAAAATT
57946763 ATCCCAAAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.52, C:0.10, G:0.13, T:0.25
Consensus pattern (21 bp):
GACTAAAATTTAAAAGTCGAA
Found at i:57947062 original size:12 final size:12
Alignment explanation
Indices: 57947045--57947078 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
57947035 CCGGCCCGCC
57947045 ATATTAATTTTT
1 ATATTAATTTTT
*
57947057 ATATTATTTTTT
1 ATATTAATTTTT
57947069 ATA-TAATTTT
1 ATATTAATTTT
57947079 AAAATATATA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
11 6 0.30
12 14 0.70
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (12 bp):
ATATTAATTTTT
Found at i:57947238 original size:30 final size:30
Alignment explanation
Indices: 57947202--57947264 Score: 117
Period size: 30 Copynumber: 2.1 Consensus size: 30
57947192 ACTTAACAAG
57947202 CAAATGTCTTTAAAATAATAACAAAATTAA
1 CAAATGTCTTTAAAATAATAACAAAATTAA
*
57947232 CAAATGTCTTTAAAATGATAACAAAATTAA
1 CAAATGTCTTTAAAATAATAACAAAATTAA
57947262 CAA
1 CAA
57947265 TAAAATAAGT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.56, C:0.11, G:0.05, T:0.29
Consensus pattern (30 bp):
CAAATGTCTTTAAAATAATAACAAAATTAA
Found at i:57947317 original size:22 final size:22
Alignment explanation
Indices: 57947291--57947333 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
57947281 TATTCAAACA
57947291 ATAATAACAAAATAGTAGCAAC
1 ATAATAACAAAATAGTAGCAAC
** *
57947313 ATAATAGTAAAATGGTAGCAA
1 ATAATAACAAAATAGTAGCAA
57947334 AATAGGAAGA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.56, C:0.09, G:0.14, T:0.21
Consensus pattern (22 bp):
ATAATAACAAAATAGTAGCAAC
Found at i:57951235 original size:69 final size:69
Alignment explanation
Indices: 57951149--57951299 Score: 187
Period size: 69 Copynumber: 2.2 Consensus size: 69
57951139 AATAGTATAA
* * * * * *
57951149 CCCTATGTTTATCGTCCCGAC-GGACTCCAATGGTTGGCATAGCCGAGCTATGGTCCTACACCTC
1 CCCTATGTTTATTGTCCCAACAGGA-TCCAATGGTCGCCATAGCCGACCTATGGTCCTAAACCTC
*
57951213 GTTAT
65 GTAAT
* * *
57951218 CCCTATGTTTATTGTCCCAACAGGATCTATTGGTCGCCATAGCCGACCTATGGTCTTAAACCTCG
1 CCCTATGTTTATTGTCCCAACAGGATCCAATGGTCGCCATAGCCGACCTATGGTCCTAAACCTCG
57951283 TAAT
66 TAAT
*
57951287 CCCCATGTTTATT
1 CCCTATGTTTATT
57951300 ATCCTAGCAG
Statistics
Matches: 70, Mismatches: 11, Indels: 2
0.84 0.13 0.02
Matches are distributed among these distances:
69 67 0.96
70 3 0.04
ACGTcount: A:0.21, C:0.29, G:0.19, T:0.32
Consensus pattern (69 bp):
CCCTATGTTTATTGTCCCAACAGGATCCAATGGTCGCCATAGCCGACCTATGGTCCTAAACCTCG
TAAT
Found at i:57951318 original size:69 final size:69
Alignment explanation
Indices: 57951186--57951344 Score: 203
Period size: 69 Copynumber: 2.3 Consensus size: 69
57951176 CAATGGTTGG
* * * * *
57951186 CATAGCCGAGCTATGGTCCTACACCTCGTTATCCCTATGTTTATTGTCCCAACAGGATCTATTGG
1 CATAGCCGAGCTATGGTCTTAAACCTCGTAATCCCCATGTTTATTATCCCAACAGGATCTATTGG
57951251 TCGC
66 TCGC
* * * *
57951255 CATAGCCGACCTATGGTCTTAAACCTCGTAATCCCCATGTTTATTATCCTAGCA-GATTTTATTG
1 CATAGCCGAGCTATGGTCTTAAACCTCGTAATCCCCATGTTTATTATCCCAACAGGA-TCTATTG
*
57951319 GTCGT
65 GTCGC
*
57951324 CATAGCCGAGTTATGGTCTTA
1 CATAGCCGAGCTATGGTCTTA
57951345 CACCCTAAAC
Statistics
Matches: 77, Mismatches: 12, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
68 2 0.03
69 75 0.97
ACGTcount: A:0.22, C:0.26, G:0.18, T:0.34
Consensus pattern (69 bp):
CATAGCCGAGCTATGGTCTTAAACCTCGTAATCCCCATGTTTATTATCCCAACAGGATCTATTGG
TCGC
Found at i:57952733 original size:23 final size:23
Alignment explanation
Indices: 57952682--57952733 Score: 54
Period size: 22 Copynumber: 2.3 Consensus size: 23
57952672 ATTGGCACCA
* *
57952682 CATTTCATACATAAAACATTAAC
1 CATTTCAAACATAAAAAATTAAC
*
57952705 CA-TTCAAACATAAACAAATT-AG
1 CATTTCAAACATAAA-AAATTAAC
57952727 CATTTCA
1 CATTTCA
57952734 TATCCATTCC
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
22 14 0.58
23 10 0.42
ACGTcount: A:0.48, C:0.21, G:0.02, T:0.29
Consensus pattern (23 bp):
CATTTCAAACATAAAAAATTAAC
Found at i:57956071 original size:24 final size:24
Alignment explanation
Indices: 57956043--57956096 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
57956033 AAACTATCCA
*
57956043 TTGGGAGGATTTGAAATTTGACTG
1 TTGGGAGGATTTGAAATTTGACCG
*
57956067 TTGGGCGGATTTGAAATTTGACCG
1 TTGGGAGGATTTGAAATTTGACCG
57956091 TTGGGA
1 TTGGGA
57956097 TGTTCCTATT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.22, C:0.07, G:0.35, T:0.35
Consensus pattern (24 bp):
TTGGGAGGATTTGAAATTTGACCG
Found at i:57956912 original size:20 final size:21
Alignment explanation
Indices: 57956889--57956928 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
57956879 AACTATTCAA
*
57956889 ATAA-TATTTTTTGAATAATT
1 ATAATTATTTTTTAAATAATT
*
57956909 ATAATTCTTTTTTAAATAAT
1 ATAATTATTTTTTAAATAAT
57956929 CAAATGATAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.40, C:0.03, G:0.03, T:0.55
Consensus pattern (21 bp):
ATAATTATTTTTTAAATAATT
Found at i:57960523 original size:43 final size:43
Alignment explanation
Indices: 57960455--57960541 Score: 138
Period size: 43 Copynumber: 2.0 Consensus size: 43
57960445 AGGGCAATCT
* *
57960455 CTGAGAACATGCAACAACTCCTCAGATCTATGCCCACAAAAAC
1 CTGAAAACATGCAACAACTCCTCAGATCCATGCCCACAAAAAC
* *
57960498 CTGAAAACATGCAACACCTCTTCAGATCCATGCCCACAAAAAC
1 CTGAAAACATGCAACAACTCCTCAGATCCATGCCCACAAAAAC
57960541 C
1 C
57960542 ACGTGTTGTC
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
43 40 1.00
ACGTcount: A:0.39, C:0.34, G:0.10, T:0.16
Consensus pattern (43 bp):
CTGAAAACATGCAACAACTCCTCAGATCCATGCCCACAAAAAC
Found at i:57966679 original size:19 final size:18
Alignment explanation
Indices: 57966655--57966690 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
57966645 TGTCATTCAT
*
57966655 GACAAATTTTCTGAGAGTA
1 GACAAAATTTCT-AGAGTA
57966674 GACAAAATTTCTAGAGT
1 GACAAAATTTCTAGAGT
57966691 GGTGGTTAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.39, C:0.11, G:0.19, T:0.31
Consensus pattern (18 bp):
GACAAAATTTCTAGAGTA
Found at i:57971752 original size:25 final size:25
Alignment explanation
Indices: 57971717--57971767 Score: 93
Period size: 25 Copynumber: 2.0 Consensus size: 25
57971707 AACAAAAACA
57971717 CAAAACGCCCCGTTTCAATTAACTC
1 CAAAACGCCCCGTTTCAATTAACTC
*
57971742 CAAAACTCCCCGTTTCAATTAACTC
1 CAAAACGCCCCGTTTCAATTAACTC
57971767 C
1 C
57971768 TCAACAGTCT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.31, C:0.37, G:0.06, T:0.25
Consensus pattern (25 bp):
CAAAACGCCCCGTTTCAATTAACTC
Found at i:57983497 original size:20 final size:20
Alignment explanation
Indices: 57983472--57983512 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
57983462 GGGTCTAACA
57983472 TATCCTCTTGCTATTCTTAG
1 TATCCTCTTGCTATTCTTAG
57983492 TATCCTCTTGCTATTCTTAG
1 TATCCTCTTGCTATTCTTAG
57983512 T
1 T
57983513 TAAGTTCACC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.15, C:0.24, G:0.10, T:0.51
Consensus pattern (20 bp):
TATCCTCTTGCTATTCTTAG
Found at i:57987137 original size:24 final size:24
Alignment explanation
Indices: 57987067--57987137 Score: 63
Period size: 23 Copynumber: 3.0 Consensus size: 24
57987057 CACATAAACG
* * * *
57987067 GGAAGCTCATGTGAGCCATGTAACG
1 GGAAGTTCATGCGAGCC-TATAACA
* * *
57987092 GGAAGTTTATCCG-GGCTATAACA
1 GGAAGTTCATGCGAGCCTATAACA
57987115 GGAAGTTCATGCGAGCCTATAAC
1 GGAAGTTCATGCGAGCCTATAAC
57987138 GGGTAGCTCC
Statistics
Matches: 35, Mismatches: 10, Indels: 3
0.73 0.21 0.06
Matches are distributed among these distances:
23 16 0.46
24 10 0.29
25 9 0.26
ACGTcount: A:0.30, C:0.20, G:0.28, T:0.23
Consensus pattern (24 bp):
GGAAGTTCATGCGAGCCTATAACA
Found at i:57989245 original size:23 final size:21
Alignment explanation
Indices: 57989215--57989264 Score: 66
Period size: 21 Copynumber: 2.3 Consensus size: 21
57989205 GTAAGCAATT
57989215 AATTATTTTTTAAAAAATTATAA
1 AATTATTTTTT-AAAAATT-TAA
*
57989238 AATTA-TTTTTAAAAATTTTA
1 AATTATTTTTTAAAAATTTAA
57989258 AATTATT
1 AATTATT
57989265 AAAAAAGCAT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
20 7 0.28
21 8 0.32
22 5 0.20
23 5 0.20
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (21 bp):
AATTATTTTTTAAAAATTTAA
Found at i:57989260 original size:20 final size:22
Alignment explanation
Indices: 57989215--57989289 Score: 70
Period size: 22 Copynumber: 3.6 Consensus size: 22
57989205 GTAAGCAATT
57989215 AATTATTTTTTAAAAAATTATAA
1 AATTA-TTTTTAAAAAATTATAA
*
57989238 AATTATTTTT-AAAAATT-TTA
1 AATTATTTTTAAAAAATTATAA
**
57989258 AATTA---TTAAAAAAGCATAA
1 AATTATTTTTAAAAAATTATAA
*
57989277 AAATATTTTTAAA
1 AATTATTTTTAAA
57989290 TAATATTTTA
Statistics
Matches: 42, Mismatches: 5, Indels: 11
0.72 0.09 0.19
Matches are distributed among these distances:
17 2 0.05
18 5 0.12
19 6 0.14
20 7 0.17
21 7 0.17
22 10 0.24
23 5 0.12
ACGTcount: A:0.53, C:0.01, G:0.01, T:0.44
Consensus pattern (22 bp):
AATTATTTTTAAAAAATTATAA
Found at i:57989307 original size:40 final size:39
Alignment explanation
Indices: 57989221--57989309 Score: 108
Period size: 39 Copynumber: 2.3 Consensus size: 39
57989211 AATTAATTAT
** *
57989221 TTTTTAAAAAATTATAAAATTATTTTTAAAAATTTTAAA
1 TTTTTAAAAAAGCATAAAAATATTTTTAAAAATTTTAAA
* *
57989260 TTATTAAAAAAGCATAAAAATATTTTTAAATAATATTT-TA
1 TTTTTAAAAAAGCATAAAAATATTTTTAAA-AAT-TTTAAA
57989300 TTTTTAAAAA
1 TTTTTAAAAA
57989310 TACAATTAAT
Statistics
Matches: 42, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
39 26 0.62
40 13 0.31
41 3 0.07
ACGTcount: A:0.52, C:0.01, G:0.01, T:0.46
Consensus pattern (39 bp):
TTTTTAAAAAAGCATAAAAATATTTTTAAAAATTTTAAA
Found at i:57992336 original size:18 final size:18
Alignment explanation
Indices: 57992313--57992351 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
57992303 AACACAATCC
*
57992313 AAAAAAAA-TCAAAATATT
1 AAAAAAAACCCAAAA-ATT
57992331 AAAAAAAACCCAAAAATT
1 AAAAAAAACCCAAAAATT
57992349 AAA
1 AAA
57992352 TCTAAAAACA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 14 0.74
19 5 0.26
ACGTcount: A:0.74, C:0.10, G:0.00, T:0.15
Consensus pattern (18 bp):
AAAAAAAACCCAAAAATT
Found at i:57992337 original size:19 final size:18
Alignment explanation
Indices: 57992313--57992351 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 18
57992303 AACACAATCC
*
57992313 AAAAAAAATCAAAATATTA
1 AAAAAAAACCAAAA-ATTA
*
57992332 AAAAAAACCCAAAAATTA
1 AAAAAAAACCAAAAATTA
57992350 AA
1 AA
57992352 TCTAAAAACA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 6 0.33
19 12 0.67
ACGTcount: A:0.74, C:0.10, G:0.00, T:0.15
Consensus pattern (18 bp):
AAAAAAAACCAAAAATTA
Found at i:58002801 original size:19 final size:17
Alignment explanation
Indices: 58002776--58002822 Score: 58
Period size: 19 Copynumber: 2.6 Consensus size: 17
58002766 TTTCAATGCA
*
58002776 TCCAATAATTATACATAT
1 TCCAATAATAATACA-AT
*
58002794 TACCAATAATAATTCAAT
1 T-CCAATAATAATACAAT
58002812 TCCAATAATAA
1 TCCAATAATAA
58002823 AATACATATT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
17 10 0.38
18 4 0.15
19 12 0.46
ACGTcount: A:0.49, C:0.17, G:0.00, T:0.34
Consensus pattern (17 bp):
TCCAATAATAATACAAT
Found at i:58005134 original size:16 final size:16
Alignment explanation
Indices: 58005086--58005138 Score: 53
Period size: 16 Copynumber: 3.6 Consensus size: 16
58005076 TTTCCTTGAT
*
58005086 TTTATATTTTATATCA
1 TTTATATATTATATCA
58005102 ---ATA-ATTA-ATCA
1 TTTATATATTATATCA
*
58005113 TCTATATATTATATCA
1 TTTATATATTATATCA
58005129 TTTATATATT
1 TTTATATATT
58005139 CTCTTTTATT
Statistics
Matches: 30, Mismatches: 2, Indels: 10
0.71 0.05 0.24
Matches are distributed among these distances:
11 4 0.13
12 3 0.10
13 3 0.10
14 3 0.10
15 4 0.13
16 13 0.43
ACGTcount: A:0.38, C:0.08, G:0.00, T:0.55
Consensus pattern (16 bp):
TTTATATATTATATCA
Found at i:58008979 original size:21 final size:21
Alignment explanation
Indices: 58008955--58008998 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
58008945 CCCTTCTAAA
58008955 AAAATTTATTCAAAGAAAGTC
1 AAAATTTATTCAAAGAAAGTC
58008976 AAAATTTATTCAAAGAAAGTC
1 AAAATTTATTCAAAGAAAGTC
58008997 AA
1 AA
58008999 GGAGAGGGCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.55, C:0.09, G:0.09, T:0.27
Consensus pattern (21 bp):
AAAATTTATTCAAAGAAAGTC
Found at i:58012922 original size:35 final size:35
Alignment explanation
Indices: 58012876--58012946 Score: 142
Period size: 35 Copynumber: 2.0 Consensus size: 35
58012866 ACCTTCACAA
58012876 CCCCTTTAGTTGAGGAAAGTGTAACTTTTCTCGGG
1 CCCCTTTAGTTGAGGAAAGTGTAACTTTTCTCGGG
58012911 CCCCTTTAGTTGAGGAAAGTGTAACTTTTCTCGGG
1 CCCCTTTAGTTGAGGAAAGTGTAACTTTTCTCGGG
58012946 C
1 C
58012947 TTTGGTTGGC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.20, C:0.21, G:0.25, T:0.34
Consensus pattern (35 bp):
CCCCTTTAGTTGAGGAAAGTGTAACTTTTCTCGGG
Found at i:58014778 original size:37 final size:37
Alignment explanation
Indices: 58014728--58014802 Score: 132
Period size: 37 Copynumber: 2.0 Consensus size: 37
58014718 ATCAAGTATA
*
58014728 AATCAGAGTTCCTAAATCATACAAATACGGTAACAGC
1 AATCAGAGTTCCTAAATCATACAAATACAGTAACAGC
*
58014765 AATCAGAGTTCCTAAATCATACAAATACAGTAAGAGC
1 AATCAGAGTTCCTAAATCATACAAATACAGTAACAGC
58014802 A
1 A
58014803 GGCAAAAATT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
37 36 1.00
ACGTcount: A:0.45, C:0.20, G:0.13, T:0.21
Consensus pattern (37 bp):
AATCAGAGTTCCTAAATCATACAAATACAGTAACAGC
Found at i:58018573 original size:37 final size:36
Alignment explanation
Indices: 58018527--58018600 Score: 87
Period size: 37 Copynumber: 2.0 Consensus size: 36
58018517 TTATGATTGT
* * *
58018527 TTATTTATAAAATATATT-ATTATTGTTATTATTTTA
1 TTATTTATAAAATAAATTGATTA-TATTATTATATTA
*
58018563 TTATATTATAAATTAAATTGATTATATTATTATATTA
1 TTAT-TTATAAAATAAATTGATTATATTATTATATTA
58018600 T
1 T
58018601 GAAATAAATT
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
36 4 0.12
37 24 0.75
38 4 0.12
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (36 bp):
TTATTTATAAAATAAATTGATTATATTATTATATTA
Found at i:58018577 original size:29 final size:29
Alignment explanation
Indices: 58018554--58018610 Score: 80
Period size: 29 Copynumber: 2.0 Consensus size: 29
58018544 TATTATTGTT
*
58018554 ATTATTTTATTATATTAT-AAATTAAATTG
1 ATTATATTATTATATTATGAAATT-AATTG
*
58018583 ATTATATTATTATATTATGAAATAAATT
1 ATTATATTATTATATTATGAAATTAATT
58018611 AAGAAAAGAC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 21 0.84
30 4 0.16
ACGTcount: A:0.44, C:0.00, G:0.04, T:0.53
Consensus pattern (29 bp):
ATTATATTATTATATTATGAAATTAATTG
Found at i:58018858 original size:3 final size:3
Alignment explanation
Indices: 58018850--58018904 Score: 53
Period size: 3 Copynumber: 19.0 Consensus size: 3
58018840 AAATAGATAT
* * *
58018850 TTA TTA TTA TTA TTA TAA TTA TTG TTA TTA TTA TT- TAA TTGA -TA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT-A TTA
58018894 TTA -TA TTA TTA
1 TTA TTA TTA TTA
58018905 GATTTATGAA
Statistics
Matches: 42, Mismatches: 6, Indels: 8
0.75 0.11 0.14
Matches are distributed among these distances:
2 4 0.10
3 37 0.88
4 1 0.02
ACGTcount: A:0.35, C:0.00, G:0.04, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:58019090 original size:15 final size:16
Alignment explanation
Indices: 58019070--58019099 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
58019060 AACAAAAAGA
58019070 AATAGAAA-GAAACAT
1 AATAGAAACGAAACAT
58019085 AATAGAAACGAAACA
1 AATAGAAACGAAACA
58019100 GGAAGAAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.67, C:0.10, G:0.13, T:0.10
Consensus pattern (16 bp):
AATAGAAACGAAACAT
Found at i:58019134 original size:10 final size:10
Alignment explanation
Indices: 58019053--58019137 Score: 62
Period size: 10 Copynumber: 8.3 Consensus size: 10
58019043 ATGAAAGCAT
*
58019053 AAAAAGAAAC
1 AAAAAGAAAG
*
58019063 AAAAAGAAAT
1 AAAAAGAAAG
* *
58019073 AGAAAGAAAC
1 AAAAAGAAAG
*
58019083 ATAATAGAAACG
1 A-AAAAGAAA-G
* *
58019095 AAACAGGAAG
1 AAAAAGAAAG
58019105 AAAAAGAAAG
1 AAAAAGAAAG
*
58019115 AAAAAAAAAG
1 AAAAAGAAAG
**
58019125 GGAAAGAAAG
1 AAAAAGAAAG
58019135 AAA
1 AAA
58019138 GGAGAAATAG
Statistics
Matches: 57, Mismatches: 16, Indels: 4
0.74 0.21 0.05
Matches are distributed among these distances:
10 44 0.77
11 12 0.21
12 1 0.02
ACGTcount: A:0.73, C:0.05, G:0.19, T:0.04
Consensus pattern (10 bp):
AAAAAGAAAG
Found at i:58019324 original size:29 final size:29
Alignment explanation
Indices: 58019283--58019340 Score: 66
Period size: 29 Copynumber: 2.0 Consensus size: 29
58019273 TTTTTTAGTA
58019283 GGGTTCATGTTGAATA-AATGATTGAATTAG
1 GGGTTCATGTTG-ATAGAATGATTG-ATTAG
* *
58019313 GGGTTTAT-TTGATAGAATTATTGATTAG
1 GGGTTCATGTTGATAGAATGATTGATTAG
58019341 AATTGATTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
28 8 0.32
29 10 0.40
30 7 0.28
ACGTcount: A:0.31, C:0.02, G:0.26, T:0.41
Consensus pattern (29 bp):
GGGTTCATGTTGATAGAATGATTGATTAG
Found at i:58020109 original size:38 final size:37
Alignment explanation
Indices: 58020048--58020139 Score: 114
Period size: 38 Copynumber: 2.5 Consensus size: 37
58020038 CGGATAGATT
* *
58020048 CGATGAGATACTGGGTATCACTTTACTTCG-ACTAGGC
1 CGATGAGACACTGGGTGTCACTTTACTTCGAACTA-GC
* *
58020085 CGATGAGACACTGGGTGTCAACTTTGCTTCGAACTATC
1 CGATGAGACACTGGGTGTC-ACTTTACTTCGAACTAGC
*
58020123 CGATGAGGCACTGGGTG
1 CGATGAGACACTGGGTG
58020140 CCAATCTGGT
Statistics
Matches: 48, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
37 17 0.35
38 27 0.56
39 4 0.08
ACGTcount: A:0.23, C:0.22, G:0.28, T:0.27
Consensus pattern (37 bp):
CGATGAGACACTGGGTGTCACTTTACTTCGAACTAGC
Found at i:58024039 original size:24 final size:25
Alignment explanation
Indices: 58023993--58024039 Score: 60
Period size: 24 Copynumber: 1.9 Consensus size: 25
58023983 AACAACATTT
* *
58023993 TAATTTTTTAATTTCTAAAATATAC
1 TAATATTTTAATTTATAAAATATAC
*
58024018 TAATATTTT-ATTTATAATATAT
1 TAATATTTTAATTTATAAAATAT
58024040 TAAATTATAT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
24 11 0.58
25 8 0.42
ACGTcount: A:0.40, C:0.04, G:0.00, T:0.55
Consensus pattern (25 bp):
TAATATTTTAATTTATAAAATATAC
Found at i:58028426 original size:37 final size:36
Alignment explanation
Indices: 58028380--58028449 Score: 113
Period size: 37 Copynumber: 1.9 Consensus size: 36
58028370 TTTAAAAGTA
* *
58028380 ATTAAAATTTAGCTCATAATTTATGAAAACAAAAAAT
1 ATTAAAATTTAACCCATAATTTATGAAAA-AAAAAAT
58028417 ATTAAAATTTAACCCATAATTTATGAAAAAAAA
1 ATTAAAATTTAACCCATAATTTATGAAAAAAAA
58028450 TAAAATAATC
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
36 4 0.13
37 27 0.87
ACGTcount: A:0.56, C:0.09, G:0.04, T:0.31
Consensus pattern (36 bp):
ATTAAAATTTAACCCATAATTTATGAAAAAAAAAAT
Found at i:58037136 original size:11 final size:11
Alignment explanation
Indices: 58037114--58037173 Score: 84
Period size: 11 Copynumber: 5.4 Consensus size: 11
58037104 AACTAATCCT
58037114 CTCTCAAATTTC
1 CTCTC-AATTTC
58037126 CTCTCAATTTC
1 CTCTCAATTTC
*
58037137 CTCTAAATTTC
1 CTCTCAATTTC
*
58037148 CTCTAAATTTC
1 CTCTCAATTTC
*
58037159 CTCTCAATTTG
1 CTCTCAATTTC
58037170 CTCT
1 CTCT
58037174 TAAATCCCTT
Statistics
Matches: 45, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
11 40 0.89
12 5 0.11
ACGTcount: A:0.22, C:0.32, G:0.02, T:0.45
Consensus pattern (11 bp):
CTCTCAATTTC
Found at i:58037157 original size:33 final size:35
Alignment explanation
Indices: 58037114--58037198 Score: 108
Period size: 33 Copynumber: 2.5 Consensus size: 35
58037104 AACTAATCCT
58037114 CTCTCAAATTTCCTCTCAATTTCCTC-TAAATTTC
1 CTCTCAAATTTCCTCTCAATTTCCTCTTAAATTTC
* *
58037148 CTCT-AAATTTCCTCTCAATTTGCTCTTAAA-TCC
1 CTCTCAAATTTCCTCTCAATTTCCTCTTAAATTTC
58037181 CT-TCCAAATTT-CTCTCAA
1 CTCT-CAAATTTCCTCTCAA
58037199 ATCCATATTT
Statistics
Matches: 46, Mismatches: 2, Indels: 7
0.84 0.04 0.13
Matches are distributed among these distances:
32 1 0.02
33 31 0.67
34 14 0.30
ACGTcount: A:0.25, C:0.32, G:0.01, T:0.42
Consensus pattern (35 bp):
CTCTCAAATTTCCTCTCAATTTCCTCTTAAATTTC
Found at i:58037199 original size:11 final size:11
Alignment explanation
Indices: 58037113--58037200 Score: 60
Period size: 11 Copynumber: 7.9 Consensus size: 11
58037103 AAACTAATCC
58037113 TCTCTCAAATT
1 TCTCTCAAATT
58037124 TCCTCTC-AATT
1 T-CTCTCAAATT
58037135 TC-CTCTAAATT
1 TCTCTC-AAATT
58037146 TC-CTCTAAATT
1 TCTCTC-AAATT
58037157 TCCTCTC-AATT
1 T-CTCTCAAATT
* *
58037168 TGCTCTTAAATC
1 T-CTCTCAAATT
*
58037180 CCT-TCCAAATT
1 TCTCT-CAAATT
58037191 TCTCTCAAAT
1 TCTCTCAAAT
58037201 CCATATTTAA
Statistics
Matches: 62, Mismatches: 7, Indels: 16
0.73 0.08 0.19
Matches are distributed among these distances:
9 3 0.05
10 2 0.03
11 44 0.71
12 10 0.16
13 3 0.05
ACGTcount: A:0.25, C:0.31, G:0.01, T:0.43
Consensus pattern (11 bp):
TCTCTCAAATT
Done.