Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr2
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 50190067
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.32
Warning! 915496 characters in sequence are not A, C, G, or T
File 150 of 161
Found at i:46692497 original size:14 final size:14
Alignment explanation
Indices: 46692480--46692527 Score: 55
Period size: 14 Copynumber: 3.6 Consensus size: 14
46692470 TATTAAAATC
46692480 TTATCATTTAACTT
1 TTATCATTTAACTT
*
46692494 TTATCA-TT-CCTT
1 TTATCATTTAACTT
**
46692506 AAATCATTTAACTT
1 TTATCATTTAACTT
46692520 TTATCATT
1 TTATCATT
46692528 AAGTAATATA
Statistics
Matches: 26, Mismatches: 6, Indels: 4
0.72 0.17 0.11
Matches are distributed among these distances:
12 7 0.27
13 4 0.15
14 15 0.58
ACGTcount: A:0.29, C:0.17, G:0.00, T:0.54
Consensus pattern (14 bp):
TTATCATTTAACTT
Found at i:46694519 original size:40 final size:37
Alignment explanation
Indices: 46694449--46694541 Score: 107
Period size: 40 Copynumber: 2.5 Consensus size: 37
46694439 CCTAGTTTGG
* * *
46694449 CACCCAGTGCCTCATTGGATAATTCGAAGTAGTAAATTGA
1 CACCCAGTGCCTCATCGGATAA-ACCAA--AGTAAATTGA
* *
46694489 TACCCAGTGCCTCATCGGTTAAACCAAAGTAAATTGA
1 CACCCAGTGCCTCATCGGATAAACCAAAGTAAATTGA
46694526 CA-CCAGTGCCTCATCG
1 CACCCAGTGCCTCATCG
46694542 ACTCGAAGTT
Statistics
Matches: 47, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
36 14 0.30
37 11 0.23
39 3 0.06
40 19 0.40
ACGTcount: A:0.31, C:0.26, G:0.18, T:0.25
Consensus pattern (37 bp):
CACCCAGTGCCTCATCGGATAAACCAAAGTAAATTGA
Found at i:46695203 original size:20 final size:21
Alignment explanation
Indices: 46695164--46695205 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
46695154 AGAACACACC
*
46695164 AATAGAAGCTCATAAGAGCTG
1 AATAGAAGCTCAGAAGAGCTG
*
46695185 AATAGAAGCTC-GGAGAGCTG
1 AATAGAAGCTCAGAAGAGCTG
46695205 A
1 A
46695206 TCCACCCAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 8 0.42
21 11 0.58
ACGTcount: A:0.40, C:0.14, G:0.29, T:0.17
Consensus pattern (21 bp):
AATAGAAGCTCAGAAGAGCTG
Found at i:46696541 original size:2 final size:2
Alignment explanation
Indices: 46696530--46696558 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
46696520 ACCATTACCT
46696530 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
46696559 AAGCAAGACA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:46701150 original size:44 final size:44
Alignment explanation
Indices: 46701098--46701183 Score: 111
Period size: 44 Copynumber: 2.0 Consensus size: 44
46701088 CTGTAACCTC
*
46701098 AGGGAGGTAAAATCCGCT-ATCTTCGATCTACTCCACTACTGCTT
1 AGGGAGGTAAAATCCG-TAATCTTCAATCTACTCCACTACTGCTT
* * * *
46701142 AGGGAGGTAAGATCTGTAATCTTCAATCTATTCCACTGCTGC
1 AGGGAGGTAAAATCCGTAATCTTCAATCTACTCCACTACTGC
46701184 CCAGGGAGAT
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
43 1 0.03
44 35 0.97
ACGTcount: A:0.26, C:0.24, G:0.20, T:0.30
Consensus pattern (44 bp):
AGGGAGGTAAAATCCGTAATCTTCAATCTACTCCACTACTGCTT
Found at i:46701177 original size:132 final size:132
Alignment explanation
Indices: 46701039--46701525 Score: 735
Period size: 132 Copynumber: 3.7 Consensus size: 132
46701029 TCCTCGATCA
* * * * *
46701039 ATTCCACTGCCGACCAGGG-GGATAGAATTACTGGCTTCAATATACTCCACTGTAACCTCAGGGA
1 ATTCCACTGCTGTCCAGGGAAG-TAGAATTACTGGCTTCAATGTACTCCACTGTAACCACAGGGA
* * * * ** *
46701103 GGTAAAATCCGCTATCTTCGATCTACTCCACTACTGCTTAGGGAGGTAAGATCTGTAATCTTCAA
65 GGTAAAATCTGCCATCTTTGATCTGCTCCACTACTGCTTAGGGAGACAAGATCTGAAATCTTCAA
46701168 TCT
130 TCT
* ** *
46701171 ATTCCACTGCTGCCCAGGG-AGATAGAATTACTGGCTTCAATGTACTCTGCTGTAACCATAGGGA
1 ATTCCACTGCTGTCCAGGGAAG-TAGAATTACTGGCTTCAATGTACTCCACTGTAACCACAGGGA
46701235 GGTAAAATCTGCCATCTTTGATCTGCTCCACTACTGCTTAGGGAGACAAGATCTGAAATCTTCAA
65 GGTAAAATCTGCCATCTTTGATCTGCTCCACTACTGCTTAGGGAGACAAGATCTGAAATCTTCAA
46701300 TCT
130 TCT
* *
46701303 ATTCCGCTGCTGTCCAGGGAAGTAGAATTACTGGCTTCAATGTACTCCACTATAACCACAGGGAG
1 ATTCCACTGCTGTCCAGGGAAGTAGAATTACTGGCTTCAATGTACTCCACTGTAACCACAGGGAG
*
46701368 GTAAAATCTGCCATCTTTGATCTGCTCCACTACTGTTTAGGGAGACAAGATCTGAAATCTTCAAT
66 GTAAAATCTGCCATCTTTGATCTGCTCCACTACTGCTTAGGGAGACAAGATCTGAAATCTTCAAT
46701433 CT
131 CT
* * *
46701435 ATTCCGCTGCTGTCCAGGGAAGTAGAATTACTGGTTTCAATGTACTCCGCTGTAACCACAGGGAG
1 ATTCCACTGCTGTCCAGGGAAGTAGAATTACTGGCTTCAATGTACTCCACTGTAACCACAGGGAG
*
46701500 GTAAAATATGCCATCTTTGATCTGCT
66 GTAAAATCTGCCATCTTTGATCTGCT
46701526 TCGCTGTCTA
Statistics
Matches: 328, Mismatches: 26, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
132 326 0.99
133 2 0.01
ACGTcount: A:0.27, C:0.24, G:0.21, T:0.29
Consensus pattern (132 bp):
ATTCCACTGCTGTCCAGGGAAGTAGAATTACTGGCTTCAATGTACTCCACTGTAACCACAGGGAG
GTAAAATCTGCCATCTTTGATCTGCTCCACTACTGCTTAGGGAGACAAGATCTGAAATCTTCAAT
CT
Found at i:46703840 original size:20 final size:20
Alignment explanation
Indices: 46703815--46703855 Score: 66
Period size: 20 Copynumber: 2.0 Consensus size: 20
46703805 AATTTGGCAG
46703815 AAAAAATC-TGAAAGAATGAA
1 AAAAAATCGT-AAAGAATGAA
46703835 AAAAAATCGTAAAGAATGAA
1 AAAAAATCGTAAAGAATGAA
46703855 A
1 A
46703856 GAACATTTGC
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 19 0.95
21 1 0.05
ACGTcount: A:0.66, C:0.05, G:0.15, T:0.15
Consensus pattern (20 bp):
AAAAAATCGTAAAGAATGAA
Found at i:46707387 original size:6 final size:6
Alignment explanation
Indices: 46707378--46707408 Score: 62
Period size: 6 Copynumber: 5.2 Consensus size: 6
46707368 AATATAAAAG
46707378 TATGTA TATGTA TATGTA TATGTA TATGTA T
1 TATGTA TATGTA TATGTA TATGTA TATGTA T
46707409 TTACAAAATT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.32, C:0.00, G:0.16, T:0.52
Consensus pattern (6 bp):
TATGTA
Found at i:46713379 original size:12 final size:13
Alignment explanation
Indices: 46713353--46713377 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
46713343 ATATTTTATT
46713353 TTAAAAAATTAAA
1 TTAAAAAATTAAA
46713366 TTAAAAAATTAA
1 TTAAAAAATTAA
46713378 TTTTAGAAGG
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:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (13 bp):
TTAAAAAATTAAA
Found at i:46714258 original size:28 final size:28
Alignment explanation
Indices: 46714209--46714262 Score: 72
Period size: 28 Copynumber: 1.9 Consensus size: 28
46714199 TCCGAAAAAT
* * *
46714209 TAATAGACAAATTTAGATAAAAAAAACA
1 TAATAGACAAATTGACAAAAAAAAAACA
*
46714237 TAATAGCCAAATTGACAAAAAAAAAA
1 TAATAGACAAATTGACAAAAAAAAAA
46714263 ATATGAACAT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 22 1.00
ACGTcount: A:0.65, C:0.09, G:0.07, T:0.19
Consensus pattern (28 bp):
TAATAGACAAATTGACAAAAAAAAAACA
Found at i:46718041 original size:2 final size:2
Alignment explanation
Indices: 46718029--46718062 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
46718019 AAAACTAATA
* *
46718029 AT AT AT TT AT AT AT AT AT AT AA AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
46718063 GAATAAACAG
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:46732344 original size:19 final size:19
Alignment explanation
Indices: 46732320--46732358 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
46732310 TTGTAATGTT
46732320 TTTATTTGCGATTATGAAC
1 TTTATTTGCGATTATGAAC
46732339 TTTATTTGCGATTATGAAC
1 TTTATTTGCGATTATGAAC
46732358 T
1 T
46732359 AACTTTTTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.26, C:0.10, G:0.15, T:0.49
Consensus pattern (19 bp):
TTTATTTGCGATTATGAAC
Found at i:46739381 original size:13 final size:13
Alignment explanation
Indices: 46739363--46739387 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
46739353 AAGAACCAAA
46739363 TAATGAAAGTTTG
1 TAATGAAAGTTTG
46739376 TAATGAAAGTTT
1 TAATGAAAGTTT
46739388 TCTTGGTTCT
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:0.40, C:0.00, G:0.20, T:0.40
Consensus pattern (13 bp):
TAATGAAAGTTTG
Found at i:46768812 original size:26 final size:27
Alignment explanation
Indices: 46768721--46768937 Score: 287
Period size: 27 Copynumber: 8.1 Consensus size: 27
46768711 ATTCATGAGG
46768721 AAATTACCGAAATACCCTCGAAGGGTA
1 AAATTACCGAAATACCCTCGAAGGGTA
* * *
46768748 AAATTACCAAAATACCCTTGAAGGGAA
1 AAATTACCGAAATACCCTCGAAGGGTA
*
46768775 AAATTACTGAAATACCCTCGAAGGGT-
1 AAATTACCGAAATACCCTCGAAGGGTA
* *
46768801 AAATTACCGAAATACCTTCAAAGGGTA
1 AAATTACCGAAATACCCTCGAAGGGTA
*
46768828 AAATTACCGAAATACCCTTGAAGGGT-
1 AAATTACCGAAATACCCTCGAAGGGTA
* * *
46768854 AACTTACCGTAATACCCTCTAAGGGTA
1 AAATTACCGAAATACCCTCGAAGGGTA
* *
46768881 AAATTATCGAAATA-CCTCTAAGGGTA
1 AAATTACCGAAATACCCTCGAAGGGTA
* *
46768907 AAATTACCGTAATACCCTCTAAGGGTA
1 AAATTACCGAAATACCCTCGAAGGGTA
46768934 AAAT
1 AAAT
46768938 GATATGACTG
Statistics
Matches: 165, Mismatches: 22, Indels: 6
0.85 0.11 0.03
Matches are distributed among these distances:
26 69 0.42
27 96 0.58
ACGTcount: A:0.41, C:0.20, G:0.16, T:0.23
Consensus pattern (27 bp):
AAATTACCGAAATACCCTCGAAGGGTA
Found at i:46768831 original size:53 final size:54
Alignment explanation
Indices: 46768721--46768937 Score: 298
Period size: 53 Copynumber: 4.1 Consensus size: 54
46768711 ATTCATGAGG
* *
46768721 AAATTACCGAAATACCCTCGAAGGGTAAAATTACCAAAATACCCT-TGAAGGGAA
1 AAATTACCGAAATACCCTCGAAGGGTAAAATTACCGAAATACCCTCT-AAGGGTA
* * *
46768775 AAATTACTGAAATACCCTCGAAGGGT-AAATTACCGAAATACCTTCAAAGGGTA
1 AAATTACCGAAATACCCTCGAAGGGTAAAATTACCGAAATACCCTCTAAGGGTA
* * *
46768828 AAATTACCGAAATACCCTTGAAGGGT-AACTTACCGTAATACCCTCTAAGGGTA
1 AAATTACCGAAATACCCTCGAAGGGTAAAATTACCGAAATACCCTCTAAGGGTA
* * *
46768881 AAATTATCGAAATA-CCTCTAAGGGTAAAATTACCGTAATACCCTCTAAGGGTA
1 AAATTACCGAAATACCCTCGAAGGGTAAAATTACCGAAATACCCTCTAAGGGTA
46768934 AAAT
1 AAAT
46768938 GATATGACTG
Statistics
Matches: 146, Mismatches: 15, Indels: 5
0.88 0.09 0.03
Matches are distributed among these distances:
52 9 0.06
53 112 0.77
54 25 0.17
ACGTcount: A:0.41, C:0.20, G:0.16, T:0.23
Consensus pattern (54 bp):
AAATTACCGAAATACCCTCGAAGGGTAAAATTACCGAAATACCCTCTAAGGGTA
Found at i:46769330 original size:28 final size:28
Alignment explanation
Indices: 46769290--46769343 Score: 81
Period size: 28 Copynumber: 1.9 Consensus size: 28
46769280 ACTGTAATGA
* *
46769290 TACTGTATTGGGTTGAGGCCCACACTGC
1 TACTGAATTGGGTTAAGGCCCACACTGC
*
46769318 TACTGAATTGGGTTAAGGCCCTCACT
1 TACTGAATTGGGTTAAGGCCCACACT
46769344 ATACTATCAC
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 23 1.00
ACGTcount: A:0.20, C:0.24, G:0.26, T:0.30
Consensus pattern (28 bp):
TACTGAATTGGGTTAAGGCCCACACTGC
Found at i:46778087 original size:8 final size:8
Alignment explanation
Indices: 46778074--46778104 Score: 53
Period size: 8 Copynumber: 3.8 Consensus size: 8
46778064 ATATTGATCT
46778074 ATATGTTA
1 ATATGTTA
46778082 ATATGTTA
1 ATATGTTA
46778090 ATATGTTA
1 ATATGTTA
46778098 ATGATGT
1 AT-ATGT
46778105 AAATCCAACG
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
8 18 0.82
9 4 0.18
ACGTcount: A:0.35, C:0.00, G:0.16, T:0.48
Consensus pattern (8 bp):
ATATGTTA
Found at i:46789730 original size:6 final size:7
Alignment explanation
Indices: 46789713--46789738 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
46789703 TCAAGTCGAT
46789713 TTTTTAA
1 TTTTTAA
46789720 TTTTTAA
1 TTTTTAA
46789727 TTTTTAA
1 TTTTTAA
46789734 TTTTT
1 TTTTT
46789739 CTTACTCAAC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (7 bp):
TTTTTAA
Found at i:46795769 original size:21 final size:22
Alignment explanation
Indices: 46795745--46795790 Score: 60
Period size: 20 Copynumber: 2.2 Consensus size: 22
46795735 TGTGCTATAT
* *
46795745 AATTTTGAATTATGATTCA-AC
1 AATTTTCAATTATGATTAATAC
46795766 AA-TTTCAATTATGATTAATAC
1 AATTTTCAATTATGATTAATAC
46795787 AATT
1 AATT
46795791 AACCAATCTA
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
20 14 0.67
21 6 0.29
22 1 0.05
ACGTcount: A:0.41, C:0.09, G:0.07, T:0.43
Consensus pattern (22 bp):
AATTTTCAATTATGATTAATAC
Found at i:46802704 original size:97 final size:90
Alignment explanation
Indices: 46802525--46802721 Score: 245
Period size: 91 Copynumber: 2.1 Consensus size: 90
46802515 TTGACTGTGT
* *
46802525 AAAAA-GCCCTCAAACTTTTTTAACAAAAGCAATTAAGCCCTTGCTTTTTTTTTTGCACTCAATT
1 AAAAAGGCCTTCAAACTTTTTCAACAAAAGCAATTAAGCCCTTGCTTTTTTTTTTGCACTCAATT
46802589 GGGTACTTGAACTTTCAAAATGCATC
66 GGGTACTTGAACTTTC-AAATGCATC
* ** *
46802615 AAAAAGGCCTTCAAACTTTTTCAAGAAAAGCAATTAAGTCCCTGATTTTTATTTTTATTTTTCAC
1 AAAAAGGCCTTCAAACTTTTTCAACAAAAGCAATTAAG-CCC---TTGCT-TTTTT-TTTTGCAC
*
46802680 TCAATTGGTTACTTGAA-TTATCAAATGCATC
60 TCAATTGGGTACTTGAACTT-TCAAATGCATC
46802711 AAAAAGGCCTT
1 AAAAAGGCCTT
46802722 TTGACCATTA
Statistics
Matches: 92, Mismatches: 7, Indels: 10
0.84 0.06 0.09
Matches are distributed among these distances:
90 5 0.05
91 29 0.32
92 3 0.03
95 3 0.03
96 27 0.29
97 25 0.27
ACGTcount: A:0.34, C:0.19, G:0.11, T:0.37
Consensus pattern (90 bp):
AAAAAGGCCTTCAAACTTTTTCAACAAAAGCAATTAAGCCCTTGCTTTTTTTTTTGCACTCAATT
GGGTACTTGAACTTTCAAATGCATC
Found at i:46802833 original size:10 final size:10
Alignment explanation
Indices: 46802820--46802956 Score: 60
Period size: 10 Copynumber: 14.3 Consensus size: 10
46802810 GACATGTGGC
46802820 AAAAAATTAT
1 AAAAAATTAT
46802830 -AAAAA--AT
1 AAAAAATTAT
46802837 -AAAAATTA-
1 AAAAAATTAT
*
46802845 ATAAAATT-T
1 AAAAAATTAT
*
46802854 ATAACAATTAT
1 A-AAAAATTAT
*
46802865 -TA-AATTAT
1 AAAAAATTAT
*
46802873 AATAAAAATAT
1 AA-AAAATTAT
*
46802884 -AAAAATTAGA
1 AAAAAATTA-T
*
46802894 AAAAAATTAG
1 AAAAAATTAT
* * *
46802904 AACAATTTGT
1 AAAAAATTAT
46802914 AAAAAATTAT
1 AAAAAATTAT
**
46802924 AAAATTTTAT
1 AAAAAATTAT
*
46802934 -AAAAATCAT
1 AAAAAATTAT
46802943 AAAAAAATTAT
1 -AAAAAATTAT
46802954 AAA
1 AAA
46802957 GTGCATAAAA
Statistics
Matches: 92, Mismatches: 22, Indels: 26
0.66 0.16 0.19
Matches are distributed among these distances:
7 7 0.08
8 6 0.07
9 26 0.28
10 31 0.34
11 22 0.24
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.31
Consensus pattern (10 bp):
AAAAAATTAT
Found at i:46802889 original size:20 final size:19
Alignment explanation
Indices: 46802866--46802956 Score: 67
Period size: 20 Copynumber: 4.5 Consensus size: 19
46802856 AACAATTATT
46802866 AAATTATAATAAAAATATAA
1 AAATTATAA-AAAAATATAA
*
46802886 AAATTAGAAAAAAAT-TAGA
1 AAATTATAAAAAAATATA-A
* *
46802905 ACAATTTGTAAAAAATTATAA
1 A-AA-TTATAAAAAAATATAA
* * *
46802926 AATTTTATAAAAATCATAAAA
1 AA-ATTATAAAAA-AATATAA
46802947 AAATTATAAA
1 AAATTATAAA
46802957 GTGCATAAAA
Statistics
Matches: 55, Mismatches: 10, Indels: 12
0.71 0.13 0.16
Matches are distributed among these distances:
18 2 0.04
19 8 0.15
20 26 0.47
21 17 0.31
22 2 0.04
ACGTcount: A:0.65, C:0.02, G:0.03, T:0.30
Consensus pattern (19 bp):
AAATTATAAAAAAATATAA
Found at i:46802927 original size:9 final size:9
Alignment explanation
Indices: 46802821--46802947 Score: 71
Period size: 9 Copynumber: 13.6 Consensus size: 9
46802811 ACATGTGGCA
46802821 AAAAATTAT
1 AAAAATTAT
46802830 AAAAA--AT
1 AAAAATTAT
46802837 AAAAATTAAT
1 AAAAATT-AT
*
46802847 AAAATTTAT
1 AAAAATTAT
*
46802856 AACAATTAT
1 AAAAATTAT
*
46802865 -TAAATTAT
1 AAAAATTAT
*
46802873 AATAAAAATAT
1 -A-AAAATTAT
*
46802884 AAAAATTAGAA
1 AAAAATT--AT
*
46802895 AAAAATTAG
1 AAAAATTAT
* *
46802904 AACAATTTGT
1 AA-AAATTAT
46802914 AAAAAATTAT
1 -AAAAATTAT
*
46802924 AAAATTTTAT
1 AAAA-ATTAT
*
46802934 AAAAATCAT
1 AAAAATTAT
46802943 AAAAA
1 AAAAA
46802948 AATTATAAAG
Statistics
Matches: 89, Mismatches: 18, Indels: 22
0.69 0.14 0.17
Matches are distributed among these distances:
7 7 0.08
8 6 0.07
9 34 0.38
10 26 0.29
11 16 0.18
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.31
Consensus pattern (9 bp):
AAAAATTAT
Found at i:46802929 original size:19 final size:19
Alignment explanation
Indices: 46802820--46802938 Score: 86
Period size: 20 Copynumber: 6.3 Consensus size: 19
46802810 GACATGTGGC
*
46802820 AAAAAATTATAAAA--AAT
1 AAAAAATTATAAAATTTAT
46802837 -AAAAATTAATAAAATTTAT
1 AAAAAATT-ATAAAATTTAT
* *
46802856 -AACAATTATTAAA-TTAT
1 AAAAAATTATAAAATTTAT
* * *
46802873 AATAAAAATATAAAAATTAGA
1 AA-AAAATTATAAAATTTA-T
* *
46802894 AAAAAATTAGAACAATTTGT
1 AAAAAATTATAA-AATTTAT
46802914 AAAAAATTATAAAATTTTAT
1 AAAAAATTATAAAA-TTTAT
46802934 AAAAA
1 AAAAA
46802939 TCATAAAAAA
Statistics
Matches: 79, Mismatches: 14, Indels: 15
0.73 0.13 0.14
Matches are distributed among these distances:
16 7 0.09
17 10 0.13
18 6 0.08
19 19 0.24
20 31 0.39
21 6 0.08
ACGTcount: A:0.65, C:0.02, G:0.03, T:0.31
Consensus pattern (19 bp):
AAAAAATTATAAAATTTAT
Found at i:46802939 original size:19 final size:19
Alignment explanation
Indices: 46802835--46802946 Score: 86
Period size: 19 Copynumber: 5.8 Consensus size: 19
46802825 ATTATAAAAA
46802835 ATAAAAATTAATAAAA-TTT
1 ATAAAAATT-ATAAAATTTT
* * *
46802854 ATAACAATTATTAAATTATA
1 ATAAAAATTATAAAATT-TT
**
46802874 ATAAAAA-TATAAAAATTAG
1 ATAAAAATTAT-AAAATTTT
* *
46802893 AAAAAAATTAGAACAATTTGT
1 ATAAAAATTATAA-AATTT-T
46802914 A-AAAAATTATAAAATTTT
1 ATAAAAATTATAAAATTTT
*
46802932 ATAAAAATCATAAAA
1 ATAAAAATTATAAAA
46802947 AAATTATAAA
Statistics
Matches: 73, Mismatches: 13, Indels: 14
0.73 0.13 0.14
Matches are distributed among these distances:
18 7 0.10
19 37 0.51
20 28 0.38
21 1 0.01
ACGTcount: A:0.62, C:0.03, G:0.03, T:0.32
Consensus pattern (19 bp):
ATAAAAATTATAAAATTTT
Found at i:46803216 original size:28 final size:29
Alignment explanation
Indices: 46803178--46803247 Score: 90
Period size: 28 Copynumber: 2.4 Consensus size: 29
46803168 TCTTTACATT
*
46803178 TTTTATAATTTTCTTATGA-CTTTATAAAA
1 TTTTATAATTTT-TTACGATCTTTATAAAA
*
46803207 TTTTAT-ATTTTTTACGATTTTTATAAAA
1 TTTTATAATTTTTTACGATCTTTATAAAA
*
46803235 TTTTACAATTTTT
1 TTTTATAATTTTT
46803248 ATATTTTTTT
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
27 5 0.14
28 19 0.53
29 12 0.33
ACGTcount: A:0.31, C:0.06, G:0.03, T:0.60
Consensus pattern (29 bp):
TTTTATAATTTTTTACGATCTTTATAAAA
Found at i:46803277 original size:19 final size:19
Alignment explanation
Indices: 46803207--46803275 Score: 79
Period size: 19 Copynumber: 3.7 Consensus size: 19
46803197 CTTTATAAAA
46803207 TTTTAT-ATTTTTTACGAT
1 TTTTATAATTTTTTACGAT
** *
46803225 TTTTATAAAATTTTACAAT
1 TTTTATAATTTTTTACGAT
*
46803244 TTTTAT-ATTTTTTTCGAT
1 TTTTATAATTTTTTACGAT
*
46803262 TTTTGTAATTTTTT
1 TTTTATAATTTTTT
46803276 TCTAATTTTA
Statistics
Matches: 41, Mismatches: 8, Indels: 3
0.79 0.15 0.06
Matches are distributed among these distances:
18 19 0.46
19 22 0.54
ACGTcount: A:0.25, C:0.04, G:0.04, T:0.67
Consensus pattern (19 bp):
TTTTATAATTTTTTACGAT
Found at i:46803284 original size:19 final size:19
Alignment explanation
Indices: 46803207--46803284 Score: 63
Period size: 19 Copynumber: 4.2 Consensus size: 19
46803197 CTTTATAAAA
*
46803207 TTTTATATTTTTTACG-AT
1 TTTTATATTTTTTTCGAAT
** *
46803225 TTTTATAAAATTTTAC-AAT
1 TTTTAT-ATTTTTTTCGAAT
46803244 TTTTATATTTTTTTCG-AT
1 TTTTATATTTTTTTCGAAT
* *
46803262 TTTTGTAATTTTTTTCTAAT
1 TTTTAT-ATTTTTTTCGAAT
46803282 TTT
1 TTT
46803285 AATTAAAATT
Statistics
Matches: 48, Mismatches: 7, Indels: 8
0.76 0.11 0.13
Matches are distributed among these distances:
18 19 0.40
19 24 0.50
20 5 0.10
ACGTcount: A:0.24, C:0.05, G:0.04, T:0.67
Consensus pattern (19 bp):
TTTTATATTTTTTTCGAAT
Found at i:46803311 original size:28 final size:28
Alignment explanation
Indices: 46803267--46803336 Score: 77
Period size: 29 Copynumber: 2.5 Consensus size: 28
46803257 TCGATTTTTG
* * *
46803267 TAATTTTTTTCTAATTTTAATTAAAATT
1 TAATATTTTTATATTTTTAATTAAAATT
** *
46803295 TAAATATTTTTATATTTTTTGTTAATATT
1 T-AATATTTTTATATTTTTAATTAAAATT
46803324 TAATATTTTTATA
1 TAATATTTTTATA
46803337 ACTTTTATTA
Statistics
Matches: 35, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
28 13 0.37
29 22 0.63
ACGTcount: A:0.34, C:0.01, G:0.01, T:0.63
Consensus pattern (28 bp):
TAATATTTTTATATTTTTAATTAAAATT
Found at i:46803342 original size:28 final size:28
Alignment explanation
Indices: 46803267--46803361 Score: 88
Period size: 28 Copynumber: 3.4 Consensus size: 28
46803257 TCGATTTTTG
* * *
46803267 TAATTTTTTTCTAA-TTTTAATTAAAATT
1 TAATATTTTTATAACTTTT-ATTAATATT
** *
46803295 TAAATATTTTTATATTTTTTGTTAATATT
1 T-AATATTTTTATAACTTTTATTAATATT
46803324 TAATATTTTTATAACTTTTATTAAT-TT
1 TAATATTTTTATAACTTTTATTAATATT
*
46803351 TTAT-TTTTTAT
1 TAATATTTTTAT
46803362 CATTTTTTTG
Statistics
Matches: 56, Mismatches: 9, Indels: 6
0.79 0.13 0.08
Matches are distributed among these distances:
26 7 0.12
27 5 0.09
28 22 0.39
29 18 0.32
30 4 0.07
ACGTcount: A:0.32, C:0.02, G:0.01, T:0.65
Consensus pattern (28 bp):
TAATATTTTTATAACTTTTATTAATATT
Found at i:46803621 original size:88 final size:88
Alignment explanation
Indices: 46803430--46803676 Score: 327
Period size: 88 Copynumber: 2.7 Consensus size: 88
46803420 ACTATGGGCG
* * *
46803430 GTTCAAGTACCCAATTGAGTGCAAAAAAAGGTAGAGGCTTAATTGCTTTTTTTTTTGAAAAAGTT
1 GTTCAAGTGCCCAATTGAGTGCAAAAAAAAGCAG-GGCTTAATTGC---TTTTTTTGAAAAAGTT
* *
46803495 TGAGGGTTCTTTTTATGTATTTTGAAA
62 TGAGGGTGCTTTTTATGTATTGTGAAA
46803522 GTTCAAGTGCCCAATTGAGTGCAAAAAAAATGCAAGGGCTTAATTGCTTTTTTT-AAAAAGTTTG
1 GTTCAAGTGCCCAATTGAGTGCAAAAAAAA-GC-AGGGCTTAATTGCTTTTTTTGAAAAAGTTTG
46803586 AGGG-GCTTTTTATGTATTGTGAAA
64 AGGGTGCTTTTTATGTATTGTGAAA
* * * *
46803610 TTTCAAGTGCCCAAGTAAGTGAAAAAAAAAAGGCAGGGCTTAATTGCTTTTTTTGAAAAAGTTTG
1 GTTCAAGTGCCCAATTGAGTG-CAAAAAAAA-GCAGGGCTTAATTGCTTTTTTTGAAAAAGTTTG
46803675 AG
64 AG
46803677 AGTTTTTTAC
Statistics
Matches: 141, Mismatches: 10, Indels: 11
0.87 0.06 0.07
Matches are distributed among these distances:
88 56 0.40
89 36 0.26
90 7 0.05
92 28 0.20
93 12 0.09
94 2 0.01
ACGTcount: A:0.33, C:0.10, G:0.22, T:0.36
Consensus pattern (88 bp):
GTTCAAGTGCCCAATTGAGTGCAAAAAAAAGCAGGGCTTAATTGCTTTTTTTGAAAAAGTTTGAG
GGTGCTTTTTATGTATTGTGAAA
Found at i:46807239 original size:3 final size:3
Alignment explanation
Indices: 46807185--46807226 Score: 84
Period size: 3 Copynumber: 14.0 Consensus size: 3
46807175 ATCATTTTTG
46807185 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
46807227 CGATTAATTA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:46807669 original size:4 final size:4
Alignment explanation
Indices: 46807660--46807695 Score: 72
Period size: 4 Copynumber: 9.0 Consensus size: 4
46807650 TTTTACTCAT
46807660 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA
46807696 CATGTCTATT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 32 1.00
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (4 bp):
TTTA
Found at i:46809405 original size:3 final size:3
Alignment explanation
Indices: 46809399--46809463 Score: 103
Period size: 3 Copynumber: 21.7 Consensus size: 3
46809389 ATTTTTGTCC
* * *
46809399 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAC TAA TAC
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
46809447 TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TA
46809464 ATTTGTTTTA
Statistics
Matches: 58, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 58 1.00
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.62
Consensus pattern (3 bp):
TAT
Found at i:46811492 original size:29 final size:29
Alignment explanation
Indices: 46811421--46811510 Score: 78
Period size: 30 Copynumber: 3.0 Consensus size: 29
46811411 GGGGATGGGA
* *
46811421 TGGGAGGAGAGTAAAAGTTTTGGGGGAAAAAAA
1 TGGGAGG-GAGTAAAA-TTTT-GGGG-AGAAAG
*
46811454 T-GG-GGAAGTAAAATTTTGGGGAGAAAG
1 TGGGAGGGAGTAAAATTTTGGGGAGAAAG
*
46811481 TGGGAGGGAGTAAAAATTTTTGGG-GAAAG
1 TGGGAGGGAGT-AAAATTTTGGGGAGAAAG
46811510 T
1 T
46811511 AAATAAGTTT
Statistics
Matches: 49, Mismatches: 5, Indels: 10
0.77 0.08 0.16
Matches are distributed among these distances:
27 5 0.10
28 6 0.12
29 15 0.31
30 18 0.37
31 2 0.04
32 2 0.04
33 1 0.02
ACGTcount: A:0.38, C:0.00, G:0.40, T:0.22
Consensus pattern (29 bp):
TGGGAGGGAGTAAAATTTTGGGGAGAAAG
Found at i:46811499 original size:30 final size:30
Alignment explanation
Indices: 46811421--46811510 Score: 80
Period size: 29 Copynumber: 3.0 Consensus size: 30
46811411 GGGGATGGGA
* * *
46811421 TGGGAGGAGAGTAAAAGTTTTGGGGGAAAAAAA
1 TGGGAGG-GAGTAAAAATTTT-GGGG-AGAAAG
*
46811454 T-GG-GGAAGT-AAAATTTTGGGGAGAAAG
1 TGGGAGGGAGTAAAAATTTTGGGGAGAAAG
*
46811481 TGGGAGGGAGTAAAAATTTTTGGG-GAAAG
1 TGGGAGGGAGTAAAAATTTTGGGGAGAAAG
46811510 T
1 T
46811511 AAATAAGTTT
Statistics
Matches: 48, Mismatches: 6, Indels: 10
0.75 0.09 0.16
Matches are distributed among these distances:
27 5 0.10
28 6 0.12
29 18 0.38
30 14 0.29
31 2 0.04
32 2 0.04
33 1 0.02
ACGTcount: A:0.38, C:0.00, G:0.40, T:0.22
Consensus pattern (30 bp):
TGGGAGGGAGTAAAAATTTTGGGGAGAAAG
Found at i:46814086 original size:24 final size:21
Alignment explanation
Indices: 46814055--46814103 Score: 53
Period size: 23 Copynumber: 2.2 Consensus size: 21
46814045 CTCTAGTTTT
*
46814055 TCTCTTCACCTTATTTCGGAACA
1 TCTCTTCA-CTTATTT-GCAACA
*
46814078 TCTCGTTCACTTGTTTGCAACA
1 TCTC-TTCACTTATTTGCAACA
46814100 TCTC
1 TCTC
46814104 CTCTCTCCAT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
22 9 0.39
23 10 0.43
24 4 0.17
ACGTcount: A:0.18, C:0.31, G:0.10, T:0.41
Consensus pattern (21 bp):
TCTCTTCACTTATTTGCAACA
Found at i:46815661 original size:11 final size:11
Alignment explanation
Indices: 46815633--46815702 Score: 60
Period size: 11 Copynumber: 6.6 Consensus size: 11
46815623 TAAAAAAATA
46815633 AAAAAGTATTTT
1 AAAAA-TATTTT
46815645 AAAAATATTTT
1 AAAAATATTTT
*
46815656 CAAAATA----
1 AAAAATATTTT
**
46815663 AAAAA-ATTAA
1 AAAAATATTTT
46815673 AAAAAGTATTTT
1 AAAAA-TATTTT
46815685 AAAAATATTTT
1 AAAAATATTTT
46815696 AAAAATA
1 AAAAATA
46815703 AAAATAAAAA
Statistics
Matches: 48, Mismatches: 4, Indels: 13
0.74 0.06 0.20
Matches are distributed among these distances:
6 1 0.02
7 4 0.08
10 5 0.10
11 25 0.52
12 13 0.27
ACGTcount: A:0.61, C:0.01, G:0.03, T:0.34
Consensus pattern (11 bp):
AAAAATATTTT
Found at i:46815723 original size:40 final size:39
Alignment explanation
Indices: 46815623--46815706 Score: 143
Period size: 40 Copynumber: 2.2 Consensus size: 39
46815613 AAAAAACTTT
*
46815623 TAAAAAAAT-AAAAAAGTATTTTAAAAATATTTTCAAAA
1 TAAAAAAATAAAAAAAGTATTTTAAAAATATTTTAAAAA
46815661 TAAAAAAATTAAAAAAAGTATTTTAAAAATATTTTAAAAA
1 TAAAAAAA-TAAAAAAAGTATTTTAAAAATATTTTAAAAA
46815701 TAAAAA
1 TAAAAA
46815707 TAAAAATAAA
Statistics
Matches: 43, Mismatches: 1, Indels: 2
0.93 0.02 0.04
Matches are distributed among these distances:
38 8 0.19
39 1 0.02
40 34 0.79
ACGTcount: A:0.65, C:0.01, G:0.02, T:0.31
Consensus pattern (39 bp):
TAAAAAAATAAAAAAAGTATTTTAAAAATATTTTAAAAA
Found at i:46828736 original size:12 final size:12
Alignment explanation
Indices: 46828719--46828744 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
46828709 AGGATATGCA
46828719 ATCTTAGATATG
1 ATCTTAGATATG
46828731 ATCTTAGATATG
1 ATCTTAGATATG
46828743 AT
1 AT
46828745 ATATGCAATC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.35, C:0.08, G:0.15, T:0.42
Consensus pattern (12 bp):
ATCTTAGATATG
Found at i:46828767 original size:19 final size:20
Alignment explanation
Indices: 46828731--46828778 Score: 80
Period size: 19 Copynumber: 2.4 Consensus size: 20
46828721 CTTAGATATG
46828731 ATCTTAGATATGATATATGCA
1 ATCTTAGATATGA-ATATGCA
46828752 ATCTTAGATATG-ATATGCA
1 ATCTTAGATATGAATATGCA
46828771 ATCTTAGA
1 ATCTTAGA
46828779 AGATATGATT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
19 15 0.56
21 12 0.44
ACGTcount: A:0.38, C:0.10, G:0.15, T:0.38
Consensus pattern (20 bp):
ATCTTAGATATGAATATGCA
Found at i:46828785 original size:22 final size:21
Alignment explanation
Indices: 46828736--46828804 Score: 70
Period size: 22 Copynumber: 3.2 Consensus size: 21
46828726 ATATGATCTT
46828736 AGATATGATATATGCAATCTT--
1 AGATATG--ATATGCAATCTTAA
46828757 AGATATGATATGCAATCTTAGA
1 AGATATGATATGCAATCTTA-A
* *
46828779 AGATATGATTTTGTAATCTTAA
1 AGATATGA-TATGCAATCTTAA
46828801 AGAT
1 AGAT
46828805 TTAATTTGTA
Statistics
Matches: 42, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
19 12 0.29
21 7 0.17
22 13 0.31
23 10 0.24
ACGTcount: A:0.39, C:0.07, G:0.16, T:0.38
Consensus pattern (21 bp):
AGATATGATATGCAATCTTAA
Found at i:46828814 original size:21 final size:23
Alignment explanation
Indices: 46828757--46828814 Score: 59
Period size: 22 Copynumber: 2.7 Consensus size: 23
46828747 ATGCAATCTT
* *
46828757 AGATATG-ATATGCAATCTTAGA
1 AGATATGAATTTGTAATCTTAGA
*
46828779 AGATATGATTTTGTAATCTTA-A
1 AGATATGAATTTGTAATCTTAGA
*
46828801 AGAT-TTAATTTGTA
1 AGATATGAATTTGTA
46828815 GATACCCTTT
Statistics
Matches: 30, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
21 8 0.27
22 12 0.40
23 10 0.33
ACGTcount: A:0.38, C:0.05, G:0.16, T:0.41
Consensus pattern (23 bp):
AGATATGAATTTGTAATCTTAGA
Found at i:46834744 original size:16 final size:16
Alignment explanation
Indices: 46834722--46834762 Score: 73
Period size: 16 Copynumber: 2.6 Consensus size: 16
46834712 CCATATTGCC
46834722 CAAAAAAAAGATGGCG
1 CAAAAAAAAGATGGCG
*
46834738 TAAAAAAAAGATGGCG
1 CAAAAAAAAGATGGCG
46834754 CAAAAAAAA
1 CAAAAAAAA
46834763 AACTCTACCG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.63, C:0.10, G:0.20, T:0.07
Consensus pattern (16 bp):
CAAAAAAAAGATGGCG
Found at i:46836428 original size:44 final size:43
Alignment explanation
Indices: 46836363--46836651 Score: 226
Period size: 44 Copynumber: 6.5 Consensus size: 43
46836353 GCAGATTAGT
* * *
46836363 GAAGATAGCAGATCCTATCTTCCTATATAGGTAGCGAAGTGGATC
1 GAAGAT-GCAGATCTTGTCTTCCTATAT-GGTAGCGAAGTAGATC
* * * *
46836408 GAAGATGTAGATCTTGTCTTCCCATACTGGTGGCAAAGTAGATC
1 GAAGATGCAGATCTTGTCTTCCTATA-TGGTAGCGAAGTAGATC
* * * * *
46836452 GAAGAAAGCAGATCTTGTCTTCATGTATTGG-CGTGAAGTAGATC
1 GAAG-ATGCAGATCTTGTCTTCCTATA-TGGTAGCGAAGTAGATC
* * *
46836496 GAAGATAGCAGGTCCTGTCTTCCTATATTGGTAG-GAAGTGGATC
1 GAAGAT-GCAGATCTTGTCTTCCTATA-TGGTAGCGAAGTAGATC
* * * *
46836540 GAAGATGTAGATCTTGTCTTCCCATACTGGTGGTGAAGTAGATC
1 GAAGATGCAGATCTTGTCTTCCTATA-TGGTAGCGAAGTAGATC
* * * *
46836584 GAAGAAAGCAGATCTTGTCTTCATGTATTG-A-CGTAAAGTAGATC
1 GAAG-ATGCAGATCTTGTCTTCCTATATGGTAGCG--AAGTAGATC
*
46836628 GAAGATAGCAGATCTTGCCTTCCT
1 GAAGAT-GCAGATCTTGTCTTCCT
46836652 GCACTGACAG
Statistics
Matches: 194, Mismatches: 41, Indels: 19
0.76 0.16 0.07
Matches are distributed among these distances:
42 1 0.01
43 23 0.12
44 125 0.64
45 45 0.23
ACGTcount: A:0.28, C:0.17, G:0.26, T:0.29
Consensus pattern (43 bp):
GAAGATGCAGATCTTGTCTTCCTATATGGTAGCGAAGTAGATC
Found at i:46836650 original size:132 final size:133
Alignment explanation
Indices: 46836363--46836651 Score: 490
Period size: 132 Copynumber: 2.2 Consensus size: 133
46836353 GCAGATTAGT
*
46836363 GAAGATAGCAGATCCTATCTTCCTATATAGGTAGCGAAGTGGATCGAAGATGTAGATCTTGTCTT
1 GAAGATAGCAGATCCTGTCTTCCTATATAGGTAGCGAAGTGGATCGAAGATGTAGATCTTGTCTT
* *
46836428 CCCATACTGGTGGCAAAGTAGATCGAAGAAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAG
66 CCCATACTGGTGGCAAAGTAGATCGAAGAAAGCAGATCTTGTCTTCATGTATTGACGTAAAGTAG
46836493 ATC
131 ATC
* *
46836496 GAAGATAGCAGGTCCTGTCTTCCTATATTGGTAG-GAAGTGGATCGAAGATGTAGATCTTGTCTT
1 GAAGATAGCAGATCCTGTCTTCCTATATAGGTAGCGAAGTGGATCGAAGATGTAGATCTTGTCTT
**
46836560 CCCATACTGGTGGTGAAGTAGATCGAAGAAAGCAGATCTTGTCTTCATGTATTGACGTAAAGTAG
66 CCCATACTGGTGGCAAAGTAGATCGAAGAAAGCAGATCTTGTCTTCATGTATTGACGTAAAGTAG
46836625 ATC
131 ATC
* *
46836628 GAAGATAGCAGATCTTGCCTTCCT
1 GAAGATAGCAGATCCTGTCTTCCT
46836652 GCACTGACAG
Statistics
Matches: 146, Mismatches: 10, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
132 115 0.79
133 31 0.21
ACGTcount: A:0.28, C:0.17, G:0.26, T:0.29
Consensus pattern (133 bp):
GAAGATAGCAGATCCTGTCTTCCTATATAGGTAGCGAAGTGGATCGAAGATGTAGATCTTGTCTT
CCCATACTGGTGGCAAAGTAGATCGAAGAAAGCAGATCTTGTCTTCATGTATTGACGTAAAGTAG
ATC
Found at i:46836777 original size:44 final size:44
Alignment explanation
Indices: 46836729--46836960 Score: 182
Period size: 44 Copynumber: 5.3 Consensus size: 44
46836719 AATAGCAGAT
*
46836729 CTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAGC
1 CTTGCCTCCCTGCACCGACAGCGAAGCAGATCGAAGACACCAGC
**** * * ** * * *
46836773 CTTGCCTCCCTG-GGTTACAGCGGAGCAGGTAAAAAATAGCAGC
1 CTTGCCTCCCTGCACCGACAGCGAAGCAGATCGAAGACACCAGC
* *
46836816 TCTTGCCTTCCTGCACCGACAGCGAAGCAAATCGAAGACACCAGC
1 -CTTGCCTCCCTGCACCGACAGCGAAGCAGATCGAAGACACCAGC
**** * * * * * *
46836861 CTTGCCTCCCTGGGTTG-CAGCGGAGCAG-GCAAAAAATAGCAGC
1 CTTGCCTCCCTGCACCGACAGCGAAGCAGATC-GAAGACACCAGC
*
46836904 TCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAGC
1 -CTTGCCTCCCTGCACCGACAGCGAAGCAGATCGAAGACACCAGC
*
46836949 CTTACCTCCCTG
1 CTTGCCTCCCTG
46836961 GGTTGCAGCG
Statistics
Matches: 132, Mismatches: 50, Indels: 12
0.68 0.26 0.06
Matches are distributed among these distances:
42 1 0.01
43 37 0.28
44 56 0.42
45 37 0.28
46 1 0.01
ACGTcount: A:0.26, C:0.33, G:0.24, T:0.17
Consensus pattern (44 bp):
CTTGCCTCCCTGCACCGACAGCGAAGCAGATCGAAGACACCAGC
Found at i:46836781 original size:88 final size:88
Alignment explanation
Indices: 46836632--46837049 Score: 640
Period size: 88 Copynumber: 4.8 Consensus size: 88
46836622 TAGATCGAAG
* * * * *
46836632 ATAGCAGATCTTGCCTTCCTGCACTGACAGCGAAGCAGATCGAATACACTAGCTTTGCCTCCCTA
1 ATAGCAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCCCTG
46836697 GGTTGCAGCGGAGCAGGCTAAAA
66 GGTTGCAGCGGAGCAGGCTAAAA
46836720 ATAGCAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCCCTG
1 ATAGCAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCCCTG
*
46836785 GGTTACAGCGGAGCAGG-TAAAAA
66 GGTTGCAGCGGAGCAGGCT-AAAA
* *
46836808 ATAGCAGCTCTTGCCTTCCTGCACCGACAGCGAAGCAAATCGAAGACACCAGCCTTGCCTCCCTG
1 ATAGCAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCCCTG
*
46836873 GGTTGCAGCGGAGCAGGCAAAAA
66 GGTTGCAGCGGAGCAGGCTAAAA
* *
46836896 ATAGCAGCTCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAGCCTTACCTCCCTG
1 ATAGCAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCCCTG
* *
46836961 GGTTGCAGCGGAGTAGGTTAAAA
66 GGTTGCAGCGGAGCAGGCTAAAA
* * * * * **
46836984 ATAGCAGATCTTGCATTCCTGTACCGACAGCGAAGCAGATCGATGACTCTAGCCTTATCTCCCTG
1 ATAGCAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCCCTG
46837049 G
66 G
46837050 TCAGCAGTGG
Statistics
Matches: 306, Mismatches: 22, Indels: 4
0.92 0.07 0.01
Matches are distributed among these distances:
87 1 0.00
88 305 1.00
ACGTcount: A:0.27, C:0.29, G:0.24, T:0.20
Consensus pattern (88 bp):
ATAGCAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCCCTG
GGTTGCAGCGGAGCAGGCTAAAA
Found at i:46837102 original size:44 final size:44
Alignment explanation
Indices: 46837039--46837222 Score: 212
Period size: 44 Copynumber: 4.2 Consensus size: 44
46837029 ACTCTAGCCT
* *
46837039 TATCTCCCTGGTCAGCAGTGGAATAGGTTAAAGATTGTGAATCC
1 TATCTCCCTGGTCAACAGTGGAATAGGTTGAAGATTGTGAATCC
* * *
46837083 TATCTCCCTGGTCAACAGTGGAATAGGTTGACGATTGAGAATTC
1 TATCTCCCTGGTCAACAGTGGAATAGGTTGAAGATTGTGAATCC
* * ** *
46837127 TATCCCCCTAGG--AAGTAGTGGAATAAATTGAAGATTGT-AGGTCC
1 TATCTCCCT-GGTCAA-CAGTGGAATAGGTTGAAGATTGTGA-ATCC
* *
46837171 TATCTCCCTGATCAGCAGTGGAATAGGTTGAAGATTGTGAATCC
1 TATCTCCCTGGTCAACAGTGGAATAGGTTGAAGATTGTGAATCC
46837215 TATCTCCC
1 TATCTCCC
46837223 CAAGCAACAG
Statistics
Matches: 114, Mismatches: 20, Indels: 12
0.78 0.14 0.08
Matches are distributed among these distances:
43 4 0.04
44 106 0.93
45 4 0.04
ACGTcount: A:0.28, C:0.19, G:0.24, T:0.29
Consensus pattern (44 bp):
TATCTCCCTGGTCAACAGTGGAATAGGTTGAAGATTGTGAATCC
Found at i:46837234 original size:44 final size:44
Alignment explanation
Indices: 46837054--46837246 Score: 187
Period size: 44 Copynumber: 4.4 Consensus size: 44
46837044 CCCTGGTCAG
* *
46837054 CAGTGGAATAGGTTAAAGATTGTGAATCCTATCT-CCCTGGTCAA
1 CAGTGGAATAGGTTGAAGATTGTGAATCCTATCTCCCCTAG-CAA
* * * *
46837098 CAGTGGAATAGGTTGACGATTGAGAATTCTATC-CCCCTAGGAA
1 CAGTGGAATAGGTTGAAGATTGTGAATCCTATCTCCCCTAGCAA
* ** * * *
46837141 GTAGTGGAATAAATTGAAGATTGT-AGGTCCTATCT-CCCTGATCAG
1 -CAGTGGAATAGGTTGAAGATTGTGA-ATCCTATCTCCCCT-AGCAA
*
46837186 CAGTGGAATAGGTTGAAGATTGTGAATCCTATCTCCCCAAGCAA
1 CAGTGGAATAGGTTGAAGATTGTGAATCCTATCTCCCCTAGCAA
* *
46837230 CAGTGGAGTAAGTTGAA
1 CAGTGGAATAGGTTGAA
46837247 AATAGCAGAT
Statistics
Matches: 117, Mismatches: 25, Indels: 14
0.75 0.16 0.09
Matches are distributed among these distances:
43 3 0.03
44 108 0.92
45 6 0.05
ACGTcount: A:0.31, C:0.17, G:0.25, T:0.27
Consensus pattern (44 bp):
CAGTGGAATAGGTTGAAGATTGTGAATCCTATCTCCCCTAGCAA
Found at i:46837235 original size:88 final size:88
Alignment explanation
Indices: 46837052--46837246 Score: 241
Period size: 88 Copynumber: 2.2 Consensus size: 88
46837042 CTCCCTGGTC
* * * *
46837052 AGCAGTGGAATAGGTTAAAGATTGTGAATCCTATCTCCCTGGTCAACAGTGGAATAGGTTGACGA
1 AGCAGTGGAATAAGTTGAAGATTGTGAATCCTATCTCCCTGATCAACAGTGGAATAGGTTGAAGA
* * *
46837117 TTGAGAATTCTATCCCCCTAGGA
66 TTGAGAATCCTATCCCCCAAGCA
* * * *
46837140 AGTAGTGGAATAAATTGAAGATTGT-AGGTCCTATCTCCCTGATCAGCAGTGGAATAGGTTGAAG
1 AGCAGTGGAATAAGTTGAAGATTGTGA-ATCCTATCTCCCTGATCAACAGTGGAATAGGTTGAAG
*
46837204 ATTGTGAATCCTATCTCCCCAAGCA
65 ATTGAGAATCCTATC-CCCCAAGCA
*
46837229 A-CAGTGGAGTAAGTTGAA
1 AGCAGTGGAATAAGTTGAA
46837247 AATAGCAGAT
Statistics
Matches: 90, Mismatches: 15, Indels: 4
0.83 0.14 0.04
Matches are distributed among these distances:
87 1 0.01
88 81 0.90
89 8 0.09
ACGTcount: A:0.31, C:0.17, G:0.25, T:0.27
Consensus pattern (88 bp):
AGCAGTGGAATAAGTTGAAGATTGTGAATCCTATCTCCCTGATCAACAGTGGAATAGGTTGAAGA
TTGAGAATCCTATCCCCCAAGCA
Found at i:46838051 original size:12 final size:12
Alignment explanation
Indices: 46838034--46838059 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
46838024 AGGATATGCA
46838034 ATCTTAGATATG
1 ATCTTAGATATG
46838046 ATCTTAGATATG
1 ATCTTAGATATG
46838058 AT
1 AT
46838060 ATATGCAATC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.35, C:0.08, G:0.15, T:0.42
Consensus pattern (12 bp):
ATCTTAGATATG
Found at i:46838156 original size:3 final size:3
Alignment explanation
Indices: 46838148--46838195 Score: 51
Period size: 3 Copynumber: 16.0 Consensus size: 3
46838138 TATTAAGTTG
* * * * *
46838148 TTA TTA TTA TTA TTG TTG TTG TTA TTA TTA TCA TCA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
46838196 CTATATATAC
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.27, C:0.04, G:0.06, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:46838167 original size:18 final size:18
Alignment explanation
Indices: 46838144--46838178 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
46838134 TTGTTATTAA
46838144 GTTGTTATTATTATTATT
1 GTTGTTATTATTATTATT
*
46838162 GTTGTTGTTATTATTAT
1 GTTGTTATTATTATTAT
46838179 CATCATTATT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.20, C:0.00, G:0.14, T:0.66
Consensus pattern (18 bp):
GTTGTTATTATTATTATT
Found at i:46838349 original size:19 final size:17
Alignment explanation
Indices: 46838318--46838388 Score: 67
Period size: 17 Copynumber: 4.3 Consensus size: 17
46838308 CATAACTTTT
*
46838318 ATATACA-TATATATAC
1 ATATACATTTTATATAC
*
46838334 ATTTACATTTTATATAC
1 ATATACATTTTATATAC
*
46838351 ATATACATTTTTTATATC
1 ATATACATTTTATATA-C
* *
46838369 CTA-AC-TTTTATATGC
1 ATATACATTTTATATAC
46838384 ATATA
1 ATATA
46838389 TATATACTTT
Statistics
Matches: 44, Mismatches: 8, Indels: 6
0.76 0.14 0.10
Matches are distributed among these distances:
15 3 0.07
16 14 0.32
17 24 0.55
18 3 0.07
ACGTcount: A:0.38, C:0.13, G:0.01, T:0.48
Consensus pattern (17 bp):
ATATACATTTTATATAC
Found at i:46838554 original size:30 final size:31
Alignment explanation
Indices: 46838518--46838575 Score: 91
Period size: 31 Copynumber: 1.9 Consensus size: 31
46838508 ATTATTTGTT
*
46838518 TATATATATGTA-ATTATCTTTTTTATAATC
1 TATATATATGTATATAATCTTTTTTATAATC
*
46838548 TATATATATGTATATAATTTTTTTTATA
1 TATATATATGTATATAATCTTTTTTATA
46838576 TATGTACATG
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
30 12 0.48
31 13 0.52
ACGTcount: A:0.34, C:0.03, G:0.03, T:0.59
Consensus pattern (31 bp):
TATATATATGTATATAATCTTTTTTATAATC
Found at i:46838740 original size:18 final size:18
Alignment explanation
Indices: 46838719--46838756 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
46838709 GCTTTGCATG
46838719 TTATTGATTTTTAT-TTAT
1 TTATT-ATTTTTATATTAT
*
46838737 TTATTTTTTTTATATTAT
1 TTATTATTTTTATATTAT
46838755 TT
1 TT
46838757 CTATGCCATT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 7 0.39
18 11 0.61
ACGTcount: A:0.21, C:0.00, G:0.03, T:0.76
Consensus pattern (18 bp):
TTATTATTTTTATATTAT
Found at i:46840848 original size:40 final size:40
Alignment explanation
Indices: 46840803--46840936 Score: 214
Period size: 40 Copynumber: 3.4 Consensus size: 40
46840793 AAGGTAGTGG
*
46840803 CAGACAATAACCAAACACTTTAATACAACCTAGGCAATGA
1 CAGACAATAACCAAACACTTTAATACAACCTAGACAATGA
* * *
46840843 CAGACAATAGCCAAACACTTTCATACAACCTAGATAATGA
1 CAGACAATAACCAAACACTTTAATACAACCTAGACAATGA
46840883 CAGACAATAACCAAACACTTTAATACAACCTAGACAATGA
1 CAGACAATAACCAAACACTTTAATACAACCTAGACAATGA
* *
46840923 CAAACAATATCCAA
1 CAGACAATAACCAA
46840937 TACAAAAATA
Statistics
Matches: 85, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
40 85 1.00
ACGTcount: A:0.49, C:0.25, G:0.08, T:0.18
Consensus pattern (40 bp):
CAGACAATAACCAAACACTTTAATACAACCTAGACAATGA
Found at i:46841597 original size:205 final size:205
Alignment explanation
Indices: 46841239--46841617 Score: 578
Period size: 205 Copynumber: 1.8 Consensus size: 205
46841229 CCCAAGGCTA
* *
46841239 TTAGTATGCACATGACAGACAAAAAGTTTACAAAAATCCAAACTTGTAATTCAATTTGATACAAA
1 TTAGTATGCACATGACAGACAAAAAGTTTACAAAAATCCAAACATGCAATTCAATTTGATACAAA
* * * * *
46841304 CAATAATCATATTTGAATTAATATCTAAAAAATATTTTGAAACATATTTGAATAATTCATTGACA
66 AAATAATCACATTTGAATCAACATCTAAAAAATATTTTGAAACATATTTGAATAATTCAATGACA
* *
46841369 TACACAACTTCAAATAATTCAATAACAATTGATTTGTCAAATAGGAACTTATTTGTGTCTAATTT
131 TACACAACTTCAAATAATTCAATAAAAACTGATTTGTCAAATAGGAACTTATTTGTGTCTAATTT
46841434 CCTAAGTCTC
196 CCTAAGTCTC
* * * *
46841444 TTAGTTTGCACATGGCAGACAATAAGTTTACAAAAATCCAAACATGCAATTCAGTTTGATACAAA
1 TTAGTATGCACATGACAGACAAAAAGTTTACAAAAATCCAAACATGCAATTCAATTTGATACAAA
* * * * * *
46841509 AAATAATCACATTTGAATCAACATTTAAAATATGTTTTGTATCATATTTGAATAATTCAATGGCA
66 AAATAATCACATTTGAATCAACATCTAAAAAATATTTTGAAACATATTTGAATAATTCAATGACA
*
46841574 TACACAATTTCAAATAATTCAATAAAAACTGATTTGTCAAATAG
131 TACACAACTTCAAATAATTCAATAAAAACTGATTTGTCAAATAG
46841618 AAATTAAATT
Statistics
Matches: 154, Mismatches: 20, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
205 154 1.00
ACGTcount: A:0.43, C:0.14, G:0.09, T:0.34
Consensus pattern (205 bp):
TTAGTATGCACATGACAGACAAAAAGTTTACAAAAATCCAAACATGCAATTCAATTTGATACAAA
AAATAATCACATTTGAATCAACATCTAAAAAATATTTTGAAACATATTTGAATAATTCAATGACA
TACACAACTTCAAATAATTCAATAAAAACTGATTTGTCAAATAGGAACTTATTTGTGTCTAATTT
CCTAAGTCTC
Found at i:46850997 original size:18 final size:18
Alignment explanation
Indices: 46850976--46851023 Score: 60
Period size: 18 Copynumber: 2.7 Consensus size: 18
46850966 ATTTTTTATA
*
46850976 TAGTGTGAATTTAATCTC
1 TAGTGTAAATTTAATCTC
*
46850994 TAGTTTAAATTTAATCTC
1 TAGTGTAAATTTAATCTC
* *
46851012 TGGTTTAAATTT
1 TAGTGTAAATTT
46851024 GATTTTTAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.29, C:0.08, G:0.12, T:0.50
Consensus pattern (18 bp):
TAGTGTAAATTTAATCTC
Found at i:46854479 original size:36 final size:37
Alignment explanation
Indices: 46854439--46854510 Score: 96
Period size: 36 Copynumber: 2.0 Consensus size: 37
46854429 TTAAACTTCT
46854439 AATTTTAAAA-AATTCAAAAAA-AATAAAAA-TTATTTA
1 AATTTTAAAATAATT-AAAAAATAA-AAAAATTTATTTA
*
46854475 AATTTTAAAATTATTAAAAAATAAAAAAATTTATTT
1 AATTTTAAAATAATTAAAAAATAAAAAAATTTATTT
46854511 TCAACCTTTT
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
36 21 0.66
37 11 0.34
ACGTcount: A:0.61, C:0.01, G:0.00, T:0.38
Consensus pattern (37 bp):
AATTTTAAAATAATTAAAAAATAAAAAAATTTATTTA
Found at i:46854501 original size:17 final size:17
Alignment explanation
Indices: 46854456--46854501 Score: 56
Period size: 17 Copynumber: 2.7 Consensus size: 17
46854446 AAAAATTCAA
46854456 AAAAAATAAAAATTATT
1 AAAAAATAAAAATTATT
* ** *
46854473 TAAATTTTAAAATTATT
1 AAAAAATAAAAATTATT
46854490 AAAAAATAAAAA
1 AAAAAATAAAAA
46854502 AATTTATTTT
Statistics
Matches: 21, Mismatches: 8, Indels: 0
0.72 0.28 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (17 bp):
AAAAAATAAAAATTATT
Found at i:46855747 original size:54 final size:54
Alignment explanation
Indices: 46855657--46855763 Score: 178
Period size: 54 Copynumber: 2.0 Consensus size: 54
46855647 ACCCAAGGCC
* * *
46855657 GAACAAGACAACTGGAGGCTGGAATCTCCTATAAGAATTTCCTTTCTCTCAATG
1 GAACAAGACAACTAGAGGCTGGAATCTCCCAAAAGAATTTCCTTTCTCTCAATG
*
46855711 GAACGAGACAACTAGAGGCTGGAATCTCCCAAAAGAATTTCCTTTCTCTCAAT
1 GAACAAGACAACTAGAGGCTGGAATCTCCCAAAAGAATTTCCTTTCTCTCAAT
46855764 TCTATTTTTA
Statistics
Matches: 49, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
54 49 1.00
ACGTcount: A:0.33, C:0.23, G:0.18, T:0.26
Consensus pattern (54 bp):
GAACAAGACAACTAGAGGCTGGAATCTCCCAAAAGAATTTCCTTTCTCTCAATG
Found at i:46863583 original size:21 final size:20
Alignment explanation
Indices: 46863559--46863604 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 20
46863549 CCCTTGATTA
* *
46863559 CACTTTCGTGCCCCTGATTTG
1 CACTTTCATGCCCCT-ATATG
*
46863580 CACTCTCATGCCCCTATATG
1 CACTTTCATGCCCCTATATG
46863600 CACTT
1 CACTT
46863605 ATATGGCTAT
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
20 8 0.38
21 13 0.62
ACGTcount: A:0.15, C:0.37, G:0.13, T:0.35
Consensus pattern (20 bp):
CACTTTCATGCCCCTATATG
Found at i:46884083 original size:17 final size:17
Alignment explanation
Indices: 46884057--46884090 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
46884047 TTAAATTCTA
*
46884057 AAAATAATCAATTATAC
1 AAAATAATCAATAATAC
*
46884074 AAAATTATCAATAATAC
1 AAAATAATCAATAATAC
46884091 TTAAGAAAAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.59, C:0.12, G:0.00, T:0.29
Consensus pattern (17 bp):
AAAATAATCAATAATAC
Found at i:46886355 original size:52 final size:52
Alignment explanation
Indices: 46886280--46886379 Score: 139
Period size: 52 Copynumber: 1.9 Consensus size: 52
46886270 AATTTTGGAT
**
46886280 TTTTTTTAGTATTAGGACCAAATTGAGACAATATGT-AAATGTTGAGGGTTAA
1 TTTTTTTAAAATTAGGACCAAATTGAGACAATATGTGAAAT-TTGAGGGTTAA
* * *
46886332 TTTTTTTAAAATTATGACTAAATTGATACAATATGTGAAATTTGAGGG
1 TTTTTTTAAAATTAGGACCAAATTGAGACAATATGTGAAATTTGAGGG
46886380 CTAAATTTGT
Statistics
Matches: 42, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
52 38 0.90
53 4 0.10
ACGTcount: A:0.36, C:0.05, G:0.19, T:0.40
Consensus pattern (52 bp):
TTTTTTTAAAATTAGGACCAAATTGAGACAATATGTGAAATTTGAGGGTTAA
Found at i:46890697 original size:2 final size:2
Alignment explanation
Indices: 46890690--46890714 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
46890680 AACAGATAAT
46890690 TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC T
46890715 ACCCTTCAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:46892026 original size:38 final size:38
Alignment explanation
Indices: 46891984--46892081 Score: 160
Period size: 38 Copynumber: 2.6 Consensus size: 38
46891974 CCCTATTGAG
46891984 TACATGTTAAGCATGTCTACTGCTAGTGTTGAACTGAA
1 TACATGTTAAGCATGTCTACTGCTAGTGTTGAACTGAA
* *
46892022 TACATGTTAAGCATGTCTACTGGTAGTTTTGAACTGAA
1 TACATGTTAAGCATGTCTACTGCTAGTGTTGAACTGAA
* *
46892060 TACATGTAAAGCATGTCCACTG
1 TACATGTTAAGCATGTCTACTG
46892082 TTTTTGCATT
Statistics
Matches: 56, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
38 56 1.00
ACGTcount: A:0.30, C:0.16, G:0.20, T:0.34
Consensus pattern (38 bp):
TACATGTTAAGCATGTCTACTGCTAGTGTTGAACTGAA
Found at i:46896527 original size:11 final size:11
Alignment explanation
Indices: 46896509--46896550 Score: 59
Period size: 11 Copynumber: 3.8 Consensus size: 11
46896499 CTCAAAAACG
46896509 AACAACATTTA
1 AACAACATTTA
*
46896520 ACCAACA-TTA
1 AACAACATTTA
46896530 AGACAACATTTA
1 A-ACAACATTTA
46896542 AACAACATT
1 AACAACATT
46896551 CAGACAGCAT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
10 4 0.15
11 19 0.70
12 4 0.15
ACGTcount: A:0.52, C:0.21, G:0.02, T:0.24
Consensus pattern (11 bp):
AACAACATTTA
Found at i:46896535 original size:22 final size:22
Alignment explanation
Indices: 46896510--46896561 Score: 77
Period size: 22 Copynumber: 2.4 Consensus size: 22
46896500 TCAAAAACGA
*
46896510 ACAACATTTAACCAACATTAAG
1 ACAACATTTAAACAACATTAAG
*
46896532 ACAACATTTAAACAACATTCAG
1 ACAACATTTAAACAACATTAAG
*
46896554 ACAGCATT
1 ACAACATT
46896562 AGTATGCTAA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.48, C:0.23, G:0.06, T:0.23
Consensus pattern (22 bp):
ACAACATTTAAACAACATTAAG
Found at i:46896658 original size:111 final size:111
Alignment explanation
Indices: 46896528--46896751 Score: 448
Period size: 111 Copynumber: 2.0 Consensus size: 111
46896518 TAACCAACAT
46896528 TAAGACAACATTTAAACAACATTCAGACAGCATTAGTATGCTAAAAAACGAACATCGTTTAACCA
1 TAAGACAACATTTAAACAACATTCAGACAGCATTAGTATGCTAAAAAACGAACATCGTTTAACCA
46896593 ACATTCAGACAGCATTATTATCAAGCCATTTTCTCATGGCTATATG
66 ACATTCAGACAGCATTATTATCAAGCCATTTTCTCATGGCTATATG
46896639 TAAGACAACATTTAAACAACATTCAGACAGCATTAGTATGCTAAAAAACGAACATCGTTTAACCA
1 TAAGACAACATTTAAACAACATTCAGACAGCATTAGTATGCTAAAAAACGAACATCGTTTAACCA
46896704 ACATTCAGACAGCATTATTATCAAGCCATTTTCTCATGGCTATATG
66 ACATTCAGACAGCATTATTATCAAGCCATTTTCTCATGGCTATATG
46896750 TA
1 TA
46896752 TATATATACA
Statistics
Matches: 113, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
111 113 1.00
ACGTcount: A:0.40, C:0.21, G:0.12, T:0.28
Consensus pattern (111 bp):
TAAGACAACATTTAAACAACATTCAGACAGCATTAGTATGCTAAAAAACGAACATCGTTTAACCA
ACATTCAGACAGCATTATTATCAAGCCATTTTCTCATGGCTATATG
Found at i:46902636 original size:15 final size:15
Alignment explanation
Indices: 46902611--46902645 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
46902601 AACTATATTT
*
46902611 TAATT-ATATTAGGA
1 TAATTAATATTAAGA
46902625 TAATTAATATTAAGA
1 TAATTAATATTAAGA
46902640 TAATTA
1 TAATTA
46902646 TTAAGGATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 5 0.26
15 14 0.74
ACGTcount: A:0.49, C:0.00, G:0.09, T:0.43
Consensus pattern (15 bp):
TAATTAATATTAAGA
Found at i:46910155 original size:22 final size:20
Alignment explanation
Indices: 46910101--46910155 Score: 51
Period size: 22 Copynumber: 2.7 Consensus size: 20
46910091 AAATATTTTA
*
46910101 TAAAATTTTATA-AATTATT
1 TAAATTTTTATATAATTATT
*
46910120 GAAATTTGTT-TATAATTACTTT
1 TAAATTT-TTATATAATTA--TT
46910142 TAAATTTTTATATA
1 TAAATTTTTATATA
46910156 TTTTCTTGAA
Statistics
Matches: 28, Mismatches: 3, Indels: 7
0.74 0.08 0.18
Matches are distributed among these distances:
19 7 0.25
20 7 0.25
21 2 0.07
22 12 0.43
ACGTcount: A:0.40, C:0.02, G:0.04, T:0.55
Consensus pattern (20 bp):
TAAATTTTTATATAATTATT
Found at i:46910255 original size:19 final size:20
Alignment explanation
Indices: 46910223--46910262 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
46910213 TTTTTTTATA
*
46910223 TTATTTAGAATTTTTAATTT
1 TTATTTAGAATTTTCAATTT
*
46910243 TTATTTA-AGTTTTCAATTT
1 TTATTTAGAATTTTCAATTT
46910262 T
1 T
46910263 ATACAATTTA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 11 0.61
20 7 0.39
ACGTcount: A:0.28, C:0.03, G:0.05, T:0.65
Consensus pattern (20 bp):
TTATTTAGAATTTTCAATTT
Found at i:46917955 original size:19 final size:20
Alignment explanation
Indices: 46917931--46917971 Score: 59
Period size: 19 Copynumber: 2.1 Consensus size: 20
46917921 CTACATTACA
46917931 AATAGATACTT-GTGAGT-TC
1 AATAGA-ACTTAGTGAGTCTC
46917950 AATAGAACTTAGTGAGTCTC
1 AATAGAACTTAGTGAGTCTC
46917970 AA
1 AA
46917972 CCAATATTAC
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
18 4 0.20
19 12 0.60
20 4 0.20
ACGTcount: A:0.37, C:0.12, G:0.20, T:0.32
Consensus pattern (20 bp):
AATAGAACTTAGTGAGTCTC
Found at i:46922036 original size:27 final size:27
Alignment explanation
Indices: 46922006--46922100 Score: 104
Period size: 27 Copynumber: 3.5 Consensus size: 27
46921996 CTAAGAATAA
* *
46922006 CCTTTGTGGTGAACTCTTAAA-TAATAG
1 CCTTTGTGGCGAACTCTTAAAGGAAT-G
*
46922033 CCTTTGTGGCGAACT-TTAAAAGGAATT
1 CCTTTGTGGCGAACTCTT-AAAGGAATG
*
46922060 CCTTTGTGGCGAACTCTAAAAGGAATG
1 CCTTTGTGGCGAACTCTTAAAGGAATG
* *
46922087 CTTTTGTGGTGAAC
1 CCTTTGTGGCGAAC
46922101 ACTGAATGGA
Statistics
Matches: 58, Mismatches: 7, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
26 2 0.03
27 52 0.90
28 4 0.07
ACGTcount: A:0.27, C:0.16, G:0.23, T:0.34
Consensus pattern (27 bp):
CCTTTGTGGCGAACTCTTAAAGGAATG
Found at i:46926501 original size:46 final size:44
Alignment explanation
Indices: 46926448--46926609 Score: 227
Period size: 46 Copynumber: 3.6 Consensus size: 44
46926438 TTTGAGTACT
46926448 TCTGATCAAGTGATAAAGTGATAAGTGGTAGCATTAGCTACACTTA
1 TCTGATCAAGTGA-AAAGTGATAAGTGGTAGC-TTAGCTACACTTA
*
46926494 TCTGATCAAGTGAGAAAGTGATAAGTGGTAGCCTTAGCTACTCTTA
1 TCTGATCAAGTGA-AAAGTGATAAGTGGTAG-CTTAGCTACACTTA
* *
46926540 TCTGATCAAGTGACAAAGTGATAAGTGGGAGCCTAGCTACACTTA
1 TCTGATCAAGTGA-AAAGTGATAAGTGGTAGCTTAGCTACACTTA
* *
46926585 TCTGATC-AGGGACAAGTGATAAGTG
1 TCTGATCAAGTGAAAAGTGATAAGTG
46926610 ATCATATGTA
Statistics
Matches: 107, Mismatches: 8, Indels: 5
0.89 0.07 0.04
Matches are distributed among these distances:
43 12 0.11
44 4 0.04
45 19 0.18
46 71 0.66
47 1 0.01
ACGTcount: A:0.33, C:0.15, G:0.25, T:0.28
Consensus pattern (44 bp):
TCTGATCAAGTGAAAAGTGATAAGTGGTAGCTTAGCTACACTTA
Found at i:46934632 original size:13 final size:13
Alignment explanation
Indices: 46934614--46934640 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
46934604 TCGTTACAAG
46934614 AGGAATCTAAAAC
1 AGGAATCTAAAAC
46934627 AGGAATCTAAAAC
1 AGGAATCTAAAAC
46934640 A
1 A
46934641 TGTTATTATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.56, C:0.15, G:0.15, T:0.15
Consensus pattern (13 bp):
AGGAATCTAAAAC
Found at i:46938918 original size:15 final size:16
Alignment explanation
Indices: 46938898--46938927 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
46938888 TTGTTTAAAT
46938898 TTAAAA-TTATTATTG
1 TTAAAATTTATTATTG
46938913 TTAAAATTTATTATT
1 TTAAAATTTATTATT
46938928 AAAAAATTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.40, C:0.00, G:0.03, T:0.57
Consensus pattern (16 bp):
TTAAAATTTATTATTG
Found at i:46938949 original size:16 final size:15
Alignment explanation
Indices: 46938915--46938953 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
46938905 TATTATTGTT
* *
46938915 AAAATTTATTATTAA
1 AAAATTTAATATCAA
46938930 AAAATTATAATATCAA
1 AAAATT-TAATATCAA
46938946 AAAATTTA
1 AAAATTTA
46938954 TTAATATAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
15 8 0.38
16 13 0.62
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (15 bp):
AAAATTTAATATCAA
Found at i:46938983 original size:9 final size:9
Alignment explanation
Indices: 46938954--46939001 Score: 60
Period size: 9 Copynumber: 5.1 Consensus size: 9
46938944 AAAAAATTTA
*
46938954 TTAATATAA
1 TTAATATAT
*
46938963 TAAATCATAT
1 TTAAT-ATAT
46938973 TTAATATAT
1 TTAATATAT
46938982 TTAATATAT
1 TTAATATAT
46938991 TTAATAATAT
1 TTAAT-ATAT
46939001 T
1 T
46939002 GTACTTTATA
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
9 22 0.65
10 12 0.35
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (9 bp):
TTAATATAT
Found at i:46944534 original size:35 final size:35
Alignment explanation
Indices: 46944485--46944554 Score: 131
Period size: 35 Copynumber: 2.0 Consensus size: 35
46944475 TGCCTAAAGT
46944485 AGATGTCTCAAAGTTGAAATAGTTCAATGGGACGA
1 AGATGTCTCAAAGTTGAAATAGTTCAATGGGACGA
*
46944520 AGATGTCTCGAAGTTGAAATAGTTCAATGGGACGA
1 AGATGTCTCAAAGTTGAAATAGTTCAATGGGACGA
46944555 TGTTCGCAAA
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 34 1.00
ACGTcount: A:0.36, C:0.11, G:0.27, T:0.26
Consensus pattern (35 bp):
AGATGTCTCAAAGTTGAAATAGTTCAATGGGACGA
Found at i:46957156 original size:30 final size:30
Alignment explanation
Indices: 46957122--46957181 Score: 111
Period size: 30 Copynumber: 2.0 Consensus size: 30
46957112 ACATTCCGAA
46957122 CACTACTCCGCATCCATAACCTAGCAACAC
1 CACTACTCCGCATCCATAACCTAGCAACAC
*
46957152 CACTACTCCGCATCCATAACCTATCAACAC
1 CACTACTCCGCATCCATAACCTAGCAACAC
46957182 GACTTTCCAA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.33, C:0.43, G:0.05, T:0.18
Consensus pattern (30 bp):
CACTACTCCGCATCCATAACCTAGCAACAC
Found at i:46960183 original size:18 final size:18
Alignment explanation
Indices: 46960160--46960199 Score: 71
Period size: 18 Copynumber: 2.2 Consensus size: 18
46960150 ATGTCATTTT
46960160 CTATTAACTGCAAGAAAA
1 CTATTAACTGCAAGAAAA
*
46960178 CTATTAACTGTAAGAAAA
1 CTATTAACTGCAAGAAAA
46960196 CTAT
1 CTAT
46960200 CTGGTAAACT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.47, C:0.15, G:0.10, T:0.28
Consensus pattern (18 bp):
CTATTAACTGCAAGAAAA
Found at i:46961876 original size:15 final size:15
Alignment explanation
Indices: 46961856--46961886 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
46961846 ATTCAAATTT
*
46961856 AATAAAGTTGCTATG
1 AATAAAGTTGATATG
46961871 AATAAAGTTGATATG
1 AATAAAGTTGATATG
46961886 A
1 A
46961887 GTGATGTTTG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.45, C:0.03, G:0.19, T:0.32
Consensus pattern (15 bp):
AATAAAGTTGATATG
Found at i:46965290 original size:74 final size:74
Alignment explanation
Indices: 46965202--46965537 Score: 656
Period size: 74 Copynumber: 4.6 Consensus size: 74
46965192 AACTATAAAT
46965202 AAAA-CATATATTATATTTATAATGATCTAAGAGTAGTAGAGTCAATGCCAATCTACATGAAAAG
1 AAAATCATATATTATATTTATAATGATCTAAGAGTAGTAGAGTCAATGCCAATCTACATGAAAAG
46965266 GAGAACAAA
66 GAGAACAAA
46965275 AAAATCATATATTATATTTATAATGATCTAAGAGTAGTAGAGTCAATGCCAATCTACATGAAAAG
1 AAAATCATATATTATATTTATAATGATCTAAGAGTAGTAGAGTCAATGCCAATCTACATGAAAAG
46965340 GAGAACAAA
66 GAGAACAAA
46965349 AAAATCATATATTATATTTATAATGATCTAAGAGTAGTAGAGTCAATGCCAATCTACATGAAAAG
1 AAAATCATATATTATATTTATAATGATCTAAGAGTAGTAGAGTCAATGCCAATCTACATGAAAAG
46965414 GAGAACAAA
66 GAGAACAAA
46965423 AAAATCATATATTATATTTATAATGATCTAAGAGTAGTAGAGTCAATGCCAATCTACATGAAAAG
1 AAAATCATATATTATATTTATAATGATCTAAGAGTAGTAGAGTCAATGCCAATCTACATGAAAAG
46965488 GAGAACAAA
66 GAGAACAAA
*
46965497 AAAATCATATATTATATTTATAATGATCTAAGAATAGTAGA
1 AAAATCATATATTATATTTATAATGATCTAAGAGTAGTAGA
46965538 ATTAAAGTGA
Statistics
Matches: 261, Mismatches: 1, Indels: 1
0.99 0.00 0.00
Matches are distributed among these distances:
73 4 0.02
74 257 0.98
ACGTcount: A:0.48, C:0.10, G:0.14, T:0.28
Consensus pattern (74 bp):
AAAATCATATATTATATTTATAATGATCTAAGAGTAGTAGAGTCAATGCCAATCTACATGAAAAG
GAGAACAAA
Found at i:46967553 original size:72 final size:72
Alignment explanation
Indices: 46967448--46968100 Score: 1039
Period size: 72 Copynumber: 9.1 Consensus size: 72
46967438 GAATTGACGA
* * * * * *
46967448 TGGAATTTGTCCACTCAATTGGTTCTGCAACAAGTC-TAACTGAGTGAGTTGCAACAGGTTCCCT
1 TGGAATTTGTCCACTCAATTGGTTCAGCGACAAG-CGTAAATGAATGAGTTGCAAGAGGTTCCCC
46967512 AATGATCT
65 AATGATCT
* * **
46967520 TGGAATTTTTCGACTCAATTGGTTCTCCGACAAGTC-TAAAT-AAGTGAGTTGCAAGAGGTTCCC
1 TGGAATTTGTCCACTCAATTGGTTCAGCGACAAG-CGTAAATGAA-TGAGTTGCAAGAGGTTCCC
46967583 CAATGATCT
64 CAATGATCT
46967592 TGGAATTTGTCCACTCAATTGGTTCAGCGACAAGCGTAAATGAATGAGTTGCAAGAGGTTCCCCA
1 TGGAATTTGTCCACTCAATTGGTTCAGCGACAAGCGTAAATGAATGAGTTGCAAGAGGTTCCCCA
46967657 ATGATCT
66 ATGATCT
* ** * *
46967664 TGGAATTTGTCCACTCAATTGGTTCTGC-ACCAAGTATAAATGAGTGAGTTGCAAGAGGTTTCCC
1 TGGAATTTGTCCACTCAATTGGTTCAGCGA-CAAGCGTAAATGAATGAGTTGCAAGAGGTTCCCC
46967728 AATGATCT
65 AATGATCT
46967736 TGGAATTTGTCCACTCAATTGGTTCAGCGACAAGCGTAAATGAATGAGTTGCAAGAGGTTCCCCA
1 TGGAATTTGTCCACTCAATTGGTTCAGCGACAAGCGTAAATGAATGAGTTGCAAGAGGTTCCCCA
46967801 ATGATCT
66 ATGATCT
46967808 TGGAATTTGTCCACTCAATTGGTTCAGCGACAAGCGTAAATGAATGAGTTGCAAGAGGTTCCCCA
1 TGGAATTTGTCCACTCAATTGGTTCAGCGACAAGCGTAAATGAATGAGTTGCAAGAGGTTCCCCA
46967873 ATGATCT
66 ATGATCT
46967880 TGGAATTTGTCCACTCAATTGGTTCAGCGACAAGCGTAAATGAATGAGTTGCAAGAGGTTCCCCA
1 TGGAATTTGTCCACTCAATTGGTTCAGCGACAAGCGTAAATGAATGAGTTGCAAGAGGTTCCCCA
46967945 ATGATCT
66 ATGATCT
46967952 TGGAATTTGTCCACTCAATTGGTTCAGCGACAAGCGTAAATGAATGAGTTGCAAGAGGTTCCCCA
1 TGGAATTTGTCCACTCAATTGGTTCAGCGACAAGCGTAAATGAATGAGTTGCAAGAGGTTCCCCA
46968017 ATGATCT
66 ATGATCT
* *
46968024 TGGAATTTGTCCACTCAATTGGTTC-TCTGACAAGTC-TAAATGAGTGAGTTGCAAGAGGTTCCC
1 TGGAATTTGTCCACTCAATTGGTTCAGC-GACAAG-CGTAAATGAATGAGTTGCAAGAGGTTCCC
* *
46968087 TAGTGATCT
64 CAATGATCT
46968096 TGGAA
1 TGGAA
46968101 CCGGTCCTGA
Statistics
Matches: 548, Mismatches: 26, Indels: 14
0.93 0.04 0.02
Matches are distributed among these distances:
71 4 0.01
72 540 0.99
73 4 0.01
ACGTcount: A:0.28, C:0.19, G:0.23, T:0.30
Consensus pattern (72 bp):
TGGAATTTGTCCACTCAATTGGTTCAGCGACAAGCGTAAATGAATGAGTTGCAAGAGGTTCCCCA
ATGATCT
Found at i:46969308 original size:36 final size:36
Alignment explanation
Indices: 46969268--46969339 Score: 144
Period size: 36 Copynumber: 2.0 Consensus size: 36
46969258 CTTAAAATTG
46969268 GATGCTTTTCTTTTGGCAAAATCTTGTATTTCATTT
1 GATGCTTTTCTTTTGGCAAAATCTTGTATTTCATTT
46969304 GATGCTTTTCTTTTGGCAAAATCTTGTATTTCATTT
1 GATGCTTTTCTTTTGGCAAAATCTTGTATTTCATTT
46969340 CAACTAAAAT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.19, C:0.14, G:0.14, T:0.53
Consensus pattern (36 bp):
GATGCTTTTCTTTTGGCAAAATCTTGTATTTCATTT
Found at i:46974306 original size:7 final size:7
Alignment explanation
Indices: 46974289--46974349 Score: 52
Period size: 7 Copynumber: 8.3 Consensus size: 7
46974279 AAATAAAATG
46974289 AAACAAAT
1 AAAC-AAT
46974297 AAACAAT
1 AAACAAT
*
46974304 AAATAA-
1 AAACAAT
*
46974310 AATAAAAT
1 AA-ACAAT
46974318 GAAACAAAT
1 -AAAC-AAT
46974327 AAACAAT
1 AAACAAT
46974334 AAACAAT
1 AAACAAT
*
46974341 AAAAAAT
1 AAACAAT
46974348 AA
1 AA
46974350 TCATACGGGC
Statistics
Matches: 45, Mismatches: 4, Indels: 9
0.78 0.07 0.16
Matches are distributed among these distances:
6 2 0.04
7 29 0.64
8 9 0.20
9 5 0.11
ACGTcount: A:0.75, C:0.08, G:0.02, T:0.15
Consensus pattern (7 bp):
AAACAAT
Found at i:46974313 original size:30 final size:30
Alignment explanation
Indices: 46974279--46974336 Score: 116
Period size: 30 Copynumber: 1.9 Consensus size: 30
46974269 GATGCAATGT
46974279 AAATAAAATGAAACAAATAAACAATAAATA
1 AAATAAAATGAAACAAATAAACAATAAATA
46974309 AAATAAAATGAAACAAATAAACAATAAA
1 AAATAAAATGAAACAAATAAACAATAAA
46974337 CAATAAAAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.74, C:0.07, G:0.03, T:0.16
Consensus pattern (30 bp):
AAATAAAATGAAACAAATAAACAATAAATA
Found at i:46974341 original size:14 final size:15
Alignment explanation
Indices: 46974283--46974349 Score: 66
Period size: 14 Copynumber: 4.5 Consensus size: 15
46974273 CAATGTAAAT
46974283 AAAATGAAACAAATAA
1 AAAAT-AAACAAATAA
* * *
46974299 ACAATAAATAAA-AT
1 AAAATAAACAAATAA
46974313 AAAATGAAACAAATAA
1 AAAAT-AAACAAATAA
*
46974329 ACAATAAAC-AATAA
1 AAAATAAACAAATAA
46974343 AAAATAA
1 AAAATAA
46974350 TCATACGGGC
Statistics
Matches: 41, Mismatches: 8, Indels: 6
0.75 0.15 0.11
Matches are distributed among these distances:
14 16 0.39
15 16 0.39
16 9 0.22
ACGTcount: A:0.75, C:0.07, G:0.03, T:0.15
Consensus pattern (15 bp):
AAAATAAACAAATAA
Found at i:46974347 original size:30 final size:30
Alignment explanation
Indices: 46974279--46974347 Score: 113
Period size: 30 Copynumber: 2.3 Consensus size: 30
46974269 GATGCAATGT
*
46974279 AAATAAAATGAAACAAATAAACAATAAATA
1 AAATAAAATGAAACAAATAAACAATAAACA
46974309 AAATAAAATGAAACAAATAAACAATAAACA
1 AAATAAAATGAAACAAATAAACAATAAACA
46974339 ATAA-AAAAT
1 A-AATAAAAT
46974348 AATCATACGG
Statistics
Matches: 37, Mismatches: 1, Indels: 2
0.93 0.03 0.05
Matches are distributed among these distances:
30 35 0.95
31 2 0.05
ACGTcount: A:0.74, C:0.07, G:0.03, T:0.16
Consensus pattern (30 bp):
AAATAAAATGAAACAAATAAACAATAAACA
Found at i:46975066 original size:3 final size:3
Alignment explanation
Indices: 46975046--46975122 Score: 82
Period size: 3 Copynumber: 25.7 Consensus size: 3
46975036 AAGCTAAAAC
* * * * *
46975046 ATA ACA ATA ATA ACA ATA ATA TTA ATA ATA ATA CTA ATA ATA ATA GTA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
** *
46975094 AGG ATA ACA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
46975123 GAAAGTAATG
Statistics
Matches: 58, Mismatches: 16, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
3 58 1.00
ACGTcount: A:0.61, C:0.05, G:0.04, T:0.30
Consensus pattern (3 bp):
ATA
Found at i:46976542 original size:100 final size:100
Alignment explanation
Indices: 46976383--46976977 Score: 739
Period size: 100 Copynumber: 6.0 Consensus size: 100
46976373 AATGTCAGAA
* * * * * * * * * *
46976383 AAGCAAGATTCGCCATCGTAGCTTCAATCTGTTCCACTGTATCTG-CAGGGAGGTGAGATTTACT
1 AAGCAAGATTCGTCGTCGTAGCTTCAATCTATTCCGCTGCATC-GCCTGGGAAGTAAGATTCACC
* * * * *
46976447 GTTGTAGCTTCAATCTATTT-GACTGCAAAGTCGGGG
65 GTTGTGGCTTCAATCT-TTTAAATTGCAATGTTGGGG
* * * * *
46976483 AAGGAAGATTCATTGTTGTAGCTTCAATCTATTCCGCTGCATCGCCTGGGAAGTAAGATTCGCCG
1 AAGCAAGATTCGTCGTCGTAGCTTCAATCTATTCCGCTGCATCGCCTGGGAAGTAAGATTCACCG
*
46976548 TTGTGGCATCAATCTTTTAAATTGCAATGTTGGGG
66 TTGTGGCTTCAATCTTTTAAATTGCAATGTTGGGG
* * * ** * *
46976583 AAACAAGATTCGTCGTCCTAGCTTCAATCTGTTTTGTTGCATCGCCTGGAAAGTAAGATTCACCG
1 AAGCAAGATTCGTCGTCGTAGCTTCAATCTATTCCGCTGCATCGCCTGGGAAGTAAGATTCACCG
46976648 TTGTGGCTTCAATCTTTTAAATTGCAATGTTGGGG
66 TTGTGGCTTCAATCTTTTAAATTGCAATGTTGGGG
**
46976683 AAGCAAGATTCGTCGTCGTAGCTTCAA--TATGTCTCGCTGCATTACCTGGGAAGTAAGATTCAC
1 AAGCAAGATTCGTCGTCGTAGCTTCAATCTAT-TC-CGCTGCATCGCCTGGGAAGTAAGATTCAC
46976746 CGTTGTGGCTTCAATCTTTTAAATTGCAATGTTGGGG
64 CGTTGTGGCTTCAATCTTTTAAATTGCAATGTTGGGG
* * * * *
46976783 AAGCAAGATTCGCCCTCGTAGCTTCAATCTGTTCCGCTACATCGCCTGGGAATTAAGATTCACCG
1 AAGCAAGATTCGTCGTCGTAGCTTCAATCTATTCCGCTGCATCGCCTGGGAAGTAAGATTCACCG
* *
46976848 TTGTGGCTTTAATCTTTTAAATTGCAATGTCGGGG
66 TTGTGGCTTCAATCTTTTAAATTGCAATGTTGGGG
** * * * *
46976883 AAGCAAGATTCACCATCGTAGCTTCAATCTATTCCGCTGCATCGCCTGAGAAGTAAGATTCGCCA
1 AAGCAAGATTCGTCGTCGTAGCTTCAATCTATTCCGCTGCATCGCCTGGGAAGTAAGATTCACCG
46976948 TTGTGGCTTCAATCTTTTAAATTGCAATGT
66 TTGTGGCTTCAATCTTTTAAATTGCAATGT
46976978 ATAGTTTCTT
Statistics
Matches: 428, Mismatches: 61, Indels: 12
0.85 0.12 0.02
Matches are distributed among these distances:
98 2 0.00
99 5 0.01
100 417 0.97
101 2 0.00
102 2 0.00
ACGTcount: A:0.24, C:0.20, G:0.23, T:0.33
Consensus pattern (100 bp):
AAGCAAGATTCGTCGTCGTAGCTTCAATCTATTCCGCTGCATCGCCTGGGAAGTAAGATTCACCG
TTGTGGCTTCAATCTTTTAAATTGCAATGTTGGGG
Found at i:46976551 original size:50 final size:50
Alignment explanation
Indices: 46976400--46976962 Score: 239
Period size: 50 Copynumber: 11.3 Consensus size: 50
46976390 ATTCGCCATC
* * * * * * * *
46976400 GTAGCTTCAATCTGTTCCACTGTATCTG-CAGGGAGGTGAGATTTACTGTT
1 GTAGCTTCAATCTATTCCGCTGCATC-GCCTGGGAAGTAAGATTCACCGTT
* ** * * * **
46976450 GTAGCTTCAATCTATT-TGACTGCAAAGTCGGGGAAGGAAGATTCATTGTT
1 GTAGCTTCAATCTATTCCG-CTGCATCGCCTGGGAAGTAAGATTCACCGTT
*
46976500 GTAGCTTCAATCTATTCCGCTGCATCGCCTGGGAAGTAAGATTCGCCGTT
1 GTAGCTTCAATCTATTCCGCTGCATCGCCTGGGAAGTAAGATTCACCGTT
* * * **** * ** ** *
46976550 GTGGCATCAATCTTTTAAATTGCAAT-G-TTGGGGAAACAAGATTCGTCGTC
1 GTAGCTTCAATCTATTCCGCTGC-ATCGCCT-GGGAAGTAAGATTCACCGTT
* * ** * *
46976600 CTAGCTTCAATCTGTTTTGTTGCATCGCCTGGAAAGTAAGATTCACCGTT
1 GTAGCTTCAATCTATTCCGCTGCATCGCCTGGGAAGTAAGATTCACCGTT
* * **** * * ** *
46976650 GTGGCTTCAATCTTTTAAATTGCAAT-G-TTGGGGAAGCAAGATTCGTCGTC
1 GTAGCTTCAATCTATTCCGCTGC-ATCGCCT-GGGAAGTAAGATTCACCGTT
**
46976700 GTAGCTTCAA--TATGTCTCGCTGCATTACCTGGGAAGTAAGATTCACCGTT
1 GTAGCTTCAATCTAT-TC-CGCTGCATCGCCTGGGAAGTAAGATTCACCGTT
* * **** * * * * *
46976750 GTGGCTTCAATCTTTTAAATTGCAAT-G-TTGGGGAAGCAAGATTCGCCCTC
1 GTAGCTTCAATCTATTCCGCTGC-ATCGCCT-GGGAAGTAAGATTCACCGTT
* * *
46976800 GTAGCTTCAATCTGTTCCGCTACATCGCCTGGGAATTAAGATTCACCGTT
1 GTAGCTTCAATCTATTCCGCTGCATCGCCTGGGAAGTAAGATTCACCGTT
* * * **** * * * * *
46976850 GTGGCTTTAATCTTTTAAATTGCAAT-GTCGGGGAAGCAAGATTCACCATC
1 GTAGCTTCAATCTATTCCGCTGC-ATCGCCTGGGAAGTAAGATTCACCGTT
* * *
46976900 GTAGCTTCAATCTATTCCGCTGCATCGCCTGAGAAGTAAGATTCGCCATT
1 GTAGCTTCAATCTATTCCGCTGCATCGCCTGGGAAGTAAGATTCACCGTT
*
46976950 GTGGCTTCAATCT
1 GTAGCTTCAATCT
46976963 TTTAAATTGC
Statistics
Matches: 368, Mismatches: 124, Indels: 42
0.69 0.23 0.08
Matches are distributed among these distances:
48 2 0.01
49 13 0.04
50 338 0.92
51 13 0.04
52 2 0.01
ACGTcount: A:0.24, C:0.20, G:0.23, T:0.33
Consensus pattern (50 bp):
GTAGCTTCAATCTATTCCGCTGCATCGCCTGGGAAGTAAGATTCACCGTT
Found at i:46986625 original size:11 final size:11
Alignment explanation
Indices: 46986609--46986638 Score: 60
Period size: 11 Copynumber: 2.7 Consensus size: 11
46986599 TTGAGTATAT
46986609 ATTCTTTTAAG
1 ATTCTTTTAAG
46986620 ATTCTTTTAAG
1 ATTCTTTTAAG
46986631 ATTCTTTT
1 ATTCTTTT
46986639 CATTCTTTCA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.23, C:0.10, G:0.07, T:0.60
Consensus pattern (11 bp):
ATTCTTTTAAG
Found at i:46990286 original size:100 final size:100
Alignment explanation
Indices: 46990111--46990656 Score: 619
Period size: 100 Copynumber: 5.5 Consensus size: 100
46990101 AAGAAACTAT
* * * * * *
46990111 ACATTGCAATTTAAAAGATTGAAGCTACAACGGCGAATCTTACTTCTCAGGCGATGCAGCGGAAT
1 ACATTACAATTTAAAAGATTGAAGCCACAACGGCGAATCTTACTTCCCAGACGATGCAGCAGAAC
*
46990176 AGATTGAAGCTACGACGACGAATCTTGCTTCCCCA
66 AGATTAAAGCTACGACGACGAATCTTGCTTCCCCA
* * *
46990211 ACATTGCAATTTAAAAAATTAAAGCCACAACGGCGAATCTTACTTCCCAGACGATGCAGCAGAAC
1 ACATTACAATTTAAAAGATTGAAGCCACAACGGCGAATCTTACTTCCCAGACGATGCAGCAGAAC
* **
46990276 AGATTAAAGCTACGGCGGTGAATCTTGCTTCCCCA
66 AGATTAAAGCTACGACGACGAATCTTGCTTCCCCA
46990311 ACATTACAATTTAAAAGATTGAAGCCACAACGGCGAATCTTACTTCCCAGACGATGCAGCAGAAC
1 ACATTACAATTTAAAAGATTGAAGCCACAACGGCGAATCTTACTTCCCAGACGATGCAGCAGAAC
* **
46990376 AGATTAAAGCTACGGCGGTGAATCTTGCTTCCCCA
66 AGATTAAAGCTACGACGACGAATCTTGCTTCCCCA
* *
46990411 ACATTACAATTTAAAAGATTGAAGCCACAACGGCGAATCTTACTTCCTAGGCGATGCAGCAGAAC
1 ACATTACAATTTAAAAGATTGAAGCCACAACGGCGAATCTTACTTCCCAGACGATGCAGCAGAAC
* * * * *
46990476 AGATTGAAGCTACAACGACAAATCTTCCTTCCCCG
66 AGATTAAAGCTACGACGACGAATCTTGCTTCCCCA
* * * * * * * * * * * * **
46990511 ACATTAC-AGTCAAATAGATTGAAGCTATAACAGTGAATCTCACCTCCCTGGCGGTACAGTGGAA
1 ACATTACAATTTAAA-AGATTGAAGCCACAACGGCGAATCTTACTTCCCAGACGATGCAGCAGAA
* * * ** *
46990575 CAGATTGAAGTTACGATGACGAATCTTGCTTTTCCG
65 CAGATTAAAGCTACGACGACGAATCTTGCTTCCCCA
** * ** * *
46990611 ACATTGTAA-CTAAAAGATTGAAGCTGCAACAGCGAATCTTATTTCC
1 ACATTACAATTTAAAAGATTGAAGCCACAACGGCGAATCTTACTTCC
46990657 TCGACGAGAC
Statistics
Matches: 389, Mismatches: 55, Indels: 5
0.87 0.12 0.01
Matches are distributed among these distances:
99 31 0.08
100 357 0.92
101 1 0.00
ACGTcount: A:0.34, C:0.24, G:0.19, T:0.24
Consensus pattern (100 bp):
ACATTACAATTTAAAAGATTGAAGCCACAACGGCGAATCTTACTTCCCAGACGATGCAGCAGAAC
AGATTAAAGCTACGACGACGAATCTTGCTTCCCCA
Found at i:46990480 original size:50 final size:50
Alignment explanation
Indices: 46990123--46990508 Score: 280
Period size: 50 Copynumber: 7.7 Consensus size: 50
46990113 ATTGCAATTT
* * *
46990123 AAAAGATTGAAGCTACAACGGCGAATCTTACTTCTCAGGCGATGCAGCGG
1 AAAAGATTGAAGCTACAACGGCGAATCTTACTTCCCAGACGATGCAGCAG
* * * * ****
46990173 AATAGATTGAAGCTACGACGACGAATCTTGCTTCCCCA-AC-ATTGCAATTT
1 AAAAGATTGAAGCTACAACGGCGAATCTTACTT-CCCAGACGA-TGCAGCAG
* * *
46990223 AAAAAATTAAAGCCACAACGGCGAATCTTACTTCCCAGACGATGCAGCAG
1 AAAAGATTGAAGCTACAACGGCGAATCTTACTTCCCAGACGATGCAGCAG
* * ** * * * ****
46990273 AACAGATTAAAGCTACGGCGGTGAATCTTGCTTCCCCA-AC-ATTACAATTT
1 AAAAGATTGAAGCTACAACGGCGAATCTTACTT-CCCAGACGA-TGCAGCAG
*
46990323 AAAAGATTGAAGCCACAACGGCGAATCTTACTTCCCAGACGATGCAGCAG
1 AAAAGATTGAAGCTACAACGGCGAATCTTACTTCCCAGACGATGCAGCAG
* * ** * * * ****
46990373 AACAGATTAAAGCTACGGCGGTGAATCTTGCTTCCCCA-AC-ATTACAATTT
1 AAAAGATTGAAGCTACAACGGCGAATCTTACTT-CCCAGACGA-TGCAGCAG
* * *
46990423 AAAAGATTGAAGCCACAACGGCGAATCTTACTTCCTAGGCGATGCAGCAG
1 AAAAGATTGAAGCTACAACGGCGAATCTTACTTCCCAGACGATGCAGCAG
* * * *
46990473 AACAGATTGAAGCTACAACGACAAATCTTCCTTCCC
1 AAAAGATTGAAGCTACAACGGCGAATCTTACTTCCC
46990509 CGACATTACA
Statistics
Matches: 247, Mismatches: 77, Indels: 24
0.71 0.22 0.07
Matches are distributed among these distances:
49 14 0.06
50 219 0.89
51 14 0.06
ACGTcount: A:0.34, C:0.25, G:0.19, T:0.22
Consensus pattern (50 bp):
AAAAGATTGAAGCTACAACGGCGAATCTTACTTCCCAGACGATGCAGCAG
Found at i:47004704 original size:22 final size:19
Alignment explanation
Indices: 47004671--47004734 Score: 65
Period size: 22 Copynumber: 3.2 Consensus size: 19
47004661 CTTTTTTATT
*
47004671 TTTTTAGAAAATTTTAAAA
1 TTTTTATAAAATTTTAAAA
* *
47004690 TTTTTAAATATAAATTTTGACA
1 TTTTT--ATA-AAATTTTAAAA
47004712 TTTTTATAAATATTTTAAAA
1 TTTTTATAAA-ATTTTAAAA
47004732 TTT
1 TTT
47004735 AAAAATTATT
Statistics
Matches: 36, Mismatches: 5, Indels: 7
0.75 0.10 0.15
Matches are distributed among these distances:
19 7 0.19
20 13 0.36
21 2 0.06
22 14 0.39
ACGTcount: A:0.42, C:0.02, G:0.03, T:0.53
Consensus pattern (19 bp):
TTTTTATAAAATTTTAAAA
Found at i:47004760 original size:20 final size:20
Alignment explanation
Indices: 47004732--47004773 Score: 59
Period size: 19 Copynumber: 2.1 Consensus size: 20
47004722 TATTTTAAAA
*
47004732 TTTAAAAATTATTGT-AATT
1 TTTAAAAAATATTGTGAATT
*
47004751 TTTAAAAAATATTTTGAATT
1 TTTAAAAAATATTGTGAATT
47004771 TTT
1 TTT
47004774 TTTTGTTGAG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 13 0.65
20 7 0.35
ACGTcount: A:0.40, C:0.00, G:0.05, T:0.55
Consensus pattern (20 bp):
TTTAAAAAATATTGTGAATT
Found at i:47005832 original size:21 final size:21
Alignment explanation
Indices: 47005806--47005851 Score: 92
Period size: 21 Copynumber: 2.2 Consensus size: 21
47005796 TATATATATA
47005806 TGAAAATACAACAGAAATGCT
1 TGAAAATACAACAGAAATGCT
47005827 TGAAAATACAACAGAAATGCT
1 TGAAAATACAACAGAAATGCT
47005848 TGAA
1 TGAA
47005852 CATCATTTGC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.52, C:0.13, G:0.15, T:0.20
Consensus pattern (21 bp):
TGAAAATACAACAGAAATGCT
Found at i:47012112 original size:21 final size:21
Alignment explanation
Indices: 47012086--47012127 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
47012076 TAGTCTTGAA
*
47012086 ACATTGCAGATTTTTTCAATT
1 ACATTGCAAATTTTTTCAATT
47012107 ACATTGCAAATTTTTTCAATT
1 ACATTGCAAATTTTTTCAATT
47012128 TTTGAATTCC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.31, C:0.14, G:0.07, T:0.48
Consensus pattern (21 bp):
ACATTGCAAATTTTTTCAATT
Found at i:47016127 original size:23 final size:24
Alignment explanation
Indices: 47016089--47016139 Score: 77
Period size: 23 Copynumber: 2.2 Consensus size: 24
47016079 ACTTCAATTT
*
47016089 TTTTTCTTTTATTTTCTTTGTTCC
1 TTTTTCTTTTATTTTCTTTATTCC
*
47016113 TTTTTCTTTTA-TTTCTTTATTTC
1 TTTTTCTTTTATTTTCTTTATTCC
47016136 TTTT
1 TTTT
47016140 CTTACCTTGT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
23 14 0.56
24 11 0.44
ACGTcount: A:0.06, C:0.14, G:0.02, T:0.78
Consensus pattern (24 bp):
TTTTTCTTTTATTTTCTTTATTCC
Found at i:47016153 original size:33 final size:33
Alignment explanation
Indices: 47016086--47016153 Score: 77
Period size: 33 Copynumber: 2.1 Consensus size: 33
47016076 AACACTTCAA
* * *
47016086 TTTTTTTTCTTTTATTTTCTTTGTTCCTTTTTC
1 TTTTATTTCTTTTATTTTCTTTCTTCCTTGTTC
47016119 TTTTATTTC-TTTA-TTTCTTTTCTTACCTTGTTC
1 TTTTATTTCTTTTATTTTC-TTTCTT-CCTTGTTC
47016152 TT
1 TT
47016154 CACTTGTAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
31 4 0.13
32 9 0.30
33 17 0.57
ACGTcount: A:0.06, C:0.16, G:0.03, T:0.75
Consensus pattern (33 bp):
TTTTATTTCTTTTATTTTCTTTCTTCCTTGTTC
Found at i:47021360 original size:29 final size:31
Alignment explanation
Indices: 47021311--47021369 Score: 86
Period size: 29 Copynumber: 2.0 Consensus size: 31
47021301 ATTAATTTGA
* *
47021311 ACCACAATTAAAGTTTCATGTGTATAATTAT
1 ACCACAATTAAAGATTCATGTATATAATTAT
47021342 ACCA-AATTAAA-ATTCATGTATATAATTA
1 ACCACAATTAAAGATTCATGTATATAATTA
47021370 CGCATTAAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
29 15 0.58
30 7 0.27
31 4 0.15
ACGTcount: A:0.44, C:0.12, G:0.07, T:0.37
Consensus pattern (31 bp):
ACCACAATTAAAGATTCATGTATATAATTAT
Found at i:47021537 original size:15 final size:16
Alignment explanation
Indices: 47021512--47021542 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
47021502 CAAAAGTTAT
47021512 AATTAATTTTTATAAA
1 AATTAATTTTTATAAA
47021528 AATT-ATTTTTATAAA
1 AATTAATTTTTATAAA
47021543 TTTCCTATAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 11 0.73
16 4 0.27
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (16 bp):
AATTAATTTTTATAAA
Found at i:47022957 original size:15 final size:16
Alignment explanation
Indices: 47022932--47022962 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
47022922 CAAAAGTTAT
47022932 AATTAATTTTTATAAA
1 AATTAATTTTTATAAA
47022948 AATT-ATTTTTATAAA
1 AATTAATTTTTATAAA
47022963 TTTCCTATAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 11 0.73
16 4 0.27
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (16 bp):
AATTAATTTTTATAAA
Found at i:47023147 original size:59 final size:60
Alignment explanation
Indices: 47023050--47023166 Score: 218
Period size: 59 Copynumber: 2.0 Consensus size: 60
47023040 TTATTAACAA
*
47023050 TTTTTTTTATTTGTTAATGTTAGAGGCGAGTGTTCAATCGAGTTAAGTCGAATCAAATCG
1 TTTTTTTTATTTGTCAATGTTAGAGGCGAGTGTTCAATCGAGTTAAGTCGAATCAAATCG
47023110 TTTTTTTTATTTGTCAATGTTAGAGG-GAGTGTTCAATCGAGTTAAGTCGAATCAAAT
1 TTTTTTTTATTTGTCAATGTTAGAGGCGAGTGTTCAATCGAGTTAAGTCGAATCAAAT
47023167 TAAGTAATAA
Statistics
Matches: 56, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
59 31 0.55
60 25 0.45
ACGTcount: A:0.27, C:0.09, G:0.21, T:0.42
Consensus pattern (60 bp):
TTTTTTTTATTTGTCAATGTTAGAGGCGAGTGTTCAATCGAGTTAAGTCGAATCAAATCG
Found at i:47023541 original size:23 final size:24
Alignment explanation
Indices: 47023515--47023561 Score: 78
Period size: 23 Copynumber: 2.0 Consensus size: 24
47023505 TTTTTTTAGA
47023515 AAATTTTAAAATTTTT-TAAATAT
1 AAATTTTAAAATTTTTATAAATAT
*
47023538 AAATTTTGAAATTTTTATAAATAT
1 AAATTTTAAAATTTTTATAAATAT
47023562 TTTGAATTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
23 15 0.68
24 7 0.32
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (24 bp):
AAATTTTAAAATTTTTATAAATAT
Found at i:47023571 original size:19 final size:20
Alignment explanation
Indices: 47023540--47023591 Score: 63
Period size: 19 Copynumber: 2.6 Consensus size: 20
47023530 TTAAATATAA
*
47023540 ATTTTGAAATTTTTATAAA-T
1 ATTTTG-AATTTTTAAAAATT
47023560 ATTTTGAA-TTTTAAAAATT
1 ATTTTGAATTTTTAAAAATT
*
47023579 ATTGTGAATTTTT
1 ATTTTGAATTTTT
47023592 TTTGTTGAGA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
18 8 0.29
19 10 0.36
20 10 0.36
ACGTcount: A:0.37, C:0.00, G:0.08, T:0.56
Consensus pattern (20 bp):
ATTTTGAATTTTTAAAAATT
Found at i:47025894 original size:21 final size:22
Alignment explanation
Indices: 47025864--47025906 Score: 70
Period size: 21 Copynumber: 2.0 Consensus size: 22
47025854 AAAGAAAACC
*
47025864 TTGTTGTTTTTTCA-TGTTTTG
1 TTGTTATTTTTTCACTGTTTTG
47025885 TTGTTATTTTTTCACTGTTTTG
1 TTGTTATTTTTTCACTGTTTTG
47025907 CTACAAGTTC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 13 0.65
22 7 0.35
ACGTcount: A:0.07, C:0.07, G:0.16, T:0.70
Consensus pattern (22 bp):
TTGTTATTTTTTCACTGTTTTG
Found at i:47027069 original size:20 final size:22
Alignment explanation
Indices: 47027028--47027071 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 22
47027018 AATTTAATTA
*
47027028 TTTTACTTTTATTTTTAGAAAT
1 TTTTACTTTTATTTTTACAAAT
47027050 TTTTA-TTTTATTTTT-CAAAT
1 TTTTACTTTTATTTTTACAAAT
47027070 TT
1 TT
47027072 CAATACTTTG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 6 0.29
21 10 0.48
22 5 0.24
ACGTcount: A:0.25, C:0.05, G:0.02, T:0.68
Consensus pattern (22 bp):
TTTTACTTTTATTTTTACAAAT
Found at i:47028174 original size:42 final size:42
Alignment explanation
Indices: 47028030--47028184 Score: 153
Period size: 41 Copynumber: 3.8 Consensus size: 42
47028020 TTTAAACAAA
* * * *
47028030 CGCCGCTAATGTTATGGTTTTTAGTGGCGTTTGTTTCT-GAG
1 CGCCGCTAATGTTAGGGTTTTTAGCGGCGTTTGTTTGTAAAG
* *
47028071 CGCCGCTAACT-TTAGGGCTTTTAGCGGCG-TT-TTTGATAATG
1 CGCCGCTAA-TGTTAGGGTTTTTAGCGGCGTTTGTTTG-TAAAG
* *
47028112 CGCCGCT-ATAGTTAAGGTTTTTAGTGGCGTTTGTTTGTAAAG
1 CGCCGCTAAT-GTTAGGGTTTTTAGCGGCGTTTGTTTGTAAAG
47028154 CGCCGCTAATGTT-GGAG-TTTTAGCGGCGTTT
1 CGCCGCTAATGTTAGG-GTTTTTAGCGGCGTTT
47028185 TGATGGAAAC
Statistics
Matches: 93, Mismatches: 12, Indels: 18
0.76 0.10 0.15
Matches are distributed among these distances:
39 4 0.04
40 4 0.04
41 61 0.66
42 18 0.19
43 6 0.06
ACGTcount: A:0.15, C:0.16, G:0.29, T:0.39
Consensus pattern (42 bp):
CGCCGCTAATGTTAGGGTTTTTAGCGGCGTTTGTTTGTAAAG
Found at i:47028175 original size:82 final size:82
Alignment explanation
Indices: 47028030--47028185 Score: 221
Period size: 82 Copynumber: 1.9 Consensus size: 82
47028020 TTTAAACAAA
* *
47028030 CGCCGCTAATGTTATGGTTTTTAGTGGCGTTTGTTTCTGAGCGCCGCTAACTTTAGGGCTTTTAG
1 CGCCGCTAATGTTAAGGTTTTTAGTGGCGTTTGTTTCTAAGCGCCGCTAACTTTAGGGCTTTTAG
47028095 CGGCGTTTTTGATAATG
66 CGGCGTTTTTGATAATG
*
47028112 CGCCGCT-ATAGTTAAGGTTTTTAGTGGCGTTTGTTTGTAAAGCGCCGCTAA-TGTT-GGAG-TT
1 CGCCGCTAAT-GTTAAGGTTTTTAGTGGCGTTTGTTTCT-AAGCGCCGCTAACT-TTAGG-GCTT
47028173 TTAGCGGCGTTTT
62 TTAGCGGCGTTTT
47028186 GATGGAAACG
Statistics
Matches: 67, Mismatches: 3, Indels: 8
0.86 0.04 0.10
Matches are distributed among these distances:
81 2 0.03
82 51 0.76
83 14 0.21
ACGTcount: A:0.15, C:0.16, G:0.29, T:0.40
Consensus pattern (82 bp):
CGCCGCTAATGTTAAGGTTTTTAGTGGCGTTTGTTTCTAAGCGCCGCTAACTTTAGGGCTTTTAG
CGGCGTTTTTGATAATG
Found at i:47028198 original size:82 final size:81
Alignment explanation
Indices: 47028009--47028199 Score: 212
Period size: 82 Copynumber: 2.3 Consensus size: 81
47027999 TCAGAGGGAC
* * * * *
47028009 TTAGTGGCGTTTTTAAACAAACGCCGCTAATGTTATGGTTTTTAGTGGCGTTTGTTTCTGAGCGC
1 TTAGCGGCGTTTTT-GATAAACGCCGCTAATGTTAAGGTTTTTAGTGGCGTTTGTTTCTAAGCGC
47028074 CGCTAACTTTAGGGCTT
65 CGCTAACTTTAGGGCTT
* *
47028091 TTAGCGGCGTTTTTGATAATGCGCCGCT-ATAGTTAAGGTTTTTAGTGGCGTTTGTTTGTAAAGC
1 TTAGCGGCGTTTTTGATAA-ACGCCGCTAAT-GTTAAGGTTTTTAGTGGCGTTTGTTTCT-AAGC
47028155 GCCGCTAA-TGTT-GGAG-TT
63 GCCGCTAACT-TTAGG-GCTT
47028173 TTAGCGGCG-TTTTGATGGAAACGCCGC
1 TTAGCGGCGTTTTTGAT--AAACGCCGC
47028200 AAAATACATT
Statistics
Matches: 94, Mismatches: 8, Indels: 14
0.81 0.07 0.12
Matches are distributed among these distances:
81 12 0.13
82 66 0.70
83 16 0.17
ACGTcount: A:0.18, C:0.16, G:0.28, T:0.37
Consensus pattern (81 bp):
TTAGCGGCGTTTTTGATAAACGCCGCTAATGTTAAGGTTTTTAGTGGCGTTTGTTTCTAAGCGCC
GCTAACTTTAGGGCTT
Found at i:47029648 original size:13 final size:13
Alignment explanation
Indices: 47029617--47029650 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
47029607 GACAAATCAC
47029617 TTTTCCCCCCAAA
1 TTTTCCCCCCAAA
**
47029630 AATTCCCCCCAAA
1 TTTTCCCCCCAAA
47029643 TTTTCCCC
1 TTTTCCCC
47029651 AAAAATCCCC
Statistics
Matches: 17, Mismatches: 4, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.24, C:0.47, G:0.00, T:0.29
Consensus pattern (13 bp):
TTTTCCCCCCAAA
Found at i:47030988 original size:24 final size:23
Alignment explanation
Indices: 47030960--47031057 Score: 58
Period size: 24 Copynumber: 4.2 Consensus size: 23
47030950 TAAACTTTTA
47030960 ATTTTAAAAATAATTGTAAATGTT
1 ATTTTAAAAATAATT-TAAATGTT
** * **
47030984 ATTTTTTAAATAA-TAAAACCTAT
1 ATTTTAAAAATAATTTAAATGT-T
* * *
47031007 ATTTTCAAAAATAATTT--TTATA
1 ATTTT-AAAAATAATTTAAATGTT
*
47031029 ATTTTAGAAATAATTGTAAATGTT
1 ATTTTAAAAATAATT-TAAATGTT
47031053 ATTTT
1 ATTTT
47031058 CTAAATATTA
Statistics
Matches: 52, Mismatches: 16, Indels: 12
0.65 0.20 0.15
Matches are distributed among these distances:
21 9 0.17
22 10 0.19
23 8 0.15
24 24 0.46
25 1 0.02
ACGTcount: A:0.44, C:0.03, G:0.05, T:0.48
Consensus pattern (23 bp):
ATTTTAAAAATAATTTAAATGTT
Found at i:47031063 original size:24 final size:22
Alignment explanation
Indices: 47031036--47031206 Score: 58
Period size: 21 Copynumber: 7.5 Consensus size: 22
47031026 ATAATTTTAG
47031036 AAATAATTGTAAATGTTATTTTCT
1 AAATAA-T-TAAATGTTATTTTCT
*
47031060 AAAT-ATTAACATCTATATTTTC-
1 AAATAATTAA-ATGT-TATTTTCT
*
47031082 -AATAA-TAAATTTTATAATTT-T
1 AAATAATTAAATGTTAT--TTTCT
47031103 AGAAATAATTGTAAATGTTATTTTCT
1 --AAATAA-T-TAAATGTTATTTTCT
*
47031129 AAAT-ATTAACATCTATATTTTC-
1 AAATAATTAA-ATGT-TATTTTCT
*
47031151 -AATAA-TAAATTTTATAATTT-T
1 AAATAATTAAATGTTAT--TTTCT
*
47031172 AGAAATAATTGTAAATGCTATTTTCT
1 --AAATAA-T-TAAATGTTATTTTCT
47031198 AAAT-ATTAA
1 AAATAATTAA
47031207 CATAATACAT
Statistics
Matches: 114, Mismatches: 7, Indels: 55
0.65 0.04 0.31
Matches are distributed among these distances:
19 6 0.05
20 6 0.05
21 27 0.24
22 11 0.10
23 17 0.15
24 22 0.19
25 6 0.05
26 2 0.02
27 17 0.15
ACGTcount: A:0.43, C:0.06, G:0.05, T:0.47
Consensus pattern (22 bp):
AAATAATTAAATGTTATTTTCT
Found at i:47031076 original size:69 final size:69
Alignment explanation
Indices: 47030947--47031209 Score: 438
Period size: 69 Copynumber: 3.8 Consensus size: 69
47030937 ATTTTATTGG
* * * * * *
47030947 TAATAAACTTT-TAATTTTAAAAATAATTGTAAATGTTATTTTTTAAATAATAAAACCTATATTT
1 TAATAAATTTTATAATTTTAGAAATAATTGTAAATGTTATTTTCTAAATATTAACATCTATATTT
47031011 TCAA
66 TCAA
* *
47031015 AAATAATTTTTATAATTTTAGAAATAATTGTAAATGTTATTTTCTAAATATTAACATCTATATTT
1 TAATAAATTTTATAATTTTAGAAATAATTGTAAATGTTATTTTCTAAATATTAACATCTATATTT
47031080 TCAA
66 TCAA
47031084 TAATAAATTTTATAATTTTAGAAATAATTGTAAATGTTATTTTCTAAATATTAACATCTATATTT
1 TAATAAATTTTATAATTTTAGAAATAATTGTAAATGTTATTTTCTAAATATTAACATCTATATTT
47031149 TCAA
66 TCAA
*
47031153 TAATAAATTTTATAATTTTAGAAATAATTGTAAATGCTATTTTCTAAATATTAACAT
1 TAATAAATTTTATAATTTTAGAAATAATTGTAAATGTTATTTTCTAAATATTAACAT
47031210 AATACATAAC
Statistics
Matches: 183, Mismatches: 11, Indels: 1
0.94 0.06 0.01
Matches are distributed among these distances:
68 8 0.04
69 175 0.96
ACGTcount: A:0.43, C:0.06, G:0.04, T:0.47
Consensus pattern (69 bp):
TAATAAATTTTATAATTTTAGAAATAATTGTAAATGTTATTTTCTAAATATTAACATCTATATTT
TCAA
Found at i:47031097 original size:21 final size:21
Alignment explanation
Indices: 47030976--47031172 Score: 71
Period size: 21 Copynumber: 8.8 Consensus size: 21
47030966 AAAATAATTG
* *
47030976 TAAATGTTATTTTTTAAATAA
1 TAAATTTTATATTTTAAATAA
***
47030997 TAAAACCTATATTTTCAAA-AA
1 TAAATTTTATATTTT-AAATAA
*
47031018 TAATTTTTATAATTTTAGAAATAA
1 TAAATTTTAT-ATTTT--AAATAA
* *
47031042 TTGTAAATGTTAT-TTTCTAAATAT
1 ---TAAATTTTATATTT-TAAATAA
* *
47031066 TAACA-TCTATATTTTCAATAA
1 TAA-ATTTTATATTTTAAATAA
47031087 TAAATTTTATAATTTTAGAAATAA
1 TAAATTTTAT-ATTTT--AAATAA
* *
47031111 TTGTAAATGTTAT-TTTCTAAATAT
1 ---TAAATTTTATATTT-TAAATAA
* *
47031135 TAACA-TCTATATTTTCAATAA
1 TAA-ATTTTATATTTTAAATAA
47031156 TAAATTTTATAATTTTA
1 TAAATTTTAT-ATTTTA
47031173 GAAATAATTG
Statistics
Matches: 128, Mismatches: 26, Indels: 43
0.65 0.13 0.22
Matches are distributed among these distances:
20 2 0.02
21 55 0.43
22 26 0.20
23 3 0.02
24 17 0.13
25 6 0.05
26 2 0.02
27 17 0.13
ACGTcount: A:0.43, C:0.06, G:0.04, T:0.48
Consensus pattern (21 bp):
TAAATTTTATATTTTAAATAA
Done.