Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr3
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: 100348136
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.31
Warning! 3062571 characters in sequence are not A, C, G, or T
File 120 of 290
Found at i:40848794 original size:30 final size:30
Alignment explanation
Indices: 40848760--40849091 Score: 664
Period size: 30 Copynumber: 11.1 Consensus size: 30
40848750 AAAGACACAC
40848760 TAAAAATGAATTTAAACAAATGGTTATTCA
1 TAAAAATGAATTTAAACAAATGGTTATTCA
40848790 TAAAAATGAATTTAAACAAATGGTTATTCA
1 TAAAAATGAATTTAAACAAATGGTTATTCA
40848820 TAAAAATGAATTTAAACAAATGGTTATTCA
1 TAAAAATGAATTTAAACAAATGGTTATTCA
40848850 TAAAAATGAATTTAAACAAATGGTTATTCA
1 TAAAAATGAATTTAAACAAATGGTTATTCA
40848880 TAAAAATGAATTTAAACAAATGGTTATTCA
1 TAAAAATGAATTTAAACAAATGGTTATTCA
40848910 TAAAAATGAATTTAAACAAATGGTTATTCA
1 TAAAAATGAATTTAAACAAATGGTTATTCA
40848940 TAAAAATGAATTTAAACAAATGGTTATTCA
1 TAAAAATGAATTTAAACAAATGGTTATTCA
40848970 TAAAAATGAATTTAAACAAATGGTTATTCA
1 TAAAAATGAATTTAAACAAATGGTTATTCA
40849000 TAAAAATGAATTTAAACAAATGGTTATTCA
1 TAAAAATGAATTTAAACAAATGGTTATTCA
40849030 TAAAAATGAATTTAAACAAATGGTTATTCA
1 TAAAAATGAATTTAAACAAATGGTTATTCA
40849060 TAAAAATGAATTTAAACAAATGGTTATTCA
1 TAAAAATGAATTTAAACAAATGGTTATTCA
40849090 TA
1 TA
40849092 TTCATTCTAA
Statistics
Matches: 302, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 302 1.00
ACGTcount: A:0.50, C:0.07, G:0.10, T:0.33
Consensus pattern (30 bp):
TAAAAATGAATTTAAACAAATGGTTATTCA
Found at i:40849136 original size:11 final size:10
Alignment explanation
Indices: 40849120--40849170 Score: 50
Period size: 11 Copynumber: 5.0 Consensus size: 10
40849110 TTAAATATTA
40849120 TAAAAAATAT
1 TAAAAAATAT
40849130 GTAAAAAATAT
1 -TAAAAAATAT
**
40849141 TAAAATTTATT
1 TAAAAAATA-T
*
40849152 TAAAAAAT-C
1 TAAAAAATAT
40849161 TAAAAAATAT
1 TAAAAAATAT
40849171 GTCGAATAAA
Statistics
Matches: 32, Mismatches: 6, Indels: 5
0.74 0.14 0.12
Matches are distributed among these distances:
9 8 0.25
10 7 0.22
11 17 0.53
ACGTcount: A:0.63, C:0.02, G:0.02, T:0.33
Consensus pattern (10 bp):
TAAAAAATAT
Found at i:40852007 original size:12 final size:13
Alignment explanation
Indices: 40851990--40852026 Score: 51
Period size: 12 Copynumber: 3.0 Consensus size: 13
40851980 GAACTGGACA
40851990 CGAACCGAA-CTC
1 CGAACCGAAGCTC
40852002 CGAACC-AAGCTC
1 CGAACCGAAGCTC
*
40852014 CGAACCGTAGCTC
1 CGAACCGAAGCTC
40852027 TGATGCCACT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
11 2 0.09
12 15 0.68
13 5 0.23
ACGTcount: A:0.30, C:0.41, G:0.19, T:0.11
Consensus pattern (13 bp):
CGAACCGAAGCTC
Found at i:40853468 original size:17 final size:18
Alignment explanation
Indices: 40853436--40853469 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
40853426 AATGTAAAAA
40853436 TAAATTTAATTTAATTTG
1 TAAATTTAATTTAATTTG
*
40853454 TAAATTTTA-TTAATTT
1 TAAATTTAATTTAATTT
40853470 ATATCTTTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (18 bp):
TAAATTTAATTTAATTTG
Found at i:40853928 original size:38 final size:39
Alignment explanation
Indices: 40853875--40853969 Score: 106
Period size: 38 Copynumber: 2.5 Consensus size: 39
40853865 CATTTAATTA
* *
40853875 ATTTTTTAAATTTAAAAATTCA-AAAAAGT-TAT-AAAACT
1 ATTTTTAAAATTTAAAAA-TCATAAAAA-TCTATAAAAAAT
* * *
40853913 ATTTTTAAAAATTAAACATCATTAAAATCTATAAAAAAT
1 ATTTTTAAAATTTAAAAATCATAAAAATCTATAAAAAAT
40853952 ATTTTTAAAATTTAAAAA
1 ATTTTTAAAATTTAAAAA
40853970 ATTAATTAAA
Statistics
Matches: 47, Mismatches: 7, Indels: 5
0.80 0.12 0.08
Matches are distributed among these distances:
37 4 0.09
38 22 0.47
39 21 0.45
ACGTcount: A:0.55, C:0.05, G:0.01, T:0.39
Consensus pattern (39 bp):
ATTTTTAAAATTTAAAAATCATAAAAATCTATAAAAAAT
Found at i:40854185 original size:13 final size:13
Alignment explanation
Indices: 40854167--40854192 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
40854157 TCATTATACC
40854167 AAAAAAACAACCA
1 AAAAAAACAACCA
40854180 AAAAAAACAACCA
1 AAAAAAACAACCA
40854193 TAATTGGATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.77, C:0.23, G:0.00, T:0.00
Consensus pattern (13 bp):
AAAAAAACAACCA
Found at i:40855008 original size:7 final size:7
Alignment explanation
Indices: 40854996--40855020 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
40854986 ATAAGTGCTC
40854996 TAAGATT
1 TAAGATT
40855003 TAAGATT
1 TAAGATT
40855010 TAAGATT
1 TAAGATT
40855017 TAAG
1 TAAG
40855021 TGTTTAATAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.44, C:0.00, G:0.16, T:0.40
Consensus pattern (7 bp):
TAAGATT
Found at i:40855980 original size:14 final size:15
Alignment explanation
Indices: 40855961--40855993 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
40855951 ATAAAAACTG
40855961 CTTTAATATT-TATA
1 CTTTAATATTGTATA
*
40855975 CTTTAATTTTGTATA
1 CTTTAATATTGTATA
40855990 CTTT
1 CTTT
40855994 TTATCTCTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 9 0.53
15 8 0.47
ACGTcount: A:0.27, C:0.09, G:0.03, T:0.61
Consensus pattern (15 bp):
CTTTAATATTGTATA
Found at i:40861077 original size:27 final size:26
Alignment explanation
Indices: 40861020--40861082 Score: 76
Period size: 26 Copynumber: 2.4 Consensus size: 26
40861010 TACTCTATTG
40861020 TTTTTTTTTCTTTTTACATTTCTTCA
1 TTTTTTTTTCTTTTTACATTTCTTCA
*
40861046 TTTTTTTTTCTTCTTTTC-TTTCTAT-A
1 TTTTTTTTTCTT-TTTACATTTCT-TCA
40861072 TATTTTTTTTC
1 T-TTTTTTTTC
40861083 CTTAGCAATG
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
26 19 0.58
27 14 0.42
ACGTcount: A:0.10, C:0.14, G:0.00, T:0.76
Consensus pattern (26 bp):
TTTTTTTTTCTTTTTACATTTCTTCA
Found at i:40862792 original size:19 final size:20
Alignment explanation
Indices: 40862755--40862792 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 20
40862745 TCTCTAATAT
* *
40862755 AAAATATATTTTAATATTTG
1 AAAATATATTTGAAAATTTG
40862775 AAAAT-TATTTGAAAATTT
1 AAAATATATTTGAAAATTT
40862793 TGCTAAATTA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 11 0.69
20 5 0.31
ACGTcount: A:0.47, C:0.00, G:0.05, T:0.47
Consensus pattern (20 bp):
AAAATATATTTGAAAATTTG
Found at i:40865348 original size:13 final size:13
Alignment explanation
Indices: 40865330--40865362 Score: 66
Period size: 13 Copynumber: 2.5 Consensus size: 13
40865320 AATTAGTAAT
40865330 TATTTATTAAAAA
1 TATTTATTAAAAA
40865343 TATTTATTAAAAA
1 TATTTATTAAAAA
40865356 TATTTAT
1 TATTTAT
40865363 GAATCCGAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (13 bp):
TATTTATTAAAAA
Found at i:40871270 original size:51 final size:50
Alignment explanation
Indices: 40871194--40871294 Score: 175
Period size: 51 Copynumber: 2.0 Consensus size: 50
40871184 TTCAAACTTG
* *
40871194 TTTTTGAGGCAGATAAGTTTATTTTGTCTAATGGATGAATTTTTGTAGGGA
1 TTTTTGAGGCAGATAAGTTTATTTTGTCTAAGGGAGGAATTTTTGT-GGGA
40871245 TTTTTGAGGCAGATAAGTTTATTTTGTCTAAGGGAGGAATTTTTGTGGGA
1 TTTTTGAGGCAGATAAGTTTATTTTGTCTAAGGGAGGAATTTTTGTGGGA
40871295 AAAGGGTATA
Statistics
Matches: 48, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
50 4 0.08
51 44 0.92
ACGTcount: A:0.25, C:0.04, G:0.28, T:0.44
Consensus pattern (50 bp):
TTTTTGAGGCAGATAAGTTTATTTTGTCTAAGGGAGGAATTTTTGTGGGA
Found at i:40875258 original size:5 final size:5
Alignment explanation
Indices: 40875248--40875275 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
40875238 TACCTGATAT
40875248 AAATA AAATA AAATA AAATA AAATA AAA
1 AAATA AAATA AAATA AAATA AAATA AAA
40875276 CGCAGATGAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.18
Consensus pattern (5 bp):
AAATA
Found at i:40883688 original size:43 final size:43
Alignment explanation
Indices: 40883624--40883912 Score: 339
Period size: 43 Copynumber: 6.7 Consensus size: 43
40883614 ATTGTCAACG
*
40883624 CCGCTATAGATCAGGACCTTTAGCGGCGCTTTTTACACAAACA
1 CCGCTATAGATCATGACCTTTAGCGGCGCTTTTTACACAAACA
* ** *
40883667 CCGCTATAGATCATGATCTTTAGCGGCGCTTTTTTTACAAACG
1 CCGCTATAGATCATGACCTTTAGCGGCGCTTTTTACACAAACA
*
40883710 CCGCTATAGATCATGACCTTTAGCGGCGCTTATTACACAAACA
1 CCGCTATAGATCATGACCTTTAGCGGCGCTTTTTACACAAACA
* * * *
40883753 CCGCTATAGATCAAGATCTTTAGCGGCGCTTTTTTCACAAACG
1 CCGCTATAGATCATGACCTTTAGCGGCGCTTTTTACACAAACA
* **
40883796 CCGCTATAGATCAAGACCTTTAGCGGCGCTTTTCCCACAAA-A
1 CCGCTATAGATCATGACCTTTAGCGGCGCTTTTTACACAAACA
* * * * * *
40883838 GCCACTATAGATCATGATCTTTAGCGACGCTTTTTCCATAAACG
1 -CCGCTATAGATCATGACCTTTAGCGGCGCTTTTTACACAAACA
** * *
40883882 CTACTATA-ACTCAAGACCTTTAGCGACGCTT
1 CCGCTATAGA-TCATGACCTTTAGCGGCGCTT
40883913 CAATTACAAA
Statistics
Matches: 214, Mismatches: 29, Indels: 6
0.86 0.12 0.02
Matches are distributed among these distances:
42 1 0.00
43 213 1.00
ACGTcount: A:0.27, C:0.27, G:0.17, T:0.29
Consensus pattern (43 bp):
CCGCTATAGATCATGACCTTTAGCGGCGCTTTTTACACAAACA
Found at i:40883765 original size:86 final size:85
Alignment explanation
Indices: 40883620--40883912 Score: 419
Period size: 86 Copynumber: 3.4 Consensus size: 85
40883610 TGCCATTGTC
*
40883620 AACGCCGCTATAGATCAGGACCTTTAGCGGCGCTTTTTACACAAACACCGCTATAGATCATGATC
1 AACGCCGCTATAGATCAAGACCTTTAGCGGCGC-TTTTACACAAACACCGCTATAGATCATGATC
*
40883685 TTTAGCGGCGCTTTTTTTACA
65 TTTAGCGGCGCTTTTTTCACA
* *
40883706 AACGCCGCTATAGATCATGACCTTTAGCGGCGCTTATTACACAAACACCGCTATAGATCAAGATC
1 AACGCCGCTATAGATCAAGACCTTTAGCGGCGCTT-TTACACAAACACCGCTATAGATCATGATC
40883771 TTTAGCGGCGCTTTTTTCACA
65 TTTAGCGGCGCTTTTTTCACA
* *
40883792 AACGCCGCTATAGATCAAGACCTTTAGCGGCGCTTTTCCCACAAA-AGCCACTATAGATCATGAT
1 AACGCCGCTATAGATCAAGACCTTTAGCGGCGCTTTT-ACACAAACA-CCGCTATAGATCATGAT
* * *
40883856 CTTTAGCGACGCTTTTTCCATA
64 CTTTAGCGGCGCTTTTTTCACA
** *
40883878 AACGCTACTATA-ACTCAAGACCTTTAGCGACGCTT
1 AACGCCGCTATAGA-TCAAGACCTTTAGCGGCGCTT
40883913 CAATTACAAA
Statistics
Matches: 190, Mismatches: 13, Indels: 8
0.90 0.06 0.04
Matches are distributed among these distances:
85 6 0.03
86 184 0.97
ACGTcount: A:0.28, C:0.27, G:0.17, T:0.28
Consensus pattern (85 bp):
AACGCCGCTATAGATCAAGACCTTTAGCGGCGCTTTTACACAAACACCGCTATAGATCATGATCT
TTAGCGGCGCTTTTTTCACA
Found at i:40883786 original size:129 final size:129
Alignment explanation
Indices: 40883624--40883912 Score: 382
Period size: 129 Copynumber: 2.2 Consensus size: 129
40883614 ATTGTCAACG
* * *
40883624 CCGCTATAGATCAGGACCTTTAGCGGCGCTTTTTACACAAACACCGCTATAGATCATGATCTTTA
1 CCGCTATAGATCAAGACCTTTAGCGGCGCTTTTTACACAAACACCGCTATAGATCAAGACCTTTA
*** * * *
40883689 GCGGCGCTTTTTTTACAAACGCCGCTATAGATCATGACCTTTAGCGGCGCTTATTACACAAACA
66 GCGGCGCTTTTCCCACAAAAGCCACTATAGATCATGACCTTTAGCGACGCTTATTACACAAACA
* * *
40883753 CCGCTATAGATCAAGATCTTTAGCGGCGCTTTTTTCACAAACGCCGCTATAGATCAAGACCTTTA
1 CCGCTATAGATCAAGACCTTTAGCGGCGCTTTTTACACAAACACCGCTATAGATCAAGACCTTTA
* * * * *
40883818 GCGGCGCTTTTCCCACAAAAGCCACTATAGATCATGATCTTTAGCGACGCTTTTTCCATAAACG
66 GCGGCGCTTTTCCCACAAAAGCCACTATAGATCATGACCTTTAGCGACGCTTATTACACAAACA
** *
40883882 CTACTATA-ACTCAAGACCTTTAGCGACGCTT
1 CCGCTATAGA-TCAAGACCTTTAGCGGCGCTT
40883913 CAATTACAAA
Statistics
Matches: 138, Mismatches: 21, Indels: 2
0.86 0.13 0.01
Matches are distributed among these distances:
128 1 0.01
129 137 0.99
ACGTcount: A:0.27, C:0.27, G:0.17, T:0.29
Consensus pattern (129 bp):
CCGCTATAGATCAAGACCTTTAGCGGCGCTTTTTACACAAACACCGCTATAGATCAAGACCTTTA
GCGGCGCTTTTCCCACAAAAGCCACTATAGATCATGACCTTTAGCGACGCTTATTACACAAACA
Found at i:40889676 original size:16 final size:17
Alignment explanation
Indices: 40889640--40889681 Score: 68
Period size: 16 Copynumber: 2.5 Consensus size: 17
40889630 CACTATAATC
40889640 ATTATTTTAATATATTAA
1 ATTA-TTTAATATATTAA
40889658 ATTATTTAATATA-TAA
1 ATTATTTAATATATTAA
40889674 ATTATTTA
1 ATTATTTA
40889682 TAAATAATTT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
16 11 0.46
17 9 0.38
18 4 0.17
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (17 bp):
ATTATTTAATATATTAA
Found at i:40889804 original size:7 final size:7
Alignment explanation
Indices: 40889788--40889970 Score: 59
Period size: 7 Copynumber: 26.0 Consensus size: 7
40889778 ACTAATTAAT
40889788 CTAAACC
1 CTAAACC
*
40889795 CTAAATC
1 CTAAACC
40889802 CTAAACCC
1 CTAAA-CC
*
40889810 CT-AACT
1 CTAAACC
*
40889816 CTTAACC
1 CTAAACC
*
40889823 CTCAACCC
1 CT-AAACC
40889831 CT-AACC
1 CTAAACC
40889837 ACTAAACC
1 -CTAAACC
*
40889845 TTAAACC
1 CTAAACC
*
40889852 C-CAACC
1 CTAAACC
* *
40889858 CTTAA-T
1 CTAAACC
*
40889864 CTATAACA
1 CTA-AACC
*
40889872 TTAAACC
1 CTAAACC
* *
40889879 ATAAACT
1 CTAAACC
* *
40889886 ATAACCC
1 CTAAACC
40889893 CTAAACC
1 CTAAACC
*
40889900 CTAAACT
1 CTAAACC
*
40889907 GTAAACC
1 CTAAACC
* *
40889914 ATAACCC
1 CTAAACC
40889921 CTAAACTC
1 CTAAAC-C
* *
40889929 ATAATCC
1 CTAAACC
*
40889936 ATAAACC
1 CTAAACC
* *
40889943 TTAAACT
1 CTAAACC
*
40889950 CTATACC
1 CTAAACC
* *
40889957 ATATACC
1 CTAAACC
40889964 CTAAACC
1 CTAAACC
40889971 AAAAATTCTT
Statistics
Matches: 127, Mismatches: 40, Indels: 18
0.69 0.22 0.10
Matches are distributed among these distances:
6 13 0.10
7 95 0.75
8 19 0.15
ACGTcount: A:0.41, C:0.36, G:0.01, T:0.22
Consensus pattern (7 bp):
CTAAACC
Found at i:40889897 original size:21 final size:21
Alignment explanation
Indices: 40889873--40889969 Score: 95
Period size: 21 Copynumber: 4.6 Consensus size: 21
40889863 TCTATAACAT
* * *
40889873 TAAACCATAAACTATAACCCC
1 TAAACCCTAAACTATAAACCA
*
40889894 TAAACCCTAAACTGTAAACCA
1 TAAACCCTAAACTATAAACCA
* *
40889915 TAACCCCTAAACTCATAATCCA
1 TAAACCCTAAACT-ATAAACCA
* * *
40889937 TAAACCTTAAACTCTATACCA
1 TAAACCCTAAACTATAAACCA
*
40889958 TATACCCTAAAC
1 TAAACCCTAAAC
40889970 CAAAAATTCT
Statistics
Matches: 61, Mismatches: 14, Indels: 2
0.79 0.18 0.03
Matches are distributed among these distances:
21 44 0.72
22 17 0.28
ACGTcount: A:0.44, C:0.32, G:0.01, T:0.23
Consensus pattern (21 bp):
TAAACCCTAAACTATAAACCA
Found at i:40889948 original size:43 final size:42
Alignment explanation
Indices: 40889880--40889969 Score: 110
Period size: 43 Copynumber: 2.1 Consensus size: 42
40889870 CATTAAACCA
* *
40889880 TAAACTATAACCCCTAAACCCTAAACTGTAAACCATA-ACCCC
1 TAAACTATAACCCATAAACCCTAAACTCTAAACCATATA-CCC
* * *
40889922 TAAACTCATAATCCATAAACCTTAAACTCTATACCATATACCC
1 TAAACT-ATAACCCATAAACCCTAAACTCTAAACCATATACCC
40889965 TAAAC
1 TAAAC
40889970 CAAAAATTCT
Statistics
Matches: 41, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
42 6 0.15
43 34 0.83
44 1 0.02
ACGTcount: A:0.43, C:0.32, G:0.01, T:0.23
Consensus pattern (42 bp):
TAAACTATAACCCATAAACCCTAAACTCTAAACCATATACCC
Found at i:40890435 original size:40 final size:41
Alignment explanation
Indices: 40890379--40890490 Score: 181
Period size: 41 Copynumber: 2.8 Consensus size: 41
40890369 AAATGTTTTT
*
40890379 GCGGCGCTTTTACAAAAACGTCGCTAAAGCC-TGAGCATTA
1 GCGGCGCTTTTACAAAAACGCCGCTAAAGCCTTGAGCATTA
*
40890419 GCGGCGCTTTTTCAAAAACGCCGCTAAAGCCTTGAGCATTA
1 GCGGCGCTTTTACAAAAACGCCGCTAAAGCCTTGAGCATTA
* *
40890460 GCGGCGCTTCTACAAAAACACCGCTAAAGCC
1 GCGGCGCTTTTACAAAAACGCCGCTAAAGCC
40890491 CTGAAAGGTA
Statistics
Matches: 66, Mismatches: 5, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
40 29 0.44
41 37 0.56
ACGTcount: A:0.29, C:0.29, G:0.21, T:0.21
Consensus pattern (41 bp):
GCGGCGCTTTTACAAAAACGCCGCTAAAGCCTTGAGCATTA
Found at i:40890618 original size:40 final size:39
Alignment explanation
Indices: 40890556--40890678 Score: 119
Period size: 40 Copynumber: 3.1 Consensus size: 39
40890546 AAAAATGCCG
*
40890556 CTAATACTC-ATTATTAGCGGCGTTTTCCT-TAAAGCGCCA
1 CTAATACTCGATT-TTAGCGGCGTTTT-ATATAAAGCGCCA
* *
40890595 CTAATACTCGATCTTTAGTGGCGTTTTATATAAAGCGCCG
1 CTAATACTCGAT-TTTAGCGGCGTTTTATATAAAGCGCCA
* *
40890635 CTAATGCTCGATTTTTAGCGGC-TTTTTTATGCAAA-CGCCA
1 CTAATACTCGA-TTTTAGCGGCGTTTTATAT--AAAGCGCCA
40890675 CTAA
1 CTAA
40890679 AAATGCCGCT
Statistics
Matches: 71, Mismatches: 7, Indels: 11
0.80 0.08 0.12
Matches are distributed among these distances:
39 17 0.24
40 49 0.69
41 5 0.07
ACGTcount: A:0.25, C:0.23, G:0.17, T:0.35
Consensus pattern (39 bp):
CTAATACTCGATTTTAGCGGCGTTTTATATAAAGCGCCA
Found at i:40892699 original size:15 final size:15
Alignment explanation
Indices: 40892679--40892732 Score: 64
Period size: 12 Copynumber: 3.9 Consensus size: 15
40892669 TAAAAAGAAG
40892679 TAATAAATAAATAGA
1 TAATAAATAAATAGA
40892694 TAAT-AATAAA-A-A
1 TAATAAATAAATAGA
40892706 TAA-AAAT-AATAGA
1 TAATAAATAAATAGA
40892719 TAATAAAATAAATA
1 TAAT-AAATAAATA
40892733 AATGCTCGAT
Statistics
Matches: 33, Mismatches: 0, Indels: 11
0.75 0.00 0.25
Matches are distributed among these distances:
11 2 0.06
12 8 0.24
13 5 0.15
14 6 0.18
15 8 0.24
16 4 0.12
ACGTcount: A:0.70, C:0.00, G:0.04, T:0.26
Consensus pattern (15 bp):
TAATAAATAAATAGA
Found at i:40892716 original size:25 final size:26
Alignment explanation
Indices: 40892683--40892734 Score: 81
Period size: 25 Copynumber: 2.0 Consensus size: 26
40892673 AAGAAGTAAT
40892683 AAATAAATAGATAATAATAA-AAATAA
1 AAATAAATAGATAATAA-AATAAATAA
40892709 AAAT-AATAGATAATAAAATAAATAA
1 AAATAAATAGATAATAAAATAAATAA
40892734 A
1 A
40892735 TGCTCGATGA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
24 2 0.08
25 19 0.76
26 4 0.16
ACGTcount: A:0.73, C:0.00, G:0.04, T:0.23
Consensus pattern (26 bp):
AAATAAATAGATAATAAAATAAATAA
Found at i:40892721 original size:22 final size:21
Alignment explanation
Indices: 40892687--40892730 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 21
40892677 AGTAATAAAT
40892687 AAATAGATAATAATAAAAATAA
1 AAATAGATAATAAT-AAAATAA
40892709 AAATA-ATAGATAATAAAATAA
1 AAATAGATA-ATAATAAAATAA
40892730 A
1 A
40892731 TAAATGCTCG
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
21 11 0.52
22 10 0.48
ACGTcount: A:0.73, C:0.00, G:0.05, T:0.23
Consensus pattern (21 bp):
AAATAGATAATAATAAAATAA
Found at i:40894509 original size:96 final size:96
Alignment explanation
Indices: 40894371--40895205 Score: 1058
Period size: 96 Copynumber: 8.9 Consensus size: 96
40894361 AGTTTTAATA
* * * * *
40894371 TGCTCCATTGCAACTTTAGGGAGATAAGGTTTGTAATTTGTAGCTTTAATCTGTTCCACTGTAAC
1 TGCTCCACTGCAACTTCAGGGAGATAAGATTTGTAACTTGTAGCTTTAATCTGTTCCACTGCAAC
* *
40894436 TTCAGGGAAATAAGATTCGTTATCTTCAATC
66 TTTAGGGAAATAAGATTCGCTATCTTCAATC
* * * *
40894467 TGCTTCGCTGCAACTTCAGGGAGATAAGATTTGTAATTTGTAGCTTTAATCTGTTCCACTGTAAC
1 TGCTCCACTGCAACTTCAGGGAGATAAGATTTGTAACTTGTAGCTTTAATCTGTTCCACTGCAAC
* * *
40894532 TTTAAGGAAATAAGATTCGTTATTTTCAATC
66 TTTAGGGAAATAAGATTCGCTATCTTCAATC
* * * * * *
40894563 AGCTCCACTGTAATTTCAGGGAGATAAGATTTGTAACTTGTAACTTTAATCTGGTCCACTGTAAC
1 TGCTCCACTGCAACTTCAGGGAGATAAGATTTGTAACTTGTAGCTTTAATCTGTTCCACTGCAAC
* *
40894628 TTTAAGGAAATAAGATTCGTTATCTTCAAT-
66 TTTAGGGAAATAAGATTCGCTATCTTCAATC
* * * *
40894658 TAGCTCCACTGCAATTTCAGAGAGATAAGATTTGTAACTTGTGGCTTTAATCTGTTCCACTGTAA
1 T-GCTCCACTGCAACTTCAGGGAGATAAGATTTGTAACTTGTAGCTTTAATCTGTTCCACTGCAA
* *
40894723 CTTTAGGGAAATAAGATTCACTATTTTCAATC
65 CTTTAGGGAAATAAGATTCGCTATCTTCAATC
* *
40894755 TGCTCCACTGCAACTTTAGAGAGATAAGATTTGTAACTTGTAGCTTTAATCTGTTCCACTGCAAC
1 TGCTCCACTGCAACTTCAGGGAGATAAGATTTGTAACTTGTAGCTTTAATCTGTTCCACTGCAAC
* *
40894820 TTTAGGGAAATAAGATTCACTATTTTCAATC
66 TTTAGGGAAATAAGATTCGCTATCTTCAATC
* *
40894851 TGCTCCACTGCAACTTTAGAGAGATAAGATTTGTAACTTGTAGCTTTAATCTGTTCCACTGCAAC
1 TGCTCCACTGCAACTTCAGGGAGATAAGATTTGTAACTTGTAGCTTTAATCTGTTCCACTGCAAC
* *
40894916 TTTAGGGAAATAAGATTCACTATTTTCAATC
66 TTTAGGGAAATAAGATTCGCTATCTTCAATC
* * *
40894947 TGCTCCACTGCAACTTTAGAGAGATAAGATTTGTAACTTGTAGCTTTAATCTATTCCACTGCAAC
1 TGCTCCACTGCAACTTCAGGGAGATAAGATTTGTAACTTGTAGCTTTAATCTGTTCCACTGCAAC
* * *
40895012 TTCAAGGAAATAAGATTCGCTATCTTTAATC
66 TTTAGGGAAATAAGATTCGCTATCTTCAATC
* * * *
40895043 TGCTCCATTGTAACTTC-TGG-G---AGA----TAACTTGTAGATTTAATCTG-TCCTACTGCAA
1 TGCTCCACTGCAACTTCAGGGAGATAAGATTTGTAACTTGTAGCTTTAATCTGTTCC-ACTGCAA
40895098 CTTTAGGGAAATAAGATTCGCTATCTTCAATC
65 CTTTAGGGAAATAAGATTCGCTATCTTCAATC
* * * *
40895130 TACTCCACTGTAACTTCAGGGAGATAAAATTTG-----TG--GCTTTAATCTGCTCCACTGCAAC
1 TGCTCCACTGCAACTTCAGGGAGATAAGATTTGTAACTTGTAGCTTTAATCTGTTCCACTGCAAC
* *
40895188 TTTAAGGAGATAAGATTC
66 TTTAGGGAAATAAGATTC
40895206 ACCACGGTGA
Statistics
Matches: 672, Mismatches: 54, Indels: 33
0.89 0.07 0.04
Matches are distributed among these distances:
86 3 0.00
87 69 0.10
88 2 0.00
89 35 0.05
90 3 0.00
91 5 0.01
92 2 0.00
94 1 0.00
95 1 0.00
96 550 0.82
97 1 0.00
ACGTcount: A:0.30, C:0.18, G:0.17, T:0.36
Consensus pattern (96 bp):
TGCTCCACTGCAACTTCAGGGAGATAAGATTTGTAACTTGTAGCTTTAATCTGTTCCACTGCAAC
TTTAGGGAAATAAGATTCGCTATCTTCAATC
Found at i:40895130 original size:87 final size:86
Alignment explanation
Indices: 40894980--40895205 Score: 308
Period size: 87 Copynumber: 2.6 Consensus size: 86
40894970 ATAAGATTTG
* * * *
40894980 TAACTTGTAGCTTTAATCTATTCCACTGCAACTTCAAGGAAATAAGATTCGCTATCTTTAATCTG
1 TAACTTGTAGCTTTAATCT-GTCCACTGCAACTTTAAGGAAATAAGATTCGCTATCTTCAATCTA
* *
40895045 CTCCATTGTAACTTCTGGGAGA
65 CTCCACTGTAACTTCAGGGAGA
* *
40895067 TAACTTGTAGATTTAATCTGTCCTACTGCAACTTTAGGGAAATAAGATTCGCTATCTTCAATCTA
1 TAACTTGTAGCTTTAATCTGTCC-ACTGCAACTTTAAGGAAATAAGATTCGCTATCTTCAATCTA
40895132 CTCCACTGTAACTTCAGGGAGA
65 CTCCACTGTAACTTCAGGGAGA
* * *
40895154 TAAAATTTGTGGCTTTAATCTGCTCCACTGCAACTTTAAGGAGATAAGATTC
1 T--AACTTGTAGCTTTAATCTG-TCCACTGCAACTTTAAGGAAATAAGATTC
40895206 ACCACGGTGA
Statistics
Matches: 122, Mismatches: 13, Indels: 6
0.87 0.09 0.04
Matches are distributed among these distances:
86 3 0.02
87 76 0.62
89 40 0.33
90 3 0.02
ACGTcount: A:0.30, C:0.20, G:0.16, T:0.35
Consensus pattern (86 bp):
TAACTTGTAGCTTTAATCTGTCCACTGCAACTTTAAGGAAATAAGATTCGCTATCTTCAATCTAC
TCCACTGTAACTTCAGGGAGA
Found at i:40899089 original size:19 final size:21
Alignment explanation
Indices: 40899065--40899109 Score: 62
Period size: 19 Copynumber: 2.3 Consensus size: 21
40899055 TTATAGAATT
40899065 TAATGCAT-ATG-ATGAAATG
1 TAATGCATGATGTATGAAATG
40899084 TAATGC-TGATGTATGAAATG
1 TAATGCATGATGTATGAAATG
40899104 -AATGCA
1 TAATGCA
40899110 AAAAGAGGCA
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
18 1 0.04
19 14 0.61
20 8 0.35
ACGTcount: A:0.40, C:0.07, G:0.22, T:0.31
Consensus pattern (21 bp):
TAATGCATGATGTATGAAATG
Found at i:40899922 original size:21 final size:21
Alignment explanation
Indices: 40899896--40899939 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
40899886 TTTCTGCTTC
40899896 CAACTATTCTATCTTTTTCCT
1 CAACTATTCTATCTTTTTCCT
40899917 CAACTATTCTATCTTTTTCCT
1 CAACTATTCTATCTTTTTCCT
40899938 CA
1 CA
40899940 GTTCTGAATT
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:0.20, C:0.30, G:0.00, T:0.50
Consensus pattern (21 bp):
CAACTATTCTATCTTTTTCCT
Found at i:40902020 original size:391 final size:391
Alignment explanation
Indices: 40901285--40902069 Score: 1302
Period size: 391 Copynumber: 2.0 Consensus size: 391
40901275 CTTTATCAAG
* * * *
40901285 GAATTCTTTTTCCATAGCAAGCTCTCTATTTAGCACTAAATGTGAATCAACACCCTTTTCGATAA
1 GAATTCATTTTCCATAGCAAACTCTCTATTTAGCACTAAACGTGAATCAACACCCTTTCCGATAA
* *
40901350 TGAAAATGCAATGCAATCACAACCAAAACAAAACGAAACAAGTCAATATATTTCATACAAATCTA
66 TGAAAATACAATGCAATCACAACCAAAACAAAACGAAACAAGTCAATATATTTCATAAAAATCTA
40901415 GAATTCAAAGCAAGAAATAAGAAATAAATAGAGCAACTATTCGGGTGACCACTAGGGGTTTAGTA
131 GAATTCAAAGCAAGAAATAAGAAATAAATAGAGCAACTATTCGGGTGACCACTAGGGGTTTAGTA
* *
40901480 TGGCTCTACCTAGGATAGGTTCTTAGGGCTCATTATATGTGGTTCGGTTCTAAAGTAAGGGTACC
196 TGGCTCTACCTAGGATAGGTTATTAGGGCTCATTATATGTGGTTCGGTTCTAAAGTAAAGGTACC
* * * *
40901545 TGAACCGGCAGATTTCTCGATCTTCACCGATTATAGGCTCATACGGTACCGAGTTTAGCTCAGAG
261 TGAACCAGCAGATTCCTCGATCCTCACCAATTATAGGCTCATACGGTACCGAGTTTAGCTCAGAG
*
40901610 GAATACATTTCCCTATGGCTATAC-GAAGATGAAAATCTCACGAAAACATAGGTATAAATGTACC
326 GAATACATTTCCCTATGGCTATACAG-AGATGAAAATCTCACGAAAACATAGGTACAAATGTACC
*
40901674 TT
390 CT
* * * *
40901676 GAATTCATTTTCCATGGCAAACTTTCTATTTAGCACTGAACGTGAATCAACACCCTTTCCTATAA
1 GAATTCATTTTCCATAGCAAACTCTCTATTTAGCACTAAACGTGAATCAACACCCTTTCCGATAA
* *
40901741 TGAAAATACAATGCAATCACAACCAAAACAAAATGAAACAAGTCAGTATATTTCATAAAAATCTA
66 TGAAAATACAATGCAATCACAACCAAAACAAAACGAAACAAGTCAATATATTTCATAAAAATCTA
* * *
40901806 GAATTCAAAGCAAGAAATAAGAAATAAATAGAGCACCTATTCTGGTGACCACTAGGGGTTTGGTA
131 GAATTCAAAGCAAGAAATAAGAAATAAATAGAGCAACTATTCGGGTGACCACTAGGGGTTTAGTA
*
40901871 TGGCTCTACTTAGGATAGGTTATTAGGGCTCATTATATGTGGTTCGGTTCTAAAGTAAAGGTACC
196 TGGCTCTACCTAGGATAGGTTATTAGGGCTCATTATATGTGGTTCGGTTCTAAAGTAAAGGTACC
*
40901936 TGAACCAGCAGATTCCTCGATCCTCACCAATTATAGGCTCATACGGTACCGAGTTTAGCTCAGGG
261 TGAACCAGCAGATTCCTCGATCCTCACCAATTATAGGCTCATACGGTACCGAGTTTAGCTCAGAG
* * *
40902001 GAATACATTTCCTTATGGCTATACAGAGATGAAAATCTCACGAAGACATAGGTACAGATGTACCC
326 GAATACATTTCCCTATGGCTATACAGAGATGAAAATCTCACGAAAACATAGGTACAAATGTACCC
40902066 T
391 T
40902067 GAA
1 GAA
40902070 AGAGATCCAC
Statistics
Matches: 365, Mismatches: 28, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
391 364 1.00
392 1 0.00
ACGTcount: A:0.35, C:0.19, G:0.18, T:0.27
Consensus pattern (391 bp):
GAATTCATTTTCCATAGCAAACTCTCTATTTAGCACTAAACGTGAATCAACACCCTTTCCGATAA
TGAAAATACAATGCAATCACAACCAAAACAAAACGAAACAAGTCAATATATTTCATAAAAATCTA
GAATTCAAAGCAAGAAATAAGAAATAAATAGAGCAACTATTCGGGTGACCACTAGGGGTTTAGTA
TGGCTCTACCTAGGATAGGTTATTAGGGCTCATTATATGTGGTTCGGTTCTAAAGTAAAGGTACC
TGAACCAGCAGATTCCTCGATCCTCACCAATTATAGGCTCATACGGTACCGAGTTTAGCTCAGAG
GAATACATTTCCCTATGGCTATACAGAGATGAAAATCTCACGAAAACATAGGTACAAATGTACCC
T
Found at i:40903395 original size:4 final size:4
Alignment explanation
Indices: 40903388--40903458 Score: 58
Period size: 4 Copynumber: 17.8 Consensus size: 4
40903378 AAAAAGGAGT
* * *
40903388 AATA AATA AATA ACTA AATA AATA AATA GAT- AAT- AATGAA AATA AAAA
1 AATA AATA AATA AATA AATA AATA AATA AATA AATA AAT--A AATA AATA
*
40903436 AATA GAT- AATAA AATA AATA AAT
1 AATA AATA AAT-A AATA AATA AAT
40903459 GCCTGATGAA
Statistics
Matches: 54, Mismatches: 8, Indels: 10
0.75 0.11 0.14
Matches are distributed among these distances:
3 7 0.13
4 41 0.76
5 3 0.06
6 3 0.06
ACGTcount: A:0.70, C:0.01, G:0.04, T:0.24
Consensus pattern (4 bp):
AATA
Found at i:40903413 original size:20 final size:19
Alignment explanation
Indices: 40903388--40903458 Score: 81
Period size: 20 Copynumber: 3.6 Consensus size: 19
40903378 AAAAAGGAGT
40903388 AATAAATAAATAACTAA-ATA
1 AATAAATAAATAA-TAATA-A
*
40903408 AATAAATAGATAATAATGAA
1 AATAAATAAATAATAAT-AA
*
40903428 AATAAAAAAATAGATAATAA
1 AATAAATAAATA-ATAATAA
40903448 AATAAATAAAT
1 AATAAATAAAT
40903459 GCCTGATGAA
Statistics
Matches: 44, Mismatches: 4, Indels: 6
0.81 0.07 0.11
Matches are distributed among these distances:
19 3 0.07
20 35 0.80
21 6 0.14
ACGTcount: A:0.70, C:0.01, G:0.04, T:0.24
Consensus pattern (19 bp):
AATAAATAAATAATAATAA
Found at i:40903415 original size:24 final size:23
Alignment explanation
Indices: 40903388--40903458 Score: 67
Period size: 24 Copynumber: 3.1 Consensus size: 23
40903378 AAAAAGGAGT
40903388 AATAAATAAATAACTAAATAAATA
1 AATAAATAAATAA-TAAATAAATA
* *
40903412 AATAGAT-AATAAT-GA-AAATA
1 AATAAATAAATAATAAATAAATA
* *
40903432 AAAAAATAGATAATAAAATAAATA
1 AATAAATAAATAAT-AAATAAATA
40903456 AAT
1 AAT
40903459 GCCTGATGAA
Statistics
Matches: 36, Mismatches: 7, Indels: 8
0.71 0.14 0.16
Matches are distributed among these distances:
20 10 0.28
21 6 0.17
22 1 0.03
23 6 0.17
24 13 0.36
ACGTcount: A:0.70, C:0.01, G:0.04, T:0.24
Consensus pattern (23 bp):
AATAAATAAATAATAAATAAATA
Found at i:40912235 original size:39 final size:39
Alignment explanation
Indices: 40912191--40912318 Score: 184
Period size: 39 Copynumber: 3.3 Consensus size: 39
40912181 TATGAGATTG
40912191 AAAATATCCGGACATGAGGTCCGCAGGCTATATGCTGGA
1 AAAATATCCGGACATGAGGTCCGCAGGCTATATGCTGGA
* *
40912230 AAAATATCCGGACATGAGATCCGCAGGCTATATGCTAGA
1 AAAATATCCGGACATGAGGTCCGCAGGCTATATGCTGGA
* * * ** *
40912269 AATATATCCGGACTTGAGGTCCGTAGGCTACGTGTTGGA
1 AAAATATCCGGACATGAGGTCCGCAGGCTATATGCTGGA
40912308 AAAATATCCGG
1 AAAATATCCGG
40912319 GTTAAAGACC
Statistics
Matches: 78, Mismatches: 11, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
39 78 1.00
ACGTcount: A:0.31, C:0.20, G:0.27, T:0.23
Consensus pattern (39 bp):
AAAATATCCGGACATGAGGTCCGCAGGCTATATGCTGGA
Found at i:40912332 original size:78 final size:76
Alignment explanation
Indices: 40912190--40912344 Score: 186
Period size: 78 Copynumber: 2.0 Consensus size: 76
40912180 GTATGAGATT
* * *
40912190 GAAAATATCCGGACATGAGGTCCGCAGGCTATATGCTGGAAAAATATCCGGACATGAGATCCGCA
1 GAAAATATCCGGACATGAGGTCCGCAGGCTACATGCTGGAAAAATATCCGGACATAAGACCCGCA
*
40912255 GGCTATATGCTA
66 GGCT-TACGCTA
* * * * **
40912267 GAAATATATCCGGACTTGAGGTCCGTAGGCTACGTGTTGGAAAAATATCCGG-GTTAAAGACCCG
1 GAAA-ATATCCGGACATGAGGTCCGCAGGCTACATGCTGGAAAAATATCCGGACAT-AAGACCCG
40912331 CAGGCTTACGCTA
64 CAGGCTTACGCTA
40912344 G
1 G
40912345 TAATGTATTC
Statistics
Matches: 66, Mismatches: 10, Indels: 4
0.82 0.12 0.05
Matches are distributed among these distances:
77 12 0.18
78 54 0.82
ACGTcount: A:0.30, C:0.21, G:0.27, T:0.22
Consensus pattern (76 bp):
GAAAATATCCGGACATGAGGTCCGCAGGCTACATGCTGGAAAAATATCCGGACATAAGACCCGCA
GGCTTACGCTA
Found at i:40921116 original size:19 final size:22
Alignment explanation
Indices: 40921077--40921117 Score: 61
Period size: 19 Copynumber: 2.0 Consensus size: 22
40921067 CTTATTTCTA
40921077 TTATTACTCTTAGTATATTATT
1 TTATTACTCTTAGTATATTATT
40921099 TTATT-CTCTTA-T-TATTATT
1 TTATTACTCTTAGTATATTATT
40921118 GCTTTCTTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 7 0.37
20 1 0.05
21 6 0.32
22 5 0.26
ACGTcount: A:0.24, C:0.10, G:0.02, T:0.63
Consensus pattern (22 bp):
TTATTACTCTTAGTATATTATT
Found at i:40922655 original size:25 final size:25
Alignment explanation
Indices: 40922627--40922684 Score: 98
Period size: 25 Copynumber: 2.3 Consensus size: 25
40922617 CTTTTCATTC
*
40922627 CCATATTCTCTGTTTCTTCTTGCTA
1 CCATATTCTCTCTTTCTTCTTGCTA
*
40922652 CCATATTCTTTCTTTCTTCTTGCTA
1 CCATATTCTCTCTTTCTTCTTGCTA
40922677 CCATATTC
1 CCATATTC
40922685 ACAGTTTGTA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
25 31 1.00
ACGTcount: A:0.14, C:0.29, G:0.05, T:0.52
Consensus pattern (25 bp):
CCATATTCTCTCTTTCTTCTTGCTA
Found at i:40927282 original size:32 final size:32
Alignment explanation
Indices: 40927246--40927337 Score: 159
Period size: 32 Copynumber: 2.9 Consensus size: 32
40927236 ACTATGCTAG
40927246 TTTTTTATATGTAAAACTAATGTATGATCTAC
1 TTTTTTATATGTAAAACTAATGTATGATCTAC
*
40927278 TTTTTTATATGCAAAACTAATGTATGATCTAC
1 TTTTTTATATGTAAAACTAATGTATGATCTAC
40927310 TTTTTTATATGT-AAACTTAATGTATGAT
1 TTTTTTATATGTAAAAC-TAATGTATGAT
40927338 ATTTTTTATG
Statistics
Matches: 57, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
31 4 0.07
32 53 0.93
ACGTcount: A:0.34, C:0.09, G:0.10, T:0.48
Consensus pattern (32 bp):
TTTTTTATATGTAAAACTAATGTATGATCTAC
Found at i:40929397 original size:21 final size:21
Alignment explanation
Indices: 40929345--40929399 Score: 74
Period size: 21 Copynumber: 2.6 Consensus size: 21
40929335 ACTGCTGTTT
** *
40929345 CTAATCTCATAGCTACAGTAT
1 CTAATCTCACCGCTACAGTAA
*
40929366 CCAATCTCACCGCTACAGTAA
1 CTAATCTCACCGCTACAGTAA
40929387 CTAATCTCACCGC
1 CTAATCTCACCGC
40929400 CACCGCTGTT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.31, C:0.35, G:0.09, T:0.25
Consensus pattern (21 bp):
CTAATCTCACCGCTACAGTAA
Found at i:40930003 original size:17 final size:18
Alignment explanation
Indices: 40929976--40930010 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
40929966 CATTGAGTCC
40929976 GATTATTTTTATGTTTAT
1 GATTATTTTTATGTTTAT
*
40929994 GATT-TTTTTATTTTTAT
1 GATTATTTTTATGTTTAT
40930011 CTTGTATTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 12 0.75
18 4 0.25
ACGTcount: A:0.20, C:0.00, G:0.09, T:0.71
Consensus pattern (18 bp):
GATTATTTTTATGTTTAT
Found at i:40930044 original size:7 final size:6
Alignment explanation
Indices: 40929978--40930058 Score: 76
Period size: 6 Copynumber: 13.7 Consensus size: 6
40929968 TTGAGTCCGA
* ** *
40929978 TTATTT TTATGT TTATGA TT-TTT TTATTT TTATCTT GTA-TT TTATTT
1 TTATTT TTATTT TTATTT TTATTT TTATTT TTAT-TT TTATTT TTATTT
* * *
40930025 TCATTT TTATTT TTAGTT TTATTT TTCTTT TTAT
1 TTATTT TTATTT TTATTT TTATTT TTATTT TTAT
40930059 GTCTATTTTG
Statistics
Matches: 60, Mismatches: 12, Indels: 6
0.77 0.15 0.08
Matches are distributed among these distances:
5 7 0.12
6 49 0.82
7 4 0.07
ACGTcount: A:0.16, C:0.04, G:0.05, T:0.75
Consensus pattern (6 bp):
TTATTT
Found at i:40931925 original size:30 final size:30
Alignment explanation
Indices: 40931877--40931934 Score: 73
Period size: 30 Copynumber: 1.9 Consensus size: 30
40931867 AAGATGAATT
* *
40931877 CCACACGGGCTGAGCACACGCCCGTGTGAG
1 CCACACGGGCTGAGCACACACCCATGTGAG
*
40931907 CCACATGGGCTG-GCCACACACCCATGTG
1 CCACACGGGCTGAG-CACACACCCATGTG
40931935 GCAGCCCGTG
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 1 0.04
30 23 0.96
ACGTcount: A:0.21, C:0.38, G:0.29, T:0.12
Consensus pattern (30 bp):
CCACACGGGCTGAGCACACACCCATGTGAG
Found at i:40935159 original size:22 final size:20
Alignment explanation
Indices: 40935128--40935167 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
40935118 ATATAAGATC
40935128 TATATCTATCTCTGAATTTGCA
1 TATATCTA--TCTGAATTTGCA
*
40935150 TATATGTATCTGAATTTG
1 TATATCTATCTGAATTTG
40935168 TATTTGTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 10 0.59
22 7 0.41
ACGTcount: A:0.28, C:0.12, G:0.12, T:0.47
Consensus pattern (20 bp):
TATATCTATCTGAATTTGCA
Found at i:40944891 original size:18 final size:19
Alignment explanation
Indices: 40944843--40944893 Score: 56
Period size: 17 Copynumber: 2.9 Consensus size: 19
40944833 ATATATTAAT
*
40944843 TTTTTATTT-T-TAATTCA
1 TTTTTATTTATATAAATCA
*
40944860 TTTTTAATTA-ATAAATCA
1 TTTTTATTTATATAAATCA
40944878 -TTTTATTTATATAAAT
1 TTTTTATTTATATAAAT
40944894 AAAATAATAA
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
17 16 0.57
18 12 0.43
ACGTcount: A:0.35, C:0.04, G:0.00, T:0.61
Consensus pattern (19 bp):
TTTTTATTTATATAAATCA
Found at i:40945056 original size:87 final size:87
Alignment explanation
Indices: 40944877--40945057 Score: 199
Period size: 87 Copynumber: 2.1 Consensus size: 87
40944867 TTAATAAATC
* *
40944877 ATTTTATTTATATAAATAAAATAATAAATATGTAATTATATATAAAATTATATATTATTGTGTTA
1 ATTTTATTTATATAAATAAAATAATAAATATATAATTATATATAAAATTATATATTATTATGTTA
* *
40944942 AAAATACTTTTTAATTAATATTT
66 AAAATA-TTGTTAAATAATATTT
* * * *
40944965 -TTTTATTTGTATAAATAAATTAATAATTATATAATTATATAATAAAA-TATATAATTTTTATGT
1 ATTTTATTTATATAAATAAAATAATAAATATATAATTATAT-ATAAAATTATAT-ATTATTATGT
* **
40945028 TTATCAT-TGTGTTAAAT-ATATTT
64 TAAAAATAT-TGTTAAATAATATTT
40945051 ATTTTAT
1 ATTTTAT
40945058 AAAAAAAATT
Statistics
Matches: 78, Mismatches: 11, Indels: 9
0.80 0.11 0.09
Matches are distributed among these distances:
86 7 0.09
87 53 0.68
88 18 0.23
ACGTcount: A:0.44, C:0.01, G:0.04, T:0.51
Consensus pattern (87 bp):
ATTTTATTTATATAAATAAAATAATAAATATATAATTATATATAAAATTATATATTATTATGTTA
AAAATATTGTTAAATAATATTT
Found at i:40945069 original size:17 final size:18
Alignment explanation
Indices: 40945049--40945084 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
40945039 TTAAATATAT
40945049 TTATTT-TATAAAAAAAA
1 TTATTTATATAAAAAAAA
*
40945066 TTATTTATATAATAAAAA
1 TTATTTATATAAAAAAAA
40945084 T
1 T
40945085 AAGGGCCTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 6 0.35
18 11 0.65
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (18 bp):
TTATTTATATAAAAAAAA
Found at i:40945070 original size:21 final size:22
Alignment explanation
Indices: 40945041--40945083 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
40945031 TCATTGTGTT
* *
40945041 AAATATATTTATTTTATAAAAA
1 AAATATATTTATATAATAAAAA
40945063 AAAT-TATTTATATAATAAAAA
1 AAATATATTTATATAATAAAAA
40945084 TAAGGGCCTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 15 0.79
22 4 0.21
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (22 bp):
AAATATATTTATATAATAAAAA
Found at i:40945697 original size:16 final size:17
Alignment explanation
Indices: 40945676--40945707 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
40945666 ATGCCACGTG
40945676 AATTATTT-ATATTTTA
1 AATTATTTAATATTTTA
40945692 AATTATTTAATATTTT
1 AATTATTTAATATTTT
40945708 TTAAAATTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (17 bp):
AATTATTTAATATTTTA
Found at i:40952843 original size:21 final size:21
Alignment explanation
Indices: 40952817--40952856 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
40952807 TAAAAAATAG
* *
40952817 TTTTTTGACTTTTTTGTTATT
1 TTTTTTCACTATTTTGTTATT
40952838 TTTTTTCACTATTTTGTTA
1 TTTTTTCACTATTTTGTTA
40952857 CCATTTCATT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.12, C:0.07, G:0.07, T:0.72
Consensus pattern (21 bp):
TTTTTTCACTATTTTGTTATT
Found at i:40952929 original size:23 final size:22
Alignment explanation
Indices: 40952847--40952933 Score: 75
Period size: 22 Copynumber: 3.9 Consensus size: 22
40952837 TTTTTTTCAC
* * *
40952847 TATTTTGTTACCATTTCATTAT
1 TATTTTGTTACTATTTTATTGT
** *
40952869 TATAATGTTACTATTTTGTTGT
1 TATTTTGTTACTATTTTATTGT
* * *
40952891 TATTGTATAACTTATTTTATTGT
1 TATTTTGTTAC-TATTTTATTGT
40952914 TAATTTTGTTACTATTTTAT
1 T-ATTTTGTTACTATTTTAT
40952934 AGGCATTTAC
Statistics
Matches: 49, Mismatches: 14, Indels: 3
0.74 0.21 0.05
Matches are distributed among these distances:
22 23 0.47
23 19 0.39
24 7 0.14
ACGTcount: A:0.24, C:0.07, G:0.08, T:0.61
Consensus pattern (22 bp):
TATTTTGTTACTATTTTATTGT
Found at i:40953047 original size:18 final size:18
Alignment explanation
Indices: 40953026--40953077 Score: 54
Period size: 18 Copynumber: 2.9 Consensus size: 18
40953016 GAAATATTTA
*
40953026 TTTTAATAT-TTTTAGTAT
1 TTTTAATATATTATA-TAT
*
40953044 TTTTGATATATTATATAT
1 TTTTAATATATTATATAT
*
40953062 TTTTAA-AAATTATATA
1 TTTTAATATATTATATA
40953078 AAAAATTAAT
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
17 9 0.31
18 16 0.55
19 4 0.14
ACGTcount: A:0.37, C:0.00, G:0.04, T:0.60
Consensus pattern (18 bp):
TTTTAATATATTATATAT
Found at i:40954195 original size:18 final size:20
Alignment explanation
Indices: 40954169--40954211 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
40954159 AAACATAATT
40954169 TTTTATTTAA-A-AAATATA
1 TTTTATTTAATATAAATATA
* *
40954187 TTTTCTTTAATATATATATA
1 TTTTATTTAATATAAATATA
40954207 TTTTA
1 TTTTA
40954212 AAAAATCTCA
Statistics
Matches: 20, Mismatches: 3, Indels: 2
0.80 0.12 0.08
Matches are distributed among these distances:
18 9 0.45
19 1 0.05
20 10 0.50
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (20 bp):
TTTTATTTAATATAAATATA
Found at i:40954789 original size:138 final size:137
Alignment explanation
Indices: 40954548--40954795 Score: 331
Period size: 138 Copynumber: 1.8 Consensus size: 137
40954538 AATAGTGTAA
* * *
40954548 TGTACATTCTTTTATTAATGATATGCAACCTAAACCTTAAACGTGAAACTAATTTTATGGTAGAA
1 TGTACATTCTTTTATTAATGATATGCAACCTAAACCTTAAACGTGAAACTAACTCTATGATAGAA
*
40954613 TATAATATATACAATTAACATTATGAAATTAAGATAGATTATTAAAACATGTATCCATGTATATC
66 TATAATATATACAATTAACATTATGAAATGAAGATAGATTATTAAAACATGTATCCATGTATATC
40954678 ACTTTGT
131 ACTTTGT
* * *
40954685 TGTACATT-TTTATATTAATGATATGTAAGCTTAAACAC-TAAACGTGTAACTAACTCTATGATA
1 TGTACATTCTTT-TATTAATGATATGCAA-CCTAAAC-CTTAAACGTGAAACTAACTCTATGATA
* * ** *
40954748 GATTATAATATATATAATTAGTATTAT-ATAATGAAGTTAGATTATTAA
63 GAATATAATATATACAATTAACATTATGA-AATGAAGATAGATTATTAA
40954796 TTATATGTAA
Statistics
Matches: 95, Mismatches: 12, Indels: 7
0.83 0.11 0.06
Matches are distributed among these distances:
136 3 0.03
137 24 0.25
138 67 0.71
139 1 0.01
ACGTcount: A:0.41, C:0.10, G:0.10, T:0.39
Consensus pattern (137 bp):
TGTACATTCTTTTATTAATGATATGCAACCTAAACCTTAAACGTGAAACTAACTCTATGATAGAA
TATAATATATACAATTAACATTATGAAATGAAGATAGATTATTAAAACATGTATCCATGTATATC
ACTTTGT
Found at i:40954793 original size:21 final size:20
Alignment explanation
Indices: 40954746--40954794 Score: 50
Period size: 18 Copynumber: 2.5 Consensus size: 20
40954736 AACTCTATGA
*
40954746 TAGATTATAATATATATAAT
1 TAGATTATTATATATATAAT
40954766 TAG--TATTATATA-ATGAAGT
1 TAGATTATTATATATAT-AA-T
40954785 TAGATTATTA
1 TAGATTATTA
40954795 ATTATATGTA
Statistics
Matches: 24, Mismatches: 1, Indels: 7
0.75 0.03 0.22
Matches are distributed among these distances:
17 2 0.08
18 10 0.42
19 4 0.17
20 3 0.12
21 5 0.21
ACGTcount: A:0.45, C:0.00, G:0.10, T:0.45
Consensus pattern (20 bp):
TAGATTATTATATATATAAT
Found at i:40955370 original size:23 final size:23
Alignment explanation
Indices: 40955340--40955383 Score: 88
Period size: 23 Copynumber: 1.9 Consensus size: 23
40955330 CTCCACTACC
40955340 TTAGCTTGCCAAAACTAAGGACT
1 TTAGCTTGCCAAAACTAAGGACT
40955363 TTAGCTTGCCAAAACTAAGGA
1 TTAGCTTGCCAAAACTAAGGA
40955384 TTTCTCAAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.36, C:0.20, G:0.18, T:0.25
Consensus pattern (23 bp):
TTAGCTTGCCAAAACTAAGGACT
Found at i:40959697 original size:11 final size:11
Alignment explanation
Indices: 40959677--40959718 Score: 52
Period size: 11 Copynumber: 4.0 Consensus size: 11
40959667 AAAAGCAAGC
40959677 GTTTTCATTAA
1 GTTTTCATTAA
* *
40959688 GTTTTAATTAT
1 GTTTTCATTAA
40959699 GTTTTCA-TAA
1 GTTTTCATTAA
40959709 GTTTTC-TTAA
1 GTTTTCATTAA
40959719 AGTTAATAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
10 11 0.42
11 15 0.58
ACGTcount: A:0.26, C:0.07, G:0.10, T:0.57
Consensus pattern (11 bp):
GTTTTCATTAA
Found at i:40962147 original size:26 final size:26
Alignment explanation
Indices: 40962117--40962168 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
40962107 TCACAGATAG
40962117 GCCATACCAATTTTAAGTTCATTCTC
1 GCCATACCAATTTTAAGTTCATTCTC
40962143 GCCATACCAATTTTAAGTTCATTCTC
1 GCCATACCAATTTTAAGTTCATTCTC
40962169 ACCTTGATGG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.27, C:0.27, G:0.08, T:0.38
Consensus pattern (26 bp):
GCCATACCAATTTTAAGTTCATTCTC
Found at i:40967354 original size:21 final size:22
Alignment explanation
Indices: 40967311--40967354 Score: 54
Period size: 21 Copynumber: 2.0 Consensus size: 22
40967301 TCATCTACTC
* *
40967311 AGGGTAATTATAATCCACGACA
1 AGGGTAATTATAATCAACAACA
*
40967333 AGGG-AATTATACTCAACAACA
1 AGGGTAATTATAATCAACAACA
40967354 A
1 A
40967355 CAGAACTACA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
21 15 0.79
22 4 0.21
ACGTcount: A:0.45, C:0.18, G:0.16, T:0.20
Consensus pattern (22 bp):
AGGGTAATTATAATCAACAACA
Found at i:40967958 original size:20 final size:21
Alignment explanation
Indices: 40967917--40967960 Score: 81
Period size: 21 Copynumber: 2.1 Consensus size: 21
40967907 AACCGGATGT
40967917 CATTCCACTTGTACCTTTTTC
1 CATTCCACTTGTACCTTTTTC
40967938 CATTCCACTTGTACC-TTTTC
1 CATTCCACTTGTACCTTTTTC
40967958 CAT
1 CAT
40967961 AAAGATTCAA
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
20 8 0.35
21 15 0.65
ACGTcount: A:0.16, C:0.34, G:0.05, T:0.45
Consensus pattern (21 bp):
CATTCCACTTGTACCTTTTTC
Found at i:40975930 original size:27 final size:27
Alignment explanation
Indices: 40975900--40976018 Score: 143
Period size: 27 Copynumber: 4.4 Consensus size: 27
40975890 AGGGCAAAAT
* *
40975900 GGTAATTTTACCCCACAAGGGTATCTC
1 GGTAATTTTACCCTACAAGGGTATTTC
*
40975927 GGTAATTCTACCCTAC-AGAGGTATTTC
1 GGTAATTTTACCCTACAAG-GGTATTTC
* *
40975954 GAT-ATTTCTACCCTACATGGGTATTTC
1 GGTAATTT-TACCCTACAAGGGTATTTC
* *
40975981 GGTAATTCTACCCTACAGGGGTATTTC
1 GGTAATTTTACCCTACAAGGGTATTTC
40976008 GGTAATTTTAC
1 GGTAATTTTAC
40976019 AAACCAGGGG
Statistics
Matches: 78, Mismatches: 10, Indels: 8
0.81 0.10 0.08
Matches are distributed among these distances:
26 5 0.06
27 69 0.88
28 4 0.05
ACGTcount: A:0.24, C:0.22, G:0.18, T:0.35
Consensus pattern (27 bp):
GGTAATTTTACCCTACAAGGGTATTTC
Found at i:40975976 original size:54 final size:53
Alignment explanation
Indices: 40975904--40976018 Score: 167
Period size: 54 Copynumber: 2.1 Consensus size: 53
40975894 CAAAATGGTA
40975904 ATTTTACCCCACAAGGGTATCTCGGTAATTCTACCCTACAGAGGTATTTCGAT
1 ATTTTACCCCACAAGGGTATCTCGGTAATTCTACCCTACAGAGGTATTTCGAT
* * * * *
40975957 ATTTCTACCCTACATGGGTATTTCGGTAATTCTACCCTACAGGGGTATTTCGGT
1 ATTT-TACCCCACAAGGGTATCTCGGTAATTCTACCCTACAGAGGTATTTCGAT
40976011 AATTTTAC
1 -ATTTTAC
40976019 AAACCAGGGG
Statistics
Matches: 55, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
53 4 0.07
54 47 0.85
55 4 0.07
ACGTcount: A:0.24, C:0.23, G:0.17, T:0.36
Consensus pattern (53 bp):
ATTTTACCCCACAAGGGTATCTCGGTAATTCTACCCTACAGAGGTATTTCGAT
Found at i:40976026 original size:27 final size:27
Alignment explanation
Indices: 40975972--40976071 Score: 121
Period size: 27 Copynumber: 3.7 Consensus size: 27
40975962 TACCCTACAT
* **
40975972 GGGTATTTCGGTAATTCTACCCTA-CAG
1 GGGTATTTCGGTAATTTTA-CAAACCAG
40975999 GGGTATTTCGGTAATTTTACAAACCAG
1 GGGTATTTCGGTAATTTTACAAACCAG
** *
40976026 GGGTATTTTAGTAATTTTACAAACTAG
1 GGGTATTTCGGTAATTTTACAAACCAG
*
40976053 GGGTATTTTGGTAATTTTA
1 GGGTATTTCGGTAATTTTA
40976072 TTGATCGAGG
Statistics
Matches: 65, Mismatches: 7, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
26 2 0.03
27 63 0.97
ACGTcount: A:0.27, C:0.12, G:0.22, T:0.39
Consensus pattern (27 bp):
GGGTATTTCGGTAATTTTACAAACCAG
Found at i:40976030 original size:54 final size:54
Alignment explanation
Indices: 40975900--40976071 Score: 161
Period size: 54 Copynumber: 3.2 Consensus size: 54
40975890 AGGGCAAAAT
** * * *
40975900 GGTAATTTTACCCCACAAGGGTATCTCGGTAATTCTACCCTACAGAGGTATTTC
1 GGTAATTTTACCAAACAGGGGTATTTCGGTAATTCTACCCTACAGGGGTATTTC
* ** *
40975954 GAT-ATTTCTACCCTACATGGGTATTTCGGTAATTCTACCCTACAGGGGTATTTC
1 GGTAATTT-TACCAAACAGGGGTATTTCGGTAATTCTACCCTACAGGGGTATTTC
** * ** *
40976008 GGTAATTTTA-CAAACCAGGGGTATTTTAGTAATTTTA-CAAACTAGGGGTATTTT
1 GGTAATTTTACCAAA-CAGGGGTATTTCGGTAATTCTACCCTAC-AGGGGTATTTC
40976062 GGTAATTTTA
1 GGTAATTTTA
40976072 TTGATCGAGG
Statistics
Matches: 99, Mismatches: 15, Indels: 8
0.81 0.12 0.07
Matches are distributed among these distances:
53 9 0.09
54 86 0.87
55 4 0.04
ACGTcount: A:0.27, C:0.17, G:0.19, T:0.37
Consensus pattern (54 bp):
GGTAATTTTACCAAACAGGGGTATTTCGGTAATTCTACCCTACAGGGGTATTTC
Found at i:40976083 original size:27 final size:27
Alignment explanation
Indices: 40975999--40976192 Score: 99
Period size: 27 Copynumber: 7.2 Consensus size: 27
40975989 TACCCTACAG
* * *
40975999 GGGTATTTCGGTAATTTTACAAA-CCA
1 GGGTATTTCAGTAATTTTATAAATCGA
* * *
40976025 GGGGTATTTTAGTAATTTTACAAA-CTA
1 -GGGTATTTCAGTAATTTTATAAATCGA
** **
40976052 GGGGTATTTTGGTAATTTTATTGATCGA
1 -GGGTATTTCAGTAATTTTATAAATCGA
*
40976080 GGGTATTTCAGTAATTTTGTAAATCGA
1 GGGTATTTCAGTAATTTTATAAATCGA
*** * *
40976107 GGGTAAAAC-GATAATTCTGTAAATCGA
1 GGGTATTTCAG-TAATTTTATAAATCGA
** * * *
40976134 GGGTAAAATGA-TAATTCTGTAAATCGA
1 GGGT-ATTTCAGTAATTTTATAAATCGA
*** *
40976161 GGGTAAAACAGTAATTCTATAAATCGA
1 GGGTATTTCAGTAATTTTATAAATCGA
40976188 GGGTA
1 GGGTA
40976193 AAATGGCAAT
Statistics
Matches: 140, Mismatches: 22, Indels: 10
0.81 0.13 0.06
Matches are distributed among these distances:
26 5 0.04
27 130 0.93
28 5 0.04
ACGTcount: A:0.34, C:0.09, G:0.23, T:0.35
Consensus pattern (27 bp):
GGGTATTTCAGTAATTTTATAAATCGA
Found at i:40976271 original size:27 final size:27
Alignment explanation
Indices: 40976090--40976257 Score: 246
Period size: 27 Copynumber: 6.2 Consensus size: 27
40976080 GGGTATTTCA
* *
40976090 GTAATTTTGTAAATCGAGGGTAAAACG
1 GTAATTCTGTAAATCGAGGGTAAAATG
*
40976117 ATAATTCTGTAAATCGAGGGTAAAATG
1 GTAATTCTGTAAATCGAGGGTAAAATG
* **
40976144 ATAATTCTGTAAATCGAGGGTAAAACA
1 GTAATTCTGTAAATCGAGGGTAAAATG
*
40976171 GTAATTCTATAAATCGAGGGTAAAATG
1 GTAATTCTGTAAATCGAGGGTAAAATG
* *
40976198 GCAATTCTGTAAATCGAGGGTAAAACG
1 GTAATTCTGTAAATCGAGGGTAAAATG
*
40976225 GTAATTCTGTAAATCAAGGGTAAAATG
1 GTAATTCTGTAAATCGAGGGTAAAATG
40976252 GTAATT
1 GTAATT
40976258 TTACAAGTTG
Statistics
Matches: 126, Mismatches: 15, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 126 1.00
ACGTcount: A:0.40, C:0.09, G:0.23, T:0.29
Consensus pattern (27 bp):
GTAATTCTGTAAATCGAGGGTAAAATG
Found at i:40976271 original size:54 final size:54
Alignment explanation
Indices: 40976090--40976257 Score: 273
Period size: 54 Copynumber: 3.1 Consensus size: 54
40976080 GGGTATTTCA
* *
40976090 GTAATTTTGTAAATCGAGGGTAAAACGATAATTCTGTAAATCGAGGGTAAAATG
1 GTAATTCTGTAAATCGAGGGTAAAACGGTAATTCTGTAAATCGAGGGTAAAATG
* * *
40976144 ATAATTCTGTAAATCGAGGGTAAAACAGTAATTCTATAAATCGAGGGTAAAATG
1 GTAATTCTGTAAATCGAGGGTAAAACGGTAATTCTGTAAATCGAGGGTAAAATG
* *
40976198 GCAATTCTGTAAATCGAGGGTAAAACGGTAATTCTGTAAATCAAGGGTAAAATG
1 GTAATTCTGTAAATCGAGGGTAAAACGGTAATTCTGTAAATCGAGGGTAAAATG
40976252 GTAATT
1 GTAATT
40976258 TTACAAGTTG
Statistics
Matches: 103, Mismatches: 11, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
54 103 1.00
ACGTcount: A:0.40, C:0.09, G:0.23, T:0.29
Consensus pattern (54 bp):
GTAATTCTGTAAATCGAGGGTAAAACGGTAATTCTGTAAATCGAGGGTAAAATG
Found at i:40987126 original size:18 final size:18
Alignment explanation
Indices: 40987105--40987156 Score: 61
Period size: 18 Copynumber: 2.9 Consensus size: 18
40987095 AGGAAACTGA
40987105 TGTTGTCGAAGAAGAAGT
1 TGTTGTCGAAGAAGAAGT
* **
40987123 TGTTGTAGAAGCGGAAGT
1 TGTTGTCGAAGAAGAAGT
40987141 TGTTG-CTGAAGAAGAA
1 TGTTGTC-GAAGAAGAA
40987157 AAAGTTGCTG
Statistics
Matches: 27, Mismatches: 6, Indels: 2
0.77 0.17 0.06
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.33, C:0.06, G:0.35, T:0.27
Consensus pattern (18 bp):
TGTTGTCGAAGAAGAAGT
Found at i:40997208 original size:17 final size:18
Alignment explanation
Indices: 40997188--40997221 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
40997178 TAAAAGAGTT
*
40997188 AATTA-GGATTAAATTGG
1 AATTAGGGAATAAATTGG
40997205 AATTAGGGAATAAATTG
1 AATTAGGGAATAAATTG
40997222 AATAAAAATT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.44, C:0.00, G:0.24, T:0.32
Consensus pattern (18 bp):
AATTAGGGAATAAATTGG
Found at i:40997763 original size:27 final size:27
Alignment explanation
Indices: 40997704--40997775 Score: 76
Period size: 27 Copynumber: 2.7 Consensus size: 27
40997694 AATGCCTTAT
*
40997704 TGGTGTGCTTGGGAGGATATGATATAC
1 TGGTGTGTTTGGGAGGATATGATATAC
** *
40997731 CAGTGTGTTTGGGAGGCTAT-ATTATAC
1 TGGTGTGTTTGGGAGGATATGA-TATAC
40997758 TGGTGTGTTAT-GGAGGAT
1 TGGTGTGTT-TGGGAGGAT
40997776 TTATATTATT
Statistics
Matches: 36, Mismatches: 7, Indels: 4
0.77 0.15 0.09
Matches are distributed among these distances:
26 1 0.03
27 34 0.94
28 1 0.03
ACGTcount: A:0.21, C:0.07, G:0.36, T:0.36
Consensus pattern (27 bp):
TGGTGTGTTTGGGAGGATATGATATAC
Found at i:41009424 original size:18 final size:19
Alignment explanation
Indices: 41009382--41009426 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
41009372 CAGAATTTAT
* *
41009382 TAAAAAATATTTAATATTA
1 TAAAAATTATTTAATATAA
*
41009401 TGAAAATTATTTAAT-TAA
1 TAAAAATTATTTAATATAA
41009419 TAAAAATT
1 TAAAAATT
41009427 TTACACATTT
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
18 9 0.41
19 13 0.59
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (19 bp):
TAAAAATTATTTAATATAA
Found at i:41012357 original size:11 final size:11
Alignment explanation
Indices: 41012343--41012383 Score: 55
Period size: 11 Copynumber: 3.7 Consensus size: 11
41012333 TGTTTTCTCC
41012343 CTATTTTGCTA
1 CTATTTTGCTA
*
41012354 CTATTTTACTA
1 CTATTTTGCTA
* *
41012365 TTATGTTGCTA
1 CTATTTTGCTA
41012376 CTATTTTG
1 CTATTTTG
41012384 TTGTTATTGT
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
11 24 1.00
ACGTcount: A:0.20, C:0.15, G:0.10, T:0.56
Consensus pattern (11 bp):
CTATTTTGCTA
Found at i:41012454 original size:30 final size:30
Alignment explanation
Indices: 41012420--41012482 Score: 92
Period size: 30 Copynumber: 2.1 Consensus size: 30
41012410 ACTTATTTTA
41012420 TTGTTAAATTTGTTCA-TATTTTAAAGACAT
1 TTGTTAAATTTGTT-ATTATTTTAAAGACAT
* *
41012450 TTGTTAATTTTGTTATTATTTTAGAGACAT
1 TTGTTAAATTTGTTATTATTTTAAAGACAT
41012480 TTG
1 TTG
41012483 CTTGTTAAGT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
29 1 0.03
30 29 0.97
ACGTcount: A:0.29, C:0.05, G:0.13, T:0.54
Consensus pattern (30 bp):
TTGTTAAATTTGTTATTATTTTAAAGACAT
Found at i:41026988 original size:27 final size:27
Alignment explanation
Indices: 41026916--41026991 Score: 80
Period size: 27 Copynumber: 2.8 Consensus size: 27
41026906 TCGGCGGACT
* * *
41026916 TGTTGGTGTACACCATATCACCAAACT
1 TGTTGGTGTACACCATCTCGCCAAACC
* * * *
41026943 TATTGGCGTACAACATCTCGCCAGACC
1 TGTTGGTGTACACCATCTCGCCAAACC
*
41026970 TGTTGGTGTACACCGTCTCGCC
1 TGTTGGTGTACACCATCTCGCC
41026992 GGACATATTA
Statistics
Matches: 38, Mismatches: 11, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
27 38 1.00
ACGTcount: A:0.22, C:0.30, G:0.20, T:0.28
Consensus pattern (27 bp):
TGTTGGTGTACACCATCTCGCCAAACC
Found at i:41027018 original size:55 final size:54
Alignment explanation
Indices: 41026916--41027060 Score: 128
Period size: 55 Copynumber: 2.7 Consensus size: 54
41026906 TCGGCGGACT
*
41026916 TGTTGGTGTACACCATATCACCAAACTTATTGGCGTACAACATCTCGCCAGACC
1 TGTTGGTGTACACCATATCACCAAACATATTGGCGTACAACATCTCGCCAGACC
* * * ** * * * *
41026970 TGTTGGTGTACACCGTCTCGCCGGACATATTAGGCGTATACCATCTCGCTAGACT
1 TGTTGGTGTACACCATATCACCAAACATATT-GGCGTACAACATCTCGCCAGACC
** * * ** *
41027025 TACTGGTGTATACCATCTTGCCAAACCTATTGGCGT
1 TGTTGGTGTACACCATATCACCAAACATATTGGCGT
41027061 TGTAACAGTT
Statistics
Matches: 72, Mismatches: 18, Indels: 2
0.78 0.20 0.02
Matches are distributed among these distances:
54 30 0.42
55 42 0.58
ACGTcount: A:0.23, C:0.28, G:0.20, T:0.29
Consensus pattern (54 bp):
TGTTGGTGTACACCATATCACCAAACATATTGGCGTACAACATCTCGCCAGACC
Found at i:41027777 original size:20 final size:20
Alignment explanation
Indices: 41027752--41027792 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
41027742 ACTAAAATGT
41027752 AAAATTGTGAAATTTGATGA
1 AAAATTGTGAAATTTGATGA
* *
41027772 AAAATTTTGAAATTTTATGA
1 AAAATTGTGAAATTTGATGA
41027792 A
1 A
41027793 TATATGTGCT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.46, C:0.00, G:0.15, T:0.39
Consensus pattern (20 bp):
AAAATTGTGAAATTTGATGA
Found at i:41031959 original size:19 final size:19
Alignment explanation
Indices: 41031935--41031973 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
41031925 AAAACAGACT
41031935 TGTAAATATTTATTAAAAA
1 TGTAAATATTTATTAAAAA
41031954 TGTAAATATTTATTAAAAA
1 TGTAAATATTTATTAAAAA
41031973 T
1 T
41031974 ATTTACGAAG
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:0.51, C:0.00, G:0.05, T:0.44
Consensus pattern (19 bp):
TGTAAATATTTATTAAAAA
Found at i:41032218 original size:5 final size:5
Alignment explanation
Indices: 41032208--41032235 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
41032198 TGAATACTTA
41032208 ATATT ATATT ATATT ATATT ATATT ATA
1 ATATT ATATT ATATT ATATT ATATT ATA
41032236 ATAACTAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (5 bp):
ATATT
Found at i:41040257 original size:27 final size:27
Alignment explanation
Indices: 41040239--41040487 Score: 266
Period size: 27 Copynumber: 9.2 Consensus size: 27
41040229 ACCATGTAAC
41040239 GGCAAAACAATCATTTTACCACATAAG
1 GGCAAAACAATCATTTTACCACATAAG
* ** *
41040266 GGCGAAACTGTCATTTTACCACACAAG
1 GGCAAAACAATCATTTTACCACATAAG
41040293 GGCAAAA-AAGTCATTTTACCACATAAG
1 GGCAAAACAA-TCATTTTACCACATAAG
** ***
41040320 GGCAAAACTGTCATTTTTTGACATAAG
1 GGCAAAACAATCATTTTACCACATAAG
** * * * *
41040347 GGCAAAACTGTTATTTTACCATACAAT
1 GGCAAAACAATCATTTTACCACATAAG
* *
41040374 GGCAGAACAATCATTTTGCCACATAAG
1 GGCAAAACAATCATTTTACCACATAAG
* *
41040401 GGCAAAACTATCATTTTACCACACAAG
1 GGCAAAACAATCATTTTACCACATAAG
* *
41040428 GGCAAAATAATCATTTTACCACATACG
1 GGCAAAACAATCATTTTACCACATAAG
* * *
41040455 GGCAAAACAGTCATTTTGCCACAGAAG
1 GGCAAAACAATCATTTTACCACATAAG
41040482 GGCAAA
1 GGCAAA
41040488 TGCCACATAA
Statistics
Matches: 179, Mismatches: 41, Indels: 4
0.80 0.18 0.02
Matches are distributed among these distances:
27 179 1.00
ACGTcount: A:0.39, C:0.21, G:0.16, T:0.24
Consensus pattern (27 bp):
GGCAAAACAATCATTTTACCACATAAG
Found at i:41040346 original size:81 final size:80
Alignment explanation
Indices: 41040239--41040487 Score: 302
Period size: 81 Copynumber: 3.1 Consensus size: 80
41040229 ACCATGTAAC
*
41040239 GGCAAAACAATCATTTTACCACATAAGGGCGAAACTGTCATTTTACCACACAAGGGCAAAAAAGT
1 GGCAAAACTATCATTTTACCACATAAGGGC-AAACTGTCATTTTACCACACAAGGGCAAAAAAGT
*
41040304 CATTTTACCACATAAG
65 CATTTTGCCACATAAG
* *** * * * *
41040320 GGCAAAACTGTCATTTTTTGACATAAGGGCAAAACTGTTATTTTACCATACAATGGCAGAACAA-
1 GGCAAAACTATCATTTTACCACATAAGGGC-AAACTGTCATTTTACCACACAAGGGCA-AAAAAG
41040384 TCATTTTGCCACATAAG
64 TCATTTTGCCACATAAG
* * * * * *
41040401 GGCAAAACTATCATTTTACCACACAAGGGCAAAATAATCATTTTACCACATACGGGCAAAACAGT
1 GGCAAAACTATCATTTTACCACATAAGGGCAAACT-GTCATTTTACCACACAAGGGCAAAAAAGT
*
41040466 CATTTTGCCACAGAAG
65 CATTTTGCCACATAAG
41040482 GGCAAA
1 GGCAAA
41040488 TGCCACATAA
Statistics
Matches: 139, Mismatches: 26, Indels: 6
0.81 0.15 0.04
Matches are distributed among these distances:
80 7 0.05
81 128 0.92
82 4 0.03
ACGTcount: A:0.39, C:0.21, G:0.16, T:0.24
Consensus pattern (80 bp):
GGCAAAACTATCATTTTACCACATAAGGGCAAACTGTCATTTTACCACACAAGGGCAAAAAAGTC
ATTTTGCCACATAAG
Found at i:41040493 original size:17 final size:17
Alignment explanation
Indices: 41040471--41040504 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
41040461 ACAGTCATTT
41040471 TGCCACAGAAGGGCAAA
1 TGCCACAGAAGGGCAAA
*
41040488 TGCCACATAAGGGCAAA
1 TGCCACAGAAGGGCAAA
41040505 ATAGTCATTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.41, C:0.24, G:0.26, T:0.09
Consensus pattern (17 bp):
TGCCACAGAAGGGCAAA
Found at i:41040511 original size:44 final size:44
Alignment explanation
Indices: 41040446--41040529 Score: 141
Period size: 44 Copynumber: 1.9 Consensus size: 44
41040436 AATCATTTTA
*
41040446 CCACATACGGGCAAAACAGTCATTTTGCCACAGAAGGGCAAATG
1 CCACATAAGGGCAAAACAGTCATTTTGCCACAGAAGGGCAAATG
* *
41040490 CCACATAAGGGCAAAATAGTCATTTTGCCACATAAGGGCA
1 CCACATAAGGGCAAAACAGTCATTTTGCCACAGAAGGGCA
41040530 GAACAGTTAT
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
44 37 1.00
ACGTcount: A:0.37, C:0.24, G:0.21, T:0.18
Consensus pattern (44 bp):
CCACATAAGGGCAAAACAGTCATTTTGCCACAGAAGGGCAAATG
Found at i:41040541 original size:27 final size:27
Alignment explanation
Indices: 41040488--41040542 Score: 83
Period size: 27 Copynumber: 2.0 Consensus size: 27
41040478 GAAGGGCAAA
*
41040488 TGCCACATAAGGGCAAAATAGTCATTT
1 TGCCACATAAGGGCAAAACAGTCATTT
* *
41040515 TGCCACATAAGGGCAGAACAGTTATTT
1 TGCCACATAAGGGCAAAACAGTCATTT
41040542 T
1 T
41040543 ATCAAATTGA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.35, C:0.18, G:0.20, T:0.27
Consensus pattern (27 bp):
TGCCACATAAGGGCAAAACAGTCATTT
Found at i:41043206 original size:17 final size:19
Alignment explanation
Indices: 41043174--41043211 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
41043164 ATTTGAGATC
41043174 AATTTGAAGCAAAATA-GA
1 AATTTGAAGCAAAATATGA
*
41043192 AATTTTAAG-AAAATATGA
1 AATTTGAAGCAAAATATGA
41043210 AA
1 AA
41043212 AATTTCAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 6 0.33
18 12 0.67
ACGTcount: A:0.58, C:0.03, G:0.13, T:0.26
Consensus pattern (19 bp):
AATTTGAAGCAAAATATGA
Found at i:41051618 original size:14 final size:15
Alignment explanation
Indices: 41051576--41051618 Score: 54
Period size: 15 Copynumber: 2.9 Consensus size: 15
41051566 GGTAGATCAA
41051576 CCATAAGTGAGTTCG
1 CCATAAGTGAGTTCG
*
41051591 CTATAAAG-GAGTTCG
1 CCAT-AAGTGAGTTCG
41051606 CCAT-AGTGAGTTC
1 CCATAAGTGAGTTC
41051619 TTTATGGAGT
Statistics
Matches: 24, Mismatches: 2, Indels: 5
0.77 0.06 0.16
Matches are distributed among these distances:
13 2 0.08
14 6 0.25
15 13 0.54
16 3 0.12
ACGTcount: A:0.28, C:0.19, G:0.26, T:0.28
Consensus pattern (15 bp):
CCATAAGTGAGTTCG
Found at i:41051683 original size:15 final size:14
Alignment explanation
Indices: 41051644--41051731 Score: 68
Period size: 15 Copynumber: 6.0 Consensus size: 14
41051634 TCTATAAAGA
*
41051644 AGTTTGCCATAGGTG
1 AGTTCGCCATAGG-G
* *
41051659 AGCTCACCATAGAGG
1 AGTTCGCCATAG-GG
41051674 AGTTCGCCATAGGG
1 AGTTCGCCATAGGG
*
41051688 AGTTTGCCATAGGTG
1 AGTTCGCCATAGG-G
* * *
41051703 AGTTTGCTATAAAGG
1 AGTTCGCCAT-AGGG
*
41051718 AGTTCTCCATAGGG
1 AGTTCGCCATAGGG
41051732 TTATGCACAG
Statistics
Matches: 58, Mismatches: 12, Indels: 7
0.75 0.16 0.09
Matches are distributed among these distances:
14 17 0.29
15 38 0.66
16 3 0.05
ACGTcount: A:0.25, C:0.17, G:0.31, T:0.27
Consensus pattern (14 bp):
AGTTCGCCATAGGG
Found at i:41051692 original size:44 final size:44
Alignment explanation
Indices: 41051644--41051731 Score: 122
Period size: 44 Copynumber: 2.0 Consensus size: 44
41051634 TCTATAAAGA
*
41051644 AGTTTGCCATAGGTGAGCTCACCATAGAGGAGTTCGCCATAGGG
1 AGTTTGCCATAGGTGAGCTCACCATAAAGGAGTTCGCCATAGGG
* ** * *
41051688 AGTTTGCCATAGGTGAGTTTGCTATAAAGGAGTTCTCCATAGGG
1 AGTTTGCCATAGGTGAGCTCACCATAAAGGAGTTCGCCATAGGG
41051732 TTATGCACAG
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
44 38 1.00
ACGTcount: A:0.25, C:0.17, G:0.31, T:0.27
Consensus pattern (44 bp):
AGTTTGCCATAGGTGAGCTCACCATAAAGGAGTTCGCCATAGGG
Found at i:41053350 original size:13 final size:13
Alignment explanation
Indices: 41053332--41053357 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
41053322 TAGCAACCAA
41053332 AATGGTACCAGTT
1 AATGGTACCAGTT
41053345 AATGGTACCAGTT
1 AATGGTACCAGTT
41053358 CAATACATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.23, T:0.31
Consensus pattern (13 bp):
AATGGTACCAGTT
Found at i:41054217 original size:46 final size:47
Alignment explanation
Indices: 41054131--41054219 Score: 119
Period size: 46 Copynumber: 1.9 Consensus size: 47
41054121 GTGCCTTTCA
*
41054131 TAGCCGAAGCTATCTCAGTCTCGCACACTAAGTACCATATATATATG
1 TAGCCGAAGCTATCTCAGTCTCACACACTAAGTACCATATATATATG
* * *
41054178 TAGCCGAAGCTATCATGA-T-TCACACACTAAGTGCTATATATA
1 TAGCCGAAGCTATC-TCAGTCTCACACACTAAGTACCATATATA
41054220 GCCGAAGCTA
Statistics
Matches: 37, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
46 20 0.54
47 15 0.41
48 2 0.05
ACGTcount: A:0.34, C:0.24, G:0.15, T:0.28
Consensus pattern (47 bp):
TAGCCGAAGCTATCTCAGTCTCACACACTAAGTACCATATATATATG
Found at i:41054244 original size:40 final size:40
Alignment explanation
Indices: 41054172--41054251 Score: 108
Period size: 40 Copynumber: 2.0 Consensus size: 40
41054162 GTACCATATA
* **
41054172 TATATGTAGCCGAAGCTATCATGATTCACACACTAAGTGC
1 TATATATAGCCGAAGCTATCATGAAACACACACTAAGTGC
*
41054212 TATATATAGCCGAAGCTATTC-TGAAACGCACACTAAGTGC
1 TATATATAGCCGAAGCTA-TCATGAAACACACACTAAGTGC
41054252 CAAACGTAGT
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
40 33 0.94
41 2 0.06
ACGTcount: A:0.34, C:0.23, G:0.17, T:0.26
Consensus pattern (40 bp):
TATATATAGCCGAAGCTATCATGAAACACACACTAAGTGC
Found at i:41057722 original size:59 final size:59
Alignment explanation
Indices: 41057630--41057753 Score: 230
Period size: 59 Copynumber: 2.1 Consensus size: 59
41057620 ATTTTAAATT
*
41057630 AATTACTAAACTATCCAAATGTATTTTTTAATCATTGAACCGTTAAAGTATAAACACTG
1 AATTACTAAACTATCCAAATGCATTTTTTAATCATTGAACCGTTAAAGTATAAACACTG
41057689 AATTACTAAACTATCCAAATGCATTTTTTAATCATTGAACCGTTAAAGTATAAACACTG
1 AATTACTAAACTATCCAAATGCATTTTTTAATCATTGAACCGTTAAAGTATAAACACTG
*
41057748 GATTAC
1 AATTAC
41057754 ATGGAATTTC
Statistics
Matches: 63, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
59 63 1.00
ACGTcount: A:0.40, C:0.16, G:0.09, T:0.35
Consensus pattern (59 bp):
AATTACTAAACTATCCAAATGCATTTTTTAATCATTGAACCGTTAAAGTATAAACACTG
Found at i:41061762 original size:19 final size:19
Alignment explanation
Indices: 41061738--41061777 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
41061728 ATTCATATGT
41061738 TAATGCAATTTCCTCATAA
1 TAATGCAATTTCCTCATAA
41061757 TAATGCAATTTCCTCATAA
1 TAATGCAATTTCCTCATAA
41061776 TA
1 TA
41061778 TTGCTTCTGC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.38, C:0.20, G:0.05, T:0.38
Consensus pattern (19 bp):
TAATGCAATTTCCTCATAA
Found at i:41062542 original size:217 final size:217
Alignment explanation
Indices: 41062182--41062599 Score: 782
Period size: 217 Copynumber: 1.9 Consensus size: 217
41062172 GGGGTTGGAT
41062182 AAATATCAATTTTTGAAAATCTATTGCTTTGCGCCTTGTTCTTTTTAATTCTCACTTAAGTGTTC
1 AAATATCAATTTTTGAAAATCTATTGCTTTGCGCCTTGTTCTTTTTAATTCTCACTTAAGTGTTC
*
41062247 TTCCATTACAATATTTGAAGAGTTTTCTTTGTTTTAATGGTGAAGAAATGATTCATTTTGCCAAT
66 TTCCATTACAATATTTGAAGAGTTGTCTTTGTTTTAATGGTGAAGAAATGATTCATTTTGCCAAT
41062312 TTAAGATTATTCATGACTTTGATTGTTTATTAAATTGCATAGGGAGACAACATTCCAGCACCATT
131 TTAAGATTATTCATGACTTTGATTGTTTATTAAATTGCATAGGGAGACAACATTCCAGCACCATT
41062377 CATAAGGGGAAGGGTGTTTAAC
196 CATAAGGGGAAGGGTGTTTAAC
* * *
41062399 AAATATCATTTTTTGAAAATCTATTGCTTTGTGCCTTGTTCTTTTTAATTCTCACTTAATTGTTC
1 AAATATCAATTTTTGAAAATCTATTGCTTTGCGCCTTGTTCTTTTTAATTCTCACTTAAGTGTTC
*
41062464 TTCCATTACAATATTTGAAGAGTTGTCTTTGTTTTAATGGTGAGGAAATGATTCATTTTGCCAAT
66 TTCCATTACAATATTTGAAGAGTTGTCTTTGTTTTAATGGTGAAGAAATGATTCATTTTGCCAAT
*
41062529 TTAAGATTATTCATGACTTTGATTGTTTATTAAATTGCATAGGGAGACAACGTTCCAGCACCATT
131 TTAAGATTATTCATGACTTTGATTGTTTATTAAATTGCATAGGGAGACAACATTCCAGCACCATT
41062594 CATAAG
196 CATAAG
41062600 ATTTGAAGAT
Statistics
Matches: 195, Mismatches: 6, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
217 195 1.00
ACGTcount: A:0.28, C:0.14, G:0.16, T:0.42
Consensus pattern (217 bp):
AAATATCAATTTTTGAAAATCTATTGCTTTGCGCCTTGTTCTTTTTAATTCTCACTTAAGTGTTC
TTCCATTACAATATTTGAAGAGTTGTCTTTGTTTTAATGGTGAAGAAATGATTCATTTTGCCAAT
TTAAGATTATTCATGACTTTGATTGTTTATTAAATTGCATAGGGAGACAACATTCCAGCACCATT
CATAAGGGGAAGGGTGTTTAAC
Found at i:41064939 original size:33 final size:33
Alignment explanation
Indices: 41064897--41064985 Score: 142
Period size: 33 Copynumber: 2.7 Consensus size: 33
41064887 GGATTCTGGA
41064897 GGCCGTGGTGGAATGAGGGATGGAGGCTTTGGT
1 GGCCGTGGTGGAATGAGGGATGGAGGCTTTGGT
*
41064930 GGCCGTGGTGGAATGAGGGATGGGGGCTTTGGT
1 GGCCGTGGTGGAATGAGGGATGGAGGCTTTGGT
* * *
41064963 GGACGTGGTGGCATGAGAGATGG
1 GGCCGTGGTGGAATGAGGGATGG
41064986 TTTTGGCGGT
Statistics
Matches: 52, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 52 1.00
ACGTcount: A:0.16, C:0.09, G:0.53, T:0.22
Consensus pattern (33 bp):
GGCCGTGGTGGAATGAGGGATGGAGGCTTTGGT
Found at i:41065312 original size:6 final size:6
Alignment explanation
Indices: 41065303--41065358 Score: 73
Period size: 6 Copynumber: 9.8 Consensus size: 6
41065293 AGCCGCAGTG
* *
41065303 GGAGTC GGAGTT GGAGTA GGAGT- --AGTA GGAGTA GGAGTA GGAGTA
1 GGAGTA GGAGTA GGAGTA GGAGTA GGAGTA GGAGTA GGAGTA GGAGTA
41065348 GGAGTA GGAGT
1 GGAGTA GGAGT
41065359 CGAAGCAGAA
Statistics
Matches: 45, Mismatches: 2, Indels: 6
0.85 0.04 0.11
Matches are distributed among these distances:
3 3 0.07
6 42 0.93
ACGTcount: A:0.29, C:0.02, G:0.50, T:0.20
Consensus pattern (6 bp):
GGAGTA
Found at i:41065333 original size:27 final size:27
Alignment explanation
Indices: 41065303--41065354 Score: 86
Period size: 27 Copynumber: 1.9 Consensus size: 27
41065293 AGCCGCAGTG
* *
41065303 GGAGTCGGAGTTGGAGTAGGAGTAGTA
1 GGAGTAGGAGTAGGAGTAGGAGTAGTA
41065330 GGAGTAGGAGTAGGAGTAGGAGTAG
1 GGAGTAGGAGTAGGAGTAGGAGTAG
41065355 GAGTCGAAGC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.29, C:0.02, G:0.50, T:0.19
Consensus pattern (27 bp):
GGAGTAGGAGTAGGAGTAGGAGTAGTA
Found at i:41065334 original size:21 final size:21
Alignment explanation
Indices: 41065309--41065348 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
41065299 AGTGGGAGTC
*
41065309 GGAGTTGGAGTAGGAGTAGTA
1 GGAGTAGGAGTAGGAGTAGTA
41065330 GGAGTAGGAGTAGGAGTAG
1 GGAGTAGGAGTAGGAGTAG
41065349 GAGTAGGAGT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.30, C:0.00, G:0.50, T:0.20
Consensus pattern (21 bp):
GGAGTAGGAGTAGGAGTAGTA
Found at i:41065589 original size:63 final size:63
Alignment explanation
Indices: 41065490--41065645 Score: 226
Period size: 63 Copynumber: 2.5 Consensus size: 63
41065480 GCTATGAGCG
* ** *
41065490 GAAGGATGTTGCAAAGCGGGCATTTGATTCTCCTCCTGGTTCCAACGAACATAACTT-GCAACA
1 GAAGGATGTTGCAAAGCGAGCATTTGATTCTCCTCCTCCTTCCAACGAACAGAACTTCG-AACA
* *
41065553 GAAGGATGTTGCGAAGCGAGCATTTGATTCTCCTCCTCCTTCCAACGAACAGAACTTCGAGCA
1 GAAGGATGTTGCAAAGCGAGCATTTGATTCTCCTCCTCCTTCCAACGAACAGAACTTCGAACA
41065616 GAAGGATGTTGCAAAGC-AGGCATTTGATTC
1 GAAGGATGTTGCAAAGCGA-GCATTTGATTC
41065646 ACCTGGTGCA
Statistics
Matches: 84, Mismatches: 7, Indels: 4
0.88 0.07 0.04
Matches are distributed among these distances:
62 1 0.01
63 82 0.98
64 1 0.01
ACGTcount: A:0.28, C:0.23, G:0.24, T:0.25
Consensus pattern (63 bp):
GAAGGATGTTGCAAAGCGAGCATTTGATTCTCCTCCTCCTTCCAACGAACAGAACTTCGAACA
Found at i:41067693 original size:20 final size:20
Alignment explanation
Indices: 41067666--41067715 Score: 84
Period size: 20 Copynumber: 2.5 Consensus size: 20
41067656 ATGTTAATGA
*
41067666 AAGT-ATGATTAAAATAATT
1 AAGTAATGAATAAAATAATT
41067685 AAGTAATGAATAAAATAATT
1 AAGTAATGAATAAAATAATT
41067705 AAGTAATGAAT
1 AAGTAATGAAT
41067716 GGTTACTTAA
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
19 4 0.14
20 25 0.86
ACGTcount: A:0.56, C:0.00, G:0.12, T:0.32
Consensus pattern (20 bp):
AAGTAATGAATAAAATAATT
Found at i:41073888 original size:142 final size:142
Alignment explanation
Indices: 41073632--41073914 Score: 539
Period size: 142 Copynumber: 2.0 Consensus size: 142
41073622 AATATTATGC
*
41073632 TTTGTGTTTAATGTTGAGTAATATGCAAATCATGTTTACTACTTGATAAATATGAATTGCTATCG
1 TTTGTGTTTAATGTTGAGTAATATGCAAATCATGTTTACTACTTGATAAATATGAATTGCTACCG
* *
41073697 AGTATCGGTTCCGATATTCCATGGAGGGCGACAAATGTGAGATCGAGGGAAAAATCCCGTTTGAA
66 AGTATCGGTTCCGATATTCCATGGAAGACGACAAATGTGAGATCGAGGGAAAAATCCCGTTTGAA
41073762 CCTTAGGAATAA
131 CCTTAGGAATAA
41073774 TTTGTGTTTAATGTTGAGTAATATGCAAATCATGTTTACTACTTGATAAATATGAATTGCTACCG
1 TTTGTGTTTAATGTTGAGTAATATGCAAATCATGTTTACTACTTGATAAATATGAATTGCTACCG
41073839 AGTATCGGTTCCGATATTCCATGGAAGACGACAAATGTGAGATCGAGGGAAAAATCCCGTTTGAA
66 AGTATCGGTTCCGATATTCCATGGAAGACGACAAATGTGAGATCGAGGGAAAAATCCCGTTTGAA
41073904 CCTTAGGAATA
131 CCTTAGGAATA
41073915 GATTAGGATA
Statistics
Matches: 138, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
142 138 1.00
ACGTcount: A:0.32, C:0.14, G:0.22, T:0.32
Consensus pattern (142 bp):
TTTGTGTTTAATGTTGAGTAATATGCAAATCATGTTTACTACTTGATAAATATGAATTGCTACCG
AGTATCGGTTCCGATATTCCATGGAAGACGACAAATGTGAGATCGAGGGAAAAATCCCGTTTGAA
CCTTAGGAATAA
Found at i:41074034 original size:74 final size:74
Alignment explanation
Indices: 41073913--41074061 Score: 289
Period size: 74 Copynumber: 2.0 Consensus size: 74
41073903 ACCTTAGGAA
41073913 TAGATTAGGATACAAGTGACATGTCACTAGGATGGTTGAGCATCCGAACTCATTGAGTTGAGTCC
1 TAGATTAGGATACAAGTGACATGTCACTAGGATGGTTGAGCATCCGAACTCATTGAGTTGAGTCC
41073978 GAGTTCACC
66 GAGTTCACC
*
41073987 TAGATTAGGATACAAGTGACATGTCACTAGGATGGTTGAGCATCCGAACTCGTTGAGTTGAGTCC
1 TAGATTAGGATACAAGTGACATGTCACTAGGATGGTTGAGCATCCGAACTCATTGAGTTGAGTCC
41074052 GAGTTCACC
66 GAGTTCACC
41074061 T
1 T
41074062 GTGGATGCGA
Statistics
Matches: 74, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
74 74 1.00
ACGTcount: A:0.28, C:0.19, G:0.26, T:0.28
Consensus pattern (74 bp):
TAGATTAGGATACAAGTGACATGTCACTAGGATGGTTGAGCATCCGAACTCATTGAGTTGAGTCC
GAGTTCACC
Found at i:41074144 original size:47 final size:47
Alignment explanation
Indices: 41074026--41074197 Score: 248
Period size: 47 Copynumber: 3.7 Consensus size: 47
41074016 GGATGGTTGA
*
41074026 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACCTGTG-GATGCGAA-T--
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTT---C-GTGAGATG-TAACTAG
41074074 G--TCCGAACTCGTTGAGTTGAGTCCGAGTTCGTGAGATGTAACTAG
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCGTGAGATGTAACTAG
41074119 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCGTGAGATGTAACTAG
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCGTGAGATGTAACTAG
41074166 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTC
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTC
41074198 ACTTATGGAT
Statistics
Matches: 117, Mismatches: 1, Indels: 13
0.89 0.01 0.10
Matches are distributed among these distances:
42 5 0.04
43 6 0.05
45 1 0.01
46 28 0.24
47 76 0.65
48 1 0.01
ACGTcount: A:0.22, C:0.21, G:0.30, T:0.28
Consensus pattern (47 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCGTGAGATGTAACTAG
Found at i:41074246 original size:46 final size:45
Alignment explanation
Indices: 41074030--41074248 Score: 185
Period size: 47 Copynumber: 4.7 Consensus size: 45
41074020 GGTTGAGCAT
* * * * *
41074030 CCGAACTCGTTGAGTTGAGTCCGAGTTCACCTGTGGATGCGAATG-T
1 CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGA-AC-AAGGCA
* * * *
41074076 CCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGAGATGTAACTAGGCA
1 CCGAACTCGTTGAGTTGAGTCCGAGTTCACT--TATGGAACAAGGCA
* * * *
41074122 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGAGATGTAACTAGGCA
1 -CCGAACTCGTTGAGTTGAGTCCGAGTTCACT--TATGGAACAAGGCA
*
41074169 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATACGAACGC-
1 -CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGA-AC-AAGGCA
*
41074216 CCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTA
1 CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTA
41074249 GGGGCGGGTT
Statistics
Matches: 151, Mismatches: 15, Indels: 14
0.84 0.08 0.08
Matches are distributed among these distances:
45 2 0.01
46 65 0.43
47 80 0.53
48 4 0.03
ACGTcount: A:0.22, C:0.21, G:0.29, T:0.28
Consensus pattern (45 bp):
CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGAACAAGGCA
Found at i:41076673 original size:17 final size:17
Alignment explanation
Indices: 41076651--41076686 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
41076641 AATCTCAGAA
41076651 TACTTCTGCAGCCAGTG
1 TACTTCTGCAGCCAGTG
41076668 TACTTCTGCAGCCAGTG
1 TACTTCTGCAGCCAGTG
41076685 TA
1 TA
41076687 GGGAACTCGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.19, C:0.28, G:0.22, T:0.31
Consensus pattern (17 bp):
TACTTCTGCAGCCAGTG
Found at i:41082737 original size:30 final size:34
Alignment explanation
Indices: 41082675--41082740 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 34
41082665 CGAAACGAAC
41082675 TATTACTCGTATATACGTGAAGTACATGGAAATGA
1 TATTACTCGTATATACGTGAAG-ACATGGAAATGA
*
41082710 TATTACTTG-ATATAC-TGAAG-CAT-GAAATGA
1 TATTACTCGTATATACGTGAAGACATGGAAATGA
41082740 T
1 T
41082741 TGTTACATGT
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
30 8 0.27
31 3 0.10
33 5 0.17
34 6 0.20
35 8 0.27
ACGTcount: A:0.38, C:0.11, G:0.18, T:0.33
Consensus pattern (34 bp):
TATTACTCGTATATACGTGAAGACATGGAAATGA
Found at i:41087410 original size:39 final size:39
Alignment explanation
Indices: 41087367--41087443 Score: 118
Period size: 39 Copynumber: 2.0 Consensus size: 39
41087357 CCCCAGTCAG
* *
41087367 TCAACAAAATGCAAAATTTACTAGAATGCTTAGTGGGAT
1 TCAACAAAATGCAAAATTAACCAGAATGCTTAGTGGGAT
* *
41087406 TCAACAAAATGGAAAATTAACCAGAATTCTTAGTGGGA
1 TCAACAAAATGCAAAATTAACCAGAATGCTTAGTGGGA
41087444 CTGAAAGGAT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
39 34 1.00
ACGTcount: A:0.43, C:0.13, G:0.18, T:0.26
Consensus pattern (39 bp):
TCAACAAAATGCAAAATTAACCAGAATGCTTAGTGGGAT
Found at i:41093228 original size:15 final size:15
Alignment explanation
Indices: 41093205--41093239 Score: 61
Period size: 15 Copynumber: 2.3 Consensus size: 15
41093195 TACACCGTTT
*
41093205 GATACAACCATTATC
1 GATATAACCATTATC
41093220 GATATAACCATTATC
1 GATATAACCATTATC
41093235 GATAT
1 GATAT
41093240 GATAAGAGCC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.40, C:0.20, G:0.09, T:0.31
Consensus pattern (15 bp):
GATATAACCATTATC
Found at i:41095191 original size:21 final size:21
Alignment explanation
Indices: 41095165--41095207 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
41095155 GGTTCGCTGT
*
41095165 ATTGGATTAGAGGTGTATTGG
1 ATTGGATTAGAGGTGTAATGG
41095186 ATTGGATTAGAGGTGTAATGG
1 ATTGGATTAGAGGTGTAATGG
41095207 A
1 A
41095208 ATAGAGGTGT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.28, C:0.00, G:0.37, T:0.35
Consensus pattern (21 bp):
ATTGGATTAGAGGTGTAATGG
Found at i:41095207 original size:16 final size:16
Alignment explanation
Indices: 41095188--41095220 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
41095178 TGTATTGGAT
*
41095188 TGGATTAGAGGTGTAA
1 TGGAATAGAGGTGTAA
41095204 TGGAATAGAGGTGTAA
1 TGGAATAGAGGTGTAA
41095220 T
1 T
41095221 AGCAAATCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.33, C:0.00, G:0.36, T:0.30
Consensus pattern (16 bp):
TGGAATAGAGGTGTAA
Found at i:41095265 original size:45 final size:44
Alignment explanation
Indices: 41095199--41095293 Score: 136
Period size: 45 Copynumber: 2.1 Consensus size: 44
41095189 GGATTAGAGG
* *
41095199 TGTAATGGAATAGAGGTGTAATAGCAAATCAACTGTTTGGTTGAA
1 TGTAATGGAATAGAGGCGTAATAGCAAAAC-ACTGTTTGGTTGAA
* **
41095244 TGTAATGGAATAGAGGCGTAATAGTAAAACTGTGTTTGGTTGAA
1 TGTAATGGAATAGAGGCGTAATAGCAAAACACTGTTTGGTTGAA
41095288 TGTAAT
1 TGTAAT
41095294 AGAGGTGTAA
Statistics
Matches: 45, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
44 18 0.40
45 27 0.60
ACGTcount: A:0.35, C:0.05, G:0.27, T:0.33
Consensus pattern (44 bp):
TGTAATGGAATAGAGGCGTAATAGCAAAACACTGTTTGGTTGAA
Found at i:41095476 original size:18 final size:17
Alignment explanation
Indices: 41095455--41095489 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
41095445 TTATTATTTA
*
41095455 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
41095473 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
41095490 TCTTAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:41095483 original size:28 final size:27
Alignment explanation
Indices: 41095413--41095485 Score: 76
Period size: 27 Copynumber: 2.7 Consensus size: 27
41095403 TTTATTATCA
*
41095413 AAAATAAATAATTTAATCATATTTAAAC
1 AAAATATATAATTTAAT-ATATTTAAAC
* * **
41095441 ATAAT-TATTATTTAATATATTTTAATT
1 AAAATATATAATTTAATATA-TTTAAAC
41095468 AAAATATATAATTTAATA
1 AAAATATATAATTTAATA
41095486 AAATTCTTAA
Statistics
Matches: 36, Mismatches: 7, Indels: 4
0.77 0.15 0.09
Matches are distributed among these distances:
26 3 0.08
27 18 0.50
28 15 0.42
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (27 bp):
AAAATATATAATTTAATATATTTAAAC
Found at i:41095602 original size:144 final size:154
Alignment explanation
Indices: 41095374--41095654 Score: 447
Period size: 144 Copynumber: 1.9 Consensus size: 154
41095364 ATGATTATTG
41095374 TTATTGTTATTTAAATTTTAATAAGATTATTTATTATCAAAAATAAATAATTTAATCATATTTAA
1 TTATTGTTATTTAAATTTTAATAAGATTA--TATTATCAAAAATAAATAATTTAATCATATTTAA
41095439 ACATAATTATTATT--TA-A-T-ATAT-TT-TAATTAAAATATATAATTTAATAAAATTCTTAAT
64 ACATAATTATTATTAATATATTAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAAT
41095497 AATTAGCAGAAATTTGTTTTGGTAAA
129 AATTAGCAGAAATTTGTTTTGGTAAA
*
41095523 TTATT-TTATTTAAATTTTAATAAGATTA-A-TATCAATAATAAATAATTTAATCATATTTAAAC
1 TTATTGTTATTTAAATTTTAATAAGATTATATTATCAAAAATAAATAATTTAATCATATTTAAAC
41095585 ATAATTATTATTAAATATATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAAT
66 ATAATTATTATT-AATATATT-AATATATTATAATTAAAATATATAATTTAATAAAATTCTTAAT
41095650 AATTA
129 AATTA
41095655 ATATTCTTAT
Statistics
Matches: 122, Mismatches: 1, Indels: 14
0.89 0.01 0.10
Matches are distributed among these distances:
144 44 0.36
145 1 0.01
147 2 0.02
148 24 0.20
149 6 0.05
151 4 0.03
152 2 0.02
153 39 0.32
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (154 bp):
TTATTGTTATTTAAATTTTAATAAGATTATATTATCAAAAATAAATAATTTAATCATATTTAAAC
ATAATTATTATTAATATATTAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAA
TTAGCAGAAATTTGTTTTGGTAAA
Found at i:41095607 original size:25 final size:25
Alignment explanation
Indices: 41095575--41095629 Score: 69
Period size: 25 Copynumber: 2.2 Consensus size: 25
41095565 TAATTTAATC
*
41095575 ATAT-TTAAACATAATTATTATT-AA
1 ATATATTAAACAT-ATTATAATTAAA
*
41095599 ATATATTAAATATATTATAATTAAA
1 ATATATTAAACATATTATAATTAAA
41095624 ATATAT
1 ATATAT
41095630 AATTTAATAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
24 12 0.44
25 15 0.56
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (25 bp):
ATATATTAAACATATTATAATTAAA
Found at i:41097861 original size:23 final size:23
Alignment explanation
Indices: 41097826--41097870 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
41097816 CTTTTAGAGT
*
41097826 TTTACTATCACAAATATAATATA
1 TTTACAATCACAAATATAATATA
*
41097849 TTTACAATTACAAATATAATAT
1 TTTACAATCACAAATATAATAT
41097871 TAGTTTAGAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.49, C:0.11, G:0.00, T:0.40
Consensus pattern (23 bp):
TTTACAATCACAAATATAATATA
Found at i:41099988 original size:18 final size:18
Alignment explanation
Indices: 41099955--41099989 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
41099945 TTGAGAAAAG
*
41099955 AATTTAATTGACTAATTT
1 AATTTAATTAACTAATTT
*
41099973 AATTTAATTAATTAATT
1 AATTTAATTAACTAATT
41099990 AATATTTTTT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.43, C:0.03, G:0.03, T:0.51
Consensus pattern (18 bp):
AATTTAATTAACTAATTT
Found at i:41105743 original size:18 final size:18
Alignment explanation
Indices: 41105687--41105743 Score: 53
Period size: 18 Copynumber: 3.2 Consensus size: 18
41105677 CCGGATGATA
41105687 GTCAATAACCAGATTATT
1 GTCAATAACCAGATTATT
** * * *
41105705 GTCTTTTATCA-ATTCAAT
1 GTCAATAACCAGATT-ATT
41105723 GTCAATAACCAGATTATT
1 GTCAATAACCAGATTATT
41105741 GTC
1 GTC
41105744 TTTTATCAAA
Statistics
Matches: 27, Mismatches: 10, Indels: 4
0.66 0.24 0.10
Matches are distributed among these distances:
17 3 0.11
18 21 0.78
19 3 0.11
ACGTcount: A:0.33, C:0.18, G:0.11, T:0.39
Consensus pattern (18 bp):
GTCAATAACCAGATTATT
Found at i:41107654 original size:23 final size:23
Alignment explanation
Indices: 41107625--41107722 Score: 171
Period size: 23 Copynumber: 4.3 Consensus size: 23
41107615 ATAAGTGCCA
41107625 CACTGATATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
41107648 CACTGATATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
*
41107671 CACTG-GATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
*
41107693 CACTGAAATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
41107716 CACTGAT
1 CACTGAT
41107723 CAATAACACT
Statistics
Matches: 71, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
22 21 0.30
23 50 0.70
ACGTcount: A:0.31, C:0.27, G:0.22, T:0.20
Consensus pattern (23 bp):
CACTGATATGTAGCCGAAGCTAC
Found at i:41107690 original size:45 final size:45
Alignment explanation
Indices: 41107632--41107720 Score: 169
Period size: 45 Copynumber: 2.0 Consensus size: 45
41107622 CCACACTGAT
*
41107632 ATGTAGCCGAAGCTACCACTGATATGTAGCCGAAGCTACCACTGG
1 ATGTAGCCGAAGCTACCACTGAAATGTAGCCGAAGCTACCACTGG
41107677 ATGTAGCCGAAGCTACCACTGAAATGTAGCCGAAGCTACCACTG
1 ATGTAGCCGAAGCTACCACTGAAATGTAGCCGAAGCTACCACTG
41107721 ATCAATAACA
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
45 43 1.00
ACGTcount: A:0.30, C:0.27, G:0.24, T:0.19
Consensus pattern (45 bp):
ATGTAGCCGAAGCTACCACTGAAATGTAGCCGAAGCTACCACTGG
Found at i:41116331 original size:73 final size:73
Alignment explanation
Indices: 41116212--41116359 Score: 287
Period size: 73 Copynumber: 2.0 Consensus size: 73
41116202 GGGTAAAAAT
*
41116212 ATGTATAATTTACGGTTTATCAAATACCCCCACACTTAAGCATTTGCTTGTCCTCAAGCAACATT
1 ATGTATAATTTACGGTTTATCAAATACCCCCACACTTAAGCATTTGCTTGTCCTCAAGCAAAATT
41116277 CTCAACTC
66 CTCAACTC
41116285 ATGTATAATTTACGGTTTATCAAATACCCCCACACTTAAGCATTTGCTTGTCCTCAAGCAAAATT
1 ATGTATAATTTACGGTTTATCAAATACCCCCACACTTAAGCATTTGCTTGTCCTCAAGCAAAATT
41116350 CTCAACTC
66 CTCAACTC
41116358 AT
1 AT
41116360 AATCAAAATA
Statistics
Matches: 74, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
73 74 1.00
ACGTcount: A:0.31, C:0.26, G:0.09, T:0.33
Consensus pattern (73 bp):
ATGTATAATTTACGGTTTATCAAATACCCCCACACTTAAGCATTTGCTTGTCCTCAAGCAAAATT
CTCAACTC
Found at i:41117810 original size:18 final size:17
Alignment explanation
Indices: 41117765--41117802 Score: 76
Period size: 17 Copynumber: 2.2 Consensus size: 17
41117755 TGTCAAAGGG
41117765 AAACAAATGAATCTTAA
1 AAACAAATGAATCTTAA
41117782 AAACAAATGAATCTTAA
1 AAACAAATGAATCTTAA
41117799 AAAC
1 AAAC
41117803 TTAATGAAAG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.61, C:0.13, G:0.05, T:0.21
Consensus pattern (17 bp):
AAACAAATGAATCTTAA
Done.