Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D12
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: 58873029
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.33
Warning! 639818 characters in sequence are not A, C, G, or T
File 181 of 196
Found at i:53103598 original size:12 final size:12
Alignment explanation
Indices: 53103581--53103613 Score: 59
Period size: 11 Copynumber: 2.8 Consensus size: 12
53103571 AACTAATCCT
53103581 CTCTCAAATTTG
1 CTCTCAAATTTG
53103593 CTCTC-AATTTG
1 CTCTCAAATTTG
53103604 CTCTCAAATT
1 CTCTCAAATT
53103614 CCTTCCAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 11 0.55
12 9 0.45
ACGTcount: A:0.24, C:0.27, G:0.06, T:0.42
Consensus pattern (12 bp):
CTCTCAAATTTG
Found at i:53103685 original size:50 final size:51
Alignment explanation
Indices: 53103594--53103691 Score: 128
Period size: 50 Copynumber: 1.9 Consensus size: 51
53103584 TCAAATTTGC
* *
53103594 TCTCAATTTGCTCTCAAATTCCTTCCAAATTTCTCTGAAATCCATATTAAA
1 TCTCAATTGGCTCCCAAATTCCTTCCAAATTTCTCTGAAATCCATATTAAA
* * *
53103645 TCTCAATTGGCTCCCAATTTCC-TCTC-AATTTCTCTTAAATCCCTATT
1 TCTCAATTGGCTCCCAAATTCCTTC-CAAATTTCTCTGAAATCCATATT
53103692 TTTAAATAAT
Statistics
Matches: 41, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
50 21 0.51
51 20 0.49
ACGTcount: A:0.27, C:0.29, G:0.04, T:0.41
Consensus pattern (51 bp):
TCTCAATTGGCTCCCAAATTCCTTCCAAATTTCTCTGAAATCCATATTAAA
Found at i:53105447 original size:21 final size:21
Alignment explanation
Indices: 53105423--53105468 Score: 74
Period size: 21 Copynumber: 2.2 Consensus size: 21
53105413 GATGCCCTAT
*
53105423 CGGAGGAACCAGAATCCCCGC
1 CGGAGGAACCACAATCCCCGC
*
53105444 CGGAGGAACCACAATCGCCGC
1 CGGAGGAACCACAATCCCCGC
53105465 CGGA
1 CGGA
53105469 AGCTGGACAA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.28, C:0.37, G:0.30, T:0.04
Consensus pattern (21 bp):
CGGAGGAACCACAATCCCCGC
Found at i:53105717 original size:14 final size:14
Alignment explanation
Indices: 53105698--53105727 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
53105688 TTTAATTGAC
53105698 AAACCCTAAACCTT
1 AAACCCTAAACCTT
*
53105712 AAACCCTAATCCTT
1 AAACCCTAAACCTT
53105726 AA
1 AA
53105728 CTTAAAAATC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.43, C:0.33, G:0.00, T:0.23
Consensus pattern (14 bp):
AAACCCTAAACCTT
Found at i:53105765 original size:22 final size:22
Alignment explanation
Indices: 53105698--53105768 Score: 69
Period size: 22 Copynumber: 3.3 Consensus size: 22
53105688 TTTAATTGAC
*
53105698 AAACCCTAAACCTT-AAACCC-T
1 AAACCCTTAA-CTTAAAACCCAT
* *
53105719 -AATCCTTAACTTAAAAATCCA-
1 AAACCCTTAACTT-AAAACCCAT
53105740 AAACCCTTAACTTAAAACCCAT
1 AAACCCTTAACTTAAAACCCAT
53105762 AAACCCT
1 AAACCCT
53105769 AAACCGTAAC
Statistics
Matches: 40, Mismatches: 5, Indels: 9
0.74 0.09 0.17
Matches are distributed among these distances:
19 3 0.08
20 7 0.17
21 12 0.30
22 18 0.45
ACGTcount: A:0.45, C:0.32, G:0.00, T:0.23
Consensus pattern (22 bp):
AAACCCTTAACTTAAAACCCAT
Found at i:53105765 original size:50 final size:48
Alignment explanation
Indices: 53105705--53105861 Score: 170
Period size: 50 Copynumber: 3.0 Consensus size: 48
53105695 GACAAACCCT
* *
53105705 AAACCTTAAACCCTAATCCTTAACTTAAAAATCCAAAACCCTTAACTTA
1 AAACCCTAAACCCTAATCCTTAACTTAAAAA-CCTAAACCCTTAACTTA
53105754 AAACCCATAAACCCTAAACCGTAACCATTAACTTAAAAACACTAAACCCTTAACTTTA
1 AAACCC-TAAACCCT-AA---T--CC-TTAACTTAAAAAC-CTAAACCCTTAAC-TTA
* *
53105812 AAACCCTAAACCATAACCCTTAACTTAAAAACCCTAAACCCTTAACTTA
1 AAACCCTAAACCCTAATCCTTAACTTAAAAA-CCTAAACCCTTAACTTA
53105861 A
1 A
53105862 CTTAAAACCC
Statistics
Matches: 93, Mismatches: 4, Indels: 22
0.78 0.03 0.18
Matches are distributed among these distances:
49 9 0.10
50 33 0.35
51 5 0.05
54 1 0.01
56 5 0.05
57 31 0.33
58 9 0.10
ACGTcount: A:0.46, C:0.30, G:0.01, T:0.24
Consensus pattern (48 bp):
AAACCCTAAACCCTAATCCTTAACTTAAAAACCTAAACCCTTAACTTA
Found at i:53105772 original size:57 final size:53
Alignment explanation
Indices: 53105698--53105861 Score: 185
Period size: 57 Copynumber: 3.0 Consensus size: 53
53105688 TTTAATTGAC
* *
53105698 AAACCCTAAACCTTAAACCCTAATCCTTAACTTAAAAATCCAAAACCCTTAACTTA
1 AAACCCTAAACCCTAAA-CCTAA-CCTTAACTTAAAAA-CCTAAACCCTTAACTTA
53105754 AAACCCATAAACCCTAAACCGTAACCATTAACTTAAAAACACTAAACCCTTAACTTTA
1 AAACCC-TAAACCCTAAACC-TAACC-TTAACTTAAAAAC-CTAAACCCTTAAC-TTA
*
53105812 AAACCCTAAACCAT-AA-C---CCTTAACTTAAAAACCCTAAACCCTTAACTTA
1 AAACCCTAAACCCTAAACCTAACCTTAACTTAAAAA-CCTAAACCCTTAACTTA
53105861 A
1 A
53105862 CTTAAAACCC
Statistics
Matches: 99, Mismatches: 3, Indels: 19
0.82 0.02 0.16
Matches are distributed among these distances:
49 4 0.04
50 25 0.25
51 3 0.03
55 1 0.01
56 13 0.13
57 44 0.44
58 9 0.09
ACGTcount: A:0.46, C:0.30, G:0.01, T:0.23
Consensus pattern (53 bp):
AAACCCTAAACCCTAAACCTAACCTTAACTTAAAAACCTAAACCCTTAACTTA
Found at i:53105793 original size:28 final size:26
Alignment explanation
Indices: 53105762--53105970 Score: 114
Period size: 28 Copynumber: 8.3 Consensus size: 26
53105752 TAAAACCCAT
53105762 AAACCCTAAACCGTAACCATTAACTTAA
1 AAACCCTAAACC-TAACC-TTAACTTAA
* *
53105790 AAACACTAAA-C---CCTTAACTTTA
1 AAACCCTAAACCTAACCTTAACTTAA
53105812 AAACCCTAAACCATAACCCTTAACTTAA
1 AAACCCTAAACC-TAA-CCTTAACTTAA
53105840 AAACCCTAAACCCTTAA-CTTAACTT-A
1 AAACCCTAAA-CC-TAACCTTAACTTAA
* *
53105866 AAACCC---ACATAACCTTAAACTT-T
1 AAACCCTAAACCTAACCTT-AACTTAA
* *
53105889 TAACCCTAAACATATAACCCTTAACTT-A
1 AAACCCTAAAC--CTAA-CCTTAACTTAA
53105917 AAACCCTAAA-C-AA--TTAACTTAAA
1 AAACCCTAAACCTAACCTTAACTT-AA
* *
53105940 AAATCCTAAA-C---CGTTAACTTAA
1 AAACCCTAAACCTAACCTTAACTTAA
53105962 AAACCCTAA
1 AAACCCTAA
53105971 TCCTTGACTG
Statistics
Matches: 149, Mismatches: 13, Indels: 44
0.72 0.06 0.21
Matches are distributed among these distances:
21 10 0.07
22 31 0.21
23 32 0.21
24 2 0.01
26 9 0.06
27 9 0.06
28 47 0.32
29 9 0.06
ACGTcount: A:0.46, C:0.28, G:0.01, T:0.24
Consensus pattern (26 bp):
AAACCCTAAACCTAACCTTAACTTAA
Found at i:53105801 original size:22 final size:22
Alignment explanation
Indices: 53105776--53105970 Score: 90
Period size: 22 Copynumber: 8.0 Consensus size: 22
53105766 CCTAAACCGT
*
53105776 AACCATTAACTTAAAAACACTA
1 AACCATTAACTTAAAAACCCTA
* *
53105798 AACCCTTAACTTTAAAACCCTA
1 AACCATTAACTTAAAAACCCTA
53105820 AACCATAACCCTTAACTTAAAAACCCTA
1 AACC---A---TTAACTTAAAAACCCTA
* *
53105848 AACCCTTAACTTAACTTAAAACCCACA
1 AACCATTAACTT-A---AAAACCC-TA
**
53105875 TAACC-TTAAACTT-TTAACCCTA
1 -AACCATT-AACTTAAAAACCCTA
53105897 AA-CATATAACCCTTAACTTAAAACCCTA
1 AACCAT-TAA--CTT-A---AAAACCCTA
* *
53105925 AACAATTAACTTAAAAAATCCTA
1 AACCATTAACTT-AAAAACCCTA
*
53105948 AACCGTTAACTTAAAAACCCTA
1 AACCATTAACTTAAAAACCCTA
53105970 A
1 A
53105971 TCCTTGACTG
Statistics
Matches: 133, Mismatches: 17, Indels: 46
0.68 0.09 0.23
Matches are distributed among these distances:
20 1 0.01
21 5 0.04
22 42 0.32
23 27 0.20
26 12 0.09
27 3 0.02
28 41 0.31
29 2 0.02
ACGTcount: A:0.47, C:0.28, G:0.01, T:0.25
Consensus pattern (22 bp):
AACCATTAACTTAAAAACCCTA
Found at i:53105817 original size:15 final size:15
Alignment explanation
Indices: 53105797--53105846 Score: 50
Period size: 15 Copynumber: 3.5 Consensus size: 15
53105787 TAAAAACACT
*
53105797 AAACCCTTAACTTTA
1 AAACCCTTAACTTAA
* *
53105812 AAACCCTAAAC--CA
1 AAACCCTTAACTTAA
*
53105825 TAACCCTTAACTTAA
1 AAACCCTTAACTTAA
53105840 AAACCCT
1 AAACCCT
53105847 AAACCCTTAA
Statistics
Matches: 27, Mismatches: 6, Indels: 4
0.73 0.16 0.11
Matches are distributed among these distances:
13 10 0.37
15 17 0.63
ACGTcount: A:0.44, C:0.32, G:0.00, T:0.24
Consensus pattern (15 bp):
AAACCCTTAACTTAA
Found at i:53105877 original size:50 final size:50
Alignment explanation
Indices: 53105775--53105961 Score: 149
Period size: 50 Copynumber: 3.7 Consensus size: 50
53105765 CCCTAAACCG
*
53105775 TAACCATTAACTTAAAAACACTAAACCCTTAAC-T---TTAAAACCCTAAACCA
1 TAACCATTAACTTAAAAACCCTAAACCCTTAACTTAACTTAAAACCC---A-CA
*
53105825 TAACCCTTAACTTAAAAACCCTAAACCCTTAACTTAACTTAAAACCCACA
1 TAACCATTAACTTAAAAACCCTAAACCCTTAACTTAACTTAAAACCCACA
** * *
53105875 TAACC-TTAAACTT-TTAACCCTAAA-CATATAACCCTTAACTTAAAACCC-TA
1 TAACCATT-AACTTAAAAACCCTAAACCCT-TAA--CTTAACTTAAAACCCACA
* * *
53105925 -AACAATTAACTTAAAAAATCCTAAACCGTTAACTTAA
1 TAACCATTAACTT-AAAAACCCTAAACCCTTAACTTAA
53105962 AAACCCTAAT
Statistics
Matches: 114, Mismatches: 11, Indels: 25
0.76 0.07 0.17
Matches are distributed among these distances:
48 2 0.02
49 27 0.24
50 46 0.40
51 28 0.25
52 2 0.02
54 9 0.08
ACGTcount: A:0.46, C:0.27, G:0.01, T:0.26
Consensus pattern (50 bp):
TAACCATTAACTTAAAAACCCTAAACCCTTAACTTAACTTAAAACCCACA
Found at i:53105883 original size:77 final size:77
Alignment explanation
Indices: 53105762--53105938 Score: 211
Period size: 77 Copynumber: 2.3 Consensus size: 77
53105752 TAAAACCCAT
*
53105762 AAACCCTAAA-CCGTAACCATTAACTTAAAAACACTAAACCCTT-AACTTTAAAACCCTAAAC-C
1 AAACCCTAAACCCTTAA-C-TTAACTTAAAAACACTAAACCCTTAAACTTT-AAACCCTAAACAC
53105824 ATAACCCTTAACTTAA
63 ATAACCCTTAACTT-A
* * *
53105840 AAACCCTAAACCCTTAACTTAACTTAAAACCCAC-ATAA-CCTTAAACTTTTAACCCTAAACATA
1 AAACCCTAAACCCTTAACTTAACTTAAAA-ACACTA-AACCCTTAAACTTTAAACCCTAAACACA
53105903 TAACCCTTAACTTA
64 TAACCCTTAACTTA
**
53105917 AAACCCTAAACAATTAACTTAA
1 AAACCCTAAACCCTTAACTTAA
53105939 AAAATCCTAA
Statistics
Matches: 88, Mismatches: 6, Indels: 11
0.84 0.06 0.10
Matches are distributed among these distances:
77 47 0.53
78 36 0.41
79 5 0.06
ACGTcount: A:0.46, C:0.29, G:0.01, T:0.25
Consensus pattern (77 bp):
AAACCCTAAACCCTTAACTTAACTTAAAAACACTAAACCCTTAAACTTTAAACCCTAAACACATA
ACCCTTAACTTA
Found at i:53105898 original size:14 final size:14
Alignment explanation
Indices: 53105874--53105927 Score: 63
Period size: 14 Copynumber: 3.9 Consensus size: 14
53105864 TAAAACCCAC
*
53105874 ATAACCTTAAACTT
1 ATAACCCTAAACTT
* *
53105888 TTAACCCTAAACAT
1 ATAACCCTAAACTT
*
53105902 ATAACCCTTAACTT
1 ATAACCCTAAACTT
*
53105916 AAAACCCTAAAC
1 ATAACCCTAAAC
53105928 AATTAACTTA
Statistics
Matches: 32, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
14 32 1.00
ACGTcount: A:0.44, C:0.28, G:0.00, T:0.28
Consensus pattern (14 bp):
ATAACCCTAAACTT
Found at i:53105933 original size:21 final size:22
Alignment explanation
Indices: 53105909--53105970 Score: 81
Period size: 23 Copynumber: 2.8 Consensus size: 22
53105899 CATATAACCC
53105909 TTAACTT-AAAACCCTAAACAA
1 TTAACTTAAAAACCCTAAACAA
* **
53105930 TTAACTTAAAAAATCCTAAACCG
1 TTAACTT-AAAAACCCTAAACAA
53105953 TTAACTTAAAAACCCTAA
1 TTAACTTAAAAACCCTAA
53105971 TCCTTGACTG
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
21 7 0.20
22 10 0.29
23 18 0.51
ACGTcount: A:0.50, C:0.23, G:0.02, T:0.26
Consensus pattern (22 bp):
TTAACTTAAAAACCCTAAACAA
Found at i:53109321 original size:127 final size:124
Alignment explanation
Indices: 53109068--53109506 Score: 581
Period size: 127 Copynumber: 3.5 Consensus size: 124
53109058 AACATGATAT
* * * *
53109068 TGTAGCAAAAGCGCGTCCACGTGTGCGCGATTTCACAAATTCTTCTGATAAAACATCCTGCTTGA
1 TGTAGCAAAAGCGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTCATAAAGCATCCTGCTTGA
* *
53109133 AGCGTTTTTATACTATTTGCTCAGAAACGTCAAGTCGAAATTATTTTTTCTAGGACTTAC
66 AGCGTTTTTATACTATTTGCTCAGAAACGTCAAGTCGAAATTA-TTTTTCCAGGACCTAC
* * *
53109193 TGTAGCAAAAGCGCGTTCACGAGAGTGCGATTTCACAAATTCTTCTCATAAAGCATCCTGCTTGA
1 TGTAGCAAAAGCGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTCATAAAGCATCCTGCTTGA
* * *
53109258 AGCGTTTTTTTAAACTATATGCTCAGAAACGTTAAGTCGAAATTATTTCTTCCAGGACCTAC
66 AGCG--TTTTTATACTATTTGCTCAGAAACGTCAAGTCGAAATTATTT-TTCCAGGACCTAC
* * * * * *
53109320 TGTAACAAAAGCGCATCCACGAGGGCTCGATTTCACAAATTTTTCTCATAAAGCATCCTTCCTGA
1 TGTAGCAAAAGCGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTCATAAAGCATCCTGCTTGA
* * * * *
53109385 AGCATTTTTATACTATTTGCTCAAAAACCTCAACTCGAAATTATTTTTGCAGGACCTAC
66 AGCGTTTTTATACTATTTGCTCAGAAACGTCAAGTCGAAATTATTTTTCCAGGACCTAC
* * * * * *
53109444 TGTAGCAAAAGCGTGTACACGTGGGCGCGACTTCAGAAATTCTTCTGATAAAGCATCCTGCTT
1 TGTAGCAAAAGCGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTCATAAAGCATCCTGCTT
53109507 TGATTTTATC
Statistics
Matches: 271, Mismatches: 40, Indels: 7
0.85 0.13 0.02
Matches are distributed among these distances:
124 63 0.23
125 99 0.37
126 3 0.01
127 106 0.39
ACGTcount: A:0.29, C:0.22, G:0.17, T:0.31
Consensus pattern (124 bp):
TGTAGCAAAAGCGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTCATAAAGCATCCTGCTTGA
AGCGTTTTTATACTATTTGCTCAGAAACGTCAAGTCGAAATTATTTTTCCAGGACCTAC
Found at i:53124533 original size:126 final size:125
Alignment explanation
Indices: 53124219--53124632 Score: 711
Period size: 125 Copynumber: 3.3 Consensus size: 125
53124209 ATTTATTAAG
* * *
53124219 GAAATTGCTCCTACGTGGACGCGCTTTTGCTACAGTAGGTCTTGAAAAAATAATTTTGAGTTGAC
1 GAAATCGCTCCCACGTGGACGCGCTTTTGCTACAGTAGGTCCTGAAAAAATAATTTTGAGTTGAC
* *
53124284 GTTTCTAAGCAAATAGTATAAAAAACGCTTCAAGCAGGATGCTTTATCAGAAGAATTTCT
66 GTTTCTGAGCAAATAGTATAAAAAATGCTTCAAGCAGGATGCTTTATCAGAAGAATTTCT
* * *
53124344 GAAATCGCTCCCATGTGGACACACTTTTGCTACAGTAGGTCCTGAAAAAATAATTTTGAGTTGAC
1 GAAATCGCTCCCACGTGGACGCGCTTTTGCTACAGTAGGTCCTGAAAAAATAATTTTGAGTTGAC
*
53124409 ATTTCTGAGCAAATAGTATAAAAAATGCTTCAAGCAGGATGCTTTATCAGAAGAATTTCT
66 GTTTCTGAGCAAATAGTATAAAAAATGCTTCAAGCAGGATGCTTTATCAGAAGAATTTCT
*
53124469 GAAATCGCTCCCACCGTGGACGTGCTTTTGCTACAGTAGGTCCTGAAAAAATAATTTTGAGTTGA
1 GAAATCGCTCCCA-CGTGGACGCGCTTTTGCTACAGTAGGTCCTGAAAAAATAATTTTGAGTTGA
*
53124534 CGTTTCTGAGCAAATAGTATAAAAAATGCTTCAAGCAGGATACTTTATCAGAAGAATTTCT
65 CGTTTCTGAGCAAATAGTATAAAAAATGCTTCAAGCAGGATGCTTTATCAGAAGAATTTCT
*
53124595 GAAATCGCTCCCACGTGGACGCGTTTTTGCTACAGTAG
1 GAAATCGCTCCCACGTGGACGCGCTTTTGCTACAGTAG
53124633 CATATTTGGG
Statistics
Matches: 271, Mismatches: 17, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
125 152 0.56
126 119 0.44
ACGTcount: A:0.32, C:0.18, G:0.20, T:0.30
Consensus pattern (125 bp):
GAAATCGCTCCCACGTGGACGCGCTTTTGCTACAGTAGGTCCTGAAAAAATAATTTTGAGTTGAC
GTTTCTGAGCAAATAGTATAAAAAATGCTTCAAGCAGGATGCTTTATCAGAAGAATTTCT
Found at i:53126453 original size:50 final size:50
Alignment explanation
Indices: 53126329--53126576 Score: 284
Period size: 50 Copynumber: 4.8 Consensus size: 50
53126319 GATAATAACA
* * ** * *
53126329 TGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGTTCTCGTGAT-GG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGA-CCTCTCAT-CTCGG
* *
53126380 TGCCCATGCCATGTCCCAGACATGGTCTTATAGGGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
* * *
53126430 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGTCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
*
53126480 TGCC-ATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATGATCTTAAGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTC---ATC-T-CGG
* *
53126534 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGATCTCT
1 -TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCT
53126577 TTACCCAAAT
Statistics
Matches: 170, Mismatches: 19, Indels: 11
0.85 0.09 0.05
Matches are distributed among these distances:
49 37 0.22
50 56 0.33
51 33 0.19
52 2 0.01
53 1 0.01
54 2 0.01
55 4 0.02
56 35 0.21
ACGTcount: A:0.21, C:0.29, G:0.24, T:0.26
Consensus pattern (50 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
Found at i:53126518 original size:99 final size:104
Alignment explanation
Indices: 53126328--53126576 Score: 348
Period size: 99 Copynumber: 2.4 Consensus size: 104
53126318 TGATAATAAC
**
53126328 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGTTCTCGTGATGGTGCCCATGCCATG
1 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGA-CCTCTCGTGATGGTGCCCATGCCATG
* *
53126393 TCCCAGACATGGTCTTATAGGGGACCTCTC-ATC-T-CGG
65 TCCCAGACATGGTCTTACAGGGGACCTCTCAATCTTAAGG
* *
53126430 -TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGT-CTCGGTG-CCATGCCATG
1 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGTGAT-GGTGCCCATGCCATG
53126492 TCCCAGACATGGTCTTACAGGGGACCTCTCATGATCTTAAGG
65 TCCCAGACATGGTCTTACAGGGGACCTCTCA--ATCTTAAGG
* *
53126534 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGATCTCT
1 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGACCTCT
53126577 TTACCCAAAT
Statistics
Matches: 132, Mismatches: 8, Indels: 11
0.87 0.05 0.07
Matches are distributed among these distances:
99 40 0.30
100 10 0.08
101 36 0.27
102 3 0.02
103 1 0.01
104 2 0.02
105 40 0.30
ACGTcount: A:0.21, C:0.29, G:0.24, T:0.26
Consensus pattern (104 bp):
ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGTGATGGTGCCCATGCCATGT
CCCAGACATGGTCTTACAGGGGACCTCTCAATCTTAAGG
Found at i:53126692 original size:13 final size:13
Alignment explanation
Indices: 53126671--53126702 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
53126661 GCTTGGATCA
*
53126671 TCATCAAATAAAT
1 TCATAAAATAAAT
53126684 TCATAAAATAAAT
1 TCATAAAATAAAT
53126697 TCATAA
1 TCATAA
53126703 TTGCTGGAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.56, C:0.12, G:0.00, T:0.31
Consensus pattern (13 bp):
TCATAAAATAAAT
Found at i:53126949 original size:30 final size:30
Alignment explanation
Indices: 53126914--53126971 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
53126904 CCTCGACTCT
*
53126914 AACTTTTTCAAAATTACAATTTTGCCCCTA
1 AACTTTTACAAAATTACAATTTTGCCCCTA
* *
53126944 AACTTTTACATAATTACATTTTTGCCCC
1 AACTTTTACAAAATTACAATTTTGCCCC
53126972 AAGGCTCGGA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.31, C:0.24, G:0.03, T:0.41
Consensus pattern (30 bp):
AACTTTTACAAAATTACAATTTTGCCCCTA
Found at i:53129652 original size:37 final size:37
Alignment explanation
Indices: 53129587--53129732 Score: 233
Period size: 37 Copynumber: 4.0 Consensus size: 37
53129577 TACGTATGAT
* *
53129587 CACTTATCAC-TTG-TCCCTGATCAGATAAGTGTAGC
1 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
* *
53129622 CACCTATCACTTTGTTTCTTGATCACATAAGTGTAGC
1 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
53129659 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
1 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
*
53129696 CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGC
1 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
53129733 TAAAGCTATC
Statistics
Matches: 102, Mismatches: 7, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
35 9 0.09
36 3 0.03
37 90 0.88
ACGTcount: A:0.25, C:0.23, G:0.16, T:0.37
Consensus pattern (37 bp):
CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
Found at i:53129749 original size:46 final size:46
Alignment explanation
Indices: 53129696--53130010 Score: 396
Period size: 46 Copynumber: 6.6 Consensus size: 46
53129686 TAAGTGTAGC
* * **
53129696 CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGCTAAAGCTAT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTATAGCCGAAGCTAT
*
53129742 CACTTATCACTTTGTCTCTTGATCAGATAAGTATAGCCGAAGCTAT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTATAGCCGAAGCTAT
* *
53129788 CACTTATCACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCTGAAGCTAT
1 CACTTATCAC---T---TTGTCACTTGATCAGATAAGTATAGCCGAAGCTAT
53129840 CACTTATCACTTTGTCACTTGATCAGATAAGTATAGCCGAAGCTAT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTATAGCCGAAGCTAT
*
53129886 CACTTATCACTTTATCACTTGATCAGATAAGTATAGCCGAAGCTAT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTATAGCCGAAGCTAT
* * ** *
53129932 TACTTATCACTTTCCACTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
1 CACTTATCAC--T----TTGTCACTTGATCAGATAAGTATAGCCGAAGCTAT
*
53129984 CACTTATCACTTTATCACTTGATCAGA
1 CACTTATCACTTTGTCACTTGATCAGA
53130011 AGTACTCAAA
Statistics
Matches: 240, Mismatches: 17, Indels: 24
0.85 0.06 0.09
Matches are distributed among these distances:
46 155 0.65
48 1 0.00
49 2 0.01
50 1 0.00
52 81 0.34
ACGTcount: A:0.29, C:0.22, G:0.14, T:0.35
Consensus pattern (46 bp):
CACTTATCACTTTGTCACTTGATCAGATAAGTATAGCCGAAGCTAT
Found at i:53129818 original size:98 final size:98
Alignment explanation
Indices: 53129696--53130004 Score: 405
Period size: 98 Copynumber: 3.1 Consensus size: 98
53129686 TAAGTGTAGC
* * * *
53129696 CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGCTAAAGCTATCACTTATCACTTTGTCTCT
1 CACTTTTCAC-TTGTCACTTGATCAGATAAGTGTAGCTGAAGCTATCACTTATCACTTTGTCACT
53129761 TGATCAGATAAGTATAGCCGAAGCTATCACTTAT
65 TGATCAGATAAGTATAGCCGAAGCTATCACTTAT
53129795 CACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCTGAAGCTATCACTTATCACTTTGTCACTT
1 CACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCTGAAGCTATCACTTATCACTTTGTCACTT
53129860 GATCAGATAAGTATAGCCGAAGCTATCACTTAT
66 GATCAGATAAGTATAGCCGAAGCTATCACTTAT
* * *
53129893 CAC-TTT-A----TCACTTGATCAGATAAGTATAGCCGAAGCTATTACTTATCACTTTCCACTTG
1 CACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCTGAAGCTATCACTTATCAC--T----TTG
* ** *
53129952 TCACTTGATCAGATAAGTGTAGCTAAAGCTACCACTTAT
60 TCACTTGATCAGATAAGTATAGCCGAAGCTATCACTTAT
53129991 CACTTTATCACTTG
1 CACTTT-TCACTTG
53130005 ATCAGAAGTA
Statistics
Matches: 186, Mismatches: 11, Indels: 20
0.86 0.05 0.09
Matches are distributed among these distances:
92 39 0.21
94 1 0.01
96 1 0.01
97 3 0.02
98 129 0.69
99 11 0.06
100 1 0.01
101 1 0.01
ACGTcount: A:0.29, C:0.22, G:0.14, T:0.35
Consensus pattern (98 bp):
CACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCTGAAGCTATCACTTATCACTTTGTCACTT
GATCAGATAAGTATAGCCGAAGCTATCACTTAT
Found at i:53129862 original size:144 final size:144
Alignment explanation
Indices: 53129695--53130010 Score: 533
Period size: 144 Copynumber: 2.2 Consensus size: 144
53129685 ATAAGTGTAG
* * * * *
53129695 CCACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGCTAAAGCTATCACTTATCACTTTGTCTC
1 CCACTTATCACTTTGTCACTTGATCAGATAAGTATAGCCAAAGCTATCACTTATCACTTTATCAC
*
53129760 TTGATCAGATAAGTATAGCCGAAGCTATCACTTATCACTTTTCACTTGTCACTTGATCAGATAAG
66 TTGATCAGATAAGTATAGCCGAAGCTATCACTTATCACTTTCCACTTGTCACTTGATCAGATAAG
*
53129825 TGTAGCTGAAGCTA
131 TGTAGCTAAAGCTA
* *
53129839 TCACTTATCACTTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACTTATCACTTTATCAC
1 CCACTTATCACTTTGTCACTTGATCAGATAAGTATAGCCAAAGCTATCACTTATCACTTTATCAC
*
53129904 TTGATCAGATAAGTATAGCCGAAGCTATTACTTATCACTTTCCACTTGTCACTTGATCAGATAAG
66 TTGATCAGATAAGTATAGCCGAAGCTATCACTTATCACTTTCCACTTGTCACTTGATCAGATAAG
53129969 TGTAGCTAAAGCTA
131 TGTAGCTAAAGCTA
*
53129983 CCACTTATCACTTTATCACTTGATCAGA
1 CCACTTATCACTTTGTCACTTGATCAGA
53130011 AGTACTCAAA
Statistics
Matches: 160, Mismatches: 12, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
144 160 1.00
ACGTcount: A:0.29, C:0.22, G:0.14, T:0.35
Consensus pattern (144 bp):
CCACTTATCACTTTGTCACTTGATCAGATAAGTATAGCCAAAGCTATCACTTATCACTTTATCAC
TTGATCAGATAAGTATAGCCGAAGCTATCACTTATCACTTTCCACTTGTCACTTGATCAGATAAG
TGTAGCTAAAGCTA
Found at i:53136814 original size:50 final size:50
Alignment explanation
Indices: 53136690--53136937 Score: 284
Period size: 50 Copynumber: 4.8 Consensus size: 50
53136680 GATAATAACA
* * ** * *
53136690 TGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGTTCTCGTGAT-GG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGA-CCTCTCAT-CTCGG
* *
53136741 TGCCCATGCCATGTCCCAGACATGGTCTTATAGGGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
* * *
53136791 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGTCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
*
53136841 TGCC-ATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATGATCTTAAGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTC---ATC-T-CGG
* *
53136895 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGATCTCT
1 -TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCT
53136938 TTACCCAAAT
Statistics
Matches: 170, Mismatches: 19, Indels: 11
0.85 0.09 0.05
Matches are distributed among these distances:
49 37 0.22
50 56 0.33
51 33 0.19
52 2 0.01
53 1 0.01
54 2 0.01
55 4 0.02
56 35 0.21
ACGTcount: A:0.21, C:0.29, G:0.24, T:0.26
Consensus pattern (50 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
Found at i:53136879 original size:99 final size:104
Alignment explanation
Indices: 53136689--53136937 Score: 348
Period size: 99 Copynumber: 2.4 Consensus size: 104
53136679 TGATAATAAC
**
53136689 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGTTCTCGTGATGGTGCCCATGCCATG
1 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGA-CCTCTCGTGATGGTGCCCATGCCATG
* *
53136754 TCCCAGACATGGTCTTATAGGGGACCTCTC-ATC-T-CGG
65 TCCCAGACATGGTCTTACAGGGGACCTCTCAATCTTAAGG
* *
53136791 -TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGT-CTCGGTG-CCATGCCATG
1 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGTGAT-GGTGCCCATGCCATG
53136853 TCCCAGACATGGTCTTACAGGGGACCTCTCATGATCTTAAGG
65 TCCCAGACATGGTCTTACAGGGGACCTCTCA--ATCTTAAGG
* *
53136895 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGATCTCT
1 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGACCTCT
53136938 TTACCCAAAT
Statistics
Matches: 132, Mismatches: 8, Indels: 11
0.87 0.05 0.07
Matches are distributed among these distances:
99 40 0.30
100 10 0.08
101 36 0.27
102 3 0.02
103 1 0.01
104 2 0.02
105 40 0.30
ACGTcount: A:0.21, C:0.29, G:0.24, T:0.26
Consensus pattern (104 bp):
ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGTGATGGTGCCCATGCCATGT
CCCAGACATGGTCTTACAGGGGACCTCTCAATCTTAAGG
Found at i:53137053 original size:13 final size:13
Alignment explanation
Indices: 53137032--53137063 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
53137022 GCTTGGATCA
*
53137032 TCATCAAATAAAT
1 TCATAAAATAAAT
53137045 TCATAAAATAAAT
1 TCATAAAATAAAT
53137058 TCATAA
1 TCATAA
53137064 TTGCTGGAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.56, C:0.12, G:0.00, T:0.31
Consensus pattern (13 bp):
TCATAAAATAAAT
Found at i:53137310 original size:30 final size:30
Alignment explanation
Indices: 53137275--53137332 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
53137265 CCTCGACTCT
*
53137275 AACTTTTTCAAAATTACAATTTTGCCCCTA
1 AACTTTTACAAAATTACAATTTTGCCCCTA
* * *
53137305 AACTTTTACATAATTACATTTTTTCCCC
1 AACTTTTACAAAATTACAATTTTGCCCC
53137333 AAGGCTCGGA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.31, C:0.24, G:0.02, T:0.43
Consensus pattern (30 bp):
AACTTTTACAAAATTACAATTTTGCCCCTA
Found at i:53141000 original size:44 final size:44
Alignment explanation
Indices: 53140952--53141056 Score: 111
Period size: 49 Copynumber: 2.3 Consensus size: 44
53140942 TATTATTAAG
*
53140952 ATATTTAAAATATTCAATATTTTATTAAATGAAATAATATCAAA
1 ATATTTAAAATATTCAATATTTTATTAAATGAAATAACATCAAA
* ***
53140996 ATATTCAAAATAAACTATTTTGTATTTTATTAAATGAAATAACATCAAA
1 ATATT-----TAAAATATTCAATATTTTATTAAATGAAATAACATCAAA
*
53141045 ATATTCAAAATA
1 ATATTTAAAATA
53141057 AATTATTTTT
Statistics
Matches: 49, Mismatches: 7, Indels: 10
0.74 0.11 0.15
Matches are distributed among these distances:
44 10 0.20
49 39 0.80
ACGTcount: A:0.51, C:0.07, G:0.03, T:0.39
Consensus pattern (44 bp):
ATATTTAAAATATTCAATATTTTATTAAATGAAATAACATCAAA
Found at i:53141028 original size:49 final size:49
Alignment explanation
Indices: 53140969--53141076 Score: 189
Period size: 49 Copynumber: 2.2 Consensus size: 49
53140959 AAATATTCAA
*
53140969 TATTTTATTAAATGAAATAATATCAAAATATTCAAAATAAACTATTTTG
1 TATTTTATTAAATGAAATAACATCAAAATATTCAAAATAAACTATTTTG
* *
53141018 TATTTTATTAAATGAAATAACATCAAAATATTCAAAATAAATTATTTTT
1 TATTTTATTAAATGAAATAACATCAAAATATTCAAAATAAACTATTTTG
53141067 TATTTTATTA
1 TATTTTATTA
53141077 CATTAATATA
Statistics
Matches: 56, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
49 56 1.00
ACGTcount: A:0.47, C:0.06, G:0.03, T:0.44
Consensus pattern (49 bp):
TATTTTATTAAATGAAATAACATCAAAATATTCAAAATAAACTATTTTG
Found at i:53141526 original size:18 final size:18
Alignment explanation
Indices: 53141500--53141542 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
53141490 GACTAGAACA
* * *
53141500 AGGAAACATATAAGGGTT
1 AGGATACATAAAAGGGCT
53141518 AGGATACATAAAAGGGCT
1 AGGATACATAAAAGGGCT
53141536 AGGATAC
1 AGGATAC
53141543 GCACCTGGCA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.44, C:0.09, G:0.28, T:0.19
Consensus pattern (18 bp):
AGGATACATAAAAGGGCT
Found at i:53143152 original size:33 final size:34
Alignment explanation
Indices: 53143115--53143179 Score: 89
Period size: 35 Copynumber: 1.9 Consensus size: 34
53143105 ACAAAATTTT
*
53143115 ATAAATAATAAA-TT-AATAATTATTTAAAAATGC
1 ATAAATAAAAAACTTAAATAA-TATTTAAAAATGC
53143148 ATAAATAAAAAATCTTAAATAATATTTAAAAA
1 ATAAATAAAAAA-CTTAAATAATATTTAAAAA
53143180 ATAAATTTAA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
33 11 0.39
35 12 0.43
36 5 0.18
ACGTcount: A:0.62, C:0.03, G:0.02, T:0.34
Consensus pattern (34 bp):
ATAAATAAAAAACTTAAATAATATTTAAAAATGC
Found at i:53143355 original size:22 final size:22
Alignment explanation
Indices: 53143330--53143374 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
53143320 TAGGGATGTA
53143330 AGAGAAATTTAAGAGAAAATTG
1 AGAGAAATTTAAGAGAAAATTG
* * *
53143352 AGAGCAATTTGAGAGGAAATTG
1 AGAGAAATTTAAGAGAAAATTG
53143374 A
1 A
53143375 TAATATAATT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.49, C:0.02, G:0.27, T:0.22
Consensus pattern (22 bp):
AGAGAAATTTAAGAGAAAATTG
Found at i:53149436 original size:6 final size:6
Alignment explanation
Indices: 53149425--53149458 Score: 68
Period size: 6 Copynumber: 5.7 Consensus size: 6
53149415 CCATATCAAA
53149425 CAAAGG CAAAGG CAAAGG CAAAGG CAAAGG CAAA
1 CAAAGG CAAAGG CAAAGG CAAAGG CAAAGG CAAA
53149459 ATGTTGTTGG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.53, C:0.18, G:0.29, T:0.00
Consensus pattern (6 bp):
CAAAGG
Found at i:53156432 original size:37 final size:37
Alignment explanation
Indices: 53156378--53156473 Score: 120
Period size: 37 Copynumber: 2.6 Consensus size: 37
53156368 ATATATTGTA
* * *
53156378 AGGTTATCAGTCCAGGCTAAACCTATAACATAACATC
1 AGGTTACCAGTCTAGGCTAAACCTATAAAATAACATC
* * *
53156415 AGGTTACCAGTCTAGGCTAAATCTATAAAATGACATT
1 AGGTTACCAGTCTAGGCTAAACCTATAAAATAACATC
* *
53156452 AAGTTACAAGTCTAGGCTAAAC
1 AGGTTACCAGTCTAGGCTAAAC
53156474 ATGTGTCACA
Statistics
Matches: 50, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
37 50 1.00
ACGTcount: A:0.39, C:0.20, G:0.16, T:0.26
Consensus pattern (37 bp):
AGGTTACCAGTCTAGGCTAAACCTATAAAATAACATC
Found at i:53160801 original size:34 final size:34
Alignment explanation
Indices: 53160755--53160844 Score: 110
Period size: 34 Copynumber: 2.6 Consensus size: 34
53160745 GTTTTTTTTT
*
53160755 AAAATGAACTAAATTAGGTTTTTGGGGTTTTAA-
1 AAAATTAACTAAATTAGGTTTTTGGGGTTTTAAG
* * *
53160788 ATAAATTAACTAAATTTGGGTTTTGGGTTTTTAAG
1 A-AAATTAACTAAATTAGGTTTTTGGGGTTTTAAG
*
53160823 AAAATTAATTAAATTATGGTTT
1 AAAATTAACTAAATTA-GGTTT
53160845 AGTTTTTTTA
Statistics
Matches: 47, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
33 1 0.02
34 41 0.87
35 5 0.11
ACGTcount: A:0.37, C:0.02, G:0.18, T:0.43
Consensus pattern (34 bp):
AAAATTAACTAAATTAGGTTTTTGGGGTTTTAAG
Found at i:53161120 original size:126 final size:126
Alignment explanation
Indices: 53160889--53161473 Score: 764
Period size: 126 Copynumber: 4.6 Consensus size: 126
53160879 GAATAGACAA
* * * * *
53160889 TGTAAAAAATGTTTCAAGTAGGATGCCCTGTCAGCAAAATTACTAAAAAAAAGTTCCCACGTGGA
1 TGTAAAAAATGCTTCAAGCAGGATGCACTGTCAGCAAAATTACT-GAAAAAAGCTCCCACGTGGA
* * * *
53160954 TGCTTTTTTTCTATAGTTATTCCTAAAAAAATAATTTTGAGAAGAATGTTCAGAACAAATAG
65 CGCTCTTTTTCTACAGATATTCCTAAAAAAATAATTTTGAGAAGAATGTTCAGAACAAATAG
*
53161016 TGTAAAAAATGCTTCAAGCATGATGCACTGTCAGCAAAATTACTGAAAAAAGCTCCCACGTGGAC
1 TGTAAAAAATGCTTCAAGCAGGATGCACTGTCAGCAAAATTACTGAAAAAAGCTCCCACGTGGAC
* ** * * * * *
53161081 GCTCTTTTTCTACA-ATAGTTCCTGAAAAAATAATTTTGAGAAG-GCGATTCTGAATAGACAA
66 GCTCTTTTTCTACAGATA-TTCCTAAAAAAATAATTTTGAGAAGAATG-TTCAGAACAAATAG
* * * * *
53161142 TGTAAAAAATGTTTCAAGTAGGATGCCCTGTCAGCAAAATTACTAAAAAAAAGTTCCCACGTGGA
1 TGTAAAAAATGCTTCAAGCAGGATGCACTGTCAGCAAAATTACT-GAAAAAAGCTCCCACGTGGA
* * *
53161207 TGCTTTTTTTCTACAGTTATTCCTAAAAAAATAATTTTGAGAAGAATGTTCAGAACAAATAG
65 CGCTCTTTTTCTACAGATATTCCTAAAAAAATAATTTTGAGAAGAATGTTCAGAACAAATAG
*
53161269 TGTAAAAAATGCTTCAAGCATGATGCACTGTCAGCAAAATTACTGAAAAAAGCTCCCACGTGGAC
1 TGTAAAAAATGCTTCAAGCAGGATGCACTGTCAGCAAAATTACTGAAAAAAGCTCCCACGTGGAC
* ** *
53161334 GCTCTTTTTCTACA-ATAGTTCCTGAAAAAATAATTTTGAGAAGACGGTTCTGAACAAATAG
66 GCTCTTTTTCTACAGATA-TTCCTAAAAAAATAATTTTGAGAAGAATGTTCAGAACAAATAG
* * * * * *
53161395 TGT-AAAAACGCTTCAAGCAGGATGCACTGTCAGCAAAATTATTGGAAAAATCTCTCACGTGTAC
1 TGTAAAAAATGCTTCAAGCAGGATGCACTGTCAGCAAAATTACTGAAAAAAGCTCCCACGTGGAC
53161459 GCTCTTTTTCTACAG
66 GCTCTTTTTCTACAG
53161474 TAGCTCATGT
Statistics
Matches: 396, Mismatches: 55, Indels: 15
0.85 0.12 0.03
Matches are distributed among these distances:
125 73 0.18
126 176 0.44
127 144 0.36
128 3 0.01
ACGTcount: A:0.37, C:0.17, G:0.17, T:0.29
Consensus pattern (126 bp):
TGTAAAAAATGCTTCAAGCAGGATGCACTGTCAGCAAAATTACTGAAAAAAGCTCCCACGTGGAC
GCTCTTTTTCTACAGATATTCCTAAAAAAATAATTTTGAGAAGAATGTTCAGAACAAATAG
Found at i:53161302 original size:253 final size:253
Alignment explanation
Indices: 53160854--53161435 Score: 1058
Period size: 253 Copynumber: 2.3 Consensus size: 253
53160844 TAGTTTTTTT
53160854 AAAATAATTTTGAGAAGGCGATTCTGAATAGACAATGTAAAAAATGTTTCAAGTAGGATGCCCTG
1 AAAATAATTTTGAGAAGGCGATTCTGAATAGACAATGTAAAAAATGTTTCAAGTAGGATGCCCTG
*
53160919 TCAGCAAAATTACTAAAAAAAAGTTCCCACGTGGATGCTTTTTTTCTATAGTTATTCCTAAAAAA
66 TCAGCAAAATTACTAAAAAAAAGTTCCCACGTGGATGCTTTTTTTCTACAGTTATTCCTAAAAAA
53160984 ATAATTTTGAGAAGAATGTTCAGAACAAATAGTGTAAAAAATGCTTCAAGCATGATGCACTGTCA
131 ATAATTTTGAGAAGAATGTTCAGAACAAATAGTGTAAAAAATGCTTCAAGCATGATGCACTGTCA
53161049 GCAAAATTACTGAAAAAAGCTCCCACGTGGACGCTCTTTTTCTACAATAGTTCCTGAA
196 GCAAAATTACTGAAAAAAGCTCCCACGTGGACGCTCTTTTTCTACAATAGTTCCTGAA
53161107 AAAATAATTTTGAGAAGGCGATTCTGAATAGACAATGTAAAAAATGTTTCAAGTAGGATGCCCTG
1 AAAATAATTTTGAGAAGGCGATTCTGAATAGACAATGTAAAAAATGTTTCAAGTAGGATGCCCTG
53161172 TCAGCAAAATTACTAAAAAAAAGTTCCCACGTGGATGCTTTTTTTCTACAGTTATTCCTAAAAAA
66 TCAGCAAAATTACTAAAAAAAAGTTCCCACGTGGATGCTTTTTTTCTACAGTTATTCCTAAAAAA
53161237 ATAATTTTGAGAAGAATGTTCAGAACAAATAGTGTAAAAAATGCTTCAAGCATGATGCACTGTCA
131 ATAATTTTGAGAAGAATGTTCAGAACAAATAGTGTAAAAAATGCTTCAAGCATGATGCACTGTCA
53161302 GCAAAATTACTGAAAAAAGCTCCCACGTGGACGCTCTTTTTCTACAATAGTTCCTGAA
196 GCAAAATTACTGAAAAAAGCTCCCACGTGGACGCTCTTTTTCTACAATAGTTCCTGAA
* * * * * * * * * *
53161360 AAAATAATTTTGAGAAGACGGTTCTGAACAAATAGTGT-AAAAACGCTTCAAGCAGGATGCACTG
1 AAAATAATTTTGAGAAGGCGATTCTGAATAGACAATGTAAAAAATGTTTCAAGTAGGATGCCCTG
53161424 TCAGCAAAATTA
66 TCAGCAAAATTA
53161436 TTGGAAAAAT
Statistics
Matches: 318, Mismatches: 11, Indels: 1
0.96 0.03 0.00
Matches are distributed among these distances:
252 34 0.11
253 284 0.89
ACGTcount: A:0.39, C:0.16, G:0.17, T:0.28
Consensus pattern (253 bp):
AAAATAATTTTGAGAAGGCGATTCTGAATAGACAATGTAAAAAATGTTTCAAGTAGGATGCCCTG
TCAGCAAAATTACTAAAAAAAAGTTCCCACGTGGATGCTTTTTTTCTACAGTTATTCCTAAAAAA
ATAATTTTGAGAAGAATGTTCAGAACAAATAGTGTAAAAAATGCTTCAAGCATGATGCACTGTCA
GCAAAATTACTGAAAAAAGCTCCCACGTGGACGCTCTTTTTCTACAATAGTTCCTGAA
Found at i:53163203 original size:11 final size:10
Alignment explanation
Indices: 53163175--53163227 Score: 58
Period size: 10 Copynumber: 5.3 Consensus size: 10
53163165 TTTAAAATAC
53163175 TTTTTTAAA-
1 TTTTTTAAAT
53163184 -TTTTTAAAT
1 TTTTTTAAAT
53163193 TTTTTTAAAAT
1 TTTTTT-AAAT
53163204 ACTTTTTT-AAT
1 --TTTTTTAAAT
53163215 TTTTTTAAAT
1 TTTTTTAAAT
53163225 TTT
1 TTT
53163228 AAAATATTTT
Statistics
Matches: 38, Mismatches: 0, Indels: 11
0.78 0.00 0.22
Matches are distributed among these distances:
8 8 0.21
9 6 0.16
10 11 0.29
11 7 0.18
13 6 0.16
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.68
Consensus pattern (10 bp):
TTTTTTAAAT
Found at i:53163203 original size:31 final size:32
Alignment explanation
Indices: 53163165--53163227 Score: 110
Period size: 31 Copynumber: 2.0 Consensus size: 32
53163155 ATTTTTTTAG
53163165 TTTAAAATACTTTTTTAA-ATTTTTAAATTTT
1 TTTAAAATACTTTTTTAATATTTTTAAATTTT
*
53163196 TTTAAAATACTTTTTTAATTTTTTTAAATTTT
1 TTTAAAATACTTTTTTAATATTTTTAAATTTT
53163228 AAAATATTTT
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
31 18 0.60
32 12 0.40
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.63
Consensus pattern (32 bp):
TTTAAAATACTTTTTTAATATTTTTAAATTTT
Found at i:53163225 original size:40 final size:41
Alignment explanation
Indices: 53163175--53163273 Score: 146
Period size: 40 Copynumber: 2.4 Consensus size: 41
53163165 TTTAAAATAC
* *
53163175 TTTTTTAAATTTTTAAATTTTTTTAAAATACTTTTTTAA-T
1 TTTTTTAAATTTTTAAATATTTTTAAAATACTGTTTTAATT
*
53163215 TTTTTTAAATTTTAAAATATTTTTAAAATACTGTTTTAATT
1 TTTTTTAAATTTTTAAATATTTTTAAAATACTGTTTTAATT
*
53163256 TTTGTTTTAATTTTTAAA
1 TTT-TTTAAATTTTTAAA
53163274 ATAAATTTTT
Statistics
Matches: 52, Mismatches: 5, Indels: 2
0.88 0.08 0.03
Matches are distributed among these distances:
40 36 0.69
41 4 0.08
42 12 0.23
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.63
Consensus pattern (41 bp):
TTTTTTAAATTTTTAAATATTTTTAAAATACTGTTTTAATT
Found at i:53163253 original size:13 final size:11
Alignment explanation
Indices: 53163165--53163244 Score: 50
Period size: 11 Copynumber: 7.8 Consensus size: 11
53163155 ATTTTTTTAG
53163165 TTTAAAATACTT
1 TTTAAAATA-TT
*
53163177 TTT-TAA-ATT
1 TTTAAAATATT
*
53163186 TTT-AAATTTT
1 TTTAAAATATT
53163196 TTTAAAATACTT
1 TTTAAAATA-TT
*
53163208 TTT-TAAT-TT
1 TTTAAAATATT
*
53163217 TTT-TAA-A-T
1 TTTAAAATATT
53163225 TTTAAAATATT
1 TTTAAAATATT
53163236 TTTAAAATA
1 TTTAAAATA
53163245 CTGTTTTAAT
Statistics
Matches: 55, Mismatches: 6, Indels: 15
0.72 0.08 0.20
Matches are distributed among these distances:
8 4 0.07
9 17 0.31
10 7 0.13
11 19 0.35
12 8 0.15
ACGTcount: A:0.39, C:0.03, G:0.00, T:0.59
Consensus pattern (11 bp):
TTTAAAATATT
Found at i:53163263 original size:12 final size:12
Alignment explanation
Indices: 53163246--53163270 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
53163236 TTTAAAATAC
53163246 TGTTTTAATTTT
1 TGTTTTAATTTT
53163258 TGTTTTAATTTT
1 TGTTTTAATTTT
53163270 T
1 T
53163271 AAAATAAATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.16, C:0.00, G:0.08, T:0.76
Consensus pattern (12 bp):
TGTTTTAATTTT
Found at i:53165096 original size:24 final size:24
Alignment explanation
Indices: 53165042--53165096 Score: 67
Period size: 25 Copynumber: 2.2 Consensus size: 24
53165032 GAACTTCTAA
*
53165042 TTTATTAAAAATATAAAAATAAAT
1 TTTATTAAAAATATAAAAACAAAT
*
53165066 TTCTATT-AAAATATTAAAAACAACT
1 TT-TATTAAAAATA-TAAAAACAAAT
53165091 TTTATT
1 TTTATT
53165097 TTATTAAATG
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
24 12 0.44
25 15 0.56
ACGTcount: A:0.53, C:0.05, G:0.00, T:0.42
Consensus pattern (24 bp):
TTTATTAAAAATATAAAAACAAAT
Found at i:53165149 original size:94 final size:93
Alignment explanation
Indices: 53165044--53165239 Score: 313
Period size: 95 Copynumber: 2.1 Consensus size: 93
53165034 ACTTCTAATT
*
53165044 TATTAAAAATATAAAAA-TAAATTTCTATTAAAATATTAAAAACAACTTTTATTTTATTAAATGA
1 TATTAAAAATATAAAAAGTAAATTACTATTAAAATATTAAAAACAACTTTTATTTTATTAAATGA
*
53165108 AACAATATAAAAAACCAATTTGTACAAGTA
66 AACAATAT-AAAAA-CAATTTGTACAAATA
**
53165138 TATTAAAAATATAAAAAGTAAATTACTATTACTATATTAAAAACAACTTTTATTTTATTAAATGA
1 TATTAAAAATATAAAAAGTAAATTACTATTAAAATATTAAAAACAACTTTTATTTTATTAAATGA
* *
53165203 AACAATATAAAAATAGTTTGTACAAATA
66 AACAATATAAAAACAATTTGTACAAATA
53165231 TATTAAAAA
1 TATTAAAAA
53165240 ATCCATGTTG
Statistics
Matches: 95, Mismatches: 6, Indels: 3
0.91 0.06 0.03
Matches are distributed among these distances:
93 21 0.22
94 22 0.23
95 52 0.55
ACGTcount: A:0.54, C:0.07, G:0.04, T:0.36
Consensus pattern (93 bp):
TATTAAAAATATAAAAAGTAAATTACTATTAAAATATTAAAAACAACTTTTATTTTATTAAATGA
AACAATATAAAAACAATTTGTACAAATA
Found at i:53167033 original size:23 final size:23
Alignment explanation
Indices: 53166998--53167050 Score: 88
Period size: 23 Copynumber: 2.3 Consensus size: 23
53166988 AGTGTTATTG
*
53166998 ATCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGGAGCTTCGGCTACAT
*
53167021 TTCAGTGGGAGCTTCGGCTACAT
1 ATCAGTGGGAGCTTCGGCTACAT
53167044 ATCAGTG
1 ATCAGTG
53167051 TGGCACTTAT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.21, C:0.21, G:0.28, T:0.30
Consensus pattern (23 bp):
ATCAGTGGGAGCTTCGGCTACAT
Found at i:53167222 original size:38 final size:37
Alignment explanation
Indices: 53167180--53167252 Score: 103
Period size: 38 Copynumber: 1.9 Consensus size: 37
53167170 ATGTGTAGAA
* *
53167180 TTGAATTGAATATTGACTTGAAAA-TGGAAAAGTGAATT
1 TTGAATTGAATAGTGA-TT-AAAAGTGAAAAAGTGAATT
53167218 TTGAATTGAATAGTGATTAAAAGTGAAAAAGTGAA
1 TTGAATTGAATAGTGATTAAAAGTGAAAAAGTGAA
53167253 ATTATGAAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
36 4 0.12
37 13 0.41
38 15 0.47
ACGTcount: A:0.45, C:0.01, G:0.22, T:0.32
Consensus pattern (37 bp):
TTGAATTGAATAGTGATTAAAAGTGAAAAAGTGAATT
Found at i:53171884 original size:19 final size:21
Alignment explanation
Indices: 53171849--53171894 Score: 78
Period size: 19 Copynumber: 2.3 Consensus size: 21
53171839 ATGCATGTAT
53171849 ATAAAAACATAAAGTATAAAA
1 ATAAAAACATAAAGTATAAAA
53171870 ATAAAAA-AT-AAGTATAAAA
1 ATAAAAACATAAAGTATAAAA
53171889 ATAAAA
1 ATAAAA
53171895 GTAATAATAA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
19 16 0.64
20 2 0.08
21 7 0.28
ACGTcount: A:0.74, C:0.02, G:0.04, T:0.20
Consensus pattern (21 bp):
ATAAAAACATAAAGTATAAAA
Found at i:53176297 original size:39 final size:37
Alignment explanation
Indices: 53176230--53176322 Score: 98
Period size: 39 Copynumber: 2.5 Consensus size: 37
53176220 ACCAGAATGG
* *
53176230 CACCCAGTGCCTCATCGGATAGTTCGAAGCAATAGTTGA
1 CACCCAGTGCCTCATCGGAAAGTCCGAAG-AA-AGTTGA
* *
53176269 CACCCAGTGTCTCATCGGCAAAG-CCGAAGAAAGTTGG
1 CACCCAGTGCCTCATCGG-AAAGTCCGAAGAAAGTTGA
* *
53176306 TACCCAGTACCTCATCG
1 CACCCAGTGCCTCATCG
53176323 AATCTATCCG
Statistics
Matches: 46, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
37 19 0.41
38 2 0.04
39 22 0.48
40 3 0.07
ACGTcount: A:0.28, C:0.29, G:0.23, T:0.20
Consensus pattern (37 bp):
CACCCAGTGCCTCATCGGAAAGTCCGAAGAAAGTTGA
Found at i:53177448 original size:17 final size:16
Alignment explanation
Indices: 53177416--53177449 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
53177406 TTGGCTATTC
*
53177416 TGTTTCTTTCTTCTTT
1 TGTTTCTTTATTCTTT
53177432 TGTTTCTTTTATTCTTT
1 TGTTTC-TTTATTCTTT
53177449 T
1 T
53177450 ATTTTAACTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.03, C:0.15, G:0.06, T:0.76
Consensus pattern (16 bp):
TGTTTCTTTATTCTTT
Found at i:53177497 original size:14 final size:14
Alignment explanation
Indices: 53177438--53177488 Score: 50
Period size: 14 Copynumber: 3.6 Consensus size: 14
53177428 CTTTTGTTTC
*
53177438 TTTTA-TTCTTTTA
1 TTTTATTTCCTTTA
* *
53177451 TTTTAACTTACTTTA
1 TTTT-ATTTCCTTTA
*
53177466 CTTTATTTCCTTTA
1 TTTTATTTCCTTTA
53177480 TTTTATTTC
1 TTTTATTTC
53177489 TTTTGTTTTC
Statistics
Matches: 30, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
13 4 0.13
14 17 0.57
15 9 0.30
ACGTcount: A:0.18, C:0.14, G:0.00, T:0.69
Consensus pattern (14 bp):
TTTTATTTCCTTTA
Found at i:53178414 original size:16 final size:16
Alignment explanation
Indices: 53178393--53178425 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
53178383 CTTAGAAAAA
53178393 AACGCCGCTAAAGAAC
1 AACGCCGCTAAAGAAC
53178409 AACGCCGCTAAAGAAC
1 AACGCCGCTAAAGAAC
53178425 A
1 A
53178426 TGTTCTTTAG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.45, C:0.30, G:0.18, T:0.06
Consensus pattern (16 bp):
AACGCCGCTAAAGAAC
Found at i:53179204 original size:24 final size:24
Alignment explanation
Indices: 53179164--53179216 Score: 61
Period size: 25 Copynumber: 2.1 Consensus size: 24
53179154 ACTGTTATAA
* *
53179164 AAAATTATAAAATTAAAATAAATT
1 AAAATTACAAAATTAAAAAAAATT
*
53179188 AAAATTACATAAATAAAAAAAATATT
1 AAAATTACA-AAATTAAAAAAA-ATT
53179214 AAA
1 AAA
53179217 TAGTATTAAG
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
24 8 0.33
25 10 0.42
26 6 0.25
ACGTcount: A:0.70, C:0.02, G:0.00, T:0.28
Consensus pattern (24 bp):
AAAATTACAAAATTAAAAAAAATT
Found at i:53180481 original size:30 final size:30
Alignment explanation
Indices: 53180447--53180509 Score: 117
Period size: 30 Copynumber: 2.1 Consensus size: 30
53180437 ACTTAACAAG
*
53180447 CAAATGTCTCTAAAATAATAACAAAATTAA
1 CAAATGCCTCTAAAATAATAACAAAATTAA
53180477 CAAATGCCTCTAAAATAATAACAAAATTAA
1 CAAATGCCTCTAAAATAATAACAAAATTAA
53180507 CAA
1 CAA
53180510 TAAAACTAGT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.57, C:0.16, G:0.03, T:0.24
Consensus pattern (30 bp):
CAAATGCCTCTAAAATAATAACAAAATTAA
Found at i:53185356 original size:97 final size:99
Alignment explanation
Indices: 53185253--53185455 Score: 268
Period size: 97 Copynumber: 2.1 Consensus size: 99
53185243 TTTTTAATTC
* *
53185253 ATATTTTTAATTAATAACTCTTTTATTTATA-TAAATAAAATAATAAGCATGTAATTATATAAT-
1 ATATTTTTAATTAATAACTCATTTATTTATACT-AATAAAATAATAAACATGTAATTATATAATG
53185316 AAA-AATATATTTTATATATATCATTAAGTTAAAA
65 AAATAATATATTTTATATATATCATTAAGTTAAAA
* * * * *
53185350 ATATTTTTAATTAATAACTCATTTATTTATACTTATAAATTAATAAATATGTCATTCTATAATGA
1 ATATTTTTAATTAATAACTCATTTATTTATACTAATAAAATAATAAACATGTAATTATATAATGA
* * * * *
53185415 AATTATATATTTTATATTTATTATTATGTTAAAT
66 AATAATATATTTTATATATATCATTAAGTTAAAA
53185449 ATATTTT
1 ATATTTT
53185456 ATTGTAACTA
Statistics
Matches: 91, Mismatches: 12, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
97 54 0.59
98 4 0.04
99 33 0.36
ACGTcount: A:0.44, C:0.04, G:0.03, T:0.49
Consensus pattern (99 bp):
ATATTTTTAATTAATAACTCATTTATTTATACTAATAAAATAATAAACATGTAATTATATAATGA
AATAATATATTTTATATATATCATTAAGTTAAAA
Found at i:53191187 original size:46 final size:46
Alignment explanation
Indices: 53191109--53191293 Score: 307
Period size: 46 Copynumber: 4.0 Consensus size: 46
53191099 ACATTACTAT
* *
53191109 AACTCAGTATGGTTTTCTTCACGGAAATACCATACCTACTTTTCAC
1 AACTCAGTATGGTTTTCTTCACTGAAACACCATACCTACTTTTCAC
* *
53191155 AACTCAGTATGGTTTTCTTTACTGAAACACCATACCTACTTTTAAC
1 AACTCAGTATGGTTTTCTTCACTGAAACACCATACCTACTTTTCAC
*
53191201 AACTCAGTATGGTTTTCTTCACTGAAACACCATACCTACTTTTCAT
1 AACTCAGTATGGTTTTCTTCACTGAAACACCATACCTACTTTTCAC
* *
53191247 AACTTAGTATGGTTTTCTTCACCGAAACACCATACCTACTTTTCAC
1 AACTCAGTATGGTTTTCTTCACTGAAACACCATACCTACTTTTCAC
53191293 A
1 A
53191294 CATTGCCATG
Statistics
Matches: 129, Mismatches: 10, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
46 129 1.00
ACGTcount: A:0.29, C:0.26, G:0.09, T:0.36
Consensus pattern (46 bp):
AACTCAGTATGGTTTTCTTCACTGAAACACCATACCTACTTTTCAC
Found at i:53195515 original size:157 final size:157
Alignment explanation
Indices: 53195269--53195573 Score: 540
Period size: 157 Copynumber: 1.9 Consensus size: 157
53195259 ATGAGTCTCA
*
53195269 AGATGAACGCTCCAGATCCAGTTCGGCGCAGGTTAGTTTGGATTTCTTCTTCTCATCTTTTGATT
1 AGATGAACGCTCCAGATCCAGTTCGGCGCAGGTTAGTTTGGATTTCTTCCTCTCATCTTTTGATT
* *
53195334 CTTATGTTATATCTTGGTTAAAAAAGAAAAAAAATTGCTGATTGAGTTTGATAATGTTCGCAGGC
66 CTTATGTTATATCATAGTTAAAAAAGAAAAAAAATTGCTGATTGAGTTTGATAATGTTCGCAGGC
53195399 GGTGTCAGGGGATCAGGAACACCAACG
131 GGTGTCAGGGGATCAGGAACACCAACG
* *
53195426 AGATGAACGCTCCAGATCCAGTTGGGCGCAGGTTAGTTTGGATTTCTTCCTCTGATCTTTTGATT
1 AGATGAACGCTCCAGATCCAGTTCGGCGCAGGTTAGTTTGGATTTCTTCCTCTCATCTTTTGA-T
53195491 TCTTATGTTATATCATAGTT-AAAAAGAAAAAAAATTGCTGATTGAGTTTGATAATGTTCGCAGG
65 TCTTATGTTATATCATAGTTAAAAAAGAAAAAAAATTGCTGATTGAGTTTGATAATGTTCGCAGG
*
53195555 TGGTGTCAGGGGATCAGGA
130 CGGTGTCAGGGGATCAGGA
53195574 TCACGAAAAA
Statistics
Matches: 141, Mismatches: 6, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
157 122 0.87
158 19 0.13
ACGTcount: A:0.27, C:0.15, G:0.24, T:0.33
Consensus pattern (157 bp):
AGATGAACGCTCCAGATCCAGTTCGGCGCAGGTTAGTTTGGATTTCTTCCTCTCATCTTTTGATT
CTTATGTTATATCATAGTTAAAAAAGAAAAAAAATTGCTGATTGAGTTTGATAATGTTCGCAGGC
GGTGTCAGGGGATCAGGAACACCAACG
Found at i:53214336 original size:48 final size:48
Alignment explanation
Indices: 53214280--53214373 Score: 188
Period size: 48 Copynumber: 2.0 Consensus size: 48
53214270 ATTTTAGTAA
53214280 AAACATAAAAAATAATTTATTGTAATTTGTTATTTATATTTCAATACT
1 AAACATAAAAAATAATTTATTGTAATTTGTTATTTATATTTCAATACT
53214328 AAACATAAAAAATAATTTATTGTAATTTGTTATTTATATTTCAATA
1 AAACATAAAAAATAATTTATTGTAATTTGTTATTTATATTTCAATA
53214374 TATGAAATAT
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
48 46 1.00
ACGTcount: A:0.45, C:0.05, G:0.04, T:0.46
Consensus pattern (48 bp):
AAACATAAAAAATAATTTATTGTAATTTGTTATTTATATTTCAATACT
Found at i:53214647 original size:16 final size:17
Alignment explanation
Indices: 53214621--53214655 Score: 63
Period size: 16 Copynumber: 2.1 Consensus size: 17
53214611 GGTTCGCTGT
53214621 ATTGAAATAGAGGCGTA
1 ATTGAAATAGAGGCGTA
53214638 ATTG-AATAGAGGCGTA
1 ATTGAAATAGAGGCGTA
53214654 AT
1 AT
53214656 AGCAATTCAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 14 0.78
17 4 0.22
ACGTcount: A:0.40, C:0.06, G:0.29, T:0.26
Consensus pattern (17 bp):
ATTGAAATAGAGGCGTA
Found at i:53214690 original size:45 final size:44
Alignment explanation
Indices: 53214635--53214731 Score: 133
Period size: 44 Copynumber: 2.2 Consensus size: 44
53214625 AAATAGAGGC
*
53214635 GTAATTGAATAGAGGCGTAATAGCAATTCAAT-TGTTTGGTTGAAT
1 GTAATGGAATAGAGGCGTAATAG-AATTC-ATGTGTTTGGTTGAAT
* *
53214680 GTAATGGAATAGAGGCGTAATAGTATTCTTGTGTTTGGTTGAAT
1 GTAATGGAATAGAGGCGTAATAGAATTCATGTGTTTGGTTGAAT
*
53214724 GGAATGGA
1 GTAATGGA
53214732 GGTGTAAGAA
Statistics
Matches: 47, Mismatches: 4, Indels: 3
0.87 0.07 0.06
Matches are distributed among these distances:
43 1 0.02
44 24 0.51
45 22 0.47
ACGTcount: A:0.31, C:0.05, G:0.29, T:0.35
Consensus pattern (44 bp):
GTAATGGAATAGAGGCGTAATAGAATTCATGTGTTTGGTTGAAT
Found at i:53215017 original size:59 final size:57
Alignment explanation
Indices: 53214858--53215033 Score: 158
Period size: 59 Copynumber: 3.0 Consensus size: 57
53214848 TTAATCATAT
* * *
53214858 TTTAACATAATTATTATTAAAAATATTTTAATTAAAATATATAATTTAATAAAATTC
1 TTTAACATAATTATTATTAAATATATTTTAATTAAAATATATAATCTAATAAAATTA
* * * ** * * *
53214915 TTAATAATCA-ATATTCTTATATAAATTTACTAAAATCATAATATATGATACT-ATAAAATATAA
1 TT--TAA-CATA-ATTATTAT-TAAATATATTTTAATTAAAATATATAAT-CTAATAAAAT-T-A
*
53214978 TTTAACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATT
1 TTTAACATAATTATTATTAAATATATTTTAATTAAAATATATAATCTAATAAAATT
53215034 CTTAATAATC
Statistics
Matches: 89, Mismatches: 20, Indels: 19
0.70 0.16 0.15
Matches are distributed among these distances:
57 2 0.02
58 2 0.02
59 32 0.36
60 18 0.20
61 31 0.35
62 2 0.02
63 2 0.02
ACGTcount: A:0.51, C:0.05, G:0.01, T:0.44
Consensus pattern (57 bp):
TTTAACATAATTATTATTAAATATATTTTAATTAAAATATATAATCTAATAAAATTA
Found at i:53215019 original size:18 final size:17
Alignment explanation
Indices: 53214998--53215032 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
53214988 TTATTATTAA
*
53214998 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
53215016 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
53215033 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:53215052 original size:16 final size:16
Alignment explanation
Indices: 53215031--53215073 Score: 70
Period size: 16 Copynumber: 2.8 Consensus size: 16
53215021 ATTTAATAAA
*
53215031 ATTCTTAATAATCAAT
1 ATTCTTAATAACCAAT
53215047 ATTCTTAATAACCAAT
1 ATTCTTAATAACCAAT
53215063 ATTCTT-ATAAC
1 ATTCTTAATAAC
53215074 AAAAATTCAA
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
15 5 0.19
16 21 0.81
ACGTcount: A:0.42, C:0.16, G:0.00, T:0.42
Consensus pattern (16 bp):
ATTCTTAATAACCAAT
Found at i:53226852 original size:14 final size:15
Alignment explanation
Indices: 53226827--53226855 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
53226817 CCATTCAATT
53226827 AATCAGTTCATAACA
1 AATCAGTTCATAACA
53226842 AATCA-TTCATAACA
1 AATCAGTTCATAACA
53226856 TATTCAATTC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.48, C:0.21, G:0.03, T:0.28
Consensus pattern (15 bp):
AATCAGTTCATAACA
Found at i:53227177 original size:41 final size:40
Alignment explanation
Indices: 53227070--53227180 Score: 120
Period size: 41 Copynumber: 2.8 Consensus size: 40
53227060 CGGATAATTT
*
53227070 GAAGTAATAAGTTGACACCCAATGTCTCATCG-GCTAAACC
1 GAAGTAATAA-TTGACACCCAATGTCTCATCGAACTAAACC
* * * * *
53227110 GAAGT-A-AATTGGCACCCAATGCCTCATCGAATTAATCG
1 GAAGTAATAATTGACACCCAATGTCTCATCGAACTAAACC
*
53227148 GAAGTAATAGATTGACACCCAGTGTCTCATCGA
1 GAAGTAATA-ATTGACACCCAATGTCTCATCGA
53227181 CTCGTAGTTG
Statistics
Matches: 58, Mismatches: 9, Indels: 7
0.78 0.12 0.09
Matches are distributed among these distances:
37 19 0.33
38 11 0.19
39 2 0.03
40 6 0.10
41 20 0.34
ACGTcount: A:0.34, C:0.23, G:0.19, T:0.23
Consensus pattern (40 bp):
GAAGTAATAATTGACACCCAATGTCTCATCGAACTAAACC
Found at i:53238452 original size:25 final size:25
Alignment explanation
Indices: 53238345--53238504 Score: 140
Period size: 25 Copynumber: 6.6 Consensus size: 25
53238335 TTGTTATGCA
*
53238345 CTAATGAA-CAGAGAGCACTGAAGTG
1 CTAAT-AATCAGAGAGCACTGACGTG
*
53238370 CT-AT-A-CAGAGAGCACAGACGTG
1 CTAATAATCAGAGAGCACTGACGTG
* * *
53238392 CTAGTAATCAAAGAGCACTAACGTG
1 CTAATAATCAGAGAGCACTGACGTG
*
53238417 CTAATAATCAGAGAGCACTGATGTG
1 CTAATAATCAGAGAGCACTGACGTG
* * *
53238442 CTAATAATCAGATAACACAT-ATGTG
1 CTAATAATCAGAGAGCAC-TGACGTG
*
53238467 CT-A-AA-CAGAGAGCAGTGACGTG
1 CTAATAATCAGAGAGCACTGACGTG
53238489 CTAA-ATATCAGAGAGC
1 CTAATA-ATCAGAGAGC
53238505 GCGCTAGAGT
Statistics
Matches: 111, Mismatches: 16, Indels: 16
0.78 0.11 0.11
Matches are distributed among these distances:
21 1 0.01
22 31 0.28
23 5 0.05
24 5 0.05
25 68 0.61
26 1 0.01
ACGTcount: A:0.39, C:0.18, G:0.23, T:0.19
Consensus pattern (25 bp):
CTAATAATCAGAGAGCACTGACGTG
Found at i:53241161 original size:12 final size:12
Alignment explanation
Indices: 53241144--53241169 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
53241134 ACTTTTTTAA
53241144 AAAAAAGAAAAG
1 AAAAAAGAAAAG
53241156 AAAAAAGAAAAG
1 AAAAAAGAAAAG
53241168 AA
1 AA
53241170 TCTCCTAGTA
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:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (12 bp):
AAAAAAGAAAAG
Found at i:53244541 original size:42 final size:41
Alignment explanation
Indices: 53244487--53244598 Score: 129
Period size: 42 Copynumber: 2.7 Consensus size: 41
53244477 GATTTATGTA
* * *
53244487 TAAGACCATGTCTGGGACATCGGCATT-ATATTTGATTTCGTG
1 TAAGACCCTGTCTGGGACAT-GGCATTGATA-TTGATTACATG
53244529 TAAGACCCTGTCTGGGACAGTGGCATTGATATTGATTACATG
1 TAAGACCCTGTCTGGGACA-TGGCATTGATATTGATTACATG
*
53244571 TAAGACCAC-GTCTGGGACGTTGGCATTG
1 TAAGACC-CTGTCTGGGAC-ATGGCATTG
53244599 TACGAGTTTT
Statistics
Matches: 62, Mismatches: 4, Indels: 8
0.84 0.05 0.11
Matches are distributed among these distances:
42 57 0.92
43 5 0.08
ACGTcount: A:0.24, C:0.18, G:0.27, T:0.31
Consensus pattern (41 bp):
TAAGACCCTGTCTGGGACATGGCATTGATATTGATTACATG
Found at i:53244940 original size:17 final size:18
Alignment explanation
Indices: 53244896--53244940 Score: 51
Period size: 17 Copynumber: 2.6 Consensus size: 18
53244886 TATGAAATTT
53244896 TGATATGAAATGTGAGTA
1 TGATATGAAATGTGAGTA
*
53244914 TGAT-TAAAATGATGA-TA
1 TGATATGAAATG-TGAGTA
53244931 T-ATATGAAAT
1 TGATATGAAAT
53244941 ATATGATAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 5
0.77 0.07 0.17
Matches are distributed among these distances:
16 2 0.09
17 14 0.61
18 7 0.30
ACGTcount: A:0.44, C:0.00, G:0.20, T:0.36
Consensus pattern (18 bp):
TGATATGAAATGTGAGTA
Found at i:53250124 original size:36 final size:36
Alignment explanation
Indices: 53250083--53250273 Score: 240
Period size: 36 Copynumber: 5.0 Consensus size: 36
53250073 CTAAGGCTAA
53250083 CACTTATCACTTTGTT-ACTTGATCAGATAAGTATAG
1 CACTTATCACTTT-TTCACTTGATCAGATAAGTATAG
53250119 CACTTATCACTTTTTCACTTGATCAGATAAGTATAG
1 CACTTATCACTTTTTCACTTGATCAGATAAGTATAG
53250155 CACTTATCACTTTTTCACTTGATCAGATAAGTGTAGCTAAAG
1 CACTTATCACTTTTTCACTTGATCAGATAA--GTA--T--AG
* * *
53250197 CTACCACTTATCACTTTGTCTCTTGATCAGATAAGTGTAG
1 ----CACTTATCACTTTTTCACTTGATCAGATAAGTATAG
*
53250237 CACTTATCACTTTTTCACTTGATCAGATAAGTGTAG
1 CACTTATCACTTTTTCACTTGATCAGATAAGTATAG
53250273 C
1 C
53250274 TAAAGCTACC
Statistics
Matches: 139, Mismatches: 5, Indels: 22
0.84 0.03 0.13
Matches are distributed among these distances:
35 2 0.01
36 98 0.71
38 3 0.02
40 3 0.02
42 3 0.02
44 2 0.01
46 28 0.20
ACGTcount: A:0.29, C:0.20, G:0.14, T:0.38
Consensus pattern (36 bp):
CACTTATCACTTTTTCACTTGATCAGATAAGTATAG
Found at i:53250205 original size:82 final size:81
Alignment explanation
Indices: 53249994--53250309 Score: 350
Period size: 82 Copynumber: 3.9 Consensus size: 81
53249984 TACGTATGAT
* * * *
53249994 CACTTATCAC-TTGTC-CCTGATCAGATAAGTGTAGCTAGGCTACCACTTATCACTTTCTCACTT
1 CACTTATCACTTTTTCACTTGATCAGATAAGTGTAGCTAAGCTACCACTTATCACTTTATCACTT
53250057 GATCAGATAAGTGTAGCTAAGG
66 GATCAGATAA--GTA--T-A-G
*
53250079 CTAACACTTATCACTTTGTT-ACTTGATCAGATAA--GTA--T-AG----CACTTATCACTTTTT
1 ----CACTTATCACTTT-TTCACTTGATCAGATAAGTGTAGCTAAGCTACCACTTATCACTTTAT
53250134 CACTTGATCAGATAAGTATAG
61 CACTTGATCAGATAAGTATAG
* *
53250155 CACTTATCACTTTTTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTGTCTCT
1 CACTTATCACTTTTTCACTTGATCAGATAAGTGTAGCT-AAGCTACCACTTATCACTTTATCACT
*
53250220 TGATCAGATAAGTGTAG
65 TGATCAGATAAGTATAG
*
53250237 CACTTATCACTTTTTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTATCTCT
1 CACTTATCACTTTTTCACTTGATCAGATAAGTGTAGCT-AAGCTACCACTTATCACTTTATCACT
53250302 TGATCAGA
65 TGATCAGA
53250310 AGTACTCAAA
Statistics
Matches: 205, Mismatches: 8, Indels: 35
0.83 0.03 0.14
Matches are distributed among these distances:
71 2 0.01
72 27 0.13
74 3 0.01
76 2 0.01
77 1 0.00
78 3 0.01
80 3 0.01
82 134 0.65
86 1 0.00
87 1 0.00
89 13 0.06
90 2 0.01
91 13 0.06
ACGTcount: A:0.29, C:0.22, G:0.14, T:0.36
Consensus pattern (81 bp):
CACTTATCACTTTTTCACTTGATCAGATAAGTGTAGCTAAGCTACCACTTATCACTTTATCACTT
GATCAGATAAGTATAG
Found at i:53250209 original size:118 final size:118
Alignment explanation
Indices: 53250037--53250273 Score: 413
Period size: 118 Copynumber: 2.0 Consensus size: 118
53250027 GCTAGGCTAC
*
53250037 CACTTATCACTTTCTCACTTGATCAGATAAGTGTAGCTAAGGCTAACACTTATCACTTTGT-TAC
1 CACTTATCACTTTCTCACTTGATCAGATAAGTGTAGCTAAAGCTAACACTTATCACTTTGTCT-C
53250101 TTGATCAGATAAGTATAGCACTTATCACTTTTTCACTTGATCAGATAAGTATAG
65 TTGATCAGATAAGTATAGCACTTATCACTTTTTCACTTGATCAGATAAGTATAG
* *
53250155 CACTTATCACTTTTTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTGTCTCT
1 CACTTATCACTTTCTCACTTGATCAGATAAGTGTAGCTAAAGCTAACACTTATCACTTTGTCTCT
* *
53250220 TGATCAGATAAGTGTAGCACTTATCACTTTTTCACTTGATCAGATAAGTGTAG
66 TGATCAGATAAGTATAGCACTTATCACTTTTTCACTTGATCAGATAAGTATAG
53250273 C
1 C
53250274 TAAAGCTACC
Statistics
Matches: 113, Mismatches: 5, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
118 112 0.99
119 1 0.01
ACGTcount: A:0.29, C:0.20, G:0.14, T:0.37
Consensus pattern (118 bp):
CACTTATCACTTTCTCACTTGATCAGATAAGTGTAGCTAAAGCTAACACTTATCACTTTGTCTCT
TGATCAGATAAGTATAGCACTTATCACTTTTTCACTTGATCAGATAAGTATAG
Found at i:53253459 original size:4 final size:4
Alignment explanation
Indices: 53253437--53253472 Score: 54
Period size: 4 Copynumber: 9.0 Consensus size: 4
53253427 GTGGGAAAAG
* *
53253437 ACAT GCAT ACAT GCAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
53253473 GGGCTTTTCT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
4 28 1.00
ACGTcount: A:0.44, C:0.25, G:0.06, T:0.25
Consensus pattern (4 bp):
ACAT
Found at i:53253786 original size:9 final size:9
Alignment explanation
Indices: 53253774--53253816 Score: 61
Period size: 9 Copynumber: 4.9 Consensus size: 9
53253764 TTTTGTTAAA
53253774 AATTACCCG
1 AATTACCCG
53253783 AATTACCCG
1 AATTACCCG
*
53253792 -ATTAACCG
1 AATTACCCG
*
53253800 AATTAACCG
1 AATTACCCG
53253809 AATTACCC
1 AATTACCC
53253817 AAAAATTACC
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
8 7 0.23
9 24 0.77
ACGTcount: A:0.37, C:0.30, G:0.09, T:0.23
Consensus pattern (9 bp):
AATTACCCG
Found at i:53253800 original size:17 final size:17
Alignment explanation
Indices: 53253775--53253809 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
53253765 TTTGTTAAAA
* *
53253775 ATTACCCGAATTACCCG
1 ATTAACCGAATTAACCG
53253792 ATTAACCGAATTAACCG
1 ATTAACCGAATTAACCG
53253809 A
1 A
53253810 ATTACCCAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.37, C:0.29, G:0.11, T:0.23
Consensus pattern (17 bp):
ATTAACCGAATTAACCG
Found at i:53271004 original size:86 final size:86
Alignment explanation
Indices: 53270884--53271057 Score: 303
Period size: 86 Copynumber: 2.0 Consensus size: 86
53270874 AAATCGGACA
* *
53270884 CAAACATTTATAACAATAGAGAGTCCAAATATAGATAAGCATATTTAGCAGTAACAAACTCTTCA
1 CAAACATTTATAACAATAAAGAGTCCAAATATAGATAAGCATATTTAGCAGTAACAAACTCGTCA
53270949 AATTAGTAGACACAACTTTCT
66 AATTAGTAGACACAACTTTCT
* * *
53270970 CAAACATTTATAATAATAAAGGGTCCAAATATAGATGAGCATATTTAGCAGTAACAAACTCGTCA
1 CAAACATTTATAACAATAAAGAGTCCAAATATAGATAAGCATATTTAGCAGTAACAAACTCGTCA
53271035 AATTAGTAGACACAACTTTCT
66 AATTAGTAGACACAACTTTCT
53271056 CA
1 CA
53271058 GAGTCTCATG
Statistics
Matches: 83, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
86 83 1.00
ACGTcount: A:0.44, C:0.17, G:0.11, T:0.28
Consensus pattern (86 bp):
CAAACATTTATAACAATAAAGAGTCCAAATATAGATAAGCATATTTAGCAGTAACAAACTCGTCA
AATTAGTAGACACAACTTTCT
Found at i:53275180 original size:2 final size:2
Alignment explanation
Indices: 53275167--53275210 Score: 70
Period size: 2 Copynumber: 22.0 Consensus size: 2
53275157 AGGAAATGCG
* *
53275167 CA CA CA CG CA CA CA CG CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
53275209 CA
1 CA
53275211 AAAAGAAAAC
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.45, C:0.50, G:0.05, T:0.00
Consensus pattern (2 bp):
CA
Found at i:53276667 original size:20 final size:19
Alignment explanation
Indices: 53276654--53276698 Score: 54
Period size: 20 Copynumber: 2.3 Consensus size: 19
53276644 TTTAATTGTA
53276654 TAAAAATTAATTTATCATTT
1 TAAAAATTAATTTA-CATTT
* *
53276674 TAAAAATTAATATATATTAT
1 TAAAAATTAATTTACATT-T
53276694 TAAAA
1 TAAAA
53276699 CTAAACACCG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 3 0.14
20 19 0.86
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.44
Consensus pattern (19 bp):
TAAAAATTAATTTACATTT
Found at i:53279412 original size:11 final size:10
Alignment explanation
Indices: 53279394--53279531 Score: 60
Period size: 10 Copynumber: 14.0 Consensus size: 10
53279384 AAATTAAAAC
53279394 AAAA-ATTTA
1 AAAATATTTA
53279403 AAAAGTATTTTA
1 AAAA-TA-TTTA
53279415 AAAATATTT-
1 AAAATATTTA
*
53279424 TAAA-A-TTA
1 AAAATATTTA
* *
53279432 AAAAAATTAA
1 AAAATATTTA
53279442 AAAAGTATTTTA
1 AAAA-TA-TTTA
*
53279454 AAAATATTTT
1 AAAATATTTA
*
53279464 AAAAT-TTAAA
1 AAAATATT-TA
53279474 AAAAGTATTTTA
1 AAAA-TA-TTTA
* *
53279486 AAAGTATTTT
1 AAAATATTTA
**
53279496 AAAAT-TAAA
1 AAAATATTTA
53279505 AAAAT-TTTA
1 AAAATATTTA
*
53279514 AAAA-A-ATA
1 AAAATATTTA
53279522 AAAATATTTA
1 AAAATATTTA
53279532 TTATTCGGGC
Statistics
Matches: 95, Mismatches: 19, Indels: 29
0.66 0.13 0.20
Matches are distributed among these distances:
7 2 0.02
8 10 0.11
9 23 0.24
10 30 0.32
11 9 0.09
12 19 0.20
13 2 0.02
ACGTcount: A:0.60, C:0.00, G:0.03, T:0.37
Consensus pattern (10 bp):
AAAATATTTA
Found at i:53279445 original size:39 final size:39
Alignment explanation
Indices: 53279376--53279477 Score: 150
Period size: 39 Copynumber: 2.5 Consensus size: 39
53279366 ACCAAAAATT
*
53279376 TATTTTAAAAATTAAAACAAAAATTTAAAAAGTATTTTAAAAA
1 TATTTT-AAAATT--AA-AAAAATTAAAAAAGTATTTTAAAAA
53279419 TATTTTAAAATTAAAAAAATTAAAAAAGTATTTTAAAAA
1 TATTTTAAAATTAAAAAAATTAAAAAAGTATTTTAAAAA
53279458 TATTTTAAAATTTAAAAAAA
1 TATTTTAAAA-TTAAAAAAA
53279478 GTATTTTAAA
Statistics
Matches: 57, Mismatches: 1, Indels: 5
0.90 0.02 0.08
Matches are distributed among these distances:
39 34 0.60
40 11 0.19
42 6 0.11
43 6 0.11
ACGTcount: A:0.61, C:0.01, G:0.02, T:0.36
Consensus pattern (39 bp):
TATTTTAAAATTAAAAAAATTAAAAAAGTATTTTAAAAA
Found at i:53279451 original size:71 final size:70
Alignment explanation
Indices: 53279376--53279510 Score: 191
Period size: 71 Copynumber: 1.9 Consensus size: 70
53279366 ACCAAAAATT
53279376 TATTTTAAAAATTAAAACAAAAATTT-AAAAAGTATTTTAAAAATATTTTAAAATTAAAAAAATT
1 TATTTTAAAAA-T-AAACAAAAATTTAAAAAAGTATTTTAAAAATATTTTAAAATTAAAAAAATT
53279440 AAAAAAG
64 AAAAAAG
**** *
53279447 TATTTTAAAAATATTTTAAAATTTAAAAAAAGTATTTTAAAAGTATTTTAAAATTAAAAAAATT
1 TATTTTAAAAATAAACAAAAATTT-AAAAAAGTATTTTAAAAATATTTTAAAATTAAAAAAATT
53279511 TTAAAAAAAT
Statistics
Matches: 57, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
69 8 0.14
70 1 0.02
71 48 0.84
ACGTcount: A:0.59, C:0.01, G:0.03, T:0.38
Consensus pattern (70 bp):
TATTTTAAAAATAAACAAAAATTTAAAAAAGTATTTTAAAAATATTTTAAAATTAAAAAAATTAA
AAAAG
Found at i:53279481 original size:32 final size:31
Alignment explanation
Indices: 53279434--53279508 Score: 125
Period size: 32 Copynumber: 2.4 Consensus size: 31
53279424 TAAAATTAAA
53279434 AAAATT-AAAAAAGTATTTTAAAAATATTTT
1 AAAATTAAAAAAAGTATTTTAAAAATATTTT
*
53279464 AAAATTTAAAAAAAGTATTTTAAAAGTATTTT
1 AAAA-TTAAAAAAAGTATTTTAAAAATATTTT
53279496 AAAATTAAAAAAA
1 AAAATTAAAAAAA
53279509 TTTTAAAAAA
Statistics
Matches: 42, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
30 4 0.10
31 11 0.26
32 27 0.64
ACGTcount: A:0.60, C:0.00, G:0.04, T:0.36
Consensus pattern (31 bp):
AAAATTAAAAAAAGTATTTTAAAAATATTTT
Found at i:53297209 original size:61 final size:61
Alignment explanation
Indices: 53297141--53297263 Score: 201
Period size: 61 Copynumber: 2.0 Consensus size: 61
53297131 CTTCTGTATA
* **
53297141 TGCATGAATTTATGGGTGTTGGTGTTTGTGTAAGGGTGTATTTATTGTGCATATGTGTTGT
1 TGCATGAATTTATGGGTGTTGGTGTTAGTGTAAGGGTGTACGTATTGTGCATATGTGTTGT
* *
53297202 TGCATGAATTTATGGGTGTTGGTGTTAGTGTAAGGGTGTGCGTATTGTGCATGTGTGTTGT
1 TGCATGAATTTATGGGTGTTGGTGTTAGTGTAAGGGTGTACGTATTGTGCATATGTGTTGT
53297263 T
1 T
53297264 TTTGTATGTG
Statistics
Matches: 57, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
61 57 1.00
ACGTcount: A:0.15, C:0.04, G:0.35, T:0.46
Consensus pattern (61 bp):
TGCATGAATTTATGGGTGTTGGTGTTAGTGTAAGGGTGTACGTATTGTGCATATGTGTTGT
Found at i:53310778 original size:100 final size:104
Alignment explanation
Indices: 53310666--53310855 Score: 282
Period size: 100 Copynumber: 1.9 Consensus size: 104
53310656 TTATTACACA
* * *
53310666 TGTAATTTTTAAAATTTT-AAAGGTAAATTATTTAAAAGATAATGTTAAAAAATAAAAT-AAT-A
1 TGTAAGTTTTAAAATTTTAAAAAGTAAATTATTTAAAAGATAACGTT-AAAAATAAAATAAATAA
*
53310728 -AAAAATT-TAAAAATCAACATTAAGCGATAAGTAATATG
65 TAAAAATTAAAAAAATCAACATTAAGCGATAAGTAATATG
*
53310766 TGTAAGTTTTAAAATTTTAAAAAGTAAATTATTTTAAAGATAACGTTAAAAATAAAATAAAATAA
1 TGTAAGTTTTAAAATTTTAAAAAGTAAATTATTTAAAAGATAACGTTAAAAATAAAAT-AAATAA
53310831 TAAAAATTAAAAAAATCAACATTAA
65 TAAAAATTAAAAAAATCAACATTAA
53310856 ACCCTTATCT
Statistics
Matches: 79, Mismatches: 5, Indels: 7
0.87 0.05 0.08
Matches are distributed among these distances:
100 28 0.35
101 25 0.32
102 3 0.04
103 1 0.01
104 7 0.09
105 15 0.19
ACGTcount: A:0.56, C:0.03, G:0.07, T:0.33
Consensus pattern (104 bp):
TGTAAGTTTTAAAATTTTAAAAAGTAAATTATTTAAAAGATAACGTTAAAAATAAAATAAATAAT
AAAAATTAAAAAAATCAACATTAAGCGATAAGTAATATG
Found at i:53329568 original size:13 final size:11
Alignment explanation
Indices: 53329538--53329582 Score: 56
Period size: 11 Copynumber: 4.0 Consensus size: 11
53329528 TTAGTTAACA
53329538 AATATTTTATT
1 AATATTTTATT
53329549 AATATTTTACTT
1 AATATTTTA-TT
53329561 AGATA-TTTATT
1 A-ATATTTTATT
*
53329572 ATTATTTTATT
1 AATATTTTATT
53329583 TAGAAAATGG
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
10 2 0.07
11 18 0.60
12 7 0.23
13 3 0.10
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.62
Consensus pattern (11 bp):
AATATTTTATT
Found at i:53329569 original size:23 final size:23
Alignment explanation
Indices: 53329543--53329586 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
53329533 TAACAAATAT
53329543 TTTATTAATATTTTACTTAGATA
1 TTTATTAATATTTTACTTAGATA
* *
53329566 TTTATTATTATTTTATTTAGA
1 TTTATTAATATTTTACTTAGA
53329587 AAATGGTAGA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.32, C:0.02, G:0.05, T:0.61
Consensus pattern (23 bp):
TTTATTAATATTTTACTTAGATA
Found at i:53332032 original size:9 final size:9
Alignment explanation
Indices: 53332018--53332048 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
53332008 GTTAAACGAA
53332018 TCGAGTTAT
1 TCGAGTTAT
*
53332027 TCGAGTTAA
1 TCGAGTTAT
53332036 TCGAGTTAT
1 TCGAGTTAT
53332045 TCGA
1 TCGA
53332049 ATCAACTCGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.26, C:0.13, G:0.23, T:0.39
Consensus pattern (9 bp):
TCGAGTTAT
Found at i:53332119 original size:9 final size:9
Alignment explanation
Indices: 53332102--53332138 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
53332092 TGAGTTTTCG
53332102 AATTCGAAT
1 AATTCGAAT
*
53332111 AACTCGAAT
1 AATTCGAAT
53332120 AATTCGAAT
1 AATTCGAAT
53332129 AATTCGAAT
1 AATTCGAAT
53332138 A
1 A
53332139 TCAAACTATA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.46, C:0.14, G:0.11, T:0.30
Consensus pattern (9 bp):
AATTCGAAT
Found at i:53333185 original size:5 final size:5
Alignment explanation
Indices: 53333175--53333200 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
53333165 CTCGAAAATT
53333175 TTCGA TTCGA TTCGA TTCGA TTCGA T
1 TTCGA TTCGA TTCGA TTCGA TTCGA T
53333201 CGAATGCTCA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.19, C:0.19, G:0.19, T:0.42
Consensus pattern (5 bp):
TTCGA
Found at i:53334763 original size:28 final size:31
Alignment explanation
Indices: 53334705--53334766 Score: 85
Period size: 30 Copynumber: 2.1 Consensus size: 31
53334695 TTATTGAATT
*
53334705 TTTAATAAATTATTTATACAATTATTCAAAA
1 TTTAATAAAATATTTATACAATTATTCAAAA
*
53334736 TTTAA-AAAATATTTATATAATT-TT-AAAA
1 TTTAATAAAATATTTATACAATTATTCAAAA
53334764 TTT
1 TTT
53334767 TCATTGCGTA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
28 7 0.24
29 2 0.07
30 15 0.52
31 5 0.17
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (31 bp):
TTTAATAAAATATTTATACAATTATTCAAAA
Found at i:53335620 original size:5 final size:5
Alignment explanation
Indices: 53335612--53335647 Score: 54
Period size: 5 Copynumber: 6.8 Consensus size: 5
53335602 AGTTAAGTTA
53335612 TATAT TATATT ATATAT TATAT TATAT TATAT TATA
1 TATAT TATA-T -TATAT TATAT TATAT TATAT TATA
53335648 AAAGAAATAA
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
5 23 0.79
6 2 0.07
7 4 0.14
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (5 bp):
TATAT
Found at i:53335626 original size:12 final size:12
Alignment explanation
Indices: 53335609--53335647 Score: 64
Period size: 12 Copynumber: 3.4 Consensus size: 12
53335599 AAAAGTTAAG
53335609 TTATATATTATA
1 TTATATATTATA
53335621 TTATATATTATA
1 TTATATATTATA
53335633 -T-TATATTATA
1 TTATATATTATA
53335643 TTATA
1 TTATA
53335648 AAAGAAATAA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
10 9 0.36
11 2 0.08
12 14 0.56
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (12 bp):
TTATATATTATA
Found at i:53337755 original size:12 final size:11
Alignment explanation
Indices: 53337727--53337767 Score: 55
Period size: 12 Copynumber: 3.5 Consensus size: 11
53337717 ATTAAAATTT
53337727 AATAATATATAA
1 AATAA-ATATAA
53337739 AATAAATATAA
1 AATAAATATAA
53337750 ATATAAATATGAA
1 A-ATAAATAT-AA
53337763 AATAA
1 AATAA
53337768 TTATTTTGAT
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
11 7 0.26
12 17 0.63
13 3 0.11
ACGTcount: A:0.68, C:0.00, G:0.02, T:0.29
Consensus pattern (11 bp):
AATAAATATAA
Found at i:53342803 original size:180 final size:180
Alignment explanation
Indices: 53342568--53343103 Score: 1009
Period size: 180 Copynumber: 3.0 Consensus size: 180
53342558 GGAGATTTCG
53342568 AGCTTAATTCCACATGTAGTGTGGTTGTAGGATACATGCCATCTTTACTCCCACAAATTTTATCT
1 AGCTTAATTCCACATGTAGTGTGGTTGTAGGATACATGCCATCTTTACTCCCACAAATTTTATCT
* * *
53342633 TGATCTTTCCGAGTGTTAATGGTAAAATTTTATAATATTAGAGTTCAAAAACCACACTGTCTACA
66 TGATCTTTCCAAGTGTTAATGGTAAAATTTTATAATATCAGAGTTGAAAAACCACACTGTCTACA
*
53342698 CTGATACTAGTTTCATACTAGCAGATTATGTTACAATTTGTAAAACTTCA
131 CCGATACTAGTTTCATACTAGCAGATTATGTTACAATTTGTAAAACTTCA
53342748 AGCTTAATTCCACATGTAGTGTGGTTGTAGGATACATGCCATCTTTACTCCCACAAATTTTATCT
1 AGCTTAATTCCACATGTAGTGTGGTTGTAGGATACATGCCATCTTTACTCCCACAAATTTTATCT
53342813 TGATCTTTCCAAGTGTTAATGGTAAAATTTTATAATATCAGAGTTGAAAAACCACACTGTCTACA
66 TGATCTTTCCAAGTGTTAATGGTAAAATTTTATAATATCAGAGTTGAAAAACCACACTGTCTACA
53342878 CCGATACTAGTTTCATACTAGCAGATTATGTTACAATTTGTAAAACTTCA
131 CCGATACTAGTTTCATACTAGCAGATTATGTTACAATTTGTAAAACTTCA
* *
53342928 AGCTTAATTCCACATGTAGTGTGGTTGTAGGATACAAGCCATCTTTACTCCCACAAATTTTATAT
1 AGCTTAATTCCACATGTAGTGTGGTTGTAGGATACATGCCATCTTTACTCCCACAAATTTTATCT
53342993 TGATCTTTCCAAGTGTTAATGGTAAAATTTTATAATATCAGAGTTGAAAAACCACACTGTCTACA
66 TGATCTTTCCAAGTGTTAATGGTAAAATTTTATAATATCAGAGTTGAAAAACCACACTGTCTACA
*
53343058 CCGATACTAGTTTCATACTAGCAGGTTATGTTACAATTTGTAAAAC
131 CCGATACTAGTTTCATACTAGCAGATTATGTTACAATTTGTAAAAC
53343104 ATTATACTGA
Statistics
Matches: 349, Mismatches: 7, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
180 349 1.00
ACGTcount: A:0.32, C:0.18, G:0.14, T:0.36
Consensus pattern (180 bp):
AGCTTAATTCCACATGTAGTGTGGTTGTAGGATACATGCCATCTTTACTCCCACAAATTTTATCT
TGATCTTTCCAAGTGTTAATGGTAAAATTTTATAATATCAGAGTTGAAAAACCACACTGTCTACA
CCGATACTAGTTTCATACTAGCAGATTATGTTACAATTTGTAAAACTTCA
Found at i:53349764 original size:22 final size:23
Alignment explanation
Indices: 53349725--53349780 Score: 62
Period size: 22 Copynumber: 2.5 Consensus size: 23
53349715 TGTATGTTGA
*
53349725 ATATGTTT-AAAATGTTTTAATT
1 ATATATTTGAAAATGTTTTAATT
* *
53349747 AT-TATTTGAAAATTTTTTTATT
1 ATATATTTGAAAATGTTTTAATT
53349769 ATGATATTTGAA
1 AT-ATATTTGAA
53349781 TTGATAAGCT
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
21 4 0.14
22 16 0.57
24 8 0.29
ACGTcount: A:0.36, C:0.00, G:0.09, T:0.55
Consensus pattern (23 bp):
ATATATTTGAAAATGTTTTAATT
Found at i:53350756 original size:25 final size:26
Alignment explanation
Indices: 53350718--53350767 Score: 77
Period size: 25 Copynumber: 2.0 Consensus size: 26
53350708 TACTGTATAC
53350718 TAATTAAAATTAATATTTAA-CATTA
1 TAATTAAAATTAATATTTAAGCATTA
53350743 TAATTATAAA-TAATATTTAAGCATT
1 TAATTA-AAATTAATATTTAAGCATT
53350768 TCCAAATAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
25 16 0.70
26 7 0.30
ACGTcount: A:0.50, C:0.04, G:0.02, T:0.44
Consensus pattern (26 bp):
TAATTAAAATTAATATTTAAGCATTA
Found at i:53352016 original size:16 final size:15
Alignment explanation
Indices: 53351995--53352024 Score: 51
Period size: 15 Copynumber: 1.9 Consensus size: 15
53351985 ATCGGTCCAA
53351995 TTAAAAATAATTAAAT
1 TTAAAAA-AATTAAAT
53352011 TTAAAAAAATTAAA
1 TTAAAAAAATTAAA
53352025 AATACTGGTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (15 bp):
TTAAAAAAATTAAAT
Found at i:53355472 original size:20 final size:21
Alignment explanation
Indices: 53355437--53355478 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
53355427 CATGAATAAC
*
53355437 AAATCTATAATATATACCAAT
1 AAATCTATAATATATAACAAT
*
53355458 AAATCTAT-TTATATAACAAT
1 AAATCTATAATATATAACAAT
53355478 A
1 A
53355479 TCTCTATTGG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 11 0.58
21 8 0.42
ACGTcount: A:0.52, C:0.12, G:0.00, T:0.36
Consensus pattern (21 bp):
AAATCTATAATATATAACAAT
Found at i:53355481 original size:18 final size:18
Alignment explanation
Indices: 53355401--53355481 Score: 58
Period size: 18 Copynumber: 4.3 Consensus size: 18
53355391 ATTGTTCACC
*
53355401 ATATCTATTTATATAACA
1 ATATCTATATATATAACA
* *
53355419 ACATCT-TACATGAATAACA
1 ATATCTATATAT--ATAACA
*
53355438 A-ATCTATAATATATACCA
1 ATATCTAT-ATATATAACA
*
53355456 ATAAATCTATTTATATAACA
1 AT--ATCTATATATATAACA
53355476 ATATCT
1 ATATCT
53355482 CTATTGGTCC
Statistics
Matches: 49, Mismatches: 7, Indels: 14
0.70 0.10 0.20
Matches are distributed among these distances:
17 3 0.06
18 19 0.39
19 8 0.16
20 13 0.27
21 6 0.12
ACGTcount: A:0.47, C:0.15, G:0.01, T:0.37
Consensus pattern (18 bp):
ATATCTATATATATAACA
Found at i:53355484 original size:20 final size:20
Alignment explanation
Indices: 53355404--53355486 Score: 57
Period size: 20 Copynumber: 4.3 Consensus size: 20
53355394 GTTCACCATA
*
53355404 TCTATTTATATAACAACATC
1 TCTATTTATATAACAATATC
* *
53355424 T-TACATGA-ATAACAA-ATC
1 TCTA-TTTATATAACAATATC
* * * **
53355442 TATA-ATATATACCAATAAA
1 TCTATTTATATAACAATATC
53355461 TCTATTTATATAACAATATC
1 TCTATTTATATAACAATATC
53355481 TCTATT
1 TCTATT
53355487 GGTCCTACAC
Statistics
Matches: 46, Mismatches: 12, Indels: 10
0.68 0.18 0.15
Matches are distributed among these distances:
17 1 0.02
18 10 0.22
19 15 0.33
20 20 0.43
ACGTcount: A:0.45, C:0.16, G:0.01, T:0.39
Consensus pattern (20 bp):
TCTATTTATATAACAATATC
Found at i:53356348 original size:21 final size:21
Alignment explanation
Indices: 53356303--53356355 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
53356293 AACGGTGGCT
* **
53356303 GTGAGATTAGTTACTGTAGTA
1 GTGAGATTAGATACTGTAACA
*
53356324 GTGAGATTAGATACTGTAACG
1 GTGAGATTAGATACTGTAACA
53356345 GTGAGATTAGA
1 GTGAGATTAGA
53356356 AACAGCGGTG
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.32, C:0.06, G:0.30, T:0.32
Consensus pattern (21 bp):
GTGAGATTAGATACTGTAACA
Found at i:53363387 original size:20 final size:21
Alignment explanation
Indices: 53363349--53363388 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
53363339 TATTTTTAAA
53363349 TAAAAAATATTAATGTATTTT
1 TAAAAAATATTAATGTATTTT
* *
53363370 TAAATAATA-TAATTTATTT
1 TAAAAAATATTAATGTATTT
53363389 CAAATATAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (21 bp):
TAAAAAATATTAATGTATTTT
Found at i:53363387 original size:28 final size:24
Alignment explanation
Indices: 53363330--53363387 Score: 64
Period size: 25 Copynumber: 2.3 Consensus size: 24
53363320 TTTTATGTAT
53363330 ATTTATTATTATTTTTAAATAAAA
1 ATTTATTATTATTTTTAAATAAAA
*
53363354 A-ATATTAATGTATTTTTAAATAATATA
1 ATTTATT-AT-TATTTTTAAATAA-A-A
53363381 ATTTATT
1 ATTTATT
53363388 TCAAATATAA
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
23 4 0.15
24 3 0.11
25 13 0.48
26 1 0.04
27 2 0.07
28 4 0.15
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (24 bp):
ATTTATTATTATTTTTAAATAAAA
Found at i:53364297 original size:25 final size:25
Alignment explanation
Indices: 53364269--53364319 Score: 93
Period size: 25 Copynumber: 2.0 Consensus size: 25
53364259 AATTAAGTCC
53364269 AGAATAAGTCTTAAATCTTCAGGAT
1 AGAATAAGTCTTAAATCTTCAGGAT
*
53364294 AGAATAAGTCTTGAATCTTCAGGAT
1 AGAATAAGTCTTAAATCTTCAGGAT
53364319 A
1 A
53364320 TGTTGTTTCG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.39, C:0.12, G:0.18, T:0.31
Consensus pattern (25 bp):
AGAATAAGTCTTAAATCTTCAGGAT
Found at i:53371089 original size:20 final size:20
Alignment explanation
Indices: 53371055--53371096 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
53371045 AACTATTTAA
** *
53371055 ATAATATTATTTGAATAGTT
1 ATAATATTAAATGAATAATT
53371075 ATAATATTAAATGAATAATT
1 ATAATATTAAATGAATAATT
53371095 AT
1 AT
53371097 GTATTTATTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.48, C:0.00, G:0.07, T:0.45
Consensus pattern (20 bp):
ATAATATTAAATGAATAATT
Found at i:53373290 original size:26 final size:26
Alignment explanation
Indices: 53373255--53373305 Score: 93
Period size: 26 Copynumber: 2.0 Consensus size: 26
53373245 AATGTGAAAG
*
53373255 GGGGTTGCTATGTGCTGATTCCCCGA
1 GGGGTTGCTAAGTGCTGATTCCCCGA
53373281 GGGGTTGCTAAGTGCTGATTCCCCG
1 GGGGTTGCTAAGTGCTGATTCCCCG
53373306 GTTCATTGGT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.12, C:0.24, G:0.35, T:0.29
Consensus pattern (26 bp):
GGGGTTGCTAAGTGCTGATTCCCCGA
Found at i:53373317 original size:103 final size:104
Alignment explanation
Indices: 53373177--53373399 Score: 369
Period size: 103 Copynumber: 2.2 Consensus size: 104
53373167 TGTATATAAA
** * *
53373177 AGGGGTTGCTGTGTGCTGATTCCCCGATTTATGGGTGGTGCTATGTGCG-TGATCCACCATATCT
1 AGGGGTTGCTAAGTGCTGATTCCCCGATTCATGGGTGGTGCTAAGTGCGAT-ATCCACCATATCT
53373241 TTGAAATGTGAAAGGGGGTTGCTATGTGCTGATT-CCCCG
65 TTGAAATGTGAAAGGGGGTTGCTATGTGCTGATTCCCCCG
* *
53373280 AGGGGTTGCTAAGTGCTGATTCCCCGGTTCATTGGTGGTGCTAAGTGCGATATCCACCATATCTT
1 AGGGGTTGCTAAGTGCTGATTCCCCGATTCATGGGTGGTGCTAAGTGCGATATCCACCATATCTT
53373345 TGAAATGTGAAAGGGGGTTGCTATGTGCTGATTCCCCCG
66 TGAAATGTGAAAGGGGGTTGCTATGTGCTGATTCCCCCG
53373384 AGGGGTTGCTAAGTGC
1 AGGGGTTGCTAAGTGC
53373400 GATATCCATT
Statistics
Matches: 112, Mismatches: 6, Indels: 3
0.93 0.05 0.02
Matches are distributed among these distances:
103 90 0.80
104 22 0.20
ACGTcount: A:0.18, C:0.19, G:0.32, T:0.31
Consensus pattern (104 bp):
AGGGGTTGCTAAGTGCTGATTCCCCGATTCATGGGTGGTGCTAAGTGCGATATCCACCATATCTT
TGAAATGTGAAAGGGGGTTGCTATGTGCTGATTCCCCCG
Found at i:53373451 original size:71 final size:72
Alignment explanation
Indices: 53373318--53373469 Score: 252
Period size: 71 Copynumber: 2.1 Consensus size: 72
53373308 TCATTGGTGG
* *
53373318 TGCTAAGTGCGATATCCACCATATCTTTGAAATGTGAAAGGGGGTTGCTATGTGCTGATTCCCCC
1 TGCTAAGTGCGATATCCACCATATATTTGAAATGTAAAAGGGGGTTGCTATGTGCTGATTCCCCC
53373383 GAGGGGT
66 GAGGGGT
***
53373390 TGCTAAGTGCGATATCCATTGTATATTTGAAATG-AAAAGGGGGTTGCTATGTGCTGATTCCCCC
1 TGCTAAGTGCGATATCCACCATATATTTGAAATGTAAAAGGGGGTTGCTATGTGCTGATTCCCCC
53373454 GAGGGGT
66 GAGGGGT
53373461 TGCTAAGTG
1 TGCTAAGTG
53373470 ATGATTCCCC
Statistics
Matches: 75, Mismatches: 5, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
71 45 0.60
72 30 0.40
ACGTcount: A:0.23, C:0.17, G:0.30, T:0.30
Consensus pattern (72 bp):
TGCTAAGTGCGATATCCACCATATATTTGAAATGTAAAAGGGGGTTGCTATGTGCTGATTCCCCC
GAGGGGT
Found at i:53375541 original size:8 final size:8
Alignment explanation
Indices: 53375528--53375552 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
53375518 GGAAGTCAAA
53375528 AGTAGTCG
1 AGTAGTCG
53375536 AGTAGTCG
1 AGTAGTCG
53375544 AGTAGTCG
1 AGTAGTCG
53375552 A
1 A
53375553 TTGTGTCCGT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.28, C:0.12, G:0.36, T:0.24
Consensus pattern (8 bp):
AGTAGTCG
Found at i:53375912 original size:43 final size:42
Alignment explanation
Indices: 53375786--53375913 Score: 127
Period size: 43 Copynumber: 3.0 Consensus size: 42
53375776 TGGGATTTTT
* * * *
53375786 GATATGTGTTATCGTGTAAGACCACATCAGGGATGTTGGCATC
1 GATATGTGTTA-CATGTAAGACCACGTCTGGGACGTTGGCATC
*
53375829 GACTTATGT-TTACATGTAAGACC-CTGTCTGAGACAG-TGGCATC
1 GA--TATGTGTTACATGTAAGACCAC-GTCTGGGAC-GTTGGCATC
*
53375872 GATATGTGATTACATGTAAGACCACGTCTGGGGCGTTGGCAT
1 GATATGTG-TTACATGTAAGACCACGTCTGGGACGTTGGCAT
53375914 TGTACGAGCT
Statistics
Matches: 70, Mismatches: 7, Indels: 16
0.75 0.08 0.17
Matches are distributed among these distances:
41 5 0.07
42 2 0.03
43 53 0.76
44 5 0.07
45 5 0.07
ACGTcount: A:0.25, C:0.18, G:0.27, T:0.30
Consensus pattern (42 bp):
GATATGTGTTACATGTAAGACCACGTCTGGGACGTTGGCATC
Found at i:53380183 original size:27 final size:27
Alignment explanation
Indices: 53380145--53380196 Score: 104
Period size: 27 Copynumber: 1.9 Consensus size: 27
53380135 TGAAATGAAG
53380145 TTGGTGTGGTTTATTAATGTTTGAGGT
1 TTGGTGTGGTTTATTAATGTTTGAGGT
53380172 TTGGTGTGGTTTATTAATGTTTGAG
1 TTGGTGTGGTTTATTAATGTTTGAG
53380197 ATTCGGTTTC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.15, C:0.00, G:0.33, T:0.52
Consensus pattern (27 bp):
TTGGTGTGGTTTATTAATGTTTGAGGT
Found at i:53381921 original size:21 final size:20
Alignment explanation
Indices: 53381895--53382005 Score: 87
Period size: 21 Copynumber: 5.3 Consensus size: 20
53381885 CACAAAAGCA
* *
53381895 CATAAGTGCTAAACAGAAACC
1 CATAAGAGCTGAAC-GAAACC
* * *
53381916 CATAAGGGCTGAACGGAAGCT
1 CATAAGAGCTGAAC-GAAACC
53381937 CATAAGAGCTGAACGAAAACC
1 CATAAGAGCTGAACG-AAACC
* * * *
53381958 CATAAGGGTTGAACGGAAGCT
1 CATAAGAGCTGAAC-GAAACC
*
53381979 CGTAAGAGCTGAACGAAAACC
1 CATAAGAGCTGAACG-AAACC
53382000 CATAAG
1 CATAAG
53382006 GGTTGAACGG
Statistics
Matches: 69, Mismatches: 18, Indels: 6
0.74 0.19 0.06
Matches are distributed among these distances:
20 2 0.03
21 66 0.96
22 1 0.01
ACGTcount: A:0.41, C:0.21, G:0.24, T:0.14
Consensus pattern (20 bp):
CATAAGAGCTGAACGAAACC
Found at i:53381942 original size:42 final size:41
Alignment explanation
Indices: 53381890--53382093 Score: 212
Period size: 42 Copynumber: 4.9 Consensus size: 41
53381880 GGTTGCACAA
* * *
53381890 AAGCACATAAGTGCTAAACAGAAACCCATAAGGGCTGAACGG
1 AAGCTCATAAGAGCTAAAC-GAAACCCATAAGGGTTGAACGG
*
53381932 AAGCTCATAAGAGCTGAACGAAAACCCATAAGGGTTGAACGG
1 AAGCTCATAAGAGCTAAACG-AAACCCATAAGGGTTGAACGG
* *
53381974 AAGCTCGTAAGAGCTGAACGAAAACCCATAAGGGTTGAACGG
1 AAGCTCATAAGAGCTAAACG-AAACCCATAAGGGTTGAACGG
* * ** **
53382016 AAGCTCGTAAGAGTTGAAAAAAAACCCATAAGGG-TGAAACTA
1 AAGCTCATAAGAGCT-AAACGAAACCCATAAGGGTTG-AACGG
* * *
53382058 AAGCTCAAAAGAGCTTAACGGAAACTCATAAGGGTT
1 AAGCTCATAAGAGCTAAAC-GAAACCCATAAGGGTT
53382094 AAAATGAAAT
Statistics
Matches: 139, Mismatches: 18, Indels: 9
0.84 0.11 0.05
Matches are distributed among these distances:
41 5 0.04
42 131 0.94
43 3 0.02
ACGTcount: A:0.42, C:0.18, G:0.25, T:0.15
Consensus pattern (41 bp):
AAGCTCATAAGAGCTAAACGAAACCCATAAGGGTTGAACGG
Found at i:53382012 original size:21 final size:21
Alignment explanation
Indices: 53381911--53382050 Score: 109
Period size: 21 Copynumber: 6.7 Consensus size: 21
53381901 TGCTAAACAG
* *
53381911 AAACCCATAAGGGCTGAACGG
1 AAACCCATAAGGGTTGAACGA
* * * *
53381932 AAGCTCATAAGAGCTGAACGA
1 AAACCCATAAGGGTTGAACGA
*
53381953 AAACCCATAAGGGTTGAACGG
1 AAACCCATAAGGGTTGAACGA
* * * * *
53381974 AAGCTCGTAAGAGCTGAACGA
1 AAACCCATAAGGGTTGAACGA
*
53381995 AAACCCATAAGGGTTGAACGG
1 AAACCCATAAGGGTTGAACGA
* * * * **
53382016 AAGCTCGTAAGAGTTGAAAAA
1 AAACCCATAAGGGTTGAACGA
53382037 AAACCCATAAGGGT
1 AAACCCATAAGGGT
53382051 GAAACTAAAG
Statistics
Matches: 87, Mismatches: 32, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
21 87 1.00
ACGTcount: A:0.41, C:0.19, G:0.26, T:0.14
Consensus pattern (21 bp):
AAACCCATAAGGGTTGAACGA
Found at i:53382021 original size:84 final size:84
Alignment explanation
Indices: 53381911--53382093 Score: 242
Period size: 84 Copynumber: 2.2 Consensus size: 84
53381901 TGCTAAACAG
* ** *
53381911 AAACCCATAAGGGCTGAACGGAAGCTCATAAGAGCTGAACGAAAACCCATAAGGGTTG-AACGGA
1 AAACCCATAAGGGTTGAACGGAAGCTCATAAGAGCTGAAAAAAAACCCATAAGGG-TGAAACGAA
**
53381975 AGCTCGTAAGAGCTGAACGA
65 AGCTCAAAAGAGCTGAACGA
* * *
53381995 AAACCCATAAGGGTTGAACGGAAGCTCGTAAGAGTTGAAAAAAAACCCATAAGGGTGAAACTAAA
1 AAACCCATAAGGGTTGAACGGAAGCTCATAAGAGCTGAAAAAAAACCCATAAGGGTGAAACGAAA
* *
53382060 GCTCAAAAGAGCTTAACGG
66 GCTCAAAAGAGCTGAACGA
*
53382079 AAACTCATAAGGGTT
1 AAACCCATAAGGGTT
53382094 AAAATGAAAT
Statistics
Matches: 86, Mismatches: 12, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
83 2 0.02
84 84 0.98
ACGTcount: A:0.42, C:0.18, G:0.25, T:0.15
Consensus pattern (84 bp):
AAACCCATAAGGGTTGAACGGAAGCTCATAAGAGCTGAAAAAAAACCCATAAGGGTGAAACGAAA
GCTCAAAAGAGCTGAACGA
Found at i:53382383 original size:45 final size:46
Alignment explanation
Indices: 53382298--53382384 Score: 113
Period size: 45 Copynumber: 1.9 Consensus size: 46
53382288 TTTTCAATTC
* * * *
53382298 ATAAATTAACAATATTTCATTTTTTTAACAATATGCTAAATACATA
1 ATAAATTAACAACATTCCATTTTTTCAACAATATACTAAATACATA
* *
53382344 ATAATTTAACAACATTCCA-TTTTTCAACAATATATTAAATA
1 ATAAATTAACAACATTCCATTTTTTCAACAATATACTAAATA
53382385 TGTAACATCA
Statistics
Matches: 35, Mismatches: 6, Indels: 1
0.83 0.14 0.02
Matches are distributed among these distances:
45 19 0.54
46 16 0.46
ACGTcount: A:0.46, C:0.13, G:0.01, T:0.40
Consensus pattern (46 bp):
ATAAATTAACAACATTCCATTTTTTCAACAATATACTAAATACATA
Found at i:53384212 original size:31 final size:32
Alignment explanation
Indices: 53384171--53384230 Score: 79
Period size: 31 Copynumber: 1.9 Consensus size: 32
53384161 AATAATAAAA
*
53384171 TATCTCATTAAA-ATATTA-ATAAAATAATATT
1 TATCTAATTAAATA-ATTATATAAAATAATATT
*
53384202 TATCTAATTAAATAATTATATAATATAAT
1 TATCTAATTAAATAATTATATAAAATAAT
53384231 TAAAATATCT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
31 15 0.60
32 10 0.40
ACGTcount: A:0.52, C:0.05, G:0.00, T:0.43
Consensus pattern (32 bp):
TATCTAATTAAATAATTATATAAAATAATATT
Found at i:53385582 original size:8 final size:8
Alignment explanation
Indices: 53385560--53385593 Score: 50
Period size: 8 Copynumber: 4.2 Consensus size: 8
53385550 TTTCTATATT
53385560 TTTTAAAA
1 TTTTAAAA
* *
53385568 ATATAAAA
1 TTTTAAAA
53385576 TTTTAAAA
1 TTTTAAAA
53385584 TTTTAAAA
1 TTTTAAAA
53385592 TT
1 TT
53385594 ACCCTTGTGT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
8 22 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (8 bp):
TTTTAAAA
Found at i:53391872 original size:22 final size:23
Alignment explanation
Indices: 53391844--53391888 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
53391834 ATACAATCTT
53391844 AGATATGA-TATGTAATCATAGA
1 AGATATGATTATGTAATCATAGA
*
53391866 AGATATGATTTTGTAATCATAGA
1 AGATATGATTATGTAATCATAGA
53391889 GATTTAATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
22 8 0.38
23 13 0.62
ACGTcount: A:0.42, C:0.04, G:0.18, T:0.36
Consensus pattern (23 bp):
AGATATGATTATGTAATCATAGA
Found at i:53391898 original size:22 final size:23
Alignment explanation
Indices: 53391854--53391898 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
53391844 AGATATGATA
*
53391854 TGTAATCATAGAAGATATGATTT
1 TGTAATCATAGAAGATATAATTT
*
53391877 TGTAATCATAG-AGATTTAATTT
1 TGTAATCATAGAAGATATAATTT
53391899 GTAGATATCC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 9 0.45
23 11 0.55
ACGTcount: A:0.38, C:0.04, G:0.16, T:0.42
Consensus pattern (23 bp):
TGTAATCATAGAAGATATAATTT
Done.