Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr01 ID=Chr01-JGI_221_v2.0
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: 55868233
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 983842 characters in sequence are not A, C, G, or T
File 134 of 187
Found at i:40510815 original size:33 final size:30
Alignment explanation
Indices: 40510754--40510815 Score: 79
Period size: 33 Copynumber: 2.0 Consensus size: 30
40510744 TAATTTATTT
* *
40510754 TTATATTATATAAAAATTAAATATATTATA
1 TTATATTATATAAAAATTAAAAAAATTATA
40510784 TTATATTATATTATAAATATTAAAAAAATTAT
1 TTATATTATA-TA-AAA-ATTAAAAAAATTAT
40510816 TAAGTCACTG
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
30 10 0.37
31 2 0.07
32 3 0.11
33 12 0.44
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (30 bp):
TTATATTATATAAAAATTAAAAAAATTATA
Found at i:40511787 original size:40 final size:39
Alignment explanation
Indices: 40511668--40511791 Score: 113
Period size: 40 Copynumber: 3.1 Consensus size: 39
40511658 GCTTTTGGAC
* * * *
40511668 AAAAAACGCCACTAAAAATCAAGCAGTAGCGGCGCTTTTG
1 AAAAAACGCCGCTAAAAAT-AAGCATTAGCGGCGATTTTT
* ** * * *
40511708 GAAAAACGCCGCTAAAGGTTGATCATTAGCAGCGATTTTT
1 AAAAAACGCCGCTAAA-AATAAGCATTAGCGGCGATTTTT
* *
40511748 AAAAAACGCCGCTAAAAATAAGCTTTAGCGGCGTTTTTT
1 AAAAAACGCCGCTAAAAATAAGCATTAGCGGCGATTTTT
*
40511787 TAAAA
1 AAAAA
40511792 GCACCGCAAA
Statistics
Matches: 64, Mismatches: 19, Indels: 3
0.74 0.22 0.03
Matches are distributed among these distances:
39 20 0.31
40 43 0.67
41 1 0.02
ACGTcount: A:0.38, C:0.19, G:0.19, T:0.24
Consensus pattern (39 bp):
AAAAAACGCCGCTAAAAATAAGCATTAGCGGCGATTTTT
Found at i:40511956 original size:40 final size:41
Alignment explanation
Indices: 40511844--40512006 Score: 267
Period size: 41 Copynumber: 4.0 Consensus size: 41
40511834 TTTTGGGGTA
*
40511844 TTTAGCGGCATTTTCTGAA-AAGCGCCGCTAATGCTCAGGTC
1 TTTAGCGGCGTTTT-TGAATAAGCGCCGCTAATGCTCAGGTC
40511885 TTTAGCGGCGTTTTTGAATAAGCGCCGCTAATGCTCAGGTC
1 TTTAGCGGCGTTTTTGAATAAGCGCCGCTAATGCTCAGGTC
*
40511926 TTTAGCGGCGTTTTT-AATAAGCGCCGCTAATTCTCAGGTC
1 TTTAGCGGCGTTTTTGAATAAGCGCCGCTAATGCTCAGGTC
* *
40511966 TTTAGCGGCGTTTTTTAATAAGCGCCGCTAATTCTCAGGTC
1 TTTAGCGGCGTTTTTGAATAAGCGCCGCTAATGCTCAGGTC
40512007 NNNNNNNNNN
Statistics
Matches: 118, Mismatches: 2, Indels: 4
0.95 0.02 0.03
Matches are distributed among these distances:
40 43 0.36
41 75 0.64
ACGTcount: A:0.20, C:0.23, G:0.24, T:0.33
Consensus pattern (41 bp):
TTTAGCGGCGTTTTTGAATAAGCGCCGCTAATGCTCAGGTC
Found at i:40511986 original size:81 final size:82
Alignment explanation
Indices: 40511844--40512006 Score: 267
Period size: 81 Copynumber: 2.0 Consensus size: 82
40511834 TTTTGGGGTA
40511844 TTTAGCGGCATTTTCTGAAAAGCGCCGCTAATGCTCAGGTCTTTAGCGGCGTTTTTGAATAAGCG
1 TTTAGCGGCATTTTCTGAAAAGCGCCGCTAATGCTCAGGTCTTTAGCGGCGTTTTTGAATAAGCG
40511909 CCGCTAATGCTCAGGTC
66 CCGCTAATGCTCAGGTC
* * *
40511926 TTTAGCGGCGTTTT-T-AATAAGCGCCGCTAATTCTCAGGTCTTTAGCGGCGTTTTTTAATAAGC
1 TTTAGCGGCATTTTCTGAA-AAGCGCCGCTAATGCTCAGGTCTTTAGCGGCGTTTTTGAATAAGC
*
40511989 GCCGCTAATTCTCAGGTC
65 GCCGCTAATGCTCAGGTC
40512007 NNNNNNNNNN
Statistics
Matches: 76, Mismatches: 4, Indels: 3
0.92 0.05 0.04
Matches are distributed among these distances:
80 2 0.03
81 61 0.80
82 13 0.17
ACGTcount: A:0.20, C:0.23, G:0.24, T:0.33
Consensus pattern (82 bp):
TTTAGCGGCATTTTCTGAAAAGCGCCGCTAATGCTCAGGTCTTTAGCGGCGTTTTTGAATAAGCG
CCGCTAATGCTCAGGTC
Found at i:40512164 original size:41 final size:41
Alignment explanation
Indices: 40512107--40512280 Score: 303
Period size: 41 Copynumber: 4.2 Consensus size: 41
40512097 NNNNNNNNNN
40512107 GCTAATGCTCAGGTCTTTAGCGGCGTTTTTTAATAAGCGCC
1 GCTAATGCTCAGGTCTTTAGCGGCGTTTTTTAATAAGCGCC
40512148 GCTAATGCTCAGGTCTTTAGCGGCGTTTTTTAATAAGCGCC
1 GCTAATGCTCAGGTCTTTAGCGGCGTTTTTTAATAAGCGCC
* * *
40512189 GCTAATTCTTAGGTCTTTAGCGACGTTTTTTAATAAGCGCC
1 GCTAATGCTCAGGTCTTTAGCGGCGTTTTTTAATAAGCGCC
*
40512230 GCGAATGCTCAGGTCTTTAGCGGCGTTTTTTAATAAGCGCC
1 GCTAATGCTCAGGTCTTTAGCGGCGTTTTTTAATAAGCGCC
*
40512271 GCCAATGCTC
1 GCTAATGCTC
40512281 GTACCTTTAG
Statistics
Matches: 125, Mismatches: 8, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
41 125 1.00
ACGTcount: A:0.20, C:0.22, G:0.24, T:0.34
Consensus pattern (41 bp):
GCTAATGCTCAGGTCTTTAGCGGCGTTTTTTAATAAGCGCC
Found at i:40512289 original size:41 final size:40
Alignment explanation
Indices: 40512107--40512300 Score: 273
Period size: 41 Copynumber: 4.7 Consensus size: 40
40512097 NNNNNNNNNN
40512107 GCTAATGCTCAGGTCTTTAGCGGCGTTTTTTAATAAGCGCC
1 GCTAATGCTCA-GTCTTTAGCGGCGTTTTTTAATAAGCGCC
40512148 GCTAATGCTCAGGTCTTTAGCGGCGTTTTTTAATAAGCGCC
1 GCTAATGCTCA-GTCTTTAGCGGCGTTTTTTAATAAGCGCC
* * *
40512189 GCTAATTCTTAGGTCTTTAGCGACGTTTTTTAATAAGCGCC
1 GCTAATGCTCA-GTCTTTAGCGGCGTTTTTTAATAAGCGCC
*
40512230 GCGAATGCTCAGGTCTTTAGCGGCGTTTTTTAATAAGCGCC
1 GCTAATGCTCA-GTCTTTAGCGGCGTTTTTTAATAAGCGCC
* *
40512271 GCCAATGCTC-GTACCTTTAGCGGTGTTTTT
1 GCTAATGCTCAGT--CTTTAGCGGCGTTTTT
40512301 GAGGAAGCGC
Statistics
Matches: 142, Mismatches: 9, Indels: 4
0.92 0.06 0.03
Matches are distributed among these distances:
39 2 0.01
41 140 0.99
ACGTcount: A:0.19, C:0.22, G:0.24, T:0.36
Consensus pattern (40 bp):
GCTAATGCTCAGTCTTTAGCGGCGTTTTTTAATAAGCGCC
Found at i:40512458 original size:26 final size:26
Alignment explanation
Indices: 40512410--40512460 Score: 66
Period size: 26 Copynumber: 2.0 Consensus size: 26
40512400 AAAATGGATA
** * *
40512410 AATTTGAAATAATGACACGTAGAAAT
1 AATTTGAAATAAAAAAACATAGAAAT
40512436 AATTTGAAATAAAAAAACATAGAAA
1 AATTTGAAATAAAAAAACATAGAAA
40512461 AATATTTGTT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.59, C:0.06, G:0.12, T:0.24
Consensus pattern (26 bp):
AATTTGAAATAAAAAAACATAGAAAT
Found at i:40513997 original size:66 final size:65
Alignment explanation
Indices: 40513890--40514060 Score: 218
Period size: 66 Copynumber: 2.6 Consensus size: 65
40513880 GAGCAAGTTA
* * * * *
40513890 CACAACTTAAAGCGGAGGCAACATCGAGAGAAGCTGAGGTTCAA-AAAAGATATGAAGAATTCCA
1 CACAACTTAAAGCAGATGCAGCAGCGAGAGAAGCTGAGGTTCAACAAAAG-TATGAAGAAATCCA
40513954 G
65 G
*
40513955 CTACAACTTAAAGCAGATGCAGCAGCGAGAGAAGCTGAGGTTCAACGAAAGTATGAAGAAATCCA
1 C-ACAACTTAAAGCAGATGCAGCAGCGAGAGAAGCTGAGGTTCAACAAAAGTATGAAGAAATCCA
40514020 G
65 G
* * * *
40514021 CAGCAGCTTAAAGCAGATGCGGCAGCAAGAGAAGCAGAGG
1 CA-CAACTTAAAGCAGATGCAGCAGCGAGAGAAGCTGAGG
40514061 CGGTAGCGAG
Statistics
Matches: 93, Mismatches: 10, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
65 2 0.02
66 87 0.94
67 4 0.04
ACGTcount: A:0.41, C:0.18, G:0.27, T:0.13
Consensus pattern (65 bp):
CACAACTTAAAGCAGATGCAGCAGCGAGAGAAGCTGAGGTTCAACAAAAGTATGAAGAAATCCAG
Found at i:40514057 original size:21 final size:21
Alignment explanation
Indices: 40514031--40514075 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
40514021 CAGCAGCTTA
*
40514031 AAGCAGATGCGGCAGCAAGAG
1 AAGCAGAGGCGGCAGCAAGAG
* *
40514052 AAGCAGAGGCGGTAGCGAGAG
1 AAGCAGAGGCGGCAGCAAGAG
40514073 AAG
1 AAG
40514076 TACAGGCTAC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.38, C:0.16, G:0.42, T:0.04
Consensus pattern (21 bp):
AAGCAGAGGCGGCAGCAAGAG
Found at i:40514082 original size:21 final size:21
Alignment explanation
Indices: 40514039--40514082 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
40514029 TAAAGCAGAT
*
40514039 GCGGCAGCAAGAGAAGCAGAG
1 GCGGCAGCAAGAGAAGCACAG
* * *
40514060 GCGGTAGCGAGAGAAGTACAG
1 GCGGCAGCAAGAGAAGCACAG
40514081 GC
1 GC
40514083 TACAGCGAGG
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.34, C:0.18, G:0.43, T:0.05
Consensus pattern (21 bp):
GCGGCAGCAAGAGAAGCACAG
Found at i:40514089 original size:21 final size:21
Alignment explanation
Indices: 40514065--40514143 Score: 95
Period size: 21 Copynumber: 3.8 Consensus size: 21
40514055 CAGAGGCGGT
* *
40514065 AGCGAGAGAAGTACAGGCTAC
1 AGCGAGGGAAGTAGAGGCTAC
* * *
40514086 AGCGAGGGAAGCAGAAGCTAT
1 AGCGAGGGAAGTAGAGGCTAC
*
40514107 AGCGAGGGAAGTAGAGGCTGC
1 AGCGAGGGAAGTAGAGGCTAC
*
40514128 AGCGAGGGAAGCAGAG
1 AGCGAGGGAAGTAGAG
40514144 CAGCGTCAAA
Statistics
Matches: 48, Mismatches: 10, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 48 1.00
ACGTcount: A:0.35, C:0.15, G:0.42, T:0.08
Consensus pattern (21 bp):
AGCGAGGGAAGTAGAGGCTAC
Found at i:40514504 original size:43 final size:43
Alignment explanation
Indices: 40514451--40514747 Score: 252
Period size: 43 Copynumber: 6.9 Consensus size: 43
40514441 ATCTGCCAAA
* * * * *
40514451 TTTAGTGGCGTTTTTGGTAAAAGCGCCGCTAAATATAAGGGTC
1 TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGATCAGGGTC
* * *
40514494 TTTAGCGGCGTTTGTGGAAAAAGCGCCACTAAAGATCATGGTC
1 TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGATCAGGGTC
* * * *
40514537 TTTAGCGGCGTTTATGGGGAAAGCGCCGCTAAAGATTAGGTTC
1 TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGATCAGGGTC
* *** * *
40514580 TTTAGTGGCGTTTGTGGTCTAAGCGCCGCTATAGATCAGAGTC
1 TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGATCAGGGTC
* * ****
40514623 TTTTGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGACCCTAATC
1 TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGATCAGGGTC
* * * * * ** *
40514666 TTTAGCGGCGCTTGTCGCAAAAACGCCGCTAAAGACCTTGATC
1 TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGATCAGGGTC
* * ** *
40514709 TTTAGCGGCGCTTCTAGCAAAAAACGCCGCTAAAGATCA
1 TTTAGCGGCGTTTGT-GGGAAAAGCGCCGCTAAAGATCA
40514748 ACACTTTTAG
Statistics
Matches: 207, Mismatches: 46, Indels: 1
0.81 0.18 0.00
Matches are distributed among these distances:
43 189 0.91
44 18 0.09
ACGTcount: A:0.25, C:0.21, G:0.27, T:0.27
Consensus pattern (43 bp):
TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGATCAGGGTC
Found at i:40514693 original size:129 final size:129
Alignment explanation
Indices: 40514451--40514700 Score: 320
Period size: 129 Copynumber: 1.9 Consensus size: 129
40514441 ATCTGCCAAA
* * *
40514451 TTTAGTGGCGTTTTTGGTAAAAGCGCCGCTAAATATAAGGGTCTTTAGCGGCGTTTGTGGAAAAA
1 TTTAGTGGCGTTTGTGGTAAAAGCGCCGCTAAAGATAAGAGTCTTTAGCGGCGTTTGTGGAAAAA
* ** * * ** *
40514516 GCGCCACTAAAGATCATGGTCTTTAGCGGCGTTTATGGGGAAAGCGCCGCTAAAGATTAGGTTC
66 GCGCCACTAAAGACCATAATCTTTAGCGGCGCTTATCGCAAAAACGCCGCTAAAGATTAGGTTC
** * * * *
40514580 TTTAGTGGCGTTTGTGGTCTAAGCGCCGCTATAGATCAGAGTCTTTTGCGGCGTTTGTGGGAAAA
1 TTTAGTGGCGTTTGTGGTAAAAGCGCCGCTAAAGATAAGAGTCTTTAGCGGCGTTTGTGGAAAAA
* * *
40514645 GCGCCGCTAAAGACCCTAATCTTTAGCGGCGCTTGTCGCAAAAACGCCGCTAAAGA
66 GCGCCACTAAAGACCATAATCTTTAGCGGCGCTTATCGCAAAAACGCCGCTAAAGA
40514701 CCTTGATCTT
Statistics
Matches: 101, Mismatches: 20, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
129 101 1.00
ACGTcount: A:0.24, C:0.19, G:0.29, T:0.28
Consensus pattern (129 bp):
TTTAGTGGCGTTTGTGGTAAAAGCGCCGCTAAAGATAAGAGTCTTTAGCGGCGTTTGTGGAAAAA
GCGCCACTAAAGACCATAATCTTTAGCGGCGCTTATCGCAAAAACGCCGCTAAAGATTAGGTTC
Found at i:40514711 original size:129 final size:128
Alignment explanation
Indices: 40514451--40514765 Score: 310
Period size: 129 Copynumber: 2.4 Consensus size: 128
40514441 ATCTGCCAAA
* * *
40514451 TTTAGTGGCGTTTTTGGTAAAAGCGCCGCTAAATATAAGGGTCTTTAGCGGCGTTTGTGGAAAAA
1 TTTAGTGGCGTTTGTGGTAAAAGCGCCGCTAAAGATAAGAGTCTTTAGCGGCGTTTGTGGAAAAA
* ** * * ** * *
40514516 GCGCCACTAAAGATCATGGTCTTTAGCGGCGTTTATGGGGAAAGCGCCGCTAAAGATTAGGTTC
66 GCGCCACTAAAGACCATAATCTTTAGCGGCGCTTATCGCAAAAACGCCGCTAAAGATTA-GATC
** * * * *
40514580 TTTAGTGGCGTTTGTGGTCTAAGCGCCGCTATAGATCAGAGTCTTTTGCGGCGTTTGTGGGAAAA
1 TTTAGTGGCGTTTGTGGTAAAAGCGCCGCTAAAGATAAGAGTCTTTAGCGGCGTTTGTGGAAAAA
* * *
40514645 GCGCCGCTAAAGACCCTAATCTTTAGCGGCGCTTGTCGCAAAAACGCCGCTAAAGACCTT-GATC
66 GCGCCACTAAAGACCATAATCTTTAGCGGCGCTTATCGCAAAAACGCCGCTAAAGA--TTAGATC
* * * ** * * *
40514709 TTTAGCGGCGCTTCTAGCAAAAAACGCCGCTAAAGATCAACACT-TTTAGCGGCGTTT
1 TTTAGTGGCGTTTGT-GGTAAAAGCGCCGCTAAAGAT-AAGAGTCTTTAGCGGCGTTT
40514766 ATTTCTAAAA
Statistics
Matches: 148, Mismatches: 34, Indels: 7
0.78 0.18 0.04
Matches are distributed among these distances:
129 116 0.78
130 27 0.18
131 5 0.03
ACGTcount: A:0.25, C:0.21, G:0.27, T:0.28
Consensus pattern (128 bp):
TTTAGTGGCGTTTGTGGTAAAAGCGCCGCTAAAGATAAGAGTCTTTAGCGGCGTTTGTGGAAAAA
GCGCCACTAAAGACCATAATCTTTAGCGGCGCTTATCGCAAAAACGCCGCTAAAGATTAGATC
Found at i:40514757 original size:44 final size:43
Alignment explanation
Indices: 40514641--40514762 Score: 131
Period size: 43 Copynumber: 2.8 Consensus size: 43
40514631 CGTTTGTGGG
* * * *
40514641 AAAAGCGCCGCTAAAGACCCTA-ATCTTTAGCGGCGCTTGTCGC
1 AAAAACGCCGCTAAAGA-CCAACATCTTTAGCGGCGCTTCTAGC
***
40514684 AAAAACGCCGCTAAAGACCTTGATCTTTAGCGGCGCTTCTAGC
1 AAAAACGCCGCTAAAGACCAACATCTTTAGCGGCGCTTCTAGC
*
40514727 AAAAAACGCCGCTAAAGATCAACA-CTTTTAGCGGCG
1 -AAAAACGCCGCTAAAGACCAACATC-TTTAGCGGCG
40514763 TTTATTTCTA
Statistics
Matches: 68, Mismatches: 8, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
42 3 0.04
43 36 0.53
44 29 0.43
ACGTcount: A:0.30, C:0.28, G:0.21, T:0.20
Consensus pattern (43 bp):
AAAAACGCCGCTAAAGACCAACATCTTTAGCGGCGCTTCTAGC
Found at i:40517861 original size:38 final size:38
Alignment explanation
Indices: 40517828--40517935 Score: 126
Period size: 38 Copynumber: 2.8 Consensus size: 38
40517818 CATGTTCAAT
*
40517828 ATGCCTACTGTTACTATTGAACTGAATACATGTTAAGC
1 ATGCCTACTATTACTATTGAACTGAATACATGTTAAGC
* * *
40517866 ATGCCTACTATTACTGTTGAACTTAATACATGTTACGC
1 ATGCCTACTATTACTATTGAACTGAATACATGTTAAGC
* * ** * *
40517904 ATGTCTAATGCTATTATTGAACTAAATACATG
1 ATGCCTACTATTACTATTGAACTGAATACATG
40517936 ATAAAACATG
Statistics
Matches: 59, Mismatches: 11, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
38 59 1.00
ACGTcount: A:0.32, C:0.18, G:0.14, T:0.36
Consensus pattern (38 bp):
ATGCCTACTATTACTATTGAACTGAATACATGTTAAGC
Found at i:40523724 original size:52 final size:52
Alignment explanation
Indices: 40523662--40523762 Score: 193
Period size: 52 Copynumber: 1.9 Consensus size: 52
40523652 GTAGATATGC
*
40523662 AAAGTCCTACCCCTATCCTCTACACACCAACTCCGATCATCCCAACGCACCA
1 AAAGTCCTACCCCTATCCTCTACACACCAACTCCGACCATCCCAACGCACCA
40523714 AAAGTCCTACCCCTATCCTCTACACACCAACTCCGACCATCCCAACGCA
1 AAAGTCCTACCCCTATCCTCTACACACCAACTCCGACCATCCCAACGCA
40523763 TCACATGGGG
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
52 48 1.00
ACGTcount: A:0.31, C:0.47, G:0.06, T:0.17
Consensus pattern (52 bp):
AAAGTCCTACCCCTATCCTCTACACACCAACTCCGACCATCCCAACGCACCA
Found at i:40526257 original size:14 final size:15
Alignment explanation
Indices: 40526240--40526271 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
40526230 ATAACGGTTG
40526240 GAAAAT-TAAGTATT
1 GAAAATGTAAGTATT
40526254 GAAAATGTAAGTATT
1 GAAAATGTAAGTATT
40526269 GAA
1 GAA
40526272 TTTAAGTTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 6 0.35
15 11 0.65
ACGTcount: A:0.50, C:0.00, G:0.19, T:0.31
Consensus pattern (15 bp):
GAAAATGTAAGTATT
Found at i:40531015 original size:42 final size:41
Alignment explanation
Indices: 40530969--40531091 Score: 149
Period size: 42 Copynumber: 3.0 Consensus size: 41
40530959 ATGCTATCAT
40530969 ATATCGATGCCAATAG-CCCAGCTATGGTCTTACACAAATCTC
1 ATATCGATGCCAAT-GTCCCAGC-ATGGTCTTACACAAATCTC
* * * * *
40531011 ATATCAATGCCAATGTCCCAAACATGGTTTTACACGAATCTT
1 ATATCGATGCCAATGTCCC-AGCATGGTCTTACACAAATCTC
* *
40531053 ATATCGATGTCAATGTCCCAGAATGGTCTTACACAAATC
1 ATATCGATGCCAATGTCCCAGCATGGTCTTACACAAATC
40531092 ACATCGCAGT
Statistics
Matches: 68, Mismatches: 11, Indels: 5
0.81 0.13 0.06
Matches are distributed among these distances:
41 17 0.25
42 49 0.72
43 2 0.03
ACGTcount: A:0.33, C:0.25, G:0.14, T:0.28
Consensus pattern (41 bp):
ATATCGATGCCAATGTCCCAGCATGGTCTTACACAAATCTC
Found at i:40531457 original size:21 final size:21
Alignment explanation
Indices: 40531433--40531474 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
40531423 TTTTCCCCTA
*
40531433 AACTTTCACATTTTTGCAATT
1 AACTTTCACATTTTTACAATT
40531454 AACTTTCACATTTTTACAATT
1 AACTTTCACATTTTTACAATT
40531475 TCGTCCTTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.31, C:0.19, G:0.02, T:0.48
Consensus pattern (21 bp):
AACTTTCACATTTTTACAATT
Found at i:40532556 original size:18 final size:18
Alignment explanation
Indices: 40532533--40532571 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
40532523 ACACGGGCTA
40532533 GGCCAAGTTAGGCGTATG
1 GGCCAAGTTAGGCGTATG
* *
40532551 GGCCAAGTTGGGCGTGTG
1 GGCCAAGTTAGGCGTATG
40532569 GGC
1 GGC
40532572 TACACGTGCA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.15, C:0.18, G:0.46, T:0.21
Consensus pattern (18 bp):
GGCCAAGTTAGGCGTATG
Found at i:40532587 original size:17 final size:17
Alignment explanation
Indices: 40532565--40532602 Score: 67
Period size: 17 Copynumber: 2.2 Consensus size: 17
40532555 AAGTTGGGCG
*
40532565 TGTGGGCTACACGTGCA
1 TGTGGGCTACACGAGCA
40532582 TGTGGGCTACACGAGCA
1 TGTGGGCTACACGAGCA
40532599 TGTG
1 TGTG
40532603 AGCCCACACA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.18, C:0.21, G:0.37, T:0.24
Consensus pattern (17 bp):
TGTGGGCTACACGAGCA
Found at i:40552738 original size:2 final size:2
Alignment explanation
Indices: 40552731--40552757 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
40552721 GCATCAAATC
40552731 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
40552758 CACATTATAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:40555404 original size:5 final size:5
Alignment explanation
Indices: 40555396--40555440 Score: 63
Period size: 5 Copynumber: 8.8 Consensus size: 5
40555386 AATACAACAC
* *
40555396 AAAAG AAAAG AAAAAG AGAGG AAAAG AAAAG AAAAG AAAAG AAAA
1 AAAAG AAAAG -AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAAA
40555441 AAATGGCTTC
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
5 30 0.86
6 5 0.14
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (5 bp):
AAAAG
Found at i:40556048 original size:5 final size:5
Alignment explanation
Indices: 40556038--40556067 Score: 60
Period size: 5 Copynumber: 6.0 Consensus size: 5
40556028 ATTTACCTCT
40556038 TACCA TACCA TACCA TACCA TACCA TACCA
1 TACCA TACCA TACCA TACCA TACCA TACCA
40556068 CCACCATTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 25 1.00
ACGTcount: A:0.40, C:0.40, G:0.00, T:0.20
Consensus pattern (5 bp):
TACCA
Found at i:40556437 original size:22 final size:21
Alignment explanation
Indices: 40556390--40556436 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
40556380 TTAGTAAATA
**
40556390 TAAAATTACATTTTGACCCCC
1 TAAAATTACATTTCAACCCCC
*
40556411 TAAAATTTCATTTCAACCCCC
1 TAAAATTACATTTCAACCCCC
40556432 TAAAA
1 TAAAA
40556437 AAATATTTTC
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.38, C:0.28, G:0.02, T:0.32
Consensus pattern (21 bp):
TAAAATTACATTTCAACCCCC
Found at i:40559867 original size:16 final size:17
Alignment explanation
Indices: 40559839--40559870 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
40559829 AGAGTTAAAA
40559839 TTAAAATTCTAAAATTT
1 TTAAAATTCTAAAATTT
40559856 TTAAAA-TCTAAAATT
1 TTAAAATTCTAAAATT
40559871 GATTAAAATA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.50, C:0.06, G:0.00, T:0.44
Consensus pattern (17 bp):
TTAAAATTCTAAAATTT
Found at i:40559876 original size:17 final size:16
Alignment explanation
Indices: 40559838--40559879 Score: 57
Period size: 17 Copynumber: 2.5 Consensus size: 16
40559828 AAGAGTTAAA
40559838 ATTAAAATTCTAAAATT
1 ATTAAAA-TCTAAAATT
*
40559855 TTTAAAATCTAAAATT
1 ATTAAAATCTAAAATT
40559871 GATTAAAAT
1 -ATTAAAAT
40559880 AAATATGAGA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
16 9 0.41
17 13 0.59
ACGTcount: A:0.52, C:0.05, G:0.02, T:0.40
Consensus pattern (16 bp):
ATTAAAATCTAAAATT
Found at i:40560070 original size:17 final size:17
Alignment explanation
Indices: 40560048--40560081 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
40560038 TGAATAAATT
40560048 ATTAAAAA-AATAAAAAC
1 ATTAAAAATAA-AAAAAC
40560065 ATTAAAAATAAAAAAAC
1 ATTAAAAATAAAAAAAC
40560082 TAGTTCAACT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 14 0.88
18 2 0.12
ACGTcount: A:0.76, C:0.06, G:0.00, T:0.18
Consensus pattern (17 bp):
ATTAAAAATAAAAAAAC
Found at i:40560305 original size:27 final size:27
Alignment explanation
Indices: 40560275--40560326 Score: 77
Period size: 27 Copynumber: 1.9 Consensus size: 27
40560265 ATACAATATA
* *
40560275 AATATTCAAAATTTTCATTTATACCAT
1 AATATCCAAAATTTTAATTTATACCAT
*
40560302 AATATCCACAATTTTAATTTATACC
1 AATATCCAAAATTTTAATTTATACC
40560327 TAAGTAAGTC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.40, C:0.17, G:0.00, T:0.42
Consensus pattern (27 bp):
AATATCCAAAATTTTAATTTATACCAT
Found at i:40564758 original size:17 final size:16
Alignment explanation
Indices: 40564706--40564760 Score: 65
Period size: 16 Copynumber: 3.4 Consensus size: 16
40564696 CTGGAGCAAC
40564706 AACTATTGTTTAGAAT
1 AACTATTGTTTAGAAT
** * *
40564722 AGTTGTTGTTTAGAAC
1 AACTATTGTTTAGAAT
40564738 AACTATTGTTTGAGAAT
1 AACTATTGTTT-AGAAT
40564755 AACTAT
1 AACTAT
40564761 GTCCAAAATA
Statistics
Matches: 30, Mismatches: 8, Indels: 1
0.77 0.21 0.03
Matches are distributed among these distances:
16 20 0.67
17 10 0.33
ACGTcount: A:0.35, C:0.07, G:0.16, T:0.42
Consensus pattern (16 bp):
AACTATTGTTTAGAAT
Found at i:40570662 original size:9 final size:9
Alignment explanation
Indices: 40570648--40570687 Score: 62
Period size: 9 Copynumber: 4.4 Consensus size: 9
40570638 TTTGGTTAAA
40570648 AATTAACCG
1 AATTAACCG
40570657 AATTAACCG
1 AATTAACCG
*
40570666 AATTACCCG
1 AATTAACCG
*
40570675 AATTACCCG
1 AATTAACCG
40570684 AATT
1 AATT
40570688 GAATCACTAC
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
9 30 1.00
ACGTcount: A:0.40, C:0.25, G:0.10, T:0.25
Consensus pattern (9 bp):
AATTAACCG
Found at i:40570973 original size:39 final size:39
Alignment explanation
Indices: 40570886--40571002 Score: 191
Period size: 39 Copynumber: 3.0 Consensus size: 39
40570876 ACTTAAGAGT
*
40570886 TAGACTTTAGTTTTATTTTTATTGGGTT-GGTAATTGGG
1 TAGACTTTAGTTTTAGTTTTATTGGGTTGGGTAATTGGG
* * *
40570924 TAGACCTTAGTTTTAGTTCTATTGGGTTGGGTAATTTGG
1 TAGACTTTAGTTTTAGTTTTATTGGGTTGGGTAATTGGG
40570963 TAGACTTTAGTTTTAGTTTTATTGGGTTGGGTAATTGGG
1 TAGACTTTAGTTTTAGTTTTATTGGGTTGGGTAATTGGG
40571002 T
1 T
40571003 TGGGTTGGAT
Statistics
Matches: 71, Mismatches: 7, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
38 25 0.35
39 46 0.65
ACGTcount: A:0.18, C:0.04, G:0.28, T:0.50
Consensus pattern (39 bp):
TAGACTTTAGTTTTAGTTTTATTGGGTTGGGTAATTGGG
Found at i:40571001 original size:13 final size:13
Alignment explanation
Indices: 40570983--40571007 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
40570973 TTTTAGTTTT
40570983 ATTGGGTTGGGTA
1 ATTGGGTTGGGTA
40570996 ATTGGGTTGGGT
1 ATTGGGTTGGGT
40571008 TGGATAATTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.12, C:0.00, G:0.48, T:0.40
Consensus pattern (13 bp):
ATTGGGTTGGGTA
Found at i:40571616 original size:16 final size:15
Alignment explanation
Indices: 40571591--40571624 Score: 50
Period size: 16 Copynumber: 2.2 Consensus size: 15
40571581 AAATTTGATA
*
40571591 ATAATTAATATACATT
1 ATAATAAATATA-ATT
40571607 ATAATAAATATAATT
1 ATAATAAATATAATT
40571622 ATA
1 ATA
40571625 TATTAGTTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 6 0.35
16 11 0.65
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.41
Consensus pattern (15 bp):
ATAATAAATATAATT
Found at i:40571745 original size:29 final size:29
Alignment explanation
Indices: 40571691--40571746 Score: 69
Period size: 29 Copynumber: 1.9 Consensus size: 29
40571681 GCTTTTAAAG
* * *
40571691 ATATTTACAAAAAGAGACAGCTAATTTCA
1 ATATTCACAAAAAGAGACACCAAATTTCA
40571720 ATATTCACAAAAAGA-ACAACCAAATTT
1 ATATTCACAAAAAGAGAC-ACCAAATTT
40571747 TGCAAATAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
28 2 0.09
29 21 0.91
ACGTcount: A:0.52, C:0.16, G:0.07, T:0.25
Consensus pattern (29 bp):
ATATTCACAAAAAGAGACACCAAATTTCA
Found at i:40579264 original size:27 final size:28
Alignment explanation
Indices: 40579234--40579294 Score: 65
Period size: 27 Copynumber: 2.2 Consensus size: 28
40579224 TATTATAAAA
40579234 TTAATTAA-AA-TTAAATATTTTAATAAT
1 TTAATTAACAATTTAAATATTTT-ATAAT
* *
40579261 TTAA-GAACAATTTAATTATTTTATAAT
1 TTAATTAACAATTTAAATATTTTATAAT
*
40579288 TAAATTA
1 TTAATTA
40579295 TATTTTGGAC
Statistics
Matches: 27, Mismatches: 4, Indels: 5
0.75 0.11 0.14
Matches are distributed among these distances:
26 2 0.07
27 14 0.52
28 11 0.41
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.48
Consensus pattern (28 bp):
TTAATTAACAATTTAAATATTTTATAAT
Found at i:40582458 original size:30 final size:30
Alignment explanation
Indices: 40582416--40582495 Score: 83
Period size: 29 Copynumber: 2.7 Consensus size: 30
40582406 GAGTAAGTTG
* *
40582416 CTCACACAAGCTGACATTATATCAGGGTTC
1 CTCAAACAAGCTGACATTATATCAAGGTTC
* *** *
40582446 CTCAAGCAAGCTGA-AACGTATCAAGGTTG
1 CTCAAACAAGCTGACATTATATCAAGGTTC
40582475 CTCAAACAAGCTGAC-TTATAT
1 CTCAAACAAGCTGACATTATAT
40582496 TAGGTTACCC
Statistics
Matches: 38, Mismatches: 11, Indels: 3
0.73 0.21 0.06
Matches are distributed among these distances:
29 26 0.68
30 12 0.32
ACGTcount: A:0.34, C:0.24, G:0.17, T:0.25
Consensus pattern (30 bp):
CTCAAACAAGCTGACATTATATCAAGGTTC
Found at i:40590742 original size:2 final size:2
Alignment explanation
Indices: 40590731--40590773 Score: 79
Period size: 2 Copynumber: 22.0 Consensus size: 2
40590721 AACATAAGAA
40590731 AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
40590772 AT
1 AT
40590774 TCTTTCTTTA
Statistics
Matches: 40, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 39 0.98
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:40593782 original size:36 final size:36
Alignment explanation
Indices: 40593689--40593782 Score: 152
Period size: 36 Copynumber: 2.6 Consensus size: 36
40593679 GCTGCAGGTT
* *
40593689 CTGGAGGAGGCTGCAATGGGTCTGGAACTAGTGGAG
1 CTGGTGGAGGCTGCAATGGGTTTGGAACTAGTGGAG
40593725 CTGGTGGAGGCTGCAATGGGTTTGGAACTAGTGGAG
1 CTGGTGGAGGCTGCAATGGGTTTGGAACTAGTGGAG
* *
40593761 CTGGTGGCGGCTGAAATGGGTT
1 CTGGTGGAGGCTGCAATGGGTT
40593783 AGGAGGGAGC
Statistics
Matches: 54, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
36 54 1.00
ACGTcount: A:0.19, C:0.13, G:0.45, T:0.23
Consensus pattern (36 bp):
CTGGTGGAGGCTGCAATGGGTTTGGAACTAGTGGAG
Found at i:40593821 original size:33 final size:33
Alignment explanation
Indices: 40593766--40593875 Score: 141
Period size: 33 Copynumber: 3.3 Consensus size: 33
40593756 TGGAGCTGGT
* * * * *
40593766 GGCGGCTGAAATGGGTTAGGAGGGAGCACTGGG-
1 GGCGGCAGAAGTGGGTTTGGAGGAAG-AATGGGC
*
40593799 GGTGGCAGAAGTGGGTTTGGAGGAAGAATGGGC
1 GGCGGCAGAAGTGGGTTTGGAGGAAGAATGGGC
40593832 GGCGGCAGAAGTGGGTTTGGAGGAAGAATGGGC
1 GGCGGCAGAAGTGGGTTTGGAGGAAGAATGGGC
*
40593865 GGCGGAAGAAG
1 GGCGGCAGAAG
40593876 CTGGTTGGGA
Statistics
Matches: 68, Mismatches: 8, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
32 5 0.07
33 63 0.93
ACGTcount: A:0.25, C:0.09, G:0.52, T:0.15
Consensus pattern (33 bp):
GGCGGCAGAAGTGGGTTTGGAGGAAGAATGGGC
Found at i:40593841 original size:15 final size:15
Alignment explanation
Indices: 40593820--40593874 Score: 56
Period size: 15 Copynumber: 3.5 Consensus size: 15
40593810 TGGGTTTGGA
40593820 GGAAGAATGGGCGGC
1 GGAAGAATGGGCGGC
* * *
40593835 GGCAGAAGTGGGTTTGGA
1 GGAAGAA-TGGG--CGGC
40593853 GGAAGAATGGGCGGC
1 GGAAGAATGGGCGGC
40593868 GGAAGAA
1 GGAAGAA
40593875 GCTGGTTGGG
Statistics
Matches: 31, Mismatches: 6, Indels: 6
0.72 0.14 0.14
Matches are distributed among these distances:
15 15 0.48
16 4 0.13
17 4 0.13
18 8 0.26
ACGTcount: A:0.29, C:0.09, G:0.51, T:0.11
Consensus pattern (15 bp):
GGAAGAATGGGCGGC
Found at i:40593859 original size:18 final size:17
Alignment explanation
Indices: 40593805--40593863 Score: 59
Period size: 18 Copynumber: 3.5 Consensus size: 17
40593795 TGGGGGTGGC
40593805 AGAAGTGGGTTTGGAGGA
1 AGAA-TGGGTTTGGAGGA
* * *
40593823 AGAATGGG--CGGCGGC
1 AGAATGGGTTTGGAGGA
40593838 AGAAGTGGGTTTGGAGGA
1 AGAA-TGGGTTTGGAGGA
40593856 AGAATGGG
1 AGAATGGG
40593864 CGGCGGAAGA
Statistics
Matches: 32, Mismatches: 6, Indels: 7
0.71 0.13 0.16
Matches are distributed among these distances:
15 8 0.25
16 4 0.12
17 8 0.25
18 12 0.38
ACGTcount: A:0.27, C:0.05, G:0.51, T:0.17
Consensus pattern (17 bp):
AGAATGGGTTTGGAGGA
Found at i:40598301 original size:22 final size:22
Alignment explanation
Indices: 40598276--40598319 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
40598266 TTTTTGACAA
40598276 AGGCTTGTTTAAATGTCTGAAT
1 AGGCTTGTTTAAATGTCTGAAT
40598298 AGGCTTGTTTAAATGTCTGAAT
1 AGGCTTGTTTAAATGTCTGAAT
40598320 TAAATAAGAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.27, C:0.09, G:0.23, T:0.41
Consensus pattern (22 bp):
AGGCTTGTTTAAATGTCTGAAT
Found at i:40603744 original size:51 final size:51
Alignment explanation
Indices: 40603659--40603841 Score: 258
Period size: 51 Copynumber: 3.6 Consensus size: 51
40603649 TCAAACACAC
* *
40603659 CAGTAACAGTAATCAGTAACGGTAACAGTGTTCGACACACAAAGTGCCGAAT
1 CAGTAACAGTAA-CAGTAACAGTAACAGTATTCGACACACAAAGTGCCGAAT
* * * **
40603711 CGGTAACGGTAACAGTAACAGTAACAATATTCGACACACAAAGTATCGAAT
1 CAGTAACAGTAACAGTAACAGTAACAGTATTCGACACACAAAGTGCCGAAT
* *
40603762 CAGTAACAGTAACAGTAACAGTAACAGTATTCAACACACAAAGTGCTGAAT
1 CAGTAACAGTAACAGTAACAGTAACAGTATTCGACACACAAAGTGCCGAAT
* *
40603813 CTGTAACAGTAACGGTAACAGTAACAGTA
1 CAGTAACAGTAACAGTAACAGTAACAGTA
40603842 GTCGGTACAT
Statistics
Matches: 115, Mismatches: 16, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
51 105 0.91
52 10 0.09
ACGTcount: A:0.42, C:0.20, G:0.19, T:0.20
Consensus pattern (51 bp):
CAGTAACAGTAACAGTAACAGTAACAGTATTCGACACACAAAGTGCCGAAT
Found at i:40603773 original size:6 final size:6
Alignment explanation
Indices: 40603762--40603790 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
40603752 AGTATCGAAT
40603762 CAGTAA CAGTAA CAGTAA CAGTAA CAGTA
1 CAGTAA CAGTAA CAGTAA CAGTAA CAGTA
40603791 TTCAACACAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.48, C:0.17, G:0.17, T:0.17
Consensus pattern (6 bp):
CAGTAA
Found at i:40604269 original size:26 final size:25
Alignment explanation
Indices: 40604240--40604289 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
40604230 CAATTCAATA
40604240 ATTCAATTCAAAC-CATTTCAATTTCT
1 ATTCAA-T-AAACACATTTCAATTTCT
*
40604266 ATTCAATAATCACATTTCAATTTC
1 ATTCAATAAACACATTTCAATTTC
40604290 ACTTTCTTAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
24 3 0.14
25 13 0.59
26 6 0.27
ACGTcount: A:0.36, C:0.22, G:0.00, T:0.42
Consensus pattern (25 bp):
ATTCAATAAACACATTTCAATTTCT
Found at i:40605327 original size:8 final size:8
Alignment explanation
Indices: 40605314--40605368 Score: 51
Period size: 8 Copynumber: 6.8 Consensus size: 8
40605304 GTTTATTTAA
40605314 AATATAAT
1 AATATAAT
40605322 AATATAAT
1 AATATAAT
40605330 AATATAAT
1 AATATAAT
* *
40605338 -ATAATTTAC
1 AAT-A-TAAT
40605347 AATATAAT
1 AATATAAT
40605355 AA-ATTAAT
1 AATA-TAAT
40605363 AATATA
1 AATATA
40605369 CTTCAAAAAA
Statistics
Matches: 38, Mismatches: 4, Indels: 10
0.73 0.08 0.19
Matches are distributed among these distances:
7 3 0.08
8 29 0.76
9 4 0.11
10 2 0.05
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (8 bp):
AATATAAT
Found at i:40612749 original size:34 final size:34
Alignment explanation
Indices: 40612711--40612775 Score: 103
Period size: 34 Copynumber: 1.9 Consensus size: 34
40612701 CGAATACTTG
*
40612711 ATAAACATGACTTTTGCTACTGCATTGATCTATC
1 ATAAACATGACTATTGCTACTGCATTGATCTATC
* *
40612745 ATAAACATGTCTATTGCTACTGTATTGATCT
1 ATAAACATGACTATTGCTACTGCATTGATCT
40612776 GTTATAATCA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
34 28 1.00
ACGTcount: A:0.29, C:0.18, G:0.12, T:0.40
Consensus pattern (34 bp):
ATAAACATGACTATTGCTACTGCATTGATCTATC
Found at i:40612788 original size:34 final size:35
Alignment explanation
Indices: 40612711--40612794 Score: 100
Period size: 34 Copynumber: 2.5 Consensus size: 35
40612701 CGAATACTTG
* *
40612711 ATAAACATGAC-TTTTGCTACTGCATTGATCTATC
1 ATAAACATGTCATATTGCTACTGCATTGATCTATC
* * *
40612745 ATAAACATGTC-TATTGCTACTGTATTGATCTGTT
1 ATAAACATGTCATATTGCTACTGCATTGATCTATC
*
40612779 ATAATCATGTCATATT
1 ATAAACATGTCATATT
40612795 ACATTGCATG
Statistics
Matches: 43, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
34 39 0.91
35 4 0.09
ACGTcount: A:0.30, C:0.17, G:0.12, T:0.42
Consensus pattern (35 bp):
ATAAACATGTCATATTGCTACTGCATTGATCTATC
Found at i:40613636 original size:2 final size:2
Alignment explanation
Indices: 40613631--40613657 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
40613621 TGAGGTTTGA
40613631 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
40613658 CTNNNNNNNN
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:40613941 original size:30 final size:29
Alignment explanation
Indices: 40613877--40613946 Score: 79
Period size: 30 Copynumber: 2.3 Consensus size: 29
40613867 AATTTTATAC
* *
40613877 AATTAATTAAAATATTTAGTTTTTCCTTAG
1 AATTAATTAAAATATTTAATTTTT-CTTAA
40613907 AATTAATTAAAATAATTTAATTTTT-TTAAA
1 AATTAATTAAAAT-ATTTAATTTTTCTT-AA
*
40613937 AATTATTTAA
1 AATTAATTAA
40613947 GAAATTAAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
29 2 0.06
30 23 0.66
31 10 0.29
ACGTcount: A:0.44, C:0.03, G:0.03, T:0.50
Consensus pattern (29 bp):
AATTAATTAAAATATTTAATTTTTCTTAA
Found at i:40615274 original size:16 final size:16
Alignment explanation
Indices: 40615250--40615280 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
40615240 ATACTATATT
*
40615250 TAATCAAATTATTTTA
1 TAATAAAATTATTTTA
40615266 TAATAAAATTATTTT
1 TAATAAAATTATTTT
40615281 TTATGATATT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.52
Consensus pattern (16 bp):
TAATAAAATTATTTTA
Found at i:40615524 original size:15 final size:15
Alignment explanation
Indices: 40615501--40615542 Score: 57
Period size: 15 Copynumber: 2.8 Consensus size: 15
40615491 AAAACATAAC
*
40615501 TAATTTTAATTAAAA
1 TAATATTAATTAAAA
*
40615516 TAATATTAAATAAAA
1 TAATATTAATTAAAA
*
40615531 TAATAATAATTA
1 TAATATTAATTA
40615543 CTAATACTTT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (15 bp):
TAATATTAATTAAAA
Found at i:40615597 original size:16 final size:18
Alignment explanation
Indices: 40615566--40615598 Score: 52
Period size: 16 Copynumber: 1.9 Consensus size: 18
40615556 TTTATATTTT
40615566 ATATTGTTCTTAAATAAA
1 ATATTGTTCTTAAATAAA
40615584 ATATT-TTC-TAAATAA
1 ATATTGTTCTTAAATAA
40615599 TAATTAAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 7 0.47
17 3 0.20
18 5 0.33
ACGTcount: A:0.45, C:0.06, G:0.03, T:0.45
Consensus pattern (18 bp):
ATATTGTTCTTAAATAAA
Found at i:40620975 original size:12 final size:12
Alignment explanation
Indices: 40620958--40620998 Score: 59
Period size: 11 Copynumber: 3.6 Consensus size: 12
40620948 CCGTATACAA
40620958 TTTTTTTTGATT
1 TTTTTTTTGATT
*
40620970 TTTTTTTCGA-T
1 TTTTTTTTGATT
40620981 TTTTTTTT-ATT
1 TTTTTTTTGATT
40620992 TTTTTTT
1 TTTTTTT
40620999 CACGAGTCTA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
10 1 0.04
11 16 0.62
12 9 0.35
ACGTcount: A:0.07, C:0.02, G:0.05, T:0.85
Consensus pattern (12 bp):
TTTTTTTTGATT
Found at i:40620985 original size:22 final size:22
Alignment explanation
Indices: 40620957--40620999 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
40620947 ACCGTATACA
40620957 ATTTTTTTTGATTTTTTTTTCG
1 ATTTTTTTTGATTTTTTTTTCG
*
40620979 ATTTTTTTTTATTTTTTTTTC
1 ATTTTTTTTGATTTTTTTTTC
40621000 ACGAGTCTAC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.09, C:0.05, G:0.05, T:0.81
Consensus pattern (22 bp):
ATTTTTTTTGATTTTTTTTTCG
Found at i:40620998 original size:10 final size:10
Alignment explanation
Indices: 40620957--40620998 Score: 57
Period size: 10 Copynumber: 4.0 Consensus size: 10
40620947 ACCGTATACA
*
40620957 ATTTTTTTTG
1 ATTTTTTTTT
40620967 ATTTTTTTTT
1 ATTTTTTTTT
40620977 CGATTTTTTTTT
1 --ATTTTTTTTT
40620989 ATTTTTTTTT
1 ATTTTTTTTT
40620999 CACGAGTCTA
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
10 19 0.66
12 10 0.34
ACGTcount: A:0.10, C:0.02, G:0.05, T:0.83
Consensus pattern (10 bp):
ATTTTTTTTT
Found at i:40625464 original size:2 final size:2
Alignment explanation
Indices: 40625457--40625504 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
40625447 AATAATGATA
40625457 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
40625499 AT AT AT
1 AT AT AT
40625505 GATAACAATA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:40627351 original size:41 final size:41
Alignment explanation
Indices: 40627289--40627395 Score: 160
Period size: 41 Copynumber: 2.6 Consensus size: 41
40627279 TTACACTGGT
* * *
40627289 TAACATCCTTTTCAATCTTTTCATTTGTTATCCTTTTCAGA
1 TAACTTCCTTTTCAACCTTTTCATTTATTATCCTTTTCAGA
* *
40627330 TAACTTCCTTTTTAACCTTTTCATTTATTATCCTTTTCGGA
1 TAACTTCCTTTTCAACCTTTTCATTTATTATCCTTTTCAGA
*
40627371 TAACTTCCTTTTCAACATTTTCATT
1 TAACTTCCTTTTCAACCTTTTCATT
40627396 GATTCAGAAA
Statistics
Matches: 59, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
41 59 1.00
ACGTcount: A:0.21, C:0.22, G:0.04, T:0.52
Consensus pattern (41 bp):
TAACTTCCTTTTCAACCTTTTCATTTATTATCCTTTTCAGA
Found at i:40628491 original size:19 final size:19
Alignment explanation
Indices: 40628463--40628505 Score: 79
Period size: 19 Copynumber: 2.3 Consensus size: 19
40628453 TCTTTACGAT
40628463 TTAA-TCCTTTTTACTTAA
1 TTAACTCCTTTTTACTTAA
40628481 TTAACTCCTTTTTACTTAA
1 TTAACTCCTTTTTACTTAA
40628500 TTAACT
1 TTAACT
40628506 ATTTAAACCT
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
18 4 0.17
19 20 0.83
ACGTcount: A:0.28, C:0.19, G:0.00, T:0.53
Consensus pattern (19 bp):
TTAACTCCTTTTTACTTAA
Found at i:40629556 original size:30 final size:30
Alignment explanation
Indices: 40629521--40629587 Score: 116
Period size: 30 Copynumber: 2.2 Consensus size: 30
40629511 TTACCAGTAG
40629521 CACACGGTCGTGTCAACCAACTGTGTAAGA
1 CACACGGTCGTGTCAACCAACTGTGTAAGA
* *
40629551 CACACGATCGTGTCAACCAACTGTGTGAGA
1 CACACGGTCGTGTCAACCAACTGTGTAAGA
40629581 CACACGG
1 CACACGG
40629588 CCATGTAGCA
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
30 34 1.00
ACGTcount: A:0.30, C:0.28, G:0.24, T:0.18
Consensus pattern (30 bp):
CACACGGTCGTGTCAACCAACTGTGTAAGA
Found at i:40633762 original size:17 final size:18
Alignment explanation
Indices: 40633737--40633770 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
40633727 TAAATTGAGT
*
40633737 TCATTTTAG-TTAATAAC
1 TCATCTTAGATTAATAAC
40633754 TCATCTTAGATTAATAA
1 TCATCTTAGATTAATAA
40633771 ATGAGTTGCT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.38, C:0.12, G:0.06, T:0.44
Consensus pattern (18 bp):
TCATCTTAGATTAATAAC
Found at i:40636721 original size:87 final size:86
Alignment explanation
Indices: 40636574--40636734 Score: 216
Period size: 87 Copynumber: 1.9 Consensus size: 86
40636564 AAATTTAAGT
* * * *
40636574 TCGGTGAATTCATCAAGTCAATCTCAATAGGACCACCCAAACTTTGGGATATGAACTCATTAAAA
1 TCGGTGAATTCATCAAGTCAATCTCAATAAGACCACCCAAAATCTGGGATATAAACTCATTAAAA
40636639 GTAACAAACTTAACCTCTCAAG
66 GTAA-AAACTTAACCTCTCAAG
* * * * *
40636661 TCGGTGAATTCATCAAATTC-GTCTCAATAAGACCACCCAAAATCTGGGCTATAAATTCATTAAG
1 TCGGTGAATTCATC-AAGTCAATCTCAATAAGACCACCCAAAATCTGGGATATAAACTCATTAAA
40636725 AGTAAAAACT
65 AGTAAAAACT
40636735 CAGCCTTATG
Statistics
Matches: 64, Mismatches: 9, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
86 5 0.08
87 55 0.86
88 4 0.06
ACGTcount: A:0.39, C:0.22, G:0.14, T:0.26
Consensus pattern (86 bp):
TCGGTGAATTCATCAAGTCAATCTCAATAAGACCACCCAAAATCTGGGATATAAACTCATTAAAA
GTAAAAACTTAACCTCTCAAG
Found at i:40645017 original size:19 final size:20
Alignment explanation
Indices: 40644972--40645016 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 20
40644962 TATTTCAGTT
40644972 TAAAAAATCTAACTAAAATA
1 TAAAAAATCTAACTAAAATA
* *
40644992 TATAAAAT-TAATTAAAAT-
1 TAAAAAATCTAACTAAAATA
40645010 TAAAAAA
1 TAAAAAA
40645017 AGGGCATTTT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
18 6 0.27
19 9 0.41
20 7 0.32
ACGTcount: A:0.67, C:0.04, G:0.00, T:0.29
Consensus pattern (20 bp):
TAAAAAATCTAACTAAAATA
Found at i:40651527 original size:18 final size:19
Alignment explanation
Indices: 40651501--40651537 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
40651491 CCCACCTTCT
*
40651501 CTTTCCTCCTCCCC-CCTC
1 CTTTACTCCTCCCCTCCTC
40651519 CTTTACTCCTCCCCTCCTC
1 CTTTACTCCTCCCCTCCTC
40651538 TTTCCCCAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 13 0.76
19 4 0.24
ACGTcount: A:0.03, C:0.62, G:0.00, T:0.35
Consensus pattern (19 bp):
CTTTACTCCTCCCCTCCTC
Found at i:40651540 original size:18 final size:17
Alignment explanation
Indices: 40651499--40651540 Score: 57
Period size: 18 Copynumber: 2.4 Consensus size: 17
40651489 CACCCACCTT
*
40651499 CTCTTTCCTCCTCCCCC
1 CTCTTTACTCCTCCCCC
40651516 CTCCTTTACTCCTCCCCTC
1 CT-CTTTACTCCTCCCC-C
40651535 CTCTTT
1 CTCTTT
40651541 CCCCAAATTT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
17 2 0.09
18 17 0.77
19 3 0.14
ACGTcount: A:0.02, C:0.57, G:0.00, T:0.40
Consensus pattern (17 bp):
CTCTTTACTCCTCCCCC
Found at i:40656021 original size:43 final size:43
Alignment explanation
Indices: 40655879--40656023 Score: 136
Period size: 43 Copynumber: 3.4 Consensus size: 43
40655869 TTAAGGTTAC
* * *
40655879 CGAGATTATGTGTAAGACCAT-ATCTGGGATATGGA-ATCGATA
1 CGAGATTACGTGTAAGACCATGA-CTGGGCTATTGACATCGATA
* * * *
40655921 TGAGAATT-CGTGTAAGACCATGTCTGGGAC-ATTGGCATTGATA
1 CGAG-ATTACGTGTAAGACCATGACTGGG-CTATTGACATCGATA
* * *
40655964 TGTGATTTCGTGTAAGACCATGACTGGGCTATTGACATCGATA
1 CGAGATTACGTGTAAGACCATGACTGGGCTATTGACATCGATA
*
40656007 CGAGATTACATGTAAGA
1 CGAGATTACGTGTAAGA
40656024 TCATATCTAG
Statistics
Matches: 82, Mismatches: 15, Indels: 11
0.76 0.14 0.10
Matches are distributed among these distances:
42 27 0.33
43 55 0.67
ACGTcount: A:0.30, C:0.14, G:0.26, T:0.30
Consensus pattern (43 bp):
CGAGATTACGTGTAAGACCATGACTGGGCTATTGACATCGATA
Found at i:40656044 original size:85 final size:85
Alignment explanation
Indices: 40655888--40656045 Score: 187
Period size: 85 Copynumber: 1.9 Consensus size: 85
40655878 CCGAGATTAT
* * * *
40655888 GTGTAAGACCATATCTGGGATATGGAATCGATATGAGAATTCGTGTAAGACCATGTCTGGGACAT
1 GTGTAAGACCATATCTGGGATATGGAATCGATACGAGAATTCATGTAAGACCATATCTAGGACAT
*
40655953 TGGCATTGATATGTGATTTC
66 TAGCATTGATATGTGATTTC
* * *
40655973 GTGTAAGACCATGA-CTGGGCTATTGACATCGATACGAG-ATTACATGTAAGATCATATCTAGGA
1 GTGTAAGACCAT-ATCTGGGATATGGA-ATCGATACGAGAATT-CATGTAAGACCATATCTAGGA
*
40656036 TA-TAGCATTG
63 CATTAGCATTG
40656046 TTACAGTACT
Statistics
Matches: 61, Mismatches: 9, Indels: 6
0.80 0.12 0.08
Matches are distributed among these distances:
85 32 0.52
86 29 0.48
ACGTcount: A:0.30, C:0.14, G:0.25, T:0.30
Consensus pattern (85 bp):
GTGTAAGACCATATCTGGGATATGGAATCGATACGAGAATTCATGTAAGACCATATCTAGGACAT
TAGCATTGATATGTGATTTC
Found at i:40658614 original size:66 final size:66
Alignment explanation
Indices: 40658537--40658662 Score: 218
Period size: 66 Copynumber: 1.9 Consensus size: 66
40658527 ATTTAACAAA
40658537 ATTTTTTCTCTCATTTTCTCTCTTGCCAAACACCACTTTTT-TTATTCAAAACACATGGTTGCTG
1 ATTTTTTCTCTCATTTTCTCTCTTGCCAAACACCA-TTTTTCTTATTCAAAACACATGGTTGCTG
40658601 CT
65 CT
* *
40658603 ATTTTTTCTCTCATTTTCTCTCTTGCCAAACACCATTTTTCTTCTTCAAAACATATGGTT
1 ATTTTTTCTCTCATTTTCTCTCTTGCCAAACACCATTTTTCTTATTCAAAACACATGGTT
40658663 AGCTCATTTC
Statistics
Matches: 57, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
65 5 0.09
66 52 0.91
ACGTcount: A:0.21, C:0.25, G:0.06, T:0.47
Consensus pattern (66 bp):
ATTTTTTCTCTCATTTTCTCTCTTGCCAAACACCATTTTTCTTATTCAAAACACATGGTTGCTGC
T
Found at i:40658835 original size:21 final size:21
Alignment explanation
Indices: 40658795--40658850 Score: 76
Period size: 21 Copynumber: 2.6 Consensus size: 21
40658785 TTTTCTCTCA
* *
40658795 TTTTCTCTCTTGCCAAACACCAT
1 TTTTCT-TCTT-CAAAACACAAT
40658818 TTTTCTTCTTCAAAACACAAT
1 TTTTCTTCTTCAAAACACAAT
40658839 TTTTCTTCTTCA
1 TTTTCTTCTTCA
40658851 CTACCTAACC
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
21 21 0.68
22 4 0.13
23 6 0.19
ACGTcount: A:0.23, C:0.29, G:0.02, T:0.46
Consensus pattern (21 bp):
TTTTCTTCTTCAAAACACAAT
Found at i:40664512 original size:10 final size:11
Alignment explanation
Indices: 40664497--40664533 Score: 60
Period size: 10 Copynumber: 3.5 Consensus size: 11
40664487 CATACAAACT
40664497 AAGAAAGAAA-
1 AAGAAAGAAAG
40664507 AAGAAAGAAAG
1 AAGAAAGAAAG
40664518 AA-AAAGAAAG
1 AAGAAAGAAAG
40664528 AAGAAA
1 AAGAAA
40664534 AGAAGTCAAC
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
10 20 0.80
11 5 0.20
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (11 bp):
AAGAAAGAAAG
Found at i:40664516 original size:14 final size:14
Alignment explanation
Indices: 40664497--40664534 Score: 69
Period size: 14 Copynumber: 2.8 Consensus size: 14
40664487 CATACAAACT
40664497 AAGAAAGAAAAAGA
1 AAGAAAGAAAAAGA
40664511 AAGAAAGAAAAAGA
1 AAGAAAGAAAAAGA
40664525 AAG-AAGAAAA
1 AAGAAAGAAAA
40664535 GAAGTCAACG
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
13 7 0.29
14 17 0.71
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (14 bp):
AAGAAAGAAAAAGA
Found at i:40674103 original size:13 final size:13
Alignment explanation
Indices: 40674085--40674109 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
40674075 GTCTTGGACC
40674085 GCTCCTATGTACT
1 GCTCCTATGTACT
40674098 GCTCCTATGTAC
1 GCTCCTATGTAC
40674110 CAAAAAAAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.16, C:0.32, G:0.16, T:0.36
Consensus pattern (13 bp):
GCTCCTATGTACT
Found at i:40676106 original size:90 final size:90
Alignment explanation
Indices: 40675941--40676107 Score: 194
Period size: 90 Copynumber: 1.9 Consensus size: 90
40675931 TAATATGTTG
* * * * * * *
40675941 CCAGATGGTTGTGAATACACAACATAAATGCATATGAGAGTTGTTAGATAATGGGTGGGTGAACT
1 CCAGATGGTTCTGAATACACAACATAAATGCAAATAAAAGTTGTTAGATAATAGGTGGATGAACC
*
40676006 GCCAGTATTGCAGGTTAATACACTA
66 ACCAGTATTGCAGGTTAATACACTA
* * * *
40676031 CCAGATGGTTCTGAATACACAACTTAATTGCAAATAAAAGTTG-TCGTATAATATGTGGATGAAC
1 CCAGATGGTTCTGAATACACAACATAAATGCAAATAAAAGTTGTTAG-ATAATAGGTGGATGAAC
40676095 CACCA-TAATTGCA
65 CACCAGT-ATTGCA
40676108 AATTAATATT
Statistics
Matches: 63, Mismatches: 12, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
89 3 0.05
90 60 0.95
ACGTcount: A:0.35, C:0.15, G:0.22, T:0.28
Consensus pattern (90 bp):
CCAGATGGTTCTGAATACACAACATAAATGCAAATAAAAGTTGTTAGATAATAGGTGGATGAACC
ACCAGTATTGCAGGTTAATACACTA
Found at i:40676125 original size:90 final size:90
Alignment explanation
Indices: 40675905--40676125 Score: 191
Period size: 90 Copynumber: 2.5 Consensus size: 90
40675895 CACACCAGGT
* * *
40675905 TGTGGATAAACCA-CA-AAGTTG-AAAGTTAATATGTTGCCAGATGGTTGTGAATACACAACATA
1 TGTGGATGAACCACCATAA-TTGCAAA-TTAATATATTGCCAGATGGTTCTGAATACACAACATA
* * * *
40675967 AATGCATATGAGAGTTGTTAGATAATG
64 AATGCAAATAAAAGTTGTTAGATAATA
* * ** ** * * * *
40675994 GGTGGGTGAACTGCCAGT-ATTGCAGGTTAATACACTACCAGATGGTTCTGAATACACAACTTAA
1 TGTGGATGAACCACCA-TAATTGCAAATTAATATATTGCCAGATGGTTCTGAATACACAACATAA
* *
40676058 TTGCAAATAAAAGTTG-TCGTATAATA
65 ATGCAAATAAAAGTTGTTAG-ATAATA
*
40676084 TGTGGATGAACCACCATAATTGCAAATTAATATTTTGCCAGA
1 TGTGGATGAACCACCATAATTGCAAATTAATATATTGCCAGA
40676126 GCTTCCTCCT
Statistics
Matches: 97, Mismatches: 29, Indels: 11
0.71 0.21 0.08
Matches are distributed among these distances:
89 11 0.11
90 84 0.87
91 2 0.02
ACGTcount: A:0.36, C:0.14, G:0.21, T:0.29
Consensus pattern (90 bp):
TGTGGATGAACCACCATAATTGCAAATTAATATATTGCCAGATGGTTCTGAATACACAACATAAA
TGCAAATAAAAGTTGTTAGATAATA
Found at i:40686345 original size:238 final size:239
Alignment explanation
Indices: 40685927--40686408 Score: 831
Period size: 238 Copynumber: 2.0 Consensus size: 239
40685917 GTAGAAGAAA
* *
40685927 GAGAGCATAAGAGTAAGGATCCATATGCATTGACGATTAGAAGCCTTATGTATTCTATGCTATGC
1 GAGAGCATAAGAGTAAGGATCAATATGCATTGACGATTAGAAGCCTTATGTATGCTATGCTATGC
* * *
40685992 TTTGCACACGTTCAAATATATGTTTAGTTGAAGGACTAGTAGATGCGGTGAAAGTAACTTCTCAA
66 TTTGCACACGTCCAAATATATGTTTAGTTGAAGGACAAGTAGACGCGGTGAAAGTAACTTCTCAA
40686057 TACAAACTTTCGGATTCGTTTGTTGAGACTATTATAATTAGGAGTTTTAACAAACATGTCAAGGA
131 TACAAACTTTCGGATTCGTTTGTTGAGACTATTATAATTAGGAGTTTTAACAAACATGTCAAGGA
*
40686122 TATGAGAATGTGAAACATGACACATTTACTTCACTA-GGCAAGT
196 TATAAGAATGTGAAACATGACACATTTACTTCACTAGGGCAAGT
*
40686165 GAGAGCATAAGAGTAAGGATCAATATGCATTGGCGATTAGAAGCCTTATGTATGCTATGCTATGC
1 GAGAGCATAAGAGTAAGGATCAATATGCATTGACGATTAGAAGCCTTATGTATGCTATGCTATGC
* * *
40686230 TTTGCACATGTCCAGATATATGTTTAGTTGAAGGACAAGTAGACGTGGTGAAAGTAACTTCTCAA
66 TTTGCACACGTCCAAATATATGTTTAGTTGAAGGACAAGTAGACGCGGTGAAAGTAACTTCTCAA
* * * *
40686295 TATAACCTTTCGGATTCGTTTGTTGAGACTCTTATAATTAGGAGTTTTAACAAACATGTCAATGA
131 TACAAACTTTCGGATTCGTTTGTTGAGACTATTATAATTAGGAGTTTTAACAAACATGTCAAGGA
40686360 TATAAGAATGTGAAACATGACACATTTACTTCACTAGGGCAAGT
196 TATAAGAATGTGAAACATGACACATTTACTTCACTAGGGCAAGT
40686404 GAGAG
1 GAGAG
40686409 ATTGTTGGGA
Statistics
Matches: 229, Mismatches: 14, Indels: 1
0.94 0.06 0.00
Matches are distributed among these distances:
238 217 0.95
239 12 0.05
ACGTcount: A:0.33, C:0.14, G:0.21, T:0.31
Consensus pattern (239 bp):
GAGAGCATAAGAGTAAGGATCAATATGCATTGACGATTAGAAGCCTTATGTATGCTATGCTATGC
TTTGCACACGTCCAAATATATGTTTAGTTGAAGGACAAGTAGACGCGGTGAAAGTAACTTCTCAA
TACAAACTTTCGGATTCGTTTGTTGAGACTATTATAATTAGGAGTTTTAACAAACATGTCAAGGA
TATAAGAATGTGAAACATGACACATTTACTTCACTAGGGCAAGT
Found at i:40687968 original size:56 final size:54
Alignment explanation
Indices: 40687839--40687968 Score: 127
Period size: 56 Copynumber: 2.3 Consensus size: 54
40687829 TTCAAAAATA
*
40687839 ATATTATTTTAATAGTTTTAATATTAAATTTAATATTTATCTTTTAAAGAAGTATT
1 ATATTATTTTAATA--TTTAATATTAAATTTAATATATATCTTTTAAAGAAGTATT
* * * ** *
40687895 TTATTAATTTAATATATTTAATATTAAATTTAATCTAATAT-TTATCTTGATAAGTATT
1 ATATT-ATTTTA-ATATTTAATATTAAATTTAATAT-ATATCTT-T-TAAAGAAGTATT
40687953 ATATTATTTTAATATT
1 ATATTATTTTAATATT
40687969 AAAGTGACTA
Statistics
Matches: 60, Mismatches: 9, Indels: 10
0.76 0.11 0.13
Matches are distributed among these distances:
56 30 0.50
57 14 0.23
58 16 0.27
ACGTcount: A:0.39, C:0.02, G:0.04, T:0.55
Consensus pattern (54 bp):
ATATTATTTTAATATTTAATATTAAATTTAATATATATCTTTTAAAGAAGTATT
Found at i:40691879 original size:4 final size:4
Alignment explanation
Indices: 40691870--40691910 Score: 64
Period size: 4 Copynumber: 10.2 Consensus size: 4
40691860 GATTGTACGT
* *
40691870 TTTG TTTG TTTG TTTG TTTG TTTG TATG TTTG TTTT TTTG T
1 TTTG TTTG TTTG TTTG TTTG TTTG TTTG TTTG TTTG TTTG T
40691911 ATTTTTATCA
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
4 33 1.00
ACGTcount: A:0.02, C:0.00, G:0.22, T:0.76
Consensus pattern (4 bp):
TTTG
Found at i:40697181 original size:32 final size:31
Alignment explanation
Indices: 40697142--40697211 Score: 95
Period size: 32 Copynumber: 2.2 Consensus size: 31
40697132 CATAACAACT
40697142 CAATGACTTAAATGAAAACTTCTGAATAGTC
1 CAATGACTTAAATGAAAACTTCTGAATAGTC
* * * *
40697173 CAACTGACTTAAATGAGAGCTTTTGAATAGTT
1 CAA-TGACTTAAATGAAAACTTCTGAATAGTC
40697205 CAATGAC
1 CAATGAC
40697212 CATTTTGTAA
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
31 7 0.21
32 27 0.79
ACGTcount: A:0.39, C:0.16, G:0.16, T:0.30
Consensus pattern (31 bp):
CAATGACTTAAATGAAAACTTCTGAATAGTC
Found at i:40699946 original size:21 final size:21
Alignment explanation
Indices: 40699899--40699947 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 21
40699889 CCAGATGCCT
* *
40699899 TACCGGAGGAACCAGAATCCC
1 TACCGGAGCAACCACAATCCC
*
40699920 TGCCGGAGCAACCACAA-CCC
1 TACCGGAGCAACCACAATCCC
40699940 TCACCGGA
1 T-ACCGGA
40699948 AGCTGGACAA
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
20 4 0.17
21 19 0.83
ACGTcount: A:0.31, C:0.39, G:0.22, T:0.08
Consensus pattern (21 bp):
TACCGGAGCAACCACAATCCC
Found at i:40700216 original size:13 final size:13
Alignment explanation
Indices: 40700198--40700223 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
40700188 ACCCTAACAA
40700198 AAACCCTAACCCT
1 AAACCCTAACCCT
40700211 AAACCCTAACCCT
1 AAACCCTAACCCT
40700224 TAACTTAAAA
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:0.38, C:0.46, G:0.00, T:0.15
Consensus pattern (13 bp):
AAACCCTAACCCT
Found at i:40700411 original size:15 final size:15
Alignment explanation
Indices: 40700391--40700444 Score: 60
Period size: 15 Copynumber: 3.8 Consensus size: 15
40700381 TAAAAACTCT
40700391 AAACCCTTAACTTAA
1 AAACCCTTAACTTAA
*
40700406 AAACCC-TAAC--CA
1 AAACCCTTAACTTAA
* *
40700418 TAACCCTTAAATTAA
1 AAACCCTTAACTTAA
40700433 AAACCCTTAACT
1 AAACCCTTAACT
40700445 ATCTAAGCCC
Statistics
Matches: 30, Mismatches: 6, Indels: 6
0.71 0.14 0.14
Matches are distributed among these distances:
12 6 0.20
13 3 0.10
14 4 0.13
15 17 0.57
ACGTcount: A:0.46, C:0.30, G:0.00, T:0.24
Consensus pattern (15 bp):
AAACCCTTAACTTAA
Found at i:40700416 original size:43 final size:44
Alignment explanation
Indices: 40700211--40700414 Score: 333
Period size: 43 Copynumber: 4.7 Consensus size: 44
40700201 CCCTAACCCT
*
40700211 AAACCCT-AACCCTTAACTTAAAAATCCTAAACCCTTAACTTAA
1 AAACCCTAAACCCTTAACTTAAAAACCCTAAACCCTTAACTTAA
*
40700254 AAACCCT-AACCCTTAACTTAAAAACCCTAAACCCTTAACTTGA
1 AAACCCTAAACCCTTAACTTAAAAACCCTAAACCCTTAACTTAA
*
40700297 AAACCCTAAAACCTTAACTTAAAAACCCTAAACCCTTAACTTAA
1 AAACCCTAAACCCTTAACTTAAAAACCCTAAACCCTTAACTTAA
* *
40700341 ATACCCTAAACCTTTAACTTAAAAACCCT-AACCCTTAACTTAA
1 AAACCCTAAACCCTTAACTTAAAAACCCTAAACCCTTAACTTAA
*
40700384 AAACTCTAAACCCTTAACTTAAAAACCCTAA
1 AAACCCTAAACCCTTAACTTAAAAACCCTAA
40700415 CCATAACCCT
Statistics
Matches: 149, Mismatches: 10, Indels: 3
0.92 0.06 0.02
Matches are distributed among these distances:
43 88 0.59
44 61 0.41
ACGTcount: A:0.45, C:0.30, G:0.00, T:0.25
Consensus pattern (44 bp):
AAACCCTAAACCCTTAACTTAAAAACCCTAAACCCTTAACTTAA
Found at i:40700428 original size:22 final size:22
Alignment explanation
Indices: 40700211--40700414 Score: 333
Period size: 22 Copynumber: 9.4 Consensus size: 22
40700201 CCCTAACCCT
40700211 AAACCCT-AACCCTTAACTTAA
1 AAACCCTAAACCCTTAACTTAA
*
40700232 AAATCCTAAACCCTTAACTTAA
1 AAACCCTAAACCCTTAACTTAA
40700254 AAACCCT-AACCCTTAACTTAA
1 AAACCCTAAACCCTTAACTTAA
*
40700275 AAACCCTAAACCCTTAACTTGA
1 AAACCCTAAACCCTTAACTTAA
*
40700297 AAACCCTAAAACCTTAACTTAA
1 AAACCCTAAACCCTTAACTTAA
40700319 AAACCCTAAACCCTTAACTTAA
1 AAACCCTAAACCCTTAACTTAA
* *
40700341 ATACCCTAAACCTTTAACTTAA
1 AAACCCTAAACCCTTAACTTAA
40700363 AAACCCT-AACCCTTAACTTAA
1 AAACCCTAAACCCTTAACTTAA
*
40700384 AAACTCTAAACCCTTAACTTAA
1 AAACCCTAAACCCTTAACTTAA
40700406 AAACCCTAA
1 AAACCCTAA
40700415 CCATAACCCT
Statistics
Matches: 168, Mismatches: 12, Indels: 5
0.91 0.06 0.03
Matches are distributed among these distances:
21 46 0.27
22 122 0.73
ACGTcount: A:0.45, C:0.30, G:0.00, T:0.25
Consensus pattern (22 bp):
AAACCCTAAACCCTTAACTTAA
Found at i:40700428 original size:65 final size:66
Alignment explanation
Indices: 40700211--40700414 Score: 333
Period size: 65 Copynumber: 3.1 Consensus size: 66
40700201 CCCTAACCCT
*
40700211 AAACCCT-AACCCTTAACTTAAAAATCCTAAACCCTTAACTTAAAAACCCT-AACCCTTAACTTA
1 AAACCCTAAACCCTTAACTTAAAAACCCTAAACCCTTAACTTAAAAACCCTAAACCCTTAACTTA
40700274 A
66 A
* *
40700275 AAACCCTAAACCCTTAACTTGAAAACCCTAAAACCTTAACTTAAAAACCCTAAACCCTTAACTTA
1 AAACCCTAAACCCTTAACTTAAAAACCCTAAACCCTTAACTTAAAAACCCTAAACCCTTAACTTA
40700340 A
66 A
* * *
40700341 ATACCCTAAACCTTTAACTTAAAAACCCT-AACCCTTAACTTAAAAACTCTAAACCCTTAACTTA
1 AAACCCTAAACCCTTAACTTAAAAACCCTAAACCCTTAACTTAAAAACCCTAAACCCTTAACTTA
40700405 A
66 A
40700406 AAACCCTAA
1 AAACCCTAA
40700415 CCATAACCCT
Statistics
Matches: 129, Mismatches: 9, Indels: 3
0.91 0.06 0.02
Matches are distributed among these distances:
64 7 0.05
65 82 0.64
66 40 0.31
ACGTcount: A:0.45, C:0.30, G:0.00, T:0.25
Consensus pattern (66 bp):
AAACCCTAAACCCTTAACTTAAAAACCCTAAACCCTTAACTTAAAAACCCTAAACCCTTAACTTA
A
Found at i:40700490 original size:18 final size:18
Alignment explanation
Indices: 40700456--40700490 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
40700446 TCTAAGCCCC
* *
40700456 AAAACCCTAATCTTAACA
1 AAAACCCTAACCCTAACA
40700474 AAAACCCTAACCCTAAC
1 AAAACCCTAACCCTAAC
40700491 CCTAATATGA
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:0.49, C:0.34, G:0.00, T:0.17
Consensus pattern (18 bp):
AAAACCCTAACCCTAACA
Found at i:40700656 original size:53 final size:53
Alignment explanation
Indices: 40700493--40700718 Score: 249
Period size: 53 Copynumber: 4.2 Consensus size: 53
40700483 ACCCTAACCC
* *
40700493 TAATATGATATAATTTGATAAATTTACTAACAATTAATACAATTAAAAATTAA
1 TAATTTGATATAATTTGATAAATTTACTAACAATTAATACAATTAACAATTAA
* ** * * ** * *
40700546 TAATTTGACTAACAAAATGTTAGATTTTAC-AA-AATGTTTTGACTGGTACTAACAATTAA
1 TAATTTGA-T-ATAATTTGATA-AATTTACTAACAAT-TAAT-AC---AATTAACAATTAA
*
40700605 TAATTTGATATAATTTGATAATTTTACTAACAATTAATACAATTAACAATTAA
1 TAATTTGATATAATTTGATAAATTTACTAACAATTAATACAATTAACAATTAA
*
40700658 TAATTTGATATAATTTGATAAATTTACTAACAATTAATACAATTAATAATTAA
1 TAATTTGATATAATTTGATAAATTTACTAACAATTAATACAATTAACAATTAA
40700711 TAATTTGA
1 TAATTTGA
40700719 CTAACAAAAT
Statistics
Matches: 142, Mismatches: 21, Indels: 20
0.78 0.11 0.11
Matches are distributed among these distances:
53 77 0.54
54 4 0.03
55 11 0.08
56 17 0.12
57 11 0.08
58 4 0.03
59 18 0.13
ACGTcount: A:0.47, C:0.07, G:0.06, T:0.40
Consensus pattern (53 bp):
TAATTTGATATAATTTGATAAATTTACTAACAATTAATACAATTAACAATTAA
Found at i:40700664 original size:43 final size:46
Alignment explanation
Indices: 40700595--40700725 Score: 132
Period size: 43 Copynumber: 2.9 Consensus size: 46
40700585 TGACTGGTAC
* *
40700595 TAACAATTAATA-ATTTGATATAATTTGATAATTTTACTAACAATTAA
1 TAACAATTAATACAATT-A-ATAATTTGATAATTTGACTAACAATTAA
* *
40700642 T-ACAATT-A-ACAATTAATAATTTGATATAATTTGA-TAA-ATTTAC
1 TAACAATTAATACAATTAATAATTTG--ATAATTTGACTAACAATTAA
*
40700685 TAACAATTAATACAATTAATAA-TTAATAATTTGACTAACAA
1 TAACAATTAATACAATTAATAATTTGATAATTTGACTAACAA
40700726 AATGTTAGAT
Statistics
Matches: 70, Mismatches: 6, Indels: 18
0.74 0.06 0.19
Matches are distributed among these distances:
43 22 0.31
44 14 0.20
45 16 0.23
46 17 0.24
47 1 0.01
ACGTcount: A:0.49, C:0.08, G:0.04, T:0.40
Consensus pattern (46 bp):
TAACAATTAATACAATTAATAATTTGATAATTTGACTAACAATTAA
Found at i:40704153 original size:124 final size:124
Alignment explanation
Indices: 40703768--40704208 Score: 704
Period size: 125 Copynumber: 3.5 Consensus size: 124
40703758 CCCAAACATG
40703768 CTACTGTAGCAAAAGCGCGTCCACGAGGGCGCGATTTCAGAAATTCTTCTGATAAAGCATCCTGC
1 CTACTGTAGCAAAAGCGCGTCCACGAGGGCGCGATTTCAGAAATTCTTCTGATAAAGCATCCTGC
*
40703833 TTGAAGCATTTTTTATACTATTTGCTCAGAAACGTCAACTCGAAATTATTTTTCC-AGAAC
66 TTGAAGC-GTTTTTATACTATTTGCTCAGAAACGTCAACTCGAAATTATTTTTCCAAG-AC
* * * *
40703893 CTACTATAGAAAAAGCGCGTCCACGAAGGCACGATTTCAGAAATTCTTCTGATAAAGCATCCTGC
1 CTACTGTAGCAAAAGCGCGTCCACGAGGGCGCGATTTCAGAAATTCTTCTGATAAAGCATCCTGC
* *
40703958 TTGAAGCGTTTTTTATACTATTTACTCAGAAACGTCAACTCGAAATTATTTTTCCAGGAC
66 TTGAAGCG-TTTTTATACTATTTGCTCAGAAACGTCAACTCGAAATTATTTTTCCAAGAC
* * *
40704018 CTACTGTAGCAAAAGCGCGTCCATGAGGGCGCAATTTCAGAAATTCTTCTGATAAAACATCCTGC
1 CTACTGTAGCAAAAGCGCGTCCACGAGGGCGCGATTTCAGAAATTCTTCTGATAAAGCATCCTGC
* *
40704083 TTGAAGCGTTTTTATACTATTTGCTTAGAAATGTCAACTCGAAATTATTTTTCCAAGAC
66 TTGAAGCGTTTTTATACTATTTGCTCAGAAACGTCAACTCGAAATTATTTTTCCAAGAC
* * * *
40704142 CTACTGTAGCAAAAACGCGTCCACGTGGGCGCGACTTCAGAAATTCTTCTGATAAAGCATCTTGC
1 CTACTGTAGCAAAAGCGCGTCCACGAGGGCGCGATTTCAGAAATTCTTCTGATAAAGCATCCTGC
40704207 TT
66 TT
40704209 TGATTTTATC
Statistics
Matches: 289, Mismatches: 25, Indels: 5
0.91 0.08 0.02
Matches are distributed among these distances:
124 107 0.37
125 181 0.63
126 1 0.00
ACGTcount: A:0.30, C:0.22, G:0.17, T:0.30
Consensus pattern (124 bp):
CTACTGTAGCAAAAGCGCGTCCACGAGGGCGCGATTTCAGAAATTCTTCTGATAAAGCATCCTGC
TTGAAGCGTTTTTATACTATTTGCTCAGAAACGTCAACTCGAAATTATTTTTCCAAGAC
Found at i:40706248 original size:27 final size:27
Alignment explanation
Indices: 40706218--40706271 Score: 99
Period size: 27 Copynumber: 2.0 Consensus size: 27
40706208 CATCTCTATC
*
40706218 GTTAATGCAGGCAAAGTCCTTTGTTAA
1 GTTAATGCAGGAAAAGTCCTTTGTTAA
40706245 GTTAATGCAGGAAAAGTCCTTTGTTAA
1 GTTAATGCAGGAAAAGTCCTTTGTTAA
40706272 CTTTTTTCTA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.31, C:0.13, G:0.22, T:0.33
Consensus pattern (27 bp):
GTTAATGCAGGAAAAGTCCTTTGTTAA
Found at i:40709005 original size:32 final size:32
Alignment explanation
Indices: 40708969--40709033 Score: 121
Period size: 32 Copynumber: 2.0 Consensus size: 32
40708959 ATCATATGCA
*
40708969 TATGATTGTTGGAAATCAAAGTGTGGATTTTT
1 TATGATTGCTGGAAATCAAAGTGTGGATTTTT
40709001 TATGATTGCTGGAAATCAAAGTGTGGATTTTT
1 TATGATTGCTGGAAATCAAAGTGTGGATTTTT
40709033 T
1 T
40709034 TTTTCTTTAT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.28, C:0.05, G:0.25, T:0.43
Consensus pattern (32 bp):
TATGATTGCTGGAAATCAAAGTGTGGATTTTT
Found at i:40711549 original size:2 final size:2
Alignment explanation
Indices: 40711544--40711572 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
40711534 ATATTTCGTG
40711544 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
40711573 CATCTTCACA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:40713026 original size:16 final size:16
Alignment explanation
Indices: 40713007--40713042 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
40712997 ATTAAATTTT
*
40713007 AATATGATTATTATTA
1 AATATAATTATTATTA
*
40713023 AATATAATTATTATTC
1 AATATAATTATTATTA
40713039 AATA
1 AATA
40713043 GGTAACATGT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (16 bp):
AATATAATTATTATTA
Found at i:40717948 original size:42 final size:42
Alignment explanation
Indices: 40717887--40718049 Score: 159
Period size: 42 Copynumber: 3.8 Consensus size: 42
40717877 CGGGTTAATA
* * *
40717887 CTTCGGTTTAACTGATGATGCACTTATGTGCCAATATATTTG
1 CTTCGATTTATCTGATGATACACTTATGTGCCAATATATTTG
** * * *
40717929 CTTCGATTTATCAAATGATGCAC-TATGTGTGCAAGTATATTTT
1 CTTCGATTTATCTGATGATACACTTATGTG-CCAA-TATATTTG
* * * *
40717972 CTTCAATTTATTTGATGATACACTTATGTGTCAATATGA-CTG
1 CTTCGATTTATCTGATGATACACTTATGTGCCAATAT-ATTTG
*
40718014 CTTCGGTTTATCTGATGATACACTATATGTGCCAAT
1 CTTCGATTTATCTGATGATACACT-TATGTGCCAAT
40718050 TGCTTCGGTT
Statistics
Matches: 98, Mismatches: 18, Indels: 9
0.78 0.14 0.07
Matches are distributed among these distances:
41 6 0.06
42 47 0.48
43 39 0.40
44 6 0.06
ACGTcount: A:0.26, C:0.16, G:0.17, T:0.41
Consensus pattern (42 bp):
CTTCGATTTATCTGATGATACACTTATGTGCCAATATATTTG
Found at i:40717981 original size:43 final size:42
Alignment explanation
Indices: 40717901--40718049 Score: 122
Period size: 43 Copynumber: 3.5 Consensus size: 42
40717891 GGTTTAACTG
*
40717901 ATGATGCACTTATGTGCCAATATATTTGCTTCGATTTATCAA
1 ATGATGCACTTATGTGCCAATATATTTGCTTCAATTTATCAA
* * ***
40717943 ATGATGCAC-TATGTGTGCAAGTATATTTTCTTCAATTTATTTG
1 ATGATGCACTTATGTG-CCAA-TATATTTGCTTCAATTTATCAA
* * * ** **
40717986 ATGATACACTTATGTGTCAATATGA-CTGCTTCGGTTTATCTG
1 ATGATGCACTTATGTGCCAATAT-ATTTGCTTCAATTTATCAA
*
40718028 ATGATACACTATATGTGCCAAT
1 ATGATGCACT-TATGTGCCAAT
40718050 TGCTTCGGTT
Statistics
Matches: 88, Mismatches: 14, Indels: 9
0.79 0.13 0.08
Matches are distributed among these distances:
41 6 0.07
42 37 0.42
43 39 0.44
44 6 0.07
ACGTcount: A:0.28, C:0.15, G:0.16, T:0.41
Consensus pattern (42 bp):
ATGATGCACTTATGTGCCAATATATTTGCTTCAATTTATCAA
Found at i:40718758 original size:23 final size:23
Alignment explanation
Indices: 40718702--40718759 Score: 66
Period size: 23 Copynumber: 2.5 Consensus size: 23
40718692 TAGCTAAACT
*
40718702 TATGCCAAGTTAGCTAACATGTA
1 TATGCCAACTTAGCTAACATGTA
*
40718725 TATG-TATACTTA-CTAAACATGTA
1 TATGCCA-ACTTAGCT-AACATGTA
40718748 TATGCCAACTTA
1 TATGCCAACTTA
40718760 TGCCAAGCAT
Statistics
Matches: 29, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
22 3 0.10
23 25 0.86
24 1 0.03
ACGTcount: A:0.36, C:0.17, G:0.12, T:0.34
Consensus pattern (23 bp):
TATGCCAACTTAGCTAACATGTA
Found at i:40723858 original size:19 final size:19
Alignment explanation
Indices: 40723821--40723868 Score: 69
Period size: 19 Copynumber: 2.5 Consensus size: 19
40723811 TATACTAGGT
40723821 TTAATTATAATTAAACTTAA
1 TTAATTA-AATTAAACTTAA
* *
40723841 TTAATTAACTTAATCTTAA
1 TTAATTAAATTAAACTTAA
40723860 TTAATTAAA
1 TTAATTAAA
40723869 CATTAATCAT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
19 18 0.72
20 7 0.28
ACGTcount: A:0.48, C:0.06, G:0.00, T:0.46
Consensus pattern (19 bp):
TTAATTAAATTAAACTTAA
Found at i:40731042 original size:44 final size:43
Alignment explanation
Indices: 40730983--40731370 Score: 288
Period size: 45 Copynumber: 8.9 Consensus size: 43
40730973 GATCACATCT
*
40730983 AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGAATAAGTAAGCA
1 AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAG-AAGCA
* * *
40731027 AGCCTTATC-CTCCTGAAGTTGTAGT-GAGGCAGACTGAAGATGCA
1 AGTCTTATCTC-CCTGAAGTTGCAGTGGA-GCAGACT-AAGAAGCA
* * *
40731071 AATCTTATCTCCCTGAAGTTGCAGTGGAGTAGA-TTA-AAGCCAA
1 AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGAAG-C-A
* * * ** * *
40731114 TAATCCTATCTCCCTAAAGTTGCAGTGGAGTGGATTAA-AATCA
1 -AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGAAGCA
* * * * * * *
40731157 CAGATCTTATCTCTCTGAAGTTGCAG-AGAGCA-AAT-CGCATCG
1 -AG-TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGAAGCA
* ** * *
40731199 GGTCTTATCTCTTTGAAGTTGCAGTGGAGCAGACCCAAGAAAGCG
1 AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGA-CTAAG-AAGCA
* *
40731244 AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACCCAAGAAAGCG
1 AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGA-CTAAG-AAGCA
*
40731289 AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTCAAGAAATCA
1 AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACT-AAG-AAGCA
* * * *
40731334 AGTCTTATCCCCCTGAAATTGCAGCGGGGCAGACTAA
1 AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAA
40731371 ATAAACAAAT
Statistics
Matches: 282, Mismatches: 45, Indels: 34
0.78 0.12 0.09
Matches are distributed among these distances:
40 21 0.07
41 8 0.03
42 8 0.03
43 10 0.04
44 109 0.39
45 126 0.45
ACGTcount: A:0.30, C:0.21, G:0.24, T:0.25
Consensus pattern (43 bp):
AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGAAGCA
Found at i:40731940 original size:19 final size:19
Alignment explanation
Indices: 40731916--40731977 Score: 115
Period size: 19 Copynumber: 3.3 Consensus size: 19
40731906 AATCTTCAAG
40731916 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
*
40731935 GATATGTAATCTTAGATAT
1 GATATGCAATCTTAGATAT
40731954 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
40731973 GATAT
1 GATAT
40731978 TAGATATGAT
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 41 1.00
ACGTcount: A:0.37, C:0.08, G:0.16, T:0.39
Consensus pattern (19 bp):
GATATGCAATCTTAGATAT
Found at i:40731982 original size:12 final size:12
Alignment explanation
Indices: 40731965--40731989 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
40731955 ATATGCAATC
40731965 TTAGATATGATA
1 TTAGATATGATA
40731977 TTAGATATGATA
1 TTAGATATGATA
40731989 T
1 T
40731990 GCAATCTTAG
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:0.40, C:0.00, G:0.16, T:0.44
Consensus pattern (12 bp):
TTAGATATGATA
Found at i:40732005 original size:22 final size:23
Alignment explanation
Indices: 40731979--40732023 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
40731969 ATATGATATT
40731979 AGATATGA-TATGCAATCTTAGA
1 AGATATGATTATGCAATCTTAGA
* *
40732001 AGATATGATTTTGTAATCTTAGA
1 AGATATGATTATGCAATCTTAGA
40732024 GATTTAATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 8 0.40
23 12 0.60
ACGTcount: A:0.38, C:0.07, G:0.18, T:0.38
Consensus pattern (23 bp):
AGATATGATTATGCAATCTTAGA
Found at i:40732435 original size:2 final size:2
Alignment explanation
Indices: 40732424--40732463 Score: 55
Period size: 2 Copynumber: 20.5 Consensus size: 2
40732414 ACACATATGT
* *
40732424 TA TA -A TA TA TA TA TA TA TA TA TA TA TG TA TA TT TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
40732464 TTTTCTTTAT
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.53
Consensus pattern (2 bp):
TA
Found at i:40734382 original size:26 final size:27
Alignment explanation
Indices: 40734353--40734408 Score: 87
Period size: 26 Copynumber: 2.1 Consensus size: 27
40734343 TTAAAATTCA
40734353 TTGAGTATTAATATTTCA-ATTAATAT
1 TTGAGTATTAATATTTCAGATTAATAT
*
40734379 TTGAGTGTTAATATTTCAGTATTAATAT
1 TTGAGTATTAATATTTCAG-ATTAATAT
40734407 TT
1 TT
40734409 ATCACAAGAA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
26 17 0.63
28 10 0.37
ACGTcount: A:0.34, C:0.04, G:0.11, T:0.52
Consensus pattern (27 bp):
TTGAGTATTAATATTTCAGATTAATAT
Found at i:40734391 original size:14 final size:14
Alignment explanation
Indices: 40734330--40734408 Score: 72
Period size: 14 Copynumber: 5.6 Consensus size: 14
40734320 ATATTTTAAC
*
40734330 TAATATTTGAGTGT
1 TAATATTTGAGTAT
*
40734344 TAAAATTCATTGAGTAT
1 TAATA-T--TTGAGTAT
*
40734361 TAATATTTCA--AT
1 TAATATTTGAGTAT
*
40734373 TAATATTTGAGTGT
1 TAATATTTGAGTAT
*
40734387 TAATATTTCAGTAT
1 TAATATTTGAGTAT
40734401 TAATATTT
1 TAATATTT
40734409 ATCACAAGAA
Statistics
Matches: 52, Mismatches: 8, Indels: 10
0.74 0.11 0.14
Matches are distributed among these distances:
12 11 0.21
14 28 0.54
15 1 0.02
16 1 0.02
17 11 0.21
ACGTcount: A:0.35, C:0.04, G:0.11, T:0.49
Consensus pattern (14 bp):
TAATATTTGAGTAT
Found at i:40735349 original size:9 final size:9
Alignment explanation
Indices: 40735335--40735422 Score: 54
Period size: 11 Copynumber: 9.1 Consensus size: 9
40735325 ATATATAAAG
40735335 TTATAAAAA
1 TTATAAAAA
40735344 TTATAAAAAA
1 TTAT-AAAAA
* *
40735354 TGAAAATAAA
1 TTATAA-AAA
*
40735364 CATATAAAAAA
1 -TTAT-AAAAA
*
40735375 TTCAGAAAAAA
1 TT-A-TAAAAA
40735386 TTATAAAAA
1 TTATAAAAA
40735395 TT-TAAAAA
1 TTATAAAAA
40735403 -TATAAAAA
1 TTATAAAAA
40735411 TATATGAAAAA
1 T-TAT-AAAAA
40735422 T
1 T
40735423 GAAAATAAAA
Statistics
Matches: 61, Mismatches: 8, Indels: 18
0.70 0.09 0.21
Matches are distributed among these distances:
7 1 0.02
8 12 0.20
9 13 0.21
10 15 0.25
11 18 0.30
12 2 0.03
ACGTcount: A:0.67, C:0.02, G:0.03, T:0.27
Consensus pattern (9 bp):
TTATAAAAA
Found at i:40735390 original size:21 final size:19
Alignment explanation
Indices: 40735339--40735394 Score: 58
Period size: 21 Copynumber: 2.7 Consensus size: 19
40735329 ATAAAGTTAT
*
40735339 AAAAATTATAAAAAATGAA
1 AAAAATTATAAAAAATCAA
*
40735358 AATAAACATATAAAAAATTCAGA
1 AA-AAA-TTATAAAAAA-TCA-A
40735381 AAAAATTATAAAAA
1 AAAAATTATAAAAA
40735395 TTTAAAAATA
Statistics
Matches: 30, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
19 2 0.07
20 3 0.10
21 17 0.57
22 5 0.17
23 3 0.10
ACGTcount: A:0.71, C:0.04, G:0.04, T:0.21
Consensus pattern (19 bp):
AAAAATTATAAAAAATCAA
Found at i:40735412 original size:8 final size:8
Alignment explanation
Indices: 40735381--40735414 Score: 50
Period size: 8 Copynumber: 4.1 Consensus size: 8
40735371 AAAATTCAGA
40735381 AAAAATTAT
1 AAAAA-TAT
*
40735390 AAAAATTT
1 AAAAATAT
40735398 AAAAATAT
1 AAAAATAT
40735406 AAAAATAT
1 AAAAATAT
40735414 A
1 A
40735415 TGAAAAATGA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
8 18 0.78
9 5 0.22
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (8 bp):
AAAAATAT
Found at i:40735420 original size:10 final size:9
Alignment explanation
Indices: 40735336--40735489 Score: 54
Period size: 9 Copynumber: 16.4 Consensus size: 9
40735326 TATATAAAGT
*
40735336 TATAAAAAT
1 TATAAAAAA
40735345 TATAAAAAA
1 TATAAAAAA
*
40735354 TGAAAATAAACA
1 T-ATAA-AAA-A
40735366 TATAAAAAA
1 TATAAAAAA
*
40735375 TTCAGAAAAAA
1 -T-ATAAAAAA
40735386 T-TATAAAAA
1 TATA-AAAAA
*
40735395 T-TTAAAAA
1 TATAAAAAA
40735403 TATAAAAATA
1 TATAAAAA-A
*
40735413 TATGAAAAA
1 TATAAAAAA
40735422 TGA-AAATAAA
1 T-ATAAA-AAA
* *
40735432 -ATTAGAAA
1 TATAAAAAA
40735440 TAT---AAA
1 TATAAAAAA
40735446 TATAAATAAA
1 TATAAA-AAA
40735456 T-TCAAAAAA
1 TAT-AAAAAA
40735465 TATAGATAAAA
1 TATA-A-AAAA
*
40735476 TCTAAAAATA
1 TATAAAAA-A
40735486 TATA
1 TATA
40735490 TGAAATAGAT
Statistics
Matches: 111, Mismatches: 13, Indels: 41
0.67 0.08 0.25
Matches are distributed among these distances:
6 6 0.05
8 11 0.10
9 38 0.34
10 34 0.31
11 20 0.18
12 2 0.02
ACGTcount: A:0.67, C:0.03, G:0.04, T:0.27
Consensus pattern (9 bp):
TATAAAAAA
Found at i:40735489 original size:21 final size:19
Alignment explanation
Indices: 40735443--40735487 Score: 63
Period size: 19 Copynumber: 2.4 Consensus size: 19
40735433 TTAGAAATAT
*
40735443 AAATATAAATAAATTCAAA
1 AAATATAAATAAAATCAAA
* *
40735462 AAATATAGATAAAATCTAA
1 AAATATAAATAAAATCAAA
40735481 AAATATA
1 AAATATA
40735488 TATGAAATAG
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.67, C:0.04, G:0.02, T:0.27
Consensus pattern (19 bp):
AAATATAAATAAAATCAAA
Found at i:40735495 original size:19 final size:18
Alignment explanation
Indices: 40735460--40735513 Score: 54
Period size: 19 Copynumber: 2.9 Consensus size: 18
40735450 AATAAATTCA
* **
40735460 AAAAATATAGATAAAATCT
1 AAAAATATATAT-AAATAG
40735479 AAAAATATATATGAAATAG
1 AAAAATATATAT-AAATAG
*
40735498 ATAAATATATATAAAT
1 AAAAATATATATAAAT
40735514 TAGGACTAGA
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
18 4 0.13
19 26 0.87
ACGTcount: A:0.63, C:0.02, G:0.06, T:0.30
Consensus pattern (18 bp):
AAAAATATATATAAATAG
Found at i:40744701 original size:3 final size:3
Alignment explanation
Indices: 40744693--40744719 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
40744683 ATGAAGCTTA
40744693 AAG AAG AAG AAG AAG AAG AAG AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG
40744720 TTCAAAAATC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:40746517 original size:18 final size:18
Alignment explanation
Indices: 40746494--40746541 Score: 51
Period size: 18 Copynumber: 2.6 Consensus size: 18
40746484 ATTAAGTCAC
*
40746494 ATTATAAAATAAATTTAT
1 ATTATAAAATAAATTTAA
* **
40746512 ATTATAATATTTATTTAA
1 ATTATAAAATAAATTTAA
40746530 ATTATATAAATA
1 ATTATA-AAATA
40746542 TTAGTTAATT
Statistics
Matches: 23, Mismatches: 6, Indels: 1
0.77 0.20 0.03
Matches are distributed among these distances:
18 20 0.87
19 3 0.13
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (18 bp):
ATTATAAAATAAATTTAA
Found at i:40746549 original size:20 final size:24
Alignment explanation
Indices: 40746503--40746549 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 24
40746493 CATTATAAAA
*
40746503 TAAATTTATATTATAATATTTATT
1 TAAATTTATATTATAATATTTAGT
40746527 TAAA-TTATA-TA-AATA-TTAGT
1 TAAATTTATATTATAATATTTAGT
40746547 TAA
1 TAA
40746550 TTGTTTTGTT
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
20 7 0.32
21 4 0.18
22 2 0.09
23 5 0.23
24 4 0.18
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (24 bp):
TAAATTTATATTATAATATTTAGT
Found at i:40748530 original size:16 final size:16
Alignment explanation
Indices: 40748490--40748531 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
40748480 GCAATTAGAG
40748490 TTAGGGTTTTTGAATT
1 TTAGGGTTTTTGAATT
* * *
40748506 TTTGAGTTTTTGGATT
1 TTAGGGTTTTTGAATT
40748522 TTAGGGTTTT
1 TTAGGGTTTT
40748532 AAGAAAAAAT
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.14, C:0.00, G:0.26, T:0.60
Consensus pattern (16 bp):
TTAGGGTTTTTGAATT
Found at i:40748970 original size:2 final size:2
Alignment explanation
Indices: 40748963--40749003 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
40748953 GATAAATTTA
40748963 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
40749004 AACTTTTAAC
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:40749490 original size:96 final size:95
Alignment explanation
Indices: 40749207--40749509 Score: 406
Period size: 90 Copynumber: 3.2 Consensus size: 95
40749197 AACAACTAGC
* * * * *
40749207 TTTATTTGA-TTTTTCCTTAAAAACCCTAAATACTAAACCCCAATCTAATTTTTTTAAATTATAA
1 TTTATTTAATTTTTTCCTTAAAAACCATAAACACTAAACCCTAATCTAATTTTTTAAAATTATAA
40749271 TTAATTTACTCAAGTAACCCTAAACCCTAA
66 TTAATTTACTCAAGTAACCCTAAACCCTAA
* * *
40749301 TTTATTTGATTTTTTTCTT-AAAA--AT---C-CTAAACCCTAATCTAATTTTTAAAAAAATTAT
1 TTTATTTAATTTTTTCCTTAAAAACCATAAACACTAAACCCTAATCTAATTTTT--TAAAATTAT
40749359 AATTAATTTACTCAAGTAACCCTAAACCCTAA
64 AATTAATTTACTCAAGTAACCCTAAACCCTAA
*
40749391 TTTATTTAATTTTTTCCTTAAAAACCATAAACATTAAACCCTAATCTAATTTTTTAAAATTTATA
1 TTTATTTAATTTTTTCCTTAAAAACCATAAACACTAAACCCTAATCTAATTTTTTAAAA-TTATA
* * * *
40749456 ATTAATTTAATTAAGAAACCCTAAACCCTTA
65 ATTAATTTACTCAAGTAACCCTAAACCCTAA
40749487 TTTATTTAATTTTTTCCTTAAAA
1 TTTATTTAATTTTTTCCTTAAAA
40749510 CCCTAAAATT
Statistics
Matches: 184, Mismatches: 14, Indels: 20
0.84 0.06 0.09
Matches are distributed among these distances:
88 20 0.11
90 56 0.30
91 4 0.02
92 1 0.01
93 2 0.01
94 13 0.07
95 12 0.07
96 56 0.30
97 20 0.11
ACGTcount: A:0.39, C:0.17, G:0.02, T:0.42
Consensus pattern (95 bp):
TTTATTTAATTTTTTCCTTAAAAACCATAAACACTAAACCCTAATCTAATTTTTTAAAATTATAA
TTAATTTACTCAAGTAACCCTAAACCCTAA
Found at i:40757496 original size:26 final size:26
Alignment explanation
Indices: 40757467--40757524 Score: 64
Period size: 26 Copynumber: 2.2 Consensus size: 26
40757457 CCCGATATAT
*
40757467 GGCT-TTTCATGAGCTTTCTAATTAAA
1 GGCTCTTT-ATGAGCTTCCTAATTAAA
* * *
40757493 GGCTCTTTGTGAGGTTCCTAATTAAT
1 GGCTCTTTATGAGCTTCCTAATTAAA
40757519 GGCTCT
1 GGCTCT
40757525 CCGGAGCTTC
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
26 24 0.89
27 3 0.11
ACGTcount: A:0.21, C:0.17, G:0.21, T:0.41
Consensus pattern (26 bp):
GGCTCTTTATGAGCTTCCTAATTAAA
Found at i:40757570 original size:24 final size:25
Alignment explanation
Indices: 40757514--40757572 Score: 75
Period size: 25 Copynumber: 2.4 Consensus size: 25
40757504 AGGTTCCTAA
* *
40757514 TTAATGGCTCTCCGGAGCTTCCTGG
1 TTAATGGCTCTCCGGAGCTACCTCG
*
40757539 TTAATGGCTCTTCGGAGCTACC-CG
1 TTAATGGCTCTCCGGAGCTACCTCG
*
40757563 TTATTGGCTC
1 TTAATGGCTC
40757573 GTATAAGCTT
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
24 10 0.33
25 20 0.67
ACGTcount: A:0.14, C:0.27, G:0.25, T:0.34
Consensus pattern (25 bp):
TTAATGGCTCTCCGGAGCTACCTCG
Found at i:40759026 original size:24 final size:24
Alignment explanation
Indices: 40758994--40759044 Score: 93
Period size: 24 Copynumber: 2.1 Consensus size: 24
40758984 TCATTTTTAA
*
40758994 ATTTCGGTAATGCTTTGTAATCCT
1 ATTTCGGTAATGCTTTGTAACCCT
40759018 ATTTCGGTAATGCTTTGTAACCCT
1 ATTTCGGTAATGCTTTGTAACCCT
40759042 ATT
1 ATT
40759045 CTGGCGACGA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.22, C:0.18, G:0.16, T:0.45
Consensus pattern (24 bp):
ATTTCGGTAATGCTTTGTAACCCT
Done.