Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr6
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: 47432654
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 2298022 characters in sequence are not A, C, G, or T
File 18 of 136
Found at i:5746553 original size:33 final size:32
Alignment explanation
Indices: 5746486--5746555 Score: 88
Period size: 32 Copynumber: 2.2 Consensus size: 32
5746476 TTTTAGAATA
* * *
5746486 TGATTAATACAAATCATTGAAGAACTTAGGAT
1 TGATTAATACAAACCATTGAAAAAATTAGGAT
5746518 TGATTAATACAAACC-TATGAAAAAAATTAGGAT
1 TGATTAATACAAACCAT-TG-AAAAAATTAGGAT
5746551 TGATT
1 TGATT
5746556 GGAGATTTAA
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
31 1 0.03
32 16 0.48
33 16 0.48
ACGTcount: A:0.46, C:0.09, G:0.14, T:0.31
Consensus pattern (32 bp):
TGATTAATACAAACCATTGAAAAAATTAGGAT
Found at i:5748272 original size:114 final size:113
Alignment explanation
Indices: 5747902--5748562 Score: 820
Period size: 114 Copynumber: 5.8 Consensus size: 113
5747892 AAAAATAGTA
* * * *
5747902 TTAGCGGTGTTTTTCG-GAAAGCGCCGCAAAAAACCTAAGCCCAACGACGTCGTTTTCTGAGCTT
1 TTAGCGGCGTTTTT-GATAAAGCGCCGCAAAAAAACTAAGCCCAACGACGCCGTTTTCTGAGCTT
* *
5747966 TCGCAGATTTAGTGGCGTTTTTTAGGAAGCGCCGCTAATGCTCAGGGCT
65 TCGCGGATTTAGCGGCGTTTTTTAGGAAGCGCCGCTAATGCTCAGGGCT
* * * * *
5748015 TTAGCGGCATTTTTGAGAAAGCGCCGCAAAAAGACATAAGTCCAACGACGCCGTTTTCTAAGCTT
1 TTAGCGGCGTTTTTGATAAAGCGCCGCAAAAAAAC-TAAGCCCAACGACGCCGTTTTCTGAGCTT
* * *
5748080 TCGTGGATTTAGCGGCGTTTCTTAAGGAAGCGCCGCTAATGCTGAGGGCT
65 TCGCGGATTTAGCGGCGTTT-TTTAGGAAGCGCCGCTAATGCTCAGGGCT
* * * *
5748130 TTAGTGGCGTTTTTGATGAAGCGCCGCAAAATAAACTAAGGCCAACGACACCGTTTTCTGAGCTT
1 TTAGCGGCGTTTTTGATAAAGCGCCGCAAAA-AAACTAAGCCCAACGACGCCGTTTTCTGAGCTT
* * * *
5748195 TCACGAATTTAGTGGCGTTTTTTAGGAAGCGTCGCTAATGCTCAGGGCT
65 TCGCGGATTTAGCGGCGTTTTTTAGGAAGCGCCGCTAATGCTCAGGGCT
* * *
5748244 TTAACGGCGTTTTTGATAAAGCGCCGCAAAAAGACATTAGCCCAACGACGCCGTTTTCTGAGCTT
1 TTAGCGGCGTTTTTGATAAAGCGCCGCAAAAAAAC-TAAGCCCAACGACGCCGTTTTCTGAGCTT
* * * ** * *
5748309 TCGGGGATTTAGCGGTGTTTCTTAAAAAAGCGTCGCTAATGCTGAGGGCT
65 TCGCGGATTTAGCGGCGTTT-TTTAGGAAGCGCCGCTAATGCTCAGGGCT
* *** *
5748359 TTAGCAGCGTTTTTGGGGAAGCGCTGCAAAATAAACTAAGCCCAACGACGCCGTTTTCTGAGCTT
1 TTAGCGGCGTTTTTGATAAAGCGCCGCAAAA-AAACTAAGCCCAACGACGCCGTTTTCTGAGCTT
* * * *
5748424 TCGCGGATTTAGTGGCATTTTTTAGGAAGCGCCGCTAATGCTCAAGGAT
65 TCGCGGATTTAGCGGCGTTTTTTAGGAAGCGCCGCTAATGCTCAGGGCT
* * * *
5748473 TTAGCAGCGTTTTTGATGAAGCGCCGCAAAATAAATTAAGCCCAACGATGCCGTTTTCTGAGCTT
1 TTAGCGGCGTTTTTGATAAAGCGCCGCAAAA-AAACTAAGCCCAACGACGCCGTTTTCTGAGCTT
*
5748538 TCGGGGGATTTAGCGGCGTTTTTTA
65 TC-GCGGATTTAGCGGCGTTTTTTA
5748563 ATAAAGCGCT
Statistics
Matches: 470, Mismatches: 70, Indels: 14
0.85 0.13 0.03
Matches are distributed among these distances:
112 1 0.00
113 32 0.07
114 222 0.47
115 209 0.44
116 6 0.01
ACGTcount: A:0.24, C:0.21, G:0.26, T:0.29
Consensus pattern (113 bp):
TTAGCGGCGTTTTTGATAAAGCGCCGCAAAAAAACTAAGCCCAACGACGCCGTTTTCTGAGCTTT
CGCGGATTTAGCGGCGTTTTTTAGGAAGCGCCGCTAATGCTCAGGGCT
Found at i:5748348 original size:229 final size:229
Alignment explanation
Indices: 5747920--5748571 Score: 961
Period size: 229 Copynumber: 2.8 Consensus size: 229
5747910 GTTTTTCGGA
* *
5747920 AAGCGCCGCAAAA-AACCTAAGCCCAACGACGTCGTTTTCTGAGCTTTCGC-AGATTTAGTGGCG
1 AAGCGCCGCAAAATAAACTAAGCCCAACGACGCCGTTTTCTGAGCTTTCGCGA-ATTTAGTGGCG
* *
5747983 TTTTTTAGGAAGCGCCGCTAATGCTCAGGGCTTTAGCGGCATTTTTGAGAAAGCGCCGCAAAAAG
65 TTTTTTAGGAAGCGCCGCTAATGCTCAGGGCTTTAGCGGCGTTTTTGATAAAGCGCCGCAAAAAG
* * * * **
5748048 ACATAAGTCCAACGACGCCGTTTTCTAAGCTTTCGTGGATTTAGCGGCGTTTCTTAAGGAAGCGC
130 ACATTAGCCCAACGACGCCGTTTTCTGAGCTTTCGGGGATTTAGCGGCGTTTCTTAAAAAAGCGC
** *
5748113 CGCTAATGCTGAGGGCTTTAGTGGCGTTTTTGATG
195 CGCTAATGCTGAGGGCTTTAGCAGCGTTTTTGAGG
* * *
5748148 AAGCGCCGCAAAATAAACTAAGGCCAACGACACCGTTTTCTGAGCTTTCACGAATTTAGTGGCGT
1 AAGCGCCGCAAAATAAACTAAGCCCAACGACGCCGTTTTCTGAGCTTTCGCGAATTTAGTGGCGT
* *
5748213 TTTTTAGGAAGCGTCGCTAATGCTCAGGGCTTTAACGGCGTTTTTGATAAAGCGCCGCAAAAAGA
66 TTTTTAGGAAGCGCCGCTAATGCTCAGGGCTTTAGCGGCGTTTTTGATAAAGCGCCGCAAAAAGA
* *
5748278 CATTAGCCCAACGACGCCGTTTTCTGAGCTTTCGGGGATTTAGCGGTGTTTCTTAAAAAAGCGTC
131 CATTAGCCCAACGACGCCGTTTTCTGAGCTTTCGGGGATTTAGCGGCGTTTCTTAAAAAAGCGCC
*
5748343 GCTAATGCTGAGGGCTTTAGCAGCGTTTTTGGGG
196 GCTAATGCTGAGGGCTTTAGCAGCGTTTTTGAGG
* * *
5748377 AAGCGCTGCAAAATAAACTAAGCCCAACGACGCCGTTTTCTGAGCTTTCGCGGATTTAGTGGCAT
1 AAGCGCCGCAAAATAAACTAAGCCCAACGACGCCGTTTTCTGAGCTTTCGCGAATTTAGTGGCGT
* * * *
5748442 TTTTTAGGAAGCGCCGCTAATGCTCAAGGATTTAGCAGCGTTTTTGATGAAGCGCCGCAAAATA-
66 TTTTTAGGAAGCGCCGCTAATGCTCAGGGCTTTAGCGGCGTTTTTGATAAAGCGCCGCAAAA-AG
* * *
5748506 A-ATTAAGCCCAACGATGCCGTTTTCTGAGCTTTCGGGGGATTTAGCGGCGTTTTTTAATAAAGC
130 ACATT-AGCCCAACGACGCCGTTTTCTGAGCTTTC-GGGGATTTAGCGGCGTTTCTTAAAAAAGC
5748570 GC
193 GC
5748572 TGCAAAAAAA
Statistics
Matches: 381, Mismatches: 38, Indels: 8
0.89 0.09 0.02
Matches are distributed among these distances:
228 16 0.04
229 336 0.88
230 29 0.08
ACGTcount: A:0.25, C:0.21, G:0.26, T:0.28
Consensus pattern (229 bp):
AAGCGCCGCAAAATAAACTAAGCCCAACGACGCCGTTTTCTGAGCTTTCGCGAATTTAGTGGCGT
TTTTTAGGAAGCGCCGCTAATGCTCAGGGCTTTAGCGGCGTTTTTGATAAAGCGCCGCAAAAAGA
CATTAGCCCAACGACGCCGTTTTCTGAGCTTTCGGGGATTTAGCGGCGTTTCTTAAAAAAGCGCC
GCTAATGCTGAGGGCTTTAGCAGCGTTTTTGAGG
Found at i:5748725 original size:15 final size:15
Alignment explanation
Indices: 5748702--5748733 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
5748692 GTTGAGATTT
*
5748702 AAGGTTTAGGGGTTA
1 AAGGGTTAGGGGTTA
5748717 AAGGGTTAGGGGTTA
1 AAGGGTTAGGGGTTA
5748732 AA
1 AA
5748734 CATTTGAGGT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.31, C:0.00, G:0.41, T:0.28
Consensus pattern (15 bp):
AAGGGTTAGGGGTTA
Found at i:5748767 original size:7 final size:8
Alignment explanation
Indices: 5748750--5748778 Score: 51
Period size: 8 Copynumber: 3.8 Consensus size: 8
5748740 AGGTTAAGAG
5748750 TTAGGGAT
1 TTAGGGAT
5748758 TTAGGG-T
1 TTAGGGAT
5748765 TTAGGGAT
1 TTAGGGAT
5748773 TTAGGG
1 TTAGGG
5748779 GTCGAGTTAG
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
7 7 0.35
8 13 0.65
ACGTcount: A:0.21, C:0.00, G:0.41, T:0.38
Consensus pattern (8 bp):
TTAGGGAT
Found at i:5748770 original size:15 final size:15
Alignment explanation
Indices: 5748750--5748778 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
5748740 AGGTTAAGAG
5748750 TTAGGGATTTAGGGT
1 TTAGGGATTTAGGGT
5748765 TTAGGGATTTAGGG
1 TTAGGGATTTAGGG
5748779 GTCGAGTTAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.21, C:0.00, G:0.41, T:0.38
Consensus pattern (15 bp):
TTAGGGATTTAGGGT
Found at i:5749634 original size:21 final size:21
Alignment explanation
Indices: 5749610--5749649 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
5749600 AAAACGCCGC
5749610 AAAATAAAAATAAAATTATAA
1 AAAATAAAAATAAAATTATAA
5749631 AAAATAAAAATAAAATTAT
1 AAAATAAAAATAAAATTAT
5749650 TTGCATAGCA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (21 bp):
AAAATAAAAATAAAATTATAA
Found at i:5749784 original size:104 final size:105
Alignment explanation
Indices: 5749591--5749785 Score: 297
Period size: 105 Copynumber: 1.9 Consensus size: 105
5749581 ATAGCGGCAT
* * *
5749591 TTTTTTATAAAAACGCCGCAAAATAAAAATAAAATTATAAAAAATAAAAATAAAATTATTTGCAT
1 TTTTTCATAAAAACGCCGCAAAAAAAAAATAAAATTATAAAAAATAAAAATAAAATTATGTGCAT
5749656 AGCAAAACGGCGTCATTTTGTTCAAAATCAAATAGCATCG
66 AGCAAAACGGCGTCATTTTGTTCAAAATCAAATAGCATCG
*
5749696 TTTTTCATAAAAACGCCGCAAAAAAATAAATCAAATTATAAAAAA-AATAAA-AAAATT-TGTGC
1 TTTTTCATAAAAACGCCGCAAAAAAA-AAATAAAATTATAAAAAATAA-AAATAAAATTATGTGC
* *
5749758 ATAGCAATACGGCGTCGTTTTGTTCAAA
64 ATAGCAAAACGGCGTCATTTTGTTCAAA
5749786 TTGAAATTGC
Statistics
Matches: 82, Mismatches: 6, Indels: 5
0.88 0.06 0.05
Matches are distributed among these distances:
104 30 0.37
105 32 0.39
106 20 0.24
ACGTcount: A:0.49, C:0.13, G:0.10, T:0.28
Consensus pattern (105 bp):
TTTTTCATAAAAACGCCGCAAAAAAAAAATAAAATTATAAAAAATAAAAATAAAATTATGTGCAT
AGCAAAACGGCGTCATTTTGTTCAAAATCAAATAGCATCG
Found at i:5750622 original size:22 final size:22
Alignment explanation
Indices: 5750596--5750645 Score: 100
Period size: 22 Copynumber: 2.3 Consensus size: 22
5750586 TGTAAGTTTA
5750596 TTTTAGGGCAACTTTGAACCTT
1 TTTTAGGGCAACTTTGAACCTT
5750618 TTTTAGGGCAACTTTGAACCTT
1 TTTTAGGGCAACTTTGAACCTT
5750640 TTTTAG
1 TTTTAG
5750646 TCTAGGCACT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.22, C:0.16, G:0.18, T:0.44
Consensus pattern (22 bp):
TTTTAGGGCAACTTTGAACCTT
Found at i:5752742 original size:30 final size:30
Alignment explanation
Indices: 5752699--5752759 Score: 79
Period size: 30 Copynumber: 2.0 Consensus size: 30
5752689 TATAACTTGC
* *
5752699 ATAATTTACATAACTTATAAATTTTTAATAT
1 ATAACTTACATAACTTATAAATATTT-ATAT
*
5752730 ATAACTTA-ATAACTTATTAATATTTATAT
1 ATAACTTACATAACTTATAAATATTTATAT
5752759 A
1 A
5752760 CATTTTTAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
29 5 0.19
30 15 0.56
31 7 0.26
ACGTcount: A:0.46, C:0.07, G:0.00, T:0.48
Consensus pattern (30 bp):
ATAACTTACATAACTTATAAATATTTATAT
Found at i:5752749 original size:23 final size:22
Alignment explanation
Indices: 5752708--5752752 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 22
5752698 CATAATTTAC
*
5752708 ATAACTTATAAATTTTTAATAT
1 ATAACTTATAAATTATTAATAT
*
5752730 ATAACTTAATAACTTATTAATAT
1 ATAACTT-ATAAATTATTAATAT
5752753 TTATATACAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 7 0.35
23 13 0.65
ACGTcount: A:0.47, C:0.07, G:0.00, T:0.47
Consensus pattern (22 bp):
ATAACTTATAAATTATTAATAT
Found at i:5752795 original size:42 final size:42
Alignment explanation
Indices: 5752714--5752796 Score: 107
Period size: 42 Copynumber: 2.0 Consensus size: 42
5752704 TTACATAACT
*
5752714 TATAAATTTTTAATATATAACTTAATAACTTATTAATATTTA
1 TATAAATTTTTAATATATAACTTAAAAACTTATTAATATTTA
* *
5752756 TATACATTTTTAATATATATA-TTAAAAATTTA-TATATATTT
1 TATAAATTTTTAATATATA-ACTTAAAAACTTATTA-ATATTT
5752797 TTAATAACTT
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
41 2 0.06
42 33 0.92
43 1 0.03
ACGTcount: A:0.45, C:0.04, G:0.00, T:0.52
Consensus pattern (42 bp):
TATAAATTTTTAATATATAACTTAAAAACTTATTAATATTTA
Found at i:5752800 original size:20 final size:19
Alignment explanation
Indices: 5752768--5752811 Score: 52
Period size: 20 Copynumber: 2.3 Consensus size: 19
5752758 TACATTTTTA
*
5752768 ATATATATATTAAAAATTT
1 ATATATATATTAAAAACTT
* *
5752787 ATATATATTTTTAATAACTT
1 ATATATA-TATTAAAAACTT
5752807 ATATA
1 ATATA
5752812 CAACTTTCAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
19 7 0.33
20 14 0.67
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (19 bp):
ATATATATATTAAAAACTT
Found at i:5752831 original size:9 final size:9
Alignment explanation
Indices: 5752813--5752922 Score: 63
Period size: 9 Copynumber: 12.7 Consensus size: 9
5752803 ACTTATATAC
*
5752813 AACTTTCAT
1 AACTTACAT
5752822 AACTTACAT
1 AACTTACAT
*
5752831 AA-TAACATAAT
1 AACTTAC---AT
5752842 AACTTACAT
1 AACTTACAT
5752851 AA--TACAT
1 AACTTACAT
* *
5752858 AGCCTACAT
1 AACTTACAT
* *
5752867 GACTTGCAT
1 AACTTACAT
*
5752876 AA--TACAC
1 AACTTACAT
5752883 AACTTACAT
1 AACTTACAT
*
5752892 AAATTACAT
1 AACTTACAT
5752901 AA--TACAT
1 AACTTACAT
*
5752908 AACTTTCAT
1 AACTTACAT
5752917 AACTTA
1 AACTTA
5752923 NNNNNNNNNN
Statistics
Matches: 76, Mismatches: 15, Indels: 20
0.68 0.14 0.18
Matches are distributed among these distances:
7 18 0.24
8 3 0.04
9 48 0.63
11 4 0.05
12 3 0.04
ACGTcount: A:0.45, C:0.20, G:0.03, T:0.32
Consensus pattern (9 bp):
AACTTACAT
Found at i:5752843 original size:20 final size:19
Alignment explanation
Indices: 5752820--5752858 Score: 69
Period size: 20 Copynumber: 2.0 Consensus size: 19
5752810 TACAACTTTC
5752820 ATAACTTACATAATAACATA
1 ATAACTTACATAAT-ACATA
5752840 ATAACTTACATAATACATA
1 ATAACTTACATAATACATA
5752859 GCCTACATGA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 5 0.26
20 14 0.74
ACGTcount: A:0.54, C:0.15, G:0.00, T:0.31
Consensus pattern (19 bp):
ATAACTTACATAATACATA
Found at i:5752876 original size:25 final size:25
Alignment explanation
Indices: 5752832--5752922 Score: 94
Period size: 25 Copynumber: 3.7 Consensus size: 25
5752822 AACTTACATA
*
5752832 ATAACATA-ATAACTTACATAATAC
1 ATAACCTACATAACTTACATAATAC
* * *
5752856 ATAGCCTACATGACTTGCATAATAC
1 ATAACCTACATAACTTACATAATAC
* * *
5752881 ACAACTTACATAAATTACATAATAC
1 ATAACCTACATAACTTACATAATAC
* *
5752906 ATAACTTTCATAACTTA
1 ATAACCTACATAACTTA
5752923 NNNNNNNNNN
Statistics
Matches: 53, Mismatches: 13, Indels: 1
0.79 0.19 0.01
Matches are distributed among these distances:
24 6 0.11
25 47 0.89
ACGTcount: A:0.46, C:0.20, G:0.03, T:0.31
Consensus pattern (25 bp):
ATAACCTACATAACTTACATAATAC
Found at i:5755083 original size:44 final size:42
Alignment explanation
Indices: 5755000--5755252 Score: 229
Period size: 43 Copynumber: 5.9 Consensus size: 42
5754990 CGTTTTTAAA
** ** *
5755000 AAAAGCGCCGCTAAAGGTCATGGTCTTTAACGGCGTTTGTCAG
1 AAAAGCGCCGCTAAAGAACATGACCTTTAGCGGCGTTTG-CAG
* * **
5755043 AAAAGCGCCACTAAAAGAACATGACCTTTAGTGGCGTTTGTGG
1 AAAAGCGCCGCT-AAAGAACATGACCTTTAGCGGCGTTTGCAG
* * * * *
5755086 ATAAAGCGCCGCCAAATAACATGATCTTTAGCGGCATTTGCAAA
1 A-AAAGCGCCGCTAAAGAACATGACCTTTAGCGGCGTTTGC-AG
* * *
5755130 AAAAGCGTCGCTAAAGAACATGATCTTTAGCGGCGTTTGCGG
1 AAAAGCGCCGCTAAAGAACATGACCTTTAGCGGCGTTTGCAG
* ***
5755172 AATAAGCGCCGCTAAAGTACATGACCTTTAGCGGCGCTTT-TTT
1 AA-AAGCGCCGCTAAAGAACATGACCTTTAGCGGCG-TTTGCAG
* * *
5755215 TATAGCGCCGCTAAAGAACATGACCTTTAGCGGTGTTT
1 AAAAGCGCCGCTAAAGAACATGACCTTTAGCGGCGTTT
5755253 ATAAAAATAA
Statistics
Matches: 171, Mismatches: 34, Indels: 12
0.79 0.16 0.06
Matches are distributed among these distances:
41 3 0.02
42 32 0.19
43 102 0.60
44 34 0.20
ACGTcount: A:0.29, C:0.21, G:0.24, T:0.26
Consensus pattern (42 bp):
AAAAGCGCCGCTAAAGAACATGACCTTTAGCGGCGTTTGCAG
Found at i:5755369 original size:21 final size:22
Alignment explanation
Indices: 5755340--5755382 Score: 70
Period size: 21 Copynumber: 2.0 Consensus size: 22
5755330 TACTTTTAGT
*
5755340 GGCTCTAAAAAGCGCCGCTAAA
1 GGCTCTAAAAAACGCCGCTAAA
5755362 GGCT-TAAAAAACGCCGCTAAA
1 GGCTCTAAAAAACGCCGCTAAA
5755383 AACCTGTTCT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 16 0.80
22 4 0.20
ACGTcount: A:0.40, C:0.26, G:0.21, T:0.14
Consensus pattern (22 bp):
GGCTCTAAAAAACGCCGCTAAA
Found at i:5755914 original size:6 final size:7
Alignment explanation
Indices: 5755899--5755923 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
5755889 ATACCCTTTC
5755899 TTTTATT
1 TTTTATT
5755906 TTTTATT
1 TTTTATT
5755913 TTTTATT
1 TTTTATT
5755920 TTTT
1 TTTT
5755924 GAAATTTCCA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.12, C:0.00, G:0.00, T:0.88
Consensus pattern (7 bp):
TTTTATT
Found at i:5762159 original size:148 final size:147
Alignment explanation
Indices: 5761854--5762153 Score: 458
Period size: 148 Copynumber: 2.0 Consensus size: 147
5761844 GAATTGAGCT
**
5761854 TTGTATAAAAAATTATTTATAAATGCTAATATTCATATATATAGTATATATGAGGTTTAAAATTA
1 TTGTATAAAAAATTATTTATAAATGCTAATACACATATATATAGTATATATGAGGTTTAAAATTA
* *
5761919 AACAAATTTAAAAATAAAATGTTATATATATTTCATAAGAGTGATTATAGAAAATATATAATAAT
66 AACAAATTTAAAAATAAAATG-TATATATATTTCATAAGAATGATTATAAAAAATATATAATAAT
* ***
5761984 GTCAACAATTAGACAGCT
130 ATCAACAATTAGACAAAA
5762002 TTGTATAAAAAATTATTTATAAATGCTAATACACATATATATAGTATATATGAGGTTTAAAATTA
1 TTGTATAAAAAATTATTTATAAATGCTAATACACATATATATAGTATATATGAGGTTTAAAATTA
*
5762067 AACAAATTTAAAAATAAAATG-CTATATATTTCATAAGAATGATTATATAAATATATATATAATA
66 AACAAATTTAAAAATAAAATGTATATATATTTCATAAGAATGATTATA-AAA-A-ATATATAATA
*
5762131 ATATCAACAGTTAGACATAAA
128 ATATCAACAATTAGACA-AAA
5762152 TT
1 TT
5762154 TTAAAATCTA
Statistics
Matches: 138, Mismatches: 10, Indels: 6
0.90 0.06 0.04
Matches are distributed among these distances:
146 24 0.17
147 2 0.01
148 85 0.62
149 25 0.18
150 2 0.01
ACGTcount: A:0.49, C:0.06, G:0.08, T:0.37
Consensus pattern (147 bp):
TTGTATAAAAAATTATTTATAAATGCTAATACACATATATATAGTATATATGAGGTTTAAAATTA
AACAAATTTAAAAATAAAATGTATATATATTTCATAAGAATGATTATAAAAAATATATAATAATA
TCAACAATTAGACAAAA
Found at i:5771186 original size:106 final size:106
Alignment explanation
Indices: 5770978--5771170 Score: 271
Period size: 106 Copynumber: 1.8 Consensus size: 106
5770968 AAAAAATTAA
5770978 GAGTGTGTTGAGCTGAGTAAACAGGGTAGGGTGCTTGGGTTGTCATCCTACTTCACGTCAAAAGG
1 GAGTGTGTTGAGCTGAGTAAACAGGGTAGGGTGCTTGGGTTGTCATCCTACTTCACGTCAAAAGG
* * *
5771043 GTCAAAACACTCTTAACCAAATAATAATAATAATAAAATAG
66 GCCAAAACACTCTTAAACAAATAATAATAAGAATAAAATAG
* * * * *
5771084 GAGTGTGTTG-GCCTGAGTAACCGGGGTGGGGTGCTTGGGTTGTCATCCTTCTTCGCGTCAAAAG
1 GAGTGTGTTGAG-CTGAGTAAACAGGGTAGGGTGCTTGGGTTGTCATCCTACTTCACGTCAAAAG
* *
5771148 GGCCAATACATTCTTAAGACAAA
65 GGCCAAAACACTCTTAA-ACAAA
5771171 ACAAAAAGAA
Statistics
Matches: 76, Mismatches: 9, Indels: 3
0.86 0.10 0.03
Matches are distributed among these distances:
105 1 0.01
106 71 0.93
107 4 0.05
ACGTcount: A:0.30, C:0.17, G:0.26, T:0.27
Consensus pattern (106 bp):
GAGTGTGTTGAGCTGAGTAAACAGGGTAGGGTGCTTGGGTTGTCATCCTACTTCACGTCAAAAGG
GCCAAAACACTCTTAAACAAATAATAATAAGAATAAAATAG
Found at i:5779690 original size:34 final size:35
Alignment explanation
Indices: 5779647--5779718 Score: 110
Period size: 34 Copynumber: 2.1 Consensus size: 35
5779637 TTTTACCGCC
**
5779647 AATAGATCGATAGCATCAATTTCAAACAC-AAAAT
1 AATAGATCGATAGCATCAACGTCAAACACAAAAAT
*
5779681 AATAGATCGATAGTATCAACGTCAAACACAAAAAT
1 AATAGATCGATAGCATCAACGTCAAACACAAAAAT
5779716 AAT
1 AAT
5779719 TTACTTCTAT
Statistics
Matches: 34, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
34 26 0.76
35 8 0.24
ACGTcount: A:0.51, C:0.17, G:0.10, T:0.22
Consensus pattern (35 bp):
AATAGATCGATAGCATCAACGTCAAACACAAAAAT
Found at i:5783988 original size:21 final size:22
Alignment explanation
Indices: 5783959--5784000 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
5783949 AAAACTATTA
5783959 AAATATTCA-AAAACTTTTAAG
1 AAATATTCATAAAACTTTTAAG
* *
5783980 AAATGTTCATAAAATTTTTAA
1 AAATATTCATAAAACTTTTAA
5784001 ATATTAACCA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 8 0.44
22 10 0.56
ACGTcount: A:0.50, C:0.07, G:0.05, T:0.38
Consensus pattern (22 bp):
AAATATTCATAAAACTTTTAAG
Found at i:5789483 original size:44 final size:43
Alignment explanation
Indices: 5789133--5789515 Score: 231
Period size: 44 Copynumber: 8.7 Consensus size: 43
5789123 ACTTGATGTG
* * * * *
5789133 ATCTGCTCTATTGCAACTTCAGAGAGATAAGATCTATTACTTTA
1 ATCTGCTCCACTGCAACTTCAGGGAGATAAGATCTCTT-CTTCA
* * * * **
5789177 ATCCGCTCCACTACAACTTCAGGGAGATAGGATTATCGGCTTCA
1 ATCTGCTCCACTGCAACTTCAGGGAGATAAGA-TCTCTTCTTCA
* * * *
5789221 ATCTGCTCCACTGTAACTTCAGGGAGATAAGATTGGTCATCTTCG
1 ATCTGCTCCACTGCAACTTCAGGGAGATAAGA-T-CTCTTCTTCA
* * *
5789266 ATCTGCCCCACTGCAACTTCAGTCGAGATAAGACCTGCTTACTT-A
1 ATCTGCTCCACTGCAACTTCAG-GGAGATAAGATCT-CTT-CTTCA
* * * ** *
5789311 GTTTGCTCCACTGTAACTTCAGGGAGATAAGA-C-CTGATGT-G
1 ATCTGCTCCACTGCAACTTCAGGGAGATAAGATCTCTTCT-TCA
** * * * *
5789352 ATCCACTCTACTGCAACTTCAGAGAGATAAGATCTATTACTTTA
1 ATCTGCTCCACTGCAACTTCAGGGAGATAAGATCTCTT-CTTCA
* * * *
5789396 ATCCT-CTCCATTGCAACTTTAGGGAGATATGAT-TATTGACTTCA
1 AT-CTGCTCCACTGCAACTTCAGGGAGATAAGATCTCTT--CTTCA
*
5789440 ATCTGCTCCACTGCAACCTT-AGGGAGATAAGATTTGCTTCTTCA
1 ATCTGCTCCACTGCAA-CTTCAGGGAGATAAGATCT-CTTCTTCA
* ** * *
5789484 ATCTGCCCCACTGTGACCTCAGGGGGATAAGA
1 ATCTGCTCCACTGCAACTTCAGGGAGATAAGA
5789516 CTCCTGGCTT
Statistics
Matches: 262, Mismatches: 60, Indels: 34
0.74 0.17 0.10
Matches are distributed among these distances:
40 1 0.00
41 28 0.11
42 1 0.00
43 11 0.04
44 154 0.59
45 53 0.20
46 14 0.05
ACGTcount: A:0.27, C:0.24, G:0.19, T:0.30
Consensus pattern (43 bp):
ATCTGCTCCACTGCAACTTCAGGGAGATAAGATCTCTTCTTCA
Found at i:5789711 original size:43 final size:43
Alignment explanation
Indices: 5789658--5789902 Score: 393
Period size: 43 Copynumber: 5.7 Consensus size: 43
5789648 TGGCTTAAAG
*
5789658 CTGTTTCCCTACTCTTGGGG-AGAATAAGATTCGCCGCTTAGAT
1 CTGTTTCCCTACTCCTGGGGAAG-ATAAGATTCGCCGCTTAGAT
* *
5789701 ATGTTTCCCTACTCCTGGGGAAAATAAGATTCGCCGCTTAGAT
1 CTGTTTCCCTACTCCTGGGGAAGATAAGATTCGCCGCTTAGAT
* * *
5789744 CTGTTTCCCTACTCCTAGGGAAGATAAGATCCGCCTCTTAGAT
1 CTGTTTCCCTACTCCTGGGGAAGATAAGATTCGCCGCTTAGAT
* *
5789787 CTGTTTCCCTACTCCTGGGGAAGATAAGATTCGCCACATAGAT
1 CTGTTTCCCTACTCCTGGGGAAGATAAGATTCGCCGCTTAGAT
*
5789830 CTGTTTCCCTACTCCTGGGGAAGATAAGATTCGTCGCTTAGAT
1 CTGTTTCCCTACTCCTGGGGAAGATAAGATTCGCCGCTTAGAT
5789873 CTGTTTCCCTACTCCTGGGGAAGATAAGAT
1 CTGTTTCCCTACTCCTGGGGAAGATAAGAT
5789903 CCGCAATATT
Statistics
Matches: 186, Mismatches: 15, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
43 185 0.99
44 1 0.01
ACGTcount: A:0.23, C:0.24, G:0.22, T:0.31
Consensus pattern (43 bp):
CTGTTTCCCTACTCCTGGGGAAGATAAGATTCGCCGCTTAGAT
Found at i:5791156 original size:7 final size:6
Alignment explanation
Indices: 5791125--5791152 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
5791115 GCCTCTCTAT
5791125 TTTTCA TTTTCA TTTTCA TTTTCA TTTT
1 TTTTCA TTTTCA TTTTCA TTTTCA TTTT
5791153 TCATATTTTC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.14, C:0.14, G:0.00, T:0.71
Consensus pattern (6 bp):
TTTTCA
Found at i:5797576 original size:18 final size:19
Alignment explanation
Indices: 5797553--5797593 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
5797543 GGTCCCTGGT
*
5797553 GGCGTGGC-TCGGCTCGGA
1 GGCGTGGCTTCGGCGCGGA
*
5797571 GGCGTGGCTTTGGCGCGGA
1 GGCGTGGCTTCGGCGCGGA
5797590 GGCG
1 GGCG
5797594 CTACACGCGC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 8 0.40
19 12 0.60
ACGTcount: A:0.05, C:0.24, G:0.54, T:0.17
Consensus pattern (19 bp):
GGCGTGGCTTCGGCGCGGA
Found at i:5801153 original size:14 final size:14
Alignment explanation
Indices: 5801134--5801170 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
5801124 ATGAATTAAA
5801134 ATATGTAGATATAT
1 ATATGTAGATATAT
*
5801148 ATATGTATATATAT
1 ATATGTAGATATAT
*
5801162 GTATGTAGA
1 ATATGTAGA
5801171 AAATATGAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.41, C:0.00, G:0.16, T:0.43
Consensus pattern (14 bp):
ATATGTAGATATAT
Found at i:5801453 original size:3 final size:3
Alignment explanation
Indices: 5801447--5801486 Score: 71
Period size: 3 Copynumber: 13.3 Consensus size: 3
5801437 GTAGTAGTAC
*
5801447 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAT TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
5801487 GATATTGTAT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (3 bp):
TAA
Found at i:5801491 original size:9 final size:9
Alignment explanation
Indices: 5801447--5801492 Score: 56
Period size: 9 Copynumber: 5.1 Consensus size: 9
5801437 GTAGTAGTAC
*
5801447 TAATAATAA
1 TAATAATAT
*
5801456 TAATAATAA
1 TAATAATAT
*
5801465 TAATAATAA
1 TAATAATAT
5801474 TAATAATAT
1 TAATAATAT
*
5801483 TAATGATAT
1 TAATAATAT
5801492 T
1 T
5801493 GTATGAAAGT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
9 35 1.00
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (9 bp):
TAATAATAT
Found at i:5803572 original size:19 final size:19
Alignment explanation
Indices: 5803548--5803584 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
5803538 ACATACTTGG
5803548 ATTAAACCTTAATTAATTA
1 ATTAAACCTTAATTAATTA
*
5803567 ATTAAACCTTAGTTAATT
1 ATTAAACCTTAATTAATT
5803585 GGACCTTTGA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.43, C:0.11, G:0.03, T:0.43
Consensus pattern (19 bp):
ATTAAACCTTAATTAATTA
Found at i:5803855 original size:18 final size:18
Alignment explanation
Indices: 5803832--5803872 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
5803822 ATCCTATAAA
* *
5803832 TAGTTTGAATTTTATCTT
1 TAGTTTAAATTTGATCTT
*
5803850 TAGTTTAAATTTGATTTT
1 TAGTTTAAATTTGATCTT
5803868 TAGTT
1 TAGTT
5803873 GATATTTTCT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.24, C:0.02, G:0.12, T:0.61
Consensus pattern (18 bp):
TAGTTTAAATTTGATCTT
Found at i:5808811 original size:18 final size:18
Alignment explanation
Indices: 5808788--5808827 Score: 55
Period size: 17 Copynumber: 2.3 Consensus size: 18
5808778 AAAAGTTATC
*
5808788 AAAAAAGTGAA-AAAACA
1 AAAAAAATGAATAAAACA
*
5808805 AAAAAAATGAATAAAAGA
1 AAAAAAATGAATAAAACA
5808823 AAAAA
1 AAAAA
5808828 TAAAAAATAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 10 0.50
18 10 0.50
ACGTcount: A:0.80, C:0.03, G:0.10, T:0.07
Consensus pattern (18 bp):
AAAAAAATGAATAAAACA
Found at i:5812439 original size:12 final size:11
Alignment explanation
Indices: 5812424--5812475 Score: 70
Period size: 12 Copynumber: 4.5 Consensus size: 11
5812414 CTTTCTTGCC
5812424 TCTTTTCATTTT
1 TCTTTTC-TTTT
5812436 TC-TTTCTTTT
1 TCTTTTCTTTT
5812446 TCTTTTTCTTTT
1 TC-TTTTCTTTT
5812458 TCTTTTCTTTT
1 TCTTTTCTTTT
5812469 TCATTTT
1 TC-TTTT
5812476 TATTCTTCTT
Statistics
Matches: 37, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
10 6 0.16
11 15 0.41
12 16 0.43
ACGTcount: A:0.04, C:0.17, G:0.00, T:0.79
Consensus pattern (11 bp):
TCTTTTCTTTT
Found at i:5812441 original size:11 final size:10
Alignment explanation
Indices: 5812427--5812470 Score: 52
Period size: 11 Copynumber: 4.0 Consensus size: 10
5812417 TCTTGCCTCT
5812427 TTTCATTTTTC
1 TTTC-TTTTTC
5812438 TTTCTTTTTC
1 TTTCTTTTTC
5812448 TTTTTCTTTTTC
1 --TTTCTTTTTC
5812460 TTTTCTTTTTC
1 -TTTCTTTTTC
5812471 ATTTTTATTC
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
10 6 0.19
11 15 0.48
12 10 0.32
ACGTcount: A:0.02, C:0.18, G:0.00, T:0.80
Consensus pattern (10 bp):
TTTCTTTTTC
Found at i:5812452 original size:17 final size:17
Alignment explanation
Indices: 5812423--5812470 Score: 71
Period size: 17 Copynumber: 2.8 Consensus size: 17
5812413 TCTTTCTTGC
5812423 CTCTTTTCATTTTTCTTT
1 CTCTTTTC-TTTTTCTTT
5812441 CT-TTTTCTTTTTCTTT
1 CTCTTTTCTTTTTCTTT
*
5812457 TTCTTTTCTTTTTC
1 CTCTTTTCTTTTTC
5812471 ATTTTTATTC
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
16 10 0.36
17 16 0.57
18 2 0.07
ACGTcount: A:0.02, C:0.21, G:0.00, T:0.77
Consensus pattern (17 bp):
CTCTTTTCTTTTTCTTT
Found at i:5812452 original size:23 final size:24
Alignment explanation
Indices: 5812426--5812485 Score: 81
Period size: 23 Copynumber: 2.6 Consensus size: 24
5812416 TTCTTGCCTC
5812426 TTTTCATTTTTCTTTCTTTTTC-T
1 TTTTCATTTTTCTTTCTTTTTCAT
5812449 TTTTC-TTTTTCTTTTCTTTTTCAT
1 TTTTCATTTTTC-TTTCTTTTTCAT
*
5812473 TTTT-ATTCTTCTT
1 TTTTCATTTTTCTT
5812486 CTATTCCTTT
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
22 6 0.18
23 17 0.52
24 10 0.30
ACGTcount: A:0.05, C:0.17, G:0.00, T:0.78
Consensus pattern (24 bp):
TTTTCATTTTTCTTTCTTTTTCAT
Found at i:5812475 original size:17 final size:16
Alignment explanation
Indices: 5812424--5812499 Score: 66
Period size: 16 Copynumber: 4.6 Consensus size: 16
5812414 CTTTCTTGCC
5812424 TCTTTTCATTTTTC-TT
1 TCTTTTC-TTTTTCTTT
5812440 TCTTTTTCTTTTTCTTTT
1 TC-TTTTCTTTTTC-TTT
5812458 TCTTTTCTTTTTCATTT
1 TCTTTTCTTTTTC-TTT
* * *
5812475 T-TATTCTTCTTCTAT
1 TCTTTTCTTTTTCTTT
*
5812490 TCCTTTCTTT
1 TCTTTTCTTT
5812500 CCTCTTCGCT
Statistics
Matches: 49, Mismatches: 7, Indels: 8
0.77 0.11 0.12
Matches are distributed among these distances:
15 3 0.06
16 22 0.45
17 20 0.41
18 4 0.08
ACGTcount: A:0.05, C:0.20, G:0.00, T:0.75
Consensus pattern (16 bp):
TCTTTTCTTTTTCTTT
Found at i:5812487 original size:6 final size:6
Alignment explanation
Indices: 5812426--5812476 Score: 63
Period size: 6 Copynumber: 8.7 Consensus size: 6
5812416 TTCTTGCCTC
5812426 TTTTCAT TTTTC- -TTTCT TTTTCT TTTTCT TTTTC- TTTTCT TTTTCAT
1 TTTTC-T TTTTCT TTTTCT TTTTCT TTTTCT TTTTCT TTTTCT TTTTC-T
5812473 TTTT
1 TTTT
5812477 ATTCTTCTTC
Statistics
Matches: 40, Mismatches: 0, Indels: 8
0.83 0.00 0.17
Matches are distributed among these distances:
4 4 0.10
5 5 0.12
6 21 0.52
7 10 0.25
ACGTcount: A:0.04, C:0.16, G:0.00, T:0.80
Consensus pattern (6 bp):
TTTTCT
Found at i:5813195 original size:65 final size:65
Alignment explanation
Indices: 5813109--5813245 Score: 181
Period size: 65 Copynumber: 2.1 Consensus size: 65
5813099 GTTAGTGTAG
* * * *
5813109 GGTTCACACAGGCCAAGGACACGGGCGTGTGTCCATACCGTGTACCTCACTATTTACAAATATAA
1 GGTTCACACAGGCCAAGGACACGAGCGTGTGTCCAGACCATATACCTCACTATTTACAAATATAA
* *
5813174 GGTTCACA-AGGGCCAAGGACACGAGCGTGTGTCCAGGCCATATACCTCGCTATTTACAAA-AT-
1 GGTTCACACA-GGCCAAGGACACGAGCGTGTGTCCAGACCATATACCTCACTATTTACAAATATA
5813236 A
65 A
*
5813237 GGATCACAC
1 GGTTCACAC
5813246 GAGTGGAGGA
Statistics
Matches: 63, Mismatches: 7, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
63 8 0.13
64 3 0.05
65 52 0.83
ACGTcount: A:0.30, C:0.26, G:0.23, T:0.21
Consensus pattern (65 bp):
GGTTCACACAGGCCAAGGACACGAGCGTGTGTCCAGACCATATACCTCACTATTTACAAATATAA
Found at i:5815803 original size:26 final size:26
Alignment explanation
Indices: 5815774--5815874 Score: 139
Period size: 26 Copynumber: 3.9 Consensus size: 26
5815764 ATGGAGGAAG
* *
5815774 CTGTTGCTAGCAGCTTTGCTGCGATA
1 CTGTTACTGGCAGCTTTGCTGCGATA
*
5815800 CTGTTACTGGCAGCTTTGCTGTGATA
1 CTGTTACTGGCAGCTTTGCTGCGATA
* *
5815826 CTGTTACTGGCAGCTTTGTTGTGATA
1 CTGTTACTGGCAGCTTTGCTGCGATA
* *
5815852 CTATTACTGGCAGTTTTGCTGCG
1 CTGTTACTGGCAGCTTTGCTGCG
5815875 GTATTGGTGT
Statistics
Matches: 67, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
26 67 1.00
ACGTcount: A:0.15, C:0.20, G:0.27, T:0.39
Consensus pattern (26 bp):
CTGTTACTGGCAGCTTTGCTGCGATA
Found at i:5817968 original size:19 final size:19
Alignment explanation
Indices: 5817944--5817981 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 19
5817934 TATTTATCCT
5817944 TTATTT-TTTTTTACTTTTC
1 TTATTTCTTTTTTA-TTTTC
5817963 TTATTTCCTTTTTTATTTT
1 TTATTT-CTTTTTTATTTT
5817982 TTAAATTTGT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 6 0.35
20 4 0.24
21 7 0.41
ACGTcount: A:0.11, C:0.11, G:0.00, T:0.79
Consensus pattern (19 bp):
TTATTTCTTTTTTATTTTC
Found at i:5818371 original size:28 final size:29
Alignment explanation
Indices: 5818305--5818364 Score: 120
Period size: 29 Copynumber: 2.1 Consensus size: 29
5818295 TCATTTGATG
5818305 AAATTCTAAATATTTGGTTATTCTTAAAA
1 AAATTCTAAATATTTGGTTATTCTTAAAA
5818334 AAATTCTAAATATTTGGTTATTCTTAAAA
1 AAATTCTAAATATTTGGTTATTCTTAAAA
5818363 AA
1 AA
5818365 TTGTAAAAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.43, C:0.07, G:0.07, T:0.43
Consensus pattern (29 bp):
AAATTCTAAATATTTGGTTATTCTTAAAA
Found at i:5819464 original size:20 final size:20
Alignment explanation
Indices: 5819420--5819467 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 20
5819410 AGGTTGTCGG
5819420 AAAA-TGATTCTTTTAAAAA
1 AAAATTGATTCTTTTAAAAA
**
5819439 TGAATTGATT-TTTTGAAAAA
1 AAAATTGATTCTTTT-AAAAA
5819459 AAAATTGAT
1 AAAATTGAT
5819468 ATATATTGTA
Statistics
Matches: 23, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
19 6 0.26
20 17 0.74
ACGTcount: A:0.48, C:0.02, G:0.10, T:0.40
Consensus pattern (20 bp):
AAAATTGATTCTTTTAAAAA
Found at i:5822613 original size:42 final size:42
Alignment explanation
Indices: 5822554--5822727 Score: 341
Period size: 42 Copynumber: 4.2 Consensus size: 42
5822544 ACCAAATGAC
5822554 ATAGATCATGTATGGATGTATGGTATGGAAATTACATGCAAT
1 ATAGATCATGTATGGATGTATGGTATGGAAATTACATGCAAT
5822596 ATAGATCATGTATGGATGTATGGTATGGAAATTACATGCAAT
1 ATAGATCATGTATGGATGTATGGTATGGAAATTACATGCAAT
5822638 ATAGATCATGTATGGATGTATGGTATGGAAATTACATGCAAT
1 ATAGATCATGTATGGATGTATGGTATGGAAATTACATGCAAT
5822680 ATAGATCATGTATGGATGTATGGTATGGAAATTACATGCAAT
1 ATAGATCATGTATGGATGTATGGTATGGAAATTACATGCAAT
5822722 AT-GATC
1 ATAGATC
5822728 CAAACATGTT
Statistics
Matches: 132, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
41 4 0.03
42 128 0.97
ACGTcount: A:0.36, C:0.07, G:0.24, T:0.33
Consensus pattern (42 bp):
ATAGATCATGTATGGATGTATGGTATGGAAATTACATGCAAT
Found at i:5824948 original size:16 final size:16
Alignment explanation
Indices: 5824902--5824949 Score: 51
Period size: 16 Copynumber: 2.9 Consensus size: 16
5824892 GAAGAGAGAG
*
5824902 AAAAGAAAGAAAAAATA
1 AAAAGAAA-ACAAAATA
* *
5824919 AAAATAAAATAAAATA
1 AAAAGAAAACAAAATA
*
5824935 AAAAGAAACCAAAAT
1 AAAAGAAAACAAAAT
5824950 CCCTCAAATT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
16 19 0.73
17 7 0.27
ACGTcount: A:0.79, C:0.04, G:0.06, T:0.10
Consensus pattern (16 bp):
AAAAGAAAACAAAATA
Found at i:5830059 original size:26 final size:26
Alignment explanation
Indices: 5830030--5830083 Score: 83
Period size: 26 Copynumber: 2.1 Consensus size: 26
5830020 CTCAATATAG
*
5830030 TTTCAGAAA-TTACTAACTACTGTGCT
1 TTTCAGAAAGTT-CTAACTACCGTGCT
5830056 TTTCAGAAAGTTCTAACTACCGTGCT
1 TTTCAGAAAGTTCTAACTACCGTGCT
5830082 TT
1 TT
5830084 CTAAATTTAA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
26 24 0.92
27 2 0.08
ACGTcount: A:0.28, C:0.20, G:0.13, T:0.39
Consensus pattern (26 bp):
TTTCAGAAAGTTCTAACTACCGTGCT
Found at i:5832760 original size:13 final size:13
Alignment explanation
Indices: 5832742--5832818 Score: 70
Period size: 13 Copynumber: 5.9 Consensus size: 13
5832732 AGTTTAACAT
5832742 TGCTTTTGAAAAA
1 TGCTTTTGAAAAA
5832755 TGCTTTT-AAAAA
1 TGCTTTTGAAAAA
*
5832767 GTG-TTGTGGAAAAA
1 -TGCTT-TTGAAAAA
*
5832781 TGCTTTTGAGAAA
1 TGCTTTTGAAAAA
*
5832794 TGCTTTT-AATAAG
1 TGCTTTTGAA-AAA
*
5832807 TACTTTTGAAAA
1 TGCTTTTGAAAA
5832819 GTTTGATTTA
Statistics
Matches: 52, Mismatches: 6, Indels: 12
0.74 0.09 0.17
Matches are distributed among these distances:
12 8 0.15
13 35 0.67
14 9 0.17
ACGTcount: A:0.36, C:0.06, G:0.18, T:0.39
Consensus pattern (13 bp):
TGCTTTTGAAAAA
Found at i:5833537 original size:8 final size:8
Alignment explanation
Indices: 5833524--5833568 Score: 54
Period size: 8 Copynumber: 5.2 Consensus size: 8
5833514 AAAGGTTAGA
5833524 TTTTATTT
1 TTTTATTT
5833532 TTTTATTT
1 TTTTATTT
*
5833540 GTTTTGCTTAT
1 -TTTT-ATT-T
5833551 TTTTATTT
1 TTTTATTT
5833559 TTTTATTT
1 TTTTATTT
5833567 TT
1 TT
5833569 ATTTTTGAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
8 19 0.59
9 6 0.19
10 6 0.19
11 1 0.03
ACGTcount: A:0.11, C:0.02, G:0.04, T:0.82
Consensus pattern (8 bp):
TTTTATTT
Found at i:5834586 original size:12 final size:12
Alignment explanation
Indices: 5834569--5834595 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
5834559 TGTTTTGCAA
5834569 ATTTTTCTTATT
1 ATTTTTCTTATT
5834581 ATTTTTCTTATT
1 ATTTTTCTTATT
5834593 ATT
1 ATT
5834596 ATTTTATTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.19, C:0.07, G:0.00, T:0.74
Consensus pattern (12 bp):
ATTTTTCTTATT
Found at i:5837182 original size:3 final size:3
Alignment explanation
Indices: 5837174--5837207 Score: 61
Period size: 3 Copynumber: 11.7 Consensus size: 3
5837164 TAGTTTTTTC
5837174 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT- TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
5837208 TTTGATATGA
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.07
3 28 0.93
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (3 bp):
TTA
Found at i:5837761 original size:16 final size:17
Alignment explanation
Indices: 5837740--5837772 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
5837730 GACCACACAG
5837740 GTGG-CCACACGGGCGT
1 GTGGCCCACACGGGCGT
5837756 GTGGCCCCACACGGGCG
1 GTGG-CCCACACGGGCG
5837773 GTCTACACGA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 4 0.27
18 11 0.73
ACGTcount: A:0.12, C:0.36, G:0.42, T:0.09
Consensus pattern (17 bp):
GTGGCCCACACGGGCGT
Found at i:5847219 original size:30 final size:30
Alignment explanation
Indices: 5847185--5847264 Score: 142
Period size: 30 Copynumber: 2.7 Consensus size: 30
5847175 AATATCTCGG
5847185 TACCCATATCTTTGACTTTCTAATATTTGA
1 TACCCATATCTTTGACTTTCTAATATTTGA
*
5847215 TACCCATATCTTTGACTTTCTATTATTTGA
1 TACCCATATCTTTGACTTTCTAATATTTGA
*
5847245 TACCCATATCTTTGATTTTC
1 TACCCATATCTTTGACTTTC
5847265 CATAAACATG
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 48 1.00
ACGTcount: A:0.24, C:0.21, G:0.06, T:0.49
Consensus pattern (30 bp):
TACCCATATCTTTGACTTTCTAATATTTGA
Found at i:5847228 original size:15 final size:15
Alignment explanation
Indices: 5847210--5847260 Score: 50
Period size: 15 Copynumber: 3.4 Consensus size: 15
5847200 CTTTCTAATA
5847210 TTTGATACCCATATC
1 TTTGATACCCATATC
** * *
5847225 TTTGACTTTCTAT-TA
1 TTTGA-TACCCATATC
5847240 TTTGATACCCATATC
1 TTTGATACCCATATC
5847255 TTTGAT
1 TTTGAT
5847261 TTTCCATAAA
Statistics
Matches: 26, Mismatches: 8, Indels: 4
0.68 0.21 0.11
Matches are distributed among these distances:
14 4 0.15
15 18 0.69
16 4 0.15
ACGTcount: A:0.24, C:0.20, G:0.08, T:0.49
Consensus pattern (15 bp):
TTTGATACCCATATC
Found at i:5866017 original size:21 final size:21
Alignment explanation
Indices: 5865991--5866052 Score: 72
Period size: 21 Copynumber: 3.0 Consensus size: 21
5865981 CAACAACTTA
**
5865991 AAGCAGAGGCGACAGCGAGGG
1 AAGCAGAGGCGACAGCGAGAC
* *
5866012 AAGCAGAGGCTACAGCAAGAC
1 AAGCAGAGGCGACAGCGAGAC
5866033 AAGCAGAGGCCG-CAGCGAGA
1 AAGCAGAGG-CGACAGCGAGA
5866053 GAAACAACGA
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
21 33 0.97
22 1 0.03
ACGTcount: A:0.37, C:0.23, G:0.39, T:0.02
Consensus pattern (21 bp):
AAGCAGAGGCGACAGCGAGAC
Found at i:5869907 original size:18 final size:16
Alignment explanation
Indices: 5869868--5869912 Score: 56
Period size: 18 Copynumber: 2.7 Consensus size: 16
5869858 TCCATTTTAA
5869868 ATTTT-TATATAACAT
1 ATTTTATATATAACAT
5869883 ATGTTTATATATATACAT
1 AT-TTTATATATA-ACAT
5869901 CATTTTATATAT
1 -ATTTTATATAT
5869913 GTTATTTTAA
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
15 2 0.08
16 3 0.12
17 6 0.23
18 13 0.50
19 2 0.08
ACGTcount: A:0.38, C:0.07, G:0.02, T:0.53
Consensus pattern (16 bp):
ATTTTATATATAACAT
Found at i:5870065 original size:12 final size:12
Alignment explanation
Indices: 5870048--5870072 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
5870038 CATATTACTT
5870048 ATTTTAAGATTA
1 ATTTTAAGATTA
5870060 ATTTTAAGATTA
1 ATTTTAAGATTA
5870072 A
1 A
5870073 CCTATACTAT
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:0.44, C:0.00, G:0.08, T:0.48
Consensus pattern (12 bp):
ATTTTAAGATTA
Found at i:5874019 original size:54 final size:54
Alignment explanation
Indices: 5873961--5874079 Score: 159
Period size: 54 Copynumber: 2.2 Consensus size: 54
5873951 TGATGGGACA
*
5873961 TTAAACATGGGATAGTCTGATGGGACATTAAACACAGGA-TAGTCCGACGGGATG
1 TTAAACATGGGATAGTCTGATGGGACATTAAACA-AGGAGTAGTCCGACAGGATG
** * * *
5874015 TTAAACACAGGATAGTCTGATGGGACATTAAACATGGAGTAGTCTGCCAGGATG
1 TTAAACATGGGATAGTCTGATGGGACATTAAACAAGGAGTAGTCCGACAGGATG
*
5874069 ATAAACATGGG
1 TTAAACATGGG
5874080 GATATTAAGA
Statistics
Matches: 55, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
53 3 0.05
54 52 0.95
ACGTcount: A:0.34, C:0.14, G:0.29, T:0.23
Consensus pattern (54 bp):
TTAAACATGGGATAGTCTGATGGGACATTAAACAAGGAGTAGTCCGACAGGATG
Found at i:5874060 original size:27 final size:27
Alignment explanation
Indices: 5873944--5874048 Score: 147
Period size: 27 Copynumber: 3.9 Consensus size: 27
5873934 TGACATCGAA
* **
5873944 GATAGTGTGATGGGACATTAAACATGG
1 GATAGTCTGATGGGACATTAAACACAG
5873971 GATAGTCTGATGGGACATTAAACACAG
1 GATAGTCTGATGGGACATTAAACACAG
* * **
5873998 GATAGTCCGACGGGATGTTAAACACAG
1 GATAGTCTGATGGGACATTAAACACAG
5874025 GATAGTCTGATGGGACATTAAACA
1 GATAGTCTGATGGGACATTAAACA
5874049 TGGAGTAGTC
Statistics
Matches: 67, Mismatches: 11, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 67 1.00
ACGTcount: A:0.35, C:0.13, G:0.29, T:0.23
Consensus pattern (27 bp):
GATAGTCTGATGGGACATTAAACACAG
Found at i:5879187 original size:15 final size:15
Alignment explanation
Indices: 5879167--5879198 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
5879157 TGATAAACTA
*
5879167 AAAAATTAAGTGTTG
1 AAAAATTAAATGTTG
5879182 AAAAATTAAATGTTG
1 AAAAATTAAATGTTG
5879197 AA
1 AA
5879199 TCTAGTTTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.53, C:0.00, G:0.16, T:0.31
Consensus pattern (15 bp):
AAAAATTAAATGTTG
Found at i:5880972 original size:20 final size:22
Alignment explanation
Indices: 5880936--5880977 Score: 54
Period size: 21 Copynumber: 2.0 Consensus size: 22
5880926 CTGGATAAAT
5880936 AACTTCCAATTTCTTA-TCCTC
1 AACTTCCAATTTCTTATTCCTC
5880957 AACTT-CAATGTT-TTATTCCTC
1 AACTTCCAAT-TTCTTATTCCTC
5880978 TTTTAATTTC
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
20 7 0.37
21 12 0.63
ACGTcount: A:0.24, C:0.29, G:0.02, T:0.45
Consensus pattern (22 bp):
AACTTCCAATTTCTTATTCCTC
Found at i:5885734 original size:146 final size:147
Alignment explanation
Indices: 5885456--5885750 Score: 565
Period size: 146 Copynumber: 2.0 Consensus size: 147
5885446 CAGAGGAGGA
5885456 TTGTTTGTAGCCAAGGGATAAAAGAGAAGCTGTAAGTTTGGAGAACCACTGTCTGCTAGCTTGTT
1 TTGTTTGTAGCCAAGGGATAAAAGAGAAGCTGTAAGTTTGGAGAACCACTGTCTGCTAGCTTGTT
5885521 TTAAGCCATATAGAGATTTTTGTAATTTGCAGACTTTGCTCTTGTCTGATCCTTCAAATCCAAGG
66 TTAAGCCATATAGAGATTTTTGTAATTTGCAGACTTTGCTCTTGTCTGATCCTTCAAATCCAAGG
5885586 GGCAACTTCATGTAAAC
131 GGCAACTTCATGTAAAC
5885603 TTGTTTGTAGCC-AGGGATAAAAGAGAAGCTGTAAGTTTGGAGAACCACTGTCTGCTAGCTTGTT
1 TTGTTTGTAGCCAAGGGATAAAAGAGAAGCTGTAAGTTTGGAGAACCACTGTCTGCTAGCTTGTT
* *
5885667 TTAAGCCATATAGAGATTTTTGTAATTTTCAGACTTTGCTCTTGTCTGATCCTTCAAATCCAGGG
66 TTAAGCCATATAGAGATTTTTGTAATTTGCAGACTTTGCTCTTGTCTGATCCTTCAAATCCAAGG
5885732 GGCAACTTCATGTAAAC
131 GGCAACTTCATGTAAAC
5885749 TT
1 TT
5885751 CCTCATTCAA
Statistics
Matches: 146, Mismatches: 2, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
146 134 0.92
147 12 0.08
ACGTcount: A:0.27, C:0.17, G:0.22, T:0.34
Consensus pattern (147 bp):
TTGTTTGTAGCCAAGGGATAAAAGAGAAGCTGTAAGTTTGGAGAACCACTGTCTGCTAGCTTGTT
TTAAGCCATATAGAGATTTTTGTAATTTGCAGACTTTGCTCTTGTCTGATCCTTCAAATCCAAGG
GGCAACTTCATGTAAAC
Found at i:5886326 original size:12 final size:13
Alignment explanation
Indices: 5886309--5886340 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
5886299 TTTGGAGTTG
5886309 GTGGTTCAAT-AT
1 GTGGTTCAATCAT
5886321 GTGGTTC-ATCAT
1 GTGGTTCAATCAT
5886333 GTGGTTCA
1 GTGGTTCA
5886341 GTATTTGTGG
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
11 2 0.11
12 16 0.89
ACGTcount: A:0.19, C:0.12, G:0.28, T:0.41
Consensus pattern (13 bp):
GTGGTTCAATCAT
Found at i:5886360 original size:33 final size:33
Alignment explanation
Indices: 5886321--5886389 Score: 113
Period size: 33 Copynumber: 2.1 Consensus size: 33
5886311 GGTTCAATAT
5886321 GTGGTTC-ATCATGTGGTTCAGTATTTGTGGGTG
1 GTGGTTCAAT-ATGTGGTTCAGTATTTGTGGGTG
*
5886354 GTGGTTCAATATGTGGTTTAGTATTTGTGGGTG
1 GTGGTTCAATATGTGGTTCAGTATTTGTGGGTG
5886387 GTG
1 GTG
5886390 ATGGTGTTTC
Statistics
Matches: 34, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
33 32 0.94
34 2 0.06
ACGTcount: A:0.13, C:0.06, G:0.38, T:0.43
Consensus pattern (33 bp):
GTGGTTCAATATGTGGTTCAGTATTTGTGGGTG
Found at i:5896544 original size:21 final size:21
Alignment explanation
Indices: 5896520--5896564 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
5896510 AAAAAACATC
* *
5896520 AAATCCGAAACTTGAAACCCA
1 AAATCCAAAACTTAAAACCCA
**
5896541 AAATTTAAAACTTAAAACCCA
1 AAATCCAAAACTTAAAACCCA
5896562 AAA
1 AAA
5896565 GATAAATAAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.56, C:0.22, G:0.04, T:0.18
Consensus pattern (21 bp):
AAATCCAAAACTTAAAACCCA
Found at i:5896570 original size:21 final size:21
Alignment explanation
Indices: 5896527--5896570 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
5896517 ATCAAATCCG
* **
5896527 AAACTTGAAACCCAAAATTTA
1 AAACTTAAAACCCAAAAGATA
5896548 AAACTTAAAACCCAAAAGATA
1 AAACTTAAAACCCAAAAGATA
5896569 AA
1 AA
5896571 TAAAATAATT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.59, C:0.18, G:0.05, T:0.18
Consensus pattern (21 bp):
AAACTTAAAACCCAAAAGATA
Found at i:5902701 original size:17 final size:17
Alignment explanation
Indices: 5902679--5902712 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
5902669 TGTAGGGACT
*
5902679 AAATTGAAGGTAAAAAG
1 AAATTGAAGGCAAAAAG
*
5902696 AAATTGGAGGCAAAAAG
1 AAATTGAAGGCAAAAAG
5902713 CGTGAATTTA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.56, C:0.03, G:0.26, T:0.15
Consensus pattern (17 bp):
AAATTGAAGGCAAAAAG
Found at i:5909262 original size:5 final size:5
Alignment explanation
Indices: 5909218--5909276 Score: 59
Period size: 5 Copynumber: 11.8 Consensus size: 5
5909208 GTAACCCAAT
* * *
5909218 TTTTA -TTTA -TTTA TTTATTA TTTTA TTATA TATTA CTTTA TTTTA TTTTA
1 TTTTA TTTTA TTTTA -TT-TTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA
5909268 TTTTA TTTT
1 TTTTA TTTT
5909277 CATGTTAATA
Statistics
Matches: 45, Mismatches: 6, Indels: 6
0.79 0.11 0.11
Matches are distributed among these distances:
4 8 0.18
5 31 0.69
6 3 0.07
7 3 0.07
ACGTcount: A:0.24, C:0.02, G:0.00, T:0.75
Consensus pattern (5 bp):
TTTTA
Found at i:5917362 original size:18 final size:18
Alignment explanation
Indices: 5917339--5917376 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
5917329 CACGTTAGTG
5917339 AACAAATATATATAAATA
1 AACAAATATATATAAATA
* *
5917357 AACAAATATCTATATATA
1 AACAAATATATATAAATA
5917375 AA
1 AA
5917377 ATAAAATAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.63, C:0.08, G:0.00, T:0.29
Consensus pattern (18 bp):
AACAAATATATATAAATA
Found at i:5917824 original size:20 final size:19
Alignment explanation
Indices: 5917786--5917836 Score: 57
Period size: 20 Copynumber: 2.6 Consensus size: 19
5917776 TTAAAGGAGC
*
5917786 AATTAAATAAATTTTATTAA
1 AATTAAATAAA-TTGATTAA
*
5917806 AATTAAATGAAATTGATTAG
1 AATTAAAT-AAATTGATTAA
*
5917826 AATCAAATAAA
1 AATTAAATAAA
5917837 ATTAGGATAT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
19 3 0.11
20 21 0.78
21 3 0.11
ACGTcount: A:0.57, C:0.02, G:0.06, T:0.35
Consensus pattern (19 bp):
AATTAAATAAATTGATTAA
Found at i:5919224 original size:20 final size:22
Alignment explanation
Indices: 5919174--5919224 Score: 56
Period size: 20 Copynumber: 2.5 Consensus size: 22
5919164 CACTATTTAG
5919174 TTATTATTTTAAATATTTATCC
1 TTATTATTTTAAATATTTATCC
*
5919196 TCTA-T-TTTTAAA-ATTT-TTC
1 T-TATTATTTTAAATATTTATCC
5919215 TTATTATTTT
1 TTATTATTTT
5919225 TGTTATTTTC
Statistics
Matches: 25, Mismatches: 1, Indels: 8
0.74 0.03 0.24
Matches are distributed among these distances:
18 2 0.08
19 4 0.16
20 8 0.32
21 7 0.28
22 2 0.08
23 2 0.08
ACGTcount: A:0.27, C:0.08, G:0.00, T:0.65
Consensus pattern (22 bp):
TTATTATTTTAAATATTTATCC
Found at i:5920030 original size:20 final size:20
Alignment explanation
Indices: 5919986--5920033 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 20
5919976 AACTATTCGG
5919986 AAAA-TGATTCTTTTAAAAA
1 AAAATTGATTCTTTTAAAAA
**
5920005 TGAATTGATT-TTTTGAAAAA
1 AAAATTGATTCTTTT-AAAAA
5920025 AAAATTGAT
1 AAAATTGAT
5920034 ATATATATAT
Statistics
Matches: 23, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
19 6 0.26
20 17 0.74
ACGTcount: A:0.48, C:0.02, G:0.10, T:0.40
Consensus pattern (20 bp):
AAAATTGATTCTTTTAAAAA
Found at i:5920073 original size:13 final size:13
Alignment explanation
Indices: 5920055--5920079 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
5920045 GTATTGCTTG
5920055 AAATATTTTTTAA
1 AAATATTTTTTAA
5920068 AAATATTTTTTA
1 AAATATTTTTTA
5920080 TTATTTGACA
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:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (13 bp):
AAATATTTTTTAA
Found at i:5922869 original size:24 final size:26
Alignment explanation
Indices: 5922819--5922891 Score: 89
Period size: 24 Copynumber: 2.9 Consensus size: 26
5922809 AAAATAAAAA
*
5922819 TAAATAATTTAATCATATTTTATTAT
1 TAAATAATATAATCATATTTTATTAT
*
5922845 TAAATAATATAATTAT-TTTTA-TAT
1 TAAATAATATAATCATATTTTATTAT
* *
5922869 TAAATTATATAA-AATATTTTATT
1 TAAATAATATAATCATATTTTATT
5922892 TCAAATTATA
Statistics
Matches: 41, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
23 2 0.05
24 19 0.46
25 6 0.15
26 14 0.34
ACGTcount: A:0.45, C:0.01, G:0.00, T:0.53
Consensus pattern (26 bp):
TAAATAATATAATCATATTTTATTAT
Found at i:5922897 original size:24 final size:22
Alignment explanation
Indices: 5922833--5922902 Score: 68
Period size: 24 Copynumber: 2.9 Consensus size: 22
5922823 TAATTTAATC
*
5922833 ATATTTTATTATTAAATAATATAA
1 ATATTTTA-T-TTAAATTATATAA
*
5922857 TTATTTTTATATTAAATTATATAAA
1 ATA-TTTTAT-TTAAATTATAT-AA
5922882 ATATTTTATTTCAAATTATAT
1 ATATTTTATTT-AAATTATAT
5922903 TTTGAAATAA
Statistics
Matches: 40, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
23 2 0.05
24 29 0.73
25 9 0.22
ACGTcount: A:0.44, C:0.01, G:0.00, T:0.54
Consensus pattern (22 bp):
ATATTTTATTTAAATTATATAA
Found at i:5922942 original size:23 final size:25
Alignment explanation
Indices: 5922907--5922970 Score: 87
Period size: 23 Copynumber: 2.6 Consensus size: 25
5922897 TTATATTTTG
*
5922907 AAATAAAATATTTTATATT-AAATT
1 AAATTAAATATTTTATATTAAAATT
5922931 AAATT-AATATTTTATATTAAAATT
1 AAATTAAATATTTTATATTAAAATT
*
5922955 ATATTAAAATATTTTA
1 AAATT-AAATATTTTA
5922971 AATATTTTAT
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
23 13 0.37
24 13 0.37
26 9 0.26
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (25 bp):
AAATTAAATATTTTATATTAAAATT
Found at i:5922958 original size:18 final size:18
Alignment explanation
Indices: 5922894--5922959 Score: 62
Period size: 18 Copynumber: 3.6 Consensus size: 18
5922884 ATTTTATTTC
*
5922894 AAATTATATTTTGAAATAA
1 AAATTATATTTT-AAATTA
* *
5922913 AATATTTTATATTAAATT-
1 AA-ATTATATTTTAAATTA
*
5922931 AAATTAATATTTTATATTA
1 AAATT-ATATTTTAAATTA
5922950 AAATTATATT
1 AAATTATATT
5922960 AAAATATTTT
Statistics
Matches: 38, Mismatches: 6, Indels: 7
0.75 0.12 0.14
Matches are distributed among these distances:
17 3 0.08
18 16 0.42
19 11 0.29
20 8 0.21
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (18 bp):
AAATTATATTTTAAATTA
Found at i:5927955 original size:25 final size:25
Alignment explanation
Indices: 5927900--5927955 Score: 67
Period size: 25 Copynumber: 2.2 Consensus size: 25
5927890 ACATACTATT
* * *
5927900 TACAGAATACGCCATAAGGCCTTCA
1 TACAGAATACACCACAAGGCCTACA
* *
5927925 TTCAGAATACACCACAAGGGCTACA
1 TACAGAATACACCACAAGGCCTACA
5927950 TACAGA
1 TACAGA
5927956 GTCACATGTT
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.39, C:0.27, G:0.16, T:0.18
Consensus pattern (25 bp):
TACAGAATACACCACAAGGCCTACA
Found at i:5937466 original size:32 final size:32
Alignment explanation
Indices: 5937420--5937499 Score: 115
Period size: 32 Copynumber: 2.5 Consensus size: 32
5937410 TTTCAATCAT
*
5937420 TTCAATATCCAACAAGTTTAAAACATAATAAA
1 TTCAATATCCAACAAATTTAAAACATAATAAA
* * *
5937452 TTCAATGTCTAACAAATTTAAAACATAATAAT
1 TTCAATATCCAACAAATTTAAAACATAATAAA
*
5937484 TTCAAAATCCAACAAA
1 TTCAATATCCAACAAA
5937500 CTAATTTCAG
Statistics
Matches: 41, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
32 41 1.00
ACGTcount: A:0.53, C:0.16, G:0.03, T:0.29
Consensus pattern (32 bp):
TTCAATATCCAACAAATTTAAAACATAATAAA
Found at i:5938951 original size:21 final size:21
Alignment explanation
Indices: 5938927--5938968 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
5938917 ACACAAAAAT
*
5938927 TTACAAATTAATATGCAATTA
1 TTACAAATCAATATGCAATTA
*
5938948 TTACAAATCAATGTGCAATTA
1 TTACAAATCAATATGCAATTA
5938969 ATTTGAAAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.45, C:0.12, G:0.07, T:0.36
Consensus pattern (21 bp):
TTACAAATCAATATGCAATTA
Found at i:5941049 original size:4 final size:4
Alignment explanation
Indices: 5941040--5941076 Score: 74
Period size: 4 Copynumber: 9.2 Consensus size: 4
5941030 TTATTACTGA
5941040 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT A
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT A
5941077 TATCTGTATT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 33 1.00
ACGTcount: A:0.51, C:0.24, G:0.00, T:0.24
Consensus pattern (4 bp):
ACAT
Found at i:5945464 original size:8 final size:8
Alignment explanation
Indices: 5945451--5945485 Score: 52
Period size: 8 Copynumber: 4.1 Consensus size: 8
5945441 AAAAATTCGT
5945451 AATAATAA
1 AATAATAA
5945459 AATAATAA
1 AATAATAA
5945467 AATAATAA
1 AATAATAA
5945475 GAGATAATAA
1 -A-ATAATAA
5945485 A
1 A
5945486 TACAATATTT
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
8 16 0.64
9 2 0.08
10 7 0.28
ACGTcount: A:0.71, C:0.00, G:0.06, T:0.23
Consensus pattern (8 bp):
AATAATAA
Found at i:5951817 original size:19 final size:15
Alignment explanation
Indices: 5951779--5951808 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
5951769 ATGTTTCAAC
5951779 TTAATAATGTTGTTA
1 TTAATAATGTTGTTA
5951794 TTAATGAATGTTGTT
1 TTAAT-AATGTTGTT
5951809 GTATTTAATT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.30, C:0.00, G:0.17, T:0.53
Consensus pattern (15 bp):
TTAATAATGTTGTTA
Found at i:5961990 original size:20 final size:21
Alignment explanation
Indices: 5961932--5961990 Score: 57
Period size: 21 Copynumber: 2.8 Consensus size: 21
5961922 TTTTGAAATT
* *
5961932 ATATAAAAAATTATGAGGATA
1 ATATAAAAAATAATGAGGAGA
* *
5961953 AAATAAAAAAAAATATGAGG-GA
1 ATAT-AAAAAATA-ATGAGGAGA
5961975 ATATAAAAAATAATGA
1 ATATAAAAAATAATGA
5961991 AAAATACTAA
Statistics
Matches: 30, Mismatches: 6, Indels: 5
0.73 0.15 0.12
Matches are distributed among these distances:
20 4 0.13
21 10 0.33
22 10 0.33
23 6 0.20
ACGTcount: A:0.64, C:0.00, G:0.14, T:0.22
Consensus pattern (21 bp):
ATATAAAAAATAATGAGGAGA
Found at i:5963419 original size:11 final size:11
Alignment explanation
Indices: 5963403--5963430 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
5963393 AAAATATTAA
5963403 TTTTTTTAAAT
1 TTTTTTTAAAT
5963414 TTTTTTTAAAT
1 TTTTTTTAAAT
5963425 TTTTTT
1 TTTTTT
5963431 CAAACATGGC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (11 bp):
TTTTTTTAAAT
Found at i:5965143 original size:94 final size:95
Alignment explanation
Indices: 5965008--5965196 Score: 362
Period size: 94 Copynumber: 2.0 Consensus size: 95
5964998 CAAAGACAAG
5965008 CAATCAAAATATATATATATTTATATATATATATAAACTGAATGCAAAAGGTGATTCTTTTTTTC
1 CAATCAAAATATATATATATTTATATATATATATAAACTGAATGCAAAAGGTGATTCTTTTTTTC
5965073 GATTTATTTTTATTTTTTCGAAACAAATAA
66 GATTTATTTTTATTTTTTCGAAACAAATAA
*
5965103 CAATCAAAAT-TATATATATTTTTATATATATATAAACTGAATGCAAAAGGTGATTCTTTTTTTC
1 CAATCAAAATATATATATATTTATATATATATATAAACTGAATGCAAAAGGTGATTCTTTTTTTC
5965167 GATTTATTTTTATTTTTTCGAAACAAATAA
66 GATTTATTTTTATTTTTTCGAAACAAATAA
5965197 GAGTAAAAAA
Statistics
Matches: 93, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
94 83 0.89
95 10 0.11
ACGTcount: A:0.39, C:0.08, G:0.07, T:0.45
Consensus pattern (95 bp):
CAATCAAAATATATATATATTTATATATATATATAAACTGAATGCAAAAGGTGATTCTTTTTTTC
GATTTATTTTTATTTTTTCGAAACAAATAA
Found at i:5965219 original size:94 final size:94
Alignment explanation
Indices: 5965024--5965220 Score: 304
Period size: 94 Copynumber: 2.1 Consensus size: 94
5965014 AAATATATAT
*
5965024 ATATTTATATATATATATAAACTGAATGCAAAAGGTGATTCTTTTTTTCGATTTATTTTTATTTT
1 ATATTTTTATATATATATAAACTGAATGCAAAAGGTGATTCTTTTTTTCGATTTATTTTTATTTT
* ** * *
5965089 TTCGAAACAAATAACAATCAAAATTATAT
66 TTCGAAACAAATAACAATAAAAAAAAGAG
5965118 ATATTTTTATATATATATAAACTGAATGCAAAAGGTGATTCTTTTTTTCGATTTATTTTTATTTT
1 ATATTTTTATATATATATAAACTGAATGCAAAAGGTGATTCTTTTTTTCGATTTATTTTTATTTT
* * *
5965183 TTCGAAACAAATAAGAGTAAAAAAAAGGG
66 TTCGAAACAAATAACAATAAAAAAAAGAG
*
5965212 ATTTTTTTA
1 ATATTTTTA
5965221 CCTGTGTCGG
Statistics
Matches: 93, Mismatches: 10, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
94 93 1.00
ACGTcount: A:0.39, C:0.07, G:0.10, T:0.45
Consensus pattern (94 bp):
ATATTTTTATATATATATAAACTGAATGCAAAAGGTGATTCTTTTTTTCGATTTATTTTTATTTT
TTCGAAACAAATAACAATAAAAAAAAGAG
Found at i:5966164 original size:78 final size:79
Alignment explanation
Indices: 5966060--5966222 Score: 312
Period size: 78 Copynumber: 2.1 Consensus size: 79
5966050 ATTTAATCCC
5966060 TTATTT-GGTTAATTTTGCCTCTTTATTTACTATATTATTTATTTTAGTAACTAAAATTTATGTT
1 TTATTTAGGTTAATTTTGCCTCTTTATTTACTATATTATTTATTTTAGTAACTAAAATTTATGTT
5966124 ATTTATATTTCCTT
66 ATTTATATTTCCTT
5966138 TTATTTAGGTTAATTTT-CCTCTTTATTTACTATATTATTTATTTTAGTAACTAAAATTTATGTT
1 TTATTTAGGTTAATTTTGCCTCTTTATTTACTATATTATTTATTTTAGTAACTAAAATTTATGTT
5966202 ATTTATATTTCCTT
66 ATTTATATTTCCTT
5966216 TTATTTA
1 TTATTTA
5966223 TACACTTTAT
Statistics
Matches: 84, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
78 74 0.88
79 10 0.12
ACGTcount: A:0.26, C:0.09, G:0.06, T:0.60
Consensus pattern (79 bp):
TTATTTAGGTTAATTTTGCCTCTTTATTTACTATATTATTTATTTTAGTAACTAAAATTTATGTT
ATTTATATTTCCTT
Found at i:5966393 original size:5 final size:5
Alignment explanation
Indices: 5966378--5966415 Score: 69
Period size: 5 Copynumber: 7.8 Consensus size: 5
5966368 AACATGTTTC
5966378 TTTTA -TTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTT
1 TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTT
5966416 CTGCTTATTA
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
4 4 0.12
5 28 0.88
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (5 bp):
TTTTA
Found at i:5978056 original size:44 final size:44
Alignment explanation
Indices: 5977993--5978477 Score: 316
Period size: 44 Copynumber: 10.6 Consensus size: 44
5977983 GTTACCAAGG
* * * *
5977993 CAAATCTTATCTCCCTGAAGCTACAGTAGAGCAGATTAAAGCCA
1 CAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCTA
* * * * * * *
5978037 CAAATCTTATCTTCTTGAAGTTGTAGTAGAACAAATTGAAGCTA
1 CAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCTA
* * * * * *
5978081 AAATATCCTAT-ACCCTAAAGTTGCAGT-GAGTCGGATTAAAGTTA
1 CAA-ATCTTATCTCCCTGAAGTTGCAGTGGAG-CAGATTAAAGCTA
* * *
5978125 CCATGGCGAATCTTATTTCCTTGAAGTTGTAGTGGAGCA-AGTTAAAGCTA
1 -CA-----AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGA-TTAAAGCTA
*
5978175 CAAATCTTATCTCCCTGAAGTTGCAGTGGAGCATATTAAAGCTA
1 CAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCTA
* *
5978219 CAAATCTAATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAACTA
1 CAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCTA
* * * *
5978263 CAAATCTTATCTCGCTGAAGCTGCAGTGGAGTAGATTAAAGCGA
1 CAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCTA
* * *
5978307 CAAATCCTATAC-CTCTGAAGTTGCAGTGG-GTCAGATTAAATCTACCA
1 CAAATCTTAT-CTCCCTGAAGTTGCAGTGGAG-CAGATTAAAGCT---A
* ** *
5978354 CAGAGAGTCTTAT-TCCCCTGAAGTTGGAGTAAAACAGATTAAAGCTACAAGCTA
1 CA-A-A-TCTTATCT-CCCTGAAGTTGCAGTGGAGCAGA-T-----TA-AAGCTA
* * * * *
5978408 CAAATCTTATCTCCTTGAAGTTGTAGTGGAACAAATTGAAGCTA
1 CAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCTA
* * * *
5978452 CGAATCTCATCTCCATAAAGTTGCAG
1 CAAATCTTATCTCCCTGAAGTTGCAG
5978478 CAGAGTAGAT
Statistics
Matches: 345, Mismatches: 65, Indels: 62
0.73 0.14 0.13
Matches are distributed among these distances:
43 3 0.01
44 233 0.68
45 10 0.03
47 3 0.01
48 1 0.00
49 10 0.03
50 45 0.13
51 28 0.08
52 2 0.01
53 1 0.00
54 3 0.01
56 2 0.01
57 4 0.01
ACGTcount: A:0.34, C:0.19, G:0.19, T:0.28
Consensus pattern (44 bp):
CAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCTA
Found at i:5978217 original size:138 final size:140
Alignment explanation
Indices: 5977950--5978333 Score: 366
Period size: 138 Copynumber: 2.8 Consensus size: 140
5977940 CCATAAATCT
* *
5977950 TATACCCCTGAAGTTGCAGTGAGTCGGATTGAAGTTACCAAGGCAAATCTTATCTCCCTGAAGCT
1 TATACCCCTAAAGTTGCAGTGAGTCGGATTAAAGTTACCAAGGCAAATCTTATCTCCCTGAAGCT
* * * *
5978015 ACAGTAGAGCAGATTAAAGCCACAAATCTTATCTTCTTGAAGTTGTAGTAGAACAAATTGAAGCT
66 ACAGTAGAGCAGATTAAAGCCACAAATCTTATCTCCCTGAAGTTGCAGTAGAACAAATTAAAGCT
5978080 A-AAATATCC
131 ACAAATATCC
* * * * *
5978089 TATA-CCCTAAAGTTGCAGTGAGTCGGATTAAAGTTACCATGGCGAATCTTATTTCCTTGAAGTT
1 TATACCCCTAAAGTTGCAGTGAGTCGGATTAAAGTTACCAAGGCAAATCTTATCTCCCTGAAGCT
** * * * * *
5978153 GTAGTGGAGCA-AGTTAAAGCTACAAATCTTATCTCCCTGAAGTTGCAGTGGAGCATATTAAAGC
66 ACAGTAGAGCAGA-TTAAAGCCACAAATCTTATCTCCCTGAAGTTGCAGTAGAACAAATTAAAGC
5978217 TAC-AA-AT-C
130 TACAAATATCC
* * * *
5978225 TA-ATCTCCCTGAAGTTGCAGTGGAG-CAGATTAAA---A-CTA--CAAATCTTATCTCGCTGAA
1 TATA-C-CCCTAAAGTTGCAGT-GAGTCGGATTAAAGTTACCAAGGCAAATCTTATCTCCCTGAA
* * * * * *
5978282 GCTGCAGTGGAGTAGATTAAAGCGACAAATCCTATAC-CTCTGAAGTTGCAGT
63 GCTACAGTAGAGCAGATTAAAGCCACAAATCTTAT-CTCCCTGAAGTTGCAGT
5978334 GGGTCAGATT
Statistics
Matches: 205, Mismatches: 32, Indels: 23
0.79 0.12 0.09
Matches are distributed among these distances:
132 57 0.28
133 2 0.01
134 1 0.00
135 2 0.01
136 3 0.01
137 3 0.01
138 130 0.63
139 7 0.03
ACGTcount: A:0.33, C:0.19, G:0.20, T:0.28
Consensus pattern (140 bp):
TATACCCCTAAAGTTGCAGTGAGTCGGATTAAAGTTACCAAGGCAAATCTTATCTCCCTGAAGCT
ACAGTAGAGCAGATTAAAGCCACAAATCTTATCTCCCTGAAGTTGCAGTAGAACAAATTAAAGCT
ACAAATATCC
Found at i:5980093 original size:5 final size:5
Alignment explanation
Indices: 5980083--5980110 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
5980073 TACCAACATG
5980083 TTTAT TTTAT TTTAT TTTAT TTTAT TTT
1 TTTAT TTTAT TTTAT TTTAT TTTAT TTT
5980111 CTGCTTATTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (5 bp):
TTTAT
Found at i:5983401 original size:42 final size:42
Alignment explanation
Indices: 5983335--5983429 Score: 127
Period size: 42 Copynumber: 2.3 Consensus size: 42
5983325 ACGACCTGGA
* *
5983335 CACATGCCCATGTCTTTGCCCGTGTAACTCACAGGGCTTGGG
1 CACACGCCCATGTCCTTGCCCGTGTAACTCACAGGGCTTGGG
* * ** *
5983377 CATACGCCCATGTCCTTGCTCGTGTGGCTCACATGGCTTGGG
1 CACACGCCCATGTCCTTGCCCGTGTAACTCACAGGGCTTGGG
5983419 CACACGCCCAT
1 CACACGCCCAT
5983430 ATTCCTGGCC
Statistics
Matches: 45, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
42 45 1.00
ACGTcount: A:0.16, C:0.34, G:0.25, T:0.25
Consensus pattern (42 bp):
CACACGCCCATGTCCTTGCCCGTGTAACTCACAGGGCTTGGG
Found at i:5983443 original size:42 final size:42
Alignment explanation
Indices: 5983335--5983445 Score: 116
Period size: 42 Copynumber: 2.6 Consensus size: 42
5983325 ACGACCTGGA
* * * * **
5983335 CACATGCCCATGTCTTTGCCCGTGTAACTCACAGGGCTTGGG
1 CACACGCCCATGTCCTGGCTCGTGTGGCTCACAGGGCTTGGG
* * *
5983377 CATACGCCCATGTCCTTGCTCGTGTGGCTCACATGGCTTGGG
1 CACACGCCCATGTCCTGGCTCGTGTGGCTCACAGGGCTTGGG
*
5983419 CACACGCCCATATTCCTGGC-CGTGTGG
1 CACACGCCCAT-GTCCTGGCTCGTGTGG
5983446 TTCTAAAACG
Statistics
Matches: 58, Mismatches: 10, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
42 52 0.90
43 6 0.10
ACGTcount: A:0.14, C:0.32, G:0.27, T:0.26
Consensus pattern (42 bp):
CACACGCCCATGTCCTGGCTCGTGTGGCTCACAGGGCTTGGG
Found at i:5990898 original size:9 final size:10
Alignment explanation
Indices: 5990884--5990926 Score: 52
Period size: 10 Copynumber: 4.2 Consensus size: 10
5990874 ATTAATATCC
5990884 AAAT-AAGTA
1 AAATAAAGTA
*
5990893 AAATAAAATA
1 AAATAAAGTA
5990903 AAATAAAGTAA
1 AAATAAAGT-A
5990914 TAAATAAAGTA
1 -AAATAAAGTA
5990925 AA
1 AA
5990927 GAAAAAAATA
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
9 4 0.14
10 14 0.48
11 2 0.07
12 9 0.31
ACGTcount: A:0.72, C:0.00, G:0.07, T:0.21
Consensus pattern (10 bp):
AAATAAAGTA
Found at i:5990920 original size:17 final size:16
Alignment explanation
Indices: 5990897--5990955 Score: 57
Period size: 17 Copynumber: 3.6 Consensus size: 16
5990887 TAAGTAAAAT
5990897 AAAATAAAATAAAGTA
1 AAAATAAAATAAAGTA
*
5990913 ATAAATAAAGTAAAG-A
1 A-AAATAAAATAAAGTA
* *
5990929 AAAAAATAAATAATAATA
1 AAAATA-AAATAA-AGTA
5990947 AAAATAAAA
1 AAAATAAAA
5990956 ATTGGGTTGC
Statistics
Matches: 34, Mismatches: 5, Indels: 7
0.74 0.11 0.15
Matches are distributed among these distances:
15 4 0.12
16 8 0.24
17 16 0.47
18 6 0.18
ACGTcount: A:0.76, C:0.00, G:0.05, T:0.19
Consensus pattern (16 bp):
AAAATAAAATAAAGTA
Found at i:5990955 original size:21 final size:21
Alignment explanation
Indices: 5990893--5990957 Score: 62
Period size: 22 Copynumber: 3.0 Consensus size: 21
5990883 CAAATAAGTA
*
5990893 AAATAAAATAAA-ATAAAGTAAT
1 AAATAAAATAAAGA-AAA-AAAT
*
5990915 AAATAAAGTAAAGAAAAAAAT
1 AAATAAAATAAAGAAAAAAAT
5990936 AAATAATAATAAA-AATAAAAAT
1 AAATAA-AATAAAGAA-AAAAAT
5990958 TGGGTTGCCT
Statistics
Matches: 37, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
21 11 0.30
22 25 0.68
23 1 0.03
ACGTcount: A:0.75, C:0.00, G:0.05, T:0.20
Consensus pattern (21 bp):
AAATAAAATAAAGAAAAAAAT
Found at i:6000117 original size:2 final size:2
Alignment explanation
Indices: 6000110--6000138 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
6000100 ATAAAAGGTT
6000110 AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
6000139 TGTTAGATTA
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:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:6013344 original size:1 final size:1
Alignment explanation
Indices: 6013340--6013370 Score: 62
Period size: 1 Copynumber: 31.0 Consensus size: 1
6013330 TTCTTTTCCC
6013340 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
6013371 CATTGTCGAC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 30 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:6014757 original size:21 final size:21
Alignment explanation
Indices: 6014718--6014757 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
6014708 AGCGACTTGT
***
6014718 TTTGCAAGAAACTTGACTTAA
1 TTTGCAAGAAACCAAACTTAA
6014739 TTTGCAAGAAACCAAACTT
1 TTTGCAAGAAACCAAACTT
6014758 TAGGTCTTCA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.40, C:0.17, G:0.12, T:0.30
Consensus pattern (21 bp):
TTTGCAAGAAACCAAACTTAA
Found at i:6018481 original size:22 final size:23
Alignment explanation
Indices: 6018449--6018492 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 23
6018439 TCTATTGAAA
6018449 ATTATCAAAATTAA-TCAAAATTT
1 ATTATCAAAATTAAGT-AAAATTT
6018472 ATTA-CAAAATTAAGTAAAATT
1 ATTATCAAAATTAAGTAAAATT
6018493 CAACATGTTC
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
22 15 0.75
23 5 0.25
ACGTcount: A:0.55, C:0.07, G:0.02, T:0.36
Consensus pattern (23 bp):
ATTATCAAAATTAAGTAAAATTT
Found at i:6019870 original size:43 final size:44
Alignment explanation
Indices: 6019753--6019871 Score: 113
Period size: 44 Copynumber: 2.7 Consensus size: 44
6019743 TGTGTGTTAT
* * * *
6019753 CGTGTAAGACCACGTCTAGGACGTTGGCATCGATTTGTGATTTA
1 CGTGTAAGACCATGTCTGGGACGTTGGCATTGATATGTGATTTA
* *
6019797 CGTGTAAAACTC-TAT-TGAGGACAG-TGGCATTGATATGTGA-TTA
1 CGTGTAAGAC-CATGTCTG-GGAC-GTTGGCATTGATATGTGATTTA
6019840 CAG-GTAAGACCATGTCTGGGACGTTGGCATTG
1 C-GTGTAAGACCATGTCTGGGACGTTGGCATTG
6019872 TACAAGCCTT
Statistics
Matches: 60, Mismatches: 8, Indels: 15
0.72 0.10 0.18
Matches are distributed among these distances:
42 2 0.03
43 25 0.42
44 31 0.52
45 2 0.03
ACGTcount: A:0.25, C:0.16, G:0.29, T:0.30
Consensus pattern (44 bp):
CGTGTAAGACCATGTCTGGGACGTTGGCATTGATATGTGATTTA
Found at i:6022816 original size:33 final size:33
Alignment explanation
Indices: 6022773--6022835 Score: 99
Period size: 33 Copynumber: 1.9 Consensus size: 33
6022763 GTGGGATTCC
6022773 GTGATAAGGGCACTTCCATAATAATTCTTTTCT
1 GTGATAAGGGCACTTCCATAATAATTCTTTTCT
* * *
6022806 GTGATGAGGGCGCTTCCGTAATAATTCTTT
1 GTGATAAGGGCACTTCCATAATAATTCTTT
6022836 GTATCTTTCC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
33 27 1.00
ACGTcount: A:0.24, C:0.17, G:0.21, T:0.38
Consensus pattern (33 bp):
GTGATAAGGGCACTTCCATAATAATTCTTTTCT
Found at i:6025389 original size:78 final size:79
Alignment explanation
Indices: 6025286--6025442 Score: 307
Period size: 78 Copynumber: 2.0 Consensus size: 79
6025276 AAATGAAAAT
6025286 GTCGTGCTAGTGAATGCTAATGATATAACTCTAATGACAATAAAATATCTACTCACAATAACAGT
1 GTCGTGCTAGTGAATGCTAATGATATAACTCTAATGACAATAAAATATCTACTCACAATAACAGT
6025351 GGCAATAATCATGC
66 GGCAATAATCATGC
6025365 GTCGTGCTAG-GAATGCTAATGATATAACTCTAATGACAATAAAATATCTACTCACAATAACAGT
1 GTCGTGCTAGTGAATGCTAATGATATAACTCTAATGACAATAAAATATCTACTCACAATAACAGT
6025429 GGCAATAATCATGC
66 GGCAATAATCATGC
6025443 CATAATTACT
Statistics
Matches: 78, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
78 68 0.87
79 10 0.13
ACGTcount: A:0.39, C:0.18, G:0.15, T:0.27
Consensus pattern (79 bp):
GTCGTGCTAGTGAATGCTAATGATATAACTCTAATGACAATAAAATATCTACTCACAATAACAGT
GGCAATAATCATGC
Found at i:6025496 original size:3 final size:3
Alignment explanation
Indices: 6025488--6025557 Score: 104
Period size: 3 Copynumber: 23.3 Consensus size: 3
6025478 AAGTAAAATA
* *
6025488 AAT AAT AAT AAT AAT AAT AAT GAT AAT AAT AAT AAT AAT AAT AAT AAC
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
**
6025536 AAT AAT AAT AAT GGT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT A
6025558 GGGGCAACAA
Statistics
Matches: 59, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 59 1.00
ACGTcount: A:0.63, C:0.01, G:0.04, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:6027237 original size:44 final size:44
Alignment explanation
Indices: 6027187--6027650 Score: 267
Period size: 44 Copynumber: 10.3 Consensus size: 44
6027177 TCATTCTAAC
* *
6027187 CCACTGCAACTTCAGGG-GTATAGGAATTGTAGTTTCAATCTATT
1 CCACTGCAACTTCAGGGAG-ATAGGAATTGTAGCTTCAATCTACT
* * *
6027231 CCACTGCAACTTTAGGGAGATAGGACTTGTAGCTTCAATCTGCT
1 CCACTGCAACTTCAGGGAGATAGGAATTGTAGCTTCAATCTACT
* * * *
6027275 CCACTGCAAGTTCAGGGAGATAAGATTTGTAACTTGTAGATTTAATCTATT
1 CCACTGCAACTTCAGGGAGAT-AG----G-AA-TTGTAGCTTCAATCTACT
* * * * * *
6027326 TCACTGCAACTTCAGGGAAATA-AAACTCGCTATGGTAGATTTAATTCGAC-
1 CCACTGCAACTTCAGGGAGATAGGAA-----T-T-GTAGCTTCAA-TCTACT
* * * * * *
6027376 CCACTGTAACTTCAGAGG-CATAAGATTTGTCA-CTTTAATCTTCT
1 CCACTGCAACTTCAG-GGAGATAGGAATTGT-AGCTTCAATCTACT
** * * *
6027420 CCACTGCAACTTCAGCAAGATAAGATTTGTAGCTTCAATCTGCT
1 CCACTGCAACTTCAGGGAGATAGGAATTGTAGCTTCAATCTACT
* * * * * *
6027464 CCACTACAACTTCAGGGAGATAAGATTTTTAGCTTTAATCTGCT
1 CCACTGCAACTTCAGGGAGATAGGAATTGTAGCTTCAATCTACT
* * * * * *
6027508 -CACTGTAACTTTAGGGAGATAAGATTTGTAGTTTCAATCTGCT
1 CCACTGCAACTTCAGGGAGATAGGAATTGTAGCTTCAATCTACT
* * * * * *
6027551 CCACTGCAACTTCAAGGAGATAAGATTTGTAGTTTTAATCTGCT
1 CCACTGCAACTTCAGGGAGATAGGAATTGTAGCTTCAATCTACT
* * * * *
6027595 CCACTACAACTTCAGGAAGAT-GAGATTTGTAGCTTTAATCTGCT
1 CCACTGCAACTTCAGGGAGATAG-GAATTGTAGCTTCAATCTACT
6027639 CCACTGCAACTT
1 CCACTGCAACTT
6027651 TAAGAAGATA
Statistics
Matches: 344, Mismatches: 53, Indels: 46
0.78 0.12 0.10
Matches are distributed among these distances:
43 41 0.12
44 227 0.66
45 5 0.01
46 1 0.00
48 2 0.01
49 2 0.01
50 28 0.08
51 38 0.11
ACGTcount: A:0.29, C:0.20, G:0.18, T:0.33
Consensus pattern (44 bp):
CCACTGCAACTTCAGGGAGATAGGAATTGTAGCTTCAATCTACT
Found at i:6027553 original size:131 final size:132
Alignment explanation
Indices: 6027376--6027665 Score: 408
Period size: 131 Copynumber: 2.2 Consensus size: 132
6027366 TTAATTCGAC
* * *
6027376 CCACTGTAACTTCAGAGG-CATAAGATTTGTCACTTTAATCTTCTCCACTGCAACTTC-AGCAAG
1 CCACTGTAACTTTAG-GGAGATAAGATTTGTCACTTTAATCTGCTCCACTGCAACTTCAAG-AAG
* *
6027439 ATAAGATTTGTAGCTTCAATCTGCTCCACTACAACTTCAGGGAGATAAGATTTTTAGCTTTAATC
64 ATAAGATTTGTAGCTTCAATCTGCTCCACTACAACTTCAGGAAGATAAGATTTGTAGCTTTAATC
6027504 TGCT
129 TGCT
* *
6027508 -CACTGTAACTTTAGGGAGATAAGATTTGT-AGTTTCAATCTGCTCCACTGCAACTTCAAGGAGA
1 CCACTGTAACTTTAGGGAGATAAGATTTGTCACTTT-AATCTGCTCCACTGCAACTTCAAGAAGA
* * *
6027571 TAAGATTTGTAGTTTTAATCTGCTCCACTACAACTTCAGGAAGATGAGATTTGTAGCTTTAATCT
65 TAAGATTTGTAGCTTCAATCTGCTCCACTACAACTTCAGGAAGATAAGATTTGTAGCTTTAATCT
6027636 GCT
130 GCT
* * *
6027639 CCACTGCAACTTTAAGAAGATAAGATT
1 CCACTGTAACTTTAGGGAGATAAGATT
6027666 CGCTATGGTA
Statistics
Matches: 141, Mismatches: 13, Indels: 8
0.87 0.08 0.05
Matches are distributed among these distances:
130 6 0.04
131 110 0.78
132 25 0.18
ACGTcount: A:0.30, C:0.20, G:0.17, T:0.33
Consensus pattern (132 bp):
CCACTGTAACTTTAGGGAGATAAGATTTGTCACTTTAATCTGCTCCACTGCAACTTCAAGAAGAT
AAGATTTGTAGCTTCAATCTGCTCCACTACAACTTCAGGAAGATAAGATTTGTAGCTTTAATCTG
CT
Found at i:6027658 original size:44 final size:44
Alignment explanation
Indices: 6027376--6027665 Score: 347
Period size: 44 Copynumber: 6.6 Consensus size: 44
6027366 TTAATTCGAC
* * *
6027376 CCACTGTAACTTC-AGAGGCATAAGATTTGTCA-CTTTAATCTTCT
1 CCACTGCAACTTCAAGAAG-ATAAGATTTGT-AGCTTTAATCTGCT
*
6027420 CCACTGCAACTTC-AGCAAGATAAGATTTGTAGCTTCAATCTGCT
1 CCACTGCAACTTCAAG-AAGATAAGATTTGTAGCTTTAATCTGCT
* * * *
6027464 CCACTACAACTTCAGGGAGATAAGATTTTTAGCTTTAATCTGCT
1 CCACTGCAACTTCAAGAAGATAAGATTTGTAGCTTTAATCTGCT
* * * *
6027508 -CACTGTAACTTTAGGGAGATAAGATTTGTAG-TTTCAATCTGCT
1 CCACTGCAACTTCAAGAAGATAAGATTTGTAGCTTT-AATCTGCT
* *
6027551 CCACTGCAACTTCAAGGAGATAAGATTTGTAGTTTTAATCTGCT
1 CCACTGCAACTTCAAGAAGATAAGATTTGTAGCTTTAATCTGCT
* * *
6027595 CCACTACAACTTCAGGAAGATGAGATTTGTAGCTTTAATCTGCT
1 CCACTGCAACTTCAAGAAGATAAGATTTGTAGCTTTAATCTGCT
*
6027639 CCACTGCAACTTTAAGAAGATAAGATT
1 CCACTGCAACTTCAAGAAGATAAGATT
6027666 CGCTATGGTA
Statistics
Matches: 215, Mismatches: 25, Indels: 12
0.85 0.10 0.05
Matches are distributed among these distances:
42 3 0.01
43 36 0.17
44 170 0.79
45 6 0.03
ACGTcount: A:0.30, C:0.20, G:0.17, T:0.33
Consensus pattern (44 bp):
CCACTGCAACTTCAAGAAGATAAGATTTGTAGCTTTAATCTGCT
Found at i:6027743 original size:138 final size:131
Alignment explanation
Indices: 6027418--6027759 Score: 395
Period size: 131 Copynumber: 2.6 Consensus size: 131
6027408 CTTTAATCTT
* *
6027418 CTCCACTGCAACTTC-AGCAAGATAAGATTTGTAGCTTCAATCTGCTCCACTACAACTTCAGGGA
1 CTCCACTGCAACTTCAAG-GAGATAAGATTTGTAGCTTAAATCTGCTCCACTACAACTTCAGGGA
* * * * *
6027482 GATAAGATTTTTAGCTTTAATCTGCTCACTGTAACTTTAGGGAGATAAGATTTGTAGTTTCAATC
65 GATAAGATTTGTAGCTTTAATCTGCTCACTGCAACTTTAAGAAGATAAGATTTGTAGATTCAATC
*
6027547 TG
130 CG
* * *
6027549 CTCCACTGCAACTTCAAGGAGATAAGATTTGTAGTTTTAATCTGCTCCACTACAACTTCAGGAAG
1 CTCCACTGCAACTTCAAGGAGATAAGATTTGTAGCTTAAATCTGCTCCACTACAACTTCAGGGAG
*
6027614 ATGAGATTTGTAGCTTTAATCTGCTCCACTGCAACTTTAAGAAGATAAGATTCGCTATGGTAGAT
66 ATAAGATTTGTAGCTTTAATCTGCT-CACTGCAACTTTAAGAAGATAAGA-T---T-T-GTAGAT
6027679 TCAATCCG
124 TCAATCCG
* * * * * *
6027687 -TCCCATTGCGACTTCAAGG-GTGTAAGATCTGTAGCTTAAATCTGC-CTCACTGCAACTTTAGG
1 CT-CCACTGCAACTTCAAGGAG-ATAAGATTTGTAGCTTAAATCTGCTC-CACTACAACTTCAGG
6027749 GAGATAAGATT
63 GAGATAAGATT
6027760 CGCTATAGTG
Statistics
Matches: 179, Mismatches: 21, Indels: 15
0.83 0.10 0.07
Matches are distributed among these distances:
131 81 0.45
132 23 0.13
133 1 0.01
136 1 0.01
137 4 0.02
138 69 0.39
ACGTcount: A:0.29, C:0.20, G:0.19, T:0.32
Consensus pattern (131 bp):
CTCCACTGCAACTTCAAGGAGATAAGATTTGTAGCTTAAATCTGCTCCACTACAACTTCAGGGAG
ATAAGATTTGTAGCTTTAATCTGCTCACTGCAACTTTAAGAAGATAAGATTTGTAGATTCAATCC
G
Found at i:6037738 original size:44 final size:44
Alignment explanation
Indices: 6037688--6038151 Score: 267
Period size: 44 Copynumber: 10.3 Consensus size: 44
6037678 TCATTCTAAC
* *
6037688 CCACTGCAACTTCAGGG-GTATAGGAATTGTAGTTTCAATCTATT
1 CCACTGCAACTTCAGGGAG-ATAGGAATTGTAGCTTCAATCTACT
* * *
6037732 CCACTGCAACTTTAGGGAGATAGGACTTGTAGCTTCAATCTGCT
1 CCACTGCAACTTCAGGGAGATAGGAATTGTAGCTTCAATCTACT
* * * *
6037776 CCACTGCAAGTTCAGGGAGATAAGATTTGTAACTTGTAGATTTAATCTATT
1 CCACTGCAACTTCAGGGAGAT-AG----G-AA-TTGTAGCTTCAATCTACT
* * * * * *
6037827 TCACTGCAACTTCAGGGAAATA-AAACTCGCTATGGTAGATTTAATTCGAC-
1 CCACTGCAACTTCAGGGAGATAGGAA-----T-T-GTAGCTTCAA-TCTACT
* * * * * *
6037877 CCACTGTAACTTCAGAGG-CATAAGATTTGTCA-CTTTAATCTTCT
1 CCACTGCAACTTCAG-GGAGATAGGAATTGT-AGCTTCAATCTACT
** * * *
6037921 CCACTGCAACTTCAGCAAGATAAGATTTGTAGCTTCAATCTGCT
1 CCACTGCAACTTCAGGGAGATAGGAATTGTAGCTTCAATCTACT
* * * * * *
6037965 CCACTACAACTTCAGGGAGATAAGATTTTTAGCTTTAATCTGCT
1 CCACTGCAACTTCAGGGAGATAGGAATTGTAGCTTCAATCTACT
* * * * * *
6038009 -CACTGTAACTTTAGGGAGATAAGATTTGTAGTTTCAATCTGCT
1 CCACTGCAACTTCAGGGAGATAGGAATTGTAGCTTCAATCTACT
* * * * * *
6038052 CCACTGCAACTTCAAGGAGATAAGATTTGTAGTTTTAATCTGCT
1 CCACTGCAACTTCAGGGAGATAGGAATTGTAGCTTCAATCTACT
* * * * *
6038096 CCACTACAACTTCAGGAAGAT-GAGATTTGTAGCTTTAATCTGCT
1 CCACTGCAACTTCAGGGAGATAG-GAATTGTAGCTTCAATCTACT
6038140 CCACTGCAACTT
1 CCACTGCAACTT
6038152 TAAGAAGATA
Statistics
Matches: 344, Mismatches: 53, Indels: 46
0.78 0.12 0.10
Matches are distributed among these distances:
43 41 0.12
44 227 0.66
45 5 0.01
46 1 0.00
48 2 0.01
49 2 0.01
50 28 0.08
51 38 0.11
ACGTcount: A:0.29, C:0.20, G:0.18, T:0.33
Consensus pattern (44 bp):
CCACTGCAACTTCAGGGAGATAGGAATTGTAGCTTCAATCTACT
Found at i:6038054 original size:131 final size:132
Alignment explanation
Indices: 6037877--6038166 Score: 408
Period size: 131 Copynumber: 2.2 Consensus size: 132
6037867 TTAATTCGAC
* * *
6037877 CCACTGTAACTTCAGAGG-CATAAGATTTGTCACTTTAATCTTCTCCACTGCAACTTC-AGCAAG
1 CCACTGTAACTTTAG-GGAGATAAGATTTGTCACTTTAATCTGCTCCACTGCAACTTCAAG-AAG
* *
6037940 ATAAGATTTGTAGCTTCAATCTGCTCCACTACAACTTCAGGGAGATAAGATTTTTAGCTTTAATC
64 ATAAGATTTGTAGCTTCAATCTGCTCCACTACAACTTCAGGAAGATAAGATTTGTAGCTTTAATC
6038005 TGCT
129 TGCT
* *
6038009 -CACTGTAACTTTAGGGAGATAAGATTTGT-AGTTTCAATCTGCTCCACTGCAACTTCAAGGAGA
1 CCACTGTAACTTTAGGGAGATAAGATTTGTCACTTT-AATCTGCTCCACTGCAACTTCAAGAAGA
* * *
6038072 TAAGATTTGTAGTTTTAATCTGCTCCACTACAACTTCAGGAAGATGAGATTTGTAGCTTTAATCT
65 TAAGATTTGTAGCTTCAATCTGCTCCACTACAACTTCAGGAAGATAAGATTTGTAGCTTTAATCT
6038137 GCT
130 GCT
* * *
6038140 CCACTGCAACTTTAAGAAGATAAGATT
1 CCACTGTAACTTTAGGGAGATAAGATT
6038167 CGCTATGGTA
Statistics
Matches: 141, Mismatches: 13, Indels: 8
0.87 0.08 0.05
Matches are distributed among these distances:
130 6 0.04
131 110 0.78
132 25 0.18
ACGTcount: A:0.30, C:0.20, G:0.17, T:0.33
Consensus pattern (132 bp):
CCACTGTAACTTTAGGGAGATAAGATTTGTCACTTTAATCTGCTCCACTGCAACTTCAAGAAGAT
AAGATTTGTAGCTTCAATCTGCTCCACTACAACTTCAGGAAGATAAGATTTGTAGCTTTAATCTG
CT
Found at i:6038159 original size:44 final size:44
Alignment explanation
Indices: 6037877--6038166 Score: 347
Period size: 44 Copynumber: 6.6 Consensus size: 44
6037867 TTAATTCGAC
* * *
6037877 CCACTGTAACTTC-AGAGGCATAAGATTTGTCA-CTTTAATCTTCT
1 CCACTGCAACTTCAAGAAG-ATAAGATTTGT-AGCTTTAATCTGCT
*
6037921 CCACTGCAACTTC-AGCAAGATAAGATTTGTAGCTTCAATCTGCT
1 CCACTGCAACTTCAAG-AAGATAAGATTTGTAGCTTTAATCTGCT
* * * *
6037965 CCACTACAACTTCAGGGAGATAAGATTTTTAGCTTTAATCTGCT
1 CCACTGCAACTTCAAGAAGATAAGATTTGTAGCTTTAATCTGCT
* * * *
6038009 -CACTGTAACTTTAGGGAGATAAGATTTGTAG-TTTCAATCTGCT
1 CCACTGCAACTTCAAGAAGATAAGATTTGTAGCTTT-AATCTGCT
* *
6038052 CCACTGCAACTTCAAGGAGATAAGATTTGTAGTTTTAATCTGCT
1 CCACTGCAACTTCAAGAAGATAAGATTTGTAGCTTTAATCTGCT
* * *
6038096 CCACTACAACTTCAGGAAGATGAGATTTGTAGCTTTAATCTGCT
1 CCACTGCAACTTCAAGAAGATAAGATTTGTAGCTTTAATCTGCT
*
6038140 CCACTGCAACTTTAAGAAGATAAGATT
1 CCACTGCAACTTCAAGAAGATAAGATT
6038167 CGCTATGGTA
Statistics
Matches: 215, Mismatches: 25, Indels: 12
0.85 0.10 0.05
Matches are distributed among these distances:
42 3 0.01
43 36 0.17
44 170 0.79
45 6 0.03
ACGTcount: A:0.30, C:0.20, G:0.17, T:0.33
Consensus pattern (44 bp):
CCACTGCAACTTCAAGAAGATAAGATTTGTAGCTTTAATCTGCT
Found at i:6038244 original size:138 final size:131
Alignment explanation
Indices: 6037919--6038260 Score: 395
Period size: 131 Copynumber: 2.6 Consensus size: 131
6037909 CTTTAATCTT
* *
6037919 CTCCACTGCAACTTC-AGCAAGATAAGATTTGTAGCTTCAATCTGCTCCACTACAACTTCAGGGA
1 CTCCACTGCAACTTCAAG-GAGATAAGATTTGTAGCTTAAATCTGCTCCACTACAACTTCAGGGA
* * * * *
6037983 GATAAGATTTTTAGCTTTAATCTGCTCACTGTAACTTTAGGGAGATAAGATTTGTAGTTTCAATC
65 GATAAGATTTGTAGCTTTAATCTGCTCACTGCAACTTTAAGAAGATAAGATTTGTAGATTCAATC
*
6038048 TG
130 CG
* * *
6038050 CTCCACTGCAACTTCAAGGAGATAAGATTTGTAGTTTTAATCTGCTCCACTACAACTTCAGGAAG
1 CTCCACTGCAACTTCAAGGAGATAAGATTTGTAGCTTAAATCTGCTCCACTACAACTTCAGGGAG
*
6038115 ATGAGATTTGTAGCTTTAATCTGCTCCACTGCAACTTTAAGAAGATAAGATTCGCTATGGTAGAT
66 ATAAGATTTGTAGCTTTAATCTGCT-CACTGCAACTTTAAGAAGATAAGA-T---T-T-GTAGAT
6038180 TCAATCCG
124 TCAATCCG
* * * * * *
6038188 -TCCCATTGCGACTTCAAGG-GTGTAAGATCTGTAGCTTAAATCTGC-CTCACTGCAACTTTAGG
1 CT-CCACTGCAACTTCAAGGAG-ATAAGATTTGTAGCTTAAATCTGCTC-CACTACAACTTCAGG
6038250 GAGATAAGATT
63 GAGATAAGATT
6038261 CGCTATAGTG
Statistics
Matches: 179, Mismatches: 21, Indels: 15
0.83 0.10 0.07
Matches are distributed among these distances:
131 81 0.45
132 23 0.13
133 1 0.01
136 1 0.01
137 4 0.02
138 69 0.39
ACGTcount: A:0.29, C:0.20, G:0.19, T:0.32
Consensus pattern (131 bp):
CTCCACTGCAACTTCAAGGAGATAAGATTTGTAGCTTAAATCTGCTCCACTACAACTTCAGGGAG
ATAAGATTTGTAGCTTTAATCTGCTCACTGCAACTTTAAGAAGATAAGATTTGTAGATTCAATCC
G
Found at i:6060605 original size:22 final size:20
Alignment explanation
Indices: 6060554--6060603 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 20
6060544 TTAATAACGG
*
6060554 AATATATAGAATAATAAAAA
1 AATATATATAATAATAAAAA
* * **
6060574 AATGTTTATAATAATTCAAA
1 AATATATATAATAATAAAAA
6060594 AATATATATA
1 AATATATATA
6060604 TATATATATA
Statistics
Matches: 23, Mismatches: 7, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.60, C:0.02, G:0.04, T:0.34
Consensus pattern (20 bp):
AATATATATAATAATAAAAA
Found at i:6060747 original size:3 final size:3
Alignment explanation
Indices: 6060719--6060780 Score: 72
Period size: 3 Copynumber: 20.3 Consensus size: 3
6060709 ATAGTAACAG
* * *
6060719 TAA TAA TGA TAA TATA TAA T-A TAA TAA TAA TGA TAA TAAA TGA TAA
1 TAA TAA TAA TAA TA-A TAA TAA TAA TAA TAA TAA TAA T-AA TAA TAA
6060765 TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA T
6060781 TTAAAAAAAC
Statistics
Matches: 50, Mismatches: 6, Indels: 6
0.81 0.10 0.10
Matches are distributed among these distances:
2 2 0.04
3 42 0.84
4 6 0.12
ACGTcount: A:0.60, C:0.00, G:0.05, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:6061400 original size:10 final size:11
Alignment explanation
Indices: 6061375--6061404 Score: 53
Period size: 10 Copynumber: 2.8 Consensus size: 11
6061365 TGTTTTAGGA
6061375 AAAATAAAATG
1 AAAATAAAATG
6061386 AAAATAAAA-G
1 AAAATAAAATG
6061396 AAAATAAAA
1 AAAATAAAA
6061405 AATATATATA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 10 0.53
11 9 0.47
ACGTcount: A:0.80, C:0.00, G:0.07, T:0.13
Consensus pattern (11 bp):
AAAATAAAATG
Found at i:6062378 original size:44 final size:44
Alignment explanation
Indices: 6062324--6062522 Score: 163
Period size: 44 Copynumber: 4.5 Consensus size: 44
6062314 TGATCTACCG
** *
6062324 TTCTT-GATCTACTTCATGCCAATACATGAAGACAAGATCTGTT
1 TTCTTCGATCTACTTCACACCAATACATGAAGACAAGATCTGCT
* * * * *
6062367 TTCTTCAATCTACTTCACACCAATACATGAATATAAGATTTGCCA
1 TTCTTCGATCTACTTCACACCAATACATGAAGACAAGATCTG-CT
* *** *
6062412 TT-TTCGATCTACTTCACCACCAGTATGGGAAGACAAGAT-T-TT
1 TTCTTCGATCTACTTCA-CACCAATACATGAAGACAAGATCTGCT
* * * *
6062454 TTGACTTTGATCTACTTCACGCCGATACATGAAGACAAGATCTACT
1 TT--CTTCGATCTACTTCACACCAATACATGAAGACAAGATCTGCT
*
6062500 TTCTTCGATCTACTCCACCACCA
1 TTCTTCGATCTACTTCA-CACCA
6062523 GTATGGGGAG
Statistics
Matches: 118, Mismatches: 29, Indels: 16
0.72 0.18 0.10
Matches are distributed among these distances:
42 2 0.02
43 5 0.04
44 73 0.62
45 35 0.30
46 3 0.03
ACGTcount: A:0.30, C:0.25, G:0.12, T:0.33
Consensus pattern (44 bp):
TTCTTCGATCTACTTCACACCAATACATGAAGACAAGATCTGCT
Found at i:6062451 original size:45 final size:44
Alignment explanation
Indices: 6062401--6062539 Score: 104
Period size: 45 Copynumber: 3.1 Consensus size: 44
6062391 ACATGAATAT
*
6062401 AAGATTTGCCATTTTCGATCTACTTCACCACCAGTATGGGAAGAC
1 AAGATTT-ACATTTTCGATCTACTTCACCACCAGTATGGGAAGAC
** * * ***
6062446 AAGATTTTTTGACTTT-GATCTACTTCA-CGCC-GATACATGAAGAC
1 AAGA--TTTACATTTTCGATCTACTTCACCACCAG-TATGGGAAGAC
* * * *
6062490 AAGATCTACTTTCTTCGATCTACTCCACCACCAGTATGGGGAGAC
1 AAGATTTACATT-TTCGATCTACTTCACCACCAGTATGGGAAGAC
6062535 AAGAT
1 AAGAT
6062540 CTGGTCTTCG
Statistics
Matches: 69, Mismatches: 18, Indels: 14
0.68 0.18 0.14
Matches are distributed among these distances:
42 3 0.04
43 3 0.04
44 25 0.36
45 30 0.43
46 5 0.07
47 3 0.04
ACGTcount: A:0.29, C:0.24, G:0.17, T:0.29
Consensus pattern (44 bp):
AAGATTTACATTTTCGATCTACTTCACCACCAGTATGGGAAGAC
Found at i:6062482 original size:89 final size:89
Alignment explanation
Indices: 6062374--6062539 Score: 235
Period size: 89 Copynumber: 1.9 Consensus size: 89
6062364 GTTTTCTTCA
* * * * *
6062374 ATCTACTTCACACCAATACATGAATATAAGATTTGCCATT-TTCGATCTACTTCACCACCAGTAT
1 ATCTACTTCACACCAATACATGAAGACAAGATCT-ACATTCTTCGATCTACTCCACCACCAGTAT
6062438 GGGAAGACAAGATTTTTTGACTTTG
65 GGGAAGACAAGATTTTTTGACTTTG
* * *
6062463 ATCTACTTCACGCCGATACATGAAGACAAGATCTACTTTCTTCGATCTACTCCACCACCAGTATG
1 ATCTACTTCACACCAATACATGAAGACAAGATCTACATTCTTCGATCTACTCCACCACCAGTATG
*
6062528 GGGAGACAAGAT
66 GGAAGACAAGAT
6062540 CTGGTCTTCG
Statistics
Matches: 67, Mismatches: 9, Indels: 2
0.86 0.12 0.03
Matches are distributed among these distances:
88 3 0.04
89 64 0.96
ACGTcount: A:0.31, C:0.24, G:0.15, T:0.30
Consensus pattern (89 bp):
ATCTACTTCACACCAATACATGAAGACAAGATCTACATTCTTCGATCTACTCCACCACCAGTATG
GGAAGACAAGATTTTTTGACTTTG
Found at i:6063881 original size:50 final size:47
Alignment explanation
Indices: 6063824--6063930 Score: 144
Period size: 47 Copynumber: 2.2 Consensus size: 47
6063814 CTTTGCGAGT
* *
6063824 TTTCACCTTAGCCTCTCCATTTTTTTTT-ACTCAAGGCTCCCTTTGTAGGC
1 TTTCACCTT-G-CTCT-C-TTTTTTTTTGACTCAAAGCGCCCTTTGTAGGC
*
6063874 TTTCACCTTGGTCTCTTTTTTTTTGACTCAAAGCGCCCTTTGTAGGC
1 TTTCACCTTGCTCTCTTTTTTTTTGACTCAAAGCGCCCTTTGTAGGC
6063921 TTTCACCTTG
1 TTTCACCTTG
6063931 GTCCCACCTT
Statistics
Matches: 53, Mismatches: 3, Indels: 5
0.87 0.05 0.08
Matches are distributed among these distances:
46 9 0.17
47 31 0.58
48 3 0.06
49 1 0.02
50 9 0.17
ACGTcount: A:0.13, C:0.28, G:0.14, T:0.45
Consensus pattern (47 bp):
TTTCACCTTGCTCTCTTTTTTTTTGACTCAAAGCGCCCTTTGTAGGC
Done.