Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009585.1 Hibiscus syriacus cultivar Beakdansim tig00116962_pilon, whole genome shotgun sequence
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: 8285662
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 27 of 35
Found at i:6154721 original size:38 final size:38
Alignment explanation
Indices: 6154677--6154859 Score: 186
Period size: 37 Copynumber: 4.9 Consensus size: 38
6154667 ATTATATAAG
6154677 TTTTAAAAACTATATATTATATAAGT-TTTTCAAAATGA
1 TTTTAAAAACTATATATTATATAA-TATTTTCAAAATGA
*
6154715 TTTTAAAAATTATATATTATAT-ATATTTTCTAAAATG-
1 TTTTAAAAACTATATATTATATAATATTTTC-AAAATGA
* *
6154752 TTTTAAAATC-ATATA-T-T-TAATAACTTTCAAAA-GTA
1 TTTTAAAAACTATATATTATATAAT-ATTTTCAAAATG-A
* *
6154787 TTTTAAAAACTATATATTGTAT-ATATTTTCAAAATGT
1 TTTTAAAAACTATATATTATATAATATTTTCAAAATGA
* * *
6154824 TTTTAGAAATTATATATTATATACGTATTTTCAAAA
1 TTTTAAAAACTATATATTATATA-ATATTTTCAAAA
6154860 ACCGTTTGCA
Statistics
Matches: 121, Mismatches: 11, Indels: 25
0.77 0.07 0.16
Matches are distributed among these distances:
33 2 0.02
34 7 0.06
35 15 0.12
36 11 0.09
37 43 0.36
38 31 0.26
39 12 0.10
ACGTcount: A:0.43, C:0.05, G:0.04, T:0.47
Consensus pattern (38 bp):
TTTTAAAAACTATATATTATATAATATTTTCAAAATGA
Found at i:6154790 original size:72 final size:73
Alignment explanation
Indices: 6154704--6154841 Score: 210
Period size: 72 Copynumber: 1.9 Consensus size: 73
6154694 TATATAAGTT
*
6154704 TTTCAAAATGATTTTAAAAATTATATATTATATATATTTTCTAAAATG-TTTTA-AAATCATATA
1 TTTCAAAATGATTTTAAAAACTATATATTATATATATTTTC-AAAATGTTTTTAGAAATCATATA
6154767 TTTAATAAC
65 TTTAATAAC
* *
6154776 TTTCAAAA-GTATTTTAAAAACTATATATTGTATATATTTTCAAAATGTTTTTAGAAATTATATA
1 TTTCAAAATG-ATTTTAAAAACTATATATTATATATATTTTCAAAATGTTTTTAGAAATCATATA
6154840 TT
65 TT
6154842 ATATACGTAT
Statistics
Matches: 60, Mismatches: 3, Indels: 5
0.88 0.04 0.07
Matches are distributed among these distances:
71 7 0.12
72 42 0.70
73 11 0.18
ACGTcount: A:0.43, C:0.05, G:0.04, T:0.48
Consensus pattern (73 bp):
TTTCAAAATGATTTTAAAAACTATATATTATATATATTTTCAAAATGTTTTTAGAAATCATATAT
TTAATAAC
Found at i:6157783 original size:63 final size:63
Alignment explanation
Indices: 6157684--6157881 Score: 297
Period size: 63 Copynumber: 3.1 Consensus size: 63
6157674 CTGGAGGAGA
* * * * *
6157684 TGGTGGCTTAGTTGGAGGATGAACTGGTGACTTGGGTGCCGGGTAAGTAGGCGGTTTGGTGGT
1 TGGTGGCTTAGTAGGAGGATGAACTGGTGGCTTGGGTGCCGGGTATGTCGGTGGTTTGGTGGT
* * * *
6157747 TGGTGGCTTAGTAGGAGGACGAATTGGTGGCTTGGGTGCAGGGTATGTCGGTGGTTTGGTAGT
1 TGGTGGCTTAGTAGGAGGATGAACTGGTGGCTTGGGTGCCGGGTATGTCGGTGGTTTGGTGGT
* *
6157810 TGGTGGCTTAGTAGGAGGATGAACTGGTGGCTTGGGTGCCGGGTATGTCGGTGTTTTGGTGGA
1 TGGTGGCTTAGTAGGAGGATGAACTGGTGGCTTGGGTGCCGGGTATGTCGGTGGTTTGGTGGT
6157873 TGGTGGCTT
1 TGGTGGCTT
6157882 GGGTGGTGGG
Statistics
Matches: 120, Mismatches: 15, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
63 120 1.00
ACGTcount: A:0.13, C:0.09, G:0.46, T:0.32
Consensus pattern (63 bp):
TGGTGGCTTAGTAGGAGGATGAACTGGTGGCTTGGGTGCCGGGTATGTCGGTGGTTTGGTGGT
Found at i:6157893 original size:39 final size:38
Alignment explanation
Indices: 6157834--6157920 Score: 102
Period size: 39 Copynumber: 2.2 Consensus size: 38
6157824 GAGGATGAAC
* * *
6157834 TGGTGGCTTGGGTGCCGGGTATGTCGGTGTTTTGGTGG
1 TGGTGGCTTGGGTGCCGGGTAAGTCGGTGGTTTAGTGG
** *
6157872 ATGGTGGCTTGGGTGGTGGGTAAGTGGGTGGTTTAGTGG
1 -TGGTGGCTTGGGTGCCGGGTAAGTCGGTGGTTTAGTGG
6157911 TCGGTGGCTT
1 T-GGTGGCTT
6157921 TGTTGGAGGA
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
38 1 0.02
39 40 0.98
ACGTcount: A:0.06, C:0.08, G:0.51, T:0.36
Consensus pattern (38 bp):
TGGTGGCTTGGGTGCCGGGTAAGTCGGTGGTTTAGTGG
Found at i:6162645 original size:14 final size:14
Alignment explanation
Indices: 6162626--6162683 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
6162616 TTGTGTTTCG
6162626 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
*
6162640 CGTTGCGATTTCATTT
1 CGTTGCGATTT--TGT
6162656 CGCGTTGCGATTTTGT
1 --CGTTGCGATTTTGT
6162672 CGTTGCGATTTT
1 CGTTGCGATTTT
6162684 CATTTCGCAT
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 23 0.61
16 4 0.11
18 11 0.29
ACGTcount: A:0.09, C:0.17, G:0.26, T:0.48
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:6162647 original size:33 final size:32
Alignment explanation
Indices: 6162610--6162699 Score: 135
Period size: 32 Copynumber: 2.8 Consensus size: 32
6162600 AAAATCGCAA
*
6162610 TGCGATTTGTGTTTCGCGTTGCGATTTTGTCGT
1 TGCGATTT-TATTTCGCGTTGCGATTTTGTCGT
*
6162643 TGCGATTTCATTTCGCGTTGCGATTTTGTCGT
1 TGCGATTTTATTTCGCGTTGCGATTTTGTCGT
*
6162675 TGCGATTTTCATTTCGCATTGCGAT
1 TGCGATTTT-ATTTCGCGTTGCGAT
6162700 AGCCATTTCC
Statistics
Matches: 52, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
32 30 0.58
33 22 0.42
ACGTcount: A:0.10, C:0.18, G:0.26, T:0.47
Consensus pattern (32 bp):
TGCGATTTTATTTCGCGTTGCGATTTTGTCGT
Found at i:6162660 original size:32 final size:33
Alignment explanation
Indices: 6162621--6162699 Score: 142
Period size: 32 Copynumber: 2.4 Consensus size: 33
6162611 GCGATTTGTG
6162621 TTTCGCGTTGCGATTTTGTCGTTGCGA-TTTCA
1 TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
6162653 TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
1 TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
*
6162686 TTTCGCATTGCGAT
1 TTTCGCGTTGCGAT
6162700 AGCCATTTCC
Statistics
Matches: 45, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
32 27 0.60
33 18 0.40
ACGTcount: A:0.10, C:0.19, G:0.24, T:0.47
Consensus pattern (33 bp):
TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
Found at i:6162698 original size:19 final size:17
Alignment explanation
Indices: 6162621--6162699 Score: 62
Period size: 14 Copynumber: 4.8 Consensus size: 17
6162611 GCGATTTGTG
6162621 TTTCGCGTTGCGATTT--
1 TTTCGC-TTGCGATTTCA
*
6162637 TGTCG-TTGCGATTTCA
1 TTTCGCTTGCGATTTCA
6162653 TTTCGCGTTGCGATTT--
1 TTTCGC-TTGCGATTTCA
*
6162669 TGTCG-TTGCGATTTTCA
1 TTTCGCTTGCGA-TTTCA
6162686 TTTCGCATTGCGAT
1 TTTCGC-TTGCGAT
6162700 AGCCATTTCC
Statistics
Matches: 50, Mismatches: 4, Indels: 16
0.71 0.06 0.23
Matches are distributed among these distances:
14 15 0.30
15 3 0.06
16 12 0.24
17 4 0.08
18 10 0.20
19 6 0.12
ACGTcount: A:0.10, C:0.19, G:0.24, T:0.47
Consensus pattern (17 bp):
TTTCGCTTGCGATTTCA
Found at i:6162718 original size:20 final size:19
Alignment explanation
Indices: 6162684--6162739 Score: 67
Period size: 20 Copynumber: 2.8 Consensus size: 19
6162674 TTGCGATTTT
*
6162684 CATTTCGCATTGCGATAGC
1 CATTTCGCGTTGCGATAGC
*
6162703 CATTTCCGCGTTGCGATAGT
1 CATTT-CGCGTTGCGATAGC
*
6162723 CATTTTCGTGTTGCGAT
1 CA-TTTCGCGTTGCGAT
6162740 TTTTAAGTTT
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
19 5 0.16
20 24 0.75
21 3 0.09
ACGTcount: A:0.16, C:0.23, G:0.23, T:0.38
Consensus pattern (19 bp):
CATTTCGCGTTGCGATAGC
Found at i:6164630 original size:14 final size:14
Alignment explanation
Indices: 6164611--6164646 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
6164601 ATTGTTTAAT
6164611 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
* *
6164625 TGATTTGTAAATGT
1 TGATTTGTAAAAGA
6164639 TGATTTGT
1 TGATTTGT
6164647 TTAATTGATG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.22, T:0.47
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:6164772 original size:14 final size:14
Alignment explanation
Indices: 6164753--6164806 Score: 54
Period size: 14 Copynumber: 3.5 Consensus size: 14
6164743 CGAAATGGCT
6164753 ATCGCAACGAGAAA
1 ATCGCAACGAGAAA
6164767 ATCGCAATGCGAAATGAAA
1 ATCGCAA--CG--A-GAAA
*
6164786 ATCGCAACAAGAAA
1 ATCGCAACGAGAAA
6164800 ATCGCAA
1 ATCGCAA
6164807 TGCGATTTTC
Statistics
Matches: 34, Mismatches: 1, Indels: 10
0.76 0.02 0.22
Matches are distributed among these distances:
14 18 0.53
15 1 0.03
16 2 0.06
17 1 0.03
18 1 0.03
19 11 0.32
ACGTcount: A:0.50, C:0.20, G:0.19, T:0.11
Consensus pattern (14 bp):
ATCGCAACGAGAAA
Found at i:6164785 original size:19 final size:18
Alignment explanation
Indices: 6164762--6164811 Score: 63
Period size: 14 Copynumber: 2.9 Consensus size: 18
6164752 TATCGCAACG
6164762 AGAAAATCGCAATGCGAA
1 AGAAAATCGCAATGCGAA
6164780 ATGAAAATCGCAA--C--A
1 A-GAAAATCGCAATGCGAA
6164795 AGAAAATCGCAATGCGA
1 AGAAAATCGCAATGCGA
6164812 TTTTCATTTC
Statistics
Matches: 27, Mismatches: 0, Indels: 10
0.73 0.00 0.27
Matches are distributed among these distances:
14 11 0.41
15 2 0.07
16 1 0.04
17 1 0.04
18 1 0.04
19 11 0.41
ACGTcount: A:0.50, C:0.18, G:0.20, T:0.12
Consensus pattern (18 bp):
AGAAAATCGCAATGCGAA
Found at i:6164824 original size:33 final size:33
Alignment explanation
Indices: 6164734--6164811 Score: 111
Period size: 33 Copynumber: 2.4 Consensus size: 33
6164724 AAAACAGACT
* *** *
6164734 ATCGCAACGCGAAATGGCTATCGCAACGAGAAA
1 ATCGCAATGCGAAATGAAAATCGCAACAAGAAA
6164767 ATCGCAATGCGAAATGAAAATCGCAACAAGAAA
1 ATCGCAATGCGAAATGAAAATCGCAACAAGAAA
6164800 ATCGCAATGCGA
1 ATCGCAATGCGA
6164812 TTTTCATTTC
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 40 1.00
ACGTcount: A:0.44, C:0.22, G:0.22, T:0.13
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACAAGAAA
Found at i:6164855 original size:20 final size:20
Alignment explanation
Indices: 6164830--6164887 Score: 107
Period size: 20 Copynumber: 2.9 Consensus size: 20
6164820 TCGCATTGCG
*
6164830 ATTTTCTCGTTGCGATAGCC
1 ATTTTCGCGTTGCGATAGCC
6164850 ATTTTCGCGTTGCGATAGCC
1 ATTTTCGCGTTGCGATAGCC
6164870 ATTTTCGCGTTGCGATAG
1 ATTTTCGCGTTGCGATAG
6164888 TCAAATGAAT
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 37 1.00
ACGTcount: A:0.16, C:0.22, G:0.24, T:0.38
Consensus pattern (20 bp):
ATTTTCGCGTTGCGATAGCC
Found at i:6165967 original size:24 final size:24
Alignment explanation
Indices: 6165940--6165993 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
6165930 GTATTCGAAA
* *
6165940 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATATTGGTCAATACACGGAC
*
6165964 TTTGATATTGGTCAATACACGGAT
1 TTTGATATTGGTCAATACACGGAC
6165988 TTTGAT
1 TTTGAT
6165994 GACGTTTCGG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.24, C:0.17, G:0.20, T:0.39
Consensus pattern (24 bp):
TTTGATATTGGTCAATACACGGAC
Found at i:6168493 original size:19 final size:19
Alignment explanation
Indices: 6168471--6168599 Score: 67
Period size: 14 Copynumber: 7.7 Consensus size: 19
6168461 GGAAATTACT
*
6168471 ATCGCAATGCGAAATAAAA
1 ATCGCAATGCGAAATGAAA
*
6168490 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
6168504 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
* *
6168523 ATCGCAA--C--ACT-AAT
1 ATCGCAATGCGAAATGAAA
*
6168537 TTCGCAATGCGAAATG-AA
1 ATCGCAATGCGAAATGAAA
**
6168555 ATCGCAA--CG--A-GGGA
1 ATCGCAATGCGAAATGAAA
6168569 ATCGCAATGCGAAATG-AA
1 ATCGCAATGCGAAATGAAA
*
6168587 ATCGCAACGCGAA
1 ATCGCAATGCGAA
6168600 TTTAATTTCG
Statistics
Matches: 82, Mismatches: 12, Indels: 33
0.65 0.09 0.26
Matches are distributed among these distances:
13 1 0.01
14 26 0.32
15 3 0.04
16 7 0.09
17 3 0.04
18 24 0.29
19 18 0.22
ACGTcount: A:0.43, C:0.20, G:0.22, T:0.15
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:6168562 original size:32 final size:32
Alignment explanation
Indices: 6168471--6168595 Score: 164
Period size: 33 Copynumber: 3.8 Consensus size: 32
6168461 GGAAATTACT
* *
6168471 ATCGCAATGCGAAATAAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAAT-GAAATCGCAACGAGCGA
*
6168504 ATCGCAATGCGAAATGAAAATCGCAAC-A-CTA
1 ATCGCAATGCGAAATG-AAATCGCAACGAGCGA
*
6168535 ATTTCGCAATGCGAAATGAAATCGCAACGAGGGA
1 A--TCGCAATGCGAAATGAAATCGCAACGAGCGA
6168569 ATCGCAATGCGAAATGAAATCGCAACG
1 ATCGCAATGCGAAATGAAATCGCAACG
6168596 CGAATTTAAT
Statistics
Matches: 82, Mismatches: 5, Indels: 11
0.84 0.05 0.11
Matches are distributed among these distances:
31 2 0.02
32 37 0.45
33 41 0.50
34 2 0.02
ACGTcount: A:0.43, C:0.20, G:0.22, T:0.15
Consensus pattern (32 bp):
ATCGCAATGCGAAATGAAATCGCAACGAGCGA
Found at i:6168577 original size:65 final size:65
Alignment explanation
Indices: 6168472--6168594 Score: 212
Period size: 65 Copynumber: 1.9 Consensus size: 65
6168462 GAAATTACTA
6168472 TCGCAATGCGAAATAAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACACTAAT
1 TCGCAATGCGAAATAAAAATCGCAACGAGAGAATCGCAATGCGAAATG-AAATCGCAACACTAAT
6168537 T
65 T
* *
6168538 TCGCAATGCGAAAT-GAAATCGCAACGAGGGAATCGCAATGCGAAATGAAATCGCAAC
1 TCGCAATGCGAAATAAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAATCGCAAC
6168595 GCGAATTTAA
Statistics
Matches: 55, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
64 10 0.18
65 31 0.56
66 14 0.25
ACGTcount: A:0.43, C:0.20, G:0.21, T:0.15
Consensus pattern (65 bp):
TCGCAATGCGAAATAAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAATCGCAACACTAATT
Found at i:6168627 original size:14 final size:14
Alignment explanation
Indices: 6168610--6168666 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
6168600 TTTAATTTCG
6168610 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
6168624 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
6168643 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
6168657 CGTTGCGATT
1 CGTTGCGATT
6168667 TTCATTTTGC
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 20 0.56
16 3 0.08
17 3 0.08
19 10 0.28
ACGTcount: A:0.09, C:0.25, G:0.23, T:0.44
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:6168641 original size:33 final size:33
Alignment explanation
Indices: 6168595--6168684 Score: 144
Period size: 33 Copynumber: 2.7 Consensus size: 33
6168585 AAATCGCAAC
* *
6168595 GCGAATTTAATTTCGCGTTGCGATTCTCTCGTT
1 GCGATTTTCATTTCGCGTTGCGATTCTCTCGTT
6168628 GCGATTTTCATTTCGCGTTGCGATTCTCTCGTT
1 GCGATTTTCATTTCGCGTTGCGATTCTCTCGTT
* *
6168661 GCGATTTTCATTTTGCATTGCGAT
1 GCGATTTTCATTTCGCGTTGCGAT
6168685 AGTACTTTTT
Statistics
Matches: 53, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 53 1.00
ACGTcount: A:0.13, C:0.21, G:0.21, T:0.44
Consensus pattern (33 bp):
GCGATTTTCATTTCGCGTTGCGATTCTCTCGTT
Found at i:6168648 original size:19 final size:19
Alignment explanation
Indices: 6168624--6168684 Score: 60
Period size: 19 Copynumber: 3.5 Consensus size: 19
6168614 GCGATTCTCT
6168624 CGTTGCGATTTTCATTTCG
1 CGTTGCGATTTTCATTTCG
*
6168643 CGTTGCGA--TTC---TCT
1 CGTTGCGATTTTCATTTCG
*
6168657 CGTTGCGATTTTCATTTTG
1 CGTTGCGATTTTCATTTCG
*
6168676 CATTGCGAT
1 CGTTGCGAT
6168685 AGTACTTTTT
Statistics
Matches: 33, Mismatches: 4, Indels: 10
0.70 0.09 0.21
Matches are distributed among these distances:
14 10 0.30
16 3 0.09
17 3 0.09
19 17 0.52
ACGTcount: A:0.11, C:0.21, G:0.21, T:0.46
Consensus pattern (19 bp):
CGTTGCGATTTTCATTTCG
Found at i:6168810 original size:14 final size:14
Alignment explanation
Indices: 6168791--6168827 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
6168781 CATCAATTAA
6168791 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
6168805 ACAAATCACCTTTT
1 ACAAATCAACTTTT
6168819 ACAAATCAA
1 ACAAATCAA
6168828 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.24, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:6170683 original size:91 final size:89
Alignment explanation
Indices: 6170509--6170692 Score: 271
Period size: 91 Copynumber: 2.0 Consensus size: 89
6170499 ATTTCAAACT
* *
6170509 TTCAACCAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGTTTAGCA
1 TTCAACCAAAGACAAAACAAAGACAAATACTAACTTCACAATGTT--A-AATAAACAGTTTAGCA
6170574 GAATTGGCAGCAACCGAATAAATTTAC
63 GAATTGGCAGCAACCGAATAAATTTAC
6170601 TTCAACCAAAAGACAAAACAAAAAGACAAATACTAACTTCACAATGTT-AATAAACAGTTTAGCA
1 TTCAACC-AAAGACAAAAC--AAAGACAAATACTAACTTCACAATGTTAAATAAACAGTTTAGCA
**
6170665 GTTTTGGCAGCAACCGAATAAATTTAC
63 GAATTGGCAGCAACCGAATAAATTTAC
6170692 T
1 T
6170693 AAGCAATCTA
Statistics
Matches: 85, Mismatches: 4, Indels: 7
0.89 0.04 0.07
Matches are distributed among these distances:
91 41 0.48
92 7 0.08
93 11 0.13
95 26 0.31
ACGTcount: A:0.47, C:0.19, G:0.12, T:0.22
Consensus pattern (89 bp):
TTCAACCAAAGACAAAACAAAGACAAATACTAACTTCACAATGTTAAATAAACAGTTTAGCAGAA
TTGGCAGCAACCGAATAAATTTAC
Found at i:6172200 original size:19 final size:19
Alignment explanation
Indices: 6172176--6172223 Score: 53
Period size: 20 Copynumber: 2.5 Consensus size: 19
6172166 AAAATCACAA
*
6172176 TGCGATTTTGGTTT-CGCGT
1 TGCGATTTT-ATTTCCGCGT
*
6172195 TGCGATAGTTATTTCCGCGT
1 TGCGAT-TTTATTTCCGCGT
6172215 TGCGATTTT
1 TGCGATTTT
6172224 CATTCTCGAA
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
19 11 0.46
20 13 0.54
ACGTcount: A:0.10, C:0.17, G:0.27, T:0.46
Consensus pattern (19 bp):
TGCGATTTTATTTCCGCGT
Found at i:6172766 original size:20 final size:20
Alignment explanation
Indices: 6172741--6172833 Score: 159
Period size: 20 Copynumber: 4.7 Consensus size: 20
6172731 ACGCTATGTA
6172741 AATCGCGTTGCGAAAGTCAG
1 AATCGCGTTGCGAAAGTCAG
6172761 AATCGCGTTGCGAAAGTCAG
1 AATCGCGTTGCGAAAGTCAG
*
6172781 AATCGCGTTGCGAAAGTCAA
1 AATCGCGTTGCGAAAGTCAG
6172801 AATCGCGTTGCGAAAGTCAG
1 AATCGCGTTGCGAAAGTCAG
* *
6172821 TATCTCGTTGCGA
1 AATCGCGTTGCGA
6172834 TTTTGTATAT
Statistics
Matches: 69, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 69 1.00
ACGTcount: A:0.29, C:0.20, G:0.28, T:0.23
Consensus pattern (20 bp):
AATCGCGTTGCGAAAGTCAG
Found at i:6182196 original size:21 final size:21
Alignment explanation
Indices: 6182172--6182215 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
6182162 TGAAGATTTG
6182172 CTTGGTTCTATTAAAGAGATA
1 CTTGGTTCTATTAAAGAGATA
6182193 CTTGGTTCTATTAAAGAGATA
1 CTTGGTTCTATTAAAGAGATA
6182214 CT
1 CT
6182216 GGGTGCTCAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.32, C:0.11, G:0.18, T:0.39
Consensus pattern (21 bp):
CTTGGTTCTATTAAAGAGATA
Found at i:6187218 original size:20 final size:21
Alignment explanation
Indices: 6187193--6187247 Score: 62
Period size: 20 Copynumber: 2.7 Consensus size: 21
6187183 ATATTCATAT
6187193 ATAAAATTAGTATATATAA-A
1 ATAAAATTAGTATATATAACA
* *
6187213 ATAAAATATA-TTTAAATAACA
1 ATAAAAT-TAGTATATATAACA
6187234 ATAAAATT-GTATAT
1 ATAAAATTAGTATAT
6187248 GTCCATTTTT
Statistics
Matches: 28, Mismatches: 4, Indels: 6
0.74 0.11 0.16
Matches are distributed among these distances:
20 18 0.64
21 10 0.36
ACGTcount: A:0.58, C:0.02, G:0.04, T:0.36
Consensus pattern (21 bp):
ATAAAATTAGTATATATAACA
Found at i:6187319 original size:2 final size:2
Alignment explanation
Indices: 6187312--6187347 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
6187302 GGGGGTTTTA
6187312 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
6187348 TTGTGGAAGT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:6189146 original size:18 final size:18
Alignment explanation
Indices: 6189123--6189167 Score: 56
Period size: 18 Copynumber: 2.5 Consensus size: 18
6189113 AATATTTCCA
6189123 ATAATCTTATTC-CTACCG
1 ATAATCTTATTCTC-ACCG
* *
6189141 ATAATCCTATTCTCACTG
1 ATAATCTTATTCTCACCG
6189159 ATAATCTTA
1 ATAATCTTA
6189168 CATTCCGTAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
18 22 0.96
19 1 0.04
ACGTcount: A:0.31, C:0.24, G:0.04, T:0.40
Consensus pattern (18 bp):
ATAATCTTATTCTCACCG
Found at i:6214748 original size:12 final size:12
Alignment explanation
Indices: 6214731--6214756 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
6214721 GCCGATGCTT
6214731 TATGTCCAAGCC
1 TATGTCCAAGCC
6214743 TATGTCCAAGCC
1 TATGTCCAAGCC
6214755 TA
1 TA
6214757 CTTTGAGGTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.27, C:0.31, G:0.15, T:0.27
Consensus pattern (12 bp):
TATGTCCAAGCC
Found at i:6216558 original size:4 final size:4
Alignment explanation
Indices: 6216549--6216575 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
6216539 ATAAATGAAA
6216549 TGAG TGAG TGAG TGAG TGAG TGAG TGA
1 TGAG TGAG TGAG TGAG TGAG TGAG TGA
6216576 TTGATTAATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.26, C:0.00, G:0.48, T:0.26
Consensus pattern (4 bp):
TGAG
Found at i:6217133 original size:31 final size:31
Alignment explanation
Indices: 6217095--6217370 Score: 329
Period size: 31 Copynumber: 9.2 Consensus size: 31
6217085 TACATTTTGG
*
6217095 TACTTGAATTTAGTTTCTTGATTCAAATTGA
1 TACTTGAACTTAGTTTCTTGATTCAAATTGA
*
6217126 TACTTGAACTTAGTTTCTTAATTCAAATTGA
1 TACTTGAACTTAGTTTCTTGATTCAAATTGA
* *
6217157 CACTTGAACTTAGTTTCTTAATTCAAATTGA
1 TACTTGAACTTAGTTTCTTGATTCAAATTGA
* *
6217188 CACTTGAACTTAGTTTCTTAATTCAAATTGA
1 TACTTGAACTTAGTTTCTTGATTCAAATTGA
*
6217219 TACTTGAAC-TAGTTTCTTAATTCAAATTGA
1 TACTTGAACTTAGTTTCTTGATTCAAATTGA
*
6217249 TACTTGAGCTTAGTTTCTTG-------TTGA
1 TACTTGAACTTAGTTTCTTGATTCAAATTGA
* *
6217273 CACTTGAACTTAGTTTCTTGATCCAAATTGA
1 TACTTGAACTTAGTTTCTTGATTCAAATTGA
* * *
6217304 TACTAGAGCTTA-TCTTCTTGATCCAAATTGA
1 TACTTGAACTTAGT-TTCTTGATTCAAATTGA
* *
6217335 TACTTGAACTTA-TCTTCTTGATCCAAATTGT
1 TACTTGAACTTAGT-TTCTTGATTCAAATTGA
6217366 TACTT
1 TACTT
6217371 AAAGTAAATG
Statistics
Matches: 222, Mismatches: 14, Indels: 18
0.87 0.06 0.07
Matches are distributed among these distances:
24 22 0.10
30 30 0.14
31 170 0.77
ACGTcount: A:0.29, C:0.16, G:0.12, T:0.44
Consensus pattern (31 bp):
TACTTGAACTTAGTTTCTTGATTCAAATTGA
Found at i:6217272 original size:24 final size:24
Alignment explanation
Indices: 6217245--6217292 Score: 78
Period size: 24 Copynumber: 2.0 Consensus size: 24
6217235 TTAATTCAAA
* *
6217245 TTGATACTTGAGCTTAGTTTCTTG
1 TTGACACTTGAACTTAGTTTCTTG
6217269 TTGACACTTGAACTTAGTTTCTTG
1 TTGACACTTGAACTTAGTTTCTTG
6217293 ATCCAAATTG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.19, C:0.15, G:0.19, T:0.48
Consensus pattern (24 bp):
TTGACACTTGAACTTAGTTTCTTG
Found at i:6217303 original size:55 final size:54
Alignment explanation
Indices: 6217215--6217323 Score: 157
Period size: 55 Copynumber: 2.0 Consensus size: 54
6217205 TTAATTCAAA
* * *
6217215 TTGATACTTGAACTAGTTTCTTAATTCAAATTGATACTTGAGCTTAGT-TTCTTG
1 TTGACACTTGAACTAGTTTCTTAATCCAAATTGATACTAGAGCTTA-TCTTCTTG
*
6217269 TTGACACTTGAACTTAGTTTCTTGATCCAAATTGATACTAGAGCTTATCTTCTTG
1 TTGACACTTGAAC-TAGTTTCTTAATCCAAATTGATACTAGAGCTTATCTTCTTG
6217324 ATCCAAATTG
Statistics
Matches: 49, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
54 13 0.27
55 36 0.73
ACGTcount: A:0.26, C:0.16, G:0.15, T:0.44
Consensus pattern (54 bp):
TTGACACTTGAACTAGTTTCTTAATCCAAATTGATACTAGAGCTTATCTTCTTG
Found at i:6217331 original size:116 final size:117
Alignment explanation
Indices: 6217153--6217370 Score: 307
Period size: 116 Copynumber: 1.9 Consensus size: 117
6217143 TTAATTCAAA
* * *
6217153 TTGACACTTGAACTTAGTTTCTTAATTCAAATTGACACTTGAACTTAGTTTCTTAATTCAAATTG
1 TTGACACTTGAACTTAGTTTCTTAATCCAAATTGACACTAGAACTTAGTTTCTTAATCCAAATTG
*
6217218 ATACTTGAAC-TAGT-TTCTTAATTCAAATTGATACTTGAGCTTAGTTTCTTG
66 ATACTTGAACTTA-TCTTCTTAATCCAAATTGATACTTGAGCTTAGTTTCTTG
* * * *
6217269 TTGACACTTGAACTTAGTTTCTTGATCCAAATTGATACTAGAGCTTA-TCTTCTTGATCCAAATT
1 TTGACACTTGAACTTAGTTTCTTAATCCAAATTGACACTAGAACTTAGT-TTCTTAATCCAAATT
* *
6217333 GATACTTGAACTTATCTTCTTGATCCAAATTGTTACTT
65 GATACTTGAACTTATCTTCTTAATCCAAATTGATACTT
6217371 AAAGTAAATG
Statistics
Matches: 89, Mismatches: 10, Indels: 5
0.86 0.10 0.05
Matches are distributed among these distances:
115 1 0.01
116 67 0.75
117 21 0.24
ACGTcount: A:0.28, C:0.17, G:0.12, T:0.43
Consensus pattern (117 bp):
TTGACACTTGAACTTAGTTTCTTAATCCAAATTGACACTAGAACTTAGTTTCTTAATCCAAATTG
ATACTTGAACTTATCTTCTTAATCCAAATTGATACTTGAGCTTAGTTTCTTG
Found at i:6218033 original size:2 final size:2
Alignment explanation
Indices: 6218028--6218060 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
6218018 TTTTTTTATC
6218028 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 A
6218061 GTTAAATGCT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:6223391 original size:2 final size:2
Alignment explanation
Indices: 6223384--6223419 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
6223374 TGAATATTGA
6223384 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
6223420 TGATTTAGTG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:6229758 original size:27 final size:29
Alignment explanation
Indices: 6229728--6229791 Score: 78
Period size: 29 Copynumber: 2.3 Consensus size: 29
6229718 AGATCAATAT
*
6229728 TTTTAAATAAA-AAAGT-TAAAGACTCAA
1 TTTTAAATAAATAAAGTATAAAGACTAAA
* * *
6229755 TTTTATATAAATAAAGTATAGAGATTAAA
1 TTTTAAATAAATAAAGTATAAAGACTAAA
6229784 TTTTAAAT
1 TTTTAAAT
6229792 TAGTAAAAAA
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
27 10 0.33
28 5 0.17
29 15 0.50
ACGTcount: A:0.52, C:0.03, G:0.08, T:0.38
Consensus pattern (29 bp):
TTTTAAATAAATAAAGTATAAAGACTAAA
Found at i:6235635 original size:50 final size:50
Alignment explanation
Indices: 6235559--6235659 Score: 184
Period size: 50 Copynumber: 2.0 Consensus size: 50
6235549 CTTAGCATTA
6235559 ATTATTTATTTTCATGTACAGAAACTTCAGCGACATTGCATCAGTTGATG
1 ATTATTTATTTTCATGTACAGAAACTTCAGCGACATTGCATCAGTTGATG
* *
6235609 ATTATTTATTTTCATGTACAGGAACTTCCGCGACATTGCATCAGTTGATG
1 ATTATTTATTTTCATGTACAGAAACTTCAGCGACATTGCATCAGTTGATG
6235659 A
1 A
6235660 GCACTGTACG
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
50 49 1.00
ACGTcount: A:0.29, C:0.17, G:0.17, T:0.38
Consensus pattern (50 bp):
ATTATTTATTTTCATGTACAGAAACTTCAGCGACATTGCATCAGTTGATG
Found at i:6237165 original size:6 final size:6
Alignment explanation
Indices: 6237154--6237218 Score: 102
Period size: 6 Copynumber: 11.5 Consensus size: 6
6237144 GACACGTATT
6237154 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACC-CG
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
6237201 ACC-CG ACC-CG ACC-CG ACC
1 ACCACG ACCACG ACCACG ACC
6237219 CGAGACGATA
Statistics
Matches: 59, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
5 20 0.34
6 39 0.66
ACGTcount: A:0.29, C:0.54, G:0.17, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:6238003 original size:22 final size:22
Alignment explanation
Indices: 6237975--6238046 Score: 87
Period size: 22 Copynumber: 3.4 Consensus size: 22
6237965 GGAATGGAAA
6237975 ATCGCAACGAAAATCGTAGACT
1 ATCGCAACGAAAATCGTAGACT
* * **
6237997 ATCGCAACG--AAT-TTGGAAA
1 ATCGCAACGAAAATCGTAGACT
6238016 ATCGCAACGAAAATCGTAGACT
1 ATCGCAACGAAAATCGTAGACT
6238038 ATCGCAACG
1 ATCGCAACG
6238047 CGAAATGGAA
Statistics
Matches: 39, Mismatches: 8, Indels: 6
0.74 0.15 0.11
Matches are distributed among these distances:
19 12 0.31
20 3 0.08
21 3 0.08
22 21 0.54
ACGTcount: A:0.40, C:0.22, G:0.19, T:0.18
Consensus pattern (22 bp):
ATCGCAACGAAAATCGTAGACT
Found at i:6238014 original size:41 final size:41
Alignment explanation
Indices: 6237969--6238046 Score: 156
Period size: 41 Copynumber: 1.9 Consensus size: 41
6237959 CTATTGGGAA
6237969 TGGAAAATCGCAACGAAAATCGTAGACTATCGCAACGAATT
1 TGGAAAATCGCAACGAAAATCGTAGACTATCGCAACGAATT
6238010 TGGAAAATCGCAACGAAAATCGTAGACTATCGCAACG
1 TGGAAAATCGCAACGAAAATCGTAGACTATCGCAACG
6238047 CGAAATGGAA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 37 1.00
ACGTcount: A:0.41, C:0.21, G:0.21, T:0.18
Consensus pattern (41 bp):
TGGAAAATCGCAACGAAAATCGTAGACTATCGCAACGAATT
Found at i:6238080 original size:41 final size:41
Alignment explanation
Indices: 6238035--6238135 Score: 166
Period size: 41 Copynumber: 2.5 Consensus size: 41
6238025 AAAATCGTAG
6238035 ACTATCGCAACGCGAAATGGAAAATCACAACGCAATTTTCA
1 ACTATCGCAACGCGAAATGGAAAATCACAACGCAATTTTCA
** *
6238076 ACTATCGCAACGCGAAATGGAAAATCGTAACGCGATTTTCA
1 ACTATCGCAACGCGAAATGGAAAATCACAACGCAATTTTCA
*
6238117 ACTCTCGCAACGCGAAATG
1 ACTATCGCAACGCGAAATG
6238136 CAACGCGAAT
Statistics
Matches: 56, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
41 56 1.00
ACGTcount: A:0.38, C:0.25, G:0.18, T:0.20
Consensus pattern (41 bp):
ACTATCGCAACGCGAAATGGAAAATCACAACGCAATTTTCA
Found at i:6238139 original size:21 final size:21
Alignment explanation
Indices: 6238035--6238139 Score: 72
Period size: 21 Copynumber: 5.1 Consensus size: 21
6238025 AAAATCGTAG
*
6238035 ACTATCGCAACGCGAAATGGA
1 ACTATCGCAACGCGAAATGCA
* * * *
6238056 A-AATCACAACGC-AATTTTCA
1 ACTATCGCAACGCGAA-ATGCA
*
6238076 ACTATCGCAACGCGAAATGGA
1 ACTATCGCAACGCGAAATGCA
* * ** *
6238097 A-AATCGTAACGCGATTTTCA
1 ACTATCGCAACGCGAAATGCA
*
6238117 ACTCTCGCAACGCGAAATGCA
1 ACTATCGCAACGCGAAATGCA
6238138 AC
1 AC
6238140 GCGAATTTGC
Statistics
Matches: 58, Mismatches: 22, Indels: 8
0.66 0.25 0.09
Matches are distributed among these distances:
19 2 0.03
20 26 0.45
21 28 0.48
22 2 0.03
ACGTcount: A:0.38, C:0.26, G:0.17, T:0.19
Consensus pattern (21 bp):
ACTATCGCAACGCGAAATGCA
Found at i:6239122 original size:19 final size:20
Alignment explanation
Indices: 6239083--6239126 Score: 63
Period size: 19 Copynumber: 2.2 Consensus size: 20
6239073 CAATTTGACA
*
6239083 AAAACCGGTTGCAAATAGAC
1 AAAACCGATTGCAAATAGAC
*
6239103 AAAACCGATTG-AAATGGAC
1 AAAACCGATTGCAAATAGAC
6239122 AAAAC
1 AAAAC
6239127 ATGTAGAAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 12 0.55
20 10 0.45
ACGTcount: A:0.50, C:0.18, G:0.18, T:0.14
Consensus pattern (20 bp):
AAAACCGATTGCAAATAGAC
Found at i:6240756 original size:100 final size:100
Alignment explanation
Indices: 6240583--6240920 Score: 450
Period size: 100 Copynumber: 3.4 Consensus size: 100
6240573 CTAGCTACGT
* * * *
6240583 AATAGGTGCTACCTATTACGTTAAACTAGCTATCAGA-TTGTTTAAATGTATAATATTAAAGTAA
1 AATAGGAGCTACCTATTACGTTAAACTACCTA-CCGATTTGTTTAAATGTATAATATTAATGTAA
6240647 ACGATAAAATATTTAAAACTTAACCGGTTAAAATAA
65 ACGATAAAATATTTAAAACTTAACCGGTTAAAATAA
* * *
6240683 AATAGGAGCTACCTATTACGTTAAACTACCTATCGATTTGTTTAAAGGTGTAATATTAATGTAAA
1 AATAGGAGCTACCTATTACGTTAAACTACCTACCGATTTGTTTAAATGTATAATATTAATGTAAA
* *
6240748 CAATAAAATATTTACAAA-TTAACCTGTTAAAA-AA
66 CGATAAAATATTTA-AAACTTAACCGGTTAAAATAA
* ** *
6240782 AAGATGTTGCTACCTATTACGTTAAACTACCTACCAATTTGTTTAAATGTATAATATTAATGTAA
1 AATA-GGAGCTACCTATTACGTTAAACTACCTACCGATTTGTTTAAATGTATAATATTAATGTAA
* *
6240847 ACGATAAACTATTTACAACTTAACCGGTTAAAATAA
65 ACGATAAAATATTTAAAACTTAACCGGTTAAAATAA
* **
6240883 AATA-GACGCTACTTATTACGTTAAGTTACCTACCGATT
1 AATAGGA-GCTACCTATTACGTTAAACTACCTACCGATT
6240921 AAAATAAAAT
Statistics
Matches: 205, Mismatches: 27, Indels: 12
0.84 0.11 0.05
Matches are distributed among these distances:
99 9 0.04
100 188 0.92
101 8 0.04
ACGTcount: A:0.41, C:0.14, G:0.11, T:0.34
Consensus pattern (100 bp):
AATAGGAGCTACCTATTACGTTAAACTACCTACCGATTTGTTTAAATGTATAATATTAATGTAAA
CGATAAAATATTTAAAACTTAACCGGTTAAAATAA
Found at i:6241131 original size:108 final size:108
Alignment explanation
Indices: 6240936--6241242 Score: 443
Period size: 108 Copynumber: 2.8 Consensus size: 108
6240926 AAAATATGTG
* *
6240936 CTACCTAATATGTTGATAATATTAATAAAAAAATTAAGTAATTAACCTATTTTATTATCGTCGGA
1 CTACCTAATATGTTGATAATATTAATAACAAAA-TAAGTAATTAACCTATTTTGTTATCGTCGGA
* * * *
6241001 TTTCTAAGGGCCCATCAACTTAAACTTTGGTAACATTTTAGGCG
65 TTTCTAAGGCCCCATCAGCTTAAACTTTGATAACATTTTAGGCA
* * * *
6241045 TTACCTAATATGTTAATAATATTAATAACAAAATAAGTAATTAATCTATTTTGTTATTGTCGGAT
1 CTACCTAATATGTTGATAATATTAATAACAAAATAAGTAATTAACCTATTTTGTTATCGTCGGAT
* * ** *
6241110 TTGTAAAGTTCCATCAGCTTAAAATTTGATAACATTTTAGGCA
66 TTCTAAGGCCCCATCAGCTTAAACTTTGATAACATTTTAGGCA
* *
6241153 CTACCTAATATATTGATAATATTAATAACAAATTAAGTAATTAACCTATTTTGTTATCGTCGGAT
1 CTACCTAATATGTTGATAATATTAATAACAAAATAAGTAATTAACCTATTTTGTTATCGTCGGAT
6241218 TTCTAAGGCCCCATCAGCTTTAAAC
66 TTCTAAGGCCCCATCAGC-TTAAAC
6241243 AGGTGCAACC
Statistics
Matches: 172, Mismatches: 25, Indels: 2
0.86 0.13 0.01
Matches are distributed among these distances:
108 137 0.80
109 35 0.20
ACGTcount: A:0.36, C:0.14, G:0.11, T:0.38
Consensus pattern (108 bp):
CTACCTAATATGTTGATAATATTAATAACAAAATAAGTAATTAACCTATTTTGTTATCGTCGGAT
TTCTAAGGCCCCATCAGCTTAAACTTTGATAACATTTTAGGCA
Found at i:6246392 original size:14 final size:14
Alignment explanation
Indices: 6246360--6246405 Score: 56
Period size: 14 Copynumber: 3.1 Consensus size: 14
6246350 TTCGGTTTGA
*
6246360 AAAAAACCGATTTTTT
1 AAAAAACCGA--TTAT
*
6246376 AAAAAACCGGTTAT
1 AAAAAACCGATTAT
6246390 AAAAAACCGATTAT
1 AAAAAACCGATTAT
6246404 AA
1 AA
6246406 TATTATTAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
14 18 0.67
16 9 0.33
ACGTcount: A:0.52, C:0.13, G:0.09, T:0.26
Consensus pattern (14 bp):
AAAAAACCGATTAT
Found at i:6246493 original size:33 final size:33
Alignment explanation
Indices: 6246456--6246550 Score: 172
Period size: 33 Copynumber: 2.9 Consensus size: 33
6246446 ACGCTAAGTG
* *
6246456 AAATACTTAAATACTTCCAAGTTCGATAAATTT
1 AAATACTTAAAAACTTCCAAGTTCGATAAATTC
6246489 AAATACTTAAAAACTTCCAAGTTCGATAAATTC
1 AAATACTTAAAAACTTCCAAGTTCGATAAATTC
6246522 AAATACTTAAAAACTTCCAAGTTCGATAA
1 AAATACTTAAAAACTTCCAAGTTCGATAA
6246551 TTGAAACAAA
Statistics
Matches: 60, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 60 1.00
ACGTcount: A:0.45, C:0.17, G:0.06, T:0.32
Consensus pattern (33 bp):
AAATACTTAAAAACTTCCAAGTTCGATAAATTC
Found at i:6246570 original size:21 final size:21
Alignment explanation
Indices: 6246545--6246586 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
6246535 CTTCCAAGTT
6246545 CGATAATTGAAACAAAGTTTA
1 CGATAATTGAAACAAAGTTTA
*
6246566 CGATAATTGAAATAAAGTTTA
1 CGATAATTGAAACAAAGTTTA
6246587 AAAATAAACT
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:0.48, C:0.07, G:0.14, T:0.31
Consensus pattern (21 bp):
CGATAATTGAAACAAAGTTTA
Found at i:6259847 original size:15 final size:15
Alignment explanation
Indices: 6259827--6259875 Score: 57
Period size: 15 Copynumber: 3.3 Consensus size: 15
6259817 TTATCAAATT
6259827 TTAAAAATATAAAAA
1 TTAAAAATATAAAAA
*
6259842 TTAAAACTA-ATAAAA
1 TTAAAAATATA-AAAA
*
6259857 TT-AAAATATATAAA
1 TTAAAAATATAAAAA
6259871 TTAAA
1 TTAAA
6259876 TCTATAATTA
Statistics
Matches: 28, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
14 11 0.39
15 17 0.61
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (15 bp):
TTAAAAATATAAAAA
Found at i:6259873 original size:14 final size:14
Alignment explanation
Indices: 6259830--6259875 Score: 58
Period size: 14 Copynumber: 3.2 Consensus size: 14
6259820 TCAAATTTTA
*
6259830 AAAATATAAAAATT
1 AAAATATATAAATT
6259844 AAAACTA-ATAAAATT
1 AAAA-TATAT-AAATT
6259859 AAAATATATAAATT
1 AAAATATATAAATT
6259873 AAA
1 AAA
6259876 TCTATAATTA
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
14 15 0.54
15 13 0.46
ACGTcount: A:0.70, C:0.02, G:0.00, T:0.28
Consensus pattern (14 bp):
AAAATATATAAATT
Found at i:6262055 original size:16 final size:16
Alignment explanation
Indices: 6262032--6262092 Score: 104
Period size: 16 Copynumber: 3.8 Consensus size: 16
6262022 TAATAAATAT
6262032 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
*
6262048 ATGAACATAAACGAAC
1 ACGAACATAAACGAAC
*
6262064 ACGAACATAAATGAAC
1 ACGAACATAAACGAAC
6262080 ACGAACATAAACG
1 ACGAACATAAACG
6262093 TTGGAGACCC
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 41 1.00
ACGTcount: A:0.56, C:0.21, G:0.13, T:0.10
Consensus pattern (16 bp):
ACGAACATAAACGAAC
Found at i:6267912 original size:27 final size:26
Alignment explanation
Indices: 6267856--6267912 Score: 62
Period size: 27 Copynumber: 2.2 Consensus size: 26
6267846 AATTCAAAAA
* *
6267856 AAATATTAAAAGAAATAATATAGGAT
1 AAATATTAAAAGAAATAATATAGAAG
*
6267882 AAATA-TAAAAGAAATTGTATATAGAAG
1 AAATATTAAAAGAAA-T-AATATAGAAG
6267909 AAAT
1 AAAT
6267913 TCTAGTTCAT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
25 9 0.35
26 6 0.23
27 11 0.42
ACGTcount: A:0.61, C:0.00, G:0.12, T:0.26
Consensus pattern (26 bp):
AAATATTAAAAGAAATAATATAGAAG
Found at i:6269205 original size:28 final size:28
Alignment explanation
Indices: 6269163--6269229 Score: 118
Period size: 28 Copynumber: 2.4 Consensus size: 28
6269153 TTTGTTCGAG
*
6269163 TCGGGTCGGG-TTTTTTAAGTGTGATAT
1 TCGGGTCGGGTTTTTTTAAGTATGATAT
6269190 TCGGGTCGGGTTTTTTTAAGTATGATAT
1 TCGGGTCGGGTTTTTTTAAGTATGATAT
6269218 TCGGGTCGGGTT
1 TCGGGTCGGGTT
6269230 CGGGTTTATG
Statistics
Matches: 38, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
27 10 0.26
28 28 0.74
ACGTcount: A:0.13, C:0.09, G:0.34, T:0.43
Consensus pattern (28 bp):
TCGGGTCGGGTTTTTTTAAGTATGATAT
Found at i:6275956 original size:23 final size:23
Alignment explanation
Indices: 6275925--6275972 Score: 62
Period size: 22 Copynumber: 2.1 Consensus size: 23
6275915 TATGATACGA
*
6275925 TTTCTTCTGTTTTTATGACACGTT
1 TTTCTTCTGTCTTT-TGACACGTT
*
6275949 TTTC-TCTGTCTTTTGGCACGTT
1 TTTCTTCTGTCTTTTGACACGTT
6275971 TT
1 TT
6275973 CGATCATTTG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
22 10 0.45
23 8 0.36
24 4 0.18
ACGTcount: A:0.08, C:0.19, G:0.15, T:0.58
Consensus pattern (23 bp):
TTTCTTCTGTCTTTTGACACGTT
Found at i:6275971 original size:22 final size:24
Alignment explanation
Indices: 6275912--6275972 Score: 65
Period size: 23 Copynumber: 2.7 Consensus size: 24
6275902 ATAATTATTC
* *
6275912 CTTTATGATACG-ATTTCTTCTGT
1 CTTTATGACACGTTTTTCTTCTGT
*
6275935 TTTTATGACACGTTTTTC-TCTGT
1 CTTTATGACACGTTTTTCTTCTGT
*
6275958 CTTT-TGGCACGTTTT
1 CTTTATGACACGTTTT
6275973 CGATCATTTG
Statistics
Matches: 32, Mismatches: 5, Indels: 3
0.80 0.12 0.08
Matches are distributed among these distances:
22 10 0.31
23 18 0.56
24 4 0.12
ACGTcount: A:0.13, C:0.18, G:0.15, T:0.54
Consensus pattern (24 bp):
CTTTATGACACGTTTTTCTTCTGT
Found at i:6276555 original size:14 final size:14
Alignment explanation
Indices: 6276514--6276557 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
6276504 AAGATTTGTG
*
6276514 TGTGTGCACACATT
1 TGTGTTCACACATT
* *
6276528 TTTGGTTTACACATT
1 TGT-GTTCACACATT
6276543 TGTGTTCACACATT
1 TGTGTTCACACATT
6276557 T
1 T
6276558 TTTTCGACCT
Statistics
Matches: 24, Mismatches: 5, Indels: 2
0.77 0.16 0.06
Matches are distributed among these distances:
14 13 0.54
15 11 0.46
ACGTcount: A:0.20, C:0.18, G:0.16, T:0.45
Consensus pattern (14 bp):
TGTGTTCACACATT
Found at i:6277584 original size:22 final size:24
Alignment explanation
Indices: 6277553--6277600 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 24
6277543 TATGTTTAAA
6277553 AAAAATTAAATA-GATAATATCTT
1 AAAAATTAAATATGATAATATCTT
* *
6277576 AAAAA-TAAATATTATAATTTCTT
1 AAAAATTAAATATGATAATATCTT
6277599 AA
1 AA
6277601 TCATGTCCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
22 6 0.27
23 16 0.73
ACGTcount: A:0.56, C:0.04, G:0.02, T:0.38
Consensus pattern (24 bp):
AAAAATTAAATATGATAATATCTT
Found at i:6287091 original size:2 final size:2
Alignment explanation
Indices: 6287084--6287108 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
6287074 ATTATATCGT
6287084 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 T
6287109 CAATGATTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:6288772 original size:18 final size:18
Alignment explanation
Indices: 6288749--6288785 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
6288739 CCACCCAAGG
6288749 GGAAATAAGTGAAGCTCT
1 GGAAATAAGTGAAGCTCT
6288767 GGAAATAAGTGAAGCTCT
1 GGAAATAAGTGAAGCTCT
6288785 G
1 G
6288786 TAAAGATGAC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.38, C:0.11, G:0.30, T:0.22
Consensus pattern (18 bp):
GGAAATAAGTGAAGCTCT
Found at i:6309147 original size:21 final size:20
Alignment explanation
Indices: 6309118--6309160 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 20
6309108 TAATTTAATT
6309118 TTTTAAAATTAAT-AAATTAA
1 TTTTAAAA-TAATAAAATTAA
*
6309138 TTTTACAAATATTAAAATTAA
1 TTTTA-AAATAATAAAATTAA
6309159 TT
1 TT
6309161 AAAAATTATT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
20 8 0.40
21 12 0.60
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (20 bp):
TTTTAAAATAATAAAATTAA
Found at i:6310037 original size:199 final size:198
Alignment explanation
Indices: 6309697--6310096 Score: 746
Period size: 199 Copynumber: 2.0 Consensus size: 198
6309687 GATCTTTGCA
6309697 AAAGAACCTAAGAAGAAATGGCAGGTGTAAGGAGGGAAATGATCAACGGTGGGAAAATTTCACGG
1 AAAGAACCTAAGAAGAAATGGCAGGTGTAAGGAGGGAAATGATCAACGGTGGGAAAATTTCACGG
* *
6309762 AGGATTGCCGGACGTCCGATCCCAAGGAGGGGTCAAGTAAAAGTTGCTATATTGCTGGGGATTGC
66 AGGATTGCCGGACGTCCGATCCCAAGAAGGGGTCAAGTAAAAGTTGCAATATTGCTGGGGATTGC
*
6309827 CCATTCTGTTGCTTCTATTTTTTTCTCTAAGTAGTCGCAAGGTTGTTAAATTTCTCCCCAAAAAA
131 CCATTCTGTTGCTTCTA-TTTTTTCTCCAAGTAGTCGCAAGGTTGTTAAATTTCTCCCCAAAAAA
6309892 GTTT
195 GTTT
6309896 AAAGAACCTAAGAAGAAATGGCAGGTGTAAGGAGGGAAATGATCAACGGTGGGAAAATTTCACGG
1 AAAGAACCTAAGAAGAAATGGCAGGTGTAAGGAGGGAAATGATCAACGGTGGGAAAATTTCACGG
6309961 AGGATTGCCGGACGTCCGATCCCAAGAAGGGGTCAAGTAAAAGTTGCAATATTGCTGGGGATTGC
66 AGGATTGCCGGACGTCCGATCCCAAGAAGGGGTCAAGTAAAAGTTGCAATATTGCTGGGGATTGC
* *
6310026 CTATTCTGTTGCTTCTATTTTTTCTCCAAGTAGTCGCAAGTTTGTTAAATTTCTCCCCAAAAAAG
131 CCATTCTGTTGCTTCTATTTTTTCTCCAAGTAGTCGCAAGGTTGTTAAATTTCTCCCCAAAAAAG
6310091 TTT
196 TTT
6310094 AAA
1 AAA
6310097 AGAAGTGGGA
Statistics
Matches: 196, Mismatches: 5, Indels: 1
0.97 0.02 0.00
Matches are distributed among these distances:
198 52 0.27
199 144 0.73
ACGTcount: A:0.31, C:0.17, G:0.26, T:0.27
Consensus pattern (198 bp):
AAAGAACCTAAGAAGAAATGGCAGGTGTAAGGAGGGAAATGATCAACGGTGGGAAAATTTCACGG
AGGATTGCCGGACGTCCGATCCCAAGAAGGGGTCAAGTAAAAGTTGCAATATTGCTGGGGATTGC
CCATTCTGTTGCTTCTATTTTTTCTCCAAGTAGTCGCAAGGTTGTTAAATTTCTCCCCAAAAAAG
TTT
Found at i:6319240 original size:18 final size:18
Alignment explanation
Indices: 6319134--6319227 Score: 143
Period size: 18 Copynumber: 5.2 Consensus size: 18
6319124 AGGGATTATC
6319134 AGTGGTCCTTCGGGACAT
1 AGTGGTCCTTCGGGACAT
*
6319152 AGTGGTCTTTCGGGACAT
1 AGTGGTCCTTCGGGACAT
* *
6319170 AGTGGTCTTTCGAGACAT
1 AGTGGTCCTTCGGGACAT
* *
6319188 AGTGGTCCTTCAGGACAC
1 AGTGGTCCTTCGGGACAT
6319206 AGTGGTCCTTCGGGACAT
1 AGTGGTCCTTCGGGACAT
6319224 AGTG
1 AGTG
6319228 TTCATACGGG
Statistics
Matches: 68, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 68 1.00
ACGTcount: A:0.19, C:0.20, G:0.32, T:0.29
Consensus pattern (18 bp):
AGTGGTCCTTCGGGACAT
Found at i:6319240 original size:36 final size:36
Alignment explanation
Indices: 6319133--6319240 Score: 144
Period size: 36 Copynumber: 3.0 Consensus size: 36
6319123 GAGGGATTAT
*
6319133 CAGTGGTCCTTCGGGACATAGTGGTCTTTCGGGACA
1 CAGTGGTCCTTCGGGACATAGTGGTCATTCGGGACA
* * * * *
6319169 TAGTGGTCTTTCGAGACATAGTGGTCCTTCAGGACA
1 CAGTGGTCCTTCGGGACATAGTGGTCATTCGGGACA
* *
6319205 CAGTGGTCCTTCGGGACATAGTGTTCATACGGGACA
1 CAGTGGTCCTTCGGGACATAGTGGTCATTCGGGACA
6319241 AATTCTATGC
Statistics
Matches: 60, Mismatches: 12, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
36 60 1.00
ACGTcount: A:0.20, C:0.21, G:0.31, T:0.28
Consensus pattern (36 bp):
CAGTGGTCCTTCGGGACATAGTGGTCATTCGGGACA
Found at i:6322160 original size:22 final size:23
Alignment explanation
Indices: 6322117--6322160 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 23
6322107 GTCATTAGTG
**
6322117 GAATTAAGAAGTATAAGGTGTTA
1 GAATTAAGAAGTATAACATGTTA
*
6322140 GAATTAA-AATTATAACATGTT
1 GAATTAAGAAGTATAACATGTT
6322161 GAAAATTGAG
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
22 11 0.61
23 7 0.39
ACGTcount: A:0.45, C:0.02, G:0.18, T:0.34
Consensus pattern (23 bp):
GAATTAAGAAGTATAACATGTTA
Found at i:6323288 original size:18 final size:18
Alignment explanation
Indices: 6323264--6323317 Score: 72
Period size: 18 Copynumber: 3.0 Consensus size: 18
6323254 GAGCGATTAT
*
6323264 CAGTGGTCCTTCGGGACA
1 CAGTGGTCCTACGGGACA
* *
6323282 TAGTGGTCCTCCGGGACA
1 CAGTGGTCCTACGGGACA
*
6323300 CAATGGTCCTACGGGACA
1 CAGTGGTCCTACGGGACA
6323318 AATTCTACGC
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 31 1.00
ACGTcount: A:0.20, C:0.28, G:0.31, T:0.20
Consensus pattern (18 bp):
CAGTGGTCCTACGGGACA
Found at i:6328557 original size:91 final size:93
Alignment explanation
Indices: 6328437--6328619 Score: 264
Period size: 94 Copynumber: 2.0 Consensus size: 93
6328427 TTAATAATTT
* *
6328437 TCAAATAAATTTTGGTTCGATTAACGGTTAAAGAAAAATAAT-TT-ATTTTATTCGGTTAATAAT
1 TCAAATAAATTTGGGTTCGATTAACGGTTAAAGAAAAA-AATATTGATTTGATTCGGTTAATAAT
**
6328500 TTTCAAATAAATTTGGGTTCGATTAACGG
65 TTTCAAATAAATTTCAGTTCGATTAACGG
* *
6328529 TCAAAT-AATTTGGGTTCGATTAATGGTTAAAGAAAAAAATCAGTTGATTTGGTTCGGTTAATAA
1 TCAAATAAATTTGGGTTCGATTAACGGTTAAAGAAAAAAAT-A-TTGATTTGATTCGGTTAATAA
6328593 TTTTCAAATAAATTTCAGTTCGATTAA
64 TTTTCAAATAAATTTCAGTTCGATTAA
6328620 AGGTTAAAGA
Statistics
Matches: 81, Mismatches: 6, Indels: 6
0.87 0.06 0.06
Matches are distributed among these distances:
90 3 0.04
91 29 0.36
92 6 0.07
93 2 0.02
94 41 0.51
ACGTcount: A:0.37, C:0.08, G:0.16, T:0.39
Consensus pattern (93 bp):
TCAAATAAATTTGGGTTCGATTAACGGTTAAAGAAAAAAATATTGATTTGATTCGGTTAATAATT
TTCAAATAAATTTCAGTTCGATTAACGG
Found at i:6328564 original size:159 final size:159
Alignment explanation
Indices: 6328273--6328685 Score: 611
Period size: 159 Copynumber: 2.6 Consensus size: 159
6328263 AAAATACGGC
* * ** *
6328273 TAATAATTTTAAAATAAATTTCGGATT-GATTAACGGTTAAGGAAAAA-AA---AAATTATTTGG
1 TAATAATTTTCAAATAAATTTCGG-TTCGATTAACGGTTAAAGAAAAATAATTTATTTTATTCGG
* *
6328333 GTAATAATTTTCAAATAAATTTCGATTCGATTAACGGTCAAATAATTTCGGTTCGATTAATGGTG
65 TTAATAATTTTCAAATAAATTTCGGTTCGATTAACGGTCAAATAATTTCGGTTCGATTAATGGTG
* *
6328398 AATGAAAAAAATCGGTTGATTTGGTTCAAT
130 AAAGAAAAAAATCAGTTGATTTGGTTCAAT
*
6328428 TAATAATTTTCAAATAAATTTTGGTTCGATTAACGGTTAAAGAAAAATAATTTATTTTATTCGGT
1 TAATAATTTTCAAATAAATTTCGGTTCGATTAACGGTTAAAGAAAAATAATTTATTTTATTCGGT
* * *
6328493 TAATAATTTTCAAATAAATTTGGGTTCGATTAACGGTCAAATAATTTGGGTTCGATTAATGGTTA
66 TAATAATTTTCAAATAAATTTCGGTTCGATTAACGGTCAAATAATTTCGGTTCGATTAATGGTGA
**
6328558 AAGAAAAAAATCAGTTGATTTGGTTCGGT
131 AAGAAAAAAATCAGTTGATTTGGTTCAAT
* *
6328587 TAATAATTTTCAAATAAATTTCAGTTCGATTAAAGGTTAAAGAAAAATAATTTATTTTATTCGGT
1 TAATAATTTTCAAATAAATTTCGGTTCGATTAACGGTTAAAGAAAAATAATTTATTTTATTCGGT
* *
6328652 TAATAATTTTAAAATAAATTTTGGTTCGATTAAC
66 TAATAATTTTCAAATAAATTTCGGTTCGATTAAC
6328686 AGTTAAAGAA
Statistics
Matches: 233, Mismatches: 20, Indels: 6
0.90 0.08 0.02
Matches are distributed among these distances:
154 2 0.01
155 41 0.18
156 2 0.01
159 188 0.81
ACGTcount: A:0.39, C:0.07, G:0.15, T:0.39
Consensus pattern (159 bp):
TAATAATTTTCAAATAAATTTCGGTTCGATTAACGGTTAAAGAAAAATAATTTATTTTATTCGGT
TAATAATTTTCAAATAAATTTCGGTTCGATTAACGGTCAAATAATTTCGGTTCGATTAATGGTGA
AAGAAAAAAATCAGTTGATTTGGTTCAAT
Found at i:6328614 original size:68 final size:65
Alignment explanation
Indices: 6328529--6328749 Score: 304
Period size: 65 Copynumber: 3.4 Consensus size: 65
6328519 CGATTAACGG
* **
6328529 TCAAAT-AATTTGGGTTCGATTAATGGTTAAAGAAAAA-AATCAGTTGATTTGGTTCGGTTAATA
1 TCAAATAAATTTGGGTTCGATTAAAGGTTAAAGAAAAATAAT---TT-ATTTTATTCGGTTAATA
6328592 ATTT
62 ATTT
**
6328596 TCAAATAAATTTCAGTTCGATTAAAGGTTAAAGAAAAATAATTTATTTTATTCGGTTAATAATTT
1 TCAAATAAATTTGGGTTCGATTAAAGGTTAAAGAAAAATAATTTATTTTATTCGGTTAATAATTT
* *
6328661 TAAAATAAATTTTGGTTCGATTAACA-GTTAAAGAAAAATAATTTATTTTATTCGGTTAATAATT
1 TCAAATAAATTTGGGTTCGATTAA-AGGTTAAAGAAAAATAATTTATTTTATTCGGTTAATAATT
6328725 T
65 T
*
6328726 TTAAATAAATTTGGGTTCGATTAA
1 TCAAATAAATTTGGGTTCGATTAA
6328750 CGGTCAAATA
Statistics
Matches: 141, Mismatches: 10, Indels: 8
0.89 0.06 0.05
Matches are distributed among these distances:
65 101 0.72
66 3 0.02
67 6 0.04
68 28 0.20
69 3 0.02
ACGTcount: A:0.39, C:0.05, G:0.14, T:0.41
Consensus pattern (65 bp):
TCAAATAAATTTGGGTTCGATTAAAGGTTAAAGAAAAATAATTTATTTTATTCGGTTAATAATTT
Found at i:6328666 original size:32 final size:32
Alignment explanation
Indices: 6328630--6328733 Score: 88
Period size: 32 Copynumber: 3.2 Consensus size: 32
6328620 AGGTTAAAGA
6328630 AAAATAATTTATTTTATTCGGTTAATAATTTT
1 AAAATAATTTATTTTATTCGGTTAATAATTTT
* * * * **
6328662 AAAATAA---ATTTTGGTTCGATTAACAGTTAAAGA
1 AAAATAATTTATTTT-ATTCGGTTAATAATT---TT
6328695 AAAATAATTTATTTTATTCGGTTAATAATTTT
1 AAAATAATTTATTTTATTCGGTTAATAATTTT
*
6328727 TAAATAA
1 AAAATAA
6328734 ATTTGGGTTC
Statistics
Matches: 52, Mismatches: 13, Indels: 14
0.66 0.16 0.18
Matches are distributed among these distances:
29 5 0.10
30 11 0.21
32 13 0.25
33 7 0.13
35 11 0.21
36 5 0.10
ACGTcount: A:0.42, C:0.04, G:0.09, T:0.45
Consensus pattern (32 bp):
AAAATAATTTATTTTATTCGGTTAATAATTTT
Found at i:6328681 original size:224 final size:225
Alignment explanation
Indices: 6328427--6328869 Score: 764
Period size: 224 Copynumber: 2.0 Consensus size: 225
6328417 TTTGGTTCAA
* *
6328427 TTAATAATTTTCAAATAAATTTTGGTTCGATTAACGGTTAAAGAAAAATAATTTATTTTATTCGG
1 TTAATAATTTTAAAATAAATTTTGGTTCGATTAACAGTTAAAGAAAAATAATTTATTTTATTCGG
6328492 TTAATAATTTTCAAATAAATTTGGGTTCGATTAACGGTCAAATAATTTGGGTTCGATTAATGGTT
66 TTAATAATTTTCAAATAAATTTGGGTTCGATTAACGGTCAAATAATTTGGGTTCGATTAATGGTT
* *
6328557 AAAG-AAAAAAATCAGTTGATTTGGTTCGGTTAATAATTTTCAAATAAATTTCAGTTCGATTAAA
131 AAAGAAAAAAAATCAGTTAATTTGGTTC-ATTAATAATTTTCAAATAAATTTCAGTTCGATTAAA
*
6328621 GGTTAAAGAAAAA-TAATTTATTTTATTCGG
195 GGTTAAAGAAAAATTAATTAATTTTATTCGG
6328651 TTAATAATTTTAAAATAAATTTTGGTTCGATTAACAGTTAAAGAAAAATAATTTATTTTATTCGG
1 TTAATAATTTTAAAATAAATTTTGGTTCGATTAACAGTTAAAGAAAAATAATTTATTTTATTCGG
* *
6328716 TTAATAATTTTTAAATAAATTTGGGTTCGATTAACGGTCAAATAATTTTGGTTCGATTAATGGTT
66 TTAATAATTTTCAAATAAATTTGGGTTCGATTAACGGTCAAATAATTTGGGTTCGATTAATGGTT
* * *
6328781 AAAGAAAAAAAAATCGGTTAATTTGGTTCATTAATAATTTTCAAATAAATTTCGGTTCGATTAAT
131 AAAG-AAAAAAAATCAGTTAATTTGGTTCATTAATAATTTTCAAATAAATTTCAGTTCGATTAAA
6328846 GGTTAAAGAAAAATTAATTAATTT
195 GGTTAAAGAAAAATTAATTAATTT
6328870 AAAAAAATAA
Statistics
Matches: 206, Mismatches: 10, Indels: 4
0.94 0.05 0.02
Matches are distributed among these distances:
224 130 0.63
225 46 0.22
226 30 0.15
ACGTcount: A:0.39, C:0.06, G:0.14, T:0.41
Consensus pattern (225 bp):
TTAATAATTTTAAAATAAATTTTGGTTCGATTAACAGTTAAAGAAAAATAATTTATTTTATTCGG
TTAATAATTTTCAAATAAATTTGGGTTCGATTAACGGTCAAATAATTTGGGTTCGATTAATGGTT
AAAGAAAAAAAATCAGTTAATTTGGTTCATTAATAATTTTCAAATAAATTTCAGTTCGATTAAAG
GTTAAAGAAAAATTAATTAATTTTATTCGG
Found at i:6328738 original size:159 final size:159
Alignment explanation
Indices: 6328273--6328869 Score: 419
Period size: 159 Copynumber: 3.8 Consensus size: 159
6328263 AAAATACGGC
* * * * ** *
6328273 TAATAATTTTAAAATAAATTTCGGATT-GATTAACGGTTAAGGAAAAA-AA---AAATTATTTGG
1 TAATAATTTTCAAATAAATTTTGG-TTCGATTAAAGGTTAAAGAAAAATAATTTATTTTATTCGG
* * * * ** *** ***
6328333 GTAATAATTTTCAAATAAATTTCGATTCGATTAACGGTCAAA-TAATTTCGGTTCGATTAATGGT
65 TTAATAATTTTCAAATAAATTTCGGTTCGATTAACGGTTAAAGAAAAATAATTTATTTTAATGGT
* * *** ** *
6328397 GAATGAAAAAAATCGGTTGATTTGGTTCAAT
130 TAAAGAAAAAAATAAATAAATTTGGTTC-GT
*
6328428 TAATAATTTTCAAATAAATTTTGGTTCGATTAACGGTTAAAGAAAAATAATTTATTTTATTCGGT
1 TAATAATTTTCAAATAAATTTTGGTTCGATTAAAGGTTAAAGAAAAATAATTTATTTTATTCGGT
* * * ** *** ***
6328493 TAATAATTTTCAAATAAATTTGGGTTCGATTAACGGTCAAA-TAATTTGGGTTCGATTAATGGTT
66 TAATAATTTTCAAATAAATTTCGGTTCGATTAACGGTTAAAGAAAAATAATTTATTTTAATGGTT
* * **
6328557 AAAGAAAAAAATCAGTTGATTTGGTTCGGT
131 AAAGAAAAAAATAAATAAATTTGGTTC-GT
**
6328587 TAATAATTTTCAAATAAATTTCAGTTCGATTAAAGGTTAAAGAAAAATAATTTATTTTATTCGGT
1 TAATAATTTTCAAATAAATTTTGGTTCGATTAAAGGTTAAAGAAAAATAATTTATTTTATTCGGT
* * * *
6328652 TAATAATTTTAAAATAAATTTTGGTTCGATTAACAGTTAAAGAAAAATAATTTATTTTATTCGGT
66 TAATAATTTTCAAATAAATTTCGGTTCGATTAACGGTTAAAGAAAAATAATTTATTTTAAT-GGT
* ****
6328717 T-AA-TAATTTTTAAATAAATTTGGGTTCG-
130 TAAAGAAAAAAATAAATAAATTT-GGTTCGT
* *** * * **
6328745 -ATTAACGGTCAAAT-AATTTTGGTTCGATTAATGGTTAAAGAAAAAAAAATCGGTTAATTTGGT
1 TAATAATTTTCAAATAAATTTTGGTTCGATTAAAGGTTAAAG-AAAAATAAT---TT-ATTTTAT
* * *
6328808 TC-ATTAATAATTTTCAAATAAATTTCGGTTCGATTAATGGTTAAAGAAAAATTAATTAATTT
61 TCGGTTAATAATTTTCAAATAAATTTCGGTTCGATTAACGGTTAAAGAAAAA-TAATTTATTT
6328870 AAAAAAATAA
Statistics
Matches: 371, Mismatches: 57, Indels: 22
0.82 0.13 0.05
Matches are distributed among these distances:
154 2 0.01
155 41 0.11
156 25 0.07
157 18 0.05
159 203 0.55
160 62 0.17
161 20 0.05
ACGTcount: A:0.39, C:0.06, G:0.15, T:0.39
Consensus pattern (159 bp):
TAATAATTTTCAAATAAATTTTGGTTCGATTAAAGGTTAAAGAAAAATAATTTATTTTATTCGGT
TAATAATTTTCAAATAAATTTCGGTTCGATTAACGGTTAAAGAAAAATAATTTATTTTAATGGTT
AAAGAAAAAAATAAATAAATTTGGTTCGT
Found at i:6328769 original size:91 final size:94
Alignment explanation
Indices: 6328663--6328844 Score: 237
Period size: 95 Copynumber: 1.9 Consensus size: 94
6328653 AATAATTTTA
* * *
6328663 AAATAAATTTTGGTTCGATTAACAGTTAAAG-AAAAATAAT-TT-ATTTTATTCGGTTAATAATT
1 AAATAAATTTTGGTTCGATTAACAGTTAAAGAAAAAAAAATGTTAATTTGATTC-ATTAATAATT
* *
6328725 TTTAAATAAATTTGGGTTCGATTAACGGTC
65 TTCAAATAAATTTCGGTTCGATTAACGGTC
** *
6328755 AAAT-AATTTTGGTTCGATTAATGGTTAAAGAAAAAAAAATCGGTTAATTTGGTTCATTAATAAT
1 AAATAAATTTTGGTTCGATTAACAGTTAAAGAAAAAAAAAT--GTTAATTTGATTCATTAATAAT
6328819 TTTCAAATAAATTTCGGTTCGATTAA
64 TTTCAAATAAATTTCGGTTCGATTAA
6328845 TGGTTAAAGA
Statistics
Matches: 77, Mismatches: 8, Indels: 7
0.84 0.09 0.08
Matches are distributed among these distances:
91 24 0.31
92 12 0.16
95 34 0.44
96 7 0.09
ACGTcount: A:0.39, C:0.07, G:0.14, T:0.40
Consensus pattern (94 bp):
AAATAAATTTTGGTTCGATTAACAGTTAAAGAAAAAAAAATGTTAATTTGATTCATTAATAATTT
TCAAATAAATTTCGGTTCGATTAACGGTC
Found at i:6335448 original size:25 final size:25
Alignment explanation
Indices: 6335419--6335476 Score: 107
Period size: 25 Copynumber: 2.3 Consensus size: 25
6335409 TATTATCTAA
6335419 AAAAATAAGAATACTTTAAATTAGG
1 AAAAATAAGAATACTTTAAATTAGG
*
6335444 GAAAATAAGAATACTTTAAATTAGG
1 AAAAATAAGAATACTTTAAATTAGG
6335469 AAAAATAA
1 AAAAATAA
6335477 TACTAAATAC
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
25 31 1.00
ACGTcount: A:0.59, C:0.03, G:0.12, T:0.26
Consensus pattern (25 bp):
AAAAATAAGAATACTTTAAATTAGG
Found at i:6345814 original size:31 final size:33
Alignment explanation
Indices: 6345766--6345844 Score: 90
Period size: 34 Copynumber: 2.4 Consensus size: 33
6345756 TTTAAATAGT
*
6345766 TATTATATTTTATATT-AAT-ATAATTATATAAA
1 TATTAT-TTTTTTATTAAATAATAATTATATAAA
* *
6345798 TATTATTTTTTTATTAAAATAATATTTATATAAT
1 TATTATTTTTTTATT-AAATAATAATTATATAAA
*
6345832 TATTATTTATTTA
1 TATTATTTTTTTA
6345845 AATTTATTAA
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
31 8 0.20
32 6 0.15
33 3 0.08
34 23 0.57
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (33 bp):
TATTATTTTTTTATTAAATAATAATTATATAAA
Found at i:6345836 original size:34 final size:31
Alignment explanation
Indices: 6345756--6345867 Score: 88
Period size: 34 Copynumber: 3.6 Consensus size: 31
6345746 TTAGTATTTT
* * *
6345756 TTTAAATAGTTATTATATTTTATATTAATATA
1 TTTATATAATTATTAT-TTTTTTATTAATATA
* *
6345788 ATTATATAAATATTATTTTTTTATTAAAATAATA
1 TTTATATAATTATTATTTTTTTATT--AAT-ATA
* *
6345822 TTTATATAATTATTATTTATTTA--AATTTA
1 TTTATATAATTATTATTTTTTTATTAATATA
*
6345851 TTAAT-TAATTATT-TTTT
1 TTTATATAATTATTATTTT
6345868 GTGCTAATTA
Statistics
Matches: 66, Mismatches: 11, Indels: 11
0.75 0.12 0.12
Matches are distributed among these distances:
27 3 0.05
28 8 0.12
29 6 0.09
30 3 0.05
31 8 0.12
32 12 0.18
33 3 0.05
34 23 0.35
ACGTcount: A:0.40, C:0.00, G:0.01, T:0.59
Consensus pattern (31 bp):
TTTATATAATTATTATTTTTTTATTAATATA
Found at i:6347687 original size:21 final size:21
Alignment explanation
Indices: 6347638--6347687 Score: 75
Period size: 21 Copynumber: 2.4 Consensus size: 21
6347628 TGTCATCTCG
*
6347638 GCAGGGTTACATTCCTAGCCC
1 GCAGGGTTACATGCCTAGCCC
6347659 GCCA-GGTTACATGCCTAGCCC
1 G-CAGGGTTACATGCCTAGCCC
6347680 GCAGGGTT
1 GCAGGGTT
6347688 TTATACCATA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
20 2 0.08
21 22 0.85
22 2 0.08
ACGTcount: A:0.18, C:0.32, G:0.28, T:0.22
Consensus pattern (21 bp):
GCAGGGTTACATGCCTAGCCC
Found at i:6348265 original size:34 final size:34
Alignment explanation
Indices: 6348209--6348315 Score: 151
Period size: 34 Copynumber: 3.1 Consensus size: 34
6348199 ATAAATGTTT
*
6348209 TTAAAATACAAATTATAGTATTCGAAATTTAAAA
1 TTAAAATATAAATTATAGTATTCGAAATTTAAAA
* * * * *
6348243 TTAAAATTTAAATAATATTATTCAAAATTTAAAT
1 TTAAAATATAAATTATAGTATTCGAAATTTAAAA
*
6348277 TTAAAATATAAATTATAGTATTCGAAATTTAACA
1 TTAAAATATAAATTATAGTATTCGAAATTTAAAA
6348311 TTAAA
1 TTAAA
6348316 TTCAACTTAA
Statistics
Matches: 61, Mismatches: 12, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
34 61 1.00
ACGTcount: A:0.52, C:0.05, G:0.04, T:0.39
Consensus pattern (34 bp):
TTAAAATATAAATTATAGTATTCGAAATTTAAAA
Found at i:6348964 original size:127 final size:127
Alignment explanation
Indices: 6348738--6349371 Score: 1038
Period size: 127 Copynumber: 5.0 Consensus size: 127
6348728 CCGCTTTAAA
* *
6348738 GTCCCATAAGGAATAGTAGGTATTGACATGAATAGTTCTCGGGGGACATAACTGACATAATAGGG
1 GTCCCCTAAGGAATAATAGGTATTGACATGAATAGTTCTCGGGGGACATAACTGACATAATAGGG
* *
6348803 CAATGATAACATATTCTCTGACAAAATAATGGAAGGCGCGCCCCCGGGAATGCGCCTTCACG
66 CAATGATAACATATTCTCTGACAAAATAATGGAAGGCGCACCCCCGGGAACGCGCCTTCACG
*
6348865 GTCCCCTAAGGAATAATAGGTATTGACATGAATAGTT-TCCGGGGGACATAAGTGACATAATAGG
1 GTCCCCTAAGGAATAATAGGTATTGACATGAATAGTTCT-CGGGGGACATAACTGACATAATAGG
* * * *
6348929 GCAATGATAACATATTCTATGACAAAATAATGGAAGACGTACCCCCGAGAACGCGCCTTCACG
65 GCAATGATAACATATTCTCTGACAAAATAATGGAAGGCGCACCCCCGGGAACGCGCCTTCACG
* *
6348992 GTCCCTTAAGGAATAATAGGTATTGACATGAATAGTTCTCGGGGGACATAAATGACATAATAGGG
1 GTCCCCTAAGGAATAATAGGTATTGACATGAATAGTTCTCGGGGGACATAACTGACATAATAGGG
6349057 CAATGATAACATATTCTCTGACAAAATAATGGAAGGCGCACCCCCGGGAACGCGCCTTCACG
66 CAATGATAACATATTCTCTGACAAAATAATGGAAGGCGCACCCCCGGGAACGCGCCTTCACG
6349119 GTCCCCTAAGGAATAATAGGTATTGACATGAATAGTTCTCGGGGGACATAACTGACATAATAGGG
1 GTCCCCTAAGGAATAATAGGTATTGACATGAATAGTTCTCGGGGGACATAACTGACATAATAGGG
* *
6349184 CAATGATAACATATTCTCTGACAAAATAATGAAATGCGC-CCCCCGGGAACGCGCCTTCACG
66 CAATGATAACATATTCTCTGACAAAATAATGGAAGGCGCACCCCCGGGAACGCGCCTTCACG
* * *
6349245 GTCCCCTAAGGAATAATATGTATTGATATGAATAGTTCTCGGGGGACATAAGTGACATAATAGGG
1 GTCCCCTAAGGAATAATAGGTATTGACATGAATAGTTCTCGGGGGACATAACTGACATAATAGGG
* * * * * * *
6349310 CAATGATTATATATTCTCTGATAAAATAATAGAAGGCGCGCCCCCAGGAATGCGCCTTCACG
66 CAATGATAACATATTCTCTGACAAAATAATGGAAGGCGCACCCCCGGGAACGCGCCTTCACG
6349372 TGAATAGTAC
Statistics
Matches: 474, Mismatches: 30, Indels: 6
0.93 0.06 0.01
Matches are distributed among these distances:
126 118 0.25
127 355 0.75
128 1 0.00
ACGTcount: A:0.34, C:0.20, G:0.23, T:0.23
Consensus pattern (127 bp):
GTCCCCTAAGGAATAATAGGTATTGACATGAATAGTTCTCGGGGGACATAACTGACATAATAGGG
CAATGATAACATATTCTCTGACAAAATAATGGAAGGCGCACCCCCGGGAACGCGCCTTCACG
Found at i:6354084 original size:65 final size:65
Alignment explanation
Indices: 6353980--6354109 Score: 260
Period size: 65 Copynumber: 2.0 Consensus size: 65
6353970 CTTTGCCTAT
6353980 TGCTGGTACTTGGAAGTGATCCAATATACAGTTTTTTTTTACTGCTGCTAACTGATGAATTCGTA
1 TGCTGGTACTTGGAAGTGATCCAATATACAGTTTTTTTTTACTGCTGCTAACTGATGAATTCGTA
6354045 TGCTGGTACTTGGAAGTGATCCAATATACAGTTTTTTTTTACTGCTGCTAACTGATGAATTCGTA
1 TGCTGGTACTTGGAAGTGATCCAATATACAGTTTTTTTTTACTGCTGCTAACTGATGAATTCGTA
6354110 GTGATATCCG
Statistics
Matches: 65, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
65 65 1.00
ACGTcount: A:0.25, C:0.15, G:0.20, T:0.40
Consensus pattern (65 bp):
TGCTGGTACTTGGAAGTGATCCAATATACAGTTTTTTTTTACTGCTGCTAACTGATGAATTCGTA
Found at i:6367509 original size:39 final size:39
Alignment explanation
Indices: 6367465--6367542 Score: 156
Period size: 39 Copynumber: 2.0 Consensus size: 39
6367455 TCACCGTTAA
6367465 TTTGCCGATGAGATTTTAGTAACAAGCAAATCACTTGGG
1 TTTGCCGATGAGATTTTAGTAACAAGCAAATCACTTGGG
6367504 TTTGCCGATGAGATTTTAGTAACAAGCAAATCACTTGGG
1 TTTGCCGATGAGATTTTAGTAACAAGCAAATCACTTGGG
6367543 GCAAACCTTG
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 39 1.00
ACGTcount: A:0.31, C:0.15, G:0.23, T:0.31
Consensus pattern (39 bp):
TTTGCCGATGAGATTTTAGTAACAAGCAAATCACTTGGG
Found at i:6375225 original size:27 final size:27
Alignment explanation
Indices: 6375191--6375245 Score: 110
Period size: 27 Copynumber: 2.0 Consensus size: 27
6375181 TGCACACCAG
6375191 ACATTGGTGGGTGAATCTCTTAGCAGA
1 ACATTGGTGGGTGAATCTCTTAGCAGA
6375218 ACATTGGTGGGTGAATCTCTTAGCAGA
1 ACATTGGTGGGTGAATCTCTTAGCAGA
6375245 A
1 A
6375246 ATTTTCTGCA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.27, C:0.15, G:0.29, T:0.29
Consensus pattern (27 bp):
ACATTGGTGGGTGAATCTCTTAGCAGA
Found at i:6378824 original size:21 final size:21
Alignment explanation
Indices: 6378798--6378840 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
6378788 TTTCTGGGTT
* *
6378798 AGGGGAATCGGTACCCATTCA
1 AGGGGAACCGATACCCATTCA
*
6378819 AGGGGAACCGATACCCCTTCA
1 AGGGGAACCGATACCCATTCA
6378840 A
1 A
6378841 CGAATATGAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.30, C:0.28, G:0.26, T:0.16
Consensus pattern (21 bp):
AGGGGAACCGATACCCATTCA
Found at i:6378952 original size:67 final size:68
Alignment explanation
Indices: 6378820--6378971 Score: 191
Period size: 68 Copynumber: 2.2 Consensus size: 68
6378810 ACCCATTCAA
* * * * * *
6378820 GGGGAACCGATACCCCTTCAACGAATATGATTTCCAGAATGCTAGAGGGGAATCGGTACCCCCA-
1 GGGGAACCGATACCCCCTCAACGAATAAGAATTCCAGAAGGCTAGAGGGGAACCGATACCCCCAG
6378884 GGG
66 GGG
* * *
6378887 GGGGAACCGATACCCCCTCATCGTATAAGAAATTCCAGAAGGCTATAGGGGAACCGATA-CCCCA
1 GGGGAACCGATACCCCCTCAACGAATAAG-AATTCCAGAAGGCTAGAGGGGAACCGATACCCCCA
6378951 GGGG
65 GGGG
*
6378955 GGGGAACCGATTCCCCC
1 GGGGAACCGATACCCCC
6378972 ATGAGAAAAA
Statistics
Matches: 73, Mismatches: 10, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
67 30 0.41
68 43 0.59
ACGTcount: A:0.28, C:0.28, G:0.28, T:0.16
Consensus pattern (68 bp):
GGGGAACCGATACCCCCTCAACGAATAAGAATTCCAGAAGGCTAGAGGGGAACCGATACCCCCAG
GGG
Found at i:6379329 original size:28 final size:28
Alignment explanation
Indices: 6379274--6379344 Score: 106
Period size: 28 Copynumber: 2.5 Consensus size: 28
6379264 CATATTATGA
*
6379274 TACATGACATGAAATTGTATTAAATGTAT
1 TACATGACATG-AATTATATTAAATGTAT
* *
6379303 TACATGACATGAATTATCTTATATGTAT
1 TACATGACATGAATTATATTAAATGTAT
6379331 TACATGACATGAAT
1 TACATGACATGAAT
6379345 ATGCAGAAAA
Statistics
Matches: 39, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
28 28 0.72
29 11 0.28
ACGTcount: A:0.39, C:0.10, G:0.13, T:0.38
Consensus pattern (28 bp):
TACATGACATGAATTATATTAAATGTAT
Found at i:6379399 original size:30 final size:31
Alignment explanation
Indices: 6379359--6379417 Score: 84
Period size: 30 Copynumber: 1.9 Consensus size: 31
6379349 AGAAAAGTTC
*
6379359 TATGCACTATGTGATAAAAGTATGTAAATGA
1 TATGCACTATGTGATAAAAGTATGGAAATGA
* *
6379390 TATGC-CTATGTGTTAAAGGTATGGAAAT
1 TATGCACTATGTGATAAAAGTATGGAAAT
6379418 ACTATGTCTA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
30 20 0.80
31 5 0.20
ACGTcount: A:0.37, C:0.07, G:0.22, T:0.34
Consensus pattern (31 bp):
TATGCACTATGTGATAAAAGTATGGAAATGA
Found at i:6379708 original size:22 final size:22
Alignment explanation
Indices: 6379634--6379700 Score: 134
Period size: 22 Copynumber: 3.0 Consensus size: 22
6379624 TTATGGACAA
6379634 AATTCTACGGGCACTTCGGTGC
1 AATTCTACGGGCACTTCGGTGC
6379656 AATTCTACGGGCACTTCGGTGC
1 AATTCTACGGGCACTTCGGTGC
6379678 AATTCTACGGGCACTTCGGTGC
1 AATTCTACGGGCACTTCGGTGC
6379700 A
1 A
6379701 TTTATACGAG
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 45 1.00
ACGTcount: A:0.19, C:0.27, G:0.27, T:0.27
Consensus pattern (22 bp):
AATTCTACGGGCACTTCGGTGC
Found at i:6385711 original size:21 final size:21
Alignment explanation
Indices: 6385685--6385727 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
6385675 TTTCTGGGTT
* *
6385685 AGGGGAATCGGTACCCATTCA
1 AGGGGAACCGATACCCATTCA
*
6385706 AGGGGAACCGATACCCCTTCA
1 AGGGGAACCGATACCCATTCA
6385727 A
1 A
6385728 CGAATATGAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.30, C:0.28, G:0.26, T:0.16
Consensus pattern (21 bp):
AGGGGAACCGATACCCATTCA
Found at i:6385839 original size:67 final size:68
Alignment explanation
Indices: 6385707--6385858 Score: 191
Period size: 68 Copynumber: 2.2 Consensus size: 68
6385697 ACCCATTCAA
* * * * * *
6385707 GGGGAACCGATACCCCTTCAACGAATATGATTTCCAGAATGCTAGAGGGGAATCGGTACCCCCA-
1 GGGGAACCGATACCCCCTCAACGAATAAGAATTCCAGAAGGCTAGAGGGGAACCGATACCCCCAG
6385771 GGG
66 GGG
* * *
6385774 GGGGAACCGATACCCCCTCATCGTATAAGAAATTCCAGAAGGCTATAGGGGAACCGATA-CCCCA
1 GGGGAACCGATACCCCCTCAACGAATAAG-AATTCCAGAAGGCTAGAGGGGAACCGATACCCCCA
6385838 GGGG
65 GGGG
*
6385842 GGGGAACCGATTCCCCC
1 GGGGAACCGATACCCCC
6385859 ATGAGAAAAA
Statistics
Matches: 73, Mismatches: 10, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
67 30 0.41
68 43 0.59
ACGTcount: A:0.28, C:0.28, G:0.28, T:0.16
Consensus pattern (68 bp):
GGGGAACCGATACCCCCTCAACGAATAAGAATTCCAGAAGGCTAGAGGGGAACCGATACCCCCAG
GGG
Found at i:6386215 original size:28 final size:28
Alignment explanation
Indices: 6386160--6386230 Score: 106
Period size: 28 Copynumber: 2.5 Consensus size: 28
6386150 CATATTATGA
*
6386160 TACATGACATGAAATTGTATTAAATGTAT
1 TACATGACATG-AATTATATTAAATGTAT
* *
6386189 TACATGACATGAATTATCTTATATGTAT
1 TACATGACATGAATTATATTAAATGTAT
6386217 TACATGACATGAAT
1 TACATGACATGAAT
6386231 ATGCAGAAAA
Statistics
Matches: 39, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
28 28 0.72
29 11 0.28
ACGTcount: A:0.39, C:0.10, G:0.13, T:0.38
Consensus pattern (28 bp):
TACATGACATGAATTATATTAAATGTAT
Found at i:6386285 original size:30 final size:31
Alignment explanation
Indices: 6386245--6386303 Score: 84
Period size: 30 Copynumber: 1.9 Consensus size: 31
6386235 AGAAAAGTTC
*
6386245 TATGCACTATGTGATAAAAGTATGTAAATGA
1 TATGCACTATGTGATAAAAGTATGGAAATGA
* *
6386276 TATGC-CTATGTGTTAAAGGTATGGAAAT
1 TATGCACTATGTGATAAAAGTATGGAAAT
6386304 ACTATGTCTA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
30 20 0.80
31 5 0.20
ACGTcount: A:0.37, C:0.07, G:0.22, T:0.34
Consensus pattern (31 bp):
TATGCACTATGTGATAAAAGTATGGAAATGA
Found at i:6386592 original size:22 final size:22
Alignment explanation
Indices: 6386518--6386584 Score: 134
Period size: 22 Copynumber: 3.0 Consensus size: 22
6386508 TTATGGACAA
6386518 AATTCTACGGGCACTTCGGTGC
1 AATTCTACGGGCACTTCGGTGC
6386540 AATTCTACGGGCACTTCGGTGC
1 AATTCTACGGGCACTTCGGTGC
6386562 AATTCTACGGGCACTTCGGTGC
1 AATTCTACGGGCACTTCGGTGC
6386584 A
1 A
6386585 TTTATACGAG
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 45 1.00
ACGTcount: A:0.19, C:0.27, G:0.27, T:0.27
Consensus pattern (22 bp):
AATTCTACGGGCACTTCGGTGC
Found at i:6389315 original size:26 final size:26
Alignment explanation
Indices: 6389279--6389330 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
6389269 ATTACTATTT
6389279 TCATAGTGAAATTCTTCTACCGTTGC
1 TCATAGTGAAATTCTTCTACCGTTGC
6389305 TCATAGTGAAATTCTTCTACCGTTGC
1 TCATAGTGAAATTCTTCTACCGTTGC
6389331 CGTGGTTTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.23, C:0.23, G:0.15, T:0.38
Consensus pattern (26 bp):
TCATAGTGAAATTCTTCTACCGTTGC
Found at i:6398684 original size:98 final size:99
Alignment explanation
Indices: 6398515--6398712 Score: 389
Period size: 98 Copynumber: 2.0 Consensus size: 99
6398505 CCCATATAAA
6398515 TCTTTAATTTTAAAATGTTATTTATGCTTGTGTTAGTTCTCAGCTCACCTCTTGGTATGAATTGT
1 TCTTTAATTTTAAAATGTTATTTATGCTTGTGTTAGTTCTCAGCTCACCTCTTGGTATGAATTGT
6398580 TGTCCAGATTACTTTGAATCTATATTG-TTGGAT
66 TGTCCAGATTACTTTGAATCTATATTGTTTGGAT
6398613 TCTTTAATTTTAAAATGTTATTTATGCTTGTGTTAGTTCTCAGCTCACCTCTTGGTATGAATTGT
1 TCTTTAATTTTAAAATGTTATTTATGCTTGTGTTAGTTCTCAGCTCACCTCTTGGTATGAATTGT
6398678 TGTCCAGATTACTTTGAATCTATATTGTTTGGAT
66 TGTCCAGATTACTTTGAATCTATATTGTTTGGAT
6398712 T
1 T
6398713 TCATTTGACC
Statistics
Matches: 99, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
98 92 0.93
99 7 0.07
ACGTcount: A:0.22, C:0.13, G:0.16, T:0.48
Consensus pattern (99 bp):
TCTTTAATTTTAAAATGTTATTTATGCTTGTGTTAGTTCTCAGCTCACCTCTTGGTATGAATTGT
TGTCCAGATTACTTTGAATCTATATTGTTTGGAT
Found at i:6399241 original size:11 final size:11
Alignment explanation
Indices: 6399225--6399253 Score: 58
Period size: 11 Copynumber: 2.6 Consensus size: 11
6399215 ATCGCTTGAT
6399225 AATTAACCGAA
1 AATTAACCGAA
6399236 AATTAACCGAA
1 AATTAACCGAA
6399247 AATTAAC
1 AATTAAC
6399254 AATTAGGTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.55, C:0.17, G:0.07, T:0.21
Consensus pattern (11 bp):
AATTAACCGAA
Found at i:6403113 original size:76 final size:76
Alignment explanation
Indices: 6402987--6403138 Score: 304
Period size: 76 Copynumber: 2.0 Consensus size: 76
6402977 GGTTTTTATT
6402987 GTTACTTGTTTCATTTCACTAATACTTGTGCATTGCGGCAATGATTATATAAGCTGGTCTTGTTC
1 GTTACTTGTTTCATTTCACTAATACTTGTGCATTGCGGCAATGATTATATAAGCTGGTCTTGTTC
6403052 ATAAATGCAAA
66 ATAAATGCAAA
6403063 GTTACTTGTTTCATTTCACTAATACTTGTGCATTGCGGCAATGATTATATAAGCTGGTCTTGTTC
1 GTTACTTGTTTCATTTCACTAATACTTGTGCATTGCGGCAATGATTATATAAGCTGGTCTTGTTC
6403128 ATAAATGCAAA
66 ATAAATGCAAA
6403139 CAATATCTGT
Statistics
Matches: 76, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
76 76 1.00
ACGTcount: A:0.28, C:0.16, G:0.17, T:0.39
Consensus pattern (76 bp):
GTTACTTGTTTCATTTCACTAATACTTGTGCATTGCGGCAATGATTATATAAGCTGGTCTTGTTC
ATAAATGCAAA
Found at i:6405285 original size:15 final size:15
Alignment explanation
Indices: 6405267--6405300 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
6405257 ATTATATAAA
6405267 ATATAATGAATTATT
1 ATATAATGAATTATT
* *
6405282 ATATTATGGATTATT
1 ATATAATGAATTATT
6405297 ATAT
1 ATAT
6405301 TTTGTATTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.41, C:0.00, G:0.09, T:0.50
Consensus pattern (15 bp):
ATATAATGAATTATT
Found at i:6406225 original size:15 final size:14
Alignment explanation
Indices: 6406186--6406240 Score: 58
Period size: 15 Copynumber: 3.9 Consensus size: 14
6406176 AACTATGTAC
*
6406186 TTTATATATAAAAA
1 TTTATATATATAAA
*
6406200 TATATAATATATAAGA
1 TTTAT-ATATATAA-A
*
6406216 TTTATGTATAT-AA
1 TTTATATATATAAA
6406229 TTTATATATATA
1 TTTATATATATA
6406241 GTATATTAAG
Statistics
Matches: 33, Mismatches: 5, Indels: 6
0.75 0.11 0.14
Matches are distributed among these distances:
13 11 0.33
14 5 0.15
15 12 0.36
16 5 0.15
ACGTcount: A:0.49, C:0.00, G:0.04, T:0.47
Consensus pattern (14 bp):
TTTATATATATAAA
Found at i:6406374 original size:17 final size:18
Alignment explanation
Indices: 6406343--6406377 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
6406333 ATGTGTAAAC
6406343 AATATATAAACTATATAA
1 AATATATAAACTATATAA
*
6406361 AATAT-TAAAGTATATAA
1 AATATATAAACTATATAA
6406378 TTTATATTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 11 0.69
18 5 0.31
ACGTcount: A:0.60, C:0.03, G:0.03, T:0.34
Consensus pattern (18 bp):
AATATATAAACTATATAA
Found at i:6406384 original size:19 final size:19
Alignment explanation
Indices: 6406362--6406416 Score: 58
Period size: 21 Copynumber: 2.7 Consensus size: 19
6406352 ACTATATAAA
6406362 ATATTAAAGTATATAA-TTT
1 ATATTAAA-TATATAAGTTT
6406381 ATATTAATATAATATAAGTTT
1 ATATTAA-AT-ATATAAGTTT
6406402 ATATATAAACTATAT
1 ATAT-TAAA-TATAT
6406417 TTATATTATA
Statistics
Matches: 31, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
19 8 0.26
20 7 0.23
21 12 0.39
22 4 0.13
ACGTcount: A:0.49, C:0.02, G:0.04, T:0.45
Consensus pattern (19 bp):
ATATTAAATATATAAGTTT
Found at i:6406421 original size:13 final size:13
Alignment explanation
Indices: 6406418--6406520 Score: 55
Period size: 13 Copynumber: 7.3 Consensus size: 13
6406408 AAACTATATT
6406418 TATA-TTATAAAC
1 TATATTTATAAAC
*
6406430 TATATAATTATTATAAT
1 TATAT--TTA-TA-AAC
*
6406447 TTATATATATAAAC
1 T-ATATTTATAAAC
*
6406461 TATGTTTATATGAAC
1 TATATTTATA--AAC
*
6406476 TATATATATAAAC
1 TATATTTATAAAC
* *
6406489 TATGTATATAAAC
1 TATATTTATAAAC
*
6406502 TATATATGTATAAAT
1 TATAT-T-TATAAAC
6406517 TATA
1 TATA
6406521 AAAAGTATAT
Statistics
Matches: 70, Mismatches: 11, Indels: 17
0.71 0.11 0.17
Matches are distributed among these distances:
12 4 0.06
13 26 0.37
14 3 0.04
15 26 0.37
16 4 0.06
17 3 0.04
18 4 0.06
ACGTcount: A:0.47, C:0.05, G:0.04, T:0.45
Consensus pattern (13 bp):
TATATTTATAAAC
Found at i:6406421 original size:15 final size:15
Alignment explanation
Indices: 6406403--6406520 Score: 68
Period size: 15 Copynumber: 7.9 Consensus size: 15
6406393 TATAAGTTTA
6406403 TATATAAACTATATTT
1 TATATAAACTATA-TT
6406419 ATATTATAAACTATATAAT
1 -TA-TATAAACTATAT--T
* *
6406438 TAT-TATAA-TTTATA
1 TATATA-AACTATATT
*
6406452 TATATAAACTATGTT
1 TATATAAACTATATT
*
6406467 TATATGAACTATA--
1 TATATAAACTATATT
*
6406480 TATATAAAC--TATG
1 TATATAAACTATATT
*
6406493 TATATAAACTATATA
1 TATATAAACTATATT
* *
6406508 TGTATAAATTATA
1 TATATAAACTATA
6406521 AAAAGTATAT
Statistics
Matches: 80, Mismatches: 11, Indels: 22
0.71 0.10 0.19
Matches are distributed among these distances:
11 2 0.03
13 17 0.21
14 5 0.06
15 30 0.38
16 6 0.08
17 6 0.08
18 13 0.16
19 1 0.01
ACGTcount: A:0.47, C:0.05, G:0.03, T:0.45
Consensus pattern (15 bp):
TATATAAACTATATT
Found at i:6406428 original size:18 final size:18
Alignment explanation
Indices: 6406377--6406471 Score: 71
Period size: 18 Copynumber: 5.4 Consensus size: 18
6406367 AAAGTATATA
6406377 ATTTATATTAATATAA-TAT
1 ATTTATATT-ATA-AACTAT
6406396 AAGTTTATA-TATAAACTAT
1 -A-TTTATATTATAAACTAT
6406415 ATTTATATTATAAACTAT
1 ATTTATATTATAAACTAT
*
6406433 A--TA-ATTAT-TA-TA-
1 ATTTATATTATAAACTAT
6406445 ATTTATATATATAAACTAT
1 ATTTATAT-TATAAACTAT
*
6406464 GTTTATAT
1 ATTTATAT
6406472 GAACTATATA
Statistics
Matches: 62, Mismatches: 3, Indels: 21
0.72 0.03 0.24
Matches are distributed among these distances:
12 1 0.02
13 2 0.03
14 3 0.05
15 7 0.11
16 5 0.08
17 7 0.11
18 16 0.26
19 13 0.21
20 2 0.03
21 6 0.10
ACGTcount: A:0.45, C:0.03, G:0.02, T:0.49
Consensus pattern (18 bp):
ATTTATATTATAAACTAT
Found at i:6406488 original size:28 final size:26
Alignment explanation
Indices: 6406448--6406508 Score: 95
Period size: 28 Copynumber: 2.3 Consensus size: 26
6406438 TATTATAATT
*
6406448 TATATATATAAACTATGTTTATATGAAC
1 TATATATATAAACTATG--TATATAAAC
6406476 TATATATATAAACTATGTATATAAAC
1 TATATATATAAACTATGTATATAAAC
6406502 TATATAT
1 TATATAT
6406509 GTATAAATTA
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
26 15 0.47
28 17 0.53
ACGTcount: A:0.46, C:0.07, G:0.05, T:0.43
Consensus pattern (26 bp):
TATATATATAAACTATGTATATAAAC
Found at i:6406573 original size:2 final size:2
Alignment explanation
Indices: 6406556--6406832 Score: 56
Period size: 2 Copynumber: 135.0 Consensus size: 2
6406546 GTTTATATTA
* * *
6406556 AT AT AGT AT TT AT AT AT AT AT AT AA ACT AT AT AT GT AT GA- ACT
1 AT AT A-T AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT -AT A-T
* * * *
6406599 AT AT AA AGT AT AT AGT TT AT AA AT -T AT A- AT TT AT AT -T A- AT
1 AT AT AT A-T AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * * *
6406639 AT AGT AT AT AT AT GT AT A- ACT A- AT AT AT GT A- AT CT AT AG AT
1 AT A-T AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT
* *
6406680 -T AT AT AT AT AT AT AT AT ACT AT AT AA AGT A- AT AA AGT AT AT
1 AT AT AT AT AT AT AT AT AT A-T AT AT AT A-T AT AT AT A-T AT AT
* * * ** * *
6406721 AGT TT AT AG AA AT ACT AT GC AT AA ACT AT AT AT AT AT AT AA ACT
1 A-T AT AT AT AT AT A-T AT AT AT AT A-T AT AT AT AT AT AT AT A-T
* * * * *
6406765 AT AC AT GT AA AT AT AA ACT AT AT AT GT AT GA- ACT AT AT AT AT
1 AT AT AT AT AT AT AT AT A-T AT AT AT AT AT -AT A-T AT AT AT AT
* *
6406807 AA ACT AT AT AT GT AT AT AT -T AT AT AT
1 AT A-T AT AT AT AT AT AT AT AT AT AT AT
6406833 GTAATCTATG
Statistics
Matches: 191, Mismatches: 53, Indels: 62
0.62 0.17 0.20
Matches are distributed among these distances:
1 12 0.06
2 156 0.82
3 23 0.12
ACGTcount: A:0.47, C:0.05, G:0.06, T:0.42
Consensus pattern (2 bp):
AT
Found at i:6406580 original size:81 final size:81
Alignment explanation
Indices: 6406454--6406656 Score: 284
Period size: 81 Copynumber: 2.5 Consensus size: 81
6406444 AATTTATATA
* * * *
6406454 TATAAACTAT-GTTTATATGAACTATA-TATATAAACTATGTATATAAACTATATATGTATAAAT
1 TATAAACTATAGTTTATATTAA-TATAGTATATATA-TATATATATAAACTATATATGTATAAAC
6406517 TATAAAAAGTATATAGTT
64 TATAAAAAGTATATAGTT
* *
6406535 TATAAACTATAGTTTATATTAATATAGTATTTATATATATATATAAACTATATATGTATGAACTA
1 TATAAACTATAGTTTATATTAATATAGTATATATATATATATATAAACTATATATGTATAAACTA
*
6406600 TATAAAGTATATAGTT
66 TAAAAAGTATATAGTT
* * *
6406616 TATAAATTATAATTTATATTAATATAGTATATATATGTATA
1 TATAAACTATAGTTTATATTAATATAGTATATATATATATA
6406657 ACTAATATAT
Statistics
Matches: 109, Mismatches: 11, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
81 93 0.85
82 16 0.15
ACGTcount: A:0.46, C:0.03, G:0.07, T:0.44
Consensus pattern (81 bp):
TATAAACTATAGTTTATATTAATATAGTATATATATATATATATAAACTATATATGTATAAACTA
TAAAAAGTATATAGTT
Found at i:6406586 original size:13 final size:13
Alignment explanation
Indices: 6406448--6407049 Score: 110
Period size: 13 Copynumber: 43.5 Consensus size: 13
6406438 TATTATAATT
6406448 TATATATATAAAC
1 TATATATATAAAC
* *
6406461 TATGTTTATATGAAC
1 TA--TATATATAAAC
6406476 TATATATATAAAC
1 TATATATATAAAC
*
6406489 TATGTATATAAAC
1 TATATATATAAAC
6406502 TATATATGTATAAA-
1 TATATA--TATAAAC
*
6406516 T-TATA-A-AAAG
1 TATATATATAAAC
6406526 TATATAGTTTATAAAC
1 TATATA---TATAAAC
*
6406542 TATAGTTTATATTAA-
1 TATA---TATATAAAC
* *
6406557 TATAGTATTTATA-
1 TATA-TATATAAAC
6406570 TATATATATAAAC
1 TATATATATAAAC
*
6406583 TATATATGTATGAAC
1 TATATA--TATAAAC
*
6406598 TATATA-A-AGTA-
1 TATATATATA-AAC
* *
6406609 TATAGTTTATAAAT
1 TATA-TATATAAAC
* * *
6406623 TATA-ATTTATAT
1 TATATATATAAAC
*
6406635 TA-ATATAGTATA-
1 TATATATA-TAAAC
*
6406647 TATATGTAT-AAC
1 TATATATATAAAC
* *
6406659 TAATATATGTAATC
1 T-ATATATATAAAC
* *
6406673 TATAGATTATATA-
1 TATATA-TATAAAC
*
6406686 TATATATATATAC
1 TATATATATAAAC
*
6406699 TATATAAAGTAATAAAG
1 TATAT--A-T-ATAAAC
*
6406716 TATATAGTTTATAGAAA
1 TATATA---TATA-AAC
**
6406733 TACTATGCATAAAC
1 TA-TATATATAAAC
6406747 TATATATAT--A-
1 TATATATATAAAC
* *
6406757 TATAAACTATACA-
1 TATATA-TATAAAC
* *
6406770 TGTAAATATAAAC
1 TATATATATAAAC
*
6406783 TATATATGTATGAAC
1 TATATA--TATAAAC
6406798 TATATATATAAAC
1 TATATATATAAAC
* *
6406811 TATATATGTATATAT
1 TATATA--TATAAAC
* *
6406826 TATATATGTAATC
1 TATATATATAAAC
6406839 TATGTAGTTATTATAAAC
1 TA--TA--TA-TATAAAC
* * *
6406857 CA-ATAAACTATA-
1 TATATATA-TAAAC
6406869 TATATATATAAAC
1 TATATATATAAAC
6406882 TATACATGTAAATATAAAC
1 TAT--A--T--ATATAAAC
*
6406901 TATATATGTATGAAC
1 TATATA--TATAAAC
6406916 TATATATATAAAC
1 TATATATATAAAC
6406929 TATATAATTTATATAAAC
1 --TAT-A--TATATAAAC
*
6406947 TACATATGTATAAAC
1 T--ATATATATAAAC
* * *
6406962 TATGTATATAGAT
1 TATATATATAAAC
* * *
6406975 TAAATAAATCAAC
1 TATATATATAAAC
6406988 TATATAGATATAAAC
1 TATAT--ATATAAAC
*
6407003 TATATATATAAGC
1 TATATATATAAAC
*
6407016 TACATATGTATAAAC
1 T--ATATATATAAAC
* *
6407031 TATATATGTAATC
1 TATATATATAAAC
6407044 TATATA
1 TATATA
6407050 GTTTATATAA
Statistics
Matches: 431, Mismatches: 85, Indels: 146
0.65 0.13 0.22
Matches are distributed among these distances:
9 3 0.01
10 7 0.02
11 14 0.03
12 38 0.09
13 170 0.39
14 16 0.04
15 113 0.26
16 18 0.04
17 19 0.04
18 20 0.05
19 13 0.03
ACGTcount: A:0.47, C:0.06, G:0.06, T:0.40
Consensus pattern (13 bp):
TATATATATAAAC
Found at i:6406586 original size:15 final size:15
Alignment explanation
Indices: 6406568--6407081 Score: 137
Period size: 15 Copynumber: 34.4 Consensus size: 15
6406558 ATAGTATTTA
6406568 TATATATATATAAAC
1 TATATATATATAAAC
* *
6406583 TATATATGTATGAAC
1 TATATATATATAAAC
* * *
6406598 TATATAAAGTATATAG
1 TATATATA-TATAAAC
* * **
6406614 TTTATAAATTATAATT
1 TATATATA-TATAAAC
* *
6406630 TATAT-TA-ATATAG
1 TATATATATATAAAC
*
6406643 TATATATATGTATAAC
1 TATATATATATA-AAC
* *
6406659 TA-ATATATGTAATC
1 TATATATATATAAAC
*
6406673 TATAGAT-TAT--A-
1 TATATATATATAAAC
*
6406684 TATATATATATATAC
1 TATATATATATAAAC
* *
6406699 TATATAAAGTAATAAAG
1 TATATATA-T-ATAAAC
*
6406716 TATATAGTTTATAGAA-
1 TATATA-TATATA-AAC
**
6406732 -ATACTATGCATAAAC
1 TATA-TATATATAAAC
6406747 TATATATATATATAAAC
1 --TATATATATATAAAC
*
6406764 TATACATGTAAATATAAAC
1 TAT--A--TATATATAAAC
* *
6406783 TATATATGTATGAAC
1 TATATATATATAAAC
6406798 --TATATATATAAAC
1 TATATATATATAAAC
* *
6406811 TATATATGTATATA-
1 TATATATATATAAAC
* *
6406825 T-TATATATGTAATC
1 TATATATATATAAAC
*
6406839 TATGTAGTTATTATAAAC
1 TATATA--TA-TATAAAC
* * *
6406857 CA-ATAAACTATATA-
1 TATATATA-TATAAAC
* *
6406871 TATATATAAACTATAC
1 TATATATATA-TAAAC
* *
6406887 -ATGTAAATATAAAC
1 TATATATATATAAAC
* *
6406901 TATATATGTATGAAC
1 TATATATATATAAAC
6406916 --TATATATATAAAC
1 TATATATATATAAAC
6406929 TATATAATTTATATAAAC
1 TATAT-A--TATATAAAC
* *
6406947 TACATATGTATAAAC
1 TATATATATATAAAC
* *
6406962 --TATGTATATAGA-
1 TATATATATATAAAC
* * *
6406974 T-TAAATAAATCAAC
1 TATATATATATAAAC
*
6406988 TATATAGATATAAAC
1 TATATATATATAAAC
*
6407003 --TATATATATAAGC
1 TATATATATATAAAC
* *
6407016 TACATATGTATAAAC
1 TATATATATATAAAC
* *
6407031 --TATATATGTAATC
1 TATATATATATAAAC
6407044 TATATAGTTTATATAAAC
1 TATATA---TATATAAAC
* *
6407062 TATATA-AAAAAAAC
1 TATATATATATAAAC
6407076 TATATA
1 TATATA
6407082 AAGTATATAG
Statistics
Matches: 356, Mismatches: 95, Indels: 97
0.65 0.17 0.18
Matches are distributed among these distances:
11 6 0.02
12 3 0.01
13 73 0.21
14 32 0.09
15 136 0.38
16 29 0.08
17 29 0.08
18 35 0.10
19 13 0.04
ACGTcount: A:0.48, C:0.07, G:0.06, T:0.39
Consensus pattern (15 bp):
TATATATATATAAAC
Found at i:6406806 original size:28 final size:28
Alignment explanation
Indices: 6406775--6407081 Score: 156
Period size: 28 Copynumber: 10.5 Consensus size: 28
6406765 ATACATGTAA
*
6406775 ATATAAACTATATATGTATGAACTATAT
1 ATATAAACTATATATGTATAAACTATAT
* *
6406803 ATATAAACTATATATGTATATATTATAT
1 ATATAAACTATATATGTATAAACTATAT
* * * *
6406831 ATGTAATCTATGTAGTTAT-TATAAACCAATAA
1 ATATAAACTA--TA--TATGTATAAA-CTATAT
* ** * * *
6406863 ACTATATA-TATATATAAACTATACATGTAA
1 A-TATAAACTATATATGTA-TAAAC-TATAT
*
6406893 ATATAAACTATATATGTATGAACTATAT
1 ATATAAACTATATATGTATAAACTATAT
*
6406921 ATATAAACTATATAATTTATATAAACTACATAT
1 ATATAAACTATAT-A--TGTATAAACT--ATAT
* * * * *
6406954 GTATAAACTATGTA--TATAGATTAAAT
1 ATATAAACTATATATGTATAAACTATAT
* *
6406980 AAATCAACTATATA-GATATAAACTATAT
1 ATATAAACTATATATG-TATAAACTATAT
* *
6407008 ATATAAGCTACATATGTATAAACTATAT
1 ATATAAACTATATATGTATAAACTATAT
* * *
6407036 ATGTAATCTATATAGTTTATATAAACTATAT
1 ATATAAACTATATA---TGTATAAACTATAT
* *
6407067 AAAAAAAACTATATA
1 -ATATAAACTATATA
6407082 AAGTATATAG
Statistics
Matches: 208, Mismatches: 49, Indels: 40
0.70 0.16 0.13
Matches are distributed among these distances:
26 13 0.06
28 100 0.48
29 12 0.06
30 19 0.09
31 26 0.12
32 20 0.10
33 18 0.09
ACGTcount: A:0.49, C:0.08, G:0.06, T:0.38
Consensus pattern (28 bp):
ATATAAACTATATATGTATAAACTATAT
Found at i:6406909 original size:19 final size:19
Alignment explanation
Indices: 6406859--6406910 Score: 72
Period size: 19 Copynumber: 2.8 Consensus size: 19
6406849 TTATAAACCA
*
6406859 ATAAACTATATA--TATAT
1 ATAAACTATATATGTAAAT
*
6406876 ATAAACTATACATGTAAAT
1 ATAAACTATATATGTAAAT
6406895 ATAAACTATATATGTA
1 ATAAACTATATATGTA
6406911 TGAACTATAT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
17 11 0.37
19 19 0.63
ACGTcount: A:0.52, C:0.08, G:0.04, T:0.37
Consensus pattern (19 bp):
ATAAACTATATATGTAAAT
Found at i:6406956 original size:46 final size:47
Alignment explanation
Indices: 6406869--6406971 Score: 138
Period size: 46 Copynumber: 2.2 Consensus size: 47
6406859 ATAAACTATA
* * *
6406869 TATATATATAAACTATACATGTAAATATAAACTATATATGTATGAAC
1 TATATATATAAACTATAAATGTAAATATAAACTACATATGTATAAAC
*
6406916 TATATATATAAACTATATAAT-T-TATATAAACTACATATGTATAAAC
1 TATATATATAAACTATA-AATGTAAATATAAACTACATATGTATAAAC
*
6406962 TATGTATATA
1 TATATATATA
6406972 GATTAAATAA
Statistics
Matches: 50, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
46 30 0.60
47 18 0.36
48 2 0.04
ACGTcount: A:0.49, C:0.08, G:0.05, T:0.39
Consensus pattern (47 bp):
TATATATATAAACTATAAATGTAAATATAAACTACATATGTATAAAC
Found at i:6406970 original size:37 final size:40
Alignment explanation
Indices: 6406913--6407013 Score: 103
Period size: 33 Copynumber: 2.7 Consensus size: 40
6406903 TATATGTATG
*
6406913 AACTATAT--ATATAAACTATATA-AT--TTATATAAA-C
1 AACTATATAGATATAAACTATATATATAATTAAATAAATC
* *
6406947 TAC-ATAT-G-TATAAACTATGTATATAGATTAAATAAATC
1 AACTATATAGATATAAACTATATATATA-ATTAAATAAATC
6406985 AACTATATAGATATAAACTATATATATAA
1 AACTATATAGATATAAACTATATATATAA
6407014 GCTACATATG
Statistics
Matches: 53, Mismatches: 5, Indels: 12
0.76 0.07 0.17
Matches are distributed among these distances:
33 16 0.30
34 4 0.08
37 8 0.15
38 3 0.06
39 4 0.08
40 2 0.04
41 16 0.30
ACGTcount: A:0.51, C:0.08, G:0.04, T:0.37
Consensus pattern (40 bp):
AACTATATAGATATAAACTATATATATAATTAAATAAATC
Found at i:6407156 original size:20 final size:20
Alignment explanation
Indices: 6407131--6407181 Score: 74
Period size: 18 Copynumber: 2.8 Consensus size: 20
6407121 CATATGTATG
6407131 TATAAACTATATATAGTTTA
1 TATAAACTATATATAGTTTA
6407151 TATAAAC--TATATAGTTTA
1 TATAAACTATATATAGTTTA
6407169 TAT--ACTATATATA
1 TATAAACTATATATA
6407182 CGTAACCTAT
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
16 2 0.07
18 20 0.69
20 7 0.24
ACGTcount: A:0.45, C:0.06, G:0.04, T:0.45
Consensus pattern (20 bp):
TATAAACTATATATAGTTTA
Found at i:6407170 original size:16 final size:18
Alignment explanation
Indices: 6407076--6407172 Score: 69
Period size: 18 Copynumber: 5.3 Consensus size: 18
6407066 TAAAAAAAAC
*
6407076 TATATAAAGTATATAGTT
1 TATATAAACTATATAGTT
6407094 TATA-AAA-TATA-A-TT
1 TATATAAACTATATAGTT
* *
6407108 TATATTAATA-TAACATATGTA
1 TATA-TAA-ACT-ATATA-GTT
*
6407129 TGTATAAACTATATATAGTT
1 TATATAAAC--TATATAGTT
6407149 TATATAAACTATATAGTT
1 TATATAAACTATATAGTT
6407167 TATATA
1 TATATA
6407173 CTATATATAC
Statistics
Matches: 63, Mismatches: 6, Indels: 20
0.71 0.07 0.22
Matches are distributed among these distances:
14 6 0.10
15 1 0.02
16 6 0.10
17 5 0.08
18 21 0.33
19 2 0.03
20 13 0.21
21 8 0.13
22 1 0.02
ACGTcount: A:0.46, C:0.03, G:0.06, T:0.44
Consensus pattern (18 bp):
TATATAAACTATATAGTT
Found at i:6407561 original size:120 final size:120
Alignment explanation
Indices: 6407392--6407647 Score: 458
Period size: 120 Copynumber: 2.1 Consensus size: 120
6407382 GCCCCGTCCT
** *
6407392 CGAACCCGACTTGAAATATTATATCCAAACCAGAAAATATTTTATATATAATTAATATAAAAAAT
1 CGAACCCGACCCGAAATATTATACCCAAACCAGAAAATATTTTATATATAATTAATATAAAAAAT
* *
6407457 ATAAAATATTATTTATATATATATATAATCGGGGCGGGGCGGGGATACCTTGCCC
66 ATAAAATATTATATATATATATATATAATCGGGGCAGGGCGGGGATACCTTGCCC
*
6407512 CGAACCCGACCCGAAATATTATACCCAAACTAGAAAATATTTTATATATAATTAATATAAAAAAT
1 CGAACCCGACCCGAAATATTATACCCAAACCAGAAAATATTTTATATATAATTAATATAAAAAAT
6407577 ATAAAATATTATATATATATATATATAATCGGGGCAGGGCGGGGATACCTTGCCC
66 ATAAAATATTATATATATATATATATAATCGGGGCAGGGCGGGGATACCTTGCCC
6407632 CGAACCCGACCCGAAA
1 CGAACCCGACCCGAAA
6407648 AAAATTTCCG
Statistics
Matches: 130, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
120 130 1.00
ACGTcount: A:0.41, C:0.17, G:0.14, T:0.28
Consensus pattern (120 bp):
CGAACCCGACCCGAAATATTATACCCAAACCAGAAAATATTTTATATATAATTAATATAAAAAAT
ATAAAATATTATATATATATATATATAATCGGGGCAGGGCGGGGATACCTTGCCC
Found at i:6421796 original size:37 final size:37
Alignment explanation
Indices: 6421723--6421797 Score: 91
Period size: 37 Copynumber: 2.0 Consensus size: 37
6421713 GTTAGAAAAT
*
6421723 ATTTATATATTTTCTTTAAAAAAATTAAATTCATAAA
1 ATTTATATATTTTCTTTAAAAAAATTAAAATCATAAA
* *
6421760 ATTTATATAATTTT-TTTTACAAAATTGAAAAT-ATAAA
1 ATTTATAT-ATTTTCTTTAAAAAAATT-AAAATCATAAA
6421797 A
1 A
6421798 ATATTTAATG
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
37 24 0.73
38 9 0.27
ACGTcount: A:0.49, C:0.04, G:0.01, T:0.45
Consensus pattern (37 bp):
ATTTATATATTTTCTTTAAAAAAATTAAAATCATAAA
Found at i:6422281 original size:37 final size:37
Alignment explanation
Indices: 6422239--6422313 Score: 100
Period size: 37 Copynumber: 2.0 Consensus size: 37
6422229 CATTAAATCT
6422239 TTTTAT-AATTTCAATTT-TGTAAAAAAAATTATATAAA
1 TTTTATGAATTT-AATTTGTGTAAAAAAAA-TATATAAA
* *
6422276 TTTTATGAATTTAATTTGTTTAAAGAAAATATATAAA
1 TTTTATGAATTTAATTTGTGTAAAAAAAATATATAAA
6422313 T
1 T
6422314 ATTTTTCAAC
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
37 20 0.59
38 14 0.41
ACGTcount: A:0.47, C:0.01, G:0.05, T:0.47
Consensus pattern (37 bp):
TTTTATGAATTTAATTTGTGTAAAAAAAATATATAAA
Found at i:6422658 original size:9 final size:9
Alignment explanation
Indices: 6422646--6422670 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
6422636 AACCGGTCGA
6422646 ATCGGTCCG
1 ATCGGTCCG
6422655 ATCGGTCCG
1 ATCGGTCCG
6422664 ATCGGTC
1 ATCGGTC
6422671 GGAAGAACCG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.12, C:0.32, G:0.32, T:0.24
Consensus pattern (9 bp):
ATCGGTCCG
Found at i:6422734 original size:22 final size:21
Alignment explanation
Indices: 6422700--6422740 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
6422690 ATAATTATTT
6422700 AAAAAATTAAATAAAAATATC
1 AAAAAATTAAATAAAAATATC
*
6422721 AAAAATATTTAATAAAAATA
1 AAAAA-ATTAAATAAAAATA
6422741 ATTTTTTATA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 5 0.28
22 13 0.72
ACGTcount: A:0.71, C:0.02, G:0.00, T:0.27
Consensus pattern (21 bp):
AAAAAATTAAATAAAAATATC
Done.