Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008746.1 Hibiscus syriacus cultivar Beakdansim tig00111835_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: 2013901
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 10 of 10
Found at i:1870175 original size:20 final size:21
Alignment explanation
Indices: 1870138--1870178 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
1870128 AGATTGTGCA
1870138 GGGGGTACAGATTCCCCCCTG
1 GGGGGTACAGATTCCCCCCTG
1870159 GGGGGTATC-GATTCCCCCCT
1 GGGGGTA-CAGATTCCCCCCT
1870179 AAATGAAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 18 0.95
22 1 0.05
ACGTcount: A:0.12, C:0.34, G:0.32, T:0.22
Consensus pattern (21 bp):
GGGGGTACAGATTCCCCCCTG
Found at i:1871306 original size:24 final size:24
Alignment explanation
Indices: 1871218--1871307 Score: 60
Period size: 23 Copynumber: 3.8 Consensus size: 24
1871208 ACAATCTTAT
* * *
1871218 ATGGCACTACGGTACAA-TTCTAT
1 ATGGCACTTCGGTGCAATTTCTAC
* *
1871241 GTGGCACTTCGGTGC-ATTTTTAC
1 ATGGCACTTCGGTGCAATTTCTAC
** ** *
1871264 GCGGTTCTTCGG-GATAATTTCTAC
1 ATGGCACTTCGGTG-CAATTTCTAC
1871288 ATGGCACTTCGGTGCAATTT
1 ATGGCACTTCGGTGCAATTT
1871308 ATACGAGCTG
Statistics
Matches: 48, Mismatches: 15, Indels: 7
0.69 0.21 0.10
Matches are distributed among these distances:
22 2 0.04
23 25 0.52
24 20 0.42
25 1 0.02
ACGTcount: A:0.20, C:0.21, G:0.23, T:0.36
Consensus pattern (24 bp):
ATGGCACTTCGGTGCAATTTCTAC
Found at i:1873818 original size:2 final size:2
Alignment explanation
Indices: 1873811--1873868 Score: 116
Period size: 2 Copynumber: 29.0 Consensus size: 2
1873801 ATTAGAAAGA
1873811 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1873853 AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT
1873869 GGATAGTTTG
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 56 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1877857 original size:24 final size:23
Alignment explanation
Indices: 1877795--1877860 Score: 64
Period size: 24 Copynumber: 2.8 Consensus size: 23
1877785 TACGGTGTAA
*
1877795 TTCTATGTGGCACTTCGGTGCAT
1 TTCTATGTGGCACTTCGGTACAT
* *
1877818 TTCTACGCGGTC-CTTCAGG-ACAAT
1 TTCTATGTGG-CACTTC-GGTAC-AT
1877842 TTCTATGTGGCACTTCGGT
1 TTCTATGTGGCACTTCGGT
1877861 GCAATTTATA
Statistics
Matches: 33, Mismatches: 5, Indels: 9
0.70 0.11 0.19
Matches are distributed among these distances:
23 16 0.48
24 17 0.52
ACGTcount: A:0.15, C:0.24, G:0.24, T:0.36
Consensus pattern (23 bp):
TTCTATGTGGCACTTCGGTACAT
Found at i:1877865 original size:24 final size:24
Alignment explanation
Indices: 1877779--1877867 Score: 87
Period size: 23 Copynumber: 3.8 Consensus size: 24
1877769 CAATCTTATA
* *
1877779 TGGCACTACGGTGTAA-TTCTATG
1 TGGCACTTCGGTGCAATTTCTATG
*
1877802 TGGCACTTCGGTGC-ATTTCTACG
1 TGGCACTTCGGTGCAATTTCTATG
* *
1877825 CGGTC-CTTCAGG-ACAATTTCTATG
1 TGG-CACTTC-GGTGCAATTTCTATG
1877849 TGGCACTTCGGTGCAATTT
1 TGGCACTTCGGTGCAATTT
1877868 ATACGAGCTG
Statistics
Matches: 52, Mismatches: 8, Indels: 11
0.73 0.11 0.15
Matches are distributed among these distances:
22 1 0.02
23 28 0.54
24 23 0.44
ACGTcount: A:0.18, C:0.22, G:0.25, T:0.35
Consensus pattern (24 bp):
TGGCACTTCGGTGCAATTTCTATG
Found at i:1878598 original size:21 final size:23
Alignment explanation
Indices: 1878572--1878617 Score: 69
Period size: 21 Copynumber: 2.1 Consensus size: 23
1878562 TATAGTAGTA
*
1878572 CTGTAGCA-GGGTATCGG-TTCC
1 CTGTAGCAGGGGAATCGGTTTCC
1878593 CTGTAGCAGGGGAATCGGTTTCC
1 CTGTAGCAGGGGAATCGGTTTCC
1878616 CT
1 CT
1878618 CTTTGAATCT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 8 0.36
22 8 0.36
23 6 0.27
ACGTcount: A:0.15, C:0.24, G:0.33, T:0.28
Consensus pattern (23 bp):
CTGTAGCAGGGGAATCGGTTTCC
Found at i:1878903 original size:22 final size:22
Alignment explanation
Indices: 1878878--1878922 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
1878868 TTTGGGTGTT
1878878 ACAGATTTCGTCGGAGATGGGG
1 ACAGATTTCGTCGGAGATGGGG
1878900 ACAGATTTCGTCGGAGATGGGG
1 ACAGATTTCGTCGGAGATGGGG
1878922 A
1 A
1878923 TGGATATCAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.24, C:0.13, G:0.40, T:0.22
Consensus pattern (22 bp):
ACAGATTTCGTCGGAGATGGGG
Found at i:1879124 original size:20 final size:20
Alignment explanation
Indices: 1879101--1879145 Score: 81
Period size: 20 Copynumber: 2.2 Consensus size: 20
1879091 TTATCGCAAC
*
1879101 GCGATAGTCAGAGTCGCGTT
1 GCGATAGTCAGAATCGCGTT
1879121 GCGATAGTCAGAATCGCGTT
1 GCGATAGTCAGAATCGCGTT
1879141 GCGAT
1 GCGAT
1879146 TTACATATTT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.22, C:0.20, G:0.33, T:0.24
Consensus pattern (20 bp):
GCGATAGTCAGAATCGCGTT
Found at i:1879162 original size:20 final size:20
Alignment explanation
Indices: 1879139--1879187 Score: 73
Period size: 20 Copynumber: 2.5 Consensus size: 20
1879129 CAGAATCGCG
1879139 TTGCGATTTACATATT-TGCA
1 TTGCGATTTACATATTCT-CA
1879159 TTGCGATTTACATATTCTCA
1 TTGCGATTTACATATTCTCA
*
1879179 TTACGATTT
1 TTGCGATTT
1879188 TCTAAAATCG
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
20 26 0.96
21 1 0.04
ACGTcount: A:0.24, C:0.16, G:0.12, T:0.47
Consensus pattern (20 bp):
TTGCGATTTACATATTCTCA
Found at i:1879634 original size:16 final size:16
Alignment explanation
Indices: 1879612--1879648 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
1879602 TTAATTGGTG
*
1879612 ATAAAAATATATTAAA
1 ATAAAAATAAATTAAA
*
1879628 TTAAAAATAAATTAAA
1 ATAAAAATAAATTAAA
1879644 ATAAA
1 ATAAA
1879649 TTTAATCATC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (16 bp):
ATAAAAATAAATTAAA
Found at i:1879979 original size:21 final size:22
Alignment explanation
Indices: 1879955--1880006 Score: 72
Period size: 23 Copynumber: 2.4 Consensus size: 22
1879945 ATTCACTAGT
1879955 ATAATTTACCCTTT-A-TTTTAA
1 ATAATTTA-CCTTTAATTTTTAA
1879976 ATAATTTACCTTTAAATTTTTAA
1 ATAATTTACCTTT-AATTTTTAA
1879999 ATAATTTA
1 ATAATTTA
1880007 TGATTATATG
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
20 5 0.18
21 8 0.29
22 1 0.04
23 14 0.50
ACGTcount: A:0.38, C:0.10, G:0.00, T:0.52
Consensus pattern (22 bp):
ATAATTTACCTTTAATTTTTAA
Found at i:1880187 original size:18 final size:18
Alignment explanation
Indices: 1880164--1880206 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
1880154 AGTTTTAATA
1880164 TATTTAAATT-AAATATAT
1 TATTTAAATTAAAATAT-T
*
1880182 TATTT-ATTTAAAATATT
1 TATTTAAATTAAAATATT
1880199 TATTTAAA
1 TATTTAAA
1880207 ATTTATTTAT
Statistics
Matches: 21, Mismatches: 2, Indels: 4
0.78 0.07 0.15
Matches are distributed among these distances:
17 9 0.43
18 12 0.57
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (18 bp):
TATTTAAATTAAAATATT
Found at i:1880198 original size:13 final size:13
Alignment explanation
Indices: 1880182--1880208 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1880172 TTAAATATAT
1880182 TATTTATTTAAAA
1 TATTTATTTAAAA
1880195 TATTTATTTAAAA
1 TATTTATTTAAAA
1880208 T
1 T
1880209 TTATTTATTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (13 bp):
TATTTATTTAAAA
Found at i:1880198 original size:31 final size:28
Alignment explanation
Indices: 1880157--1880217 Score: 77
Period size: 31 Copynumber: 2.1 Consensus size: 28
1880147 AAATTTTAGT
*
1880157 TTTAATATATTTAAATTAAATATATTATTTA
1 TTTAAAATATTT-AATTAAA-AT-TTATTTA
*
1880188 TTTAAAATATTTATTTAAAATTTATTTA
1 TTTAAAATATTTAATTAAAATTTATTTA
1880216 TT
1 TT
1880218 AATAAAAATA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
28 9 0.32
29 2 0.07
30 6 0.21
31 11 0.39
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (28 bp):
TTTAAAATATTTAATTAAAATTTATTTA
Found at i:1880777 original size:14 final size:15
Alignment explanation
Indices: 1880746--1880782 Score: 51
Period size: 14 Copynumber: 2.6 Consensus size: 15
1880736 ATAAATTAAT
1880746 TAAAAT-TTTAAAAG
1 TAAAATATTTAAAAG
*
1880760 TAAATTATTTAAAA-
1 TAAAATATTTAAAAG
1880774 TAAAATATT
1 TAAAATATT
1880783 AATTACAATA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
14 13 0.65
15 7 0.35
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.41
Consensus pattern (15 bp):
TAAAATATTTAAAAG
Found at i:1889596 original size:17 final size:16
Alignment explanation
Indices: 1889550--1889597 Score: 51
Period size: 17 Copynumber: 2.9 Consensus size: 16
1889540 ATACCATACA
*
1889550 ATGATTAATTATATTT
1 ATGATTATTTATATTT
* *
1889566 ATAACCTATTTATATTT
1 ATGA-TTATTTATATTT
1889583 ATGATTATTATATAT
1 ATGATTATT-TATAT
1889598 GTATATACTT
Statistics
Matches: 25, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
16 7 0.28
17 18 0.72
ACGTcount: A:0.38, C:0.04, G:0.04, T:0.54
Consensus pattern (16 bp):
ATGATTATTTATATTT
Found at i:1893561 original size:15 final size:15
Alignment explanation
Indices: 1893541--1893622 Score: 112
Period size: 15 Copynumber: 5.5 Consensus size: 15
1893531 TTCCAGAAAA
1893541 TGAATTACTGGAATT
1 TGAATTACTGGAATT
*
1893556 TGAATTACTAGAATT
1 TGAATTACTGGAATT
**
1893571 TGAATTACTGGAAAA
1 TGAATTACTGGAATT
1893586 TGAATTACTGGAATT
1 TGAATTACTGGAATT
**
1893601 TGAATT-CTGGAAAA
1 TGAATTACTGGAATT
1893615 TGAATTAC
1 TGAATTAC
1893623 ATTTCTGTAA
Statistics
Matches: 58, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
14 12 0.21
15 46 0.79
ACGTcount: A:0.39, C:0.07, G:0.18, T:0.35
Consensus pattern (15 bp):
TGAATTACTGGAATT
Found at i:1893575 original size:30 final size:30
Alignment explanation
Indices: 1893541--1893622 Score: 130
Period size: 30 Copynumber: 2.8 Consensus size: 30
1893531 TTCCAGAAAA
**
1893541 TGAATTACTGGAATTTGAATTACTAGAATT
1 TGAATTACTGGAAAATGAATTACTAGAATT
*
1893571 TGAATTACTGGAAAATGAATTACTGGAATT
1 TGAATTACTGGAAAATGAATTACTAGAATT
1893601 TGAATT-CTGGAAAATGAATTAC
1 TGAATTACTGGAAAATGAATTAC
1893623 ATTTCTGTAA
Statistics
Matches: 49, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
29 16 0.33
30 33 0.67
ACGTcount: A:0.39, C:0.07, G:0.18, T:0.35
Consensus pattern (30 bp):
TGAATTACTGGAAAATGAATTACTAGAATT
Found at i:1893628 original size:20 final size:20
Alignment explanation
Indices: 1893605--1893674 Score: 131
Period size: 20 Copynumber: 3.5 Consensus size: 20
1893595 GGAATTTGAA
1893605 TTCTGGAAAATGAATTACAT
1 TTCTGGAAAATGAATTACAT
*
1893625 TTCTGTAAAATGAATTACAT
1 TTCTGGAAAATGAATTACAT
1893645 TTCTGGAAAATGAATTACAT
1 TTCTGGAAAATGAATTACAT
1893665 TTCTGGAAAA
1 TTCTGGAAAA
1893675 CATCTGGAAA
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 48 1.00
ACGTcount: A:0.40, C:0.10, G:0.14, T:0.36
Consensus pattern (20 bp):
TTCTGGAAAATGAATTACAT
Found at i:1893899 original size:29 final size:27
Alignment explanation
Indices: 1893843--1893908 Score: 78
Period size: 28 Copynumber: 2.3 Consensus size: 27
1893833 TTTACTAAAA
* *
1893843 TATTATTGAAATATATAAATAATATTAT
1 TATTATT-AAATATATAAAAAAAATTAT
1893871 TCATTATTAAATATATAAAAAAAATTTAT
1 T-ATTATTAAATATATAAAAAAAA-TTAT
1893900 TATATATTA
1 TAT-TATTA
1893909 TTAAAATAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
28 17 0.52
29 16 0.48
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.45
Consensus pattern (27 bp):
TATTATTAAATATATAAAAAAAATTAT
Found at i:1893940 original size:32 final size:33
Alignment explanation
Indices: 1893859--1893941 Score: 84
Period size: 32 Copynumber: 2.6 Consensus size: 33
1893849 TGAAATATAT
*
1893859 AAATAATATTAT-TCATTATTAAATATATAAAAA
1 AAAT-ATATTATATTATTATTAAATATATAAAAA
*
1893892 AAATTTATTATA-TATTATTAAA-ATA-AAAATA
1 AAATATATTATATTATTATTAAATATATAAAA-A
* *
1893923 TAATATCTTATATTATTAT
1 AAATATATTATATTATTAT
1893942 AATATAATTG
Statistics
Matches: 42, Mismatches: 5, Indels: 7
0.78 0.09 0.13
Matches are distributed among these distances:
30 4 0.10
31 13 0.31
32 21 0.50
33 4 0.10
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (33 bp):
AAATATATTATATTATTATTAAATATATAAAAA
Found at i:1893986 original size:22 final size:23
Alignment explanation
Indices: 1893961--1894004 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
1893951 GATTATTTTA
1893961 TATAATATTAAAAATA-TAATAT
1 TATAATATTAAAAATATTAATAT
* *
1893983 TATATTATTATAAATATTAATA
1 TATAATATTAAAAATATTAATA
1894005 AATATATTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 14 0.74
23 5 0.26
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (23 bp):
TATAATATTAAAAATATTAATAT
Found at i:1894009 original size:22 final size:22
Alignment explanation
Indices: 1893965--1894021 Score: 64
Period size: 21 Copynumber: 2.6 Consensus size: 22
1893955 ATTTTATATA
* *
1893965 ATATTAAAAATA-TAATATTAT
1 ATATTATAAATATTAATATAAT
1893986 ATTATTATAAATATTAATA-AAT
1 A-TATTATAAATATTAATATAAT
*
1894008 ATATTTTAAATATT
1 ATATTATAAATATT
1894022 TTAATAATTA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
21 13 0.42
22 13 0.42
23 5 0.16
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (22 bp):
ATATTATAAATATTAATATAAT
Found at i:1894020 original size:52 final size:51
Alignment explanation
Indices: 1893901--1894021 Score: 133
Period size: 54 Copynumber: 2.3 Consensus size: 51
1893891 AAAATTTATT
**
1893901 ATATATTATTAAA-A-TAAAAATATAATATCTTATATTATTATAATATAATTG
1 ATATATT-TTAAATATTAAAAATATAATA-CTTATATTATTATAATATAATAA
1893952 AT-TATTTTATATAATATTAAAAATATAATA-TTATATTATTATAAATATTAATAA
1 ATATA-TTT-TA-AATATTAAAAATATAATACTTATATTATTAT-AATA-TAATAA
1894006 ATATATTTTAAATATT
1 ATATATTTTAAATATT
1894022 TTAATAATTA
Statistics
Matches: 60, Mismatches: 2, Indels: 15
0.78 0.03 0.19
Matches are distributed among these distances:
50 3 0.05
51 6 0.10
52 20 0.33
53 7 0.12
54 22 0.37
55 2 0.03
ACGTcount: A:0.50, C:0.01, G:0.01, T:0.48
Consensus pattern (51 bp):
ATATATTTTAAATATTAAAAATATAATACTTATATTATTATAATATAATAA
Found at i:1894273 original size:42 final size:42
Alignment explanation
Indices: 1894214--1894325 Score: 206
Period size: 42 Copynumber: 2.7 Consensus size: 42
1894204 AATTACATTT
*
1894214 CGGAAAACGAATTACGTGAAACAAACACGGGAAAACGTTTTC
1 CGGAAAACGAATTACGTGAAACAAACACGGGAAAACATTTTC
*
1894256 CGGAAAACGAATTACGTGAAACAAATACGGGAAAACATTTTC
1 CGGAAAACGAATTACGTGAAACAAACACGGGAAAACATTTTC
1894298 CGGAAAACGAATTACGTGAAACAAACAC
1 CGGAAAACGAATTACGTGAAACAAACAC
1894326 TGAAATTTGG
Statistics
Matches: 67, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
42 67 1.00
ACGTcount: A:0.46, C:0.19, G:0.20, T:0.16
Consensus pattern (42 bp):
CGGAAAACGAATTACGTGAAACAAACACGGGAAAACATTTTC
Found at i:1905780 original size:12 final size:12
Alignment explanation
Indices: 1905763--1905792 Score: 60
Period size: 12 Copynumber: 2.5 Consensus size: 12
1905753 AAATTTTGGC
1905763 TTTTTTTTGTTT
1 TTTTTTTTGTTT
1905775 TTTTTTTTGTTT
1 TTTTTTTTGTTT
1905787 TTTTTT
1 TTTTTT
1905793 GAAAAAAATA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.00, C:0.00, G:0.07, T:0.93
Consensus pattern (12 bp):
TTTTTTTTGTTT
Found at i:1906165 original size:15 final size:16
Alignment explanation
Indices: 1906145--1906186 Score: 50
Period size: 15 Copynumber: 2.6 Consensus size: 16
1906135 GATTAGAATA
*
1906145 AAATAAATAAAAGAT-
1 AAATAAATAAAACATG
*
1906160 AAATAAATGAAACATG
1 AAATAAATAAAACATG
1906176 AAATAAGATAA
1 AAATAA-ATAA
1906187 TAAAGAAATC
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
15 13 0.59
16 6 0.27
17 3 0.14
ACGTcount: A:0.69, C:0.02, G:0.10, T:0.19
Consensus pattern (16 bp):
AAATAAATAAAACATG
Found at i:1916302 original size:445 final size:445
Alignment explanation
Indices: 1915473--1916366 Score: 1700
Period size: 445 Copynumber: 2.0 Consensus size: 445
1915463 TTCTGCAAGC
1915473 TTGGTGGGGGTTGGTTATGAATTCTGAATTCTGGGGAGTTATTCCTGCTACCGTTTTGTGGTATA
1 TTGGTGGGGGTTGGTTATGAATTCTGAATTCTGGGGAGTTATTCCTGCTACCGTTTTGTGGTATA
*
1915538 TCTGGAAGTATAGAAACATGTTAGTGTTTGAGGGATTGTCTTATGAGGGATCCTTCTGTTGTGGA
66 TCTGGAAGTATAGAAACATGTTAGTGTTTGAGGGATTGTCTTATGAGGGATCCTTCTGTTGCGGA
1915603 TAGGTATGGCAGACAGGAGAGTAAGGTGTTATCTCGAGCTCTGTGGGTTCCGCCTCCTGAAGGCT
131 TAGGTATGGCAGACAGGAGAGTAAGGTGTTATCTCGAGCTCTGTGGGTTCCGCCTCCTGAAGGCT
1915668 TTTTTAAATTAAATGTGGATGGTGCTGTCACAGATGATTGGATGAAAGGGGGTATAGGACGTATT
196 TTTTTAAATTAAATGTGGATGGTGCTGTCACAGATGATTGGATGAAAGGGGGTATAGGACGTATT
* *
1915733 ATTAAAGATTCAGGGGGTTATATGTTGGCTTCATTCTCTGAGGTAATTGGGAAGGAGCCTCCTAC
261 ATTAAAGATTCAAGGGGTTATATGTTGGCTTCATTCTCTGAGGCAATTGGGAAGGAGCCTCCTAC
1915798 AACTGCTGAAATGTTGGCTATTAAAAAGGGTTTGAATCTTTTCTTTGATTCTCAATGGAGTTGCA
326 AACTGCTGAAATGTTGGCTATTAAAAAGGGTTTGAATCTTTTCTTTGATTCTCAATGGAGTTGCA
1915863 AAGGTAGACTTATTGTTGAGTGTGATTGTCTTGTGGGGTTAATTGAATTAAGAAT
391 AAGGTAGACTTATTGTTGAGTGTGATTGTCTTGTGGGGTTAATTGAATTAAGAAT
*
1915918 TTGGTGGGGGTTGGTTATGAATTTTGAATTCTGGGGAGTTATTCCTGCTACCGTTTTGTGGTATA
1 TTGGTGGGGGTTGGTTATGAATTCTGAATTCTGGGGAGTTATTCCTGCTACCGTTTTGTGGTATA
*
1915983 TCTGGAAGTATAGAAACATGTTAGTGTTTGAGGGATTGTCTTATGGGGGATCCTTCTGTTGCGGA
66 TCTGGAAGTATAGAAACATGTTAGTGTTTGAGGGATTGTCTTATGAGGGATCCTTCTGTTGCGGA
* *
1916048 TAGGTGTGGCAGACAGGGGAGTAAGGTGTTATCTCGAGCTCTGTGGGTTCCGCCTCCTGAAGGCT
131 TAGGTATGGCAGACAGGAGAGTAAGGTGTTATCTCGAGCTCTGTGGGTTCCGCCTCCTGAAGGCT
1916113 TTTTTAAATTAAATGTGGATGGTGCTGTCACAGATGATTGGATGAAAGGGGGTATAGGACGGT-T
196 TTTTTAAATTAAATGTGGATGGTGCTGTCACAGATGATTGGATGAAAGGGGGTATAGGAC-GTAT
1916177 TATTAAAGATTCAAGGGGTTATATGTTGGCTTCATTCTCTGAGGCAATTGGGAAGGAGCCTCCTA
260 TATTAAAGATTCAAGGGGTTATATGTTGGCTTCATTCTCTGAGGCAATTGGGAAGGAGCCTCCTA
1916242 CAACTGCTGAAATGTTGGCTATTAAAAAGGGTTTGAATCTTTTCTTTGATTCTCAATGGAGTTGC
325 CAACTGCTGAAATGTTGGCTATTAAAAAGGGTTTGAATCTTTTCTTTGATTCTCAATGGAGTTGC
*
1916307 AAAGGTAGACTTATTGTTGAGTGTGATTGTCTTGTGGGGTTAATTGGATTAAGAAT
390 AAAGGTAGACTTATTGTTGAGTGTGATTGTCTTGTGGGGTTAATTGAATTAAGAAT
1916363 TTGG
1 TTGG
1916367 GGGTTGCCCG
Statistics
Matches: 440, Mismatches: 8, Indels: 2
0.98 0.02 0.00
Matches are distributed among these distances:
445 438 1.00
446 2 0.00
ACGTcount: A:0.23, C:0.11, G:0.30, T:0.35
Consensus pattern (445 bp):
TTGGTGGGGGTTGGTTATGAATTCTGAATTCTGGGGAGTTATTCCTGCTACCGTTTTGTGGTATA
TCTGGAAGTATAGAAACATGTTAGTGTTTGAGGGATTGTCTTATGAGGGATCCTTCTGTTGCGGA
TAGGTATGGCAGACAGGAGAGTAAGGTGTTATCTCGAGCTCTGTGGGTTCCGCCTCCTGAAGGCT
TTTTTAAATTAAATGTGGATGGTGCTGTCACAGATGATTGGATGAAAGGGGGTATAGGACGTATT
ATTAAAGATTCAAGGGGTTATATGTTGGCTTCATTCTCTGAGGCAATTGGGAAGGAGCCTCCTAC
AACTGCTGAAATGTTGGCTATTAAAAAGGGTTTGAATCTTTTCTTTGATTCTCAATGGAGTTGCA
AAGGTAGACTTATTGTTGAGTGTGATTGTCTTGTGGGGTTAATTGAATTAAGAAT
Found at i:1925327 original size:48 final size:48
Alignment explanation
Indices: 1925265--1925363 Score: 198
Period size: 48 Copynumber: 2.1 Consensus size: 48
1925255 TAACTCTTAG
1925265 AAAGTTAGATAGATAAGGATAACTACTAAGTAGTTTACTTCTAATAGA
1 AAAGTTAGATAGATAAGGATAACTACTAAGTAGTTTACTTCTAATAGA
1925313 AAAGTTAGATAGATAAGGATAACTACTAAGTAGTTTACTTCTAATAGA
1 AAAGTTAGATAGATAAGGATAACTACTAAGTAGTTTACTTCTAATAGA
1925361 AAA
1 AAA
1925364 CTTACTCCTA
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
48 51 1.00
ACGTcount: A:0.45, C:0.08, G:0.16, T:0.30
Consensus pattern (48 bp):
AAAGTTAGATAGATAAGGATAACTACTAAGTAGTTTACTTCTAATAGA
Found at i:1936532 original size:31 final size:31
Alignment explanation
Indices: 1936459--1936548 Score: 112
Period size: 31 Copynumber: 2.9 Consensus size: 31
1936449 CCGAAGGACT
*
1936459 TATCCATATGT-TCGGAAGAACATAGGT-AAC
1 TATCCATATGTCTC-GAAGGACATAGGTAAAC
* * *
1936489 TGTCAATATGTCTCTAAGGACATAGGTAAAC
1 TATCCATATGTCTCGAAGGACATAGGTAAAC
*
1936520 TATCCATATGTCTCGAAAGACATAGGTAA
1 TATCCATATGTCTCGAAGGACATAGGTAA
1936549 CCCTAGACTC
Statistics
Matches: 50, Mismatches: 8, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
30 20 0.40
31 30 0.60
ACGTcount: A:0.37, C:0.17, G:0.19, T:0.28
Consensus pattern (31 bp):
TATCCATATGTCTCGAAGGACATAGGTAAAC
Found at i:1940947 original size:11 final size:11
Alignment explanation
Indices: 1940924--1940972 Score: 80
Period size: 11 Copynumber: 4.4 Consensus size: 11
1940914 TATCTGGAAC
1940924 TCTTCTCTTTCT
1 TCTT-TCTTTCT
*
1940936 TCTTTTTTTCT
1 TCTTTCTTTCT
1940947 TCTTTCTTTCT
1 TCTTTCTTTCT
1940958 TCTTTCTTTCT
1 TCTTTCTTTCT
1940969 TCTT
1 TCTT
1940973 CCTGTGTGTT
Statistics
Matches: 35, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
11 31 0.89
12 4 0.11
ACGTcount: A:0.00, C:0.27, G:0.00, T:0.73
Consensus pattern (11 bp):
TCTTTCTTTCT
Found at i:1940953 original size:4 final size:4
Alignment explanation
Indices: 1940924--1940969 Score: 53
Period size: 4 Copynumber: 12.0 Consensus size: 4
1940914 TATCTGGAAC
*
1940924 TCTT CTCTT TC-T TCTT TTTT TC-T TCTT TCTT TC-T TCTT TCTT TCTT
1 TCTT -TCTT TCTT TCTT TCTT TCTT TCTT TCTT TCTT TCTT TCTT TCTT
1940970 CTTCCTGTGT
Statistics
Matches: 36, Mismatches: 2, Indels: 7
0.80 0.04 0.16
Matches are distributed among these distances:
3 9 0.25
4 23 0.64
5 4 0.11
ACGTcount: A:0.00, C:0.26, G:0.00, T:0.74
Consensus pattern (4 bp):
TCTT
Found at i:1940953 original size:15 final size:16
Alignment explanation
Indices: 1940929--1940969 Score: 52
Period size: 15 Copynumber: 2.8 Consensus size: 16
1940919 GGAACTCTTC
*
1940929 TCTTTC-TTCTTTTTT
1 TCTTTCTTTCTTTTCT
1940944 TC-TTCTTTC-TTTCT
1 TCTTTCTTTCTTTTCT
1940958 TCTTTCTTTCTT
1 TCTTTCTTTCTT
1940970 CTTCCTGTGT
Statistics
Matches: 22, Mismatches: 1, Indels: 5
0.79 0.04 0.18
Matches are distributed among these distances:
14 9 0.41
15 12 0.55
16 1 0.05
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (16 bp):
TCTTTCTTTCTTTTCT
Found at i:1942448 original size:46 final size:46
Alignment explanation
Indices: 1942396--1942526 Score: 172
Period size: 46 Copynumber: 2.8 Consensus size: 46
1942386 GTCGAGGGTC
* *
1942396 TATGTGGTCATTCGAGATATAGTGGTCATTTGGGACATATGTGTTA
1 TATGTGGTCATTCGAGACATAGTGGTCATTCGGGACATATGTGTTA
* * *
1942442 TATGTGGTCCTTCGGGACATAGTGGTCCTTCGGGACATATGTGTTA
1 TATGTGGTCATTCGAGACATAGTGGTCATTCGGGACATATGTGTTA
* * *
1942488 TATGTGGTCATTCGGGACATATACTGGTCCTTCGGGACA
1 TATGTGGTCATTCGAGAC--ATAGTGGTCATTCGGGACA
1942527 AATTCTATGC
Statistics
Matches: 76, Mismatches: 7, Indels: 2
0.89 0.08 0.02
Matches are distributed among these distances:
46 58 0.76
48 18 0.24
ACGTcount: A:0.21, C:0.15, G:0.29, T:0.35
Consensus pattern (46 bp):
TATGTGGTCATTCGAGACATAGTGGTCATTCGGGACATATGTGTTA
Found at i:1942468 original size:18 final size:18
Alignment explanation
Indices: 1942445--1942480 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
1942435 TGTGTTATAT
1942445 GTGGTCCTTCGGGACATA
1 GTGGTCCTTCGGGACATA
1942463 GTGGTCCTTCGGGACATA
1 GTGGTCCTTCGGGACATA
1942481 TGTGTTATAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.17, C:0.22, G:0.33, T:0.28
Consensus pattern (18 bp):
GTGGTCCTTCGGGACATA
Found at i:1943303 original size:12 final size:12
Alignment explanation
Indices: 1943265--1943303 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
1943255 TGGCAATGAG
1943265 GAAGAGAAGGAA
1 GAAGAGAAGGAA
* *
1943277 GAAAAGAAGAAA
1 GAAGAGAAGGAA
*
1943289 GAAGAGAAGGTA
1 GAAGAGAAGGAA
1943301 GAA
1 GAA
1943304 AAAAATATAG
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.62, C:0.00, G:0.36, T:0.03
Consensus pattern (12 bp):
GAAGAGAAGGAA
Found at i:1948542 original size:178 final size:180
Alignment explanation
Indices: 1948171--1948543 Score: 511
Period size: 178 Copynumber: 2.1 Consensus size: 180
1948161 TACTAAATAT
* * *
1948171 GTATCGATACGTTTAGTCCAGTATGCATCTCAAACAATTTGTACGCAAAAAGTATCGATAAACAT
1 GTATCGATACTTTTAGTCCAGTATGCATCTCAAACAATTTGCACACAAAAAGTATCGATAAACAT
* *
1948236 ATAACAAGTATCGATACTTATAATTTCTAAACCTATTTCTTTAAAAACAAATAGGTAAATTTACA
66 ATAACAAATATCGATACTTATAATTTCTAAACCTATTACTTT-AAAACAAATAGGTAAATTTACA
* *
1948301 ATGAAAATGATAAAAATCTATCGATTTAATGATAATAGGCGTAAACATAAA
130 ATGAAAACGATAAAAATCTATCGATTTAATGATAATAGACGTAAACATAAA
** * * * * **
1948352 GTATCGATACTTTTAGTTTAGTATGCTTCTC-AACAATTTGCATACACAAAGTATCGATACATGT
1 GTATCGATACTTTTAGTCCAGTATGCATCTCAAACAATTTGCACACAAAAAGTATCGATAAACAT
**
1948416 ATAACAAATATCGATACTTATAATTT-TGAAACCTATTACTTT-AAAGTAATAGGTAAATTTACA
66 ATAACAAATATCGATACTTATAATTTCT-AAACCTATTACTTTAAAACAAATAGGTAAATTTACA
*
1948479 ATGAAAACGGTAAAAATCTATC-AGTTTAATGATAATAGACGTAAACATAAA
130 ATGAAAACGATAAAAATCTATCGA-TTTAATGATAATAGACGTAAACATAAA
* *
1948530 TTATCAATACTTTT
1 GTATCGATACTTTT
1948544 TGTATATGTA
Statistics
Matches: 170, Mismatches: 20, Indels: 7
0.86 0.10 0.04
Matches are distributed among these distances:
177 1 0.01
178 77 0.45
179 1 0.01
180 64 0.38
181 27 0.16
ACGTcount: A:0.42, C:0.13, G:0.11, T:0.33
Consensus pattern (180 bp):
GTATCGATACTTTTAGTCCAGTATGCATCTCAAACAATTTGCACACAAAAAGTATCGATAAACAT
ATAACAAATATCGATACTTATAATTTCTAAACCTATTACTTTAAAACAAATAGGTAAATTTACAA
TGAAAACGATAAAAATCTATCGATTTAATGATAATAGACGTAAACATAAA
Found at i:1949559 original size:200 final size:200
Alignment explanation
Indices: 1948383--1949564 Score: 1555
Period size: 200 Copynumber: 5.9 Consensus size: 200
1948373 TATGCTTCTC
* * * * *
1948383 AACAATTTGCATACACAAAGTATCGATACATGTATAACAAATATCGATACTTATAATTTTGAAAC
1 AACAATTTGCACACAAAAAGTATCGATACACGTATAACAAGTATCGATACTTATAATTTCGAAAC
* * *
1948448 CTATTACTTTAAAGTAATAGGTAAATTTACAATGAAAACGGTAAAAATCTATCAGTTTAATGATA
66 CTATTACTTTAAAGTAATAGGTAAATTTACAATGTAAACGGTAAAAATCTACCGGTTTAATGATA
* * * * * * * *
1948513 ATAGACGTAAACATAAATTATCAATACTTTTTGTATATGTAT-AATTACTTGTATTCCAATATTC
131 ATAGGCGTAAACATAAAGTATCGATACTTATTATATAAGTATCGA-TACTTGTATTCCAATATGC
1948577 ATCACA
195 ATCACA
* * * ** * *
1948583 AAGAATTTGCATACAAAAAGTATCGATACACGTATCACAAACATCGATACCTATAATTTCGAAAT
1 AACAATTTGCACACAAAAAGTATCGATACACGTATAACAAGTATCGATACTTATAATTTCGAAAC
* *
1948648 CGATTACTTTATAGTAATAGGTAAATTTACAATGTAAACGGTAAAAATCTACCGGTTTAATGATA
66 CTATTACTTTAAAGTAATAGGTAAATTTACAATGTAAACGGTAAAAATCTACCGGTTTAATGATA
* * *
1948713 ATAGGCGTAAACATAAAGTATTCGATACTTATTATATAAGTACCAATACTTGTACTCCAATATGC
131 ATAGGCGTAAACATAAAGTA-TCGATACTTATTATATAAGTATCGATACTTGTATTCCAATATGC
1948778 ATCACA
195 ATCACA
* * * *
1948784 AACAATTTGCACGCAAAAAAAGTATCAATACGCGTATAACAAGTATCGATACTTATAATTTTGAA
1 AACAATTTGCA--CACAAAAAGTATCGATACACGTATAACAAGTATCGATACTTATAATTTCGAA
* * * * * *
1948849 ACATGTTTCTTTAAAGTAATAGGTAAATTTACAATGTAAACGATAAAAATCTATCGATTTAATGA
64 ACCTATTACTTTAAAGTAATAGGTAAATTTACAATGTAAACGGTAAAAATCTACCGGTTTAATGA
* * * * **
1948914 TAATAGGCGTAAACATAAAGTATCGATACTTTTTGTAT-AGATATCGATACTTTTAGTCCAGGAT
129 TAATAGGCGTAAACATAAAGTATCGATACTTATTATATAAG-TATCGATACTTGTATTCCAATAT
* *
1948978 GCTTCTC-
193 GCATCACA
* * * * *
1948985 AACAATTTGCACGCACAAAGTATCGATACACGTATCACAAGTATCGATACTTATAATATCGAAGC
1 AACAATTTGCACACAAAAAGTATCGATACACGTATAACAAGTATCGATACTTATAATTTCGAAAC
* *
1949050 CTATTACTTTAAAATAATAGGTAAATTTACAATGTAAATGGTAAAAATCTACCGGTTTAATGATA
66 CTATTACTTTAAAGTAATAGGTAAATTTACAATGTAAACGGTAAAAATCTACCGGTTTAATGATA
* *
1949115 ATAGGCGTAAACATAAAGTATCGATACTTATTATATAAATATCTATACTTGTATTCCAATATGCA
131 ATAGGCGTAAACATAAAGTATCGATACTTATTATATAAGTATCGATACTTGTATTCCAATATGCA
*
1949180 TCAGA
196 TCACA
* ** * * **
1949185 AACAATTTGCACGCAAAAAGTATCGATTGACGTGTCACAAGTATCGATACTTATAATTTTTAAAC
1 AACAATTTGCACACAAAAAGTATCGATACACGTATAACAAGTATCGATACTTATAATTTCGAAAC
* * * **
1949250 CTATTACTTTAAAGTATTAGGCAAATTTACAATGTAAACGGTAAAAATCTATCGAATTAATGATA
66 CTATTACTTTAAAGTAATAGGTAAATTTACAATGTAAACGGTAAAAATCTACCGGTTTAATGATA
*
1949315 ATAGGCGTAAACATAAAGTATTGATACTTATTATATAAGTATCGATACTTGTATTCCAATATGCA
131 ATAGGCGTAAACATAAAGTATCGATACTTATTATATAAGTATCGATACTTGTATTCCAATATGCA
*
1949380 TCATA
196 TCACA
* *
1949385 AACAATTTGCACACAAAAAAGTATCGATACATGTATAACAAGTATCGATACTTATAATTTCAAAA
1 AACAATTTGCACAC-AAAAAGTATCGATACACGTATAACAAGTATCGATACTTATAATTTCGAAA
* * * * *
1949450 CATATTTCTTTAAAGTAATAGGTAAATTTACAATGTAAACTGT-AAAATCTACCGGTTCAATTAT
65 CCTATTACTTTAAAGTAATAGGTAAATTTACAATGTAAACGGTAAAAATCTACCGGTTTAATGAT
* *
1949514 AATAGGCGTAAACATAAAGTATCAATACTT-TTGATATATGTATCGATACTT
130 AATAGGCGTAAACATAAAGTATCGATACTTATT-ATATAAGTATCGATACTT
1949565 TCGATCTAAA
Statistics
Matches: 854, Mismatches: 119, Indels: 18
0.86 0.12 0.02
Matches are distributed among these distances:
199 160 0.19
200 391 0.46
201 144 0.17
202 38 0.04
203 121 0.14
ACGTcount: A:0.41, C:0.14, G:0.12, T:0.33
Consensus pattern (200 bp):
AACAATTTGCACACAAAAAGTATCGATACACGTATAACAAGTATCGATACTTATAATTTCGAAAC
CTATTACTTTAAAGTAATAGGTAAATTTACAATGTAAACGGTAAAAATCTACCGGTTTAATGATA
ATAGGCGTAAACATAAAGTATCGATACTTATTATATAAGTATCGATACTTGTATTCCAATATGCA
TCACA
Found at i:1950086 original size:18 final size:18
Alignment explanation
Indices: 1950063--1950125 Score: 83
Period size: 18 Copynumber: 3.6 Consensus size: 18
1950053 TGAGACGCAA
**
1950063 TTCTTCTCAACCAAAACC
1 TTCTTCTCAACCAAAGTC
*
1950081 TTCTTCTCAA-CAATGTC
1 TTCTTCTCAACCAAAGTC
*
1950098 TTCTTCTCAACCAAGGTC
1 TTCTTCTCAACCAAAGTC
1950116 TTCTTCTCAA
1 TTCTTCTCAA
1950126 GTAAGGGCTA
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
17 14 0.35
18 26 0.65
ACGTcount: A:0.25, C:0.33, G:0.05, T:0.37
Consensus pattern (18 bp):
TTCTTCTCAACCAAAGTC
Found at i:1952285 original size:15 final size:15
Alignment explanation
Indices: 1952265--1952294 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
1952255 AGACTACTAG
1952265 AACATTGTTATGTAT
1 AACATTGTTATGTAT
*
1952280 AACATTGTTTTGTAT
1 AACATTGTTATGTAT
1952295 GTTTGGTTTA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.30, C:0.07, G:0.13, T:0.50
Consensus pattern (15 bp):
AACATTGTTATGTAT
Found at i:1952644 original size:6 final size:6
Alignment explanation
Indices: 1952633--1952669 Score: 65
Period size: 6 Copynumber: 6.2 Consensus size: 6
1952623 TGCAGTTTTC
*
1952633 AATTTG AATTTG ATTTTG AATTTG AATTTG AATTTG A
1 AATTTG AATTTG AATTTG AATTTG AATTTG AATTTG A
1952670 GCTCCACTAT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.32, C:0.00, G:0.16, T:0.51
Consensus pattern (6 bp):
AATTTG
Found at i:1952654 original size:18 final size:18
Alignment explanation
Indices: 1952628--1952669 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
1952618 AATTATGCAG
*
1952628 TTTTCAATTTGAATTTGA
1 TTTTGAATTTGAATTTGA
1952646 TTTTGAATTTGAATTTGA
1 TTTTGAATTTGAATTTGA
*
1952664 ATTTGA
1 TTTTGA
1952670 GCTCCACTAT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.29, C:0.02, G:0.14, T:0.55
Consensus pattern (18 bp):
TTTTGAATTTGAATTTGA
Found at i:1954886 original size:199 final size:199
Alignment explanation
Indices: 1954350--1955464 Score: 1400
Period size: 199 Copynumber: 5.6 Consensus size: 199
1954340 TTTTATTCAG
* * * * *
1954350 TATGCATCTCAAACAATTTGCACGTAAAATAATATCGAT--ACATGTATAACAAGTATCAATACT
1 TATGCTTCTC-AACAATTTGCACGCACAA-AGTATCGATACACATGTAT-A-AAGTATCAATACG
* *
1954413 TATAATTTCGAAACTAATTACTTTAAAATTATAGGTAAATTTACAATGTAAACGGTAAAAGTCTA
62 TATAATTTCGAAACTGATTACTTTAAAGTTATAGGTAAATTTACAATGTAAACGGTAAAAGTCTA
** * *
1954478 TTGGTTTAATGATAATAGGCGTAAACGTAAAGTAGT-GATACATTTTGTATAGGTATCGATACTT
127 CCGGTTTAATGATAATAGGCGTAAACATAAAGTA-TCGATACTTTTTGTATAGGTATCGATACTT
1954542 GTAGTCCAGA
191 GTAGTCCA-A
* * * * * *
1954552 -ATG-TACCTCAAACAATTTGCACGCAAAAAGTATCAATACACATATA-ACAAATATCAATACTT
1 TATGCT-TCTC-AACAATTTGCACGCACAAAGTATCGATACACATGTATA-AAGTATCAATACGT
* *
1954614 ATAATTTCGAAACCGATTACTTTAAAGTTATAGGTAAATTTACAATGTAAACGGTAGAAGTCTAC
63 ATAATTTCGAAACTGATTACTTTAAAGTTATAGGTAAATTTACAATGTAAACGGTAAAAGTCTAC
* * * *
1954679 CAGTTTAATAATAATAGGCGTAAACATCAAGTATCTATACTTTTTGTATAGGTATCGATACTTGT
128 CGGTTTAATGATAATAGGCGTAAACATAAAGTATCGATACTTTTTGTATAGGTATCGATACTTGT
*
1954744 AGTCCAT
193 AGTCCAA
* * **
1954751 TATGCTTCTCAAGAATTTGCACGCACAAAGTATCGACACACATGTATAAAGTATCAATACGTGGA
1 TATGCTTCTCAACAATTTGCACGCACAAAGTATCGATACACATGTATAAAGTATCAATACGTATA
* * *
1954816 ATTTTGAAACCGATTACTTTAAAGTTATAGGTAAATTTACAATGTAAACGGTAAAAGTATACCGG
66 ATTTCGAAACTGATTACTTTAAAGTTATAGGTAAATTTACAATGTAAACGGTAAAAGTCTACCGG
* * *
1954881 TTTAATGATAATAGCCGTAAACATAAAGTATCGATACTTTTTGTATATGTATTGATACTTG--GT
131 TTTAATGATAATAGGCGTAAACATAAAGTATCGATACTTTTTGTATAGGTATCGATACTTGTAGT
1954944 CCAA
196 CCAA
* *
1954948 TATGCTTCTCAACAATTTGCACGCACAAAGTATCGATACACATGTATAAAATATCGATACGTGA-
1 TATGCTTCTCAACAATTTGCACGCACAAAGTATCGATACACATGTATAAAGTATCAATACGT-AT
* * * *
1955012 AATTTCGAAACTGGTTACTTTAAAGTTATAGGTAAATTTACAGTGTAAACGGTAAAAGTCTATCA
65 AATTTCGAAACTGATTACTTTAAAGTTATAGGTAAATTTACAATGTAAACGGTAAAAGTCTACCG
* *
1955077 GTTTAATGATAAAAGGCGTAAACATAAAGTATCGATACTTTTTGTATAGGTATCGATACTTTTAG
130 GTTTAATGATAATAGGCGTAAACATAAAGTATCGATACTTTTTGTATAGGTATCGATACTTGTAG
1955142 TCCAA
195 TCCAA
* * * * *
1955147 TATGATTCTCAACAATTTGCACGCACAAAGTATCGACACATATGTATAAAGTATCGATACGCATA
1 TATGCTTCTCAACAATTTGCACGCACAAAGTATCGATACACATGTATAAAGTATCAATACGTATA
*** * * ** * *
1955212 ATTGAAAAACTGATTACTTTAAAGTTGTAGGTAAATTTACAATGTCAATAGTAAAAGTCTACTGA
66 ATTTCGAAACTGATTACTTTAAAGTTATAGGTAAATTTACAATGTAAACGGTAAAAGTCTACCGG
* *
1955277 TTTAATGATAACAGGCGTAAACATAAAGTATCGATACTTTTTGTATAGGTATCGATACTTTTAGT
131 TTTAATGATAATAGGCGTAAACATAAAGTATCGATACTTTTTGTATAGGTATCGATACTTGTAGT
1955342 CCAA
196 CCAA
* * ****
1955346 TATGCTTCT---C-----GCACGCACAAAGTATCAATACACATGTATAAAGTATCGATACACGGA
1 TATGCTTCTCAACAATTTGCACGCACAAAGTATCGATACACATGTATAAAGTATCAATACGTATA
** * * *
1955403 ATTTCGAAACTGATTACTTTAAAGTTATTTGTAAATTTACAATATTAACGATAAAAGTCTAC
66 ATTTCGAAACTGATTACTTTAAAGTTATAGGTAAATTTACAATGTAAACGGTAAAAGTCTAC
1955465 TGATATCAAG
Statistics
Matches: 807, Mismatches: 95, Indels: 33
0.86 0.10 0.04
Matches are distributed among these distances:
191 92 0.11
196 1 0.00
197 178 0.22
198 1 0.00
199 353 0.44
200 151 0.19
201 25 0.03
202 6 0.01
ACGTcount: A:0.38, C:0.14, G:0.15, T:0.33
Consensus pattern (199 bp):
TATGCTTCTCAACAATTTGCACGCACAAAGTATCGATACACATGTATAAAGTATCAATACGTATA
ATTTCGAAACTGATTACTTTAAAGTTATAGGTAAATTTACAATGTAAACGGTAAAAGTCTACCGG
TTTAATGATAATAGGCGTAAACATAAAGTATCGATACTTTTTGTATAGGTATCGATACTTGTAGT
CCAA
Found at i:1955135 original size:396 final size:395
Alignment explanation
Indices: 1954389--1955464 Score: 1447
Period size: 396 Copynumber: 2.7 Consensus size: 395
1954379 TAATATCGAT
* * * *
1954389 ACATGTATAACAAGTATCAATACTTATAATTTCGAAACTAATTACTTTAAAATTATAGGTAAATT
1 ACATGTAT-A-AAGTATCAATACGTATAATTTAGAAACTGATTACTTTAAAGTTATAGGTAAATT
* *
1954454 TACAATGTAAACGGTAAAAGTCTATTGGTTTAATGATAATAGGCGTAAACGTAAAGTAGT-GATA
64 TACAATGTAAACGGTAAAAGTCTACTGGTTTAATGATAATAGGCGTAAACATAAAGTA-TCGATA
* * *
1954518 CATTTTGTATAGGTATCGATACTTGTAGTCCAGA-ATG-TACCTCAAACAATTTGCACGCAAAAA
128 CTTTTTGTATAGGTATCGATACTTG--GTCCA-ATATGCT-TCTC-AACAATTTGCACGCACAAA
* * * *
1954581 GTATCAATACACATATA-ACAAATATCAATACTTATAATTTCGAAACCGATTACTTTAAAGTTAT
188 GTATCAATACACATGTATA-AAATATCGATACTGA-AATTTCGAAACTGATTACTTTAAAGTTAT
* * *
1954645 AGGTAAATTTACAATGTAAACGGTAGAAGTCTACCAGTTTAATAATAATAGGCGTAAACATCAAG
251 AGGTAAATTTACAATGTAAACGGTAAAAGTCTACCAGTTTAATAATAAAAGGCGTAAACATAAAG
* * * *
1954710 TATCTATACTTTTTGTATAGGTATCGATACTTGTAGTCCATTATGCTTCTCAAGAATTTGCACGC
316 TATCGATACTTTTTGTATAGGTATCGATACTTGTAGTCCAATATGATTCTCAACAATTTGCACGC
1954775 ACAAAGTATCGACAC
381 ACAAAGTATCGACAC
** * *
1954790 ACATGTATAAAGTATCAATACGTGGAATTTTGAAACCGATTACTTTAAAGTTATAGGTAAATTTA
1 ACATGTATAAAGTATCAATACGTATAATTTAGAAACTGATTACTTTAAAGTTATAGGTAAATTTA
* * *
1954855 CAATGTAAACGGTAAAAGTATACCGGTTTAATGATAATAGCCGTAAACATAAAGTATCGATACTT
66 CAATGTAAACGGTAAAAGTCTACTGGTTTAATGATAATAGGCGTAAACATAAAGTATCGATACTT
* * *
1954920 TTTGTATATGTATTGATACTTGGTCCAATATGCTTCTCAACAATTTGCACGCACAAAGTATCGAT
131 TTTGTATAGGTATCGATACTTGGTCCAATATGCTTCTCAACAATTTGCACGCACAAAGTATCAAT
*
1954985 ACACATGTATAAAATATCGATACGTGAAATTTCGAAACTGGTTACTTTAAAGTTATAGGTAAATT
196 ACACATGTATAAAATATCGATAC-TGAAATTTCGAAACTGATTACTTTAAAGTTATAGGTAAATT
* * *
1955050 TACAGTGTAAACGGTAAAAGTCTATCAGTTTAATGATAAAAGGCGTAAACATAAAGTATCGATAC
260 TACAATGTAAACGGTAAAAGTCTACCAGTTTAATAATAAAAGGCGTAAACATAAAGTATCGATAC
*
1955115 TTTTTGTATAGGTATCGATACTTTTAGTCCAATATGATTCTCAACAATTTGCACGCACAAAGTAT
325 TTTTTGTATAGGTATCGATACTTGTAGTCCAATATGATTCTCAACAATTTGCACGCACAAAGTAT
1955180 CGACAC
390 CGACAC
* * * * * *
1955186 ATATGTATAAAGTATCGATACGCATAATTGAAAAACTGATTACTTTAAAGTTGTAGGTAAATTTA
1 ACATGTATAAAGTATCAATACGTATAATTTAGAAACTGATTACTTTAAAGTTATAGGTAAATTTA
* ** * *
1955251 CAATGTCAATAGTAAAAGTCTACTGATTTAATGATAACAGGCGTAAACATAAAGTATCGATACTT
66 CAATGTAAACGGTAAAAGTCTACTGGTTTAATGATAATAGGCGTAAACATAAAGTATCGATACTT
*
1955316 TTTGTATAGGTATCGATACTTTTAGTCCAATATGCTTCT---C-----GCACGCACAAAGTATCA
131 TTTGTATAGGTATCGATAC--TTGGTCCAATATGCTTCTCAACAATTTGCACGCACAAAGTATCA
* * * **
1955373 ATACACATGTATAAAGTATCGATACACGGAATTTCGAAACTGATTACTTTAAAGTTATTTGTAAA
194 ATACACATGTATAAAATATCGATAC-TGAAATTTCGAAACTGATTACTTTAAAGTTATAGGTAAA
* * *
1955438 TTTACAATATTAACGATAAAAGTCTAC
258 TTTACAATGTAAACGGTAAAAGTCTAC
1955465 TGATATCAAG
Statistics
Matches: 600, Mismatches: 68, Indels: 25
0.87 0.10 0.04
Matches are distributed among these distances:
390 96 0.16
395 1 0.00
396 335 0.56
397 14 0.02
398 19 0.03
399 126 0.21
400 1 0.00
401 8 0.01
ACGTcount: A:0.38, C:0.14, G:0.15, T:0.33
Consensus pattern (395 bp):
ACATGTATAAAGTATCAATACGTATAATTTAGAAACTGATTACTTTAAAGTTATAGGTAAATTTA
CAATGTAAACGGTAAAAGTCTACTGGTTTAATGATAATAGGCGTAAACATAAAGTATCGATACTT
TTTGTATAGGTATCGATACTTGGTCCAATATGCTTCTCAACAATTTGCACGCACAAAGTATCAAT
ACACATGTATAAAATATCGATACTGAAATTTCGAAACTGATTACTTTAAAGTTATAGGTAAATTT
ACAATGTAAACGGTAAAAGTCTACCAGTTTAATAATAAAAGGCGTAAACATAAAGTATCGATACT
TTTTGTATAGGTATCGATACTTGTAGTCCAATATGATTCTCAACAATTTGCACGCACAAAGTATC
GACAC
Found at i:1956189 original size:108 final size:108
Alignment explanation
Indices: 1956038--1956412 Score: 308
Period size: 108 Copynumber: 3.3 Consensus size: 108
1956028 ATGTGTCCAA
** * * * *
1956038 TAATTAACCTATTTTGTTATCCTCATATTTCTAACGATCCATCAGCTTAAACTTTAGTAACATTT
1 TAATTAACCTATTTTGTTATAGTCAGATTTCTAAGGCTCCATCAACTTAAACTTTAGTAACATTT
*
1956103 TAGGTGCTACGTAATATGTTGATAATATTGATAACAAATTAAG
66 TAGGTGCTACCTAATATGTTGATAATATTGATAACAAATTAAG
* * *
1956146 TAATAAACCTATTTTGTTATGGTCGGATTTCTAAGGC-CGCATCAACTTTAAACAAACGTTACGT
1 TAATTAACCTATTTTGTTATAGTCAGATTTCTAAGGCTC-CATCAAC-TT----AAAC--T---T
* * * * * ** * *** *
1956210 TACCTATTACATTAAATAAGCGCTACTTGTTATGTT-ATTATGATTGATAA-TGTTTCCAG
55 TA-GTA--ACATT--TTAGGTGCTACCTAATATGTTGATAAT-ATTGATAACAAATT-AAG
* *
1956269 TAATTAACCTATTTTGTTATCGTCAGATTTCTAAGGCTCCATCAACTTAAACTTTGGTAACATTT
1 TAATTAACCTATTTTGTTATAGTCAGATTTCTAAGGCTCCATCAACTTAAACTTTAGTAACATTT
*
1956334 TAGGCT-CTACCTAATATGTTGATAATATTGATAACAAATCAAG
66 TAGG-TGCTACCTAATATGTTGATAATATTGATAACAAATTAAG
* *
1956377 TAATTAACATATTTTGTTATATTCAGATTTCTAAGG
1 TAATTAACCTATTTTGTTATAGTCAGATTTCTAAGG
1956413 TAACATCAGC
Statistics
Matches: 205, Mismatches: 40, Indels: 44
0.71 0.14 0.15
Matches are distributed among these distances:
107 1 0.00
108 93 0.45
109 7 0.03
110 5 0.02
112 2 0.01
113 6 0.03
115 1 0.00
116 1 0.00
118 7 0.03
119 2 0.01
121 5 0.02
122 8 0.04
123 66 0.32
124 1 0.00
ACGTcount: A:0.33, C:0.15, G:0.13, T:0.39
Consensus pattern (108 bp):
TAATTAACCTATTTTGTTATAGTCAGATTTCTAAGGCTCCATCAACTTAAACTTTAGTAACATTT
TAGGTGCTACCTAATATGTTGATAATATTGATAACAAATTAAG
Found at i:1956285 original size:231 final size:226
Alignment explanation
Indices: 1955887--1956501 Score: 835
Period size: 231 Copynumber: 2.7 Consensus size: 226
1955877 AATGTAAACA
* *
1955887 GTAATATGTTGATAATATTGATAACAAATCAAGTAATTAACCTATGTTGTTATTATCGGATTTCT
1 GTAATATGTTGATAATATTGATAACAAATCAAGTAATTAACCTATTTTGTTATAATCGGATTTCT
* *
1955952 AATGCTCCATCAGTTTTTAAC--AGGCGCTACCTATTACATTAAATAAGCGCTACTTGTTATGTT
66 AAGGC-CCATCAG-CTTTAACAAAGGCGCTACCTATTACATTAAATAAGCGCTACTTGTTATGTT
* * *
1956015 ATTATGGTTGATAATGTGTCCAATAATTAACCTATTTTGTTATCCTCATATTTCTAACGATCCAT
129 ATTATGGTTGATAATGTTTCCAGTAATTAACCTATTTTGTTATCCTCAGATTTCTAACGATCCAT
*
1956080 CAGCTTAAACTTTAGTAACATTTTAGG-TGCTAC
194 CAACTTAAACTTTAGTAACATTTTAGGCT-CTAC
* * **
1956113 GTAATATGTTGATAATATTGATAACAAATTAAGTAATAAACCTATTTTGTTATGGTCGGATTTCT
1 GTAATATGTTGATAATATTGATAACAAATCAAGTAATTAACCTATTTTGTTATAATCGGATTTCT
* * *
1956178 AAGGCCGCATCAACTTTAAACAAACGTTACGTTACCTATTACATTAAATAAGCGCTACTTGTTAT
66 AAGGCC-CATCAGCTTT-AACAAA-G--GCGCTACCTATTACATTAAATAAGCGCTACTTGTTAT
* * * *
1956243 GTTATTATGATTGATAATGTTTCCAGTAATTAACCTATTTTGTTATCGTCAGATTTCTAAGGCTC
126 GTTATTATGGTTGATAATGTTTCCAGTAATTAACCTATTTTGTTATCCTCAGATTTCTAACGATC
*
1956308 CATCAACTTAAACTTTGGTAACATTTTAGGCTCTAC
191 CATCAACTTAAACTTTAGTAACATTTTAGGCTCTAC
* * * *
1956344 CTAATATGTTGATAATATTGATAACAAATCAAGTAATTAACATATTTTGTTATATTCAGATTTCT
1 GTAATATGTTGATAATATTGATAACAAATCAAGTAATTAACCTATTTTGTTATAATCGGATTTCT
** * * * *
1956409 AAGGTAACATCAGCTTTAA-AAAGGCGCTACCTATTACGTTACATAAGCGCTACAT-ATATGTTA
66 AAGG-CCCATCAGCTTTAACAAAGGCGCTACCTATTACATTAAATAAGCGCTACTTGTTATGTTA
*
1956472 TTATGGTTGATATTGTTTCCAGTAATTAAC
130 TTATGGTTGATAATGTTTCCAGTAATTAAC
1956502 TGGTTATGTT
Statistics
Matches: 343, Mismatches: 37, Indels: 19
0.86 0.09 0.05
Matches are distributed among these distances:
225 39 0.11
226 99 0.29
228 2 0.01
229 4 0.01
230 2 0.01
231 196 0.57
232 1 0.00
ACGTcount: A:0.33, C:0.15, G:0.13, T:0.39
Consensus pattern (226 bp):
GTAATATGTTGATAATATTGATAACAAATCAAGTAATTAACCTATTTTGTTATAATCGGATTTCT
AAGGCCCATCAGCTTTAACAAAGGCGCTACCTATTACATTAAATAAGCGCTACTTGTTATGTTAT
TATGGTTGATAATGTTTCCAGTAATTAACCTATTTTGTTATCCTCAGATTTCTAACGATCCATCA
ACTTAAACTTTAGTAACATTTTAGGCTCTAC
Found at i:1957308 original size:23 final size:21
Alignment explanation
Indices: 1957270--1957312 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 21
1957260 ATAATTATTT
1957270 AAAAAATTAAATAAAAATATA
1 AAAAAATTAAATAAAAATATA
*
1957291 AAAAATATTTAATAAAAA-ATA
1 AAAAA-ATTAAATAAAAATATA
1957312 A
1 A
1957313 TTTTTTATAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 9 0.45
22 11 0.55
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (21 bp):
AAAAAATTAAATAAAAATATA
Found at i:1959395 original size:2 final size:2
Alignment explanation
Indices: 1959388--1959418 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
1959378 GTTAGTTTAT
1959388 TA TA TA TA TA TA TA TA TA TA TA TA TA -A TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1959419 ATGAATTATT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:1969644 original size:18 final size:19
Alignment explanation
Indices: 1969604--1969640 Score: 51
Period size: 17 Copynumber: 2.1 Consensus size: 19
1969594 AATATTTCAC
*
1969604 ATATAAATTAAGTTTTTAT
1 ATATAAATTAAGTCTTTAT
1969623 ATAT-AATTAA-TCTTTAT
1 ATATAAATTAAGTCTTTAT
1969640 A
1 A
1969641 ATATTTAGTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
17 7 0.41
18 6 0.35
19 4 0.24
ACGTcount: A:0.43, C:0.03, G:0.03, T:0.51
Consensus pattern (19 bp):
ATATAAATTAAGTCTTTAT
Found at i:1973137 original size:18 final size:19
Alignment explanation
Indices: 1973100--1973137 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
1973090 TGTTAGAGGG
*
1973100 AAAAAATGAATAAATGAAA
1 AAAAAATGAATAAATAAAA
*
1973119 AAAAAATGAA-GAATAAAA
1 AAAAAATGAATAAATAAAA
1973137 A
1 A
1973138 TAAGTAAAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 7 0.41
19 10 0.59
ACGTcount: A:0.76, C:0.00, G:0.11, T:0.13
Consensus pattern (19 bp):
AAAAAATGAATAAATAAAA
Found at i:1973154 original size:9 final size:10
Alignment explanation
Indices: 1973130--1973184 Score: 53
Period size: 8 Copynumber: 5.6 Consensus size: 10
1973120 AAAAATGAAG
1973130 AATAAAAATA
1 AATAAAAATA
*
1973140 AGTAAAAA-A
1 AATAAAAATA
1973149 AATAAAAATAA
1 AATAAAAAT-A
*
1973160 AAGGAAAAATA
1 AA-TAAAAATA
1973171 AAT--AAATA
1 AATAAAAATA
1973179 AATAAA
1 AATAAA
1973185 TGAAATATAT
Statistics
Matches: 36, Mismatches: 4, Indels: 10
0.72 0.08 0.20
Matches are distributed among these distances:
8 8 0.22
9 8 0.22
10 8 0.22
11 6 0.17
12 6 0.17
ACGTcount: A:0.78, C:0.00, G:0.05, T:0.16
Consensus pattern (10 bp):
AATAAAAATA
Found at i:1973196 original size:2 final size:2
Alignment explanation
Indices: 1973189--1973213 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1973179 AATAAATGAA
1973189 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 A
1973214 AATGAGTAAA
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1973551 original size:21 final size:21
Alignment explanation
Indices: 1973527--1973569 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
1973517 AACCAAATGA
1973527 ATATAAATAAATAA-AATATAT
1 ATATAAAT-AATAATAATATAT
*
1973548 ATATATATAATAATAATATAT
1 ATATAAATAATAATAATATAT
1973569 A
1 A
1973570 GTGTAAAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 5 0.25
21 15 0.75
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (21 bp):
ATATAAATAATAATAATATAT
Found at i:1974071 original size:37 final size:37
Alignment explanation
Indices: 1974030--1974134 Score: 140
Period size: 37 Copynumber: 2.8 Consensus size: 37
1974020 GTGCTTGTGG
* *
1974030 ATCCTATCTTTAGGAGTTTAAATCATAGTAGAACTCT
1 ATCCTATCTTTAGGAGTTTGAATCCTAGTAGAACTCT
* * * *
1974067 ATCCTATTTTTAGGAGTTTGAATCCTAGCAAAATTCT
1 ATCCTATCTTTAGGAGTTTGAATCCTAGTAGAACTCT
1974104 ATCCTA-CTTTTAGGAGTTTGAATCCTAGTAG
1 ATCCTATC-TTTAGGAGTTTGAATCCTAGTAG
1974135 GATGAAAAGG
Statistics
Matches: 58, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
37 58 1.00
ACGTcount: A:0.30, C:0.16, G:0.15, T:0.39
Consensus pattern (37 bp):
ATCCTATCTTTAGGAGTTTGAATCCTAGTAGAACTCT
Found at i:1975049 original size:106 final size:106
Alignment explanation
Indices: 1974865--1976655 Score: 2965
Period size: 106 Copynumber: 16.9 Consensus size: 106
1974855 GCATTGTTCC
* * * ** * *
1974865 GAGTCCAATATCCTCCGTTGTGAAGTTGAAATTGGCTTTGGAACCT-GGAAATTGTTTGTTGACA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCT-GAAATTGGGAAGTTGTTTATTGACA
* * * *
1974929 ACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTC
65 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
*
1974971 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
1975036 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
*
1975077 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTATTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
* *
1975142 CCAGCGGTCCCTTCGTCGTTAAGTTGAACTTGCGTTGTCTA
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
1975183 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
*
1975248 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTA
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
1975289 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
* *
1975354 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTACGTTTTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
1975395 GAGTCCAATATCCTTTGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
1975460 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
1975501 GAGTCCAATATCCTTCGCTGTGAAGTTAAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
*
1975566 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTATG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * *
1975607 GAGTCCAATATCCTTCGCTGTGAATTTGAAATTGGCTCTGAAATTGAGAAATTGTTTATTGATAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
* *
1975672 CCAGCGGTCCCTTCATCGTGAAGTTGAACTTGCATTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * *
1975713 GAGTCCAATATCCTTCGTTGTGAACTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
*
1975778 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTACGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
1975819 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
*
1975884 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTT
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
1975925 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGTAAATTGTTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
* * *
1975990 CCATCAGTCCCTTTGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * *
1976031 GAGTCCAATATCCTTCGTTGTGAAGTTAAAATTGGCTCT-AAACTTGAGAAGTTGTTTGTTGACA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAA-TTGGGAAGTTGTTTATTGACA
*
1976095 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTG
65 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * *
1976137 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTAAAATTGAGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
1976202 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * *
1976243 CAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
1976308 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
1976349 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTAAAATTGGGAAGTTGTTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
*
1976414 CTAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * *
1976455 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGACTCTGAAATTGAGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
1976520 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
1976561 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTATTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
* * *
1976626 CCAGCCGTTCCTTCGTTGTGAAGTTGAACT
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACT
1976656 CCACTCTCGA
Statistics
Matches: 1596, Mismatches: 86, Indels: 6
0.95 0.05 0.00
Matches are distributed among these distances:
105 7 0.00
106 1586 0.99
107 3 0.00
ACGTcount: A:0.23, C:0.18, G:0.25, T:0.34
Consensus pattern (106 bp):
GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
Found at i:1978038 original size:11 final size:11
Alignment explanation
Indices: 1978017--1978083 Score: 56
Period size: 10 Copynumber: 6.5 Consensus size: 11
1978007 TCTTTTTGAT
1978017 TTTTGTTCTTTC
1 TTTT-TTCTTTC
1978029 TTTTTTCTTT-
1 TTTTTTCTTTC
*
1978039 TGTTTTC-TTC
1 TTTTTTCTTTC
1978049 TTTTTTGC-TTC
1 TTTTTT-CTTTC
1978060 TTTTTT-TTT-
1 TTTTTTCTTTC
*
1978069 GTTTTT-TTTC
1 TTTTTTCTTTC
1978079 TTTTT
1 TTTTT
1978084 GTTCTGATTG
Statistics
Matches: 47, Mismatches: 4, Indels: 10
0.77 0.07 0.16
Matches are distributed among these distances:
9 10 0.21
10 17 0.36
11 16 0.34
12 4 0.09
ACGTcount: A:0.00, C:0.12, G:0.06, T:0.82
Consensus pattern (11 bp):
TTTTTTCTTTC
Found at i:1978039 original size:20 final size:20
Alignment explanation
Indices: 1978005--1978088 Score: 71
Period size: 20 Copynumber: 4.0 Consensus size: 20
1977995 TTTGTCCCTT
**
1978005 TTTCTTTTTGATTTTTGTTC
1 TTTCTTTTTTCTTTTTGTTC
*
1978025 TTTCTTTTTTC-TTTTGTTT
1 TTTCTTTTTTCTTTTTGTTC
* *
1978044 TCTTCTTTTTTGCTTCTTTTTTT
1 T-TTCTTTTTT-CTT-TTTGTTC
*
1978067 TTGTTTTTTTTCTTTTTGTTC
1 TT-TCTTTTTTCTTTTTGTTC
1978088 T
1 T
1978089 GATTGAATCT
Statistics
Matches: 52, Mismatches: 7, Indels: 9
0.76 0.10 0.13
Matches are distributed among these distances:
19 8 0.15
20 18 0.35
21 7 0.13
22 5 0.10
23 14 0.27
ACGTcount: A:0.01, C:0.12, G:0.07, T:0.80
Consensus pattern (20 bp):
TTTCTTTTTTCTTTTTGTTC
Found at i:1978049 original size:24 final size:23
Alignment explanation
Indices: 1978003--1978077 Score: 62
Period size: 24 Copynumber: 3.1 Consensus size: 23
1977993 TTTTTGTCCC
*
1978003 TTTTTCTTTTTGATTTTTGTTCTTTCT
1 TTTTTC-TTTTG--TTTTCTTCTTT-T
1978030 TTTTTCTTTTGTTTTCTTCTTTT
1 TTTTTCTTTTGTTTTCTTCTTTT
* * *
1978053 TTGCTTCTTTTTTTTTGTT-TTTT
1 TT-TTTCTTTTGTTTTCTTCTTTT
1978076 TT
1 TT
1978078 CTTTTTGTTC
Statistics
Matches: 43, Mismatches: 4, Indels: 6
0.81 0.08 0.11
Matches are distributed among these distances:
23 9 0.21
24 23 0.53
26 5 0.12
27 6 0.14
ACGTcount: A:0.01, C:0.11, G:0.07, T:0.81
Consensus pattern (23 bp):
TTTTTCTTTTGTTTTCTTCTTTT
Found at i:1978084 original size:29 final size:29
Alignment explanation
Indices: 1978030--1978088 Score: 77
Period size: 29 Copynumber: 2.0 Consensus size: 29
1978020 TGTTCTTTCT
1978030 TTTTTCTTTTGTTTTCTTCTTTTTTGCTTC
1 TTTTTCTTTTGTTTTCTTCTTTTTTG-TTC
*
1978060 TTTTT-TTTTGTTTT-TTTTCTTTTTGTTC
1 TTTTTCTTTTGTTTTCTTCT-TTTTTGTTC
1978088 T
1 T
1978089 GATTGAATCT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
28 7 0.26
29 15 0.56
30 5 0.19
ACGTcount: A:0.00, C:0.12, G:0.07, T:0.81
Consensus pattern (29 bp):
TTTTTCTTTTGTTTTCTTCTTTTTTGTTC
Found at i:1982597 original size:18 final size:19
Alignment explanation
Indices: 1982561--1982649 Score: 53
Period size: 19 Copynumber: 4.7 Consensus size: 19
1982551 TGTTAGAGGG
*
1982561 AAAAATGAATAAATGAAAA
1 AAAAATGAATAAATAAAAA
*
1982580 AAAAATGAA-GAATAAAAA
1 AAAAATGAATAAATAAAAA
1982598 TAAGTAAA--AA-AAATAAAAA
1 -AA--AAATGAATAAATAAAAA
* *
1982617 TAAAAGGAA-AAATAAATAA
1 AAAAATGAATAAATAAA-AA
* *
1982636 ATAAATAAATAAAT
1 AAAAATGAATAAAT
1982650 GAAATATATA
Statistics
Matches: 55, Mismatches: 8, Indels: 13
0.72 0.11 0.17
Matches are distributed among these distances:
16 3 0.05
18 17 0.31
19 28 0.51
20 4 0.07
21 3 0.05
ACGTcount: A:0.75, C:0.00, G:0.08, T:0.17
Consensus pattern (19 bp):
AAAAATGAATAAATAAAAA
Found at i:1982614 original size:9 final size:10
Alignment explanation
Indices: 1982590--1982648 Score: 57
Period size: 12 Copynumber: 5.6 Consensus size: 10
1982580 AAAAATGAAG
1982590 AATAAAAATA
1 AATAAAAATA
*
1982600 AGTAAAAA-A
1 AATAAAAATA
1982609 AATAAAAATAA
1 AATAAAAAT-A
*
1982620 AAGGAAAAATA
1 AA-TAAAAATA
1982631 AATAAATAAATA
1 AAT-AA-AAATA
1982643 AATAAA
1 AATAAA
1982649 TGAAATATAT
Statistics
Matches: 40, Mismatches: 4, Indels: 10
0.74 0.07 0.19
Matches are distributed among these distances:
9 8 0.20
10 8 0.20
11 10 0.25
12 14 0.35
ACGTcount: A:0.78, C:0.00, G:0.05, T:0.17
Consensus pattern (10 bp):
AATAAAAATA
Found at i:1982635 original size:4 final size:4
Alignment explanation
Indices: 1982626--1982655 Score: 51
Period size: 4 Copynumber: 7.2 Consensus size: 4
1982616 ATAAAAGGAA
1982626 AAAT AAAT AAAT AAAT AAAT AAAT GAAAT A
1 AAAT AAAT AAAT AAAT AAAT AAAT -AAAT A
1982656 TATATATATA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
4 21 0.84
5 4 0.16
ACGTcount: A:0.73, C:0.00, G:0.03, T:0.23
Consensus pattern (4 bp):
AAAT
Found at i:1982809 original size:21 final size:21
Alignment explanation
Indices: 1982766--1982809 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
1982756 ACCAAAAACA
*
1982766 AAAATAAATAAATATATAAAT
1 AAAATAAATAAATATACAAAT
*
1982787 AAAATATAA-AAATATACATAT
1 AAAATA-AATAAATATACAAAT
1982808 AA
1 AA
1982810 TGATAATTGG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 18 0.90
22 2 0.10
ACGTcount: A:0.70, C:0.02, G:0.00, T:0.27
Consensus pattern (21 bp):
AAAATAAATAAATATACAAAT
Found at i:1982948 original size:2 final size:2
Alignment explanation
Indices: 1982943--1982972 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1982933 TTAAAAAAAG
1982943 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1982973 ATAATATTAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1983563 original size:37 final size:37
Alignment explanation
Indices: 1983513--1983617 Score: 147
Period size: 37 Copynumber: 2.8 Consensus size: 37
1983503 GTGCTTGTGG
* * *
1983513 ATCCTATCTTTAGGAGTTTAAATCATAGTAGAACTCT
1 ATCCTATTTTTAGGAGTTTGAATCCTAGTAGAACTCT
* * *
1983550 ATCCTATTTTTAGGAGTTTGAATCCTAGCAAAATTCT
1 ATCCTATTTTTAGGAGTTTGAATCCTAGTAGAACTCT
*
1983587 ATCCTACTTTTAGGAGTTTGAATCCTAGTAG
1 ATCCTATTTTTAGGAGTTTGAATCCTAGTAG
1983618 GACGAAAAGG
Statistics
Matches: 59, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
37 59 1.00
ACGTcount: A:0.30, C:0.16, G:0.15, T:0.39
Consensus pattern (37 bp):
ATCCTATTTTTAGGAGTTTGAATCCTAGTAGAACTCT
Found at i:1983936 original size:131 final size:133
Alignment explanation
Indices: 1983642--1983995 Score: 380
Period size: 131 Copynumber: 2.7 Consensus size: 133
1983632 TTGACAGTCG
* ** *
1983642 TCTAAGGGTGACACGGCTCCTACGTGATGAGGAGATCTGGTCGGTGGATGACATTG-TTCCTACG
1 TCTAAGGGTGACACGACTATTACGTGATGAGGAGATCTGGTCGGTGGATGACA-AGATTCCTACG
* * * * * *
1983706 TTATGAGTACAT-TTTGGCCATCTTTAGGGATGATGATAACATGGTTCCTACGTGATGAGGATGA
65 TGATGAG--GATGATTGGCCATCTTTAGGGA-GATGATAACACGGTTCCTACATGATGAGGACGA
*
1983770 CTGGTTA
127 CTAGTTA
* * * * *
1983777 TCTAAGGGTGACACGGCTATTACGTGATGAGGATATTTGGTCGGGGGATGACAAGATTTCTACGT
1 TCTAAGGGTGACACGACTATTACGTGATGAGGAGATCTGGTCGGTGGATGACAAGATTCCTACGT
* *
1983842 GATGAGGATGATTGACCATCTTTA-GG-GATGATAACACGGTTTCTACATGATGAGGACGACTAG
66 GATGAGGATGATTGGCCATCTTTAGGGAGATGATAACACGGTTCCTACATGATGAGGACGACTAG
1983905 TTA
131 TTA
* * *
1983908 TCTAA-GGTAGACGCGACTCA-TACGTGATGAGGAGATCTGGTCAGTGGATGA-AACAGTTCCTA
1 TCTAAGGGT-GACACGACT-ATTACGTGATGAGGAGATCTGGTCGGTGGATGACAAGA-TTCCTA
* * *
1983970 CGCGATGAGGACGACTGGCCATCTTT
63 CGTGATGAGGATGATTGGCCATCTTT
1983996 TCACGAGAAA
Statistics
Matches: 186, Mismatches: 28, Indels: 14
0.82 0.12 0.06
Matches are distributed among these distances:
130 6 0.03
131 101 0.54
132 1 0.01
133 4 0.02
134 13 0.07
135 61 0.33
ACGTcount: A:0.25, C:0.16, G:0.30, T:0.29
Consensus pattern (133 bp):
TCTAAGGGTGACACGACTATTACGTGATGAGGAGATCTGGTCGGTGGATGACAAGATTCCTACGT
GATGAGGATGATTGGCCATCTTTAGGGAGATGATAACACGGTTCCTACATGATGAGGACGACTAG
TTA
Found at i:1984141 original size:32 final size:32
Alignment explanation
Indices: 1984093--1984210 Score: 83
Period size: 32 Copynumber: 3.5 Consensus size: 32
1984083 GAGAGAAAAC
* *
1984093 TTTGTTTTAAGGGAAACAAACTCAAAGATTTT
1 TTTGTTTCAAGAGAAACAAACTCAAAGATTTT
*** ****
1984125 TTTGTTTCAAGAGAAACTTTCTCGAGAGAGAGAAAAC
1 TTTGTTTCAAGAGAAACAAACTC---A-A-AGATTTT
* *
1984162 TTTGTTTCAAGGGAAACAGACTCAAAGATTTT
1 TTTGTTTCAAGAGAAACAAACTCAAAGATTTT
*
1984194 TTTGTTTCAGGAGAAAC
1 TTTGTTTCAAGAGAAAC
1984211 TTTCTCAAGA
Statistics
Matches: 62, Mismatches: 19, Indels: 10
0.68 0.21 0.11
Matches are distributed among these distances:
32 36 0.58
33 1 0.02
34 1 0.02
35 1 0.02
36 1 0.02
37 22 0.35
ACGTcount: A:0.36, C:0.12, G:0.19, T:0.33
Consensus pattern (32 bp):
TTTGTTTCAAGAGAAACAAACTCAAAGATTTT
Found at i:1984165 original size:69 final size:69
Alignment explanation
Indices: 1983994--1984397 Score: 611
Period size: 69 Copynumber: 5.9 Consensus size: 69
1983984 CTGGCCATCT
* * *
1983994 TTTCACGAGAAACTGTCTCAAGAGAGACAAAA-TATGTTTCAAGGGAAACAGACTCAAAGA--TT
1 TTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTTGTTTCAAGGGAAACAAACTCAAAGATTTT
1984056 TTTG
66 TTTG
* * *
1984060 TTTTAAGAGAAACTGTCTCAAGAGAGAGAAAACTTTGTTTTAAGGGAAACAAACTCAAAGATTTT
1 TTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTTGTTTCAAGGGAAACAAACTCAAAGATTTT
1984125 TTTG
66 TTTG
* * * *
1984129 TTTCAAGAGAAACTTTCTCGAGAGAGAGAAAACTTTGTTTCAAGGGAAACAGACTCAAAGATTTT
1 TTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTTGTTTCAAGGGAAACAAACTCAAAGATTTT
1984194 TTTG
66 TTTG
* * * *
1984198 TTTCAGGAGAAACTTTCTCAAGAGAGACAAAACTTTATTTCAAGGGAAATAAACTCAAAGATTTT
1 TTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTTGTTTCAAGGGAAACAAACTCAAAGATTTT
*
1984263 TAT-
66 TTTG
1984266 TTT-AAGAGAAACTGTCTCAAGAGAGACAAAACTTTGTTTCAAGGGAAACAAACTCAAAGATTTT
1 TTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTTGTTTCAAGGGAAACAAACTCAAAGA-TTT
1984330 TTTTG
65 TTTTG
* *
1984335 TTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTTGTTTCAATGGAAACAAACTCAAAGATT
1 TTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTTGTTTCAAGGGAAACAAACTCAAAGATT
1984398 ATGTCTTAAG
Statistics
Matches: 307, Mismatches: 25, Indels: 9
0.90 0.07 0.03
Matches are distributed among these distances:
66 29 0.09
67 78 0.25
68 9 0.03
69 136 0.44
70 55 0.18
ACGTcount: A:0.40, C:0.13, G:0.18, T:0.29
Consensus pattern (69 bp):
TTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTTGTTTCAAGGGAAACAAACTCAAAGATTTT
TTTG
Found at i:1984289 original size:136 final size:138
Alignment explanation
Indices: 1983994--1984397 Score: 620
Period size: 136 Copynumber: 3.0 Consensus size: 138
1983984 CTGGCCATCT
* *
1983994 TTTCACGAGAAACTGTCTCAAGAGAGACAAAA-TATGTTTCAAGGGAAACAGACTCAAAGA--TT
1 TTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTTGTTTCAAGGGAAACAGACTCAAAGATTTT
* * *
1984056 TTTGTTTTAAGAGAAACTGTCTCAAGAGAGAGAAAACTTTGTTTTAAGGGAAACAAACTCAAAGA
66 TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTTGTTTCAAGGGAAACAAACTCAAAGA
*
1984121 TTTTTTTG
131 TTTTTATG
* * *
1984129 TTTCAAGAGAAACTTTCTCGAGAGAGAGAAAACTTTGTTTCAAGGGAAACAGACTCAAAGATTTT
1 TTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTTGTTTCAAGGGAAACAGACTCAAAGATTTT
* * * *
1984194 TTTGTTTCAGGAGAAACTTTCTCAAGAGAGACAAAACTTTATTTCAAGGGAAATAAACTCAAAGA
66 TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTTGTTTCAAGGGAAACAAACTCAAAGA
1984259 TTTTTAT-
131 TTTTTATG
*
1984266 TTT-AAGAGAAACTGTCTCAAGAGAGACAAAACTTTGTTTCAAGGGAAACAAACTCAAAGATTTT
1 TTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTTGTTTCAAGGGAAACAGACTCAAAGA-TTT
* *
1984330 TTTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTTGTTTCAATGGAAACAAACTCAAAG
65 TTTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTTGTTTCAAGGGAAACAAACTCAAAG
1984395 ATT
130 ATT
1984398 ATGTCTTAAG
Statistics
Matches: 242, Mismatches: 23, Indels: 6
0.89 0.08 0.02
Matches are distributed among these distances:
135 28 0.12
136 80 0.33
137 68 0.28
138 66 0.27
ACGTcount: A:0.40, C:0.13, G:0.18, T:0.29
Consensus pattern (138 bp):
TTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTTGTTTCAAGGGAAACAGACTCAAAGATTTT
TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTTGTTTCAAGGGAAACAAACTCAAAGA
TTTTTATG
Found at i:1984376 original size:37 final size:37
Alignment explanation
Indices: 1984260--1984377 Score: 109
Period size: 37 Copynumber: 3.3 Consensus size: 37
1984250 ACTCAAAGAT
* *
1984260 TTTTATTTTAAGAGAAACTGTCTCAAGAGAGACAAAA
1 TTTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
* * *** ****
1984297 CTTTGTTTCAAGGGAAACAAACTC-A-A-AGA-TTTT
1 TTTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
1984330 TTTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
1 TTTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
1984367 TTTTGTTTCAA
1 TTTTGTTTCAA
1984378 TGGAAACAAA
Statistics
Matches: 57, Mismatches: 20, Indels: 8
0.67 0.24 0.09
Matches are distributed among these distances:
33 19 0.33
34 4 0.07
35 2 0.04
36 4 0.07
37 28 0.49
ACGTcount: A:0.38, C:0.13, G:0.16, T:0.33
Consensus pattern (37 bp):
TTTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
Found at i:1984392 original size:37 final size:36
Alignment explanation
Indices: 1984281--1984392 Score: 97
Period size: 37 Copynumber: 3.1 Consensus size: 36
1984271 GAGAAACTGT
*
1984281 CTCAAGAGAGACAAAACTTTGTTTCAAGGGAAACAAA
1 CTCAAGAGAGACAAAATTTTGTTTCAA-GGAAACAAA
**** ***
1984318 CTC-A-A-AGA-TTTTTTTTGTTTCAAGAGAAACTGT
1 CTCAAGAGAGACAAAATTTTGTTTCAAG-GAAACAAA
1984351 CTCAAGAGAGACAAAATTTTGTTTCAATGGAAACAAA
1 CTCAAGAGAGACAAAATTTTGTTTCAA-GGAAACAAA
1984388 CTCAA
1 CTCAA
1984393 AGATTATGTC
Statistics
Matches: 54, Mismatches: 15, Indels: 12
0.67 0.19 0.15
Matches are distributed among these distances:
32 1 0.02
33 18 0.33
34 4 0.07
35 2 0.04
36 4 0.07
37 24 0.44
38 1 0.02
ACGTcount: A:0.41, C:0.15, G:0.16, T:0.28
Consensus pattern (36 bp):
CTCAAGAGAGACAAAATTTTGTTTCAAGGAAACAAA
Found at i:1991906 original size:20 final size:22
Alignment explanation
Indices: 1991868--1991907 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
1991858 AAATATCAAC
*
1991868 TTTTTTATAATTTTCATTTTAT
1 TTTTTTATAAATTTCATTTTAT
1991890 TTTTTTA-AAATTT-ATTTT
1 TTTTTTATAAATTTCATTTT
1991908 TAGAGAGAGG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 5 0.29
21 5 0.29
22 7 0.41
ACGTcount: A:0.25, C:0.03, G:0.00, T:0.72
Consensus pattern (22 bp):
TTTTTTATAAATTTCATTTTAT
Found at i:1993068 original size:3 final size:3
Alignment explanation
Indices: 1993060--1993119 Score: 88
Period size: 3 Copynumber: 20.7 Consensus size: 3
1993050 AATATGTAAT
* *
1993060 TAA TAA TAA -AA AAA TAA TAA TAT TAA TAA TAA -AA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1993106 TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TA
1993120 TTATTATTTT
Statistics
Matches: 52, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
2 4 0.08
3 48 0.92
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
TAA
Found at i:1993086 original size:23 final size:23
Alignment explanation
Indices: 1993058--1993114 Score: 96
Period size: 23 Copynumber: 2.5 Consensus size: 23
1993048 ATAATATGTA
1993058 ATTAATAATAAAAAAATAATAAT
1 ATTAATAATAAAAAAATAATAAT
*
1993081 ATTAATAATAAAATAATAATAAT
1 ATTAATAATAAAAAAATAATAAT
*
1993104 AATAATAATAA
1 ATTAATAATAA
1993115 TAATATTATT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (23 bp):
ATTAATAATAAAAAAATAATAAT
Found at i:1995935 original size:2 final size:2
Alignment explanation
Indices: 1995915--1996065 Score: 116
Period size: 2 Copynumber: 77.5 Consensus size: 2
1995905 CCCACTGATG
* * *
1995915 TA TA TA CA TA CA TA CA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * * * *
1995957 TA TA TA TA TA TA TA TA TA TA TA TA -A T- TA -A TT TCC TT TT TC
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T-A TA TA TA
* * * * * *
1995997 T- TA T- TCA TT TA TT TT TA TA TA -A TA TA TT TA TT TA TA TA TG
1 TA TA TA T-A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1996037 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1996066 TTCCCTGGTT
Statistics
Matches: 121, Mismatches: 20, Indels: 16
0.77 0.13 0.10
Matches are distributed among these distances:
1 6 0.05
2 113 0.93
3 2 0.02
ACGTcount: A:0.42, C:0.05, G:0.01, T:0.53
Consensus pattern (2 bp):
TA
Found at i:1996288 original size:5 final size:5
Alignment explanation
Indices: 1996264--1996306 Score: 52
Period size: 5 Copynumber: 8.6 Consensus size: 5
1996254 ATTCATGGTA
* *
1996264 TATAT TATTAT T-TTT TATAT TATAT TATAT TATAT TATTT TAT
1 TATAT TA-TAT TATAT TATAT TATAT TATAT TATAT TATAT TAT
1996307 TTCTTTTTCT
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
4 3 0.09
5 26 0.79
6 4 0.12
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (5 bp):
TATAT
Found at i:1996322 original size:16 final size:17
Alignment explanation
Indices: 1996301--1996359 Score: 59
Period size: 17 Copynumber: 3.5 Consensus size: 17
1996291 TATTATATTA
*
1996301 TTTTATTTC-TTTTTCT
1 TTTTATTTCATTTTTAT
1996317 TTTTATTTCATTTTTAT
1 TTTTATTTCATTTTTAT
* *
1996334 CTTTATTTTATTTATT-T
1 TTTTATTTCATTT-TTAT
1996351 TATTTATTT
1 T-TTTATTT
1996360 TCTTAACTTT
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
16 9 0.25
17 18 0.50
18 9 0.25
ACGTcount: A:0.15, C:0.07, G:0.00, T:0.78
Consensus pattern (17 bp):
TTTTATTTCATTTTTAT
Found at i:1996338 original size:6 final size:5
Alignment explanation
Indices: 1996276--1996360 Score: 59
Period size: 5 Copynumber: 16.8 Consensus size: 5
1996266 TATTATTATT
* * * * * *
1996276 TTTTA TATTA TATTA TATTA TATTA TTTTA TTTCT- TTTTCT TTTTA TTTCA
1 TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTT-TA TTTT-A TTTTA TTTTA
1996327 TTTTTA TCTTTA TTTTA -TTTA TTTTA -TTTA TTTT
1 -TTTTA T-TTTA TTTTA TTTTA TTTTA TTTTA TTTT
1996361 CTTAACTTTA
Statistics
Matches: 68, Mismatches: 5, Indels: 14
0.78 0.06 0.16
Matches are distributed among these distances:
4 9 0.13
5 45 0.66
6 14 0.21
ACGTcount: A:0.21, C:0.05, G:0.00, T:0.74
Consensus pattern (5 bp):
TTTTA
Found at i:2000533 original size:99 final size:99
Alignment explanation
Indices: 2000418--2000719 Score: 487
Period size: 99 Copynumber: 3.1 Consensus size: 99
2000408 TTATAATATT
* * * * *
2000418 ATATGTATACAATAAAGCTTGAGTTGTCCCTCTAGAGTAATTGGTTAAACGCCCCTGTTTTATGG
1 ATATTTATACAATAAAGCTTGAATTGTCCCTCTAGAGCAATTGGTTAAACGCCCCAGCTTTATGG
2000483 ATAAGATTCAGCTAGCCTGATAAAGGTGATTATA
66 ATAAGATTCAGCTAGCCTGATAAAGGTGATTATA
* * * *
2000517 ATATTTATACAATAAAGCTTGAACTGTCCCTCTAGAGCAATTGGTTAAATGCCTCGGCTTTATGG
1 ATATTTATACAATAAAGCTTGAATTGTCCCTCTAGAGCAATTGGTTAAACGCCCCAGCTTTATGG
2000582 ATAAGATTCAGCTAGCCTGATAAAGGTGATTATA
66 ATAAGATTCAGCTAGCCTGATAAAGGTGATTATA
*
2000616 ATATTTATACAATAAAGCTTGAATTGTCCCTCTAGAGCAATTGGTTAAACGTCCCAGCTTTATGG
1 ATATTTATACAATAAAGCTTGAATTGTCCCTCTAGAGCAATTGGTTAAACGCCCCAGCTTTATGG
* * *
2000681 ATAAGATTCAGCTTGCCTAATAAAGGCGATTATA
66 ATAAGATTCAGCTAGCCTGATAAAGGTGATTATA
2000715 ATATT
1 ATATT
2000720 GAGTTGTCCC
Statistics
Matches: 187, Mismatches: 16, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
99 187 1.00
ACGTcount: A:0.32, C:0.16, G:0.19, T:0.33
Consensus pattern (99 bp):
ATATTTATACAATAAAGCTTGAATTGTCCCTCTAGAGCAATTGGTTAAACGCCCCAGCTTTATGG
ATAAGATTCAGCTAGCCTGATAAAGGTGATTATA
Found at i:2002029 original size:55 final size:57
Alignment explanation
Indices: 2001897--2002036 Score: 194
Period size: 58 Copynumber: 2.5 Consensus size: 57
2001887 GACCATCCAC
* * * * *
2001897 GATTTCAACTTCACGACGAAGGATATCGTGCTCACCAGCAACATTCATCTTTAGATTG
1 GATTTCAACTTCACGACGAAGGATATCGTGCCCACAACCAACATTAATC-TAAGATTG
*
2001955 GATTTCAACTTCATGACGAAGGATATCGTGCCCACAACCAAC-TTAATC-AAGATTG
1 GATTTCAACTTCACGACGAAGGATATCGTGCCCACAACCAACATTAATCTAAGATTG
*
2002010 GATTTCAACTTCACAACGAAGGATATC
1 GATTTCAACTTCACGACGAAGGATATC
2002037 CAATTCAAGG
Statistics
Matches: 74, Mismatches: 8, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
55 31 0.42
57 5 0.07
58 38 0.51
ACGTcount: A:0.33, C:0.24, G:0.16, T:0.27
Consensus pattern (57 bp):
GATTTCAACTTCACGACGAAGGATATCGTGCCCACAACCAACATTAATCTAAGATTG
Found at i:2002102 original size:119 final size:112
Alignment explanation
Indices: 2001955--2002178 Score: 299
Period size: 110 Copynumber: 1.9 Consensus size: 112
2001945 CTTTAGATTG
*
2001955 GATTTCAACTTCATGACGAAGGATATCGTGCCCACAACCAACTTAATCAAGATTGGATTTCAACT
1 GATTTCAACTTCACGACGAAGGATATCGTG----C--CCAA--T-ATCAAGATTGGATTTCAACT
* *
2002020 TCACAACGAAGGATATCCAATTCAAGGCTCAACTTCA-AT-GAAGGAGCCATCCAC
57 TCACAACGAAGAATATCCAATTCAAAGCTCAACTTCACATCGAAGGAGCCATCCAC
* * *
2002074 GATTTCAACTTCACGACGAAGGATATCGTGCCCTATATCTAGATTGGATTTCAACTTCACAATGA
1 GATTTCAACTTCACGACGAAGGATATCGTGCCCAATATCAAGATTGGATTTCAACTTCACAACGA
2002139 AGAATATCCAATTCAAAGCTCAACTTCACATCGAAGGAGC
66 AGAATATCCAATTCAAAGCTCAACTTCACATCGAAGGAGC
2002179 TTCCCAATTT
Statistics
Matches: 97, Mismatches: 6, Indels: 11
0.85 0.05 0.10
Matches are distributed among these distances:
110 53 0.55
111 3 0.03
112 8 0.08
113 3 0.03
115 1 0.01
119 29 0.30
ACGTcount: A:0.35, C:0.24, G:0.16, T:0.25
Consensus pattern (112 bp):
GATTTCAACTTCACGACGAAGGATATCGTGCCCAATATCAAGATTGGATTTCAACTTCACAACGA
AGAATATCCAATTCAAAGCTCAACTTCACATCGAAGGAGCCATCCAC
Found at i:2003195 original size:5 final size:5
Alignment explanation
Indices: 2003156--2003263 Score: 57
Period size: 5 Copynumber: 21.2 Consensus size: 5
2003146 TCATGGTATA
* * *
2003156 TATTGT TATTAT T-TTT TATAT TATAT TATAT TATTT TATTT CT-TTT
1 TATT-T TATT-T TATTT TATTT TATTT TATTT TATTT TATTT -TATTT
* *
2003202 TATTT CATTTT TATCTT TATTT TA-TT TATTT CATTT T-TTCCT TCA-TT
1 TATTT TA-TTT TAT-TT TATTT TATTT TATTT TATTT TATT--T T-ATTT
2003249 TATTT TA-TT TATTT T
1 TATTT TATTT TATTT T
2003264 CACTCCTTTT
Statistics
Matches: 83, Mismatches: 7, Indels: 25
0.72 0.06 0.22
Matches are distributed among these distances:
4 14 0.17
5 50 0.60
6 18 0.22
7 1 0.01
ACGTcount: A:0.20, C:0.06, G:0.01, T:0.72
Consensus pattern (5 bp):
TATTT
Found at i:2003223 original size:12 final size:11
Alignment explanation
Indices: 2003189--2003239 Score: 50
Period size: 11 Copynumber: 4.4 Consensus size: 11
2003179 TATTATATTA
2003189 TTTTATTTC-T
1 TTTTATTTCAT
2003199 TTTTATTTCAT
1 TTTTATTTCAT
*
2003210 TTTTATCTTTATTT
1 TTTTAT-TTCA--T
2003224 TATTTATTTCAT
1 T-TTTATTTCAT
2003236 TTTT
1 TTTT
2003240 TCCTTCATTT
Statistics
Matches: 34, Mismatches: 2, Indels: 9
0.76 0.04 0.20
Matches are distributed among these distances:
10 9 0.26
11 10 0.29
12 5 0.15
14 5 0.15
15 5 0.15
ACGTcount: A:0.16, C:0.08, G:0.00, T:0.76
Consensus pattern (11 bp):
TTTTATTTCAT
Found at i:2003229 original size:26 final size:27
Alignment explanation
Indices: 2003186--2003262 Score: 86
Period size: 30 Copynumber: 2.8 Consensus size: 27
2003176 TTATATTATA
*
2003186 TTAT-TTTATTTCTTTTTATTTCA-TTT
1 TTATCTTTATTT-TATTTATTTCATTTT
2003212 TTATCTTTATTTTATTTATTTCATTTT
1 TTATCTTTATTTTATTTATTTCATTTT
*
2003239 TTCCTTCATTTATTTTATTTATTT
1 TT--ATC-TTTATTTTATTTATTT
2003263 TCACTCCTTT
Statistics
Matches: 44, Mismatches: 2, Indels: 6
0.85 0.04 0.12
Matches are distributed among these distances:
26 14 0.32
27 12 0.27
29 2 0.05
30 16 0.36
ACGTcount: A:0.17, C:0.09, G:0.00, T:0.74
Consensus pattern (27 bp):
TTATCTTTATTTTATTTATTTCATTTT
Done.