Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr02 ID=Chr02-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 62769430
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1067035 characters in sequence are not A, C, G, or T
File 141 of 206
Found at i:43258989 original size:12 final size:12
Alignment explanation
Indices: 43258972--43258997 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
43258962 ATTAATATTA
43258972 CACATAAAATTT
1 CACATAAAATTT
43258984 CACATAAAATTT
1 CACATAAAATTT
43258996 CA
1 CA
43258998 ATTTTCACAC
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:0.50, C:0.19, G:0.00, T:0.31
Consensus pattern (12 bp):
CACATAAAATTT
Found at i:43259450 original size:15 final size:16
Alignment explanation
Indices: 43259432--43259466 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
43259422 CTTCTTCTCA
43259432 TTTTATTTC-TTTCTT
1 TTTTATTTCTTTTCTT
*
43259447 TTTTCTTTCTTTTCTT
1 TTTTATTTCTTTTCTT
43259463 TTTT
1 TTTT
43259467 TAATTTGTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 8 0.44
16 10 0.56
ACGTcount: A:0.03, C:0.14, G:0.00, T:0.83
Consensus pattern (16 bp):
TTTTATTTCTTTTCTT
Found at i:43260485 original size:15 final size:13
Alignment explanation
Indices: 43260454--43260492 Score: 78
Period size: 13 Copynumber: 3.0 Consensus size: 13
43260444 TTAAGCTATA
43260454 TGTGTGAAAATTT
1 TGTGTGAAAATTT
43260467 TGTGTGAAAATTT
1 TGTGTGAAAATTT
43260480 TGTGTGAAAATTT
1 TGTGTGAAAATTT
43260493 GATAGTTTGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 26 1.00
ACGTcount: A:0.31, C:0.00, G:0.23, T:0.46
Consensus pattern (13 bp):
TGTGTGAAAATTT
Found at i:43261071 original size:27 final size:28
Alignment explanation
Indices: 43261040--43261102 Score: 76
Period size: 29 Copynumber: 2.2 Consensus size: 28
43261030 TGAATTTTTG
*
43261040 GTGAAATTGAATATTTA-GGG-CTAAATT
1 GTGAAATTGAA-ATTTAGGGGTCTAAAAT
*
43261067 GTGAAATTTAAATTTATGGGGTCTAAAAT
1 GTGAAATTGAAATTTA-GGGGTCTAAAAT
43261096 GTGAAAT
1 GTGAAAT
43261103 AAATGAAATG
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
26 5 0.16
27 10 0.32
28 3 0.10
29 13 0.42
ACGTcount: A:0.38, C:0.03, G:0.22, T:0.37
Consensus pattern (28 bp):
GTGAAATTGAAATTTAGGGGTCTAAAAT
Found at i:43261758 original size:41 final size:40
Alignment explanation
Indices: 43261694--43261842 Score: 208
Period size: 41 Copynumber: 3.6 Consensus size: 40
43261684 TATAATTGGT
* * *
43261694 TTTCAGGCTTAATGCCTAACAGGCTTGATGCTGGTGAATTA
1 TTTCAGACTT-ATGTCTAACAGGCTTGATGCCGGTGAATTA
*
43261735 TTTCAGACTTAGTGTCTAGCAGGCTTGATGCCGGTGAATTA
1 TTTCAGACTTA-TGTCTAACAGGCTTGATGCCGGTGAATTA
* *
43261776 CTTCAGACTTTATGTCTAGCAGGCTTGATGCCGGTGAATTA
1 TTTCAGAC-TTATGTCTAACAGGCTTGATGCCGGTGAATTA
43261817 TTTCAGACTTATTGTCTAACAGGCTT
1 TTTCAGACTTA-TGTCTAACAGGCTT
43261843 CATGTTGGTG
Statistics
Matches: 98, Mismatches: 7, Indels: 6
0.88 0.06 0.05
Matches are distributed among these distances:
40 4 0.04
41 91 0.93
42 3 0.03
ACGTcount: A:0.23, C:0.18, G:0.23, T:0.36
Consensus pattern (40 bp):
TTTCAGACTTATGTCTAACAGGCTTGATGCCGGTGAATTA
Found at i:43261869 original size:82 final size:80
Alignment explanation
Indices: 43261695--43261860 Score: 217
Period size: 82 Copynumber: 2.1 Consensus size: 80
43261685 ATAATTGGTT
* * * * * *
43261695 TTCAGGCTTAATGCCTAACAGGCTTGATGCTGGTGAATTATTTCAGACTTAGTGTCTAGCAGGCT
1 TTCAGACTTTATGTCTAGCAGGCTTGATGCCGGTGAATTATTTCAGACTTAGTGTCTAACAGGCT
*
43261760 TGATGCCGGTGAATTAC
66 TCATGCCGGTG-A-TAC
*
43261777 TTCAGACTTTATGTCTAGCAGGCTTGATGCCGGTGAATTATTTCAGACTTATTGTCTAACAGGCT
1 TTCAGACTTTATGTCTAGCAGGCTTGATGCCGGTGAATTATTTCAGACTTAGTGTCTAACAGGCT
**
43261842 TCATGTTGGTG-TAC
66 TCATGCCGGTGATAC
43261856 TTCAG
1 TTCAG
43261861 TAAGCTTTAG
Statistics
Matches: 74, Mismatches: 10, Indels: 3
0.85 0.11 0.03
Matches are distributed among these distances:
79 8 0.11
82 66 0.89
ACGTcount: A:0.22, C:0.18, G:0.24, T:0.36
Consensus pattern (80 bp):
TTCAGACTTTATGTCTAGCAGGCTTGATGCCGGTGAATTATTTCAGACTTAGTGTCTAACAGGCT
TCATGCCGGTGATAC
Found at i:43265057 original size:26 final size:26
Alignment explanation
Indices: 43265021--43265071 Score: 84
Period size: 26 Copynumber: 2.0 Consensus size: 26
43265011 CACGCCGAGA
43265021 AAGAAAAGCCTTTATGGCGAAATATG
1 AAGAAAAGCCTTTATGGCGAAATATG
* *
43265047 AAGAAAAGCCTTTGTGGTGAAATAT
1 AAGAAAAGCCTTTATGGCGAAATAT
43265072 AAAAGGAAGG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.41, C:0.10, G:0.24, T:0.25
Consensus pattern (26 bp):
AAGAAAAGCCTTTATGGCGAAATATG
Found at i:43270717 original size:20 final size:18
Alignment explanation
Indices: 43270670--43270718 Score: 57
Period size: 20 Copynumber: 2.7 Consensus size: 18
43270660 CAATATAAAC
43270670 ATTAAATTAA-ATTTAAT
1 ATTAAATTAATATTTAAT
43270687 ATTAAGA-TAATCACTTTAAT
1 ATTAA-ATTAAT-A-TTTAAT
43270707 ATTAAATTAATA
1 ATTAAATTAATA
43270719 AAATACTATT
Statistics
Matches: 27, Mismatches: 0, Indels: 8
0.77 0.00 0.23
Matches are distributed among these distances:
17 8 0.30
18 1 0.04
19 3 0.11
20 15 0.56
ACGTcount: A:0.51, C:0.04, G:0.02, T:0.43
Consensus pattern (18 bp):
ATTAAATTAATATTTAAT
Found at i:43283834 original size:10 final size:10
Alignment explanation
Indices: 43283819--43283866 Score: 51
Period size: 10 Copynumber: 4.6 Consensus size: 10
43283809 TAATGTGTTG
43283819 AATTTTAATT
1 AATTTTAATT
*
43283829 AATTTTATAATA
1 AA-TTT-TAATT
*
43283841 AATTTTGATT
1 AATTTTAATT
43283851 AATTTTAATT
1 AATTTTAATT
*
43283861 TATTTT
1 AATTTT
43283867 CGACAGATTC
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
10 19 0.61
11 6 0.19
12 6 0.19
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (10 bp):
AATTTTAATT
Found at i:43286702 original size:10 final size:10
Alignment explanation
Indices: 43286687--43286721 Score: 52
Period size: 10 Copynumber: 3.4 Consensus size: 10
43286677 ACATAAGCTC
43286687 TTCTCTTTTT
1 TTCTCTTTTT
43286697 TTCTCTTTTT
1 TTCTCTTTTT
*
43286707 TTTTCTTTTCT
1 TTCTCTTTT-T
43286718 TTCT
1 TTCT
43286722 TTTATTTTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
10 18 0.82
11 4 0.18
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (10 bp):
TTCTCTTTTT
Found at i:43286729 original size:21 final size:20
Alignment explanation
Indices: 43286690--43286732 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 20
43286680 TAAGCTCTTC
43286690 TCTTTTTTTCTCTTTTTTTT
1 TCTTTTTTTCTCTTTTTTTT
43286710 TCTTTTCTTTCT-TTTATTTTT
1 TCTTTT-TTTCTCTTT-TTTTT
43286731 TC
1 TC
43286733 ACGAGCATTT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
20 9 0.43
21 12 0.57
ACGTcount: A:0.02, C:0.16, G:0.00, T:0.81
Consensus pattern (20 bp):
TCTTTTTTTCTCTTTTTTTT
Found at i:43288940 original size:25 final size:27
Alignment explanation
Indices: 43288912--43288967 Score: 73
Period size: 25 Copynumber: 2.2 Consensus size: 27
43288902 TAATTAGTAT
* *
43288912 AAAATATT-AATAATTCAAT-AAATTG
1 AAAATATTAAATAATTAAATAAAATTC
43288937 AAAA-ATTAAATAATTAAATAAAATTC
1 AAAATATTAAATAATTAAATAAAATTC
43288963 AAAAT
1 AAAAT
43288968 TTAGGAGAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
24 3 0.12
25 14 0.54
26 9 0.35
ACGTcount: A:0.62, C:0.04, G:0.02, T:0.32
Consensus pattern (27 bp):
AAAATATTAAATAATTAAATAAAATTC
Found at i:43289816 original size:30 final size:30
Alignment explanation
Indices: 43289759--43289817 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 30
43289749 GGCCTTTGAA
* * *
43289759 AATATTTACAAAGAGAGACATCTAATTTTT
1 AATATTTACAAAAAGAGACACCAAATTTTT
43289789 AATATTTACAAAAAGAGTA-ACCAAATTTT
1 AATATTTACAAAAAGAG-ACACCAAATTTT
43289818 GAAAATAGTT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
30 24 0.96
31 1 0.04
ACGTcount: A:0.47, C:0.10, G:0.08, T:0.34
Consensus pattern (30 bp):
AATATTTACAAAAAGAGACACCAAATTTTT
Found at i:43296520 original size:2 final size:2
Alignment explanation
Indices: 43296513--43296550 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
43296503 TAAGAACAAC
43296513 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
43296551 TATTTCAGTA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:43297780 original size:25 final size:24
Alignment explanation
Indices: 43297747--43297881 Score: 98
Period size: 25 Copynumber: 5.5 Consensus size: 24
43297737 ACCGATTCCG
*
43297747 GCTCTTATGAGCTTACCGATACTCA
1 GCTCGTATGAGCTTACCGATA-TCA
43297772 GCTCGTATGAGCTTACC-ATTATTCA
1 GCTCGTATGAGCTTACCGA-TA-TCA
** * *
43297797 GCTCAAAAGAGCTTACCGTTTAT-A
1 GCTCGTATGAGCTTACCG-ATATCA
43297821 GCTCGTATGAGCTTACC-ATTATTCA
1 GCTCGTATGAGCTTACCGA-TA-TCA
** * *
43297846 GCTCAAAAGAGCTTACCGTTTAT-A
1 GCTCGTATGAGCTTACCG-ATATCA
43297870 GCTCGTATGAGC
1 GCTCGTATGAGC
43297882 ATAGATGTAC
Statistics
Matches: 85, Mismatches: 17, Indels: 17
0.71 0.14 0.14
Matches are distributed among these distances:
23 2 0.02
24 27 0.32
25 52 0.61
26 4 0.05
ACGTcount: A:0.27, C:0.24, G:0.18, T:0.32
Consensus pattern (24 bp):
GCTCGTATGAGCTTACCGATATCA
Found at i:43297824 original size:49 final size:49
Alignment explanation
Indices: 43297771--43297881 Score: 222
Period size: 49 Copynumber: 2.3 Consensus size: 49
43297761 ACCGATACTC
43297771 AGCTCGTATGAGCTTACCATTATTCAGCTCAAAAGAGCTTACCGTTTAT
1 AGCTCGTATGAGCTTACCATTATTCAGCTCAAAAGAGCTTACCGTTTAT
43297820 AGCTCGTATGAGCTTACCATTATTCAGCTCAAAAGAGCTTACCGTTTAT
1 AGCTCGTATGAGCTTACCATTATTCAGCTCAAAAGAGCTTACCGTTTAT
43297869 AGCTCGTATGAGC
1 AGCTCGTATGAGC
43297882 ATAGATGTAC
Statistics
Matches: 62, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
49 62 1.00
ACGTcount: A:0.28, C:0.23, G:0.18, T:0.32
Consensus pattern (49 bp):
AGCTCGTATGAGCTTACCATTATTCAGCTCAAAAGAGCTTACCGTTTAT
Found at i:43299449 original size:4 final size:4
Alignment explanation
Indices: 43299440--43299487 Score: 96
Period size: 4 Copynumber: 12.0 Consensus size: 4
43299430 TTAGGGGTGT
43299440 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
43299488 CTATAATAAA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 44 1.00
ACGTcount: A:0.50, C:0.25, G:0.00, T:0.25
Consensus pattern (4 bp):
TACA
Found at i:43300658 original size:12 final size:12
Alignment explanation
Indices: 43300641--43300678 Score: 51
Period size: 11 Copynumber: 3.2 Consensus size: 12
43300631 TTTTATTATA
43300641 TTTTAACTTTAC
1 TTTTAACTTTAC
*
43300653 TTTTAAC-TTAA
1 TTTTAACTTTAC
43300664 TTTTAACATTTAC
1 TTTTAAC-TTTAC
43300677 TT
1 TT
43300679 AATTAAAAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
11 10 0.45
12 7 0.32
13 5 0.23
ACGTcount: A:0.29, C:0.13, G:0.00, T:0.58
Consensus pattern (12 bp):
TTTTAACTTTAC
Found at i:43304000 original size:38 final size:36
Alignment explanation
Indices: 43303922--43304030 Score: 94
Period size: 38 Copynumber: 2.8 Consensus size: 36
43303912 TCACCACCCT
* * *
43303922 ATTGAATACCTTTTAAAGCATGTTTACTGCTTGTATTAA
1 ATTGAATA-CATTT-AAGCATG-TTATTGCTAGTATTAA
43303961 ATTGAATACATGTTAAGCATGTTAATTGCTAGTGA-TAA
1 ATTGAATACAT-TTAAGCATGTT-ATTGCTAGT-ATTAA
* *
43303999 ATCGAATACAATTTAAGGATGATTATTGCTAG
1 ATTGAATAC-ATTTAAGCATG-TTATTGCTAG
43304031 CATTGATTTA
Statistics
Matches: 60, Mismatches: 5, Indels: 11
0.79 0.07 0.14
Matches are distributed among these distances:
37 2 0.03
38 43 0.72
39 15 0.25
ACGTcount: A:0.35, C:0.10, G:0.17, T:0.39
Consensus pattern (36 bp):
ATTGAATACATTTAAGCATGTTATTGCTAGTATTAA
Found at i:43304367 original size:85 final size:85
Alignment explanation
Indices: 43304132--43304380 Score: 311
Period size: 85 Copynumber: 2.9 Consensus size: 85
43304122 AAACAGTGTG
* *
43304132 GTTCAATCACGAACCAAGTGACAGTTCATTTAATCTT-CAAATATGTTGTGCACCCATAACAAGT
1 GTTCGATCACGAACCAAGTGACAGTTCATTTAAT-TTACAAATATGTTGTGCACCCACAACAAGT
** * *** * *
43304196 GATAGTAACAAAAAATATGCG
65 GGCAATAACTGCAAAGATGCA
* * * * * *
43304217 GTTCGATCATGAACCAAGTAACAGTTCGTTTAATCTACAAATTTGTTATGCACCCACAACAAGTG
1 GTTCGATCACGAACCAAGTGACAGTTCATTTAATTTACAAATATGTTGTGCACCCACAACAAGTG
*
43304282 GCACTAACTGCAAAGATGCA
66 GCAATAACTGCAAAGATGCA
* *
43304302 GTTCGATCACAAACCAAGTGGCAGTTCATTTAATTTACAAATATGTTGTGCACCCACAACAAGTG
1 GTTCGATCACGAACCAAGTGACAGTTCATTTAATTTACAAATATGTTGTGCACCCACAACAAGTG
43304367 GCAATAACTGCAAA
66 GCAATAACTGCAAA
43304381 TCAGCAATGG
Statistics
Matches: 138, Mismatches: 25, Indels: 2
0.84 0.15 0.01
Matches are distributed among these distances:
84 1 0.01
85 137 0.99
ACGTcount: A:0.37, C:0.21, G:0.16, T:0.26
Consensus pattern (85 bp):
GTTCGATCACGAACCAAGTGACAGTTCATTTAATTTACAAATATGTTGTGCACCCACAACAAGTG
GCAATAACTGCAAAGATGCA
Found at i:43308119 original size:27 final size:27
Alignment explanation
Indices: 43308089--43308144 Score: 112
Period size: 27 Copynumber: 2.1 Consensus size: 27
43308079 GTAAAATCGA
43308089 AACGTTTTATTAAAACAATTGAATTGT
1 AACGTTTTATTAAAACAATTGAATTGT
43308116 AACGTTTTATTAAAACAATTGAATTGT
1 AACGTTTTATTAAAACAATTGAATTGT
43308143 AA
1 AA
43308145 GGTGATTCGA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.43, C:0.07, G:0.11, T:0.39
Consensus pattern (27 bp):
AACGTTTTATTAAAACAATTGAATTGT
Found at i:43308700 original size:10 final size:10
Alignment explanation
Indices: 43308676--43308732 Score: 52
Period size: 9 Copynumber: 6.1 Consensus size: 10
43308666 TTTTTTATAT
43308676 ATTTATAAAA
1 ATTTATAAAA
43308686 A-TTATAAAA
1 ATTTATAAAA
43308695 ATTTAT-AAA
1 ATTTATAAAA
*
43308704 ATATTA-AATA
1 AT-TTATAAAA
*
43308714 ATTT-TCAAA
1 ATTTATAAAA
43308723 ATTT-TAAAA
1 ATTTATAAAA
43308732 A
1 A
43308733 AATTAAAATT
Statistics
Matches: 39, Mismatches: 4, Indels: 9
0.75 0.08 0.17
Matches are distributed among these distances:
9 27 0.69
10 12 0.31
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (10 bp):
ATTTATAAAA
Found at i:43308700 original size:19 final size:19
Alignment explanation
Indices: 43308676--43308732 Score: 64
Period size: 19 Copynumber: 3.1 Consensus size: 19
43308666 TTTTTTATAT
43308676 ATTTATAAAAATTATAAAA
1 ATTTATAAAAATTATAAAA
*
43308695 ATTTATAAAATATTA-AATA
1 ATTTATAAAA-ATTATAAAA
* *
43308714 ATTT-TCAAAATTTTAAAA
1 ATTTATAAAAATTATAAAA
43308732 A
1 A
43308733 AATTAAAATT
Statistics
Matches: 32, Mismatches: 4, Indels: 5
0.78 0.10 0.12
Matches are distributed among these distances:
17 3 0.09
18 8 0.25
19 17 0.53
20 4 0.12
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (19 bp):
ATTTATAAAAATTATAAAA
Found at i:43308917 original size:6 final size:6
Alignment explanation
Indices: 43308906--43308940 Score: 70
Period size: 6 Copynumber: 5.8 Consensus size: 6
43308896 TTTAGGCAAT
43308906 ATAAAA ATAAAA ATAAAA ATAAAA ATAAAA ATAAA
1 ATAAAA ATAAAA ATAAAA ATAAAA ATAAAA ATAAA
43308941 TTTTAATTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (6 bp):
ATAAAA
Found at i:43309852 original size:29 final size:28
Alignment explanation
Indices: 43309819--43309879 Score: 77
Period size: 29 Copynumber: 2.1 Consensus size: 28
43309809 AAAAACTACT
43309819 TTTTTTAAAAAATTACCGAAATGGGCCA
1 TTTTTTAAAAAATTACCGAAATGGGCCA
** * *
43309847 GTTTTTTAATTATTTACCGGAATGGGCCA
1 -TTTTTTAAAAAATTACCGAAATGGGCCA
43309876 TTTT
1 TTTT
43309880 CTCCGAAATC
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
28 4 0.14
29 24 0.86
ACGTcount: A:0.30, C:0.13, G:0.16, T:0.41
Consensus pattern (28 bp):
TTTTTTAAAAAATTACCGAAATGGGCCA
Found at i:43310121 original size:22 final size:22
Alignment explanation
Indices: 43310096--43310165 Score: 113
Period size: 22 Copynumber: 3.2 Consensus size: 22
43310086 AAATTCAATA
43310096 TCAATTTCCTTCAAAAATTCTC
1 TCAATTTCCTTCAAAAATTCTC
*
43310118 TCAATTCCCTTCAAAAATTCTC
1 TCAATTTCCTTCAAAAATTCTC
* *
43310140 TCAATTTTCTTCCAAAATTCTC
1 TCAATTTCCTTCAAAAATTCTC
43310162 TCAA
1 TCAA
43310166 ACTCTCAAAT
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 44 1.00
ACGTcount: A:0.31, C:0.29, G:0.00, T:0.40
Consensus pattern (22 bp):
TCAATTTCCTTCAAAAATTCTC
Found at i:43310171 original size:30 final size:30
Alignment explanation
Indices: 43310137--43310195 Score: 91
Period size: 30 Copynumber: 2.0 Consensus size: 30
43310127 TTCAAAAATT
* * *
43310137 CTCTCAATTTTCTTCCAAAATTCTCTCAAA
1 CTCTCAAATTCCTTCCAAAATCCTCTCAAA
43310167 CTCTCAAATTCCTTCCAAAATCCTCTCAA
1 CTCTCAAATTCCTTCCAAAATCCTCTCAA
43310196 TTTCCTTCAA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.31, C:0.34, G:0.00, T:0.36
Consensus pattern (30 bp):
CTCTCAAATTCCTTCCAAAATCCTCTCAAA
Found at i:43310172 original size:52 final size:51
Alignment explanation
Indices: 43310115--43310217 Score: 136
Period size: 52 Copynumber: 2.0 Consensus size: 51
43310105 TTCAAAAATT
* * * *
43310115 CTCTC-AATTCCCTTCAAAAATTCTCTCAATTTTCTTCCAAAATTCTCTCAAA
1 CTCTCAAATT-CCTTCAAAAATCCTCTCAATTTCCTTCAAAAAATCTC-CAAA
*
43310167 CTCTCAAATTCCTTCCAAAATCCTCTCAATTTCCTTCAAAAAATCTCCAAA
1 CTCTCAAATTCCTTCAAAAATCCTCTCAATTTCCTTCAAAAAATCTCCAAA
43310218 TCCATATTAA
Statistics
Matches: 45, Mismatches: 5, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
51 4 0.09
52 37 0.82
53 4 0.09
ACGTcount: A:0.33, C:0.32, G:0.00, T:0.35
Consensus pattern (51 bp):
CTCTCAAATTCCTTCAAAAATCCTCTCAATTTCCTTCAAAAAATCTCCAAA
Found at i:43310206 original size:21 final size:22
Alignment explanation
Indices: 43310167--43310208 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
43310157 TTCTCTCAAA
43310167 CTCTCAAATTCCTTCCAAAATC
1 CTCTCAAATTCCTTCCAAAATC
* *
43310189 CTCTCAATTTCCTTCAAAAA
1 CTCTCAAATTCCTTCCAAAA
43310209 ATCTCCAAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.33, C:0.33, G:0.00, T:0.33
Consensus pattern (22 bp):
CTCTCAAATTCCTTCCAAAATC
Found at i:43310314 original size:33 final size:31
Alignment explanation
Indices: 43310249--43310315 Score: 89
Period size: 33 Copynumber: 2.1 Consensus size: 31
43310239 TTAAATTTCA
* **
43310249 TTTTTTTAAGAAAATTTTAAATTTTTTTTAT
1 TTTTTTTAAAAAAATTTTAAATTTTTAATAT
43310280 TTTTTTTAAAAATAATTTTAAAATTTTTAATAT
1 TTTTTTTAAAAA-AATTTT-AAATTTTTAATAT
43310313 TTT
1 TTT
43310316 CAACAATGGC
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
31 11 0.35
32 6 0.19
33 14 0.45
ACGTcount: A:0.36, C:0.00, G:0.01, T:0.63
Consensus pattern (31 bp):
TTTTTTTAAAAAAATTTTAAATTTTTAATAT
Found at i:43310435 original size:14 final size:15
Alignment explanation
Indices: 43310406--43310439 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
43310396 AAATTTTAAA
43310406 TTTTATTTAAGATAT
1 TTTTATTTAAGATAT
*
43310421 TTTTATTTATG-TAT
1 TTTTATTTAAGATAT
43310435 TTTTA
1 TTTTA
43310440 GATATTTATT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 8 0.44
15 10 0.56
ACGTcount: A:0.26, C:0.00, G:0.06, T:0.68
Consensus pattern (15 bp):
TTTTATTTAAGATAT
Found at i:43334714 original size:23 final size:23
Alignment explanation
Indices: 43334670--43334716 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
43334660 TTACTTAATA
*
43334670 TTATTATTTTTAGTTATATTGTT
1 TTATTATTTCTAGTTATATTGTT
*
43334693 TTATT-TTTCTAGTTCTAGTTGTT
1 TTATTATTTCTAGTTATA-TTGTT
43334716 T
1 T
43334717 CTTATCCTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
22 10 0.48
23 11 0.52
ACGTcount: A:0.17, C:0.04, G:0.11, T:0.68
Consensus pattern (23 bp):
TTATTATTTCTAGTTATATTGTT
Found at i:43334965 original size:16 final size:15
Alignment explanation
Indices: 43334940--43334971 Score: 55
Period size: 16 Copynumber: 2.1 Consensus size: 15
43334930 TTTCACTTCG
43334940 TTTCTTATTATTATT
1 TTTCTTATTATTATT
43334955 TTTCTTTATTATTATT
1 TTTC-TTATTATTATT
43334971 T
1 T
43334972 CTTAGTTAGT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 4 0.25
16 12 0.75
ACGTcount: A:0.19, C:0.06, G:0.00, T:0.75
Consensus pattern (15 bp):
TTTCTTATTATTATT
Found at i:43336447 original size:6 final size:6
Alignment explanation
Indices: 43336436--43336482 Score: 69
Period size: 6 Copynumber: 8.0 Consensus size: 6
43336426 AAGTTTATTT
* *
43336436 TTTTTA TTTTTA TTTTAA GTTTTA -TTTTA TTTTTA TTTTTA TTTTTA
1 TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA
43336483 GTTCTTTTTA
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
5 5 0.14
6 32 0.86
ACGTcount: A:0.19, C:0.00, G:0.02, T:0.79
Consensus pattern (6 bp):
TTTTTA
Found at i:43336451 original size:5 final size:5
Alignment explanation
Indices: 43336429--43336480 Score: 52
Period size: 6 Copynumber: 9.6 Consensus size: 5
43336419 GACCATTAAG
43336429 TTTAT TTT-T TTTATT TTTAT TTTAAGT TTTAT TTTATT TTTATT TTTAT
1 TTTAT TTTAT TTTA-T TTTAT TTT-A-T TTTAT TTTA-T TTTA-T TTTAT
43336478 TTT
1 TTT
43336481 TAGTTCTTTT
Statistics
Matches: 42, Mismatches: 0, Indels: 10
0.81 0.00 0.19
Matches are distributed among these distances:
4 4 0.10
5 16 0.38
6 18 0.43
7 4 0.10
ACGTcount: A:0.17, C:0.00, G:0.02, T:0.81
Consensus pattern (5 bp):
TTTAT
Found at i:43336458 original size:12 final size:11
Alignment explanation
Indices: 43336429--43336474 Score: 51
Period size: 11 Copynumber: 4.3 Consensus size: 11
43336419 GACCATTAAG
43336429 TTTA-TTTT-T
1 TTTAGTTTTAT
*
43336438 TTTATTTTTAT
1 TTTAGTTTTAT
43336449 TTTAAGTTTTAT
1 TTT-AGTTTTAT
*
43336461 TTTATTTTTAT
1 TTTAGTTTTAT
43336472 TTT
1 TTT
43336475 TATTTTTAGT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
9 4 0.12
10 4 0.12
11 14 0.44
12 10 0.31
ACGTcount: A:0.17, C:0.00, G:0.02, T:0.80
Consensus pattern (11 bp):
TTTAGTTTTAT
Found at i:43336482 original size:23 final size:22
Alignment explanation
Indices: 43336429--43336480 Score: 79
Period size: 23 Copynumber: 2.4 Consensus size: 22
43336419 GACCATTAAG
43336429 TTTATTTT-TTTTATTTTTATT
1 TTTATTTTATTTTATTTTTATT
*
43336450 TTAAGTTTTATTTTATTTTTATT
1 TTTA-TTTTATTTTATTTTTATT
43336473 TTTATTTT
1 TTTATTTT
43336481 TAGTTCTTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
21 3 0.11
22 8 0.30
23 16 0.59
ACGTcount: A:0.17, C:0.00, G:0.02, T:0.81
Consensus pattern (22 bp):
TTTATTTTATTTTATTTTTATT
Found at i:43342204 original size:29 final size:29
Alignment explanation
Indices: 43342139--43342210 Score: 71
Period size: 29 Copynumber: 2.6 Consensus size: 29
43342129 TCATGGTGGA
*
43342139 GAAAATGAGAGGTG-A-ATGGTGGTAGAG
1 GAAAATGAGAGGTGAACAAGGTGGTAGAG
* *
43342166 GAAAA-AAGAGGTGAACAGAGGTGG-AGGG
1 GAAAATGAGAGGTGAACA-AGGTGGTAGAG
*
43342194 GAAAATGAGAGATGAAC
1 GAAAATGAGAGGTGAAC
43342211 GGCGGGGAGG
Statistics
Matches: 36, Mismatches: 5, Indels: 6
0.77 0.11 0.13
Matches are distributed among these distances:
26 7 0.19
27 6 0.17
28 9 0.25
29 14 0.39
ACGTcount: A:0.43, C:0.03, G:0.42, T:0.12
Consensus pattern (29 bp):
GAAAATGAGAGGTGAACAAGGTGGTAGAG
Found at i:43350909 original size:18 final size:18
Alignment explanation
Indices: 43350881--43350922 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
43350871 TTTTATAATG
*
43350881 TATTT-TTTTATCCTTTA
1 TATTTATTTTATCCTTCA
*
43350898 TATTTATTTTATCGTTCA
1 TATTTATTTTATCCTTCA
43350916 TATTTAT
1 TATTTAT
43350923 AAGTTGGGAT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 5 0.23
18 17 0.77
ACGTcount: A:0.21, C:0.10, G:0.02, T:0.67
Consensus pattern (18 bp):
TATTTATTTTATCCTTCA
Found at i:43363683 original size:33 final size:35
Alignment explanation
Indices: 43363638--43363704 Score: 93
Period size: 33 Copynumber: 2.0 Consensus size: 35
43363628 TTTAAAATCA
* *
43363638 TTAATACAAACAATAAAT-TATATGTATA-ATATT
1 TTAAAACAAACAATAAATATATATATATATATATT
*
43363671 TTAAAACAAACAATATATATATATATATATATAT
1 TTAAAACAAACAATAAATATATATATATATATAT
43363705 GAGTTTGAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
33 16 0.55
34 9 0.31
35 4 0.14
ACGTcount: A:0.54, C:0.06, G:0.01, T:0.39
Consensus pattern (35 bp):
TTAAAACAAACAATAAATATATATATATATATATT
Found at i:43364650 original size:11 final size:11
Alignment explanation
Indices: 43364636--43364660 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
43364626 AAAAAAATGT
43364636 AAATAAAAATA
1 AAATAAAAATA
43364647 AAATAAAAATA
1 AAATAAAAATA
43364658 AAA
1 AAA
43364661 ACGACACTAC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (11 bp):
AAATAAAAATA
Found at i:43369915 original size:18 final size:18
Alignment explanation
Indices: 43369892--43369947 Score: 76
Period size: 18 Copynumber: 3.1 Consensus size: 18
43369882 TTCACCTCCA
43369892 CAACCATCATCCACAGGC
1 CAACCATCATCCACAGGC
* *
43369910 CAACCACCATCCACAGAC
1 CAACCATCATCCACAGGC
* *
43369928 CAACCATCGTCCACAAGC
1 CAACCATCATCCACAGGC
43369946 CA
1 CA
43369948 CCCACCTACA
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
18 32 1.00
ACGTcount: A:0.36, C:0.46, G:0.09, T:0.09
Consensus pattern (18 bp):
CAACCATCATCCACAGGC
Found at i:43373733 original size:22 final size:23
Alignment explanation
Indices: 43373682--43373736 Score: 62
Period size: 22 Copynumber: 2.4 Consensus size: 23
43373672 TTTTAATTAT
43373682 TTAAAATTTAACTTATTTTGAAGA
1 TTAAAA-TTAACTTATTTTGAAGA
*
43373706 TT-AAATTAACTT-TCTTTTAA-A
1 TTAAAATTAACTTAT-TTTGAAGA
43373727 TTAAAATTAA
1 TTAAAATTAA
43373737 AATTAATTCA
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
21 4 0.14
22 19 0.68
23 3 0.11
24 2 0.07
ACGTcount: A:0.44, C:0.05, G:0.04, T:0.47
Consensus pattern (23 bp):
TTAAAATTAACTTATTTTGAAGA
Found at i:43375222 original size:60 final size:60
Alignment explanation
Indices: 43375147--43375265 Score: 220
Period size: 60 Copynumber: 2.0 Consensus size: 60
43375137 ATTTTTTTTA
*
43375147 TAATTATTTTAAAATTAATTTGTTAGTAATTTAGGATTATGTTATAAATTGTTGTGTTTG
1 TAATTATTTTAAAATTAATTTATTAGTAATTTAGGATTATGTTATAAATTGTTGTGTTTG
*
43375207 TAATTATTTTAAAATTAATTTATTAGTCATTTAGGATTATGTTATAAATTGTTGTGTTT
1 TAATTATTTTAAAATTAATTTATTAGTAATTTAGGATTATGTTATAAATTGTTGTGTTT
43375266 AGTTTAGTAT
Statistics
Matches: 57, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
60 57 1.00
ACGTcount: A:0.32, C:0.01, G:0.13, T:0.54
Consensus pattern (60 bp):
TAATTATTTTAAAATTAATTTATTAGTAATTTAGGATTATGTTATAAATTGTTGTGTTTG
Found at i:43375628 original size:77 final size:78
Alignment explanation
Indices: 43375492--43375644 Score: 220
Period size: 77 Copynumber: 2.0 Consensus size: 78
43375482 ATTAGGTTAC
** *
43375492 AAATTGTTAGTGTTTAGTATAGGGTTTTGTGATTTTTTAGTAATGTAATTTTTTTAAAAATTAAT
1 AAATTGTTAGTGTTTAGTATAGGGTTTTGTGATTTTTTAGTAATGTAATTTTTAAAAAAAATAAT
43375557 TTTATAGTTATAT
66 TTTATAGTTATAT
* * * *
43375570 AAATTTTTAGTGTTTAGT-TATGTTTTTGTGATTTTTTAGTAATGT-CTTTTTAAAAAAAAATAA
1 AAATTGTTAGTGTTTAGTATAGGGTTTTGTGATTTTTTAGTAATGTAATTTTT-AAAAAAAATAA
43375633 TTTTATAGTTAT
65 TTTTATAGTTAT
43375645 TTTGTTAGTA
Statistics
Matches: 67, Mismatches: 7, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
76 5 0.07
77 45 0.67
78 17 0.25
ACGTcount: A:0.31, C:0.01, G:0.14, T:0.54
Consensus pattern (78 bp):
AAATTGTTAGTGTTTAGTATAGGGTTTTGTGATTTTTTAGTAATGTAATTTTTAAAAAAAATAAT
TTTATAGTTATAT
Found at i:43377826 original size:33 final size:32
Alignment explanation
Indices: 43377789--43377897 Score: 128
Period size: 33 Copynumber: 3.3 Consensus size: 32
43377779 TCCATCTCAA
* * *
43377789 TACTCCGCTCCTTTCGGCCCGTATCTACTGCCG
1 TACTCCACT-CTTCCGGCCCGTATCCACTGCCG
* *
43377822 TACTCCACTCTTCCCGGCCCGTATCCACCGCTG
1 TACTCCACTCTT-CCGGCCCGTATCCACTGCCG
* *
43377855 TACTCCACTCATCCTGGCCCGTATCCACTGTCG
1 TACTCCACTCTTCC-GGCCCGTATCCACTGCCG
43377888 TACTCCACTC
1 TACTCCACTC
43377898 CTCCCAGCTC
Statistics
Matches: 65, Mismatches: 9, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
32 5 0.08
33 60 0.92
ACGTcount: A:0.13, C:0.45, G:0.15, T:0.28
Consensus pattern (32 bp):
TACTCCACTCTTCCGGCCCGTATCCACTGCCG
Found at i:43378355 original size:80 final size:79
Alignment explanation
Indices: 43378092--43378479 Score: 493
Period size: 79 Copynumber: 4.9 Consensus size: 79
43378082 AATAACTTCA
* * *
43378092 TATTTATGTAATGGATTTTTTTCCATTTTATTTATCAATTTTAT-GG-ATTTTTTTTGCAATTTA
1 TATTTATGTAATGAATTTTTTGCCATTTTATTTATCAATTTTATGGGTTTTTTTTTTGCAATTTA
**
43378155 AATAGTCAACTTCA
66 AATAGTCAACTTTG
* *
43378169 TATTTATGTAATGAATTTGTTGCCATTTTATTTATCAATTTTATGGGGTTTTTTTTTT-CTATTT
1 TATTTATGTAATGAATTTTTTGCCATTTTATTTATCAATTTTAT-GGGTTTTTTTTTTGCAATTT
*
43378233 TAATAGTCAACTTTG
65 AAATAGTCAACTTTG
*
43378248 TATTTATGTAATAAATTTTTTGCCATTTTATTTATCAATTTTATGGGTTTTTTTTTTTGCAATTT
1 TATTTATGTAATGAATTTTTTGCCATTTTATTTATCAATTTTATGGG-TTTTTTTTTTGCAATTT
43378313 AAATAGTCAACTTTG
65 AAATAGTCAACTTTG
* * * * *
43378328 TATTAATGTAATGAATTTTTTGTCATTTTATTTATCAATCTCATGAGTTTTTTTTTTTTTTTTGC
1 TATTTATGTAATGAATTTTTTGCCATTTTATTTATCAATTTTATG-G-----GTTTTTTTTTTGC
43378393 AATTTAAATAGTCAACTTTG
60 AATTTAAATAGTCAACTTTG
* *
43378413 TATTTATGTAAT-AACTTTTTTTGCCATTTTAATTATCAATATTAT--G-TTTTTTTTTGCAATT
1 TATTTATGTAATGAA--TTTTTTGCCATTTTATTTATCAATTTTATGGGTTTTTTTTTTGCAATT
43378474 TAAATA
64 TAAATA
43378480 AATAAACTTT
Statistics
Matches: 274, Mismatches: 24, Indels: 26
0.85 0.07 0.08
Matches are distributed among these distances:
77 62 0.23
78 3 0.01
79 71 0.26
80 67 0.24
81 1 0.00
84 2 0.01
85 43 0.16
86 25 0.09
ACGTcount: A:0.26, C:0.08, G:0.10, T:0.56
Consensus pattern (79 bp):
TATTTATGTAATGAATTTTTTGCCATTTTATTTATCAATTTTATGGGTTTTTTTTTTGCAATTTA
AATAGTCAACTTTG
Found at i:43378380 original size:159 final size:158
Alignment explanation
Indices: 43378092--43378479 Score: 521
Period size: 159 Copynumber: 2.4 Consensus size: 158
43378082 AATAACTTCA
** * *
43378092 TATTTATGTAATGGATTTTTTTCCATTTTATTTATCAATTTTATGGATTTTTTTTGCAATTTAAA
1 TATTTATGTAATAAATTTTTTGCCATTTTATTTATCAATTTTATGGTTTTTTTTTGCAATTTAAA
* * * *
43378157 TAGTCAACTTCATATTTATGTAATGAATTTGTTGCCATTTTATTTATCAATTTTATG-GGGTTTT
66 TAGTCAACTTCATATTAATGTAATGAATTTGTTGCCATTTTATTTATCAATCTCATGAGTGTTTT
* *
43378221 TTTTTT-CTATTTTAATAGTCAACTTTG
131 TTTTTTGCAATTTAAATAGTCAACTTTG
43378248 TATTTATGTAATAAATTTTTTGCCATTTTATTTATCAATTTTATGGGTTTTTTTTTTTGCAATTT
1 TATTTATGTAATAAATTTTTTGCCATTTTATTTATCAATTTTAT-GG--TTTTTTTTTGCAATTT
** * *
43378313 AAATAGTCAACTTTGTATTAATGTAATGAATTTTTTGTCATTTTATTTATCAATCTCATGAGTTT
63 AAATAGTCAACTTCATATTAATGTAATGAATTTGTTGCCATTTTATTTATCAATCTCATGAG---
*
43378378 TTTTTTTTTTTTTGCAATTTAAATAGTCAACTTTG
125 -TGTTTTTTTTTTGCAATTTAAATAGTCAACTTTG
* * *
43378413 TATTTATGTAATAACTTTTTTTGCCATTTTAATTATCAATATTAT-GTTTTTTTTTGCAATTTAA
1 TATTTATGTAATAA-ATTTTTTGCCATTTTATTTATCAATTTTATGGTTTTTTTTTGCAATTTAA
43378477 ATA
65 ATA
43378480 AATAAACTTT
Statistics
Matches: 204, Mismatches: 18, Indels: 14
0.86 0.08 0.06
Matches are distributed among these distances:
156 41 0.20
157 2 0.01
159 68 0.33
160 1 0.00
162 21 0.10
164 11 0.05
165 33 0.16
166 27 0.13
ACGTcount: A:0.26, C:0.08, G:0.10, T:0.56
Consensus pattern (158 bp):
TATTTATGTAATAAATTTTTTGCCATTTTATTTATCAATTTTATGGTTTTTTTTTGCAATTTAAA
TAGTCAACTTCATATTAATGTAATGAATTTGTTGCCATTTTATTTATCAATCTCATGAGTGTTTT
TTTTTTGCAATTTAAATAGTCAACTTTG
Found at i:43378452 original size:86 final size:85
Alignment explanation
Indices: 43378295--43378452 Score: 264
Period size: 85 Copynumber: 1.8 Consensus size: 85
43378285 ATTTTATGGG
* *
43378295 TTTTTTTTTTTGCAATTTAAATAGTCAACTTTGTATTAATGTAATGAATTTTTTGTCATTTTATT
1 TTTTTTTTTTTGCAATTTAAATAGTCAACTTTGTATTAATGTAATGAATTTTTTGCCATTTTAAT
43378360 TATCAATCTCATGAGTTTTT
66 TATCAATCTCATGAGTTTTT
*
43378380 TTTTTTTTTTTGCAATTTAAATAGTCAACTTTGTATTTATGTAAT-AACTTTTTTTGCCATTTTA
1 TTTTTTTTTTTGCAATTTAAATAGTCAACTTTGTATTAATGTAATGAA--TTTTTTGCCATTTTA
43378444 ATTATCAAT
64 ATTATCAAT
43378453 ATTATGTTTT
Statistics
Matches: 68, Mismatches: 3, Indels: 3
0.92 0.04 0.04
Matches are distributed among these distances:
84 2 0.03
85 44 0.65
86 22 0.32
ACGTcount: A:0.27, C:0.09, G:0.08, T:0.56
Consensus pattern (85 bp):
TTTTTTTTTTTGCAATTTAAATAGTCAACTTTGTATTAATGTAATGAATTTTTTGCCATTTTAAT
TATCAATCTCATGAGTTTTT
Found at i:43380187 original size:33 final size:33
Alignment explanation
Indices: 43380145--43380267 Score: 149
Period size: 33 Copynumber: 3.7 Consensus size: 33
43380135 AATACATGTG
* * *
43380145 TAAGACCATAGCTGAGCTATGACATTCTGATGA
1 TAAGACCATAACTGGGCTATGGCATTCTGATGA
* * **
43380178 TAAGACCATAACTGGGTTATGGCACTACAAATG-
1 TAAGACCATAACTGGGCTATGGCA-TTCTGATGA
*
43380211 TAAGACCATATCTGGGCTATGGCATTCTGATGA
1 TAAGACCATAACTGGGCTATGGCATTCTGATGA
*
43380244 TAAGACCATAACTGGGTTATGGCA
1 TAAGACCATAACTGGGCTATGGCA
43380268 CTACAAATGG
Statistics
Matches: 74, Mismatches: 14, Indels: 4
0.80 0.15 0.04
Matches are distributed among these distances:
32 5 0.07
33 64 0.86
34 5 0.07
ACGTcount: A:0.33, C:0.18, G:0.23, T:0.27
Consensus pattern (33 bp):
TAAGACCATAACTGGGCTATGGCATTCTGATGA
Found at i:43380249 original size:66 final size:66
Alignment explanation
Indices: 43380143--43380285 Score: 250
Period size: 66 Copynumber: 2.2 Consensus size: 66
43380133 TAAATACATG
43380143 TGTAAGACCATAGCTGAGCTATGACATTCTGATGATAAGACCATAACTGGGTTATGGCACTACAA
1 TGTAAGACCATAGCTGAGCTATGACATTCTGATGATAAGACCATAACTGGGTTATGGCACTACAA
43380208 A
66 A
* * *
43380209 TGTAAGACCATATCTGGGCTATGGCATTCTGATGATAAGACCATAACTGGGTTATGGCACTACAA
1 TGTAAGACCATAGCTGAGCTATGACATTCTGATGATAAGACCATAACTGGGTTATGGCACTACAA
43380274 A
66 A
*
43380275 TGGAAGACCAT
1 TGTAAGACCAT
43380286 GGCAGAGCCA
Statistics
Matches: 73, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
66 73 1.00
ACGTcount: A:0.34, C:0.18, G:0.22, T:0.26
Consensus pattern (66 bp):
TGTAAGACCATAGCTGAGCTATGACATTCTGATGATAAGACCATAACTGGGTTATGGCACTACAA
A
Found at i:43380282 original size:33 final size:33
Alignment explanation
Indices: 43380178--43380285 Score: 146
Period size: 33 Copynumber: 3.3 Consensus size: 33
43380168 ATTCTGATGA
43380178 TAAGACCATAACTGGGTTATGGCACTACAAATG
1 TAAGACCATAACTGGGTTATGGCACTACAAATG
* * * **
43380211 TAAGACCATATCTGGGCTATGGCA-TTCTGATG
1 TAAGACCATAACTGGGTTATGGCACTACAAATG
43380243 ATAAGACCATAACTGGGTTATGGCACTACAAATG
1 -TAAGACCATAACTGGGTTATGGCACTACAAATG
*
43380277 GAAGACCAT
1 TAAGACCAT
43380286 GGCAGAGCCA
Statistics
Matches: 62, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
32 5 0.08
33 52 0.84
34 5 0.08
ACGTcount: A:0.34, C:0.19, G:0.22, T:0.25
Consensus pattern (33 bp):
TAAGACCATAACTGGGTTATGGCACTACAAATG
Found at i:43380314 original size:66 final size:66
Alignment explanation
Indices: 43380146--43380319 Score: 217
Period size: 66 Copynumber: 2.6 Consensus size: 66
43380136 ATACATGTGT
* * * *
43380146 AAGACCATAGCTGAGCTATGACATTCTGATGATAAGACCATAACTGGGTTATGGCACTACAAATG
1 AAGACCATAGCAGAGCCATGGCATGCTGATGATAAGACCATAACTGGGTTATGGCACTACAAATG
*
43380211 T
66 G
* * * * *
43380212 AAGACCATATCTGGGCTATGGCATTCTGATGATAAGACCATAACTGGGTTATGGCACTACAAATG
1 AAGACCATAGCAGAGCCATGGCATGCTGATGATAAGACCATAACTGGGTTATGGCACTACAAATG
43380277 G
66 G
*
43380278 AAGACCATGGCAGAGCCATGGCAATGCATG-TG-TAAGACCATA
1 AAGACCATAGCAGAGCCATGGC-ATGC-TGATGATAAGACCATA
43380320 GTTGGACTAT
Statistics
Matches: 96, Mismatches: 10, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
66 89 0.93
67 5 0.05
68 2 0.02
ACGTcount: A:0.34, C:0.19, G:0.24, T:0.24
Consensus pattern (66 bp):
AAGACCATAGCAGAGCCATGGCATGCTGATGATAAGACCATAACTGGGTTATGGCACTACAAATG
G
Found at i:43381898 original size:20 final size:22
Alignment explanation
Indices: 43381873--43381912 Score: 66
Period size: 20 Copynumber: 1.9 Consensus size: 22
43381863 TAAATATATT
43381873 AATATATTAT-TT-TATTATAA
1 AATATATTATATTATATTATAA
43381893 AATATATTATATTATATTAT
1 AATATATTATATTATATTAT
43381913 TATATTTTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 10 0.56
21 2 0.11
22 6 0.33
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (22 bp):
AATATATTATATTATATTATAA
Found at i:43381905 original size:22 final size:20
Alignment explanation
Indices: 43381873--43381912 Score: 53
Period size: 22 Copynumber: 1.9 Consensus size: 20
43381863 TAAATATATT
*
43381873 AATATATTATTTTATTATAA
1 AATATATTATTATATTATAA
43381893 AATATATTATATTATATTAT
1 AATATA-T-TATTATATTAT
43381913 TATATTTTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 6 0.35
21 1 0.06
22 10 0.59
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (20 bp):
AATATATTATTATATTATAA
Found at i:43381909 original size:30 final size:28
Alignment explanation
Indices: 43381864--43381923 Score: 84
Period size: 30 Copynumber: 2.1 Consensus size: 28
43381854 TTTATGTTTT
*
43381864 AAATATATTAATATATTATTTTATTATA
1 AAATATATTAATATATTATTATATTATA
*
43381892 AAATATATTATATTATATTATTATATTTTA
1 AAATATATTA-A-TATATTATTATATTATA
43381922 AA
1 AA
43381924 TAAACAAAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
28 10 0.36
29 1 0.04
30 17 0.61
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (28 bp):
AAATATATTAATATATTATTATATTATA
Found at i:43382161 original size:16 final size:16
Alignment explanation
Indices: 43382140--43382175 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
43382130 AGACGAAAAA
* *
43382140 GAAAGAAAGGAAAGGG
1 GAAAGAAAAGAAAAGG
43382156 GAAAGAAAAGAAAAGG
1 GAAAGAAAAGAAAAGG
43382172 GAAA
1 GAAA
43382176 AACTAGGGTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.64, C:0.00, G:0.36, T:0.00
Consensus pattern (16 bp):
GAAAGAAAAGAAAAGG
Found at i:43388229 original size:16 final size:16
Alignment explanation
Indices: 43388210--43388247 Score: 76
Period size: 16 Copynumber: 2.4 Consensus size: 16
43388200 GAAATAATGT
43388210 TGTAATGGAAGAGAAC
1 TGTAATGGAAGAGAAC
43388226 TGTAATGGAAGAGAAC
1 TGTAATGGAAGAGAAC
43388242 TGTAAT
1 TGTAAT
43388248 AGAATAGAGA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.42, C:0.05, G:0.29, T:0.24
Consensus pattern (16 bp):
TGTAATGGAAGAGAAC
Found at i:43388540 original size:102 final size:103
Alignment explanation
Indices: 43388352--43388551 Score: 307
Period size: 102 Copynumber: 2.0 Consensus size: 103
43388342 GTTGTAATAG
* *
43388352 CATAAGGCAAAATGTTTAAATAACCAGAATACCCTTAGCAGAATTTTTTTAGGTATATTGCTATT
1 CATAAGGCAAAATGTTTAAATAACCAGAATACCCTTAACAGAATTTTTTTAGGTAGATTGCTATT
43388417 GTTATTGTTATTACATTTTAATAGGATTATTATTAAAT
66 GTTATTGTTATTACATTTTAATAGGATTATTATTAAAT
* * * *
43388455 CATAAGGCAAAAT-TCTTAAATGACCATAATACCCTTAACATAA-TTTTTTAGGTAGA-TGATTA
1 CATAAGGCAAAATGT-TTAAATAACCAGAATACCCTTAACAGAATTTTTTTAGGTAGATTG-CTA
43388517 TTGTTATTGTTATTACATTTTAATAGGATTATTAT
64 TTGTTATTGTTATTACATTTTAATAGGATTATTAT
43388552 AATTTAATAA
Statistics
Matches: 89, Mismatches: 6, Indels: 5
0.89 0.06 0.05
Matches are distributed among these distances:
101 2 0.02
102 50 0.56
103 37 0.42
ACGTcount: A:0.36, C:0.10, G:0.12, T:0.42
Consensus pattern (103 bp):
CATAAGGCAAAATGTTTAAATAACCAGAATACCCTTAACAGAATTTTTTTAGGTAGATTGCTATT
GTTATTGTTATTACATTTTAATAGGATTATTATTAAAT
Found at i:43388583 original size:26 final size:27
Alignment explanation
Indices: 43388549--43388637 Score: 82
Period size: 26 Copynumber: 3.5 Consensus size: 27
43388539 ATAGGATTAT
43388549 TATAATTTAATAATAAATAAT-TTA-A
1 TATAATTTAATAATAAATAATATTACA
* * *
43388574 TCATATTTTAAT-ATAATTATTATTACA
1 T-ATAATTTAATAATAAATAATATTACA
* *
43388601 TATAATTTAATAA-AAATAA-A-AATA
1 TATAATTTAATAATAAATAATATTACA
43388625 TATAATTTAATAA
1 TATAATTTAATAA
43388638 CATTTTTAAT
Statistics
Matches: 52, Mismatches: 8, Indels: 9
0.75 0.12 0.13
Matches are distributed among these distances:
24 15 0.29
25 9 0.17
26 25 0.48
27 3 0.06
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (27 bp):
TATAATTTAATAATAAATAATATTACA
Found at i:43390513 original size:23 final size:23
Alignment explanation
Indices: 43390487--43390576 Score: 83
Period size: 23 Copynumber: 3.8 Consensus size: 23
43390477 ATACCCGCAT
43390487 TGTTTTTATATAATATATATGCA
1 TGTTTTTATATAATATATATGCA
* *
43390510 TGTTTTTATATAATATACT-CGTA
1 TGTTTTTATATAATATA-TATGCA
*
43390533 TGGTTTTTTTATAATATATATATGCA
1 T-GTTTTTATAT-A-ATATATATGCA
* * *
43390559 TCTTTTTATGTAGTATAT
1 TGTTTTTATATAATATAT
43390577 GTATACCTGT
Statistics
Matches: 53, Mismatches: 9, Indels: 10
0.74 0.12 0.14
Matches are distributed among these distances:
23 25 0.47
24 11 0.21
25 9 0.17
26 8 0.15
ACGTcount: A:0.30, C:0.06, G:0.10, T:0.54
Consensus pattern (23 bp):
TGTTTTTATATAATATATATGCA
Found at i:43392541 original size:19 final size:18
Alignment explanation
Indices: 43392517--43392562 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 18
43392507 ATGTCTCTTT
*
43392517 TTTGCATTCATTTCATGCA
1 TTTGCATTCATTACAT-CA
43392536 TTTGCATTTCATTACATCA
1 TTTGCA-TTCATTACATCA
*
43392555 TATGCATT
1 TTTGCATT
43392563 AGACACCGTT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
18 2 0.08
19 13 0.54
20 9 0.38
ACGTcount: A:0.24, C:0.20, G:0.09, T:0.48
Consensus pattern (18 bp):
TTTGCATTCATTACATCA
Found at i:43395470 original size:17 final size:17
Alignment explanation
Indices: 43395435--43395472 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
43395425 TTGAGTCGTA
*
43395435 AAAAAAATGATGAAATG
1 AAAAAAATGATAAAATG
43395452 AAAAAAATGA-AAAAGTG
1 AAAAAAATGATAAAA-TG
43395469 AAAA
1 AAAA
43395473 TGAAAAATAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 3 0.16
17 16 0.84
ACGTcount: A:0.71, C:0.00, G:0.16, T:0.13
Consensus pattern (17 bp):
AAAAAAATGATAAAATG
Found at i:43395472 original size:14 final size:13
Alignment explanation
Indices: 43395455--43395501 Score: 51
Period size: 14 Copynumber: 3.5 Consensus size: 13
43395445 TGAAATGAAA
43395455 AAAATGAAAAAGT
1 AAAATGAAAAAGT
43395468 GAAAATGAAAAA-T
1 -AAAATGAAAAAGT
*
43395481 AAAAAATGGAAAAGT
1 --AAAATGAAAAAGT
43395496 AAAATG
1 AAAATG
43395502 GAGAGGCTAA
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
13 7 0.24
14 21 0.72
15 1 0.03
ACGTcount: A:0.68, C:0.00, G:0.17, T:0.15
Consensus pattern (13 bp):
AAAATGAAAAAGT
Found at i:43396838 original size:44 final size:44
Alignment explanation
Indices: 43396785--43397242 Score: 429
Period size: 44 Copynumber: 10.3 Consensus size: 44
43396775 TGAAAAGCAA
*
43396785 CAGATCTTGTCTTCATGTATTGACATGAAGTAGATTGAAGATAG
1 CAGATCTTGTCTTCATGTATTGACATGAAGTAGATCGAAGATAG
* * * *** * *
43396829 CAAATCTTGTCTTC-TCATACTGGTGGTGAAGTAGATCAAAGATAA
1 CAGATCTTGTCTTCAT-GTA-TTGACATGAAGTAGATCGAAGATAG
** *
43396874 TGGATCTTGTCTTCATGTATTGACATGAAATAGATCGAAGATAG
1 CAGATCTTGTCTTCATGTATTGACATGAAGTAGATCGAAGATAG
* * * *** * *
43396918 CAAATCTTGTCTTC-TCATACTGGTGGTGAAGTAGATCAAAGATAA
1 CAGATCTTGTCTTCAT-GTA-TTGACATGAAGTAGATCGAAGATAG
**
43396963 TGGATCTTGTCTTCATGTATTGACATGAAGTAGATC-AGAGATAG
1 CAGATCTTGTCTTCATGTATTGACATGAAGTAGATCGA-AGATAG
*
43397007 TAGATCTTGTCTTCATGTATTGACATGAAGTAGATCGAAGATAG
1 CAGATCTTGTCTTCATGTATTGACATGAAGTAGATCGAAGATAG
* ** * * * *
43397051 CAGATATTGTCTTCCCGTACTGGCAGCGAAGTAGATCGAAGAAAG
1 CAGATCTTGTCTTCATGTATTGACA-TGAAGTAGATCGAAGATAG
* * *
43397096 CAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGAAAG
1 CAGATCTTGTCTTCATGTATTGACATGAAGTAGATCGAAGATAG
* * * *
43397140 CAGATCTTGTTTTCATGTATT-AGCATGAAGTAGATTGAGGATAA
1 CAGATCTTGTCTTCATGTATTGA-CATGAAGTAGATCGAAGATAG
* * * * * *
43397184 CGGATCTTATCTTCCTGTACTGGCAGTGAAGTAGATCAAAGATAG
1 CAGATCTTGTCTTCATGTATTGACA-TGAAGTAGATCGAAGATAG
43397229 CAGATCTTGTCTTC
1 CAGATCTTGTCTTC
43397243 CCATATTGGT
Statistics
Matches: 328, Mismatches: 74, Indels: 23
0.77 0.17 0.05
Matches are distributed among these distances:
43 3 0.01
44 196 0.60
45 127 0.39
46 2 0.01
ACGTcount: A:0.31, C:0.14, G:0.23, T:0.32
Consensus pattern (44 bp):
CAGATCTTGTCTTCATGTATTGACATGAAGTAGATCGAAGATAG
Found at i:43396938 original size:89 final size:89
Alignment explanation
Indices: 43396787--43397242 Score: 462
Period size: 89 Copynumber: 5.1 Consensus size: 89
43396777 AAAAGCAACA
* * *
43396787 GATCTTGTCTTCATGTATTGACATGAAGTAGATTGAAGATAGCAAATCTTGTCTTCTCATACTGG
1 GATCTTGTCTTCATGTATTGACATGAAGTAGATCGAAGATAGCAGATCTTGTCTTCTCGTACTGG
* *
43396852 TGGTGAAGTAGATCAAAGATAATG
66 TCGTGAAGTAGATCAAAGATAACG
* * *
43396876 GATCTTGTCTTCATGTATTGACATGAAATAGATCGAAGATAGCAAATCTTGTCTTCTCATACTGG
1 GATCTTGTCTTCATGTATTGACATGAAGTAGATCGAAGATAGCAGATCTTGTCTTCTCGTACTGG
* *
43396941 TGGTGAAGTAGATCAAAGATAATG
66 TCGTGAAGTAGATCAAAGATAACG
*
43396965 GATCTTGTCTTCATGTATTGACATGAAGTAGATC-AGAGATAGTAGATCTTGTCTTCAT-GTA-T
1 GATCTTGTCTTCATGTATTGACATGAAGTAGATCGA-AGATAGCAGATCTTGTCTTC-TCGTACT
* * * * * *
43397027 TGACATGAAGTAGATCGAAGATAGCA
64 GGTCGTGAAGTAGATCAAAGATAACG
* ** * * * * *
43397053 GATATTGTCTTCCCGTACTGGCAGCGAAGTAGATCGAAGAAAGCAGATCTTGTCTTCAT-GTATT
1 GATCTTGTCTTCATGTATTGACA-TGAAGTAGATCGAAGATAGCAGATCTTGTCTTC-TCGTACT
* *
43397117 GG-CGTGAAGTAGATCGAAGA-AAGCA
64 GGTCGTGAAGTAGATCAAAGATAA-CG
* * * * * *
43397142 GATCTTGTTTTCATGTATT-AGCATGAAGTAGATTGAGGATAACGGATCTTATCTTC-CTGTACT
1 GATCTTGTCTTCATGTATTGA-CATGAAGTAGATCGAAGATAGCAGATCTTGTCTTCTC-GTACT
* *
43397205 GG-CAGTGAAGTAGATCAAAGATAGCA
64 GGTC-GTGAAGTAGATCAAAGATAACG
43397231 GATCTTGTCTTC
1 GATCTTGTCTTC
43397243 CCATATTGGT
Statistics
Matches: 314, Mismatches: 42, Indels: 22
0.83 0.11 0.06
Matches are distributed among these distances:
88 72 0.23
89 237 0.75
90 5 0.02
ACGTcount: A:0.31, C:0.14, G:0.23, T:0.32
Consensus pattern (89 bp):
GATCTTGTCTTCATGTATTGACATGAAGTAGATCGAAGATAGCAGATCTTGTCTTCTCGTACTGG
TCGTGAAGTAGATCAAAGATAACG
Found at i:43397250 original size:133 final size:133
Alignment explanation
Indices: 43396785--43397270 Score: 500
Period size: 133 Copynumber: 3.7 Consensus size: 133
43396775 TGAAAAGCAA
* * * ** * * *
43396785 CAGATCTTGTCTTCATGTATTGACA-TGAAGTAGATTGAAGATAGCAAATCTTGTCTTCTCATAC
1 CAGATCTTGTCTTCCTGTACTGGCAGTGAAGTAGATCAAAGATAGCAGATCTTGTCTTCACATAT
* * *
43396849 TGGTGGTGAAGTAGATCAAAGATAATG-GATCTTGTCTTCATGTATTGACATGAAATAGATCGAA
66 TGGTCGTGAAGTAGATCGAAGA-AA-GAGATCTTGTCTTCATGTATTGACATGAAGTAGATCGAA
43396913 GATAG
129 GATAG
* * ** *** **
43396918 CAAATCTTGTCTT-CTCATACTGGTGGTGAAGTAGATCAAAGATAATGGATCTTGTCTTCATGTA
1 CAGATCTTGTCTTCCT-GTACTGGCAGTGAAGTAGATCAAAGATAGCAGATCTTGTCTTCACATA
* * *
43396982 TT-GACATGAAGTAGATC-AGAGATAGTAGATCTTGTCTTCATGTATTGACATGAAGTAGATCGA
65 TTGGTCGTGAAGTAGATCGA-AGAAAG-AGATCTTGTCTTCATGTATTGACATGAAGTAGATCGA
43397045 AGATAG
128 AGATAG
* * * * * **
43397051 CAGATATTGTCTTCCCGTACTGGCAGCGAAGTAGATCGAAGAAAGCAGATCTTGTCTTCATGTAT
1 CAGATCTTGTCTTCCTGTACTGGCAGTGAAGTAGATCAAAGATAGCAGATCTTGTCTTCACATAT
* * *
43397116 TGG-CGTGAAGTAGATCGAAGAAAGCAGATCTTGTTTTCATGTATT-AGCATGAAGTAGATTGAG
66 TGGTCGTGAAGTAGATCGAAGAAAG-AGATCTTGTCTTCATGTATTGA-CATGAAGTAGATCGAA
*
43397179 GATAA
129 GATAG
* * *
43397184 CGGATCTTATCTTCCTGTACTGGCAGTGAAGTAGATCAAAGATAGCAGATCTTGTCTTCCCATAT
1 CAGATCTTGTCTTCCTGTACTGGCAGTGAAGTAGATCAAAGATAGCAGATCTTGTCTTCACATAT
* * *
43397249 TGGTGGCGAAGTCGATCGAAGA
66 TGGTCGTGAAGTAGATCGAAGA
43397271 TACAAGTCTT
Statistics
Matches: 289, Mismatches: 54, Indels: 19
0.80 0.15 0.05
Matches are distributed among these distances:
131 1 0.00
132 4 0.01
133 236 0.82
134 48 0.17
ACGTcount: A:0.31, C:0.14, G:0.24, T:0.31
Consensus pattern (133 bp):
CAGATCTTGTCTTCCTGTACTGGCAGTGAAGTAGATCAAAGATAGCAGATCTTGTCTTCACATAT
TGGTCGTGAAGTAGATCGAAGAAAGAGATCTTGTCTTCATGTATTGACATGAAGTAGATCGAAGA
TAG
Found at i:43398876 original size:23 final size:23
Alignment explanation
Indices: 43398850--43398916 Score: 82
Period size: 23 Copynumber: 2.9 Consensus size: 23
43398840 ATACACGCAT
*
43398850 TGTTTTTATACAATATATATGCA
1 TGTTTTTATATAATATATATGCA
*
43398873 TGTTTTTATATAATATACT-CGCA
1 TGTTTTTATATAATATA-TATGCA
*
43398896 TGGTTTTTTTATAATATATAT
1 T-GTTTTTATATAATATATAT
43398917 ATATGCATCT
Statistics
Matches: 37, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
23 21 0.57
24 16 0.43
ACGTcount: A:0.31, C:0.07, G:0.09, T:0.52
Consensus pattern (23 bp):
TGTTTTTATATAATATATATGCA
Found at i:43402187 original size:14 final size:14
Alignment explanation
Indices: 43402168--43402207 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
43402158 TTGATTGCCA
43402168 GTAAAATGTTTTCC
1 GTAAAATGTTTTCC
* *
43402182 GTAAAATGATTTCT
1 GTAAAATGTTTTCC
*
43402196 GGAAAATGTTTT
1 GTAAAATGTTTT
43402208 ACTTTTTTGT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.33, C:0.07, G:0.17, T:0.42
Consensus pattern (14 bp):
GTAAAATGTTTTCC
Found at i:43410250 original size:21 final size:21
Alignment explanation
Indices: 43410221--43410260 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
43410211 ATAAGTTAGG
43410221 TTAAGATAATAAATAAAAGGT
1 TTAAGATAATAAATAAAAGGT
* **
43410242 TTAATATAATCTATAAAAG
1 TTAAGATAATAAATAAAAG
43410261 AGAAAATTGG
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.55, C:0.03, G:0.10, T:0.33
Consensus pattern (21 bp):
TTAAGATAATAAATAAAAGGT
Found at i:43410299 original size:16 final size:16
Alignment explanation
Indices: 43410274--43410308 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
43410264 AAATTGGAAT
*
43410274 TAAAATAATTTTAAAA
1 TAAAAAAATTTTAAAA
43410290 TAAAAAAATTTTAAAA
1 TAAAAAAATTTTAAAA
43410306 TAA
1 TAA
43410309 CCTATATCAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (16 bp):
TAAAAAAATTTTAAAA
Found at i:43410509 original size:6 final size:6
Alignment explanation
Indices: 43410498--43410546 Score: 57
Period size: 6 Copynumber: 8.0 Consensus size: 6
43410488 GGTGACACAG
43410498 AAATAA AAATAAA AAATAA AAA-ATA AAAT-A AAATAA AAATAA TAAATAA
1 AAATAA AAAT-AA AAATAA AAATA-A AAATAA AAATAA AAATAA -AAATAA
43410547 TAAAACGAAG
Statistics
Matches: 38, Mismatches: 0, Indels: 9
0.81 0.00 0.19
Matches are distributed among these distances:
5 6 0.16
6 20 0.53
7 12 0.32
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.18
Consensus pattern (6 bp):
AAATAA
Found at i:43410514 original size:7 final size:7
Alignment explanation
Indices: 43410498--43410551 Score: 56
Period size: 7 Copynumber: 7.4 Consensus size: 7
43410488 GGTGACACAG
43410498 AAAT-AA
1 AAATAAA
43410504 AAATAAA
1 AAATAAA
43410511 AAATAAA
1 AAATAAA
43410518 AAATAAA
1 AAATAAA
*
43410525 ATAAAATAA
1 A-AATA-AA
*
43410534 AAATAAT
1 AAATAAA
43410541 AAATAATA
1 AAATAA-A
43410549 AAA
1 AAA
43410552 CGAAGTATAT
Statistics
Matches: 40, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
6 4 0.10
7 24 0.60
8 9 0.22
9 3 0.08
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (7 bp):
AAATAAA
Found at i:43410527 original size:19 final size:19
Alignment explanation
Indices: 43410498--43410543 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 19
43410488 GGTGACACAG
43410498 AAATAAAAATAAAA-AATAAA
1 AAAT-AAAATAAAATAA-AAA
43410518 AAATAAAATAAAATAAAAA
1 AAATAAAATAAAATAAAAA
*
43410537 TAATAAA
1 AAATAAA
43410544 TAATAAAACG
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
19 18 0.75
20 6 0.25
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (19 bp):
AAATAAAATAAAATAAAAA
Found at i:43412216 original size:50 final size:50
Alignment explanation
Indices: 43412162--43412621 Score: 267
Period size: 50 Copynumber: 9.2 Consensus size: 50
43412152 CGCTGCTGTA
* * *
43412162 GCTTTAATATTTTTAACCGCAATGTCAGGGAGGCAAGATTCACCATTATG
1 GCTTTAATCTTTTTAACCGCAATGTCAGGGAGGCAAGATTCACCGTTGTG
* * * **** * * * * ** * * *
43412212 GCTTTAATCTGTTCAACTGCACCACCTGAGAGGTAGGATTTGCTGCTGTA
1 GCTTTAATCTTTTTAACCGCAATGTCAGGGAGGCAAGATTCACCGTTGTG
*
43412262 GCTTTAATCTTTTTAACCGCAATGTCAGGGAGGAAAGATTCACCGTTGTG
1 GCTTTAATCTTTTTAACCGCAATGTCAGGGAGGCAAGATTCACCGTTGTG
** * ** * * * * * * * *
43412312 GCTTTAAT-TTGTTCCACTGCACCGCCTGGGAGGTAGGATTCGCTGCTGTA
1 GCTTTAATCTT-TTTAACCGCAATGTCAGGGAGGCAAGATTCACCGTTGTG
43412362 GCTTTAATCTTTTTAACCGCAATGTCAGGGAGGCAAGATTCACCGTTGTG
1 GCTTTAATCTTTTTAACCGCAATGTCAGGGAGGCAAGATTCACCGTTGTG
* *** * ** * ** * * * *
43412412 GCTTTAATCTATTCCGCTGCACCGCCTTGGAGGTAAGATTCACTGCTGTA
1 GCTTTAATCTTTTTAACCGCAATGTCAGGGAGGCAAGATTCACCGTTGTG
*
43412462 GCTTTAATCTTTTTAACCGCAGTGTCAGGG-GAGCAAGATTCACCGTTGTG
1 GCTTTAATCTTTTTAACCGCAATGTCAGGGAG-GCAAGATTCACCGTTGTG
* ** * * * * * * * * * *
43412512 GCTTTAATCTGTTCCACTGCATTGCCAGGGAAGTAACACTCGCTGCTGTG
1 GCTTTAATCTTTTTAACCGCAATGTCAGGGAGGCAAGATTCACCGTTGTG
* * * * * * * *
43412562 GCTTTAGTCTTTTTAACTGCAATATCGGGGAAGCAAGATACGCCGTCGTG
1 GCTTTAATCTTTTTAACCGCAATGTCAGGGAGGCAAGATTCACCGTTGTG
43412612 GCTTTAATCT
1 GCTTTAATCT
43412622 GCTCCACTGC
Statistics
Matches: 288, Mismatches: 118, Indels: 8
0.70 0.29 0.02
Matches are distributed among these distances:
49 3 0.01
50 283 0.98
51 2 0.01
ACGTcount: A:0.23, C:0.22, G:0.24, T:0.32
Consensus pattern (50 bp):
GCTTTAATCTTTTTAACCGCAATGTCAGGGAGGCAAGATTCACCGTTGTG
Found at i:43412633 original size:100 final size:100
Alignment explanation
Indices: 43412104--43412650 Score: 711
Period size: 100 Copynumber: 5.5 Consensus size: 100
43412094 ATCTGTTCCA
* *
43412104 CGTTGTGGCTTTAATCTGCTT-CACTGCACTGCCTGAGAGTGTAAGATTCGCTGCTGTAGCTTTA
1 CGTTGTGGCTTTAATCTG-TTCCACTGCACCGCCTGGGAG-GTAAGATTCGCTGCTGTAGCTTTA
*
43412168 ATATTTTTAACCGCAATGTCAGGGAGGCAAGATTCAC
64 ATCTTTTTAACCGCAATGTCAGGGAGGCAAGATTCAC
* * * * * * *
43412205 CATTATGGCTTTAATCTGTTCAACTGCACCACCTGAGAGGTAGGATTTGCTGCTGTAGCTTTAAT
1 CGTTGTGGCTTTAATCTGTTCCACTGCACCGCCTGGGAGGTAAGATTCGCTGCTGTAGCTTTAAT
*
43412270 CTTTTTAACCGCAATGTCAGGGAGGAAAGATTCAC
66 CTTTTTAACCGCAATGTCAGGGAGGCAAGATTCAC
* *
43412305 CGTTGTGGCTTTAATTTGTTCCACTGCACCGCCTGGGAGGTAGGATTCGCTGCTGTAGCTTTAAT
1 CGTTGTGGCTTTAATCTGTTCCACTGCACCGCCTGGGAGGTAAGATTCGCTGCTGTAGCTTTAAT
43412370 CTTTTTAACCGCAATGTCAGGGAGGCAAGATTCAC
66 CTTTTTAACCGCAATGTCAGGGAGGCAAGATTCAC
* * * *
43412405 CGTTGTGGCTTTAATCTATTCCGCTGCACCGCCTTGGAGGTAAGATTCACTGCTGTAGCTTTAAT
1 CGTTGTGGCTTTAATCTGTTCCACTGCACCGCCTGGGAGGTAAGATTCGCTGCTGTAGCTTTAAT
*
43412470 CTTTTTAACCGCAGTGTCAGGG-GAGCAAGATTCAC
66 CTTTTTAACCGCAATGTCAGGGAG-GCAAGATTCAC
** * * * * * *
43412505 CGTTGTGGCTTTAATCTGTTCCACTGCATTGCCAGGGAAGTAACACTCGCTGCTGTGGCTTTAGT
1 CGTTGTGGCTTTAATCTGTTCCACTGCACCGCCTGGGAGGTAAGATTCGCTGCTGTAGCTTTAAT
* * * * * *
43412570 CTTTTTAACTGCAATATCGGGGAAGCAAGATACGC
66 CTTTTTAACCGCAATGTCAGGGAGGCAAGATTCAC
* * ** * *
43412605 CGTCGTGGCTTTAATCTGCTCCACTGCATTGCCAGGGAGATAAGAT
1 CGTTGTGGCTTTAATCTGTTCCACTGCACCGCCTGGGAGGTAAGAT
43412651 CTGAAATTCT
Statistics
Matches: 394, Mismatches: 49, Indels: 7
0.88 0.11 0.02
Matches are distributed among these distances:
99 1 0.00
100 362 0.92
101 31 0.08
ACGTcount: A:0.22, C:0.22, G:0.24, T:0.32
Consensus pattern (100 bp):
CGTTGTGGCTTTAATCTGTTCCACTGCACCGCCTGGGAGGTAAGATTCGCTGCTGTAGCTTTAAT
CTTTTTAACCGCAATGTCAGGGAGGCAAGATTCAC
Found at i:43412687 original size:46 final size:46
Alignment explanation
Indices: 43412637--43413357 Score: 222
Period size: 44 Copynumber: 16.4 Consensus size: 46
43412627 ACTGCATTGC
** *
43412637 CAGGGAGATAAGATCTGAAATTCTTCGGTCTATTCCACTGTAACCT
1 CAGGGAGATAAGATCTGAAATTCTTCAATCTATTCCACTGTAATCT
** ***
43412683 CA-GG-GATAAGATCCT-TTATT-TT-AATCCGCTCCACTGTAATCT
1 CAGGGAGATAAGAT-CTGAAATTCTTCAATCTATTCCACTGTAATCT
* * * * * **
43412725 TAGGGAGATAGGAT-T-ACCA-GCTTCAATCTGTTCTTCTGTAATCT
1 CAGGGAGATAAGATCTGA-AATTCTTCAATCTATTCCACTGTAATCT
** *
43412769 CAGGGAGATAAGATCTGAAATTCTTCGGTCTATTGCACTGTAATCT
1 CAGGGAGATAAGATCTGAAATTCTTCAATCTATTCCACTGTAATCT
* * * * * * *
43412815 CAGGGAAATAAGACCTG--A---TGCGATCTACTCTACTATAA-CTT
1 CAGGGAGATAAGATCTGAAATTCTTCAATCTATTCCACTGTAATC-T
* ** * ** ** *
43412856 TAGAAAGAGAAGATCCT-TTATT-TT-AATCTGCTCCACTTTAATCT
1 CAGGGAGATAAGAT-CTGAAATTCTTCAATCTATTCCACTGTAATCT
* * * ** * *
43412900 CAGGGAGATAGGAT-T--ACTAGCTTCAATCTGCTCCGCAGTAATCT
1 CAGGGAGATAAGATCTGAAAT-TCTTCAATCTATTCCACTGTAATCT
* **
43412944 AAGGGAGATAAGATCTGAAATTCTTCGGTCTATTCCACTGTAATCT
1 CAGGGAGATAAGATCTGAAATTCTTCAATCTATTCCACTGTAATCT
* * * * *
43412990 CAGGGAGATAAGACCTG--A-T-GT-GATCTACTCTACTGTAA-CTT
1 CAGGGAGATAAGATCTGAAATTCTTCAATCTATTCCACTGTAATC-T
* ** ***
43413031 CAGAGAGATAAGATACT-TTATT-TT-AATCCGCTCCACTGTAATCT
1 CAGGGAGATAAGAT-CTGAAATTCTTCAATCTATTCCACTGTAATCT
* * * *
43413075 CAGAGAGATAGGAT-T-ACCAA--CTTCAATCTACTCCACTGTAACCT
1 CAGGGAGATAAGATCTGA--AATTCTTCAATCTATTCCACTGTAATCT
* **
43413119 CAGGGAGATAAGATCTGAAATTTTTCGGTCTATTCCACTGTAATCT
1 CAGGGAGATAAGATCTGAAATTCTTCAATCTATTCCACTGTAATCT
* * ** * * * *
43413165 TAGGGAGACAAGGCCTG--A---TGCGATCTACTCTACTGTAA-CTT
1 CAGGGAGATAAGATCTGAAATTCTTCAATCTATTCCACTGTAATC-T
* ***
43413206 CAGAGAGATAAGATCCTTG--ATT-TT-AATCCGCTCCACTGTAATCT
1 CAGGGAGATAAGAT-C-TGAAATTCTTCAATCTATTCCACTGTAATCT
* * ** **
43413250 TAGGGAGATAGGAT-T-ACCAA--CTTCAATCTGCTCCGTTGTAATCT
1 CAGGGAGATAAGATCTGA--AATTCTTCAATCTATTCCACTGTAATCT
* **
43413294 CAGGAAGATAAGATCTGAAATTCTTCGGTCTATTCCACTGTAATCT
1 CAGGGAGATAAGATCTGAAATTCTTCAATCTATTCCACTGTAATCT
* *
43413340 CAGGGAGACAAGACCTGA
1 CAGGGAGATAAGATCTGA
43413358 TGCGATCTAC
Statistics
Matches: 494, Mismatches: 129, Indels: 104
0.68 0.18 0.14
Matches are distributed among these distances:
40 3 0.01
41 78 0.16
42 24 0.05
43 19 0.04
44 218 0.44
45 14 0.03
46 136 0.28
47 2 0.00
ACGTcount: A:0.30, C:0.21, G:0.19, T:0.31
Consensus pattern (46 bp):
CAGGGAGATAAGATCTGAAATTCTTCAATCTATTCCACTGTAATCT
Found at i:43412985 original size:175 final size:175
Alignment explanation
Indices: 43412673--43413482 Score: 1257
Period size: 175 Copynumber: 4.6 Consensus size: 175
43412663 GGTCTATTCC
* *
43412673 ACTGTAACCTCAG-G-GATAAGATCCTTTATTTTAATCCGCTCCACTGTAATCTTAGGGAGATAG
1 ACTGTAACTTCAGAGAGATAAGATCCTTTATTTTAATCCGCTCCACTGTAATCTCAGGGAGATAG
* **
43412736 GATTACCAGCTTCAATCTGTTCTTCTGTAATCTCAGGGAGATAAGATCTGAAATTCTTCGGTCTA
66 GATTACCAGCTTCAATCTGCTCCGCTGTAATCTCAGGGAGATAAGATCTGAAATTCTTCGGTCTA
* * *
43412801 TTGCACTGTAATCTCAGGGAAATAAGACCTGATGCGATCTACTCT
131 TTCCACTGTAATCTCAGGGAGACAAGACCTGATGCGATCTACTCT
* * * * * *
43412846 ACTATAACTTTAGAAAGAGAAGATCCTTTATTTTAATCTGCTCCACTTTAATCTCAGGGAGATAG
1 ACTGTAACTTCAGAGAGATAAGATCCTTTATTTTAATCCGCTCCACTGTAATCTCAGGGAGATAG
* * *
43412911 GATTACTAGCTTCAATCTGCTCCGCAGTAATCTAAGGGAGATAAGATCTGAAATTCTTCGGTCTA
66 GATTACCAGCTTCAATCTGCTCCGCTGTAATCTCAGGGAGATAAGATCTGAAATTCTTCGGTCTA
* *
43412976 TTCCACTGTAATCTCAGGGAGATAAGACCTGATGTGATCTACTCT
131 TTCCACTGTAATCTCAGGGAGACAAGACCTGATGCGATCTACTCT
* *
43413021 ACTGTAACTTCAGAGAGATAAGATACTTTATTTTAATCCGCTCCACTGTAATCTCAGAGAGATAG
1 ACTGTAACTTCAGAGAGATAAGATCCTTTATTTTAATCCGCTCCACTGTAATCTCAGGGAGATAG
* * * * *
43413086 GATTACCAACTTCAATCTACTCCACTGTAACCTCAGGGAGATAAGATCTGAAATTTTTCGGTCTA
66 GATTACCAGCTTCAATCTGCTCCGCTGTAATCTCAGGGAGATAAGATCTGAAATTCTTCGGTCTA
* *
43413151 TTCCACTGTAATCTTAGGGAGACAAGGCCTGATGCGATCTACTCT
131 TTCCACTGTAATCTCAGGGAGACAAGACCTGATGCGATCTACTCT
* *
43413196 ACTGTAACTTCAGAGAGATAAGATCCTTGATTTTAATCCGCTCCACTGTAATCTTAGGGAGATAG
1 ACTGTAACTTCAGAGAGATAAGATCCTTTATTTTAATCCGCTCCACTGTAATCTCAGGGAGATAG
* * *
43413261 GATTACCAACTTCAATCTGCTCCGTTGTAATCTCAGGAAGATAAGATCTGAAATTCTTCGGTCTA
66 GATTACCAGCTTCAATCTGCTCCGCTGTAATCTCAGGGAGATAAGATCTGAAATTCTTCGGTCTA
43413326 TTCCACTGTAATCTCAGGGAGACAAGACCTGATGCGATCTACTCT
131 TTCCACTGTAATCTCAGGGAGACAAGACCTGATGCGATCTACTCT
* * *
43413371 ACTGTAACTTTAGAGAGATAAGATCTTTTATTTTAATTCGCTCCACTGTAATCTCAGGGAGATAG
1 ACTGTAACTTCAGAGAGATAAGATCCTTTATTTTAATCCGCTCCACTGTAATCTCAGGGAGATAG
*
43413436 GATTACTAGCTTCAATCAT-CTCCGCTGTAATCTCAGGGAGATAAGAT
66 GATTACCAGCTTCAATC-TGCTCCGCTGTAATCTCAGGGAGATAAGAT
43413483 TTCTGGCTTC
Statistics
Matches: 576, Mismatches: 58, Indels: 4
0.90 0.09 0.01
Matches are distributed among these distances:
173 10 0.02
175 565 0.98
176 1 0.00
ACGTcount: A:0.30, C:0.20, G:0.19, T:0.31
Consensus pattern (175 bp):
ACTGTAACTTCAGAGAGATAAGATCCTTTATTTTAATCCGCTCCACTGTAATCTCAGGGAGATAG
GATTACCAGCTTCAATCTGCTCCGCTGTAATCTCAGGGAGATAAGATCTGAAATTCTTCGGTCTA
TTCCACTGTAATCTCAGGGAGACAAGACCTGATGCGATCTACTCT
Found at i:43413259 original size:44 final size:43
Alignment explanation
Indices: 43412665--43413482 Score: 210
Period size: 44 Copynumber: 18.7 Consensus size: 43
43412655 AATTCTTCGG
* * * *
43412665 TCTATTCCACTGTAACCTCA-GG-GATAAGATCCTTTATTTTAA
1 TCTACTCCACTGTAATCTTAGGGAGATAAGATCC-TGATTTTAA
** * * * *
43412707 TCCGCTCCACTGTAATCTTAGGGAGATAGGATTACCAG-CTTCAA
1 TCTACTCCACTGTAATCTTAGGGAGATAAGA-T-CCTGATTTTAA
** ** * **
43412751 TCTGTTCTTCTGTAATCTCAGGGAGATAAGAT-CTGAAATTCTTCGG
1 TCTACTCCACTGTAATCTTAGGGAGATAAGATCCTG--ATT-TT-AA
* * * * ***
43412797 TCTATTGCACTGTAATCTCAGGGAAATAAGA-CCTGA-TGCGA
1 TCTACTCCACTGTAATCTTAGGGAGATAAGATCCTGATTTTAA
* * ** * *
43412838 TCTACTCTACTATAA-CTTTAGAAAGAGAAGATCCTTTATTTTAA
1 TCTACTCCACTGTAATC-TTAGGGAGATAAGATCC-TGATTTTAA
* * * * * * *
43412882 TCTGCTCCACTTTAATCTCAGGGAGATAGGATTACT-AGCTTCAA
1 TCTACTCCACTGTAATCTTAGGGAGATAAGA-TCCTGA-TTTTAA
* * * * **
43412926 TCTGCTCCGCAGTAATCTAAGGGAGATAAGAT-CTGAAATTCTTCGG
1 TCTACTCCACTGTAATCTTAGGGAGATAAGATCCTG--ATT-TT-AA
* * * *
43412972 TCTATTCCACTGTAATCTCAGGGAGATAAGA-CCTGA-TGTGA
1 TCTACTCCACTGTAATCTTAGGGAGATAAGATCCTGATTTTAA
* * * *
43413013 TCTACTCTACTGTAA-CTTCAGAGAGATAAGATACTTTATTTTAA
1 TCTACTCCACTGTAATCTT-AGGGAGATAAGAT-CCTGATTTTAA
** * * * * * *
43413057 TCCGCTCCACTGTAATCTCAGAGAGATAGGATTACC-AACTTCAA
1 TCTACTCCACTGTAATCTTAGGGAGATAAGA-T-CCTGATTTTAA
* * **
43413101 TCTACTCCACTGTAACCTCAGGGAGATAAGAT-CTGAAATTTTTCGG
1 TCTACTCCACTGTAATCTTAGGGAGATAAGATCCTG--A-TTTT-AA
* * * ***
43413147 TCTATTCCACTGTAATCTTAGGGAGACAAG-GCCTGA-TGCGA
1 TCTACTCCACTGTAATCTTAGGGAGATAAGATCCTGATTTTAA
* *
43413188 TCTACTCTACTGTAA-CTTCAGAGAGATAAGATCCTTGATTTTAA
1 TCTACTCCACTGTAATCTT-AGGGAGATAAGATCC-TGATTTTAA
** * * * *
43413232 TCCGCTCCACTGTAATCTTAGGGAGATAGGATTACC-AACTTCAA
1 TCTACTCCACTGTAATCTTAGGGAGATAAGA-T-CCTGATTTTAA
* ** * * **
43413276 TCTGCTCCGTTGTAATCTCAGGAAGATAAGAT-CTGAAATTCTTCGG
1 TCTACTCCACTGTAATCTTAGGGAGATAAGATCCTG--ATT-TT-AA
* * * ***
43413322 TCTATTCCACTGTAATCTCAGGGAGACAAGA-CCTGA-TGCGA
1 TCTACTCCACTGTAATCTTAGGGAGATAAGATCCTGATTTTAA
* * * *
43413363 TCTACTCTACTGTAA-CTTTAGAGAGATAAGATCTTTTATTTTAA
1 TCTACTCCACTGTAATC-TTAGGGAGATAAGATC-CTGATTTTAA
* * * * * *
43413407 T-TCGCTCCACTGTAATCTCAGGGAGATAGGATTACT-AGCTTCAA
1 TCT-ACTCCACTGTAATCTTAGGGAGATAAGA-TCCTGA-TTTTAA
* *
43413451 TC-ATCTCCGCTGTAATCTCAGGGAGATAAGAT
1 TCTA-CTCCACTGTAATCTTAGGGAGATAAGAT
43413483 TTCTGGCTTC
Statistics
Matches: 556, Mismatches: 162, Indels: 115
0.67 0.19 0.14
Matches are distributed among these distances:
40 7 0.01
41 98 0.18
42 24 0.04
43 23 0.04
44 264 0.47
45 21 0.04
46 119 0.21
ACGTcount: A:0.29, C:0.21, G:0.18, T:0.32
Consensus pattern (43 bp):
TCTACTCCACTGTAATCTTAGGGAGATAAGATCCTGATTTTAA
Found at i:43414935 original size:7 final size:7
Alignment explanation
Indices: 43414925--43414966 Score: 59
Period size: 7 Copynumber: 6.0 Consensus size: 7
43414915 CTATTTTTAC
43414925 TTTTTCA
1 TTTTTCA
43414932 TTTTTCA
1 TTTTTCA
43414939 TTTTTTCA
1 -TTTTTCA
43414947 -TTTTCA
1 TTTTTCA
*
43414953 CTTTTCA
1 TTTTTCA
43414960 TTTTTCA
1 TTTTTCA
43414967 CATTTTTTTT
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
6 6 0.19
7 19 0.59
8 7 0.22
ACGTcount: A:0.14, C:0.17, G:0.00, T:0.69
Consensus pattern (7 bp):
TTTTTCA
Found at i:43414936 original size:14 final size:14
Alignment explanation
Indices: 43414917--43414964 Score: 62
Period size: 15 Copynumber: 3.4 Consensus size: 14
43414907 TAGCCTCTCT
43414917 ATTTTTACTTTTTC
1 ATTTTTACTTTTTC
*
43414931 ATTTTTCATTTTTTC
1 ATTTTT-ACTTTTTC
*
43414946 ATTTTCAC-TTTTC
1 ATTTTTACTTTTTC
43414959 ATTTTT
1 ATTTTT
43414965 CACATTTTTT
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
13 10 0.34
14 7 0.24
15 12 0.41
ACGTcount: A:0.15, C:0.15, G:0.00, T:0.71
Consensus pattern (14 bp):
ATTTTTACTTTTTC
Found at i:43414941 original size:21 final size:21
Alignment explanation
Indices: 43414917--43414973 Score: 69
Period size: 21 Copynumber: 2.6 Consensus size: 21
43414907 TAGCCTCTCT
*
43414917 ATTTTTACTTTTTCATTTTTC
1 ATTTTTACTTTTTCACTTTTC
* *
43414938 ATTTTTTCATTTTCACTTTTC
1 ATTTTTACTTTTTCACTTTTC
43414959 ATTTTTCACATTTTT
1 ATTTTT-AC-TTTTT
43414974 TTTTGACTCA
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
21 24 0.83
22 1 0.03
23 4 0.14
ACGTcount: A:0.16, C:0.16, G:0.00, T:0.68
Consensus pattern (21 bp):
ATTTTTACTTTTTCACTTTTC
Found at i:43414965 original size:14 final size:15
Alignment explanation
Indices: 43414917--43414972 Score: 64
Period size: 14 Copynumber: 3.9 Consensus size: 15
43414907 TAGCCTCTCT
*
43414917 ATTTTT-ACTTTTTC
1 ATTTTTCACATTTTC
**
43414931 ATTTTTCATTTTTTC
1 ATTTTTCACATTTTC
43414946 A-TTTTCAC-TTTTC
1 ATTTTTCACATTTTC
43414959 ATTTTTCACATTTT
1 ATTTTTCACATTTT
43414973 TTTTTGACTC
Statistics
Matches: 37, Mismatches: 2, Indels: 5
0.84 0.05 0.11
Matches are distributed among these distances:
13 6 0.16
14 19 0.51
15 12 0.32
ACGTcount: A:0.16, C:0.16, G:0.00, T:0.68
Consensus pattern (15 bp):
ATTTTTCACATTTTC
Found at i:43415869 original size:18 final size:20
Alignment explanation
Indices: 43415846--43415886 Score: 68
Period size: 18 Copynumber: 2.1 Consensus size: 20
43415836 TGGCCTCTCC
43415846 TTTTTTTTC-CTTTTTTC-T
1 TTTTTTTTCTCTTTTTTCAT
43415864 TTTTTTTTCTCTTTTTTCAT
1 TTTTTTTTCTCTTTTTTCAT
43415884 TTT
1 TTT
43415887 CATTTTGACT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
18 9 0.43
19 8 0.38
20 4 0.19
ACGTcount: A:0.02, C:0.15, G:0.00, T:0.83
Consensus pattern (20 bp):
TTTTTTTTCTCTTTTTTCAT
Found at i:43420393 original size:21 final size:21
Alignment explanation
Indices: 43420364--43420403 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
43420354 ATAAGTTAGG
43420364 TTAAGATAATAAATAAAAGGT
1 TTAAGATAATAAATAAAAGGT
* **
43420385 TTAATATAATCTATAAAAG
1 TTAAGATAATAAATAAAAG
43420404 AGAAAATTGG
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.55, C:0.03, G:0.10, T:0.33
Consensus pattern (21 bp):
TTAAGATAATAAATAAAAGGT
Found at i:43420442 original size:16 final size:16
Alignment explanation
Indices: 43420417--43420451 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
43420407 AAATTGGAAT
*
43420417 TAAAATAATTTTAAAA
1 TAAAAAAATTTTAAAA
43420433 TAAAAAAATTTTAAAA
1 TAAAAAAATTTTAAAA
43420449 TAA
1 TAA
43420452 CCTATATCAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (16 bp):
TAAAAAAATTTTAAAA
Found at i:43420657 original size:7 final size:7
Alignment explanation
Indices: 43420641--43420689 Score: 57
Period size: 7 Copynumber: 7.1 Consensus size: 7
43420631 GGTGACACAG
43420641 AAAT-AA
1 AAATAAA
43420647 AAATAAA
1 AAATAAA
43420654 AAATAAA
1 AAATAAA
43420661 AAATAAA
1 AAATAAA
43420668 ATAA-AAA
1 A-AATAAA
*
43420675 TAATAAA
1 AAATAAA
*
43420682 TAATAAA
1 AAATAAA
43420689 A
1 A
43420690 CGAAGTATAT
Statistics
Matches: 38, Mismatches: 2, Indels: 5
0.84 0.04 0.11
Matches are distributed among these distances:
6 6 0.16
7 30 0.79
8 2 0.05
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.18
Consensus pattern (7 bp):
AAATAAA
Found at i:43420659 original size:13 final size:13
Alignment explanation
Indices: 43420641--43420684 Score: 63
Period size: 13 Copynumber: 3.5 Consensus size: 13
43420631 GGTGACACAG
43420641 AAATAAAAATAAA
1 AAATAAAAATAAA
*
43420654 AAATAAAAA-ATA
1 AAATAAAAATAAA
*
43420666 AAATAAAAATAAT
1 AAATAAAAATAAA
43420679 AAATAA
1 AAATAA
43420685 TAAAACGAAG
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
12 11 0.41
13 16 0.59
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.18
Consensus pattern (13 bp):
AAATAAAAATAAA
Found at i:43420671 original size:25 final size:26
Alignment explanation
Indices: 43420641--43420689 Score: 82
Period size: 25 Copynumber: 1.9 Consensus size: 26
43420631 GGTGACACAG
43420641 AAATAAAAATAAAAAATAA-AAAATA
1 AAATAAAAATAAAAAATAATAAAATA
*
43420666 AAATAAAAATAATAAATAATAAAA
1 AAATAAAAATAAAAAATAATAAAA
43420690 CGAAGTATAT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
25 18 0.82
26 4 0.18
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.18
Consensus pattern (26 bp):
AAATAAAAATAAAAAATAATAAAATA
Found at i:43421127 original size:9 final size:9
Alignment explanation
Indices: 43421109--43421267 Score: 50
Period size: 10 Copynumber: 16.1 Consensus size: 9
43421099 ACCCATTTTT
43421109 ATTTTAAAA
1 ATTTTAAAA
43421118 ATTTTTAAAA
1 A-TTTTAAAA
**
43421128 ATTAAAAAATA
1 ATT-TTAAA-A
43421139 TATTTTAAAAA
1 -ATTTT-AAAA
43421150 TATTTTAAAA
1 -ATTTTAAAA
*
43421160 ATATTTTAAA
1 AT-TTTAAAA
**
43421170 ATTAAAAAA
1 ATTTTAAAA
* **
43421179 AATAAAAAA
1 ATTTTAAAA
43421188 TTATTTTAAAA
1 --ATTTTAAAA
43421199 TTATTTT-AAA
1 --ATTTTAAAA
*
43421209 ATTTAAAAAA
1 ATTT-TAAAA
**
43421219 ATTAAAAAA
1 ATTTTAAAA
43421228 GTATTTTAAAA
1 --ATTTTAAAA
*
43421239 ATATTTTAAA
1 AT-TTTAAAA
*
43421249 ATTTAAAAA
1 ATTTTAAAA
*
43421258 AATTTAAAA
1 ATTTTAAAA
43421267 A
1 A
43421268 GTATGTAAAA
Statistics
Matches: 116, Mismatches: 21, Indels: 26
0.71 0.13 0.16
Matches are distributed among these distances:
8 4 0.03
9 37 0.32
10 41 0.35
11 28 0.24
12 6 0.05
ACGTcount: A:0.60, C:0.00, G:0.01, T:0.40
Consensus pattern (9 bp):
ATTTTAAAA
Found at i:43421150 original size:13 final size:13
Alignment explanation
Indices: 43421132--43421163 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
43421122 TTAAAAATTA
43421132 AAAAATATATTTT
1 AAAAATATATTTT
43421145 -AAAA-ATATTTT
1 AAAAATATATTTT
43421156 AAAAATAT
1 AAAAATAT
43421164 TTTAAAATTA
Statistics
Matches: 17, Mismatches: 0, Indels: 4
0.81 0.00 0.19
Matches are distributed among these distances:
11 7 0.41
12 8 0.47
13 2 0.12
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (13 bp):
AAAAATATATTTT
Found at i:43421154 original size:11 final size:11
Alignment explanation
Indices: 43421108--43421289 Score: 96
Period size: 11 Copynumber: 17.9 Consensus size: 11
43421098 GACCCATTTT
43421108 TATTTTAAAAA
1 TATTTTAAAAA
43421119 T-TTTT-AAAA
1 TATTTTAAAAA
**
43421128 -ATTAAAAAATA
1 TATTTTAAAA-A
43421139 TATTTTAAAAA
1 TATTTTAAAAA
43421150 TATTTTAAAAA
1 TATTTTAAAAA
43421161 TATTTT--AAA
1 TATTTTAAAAA
43421170 -A--TTAAAAA
1 TATTTTAAAAA
** *
43421178 -AAATAAAAAA
1 TATTTTAAAAA
*
43421188 TTATTTTAAAAT
1 -TATTTTAAAAA
43421200 TATTTT--AAA
1 TATTTTAAAAA
43421209 -A-TTTAAAAA
1 TATTTTAAAAA
* *
43421218 -AATTAAAAAA
1 TATTTTAAAAA
43421228 GTATTTTAAAAA
1 -TATTTTAAAAA
43421240 TATTTT--AAA
1 TATTTTAAAAA
43421249 -A-TTTAAAAA
1 TATTTTAAAAA
*
43421258 -AATTTAAAAA
1 TATTTTAAAAA
* *
43421268 GTATGTAAAAAA
1 -TATTTTAAAAA
43421280 TATTTTAAAA
1 TATTTTAAAA
43421290 TTAAAAAAAT
Statistics
Matches: 133, Mismatches: 18, Indels: 40
0.70 0.09 0.21
Matches are distributed among these distances:
6 2 0.02
7 6 0.05
8 7 0.05
9 22 0.17
10 28 0.21
11 40 0.30
12 28 0.21
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.40
Consensus pattern (11 bp):
TATTTTAAAAA
Found at i:43421226 original size:40 final size:40
Alignment explanation
Indices: 43421108--43421299 Score: 248
Period size: 40 Copynumber: 4.8 Consensus size: 40
43421098 GACCCATTTT
* *
43421108 TATTTTAAAAAT-TTTTAAAAATTAAAAAATATATTTTAAAAA-
1 TATTTTAAAAATATTTT-AAAATTTAAAAA-A-A-TTAAAAAAG
* *
43421150 TATTTTAAAAATATTTTAAAA-TTAAAAAAAATAAAAAAT
1 TATTTTAAAAATATTTTAAAATTTAAAAAAATTAAAAAAG
*
43421189 TATTTTAAAATTATTTTAAAATTTAAAAAAATTAAAAAAG
1 TATTTTAAAAATATTTTAAAATTTAAAAAAATTAAAAAAG
*
43421229 TATTTTAAAAATATTTTAAAATTTAAAAAAATTTAAAAAG
1 TATTTTAAAAATATTTTAAAATTTAAAAAAATTAAAAAAG
* *
43421269 TATGTAAAAAATATTTTAAAA-TTAAAAAAAT
1 TATTTTAAAAATATTTTAAAATTTAAAAAAAT
43421300 AAATATATTT
Statistics
Matches: 137, Mismatches: 10, Indels: 9
0.88 0.06 0.06
Matches are distributed among these distances:
38 6 0.04
39 31 0.23
40 74 0.54
41 6 0.04
42 16 0.12
43 4 0.03
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (40 bp):
TATTTTAAAAATATTTTAAAATTTAAAAAAATTAAAAAAG
Found at i:43427264 original size:20 final size:21
Alignment explanation
Indices: 43427239--43427278 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
43427229 ACATAATTCG
*
43427239 ATATTATA-CTATTTCAAACC
1 ATATTATATATATTTCAAACC
43427259 ATATTATATATATTTCAAAC
1 ATATTATATATATTTCAAAC
43427279 GTAATTTGGA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 8 0.44
21 10 0.56
ACGTcount: A:0.42, C:0.15, G:0.00, T:0.42
Consensus pattern (21 bp):
ATATTATATATATTTCAAACC
Found at i:43427706 original size:26 final size:26
Alignment explanation
Indices: 43427677--43427739 Score: 83
Period size: 26 Copynumber: 2.4 Consensus size: 26
43427667 TAAGTAAATC
43427677 AAATTATTAAATA-CATAAATTTATAT
1 AAATTATTAAATATCATAAATTTA-AT
* *
43427703 AAATTTTTATATATCATAAATTTAAT
1 AAATTATTAAATATCATAAATTTAAT
*
43427729 AAATTAATAAA
1 AAATTATTAAA
43427740 ACTTGGTTTA
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
26 21 0.68
27 10 0.32
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.43
Consensus pattern (26 bp):
AAATTATTAAATATCATAAATTTAAT
Found at i:43428547 original size:13 final size:13
Alignment explanation
Indices: 43428526--43428576 Score: 57
Period size: 13 Copynumber: 3.9 Consensus size: 13
43428516 AATTCTTCAT
*
43428526 TGCTCTTGAAAAG
1 TGCTTTTGAAAAG
*
43428539 TGCTTTTGAAAAT
1 TGCTTTTGAAAAG
* *
43428552 TGCTATGGAAAAG
1 TGCTTTTGAAAAG
*
43428565 TACTTTTGAAAA
1 TGCTTTTGAAAA
43428577 TTTTGATTAT
Statistics
Matches: 30, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
13 30 1.00
ACGTcount: A:0.35, C:0.10, G:0.20, T:0.35
Consensus pattern (13 bp):
TGCTTTTGAAAAG
Found at i:43428553 original size:26 final size:26
Alignment explanation
Indices: 43428524--43428578 Score: 83
Period size: 26 Copynumber: 2.1 Consensus size: 26
43428514 CCAATTCTTC
* * *
43428524 ATTGCTCTTGAAAAGTGCTTTTGAAA
1 ATTGCTATGGAAAAGTACTTTTGAAA
43428550 ATTGCTATGGAAAAGTACTTTTGAAA
1 ATTGCTATGGAAAAGTACTTTTGAAA
43428576 ATT
1 ATT
43428579 TTGATTATTT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.35, C:0.09, G:0.18, T:0.38
Consensus pattern (26 bp):
ATTGCTATGGAAAAGTACTTTTGAAA
Found at i:43430707 original size:72 final size:72
Alignment explanation
Indices: 43430624--43430788 Score: 226
Period size: 72 Copynumber: 2.3 Consensus size: 72
43430614 AAAATCACAT
* *
43430624 ATAAACAACTATTGATAAAAATA-ATTTAGTAAAAAAT-AAGTAGAACATAAATTCAATATCTAA
1 ATAAACAACTATTGATAAAAATAGA-TTA-CAAAAAATCAAGTAGAACATAAATTCAATATCCAA
*
43430687 AGACCAAAC
64 AAACCAAAC
* * * *
43430696 ATAAACAACTATTAATAAAACTAGATTACACATAATCAAGTAGAACATAAATTCAATATCCAAAA
1 ATAAACAACTATTGATAAAAATAGATTACAAAAAATCAAGTAGAACATAAATTCAATATCCAAAA
43430761 ACCAAAC
66 ACCAAAC
*
43430768 ATAAATAACTATTGATAAAAA
1 ATAAACAACTATTGATAAAAA
43430789 CATACTTCGT
Statistics
Matches: 81, Mismatches: 10, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
71 5 0.06
72 75 0.93
73 1 0.01
ACGTcount: A:0.57, C:0.13, G:0.05, T:0.24
Consensus pattern (72 bp):
ATAAACAACTATTGATAAAAATAGATTACAAAAAATCAAGTAGAACATAAATTCAATATCCAAAA
ACCAAAC
Found at i:43432017 original size:20 final size:20
Alignment explanation
Indices: 43431994--43432108 Score: 68
Period size: 20 Copynumber: 5.2 Consensus size: 20
43431984 AACTATATAC
43431994 ATGAACAAATAACAGTATTA
1 ATGAACAAATAACAGTATTA
* * * *
43432014 ATGAATAAAAAATTTAACTATATA
1 ATGAACAAATAA---CAGTAT-TA
43432038 CATGAACAAATAACAGTATTA
1 -ATGAACAAATAACAGTATTA
* * * *
43432059 ATGAATAAAAAATTTAACTATATA
1 ATGAACAAATAA---CAGTAT-TA
43432083 CATGAACAAATAACAGTATTA
1 -ATGAACAAATAACAGTATTA
43432104 ATGAA
1 ATGAA
43432109 GCTTGTTGCC
Statistics
Matches: 69, Mismatches: 16, Indels: 20
0.66 0.15 0.19
Matches are distributed among these distances:
20 25 0.36
21 4 0.06
22 8 0.12
23 8 0.12
24 4 0.06
25 20 0.29
ACGTcount: A:0.56, C:0.09, G:0.08, T:0.28
Consensus pattern (20 bp):
ATGAACAAATAACAGTATTA
Found at i:43432024 original size:45 final size:45
Alignment explanation
Indices: 43431973--43432108 Score: 272
Period size: 45 Copynumber: 3.0 Consensus size: 45
43431963 TTACATATGT
43431973 ATAAAAAATTTAACTATATACATGAACAAATAACAGTATTAATGA
1 ATAAAAAATTTAACTATATACATGAACAAATAACAGTATTAATGA
43432018 ATAAAAAATTTAACTATATACATGAACAAATAACAGTATTAATGA
1 ATAAAAAATTTAACTATATACATGAACAAATAACAGTATTAATGA
43432063 ATAAAAAATTTAACTATATACATGAACAAATAACAGTATTAATGA
1 ATAAAAAATTTAACTATATACATGAACAAATAACAGTATTAATGA
43432108 A
1 A
43432109 GCTTGTTGCC
Statistics
Matches: 91, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 91 1.00
ACGTcount: A:0.56, C:0.09, G:0.07, T:0.29
Consensus pattern (45 bp):
ATAAAAAATTTAACTATATACATGAACAAATAACAGTATTAATGA
Found at i:43434840 original size:72 final size:72
Alignment explanation
Indices: 43434691--43434855 Score: 226
Period size: 72 Copynumber: 2.3 Consensus size: 72
43434681 ACGAAGTATG
* * * *
43434691 TTTTTATCAATAGTTATTTATGTTTGGTTTTTGGATATTGAATTTATGTTCTACTTGATTATGTG
1 TTTTTATCAATAGTTGTTTATGTTTGGTCTTTAGATATTGAATTTATGTTCTACTTGATTATGTC
43434756 TAATCTA
66 TAATCTA
* * * *
43434763 GTTTTATTAATAGTTGTTTATGTTTGGTCTTTAGATATTGAATTTATGTTCTACTT-ATTTTTTA
1 TTTTTATCAATAGTTGTTTATGTTTGGTCTTTAGATATTGAATTTATGTTCTACTTGATTATGT-
43434827 CTAAAT-TA
65 CT-AATCTA
43434835 TTTTTATCAATAGTTGTTTAT
1 TTTTTATCAATAGTTGTTTAT
43434856 ATGTGATTTT
Statistics
Matches: 81, Mismatches: 10, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
71 5 0.06
72 73 0.90
73 3 0.04
ACGTcount: A:0.24, C:0.05, G:0.13, T:0.57
Consensus pattern (72 bp):
TTTTTATCAATAGTTGTTTATGTTTGGTCTTTAGATATTGAATTTATGTTCTACTTGATTATGTC
TAATCTA
Found at i:43438698 original size:12 final size:12
Alignment explanation
Indices: 43438681--43438710 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
43438671 GAATATAGTT
*
43438681 GCCCATCTTCTG
1 GCCCATCTTCTA
43438693 GCCCATCTTCTA
1 GCCCATCTTCTA
43438705 GCCCAT
1 GCCCAT
43438711 AAGGGTTTTC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.13, C:0.43, G:0.13, T:0.30
Consensus pattern (12 bp):
GCCCATCTTCTA
Found at i:43439522 original size:79 final size:77
Alignment explanation
Indices: 43439427--43439570 Score: 216
Period size: 79 Copynumber: 1.8 Consensus size: 77
43439417 TGAAAAATAA
** * *
43439427 AAAATAAAATTTAATTTAGATGATAAATTTATTAAGGTTTCCTTAAAAGAAATTGAGGATTTCAA
1 AAAATAAAATAAAATTTAGATGATAAATCTATCAAGGTTT-CTTAAAAGAAATTGAGG-TTTCAA
43439492 CAGGGAAATAAAAT
64 CAGGGAAATAAAAT
* *
43439506 AAAATAAAATAAAATTTAGATGGTGAATCTATCAAGGTTTCTTAAAAGAAATTGAGGTTTCAACA
1 AAAATAAAATAAAATTTAGATGATAAATCTATCAAGGTTTCTTAAAAGAAATTGAGGTTTCAACA
43439571 AGGCATCACT
Statistics
Matches: 59, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
77 8 0.14
78 17 0.29
79 34 0.58
ACGTcount: A:0.47, C:0.06, G:0.15, T:0.32
Consensus pattern (77 bp):
AAAATAAAATAAAATTTAGATGATAAATCTATCAAGGTTTCTTAAAAGAAATTGAGGTTTCAACA
GGGAAATAAAAT
Found at i:43440387 original size:20 final size:19
Alignment explanation
Indices: 43440350--43440387 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
43440340 TTGACAAAAT
*
43440350 AAAACCACGAATTGTGGAC
1 AAAACCACGAAATGTGGAC
43440369 AAAACCACGATAATGTGGA
1 AAAACCACGA-AATGTGGA
43440388 ATGAAATTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.45, C:0.18, G:0.21, T:0.16
Consensus pattern (19 bp):
AAAACCACGAAATGTGGAC
Found at i:43442646 original size:2 final size:2
Alignment explanation
Indices: 43442639--43442670 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
43442629 ATGAAGATGG
43442639 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
43442671 CATTTCCAGG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:43442830 original size:2 final size:2
Alignment explanation
Indices: 43442823--43442861 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
43442813 CACAATTATT
*
43442823 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TT TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
43442862 TTTCCTTTCT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (2 bp):
TA
Found at i:43455261 original size:13 final size:13
Alignment explanation
Indices: 43455243--43455267 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
43455233 ATTATTTCAA
43455243 ATTTTTAATTAAT
1 ATTTTTAATTAAT
43455256 ATTTTTAATTAA
1 ATTTTTAATTAA
43455268 AAAATATACC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (13 bp):
ATTTTTAATTAAT
Found at i:43460164 original size:25 final size:25
Alignment explanation
Indices: 43460108--43460165 Score: 89
Period size: 25 Copynumber: 2.3 Consensus size: 25
43460098 AACCATTTCA
* *
43460108 AACCCAATAGCCTAAACATCCAGCC
1 AACCCATTAGCCTAAACATCAAGCC
*
43460133 AACCCATTTGCCTAAACATCAAGCC
1 AACCCATTAGCCTAAACATCAAGCC
43460158 AACCCATT
1 AACCCATT
43460166 CTTGCATGCA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 30 1.00
ACGTcount: A:0.38, C:0.38, G:0.07, T:0.17
Consensus pattern (25 bp):
AACCCATTAGCCTAAACATCAAGCC
Found at i:43462389 original size:50 final size:50
Alignment explanation
Indices: 43462331--43462668 Score: 302
Period size: 51 Copynumber: 6.7 Consensus size: 50
43462321 TCATTCGATA
* * *
43462331 CACGTAGTAGCCTTCACATAGTGCTACACACGTTATCAAGTTTTACGGTT
1 CACGTAGTAGCCTTCACATAGTACTACACACGTGACCAAGTTTTACGGTT
* **
43462381 CACGTAGTAGCCTTCACATAGTACTACACACATGATAAAGTTTTACGGTT
1 CACGTAGTAGCCTTCACATAGTACTACACACGTGACCAAGTTTTACGGTT
** * *
43462431 TGCGTAGTAGCCTTCACATAGTACTACACACATGACCAAAGCTTTT-CGGTA
1 CACGTAGTAGCCTTCACATAGTACTACACACGTGACC-AAG-TTTTACGGTT
* * * * * *** *
43462482 CACATAATAGCTTTCACTTAGTACTACACATGTGACCATCATTTATCGATT
1 CACGTAGTAGCCTTCACATAGTACTACACACGTGACCAAGTTTTA-CGGTT
* ** * *
43462533 CACGTAGTAGACTTCACACCGTACTACACACGTGACCAAAGCTTCT-CGGTA
1 CACGTAGTAGCCTTCACATAGTACTACACACGTGACC-AAG-TTTTACGGTT
* * * * *** *
43462584 CACATTGTAGCCTTCACTTAGTACTACACATGTGACCATCATTTATCGATT
1 CACGTAGTAGCCTTCACATAGTACTACACACGTGACCAAGTTTTA-CGGTT
* *
43462635 CACGTAGTAGACTTCACACAGTACTACACACGTG
1 CACGTAGTAGCCTTCACATAGTACTACACACGTG
43462669 TTCATCGATA
Statistics
Matches: 225, Mismatches: 55, Indels: 15
0.76 0.19 0.05
Matches are distributed among these distances:
49 5 0.02
50 81 0.36
51 132 0.59
52 5 0.02
53 2 0.01
ACGTcount: A:0.30, C:0.26, G:0.15, T:0.29
Consensus pattern (50 bp):
CACGTAGTAGCCTTCACATAGTACTACACACGTGACCAAGTTTTACGGTT
Found at i:43462666 original size:102 final size:102
Alignment explanation
Indices: 43462433--43462668 Score: 400
Period size: 102 Copynumber: 2.3 Consensus size: 102
43462423 TTACGGTTTG
* * * * *
43462433 CGTAGTAGCCTTCACATAGTACTACACACATGACCAAAGCTTTTCGGTACACATAATAGCTTTCA
1 CGTAGTAGACTTCACACAGTACTACACACGTGACCAAAGCTTCTCGGTACACATAATAGCCTTCA
43462498 CTTAGTACTACACATGTGACCATCATTTATCGATTCA
66 CTTAGTACTACACATGTGACCATCATTTATCGATTCA
* **
43462535 CGTAGTAGACTTCACACCGTACTACACACGTGACCAAAGCTTCTCGGTACACATTGTAGCCTTCA
1 CGTAGTAGACTTCACACAGTACTACACACGTGACCAAAGCTTCTCGGTACACATAATAGCCTTCA
43462600 CTTAGTACTACACATGTGACCATCATTTATCGATTCA
66 CTTAGTACTACACATGTGACCATCATTTATCGATTCA
43462637 CGTAGTAGACTTCACACAGTACTACACACGTG
1 CGTAGTAGACTTCACACAGTACTACACACGTG
43462669 TTCATCGATA
Statistics
Matches: 125, Mismatches: 9, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
102 125 1.00
ACGTcount: A:0.30, C:0.27, G:0.14, T:0.28
Consensus pattern (102 bp):
CGTAGTAGACTTCACACAGTACTACACACGTGACCAAAGCTTCTCGGTACACATAATAGCCTTCA
CTTAGTACTACACATGTGACCATCATTTATCGATTCA
Found at i:43463842 original size:11 final size:12
Alignment explanation
Indices: 43463814--43463846 Score: 50
Period size: 11 Copynumber: 2.8 Consensus size: 12
43463804 GCCCAAACGT
43463814 CGAAATTTTCGAA
1 CGAAATTTTC-AA
43463827 CGAAATTTTC-A
1 CGAAATTTTCAA
43463838 CGAAATTTT
1 CGAAATTTT
43463847 TCAGTGAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 10 0.50
13 10 0.50
ACGTcount: A:0.36, C:0.15, G:0.12, T:0.36
Consensus pattern (12 bp):
CGAAATTTTCAA
Found at i:43466030 original size:19 final size:19
Alignment explanation
Indices: 43466006--43466044 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
43465996 AGGTCGAAGA
43466006 GTTTGTTTCATTCTCATTT
1 GTTTGTTTCATTCTCATTT
43466025 GTTTGTTTCATTCTCATTT
1 GTTTGTTTCATTCTCATTT
43466044 G
1 G
43466045 ATGATAACAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.10, C:0.15, G:0.13, T:0.62
Consensus pattern (19 bp):
GTTTGTTTCATTCTCATTT
Found at i:43474783 original size:85 final size:86
Alignment explanation
Indices: 43474640--43474812 Score: 235
Period size: 85 Copynumber: 2.0 Consensus size: 86
43474630 TGTTATACTC
* *
43474640 TAAAATCATGTTAACAGTTCAGTGTTGGAGAAGAAGAAAAAATTTATTGATT-AAAAAAAAAGAG
1 TAAAATCATGTTAACAGTTCAGTGTTGGAGAAGAAGAAAAAATTGATCGATTAAAAAAAAAAGAG
* *
43474704 TTGTGCATGCAACAGTAGTGA
66 TTGTGCATGCAACAATAGAGA
* * * *
43474725 TAAAATCATGTTAAGAGTTC-GTTGTTGGAGAA-AAGGCAAAACTTGATCGATTAGAAAAAAAAG
1 TAAAATCATGTTAACAGTTCAG-TGTTGGAGAAGAA-GAAAAAATTGATCGATTAAAAAAAAAAG
43474788 AGTTGTGCATGCAACAATAGAGA
64 AGTTGTGCATGCAACAATAGAGA
43474811 TA
1 TA
43474813 GAATAGCTAA
Statistics
Matches: 77, Mismatches: 8, Indels: 5
0.86 0.09 0.06
Matches are distributed among these distances:
84 3 0.04
85 42 0.55
86 32 0.42
ACGTcount: A:0.44, C:0.08, G:0.22, T:0.26
Consensus pattern (86 bp):
TAAAATCATGTTAACAGTTCAGTGTTGGAGAAGAAGAAAAAATTGATCGATTAAAAAAAAAAGAG
TTGTGCATGCAACAATAGAGA
Found at i:43478667 original size:20 final size:20
Alignment explanation
Indices: 43478642--43478681 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
43478632 ACTTGTACAG
43478642 GTTTGCACTTCGGTGCCTCT
1 GTTTGCACTTCGGTGCCTCT
43478662 GTTTGCACTTCGGTGCCTCT
1 GTTTGCACTTCGGTGCCTCT
43478682 AACTTCAGAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.05, C:0.30, G:0.25, T:0.40
Consensus pattern (20 bp):
GTTTGCACTTCGGTGCCTCT
Found at i:43481681 original size:33 final size:34
Alignment explanation
Indices: 43481636--43481708 Score: 96
Period size: 33 Copynumber: 2.2 Consensus size: 34
43481626 TAACTCTACA
43481636 CATTCAGACTCCTTTCTATTAACAA-ATTTAACAT
1 CATTCAGACTCCTTTCTATTAACAACA-TTAACAT
* * *
43481670 CATTCA-ACTCCTTTTTATTTACAACATTACCAT
1 CATTCAGACTCCTTTCTATTAACAACATTAACAT
43481703 CATTCA
1 CATTCA
43481709 TTTCTCTGTT
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
33 28 0.80
34 7 0.20
ACGTcount: A:0.33, C:0.26, G:0.01, T:0.40
Consensus pattern (34 bp):
CATTCAGACTCCTTTCTATTAACAACATTAACAT
Found at i:43485604 original size:9 final size:9
Alignment explanation
Indices: 43485590--43485641 Score: 61
Period size: 9 Copynumber: 5.6 Consensus size: 9
43485580 TTTGGTTAAA
43485590 AATTAACCG
1 AATTAACCG
*
43485599 AATTAACCTAA
1 AATTAACC--G
43485610 AATTAACCG
1 AATTAACCG
43485619 AATT-ACCTG
1 AATTAACC-G
43485628 AATTAACCG
1 AATTAACCG
43485637 AATTA
1 AATTA
43485642 TATTTTATTA
Statistics
Matches: 37, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
8 3 0.08
9 23 0.62
10 3 0.08
11 8 0.22
ACGTcount: A:0.46, C:0.19, G:0.08, T:0.27
Consensus pattern (9 bp):
AATTAACCG
Found at i:43485613 original size:20 final size:20
Alignment explanation
Indices: 43485588--43485641 Score: 85
Period size: 20 Copynumber: 2.8 Consensus size: 20
43485578 TTTTTGGTTA
43485588 AAAATTAACCGAATTAACCT
1 AAAATTAACCGAATTAACCT
43485608 AAAATTAACCGAATT-ACCT
1 AAAATTAACCGAATTAACCT
*
43485627 -GAATTAACCGAATTA
1 AAAATTAACCGAATTA
43485642 TATTTTATTA
Statistics
Matches: 32, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
18 13 0.41
19 4 0.12
20 15 0.47
ACGTcount: A:0.48, C:0.19, G:0.07, T:0.26
Consensus pattern (20 bp):
AAAATTAACCGAATTAACCT
Found at i:43486099 original size:45 final size:45
Alignment explanation
Indices: 43486045--43486130 Score: 138
Period size: 45 Copynumber: 1.9 Consensus size: 45
43486035 TGTTAGAGAT
43486045 TTTAATTTTAGACTTTAGTTTTATTGGGTT-GGTAATTGGGTAGAC
1 TTTAATTTTAG-CTTTAGTTTTATTGGGTTGGGTAATTGGGTAGAC
* *
43486090 TTTAGTTTTAGTTTTAGTTTTATTGGGTTGGGTAATTGGGT
1 TTTAATTTTAGCTTTAGTTTTATTGGGTTGGGTAATTGGGT
43486131 TGTGTTGGAT
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
44 17 0.45
45 21 0.55
ACGTcount: A:0.19, C:0.02, G:0.27, T:0.52
Consensus pattern (45 bp):
TTTAATTTTAGCTTTAGTTTTATTGGGTTGGGTAATTGGGTAGAC
Found at i:43488567 original size:13 final size:13
Alignment explanation
Indices: 43488549--43488574 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
43488539 TAGTCAATAG
43488549 TTCCTTTCTTTTT
1 TTCCTTTCTTTTT
43488562 TTCCTTTCTTTTT
1 TTCCTTTCTTTTT
43488575 AGTTCATCTC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (13 bp):
TTCCTTTCTTTTT
Found at i:43497285 original size:4 final size:4
Alignment explanation
Indices: 43497276--43497341 Score: 132
Period size: 4 Copynumber: 16.5 Consensus size: 4
43497266 TGTAACAATC
43497276 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
43497324 ATGT ATGT ATGT ATGT AT
1 ATGT ATGT ATGT ATGT AT
43497342 ATTGAATTCG
Statistics
Matches: 62, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 62 1.00
ACGTcount: A:0.26, C:0.00, G:0.24, T:0.50
Consensus pattern (4 bp):
ATGT
Done.