Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008323.1 Hibiscus syriacus cultivar Beakdansim tig00111027_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: 5101972
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 16 of 26
Found at i:3082724 original size:216 final size:214
Alignment explanation
Indices: 3082352--3082780 Score: 840
Period size: 216 Copynumber: 2.0 Consensus size: 214
3082342 CTTGTTCATA
3082352 TAATCAATTAAGCTCATATCATATATCTTATAGCATATACAATAATCACTAAACACATATATCAT
1 TAATCAATTAAGCTCATATCATATATCTTATAGCATATACAATAATCACTAAACACATATATCAT
3082417 CTACAGTACATTCCATGTTATCTCTTATTAGCCCAGTGCACCTGTGAGAACTGTAGATATGTGAG
66 CTACAGTACATTCCATGTTATCTCTTATTAGCCCAGTGCACCTGTGAGAACTGTAGATATGTGAG
3082482 TTTATTGAGGTTGTGCACCACTATGCTGTCACCACAGCTCATATAAATGTCCCGAAGGACCTATC
131 TTTATTGAGGTTGTGCACCACTATGCTGTCACCACAGCTCATATAAATGTCCCGAAGGACCTATC
3082547 CAGAGGTCACAAAGACCCG
196 CAGAGGTCACAAAGACCCG
3082566 TAATCAATTAAGCTCATATCATATATCTTATAGCATATACAATAATCACTAACACACATATATCA
1 TAATCAATTAAGCTCATATCATATATCTTATAGCATATACAATAATCACTAA-ACACATATATCA
3082631 TCTACAGTACATTCCATGTTATCTCTTATTAGCCCATGTGCACCTGTGAGAACTGTAGATATGTG
65 TCTACAGTACATTCCATGTTATCTCTTATTAGCCCA-GTGCACCTGTGAGAACTGTAGATATGTG
3082696 AGTTTATTGAGGTTGTGCACCACTATGCTGTCACCACAGCTCATATAAATGTCCCGAAGGACCTA
129 AGTTTATTGAGGTTGTGCACCACTATGCTGTCACCACAGCTCATATAAATGTCCCGAAGGACCTA
3082761 TCCAGAGGTCACAAAGACCC
194 TCCAGAGGTCACAAAGACCC
3082781 CGGTAACTAT
Statistics
Matches: 213, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
214 52 0.24
215 48 0.23
216 113 0.53
ACGTcount: A:0.33, C:0.23, G:0.15, T:0.30
Consensus pattern (214 bp):
TAATCAATTAAGCTCATATCATATATCTTATAGCATATACAATAATCACTAAACACATATATCAT
CTACAGTACATTCCATGTTATCTCTTATTAGCCCAGTGCACCTGTGAGAACTGTAGATATGTGAG
TTTATTGAGGTTGTGCACCACTATGCTGTCACCACAGCTCATATAAATGTCCCGAAGGACCTATC
CAGAGGTCACAAAGACCCG
Found at i:3082817 original size:30 final size:30
Alignment explanation
Indices: 3082758--3082853 Score: 149
Period size: 30 Copynumber: 3.2 Consensus size: 30
3082748 CCCGAAGGAC
* *
3082758 CTATCCAGAGGTCACAAAGA-CCCCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
3082787 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
*
3082817 CTGTCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
*
3082847 CTGTCCA
1 CTATCCA
3082854 TATGTTCCTT
Statistics
Matches: 63, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
29 19 0.30
30 44 0.70
ACGTcount: A:0.31, C:0.27, G:0.21, T:0.21
Consensus pattern (30 bp):
CTATCCAGAGGTCATAAAGATCCTCGGTAA
Found at i:3082884 original size:31 final size:30
Alignment explanation
Indices: 3082842--3082939 Score: 117
Period size: 31 Copynumber: 3.2 Consensus size: 30
3082832 AAAGATCCTC
*
3082842 GGTAACTGTCCATATGTTCCTTAGAACATA
1 GGTAACTGTCCATATGTTCCATAGAACATA
* *
3082872 GGTATACTGTCCATATGTCTCGAAAG-ACATA
1 GGTA-ACTGTCCATATGT-TCCATAGAACATA
*
3082903 GGTAAAACTGTCCATATGTTCCGTAGAACATA
1 GGT--AACTGTCCATATGTTCCATAGAACATA
3082935 GGTAA
1 GGTAA
3082940 ACCCTCGACT
Statistics
Matches: 57, Mismatches: 6, Indels: 10
0.78 0.08 0.14
Matches are distributed among these distances:
30 6 0.11
31 25 0.44
32 25 0.44
33 1 0.02
ACGTcount: A:0.33, C:0.18, G:0.19, T:0.30
Consensus pattern (30 bp):
GGTAACTGTCCATATGTTCCATAGAACATA
Found at i:3084109 original size:21 final size:21
Alignment explanation
Indices: 3084079--3084123 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
3084069 ATTCTGTCGT
* *
3084079 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
3084100 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
3084121 TTG
1 TTG
3084124 CCCAGAAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:3089816 original size:24 final size:24
Alignment explanation
Indices: 3089789--3089850 Score: 115
Period size: 24 Copynumber: 2.6 Consensus size: 24
3089779 CTATTCTTTC
3089789 GCTTCAATTGAGCTCGAATTTCAG
1 GCTTCAATTGAGCTCGAATTTCAG
3089813 GCTTCAATTGAGCTCGAATTTCAG
1 GCTTCAATTGAGCTCGAATTTCAG
*
3089837 GCTTCAATCGAGCT
1 GCTTCAATTGAGCT
3089851 TCTAAATTTT
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 37 1.00
ACGTcount: A:0.24, C:0.23, G:0.21, T:0.32
Consensus pattern (24 bp):
GCTTCAATTGAGCTCGAATTTCAG
Found at i:3091726 original size:15 final size:15
Alignment explanation
Indices: 3091706--3091751 Score: 55
Period size: 13 Copynumber: 3.3 Consensus size: 15
3091696 TTATATTTTA
3091706 AAATAAATTTATATT
1 AAATAAATTTATATT
3091721 AAAT-AATTTA-A--
1 AAATAAATTTATATT
3091732 AATATAAATTTATATT
1 AA-ATAAATTTATATT
3091748 AAAT
1 AAAT
3091752 TATTTAATTC
Statistics
Matches: 26, Mismatches: 0, Indels: 10
0.72 0.00 0.28
Matches are distributed among these distances:
11 2 0.08
12 2 0.08
13 7 0.27
14 7 0.27
15 6 0.23
16 2 0.08
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (15 bp):
AAATAAATTTATATT
Found at i:3091730 original size:14 final size:14
Alignment explanation
Indices: 3091706--3091757 Score: 52
Period size: 14 Copynumber: 3.7 Consensus size: 14
3091696 TTATATTTTA
3091706 AAATAAATTTATATT
1 AAAT-AATTTATATT
* *
3091721 AAATAATTTAAAAT
1 AAATAATTTATATT
*
3091735 ATA-AATTTATATT
1 AAATAATTTATATT
*
3091748 AAATTATTTA
1 AAATAATTTA
3091758 ATTCTTAGTT
Statistics
Matches: 29, Mismatches: 7, Indels: 3
0.74 0.18 0.08
Matches are distributed among these distances:
13 10 0.34
14 15 0.52
15 4 0.14
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (14 bp):
AAATAATTTATATT
Found at i:3091743 original size:27 final size:26
Alignment explanation
Indices: 3091700--3091758 Score: 91
Period size: 27 Copynumber: 2.2 Consensus size: 26
3091690 TACTTTTTAT
*
3091700 ATTTTAAAATAAATTTATATTAAATA
1 ATTTAAAAATAAATTTATATTAAATA
*
3091726 ATTTAAAATATAAATTTATATTAAATT
1 ATTTAAAA-ATAAATTTATATTAAATA
3091753 ATTTAA
1 ATTTAA
3091759 TTCTTAGTTT
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
26 7 0.23
27 23 0.77
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (26 bp):
ATTTAAAAATAAATTTATATTAAATA
Found at i:3092538 original size:21 final size:21
Alignment explanation
Indices: 3092500--3092539 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
3092490 TAGCACGAAA
*
3092500 CATATATAGTTTGTTAAAATT
1 CATATATAGTTTATTAAAATT
3092521 CATATATA-TTTATATAAAA
1 CATATATAGTTTAT-TAAAA
3092540 ATATAAAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.45, C:0.05, G:0.05, T:0.45
Consensus pattern (21 bp):
CATATATAGTTTATTAAAATT
Found at i:3095916 original size:15 final size:15
Alignment explanation
Indices: 3095892--3095927 Score: 63
Period size: 15 Copynumber: 2.4 Consensus size: 15
3095882 GCATCATTAA
*
3095892 ATTAATTTATAAAAT
1 ATTAAATTATAAAAT
3095907 ATTAAATTATAAAAT
1 ATTAAATTATAAAAT
3095922 ATTAAA
1 ATTAAA
3095928 CGCATAATTA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (15 bp):
ATTAAATTATAAAAT
Found at i:3112938 original size:20 final size:20
Alignment explanation
Indices: 3112910--3112961 Score: 79
Period size: 20 Copynumber: 2.6 Consensus size: 20
3112900 ATATTTCTTA
3112910 TTTTAAATAAAATTAGTGAT
1 TTTTAAATAAAATTAGTGAT
*
3112930 TTTTGAATAAAATTAGTGA-
1 TTTTAAATAAAATTAGTGAT
*
3112949 TTTTAAAAAAAAT
1 TTTTAAATAAAAT
3112962 CTAATAATTT
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 11 0.38
20 18 0.62
ACGTcount: A:0.48, C:0.00, G:0.10, T:0.42
Consensus pattern (20 bp):
TTTTAAATAAAATTAGTGAT
Found at i:3115922 original size:51 final size:51
Alignment explanation
Indices: 3115841--3115939 Score: 162
Period size: 51 Copynumber: 1.9 Consensus size: 51
3115831 GACGTTAATA
3115841 TGTTGATTGTGATATAATAAAATATAATTCTAGAATCTTAAACAATTAGAC
1 TGTTGATTGTGATATAATAAAATATAATTCTAGAATCTTAAACAATTAGAC
* * * *
3115892 TGTTGATTGTGATATGATAAATTATGATTCTATAATCTTAAACAATTA
1 TGTTGATTGTGATATAATAAAATATAATTCTAGAATCTTAAACAATTA
3115940 TATAGCTCAG
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
51 44 1.00
ACGTcount: A:0.40, C:0.07, G:0.12, T:0.40
Consensus pattern (51 bp):
TGTTGATTGTGATATAATAAAATATAATTCTAGAATCTTAAACAATTAGAC
Found at i:3121015 original size:20 final size:20
Alignment explanation
Indices: 3120977--3121015 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
3120967 TAATTAATTC
*
3120977 AATATTAATAAATATATAAA
1 AATATTAATAAAGATATAAA
3120997 AATATTAA-ATAAGATATAA
1 AATATTAATA-AAGATATAA
3121016 TTATATTGAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 1 0.06
20 16 0.94
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.33
Consensus pattern (20 bp):
AATATTAATAAAGATATAAA
Found at i:3123203 original size:15 final size:16
Alignment explanation
Indices: 3123173--3123203 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
3123163 GTGGGAATAA
3123173 AAGATTACTAGGGAAT
1 AAGATTACTAGGGAAT
3123189 AAGATTACT-GGGAAT
1 AAGATTACTAGGGAAT
3123204 GTTACATTAC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 6 0.40
16 9 0.60
ACGTcount: A:0.42, C:0.06, G:0.26, T:0.26
Consensus pattern (16 bp):
AAGATTACTAGGGAAT
Found at i:3124626 original size:29 final size:30
Alignment explanation
Indices: 3124594--3124674 Score: 121
Period size: 29 Copynumber: 2.8 Consensus size: 30
3124584 TTCCAGAAAA
**
3124594 TGAATTACTGGAATTTGAA-TACTGAAATT
1 TGAATTACTGGAAAATGAATTACTGAAATT
*
3124623 TGAATTACTGGAAAATGAATTACTGGAATT
1 TGAATTACTGGAAAATGAATTACTGAAATT
3124653 TGAATT-CTGGAAAATGAATTAC
1 TGAATTACTGGAAAATGAATTAC
3124675 ATTTCTGTAA
Statistics
Matches: 48, Mismatches: 3, Indels: 2
0.91 0.06 0.04
Matches are distributed among these distances:
29 33 0.69
30 15 0.31
ACGTcount: A:0.40, C:0.07, G:0.19, T:0.35
Consensus pattern (30 bp):
TGAATTACTGGAAAATGAATTACTGAAATT
Found at i:3124631 original size:15 final size:15
Alignment explanation
Indices: 3124594--3124658 Score: 80
Period size: 15 Copynumber: 4.4 Consensus size: 15
3124584 TTCCAGAAAA
*
3124594 TGAATTACTGGAATT
1 TGAATTACTGAAATT
3124609 TGAA-TACTGAAATT
1 TGAATTACTGAAATT
*
3124623 TGAATTACTGGAAA-A
1 TGAATTACT-GAAATT
*
3124638 TGAATTACTGGAATT
1 TGAATTACTGAAATT
3124653 TGAATT
1 TGAATT
3124659 CTGGAAAATG
Statistics
Matches: 43, Mismatches: 4, Indels: 6
0.81 0.08 0.11
Matches are distributed among these distances:
14 16 0.37
15 23 0.53
16 4 0.09
ACGTcount: A:0.38, C:0.06, G:0.18, T:0.37
Consensus pattern (15 bp):
TGAATTACTGAAATT
Found at i:3124652 original size:44 final size:44
Alignment explanation
Indices: 3124589--3124674 Score: 138
Period size: 44 Copynumber: 2.0 Consensus size: 44
3124579 TGGTTTTCCA
*
3124589 GAAAATGAATTACTGGAATTTGAATACT-GAAATTTGAATTACTG
1 GAAAATGAATTACTGGAATTTGAATACTGGAAA-ATGAATTACTG
*
3124633 GAAAATGAATTACTGGAATTTGAATTCTGGAAAATGAATTAC
1 GAAAATGAATTACTGGAATTTGAATACTGGAAAATGAATTAC
3124675 ATTTCTGTAA
Statistics
Matches: 39, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
44 35 0.90
45 4 0.10
ACGTcount: A:0.42, C:0.07, G:0.19, T:0.33
Consensus pattern (44 bp):
GAAAATGAATTACTGGAATTTGAATACTGGAAAATGAATTACTG
Found at i:3124680 original size:20 final size:20
Alignment explanation
Indices: 3124657--3124726 Score: 131
Period size: 20 Copynumber: 3.5 Consensus size: 20
3124647 GGAATTTGAA
3124657 TTCTGGAAAATGAATTACAT
1 TTCTGGAAAATGAATTACAT
*
3124677 TTCTGTAAAATGAATTACAT
1 TTCTGGAAAATGAATTACAT
3124697 TTCTGGAAAATGAATTACAT
1 TTCTGGAAAATGAATTACAT
3124717 TTCTGGAAAA
1 TTCTGGAAAA
3124727 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:3124948 original size:28 final size:28
Alignment explanation
Indices: 3124892--3124995 Score: 99
Period size: 28 Copynumber: 3.5 Consensus size: 28
3124882 CTTTACTAAA
3124892 ATATTATTGAAATATATATAAATAATATTAT
1 ATATTATT-AAATATA-A-AAATAATATTAT
3124923 -TCATTATTAAATATAAAAA-AATTATTAT
1 AT-ATTATTAAATATAAAAATAA-TATTAT
3124951 ATATTATTAAA-ATAAAAATATAATATCT-T
1 ATATTATTAAATAT-AAAA-ATAATAT-TAT
3124980 ATATTATTATAATATA
1 ATATTATTA-AATATA
3124996 TTTGATTATT
Statistics
Matches: 64, Mismatches: 0, Indels: 19
0.77 0.00 0.23
Matches are distributed among these distances:
27 4 0.06
28 22 0.34
29 16 0.25
30 14 0.22
31 8 0.12
ACGTcount: A:0.53, C:0.02, G:0.01, T:0.44
Consensus pattern (28 bp):
ATATTATTAAATATAAAAATAATATTAT
Found at i:3124976 original size:24 final size:27
Alignment explanation
Indices: 3124892--3124981 Score: 69
Period size: 30 Copynumber: 3.3 Consensus size: 27
3124882 CTTTACTAAA
* * *
3124892 ATATTATTGAAATATATATAAATAATATT
1 ATATTATT-AAATATA-AAAAATTATAAT
*
3124921 ATTCATTATTAAATATAAAAAAATTATTAT
1 A-T-ATTATTAAATAT-AAAAAATTATAAT
3124951 ATATTATTAAA-AT-AAAAA-TATAAT
1 ATATTATTAAATATAAAAAATTATAAT
*
3124975 ATCTTAT
1 ATATTAT
3124982 ATTATTATAA
Statistics
Matches: 52, Mismatches: 6, Indels: 11
0.75 0.09 0.16
Matches are distributed among these distances:
24 11 0.21
25 5 0.10
27 2 0.04
28 9 0.17
29 2 0.04
30 16 0.31
31 7 0.13
ACGTcount: A:0.53, C:0.02, G:0.01, T:0.43
Consensus pattern (27 bp):
ATATTATTAAATATAAAAAATTATAAT
Found at i:3125003 original size:18 final size:18
Alignment explanation
Indices: 3124969--3125049 Score: 57
Period size: 18 Copynumber: 4.7 Consensus size: 18
3124959 AAAATAAAAA
*
3124969 TATAATATCTTATATTAT
1 TATAATATATTATATTAT
3124987 TATAATATATT-TGATTAT
1 TATAATATATTAT-ATTAT
*
3125005 T-T--TATATAATATTA-
1 TATAATATATTATATTAT
* *
3125019 AAAATATAATATTATATTAT
1 TATA-AT-ATATTATATTAT
3125039 TATAA-ATATTA
1 TATAATATATTA
3125050 ATAAATATAT
Statistics
Matches: 48, Mismatches: 7, Indels: 17
0.67 0.10 0.24
Matches are distributed among these distances:
15 9 0.19
16 1 0.02
17 8 0.17
18 17 0.35
19 11 0.23
20 2 0.04
ACGTcount: A:0.46, C:0.01, G:0.01, T:0.52
Consensus pattern (18 bp):
TATAATATATTATATTAT
Found at i:3125026 original size:31 final size:30
Alignment explanation
Indices: 3124980--3125061 Score: 87
Period size: 31 Copynumber: 2.6 Consensus size: 30
3124970 ATAATATCTT
*
3124980 ATATTATTATAATATATTTGATTATT-TTATATA
1 ATATTAATA-AATATATTT-A-TATTATTATA-A
3125013 ATATTAA-AAATATAATATTATATTATTATAA
1 ATATTAATAAATAT-AT-TTATATTATTATAA
3125044 ATATTAATAAATATATTT
1 ATATTAATAAATATATTT
3125062 TAAATATTTT
Statistics
Matches: 44, Mismatches: 1, Indels: 11
0.79 0.02 0.20
Matches are distributed among these distances:
30 2 0.05
31 19 0.43
32 15 0.34
33 8 0.18
ACGTcount: A:0.48, C:0.00, G:0.01, T:0.51
Consensus pattern (30 bp):
ATATTAATAAATATATTTATATTATTATAA
Found at i:3125034 original size:22 final size:23
Alignment explanation
Indices: 3125009--3125052 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
3124999 GATTATTTTA
3125009 TATAATATTAAAAATA-TAATAT
1 TATAATATTAAAAATATTAATAT
* *
3125031 TATATTATTATAAATATTAATA
1 TATAATATTAAAAATATTAATA
3125053 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:3125057 original size:22 final size:22
Alignment explanation
Indices: 3124980--3125069 Score: 64
Period size: 21 Copynumber: 4.2 Consensus size: 22
3124970 ATAATATCTT
* *
3124980 ATATTATTATAATATATT-TGA
1 ATATTAATATAATATATTATAA
* * *
3125001 TTATT-TTAT-ATAATATTAAAA
1 ATATTAATATAAT-ATATTATAA
*
3125022 ATA-TAATATTATATTATTATAA
1 ATATTAATATAATA-TATTATAA
*
3125044 ATATTAATA-AATATATTTTAA
1 ATATTAATATAATATATTATAA
3125065 ATATT
1 ATATT
3125070 TTAATAATTA
Statistics
Matches: 55, Mismatches: 8, Indels: 12
0.73 0.11 0.16
Matches are distributed among these distances:
19 2 0.04
20 10 0.18
21 23 0.42
22 15 0.27
23 5 0.09
ACGTcount: A:0.48, C:0.00, G:0.01, T:0.51
Consensus pattern (22 bp):
ATATTAATATAATATATTATAA
Found at i:3125068 original size:52 final size:52
Alignment explanation
Indices: 3124949--3125069 Score: 135
Period size: 52 Copynumber: 2.3 Consensus size: 52
3124939 AAAAATTATT
*
3124949 ATATATTATTAAA-A-TAAAAATATAATATCTTATATTATTATAATATATTTGA
1 ATATATT-TTAAATATTAAAAATATAATA-CTTATATTATTATAATATATTTAA
*
3125001 TTAT-TTTATATAATATTAAAAATATAATA-TTATATTATTATAA-ATATTAATAA
1 ATATATTT-TA-AATATTAAAAATATAATACTTATATTATTATAATATATT--TAA
3125054 ATATATTTTAAATATT
1 ATATATTTTAAATATT
3125070 TTAATAATTA
Statistics
Matches: 59, Mismatches: 3, Indels: 14
0.78 0.04 0.18
Matches are distributed among these distances:
50 1 0.02
51 9 0.15
52 25 0.42
53 8 0.14
54 16 0.27
ACGTcount: A:0.50, C:0.01, G:0.01, T:0.49
Consensus pattern (52 bp):
ATATATTTTAAATATTAAAAATATAATACTTATATTATTATAATATATTTAA
Found at i:3125303 original size:42 final size:42
Alignment explanation
Indices: 3125256--3125375 Score: 231
Period size: 42 Copynumber: 2.9 Consensus size: 42
3125246 ATGAATTACA
*
3125256 TTCCGGAAAACGAATTACGTGAAACAAACACGGGAAAACGTT
1 TTCCGGAAAACGAATTACGTGAAACAAACACGGGAAAACATT
3125298 TTCCGGAAAACGAATTACGTGAAACAAACACGGGAAAACATT
1 TTCCGGAAAACGAATTACGTGAAACAAACACGGGAAAACATT
3125340 TTCCGGAAAACGAATTACGTGAAACAAACACGGGAA
1 TTCCGGAAAACGAATTACGTGAAACAAACACGGGAA
3125376 TTCGGGGAAA
Statistics
Matches: 77, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
42 77 1.00
ACGTcount: A:0.44, C:0.19, G:0.21, T:0.16
Consensus pattern (42 bp):
TTCCGGAAAACGAATTACGTGAAACAAACACGGGAAAACATT
Found at i:3127302 original size:64 final size:63
Alignment explanation
Indices: 3127211--3127375 Score: 187
Period size: 64 Copynumber: 2.6 Consensus size: 63
3127201 GCATCCCTTG
* *
3127211 ACAGGTGCATCGATGCACTATCC--ATGCATCGGTGCATAAAT-CCTATTCGATGTT-TGTATTT
1 ACAGGTGCATCGATGCAC--TCCTTATGCATCGATGCATAAATACC-ATTCGATGTTAT-TAATT
3127272 TA
62 TA
* *
3127274 AGCAGGTGCATCGATGCACTCCTTATGCATCGATGCATTAATAGCATTCGATGTTCATTAATTTA
1 A-CAGGTGCATCGATGCACTCCTTATGCATCGATGCATAAATACCATTCGATGTT-ATTAATTTA
3127339 A-ATGAGTGCATCGATGCACTCCTTATGCATCGATGCA
1 ACA-G-GTGCATCGATGCACTCCTTATGCATCGATGCA
3127376 CCTTCAACAA
Statistics
Matches: 90, Mismatches: 4, Indels: 14
0.83 0.04 0.13
Matches are distributed among these distances:
62 3 0.03
63 2 0.02
64 44 0.49
65 40 0.44
66 1 0.01
ACGTcount: A:0.27, C:0.21, G:0.19, T:0.33
Consensus pattern (63 bp):
ACAGGTGCATCGATGCACTCCTTATGCATCGATGCATAAATACCATTCGATGTTATTAATTTA
Found at i:3130240 original size:16 final size:18
Alignment explanation
Indices: 3130207--3130243 Score: 51
Period size: 16 Copynumber: 2.2 Consensus size: 18
3130197 TTAAGAATTT
*
3130207 ATATTTTATTTTCTAAAA
1 ATATTTTATTTTCAAAAA
3130225 ATATTTT-TTTT-AAAAA
1 ATATTTTATTTTCAAAAA
3130241 ATA
1 ATA
3130244 GTCTAGAGTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
16 7 0.39
17 4 0.22
18 7 0.39
ACGTcount: A:0.43, C:0.03, G:0.00, T:0.54
Consensus pattern (18 bp):
ATATTTTATTTTCAAAAA
Found at i:3145366 original size:14 final size:14
Alignment explanation
Indices: 3145330--3145359 Score: 51
Period size: 15 Copynumber: 2.1 Consensus size: 14
3145320 TGTGTGTTGT
3145330 TTATATTTTAAAAA
1 TTATATTTTAAAAA
3145344 TTCATATTTTAAAAA
1 TT-ATATTTTAAAAA
3145359 T
1 T
3145360 ATTATTTAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 2 0.13
15 13 0.87
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (14 bp):
TTATATTTTAAAAA
Found at i:3155491 original size:20 final size:21
Alignment explanation
Indices: 3155466--3155517 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
3155456 TTTTCCCAAT
*
3155466 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
3155486 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
3155507 TCGCAATGCGA
1 TCGCAATGCGA
3155518 TACTGACTAT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
20 11 0.42
21 15 0.58
ACGTcount: A:0.38, C:0.19, G:0.25, T:0.17
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:3155531 original size:20 final size:20
Alignment explanation
Indices: 3155506--3155579 Score: 69
Period size: 20 Copynumber: 3.6 Consensus size: 20
3155496 AATTGGGAAA
*
3155506 ATCGCAATGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* * *
3155526 ATCGCAATGCGATAAT-ACAAA
1 ATCGCAACGCGATACTGAC--T
*
3155547 ATCGCAACGAGATACTGACT
1 ATCGCAACGCGATACTGACT
*
3155567 TTCGCAACGCGAT
1 ATCGCAACGCGAT
3155580 TTACATAGCA
Statistics
Matches: 43, Mismatches: 8, Indels: 6
0.75 0.14 0.11
Matches are distributed among these distances:
19 2 0.05
20 26 0.60
21 13 0.30
22 2 0.05
ACGTcount: A:0.35, C:0.24, G:0.19, T:0.22
Consensus pattern (20 bp):
ATCGCAACGCGATACTGACT
Found at i:3155845 original size:27 final size:27
Alignment explanation
Indices: 3155789--3155848 Score: 75
Period size: 27 Copynumber: 2.2 Consensus size: 27
3155779 ATCGCCGGCG
* *
3155789 AAATCCCTCACAACCATTCACAGTCAA
1 AAATCCCTCACAACCATTCAAAATCAA
* *
3155816 AAATCCCTCACAATCATTCAGAAATGAA
1 AAATCCCTCACAACCATTCA-AAATCAA
3155844 AAATC
1 AAATC
3155849 AACCTCCGAG
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
27 19 0.68
28 9 0.32
ACGTcount: A:0.45, C:0.30, G:0.05, T:0.20
Consensus pattern (27 bp):
AAATCCCTCACAACCATTCAAAATCAA
Found at i:3156136 original size:19 final size:19
Alignment explanation
Indices: 3156098--3156153 Score: 85
Period size: 19 Copynumber: 2.9 Consensus size: 19
3156088 TTCGAGAATG
3156098 AAAATCGCAACGCGGAAATA
1 AAAATCGCAACGC-GAAATA
**
3156118 ACTATCGCAACGCGAAATA
1 AAAATCGCAACGCGAAATA
3156137 AAAATCGCAACGCGAAA
1 AAAATCGCAACGCGAAA
3156154 CCAAAACCGC
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
19 21 0.66
20 11 0.34
ACGTcount: A:0.48, C:0.23, G:0.18, T:0.11
Consensus pattern (19 bp):
AAAATCGCAACGCGAAATA
Found at i:3156164 original size:19 final size:19
Alignment explanation
Indices: 3156123--3156164 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
3156113 AAATAACTAT
* *
3156123 CGCAACGCGAAATAAAAAT
1 CGCAACGCGAAACAAAAAC
*
3156142 CGCAACGCGAAACCAAAAC
1 CGCAACGCGAAACAAAAAC
3156161 CGCA
1 CGCA
3156165 TTGCGATTTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.48, C:0.31, G:0.17, T:0.05
Consensus pattern (19 bp):
CGCAACGCGAAACAAAAAC
Found at i:3156205 original size:33 final size:33
Alignment explanation
Indices: 3156163--3156294 Score: 201
Period size: 33 Copynumber: 4.0 Consensus size: 33
3156153 ACCAAAACCG
**
3156163 CATTGCGATTTTCATTTCGCGTTGCGATTCTCT
1 CATTGCGATAGTCATTTCGCGTTGCGATTCTCT
**
3156196 CATTGCGATTTTCATTTCGCGTTGCGATTCTCT
1 CATTGCGATAGTCATTTCGCGTTGCGATTCTCT
*
3156229 CATCGCGATAGTCATTTCGCGTTGCGATTCTCT
1 CATTGCGATAGTCATTTCGCGTTGCGATTCTCT
*
3156262 CGTTGCGATAGTCATTTCCGCGTTGCGATTCTC
1 CATTGCGATAGTCATTT-CGCGTTGCGATTCTC
3156295 ATTATCTCGT
Statistics
Matches: 93, Mismatches: 5, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
33 78 0.84
34 15 0.16
ACGTcount: A:0.13, C:0.26, G:0.20, T:0.41
Consensus pattern (33 bp):
CATTGCGATAGTCATTTCGCGTTGCGATTCTCT
Found at i:3156296 original size:20 final size:20
Alignment explanation
Indices: 3156262--3156319 Score: 64
Period size: 20 Copynumber: 2.9 Consensus size: 20
3156252 GCGATTCTCT
**
3156262 CGTTGCGATAGTCATTTCCG
1 CGTTGCGATTCTCATTTCCG
*
3156282 CGTTGCGATTCTCATTAT-CT
1 CGTTGCGATTCTCATT-TCCG
*
3156302 CGTTGCGATTTTCATTTC
1 CGTTGCGATTCTCATTTC
3156320 AACCAAAAGG
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
19 1 0.03
20 30 0.94
21 1 0.03
ACGTcount: A:0.14, C:0.24, G:0.19, T:0.43
Consensus pattern (20 bp):
CGTTGCGATTCTCATTTCCG
Found at i:3158488 original size:42 final size:42
Alignment explanation
Indices: 3158412--3158614 Score: 203
Period size: 42 Copynumber: 4.8 Consensus size: 42
3158402 GACTCGCCTG
* * * * * *
3158412 TCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCCCCTA
1 TCATTCCTCAAGAGTCCCCTCCCACCGTTCAAGAGGCCACTA
* *
3158454 TCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCCACTG
1 TCATTCCTCAAGAGTCCCCTCCCACCGTTCAAGAGGCCACTA
* * * * * * *
3158496 TAATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCCCCTA
1 TCATTCCTCAAGAGTCCCCTCCCACCGTTCAAGAGGCCACTA
*
3158538 TCATTCCTCAAGAGTCCCCTCCCACCGTTCAAGAGGCCACTG
1 TCATTCCTCAAGAGTCCCCTCCCACCGTTCAAGAGGCCACTA
* * *
3158580 TCA-TCGTTGAAGAGGT-CCCTCCCACCATTCAAGAG
1 TCATTC-CTCAAGA-GTCCCCTCCCACCGTTCAAGAG
3158615 CCCGATTCAC
Statistics
Matches: 131, Mismatches: 28, Indels: 4
0.80 0.17 0.02
Matches are distributed among these distances:
41 2 0.02
42 127 0.97
43 2 0.02
ACGTcount: A:0.23, C:0.36, G:0.18, T:0.23
Consensus pattern (42 bp):
TCATTCCTCAAGAGTCCCCTCCCACCGTTCAAGAGGCCACTA
Found at i:3158569 original size:21 final size:21
Alignment explanation
Indices: 3158545--3158614 Score: 61
Period size: 21 Copynumber: 3.3 Consensus size: 21
3158535 CTATCATTCC
3158545 TCAAGAGTCCCCTCCCACCGT
1 TCAAGAGTCCCCTCCCACCGT
* * ** *
3158566 TCAAGAGGCCACTGTCATCGT
1 TCAAGAGTCCCCTCCCACCGT
* *
3158587 TGAAGAGGT-CCCTCCCACCAT
1 TCAAGA-GTCCCCTCCCACCGT
3158608 TCAAGAG
1 TCAAGAG
3158615 CCCGATTCAC
Statistics
Matches: 35, Mismatches: 13, Indels: 3
0.69 0.25 0.06
Matches are distributed among these distances:
20 1 0.03
21 33 0.94
22 1 0.03
ACGTcount: A:0.24, C:0.36, G:0.20, T:0.20
Consensus pattern (21 bp):
TCAAGAGTCCCCTCCCACCGT
Found at i:3158593 original size:84 final size:84
Alignment explanation
Indices: 3158409--3158580 Score: 326
Period size: 84 Copynumber: 2.0 Consensus size: 84
3158399 CCCGACTCGC
* *
3158409 CTGTCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCCCCTATCATTCCTCGAGAGTCCCCT
1 CTGTAATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCCCCTATCATTCCTCAAGAGTCCCCT
3158474 CCCACCGTTCAAGAGGCCA
66 CCCACCGTTCAAGAGGCCA
3158493 CTGTAATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCCCCTATCATTCCTCAAGAGTCCCCT
1 CTGTAATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCCCCTATCATTCCTCAAGAGTCCCCT
3158558 CCCACCGTTCAAGAGGCCA
66 CCCACCGTTCAAGAGGCCA
3158577 CTGT
1 CTGT
3158581 CATCGTTGAA
Statistics
Matches: 86, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
84 86 1.00
ACGTcount: A:0.22, C:0.37, G:0.17, T:0.23
Consensus pattern (84 bp):
CTGTAATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCCCCTATCATTCCTCAAGAGTCCCCT
CCCACCGTTCAAGAGGCCA
Found at i:3158614 original size:84 final size:84
Alignment explanation
Indices: 3158409--3158614 Score: 270
Period size: 84 Copynumber: 2.5 Consensus size: 84
3158399 CCCGACTCGC
* * * * * *
3158409 CTGTCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCCCCTATCATTCCTCGAGAGTCCCCT
1 CTGTAATCCCTCAAGAGTCCACTCCCACCATTCAAGAGGCCCCTATCATTCCTCAAGAGTCCCCT
3158474 CCCACCGTTCAAGAGGCCA
66 CCCACCGTTCAAGAGGCCA
* * * *
3158493 CTGTAATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCCCCTATCATTCCTCAAGAGTCCCCT
1 CTGTAATCCCTCAAGAGTCCACTCCCACCATTCAAGAGGCCCCTATCATTCCTCAAGAGTCCCCT
3158558 CCCACCGTTCAAGAGGCCA
66 CCCACCGTTCAAGAGGCCA
* ** *
3158577 CTGTCATCGTTGAAGAGGTCC-CTCCCACCATTCAAGAG
1 CTGTAATCCCTCAAGA-GTCCACTCCCACCATTCAAGAG
3158615 CCCGATTCAC
Statistics
Matches: 111, Mismatches: 10, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
84 107 0.96
85 4 0.04
ACGTcount: A:0.23, C:0.36, G:0.18, T:0.23
Consensus pattern (84 bp):
CTGTAATCCCTCAAGAGTCCACTCCCACCATTCAAGAGGCCCCTATCATTCCTCAAGAGTCCCCT
CCCACCGTTCAAGAGGCCA
Found at i:3159990 original size:14 final size:14
Alignment explanation
Indices: 3159971--3160006 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
3159961 ATTGTTTAAT
3159971 TGATTTGTAAAAGG
1 TGATTTGTAAAAGG
*
3159985 TGATTTGTAAAAGT
1 TGATTTGTAAAAGG
3159999 TGATTTGT
1 TGATTTGT
3160007 TTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.31, C:0.00, G:0.25, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGG
Found at i:3160137 original size:19 final size:19
Alignment explanation
Indices: 3160113--3160171 Score: 74
Period size: 19 Copynumber: 3.4 Consensus size: 19
3160103 AAAAAGTACT
3160113 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
3160132 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
3160146 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
3160165 ATCGCAA
1 ATCGCAA
3160172 CGAGAAATTA
Statistics
Matches: 33, Mismatches: 2, Indels: 10
0.73 0.04 0.22
Matches are distributed among these distances:
14 10 0.30
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 17 0.52
ACGTcount: A:0.46, C:0.19, G:0.22, T:0.14
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:3160155 original size:33 final size:33
Alignment explanation
Indices: 3160113--3160176 Score: 128
Period size: 33 Copynumber: 1.9 Consensus size: 33
3160103 AAAAAGTACT
3160113 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
3160146 ATCGCAATGCGAAATGAAAATCGCAACGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGA
3160177 AATTAAATTC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.45, C:0.19, G:0.23, T:0.12
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:3160178 original size:19 final size:19
Alignment explanation
Indices: 3160113--3160179 Score: 63
Period size: 19 Copynumber: 3.8 Consensus size: 19
3160103 AAAAAGTACT
* *
3160113 ATCGCAATGCGAAATGAAA
1 ATCGCAACGAGAAATGAAA
3160132 ATCGCAACGAG--A-G--A
1 ATCGCAACGAGAAATGAAA
* *
3160146 ATCGCAATGCGAAATGAAA
1 ATCGCAACGAGAAATGAAA
3160165 ATCGCAACGAGAAAT
1 ATCGCAACGAGAAAT
3160180 TAAATTCGCG
Statistics
Matches: 37, Mismatches: 6, Indels: 10
0.70 0.11 0.19
Matches are distributed among these distances:
14 10 0.27
16 2 0.05
17 2 0.05
19 23 0.62
ACGTcount: A:0.46, C:0.18, G:0.22, T:0.13
Consensus pattern (19 bp):
ATCGCAACGAGAAATGAAA
Found at i:3160230 original size:33 final size:32
Alignment explanation
Indices: 3160188--3160310 Score: 151
Period size: 33 Copynumber: 3.8 Consensus size: 32
3160178 ATTAAATTCG
*
3160188 CGTTGCGATTTTCATTTCGCATTGTGATTCCCT
1 CGTTGCGATTTTCATTTCGCATTGAGATT-CCT
**
3160221 CGTTGCGATTTTCATTTCGCATTGAGAAATT-AG
1 CGTTGCGATTTTCATTTCGCATTGAG--ATTCCT
*
3160254 CGTTACGATTTTCATTTCGCATT-ACGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGA-GATTC-CT
3160287 CGTTGCGATTTTCATTTCGCATTG
1 CGTTGCGATTTTCATTTCGCATTG
3160311 CGATAGTAAT
Statistics
Matches: 77, Mismatches: 7, Indels: 11
0.81 0.07 0.12
Matches are distributed among these distances:
31 3 0.04
32 1 0.01
33 70 0.91
35 3 0.04
ACGTcount: A:0.17, C:0.21, G:0.18, T:0.44
Consensus pattern (32 bp):
CGTTGCGATTTTCATTTCGCATTGAGATTCCT
Found at i:3160272 original size:66 final size:66
Alignment explanation
Indices: 3160181--3160310 Score: 215
Period size: 66 Copynumber: 2.0 Consensus size: 66
3160171 ACGAGAAATT
* * **
3160181 AAATTCGCGTTGCGATTTTCATTTCGCATTGTGATTCCCTCGTTGCGATTTTCATTTCGCATTGA
1 AAATTAGCGTTACGATTTTCATTTCGCATTACGATTCCCTCGTTGCGATTTTCATTTCGCATTGA
3160246 G
66 G
*
3160247 AAATTAGCGTTACGATTTTCATTTCGCATTACGATTCTCTCGTTGCGATTTTCATTTCGCATTG
1 AAATTAGCGTTACGATTTTCATTTCGCATTACGATTCCCTCGTTGCGATTTTCATTTCGCATTG
3160311 CGATAGTAAT
Statistics
Matches: 59, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
66 59 1.00
ACGTcount: A:0.18, C:0.21, G:0.18, T:0.43
Consensus pattern (66 bp):
AAATTAGCGTTACGATTTTCATTTCGCATTACGATTCCCTCGTTGCGATTTTCATTTCGCATTGA
G
Found at i:3160280 original size:19 final size:19
Alignment explanation
Indices: 3160256--3160314 Score: 56
Period size: 19 Copynumber: 3.4 Consensus size: 19
3160246 GAAATTAGCG
3160256 TTACGATTTTCATTTCGCA
1 TTACGATTTTCATTTCGCA
*
3160275 TTACGA--TTC-TCTCG--
1 TTACGATTTTCATTTCGCA
*
3160289 TTGCGATTTTCATTTCGCA
1 TTACGATTTTCATTTCGCA
*
3160308 TTGCGAT
1 TTACGAT
3160315 AGTAATTTCC
Statistics
Matches: 32, Mismatches: 3, Indels: 10
0.71 0.07 0.22
Matches are distributed among these distances:
14 5 0.16
16 7 0.22
17 7 0.22
19 13 0.41
ACGTcount: A:0.17, C:0.22, G:0.15, T:0.46
Consensus pattern (19 bp):
TTACGATTTTCATTTCGCA
Found at i:3162639 original size:12 final size:12
Alignment explanation
Indices: 3162606--3162642 Score: 65
Period size: 12 Copynumber: 3.1 Consensus size: 12
3162596 TCTTCGGGGA
*
3162606 CTTTTTCTTATT
1 CTTTTTCTTCTT
3162618 CTTTTTCTTCTT
1 CTTTTTCTTCTT
3162630 CTTTTTCTTCTT
1 CTTTTTCTTCTT
3162642 C
1 C
3162643 AGAATTATAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.03, C:0.24, G:0.00, T:0.73
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:3162851 original size:24 final size:24
Alignment explanation
Indices: 3162817--3162870 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
3162807 ATGAAACATC
*
3162817 ATCAAAATCCGAGTATTGACCAAT
1 ATCAAAATCCGAGTATTGACCAAG
* *
3162841 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
3162865 ATCAAA
1 ATCAAA
3162871 TTTCGAATAC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.41, C:0.20, G:0.17, T:0.22
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:3163680 original size:20 final size:21
Alignment explanation
Indices: 3163655--3163706 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
3163645 TTTTCCTAAT
*
3163655 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
**
3163675 TCGCAATGCGAATTTGGAAAA
1 TCGCAATGCGAATTAAGAAAA
3163696 TCGCAATGCGA
1 TCGCAATGCGA
3163707 TACTAACTAT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 12 0.43
21 16 0.57
ACGTcount: A:0.38, C:0.17, G:0.23, T:0.21
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:3163720 original size:20 final size:20
Alignment explanation
Indices: 3163695--3163762 Score: 73
Period size: 20 Copynumber: 3.4 Consensus size: 20
3163685 AATTTGGAAA
* *
3163695 ATCGCAATGCGATACTAACT
1 ATCGCAATGAGATTCTAACT
* *
3163715 ATCGCAACGAGATTCTGACT
1 ATCGCAATGAGATTCTAACT
* **
3163735 TTCGCAATGAGATTCTAAAA
1 ATCGCAATGAGATTCTAACT
3163755 ATCGCAAT
1 ATCGCAAT
3163763 CATCTTCAAA
Statistics
Matches: 38, Mismatches: 10, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
20 38 1.00
ACGTcount: A:0.35, C:0.22, G:0.16, T:0.26
Consensus pattern (20 bp):
ATCGCAATGAGATTCTAACT
Found at i:3164070 original size:20 final size:20
Alignment explanation
Indices: 3163975--3164062 Score: 106
Period size: 20 Copynumber: 4.4 Consensus size: 20
3163965 CAACGGGGAA
3163975 ATCGCAACGCGAAAATGGCT
1 ATCGCAACGCGAAAATGGCT
3163995 ATCGCAACGCGAAAATGGCT
1 ATCGCAACGCGAAAATGGCT
*** ***
3164015 ATCGCAATTTG-AAATGAAAA
1 ATCGCAACGCGAAAATG-GCT
3164035 ATCGCAACGCGAAAATGGCT
1 ATCGCAACGCGAAAATGGCT
3164055 ATCGCAAC
1 ATCGCAAC
3164063 TAGAAAATCG
Statistics
Matches: 54, Mismatches: 12, Indels: 4
0.77 0.17 0.06
Matches are distributed among these distances:
19 5 0.09
20 44 0.81
21 5 0.09
ACGTcount: A:0.39, C:0.23, G:0.22, T:0.17
Consensus pattern (20 bp):
ATCGCAACGCGAAAATGGCT
Found at i:3164113 original size:33 final size:33
Alignment explanation
Indices: 3164076--3164146 Score: 79
Period size: 33 Copynumber: 2.2 Consensus size: 33
3164066 AAAATCGCAA
3164076 TGCGAAATGAAAATCGCATTGCAATTTTCTCGT
1 TGCGAAATGAAAATCGCATTGCAATTTTCTCGT
** ** ** *
3164109 TGCGATTTTCATTTCGCATTGCGATTTTCTCGT
1 TGCGAAATGAAAATCGCATTGCAATTTTCTCGT
3164142 TGCGA
1 TGCGA
3164147 TAGTCAGTTT
Statistics
Matches: 31, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.21, C:0.20, G:0.20, T:0.39
Consensus pattern (33 bp):
TGCGAAATGAAAATCGCATTGCAATTTTCTCGT
Found at i:3164116 original size:14 final size:14
Alignment explanation
Indices: 3164094--3164147 Score: 54
Period size: 14 Copynumber: 3.5 Consensus size: 14
3164084 GAAAATCGCA
*
3164094 TTGCAATTTTCTCG
1 TTGCGATTTTCTCG
3164108 TTGCGATTTTCATTTCG
1 TTGCGATTTTC---TCG
3164125 CATTGCGATTTTCTCG
1 --TTGCGATTTTCTCG
3164141 TTGCGAT
1 TTGCGAT
3164148 AGTCAGTTTC
Statistics
Matches: 34, Mismatches: 1, Indels: 10
0.76 0.02 0.22
Matches are distributed among these distances:
14 17 0.50
16 3 0.09
17 3 0.09
19 11 0.32
ACGTcount: A:0.13, C:0.20, G:0.19, T:0.48
Consensus pattern (14 bp):
TTGCGATTTTCTCG
Found at i:3164293 original size:14 final size:14
Alignment explanation
Indices: 3164274--3164310 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
3164264 CATCAATTAA
3164274 ACAAATCAACATTT
1 ACAAATCAACATTT
* *
3164288 ACAAATCATCTTTT
1 ACAAATCAACATTT
3164302 ACAAATCAA
1 ACAAATCAA
3164311 TTAAACAATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACATTT
Found at i:3166201 original size:20 final size:19
Alignment explanation
Indices: 3166178--3166245 Score: 82
Period size: 20 Copynumber: 3.5 Consensus size: 19
3166168 GAAACTTAAA
3166178 ATCGCAACGCGAAAATGACT
1 ATCGCAACGCG-AAATGACT
*
3166198 ATCGCAACGCGGAAATGGCT
1 ATCGCAACGC-GAAATGACT
* **
3166218 ATCGCAATGCGAAATGAAA
1 ATCGCAACGCGAAATGACT
3166237 ATCGCAACG
1 ATCGCAACG
3166246 ACAAAATCGC
Statistics
Matches: 41, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
19 14 0.34
20 26 0.63
21 1 0.02
ACGTcount: A:0.38, C:0.24, G:0.24, T:0.15
Consensus pattern (19 bp):
ATCGCAACGCGAAATGACT
Found at i:3166253 original size:14 final size:14
Alignment explanation
Indices: 3166234--3166284 Score: 57
Period size: 14 Copynumber: 3.4 Consensus size: 14
3166224 ATGCGAAATG
3166234 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
3166248 AAAATCGCAATGCGAA
1 AAAATCGCAA--CGAC
3166264 ATGAAATCGCAACGAC
1 A--AAATCGCAACGAC
3166280 AAAAT
1 AAAAT
3166285 TTCGCATTGC
Statistics
Matches: 31, Mismatches: 2, Indels: 8
0.76 0.05 0.20
Matches are distributed among these distances:
14 14 0.45
16 8 0.26
18 9 0.29
ACGTcount: A:0.51, C:0.22, G:0.16, T:0.12
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:3166276 original size:32 final size:33
Alignment explanation
Indices: 3166218--3166284 Score: 127
Period size: 32 Copynumber: 2.1 Consensus size: 33
3166208 GGAAATGGCT
3166218 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
3166251 ATCGCAATGCGAAATG-AAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
3166283 AT
1 AT
3166285 TTCGCATTGC
Statistics
Matches: 34, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
32 18 0.53
33 16 0.47
ACGTcount: A:0.48, C:0.21, G:0.18, T:0.13
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGACAAA
Found at i:3166310 original size:14 final size:14
Alignment explanation
Indices: 3166291--3166379 Score: 79
Period size: 14 Copynumber: 5.7 Consensus size: 14
3166281 AAATTTCGCA
3166291 TTGCGATTTTGTCG
1 TTGCGATTTTGTCG
*
3166305 TTGCGATTTCATTTCG
1 TTGCGATTT--TGTCG
3166321 CATTGCGATTTTGTCG
1 --TTGCGATTTTGTCG
*
3166337 TTGCGATTTTCATTTCG
1 TTGCGA-TTT--TGTCG
3166354 CATTGCGATTTTGTCG
1 --TTGCGATTTTGTCG
3166370 TTGCGATTTT
1 TTGCGATTTT
3166380 CATTTCGCAT
Statistics
Matches: 62, Mismatches: 4, Indels: 18
0.74 0.05 0.21
Matches are distributed among these distances:
14 25 0.40
15 3 0.05
16 12 0.19
17 4 0.06
18 12 0.19
19 6 0.10
ACGTcount: A:0.11, C:0.17, G:0.22, T:0.49
Consensus pattern (14 bp):
TTGCGATTTTGTCG
Found at i:3166353 original size:33 final size:33
Alignment explanation
Indices: 3166283--3166395 Score: 219
Period size: 33 Copynumber: 3.5 Consensus size: 33
3166273 CAACGACAAA
3166283 ATTTCGCATTGCGATTTTGTCGTTGCGA-TTTC
1 ATTTCGCATTGCGATTTTGTCGTTGCGATTTTC
3166315 ATTTCGCATTGCGATTTTGTCGTTGCGATTTTC
1 ATTTCGCATTGCGATTTTGTCGTTGCGATTTTC
3166348 ATTTCGCATTGCGATTTTGTCGTTGCGATTTTC
1 ATTTCGCATTGCGATTTTGTCGTTGCGATTTTC
3166381 ATTTCGCATTGCGAT
1 ATTTCGCATTGCGAT
3166396 AGCCATTTCC
Statistics
Matches: 80, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
32 28 0.35
33 52 0.65
ACGTcount: A:0.13, C:0.19, G:0.21, T:0.47
Consensus pattern (33 bp):
ATTTCGCATTGCGATTTTGTCGTTGCGATTTTC
Found at i:3166414 original size:20 final size:19
Alignment explanation
Indices: 3166380--3166434 Score: 65
Period size: 20 Copynumber: 2.8 Consensus size: 19
3166370 TTGCGATTTT
*
3166380 CATTTCGCATTGCGATAGC
1 CATTTCGCGTTGCGATAGC
*
3166399 CATTTCCGCGTTGCGATAGT
1 CATTT-CGCGTTGCGATAGC
*
3166419 CATTTTCGTGTTGCGA
1 CA-TTTCGCGTTGCGA
3166435 AAGTAAACTA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
19 5 0.16
20 23 0.74
21 3 0.10
ACGTcount: A:0.16, C:0.24, G:0.24, T:0.36
Consensus pattern (19 bp):
CATTTCGCGTTGCGATAGC
Found at i:3166942 original size:18 final size:18
Alignment explanation
Indices: 3166916--3166960 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
3166906 GTCGATCAGA
*
3166916 TGATGGCTCTGGGTGAGG
1 TGATGGCTCTGGGCGAGG
*
3166934 TGATAGCTCTGGGCGAGG
1 TGATGGCTCTGGGCGAGG
3166952 TGATGGCTC
1 TGATGGCTC
3166961 CCGAAGTGGA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.13, C:0.16, G:0.44, T:0.27
Consensus pattern (18 bp):
TGATGGCTCTGGGCGAGG
Found at i:3168314 original size:20 final size:20
Alignment explanation
Indices: 3168281--3168334 Score: 56
Period size: 20 Copynumber: 2.7 Consensus size: 20
3168271 AATAGTTTCT
3168281 GAAAATGA-TAATCGAAACAC
1 GAAAATGACT-ATCGAAACAC
* *
3168301 GAAAATGACTATCGCAACGC
1 GAAAATGACTATCGAAACAC
**
3168321 GAATTTGACTATCG
1 GAAAATGACTATCG
3168335 CAACGAGAGA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
20 28 0.97
21 1 0.03
ACGTcount: A:0.43, C:0.19, G:0.19, T:0.20
Consensus pattern (20 bp):
GAAAATGACTATCGAAACAC
Found at i:3168620 original size:20 final size:21
Alignment explanation
Indices: 3168595--3168644 Score: 59
Period size: 22 Copynumber: 2.4 Consensus size: 21
3168585 CTCTGAGAGA
3168595 TGGAGAT-AGACGGATTTCGC
1 TGGAGATGAGACGGATTTCGC
*
3168615 TGGAGATGGGGACGGATTTCG-
1 TGGAGAT-GAGACGGATTTCGC
3168636 TCGGAGATG
1 T-GGAGATG
3168645 GGTGAGAGAG
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
20 7 0.27
21 2 0.08
22 17 0.65
ACGTcount: A:0.22, C:0.12, G:0.42, T:0.24
Consensus pattern (21 bp):
TGGAGATGAGACGGATTTCGC
Found at i:3168631 original size:22 final size:22
Alignment explanation
Indices: 3168603--3168646 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
3168593 GATGGAGATA
3168603 GACGGATTTCG-CTGGAGATGGG
1 GACGGATTTCGTC-GGAGATGGG
3168625 GACGGATTTCGTCGGAGATGGG
1 GACGGATTTCGTCGGAGATGGG
3168647 TGAGAGAGTG
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 20 0.95
23 1 0.05
ACGTcount: A:0.18, C:0.14, G:0.45, T:0.23
Consensus pattern (22 bp):
GACGGATTTCGTCGGAGATGGG
Found at i:3168860 original size:20 final size:20
Alignment explanation
Indices: 3168835--3168886 Score: 86
Period size: 20 Copynumber: 2.6 Consensus size: 20
3168825 ATTATGTATT
3168835 ATCGCGTTGCGAAAGTCAGA
1 ATCGCGTTGCGAAAGTCAGA
*
3168855 ATCGCGTTGCGAAAGTCAGT
1 ATCGCGTTGCGAAAGTCAGA
*
3168875 ATCTCGTTGCGA
1 ATCGCGTTGCGA
3168887 TTTTGTATTA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.25, C:0.21, G:0.29, T:0.25
Consensus pattern (20 bp):
ATCGCGTTGCGAAAGTCAGA
Found at i:3168923 original size:20 final size:20
Alignment explanation
Indices: 3168814--3168948 Score: 76
Period size: 20 Copynumber: 6.7 Consensus size: 20
3168804 CGCTTTGAAA
*
3168814 ATCGCATTGCGATTATGT-ATT
1 ATCGCATTGCGA-TA-GTAAGT
* * * *
3168835 ATCGCGTTGCGAAAGTCAGA
1 ATCGCATTGCGATAGTAAGT
* * *
3168855 ATCGCGTTGCGAAAGTCAGT
1 ATCGCATTGCGATAGTAAGT
* * * *
3168875 ATCTCGTTGCGATTTTGT-ATT
1 ATCGCATTGCGA--TAGTAAGT
3168896 ATCGCATTGCGATAGTAAGT
1 ATCGCATTGCGATAGTAAGT
* * *
3168916 ATCACATTGTGATAGTCAGT
1 ATCGCATTGCGATAGTAAGT
*
3168936 ATTGCATTGCGAT
1 ATCGCATTGCGAT
3168949 TTTCCCAATT
Statistics
Matches: 91, Mismatches: 19, Indels: 9
0.76 0.16 0.08
Matches are distributed among these distances:
19 5 0.05
20 61 0.67
21 23 0.25
22 2 0.02
ACGTcount: A:0.25, C:0.16, G:0.24, T:0.35
Consensus pattern (20 bp):
ATCGCATTGCGATAGTAAGT
Found at i:3168933 original size:61 final size:61
Alignment explanation
Indices: 3168817--3168951 Score: 164
Period size: 61 Copynumber: 2.2 Consensus size: 61
3168807 TTTGAAAATC
* * * * *
3168817 GCATTGCGATTATGTATTATCGCGTTGCGAAAGTCAGAATCGCGTTGCGAAAGTCAGTATCT
1 GCATTGCGATTTTGTATTATCGCATTGCGAAAGTAAGAATCACATTGCGAAAGTCAGTAT-T
* * * * *
3168879 -CGTTGCGATTTTGTATTATCGCATTGCGATAGTAAGTATCACATTGTGATAGTCAGTATT
1 GCATTGCGATTTTGTATTATCGCATTGCGAAAGTAAGAATCACATTGCGAAAGTCAGTATT
3168939 GCATTGCGATTTT
1 GCATTGCGATTTT
3168952 CCCAATTCGC
Statistics
Matches: 61, Mismatches: 11, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
60 1 0.02
61 60 0.98
ACGTcount: A:0.24, C:0.16, G:0.24, T:0.36
Consensus pattern (61 bp):
GCATTGCGATTTTGTATTATCGCATTGCGAAAGTAAGAATCACATTGCGAAAGTCAGTATT
Found at i:3169932 original size:23 final size:22
Alignment explanation
Indices: 3169899--3169941 Score: 59
Period size: 23 Copynumber: 1.9 Consensus size: 22
3169889 TTGGTATTGG
*
3169899 AAACAAGATAAAAAATAAGATTA
1 AAACAAAATAAAAAA-AAGATTA
*
3169922 AAACAAAATAAAGAAAAGAT
1 AAACAAAATAAAAAAAAGAT
3169942 AAAGGAATTG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 5 0.28
23 13 0.72
ACGTcount: A:0.72, C:0.05, G:0.09, T:0.14
Consensus pattern (22 bp):
AAACAAAATAAAAAAAAGATTA
Found at i:3178364 original size:13 final size:14
Alignment explanation
Indices: 3178345--3178386 Score: 50
Period size: 15 Copynumber: 2.9 Consensus size: 14
3178335 TTCTTCGATC
3178345 TAATTTAATAAAAA
1 TAATTTAATAAAAA
3178359 -AATTTAAAATAAAAA
1 TAATTT--AATAAAAA
*
3178374 TAATTAAATAAAA
1 TAATTTAATAAAA
3178387 TGTTGATTTA
Statistics
Matches: 24, Mismatches: 1, Indels: 6
0.77 0.03 0.19
Matches are distributed among these distances:
13 5 0.21
14 7 0.29
15 8 0.33
16 4 0.17
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (14 bp):
TAATTTAATAAAAA
Found at i:3178371 original size:15 final size:14
Alignment explanation
Indices: 3178345--3178386 Score: 50
Period size: 14 Copynumber: 2.9 Consensus size: 14
3178335 TTCTTCGATC
*
3178345 TAATTTAATAAAAA
1 TAATTAAATAAAAA
3178359 -AATTTAAAATAAAAA
1 TAA-TT-AAATAAAAA
3178374 TAATTAAATAAAA
1 TAATTAAATAAAA
3178387 TGTTGATTTA
Statistics
Matches: 24, Mismatches: 1, Indels: 6
0.77 0.03 0.19
Matches are distributed among these distances:
13 2 0.08
14 10 0.42
15 10 0.42
16 2 0.08
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (14 bp):
TAATTAAATAAAAA
Found at i:3198904 original size:2 final size:2
Alignment explanation
Indices: 3198897--3198923 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
3198887 CTTCTATCTT
3198897 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 T
3198924 TAATTAAGTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3203621 original size:17 final size:17
Alignment explanation
Indices: 3203599--3203641 Score: 70
Period size: 17 Copynumber: 2.5 Consensus size: 17
3203589 ATATTATTCG
3203599 AACGAGTCC-CGAAGCCA
1 AACGAG-CCTCGAAGCCA
3203616 AACGAGCCTCGAAGCCA
1 AACGAGCCTCGAAGCCA
3203633 AACGAGCCT
1 AACGAGCCT
3203642 GTGCAAATTG
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
16 2 0.08
17 23 0.92
ACGTcount: A:0.35, C:0.35, G:0.23, T:0.07
Consensus pattern (17 bp):
AACGAGCCTCGAAGCCA
Found at i:3204699 original size:194 final size:194
Alignment explanation
Indices: 3204295--3204864 Score: 469
Period size: 194 Copynumber: 2.9 Consensus size: 194
3204285 TGAATTGTTT
* *
3204295 TATTTACTTGCATATACGGTAACGGTAATAGTTCTTCTTTGATTAAATTGTGCAACCAGTCCTTC
1 TATTTAATTGCATATACGGTAATGGTAATAGTTCTTCTTT--TT-AATT-TGCAA-CAGTCCTTC
* * * * * *
3204360 TACAGTTATCAAATTCTAAATTTTGTTCTTAATCATCCCTCATCATTGTCGATATGTCCGAGTGG
61 TACAATTACCAAATTCTAAATTTAGTCCTTAATCATCCCTCAACATTGTCGATATGCCCGAGTGG
* * * * *
3204425 TTAAGGAGTCAGACTCGAAATCTGATGGGCTACGCCTGCGCAGGTTCGAATCCTGCTGTCGACGC
126 TTAAGGAGTCAGACTCAAAATCAGATGGGCTACGCCTGCGAAGGTTCGAATCCTACTGTAGACGC
*
3204490 TTTT
191 TTTC
* ** * * *
3204494 TCTCCAATTGCATATTCGGTAATGGTAATAGTTCTTCGTTTTAATTTGCAACAATCCTTCTACAA
1 TATTTAATTGCATATACGGTAATGGTAATAGTTCTTCTTTTTAATTTGCAACAGTCCTTCTACAA
* * * **
3204559 TTACCAAATATC-ATATTTAGTCCTTGATCGGT-TTTCAACATTGTCGATATGCCCGAGTGGTTA
66 TTACCAAAT-TCTAAATTTAGTCCTTAATC-ATCCCTCAACATTGTCGATATGCCCGAGTGGTTA
** * * * * *
3204622 ATTAGTCAGACTCAAAATCAGATGTG-TTCTTCCTGCGAAGGTTCG-ATCCTACTGTTATATGCT
129 AGGAGTCAGACTCAAAATCAGATGGGCTAC-GCCTGCGAAGGTTCGAATCCTACTG-TAGACGCT
3204685 TTC
192 TTC
* *
3204688 TATTTAATTGCACATACGGTAAT-G--ATAGTTCTT-TTGTTTATTTTGCACACAGTCCTTCTAC
1 TATTTAATTGCATATACGGTAATGGTAATAGTTCTTCTT-TTTAATTTGCA-ACAGTCCTTCTAC
** * ** * * ** *
3204749 CTTTA-GAAGA-TCTGAGTTTTAGTCCTTAA-CTAACCCTCACCGGTGTCGATATGTCCGAGTGG
64 AATTACCAA-ATTCT-AAATTTAGTCCTTAATC-ATCCCTCAACATTGTCGATATGCCCGAGTGG
* ** * * * * *
3204811 TTAAGGAGACAGACTTGAAATCTGTTGGGCTATGCCTGCGCAGGCTCGAATCCT
126 TTAAGGAGTCAGACTCAAAATCAGATGGGCTACGCCTGCGAAGGTTCGAATCCT
3204865 GTTGTCGACG
Statistics
Matches: 291, Mismatches: 68, Indels: 30
0.75 0.17 0.08
Matches are distributed among these distances:
190 3 0.01
191 22 0.08
192 83 0.29
193 17 0.06
194 119 0.41
195 8 0.03
196 4 0.01
197 2 0.01
199 33 0.11
ACGTcount: A:0.25, C:0.21, G:0.19, T:0.36
Consensus pattern (194 bp):
TATTTAATTGCATATACGGTAATGGTAATAGTTCTTCTTTTTAATTTGCAACAGTCCTTCTACAA
TTACCAAATTCTAAATTTAGTCCTTAATCATCCCTCAACATTGTCGATATGCCCGAGTGGTTAAG
GAGTCAGACTCAAAATCAGATGGGCTACGCCTGCGAAGGTTCGAATCCTACTGTAGACGCTTTC
Found at i:3206551 original size:76 final size:76
Alignment explanation
Indices: 3206429--3206576 Score: 260
Period size: 76 Copynumber: 1.9 Consensus size: 76
3206419 TTCTTGATAG
* * *
3206429 ACTCTTGCATTAGATAATCTCTTTGATTTTGAACATCTTGAGATGATAAATTGAATACGATCAGT
1 ACTCTTGCATTAGATAATCTCTTTGATTTTGAACATCTAGACATGATAAATCGAATACGATCAGT
3206494 TCCAAAGCTTC
66 TCCAAAGCTTC
*
3206505 ACTCTTGCATTAGATAATCTCTTTGATTTTGAACATCTAGACATGATAAATCGAATGCGATCAGT
1 ACTCTTGCATTAGATAATCTCTTTGATTTTGAACATCTAGACATGATAAATCGAATACGATCAGT
3206570 TCCAAAG
66 TCCAAAG
3206577 TTTCGCCTAC
Statistics
Matches: 68, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
76 68 1.00
ACGTcount: A:0.32, C:0.18, G:0.15, T:0.35
Consensus pattern (76 bp):
ACTCTTGCATTAGATAATCTCTTTGATTTTGAACATCTAGACATGATAAATCGAATACGATCAGT
TCCAAAGCTTC
Found at i:3216996 original size:23 final size:23
Alignment explanation
Indices: 3216965--3217009 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
3216955 TCGGAACATA
* *
3216965 TATGTGGTCCTTCGGGACAATTC
1 TATGAGGTCCTTCAGGACAATTC
*
3216988 TATGAGGTCCTTCAGGATAATT
1 TATGAGGTCCTTCAGGACAATT
3217010 TTATATGGCA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.22, C:0.18, G:0.24, T:0.36
Consensus pattern (23 bp):
TATGAGGTCCTTCAGGACAATTC
Found at i:3217793 original size:25 final size:24
Alignment explanation
Indices: 3217750--3217816 Score: 91
Period size: 25 Copynumber: 2.8 Consensus size: 24
3217740 CCGAAGTACG
3217750 ACATAG-ATTTGTCCCGAATGACC
1 ACATAGAATTTGTCCCGAATGACC
* *
3217773 GCATAGAAATTTGTCCTGAATGACC
1 ACATAG-AATTTGTCCCGAATGACC
*
3217798 ACATAGAATTTGTCTCGAA
1 ACATAGAATTTGTCCCGAA
3217817 GGATCGCGTA
Statistics
Matches: 37, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
23 5 0.14
24 11 0.30
25 21 0.57
ACGTcount: A:0.33, C:0.21, G:0.18, T:0.28
Consensus pattern (24 bp):
ACATAGAATTTGTCCCGAATGACC
Found at i:3218531 original size:20 final size:22
Alignment explanation
Indices: 3218506--3218545 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
3218496 TGTTGTATAT
3218506 AGCCG-TTGGGGATG-TTTTGG
1 AGCCGTTTGGGGATGATTTTGG
3218526 AGCCGTTTGGGGATGATTTT
1 AGCCGTTTGGGGATGATTTT
3218546 TCTACTCAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 5 0.28
21 9 0.50
22 4 0.22
ACGTcount: A:0.12, C:0.10, G:0.40, T:0.38
Consensus pattern (22 bp):
AGCCGTTTGGGGATGATTTTGG
Found at i:3218762 original size:21 final size:21
Alignment explanation
Indices: 3218736--3218791 Score: 112
Period size: 21 Copynumber: 2.7 Consensus size: 21
3218726 AGTGCAGGTA
3218736 CATGGATGCACTGCAGGGATG
1 CATGGATGCACTGCAGGGATG
3218757 CATGGATGCACTGCAGGGATG
1 CATGGATGCACTGCAGGGATG
3218778 CATGGATGCACTGC
1 CATGGATGCACTGC
3218792 GACACCATTT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.23, C:0.21, G:0.36, T:0.20
Consensus pattern (21 bp):
CATGGATGCACTGCAGGGATG
Found at i:3218890 original size:29 final size:29
Alignment explanation
Indices: 3218869--3218926 Score: 91
Period size: 30 Copynumber: 2.0 Consensus size: 29
3218859 AAACTTTGAA
3218869 TAAATTCAATT-AAGTCCAAAAACATTTTG
1 TAAATTCAATTCAAGTCCAAAAACA-TTTG
3218898 TAAATTCAATTCAAGTCCAAAAACCATTT
1 TAAATTCAATTCAAGTCCAAAAA-CATTT
3218927 TTCCTTAAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
29 11 0.41
30 14 0.52
31 2 0.07
ACGTcount: A:0.45, C:0.17, G:0.05, T:0.33
Consensus pattern (29 bp):
TAAATTCAATTCAAGTCCAAAAACATTTG
Found at i:3218916 original size:30 final size:30
Alignment explanation
Indices: 3218869--3218927 Score: 102
Period size: 29 Copynumber: 2.0 Consensus size: 30
3218859 AAACTTTGAA
3218869 TAAATTCAATTAAGTCCAAAAA-CATTTTG
1 TAAATTCAATTAAGTCCAAAAACCATTTTG
3218898 TAAATTCAATTCAAGTCCAAAAACCATTTT
1 TAAATTCAATT-AAGTCCAAAAACCATTTT
3218928 TCCTTAAATT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
29 11 0.39
30 11 0.39
31 6 0.21
ACGTcount: A:0.44, C:0.17, G:0.05, T:0.34
Consensus pattern (30 bp):
TAAATTCAATTAAGTCCAAAAACCATTTTG
Found at i:3222255 original size:20 final size:19
Alignment explanation
Indices: 3222169--3222259 Score: 57
Period size: 20 Copynumber: 4.9 Consensus size: 19
3222159 GTTGCAGCCT
* *
3222169 TGATGCATGGATGCATGGCA
1 TGATGCATCGATGCATTG-A
* *
3222189 GGATGCATCGATGCACT-A
1 TGATGCATCGATGCATTGA
* *
3222207 AG-TGCATTCGATG-TTTGA
1 TGATGCA-TCGATGCATTGA
*
3222225 -G-TGCATGGATGCATTGCA
1 TGATGCATCGATGCATTG-A
3222243 TGATGCATCGATGCATT
1 TGATGCATCGATGCATT
3222260 AGTGCAGGTG
Statistics
Matches: 55, Mismatches: 10, Indels: 12
0.71 0.13 0.16
Matches are distributed among these distances:
16 5 0.09
17 13 0.24
18 10 0.18
19 1 0.02
20 26 0.47
ACGTcount: A:0.24, C:0.16, G:0.30, T:0.30
Consensus pattern (19 bp):
TGATGCATCGATGCATTGA
Found at i:3222294 original size:21 final size:21
Alignment explanation
Indices: 3222268--3222313 Score: 83
Period size: 21 Copynumber: 2.2 Consensus size: 21
3222258 TTAGTGCAGG
3222268 TGCATGAATGCACTGCAGGGA
1 TGCATGAATGCACTGCAGGGA
*
3222289 TGCATGGATGCACTGCAGGGA
1 TGCATGAATGCACTGCAGGGA
3222310 TGCA
1 TGCA
3222314 CTTTGACACC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.26, C:0.20, G:0.35, T:0.20
Consensus pattern (21 bp):
TGCATGAATGCACTGCAGGGA
Found at i:3222416 original size:29 final size:29
Alignment explanation
Indices: 3222395--3222452 Score: 91
Period size: 30 Copynumber: 2.0 Consensus size: 29
3222385 AAACTTTGAA
3222395 TAAATTCAATT-AAGTCCAAAAACATTTTG
1 TAAATTCAATTCAAGTCCAAAAACA-TTTG
3222424 TAAATTCAATTCAAGTCCAAAAACCATTT
1 TAAATTCAATTCAAGTCCAAAAA-CATTT
3222453 TGCCTTAAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
29 11 0.41
30 14 0.52
31 2 0.07
ACGTcount: A:0.45, C:0.17, G:0.05, T:0.33
Consensus pattern (29 bp):
TAAATTCAATTCAAGTCCAAAAACATTTG
Found at i:3222442 original size:30 final size:30
Alignment explanation
Indices: 3222395--3222454 Score: 104
Period size: 29 Copynumber: 2.0 Consensus size: 30
3222385 AAACTTTGAA
3222395 TAAATTCAATTAAGTCCAAAAA-CATTTTG
1 TAAATTCAATTAAGTCCAAAAACCATTTTG
3222424 TAAATTCAATTCAAGTCCAAAAACCATTTTG
1 TAAATTCAATT-AAGTCCAAAAACCATTTTG
3222455 CCTTAAATTG
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
29 11 0.38
30 11 0.38
31 7 0.24
ACGTcount: A:0.43, C:0.17, G:0.07, T:0.33
Consensus pattern (30 bp):
TAAATTCAATTAAGTCCAAAAACCATTTTG
Found at i:3226036 original size:21 final size:21
Alignment explanation
Indices: 3226012--3226135 Score: 178
Period size: 21 Copynumber: 5.7 Consensus size: 21
3226002 AAAGTGACAT
3226012 AGTACACAAAGTACTACTCCA
1 AGTACACAAAGTACTACTCCA
*
3226033 AGTACACAAAGTACTATTGCCA
1 AGTACACAAAGTACTACT-CCA
3226055 TAGTACACAAAGTACTACTCCA
1 -AGTACACAAAGTACTACTCCA
3226077 AGTACACAAAGTACT-CATGCCA
1 AGTACACAAAGTACTAC-T-CCA
3226099 TAGTACACAAAGTACTACTCCA
1 -AGTACACAAAGTACTACTCCA
*
3226121 AGTACATAAAGTACT
1 AGTACACAAAGTACT
3226136 CTTATGAAAA
Statistics
Matches: 94, Mismatches: 3, Indels: 12
0.86 0.03 0.11
Matches are distributed among these distances:
20 1 0.01
21 47 0.50
22 12 0.13
23 33 0.35
24 1 0.01
ACGTcount: A:0.42, C:0.25, G:0.11, T:0.22
Consensus pattern (21 bp):
AGTACACAAAGTACTACTCCA
Found at i:3226059 original size:44 final size:44
Alignment explanation
Indices: 3226009--3226136 Score: 231
Period size: 44 Copynumber: 2.9 Consensus size: 44
3225999 CACAAAGTGA
3226009 CATAGTACACAAAGTACTACTCCAAGTACACAAAGTACT-ATTGC
1 CATAGTACACAAAGTACTACTCCAAGTACACAAAGTACTCA-TGC
3226053 CATAGTACACAAAGTACTACTCCAAGTACACAAAGTACTCATGC
1 CATAGTACACAAAGTACTACTCCAAGTACACAAAGTACTCATGC
*
3226097 CATAGTACACAAAGTACTACTCCAAGTACATAAAGTACTC
1 CATAGTACACAAAGTACTACTCCAAGTACACAAAGTACTC
3226137 TTATGAAAAT
Statistics
Matches: 82, Mismatches: 1, Indels: 2
0.96 0.01 0.02
Matches are distributed among these distances:
44 81 0.99
45 1 0.01
ACGTcount: A:0.41, C:0.26, G:0.11, T:0.22
Consensus pattern (44 bp):
CATAGTACACAAAGTACTACTCCAAGTACACAAAGTACTCATGC
Found at i:3231584 original size:43 final size:42
Alignment explanation
Indices: 3231536--3231895 Score: 231
Period size: 43 Copynumber: 8.4 Consensus size: 42
3231526 AATAGAGGCA
* *
3231536 TCAATTATAAAGGTAGAAAGTGAGATTCAGAAAATTAGGGACC
1 TCAATTATAAAGGTAGAAAGTGAGATTAAAAAAATTAGGG-CC
* * * *
3231579 TCAATTATAAAGGT-GAAAAGCG-GTACTGAAAAAATTAGGGGCG
1 TCAATTATAAAGGTAG-AAAGTGAG-ATTAAAAAAATTA-GGGCC
* *
3231622 TCAATTATAAAAGTA-AAATTTGAGATTAAAAAAATTATGGGCC
1 TCAATTATAAAGGTAGAAA-GTGAGATTAAAAAAATTA-GGGCC
* *
3231665 TCAATTATGAAGGTAGAAAGTG-GCAATTTTTTAAAAAAAAATTAGAGGCT
1 TCAATTATAAAGGTAGAAAGTGAG--A----TT--AAAAAAATTAG-GGCC
* *
3231715 TTAATTATAAAGGTAAAAAGTGAGA-TAAAAAAA-TAGGGCCC
1 TCAATTATAAAGGTAGAAAGTGAGATTAAAAAAATTAGGG-CC
* * * * *
3231756 TCAATTATATAGGTAGAAAATAAGATTGAAAAAAATAAGGGGTC
1 TCAATTATAAAGGTAGAAAGTGAGATT-AAAAAAATTA-GGGCC
*
3231800 TTAATTATAAAGGTA-AAAGTGAGA-T-AAAAAA-TAGGGCCC
1 TCAATTATAAAGGTAGAAAGTGAGATTAAAAAAATTAGGG-CC
* * * * *
3231839 TCAATTATATA-GTAGAAAATAAGATTGAAAAAAATAAGGGGTC
1 TCAATTATAAAGGTAGAAAGTGAGATT-AAAAAAATTA-GGGCC
*
3231882 TTAATTAT-AAGGTA
1 TCAATTATAAAGGTA
3231896 AAATTAGGGG
Statistics
Matches: 246, Mismatches: 41, Indels: 60
0.71 0.12 0.17
Matches are distributed among these distances:
38 6 0.02
39 18 0.07
40 9 0.04
41 24 0.10
42 22 0.09
43 100 0.41
44 27 0.11
45 3 0.01
48 2 0.01
49 2 0.01
50 32 0.13
51 1 0.00
ACGTcount: A:0.47, C:0.07, G:0.20, T:0.26
Consensus pattern (42 bp):
TCAATTATAAAGGTAGAAAGTGAGATTAAAAAAATTAGGGCC
Found at i:3231739 original size:93 final size:91
Alignment explanation
Indices: 3231607--3231856 Score: 247
Period size: 93 Copynumber: 2.8 Consensus size: 91
3231597 AGCGGTACTG
* **
3231607 AAAAAATTAGGGGCGTCAATTATAAAAGTAAAATTTGAGATTAAAAAAATTATGGG-CCTCAATT
1 AAAAAATTAGAGGCGTCAATTATAAAAGTAAAAAGTGAGA-TAAAAAAA-TA-GGGCCCTCAATT
3231671 ATGA-AGGTAGAAAGTGGCAATTTTTTAAA
63 AT-ATAGGTAGAAAGTGGCAATTTTTTAAA
* * *
3231700 AAAAAATTAGAGGCTTTAATTATAAAGGTAAAAAGTGAGATAAAAAAATAGGGCCCTCAATTATA
1 AAAAAATTAGAGGCGTCAATTATAAAAGTAAAAAGTGAGATAAAAAAATAGGGCCCTCAATTATA
* ** *
3231765 TAGGTAGAAAAT---AA--GATT-GA
66 TAGGTAGAAAGTGGCAATTTTTTAAA
* *
3231785 AAAAAA-TA-AGGGGTCTTAATTATAAAGGT-AAAAGTGAGAT-AAAAAATAGGGCCCTCAATTA
1 AAAAAATTAGAGGCGTC--AATTATAAAAGTAAAAAGTGAGATAAAAAAATAGGGCCCTCAATTA
3231846 TATA-GTAGAAA
64 TATAGGTAGAAA
3231857 ATAAGATTGA
Statistics
Matches: 140, Mismatches: 13, Indels: 19
0.81 0.08 0.11
Matches are distributed among these distances:
82 7 0.05
83 29 0.21
84 13 0.09
85 19 0.14
86 2 0.01
88 2 0.01
90 4 0.03
91 22 0.16
92 8 0.06
93 34 0.24
ACGTcount: A:0.48, C:0.06, G:0.19, T:0.26
Consensus pattern (91 bp):
AAAAAATTAGAGGCGTCAATTATAAAAGTAAAAAGTGAGATAAAAAAATAGGGCCCTCAATTATA
TAGGTAGAAAGTGGCAATTTTTTAAA
Found at i:3231876 original size:82 final size:84
Alignment explanation
Indices: 3231715--3231898 Score: 338
Period size: 82 Copynumber: 2.2 Consensus size: 84
3231705 ATTAGAGGCT
3231715 TTAATTATAAAGGTAAAAAGTGAGATAAAAAAATAGGGCCCTCAATTATATAGGTAGAAAATAAG
1 TTAATTATAAAGGT-AAAAGTGAGATAAAAAAATAGGGCCCTCAATTATATAGGTAGAAAATAAG
3231780 ATTGAAAAAAATAAGGGGTC
65 ATTGAAAAAAATAAGGGGTC
3231800 TTAATTATAAAGGTAAAAGTGAGAT-AAAAAATAGGGCCCTCAATTATATA-GTAGAAAATAAGA
1 TTAATTATAAAGGTAAAAGTGAGATAAAAAAATAGGGCCCTCAATTATATAGGTAGAAAATAAGA
3231863 TTGAAAAAAATAAGGGGTC
66 TTGAAAAAAATAAGGGGTC
3231882 TTAATTAT-AAGGTAAAA
1 TTAATTATAAAGGTAAAA
3231899 TTAGGGGTCA
Statistics
Matches: 99, Mismatches: 0, Indels: 4
0.96 0.00 0.04
Matches are distributed among these distances:
81 9 0.09
82 40 0.40
83 25 0.25
84 11 0.11
85 14 0.14
ACGTcount: A:0.51, C:0.05, G:0.19, T:0.25
Consensus pattern (84 bp):
TTAATTATAAAGGTAAAAGTGAGATAAAAAAATAGGGCCCTCAATTATATAGGTAGAAAATAAGA
TTGAAAAAAATAAGGGGTC
Found at i:3231942 original size:43 final size:43
Alignment explanation
Indices: 3231895--3231988 Score: 111
Period size: 43 Copynumber: 2.2 Consensus size: 43
3231885 ATTATAAGGT
*
3231895 AAAATTAGGGG-TCACAATAAAAAGGTAGAAAG-TGAGATTGAAA
1 AAAATTAGGGGCTCA-AATAAAAAGGTAAAAAGTTG-GATTGAAA
* * * *
3231938 AAAATTTGGGGCTCAATTATAGAGGTAAAAAGTTGGATTGAAA
1 AAAATTAGGGGCTCAAATAAAAAGGTAAAAAGTTGGATTGAAA
3231981 AAAATTAG
1 AAAATTAG
3231989 AAACCTCAAT
Statistics
Matches: 43, Mismatches: 6, Indels: 4
0.81 0.11 0.08
Matches are distributed among these distances:
43 38 0.88
44 5 0.12
ACGTcount: A:0.48, C:0.04, G:0.24, T:0.23
Consensus pattern (43 bp):
AAAATTAGGGGCTCAAATAAAAAGGTAAAAAGTTGGATTGAAA
Found at i:3232072 original size:43 final size:42
Alignment explanation
Indices: 3231973--3232072 Score: 112
Period size: 43 Copynumber: 2.3 Consensus size: 42
3231963 TAAAAAGTTG
*
3231973 GATTGAAAAAAATTAGAAACCTCAATTAAAAAGATAAAAATAA
1 GATT-AAAAAAATTAAAAACCTCAATTAAAAAGATAAAAATAA
* * * *
3232016 GATTAACAGAATTAAAAACTTCAATTATAAAA-ATAAAAAATAT
1 GATTAAAAAAATTAAAAACCTCAATTA-AAAAGAT-AAAAATAA
*
3232059 TATTAAAAAAATTA
1 GATTAAAAAAATTA
3232073 TATATCCTAT
Statistics
Matches: 47, Mismatches: 8, Indels: 4
0.80 0.14 0.07
Matches are distributed among these distances:
42 21 0.45
43 26 0.55
ACGTcount: A:0.62, C:0.06, G:0.06, T:0.26
Consensus pattern (42 bp):
GATTAAAAAAATTAAAAACCTCAATTAAAAAGATAAAAATAA
Found at i:3234907 original size:152 final size:151
Alignment explanation
Indices: 3234730--3235032 Score: 588
Period size: 152 Copynumber: 2.0 Consensus size: 151
3234720 AAGTAAATAT
*
3234730 TCATTTTGGTTAATATTCTTTTTTTATAATATTTTGACCTCCATTATTTCATTTGATAAAAAAAC
1 TCATTTTGGTTAATATTCCTTTTTTATAATATTTTGACCTCCATTATTTCATTTGATAAAAAAAC
3234795 ATCCCTATTATGAAGCGTTGATCCTTTTCTAACTAATGAACTCTATCCATGAATGGATTTTTTCC
66 ATCCCTATTATGAAGCGTTGATCCTTTTCTAACTAATGAACTCTATCCATGAATGGATTTTTTCC
3234860 CGAAATAATGTTTGGGGTCAAA
131 CGAAATAATG-TTGGGGTCAAA
3234882 TCATTTTGGTTAATATTCCTTTTTTATAATATTTTGACCTCCATTATTTCATTTGATAAAAAAAC
1 TCATTTTGGTTAATATTCCTTTTTTATAATATTTTGACCTCCATTATTTCATTTGATAAAAAAAC
3234947 ATCCCTATTATGAAGCGTTGATCCTTTTCTAACTAATGAACTCTATCCATGAATGGATTTTTTCC
66 ATCCCTATTATGAAGCGTTGATCCTTTTCTAACTAATGAACTCTATCCATGAATGGATTTTTTCC
3235012 CGAAATAATGTTGGGGTCAAA
131 CGAAATAATGTTGGGGTCAAA
3235033 ATAATAAAAA
Statistics
Matches: 150, Mismatches: 1, Indels: 1
0.99 0.01 0.01
Matches are distributed among these distances:
151 11 0.07
152 139 0.93
ACGTcount: A:0.30, C:0.16, G:0.12, T:0.42
Consensus pattern (151 bp):
TCATTTTGGTTAATATTCCTTTTTTATAATATTTTGACCTCCATTATTTCATTTGATAAAAAAAC
ATCCCTATTATGAAGCGTTGATCCTTTTCTAACTAATGAACTCTATCCATGAATGGATTTTTTCC
CGAAATAATGTTGGGGTCAAA
Found at i:3235254 original size:2 final size:2
Alignment explanation
Indices: 3235242--3235276 Score: 61
Period size: 2 Copynumber: 17.0 Consensus size: 2
3235232 CGTGGCATTA
3235242 AT AT CAT 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
3235277 GGTTGCCTTT
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 30 0.94
3 2 0.06
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:3235775 original size:2 final size:2
Alignment explanation
Indices: 3235768--3235793 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
3235758 TCAATATGGG
3235768 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
3235794 GCTATTATGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3239565 original size:18 final size:18
Alignment explanation
Indices: 3239539--3239576 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
3239529 ATAGGAATGC
3239539 ATAAATATCTTTATAGAT
1 ATAAATATCTTTATAGAT
*
3239557 ATAATTATCTTTATAGAT
1 ATAAATATCTTTATAGAT
3239575 AT
1 AT
3239577 GATGTCTGCA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.42, C:0.05, G:0.05, T:0.47
Consensus pattern (18 bp):
ATAAATATCTTTATAGAT
Found at i:3240349 original size:47 final size:47
Alignment explanation
Indices: 3240295--3240385 Score: 164
Period size: 47 Copynumber: 1.9 Consensus size: 47
3240285 CTTTTTCCAG
*
3240295 TTTCACTTTTTATCTTTATAATTAAAACTCTTACTTTTTTCAATTAA
1 TTTCACTTTTTATCTTTATAATTAAAACTCTTAATTTTTTCAATTAA
*
3240342 TTTCACTTTTTATCTTTATAATTAAAATTCTTAATTTTTTCAAT
1 TTTCACTTTTTATCTTTATAATTAAAACTCTTAATTTTTTCAAT
3240386 CATATTTTTA
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
47 42 1.00
ACGTcount: A:0.30, C:0.13, G:0.00, T:0.57
Consensus pattern (47 bp):
TTTCACTTTTTATCTTTATAATTAAAACTCTTAATTTTTTCAATTAA
Found at i:3242578 original size:18 final size:17
Alignment explanation
Indices: 3242550--3242590 Score: 55
Period size: 18 Copynumber: 2.4 Consensus size: 17
3242540 CAAAGGCCCA
* *
3242550 AAATTATAAATTTATAT
1 AAATTAAAAATATATAT
3242567 ATAATTAAAAATATATAT
1 A-AATTAAAAATATATAT
3242585 AAATTA
1 AAATTA
3242591 TTTATTTAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
17 6 0.29
18 15 0.71
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (17 bp):
AAATTAAAAATATATAT
Found at i:3245901 original size:25 final size:25
Alignment explanation
Indices: 3245867--3245917 Score: 61
Period size: 25 Copynumber: 2.0 Consensus size: 25
3245857 ATCTGAAATA
*
3245867 AAAGTATAAT-TATATCATATATATTT
1 AAAGTATAATGTA-ATAATATAT-TTT
3245893 AAAG-ATAATGTAATAATATATTTT
1 AAAGTATAATGTAATAATATATTTT
3245917 A
1 A
3245918 TAAATATGAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
24 4 0.17
25 13 0.57
26 6 0.26
ACGTcount: A:0.49, C:0.02, G:0.06, T:0.43
Consensus pattern (25 bp):
AAAGTATAATGTAATAATATATTTT
Found at i:3246953 original size:35 final size:37
Alignment explanation
Indices: 3246882--3246954 Score: 98
Period size: 35 Copynumber: 2.0 Consensus size: 37
3246872 GTTGGAAAGT
*
3246882 ATTTATATATTTTCTTTAAAAAAATTAAATTCATAAA
1 ATTTATATATTTTCTTTAAAAAAATTAAAATCATAAA
*
3246919 ATTTATATA-TTT-TTTAACAAAATTAAAAAT-ATAAA
1 ATTTATATATTTTCTTTAAAAAAATT-AAAATCATAAA
3246954 A
1 A
3246955 AGGTTTAATG
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
35 17 0.52
36 7 0.21
37 9 0.27
ACGTcount: A:0.52, C:0.04, G:0.00, T:0.44
Consensus pattern (37 bp):
ATTTATATATTTTCTTTAAAAAAATTAAAATCATAAA
Found at i:3253863 original size:190 final size:189
Alignment explanation
Indices: 3253542--3253890 Score: 655
Period size: 190 Copynumber: 1.8 Consensus size: 189
3253532 AATTGGTAAT
3253542 CAGAGCTGGTTTTGTGATCCAAAATCAAGTAGTTCAAGCTGGGAAACAAGGAAGATGCAGAAGAC
1 CAGAGCTGGTTTTGTGATCCAAAATCAAGTAGTTCAAGCTGGGAAACAAGGAAGATGCAGAAGAC
*
3253607 TGGAACCAGTGAGGTACCAGACAGACCATAGAGGAGAAAGAGGAATATTTACCGTCGTGGTGGAC
66 TGGAACCAGTGAGGTACCAAACAGACCATAGAGGAGAAAGAGGAATATTTACCGTCGTGGTGGAC
3253672 AGAGCAGAAAGCT-GTTGGAAGGAAGGATTCAGACACTAGAAGAAGGAATGACTGAGAA
131 AGAGCAGAAAGCTAGTTGGAAGGAAGGATTCAGACACTAGAAGAAGGAATGACTGAGAA
3253730 CAGAGCTGGTTTTGTGATCCAAAATCAAGTAGTTCAAGCTGGGAAAGACAAGGAAGATGCAGAAG
1 CAGAGCTGGTTTTGTGATCCAAAATCAAGTAGTTCAAGCTGGG-AA-ACAAGGAAGATGCAGAAG
3253795 ACTGGAACCAGTGAGGTACCAAACAGACCATAGAGGAGAAAGAGGAATATTTACCGTCGTGGTGG
64 ACTGGAACCAGTGAGGTACCAAACAGACCATAGAGGAGAAAGAGGAATATTTACCGTCGTGGTGG
3253860 ACAGAGCAGAAAGCTGAGTTGGAAGGAAGGA
129 ACAGAGCAGAAAGCT-AGTTGGAAGGAAGGA
3253891 ATCAAGCAGC
Statistics
Matches: 156, Mismatches: 1, Indels: 4
0.97 0.01 0.02
Matches are distributed among these distances:
188 43 0.28
189 2 0.01
190 97 0.62
192 14 0.09
ACGTcount: A:0.38, C:0.14, G:0.31, T:0.17
Consensus pattern (189 bp):
CAGAGCTGGTTTTGTGATCCAAAATCAAGTAGTTCAAGCTGGGAAACAAGGAAGATGCAGAAGAC
TGGAACCAGTGAGGTACCAAACAGACCATAGAGGAGAAAGAGGAATATTTACCGTCGTGGTGGAC
AGAGCAGAAAGCTAGTTGGAAGGAAGGATTCAGACACTAGAAGAAGGAATGACTGAGAA
Found at i:3258852 original size:15 final size:15
Alignment explanation
Indices: 3258834--3258862 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
3258824 AGATTGTTGC
3258834 CCCCAAGATTCAGTA
1 CCCCAAGATTCAGTA
3258849 CCCCAAGATTCAGT
1 CCCCAAGATTCAGT
3258863 TTCCTTCCGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.31, C:0.34, G:0.14, T:0.21
Consensus pattern (15 bp):
CCCCAAGATTCAGTA
Found at i:3262889 original size:30 final size:30
Alignment explanation
Indices: 3262855--3262949 Score: 106
Period size: 30 Copynumber: 3.2 Consensus size: 30
3262845 ATTTGTGAAC
*
3262855 AATAAATAAATGAACACGAACACCTTCAAA
1 AATAAATAAACGAACACGAACACCTTCAAA
* * *
3262885 AATAAAAAAACGAACACGAACACGATATTAAA
1 AATAAATAAACGAACACGAACAC-CT-TCAAA
*
3262917 AAT--TTAAACGAACACGAACACCTTC-AA
1 AATAAATAAACGAACACGAACACCTTCAAA
3262944 AATAAA
1 AATAAA
3262950 CGAACGAGCA
Statistics
Matches: 52, Mismatches: 9, Indels: 9
0.74 0.13 0.13
Matches are distributed among these distances:
27 5 0.10
28 1 0.02
29 1 0.02
30 37 0.71
31 1 0.02
32 7 0.13
ACGTcount: A:0.58, C:0.19, G:0.07, T:0.16
Consensus pattern (30 bp):
AATAAATAAACGAACACGAACACCTTCAAA
Found at i:3268748 original size:1 final size:1
Alignment explanation
Indices: 3268744--3268801 Score: 71
Period size: 1 Copynumber: 58.0 Consensus size: 1
3268734 AAATTTTGGC
* * * * *
3268744 TTTTTTTTTGTTTTTTTTTTGTTTTTTTGTTTTTTTTTTGTTTTTTTTTTGTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
3268802 AAAATTACAA
Statistics
Matches: 47, Mismatches: 10, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
1 47 1.00
ACGTcount: A:0.00, C:0.00, G:0.09, T:0.91
Consensus pattern (1 bp):
T
Found at i:3268758 original size:11 final size:11
Alignment explanation
Indices: 3268744--3268801 Score: 95
Period size: 11 Copynumber: 5.5 Consensus size: 11
3268734 AAATTTTGGC
3268744 TTTTTTTTTGT
1 TTTTTTTTTGT
3268755 TTTTTTTTTG-
1 TTTTTTTTTGT
3268765 --TTTTTTTGT
1 TTTTTTTTTGT
3268774 TTTTTTTTTGT
1 TTTTTTTTTGT
3268785 TTTTTTTTTGT
1 TTTTTTTTTGT
3268796 TTTTTT
1 TTTTTT
3268802 AAAATTACAA
Statistics
Matches: 44, Mismatches: 0, Indels: 6
0.88 0.00 0.12
Matches are distributed among these distances:
8 8 0.18
11 36 0.82
ACGTcount: A:0.00, C:0.00, G:0.09, T:0.91
Consensus pattern (11 bp):
TTTTTTTTTGT
Found at i:3268762 original size:30 final size:30
Alignment explanation
Indices: 3268727--3268794 Score: 91
Period size: 30 Copynumber: 2.2 Consensus size: 30
3268717 TCGTTTGCAA
3268727 TTTTTTGAAATTTTGGCTTTTTTTTTGTTTT
1 TTTTTTG-AATTTTGGCTTTTTTTTTGTTTT
** * *
3268758 TTTTTTGTTTTTTTGTTTTTTTTTTGTTTT
1 TTTTTTGAATTTTGGCTTTTTTTTTGTTTT
3268788 TTTTTTG
1 TTTTTTG
3268795 TTTTTTTAAA
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
30 26 0.79
31 7 0.21
ACGTcount: A:0.04, C:0.01, G:0.12, T:0.82
Consensus pattern (30 bp):
TTTTTTGAATTTTGGCTTTTTTTTTGTTTT
Found at i:3268790 original size:19 final size:19
Alignment explanation
Indices: 3268746--3268801 Score: 96
Period size: 19 Copynumber: 2.9 Consensus size: 19
3268736 ATTTTGGCTT
3268746 TTTTTTTGTTTTTTTTTTG
1 TTTTTTTGTTTTTTTTTTG
3268765 TTTTTTTGTTTTTTTTTTG
1 TTTTTTTGTTTTTTTTTTG
3268784 TTTTTTT-TTTGTTTTTTT
1 TTTTTTTGTTT-TTTTTTT
3268802 AAAATTACAA
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
18 3 0.08
19 33 0.92
ACGTcount: A:0.00, C:0.00, G:0.09, T:0.91
Consensus pattern (19 bp):
TTTTTTTGTTTTTTTTTTG
Found at i:3268795 original size:30 final size:30
Alignment explanation
Indices: 3268744--3268801 Score: 116
Period size: 30 Copynumber: 1.9 Consensus size: 30
3268734 AAATTTTGGC
3268744 TTTTTTTTTGTTTTTTTTTTGTTTTTTTGT
1 TTTTTTTTTGTTTTTTTTTTGTTTTTTTGT
3268774 TTTTTTTTTGTTTTTTTTTTGTTTTTTT
1 TTTTTTTTTGTTTTTTTTTTGTTTTTTT
3268802 AAAATTACAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.00, C:0.00, G:0.09, T:0.91
Consensus pattern (30 bp):
TTTTTTTTTGTTTTTTTTTTGTTTTTTTGT
Found at i:3276943 original size:13 final size:13
Alignment explanation
Indices: 3276925--3276950 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3276915 TTATATGATA
3276925 ATTAATAATTTTT
1 ATTAATAATTTTT
3276938 ATTAATAATTTTT
1 ATTAATAATTTTT
3276951 GTAATAAATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (13 bp):
ATTAATAATTTTT
Found at i:3277494 original size:2 final size:2
Alignment explanation
Indices: 3277433--3277474 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
3277423 ACTTTGTATG
3277433 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
3277475 CACATATGGA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3285214 original size:46 final size:45
Alignment explanation
Indices: 3285154--3285241 Score: 140
Period size: 45 Copynumber: 1.9 Consensus size: 45
3285144 AAATAGCCTG
* * *
3285154 AGTGCATCGATGCATGGTCTTGTGCATCGATGCATCAAATGCACTA
1 AGTGCATCGATGCATGGT-ATGTGAATCGATGCATAAAATGCACTA
3285200 AGTGCATCGATGCATGGTATGTGAATCGATGCATAAAATGCA
1 AGTGCATCGATGCATGGTATGTGAATCGATGCATAAAATGCA
3285242 TTCGATGTTC
Statistics
Matches: 39, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
45 21 0.54
46 18 0.46
ACGTcount: A:0.30, C:0.18, G:0.25, T:0.27
Consensus pattern (45 bp):
AGTGCATCGATGCATGGTATGTGAATCGATGCATAAAATGCACTA
Found at i:3303570 original size:16 final size:17
Alignment explanation
Indices: 3303538--3303570 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
3303528 TCCAACTACA
*
3303538 CCATTTTGATCCGAAAC
1 CCATTTTGATCCAAAAC
3303555 CCATTTT-ATCCAAAAC
1 CCATTTTGATCCAAAAC
3303571 TTTAAAGAGA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.33, C:0.30, G:0.06, T:0.30
Consensus pattern (17 bp):
CCATTTTGATCCAAAAC
Found at i:3308404 original size:20 final size:21
Alignment explanation
Indices: 3308376--3308418 Score: 70
Period size: 20 Copynumber: 2.1 Consensus size: 21
3308366 TGGTGCAGAG
*
3308376 GGAATCGATTCCCCCTTT-AA
1 GGAACCGATTCCCCCTTTGAA
3308396 GGAACCGATTCCCCCTTTGAA
1 GGAACCGATTCCCCCTTTGAA
3308417 GG
1 GG
3308419 GGTATCGATT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
20 17 0.81
21 4 0.19
ACGTcount: A:0.23, C:0.30, G:0.21, T:0.26
Consensus pattern (21 bp):
GGAACCGATTCCCCCTTTGAA
Found at i:3310741 original size:40 final size:40
Alignment explanation
Indices: 3310686--3310766 Score: 144
Period size: 40 Copynumber: 2.0 Consensus size: 40
3310676 TAAATGTGAT
* *
3310686 AAATGGGAGAAGTGTTAAAGTAAGGGGGAGTAATTTCAAA
1 AAATGGGAGAAGTGTTAAAATAAAGGGGAGTAATTTCAAA
3310726 AAATGGGAGAAGTGTTAAAATAAAGGGGAGTAATTTCAAA
1 AAATGGGAGAAGTGTTAAAATAAAGGGGAGTAATTTCAAA
3310766 A
1 A
3310767 CTTAATTTCA
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 39 1.00
ACGTcount: A:0.46, C:0.02, G:0.30, T:0.22
Consensus pattern (40 bp):
AAATGGGAGAAGTGTTAAAATAAAGGGGAGTAATTTCAAA
Found at i:3310754 original size:21 final size:21
Alignment explanation
Indices: 3310660--3310755 Score: 72
Period size: 21 Copynumber: 4.4 Consensus size: 21
3310650 GATTTAACAA
3310660 AAAGGGAGAGAAGTGTTAAATGTGAT
1 AAAGGG-GAGAAGTGTTAAA----AT
* *
3310686 AAATGGGAGAAGTGTTAAAGT
1 AAAGGGGAGAAGTGTTAAAAT
* *
3310707 AAGGGGGAGTAA-T-TTCAAA-
1 AAAGGGGAG-AAGTGTTAAAAT
*
3310726 AAATGGGAGAAGTGTTAAAAT
1 AAAGGGGAGAAGTGTTAAAAT
3310747 AAAGGGGAG
1 AAAGGGGAG
3310756 TAATTTCAAA
Statistics
Matches: 56, Mismatches: 10, Indels: 13
0.71 0.13 0.16
Matches are distributed among these distances:
18 2 0.04
19 8 0.14
20 9 0.16
21 17 0.30
22 2 0.04
25 13 0.23
26 5 0.09
ACGTcount: A:0.44, C:0.01, G:0.34, T:0.21
Consensus pattern (21 bp):
AAAGGGGAGAAGTGTTAAAAT
Found at i:3310766 original size:21 final size:20
Alignment explanation
Indices: 3310710--3310766 Score: 57
Period size: 21 Copynumber: 2.9 Consensus size: 20
3310700 TTAAAGTAAG
3310710 GGGGAGTAATTTC-AAAAAA
1 GGGGAGTAATTTCAAAAAAA
*
3310729 TGGGAG-AAGTGTT-AAAATAAA
1 GGGGAGTAA-T-TTCAAAA-AAA
3310750 GGGGAGTAATTTCAAAA
1 GGGGAGTAATTTCAAAA
3310767 CTTAATTTCA
Statistics
Matches: 30, Mismatches: 2, Indels: 10
0.71 0.05 0.24
Matches are distributed among these distances:
18 2 0.07
19 6 0.20
20 7 0.23
21 13 0.43
22 2 0.07
ACGTcount: A:0.46, C:0.04, G:0.28, T:0.23
Consensus pattern (20 bp):
GGGGAGTAATTTCAAAAAAA
Found at i:3333790 original size:20 final size:20
Alignment explanation
Indices: 3333767--3333804 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
3333757 CCCGTTGACC
3333767 GTTGACCGACGTTGACCACT
1 GTTGACCGACGTTGACCACT
* *
3333787 GTTGACCGGCTTTGACCA
1 GTTGACCGACGTTGACCA
3333805 GGCATTAAAC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.18, C:0.29, G:0.26, T:0.26
Consensus pattern (20 bp):
GTTGACCGACGTTGACCACT
Found at i:3336767 original size:42 final size:43
Alignment explanation
Indices: 3336583--3336791 Score: 357
Period size: 43 Copynumber: 4.9 Consensus size: 43
3336573 CAGATGCCCG
*
3336583 AGGTCCCTTTGCTGTGTGCAAGGGTAAGCCTTATAGTTCCCCC
1 AGGTCCCTTTGCTGTGTGCAAGGGTAAGCCTTACAGTTCCCCC
* *
3336626 AAGTCCCTTTACTGTGTGCAAGGGTAAGCCTTACAGTTCCCCC
1 AGGTCCCTTTGCTGTGTGCAAGGGTAAGCCTTACAGTTCCCCC
*
3336669 AGGTCCCTTTGCTGTGTTCAAGGGTAAGCCTTACAGTTCCCCC
1 AGGTCCCTTTGCTGTGTGCAAGGGTAAGCCTTACAGTTCCCCC
*
3336712 AGGTTCCTTTGCTGTGTGCAAGGGTAAGCCTTACAGTT-CCCC
1 AGGTCCCTTTGCTGTGTGCAAGGGTAAGCCTTACAGTTCCCCC
*
3336754 AGGTTCCTTTGCTGTGTGCAAGGGTAAGCCTTACAGTT
1 AGGTCCCTTTGCTGTGTGCAAGGGTAAGCCTTACAGTT
3336792 TTCCCAGGCT
Statistics
Matches: 158, Mismatches: 8, Indels: 1
0.95 0.05 0.01
Matches are distributed among these distances:
42 42 0.27
43 116 0.73
ACGTcount: A:0.18, C:0.27, G:0.25, T:0.31
Consensus pattern (43 bp):
AGGTCCCTTTGCTGTGTGCAAGGGTAAGCCTTACAGTTCCCCC
Found at i:3336815 original size:43 final size:42
Alignment explanation
Indices: 3336589--3336815 Score: 312
Period size: 43 Copynumber: 5.3 Consensus size: 42
3336579 CCCGAGGTCC
* * *
3336589 CTTTGCTGTGTGCAAGGGTAAGCCTTATAGTTCCCCCAAGTCC
1 CTTTGCTGTGTGCAAGGGTAAGCCTTACAGTTCCCCCAGGT-T
* *
3336632 CTTTACTGTGTGCAAGGGTAAGCCTTACAGTTCCCCCAGGTCC
1 CTTTGCTGTGTGCAAGGGTAAGCCTTACAGTTCCCCCAGGT-T
*
3336675 CTTTGCTGTGTTCAAGGGTAAGCCTTACAGTTCCCCCAGGTT
1 CTTTGCTGTGTGCAAGGGTAAGCCTTACAGTTCCCCCAGGTT
3336717 CCTTTGCTGTGTGCAAGGGTAAGCCTTACAGTT-CCCCAGGTT
1 -CTTTGCTGTGTGCAAGGGTAAGCCTTACAGTTCCCCCAGGTT
**
3336759 CCTTTGCTGTGTGCAAGGGTAAGCCTTACAGTTTTCCCAGGCTT
1 -CTTTGCTGTGTGCAAGGGTAAGCCTTACAGTTCCCCCAGG-TT
* *
3336803 TTTTGCTATGTGC
1 CTTTGCTGTGTGC
3336816 TAGTATAAAA
Statistics
Matches: 171, Mismatches: 10, Indels: 6
0.91 0.05 0.03
Matches are distributed among these distances:
42 42 0.25
43 127 0.74
44 2 0.01
ACGTcount: A:0.17, C:0.26, G:0.24, T:0.33
Consensus pattern (42 bp):
CTTTGCTGTGTGCAAGGGTAAGCCTTACAGTTCCCCCAGGTT
Found at i:3342994 original size:23 final size:23
Alignment explanation
Indices: 3342960--3343026 Score: 73
Period size: 23 Copynumber: 2.9 Consensus size: 23
3342950 ATCTTATATA
3342960 GCACTTCA-GTGCATTTCTACGCG
1 GCACTT-AGGTGCATTTCTACGCG
* *
3342983 GCACTTAGGTGCAATTCTACGTG
1 GCACTTAGGTGCATTTCTACGCG
* * *
3343006 GTACTTCGGTGCATTTATACG
1 GCACTTAGGTGCATTTCTACG
3343027 AGCTGTGGTG
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
22 1 0.03
23 36 0.97
ACGTcount: A:0.19, C:0.24, G:0.24, T:0.33
Consensus pattern (23 bp):
GCACTTAGGTGCATTTCTACGCG
Done.