Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008709.1 Hibiscus syriacus cultivar Beakdansim tig00111758_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: 3030657
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 14 of 15
Found at i:2734756 original size:42 final size:42
Alignment explanation
Indices: 2734710--2734901 Score: 194
Period size: 42 Copynumber: 4.6 Consensus size: 42
2734700 GGTTAAACAA
*
2734710 TAGCGGCATTTATAGTAAAAACGCCGCAATATAGTAGACATG
1 TAGCGGCGTTTATAGTAAAAACGCCGCAATATAGTAGACATG
*
2734752 TAGCGGCGTTTATAGTAAAAATGCCGCAATATAGTAGACATG
1 TAGCGGCGTTTATAGTAAAAACGCCGCAATATAGTAGACATG
* * * *
2734794 TAGCGGCGTTT-TAGCT-AAAACACCGTAATATATTTA-ACATT
1 TAGCGGCGTTTATAG-TAAAAACGCCGCAATATA-GTAGACATG
** * * * *
2734835 TAGCGGCGTTTATACCAAAAACGCCGTAATAGAGTGGTAAAT-
1 TAGCGGCGTTTATAGTAAAAACGCCGCAATATAGTAG-ACATG
* * *
2734877 TAGCGGCGTTTTTTGTATAAACGCC
1 TAGCGGCGTTTATAGTAAAAACGCC
2734902 ATAAAAAACA
Statistics
Matches: 125, Mismatches: 19, Indels: 12
0.80 0.12 0.08
Matches are distributed among these distances:
41 32 0.26
42 90 0.72
43 3 0.02
ACGTcount: A:0.34, C:0.17, G:0.21, T:0.28
Consensus pattern (42 bp):
TAGCGGCGTTTATAGTAAAAACGCCGCAATATAGTAGACATG
Found at i:2734814 original size:83 final size:83
Alignment explanation
Indices: 2734710--2734888 Score: 193
Period size: 83 Copynumber: 2.1 Consensus size: 83
2734700 GGTTAAACAA
* * ** *
2734710 TAGCGGCATTTATAGTAAAAACGCCGCAATATA-GTAGACATGTAGCGGCGTTTATAGTAAAAAT
1 TAGCGGCGTTT-TAGTAAAAACACCGCAATATATGTA-ACATGTAGCGGCGTTTATACCAAAAAC
* *
2734774 GCCGCAATATAGTAG-ACAT
64 GCCGCAATAGAGTAGTAAAT
* * *
2734793 GTAGCGGCGTTTTAGCT-AAAACACCGTAATATATTTAACATTTAGCGGCGTTTATACCAAAAAC
1 -TAGCGGCGTTTTAG-TAAAAACACCGCAATATATGTAACATGTAGCGGCGTTTATACCAAAAAC
* *
2734857 GCCGTAATAGAGTGGTAAAT
64 GCCGCAATAGAGTAGTAAAT
2734877 TAGCGGCGTTTT
1 TAGCGGCGTTTT
2734889 TTGTATAAAC
Statistics
Matches: 80, Mismatches: 12, Indels: 7
0.81 0.12 0.07
Matches are distributed among these distances:
83 64 0.80
84 16 0.20
ACGTcount: A:0.34, C:0.16, G:0.22, T:0.28
Consensus pattern (83 bp):
TAGCGGCGTTTTAGTAAAAACACCGCAATATATGTAACATGTAGCGGCGTTTATACCAAAAACGC
CGCAATAGAGTAGTAAAT
Found at i:2736074 original size:52 final size:52
Alignment explanation
Indices: 2735960--2736118 Score: 293
Period size: 52 Copynumber: 3.1 Consensus size: 52
2735950 TACTGAACAA
2735960 TATGGTGAAGACTGTTTATGCATAAGTACTTTAATG-TTCTAAATTATAATG
1 TATGGTGAAGACTGTTTATGCATAAGTACTTTAATGTTTCTAAATTATAATG
*
2736011 TATGTTGAAGACTGTTTATGCATAAGTACTTTAATGTTTCTAAATTATAATG
1 TATGGTGAAGACTGTTTATGCATAAGTACTTTAATGTTTCTAAATTATAATG
2736063 TATGGTGAAGACTGTTTATGCATAAGTACTTTAATGTTTTCTAAATTATAATG
1 TATGGTGAAGACTGTTTATGCATAAGTACTTTAATG-TTTCTAAATTATAATG
2736116 TAT
1 TAT
2736119 TTTGTTGTTA
Statistics
Matches: 104, Mismatches: 2, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
51 35 0.34
52 50 0.48
53 19 0.18
ACGTcount: A:0.33, C:0.08, G:0.16, T:0.43
Consensus pattern (52 bp):
TATGGTGAAGACTGTTTATGCATAAGTACTTTAATGTTTCTAAATTATAATG
Found at i:2736462 original size:41 final size:44
Alignment explanation
Indices: 2736382--2736462 Score: 107
Period size: 41 Copynumber: 1.9 Consensus size: 44
2736372 TCGCGTTCTT
* *
2736382 ATAACAAACGCCGTAAAATATTTGTATTTTATTGGCGTTTTTAA
1 ATAACAAACGCCGCAAAATATTTGTATTTTAATGGCGTTTTTAA
2736426 ATAA-AAACGCCGCAAAA-A-TTGT-TTATTAATGGCGTTT
1 ATAACAAACGCCGCAAAATATTTGTATT-TTAATGGCGTTT
2736463 ATAACAATCG
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
40 2 0.06
41 15 0.44
42 1 0.03
43 12 0.35
44 4 0.12
ACGTcount: A:0.36, C:0.12, G:0.15, T:0.37
Consensus pattern (44 bp):
ATAACAAACGCCGCAAAATATTTGTATTTTAATGGCGTTTTTAA
Found at i:2740638 original size:21 final size:21
Alignment explanation
Indices: 2740614--2740672 Score: 73
Period size: 21 Copynumber: 2.8 Consensus size: 21
2740604 TGATTTATTA
**
2740614 TTATGGATTTCATTTTTCTTG
1 TTATGGATTTCAAGTTTCTTG
* *
2740635 TTATGGATTTTAAGTTTGTTG
1 TTATGGATTTCAAGTTTCTTG
*
2740656 TTATGGATGTCAAGTTT
1 TTATGGATTTCAAGTTT
2740673 ATTGGAAAAT
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.19, C:0.05, G:0.20, T:0.56
Consensus pattern (21 bp):
TTATGGATTTCAAGTTTCTTG
Found at i:2740869 original size:43 final size:42
Alignment explanation
Indices: 2740800--2741071 Score: 177
Period size: 43 Copynumber: 6.4 Consensus size: 42
2740790 TTTGTATCTT
* * * *
2740800 AAAACGCCGCTATAGATATGACATTTTGCGGCGTTTGTTCTAA
1 AAAACGCCGCTATATACAAGACATTTTGCGGCGTTTG-TCGAA
* * * * *
2740843 AAAACGCCGCTATATACCAGATATTTTGCGGTGTTTGTGGGA
1 AAAACGCCGCTATATACAAGACATTTTGCGGCGTTTGTCGAA
* * * *
2740885 AAAACGCCGCTAAATATCAAGACCTATTGCGGCGTTTGTGGAA
1 AAAACGCCGCTATATA-CAAGACATTTTGCGGCGTTTGTCGAA
* * * * * *
2740928 AAAACGCCGCTAAATCTCAACACCTATTGCGGCGTTTGTGGAA
1 AAAACGCCGCTATAT-ACAAGACATTTTGCGGCGTTTGTCGAA
* * * * * * *
2740971 AAAACGCCGCTAAATCTCAACACCTATTGCGGCGTTTGTTGGA
1 AAAACGCCGCTATAT-ACAAGACATTTTGCGGCGTTTGTCGAA
** * * * * * *
2741014 AAAATACCGCCAAATATCAACACCTATTGCGGCGTTTGTTG-A
1 AAAACGCCGCTATATA-CAAGACATTTTGCGGCGTTTGTCGAA
*
2741056 CAAACGCCGCTATATA
1 AAAACGCCGCTATATA
2741072 TCGTTACCTA
Statistics
Matches: 197, Mismatches: 29, Indels: 7
0.85 0.12 0.03
Matches are distributed among these distances:
42 29 0.15
43 168 0.85
ACGTcount: A:0.30, C:0.22, G:0.21, T:0.26
Consensus pattern (42 bp):
AAAACGCCGCTATATACAAGACATTTTGCGGCGTTTGTCGAA
Found at i:2740922 original size:86 final size:86
Alignment explanation
Indices: 2740825--2741073 Score: 276
Period size: 86 Copynumber: 2.9 Consensus size: 86
2740815 ATATGACATT
* * * * * *
2740825 TTGCGGCGTTTGTTCTAAAAAACGCCGCTATATAC-CAGATA-TTTTGCGGTGTTTGTGGGAAAA
1 TTGCGGCGTTTGTTCGAAAAAACGCCGCTAAAT-CTCA-ACACTATTGCGGCGTTTGTGGAAAAA
*
2740888 ACGCCGCTAAATATCAAGACCTA
64 ACGCCGCTAAATATCAACACCTA
*
2740911 TTGCGGCGTTTG-TGGAAAAAACGCCGCTAAATCTCAACACCTATTGCGGCGTTTGTGGAAAAAA
1 TTGCGGCGTTTGTTCGAAAAAACGCCGCTAAATCTCAACA-CTATTGCGGCGTTTGTGGAAAAAA
*
2740975 CGCCGCTAAATCTCAACACCTA
65 CGCCGCTAAATATCAACACCTA
* * * * *
2740997 TTGCGGCGTTTGTTGGAAAAATA--CCGCCAAATATCAACACCTATTGCGGCGTTTGTTG-ACAA
1 TTGCGGCGTTTGTTCGAAAAA-ACGCCGCTAAATCTCAACA-CTATTGCGGCGTTTGTGGAAAAA
*
2741059 ACGCCGCTATATATC
64 ACGCCGCTAAATATC
2741074 GTTACCTATT
Statistics
Matches: 143, Mismatches: 15, Indels: 11
0.85 0.09 0.07
Matches are distributed among these distances:
84 3 0.02
85 35 0.24
86 96 0.67
87 8 0.06
88 1 0.01
ACGTcount: A:0.29, C:0.23, G:0.21, T:0.27
Consensus pattern (86 bp):
TTGCGGCGTTTGTTCGAAAAAACGCCGCTAAATCTCAACACTATTGCGGCGTTTGTGGAAAAAAC
GCCGCTAAATATCAACACCTA
Found at i:2742195 original size:11 final size:12
Alignment explanation
Indices: 2742164--2742196 Score: 52
Period size: 11 Copynumber: 2.9 Consensus size: 12
2742154 AAACTTATAT
2742164 AATTTTTT-CTC
1 AATTTTTTCCTC
2742175 AATTTTTTCCTC
1 AATTTTTTCCTC
2742187 -ATTTTTTCCT
1 AATTTTTTCCT
2742197 TTGGGCCTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 18 0.86
12 3 0.14
ACGTcount: A:0.15, C:0.21, G:0.00, T:0.64
Consensus pattern (12 bp):
AATTTTTTCCTC
Found at i:2744761 original size:20 final size:20
Alignment explanation
Indices: 2744733--2744772 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
2744723 AATCGGTTTT
* *
2744733 TTTTTAAACCGGATCGTATA
1 TTTTAAAACCGGATAGTATA
2744753 TTTTAAAACCGGATAGTATA
1 TTTTAAAACCGGATAGTATA
2744773 ACCGGTTTGA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.35, C:0.12, G:0.15, T:0.38
Consensus pattern (20 bp):
TTTTAAAACCGGATAGTATA
Found at i:2749817 original size:2 final size:2
Alignment explanation
Indices: 2749810--2749874 Score: 130
Period size: 2 Copynumber: 32.5 Consensus size: 2
2749800 TGTATTGAAT
2749810 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2749852 TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA T
2749875 GATTAAATTT
Statistics
Matches: 63, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 63 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2750209 original size:50 final size:50
Alignment explanation
Indices: 2750155--2750249 Score: 147
Period size: 50 Copynumber: 1.9 Consensus size: 50
2750145 TGAAGTGATA
*
2750155 AAATTT-AATAAAAAATTATATTTTATTAAAACTCGTCACCTCGACATTAC
1 AAATTTAAATAAAAAA-TATATTTTATTAAAACTCATCACCTCGACATTAC
* *
2750205 AAATTTAAATAAAAAATATTTTTTATTAGAACTCATCACCTCGAC
1 AAATTTAAATAAAAAATATATTTTATTAAAACTCATCACCTCGAC
2750250 GTGACGAATT
Statistics
Matches: 41, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
50 32 0.78
51 9 0.22
ACGTcount: A:0.44, C:0.16, G:0.04, T:0.36
Consensus pattern (50 bp):
AAATTTAAATAAAAAATATATTTTATTAAAACTCATCACCTCGACATTAC
Found at i:2750260 original size:50 final size:50
Alignment explanation
Indices: 2750155--2750260 Score: 142
Period size: 50 Copynumber: 2.1 Consensus size: 50
2750145 TGAAGTGATA
* *
2750155 AAATTTAATAAAAAATTATATTTTATTAAAACTCGTCACCTCGACATTAC
1 AAATTTAATAAAAAATTATATTTTATTAAAACTCATCACCTCGACATGAC
* * *
2750205 AAATTTAAATAAAAAA-TATTTTTTATTAGAACTCATCACCTCGACGTGAC
1 AAATTT-AATAAAAAATTATATTTTATTAAAACTCATCACCTCGACATGAC
*
2750255 GAATTT
1 AAATTT
2750261 TTTTAAATAC
Statistics
Matches: 49, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
50 40 0.82
51 9 0.18
ACGTcount: A:0.42, C:0.15, G:0.07, T:0.36
Consensus pattern (50 bp):
AAATTTAATAAAAAATTATATTTTATTAAAACTCATCACCTCGACATGAC
Found at i:2751625 original size:90 final size:90
Alignment explanation
Indices: 2751507--2751683 Score: 354
Period size: 90 Copynumber: 2.0 Consensus size: 90
2751497 ACATCAACTT
2751507 CAATTCCAATTCAATGGAAAATCCCCACATTTTCCCACCTATTGAAATACCTCACACTTGTAAAA
1 CAATTCCAATTCAATGGAAAATCCCCACATTTTCCCACCTATTGAAATACCTCACACTTGTAAAA
2751572 TAGGACACTTCTTTCACTACAGCAA
66 TAGGACACTTCTTTCACTACAGCAA
2751597 CAATTCCAATTCAATGGAAAATCCCCACATTTTCCCACCTATTGAAATACCTCACACTTGTAAAA
1 CAATTCCAATTCAATGGAAAATCCCCACATTTTCCCACCTATTGAAATACCTCACACTTGTAAAA
2751662 TAGGACACTTCTTTCACTACAG
66 TAGGACACTTCTTTCACTACAG
2751684 TAAAAGTGTT
Statistics
Matches: 87, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
90 87 1.00
ACGTcount: A:0.35, C:0.29, G:0.08, T:0.28
Consensus pattern (90 bp):
CAATTCCAATTCAATGGAAAATCCCCACATTTTCCCACCTATTGAAATACCTCACACTTGTAAAA
TAGGACACTTCTTTCACTACAGCAA
Found at i:2751900 original size:83 final size:82
Alignment explanation
Indices: 2751785--2752134 Score: 237
Period size: 83 Copynumber: 4.3 Consensus size: 82
2751775 TTTATCGGCG
* * *
2751785 TTTTTCCAACAAACGCCGCAATAAAGTGGTAATTTAGCGGCGTTTATAGCT-AAAACGCCGGAAG
1 TTTTTCCAACAAACGCCGCAATAGAGTAGTAATTTAGCGGCGTTTATA--TAAAAACGCCGCAAG
* *
2751849 ATATTTGTTT-TCAGTGGCA
64 AGAGTTGTTTAT-AGTGGCA
* * ** * *
2751868 TTTTTTCAATAAACGCCGCAATAGAGTAGTAATTTAATGGCGTTTGTATAAAAACGCCGCAATAG
1 TTTTTCCAACAAACGCCGCAATAGAGTAGTAATTTAGCGGCGTTTATATAAAAACGCCGCAAGAG
* *
2751933 GGTTGTTTATAGTGGCG
66 AGTTGTTTATAGTGGCA
* * * * * * *
2751950 TTTGTCCAACAAACGACGCTATAGAGAATTAATTTAGCGGCGTTTATCA-AACAAACGCCACAAT
1 TTTTTCCAACAAACGCCGCAATAGAGTAGTAATTTAGCGGCGTTTAT-ATAA-AAACGCCGCAAG
* *
2752014 AG-GTTTGTTTATAGCGGCG
64 AGAG-TTGTTTATAGTGGCA
** ** * * * * * * * * *
2752033 TTAGTGTAAAAAATGGCGTAATAGATTAATAATTTAGCGGCGTTTGTATAACAAACGCCGCCATA
1 TTTTTCCAACAAACGCCGCAATAGAGTAGTAATTTAGCGGCGTTTATATAA-AAACGCCGCAAGA
*
2752098 TG-TTTGTTTATAGTGGCA
65 -GAGTTGTTTATAGTGGCA
* *
2752116 GTTTT--AAAAAACGCCGCAA
1 TTTTTCCAACAAACGCCGCAA
2752135 AAACGTGTAC
Statistics
Matches: 212, Mismatches: 48, Indels: 16
0.77 0.17 0.06
Matches are distributed among these distances:
81 12 0.06
82 65 0.31
83 134 0.63
84 1 0.00
ACGTcount: A:0.32, C:0.16, G:0.21, T:0.31
Consensus pattern (82 bp):
TTTTTCCAACAAACGCCGCAATAGAGTAGTAATTTAGCGGCGTTTATATAAAAACGCCGCAAGAG
AGTTGTTTATAGTGGCA
Found at i:2751964 original size:41 final size:40
Alignment explanation
Indices: 2751878--2752034 Score: 111
Period size: 41 Copynumber: 3.8 Consensus size: 40
2751868 TTTTTTCAAT
* * **
2751878 AAACGCCGCAATAGAGTAGTAATTTAATGGCGTTTGT-ATAA-
1 AAACGCCGCAATAGGGTTGT--TTTAGCGGCGTTTGTCA-AAC
* *
2751919 AAACGCCGCAATAGGGTTGTTTATAGTGGCGTTTGTCCAAC
1 AAACGCCGCAATAGGGTTGTTT-TAGCGGCGTTTGTCAAAC
* * * ** *
2751960 AAACGACGCTATAGAGAATTAATTTAGCGGCGTTTATCAAAC
1 AAACGCCGCAATAG-G-GTTGTTTTAGCGGCGTTTGTCAAAC
* *
2752002 AAACGCCACAATAGGTTTGTTTATAGCGGCGTT
1 AAACGCCGCAATAGGGTTGTTT-TAGCGGCGTT
2752035 AGTGTAAAAA
Statistics
Matches: 92, Mismatches: 18, Indels: 12
0.75 0.15 0.10
Matches are distributed among these distances:
39 2 0.02
40 18 0.20
41 41 0.45
42 27 0.29
43 4 0.04
ACGTcount: A:0.32, C:0.17, G:0.23, T:0.29
Consensus pattern (40 bp):
AAACGCCGCAATAGGGTTGTTTTAGCGGCGTTTGTCAAAC
Found at i:2752568 original size:22 final size:22
Alignment explanation
Indices: 2752536--2752589 Score: 63
Period size: 22 Copynumber: 2.4 Consensus size: 22
2752526 GTGTTTTTCT
*
2752536 GCTTTCGAATACAAAAATAATA
1 GCTTTCAAATACAAAAATAATA
** *
2752558 GCTTTCAAATATGATAATAATA
1 GCTTTCAAATACAAAAATAATA
2752580 GCTTTTCAAA
1 GC-TTTCAAA
2752590 ACGTGAACAA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
22 20 0.74
23 7 0.26
ACGTcount: A:0.44, C:0.13, G:0.09, T:0.33
Consensus pattern (22 bp):
GCTTTCAAATACAAAAATAATA
Found at i:2756151 original size:18 final size:18
Alignment explanation
Indices: 2756115--2756151 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
2756105 AATATTGATT
*
2756115 TGATTAATTTAGTATCGA
1 TGATTAATTTAGTAGCGA
*
2756133 TGATTAATTTAGTCGCGA
1 TGATTAATTTAGTAGCGA
2756151 T
1 T
2756152 AATTCTTGAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.30, C:0.08, G:0.19, T:0.43
Consensus pattern (18 bp):
TGATTAATTTAGTAGCGA
Found at i:2756628 original size:27 final size:26
Alignment explanation
Indices: 2756578--2756654 Score: 104
Period size: 24 Copynumber: 3.0 Consensus size: 26
2756568 CATAGGATGC
*
2756578 ATGAAATGTTGTTTTTAAGAGACAAATA
1 ATGAAGTGTTG-TTTTAAGAGACAAA-A
2756606 ATGAAGTGTTGTTTTAAGAGAC--AA
1 ATGAAGTGTTGTTTTAAGAGACAAAA
*
2756630 ATGAAGTATTGTTTTAAGAGACAAA
1 ATGAAGTGTTGTTTTAAGAGACAAA
2756655 CTTATTATGA
Statistics
Matches: 45, Mismatches: 2, Indels: 6
0.85 0.04 0.11
Matches are distributed among these distances:
24 22 0.49
25 1 0.02
26 1 0.02
27 11 0.24
28 10 0.22
ACGTcount: A:0.42, C:0.04, G:0.21, T:0.34
Consensus pattern (26 bp):
ATGAAGTGTTGTTTTAAGAGACAAAA
Found at i:2762891 original size:44 final size:44
Alignment explanation
Indices: 2762812--2763082 Score: 298
Period size: 44 Copynumber: 6.2 Consensus size: 44
2762802 TTTTATTAAC
* *
2762812 AAACGTCGCTATATATCA-ACCTTTAGCGGCGTTTGTATTCTAA
1 AAACGCCGCTATATACCAGACCTTTAGCGGCGTTTGTATTCTAA
* * * * *
2762855 AAACGCCGTTATATACCAGACCTTTAACGACATTTGTATCCTAA
1 AAACGCCGCTATATACCAGACCTTTAGCGGCGTTTGTATTCTAA
* * * **
2762899 AAAGGACGCTATATACCAGATCTTTAGCGGTATTTGTATTCTAA
1 AAACGCCGCTATATACCAGACCTTTAGCGGCGTTTGTATTCTAA
* * * *
2762943 AAACGCCGCTATATACCAGACCTTTAGCGGAGTTTATATACTGA
1 AAACGCCGCTATATACCAGACCTTTAGCGGCGTTTGTATTCTAA
* * * * * **
2762987 AAGCGTCGTTATATACCAAAACTTTAGCGGCGTTT-T-TAATAA
1 AAACGCCGCTATATACCAGACCTTTAGCGGCGTTTGTATTCTAA
*
2763029 AAACGCCGCTATATACCAGACCTTTAGCGGCGTTTGTA-TCCAA
1 AAACGCCGCTATATACCAGACCTTTAGCGGCGTTTGTATTCTAA
2763072 AAACGCCGCTA
1 AAACGCCGCTA
2763083 AATCTCAAAA
Statistics
Matches: 186, Mismatches: 39, Indels: 6
0.81 0.17 0.03
Matches are distributed among these distances:
42 34 0.18
43 30 0.16
44 122 0.66
ACGTcount: A:0.31, C:0.22, G:0.17, T:0.30
Consensus pattern (44 bp):
AAACGCCGCTATATACCAGACCTTTAGCGGCGTTTGTATTCTAA
Found at i:2763108 original size:86 final size:84
Alignment explanation
Indices: 2762940--2763187 Score: 220
Period size: 86 Copynumber: 2.9 Consensus size: 84
2762930 ATTTGTATTC
* * * * * *
2762940 TAAAAACGCCGCTATATACCAGACCTTTAGCGGAGTTTATATACTGAAAGCGTCGTTATATAC-C
1 TAAAAACGCCGCTATATACCAGACCTTTAGCGGCGTTT-TAT-CTAAAAACGCCGCTAAAT-CTC
*
2763004 AAAA-CT-TTAGCGGCGTTTTTAA
63 AAAACCTATTA-CAGCG-TTTTAA
*
2763026 TAAAAACGCCGCTATATACCAGACCTTTAGCGGCGTTTGTATCCAAAAACGCCGCTAAATCTCAA
1 TAAAAACGCCGCTATATACCAGACCTTTAGCGGCGTTT-TATCTAAAAACGCCGCTAAATCTCAA
*
2763091 AACCTATTACAGTGTTTTAA
65 AACCTATTACAGCGTTTTAA
* * *
2763111 -AACAAACGCCGCTAAATATCAGAACCTATT-GCGGCATTTT-TCGTTAACAAACGCCGCTAAAT
1 TAA-AAACGCCGCTATATACCAG-ACCT-TTAGCGGCGTTTTATC--TAA-AAACGCCGCTAAAT
* *
2763173 ATCAGAACCTATTAC
60 CTCAAAACCTATTAC
2763188 GGCATTTTTC
Statistics
Matches: 137, Mismatches: 16, Indels: 17
0.81 0.09 0.10
Matches are distributed among these distances:
84 5 0.04
85 41 0.30
86 59 0.43
87 32 0.23
ACGTcount: A:0.34, C:0.23, G:0.15, T:0.27
Consensus pattern (84 bp):
TAAAAACGCCGCTATATACCAGACCTTTAGCGGCGTTTTATCTAAAAACGCCGCTAAATCTCAAA
ACCTATTACAGCGTTTTAA
Found at i:2763169 original size:45 final size:45
Alignment explanation
Indices: 2763111--2763211 Score: 193
Period size: 45 Copynumber: 2.2 Consensus size: 45
2763101 AGTGTTTTAA
*
2763111 AACAAACGCCGCTAAATATCAGAACCTATTGCGGCATTTTTCGTT
1 AACAAACGCCGCTAAATATCAGAACCTATTACGGCATTTTTCGTT
2763156 AACAAACGCCGCTAAATATCAGAACCTATTACGGCATTTTTCGTT
1 AACAAACGCCGCTAAATATCAGAACCTATTACGGCATTTTTCGTT
2763201 AACAAACGCCG
1 AACAAACGCCG
2763212 TGAACTTTAG
Statistics
Matches: 55, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
45 55 1.00
ACGTcount: A:0.34, C:0.26, G:0.15, T:0.26
Consensus pattern (45 bp):
AACAAACGCCGCTAAATATCAGAACCTATTACGGCATTTTTCGTT
Found at i:2766733 original size:21 final size:21
Alignment explanation
Indices: 2766707--2766757 Score: 93
Period size: 21 Copynumber: 2.4 Consensus size: 21
2766697 GCGAACATCA
*
2766707 CGTTGCGATTTATTCCAAGTT
1 CGTTGCGATTTATTCCAAATT
2766728 CGTTGCGATTTATTCCAAATT
1 CGTTGCGATTTATTCCAAATT
2766749 CGTTGCGAT
1 CGTTGCGAT
2766758 AGTCTAAAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.20, C:0.20, G:0.20, T:0.41
Consensus pattern (21 bp):
CGTTGCGATTTATTCCAAATT
Found at i:2766806 original size:6 final size:6
Alignment explanation
Indices: 2766795--2766819 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
2766785 GACACGTATT
2766795 ACCACG ACCACG ACCACG ACCACG A
1 ACCACG ACCACG ACCACG ACCACG A
2766820 GACGAGACGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.36, C:0.48, G:0.16, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:2767605 original size:21 final size:19
Alignment explanation
Indices: 2767572--2767730 Score: 120
Period size: 19 Copynumber: 7.7 Consensus size: 19
2767562 CGTTGCGATT
* *
2767572 TTGGACTATCGCAACGAAT
1 TTGGAATATCGCAACGAAC
2767591 TTGGAATAAATCGCAACGCGAAC
1 TTGGAAT--ATCGCAA--CGAAC
*
2767614 TTGGACTATCGCAACGAAC
1 TTGGAATATCGCAACGAAC
* *
2767633 TTGGACTATCGCAACGAAT
1 TTGGAATATCGCAACGAAC
*
2767652 TTGTAATAAATCGCAACGCGAAC
1 TTGGAAT--ATCGCAA--CGAAC
* * *
2767675 TTGGACTATCGCAACAAAT
1 TTGGAATATCGCAACGAAC
2767694 TTGGAATAAATCGCAACGCGAAC
1 TTGGAAT--ATCGCAA--CGAAC
*
2767717 TTGGACTATCGCAA
1 TTGGAATATCGCAA
2767731 TGCGATAGTC
Statistics
Matches: 113, Mismatches: 15, Indels: 22
0.75 0.10 0.15
Matches are distributed among these distances:
19 43 0.38
21 42 0.37
23 28 0.25
ACGTcount: A:0.35, C:0.22, G:0.20, T:0.23
Consensus pattern (19 bp):
TTGGAATATCGCAACGAAC
Found at i:2767667 original size:61 final size:61
Alignment explanation
Indices: 2767572--2767698 Score: 227
Period size: 61 Copynumber: 2.1 Consensus size: 61
2767562 CGTTGCGATT
*
2767572 TTGGACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTGGACTATCGCAACGAAC
1 TTGGACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTGGACTATCGCAACAAAC
* *
2767633 TTGGACTATCGCAACGAATTTGTAATAAATCGCAACGCGAACTTGGACTATCGCAACAAAT
1 TTGGACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTGGACTATCGCAACAAAC
2767694 TTGGA
1 TTGGA
2767699 ATAAATCGCA
Statistics
Matches: 63, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
61 63 1.00
ACGTcount: A:0.35, C:0.21, G:0.20, T:0.24
Consensus pattern (61 bp):
TTGGACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTGGACTATCGCAACAAAC
Found at i:2767675 original size:42 final size:42
Alignment explanation
Indices: 2767621--2767730 Score: 188
Period size: 42 Copynumber: 2.7 Consensus size: 42
2767611 AACTTGGACT
* *
2767621 ATCGCAA--CGAACTTGGACTATCGCAACGAATTTGTAATAA
1 ATCGCAACGCGAACTTGGACTATCGCAACAAATTTGGAATAA
2767661 ATCGCAACGCGAACTTGGACTATCGCAACAAATTTGGAATAA
1 ATCGCAACGCGAACTTGGACTATCGCAACAAATTTGGAATAA
2767703 ATCGCAACGCGAACTTGGACTATCGCAA
1 ATCGCAACGCGAACTTGGACTATCGCAA
2767731 TGCGATAGTC
Statistics
Matches: 66, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
40 7 0.11
42 59 0.89
ACGTcount: A:0.36, C:0.23, G:0.19, T:0.22
Consensus pattern (42 bp):
ATCGCAACGCGAACTTGGACTATCGCAACAAATTTGGAATAA
Found at i:2768283 original size:31 final size:31
Alignment explanation
Indices: 2768240--2768306 Score: 100
Period size: 31 Copynumber: 2.2 Consensus size: 31
2768230 ATTGAAGTTT
* *
2768240 AATTTTTTTAATTTAATTACT-TAACTTTTA
1 AATTTTTCTAATTTAATCACTCTAACTTTTA
2768270 AATTATTTCTAATTTAATCACTCTAACTTTTA
1 AATT-TTTCTAATTTAATCACTCTAACTTTTA
2768302 AATTT
1 AATTT
2768307 AAATTTTTTA
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
30 4 0.12
31 16 0.48
32 13 0.39
ACGTcount: A:0.34, C:0.10, G:0.00, T:0.55
Consensus pattern (31 bp):
AATTTTTCTAATTTAATCACTCTAACTTTTA
Found at i:2774685 original size:3 final size:3
Alignment explanation
Indices: 2774677--2774711 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
2774667 ATTTCTTTCT
2774677 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
2774712 TATATGTGAG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (3 bp):
TTC
Found at i:2776589 original size:138 final size:138
Alignment explanation
Indices: 2776164--2776693 Score: 734
Period size: 135 Copynumber: 3.9 Consensus size: 138
2776154 GGGTGTTACA
* * * ** *
2776164 CATGTCCCCCGGGGGCATTATTCATATCAGTACTTATCATGTTTGAGGGGGTGCAAAAAAGTGGT
1 CATGTCCCCC-GGGGCACTATTCATGTCAGTACCTATCATGTTTGAGGGGACGCAACAAAGTGGT
* * * *
2776229 GAAAGCACATTTCA-AGGG-GCACCTTCCATTATTTTGTCAGATAATATGTTATAATTACCCTAT
65 GAAAGCGCATTTCAGGGGGCGCACCTTCCATTATTTTGTCAGAGAATATGTTATAATTTCCCTAT
2776292 TATGTCACT
130 TATGTCACT
* * *
2776301 CATGTCCCCCGGGGCACTATTCATGTTAGTAACTATCATGTTTGAGGGGACGCAGCAAAGTGGTG
1 CATGTCCCCCGGGGCACTATTCATGTCAGTACCTATCATGTTTGAGGGGACGCAACAAAGTGGTG
** * *
2776366 AAAGCGTGTTTCAGGGGGCGTA---TCCATTATTTTGTCAGAGAATATGTTATAATTGCCCTATT
66 AAAGCGCATTTCAGGGGGCGCACCTTCCATTATTTTGTCAGAGAATATGTTATAATTTCCCTATT
2776428 ATGTCACT
131 ATGTCACT
* * * *
2776436 CATATCCCCCGGGGCACTATTTATGTCATTACCTATTATGTTTGAGGGGACGCAACAAAGTGGTG
1 CATGTCCCCCGGGGCACTATTCATGTCAGTACCTATCATGTTTGAGGGGACGCAACAAAGTGGTG
*
2776501 AAAGCGCATTTCAGGGGGCACACCTTCCATTATTTTGTCAGAGAATATGTTATAATTTCCCTATT
66 AAAGCGCATTTCAGGGGGCGCACCTTCCATTATTTTGTCAGAGAATATGTTATAATTTCCCTATT
*
2776566 GTGTCACT
131 ATGTCACT
* *
2776574 CATGTCCCCCGGGGCACTATTCATGTCAGTACATATCATGTTTGAGGGGACGCAGCAAA---GTG
1 CATGTCCCCCGGGGCACTATTCATGTCAGTACCTATCATGTTTGAGGGGACGCAACAAAGTGGTG
* ** *
2776636 AAAGCGCGTTTCAGGGGATGCGCCTTCCATTATTTTGTCAGAGAATATGTTATAATTT
66 AAAGCGCATTTCAGGGGGCGCACCTTCCATTATTTTGTCAGAGAATATGTTATAATTT
2776694 GTTGAAAACA
Statistics
Matches: 348, Mismatches: 40, Indels: 12
0.87 0.10 0.03
Matches are distributed among these distances:
135 178 0.51
136 56 0.16
137 13 0.04
138 101 0.29
ACGTcount: A:0.26, C:0.20, G:0.23, T:0.32
Consensus pattern (138 bp):
CATGTCCCCCGGGGCACTATTCATGTCAGTACCTATCATGTTTGAGGGGACGCAACAAAGTGGTG
AAAGCGCATTTCAGGGGGCGCACCTTCCATTATTTTGTCAGAGAATATGTTATAATTTCCCTATT
ATGTCACT
Found at i:2776687 original size:273 final size:270
Alignment explanation
Indices: 2776168--2776692 Score: 797
Period size: 273 Copynumber: 1.9 Consensus size: 270
2776158 GTTACACATG
* * **
2776168 TCCCCCGGGGGCATTATTCATATCAGTACTTATCATGTTTGAGGGGGTGCAAAAAAGTGGTGAAA
1 TCCCCCGGGGGCACTATTCATATCAGTACCTATCATGTTTGAGGGGACGCAAAAAAGTGGTGAAA
*
2776233 GCACATTTCAAGGGGCACCTTCCATTATTTTGTCAGATAATATGTTATAATTACCCTATTATGTC
66 GCACATTTCAAGGGGCACCTTCCATTATTTTGTCAGAGAATATGTTATAATTACCCTATTATGTC
*
2776298 ACTCATGTCCCCCGGGGCACTATTCATGTTAGTAACTATCATGTTTGAGGGGACGCAGCAAAGTG
131 ACTCATGTCCCCCGGGGCACTATTCATGTCAGTAACTATCATGTTTGAGGGGACGCAGCAAA--G
*
2776363 GTGAAAGCGTGTTTCAGGGGGCGTATCCATTATTTTGTCAGAGAATATGTTATAATTGCCCTATT
194 GTGAAAGCGCGTTTCAGGGGGCGTATCCATTATTTTGTCAGAGAATATGTTATAATTGCCCTATT
2776428 ATGTCACTCATA
259 ATGTCACTCATA
* * * * *
2776440 TCCCCC-GGGGCACTATTTATGTCATTACCTATTATGTTTGAGGGGACGCAACAAAGTGGTGAAA
1 TCCCCCGGGGGCACTATTCATATCAGTACCTATCATGTTTGAGGGGACGCAAAAAAGTGGTGAAA
* * * *
2776504 GCGCATTTCAGGGGGCACACCTTCCATTATTTTGTCAGAGAATATGTTATAATTTCCCTATTGTG
66 GCACATTTCAAGGGG--CACCTTCCATTATTTTGTCAGAGAATATGTTATAATTACCCTATTATG
2776569 TCACTCATGTCCCCCGGGGCACTATTCATGTCAGT-ACATATCATGTTTGAGGGGACGCAGCAAA
129 TCACTCATGTCCCCCGGGGCACTATTCATGTCAGTAAC-TATCATGTTTGAGGGGACGCAGCAAA
2776633 -GTGAAAGCGCGTTTCAGGGGATGCGCCT-TCCATTATTTTGTCAGAGAATATGTTATAATT
193 GGTGAAAGCGCGTTTCAGGGG--GCG--TATCCATTATTTTGTCAGAGAATATGTTATAATT
2776693 TGTTGAAAAC
Statistics
Matches: 230, Mismatches: 16, Indels: 13
0.89 0.06 0.05
Matches are distributed among these distances:
270 19 0.08
271 62 0.27
272 11 0.05
273 137 0.60
274 1 0.00
ACGTcount: A:0.26, C:0.20, G:0.23, T:0.32
Consensus pattern (270 bp):
TCCCCCGGGGGCACTATTCATATCAGTACCTATCATGTTTGAGGGGACGCAAAAAAGTGGTGAAA
GCACATTTCAAGGGGCACCTTCCATTATTTTGTCAGAGAATATGTTATAATTACCCTATTATGTC
ACTCATGTCCCCCGGGGCACTATTCATGTCAGTAACTATCATGTTTGAGGGGACGCAGCAAAGGT
GAAAGCGCGTTTCAGGGGGCGTATCCATTATTTTGTCAGAGAATATGTTATAATTGCCCTATTAT
GTCACTCATA
Found at i:2777484 original size:13 final size:13
Alignment explanation
Indices: 2777468--2777492 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2777458 CTATTATACT
2777468 TGAAATTTATGTC
1 TGAAATTTATGTC
2777481 TGAAATTTATGT
1 TGAAATTTATGT
2777493 TAGAGTGTCA
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:0.32, C:0.04, G:0.16, T:0.48
Consensus pattern (13 bp):
TGAAATTTATGTC
Found at i:2778357 original size:21 final size:21
Alignment explanation
Indices: 2778333--2778412 Score: 81
Period size: 21 Copynumber: 3.8 Consensus size: 21
2778323 AAAACCCTGC
*
2778333 GGGCTAGGCATGTAACCTTGT
1 GGGCTAGGTATGTAACCTTGT
* * *
2778354 GGGCTGGGTATGTACCCCTGT
1 GGGCTAGGTATGTAACCTTGT
* *
2778375 AGGCTGGGTATGT-ACTCTTGT
1 GGGCTAGGTATGTAAC-CTTGT
*
2778396 GGGCTAGGAATGTAACC
1 GGGCTAGGTATGTAACC
2778413 CTGCATAGAT
Statistics
Matches: 47, Mismatches: 10, Indels: 4
0.77 0.16 0.07
Matches are distributed among these distances:
20 1 0.02
21 44 0.94
22 2 0.04
ACGTcount: A:0.17, C:0.19, G:0.35, T:0.29
Consensus pattern (21 bp):
GGGCTAGGTATGTAACCTTGT
Found at i:2780088 original size:28 final size:28
Alignment explanation
Indices: 2780057--2780132 Score: 91
Period size: 30 Copynumber: 2.6 Consensus size: 28
2780047 TAATTAGCAC
2780057 AAATAATAATTA-ATTAATAAATTTAAAT
1 AAATAATAATTATA-TAATAAATTTAAAT
* *
2780085 AAATAATAATTATATAATATATTTTAATAA
1 AAATAATAATTATATAATA-AATTTAA-AT
*
2780115 AAATAATATTTATATAAT
1 AAATAATAATTATATAAT
2780133 TATATTAATA
Statistics
Matches: 42, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
28 17 0.40
29 7 0.17
30 18 0.43
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (28 bp):
AAATAATAATTATATAATAAATTTAAAT
Found at i:2780150 original size:14 final size:14
Alignment explanation
Indices: 2780082--2780150 Score: 52
Period size: 14 Copynumber: 4.9 Consensus size: 14
2780072 AATAAATTTA
2780082 AATAAATAATA-ATT
1 AATAAA-AATATATT
* *
2780096 -ATATAATATATTTT
1 AATA-AAAATATATT
2780110 AATAAAAATAATATT
1 AATAAAAAT-ATATT
* * *
2780125 TATATAATTATATT
1 AATAAAAATATATT
2780139 AATAAAAATATA
1 AATAAAAATATA
2780151 AAAACTATTT
Statistics
Matches: 41, Mismatches: 10, Indels: 8
0.69 0.17 0.14
Matches are distributed among these distances:
13 6 0.15
14 22 0.54
15 13 0.32
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (14 bp):
AATAAAAATATATT
Found at i:2782116 original size:15 final size:14
Alignment explanation
Indices: 2782089--2782118 Score: 51
Period size: 15 Copynumber: 2.1 Consensus size: 14
2782079 TTCTTATTTT
2782089 TATTTAATTATTAA
1 TATTTAATTATTAA
2782103 TATTTAATTTATTAA
1 TATTTAA-TTATTAA
2782118 T
1 T
2782119 TAAATATTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 7 0.47
15 8 0.53
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (14 bp):
TATTTAATTATTAA
Found at i:2782127 original size:26 final size:25
Alignment explanation
Indices: 2782084--2782135 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 25
2782074 ATATTTTCTT
* * *
2782084 ATTTTTATTTAATTATTAATATTTA
1 ATTTTTAATTAAATATTAATAATTA
2782109 ATTTATTAATTAAATATTAATAATTA
1 ATTT-TTAATTAAATATTAATAATTA
2782135 A
1 A
2782136 ATATTGTAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
25 4 0.17
26 19 0.83
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (25 bp):
ATTTTTAATTAAATATTAATAATTA
Found at i:2782134 original size:14 final size:14
Alignment explanation
Indices: 2782092--2782140 Score: 57
Period size: 14 Copynumber: 3.6 Consensus size: 14
2782082 TTATTTTTAT
*
2782092 TTAATTATTAAT-A
1 TTAAATATTAATAA
* *
2782105 TTTAAT-TTATTAA
1 TTAAATATTAATAA
2782118 TTAAATATTAATAA
1 TTAAATATTAATAA
2782132 TTAAATATT
1 TTAAATATT
2782141 GTAAATATTC
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
12 4 0.14
13 10 0.34
14 15 0.52
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (14 bp):
TTAAATATTAATAA
Found at i:2782629 original size:19 final size:19
Alignment explanation
Indices: 2782605--2782650 Score: 92
Period size: 19 Copynumber: 2.4 Consensus size: 19
2782595 AAGGTAAAAT
2782605 AGCGAGAATGGTCGAGTGG
1 AGCGAGAATGGTCGAGTGG
2782624 AGCGAGAATGGTCGAGTGG
1 AGCGAGAATGGTCGAGTGG
2782643 AGCGAGAA
1 AGCGAGAA
2782651 ATGATGATGT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.30, C:0.11, G:0.46, T:0.13
Consensus pattern (19 bp):
AGCGAGAATGGTCGAGTGG
Found at i:2782821 original size:23 final size:23
Alignment explanation
Indices: 2782777--2782821 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
2782767 AACATATTAG
**
2782777 GTAGCGCTTATATAATGTAATAT
1 GTAGCGCTTATATAATAAAATAT
2782800 GTAGCGCTTATATAATAAAATA
1 GTAGCGCTTATATAATAAAATA
2782822 GGCATTTAAC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.40, C:0.09, G:0.16, T:0.36
Consensus pattern (23 bp):
GTAGCGCTTATATAATAAAATAT
Found at i:2782883 original size:87 final size:87
Alignment explanation
Indices: 2782737--2782899 Score: 290
Period size: 87 Copynumber: 1.9 Consensus size: 87
2782727 AATGTTATAT
* *
2782737 CATTTAACCGGAAATATTAACAAGTATAATAACATATTAGGTAGCGCTTATATAATGTAATATGT
1 CATTTAACCGGAAATATTAACAAGTACAATAACATATTAGGTAGCGCTTATATAATGTAATAGGT
2782802 AGCGCTTATATAATAAAATAGG
66 AGCGCTTATATAATAAAATAGG
* *
2782824 CATTTAACCGGAAATATTATCAAGTACAATAACATATTAGGTAGCTCTTATATAATGTAATAGGT
1 CATTTAACCGGAAATATTAACAAGTACAATAACATATTAGGTAGCGCTTATATAATGTAATAGGT
2782889 AGCGCTTATAT
66 AGCGCTTATAT
2782900 TGACCTATTT
Statistics
Matches: 72, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
87 72 1.00
ACGTcount: A:0.40, C:0.12, G:0.15, T:0.33
Consensus pattern (87 bp):
CATTTAACCGGAAATATTAACAAGTACAATAACATATTAGGTAGCGCTTATATAATGTAATAGGT
AGCGCTTATATAATAAAATAGG
Found at i:2783323 original size:200 final size:196
Alignment explanation
Indices: 2782894--2783625 Score: 751
Period size: 200 Copynumber: 3.6 Consensus size: 196
2782884 TAGGTAGCGC
* ** * *
2782894 TTATATTGACCTATTTTCAAAGT-AAACCGGTATATTTATACCGGTAACATTGCAAATTTACCTA
1 TTATGTTGACCTATTTTCTCA-TAAAACCGGTATATTTATACCGGTTACATTGTAAATTTACCTA
* * * ** * *
2782958 TTACATTATTATTATCGGTTACGATGTTTTTTAGATCAATACAATTT-TAAATGTATCGACACTT
65 TTACATTATAATTATCGGTTTCGATATTTTTGGGATCGATAC-TTTTATAAATGTATCGACACTT
* ** * *
2783022 TATGCTTGCACCTGGTTGAGCATTCATATTTCATTCTGGAAAAAAGTATCGACACAAACTAACAA
129 TATGGTTGCACCT-GTT-----TTGGTA-TTCATTCTGGACAAAAGTATCGACACAAA-TTACAA
*
2783087 CGTGTCGATACA
186 -ATGTCGATACA
* *
2783099 TTAT-TTAGACCTATTCTCTCATAAAACCGGTATATTTATACCGGTTACATTGAAAATTTACCTA
1 TTATGTT-GACCTATTTTCTCATAAAACCGGTATATTTATACCGGTTACATTGTAAATTTACCTA
* * * * * *
2783163 TTATATTATACTTATGGGTTTCGATATTTTCGGGATCGTTACTTGTTATAAATGTATCAACACTT
65 TTACATTATAATTATCGGTTTCGATATTTTTGGGATCGATACTT-TTATAAATGTATCGACACTT
*
2783228 TATGGTTGCACCAT-TTTTGGTATTCATTCTGGACCAAAAGTATCAACACAAATTTATCAAATGT
129 TATGGTTGCACC-TGTTTTGGTATTCATTCTGGA-CAAAAGTATCGACACAAA-TTA-CAAATGT
*
2783292 CGATACT
190 CGATACA
* * * * * *
2783299 TTATGATGACCTATTTTATCATAAAACTGGTATATTTTTATCGGTTACATTGTAAATTTACCTAA
1 TTATGTTGACCTATTTTCTCATAAAACCGGTATATTTATACCGGTTACATTGTAAATTTACCTAT
* *
2783364 TACATTATAATTATCGGTTTTGATGTTTTTGGGATCGATACTTTTAATAAATGTATCGACACTTT
66 TACATTATAATTATCGGTTTCGATATTTTTGGGATCGATACTTTT-ATAAATGTATCGACACTTT
* *
2783429 ATGCG-TGCACCTCG-TTTGTGCATTCATCCTGGACAATAAGTATCGACACAAATTACACAAGTG
130 ATG-GTTGCACCT-GTTTTG-GTATTCATTCTGGACAA-AAGTATCGACACAAATTACA-AA-TG
2783492 TCGATACA
189 TCGATACA
* * * * * *
2783500 TTATGTTGACATGTTTTCTAAT-TAACCGGTATATTTATACCGGTTATATTGTTAATTTACCTAT
1 TTATGTTGACCTATTTTCTCATAAAACCGGTATATTTATACCGGTTACATTGTAAATTTACCTAT
* * *
2783564 TACATTATAATTATTGGTTTTGATATTTTTTGGG-TCGATACTTGTATAAAATGTATCGACAC
66 TACATTATAATTATCGGTTTCGATA-TTTTTGGGATCGATACTTTTAT-AAATGTATCGACAC
2783626 ATATTTAGGT
Statistics
Matches: 447, Mismatches: 62, Indels: 41
0.81 0.11 0.07
Matches are distributed among these distances:
199 18 0.04
200 243 0.54
201 65 0.15
204 4 0.01
205 89 0.20
206 27 0.06
207 1 0.00
ACGTcount: A:0.31, C:0.16, G:0.14, T:0.40
Consensus pattern (196 bp):
TTATGTTGACCTATTTTCTCATAAAACCGGTATATTTATACCGGTTACATTGTAAATTTACCTAT
TACATTATAATTATCGGTTTCGATATTTTTGGGATCGATACTTTTATAAATGTATCGACACTTTA
TGGTTGCACCTGTTTTGGTATTCATTCTGGACAAAAGTATCGACACAAATTACAAATGTCGATAC
A
Found at i:2785109 original size:22 final size:22
Alignment explanation
Indices: 2785079--2785121 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
2785069 GCGAGTCTAT
* *
2785079 GAATGCTTTGTTAAATCATTTG
1 GAATACTTTGTAAAATCATTTG
*
2785101 GAATACTTTGTAAAATTATTT
1 GAATACTTTGTAAAATCATTT
2785122 TGAAATTGTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.33, C:0.07, G:0.14, T:0.47
Consensus pattern (22 bp):
GAATACTTTGTAAAATCATTTG
Found at i:2786365 original size:19 final size:19
Alignment explanation
Indices: 2786329--2786366 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
2786319 TAAGCAAGAG
*
2786329 AGGAACAGAGTTTCTTGTT
1 AGGAACAGAGTTTATTGTT
2786348 AGGAACA-AGATTTATTGTT
1 AGGAACAGAG-TTTATTGTT
2786367 TCAACAATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 2 0.12
19 15 0.88
ACGTcount: A:0.32, C:0.08, G:0.24, T:0.37
Consensus pattern (19 bp):
AGGAACAGAGTTTATTGTT
Found at i:2789676 original size:22 final size:21
Alignment explanation
Indices: 2789634--2789673 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
2789624 GAGTTTGTTT
*
2789634 TCATTTTTCAATTTTGAAATA
1 TCATTTTTCAATTTTAAAATA
2789655 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
2789674 ATAATTTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.07, G:0.03, T:0.55
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAATA
Found at i:2792308 original size:19 final size:22
Alignment explanation
Indices: 2792280--2792334 Score: 62
Period size: 24 Copynumber: 2.5 Consensus size: 22
2792270 GCAACCTGCA
2792280 TTTATAATAAAATT-TA-TA-AT
1 TTTAT-ATAAAATTATACTACAT
2792300 TTTATATAATAATTATACTATCAT
1 TTTATATAA-AATTATACTA-CAT
2792324 TTTATATAAAA
1 TTTATATAAAA
2792335 ACACAAAAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
19 4 0.13
20 9 0.30
21 2 0.07
22 2 0.07
23 2 0.07
24 11 0.37
ACGTcount: A:0.47, C:0.04, G:0.00, T:0.49
Consensus pattern (22 bp):
TTTATATAAAATTATACTACAT
Found at i:2792406 original size:3 final size:3
Alignment explanation
Indices: 2792398--2792492 Score: 172
Period size: 3 Copynumber: 31.7 Consensus size: 3
2792388 TTTTTACCCA
*
2792398 TAT TAT TAT TAT TAT TAT TAT TAT TAT CAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
*
2792446 TAT TAT TAT TAT TAT TAT TAT TAT TAT CAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
2792493 AATATATTAA
Statistics
Matches: 88, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 88 1.00
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:2792535 original size:21 final size:21
Alignment explanation
Indices: 2792491--2792535 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 21
2792481 TTATTATTAT
* *
2792491 TAAATATATTAAATACATATA
1 TAAATATATTAAAAAAATATA
2792512 TAAATATTATTAAAAAAATA-A
1 TAAATA-TATTAAAAAAATATA
2792533 TAA
1 TAA
2792536 TTACAGGCCC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 10 0.48
22 11 0.52
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (21 bp):
TAAATATATTAAAAAAATATA
Found at i:2793073 original size:15 final size:15
Alignment explanation
Indices: 2793045--2793086 Score: 50
Period size: 15 Copynumber: 2.8 Consensus size: 15
2793035 ACCACTCAGC
2793045 AAAGAAACAG-AAAAG
1 AAAGAAA-AGAAAAAG
*
2793060 AAAGGAAAGAAAAAG
1 AAAGAAAAGAAAAAG
*
2793075 GAAGAAAAGAAA
1 AAAGAAAAGAAA
2793087 CTTACCGAGG
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
14 2 0.09
15 21 0.91
ACGTcount: A:0.74, C:0.02, G:0.24, T:0.00
Consensus pattern (15 bp):
AAAGAAAAGAAAAAG
Found at i:2793628 original size:30 final size:29
Alignment explanation
Indices: 2793594--2793652 Score: 73
Period size: 30 Copynumber: 2.0 Consensus size: 29
2793584 TAAAATAATA
2793594 TATTTAGGATAAATAACAGATTTAATCCCT
1 TATTTAGGATAAATAACA-ATTTAATCCCT
** * *
2793624 TATTTTTGATAAATAATATTTTAATCCCT
1 TATTTAGGATAAATAACAATTTAATCCCT
2793653 AGTTTATATT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
29 10 0.40
30 15 0.60
ACGTcount: A:0.37, C:0.12, G:0.07, T:0.44
Consensus pattern (29 bp):
TATTTAGGATAAATAACAATTTAATCCCT
Found at i:2805298 original size:25 final size:25
Alignment explanation
Indices: 2805273--2805320 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 25
2805263 TACTTGAAGA
*
2805273 AAAAAG-AGAAAAGAAAAGAAAAAG
1 AAAAAGAAAAAAAGAAAAGAAAAAG
*
2805297 AAAAAGAAAAAAAGAGAAGAAAAA
1 AAAAAGAAAAAAAGAAAAGAAAAA
2805321 AAATGAGGGG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 6 0.29
25 15 0.71
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (25 bp):
AAAAAGAAAAAAAGAAAAGAAAAAG
Found at i:2805300 original size:16 final size:15
Alignment explanation
Indices: 2805272--2805323 Score: 61
Period size: 15 Copynumber: 3.5 Consensus size: 15
2805262 ATACTTGAAG
*
2805272 AAAAAAGAGAAAAGA
1 AAAAAAAAGAAAAGA
2805287 AAAGAAAAAGAAAA-A
1 AAA-AAAAAGAAAAGA
* *
2805302 GAAAAAAAGAGAAGA
1 AAAAAAAAGAAAAGA
2805317 AAAAAAA
1 AAAAAAA
2805324 TGAGGGGTCA
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
14 9 0.29
15 13 0.42
16 9 0.29
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (15 bp):
AAAAAAAAGAAAAGA
Found at i:2805308 original size:19 final size:18
Alignment explanation
Indices: 2805269--2805320 Score: 63
Period size: 17 Copynumber: 2.8 Consensus size: 18
2805259 ATTATACTTG
2805269 AAGAAAAAAGAGAAAAGAA
1 AAGAAAAAAGA-AAAAGAA
2805288 AAG-AAAAAGAAAAAGAA
1 AAGAAAAAAGAAAAAGAA
2805305 AA-AAAGAGAAGAAAAA
1 AAGAAA-A-AAGAAAAA
2805321 AAATGAGGGG
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
17 11 0.37
18 8 0.27
19 11 0.37
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (18 bp):
AAGAAAAAAGAAAAAGAA
Found at i:2805319 original size:12 final size:11
Alignment explanation
Indices: 2805272--2805323 Score: 54
Period size: 11 Copynumber: 4.5 Consensus size: 11
2805262 ATACTTGAAG
2805272 AAAAAAGAGAA
1 AAAAAAGAGAA
2805283 AAGAAAAGA-AA
1 AA-AAAAGAGAA
2805294 AAGAAAA-AGAA
1 AA-AAAAGAGAA
2805305 AAAAAGAGAAGAA
1 AAAAA-AG-AGAA
2805318 AAAAAA
1 AAAAAA
2805324 TGAGGGGTCA
Statistics
Matches: 36, Mismatches: 0, Indels: 9
0.80 0.00 0.20
Matches are distributed among these distances:
10 4 0.11
11 16 0.44
12 7 0.19
13 9 0.25
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (11 bp):
AAAAAAGAGAA
Found at i:2805664 original size:16 final size:16
Alignment explanation
Indices: 2805638--2805682 Score: 56
Period size: 16 Copynumber: 2.8 Consensus size: 16
2805628 TTTGAATACA
*
2805638 ATTCTATTTATTTCAAG
1 ATTCAATTTATTT-AAG
*
2805655 -TTCAATTTATTTGAG
1 ATTCAATTTATTTAAG
2805670 ATTCAATTTATTT
1 ATTCAATTTATTT
2805683 TTGAAAATTC
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
15 2 0.08
16 23 0.92
ACGTcount: A:0.29, C:0.09, G:0.07, T:0.56
Consensus pattern (16 bp):
ATTCAATTTATTTAAG
Found at i:2807438 original size:83 final size:83
Alignment explanation
Indices: 2806482--2807435 Score: 1653
Period size: 83 Copynumber: 11.5 Consensus size: 83
2806472 CAATATACTC
2806482 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAATCAATCATTGAATT
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAATCAATCATTGAATT
2806547 TAGAAGATGAATTTGTTA
66 TAGAAGATGAATTTGTTA
2806565 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTT-GACAGAATCAATCA-TGAATT
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAATCAATCATTGAATT
2806628 TAGAAGATGAATTTGTTA
66 TAGAAGATGAATTTGTTA
*
2806646 ATAGCATCTTCTAGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAATCAATCATTGAATT
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAATCAATCATTGAATT
2806711 TAGAAGATGAATTTGTTA
66 TAGAAGATGAATTTGTTA
2806729 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAATCAATCATTGAATT
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAATCAATCATTGAATT
2806794 TAGAAGATGAATTTGTTA
66 TAGAAGATGAATTTGTTA
2806812 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAATCAATCATTGAATT
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAATCAATCATTGAATT
* **
2806877 TGGAAGATGAATTTGCCA
66 TAGAAGATGAATTTGTTA
2806895 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAATCAATCATTGAATT
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAATCAATCATTGAATT
* **
2806960 TGGAAGATGAATTTGCCA
66 TAGAAGATGAATTTGTTA
* *
2806978 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGACAGAATCAATCACTGAATT
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAATCAATCATTGAATT
2807043 TAGAAGATGAATTTGTTA
66 TAGAAGATGAATTTGTTA
*
2807061 ATAGCATCTTTTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAATCAATCATTGAATT
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAATCAATCATTGAATT
* **
2807126 TGGAAGATGAATTTGCCA
66 TAGAAGATGAATTTGTTA
* *
2807144 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGACAGAATCAATCACTGAATT
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAATCAATCATTGAATT
2807209 TAGAAGATGAATTTGTTA
66 TAGAAGATGAATTTGTTA
*
2807227 ATAGCATCTTCTGAAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAATCAATCATTGAATT
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAATCAATCATTGAATT
* * **
2807292 TGGAAGATAAATTTGCCA
66 TAGAAGATGAATTTGTTA
*
2807310 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGG-CAGAACCAATCATTGAAT
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGG-TTGGACAGAATCAATCATTGAAT
* **
2807374 TTGGAAGATGAATTTGCCA
65 TTAGAAGATGAATTTGTTA
*
2807393 ATAGCATCTTCTGGAAATGTTCTTTGAGTTATCTGATCTGGTT
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTT
2807436 TGGTAGGAAC
Statistics
Matches: 835, Mismatches: 33, Indels: 7
0.95 0.04 0.01
Matches are distributed among these distances:
81 66 0.08
82 30 0.04
83 735 0.88
84 4 0.00
ACGTcount: A:0.29, C:0.12, G:0.22, T:0.38
Consensus pattern (83 bp):
ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAATCAATCATTGAATT
TAGAAGATGAATTTGTTA
Found at i:2808368 original size:113 final size:113
Alignment explanation
Indices: 2808165--2808952 Score: 1306
Period size: 113 Copynumber: 7.0 Consensus size: 113
2808155 ATTCAAATCT
* *
2808165 ATCAATTGATGGATTATTTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAA
1 ATCACTTGATGGATTATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAA
2808230 GAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGTCTGAATTC
66 GAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGTCTGAATTC
2808278 ATCACTTGATGGATTATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAA
1 ATCACTTGATGGATTATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAA
2808343 GAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGTCTGAATTC
66 GAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGTCTGAATTC
*
2808391 ATCACTTGATGGATTATCTTTTCTAGAGAAAGTTCATAATGAGAAGAACTCATCT-------GAA
1 ATCACTTGATGGATTATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAA
2808449 GAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGTCTGAATTC
66 GAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGTCTGAATTC
2808497 ATCACTTGATGGATTATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAA
1 ATCACTTGATGGATTATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAA
** *
2808562 GAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAATCC
66 GAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGTCTGAATTC
* *
2808610 ATCATTTGATGGATCATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAA
1 ATCACTTGATGGATTATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAA
* **
2808675 GAAGAAGTTCATAATGAGAAGAATTTGTTTAACCTTTTACCTGAATTC
66 GAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGTCTGAATTC
* *
2808723 ATCATTTGATGGATCATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAA
1 ATCACTTGATGGATTATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAA
**
2808788 GAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAATTC
66 GAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGTCTGAATTC
* * *
2808836 ATCAATTGATGGATTATCTTTTCCGGAG-AAGTTCATAATGAGAAGAACTCATCTGAAGAAGAAA
1 ATCACTTGATGGATTATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAA
* * * *
2808900 GAAGAAGTTCATAATAAGAAGAACTTGTTCAACTTTTTGTAT-AATTC
66 GAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGTCTGAATTC
2808947 TATCAC
1 -ATCAC
2808953 AGAAGGAGAT
Statistics
Matches: 644, Mismatches: 23, Indels: 17
0.94 0.03 0.02
Matches are distributed among these distances:
106 105 0.16
111 5 0.01
112 75 0.12
113 459 0.71
ACGTcount: A:0.37, C:0.13, G:0.19, T:0.31
Consensus pattern (113 bp):
ATCACTTGATGGATTATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAA
GAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGTCTGAATTC
Found at i:2808468 original size:17 final size:17
Alignment explanation
Indices: 2808420--2808471 Score: 63
Period size: 17 Copynumber: 3.1 Consensus size: 17
2808410 TTTCTAGAGA
2808420 AAGTTCATAATGAGAAG
1 AAGTTCATAATGAGAAG
* *
2808437 AA-CTCAT-CTGAAGAAG
1 AAGTTCATAATG-AGAAG
2808453 AAGTTCATAATGAGAAG
1 AAGTTCATAATGAGAAG
2808470 AA
1 AA
2808472 TTTGTTCAAC
Statistics
Matches: 28, Mismatches: 4, Indels: 6
0.74 0.11 0.16
Matches are distributed among these distances:
15 2 0.07
16 11 0.39
17 13 0.46
18 2 0.07
ACGTcount: A:0.48, C:0.10, G:0.21, T:0.21
Consensus pattern (17 bp):
AAGTTCATAATGAGAAG
Found at i:2808776 original size:332 final size:333
Alignment explanation
Indices: 2808165--2808937 Score: 1298
Period size: 332 Copynumber: 2.3 Consensus size: 333
2808155 ATTCAAATCT
*
2808165 ATCAATTGATGGATTATTTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAA
1 ATCAATTGATGGATTATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAA
** * *
2808230 GAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGTCTGAATTCATCACTTGATGGATTAT
66 GAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAATCCATCACTTGATGGATCAT
2808295 CTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGA
131 CTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGA
** * *
2808360 GAAGAATTTGTTCAACCTTTTGTCTGAATTCATCACTTGATGGATTATCTTTTCTAGAGAAAGTT
196 GAAGAATTTGTTCAACCTTTTACCTGAATTCATCACTTGATGGATCATCTTTTCCAGAGAAAGTT
**
2808425 CATAATGAGAAGAACTCATCT-GAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGT
261 CATAATGAGAAGAACTCATCTAGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTAC
2808489 CTGAATTC
326 CTGAATTC
*
2808497 ATCACTTGATGGATTATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAA
1 ATCAATTGATGGATTATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAA
*
2808562 GAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAATCCATCATTTGATGGATCAT
66 GAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAATCCATCACTTGATGGATCAT
2808627 CTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGA
131 CTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGA
* *
2808692 GAAGAATTTGTTTAACCTTTTACCTGAATTCATCATTTGATGGATCATCTTTTCCAGAGAAAGTT
196 GAAGAATTTGTTCAACCTTTTACCTGAATTCATCACTTGATGGATCATCTTTTCCAGAGAAAGTT
2808757 CATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACC
261 CATAATGAGAAGAACTCATCT-----A-GAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACC
2808822 TTTTACCTGAATTC
320 TTTTACCTGAATTC
* *
2808836 ATCAATTGATGGATTATCTTTTCCGGAG-AAGTTCATAATGAGAAGAACTCATCTGAAGAAGAAA
1 ATCAATTGATGGATTATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAA
* * *
2808900 GAAGAAGTTCATAATAAGAAGAACTTGTTCAACTTTTT
66 GAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTT
2808938 GTATAATTCT
Statistics
Matches: 413, Mismatches: 21, Indels: 8
0.93 0.05 0.02
Matches are distributed among these distances:
332 268 0.65
338 70 0.17
339 75 0.18
ACGTcount: A:0.37, C:0.13, G:0.19, T:0.31
Consensus pattern (333 bp):
ATCAATTGATGGATTATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAA
GAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAATCCATCACTTGATGGATCAT
CTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGA
GAAGAATTTGTTCAACCTTTTACCTGAATTCATCACTTGATGGATCATCTTTTCCAGAGAAAGTT
CATAATGAGAAGAACTCATCTAGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTAC
CTGAATTC
Found at i:2809044 original size:95 final size:93
Alignment explanation
Indices: 2808918--2809105 Score: 216
Period size: 95 Copynumber: 2.0 Consensus size: 93
2808908 TCATAATAAG
* * * * * * * * *
2808918 AAGAACTTGTTCAACTTTTTGTATAATTCTATCACAGAAGGAGATAGATTAGCATCAGCCTTTCT
1 AAGAACTTATTCAACCTTTTGAATAACTCTATCACAGAAAGAAAGAGATCAGCATCAGCC---CC
2808983 AG-AGAAAGTTCATAATGAGAAGAACTCATC
63 AGTAGAAAGTTCATAATGAGAAGAACTCATC
* * * * *
2809013 AAGAGCTTATTCAACCTTTTGAATGACTCTATCACAGAAAGAAAGAGGTCAGTATCATCCCCAGT
1 AAGAACTTATTCAACCTTTTGAATAACTCTATCACAGAAAGAAAGAGATCAGCATCAGCCCCAGT
2809078 AGAAAGTTCATAATGAGAAGAACTCATC
66 AGAAAGTTCATAATGAGAAGAACTCATC
2809106 TGAAGAAAGA
Statistics
Matches: 78, Mismatches: 14, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
92 3 0.04
93 28 0.36
95 47 0.60
ACGTcount: A:0.38, C:0.18, G:0.17, T:0.28
Consensus pattern (93 bp):
AAGAACTTATTCAACCTTTTGAATAACTCTATCACAGAAAGAAAGAGATCAGCATCAGCCCCAGT
AGAAAGTTCATAATGAGAAGAACTCATC
Found at i:2809269 original size:3 final size:3
Alignment explanation
Indices: 2809261--2809333 Score: 137
Period size: 3 Copynumber: 24.3 Consensus size: 3
2809251 TACCCATATC
2809261 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
*
2809309 ATT ATT ATC ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT A
2809334 AATATATTAA
Statistics
Matches: 68, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
3 68 1.00
ACGTcount: A:0.34, C:0.01, G:0.00, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:2809376 original size:21 final size:21
Alignment explanation
Indices: 2809332--2809376 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 21
2809322 TTATTATTAT
* *
2809332 TAAATATATTAAATACATATA
1 TAAATATATTAAAAAAATATA
2809353 TAAATATTATTAAAAAAATA-A
1 TAAATA-TATTAAAAAAATATA
2809374 TAA
1 TAA
2809377 TTACAGGCCC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 10 0.48
22 11 0.52
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (21 bp):
TAAATATATTAAAAAAATATA
Found at i:2809912 original size:15 final size:15
Alignment explanation
Indices: 2809884--2809925 Score: 50
Period size: 15 Copynumber: 2.8 Consensus size: 15
2809874 ACCACTCAGC
2809884 AAAGAAACAG-AAAAG
1 AAAGAAA-AGAAAAAG
*
2809899 AAAGGAAAGAAAAAG
1 AAAGAAAAGAAAAAG
*
2809914 GAAGAAAAGAAA
1 AAAGAAAAGAAA
2809926 CTTACCGAGG
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
14 2 0.09
15 21 0.91
ACGTcount: A:0.74, C:0.02, G:0.24, T:0.00
Consensus pattern (15 bp):
AAAGAAAAGAAAAAG
Found at i:2810483 original size:30 final size:29
Alignment explanation
Indices: 2810449--2810507 Score: 73
Period size: 30 Copynumber: 2.0 Consensus size: 29
2810439 TAAAATAATA
2810449 TATTTAGGATAAATAACAGATTTAATCCCT
1 TATTTAGGATAAATAACA-ATTTAATCCCT
** * *
2810479 TATTTTTGATAAATAATATTTTAATCCCT
1 TATTTAGGATAAATAACAATTTAATCCCT
2810508 AGTTTATATT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
29 10 0.40
30 15 0.60
ACGTcount: A:0.37, C:0.12, G:0.07, T:0.44
Consensus pattern (29 bp):
TATTTAGGATAAATAACAATTTAATCCCT
Found at i:2813296 original size:18 final size:18
Alignment explanation
Indices: 2813275--2813310 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
2813265 GTATCGACAC
2813275 TTTATAGGCGCTAAAACT
1 TTTATAGGCGCTAAAACT
2813293 TTTATAGGCGCTAAAACT
1 TTTATAGGCGCTAAAACT
2813311 GATTCTCTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Consensus pattern (18 bp):
TTTATAGGCGCTAAAACT
Found at i:2813530 original size:182 final size:183
Alignment explanation
Indices: 2813293--2813643 Score: 465
Period size: 182 Copynumber: 1.9 Consensus size: 183
2813283 CGCTAAAACT
* *
2813293 TTTATAGGCGCTAAAACTGATTCTCTTTTAAATTCACTAAGTGTCGATACTTATATTAAACTACC
1 TTTATAGGCGCTAAAAATGATTCTCTTTTAAATTCACAAAGTGTCGATACTTATATTAAACTACC
* ** ** * *
2813358 GACACTTTAAATATATCTTGT-AGCTCTTTACCGGTTTTATCATTTCGAT-ACCGATTTTGTC-A
66 GACACGTTAAATATATCCGGTAAG-GATTTACCGGTATTATCATTTCG-TGACCGATTTTATCGA
* *
2813420 TATTTTTACCTGTTATATCGTTGTGGATCGATACATTTTTATAAAGTATCGACAC
129 TATTTTTACCTGTTATATCGATATGGATCGATACATTTTTATAAAGTATCGACAC
* * * * *
2813475 TTTATAGGCGTTAAAAATGCTTCTCTTTTAAATTCACAAAGTGTCGATCCTTATATTAAAGTATC
1 TTTATAGGCGCTAAAAATGATTCTCTTTTAAATTCACAAAGTGTCGATACTTATATTAAACTACC
* * * * *
2813540 GACACGTTCAATATATCCGGTAAGGATTTACTGGTATTGTCTTTTCGTGACCGGTTTTATCGATA
66 GACACGTTAAATATATCCGGTAAGGATTTACCGGTATTATCATTTCGTGACCGATTTTATCGATA
*
2813605 TTTTTACCTGTTATATTGATATGGATCGATACATTTTTA
131 TTTTTACCTGTTATATCGATATGGATCGATACATTTTTA
2813644 ATTTGGATCG
Statistics
Matches: 144, Mismatches: 22, Indels: 5
0.84 0.13 0.03
Matches are distributed among these distances:
181 1 0.01
182 102 0.71
183 41 0.28
ACGTcount: A:0.28, C:0.16, G:0.14, T:0.42
Consensus pattern (183 bp):
TTTATAGGCGCTAAAAATGATTCTCTTTTAAATTCACAAAGTGTCGATACTTATATTAAACTACC
GACACGTTAAATATATCCGGTAAGGATTTACCGGTATTATCATTTCGTGACCGATTTTATCGATA
TTTTTACCTGTTATATCGATATGGATCGATACATTTTTATAAAGTATCGACAC
Found at i:2814274 original size:15 final size:15
Alignment explanation
Indices: 2814243--2814273 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
2814233 ATATTTTTTA
2814243 TTAATTTAAATAATT
1 TTAATTTAAATAATT
2814258 TTAA-TTAAATAATT
1 TTAATTTAAATAATT
2814272 TT
1 TT
2814274 TCTATCCAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 12 0.75
15 4 0.25
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (15 bp):
TTAATTTAAATAATT
Found at i:2817325 original size:18 final size:18
Alignment explanation
Indices: 2817261--2817326 Score: 57
Period size: 18 Copynumber: 3.7 Consensus size: 18
2817251 AATCTAAATG
* *
2817261 TTTACAGTTATCATATGAT
1 TTTACAGTTATAAGAT-AT
**
2817280 TTT-CAGTTATTGGATA-
1 TTTACAGTTATAAGATAT
2817296 TTTACA-TATATAAGATAT
1 TTTACAGT-TATAAGATAT
2817314 TTTACAGTTATAA
1 TTTACAGTTATAA
2817327 AATACAGATT
Statistics
Matches: 38, Mismatches: 5, Indels: 9
0.73 0.10 0.17
Matches are distributed among these distances:
16 4 0.11
17 10 0.26
18 20 0.53
19 4 0.11
ACGTcount: A:0.35, C:0.08, G:0.11, T:0.47
Consensus pattern (18 bp):
TTTACAGTTATAAGATAT
Found at i:2817493 original size:43 final size:43
Alignment explanation
Indices: 2817439--2817523 Score: 134
Period size: 43 Copynumber: 2.0 Consensus size: 43
2817429 TCAATTATCA
*
2817439 GTTATCAGTTATTAGATCAACTTTGGTACATTTGTGTATCAAC
1 GTTATCAGTTATCAGATCAACTTTGGTACATTTGTGTATCAAC
* * *
2817482 GTTATCAGTTATCAGATTAGCTTTGGTATATTTGTGTATCAA
1 GTTATCAGTTATCAGATCAACTTTGGTACATTTGTGTATCAA
2817524 TGTTCAGCAC
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
43 38 1.00
ACGTcount: A:0.27, C:0.12, G:0.18, T:0.44
Consensus pattern (43 bp):
GTTATCAGTTATCAGATCAACTTTGGTACATTTGTGTATCAAC
Found at i:2818982 original size:18 final size:18
Alignment explanation
Indices: 2818959--2818996 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
2818949 TGATTTTTAA
2818959 AAAATAAAAAATAAATAG
1 AAAATAAAAAATAAATAG
2818977 AAAATAAAAAATAAATAG
1 AAAATAAAAAATAAATAG
2818995 AA
1 AA
2818997 TTTTTTTATT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.79, C:0.00, G:0.05, T:0.16
Consensus pattern (18 bp):
AAAATAAAAAATAAATAG
Found at i:2819138 original size:16 final size:17
Alignment explanation
Indices: 2819106--2819138 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
2819096 AAAAAAATAA
*
2819106 TTCTAATTTATTTTTAC
1 TTCTAATTTACTTTTAC
2819123 TTCTAATTT-CTTTTAC
1 TTCTAATTTACTTTTAC
2819139 CGTTATCAAG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.21, C:0.15, G:0.00, T:0.64
Consensus pattern (17 bp):
TTCTAATTTACTTTTAC
Found at i:2828389 original size:32 final size:30
Alignment explanation
Indices: 2828315--2828435 Score: 143
Period size: 30 Copynumber: 3.9 Consensus size: 30
2828305 GAATGACCTA
* * *
2828315 TCCATATGTTCCGAAGAACATAGGTAAATG
1 TCCATATGTCCCGAAGGACATAGGTAACTG
2828345 TCCATATGTCCCGAAGGACATAGGTAATCCTG
1 TCCATATGTCCCGAAGGACATAGGTAA--CTG
* * *
2828377 TCCATATATCCCGAATGACATAGGTAAACTA
1 TCCATATGTCCCGAAGGACATAGGT-AACTG
* *
2828408 TCCATATGTCTCGAAAGACATAGGTAAC
1 TCCATATGTCCCGAAGGACATAGGTAAC
2828436 CCTCGACTCT
Statistics
Matches: 79, Mismatches: 9, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
30 28 0.35
31 24 0.30
32 25 0.32
33 2 0.03
ACGTcount: A:0.35, C:0.21, G:0.18, T:0.26
Consensus pattern (30 bp):
TCCATATGTCCCGAAGGACATAGGTAACTG
Found at i:2836709 original size:27 final size:25
Alignment explanation
Indices: 2836665--2836716 Score: 61
Period size: 27 Copynumber: 2.0 Consensus size: 25
2836655 TTTCTCAAAC
*
2836665 CCTCTCTTCTTTCTTAAACTCATCCAT
1 CCTCTCTTCTCTCTTAAA-TC-TCCAT
2836692 CCTCTCTT-TCTCTCTAAATCTCCAT
1 CCTCTCTTCTCTCT-TAAATCTCCAT
2836717 TTTTGCCAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
25 5 0.22
26 6 0.26
27 12 0.52
ACGTcount: A:0.17, C:0.38, G:0.00, T:0.44
Consensus pattern (25 bp):
CCTCTCTTCTCTCTTAAATCTCCAT
Found at i:2839780 original size:17 final size:20
Alignment explanation
Indices: 2839758--2839801 Score: 58
Period size: 17 Copynumber: 2.3 Consensus size: 20
2839748 GACGCTATCT
2839758 AAAATATT-T-AA-AAATAA
1 AAAATATTATAAACAAATAA
2839775 AAAATATTATAAACAAATAA
1 AAAATATTATAAACAAATAA
2839795 ATAAATA
1 A-AAATA
2839802 AAATAAAATT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
17 8 0.35
18 1 0.04
19 2 0.09
20 7 0.30
21 5 0.22
ACGTcount: A:0.70, C:0.02, G:0.00, T:0.27
Consensus pattern (20 bp):
AAAATATTATAAACAAATAA
Found at i:2839807 original size:21 final size:20
Alignment explanation
Indices: 2839769--2839808 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
2839759 AAATATTTAA
**
2839769 AAATAAAAAATATTATAAAC
1 AAATAAAAAATAAAATAAAC
2839789 AAATAAATAAATAAAATAAA
1 AAATAAA-AAATAAAATAAA
2839809 ATTTTGATAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 7 0.41
21 10 0.59
ACGTcount: A:0.75, C:0.03, G:0.00, T:0.23
Consensus pattern (20 bp):
AAATAAAAAATAAAATAAAC
Found at i:2841760 original size:24 final size:24
Alignment explanation
Indices: 2841713--2841759 Score: 87
Period size: 23 Copynumber: 2.0 Consensus size: 24
2841703 TGTTAAGGTT
2841713 CAAAATTTAATTTTTTTTCTAAAA
1 CAAAATTTAATTTTTTTTCTAAAA
2841737 CAAAATTT-ATTTTTTTTCTAAAA
1 CAAAATTTAATTTTTTTTCTAAAA
2841760 AACTTATTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
23 15 0.65
24 8 0.35
ACGTcount: A:0.40, C:0.09, G:0.00, T:0.51
Consensus pattern (24 bp):
CAAAATTTAATTTTTTTTCTAAAA
Found at i:2842888 original size:21 final size:20
Alignment explanation
Indices: 2842846--2842888 Score: 50
Period size: 21 Copynumber: 2.1 Consensus size: 20
2842836 CTTGAGCACA
**
2842846 CATATTTAAACCATTTTTAT
1 CATATTTAAACCATTTAGAT
*
2842866 CATATATTAAACCCTTTAGAT
1 CATAT-TTAAACCATTTAGAT
2842887 CA
1 CA
2842889 ATCCAAAGCA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
20 5 0.26
21 14 0.74
ACGTcount: A:0.37, C:0.19, G:0.02, T:0.42
Consensus pattern (20 bp):
CATATTTAAACCATTTAGAT
Found at i:2844933 original size:27 final size:26
Alignment explanation
Indices: 2844877--2844933 Score: 71
Period size: 26 Copynumber: 2.2 Consensus size: 26
2844867 TCAGGTCGAG
*
2844877 TTCGGGTCGGGTGGAAGGTTATATTT
1 TTCGGGTCGGGTGGAAGGTTATAATT
*
2844903 TTCGGGTCGGGT-GAATGATTTATAATT
1 TTCGGGTCGGGTGGAA-G-GTTATAATT
2844930 TTCG
1 TTCG
2844934 AGCTAGGCCT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
25 3 0.11
26 13 0.48
27 11 0.41
ACGTcount: A:0.18, C:0.09, G:0.33, T:0.40
Consensus pattern (26 bp):
TTCGGGTCGGGTGGAAGGTTATAATT
Found at i:2845064 original size:17 final size:17
Alignment explanation
Indices: 2845038--2845070 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
2845028 TCTAAAATTA
2845038 TTATAGATTTTCTATTT
1 TTATAGATTTTCTATTT
*
2845055 TTATATATTTTCTATT
1 TTATAGATTTTCTATT
2845071 GAAAATATGT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.24, C:0.06, G:0.03, T:0.67
Consensus pattern (17 bp):
TTATAGATTTTCTATTT
Found at i:2846587 original size:11 final size:11
Alignment explanation
Indices: 2846571--2846619 Score: 71
Period size: 11 Copynumber: 4.2 Consensus size: 11
2846561 AAATTTTAGT
2846571 TATTAATAAAA
1 TATTAATAAAA
2846582 TATTAATAAAA
1 TATTAATAAAA
2846593 TAAATTTAATAAAA
1 T--A-TTAATAAAA
2846607 TATTAATAAAA
1 TATTAATAAAA
2846618 TA
1 TA
2846620 AATTCGAGTT
Statistics
Matches: 35, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
11 23 0.66
12 1 0.03
13 1 0.03
14 10 0.29
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (11 bp):
TATTAATAAAA
Found at i:2846603 original size:14 final size:14
Alignment explanation
Indices: 2846579--2846623 Score: 60
Period size: 14 Copynumber: 3.4 Consensus size: 14
2846569 GTTATTAATA
2846579 AAATATTAATAAAAT
1 AAAT-TTAATAAAAT
2846594 AAATTTAATAAAAT
1 AAATTTAATAAAAT
2846608 --A-TTAATAAAAT
1 AAATTTAATAAAAT
2846619 AAATT
1 AAATT
2846624 CGAGTTATTA
Statistics
Matches: 27, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
11 10 0.37
12 1 0.04
13 1 0.04
14 11 0.41
15 4 0.15
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (14 bp):
AAATTTAATAAAAT
Found at i:2846607 original size:25 final size:25
Alignment explanation
Indices: 2846573--2846623 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
2846563 ATTTTAGTTA
2846573 TTAATAAAATATTAATAAAATAAAT
1 TTAATAAAATATTAATAAAATAAAT
2846598 TTAATAAAATATTAATAAAATAAAT
1 TTAATAAAATATTAATAAAATAAAT
2846623 T
1 T
2846624 CGAGTTATTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (25 bp):
TTAATAAAATATTAATAAAATAAAT
Found at i:2847814 original size:21 final size:21
Alignment explanation
Indices: 2847781--2847841 Score: 72
Period size: 21 Copynumber: 2.9 Consensus size: 21
2847771 TCTTAAAATG
2847781 ATATGAAAATAAAATATAAAAC
1 ATATG-AAATAAAATATAAAAC
2847803 ATAT-AATATAAAAT-TATAAAC
1 ATATGAA-ATAAAATATA-AAAC
*
2847824 ATATGAAAAAAAATATAA
1 ATATGAAATAAAATATAA
2847842 CTTATATATT
Statistics
Matches: 34, Mismatches: 1, Indels: 9
0.77 0.02 0.20
Matches are distributed among these distances:
20 4 0.12
21 22 0.65
22 8 0.24
ACGTcount: A:0.67, C:0.03, G:0.03, T:0.26
Consensus pattern (21 bp):
ATATGAAATAAAATATAAAAC
Found at i:2861918 original size:51 final size:51
Alignment explanation
Indices: 2861838--2861936 Score: 162
Period size: 51 Copynumber: 1.9 Consensus size: 51
2861828 CTAAGATTAA
* *
2861838 TAAAATGTATAGGAATCAATCAATGGAAGAAAAATGCTTAAAGTGCACTGG
1 TAAAATGTATAGGAACCAATCAATAGAAGAAAAATGCTTAAAGTGCACTGG
* *
2861889 TAAAATGTGTAGGAACCAATCAATAGAAGAGAAATGCTTAAAGTGCAC
1 TAAAATGTATAGGAACCAATCAATAGAAGAAAAATGCTTAAAGTGCAC
2861937 AAGTATGAAT
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:0.45, C:0.11, G:0.21, T:0.22
Consensus pattern (51 bp):
TAAAATGTATAGGAACCAATCAATAGAAGAAAAATGCTTAAAGTGCACTGG
Found at i:2864745 original size:63 final size:63
Alignment explanation
Indices: 2864624--2864749 Score: 209
Period size: 63 Copynumber: 2.0 Consensus size: 63
2864614 ATTACTCAGC
*
2864624 ATGGAACCAAGTCTGGAACCTTTTATATACTCTCCTTAGCCTGGTTTTCATTTATTTATATAT
1 ATGGAACCAAGTCTGGAACCTTTTATATACTCTCCATAGCCTGGTTTTCATTTATTTATATAT
* *
2864687 ATGGAACCAAGTCTGGAACCTTTTATATTACTCTTCATCGCCTGGTTTTCATTT-TTTATATAT
1 ATGGAACCAAGTCTGGAACCTTTTATA-TACTCTCCATAGCCTGGTTTTCATTTATTTATATAT
2864750 CAAAACTTTA
Statistics
Matches: 59, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
63 36 0.61
64 23 0.39
ACGTcount: A:0.25, C:0.19, G:0.13, T:0.44
Consensus pattern (63 bp):
ATGGAACCAAGTCTGGAACCTTTTATATACTCTCCATAGCCTGGTTTTCATTTATTTATATAT
Found at i:2869057 original size:21 final size:21
Alignment explanation
Indices: 2869040--2869080 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
2869030 AAAATTAATC
*
2869040 AATAATATATTAATATTATTAA
1 AATAATA-ATTAATATTAATAA
*
2869062 AATAATAATTATTATTAAT
1 AATAATAATTAATATTAAT
2869081 TTAAATATAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 10 0.59
22 7 0.41
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (21 bp):
AATAATAATTAATATTAATAA
Found at i:2870209 original size:3 final size:3
Alignment explanation
Indices: 2870203--2870279 Score: 88
Period size: 3 Copynumber: 26.3 Consensus size: 3
2870193 ATAATATATT
* *
2870203 TAA TAA TAA T-A TAA T-A TATA TAA T-A TAA TAA TAA TAT TTA TAA
1 TAA TAA TAA TAA TAA TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA
**
2870246 TAA TAA TAA TAA TAA TAA TTT TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
2870280 TTAAGTAAAA
Statistics
Matches: 62, Mismatches: 8, Indels: 8
0.79 0.10 0.10
Matches are distributed among these distances:
2 6 0.10
3 53 0.85
4 3 0.05
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (3 bp):
TAA
Found at i:2870211 original size:15 final size:14
Alignment explanation
Indices: 2870191--2870283 Score: 94
Period size: 15 Copynumber: 7.0 Consensus size: 14
2870181 TGGACCGTTG
2870191 TAATAATATATTTAA
1 TAATAATA-ATTTAA
2870206 TAATAAT-A--TAA
1 TAATAATAATTTAA
*
2870217 T-ATATATAATATAA
1 TAATA-ATAATTTAA
2870231 TAATAAT-ATTT-A
1 TAATAATAATTTAA
2870243 TAATAATAA--TAA
1 TAATAATAATTTAA
2870255 TAATAATAATTTTAA
1 TAATAATAA-TTTAA
2870270 TAATAATAATTTAA
1 TAATAATAATTTAA
2870284 GTAAAATGAA
Statistics
Matches: 67, Mismatches: 1, Indels: 21
0.75 0.01 0.24
Matches are distributed among these distances:
10 3 0.04
11 7 0.10
12 19 0.28
13 5 0.07
14 11 0.16
15 22 0.33
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (14 bp):
TAATAATAATTTAA
Found at i:2870223 original size:9 final size:9
Alignment explanation
Indices: 2870193--2870256 Score: 58
Period size: 9 Copynumber: 6.7 Consensus size: 9
2870183 GACCGTTGTA
2870193 ATAATATAT
1 ATAATATAT
*
2870202 TTAATAATAAT
1 ATAAT-AT-AT
2870213 ATAATATAT
1 ATAATATAT
2870222 ATAATATAAT
1 ATAATAT-AT
*
2870232 AATAATATTT
1 -ATAATATAT
2870242 ATAATA-AT
1 ATAATATAT
2870250 AATAATA
1 -ATAATA
2870257 ATAATAATTT
Statistics
Matches: 46, Mismatches: 4, Indels: 10
0.77 0.07 0.17
Matches are distributed among these distances:
8 1 0.02
9 25 0.54
10 7 0.15
11 13 0.28
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (9 bp):
ATAATATAT
Found at i:2870275 original size:12 final size:12
Alignment explanation
Indices: 2870191--2870276 Score: 77
Period size: 12 Copynumber: 6.8 Consensus size: 12
2870181 TGGACCGTTG
2870191 TAATAATATATT-
1 TAATAATA-ATTA
2870203 TAATAATAA-TA
1 TAATAATAATTA
2870214 TAATATATATAATATAA
1 T-A-ATA-ATAAT-T-A
*
2870231 TAATAATATTTA
1 TAATAATAATTA
*
2870243 TAATAATAATAA
1 TAATAATAATTA
*
2870255 TAATAATAATTT
1 TAATAATAATTA
2870267 TAATAATAAT
1 TAATAATAAT
2870277 AATTTAAGTA
Statistics
Matches: 62, Mismatches: 5, Indels: 14
0.77 0.06 0.17
Matches are distributed among these distances:
10 1 0.02
11 2 0.03
12 40 0.65
13 4 0.06
14 8 0.13
15 3 0.05
16 2 0.03
17 2 0.03
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (12 bp):
TAATAATAATTA
Found at i:2871171 original size:76 final size:76
Alignment explanation
Indices: 2870433--2871144 Score: 1311
Period size: 76 Copynumber: 9.4 Consensus size: 76
2870423 GAGGTCTTAA
* *
2870433 AAACATCATGCACTGCAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
2870498 AGGCTTTTTGG
66 AGGCTTTTTGG
2870509 AAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
2870574 AGGCTTTTTGG
66 AGGCTTTTTGG
2870585 AAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
2870650 AGGCTTTTTGG
66 AGGCTTTTTGG
2870661 AAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
2870726 AGGCTTTTTGG
66 AGGCTTTTTGG
* *
2870737 AAACATCATGCACTGAAGGGCTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGATCCCGA
1 AAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
2870802 AGGCTTTTTGG
66 AGGCTTTTTGG
* * *
2870813 AAACATCATGCACTG-AGGACTTACAGATGACCCGAAGGCTTTGAAAACATCGAAAAGCTACCGA
1 AAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
2870877 AGGCTTTTTGG
66 AGGCTTTTTGG
*
2870888 AAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
2870953 AGGC-TTTTGG
66 AGGCTTTTTGG
*
2870963 AAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
2871028 AGGCTTTTTGG
66 AGGCTTTTTGG
*
2871039 AAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
2871104 AGGCTTTTTGG
66 AGGCTTTTTGG
*
2871115 AAACATCATGCACTGAAGGACTTACAGATG
1 AAACATCATGCACTGAAGGGCTTACAGATG
2871145 TGGGAAATAG
Statistics
Matches: 620, Mismatches: 14, Indels: 4
0.97 0.02 0.01
Matches are distributed among these distances:
75 145 0.23
76 475 0.77
ACGTcount: A:0.35, C:0.22, G:0.22, T:0.21
Consensus pattern (76 bp):
AAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
AGGCTTTTTGG
Found at i:2872295 original size:54 final size:54
Alignment explanation
Indices: 2872213--2872368 Score: 258
Period size: 54 Copynumber: 2.9 Consensus size: 54
2872203 AGAATAGCAG
***
2872213 GTTCGTAAAACATTTGACAGTGCATTCATCCTTTCCTGTGGCTTCTGCTCAGAT
1 GTTCGTAAAACATTTGACAACACATTCATCCTTTCCTGTGGCTTCTGCTCAGAT
* *
2872267 GTTCGTAAAACATTTGACAACACATTCATCCTTTCCTGTGGTTTCTGTTCAGAT
1 GTTCGTAAAACATTTGACAACACATTCATCCTTTCCTGTGGCTTCTGCTCAGAT
*
2872321 GTTCGTAAAACATTTGACAACACATTCATCCTTTACTGTGGCTTCTGC
1 GTTCGTAAAACATTTGACAACACATTCATCCTTTCCTGTGGCTTCTGC
2872369 CAAGATTTCT
Statistics
Matches: 94, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
54 94 1.00
ACGTcount: A:0.23, C:0.24, G:0.16, T:0.37
Consensus pattern (54 bp):
GTTCGTAAAACATTTGACAACACATTCATCCTTTCCTGTGGCTTCTGCTCAGAT
Found at i:2874280 original size:21 final size:20
Alignment explanation
Indices: 2874194--2874351 Score: 86
Period size: 21 Copynumber: 7.8 Consensus size: 20
2874184 AAATGACCAA
**
2874194 CAAAATCGCAACGCGA-AAT
1 CAAAATCGCAACGCGATTTT
* ***
2874213 AAAAATCGCAACGCGATCCC
1 CAAAATCGCAACGCGATTTT
* ** *
2874233 CAGAATCGCAAATC-AGTTTC
1 CAAAATCGCAACGCGA-TTTT
2874253 CAAAATCGCAACGCGATTCTT
1 CAAAATCGCAACGCGATT-TT
* * * *
2874274 GAAAATCGCAATGCGATAGTA
1 CAAAATCGCAACGCGAT-TTT
* **
2874295 CAAATTCGCATTGCGATTTT
1 CAAAATCGCAACGCGATTTT
* *
2874315 CCAAAATCGCAACGCGAATAT
1 -CAAAATCGCAACGCGATTTT
*
2874336 GAAAATCGCAACGCGA
1 CAAAATCGCAACGCGA
2874352 ACACATAAAT
Statistics
Matches: 104, Mismatches: 29, Indels: 11
0.72 0.20 0.08
Matches are distributed among these distances:
19 16 0.15
20 41 0.39
21 47 0.45
ACGTcount: A:0.39, C:0.25, G:0.17, T:0.19
Consensus pattern (20 bp):
CAAAATCGCAACGCGATTTT
Found at i:2874380 original size:20 final size:20
Alignment explanation
Indices: 2874318--2874511 Score: 221
Period size: 20 Copynumber: 9.7 Consensus size: 20
2874308 CGATTTTCCA
* ** *
2874318 AAATCGCAACGCGAATATGA
1 AAATCGCAACGCGTATCCGT
* *
2874338 AAATCGCAACGCG-AACACAT
1 AAATCGCAACGCGTATC-CGT
2874358 AAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
2874378 AAATCGCAACGTGTATCCGT
1 AAATCGCAACGCGTATCCGT
**
2874398 AAATCGCAACGCGTATGGGT
1 AAATCGCAACGCGTATCCGT
*
2874418 AAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
2874438 ATATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
* * *
2874458 AAATCGCAACG-ATAATACAT
1 AAATCGCAACGCGT-ATCCGT
2874478 AAAATCGCAACGCGTATCCGT
1 -AAATCGCAACGCGTATCCGT
2874499 AAATCGCAACGCG
1 AAATCGCAACGCG
2874512 ATATTTAAAG
Statistics
Matches: 146, Mismatches: 23, Indels: 10
0.82 0.13 0.06
Matches are distributed among these distances:
19 2 0.01
20 126 0.86
21 17 0.12
22 1 0.01
ACGTcount: A:0.36, C:0.26, G:0.20, T:0.19
Consensus pattern (20 bp):
AAATCGCAACGCGTATCCGT
Found at i:2874402 original size:60 final size:60
Alignment explanation
Indices: 2874318--2874511 Score: 253
Period size: 60 Copynumber: 3.2 Consensus size: 60
2874308 CGATTTTCCA
* ** * *
2874318 AAATCGCAACGCGAATATGAAAATCGCAACGCGAACACATAAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGT
* * *** *
2874378 AAATCGCAACGTGTATCCGTAAATCGCAACGCGTATGGGTAAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGT
* **
2874438 ATATCGCAACGCGTATCCGTAAATCGCAACGATAATACATAAAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACAT-AAATCGCAACGCGTATCCGT
2874499 AAATCGCAACGCG
1 AAATCGCAACGCG
2874512 ATATTTAAAG
Statistics
Matches: 112, Mismatches: 21, Indels: 1
0.84 0.16 0.01
Matches are distributed among these distances:
60 81 0.72
61 31 0.28
ACGTcount: A:0.36, C:0.26, G:0.20, T:0.19
Consensus pattern (60 bp):
AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGT
Found at i:2874930 original size:33 final size:33
Alignment explanation
Indices: 2874891--2874961 Score: 106
Period size: 33 Copynumber: 2.2 Consensus size: 33
2874881 TTCACTTAGA
* *
2874891 TTTCATTTCGCGTTACGATTCTGTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTCCGAT
* *
2874924 TTTCATTTCGCGTTGCTATTCTCTCGTTCCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTCCGAT
2874957 TTTCA
1 TTTCA
2874962 AGTTAGTATT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.11, C:0.24, G:0.17, T:0.48
Consensus pattern (33 bp):
TTTCATTTCGCGTTACGATTCTCTCGTTCCGAT
Found at i:2875085 original size:20 final size:20
Alignment explanation
Indices: 2875041--2875150 Score: 108
Period size: 21 Copynumber: 5.8 Consensus size: 20
2875031 TGCAGAAGAG
*
2875041 TCGCAACGAGATAAATGAAAA
1 TCGCAACGAGA-GAATGAAAA
***
2875062 TCGCAACGAGAGAATGACTG
1 TCGCAACGAGAGAATGAAAA
2875082 TCGCAACGAGAGAAATGAAAA
1 TCGCAACGAGAG-AATGAAAA
2875103 TCGCAAC--GAG-A-G--AA
1 TCGCAACGAGAGAATGAAAA
*
2875117 TCGCAACGCGA-AATGAAAA
1 TCGCAACGAGAGAATGAAAA
2875136 TCGCAACGAGAGAAT
1 TCGCAACGAGAGAAT
2875151 CGCAACGCGA
Statistics
Matches: 73, Mismatches: 8, Indels: 17
0.74 0.08 0.17
Matches are distributed among these distances:
14 9 0.12
16 4 0.05
17 2 0.03
19 15 0.21
20 20 0.27
21 23 0.32
ACGTcount: A:0.45, C:0.18, G:0.25, T:0.12
Consensus pattern (20 bp):
TCGCAACGAGAGAATGAAAA
Found at i:2875098 original size:41 final size:38
Alignment explanation
Indices: 2875034--2875150 Score: 145
Period size: 41 Copynumber: 3.1 Consensus size: 38
2875024 TTCAATTTGC
* *
2875034 AGAAGAGTCGCAACGAGATAAATGAAAATCGCAACGAG
1 AGAATAGTCGCAACGAGAGAAATGAAAATCGCAACGAG
2875072 AGAATGACTGTCGCAACGAGAGAAATGAAAATCGCAACGAG
1 AGAAT-A--GTCGCAACGAGAGAAATGAAAATCGCAACGAG
*
2875113 AG-A-A-TCGCAAC--GCGAAATGAAAATCGCAACGAG
1 AGAATAGTCGCAACGAGAGAAATGAAAATCGCAACGAG
2875146 AGAAT
1 AGAAT
2875151 CGCAACGCGA
Statistics
Matches: 71, Mismatches: 3, Indels: 13
0.82 0.03 0.15
Matches are distributed among these distances:
33 23 0.32
34 1 0.01
35 7 0.10
38 5 0.07
39 1 0.01
40 1 0.01
41 33 0.46
ACGTcount: A:0.46, C:0.17, G:0.26, T:0.11
Consensus pattern (38 bp):
AGAATAGTCGCAACGAGAGAAATGAAAATCGCAACGAG
Found at i:2875120 original size:14 final size:14
Alignment explanation
Indices: 2875101--2875157 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
2875091 GAGAAATGAA
2875101 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
2875115 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
2875134 AATCGCAACGAGAG
1 AATCGCAACGAGAG
2875148 AATCGCAACG
1 AATCGCAACG
2875158 CGAAACCAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 20 0.56
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.28
ACGTcount: A:0.44, C:0.23, G:0.25, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:2875133 original size:33 final size:33
Alignment explanation
Indices: 2875093--2875173 Score: 144
Period size: 33 Copynumber: 2.5 Consensus size: 33
2875083 CGCAACGAGA
2875093 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
2875126 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
**
2875159 GAAACCAAAATCGCA
1 GAAATGAAAATCGCA
2875174 TTGCGATTTT
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
33 46 1.00
ACGTcount: A:0.47, C:0.22, G:0.22, T:0.09
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:2875191 original size:19 final size:19
Alignment explanation
Indices: 2875169--2875266 Score: 81
Period size: 19 Copynumber: 5.7 Consensus size: 19
2875159 GAAACCAAAA
*
2875169 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
2875188 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
2875202 TCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
2875221 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* * *
2875235 TCTCGTTGCGATTGTCATC
1 TCGCGTTGCGATTTTCATT
2875254 TCGCGTTGCGATT
1 TCGCGTTGCGATT
2875267 CTCTCGTTGC
Statistics
Matches: 63, Mismatches: 6, Indels: 20
0.71 0.07 0.22
Matches are distributed among these distances:
14 20 0.32
16 5 0.08
17 6 0.10
19 32 0.51
ACGTcount: A:0.10, C:0.24, G:0.22, T:0.43
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:2875210 original size:14 final size:14
Alignment explanation
Indices: 2875191--2875280 Score: 81
Period size: 14 Copynumber: 5.7 Consensus size: 14
2875181 TTTCATTTCG
2875191 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
2875205 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
2875224 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
2875238 CGTTGCGATTGTCATCT
1 CGTTGCGA-T-TC-TCT
2875255 CGCGTTGCGATTCTCT
1 --CGTTGCGATTCTCT
2875271 CGTTGCGATT
1 CGTTGCGATT
2875281 TTCATTTCAA
Statistics
Matches: 64, Mismatches: 2, Indels: 20
0.74 0.02 0.23
Matches are distributed among these distances:
14 28 0.44
15 1 0.02
16 8 0.12
17 8 0.12
18 1 0.02
19 18 0.28
ACGTcount: A:0.09, C:0.26, G:0.23, T:0.42
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:2875216 original size:33 final size:33
Alignment explanation
Indices: 2875174--2875288 Score: 212
Period size: 33 Copynumber: 3.5 Consensus size: 33
2875164 CAAAATCGCA
2875174 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
2875207 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
* *
2875240 TTGCGATTGTCATCTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
2875273 TTGCGATTTTCATTTC
1 TTGCGATTTTCATTTC
2875289 AACCAAAAGA
Statistics
Matches: 78, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 78 1.00
ACGTcount: A:0.10, C:0.24, G:0.21, T:0.45
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
Found at i:2876631 original size:18 final size:18
Alignment explanation
Indices: 2876610--2876645 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
2876600 GTTTGAAAAG
2876610 AAACTTCTTAATGAAGAC
1 AAACTTCTTAATGAAGAC
2876628 AAACTTCTTAATGAAGAC
1 AAACTTCTTAATGAAGAC
2876646 GATCATGCAG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.44, C:0.17, G:0.11, T:0.28
Consensus pattern (18 bp):
AAACTTCTTAATGAAGAC
Found at i:2876856 original size:114 final size:114
Alignment explanation
Indices: 2876656--2876878 Score: 374
Period size: 114 Copynumber: 2.0 Consensus size: 114
2876646 GATCATGCAG
* * *
2876656 TTCATCTTTCAATTCCAATGATTGGTTCTGGGATTCCTACCGAACCAAATCAGATAACTCAAAGA
1 TTCATCTTTCAAATCCAATGATTGGTTCTGGGATTCATACCAAACCAAATCAGATAACTCAAAGA
*
2876721 ACACTTCCAGAAGATGCTATTGGGTCTCCTTATTTCTACTATGAGCAAA
66 ACACTTCCAGAAGATGCTATTGAGTCTCCTTATTTCTACTATGAGCAAA
* * *
2876770 TTCATCTTTCAAATCTAATGATTGGTTTTGGGGTTCATACCAAACCAAATCAGATAACTCAAAGA
1 TTCATCTTTCAAATCCAATGATTGGTTCTGGGATTCATACCAAACCAAATCAGATAACTCAAAGA
*
2876835 ACACTTCCAGAAGATGCTATTGAGTCTTCTTATTTCTACTATGA
66 ACACTTCCAGAAGATGCTATTGAGTCTCCTTATTTCTACTATGA
2876879 TCACATGGCA
Statistics
Matches: 101, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
114 101 1.00
ACGTcount: A:0.31, C:0.21, G:0.14, T:0.33
Consensus pattern (114 bp):
TTCATCTTTCAAATCCAATGATTGGTTCTGGGATTCATACCAAACCAAATCAGATAACTCAAAGA
ACACTTCCAGAAGATGCTATTGAGTCTCCTTATTTCTACTATGAGCAAA
Found at i:2884913 original size:22 final size:22
Alignment explanation
Indices: 2884883--2884940 Score: 66
Period size: 22 Copynumber: 2.7 Consensus size: 22
2884873 TTTATAAAAC
*
2884883 TATTCAAATAATATATTAATAT
1 TATTAAAATAATATATTAATAT
*
2884905 TATTAAAATAATA-ATTATTAT
1 TATTAAAATAATATATTAATAT
*
2884926 TAATTTAAAT-ATATA
1 T-ATTAAAATAATATA
2884941 ACAATAAAAT
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
21 11 0.35
22 20 0.65
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.47
Consensus pattern (22 bp):
TATTAAAATAATATATTAATAT
Found at i:2886063 original size:3 final size:3
Alignment explanation
Indices: 2886057--2886130 Score: 73
Period size: 3 Copynumber: 25.3 Consensus size: 3
2886047 ATAATATATT
* **
2886057 TAA TAA TAA T-A TAA T-A TATA TAA T-A TAA TAA TAA TAT TTC TAA
1 TAA TAA TAA TAA TAA TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA
**
2886100 TAA TAA TAA TAA TAA TTT TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
2886131 TTAAGTAAAA
Statistics
Matches: 58, Mismatches: 9, Indels: 8
0.77 0.12 0.11
Matches are distributed among these distances:
2 6 0.10
3 49 0.84
4 3 0.05
ACGTcount: A:0.57, C:0.01, G:0.00, T:0.42
Consensus pattern (3 bp):
TAA
Found at i:2886126 original size:12 final size:12
Alignment explanation
Indices: 2886045--2886127 Score: 64
Period size: 12 Copynumber: 6.8 Consensus size: 12
2886035 TGGACCGTTG
2886045 TAATAATATATT-
1 TAATAATA-ATTA
2886057 TAATAATAA-TA
1 TAATAATAATTA
*
2886068 TAATATATATAATA
1 TAATA-ATA-ATTA
2886082 TAATAATAA-TA
1 TAATAATAATTA
** *
2886093 TTTCTAATAATAA
1 -TAATAATAATTA
*
2886106 TAATAATAATTT
1 TAATAATAATTA
2886118 TAATAATAAT
1 TAATAATAAT
2886128 AATTTAAGTA
Statistics
Matches: 58, Mismatches: 7, Indels: 12
0.75 0.09 0.16
Matches are distributed among these distances:
10 1 0.02
11 8 0.14
12 37 0.64
13 5 0.09
14 7 0.12
ACGTcount: A:0.55, C:0.01, G:0.00, T:0.43
Consensus pattern (12 bp):
TAATAATAATTA
Found at i:2886386 original size:76 final size:76
Alignment explanation
Indices: 2886284--2886942 Score: 1223
Period size: 76 Copynumber: 8.7 Consensus size: 76
2886274 GAGGTTTTAA
* *
2886284 AAACATCATGCACTGCAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
2886349 AGGCTTTTTGG
66 AGGCTTTTTGG
2886360 AAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
2886425 AGGCTTTTTGG
66 AGGCTTTTTGG
2886436 AAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAACATC-AAAAGCTCCCGA
1 AAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
2886500 AGGCTTTTTGG
66 AGGCTTTTTGG
2886511 AAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
2886576 AGGCTTTTTGG
66 AGGCTTTTTGG
*
2886587 AAACATCATGCACTGAAGGGCTTACAGATGACCCGAAAGCTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
2886652 AGGCTTTTTGG
66 AGGCTTTTTGG
* *
2886663 AAACATCATGCACTGAAGGGCTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGATCCCGA
1 AAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
2886728 AGGCTTTTTGG
66 AGGCTTTTTGG
* *
2886739 AAACATCATGCACTG-AGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTACCGA
1 AAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
2886803 AGGCTTTTTGG
66 AGGCTTTTTGG
*
2886814 AAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
2886879 AGGCTTTTTGG
66 AGGCTTTTTGG
*
2886890 AAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTGAAAACATCA
1 AAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAACATCA
2886943 TGCACTGAAG
Statistics
Matches: 568, Mismatches: 13, Indels: 4
0.97 0.02 0.01
Matches are distributed among these distances:
75 146 0.26
76 422 0.74
ACGTcount: A:0.35, C:0.22, G:0.22, T:0.21
Consensus pattern (76 bp):
AAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
AGGCTTTTTGG
Found at i:2886543 original size:151 final size:152
Alignment explanation
Indices: 2886284--2886942 Score: 1223
Period size: 151 Copynumber: 4.3 Consensus size: 152
2886274 GAGGTTTTAA
* *
2886284 AAACATCATGCACTGCAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
2886349 AGGCTTTTTGGAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAACATCAA
66 AGGCTTTTTGGAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAACATCAA
2886414 AAAGCTCCCGAAGGCTTTTTGG
131 AAAGCTCCCGAAGGCTTTTTGG
2886436 AAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAACATC-AAAAGCTCCCGA
1 AAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
2886500 AGGCTTTTTGGAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAACATCAA
66 AGGCTTTTTGGAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAACATCAA
2886565 AAAGCTCCCGAAGGCTTTTTGG
131 AAAGCTCCCGAAGGCTTTTTGG
*
2886587 AAACATCATGCACTGAAGGGCTTACAGATGACCCGAAAGCTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
*
2886652 AGGCTTTTTGGAAACATCATGCACTGAAGGGCTTACAGATGACCCTAAGGCTTTGAAAACATCAA
66 AGGCTTTTTGGAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAACATCAA
*
2886717 AAAGATCCCGAAGGCTTTTTGG
131 AAAGCTCCCGAAGGCTTTTTGG
* *
2886739 AAACATCATGCACTG-AGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTACCGA
1 AAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
*
2886803 AGGCTTTTTGGAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTGAAAACATCAA
66 AGGCTTTTTGGAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAACATCAA
2886868 AAAGCTCCCGAAGGCTTTTTGG
131 AAAGCTCCCGAAGGCTTTTTGG
*
2886890 AAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTGAAAACATCA
1 AAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAACATCA
2886943 TGCACTGAAG
Statistics
Matches: 492, Mismatches: 13, Indels: 4
0.97 0.03 0.01
Matches are distributed among these distances:
151 295 0.60
152 197 0.40
ACGTcount: A:0.35, C:0.22, G:0.22, T:0.21
Consensus pattern (152 bp):
AAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
AGGCTTTTTGGAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAACATCAA
AAAGCTCCCGAAGGCTTTTTGG
Found at i:2886679 original size:227 final size:226
Alignment explanation
Indices: 2886284--2886942 Score: 1228
Period size: 227 Copynumber: 2.9 Consensus size: 226
2886274 GAGGTTTTAA
2886284 AAACATCATGCACTGCAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTG-AGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
2886349 AGGCTTTTTGGAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAACATCAA
65 AGGCTTTTTGGAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAACATCAA
2886414 AAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTT
130 AAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTT
*
2886479 GAAAACATCAAAAGCTCCCGAAGGCTTTTTGG
195 GAAAACATCAAAAGATCCCGAAGGCTTTTTGG
*
2886511 AAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTG-AGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
*
2886576 AGGCTTTTTGGAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAAGCTTTGAAAACATCAA
65 AGGCTTTTTGGAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAACATCAA
*
2886641 AAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGGCTTACAGATGACCCTAAGGCTTT
130 AAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTT
2886706 GAAAACATCAAAAAGATCCCGAAGGCTTTTTGG
195 GAAAACATC-AAAAGATCCCGAAGGCTTTTTGG
*
2886739 AAACATCATGCACTGAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTACCGAA
1 AAACATCATGCACTGAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGAA
*
2886804 GGCTTTTTGGAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTGAAAACATCAAA
66 GGCTTTTTGGAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAACATCAAA
*
2886869 AAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTG
131 AAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTG
2886934 AAAACATCA
196 AAAACATCA
2886943 TGCACTGAAG
Statistics
Matches: 420, Mismatches: 11, Indels: 3
0.97 0.03 0.01
Matches are distributed among these distances:
226 1 0.00
227 382 0.91
228 37 0.09
ACGTcount: A:0.35, C:0.22, G:0.22, T:0.21
Consensus pattern (226 bp):
AAACATCATGCACTGAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGAA
GGCTTTTTGGAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAACATCAAA
AAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTG
AAAACATCAAAAGATCCCGAAGGCTTTTTGG
Found at i:2886940 original size:45 final size:45
Alignment explanation
Indices: 2886874--2886987 Score: 201
Period size: 45 Copynumber: 2.5 Consensus size: 45
2886864 TCAAAAAGCT
*
2886874 CCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGGCTTACAGATGA
1 CCCGAAGG--TTTTGAAAACATCATGCACTGAAGGGCTTACAGATGA
2886921 CCCGAAGGTTTTGAAAACATCATGCACTGAAGGGCTTACAGATGA
1 CCCGAAGGTTTTGAAAACATCATGCACTGAAGGGCTTACAGATGA
2886966 CCCGAAGGTTTTGAAAACATCA
1 CCCGAAGGTTTTGAAAACATCA
2886988 AAAAGCTCCC
Statistics
Matches: 66, Mismatches: 1, Indels: 2
0.96 0.01 0.03
Matches are distributed among these distances:
45 58 0.88
47 8 0.12
ACGTcount: A:0.32, C:0.21, G:0.24, T:0.23
Consensus pattern (45 bp):
CCCGAAGGTTTTGAAAACATCATGCACTGAAGGGCTTACAGATGA
Found at i:2886950 original size:121 final size:122
Alignment explanation
Indices: 2886799--2887040 Score: 450
Period size: 121 Copynumber: 2.0 Consensus size: 122
2886789 CAAAAAGCTA
*
2886799 CCGAAGGCTTTTTGGAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTGAAAACA
1 CCGAAGGC-TTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTGAAAACA
*
2886864 TCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGGCTTACAGATGAC
65 TCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGAC
2886922 CCGAAGG-TTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTGAAAACAT
1 CCGAAGGCTTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTGAAAACAT
2886986 CAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATG
66 CAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATG
2887041 TGGGAAATAG
Statistics
Matches: 117, Mismatches: 2, Indels: 2
0.97 0.02 0.02
Matches are distributed among these distances:
121 110 0.94
123 7 0.06
ACGTcount: A:0.33, C:0.21, G:0.23, T:0.23
Consensus pattern (122 bp):
CCGAAGGCTTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTGAAAACAT
CAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGAC
Found at i:2888192 original size:54 final size:54
Alignment explanation
Indices: 2888110--2888265 Score: 240
Period size: 54 Copynumber: 2.9 Consensus size: 54
2888100 AGAATAGCAG
***
2888110 GTTCGTAAAACATTTGACAGTGCATTCATCCTTTCCTGTGGCTTCTGCTCAGAT
1 GTTCGTAAAACATTTGACAACACATTCATCCTTTCCTGTGGCTTCTGCTCAGAT
* * *
2888164 GTTCGTAAAACATTTGACAACACATTCATCCTTTCCTGTGGTTTTTGTTCAGAT
1 GTTCGTAAAACATTTGACAACACATTCATCCTTTCCTGTGGCTTCTGCTCAGAT
* *
2888218 GTTCGTAAAACATTTGACAACACATTCATCTTTTACTGTGGCTTCTGC
1 GTTCGTAAAACATTTGACAACACATTCATCCTTTCCTGTGGCTTCTGC
2888266 CAAGATTTCT
Statistics
Matches: 91, Mismatches: 11, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
54 91 1.00
ACGTcount: A:0.23, C:0.22, G:0.16, T:0.38
Consensus pattern (54 bp):
GTTCGTAAAACATTTGACAACACATTCATCCTTTCCTGTGGCTTCTGCTCAGAT
Found at i:2889550 original size:133 final size:128
Alignment explanation
Indices: 2889355--2889591 Score: 307
Period size: 133 Copynumber: 1.8 Consensus size: 128
2889345 AAGTAAATTT
* * * * *
2889355 ATTAATTTATATAAATAAGATATTTATTTAGAAATATCAGAAAAGAGCTTCTAGGTGTTTTAAGA
1 ATTAATATATATAAATAAAATATTTATTTAGAAATATCAGAAAACAGCATCTAGGTGCTTTAAGA
*
2889420 C-ATCTCCTTCCTTTGATATTAAAAAATAAATAAATATTAAAAAATTTATCTAAAAAATAATAG
66 CTATC-CCTTCCTTTGATATTAAAAAATAAATAAACATTAAAAAATTTATCTAAAAAATAATAG
* *
2889483 ATTAATATATA-AAAGTAAAATATTTATTTATTGAAAATTATCATAAAACAGACATCTAGTTGCT
1 ATTAATATATATAAA-TAAAATATTTATTTA--G-AAA-TATCAGAAAACAG-CATCTAGGTGCT
* *
2889547 TTAAGACTATCCTTTTCTTTGATATTAAAAAATAAATAAACATTA
60 TTAAGACTATCCCTTCCTTTGATATTAAAAAATAAATAAACATTA
2889592 TTATAAATTT
Statistics
Matches: 92, Mismatches: 10, Indels: 9
0.83 0.09 0.08
Matches are distributed among these distances:
127 3 0.03
128 24 0.26
130 1 0.01
131 3 0.03
132 11 0.12
133 47 0.51
134 3 0.03
ACGTcount: A:0.46, C:0.08, G:0.08, T:0.38
Consensus pattern (128 bp):
ATTAATATATATAAATAAAATATTTATTTAGAAATATCAGAAAACAGCATCTAGGTGCTTTAAGA
CTATCCCTTCCTTTGATATTAAAAAATAAATAAACATTAAAAAATTTATCTAAAAAATAATAG
Found at i:2889635 original size:22 final size:21
Alignment explanation
Indices: 2889610--2889658 Score: 55
Period size: 22 Copynumber: 2.3 Consensus size: 21
2889600 TTTTTATAAA
*
2889610 ATTAATCAAATAATATATTAA-T
1 ATTAATAAAATAATA-A-TAATT
*
2889632 ATTATTAAAATAATAATAATT
1 ATTAATAAAATAATAATAATT
2889653 ATTAAT
1 ATTAAT
2889659 TTAAATATAT
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
20 3 0.13
21 7 0.30
22 13 0.57
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (21 bp):
ATTAATAAAATAATAATAATT
Found at i:2889664 original size:22 final size:21
Alignment explanation
Indices: 2889617--2889670 Score: 56
Period size: 22 Copynumber: 2.4 Consensus size: 21
2889607 AAAATTAATC
2889617 AAATAATATATTAATATTATTA
1 AAATAATA-ATTAATATTATTA
*
2889639 AAATAATAA-TAATTATTAATTT
1 AAATAATAATTAA-TATT-ATTA
2889661 AAATATATAA
1 AAATA-ATAA
2889671 CAATAAAATA
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
20 3 0.11
21 5 0.18
22 16 0.57
23 4 0.14
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (21 bp):
AAATAATAATTAATATTATTA
Found at i:2890445 original size:3 final size:3
Alignment explanation
Indices: 2890439--2890515 Score: 88
Period size: 3 Copynumber: 26.3 Consensus size: 3
2890429 ATAATATATT
* *
2890439 TAA TAA TAA T-A TAA T-A TATA TAA T-A TAA TAA TAA TAA TAT TTA
1 TAA TAA TAA TAA TAA TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA
**
2890482 TAA TAA TAA TAA TAA TAA TTT TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
2890516 TTAAGTAAAA
Statistics
Matches: 62, Mismatches: 8, Indels: 8
0.79 0.10 0.10
Matches are distributed among these distances:
2 6 0.10
3 53 0.85
4 3 0.05
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (3 bp):
TAA
Found at i:2890459 original size:9 final size:9
Alignment explanation
Indices: 2890429--2890495 Score: 54
Period size: 9 Copynumber: 7.7 Consensus size: 9
2890419 TGGGCTTGTA
2890429 ATAATATAT
1 ATAATATAT
*
2890438 TTAATAATAAT
1 ATAAT-AT-AT
2890449 ATAATATAT
1 ATAATATAT
2890458 ATAATATA-
1 ATAATATAT
2890466 AT-A-ATA-
1 ATAATATAT
*
2890472 ATAATATTT
1 ATAATATAT
2890481 ATAATA-AT
1 ATAATATAT
2890489 AATAATA
1 -ATAATA
2890496 ATAATTTTAA
Statistics
Matches: 48, Mismatches: 4, Indels: 12
0.75 0.06 0.19
Matches are distributed among these distances:
6 5 0.10
7 2 0.04
8 5 0.10
9 26 0.54
10 4 0.08
11 6 0.12
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (9 bp):
ATAATATAT
Found at i:2890511 original size:12 final size:13
Alignment explanation
Indices: 2890427--2890519 Score: 88
Period size: 12 Copynumber: 7.2 Consensus size: 13
2890417 TTTGGGCTTG
2890427 TAATAAT-ATATT
1 TAATAATAATATT
2890439 TAATAATAATA-T
1 TAATAATAATATT
* *
2890451 AATATATATAATATAA
1 TA-ATA-ATAATAT-T
2890467 TAATAATAATATT
1 TAATAATAATATT
*
2890480 T-ATAATAATA-A
1 TAATAATAATATT
2890491 TAATAATAAT-TT
1 TAATAATAATATT
2890503 TAATAATAATAATT
1 TAATAATAAT-ATT
2890517 TAA
1 TAA
2890520 GTAAAATGAA
Statistics
Matches: 66, Mismatches: 6, Indels: 16
0.75 0.07 0.18
Matches are distributed among these distances:
11 1 0.02
12 36 0.55
13 7 0.11
14 18 0.27
15 3 0.05
16 1 0.02
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (13 bp):
TAATAATAATATT
Found at i:2903501 original size:146 final size:144
Alignment explanation
Indices: 2903313--2903694 Score: 460
Period size: 146 Copynumber: 2.7 Consensus size: 144
2903303 TTTATTTTTA
* * * *
2903313 TAAATAAGATATTTATTTACTTAGAAATATCAGAAAAAGACTTCTAGGTGCTTTAAGATAGCCCA
1 TAAATAAGATATTTATTTATTTAAAAATATCAGAAAAGGACTTCTAGGTGCTTTAAGATAGCACA
2903378 TTTCTTAATATTAAAAAATAAATAAATATTAATAA-A-ACATTTCTCTA-AAAATAATTAAAATA
66 TTTCTTAATATTAAAAAATAAATAAATATTAATAATAGACATTTCTCTATAAAA-AA-TAAAA-A
2903440 AATT-AATATATAATTT
128 AATTAAATATATAATTT
* *
2903456 ATAAAAATAAGATATTTATTTATTTAAAAATATCAGAAAAGGACTTCTAGGTACTTTAAGATAAC
1 -T--AAATAAGATATTTATTTATTTAAAAATATCAGAAAAGGACTTCTAGGTGCTTTAAGATAGC
** * * * *
2903521 ACATTTCTTAATATCGAAAAATAAATAAATATTAATAATATGATATTTTTTTATAAAAAATAATA
63 ACATTTCTTAATATTAAAAAATAAATAAATATTAATAATA-GACATTTCTCTATAAAAAATAAAA
2903586 AAATTAAATATATAATTT
127 AAATTAAATATATAATTT
* * * * * *
2903604 T-TAT-A-ATATTTATTTATTT-AAAATACCAGAATAGGACATCTAGTTGCTTTAAGACT-G-TC
1 TAAATAAGATATTTATTTATTTAAAAATATCAGAAAAGGACTTCTAGGTGCTTTAAGA-TAGCAC
2903663 ATTTCTTAATATTAAAAAATAAATAAATATTA
65 ATTTCTTAATATTAAAAAATAAATAAATATTA
2903695 TTATTTAAAC
Statistics
Matches: 208, Mismatches: 22, Indels: 20
0.83 0.09 0.08
Matches are distributed among these distances:
140 31 0.15
141 30 0.14
142 15 0.07
143 1 0.00
144 3 0.01
146 91 0.44
147 7 0.03
148 16 0.08
149 10 0.05
150 4 0.02
ACGTcount: A:0.48, C:0.07, G:0.07, T:0.38
Consensus pattern (144 bp):
TAAATAAGATATTTATTTATTTAAAAATATCAGAAAAGGACTTCTAGGTGCTTTAAGATAGCACA
TTTCTTAATATTAAAAAATAAATAAATATTAATAATAGACATTTCTCTATAAAAAATAAAAAAAT
TAAATATATAATTT
Done.