Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000260.1 Hibiscus syriacus cultivar Beakdansim tig00000477_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: 5583615
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 10 of 26
Found at i:1857282 original size:12 final size:13
Alignment explanation
Indices: 1857242--1857287 Score: 51
Period size: 13 Copynumber: 3.5 Consensus size: 13
1857232 AATATATAAA
*
1857242 AAAATAAAAATAGT
1 AAAATAAAAACA-T
1857256 AAAA-AAACAACAT
1 AAAATAAA-AACAT
1857269 AAAATAAAAA-AT
1 AAAATAAAAACAT
1857281 AAAATAA
1 AAAATAA
1857288 GTACAAGGAC
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
12 9 0.31
13 10 0.34
14 10 0.34
ACGTcount: A:0.78, C:0.04, G:0.02, T:0.15
Consensus pattern (13 bp):
AAAATAAAAACAT
Found at i:1857442 original size:4 final size:4
Alignment explanation
Indices: 1857429--1857457 Score: 51
Period size: 4 Copynumber: 7.5 Consensus size: 4
1857419 CGAATATTAG
1857429 AAAT -AAT AAAT AAAT AAAT AAAT AAAT AA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AA
1857458 CAATGATTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
3 3 0.12
4 21 0.88
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (4 bp):
AAAT
Found at i:1857652 original size:134 final size:137
Alignment explanation
Indices: 1857338--1857864 Score: 686
Period size: 138 Copynumber: 3.8 Consensus size: 137
1857328 AAAATTCAAG
* * * * * **
1857338 AAAATAAAAGTCAGTAGTTAGCAGAGTTCGAACCATAATAATGCAGATCTTACCCCGGATCAAAT
1 AAAATAAAAGTCAGTAGTTAGCAGAGTCCAAACCATAATAATGCGGATCATACCCCAGATCGGAT
*
1857403 CACCACAAGGTCGAATCGAATATTAGAAATAATAAATAAATAAATAAATAAATAACAATGATTAA
66 CACCACAAGGCCGAATCGAATATTAG-AATAATAAATAAATAAATAAATAAATAACAATGATTAA
1857468 AGTGTAAT
130 AGTGTAAT
* * *
1857476 AAAATAAAAGTCAGTAG-TA-CTTAGAGTCCGAACCATAATAATGCGGATCATACCCTAGATTGG
1 AAAATAAAAGTCAGTAGTTAGC--AGAGTCCAAACCATAATAATGCGGATCATACCCCAGATCGG
*
1857539 TTCACCACAAGGCCGAATCGAATATTAG-A-AAT-AATAAATAAATAAATAAATAACAATGATTA
64 ATCACCACAAGGCCGAATCGAATATTAGAATAATAAATAAATAAATAAATAAATAACAATGATTA
1857601 AAGTGTAAT
129 AAGTGTAAT
* * * * *
1857610 AAAATAAAAGTTAGTAGTTAGCAGAGTCCAAACTATAATAATGTGGATCATACCCCGGATCGGGT
1 AAAATAAAAGTCAGTAGTTAGCAGAGTCCAAACCATAATAATGCGGATCATACCCCAGATCGGAT
* *
1857675 CACCACAAGGCTGAATTGAATATTAGAAATAATAAATAAATAAATAAATAAATAACAATGATTAA
66 CACCACAAGGCCGAATCGAATATTAG-AATAATAAATAAATAAATAAATAAATAACAATGATTAA
*
1857740 AGTGCAAT
130 AGTGTAAT
* * * * * * * * *
1857748 AGAATAAAATTTAGTTGTTAGCAGAATCAAAACCATAATAAAGCGAATCATACCCCAGATTGGAT
1 AAAATAAAAGTCAGTAGTTAGCAGAGTCCAAACCATAATAATGCGGATCATACCCCAGATCGGAT
* * *
1857813 CACGACAAGGCCGAATTGAATATTAGAATCAATAAGTAAATAAATAAATAAA
66 CACCACAAGGCCGAATCGAATATTAGAAT-AATAAATAAATAAATAAATAAA
1857865 CAATAAAATA
Statistics
Matches: 344, Mismatches: 36, Indels: 18
0.86 0.09 0.05
Matches are distributed among these distances:
134 115 0.33
135 5 0.01
136 4 0.01
137 8 0.02
138 212 0.62
ACGTcount: A:0.48, C:0.13, G:0.15, T:0.24
Consensus pattern (137 bp):
AAAATAAAAGTCAGTAGTTAGCAGAGTCCAAACCATAATAATGCGGATCATACCCCAGATCGGAT
CACCACAAGGCCGAATCGAATATTAGAATAATAAATAAATAAATAAATAAATAACAATGATTAAA
GTGTAAT
Found at i:1857714 original size:4 final size:4
Alignment explanation
Indices: 1857701--1857729 Score: 51
Period size: 4 Copynumber: 7.5 Consensus size: 4
1857691 TGAATATTAG
1857701 AAAT -AAT AAAT AAAT AAAT AAAT AAAT AA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AA
1857730 CAATGATTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
3 3 0.12
4 21 0.88
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (4 bp):
AAAT
Found at i:1857824 original size:272 final size:272
Alignment explanation
Indices: 1857338--1857868 Score: 755
Period size: 272 Copynumber: 1.9 Consensus size: 272
1857328 AAAATTCAAG
* * *
1857338 AAAATAAAAGTCAGTAGTTAGCAGAGTTCGAACCATAATAATGCAGATCTTACCCCGGATCAAAT
1 AAAATAAAAGTCAGTAGTTAGCAGAGTCCAAACCATAATAATGCAGATCATACCCCGGATCAAAT
1857403 CACCACAAGGTCGAATCGAATATTAGAAATAATAAATAAATAAATAAATAAATAACAATGATTAA
66 CACCACAAGGTCGAATCGAATATTAGAAATAATAAATAAATAAATAAATAAATAACAATGATTAA
* * ** * * *
1857468 AGTGTAATAAAATAAAAGTCAGTAGTACTTAGAGTCCGAACCATAATAATGCGGATCATACCCTA
131 AGTGCAATAAAATAAAAGTCAGTAGTAC-TAGAATCAAAACCATAATAAAGCGAATCATACCCCA
*
1857533 GATTGGTTCACCACAAGGCCGAATCGAATATTAGAAAT-AATAAATAAATAAATAAAT-AACAAT
195 GATTGGATCACCACAAGGCCGAATCGAATATTAG-AATCAATAAATAAATAAATAAATAAACAAT
1857596 GATTAAAGTGTAAT
259 GATTAAAGTGTAAT
* * ** ***
1857610 AAAATAAAAGTTAGTAGTTAGCAGAGTCCAAACTATAATAATGTGGATCATACCCCGGATCGGGT
1 AAAATAAAAGTCAGTAGTTAGCAGAGTCCAAACCATAATAATGCAGATCATACCCCGGATCAAAT
*
1857675 CACCACAAGG-CTGAATTGAATATTAGAAATAATAAATAAATAAATAAATAAATAACAATGATTA
66 CACCACAAGGTC-GAATCGAATATTAGAAATAATAAATAAATAAATAAATAAATAACAATGATTA
* * * *
1857739 AAGTGCAATAGAATAAAATTTAGTTGTTAGC-AGAATCAAAACCATAATAAAGCGAATCATACCC
130 AAGTGCAATAAAATAAAAGTCAGTAG-TA-CTAGAATCAAAACCATAATAAAGCGAATCATACCC
* * *
1857803 CAGATTGGATCACGACAAGGCCGAATTGAATATTAGAATCAATAAGTAAATAAATAAATAAACAA
193 CAGATTGGATCACCACAAGGCCGAATCGAATATTAGAATCAATAAATAAATAAATAAATAAACAA
1857868 T
258 T
1857869 AAAATAAATA
Statistics
Matches: 228, Mismatches: 26, Indels: 9
0.87 0.10 0.03
Matches are distributed among these distances:
271 4 0.02
272 215 0.94
273 8 0.04
274 1 0.00
ACGTcount: A:0.48, C:0.14, G:0.15, T:0.24
Consensus pattern (272 bp):
AAAATAAAAGTCAGTAGTTAGCAGAGTCCAAACCATAATAATGCAGATCATACCCCGGATCAAAT
CACCACAAGGTCGAATCGAATATTAGAAATAATAAATAAATAAATAAATAAATAACAATGATTAA
AGTGCAATAAAATAAAAGTCAGTAGTACTAGAATCAAAACCATAATAAAGCGAATCATACCCCAG
ATTGGATCACCACAAGGCCGAATCGAATATTAGAATCAATAAATAAATAAATAAATAAACAATGA
TTAAAGTGTAAT
Found at i:1857930 original size:28 final size:28
Alignment explanation
Indices: 1857896--1857957 Score: 90
Period size: 28 Copynumber: 2.2 Consensus size: 28
1857886 GAGTGCAAAA
*
1857896 AAATAAAAGTTAGTAGTTAATTTG-AAGT
1 AAATAAAAGTTAGTAGTTAATATGCAA-T
*
1857924 AAATAAAAGTTAGTGGTTAATATGCAAT
1 AAATAAAAGTTAGTAGTTAATATGCAAT
1857952 AAATAA
1 AAATAA
1857958 TATAGCAAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
28 29 0.94
29 2 0.06
ACGTcount: A:0.50, C:0.02, G:0.16, T:0.32
Consensus pattern (28 bp):
AAATAAAAGTTAGTAGTTAATATGCAAT
Found at i:1864646 original size:21 final size:21
Alignment explanation
Indices: 1864620--1864665 Score: 83
Period size: 21 Copynumber: 2.2 Consensus size: 21
1864610 GTTTCGACAT
*
1864620 GATGTATGACATTATTACTGG
1 GATGTACGACATTATTACTGG
1864641 GATGTACGACATTATTACTGG
1 GATGTACGACATTATTACTGG
1864662 GATG
1 GATG
1864666 AACCATTTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.28, C:0.11, G:0.26, T:0.35
Consensus pattern (21 bp):
GATGTACGACATTATTACTGG
Found at i:1868897 original size:10 final size:10
Alignment explanation
Indices: 1868882--1868906 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
1868872 TGCACAACAT
1868882 TTTAGTTGTA
1 TTTAGTTGTA
1868892 TTTAGTTGTA
1 TTTAGTTGTA
1868902 TTTAG
1 TTTAG
1868907 GTTATATTTG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.20, C:0.00, G:0.20, T:0.60
Consensus pattern (10 bp):
TTTAGTTGTA
Found at i:1870572 original size:31 final size:33
Alignment explanation
Indices: 1870534--1870599 Score: 100
Period size: 35 Copynumber: 2.0 Consensus size: 33
1870524 TCTCACCTCT
1870534 ATTCTTACATA-C-GTTCAAAGAAAGAATAAAA
1 ATTCTTACATACCAGTTCAAAGAAAGAATAAAA
1870565 ATTCTTACATACTCAAGTTCAAAGAAAGAATAAAA
1 ATTCTTACATAC-C-AGTTCAAAGAAAGAATAAAA
1870600 CAAGGAGGAA
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
31 11 0.35
33 1 0.03
35 19 0.61
ACGTcount: A:0.52, C:0.14, G:0.09, T:0.26
Consensus pattern (33 bp):
ATTCTTACATACCAGTTCAAAGAAAGAATAAAA
Found at i:1871968 original size:19 final size:19
Alignment explanation
Indices: 1871944--1871983 Score: 71
Period size: 19 Copynumber: 2.1 Consensus size: 19
1871934 CACTTAAGAG
*
1871944 AATGAATCGAAAAGAGTAC
1 AATGAATCCAAAAGAGTAC
1871963 AATGAATCCAAAAGAGTAC
1 AATGAATCCAAAAGAGTAC
1871982 AA
1 AA
1871984 AAGTGTCCTA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.55, C:0.12, G:0.17, T:0.15
Consensus pattern (19 bp):
AATGAATCCAAAAGAGTAC
Found at i:1874206 original size:20 final size:22
Alignment explanation
Indices: 1874181--1874227 Score: 62
Period size: 23 Copynumber: 2.2 Consensus size: 22
1874171 GTTGATGGTA
*
1874181 AAGATG-AAAGAAAA-AAGAAC
1 AAGATGAAAAGAAAATAAAAAC
1874201 AAGATGATAAAGAAAATAAAAAC
1 AAGATGA-AAAGAAAATAAAAAC
1874224 AAGA
1 AAGA
1874228 AGAAGAATGA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
20 6 0.26
22 8 0.35
23 9 0.39
ACGTcount: A:0.70, C:0.04, G:0.17, T:0.09
Consensus pattern (22 bp):
AAGATGAAAAGAAAATAAAAAC
Found at i:1879365 original size:75 final size:75
Alignment explanation
Indices: 1879286--1879459 Score: 269
Period size: 75 Copynumber: 2.3 Consensus size: 75
1879276 CCATTATAAG
* * *
1879286 ATGGGGGTATCGGTA-CCTCCTGGGGGGTATCGGTACCCTCCAAGCAATTTGTTATTTCTCGGAG
1 ATGGGGGTATCGGTACCCT-ATGGGGGGTATCGGTACCCTCCAAGAAATCTGTTATTTCTCGGAG
*
1879350 CCAAATCTTAT
65 CCAAATCTTAC
* *
1879361 ATGGGGGTATCGGTACCCTATTGGGGGTATCGGTACCCTCCAAGAAATCTGTTATTTCTCGGAGT
1 ATGGGGGTATCGGTACCCTATGGGGGGTATCGGTACCCTCCAAGAAATCTGTTATTTCTCGGAGC
1879426 CAAATCTTAC
66 CAAATCTTAC
*
1879436 ATGGGGGTATCGGTACCCTCTGGG
1 ATGGGGGTATCGGTACCCTATGGG
1879460 CAATCTGGTT
Statistics
Matches: 90, Mismatches: 8, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
75 87 0.97
76 3 0.03
ACGTcount: A:0.20, C:0.22, G:0.28, T:0.30
Consensus pattern (75 bp):
ATGGGGGTATCGGTACCCTATGGGGGGTATCGGTACCCTCCAAGAAATCTGTTATTTCTCGGAGC
CAAATCTTAC
Found at i:1879387 original size:20 final size:20
Alignment explanation
Indices: 1879362--1879399 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
1879352 AAATCTTATA
1879362 TGGGGGTATCGGTACCCTAT
1 TGGGGGTATCGGTACCCTAT
1879382 TGGGGGTATCGGTACCCT
1 TGGGGGTATCGGTACCCT
1879400 CCAAGAAATC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.13, C:0.21, G:0.37, T:0.29
Consensus pattern (20 bp):
TGGGGGTATCGGTACCCTAT
Found at i:1882065 original size:21 final size:21
Alignment explanation
Indices: 1882041--1882101 Score: 70
Period size: 21 Copynumber: 2.9 Consensus size: 21
1882031 ACCCCGTGGA
1882041 GGGTATCGGTACCCTCCTGGG
1 GGGTATCGGTACCCTCCTGGG
* **
1882062 GGGTATCGGTACCCACTCAAGG
1 GGGTATCGGTACCCTC-CTGGG
*
1882084 GGGTATCGATA-CCTCCTG
1 GGGTATCGGTACCCTCCTG
1882102 CTCCCAAAAT
Statistics
Matches: 32, Mismatches: 7, Indels: 3
0.76 0.17 0.07
Matches are distributed among these distances:
20 1 0.03
21 18 0.56
22 13 0.41
ACGTcount: A:0.16, C:0.28, G:0.33, T:0.23
Consensus pattern (21 bp):
GGGTATCGGTACCCTCCTGGG
Found at i:1887975 original size:76 final size:76
Alignment explanation
Indices: 1887851--1888042 Score: 300
Period size: 76 Copynumber: 2.5 Consensus size: 76
1887841 CCGTTATAAG
* *
1887851 ATGGGGGTATCA-GTA-CCTCCT-GGGGGTATCGGTACCCTCTGAGCAATCTGTTATTTCTCGGA
1 ATGGGGGTAT-AGGTACCCTCTTGGGGGGTATCGGTACCCTCCGAGCAATCTGTTATTTCTCGGA
*
1887913 GCCAAATCTTAT
65 GCCAAATCTTAC
1887925 ATGGGGGTATAGGTACCCTCTTGGGGGGTATCGGTACCCTCCGAGCAATCTGTTATTTCTCGGAG
1 ATGGGGGTATAGGTACCCTCTTGGGGGGTATCGGTACCCTCCGAGCAATCTGTTATTTCTCGGAG
1887990 CCAAATCTTAC
66 CCAAATCTTAC
* *
1888001 ATGGGGATATCGGTACCCTCTTGGGGGGGTATCGGTACCCTC
1 ATGGGGGTATAGGTACCCTCTT-GGGGGGTATCGGTACCCTC
1888043 TGGGCAATAT
Statistics
Matches: 109, Mismatches: 5, Indels: 5
0.92 0.04 0.04
Matches are distributed among these distances:
73 1 0.01
74 13 0.12
75 5 0.05
76 71 0.65
77 19 0.17
ACGTcount: A:0.19, C:0.23, G:0.29, T:0.29
Consensus pattern (76 bp):
ATGGGGGTATAGGTACCCTCTTGGGGGGTATCGGTACCCTCCGAGCAATCTGTTATTTCTCGGAG
CCAAATCTTAC
Found at i:1895804 original size:20 final size:20
Alignment explanation
Indices: 1895779--1895817 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
1895769 GTATATTGGG
*
1895779 CTATTGTCTATTGTTTATGC
1 CTATTGTCTATTGTATATGC
1895799 CTATTGTCTATTGTATATG
1 CTATTGTCTATTGTATATG
1895818 GTTATGGAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.18, C:0.13, G:0.15, T:0.54
Consensus pattern (20 bp):
CTATTGTCTATTGTATATGC
Found at i:1895910 original size:44 final size:44
Alignment explanation
Indices: 1895819--1895941 Score: 185
Period size: 44 Copynumber: 2.8 Consensus size: 44
1895809 TTGTATATGG
* *
1895819 TTATGGA-ATAATGGAAAGTGTATTGGTAAAAATAAGCTTACGAGC
1 TTATGGATA-AATGGTAAGTATATTGGT-AAAATAAGCTTACGAGC
1895864 TTATGGATAAATGGTAAGTATATTGGTAAAATAAGCTTACGAGC
1 TTATGGATAAATGGTAAGTATATTGGTAAAATAAGCTTACGAGC
**
1895908 TTATAAATAAATGGTAAGTATATTGGTAAAATAA
1 TTATGGATAAATGGTAAGTATATTGGTAAAATAA
1895942 ATAAATGGTA
Statistics
Matches: 73, Mismatches: 4, Indels: 3
0.91 0.05 0.04
Matches are distributed among these distances:
44 49 0.67
45 23 0.32
46 1 0.01
ACGTcount: A:0.42, C:0.05, G:0.21, T:0.32
Consensus pattern (44 bp):
TTATGGATAAATGGTAAGTATATTGGTAAAATAAGCTTACGAGC
Found at i:1895941 original size:28 final size:28
Alignment explanation
Indices: 1895910--1895969 Score: 120
Period size: 28 Copynumber: 2.1 Consensus size: 28
1895900 TTACGAGCTT
1895910 ATAAATAAATGGTAAGTATATTGGTAAA
1 ATAAATAAATGGTAAGTATATTGGTAAA
1895938 ATAAATAAATGGTAAGTATATTGGTAAA
1 ATAAATAAATGGTAAGTATATTGGTAAA
1895966 ATAA
1 ATAA
1895970 GCTTACGAGC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 32 1.00
ACGTcount: A:0.52, C:0.00, G:0.17, T:0.32
Consensus pattern (28 bp):
ATAAATAAATGGTAAGTATATTGGTAAA
Found at i:1895952 original size:72 final size:72
Alignment explanation
Indices: 1895870--1896013 Score: 261
Period size: 72 Copynumber: 2.0 Consensus size: 72
1895860 GAGCTTATGG
*
1895870 ATAAATGGTAAGTATATTGGTAAAATAAGCTTACGAGCTTATAAATAAATGGTAAGTATATTGGT
1 ATAAATGGTAAGTATATTGGTAAAATAAGCTTACGAGCTTATAAATAAATGGTAAGTATAATGGT
1895935 AAAATAA
66 AAAATAA
**
1895942 ATAAATGGTAAGTATATTGGTAAAATAAGCTTACGAGCTTATGGATAAATGGTAAGTATAATGGT
1 ATAAATGGTAAGTATATTGGTAAAATAAGCTTACGAGCTTATAAATAAATGGTAAGTATAATGGT
1896007 AAAATAA
66 AAAATAA
1896014 GCTTACGAGC
Statistics
Matches: 69, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
72 69 1.00
ACGTcount: A:0.45, C:0.04, G:0.19, T:0.31
Consensus pattern (72 bp):
ATAAATGGTAAGTATATTGGTAAAATAAGCTTACGAGCTTATAAATAAATGGTAAGTATAATGGT
AAAATAA
Found at i:1895973 original size:116 final size:117
Alignment explanation
Indices: 1895828--1896057 Score: 408
Period size: 116 Copynumber: 2.0 Consensus size: 117
1895818 GTTATGGAAT
* *
1895828 AATGGAAAGTGTATTGGTAAAAATAAGCTTACGAGCTTATGGATAAATGGTAAGTATATTGGTAA
1 AATGGAAAGTATATTGGTAAAAATAAGCTTACGAGCTTATGGATAAATGGTAAGTATAATGGTAA
1895893 AATAAGCTTACGAGCTTATAAATAAATGGTAAGTATATTGGTAAAATAAATA
66 AATAAGCTTACGAGCTTATAAATAAATGGTAAGTATATTGGTAAAATAAATA
*
1895945 AATGGTAAGTATATTGGT-AAAATAAGCTTACGAGCTTATGGATAAATGGTAAGTATAATGGTAA
1 AATGGAAAGTATATTGGTAAAAATAAGCTTACGAGCTTATGGATAAATGGTAAGTATAATGGTAA
**
1896009 AATAAGCTTACGAGCTTATGGATAAATGGTAAGTATATTGGTAAAATAA
66 AATAAGCTTACGAGCTTATAAATAAATGGTAAGTATATTGGTAAAATAA
1896058 GCTTACGAGC
Statistics
Matches: 108, Mismatches: 5, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
116 92 0.85
117 16 0.15
ACGTcount: A:0.43, C:0.05, G:0.21, T:0.31
Consensus pattern (117 bp):
AATGGAAAGTATATTGGTAAAAATAAGCTTACGAGCTTATGGATAAATGGTAAGTATAATGGTAA
AATAAGCTTACGAGCTTATAAATAAATGGTAAGTATATTGGTAAAATAAATA
Found at i:1895991 original size:24 final size:24
Alignment explanation
Indices: 1895964--1896035 Score: 59
Period size: 24 Copynumber: 3.2 Consensus size: 24
1895954 TATATTGGTA
1895964 AAATAAGCTTACGAGCTTATGGAT
1 AAATAAGCTTACGAGCTTATGGAT
*
1895988 AAAT--G-GTA--AG-TATAATGG-T
1 AAATAAGCTTACGAGCT-T-ATGGAT
1896007 AAAATAAGCTTACGAGCTTATGGAT
1 -AAATAAGCTTACGAGCTTATGGAT
1896032 AAAT
1 AAAT
1896036 GGTAAGTATA
Statistics
Matches: 36, Mismatches: 2, Indels: 20
0.62 0.03 0.34
Matches are distributed among these distances:
18 1 0.03
19 4 0.11
20 8 0.22
21 2 0.06
22 2 0.06
23 2 0.06
24 12 0.33
25 4 0.11
26 1 0.03
ACGTcount: A:0.42, C:0.08, G:0.21, T:0.29
Consensus pattern (24 bp):
AAATAAGCTTACGAGCTTATGGAT
Found at i:1895993 original size:44 final size:44
Alignment explanation
Indices: 1895942--1896086 Score: 263
Period size: 44 Copynumber: 3.2 Consensus size: 44
1895932 GGTAAAATAA
1895942 ATAAATGGTAAGTATATTGGTAAAATAAGCTTACGAGCTTATGG
1 ATAAATGGTAAGTATATTGGTAAAATAAGCTTACGAGCTTATGG
*
1895986 ATAAATGGTAAGTATAATGGTAAAATAAGCTTACGAGCTTATGG
1 ATAAATGGTAAGTATATTGGTAAAATAAGCTTACGAGCTTATGG
1896030 ATAAATGGTAAGTATATTGGTAAAATAAGCTTACGAGCTTATGG
1 ATAAATGGTAAGTATATTGGTAAAATAAGCTTACGAGCTTATGG
1896074 TATTAAATGGTAA
1 -A-TAAATGGTAA
1896087 ATATTGCACA
Statistics
Matches: 97, Mismatches: 2, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
44 86 0.89
45 1 0.01
46 10 0.10
ACGTcount: A:0.40, C:0.06, G:0.22, T:0.32
Consensus pattern (44 bp):
ATAAATGGTAAGTATATTGGTAAAATAAGCTTACGAGCTTATGG
Found at i:1896074 original size:24 final size:24
Alignment explanation
Indices: 1896002--1896075 Score: 61
Period size: 24 Copynumber: 3.2 Consensus size: 24
1895992 GGTAAGTATA
1896002 ATGGTAAAATAAGCTTACGAGCTT
1 ATGGTAAAATAAGCTTACGAGCTT
* **
1896026 ATGG-ATAAAT--G-GTA--AGTAT
1 ATGGTA-AAATAAGCTTACGAGCTT
1896045 ATTGGTAAAATAAGCTTACGAGCTT
1 A-TGGTAAAATAAGCTTACGAGCTT
1896070 ATGGTA
1 ATGGTA
1896076 TTAAATGGTA
Statistics
Matches: 36, Mismatches: 6, Indels: 16
0.62 0.10 0.28
Matches are distributed among these distances:
19 4 0.11
20 7 0.19
21 3 0.08
22 2 0.06
23 3 0.08
24 13 0.36
25 4 0.11
ACGTcount: A:0.38, C:0.08, G:0.23, T:0.31
Consensus pattern (24 bp):
ATGGTAAAATAAGCTTACGAGCTT
Found at i:1899687 original size:22 final size:22
Alignment explanation
Indices: 1899657--1899704 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 22
1899647 CTATGGCGAC
*
1899657 ATCCGTCCCCATATCCAACAAA
1 ATCCATCCCCATATCCAACAAA
* * *
1899679 ATCCATCCCCATCTCCGACGAA
1 ATCCATCCCCATATCCAACAAA
1899701 ATCC
1 ATCC
1899705 GTCTATCTCC
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.31, C:0.44, G:0.06, T:0.19
Consensus pattern (22 bp):
ATCCATCCCCATATCCAACAAA
Found at i:1900144 original size:19 final size:20
Alignment explanation
Indices: 1900097--1900199 Score: 58
Period size: 20 Copynumber: 5.5 Consensus size: 20
1900087 GTCAAATTCA
*
1900097 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATTGTCATTTTCG
* * *
1900117 TGTTACGATTTTCA-TTTCG
1 CGTTGCGATTGTCATTTTCG
*
1900136 CGTTGCGA-T-T-A---TCT
1 CGTTGCGATTGTCATTTTCG
* **
1900150 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATTGTCATTTTCG
*
1900170 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATTGTCATTTTCG
**
1900190 TATTGCGATT
1 CGTTGCGATT
1900200 TTAAGTTTCA
Statistics
Matches: 63, Mismatches: 14, Indels: 12
0.71 0.16 0.13
Matches are distributed among these distances:
14 10 0.16
16 2 0.03
17 2 0.03
18 1 0.02
19 11 0.17
20 37 0.59
ACGTcount: A:0.17, C:0.18, G:0.22, T:0.42
Consensus pattern (20 bp):
CGTTGCGATTGTCATTTTCG
Found at i:1900189 original size:20 final size:19
Alignment explanation
Indices: 1900082--1900186 Score: 76
Period size: 20 Copynumber: 5.6 Consensus size: 19
1900072 AAAATCGCAA
* *
1900082 CGATAGTCAAATTCACGTTG
1 CGATAGTC-ATTTCGCGTTG
* *
1900102 CGATAGTCATTTTCGTGTTA
1 CGATAGTCA-TTTCGCGTTG
**
1900122 CGATTTTCATTTCGCGTTG
1 CGATAGTCATTTCGCGTTG
*
1900141 CGAT--T-A--TCTCGTTG
1 CGATAGTCATTTCGCGTTG
*
1900155 CGATAGTCAAATTCGCGTTG
1 CGATAGTC-ATTTCGCGTTG
1900175 CGATAGTCATTT
1 CGATAGTCATTT
1900187 TCGTATTGCG
Statistics
Matches: 67, Mismatches: 11, Indels: 15
0.72 0.12 0.16
Matches are distributed among these distances:
14 11 0.16
16 2 0.03
17 1 0.01
18 1 0.01
19 16 0.24
20 36 0.54
ACGTcount: A:0.21, C:0.19, G:0.21, T:0.39
Consensus pattern (19 bp):
CGATAGTCATTTCGCGTTG
Found at i:1900220 original size:73 final size:73
Alignment explanation
Indices: 1900082--1900220 Score: 181
Period size: 73 Copynumber: 1.9 Consensus size: 73
1900072 AAAATCGCAA
* * * ***
1900082 CGATAGTCAAATTCACGTTGCGATAGTCATTTTCGTGTTACGATTTTCATTTCGCGTTGCGATTA
1 CGATAGTCAAATTCACGTTGCGATAGTCATTTTCGTATTACGATTTTAATTTCGAGAAACGATTA
1900147 TCTCGTTG
66 TCTCGTTG
* * *
1900155 CGATAGTCAAATTCGCGTTGCGATAGTCATTTTCGTATTGCGATTTTAAGTTTC-AGAAACTATT
1 CGATAGTCAAATTCACGTTGCGATAGTCATTTTCGTATTACGATTTTAA-TTTCGAGAAACGATT
1900219 AT
65 AT
1900221 TCTTCTGCAA
Statistics
Matches: 56, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
73 52 0.93
74 4 0.07
ACGTcount: A:0.23, C:0.17, G:0.19, T:0.40
Consensus pattern (73 bp):
CGATAGTCAAATTCACGTTGCGATAGTCATTTTCGTATTACGATTTTAATTTCGAGAAACGATTA
TCTCGTTG
Found at i:1902124 original size:20 final size:20
Alignment explanation
Indices: 1902099--1902148 Score: 82
Period size: 20 Copynumber: 2.5 Consensus size: 20
1902089 CGAAACTTAA
1902099 ATCGCAACGCGAAAATGACT
1 ATCGCAACGCGAAAATGACT
* *
1902119 ATCGCAACACGGAAATGACT
1 ATCGCAACGCGAAAATGACT
1902139 ATCGCAACGC
1 ATCGCAACGC
1902149 AAATTTAGTT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.38, C:0.28, G:0.20, T:0.14
Consensus pattern (20 bp):
ATCGCAACGCGAAAATGACT
Found at i:1902178 original size:19 final size:19
Alignment explanation
Indices: 1902156--1902192 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
1902146 CGCAAATTTA
1902156 GTTTCGCGTTGCGATTTTG
1 GTTTCGCGTTGCGATTTTG
*
1902175 GTTTTGCGTTGCGATTTT
1 GTTTCGCGTTGCGATTTT
1902193 AAGTTTCATA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.05, C:0.14, G:0.30, T:0.51
Consensus pattern (19 bp):
GTTTCGCGTTGCGATTTTG
Found at i:1904214 original size:14 final size:14
Alignment explanation
Indices: 1904177--1904238 Score: 52
Period size: 14 Copynumber: 4.3 Consensus size: 14
1904167 TTACTTGTTT
* *
1904177 AATTAATTTATAAA
1 AATTGATTTGTAAA
1904191 AATTGATTTGTAAA
1 AATTGATTTGTAAA
* *
1904205 AGTTGATTTGTTTAA
1 AATTGATTTG-TAAA
* *
1904220 TATTGATGTGTAAA
1 AATTGATTTGTAAA
1904234 TAATT
1 -AATT
1904239 CTTATTTGTG
Statistics
Matches: 37, Mismatches: 9, Indels: 3
0.76 0.18 0.06
Matches are distributed among these distances:
14 24 0.65
15 13 0.35
ACGTcount: A:0.40, C:0.00, G:0.13, T:0.47
Consensus pattern (14 bp):
AATTGATTTGTAAA
Found at i:1904362 original size:20 final size:20
Alignment explanation
Indices: 1904337--1904410 Score: 112
Period size: 20 Copynumber: 3.7 Consensus size: 20
1904327 AGGTACACTT
* **
1904337 TCGCAACGCTAAATTCAAAA
1 TCGCAACGCGAAAGCCAAAA
*
1904357 TCGCAATGCGAAAGCCAAAA
1 TCGCAACGCGAAAGCCAAAA
1904377 TCGCAACGCGAAAGCCAAAA
1 TCGCAACGCGAAAGCCAAAA
1904397 TCGCAACGCGAAAG
1 TCGCAACGCGAAAG
1904411 TCAATTCGCA
Statistics
Matches: 49, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 49 1.00
ACGTcount: A:0.43, C:0.27, G:0.19, T:0.11
Consensus pattern (20 bp):
TCGCAACGCGAAAGCCAAAA
Found at i:1904426 original size:19 final size:20
Alignment explanation
Indices: 1904404--1904446 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 20
1904394 AAATCGCAAC
*
1904404 GCGAAAGTC-AATTCGCATT
1 GCGAAAGTCTAATACGCATT
* *
1904423 GCGATAGTCTAATACGCTTT
1 GCGAAAGTCTAATACGCATT
1904443 GCGA
1 GCGA
1904447 TTTTCTCGTT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
19 8 0.40
20 12 0.60
ACGTcount: A:0.28, C:0.21, G:0.23, T:0.28
Consensus pattern (20 bp):
GCGAAAGTCTAATACGCATT
Found at i:1904478 original size:20 final size:20
Alignment explanation
Indices: 1904453--1904785 Score: 293
Period size: 20 Copynumber: 17.9 Consensus size: 20
1904443 GCGATTTTCT
* *
1904453 CGTTGCGATAGTCAAATACC
1 CGTTGCGATAGTCAAATTCG
*
1904473 CGTTGCGATAATCAAATTCG
1 CGTTGCGATAGTCAAATTCG
1904493 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCAAATTCG
*
1904513 CGTTGCGATAGTTAAATTCG
1 CGTTGCGATAGTCAAATTCG
*
1904533 CGTTGCGAT--T----TTCT
1 CGTTGCGATAGTCAAATTCG
*
1904547 CGTTGCGATAGTCAAATAAC-
1 CGTTGCGATAGTCAAAT-TCG
*
1904567 CGTTGCGATAATCAAATTCG
1 CGTTGCGATAGTCAAATTCG
*
1904587 CGTTGCGAT--T----TTCT
1 CGTTGCGATAGTCAAATTCG
* * *
1904601 CGTTGCTATAGTCAAATACC
1 CGTTGCGATAGTCAAATTCG
*
1904621 CGTTGCGATAATCAAATTCG
1 CGTTGCGATAGTCAAATTCG
*
1904641 TGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCAAATTCG
* *
1904661 CGTAGCGAT--T----TTTG
1 CGTTGCGATAGTCAAATTCG
*
1904675 CGTTGCGATAGTCATATTCG
1 CGTTGCGATAGTCAAATTCG
1904695 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCAAATTCG
*
1904715 CGTTGCGAT--T----TTTG
1 CGTTGCGATAGTCAAATTCG
* *
1904729 AGTTGCGATAATCAAATTCG
1 CGTTGCGATAGTCAAATTCG
*
1904749 CGTTGCGATAGTCAAATTTG
1 CGTTGCGATAGTCAAATTCG
*
1904769 CGTTGCGATATTCAAAT
1 CGTTGCGATAGTCAAAT
1904786 GAATGTGTAA
Statistics
Matches: 255, Mismatches: 32, Indels: 52
0.75 0.09 0.15
Matches are distributed among these distances:
14 45 0.18
16 4 0.02
18 4 0.02
19 1 0.00
20 200 0.78
21 1 0.00
ACGTcount: A:0.25, C:0.19, G:0.22, T:0.34
Consensus pattern (20 bp):
CGTTGCGATAGTCAAATTCG
Found at i:1904575 original size:54 final size:54
Alignment explanation
Indices: 1904493--1904649 Score: 244
Period size: 54 Copynumber: 2.9 Consensus size: 54
1904483 ATCAAATTCG
* * *
1904493 CGTTGCGATAGTCAAAT-TCGCGTTGCGATAGTTAAATTCGCGTTGCGATTTTCT
1 CGTTGCGATAGTCAAATAAC-CGTTGCGATAATCAAATTCGCGTTGCGATTTTCT
1904547 CGTTGCGATAGTCAAATAACCGTTGCGATAATCAAATTCGCGTTGCGATTTTCT
1 CGTTGCGATAGTCAAATAACCGTTGCGATAATCAAATTCGCGTTGCGATTTTCT
* * *
1904601 CGTTGCTATAGTCAAATACCCGTTGCGATAATCAAATTCGTGTTGCGAT
1 CGTTGCGATAGTCAAATAACCGTTGCGATAATCAAATTCGCGTTGCGAT
1904650 AGTCAAATTC
Statistics
Matches: 96, Mismatches: 6, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
54 95 0.99
55 1 0.01
ACGTcount: A:0.24, C:0.20, G:0.22, T:0.34
Consensus pattern (54 bp):
CGTTGCGATAGTCAAATAACCGTTGCGATAATCAAATTCGCGTTGCGATTTTCT
Found at i:1904625 original size:74 final size:74
Alignment explanation
Indices: 1904413--1904723 Score: 341
Period size: 74 Copynumber: 4.2 Consensus size: 74
1904403 CGCGAAAGTC
* * * *
1904413 AATTCGCATTGCGATAGTCTAATACGCTTTGCGATTTTCTCGTTGCGATAGTCAAATACCCGTTG
1 AATTCGCGTTGCGATAGTCAAATTCGCGTTGCGATTTTCTCGTTGCGATAGTCAAATACCCGTTG
1904478 CGATAATCA
66 CGATAATCA
* *
1904487 AATTCGCGTTGCGATAGTCAAATTCGCGTTGCGATAGTTAAATTCGCGTTGCGAT--T----TTC
1 AATTCGCGTTGCGATAGTCAAATTCGCGTTGCG--A-TT---TTCTCGTTGCGATAGTCAAATAC
* *
1904546 TCGTTGCGATAGTCA
60 CCGTTGCGATAATCA
* * *
1904561 AATAAC-CGTTGCGATAATCAAATTCGCGTTGCGATTTTCTCGTTGCTATAGTCAAATACCCGTT
1 AAT-TCGCGTTGCGATAGTCAAATTCGCGTTGCGATTTTCTCGTTGCGATAGTCAAATACCCGTT
1904625 GCGATAATCA
65 GCGATAATCA
* * * * *
1904635 AATTCGTGTTGCGATAGTCAAATTCGCGTAGCGATTTT-TGCGTTGCGATAGTCATATTCGCGTT
1 AATTCGCGTTGCGATAGTCAAATTCGCGTTGCGATTTTCT-CGTTGCGATAGTCAAATACCCGTT
*
1904699 GCGATAGTCA
65 GCGATAATCA
1904709 AATTCGCGTTGCGAT
1 AATTCGCGTTGCGAT
1904724 TTTTGAGTTG
Statistics
Matches: 197, Mismatches: 25, Indels: 30
0.78 0.10 0.12
Matches are distributed among these distances:
68 11 0.06
70 1 0.01
71 2 0.01
72 1 0.01
73 2 0.01
74 163 0.83
75 1 0.01
76 1 0.01
77 2 0.01
78 1 0.01
80 12 0.06
ACGTcount: A:0.24, C:0.20, G:0.22, T:0.34
Consensus pattern (74 bp):
AATTCGCGTTGCGATAGTCAAATTCGCGTTGCGATTTTCTCGTTGCGATAGTCAAATACCCGTTG
CGATAATCA
Found at i:1904679 original size:54 final size:54
Alignment explanation
Indices: 1904621--1904777 Score: 260
Period size: 54 Copynumber: 2.9 Consensus size: 54
1904611 GTCAAATACC
* *
1904621 CGTTGCGATAATCAAATTCGTGTTGCGATAGTCAAATTCGCGTAGCGATTTTTG
1 CGTTGCGATAATCAAATTCGCGTTGCGATAGTCAAATTCGCGTTGCGATTTTTG
* *
1904675 CGTTGCGATAGTCATATTCGCGTTGCGATAGTCAAATTCGCGTTGCGATTTTTG
1 CGTTGCGATAATCAAATTCGCGTTGCGATAGTCAAATTCGCGTTGCGATTTTTG
* *
1904729 AGTTGCGATAATCAAATTCGCGTTGCGATAGTCAAATTTGCGTTGCGAT
1 CGTTGCGATAATCAAATTCGCGTTGCGATAGTCAAATTCGCGTTGCGAT
1904778 ATTCAAATGA
Statistics
Matches: 95, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
54 95 1.00
ACGTcount: A:0.23, C:0.17, G:0.25, T:0.35
Consensus pattern (54 bp):
CGTTGCGATAATCAAATTCGCGTTGCGATAGTCAAATTCGCGTTGCGATTTTTG
Found at i:1904966 original size:18 final size:18
Alignment explanation
Indices: 1904940--1904980 Score: 64
Period size: 18 Copynumber: 2.3 Consensus size: 18
1904930 AGGTGAAGCC
*
1904940 GATTGTGATTGGGATTTT
1 GATTGTGATTGCGATTTT
*
1904958 GATTTTGATTGCGATTTT
1 GATTGTGATTGCGATTTT
1904976 GATTG
1 GATTG
1904981 CCTTTTTCTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.17, C:0.02, G:0.29, T:0.51
Consensus pattern (18 bp):
GATTGTGATTGCGATTTT
Found at i:1907034 original size:14 final size:14
Alignment explanation
Indices: 1907015--1907051 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
1907005 TCCCGTAGCA
1907015 TTTTCTTCGGGGAC
1 TTTTCTTCGGGGAC
*
1907029 TTTTCTTCGGGGAT
1 TTTTCTTCGGGGAC
1907043 TTCTTCTTC
1 TT-TTCTTC
1907052 TTCTTTTTAT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
14 15 0.71
15 6 0.29
ACGTcount: A:0.05, C:0.22, G:0.22, T:0.51
Consensus pattern (14 bp):
TTTTCTTCGGGGAC
Found at i:1907272 original size:24 final size:24
Alignment explanation
Indices: 1907238--1907290 Score: 88
Period size: 24 Copynumber: 2.2 Consensus size: 24
1907228 CTGAGACATC
1907238 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
* *
1907262 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
1907286 ATCAA
1 ATCAA
1907291 GTTTCGAATA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.40, C:0.21, G:0.19, T:0.21
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:1908137 original size:20 final size:20
Alignment explanation
Indices: 1908112--1908320 Score: 131
Period size: 20 Copynumber: 10.2 Consensus size: 20
1908102 GAAATTCAGT
*
1908112 GTTGCGACAGTCAGAATCGC
1 GTTGCGATAGTCAGAATCGC
**
1908132 GTTGCGATTATGT-ATTATCGC
1 GTTGCGA-TA-GTCAGAATCGC
1908153 GTTGCGATAGTCAGAATCGC
1 GTTGCGATAGTCAGAATCGC
**
1908173 GTTGCGATTATGT-ATTATCGC
1 GTTGCGA-TA-GTCAGAATCGC
*
1908194 GTTGCGATAGTCAGAATCAC
1 GTTGCGATAGTCAGAATCGC
* ** *
1908214 ATTGCGATTATGT-ATTATTGC
1 GTTGCGA-TA-GTCAGAATCGC
* **
1908235 GTTGTGATTATGT-ATTATCGC
1 GTTGCGA-TA-GTCAGAATCGC
*
1908256 GTTGTGATAGTCAGAATCGC
1 GTTGCGATAGTCAGAATCGC
* * *
1908276 GTTGCGAT-TTACATATTCGC
1 GTTGCGATAGT-CAGAATCGC
* *
1908296 ATTGCGATAGTCAAAATCGC
1 GTTGCGATAGTCAGAATCGC
1908316 GTTGC
1 GTTGC
1908321 AAATCTGGAA
Statistics
Matches: 149, Mismatches: 29, Indels: 22
0.75 0.14 0.11
Matches are distributed among these distances:
19 7 0.05
20 75 0.50
21 61 0.41
22 6 0.04
ACGTcount: A:0.23, C:0.17, G:0.25, T:0.35
Consensus pattern (20 bp):
GTTGCGATAGTCAGAATCGC
Found at i:1908169 original size:41 final size:41
Alignment explanation
Indices: 1908112--1908238 Score: 218
Period size: 41 Copynumber: 3.1 Consensus size: 41
1908102 GAAATTCAGT
*
1908112 GTTGCGACAGTCAGAATCGCGTTGCGATTATGTATTATCGC
1 GTTGCGATAGTCAGAATCGCGTTGCGATTATGTATTATCGC
1908153 GTTGCGATAGTCAGAATCGCGTTGCGATTATGTATTATCGC
1 GTTGCGATAGTCAGAATCGCGTTGCGATTATGTATTATCGC
* * *
1908194 GTTGCGATAGTCAGAATCACATTGCGATTATGTATTATTGC
1 GTTGCGATAGTCAGAATCGCGTTGCGATTATGTATTATCGC
1908235 GTTG
1 GTTG
1908239 TGATTATGTA
Statistics
Matches: 82, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 82 1.00
ACGTcount: A:0.23, C:0.17, G:0.26, T:0.35
Consensus pattern (41 bp):
GTTGCGATAGTCAGAATCGCGTTGCGATTATGTATTATCGC
Found at i:1908275 original size:82 final size:82
Alignment explanation
Indices: 1908112--1908283 Score: 206
Period size: 82 Copynumber: 2.1 Consensus size: 82
1908102 GAAATTCAGT
* * *
1908112 GTTGCGACAGTCAGAATCGCGTTGCGATTATGTATTATCGCGTTGCGATAGTCAGAATCGCGTTG
1 GTTGCGATAGTCAGAATCACATTGCGATTATGTATTATCGCGTTGCGATAGTCAGAATCGCGTTG
**
1908177 CGATTATGTATTATCGC
66 CGATTATGTAGAATCGC
* * **
1908194 GTTGCGATAGTCAGAATCACATTGCGATTATGTATTATTGCGTTGTGATTATGT-ATTATCGCGT
1 GTTGCGATAGTCAGAATCACATTGCGATTATGTATTATCGCGTTGCGA-TA-GTCAGAATCGCGT
*
1908258 TGTGA-TA-GTCAGAATCGC
64 TGCGATTATGT-AGAATCGC
1908276 GTTGCGAT
1 GTTGCGAT
1908284 TTACATATTC
Statistics
Matches: 77, Mismatches: 10, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
81 2 0.03
82 59 0.77
83 14 0.18
84 2 0.03
ACGTcount: A:0.23, C:0.16, G:0.26, T:0.35
Consensus pattern (82 bp):
GTTGCGATAGTCAGAATCACATTGCGATTATGTATTATCGCGTTGCGATAGTCAGAATCGCGTTG
CGATTATGTAGAATCGC
Found at i:1908372 original size:19 final size:19
Alignment explanation
Indices: 1908348--1908384 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
1908338 TGCCATACTG
* *
1908348 GAGATCGCGTTGCGATTTA
1 GAGATCGCATTACGATTTA
1908367 GAGATCGCATTACGATTT
1 GAGATCGCATTACGATTT
1908385 TGTTGGTCAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.24, C:0.16, G:0.27, T:0.32
Consensus pattern (19 bp):
GAGATCGCATTACGATTTA
Found at i:1911622 original size:60 final size:60
Alignment explanation
Indices: 1911558--1911694 Score: 181
Period size: 60 Copynumber: 2.3 Consensus size: 60
1911548 ATAGTCGAGT
*
1911558 GACCATTTTGTAACTTTTAATAGTTAGGTGAT-TCAACAAAACTAT-ATCCTATAGTTGGGG
1 GACCATTTTGTAACTTTTAATAG-TAGATGATCTCAAC-AAACTATCATCCTATAGTTGGGG
* * * *
1911618 GACCATTTTGTAACTTATAATAGTCGATGGTCTCAACAAAGTATCATCCTATAGTTGGGG
1 GACCATTTTGTAACTTTTAATAGTAGATGATCTCAACAAACTATCATCCTATAGTTGGGG
1911678 GACCATTTTTGT-ACTTT
1 GACCA-TTTTGTAACTTT
1911695 ACCCATTATT
Statistics
Matches: 68, Mismatches: 6, Indels: 6
0.85 0.08 0.08
Matches are distributed among these distances:
59 11 0.16
60 51 0.75
61 6 0.09
ACGTcount: A:0.29, C:0.15, G:0.18, T:0.37
Consensus pattern (60 bp):
GACCATTTTGTAACTTTTAATAGTAGATGATCTCAACAAACTATCATCCTATAGTTGGGG
Found at i:1913322 original size:29 final size:29
Alignment explanation
Indices: 1913280--1913345 Score: 105
Period size: 29 Copynumber: 2.3 Consensus size: 29
1913270 AATGTATGTA
* *
1913280 TGATTCTGCATGGGATTATATCCCCGTCC
1 TGATTCTACATGGGATTAAATCCCCGTCC
1913309 TGATTCTACATGGGATTAAATCCCCGTCC
1 TGATTCTACATGGGATTAAATCCCCGTCC
*
1913338 TGTTTCTA
1 TGATTCTA
1913346 TTTTGTGATC
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
29 34 1.00
ACGTcount: A:0.20, C:0.26, G:0.18, T:0.36
Consensus pattern (29 bp):
TGATTCTACATGGGATTAAATCCCCGTCC
Found at i:1915825 original size:18 final size:18
Alignment explanation
Indices: 1915781--1915826 Score: 53
Period size: 17 Copynumber: 2.7 Consensus size: 18
1915771 ATTTAACCCA
*
1915781 ACCCA-TTGACAGAACCG
1 ACCCAGTTGACCGAACCG
1915798 ACCC-GTTGACCGAACC-
1 ACCCAGTTGACCGAACCG
1915814 AGCCCAGTTGACC
1 A-CCCAGTTGACC
1915827 ATTGAGTTTG
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
16 1 0.04
17 17 0.68
18 7 0.28
ACGTcount: A:0.28, C:0.39, G:0.20, T:0.13
Consensus pattern (18 bp):
ACCCAGTTGACCGAACCG
Found at i:1916465 original size:29 final size:29
Alignment explanation
Indices: 1916432--1916494 Score: 90
Period size: 29 Copynumber: 2.2 Consensus size: 29
1916422 TGCATACATG
*
1916432 ATTCTGCATAGGATTATATCCCCATCCTA
1 ATTCTGCATAGGATTAAATCCCCATCCTA
* *
1916461 ATTCTGCATGGGATTAAATCCCCGTCCTA
1 ATTCTGCATAGGATTAAATCCCCATCCTA
*
1916490 TTTCT
1 ATTCT
1916495 ATTTTGGGAT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.24, C:0.27, G:0.13, T:0.37
Consensus pattern (29 bp):
ATTCTGCATAGGATTAAATCCCCATCCTA
Found at i:1919563 original size:124 final size:125
Alignment explanation
Indices: 1919427--1919662 Score: 411
Period size: 124 Copynumber: 1.9 Consensus size: 125
1919417 ATTATTACTT
* *
1919427 TTTATTTTATTTTCATTTTAGTCATATGAATATATATATATATATAATTAAAATATTTATTTATT
1 TTTATTTTATTTTCAATTTAGTCATATGAACATATATATATATATAATTAAAATATTTATTTATT
*
1919492 AAAGAAAGAACTATCTTAAAGTAACTAGATGTCCTATTCTGATATTTATTAATTACAATA
66 AAAGAAAGAACTATCTTAAAGTAACTAGATGTCCTATTCTAATATTTATTAATTACAATA
*
1919552 TTTA-TTTATTTTCAATTTCGTCATATGAACATATATATATATATAATTAAAATATTTATTTATT
1 TTTATTTTATTTTCAATTTAGTCATATGAACATATATATATATATAATTAAAATATTTATTTATT
* *
1919616 AAAGAAAGCACTATCTTAAAGTAACTAGATGTCCTATTTTAATATTT
66 AAAGAAAGAACTATCTTAAAGTAACTAGATGTCCTATTCTAATATTT
1919663 TAAAATAAAT
Statistics
Matches: 105, Mismatches: 6, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
124 101 0.96
125 4 0.04
ACGTcount: A:0.39, C:0.08, G:0.06, T:0.46
Consensus pattern (125 bp):
TTTATTTTATTTTCAATTTAGTCATATGAACATATATATATATATAATTAAAATATTTATTTATT
AAAGAAAGAACTATCTTAAAGTAACTAGATGTCCTATTCTAATATTTATTAATTACAATA
Found at i:1921100 original size:15 final size:16
Alignment explanation
Indices: 1921070--1921103 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
1921060 GTACTAACCA
*
1921070 TTTTATCTTTTCTTAT
1 TTTTATCTATTCTTAT
1921086 TTTTATCTATT-TTAT
1 TTTTATCTATTCTTAT
1921101 TTT
1 TTT
1921104 GTTATAACTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 7 0.41
16 10 0.59
ACGTcount: A:0.15, C:0.09, G:0.00, T:0.76
Consensus pattern (16 bp):
TTTTATCTATTCTTAT
Found at i:1924880 original size:89 final size:88
Alignment explanation
Indices: 1924723--1924985 Score: 292
Period size: 89 Copynumber: 3.0 Consensus size: 88
1924713 TATACTCATA
* ** *
1924723 CTATATTATTATATATACAATAAAGCTTGAGTTGTCCCCTAAAGCAATTGGTTAATCGTCCTGGC
1 CTATATTATTATATATACAATAAAACTTGAGTTGTCCCCTAAAGCAATTGGTTAATCACCCCGGC
1924788 TTTATGGATAATATTCAACTAGC
66 TTTATGGATAATATTCAACTAGC
* * *
1924811 CTATATTATTATATATACATTAAAACTTGAGTTATTCCCCTAAAGCAATTGGTTAATCACCCCGT
1 CTATATTATTATATATACAATAAAACTTGAGTT-GTCCCCTAAAGCAATTGGTTAATCACCCCGG
*
1924876 CTTTATGGATAATATTCAGCTAGC
65 CTTTATGGATAATATTCAACTAGC
* * * *
1924900 CTGT-TATACTATTATATGCAAT--AA----AGTTGTCCCTCTAGAGCAATTGGTTAAT-AGCCC
1 CTATAT-TATTA-TATATACAATAAAACTTGAGTTGTCCC-CTAAAGCAATTGGTTAATCA-CCC
*
1924957 CGACTTTATGGATAAGT-TTCAACTAGC
62 CGGCTTTATGGATAA-TATTCAACTAGC
1924984 CT
1 CT
1924986 GATTGAGGCA
Statistics
Matches: 153, Mismatches: 16, Indels: 16
0.83 0.09 0.09
Matches are distributed among these distances:
83 5 0.03
84 49 0.32
85 1 0.01
88 34 0.22
89 56 0.37
90 8 0.05
ACGTcount: A:0.31, C:0.19, G:0.14, T:0.36
Consensus pattern (88 bp):
CTATATTATTATATATACAATAAAACTTGAGTTGTCCCCTAAAGCAATTGGTTAATCACCCCGGC
TTTATGGATAATATTCAACTAGC
Found at i:1925065 original size:11 final size:11
Alignment explanation
Indices: 1925049--1925073 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
1925039 GAAGTTGTTG
1925049 TAAAGATGGAC
1 TAAAGATGGAC
1925060 TAAAGATGGAC
1 TAAAGATGGAC
1925071 TAA
1 TAA
1925074 GGGAATTAAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.48, C:0.08, G:0.24, T:0.20
Consensus pattern (11 bp):
TAAAGATGGAC
Found at i:1927138 original size:64 final size:63
Alignment explanation
Indices: 1927032--1927207 Score: 178
Period size: 64 Copynumber: 2.8 Consensus size: 63
1927022 TTGGACTCCT
* * * *
1927032 AGTGCATCGGTGCACT-AAGAGTGCACCGATGCATGAAGTGCATTCGATGTTTGAA-AAAT-AG
1 AGTGCATCGATGCA-TGGAGAGTGCATCGATGCATGAAATGCATTCGATGTTTGAATAAATCAG
* *** * *
1927093 CCTGGTGCATCGATGCATGGCTTGTGCATCGATGCATCAAATGCATTCGATGTTTTAATTAAATC
1 ---AGTGCATCGATGCATGGAGAGTGCATCGATGCATGAAATGCATTCGATGTTTGAA-TAAATC
1927158 AG
62 AG
* *
1927160 AGTGCATCGATGCATGGAGAGTGCATCGGTGCATGGAATGCATTCGAT
1 AGTGCATCGATGCATGGAGAGTGCATCGATGCATGAAATGCATTCGAT
1927208 ATTTCAATTT
Statistics
Matches: 91, Mismatches: 17, Indels: 8
0.78 0.15 0.07
Matches are distributed among these distances:
63 1 0.01
64 84 0.92
66 4 0.04
67 2 0.02
ACGTcount: A:0.27, C:0.18, G:0.27, T:0.28
Consensus pattern (63 bp):
AGTGCATCGATGCATGGAGAGTGCATCGATGCATGAAATGCATTCGATGTTTGAATAAATCAG
Found at i:1927182 original size:19 final size:19
Alignment explanation
Indices: 1927158--1927196 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
1927148 TAATTAAATC
1927158 AGAGTGCATCGATGCATGG
1 AGAGTGCATCGATGCATGG
*
1927177 AGAGTGCATCGGTGCATGG
1 AGAGTGCATCGATGCATGG
1927196 A
1 A
1927197 ATGCATTCGA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.26, C:0.15, G:0.38, T:0.21
Consensus pattern (19 bp):
AGAGTGCATCGATGCATGG
Found at i:1934269 original size:41 final size:43
Alignment explanation
Indices: 1934188--1934280 Score: 104
Period size: 41 Copynumber: 2.2 Consensus size: 43
1934178 TCAGGTCAGT
* * * *
1934188 CTTTCGAGCATGATGCTTAAATCCTTCGGGTCATCTGTAAG-C
1 CTTTCGAGCAAGATGCATAAATCCTTCGGCTCATCCGTAAGAC
*
1934230 CTTTCGAGCAAGATG-ATAAGTCCTTCAGGCT-ATCCGTAAGAC
1 CTTTCGAGCAAGATGCATAAATCCTTC-GGCTCATCCGTAAGAC
1934272 C-TTCGAGCA
1 CTTTCGAGCA
1934281 GAATGTTTTC
Statistics
Matches: 44, Mismatches: 5, Indels: 5
0.81 0.09 0.09
Matches are distributed among these distances:
41 25 0.57
42 19 0.43
ACGTcount: A:0.25, C:0.25, G:0.22, T:0.29
Consensus pattern (43 bp):
CTTTCGAGCAAGATGCATAAATCCTTCGGCTCATCCGTAAGAC
Found at i:1934537 original size:138 final size:138
Alignment explanation
Indices: 1934289--1934789 Score: 681
Period size: 138 Copynumber: 3.6 Consensus size: 138
1934279 CAGAATGTTT
* * * *
1934289 TCAACATTTCCAGAAGAAGTTCATAATAAGAAGAACTTATCTGAAGAGGAAGAAGAAATTCATAA
1 TCAACATTTCCAGAAGAAGTTCATAATGAGAAGAACTTATCTAAAGAAGAAGAAGAAGTTCATAA
* * *
1934354 TGAGAAGAACTTTTTCAACCTTAG-CTCGATTCATCACATATGGAGTTGAATCAACAACACCTTA
66 TGAGAAGAACTTGTTCAACCTT-GCCTTGATTCATCGCATATGGAGTTGAATCAACAACACCTTA
1934418 CTTGAGGCA
130 CTTGAGGCA
* *
1934427 TCAACATTTCCAGAAGAAGTTCATAATGAGAAGAACTTATCTGAAGAAGAAGAACAAGTTCATAA
1 TCAACATTTCCAGAAGAAGTTCATAATGAGAAGAACTTATCTAAAGAAGAAGAAGAAGTTCATAA
* * **
1934492 TGAGAAAAACTTGTTCAACCATGCCTTGATTCATCGCATATGGAGTTGAATCAACAACGGCTTAC
66 TGAGAAGAACTTGTTCAACCTTGCCTTGATTCATCGCATATGGAGTTGAATCAACAACACCTTAC
1934557 TTGAGGCA
131 TTGAGGCA
* * * *
1934565 TCAATATTTCCGGAAGAAGTTCATAATGAGAAGAATTTATCTAAAGAGGAAGAAGAAGTTCATAA
1 TCAACATTTCCAGAAGAAGTTCATAATGAGAAGAACTTATCTAAAGAAGAAGAAGAAGTTCATAA
* * *
1934630 TGAGAAGAACTTGTTCAACCTTGCCTTGATTCATCGTATATGGAGTTGAATCAACGACACCTCAC
66 TGAGAAGAACTTGTTCAACCTTGCCTTGATTCATCGCATATGGAGTTGAATCAACAACACCTTAC
* *
1934695 TTAAGACA
131 TTGAGGCA
* *
1934703 TCAACA-TTCAATGGAAG-AGTTCATAATGAGAAAAACTCGTA-C-AAAG-AGAAAGAAGAAGTT
1 TCAACATTTCCA--GAAGAAGTTCATAATGAGAAGAACT--TATCTAAAGAAG-AAGAAGAAGTT
*
1934763 CATAATGACAAGAACTTGTTCAACCTT
61 CATAATGAGAAGAACTTGTTCAACCTT
1934790 TTGCTACATT
Statistics
Matches: 324, Mismatches: 33, Indels: 12
0.88 0.09 0.03
Matches are distributed among these distances:
137 5 0.02
138 312 0.96
139 5 0.02
140 2 0.01
ACGTcount: A:0.40, C:0.17, G:0.18, T:0.26
Consensus pattern (138 bp):
TCAACATTTCCAGAAGAAGTTCATAATGAGAAGAACTTATCTAAAGAAGAAGAAGAAGTTCATAA
TGAGAAGAACTTGTTCAACCTTGCCTTGATTCATCGCATATGGAGTTGAATCAACAACACCTTAC
TTGAGGCA
Found at i:1934599 original size:17 final size:17
Alignment explanation
Indices: 1934577--1934638 Score: 52
Period size: 17 Copynumber: 3.4 Consensus size: 17
1934567 AATATTTCCG
1934577 GAAGAAGTTCATAATGA
1 GAAGAAGTTCATAATGA
* * *
1934594 GAAGAATTTATCTAAAGAGGAA
1 GAAGAA-GT-TC-ATA-ATG-A
1934616 GAAGAAGTTCATAATGA
1 GAAGAAGTTCATAATGA
1934633 GAAGAA
1 GAAGAA
1934639 CTTGTTCAAC
Statistics
Matches: 34, Mismatches: 6, Indels: 10
0.68 0.12 0.20
Matches are distributed among these distances:
17 13 0.38
18 3 0.09
19 4 0.12
20 4 0.12
21 3 0.09
22 7 0.21
ACGTcount: A:0.50, C:0.05, G:0.24, T:0.21
Consensus pattern (17 bp):
GAAGAAGTTCATAATGA
Found at i:1934645 original size:20 final size:19
Alignment explanation
Indices: 1934583--1934646 Score: 51
Period size: 20 Copynumber: 3.3 Consensus size: 19
1934573 TCCGGAAGAA
1934583 GTTCATAATGAGAAGAATT
1 GTTCATAATGAGAAGAATT
* **
1934602 -TATC-TAAAGAGGAAGAAGAA
1 GT-TCATAATGA-GAAGAA-TT
1934622 GTTCATAATGAGAAGAACTT
1 GTTCATAATGAGAAGAA-TT
1934642 GTTCA
1 GTTCA
1934647 ACCTTGCCTT
Statistics
Matches: 33, Mismatches: 7, Indels: 9
0.67 0.14 0.18
Matches are distributed among these distances:
18 6 0.18
19 8 0.24
20 13 0.39
21 6 0.18
ACGTcount: A:0.44, C:0.08, G:0.22, T:0.27
Consensus pattern (19 bp):
GTTCATAATGAGAAGAATT
Found at i:1935913 original size:18 final size:18
Alignment explanation
Indices: 1935890--1935931 Score: 84
Period size: 18 Copynumber: 2.3 Consensus size: 18
1935880 TTTGGTGTAA
1935890 CGGTGGTCGACGGTCGGC
1 CGGTGGTCGACGGTCGGC
1935908 CGGTGGTCGACGGTCGGC
1 CGGTGGTCGACGGTCGGC
1935926 CGGTGG
1 CGGTGG
1935932 CCGGCTTTCC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.05, C:0.26, G:0.52, T:0.17
Consensus pattern (18 bp):
CGGTGGTCGACGGTCGGC
Found at i:1939103 original size:14 final size:13
Alignment explanation
Indices: 1939072--1939101 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
1939062 CAAACACTAT
1939072 AAAATATTATCCA
1 AAAATATTATCCA
*
1939085 AAAATATTTTCCA
1 AAAATATTATCCA
1939098 AAAA
1 AAAA
1939102 ATGTAATTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.57, C:0.13, G:0.00, T:0.30
Consensus pattern (13 bp):
AAAATATTATCCA
Found at i:1942706 original size:20 final size:21
Alignment explanation
Indices: 1942680--1942728 Score: 80
Period size: 21 Copynumber: 2.3 Consensus size: 21
1942670 TTATCCAGGA
*
1942680 AAAAAAACCGGTCTGGGGTTT
1 AAAAAATCCGGTCTGGGGTTT
*
1942701 AAAAAATTCGGTCTGGGGTTT
1 AAAAAATCCGGTCTGGGGTTT
1942722 AAAAAAT
1 AAAAAAT
1942729 TGGAAGACCG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.39, C:0.10, G:0.24, T:0.27
Consensus pattern (21 bp):
AAAAAATCCGGTCTGGGGTTT
Found at i:1942728 original size:21 final size:21
Alignment explanation
Indices: 1942688--1942729 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
1942678 GAAAAAAAAC
1942688 CGGTCTGGGGTTTAAAAAATT
1 CGGTCTGGGGTTTAAAAAATT
1942709 CGGTCTGGGGTTTAAAAAATT
1 CGGTCTGGGGTTTAAAAAATT
1942730 GGAAGACCGG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.29, C:0.10, G:0.29, T:0.33
Consensus pattern (21 bp):
CGGTCTGGGGTTTAAAAAATT
Found at i:1945811 original size:18 final size:18
Alignment explanation
Indices: 1945788--1945822 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
1945778 GTAGAATTTC
1945788 TCCCGAAGGACCACTATG
1 TCCCGAAGGACCACTATG
1945806 TCCCGAAGGACCACTAT
1 TCCCGAAGGACCACTAT
1945823 CACATATCAC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.29, C:0.34, G:0.20, T:0.17
Consensus pattern (18 bp):
TCCCGAAGGACCACTATG
Found at i:1955809 original size:25 final size:23
Alignment explanation
Indices: 1955770--1955824 Score: 74
Period size: 24 Copynumber: 2.3 Consensus size: 23
1955760 ATTTTGTGAC
* *
1955770 TTTTTTTGGCTTTTTTATTTTTCT
1 TTTTTTTGGCCTTTTT-CTTTTCT
1955794 TTTTTTTCGGCCTTTTTCTTTTCT
1 TTTTTTT-GGCCTTTTTCTTTTCT
1955818 TTTTTTT
1 TTTTTTT
1955825 AAAAAATAGC
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
24 20 0.71
25 8 0.29
ACGTcount: A:0.02, C:0.13, G:0.07, T:0.78
Consensus pattern (23 bp):
TTTTTTTGGCCTTTTTCTTTTCT
Found at i:1956626 original size:43 final size:47
Alignment explanation
Indices: 1956578--1956682 Score: 130
Period size: 49 Copynumber: 2.3 Consensus size: 47
1956568 ATAACTAAAG
1956578 AATAAAATAATAATAAACT-AAACA-TGTCTTAA-CT-C-TAATTCAT
1 AATAAAATAATAAT-AACTAAAACATTGTCTTAACCTACTTAATTCAT
* *
1956621 AATAAAATAATAATAACTAAAACATTGTTTTAACCTAGCCTTAATTCCT
1 AATAAAATAATAATAACTAAAACATTGTCTTAACCTA--CTTAATTCAT
1956670 AATAAAATAATAA
1 AATAAAATAATAA
1956683 ATTTGATCCT
Statistics
Matches: 53, Mismatches: 2, Indels: 8
0.84 0.03 0.13
Matches are distributed among these distances:
42 4 0.08
43 19 0.36
44 7 0.13
45 2 0.04
48 1 0.02
49 20 0.38
ACGTcount: A:0.51, C:0.13, G:0.03, T:0.32
Consensus pattern (47 bp):
AATAAAATAATAATAACTAAAACATTGTCTTAACCTACTTAATTCAT
Found at i:1957393 original size:20 final size:21
Alignment explanation
Indices: 1957355--1957395 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
1957345 CATCCTTCAG
1957355 GTATCGATACTACCCCTTACA
1 GTATCGATACTACCCCTTACA
1957376 GTATCGATACTA-CCCTTACA
1 GTATCGATACTACCCCTTACA
1957396 AAATACTCAT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 8 0.40
21 12 0.60
ACGTcount: A:0.29, C:0.32, G:0.10, T:0.29
Consensus pattern (21 bp):
GTATCGATACTACCCCTTACA
Found at i:1959532 original size:2 final size:2
Alignment explanation
Indices: 1959525--1959552 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1959515 CTTCAAATAC
1959525 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1959553 GAAACACGTC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1960316 original size:53 final size:53
Alignment explanation
Indices: 1960231--1960452 Score: 345
Period size: 53 Copynumber: 4.2 Consensus size: 53
1960221 AAGTATGTCG
* * * *
1960231 AGTGTCGAAATGGTAATTAAAAAACTCATTATGAATTCCATGGATGCTCACAT
1 AGTGTCGAAATGGTAATTCACAAACTTATTATGAATTCCATGGATGCACACAT
* *
1960284 AGTGCCGAAATGGTAATTCACAAACTTATTATGAATTTCATGGATGCACACAT
1 AGTGTCGAAATGGTAATTCACAAACTTATTATGAATTCCATGGATGCACACAT
* *
1960337 AGTGTTGAAATGGTAATTCACAAACTAATTATGAATTCCATGGATGCACACAT
1 AGTGTCGAAATGGTAATTCACAAACTTATTATGAATTCCATGGATGCACACAT
* * *
1960390 AGTGCCGAAATGGTAATTCACAAACTTATTATGAATTCCATTGATGTACACAT
1 AGTGTCGAAATGGTAATTCACAAACTTATTATGAATTCCATGGATGCACACAT
1960443 AGTGTCGAAA
1 AGTGTCGAAA
1960453 GTACATATTG
Statistics
Matches: 153, Mismatches: 16, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
53 153 1.00
ACGTcount: A:0.37, C:0.16, G:0.17, T:0.30
Consensus pattern (53 bp):
AGTGTCGAAATGGTAATTCACAAACTTATTATGAATTCCATGGATGCACACAT
Found at i:1961816 original size:19 final size:19
Alignment explanation
Indices: 1961792--1961831 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
1961782 ACACTTCTCC
1961792 CATTTATCATTTTAAAACA
1 CATTTATCATTTTAAAACA
1961811 CATTTATCATTTTAAAACA
1 CATTTATCATTTTAAAACA
1961830 CA
1 CA
1961832 CACTTACACT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.42, C:0.17, G:0.00, T:0.40
Consensus pattern (19 bp):
CATTTATCATTTTAAAACA
Found at i:1963439 original size:409 final size:409
Alignment explanation
Indices: 1962680--1963499 Score: 1640
Period size: 409 Copynumber: 2.0 Consensus size: 409
1962670 CCAGCTTTGG
1962680 AAAACAGATTACTCAAAATACAACCGTAAACAAGAGATGAACAAAGTTTTTTATTAGGAACAAGA
1 AAAACAGATTACTCAAAATACAACCGTAAACAAGAGATGAACAAAGTTTTTTATTAGGAACAAGA
1962745 TTTACGGTTTCAACAATTTCAGCAAAAATAATCTGAGGTAGGTTGATTTTAATATTGTTTTCGAA
66 TTTACGGTTTCAACAATTTCAGCAAAAATAATCTGAGGTAGGTTGATTTTAATATTGTTTTCGAA
1962810 ACAATGTAACCACCAAAGATCTAAGGCTCTAAGAGTAGAATAACGACCTCCAGATGGTCAAAACC
131 ACAATGTAACCACCAAAGATCTAAGGCTCTAAGAGTAGAATAACGACCTCCAGATGGTCAAAACC
1962875 ACCAAGAAATCATTAGATGAAGAAAACGTTCATGAAGGTCTAGGACACTTGCACTATCCCTTCTT
196 ACCAAGAAATCATTAGATGAAGAAAACGTTCATGAAGGTCTAGGACACTTGCACTATCCCTTCTT
1962940 TTATAACGAGATCCTAAAACCTGTTTTTCATTTAAAATCCCTTCATTATCTAATCCGAATGTATT
261 TTATAACGAGATCCTAAAACCTGTTTTTCATTTAAAATCCCTTCATTATCTAATCCGAATGTATT
1963005 GGCTATGTAAGCCGATTCAATATATAAGAATTGTCCTAGAAGGTAGGAACGAATTCCTATGGTTT
326 GGCTATGTAAGCCGATTCAATATATAAGAATTGTCCTAGAAGGTAGGAACGAATTCCTATGGTTT
1963070 CGGTTTCAGTTTGGTCTTT
391 CGGTTTCAGTTTGGTCTTT
1963089 AAAACAGATTACTCAAAATACAACCGTAAACAAGAGATGAACAAAGTTTTTTATTAGGAACAAGA
1 AAAACAGATTACTCAAAATACAACCGTAAACAAGAGATGAACAAAGTTTTTTATTAGGAACAAGA
1963154 TTTACGGTTTCAACAATTTCAGCAAAAATAATCTGAGGTAGGTTGATTTTAATATTGTTTTCGAA
66 TTTACGGTTTCAACAATTTCAGCAAAAATAATCTGAGGTAGGTTGATTTTAATATTGTTTTCGAA
1963219 ACAATGTAACCACCAAAGATCTAAGGCTCTAAGAGTAGAATAACGACCTCCAGATGGTCAAAACC
131 ACAATGTAACCACCAAAGATCTAAGGCTCTAAGAGTAGAATAACGACCTCCAGATGGTCAAAACC
1963284 ACCAAGAAATCATTAGATGAAGAAAACGTTCATGAAGGTCTAGGACACTTGCACTATCCCTTCTT
196 ACCAAGAAATCATTAGATGAAGAAAACGTTCATGAAGGTCTAGGACACTTGCACTATCCCTTCTT
1963349 TTATAACGAGATCCTAAAACCTGTTTTTCATTTAAAATCCCTTCATTATCTAATCCGAATGTATT
261 TTATAACGAGATCCTAAAACCTGTTTTTCATTTAAAATCCCTTCATTATCTAATCCGAATGTATT
1963414 GGCTATGTAAGCCGATTCAATATATAAGAATTGTCCTAGAAGGTAGGAACGAATTCCTATGGTTT
326 GGCTATGTAAGCCGATTCAATATATAAGAATTGTCCTAGAAGGTAGGAACGAATTCCTATGGTTT
1963479 CGGTTTCAGTTTGGTCTTT
391 CGGTTTCAGTTTGGTCTTT
1963498 AA
1 AA
1963500 CACAAACGGC
Statistics
Matches: 411, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
409 411 1.00
ACGTcount: A:0.36, C:0.17, G:0.16, T:0.30
Consensus pattern (409 bp):
AAAACAGATTACTCAAAATACAACCGTAAACAAGAGATGAACAAAGTTTTTTATTAGGAACAAGA
TTTACGGTTTCAACAATTTCAGCAAAAATAATCTGAGGTAGGTTGATTTTAATATTGTTTTCGAA
ACAATGTAACCACCAAAGATCTAAGGCTCTAAGAGTAGAATAACGACCTCCAGATGGTCAAAACC
ACCAAGAAATCATTAGATGAAGAAAACGTTCATGAAGGTCTAGGACACTTGCACTATCCCTTCTT
TTATAACGAGATCCTAAAACCTGTTTTTCATTTAAAATCCCTTCATTATCTAATCCGAATGTATT
GGCTATGTAAGCCGATTCAATATATAAGAATTGTCCTAGAAGGTAGGAACGAATTCCTATGGTTT
CGGTTTCAGTTTGGTCTTT
Found at i:1964562 original size:20 final size:21
Alignment explanation
Indices: 1964509--1964570 Score: 63
Period size: 20 Copynumber: 2.9 Consensus size: 21
1964499 TTCCCCTGTG
1964509 GGGGGGAATCGGTTCCCCTTCAAA
1 GGGGGG-ATCGGTT-CCC-TCAAA
* *
1964533 GGGGGAATCGGTTCCCTC-AT
1 GGGGGGATCGGTTCCCTCAAA
*
1964553 GGGGGGATCGATTCCCTC
1 GGGGGGATCGGTTCCCTC
1964571 TGCACCAAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
20 17 0.50
21 2 0.06
22 3 0.09
23 7 0.21
24 5 0.15
ACGTcount: A:0.16, C:0.26, G:0.35, T:0.23
Consensus pattern (21 bp):
GGGGGGATCGGTTCCCTCAAA
Found at i:1970776 original size:20 final size:21
Alignment explanation
Indices: 1970738--1970776 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 21
1970728 TCATTTTCAT
*
1970738 AAATATTATGAAAATATATCA
1 AAATATTATGAAAACATATCA
*
1970759 AAATATTGT-AAAACATAT
1 AAATATTATGAAAACATAT
1970777 TTTTATCAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 8 0.50
21 8 0.50
ACGTcount: A:0.56, C:0.05, G:0.05, T:0.33
Consensus pattern (21 bp):
AAATATTATGAAAACATATCA
Found at i:1982032 original size:29 final size:30
Alignment explanation
Indices: 1981979--1982055 Score: 86
Period size: 29 Copynumber: 2.6 Consensus size: 30
1981969 TGTAGTAAAT
* *
1981979 AGACTTAATTAA-TTTTTGGTTAGGTTTGA
1 AGACTTAATTAATTTTTTAGTAAGGTTTGA
* *
1982008 TGGCTTAATTAATTTTTTAG-AAGGTTTGA
1 AGACTTAATTAATTTTTTAGTAAGGTTTGA
*
1982037 AGACTTATTTTAATTTTTT
1 AGACTTA-ATTAATTTTTT
1982056 TAAAAATAAA
Statistics
Matches: 39, Mismatches: 7, Indels: 3
0.80 0.14 0.06
Matches are distributed among these distances:
29 23 0.59
30 16 0.41
ACGTcount: A:0.27, C:0.04, G:0.17, T:0.52
Consensus pattern (30 bp):
AGACTTAATTAATTTTTTAGTAAGGTTTGA
Found at i:1983774 original size:35 final size:35
Alignment explanation
Indices: 1983728--1983808 Score: 135
Period size: 35 Copynumber: 2.3 Consensus size: 35
1983718 ACAGTTAATC
*
1983728 GAACCAAACTATTTGAGGAAATAATTAAATGACTG
1 GAACCAAACTATTTGAGAAAATAATTAAATGACTG
* *
1983763 GAACCAAACTATTTGAGAAAATAATTAACTGATTG
1 GAACCAAACTATTTGAGAAAATAATTAAATGACTG
1983798 GAACCAAACTA
1 GAACCAAACTA
1983809 ACTTTCCTCA
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
35 43 1.00
ACGTcount: A:0.47, C:0.14, G:0.15, T:0.25
Consensus pattern (35 bp):
GAACCAAACTATTTGAGAAAATAATTAAATGACTG
Found at i:1986711 original size:6 final size:6
Alignment explanation
Indices: 1986700--1986724 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
1986690 AAATTATTAA
1986700 TAATAT TAATAT TAATAT TAATAT T
1 TAATAT TAATAT TAATAT TAATAT T
1986725 TATGTATTGA
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (6 bp):
TAATAT
Found at i:1990726 original size:94 final size:96
Alignment explanation
Indices: 1990589--1990769 Score: 260
Period size: 95 Copynumber: 1.9 Consensus size: 96
1990579 CTTATTGCTC
* *
1990589 ATTAAGCTCATTAAAATTTTTGTTCGACTTGTACTCGTT-AAAAAATTGCTCGACTCATTGCTTG
1 ATTAAGCTCATTAAAATTTTTGTTCCACTTGTACTCGTTAAAAAAATTGCTCGACACATTGCTTG
*
1990653 TTAAGT-TTGTTGCTCATTAAACACGTTGTTT
66 -TAAATCTTGTTGCTCATTAAACACGTTGTTT
* * * *
1990684 ATTAAGCTCTTTAAAA-TTTTGTTCCATTTGTGCTCGTTAAAAAAATTGCTCGACACGTTGCTTG
1 ATTAAGCTCATTAAAATTTTTGTTCCACTTGTACTCGTTAAAAAAATTGCTCGACACATTGCTTG
*
1990748 TAAATCTTGTTGTTCATTAAAC
66 TAAATCTTGTTGCTCATTAAAC
1990770 TCATTGCTTG
Statistics
Matches: 76, Mismatches: 8, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
94 23 0.30
95 53 0.70
ACGTcount: A:0.27, C:0.16, G:0.14, T:0.43
Consensus pattern (96 bp):
ATTAAGCTCATTAAAATTTTTGTTCCACTTGTACTCGTTAAAAAAATTGCTCGACACATTGCTTG
TAAATCTTGTTGCTCATTAAACACGTTGTTT
Found at i:1990786 original size:95 final size:95
Alignment explanation
Indices: 1990582--1990786 Score: 243
Period size: 95 Copynumber: 2.2 Consensus size: 95
1990572 GACTCGACTT
* * * *
1990582 ATTGCTCATTAAGCTCATTAAAATTTTTGTTCGACTTGTACTCGTTAAAAAATTGCTCGACTCAT
1 ATTGCTTATAAAGCTCATTAAAATTTTTGTTCCACTTGTACTCGTTAAAAAATTGCTCGACACAT
*
1990647 TGCTTGTTAAGTTTGTTGCTCATTAAACAC
66 TGCTTGTTAAATTTGTTGCTCATTAAACAC
* * * * * * *
1990677 GTTGTTTATTAAGCTCTTTAAAA-TTTTGTTCCATTTGTGCTCGTTAAAAAAATTGCTCGACACG
1 ATTGCTTATAAAGCTCATTAAAATTTTTGTTCCACTTGTACTCGTT-AAAAAATTGCTCGACACA
* *
1990741 TTGCTTG-TAAATCTTGTTGTTCATTAAACTC
65 TTGCTTGTTAAAT-TTGTTGCTCATTAAACAC
*
1990772 ATTGCTTGTAAAGCT
1 ATTGCTTATAAAGCT
1990787 TATAAAAAAT
Statistics
Matches: 92, Mismatches: 16, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
94 23 0.25
95 69 0.75
ACGTcount: A:0.26, C:0.17, G:0.15, T:0.42
Consensus pattern (95 bp):
ATTGCTTATAAAGCTCATTAAAATTTTTGTTCCACTTGTACTCGTTAAAAAATTGCTCGACACAT
TGCTTGTTAAATTTGTTGCTCATTAAACAC
Found at i:1991079 original size:45 final size:44
Alignment explanation
Indices: 1990995--1991080 Score: 113
Period size: 45 Copynumber: 1.9 Consensus size: 44
1990985 GTAAAATATT
*
1990995 AATTAACAATTTAGTATTTTTTATTGTTTATTAGAAAATTAATA
1 AATTAACAATTTAGTATTTTTTATTATTTATTAGAAAATTAATA
*
1991039 AATTAACAATTTA-TCATCTTTTTATTATCTT-TTAGTAAATTA
1 AATTAACAATTTAGT-AT-TTTTTATTAT-TTATTAGAAAATTA
1991081 GTAATTTTTT
Statistics
Matches: 37, Mismatches: 2, Indels: 5
0.84 0.05 0.11
Matches are distributed among these distances:
43 1 0.03
44 15 0.41
45 19 0.51
46 2 0.05
ACGTcount: A:0.38, C:0.06, G:0.05, T:0.51
Consensus pattern (44 bp):
AATTAACAATTTAGTATTTTTTATTATTTATTAGAAAATTAATA
Found at i:1993373 original size:5 final size:6
Alignment explanation
Indices: 1993356--1993380 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
1993346 TCATTTGCAA
1993356 TCTTTT TCTTTT TCTTTT TCTTTT T
1 TCTTTT TCTTTT TCTTTT TCTTTT T
1993381 AGGTACTTTC
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:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (6 bp):
TCTTTT
Found at i:1999226 original size:20 final size:21
Alignment explanation
Indices: 1999205--1999245 Score: 73
Period size: 22 Copynumber: 1.9 Consensus size: 21
1999195 TGATCGTTAC
1999205 ATATGATATTTATCATGAACA
1 ATATGATATTTATCATGAACA
1999226 TATATGATATTTATCATGAA
1 -ATATGATATTTATCATGAA
1999246 TGATATTTCA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.41, C:0.07, G:0.10, T:0.41
Consensus pattern (21 bp):
ATATGATATTTATCATGAACA
Found at i:1999452 original size:40 final size:39
Alignment explanation
Indices: 1999394--1999491 Score: 135
Period size: 40 Copynumber: 2.5 Consensus size: 39
1999384 ACATATCGAT
*
1999394 TAAGCACTTCGGTGCATATGGTGGGCACGACCTTATGTG
1 TAAGCACTTCGGTGCATATGGTGGGCACGACCTTATGAG
* *
1999433 TAATGCACTTCGGTGCATATTGTGGGCACTACCTTATGAG
1 TAA-GCACTTCGGTGCATATGGTGGGCACGACCTTATGAG
*
1999473 TAAGCA-TTACAGTGCATAT
1 TAAGCACTT-CGGTGCATAT
1999492 ATTTGACTTG
Statistics
Matches: 53, Mismatches: 4, Indels: 4
0.87 0.07 0.07
Matches are distributed among these distances:
38 2 0.04
39 15 0.28
40 36 0.68
ACGTcount: A:0.24, C:0.19, G:0.26, T:0.31
Consensus pattern (39 bp):
TAAGCACTTCGGTGCATATGGTGGGCACGACCTTATGAG
Found at i:2002025 original size:16 final size:16
Alignment explanation
Indices: 2002004--2002057 Score: 54
Period size: 16 Copynumber: 3.1 Consensus size: 16
2001994 AATGTAATTT
2002004 TTATTTTTTATTTAAA
1 TTATTTTTTATTTAAA
2002020 TTATTTTAGTTTTAATTTAAA
1 TTA--TT--TTTT-ATTTAAA
*
2002041 TTATTTTTTGTTTAAA
1 TTATTTTTTATTTAAA
2002057 T
1 T
2002058 CAACTTAGAT
Statistics
Matches: 32, Mismatches: 1, Indels: 10
0.74 0.02 0.23
Matches are distributed among these distances:
16 10 0.31
17 4 0.12
18 2 0.06
19 2 0.06
20 4 0.12
21 10 0.31
ACGTcount: A:0.30, C:0.00, G:0.04, T:0.67
Consensus pattern (16 bp):
TTATTTTTTATTTAAA
Found at i:2002055 original size:21 final size:21
Alignment explanation
Indices: 2002002--2002047 Score: 74
Period size: 21 Copynumber: 2.2 Consensus size: 21
2001992 AGAATGTAAT
* *
2002002 TTTTATTTTTTATTTAAATTA
1 TTTTAGTTTTAATTTAAATTA
2002023 TTTTAGTTTTAATTTAAATTA
1 TTTTAGTTTTAATTTAAATTA
2002044 TTTT
1 TTTT
2002048 TTGTTTAAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.28, C:0.00, G:0.02, T:0.70
Consensus pattern (21 bp):
TTTTAGTTTTAATTTAAATTA
Found at i:2002144 original size:20 final size:21
Alignment explanation
Indices: 2002119--2002164 Score: 85
Period size: 20 Copynumber: 2.2 Consensus size: 21
2002109 ATAATTTAGA
2002119 TAAATTATATTAT-TTTAGTT
1 TAAATTATATTATGTTTAGTT
2002139 TAAATTATATTATGTTTAGTT
1 TAAATTATATTATGTTTAGTT
2002160 TAAAT
1 TAAAT
2002165 GAAGTTTAGT
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
20 13 0.52
21 12 0.48
ACGTcount: A:0.37, C:0.00, G:0.07, T:0.57
Consensus pattern (21 bp):
TAAATTATATTATGTTTAGTT
Found at i:2003569 original size:23 final size:23
Alignment explanation
Indices: 2003541--2003641 Score: 78
Period size: 23 Copynumber: 4.3 Consensus size: 23
2003531 TTTGTGTTCA
***
2003541 TTCATTTAACATTTGTGAACATG
1 TTCATTTAACATTTACAAACATG
*
2003564 TTCATTTAACATTCACAAACATG
1 TTCATTTAACATTTACAAACATG
* *
2003587 TTCGTTTAA-ATGTTCACGAACATG
1 TTCATTTAACAT-TT-ACAAACATG
** * **
2003611 TTTGTTTAACGTTTGTAAACATG
1 TTCATTTAACATTTACAAACATG
2003634 TTCATTTA
1 TTCATTTA
2003642 GTGTCCGTTT
Statistics
Matches: 61, Mismatches: 14, Indels: 6
0.75 0.17 0.07
Matches are distributed among these distances:
22 2 0.03
23 40 0.66
24 18 0.30
25 1 0.02
ACGTcount: A:0.31, C:0.15, G:0.12, T:0.43
Consensus pattern (23 bp):
TTCATTTAACATTTACAAACATG
Found at i:2003608 original size:24 final size:23
Alignment explanation
Indices: 2003557--2003620 Score: 76
Period size: 24 Copynumber: 2.7 Consensus size: 23
2003547 TAACATTTGT
*
2003557 GAACATGTTCATTTAACATTCAC
1 GAACATGTTCGTTTAACATTCAC
*
2003580 AAACATGTTCGTTTAA-ATGTTCAC
1 GAACATGTTCGTTTAACA--TTCAC
*
2003604 GAACATGTTTGTTTAAC
1 GAACATGTTCGTTTAAC
2003621 GTTTGTAAAC
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
22 1 0.03
23 14 0.41
24 19 0.56
ACGTcount: A:0.33, C:0.17, G:0.12, T:0.38
Consensus pattern (23 bp):
GAACATGTTCGTTTAACATTCAC
Found at i:2005042 original size:39 final size:39
Alignment explanation
Indices: 2004983--2005061 Score: 131
Period size: 39 Copynumber: 2.0 Consensus size: 39
2004973 TACAAATGTT
2004983 ATTTTTGAGCCATTTAGTCCCCTTAAGATTAATATTTTC
1 ATTTTTGAGCCATTTAGTCCCCTTAAGATTAATATTTTC
* * *
2005022 ATTTTTGAGCCATTTTGTCCCTTTAAGATTAATCTTTTC
1 ATTTTTGAGCCATTTAGTCCCCTTAAGATTAATATTTTC
2005061 A
1 A
2005062 ATCGGTATTT
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
39 37 1.00
ACGTcount: A:0.24, C:0.18, G:0.10, T:0.48
Consensus pattern (39 bp):
ATTTTTGAGCCATTTAGTCCCCTTAAGATTAATATTTTC
Found at i:2007449 original size:17 final size:17
Alignment explanation
Indices: 2007423--2007463 Score: 73
Period size: 17 Copynumber: 2.4 Consensus size: 17
2007413 AAGCTCATAT
*
2007423 ACACTTTGTCTACAACC
1 ACACTCTGTCTACAACC
2007440 ACACTCTGTCTACAACC
1 ACACTCTGTCTACAACC
2007457 ACACTCT
1 ACACTCT
2007464 CCTAAAGCAG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.29, C:0.39, G:0.05, T:0.27
Consensus pattern (17 bp):
ACACTCTGTCTACAACC
Found at i:2011812 original size:15 final size:15
Alignment explanation
Indices: 2011778--2011833 Score: 53
Period size: 14 Copynumber: 3.6 Consensus size: 15
2011768 CATTTTAATA
2011778 ATTTTT-ATTAATTTG
1 ATTTTTCATT-ATTTG
2011793 A-TTTTCATTATTTG
1 ATTTTTCATTATTTG
*
2011807 ATTTTTAACTTATTTAG
1 ATTTTTCA-TTATTT-G
2011824 ATTTTCTCAT
1 ATTTT-TCAT
2011834 AGTTTTACAA
Statistics
Matches: 34, Mismatches: 2, Indels: 8
0.77 0.05 0.18
Matches are distributed among these distances:
14 10 0.29
15 9 0.26
16 6 0.18
17 7 0.21
18 2 0.06
ACGTcount: A:0.25, C:0.07, G:0.05, T:0.62
Consensus pattern (15 bp):
ATTTTTCATTATTTG
Found at i:2013154 original size:184 final size:187
Alignment explanation
Indices: 2012845--2013216 Score: 723
Period size: 184 Copynumber: 2.0 Consensus size: 187
2012835 CTAAATTGAA
2012845 TTAATTCAAAATTTAAGGGCAAAATTACAAATGGTGACCAAAATGAATTACGCATCAAAAGTAAA
1 TTAATTCAAAATTTAAGGGCAAAATTACAAATGGTGACCAAAATGAATTACGCATCAAAAGTAAA
2012910 GGGACTACGGAAATAATTTAACTATTTGTTAATTATAACCTAGTCCCCCTATAAATAGCCCAAAA
66 GGGACTACGGAAATAATTTAACTATTTGTTAATTATAACCTAGTCCCCCTATAAATAGCCCAAAA
2012975 ACCCCATTTTA-TTAA-TTTTCATTCTAC-CTTCAAAATCCCTCCCCCAAAACTCTC
131 ACCCCATTTTATTTAATTTTTCATTCTACACTTCAAAATCCCTCCCCCAAAACTCTC
2013029 TTAATTCAAAATTTAAGGGCAAAATTACAAATGGTGACCAAAATGAATTACGCATCAAAAGTAAA
1 TTAATTCAAAATTTAAGGGCAAAATTACAAATGGTGACCAAAATGAATTACGCATCAAAAGTAAA
2013094 GGGACTACGGAAATAATTTAACTATTTGTTAATTATAACCTAGTCCCCCTATAAATAGCCCAAAA
66 GGGACTACGGAAATAATTTAACTATTTGTTAATTATAACCTAGTCCCCCTATAAATAGCCCAAAA
2013159 ACCCCATTTTATTTAATTTTTCATTCTACACTTCAAAATCCCTCCCCCAAAACTCTC
131 ACCCCATTTTATTTAATTTTTCATTCTACACTTCAAAATCCCTCCCCCAAAACTCTC
2013216 T
1 T
2013217 CAAGCTTTTG
Statistics
Matches: 185, Mismatches: 0, Indels: 3
0.98 0.00 0.02
Matches are distributed among these distances:
184 141 0.76
185 4 0.02
186 12 0.06
187 28 0.15
ACGTcount: A:0.39, C:0.22, G:0.09, T:0.30
Consensus pattern (187 bp):
TTAATTCAAAATTTAAGGGCAAAATTACAAATGGTGACCAAAATGAATTACGCATCAAAAGTAAA
GGGACTACGGAAATAATTTAACTATTTGTTAATTATAACCTAGTCCCCCTATAAATAGCCCAAAA
ACCCCATTTTATTTAATTTTTCATTCTACACTTCAAAATCCCTCCCCCAAAACTCTC
Found at i:2013316 original size:2 final size:2
Alignment explanation
Indices: 2013304--2013444 Score: 83
Period size: 2 Copynumber: 74.5 Consensus size: 2
2013294 CACCATTTAT
* *
2013304 TA TA GTA TA TA TA TA TA TA T- TA CA TA TT TA CTA TA T- TA TA T-
1 TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA
2013345 TA TA TA GTA TA TA TA TA TA T- TA TA T- TA TA TA TA -A 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
* * * * *
2013385 T- TA TA TA GTA TT TT TG TA TA -A TA TA CA T- TA T- TA TA TCG TA
1 TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T-A TA
2013425 TA T- TA TA TA T- TA TA -A TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA T
2013445 TATTATTTTT
Statistics
Matches: 110, Mismatches: 11, Indels: 36
0.70 0.07 0.23
Matches are distributed among these distances:
1 13 0.12
2 88 0.80
3 9 0.08
ACGTcount: A:0.42, C:0.03, G:0.04, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2013350 original size:7 final size:7
Alignment explanation
Indices: 2013301--2013450 Score: 93
Period size: 7 Copynumber: 21.9 Consensus size: 7
2013291 CACCACCATT
2013301 TATTATA
1 TATTATA
2013308 GTA-TATA
1 -TATTATA
2013315 TA-TATA
1 TATTATA
*
2013321 TATTACA
1 TATTATA
2013328 TATT-TA
1 TATTATA
2013334 CTA-TATTA
1 -TATTA-TA
2013342 TATTATA
1 TATTATA
*
2013349 TAGTATA
1 TATTATA
2013356 TA-TATA
1 TATTATA
2013362 TATTATA
1 TATTATA
2013369 T-TATATA
1 TAT-TATA
*
2013376 TAATATA
1 TATTATA
2013383 TATTATA
1 TATTATA
*
2013390 TAGTAT-
1 TATTATA
* *
2013396 TTTTGTA
1 TATTATA
*
2013403 TAATATA
1 TATTATA
*
2013410 CATTATTA
1 TATTA-TA
**
2013418 TATCGTA
1 TATTATA
2013425 TATTATA
1 TATTATA
2013432 TATTATA
1 TATTATA
2013439 -A-TATA
1 TATTATA
2013444 TTATTAT
1 -TATTAT
2013451 TTTTTTTGAT
Statistics
Matches: 110, Mismatches: 19, Indels: 26
0.71 0.12 0.17
Matches are distributed among these distances:
5 4 0.04
6 21 0.19
7 72 0.65
8 13 0.12
ACGTcount: A:0.41, C:0.03, G:0.03, T:0.53
Consensus pattern (7 bp):
TATTATA
Found at i:2013370 original size:39 final size:39
Alignment explanation
Indices: 2013301--2013450 Score: 126
Period size: 41 Copynumber: 3.7 Consensus size: 39
2013291 CACCACCATT
2013301 TATTATAGTA-TATATATATATATTACATATTTACTATAT-TA
1 TATTATA-TAGTATATATATATATT--ATATTTA-TATATATA
2013342 TATTATATAGTATATATATATATTATATTATATATAATATA
1 TATTATATAGTATATATATATATTATATT-TATAT-ATATA
* * * * * *
2013383 TATTATATAGTATTTTTGTATAATATACATTATTATATCGTA
1 TATTATATAGTATATATATATATTATA-TTTA-TATAT-ATA
*
2013425 TATTATATATTATA-ATATATTATTAT
1 TATTATATAGTATATATATA-TATTAT
2013451 TTTTTTTGAT
Statistics
Matches: 90, Mismatches: 11, Indels: 15
0.78 0.09 0.13
Matches are distributed among these distances:
39 8 0.09
40 6 0.07
41 53 0.59
42 23 0.26
ACGTcount: A:0.41, C:0.03, G:0.03, T:0.53
Consensus pattern (39 bp):
TATTATATAGTATATATATATATTATATTTATATATATA
Found at i:2014949 original size:12 final size:12
Alignment explanation
Indices: 2014932--2014966 Score: 61
Period size: 12 Copynumber: 2.9 Consensus size: 12
2014922 GTGGGGTAGG
2014932 AATTATTATTTT
1 AATTATTATTTT
2014944 AATTATTATTTT
1 AATTATTATTTT
*
2014956 GATTATTATTT
1 AATTATTATTT
2014967 CTCCCTTACT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.31, C:0.00, G:0.03, T:0.66
Consensus pattern (12 bp):
AATTATTATTTT
Found at i:2018981 original size:77 final size:79
Alignment explanation
Indices: 2018806--2019001 Score: 207
Period size: 77 Copynumber: 2.5 Consensus size: 79
2018796 TTTTGTGCTA
* * * * * * *
2018806 GATTTCAACTTCACGATGAAGGATATCATGCTCAATTCATCCACGATCGACTCAACTTTACGATG
1 GATTTCAACTTCACGACGAAGGATATCATACTCAAGTCATCCAAGATCGACTCAACTTCAAGACG
*
2018871 AAAGAGTCATCCAC
66 AAAGAGTAATCCAC
* *
2018885 GATTTCAACTTCATGACGAAGGATATCATACTC-AGTCATCCAAGAT-GGCTCAACTTCAAGACG
1 GATTTCAACTTCACGACGAAGGATATCATACTCAAGTCATCCAAGATCGACTCAACTTCAAGACG
* ***
2018948 AATGAGTAATCTTT
66 AAAGAGTAATCCAC
* * * * *
2018962 GATTTTAACTTCACAACGAATGATATCTTGCTCAAGTCAT
1 GATTTCAACTTCACGACGAAGGATATCATACTCAAGTCAT
2019002 TCGGGATCAA
Statistics
Matches: 96, Mismatches: 20, Indels: 3
0.81 0.17 0.03
Matches are distributed among these distances:
77 49 0.51
78 17 0.18
79 30 0.31
ACGTcount: A:0.33, C:0.22, G:0.15, T:0.29
Consensus pattern (79 bp):
GATTTCAACTTCACGACGAAGGATATCATACTCAAGTCATCCAAGATCGACTCAACTTCAAGACG
AAAGAGTAATCCAC
Found at i:2019392 original size:133 final size:133
Alignment explanation
Indices: 2019154--2019453 Score: 350
Period size: 133 Copynumber: 2.3 Consensus size: 133
2019144 ATCAACTGCG
* * *
2019154 ATTTAGCTTAACTCAACAACGATGAGTTATTTCCCATTCCATATTTCGAGCTAGATTTCAACTTA
1 ATTTAGCTTAACTCAACAACGATGAGCTATTTTCCATTCCAGATTTCGAGCTAGATTTCAACTTA
* ** * *
2019219 ACGATGAAGGATATCATGCTTAAGTCATCCAAGGTCGACTCAACTAAATGACGAAGGAGTCAACC
66 ACAAAAAAGGATATCAAGCTTAAGTCATCCAAGATCGACTCAACTAAATGACGAAGGAGTCAACC
2019284 ACA
131 ACA
* * * * *
2019287 ATTTAGCTTAACTCAATAACGATGAGCTATTTTTCATTCTAGATTTCGAG-TCGGATTTCAAGTT
1 ATTTAGCTTAACTCAACAACGATGAGCTATTTTCCATTCCAGATTTCGAGCT-AGATTTCAACTT
* * * ** * * *
2019351 AACAAAAAAGGATATCAAGCTTGAGTCATCCGAGATTGACTCAACTTCATGATGAATGAGTCATC
65 AACAAAAAAGGATATCAAGCTTAAGTCATCCAAGATCGACTCAACTAAATGACGAAGGAGTCAAC
*
2019416 CATA
130 CACA
** * *
2019420 ACATAGTTTAACTCAACAACGATGAACTATTTTC
1 ATTTAGCTTAACTCAACAACGATGAGCTATTTTC
2019454 ATCCAACTTA
Statistics
Matches: 138, Mismatches: 28, Indels: 2
0.82 0.17 0.01
Matches are distributed among these distances:
132 1 0.01
133 137 0.99
ACGTcount: A:0.35, C:0.20, G:0.15, T:0.30
Consensus pattern (133 bp):
ATTTAGCTTAACTCAACAACGATGAGCTATTTTCCATTCCAGATTTCGAGCTAGATTTCAACTTA
ACAAAAAAGGATATCAAGCTTAAGTCATCCAAGATCGACTCAACTAAATGACGAAGGAGTCAACC
ACA
Found at i:2020942 original size:15 final size:15
Alignment explanation
Indices: 2020919--2020978 Score: 50
Period size: 15 Copynumber: 3.9 Consensus size: 15
2020909 TTTTAATATT
*
2020919 TTTTTATTATTTTGA
1 TTTTCATTATTTTGA
2020934 TTTTCATTATTTAT-A
1 TTTTCATTATTT-TGA
* * *
2020949 TTTTAACTTATTTAGT
1 TTTTCA-TTATTTTGA
2020965 TTTTCTATTATTTT
1 TTTTC-ATTATTTT
2020979 TACCATAATT
Statistics
Matches: 35, Mismatches: 6, Indels: 7
0.73 0.12 0.15
Matches are distributed among these distances:
15 17 0.49
16 17 0.49
17 1 0.03
ACGTcount: A:0.22, C:0.05, G:0.03, T:0.70
Consensus pattern (15 bp):
TTTTCATTATTTTGA
Found at i:2025181 original size:24 final size:21
Alignment explanation
Indices: 2025154--2025206 Score: 70
Period size: 24 Copynumber: 2.4 Consensus size: 21
2025144 AGGAAAAAAG
2025154 AAAAAGAGAAAAGTAAAAAATGTA
1 AAAAAGAGAAAA-T-AAAAATG-A
*
2025178 AAAAAGAGAAAATAATAATGA
1 AAAAAGAGAAAATAAAAATGA
2025199 AAAAAGAG
1 AAAAAGAG
2025207 GTTTCAAGAT
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
21 9 0.32
22 6 0.21
23 1 0.04
24 12 0.43
ACGTcount: A:0.72, C:0.00, G:0.17, T:0.11
Consensus pattern (21 bp):
AAAAAGAGAAAATAAAAATGA
Found at i:2026162 original size:18 final size:20
Alignment explanation
Indices: 2026120--2026168 Score: 66
Period size: 21 Copynumber: 2.5 Consensus size: 20
2026110 TAGTGAACAT
2026120 TATCGATACTGATGCAAGTAG
1 TATCGATACTGATG-AAGTAG
*
2026141 TATCGATACTGATG-TG-AG
1 TATCGATACTGATGAAGTAG
2026159 TATCGATACT
1 TATCGATACT
2026169 AAGAGAATGG
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
18 12 0.44
19 1 0.04
21 14 0.52
ACGTcount: A:0.31, C:0.14, G:0.22, T:0.33
Consensus pattern (20 bp):
TATCGATACTGATGAAGTAG
Found at i:2026768 original size:51 final size:52
Alignment explanation
Indices: 2026699--2026797 Score: 155
Period size: 51 Copynumber: 1.9 Consensus size: 52
2026689 AATGCCTAAC
*
2026699 TGTGCAATCATGCAAGTTAGATGAAAGGCTAAATGCCTTTGAG-TAAAGAAT
1 TGTGCAATAATGCAAGTTAGATGAAAGGCTAAATGCCTTTGAGATAAAGAAT
* * *
2026750 TGTGCCATAATGCCAGTTAGATGAAAGGTTAAATGCCTTTGAGATAAA
1 TGTGCAATAATGCAAGTTAGATGAAAGGCTAAATGCCTTTGAGATAAA
2026798 AGACTAAATG
Statistics
Matches: 43, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
51 39 0.91
52 4 0.09
ACGTcount: A:0.36, C:0.12, G:0.23, T:0.28
Consensus pattern (52 bp):
TGTGCAATAATGCAAGTTAGATGAAAGGCTAAATGCCTTTGAGATAAAGAAT
Found at i:2026976 original size:81 final size:81
Alignment explanation
Indices: 2026751--2027183 Score: 584
Period size: 81 Copynumber: 5.3 Consensus size: 81
2026741 GTAAAGAATT
* *
2026751 GTGCC-ATAATGCCAGTTAGATGAAAGGTTAAATGCCTTTGAGATAAAAGACTAAATGGCTAGTT
1 GTGCCAATAATG-CAGTTAGATGAAAGGTTAAATGCCTTTGAGATAAAATACTAAATGCCTAGTT
* *
2026815 GTTCATTTGGCAGAAAA
65 GTGCATTTGGCAGAAAG
* *
2026832 GTGCCAATAATGCCGGTTAGATGAAAGCTTAAATGCCTTTGAGATAAAATACTAAATGCCTAGTT
1 GTGCCAATAATG-CAGTTAGATGAAAGGTTAAATGCCTTTGAGATAAAATACTAAATGCCTAGTT
*
2026897 GTGCATTTGGTAGAAAG
65 GTGCATTTGGCAGAAAG
* *
2026914 GTGCCAATAATGCAGTTAGATAAAAGGTTAAATGCCTTTGAGATAAAATACTAAATGTCTAGTTG
1 GTGCCAATAATGCAGTTAGATGAAAGGTTAAATGCCTTTGAGATAAAATACTAAATGCCTAGTTG
*
2026979 TGTATTTGGCAGAAAG
66 TGCATTTGGCAGAAAG
* **
2026995 GTGCCAATAATGCAGTTAGATGAAAGGTTAAATGGCTTTGAGATAAAATACTAAATGCCTAACTG
1 GTGCCAATAATGCAGTTAGATGAAAGGTTAAATGCCTTTGAGATAAAATACTAAATGCCTAGTTG
*
2027060 TGCATTTCGCAGAAAG
66 TGCATTTGGCAGAAAG
** * * * *
2027076 GTGCCAATAATGCAGTTAGATGAAAGACTAAATGCCTTTGGGATGAAAGACTAAATGCCTAACTA
1 GTGCCAATAATGCAGTTAGATGAAAGGTTAAATGCCTTTGAGATAAAATACTAAATGCCT-AGT-
**
2027141 TGT-TTTTTGGCAGAAAG
64 TGTGCATTTGGCAGAAAG
* *
2027158 GTGACACTAATGCAGGTTAGAT-AAAG
1 GTGCCAATAATGCA-GTTAGATGAAAG
2027184 AGCAAGGCAT
Statistics
Matches: 315, Mismatches: 33, Indels: 7
0.89 0.09 0.02
Matches are distributed among these distances:
81 196 0.62
82 109 0.35
83 10 0.03
ACGTcount: A:0.36, C:0.12, G:0.23, T:0.28
Consensus pattern (81 bp):
GTGCCAATAATGCAGTTAGATGAAAGGTTAAATGCCTTTGAGATAAAATACTAAATGCCTAGTTG
TGCATTTGGCAGAAAG
Found at i:2027109 original size:22 final size:23
Alignment explanation
Indices: 2027084--2027133 Score: 66
Period size: 23 Copynumber: 2.2 Consensus size: 23
2027074 AGGTGCCAAT
2027084 AATGCAGTT-AGATGAAAGACTA
1 AATGCAGTTGAGATGAAAGACTA
** *
2027106 AATGCCTTTGGGATGAAAGACTA
1 AATGCAGTTGAGATGAAAGACTA
2027129 AATGC
1 AATGC
2027134 CTAACTATGT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
22 7 0.29
23 17 0.71
ACGTcount: A:0.40, C:0.12, G:0.24, T:0.24
Consensus pattern (23 bp):
AATGCAGTTGAGATGAAAGACTA
Found at i:2030142 original size:18 final size:18
Alignment explanation
Indices: 2030119--2030153 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
2030109 TATTATATGG
*
2030119 TTCCATGTTATAATTGTT
1 TTCCATATTATAATTGTT
*
2030137 TTCCATATTATAGTTGT
1 TTCCATATTATAATTGT
2030154 GTCATTAGTA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.23, C:0.11, G:0.11, T:0.54
Consensus pattern (18 bp):
TTCCATATTATAATTGTT
Found at i:2033797 original size:2 final size:2
Alignment explanation
Indices: 2033762--2033787 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
2033752 TATACTATGT
2033762 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
2033788 AACTTATATA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2034203 original size:3 final size:3
Alignment explanation
Indices: 2034195--2034242 Score: 96
Period size: 3 Copynumber: 16.0 Consensus size: 3
2034185 CCCGACCCTG
2034195 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
2034243 TGAACTATAT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 45 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:2034696 original size:29 final size:28
Alignment explanation
Indices: 2034656--2034721 Score: 89
Period size: 28 Copynumber: 2.3 Consensus size: 28
2034646 TAAAAGTACT
*
2034656 AGAAATTAAGGGGCAGAAATATAAATAAC
1 AGAAATTAA-GGGCAAAAATATAAATAAC
*
2034685 A-AAATTGAAGGGCAAAAATATAAATTAC
1 AGAAATT-AAGGGCAAAAATATAAATAAC
2034713 AGAAATTAA
1 AGAAATTAA
2034722 ACAATCAAAT
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
28 25 0.76
29 8 0.24
ACGTcount: A:0.58, C:0.06, G:0.17, T:0.20
Consensus pattern (28 bp):
AGAAATTAAGGGCAAAAATATAAATAAC
Found at i:2035960 original size:21 final size:21
Alignment explanation
Indices: 2035936--2035979 Score: 79
Period size: 21 Copynumber: 2.1 Consensus size: 21
2035926 AATATGTGAA
2035936 TCGCATTGCGATTTTCCAAAT
1 TCGCATTGCGATTTTCCAAAT
*
2035957 TCGCGTTGCGATTTTCCAAAT
1 TCGCATTGCGATTTTCCAAAT
2035978 TC
1 TC
2035980 TCAACGCGAA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.20, C:0.25, G:0.16, T:0.39
Consensus pattern (21 bp):
TCGCATTGCGATTTTCCAAAT
Found at i:2035988 original size:21 final size:21
Alignment explanation
Indices: 2035943--2035988 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
2035933 GAATCGCATT
***
2035943 GCGATTTTCCAAATTCGCGTT
1 GCGATTTTCCAAATTCGCAAC
*
2035964 GCGATTTTCCAAATTCTCAAC
1 GCGATTTTCCAAATTCGCAAC
2035985 GCGA
1 GCGA
2035989 ATATGTAAAT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.24, C:0.26, G:0.17, T:0.33
Consensus pattern (21 bp):
GCGATTTTCCAAATTCGCAAC
Found at i:2036021 original size:20 final size:20
Alignment explanation
Indices: 2035998--2036056 Score: 82
Period size: 20 Copynumber: 3.0 Consensus size: 20
2035988 AATATGTAAA
2035998 TCGCAACAAAGAAGTCAAAT
1 TCGCAACAAAGAAGTCAAAT
* *
2036018 TCGCAACACATAAGTCAAAT
1 TCGCAACAAAGAAGTCAAAT
**
2036038 TCGCTTCAAAGAAGTCAAA
1 TCGCAACAAAGAAGTCAAA
2036057 ACGCATTTAT
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.46, C:0.22, G:0.14, T:0.19
Consensus pattern (20 bp):
TCGCAACAAAGAAGTCAAAT
Found at i:2036235 original size:20 final size:22
Alignment explanation
Indices: 2036178--2036235 Score: 75
Period size: 22 Copynumber: 2.7 Consensus size: 22
2036168 CTACGGCGAC
* **
2036178 ATCCGTCCCCATCTCCGACGTA
1 ATCCGTCCTCATCTCCGACAAA
2036200 ATCCGTCCTCATCTCCGACAAA
1 ATCCGTCCTCATCTCCGACAAA
2036222 ATCCGT-CT-ATCTCC
1 ATCCGTCCTCATCTCC
2036236 ATCTCTCATA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
20 6 0.18
21 2 0.06
22 25 0.76
ACGTcount: A:0.21, C:0.43, G:0.10, T:0.26
Consensus pattern (22 bp):
ATCCGTCCTCATCTCCGACAAA
Found at i:2038807 original size:21 final size:21
Alignment explanation
Indices: 2038781--2038878 Score: 117
Period size: 21 Copynumber: 4.7 Consensus size: 21
2038771 GATGCACCTG
2038781 TCATCGTTCAAGAGGCCCCTC
1 TCATCGTTCAAGAGGCCCCTC
2038802 TCATCGTTCAAGAGGCCCCTC
1 TCATCGTTCAAGAGGCCCCTC
* * *
2038823 -CTACCGTTCAAGAGGCCTCTG
1 TC-ATCGTTCAAGAGGCCCCTC
* *
2038844 TCATCGTTTAAGAGGTCCCTC
1 TCATCGTTCAAGAGGCCCCTC
* *
2038865 CCACCGTTCAAGAG
1 TCATCGTTCAAGAG
2038879 CCCGATTCAT
Statistics
Matches: 64, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
20 1 0.02
21 62 0.97
22 1 0.02
ACGTcount: A:0.20, C:0.35, G:0.20, T:0.24
Consensus pattern (21 bp):
TCATCGTTCAAGAGGCCCCTC
Found at i:2038832 original size:42 final size:42
Alignment explanation
Indices: 2038785--2038878 Score: 143
Period size: 42 Copynumber: 2.2 Consensus size: 42
2038775 CACCTGTCAT
*
2038785 CGTTCAAGAGGCCCCTCTCATCGTTCAAGAGGCCCCTCCTAC
1 CGTTCAAGAGGCCCCTCTCATCGTTCAAGAGGCCCCTCCCAC
* * * *
2038827 CGTTCAAGAGGCCTCTGTCATCGTTTAAGAGGTCCCTCCCAC
1 CGTTCAAGAGGCCCCTCTCATCGTTCAAGAGGCCCCTCCCAC
2038869 CGTTCAAGAG
1 CGTTCAAGAG
2038879 CCCGATTCAT
Statistics
Matches: 47, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
42 47 1.00
ACGTcount: A:0.20, C:0.35, G:0.21, T:0.23
Consensus pattern (42 bp):
CGTTCAAGAGGCCCCTCTCATCGTTCAAGAGGCCCCTCCCAC
Found at i:2040334 original size:14 final size:14
Alignment explanation
Indices: 2040315--2040351 Score: 74
Period size: 14 Copynumber: 2.6 Consensus size: 14
2040305 GCTTGTTTAA
2040315 TTGATTTGTAAAAG
1 TTGATTTGTAAAAG
2040329 TTGATTTGTAAAAG
1 TTGATTTGTAAAAG
2040343 TTGATTTGT
1 TTGATTTGT
2040352 TTAATTGATG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.30, C:0.00, G:0.22, T:0.49
Consensus pattern (14 bp):
TTGATTTGTAAAAG
Found at i:2040352 original size:78 final size:76
Alignment explanation
Indices: 2040225--2040415 Score: 296
Period size: 78 Copynumber: 2.5 Consensus size: 76
2040215 GGTACACTTC
*
2040225 TTTTGCTTGTTTAATTGAATTT-T-ACATTGATTTGTAAAAGTTGATTTGTTTAATTGATGAGGA
1 TTTTGCTTGTTTAATTG-ATTTGTAAAATTGATTTGTAAAAGTTGATTTGTTTAATTGATGAGGA
2040288 AATAAGAATTATT
65 AATAAGAATTA-T
* *
2040301 TTTTGCTTGTTTAATTGATTTGTAAAAGTTGATTTGTAAAAGTTGATTTGTTTAATTGATGTGTA
1 TTTTGCTTGTTTAATTGATTTGTAAAA-TTGATTTGTAAAAGTTGATTTGTTTAATTGATGAGGA
2040366 AATAAGAATTAT
65 AATAAGAATTAT
2040378 TTTTGTCTTGTTTAATTGATTTGTAAAATTTGATTTGT
1 TTTTG-CTTGTTTAATTGATTTGTAAAA-TTGATTTGT
2040416 TGTTTATTCA
Statistics
Matches: 107, Mismatches: 4, Indels: 6
0.91 0.03 0.05
Matches are distributed among these distances:
75 4 0.04
76 18 0.17
77 8 0.07
78 77 0.72
ACGTcount: A:0.29, C:0.02, G:0.17, T:0.51
Consensus pattern (76 bp):
TTTTGCTTGTTTAATTGATTTGTAAAATTGATTTGTAAAAGTTGATTTGTTTAATTGATGAGGAA
ATAAGAATTAT
Found at i:2040403 original size:37 final size:37
Alignment explanation
Indices: 2040270--2040404 Score: 105
Period size: 37 Copynumber: 3.5 Consensus size: 37
2040260 AAAAGTTGAT
* *
2040270 TTGTTTAATTGATGAGGAAATAAGAATTATTTTT-TGC
1 TTGTTTAATTGATGTGTAAATAAGAATTATTTTTGT-C
* * * ***
2040307 TTGTTTAATTGATTTGTAAA-AGTTGATTTGTAAAAGTTGAT-
1 TTGTTTAATTGATGTGTAAATA--AGA-AT-T-ATTTTTG-TC
2040348 TTGTTTAATTGATGTGTAAATAAGAATTATTTTTGTC
1 TTGTTTAATTGATGTGTAAATAAGAATTATTTTTGTC
*
2040385 TTGTTTAATTGATTTGTAAA
1 TTGTTTAATTGATGTGTAAA
2040405 ATTTGATTTG
Statistics
Matches: 74, Mismatches: 15, Indels: 18
0.69 0.14 0.17
Matches are distributed among these distances:
36 2 0.03
37 40 0.54
38 3 0.04
39 2 0.03
40 3 0.04
41 22 0.30
42 1 0.01
43 1 0.01
ACGTcount: A:0.31, C:0.01, G:0.18, T:0.50
Consensus pattern (37 bp):
TTGTTTAATTGATGTGTAAATAAGAATTATTTTTGTC
Found at i:2040511 original size:20 final size:20
Alignment explanation
Indices: 2040468--2040572 Score: 102
Period size: 20 Copynumber: 5.2 Consensus size: 20
2040458 TTGAAGGTAC
* *
2040468 AATTTCGCAACGCGAAAATAA
1 AATTT-GCAACGCGAAAGTCA
2040489 AATTTGCAACGCGAAAGTCA
1 AATTTGCAACGCGAAAGTCA
* *** *
2040509 AATTCGCGTTGCGATAGTCA
1 AATTTGCAACGCGAAAGTCA
* *
2040529 AATTCGCAACGCGATAGTCA
1 AATTTGCAACGCGAAAGTCA
* *
2040549 AATTTGCAACGCAAAACTCA
1 AATTTGCAACGCGAAAGTCA
2040569 AATT
1 AATT
2040573 CACATTGCGA
Statistics
Matches: 70, Mismatches: 14, Indels: 1
0.82 0.16 0.01
Matches are distributed among these distances:
20 65 0.93
21 5 0.07
ACGTcount: A:0.39, C:0.21, G:0.17, T:0.23
Consensus pattern (20 bp):
AATTTGCAACGCGAAAGTCA
Found at i:2040570 original size:60 final size:60
Alignment explanation
Indices: 2040471--2040583 Score: 163
Period size: 60 Copynumber: 1.9 Consensus size: 60
2040461 AAGGTACAAT
* * * *
2040471 TTCGCAACGCGAAAATAAAATTTGCAACGCGAAAGTCAAATTCGCGTTGCGATAGTCAAA
1 TTCGCAACGCGAAAATAAAATTTGCAACGCAAAACTCAAATTCACATTGCGATAGTCAAA
* * *
2040531 TTCGCAACGCGATAGTCAAATTTGCAACGCAAAACTCAAATTCACATTGCGAT
1 TTCGCAACGCGAAAATAAAATTTGCAACGCAAAACTCAAATTCACATTGCGAT
2040584 TTTTAGTTTG
Statistics
Matches: 46, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
60 46 1.00
ACGTcount: A:0.37, C:0.22, G:0.18, T:0.23
Consensus pattern (60 bp):
TTCGCAACGCGAAAATAAAATTTGCAACGCAAAACTCAAATTCACATTGCGATAGTCAAA
Found at i:2040958 original size:18 final size:18
Alignment explanation
Indices: 2040935--2040970 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
2040925 AAGCCGGTTG
*
2040935 TGATTGGGATTTTGATTT
1 TGATTGCGATTTTGATTT
2040953 TGATTGCGATTTTGATTT
1 TGATTGCGATTTTGATTT
2040971 CCTTTTGCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.17, C:0.03, G:0.25, T:0.56
Consensus pattern (18 bp):
TGATTGCGATTTTGATTT
Found at i:2043265 original size:24 final size:24
Alignment explanation
Indices: 2043231--2043286 Score: 78
Period size: 24 Copynumber: 2.3 Consensus size: 24
2043221 CTGAAACATC
*
2043231 ATCAAAATCC-GAGTATTAACCAAG
1 ATCAAATTCCGGA-TATTAACCAAG
*
2043255 ATCAAATTCCGGATATTGACCAAG
1 ATCAAATTCCGGATATTAACCAAG
2043279 ATCAAATT
1 ATCAAATT
2043287 TTGAATACTG
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
24 27 0.93
25 2 0.07
ACGTcount: A:0.43, C:0.20, G:0.12, T:0.25
Consensus pattern (24 bp):
ATCAAATTCCGGATATTAACCAAG
Found at i:2043298 original size:24 final size:24
Alignment explanation
Indices: 2043231--2043298 Score: 64
Period size: 24 Copynumber: 2.8 Consensus size: 24
2043221 CTGAAACATC
* * * *
2043231 ATCAAAATCCGAGTATTAACCAAG
1 ATCAAATTCCGAATACTGACCAAG
* *
2043255 ATCAAATTCCGGATATTGACCAAG
1 ATCAAATTCCGAATACTGACCAAG
**
2043279 ATCAAATTTTGAATACTGAC
1 ATCAAATTCCGAATACTGAC
2043299 TAGTACTCAC
Statistics
Matches: 36, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 36 1.00
ACGTcount: A:0.41, C:0.19, G:0.13, T:0.26
Consensus pattern (24 bp):
ATCAAATTCCGAATACTGACCAAG
Found at i:2044062 original size:14 final size:15
Alignment explanation
Indices: 2044026--2044063 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
2044016 GAAATCATTG
2044026 AAAAATTATATAGAA
1 AAAAATTATATAGAA
*
2044041 ATAAAATTATGTA-AA
1 A-AAAATTATATAGAA
2044056 AAAAATTA
1 AAAAATTA
2044064 GAGATGGGGA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
14 7 0.33
15 4 0.19
16 10 0.48
ACGTcount: A:0.66, C:0.00, G:0.05, T:0.29
Consensus pattern (15 bp):
AAAAATTATATAGAA
Done.