Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr5
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: 55438857
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 1812582 characters in sequence are not A, C, G, or T
File 59 of 167
Found at i:18498255 original size:48 final size:48
Alignment explanation
Indices: 18498120--18498258 Score: 152
Period size: 48 Copynumber: 2.9 Consensus size: 48
18498110 AATGGTGAAT
* * * * *
18498120 TGCCGATGCCATGTTCCAAACATGGTTTTACACTGGCTCACATGTCGA
1 TGCCGATGCCATGTCCCAAACATGGTCTTACACTGGCTCTCATCTCAA
* * ** * * *
18498168 GGTCGATGCCATGTCTTACACATGGTCTTACACTAGCTCTCGTCTCAA
1 TGCCGATGCCATGTCCCAAACATGGTCTTACACTGGCTCTCATCTCAA
* *
18498216 TGCCGATGGCATGTCCCAGACATGGTCTTACACTGGCTCTCAT
1 TGCCGATGCCATGTCCCAAACATGGTCTTACACTGGCTCTCAT
18498259 TGTGCCCGGT
Statistics
Matches: 71, Mismatches: 20, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
48 71 1.00
ACGTcount: A:0.21, C:0.29, G:0.21, T:0.29
Consensus pattern (48 bp):
TGCCGATGCCATGTCCCAAACATGGTCTTACACTGGCTCTCATCTCAA
Found at i:18500277 original size:41 final size:41
Alignment explanation
Indices: 18500232--18500344 Score: 145
Period size: 41 Copynumber: 2.8 Consensus size: 41
18500222 TTGTATATAA
* * *
18500232 CACCGGCATAAAGCCTGCTAGGCACCAAGCCCGATACATTT
1 CACCGGCACAAAGCCTGCTAGGCACAAAGCCCGATACAATT
* * * * *
18500273 CACCGGCACAAAGCCTGCTAGACATAAAGTCTGATATAATT
1 CACCGGCACAAAGCCTGCTAGGCACAAAGCCCGATACAATT
*
18500314 CACCGGCACAAAGCCTGCTAGGCATAAAGCC
1 CACCGGCACAAAGCCTGCTAGGCACAAAGCC
18500345 TGAACTTACA
Statistics
Matches: 62, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
41 62 1.00
ACGTcount: A:0.33, C:0.31, G:0.19, T:0.17
Consensus pattern (41 bp):
CACCGGCACAAAGCCTGCTAGGCACAAAGCCCGATACAATT
Found at i:18501600 original size:42 final size:42
Alignment explanation
Indices: 18501537--18501635 Score: 135
Period size: 42 Copynumber: 2.4 Consensus size: 42
18501527 CTCTCGGTAT
* *
18501537 CGCACACTTAGTGCCCGTTATTCAACATCATTATTATAATTC
1 CGCACACTTAGTGCCCATTATTCAACATCATCATTATAATTC
* * *
18501579 CGCACACTTAGTGCCTATTATTCAACATCATCATTTTAATTT
1 CGCACACTTAGTGCCCATTATTCAACATCATCATTATAATTC
**
18501621 TACACACTTAGTGCC
1 CGCACACTTAGTGCC
18501636 ATTCATATAG
Statistics
Matches: 50, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
42 50 1.00
ACGTcount: A:0.28, C:0.26, G:0.09, T:0.36
Consensus pattern (42 bp):
CGCACACTTAGTGCCCATTATTCAACATCATCATTATAATTC
Found at i:18507739 original size:27 final size:27
Alignment explanation
Indices: 18507700--18507752 Score: 97
Period size: 27 Copynumber: 2.0 Consensus size: 27
18507690 GGATAAGTTT
*
18507700 TAGAATTATTAAAATACCCCTGTAGGA
1 TAGAATTACTAAAATACCCCTGTAGGA
18507727 TAGAATTACTAAAATACCCCTGTAGG
1 TAGAATTACTAAAATACCCCTGTAGG
18507753 GTAGGACTAC
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.40, C:0.17, G:0.15, T:0.28
Consensus pattern (27 bp):
TAGAATTACTAAAATACCCCTGTAGGA
Found at i:18514273 original size:27 final size:26
Alignment explanation
Indices: 18514229--18514280 Score: 68
Period size: 27 Copynumber: 2.0 Consensus size: 26
18514219 GGACTACCGA
*
18514229 TTTACCCCTAGAGGGTAAAATGACTAT
1 TTTACCCCTAGAGCGT-AAATGACTAT
* *
18514256 TTTACCCCTTGTGCGTAAATGACTA
1 TTTACCCCTAGAGCGTAAATGACTA
18514281 ACTTGTGTGA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
26 9 0.41
27 13 0.59
ACGTcount: A:0.29, C:0.21, G:0.17, T:0.33
Consensus pattern (26 bp):
TTTACCCCTAGAGCGTAAATGACTAT
Found at i:18514922 original size:27 final size:26
Alignment explanation
Indices: 18514878--18514928 Score: 66
Period size: 27 Copynumber: 1.9 Consensus size: 26
18514868 CACGCTGCAA
*
18514878 TCTGGTGGCCTCGCCACATATATCTGT
1 TCTGGTGACCTCGCCACA-ATATCTGT
* *
18514905 TCTGGTGACTTCGTCACAATATCT
1 TCTGGTGACCTCGCCACAATATCT
18514929 AGCAGCCTCG
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
26 6 0.29
27 15 0.71
ACGTcount: A:0.18, C:0.27, G:0.20, T:0.35
Consensus pattern (26 bp):
TCTGGTGACCTCGCCACAATATCTGT
Found at i:18515008 original size:27 final size:26
Alignment explanation
Indices: 18514970--18515029 Score: 66
Period size: 27 Copynumber: 2.3 Consensus size: 26
18514960 ACATATATAT
* *
18514970 ATATTTGTTCTGGTGGCCTAGCCACA
1 ATATCTGTTCTGGTGACCTAGCCACA
* * *
18514996 ATATCTGTATCTGGTGACTTCGTCACA
1 ATATCTGT-TCTGGTGACCTAGCCACA
18515023 ATATCTG
1 ATATCTG
18515030 GTAGCCTCGC
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
26 7 0.25
27 21 0.75
ACGTcount: A:0.22, C:0.22, G:0.20, T:0.37
Consensus pattern (26 bp):
ATATCTGTTCTGGTGACCTAGCCACA
Found at i:18515874 original size:22 final size:22
Alignment explanation
Indices: 18515846--18515897 Score: 77
Period size: 22 Copynumber: 2.4 Consensus size: 22
18515836 GGCCTTTAGT
*
18515846 CGTCCTGTCTACGGCGTTGAGC
1 CGTCCTGTCTACGGCATTGAGC
*
18515868 CGTCCTGTCTACGGTATTGAGC
1 CGTCCTGTCTACGGCATTGAGC
*
18515890 CATCCTGT
1 CGTCCTGT
18515898 TGACTTAGTG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.12, C:0.31, G:0.27, T:0.31
Consensus pattern (22 bp):
CGTCCTGTCTACGGCATTGAGC
Found at i:18521055 original size:144 final size:144
Alignment explanation
Indices: 18520795--18521061 Score: 405
Period size: 144 Copynumber: 1.9 Consensus size: 144
18520785 TCAAATACCA
* *
18520795 ATGCCATGTCCCTAACATGGTCTTACATGAATCCACATATCATCCCCGATGCCATGTCCTAGACA
1 ATGCCATGTCCCTAACATGGTCTTACATCAAGCCACATATCATCCCCGATGCCATGTCCTAGACA
* *
18520860 TGGTCTTACACTGGCACACATATCATCGCTGATGCCATTTCCCAGACATGGTCTTACATAGGCAC
66 TGGTCTTACACAGGCACACATATCATCGCTGATGCCATATCCCAGACATGGTCTTACATAGGCAC
18520925 ATATATCGTCGCCG
131 ATATATCGTCGCCG
* * *
18520939 ATGCCATGTCCC-AGACATGGTCTTACA-CAGGCACATATATCATCGCCGATGCCATGTCCTAGA
1 ATGCCATGTCCCTA-ACATGGTCTTACATCAAGC-CACATATCATCCCCGATGCCATGTCCTAGA
* *
18521002 CATGGTCTTACACAGGCACATATATCATC-ATCGATGCCATATCCCAGACATGGTCTTACA
64 CATGGTCTTACACAGGCACACATATCATCGCT-GATGCCATATCCCAGACATGGTCTTACA
18521062 CAGAATCTCA
Statistics
Matches: 111, Mismatches: 9, Indels: 6
0.88 0.07 0.05
Matches are distributed among these distances:
143 4 0.04
144 107 0.96
ACGTcount: A:0.27, C:0.30, G:0.17, T:0.26
Consensus pattern (144 bp):
ATGCCATGTCCCTAACATGGTCTTACATCAAGCCACATATCATCCCCGATGCCATGTCCTAGACA
TGGTCTTACACAGGCACACATATCATCGCTGATGCCATATCCCAGACATGGTCTTACATAGGCAC
ATATATCGTCGCCG
Found at i:18521062 original size:48 final size:48
Alignment explanation
Indices: 18520795--18521064 Score: 364
Period size: 48 Copynumber: 5.6 Consensus size: 48
18520785 TCAAATACCA
* ** * *
18520795 ATGCCATGTCCCTA-ACATGGTCTTACATGAATC-CACATATCATCCCCG
1 ATGCCATGTCCC-AGACATGGTCTTACA-CAGGCACATATATCATCGCCG
* * * *
18520843 ATGCCATGTCCTAGACATGGTCTTACACTGGCACACATATCATCGCTG
1 ATGCCATGTCCCAGACATGGTCTTACACAGGCACATATATCATCGCCG
* * *
18520891 ATGCCATTTCCCAGACATGGTCTTACATAGGCACATATATCGTCGCCG
1 ATGCCATGTCCCAGACATGGTCTTACACAGGCACATATATCATCGCCG
18520939 ATGCCATGTCCCAGACATGGTCTTACACAGGCACATATATCATCGCCG
1 ATGCCATGTCCCAGACATGGTCTTACACAGGCACATATATCATCGCCG
* **
18520987 ATGCCATGTCCTAGACATGGTCTTACACAGGCACATATATCATCATCG
1 ATGCCATGTCCCAGACATGGTCTTACACAGGCACATATATCATCGCCG
*
18521035 ATGCCATATCCCAGACATGGTCTTACACAG
1 ATGCCATGTCCCAGACATGGTCTTACACAG
18521065 AATCTCATTT
Statistics
Matches: 198, Mismatches: 22, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
47 2 0.01
48 196 0.99
ACGTcount: A:0.27, C:0.30, G:0.17, T:0.26
Consensus pattern (48 bp):
ATGCCATGTCCCAGACATGGTCTTACACAGGCACATATATCATCGCCG
Found at i:18529165 original size:39 final size:39
Alignment explanation
Indices: 18529122--18529259 Score: 138
Period size: 39 Copynumber: 3.5 Consensus size: 39
18529112 CCAGACATAT
*
18529122 TTCCAACACGTAGCCTGCGGACCTTAAGTCCG-GTTATAA
1 TTCCAACACATAGCCTGCGGACCTTAAGTCCGAG-TATAA
*
18529161 TTCCAGCACATAGCCTGCGGACCTTAAGTCCGAGTATAA
1 TTCCAACACATAGCCTGCGGACCTTAAGTCCGAGTATAA
* * * * * *
18529200 TTCCAGCATATAGCCGGCAGGTCTTTAAGCCCG-GATATAA
1 TTCCAACACATAGCCTGC-GGACCTTAAGTCCGAG-TATAA
*
18529240 TTCCAGA-ATATAGCCTGCGG
1 TTCCA-ACACATAGCCTGCGG
18529260 GTCTTTAAGC
Statistics
Matches: 86, Mismatches: 9, Indels: 8
0.83 0.09 0.08
Matches are distributed among these distances:
39 54 0.63
40 32 0.37
ACGTcount: A:0.27, C:0.27, G:0.22, T:0.25
Consensus pattern (39 bp):
TTCCAACACATAGCCTGCGGACCTTAAGTCCGAGTATAA
Found at i:18529239 original size:40 final size:39
Alignment explanation
Indices: 18529132--18529275 Score: 164
Period size: 40 Copynumber: 3.6 Consensus size: 39
18529122 TTCCAACACG
* * * * *
18529132 TAGCCTGCGGACCTTAAGTCCGGTTATAATTCCAGCACA
1 TAGCCTGCGGTCTTTAAGCCCGGATATAATTCCAGCATA
* * *
18529171 TAGCCTGCGGACCTTAAGTCC-GAGTATAATTCCAGCATA
1 TAGCCTGCGGTCTTTAAGCCCGGA-TATAATTCCAGCATA
* *
18529210 TAGCCGGCAGGTCTTTAAGCCCGGATATAATTCCAGAATA
1 TAGCCTGC-GGTCTTTAAGCCCGGATATAATTCCAGCATA
18529250 TAGCCTGCGGGTCTTTAAGCCCGGAT
1 TAGCCTGC-GGTCTTTAAGCCCGGAT
18529276 TCACATCAAA
Statistics
Matches: 93, Mismatches: 9, Indels: 5
0.87 0.08 0.05
Matches are distributed among these distances:
38 1 0.01
39 42 0.45
40 48 0.52
41 2 0.02
ACGTcount: A:0.26, C:0.26, G:0.23, T:0.26
Consensus pattern (39 bp):
TAGCCTGCGGTCTTTAAGCCCGGATATAATTCCAGCATA
Found at i:18537861 original size:37 final size:37
Alignment explanation
Indices: 18537807--18537879 Score: 103
Period size: 37 Copynumber: 2.0 Consensus size: 37
18537797 GAGCTCTAAA
* *
18537807 GACCCGATGACTACGTGTGG-GAATTTTGTCCGGGTAT
1 GACCCGATAACTACGTGTGGAG-ATTATGTCCGGGTAT
*
18537844 GACCCGATAACTTCGTGTGGAGATTATGTCCGGGTA
1 GACCCGATAACTACGTGTGGAGATTATGTCCGGGTA
18537880 AGACTTCGTA
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
37 31 0.97
38 1 0.03
ACGTcount: A:0.21, C:0.19, G:0.32, T:0.29
Consensus pattern (37 bp):
GACCCGATAACTACGTGTGGAGATTATGTCCGGGTAT
Found at i:18541214 original size:184 final size:185
Alignment explanation
Indices: 18540896--18541261 Score: 691
Period size: 184 Copynumber: 2.0 Consensus size: 185
18540886 CACTATCAAG
18540896 CTATAAACTCCAGAGTATTGTAATACGTGTATTAAACACTTTCAAGTGAGTGGCATGTATAAGGA
1 CTATAAACTCCAGAGTATTGTAATACGTGTATTAAACACTTTCAAGTGAGTGGCATGTATAAGGA
*
18540961 CTAGTTTTTATATTAGATGTTGTTATGATTAGCCAAATGTATCGGCTTATATTGATCTATTGTAT
66 CTAGTTTTTATATTAGATGTTGTTATGATTAGCCAAATGTATCGGCTTATATTGATCTATTGGAT
*
18541026 ATAGCCATGAGATGTAG-CTTATTATGGTTATGGCTTGTAAGCCTAATTATTCCTA
131 ATAGCCATGAGATGT-GCCTTATTATGGTTATGGCTTGTAAACCTAATTATTCCTA
18541081 CTAT-AACTCCAGAGTATTGTAATACGTGTATTAAACACTTTCAAGTGAGTGGCATGTATAAGGA
1 CTATAAACTCCAGAGTATTGTAATACGTGTATTAAACACTTTCAAGTGAGTGGCATGTATAAGGA
18541145 CTAGTTTTTATATTAGATGTTGTTATGATTAGCCAAATGTATCGGCTTATATTGATCTATTGGAT
66 CTAGTTTTTATATTAGATGTTGTTATGATTAGCCAAATGTATCGGCTTATATTGATCTATTGGAT
18541210 ATAGCCATGAGATGTGCCTTATTATGGTTATGGCTTGTAAACCTAATTATTC
131 ATAGCCATGAGATGTGCCTTATTATGGTTATGGCTTGTAAACCTAATTATTC
18541262 TTGCTATGGG
Statistics
Matches: 178, Mismatches: 2, Indels: 3
0.97 0.01 0.02
Matches are distributed among these distances:
183 1 0.01
184 173 0.97
185 4 0.02
ACGTcount: A:0.30, C:0.13, G:0.19, T:0.39
Consensus pattern (185 bp):
CTATAAACTCCAGAGTATTGTAATACGTGTATTAAACACTTTCAAGTGAGTGGCATGTATAAGGA
CTAGTTTTTATATTAGATGTTGTTATGATTAGCCAAATGTATCGGCTTATATTGATCTATTGGAT
ATAGCCATGAGATGTGCCTTATTATGGTTATGGCTTGTAAACCTAATTATTCCTA
Found at i:18548804 original size:25 final size:25
Alignment explanation
Indices: 18548766--18548817 Score: 68
Period size: 25 Copynumber: 2.1 Consensus size: 25
18548756 TTTGGCTTGA
*
18548766 CATTTACTAAGCAACATCAGATATT
1 CATTTACTAAGCAACATCAAATATT
* * *
18548791 CATTTATTAGGCAATATCAAATATT
1 CATTTACTAAGCAACATCAAATATT
18548816 CA
1 CA
18548818 AATTATTTTT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.40, C:0.17, G:0.08, T:0.35
Consensus pattern (25 bp):
CATTTACTAAGCAACATCAAATATT
Found at i:18555911 original size:16 final size:16
Alignment explanation
Indices: 18555890--18555920 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
18555880 GCATTGGAAC
18555890 TTTTATTTTATTTTAT
1 TTTTATTTTATTTTAT
*
18555906 TTTTATTTTTTTTTA
1 TTTTATTTTATTTTA
18555921 CTTAGCTAAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (16 bp):
TTTTATTTTATTTTAT
Found at i:18556392 original size:48 final size:48
Alignment explanation
Indices: 18556334--18556431 Score: 151
Period size: 48 Copynumber: 2.0 Consensus size: 48
18556324 AAGGACCGAA
* * *
18556334 GAGATGAACTTCGAAAGTCCGAATCAAGGAAAAGGAGCAAATCCTGCT
1 GAGATAAACTTCGAAAATCCGAATCAAGGAAAAGGAGCAAACCCTGCT
* *
18556382 GAGATAAACTTCGAAAATCTGAATCAAGGAAATGGAGCAAACCCTGCT
1 GAGATAAACTTCGAAAATCCGAATCAAGGAAAAGGAGCAAACCCTGCT
18556430 GA
1 GA
18556432 AAATCCTATC
Statistics
Matches: 45, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
48 45 1.00
ACGTcount: A:0.41, C:0.18, G:0.23, T:0.17
Consensus pattern (48 bp):
GAGATAAACTTCGAAAATCCGAATCAAGGAAAAGGAGCAAACCCTGCT
Found at i:18563976 original size:90 final size:90
Alignment explanation
Indices: 18563817--18564072 Score: 271
Period size: 90 Copynumber: 2.8 Consensus size: 90
18563807 AAGATCAATG
* ** * ** * * *
18563817 TGGGTGGATGATCCACCAGTGTTGCAGGTTAATATGCTGCCAGGTGGTTGTGAATACGCAACGTA
1 TGGGTGGATGAACCAAAAATGTTGCAGGTTAATACACTGCCAGATGGTTGTGAATGCACAACG-A
18563882 -TTTGCAGATAAGAGCTACCAAAAAA
65 GTTTGCAGATAAGAGCTACCAAAAAA
* * *
18563907 TGGGTGGATTAACCAAAAATGTTGCATGTTAATACACTGCTAGATGGTTGTGAATGCACAACGAG
1 TGGGTGGATGAACCAAAAATGTTGCAGGTTAATACACTGCCAGATGGTTGTGAATGCACAACGAG
* * *
18563972 TTTGCATATAAGAGCTGCCAGAAAA
66 TTTGCAGATAAGAGCTACCAAAAAA
** * ** * * * * *
18563997 TTTGTGGATGAACTACTAGTGTTCCAGGTTAATACATTTCCAGATGTTTGTGAATGCACAACGAG
1 TGGGTGGATGAACCAAAAATGTTGCAGGTTAATACACTGCCAGATGGTTGTGAATGCACAACGAG
18564062 TTTGCAGATAA
66 TTTGCAGATAA
18564073 TAGTTGCTAG
Statistics
Matches: 136, Mismatches: 29, Indels: 2
0.81 0.17 0.01
Matches are distributed among these distances:
89 1 0.01
90 135 0.99
ACGTcount: A:0.31, C:0.15, G:0.25, T:0.29
Consensus pattern (90 bp):
TGGGTGGATGAACCAAAAATGTTGCAGGTTAATACACTGCCAGATGGTTGTGAATGCACAACGAG
TTTGCAGATAAGAGCTACCAAAAAA
Found at i:18564799 original size:86 final size:86
Alignment explanation
Indices: 18564639--18564800 Score: 211
Period size: 86 Copynumber: 1.9 Consensus size: 86
18564629 CGACCGTGTG
*
18564639 GAGGGTTCTTGGCGGTATGAGATTCAAACTATCTTAGGGTTTCAATGGTACATGGTCGTGTGAAA
1 GAGGGTTCTTGGCGGTATGAGATTCAAACTATCCTAGGGTTTCAATGGTACATGGTCGTGTGAAA
*
18564704 GGCCGTGTGGTTAGCTGTGGA
66 GGCCATGTGGTTAGCTGTGGA
** * * *
18564725 GAGGGTTCTTGGTTGTGTGAGATTCGAGCTATCCTAGGGTTTCAGA-GGTACATGG-CAGTGTGA
1 GAGGGTTCTTGGCGGTATGAGATTCAAACTATCCTAGGGTTTCA-ATGGTACATGGTC-GTGTGA
**
18564788 GGGGCCATGTGGT
64 AAGGCCATGTGGT
18564801 CCACATGCCC
Statistics
Matches: 65, Mismatches: 9, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
85 1 0.02
86 63 0.97
87 1 0.02
ACGTcount: A:0.19, C:0.13, G:0.37, T:0.31
Consensus pattern (86 bp):
GAGGGTTCTTGGCGGTATGAGATTCAAACTATCCTAGGGTTTCAATGGTACATGGTCGTGTGAAA
GGCCATGTGGTTAGCTGTGGA
Found at i:18570526 original size:44 final size:44
Alignment explanation
Indices: 18570457--18570548 Score: 130
Period size: 44 Copynumber: 2.1 Consensus size: 44
18570447 CCGAAGTAAC
* *
18570457 AGTAGCAGTACGACACACATGGTGCCTCATCGACTCAAAGTCGA
1 AGTAACAGTACGACACACATAGTGCCTCATCGACTCAAAGTCGA
** * *
18570501 AGTAACAGTACGACACTTATAGTGCCTCATTGACTCAAGGTCGA
1 AGTAACAGTACGACACACATAGTGCCTCATCGACTCAAAGTCGA
18570545 AGTA
1 AGTA
18570549 TCCCTGAACA
Statistics
Matches: 42, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
44 42 1.00
ACGTcount: A:0.33, C:0.24, G:0.22, T:0.22
Consensus pattern (44 bp):
AGTAACAGTACGACACACATAGTGCCTCATCGACTCAAAGTCGA
Found at i:18571361 original size:16 final size:17
Alignment explanation
Indices: 18571330--18571362 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
18571320 AATTTCTATC
18571330 CAATTTATACCCTAATT
1 CAATTTATACCCTAATT
*
18571347 CAATTTA-ATCCTAATT
1 CAATTTATACCCTAATT
18571363 AACTAATTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.36, C:0.21, G:0.00, T:0.42
Consensus pattern (17 bp):
CAATTTATACCCTAATT
Found at i:18571750 original size:11 final size:11
Alignment explanation
Indices: 18571730--18571764 Score: 52
Period size: 12 Copynumber: 3.0 Consensus size: 11
18571720 AAAACCCTAG
18571730 TTTTTCCTTTTC
1 TTTTT-CTTTTC
18571742 TTTTTCTTTTC
1 TTTTTCTTTTC
18571753 TTCTTTCTTTTC
1 TT-TTTCTTTTC
18571765 CCTCTGTTTC
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
11 8 0.36
12 14 0.64
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (11 bp):
TTTTTCTTTTC
Found at i:18572190 original size:21 final size:21
Alignment explanation
Indices: 18572164--18572205 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
18572154 TTTATAATTT
*
18572164 AATATCAATTAAATAATAATA
1 AATATCAATTAAATAAAAATA
* *
18572185 AATATCTATTTAATAAAAATA
1 AATATCAATTAAATAAAAATA
18572206 TATGTATTAC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.60, C:0.05, G:0.00, T:0.36
Consensus pattern (21 bp):
AATATCAATTAAATAAAAATA
Found at i:18573983 original size:15 final size:15
Alignment explanation
Indices: 18573963--18573992 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
18573953 AAATGGTTTC
18573963 ATGGGATTTAGCCAA
1 ATGGGATTTAGCCAA
18573978 ATGGGATTTAGCCAA
1 ATGGGATTTAGCCAA
18573993 TTGTCTTGGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.33, C:0.13, G:0.27, T:0.27
Consensus pattern (15 bp):
ATGGGATTTAGCCAA
Found at i:18576934 original size:22 final size:22
Alignment explanation
Indices: 18576909--18576972 Score: 74
Period size: 22 Copynumber: 2.9 Consensus size: 22
18576899 ATCTACAAAC
*
18576909 ACTGGTGGTTCATCCACAACTT
1 ACTGGTGGTTCATCAACAACTT
** * * *
18576931 ACTGGCAGTTTATCTACAAATT
1 ACTGGTGGTTCATCAACAACTT
18576953 ACTGGTGGTTCATCAACAAC
1 ACTGGTGGTTCATCAACAAC
18576973 CCCAGTGTGT
Statistics
Matches: 32, Mismatches: 10, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
22 32 1.00
ACGTcount: A:0.28, C:0.23, G:0.17, T:0.31
Consensus pattern (22 bp):
ACTGGTGGTTCATCAACAACTT
Found at i:18578427 original size:88 final size:88
Alignment explanation
Indices: 18578239--18578416 Score: 320
Period size: 88 Copynumber: 2.0 Consensus size: 88
18578229 ACATGCCATT
* *
18578239 GAACAAAATAAGAGTATCTATATACCAAAACTAGACAAGATGATAGTGTGTTGATTCTACAATCG
1 GAACAAAATAAGAGTATCTATATACCAAAACTAGACAAGATGATAGTGTGTTGATTCTACAACCA
18578304 TCTCCCAATCTTCACGAGTCCAC
66 TCTCCCAATCTTCACGAGTCCAC
* *
18578327 GAACAAAATAAGAGTATCTATATACCAAAGCTAGACAAGATGATAGTGTGTTGATTCTTCAACCA
1 GAACAAAATAAGAGTATCTATATACCAAAACTAGACAAGATGATAGTGTGTTGATTCTACAACCA
18578392 TCTCCCAATCTTCACGAGTCCAC
66 TCTCCCAATCTTCACGAGTCCAC
18578415 GA
1 GA
18578417 GCTCTGTAAG
Statistics
Matches: 86, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
88 86 1.00
ACGTcount: A:0.37, C:0.22, G:0.15, T:0.26
Consensus pattern (88 bp):
GAACAAAATAAGAGTATCTATATACCAAAACTAGACAAGATGATAGTGTGTTGATTCTACAACCA
TCTCCCAATCTTCACGAGTCCAC
Found at i:18582692 original size:56 final size:56
Alignment explanation
Indices: 18582618--18582759 Score: 160
Period size: 56 Copynumber: 2.5 Consensus size: 56
18582608 TAAGTAAGTC
* *
18582618 TTTGTGGCTATCTCTATTAAAAGAAGCCTTTATGACGATCTCAGTTATAGGAATCA
1 TTTGTGGCTATCTCTATTAAAAGAAGCCTTTATGACGATCTCAGTTAAAGGAAGCA
* * * * * * *
18582674 TTTGTGGCAATATCTATTAAATA-AAGCCTTTGTGGCTATCTCTGTTAAAGGAAGCC
1 TTTGTGGCTATCTCTATTAAA-AGAAGCCTTTATGACGATCTCAGTTAAAGGAAGCA
* *
18582730 TTTGTGACTATCTCTGTTAAAAGGAAGCCT
1 TTTGTGGCTATCTCTATTAAAA-GAAGCCT
18582760 CTGTGGTGAT
Statistics
Matches: 70, Mismatches: 13, Indels: 5
0.80 0.15 0.06
Matches are distributed among these distances:
55 1 0.01
56 62 0.89
57 7 0.10
ACGTcount: A:0.29, C:0.16, G:0.19, T:0.36
Consensus pattern (56 bp):
TTTGTGGCTATCTCTATTAAAAGAAGCCTTTATGACGATCTCAGTTAAAGGAAGCA
Found at i:18582764 original size:29 final size:28
Alignment explanation
Indices: 18582617--18582793 Score: 130
Period size: 28 Copynumber: 6.2 Consensus size: 28
18582607 ATAAGTAAGT
*
18582617 CTTTGTGGCTATCTCTATTAAAA-GAAGC
1 CTTTGT-GCTATCTCTGTTAAAAGGAAGC
* * * * *
18582645 CTTTATGACGATCTCAGTT-ATAGGAATC
1 CTTTGTG-CTATCTCTGTTAAAAGGAAGC
* * * *
18582673 ATTTGTGGCAATATCTATTAAATA--AAGC
1 CTTTGT-GCTATCTCTGTTAAA-AGGAAGC
18582701 CTTTGTGGCTATCTCTGTT-AAAGGAAGC
1 CTTTGT-GCTATCTCTGTTAAAAGGAAGC
18582729 CTTTGTGACTATCTCTGTTAAAAGGAAGC
1 CTTTGTG-CTATCTCTGTTAAAAGGAAGC
* *
18582758 CTCTGTGGTGATCTCTGTTAAAAAGGAAGC
1 CTTTGTGCT-ATCTCTGTT-AAAAGGAAGC
*
18582788 CCTTGT
1 CTTTGT
18582794 TACAATCTTT
Statistics
Matches: 116, Mismatches: 22, Indels: 20
0.73 0.14 0.13
Matches are distributed among these distances:
26 1 0.01
27 6 0.05
28 68 0.59
29 26 0.22
30 15 0.13
ACGTcount: A:0.28, C:0.17, G:0.20, T:0.35
Consensus pattern (28 bp):
CTTTGTGCTATCTCTGTTAAAAGGAAGC
Found at i:18589015 original size:26 final size:26
Alignment explanation
Indices: 18588984--18589080 Score: 167
Period size: 26 Copynumber: 3.7 Consensus size: 26
18588974 TGAAATGCCC
18588984 ATCATGGAACATTTACCTAAACCATT
1 ATCATGGAACATTTACCTAAACCATT
*
18589010 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAAACCATT
* *
18589036 ATCATGGAATATTTACCTAATCCATT
1 ATCATGGAACATTTACCTAAACCATT
18589062 ATCATGGAACATTTACCTA
1 ATCATGGAACATTTACCTA
18589081 TTTTAAGTGC
Statistics
Matches: 67, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 67 1.00
ACGTcount: A:0.36, C:0.23, G:0.08, T:0.33
Consensus pattern (26 bp):
ATCATGGAACATTTACCTAAACCATT
Found at i:18594687 original size:29 final size:28
Alignment explanation
Indices: 18594594--18594764 Score: 130
Period size: 29 Copynumber: 6.4 Consensus size: 28
18594584 TATATTAAGT
* *
18594594 CCGCACACTCAGTGCTATATAATC-AAC
1 CCGCACACTTAGTGCTATACAATCAAAC
* *
18594621 TCGCACACTTAGTGCTATATAATCAAAC
1 CCGCACACTTAGTGCTATACAATCAAAC
* * *
18594649 TCGCACACTTAGTGCTGTACAATTTAAAC
1 CCGCACACTTAGTGCTATACAA-TCAAAC
* *
18594678 CCGCACACTTAGCGC-ATATAATCAAAC
1 CCGCACACTTAGTGCTATACAATCAAAC
*
18594705 TCG--CAC--A---CTAT--AATCAAAC
1 CCGCACACTTAGTGCTATACAATCAAAC
* * *
18594724 TCGCACACTTAGTGCTGTACAATTTAAAC
1 CCGCACACTTAGTGCTATACAA-TCAAAC
18594753 CCGCACACTTAG
1 CCGCACACTTAG
18594765 CGCCAATCTC
Statistics
Matches: 117, Mismatches: 14, Indels: 24
0.75 0.09 0.15
Matches are distributed among these distances:
19 11 0.09
20 1 0.01
21 5 0.04
23 2 0.02
25 3 0.03
26 3 0.03
27 29 0.25
28 29 0.25
29 34 0.29
ACGTcount: A:0.34, C:0.29, G:0.12, T:0.25
Consensus pattern (28 bp):
CCGCACACTTAGTGCTATACAATCAAAC
Found at i:18594712 original size:27 final size:28
Alignment explanation
Indices: 18594595--18594713 Score: 161
Period size: 27 Copynumber: 4.3 Consensus size: 28
18594585 ATATTAAGTC
*
18594595 CGCACACTCAGTGCTATATAATC-AACT
1 CGCACACTTAGTGCTATATAATCAAACT
18594622 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
* * * *
18594650 CGCACACTTAGTGCTGTACAATTTAAACC
1 CGCACACTTAGTGCTATATAA-TCAAACT
*
18594679 CGCACACTTAGCGC-ATATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
18594706 CGCACACT
1 CGCACACT
18594714 ATAATCAAAC
Statistics
Matches: 80, Mismatches: 10, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
27 35 0.44
28 27 0.34
29 18 0.22
ACGTcount: A:0.34, C:0.29, G:0.12, T:0.25
Consensus pattern (28 bp):
CGCACACTTAGTGCTATATAATCAAACT
Found at i:18594718 original size:19 final size:19
Alignment explanation
Indices: 18594694--18594732 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
18594684 ACTTAGCGCA
18594694 TATAATCAAACTCGCACAC
1 TATAATCAAACTCGCACAC
18594713 TATAATCAAACTCGCACAC
1 TATAATCAAACTCGCACAC
18594732 T
1 T
18594733 TAGTGCTGTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.41, C:0.31, G:0.05, T:0.23
Consensus pattern (19 bp):
TATAATCAAACTCGCACAC
Found at i:18598811 original size:43 final size:43
Alignment explanation
Indices: 18598750--18598832 Score: 166
Period size: 43 Copynumber: 1.9 Consensus size: 43
18598740 AATAGATTGG
18598750 ATACAAGTGACATGTCACTAGGATGGTTGAGCATCCGAACAGA
1 ATACAAGTGACATGTCACTAGGATGGTTGAGCATCCGAACAGA
18598793 ATACAAGTGACATGTCACTAGGATGGTTGAGCATCCGAAC
1 ATACAAGTGACATGTCACTAGGATGGTTGAGCATCCGAAC
18598833 TCGTTGAGTT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 40 1.00
ACGTcount: A:0.34, C:0.19, G:0.25, T:0.22
Consensus pattern (43 bp):
ATACAAGTGACATGTCACTAGGATGGTTGAGCATCCGAACAGA
Found at i:18613962 original size:30 final size:30
Alignment explanation
Indices: 18613928--18613987 Score: 102
Period size: 30 Copynumber: 2.0 Consensus size: 30
18613918 TTGAATACAA
18613928 AGCAAAGAATAAAAATTAAAGCGTTTCTTC
1 AGCAAAGAATAAAAATTAAAGCGTTTCTTC
* *
18613958 AGCAAAGAATAACAATTAAAGTGTTTCTTC
1 AGCAAAGAATAAAAATTAAAGCGTTTCTTC
18613988 TTTGGAATCT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.45, C:0.13, G:0.13, T:0.28
Consensus pattern (30 bp):
AGCAAAGAATAAAAATTAAAGCGTTTCTTC
Found at i:18615407 original size:18 final size:19
Alignment explanation
Indices: 18615366--18615408 Score: 52
Period size: 18 Copynumber: 2.3 Consensus size: 19
18615356 ACAATACAAC
* *
18615366 TATGACATTAATCAATGAT
1 TATGACAATAATCAATAAT
*
18615385 GATGACAAT-ATCAATAAT
1 TATGACAATAATCAATAAT
18615403 TATGAC
1 TATGAC
18615409 GTGATTAATA
Statistics
Matches: 20, Mismatches: 4, Indels: 1
0.80 0.16 0.04
Matches are distributed among these distances:
18 13 0.65
19 7 0.35
ACGTcount: A:0.44, C:0.12, G:0.12, T:0.33
Consensus pattern (19 bp):
TATGACAATAATCAATAAT
Found at i:18646039 original size:43 final size:44
Alignment explanation
Indices: 18645949--18646070 Score: 156
Period size: 43 Copynumber: 2.8 Consensus size: 44
18645939 GCAAAAATTT
* * *
18645949 GATGCATTGGAAGAATCTTGAAACAAACTTTGTAATTTAAATGA
1 GATGCATTGGAACAAACTTGGAACAAACTTTGTAATTTAAATGA
* * *
18645993 GATGCATTGTACCAAACTTGGAACAAA-TTTGTAATTTAAATTA
1 GATGCATTGGAACAAACTTGGAACAAACTTTGTAATTTAAATGA
* * *
18646036 GATGCATTGGAATAAACTTTGAACAAACTCTGTAA
1 GATGCATTGGAACAAACTTGGAACAAACTTTGTAA
18646071 AATATATATC
Statistics
Matches: 66, Mismatches: 11, Indels: 2
0.84 0.14 0.03
Matches are distributed among these distances:
43 38 0.58
44 28 0.42
ACGTcount: A:0.40, C:0.11, G:0.16, T:0.32
Consensus pattern (44 bp):
GATGCATTGGAACAAACTTGGAACAAACTTTGTAATTTAAATGA
Found at i:18650807 original size:30 final size:30
Alignment explanation
Indices: 18650771--18650839 Score: 120
Period size: 30 Copynumber: 2.3 Consensus size: 30
18650761 ACTTTTCTCA
* *
18650771 ACTAGCCACTCCTTTTCCACCACCAACTCC
1 ACTAGCCACACCTTTTCCACCACCAACTAC
18650801 ACTAGCCACACCTTTTCCACCACCAACTAC
1 ACTAGCCACACCTTTTCCACCACCAACTAC
18650831 ACTAGCCAC
1 ACTAGCCAC
18650840 NNNNNNNNNN
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
30 37 1.00
ACGTcount: A:0.28, C:0.48, G:0.04, T:0.20
Consensus pattern (30 bp):
ACTAGCCACACCTTTTCCACCACCAACTAC
Found at i:18659970 original size:75 final size:75
Alignment explanation
Indices: 18659847--18660189 Score: 417
Period size: 72 Copynumber: 4.5 Consensus size: 75
18659837 TTTTGTTTTC
*
18659847 AAAATCAACTCATATTGCTAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTTCT
1 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTTCT
*
18659912 ATTGTT-AAAA
66 GTT-TTAAAAA
**
18659922 AAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTTCT
1 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTTCT
*
18659987 GTTTT---CA
66 GTTTTAAAAA
* * * ** * * *
18659994 AAATTTAACTTATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTATTTTCAATTTCT
1 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTTCT
18660059 GTTTTCAAAAAAAA
66 GTTTT----AAAAA
* * *
18660073 AAAATCAACTTATATTGCGAGAGGTGAGTTGAGCCTC-GGTTCACATGCTGAGGTATTTTCAATT
1 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGG---ACACGCTGAGGTAATTTCAATT
18660137 TCTGTTTTTAAAAA
63 TCTG-TTTTAAAAA
*
18660151 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCTTCAG
1 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAG
18660190 ATTACACACT
Statistics
Matches: 235, Mismatches: 21, Indels: 20
0.85 0.08 0.07
Matches are distributed among these distances:
72 65 0.28
74 2 0.01
75 64 0.27
78 41 0.17
79 35 0.15
81 24 0.10
82 4 0.02
ACGTcount: A:0.33, C:0.15, G:0.20, T:0.32
Consensus pattern (75 bp):
AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTTCT
GTTTTAAAAA
Found at i:18660424 original size:72 final size:73
Alignment explanation
Indices: 18660343--18660484 Score: 232
Period size: 72 Copynumber: 2.0 Consensus size: 73
18660333 TCAAAATTAG
* * *
18660343 CTCATATTGCAAGAGGTGAGTTGAGCCTCGGGGCACGCTGAGGTATTTTCAATTTTTG-TGTTTT
1 CTCATATTGCAAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAATTTTCGTTGTTTT
18660407 AATTTCAA
66 AATTTCAA
* *
18660415 CTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAATTTTCGTTTTTTT
1 CTCATATTGCAAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAATTTTCGTTGTTTT
18660480 AATTT
66 AATTT
18660485 ATGTTTCAAA
Statistics
Matches: 64, Mismatches: 5, Indels: 1
0.91 0.07 0.01
Matches are distributed among these distances:
72 54 0.84
73 10 0.16
ACGTcount: A:0.22, C:0.15, G:0.24, T:0.39
Consensus pattern (73 bp):
CTCATATTGCAAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAATTTTCGTTGTTTT
AATTTCAA
Found at i:18660663 original size:73 final size:71
Alignment explanation
Indices: 18660476--18660675 Score: 247
Period size: 73 Copynumber: 2.8 Consensus size: 71
18660466 ATTTTCGTTT
** * * *
18660476 TTTTAATTTATGTTTCAAAAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCAAGACGCT
1 TTTTAATTTATG-TTCATCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAACACACT
18660541 GAGGTAA
65 GAGGTAA
* * **
18660548 TTTCAATTTTTGTTTGTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACAC
1 TTTTAATTTATGTTCATCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCA--ACACAC
**
18660613 TGAGGTGG
64 TGAGGTAA
* * *
18660621 TTTTAATTTATGTTCATCAAAAATTAGCTCATATTGCAAGAGGTGAGTTGAGCCT
1 TTTTAATTTATGTTCATCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCT
18660676 TGGCTCACAC
Statistics
Matches: 108, Mismatches: 18, Indels: 3
0.84 0.14 0.02
Matches are distributed among these distances:
71 40 0.37
72 10 0.09
73 58 0.54
ACGTcount: A:0.32, C:0.14, G:0.21, T:0.33
Consensus pattern (71 bp):
TTTTAATTTATGTTCATCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAACACACTG
AGGTAA
Found at i:18660685 original size:73 final size:73
Alignment explanation
Indices: 18660476--18660704 Score: 225
Period size: 73 Copynumber: 3.1 Consensus size: 73
18660466 ATTTTCGTTT
** * *
18660476 TTTTAATTTATGTTTCAAAAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCC-T--CAAGAC
1 TTTTAATTTATG-TTCATCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTGGC-ACAC
*
18660538 GCTGAGGTAA
64 ACTGAGGTAA
* * ** *
18660548 TTTCAATTTTTGTTTGTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGG-ACACA
1 TTTTAATTTATGTTCATCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCT-TGGCACACA
**
18660612 CTGAGGTGG
65 CTGAGGTAA
* * *
18660621 TTTTAATTTATGTTCATCAAAAATTAGCTCATATTGCAAGAGGTGAGTTGAGCCTTGGCTCACAC
1 TTTTAATTTATGTTCATCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTGG--CACAC
*
18660686 GCTGAGGT-A
64 ACTGAGGTAA
18660695 TTTTCAATTT
1 TTTT-AATTT
18660705 CTGGTTTTCA
Statistics
Matches: 127, Mismatches: 22, Indels: 13
0.78 0.14 0.08
Matches are distributed among these distances:
71 37 0.29
72 12 0.09
73 58 0.46
74 4 0.03
75 16 0.13
ACGTcount: A:0.30, C:0.15, G:0.21, T:0.34
Consensus pattern (73 bp):
TTTTAATTTATGTTCATCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTGGCACACAC
TGAGGTAA
Found at i:18660714 original size:14 final size:14
Alignment explanation
Indices: 18660695--18660729 Score: 61
Period size: 14 Copynumber: 2.5 Consensus size: 14
18660685 CGCTGAGGTA
18660695 TTTTCAATTTCTGG
1 TTTTCAATTTCTGG
*
18660709 TTTTCAATTTCTGT
1 TTTTCAATTTCTGG
18660723 TTTTCAA
1 TTTTCAA
18660730 AAATCGACTC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.17, C:0.14, G:0.09, T:0.60
Consensus pattern (14 bp):
TTTTCAATTTCTGG
Found at i:18660764 original size:162 final size:162
Alignment explanation
Indices: 18660548--18661045 Score: 617
Period size: 162 Copynumber: 3.0 Consensus size: 162
18660538 GCTGAGGTAA
* * *
18660548 TTTCAATTTTTGTTTGTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACAC
1 TTTCAATTTCTGTTTATCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGC
** * * * * *
18660613 TGAGGTGGTTTTAATTTATGTTCATCAAAAATTAGCTCATATTGCAAGAGGTGAGTTGAGCCTTG
66 TGAGGTAATTTCAATTTATGTTAATCAAAAATTAACTCATATTGCGAGAGGTGAGTTGAGCCTAG
18660678 GCTCACACGCTGAGGTATTTTCAATTTCTGGT
131 GCTCACACGCTGAGGTATTTTCAATTTCTGGT
* * *
18660710 TTTCAATTTCTGTTTTTCAAAAATCGACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGACACGC
1 TTTCAATTTCTGTTTATCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGC
* ** *
18660775 TGAGGTAATTTCAATTTCTGTTTGTCAAAAATTAACTCATATTGCGAGAGGTGAGTTGAGCCTCG
66 TGAGGTAATTTCAATTTATGTTAATCAAAAATTAACTCATATTGCGAGAGGTGAGTTGAGCCTAG
* *
18660840 GCTCACATGCTGAGGTCTTTTCAATTTCT-GT
131 GCTCACACGCTGAGGTATTTTCAATTTCTGGT
** *
18660871 TCTTCAATTTCTGTTCGTAAAAAAAAAATCAACTCATATTGCTAGAGGTGAGTTGAGCCTCAGGA
1 T-TTCAATTTCTGTT--T--ATCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGA
* * ** *
18660936 CACGCTGAGGTAATATCAATTTCTGTTGTTAAAAAAAAATCAACTCATATTGCGAGAGGTGAGTT
61 CACGCTGAGGTAATTTCAA-TT-T-ATGTTAATCAAAAATTAACTCATATTGCGAGAGGTGAGTT
* *
18661001 GAGCCTCAGG---ACACGCTGAGGTATTTTTAAATTTCTGTT
123 GAGCCT-AGGCTCACACGCTGAGGTA-TTTTCAATTTCTGGT
18661040 TTTCAA
1 TTTCAA
18661046 AAATCAACTC
Statistics
Matches: 291, Mismatches: 34, Indels: 16
0.85 0.10 0.05
Matches are distributed among these distances:
161 3 0.01
162 156 0.54
164 1 0.00
166 57 0.20
167 13 0.04
168 17 0.06
169 42 0.14
170 2 0.01
ACGTcount: A:0.28, C:0.17, G:0.21, T:0.34
Consensus pattern (162 bp):
TTTCAATTTCTGTTTATCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGC
TGAGGTAATTTCAATTTATGTTAATCAAAAATTAACTCATATTGCGAGAGGTGAGTTGAGCCTAG
GCTCACACGCTGAGGTATTTTCAATTTCTGGT
Found at i:18660814 original size:235 final size:232
Alignment explanation
Indices: 18660335--18661080 Score: 661
Period size: 235 Copynumber: 3.2 Consensus size: 232
18660325 CTACTTTTTC
* * * * * *
18660335 AAAATTAGCTCATATTGCAAGAGGTGAGTTGAGCCTCGGGGCACGCTGAGGTATTTTCAATTTTT
1 AAAATTAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACACTGAGGTATTTTCAATTTAT
** * *
18660400 GTGTTTTAATTTCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTC
66 GTGTTAAAAATTCAACTCATATTGCAAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTC
* *
18660465 AATTTTCGTTTTTTTAATTTATGTTTCAAAAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGC
131 AATTTTCGTGTTTTCAATTTATGTTTCAAAAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGC
* *
18660530 CTCAAGACGCTGAGGTAATTTCAATTTTTGTTTGTCA
196 CTCAACACGCTGAGGTAATTTCAATTTCTGTTTGTCA
* *
18660567 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACACTGAGGTGGTTTT-AATTTA
1 AAAATTAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACACTGAGGT-ATTTTCAATTTA
* *
18660631 TGT-TCATCAAAAATT-AGCTCATATTGCAAGAGGTGAGTTGAGCCT-TGGCTCACACGCTGAGG
65 TGTGT--T-AAAAATTCAACTCATATTGCAAGAGGTGAGTTGAGCCTCAGG---ACACGCTGAGG
* *** * *
18660693 TATTTTCAA-TTTC-TGGTTTTCAATTTCTGTTT-TTCAAAAATCGACTCATATTGCGAGAGGTG
124 TATTTTCAATTTTCGT-GTTTTCAATTTATGTTTCAAAAAAAATCAACTCATATTGCGAGAAGTG
*
18660755 AGTTGAGCCTCGGGACACGCTGAGGTAATTTCAATTTCTGTTTGTCA
188 AGTTGAGCCTC--AACACGCTGAGGTAATTTCAATTTCTGTTTGTCA
*
18660802 AAAATTAACTCATATTGCGAGAGGTGAGTTGAGCCTC-GGCTCACATGCTGAGGTCTTTTCAATT
1 AAAATTAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGG-ACACA--CTGAGG-----T--A--
* * * *
18660866 TCTGTTCTTCAATTTCTGTTCGTAAAAAAAAAATCAACTCATATTGCTAGAGGTGAGTTGAGCCT
54 ----TT-TTCAATTTATG-T-GT---TAAAAATTCAACTCATATTGCAAGAGGTGAGTTGAGCCT
* * *
18660931 CAGGACACGCTGAGGTAATATCAA-TTTC-TG---------T-TG-TTAAAAAAAAATCAACTCA
109 CAGGACACGCTGAGGTATTTTCAATTTTCGTGTTTTCAATTTATGTTTCAAAAAAAATCAACTCA
* * * *
18660983 TATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTTAAATTTCTGTTTTTCA
174 TATTGCGAGAAGTGAGTTGAGCCTCA--ACACGCTGAGGTA-ATTTCAATTTCTGTTTGTCA
* * * *
18661045 AAAATCAACTCATATTGAGAGATGTGAATTGAGCCT
1 AAAATTAACTCATATTGCGAGAGGTGAGTTGAGCCT
18661081 TGGGTTCACA
Statistics
Matches: 427, Mismatches: 50, Indels: 63
0.79 0.09 0.12
Matches are distributed among these distances:
231 1 0.00
232 56 0.13
233 70 0.16
234 24 0.06
235 91 0.21
237 6 0.01
241 2 0.00
242 53 0.12
243 50 0.12
249 2 0.00
250 2 0.00
251 7 0.02
252 2 0.00
253 23 0.05
254 7 0.02
255 29 0.07
256 2 0.00
ACGTcount: A:0.28, C:0.16, G:0.22, T:0.34
Consensus pattern (232 bp):
AAAATTAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACACTGAGGTATTTTCAATTTAT
GTGTTAAAAATTCAACTCATATTGCAAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTC
AATTTTCGTGTTTTCAATTTATGTTTCAAAAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGC
CTCAACACGCTGAGGTAATTTCAATTTCTGTTTGTCA
Found at i:18660829 original size:73 final size:74
Alignment explanation
Indices: 18660710--18660871 Score: 245
Period size: 73 Copynumber: 2.2 Consensus size: 74
18660700 AATTTCTGGT
* * *
18660710 TTTCAATTTCTGTTTTTCAAAAATCGACTCATATTGCGAGAGGTGAGTTGAGCCTCGG-GACACG
1 TTTCAATTTCTGTTTGTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGCCACACG
18660774 CTGAGGTAA
66 CTGAGGTAA
* *
18660783 TTTCAATTTCTGTTTGTCAAAAATTAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGCTCACAT
1 TTTCAATTTCTGTTTGTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGC-CACAC
**
18660848 GCTGAGGTCT
65 GCTGAGGTAA
18660858 TTTCAATTTCTGTT
1 TTTCAATTTCTGTT
18660872 CTTCAATTTC
Statistics
Matches: 80, Mismatches: 7, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
73 55 0.69
75 25 0.31
ACGTcount: A:0.24, C:0.18, G:0.22, T:0.36
Consensus pattern (74 bp):
TTTCAATTTCTGTTTGTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGCCACACG
CTGAGGTAA
Found at i:18660878 original size:14 final size:14
Alignment explanation
Indices: 18660859--18660886 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
18660849 CTGAGGTCTT
18660859 TTCAATTTCTGTTC
1 TTCAATTTCTGTTC
18660873 TTCAATTTCTGTTC
1 TTCAATTTCTGTTC
18660887 GTAAAAAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.14, C:0.21, G:0.07, T:0.57
Consensus pattern (14 bp):
TTCAATTTCTGTTC
Found at i:18661001 original size:76 final size:77
Alignment explanation
Indices: 18660874--18661080 Score: 287
Period size: 76 Copynumber: 2.7 Consensus size: 77
18660864 TTTCTGTTCT
* *
18660874 TCAATTTCTGTTCGTAAAAAAAAAATCAACTCATATTGCTAGAGGTGAGTTGAGCCTCAGGACAC
1 TCAATTTCTGTT-GTTAAAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACAC
18660939 GCTGAGGTA-ATA
65 GCTGAGGTATATA
18660951 TCAATTTCTGTTGTTAAAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACG
1 TCAATTTCTGTTGTTAAAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACG
* *
18661016 CTGAGGTATTTT
66 CTGAGGTATATA
* ** * * *
18661028 TAAATTTCTGTT-TT--TCAAAAATCAACTCATATTGAGAGATGTGAATTGAGCCT
1 TCAATTTCTGTTGTTAAAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCT
18661081 TGGGTTCACA
Statistics
Matches: 119, Mismatches: 10, Indels: 5
0.89 0.07 0.04
Matches are distributed among these distances:
74 34 0.29
76 61 0.51
77 24 0.20
ACGTcount: A:0.33, C:0.15, G:0.20, T:0.31
Consensus pattern (77 bp):
TCAATTTCTGTTGTTAAAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACG
CTGAGGTATATA
Found at i:18662588 original size:61 final size:61
Alignment explanation
Indices: 18662505--18662985 Score: 912
Period size: 61 Copynumber: 7.9 Consensus size: 61
18662495 ACTTTTCTCA
* *
18662505 ACTAGCCACTC-CTTTTCCACCACCAACTCCACTAGCCACACCTTTTCCACCACCAACTCC
1 ACTAGCCACTCTTTTTTCCACCACCAACTCCACTAGCCACACCTTGTCCACCACCAACTCC
18662565 ACTAGCCACTCTTTTTTCCACCACCAACTCCACTAGCCACACCTTGTCCACCACCAACTCC
1 ACTAGCCACTCTTTTTTCCACCACCAACTCCACTAGCCACACCTTGTCCACCACCAACTCC
18662626 ACTAGCCACTCTTTTTTCCACCACCAACTCCACTAGCCACACCTTGTCCACCACCAACTCC
1 ACTAGCCACTCTTTTTTCCACCACCAACTCCACTAGCCACACCTTGTCCACCACCAACTCC
18662687 ACTAGCCACTCTTTTTTCCACCACCAACTCCACTAGCCACACCTTGTCCACCACCAACTCC
1 ACTAGCCACTCTTTTTTCCACCACCAACTCCACTAGCCACACCTTGTCCACCACCAACTCC
18662748 ACTAGCCACTCTTTTTTCCACCACCAACTCCACTAGCCACACCTTGTCCACCACCAACTCC
1 ACTAGCCACTCTTTTTTCCACCACCAACTCCACTAGCCACACCTTGTCCACCACCAACTCC
18662809 ACTAGCCACTCTTTTTTCCACCACCAACTCCACTAGCCACACCTTGTCCACCACCAACTCC
1 ACTAGCCACTCTTTTTTCCACCACCAACTCCACTAGCCACACCTTGTCCACCACCAACTCC
18662870 ACTAGCCACTCTTTTTTCCACCACCAACTCCACTAGCCACACCTTGTCCACCACCAACTCC
1 ACTAGCCACTCTTTTTTCCACCACCAACTCCACTAGCCACACCTTGTCCACCACCAACTCC
* *
18662931 ACTAGCCACTC-TTTTTCCACCACTAACTCCACTAGCCACACCTTCTCCACCACCA
1 ACTAGCCACTCTTTTTTCCACCACCAACTCCACTAGCCACACCTTGTCCACCACCA
18662986 CTTGTACCTA
Statistics
Matches: 416, Mismatches: 4, Indels: 2
0.99 0.01 0.00
Matches are distributed among these distances:
60 53 0.13
61 363 0.87
ACGTcount: A:0.25, C:0.48, G:0.05, T:0.23
Consensus pattern (61 bp):
ACTAGCCACTCTTTTTTCCACCACCAACTCCACTAGCCACACCTTGTCCACCACCAACTCC
Found at i:18664205 original size:320 final size:320
Alignment explanation
Indices: 18663623--18664262 Score: 1271
Period size: 320 Copynumber: 2.0 Consensus size: 320
18663613 CACTTAAATG
18663623 TCAAATTGAATTCGTATTTTTGAAAATCAAGACAACATGTGTTTAATAAGATACCAATTTTGGGC
1 TCAAATTGAATTCGTATTTTTGAAAATCAAGACAACATGTGTTTAATAAGATACCAATTTTGGGC
18663688 GTCGCGAGGGTGCCAATACCTTCCTCGTGCGTAACCGACTCCCGAACCCTAAATTTTCTCTGGAT
66 GTCGCGAGGGTGCCAATACCTTCCTCGTGCGTAACCGACTCCCGAACCCTAAATTTTCTCTGGAT
18663753 TTTAACGTAGACCTAAACTCAGCCTTTTATTTGTTTTAATAAAAGATCTAATAGGTGTCCGATCA
131 TTTAACGTAGACCTAAACTCAGCCTTTTATTTGTTTTAATAAAAGATCTAATAGGTGTCCGATCA
18663818 CACCTAGGAAAAAGGATCGGTGGCGACTCCCTATTTATTTCAAAAATCAAACATCAAATTTCAAA
196 CACCTAGGAAAAAGGATCGGTGGCGACTCCCTATTTATTTCAAAAATCAAACATCAAATTTCAAA
18663883 AAATTTTCAATAAATCGCCACAATTAGCGACCAAGCTAAGCTAAAATTTTTACGTCGCTA
261 AAATTTTCAATAAATCGCCACAATTAGCGACCAAGCTAAGCTAAAATTTTTACGTCGCTA
18663943 TCAAATTGAATTCGTATTTTTGAAAATCAAGACAACATGTGTTTAATAAGATACCAATTTTGGGC
1 TCAAATTGAATTCGTATTTTTGAAAATCAAGACAACATGTGTTTAATAAGATACCAATTTTGGGC
18664008 GTCGCGAGGGTGCCAATACCTTCCTCGTGCGTAACCGACTCCCGAACCCTAAATTTTCTCTGGAT
66 GTCGCGAGGGTGCCAATACCTTCCTCGTGCGTAACCGACTCCCGAACCCTAAATTTTCTCTGGAT
18664073 TTTAACGTAGACCTAAACTCAGCCTTTTATTTGTTTTAATAAAAGATCTAATAGGTGTCCGATCA
131 TTTAACGTAGACCTAAACTCAGCCTTTTATTTGTTTTAATAAAAGATCTAATAGGTGTCCGATCA
*
18664138 CACCTAGGAAAAAGGATCGGTGGCGACTCCCTATTTATTTCAAAAATCAAACGTCAAATTTCAAA
196 CACCTAGGAAAAAGGATCGGTGGCGACTCCCTATTTATTTCAAAAATCAAACATCAAATTTCAAA
18664203 AAATTTTCAATAAATCGCCACAATTAGCGACCAAGCTAAGCTAAAATTTTTACGTCGCTA
261 AAATTTTCAATAAATCGCCACAATTAGCGACCAAGCTAAGCTAAAATTTTTACGTCGCTA
18664263 CAATGACAGT
Statistics
Matches: 319, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
320 319 1.00
ACGTcount: A:0.33, C:0.21, G:0.15, T:0.30
Consensus pattern (320 bp):
TCAAATTGAATTCGTATTTTTGAAAATCAAGACAACATGTGTTTAATAAGATACCAATTTTGGGC
GTCGCGAGGGTGCCAATACCTTCCTCGTGCGTAACCGACTCCCGAACCCTAAATTTTCTCTGGAT
TTTAACGTAGACCTAAACTCAGCCTTTTATTTGTTTTAATAAAAGATCTAATAGGTGTCCGATCA
CACCTAGGAAAAAGGATCGGTGGCGACTCCCTATTTATTTCAAAAATCAAACATCAAATTTCAAA
AAATTTTCAATAAATCGCCACAATTAGCGACCAAGCTAAGCTAAAATTTTTACGTCGCTA
Found at i:18666421 original size:20 final size:20
Alignment explanation
Indices: 18666396--18666435 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
18666386 AGCAACAATA
18666396 TTTAATGTGGGAGTGGTTTG
1 TTTAATGTGGGAGTGGTTTG
18666416 TTTAATGTGGGAGTGGTTTG
1 TTTAATGTGGGAGTGGTTTG
18666436 GTTGATGTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.15, C:0.00, G:0.40, T:0.45
Consensus pattern (20 bp):
TTTAATGTGGGAGTGGTTTG
Found at i:18666443 original size:20 final size:20
Alignment explanation
Indices: 18666397--18666443 Score: 76
Period size: 20 Copynumber: 2.4 Consensus size: 20
18666387 GCAACAATAT
*
18666397 TTAATGTGGGAGTGGTTTGT
1 TTAATGTGGGAGTGGTTTGG
18666417 TTAATGTGGGAGTGGTTTGG
1 TTAATGTGGGAGTGGTTTGG
*
18666437 TTGATGT
1 TTAATGT
18666444 TTAGGCTAGA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.15, C:0.00, G:0.40, T:0.45
Consensus pattern (20 bp):
TTAATGTGGGAGTGGTTTGG
Found at i:18666878 original size:23 final size:22
Alignment explanation
Indices: 18666835--18666878 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
18666825 ATAAAAAATT
**
18666835 AATATTTTAATAAATGGATAAA
1 AATATTTTAATAAATAAATAAA
*
18666857 AATATTTTATGTAAATAAATAA
1 AATATTTTA-ATAAATAAATAA
18666879 GTTTGATCAT
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
22 9 0.50
23 9 0.50
ACGTcount: A:0.55, C:0.00, G:0.07, T:0.39
Consensus pattern (22 bp):
AATATTTTAATAAATAAATAAA
Found at i:18671150 original size:6 final size:6
Alignment explanation
Indices: 18671104--18671136 Score: 66
Period size: 6 Copynumber: 5.5 Consensus size: 6
18671094 CAGCAGAAAG
18671104 AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAA
1 AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAA
18671137 TATTAAAAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (6 bp):
AAAGAA
Found at i:18673257 original size:25 final size:25
Alignment explanation
Indices: 18673209--18673260 Score: 70
Period size: 25 Copynumber: 2.1 Consensus size: 25
18673199 GTTCTTCGTT
**
18673209 TTTTTTTCTTTGTCGATTTCTTTTC
1 TTTTTTTCTTTGTCGAAATCTTTTC
18673234 TTTTTTTCTTT-TCGAAATCGTTTTC
1 TTTTTTTCTTTGTCGAAATC-TTTTC
18673259 TT
1 TT
18673261 AAGAAAATTA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
24 6 0.25
25 18 0.75
ACGTcount: A:0.08, C:0.15, G:0.08, T:0.69
Consensus pattern (25 bp):
TTTTTTTCTTTGTCGAAATCTTTTC
Found at i:18686840 original size:46 final size:44
Alignment explanation
Indices: 18686758--18687202 Score: 279
Period size: 44 Copynumber: 10.3 Consensus size: 44
18686748 ATAATACAGG
** *
18686758 TCTTATCTCCCTGAGATTACAGTGGAATAGACCAAAGAATTTCAGA
1 TCTTATCTCCCTGAGATTACAGTGGAGCAGATCAAAGAA--TCAGA
* *
18686804 TCTTATCTCCCGGAGATTACAGCGGAGCAGATCAAAG-AT-AGTAA
1 TCTTATCTCCCTGAGATTACAGTGGAGCAGATCAAAGAATCAG--A
* * * * *
18686848 TCCTATCTCCTTGAGATTACAATGGAGCGGATTAAAG-----GA
1 TCTTATCTCCCTGAGATTACAGTGGAGCAGATCAAAGAATCAGA
* * * * *
18686887 TCTTATCTCTCTGA-AGTTACAGTAGAGAAGATC--A-CATCAGG
1 TCTTATCTCCCTGAGA-TTACAGTGGAGCAGATCAAAGAATCAGA
* *
18686928 TCTTATCTCCCTGAGATTACAGTGGAACAGACCAAAGAATTTCAGA
1 TCTTATCTCCCTGAGATTACAGTGGAGCAGATCAAAGAA--TCAGA
* ** * *
18686974 TCTTATCTCCCTGAGGTTACAGTGGAGCAGATTGAAGCCA-GAGA
1 TCTTATCTCCCTGAGATTACAGTGGAGCAGATCAAAG-AATCAGA
** *
18687018 TCTTATCTCCCTGAGATTACAGCAGAGCAGATTAAAG-AT-AGTAA
1 TCTTATCTCCCTGAGATTACAGTGGAGCAGATCAAAGAATCAG--A
* * * * *
18687062 TCCTATCTCCTTGAGATTACAATGGAGCGGATTAAAG-----GA
1 TCTTATCTCCCTGAGATTACAGTGGAGCAGATCAAAGAATCAGA
* * * * *
18687101 TCTTATCTCTCTGA-AGTTACAGTAGAGAAGATC--A-CATCAGG
1 TCTTATCTCCCTGAGA-TTACAGTGGAGCAGATCAAAGAATCAGA
* *
18687142 TCTTATCTCCCTGAGATTACAGTGGAACAGACCAAAGAATTTCAGA
1 TCTTATCTCCCTGAGATTACAGTGGAGCAGATCAAAGAA--TCAGA
18687188 TCTTATCTCCCTGAG
1 TCTTATCTCCCTGAG
18687203 NNNNNNNNNN
Statistics
Matches: 308, Mismatches: 61, Indels: 60
0.72 0.14 0.14
Matches are distributed among these distances:
37 2 0.01
38 2 0.01
39 48 0.16
41 56 0.18
42 7 0.02
43 3 0.01
44 101 0.33
45 1 0.00
46 87 0.28
47 1 0.00
ACGTcount: A:0.32, C:0.20, G:0.20, T:0.27
Consensus pattern (44 bp):
TCTTATCTCCCTGAGATTACAGTGGAGCAGATCAAAGAATCAGA
Found at i:18687129 original size:214 final size:214
Alignment explanation
Indices: 18686801--18687202 Score: 777
Period size: 214 Copynumber: 1.9 Consensus size: 214
18686791 AAAGAATTTC
*
18686801 AGATCTTATCTCCCGGAGATTACAGCGGAGCAGATCAAAGATAGTAATCCTATCTCCTTGAGATT
1 AGATCTTATCTCCCGGAGATTACAGCAGAGCAGATCAAAGATAGTAATCCTATCTCCTTGAGATT
18686866 ACAATGGAGCGGATTAAAGGATCTTATCTCTCTGAAGTTACAGTAGAGAAGATCACATCAGGTCT
66 ACAATGGAGCGGATTAAAGGATCTTATCTCTCTGAAGTTACAGTAGAGAAGATCACATCAGGTCT
18686931 TATCTCCCTGAGATTACAGTGGAACAGACCAAAGAATTTCAGATCTTATCTCCCTGAGGTTACAG
131 TATCTCCCTGAGATTACAGTGGAACAGACCAAAGAATTTCAGATCTTATCTCCCTGAGGTTACAG
18686996 TGGAGCAGATTGAAGCCAG
196 TGGAGCAGATTGAAGCCAG
* *
18687015 AGATCTTATCTCCCTGAGATTACAGCAGAGCAGATTAAAGATAGTAATCCTATCTCCTTGAGATT
1 AGATCTTATCTCCCGGAGATTACAGCAGAGCAGATCAAAGATAGTAATCCTATCTCCTTGAGATT
18687080 ACAATGGAGCGGATTAAAGGATCTTATCTCTCTGAAGTTACAGTAGAGAAGATCACATCAGGTCT
66 ACAATGGAGCGGATTAAAGGATCTTATCTCTCTGAAGTTACAGTAGAGAAGATCACATCAGGTCT
18687145 TATCTCCCTGAGATTACAGTGGAACAGACCAAAGAATTTCAGATCTTATCTCCCTGAG
131 TATCTCCCTGAGATTACAGTGGAACAGACCAAAGAATTTCAGATCTTATCTCCCTGAG
18687203 NNNNNNNNNN
Statistics
Matches: 185, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
214 185 1.00
ACGTcount: A:0.32, C:0.20, G:0.21, T:0.27
Consensus pattern (214 bp):
AGATCTTATCTCCCGGAGATTACAGCAGAGCAGATCAAAGATAGTAATCCTATCTCCTTGAGATT
ACAATGGAGCGGATTAAAGGATCTTATCTCTCTGAAGTTACAGTAGAGAAGATCACATCAGGTCT
TATCTCCCTGAGATTACAGTGGAACAGACCAAAGAATTTCAGATCTTATCTCCCTGAGGTTACAG
TGGAGCAGATTGAAGCCAG
Found at i:18696173 original size:18 final size:18
Alignment explanation
Indices: 18696152--18696191 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
18696142 TGGGCTTCCC
18696152 ATTTATATTTT-TTTTTCT
1 ATTT-TATTTTATTTTTCT
*
18696170 ATTTTCTTTTATTTTTCT
1 ATTTTATTTTATTTTTCT
18696188 ATTT
1 ATTT
18696192 CAACTGTTTC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 5 0.25
18 15 0.75
ACGTcount: A:0.15, C:0.07, G:0.00, T:0.78
Consensus pattern (18 bp):
ATTTTATTTTATTTTTCT
Found at i:18696992 original size:20 final size:19
Alignment explanation
Indices: 18696958--18696996 Score: 60
Period size: 20 Copynumber: 2.0 Consensus size: 19
18696948 TAACATTATT
18696958 ATTAAATACAATTTAATAA
1 ATTAAATACAATTTAATAA
*
18696977 ATTAATATATAATTTAATAA
1 ATTAA-ATACAATTTAATAA
18696997 TATTCTTAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 5 0.28
20 13 0.72
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.41
Consensus pattern (19 bp):
ATTAAATACAATTTAATAA
Found at i:18697059 original size:23 final size:21
Alignment explanation
Indices: 18697028--18697070 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
18697018 TAAAATATGA
18697028 ATTAAAAAATCATAATATATAAT
1 ATTAAAAAA--ATAATATATAAT
*
18697051 ATTATAAAAATAATATATAA
1 ATTAAAAAAATAATATATAA
18697071 CCTACTTTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 11 0.58
23 8 0.42
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (21 bp):
ATTAAAAAAATAATATATAAT
Found at i:18698937 original size:40 final size:40
Alignment explanation
Indices: 18698877--18699060 Score: 221
Period size: 40 Copynumber: 4.6 Consensus size: 40
18698867 TATTCGAATG
*
18698877 ATATCCGGGCTAAG-TCCCGAAGGCTTTTATGCTAGTGACT
1 ATATCCGGGCTAAGAT-CCGAAGGCATTTATGCTAGTGACT
* * *
18698917 ATATCCGGACTAAGATCCGAAGGCATTTGTGCGAGTTG-CT
1 ATATCCGGGCTAAGATCCGAAGGCATTTATGCTAG-TGACT
* * * *
18698957 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGCGATT
1 ATATCCGGGCTAAGATCCGAAGGCATTTATGCTAGTGACT
* *
18698997 ATATCCGGGCTAAG-TCCCAAAGGCATTTATGCTAGTGACC
1 ATATCCGGGCTAAGAT-CCGAAGGCATTTATGCTAGTGACT
*
18699037 ATATCCGGGCTAAGACCCGAAGGC
1 ATATCCGGGCTAAGATCCGAAGGC
18699061 CTTGTGCAAG
Statistics
Matches: 122, Mismatches: 17, Indels: 10
0.82 0.11 0.07
Matches are distributed among these distances:
39 1 0.01
40 118 0.97
41 3 0.02
ACGTcount: A:0.26, C:0.23, G:0.26, T:0.25
Consensus pattern (40 bp):
ATATCCGGGCTAAGATCCGAAGGCATTTATGCTAGTGACT
Found at i:18699010 original size:80 final size:80
Alignment explanation
Indices: 18698877--18699060 Score: 246
Period size: 80 Copynumber: 2.3 Consensus size: 80
18698867 TATTCGAATG
* * * *
18698877 ATATCCGGGCTAAGTCCCGAAGGCTTTTATGCTAGTGACTATATCCGGACTAAGAT-CCGAAGGC
1 ATATCCGGGCTAAGACCCGAAGGCATTTATGCTAGCGACTATATCCGGACTAAG-TCCCAAAGGC
* *
18698941 ATTTGTGCGAGTTG-CT
65 ATTTATGCGAG-TGACC
* * *
18698957 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGCGATTATATCCGGGCTAAGTCCCAAAGGCA
1 ATATCCGGGCTAAGACCCGAAGGCATTTATGCTAGCGACTATATCCGGACTAAGTCCCAAAGGCA
*
18699022 TTTATGCTAGTGACC
66 TTTATGCGAGTGACC
18699037 ATATCCGGGCTAAGACCCGAAGGC
1 ATATCCGGGCTAAGACCCGAAGGC
18699061 CTTGTGCAAG
Statistics
Matches: 92, Mismatches: 10, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
79 3 0.03
80 89 0.97
ACGTcount: A:0.26, C:0.23, G:0.26, T:0.25
Consensus pattern (80 bp):
ATATCCGGGCTAAGACCCGAAGGCATTTATGCTAGCGACTATATCCGGACTAAGTCCCAAAGGCA
TTTATGCGAGTGACC
Found at i:18704289 original size:40 final size:38
Alignment explanation
Indices: 18704197--18704293 Score: 104
Period size: 40 Copynumber: 2.5 Consensus size: 38
18704187 ACCATCTCCG
* *
18704197 TCCAACCCAACACACCATGTGGAGATAAAATCGACCCA
1 TCCAACCCTACACACCATATGGAGATAAAATCGACCCA
* * * * * *
18704235 CCCATCCTTGCACACCGTATATGGGGATATAATCGACCCA
1 TCCAACCCTACACACC--ATATGGAGATAAAATCGACCCA
18704275 TCCAACCCTACACACCATA
1 TCCAACCCTACACACCATA
18704294 AAGTACCGCA
Statistics
Matches: 45, Mismatches: 12, Indels: 4
0.74 0.20 0.07
Matches are distributed among these distances:
38 14 0.31
40 31 0.69
ACGTcount: A:0.34, C:0.36, G:0.12, T:0.18
Consensus pattern (38 bp):
TCCAACCCTACACACCATATGGAGATAAAATCGACCCA
Found at i:18709955 original size:27 final size:27
Alignment explanation
Indices: 18709924--18710101 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
18709914 TAAATTGTAC
18709924 AGCACTAAGTGTGCGATTTGACTATGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* ** *
18709951 TGCACTAAGTGTGCGAAATGAATATG-
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
18709977 ATGCACTAAGTGTGCGAATTGACCATGC
1 A-GCACTAAGTGTGCGATTTGACTATGT
*
18710005 GGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGA-TTTGACTATGT
* *
18710033 AGCACTAAGTGTGCGATTTGATTACGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
18710060 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGATTTGACTATGT
*
18710087 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
18710102 GACTCAATAT
Statistics
Matches: 129, Mismatches: 19, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 23 0.18
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (27 bp):
AGCACTAAGTGTGCGATTTGACTATGT
Found at i:18710038 original size:82 final size:81
Alignment explanation
Indices: 18709925--18710080 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
18709915 AAATTGTACA
* *
18709925 GCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATG-ATGCACTAAGTG
1 GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTA-GCACTAAGTG
18709989 TGCGAATTGACCATGCG
65 TGCGAATTGACCATGCG
** *
18710006 GCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACGTAGCACTAAGTG
1 GCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTG
*
18710071 TGCGAGTTGA
65 TGCGAATTGA
18710081 TTATATAGCA
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 15 0.22
82 51 0.76
83 1 0.01
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.29
Consensus pattern (81 bp):
GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTGT
GCGAATTGACCATGCG
Found at i:18710092 original size:82 final size:81
Alignment explanation
Indices: 18709921--18710101 Score: 229
Period size: 82 Copynumber: 2.2 Consensus size: 81
18709911 GATTAAATTG
* *
18709921 TACAGCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATGATGCACTAA
1 TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
18709986 GTGTGCGAATTGACCA
66 GTGTGCGAATTGACCA
* * ** *
18710002 TGCGGCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACG-TAGCACT
1 TACAGCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGAT-GCACT
* **
18710066 AAGTGTGCGAGTTGATTA
64 AAGTGTGCGAATTGACCA
* *
18710084 TATAGCACTGAGTGTGCG
1 TACAGCACTAAGTGTGCG
18710102 GACTCAATAT
Statistics
Matches: 84, Mismatches: 14, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
81 18 0.21
82 66 0.79
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (81 bp):
TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
GTGTGCGAATTGACCA
Found at i:18712389 original size:24 final size:24
Alignment explanation
Indices: 18712362--18712418 Score: 71
Period size: 24 Copynumber: 2.4 Consensus size: 24
18712352 CTATCTAGAG
*
18712362 CTTCTCGATATGCTTCTTTGTGAA
1 CTTCTCGATAAGCTTCTTTGTGAA
* *
18712386 CTTC-CTAATAAGGTTCTTTGTGAA
1 CTTCTC-GATAAGCTTCTTTGTGAA
18712410 CTTCTCGAT
1 CTTCTCGAT
18712419 TAAGGCTCTT
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
23 1 0.04
24 25 0.93
25 1 0.04
ACGTcount: A:0.19, C:0.21, G:0.16, T:0.44
Consensus pattern (24 bp):
CTTCTCGATAAGCTTCTTTGTGAA
Found at i:18712428 original size:25 final size:24
Alignment explanation
Indices: 18712376--18712428 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 24
18712366 TCGATATGCT
* *
18712376 TCTTTGTGAACTTCCTAATAAGGT
1 TCTTTGTGAACTTCCGAATAAGGC
*
18712400 TCTTTGTGAACTTCTCGATTAAGGC
1 TCTTTGTGAACTTC-CGAATAAGGC
18712425 TCTT
1 TCTT
18712429 ATGAGCTTCC
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
24 14 0.56
25 11 0.44
ACGTcount: A:0.21, C:0.19, G:0.17, T:0.43
Consensus pattern (24 bp):
TCTTTGTGAACTTCCGAATAAGGC
Found at i:18714343 original size:14 final size:13
Alignment explanation
Indices: 18714319--18714360 Score: 50
Period size: 14 Copynumber: 3.2 Consensus size: 13
18714309 GCTATTAACC
18714319 AAAAAAT-AATACA
1 AAAAAATAAATA-A
18714332 AAAAAATAAATAA
1 AAAAAATAAATAA
*
18714345 AACAACATAAATAA
1 AA-AAAATAAATAA
18714359 AA
1 AA
18714361 CATTTTTCCT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
13 10 0.38
14 16 0.62
ACGTcount: A:0.79, C:0.07, G:0.00, T:0.14
Consensus pattern (13 bp):
AAAAAATAAATAA
Found at i:18716798 original size:29 final size:29
Alignment explanation
Indices: 18716764--18716821 Score: 116
Period size: 29 Copynumber: 2.0 Consensus size: 29
18716754 CTATTACAAC
18716764 AATAAAAATTTTCAAACCACAATTAAATT
1 AATAAAAATTTTCAAACCACAATTAAATT
18716793 AATAAAAATTTTCAAACCACAATTAAATT
1 AATAAAAATTTTCAAACCACAATTAAATT
18716822 CAGAACCGAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.55, C:0.14, G:0.00, T:0.31
Consensus pattern (29 bp):
AATAAAAATTTTCAAACCACAATTAAATT
Found at i:18724201 original size:44 final size:44
Alignment explanation
Indices: 18724144--18724230 Score: 115
Period size: 44 Copynumber: 2.0 Consensus size: 44
18724134 GCCTCAAGGC
**
18724144 CTTATCTCTCTGAGGTAGCAA-GAGAGCAGGTTGAAGATTGAAGT
1 CTTATCTCTCTGAGGTAGCAAGGA-AGCAGACTGAAGATTGAAGT
*
18724188 CTTATCT-TCCTGAGGTAGTAAGGAAGCAGACTGAAGATTGAAG
1 CTTATCTCT-CTGAGGTAGCAAGGAAGCAGACTGAAGATTGAAG
18724231 ATTGGAAGAG
Statistics
Matches: 38, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
43 1 0.03
44 35 0.92
45 2 0.05
ACGTcount: A:0.31, C:0.14, G:0.29, T:0.26
Consensus pattern (44 bp):
CTTATCTCTCTGAGGTAGCAAGGAAGCAGACTGAAGATTGAAGT
Found at i:18724222 original size:148 final size:148
Alignment explanation
Indices: 18724019--18724461 Score: 735
Period size: 148 Copynumber: 3.0 Consensus size: 148
18724009 ATCGGCAATG
* * * *
18724019 GAGCAGATTGAAGATTGAAGTCTTATCTTCCCGAGGTAGCAAGGAAGTAGACTGAAGATTAAAGA
1 GAGCAGGTTGAAGATTGAAGTCTTATCTTCCTGAGGTAGCAAGGAAGCAGACTGAAGATTGAAGA
*
18724084 TTGGAAGAGGCGAATCTTATCTCCATGTATTGGCAATGGAGCAGATTTAAGCCTCAAGGCCTTAT
66 TTGGAAGAGGCGAATCTTATCTCCATGTACTGGCAATGGAGCAGATTTAAGCCTCAAGGCCTTAT
18724149 CTCTCTGAGGTAGCAAGA
131 CTCTCTGAGGTAGCAAGA
*
18724167 GAGCAGGTTGAAGATTGAAGTCTTATCTTCCTGAGGTAGTAAGGAAGCAGACTGAAGATTGAAGA
1 GAGCAGGTTGAAGATTGAAGTCTTATCTTCCTGAGGTAGCAAGGAAGCAGACTGAAGATTGAAGA
*
18724232 TTGGAAGAGGCGAATCTTATCTCCATGTACTGGCAATGGAGTAGATTTAAGCCTCAAGGCCTTAT
66 TTGGAAGAGGCGAATCTTATCTCCATGTACTGGCAATGGAGCAGATTTAAGCCTCAAGGCCTTAT
18724297 CTCTCTGAGGTAGCAAGA
131 CTCTCTGAGGTAGCAAGA
* * * *
18724315 GAGTAAGTTAAAGATTGAAGTCTTATCTTCCTAAGGTAGCAAGGAAGCAGACTGAAGATTGAAGA
1 GAGCAGGTTGAAGATTGAAGTCTTATCTTCCTGAGGTAGCAAGGAAGCAGACTGAAGATTGAAGA
* * *
18724380 ATGGAAGAGGCGAATCTTATCTCCATGTACTGGCAATGGAGCAGATTTAAGCCTCAAAGCCTCAT
66 TTGGAAGAGGCGAATCTTATCTCCATGTACTGGCAATGGAGCAGATTTAAGCCTCAAGGCCTTAT
*
18724445 CT-TCCTGAGGTAACAAG
131 CTCT-CTGAGGTAGCAAG
18724462 GAAACAGACT
Statistics
Matches: 277, Mismatches: 17, Indels: 2
0.94 0.06 0.01
Matches are distributed among these distances:
147 1 0.00
148 276 1.00
ACGTcount: A:0.32, C:0.16, G:0.26, T:0.26
Consensus pattern (148 bp):
GAGCAGGTTGAAGATTGAAGTCTTATCTTCCTGAGGTAGCAAGGAAGCAGACTGAAGATTGAAGA
TTGGAAGAGGCGAATCTTATCTCCATGTACTGGCAATGGAGCAGATTTAAGCCTCAAGGCCTTAT
CTCTCTGAGGTAGCAAGA
Found at i:18728319 original size:29 final size:29
Alignment explanation
Indices: 18728256--18728323 Score: 93
Period size: 29 Copynumber: 2.3 Consensus size: 29
18728246 TAATCAACCG
18728256 CGCACACTTAGTGCCATGCACTTTAAACT
1 CGCACACTTAGTGCCATGCACTTTAAACT
* **
18728285 CACACACTTAGTGCCATGCA-TTTCAAGTT
1 CGCACACTTAGTGCCATGCACTTT-AAACT
18728314 CGCACACTTA
1 CGCACACTTA
18728324 CCTTTTCCGC
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
28 3 0.09
29 31 0.91
ACGTcount: A:0.28, C:0.31, G:0.13, T:0.28
Consensus pattern (29 bp):
CGCACACTTAGTGCCATGCACTTTAAACT
Found at i:18728435 original size:174 final size:174
Alignment explanation
Indices: 18728145--18728472 Score: 629
Period size: 174 Copynumber: 1.9 Consensus size: 174
18728135 AACTCAAGGT
*
18728145 ACTTACCTTTTCCGCTGTCCAAAATCGACTCGGTAAAGTCGCACCCTTCATGTAAATAATTTATA
1 ACTTACCTTTTCCGCTGTCCAAAATCGACTCGGTAAAGTCGCACCCTTAATGTAAATAATTTATA
18728210 GAAAATATATATTGGGTTCGCACACATAGTGCTTAATAATCAACCGCGCACACTTAGTGCCATGC
66 GAAAATATATATTGGGTTCGCACACATAGTGCTTAATAATCAACCGCGCACACTTAGTGCCATGC
18728275 ACTTTAAACTCACACACTTAGTGCCATGCATTTCAAGTTCGCAC
131 ACTTTAAACTCACACACTTAGTGCCATGCATTTCAAGTTCGCAC
18728319 ACTTACCTTTTCCGCTGTCCAAAATCGACTCGGTAAAGTCGCACCCTTAATGTAAATAATTTATA
1 ACTTACCTTTTCCGCTGTCCAAAATCGACTCGGTAAAGTCGCACCCTTAATGTAAATAATTTATA
*
18728384 GAAAATATATATTGGGTTCGCACACATAGTGCTTAATAATCAACCGCGCACACTTAGTGCCATGT
66 GAAAATATATATTGGGTTCGCACACATAGTGCTTAATAATCAACCGCGCACACTTAGTGCCATGC
*
18728449 ACTTTAAACTCGCACACTTAGTGC
131 ACTTTAAACTCACACACTTAGTGC
18728473 TGTACAATTT
Statistics
Matches: 151, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
174 151 1.00
ACGTcount: A:0.31, C:0.25, G:0.15, T:0.30
Consensus pattern (174 bp):
ACTTACCTTTTCCGCTGTCCAAAATCGACTCGGTAAAGTCGCACCCTTAATGTAAATAATTTATA
GAAAATATATATTGGGTTCGCACACATAGTGCTTAATAATCAACCGCGCACACTTAGTGCCATGC
ACTTTAAACTCACACACTTAGTGCCATGCATTTCAAGTTCGCAC
Found at i:18728464 original size:29 final size:30
Alignment explanation
Indices: 18728425--18728503 Score: 110
Period size: 29 Copynumber: 2.7 Consensus size: 30
18728415 CTTAATAATC
18728425 AACCGCGCACACTTAGTGCCATGTAC-TTTA
1 AACC-CGCACACTTAGTGCCATGTACATTTA
*
18728455 AACTCGCACACTTAGTG-C-TGTACAATTTA
1 AACCCGCACACTTAGTGCCATGTAC-ATTTA
18728484 AACCCGCACACTTAGTGCCA
1 AACCCGCACACTTAGTGCCA
18728504 ATCTCATGAC
Statistics
Matches: 43, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
27 5 0.12
28 1 0.02
29 33 0.77
30 4 0.09
ACGTcount: A:0.29, C:0.30, G:0.15, T:0.25
Consensus pattern (30 bp):
AACCCGCACACTTAGTGCCATGTACATTTA
Found at i:18736258 original size:27 final size:27
Alignment explanation
Indices: 18736228--18736405 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
18736218 ATATTGAGTC
* * * *
18736228 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAGTCAAAT
* *
18736255 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
18736282 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAAA-T
** * *
18736310 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAGTCAAAT
* **
18736337 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAGTCAAAT
*
18736364 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
18736391 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
18736406 GTACAATTTA
Statistics
Matches: 130, Mismatches: 18, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 24 0.18
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAGTCAAAT
Found at i:18736367 original size:82 final size:81
Alignment explanation
Indices: 18736249--18736404 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
18736239 TGCTATATAA
* *
18736249 TCAACTCGCACACTTAGTGCTACGTAATCAAATCGCACACTTAGTGCTACATAGTCAAACTCGCA
1 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAA-TCGCA
18736314 CACTTAGTGCCGCATGG
65 CACTTAGTGCCGCATGG
* * **
18736331 TCAATTCGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAATCGCA
1 TCAACTCGCACACTTAGTGCTA-CATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCA
18736395 CACTTAGTGC
65 CACTTAGTGC
18736405 TGTACAATTT
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 16 0.24
82 51 0.76
ACGTcount: A:0.29, C:0.28, G:0.15, T:0.27
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCAC
ACTTAGTGCCGCATGG
Found at i:18750406 original size:92 final size:93
Alignment explanation
Indices: 18750269--18750446 Score: 295
Period size: 92 Copynumber: 1.9 Consensus size: 93
18750259 CATTTCTTAG
* * *
18750269 CCTTTATTTACTTTTGTTAAGATTGAGCTCTGATTAGATATTTTGTTTTGGGTTTAATTGTTGAT
1 CCTTTATTTACTTTTATTAAGATTGAACTCTGATTAGAGATTTTGTTTTGGGTTTAATTGTTGAT
18750334 TCATCTTTTTTCTATTATTTCTTCTTCA
66 TCATCTTTTTTCTATTATTTCTTCTTCA
* * *
18750362 CCTTTATTTAC-TTTATTAGGATTGAACTCTTATTAGAGATTTTGTTTTGGGTTTAATTGTTTAT
1 CCTTTATTTACTTTTATTAAGATTGAACTCTGATTAGAGATTTTGTTTTGGGTTTAATTGTTGAT
18750426 TCATCTTTTTTCTATTATTTC
66 TCATCTTTTTTCTATTATTTC
18750447 CTGGTAGCTC
Statistics
Matches: 79, Mismatches: 6, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
92 68 0.86
93 11 0.14
ACGTcount: A:0.19, C:0.11, G:0.12, T:0.57
Consensus pattern (93 bp):
CCTTTATTTACTTTTATTAAGATTGAACTCTGATTAGAGATTTTGTTTTGGGTTTAATTGTTGAT
TCATCTTTTTTCTATTATTTCTTCTTCA
Found at i:18751969 original size:20 final size:19
Alignment explanation
Indices: 18751924--18751961 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
18751914 TATCCAAACA
18751924 CCAGAAAAGTAAATCATTT
1 CCAGAAAAGTAAATCATTT
18751943 CCAGAAAAGTAAATCATTT
1 CCAGAAAAGTAAATCATTT
18751962 TTCAGAAATC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.47, C:0.16, G:0.11, T:0.26
Consensus pattern (19 bp):
CCAGAAAAGTAAATCATTT
Found at i:18753207 original size:26 final size:28
Alignment explanation
Indices: 18753177--18753229 Score: 74
Period size: 28 Copynumber: 2.0 Consensus size: 28
18753167 AAACTTTTCT
*
18753177 AAAAG-AAAAC-TCAAGAGAAATTATTG
1 AAAAGAAAAACTTAAAGAGAAATTATTG
*
18753203 AAAAGAAAAACTTAAAGAGAATTTATT
1 AAAAGAAAAACTTAAAGAGAAATTATT
18753230 AACTCAAAAG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
26 5 0.22
27 5 0.22
28 13 0.57
ACGTcount: A:0.58, C:0.06, G:0.13, T:0.23
Consensus pattern (28 bp):
AAAAGAAAAACTTAAAGAGAAATTATTG
Found at i:18756109 original size:40 final size:40
Alignment explanation
Indices: 18756072--18756242 Score: 308
Period size: 40 Copynumber: 4.3 Consensus size: 40
18756062 GCTACTCGTT
* *
18756072 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATT-TAGTAACTCGCA
18756112 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
18756152 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
18756192 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
18756232 CAAATGCCTTC
1 CAAATGCCTTC
18756243 NNNNNNNNNN
Statistics
Matches: 128, Mismatches: 2, Indels: 2
0.97 0.02 0.02
Matches are distributed among these distances:
40 126 0.98
41 2 0.02
ACGTcount: A:0.27, C:0.28, G:0.20, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
Found at i:18766028 original size:14 final size:14
Alignment explanation
Indices: 18766009--18766038 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
18765999 TAATCTGCAT
18766009 TGGATGGCCTTGAG
1 TGGATGGCCTTGAG
18766023 TGGATGGCCTTGAG
1 TGGATGGCCTTGAG
18766037 TG
1 TG
18766039 CCGGATGGAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.13, C:0.13, G:0.43, T:0.30
Consensus pattern (14 bp):
TGGATGGCCTTGAG
Found at i:18770444 original size:15 final size:16
Alignment explanation
Indices: 18770407--18770436 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
18770397 ATAAGTGTTG
18770407 AAAATATAAAATGAAA
1 AAAATATAAAATGAAA
18770423 AAAATAT-AAATGAA
1 AAAATATAAAATGAA
18770437 TTAAATATTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.73, C:0.00, G:0.07, T:0.20
Consensus pattern (16 bp):
AAAATATAAAATGAAA
Found at i:18774357 original size:175 final size:175
Alignment explanation
Indices: 18774066--18774415 Score: 700
Period size: 175 Copynumber: 2.0 Consensus size: 175
18774056 TTTGAAATTT
18774066 CGACAGCATATAGAAGAAGAATGAGCTGATTTTGGTTCATTTTTCCCATTTTATTTCATTAAAAT
1 CGACAGCATATAGAAGAAGAATGAGCTGATTTTGGTTCATTTTTCCCATTTTATTTCATTAAAAT
18774131 GCCAAATGACCAAAATACCCTTAAGTCATTTCTTTAAAATTTCATCCATGAAAGCCCATTTTTGT
66 GCCAAATGACCAAAATACCCTTAAGTCATTTCTTTAAAATTTCATCCATGAAAGCCCATTTTTGT
18774196 CCAAAAACTTAGAAATTGGGCAAATTGCTCTCCAAGACCTTCTAA
131 CCAAAAACTTAGAAATTGGGCAAATTGCTCTCCAAGACCTTCTAA
18774241 CGACAGCATATAGAAGAAGAATGAGCTGATTTTGGTTCATTTTTCCCATTTTATTTCATTAAAAT
1 CGACAGCATATAGAAGAAGAATGAGCTGATTTTGGTTCATTTTTCCCATTTTATTTCATTAAAAT
18774306 GCCAAATGACCAAAATACCCTTAAGTCATTTCTTTAAAATTTCATCCATGAAAGCCCATTTTTGT
66 GCCAAATGACCAAAATACCCTTAAGTCATTTCTTTAAAATTTCATCCATGAAAGCCCATTTTTGT
18774371 CCAAAAACTTAGAAATTGGGCAAATTGCTCTCCAAGACCTTCTAA
131 CCAAAAACTTAGAAATTGGGCAAATTGCTCTCCAAGACCTTCTAA
18774416 TTTATAATCT
Statistics
Matches: 175, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
175 175 1.00
ACGTcount: A:0.34, C:0.20, G:0.13, T:0.33
Consensus pattern (175 bp):
CGACAGCATATAGAAGAAGAATGAGCTGATTTTGGTTCATTTTTCCCATTTTATTTCATTAAAAT
GCCAAATGACCAAAATACCCTTAAGTCATTTCTTTAAAATTTCATCCATGAAAGCCCATTTTTGT
CCAAAAACTTAGAAATTGGGCAAATTGCTCTCCAAGACCTTCTAA
Found at i:18778205 original size:46 final size:46
Alignment explanation
Indices: 18778053--18778271 Score: 185
Period size: 46 Copynumber: 4.7 Consensus size: 46
18778043 TCATTTGTGT
* * *
18778053 GCTAGTGTAAGACATGTCTAGGACATGCATCGGCCAC-ATTATGAGA
1 GCTAGTGTAAGACATGTCTGGGACATGCATCGGCCTCGA-GATGAGA
* * * * *
18778099 GCTAGTGTAAGACGATGTCTGAGACATGGCATCGACATTGAGACGAGA
1 GCTAGTGTAAGAC-ATGTCTGGGACAT-GCATCGGCCTCGAGATGAGA
*
18778147 GCTAGAGTAAGACATGTCTGGGACATGCATCGGCCTCGAGATGTA-A
1 GCTAGTGTAAGACATGTCTGGGACATGCATCGGCCTCGAGATG-AGA
* * * * * * *
18778193 GCCAGTGTAAGACATGTTTGGGACATGTATTGG-ATAGTGATGAGTAA
1 GCTAGTGTAAGACATGTCTGGGACATGCATCGGCCTCGAGATGAG--A
* * *
18778240 G-TTGTGTAAGACATGTTTGGGACATGTATCGG
1 GCTAGTGTAAGACATGTCTGGGACATGCATCGG
18778272 ATAGTGATGA
Statistics
Matches: 141, Mismatches: 25, Indels: 14
0.78 0.14 0.08
Matches are distributed among these distances:
44 1 0.01
45 6 0.04
46 83 0.59
47 26 0.18
48 24 0.17
49 1 0.01
ACGTcount: A:0.29, C:0.15, G:0.31, T:0.26
Consensus pattern (46 bp):
GCTAGTGTAAGACATGTCTGGGACATGCATCGGCCTCGAGATGAGA
Found at i:18778274 original size:46 final size:46
Alignment explanation
Indices: 18778197--18778291 Score: 181
Period size: 46 Copynumber: 2.1 Consensus size: 46
18778187 ATGTAAGCCA
*
18778197 GTGTAAGACATGTTTGGGACATGTATTGGATAGTGATGAGTAAGTT
1 GTGTAAGACATGTTTGGGACATGTATCGGATAGTGATGAGTAAGTT
18778243 GTGTAAGACATGTTTGGGACATGTATCGGATAGTGATGAGTAAGTT
1 GTGTAAGACATGTTTGGGACATGTATCGGATAGTGATGAGTAAGTT
18778289 GTG
1 GTG
18778292 AGTGGTGCAG
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
46 48 1.00
ACGTcount: A:0.27, C:0.05, G:0.34, T:0.34
Consensus pattern (46 bp):
GTGTAAGACATGTTTGGGACATGTATCGGATAGTGATGAGTAAGTT
Found at i:18779231 original size:535 final size:535
Alignment explanation
Indices: 18778222--18779295 Score: 2148
Period size: 535 Copynumber: 2.0 Consensus size: 535
18778212 GGGACATGTA
18778222 TTGGATAGTGATGAGTAAGTTGTGTAAGACATGTTTGGGACATGTATCGGATAGTGATGAGTAAG
1 TTGGATAGTGATGAGTAAGTTGTGTAAGACATGTTTGGGACATGTATCGGATAGTGATGAGTAAG
18778287 TTGTGAGTGGTGCAGGTATCTATTTGAAATGCATGAGATGTAAGCTCAATATATGCTATGTGAAT
66 TTGTGAGTGGTGCAGGTATCTATTTGAAATGCATGAGATGTAAGCTCAATATATGCTATGTGAAT
18778352 TGTATTGGATAGTGATGAGTAAGTTGTGCTTATGCCTACTTTTGTACTATGAGCATGATGATGTA
131 TGTATTGGATAGTGATGAGTAAGTTGTGCTTATGCCTACTTTTGTACTATGAGCATGATGATGTA
18778417 TGGTAAAGTTGTTGTTATATGTATTTTCATGCAACTTACTAAGCTTTATGCTTACTCCCCCTCCT
196 TGGTAAAGTTGTTGTTATATGTATTTTCATGCAACTTACTAAGCTTTATGCTTACTCCCCCTCCT
18778482 TTCCATTTTCTTATAGTGTCGCTTAATTAGCACGAAGATCATCGGACGTCGGAGGCATCGATCAC
261 TTCCATTTTCTTATAGTGTCGCTTAATTAGCACGAAGATCATCGGACGTCGGAGGCATCGATCAC
18778547 ACTATCATCCGAAGCACTTGGTATAATTAGATCTTTTATTTTGATTATGGCATGTATAGGACCCT
326 ACTATCATCCGAAGCACTTGGTATAATTAGATCTTTTATTTTGATTATGGCATGTATAGGACCCT
18778612 GACTTTTGAGTTTTGTGTCATTGTTAATTAGCCAAATGTGTTGGCTTACTTCAGCAGTTGATTTA
391 GACTTTTGAGTTTTGTGTCATTGTTAATTAGCCAAATGTGTTGGCTTACTTCAGCAGTTGATTTA
18778677 TTTTGTATAAGGCCATGGAAAATGCTAATATTGAAAGTTTATATACGAATGCAAGATAGTCTTTC
456 TTTTGTATAAGGCCATGGAAAATGCTAATATTGAAAGTTTATATACGAATGCAAGATAGTCTTTC
18778742 ATGAATGTGAAATTG
521 ATGAATGTGAAATTG
18778757 TTGGATAGTGATGAGTAAGTTGTGTAAGACATGTTTGGGACATGTATCGGATAGTGATGAGTAAG
1 TTGGATAGTGATGAGTAAGTTGTGTAAGACATGTTTGGGACATGTATCGGATAGTGATGAGTAAG
18778822 TTGTGAGTGGTGCAGGTATCTATTTGAAATGCATGAGATGTAAGCTCAATATATGCTATGTGAAT
66 TTGTGAGTGGTGCAGGTATCTATTTGAAATGCATGAGATGTAAGCTCAATATATGCTATGTGAAT
18778887 TGTATTGGATAGTGATGAGTAAGTTGTGCTTATGCCTACTTTTGTACTATGAGCATGATGATGTA
131 TGTATTGGATAGTGATGAGTAAGTTGTGCTTATGCCTACTTTTGTACTATGAGCATGATGATGTA
18778952 TGGTAAAGTTGTTGTTATATGTATTTTCATGCAACTTACTAAGCTTTATGCTTACTCCCCCTCCT
196 TGGTAAAGTTGTTGTTATATGTATTTTCATGCAACTTACTAAGCTTTATGCTTACTCCCCCTCCT
18779017 TTCCATTTTCTTATAGTGTCGCTTAATTAGCACGAAGATCATCGGACGTCGGAGGCATCGATCAC
261 TTCCATTTTCTTATAGTGTCGCTTAATTAGCACGAAGATCATCGGACGTCGGAGGCATCGATCAC
18779082 ACTATCATCCGAAGCACTTGGTATAATTAGATCTTTTATTTTGATTATGGCATGTATAGGACCCT
326 ACTATCATCCGAAGCACTTGGTATAATTAGATCTTTTATTTTGATTATGGCATGTATAGGACCCT
18779147 GACTTTTGAGTTTTGTGTCATTGTTAATTAGCCAAATGTGTTGGCTTACTTCAGCAGTTGATTTA
391 GACTTTTGAGTTTTGTGTCATTGTTAATTAGCCAAATGTGTTGGCTTACTTCAGCAGTTGATTTA
18779212 TTTTGTATAAGGCCATGGAAAATGCTAATATTGAAAGTTTATATACGAATGCAAGATAGTCTTTC
456 TTTTGTATAAGGCCATGGAAAATGCTAATATTGAAAGTTTATATACGAATGCAAGATAGTCTTTC
18779277 ATGAATGTGAAATTG
521 ATGAATGTGAAATTG
18779292 TTGG
1 TTGG
18779296 CATGGTTGAA
Statistics
Matches: 539, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
535 539 1.00
ACGTcount: A:0.27, C:0.13, G:0.23, T:0.37
Consensus pattern (535 bp):
TTGGATAGTGATGAGTAAGTTGTGTAAGACATGTTTGGGACATGTATCGGATAGTGATGAGTAAG
TTGTGAGTGGTGCAGGTATCTATTTGAAATGCATGAGATGTAAGCTCAATATATGCTATGTGAAT
TGTATTGGATAGTGATGAGTAAGTTGTGCTTATGCCTACTTTTGTACTATGAGCATGATGATGTA
TGGTAAAGTTGTTGTTATATGTATTTTCATGCAACTTACTAAGCTTTATGCTTACTCCCCCTCCT
TTCCATTTTCTTATAGTGTCGCTTAATTAGCACGAAGATCATCGGACGTCGGAGGCATCGATCAC
ACTATCATCCGAAGCACTTGGTATAATTAGATCTTTTATTTTGATTATGGCATGTATAGGACCCT
GACTTTTGAGTTTTGTGTCATTGTTAATTAGCCAAATGTGTTGGCTTACTTCAGCAGTTGATTTA
TTTTGTATAAGGCCATGGAAAATGCTAATATTGAAAGTTTATATACGAATGCAAGATAGTCTTTC
ATGAATGTGAAATTG
Found at i:18782594 original size:18 final size:18
Alignment explanation
Indices: 18782556--18782594 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
18782546 TGACATGGCA
*
18782556 AAAAAAAAAAAAAATCAT
1 AAAAAAAAAAAAAACCAT
* *
18782574 AAAACAAAAAAAAACCCT
1 AAAAAAAAAAAAAACCAT
18782592 AAA
1 AAA
18782595 TCCCTAAACC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.79, C:0.13, G:0.00, T:0.08
Consensus pattern (18 bp):
AAAAAAAAAAAAAACCAT
Found at i:18783096 original size:117 final size:117
Alignment explanation
Indices: 18782888--18783098 Score: 323
Period size: 117 Copynumber: 1.8 Consensus size: 117
18782878 TTTGATTTGT
* * * *
18782888 TGGTTATTTGTGATTTAGCATTGCAATTTGAGTGCGACAATGTAGGGTTTGTTTTGTCAATTTTT
1 TGGTTAATTGTGATTTAGCATTGCAATTTCAGTGCCACAATGTAGGGTTTGTTTTGTCAATTTAT
*
18782953 GATGCGATAGTGGTCCCGATGTTGTTGATAAAACTGTTGTAAAAATTGTATA
66 GATGCGATAGTGGTCCCGATGATGTTGATAAAACTGTTGTAAAAATTGTATA
** ** * *
18783005 TGGTTAATTGTGATTTATTATTGCAATTTCAGTGCCAGGATGTAGGGTTTGTTTTTTCGATTTAT
1 TGGTTAATTGTGATTTAGCATTGCAATTTCAGTGCCACAATGTAGGGTTTGTTTTGTCAATTTAT
18783070 GATGCGATAGTGGTCCCGATGATGTTGAT
66 GATGCGATAGTGGTCCCGATGATGTTGAT
18783099 TTCTATTACC
Statistics
Matches: 83, Mismatches: 11, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
117 83 1.00
ACGTcount: A:0.23, C:0.09, G:0.26, T:0.43
Consensus pattern (117 bp):
TGGTTAATTGTGATTTAGCATTGCAATTTCAGTGCCACAATGTAGGGTTTGTTTTGTCAATTTAT
GATGCGATAGTGGTCCCGATGATGTTGATAAAACTGTTGTAAAAATTGTATA
Found at i:18783986 original size:51 final size:51
Alignment explanation
Indices: 18783927--18784078 Score: 232
Period size: 51 Copynumber: 3.0 Consensus size: 51
18783917 GTTGCTGGTA
* * * *
18783927 ATGAATATGCTAGTAATTCTGCAACCTCAGATGGAGTGGATAATGTTGCTG
1 ATGAATATGCTGGTGATTTTGCAACATCAGATGGAGTGGATAATGTTGCTG
* * *
18783978 ATGAATATGTTGGTGATTTTACAACATCAGATGGAGTGGATAATATTGCTG
1 ATGAATATGCTGGTGATTTTGCAACATCAGATGGAGTGGATAATGTTGCTG
*
18784029 ATGAATATGCTGGTGATTTTGCAACATCAGATGGACTGGATAATGTTGCT
1 ATGAATATGCTGGTGATTTTGCAACATCAGATGGAGTGGATAATGTTGCT
18784079 ACTGCACGTA
Statistics
Matches: 90, Mismatches: 11, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
51 90 1.00
ACGTcount: A:0.30, C:0.11, G:0.26, T:0.34
Consensus pattern (51 bp):
ATGAATATGCTGGTGATTTTGCAACATCAGATGGAGTGGATAATGTTGCTG
Found at i:18787840 original size:33 final size:33
Alignment explanation
Indices: 18787803--18787882 Score: 85
Period size: 32 Copynumber: 2.5 Consensus size: 33
18787793 TCACGATTTG
* ** *
18787803 GTTTTAAGGGATTTCATGATTTTGTTCCTAATA
1 GTTTTAAGGGATTTCACGATTTCATTCCTAAAA
*
18787836 GTTTT-AGGGA-TTCAACGATTTCATTCGTAAAA
1 GTTTTAAGGGATTTC-ACGATTTCATTCCTAAAA
18787868 GTTTTAA-GGATTTCA
1 GTTTTAAGGGATTTCA
18787883 AGAAGATTTC
Statistics
Matches: 39, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
31 3 0.08
32 27 0.69
33 9 0.23
ACGTcount: A:0.28, C:0.10, G:0.19, T:0.44
Consensus pattern (33 bp):
GTTTTAAGGGATTTCACGATTTCATTCCTAAAA
Found at i:18806895 original size:40 final size:40
Alignment explanation
Indices: 18806618--18806881 Score: 349
Period size: 40 Copynumber: 6.6 Consensus size: 40
18806608 CGAATGATGT
* * * *
18806618 CCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTATAA
* * *
18806658 CCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTA-ATT
1 CCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTATA-A
*
18806698 CCGGGCTAAG-CCCGAAGGCATTGGTGCGAGTTACTA-AA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
* *
18806736 TCCGAGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 -CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
18806777 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
18806817 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
* *
18806857 CCGGGCTATGTCCCAAAGGCATTTG
1 CCGGGCTAAGTCCCGAAGGCATTTG
18806882 AACGAGTAGC
Statistics
Matches: 201, Mismatches: 16, Indels: 14
0.87 0.07 0.06
Matches are distributed among these distances:
39 33 0.16
40 158 0.79
41 10 0.05
ACGTcount: A:0.25, C:0.23, G:0.27, T:0.25
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
Found at i:18806912 original size:159 final size:159
Alignment explanation
Indices: 18806618--18806914 Score: 379
Period size: 159 Copynumber: 1.9 Consensus size: 159
18806608 CGAATGATGT
*
18806618 CCGGGCTAAGTCCCGAAGGCTTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAGGCATTTG
1 CCGGGCTAAGTCCCGAAGGCTTTGTGCTAAGTGACCATAACCGGACTAAGATCCGAAGGCATTTG
* * ** *
18806683 TGCGAGATACTAATTCCGGGCTAAGCCCGAAGGCATTGGTGCGAGTTACTAAATCCGAGTTAAGT
66 TGCGAGATACTAATACCGGGCTAAGCCCAAAGGCATTGGAACGAGTTACTAAATCCGAGTTAAAT
18806748 CCCGAAGGCATTTGTGCGAGTTACTATAA
131 CCCGAAGGCATTTGTGCGAGTTACTATAA
* * * *
18806777 CCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTATAACCGGGCTAAG-TCCCGAAGGCATT
1 CCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATAACCGGACTAAGAT-CCGAAGGCATT
* * * *
18806840 TGTGCGAGTTACT-ATAACCGGGCTATGTCCCAAAGGCATTTGAACGAG-TAGCTATATCCG-GT
64 TGTGCGAGATACTAAT-ACCGGGCTAAG-CCCAAAGGCATTGGAACGAGTTA-CTAAATCCGAGT
*
18806902 TAAATTCCGAAGG
126 TAAATCCCGAAGG
18806915 TACGTGATTT
Statistics
Matches: 118, Mismatches: 15, Indels: 10
0.83 0.10 0.07
Matches are distributed among these distances:
158 3 0.03
159 84 0.71
160 31 0.26
ACGTcount: A:0.26, C:0.22, G:0.27, T:0.25
Consensus pattern (159 bp):
CCGGGCTAAGTCCCGAAGGCTTTGTGCTAAGTGACCATAACCGGACTAAGATCCGAAGGCATTTG
TGCGAGATACTAATACCGGGCTAAGCCCAAAGGCATTGGAACGAGTTACTAAATCCGAGTTAAAT
CCCGAAGGCATTTGTGCGAGTTACTATAA
Found at i:18821739 original size:48 final size:48
Alignment explanation
Indices: 18821515--18821738 Score: 301
Period size: 48 Copynumber: 4.7 Consensus size: 48
18821505 AGTACCAATT
* * *
18821515 CCATGTCCCCGACATGGTCTTACAT--GAATTCACATATCATCGTCGATG
1 CCATGTCCCAGACATGGTCTTACATAGGCA--CACATATCATCGCCGATG
*
18821563 GCATGTCCCAGACATGGTCTTACACTA-GCACACATATCATCGCCGATG
1 CCATGTCCCAGACATGGTCTTACA-TAGGCACACATATCATCGCCGATG
* * *
18821611 CCATGTCCCAAACATGGTCTTACACAGACACACATATCATCGCCGATG
1 CCATGTCCCAGACATGGTCTTACATAGGCACACATATCATCGCCGATG
* * * *
18821659 CCATGTCCCAGACATGATCTTACACAGGCACATATATCATCGCTGATG
1 CCATGTCCCAGACATGGTCTTACATAGGCACACATATCATCGCCGATG
18821707 CCATGTCCCAGACATGGTCTTACATAGGCACA
1 CCATGTCCCAGACATGGTCTTACATAGGCACA
18821739 TTCAGCACAG
Statistics
Matches: 158, Mismatches: 15, Indels: 6
0.88 0.08 0.03
Matches are distributed among these distances:
47 1 0.01
48 154 0.97
49 1 0.01
50 2 0.01
ACGTcount: A:0.28, C:0.31, G:0.17, T:0.24
Consensus pattern (48 bp):
CCATGTCCCAGACATGGTCTTACATAGGCACACATATCATCGCCGATG
Found at i:18824106 original size:13 final size:13
Alignment explanation
Indices: 18824068--18824119 Score: 63
Period size: 13 Copynumber: 4.1 Consensus size: 13
18824058 AGTTTGGCAA
18824068 TGCTTTTG-AAAG
1 TGCTTTTGAAAAG
*
18824080 TGC-TGTGAAAAAG
1 TGCTTTTG-AAAAG
*
18824093 TGCTTTTGATAAG
1 TGCTTTTGAAAAG
18824106 TGCTTTTGAAAAG
1 TGCTTTTGAAAAG
18824119 T
1 T
18824120 TTGGTTTAAA
Statistics
Matches: 33, Mismatches: 4, Indels: 5
0.79 0.10 0.12
Matches are distributed among these distances:
11 3 0.09
12 3 0.09
13 24 0.73
14 3 0.09
ACGTcount: A:0.29, C:0.08, G:0.25, T:0.38
Consensus pattern (13 bp):
TGCTTTTGAAAAG
Found at i:18825192 original size:15 final size:15
Alignment explanation
Indices: 18825167--18825235 Score: 86
Period size: 15 Copynumber: 4.6 Consensus size: 15
18825157 GAGATGACAT
*
18825167 GAAAACCAAGATAAA
1 GAAATCCAAGATAAA
* *
18825182 GAAGTCCAAGAAAAA
1 GAAATCCAAGATAAA
*
18825197 GAAATCCATGATAAA
1 GAAATCCAAGATAAA
18825212 GAAATCCAAGATACAA
1 GAAATCCAAGATA-AA
18825228 -AAATCCAA
1 GAAATCCAA
18825236 AATACTATAT
Statistics
Matches: 46, Mismatches: 7, Indels: 2
0.84 0.13 0.04
Matches are distributed among these distances:
15 44 0.96
16 2 0.04
ACGTcount: A:0.59, C:0.16, G:0.13, T:0.12
Consensus pattern (15 bp):
GAAATCCAAGATAAA
Found at i:18831890 original size:96 final size:96
Alignment explanation
Indices: 18831726--18832008 Score: 557
Period size: 96 Copynumber: 2.9 Consensus size: 96
18831716 TCTGGATATG
*
18831726 GACTGGTTAACTCAACATGAAGCAGTGGTAAACTGCAAACAAAATCATATTGTATTGAAATTTTA
1 GACTGGTTAACTCAACATGAAACAGTGGTAAACTGCAAACAAAATCATATTGTATTGAAATTTTA
18831791 GAATGGTGAAATGCTCTGTATTGAATGTATA
66 GAATGGTGAAATGCTCTGTATTGAATGTATA
18831822 GACTGGTTAACTCAACATGAAACAGTGGTAAACTGCAAACAAAATCATATTGTATTGAAATTTTA
1 GACTGGTTAACTCAACATGAAACAGTGGTAAACTGCAAACAAAATCATATTGTATTGAAATTTTA
18831887 GAATGGTGAAATGCTCTGTATTGAATGTATA
66 GAATGGTGAAATGCTCTGTATTGAATGTATA
18831918 GACTGGTTAACTCAACATGAAACAGTGGTAAACTGCAAACAAAATCATATTGTATTGAAATTTTA
1 GACTGGTTAACTCAACATGAAACAGTGGTAAACTGCAAACAAAATCATATTGTATTGAAATTTTA
18831983 GAATGGTGAAATGCTCTGTATTGAAT
66 GAATGGTGAAATGCTCTGTATTGAAT
18832009 CTAATAAAGT
Statistics
Matches: 186, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
96 186 1.00
ACGTcount: A:0.38, C:0.12, G:0.19, T:0.31
Consensus pattern (96 bp):
GACTGGTTAACTCAACATGAAACAGTGGTAAACTGCAAACAAAATCATATTGTATTGAAATTTTA
GAATGGTGAAATGCTCTGTATTGAATGTATA
Found at i:18848969 original size:27 final size:26
Alignment explanation
Indices: 18848925--18848976 Score: 68
Period size: 27 Copynumber: 2.0 Consensus size: 26
18848915 CTCGCTGCAA
*
18848925 TCTGGTGGCCTCGCCACATATATCTGT
1 TCTGGTGACCTCGCCACA-ATATCTGT
* *
18848952 TCTGGTGACTTCGTCACAATATCTG
1 TCTGGTGACCTCGCCACAATATCTG
18848977 GCAGCCTCGC
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
26 7 0.32
27 15 0.68
ACGTcount: A:0.17, C:0.27, G:0.21, T:0.35
Consensus pattern (26 bp):
TCTGGTGACCTCGCCACAATATCTGT
Found at i:18849025 original size:67 final size:67
Alignment explanation
Indices: 18848906--18849059 Score: 265
Period size: 67 Copynumber: 2.3 Consensus size: 67
18848896 GAGGAAGCGT
*
18848906 TCTGGCAGCCTCGCTGCAATCTGGTGGCCTCGCCACATATATCTGTTCTGGTGACTTCGTCACAA
1 TCTGGCAGCCTCGCTGCAATCTGGTGGCCTAGCCACATATATCTGTTCTGGTGACTTCGTCACAA
18848971 TA
66 TA
*
18848973 TCTGGCAGCCTCGCTGCAATCTGGTGGCCTAGCCAC-TATATCTGTATTTGGTGACTTCGTCACA
1 TCTGGCAGCCTCGCTGCAATCTGGTGGCCTAGCCACATATATCTGT-TCTGGTGACTTCGTCACA
18849037 ATA
65 ATA
*
18849040 TCTGGAAGCCTCGCTGCAAT
1 TCTGGCAGCCTCGCTGCAAT
18849060 TTTTGTGGTT
Statistics
Matches: 83, Mismatches: 3, Indels: 2
0.94 0.03 0.02
Matches are distributed among these distances:
66 9 0.11
67 74 0.89
ACGTcount: A:0.19, C:0.29, G:0.23, T:0.30
Consensus pattern (67 bp):
TCTGGCAGCCTCGCTGCAATCTGGTGGCCTAGCCACATATATCTGTTCTGGTGACTTCGTCACAA
TA
Found at i:18854180 original size:43 final size:42
Alignment explanation
Indices: 18854126--18854232 Score: 153
Period size: 43 Copynumber: 2.5 Consensus size: 42
18854116 TGAGATTACA
* *
18854126 TGTAAGACCATGTTTGGGACATTGGCAT-TGTATTGTGATTATG
1 TGTAAGACCATGTCTGGGACATTGGCATAT-TAAT-TGATTATG
18854169 TGTAAGACCATGTCTGGGACATTGGCATCATTAATTGATTATG
1 TGTAAGACCATGTCTGGGACATTGGCAT-ATTAATTGATTATG
*
18854212 TGTAAGACCCTGTCTGGGACA
1 TGTAAGACCATGTCTGGGACA
18854233 GTAGCATCGA
Statistics
Matches: 59, Mismatches: 3, Indels: 4
0.89 0.05 0.06
Matches are distributed among these distances:
43 55 0.93
44 3 0.05
45 1 0.02
ACGTcount: A:0.25, C:0.14, G:0.26, T:0.35
Consensus pattern (42 bp):
TGTAAGACCATGTCTGGGACATTGGCATATTAATTGATTATG
Found at i:18857493 original size:15 final size:15
Alignment explanation
Indices: 18857458--18857497 Score: 55
Period size: 15 Copynumber: 2.6 Consensus size: 15
18857448 CTTTTTCTAC
18857458 CAAATTATAAACAATT
1 CAAA-TATAAACAATT
18857474 CAAATATACAACAATT
1 CAAATATA-AACAATT
18857490 -AAATATAA
1 CAAATATAA
18857498 TCATACCATA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
14 1 0.04
15 11 0.48
16 11 0.48
ACGTcount: A:0.60, C:0.12, G:0.00, T:0.28
Consensus pattern (15 bp):
CAAATATAAACAATT
Found at i:18860142 original size:84 final size:85
Alignment explanation
Indices: 18859932--18860277 Score: 295
Period size: 84 Copynumber: 4.1 Consensus size: 85
18859922 ACCACCACTG
* * ** * * ** *
18859932 ATTTGCAATTACTGTCACTTGTCATG-GGGCACAACATATTTACATATTAAACAAACTACCACTT
1 ATTTGCAGTTACTGCCACTTGTTGTGAGTGCACAACATATTTACAGAGCAAACAAACTGCCACTT
* *
18859996 GGTTCGTTATTGAACCACACT
66 GGTTTGTGATTGAACCACA-T
* ** * * ** *
18860017 GTTTTTAGTTACTGCCGCTTGTTGTGAGTGCACGACATATTTGTAG-GCAAACAAACTGTCACTT
1 ATTTGCAGTTACTGCCACTTGTTGTGAGTGCACAACATATTTACAGAGCAAACAAACTGCCACTT
*
18860081 GGTTTGTGATTGAACCATAT
66 GGTTTGTGATTGAACCACAT
* * * ** * *
18860101 ATTTGCAGTTACTGCCACTTTTTGTGGGTGCACAATATATTTACAGATTAAACAAAGTGCCACTC
1 ATTTGCAGTTACTGCCACTTGTTGTGAGTGCACAACATATTTACAGAGCAAACAAACTGCCACTT
18860166 GGTTTGTGATTGAACCACAT
66 GGTTTGTGATTGAACCACAT
* * * * ** *
18860186 A-TTGCAGTTACT-CAAACTTGTTGTGAGTACACAACATATTTGCATATTAAACAAATTGCCACT
1 ATTTGCAGTTACTGC-CACTTGTTGTGAGTGCACAACATATTTACAGAGCAAACAAACTGCCACT
** *
18860249 CAGTTCGTGATTGAACCACACT
65 TGGTTTGTGATTGAACCACA-T
*
18860271 GTTTGCA
1 ATTTGCA
18860278 AATTGAACTA
Statistics
Matches: 209, Mismatches: 47, Indels: 9
0.79 0.18 0.03
Matches are distributed among these distances:
83 1 0.00
84 107 0.51
85 82 0.39
86 19 0.09
ACGTcount: A:0.29, C:0.20, G:0.17, T:0.34
Consensus pattern (85 bp):
ATTTGCAGTTACTGCCACTTGTTGTGAGTGCACAACATATTTACAGAGCAAACAAACTGCCACTT
GGTTTGTGATTGAACCACAT
Found at i:18868163 original size:5 final size:5
Alignment explanation
Indices: 18868155--18868180 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
18868145 AGTAAATACT
18868155 TTTTA TTTTA TTTTA TTTTA TTTTA T
1 TTTTA TTTTA TTTTA TTTTA TTTTA T
18868181 CCAATTTTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (5 bp):
TTTTA
Found at i:18873225 original size:17 final size:18
Alignment explanation
Indices: 18873192--18873230 Score: 62
Period size: 17 Copynumber: 2.2 Consensus size: 18
18873182 TTCATGAACT
18873192 ACACTAGGGTTTCTAGGGC
1 ACACTAGGG-TTCTAGGGC
18873211 ACACTAGGG-TCTAGGGC
1 ACACTAGGGTTCTAGGGC
18873228 ACA
1 ACA
18873231 TTCTTTGAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
17 11 0.55
19 9 0.45
ACGTcount: A:0.26, C:0.23, G:0.31, T:0.21
Consensus pattern (18 bp):
ACACTAGGGTTCTAGGGC
Found at i:18877022 original size:93 final size:93
Alignment explanation
Indices: 18876909--18877080 Score: 317
Period size: 93 Copynumber: 1.8 Consensus size: 93
18876899 CGCCCATAAG
* *
18876909 CGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
18876974 ACGAGTTCGGATGCCTAGTTACATCTCA
66 ACGAGTTCGGATGCCTAGTTACATCTCA
*
18877002 CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
18877067 ACGAGTTCGGATGC
66 ACGAGTTCGGATGC
18877081 TCAACCATCC
Statistics
Matches: 76, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
93 76 1.00
ACGTcount: A:0.28, C:0.30, G:0.22, T:0.21
Consensus pattern (93 bp):
CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
ACGAGTTCGGATGCCTAGTTACATCTCA
Found at i:18877077 original size:46 final size:46
Alignment explanation
Indices: 18876902--18877077 Score: 216
Period size: 46 Copynumber: 3.8 Consensus size: 46
18876892 TGTAACCCGC
* * *
18876902 CCATAAGCGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
* *
18876948 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTT-ACAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGA---C-A-TTCGCAT
*
18876998 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
*
18877041 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGA
18877078 TGCTCAACCA
Statistics
Matches: 111, Mismatches: 10, Indels: 18
0.80 0.07 0.13
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
44 2 0.02
45 2 0.02
46 63 0.57
47 29 0.26
48 2 0.02
49 2 0.02
50 3 0.03
51 2 0.02
ACGTcount: A:0.29, C:0.30, G:0.21, T:0.20
Consensus pattern (46 bp):
CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
Found at i:18884601 original size:93 final size:93
Alignment explanation
Indices: 18884494--18884664 Score: 315
Period size: 93 Copynumber: 1.8 Consensus size: 93
18884484 GCCCCTAAGT
* *
18884494 GAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
18884559 CGAGTTCGGATGCCTAGTTACATCTCAC
66 CGAGTTCGGATGCCTAGTTACATCTCAC
*
18884587 GAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
18884652 CGAGTTCGGATGC
66 CGAGTTCGGATGC
18884665 TCAACCATCC
Statistics
Matches: 75, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
93 75 1.00
ACGTcount: A:0.28, C:0.29, G:0.22, T:0.21
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
CGAGTTCGGATGCCTAGTTACATCTCAC
Found at i:18884661 original size:46 final size:46
Alignment explanation
Indices: 18884489--18884661 Score: 219
Period size: 46 Copynumber: 3.7 Consensus size: 46
18884479 AACCCGCCCC
* * *
18884489 TAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA
*
18884535 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTT-ACAT-C-
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGA---C-A-TTCGCATCCA
* *
18884583 TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA
18884628 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
18884662 TGCTCAACCA
Statistics
Matches: 109, Mismatches: 9, Indels: 18
0.80 0.07 0.13
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
44 2 0.02
45 2 0.02
46 61 0.56
47 29 0.27
48 2 0.02
49 2 0.02
50 3 0.03
51 2 0.02
ACGTcount: A:0.29, C:0.28, G:0.21, T:0.21
Consensus pattern (46 bp):
TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA
Found at i:18885118 original size:30 final size:30
Alignment explanation
Indices: 18885084--18885143 Score: 93
Period size: 30 Copynumber: 2.0 Consensus size: 30
18885074 ATTTAATACG
18885084 AACTTTGGAAAAATTACACTTTTGCCCCTA
1 AACTTTGGAAAAATTACACTTTTGCCCCTA
* * *
18885114 AACTTTTGCATAATTACACTTTTGCCCCTA
1 AACTTTGGAAAAATTACACTTTTGCCCCTA
18885144 GGCTCGGGAA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.30, C:0.25, G:0.08, T:0.37
Consensus pattern (30 bp):
AACTTTGGAAAAATTACACTTTTGCCCCTA
Found at i:18887954 original size:24 final size:24
Alignment explanation
Indices: 18887922--18887972 Score: 84
Period size: 24 Copynumber: 2.1 Consensus size: 24
18887912 AAGTCTGTCA
**
18887922 GGATAGGATTTAGGAGTTGATAAG
1 GGATAGGATTTAGGAGCAGATAAG
18887946 GGATAGGATTTAGGAGCAGATAAG
1 GGATAGGATTTAGGAGCAGATAAG
18887970 GGA
1 GGA
18887973 GGAAATCTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.35, C:0.02, G:0.39, T:0.24
Consensus pattern (24 bp):
GGATAGGATTTAGGAGCAGATAAG
Found at i:18893868 original size:24 final size:24
Alignment explanation
Indices: 18893836--18893910 Score: 132
Period size: 24 Copynumber: 3.1 Consensus size: 24
18893826 AAGTCTGTCA
18893836 GGATAGGATTTAGGAGTTGATAAG
1 GGATAGGATTTAGGAGTTGATAAG
18893860 GGATAGGATTTAGGAGTTGATAAG
1 GGATAGGATTTAGGAGTTGATAAG
**
18893884 GGATAGGATTTAGGAGCAGATAAG
1 GGATAGGATTTAGGAGTTGATAAG
18893908 GGA
1 GGA
18893911 GGAAATCTAG
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 49 1.00
ACGTcount: A:0.35, C:0.01, G:0.39, T:0.25
Consensus pattern (24 bp):
GGATAGGATTTAGGAGTTGATAAG
Found at i:18893922 original size:48 final size:48
Alignment explanation
Indices: 18893836--18893933 Score: 119
Period size: 48 Copynumber: 2.0 Consensus size: 48
18893826 AAGTCTGTCA
** * *
18893836 GGATAGGATTTAGGAGTTGATAAGGGATAGGATTTAGGAGTTGAT-AAG
1 GGATAGGATTTAGGAGCAGATAAGGGA-AGGATCTAGGAGCTGATCAAG
18893884 GGATAGGATTTAGGAGCAGATAAGGG-AGGAAATCTAGGAGCTGATCAAG
1 GGATAGGATTTAGGAGCAGATAAGGGAAGG--ATCTAGGAGCTGATCAAG
18893933 G
1 G
18893934 AACAAGAGGT
Statistics
Matches: 43, Mismatches: 4, Indels: 5
0.83 0.08 0.10
Matches are distributed among these distances:
46 3 0.07
48 36 0.84
49 4 0.09
ACGTcount: A:0.35, C:0.04, G:0.38, T:0.23
Consensus pattern (48 bp):
GGATAGGATTTAGGAGCAGATAAGGGAAGGATCTAGGAGCTGATCAAG
Found at i:18897749 original size:40 final size:43
Alignment explanation
Indices: 18897718--18897869 Score: 159
Period size: 43 Copynumber: 3.6 Consensus size: 43
18897708 TGATTCCTGC
* * *
18897718 AAGACCACGTTTGGGACATTGGCATCGATTTGTGATTTACGTGT
1 AAGACCACGTCTGGGACATTGGCATCGA-TTGTGAGTTACATGT
* * * *
18897762 AAGACCATGTCTGGGACATCGGCATTG--TATGAGTT-CATGT
1 AAGACCACGTCTGGGACATTGGCATCGATTGTGAGTTACATGT
** *
18897802 AAGACCTTGTCTGGGACAGTGGCATCGATATGTGA-TTACATGT
1 AAGACCACGTCTGGGACATTGGCATCGAT-TGTGAGTTACATGT
*
18897845 AAGACCACGTCTGGGACGTTGGCAT
1 AAGACCACGTCTGGGACATTGGCAT
18897870 TGTACAAGCT
Statistics
Matches: 88, Mismatches: 16, Indels: 9
0.78 0.14 0.08
Matches are distributed among these distances:
40 27 0.31
41 6 0.07
42 2 0.02
43 30 0.34
44 23 0.26
ACGTcount: A:0.24, C:0.18, G:0.28, T:0.30
Consensus pattern (43 bp):
AAGACCACGTCTGGGACATTGGCATCGATTGTGAGTTACATGT
Found at i:18909440 original size:2 final size:2
Alignment explanation
Indices: 18909433--18909462 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
18909423 GAAGAAAAAT
18909433 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
18909463 AGAAGAGGTG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:18913474 original size:14 final size:14
Alignment explanation
Indices: 18913455--18913487 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
18913445 AAGGTTGATG
*
18913455 CTTATGTAATGTAT
1 CTTATGAAATGTAT
18913469 CTTATGAAATGTAT
1 CTTATGAAATGTAT
18913483 -TTATG
1 CTTATG
18913488 GTATAAATGA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 5 0.28
14 13 0.72
ACGTcount: A:0.30, C:0.06, G:0.15, T:0.48
Consensus pattern (14 bp):
CTTATGAAATGTAT
Found at i:18918890 original size:22 final size:22
Alignment explanation
Indices: 18918864--18918935 Score: 110
Period size: 22 Copynumber: 3.3 Consensus size: 22
18918854 CTAAGTCAAT
*
18918864 AGGACGGCTCAACGCCATAGAC
1 AGGACGGCTCAACGCCGTAGAC
*
18918886 AGGACGACTCAAC-CCTGTAGAC
1 AGGACGGCTCAACGCC-GTAGAC
18918908 AGGACGGCTCAACGCCGTAGAC
1 AGGACGGCTCAACGCCGTAGAC
18918930 AGGACG
1 AGGACG
18918936 ACTAAAAGCC
Statistics
Matches: 45, Mismatches: 3, Indels: 4
0.87 0.06 0.08
Matches are distributed among these distances:
21 2 0.04
22 41 0.91
23 2 0.04
ACGTcount: A:0.31, C:0.31, G:0.29, T:0.10
Consensus pattern (22 bp):
AGGACGGCTCAACGCCGTAGAC
Found at i:18918946 original size:22 final size:21
Alignment explanation
Indices: 18918881--18918948 Score: 73
Period size: 22 Copynumber: 3.1 Consensus size: 21
18918871 CTCAACGCCA
* *
18918881 TAGACAGGACGACTCAACCCTG
1 TAGACAGGACGACTAAAGCC-G
* *
18918903 TAGACAGGACGGCTCAACGCCG
1 TAGACAGGACGACT-AAAGCCG
18918925 TAGACAGGACGACTAAAAGCCG
1 TAGACAGGACGACT-AAAGCCG
18918947 TA
1 TA
18918949 AATATCTCAA
Statistics
Matches: 38, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
22 35 0.92
23 3 0.08
ACGTcount: A:0.34, C:0.28, G:0.26, T:0.12
Consensus pattern (21 bp):
TAGACAGGACGACTAAAGCCG
Found at i:18921280 original size:48 final size:50
Alignment explanation
Indices: 18921214--18921331 Score: 116
Period size: 48 Copynumber: 2.4 Consensus size: 50
18921204 TAGTTCTCTG
** * * **
18921214 GAGCTTCCCAATAT-TGGCTCCCTTGAACTTCCCGATA-TTGGCTCGTAT
1 GAGCTTCCCGTTATATGGCTCCCTGGAACTTCCCGATACATGGCTCACAT
* * * *
18921262 GAGCTTCTCGTTA-ATGGCTCTCTGGAGCTTCCCGTTACATGGCTCACAT
1 GAGCTTCCCGTTATATGGCTCCCTGGAACTTCCCGATACATGGCTCACAT
*
18921311 GAGTTTCCCGTTATATGGCTC
1 GAGCTTCCCGTTATATGGCTC
18921332 GAAAGAGCAT
Statistics
Matches: 55, Mismatches: 12, Indels: 4
0.77 0.17 0.06
Matches are distributed among these distances:
48 29 0.53
49 19 0.35
50 7 0.13
ACGTcount: A:0.17, C:0.28, G:0.21, T:0.34
Consensus pattern (50 bp):
GAGCTTCCCGTTATATGGCTCCCTGGAACTTCCCGATACATGGCTCACAT
Found at i:18921318 original size:25 final size:24
Alignment explanation
Indices: 18921214--18921331 Score: 85
Period size: 24 Copynumber: 4.8 Consensus size: 24
18921204 TAGTTCTCTG
** * * *
18921214 GAGCTTCCCAATATTGGCTCCCTT
1 GAGCTTCCCGTTAATGGCTCACAT
* * * **
18921238 GAACTTCCCGATATTGGCTCGTAT
1 GAGCTTCCCGTTAATGGCTCACAT
* *
18921262 GAGCTTCTCGTTAATGGCTCTC-T
1 GAGCTTCCCGTTAATGGCTCACAT
18921285 GGAGCTTCCCGTTACATGGCTCACAT
1 -GAGCTTCCCGTTA-ATGGCTCACAT
*
18921311 GAGTTTCCCGTTATATGGCTC
1 GAGCTTCCCGTTA-ATGGCTC
18921332 GAAAGAGCAT
Statistics
Matches: 76, Mismatches: 15, Indels: 5
0.79 0.16 0.05
Matches are distributed among these distances:
23 1 0.01
24 47 0.62
25 27 0.36
26 1 0.01
ACGTcount: A:0.17, C:0.28, G:0.21, T:0.34
Consensus pattern (24 bp):
GAGCTTCCCGTTAATGGCTCACAT
Found at i:18922839 original size:22 final size:22
Alignment explanation
Indices: 18922813--18922855 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
18922803 GATAACAACA
*
18922813 AAATATTCATAGACATGTTCAC
1 AAATATTCATAGACATATTCAC
18922835 AAATATTCATAGACATATTCA
1 AAATATTCATAGACATATTCA
18922856 TAGACATGTT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.44, C:0.16, G:0.07, T:0.33
Consensus pattern (22 bp):
AAATATTCATAGACATATTCAC
Found at i:18922852 original size:12 final size:12
Alignment explanation
Indices: 18922815--18922868 Score: 67
Period size: 12 Copynumber: 4.7 Consensus size: 12
18922805 TAACAACAAA
18922815 ATATTCATAGAC
1 ATATTCATAGAC
* *
18922827 ATGTTCACA-A-
1 ATATTCATAGAC
18922837 ATATTCATAGAC
1 ATATTCATAGAC
18922849 ATATTCATAGAC
1 ATATTCATAGAC
*
18922861 ATGTTCAT
1 ATATTCAT
18922869 CACAAGAATT
Statistics
Matches: 35, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
10 7 0.20
11 2 0.06
12 26 0.74
ACGTcount: A:0.39, C:0.17, G:0.09, T:0.35
Consensus pattern (12 bp):
ATATTCATAGAC
Done.