Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018397375.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_784.0, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 34138
ACGTcount: A:0.26, C:0.09, G:0.09, T:0.25
Warning! 10869 characters in sequence are not A, C, G, or T
Found at i:2892 original size:172 final size:171
Alignment explanation
Indices: 2507--2897 Score: 399
Period size: 172 Copynumber: 2.3 Consensus size: 171
2497 TGGAACATTT
* * **
2507 AGAAAAAGCCATTCA-TTGACAAGAATAGTCCATTTATAGTCACCCATTCCTTCAAAAGTTTTAT
1 AGAAAAAGGCATTCATTTG-CAAGAAAAGTCCATTTATAGTCACCCATTCCTTCAAAAGCCTTAT
* * *
2571 TACTCGTTTTAAATTATTTTATAATCTTATAATTGATTTTAAGTTCAATTATTTTACATTTTTGG
65 TACTCGCTTTAAATTATTGTATAATCTCATAATTGATTTTAAGTTCAATTATTTTACATTTTTGG
* * * * * **
2636 TCGAAACAGACTATAATTTAATGTCTATTTAGAGAAACGTGA
130 TCAAAAAAAACCATAATTGAATGTCTACCTAGAGAAACGTGA
* * * * **********
2678 AGAAAAACGTATTCGTTGGCAANNNNNNNNNNTTTATAGTCACCCATTCCTTCGAAAA-CCTTAT
1 AGAAAAAGGCATTCATTTGCAAGAAAAGTCCATTTATAGTCACCCATTCCTTC-AAAAGCCTTAT
* * * * *
2742 TACTTGCTTTAACTTATTGTATAATGTCATAATTGATTTTAAGTTGAATTGTTTTTACATTTTTG
65 TACTCGCTTTAAATTATTGTATAATCTCATAATTGATTTTAAGTTCAATT-ATTTTACATTTTTG
* **
2807 GTTAAAAAAAACCATAATTGAATGTCTACCTCTAGAAACGTGA
129 GTCAAAAAAAACCATAATTGAATGTCTACCTAGAGAAACGTGA
* *
2850 AGGAAAAGGCATTCATTTGCAAGAAAAGTTCATTTATAGTCACCCATT
1 AGAAAAAGGCATTCATTTGCAAGAAAAGTCCATTTATAGTCACCCATT
2898 NNNNNNNNNN
Statistics
Matches: 167, Mismatches: 50, Indels: 5
0.75 0.23 0.02
Matches are distributed among these distances:
171 82 0.49
172 85 0.51
ACGTcount: A:0.34, C:0.14, G:0.12, T:0.37
Consensus pattern (171 bp):
AGAAAAAGGCATTCATTTGCAAGAAAAGTCCATTTATAGTCACCCATTCCTTCAAAAGCCTTATT
ACTCGCTTTAAATTATTGTATAATCTCATAATTGATTTTAAGTTCAATTATTTTACATTTTTGGT
CAAAAAAAACCATAATTGAATGTCTACCTAGAGAAACGTGA
Found at i:4293 original size:171 final size:162
Alignment explanation
Indices: 4062--4376 Score: 316
Period size: 171 Copynumber: 1.9 Consensus size: 162
4052 AAAGCTATTG
* * *
4062 AAGGAATGAGTGACTATAAATGGACTATTCCTGTCACTGAATGGCTTTTTCAAAATGTTTCCT-G
1 AAGGAATGAGTGACTATAAATGGACTATTCCTGTCAATGAATGCCTTTTGCAAAATGTTT-CTAG
* * ** *
4126 AGGTAAACATTTAATTATTATCTGTTTT-AA-TGAAAAT-TATAAAAAAATTCAATTTAAAATTA
65 AGGTAAACATTCAATTATGAT-TGTTTTAAACAAAAAATGTA-AAAAAAATTCAACTTAAAATTA
*
4188 ACTATGAGTTTATAAAACCATTTAAAACGAGTAAT
128 ACTATGAGATTATAAAACCATTTAAAACGAGTAAT
* * ***
4223 AAGNNNNNNNNNNGAATGAGTGACTATAAATGGACTTTTCTTG-CAAATGAATGCCTTTTGCTTC
1 AAG----------GAATGAGTGACTATAAATGGACTATTCCTGTC-AATGAATGCCTTTTGCAAA
* *
4287 ATGTTTCTAGAGGTAAACATTCAATTATGGTTTTTTTAAACAAAAAATGTAAAAAAAATTCAACT
55 ATGTTTCTAGAGGTAAACATTCAATTATGATTGTTTTAAACAAAAAATGTAAAAAAAATTCAACT
*
4352 TAAAATTAATTATGAGATTATAAAA
120 TAAAATTAACTATGAGATTATAAAA
4377 TAATNNNNNN
Statistics
Matches: 122, Mismatches: 17, Indels: 19
0.77 0.11 0.12
Matches are distributed among these distances:
161 3 0.02
170 8 0.07
171 68 0.56
172 41 0.34
173 2 0.02
ACGTcount: A:0.39, C:0.10, G:0.13, T:0.35
Consensus pattern (162 bp):
AAGGAATGAGTGACTATAAATGGACTATTCCTGTCAATGAATGCCTTTTGCAAAATGTTTCTAGA
GGTAAACATTCAATTATGATTGTTTTAAACAAAAAATGTAAAAAAAATTCAACTTAAAATTAACT
ATGAGATTATAAAACCATTTAAAACGAGTAAT
Found at i:4426 original size:172 final size:161
Alignment explanation
Indices: 4236--4552 Score: 321
Period size: 172 Copynumber: 1.9 Consensus size: 161
4226 NNNNNNNNNN
* * * * *
4236 GAATGAGTGACTATAAATGGACTTTTCTTGCAAATGAATGCCTTTTGCTTCATGTTTCTAGAGGT
1 GAATGAGTGACTATAAATGGACTTTACTTGCAAATAAATACCTTTTGCTTCACGTTTCTAGAAGT
* ** * *
4301 AAACATTCAATTATGGT-TTTTTTAAACAAAAAATGTAAAAAAAATTCAACTTAAAATTAATTAT
66 AAACATTCAATTATAGTCTGCTTCAAAC-AAAAATGT-AAAAAAATTCAACTTAAAATCAATTAT
*
4365 GAGATTATAAAATAATNNNNNNNNNNTAATAAGGTTTTCGAAG
129 AAGATTATAAAATAAT----------TAATAAGGTTTTCGAAG
* * * * **
4408 GAATGGGTGACTATAAATGGACTTTACTTGCCAATAAATACGTTTTTCTTCACGTTTCTCTAAGT
1 GAATGAGTGACTATAAATGGACTTTACTTGCAAATAAATACCTTTTGCTTCACGTTTCTAGAAGT
* * * * *
4473 AGAGATTCAATTATAGTCTGCTTCGATCAAAAATGTAAAATAATTCAACTTAAAATCAATTATAA
66 AAACATTCAATTATAGTCTGCTTCAAACAAAAATGTAAAAAAATTCAACTTAAAATCAATTATAA
4538 GATTATAAAATAATT
131 GATTATAAAATAATT
4553 TNNNNNNNNN
Statistics
Matches: 122, Mismatches: 22, Indels: 13
0.78 0.14 0.08
Matches are distributed among these distances:
161 1 0.01
171 40 0.33
172 76 0.62
173 5 0.04
ACGTcount: A:0.38, C:0.11, G:0.13, T:0.35
Consensus pattern (161 bp):
GAATGAGTGACTATAAATGGACTTTACTTGCAAATAAATACCTTTTGCTTCACGTTTCTAGAAGT
AAACATTCAATTATAGTCTGCTTCAAACAAAAATGTAAAAAAATTCAACTTAAAATCAATTATAA
GATTATAAAATAATTAATAAGGTTTTCGAAG
Found at i:5131 original size:171 final size:161
Alignment explanation
Indices: 4828--5139 Score: 349
Period size: 171 Copynumber: 1.9 Consensus size: 161
4818 NNNNNNTAAC
* * * * *
4828 TTAAAATCAATTATGAGATTATAAAACAATTTAAAGTGAGTAATAAGGTTGTTGAAGGAATGAGT
1 TTAAAACCAATTACGAGATTATAAAACAATTTAAAGCGAGTAATAAGGCTATTGAAGGAATGAGT
** * * *
4893 GACTATAAATGGACTTTTCTTTTATATGAATGACTTTTTATACACGTTTCTCGAGGTAAGCATTC
66 GACTATAAATAAACTTTTCTTCTATATGAATGACTTTTTATACACGTTTCTCAAGCTAAGCATTC
4958 AATTGTAGTCTGNNNNNNNNNNAAATATAAAAAAATTTAGA
131 AATTGTAGTCTG----------AAATATAAAAAAATTTAGA
* *
4999 TTAAAACCAATTACGAGGTTAT-AAACTAATTTAAAGCGAGTAATAAGGCTATTGAAGGAATGGG
1 TTAAAACCAATTACGAGATTATAAAAC-AATTTAAAGCGAGTAATAAGGCTATTGAAGGAATGAG
* * * * *
5063 TGACTATAAATAAATTTTTCTTCTATATGAAT-AGCTTTTTCTACAGGTTTCTTAAGCTAGGCAT
65 TGACTATAAATAAACTTTTCTTCTATATGAATGA-CTTTTTATACACGTTTCTCAAGCTAAGCAT
5127 TCAATTGTAGTCT
129 TCAATTGTAGTCT
5140 ATTTTAAGCT
Statistics
Matches: 122, Mismatches: 17, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
170 5 0.04
171 117 0.96
ACGTcount: A:0.36, C:0.10, G:0.16, T:0.35
Consensus pattern (161 bp):
TTAAAACCAATTACGAGATTATAAAACAATTTAAAGCGAGTAATAAGGCTATTGAAGGAATGAGT
GACTATAAATAAACTTTTCTTCTATATGAATGACTTTTTATACACGTTTCTCAAGCTAAGCATTC
AATTGTAGTCTGAAATATAAAAAAATTTAGA
Found at i:6188 original size:171 final size:171
Alignment explanation
Indices: 5903--6216 Score: 418
Period size: 171 Copynumber: 1.8 Consensus size: 171
5893 NNNNNNNNNN
* * * * **
5903 AAAATCAATTATGAGATCATAAAATAATTTAAAGCGAGTAATAAGGCTTTTGAAAGAATTGGTAA
1 AAAATCAAATATAAGATCATAAAATAATTTAAAGCAAGTAATAAAGCTTTTGAAAGAATAAGTAA
* * *
5968 CTATAAATGGACTTTAATTGCCAACGAATACGTTTTTCTTCACGTTTCTCTATGTAGAG-ATTCA
66 CTATAAATGGACTTTAATTGCCAACGAATACGTTTTTCTACACGTTTCTCGATGCAG-GCATTCA
*
6032 ATTATAGTCTGTTTCGATCAAAAATGTAAAAAAATTCAACTT
130 ATTATAGTATGTTTCGATCAAAAATGTAAAAAAATTCAACTT
* * *
6074 AAAATCAAATATAAGATTATAAAATAATTTAAAGCAAGTAATAAAGCTTTTGAAGGAATAAGTGA
1 AAAATCAAATATAAGATCATAAAATAATTTAAAGCAAGTAATAAAGCTTTTGAAAGAATAAGTAA
* * * * *
6139 CTATAAATTGACTTT-TTTTCTCAAGGAAT-GGCTTTTTCTACACGTTTCTCGATGCAGGCATTC
66 CTATAAATGGACTTTAATTGC-CAACGAATACG-TTTTTCTACACGTTTCTCGATGCAGGCATTC
6202 AATTATAGTATGTTT
129 AATTATAGTATGTTT
6217 TAACCAANNN
Statistics
Matches: 122, Mismatches: 18, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
170 5 0.04
171 117 0.96
ACGTcount: A:0.39, C:0.12, G:0.14, T:0.35
Consensus pattern (171 bp):
AAAATCAAATATAAGATCATAAAATAATTTAAAGCAAGTAATAAAGCTTTTGAAAGAATAAGTAA
CTATAAATGGACTTTAATTGCCAACGAATACGTTTTTCTACACGTTTCTCGATGCAGGCATTCAA
TTATAGTATGTTTCGATCAAAAATGTAAAAAAATTCAACTT
Found at i:7515 original size:170 final size:168
Alignment explanation
Indices: 7164--7962 Score: 572
Period size: 170 Copynumber: 4.7 Consensus size: 168
7154 NNNNNNNNGA
* * * * * * *
7164 TGACTATAAATGGACTTCTCTTCCCA-ATGAATA-CTTTTCACTTCACGTTTCTCAAGGTAGACA
1 TGACTATAAATGGACTTTTCTT-CTATATGAATAGCTTTT-TCTACACATTTCTTAAGGTAGGCA
* * * * * * *
7227 TTCAATTATACTCTATTTTAA-CTAAAAACATGAAAAAATTCAACTAAAAATCAATTATGAGATT
64 TTCAATTATAGT-TGTTTTAAGCT-AAAATATAAAAAAAAT-AACTTAAAACCAATTATGAGATT
********* * * *
7291 ATAAAACAANNNNNNNNNNGTAATAAGTCT-TTTAATAGAATGGG
126 ATAAAACAA-TTTAAGCGAGTAATAAGGCTATTGAA-GGAATGGG
* * ** * *
7335 TGACTATAAATGGACTTTTCTTCTATATGAATGGCTTTTTCTATATGTTTCTCAAGGTAGACATT
1 TGACTATAAATGGACTTTTCTTCTATATGAATAGCTTTTTCTACACATTTCTTAAGGTAGGCATT
*
7400 CAATTATAGTATGTTTTAAGCTAAAATATAAAAAAAATAGCTTAAAACCAATTATGAGATTATAA
66 CAATTATAGT-TGTTTTAAGCTAAAATATAAAAAAAATAACTTAAAACCAATTATGAGATTATAA
* *
7465 AATAATTTATAGCGAGTAATAAGGCTATTGAAGAAATGGG
130 AACAATTTA-AGCGAGTAATAAGGCTATTGAAGGAATGGG
* * *
7505 TGACTATAAATGGACTTTTCTTCTATATGAATAGATTTTTCTACACATATCTTGAGGTAGGCATT
1 TGACTATAAATGGACTTTTCTTCTATATGAATAGCTTTTTCTACACATTTCTTAAGGTAGGCATT
* * * * * *
7570 CAATTGTAG-TCTATTAAGCTAAAATGTAAAAAAACTCAACTTACAACCAATTATGAGATTATAA
66 CAATTATAGTTGTTTTAAGCTAAAATATAAAAAAAAT-AACTTAAAACCAATTATGAGATTATAA
********** *
7634 AACAATTTAAAGCNNNNNNNNNNGCTGTTGAAGGAATGGG
130 AACAATTT-AAGCGAGTAATAAGGCTATTGAAGGAATGGG
* ** * * *
7674 TGACTATAAATGGAGTACTCTTGTCA-ATGAATGGC-TTTTCTATACATTTCTTAAGGTAGGCAT
1 TGACTATAAATGGACTTTTCTTCT-ATATGAATAGCTTTTTCTACACATTTCTTAAGGTAGGCAT
* * * * **
7737 TCAATTATAATCTGTTTTAACCAAAAATAGAAAAAACTTTAACTTAAAACCAATTATGAGATTAT
65 TCAATTATAGT-TGTTTTAAGCTAAAATATAAAAAA-AATAACTTAAAACCAATTATGAGATTAT
*********
7802 ANNNNNNNNNNAAGCGAGTAATAAGGCTATTGAAGGAATGGG
128 A-AAACAATTTAAGCGAGTAATAAGGCTATTGAAGGAATGGG
* * * * *
7844 -GACTATAAATAGATTTTTCTTCTATATGAATAGCTTTTTCTACACGTTTCTTGAGCTAGGCATT
1 TGACTATAAATGGACTTTTCTTCTATATGAATAGCTTTTTCTACACATTTCTTAAGGTAGGCATT
* * * * ** * *
7908 CAGTTGCT-GTTTATTTTAAGCGAAAATGCAAAAAAATTCAACTTAAAATCAATTA
66 CAATT-ATAG-TTGTTTTAAGCTAAAATATAAAAAAAAT-AACTTAAAACCAATTA
7963 NNNNNNNNNN
Statistics
Matches: 492, Mismatches: 119, Indels: 35
0.76 0.18 0.05
Matches are distributed among these distances:
168 57 0.12
169 105 0.21
170 238 0.48
171 85 0.17
172 7 0.01
ACGTcount: A:0.37, C:0.12, G:0.14, T:0.33
Consensus pattern (168 bp):
TGACTATAAATGGACTTTTCTTCTATATGAATAGCTTTTTCTACACATTTCTTAAGGTAGGCATT
CAATTATAGTTGTTTTAAGCTAAAATATAAAAAAAATAACTTAAAACCAATTATGAGATTATAAA
ACAATTTAAGCGAGTAATAAGGCTATTGAAGGAATGGG
Found at i:7773 original size:169 final size:168
Alignment explanation
Indices: 7164--8205 Score: 556
Period size: 170 Copynumber: 6.1 Consensus size: 168
7154 NNNNNNNNGA
* * * * * *
7164 TGACTATAAATGGACTTCTCTTCCCA-ATGAAT-ACTTTTC-ACTTCACGTTTCTCAAGGTAGAC
1 TGACTATAAATGGACTTTTCTT-CTATATGAATGGCTTTTCTA--T-ACATTTCTTAAGGTAGGC
* * * * * * *
7226 ATTCAATTATACTCTATTTTAACTAAAAACATGAAAAAATTCAACTAAAAATCAATTATGAGATT
62 ATTCAATTATAGTCTGTTTTAACCAAAAATA-GAAAAAACT-AACTTAAAACCAATTATGAGATT
********** * * *
7291 ATAAAACAANNNNNNNNNNGTAATAAGTCT-TTTAATAGAATGGG
125 ATAAAACAATTTAAAGCGAGTAATAAGGCTATTGAA-GGAATGGG
** * *
7335 TGACTATAAATGGACTTTTCTTCTATATGAATGGCTTTTTCTATATGTTTCTCAAGGTAGACATT
1 TGACTATAAATGGACTTTTCTTCTATATGAATGGC-TTTTCTATACATTTCTTAAGGTAGGCATT
* * * *
7400 CAATTATAGTATGTTTTAAGCTAAAATATA-AAAAAAATAGCTTAAAACCAATTATGAGATTATA
65 CAATTATAGTCTGTTTTAA-CCAAAA-ATAGAAAAAACTAACTTAAAACCAATTATGAGATTATA
* * *
7464 AAATAATTTATAGCGAGTAATAAGGCTATTGAAGAAATGGG
128 AAACAATTTAAAGCGAGTAATAAGGCTATTGAAGGAATGGG
** * * *
7505 TGACTATAAATGGACTTTTCTTCTATATGAATAGATTTTTCTACACATATCTTGAGGTAGGCATT
1 TGACTATAAATGGACTTTTCTTCTATATGAAT-GGCTTTTCTATACATTTCTTAAGGTAGGCATT
* * * * *
7570 CAATTGTAGTC--TATTAAGCTAAAAT-GTAAAAAAACTCAACTTACAACCAATTATGAGATTAT
65 CAATTATAGTCTGTTTTAACCAAAAATAG--AAAAAACT-AACTTAAAACCAATTATGAGATTAT
********** *
7632 AAAACAATTTAAAGCNNNNNNNNNNGCTGTTGAAGGAATGGG
127 AAAACAATTTAAAGCGAGTAATAAGGCTATTGAAGGAATGGG
* ** *
7674 TGACTATAAATGGAGTACTCTTGTCA-ATGAATGGCTTTTCTATACATTTCTTAAGGTAGGCATT
1 TGACTATAAATGGACTTTTCTTCT-ATATGAATGGCTTTTCTATACATTTCTTAAGGTAGGCATT
*
7738 CAATTATAATCTGTTTTAACCAAAAATAGAAAAAACTTTAACTTAAAACCAATTATGAGATTATA
65 CAATTATAGTCTGTTTTAACCAAAAATAGAAAAAAC--TAACTTAAAACCAATTATGAGATTATA
**********
7803 NNNNNNNNNNAAGCGAGTAATAAGGCTATTGAAGGAATGGG
128 AAACAATTTAAAGCGAGTAATAAGGCTATTGAAGGAATGGG
* * * * * * *
7844 -GACTATAAATAGATTTTTCTTCTATATGAATAGCTTTTTCTACACGTTTCTTGAGCTAGGCATT
1 TGACTATAAATGGACTTTTCTTCTATATGAATGGC-TTTTCTATACATTTCTTAAGGTAGGCATT
* * * * * * * * ********
7908 CAGTTGCT-GTTTATTTTAAGCGAAAAT-GCAAAAAAATTCAACTTAAAATCAATTANNNNNNNN
65 CAATT-ATAGTCTGTTTTAACCAAAAATAG--AAAAAACT-AACTTAAAACCAATTATGAGATTA
** * * *
7971 NNAAACCATTTAAAGCGAATAATAAGGCT-TTCGAAGTAATGGG
126 TAAAACAATTTAAAGCGAGTAATAAGGCTATT-GAAGGAATGGG
* * * * * * * **
8014 TGGCTATAAATGGAATTTTCTTACCA-ATTAATGTG-TTTT-T-TCATATTTCTTGAGATAAACA
1 TGACTATAAATGGACTTTTCTT-CTATATGAATG-GCTTTTCTAT-ACATTTCTTAAGGTAGGCA
* * * * * * *
8075 TTCAATTATTA-TCTATTTTAACAAAAAAAAGTAATAAAATTTAATTTAAAATCAATTATAAGAT
63 TTCAATTA-TAGTCTGTTTTAACCAAAAATAG-AA-AAAA-CTAACTTAAAACCAATTATGAGAT
* * * * * *
8139 TATAAAAAAATTTAGAGCGAGTAATAAAGCTTTTGAACGAAT-GA
124 TATAAAACAATTTAAAGCGAGTAATAAGGCTATTGAAGGAATGGG
* *
8183 CGACTATAAATGGTCTTTTCTTC
1 TGACTATAAATGGACTTTTCTTC
8206 CCAAAGAATG
Statistics
Matches: 657, Mismatches: 179, Indels: 73
0.72 0.20 0.08
Matches are distributed among these distances:
166 2 0.00
167 3 0.00
168 50 0.08
169 170 0.26
170 302 0.46
171 111 0.17
172 11 0.02
173 7 0.01
174 1 0.00
ACGTcount: A:0.37, C:0.12, G:0.13, T:0.34
Consensus pattern (168 bp):
TGACTATAAATGGACTTTTCTTCTATATGAATGGCTTTTCTATACATTTCTTAAGGTAGGCATTC
AATTATAGTCTGTTTTAACCAAAAATAGAAAAAACTAACTTAAAACCAATTATGAGATTATAAAA
CAATTTAAAGCGAGTAATAAGGCTATTGAAGGAATGGG
Found at i:8562 original size:171 final size:161
Alignment explanation
Indices: 8336--8652 Score: 295
Period size: 171 Copynumber: 1.9 Consensus size: 161
8326 NNNGCTAGTA
* * * **
8336 ATAAGGCTTTTGAAGGAATGAGTGATTGTAAAGAGACTTATCCTGCCAATGAATGCATTTTTCTT
1 ATAAAGCTTTTGAAGGAATGAGTGACTATAAAGAGACTTATCCTGCCAATGAATGCATTTTAATT
* * *
8401 CACGTTTTCTCAA-G-TAGACATTCAATTATAGT-CTATTTTCATC-AAAAATG-AAAATAAATT
66 CAAG-CTTCTCAAGGCAAG-CATTCAATTAT-GTACTATTTTC-TCAAAAAATGTAAAA-AAATT
8461 CAACTTAAAATCAATTATGAGATTATAAAACAATTT
126 CAACTTAAAATCAATTATGAGATTATAAAACAATTT
* * ** *
8497 NNNNNNNNNNATAAAGCTTTTGAAGGAATGGGTGACTATAAATG-GACTTTTTTTGCCATTGAAT
1 ----------ATAAAGCTTTTGAAGGAATGAGTGACTATAAA-GAGACTTATCCTGCCAATGAAT
* * *
8561 GCATTTTAATTCAAGCTTCTTAAGGCAAGCATTCAATTATTTACTGTTTTCTCAAAAAATGTAAA
55 GCATTTTAATTCAAGCTTCTCAAGGCAAGCATTCAATTATGTACTATTTTCTCAAAAAATGTAAA
*
8626 AACATTCAACTTAAAATCAATTATGAG
120 AAAATTCAACTTAAAATCAATTATGAG
8653 NNNNNNNNNN
Statistics
Matches: 123, Mismatches: 17, Indels: 12
0.81 0.11 0.08
Matches are distributed among these distances:
170 9 0.07
171 107 0.87
172 7 0.06
ACGTcount: A:0.36, C:0.13, G:0.13, T:0.35
Consensus pattern (161 bp):
ATAAAGCTTTTGAAGGAATGAGTGACTATAAAGAGACTTATCCTGCCAATGAATGCATTTTAATT
CAAGCTTCTCAAGGCAAGCATTCAATTATGTACTATTTTCTCAAAAAATGTAAAAAAATTCAACT
TAAAATCAATTATGAGATTATAAAACAATTT
Found at i:9061 original size:173 final size:167
Alignment explanation
Indices: 8773--9965 Score: 716
Period size: 171 Copynumber: 7.0 Consensus size: 167
8763 NNNNTAAGAC
* * * * **
8773 AATTTAAAGTGAGTAATAAGGCTTTTGAAAAAATGGGTAACTATAAATAGATTTTTCTTCTCAAT
1 AATTTAAAGTGAGTAATAAGGCTTTTGAAGAAATGGGTGACTATAAATGGACTTTTCTTAGCAAT
* * * * *
8838 AAATGACTTTTTCTACACGTTTCTTGAGACAGACATTCAATTATAGTCTGTTTTAATGAAATATG
66 AAAT-AC-TTTTCTTCATGTTTCTTAAG-CAGACATTCAATTATAGTCTGTTTT-ATCAAAAATG
* *
8903 AAAAAAAATTGAACTTAAAATCAATTATGAGTTCATAAAACT
127 AAAAAAAATTCAACTTAAAATCAATTATGAGATCATAAAA-T
* * * *
8945 -ATTTAAAGCGAGTAATAAGGCTATTGAAGGAATGGGGGTGACTATAAAGGGACTTTTCTTAGCA
1 AATTTAAAGTGAGTAATAAGGCTTTTGAAGAAAT--GGGTGACTATAAATGGACTTTTCTTAGCA
* *
9009 ATGAATACATTTTGCTTCATGTTTCTCTAAGCAGATATTCAATTATAGTCTGTTTTATCTAAAAA
64 ATAAATAC-TTTT-CTTCATGTTTCT-TAAGCAGACATTCAATTATAGTCTGTTTTATC-AAAAA
* * *
9074 TAAAAAAAAATTCAACTCAAAATCAATTATGAGATCATTAAAT
125 TGAAAAAAAATTCAACTTAAAATCAATTATGAGATCATAAAAT
* * * *
9117 AATTTAAAGTGAGTAATAAGGCTTATGAAGAAATGGGTGACTAGAAATGAACTTTCCTTA-CAAA
1 AATTTAAAGTGAGTAATAAGGCTTTTGAAGAAATGGGTGACTATAAATGGACTTTTCTTAGC-AA
* * * * * *
9181 TAAATACCTTCTCCTTCATGCTTCTTAAGGTAGACATTCAATTATGGTTTGTTTTAACTAAAAAT
65 TAAATA-CTT-TTCTTCATGTTTCTTAA-GCAGACATTCAATTATAGTCTGTTTTATC-AAAAAT
9246 GAAAAAGAATATTCAACTTAAAATCAATTATGAGATCATAAAAT
126 GAAAAA-AA-ATTCAACTTAAAATCAATTATGAGATCATAAAAT
** * * * * *
9290 AATTTAAAAAGAGTAATAAGGCTTTTTACGGAATAGTTGA-TAATAAATGGACTTTTCTT-GCCA
1 AATTTAAAGTGAGTAATAAGGCTTTTGAAGAAATGGGTGACT-ATAAATGGACTTTTCTTAG-CA
* * * * * *
9353 ATGAATGTGCTTTTCTTCATGTTTCTCGAGGCA-AGCATTCAATTATAGTCTATTTTATCCAAAA
64 AT-AA-ATACTTTTCTTCATGTTTCT-TAAGCAGA-CATTCAATTATAGTCTGTTTTATCAAAAA
* *
9417 T-ATAAAAACATTCAACTTAAAATCAATTATGAGATTATAAAAT
125 TGA-AAAAAAATTCAACTTAAAATCAATTATGAGATCATAAAAT
********************* * * **
9460 AATTTAANNNNNNNNNNNNNNNNNNNNNAGGAATGGGTGACTATAAATGGAATTTTCTTCTCAAT
1 AATTTAAAGTGAGTAATAAGGCTTTTGAAGAAATGGGTGACTATAAATGGACTTTTCTTAGCAAT
* * * * * * *
9525 GAATGGCTTTTTTTACACGTTT-TCTAAGGTAAACATTCAATTATTA-TCTGTTTTAATGAAAAA
66 AAAT-ACTTTTCTT-CATGTTTCT-TAA-GCAGACATTCAATTA-TAGTCTGTTTT-ATCAAAAA
* * * * * * * *
9588 TGTAAAAAAATTCAATTTAAAATTAACTATAAGTTTATAAAAC
125 TGAAAAAAAATTCAACTTAAAATCAATTATGAGATCATAAAAT
* * ********** *
9631 CATTTAAAGCGAGTAATANNNNNNNNNNAGGAATGGGTGACTATAAATGGACTTTTCTT-GCAAA
1 AATTTAAAGTGAGTAATAAGGCTTTTGAAGAAATGGGTGACTATAAATGGACTTTTCTTAGC-AA
* * * * * * * * * * *
9695 TGAATGTCTTTTTTTTTATGCTTCTTGAAGTAGGCATTCAATTATACTCTATTTCAACCAAAAAT
65 TAAAT-AC-TTTTCTTCATGTTTCTT-AAGCAGACATTCAATTATAGTCTGTTT-TATCAAAAAT
* * * *
9760 ATAAAACAAAATT-AACTTAAAATCAATTATGAGATTATCAAAC
126 -GAAAA-AAAATTCAACTTAAAATCAATTATGAGATCATAAAAT
* * * * * * *
9803 AATTTAAAGCGTGTAATAAGGCTTTT-AAAAGAATTGGTGACTATAAATAGACTTTTCCTATCAA
1 AATTTAAAGTGAGTAATAAGGCTTTTGAAGA-AATGGGTGACTATAAATGGACTTTTCTTAGCAA
* * * * * ** * * *
9867 TGAATGCATTTTGCTTCATGTTTCTCAGGGCAGACATTCTATTATCTTATATTTTAAGCAAAAAT
65 TAAATAC-TTTT-CTTCATGTTTCTTA-AGCAGACATTCAATTATAGTCTGTTTT-ATCAAAAAT
* *
9932 GTAAAAAAATTCAACTTAAAATCAATTATTAGAT
126 GAAAAAAAATTCAACTTAAAATCAATTATGAGAT
9966 TCTAAGACAA
Statistics
Matches: 800, Mismatches: 178, Indels: 87
0.75 0.17 0.08
Matches are distributed among these distances:
168 1 0.00
169 12 0.01
170 107 0.13
171 270 0.34
172 145 0.18
173 254 0.32
174 10 0.01
175 1 0.00
ACGTcount: A:0.38, C:0.11, G:0.13, T:0.35
Consensus pattern (167 bp):
AATTTAAAGTGAGTAATAAGGCTTTTGAAGAAATGGGTGACTATAAATGGACTTTTCTTAGCAAT
AAATACTTTTCTTCATGTTTCTTAAGCAGACATTCAATTATAGTCTGTTTTATCAAAAATGAAAA
AAAATTCAACTTAAAATCAATTATGAGATCATAAAAT
Found at i:9244 original size:171 final size:170
Alignment explanation
Indices: 8773--9466 Score: 679
Period size: 173 Copynumber: 4.0 Consensus size: 170
8763 NNNNTAAGAC
* * * * *
8773 AATTTAAAGTGAGTAATAAGGCTTTTGAAAAAATGGGTAACTATAAAT-AGATTTTTCTTCTCAA
1 AATTTAAAGTGAGTAATAAGGCTTATGAAGAAATGGGTGACTATAAATGA-ACTTTTCTT-ACAA
* * * * * *
8837 TAAATGA-CTTTTTCTACACGTTTCTTGAGACAGACATTCAATTATAGTCTGTTTTAA-TGAAAT
64 TAAAT-ACCTTTTCCTTCATGTTTCTTAAGGCAGACATTCAATTATAGTCTGTTTTAACT-AAAA
* * *
8900 ATGAAAAAAAATTGAACTTAAAATCAATTATGAGTTCATAAAACT
127 ATAAAAAAAAATTCAACTTAAAATCAATTATGAGATCATAAAA-T
* * * *
8945 -ATTTAAAGCGAGTAATAAGGC-TATTGAAGGAATGGGGGTGACTATAAAGGGACTTTTCTTAGC
1 AATTTAAAGTGAGTAATAAGGCTTA-TGAAGAAAT--GGGTGACTATAAATGAACTTTTCTTA-C
* * * * *
9008 AATGAATACATTTTGCTTCATGTTTCTCTAA-GCAGATATTCAATTATAGTCTGTTTTATCTAAA
62 AATAAATACCTTTTCCTTCATGTTTCT-TAAGGCAGACATTCAATTATAGTCTGTTTTAACTAAA
* *
9072 AATAAAAAAAAATTCAACTCAAAATCAATTATGAGATCATTAAAT
126 AATAAAAAAAAATTCAACTTAAAATCAATTATGAGATCATAAAAT
* *
9117 AATTTAAAGTGAGTAATAAGGCTTATGAAGAAATGGGTGACTAGAAATGAACTTTCCTTACAAAT
1 AATTTAAAGTGAGTAATAAGGCTTATGAAGAAATGGGTGACTATAAATGAACTTTTCTTAC-AAT
* * * * *
9182 AAATACCTTCTCCTTCATGCTTCTTAAGGTAGACATTCAATTATGGTTTGTTTTAACTAAAAATG
65 AAATACCTTTTCCTTCATGTTTCTTAAGGCAGACATTCAATTATAGTCTGTTTTAACTAAAAAT-
*
9247 AAAAAGAATATTCAACTTAAAATCAATTATGAGATCATAAAAT
129 AAAAA-AAAATTCAACTTAAAATCAATTATGAGATCATAAAAT
** * * * * * * * *
9290 AATTTAAAAAGAGTAATAAGGCTTTTTACGGAATAGTTGA-TAATAAATGGACTTTTCTTGCCAA
1 AATTTAAAGTGAGTAATAAGGCTTATGAAGAAATGGGTGACT-ATAAATGAACTTTTCTT-ACAA
* ** ** * * *
9354 TGAATGTGCTTTT-CTTCATGTTTCTCGAGGCA-AGCATTCAATTATAGTCTATTTTATC-CAAA
64 TAAAT-ACCTTTTCCTTCATGTTTCTTAAGGCAGA-CATTCAATTATAGTCTGTTTTAACTAAAA
* * *
9416 ATATAAAAACATTCAACTTAAAATCAATTATGAGATTATAAAAT
127 ATAAAAAAAAATTCAACTTAAAATCAATTATGAGATCATAAAAT
9460 AATTTAA
1 AATTTAA
9467 NNNNNNNNNN
Statistics
Matches: 433, Mismatches: 71, Indels: 38
0.80 0.13 0.07
Matches are distributed among these distances:
170 47 0.11
171 106 0.24
172 14 0.03
173 256 0.59
174 10 0.02
ACGTcount: A:0.40, C:0.12, G:0.14, T:0.35
Consensus pattern (170 bp):
AATTTAAAGTGAGTAATAAGGCTTATGAAGAAATGGGTGACTATAAATGAACTTTTCTTACAATA
AATACCTTTTCCTTCATGTTTCTTAAGGCAGACATTCAATTATAGTCTGTTTTAACTAAAAATAA
AAAAAAATTCAACTTAAAATCAATTATGAGATCATAAAAT
Found at i:9400 original size:344 final size:342
Alignment explanation
Indices: 8773--9466 Score: 834
Period size: 344 Copynumber: 2.0 Consensus size: 342
8763 NNNNTAAGAC
* * * * *
8773 AATTTAAAGTGAGTAATAAGGCTTTTGAAAAAATGGGTAACTATAAATAGATTTTTCTTCTCAAT
1 AATTTAAAGTGAGTAATAAGGCTTATGAAAAAATGGGTAACTAGAAATAGACTTTCCTTCTAAAT
* * * * *
8838 AAATGACTTTTTCTACACGTTTCTTGAGACAGACATTCAATTATAGTCTGTTTTAATGAAATATG
66 AAATGACTTCTCCTACACGCTTCTTAAGACAGACATTCAATTATAGTCTGTTTTAATGAAAAATG
* * **
8903 AAAAAAAATTGAACTTAAAATCAATTATGAGTTCATAAAACTATTTAAAGCGAGTAATAAGGCTA
131 AAAAAAAATTCAACTTAAAATCAATTATGAGATCATAAAACTATTTAAAAAGAGTAATAAGGCTA
*
8968 TTGAAGGAATGGGGGTGACTATAAAGGGACTTTTCTTAGCAATGAATACATTTTGCTTCATGTTT
196 TTGAAGGAAT-GAGGTGACTATAAAGGGACTTTTCTTAGCAATGAATACATTTTGCTTCATGTTT
* * *
9033 CTCTAAGCAGATATTCAATTATAGTCTGTTTTATCTAAAAATAAAAAAAAATTCAACTCAAAATC
260 CTCGAAGCAGACATTCAATTATAGTCTATTTTATC-AAAAATAAAAAAAAATTCAACTCAAAATC
*
9098 AATTATGAGATCATTAAAT
324 AATTATGAGATCATAAAAT
* *
9117 AATTTAAAGTGAGTAATAAGGCTTATGAAGAAATGGGTGACTAGAAAT-GAACTTTCCTTAC-AA
1 AATTTAAAGTGAGTAATAAGGCTTATGAAAAAATGGGTAACTAGAAATAG-ACTTTCCTT-CTAA
* * ** * *
9180 ATAAAT-ACCTTCTCCTTCATGCTTCTTAAGGTAGACATTCAATTATGGTTTGTTTTAACT-AAA
64 ATAAATGA-CTTCTCCTACACGCTTCTTAAGACAGACATTCAATTATAGTCTGTTTTAA-TGAAA
9243 AATGAAAAAGAATATTCAACTTAAAATCAATTATGAGATCATAAAA-TAATTTAAAAAGAGTAAT
127 AATGAAAAA-AA-ATTCAACTTAAAATCAATTATGAGATCATAAAACT-ATTTAAAAAGAGTAAT
* * * * * *
9307 AAGGCTTTTTACGGAAT-AGTTGA-TAATAAATGGACTTTTCTT-GCCAATGAATGTGC-TTTT-
189 AAGGCTATTGAAGGAATGAGGTGACT-ATAAAGGGACTTTTCTTAG-CAATGAA--TACATTTTG
* * * *
9367 CTTCATGTTTCTCGAGGCA-AGCATTCAATTATAGTCTATTTTATCCAAAATATAAAAACATTCA
250 CTTCATGTTTCTCGAAGCAGA-CATTCAATTATAGTCTATTTTATCAAAAATAAAAAAAAATTCA
* *
9431 ACTTAAAATCAATTATGAGATTATAAAAT
314 ACTCAAAATCAATTATGAGATCATAAAAT
9460 AATTTAA
1 AATTTAA
9467 NNNNNNNNNN
Statistics
Matches: 299, Mismatches: 39, Indels: 25
0.82 0.11 0.07
Matches are distributed among these distances:
343 54 0.18
344 175 0.59
345 9 0.03
346 61 0.20
ACGTcount: A:0.40, C:0.12, G:0.14, T:0.35
Consensus pattern (342 bp):
AATTTAAAGTGAGTAATAAGGCTTATGAAAAAATGGGTAACTAGAAATAGACTTTCCTTCTAAAT
AAATGACTTCTCCTACACGCTTCTTAAGACAGACATTCAATTATAGTCTGTTTTAATGAAAAATG
AAAAAAAATTCAACTTAAAATCAATTATGAGATCATAAAACTATTTAAAAAGAGTAATAAGGCTA
TTGAAGGAATGAGGTGACTATAAAGGGACTTTTCTTAGCAATGAATACATTTTGCTTCATGTTTC
TCGAAGCAGACATTCAATTATAGTCTATTTTATCAAAAATAAAAAAAAATTCAACTCAAAATCAA
TTATGAGATCATAAAAT
Found at i:10819 original size:172 final size:162
Alignment explanation
Indices: 10561--10873 Score: 341
Period size: 172 Copynumber: 1.9 Consensus size: 162
10551 NNNNNNNNNN
*
10561 ATAAATGGACTTTACTTGCCAACGAATACGTTTTTCTTCACGTTTCTCTAAGTAAACATTCAATT
1 ATAAATGGACTTTACTTGCCAACGAATACGTTTTTCTTCACGTTTCTCTAAGCAAACATTCAATT
* *
10626 ATAGTCTGTTTCGACCAAAAATGTAAAAAAAATTTAACTTAAAATCAATTATAAGATTATAAAA-
66 ATAGTCTGTTTCAACCAAAAATGTAAAAAAAATTCAACTTAAAATCAATTATAAGATTATAAAAC
10690 TAATTTAAAGCGNNNNNNNNNNCTTTTGAAGGAATGACTGACT
131 T-ATTTAAAGCG----------CTTTTGAAGGAATGACTGACT
* * * *
10733 ATAAATTGACTTTTCTT-CTCAAGGAATA-GCTTTTTCTAT-ACGTTTCTC-AATGCAAGCATTC
1 ATAAATGGACTTTACTTGC-CAACGAATACG-TTTTTCT-TCACGTTTCTCTAA-GCAAACATTC
* ** *
10794 AATTATAGTCTAGTTT-AATCAAAAATGTAAAAAAAATTCAACTTAAAATCTGTTATGAGATTAT
62 AATTATAGTCT-GTTTCAACCAAAAATGTAAAAAAAATTCAACTTAAAATCAATTATAAGATTAT
10858 AAAACTATTTAAAGCG
126 AAAACTATTTAAAGCG
10874 AGTAATANNN
Statistics
Matches: 124, Mismatches: 11, Indels: 12
0.84 0.07 0.08
Matches are distributed among these distances:
171 4 0.03
172 114 0.92
173 6 0.05
ACGTcount: A:0.38, C:0.13, G:0.11, T:0.35
Consensus pattern (162 bp):
ATAAATGGACTTTACTTGCCAACGAATACGTTTTTCTTCACGTTTCTCTAAGCAAACATTCAATT
ATAGTCTGTTTCAACCAAAAATGTAAAAAAAATTCAACTTAAAATCAATTATAAGATTATAAAAC
TATTTAAAGCGCTTTTGAAGGAATGACTGACT
Found at i:11875 original size:21 final size:21
Alignment explanation
Indices: 11846--11885 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
11836 GAATGGGTGA
11846 CAATAAATGGACTTTTCTTGC
1 CAATAAATGGACTTTTCTTGC
* *
11867 CAATGAATGTACTTTTCTT
1 CAATAAATGGACTTTTCTT
11886 CATGTTTCTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.28, C:0.17, G:0.12, T:0.42
Consensus pattern (21 bp):
CAATAAATGGACTTTTCTTGC
Found at i:12834 original size:513 final size:511
Alignment explanation
Indices: 11237--14090 Score: 2127
Period size: 514 Copynumber: 5.6 Consensus size: 511
11227 NNNNNNNNNN
* * * * * *
11237 TTTAACCAAAAATAT-AAAAAAATTTAACTGAAAATCAATTATTAGATTC-TAAAATAGTTTAGA
1 TTTAACCAAAAATATAAAAAAAATTCAACTTAAAATCAATTATGAGA-TCATAAAACAATTTAAA
* * ** * **
11300 GCGAGTAATAAGGCTTTTGAAGGAATGGGTGACTGTAAAT-GAACTTTTCTTGAAAATGAATGTG
65 GC-AGTAATAAGGCTTTTGAAGGAATGGGTGACTATAAATAG-ACTTTACTTGCCAACGAATGAC
* * * * *
11364 TTTTTCTTCATGTTTCT-TGAGATAGACATTAAATTATA-GTATGTTTTC-ATCAAAAATGTTAG
128 TTTTTCTTCATGTTTCTCTAAG-TAGACATTCAATTATATG-ATG-TTTCAACCAAAAATGTAAA
* * * *****
11426 AAAACTCAACTTAAAATCAATTATCAG-TTAATAAAACAATTTAAAGTGAGTAAT-AAGNNNNNN
190 AAAATTCAACTTAAAATCAATTATAAGATT-ATAAAACAATTTAAAGCGAGTAATAAAG-CTTTT
***** * * * * *
11489 NNNNAAATGAGTGACTATAAATGGACTTTTCTTATCAATAAATGGCTTTCTCTACACGTTTC-CT
253 GAAGGAATGGGTGACTATAAATGAACTTTTCTTCTCAATGAATGGCTTTTTCTACACGTTTCTC-
* * * *
11553 GA-GACAGGCT-TTCAATTATAGCCTATTTTAATGAAAAATGA-AACAAAGA-TCAACTTAAAAT
317 GATG-CAGG-TATTCAATTATAGTCTGTTTTAATAAAAAAT-ATAA-AAA-ATTTAACTTAAAAT
* * * * * *
11614 CAATTATGAGTTTATAAAACCATTTAAAGCGAGCAATTAA-GCTTTTGAAAGAATGGGTAACTAG
377 CAATTATGAG-TTATAAAACTATTTAAAGCGAGTAA-TAAGGCTTTTGAAGGAATGAGTGACTAT
* * * * * *
11678 AAATCGA-TTTTCCTTACAAATGACTACCTTTTCCTTCATGTTTCTTG-AGATAGACATTCAATT
440 AAATAGACTTTT-CATGCAAATGAATGCCTTTTTCTTCATGTTTCTTGAAG-TAGACATTCAATT
*
11741 ATGGTTT-T
503 ATGATTTGT
*
11749 TTGTAA-CAAAAA-ATAAAAAACATATTCAACTTAAAATCAATTATGTGATCATAAAACAATTTA
1 TT-TAACCAAAAATATAAAAAA-A-ATTCAACTTAAAATCAATTATGAGATCATAAAACAATTTA
* * * * * *
11812 AAACGAGTAATAAGGCTTTTGACGGAATGGGTGACAATAAATGGACTTTTCTTGCCAATGAATGT
63 AAGC-AGTAATAAGGCTTTTGAAGGAATGGGTGACTATAAATAGACTTTACTTGCCAACGAATG-
* * * * * * *
11877 AC-TTTTCTTCATGTTTCT-TGAGGCA-AGCATTCAATTATCGTCTAT-TTT-ATCTAAAAATAT
126 ACTTTTTCTTCATGTTTCTCT-AAGTAGA-CATTCAATTAT-AT-GATGTTTCAACCAAAAATGT
* * * * *
11937 AAAAAAAAATTCAACCTAAAATAAATTATGAGATTATAAAATAATTTAAAGCGAGTAAT-AAGNN
187 --AAAAAAATTCAACTTAAAATCAATTATAAGATTATAAAACAATTTAAAGCGAGTAATAAAG-C
******** * * *
12001 NNNNNNNNGAATGGGTGACAATAAATGGACTTTTCTTCTCAATGAATGGC-TTTTCATACACATT
249 TTTTGAAGGAATGGGTGACTATAAATGAACTTTTCTTCTCAATGAATGGCTTTTTC-TACACGTT
* * * *** * * ***
12065 TCAT-AAGGTAAACATTCAATTATTA-TCTGTTTTAACAAAAAATGTAAAAAAATTTAACTNNNN
313 TC-TCGATGCAGGTATTCAATTA-TAGTCTGTTTTAATAAAAAATAT-AAAAAATTTAACT-TAA
*************** * * *
12128 NNNNNNNNNNNNNNNATAAAACCATTTAAAGCGAGTAATAAGGCGTTTGAAGGAATGGGTGACTA
374 AATCAATTATGAGTTATAAAACTATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGAGTGACTA
* * * * *
12193 TAAA-AGGACTTTTCTTGCAAATTAATGCCTTTTCCTTCATGTTTCTAGAGGTAGACATTCAATT
439 TAAATA-GACTTTTCATGCAAATGAATGCCTTTTTCTTCATGTTTCTTGAAGTAGACATTCAATT
*
12257 ATGGTTTGT
503 ATGATTTGT
* * * * *
12266 TTTAA-CAAAAAAAGTAAAAATAAGTCAACTTAGAATCAATTCTGAGATCATAAAACAATTTAAA
1 TTTAACCAAAAATA-TAAAAAAAATTCAACTTAAAATCAATTATGAGATCATAAAACAATTTAAA
********** *
12330 GCGAGTAANNNNNNNNNNGAAGGAATGGGTGACTATAAATAGACTTTACTTGCCAGCGAATG-CG
65 GC-AGTAATAAGGCTTTTGAAGGAATGGGTGACTATAAATAGACTTTACTTGCCAACGAATGAC-
* *
12394 TTTTTCTTCATGTTTCTCTAAGTAGACATTCAACTGTA-GACTGTTTCAACCAAAAATGTAAAAA
128 TTTTTCTTCATGTTTCTCTAAGTAGACATTCAATTATATGA-TGTTTCAACCAAAAATGTAAAAA
* * *
12458 TATTCAACTTAAAATCAATTATAAGATTATAAAACAATTTAAAGCAAGTACTAAAGCTTTTGAAG
192 AATTCAACTTAAAATCAATTATAAGATTATAAAACAATTTAAAGCGAGTAATAAAGCTTTTGAAG
* *
12523 GAATGGGTGATTATAAATTAACTTTTCTTCTCAATGAATGGC-TTTTCTACACGTTTCTCGATGC
257 GAATGGGTGACTATAAATGAACTTTTCTTCTCAATGAATGGCTTTTTCTACACGTTTCTCGATGC
**
12587 AGGTATTCAATTATAGTCTGTTTTAACCAAAAATATAAAAGAATTTAACTTAAAATCAATTATGA
322 AGGTATTCAATTATAGTCTGTTTTAATAAAAAATATAAAA-AATTTAACTTAAAATCAATTATGA
* **********
12652 GATTATTAAACTATTTAAANNNNNNNNNNAGGCTTTTGAAGGAATGAGTGACTATAAATAGACTT
386 G-TTATAAAACTATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGAGTGACTATAAATAGACTT
* * * * *
12717 TTCATGCTAATGAATGTCTTTTTTTTCATGTTTCTTGAAGTAAACATTAAATTAT-ATTCTGT
450 TTCATGCAAATGAATGCCTTTTTCTTCATGTTTCTTGAAGTAGACATTCAATTATGATT-TGT
* *
12779 TTTAACCAAAAATATAAAAAAAATTTAACTTAAAA-CTAATTATGAGATTATAAAACAATTTAAN
1 TTTAACCAAAAATATAAAAAAAATTCAACTTAAAATC-AATTATGAGATCATAAAACAATTTAA-
********* * * * * *
12843 NNNNNNNNNAAGGCTTTTGAAGGAATTGGTGACTATAAGTAGACTTTTCTTGACAATGAATGACT
64 AGCAGTAATAAGGCTTTTGAAGGAATGGGTGACTATAAATAGACTTTACTTGCCAACGAATGACT
* * * * * * *
12908 TTTTCCTCACGTTTCTC-AAGGTAGATATTCGATTATATTATGTTTTAACCAAAAATATAAAAAA
129 TTTTCTTCATGTTTCTCTAA-GTAGACATTCAATTATATGATGTTTCAACCAAAAATGTAAAAAA
* * * * ********
12972 ATTAAACTTCAAATCAATTATCAGATTATAAAACAATTTAAAGTGAGTAATAANNNNNNNNNNAA
193 ATTCAACTTAAAATCAATTATAAGATTATAAAACAATTTAAAGCGAGTAATAA--AGCTTTTGAA
* * * * *
13037 --AATGAGTGACTATAAATGGACTTTTCTTCACAATGAATGGCTTTTTCAACACGTTTCTTGA-G
256 GGAATGGGTGACTATAAATGAACTTTTCTTCTCAATGAATGGCTTTTTCTACACGTTTCTCGATG
* * * * * * *
13099 ACAGGCT-TTTAATTATAGCCTGTTCTAATGAAAAATGTAAAAAAATCAACTTAAAATCAATTAT
321 -CAGG-TATTCAATTATAGTCTGTTTTAATAAAAAATATAAAAAATTTAACTTAAAATCAATTAT
* ********** *
13163 GAGTTTATAAAACCATTTAAAGCGNNNNNNNNNNCTTTTGAAGGAATTG-GTGACTATAAATGGA
384 GAG-TTATAAAACTATTTAAAGCGAGTAATAAGGCTTTTGAAGGAA-TGAGTGACTATAAATAGA
* * * * * *
13227 CTTTTCTTGCAAATGAATGCCTTTTTCTTCATG-TTCTCGAGGTACACATTTAATTATGGTTTGT
447 CTTTTCATGCAAATGAATGCCTTTTTCTTCATGTTTCTTGAAGTAGACATTCAATTATGATTTGT
* * * *
13291 TTTAACCAAAAATGTAAAAAACATTCAACTTAAAATCAATTATGAGATCATAAAATAATTTAAAA
1 TTTAACCAAAAATATAAAAAAAATTCAACTTAAAATCAATTATGAGATCATAAAACAATTTAAAG
********* * *
13356 CNNNNNNNNNNGCTTTTGAAGGAATGAGTGACTATAAATGGACTTTACTTGCCAACGAA-GACAT
66 C-AGTAATAAGGCTTTTGAAGGAATGGGTGACTATAAATAGACTTTACTTGCCAACGAATGAC-T
* * * * *
13420 TTTTCTTCATGTTTCTCGAAGTAGACATTCAATTATA-GTCTGTTTCGATCAAAAATGCAAAAAA
129 TTTTCTTCATGTTTCTCTAAGTAGACATTCAATTATATG-ATGTTTCAACCAAAAATGTAAAAAA
********** * *
13484 ATTCAACTTAAAATCAATTATNNNNNNNNNNAACAATTTAAAGCGAGTAATAAAGCTGTTAAAGG
193 ATTCAACTTAAAATCAATTATAAGATTATAAAACAATTTAAAGCGAGTAATAAAGCTTTTGAAGG
* * * *
13549 AATAGGTGACTATAAATTAACTTTTTTTTCTCAAAGAATGGCTTTTTCTACACGTTTCTCGATGC
258 AATGGGTGACTATAAATGAAC-TTTTCTTCTCAATGAATGGCTTTTTCTACACGTTTCTCGATGC
* *
13614 ATGCATTCAATTAT-GATCTGTTTTAATAAAAAATATAAAAAAATTTAACTTAAAATCAATTATG
322 AGGTATTCAATTATAG-TCTGTTTTAATAAAAAATAT-AAAAAATTTAACTTAAAATCAATTATG
* *
13678 ATGTTATAAAACTATTTAAAGCGAGTAATAAGGCTTTTGAAGGAAT-AGGTGACTATAAATGGAA
385 A-GTTATAAAACTATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGA-GTGACTATAAATAGAC
* * ** * *
13742 TTTTCATGCTAATCAATGTATTTTT-TTGTATGTTTCTTGAAGTAGACATTCAATTAT-ACTCTG
448 TTTTCATGCAAATGAATGCCTTTTTCTT-CATGTTTCTTGAAGTAGACATTCAATTATGA-TTTG
13805 T
511 T
* * * * *
13806 TTCAACCAAAATTAT-AAAAAAATTTAACTTAAAATCAATTATGAGATTATAAAATAATTTAAAG
1 TTTAACCAAAAATATAAAAAAAATTCAACTTAAAATCAATTATGAGATCATAAAACAATTTAAAG
* * * * * * *
13870 CATGTAATAAGGCTTTTGAAAGAATTGGTGACTATAAATAGACTTTTCCTACCAATGAATGCCTT
66 CA-GTAATAAGGCTTTTGAAGGAATGGGTGACTATAAATAGACTTTACTTGCCAACGAATGACTT
* * * * * *
13935 TTTCTTCATGTTTCT-TAGGGTAGACATTCTATTATATTATGTTTTAAACAAATATGTAAAAAAA
130 TTTCTTCATGTTTCTCTA-AGTAGACATTCAATTATATGATGTTTCAACCAAAAATGTAAAAAAA
* * * * **
13999 TTTAACTTAAAATCAATTATTAGATTCTAAGACAATTTAAAGCGAGTAATATGGCTTTTGAAGGA
194 TTCAACTTAAAATCAATTATAAGATTATAAAACAATTTAAAGCGAGTAATAAAGCTTTTGAAGGA
*
14064 ATGGGTGACTGTAAATGAACTTTTCTT
259 ATGGGTGACTATAAATGAACTTTTCTT
14091 GCAAATGAAT
Statistics
Matches: 1841, Mismatches: 419, Indels: 163
0.76 0.17 0.07
Matches are distributed among these distances:
510 2 0.00
511 5 0.00
512 259 0.14
513 545 0.30
514 582 0.32
515 58 0.03
516 365 0.20
517 19 0.01
518 6 0.00
ACGTcount: A:0.38, C:0.12, G:0.13, T:0.34
Consensus pattern (511 bp):
TTTAACCAAAAATATAAAAAAAATTCAACTTAAAATCAATTATGAGATCATAAAACAATTTAAAG
CAGTAATAAGGCTTTTGAAGGAATGGGTGACTATAAATAGACTTTACTTGCCAACGAATGACTTT
TTCTTCATGTTTCTCTAAGTAGACATTCAATTATATGATGTTTCAACCAAAAATGTAAAAAAATT
CAACTTAAAATCAATTATAAGATTATAAAACAATTTAAAGCGAGTAATAAAGCTTTTGAAGGAAT
GGGTGACTATAAATGAACTTTTCTTCTCAATGAATGGCTTTTTCTACACGTTTCTCGATGCAGGT
ATTCAATTATAGTCTGTTTTAATAAAAAATATAAAAAATTTAACTTAAAATCAATTATGAGTTAT
AAAACTATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGAGTGACTATAAATAGACTTTTCATG
CAAATGAATGCCTTTTTCTTCATGTTTCTTGAAGTAGACATTCAATTATGATTTGT
Found at i:13389 original size:171 final size:171
Alignment explanation
Indices: 11237--14101 Score: 1770
Period size: 171 Copynumber: 16.7 Consensus size: 171
11227 NNNNNNNNNN
* * * * * * * *
11237 TTTAACCAAAAATATAAAAAAATTTAACTGAAAATCAATTATTAGATTCTAAAATAGTTTAGAGC
1 TTTAACCAAAAATGTAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACAATTTAAAGC
* * * * * **
11302 GAGTAATAAGGCTTTTGAAGGAATGGGTGACTGTAAATGAACTTTTCTTGAAAATGAATGTGTTT
66 GAGTAAAAAGGCTTTTGAAGGAATGAGTGACTATAAATGGACTTTTCTTGCAAATGAATGCCTTT
* * *
11367 TTCTTCATGTTTCTTG-AGATAGACATTAAATTATAGTATGT
131 TTCTTCATGTTTCTCGAAG-TAGACATTCAATTATAGTCTGT
* * * * * *
11408 TTTCATCAAAAATGTTAGAAAACTCAACTTAAAATCAATTATCAG-TTAATAAAACAATTTAAAG
1 TTTAACCAAAAATGTAAAAAAATTCAACTTAAAATCAATTATGAGATT-ATAAAACAATTTAAAG
* * *********** * * *
11472 TGAGTAATAAGNNNNNNNNNNAAATGAGTGACTATAAATGGACTTTTCTTATC-AATAAATGGCT
65 CGAGTAAAAAGGCTTTTGAAGGAATGAGTGACTATAAATGGACTTTTCTT-GCAAATGAATGCCT
* * * * * * * *
11536 TTCTCTACACGTTTC-CTG-AGACAGGCTTTCAATTATAGCCTAT
129 TTTTCTTCATGTTTCTC-GAAG-TAGACATTCAATTATAGTCTGT
** * *
11579 TTTAATGAAAAATG-AAACAAAGA-TCAACTTAAAATCAATTATGAGTTTATAAAACCATTTAAA
1 TTTAACCAAAAATGTAAA-AAA-ATTCAACTTAAAATCAATTATGAGATTATAAAACAATTTAAA
* * * * * * * * * *
11642 GCGAGCAATTAA-GCTTTTGAAAGAATGGGTAACTAGAAATCGA-TTTTCCTTACAAATGACTAC
64 GCGAGTAA-AAAGGCTTTTGAAGGAATGAGTGACTATAAATGGACTTTT-CTTGCAAATGAATGC
* * * *
11705 CTTTTCCTTCATGTTTCTTG-AGATAGACATTCAATTATGGT-TTT
127 CTTTTTCTTCATGTTTCTCGAAG-TAGACATTCAATTATAGTCTGT
* * * *
11749 TTGTAACAAAAAAT-AAAAAACATATTCAACTTAAAATCAATTATGTGATCATAAAACAATTTAA
1 TT-TAACCAAAAATGTAAAAA-A-ATTCAACTTAAAATCAATTATGAGATTATAAAACAATTTAA
* * * * * * *
11813 AACGAGTAATAAGGCTTTTGACGGAATGGGTGACAATAAATGGACTTTTCTTGCCAATGAATGTA
63 AGCGAGTAAAAAGGCTTTTGAAGGAATGAGTGACTATAAATGGACTTTTCTTGCAAATGAATG-C
* * * * *
11878 C-TTTTCTTCATGTTTCTTGAGGCA-AGCATTCAATTATCGTCTAT
127 CTTTTTCTTCATGTTTCTCGAAGTAGA-CATTCAATTATAGTCTGT
* * * * * *
11922 TTTATCTAAAAATATAAAAAAAAATTCAACCTAAAATAAATTATGAGATTATAAAATAATTTAAA
1 TTTAACCAAAAATGT--AAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACAATTTAAA
* ********** * * * *
11987 GCGAGTAATAAGNNNNNNNNNNGAATGGGTGACAATAAATGGACTTTTCTT-CTCAATGAATGGC
64 GCGAGTAAAAAGGCTTTTGAAGGAATGAGTGACTATAAATGGACTTTTCTTGC-AAATGAATGCC
* ** *
12051 -TTTTCATACACATTTCAT--AAGGTAAACATTCAATTATTA-TCTGT
128 TTTTTC-TTCATGTTTC-TCGAA-GTAGACATTCAATTA-TAGTCTGT
* * ******************* *
12095 TTTAACAAAAAATGTAAAAAAATTTAACTNNNNNNNNNNNNNNNNNNNATAAAACCATTTAAAGC
1 TTTAACCAAAAATGTAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACAATTTAAAGC
* * * * *
12160 GAGTAATAAGGCGTTTGAAGGAATGGGTGACTATAAAAGGACTTTTCTTGCAAATTAATGCCTTT
66 GAGTAAAAAGGCTTTTGAAGGAATGAGTGACTATAAATGGACTTTTCTTGCAAATGAATGCCTTT
* * * * *
12225 TCCTTCATGTTTCTAGAGGTAGACATTCAATTATGGTTTGT
131 TTCTTCATGTTTCTCGAAGTAGACATTCAATTATAGTCTGT
* * * * * *
12266 TTTAACAAAAAAAGTAAAAATAAGTCAACTTAGAATCAATTCTGAGATCATAAAACAATTTAAAG
1 TTTAACCAAAAATGTAAAAA-AATTCAACTTAAAATCAATTATGAGATTATAAAACAATTTAAAG
********** * * * * ** *
12331 CGAGTAANNNNNNNNNNGAAGGAATGGGTGACTATAAATAGACTTTACTTGCCAGCGAATGCGTT
65 CGAGTAAAAAGGCTTTTGAAGGAATGAGTGACTATAAATGGACTTTTCTTGCAAATGAATGCCTT
* * * *
12396 TTTCTTCATGTTTCTCTAAGTAGACATTCAACTGTAGACTGT
130 TTTCTTCATGTTTCTCGAAGTAGACATTCAATTATAGTCTGT
* * *
12438 TTCAACCAAAAATGTAAAAATATTCAACTTAAAATCAATTATAAGATTATAAAACAATTTAAAGC
1 TTTAACCAAAAATGTAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACAATTTAAAGC
* * * * ** * *
12503 AAGTACTAAA-GCTTTTGAAGGAATGGGTGATTATAAATTAACTTTTCTT-CTCAATGAATGGC-
66 GAGTA-AAAAGGCTTTTGAAGGAATGAGTGACTATAAATGGACTTTTCTTGC-AAATGAATGCCT
* * * * **
12565 TTTTCTACACGTTTCTCGATGCAGGTATTCAATTATAGTCTGT
129 TTTTCTTCATGTTTCTCGAAGTAGACATTCAATTATAGTCTGT
* * * * * **
12608 TTTAACCAAAAATATAAAAGAATTTAACTTAAAATCAATTATGAGATTATTAAACTATTTAAANN
1 TTTAACCAAAAATGTAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACAATTTAAAGC
******** * * * *
12673 NNNNNNNNAGGCTTTTGAAGGAATGAGTGACTATAAATAGACTTTTCATGCTAATGAATGTCTTT
66 GAGTAAAAAGGCTTTTGAAGGAATGAGTGACTATAAATGGACTTTTCTTGCAAATGAATGCCTTT
* * * * *
12738 TTTTTCATGTTTCTTGAAGTAAACATTAAATTATATTCTGT
131 TTCTTCATGTTTCTCGAAGTAGACATTCAATTATAGTCTGT
* * *
12779 TTTAACCAAAAATATAAAAAAAATTTAACTTAAAA-CTAATTATGAGATTATAAAACAATTTAAN
1 TTTAACCAAAAATGT-AAAAAAATTCAACTTAAAATC-AATTATGAGATTATAAAACAATTTAAA
********* * * *
12843 NNNNNNNNNAAGGCTTTTGAAGGAATTG-GTGACTATAAGTAGACTTTTCTTG-ACAATGAATGA
64 GCGAGTAAAAAGGCTTTTGAAGGAA-TGAGTGACTATAAATGGACTTTTCTTGCA-AATGAATGC
* * * * * *
12906 CTTTTTCCTCACGTTTCTC-AAGGTAGATATTCGATTATATTATGT
127 CTTTTTCTTCATGTTTCTCGAA-GTAGACATTCAATTATAGTCTGT
* * * * *
12951 TTTAACCAAAAATATAAAAAAATTAAACTTCAAATCAATTATCAGATTATAAAACAATTTAAAGT
1 TTTAACCAAAAATGTAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACAATTTAAAGC
********* *
13016 GAGTAATAANNNNNNNNNNAA--AATGAGTGACTATAAATGGACTTTTCTT-CACAATGAATGGC
66 GAGTAA-AA-AGGCTTTTGAAGGAATGAGTGACTATAAATGGACTTTTCTTGCA-AATGAATGCC
** * * * * * * *
13078 TTTTTCAACACGTTTCTTG-AGACAGGCTTTTAATTATAGCCTGT
128 TTTTTCTTCATGTTTCTCGAAG-TAGACATTCAATTATAGTCTGT
* ** * *
13122 TCTAATGAAAAATGTAAAAAAA-TCAACTTAAAATCAATTATGAGTTTATAAAACCATTTAAAGC
1 TTTAACCAAAAATGTAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACAATTTAAAGC
**********
13186 GNNNNNNNNNNCTTTTGAAGGAATTG-GTGACTATAAATGGACTTTTCTTGCAAATGAATGCCTT
66 GAGTAAAAAGGCTTTTGAAGGAA-TGAGTGACTATAAATGGACTTTTCTTGCAAATGAATGCCTT
* * * * *
13250 TTTCTTCATG-TTCTCGAGGTACACATTTAATTATGGTTTGT
130 TTTCTTCATGTTTCTCGAAGTAGACATTCAATTATAGTCTGT
* * *
13291 TTTAACCAAAAATGTAAAAAACATTCAACTTAAAATCAATTATGAGATCATAAAATAATTTAAAA
1 TTTAACCAAAAATGTAAAAAA-ATTCAACTTAAAATCAATTATGAGATTATAAAACAATTTAAAG
********** * * * *
13356 CNNNNNNNNNNGCTTTTGAAGGAATGAGTGACTATAAATGGACTTTACTTGCCAACGAA-GACAT
65 CGAGTAAAAAGGCTTTTGAAGGAATGAGTGACTATAAATGGACTTTTCTTGCAAATGAATG-CCT
13420 TTTTCTTCATGTTTCTCGAAGTAGACATTCAATTATAGTCTGT
129 TTTTCTTCATGTTTCTCGAAGTAGACATTCAATTATAGTCTGT
** * * **********
13463 TTCGATCAAAAATGCAAAAAAATTCAACTTAAAATCAATTATNNNNNNNNNNAACAATTTAAAGC
1 TTTAACCAAAAATGTAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACAATTTAAAGC
* * ** * * *
13528 GAGTAATAAA-GCTGTTAAAGGAAT-AGGTGACTATAAATTAACTTTTTTTTCTCAAA-GAATGG
66 GAGTAA-AAAGGCTTTTGAAGGAATGA-GTGACTATAAATGGAC-TTTTCTT-GCAAATGAATGC
* * * *
13590 CTTTTTCTACACGTTTCTCGATGCATG-CATTCAATTAT-GATCTGT
127 CTTTTTCTTCATGTTTCTCGAAGTA-GACATTCAATTATAG-TCTGT
** * * *
13635 TTTAATAAAAAATATAAAAAAATTTAACTTAAAATCAATTATGATG-TTATAAAACTATTTAAAG
1 TTTAACCAAAAATGTAAAAAAATTCAACTTAAAATCAATTATGA-GATTATAAAACAATTTAAAG
* * * * * **
13699 CGAGTAATAAGGCTTTTGAAGGAAT-AGGTGACTATAAATGGAATTTTCATGCTAATCAATGTAT
65 CGAGTAAAAAGGCTTTTGAAGGAATGA-GTGACTATAAATGGACTTTTCTTGCAAATGAATGCCT
* * *
13763 TTTT-TTGTATGTTTCTTGAAGTAGACATTCAATTATACTCTGT
129 TTTTCTT-CATGTTTCTCGAAGTAGACATTCAATTATAGTCTGT
* * * * *
13806 TTCAACCAAAATTATAAAAAAATTTAACTTAAAATCAATTATGAGATTATAAAATAATTTAAAGC
1 TTTAACCAAAAATGTAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACAATTTAAAGC
* * * * * *
13871 -ATGTAATAAGGCTTTTGAAAGAATTG-GTGACTATAAATAGACTTTTCCTACCAATGAATGCCT
66 GA-GTAAAAAGGCTTTTGAAGGAA-TGAGTGACTATAAATGGACTTTTCTTGCAAATGAATGCCT
* * * * *
13934 TTTTCTTCATGTTTCT-TAGGGTAGACATTCTATTATATTATGT
129 TTTTCTTCATGTTTCTCGA-AGTAGACATTCAATTATAGTCTGT
* * * * * *
13977 TTTAAACAAATATGTAAAAAAATTTAACTTAAAATCAATTATTAGATTCTAAGACAATTTAAAGC
1 TTTAACCAAAAATGTAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACAATTTAAAGC
* * * * *
14042 GAGTAATATGGCTTTTGAAGGAATGGGTGACTGTAAATGAACTTTTCTTGCAAATGAATG
66 GAGTAAAAAGGCTTTTGAAGGAATGAGTGACTATAAATGGACTTTTCTTGCAAATGAATG
14102 TGCNNNNNNN
Statistics
Matches: 2080, Mismatches: 531, Indels: 166
0.75 0.19 0.06
Matches are distributed among these distances:
168 5 0.00
169 39 0.02
170 247 0.12
171 1066 0.51
172 574 0.28
173 140 0.07
174 4 0.00
175 5 0.00
ACGTcount: A:0.38, C:0.12, G:0.13, T:0.34
Consensus pattern (171 bp):
TTTAACCAAAAATGTAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACAATTTAAAGC
GAGTAAAAAGGCTTTTGAAGGAATGAGTGACTATAAATGGACTTTTCTTGCAAATGAATGCCTTT
TTCTTCATGTTTCTCGAAGTAGACATTCAATTATAGTCTGT
Found at i:13456 original size:341 final size:340
Alignment explanation
Indices: 11237--14101 Score: 1464
Period size: 343 Copynumber: 8.4 Consensus size: 340
11227 NNNNNNNNNN
* * * * * * *
11237 TTTAACCAAAAATATAAAAAAATTTAACTGAAAATCAATTATTAGATTC-TAAAATAGTTTAGAG
1 TTTAACCAAAAATATAAAAAAATTCAACTTAAAATCAATTATGAGA-TCATAAAACAATTTAAAA
* * * * * ** * *
11301 CGAGTAATAAGGCTTTTGAAGGAATGGGTGACTGTAAAT-GAACTTTTCTTGAAAATGAATGTGT
65 CGA-AAAAAAGGCTTTTGAAGGAATGAGTGACTATAAATAG-ACTTTACTTGCCAACGAATG-CT
* * * * * *
11365 TTTTCTTCATGTTTCTTG-AGATAGACATTAAATTATAGTATGTTTTC-ATCAAAAATGTTAGAA
127 TTTTCTTCATGTTTCTCGAAG-TAGACATTCAATTATAGTCTG-TTTCAACCAAAAATGTAAAAA
* * ** * *******
11428 AACTCAACTTAAAATCAATTATCAG-TTAATAAAACAATTTAAAGTGAGTAAT-AAGNNNNNNNN
190 AATTCAACTTAAAATCAATTATGAGATT-ATAAAACAATTTAAAGCAAGTACTAAAG-CTTTTGA
*** * * * * * *
11491 NNAAATGAGTGACTATAAATGGACTTTTCTTATC-AATAAATGGCTTTCTCTACACGTTTC-CTG
253 AGGAATGGGTGACTATAAATGGACTTTTCTT-GCAAATGAATGCCTTTTTCTTCACGTTTCTC-G
** * * * ** *
11554 AGACAGGCTTTCAATTATAGCCTAT
316 AGGTAGACATTCAATTATGGTTTGT
** * * * *
11579 TTTAATGAAAAATGA-AACAAAGA-TCAACTTAAAATCAATTATGAGTTTATAAAACCATTTAAA
1 TTTAACCAAAAAT-ATAA-AAAAATTCAACTTAAAATCAATTATGAGATCATAAAACAATTTAAA
* ** * * * * * * * * * * * *
11642 GCGAGCAATTAA-GCTTTTGAAAGAATGGGTAACTAGAAATCGATTTTCCTTACAAATGACTACC
64 ACGA--AAAAAAGGCTTTTGAAGGAATGAGTGACTATAAATAGACTTTACTTGCCAACGAAT-GC
* * * * * * *
11706 TTTTCCTTCATGTTTCTTG-AGATAGACATTCAATTATGGT-TTTTTGTAACAAAAAAT-AAAAA
126 TTTTTCTTCATGTTTCTCGAAG-TAGACATTCAATTATAGTCTGTTT-CAACCAAAAATGTAAAA
* * * * * *
11768 ACATATTCAACTTAAAATCAATTATGTGATCATAAAACAATTTAAAACGAGTAATAAGGCTTTTG
189 A-A-ATTCAACTTAAAATCAATTATGAGATTATAAAACAATTTAAAGCAAGTACTAAAGCTTTTG
* * * * * *
11833 ACGGAATGGGTGACAATAAATGGACTTTTCTTGCCAATGAATGTAC-TTTTCTTCATGTTTCTTG
252 AAGGAATGGGTGACTATAAATGGACTTTTCTTGCAAATGAATG-CCTTTTTCTTCACGTTTCTCG
* * * *
11897 AGGCA-AGCATTCAATTATCGTCTAT
316 AGGTAGA-CATTCAATTATGGTTTGT
* * * * * *
11922 TTTATCTAAAAATATAAAAAAAAATTCAACCTAAAATAAATTATGAGATTATAAAATAATTTAAA
1 TTTAACCAAAAATAT--AAAAAAATTCAACTTAAAATCAATTATGAGATCATAAAACAATTTAAA
* * * ********** * * * * *
11987 GCGAGTAATAAGNNNNNNNNNNGAATGGGTGACAATAAATGGACTTTTCTT-CTCAATGAATGGC
64 ACGA-AAAAAAGGCTTTTGAAGGAATGAGTGACTATAAATAGACTTTACTTGC-CAACGAAT-GC
* ** * * *
12051 -TTTTCATACACATTTCAT--AAGGTAAACATTCAATTATTA-TCTGTTTTAACAAAAAATGTAA
126 TTTTTC-TTCATGTTTC-TCGAA-GTAGACATTCAATTA-TAGTCTGTTTCAACCAAAAATGTAA
* ******************* * * * * *
12112 AAAAATTTAACTNNNNNNNNNNNNNNNNNNNATAAAACCATTTAAAGCGAGTAATAAGGCGTTTG
187 AAAAATTCAACTTAAAATCAATTATGAGATTATAAAACAATTTAAAGCAAGTACTAAAGCTTTTG
* * * * *
12177 AAGGAATGGGTGACTATAAAAGGACTTTTCTTGCAAATTAATGCCTTTTCCTTCATGTTTCTAGA
252 AAGGAATGGGTGACTATAAATGGACTTTTCTTGCAAATGAATGCCTTTTTCTTCACGTTTCTCGA
12242 GGTAGACATTCAATTATGGTTTGT
317 GGTAGACATTCAATTATGGTTTGT
* * * *
12266 TTTAA-CAAAAAAAGTAAAAATAAGTCAACTTAGAATCAATTCTGAGATCATAAAACAATTTAAA
1 TTTAACCAAAAATA-TAAAAA-AATTCAACTTAAAATCAATTATGAGATCATAAAACAATTTAAA
* * ********** * *
12330 GCGAGTAANNNNNNNNNNGAAGGAATGGGTGACTATAAATAGACTTTACTTGCCAGCGAATGCGT
64 ACGA-AAAAAAGGCTTTTGAAGGAATGAGTGACTATAAATAGACTTTACTTGCCAACGAATGC-T
* * * * *
12395 TTTTCTTCATGTTTCTCTAAGTAGACATTCAACTGTAGACTGTTTCAACCAAAAATGTAAAAATA
127 TTTTCTTCATGTTTCTCGAAGTAGACATTCAATTATAGTCTGTTTCAACCAAAAATGTAAAAAAA
*
12460 TTCAACTTAAAATCAATTATAAGATTATAAAACAATTTAAAGCAAGTACTAAAGCTTTTGAAGGA
192 TTCAACTTAAAATCAATTATGAGATTATAAAACAATTTAAAGCAAGTACTAAAGCTTTTGAAGGA
* ** * * * * *
12525 ATGGGTGATTATAAATTAACTTTTCTT-CTCAATGAATGGC-TTTTCTACACGTTTCTCGATGCA
257 ATGGGTGACTATAAATGGACTTTTCTTGC-AAATGAATGCCTTTTTCTTCACGTTTCTCGAGGTA
** * *
12588 GGTATTCAATTATAGTCTGT
321 GACATTCAATTATGGTTTGT
* * * * * *
12608 TTTAACCAAAAATATAAAAGAATTTAACTTAAAATCAATTATGAGATTATTAAACTATTTAAANN
1 TTTAACCAAAAATATAAAAAAATTCAACTTAAAATCAATTATGAGATCATAAAACAATTTAAA-A
******** * * * *
12673 NNNNNNNNAGGCTTTTGAAGGAATGAGTGACTATAAATAGACTTTTCATGCTAATGAATGTCTTT
65 CGAAAAAAAGGCTTTTGAAGGAATGAGTGACTATAAATAGACTTTACTTGCCAACGAATG-CTTT
* * * * * * *
12738 TTTTTCATGTTTCTTGAAGTAAACATTAAATTATATTCTGTTTTAACCAAAAATATAAAAAAAAT
129 TTCTTCATGTTTCTCGAAGTAGACATTCAATTATAGTCTGTTTCAACCAAAAATGT-AAAAAAAT
* ********** *
12803 TTAACTTAAAA-CTAATTATGAGATTATAAAACAATTTAANNNNNNNNNNAAGGCTTTTGAAGGA
193 TCAACTTAAAATC-AATTATGAGATTATAAAACAATTTAAAGCAAGTACTAAAGCTTTTGAAGGA
* * * * * *
12867 ATTGGTGACTATAAGTAGACTTTTCTTG-ACAATGAATGACTTTTTCCTCACGTTTCTCAAGGTA
257 ATGGGTGACTATAAATGGACTTTTCTTGCA-AATGAATGCCTTTTTCTTCACGTTTCTCGAGGTA
* * *
12931 GATATTCGATTAT-ATTATGT
321 GACATTCAATTATGGTT-TGT
* * * * **
12951 TTTAACCAAAAATATAAAAAAATTAAACTTCAAATCAATTATCAGATTATAAAACAATTTAAAGT
1 TTTAACCAAAAATATAAAAAAATTCAACTTAAAATCAATTATGAGATCATAAAACAATTTAAAAC
********** * * *
13016 GAGTAATAANNNNNNNNNNAA--AATGAGTGACTATAAATGGACTTTTCTT-CACAATGAATGGC
66 GA--AA-AAAAGGCTTTTGAAGGAATGAGTGACTATAAATAGACTTTACTTGC-CAACGAAT-GC
** * * * * * * * **
13078 TTTTTCAACACGTTTCTTG-AGACAGGCTTTTAATTATAGCCTG-TTCTAATGAAAAATGTAAAA
126 TTTTTCTTCATGTTTCTCGAAG-TAGACATTCAATTATAGTCTGTTTC-AACCAAAAATGTAAAA
* * ***********
13141 AAA-TCAACTTAAAATCAATTATGAGTTTATAAAACCATTTAAAGCGNNNNNNNNNNCTTTTGAA
189 AAATTCAACTTAAAATCAATTATGAGATTATAAAACAATTTAAAGCAAGTACTAAAGCTTTTGAA
* *
13205 GGAATTGGTGACTATAAATGGACTTTTCTTGCAAATGAATGCCTTTTTCTTCATG-TTCTCGAGG
254 GGAATGGGTGACTATAAATGGACTTTTCTTGCAAATGAATGCCTTTTTCTTCACGTTTCTCGAGG
* *
13269 TACACATTTAATTATGGTTTGT
319 TAGACATTCAATTATGGTTTGT
* *
13291 TTTAACCAAAAATGTAAAAAACATTCAACTTAAAATCAATTATGAGATCATAAAATAATTTAAAA
1 TTTAACCAAAAATATAAAAAA-ATTCAACTTAAAATCAATTATGAGATCATAAAACAATTTAAAA
********* *
13356 CNNNNNNNNNNGCTTTTGAAGGAATGAGTGACTATAAATGGACTTTACTTGCCAACGAA-GACAT
65 C-GAAAAAAAGGCTTTTGAAGGAATGAGTGACTATAAATAGACTTTACTTGCCAACGAATG-C-T
* * *
13420 TTTTCTTCATGTTTCTCGAAGTAGACATTCAATTATAGTCTGTTTCGATCAAAAATGCAAAAAAA
127 TTTTCTTCATGTTTCTCGAAGTAGACATTCAATTATAGTCTGTTTCAACCAAAAATGTAAAAAAA
********** * * * *
13485 TTCAACTTAAAATCAATTATNNNNNNNNNNAACAATTTAAAGCGAGTAATAAAGCTGTTAAAGGA
192 TTCAACTTAAAATCAATTATGAGATTATAAAACAATTTAAAGCAAGTACTAAAGCTTTTGAAGGA
* ** * * * * * *
13550 ATAGGTGACTATAAATTAACTTTTTTTTCTCAAA-GAATGGCTTTTTCTACACGTTTCTCGATGC
257 ATGGGTGACTATAAATGGAC-TTTTCTT-GCAAATGAATGCCTTTTTCTTCACGTTTCTCGAGGT
* *
13614 ATG-CATTCAATTATGATCTGT
320 A-GACATTCAATTATGGTTTGT
** * * * *
13635 TTTAATAAAAAATATAAAAAAATTTAACTTAAAATCAATTATGATG-TTATAAAACTATTTAAAG
1 TTTAACCAAAAATATAAAAAAATTCAACTTAAAATCAATTATGA-GATCATAAAACAATTTAAAA
* * * * * * *
13699 CGAGTAATAAGGCTTTTGAAGGAAT-AGGTGACTATAAATGGAATTTTCATGCTAATC-AATG-T
65 CGA-AAAAAAGGCTTTTGAAGGAATGA-GTGACTATAAATAGACTTTACTTGCCAA-CGAATGCT
* * * * * *
13761 ATTTTTTTGTATGTTTCTTGAAGTAGACATTCAATTATACTCTGTTTCAACCAAAATTATAAAAA
127 -TTTTCTT-CATGTTTCTCGAAGTAGACATTCAATTATAGTCTGTTTCAACCAAAAATGTAAAAA
* * * * * *
13826 AATTTAACTTAAAATCAATTATGAGATTATAAAATAATTTAAAGCATGTAATAAGGCTTTTGAAA
190 AATTCAACTTAAAATCAATTATGAGATTATAAAACAATTTAAAGCAAGTACTAAAGCTTTTGAAG
* * * * * * *
13891 GAATTGGTGACTATAAATAGACTTTTCCTACCAATGAATGCCTTTTTCTTCATGTTTCT-TAGGG
255 GAATGGGTGACTATAAATGGACTTTTCTTGCAAATGAATGCCTTTTTCTTCACGTTTCTCGA-GG
* *
13955 TAGACATTCTATTAT-ATTATGT
319 TAGACATTCAATTATGGTT-TGT
* * * * * * *
13977 TTTAAACAAATATGTAAAAAAATTTAACTTAAAATCAATTATTAGATTC-TAAGACAATTTAAAG
1 TTTAACCAAAAATATAAAAAAATTCAACTTAAAATCAATTATGAGA-TCATAAAACAATTTAAAA
* * * * * * * *
14041 CGAGTAATATGGCTTTTGAAGGAATGGGTGACTGTAAAT-GAACTTTTCTTGCAAATGAATG
65 CGA-AAAAAAGGCTTTTGAAGGAATGAGTGACTATAAATAG-ACTTTACTTGCCAACGAATG
14102 TGCNNNNNNN
Statistics
Matches: 1933, Mismatches: 501, Indels: 178
0.74 0.19 0.07
Matches are distributed among these distances:
339 6 0.00
340 46 0.02
341 355 0.18
342 502 0.26
343 712 0.37
344 191 0.10
345 109 0.06
346 12 0.01
ACGTcount: A:0.38, C:0.12, G:0.13, T:0.34
Consensus pattern (340 bp):
TTTAACCAAAAATATAAAAAAATTCAACTTAAAATCAATTATGAGATCATAAAACAATTTAAAAC
GAAAAAAAGGCTTTTGAAGGAATGAGTGACTATAAATAGACTTTACTTGCCAACGAATGCTTTTT
CTTCATGTTTCTCGAAGTAGACATTCAATTATAGTCTGTTTCAACCAAAAATGTAAAAAAATTCA
ACTTAAAATCAATTATGAGATTATAAAACAATTTAAAGCAAGTACTAAAGCTTTTGAAGGAATGG
GTGACTATAAATGGACTTTTCTTGCAAATGAATGCCTTTTTCTTCACGTTTCTCGAGGTAGACAT
TCAATTATGGTTTGT
Found at i:19233 original size:171 final size:171
Alignment explanation
Indices: 18931--20937 Score: 1532
Period size: 171 Copynumber: 11.7 Consensus size: 171
18921 NNNNNNNNNN
* * * * * * *
18931 AGCGTGTAATAAGGCTTTTGAAAGAATTGGTGACTATAAATAGACTTTTCCTACTAATGAATGCC
1 AGCGAGTAATAAGGCTTTTGAAAGAATGGGTGACTATAAATGGACTTTTCTTGCAAATGAATACC
* *
18996 TTTTTCTTCATGTTTCTC-ATGGTAGACATTCTATTATATTATGTTTTAACCAAAAATGTAAAAA
66 TTTTTCTTCATGTTTCTCGA-GGTAGACATTCAATTATAGTATGTTTTAACCAAAAATGTAAAAA
* * * **
19060 AATTCAACTTAAAATCAATTATTAGATTCTAAGACAATTTNN
130 AATTCAACTTAAAATCAATTATGAGATTATAAAACAATTTAA
********** * * * **
19102 NNNNNNNNNNAAGGCTTTTGAAGGAATGGGTGACTGTAAATGAACTTTTCTTGCAAATGAATATG
1 AGCGAGTAATAAGGCTTTTGAAAGAATGGGTGACTATAAATGGACTTTTCTTGCAAATGAATACC
* * *
19167 TTTTTCTTCATGTTTCTCGAGGTAGACATTCAATTATAGTATGTTTTCACCAAGAATGTTAAAAA
66 TTTTTCTTCATGTTTCTCGAGGTAGACATTCAATTATAGTATGTTTTAACCAAAAATGTAAAAAA
* *
19232 ATTCAACTTAAAATCAATTATCAGATAATAAAACAATTTAA
131 ATTCAACTTAAAATCAATTATGAGATTATAAAACAATTTAA
* * * * **
19273 AGTGAGTAATAAGGCTTTTGAAAAAATGAGTGACTATAAATGGACTTTTCTT-CTTAATGAATGG
1 AGCGAGTAATAAGGCTTTTGAAAGAATGGGTGACTATAAATGGACTTTTCTTGC-AAATGAATAC
* * ** ** ** **
19337 CTTTTTCTACACGTTTC-CTGAGACAGACATTCAATTATAGCCTGTTTTAATGAAAAATACAAAA
65 CTTTTTCTTCATGTTTCTC-GAGGTAGACATTCAATTATAGTATGTTTTAACCAAAAATGTAAAA
* *
19401 CAAA-TCAACTTAAAATCAATTATGAGTTTATAAAACCATTTAA
129 -AAATTCAACTTAAAATCAATTATGAGATTATAAAACAATTTAA
* *
19444 AGCGAGTAATAAGGCTTTTGAAGGAATGGGTGACTATAAATGGACTTTTCTTGCAAATGAATGCC
1 AGCGAGTAATAAGGCTTTTGAAAGAATGGGTGACTATAAATGGACTTTTCTTGCAAATGAATACC
* * * *
19509 TTTTCCTTCATG-TTCTTGAGGTAGACATTCAATTATGGTTTGTTTTAACCAAAAATGTAAAAAA
66 TTTTTCTTCATGTTTCTCGAGGTAGACATTCAATTATAGTATGTTTTAACCAAAAATGT-AAAAA
* * *
19573 AATT-AATTTAAAATCAATTATGAGATCATAAAATAATTTAA
130 AATTCAACTTAAAATCAATTATGAGATTATAAAACAATTTAA
* * * * *
19614 AGCGAGTAATAAGACTTTTGAAAGAATGGGTGACTATAAATGGACTTTACTTGCCAACGAATACA
1 AGCGAGTAATAAGGCTTTTGAAAGAATGGGTGACTATAAATGGACTTTTCTTGCAAATGAATACC
* * * * * ** *
19679 TTTTTCTTCATGTTTCTCTAAGTGGACTTTCAATTATAGTCTGTTTCGATCAAAAATGTAAAAAA
66 TTTTTCTTCATGTTTCTCGAGGTAGACATTCAATTATAGTATGTTTTAACCAAAAATGTAAAAAA
* * ********
19744 ATTCAACTTAAAATCAATTATAAAATTATAAAATNNNNNNN
131 ATTCAACTTAAAATCAATTATGAGATTATAAAACAATTTAA
*** * * *
19785 NNNGAGTAATAAAGCTTTTGAAAGAATGGGTGACTATAAATGGACTTTTCTTCCCAAA-GAATAG
1 AGCGAGTAATAAGGCTTTTGAAAGAATGGGTGACTATAAATGGACTTTTCTT-GCAAATGAATAC
* * * * * *
19849 CTTGTTT-TACATGTTTCTCAATGCAGACATTCAATTATAGTCTGTTTTAACCAAAAATATAAAA
65 CTT-TTTCTTCATGTTTCTCGAGGTAGACATTCAATTATAGTATGTTTTAACCAAAAATGTAAAA
***********
19913 AAATTTNNNNNNNNNNCAATTATGAGATTATAAAACAATTTAA
129 AAATTCAACTTAAAATCAATTATGAGATTATAAAACAATTTAA
* * * * * * * *
19956 AGCAAGTAATAAGGCTTTT-CAAGAAATTGGTGACTATAAATAGACTTTTCCTACCAATGAATGC
1 AGCGAGTAATAAGGCTTTTGAAAG-AATGGGTGACTATAAATGGACTTTTCTTGCAAATGAATAC
* * * * * * ** *
20020 ATTTTTCTTTACGTTTCT-TAGGGTAGACATTCTATTATATTATGTTTTAATAAAAAATGTAAGA
65 CTTTTTCTTCATGTTTCTCGA-GGTAGACATTCAATTATAGTATGTTTTAACCAAAAATGTAAAA
* *
20084 AAATTCAACTTAAAATCAATTATTAGATTCTAAAACAATTTAA
129 AAATTCAACTTAAAATCAATTATGAGATTATAAAACAATTTAA
* * * * * * * **
20127 TGCGAGTAATAAAGATTTTGAAGGAATGGGTGACTGTAAAT-AAATTTTACTTGCAAATGAATGT
1 AGCGAGTAATAAGGCTTTTGAAAGAATGGGTGACTATAAATGGACTTTT-CTTGCAAATGAATAC
* * ** * *
20191 GTTTTTCTTTATGTTTCTTAAGGTAGACATTCAATTATAGTATGTTTTCACCAAAAATGTTAAAA
65 CTTTTTCTTCATGTTTCTCGAGGTAGACATTCAATTATAGTATGTTTTAACCAAAAATGTAAAAA
* * *
20256 AATTCAACTTAAAATCAATTATCAGATAATAAAATAATTTAA
130 AATTCAACTTAAAATCAATTATGAGATTATAAAACAATTTAA
* ********** * * * * **
20298 AGTGAGTAATAAGGCTNNNNNNNNNNTGAGTGACTATAAATAGACTTTT-TTTCTTAATGAATGT
1 AGCGAGTAATAAGGCTTTTGAAAGAATGGGTGACTATAAATGGACTTTTCTTGC-AAATGAATAC
* * * ** ** ** *
20362 CTTTTTCTACACGTTTCTTGAGACA-AGCATTCAATTATAGCCTGTTTTAATAAAAAATGCAAAA
65 CTTTTTCTTCATGTTTCTCGAGGTAGA-CATTCAATTATAGTATGTTTTAACCAAAAATGTAAAA
* * *
20426 AAAATCAACTTAAAATCAATTATGAGTTTATAAAACCATTTAA
129 AAATTCAACTTAAAATCAATTATGAGATTATAAAACAATTTAA
************* * * * *
20469 AGCGAGTNNNNNNNNNNNNNAAGGAATAGGTGACTATAAATGGACTTTTATTGCAAATGAAGGA-
1 AGCGAGTAATAAGGCTTTTGAAAGAATGGGTGACTATAAATGGACTTTTCTTGCAAATGAA-TAC
* * * * * *
20533 CTTTTCCTTCAT-ATTCTTGAGATAGACATTCAATTATGGTTTGTTTTAACCAAAAATGTAAAAA
65 CTTTTTCTTCATGTTTCTCGAGGTAGACATTCAATTATAGTATGTTTTAACCAAAAATGT-AAAA
* * * *
20597 AAACTCAACTGAAAATCAATTATGAGATCATAAAATAATTTAA
129 AAATTCAACTTAAAATCAATTATGAGATTATAAAACAATTTAA
********** * * * * * * ***
20640 AGCGAGTAATNNNNNNNNNNAAGGAATAGGTGACTATAAATAGACTTTTCTTACCAACGAATGTG
1 AGCGAGTAATAAGGCTTTTGAAAGAATGGGTGACTATAAATGGACTTTTCTTGCAAATGAATACC
* ** * * * * *
20705 TTTTTCTTCATGTTTTTTTAAGTAGACATTTAATTATTA-TCTATTTTGACCAAAAATGTAAAAA
66 TTTTTCTTCATGTTTCTCGAGGTAGACATTCAATTA-TAGTATGTTTTAACCAAAAATGTAAAAA
* * *
20769 AAGTCAACTTAAAATCAATTATAAGATTATAAAACATTTTAA
130 AATTCAACTTAAAATCAATTATGAGATTATAAAACAATTTAA
* * * * *
20811 AGCGAGTAATAAAGCTTTTGAAGGAATGGATGACTATAAATTGACTTTTGTT-CACAA-GAAATG
1 AGCGAGTAATAAGGCTTTTGAAAGAATGGGTGACTATAAATGGACTTTTCTTGCA-AATG-AAT-
* * * * * * *
20874 A-CTTTTTATACACGTTTCTCAATGTAGGCATTCAATTATAGTCTGTTTTAACCAAAAATGTAAA
63 ACCTTTTTCTTCATGTTTCTCGAGGTAGACATTCAATTATAGTATGTTTTAACCAAAAATGTAAA
20938 NNNNNNNNNN
Statistics
Matches: 1437, Mismatches: 366, Indels: 66
0.77 0.20 0.04
Matches are distributed among these distances:
170 210 0.15
171 1169 0.81
172 57 0.04
173 1 0.00
ACGTcount: A:0.38, C:0.11, G:0.13, T:0.35
Consensus pattern (171 bp):
AGCGAGTAATAAGGCTTTTGAAAGAATGGGTGACTATAAATGGACTTTTCTTGCAAATGAATACC
TTTTTCTTCATGTTTCTCGAGGTAGACATTCAATTATAGTATGTTTTAACCAAAAATGTAAAAAA
ATTCAACTTAAAATCAATTATGAGATTATAAAACAATTTAA
Found at i:20933 original size:513 final size:511
Alignment explanation
Indices: 18931--20932 Score: 1873
Period size: 513 Copynumber: 3.9 Consensus size: 511
18921 NNNNNNNNNN
* * * * * * * * * *
18931 AGCGTGTAATAAGGCTTTTGAAAGAATTGGTGACTATAAATAGACTTTTCCTACTAATGAATGCC
1 AGCGAGTAATAAGGCTTTTCAAGGAATAGGTGACTATAAATGGACTTTTCTTGCAAATGAAGGAC
* * * *
18996 TTTTTCTTCATGTT-TCTCATGGTAGACATTCTATTAT-ATTATGTTTTAACCAAAAATGTAAAA
66 TTTTCCTTCAT-TTCT-TGA-GGTAGACATTCAATTATGGTT-TGTTTTAACCAAAAATGTAAAA
* * * * ************ ***
19059 AAATTCAACTTAAAATCAATTATTAGATTC-TAAGACAATTTNNNNNNNNNNNNAAGGCTTTTGA
127 AAAATCAACTTAAAATCAATTATGAGA-TCATAAAATAATTTAAAGCGAGTAATAAAAATTTTGA
* * *
19123 AGGAATGGGTGACTGTAAAT-GAACTTTTCTTGCAAATGAATATGTTTTTCTTCATGTTTCTCGA
191 AGGAATGGGTGACTATAAATAG-ACTTTTCTTGCAAACGAATATGTTTTTCTTCATGTTTCTCTA
* * *
19187 GGTAGACATTCAATTATAGTATGTTTTCACCAAGAATGTTAAAAAATTCAACTTAAAATCAATTA
255 AGTAGACATTCAATTATAGTATGTTTTCACCAAAAATGTAAAAAAATTCAACTTAAAATCAATTA
* * *
19252 TCAGATAATAAAACAATTTAAAGTGAGTAATAAGGCTTTTGAAAAAATGAGTGACTATAAATGGA
320 TAAGATAATAAAACAATTTAAAGTGAGTAATAAAGCTTTTGAAAGAATGAGTGACTATAAATGGA
* * *
19317 CTTTTCTTCTTAATGAATGGCTTTTTCTACACGTTTC-CTGAGACAGACATTCAATTATAGCCTG
385 CTTTTCTTCTCAATGAATGACTTTTTCTACACGTTTCTC-AAGACAGACATTCAATTATAGCCTG
** *
19381 TTTTAATGAAAAATACAAAACAAATCAACTTAAAATCAATTATGAGTTTATAAAACCATTTAA
449 TTTTAACCAAAAATACAAAAAAAATCAACTTAAAATCAATTATGAGTTTATAAAACCATTTAA
* * * *
19444 AGCGAGTAATAAGGCTTTTGAAGGAATGGGTGACTATAAATGGACTTTTCTTGCAAATGAATGCC
1 AGCGAGTAATAAGGCTTTTCAAGGAATAGGTGACTATAAATGGACTTTTCTTGCAAATGAAGGAC
19509 TTTTCCTTCATGTTCTTGAGGTAGACATTCAATTATGGTTTGTTTTAACCAAAAATGTAAAAAAA
66 TTTTCCTTCAT-TTCTTGAGGTAGACATTCAATTATGGTTTGTTTTAACCAAAAATGTAAAAAAA
* * * * *
19574 ATTAATTTAAAATCAATTATGAGATCATAAAATAATTTAAAGCGAGTAATAAGACTTTTGAAAGA
130 ATCAACTTAAAATCAATTATGAGATCATAAAATAATTTAAAGCGAGTAATAAAAATTTTGAAGGA
* * * ** *
19639 ATGGGTGACTATAAATGGACTTTACTTGCCAACGAATACATTTTTCTTCATGTTTCTCTAAGTGG
195 ATGGGTGACTATAAATAGACTTTTCTTGCAAACGAATATGTTTTTCTTCATGTTTCTCTAAGTAG
* * * *
19704 ACTTTCAATTATAGTCTG-TTTCGATCAAAAATGTAAAAAAATTCAACTTAAAATCAATTATAAA
260 ACATTCAATTATAGTATGTTTTC-ACCAAAAATGTAAAAAAATTCAACTTAAAATCAATTATAAG
* *********** *
19768 ATTATAAAATNNNNNNNNNNGAGTAATAAAGCTTTTGAAAGAATGGGTGACTATAAATGGACTTT
324 ATAATAAAACAATTTAAAGTGAGTAATAAAGCTTTTGAAAGAATGAGTGACTATAAATGGACTTT
* * * *
19833 TCTTCCCAAAGAAT-AGCTTGTTT-TACATGTTTCTCAATG-CAGACATTCAATTATAGTCTGTT
389 TCTTCTCAATGAATGA-CTT-TTTCTACACGTTTCTCAA-GACAGACATTCAATTATAGCCTGTT
* * *********** * *
19895 TTAACCAAAAATATAAAAAAATTTNNNNNNNNNNCAATTATGAGATTATAAAACAATTTAA
451 TTAACCAAAAATACAAAAAAAATCAACTTAAAATCAATTATGAGTTTATAAAACCATTTAA
* * * * * * * *
19956 AGCAAGTAATAAGGCTTTTCAAGAAATTGGTGACTATAAATAGACTTTTCCTACCAATGAATGCA
1 AGCGAGTAATAAGGCTTTTCAAGGAATAGGTGACTATAAATGGACTTTTCTTGCAAATGAA-GGA
* * * * * ** *
20021 TTTTTCTTTACGTTTCTT-AGGGTAGACATTCTATTAT-ATTATGTTTTAATAAAAAATGTAAGA
65 CTTTTCCTT-CATTTCTTGA-GGTAGACATTCAATTATGGTT-TGTTTTAACCAAAAATGTAAAA
* * * * *
20084 AAATTCAACTTAAAATCAATTATTAGATTC-TAAAACAATTTAATGCGAGTAATAAAGATTTTGA
127 AAAATCAACTTAAAATCAATTATGAGA-TCATAAAATAATTTAAAGCGAGTAATAAAAATTTTGA
* * * * *
20148 AGGAATGGGTGACTGTAAATA-AATTTTACTTGCAAATGAATGTGTTTTTCTTTATGTTTCT-TA
191 AGGAATGGGTGACTATAAATAGACTTTT-CTTGCAAACGAATATGTTTTTCTTCATGTTTCTCTA
*
20211 AGGTAGACATTCAATTATAGTATGTTTTCACCAAAAATGTTAAAAAATTCAACTTAAAATCAATT
255 A-GTAGACATTCAATTATAGTATGTTTTCACCAAAAATGTAAAAAAATTCAACTTAAAATCAATT
* * * ********** *
20276 ATCAGATAATAAAATAATTTAAAGTGAGTAATAAGGCTNNNNNNNNNNTGAGTGACTATAAATAG
319 ATAAGATAATAAAACAATTTAAAGTGAGTAATAAAGCTTTTGAAAGAATGAGTGACTATAAATGG
* * * **
20341 ACTTTTTTTCTTAATGAATGTCTTTTTCTACACGTTTCTTGAGACA-AGCATTCAATTATAGCCT
384 ACTTTTCTTCTCAATGAATGACTTTTTCTACACGTTTCTCAAGACAGA-CATTCAATTATAGCCT
** *
20405 GTTTTAATAAAAAATGCAAAAAAAATCAACTTAAAATCAATTATGAGTTTATAAAACCATTTAA
448 GTTTTAACCAAAAATACAAAAAAAATCAACTTAAAATCAATTATGAGTTTATAAAACCATTTAA
************* *
20469 AGCGAGTNNNNNNNNNNNNNAAGGAATAGGTGACTATAAATGGACTTTTATTGCAAATGAAGGAC
1 AGCGAGTAATAAGGCTTTTCAAGGAATAGGTGACTATAAATGGACTTTTCTTGCAAATGAAGGAC
*
20534 TTTTCCTTCATATTCTTGAGATAGACATTCAATTATGGTTTGTTTTAACCAAAAATGTAAAAAAA
66 TTTTCCTTCAT-TTCTTGAGGTAGACATTCAATTATGGTTTGTTTTAACCAAAAATGTAAAAAAA
* **********
20599 ACTCAACTGAAAATCAATTATGAGATCATAAAATAATTTAAAGCGAGTAATNNNNNNNNNNAAGG
130 A-TCAACTTAAAATCAATTATGAGATCATAAAATAATTTAAAGCGAGTAATAAAAATTTTGAAGG
* * * * * *
20664 AATAGGTGACTATAAATAGACTTTTCTTACCAACGAATGTGTTTTTCTTCATGTTTTTTTAAGTA
194 AATGGGTGACTATAAATAGACTTTTCTTGCAAACGAATATGTTTTTCTTCATGTTTCTCTAAGTA
* * * * *
20729 GACATTTAATTATTA-TCTATTTTGACCAAAAATGTAAAAAAAGTCAACTTAAAATCAATTATAA
259 GACATTCAATTA-TAGTATGTTTTCACCAAAAATGTAAAAAAATTCAACTTAAAATCAATTATAA
* * * * *
20793 GATTATAAAACATTTTAAAGCGAGTAATAAAGCTTTTGAAGGAATG-GATGACTATAAATTGACT
323 GATAATAAAACAATTTAAAGTGAGTAATAAAGCTTTTGAAAGAATGAG-TGACTATAAATGGACT
* * * * * *
20857 TTTGTTCACAA-GAAATGACTTTTTATACACGTTTCTCAATG-TAGGCATTCAATTATAGTCTGT
387 TTTCTTCTCAATG-AATGACTTTTTCTACACGTTTCTCAA-GACAGACATTCAATTATAGCCTGT
20920 TTTAACCAAAAAT
450 TTTAACCAAAAAT
20933 GTAAANNNNN
Statistics
Matches: 1183, Mismatches: 273, Indels: 66
0.78 0.18 0.04
Matches are distributed among these distances:
511 8 0.01
512 451 0.38
513 704 0.60
514 20 0.02
ACGTcount: A:0.37, C:0.11, G:0.13, T:0.35
Consensus pattern (511 bp):
AGCGAGTAATAAGGCTTTTCAAGGAATAGGTGACTATAAATGGACTTTTCTTGCAAATGAAGGAC
TTTTCCTTCATTTCTTGAGGTAGACATTCAATTATGGTTTGTTTTAACCAAAAATGTAAAAAAAA
TCAACTTAAAATCAATTATGAGATCATAAAATAATTTAAAGCGAGTAATAAAAATTTTGAAGGAA
TGGGTGACTATAAATAGACTTTTCTTGCAAACGAATATGTTTTTCTTCATGTTTCTCTAAGTAGA
CATTCAATTATAGTATGTTTTCACCAAAAATGTAAAAAAATTCAACTTAAAATCAATTATAAGAT
AATAAAACAATTTAAAGTGAGTAATAAAGCTTTTGAAAGAATGAGTGACTATAAATGGACTTTTC
TTCTCAATGAATGACTTTTTCTACACGTTTCTCAAGACAGACATTCAATTATAGCCTGTTTTAAC
CAAAAATACAAAAAAAATCAACTTAAAATCAATTATGAGTTTATAAAACCATTTAA
Found at i:21513 original size:170 final size:161
Alignment explanation
Indices: 21337--21648 Score: 331
Period size: 170 Copynumber: 1.9 Consensus size: 161
21327 TGCAAAAAAG
*
21337 TCAACTTAAAATCAATTATAAGATTATAAAATAATTTAAAATGAGTAATAAAACTTTTGAAGCAA
1 TCAACTTAAAATCAATTATAAGATTATAAAATAATTTAAAACGAGTAATAAAACTTTTGAAGCAA
* *
21402 TAGATGACTATAAATTGACTTTT-TTCTCAAAAAATGACTTTTTCAACACGTTTCTC-AAGGTAA
66 TAGATGACTATAAATAGACTTTTCTTCTCAAAAAATGACTTTTTCAACACGTTTCTCTAA-GAAA
*
21465 GCATTCAATTATAGTCTGTTTTAACCNNNNNNNNNNAACAAT
130 ACATTCAATTATAGTCTGTTTTAACC----------AACAAT
* * * * * * *
21507 TCAACTTAAAATCAATTCTGAGCTTATAAAATAATTTGAAGCGAGTAATAATACTTTTGAAGGAA
1 TCAACTTAAAATCAATTATAAGATTATAAAATAATTTAAAACGAGTAATAAAACTTTTGAAGCAA
* * * ** * * **
21572 TTGATGACTCTAAATAGATTTTTCTTCTCAATGAATGGCTTTTTCTACTTGTTTCTCTAAGAAAA
66 TAGATGACTATAAATAGACTTTTCTTCTCAAAAAATGACTTTTTCAACACGTTTCTCTAAGAAAA
21637 CATTCAATTATA
131 CATTCAATTATA
21649 ACCTGTNNNN
Statistics
Matches: 120, Mismatches: 20, Indels: 3
0.84 0.14 0.02
Matches are distributed among these distances:
170 76 0.63
171 42 0.35
172 2 0.02
ACGTcount: A:0.38, C:0.13, G:0.10, T:0.36
Consensus pattern (161 bp):
TCAACTTAAAATCAATTATAAGATTATAAAATAATTTAAAACGAGTAATAAAACTTTTGAAGCAA
TAGATGACTATAAATAGACTTTTCTTCTCAAAAAATGACTTTTTCAACACGTTTCTCTAAGAAAA
CATTCAATTATAGTCTGTTTTAACCAACAAT
Found at i:22420 original size:171 final size:170
Alignment explanation
Indices: 22237--22834 Score: 525
Period size: 171 Copynumber: 3.5 Consensus size: 170
22227 ATTTAAGAAG
* * *******
22237 ACATTGAATTATAGTCTGTTTTACCTAAGAATGTAAAAAAATTCAACTTAAAATTAATNNNNNNN
1 ACATTCAATTATAGTCTGTTTTACCTAAGAATGTAAAAAAATTCAACTTAAAATCAATTATCAGA
*** * *
22302 NNNTAAAACAATTTAAAGCGAGTAATAAGGCTGTTAAAGGAATGGGTGACTCTAAATTGACTTTT
66 TCATAAAACAATTTAAAGCGAGTAATAAGGCTGTTAAAGGAATGGGTGACTATAAATAGACTTTT
*
22367 CTT-CTCAATAAATGGCCTTTTCTACTTGTTTCTCTAGGTAA
131 CTTGCT-AATGAATGGCCTTTTCT-CTTGTTTCTCTAGGTAA
* * * * *
22408 ACATTAAATTATA-ACATGTTTTA-ATAGAGAATGTAAAAAAATGCAAGC-TAAAATCAATTATG
1 ACATTCAATTATAGTC-TGTTTTACCTA-AGAATGTAAAAAAATTCAA-CTTAAAATCAATTATC
* * * * * *
22470 AGTTTATAAAACAATTTAAAGAGAGTAATAAGGC--TTACGAAGGAATGGGTGACTAGAAATGGC
63 AGATCATAAAACAATTTAAAGCGAGTAATAAGGCTGTTA--AAGGAATGGGTGACTATAAATAGA
* * * * **
22533 CTTTTCTTGCAAATGAAT-ACCTTTCCTTTATGTTTCT-TGAGGTCG
126 CTTTTCTTGCTAATGAATGGCCTTTTCTCT-TGTTTCTCT-AGGTAA
* * * * * *
22578 ACATTCAATCATGGTTTGTTTTAACAAAAAATGTAAAAATAATTCAACTTAAAATCAATTATCAG
1 ACATTCAATTATAGTCTGTTTTACCTAAGAATGTAAAAA-AATTCAACTTAAAATCAATTATCAG
* * *
22643 ATCATAAAACAATTTAAAGCAAGTAATAAGGCTGTTGACA-GAATGGGTGACAATAAATAGACTT
65 ATCATAAAACAATTTAAAGCGAGTAATAAGGCTGTT-AAAGGAATGGGTGACTATAAATAGACTT
** * * * *
22707 TTCTTGCTAATGAATGTGTTTTTTTTCATGTTTCTCAAGGCAA
129 TTCTTGCTAATGAATG-GCCTTTTCTCTTGTTTCTCTAGGTAA
* * *
22750 GCATTCAATTATAGTCTGTTTTATCC-AA-AATTGTAAAAAAATTCAACTTATAATCAATTATGA
1 ACATTCAATTATAGTCTGTTTTA-CCTAAGAA-TGTAAAAAAATTCAACTTAAAATCAATTATCA
* *
22813 GATTATAAAATAATTTAAAGCG
64 GATCATAAAACAATTTAAAGCG
22835 NNNNNNNNNN
Statistics
Matches: 339, Mismatches: 68, Indels: 40
0.76 0.15 0.09
Matches are distributed among these distances:
169 5 0.01
170 50 0.15
171 234 0.69
172 42 0.12
173 7 0.02
174 1 0.00
ACGTcount: A:0.38, C:0.12, G:0.14, T:0.34
Consensus pattern (170 bp):
ACATTCAATTATAGTCTGTTTTACCTAAGAATGTAAAAAAATTCAACTTAAAATCAATTATCAGA
TCATAAAACAATTTAAAGCGAGTAATAAGGCTGTTAAAGGAATGGGTGACTATAAATAGACTTTT
CTTGCTAATGAATGGCCTTTTCTCTTGTTTCTCTAGGTAA
Found at i:25641 original size:171 final size:171
Alignment explanation
Indices: 23483--25999 Score: 1389
Period size: 171 Copynumber: 14.8 Consensus size: 171
23473 NNNNNNNNNN
* * ** * *
23483 AAAGTCCATTTCTAGTCACCCATTCTTTCAAAAGCCTTATTACTCGCTTTAAATAATTTTGTAAT
1 AAAGTCCATTTATAGTCACCCATTCCTTCAAAAGCCTTATTACTCGCTTTAAATTGTTTTATAAA
* * **********
23548 CCCATAATTGATTTTAAGTTGAATTCTTTTTACATTTTTGGTTAAAACAGACTATNNNNNNNNNN
66 CTCATAATTGATTTTAAGTTGAATT-TTTTTACATTTTTGATTAAAACAGACTATAATTGAATGT
** * * * * *
23613 CTACCTCAAGAAACTTAAAGGAAAAGGCATTCATTTGCAAGA
130 CTACCTTGAGAAACATGATGAAAAAGGCATTCATTGGCAAGA
* * ********** *
23655 AACA-TCCATTTATAATCACCCATTCTTTCAAAAGCCTTATTNNNNNNNNNNAATGGTTTTATAA
1 AA-AGTCCATTTATAGTCACCCATTCCTTCAAAAGCCTTATTACTCGCTTTAAATTGTTTTATAA
* * * * **
23719 ACTCATAATTGATTTTAAGTTGAGTTGTTTT-CCTTTTTCTATTAAAACAGAGAATAATTGAATG
65 ACTCATAATTGATTTTAAGTTGAATTTTTTTACATTTTT-GATTAAAACAGACTATAATTGAATG
* ** * **
23783 TCTACCTCGAGAAATGTGAAGAAAAATTCATTCATTGGCAAGA
129 TCTACCTTGAGAAACATGATGAAAAAGGCATTCATTGGCAAGA
* * * * * ********** **
23826 AAAGTCTATATATTGTCACCTAGTCCTTCAAAAGCCTTATNNNNNNNNNNAAACAGTTTTATAAA
1 AAAGTCCATTTATAGTCACCCATTCCTTCAAAAGCCTTATTACTCGCTTTAAATTGTTTTATAAA
* * *
23891 CTCACAATTGATTTTAAGTTGAATTGTTTTACATTTTTTG-TTTAAACA-AGCTATAATTGAATG
66 CTCATAATTGATTTTAAGTTGAATTTTTTTACA-TTTTTGATTAAAACAGA-CTATAATTGAATG
* ** * *
23954 -CTTGCCTCAAAAAACAT-ATAGAAAAAGCCATTCATTGAG-AAGA
129 TC-TACCTTGAGAAACATGAT-GAAAAAGGCATTCATTG-GCAAGA
* * * * * *
23997 AAAGTCCATTTAGAATTACCAATTCCTTCAAAAGCCTTATTACTAGCTTTAAATTG-TTTATAAG
1 AAAGTCCATTTATAGTCACCCATTCCTTCAAAAGCCTTATTACTCGCTTTAAATTGTTTTATAAA
* * * * *
24061 CTCATAATTGATTTTAAGTTG-AGTTTTTCATATTTTTGGTTAAAACAGATTATAATTGAATG-C
66 CTCATAATTGATTTTAAGTTGAATTTTTTTACATTTTTGATTAAAACAGACTATAATTGAATGTC
* * ** ** *
24124 TTACCTCGAGAAACATG-TAAAAAAAGTTATTTTTTGAG-AAAA
131 -TACCTTGAGAAACATGAT-GAAAAAGGCATTCATTG-GCAAGA
* ** * * * *
24166 AAAGTCAATTTCGAGTCACCCATTTCTTCAAAAGCTTTATTACTCGCTTTAAATTGTTTTATGAT
1 AAAGTCCATTTATAGTCACCCATTCCTTCAAAAGCCTTATTACTCGCTTTAAATTGTTTTATAAA
* * * **
24231 CTTATAATTGATTTTAAGTTGAA-TTTTTTACATTTATGGTCGAAACAGACTATAATTGAATGTC
66 CTCATAATTGATTTTAAGTTGAATTTTTTTACATTTTTGATTAAAACAGACTATAATTGAATGTC
* * * *
24295 TA--TTGAGAGAAACATGAAGAAAAATGCATTCGTTAGCAAGA
131 TACCTT--GAGAAACATGATGAAAAAGGCATTCATTGGCAAGA
* * * * * *
24336 AAAGTCCATTTATCGTCACCCATTCTTTCAAAAGTCTTATCACTCGCTTTAAATTGTTTTATGAT
1 AAAGTCCATTTATAGTCACCCATTCCTTCAAAAGCCTTATTACTCGCTTTAAATTGTTTTATAAA
* ********** * *
24401 CTCATTATTGATTTTAAGTTGAATTTTTTTTACANNNNNNNNNNAAACAAACCATAATTGAATGT
66 CTCATAATTGATTTTAAGTTGAA-TTTTTTTACATTTTTGATTAAAACAGACTATAATTGAATGT
* * * * * *
24466 CTACCTCGAG-AATATAAAGGAAAAGGCATTCATTTGCAAGA
130 CTACCTTGAGAAACATGATGAAAAAGGCATTCATTGGCAAGA
* * ********** *
24507 AAAGTCCATTTATGGTCACTCATTCCTTCAAAANNNNNNNNNNTCGCTTTAAATGGTTTTATAAA
1 AAAGTCCATTTATAGTCACCCATTCCTTCAAAAGCCTTATTACTCGCTTTAAATTGTTTTATAAA
* *
24572 CTCATAATTAATTTTACA-TTAAATTTTTTTACATTTTTCG-TTAAAACAGA-TAATAATTGAAT
66 CTCATAATTGATTTTA-AGTTGAATTTTTTTACATTTTT-GATTAAAACAGACT-ATAATTGAAT
* * * *********
24634 GTTTA-C-TGTAGGAAACGT-ATAGAAAAAGTCATTCANNNNNNNNN
128 GTCTACCTTG-A-GAAACATGAT-GAAAAAGGCATTCATTGGCAAGA
* ** * * * ***
24678 NAAGTCCATTTATAGTCACCCATTGTTTTAAAAGCCTTATTACTCGTTTTAAATTATTTTATNNN
1 AAAGTCCATTTATAGTCACCCATTCCTTCAAAAGCCTTATTACTCGCTTTAAATTGTTTTATAAA
******* * *
24743 NNNNNNNTTGATTTTAAGTTGAATTTTTTTACATTTTTGAATGAAACAGACTATAATTGAATG-C
66 CTCATAATTGATTTTAAGTTGAATTTTTTTACATTTTTGATTAAAACAGACTATAATTGAATGTC
** * * * *
24807 T-TGTTGAGAAACATGAAG-AAAAGTGAATGT-ATTAGCAAAA
131 TACCTTGAGAAACATGATGAAAAAG-GCAT-TCATTGGCAAGA
** * * * * * *
24847 AAAGTCCATTGGTAGTCTCCCATTCATTCAAAAACCTTTTTACTCGCTTCAAATGGTTTTATAAA
1 AAAGTCCATTTATAGTCACCCATTCCTTCAAAAGCCTTATTACTCGCTTTAAATTGTTTTATAAA
* ** *
24912 CTCATAATTAATTTTAAGTTGAATTTTTTTGA-ATTTTCCATTAAAATAGA-TAATAATTGAATG
66 CTCATAATTGATTTTAAGTTGAATTTTTTT-ACATTTTTGATTAAAACAGACT-ATAATTGAATG
* * * * *
24975 TTTACC-TCAGGAAACGTG-TAAAAAAGCCATTCATTGAG-AAGA
129 TCTACCTTGA-GAAACATGATGAAAAAGGCATTCATTG-GCAAGA
* ** * *
25017 AAAGTCCATTTATAGTCACCCATTCTTTCAAAAGTTTTATTACTCGCTTTAAATTATTTTATAAT
1 AAAGTCCATTTATAGTCACCCATTCCTTCAAAAGCCTTATTACTCGCTTTAAATTGTTTTATAAA
*
25082 CTCATAATTGATTTTAAGTTGAATTTGTTTACATTTTTGGA-TAAAACAGACTATAATTGAATG-
66 CTCATAATTGATTTTAAGTTGAATTTTTTTACATTTTT-GATTAAAACAGACTATAATTGAATGT
* * * *
25145 CTTGCCTAGAGAAACATGAAGAAAAATGCATTCATTGGCAAGA
130 C-TACCTTGAGAAACATGATGAAAAAGGCATTCATTGGCAAGA
********** * * *
25188 AANNNNNNNNNNTAGTGACCCATTCTTTCAAAAGCCTTATTACTCGCTTAAAATTGTTTTATAAA
1 AAAGTCCATTTATAGTCACCCATTCCTTCAAAAGCCTTATTACTCGCTTTAAATTGTTTTATAAA
* * * * ** ** * *
25253 CTCATAATTGAATTTAACTTAAATTTTTTTACATTCTCCATTAAAACAGGTTATAATTAAATGTT
66 CTCATAATTGATTTTAAGTTGAATTTTTTTACATTTTTGATTAAAACAGACTATAATTGAATGTC
* * * * **********
25318 TTCCTAGAGAAACAAG-TAGAAAAAGCCATNNNNNNNNNNGA
131 TACCTTGAGAAACATGAT-GAAAAAGGCATTCATTGGCAAGA
* * * * *
25359 AAAGTCCATTTAGAGTCATCCATTCCTTCAAAAACCTTATTACTCACTTCAAATTGTTTTATAAA
1 AAAGTCCATTTATAGTCACCCATTCCTTCAAAAGCCTTATTACTCGCTTTAAATTGTTTTATAAA
********** * * *
25424 CTCATAATTGATTTTAAGTNNNNNNNNNNTACATTTTT-AGTTAAAACAAACCATAATTAAATGT
66 CTCATAATTGATTTTAAGTTGAATTTTTTTACATTTTTGA-TTAAAACAGACTATAATTGAATGT
* *
25488 CTACCTTGAGAAACATGATGGAAAAGGTATTCATTGGCAAGA
130 CTACCTTGAGAAACATGATGAAAAAGGCATTCATTGGCAAGA
* * * ** * * *
25530 AAAGTCTATTTATAATCACCGATTTTTTCAAAAGCCTTATTACACGCTTTAAATGGTTTTACAAA
1 AAAGTCCATTTATAGTCACCCATTCCTTCAAAAGCCTTATTACTCGCTTTAAATTGTTTTATAAA
* * * ** *
25595 CTCATAATTAATTTTAAGTTGAATTTTTTTATATTTTTTATTAAAACAGAAAATAATTGAATGTT
66 CTCATAATTGATTTTAAGTTGAATTTTTTTACATTTTTGATTAAAACAGACTATAATTGAATGTC
* * * *
25660 TACC-TCAGGAAATATG-TAGAAAAAGCCATTCAGTGAG-AAGA
131 TACCTTGA-GAAACATGAT-GAAAAAGGCATTCATTG-GCAAGA
* * * *********** * *
25701 AAAATCCATTTATAGTCACCCATTCTTTCAAAAACNNNNNNNNNNACTTTAAATTATTTTATAAT
1 AAAGTCCATTTATAGTCACCCATTCCTTCAAAAGCCTTATTACTCGCTTTAAATTGTTTTATAAA
* **********
25766 CTCATAATTG-TTTATAAGTTAAATTTTTTTACATTTTTNNNNNNNNNNGACTATAATTGAATG-
66 CTCATAATTGATTT-TAAGTTGAATTTTTTTACATTTTTGATTAAAACAGACTATAATTGAATGT
* * ** *
25829 CTTGCCTCG-GAAA-AT-ATGAAGAAA-ATATATCCATTGACAAGA
130 C-TACCTTGAGAAACATGATGAA-AAAGGCAT-T-CATTGGCAAGA
* * *
25871 ATAGTCCATTTAGAATCACCCATTCCTTCAAAAGCCTTATTACTCGCTTTAAATTGTTTTATAAA
1 AAAGTCCATTTATAGTCACCCATTCCTTCAAAAGCCTTATTACTCGCTTTAAATTGTTTTATAAA
* * * * ** * **
25936 CTGATAATAT-ATTTTAACTTAAATTTTTTTACATTCTCCATTAAAATAGGTTATAATTGAATGT
66 CTCATAAT-TGATTTTAAGTTGAATTTTTTTACATTTTTGATTAAAACAGACTATAATTGAATGT
26000 TTTCCTAGAG
Statistics
Matches: 1741, Mismatches: 531, Indels: 147
0.72 0.22 0.06
Matches are distributed among these distances:
168 19 0.01
169 224 0.13
170 472 0.27
171 908 0.52
172 111 0.06
173 6 0.00
174 1 0.00
ACGTcount: A:0.35, C:0.14, G:0.11, T:0.36
Consensus pattern (171 bp):
AAAGTCCATTTATAGTCACCCATTCCTTCAAAAGCCTTATTACTCGCTTTAAATTGTTTTATAAA
CTCATAATTGATTTTAAGTTGAATTTTTTTACATTTTTGATTAAAACAGACTATAATTGAATGTC
TACCTTGAGAAACATGATGAAAAAGGCATTCATTGGCAAGA
Found at i:31551 original size:171 final size:170
Alignment explanation
Indices: 31283--32729 Score: 969
Period size: 171 Copynumber: 8.4 Consensus size: 170
31273 TAAAATAGGT
* *** *
31283 TATAATTGAATGTTTTCCT-AGAGAAACAACTAGAAAAAGCCATTCATTGAGAAGAAAAGTCTAT
1 TATAATTGAATG-TTACCTCA-AGAAACATGAAGAAAAAGCCATTCATTGAGAAGAAAAGTCCAT
* * * * * *
31347 TTAGAGTCATCCATTCCTTCAAAAACCTTATTACTCGCTTCAAATTGTTTTGTAAGCTCATAATT
64 TTATAGTCACCCATTCCTTCAAAAGCCTTATTACTCGCTTTAAATTGTTTTATAAACTCATAATT
* *
31412 GATTTTTAGTTGAATTGTTTTTACATTTTTGGTTAAAATAGAC
129 GATTTTAAGTTGAATT-TTTTTACATTTTTGGTTAAAACAGAC
* * *
31455 TATAATTGAATGTTACCTCAAGAAACATGTAGAAAAAGTCATTTC-TTGAGAAGAAAAGTCAATT
1 TATAATTGAATGTTACCTCAAGAAACATGAAGAAAAAGCCA-TTCATTGAGAAGAAAAGTCCATT
* * ****************
31519 TATAGTCACCCATTCCTTCAAAAGCTTTATTACTTGCTTTAAANNNNNNNNNNNNNNNNTAATTG
65 TATAGTCACCCATTCCTTCAAAAGCCTTATTACTCGCTTTAAATTGTTTTATAAACTCATAATTG
* *
31584 ATTTTAAGTTGAATTTTTTTACATTTTTGGTCAAAATAGAC
130 ATTTTAAGTTGAATTTTTTTACATTTTTGGTTAAAACAGAC
* * * * * ** * * * *
31625 TATAATTAAATATCTGCTTGGAA-AAACGCGAAGCAAAATG-CATTCGTTGATAAGAAAAGTTTC
1 TATAATTGAATGT-TACCT-CAAGAAACATGAAG-AAAAAGCCATTCATTGAGAAGAAAAG-TCC
* ***********
31688 -TTTATAGTCACCCATTCCTTCAAAAGCCTTATTACTCGCTTTAAATTATTTTANNNNNNNNNNN
62 ATTTATAGTCACCCATTCCTTCAAAAGCCTTATTACTCGCTTTAAATTGTTTTATAAACTCATAA
* * * * *
31752 NTGATTTTAAGTTAAATTTTTTTATATTTTTAGATAAAACAGAC
127 TTGATTTTAAGTTGAATTTTTTTACATTTTTGGTTAAAACAGAC
* * *** *
31796 TATAATTGAATGGTTGCCTCGAGAAACATGAAGAAAAATATATTCTTTG-GTAAGAAAAGTCCAT
1 TATAATTGAAT-GTTACCTCAAGAAACATGAAGAAAAAGCCATTCATTGAG-AAGAAAAGTCCAT
* * *
31860 TTATAGTTACCCATTCCTTCAAAAACCTTATTACTCGCTGTAAATTGTTTTATAAACTCATAATT
64 TTATAGTCACCCATTCCTTCAAAAGCCTTATTACTCGCTTTAAATTGTTTTATAAACTCATAATT
* * * *** **
31925 GATTTTAACTTGACTTTTTTTACATTCTCCATTAAAACAGGT
129 GATTTTAAGTTGAATTTTTTTACATTTTTGGTTAAAACAGAC
* * * * *
31967 TATAATTGAACAT-TTTCCTAAGAGAAACAAGTAGAAAAAGCCATTCATTGATAAGAAAAGTCCA
1 TATAATTG-A-ATGTTACCTCA-AGAAACATGAAGAAAAAGCCATTCATTGAGAAGAAAAGTCCA
* ** * * * *
32031 TTTAGAGTCATTCATTCCTTCAAAAACCTTATTACTCGATTTAAATTGTTTTATGAACTCAAAAT
63 TTTATAGTCACCCATTCCTTCAAAAGCCTTATTACTCGCTTTAAATTGTTTTATAAACTCATAAT
* * *
32096 TGATTTTAAGTCGAATTGTTTTACATTTTTGGATAAAACAGAC
128 TGATTTTAAGTTGAATTTTTTTACATTTTTGGTTAAAACAGAC
* ** * *
32139 TATAATTGAATGATTTCCTTGAGAAACATGAAGAAAAA-CATATTCATTG-GCAAGAAAAGTCTA
1 TATAATTGAATG-TTACCTCAAGAAACATGAAGAAAAAGC-CATTCATTGAG-AAGAAAAGTCCA
**************** * * *
32202 TTTATAGNNNNNNNNNNNNNNNNAAGCCTTATTACTCACTTTAAATGGTTTTGTAAACTCATAAT
63 TTTATAGTCACCCATTCCTTCAAAAGCCTTATTACTCGCTTTAAATTGTTTTATAAACTCATAAT
* * ** *
32267 TAATTTTAAGTTGAGTTTTTTTGTATTTTTGGTTCAAACA-AGC
128 TGATTTTAAGTTGAATTTTTTTACATTTTTGGTTAAAACAGA-C
* * * * * *** *
32310 CACAATTGAATGTCTACCT-AGAGAAACATGATGGAAAAGGCATTCATTTTCAAAAAAAGTCCAT
1 TATAATTGAATGT-TACCTCA-AGAAACATGAAGAAAAAGCCATTCATTGAGAAGAAAAGTCCAT
* * * * * **********
32374 TCATAGTTACCTATTCCTTCAAAAGCCTTATTACTCACTTTAAATGGTTNNNNNNNNNNATAATT
64 TTATAGTCACCCATTCCTTCAAAAGCCTTATTACTCGCTTTAAATTGTTTTATAAACTCATAATT
* ** *
32439 AATTTTAAGTTGAATTTTTTTACATTTTTCATTAAATATAGA-
129 GATTTTAAGTTGAATTTTTTTACATTTTTGGTTAAA-ACAGAC
* * *
32481 TAATAATTGAATGTTTACCTCAGGAAACATGTAGAAAAAGCCATTCATTAAGAAGAAAAGTCCAT
1 T-ATAATTGAATG-TTACCTCAAGAAACATGAAGAAAAAGCCATTCATTGAGAAGAAAAGTCCAT
* * * ********** * *
32546 TTATAGCCACCCATTCTTTCGAAAGCCTTANNNNNNNNNNTAAATTATTTTATAATCTCATAATT
64 TTATAGTCACCCATTCCTTCAAAAGCCTTATTACTCGCTTTAAATTGTTTTATAAACTCATAATT
* * * *
32611 GATTTCAAGTTGAATTTGTTTATATTTTTGGATAAAACAGAC
129 GATTTTAAGTTGAATTTTTTTACATTTTTGGTTAAAACAGAC
* * *
32653 TATAATTGAATGCTTGCCTTGAA-AAACATGAAGAAAAA-CGCATTCATTGACAAGAAAAGTCCA
1 TATAATTGAATG-TTACC-TCAAGAAACATGAAGAAAAAGC-CATTCATTGAGAAGAAAAGTCCA
32716 TTTATAGTCACCCA
63 TTTATAGTCACCCA
32730 NNNNNNNNNN
Statistics
Matches: 972, Mismatches: 270, Indels: 67
0.74 0.21 0.05
Matches are distributed among these distances:
170 52 0.05
171 632 0.65
172 283 0.29
173 5 0.01
ACGTcount: A:0.35, C:0.13, G:0.12, T:0.35
Consensus pattern (170 bp):
TATAATTGAATGTTACCTCAAGAAACATGAAGAAAAAGCCATTCATTGAGAAGAAAAGTCCATTT
ATAGTCACCCATTCCTTCAAAAGCCTTATTACTCGCTTTAAATTGTTTTATAAACTCATAATTGA
TTTTAAGTTGAATTTTTTTACATTTTTGGTTAAAACAGAC
Found at i:32275 original size:514 final size:498
Alignment explanation
Indices: 31755--32722 Score: 996
Period size: 514 Copynumber: 1.9 Consensus size: 498
31745 NNNNNNNNTG
* * * *
31755 ATTTTAAGTTAAATTTTTTTATATTTTTAGATAAAAC-AGACTATAATTGAATGGT-TGCCTCGA
1 ATTTTAAGTTAAATTTTTTTATATTTTTAGATAAAACAAG-CCACAATTGAAT-GTCTACCTAGA
* * * *
31818 GAAACATGAAGAAAAATATATTC-TTTGGT-AAGAAAAGTCCATTTATAGTTACCCATTCCTTCA
64 GAAACATGAAGAAAAAGACATTCATTT--TCAAAAAAAGTCCATTCATAGTTACCCATTCCTTCA
* * * *
31881 AAAACCTTATTACTCGCTGTAAATTGTTTTATAAACTCATAATTGATTTTAACTTGACTTTTTTT
127 AAAACCTTATTACTCACTGTAAATGGTTTTATAAACTCATAATTAATTTTAACTTGAATTTTTTT
* * *
31946 ACATTCTCCATTAAA-ACAGGTTATAATTGAACATTTTCCTAAGAGAAACAAGTAGAAAAAGCCA
192 ACATTCTCCATTAAATACAGATAATAATTGAACATTTACCTAAG-GAAACAAGTAGAAAAAGCCA
* * * **
32010 TTCATTGATAAGAAAAGTCCATTTAGAGTCATTCATTCCTTCAAAAACCTTATTACTCGATTTAA
256 TTCATTAAGAAGAAAAGTCCATTTAGAGCCACCCATTCCTTCAAAAACCTTATTACTCGATTTAA
* *
32075 ATTGTTTTATGAA-CTCAAAATTGATTTTAAGTCGAA-TTGTTTTACATTTTTGGATAAAACAGA
321 ATTATTTTAT-AATCTCAAAATTGATTTCAAGTCGAATTTG-TTTACATTTTTGGATAAAACAGA
* * * * *
32138 CTATAATTGAATGATTTCCTTGAGAAACATGAAGAAAAACATATTCATTGGCAAGAAAAGTCTAT
384 CTATAATTGAATGATTGCCTTGAAAAACATGAAGAAAAACACATTCATTGACAAGAAAAGTCCAT
32203 TTATAGNNNNNNNNNNNNNNNNAAGCCTTATTACTCACTTTAAATGGTTTTGTAAACTCATAATT
449 TTATAG----------------AAGCCTTATTACTCACTTTAAATGGTTTTGTAAACTCATAATT
32268 A
498 A
* * * * * *
32269 ATTTTAAGTTGAGTTTTTTTGTATTTTTGGTTCAAACAAGCCACAATTGAATGTCTACCTAGAGA
1 ATTTTAAGTTAAATTTTTTTATATTTTTAGATAAAACAAGCCACAATTGAATGTCTACCTAGAGA
* * * * *
32334 AACATGATGGAAAAGGCATTCATTTTCAAAAAAAGTCCATTCATAGTTACCTATTCCTTCAAAAG
66 AACATGAAGAAAAAGACATTCATTTTCAAAAAAAGTCCATTCATAGTTACCCATTCCTTCAAAAA
* ********** *
32399 CCTTATTACTCACTTTAAATGGTTNNNNNNNNNNATAATTAATTTTAAGTTGAATTTTTTTACAT
131 CCTTATTACTCACTGTAAATGGTTTTATAAACTCATAATTAATTTTAACTTGAATTTTTTTACAT
* * * ** * *
32464 TTTTCATTAAATATAGATAATAATTGAATGTTTACCTCAGGAAACATGTAGAAAAAGCCATTCAT
196 TCTCCATTAAATACAGATAATAATTGAACATTTACCTAAGGAAACAAGTAGAAAAAGCCATTCAT
* * * * **********
32529 TAAGAAGAAAAGTCCATTTATAGCCACCCATTCTTTCGAAAGCCTTANNNNNNNNNNTAAATTAT
261 TAAGAAGAAAAGTCCATTTAGAGCCACCCATTCCTTCAAAAACCTTATTACTCGATTTAAATTAT
* * *
32594 TTTATAATCTCATAATTGATTTCAAGTTGAATTTGTTTATATTTTTGGATAAAACAGACTATAAT
326 TTTATAATCTCAAAATTGATTTCAAGTCGAATTTGTTTACATTTTTGGATAAAACAGACTATAAT
* *
32659 TGAATGCTTGCCTTGAAAAACATGAAGAAAAACGCATTCATTGACAAGAAAAGTCCATTTATAG
391 TGAATGATTGCCTTGAAAAACATGAAGAAAAACACATTCATTGACAAGAAAAGTCCATTTATAG
32723 TCACCCANNN
Statistics
Matches: 371, Mismatches: 76, Indels: 14
0.80 0.16 0.03
Matches are distributed among these distances:
513 5 0.01
514 337 0.91
515 29 0.08
ACGTcount: A:0.36, C:0.13, G:0.12, T:0.36
Consensus pattern (498 bp):
ATTTTAAGTTAAATTTTTTTATATTTTTAGATAAAACAAGCCACAATTGAATGTCTACCTAGAGA
AACATGAAGAAAAAGACATTCATTTTCAAAAAAAGTCCATTCATAGTTACCCATTCCTTCAAAAA
CCTTATTACTCACTGTAAATGGTTTTATAAACTCATAATTAATTTTAACTTGAATTTTTTTACAT
TCTCCATTAAATACAGATAATAATTGAACATTTACCTAAGGAAACAAGTAGAAAAAGCCATTCAT
TAAGAAGAAAAGTCCATTTAGAGCCACCCATTCCTTCAAAAACCTTATTACTCGATTTAAATTAT
TTTATAATCTCAAAATTGATTTCAAGTCGAATTTGTTTACATTTTTGGATAAAACAGACTATAAT
TGAATGATTGCCTTGAAAAACATGAAGAAAAACACATTCATTGACAAGAAAAGTCCATTTATAGA
AGCCTTATTACTCACTTTAAATGGTTTTGTAAACTCATAATTA
Found at i:32319 original size:343 final size:342
Alignment explanation
Indices: 31753--32418 Score: 710
Period size: 343 Copynumber: 1.9 Consensus size: 342
31743 NNNNNNNNNN
* * * *
31753 TGATTTTAAGTTAAATTTTTTTATATTTTTAGATAAAACAGACTATAATTGAATGGTTGCCTCGA
1 TGATTTTAAGTCAAATTGTTTTACATTTTTAGATAAAACAGACTATAATTGAATGATTGCCTCGA
* * *
31818 GAAACATGAAGAAAAATATATTCTTTGGTAAGAAAAGTCCATTTATAGTTACCCATTCCTTCAAA
66 GAAACATGAAGAAAAACATATTCATTGGCAAGAAAAGTCCATTTATAGTTACCCATTCCTTCAAA
* * *
31883 AACCTTATTACTCGCTGTAAATTGTTTTATAAACTCATAATTGATTTTAACTTGACTTTTTTTAC
131 AACCTTATTACTCACTGTAAATGGTTTTATAAACTCATAATTAATTTTAACTTGACTTTTTTTAC
* ** * * *
31948 ATTCTCCATTAAAACAGGTTATAATTGAACATTTTCCTAAGAGAAACAAG-TAGAAAAAGCCATT
196 ATTCTCCATTAAAACAAGCCACAATTGAACATCTACCT-AGAGAAACAAGAT-GAAAAAGCCATT
* * *
32012 CATTGAT-AAGAAAAGTCCATTTAGAGTCA-TTCATTCCTTCAAAAACCTTATTACTCGA-TTTA
259 CATT-ATCAAAAAAAGTCCATTCAGAGTCACCT-ATTCCTTCAAAAACCTTATTACTC-ACTTTA
32074 AATTGTTTTATGAACTCAAAAT
321 AATTGTTTTATGAACTCAAAAT
* * * *
32096 TGATTTTAAGTCGAATTGTTTTACATTTTTGGATAAAACAGACTATAATTGAATGATTTCCTTGA
1 TGATTTTAAGTCAAATTGTTTTACATTTTTAGATAAAACAGACTATAATTGAATGATTGCCTCGA
* ****************
32161 GAAACATGAAGAAAAACATATTCATTGGCAAGAAAAGTCTATTTATAGNNNNNNNNNNNNNNNNA
66 GAAACATGAAGAAAAACATATTCATTGGCAAGAAAAGTCCATTTATAGTTACCCATTCCTTCAAA
* * * * * **
32226 AGCCTTATTACTCACTTTAAATGGTTTTGTAAACTCATAATTAATTTTAAGTTGAGTTTTTTTGT
131 AACCTTATTACTCACTGTAAATGGTTTTATAAACTCATAATTAATTTTAACTTGACTTTTTTTAC
* *** * ** * * *
32291 ATTTTTGGTTCAAACAAGCCACAATTGAATGTCTACCTAGAGAAACATGATGGAAAAGGCATTCA
196 ATTCTCCATTAAAACAAGCCACAATTGAACATCTACCTAGAGAAACAAGATGAAAAAGCCATTCA
* * * *
32356 TTTTCAAAAAAAGTCCATTCATAGTTACCTATTCCTTCAAAAGCCTTATTACTCACTTTAAAT
261 TTATCAAAAAAAGTCCATTCAGAGTCACCTATTCCTTCAAAAACCTTATTACTCACTTTAAAT
32419 GGTTNNNNNN
Statistics
Matches: 258, Mismatches: 61, Indels: 9
0.79 0.19 0.03
Matches are distributed among these distances:
341 2 0.01
342 72 0.28
343 184 0.71
ACGTcount: A:0.36, C:0.14, G:0.12, T:0.36
Consensus pattern (342 bp):
TGATTTTAAGTCAAATTGTTTTACATTTTTAGATAAAACAGACTATAATTGAATGATTGCCTCGA
GAAACATGAAGAAAAACATATTCATTGGCAAGAAAAGTCCATTTATAGTTACCCATTCCTTCAAA
AACCTTATTACTCACTGTAAATGGTTTTATAAACTCATAATTAATTTTAACTTGACTTTTTTTAC
ATTCTCCATTAAAACAAGCCACAATTGAACATCTACCTAGAGAAACAAGATGAAAAAGCCATTCA
TTATCAAAAAAAGTCCATTCAGAGTCACCTATTCCTTCAAAAACCTTATTACTCACTTTAAATTG
TTTTATGAACTCAAAAT
Done.