Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018397974.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_128.0, 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: 21303
ACGTcount: A:0.28, C:0.09, G:0.09, T:0.28
Warning! 5695 characters in sequence are not A, C, G, or T
Found at i:365 original size:171 final size:166
Alignment explanation
Indices: 138--669 Score: 586
Period size: 172 Copynumber: 3.1 Consensus size: 166
128 NNNNNNNNNN
* *
138 TTTAAAGTGAGTAATAAGGCTTTTGAAGGCAT-GTGTGACTATAAATGGACTTTTCTTATTAATG
1 TTTAAAGCGAGTAATAA-GCTTTTGAAGGCATAG-GTGACTATAAATGGACTTTTCTTATCAATG
* ** * * *
202 GATATCTTTTTCTTCATGTTTCCTAAGACAAACATTCAATTATTATATGTTTTAA-ACAACAATG
64 GATATCTTTTTCTTCACGTTT-CTAAGGTAGACATTCAATTATTATCTATTTTAATA-AA-AATG
266 TAAAAAATTAGACTTAAAATCAATTATGAGATTATAAAACCA
126 TAAAAAATTA-ACTTAAAATCAATTATGAGATTATAAAACCA
* * * * *
308 TTTAAAGGGAGTAATAAGATTTTCGAAGGTATAGATGACTATAAATGGACTTTTTCTTACCAATG
1 TTTAAAGCGAGTAATAAGCTTTT-GAAGGCATAGGTGACTATAAATGGAC-TTTTCTTATCAATG
** * * *
373 GATCCCTTTTACTTCACGTTTCTAGTGGTAGACATTCAATTATAATCTATTTTAATAAAAACT-T
64 GATATCTTTTTCTTCACGTTTCTA-AGGTAGACATTCAATTATTATCTATTTTAATAAAAA-TGT
* * * *
437 CAAAAAAACTCAACTTAAAATCAATTATGAGATTTTAAAGCCG
127 --AAAAAA-TTAACTTAAAATCAATTATGAGATTATAAAACCA
* * *
480 TTTAAAGCGAGTAATAAGCCTTTTGAAAGCATAGGTGACTATAAATGGACTTTTCTTGTCAATGC
1 TTTAAAGCGAGTAATAAG-CTTTTGAAGGCATAGGTGACTATAAATGGACTTTTCTTATCAATGG
*
545 ATATCTTTTTCTTCACGTTTCTGAAGGTAGATATTCAATTA-TAGTCTATTTTAATAAAAAATAT
65 ATATCTTTTTCTTCACGTTTCT-AAGGTAGACATTCAATTATTA-TCTATTTTAAT--AAAA-AT
* *
609 AGAAAAAAATTACCTTAAAATCAATTATGAGATTATAAAACCA
125 -GTAAAAAATTAACTTAAAATCAATTATGAGATTATAAAACCA
* *
652 TTTAAAGCAAGTAGTAAG
1 TTTAAAGCGAGTAATAAG
670 GCNNNNNNNN
Statistics
Matches: 302, Mismatches: 43, Indels: 32
0.80 0.11 0.08
Matches are distributed among these distances:
169 5 0.02
170 45 0.15
171 113 0.37
172 121 0.40
173 17 0.06
174 1 0.00
ACGTcount: A:0.38, C:0.12, G:0.13, T:0.36
Consensus pattern (166 bp):
TTTAAAGCGAGTAATAAGCTTTTGAAGGCATAGGTGACTATAAATGGACTTTTCTTATCAATGGA
TATCTTTTTCTTCACGTTTCTAAGGTAGACATTCAATTATTATCTATTTTAATAAAAATGTAAAA
AATTAACTTAAAATCAATTATGAGATTATAAAACCA
Found at i:1573 original size:171 final size:169
Alignment explanation
Indices: 1223--1847 Score: 600
Period size: 171 Copynumber: 3.7 Consensus size: 169
1213 NNNNNNNNNN
* *
1223 TTGAATTTTTTTATATTTTTTATTAAAACATATTATAATTAAAT-GCATACCTCAAGAAACATGA
1 TTGAATTTTTTTACA-TTTTTATTAAAACATATTATAATTAAATATC-TACCTCAAGAAACATGA
* * * * * *
1287 AGAAAATAATATCCATTGGCAAGAAAAGTCCATTTATTGTCTCCCATGCCTTCGAAAGCTTTATT
64 AGAAAA-GATATCCATTGGCAAGAAAAGTTCATTTATAGTCACCCATGCCTTCAAAAGCCTTATT
** * * *
1352 ACTCATTTTAAAT-TGATTTATAATCTTATAATTGATTTTAAG
128 ACTCGCTTTAAATGT-TTTTCTAATCTCATAATTGATTTTAAG
* *
1394 TT-AATTTTTTTTACATTTTATATTAAAAAATATTATAAGTAAATATCTACCTCAAGAAACATGA
1 TTGAA-TTTTTTTACATTTT-TATTAAAACATATTATAATTAAATATCTACCTCAAGAAACATGA
* *
1458 AGAAAAGATATCCATTGACAAAAAAAGTTCATTTATAGTCACCCATGCCTTCAAAAGCCTTATTA
64 AGAAAAGATATCCATTGGCAAGAAAAGTTCATTTATAGTCACCCATGCCTTCAAAAGCCTTATTA
* * *
1523 GTCGCCTTAAATGTTTTTCTAATCTCATAATTAATTTTAAG
129 CTCGCTTTAAATGTTTTTCTAATCTCATAATTGATTTTAAG
* * * * * * * *
1564 TTGAATTTTTTTACATTTTTGGTTGAAACAGATTATAATTCAATATCTGCCTTAGGAAACATAAA
1 TTGAATTTTTTTACATTTTT-ATTAAAACATATTATAATTAAATATCTACCTCAAGAAACATGAA
* * ** *
1629 GAAAAAGATATCCATTGGTAAGAAAAG-TCTATTTATAATCAATCATGCCTTCAAAAGCCGTATT
65 G-AAAAGATATCCATTGGCAAGAAAAGTTC-ATTTATAGTCACCCATGCCTTCAAAAGCCTTATT
* * * *
1693 ACTTGCTTTGAATAGTTTTAC-AATCTCATAACTGATTTTAAG
128 ACTCGCTTTAAAT-GTTTTTCTAATCTCATAATTGATTTTAAG
** * * * * * * * *
1735 TTGAATTTTTTTATTTTTTTTATGAACACAAACTGTAATTGAATGTCTTCCTCAAGAAACATGAA
1 TTGAATTTTTTTA-CATTTTTATTAAAACATATTATAATTAAATATCTACCTCAAGAAACATGAA
** * * *
1800 -AAAGAGGCCATTCATTCAG-AAGAAAAGTTCA-TTATAGCCACCCATGCC
65 GAAA-A-GATATCCATT-GGCAAGAAAAGTTCATTTATAGTCACCCATGCC
1848 NNNNNNNNNN
Statistics
Matches: 373, Mismatches: 67, Indels: 29
0.80 0.14 0.06
Matches are distributed among these distances:
169 4 0.01
170 155 0.42
171 199 0.53
172 15 0.04
ACGTcount: A:0.37, C:0.14, G:0.11, T:0.38
Consensus pattern (169 bp):
TTGAATTTTTTTACATTTTTATTAAAACATATTATAATTAAATATCTACCTCAAGAAACATGAAG
AAAAGATATCCATTGGCAAGAAAAGTTCATTTATAGTCACCCATGCCTTCAAAAGCCTTATTACT
CGCTTTAAATGTTTTTCTAATCTCATAATTGATTTTAAG
Found at i:1846 original size:341 final size:341
Alignment explanation
Indices: 1223--1847 Score: 724
Period size: 341 Copynumber: 1.8 Consensus size: 341
1213 NNNNNNNNNN
* * * *
1223 TTGAATTTTTTTATATTTTTTATTAAAACATATTATAATTAAATGCATACCTCAAGAAACATGAA
1 TTGAATTTTTTTACATTTTTGATTAAAACAGATTATAATTAAATGCATACCTCAAGAAACATAAA
** ** * **
1288 GAAAATAATATCCATTGGCAAGAAAAGTCCATTTATTGTCTCCCATGCCTTCGAAAGCTTTATTA
66 GAAAATAATATCCATTGGCAAGAAAAGTCCATTTATAATCAACCATGCCTTCAAAAGCCGTATTA
* * * * * *
1353 CTCATTTTAAATTGATTTATAATCTTATAATTGATTTTAAGTTAATTTTTTTTACATTTTATATT
131 CTCACTTTAAATAGATTTACAATCTCATAACTGATTTTAAGTTAATTTTTTTTACATTTTATATG
* * *
1418 AAAAAATATTATAAGTAAATATCTACCTCAAGAAACATGAAGAAAAGATATCCATTGACAAAAAA
196 AAAAAATACTATAAGTAAATATCTACCTCAAGAAACATGAAGAAAAGACATCCATTCACAAAAAA
*
1483 AGTTCATTTATAGTCACCCATGCCTTCAAAAGCCTTATTAGTCGCCTTAAATGTTTTTCTAATCT
261 AGTTCATTTATAGCCACCCATGCCTTCAAAAGCCTTATTAGTCGCCTTAAATGTTTTTCTAATCT
1548 CATAATTAATTTTAAG
326 CATAATTAATTTTAAG
* * * * *
1564 TTGAATTTTTTTACATTTTTGGTTGAAACAGATTATAATTCAATAT-C-TGCCTTAGGAAACATA
1 TTGAATTTTTTTACATTTTTGATTAAAACAGATTATAATT-AA-ATGCATACCTCAAGAAACATA
* * *
1627 AAGAAAA-AGATATCCATTGGTAAGAAAAGTCTATTTATAATCAATCATGCCTTCAAAAGCCGTA
64 AAGAAAATA-ATATCCATTGGCAAGAAAAGTCCATTTATAATCAACCATGCCTTCAAAAGCCGTA
** * * ** *
1691 TTACTTGCTTTGAATAGTTTTACAATCTCATAACTGATTTTAAGTTGAA-TTTTTTTATTTTTTT
128 TTACTCACTTTAAATAGATTTACAATCTCATAACTGATTTTAAGTT-AATTTTTTTTACATTTTA
* * * * * * * *
1755 TATGAACACAA-ACTGTAATTGAATGTCTTCCTCAAGAAACATGAA-AAAGAGGCCATTCATTCA
192 TATGAA-AAAATACTATAAGTAAATATCTACCTCAAGAAACATGAAGAAA-A-GACATCCATTCA
* *
1818 GAAGAAAAGTTCA-TTATAGCCACCCATGCC
254 CAAAAAAAGTTCATTTATAGCCACCCATGCC
1848 NNNNNNNNNN
Statistics
Matches: 231, Mismatches: 46, Indels: 14
0.79 0.16 0.05
Matches are distributed among these distances:
340 4 0.02
341 198 0.86
342 27 0.12
343 2 0.01
ACGTcount: A:0.37, C:0.14, G:0.11, T:0.38
Consensus pattern (341 bp):
TTGAATTTTTTTACATTTTTGATTAAAACAGATTATAATTAAATGCATACCTCAAGAAACATAAA
GAAAATAATATCCATTGGCAAGAAAAGTCCATTTATAATCAACCATGCCTTCAAAAGCCGTATTA
CTCACTTTAAATAGATTTACAATCTCATAACTGATTTTAAGTTAATTTTTTTTACATTTTATATG
AAAAAATACTATAAGTAAATATCTACCTCAAGAAACATGAAGAAAAGACATCCATTCACAAAAAA
AGTTCATTTATAGCCACCCATGCCTTCAAAAGCCTTATTAGTCGCCTTAAATGTTTTTCTAATCT
CATAATTAATTTTAAG
Found at i:2499 original size:171 final size:170
Alignment explanation
Indices: 2176--2589 Score: 507
Period size: 171 Copynumber: 2.4 Consensus size: 170
2166 ACATTTTTTA
* * * * ** ** *
2176 TTAAAATAGATTACAATTGAATGTCTACCACTA-GAAATGTGAAGAAAAAGGGATCCATTGGAAA
1 TTAAAATAGATAATAACTGAATGTCTACCTC-AGGAAACATGAAGAAAAAGATATCCATTGGCAA
* * *
2240 GAAAAAGTCCATTTATAGTCACCTATGCCTTCGAAAGTCTTATTACTCTCTTTAAATGGTTTTAT
65 G-AAAAGTCCATTTATAGTCACCTATGCCTTCAAAAGCCTTATTACTCGCTTTAAATGGTTTTAT
2305 AATCTCATAATTAATTTAAGTTGAATTT-TTTTACATTGTT-G
129 AATCTCATAATTAATTTAAGTTGAATTTGTTTT-CATTGTTAG
** * * *
2346 TTTAAAATAGATAATAA-TGGAATGTCTGTCTTAGGAAACATGAAGAACAAGATATCCATTAGCA
1 -TTAAAATAGATAATAACT-GAATGTCTACCTCAGGAAACATGAAGAAAAAGATATCCATTGGCA
* * **
2410 AGAAAAGTCCCTTTATAGTCACAC-ATGCCTTCAAAAGCCTTATTACTCGCTTTAATTTTTTTTA
64 AGAAAAGTCCATTTATAGTCAC-CTATGCCTTCAAAAGCCTTATTACTCGCTTTAAATGGTTTTA
*
2474 TAATCTCATAA-TAGATTTGAAGTTGAATTTGTTTTCATTTTTAG
128 TAATCTCATAATTA-ATTT-AAGTTGAATTTGTTTTCATTGTTAG
*
2518 TTAAAATAGATAATAACTGAATGTTTACCTCAGGAAACATGAAGAAAAAGATATCCATTGGCAAG
1 TTAAAATAGATAATAACTGAATGTCTACCTCAGGAAACATGAAGAAAAAGATATCCATTGGCAAG
2583 AAAAGTC
66 AAAAGTC
2590 TATNNNNNNN
Statistics
Matches: 208, Mismatches: 27, Indels: 16
0.83 0.11 0.06
Matches are distributed among these distances:
169 2 0.01
170 70 0.34
171 130 0.62
172 6 0.03
ACGTcount: A:0.37, C:0.13, G:0.14, T:0.35
Consensus pattern (170 bp):
TTAAAATAGATAATAACTGAATGTCTACCTCAGGAAACATGAAGAAAAAGATATCCATTGGCAAG
AAAAGTCCATTTATAGTCACCTATGCCTTCAAAAGCCTTATTACTCGCTTTAAATGGTTTTATAA
TCTCATAATTAATTTAAGTTGAATTTGTTTTCATTGTTAG
Found at i:6582 original size:170 final size:169
Alignment explanation
Indices: 5441--6716 Score: 798
Period size: 171 Copynumber: 7.5 Consensus size: 169
5431 ATTTAAAAGT
* * * * *
5441 TTTTATAATCCCATAATTAATTTTAAGCTAAATATTTTTATATTTTTTATTAAAATAGATTATAA
1 TTTTATAAT-TCATAATTGATTTTAAGTTAAATTTTTTTATATTTTTTATTAAAACAGATTATAA
* * ** * * *
5506 TTTAATATCTA-CTTGGGGAAACATAAAGAAAATGATATCCGTT-GATAAGAAAAGT-TCATTTA
65 TTGAATGTCTACCTT-AAGAAACATGAAGAAAAAGATATCCATTCG-TAAGAAAAGTCT-ATTTA
* * *
5568 TAGTC-ACCATTGCCTTCGAAAGCCTTATTACTCG-TTATAAATGG
127 TAG-CAACCA-TGCCTTCGAAAGCCGTATTACTCGCCT-TAAATTG
**********
5612 TTTTATAATCTCATAATTGATTTTAAGTT-ANNNNNNNNNNATTTTTTATTAAAACAGATTATAA
1 TTTTATAAT-TCATAATTGATTTTAAGTTAAATTTTTTTATATTTTTTATTAAAACAGATTATAA
* * * * **
5676 TTGAATATCTACCTTAAGATACCTGAACAAAAAGATATCCATTAATAAGAAAAGT-TCATTTATA
65 TTGAATGTCTACCTTAAGAAACATGAAGAAAAAGATATCCATTCGTAAGAAAAGTCT-ATTTATA
* * * * * * ** * * *
5740 GTTACCCATACCTTCAAAAGCCTTTTTGGTCACTTTAAATAG
129 G-CAACCATGCCTTCGAAAGCCGTATTACTCGCCTTAAATTG
********** *
5782 TTTTATAATCTCATAATTGATNNNNNNNNNNATTTTTTTATATTTTTTATTAAAACAAATTATAA
1 TTTTATAAT-TCATAATTGATTTTAAGTTAAATTTTTTTATATTTTTTATTAAAACAGATTATAA
* * * * * * *
5847 TTAAAT-TCTTATCTCAAGAAACATGAAGAAAATGATATCTATTGGCAAGAAAAGTCTATTTATA
65 TTGAATGTC-TACCTTAAGAAACATGAAGAAAAAGATATCCATTCGTAAGAAAAGTCTATTTATA
*** ** * *
5911 GTCTTTCATGCCTTCGAAAGCTTTATTACTCGCTTTAAATGG
129 G-CAACCATGCCTTCGAAAGCCGTATTACTCGCCTTAAATTG
* ********** * *
5953 ATTTATAATCTCATAATTGATTTTANNNNNNNNNNTTTTATATTTTATATTATAAA-ATATTATA
1 TTTTATAAT-TCATAATTGATTTTAAGTTAAATTTTTTTATATTTTTTATTA-AAACAGATTATA
* * * * *
6017 ATTGAATATCTACCTCAAGAAACATGAAGAAAAAAATATCCATTGGCT-AGAAAAGTCCATTTAT
64 ATTGAATGTCTACCTTAAGAAACATGAAGAAAAAGATATCCATTCG-TAAGAAAAGTCTATTTAT
* * * * *
6081 AGTCACCCATGTCTTCAAAAGCCTTATTAGTCGCCTTAAATAT-
128 AG-CAACCATGCCTTCGAAAGCCGTATTACTCGCCTTAAAT-TG
* * * * *
6124 TTTTCTAATGTCATAATTGATTTTAAGTTAAATTTTTTTACATTTTTTGTTGAAACAGATAATAA
1 TTTTATAAT-TCATAATTGATTTTAAGTTAAATTTTTTTATATTTTTTATTAAAACAGATTATAA
* * * * * *
6189 TTGAATGTCTGCCTTAGGATATATGAAGAAAAAGATATCCATTGGTAAAAAAAGTCTATTTATAA
65 TTGAATGTCTACCTTAAGAAACATGAAGAAAAAGATATCCATTCGTAAGAAAAGTCTATTTAT-A
* * * *
6254 TCAACCATGCCTTCGAAAGCCGTATTACTTGCCTTGAATAG
129 GCAACCATGCCTTCGAAAGCCGTATTACTCGCCTTAAATTG
* * * * *
6295 TTTTACAATTACATAATTGATTTTAAGTTAACTTTTTTTATATTTTTTATTAAAACAAACTGTAA
1 TTTTATAATT-CATAATTGATTTTAAGTTAAATTTTTTTATATTTTTTATTAAAACAGATTATAA
* * * ** * **
6360 TTGAATGTCTTCCTTGAGAAACATGAAAAAAAAGCCATTCATTCACAAGAAAAGTCTATTTATAG
65 TTGAATGTCTACCTTAAGAAACATGAAGAAAAAGATATCCATTCGTAAGAAAAGTCTATTTATAG
* ********* *
6425 CCACTCATGCCTTC-AAANNNNNNNNNNCTCGCTTTAAATTG
130 CAAC-CATGCCTTCGAAA-GCCGTATTACTCGCCTTAAATTG
* * *
6466 TTTTATAATCTCATAATT-AGTTTAAGTTAAATTTTTTTATATTTTTTATTCAAACAGATTTTAA
1 TTTTATAAT-TCATAATTGATTTTAAGTTAAATTTTTTTATATTTTTTATTAAAACAGATTATAA
* * * * *
6530 TTAAATGTGTACCTTAAGAAACATGAAGAAAAAGATATCCATTTGTAAGAAAAATCCATTTATAG
65 TTGAATGTCTACCTTAAGAAACATGAAGAAAAAGATATCCATTCGTAAGAAAAGTCTATTTATAG
* * * * * * *****
6595 TCATCAATGCCATCGAAAGCCTTATTACTTGCTTTANNNNN
130 -CAACCATGCCTTCGAAAGCCGTATTACTCGCCTTAAATTG
***** * *
6636 NNNNNTAATCTCATAATTGATTTTAAGTT-AATTTGTTTCTATATTTTTTATTAAAATAGATAAT
1 TTTTATAAT-TCATAATTGATTTTAAGTTAAATTT-TTT-TATATTTTTTATTAAAACAGATTAT
*
6700 AATTGAATATCTACCTT
63 AATTGAATGTCTACCTT
6717 GTGAANNNNN
Statistics
Matches: 851, Mismatches: 230, Indels: 47
0.75 0.20 0.04
Matches are distributed among these distances:
170 259 0.30
171 549 0.65
172 43 0.05
ACGTcount: A:0.36, C:0.12, G:0.10, T:0.39
Consensus pattern (169 bp):
TTTTATAATTCATAATTGATTTTAAGTTAAATTTTTTTATATTTTTTATTAAAACAGATTATAAT
TGAATGTCTACCTTAAGAAACATGAAGAAAAAGATATCCATTCGTAAGAAAAGTCTATTTATAGC
AACCATGCCTTCGAAAGCCGTATTACTCGCCTTAAATTG
Found at i:7307 original size:169 final size:160
Alignment explanation
Indices: 7126--7600 Score: 382
Period size: 172 Copynumber: 2.8 Consensus size: 160
7116 NAAAATCATT
* * *
7126 TAAAGGGAGTAATAAGACTTTCGAAGGCATAGGTG-ATAAATGGACTTTTTCTTACCAATGGATC
1 TAAAGCGAGTAATAAGACTTTCGAAGGCATAGGTGAATAAATGGAC-TTTTCTTACCAATAGATA
*
7190 CCTTTTCCTTCACGTTTCT-AGTGGTAGACATTCAATTATAATCTATGTTAATAAAAAATATA-A
65 CCTTTTCCTTCACGTTTCTCA-AGGTAGACATTCAATTATAATCTATGTTAATAAAAAATATAGA
*
7253 AAAAACTCAACCTAAAATCAATTATGAGATTA
129 AAAAAATCAACCTAAAATCAATTATGAGATTA
* * * *
7285 TAAANNNNNNNNNNGCGAGTAATAAGTCTTTTGAAGGCATGGGTGACTATAAATTGACTTTTCTT
1 TAAA----------GCGAGTAATAAGACTTTCGAAGGCATAGGTGA--ATAAATGGACTTTTCTT
** * * * * * *
7350 GTCAATAGATATCTTTTTCTTCACGTTTCTCAAGGTAGATATTCAATTATTATCTATTTTCATAA
54 ACCAATAGATACCTTTTCCTTCACGTTTCTCAAGGTAGACATTCAATTATAATCTATGTTAATAA
* *
7415 AAAATATAGAAAAAAATTAACTTAAAATCAATTATGAGATTA
119 AAAATATAGAAAAAAATCAACCTAAAATCAATTATGAGATTA
* * ** * *
7457 TAAAACCATTTATAGCAAATAATAAGGTTTTCGATGGCATTGGTGACTATAAATGGACTTTTCTT
1 T------A---A-AGCGAGTAATAAGACTTTCGAAGGCATAGGTGA--ATAAATGGACTTTTCTT
* * * * * * * * *
7522 GCGAATGGATATCTTTTTCTTCACATTTCTCAAGGTACACAATCAATTATAATCTATTTTAATAA
54 ACCAATAGATACCTTTTCCTTCACGTTTCTCAAGGTAGACATTCAATTATAATCTATGTTAATAA
7587 AAAATATA-AAAAAA
119 AAAATATAGAAAAAA
7601 TTTAACTTAA
Statistics
Matches: 255, Mismatches: 36, Indels: 38
0.78 0.11 0.12
Matches are distributed among these distances:
159 4 0.02
169 27 0.11
171 73 0.29
172 148 0.58
178 1 0.00
181 1 0.00
182 1 0.00
ACGTcount: A:0.37, C:0.13, G:0.13, T:0.35
Consensus pattern (160 bp):
TAAAGCGAGTAATAAGACTTTCGAAGGCATAGGTGAATAAATGGACTTTTCTTACCAATAGATAC
CTTTTCCTTCACGTTTCTCAAGGTAGACATTCAATTATAATCTATGTTAATAAAAAATATAGAAA
AAAATCAACCTAAAATCAATTATGAGATTA
Found at i:7504 original size:172 final size:171
Alignment explanation
Indices: 6823--7924 Score: 736
Period size: 171 Copynumber: 6.5 Consensus size: 171
6813 NNNNNNNNNG
* * * * ** * * *
6823 TAAATGGACTTTTCTTGCCAATGTATATCCTTTTCTTCATGTTTCTTGAGGTAAACATTCAGTTC
1 TAAATGGACTTTTCTTGTCAATGGATATCTTTTTCTTCACGTTTCTCAAGGTAGACATTCAATTA
* * ** * *
6888 TTATCTGTTTTAACCAAAAATGT-AAAAAAATAAAACTTAAAATCAATTATGAGATTATAAAAAC
66 TAATCTATTTTAATAAAAAATATAAAAAAAAT-TAACTTAAAATCAATTATGAGATTAT-AAAAC
********* * *
6952 -ATTTAAAGCGANNNNNNNNNNTTTT-GAAGGTA-TGTGTAACTA
129 TATTTAAAGCGA-GTAATAAGGTTTTCGAAGGCATTG-GTGACTA
** **
6994 TAAATGGACTTTTCTTG-CTAATGGATATCTTTTTCTTCATATTTC-CTAAGACAGACATTCAAT
1 TAAATGGACTTTTCTTGTC-AATGGATATCTTTTTCTTCACGTTTCTC-AAGGTAGACATTCAAT
* * ** **********
7057 TATTATCT-GTTTAA-AACAACAAT-GCAAAAAAATTCAACTTAAAATCAATTNNNNNNNNNNAA
64 TATAATCTATTTTAATAA-AA-AATATAAAAAAAATT-AACTTAAAATCAATTATGAGATTATAA
* ** *
7119 AA-TCATTTAAAGGGAGTAATAAGACTTTCGAAGGCATAGGTG---A
126 AACT-ATTTAAAGCGAGTAATAAGGTTTTCGAAGGCATTGGTGACTA
** ** * *
7162 TAAATGGACTTTTTCTTACCAATGGATCCCTTTTCCTTCACGTTTCT-AGTGGTAGACATTCAAT
1 TAAATGGAC-TTTTCTTGTCAATGGATATCTTTTTCTTCACGTTTCTCA-AGGTAGACATTCAAT
* * * * **
7226 TATAATCTATGTTAATAAAAAATATAAAAAAACTCAACCTAAAATCAATTATGAGATTATAAANN
64 TATAATCTATTTTAATAAAAAATATAAAAAAAATTAACTTAAAATCAATTATGAGATTATAAAAC
******** * *
7291 NNNNNNNNGCGAGTAATAA-GTCTTTTGAAGGCATGGGTGACTA
129 TATTTAAAGCGAGTAATAAGGT-TTTCGAAGGCATTGGTGACTA
* * *
7334 TAAATTGACTTTTCTTGTCAATAGATATCTTTTTCTTCACGTTTCTCAAGGTAGATATTCAATTA
1 TAAATGGACTTTTCTTGTCAATGGATATCTTTTTCTTCACGTTTCTCAAGGTAGACATTCAATTA
* * *
7399 TTATCTATTTTCATAAAAAATATAGAAAAAAATTAACTTAAAATCAATTATGAGATTATAAAACC
66 TAATCTATTTTAATAAAAAATATA-AAAAAAATTAACTTAAAATCAATTATGAGATTATAAAACT
* * * *
7464 ATTTATAGCAAATAATAAGGTTTTCGATGGCATTGGTGACTA
130 ATTTAAAGCGAGTAATAAGGTTTTCGAAGGCATTGGTGACTA
* * *
7506 TAAATGGACTTTTCTTG-CGAATGGATATCTTTTTCTTCACATTTCTCAAGGTACACAATCAATT
1 TAAATGGACTTTTCTTGTC-AATGGATATCTTTTTCTTCACGTTTCTCAAGGTAGACATTCAATT
* ********** *
7570 ATAATCTATTTTAATAAAAAATATAAAAAAATTTAACTTAAANNNNNNNNNNAGATTATAAAATT
65 ATAATCTATTTTAATAAAAAATATAAAAAAAATTAACTTAAAATCAATTATGAGATTATAAAACT
* *
7635 ATTTAAAGCGAGTAATAAGGCTTTT-GAAGGCA-TGAGTGGCAA
130 ATTTAAAGCGAGTAATAAGG-TTTTCGAAGGCATTG-GTGACTA
* * * * *
7677 TAAATAGACTTTTCTTGTGAA-GGA-ATGGCTTCTTT-TTCATGTTTCTCAAAGAAGACATTCAA
1 TAAATGGACTTTTCTTGTCAATGGATAT--CTT-TTTCTTCACGTTTCTCAAGGTAGACATTCAA
* * * * * * *
7739 TTACAGTTTGTTTTAATAAAAAATAT-AAAAAAATTCAACTTAAAATTAATTATGTGATTGTAAA
63 TTATAATCTATTTTAATAAAAAATATAAAAAAAATT-AACTTAAAATCAATTATGAGATTATAAA
* * * * *
7803 ACTATTTAAAGTGAGTAATAAGGCTTTCAAAGACAATGGTGACTA
127 ACTATTTAAAGCGAGTAATAAGGTTTTCGAAGGCATTGGTGACTA
* ** * * * * * * *
7848 TAAATGGACTTTTTTTACCAATGGATATCATTTTCTTTATGTTTCCCAAAGTAGATATTAAATTA
1 TAAATGGACTTTTCTTGTCAATGGATATCTTTTTCTTCACGTTTCTCAAGGTAGACATTCAATTA
*
7913 TAATCTGTTTTA
66 TAATCTATTTTA
7925 NNNNNNNNNN
Statistics
Matches: 711, Mismatches: 182, Indels: 76
0.73 0.19 0.08
Matches are distributed among these distances:
168 11 0.02
169 95 0.13
170 48 0.07
171 390 0.55
172 163 0.23
173 4 0.01
ACGTcount: A:0.37, C:0.12, G:0.12, T:0.36
Consensus pattern (171 bp):
TAAATGGACTTTTCTTGTCAATGGATATCTTTTTCTTCACGTTTCTCAAGGTAGACATTCAATTA
TAATCTATTTTAATAAAAAATATAAAAAAAATTAACTTAAAATCAATTATGAGATTATAAAACTA
TTTAAAGCGAGTAATAAGGTTTTCGAAGGCATTGGTGACTA
Found at i:8661 original size:170 final size:170
Alignment explanation
Indices: 8379--8758 Score: 444
Period size: 170 Copynumber: 2.2 Consensus size: 170
8369 NNNNNTATAT
* * * * **
8379 GTGACTATAAGTGGATTTTTCTTACCAATGGAGATCTTTTTCTTCATGTTTCAAGAGGTAGACAT
1 GTGACTATAAATGGACTTTTCTTACCAATGGATATC-TTTTCTTCATGTATCAAGAGAAAGACAT
*** * * * *
8444 TAAATTATAATTTGTTTGAGTAAGAAATATAAAAAAATCAGCTTAAAATCT-ATTATGAGATTTT
65 TAAATTATAATCCATTTGAATAAAAAATATAAAAAAATCAACTTAAAAT-TAATTATGAGATTGT
* * * * *
8508 AAAAAC-ATTCGAAGCGAGTAATAAGGTTTTCGAAGGAATG-G
129 -AAAACTATTCAAAGCGAGTAATAAAGCTTTCAAAGGAATGAC
* **
8549 GTGACTATAAATGGACTTTTCTTACAAATGGATATCTTTTCTTCATGTATCTTGAGAAAGACATT
1 GTGACTATAAATGGACTTTTCTTACCAATGGATATCTTTTCTTCATGTATCAAGAGAAAGACATT
* * *
8614 CAATTATAATCCATTTTAATAAAAAATATTAAAAAATTCAACTTAAAATTAATTATGAGATTGTA
66 AAATTATAATCCATTTGAATAAAAAATA-TAAAAAAATCAACTTAAAATTAATTATGAGATTGTA
* *
8679 AAACTATTCAAAGCGGGTAATAAAGCTTTCAAAGGTATGAC
130 AAACTATTCAAAGCGAGTAATAAAGCTTTCAAAGGAATGAC
* *
8720 G-GATTATAAATGGACTTTTCTTACCAATGGATATATTTT
1 GTGACTATAAATGGACTTTTCTTACCAATGGATATCTTTT
8759 TTTTTACGTT
Statistics
Matches: 177, Mismatches: 29, Indels: 8
0.83 0.14 0.04
Matches are distributed among these distances:
169 51 0.29
170 125 0.71
171 1 0.01
ACGTcount: A:0.38, C:0.11, G:0.15, T:0.36
Consensus pattern (170 bp):
GTGACTATAAATGGACTTTTCTTACCAATGGATATCTTTTCTTCATGTATCAAGAGAAAGACATT
AAATTATAATCCATTTGAATAAAAAATATAAAAAAATCAACTTAAAATTAATTATGAGATTGTAA
AACTATTCAAAGCGAGTAATAAAGCTTTCAAAGGAATGAC
Found at i:12120 original size:171 final size:170
Alignment explanation
Indices: 11629--12399 Score: 727
Period size: 171 Copynumber: 4.5 Consensus size: 170
11619 NNNNNNNNNN
* * *
11629 TTAAATGGTTTTATAATCTCATAATTGATTTTAAGTTGATTTTTTT-TATTTTTTACTAAAACAA
1 TTAAATGGTTTTATAATCTCATAATTGATTTTAAGTTAATTTTTTTATA-TTTTTATTAAAACAG
* * * * * *
11693 ATTATAATTGAATGTTTTCCTCAGGAAACATAAAG-AAAAGATATCCATTGGAAAAAAATAGTCT
65 ATTATAATTGAATGTCTACCTCAAGAAACATAAAGAAAAAGATATCCATTGGTAAGAAATAGTCC
* *
11757 ATTTATAGTCACCCATGCCTTCGAAAG-CTCTATTACTCTCT
130 ATTTATAGTCACCCATACCTTCGAAAGTCT-TATTACTCGCT
***********
11798 TTAAAT-GTGTTTATAATCTCATAATTGATTTTAAGTTGANNNNNNNNNNCTTTTTATTAAAACA
1 TTAAATGGT-TTTATAATCTCATAATTGATTTTAAGTT-AATTTTTTTATATTTTTATTAAAACA
* ** ** *
11862 GATTATAATTAAATGTCTACCTTGAGAAATGTTAA-AAAAA-A-ATCCATTGGTAAGAAA-AGTC
64 GATTATAATTGAATGTCTACCTCAAGAAACATAAAGAAAAAGATATCCATTGGTAAGAAATAGTC
* * * *
11923 CATTTATAGTCACTCATGCCTTCGAAAGTCTTAATACTTGCT
129 CATTTATAGTCACCCATACCTTCGAAAGTCTTATTACTCGCT
* * * *
11965 TTAAATGGCTTTATAATCTCATAATTGATTTTAAGTATAATTTTTTCACATTTTTGGTTGAAAA-
1 TTAAATGGTTTTATAATCTCATAATTGATTTTAAGT-TAATTTTTTTATATTTTT-ATT-AAAAC
* * * * * *
12029 AGATAATAATTGAATGTCTGCCTCAAAAAACGTAAAGAAAAATATATCCATTGGCAAGAAA-AGT
63 AGATTATAATTGAATGTCTACCTCAAGAAACATAAAGAAAAAGATATCCATTGGTAAGAAATAGT
* * * *
12093 CCATTTATAATTAGCCATACCTTCGAAAGCCTTATTACTCGCT
128 CCATTTATAGTCACCCATACCTTCGAAAGTCTTATTACTCGCT
* * * * * * * *
12136 TTGAATAGTTTTACACTCTTATAATAGATTTTAAGCTAAATTTTTTTATATTTTTTATTCAAACA
1 TTAAATGGTTTTATAATCTCATAATTGATTTTAAG-TTAATTTTTTTATA-TTTTTATTAAAACA
* * * * ** * * *
12201 AATTATGATTTAATATCTACCTCTGGAAATATGAAGAAGAAGATATCCATTGGTAAGAAATA-TC
64 GATTATAATTGAATGTCTACCTCAAGAAACATAAAGAAAAAGATATCCATTGGTAAGAAATAGTC
* * * *
12265 CACTTATAGTCACCCATACCTTTGAAAATCTTATTACTCGTT
129 CATTTATAGTCACCCATACCTTCGAAAGTCTTATTACTCGCT
* * * *
12307 TTAAATGATTTTATAATCTCATAATTGACTTTAAGTTAGTTTTTTTTTATATTTTTATTAAAATA
1 TTAAATGGTTTTATAATCTCATAATTGATTTTAAGTTA--ATTTTTTTATATTTTTATTAAAACA
12372 GATTATAATTGAATGTCTACCTCAAGAA
64 GATTATAATTGAATGTCTACCTCAAGAA
12400 NNNNNNNNNN
Statistics
Matches: 472, Mismatches: 112, Indels: 34
0.76 0.18 0.06
Matches are distributed among these distances:
167 77 0.16
168 50 0.11
169 44 0.09
170 48 0.10
171 236 0.50
172 17 0.04
ACGTcount: A:0.36, C:0.13, G:0.11, T:0.39
Consensus pattern (170 bp):
TTAAATGGTTTTATAATCTCATAATTGATTTTAAGTTAATTTTTTTATATTTTTATTAAAACAGA
TTATAATTGAATGTCTACCTCAAGAAACATAAAGAAAAAGATATCCATTGGTAAGAAATAGTCCA
TTTATAGTCACCCATACCTTCGAAAGTCTTATTACTCGCT
Found at i:12731 original size:58 final size:58
Alignment explanation
Indices: 12641--12757 Score: 225
Period size: 58 Copynumber: 2.0 Consensus size: 58
12631 GCCTTATTAC
12641 TCGGTTTTAATGTTTTTATAATTGAATAATAGATTTTAAGTTGAATTTTTTTATATTT
1 TCGGTTTTAATGTTTTTATAATTGAATAATAGATTTTAAGTTGAATTTTTTTATATTT
*
12699 TCGGTTTTAATGTTTTTATAATTTAATAATAGATTTTAAGTTGAATTTTTTTATATTT
1 TCGGTTTTAATGTTTTTATAATTGAATAATAGATTTTAAGTTGAATTTTTTTATATTT
12757 T
1 T
12758 TAATTAAAAT
Statistics
Matches: 58, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
58 58 1.00
ACGTcount: A:0.29, C:0.02, G:0.11, T:0.58
Consensus pattern (58 bp):
TCGGTTTTAATGTTTTTATAATTGAATAATAGATTTTAAGTTGAATTTTTTTATATTT
Found at i:12735 original size:29 final size:29
Alignment explanation
Indices: 12645--12737 Score: 77
Period size: 29 Copynumber: 3.2 Consensus size: 29
12635 TATTACTCGG
*
12645 TTTTAATGTTTTTATAATTGAATAATAGA
1 TTTTAATGTTTTTATAATTTAATAATAGA
** * *
12674 TTTTAA-GTTGAATTT-T--TTTATATTTTCGG
1 TTTTAATGTT---TTTATAATTTA-ATAATAGA
12703 TTTTAATGTTTTTATAATTTAATAATAGA
1 TTTTAATGTTTTTATAATTTAATAATAGA
12732 TTTTAA
1 TTTTAA
12738 GTTGAATTTT
Statistics
Matches: 47, Mismatches: 9, Indels: 16
0.65 0.12 0.22
Matches are distributed among these distances:
27 3 0.06
28 7 0.15
29 26 0.55
30 8 0.17
31 3 0.06
ACGTcount: A:0.32, C:0.01, G:0.10, T:0.57
Consensus pattern (29 bp):
TTTTAATGTTTTTATAATTTAATAATAGA
Found at i:12888 original size:228 final size:226
Alignment explanation
Indices: 12473--12889 Score: 609
Period size: 228 Copynumber: 1.8 Consensus size: 226
12463 GCTTTATTAC
*
12473 TCGGTTTAAATGTTTTATAATTTAATAATAGATTTTAAGCTGAATTTTTTATATTTTTTATTAAA
1 TCGGTTTAAATGTTTTATAATTTAATAATAGATTTTAAGCTGAATTTTTTATATTTTTAATTAAA
*
12538 ATAAATTATAATTAAATGTCTACTACTAGAAACGTGAAAAAACGATATCCATTAGCAAGAAAAGT
66 ATAAATTATAATTAAATGTCTACTACGAGAAACGTGAAAAAACGATATCCATTAGCAAGAAAAGT
*********** * * ** * *
12603 CCATNNNNNNNNNNTCATGCCTTCGAAAGCCTTATTACTCGGTTTTAATGTTTTTATAATTGAAT
131 CCATTTATAGTCTCCCATACCTTCGAAAGCCTTATTACACACTTTAAATGGTTTTATAATTGAAT
12668 AATAGATTTTAAGTTGAATTTTTTTATATTT
196 AATAGATTTTAAGTTGAATTTTTTTATATTT
* *
12699 TCGGTTTTAATGTTTTTATAATTTAATAATAGATTTTAAGTTGAATTTTTTTATATTTTTAATTA
1 TCGGTTTAAATG-TTTTATAATTTAATAATAGATTTTAAGCTGAA-TTTTTTATATTTTTAATTA
* *
12764 AAATAAATTATAATTAAATGTCTACTACGAGAAACGTGAAAAAATGATATCCATTGGCAAGAAAA
64 AAATAAATTATAATTAAATGTCTACTACGAGAAACGTGAAAAAACGATATCCATTAGCAAGAAAA
12829 GTCCATTTATAGTCTCCCATACCTTCGAAAGCCTTATTACACACTTTAAATGGTTTTATAA
129 GTCCATTTATAGTCTCCCATACCTTCGAAAGCCTTATTACACACTTTAAATGGTTTTATAA
12890 ACTCATAATT
Statistics
Matches: 166, Mismatches: 23, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
226 11 0.07
227 31 0.19
228 124 0.75
ACGTcount: A:0.36, C:0.10, G:0.11, T:0.41
Consensus pattern (226 bp):
TCGGTTTAAATGTTTTATAATTTAATAATAGATTTTAAGCTGAATTTTTTATATTTTTAATTAAA
ATAAATTATAATTAAATGTCTACTACGAGAAACGTGAAAAAACGATATCCATTAGCAAGAAAAGT
CCATTTATAGTCTCCCATACCTTCGAAAGCCTTATTACACACTTTAAATGGTTTTATAATTGAAT
AATAGATTTTAAGTTGAATTTTTTTATATTT
Found at i:13607 original size:339 final size:332
Alignment explanation
Indices: 13175--13828 Score: 689
Period size: 339 Copynumber: 1.9 Consensus size: 332
13165 CTTTAAAACC
* * * *
13175 CTTATTAGTCGCTTTAAATGTTTTTATACTCTCAAAACTAATTTTAAGTTGAATTTTTTTATATT
1 CTTATTACTCGCTTTAAATGGTTTTATAATCTCAAAACTAATTTTAAGTTGAATTTTTTTACATT
*
13240 TTTTATTAAAACAGATAATAATTAAATGTCTGCATCAAGAAACGTAAAGAGAAAGATATCCATTG
66 TTTTATTAAAACAGATAATAATTAAATGTCTGCATCAAGAAACGTAAAGAAAAAGATATCCATTG
* * * * *
13305 GCAAGAAAAGTGC-ATTTATAATCAGCT-ATGCCTTCGAAAGCCTTATTACTCGCTTTGAATAG-
131 GCAAGAAAAG-ACTATTTAT-ATCAACTCATGCCTTCAAAAGCCTTATTACACGCTTTAAAT-GT
* * * * *
13367 TTTTACAA-CGTCATAATTGATTTTAAGTTGAATTTTTTTAGATTTTTTA-TTAAAACACATTAT
193 TTTTACAATC-TCATAATTAATTTTAAGTTAAATTTTTTTACA-TTTTTAGTCAAAACACATAAT
* * * *
13430 AATTGAATG-CTTTCCTCAGGAAACATGAAG-AAAAGATATCCATTGGTAAGAAAAATCNNNNNN
256 AATTGAATGTC-TGCCTCAGAAAACATAAAGAAAAAGATATCCATTGGCAAGAAAAATC------
13493 NNNNCACACATACCTTCGAAAGT
314 ----CACACATACCTTCGAAAGT
* * *
13516 CTTATTACTCGCTTTAAATGGTTTTATGAAT-TCATAATTGATTTTAAGTT-AATTTTTTTACA-
1 CTTATTACTCGCTTTAAATGGTTTTAT-AATCTCAAAACTAATTTTAAGTTGAATTTTTTTACAT
* ********** * *
13578 TTTTTATTAAAACAGATTATAATTAAATGTNNNNNNNNNNAAACGTGAAGAAAAAGATATTCATT
65 TTTTTATTAAAACAGATAATAATTAAATGTCTGCATCAAGAAACGTAAAGAAAAAGATATCCATT
* *
13643 GGCAAGAAAAGACTATTTATATTAACTCATGCCTTCAAAAGCCTTATTAGACGCTTTAAATGTTT
130 GGCAAGAAAAGACTATTTATATCAACTCATGCCTTCAAAAGCCTTATTACACGCTTTAAATGTTT
* * * *
13708 TTATAATCTTATAATTAATTTTAAGTTAAATTTTTTTACATTTTTAGTCGAAACAGATAATAATT
195 TTACAATCTCATAATTAATTTTAAGTTAAATTTTTTTACATTTTTAGTCAAAACACATAATAATT
* * *
13773 GAATGTCTGCCTTAGAAAACGTAAAGAAAAAGATATCCATTGGCAAGAAAAGTCCA
260 GAATGTCTGCCTCAGAAAACATAAAGAAAAAGATATCCATTGGCAAGAAAAATCCA
13829 TTTATAATCC
Statistics
Matches: 261, Mismatches: 44, Indels: 27
0.79 0.13 0.08
Matches are distributed among these distances:
330 2 0.01
338 13 0.05
339 165 0.63
340 38 0.15
341 41 0.16
342 2 0.01
ACGTcount: A:0.37, C:0.12, G:0.12, T:0.37
Consensus pattern (332 bp):
CTTATTACTCGCTTTAAATGGTTTTATAATCTCAAAACTAATTTTAAGTTGAATTTTTTTACATT
TTTTATTAAAACAGATAATAATTAAATGTCTGCATCAAGAAACGTAAAGAAAAAGATATCCATTG
GCAAGAAAAGACTATTTATATCAACTCATGCCTTCAAAAGCCTTATTACACGCTTTAAATGTTTT
TACAATCTCATAATTAATTTTAAGTTAAATTTTTTTACATTTTTAGTCAAAACACATAATAATTG
AATGTCTGCCTCAGAAAACATAAAGAAAAAGATATCCATTGGCAAGAAAAATCCACACATACCTT
CGAAAGT
Found at i:13821 original size:171 final size:170
Alignment explanation
Indices: 13100--13898 Score: 672
Period size: 171 Copynumber: 4.7 Consensus size: 170
13090 TGAATATCTA
* * * * * * *
13100 CCTCAGGAAATGTGAAGAAAAATATATTCATTGGCAAAAAAAAGTCCATTTATATTAAGC-CATG
1 CCTCAGAAAACGTAAAGAAAAAGATATCCATTGGC-AAGAAAAGACCATTTATATTAA-CTCATG
** * * * * *
13164 CCTTTAAAACCCTTATTAGTCGCTTTAAATGTTTTTATACTCTCAAAACTAATTTTAAGTTGAAT
64 CCTTCGAAAGCCTTATTACTCGCTTTAAATG-TTTTATAATCTCATAATTAATTTTAAGTTGAAT
*
13229 TTTTTTATATTTTTTATTAAAACAGATAATAATTAAATGTCTG
128 TTTTTTACATTTTTTATTAAAACAGATAATAATTAAATGTCTG
* * ** * *
13272 CATCA-AGAAACGTAAAGAGAAAGATATCCATTGGCAAGAAAAGTGCATTTATAATCAGCT-ATG
1 CCTCAGA-AAACGTAAAGAAAAAGATATCCATTGGCAAGAAAAGACCATTTAT-ATTAACTCATG
* * *
13335 CCTTCGAAAGCCTTATTACTCGCTTTGAATAGTTTTACAA-CGTCATAATTGATTTTAAGTTGAA
64 CCTTCGAAAGCCTTATTACTCGCTTTAAAT-GTTTTATAATC-TCATAATTAATTTTAAGTTGAA
* * * * *
13399 TTTTTTTAGATTTTTTATTAAAACACATTATAATTGAATG-CTTT
127 TTTTTTTACATTTTTTATTAAAACAGATAATAATTAAATGTC-TG
* * * * *********** * *
13443 CCTCAGGAAACATGAAG-AAAAGATATCCATTGGTAAGAAAA-ATCNNNNNNNNNNCACACATAC
1 CCTCAGAAAACGTAAAGAAAAAGATATCCATTGGCAAGAAAAGA-CCATTTATATTAACTCATGC
* *
13506 CTTCGAAAGTCTTATTACTCGCTTTAAATGGTTTTATGAAT-TCATAATTGATTTTAAGTT-AAT
65 CTTCGAAAGCCTTATTACTCGCTTTAAAT-GTTTTAT-AATCTCATAATTAATTTTAAGTTGAAT
* ***
13569 TTTTTTACA-TTTTTATTAAAACAGATTATAATTAAATGTNNN
128 TTTTTTACATTTTTTATTAAAACAGATAATAATTAAATGTCTG
******* * * *
13611 NNNNNNNAAACGTGAAGAAAAAGATATTCATTGGCAAGAAAAGACTATTTATATTAACTCATGCC
1 CCTCAGAAAACGTAAAGAAAAAGATATCCATTGGCAAGAAAAGACCATTTATATTAACTCATGCC
* ** * *
13676 TTCAAAAGCCTTATTAGACGCTTTAAATGTTTTTATAATCTTATAATTAATTTTAAGTTAAATTT
66 TTCGAAAGCCTTATTACTCGCTTTAAATG-TTTTATAATCTCATAATTAATTTTAAGTTGAATTT
** *
13741 TTTTACA-TTTTTAGTCGAAACAGATAATAATTGAATGTCTG
130 TTTTACATTTTTTA-TTAAAACAGATAATAATTAAATGTCTG
* * * *
13782 CCTTAGAAAACGTAAAGAAAAAGATATCCATTGGCAAGAAAAGTCCATTTATAAT-CCGTCATGC
1 CCTCAGAAAACGTAAAGAAAAAGATATCCATTGGCAAGAAAAGACCATTTATATTAAC-TCATGC
* *
13846 CTTCGAAAGCCTTATTAC-CTGCTTTAAATAGTTTTACAAT-TTATAATTAATTT
65 CTTCGAAAGCCTTATTACTC-GCTTTAAAT-GTTTTATAATCTCATAATTAATTT
13899 AANNNNNNNN
Statistics
Matches: 496, Mismatches: 110, Indels: 44
0.76 0.17 0.07
Matches are distributed among these distances:
168 40 0.08
169 89 0.18
170 113 0.23
171 222 0.45
172 32 0.06
ACGTcount: A:0.37, C:0.13, G:0.12, T:0.36
Consensus pattern (170 bp):
CCTCAGAAAACGTAAAGAAAAAGATATCCATTGGCAAGAAAAGACCATTTATATTAACTCATGCC
TTCGAAAGCCTTATTACTCGCTTTAAATGTTTTATAATCTCATAATTAATTTTAAGTTGAATTTT
TTTACATTTTTTATTAAAACAGATAATAATTAAATGTCTG
Found at i:14451 original size:168 final size:166
Alignment explanation
Indices: 14147--14788 Score: 525
Period size: 169 Copynumber: 3.8 Consensus size: 166
14137 NNNNNNNCAA
* * * ** * *
14147 ATTATAATTTAATGTTTACCTCT-AGAAACATGAAGAAAAAGATATCCATTGGTAAGAAAAATCT
1 ATTATAATTGAATGTCTACCT-TGAG-AACAT-AAAAAAAAGATATCCATTGACAAGAAAAGTCC
* * * * *
14211 ACTTATAGTCACACATACCTTTGAAAGCCTTATTACTCGCTTTAAATAGTTTTATAATTTCATAA
63 ATTTATAGTCACCCATGCCTTCGAAAGCCTTATTACTCGCTTTAAATAGTTTTATAATCTCATAA
*
14276 CTGATTTTAAGTTCATTTTTTCACATTTTTATTAAAACAG
128 TTGATTTTAAGTTCATTTTTT-ACATTTTTATTAAAACAG
* * * *
14316 ATTATAAGTGAATGTCTACCTTGAGTAATATAAAAAATAAGATATCCATTCACAAAAAAAGTCCA
1 ATTATAATTGAATGTCTACCTTGAG-AACATAAAAAA-AAGATATCCATTGACAAGAAAAGTCCA
* * * *
14381 TTTATAGTC-CCCATGCCTTCGACAGCCTTATTACTCTCTTTAAATGGTTTTACAATCTCATAAT
64 TTTATAGTCACCCATGCCTTCGAAAGCCTTATTACTCGCTTTAAATAGTTTTATAATCTCATAAT
********
14445 TGATTTTNNNNNNNNNNTTTTTACATTTTTATTAAAACAG
129 TGATTTT--AAGTTCATTTTTTACATTTTTATTAAAACAG
* * ** * * * * * *
14485 ATTATAATTGAATGTTTACCTCGAGAGGAGTGAAGAAAAGATATCCGTTGGCAAGAAATGTTCAT
1 ATTATAATTGAATGTCTACCTTGAGAACA-TAAAAAAAAGATATCCATTGACAAGAAAAGTCCAT
* * * * *
14550 TTATAGTCACCCATGCCTTCAAAAGCCTTATTACTCGATTTAAAGATTTTTATAATCCCATAATT
65 TTATAGTCACCCATGCCTTCGAAAGCCTTATTACTCGCTTTAAATAGTTTTATAATCTCATAATT
* ******** * *
14615 AATTTNNNNNNNNNNTTTTTTATATTTTTTATTAAAACAT
130 GATTT--TAAGTTCATTTTTTACA-TTTTTATTAAAACAG
* * ** * * * *
14655 ATTATAATTTAATATCTATTTTAAAAAACATAAAGAAAATGATATCCATTGATAAGAAAAGTCCA
1 ATTATAATTGAATGTCTACCTT-GAGAACATAAA-AAAAAGATATCCATTGACAAGAAAAGTCCA
* * **
14720 TTTATAGTTA-CCATTGCCTTTGAAAGCCTTATTACTCATTTTAAATAGTTTTATAATCTCATAA
64 TTTATAGTCACCCA-TGCCTTCGAAAGCCTTATTACTCGCTTTAAATAGTTTTATAATCTCATAA
14784 TTGAT
128 TTGAT
14789 NNNNNNNNNN
Statistics
Matches: 377, Mismatches: 84, Indels: 22
0.78 0.17 0.05
Matches are distributed among these distances:
168 91 0.24
169 163 0.43
170 41 0.11
171 82 0.22
ACGTcount: A:0.36, C:0.14, G:0.10, T:0.38
Consensus pattern (166 bp):
ATTATAATTGAATGTCTACCTTGAGAACATAAAAAAAAGATATCCATTGACAAGAAAAGTCCATT
TATAGTCACCCATGCCTTCGAAAGCCTTATTACTCGCTTTAAATAGTTTTATAATCTCATAATTG
ATTTTAAGTTCATTTTTTACATTTTTATTAAAACAG
Found at i:15240 original size:170 final size:171
Alignment explanation
Indices: 15009--15391 Score: 398
Period size: 170 Copynumber: 2.2 Consensus size: 171
14999 NNNNNNNNNN
* * * *
15009 AAAAATTCAGCTTAAAATCTATTATAAGATTTTAAAAACATTCAAAGCGAGTAAGAAGGCTTTCG
1 AAAAATTCAACTTAAAACCAATTATAAGATTGTAAAAACATTCAAAGCGAGTAAGAAGGCTTTCG
* *
15074 AAAGCATTTG-TGACTATAAATAG-ATTTTTCTTACCAATGGATATCTTT-TCTTCATGTTTCCC
66 AAAGCA-TGGCTGACTATAAAT-GCACTTTTCTTACCAATGGATATCTTTCTCTTCATGTTTCCC
* * * * *
15136 GAGAAA-AGTATTCAATTATAATGTGTTTTAATAAAAAATCTAA
129 GAGAAAGA-CATTCAATTATAATCTGTTTCAACAAAAAATATAA
* * * * *
15179 AAAAATTCAACTTAAAACCAATTATGAGGTTGT-AAAACTTTTCAAAGCGAGTAATAAGGCTTTT
1 AAAAATTCAACTTAAAACCAATTATAAGATTGTAAAAAC-ATTCAAAGCGAGTAAGAAGGCTTTC
* * * * * **
15243 GAAGGCATGGCTGATTATAAATGCACTTTTCTTGCCAATTGATATCTTTCTCTTTATGTTTCTTG
65 GAAAGCATGGCTGACTATAAATGCACTTTTCTTACCAATGGATATCTTTCTCTTCATGTTTCCCG
** * * *
15308 AGGCAGACATTCAATTATTATCTGTTTCAACCAAAAATATAG
130 AGAAAGACATTCAATTATAATCTGTTTCAACAAAAAATATAA
** * * *
15350 AAAAATTCAACTTAAAATTAGTTATGAGATTATAAAAACATT
1 AAAAATTCAACTTAAAACCAATTATAAGATTGTAAAAACATT
15392 TANNNNNNNN
Statistics
Matches: 173, Mismatches: 34, Indels: 11
0.79 0.16 0.05
Matches are distributed among these distances:
169 8 0.05
170 87 0.50
171 72 0.42
172 6 0.03
ACGTcount: A:0.38, C:0.13, G:0.13, T:0.36
Consensus pattern (171 bp):
AAAAATTCAACTTAAAACCAATTATAAGATTGTAAAAACATTCAAAGCGAGTAAGAAGGCTTTCG
AAAGCATGGCTGACTATAAATGCACTTTTCTTACCAATGGATATCTTTCTCTTCATGTTTCCCGA
GAAAGACATTCAATTATAATCTGTTTCAACAAAAAATATAA
Found at i:17672 original size:170 final size:164
Alignment explanation
Indices: 17366--17728 Score: 433
Period size: 170 Copynumber: 2.2 Consensus size: 164
17356 NNNNNNNNNN
* * * * *
17366 CGCTTTAAATGGTTTTACAATCTCATAATTGATTTTAAGTTGAATAATTTTACATTTTTATTAAA
1 CGCTGTAAATAGTTTTATAATCTCATAATAGATTTTAAGTTAAATAATTTTACATTTTTATTAAA
* * * ** *
17431 ACAGATTATAAGTGAATGTTTACCTCGATAAAAGTGAAGATATCCATTGGTAAGAAAAGTCAATT
66 ACAGATTATAAGTGAATATCTACCTCGACAAAAGAAAAGATATCCATTAGTAAGAAAAGTCAATT
17496 TATAGTCACC-TATGCCTTCGAAAGCCTTATTACC
131 TATAGTCACCAT-TGCCTTCGAAAGCCTTATTACC
* * * * *
17530 CGGTGTAAATATTTTTATAATCTAATAATAGATTTTAAGTTAAAT-TTTTTATATTTTTTATTAA
1 CGCTGTAAATAGTTTTATAATCTCATAATAGATTTTAAGTTAAATAATTTTACA-TTTTTATTAA
* *
17594 AACAGATTATAATTTAATATCTACCTCAAGAAACATAAAGAAAAAGATATCCATTAGTAAGAAAA
65 AACAGATTATAAGTGAATATCTACCTC--G--ACA-AAAG-AAAAGATATCCATTAGTAAGAAAA
* * *
17659 GTCTATTTATAGTCATCATTGCCTTCGAAAGCCTTATTACT
124 GTCAATTTATAGTCACCATTGCCTTCGAAAGCCTTATTACC
* *
17700 CGCTTTAAATGGTTTTATAATCTCATAAT
1 CGCTGTAAATAGTTTTATAATCTCATAAT
17729 NNNNNNNNNN
Statistics
Matches: 165, Mismatches: 26, Indels: 10
0.82 0.13 0.05
Matches are distributed among these distances:
163 6 0.04
164 70 0.42
166 1 0.01
168 2 0.01
169 4 0.02
170 81 0.49
171 1 0.01
ACGTcount: A:0.37, C:0.13, G:0.11, T:0.39
Consensus pattern (164 bp):
CGCTGTAAATAGTTTTATAATCTCATAATAGATTTTAAGTTAAATAATTTTACATTTTTATTAAA
ACAGATTATAAGTGAATATCTACCTCGACAAAAGAAAAGATATCCATTAGTAAGAAAAGTCAATT
TATAGTCACCATTGCCTTCGAAAGCCTTATTACC
Found at i:18512 original size:170 final size:171
Alignment explanation
Indices: 17831--19016 Score: 625
Period size: 171 Copynumber: 7.0 Consensus size: 171
17821 NNNNNNNNTT
* * * * *** * *
17831 TAAAAAGTTCAGCTTAAAATCTATTATTAGATTTTTAAAACATTCAAAGCGAGTAATAAGGCTTT
1 TAAAAAATTCAACTTAAAATCAATTATGAGATTACAAAAACATTTAAAGCGAGTAAAAAGGCTTT
* * * * * * * *
17896 CGAAAGCATGTGTGACTATAAATGGACTTTTCTTG-CCAATGGATATCTTTCTCTTTACATTTCT
66 CGAAGGCATGGGTGACTATAAATGAACTTTTCTTGACGAATGAATATCTTTTTCTTCACGTTTCT
** * * * **
17960 TGAGGCAGACATTCAATTACT-ATCTGTTTCAACCAAAAATA
131 CAAAGTAGACATTCAATTA-TAATCTGTTTTAATAAAAAATA
* * * * * * * *
18001 TAAAAAAATTCAACTTCAAATTAGTTATGAGATTATAAAAATATTTAAAGCGACTAATAAGGGTT
1 T-AAAAAATTCAACTTAAAATCAATTATGAGATTACAAAAACATTTAAAGCGAGTAAAAAGGCTT
*********** * * * * * * * *
18066 TTNNNNNNNNNNGTTAATATAAATGGACTTTTTTTG-CCAATGAATATATTGTTCTTCACATTTC
65 TCGAAGGCATGGGTGACTATAAATGAACTTTTCTTGACGAATGAATATCTTTTTCTTCACGTTTC
* * * * *
18130 -CTGAGGTAGATATTCAATTATAATTTGTTTTAATAAAAAATG
130 TC-AAAGTAGACATTCAATTATAATCTGTTTTAATAAAAAATA
** * * * * *****
18172 TAAAAAAATTCAA-TCTAAAATTGATTATGAGATTATAAAACCATTTAAAGCGGGTAATANNNNN
1 T-AAAAAATTCAACT-TAAAATCAATTATGAGATTACAAAAACATTTAAAGCGAGTAAAAAGGCT
***** * * * * * * *
18236 NNNNNAGGTATGAGAGACTATAAAT-AGACTTTTCTTG-CTAGTGGATATCTTTTTCTTCACATT
64 TTCGAAGGCATGGGTGACTATAAATGA-ACTTTTCTTGACGAATGAATATCTTTTTCTTCACGTT
* * * * *
18299 TC-CTTAGGAAGACATTCAATTATTATCTGTTTTACCT-AAAAATA
128 TCTC-AAAGTAGACATTCAATTATAATCTGTTTTA-ATAAAAAATA
* * * *
18343 TAAAAACATTAAACTTAAAATCAATTATGAGTTTAAAAAAATATTTAAAGCGAGTAAAAAGGCTT
1 TAAAAA-ATTCAACTTAAAATCAATTATGAGATTACAAAAACATTTAAAGCGAGTAAAAAGGCTT
*
18408 TCGAAGGCATGGGTGACTATAAATGAAC-TTTCTTGAC-AATGAATATCTTTTTATTCACGTTTC
65 TCGAAGGCATGGGTGACTATAAATGAACTTTTCTTGACGAATGAATATCTTTTTCTTCACGTTTC
* * *
18471 TCAAAGTACATATTCAATTATAATCTATTTTAATAAAAAATA
130 TCAAAGTAGACATTCAATTATAATCTGTTTTAATAAAAAATA
* * * * *
18513 TAAAAAAATT-AACTTAAAATTAATTATGAGATTACATAACCGTTTAATGCGAGTAATAAA-GCT
1 T-AAAAAATTCAACTTAAAATCAATTATGAGATTACAAAAACATTTAAAGCGAGTAA-AAAGGCT
* * * * * **
18576 TTCGAAGGCAAT-GGTGGCTATAAATGGACTTTTCTT-ACTAATGGATATCTTTTTCTTTATATT
64 TTCGAAGGC-ATGGGTGACTATAAATGAACTTTTCTTGACGAATGAATATCTTTTTCTTCACGTT
* *** * * * * *******
18639 TCCCGCGGTAGATATTAAATTATAATTTGTCTTAATANNNNNNNN
128 TCTCAAAGTAGACATTCAATTATAATCTGTTTTAATA-AAAAATA
** * * * ** * * *
18684 NNAAAAATTCAGCTTAAAATCTATTAT-TGATTTTAAAAACATTTAAACCAAGTAATAAGGCTTT
1 TAAAAAATTCAACTTAAAATCAATTATGAGATTACAAAAACATTTAAAGCGAGTAAAAAGGCTTT
* * * * * * * *
18748 CGAAGGTATGGTTGATTATAAATGGACTTTTCTTG-CCAATGGATGTC-TTTTCTTCACTTTTCT
66 CGAAGGCATGGGTGACTATAAATGAACTTTTCTTGACGAATGAATATCTTTTTCTTCACGTTTCT
* * ****
18811 CGAAGTAAACATTCAATTATAATCTGTTTTAATAAAANNNN
131 CAAAGTAGACATTCAATTATAATCTGTTTTAATAAAAAATA
****** * * * * *
18852 NNNNNNATTCAACCTAAAATCAATTATGAGATTGCAAAACCATTTAAAGAGAGTAATAAGG-TAT
1 TAAAAAATTCAACTTAAAATCAATTATGAGATTACAAAAACATTTAAAGCGAGTAAAAAGGCT-T
* * * * * *
18916 CCGAAGGAATGGGCGACTATAAATAAACTTTTCTTG-CGAAT-AGAT-TTTTTTTTTTCACGTTT
65 TCGAAGGCATGGGTGACTATAAATGAACTTTTCTTGACGAATGA-ATATCTTTTTCTTCACGTTT
* *
18978 CTCAAGGTAGACATTCAATTATAATCTATTTTAATAAAA
129 CTCAAAGTAGACATTCAATTATAATCTGTTTTAATAAAA
19017 NNNNNNNNNN
Statistics
Matches: 780, Mismatches: 210, Indels: 53
0.75 0.20 0.05
Matches are distributed among these distances:
168 26 0.03
169 220 0.28
170 197 0.25
171 334 0.43
172 3 0.00
ACGTcount: A:0.37, C:0.12, G:0.12, T:0.36
Consensus pattern (171 bp):
TAAAAAATTCAACTTAAAATCAATTATGAGATTACAAAAACATTTAAAGCGAGTAAAAAGGCTTT
CGAAGGCATGGGTGACTATAAATGAACTTTTCTTGACGAATGAATATCTTTTTCTTCACGTTTCT
CAAAGTAGACATTCAATTATAATCTGTTTTAATAAAAAATA
Found at i:18585 original size:169 final size:171
Alignment explanation
Indices: 18251--19016 Score: 447
Period size: 169 Copynumber: 4.5 Consensus size: 171
18241 AGGTATGAGA
* * * * * *
18251 GACTATAAAT-AGACTTTTCTTGCTAGTGGATATCTTTTTCTTCACATTTCCTTAGGAAG-AC--
1 GACTATAAATGA-ACTTTTCTTACTAATGAATATCTTTTTATTCACGTTT-CTCA--AAGTACAT
* * * * *
18312 ATTCAATTATTATCTGTTTTACCTAAAAATATAAAAACATTAAACTTAAAATCAATTATGAGTTT
62 ATTCAATTATAATCTATTTTACATAAAAATATAAAAAAATTAAACTTAAAATCAATTATGAGATT
*
18377 AAAAAAATATTTAAAGCGAGTAAAAAGGCTTTCGAAGGC-ATGGGT
127 AAAAAAACATTTAAAGCGAGTAAAAAGGCTTTCGAAGGCAAT-GGT
18422 GACTATAAATGAAC-TTTCTTGAC-AATGAATATCTTTTTATTCACGTTTCTCAAAGTACATATT
1 GACTATAAATGAACTTTTCTT-ACTAATGAATATCTTTTTATTCACGTTTCTCAAAGTACATATT
* *
18485 CAATTATAATCTATTTTA-ATAAAAAATATAAAAAAATT-AACTTAAAATTAATTATGAGATTAC
65 CAATTATAATCTATTTTACAT-AAAAATATAAAAAAATTAAACTTAAAATCAATTATGAGATTAA
* * * *
18548 ATAACCGTTTAATGCGAGTAATAAA-GCTTTCGAAGGCAATGGT
129 AAAAACATTTAAAGCGAGTAA-AAAGGCTTTCGAAGGCAATGGT
* * * * * ** * *** * *
18591 GGCTATAAATGGACTTTTCTTACTAATGGATATCTTTTTCTTTATATTTCCCGCGGTAGATATTA
1 GACTATAAATGAACTTTTCTTACTAATGAATATCTTTTTATTCACGTTTCTCAAAGTACATATTC
* * * ********* * * * * **
18656 AATTATAATTTGTCTTA-ATANNNNNNNNNNAAAAATTCAGCTTAAAATCTATTAT-TGATTTTA
66 AATTATAATCTATTTTACATA-AAAATATAAAAAAATTAAACTTAAAATCAATTATGAGATTAAA
* * * *
18719 AAAACATTTAAACCAAGTAATAAGGCTTTCGAAGG-TATGGTT
130 AAAACATTTAAAGCGAGTAAAAAGGCTTTCGAAGGCAATGG-T
* * * * * * * * * * *
18761 GATTATAAATGGACTTTTCTTGCCAATGGATGTC-TTTTCTTCACTTTTCTCGAAGTAAACATTC
1 GACTATAAATGAACTTTTCTTACTAATGAATATCTTTTTATTCACGTTTCTCAAAGTACATATTC
* ********** * * **
18825 AATTATAATCTGTTTTA-ATAAAANNNNNNNNNNATTCAACCTAAAATCAATTATGAGATTGCAA
66 AATTATAATCTATTTTACATAAAAATATAAAAAAATTAAACTTAAAATCAATTATGAGATTAAAA
* * * * *
18889 AACCATTTAAAGAGAGTAATAAGG-TATCCGAAGG-AATGGGC
131 AAACATTTAAAGCGAGTAAAAAGGCT-TTCGAAGGCAAT-GGT
* * * * * * * *
18930 GACTATAAATAAACTTTTCTTGCGAAT-AGAT-TTTTTTTTTTCACGTTTCTCAAGGTAGACATT
1 GACTATAAATGAACTTTTCTTACTAATGA-ATATCTTTTTATTCACGTTTCTCAAAGTACATATT
18993 CAATTATAATCTATTTTA-ATAAAA
65 CAATTATAATCTATTTTACATAAAA
19017 NNNNNNNNNN
Statistics
Matches: 471, Mismatches: 105, Indels: 40
0.76 0.17 0.06
Matches are distributed among these distances:
167 3 0.01
168 28 0.06
169 224 0.48
170 188 0.40
171 27 0.06
172 1 0.00
ACGTcount: A:0.36, C:0.12, G:0.12, T:0.36
Consensus pattern (171 bp):
GACTATAAATGAACTTTTCTTACTAATGAATATCTTTTTATTCACGTTTCTCAAAGTACATATTC
AATTATAATCTATTTTACATAAAAATATAAAAAAATTAAACTTAAAATCAATTATGAGATTAAAA
AAACATTTAAAGCGAGTAAAAAGGCTTTCGAAGGCAATGGT
Found at i:19423 original size:170 final size:170
Alignment explanation
Indices: 19117--19725 Score: 660
Period size: 170 Copynumber: 3.6 Consensus size: 170
19107 NNNNNNNNNN
* * * *
19117 GTTTCTCAAGGTACATATTCAATTATAATCTATTTTAATAAAAAATATAAAAAAGTTAACTTAAA
1 GTTTCTCGAGGTAGACATTCAATTATAATCTATTTTAATAAAAAATATAAAAAATTTAACTTAAA
* * * * * *
19182 ATCAATTATGGGATTATATAACCATTTAATGAGAGTAATAAGGCTTTCGAAGGCAAT-GGTGGCA
66 ATCAATTATGAGATTGTAAAACCATTTAAAGAGAGTAATAAGGCTTTCGAAGGC-ATGGGTGACT
* *
19246 ATAAATGGACTTTTCTTACTAATGGATATCTTTTTCTTTAT
130 ATAAATGGACTTTTCTTACCAATGGATATCTTTTTCTTCAT
* * * * * *
19287 GTTTCCCGAGGTAGATATTAAATTATAATCTGTCTTAATAAAAAATATAAAAAAATTTAGCTTAA
1 GTTTCTCGAGGTAGACATTCAATTATAATCTATTTTAATAAAAAATAT-AAAAAATTTAACTTAA
* * * ** *
19352 AATCTATTAT-TGATTGTAAAAACATTTAAACCGAGTAATAAGGCTTTCGAA-GCTATGGGTGAT
65 AATCAATTATGAGATTGTAAAACCATTTAAAGAGAGTAATAAGGCTTTCGAAGGC-ATGGGTGAC
* * *
19415 TGTAAATGGTCTTTTCTTACCAATGGATGTC-TTTTCTTCACT
129 TATAAATGGACTTTTCTTACCAATGGATATCTTTTTCTTCA-T
* * * *
19457 -TTTCTTGAGGTAAACATTCAATTATAATCTATTTT-A-AAAAAATGTAAAAAATTTTAACATAA
1 GTTTCTCGAGGTAGACATTCAATTATAATCTATTTTAATAAAAAATATAAAAAA-TTTAACTTAA
* * *** *
19519 AATCAATTATGAGATTGCAAAACCAATTAAAGAGAGTAATAAGGCAACCGAAGGCATGGGAGACT
65 AATCAATTATGAGATTGTAAAACCATTTAAAGAGAGTAATAAGGCTTTCGAAGGCATGGGTGACT
* * * * *
19584 ATAAATAGACTTTTCTTGCCAATAGATATTTTTTTCTTCAC
130 ATAAATGGACTTTTCTTACCAATGGATATCTTTTTCTTCAT
* ** *
19625 GTTTCTCGAGATAGACATTCAATTATAATCCGTTTTAAT-AAAAATGTAAAAAA-TTAACTTAAA
1 GTTTCTCGAGGTAGACATTCAATTATAATCTATTTTAATAAAAAATATAAAAAATTTAACTTAAA
* * * *
19688 ATCAATTATGAAATTATAAAACTATTTAAAGTGAGTAA
66 ATCAATTATGAGATTGTAAAACCATTTAAAGAGAGTAA
19726 NNNNNNNNNN
Statistics
Matches: 362, Mismatches: 67, Indels: 22
0.80 0.15 0.05
Matches are distributed among these distances:
166 6 0.02
167 25 0.07
168 105 0.29
169 81 0.22
170 122 0.34
171 23 0.06
ACGTcount: A:0.40, C:0.11, G:0.13, T:0.36
Consensus pattern (170 bp):
GTTTCTCGAGGTAGACATTCAATTATAATCTATTTTAATAAAAAATATAAAAAATTTAACTTAAA
ATCAATTATGAGATTGTAAAACCATTTAAAGAGAGTAATAAGGCTTTCGAAGGCATGGGTGACTA
TAAATGGACTTTTCTTACCAATGGATATCTTTTTCTTCAT
Found at i:20335 original size:171 final size:170
Alignment explanation
Indices: 19866--21303 Score: 738
Period size: 171 Copynumber: 8.4 Consensus size: 170
19856 NNNNNNNNNN
* * * * *
19866 AGGTAGACATTAAATTATAATTTGTTTGAATAAAAAATA-TAAAAAAAATTCAGCTTAAAATCTA
1 AGGTAGACATTCAATTATAATCTGTTTTAATAAAAAA-AGT-AAAAAAATTCAACTTAAAATCAA
* * *********
19930 TTATGAGATTTTAAAAACATTCAAAGCGACTAATAAGG-TTTTCGAAGGCATNNNNNNNNNNAAA
64 TTATGAGATTATAAAAACATTCAAAGCGAGTAATAAGGCTTTT-GAAGGCAT-GGATAATATAAA
* * *
19994 TGGACTTTTCTTGCCAATGGATATC-TTTTCTTCATGTTT-CTCA
127 TGGACTTTTCTTACCAATGGATATCTTTTTCTTCACGTTTCCT-G
* * * * * * *
20037 AAGAAGACATTTAATTACAATCTGTTTTCATAAGAAATA-TAAAAATATTCAACTTAAAATCAAT
1 AGGTAGACATTCAATTATAATCTGTTTTAATAA-AAAAAGTAAAAAAATTCAACTTAAAATCAAT
********** * * * * *
20101 TA-NNNNNNNNNNAAACTATTCAAAGCGGGTAATAAGGCTTTCGATGGCATGGTTGATTATAAAT
65 TATGAGATTATAAAAAC-ATTCAAAGCGAGTAATAAGGCTTTTGAAGGCATGGAT-AATATAAAT
* *
20165 GGACTTTTCTTACCAATGGATATCTTTTTCTTTACGTTTCCTT
128 GGACTTTTCTTACCAATGGATATCTTTTTCTTCACGTTTCCTG
* * * * * *
20208 AGGCAGACATTCAATTATTATCTGTTTCAACAAAAAAAGTAAAAAAATTTAACTGAAAATCAATT
1 AGGTAGACATTCAATTATAATCTGTTTTAATAAAAAAAGTAAAAAAATTCAACTTAAAATCAATT
* * * *
20273 ATGAGATTATAAAAACATTCAAAGTGACTAATAATGCTTTTGAAGGCATAAGATAATATAAATGG
66 ATGAGATTATAAAAACATTCAAAGCGAGTAATAAGGCTTTTGAAGGCAT-GGATAATATAAATGG
* ********** *
20338 GCTTTTCTTNNNNNNNNNNATCTTTTTGTTCACGTTTCCTG
130 ACTTTTCTTACCAATGGATATCTTTTTCTTCACGTTTCCTG
* * * *
20379 AGTTAGACATTCAATTATAATTTGTTTTAA-AAAAATATGTAAAAAAATTCAACTTAAAATAAAT
1 AGGTAGACATTCAATTATAATCTGTTTTAATAAAAA-AAGTAAAAAAATTCAACTTAAAATCAAT
* ** * * * * * * *
20443 TATGAGATTGTAAATCCATTTAAAGCGAGTAATAAAGCTTCTGCAGGTATGGGTAATTATAAATA
65 TATGAGATTATAAAAACATTCAAAGCGAGTAATAAGGCTTTTGAAGGCATGGATAA-TATAAATG
* * * * *
20508 GACTCTTT-TTGCCAATGGATATATTTTTCTTCAAGTTT-TTCA
129 GACT-TTTCTTACCAATGGATATCTTTTTCTTCACGTTTCCT-G
* * * * * * * *
20550 AGTTTCG-TATTAAATTATAATCTATTTTAATAAAAATA-TAAAAAAA-T-AAGTTAAAATTAAT
1 AG-GTAGACATTCAATTATAATCTGTTTTAATAAAAAAAGTAAAAAAATTCAACTTAAAATCAAT
* * * ********** * * * *
20611 TATGAGATTATAAAACCATTTAAAGTGAGTAATANNNNNNNNNNAGGTATGGGTGACTATAAGTG
65 TATGAGATTATAAAAACATTCAAAGCGAGTAATAAGGCTTTTGAAGGCATGGAT-AATATAAATG
* * * **
20676 GATTTTTCTTACCAATGGATATCTTTTTCTTTATGTTTCGAG
129 GACTTTTCTTACCAATGGATATCTTTTTCTTCACGTTTCCTG
* * * * * ********* * *
20718 AGGGAGACATTAAATTATAATTTGTTTGAAT-AAAAAATTNNNNNNNNNNCAGCTTAAAATCTAT
1 AGGTAGACATTCAATTATAATCTGTTTTAATAAAAAAAGT-AAAAAAATTCAACTTAAAATCAAT
* * ** * * *
20782 TATGAGATTTTAAAAACATTCAAAGTGAGTAATAAGGCTTTCAAAGGCATGGACAACAATCAAAA
65 TATGAGATTATAAAAACATTCAAAGCGAGTAATAAGGCTTTTGAAGGCATGGATAA-TAT-AAAT
* * * * *
20847 GAACTTTTCTTTCCAATGGATATC-TTTTCTTCATGTTTTCTA
128 GGACTTTTCTTACCAATGGATATCTTTTTCTTCACGTTTCCTG
* * * * *
20889 AGGAAAAAATTCAATTATAATATATTTTAATAAAAAAA-TAAAAAAAATTCAACTTAAAATCAAT
1 AGGTAGACATTCAATTATAATCTGTTTTAATAAAAAAAGT-AAAAAAATTCAACTTAAAATCAAT
* ** * *
20953 TATTG-GATTGTAAAATTATTCAAAGCGAGTAATAAGGGC-TTCGAAGGCAT-GACTGATTATAA
65 TA-TGAGATTATAAAAACATTCAAAGCGAGTAATAA-GGCTTTTGAAGGCATGGA-T-AATATAA
********** * * *
21015 ATGGACTTNNNNNNNNNNTGAATAACTTTTTCTTTACGTTTCCTG
126 ATGGACTTTTCTTACCAATGGATATCTTTTTCTTCACGTTTCCTG
* * ** * * * **
21060 AGGTAAACATTCAATTATTATCTAATTCAACAAAAAATGTAAAAAAATTCAACTTAAAATCAANN
1 AGGTAGACATTCAATTATAATCTGTTTTAATAAAAAAAGTAAAAAAATTCAACTTAAAATCAATT
******** * * * * * *
21125 NNNNNNNNATCAAAACATTTAAAGCGACTAATAAGGCTTTTGAAGGTATAGATTCATATAAATGG
66 ATGAGATTATAAAAACATTCAAAGCGAGTAATAAGGCTTTTGAAGGCATGGA-TAATATAAATGG
* * * * *
21190 ACGTTTCTTGCCAATGAATATC-TTTTCTTCATGTTTCCTA
130 ACTTTTCTTACCAATGGATATCTTTTTCTTCACGTTTCCTG
* * * * *
21230 AGGTAGATATTCAATTAAAATTTGTTTTAATAAAAAATGTAAAACAATTCAACTTAAAATCAATT
1 AGGTAGACATTCAATTATAATCTGTTTTAATAAAAAAAGTAAAAAAATTCAACTTAAAATCAATT
21295 ATGAGATTA
66 ATGAGATTA
Statistics
Matches: 922, Mismatches: 310, Indels: 71
0.71 0.24 0.05
Matches are distributed among these distances:
167 9 0.01
168 111 0.12
169 6 0.01
170 186 0.20
171 549 0.60
172 61 0.07
ACGTcount: A:0.38, C:0.11, G:0.12, T:0.34
Consensus pattern (170 bp):
AGGTAGACATTCAATTATAATCTGTTTTAATAAAAAAAGTAAAAAAATTCAACTTAAAATCAATT
ATGAGATTATAAAAACATTCAAAGCGAGTAATAAGGCTTTTGAAGGCATGGATAATATAAATGGA
CTTTTCTTACCAATGGATATCTTTTTCTTCACGTTTCCTG
Done.