Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018397483.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_5010.0, 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: 13429
ACGTcount: A:0.34, C:0.10, G:0.12, T:0.32
Warning! 1684 characters in sequence are not A, C, G, or T
Found at i:3342 original size:170 final size:169
Alignment explanation
Indices: 2252--3646 Score: 1212
Period size: 171 Copynumber: 8.2 Consensus size: 169
2242 NNNNNNNNNN
* * * * * * *
2252 AAATCAATTATGAGATTATAAAACCATTTAAAGCAAGTAATAAGACTTTTGATGAAATGGGTGAC
1 AAATCAATTATGAGATTATAAAACTATTTAAAGCGAGTAATAAGGCTTTTAAAGGAATGGATGAC
* * ** * * *
2317 TATAAATGGACTTTTGTTGTCAATAAATGTATTTTT-TTCACGTTTCTTAAGTTAGACATTCAAT
66 TATAAATGGACTTTTGTTGCCAATGAATGCCTTTTTCTTCATGTTTCTCAAGGTAGACATTCAAT
* * * * *
2381 TATTGTTTGTTTTAATGAAAAATATAAAAATAATCAATTTA
131 TATAGTCTGTTTTAA-CAAAAATATAAAAA-ATTCAACTTA
* * * * * * * *
2422 AAATGAATTATGAAATT-TAAAAACCATTTAAAGAGAATAATATGACTTTTGAAA-TAAT-GAGT
1 AAATCAATTATGAGATTAT-AAAACTATTTAAAGCGAGTAATAAGGCTTTT-AAAGGAATGGA-T
* * * * ** *
2484 GACTATAAATGGACTTTTTTTAG-CAATAAATACCTTTTTCTTAATGTTTCTTGAGATAGACATT
63 GACTATAAATGGACTTTTGTT-GCCAATGAATGCCTTTTTCTTCATGTTTCTCAAGGTAGACATT
* * * *
2548 TAATTATAGTCTGTTTTAACAAAATATGTAAAGAAATTCAACCTC
127 CAATTATAGTCTGTTTTAACAAAA-ATATAAA-AAATTCAACTTA
* * *
2593 AAATCAATTATGAGATTATAAAACCT-TTTAAAGTGATTAATAAGGCTTTTGAAGGAATGTG-TG
1 AAATCAATTATGAGATTATAAAA-CTATTTAAAGCGAGTAATAAGGCTTTTAAAGGAATG-GATG
* ** * * * *
2656 ACTATAAAAGGAC-TTTGCTT-CTCAATGAATGGTTTTTTGTACACGTTTC-CTAAGGCAGACAT
64 ACTATAAATGGACTTTTG-TTGC-CAATGAATGCCTTTTTCTTCATGTTTCTC-AAGGTAGACAT
* * * *
2718 TTAATTATAATCTGTTCTAACTAAAAAT-TAAACAAATTCAACCT-
126 TCAATTATAGTCTGTTTTAAC-AAAAATATAAA-AAATTCAACTTA
* * * * *
2762 AAATCAATTATGAGATTATAAGACCATTTAGAGCGAGTAATAAGGCTTGTGAAA-GAATGAATGA
1 AAATCAATTATGAGATTATAAAACTATTTAAAGCGAGTAATAAGGCTT-TTAAAGGAATGGATGA
* * * * ** *
2826 CTATAAATAGACTTTTTTTGCCAATGAATGCCTATTTCTTTACATTTCTCTAGGTAGACATTCAA
65 CTATAAATGGACTTTTGTTGCCAATGAATGCCTTTTTCTTCATGTTTCTCAAGGTAGACATTCAA
* *
2891 TTATAGTCTATTTTAACTAAAAATATGCAAAAATTCAACTTA
130 TTATAGTCTGTTTTAAC-AAAAATAT-AAAAAATTCAACTTA
** * * * *
2933 AAATCAATTATGAGATGCTAAAACTATCTACAGCGAATAATAAGGCTTTTGAAA-AAAT-GAGTG
1 AAATCAATTATGAGATTATAAAACTATTTAAAGCGAGTAATAAGGCTTTT-AAAGGAATGGA-TG
* * * * * * * *
2996 ACTATAAACGGACTTTTCTTGCCAGA-GAATGCCTTTTTCTTCGTATATCCCAAGGTAAACATTG
64 ACTATAAATGGACTTTTGTTGCCA-ATGAATGCCTTTTTCTTCATGTTTCTCAAGGTAGACATTC
* * * *
3060 AATTATAATCTGTATTAATCAAAAATATAAAAAAAATTGAACATA
128 AATTATAGTCTGTTTTAA-CAAAAATAT--AAAAAATTCAACTTA
* * * * * *
3105 AGACCAATTTTGAGATTATAAAA-TCATTTAAAGTGAGCAATAAGGCTTTTAAAGGAATGGGTGA
1 AAATCAATTATGAGATTATAAAACT-ATTTAAAGCGAGTAATAAGGCTTTTAAAGGAATGGATGA
* ** * * *
3169 CTATAAATGGACTTTTGTTGCTAATGAATGATTTTTTCTTCATGTTTCCCAAGGTAGACTTTTAA
65 CTATAAATGGACTTTTGTTGCCAATGAATGCCTTTTTCTTCATGTTTCTCAAGGTAGACATTCAA
* * *
3234 TTATAGTCGGTTTTAACTAAAATGTAAAAAACTTCAACTTA
130 TTATAGTCTGTTTTAACAAAAATATAAAAAA-TTCAACTTA
* * *
3275 AAATCAATTATGGGATTATAAAACTATTTAAAGCGAGCAATAAAGCTTTTAAAGGAATGGATGAC
1 AAATCAATTATGAGATTATAAAACTATTTAAAGCGAGTAATAAGGCTTTTAAAGGAATGGATGAC
* * * * * *
3340 TATAAATGAACTTTTTTTGCCAATGAATGCCTTTTTCTTTATGTTTCTGAAGGTAAAAATTCAAT
66 TATAAATGGACTTTTGTTGCCAATGAATGCCTTTTTCTTCATGTTTCTCAAGGTAGACATTCAAT
* * * * *
3405 TATAGTCCGTTTTGACGAAAAATGTAAAAGAATTTAACTAA
131 TATAGTCTGTTTTAAC-AAAAATATAAAA-AATTCAACTTA
*
3446 AAACCAATTATGAGATTATAAAA-TCATTTAAAGCGAGTAATAAGGCTTTTAAAGGAATAGGA-G
1 AAATCAATTATGAGATTATAAAACT-ATTTAAAGCGAGTAATAAGGCTTTTAAAGGAAT-GGATG
* * * * * **
3509 ACTATAAATGAACTTTTCTTGCCCATGAATGGCTTTATCTTTACAT-TTT-TCAAATTAGACATT
64 ACTATAAATGGACTTTTGTTGCCAATGAATGCCTTTTTC-TT-CATGTTTCTCAAGGTAGACATT
*
3572 CAATCATAGTCTGTTTTAACCAAAAATATAAAAAAATTCAACTTA
127 CAATTATAGTCTGTTTTAA-CAAAAATAT-AAAAAATTCAACTTA
* * *
3617 AAATTAATTTTAAGATTATAAAACTATTTA
1 AAATCAATTATGAGATTATAAAACTATTTA
3647 NNNNNNNNNN
Statistics
Matches: 993, Mismatches: 186, Indels: 91
0.78 0.15 0.07
Matches are distributed among these distances:
168 1 0.00
169 122 0.12
170 255 0.26
171 464 0.47
172 147 0.15
173 4 0.00
ACGTcount: A:0.39, C:0.11, G:0.13, T:0.36
Consensus pattern (169 bp):
AAATCAATTATGAGATTATAAAACTATTTAAAGCGAGTAATAAGGCTTTTAAAGGAATGGATGAC
TATAAATGGACTTTTGTTGCCAATGAATGCCTTTTTCTTCATGTTTCTCAAGGTAGACATTCAAT
TATAGTCTGTTTTAACAAAAATATAAAAAATTCAACTTA
Found at i:3606 original size:342 final size:334
Alignment explanation
Indices: 2252--3646 Score: 1149
Period size: 341 Copynumber: 4.1 Consensus size: 334
2242 NNNNNNNNNN
* * * * * *
2252 AAATCAATTATGAGATTATAAAACCATTTAAAGC-AAGTAATAAGACTTTTGATGAAATGGGTGA
1 AAATCAATTATGAGATTATAAAACTATTTAAAGCGAA-TAATAAGGCTTTTAAAGGAATGGATGA
* * * * ** * * *
2316 CTATAAATGGACTTTTGTTGTCAATAAATGTATTTTT-TTCACGTTTCTTAAGTTAGACATTCAA
65 CTATAAAAGGACTTTTCTTGCCAATGAATGCCTTTTTCTTCATGTTTC-TAAGGTAAACATTCAA
** * * * * * ** *
2380 TTATTGTTTGTTTTAATGAAAAATATAAAAATAATCAATTTAAAATGAATTATGAAATT-TAAAA
129 TTATAATCTGTTTTAA-CAAAAAT-TAAAAA-ATTCAACTAAAAACCAATTATGAGATTAT-AAA
* * * * * * * * *
2444 ACCATTTAAAGAGAATAATATGACTTTTGAAA-TAATGAGTGACTATAAATGGACTTTTTTTAG-
190 ATCATTTAAAGCGAGTAATAAGGCTTTT-AAAGGAATG-GAGACTATAAATGAACTTTTCTT-GC
* ** * *
2507 CAATAAAT-ACCTTTT-TCTTA-ATGTTTCTTGAGATAGACATTTAATTATAGTCTGTTTTAACA
252 CAATGAATGA-CTTTTCT-TTACAT-TTT-TCAAGGTAGACATTCAATTATAGTCTGTTTTAACA
* * *
2569 AAATATGTAAAGAAATTCAACCTC
313 AAA-ATATAAA-AAATTCAACTTA
* * *
2593 AAATCAATTATGAGATTATAAAACCT-TTTAAAGTGATTAATAAGGCTTTTGAAGGAATGTG-TG
1 AAATCAATTATGAGATTATAAAA-CTATTTAAAGCGAATAATAAGGCTTTTAAAGGAATG-GATG
* ** * * * * * *
2656 ACTATAAAAGGACTTTGCTT-CTCAATGAATGGTTTTTTGTACACGTTTCCTAAGGCAGACATTT
64 ACTATAAAAGGACTTTTCTTGC-CAATGAATGCCTTTTTCTTCATGTTT-CTAAGGTAAACATTC
* *
2720 AATTATAATCTGTTCTAACTAAAAATTAAACAAATTCAACCT--AAATCAATTATGAGATTATAA
127 AATTATAATCTGTTTTAAC-AAAAATTAAA-AAATTCAA-CTAAAAACCAATTATGAGATTATAA
* * * * * *
2783 GACCATTTAGAGCGAGTAATAAGGCTTGTGAAA-GAATGAATGACTATAAAT-AGACTTTTTTTG
189 AATCATTTAAAGCGAGTAATAAGGCTT-TTAAAGGAATGGA-GACTATAAATGA-ACTTTTCTTG
* * * *
2846 CCAATGAATGCCTATTTCTTTACATTTCTCTAGGTAGACATTCAATTATAGTCTATTTTAACTAA
251 CCAATGAATGACT-TTTCTTTACATTTTTCAAGGTAGACATTCAATTATAGTCTGTTTTAAC-AA
*
2911 AAATATGCAAAAATTCAACTTA
314 AAATAT-AAAAAATTCAACTTA
** * * *
2933 AAATCAATTATGAGATGCTAAAACTATCTACAGCGAATAATAAGGCTTTTGAAA-AAAT-GAGTG
1 AAATCAATTATGAGATTATAAAACTATTTAAAGCGAATAATAAGGCTTTT-AAAGGAATGGA-TG
* * * * * *
2996 ACTATAAACGGACTTTTCTTGCCAGA-GAATGCCTTTTTCTTCGTATATCCCAAGGTAAACATTG
64 ACTATAAAAGGACTTTTCTTGCCA-ATGAATGCCTTTTTCTTCATGT-TTCTAAGGTAAACATTC
* * * *
3060 AATTATAATCTGTATTAATCAAAAATATAAAAAAAATTGAAC-ATAAGACCAATTTTGAGATTAT
127 AATTATAATCTGTTTTAA-CAAAAAT-T--AAAAAATTCAACTA-AAAACCAATTATGAGATTAT
* * * * *
3124 AAAATCATTTAAAGTGAGCAATAAGGCTTTTAAAGGAATGGGTGACTATAAATGGACTTTTGTTG
187 AAAATCATTTAAAGCGAGTAATAAGGCTTTTAAAGGAAT-GGAGACTATAAATGAACTTTTCTTG
* * * * * * *
3189 CTAATGAATGA-TTTT-TTCTTCATGTTTCCCAAGGTAGACTTTTAATTATAGTCGGTTTTAACT
251 CCAATGAATGACTTTTCTT-TACAT-TTT-TCAAGGTAGACATTCAATTATAGTCTGTTTTAACA
*
3252 AAAATGTAAAAAACTTCAACTTA
313 AAAATATAAAAAA-TTCAACTTA
* ** *
3275 AAATCAATTATGGGATTATAAAACTATTTAAAGCGAGCAATAAAGCTTTTAAAGGAATGGATGAC
1 AAATCAATTATGAGATTATAAAACTATTTAAAGCGAATAATAAGGCTTTTAAAGGAATGGATGAC
* * * * *
3340 TATAAATGAACTTTTTTTGCCAATGAATGCCTTTTTCTTTATGTTTCTGAAGGTAAAAATTCAAT
66 TATAAAAGGACTTTTCTTGCCAATGAATGCCTTTTTCTTCATGTTTCT-AAGGTAAACATTCAAT
* * * *
3405 TATAGTCCGTTTTGACGAAAAATGTAAAAGAATTTAACTAAAAACCAATTATGAGATTATAAAAT
130 TATAATCTGTTTTAAC-AAAAAT-TAAAA-AATTCAACTAAAAACCAATTATGAGATTATAAAAT
*
3470 CATTTAAAGCGAGTAATAAGGCTTTTAAAGGAATAGGAGACTATAAATGAACTTTTCTTGCCCAT
192 CATTTAAAGCGAGTAATAAGGCTTTTAAAGGAAT-GGAGACTATAAATGAACTTTTCTTGCCAAT
* ** *
3535 GAATGGCTTTATCTTTACATTTTTCAAATTAGACATTCAATCATAGTCTGTTTTAACCAAAAATA
256 GAATGACTTT-TCTTTACATTTTTCAAGGTAGACATTCAATTATAGTCTGTTTTAA-CAAAAATA
3600 TAAAAAAATTCAACTTA
319 T-AAAAAATTCAACTTA
* * *
3617 AAATTAATTTTAAGATTATAAAACTATTTA
1 AAATCAATTATGAGATTATAAAACTATTTA
3647 NNNNNNNNNN
Statistics
Matches: 851, Mismatches: 150, Indels: 105
0.77 0.14 0.09
Matches are distributed among these distances:
338 1 0.00
339 3 0.00
340 233 0.27
341 251 0.29
342 243 0.29
343 117 0.14
344 3 0.00
ACGTcount: A:0.39, C:0.11, G:0.13, T:0.36
Consensus pattern (334 bp):
AAATCAATTATGAGATTATAAAACTATTTAAAGCGAATAATAAGGCTTTTAAAGGAATGGATGAC
TATAAAAGGACTTTTCTTGCCAATGAATGCCTTTTTCTTCATGTTTCTAAGGTAAACATTCAATT
ATAATCTGTTTTAACAAAAATTAAAAAATTCAACTAAAAACCAATTATGAGATTATAAAATCATT
TAAAGCGAGTAATAAGGCTTTTAAAGGAATGGAGACTATAAATGAACTTTTCTTGCCAATGAATG
ACTTTTCTTTACATTTTTCAAGGTAGACATTCAATTATAGTCTGTTTTAACAAAAATATAAAAAA
TTCAACTTA
Found at i:4588 original size:170 final size:168
Alignment explanation
Indices: 4073--6508 Score: 1361
Period size: 171 Copynumber: 14.3 Consensus size: 168
4063 NNNNNNNNNN
* *
4073 AAAGTGAGTAATAAGGCTTTTGAAAGAA-TGAGTGACTATAAATGAACTTTTCTTA-CTAATGAA
1 AAAGCGAGTAATAAGGCTTTTGAAGGAATTG-GTGACTATAAATGAACTTTT-TTATC-AATGAA
**** * * * * * *
4136 TACCTTTTTCTTTGTGTTTCCCAAGGTGGACATTCAATTATAATCTATTCTAACCAAAAATATAA
63 TACC-TTTTCTTCACATTTCTCGAGGTAGACATTCAATTATAATCTGTTTTAACTAAAAATATAA
* * * *
4201 AAATATTCATCCTAAAATCAATTATGAGATTATAAAACTATTT
127 AAAAATTAAACTTAAAATCAATTATGAGATTATAAAAC-ATTT
********** * * * *
4244 ANNNNNNNNNNTCAGGCTTTTGAAGGAATGGGTGACTATAAATAAACTTTTTTTACCAATGAATG
1 AAAGCGAGTAATAAGGCTTTTGAAGGAATTGGTGACTATAAATGAAC-TTTTTTATCAATGAAT-
** * * * * * * **
4309 ATTTTTTTTCTTCATATTTCCCAAGGTAGACATTTAATTATAGTCTGTTTTAAC-CAAAAGGTAA
64 A--CCTTTTCTTCACATTTCTCGAGGTAGACATTCAATTATAATCTGTTTTAACTAAAAATATAA
* * * * **
4373 AAAATTTCAACCTAAAATTAATTATTTGATTATAAAACTATTT
127 AAAAATTAAACTTAAAATCAATTATGAGATTATAAAAC-ATTT
** * * *
4416 AAAGCGAGTAATAATCCTTTTGAAGGAATAGGTGACTATAAACGGACTTTTCTTAT-AAGTGAAT
1 AAAGCGAGTAATAAGGCTTTTGAAGGAATTGGTGACTATAAATGAACTTTT-TTATCAA-TGAAT
* * * * * **
4480 GCCTTTTGCTTCACATTTGTCAAGGTAAACATTCAATTATAACCTGTTTT-AGGAAAAATATAAA
64 ACCTTTT-CTTCACATTTCTCGAGGTAGACATTCAATTATAATCTGTTTTAACTAAAAATATAAA
* * * * *
4544 GAACTTGAACATAAAATCAATTTTGAGATTATAAAATCATTT
128 AAAATTAAACTTAAAATCAATTATGAGATTATAAAA-CATTT
* ** * * ** *
4586 AAAGCGAGTAATAAAGAC-TTT-AAAAAAATGAGCGACTATAAATGGTCTTTTTTTGTCAATGAA
1 AAAGCGAGTAAT-AAGGCTTTTGAAGGAATTG-GTGACTATAAATGAAC-TTTTTTATCAATGAA
* * * * * * * *****
4649 TGCCTTTTTTTATATATTTTTTGAGGTAGACATTCAATTATAATCTGTTTTAACCAAAAANNNNN
63 TACCTTTTCTT-CACATTTCTCGAGGTAGACATTCAATTATAATCTGTTTTAACTAAAAATATAA
***** * *
4714 NNNNNTTCAACTTAAAATTAATTATGAGATTATAAAACCATTT
127 AAAAATTAAACTTAAAATCAATTATGAGATTATAAAA-CATTT
* * * * * *
4757 AAAACGTGTAATAAGGCTTTCGAAAGAATTGGTGATTATAAAATGAACTTTTTTAATCAATAAAT
1 AAAGCGAGTAATAAGGCTTTTGAAGGAATTGGTGACTAT-AAATGAACTTTTTT-ATCAATGAAT
** *
4822 ATCCTTTT-TT-ATGTTTCTCGAGGTAGACATTCAATTATAGTCTGTTTTAACTAAAAATATAAA
64 A-CCTTTTCTTCACATTTCTCGAGGTAGACATTCAATTATAATCTGTTTTAACTAAAAATATAAA
*
4885 AAAATTTAACTTAAAATCAATTATGAGATTATAAAACTATTT
128 AAAATTAAACTTAAAATCAATTATGAGATTATAAAAC-ATTT
* * *
4927 AAAGAGAGTAATAAGGCTTTTGAAGG-ATTGAATAACTATAAATGAACTGTTTTTATCAATGAAT
1 AAAGCGAGTAATAAGGCTTTTGAAGGAATTG-GTGACTATAAATGAACT-TTTTTATCAATGAAT
* * * * *
4991 ACCTGTTTCTTCACGTTTCAT-AAGGTAAATATTCAATTATAATCTGTTTTAACTAAAAATGTAA
64 ACCT-TTTCTTCACATTTC-TCGAGGTAGACATTCAATTATAATCTGTTTTAACTAAAAATATAA
*
5055 AACAAATTAAACCTAAAATCAATTATGAGATTATAAAACCATTT
127 AA-AAATTAAACTTAAAATCAATTATGAGATTATAAAA-CATTT
* * *
5099 AAAGCGAGTAATAAGGCTTGTGAAGAAATTGGTGACTATAAATGAACTTTTTTTTACCAATGAAT
1 AAAGCGAGTAATAAGGCTTTTGAAGGAATTGGTGACTATAAATGAAC--TTTTTTATCAATGAAT
* * *
5164 ACCTTTTTCTTCACATTTCTCGAGGTTGACATTCAATTATAATCTGTTTTAACAAAAAATGTAAA
64 ACC-TTTTCTTCACATTTCTCGAGGTAGACATTCAATTATAATCTGTTTTAACTAAAAATATAAA
***********
5229 AAAATTCNNNNNNNNNNCAATTATGAGATTATAAAACTATTT
128 AAAATTAAACTTAAAATCAATTATGAGATTATAAAAC-ATTT
* * ** * *
5271 AAAACGAGTAATAAGGCATTTGAAGGAATAAGTAACTATAAAT-AGACTTTTCTTGTCAATGAAT
1 AAAGCGAGTAATAAGGCTTTTGAAGGAATTGGTGACTATAAATGA-ACTTTT-TTATCAATGAAT
* * * * * * *
5335 ACCTTTTTCTTTACGTTTTTCGAGGTAAACATTCAATTATTATCTGTTTTAACAAAAAATGTAAA
64 ACC-TTTTCTTCACATTTCTCGAGGTAGACATTCAATTATAATCTGTTTTAACTAAAAATATAAA
* * *
5400 AATAA-TCAACTTAAAAT-ATATTATGAGATTGTAAAACCGTTT
128 AA-AATTAAACTTAAAATCA-ATTATGAGATTATAAAA-CATTT
* ********** * ** *
5442 AAAGCGAGTGATAAGGCTTTTGAAGGNNNNNNNNNNTATAAATGGACTTTTCTTGCCAATAAATA
1 AAAGCGAGTAATAAGGCTTTTGAAGGAATTGGTGACTATAAATGAACTTTT-TTATCAATGAATA
* * * * *
5507 CTTTTTTCTTCA-AGGTTCTCGAGGTAGACATTCAATTATAGTCTGTTTTAACGAAAAATGT-AA
65 C-CTTTTCTTCACA-TTTCTCGAGGTAGACATTCAATTATAATCTGTTTTAACTAAAAATATAAA
********** *
5570 AAAATTNNNNNNNNNNTTAATTATGAGATTATAAAACCATTT
128 AAAATTAAACTTAAAATCAATTATGAGATTATAAAA-CATTT
* ** * * * *
5612 AAAGCGAATAATAAAACTTTTGATA-GAATGGGTGACTATAAATGGACTTTTGTTGTCAATAAAT
1 AAAGCGAGTAATAAGGCTTTTGA-AGGAATTGGTGACTATAAATGAACTTTT-TTATCAATGAAT
* * * ** ** * *
5676 GCCTTTT-TTCACGTTTTTTAAGGTAGACATTCAATTATTGTCTATTTTAA-TGAAAAATGTAAA
64 ACCTTTTCTTCACATTTCTCGAGGTAGACATTCAATTATAATCTGTTTTAACT-AAAAATATAAA
*
5739 AATAA-TAAACTTAAAATTAATTATGAGATT-TAAAAACTATTT
128 AA-AATTAAACTTAAAATCAATTATGAGATTAT-AAAAC-ATTT
** ** * * *
5781 AAAAAGAGTAATAAGGCTTTTGAAATAATGGGTGACTATAAATGAACTTTTTT-TGGTAATAAAT
1 AAAGCGAGTAATAAGGCTTTTGAAGGAATTGGTGACTATAAATGAACTTTTTTAT--CAATGAAT
* * * * * * *
5845 ACCTTTTTCTTCACGTTTCTTGAGGTAGACATTTAATTATAGTCCGTTTTGA-TAAAAAATGTAA
64 ACC-TTTTCTTCACATTTCTCGAGGTAGACATTCAATTATAATCTGTTTTAACT-AAAAATATAA
* * * * *
5909 ACAAATTCAACTTAAAATCTATTATAAGATGATAAAACCATTT
127 AAAAATTAAACTTAAAATCAATTATGAGATTATAAAA-CATTT
* * ********** * * * * *
5952 AAAGTGATTAATAANNNNNNNNNNGGAATGGGTGACTGTAAATGGACTTTGCTTCTCAATGAATA
1 AAAGCGAGTAATAAGGCTTTTGAAGGAATTGGTGACTATAAATGAACTTT-TTTATCAATGAATA
* * * * * * * ** *
6017 -GTTTTTTATACACGTTT-TCTAAGGTAGACATTCAGTTATAATCTGTTCTAAC-CAAAAGCTAN
65 CCTTTTCT-T-CACATTTCTC-GAGGTAGACATTCAATTATAATCTGTTTTAACTAAAAATATAA
********* * **
6079 NNNNNNNNNACCT-AAATCAATTATGAGATTATAAGGCCATTT
127 AAAAATTAAACTTAAAATCAATTATGAGATTATAA-AACATTT
* * * * **
6121 AAAGCGAGCAATAAAGCTTATGAAGGAA-TGGATGACTATAAATAGAATTTTTTTGCCAATGAAT
1 AAAGCGAGTAATAAGGCTTTTGAAGGAATTGG-TGACTATAAAT-GAACTTTTTTATCAATGAAT
* * * **********
6185 ACCTATTTCTTTACATTTCTTGAGGTAGACATTCAATTATAGTCTGTTTTNNNNNNNNNNATAAA
64 ACCT-TTTCTTCACATTTCTCGAGGTAGACATTCAATTATAATCTGTTTTAACTAAAAATATAAA
* * *
6250 ACAATTTAACTTAAAATCAATTATGAGATTATAAAACTATCT
128 AAAATTAAACTTAAAATCAATTATGAGATTATAAAAC-ATTT
* ** * * * * **
6292 ACAGCGAGTAATAAGGCTTTTGAAAAAAATGGTAACTATAAACGGACTTTTCTTGCCAGA-GAAT
1 AAAGCGAGTAATAAGGCTTTTGAAGGAATTGGTGACTATAAATGAACTTTT-TTATCA-ATGAAT
* * * * * * *
6356 ACCTTTTTCTTCGCATATCTC-AGGGTAAAGATTGAATTATAATATGTATTAA-TCAAAAATGTA
64 ACC-TTTTCTTCACATTTCTCGA-GGTAGACATTCAATTATAATCTGTTTTAACT-AAAAA--TA
* * ** * *
6419 AAAAAAAATTGAACAGAAGATCAATTTTGAGATTATAAAATCATTT
124 TAAAAAAATTAAACTTAAAATCAATTATGAGATTATAAAA-CATTT
* * *
6465 AAAGCAAGCAATAAGGCTTTTGAAGGAATGGGTGACTATAAATG
1 AAAGCGAGTAATAAGGCTTTTGAAGGAATTGGTGACTATAAATG
6509 NNNNNNNNNN
Statistics
Matches: 1730, Mismatches: 449, Indels: 170
0.74 0.19 0.07
Matches are distributed among these distances:
167 1 0.00
168 53 0.03
169 217 0.13
170 382 0.22
171 613 0.35
172 266 0.15
173 195 0.11
174 3 0.00
ACGTcount: A:0.38, C:0.11, G:0.13, T:0.35
Consensus pattern (168 bp):
AAAGCGAGTAATAAGGCTTTTGAAGGAATTGGTGACTATAAATGAACTTTTTTATCAATGAATAC
CTTTTCTTCACATTTCTCGAGGTAGACATTCAATTATAATCTGTTTTAACTAAAAATATAAAAAA
ATTAAACTTAAAATCAATTATGAGATTATAAAACATTT
Found at i:7358 original size:343 final size:341
Alignment explanation
Indices: 6937--11270 Score: 1521
Period size: 341 Copynumber: 12.7 Consensus size: 341
6927 CTCTACACAT
* * * * * *
6937 TTTTTAATGTATACATTCAATCATAGTCTGTTTTAACCAAATATATAAAAAAATTTAACTTAAAA
1 TTTTTAAGGTAGACATTTAATTATAGTCTGTTTTAA-CAAAAATGTAAAAAAATTTAACTTAAAA
* * *
7002 TTAATTTTGAGATTATAAAACTATTTAAACCGAGCAGTTAGGCTTTTGAAAAAATG-GATGACTA
65 TTAATTATGAGATTATAAAACTATTTAAACCGAGCAATAAGGCTTTTGAAAAAATGAG-TGACTA
** * * * *
7066 TAAATAGAA-TTGTT-TTTATCAATGAATACATTTTTCTTCATATTTCTTGAGATAGACATTCAA
129 TAAAT-GAACTT-TTCTTCCT-AATGAATACATTTTTCTTCACATTTCCTAAGACAGACATTCAA
* ********** * * *
7129 TTATAGTCNNNNNNNNNNAAAAATGTAAAA-AAGTTCAACTTAAAATTAATTATGAGATCATAAA
191 TTATAATCTGTTCGAACCAAAAATATAAAAGAA-TTCAACCTAAAATCAATTATGAGATCATAAA
* * * **********
7193 ACCT-TTTAAAGGGTGTAATAAGGCTTTTGAAGGAATGGGTGACNNNNNNNNNNCTTTTTTTACC
255 A-CTATTTAAAGCGAGTAATAAGGCTTTTGAAAGAATGGGTGACTATAAATAGACTTTTTTTACC
7257 AATGAAT-ATCTTTTTCTTTACG
319 AATGAATGATCTTTTTCTTTACG
*
7279 TTTCTTAAGGTAGACATTTAATTATAGTTTGTTTTAACTAAAAATGTAAAAAAATTTAACTTAAA
1 TTT-TTAAGGTAGACATTTAATTATAGTCTGTTTTAAC-AAAAATGTAAAAAAATTTAACTTAAA
* * * **
7344 ATTAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGAGTGACTA
64 ATTAATTATGAGATTATAAAACTATTTAAACCGAGCAATAAGGCTTTTGAAAAAATGAGTGACTA
* * * * *
7409 TAAATGAACTTTTCTTCCTAATGAATACTTTTTTCTTTACGTTTCCTAAGGCAGATATTCAATTA
129 TAAATGAACTTTTCTTCCTAATGAATACATTTTTCTTCACATTTCCTAAGACAGACATTCAATTA
* * *
7474 TAATGTGTTCGAACCAAAAATATAAAAGAATTCATCCTAAAATCAATTATGAGATTATAAAACTA
194 TAATCTGTTCGAACCAAAAATATAAAAGAATTCAACCTAAAATCAATTATGAGATCATAAAACTA
* *
7539 TTTAAAGCGAGTAATCAGGCTTTTGAAAGAATGGGTGACTATAAATAGACTTTTTTTGCCAATGA
259 TTTAAAGCGAGTAATAAGGCTTTTGAAAGAATGGGTGACTATAAATAGACTTTTTTTACCAATGA
* *
7604 ATGATTTTTTTCTTTATG
324 ATGATCTTTTTCTTTACG
* *
7622 TTTTCTAAGGTAGACATTTAATTATAGTCTGTTTTAACCAAAATGT-AAAAAATTTCAACCTAAA
1 TTTT-TAAGGTAGACATTTAATTATAGTCTGTTTTAACAAAAATGTAAAAAAATTT-AACTTAAA
* ** ** * * **
7686 GTTAATTATTTGATTATAAAACTATTTAAAGTGAGTAATAAGCCTTTTGAAGGAAT-AGGTGACT
64 ATTAATTATGAGATTATAAAACTATTTAAACCGAGCAATAAGGCTTTTGAAAAAATGA-GTGACT
* * * * * * * * *
7750 CTAAACGGACTTTTCTT-ATAAGTGAATGCCTTTTGCTTCATATTT-CTCATCGTA-A-ACATTC
128 ATAAATGAACTTTTCTTCCTAA-TGAATACATTTTTCTTCACATTTCCT-A-AG-ACAGACATTC
* * ** ** * * * *
7811 AATTAGAACCTGTT-TTAGGAAAAATAT-AAAGAAATTGAACATAAAATCTATT-TTAGGA-CTA
189 AATTATAATCTGTTCGAACCAAAAATATAAAAG-AATTCAACCTAAAATCAATTATGA-GATC-A
********** *
7872 TAAAA-TCATTTAAAGCGAGTANNNNNNNNNNTG-AAGAAATGGGTGACTATAAAT-GTTCTTTT
251 TAAAACT-ATTTAAAGCGAGTAATAAGGCTTTTGAAAG-AATGGGTGACTATAAATAG-ACTTTT
* * ** *
7934 TTT-TCAATGAATG-CCTTTTTCTGCATG
313 TTTACCAATGAATGATCTTTTTCTTTACG
* * * * *
7961 TTTCTTGAGGTAGACATTCAATTATAATCTGTTTTTAACCAAAAATATAAAAAAAATTCAACTTA
1 TTT-TTAAGGTAGACATTTAATTATAGTCTG-TTTTAA-CAAAAATGT-AAAAAAATTTAACTTA
********** * * * * * * *
8026 AANNNNNNNNNNAGATTATAAAACCATTTAAAACGTGTAATAAGGCTTTCGAAAGAATGGGTGAC
62 AAATTAATTATGAGATTATAAAACTATTTAAACCGAGCAATAAGGCTTTTGAAAAAATGAGTGAC
* * * * * * ** * **
8091 TATAAATGGATTTTTTTTACC-ACTAAATATC-TTTTTCTTTATGTTT-CTCGAGGTAGACATTC
127 TATAAATGAACTTTTCTT-CCTAATGAATA-CATTTTTCTTCACATTTCCT-AAGACAGACATTC
* * ** * ********** * * * *
8153 AATTACAGTCTGTTTTAACTAAAAANNNNNNNNNNTTTAACTTAAAATCAATTATGAGTTTATAA
189 AATTATAATCTGTTCGAACCAAAAATATAAAAGAATTCAACCTAAAATCAATTATGAGATCATAA
* * * * * * * *
8218 AACCATCTAAAGTGAGTAATAAAGCTTTTGAAGGAGTGGGTGACTATAAATAAACTTTTCTTACC
254 AACTATTTAAAGCGAGTAATAAGGCTTTTGAAAGAATGGGTGACTATAAATAGACTTTTTTTACC
* ********
8283 AATGAATG-CCTTTTNNNNNNNNN
319 AATGAATGATCTTTT-TCTTTACG
* ** * * * * * * *
8306 NTTCCAAGGTAAACATTCAATTATAATCTATTCTAACCAAAAATGT-AAAAAATTCAACCTAAAA
1 TTTTTAAGGTAGACATTTAATTATAGTCTGTTTTAA-CAAAAATGTAAAAAAATTTAACTTAAAA
********** * * * * *
8370 NNNNNNNNNNGATTATAAAACTATTTAAACTGAGTAATAAGGCTTATGAAGAAAT-AGGTAACTA
65 TTAATTATGAGATTATAAAACTATTTAAACCGAGCAATAAGGCTTTTGAAAAAATGA-GTGACTA
* * * * * * ***
8434 TAAATGGACTTTTTTTTACC-AAT-AAGTACCTTTTGCTTCACATTTCTTGAGGTTGACATTCAA
129 TAAATGAAC-TTTTCTT-CCTAATGAA-TACATTTTTCTTCACATTTCCTAAGACAGACATTCAA
* * ** ** * * * *********
8497 TTATAGTTTGTTTTAACCCTAAATGTAAAAAAATTCAACTTAAAATCANNNNNNNNNNT-ATAAA
191 TTATAATCTGTTCGAACCAAAAATATAAAAGAATTCAACCTAAAATCA-ATTATGAGATCATAAA
* * * * * * * ** *
8561 CCCATTTAAAGCGAGTAATAAGACCTTTGAAGGAATGGGTAACTATAAATGGACTTTGCTTGCCA
255 ACTATTTAAAGCGAGTAATAAGGCTTTTGAAAGAATGGGTGACTATAAATAGACTTTTTTTACCA
*
8626 ATGAAT-ATCGTTTTCTTTACG
320 ATGAATGATCTTTTTCTTTACG
* * * * *
8647 TTTCTTAAGGTAGACATTCAATTATTA-TTTGTTTTAACAAAAAATGTAAAATTAA-TCAAATTA
1 TTT-TTAAGGTAGACATTTAATTA-TAGTCTGTTTTAAC-AAAAATGTAAAA-AAATTTAACTTA
* * ********** * ** *
8710 AAATCAATTATGAGATTGTAAAACTNNNNNNNNNNAGTAATAAGGCTTTTGAAGGAAT-AGGAGA
62 AAATTAATTATGAGATTATAAAACTATTTAAACCGAGCAATAAGGCTTTTGAAAAAATGA-GTGA
* * * * * ** * * *
8774 CTATTAATGGATTTTTATTGCC-AATAAAT-TTTTTTTCTTCA-ACTTTCTTGAGGCAGACATTC
126 CTATAAATGAACTTTTCTT-CCTAATGAATACATTTTTCTTCACA-TTTCCTAAGACAGACATTC
* * * * ********** *
8836 AATTATAGTCTGTTTTG-ACAAAAAATGTAAAANNNNNNNNNNTAAAATCAATTATGAGATTATA
189 AATTATAATCTG-TTCGAACCAAAAATATAAAAGAATTCAACCTAAAATCAATTATGAGATCATA
* * * * ** * * * **
8900 AAACCATTTAAAGCGAATAAAAAGACTTTTGATGGAATGTGTGACTATAAATGGACTTTTATTGT
253 AAACTATTTAAAGCGAGTAATAAGGCTTTTGAAAGAATGGGTGACTATAAATAGACTTTTTTTAC
* * *
8965 CAATAAATG-TC-TTTT-TTCATG
318 CAATGAATGATCTTTTTCTTTACG
* * *
8986 TTTCTTAAGGTAGACATTTAATTACT-GTCTGTTTTAATGAAAAATATAAAAATAA-TCAACTTA
1 TTT-TTAAGGTAGACATTTAATTA-TAGTCTGTTTTAA-CAAAAATGTAAAAA-AATTTAACTTA
* ** * * * *
9049 AAATTAATTATGAGATT-TAAAAACCATTTAAACAAAAGTAATAAGGCTTTTGAAATAATGGGTA
62 AAATTAATTATGAGATTAT-AAAACTATTTAAAC-CGAGCAATAAGGCTTTTGAAAAAATGAGTG
* * *** * * * ** ** *
9113 ACTATAAATGGACTTTTTTTGAAAATAAATACCTTTTTCTTCACGTTTTTTAAGGTAGACATTTA
125 ACTATAAATGAACTTTTCTTCCTAATGAATACATTTTTCTTCACATTTCCTAAGACAGACATTCA
* * * * * *
9178 ATTATAGTCTGTTTG-ACCAAAAATGTAAGAA-AATTCAACTTAAAATTAATTATGAGATTATAA
190 ATTATAATCTGTTCGAACCAAAAATATAA-AAGAATTCAACCTAAAATCAATTATGAGATCATAA
********** * * * * ** *
9241 NNNNNNNNNNAGTGATTAATAAGGCTTTTGAAGGAATGGGTGACTATAAATGGACTTTGCTTATC
254 AACTATTTAAAGCGAGTAATAAGGCTTTTGAAAGAATGGGTGACTATAAATAGACTTTTTTTACC
* * * **
9306 AATGAACGGT-TTTTTGTACACG
319 AATGAATGATCTTTTTCTTTACG
* * * * * * ********** *
9328 TTTCCTAAAGTAGACATTCAATTATAATCTGTTCTAACCAAAA-GCTANNNNNNNNNNACCT-AA
1 TTT-TTAAGGTAGACATTTAATTATAGTCTGTTTTAACAAAAATG-TAAAAAAATTTAACTTAAA
* * * * * *
9391 ATCAATTATGAGATTATAAGACTATTTAAAGCGAGCAATAAGGCTTATGAAGAAATGAGTGACAA
64 ATTAATTATGAGATTATAAAACTATTTAAACCGAGCAATAAGGCTTTTGAAAAAATGAGTGACTA
* * * * * * * * *
9456 TAAAT-AGACTTTTTTTTACAAATAAATACCTATTTCTTTACATTT-CTCGAGGCAGACATTCAA
129 TAAATGA-AC-TTTTCTTCCTAATGAATACATTTTTCTTCACATTTCCT-AAGACAGACATTCAA
* * ** * * * *
9519 TTATAGTCCGTTTTAACCAAAAATGTGAAAA-AATTCAACTTACAATCAATTATGAGATTATAAA
191 TTATAATCTGTTCGAACCAAAAATAT-AAAAGAATTCAACCTAAAATCAATTATGAGATCATAAA
* * * * * * * * ** * *
9583 ACCATCTACAGCGAGTAATAAGGTTTTTTAAAAAATAGGTGACTCTAAACGGACTTTTCTTGCCA
255 ACTATTTAAAGCGAGTAATAAGGCTTTTGAAAGAATGGGTGACTATAAATAGACTTTTTTTACCA
*
9648 GA-GAATG--CCTTTTCTTT--G
320 -ATGAATGATCTTTTTCTTTACG
* * * * * * ********
9666 TATATCTCAAGGTAAACATTGAATTATAATCTATATTAATCAAAAATGTAAAAAAANNNNNNNNN
1 T-T-T-TTAAGGTAGACATTTAATTATAGTCTGTTTTAA-CAAAAATGTAAAAAAA-TTTAACTT
* * * * * * *** *
9731 NAGATCAATTTTGAGATTATAAAA-TCATTTAGAGCGAGCAATAAGGCTTTTGACGGAATGGGTG
61 AAAATTAATTATGAGATTATAAAACT-ATTTAAACCGAGCAATAAGGCTTTTGAAAAAATGAGTG
* * * * * * * ** * * *
9795 ACTATAAATGGACTTTTTTTGCAAATGAATGA-TTTTTTCTACACGTTTCCTAAGGTAAATATTT
125 ACTATAAATGAACTTTTCTTCCTAATGAAT-ACATTTTTCTTCACATTTCCTAAGACAGACATTC
* ** ** * * ** *
9859 AATTATAGTCAATTTTAACC-AAAATGTAAAA-AACTTCAACTTAAAATTGATTATGAGATTATA
189 AATTATAATCTGTTCGAACCAAAAATATAAAAGAA-TTCAACCTAAAATCAATTATGAGATCATA
* * * *
9922 AAA-TCATTTAAGGCAAGGAATAAGGCTTTTG-AAGAAATGGGTGACTGTAAATAGACTTTTTTT
253 AAACT-ATTTAAAGCGAGTAATAAGGCTTTTGAAAG-AATGGGTGACTATAAATAGACTTTTTTT
* * *
9985 GCCAATGAATG-CCTTTTTCTTTATG
316 ACCAATGAATGATCTTTTTCTTTACG
* * * * * * * *
10010 TTTCTAAAGGTAAAAATTCAATTCTAGTCTGTTTTAACTAAAAATGTAAAAGAATTCAACTAAAA
1 TTT-TTAAGGTAGACATTTAATTATAGTCTGTTTTAAC-AAAAATGTAAAAAAATTTAACTTAAA
* * * ***********
10075 ATCAATTATGAGATTA-AAATA-TCATTTAAAGCGAGTAATAAGGCTTTTGAAGNNNNNNNNNNC
64 ATTAATTATGAGATTATAAA-ACT-ATTTAAACCGAGCAATAAGGCTTTTGAAAAAATGAGTGAC
* * * * * * ** * **
10138 TATAAATGGACTTTTCTT-GTCAATGAATGCCTTTCTCTTCACGTTTTTTGAGGTAGACATTCAA
127 TATAAATGAACTTTTCTTCCT-AATGAATACATTTTTCTTCACATTTCCTAAGACAGACATTCAA
* * ** * * * * *
10202 TCATAGTCTGTTTTAACCAAAACTATAAAAAAATTCAACTTAAAATTAATTTTGAGA-CTATAAA
191 TTATAATCTGTTCGAACCAAAAATATAAAAGAATTCAACCTAAAATCAATTATGAGATC-ATAAA
* * * *
10266 ACTATTTAAAGCGAGTAGTAAGGCTTTTG-AAGAAATGAGTGACTATCAATAGACTTTTTTTTAT
255 ACTATTTAAAGCGAGTAATAAGGCTTTTGAAAG-AATGGGTGACTATAAATAGAC-TTTTTTTAC
* **
10330 CAATGAATG--CATTTTTCTTGATA
318 CAATGAATGATC-TTTTTCTTTACG
* * * ************
10353 TTTCTTGAGATAGACATTCAATTATAGTCTGTTTTAACCAAAAATGTAAAANNNNNNNNNNNNAA
1 TTT-TTAAGGTAGACATTTAATTATAGTCTGTTTTAA-CAAAAATGTAAAAAAATTTAACTTAAA
* * ** * *
10418 ATTAATTATGAGATTATAAAACTATTTAAAGCGAGTAATAATACTTTTGAAGAAATCAGTGACTA
64 ATTAATTATGAGATTATAAAACTATTTAAACCGAGCAATAAGGCTTTTGAAAAAATGAGTGACTA
* * * ** * * *
10483 TAAATGAACTTTTCTTACC-AATGAATACCTTTTTGTTTATGTTTCCCAAGGCAAACATTCAATT
129 TAAATGAACTTTTCTT-CCTAATGAATACATTTTTCTTCACATTTCCTAAGACAGACATTCAATT
* * * * **********
10547 ATAATCTGCTCCAACC-AAAATATAAAAAAATTCATCCTAAAATCAANNNNNNNNNNATAAAACT
193 ATAATCTGTTCGAACCAAAAATATAAAAGAATTCAACCTAAAATCAATTATGAGATCATAAAACT
* * * ** * * *
10611 ATTTAAAGCGAGTAATCATGCTTTTGAAGGAATGACTAACTATAAATAGACTCTTTTTGCCAATG
258 ATTTAAAGCGAGTAATAAGGCTTTTGAAAGAATGGGTGACTATAAATAGACTTTTTTTACCAATG
* * *
10676 AATGATTTTTTTCTTCATG
323 AATGATCTTTTTCTTTACG
** * * * * * *
10695 TTTCCCAAGGTAGACATTTAATTATAGTTTGTTTTAACCATAATGTAAAAAAGTTCAACCTAAAA
1 TTT-TTAAGGTAGACATTTAATTATAGTCTGTTTTAACAAAAATGTAAAAAAATTTAACTTAAAA
* ** * * * **
10760 TCAATTATTTGATTATAAAACTATTTAAAGC-ATGTAATAAGGCTTTCGAAGGAAT-AGGTGACT
65 TTAATTATGAGATTATAAAACTATTTAAACCGA-GCAATAAGGCTTTTGAAAAAATGA-GTGACT
* * * * * ** ** ** *
10823 ATAAACGGACTTTTCTT-ATAAGTGAATGCCTTTTGATTCATGTTT-CTCAAGGTAAACATTCAA
128 ATAAATGAACTTTTCTTCCTAA-TGAATACATTTTTCTTCACATTTCCT-AAGACAGACATTCAA
* ** ** * * * *
10886 TTATAACCTGTT-TTAGGAAAAATAT-AAAGAAATTGAACATAAAATCAATTTTGGGA-CTATAA
191 TTATAATCTGTTCGAACCAAAAATATAAAAG-AATTCAACCTAAAATCAATTATGAGATC-ATAA
* *
10948 AA-TCAGTTAAAGCGAGTAATAAGGCTTTTG-AAGAAATGGGTGACCATAAAT-GATCTTTTTTT
254 AACT-ATTTAAAGCGAGTAATAAGGCTTTTGAAAG-AATGGGTGACTATAAATAGA-CTTTTTTT
** * * * *
11010 GTCAATGAATG-CCTTTTCCTTCATG
316 ACCAATGAATGATCTTTTTCTTTACG
* * ********
11035 TTTCCTAAGGTAGACATTCAATTATAGTCTGTTTTAACTAAAAATGTAAAAAAATTTNNNNNNNN
1 TTT-TTAAGGTAGACATTTAATTATAGTCTGTTTTAAC-AAAAATGTAAAAAAATTTAACTTAAA
*** * * * *** * *
11100 NNCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGATGGAGTGGGTGACTA
64 ATTAATTATGAGATTATAAAACTATTTAAACCGAGCAATAAGGCTTTTGAAAAAATGAGTGACTA
* * * * **
11165 TAAATGAACTTTTCTTACC-AACGAATACCTCTTTCTTCACATTTCCCAAGGTAGACATTCAATT
129 TAAATGAACTTTTCTT-CCTAATGAATACATTTTTCTTCACATTTCCTAAGACAGACATTCAATT
* * * * *
11229 ATAATCTGTTCTAACTAAAAATGTAAAAAAATTCAACTTAAA
193 ATAATCTGTTCGAACCAAAAATATAAAAGAATTCAACCTAAA
11271 NNNNNNNNNN
Statistics
Matches: 3045, Mismatches: 810, Indels: 274
0.74 0.20 0.07
Matches are distributed among these distances:
338 3 0.00
339 148 0.05
340 354 0.12
341 999 0.33
342 913 0.30
343 575 0.19
344 51 0.02
345 2 0.00
ACGTcount: A:0.37, C:0.12, G:0.13, T:0.35
Consensus pattern (341 bp):
TTTTTAAGGTAGACATTTAATTATAGTCTGTTTTAACAAAAATGTAAAAAAATTTAACTTAAAAT
TAATTATGAGATTATAAAACTATTTAAACCGAGCAATAAGGCTTTTGAAAAAATGAGTGACTATA
AATGAACTTTTCTTCCTAATGAATACATTTTTCTTCACATTTCCTAAGACAGACATTCAATTATA
ATCTGTTCGAACCAAAAATATAAAAGAATTCAACCTAAAATCAATTATGAGATCATAAAACTATT
TAAAGCGAGTAATAAGGCTTTTGAAAGAATGGGTGACTATAAATAGACTTTTTTTACCAATGAAT
GATCTTTTTCTTTACG
Found at i:9963 original size:170 final size:168
Alignment explanation
Indices: 6700--12295 Score: 2516
Period size: 171 Copynumber: 32.7 Consensus size: 168
6690 NNNNNNNNNN
* * * * *
6700 GCTTTTGAAGGAATGGGTGACTATAAATGAACTTTTTTTTTTC-AATGAATGCCTTTTTCTTTAT
1 GCTTTTGAAGAAATGGGTGACTATAAATGGAC--TTTTTTTGCAAATGAATGACTTTTTCTTCAT
* * * ** *
6764 GTTT-CTAAAGGTAAAAATTGAATCGTAGTCTGTTTTAACCAAAAATGTAAAAGAATTCTAC-TA
64 GTTTCCT-AAGGTAGACATTCAATTATAGTCTGTTTTAACC-AAAATGTAAAA-AATTCAACTTA
* * ******
6827 CAAATTAATTATGAAATTATAAAATCATTTAAAGCGAGTNNNNNN
126 -AAATCAATTATGAGATTATAAAA-CATTTAAAGCGAGTAATAAG
**** * * * * * * * * **
6872 NNNNTTGAA-AGAATGAGAGACTATAAATGGACTATTCTTGCTAATGAATGCCTTTCTCTACACA
1 GCTTTTGAAGA-AATGGGTGACTATAAATGGACTTTTTTTGCAAATGAATGACTTTTTCTTCATG
** * * * * *
6936 TTTTTTAATGTATACATTCAATCATAGTCTGTTTTAACCAAATATATAAAAAAATTTAACTTAAA
65 TTTCCTAAGGTAGACATTCAATTATAGTCTGTTTTAACCAAA-ATGT-AAAAAATTCAACTTAAA
* * * * * *
7001 ATTAATTTTGAGATTATAAAACTATTTAAACCGAGCAGTTAG
128 ATCAATTATGAGATTATAAAAC-ATTTAAAGCGAGTAATAAG
* * * * *
7043 GCTTTTGAAAAAATGGATGACTATAAATAGAATTGTTTTTATC-AATGAAT-ACATTTTTCTTCA
1 GCTTTTGAAGAAATGGGTGACTATAAATGGACTT-TTTTT-GCAAATGAATGAC-TTTTTCTTCA
* * * * **********
7106 TATTTCTTGAGATAGACATTCAATTATAGTCNNNNNNNNNNAAAAATGTAAAAAAGTTCAACTTA
63 TGTTTCCTAAGGTAGACATTCAATTATAGTC-TGTTTTAACCAAAATGTAAAAAA-TTCAACTTA
* * * * *
7171 AAATTAATTATGAGATCATAAAACCTTTTAAAGGGTGTAATAAG
126 AAATCAATTATGAGATTATAAAA-CATTTAAAGCGAGTAATAAG
* ********** * * * *
7215 GCTTTTGAAGGAATGGGTGACNNNNNNNNNNCTTTTTTTACCAATGAAT-ATCTTTTTCTTTACG
1 GCTTTTGAAGAAATGGGTGACTATAAATGGACTTTTTTTGCAAATGAATGA-CTTTTTCTTCATG
* * * * *
7279 TTTCTTAAGGTAGACATTTAATTATAGTTTGTTTTAACTAAAAATGTAAAAAAATTTAACTTAAA
65 TTTCCTAAGGTAGACATTCAATTATAGTCTGTTTTAAC-CAAAATGT-AAAAAATTCAACTTAAA
*
7344 ATTAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAG
128 ATCAATTATGAGATTATAAAA-CATTTAAAGCGAGTAATAAG
* * * * * * * *
7386 GCTTTTGAAGGAATGAGTGACTATAAATGAACTTTTCTTCCTAATGAAT-ACTTTTTTCTTTACG
1 GCTTTTGAAGAAATGGGTGACTATAAATGGACTTTTTTTGCAAATGAATGAC-TTTTTCTTCATG
* * * * ** * * *
7450 TTTCCTAAGGCAGATATTCAATTATAATGTGTTCGAACCAAAAATATAAAAGAATTCATCCTAAA
65 TTTCCTAAGGTAGACATTCAATTATAGTCTGTTTTAACC-AAAATGTAAAA-AATTCAACTTAAA
*
7515 ATCAATTATGAGATTATAAAACTATTTAAAGCGAGTAATCAG
128 ATCAATTATGAGATTATAAAAC-ATTTAAAGCGAGTAATAAG
* * * *
7557 GCTTTTGAA-AGAATGGGTGACTATAAATAGACTTTTTTTGCCAATGAATGATTTTTTTCTTTAT
1 GCTTTTGAAGA-AATGGGTGACTATAAATGGACTTTTTTTGCAAATGAATGA-CTTTTTCTTCAT
* * *
7621 GTTTTCTAAGGTAGACATTTAATTATAGTCTGTTTTAACCAAAATGTAAAAAATTTCAACCTAAA
64 GTTTCCTAAGGTAGACATTCAATTATAGTCTGTTTTAACCAAAATGTAAAAAA-TTCAACTTAAA
* * ** *
7686 GTTAATTATTTGATTATAAAACTATTTAAAGTGAGTAATAAG
128 ATCAATTATGAGATTATAAAAC-ATTTAAAGCGAGTAATAAG
* * * * * * ** * * * *
7728 CCTTTTGAAGGAATAGGTGACTCTAAACGGACTTTTCTTATAAGTGAATGCCTTTTGCTTCATAT
1 GCTTTTGAAGAAATGGGTGACTATAAATGGACTTTTTTTGCAAATGAATGACTTTTTCTTCATGT
** * * ** *** * * *
7793 TT-CTCATCGTAAACATTCAATTAGAACCTGTTTTAGGAAAAATATAAAGAAATTGAACATAAAA
66 TTCCT-AAGGTAGACATTCAATTATAGTCTGTTTTAACCAAAATGTAAA-AAATTCAACTTAAAA
* * * *****
7857 TCTATT-TTAGGACTATAAAATCATTTAAAGCGAGTANNNNN
129 TCAATTATGA-GATTATAAAA-CATTTAAAGCGAGTAATAAG
***** ** * * *
7898 NNNNNTGAAGAAATGGGTGACTATAAATGTTCTTTTTTTTC-AATGAATGCCTTTTTCTGCATGT
1 GCTTTTGAAGAAATGGGTGACTATAAATGGACTTTTTTTGCAAATGAATGACTTTTTCTTCATGT
* * * *
7962 TTCTTGAGGTAGACATTCAATTATAATCTGTTTTTAACCAAAAATATAAAAAAAATTCAACTTAA
66 TTCCTAAGGTAGACATTCAATTATAGTCTG-TTTTAACC-AAAATGT--AAAAAATTCAACTTAA
********** * *
8027 ANNNNNNNNNNAGATTATAAAACCATTTAAAACGTGTAATAAG
127 AATCAATTATGAGATTATAAAA-CATTTAAAGCGAGTAATAAG
* * * * * * *
8070 GCTTTCGAA-AGAATGGGTGACTATAAATGGATTTTTTTTACCACTAAAT-ATCTTTTTCTTTAT
1 GCTTTTGAAGA-AATGGGTGACTATAAATGGACTTTTTTTGCAAATGAATGA-CTTTTTCTTCAT
* * * ********* *
8133 GTTT-CTCGAGGTAGACATTCAATTACAGTCTGTTTTAACTAAAAANNNNNNNNNNTTTAACTTA
64 GTTTCCT-AAGGTAGACATTCAATTATAGTCTGTTTTAAC-CAAAA-TGTAAAAAATTCAACTTA
* * * *
8197 AAATCAATTATGAGTTTATAAAACCATCTAAAGTGAGTAATAAA
126 AAATCAATTATGAGATTATAAAA-CATTTAAAGCGAGTAATAAG
* * ** * * * * ********
8241 GCTTTTGAAGGAGTGGGTGACTATAAATAAACTTTTCTTACCAATGAATGCCTTTTNNNNNNNNN
1 GCTTTTGAAGAAATGGGTGACTATAAATGGACTTTTTTTGCAAATGAATGACTTTT-TCTTCATG
* * * * * *
8306 NTTCC-AAGGTAAACATTCAATTATAATCTATTCTAACCAAAAATGTAAAAAATTCAACCTAAAA
65 TTTCCTAAGGTAGACATTCAATTATAGTCTGTTTTAACC-AAAATGTAAAAAATTCAACTTAAAA
**********
8370 NNNNNNNNNNGATTATAAAACTATTTAAA-CTGAGTAATAAG
129 TCAATTATGAGATTATAAAAC-ATTTAAAGC-GAGTAATAAG
* * * * * *
8411 GCTTATGAAGAAATAGGTAACTATAAATGGACTTTTTTTTACCAAT-AA-GTACCTTTTGCTTCA
1 GCTTTTGAAGAAATGGGTGACTATAAATGGAC-TTTTTTTGCAAATGAATG-A-CTTTTTCTTCA
** * * * * *
8474 CATTTCTTGAGGTTGACATTCAATTATAGTTTGTTTTAACCCTAAATGTAAAAAAATTCAACTTA
63 TGTTTCCTAAGGTAGACATTCAATTATAGTCTGTTTTAA-CCAAAATGT-AAAAAATTCAACTTA
********** *
8539 AAATCANNNNNNNNNNTATAAACCCATTTAAAGCGAGTAATAAG
126 AAATCAATTATGAGATTATAAA-ACATTTAAAGCGAGTAATAAG
* * * * ** * * * *
8583 ACCTTTGAAGGAATGGGTAACTATAAATGGACTTTGCTTGCCAATGAAT-ATCGTTTTCTTTACG
1 GCTTTTGAAGAAATGGGTGACTATAAATGGACTTTTTTTGCAAATGAATGA-CTTTTTCTTCATG
* * * *
8647 TTTCTTAAGGTAGACATTCAATTATTA-TTTGTTTTAACAAAAAATGTAAAATTAA-TCAAATTA
65 TTTCCTAAGGTAGACATTCAATTA-TAGTCTGTTTTAAC-CAAAATGTAAAA--AATTCAACTTA
* ********
8710 AAATCAATTATGAGATTGTAAAAC-TNNNNNNNNNNAGTAATAAG
126 AAATCAATTATGAGATTATAAAACAT--TTAAAGCGAGTAATAAG
* * * * * * ** **
8754 GCTTTTGAAGGAATAGGAGACTATTAATGGA-TTTTTATTGCCAATAAAT-TTTTTTTCTTCAAC
1 GCTTTTGAAGAAATGGGTGACTATAAATGGACTTTTT-TTGCAAATGAATGACTTTTTCTTCATG
* * * * * *********
8817 TTTCTTGAGGCAGACATTCAATTATAGTCTGTTTTGACAAAAAATGTAAAANNNNNNNNNNTAAA
65 TTTCCTAAGGTAGACATTCAATTATAGTCTGTTTTAAC-CAAAATGTAAAA-AATTCAACTTAAA
* *
8882 ATCAATTATGAGATTATAAAACCATTTAAAGCGAATAAAAAG
128 ATCAATTATGAGATTATAAAA-CATTTAAAGCGAGTAATAAG
* * * * * * *
8924 ACTTTTGATGGAATGTGTGACTATAAATGGACTTTTATTGTC-AATAAATGTC-TTTT-TTCATG
1 GCTTTTGAAGAAATGGGTGACTATAAATGGACTTTTTTTG-CAAATGAATGACTTTTTCTTCATG
* * ** * *
8986 TTTCTTAAGGTAGACATTTAATTACT-GTCTGTTTTAATGAAAAATATAAAAATAATCAACTTAA
65 TTTCCTAAGGTAGACATTCAATTA-TAGTCTGTTTTAA-CCAAAATGTAAAAA-ATTCAACTTAA
* *
9050 AATTAATTATGAGATT-TAAAAACCATTTAAA-CAAAAGTAATAAG
127 AATCAATTATGAGATTAT-AAAA-CATTTAAAGC--GAGTAATAAG
* * * *
9094 GCTTTTGAA-ATAATGGGTAACTATAAATGGACTTTTTTTGAAAATAAAT-ACCTTTTTCTTCAC
1 GCTTTTGAAGA-AATGGGTGACTATAAATGGACTTTTTTTGCAAATGAATGA-CTTTTTCTTCAT
** * *
9157 GTTTTTTAAGGTAGACATTTAATTATAGTCTG-TTTGACCAAAAATGTAAGAAAATTCAACTTAA
64 GTTTCCTAAGGTAGACATTCAATTATAGTCTGTTTTAACC-AAAATGTAA-AAAATTCAACTTAA
* ********* * *
9221 AATTAATTATGAGATTATAANNNNNNNNNNAGTGATTAATAAG
127 AATCAATTATGAGATTATAA-AACATTTAAAGCGAGTAATAAG
* * * ** * * *
9264 GCTTTTGAAGGAATGGGTGACTATAAATGGACTTTGCTTAT-C-AATGAACGGTTTTTTGTACAC
1 GCTTTTGAAGAAATGGGTGACTATAAATGGACTTT--TTTTGCAAATGAATGACTTTTTCTTCAT
* * * ********* *
9327 GTTTCCTAAAGTAGACATTCAATTATAATCTGTTCTAACCAAAA-GCTANNNNNNNNNNACCT-A
64 GTTTCCTAAGGTAGACATTCAATTATAGTCTGTTTTAACCAAAATG-TA-AAAAATTCAACTTAA
* *
9390 AATCAATTATGAGATTATAAGACTATTTAAAGCGAGCAATAAG
127 AATCAATTATGAGATTATAAAAC-ATTTAAAGCGAGTAATAAG
* * * * * * * * *
9433 GCTTATGAAGAAATGAGTGACAATAAATAGACTTTTTTTTACAAATAAAT-ACCTATTTCTTTAC
1 GCTTTTGAAGAAATGGGTGACTATAAATGGAC-TTTTTTTGCAAATGAATGA-CTTTTTCTTCAT
* * * *
9497 ATTT-CTCGAGGCAGACATTCAATTATAGTCCGTTTTAACCAAAAATGTGAAAAAATTCAACTTA
64 GTTTCCT-AAGGTAGACATTCAATTATAGTCTGTTTTAACC-AAAATGT-AAAAAATTCAACTTA
* * *
9561 CAATCAATTATGAGATTATAAAACCATCTACAGCGAGTAATAAG
126 AAATCAATTATGAGATTATAAAA-CATTTAAAGCGAGTAATAAG
* * * * * * * * *
9605 GTTTTTTAAAAAATAGGTGACTCTAAACGGACTTTTCTTGCCAGA-GAATG-CCTTTTCTT--TG
1 GCTTTTGAAGAAATGGGTGACTATAAATGGACTTTTTTTG-CAAATGAATGACTTTTTCTTCATG
* * * * * * *******
9666 TATAT-CTCAAGGTAAACATTGAATTATAATCTATATTAATCAAAAATGTAAAAAAANNNNNNNN
65 T-T-TCCT-AAGGTAGACATTCAATTATAGTCTGTTTTAA-CCAAAATGT-AAAAAA-TTCAACT
** * * * *
9730 NNAGATCAATTTTGAGATTATAAAATCATTTAGAGCGAGCAATAAG
124 TAAAATCAATTATGAGATTATAAAA-CATTTAAAGCGAGTAATAAG
* * * * *
9776 GCTTTTGACGGAATGGGTGACTATAAATGGACTTTTTTTGCAAATGAATGATTTTTTCTACACGT
1 GCTTTTGAAGAAATGGGTGACTATAAATGGACTTTTTTTGCAAATGAATGACTTTTTCTTCATGT
* * * **
9841 TTCCTAAGGTAAATATTTAATTATAGTCAATTTTAACCAAAATGTAAAAAACTTCAACTTAAAAT
66 TTCCTAAGGTAGACATTCAATTATAGTCTGTTTTAACCAAAATGTAAAAAA-TTCAACTTAAAAT
** * * *
9906 TGATTATGAGATTATAAAATCATTTAAGGCAAGGAATAAG
130 CAATTATGAGATTATAAAA-CATTTAAAGCGAGTAATAAG
* * * * *
9946 GCTTTTGAAGAAATGGGTGACTGTAAATAGACTTTTTTTGCCAATGAATGCCTTTTTCTTTATGT
1 GCTTTTGAAGAAATGGGTGACTATAAATGGACTTTTTTTGCAAATGAATGACTTTTTCTTCATGT
* * * * *
10011 TT-CTAAAGGTAAAAATTCAATTCTAGTCTGTTTTAACTAAAAATGTAAAAGAATTCAACTAAAA
66 TTCCT-AAGGTAGACATTCAATTATAGTCTGTTTTAAC-CAAAATGTAAAA-AATTCAACTTAAA
10075 ATCAATTATGAGATTA-AAATATCATTTAAAGCGAGTAATAAG
128 ATCAATTATGAGATTATAAA-A-CATTTAAAGCGAGTAATAAG
********** * * * *
10117 GCTTTTGAAGNNNNNNNNNNCTATAAATGGACTTTTCTTGTC-AATGAATGCCTTTCTCTTCACG
1 GCTTTTGAAGAAATGGGTGACTATAAATGGACTTTTTTTG-CAAATGAATGACTTTTTCTTCATG
** * * *
10181 TTTTTTGAGGTAGACATTCAATCATAGTCTGTTTTAACCAAAACTATAAAAAAATTCAACTTAAA
65 TTTCCTAAGGTAGACATTCAATTATAGTCTGTTTTAACCAAAA-TGT-AAAAAATTCAACTTAAA
* * * *
10246 ATTAATTTTGAGACTATAAAACTATTTAAAGCGAGTAGTAAG
128 ATCAATTATGAGATTATAAAAC-ATTTAAAGCGAGTAATAAG
* * * * *
10288 GCTTTTGAAGAAATGAGTGACTATCAATAGACTTTTTTT-TATCAATGAATG-CATTTTTCTTGA
1 GCTTTTGAAGAAATGGGTGACTATAAATGGACTTTTTTTGCA--AATGAATGAC-TTTTTCTTCA
* * * * ***********
10351 TATTTCTTGAGATAGACATTCAATTATAGTCTGTTTTAACCAAAAATGTAAAANNNNNNNNNNNN
63 TGTTTCCTAAGGTAGACATTCAATTATAGTCTGTTTTAACC-AAAATGTAAAA-AATTCAACTTA
* *
10416 AAATTAATTATGAGATTATAAAACTATTTAAAGCGAGTAATAAT
126 AAATCAATTATGAGATTATAAAAC-ATTTAAAGCGAGTAATAAG
* ** * * * * * *
10460 ACTTTTGAAGAAATCAGTGACTATAAATGAACTTTTCTTACCAATGAAT-ACCTTTTTGTTTATG
1 GCTTTTGAAGAAATGGGTGACTATAAATGGACTTTTTTTGCAAATGAATGA-CTTTTTCTTCATG
* * * * * ** * * *
10524 TTTCCCAAGGCAAACATTCAATTATAATCTGCTCCAACCAAAATATAAAAAAATTCATCCTAAAA
65 TTTCCTAAGGTAGACATTCAATTATAGTCTGTTTTAACCAAAATGT-AAAAAATTCAACTTAAAA
********** * *
10589 TCAANNNNNNNNNNATAAAACTATTTAAAGCGAGTAATCAT
129 TCAATTATGAGATTATAAAAC-ATTTAAAGCGAGTAATAAG
* ** * * * * *
10630 GCTTTTGAAGGAATGACTAACTATAAATAGACTCTTTTTGCCAATGAATGATTTTTTTCTTCATG
1 GCTTTTGAAGAAATGGGTGACTATAAATGGACTTTTTTTGCAAATGAATGA-CTTTTTCTTCATG
* * * * *
10695 TTTCCCAAGGTAGACATTTAATTATAGTTTGTTTTAACCATAATGTAAAAAAGTTCAACCTAAAA
65 TTTCCTAAGGTAGACATTCAATTATAGTCTGTTTTAACCAAAATGTAAAAAA-TTCAACTTAAAA
**
10760 TCAATTATTTGATTATAAAACTATTTAAAGC-ATGTAATAAG
129 TCAATTATGAGATTATAAAAC-ATTTAAAGCGA-GTAATAAG
* * * * * ** * * **
10801 GCTTTCGAAGGAATAGGTGACTATAAACGGACTTTTCTTATAAGTGAATGCCTTTTGATTCATGT
1 GCTTTTGAAGAAATGGGTGACTATAAATGGACTTTTTTTGCAAATGAATGACTTTTTCTTCATGT
* ** *** * * *
10866 TT-CTCAAGGTAAACATTCAATTATAACCTGTTTTAGGAAAAATATAAAGAAATTGAACATAAAA
66 TTCCT-AAGGTAGACATTCAATTATAGTCTGTTTTAACCAAAATGTAAA-AAATTCAACTTAAAA
* * * *
10930 TCAATTTTGGGACTATAAAATCAGTTAAAGCGAGTAATAAG
129 TCAATTATGAGATTATAAAA-CATTTAAAGCGAGTAATAAG
* * *
10971 GCTTTTGAAGAAATGGGTGACCATAAAT-GATCTTTTTTTGTC-AATGAATGCCTTTTCCTTCAT
1 GCTTTTGAAGAAATGGGTGACTATAAATGGA-CTTTTTTTG-CAAATGAATGACTTTTTCTTCAT
* ********
11034 GTTTCCTAAGGTAGACATTCAATTATAGTCTGTTTTAACTAAAAATGTAAAAAAATTTNNNNNNN
64 GTTTCCTAAGGTAGACATTCAATTATAGTCTGTTTTAAC-CAAAATGT-AAAAAATTCAACTTAA
***
11099 NNNCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAG
127 AATCAATTATGAGATTATAAAA-CATTTAAAGCGAGTAATAAG
* * * * * * * * * **
11142 GCTTTTGATGGAGTGGGTGACTATAAATGAACTTTTCTTACCAACGAAT-ACCTCTTTCTTCACA
1 GCTTTTGAAGAAATGGGTGACTATAAATGGACTTTTTTTGCAAATGAATGA-CTTTTTCTTCATG
* * * *
11206 TTTCCCAAGGTAGACATTCAATTATAATCTGTTCTAACTAAAAATGTAAAAAAATTCAACTTAAA
65 TTTCCTAAGGTAGACATTCAATTATAGTCTGTTTTAAC-CAAAATGT-AAAAAATTCAACTTAAA
***********************
11271 NNNNNNNNNNNNNNNNNNNNNNNNTTTAAAGCGAGTAATAAG
128 -ATCAATTATGAGATTATAAAACATTTAAAGCGAGTAATAAG
* * * *
11313 GCTTGTGAAGAAATAGGTGACTATAAATGGACTTTTTTTTTACCAATGAAT-ATCTTTTTCTTCA
1 GCTTTTGAAGAAATGGGTGACTATAAATGGAC--TTTTTTTGCAAATGAATGA-CTTTTTCTTCA
** * * * * *
11377 CATTT-CTCGAGGTTGACATCCAATTATAGTCTGTTTTAATCAAAAATATAAAAAAATTCAACTT
63 TGTTTCCT-AAGGTAGACATTCAATTATAGTCTGTTTTAA-CCAAAATGT-AAAAAATTCAACTT
*******************************
11441 AAAATCAATTNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNAAG
125 AAAATCAATT-ATGAGATTATAAAACATTTAAAGCGAGTAATAAG
* * * * * *
11486 GCTTTTGAAGAAATGGGAGACTATAAATGGACTTTTCTTGCCAATGAATGCCTTTTT-TTAACTA
1 GCTTTTGAAGAAATGGGTGACTATAAATGGACTTTTTTTGCAAATGAATGACTTTTTCTTCA-TG
* * * * * * * *
11550 TTT--TGAGATAGACATTCAATCATACTCTGTTTTAACAAAAAATATAGAAACATTGAACTTAAA
65 TTTCCTAAGGTAGACATTCAATTATAGTCTGTTTTAAC-CAAAATGTA-AAAAATTCAACTTAAA
*********
11613 ATCAATTATGAGATTNNNNNNNNNNTTAAAGCGAGTAATAAG
128 ATCAATTATGAGATT-ATAAAACATTTAAAGCGAGTAATAAG
* * * * * * * *
11655 GCTTCTGAA-AGAATAGATGATTTTAAATGGACTTTTCTTGTC-TATGAAAG-CTTTTTTCTTCA
1 GCTTTTGAAGA-AATGGGTGACTATAAATGGACTTTTTTTG-CAAATGAATGAC-TTTTTCTTCA
** * * * * * *
11717 CCTTT-CTCAAGGTAGACATTCAATTATAATTTGTTTTGACTAAAAATATAAAAAAAATTAAACT
63 TGTTTCCT-AAGGTAGACATTCAATTATAGTCTGTTTTAAC-CAAAATGT--AAAAAATTCAACT
* * * *
11781 TAAAATCAATTTTGGGATTCTAAAACCATTTAAAGCGAGCAATAAG
124 TAAAATCAATTATGAGATTATAAAA-CATTTAAAGCGAGTAATAAG
* ********** * *
11827 GCTTTTGAAGGANNNNNNNNNNATAAATGAACTTTTTTTGTC-AATGAATGCCTTTTTCTTCAT-
1 GCTTTTGAAGAAATGGGTGACTATAAATGGACTTTTTTTG-CAAATGAATGACTTTTTCTTCATG
* * * * **
11890 ATTCTTCAAGATAGACATTCAATTATAGTCTGTTTTGATA-GAAAATACAAGAAAATTCAACTTA
65 TTTCCT-AAGGTAGACATTCAATTATAGTCTGTTTT-A-ACCAAAATGTAA-AAAATTCAACTTA
* * * *
11954 AAATCAAATATGAGATTATAAAATTATTTAAAGTGGGTAATAAG
126 AAATCAATTATGAGATTATAAAA-CATTTAAAGCGAGTAATAAG
* ** * * * *
11998 GCTTTTGAAGGAATAAGTGACTATAAATGGACTATTTTTGTC-AATGAAT-ACCTTTTTCCTGAC
1 GCTTTTGAAGAAATGGGTGACTATAAATGGACTTTTTTTG-CAAATGAATGA-CTTTTTCTTCAT
* * * * * * * * * * * *
12061 GTTTCTTGATGCAGACATTCAATTATAATATGTTCTAGCAAAAAATATAAAAAAATCCAACGTAA
64 GTTTCCTAAGGTAGACATTCAATTATAGTCTGTTTTAAC-CAAAATGT-AAAAAATTCAACTTAA
* * * *
12126 AATCAATTATGAGATTAAAAAATTATTTAAGGCGAGTAATAGG
127 AATCAATTATGAGATTATAAAA-CATTTAAAGCGAGTAATAAG
* * * *
12169 GCTTATGAAGAAATGGATGACTATAAATGGACTTTTTTTGCCAATGAATG-CTTTTTTTCTCATG
1 GCTTTTGAAGAAATGGGTGACTATAAATGGACTTTTTTTGCAAATGAATGACTTTTTCT-TCATG
* * *
12233 TTT-CTAGATGTTGACATTCAATTATAGTCTATTTTAACCAAAAATGTAAAAAAATTCAACTTA
65 TTTCCTA-AGGTAGACATTCAATTATAGTCTGTTTTAACC-AAAATGT-AAAAAATTCAACTTA
12296 NNNNNNNNNN
Statistics
Matches: 4069, Mismatches: 1164, Indels: 383
0.72 0.21 0.07
Matches are distributed among these distances:
168 10 0.00
169 306 0.08
170 966 0.24
171 1832 0.45
172 757 0.19
173 194 0.05
174 4 0.00
ACGTcount: A:0.36, C:0.11, G:0.13, T:0.35
Consensus pattern (168 bp):
GCTTTTGAAGAAATGGGTGACTATAAATGGACTTTTTTTGCAAATGAATGACTTTTTCTTCATGT
TTCCTAAGGTAGACATTCAATTATAGTCTGTTTTAACCAAAATGTAAAAAATTCAACTTAAAATC
AATTATGAGATTATAAAACATTTAAAGCGAGTAATAAG
Found at i:11996 original size:343 final size:330
Alignment explanation
Indices: 11508--12178 Score: 643
Period size: 343 Copynumber: 2.0 Consensus size: 330
11498 ATGGGAGACT
* *
11508 ATAAATGGACTTTTCTTGCCAATGAATGCCTTTTTTTAACTATTTTGAGATAGACATTCAATCAT
1 ATAAATGAACTTTTCTTGCCAATGAATGCCTTTTTTTAACTATTTTAAGATAGACATTCAATCAT
* * * **********
11573 ACTCTGTTTTAACAAAAAATATAGAAACATTGAACTTAAAATCAATTATGAGATTNNNNNNNNNN
66 ACTCTGTTTTAACAAAAAATAAAGAAACATTCAACTTAAAATCAAATATGAGATTATAAAATTAT
* * *
11638 TTAAAGCGAGTAATAAGGCTTCTGAAAGAAT-AGATGATTTTAAATGGACT-TTTCTTGTCTATG
131 TTAAAGCGAGTAATAAGGCTTCTGAAAGAATAAG-TGACTATAAATGGACTATTT-TTGTCAATG
* * * * * *
11701 AA-AGCTTTTTTCTTCACCTTTCTCAAGGTAGACATTCAATTATAATTTGTT-TTGACTAAAAAT
194 AATA-CCTTTTTCCTCACCTTTCTCAAGGCAGACATTCAATTATAATATGTTCTAG-CAAAAAAT
* * * * **
11764 ATAAAAAAAATTAAACTTAAAATCAATTTTGGGATTCTAAAACCATTTAAAGCGAGCAATAAGGC
257 AT-AAAAAAATCAAACGTAAAATCAATTATGAGATTAAAAAACCATTTAAAGCGAGCAATAAGGC
*
11829 TTTTGAAGGA
321 TTATGAAGGA
* * *
11839 NNNNNNNNNNATAAATGAACTTTTTTTGTCAATGAATGCCTTTTTCTTCA-TATTCTTCAAGATA
1 ----------ATAAATGAACTTTTCTTGCCAATGAATGCCTTTTT-TTAACTATT-TT-AAGATA
* * * * *
11903 GACATTCAATTATAGTCTGTTTTGATAGAAAATACAAGAAA-ATTCAACTTAAAATCAAATATGA
53 GACATTCAATCATACTCTGTTTTAACAAAAAATA-AAGAAACATTCAACTTAAAATCAAATATGA
* * * *
11967 GATTATAAAATTATTTAAAGTGGGTAATAAGGCTTTTGAAGGAATAAGTGACTATAAATGGACTA
117 GATTATAAAATTATTTAAAGCGAGTAATAAGGCTTCTGAAAGAATAAGTGACTATAAATGGACTA
* * ** *
12032 TTTTTGTCAATGAATACCTTTTTCCTGACGTTTCTTGATGCAGACATTCAATTATAATATGTTCT
182 TTTTTGTCAATGAATACCTTTTTCCTCACCTTTCTCAAGGCAGACATTCAATTATAATATGTTCT
* ** *
12097 AGCAAAAAATATAAAAAAATCCAACGTAAAATCAATTATGAGATTAAAAAATTATTTAAGGCGAG
247 AGCAAAAAATATAAAAAAATCAAACGTAAAATCAATTATGAGATTAAAAAACCATTTAAAGCGAG
* *
12162 TAATAGGGCTTATGAAG
312 CAATAAGGCTTATGAAG
12179 AAATGGATGA
Statistics
Matches: 268, Mismatches: 54, Indels: 15
0.80 0.16 0.04
Matches are distributed among these distances:
341 36 0.13
342 62 0.23
343 157 0.59
344 13 0.05
ACGTcount: A:0.38, C:0.11, G:0.13, T:0.35
Consensus pattern (330 bp):
ATAAATGAACTTTTCTTGCCAATGAATGCCTTTTTTTAACTATTTTAAGATAGACATTCAATCAT
ACTCTGTTTTAACAAAAAATAAAGAAACATTCAACTTAAAATCAAATATGAGATTATAAAATTAT
TTAAAGCGAGTAATAAGGCTTCTGAAAGAATAAGTGACTATAAATGGACTATTTTTGTCAATGAA
TACCTTTTTCCTCACCTTTCTCAAGGCAGACATTCAATTATAATATGTTCTAGCAAAAAATATAA
AAAAATCAAACGTAAAATCAATTATGAGATTAAAAAACCATTTAAAGCGAGCAATAAGGCTTATG
AAGGA
Found at i:13416 original size:171 final size:171
Alignment explanation
Indices: 12401--13429 Score: 744
Period size: 171 Copynumber: 6.0 Consensus size: 171
12391 NNNNNAAGCA
* ***
12401 AGTAATAAGGCTTTCG-AAGGCATGGGTGACTATAAATGGACTTTTTTTGTTGATGAATGACTTT
1 AGTAATAAGGCTTT-GAAAGGCATGGGTGACTATAAATGGACTTTTCTTGCCAATGAATGACTTT
* * * * * ** *
12465 TTCTCCATGTTTCCCAAGGCCAACACTCAATTCTAAT-TTTTTTAACAAAAAATGTAAACAAATT
65 TTCTTCATGTTTCTCAAGGCAAACACTCAATTATAATCTGTTTTAATGAAAAATGTAAAAAAATT
** * * *
12529 CAACTTGGAATCAATTTTGAGATTATAAAACCATTCAAAGCG
130 CAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGTG
* * * * * * * *** *
12571 TGTAATAAAGCTCTGGAAGGGATGGGTGGCTATAAATGGACTTTTTTTATGAATGAGTGACTTTT
1 AGTAATAAGGCTTTGAAAGGCATGGGTGACTATAAATGGACTTTTCTTGCCAATGAATGACTTTT
* * ** * * * *
12636 TCTTCACGTTTTTCAAGATAAACACTAAATTATAATCTGTTTTGATGAAAAATGCAAAAAGATTC
66 TCTTCATGTTTCTCAAGGCAAACACTCAATTATAATCTGTTTTAATGAAAAATGTAAAAAAATTC
********** *
12701 AACTTNNNNNNNNNNATGAGATTATAAAACCATTTAAAGTA
131 AACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGTG
* * ** * * *
12742 AGTATTAAGCCTTCCAAAGGCATGGATGACTACAAATAGACTTTTCTTGCCAATGAAT-AGCTTT
1 AGTAATAAGGCTTTGAAAGGCATGGGTGACTATAAATGGACTTTTCTTGCCAATGAATGA-CTTT
** * *
12806 TTCTTCATGTTTC-CAAAAACCAACACTCAATTATAATCTGTTTTGATGAAAAATGTAAAAAAAC
65 TTCTTCATGTTTCTC-AAGGCAAACACTCAATTATAATCTGTTTTAATGAAAAATGTAAAAAAA-
* * * *
12870 TT-AACTTAAAATTAATTATGAGACTATAAAATCATTCAAAGTG
128 TTCAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGTG
********** * * **
12913 AGTAATAAGGCTTTGAAANNNNNNNNNNACTATAAATGGACTTTTCTTGCCCATAAATGTTTTTT
1 AGTAATAAGGCTTTGAAAGGCATGGGTGACTATAAATGGACTTTTCTTGCCAATGAATGACTTTT
* * * * * * * *
12978 TCTTCATGTTTCCCAAGGCAGATATTCAAATATAGTATAT-TTTAATAAAAAATTCAAAAATCTA
66 TCTTCATGTTTCTCAAGGCAAACACTCAATTATA--ATCTGTTT--T----AA-TGAAAAATGTA
* * * * * *
13042 AAAAAATTCAGCTTAAACTTAATAATGAGATCATAAAACCATTTAAAGCG
122 AAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGTG
* * * * * ** * *
13092 TGTAATAAAGTTTTAGAAA-GCATGGGTGGCTATAAATGGACTTTTTTTTATCAATAAATGGCTT
1 AGTAATAAGGCTTT-GAAAGGCATGGGTGACTATAAATGGAC-TTTTCTTGCCAATGAATGACTT
* * * * * ** * *
13156 TTTCTTCATGTTTTTCAAGGTAAATACTAAATTATAATCTGTTTTGACCAAACGA-GTAAAACAA
64 TTTCTTCATGTTTCTCAAGGCAAACACTCAATTATAATCTGTTTTAATGAAA-AATGTAAAAAAA
* *
13220 TTCAACTTAAAATCAATAATGAGATTATAAAATCATTTAAAGTG
128 TTCAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGTG
* * * * *
13264 AGAAATAAGGCTTTGAAAGGTATGGGTGACCATAAATGGACATTTCTTGCCAATGAATCA-TATT
1 AGTAATAAGGCTTTGAAAGGCATGGGTGACTATAAATGGACTTTTCTTGCCAATGAATGACT-TT
* * * *
13328 TTCTTCATATTTCTCAAGGCAAACACTCAATTATAATATGTTTTAATTAAAAATATAAAAAAATT
65 TTCTTCATGTTTCTCAAGGCAAACACTCAATTATAATCTGTTTTAATGAAAAATGTAAAAAAATT
* * *
13393 TAACTTCAAATCAATTATGAGATTATAAAATCATTTA
130 CAACTTAAAATCAATTATGAGATTATAAAACCATTTA
Statistics
Matches: 650, Mismatches: 185, Indels: 47
0.74 0.21 0.05
Matches are distributed among these distances:
169 1 0.00
170 85 0.13
171 344 0.53
172 84 0.13
173 5 0.01
174 1 0.00
177 1 0.00
178 6 0.01
179 74 0.11
180 49 0.08
ACGTcount: A:0.38, C:0.13, G:0.13, T:0.34
Consensus pattern (171 bp):
AGTAATAAGGCTTTGAAAGGCATGGGTGACTATAAATGGACTTTTCTTGCCAATGAATGACTTTT
TCTTCATGTTTCTCAAGGCAAACACTCAATTATAATCTGTTTTAATGAAAAATGTAAAAAAATTC
AACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGTG
Done.