Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018398435.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_1735.0, 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: 16388
ACGTcount: A:0.29, C:0.10, G:0.11, T:0.28
Warning! 3769 characters in sequence are not A, C, G, or T
Found at i:388 original size:171 final size:172
Alignment explanation
Indices: 1--1215 Score: 477
Period size: 171 Copynumber: 7.1 Consensus size: 172
* * * *
1 CTAATGGATATCTTTTTCTTCATGTTTCATGAGCCAAACAATCAATTGTTATTTGTTTTAACCAA
1 CTAATGGATATCTTTTTCTTCATGTTTCATGAGACAAACATTCAATTATTATCTGTTTTAACC-A
* * * *
66 AAACATAAAAAAAAATT-CATTTTAAAATCAATTAGGAGATTATAGAAATATTTAAAGCGAGTAA
65 AAA-ATATAAAAAAATTCCATCTTAAAATCAATTAGGAGATTATAAAAATATTTAAACCGAGTAA
*
130 TATGGCTTTTGAAGGCATGGATGACTATAGATGGACTTTTCTTG
129 TAAGGCTTTTGAAGGCATGGATGACTATAGATGGACTTTTCTTG
********** * *
174 CTAATGGATATCTTTTTCTTCANNNNNNNNNNGATAGACATTCAATTATTATCTGTTTTAACCAA
1 CTAATGGATATCTTTTTCTTCATGTTTCATGAGACAAACATTCAATTATTATCTGTTTTAACCAA
* *
239 AAATATAAAAAAATTCCA-CTTAAAGTCAATTATGAGATTATAAAAATATTTAAACCGAGTAATA
66 AAATATAAAAAAATTCCATCTTAAAATCAATTAGGAGATTATAAAAATATTTAAACCGAGTAATA
** * **********
303 AGGCTTTTGAAGGTGTGGGTGNNNNNNNNNNGACTTTTCTTG
131 AGGCTTTTGAAGGCATGGATGACTATAGATGGACTTTTCTTG
* ** * *
345 CTAATGAATATCTTTTTCTTCATGTTTTTTGAGGCAAACATTCAATTATTATCTGTTTTAACTAA
1 CTAATGGATATCTTTTTCTTCATGTTTCATGAGACAAACATTCAATTATTATCTGTTTTAACCAA
* * ********** * *
410 AAACATAAAAAAATTCAATC-TAAAATCAATTNNNNNNNNNNAAAAACATTTAAAACGAGTAATA
66 AAATATAAAAAAATTCCATCTTAAAATCAATTAGGAGATTATAAAAATATTTAAACCGAGTAATA
* * * * * *
474 AGGCTTTCGAAGGCATATG-TGACTATAAAAGAACTTTTTTTG
131 AGGCTTTTGAAGGCAT-GGATGACTATAGATGGACTTTTCTTG
* * ** * * * * * **
516 CAAATGGATATCTTTTTCTTCACGTATCTCA--AGGTAGATATTCAATTATAATCTATTTGAATA
1 CTAATGGATATCTTTTTCTTCATGT-T-TCATGAGACAAACATTCAATTATTATCTGTTTTAACC
********** * * *
579 AAAAATAT-AAAAAANNNNNNNNNNAAATCAATTAGGAGGTTAT-AAAATCATTTAAAGCTAGTA
64 AAAAATATAAAAAAATTCCATCTTAAAATCAATTAGGAGATTATAAAAAT-ATTTAAACCGAGTA
* * * * * *
642 GTAAGGCTTTCGAACGCATGGGTGACTATAAATAGACTTTTCTTG
128 ATAAGGCTTTTGAAGGCATGGATGACTATAGATGGACTTTTCTTG
* * * * * *
687 -TCAATGGATTTCTTTTCCTTCACAT-TTTCCA--AGGCAGACACTC-A--ATTATCTATTTTAA
1 CT-AATGGATATCTTTTTCTT--CATGTTT-CATGAGACAAACATTCAATTATTATCTGTTTTAA
** * *** * * **
745 TAAAAAAT-TAAAAAAATT--AACTTAAAATCAATTTTCAGGTTAT-AAAATCATGTAAAGTGAG
62 CCAAAAATATAAAAAAATTCCATCTTAAAATCAATTAGGAGATTATAAAAAT-ATTTAAACCGAG
* ** ********** * *
806 TACTAAGGCTTCCGANNNNNNNNNNGACTATACATAGACTTTTCTTG
126 TAATAAGGCTTTTGAAGGCATGGATGACTATAGATGGACTTTTCTTG
* * * * * * **
853 CCAACGGATATCTTTTTCTTCATGTTTC-TCAAGGCAAACATTCAATTTTTGTCTGTTTTAATGA
1 CTAATGGATATCTTTTTCTTCATGTTTCAT-GAGACAAACATTCAATTATTATCTGTTTTAACCA
* * ********** * * * * *
917 AAAATGTAAAAACA-TNNNNNNNNNNATTAATTATGAGATTATAAAAACATTTAAGCCGTGTAAT
65 AAAATATAAAAAAATTCCATCTTAAAATCAATTAGGAGATTATAAAAATATTTAAACCGAGTAAT
* * * *
981 AAGGCTTTCGAAGTCAT-GAGTGACTATAAATGGACTTTTGTTG
130 AAGGCTTTTGAAGGCATGGA-TGACTATAGATGGACTTTTCTTG
* * * * * * * **
1024 CCAATGGATATCTTTTTCTTTATATTTCCTAAGGCAGACATTCAATTATTATCT-TTTTAACNNN
1 CTAATGGATATCTTTTTCTTCATGTTTCATGAGACAAACATTCAATTATTATCTGTTTTAAC-CA
******* * * * ** * *
1088 NNNNNNNAAAAAACTT-AAT-TTAAAATCAATTACGAGATTCGAAAAACATTTAAAGCGAGTAAT
65 AAAATATAAAAAAATTCCATCTTAAAATCAATTAGGAGATTATAAAAATATTTAAACCGAGTAAT
* * * *
1151 AAGGCTTTTAAAAG--TGTGAGTGACTATAAATGGACTTTTCATG
130 AAGGCTTTTGAAGGCATG-GA-TGACTATAGATGGACTTTTCTTG
* *
1194 CCAATGAATATCTTTTTCTTCA
1 CTAATGGATATCTTTTTCTTCA
1216 CATTTCTTGA
Statistics
Matches: 766, Mismatches: 245, Indels: 65
0.71 0.23 0.06
Matches are distributed among these distances:
164 4 0.01
165 3 0.00
166 90 0.12
167 2 0.00
168 27 0.04
169 19 0.02
170 112 0.15
171 443 0.58
172 16 0.02
173 50 0.07
ACGTcount: A:0.35, C:0.12, G:0.13, T:0.34
Consensus pattern (172 bp):
CTAATGGATATCTTTTTCTTCATGTTTCATGAGACAAACATTCAATTATTATCTGTTTTAACCAA
AAATATAAAAAAATTCCATCTTAAAATCAATTAGGAGATTATAAAAATATTTAAACCGAGTAATA
AGGCTTTTGAAGGCATGGATGACTATAGATGGACTTTTCTTG
Found at i:1877 original size:171 final size:169
Alignment explanation
Indices: 1629--2041 Score: 506
Period size: 171 Copynumber: 2.4 Consensus size: 169
1619 NNNNNNNNNN
* * * *
1629 TAAATGGACTTTTCTTGCCAATGAATATCTTTTTCTTCTTGTTTCTTGAGGTAGACATTCAATTT
1 TAAATGGACTTTTCTTGCCAATGGATATCTTTTTCTTCATGTTAC-TGAGGCAGACATTCAATTT
* * * * **
1694 TAATCTGTTTTAATAAAAAATGTAAA-ATAATTCAACTTAAAATCAATTATGAGGCTATAAAATT
65 T-ATCTGTTTTAACAAAAAACGTAAAGA-AATTCAACTTAAAACCAATTATGAGACTATAAAAAC
** *
1758 ATTTAAAGCTAGTAATAAGGCTTTTGAAGCCAT-AGGTGACTA
128 ATTTAAAGAGAGTAATAAGGCTTTTCAAGCCATGA-GTGACTA
* * *
1800 TAAATGGACTTTTGTTGCCAATGGATAACTTTTTCTTCATGTCTACTGAGGCAGACATTTAATTC
1 TAAATGGACTTTTCTTGCCAATGGATATCTTTTTCTTCATGT-TACTGAGGCAGACATTCAATT-
* * *
1865 TTATCTGTTTTAACCAAAAACGTAAAGAATTTCAACTTAAAACCAATTATGAGATTATAAAAACA
64 TTATCTGTTTTAACAAAAAACGTAAAGAAATTCAACTTAAAACCAATTATGAGACTATAAAAACA
* * *
1930 TTTACAGAGAGTAATAAGGCTTTTCAAGTCGTGAGTGACTA
129 TTTAAAGAGAGTAATAAGGCTTTTCAAGCCATGAGTGACTA
* * * *
1971 TAAATGGACTTTTTTTGCCAATGGATATCTTTTTCTTCATGTTTCCTGAGGCAAACAATCAATTG
1 TAAATGGACTTTTCTTGCCAATGGATATCTTTTTCTTCATG-TTACTGAGGCAGACATTCAATT-
2036 TTATCT
64 TTATCT
2042 NNNNNNNNNN
Statistics
Matches: 208, Mismatches: 29, Indels: 10
0.84 0.12 0.04
Matches are distributed among these distances:
171 201 0.97
172 7 0.03
ACGTcount: A:0.34, C:0.14, G:0.14, T:0.38
Consensus pattern (169 bp):
TAAATGGACTTTTCTTGCCAATGGATATCTTTTTCTTCATGTTACTGAGGCAGACATTCAATTTT
ATCTGTTTTAACAAAAAACGTAAAGAAATTCAACTTAAAACCAATTATGAGACTATAAAAACATT
TAAAGAGAGTAATAAGGCTTTTCAAGCCATGAGTGACTA
Found at i:2450 original size:171 final size:170
Alignment explanation
Indices: 2151--3325 Score: 552
Period size: 171 Copynumber: 6.9 Consensus size: 170
2141 NGCCAAACAA
* * * *
2151 TCAATTGTTATCTGTTTTAACCAAAAACATAAAAAAATTCAATTTCAAATCAATTAGGAGATTAT
1 TCAATTATTATCTGTTTTAACTAAAAACATAAAAAAATTCAA-TTAAAATCAATTATGAGATTAT
* * *
2216 AGAAACATTTAAAGCGAGTAATATGGCTTTTGAAGGCATAGATGACAATAAATGGATTTTTCTTG
65 AAAAACATTTAAAGCGAGTAATAAGGCTTTTGAAGGCATAGATGACAATAAATGGACTTTTCTTG
* * ********** *
2281 CTAATGGATATCTTTTTCTTCANNNNNNNNNNGATAGACAT
130 CAAATGAATATCTTTTTCTTCATATTTTTTGAGACAGACAT
* *
2322 TCAATTATTATCTGTTTTAACTAAAAACATAAAAAAATTCTACTTAAAGTCAATTATGAGATTAT
1 TCAATTATTATCTGTTTTAACTAAAAACATAAAAAAATTC-AATTAAAATCAATTATGAGATTAT
* ********** ** * * *
2387 AAAAATATTTNNNNNNNNNNATAAGGCTTTTGAAGGTGTGGGTGACTATAAATGGACTTTTCTTG
65 AAAAACATTTAAAGCGAGTAATAAGGCTTTTGAAGGCATAGATGACAATAAATGGACTTTTCTTG
*
2452 CAAATGAATATCTTTTTCTTCATATTTTTTGAGGCAGACAT
130 CAAATGAATATCTTTTTCTTCATATTTTTTGAGACAGACAT
* *
2493 TCAATTATTATCTGTTTTAACTCAAAATATAAAAAAATTCAATTAAAAATCAATTATGAGATTAT
1 TCAATTATTATCTGTTTTAACTAAAAACATAAAAAAATTCAATT-AAAATCAATTATGAGATTAT
********** * * *
2558 AAAAANNNNNNNNNNGAGTAATAAGGCTTTCGAAGGCATATG-TGACCATAAATGAACTTTTCTT
65 AAAAACATTTAAAGCGAGTAATAAGGCTTTTGAAGGCATA-GATGACAATAAATGGACTTTTCTT
* * * ** * * ** ** *
2622 GCCAGTGGATATCTTTTTCTTCACGTCTCTCAAGGTAGATAT
129 GCAAATGAATATCTTTTTCTTCATATTTTTTGAGACAGACAT
* * * * * * *
2664 TCAATTA-TAGTCTATTTGAA-TAAAAAATATAAAAAAATTTAACCTAAAATCAATTAGGAGGTT
1 TCAATTATTA-TCTGTTTTAACT-AAAAACATAAAAAAATTCAA-TTAAAATCAATTATGAGATT
** * * * * * * * * *
2727 ATAAAATTATTTAAAGCTAGTAATAAGGCTTTCGAACGCATGGGTAACTATAAATAGACTTGTCT
63 ATAAAAACATTTAAAGCGAGTAATAAGGCTTTTGAAGGCATAGATGACAATAAATGGACTTTTCT
* * * **** * *
2792 TGTC-AAT-AGATTTCTTTTCCTTCATGTTTCCCAAGGCAGACAC
128 TG-CAAATGA-ATATCTTTTTCTTCATATTTTTTGAGACAGACAT
* * * * * * *
2835 TC-A--ATTACCTATTTTAA-TAAAAAAATAAAAAAAATCAACTTAAAATCAATTTTTAGGTTAT
1 TCAATTATTATCTGTTTTAACTAAAAACATAAAAAAATTCAA-TTAAAATCAATTATGAGATTAT
* * * * ** * * * * *
2896 AAAATCATGTAAAGTGAGTACTAAGGCTTCCGATGGCA-ATGGTGACTATACATAGACTTTTCTT
65 AAAAACATTTAAAGCGAGTAATAAGGCTTTTGAAGGCATA-GATGACAATAAATGGACTTTTCTT
** * * * * ** *
2960 ATAGATGGATATCTTTTTCTTCATGTTTCTCAAGGCAGACAT
129 GCAAATGAATATCTTTTTCTTCATATTTTTTGAGACAGACAT
* * * * ** *
3002 TCAATAATTATCTGATTGAA-TAAAAA-ATGTAAAAACATTCAACCCAAAATTAATTATGAGATT
1 TCAATTATTATCTGTTTTAACTAAAAACA--TAAAAAAATTCAA-TTAAAATCAATTATGAGATT
* ** * * ** * *
3065 ATAAAAATATTT-AAGCCTTGTAATAAGGCTTTCGAAGTCAT-GAGTGAGTATAAACGGACTTCT
63 ATAAAAACATTTAAAG-CGAGTAATAAGGCTTTTGAAGGCATAGA-TGACAATAAATGGACTTTT
* * * * * ** *
3128 CTTGCCAATGGATTTCTTTTTATTTATA-TTTTCAAGGCAGACAT
126 CTTGCAAATGAATATCTTTTTCTTCATATTTTTTGAGACAGACAT
********** * *
3172 TCAATTATTATCT-TTTTAACCNNNNNNNNNNAAAAACTT-AATTTAAAATCAATTACGAGATT-
1 TCAATTATTATCTGTTTTAA-CTAAAAACATAAAAAAATTCAA-TTAAAATCAATTATGAGATTA
* * * *
3234 TGAAAAATATTATTTAAAGCGAGTAATAAGGCTTTTAAAGGCGT-GAGTGACTATAAATGGACTT
64 T--AAAA-A-CATTTAAAGCGAGTAATAAGGCTTTTGAAGGCATAGA-TGACAATAAATGGACTT
* *
3298 TTCATGCCAATGAATATCTTTTTCTTCA
124 TTCTTGCAAATGAATATCTTTTTCTTCA
3326 CGTTTCTTGA
Statistics
Matches: 770, Mismatches: 205, Indels: 57
0.75 0.20 0.06
Matches are distributed among these distances:
167 121 0.16
168 12 0.02
169 25 0.03
170 65 0.08
171 476 0.62
172 68 0.09
173 3 0.00
ACGTcount: A:0.37, C:0.12, G:0.13, T:0.35
Consensus pattern (170 bp):
TCAATTATTATCTGTTTTAACTAAAAACATAAAAAAATTCAATTAAAATCAATTATGAGATTATA
AAAACATTTAAAGCGAGTAATAAGGCTTTTGAAGGCATAGATGACAATAAATGGACTTTTCTTGC
AAATGAATATCTTTTTCTTCATATTTTTTGAGACAGACAT
Found at i:2923 original size:167 final size:168
Alignment explanation
Indices: 2675--3100 Score: 425
Period size: 167 Copynumber: 2.5 Consensus size: 168
2665 CAATTATAGT
* * * *
2675 CTATTTGAATAAAAAATATAAAAAAATTTAACCTAAAATCAATTAGGAGGTTATAAAATTATTTA
1 CTATTTGAATAAAAAATATAAAAAAAATCAACCTAAAATCAATTAGGAGGTTATAAAATCATGTA
* *
2740 AAGCTAGTAATAAGGCTTTCGAACGC-ATGGGTAACTATAAATAGACTTGTCTTGTCA-ATAGAT
66 AAGCTAGTAATAAGGCTTCCGAACGCAAT-GGTAACTATAAATAGACTTGTCTTAT-AGATAGAT
*
2803 TTCTTTTCCTTCATGTTTCCCAAGGCAGACACTCAATTAC
129 ATCTTTTCCTTCATGTTTCCCAAGGCAGACACTCAATTAC
* * ***
2843 CTATTTTAATAAAAAA-ATAAAAAAAATCAACTTAAAATCAATTTTTAGGTTATAAAATCATGTA
1 CTATTTGAATAAAAAATATAAAAAAAATCAACCTAAAATCAATTAGGAGGTTATAAAATCATGTA
* ** * * * *
2907 AAG-TGAGTACTAAGGCTTCCGATGGCAATGGTGACTATACATAGACTTTTCTTATAGATGGATA
66 AAGCT-AGTAATAAGGCTTCCGAACGCAATGGTAACTATAAATAGACTTGTCTTATAGATAGATA
* * * *
2971 TCTTTTTCTTCATGTTTCTCAAGGCAGACATTCAATAATTAT
130 TCTTTTCCTTCATGTTTCCCAAGGCAGACACTC---AATTAC
* * * * * * *
3013 CTGA-TTGAATAAAAAATGTAAAAACATTCAACCCAAAATTAATTATGAGATTATAAAAAT-AT-
1 CT-ATTTGAATAAAAAATATAAAAAAAATCAACCTAAAATCAATTAGGAGGTTAT-AAAATCATG
* * *
3075 TTAAGCCTTGTAATAAGGCTTTCGAA
64 TAAAG-CTAGTAATAAGGCTTCCGAA
3101 GTCATGAGTG
Statistics
Matches: 209, Mismatches: 38, Indels: 19
0.79 0.14 0.07
Matches are distributed among these distances:
166 2 0.01
167 117 0.56
168 17 0.08
170 22 0.11
171 45 0.22
172 6 0.03
ACGTcount: A:0.40, C:0.13, G:0.13, T:0.34
Consensus pattern (168 bp):
CTATTTGAATAAAAAATATAAAAAAAATCAACCTAAAATCAATTAGGAGGTTATAAAATCATGTA
AAGCTAGTAATAAGGCTTCCGAACGCAATGGTAACTATAAATAGACTTGTCTTATAGATAGATAT
CTTTTCCTTCATGTTTCCCAAGGCAGACACTCAATTAC
Found at i:4580 original size:171 final size:171
Alignment explanation
Indices: 4396--6671 Score: 787
Period size: 171 Copynumber: 13.3 Consensus size: 171
4386 AAATTCAATC
* * *
4396 TAAAATTAATTATGAGATTATAAAAACATTTAAAGCGTGTAATAAAGCTTTTGAAGTCATGGGTG
1 TAAAATCAATTATGAGATTATAAAAATATTTAAAGCGTGTAATAAGGCTTTTGAAGTCATGGGTG
* * *
4461 ACTACAAATGGACTTTTCTTGCCAATGGATATCTTTTTCTTC-TCATTT-CTCGAGGTAGACATT
66 ACTACAAAGGGACTTTTCTAGCCAATGGATATCTTTTTCTTCAT-ATTTCCT-GAGGCAGACATT
* * **********
4524 CAATTATAATCTGTTTTAATAAAAAATGTNNNNNNNNNNAACT
129 CAATTATAATATGTTTTAACAAAAAATGTAAAGAATTACAACT
* * * * *
4567 TAAAATCAATTATGAGGTTATAAAATTATTTAAAGC-TAGTGATAAGGCTTTTGAAGCCATAGGT
1 TAAAATCAATTATGAGATTATAAAAATATTTAAAGCGT-GTAATAAGGCTTTTGAAGTCATGGGT
* * * *
4631 GACTATAAAGGGACTTTTCTAGCTAATGGATATCTTTTTCTTCATGTTTCCTGATGCAGACATTC
65 GACTACAAAGGGACTTTTCTAGCCAATGGATATCTTTTTCTTCATATTTCCTGAGGCAGACATTC
* * *
4696 AATTTTCATATGTTTTAACCAAAAATGTAAAGAATTACAACT
130 AATTATAATATGTTTTAACAAAAAATGTAAAGAATTACAACT
* * * *
4738 TAAAATCAATTATGAGATTATAAAAATATTTAATGAGAGTAATAAGGCTTTTCAAGTCATGGGTG
1 TAAAATCAATTATGAGATTATAAAAATATTTAAAGCGTGTAATAAGGCTTTTGAAGTCATGGGTG
********** * ** * * * *
4803 ACTANNNNNNNNNNTTTCTTA-CCAATGGATATCTTTTTCTTCATCTTTTGTAAGGCAAAAAATC
66 ACTACAAAGGGACTTTTC-TAGCCAATGGATATCTTTTTCTTCATATTTCCTGAGGCAGACATTC
* * * ********* * *
4867 AATTGTTATCTGTTTTAACNNNNNNNNNNAAAAAATT-CAATT
130 AATTATAATATGTTTTAAC-AAAAAATGTAAAGAATTACAACT
* * * * * * * ****
4909 TGAAATCAATTAGGAGATTATAAAAACATTTAAAGCGAGTAATATGGCTTTCGAAGGCATGANNN
1 TAAAATCAATTATGAGATTATAAAAATATTTAAAGCGTGTAATAAGGCTTTTGAAGTCATGGGTG
******* * * * * * * *
4974 NNNNNNNATGGACTTTTCTTGCTAATAGATATCTTTTTCTTC-TCGTTT-CTCGAGGTAGATATT
66 ACTACAAAGGGACTTTTCTAGCCAATGGATATCTTTTTCTTCAT-ATTTCCT-GAGGCAGACATT
* * ******** * *
5037 CAATTATAATCTATTTTNNNNNNNNNNAT-AAAAAAATTA-AACT
129 CAATTATAATATGTTTT--AACAAAAAATGTAAAGAATTACAACT
* * * *
5080 TAAAATCAATTAGGACG-TTATAAAAACT-TTTAAAGCGAGTAATAAGGCTTTTCAAGCCATGGG
1 TAAAATCAATTATGA-GATTATAAAAA-TATTTAAAGCGTGTAATAAGGCTTTTGAAGTCATGGG
* * ********** * * * * *
5143 TGACTATAAATGGACTTTTCTTA-CCAANNNNNNNNNNTTTCTTCATGTTTCATAAGGCAAACAA
64 TGACTACAAAGGGACTTTTC-TAGCCAATGGATATCTTTTTCTTCATATTTCCTGAGGCAGACAT
* * * * * * * *
5207 TCAATTGTTATCTATTTTAACCAAAAATATAAAAAAATT-CAATT
128 TCAATTATAATATGTTTTAACAAAAAATGT-AAAGAATTACAACT
* * * * * * * *
5251 TGAAATCAATTAGGAGGTTATAGAAATATTTAAAGCGAGTAATATGGCTTTTGAAGGCATGGATG
1 TAAAATCAATTATGAGATTATAAAAATATTTAAAGCGTGTAATAAGGCTTTTGAAGTCATGGGTG
* * ********** * * * *
5316 ACTATAAATGGACTNNNNNNNNNNATGGATATCTTTTTCTTCATGTTTCTTAAGGCAAACATTCA
66 ACTACAAAGGGACTTTTCTAGCCAATGGATATCTTTTTCTTCATATTTCCTGAGGCAGACATTCA
* * * * *
5381 ATTATTATCTGTTTTAACCAAAAACAT-AAAAAAATT-CTACT
131 ATTATAATATGTTTTAA-CAAAAA-ATGTAAAGAATTACAACT
* * * * *
5422 TAAAGTGAATTATGAGATTATAAAAATATTTAAAGTGAGTAATAAGGCTTTTGAAGGT-GTGGGT
1 TAAAATCAATTATGAGATTATAAAAATATTTAAAGCGTGTAATAAGGCTTTTGAA-GTCATGGGT
********** * * * * * ** *
5486 GANNNNNNNNNNACTTTTCTTGCTAATGAATATCTTTTTCTGCATGTTTTTTGAGGCAAACATTC
65 GACTACAAAGGGACTTTTCTAGCCAATGGATATCTTTTTCTTCATATTTCCTGAGGCAGACATTC
* * * * *
5551 AATTATTATTTGTTTTAACGAAAAACAT-AAAAAAATT-CAATT
130 AATTATAATATGTTTTAAC-AAAAA-ATGTAAAGAATTACAACT
* * * *******************
5593 TAAAATCAATTATGAGATTTTAAAAACATTTAAAGCGAGNNNNNNNNNNNNNNNNNNNNNAT--G
1 TAAAATCAATTATGAGATTATAAAAATATTTAAAGCGTG--TAATAAGGCTTTTGAAGTCATGGG
* * * ** * * * *
5656 TGACTATAAATGGACTTTTCTTGCCAATGGATATCTTTTTCTTCACGTCT-CTCAAGGTAGATAT
64 TGACTACAAAGGGACTTTTCTAGCCAATGGATATCTTTTTCTTCATATTTCCT-GAGGCAGACAT
* * * * * * *
5720 TCAATTATAATCTATTTGAATAAAAAATATAAAAACATT-TAACT
128 TCAATTATAATATGTTTTAACAAAAAATGTAAAGA-ATTACAACT
* * * **
5764 TAAAATCAATTAGGAGGTTAT-AAAATCAATTAAAGC-TAGTAATAAGGCTTTCAAACG-CATGG
1 TAAAATCAATTATGAGATTATAAAAAT-ATTTAAAGCGT-GTAATAAGGCTTTTGAA-GTCATGG
* * * * * * * ** * *
5826 GTGACTATAAATGGACTTTTCTTGTCAATGGATTTCTTTTCCTTCACATTTCCCAAGACAGACAC
63 GTGACTACAAAGGGACTTTTCTAGCCAATGGATATCTTTTTCTTCATATTTCCTGAGGCAGACAT
** * * * * * **
5891 TCAATTATTTTCT-TTTTAACCAAAAATATAAAAAAAGT-CATTT
128 TCAATTATAATATGTTTTAACAAAAAATGT-AAAGAATTACAACT
* * ** * * * *
5934 TAAAATCAATTACGAGATTATAAAAACATTTAAAGCAAGTAATAAGGCTTTTAAAGGCGTGAGTG
1 TAAAATCAATTATGAGATTATAAAAATATTTAAAGCGTGTAATAAGGCTTTTGAAGTCATGGGTG
* * * * * * * *
5999 ACTATAAATGGACTTTT-TCATGCCAATGAATATCTTTTCCTTC-TCGTTTCTTGAGGTAGGCAT
66 ACTACAAAGGGACTTTTCT-A-GCCAATGGATATCTTTTTCTTCAT-ATTTCCTGAGGCAGACAT
* * * * * *
6062 TCAATTGTAATATATTTTAATAAAAAATATAAAAACATT-TAACT
128 TCAATTATAATATGTTTTAACAAAAAATGTAAAGA-ATTACAACT
* * * * * ** *
6106 TAAAATCAATTAGGAGGA-TATAAAATTATTTAAAGCGAGTAATAGGGCTTTCGAAGGAATAGGT
1 TAAAATCAATTATGA-GATTATAAAAATATTTAAAGCGTGTAATAAGGCTTTTGAAGTCATGGGT
* * * * * * * *
6170 GACTATAAATGGACTATTTCTA-CCAATGAATTTCTTTCTCTTCACATTTCTTGAGGTAGACATT
65 GACTACAAAGGGACT-TTTCTAGCCAATGGATATCTTTTTCTTCATATTTCCTGAGGCAGACATT
* * ** *** *
6234 CAATTCTAATCTGTTTTATTAAAAAACAAAAAAAAATT-CAACT
129 CAATTATAATATGTTTTAACAAAAAA-TGTAAAGAATTACAACT
********** * * * *
6277 TAAAATCAATTA-NNNNNNNNNNAAATCATTTAAAGCGAGTAATAAGGCTCTCGAAGTCATAGGT
1 TAAAATCAATTATGAGATTATAAAAAT-ATTTAAAGCGTGTAATAAGGCTTTTGAAGTCATGGGT
* * * * * * **
6341 GACTATAAATGGACTTTTCTTGCCAATGGATATCTTTTCCTTC-TCTTTTCTCGAGATAGACATT
65 GACTACAAAGGGACTTTTCTAGCCAATGGATATCTTTTTCTTCATATTTCCT-GAGGCAGACATT
* * * * * *
6405 CAATTATAATCTATTTTAATACAAAATAGAAAAAAATT-CAACT
129 CAATTATAATATGTTTTAACAAAAAAT-GTAAAGAATTACAACT
* * * * *
6448 TACAATCAATTATGAGGTTATAAAATTATTTAAAGC-TAGTAATAAGGCTTTCGAAGCCATGGGT
1 TAAAATCAATTATGAGATTATAAAAATATTTAAAGCGT-GTAATAAGGCTTTTGAAGTCATGGGT
* ** * * * * *
6512 GACTATAAATAGACTTTTTTTA-TCAATGG-TAATCTTTTTCTTCATGTTTCCTAAGGTAGACAT
65 GACTACAAAGGGAC-TTTTCTAGCCAATGGAT-ATCTTTTTCTTCATATTTCCTGAGGCAGACAT
* * * * * *
6575 TCAATTTTTATCTGTTTTAACAAAAAACGTAAAGAATTTCAACG
128 TCAATTATAATATGTTTTAACAAAAAATGTAAAGAATTACAACT
* * ***
6619 TAAAATTAATTATGAGATTATAAAGATATTTAAAGAAAGTAATAAGGCTTTTG
1 TAAAATCAATTATGAGATTATAAAAATATTTAAAGCGTGTAATAAGGCTTTTG
6672 NNNNNNNNNN
Statistics
Matches: 1584, Mismatches: 456, Indels: 130
0.73 0.21 0.06
Matches are distributed among these distances:
169 8 0.01
170 126 0.08
171 1309 0.83
172 131 0.08
173 9 0.01
174 1 0.00
ACGTcount: A:0.36, C:0.12, G:0.13, T:0.35
Consensus pattern (171 bp):
TAAAATCAATTATGAGATTATAAAAATATTTAAAGCGTGTAATAAGGCTTTTGAAGTCATGGGTG
ACTACAAAGGGACTTTTCTAGCCAATGGATATCTTTTTCTTCATATTTCCTGAGGCAGACATTCA
ATTATAATATGTTTTAACAAAAAATGTAAAGAATTACAACT
Found at i:6029 original size:513 final size:513
Alignment explanation
Indices: 4380--6669 Score: 1346
Period size: 513 Copynumber: 4.5 Consensus size: 513
4370 NNNNNNAAAC
* * ** *
4380 ATAAAAAAATTCAATC-TAAAATTAATTATGAGATTATAAAAACATTTAAAGCGTGTAATAAAGC
1 ATAAAAAAATTC-ATCTTAAAATCAATTATGAGATTATAAAAATATTTAAAGCAAGTAATAAGGC
* * * * * * *
4444 TTTTGAAGTCATGGGTGACTACAAATGGAC-TTTTCTTGCCAATGGATATCTTTTTCTTC-TCAT
65 TTTTGAAGGCGTGGGTGACTATAAATAGACTTTTTCATGCCAATGAATATCTTTTTCTTCAT-GT
* * * * ** **********
4507 TTCTCGAGGTAGACATTCAATTATAATCTGTTTTAATAAAAAATGTNNNNNNNNNNAACTTAAAA
129 TTCTTGAGGTAGACATTCAATTATTATATGTTTTAACAAAAAACATAAAAAAATTCAACTTAAAA
* * * * * * **
4572 TCAATTATGAGGTTATAAAATTATTTAAAGCTAGTGATAAGGCTTTTGAAGCCATAGGTGACTAT
194 TCAATTATGAGATTATAAAAATATTTAAAGCGAGTAATAGGGCTTTCGAAGGAATAGGTGACTAT
* * * * ** * * * *
4637 AAAGGGACT-TTTCTAGCTAATGGATATCTTTTTCTTCATGTTTC-CTGATGCAGACATTCAATT
259 AAATGGACTATTTCTA-CCAATGAATATCTTTCTCTTCACATCTCTC-AAGGTAGACATTCAATT
* * * * * ** * * * *
4700 TTCATATGTTTTAACCAAAAATGT-AAAGAATTACAACTTAAAATCAATTATGAGATTATAAAAA
322 ATAATCTATTTGAATAAAAAATATAAAAAAATT-CAACTTAAAATCAATTAGGAGGTTAT-AAAA
* * ********** *
4764 T-ATTTAATGAGAGTAATAAGGCTTTTC-AAGTCATGGGTGACTANNNNNNNNNNTTTCTTACCA
385 TCATTTAAAGCGAGTAATAAGGC-TTTCGAAG-CATGGGTGACTATAAATGGACTTTTCTTGCCA
* * * * * * * * * *****
4827 ATGGATATCTTTTTCTTCATCTTTTGT-AAGGCAAAAAATCAATTGTTATCTGTTTTAACNNNNN
448 ATGGATATCTTTTCCTTCA-CATTTCTCAAGACAGACATTCAATTATTATCTATTTTAACCAAAA
**
4891 NN
512 AT
*** * * * * *
4893 NNNAAAAAATTCAAT-TTGAAATCAATTAGGAGATTATAAAAACATTTAAAGCGAGTAATATGGC
1 ATAAAAAAATTC-ATCTTAAAATCAATTATGAGATTATAAAAATATTTAAAGCAAGTAATAAGGC
* * *********** * * *
4957 TTTCGAAGGCATGANNNNNNNNNNATGGAC-TTTTCTTGCTAAT-AGATATCTTTTTCTTC-TCG
65 TTTTGAAGGCGTGGGTGACTATAAATAGACTTTTTCATGCCAATGA-ATATCTTTTTCTTCAT-G
* * * * * ********** *
5019 TTTCTCGAGGTAGATATTCAATTATAATCTATTTTNNNNNNNNNNATAAAAAAATTAAACTTAAA
128 TTTCTTGAGGTAGACATTCAATTATTATATGTTTTAACAAAAAACATAAAAAAATTCAACTTAAA
* * ** *
5084 ATCAATTAGGACG-TTATAAAAACT-TTTAAAGCGAGTAATAAGGCTTTTC-AAGCCATGGGTGA
193 ATCAATTATGA-GATTATAAAAA-TATTTAAAGCGAGTAATAGGGC-TTTCGAAGGAATAGGTGA
********* ** * * * *
5146 CTATAAATGGACT-TTTCTTACCAANNNNNNNNNNTT-TCTTCATGTTTCAT-AAGGCAAACAAT
255 CTATAAATGGACTATTTC-TACCAA-TGAATATCTTTCTCTTCACATCTC-TCAAGGTAGACATT
* * * ** * *
5208 CAATTGTTATCTATTTTAACCAAAAATATAAAAAAATTCAATTTGAAATCAATTAGGAGGTTATA
317 CAATTATAATCTATTTGAATAAAAAATATAAAAAAATTCAACTTAAAATCAATTAGGAGGTTATA
* * * *******
5273 GAAAT-ATTTAAAGCGAGTAATATGGCTTTTGAAGGCATGGATGACTATAAATGGACTNNNNNNN
382 -AAATCATTTAAAGCGAGTAATAAGGCTTTCGAA-GCATGGGTGACTATAAATGGACTTTTCTTG
*** * ** * * * *
5337 NNNATGGATATCTTTTTCTTCATGTTTCTTAAGGCAAACATTCAATTATTATCTGTTTTAACCAA
445 CCAATGGATATCTTTTCCTTCACATTTCTCAAGACAGACATTCAATTATTATCTATTTTAACCAA
*
5402 AAAC
510 AAAT
* * **
5406 ATAAAAAAATTC-TACTTAAAGTGAATTATGAGATTATAAAAATATTTAAAGTGAGTAATAAGGC
1 ATAAAAAAATTCAT-CTTAAAATCAATTATGAGATTATAAAAATATTTAAAGCAAGTAATAAGGC
* ********** * * *
5470 TTTTGAAGGTGTGGGTGANNNNNNNNNNAC-TTTTCTTGCTAATGAATATCTTTTTCTGCATGTT
65 TTTTGAAGGCGTGGGTGACTATAAATAGACTTTTTCATGCCAATGAATATCTTTTTCTTCATGTT
* * * * * *
5534 TTTTGAGGCAAACATTCAATTATTATTTGTTTTAACGAAAAACATAAAAAAATTCAATTTAAAAT
130 TCTTGAGGTAGACATTCAATTATTATATGTTTTAACAAAAAACATAAAAAAATTCAACTTAAAAT
* * ********************* *
5599 CAATTATGAGATTTTAAAAACATTTAAAGCGAGNNNNNNNNNNNNNNNNNNNNNATGTGACTATA
195 CAATTATGAGATTATAAAAATATTTAAAGCGAGTAATAGGGCTTTCGAAGGAATAGGTGACTATA
* * * * *
5664 AATGGACT-TTTCTTGCCAATGGATATCTTTTTCTTCACGTCTCTCAAGGTAGATATTCAATTAT
260 AATGGACTATTTC-TACCAATGAATATCTTTCTCTTCACATCTCTCAAGGTAGACATTCAATTAT
* * *
5728 AATCTATTTGAATAAAAAATATAAAAACATTTAACTTAAAATCAATTAGGAGGTTATAAAATCAA
324 AATCTATTTGAATAAAAAATATAAAAAAATTCAACTTAAAATCAATTAGGAGGTTATAAAATCAT
* * *
5793 TTAAAGCTAGTAATAAGGCTTTCAAACGCATGGGTGACTATAAATGGACTTTTCTTGTCAATGGA
389 TTAAAGCGAGTAATAAGGCTTTCGAA-GCATGGGTGACTATAAATGGACTTTTCTTGCCAATGGA
* * * *
5858 TTTCTTTTCCTTCACATTTCCCAAGACAGACACTCAATTATTTTCT-TTTTAACCAAAAAT
453 TATCTTTTCCTTCACATTTCTCAAGACAGACATTCAATTATTATCTATTTTAACCAAAAAT
* * * *
5918 ATAAAAAAAGTCATTTTAAAATCAATTACGAGATTATAAAAACATTTAAAGCAAGTAATAAGGCT
1 ATAAAAAAATTCATCTTAAAATCAATTATGAGATTATAAAAATATTTAAAGCAAGTAATAAGGCT
* * * *
5983 TTTAAAGGCGTGAGTGACTATAAATGGACTTTTTCATGCCAATGAATATCTTTTCCTTC-TCGTT
66 TTTGAAGGCGTGGGTGACTATAAATAGACTTTTTCATGCCAATGAATATCTTTTTCTTCAT-GTT
* * * * * * * *
6047 TCTTGAGGTAGGCATTCAATTGTAATATATTTTAATAAAAAATATAAAAACATTTAACTTAAAAT
130 TCTTGAGGTAGACATTCAATTATTATATGTTTTAACAAAAAACATAAAAAAATTCAACTTAAAAT
* *
6112 CAATTAGGAGGA-TATAAAATTATTTAAAGCGAGTAATAGGGCTTTCGAAGGAATAGGTGACTAT
195 CAATTATGA-GATTATAAAAATATTTAAAGCGAGTAATAGGGCTTTCGAAGGAATAGGTGACTAT
* * ** *
6176 AAATGGACTATTTCTACCAATGAATTTCTTTCTCTTCACATTTCTTGAGGTAGACATTCAATTCT
259 AAATGGACTATTTCTACCAATGAATATCTTTCTCTTCACATCTCTCAAGGTAGACATTCAATTAT
* * * * * **********
6241 AATCTGTTTTATTAAAAAACAAAAAAAAATTCAACTTAAAATCAATTANNNNNNNNNNAAATCAT
324 AATCTATTTGAATAAAAAATATAAAAAAATTCAACTTAAAATCAATTAGGAGGTTATAAAATCAT
* *
6306 TTAAAGCGAGTAATAAGGCTCTCGAAGTCATAGGTGACTATAAATGGACTTTTCTTGCCAATGGA
389 TTAAAGCGAGTAATAAGGCTTTCGAAG-CATGGGTGACTATAAATGGACTTTTCTTGCCAATGGA
* * * * * *
6371 TATCTTTTCCTTCTCTTTTCTCGAGATAGACATTCAATTATAATCTATTTTAA-TACAAAAT
453 TATCTTTTCCTTCACATTTCTCAAGACAGACATTCAATTATTATCTATTTTAACCA-AAAAT
* * * * * *
6432 AGAAAAAAATTCAACTTACAATCAATTATGAGGTTATAAAATTATTTAAAGCTAGTAATAAGGCT
1 ATAAAAAAATTCATCTTAAAATCAATTATGAGATTATAAAAATATTTAAAGCAAGTAATAAGGCT
* * * * *
6497 TTCGAAGCCATGGGTGACTATAAATAGACTTTTTTTAT--CAATG-GTAATCTTTTTCTTCATGT
66 TTTGAAGGCGTGGGTGACTATAAATAGAC-TTTTTCATGCCAATGAAT-ATCTTTTTCTTCATGT
* * * * * * * *
6559 TTCCTAAGGTAGACATTCAATTTTTATCTGTTTTAACAAAAAACGTAAAGAATTTCAACGTAAAA
129 TTCTTGAGGTAGACATTCAATTATTATATGTTTTAACAAAAAACATAAAAAAATTCAACTTAAAA
* * ** *
6624 TTAATTATGAGATTATAAAGATATTTAAAGAAAGTAATAAGGCTTT
194 TCAATTATGAGATTATAAAAATATTTAAAGCGAGTAATAGGGCTTT
6670 TGNNNNNNNN
Statistics
Matches: 1354, Mismatches: 387, Indels: 72
0.75 0.21 0.04
Matches are distributed among these distances:
511 1 0.00
512 105 0.08
513 1126 0.83
514 115 0.08
515 7 0.01
ACGTcount: A:0.36, C:0.12, G:0.13, T:0.35
Consensus pattern (513 bp):
ATAAAAAAATTCATCTTAAAATCAATTATGAGATTATAAAAATATTTAAAGCAAGTAATAAGGCT
TTTGAAGGCGTGGGTGACTATAAATAGACTTTTTCATGCCAATGAATATCTTTTTCTTCATGTTT
CTTGAGGTAGACATTCAATTATTATATGTTTTAACAAAAAACATAAAAAAATTCAACTTAAAATC
AATTATGAGATTATAAAAATATTTAAAGCGAGTAATAGGGCTTTCGAAGGAATAGGTGACTATAA
ATGGACTATTTCTACCAATGAATATCTTTCTCTTCACATCTCTCAAGGTAGACATTCAATTATAA
TCTATTTGAATAAAAAATATAAAAAAATTCAACTTAAAATCAATTAGGAGGTTATAAAATCATTT
AAAGCGAGTAATAAGGCTTTCGAAGCATGGGTGACTATAAATGGACTTTTCTTGCCAATGGATAT
CTTTTCCTTCACATTTCTCAAGACAGACATTCAATTATTATCTATTTTAACCAAAAAT
Found at i:6662 original size:342 final size:340
Alignment explanation
Indices: 4396--6667 Score: 1249
Period size: 342 Copynumber: 6.6 Consensus size: 340
4386 AAATTCAATC
* * * ** * * *
4396 TAAAATTAATTATGAGATTATAAAAACATTTAAAGCGT-GTAATAAAGCTTTTGAAGTCATGGGT
1 TAAAATCAATTAGGAGGTTATAAAATTATTTAAAGC-TAGTAATAAGGCTTTCGAAGCCATGGGT
* * ** * *
4460 GACTACAAATGGACTTTTCTTGCCAATGGATATCTTTTTCTTCTCATTT-CTCGAGGTAGACATT
65 GACTATAAATGGACTTTTTTTATCAATGGA-ATCTTTTTCTTCACATTTCCT-AAGGTAGACATT
* * * ** ********** * *
4524 CAATTATAATCTGTTTTAATAAAAAATGTNNNNNNNNNNAACTTAAAATCAATTATGAGGTTATA
128 CAATTTTTATCTGTTTTAACAAAAAACATAAAAAAATTCAACTTAAAATCAATTACGAGATTATA
* * * ** * * *
4589 AAATTATTTAAAGCTAGTGATAAGGCTTTTGAAGCCAT-AGGTGACTATAAAGGGACTTTTCTAG
193 AAA-TATTTAAAGCAAGTAATAAGGCTCTCAAAGGCATGA-GTGACTATAAATGGACTTTTCTTG
* * * * * * * * **
4653 CTAATGGATATCTTTTTCTTCAT-GTTTC-CTGATGCAGACATTCAATTTTCATATGTTTTAACC
256 CCAATGGATATCTTTTCCTTC-TCGTTTCTC-GAGGTAGACATTCAATTATAATCTATTTTAATA
* * *
4716 AAAAATGTAAAGA-ATTACAACT
319 AAAAATATAAAAACATT-TAACT
* * * * ** *
4738 TAAAATCAATTATGAGATTATAAAAATATTTAATGAGAGTAATAAGGCTTTTC-AAGTCATGGGT
1 TAAAATCAATTAGGAGGTTATAAAATTATTTAAAGCTAGTAATAAGGC-TTTCGAAGCCATGGGT
********** * * ** * * * *
4802 GACTANNNNNNNNNNTTTCTTACCAATGGATATCTTTTTCTTCATC-TTTTGTAAGGCAAAAAAT
65 GACTATAAATGGACTTTTTTTATCAATGGA-ATCTTTTTCTTCA-CATTTCCTAAGGTAGACATT
* ********** * * *
4866 CAATTGTTATCTGTTTTAACNNNNNNNNNNAAAAAATTCAATTTGAAATCAATTAGGAGATTATA
128 CAATTTTTATCTGTTTTAACAAAAAACATAAAAAAATTCAACTTAAAATCAATTACGAGATTAT-
* * * * * **********
4931 AAAACATTTAAAGCGAGTAATATGGCTTTCGAAGGCATGANNNNNNNNNNATGGACTTTTCTTGC
192 AAAATATTTAAAGCAAGTAATAAGGCTCTCAAAGGCATGAGTGACTATAAATGGACTTTTCTTGC
* * * * *******
4996 TAATAGATATCTTTTTCTTCTCGTTTCTCGAGGTAGATATTCAATTATAATCTATTTTNNNNNNN
257 CAATGGATATCTTTTCCTTCTCGTTTCTCGAGGTAGACATTCAATTATAATCTATTTTAATAAAA
*** * *
5061 NNNATAAAAAAATTAAACT
322 AATATAAAAACATTTAACT
* * *
5080 TAAAATCAATTAGGACGTTATAAAAACT-TTTAAAGCGAGTAATAAGGCTTTTC-AAGCCATGGG
1 TAAAATCAATTAGGAGGTTAT-AAAATTATTTAAAGCTAGTAATAAGGC-TTTCGAAGCCATGGG
* * ********* ** * * * *
5143 TGACTATAAATGGACTTTTCTTACCAANNNNNNNNNNTTTCTTCATGTTTCATAAGGCAAACAAT
64 TGACTATAAATGGACTTTTTTTATCAA-TGGAATCTTTTTCTTCACATTTCCTAAGGTAGACATT
* * * * * * * *
5208 CAATTGTTATCTATTTTAACCAAAAATATAAAAAAATTCAATTTGAAATCAATTAGGAGGTTATA
128 CAATTTTTATCTGTTTTAACAAAAAACATAAAAAAATTCAACTTAAAATCAATTACGAGATTATA
* * * ** *******
5273 GAAATATTTAAAGCGAGTAATATGGCTTTTGAAGGCATG-GATGACTATAAATGGACTNNNNNNN
193 -AAATATTTAAAGCAAGTAATAAGGCTCTCAAAGGCATGAG-TGACTATAAATGGACTTTTCTTG
*** * ** * * * * **
5337 NNNATGGATATCTTTTTCTTCAT-GTTTCTTAAGGCAAACATTCAATTATTATCTGTTTTAACCA
256 CCAATGGATATCTTTTCCTTC-TCGTTTCTCGAGGTAGACATTCAATTATAATCTATTTTAATAA
* *
5401 AAAACATAAAAAAATTCT-ACT
320 AAAATATAAAAACATT-TAACT
* * * * * * ***
5422 TAAAGTGAATTATGAGATTATAAAAATATTTAAAG-TGAGTAATAAGGCTTTTGAAGGTGTGGGT
1 TAAAATCAATTAGGAGGTTATAAAATTATTTAAAGCT-AGTAATAAGGCTTTCGAAGCCATGGGT
********** * * * * ** ** * * *
5486 GANNNNNNNNNNACTTTTCTT-GCTAATGAATATCTTTTTCTGCATGTTTTTTGAGGCAAACATT
65 GACTATAAATGGACTTTTTTTATC-AATGGA-ATCTTTTTCTTCACATTTCCTAAGGTAGACATT
* * * * * *
5550 CAATTATTATTTGTTTTAACGAAAAACATAAAAAAATTCAATTTAAAATCAATTATGAGATTTTA
128 CAATTTTTATCTGTTTTAACAAAAAACATAAAAAAATTCAACTTAAAATCAATTACGAGATTAT-
* * *******************
5615 AAAACATTTAAAGCGAGNNNNNNNNNNNNNNNNNNNNNAT--GTGACTATAAATGGACTTTTCTT
192 AAAATATTTAAAGCAAG--TAATAAGGCTCTCAAAGGCATGAGTGACTATAAATGGACTTTTCTT
* * * * * *
5678 GCCAATGGATATCTTTTTCTTCACGTCTCTCAAGGTAGATATTCAATTATAATCTATTTGAATAA
255 GCCAATGGATATCTTTTCCTTCTCGTTTCTCGAGGTAGACATTCAATTATAATCTATTTTAATAA
5743 AAAATATAAAAACATTTAACT
320 AAAATATAAAAACATTTAACT
* * *
5764 TAAAATCAATTAGGAGGTTATAAAATCAATTAAAGCTAGTAATAAGGCTTTC-AAACGCATGGGT
1 TAAAATCAATTAGGAGGTTATAAAATTATTTAAAGCTAGTAATAAGGCTTTCGAAGC-CATGGGT
* * * * * ** *
5828 GACTATAAATGGACTTTTCTTGTCAATGGATTTCTTTTCCTTCACATTTCCCAAGACAGACACTC
65 GACTATAAATGGACTTTTTTTATCAATGGA-ATCTTTTTCTTCACATTTCCTAAGGTAGACATTC
* * * **
5893 AATTATTT-TCT-TTTTAACCAAAAATATAAAAAAAGTCATTTTAAAATCAATTACGAGATTATA
129 AATT-TTTATCTGTTTTAACAAAAAACATAAAAAAATTCAACTTAAAATCAATTACGAGATTAT-
* * * * *
5956 AAAACATTTAAAGCAAGTAATAAGGCTTTTAAAGGCGTGAGTGACTATAAATGGACTTTTTCATG
192 AAAATATTTAAAGCAAGTAATAAGGCTCTCAAAGGCATGAGTGACTATAAATGGAC-TTTTCTTG
* * * * *
6021 CCAATGAATATCTTTTCCTTCTCGTTTCTTGAGGTAGGCATTCAATTGTAATATATTTTAATAAA
256 CCAATGGATATCTTTTCCTTCTCGTTTCTCGAGGTAGACATTCAATTATAATCTATTTTAATAAA
6086 AAATATAAAAACATTTAACT
321 AAATATAAAAACATTTAACT
* * * ** *
6106 TAAAATCAATTAGGAGGATATAAAATTATTTAAAGCGAGTAATAGGGCTTTCGAAGGAATAGGTG
1 TAAAATCAATTAGGAGGTTATAAAATTATTTAAAGCTAGTAATAAGGCTTTCGAAGCCATGGGTG
* * * * * *
6171 ACTATAAATGGACTATTTCTACCAAT-GAATTTCTTTCTCTTCACATTTCTTGAGGTAGACATTC
66 ACTATAAATGGACTTTTTTTATCAATGGAA--TCTTTTTCTTCACATTTCCTAAGGTAGACATTC
* * ** * **********
6235 AATTCTAATCTGTTTTATTAAAAAACAAAAAAAAATTCAACTTAAAATCAATTANNNNNNNNNNA
129 AATTTTTATCTGTTTTAACAAAAAACATAAAAAAATTCAACTTAAAATCAATTACGAGATTATAA
* * *
6300 AATCATTTAAAGCGAGTAATAAGGCTCTCGAAGTCAT-AGGTGACTATAAATGGACTTTTCTTGC
194 AAT-ATTTAAAGCAAGTAATAAGGCTCTCAAAGGCATGA-GTGACTATAAATGGACTTTTCTTGC
* * *
6364 CAATGGATATCTTTTCCTTCTCTTTTCTCGAGATAGACATTCAATTATAATCTATTTTAATACAA
257 CAATGGATATCTTTTCCTTCTCGTTTCTCGAGGTAGACATTCAATTATAATCTATTTTAATAAAA
* * *
6429 AATAGAAAAAAATTCAACT
322 AATATAAAAACATTTAACT
* *
6448 TACAATCAATTATGAGGTTATAAAATTATTTAAAGCTAGTAATAAGGCTTTCGAAGCCATGGGTG
1 TAAAATCAATTAGGAGGTTATAAAATTATTTAAAGCTAGTAATAAGGCTTTCGAAGCCATGGGTG
* **
6513 ACTATAAATAGACTTTTTTTATCAATGGTAATCTTTTTCTTCATGTTTCCTAAGGTAGACATTCA
66 ACTATAAATGGACTTTTTTTATCAATGG-AATCTTTTTCTTCACATTTCCTAAGGTAGACATTCA
* * * * * *
6578 ATTTTTATCTGTTTTAACAAAAAACGTAAAGAATTTCAACGTAAAATTAATTATGAGATTATAAA
130 ATTTTTATCTGTTTTAACAAAAAACATAAAAAAATTCAACTTAAAATCAATTACGAGATTATAAA
*
6643 GATATTTAAAGAAAGTAATAAGGCT
195 -ATATTTAAAGCAAGTAATAAGGCT
6668 TTTGNNNNNN
Statistics
Matches: 1449, Mismatches: 438, Indels: 86
0.73 0.22 0.04
Matches are distributed among these distances:
339 1 0.00
341 95 0.07
342 1241 0.86
343 108 0.07
344 4 0.00
ACGTcount: A:0.36, C:0.12, G:0.13, T:0.35
Consensus pattern (340 bp):
TAAAATCAATTAGGAGGTTATAAAATTATTTAAAGCTAGTAATAAGGCTTTCGAAGCCATGGGTG
ACTATAAATGGACTTTTTTTATCAATGGAATCTTTTTCTTCACATTTCCTAAGGTAGACATTCAA
TTTTTATCTGTTTTAACAAAAAACATAAAAAAATTCAACTTAAAATCAATTACGAGATTATAAAA
TATTTAAAGCAAGTAATAAGGCTCTCAAAGGCATGAGTGACTATAAATGGACTTTTCTTGCCAAT
GGATATCTTTTCCTTCTCGTTTCTCGAGGTAGACATTCAATTATAATCTATTTTAATAAAAAATA
TAAAAACATTTAACT
Found at i:8303 original size:172 final size:167
Alignment explanation
Indices: 7256--8482 Score: 771
Period size: 171 Copynumber: 7.2 Consensus size: 167
7246 NNNNNNNTTA
* * * * * *
7256 GAAGGCATGGATAACTATAAATGAACTTTTCTTGCTAATGGATATCTTTCTCTTCATGTTTCTTG
1 GAAGGCATGGGTGACTATAAATGGACTTTTCTTGC----CGATATCTTTTTCTTCATGTTTCTCG
* * *** *
7321 AGGCAGACATTCTATTATTATCTATTTTAA-CTAAAAACGT-AAAAAATTCTGCTTAAAGTCAAT
62 AGGCAGACATTCAATTATTATCTGTTTTAATC-AAAAACGTAAAAAAATTCAATTTAAAATCAAT
* * **
7384 TATGAGATTATAAAAATATTTAAAGTGATTAATAAGGCTTTT
126 TATGAGATTATAAAAACATTTAAAGCGAGGAATAAGGCTTTT
** ** * * * **
7426 GAAGGTGTGACTGACTATAAATGGACTTTTCCTGCGAATGAATATCTTTTTCTTCATGTTTTTTT
1 GAAGGCATGGGTGACTATAAATGGACTTTTCTTGC---CG-ATATCTTTTTCTTCATGTTTCTCG
* * * *
7491 AGGCAGACATTCAATTATTATTTG-TTTAA-CTAAAAACATAAAAAAATTCAATCTAAAATCAAN
62 AGGCAGACATTCAATTATTATCTGTTTTAATC-AAAAACGTAAAAAAATTCAATTTAAAATCAAT
********* * *
7554 NNNNNNNNNATAAAAACATTTAAAGCGAGTAATAAGGCTTTC
126 TATGAGATTATAAAAACATTTAAAGCGAGGAATAAGGCTTTT
* ** * * * * *
7596 GAAGGAATATGTGTCTATAAATGGACTTTTCTTGCCAATAGATATCTTTTTTTTAATGTCTCTCA
1 GAAGGCATGGGTGACTATAAATGGACTTTTCTTGCC----GATATCTTTTTCTTCATGTTTCTCG
* * * * * * ** * * * *
7661 AGGTAGATATTCAATTATAATCTATTTGAATAAAAAATTTAAAGAAATTTAACTCAAAATCAATT
62 AGGCAGACATTCAATTATTATCTGTTTTAATCAAAAACGTAAAAAAATTCAATTTAAAATCAATT
* * * * * * *
7726 AGGAGGTTATAAAATCATTTAAAGCTAGTAATACGGCTTTC
127 ATGAGATTATAAAAACATTTAAAGCGAGGAATAAGGCTTTT
* * * * * * * *
7767 AAACGCATGGGTGACTATAAGTGGACTTTTCTTGCCAATGGATTTCTTTTCCTTCACGTTTCCCA
1 GAAGGCATGGGTGACTATAAATGGACTTTTCTTGCC----GATATCTTTTTCTTCATGTTTCTCG
* * * * * *
7832 AGGCAGACACTCAATTATTATCTATTTTAAT-AAAAA-ATAAAAAAAATCAACTTAAAACCAATT
62 AGGCAGACATTCAATTATTATCTGTTTTAATCAAAAACGTAAAAAAATTCAATTTAAAATCAATT
* * * * * **
7895 ATGAGGTTATAAAATC-TTGTAAAGTGAGTACTAAGGCTTCC
127 ATGAGATTATAAAAACATT-TAAAGCGAGGAATAAGGCTTTT
* * * ******* * ** *
7936 GATGGCATGGGTGACTATACATAGACTTTNNNNNNNNNNGGATATATTTTTCTTCACATTTCTCA
1 GAAGGCATGGGTGACTATAAATGGACTTT----TCTTGCCGATATCTTTTTCTTCATGTTTCTCG
* * * * * **
8001 AGGCAGGCATTCAATTATTATCTGTTTTAGTGAAAAATGTAAAAACATTCAACCTAAAATCAATT
62 AGGCAGACATTCAATTATTATCTGTTTTAATCAAAAACGTAAAAAAATTCAATTTAAAATCAATT
* * * * *
8066 ATGAGATTATAAAAATATTTAAGGCGTGTAATAAGGCTTTC
127 ATGAGATTATAAAAACATTTAAAGCGAGGAATAAGGCTTTT
* * * ****** *
8107 AAAGGTATGGGTGATTATAAATGGACTTTTCTTGCCNNNNNNNNNNTTTTTCTTCATGTTTCCCG
1 GAAGGCATGGGTGACTATAAATGGACTTTTCTTGCC----GATATCTTTTTCTTCATGTTTCTCG
* * * * *
8172 AGGCAGACAGTCAATTATTATCTGTTTTAATTAAAAACATAAAAAAAATTCAATTTTAAATTAAT
62 AGGCAGACATTCAATTATTATCTGTTTTAATCAAAAACGT-AAAAAAATTCAATTTAAAATCAAT
8237 TATGAGATTATAAAAACATTTAAAGCGAGGAATATA-GCTTTT
126 TATGAGATTATAAAAACATTTAAAGCGAGGAATA-AGGCTTTT
* ****** *
8279 GAAGGCATGGGTAACTATAAATGGACTTTTNNNNNNNNNNGATATCTTTTTCTTCATGTTTCTTG
1 GAAGGCATGGGTGACTATAAATGGACTTTT----CTTGCCGATATCTTTTTCTTCATGTTTCTCG
* * * * *
8344 AGGCAAACATTCAGTTATTATCTATTTTAACCGAAAACGTAAAAAAATTCAATTTAAAATCAATT
62 AGGCAGACATTCAATTATTATCTGTTTTAATCAAAAACGTAAAAAAATTCAATTTAAAATCAATT
* *
8409 ATGAGATTAGAAAAACATTCAAAGC-AGGTAATAAGGCTTTT
127 ATGAGATTATAAAAACATTTAAAGCGAGG-AATAAGGCTTTT
* *
8450 GAAGTCATGGGTGACTATAAATGAACTTTTCTT
1 GAAGGCATGGGTGACTATAAATGGACTTTTCTT
8483 ACCAATGNNN
Statistics
Matches: 810, Mismatches: 219, Indels: 59
0.74 0.20 0.05
Matches are distributed among these distances:
168 2 0.00
169 139 0.17
170 195 0.24
171 342 0.42
172 131 0.16
173 1 0.00
ACGTcount: A:0.36, C:0.12, G:0.14, T:0.35
Consensus pattern (167 bp):
GAAGGCATGGGTGACTATAAATGGACTTTTCTTGCCGATATCTTTTTCTTCATGTTTCTCGAGGC
AGACATTCAATTATTATCTGTTTTAATCAAAAACGTAAAAAAATTCAATTTAAAATCAATTATGA
GATTATAAAAACATTTAAAGCGAGGAATAAGGCTTTT
Found at i:11576 original size:169 final size:169
Alignment explanation
Indices: 11194--11907 Score: 634
Period size: 171 Copynumber: 4.2 Consensus size: 169
11184 NNNNNNNNNN
* * *
11194 TATAAATGGACTTTTCTTGCCAATGGATATCTTTTTCTTCACGTCTCACAAAGTAGAAATTCAAT
1 TATAAATGGACTTTTCTTGCCAATGGATATCTTTTTCTTCACGTTTCACAAGGTAGACATTCAAT
* * * *
11259 TATAATCTATTTGAATAAAAAATGTAAAGAAATTTAACTTAAAATCAATTAAGAGGTTATAAAAT
66 TATTATCTATTTCAATAAAAAA-GTAAAAAAATTCAACTTAAAATCAATTAAGAGGTTATAAAAT
*
11324 CATTTAAAGCTAGTAATAT-A-GCTTTCGAACGCATGGGTGAC
130 CATTTAAAG-T-G-AATATAAGGCTTTCGAAGGCATGGGTGAC
* * *
11365 TATAAATGGACTTTTCTTGCCAATGGATTTCTTTTCCTTCACGTTTCCCAAGGTAGACATTCAAT
1 TATAAATGGACTTTTCTTGCCAATGGATATCTTTTTCTTCACGTTTCACAAGGTAGACATTCAAT
* * * * *
11430 TATTATCTATTTTATTAAAAAA-TAAAAAAAATCAACTTAAAACCAATTATGAGGTTATAAAATC
66 TATTATCTATTTCAATAAAAAAGTAAAAAAATTCAACTTAAAATCAATTAAGAGGTTATAAAATC
* * *
11494 ATGTAAAGTGAATACTAAGGCTTCCGATGGCATGGGTGAC
131 ATTTAAAGTGAATA-TAAGGCTTTCGAAGGCATGGGTGAC
* * * * * * * *
11534 TATACATAGACTTTTCTTACCAATGGATATATTTTTCTTCACGTTTCTCAAGGCAGGCAATCAAT
1 TATAAATGGACTTTTCTTGCCAATGGATATCTTTTTCTTCACGTTTCACAAGGTAGACATTCAAT
* * * * * *
11599 TATTATCTGTTTCAACAAAAAATGTAAAAACATTCAACCTAAAATCAATTACGAGATTATAAAAA
66 TATTATCTATTTCAATAAAAAA-GTAAAAAAATTCAACTTAAAATCAATTAAGAGGTTAT-AAAA
* * * *
11664 T-ATTTAAGGCGTGTA-ATAAGGCTTTCAAAGGTATGGGTGAC
129 TCATTTAA--AGTGAATATAAGGCTTTCGAAGGCATGGGTGAC
*************** * * * * *
11705 TATAAATGGACTTTTCTTGCCAATGNNNNNNNNNNNNNNNATGTTTCCCGAGGCAGACAGTCAAT
1 TATAAATGGACTTTTCTTGCCAATGGATATCTTTTTCTTCACGTTTCACAAGGTAGACATTCAAT
* * * * * * *
11770 TATTATCTGTTTTAATCAAAAACA-TAAAAGAATTCAATTTAAAATTAATTATGAGATTATAAAA
66 TATTATCTATTTCAAT-AAAAA-AGTAAAAAAATTCAACTTAAAATCAATTAAGAGGTTATAAAA
* * *
11834 ACATTTAAAGCGAGGAATATAA--CTTTTGAAGGCATGGGTGAC
129 TCATTTAAA--G-TGAATATAAGGCTTTCGAAGGCATGGGTGAC
*
11876 TATAAATGGACTTTTCTTGCTAATGGATATCT
1 TATAAATGGACTTTTCTTGCCAATGGATATCT
11908 NNNNNNNNNN
Statistics
Matches: 437, Mismatches: 91, Indels: 30
0.78 0.16 0.05
Matches are distributed among these distances:
166 4 0.01
167 2 0.00
168 2 0.00
169 135 0.31
170 4 0.01
171 268 0.61
172 13 0.03
173 9 0.02
ACGTcount: A:0.37, C:0.14, G:0.14, T:0.33
Consensus pattern (169 bp):
TATAAATGGACTTTTCTTGCCAATGGATATCTTTTTCTTCACGTTTCACAAGGTAGACATTCAAT
TATTATCTATTTCAATAAAAAAGTAAAAAAATTCAACTTAAAATCAATTAAGAGGTTATAAAATC
ATTTAAAGTGAATATAAGGCTTTCGAAGGCATGGGTGAC
Found at i:12944 original size:171 final size:169
Alignment explanation
Indices: 12660--12983 Score: 420
Period size: 171 Copynumber: 1.9 Consensus size: 169
12650 NNNTCAAGGC
* * * * *
12660 AGACATTCAATTATTATCTGTTTTAACTAAAACTGTAAAAAATTCAATTTAAAATCAATTATGAG
1 AGACATTCAATTATAATCTGTTTTAACTAAAAATATAAAAAACTCAACTTAAAATCAATTATGAG
* * * *
12725 TTTATAAAAACATTTAAGGCGAGTAATGAGGTTTTCAAAAGTATGGGTGCCTATAAATGGACTTT
66 TTTATAAAAACATTTAAAGAGAGTAATAAGGTTTT-AAAAGTATGGGTGACTATAAATGGACTTT
*
12790 TCTTAACAGTGGATATCTTTTTCCTCTCGTTTATCGAGAT
130 TCTTAACAATGGATATCTTTTTCCTCTCGTTTATCGAGAT
*
12830 AGACATTCAATTATAATCTGTTTT-ATTAAAAAATATAAAAAAACTCAACTTAAAATCAATTATG
1 AGACATTCAATTATAATCTGTTTTAACT-AAAAATAT-AAAAAACTCAACTTAAAATCAATTATG
* * * *
12894 AAG-TTATAAAATCATTTAAAGAGAGTAGTAAGGCTTTT-GAAGTCATGGGTGATTATAAATGGA
64 -AGTTTATAAAAACATTTAAAGAGAGTAATAAGG-TTTTAAAAGT-ATGGGTGACTATAAATGGA
**
12957 CTTTTCTTTCCAATGGATATCTTTTTC
126 CTTTTCTTAACAATGGATATCTTTTTC
12984 TTCATGTTTC
Statistics
Matches: 132, Mismatches: 17, Indels: 9
0.84 0.11 0.06
Matches are distributed among these distances:
169 2 0.02
170 33 0.25
171 91 0.69
172 6 0.05
ACGTcount: A:0.37, C:0.11, G:0.14, T:0.37
Consensus pattern (169 bp):
AGACATTCAATTATAATCTGTTTTAACTAAAAATATAAAAAACTCAACTTAAAATCAATTATGAG
TTTATAAAAACATTTAAAGAGAGTAATAAGGTTTTAAAAGTATGGGTGACTATAAATGGACTTTT
CTTAACAATGGATATCTTTTTCCTCTCGTTTATCGAGAT
Found at i:13025 original size:171 final size:171
Alignment explanation
Indices: 12666--13065 Score: 411
Period size: 171 Copynumber: 2.3 Consensus size: 171
12656 AGGCAGACAT
* * *
12666 TCAATTATTATCTGTTTTAACT--AAAAC-TGTAAAAAATTCAATTTAAAATCAATTATG-AGTT
1 TCAATTATAATCTGTTTTAA-TAAAAAACAT-AAAAAAATTCAACTTAAAATCAATTATGAAGTT
* * * *
12727 TATAAAAACATTTAAGGCGAGTAATGAGGTTTTCAAAAGTATGGGTGCCTATAAATGGACTTTTC
64 TATAAAAACATTTAAAGAGAGTAATAAGGTTTT-AAAAGTATGGGTGACTATAAATGGACTTTTC
* * *
12792 TTAACAGTGGATATCTTTTTCCTCTCGTTTATCGAGATAGACAT
128 TTAACAATGGATATCTTTTTCCTCTCGTTTATCGAGATAAACAA
* * *
12836 TCAATTATAATCTGTTTTATTAAAAAATATAAAAAAACTCAACTTAAAATCAATTATGAAG-TTA
1 TCAATTATAATCTGTTTTAATAAAAAACATAAAAAAATTCAACTTAAAATCAATTATGAAGTTTA
* * * *
12900 TAAAATCATTTAAAGAGAGTAGTAAGGCTTTT-GAAGTCATGGGTGATTATAAATGGACTTTTCT
66 TAAAAACATTTAAAGAGAGTAATAAGG-TTTTAAAAGT-ATGGGTGACTATAAATGGACTTTTCT
** * * *
12964 TTCCAATGGATATCTTTTTCTTCAT-GTTT-CCTGAGGTAAACAA
129 TAACAATGGATATCTTTTTCCTC-TCGTTTATC-GAGATAAACAA
* * * * * * * *
13007 TCAATTGTTATTTGTTTTAATCAAAAACATAAAAATATTTAAGTTGAAATCAATTATGA
1 TCAATTATAATCTGTTTTAATAAAAAACATAAAAAAATTCAACTTAAAATCAATTATGA
13066 NNNNNNNNNN
Statistics
Matches: 189, Mismatches: 33, Indels: 15
0.80 0.14 0.06
Matches are distributed among these distances:
169 1 0.01
170 23 0.12
171 157 0.83
172 8 0.04
ACGTcount: A:0.38, C:0.11, G:0.13, T:0.38
Consensus pattern (171 bp):
TCAATTATAATCTGTTTTAATAAAAAACATAAAAAAATTCAACTTAAAATCAATTATGAAGTTTA
TAAAAACATTTAAAGAGAGTAATAAGGTTTTAAAAGTATGGGTGACTATAAATGGACTTTTCTTA
ACAATGGATATCTTTTTCCTCTCGTTTATCGAGATAAACAA
Found at i:13825 original size:172 final size:171
Alignment explanation
Indices: 13247--13990 Score: 646
Period size: 170 Copynumber: 4.4 Consensus size: 171
13237 NNNATTTAAT
* * *
13247 TTAAAATCAATTATGAGATTATAAAA-CATTTAAAGCAAGTAATAAGG-TTTTCGAAGACATGAG
1 TTAAAATCAATTATGAGATTATAAAATCATTTAAAGCTAGTAATAAGGCTTTT-GAAGCCATGGG
* * *
13310 TGACTATAAATGGACTTTTCTTAG-CAATGCATATCTTTTTCTTCTTGTTTCTCGAAGTAGACAT
65 TGACTATAAATGGACTTTTCTT-GTCAATGGATATCTTTTTCTTCTTGTTTCTCGAGGAAGACAT
* * ********************
13374 TTAATTATAATCT-GTTTAATNNNNNNNNNNNNNNNNNNNNAC
129 TCAATTATAATCTATTTTAATAAAAAACATAAAAAAATTCAAC
* * * * * *
13416 TTAAAATCCATTAGGGGGTTATAAAATCATTTAAAGCT-GTTAATAAGGCTTTTGAAGGCATGAG
1 TTAAAATCAATTATGAGATTATAAAATCATTTAAAGCTAG-TAATAAGGCTTTTGAAGCCATGGG
* *
13480 TGACTATAAATGTACTTTTCTTGTCAATGGATAT-TTTTTCTT-TATGTTTCTGGAGGAAGACAT
65 TGACTATAAATGGACTTTTCTTGTCAATGGATATCTTTTTCTTCT-TGTTTCTCGAGGAAGACAT
* * *
13543 TCAATTATAATTTATTTTAATAAAAAACACAAAAAAATTAAAC
129 TCAATTATAATCTATTTTAATAAAAAACATAAAAAAATTCAAC
* * **********
13586 TTAAAATCAATTATGAGATTATAAAGTCATTTAAAGCGAGTAATAAGGCTTNNNNNNNNNNGGGT
1 TTAAAATCAATTATGAGATTATAAAATCATTTAAAGCTAGTAATAAGGCTTTTGAAGCCATGGGT
* * *
13651 GACTATAAATGGACTTTTCTTGCCAATGGATATCTTTTTCTTCTTGTTTCTCAAGGTAGACATTC
66 GACTATAAATGGACTTTTCTTGTCAATGGATATCTTTTTCTTCTTGTTTCTCGAGGAAGACATTC
* *
13716 AATAATAATCTATTTTAATAAAAAAATATAAAAAAATTCAAC
131 AATTATAATCTATTTTAAT-AAAAAACATAAAAAAATTCAAC
* * * *
13758 TTACAATCAATTATGAGGTTATAAAA-CTATTAAAAGCTAGTAATAAGTCTTTTGAAGCCATGGG
1 TTAAAATCAATTATGAGATTATAAAATC-ATTTAAAGCTAGTAATAAGGCTTTTGAAGCCATGGG
* * * *
13822 TGACTATAAATAGACTTTTCTTATCAATGG-TAATCTTTTTCTTCATGTTTC-CTGAGGCAGACA
65 TGACTATAAATGGACTTTTCTTGTCAATGGAT-ATCTTTTTCTTCTTGTTTCTC-GAGGAAGACA
* * * * * * * *
13885 TTTAATTCTTATCTGTTTTAACAAAAAGCATAAAGAATTTCAAC
128 TTCAATTATAATCTATTTTAATAAAAAACATAAAAAAATTCAAC
* ** *
13929 GTAAAATCAATTATGAGATTATAAAGAT-ATTTAAAGAAAGTAATAAGGCTTTTGAAGTCATG
1 TTAAAATCAATTATGAGATTATAAA-ATCATTTAAAGCTAGTAATAAGGCTTTTGAAGCCATG
13991 NNNNNNNNNN
Statistics
Matches: 459, Mismatches: 101, Indels: 28
0.78 0.17 0.05
Matches are distributed among these distances:
168 1 0.00
169 59 0.13
170 143 0.31
171 120 0.26
172 136 0.30
ACGTcount: A:0.36, C:0.11, G:0.13, T:0.36
Consensus pattern (171 bp):
TTAAAATCAATTATGAGATTATAAAATCATTTAAAGCTAGTAATAAGGCTTTTGAAGCCATGGGT
GACTATAAATGGACTTTTCTTGTCAATGGATATCTTTTTCTTCTTGTTTCTCGAGGAAGACATTC
AATTATAATCTATTTTAATAAAAAACATAAAAAAATTCAAC
Found at i:14598 original size:171 final size:170
Alignment explanation
Indices: 14243--15506 Score: 1247
Period size: 171 Copynumber: 7.4 Consensus size: 170
14233 NNNNNNNCTT
* * * * *
14243 TAAATGGACTTTTCTTGCTAATGGATATCTTTTTCTTCATGTGTCTAGAGGTAGATATTCAATTA
1 TAAATGGACTTTTCTTGCCAATGGATATCTTTTTCTTCATGTTTCTCGAGGCAGACATTCAATTA
* ** * * * *
14308 TAATCTATTTTAATGAAAAATATAAAAAAAATTAAACTTAAAATCAATTAGCA-AGTAATAAAAA
66 TTATCTATTTTAACAAAAAACAT-AAAAAAATTCAACTTAAAATCAATTAGGAGA-TTATAAAAA
* * * * *
14372 TATTTAAAGAGAGTAATAAGCCTTTTC-AAGTCATGGGTGACAA
129 CATTTAAAGCGAGTAATAAGGC-TTTCGAAGGCAT-GGTGACTA
* * * * * *
14415 TAAATGGACTTTTCTGGCTAATGGATATCTTTTTCTTCATGTTTCTTGAGGCAAACAATCAATTG
1 TAAATGGACTTTTCTTGCCAATGGATATCTTTTTCTTCATGTTTCTCGAGGCAGACATTCAATTA
* * * * * * *
14480 CTATCTGTTTTAACCAAAAACATAAAAAAATTTAATTTGAAATCAATTAGGAGATTATAGAAACA
66 TTATCTATTTTAACAAAAAACATAAAAAAATTCAACTTAAAATCAATTAGGAGATTATAAAAACA
* * *
14545 TTTAAAGCGAGTAATATGGCTTTAGAAGGCATGGATAACTA
131 TTTAAAGCGAGTAATAAGGCTTTCGAAGGCATGG-TGACTA
* * *
14586 TAAATGGACTTTTCTTGCTAATGGATATCTTTTTTTTCATGTTTCTTGAGGCAGACATTCAATTA
1 TAAATGGACTTTTCTTGCCAATGGATATCTTTTTCTTCATGTTTCTCGAGGCAGACATTCAATTA
* * * * * * * *
14651 TTATTTGTTTTAACCAAAAACGT-AAAAAATTCTACTTAAAGTCAATTATGAGATTATAAAAATA
66 TTATCTATTTTAACAAAAAACATAAAAAAATTCAACTTAAAATCAATTAGGAGATTATAAAAACA
* * **
14715 TTTAAAGCAAGTAATAAGGCTTTTGAAGGTGTGGGTGACTA
131 TTTAAAGCGAGTAATAAGGCTTTCGAAGGCAT-GGTGACTA
* * * *
14756 TAAATGGACTTTTCTTGCGAATGAATATCTTTTTCTTCATGTTTTTTGAGGCAGACATTCAATTA
1 TAAATGGACTTTTCTTGCCAATGGATATCTTTTTCTTCATGTTTCTCGAGGCAGACATTCAATTA
* *
14821 TTATCTA-TTTAACTAAAAACAT-AAAAAATTCAA-TCTAAAATCAATTATGAGATTATAAAAAC
66 TTATCTATTTTAACAAAAAACATAAAAAAATTCAACT-TAAAATCAATTAGGAGATTATAAAAAC
* *
14883 ATTTAGAGCGAGTAATAAGGCTTTCGAAGGCATATGTGACTA
130 ATTTAAAGCGAGTAATAAGGCTTTCGAAGGCAT-GGTGACTA
* * * * * *
14925 TAAATGGACTTTTCTTGCCAATGGATATCTTTTTCTTCACGTCTCACAAAGTC-GAAATTCAATT
1 TAAATGGACTTTTCTTGCCAATGGATATCTTTTTCTTCATGTTTCTC-GAGGCAGACATTCAATT
* * * * ** * * * *
14989 ATAATTTATTTGAATAAAAAATGTAAAGAAATTTAACTTAAAATCAATTAGGAGGTTATAAAATC
65 ATTATCTATTTTAACAAAAAACATAAAAAAATTCAACTTAAAATCAATTAGGAGATTATAAAAAC
* * * *
15054 ATTTAAAGCTAGTAATACGGCTTTCGAACGCATCGGTGACTT
130 ATTTAAAGCGAGTAATAAGGCTTTCGAAGGCAT-GGTGACTA
* * * * * *
15096 TAAATGGACTTTTCTTGCCAATGGATTTC-TTTTCTTTCACGTTTCCCAAGGTAGACACTCAATT
1 TAAATGGACTTTTCTTGCCAATGGATATCTTTTTC-TTCATGTTTCTCGAGGCAGACATTCAATT
* * * * *
15160 ATTATCTATTTTAA-TAAAAA-ATAAAAAAAATCAACTTAAAATCAATTATGAGGTTATAAAATC
65 ATTATCTATTTTAACAAAAAACATAAAAAAATTCAACTTAAAATCAATTAGGAGATTATAAAAAC
* * * * * * *
15223 ATGTAAAGTGAGTACTAAGGCTTCCCATGGTATAGGTGACTA
130 ATTTAAAGCGAGTAATAAGGCTTTCGAAGGCAT-GGTGACTA
* * * ** * *
15265 TACAT--ACTCTTGTCTTACCAATGGATATATTTTTCTTCACATTTCTCAAGGCAGGCATTCAAT
1 TAAATGGACT-TT-TCTTGCCAATGGATATCTTTTTCTTCATGTTTCTCGAGGCAGACATTCAAT
* * ** * * * *
15328 TATTATCTGTTTGAACAAAAAATGTAAAAATATTCAACCTAAAATCAATTACGATATTATAAAAA
64 TATTATCTATTTTAACAAAAAACATAAAAAAATTCAACTTAAAATCAATTAGGAGATTATAAAAA
* * * * **
15393 TATTTAAGGCGTGTAATAAGGCTTTCAAAGTTATGAGTGACTA
129 CATTTAAAGCGAGTAATAAGGCTTTCGAAGGCATG-GTGACTA
* * *
15436 TAAATGGACTTTTCTTTCCAATGGATATCTTTTTCTTCATGTTTCCCGAGGCAGACAGTCAATTA
1 TAAATGGACTTTTCTTGCCAATGGATATCTTTTTCTTCATGTTTCTCGAGGCAGACATTCAATTA
15501 TTATCT
66 TTATCT
15507 NNNNNNNNNN
Statistics
Matches: 909, Mismatches: 164, Indels: 39
0.82 0.15 0.04
Matches are distributed among these distances:
167 3 0.00
168 3 0.00
169 261 0.29
170 173 0.19
171 388 0.43
172 78 0.09
173 3 0.00
ACGTcount: A:0.37, C:0.13, G:0.14, T:0.36
Consensus pattern (170 bp):
TAAATGGACTTTTCTTGCCAATGGATATCTTTTTCTTCATGTTTCTCGAGGCAGACATTCAATTA
TTATCTATTTTAACAAAAAACATAAAAAAATTCAACTTAAAATCAATTAGGAGATTATAAAAACA
TTTAAAGCGAGTAATAAGGCTTTCGAAGGCATGGTGACTA
Found at i:15219 original size:340 final size:339
Alignment explanation
Indices: 14243--15506 Score: 1318
Period size: 340 Copynumber: 3.7 Consensus size: 339
14233 NNNNNNNCTT
* * * * * *
14243 TAAATGGACTTTTCTTGCTAATGGATATCTTTTTCTTCATGTGTCTA-GAGGTAGATATTCAATT
1 TAAATGGACTTTTCTTGCCAATGGATATCTTTTTCTTCACGTTTC-ACAAGGCAGACATTCAATT
* * ** * * *
14307 ATAATCTATTTTAATGAAAAATATAAAAAAAATTAAACTTAAAATCAATTAGCA-AGTAATAAAA
65 ATAATCTATTTGAA-CAAAAA-ATGTAAAAAATTTAACTTAAAATCAATTAGGAGA-TTATAAAA
** * * * *
14371 ATATTTAAAGAGAGTAATAAGCCTTTTCAAGTCATGGGTGACAATAAATGGACTTTTCTGGCTAA
127 ATATTTAAAGCTAGTAATAAGGC-TTTCAAGTCATGGGTGACTATAAATGGACTTTTCTTGCCAA
** * ** * *
14436 TGGATATCTTTTTCTTCATGTTTCTTGAGGCAAACAATCAATTGCTATCTGTTTTAACCAAAAAC
191 TGGATATCTTTTTCTTCATGTTTCCCGAGGCAGACAATCAATTATTATCTATTTTAACTAAAAAC
* * * * *
14501 ATAAAAAAATTTAATTTGAAATCAATTAGGAGATTATAGAAACATTTAAAGCGAGTAATATGGCT
256 ATAAAAAAATTCAA-TTAAAATCAATTATGAGATTATAAAAACATTTAAAGCGAGTAATAAGGCT
* *
14566 TTAGAAGGCAT-GGATAACTA
320 TTCGAAGGCATAGG-TGACTA
* * * ***
14586 TAAATGGACTTTTCTTGCTAATGGATATCTTTTTTTTCATGTTTCTTGAGGCAGACATTCAATTA
1 TAAATGGACTTTTCTTGCCAATGGATATCTTTTTCTTCACGTTTCACAAGGCAGACATTCAATTA
* * * * * * * *
14651 TTATTTGTTTTAACCAAAAACGTAAAAAATTCT-ACTTAAAGTCAATTATGAGATTATAAAAATA
66 TAATCTATTTGAACAAAAAATGTAAAAAATT-TAACTTAAAATCAATTAGGAGATTATAAAAATA
* * * *
14715 TTTAAAGCAAGTAATAAGGCTTTTGAAGGT-GTGGGTGACTATAAATGGACTTTTCTTGCGAATG
130 TTTAAAGCTAGTAATAAGGC-TTTCAA-GTCATGGGTGACTATAAATGGACTTTTCTTGCCAATG
* *** *
14779 AATATCTTTTTCTTCATGTTTTTTGAGGCAGACATTCAATTATTATCTA-TTTAACTAAAAACAT
193 GATATCTTTTTCTTCATGTTTCCCGAGGCAGACAATCAATTATTATCTATTTTAACTAAAAACAT
*
14843 -AAAAAATTCAATCTAAAATCAATTATGAGATTATAAAAACATTTAGAGCGAGTAATAAGGCTTT
258 AAAAAAATTCAAT-TAAAATCAATTATGAGATTATAAAAACATTTAAAGCGAGTAATAAGGCTTT
*
14907 CGAAGGCATATGTGACTA
322 CGAAGGCATAGGTGACTA
* * *
14925 TAAATGGACTTTTCTTGCCAATGGATATCTTTTTCTTCACGTCTCACAAAGTC-GAAATTCAATT
1 TAAATGGACTTTTCTTGCCAATGGATATCTTTTTCTTCACGTTTCAC-AAGGCAGACATTCAATT
* * *
14989 ATAATTTATTTGAATAAAAAATGTAAAGAAATTTAACTTAAAATCAATTAGGAGGTTAT-AAAAT
65 ATAATCTATTTGAACAAAAAATGTAAA-AAATTTAACTTAAAATCAATTAGGAGATTATAAAAAT
* * *
15053 CATTTAAAGCTAGTAATACGGCTTTCGAACG-CATCGGTGACTTTAAATGGACTTTTCTTGCCAA
129 -ATTTAAAGCTAGTAATAAGGCTTTC-AA-GTCATGGGTGACTATAAATGGACTTTTCTTGCCAA
* * * * *
15117 TGGATTTC-TTTTCTTTCACGTTTCCCAAGGTAGACACTCAATTATTATCTATTTTAA-TAAAAA
191 TGGATATCTTTTTC-TTCATGTTTCCCGAGGCAGACAATCAATTATTATCTATTTTAACTAAAAA
* * * * * *
15180 -ATAAAAAAAATCAACTTAAAATCAATTATGAGGTTATAAAATCATGTAAAGTGAGTACTAAGGC
255 CATAAAAAAATTCAA-TTAAAATCAATTATGAGATTATAAAAACATTTAAAGCGAGTAATAAGGC
* * * *
15244 TTCCCATGGTATAGGTGACTA
319 TTTCGAAGGCATAGGTGACTA
* * * * * *
15265 TACAT--ACTCTTGTCTTACCAATGGATATATTTTTCTTCACATTTCTCAAGGCAGGCATTCAAT
1 TAAATGGACT-TT-TCTTGCCAATGGATATCTTTTTCTTCACGTTTCACAAGGCAGACATTCAAT
* * * * * *
15328 TATTATCTGTTTGAACAAAAAATGTAAAAATATTCAACCTAAAATCAATTACGATATTATAAAAA
64 TATAATCTATTTGAACAAAAAATGTAAAAA-ATTTAACTTAAAATCAATTAGGAGATTATAAAAA
* * * *
15393 TATTTAAGGCGT-GTAATAAGGCTTTCAAAGTTATGAGTGACTATAAATGGACTTTTCTTTCCAA
128 TATTTAAAGC-TAGTAATAAGGCTTTC-AAGTCATGGGTGACTATAAATGGACTTTTCTTGCCAA
*
15457 TGGATATCTTTTTCTTCATGTTTCCCGAGGCAGACAGTCAATTATTATCT
191 TGGATATCTTTTTCTTCATGTTTCCCGAGGCAGACAATCAATTATTATCT
15507 NNNNNNNNNN
Statistics
Matches: 776, Mismatches: 121, Indels: 51
0.82 0.13 0.05
Matches are distributed among these distances:
338 4 0.01
339 166 0.21
340 384 0.49
341 146 0.19
342 7 0.01
343 69 0.09
ACGTcount: A:0.37, C:0.13, G:0.14, T:0.36
Consensus pattern (339 bp):
TAAATGGACTTTTCTTGCCAATGGATATCTTTTTCTTCACGTTTCACAAGGCAGACATTCAATTA
TAATCTATTTGAACAAAAAATGTAAAAAATTTAACTTAAAATCAATTAGGAGATTATAAAAATAT
TTAAAGCTAGTAATAAGGCTTTCAAGTCATGGGTGACTATAAATGGACTTTTCTTGCCAATGGAT
ATCTTTTTCTTCATGTTTCCCGAGGCAGACAATCAATTATTATCTATTTTAACTAAAAACATAAA
AAAATTCAATTAAAATCAATTATGAGATTATAAAAACATTTAAAGCGAGTAATAAGGCTTTCGAA
GGCATAGGTGACTA
Found at i:16091 original size:172 final size:171
Alignment explanation
Indices: 15741--16100 Score: 389
Period size: 172 Copynumber: 2.1 Consensus size: 171
15731 NNNNNNNNNN
* * * ** *
15741 ATATCTTTTTCTTCATGTTTCTTGAGGCAGACATTCAATTATTATCTATTTTAATCGAAAACGTA
1 ATATCTTTTTCTTCATGTTTCTTGAGACAGACATTCAATTATAAACTATTTTAATAAAAAACATA
* ** * *
15806 AAAAGATTCAATTTAAAATCAATTATGAGATTAGAAAAACATTCAAAGCGAGTAATAAGGCTTTT
66 AAAAAATTCAACATAAAATCAATTATGAGATTAGAAAAACATTCAAAGCAAGTAATAAGGCTTTC
* * ********** *
15871 GAAGTCATGGGTGACNNNNNNNNNNCTTTTCTTGCCAATGG
131 GAAGTCATGGATAACTACACATGGACTTTTCTTACCAATGG
* * *
15912 ATATCTTTTTCTTCATGTTTTTTGAGATAGACATTCAATTATAAACTATTTTAATAAAAAAATAT
1 ATATCTTTTTCTTCATGTTTCTTGAGACAGACATTCAATTATAAACTATTTTAAT-AAAAAACAT
* * *
15977 AAAAAAATTCAACATAAAATTAATTATGAGATTA-AAAAACTATTTAAATCAAGTAATAAGGCTT
65 AAAAAAATTCAACATAAAATCAATTATGAGATTAGAAAAAC-ATTCAAAGCAAGTAATAAGGCTT
* *
16041 TCGCAGTCATGGATAACTACACATGGACTTTTCTTATCAATGG
129 TCGAAGTCATGGATAACTACACATGGACTTTTCTTACCAATGG
* *
16084 GTATCTTTTCCTTCATG
1 ATATCTTTTTCTTCATG
16101 ATTCCCAAGG
Statistics
Matches: 153, Mismatches: 34, Indels: 3
0.81 0.18 0.02
Matches are distributed among these distances:
171 56 0.37
172 97 0.63
ACGTcount: A:0.36, C:0.13, G:0.12, T:0.36
Consensus pattern (171 bp):
ATATCTTTTTCTTCATGTTTCTTGAGACAGACATTCAATTATAAACTATTTTAATAAAAAACATA
AAAAAATTCAACATAAAATCAATTATGAGATTAGAAAAACATTCAAAGCAAGTAATAAGGCTTTC
GAAGTCATGGATAACTACACATGGACTTTTCTTACCAATGG
Done.