Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018401206.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_4354.1, 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: 3638
ACGTcount: A:0.36, C:0.12, G:0.13, T:0.35
Warning! 144 characters in sequence are not A, C, G, or T
Found at i:487 original size:171 final size:168
Alignment explanation
Indices: 1--692 Score: 459
Period size: 171 Copynumber: 4.0 Consensus size: 168
* * * *
1 TAAGGCTTTTGAAGGAATGAGTGATTATAAATGGACTTTTCTTGCTAATGAATGCT-TTCTTCTT
1 TAAGGCTTTTGAAGGAATAAGTGACTATAAATGGACTTTTCTTGCCAATGAAT-CTCTTATTCTT
* * * * ******** *
65 CATGTTTCTCAATGTAGACATTCAATTATAGTCTGTNNNNNNNNNNAATA-TAAAAAAA-ATCAA
65 CACGTTTC-CAAGGGAGACATTCAATTATA-TCTAT--TTTAACAAAAAACTAAAAAAATA-CAA
* * *
128 CTTAAAATCAATTATTAGACTATAAAA-TCATTTAAAATGAGTAA
125 CTTAAAATCAATTATGAGATTATAAAACT-ATTTAAAGTGAGTAA
********** * * *
172 TAAGGCTTTTGAAGNNNNNNNNNNCAATAAATAGACTTTTCTTGTCAATGAATGCT-TTATTCTT
1 TAAGGCTTTTGAAGGAATAAGTGACTATAAATGGACTTTTCTTGCCAATGAAT-CTCTTATTCTT
* * * *** *
236 CATGTTTCCTAGGGTAGGCATTCAATTATCATCTATTTT-ACCCTAAACTACAACAAAATTCAAC
65 CACGTTTCCAAGGG-AGACATTCAATTAT-ATCTATTTTAACAAAAAACTA-AA-AAAATACAAC
* * *
300 TCAAAATTAATTATGAGAGTATAAAACTATTTAAAGTGAGTAA
126 TTAAAATCAATTATGAGATTATAAAACTATTTAAAGTGAGTAA
* ***********
343 TAAGTCTTTNNNNNNNNNNGGTGACTATAAATGGACTTTTCTTGCCAATGAATCTCTTATTCTTC
1 TAAGGCTTTTGAAGGAATAAGTGACTATAAATGGACTTTTCTTGCCAATGAATCTCTTATTCTTC
* * *
408 ACGTTTCTCAAGGGAGACATTCAATTATAGTCTGTTTTAACAAAAAACGTAAAACAATGCAACTT
66 ACGTTTC-CAAGGGAGACATTCAATTATA-TCTATTTTAACAAAAAAC-TAAAAAAATACAACTT
* *
473 AAAATCAGTTATGAGATTATAAAA-TAATTTAAAGTGAATAA
128 AAAATCAATTATGAGATTATAAAACT-ATTTAAAGTGAGTAA
* ** *
514 TATGGCTTTTGAAGGAATAAGTGACTATAAATAGG-CTTTTCTT-CTCAATGAATAGCTTTTTCT
1 TAAGGCTTTTGAAGGAATAAGTGACTATAAAT-GGACTTTTCTTGC-CAATGAATCTCTTATTCT
* * * * *
577 ACACGTTTCCCAAGGTAAACATTCAATTATAATCTATTTTAATGAAAAATA-TAAAAAAATTAAA
64 TCACGTTT-CCAAGGGAGACATTCAATTAT-ATCTATTTTAA-CAAAAA-ACTAAAAAAA-TACA
* * *
641 ACTTAAAACCAATTATGAGATTATAAAACCATTTAAAGCGAGTAA
124 ACTTAAAATCAATTATGAGATTATAAAACTATTTAAAGTGAGTAA
686 TAAGGCT
1 TAAGGCT
693 NNNNNNNNNN
Statistics
Matches: 406, Mismatches: 94, Indels: 41
0.75 0.17 0.08
Matches are distributed among these distances:
168 2 0.00
169 2 0.00
170 10 0.02
171 318 0.78
172 71 0.17
173 3 0.01
ACGTcount: A:0.37, C:0.13, G:0.12, T:0.34
Consensus pattern (168 bp):
TAAGGCTTTTGAAGGAATAAGTGACTATAAATGGACTTTTCTTGCCAATGAATCTCTTATTCTTC
ACGTTTCCAAGGGAGACATTCAATTATATCTATTTTAACAAAAAACTAAAAAAATACAACTTAAA
ATCAATTATGAGATTATAAAACTATTTAAAGTGAGTAA
Found at i:716 original size:172 final size:160
Alignment explanation
Indices: 533--845 Score: 378
Period size: 172 Copynumber: 1.9 Consensus size: 160
523 TGAAGGAATA
** * *
533 AGTGACTATAAATAGGCTTTTCTTCTCAATGAAT-AGCTTTTTCTACACGTTTCCCAAGGTAAAC
1 AGTGACTATAAATAAACTTTTCTTCTCAATGAATGA-CTTTTTCTACACGTTTCCCAAAGCAAAC
597 ATTCAATTATA-ATCTATTTTAATGAAAAATATAAAAAAATTAAAACTTAAAACCAATTATGAGA
65 ATTCAATTATAGA-CTATTTTAATGAAAAATATAAAAAAATT-AAACTTAAAACCAATTATGAGA
661 TTATAAAACCATTTAAAGCGAGTAATAAGGCTNNNNNNNNNNNG
128 TTATAAAACCATTTAAAGCGAGTAATAAGGCT-----------G
* *
705 AGTGACTATAAATAAACTTTTCTTCTCAATGAATGACTTTTTTTACACGTTTCCCAAAGCAGACA
1 AGTGACTATAAATAAACTTTTCTTCTCAATGAATGACTTTTTCTACACGTTTCCCAAAGCAAACA
* * * * * *
770 TTCAGTTATAGACTATTTTATTGAAAAATGTAAAAAAATTCAACTTATAATCAATTATGAGATTA
66 TTCAATTATAGACTATTTTAATGAAAAATATAAAAAAATTAAACTTAAAACCAATTATGAGATTA
835 TAAAACCATTT
131 TAAAACCATTT
846 NNNNNNNNNN
Statistics
Matches: 127, Mismatches: 12, Indels: 5
0.88 0.08 0.03
Matches are distributed among these distances:
171 33 0.26
172 92 0.72
173 2 0.02
ACGTcount: A:0.40, C:0.13, G:0.10, T:0.34
Consensus pattern (160 bp):
AGTGACTATAAATAAACTTTTCTTCTCAATGAATGACTTTTTCTACACGTTTCCCAAAGCAAACA
TTCAATTATAGACTATTTTAATGAAAAATATAAAAAAATTAAACTTAAAACCAATTATGAGATTA
TAAAACCATTTAAAGCGAGTAATAAGGCTG
Found at i:816 original size:343 final size:331
Alignment explanation
Indices: 363--1021 Score: 653
Period size: 343 Copynumber: 2.0 Consensus size: 331
353 NNNNNNNNNG
** * * * *
363 GTGACTATAAATGGACTTTTCTTGCCAATGAATCTCTTATTCTTCACGTTTCTCAAGGGAGACAT
1 GTGACTATAAATAAACTTTTCTTGCCAATGAATCACTTATTCTTCACGTTTCCCAAAGCAGACAT
* * * *
428 TCAATTATAGTCTGTTTTAACAAAAAACGTAAAACAATGCAACTTAAAATCAGTTATGAGATTAT
66 TCAATTATAGACTATTTTAACAAAAAACGTAAAAAAATGCAACTTAAAATCAATTATGAGATTAT
* * *
493 AAAATAATTT-AAAGTGAATAATATGGCTTTTGAAGGAATAAGTGACTATAAATAGG-CTTTTCT
131 AAAACAATTTAAAAGTGAATAATA-GGCTTTTGAAGAAATAAGTGACTATAAAT-GGACTTTTCC
* * *
556 TCTCAATGAAT-AGCTTTTTCTACACGTTTCCCAAGGTAAACATTCAATTATAATCTATTTTAAT
194 TCTCAATGAATGA-CATTTTCTACACGTTTCCCAAGGCAAACATTCAATTATAATATATTTTAAT
*
620 GAAAAATATAAAAAAATTAAAACTTAAAACCAATTATGAGATTATAAAACCATTTAAAGCGAGTA
258 GAAAAATAT-AAAAAATTAAAACTTAAAACCAATTATAAGATTATAAAACCATTTAAAGCGAGTA
685 ATAAGGCTNNNNNNNNNNNGA
322 ATAAGGCT-----------GA
* *
706 GTGACTATAAATAAACTTTTCTT-CTCAATGAATGACTT-TTTTTACACGTTTCCCAAAGCAGAC
1 GTGACTATAAATAAACTTTTCTTGC-CAATGAATCACTTATTCTT-CACGTTTCCCAAAGCAGAC
* *** * * *
769 ATTCAGTTATAGACTATTTTATTGAAAAATGTAAAAAAATTCAACTTATAATCAATTATGAGATT
64 ATTCAATTATAGACTATTTTAACAAAAAACGTAAAAAAATGCAACTTAAAATCAATTATGAGATT
* ************* *
834 ATAAAACCATTTNNNNNNNNNNNNNAGGCTTTTGAAGAAATGAGTGACTATAAATGGACTTTTCC
129 ATAAAACAATTTAAAAGTGAATAATAGGCTTTTGAAGAAATAAGTGACTATAAATGGACTTTTCC
* * * * * * *
899 TCTCAATGAATGACATTTTCTATACGTTTCTCGAGGCAAGCATTTAATTATAGTATGTTTTAATG
194 TCTCAATGAATGACATTTTCTACACGTTTCCCAAGGCAAACATTCAATTATAATATATTTTAATG
* ** **
964 AAAAATATTAAAAATTTTAACTTAAATTCAATTATAAGATTATAAAACCATTTAAAGC
259 AAAAATATAAAAAATTAAAACTTAAAACCAATTATAAGATTATAAAACCATTTAAAGC
1022 CATTTAAAAT
Statistics
Matches: 259, Mismatches: 52, Indels: 11
0.80 0.16 0.03
Matches are distributed among these distances:
342 51 0.20
343 206 0.80
344 2 0.01
ACGTcount: A:0.38, C:0.13, G:0.12, T:0.34
Consensus pattern (331 bp):
GTGACTATAAATAAACTTTTCTTGCCAATGAATCACTTATTCTTCACGTTTCCCAAAGCAGACAT
TCAATTATAGACTATTTTAACAAAAAACGTAAAAAAATGCAACTTAAAATCAATTATGAGATTAT
AAAACAATTTAAAAGTGAATAATAGGCTTTTGAAGAAATAAGTGACTATAAATGGACTTTTCCTC
TCAATGAATGACATTTTCTACACGTTTCCCAAGGCAAACATTCAATTATAATATATTTTAATGAA
AAATATAAAAAATTAAAACTTAAAACCAATTATAAGATTATAAAACCATTTAAAGCGAGTAATAA
GGCTGA
Found at i:910 original size:171 final size:158
Alignment explanation
Indices: 704--1017 Score: 301
Period size: 171 Copynumber: 1.9 Consensus size: 158
694 NNNNNNNNNN
* * *
704 GAGTGACTATAAATAAACTTTTCTTCTCAATGAATGACTTTTTTTACACGTTTCCCAAAGC-AGA
1 GAGTGACTATAAATAAACTTTTCCTCTCAATGAATGACATTTTCTACACGTTTCCCAAAGCAAG-
* * * *
768 CATTCAGTTATAG-ACTATTTTATTGAAAAATGTAAAAAAATTCAACTTATAA-TCAATTATGAG
65 CATTCAATTATAGTA-TATTTTAATGAAAAATATAAAAAAATTCAACTTA-AATTCAATTATAAG
831 ATTATAAAACCATTTNNNNNNNNNNNNNAGGCTTTTGAAGAAAT
128 ATTATAAAACCATTT-------------AGGCTTTTGAAGAAAT
** * * * *
875 GAGTGACTATAAATGGACTTTTCCTCTCAATGAATGACATTTTCTATACGTTTCTCGAGGCAAGC
1 GAGTGACTATAAATAAACTTTTCCTCTCAATGAATGACATTTTCTACACGTTTCCCAAAGCAAGC
* * * * *
940 ATTTAATTATAGTATGTTTTAATGAAAAATATTAAAAATTTTAACTTAAATTCAATTATAAGATT
66 ATTCAATTATAGTATATTTTAATGAAAAATATAAAAAAATTCAACTTAAATTCAATTATAAGATT
1005 ATAAAACCATTTA
131 ATAAAACCATTTA
1018 AAGCCATTTA
Statistics
Matches: 122, Mismatches: 18, Indels: 19
0.77 0.11 0.12
Matches are distributed among these distances:
158 1 0.01
170 2 0.02
171 116 0.95
172 3 0.02
ACGTcount: A:0.37, C:0.12, G:0.11, T:0.36
Consensus pattern (158 bp):
GAGTGACTATAAATAAACTTTTCCTCTCAATGAATGACATTTTCTACACGTTTCCCAAAGCAAGC
ATTCAATTATAGTATATTTTAATGAAAAATATAAAAAAATTCAACTTAAATTCAATTATAAGATT
ATAAAACCATTTAGGCTTTTGAAGAAAT
Found at i:2417 original size:170 final size:169
Alignment explanation
Indices: 1027--3638 Score: 1524
Period size: 171 Copynumber: 15.3 Consensus size: 169
1017 AAAGCCATTT
* * *
1027 AAAATGTAAAAAAATTCAACTTAAAATCGATTATGAGATTATAAAA-TATTTTAAAGCAAGTAAT
1 AAAATGTAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACCA-TTTAAAGCGAGTAAT
********** *
1091 AAGGCTTTTGAAGNNNNNNNNNNCTATAAATGGACTTTTTTTATCAATGAATGGTTTTTTCTTCA
65 AAGGCTTTTGAAGGAATGGGTGACTATAAATGGACTTTTTTTATCAATGAAT-GCTTTTTCTTCA
* * * * **
1156 CGTTT-CTAGAGTAGGCATTCAATTATAGTCTATTTTAATTA
129 TGTTTCCAAG-GTAGACATTCAATTATAGTCTGTTTTAACCA
** * * *
1197 AAAATACAAAACAATTCAACTTAAAATTAA-T-TGAGATTATAAGACCATTTAAAGCGAGTAATA
1 AAAATGTAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATA
* * * * **
1260 AGGCTATTGAAGGAATGGGTGAATATAAGTGGA-TTTTTCTTATCAATGAATAGTTTTTTCAGCA
66 AGGCTTTTGAAGGAATGGGTGACTATAAATGGACTTTTT-TTATCAATGAAT-GCTTTTTCTTCA
* * *
1324 CGTTTCTCGAA-ATAGACATTCAATTATATTCTGTTTTAACCA
129 TGTTTC-C-AAGGTAGACATTCAATTATAGTCTGTTTTAACCA
* * * *********
1366 AAAATATTAAAAAAATT-AACTTAAAATCAATTATTAGACTATAAAACCATTTAAANNNNNNNNN
1 AAAAT-GTAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAAT
* * * * * *
1430 NAGGCTTTTGAAGGAATGGGTGACAATAAATAGACTTTTTTTGTCAATAAATGCCTTTTTCGTCA
65 AAGGCTTTTGAAGGAATGGGTGACTATAAATGGACTTTTTTTATCAATGAATG-CTTTTTCTTCA
* * *
1495 TGTTTCTCAACGTAGACATTCAATTATAATCTGTTTTAACAA
129 TGTTTC-CAAGGTAGACATTCAATTATAGTCTGTTTTAACCA
* * * * * * * *
1537 AAAATGTAACGAAACAATTGAACCTAAAATCAGTTTTGATATTATATAACCATTTAGAGGGAGTA
1 AAAATGTAA--AAA-AATTCAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTA
* * * * * * *
1602 ATAAGGCTTTTGAAGGATTGAGTGGCAATAAGTAGA-TTTTTCTTCTCAATGAATGGCTTTTTCT
63 ATAAGGCTTTTGAAGGAATGGGTGACTATAAATGGACTTTTT-TTATCAATGAAT-GCTTTTTCT
* * * * * * * * ***
1666 ACATGTTTCCTAAGGCAAATAGTCAGTTATAGACTATTTTATTGA
126 TCATGTTTCC-AAGGTAGACATTCAATTATAGTCTGTTTTAACCA
** * * * * * * *
1711 AAAACATAAAGAAATTCAACTGAAAATCAATCATGAGATTATATAACCATATACAGCAAGTAATA
1 AAAATGTAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATA
** * * * * ** *
1776 AGGCTTTCCAAGGAATGGGTGACTATAAATAGACTTTTCTTCTCAATGAATGCATTTTCTAAACG
66 AGGCTTTTGAAGGAATGGGTGACTATAAATGGACTTTTTTTATCAATGAATGCTTTTTCTTCATG
** * * * **
1841 TTTCTTGAGGTTCG-CATTTAATTATTGTCTGTTTTAATAA
131 TTTC-CAAGG-TAGACATTCAATTATAGTCTGTTTTAACCA
* * **********
1881 AAAATGTTAAAAACTTCAACTTAAAATCAATTATGAGATTATAANNNNNNNNNNAGCGAGTAATA
1 AAAATGTAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATA
* * * * * * *
1946 AGACTTTTGAAGGAATAGGTGACTATCAATGGACTTTTCTTCTCAATGAATGGATTTCTT-TACA
66 AGGCTTTTGAAGGAATGGGTGACTATAAATGGACTTTTTTTATCAATGAAT-GCTTT-TTCTTCA
* * * * *
2010 CGTTTCCTAAGGTA-AGCATTTAATTATAGTTTGTTTGAA-TA
129 TGTTTCC-AAGGTAGA-CATTCAATTATAGTCTGTTTTAACCA
* *** *
2051 TAAAATGTAAAAAAATTCAACTTGAAATCAATTATGAGATTATAAAATTTTTTAAAG-TAGGTAA
1 -AAAATGTAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCGA-GTAA
* * * * *
2115 TATGGCTTTTGAATGAATGTGTGACTATAAATAGACTTTTTTTACCAATGAATGCCTTTTTCTTC
64 TAAGGCTTTTGAAGGAATGGGTGACTATAAATGGACTTTTTTTATCAATGAATG-CTTTTTCTTC
* * * *
2180 ATGTTCTCTAGGGTAGGCTTTCAATTATAGTCTGTTTTAACCA
128 ATGTT-TCCAAGGTAGACATTCAATTATAGTCTGTTTTAACCA
********** * * *
2223 AAAANNNNNNNNNNTTCAACTTAAAATTAATTATGAGATTATAGAACTATTTAAAGCGAGTAATA
1 AAAATGTAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATA
* * *
2288 AGGCTTTTGAAGGAATGGATGACAATAAATGGACTTTTTTTGTCAATGAATGCTTTTTCTTCATG
66 AGGCTTTTGAAGGAATGGGTGACTATAAATGGACTTTTTTTATCAATGAATGCTTTTTCTTCATG
* * *
2353 TTTCGCAATGTAGATATTCAATTATAGCCTGTTTTAACCA
131 TTTC-CAAGGTAGACATTCAATTATAGTCTGTTTTAACCA
* * * ********** *
2393 AAAATGCAAAAGCAA-TCAACTTAAAATCAATTATTAGNNNNNNNNNNCATTTAAAGTGAGTAAT
1 AAAATGTAAAA-AAATTCAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAAT
* * * * ** *
2457 AAGGCTTGTAAAGGAATGAGTGA-TAATAAATAGA-TTTTTCTTGCCAATGAATGCCATTTTCTT
65 AAGGCTTTTGAAGGAATGGGTGACT-ATAAATGGACTTTTT-TTATCAATGAATG-CTTTTTCTT
* * * * *
2520 CATGTTTCTCGATGTAAACATTCAATTATAATTTGTTTTAACCA
127 CATGTTTC-CAAGGTAGACATTCAATTATAGTCTGTTTTAACCA
* * * * * * * *****
2564 AAACA-GTAAAAAAA-TGAACTTAAAATTAGTTTTGTGATTATAAAACAATTTAAAGTGANNNNN
1 AAA-ATGTAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAAT
***** * * * * *
2627 NNNNNTTTTGGAGGAATGGGTGACTAT-AATGGAACTTTTCTTACCAAAGAATGCATTTTTCATC
65 AAGGCTTTTGAAGGAATGGGTGACTATAAATGG-ACTTTTTTTATCAATGAATGC-TTTTTCTTC
* * * ** * * *
2691 ACGTTTCTCGAGATAGA-AAACTATTACT-GTCTATTTTAACAA
128 ATGTTTC-CAAGGTAGACATTCAATTA-TAGTCTGTTTTAACCA
* * * * * *
2733 AAAATATAAAAAAATTCAACTTCAAATCAGTTAT-AGGTTTATAAAATCATTTAAAGCTAGTAAT
1 AAAATGTAAAAAAATTCAACTTAAAATCAATTATGA-GATTATAAAACCATTTAAAGCGAGTAAT
* * * *
2797 AAGGCTTTTGAAGGAATGGGTGACTGTAAATAGATTTTTTTTCAT-AATGAATGACTTTTTCTAC
65 AAGGCTTTTGAAGGAATGGGTGACTATAAATGGACTTTTTTT-ATCAATGAATG-CTTTTTCTTC
* * * * ***
2861 ATGTTTTCCTAGGCA-AGCATTCAATTATAGTATATTTTATTGA
128 ATG-TTTCCAAGGTAGA-CATTCAATTATAGTCTGTTTTAACCA
* * *
2904 AAAATGTAAAAAAATTCAACTTAAAATTAATTATGAGAGTATAAAATCATTTAAAGCGAGTAATA
1 AAAATGTAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATA
* * * * * * * *
2969 AGGCTTTTGAAAGAATAGGCGACTATCAGTGGACTTTTCTTCTCAATGAATGGCTTTTTCTACAT
66 AGGCTTTTGAAGGAATGGGTGACTATAAATGGACTTTTTTTATCAATGAAT-GCTTTTTCTTCAT
** * ***
3034 GTTTCCTAAGACA-AGCATTCAATTATTA-TCTATTTTAANNN
130 GTTTCC-AAGGTAGA-CATTCAATTA-TAGTCTGTTTTAACCA
******* * * *
3075 NNNNNNNAAAAAAATTAAACTTAAAATCAATTATGAGATTATAAAACCATTCAAAGCGCGTAATA
1 AAAATGTAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATA
* * * ** *
3140 AGGCTTTTGAAGGAATGAGTGATTATAAATGGACTTTTTCTGCCACA-GAATTCCTTTTTCTTCA
66 AGGCTTTTGAAGGAATGGGTGACTATAAATGGACTTTTTTTATCA-ATGAA-TGCTTTTTCTTCA
** * * * * * *
3204 CATTTCCTAGGGCAGTCATTCAATTATACTCTATTTTAACTA
129 TGTTTCC-AAGGTAGACATTCAATTATAGTCTGTTTTAACCA
** * * * *
3246 AAAATACAAAATAATTCAACTTAAAATTAATTATGAGGTTATAAAACCATTTAAAGCTAGTAATA
1 AAAATGTAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATA
*********** * * * *
3311 AGGCTTTNNNNNNNNNNAGTGACTATAAGTGGACTTTTTTTCTCAATGAATGACTTTTTCTACAC
66 AGGCTTTTGAAGGAATGGGTGACTATAAATGGACTTTTTTTATCAATGAATG-CTTTTTCTTCAT
* * * ** * ***
3376 GTTTCTCGAGGCA-AGCATTCATTTATAACCTATTTTATTGA
130 GTTTC-CAAGGTAGA-CATTCAATTATAGTCTGTTTTAACCA
* * *********
3417 AAAATGTAATAAAATTCAACTTAAAATCAATTATGAGATTATAAAACAATTTAAAGNNNNNNNNN
1 AAAATGTAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATA
* * * ** * * *
3482 NGTCTTTTGAAGGAATGGGTGACTATAAATGGA-TATTTCTTGCCAATAAATCCCTTCTTCTTCA
66 AGGCTTTTGAAGGAATGGGTGACTATAAATGGACT-TTTTTTATCAATGAAT-GCTTTTTCTTCA
* *
3546 TGTTTCTCACA-GTAGTCATTCAATTATAGTCTGTTTTAA-AA
129 TGTTTC-CA-AGGTAGACATTCAATTATAGTCTGTTTTAACCA
* * *
3587 AAAATGTAAAACAATTCAACTTAAAATCAGTTATGAGATTATAAAACAATTT
1 AAAATGTAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACCATTT
Statistics
Matches: 1850, Mismatches: 520, Indels: 144
0.74 0.21 0.06
Matches are distributed among these distances:
167 5 0.00
168 75 0.04
169 84 0.05
170 514 0.28
171 1019 0.55
172 29 0.02
173 10 0.01
174 113 0.06
175 1 0.00
ACGTcount: A:0.36, C:0.12, G:0.13, T:0.35
Consensus pattern (169 bp):
AAAATGTAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATA
AGGCTTTTGAAGGAATGGGTGACTATAAATGGACTTTTTTTATCAATGAATGCTTTTTCTTCATG
TTTCCAAGGTAGACATTCAATTATAGTCTGTTTTAACCA
Found at i:3440 original size:342 final size:342
Alignment explanation
Indices: 1027--3472 Score: 1039
Period size: 341 Copynumber: 7.2 Consensus size: 342
1017 AAAGCCATTT
* * * *
1027 AAAATGTAAAAAAATTCAACTTAAAATCGATTATGAGATTATAAAA-TATTTTAAAGCAAGTAAT
1 AAAATATAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACCA-TTTAAAGCGAGTAAT
********** * * ** *
1091 AAGGCTTTTGAAGNNNNNNNNNNCTATAAATGGACTTTTTT--TATCAATGAATGGTTTTTTCTT
65 AAGGCTTTTGAAGGAATGAGTGACTATAAATAGA-TTTTTTGCCAT-AATGAATGACTTTTTCTA
* * * * * * * *
1154 CA-CGTTT-CTAGAGTAGGCATTCAATTATAGTCTATTTTAATTAAAAATACAAAACAATTCAAC
128 CATCATTTCCTAG-GCAAGCATTCAATTATACTATATTTTACTGAAAAATACAAAAAAATTCAAC
* * * * * *
1217 TTAAAATTAA-T-TGAGATTATAAGACCATTTAAAGCGAGTAATAAGGCTATTGAAGGAATGGGT
192 TTAAAATTAATTATGAGAGTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAAGAATAGGC
* * * * * *
1280 GAATATAAGTGGATTTTTCTTATCAATGAAT-AGTTTTT-TCAGCACGTTTCTCGAA-A-TAGAC
257 GACTATAAGTGGACTTTTCTTCTCAATGAATGACTTTTTCT-A-CACGTTTC-CTAAGACAAG-C
** * **
1341 ATTCAATTATATTCTGTTTTAACCA
318 ATTCAATTATAACCTATTTTAATGA
* * *********
1366 AAAATATTAAAAAAATT-AACTTAAAATCAATTATTAGACTATAAAACCATTTAAANNNNNNNNN
1 AAAATA-TAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAAT
* * * * * *
1430 NAGGCTTTTGAAGGAATGGGTGACAATAAATAGACTTTTTTTGTC--AATAAATGCCTTTTTCGT
65 AAGGCTTTTGAAGGAATGAGTGACTATAAATAGA--TTTTTTGCCATAATGAATGACTTTTTC-T
* * * * * * * * * *
1493 -CAT-GTTTCTCAACG-TAGACATTCAATTATAATCTGTTTTAAC-AAAAAATGTAACGAAACAA
127 ACATCATTTC-CTAGGCAAG-CATTCAATTATACTATATTTT-ACTGAAAAA--T-ACAAAAAAA
* * * * * * * * * * *
1554 TTGAACCTAAAATCAGTTTTGATATTATATAACCATTTAGAGGGAGTAATAAGGCTTTTGAAGGA
186 TTCAACTTAAAATTAATTATGAGAGTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAAGA
* * * * * * *
1619 TTGAGTG-G-CAATAAGTAGATTTTTCTTCTCAATGAATGGCTTTTTCTACATGTTTCCTAAGGC
251 AT-AG-GCGACTATAAGTGGACTTTTCTTCTCAATGAATGACTTTTTCTACACGTTTCCTAAGAC
** * * *
1682 AAATAGTCAGTTATAGA-CTATTTTATTGA
314 AAGCATTCAATTATA-ACCTATTTTAATGA
* * * * * * * *
1711 AAAACATAAAGAAATTCAACTGAAAATCAATCATGAGATTATATAACCATATACAGCAAGTAATA
1 AAAATATAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATA
** * *
1776 AGGCTTTCCAAGGAATGGGTGACTATAAATAGACTTTTCTT--C-TCAATGAATG-CATTTTCTA
66 AGGCTTTTGAAGGAATGAGTGACTATAAATAGA-TTTT-TTGCCAT-AATGAATGACTTTTTCTA
* * * *** * ** * * * * *** *
1837 -AACGTTTCTTGAGGTTCGCATTTAATTATTGTCTGTTTTAATAAAAAATGTTAAAAACTTCAAC
128 CATCATTTCCT-AGGCAAGCATTCAATTATACTATATTTTACTGAAAAATACAAAAAAATTCAAC
* * ********** * * *
1901 TTAAAATCAATTATGAGATTATAANNNNNNNNNNAGCGAGTAATAAGACTTTTGAAGGAATAGGT
192 TTAAAATTAATTATGAGAGTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAAGAATAGGC
**
1966 GACTATCAA-TGGACTTTTCTTCTCAATGAATGGA-TTTCTT-TACACGTTTCCTAAGGTAAGCA
257 GACTAT-AAGTGGACTTTTCTTCTCAATGAAT-GACTTT-TTCTACACGTTTCCTAAGACAAGCA
* *** * *
2028 TTTAATTATAGTTTGTTTGAAT-A
319 TTCAATTATAACCTATTTTAATGA
* * *** *
2051 TAAAATGTAAAAAAATTCAACTTGAAATCAATTATGAGATTATAAAATTTTTTAAAG-TAGGTAA
1 -AAAATATAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCGA-GTAA
* * * * *
2115 TATGGCTTTTGAATGAATGTGTGACTATAAATAGACTTTTTTTACC--AATGAATGCCTTTTTCT
64 TAAGGCTTTTGAAGGAATGAGTGACTATAAATAGA--TTTTTTGCCATAATGAATGACTTTTTCT
* * * * * * * **********
2178 ---TCATGTTCTCTAGGGTAGGCTTTCAATTATAGTCTGTTTTAAC-CAAAAANNNNNNNNNNTT
127 ACATCAT-TTC-CTA-GGCAAGCATTCAATTATACTATATTTT-ACTGAAAAATACAAAAAAATT
* * * *
2239 CAACTTAAAATTAATTATGAGATTATAGAACTATTTAAAGCGAGTAATAAGGCTTTTGAAGGAAT
188 CAACTTAAAATTAATTATGAGAGTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAAGAAT
* * * * * * * *
2304 -GGATGACAATAAATGGACTTTTTTTGTCAATGAATG-CTTTTTCTTCATGTTTCGC-AATG--T
253 AGG-CGACTATAAGTGGACTTTTCTTCTCAATGAATGACTTTTTCTACACGTTTC-CTAA-GACA
* * * **
2364 AGATATTCAATTATAGCCTGTTTTAACCA
315 AG-CATTCAATTATAACCTATTTTAATGA
** * * ********** *
2393 AAAATGCAAAAGCAA-TCAACTTAAAATCAATTATTAGNNNNNNNNNNCATTTAAAGTGAGTAAT
1 AAAATATAAAA-AAATTCAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAAT
* * * *
2457 AAGGCTTGTAAAGGAATGAGTGA-TAATAAATAGATTTTTCTTGCC--AATGAATGCCATTTTCT
65 AAGGCTTTTGAAGGAATGAGTGACT-ATAAATAGA-TTTT-TTGCCATAATGAATGACTTTTTCT
* * * * * * * * * *
2519 TCAT-GTTTCTCGATGTAAACATTCAATTATAATTTGTTTTAAC-CAAAACAGT--AAAAAAA-T
127 ACATCATTTC-CTAGGCAAGCATTCAATTATACTATATTTT-ACTGAAAA-A-TACAAAAAAATT
* * * * * * * ********** * *
2579 GAACTTAAAATTAGTTTTGTGATTATAAAACAATTTAAAGTGANNNNNNNNNNTTTTGGAGGAAT
188 CAACTTAAAATTAATTATGAGAGTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAAGAAT
* * * *
2644 GGGTGACTATAA-TGGAACTTTTCTTAC-CAAAGAATG-CATTTTTC-ATCACGTTT-CTCGAGA
253 AGGCGACTATAAGTGG-ACTTTTCTT-CTCAATGAATGAC-TTTTTCTA-CACGTTTCCT-AAGA
* * ** * ** **
2704 -TAGAAAACTATTACT-GTCTATTTTAACAA
313 CAAGCATTCAATTA-TAACCTATTTTAATGA
* * * * *
2733 AAAATATAAAAAAATTCAACTTCAAATCAGTTAT-AGGTTTATAAAATCATTTAAAGCTAGTAAT
1 AAAATATAAAAAAATTCAACTTAAAATCAATTATGA-GATTATAAAACCATTTAAAGCGAGTAAT
* * **
2797 AAGGCTTTTGAAGGAATGGGTGACTGTAAATAGATTTTTTTTCATAATGAATGACTTTTTCTACA
65 AAGGCTTTTGAAGGAATGAGTGACTATAAATAGATTTTTTGCCATAATGAATGACTTTTTCTACA
** * * **
2862 TGTTTTCCTAGGCAAGCATTCAATTATAGTATATTTTATTGAAAAATGTAAAAAAATTCAACTTA
130 TCATTTCCTAGGCAAGCATTCAATTATACTATATTTTACTGAAAAATACAAAAAAATTCAACTTA
*
2927 AAATTAATTATGAGAGTATAAAATCATTTAAAGCGAGTAATAAGGCTTTTGAAAGAATAGGCGAC
195 AAATTAATTATGAGAGTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAAGAATAGGCGAC
* * *
2992 TATCAGTGGACTTTTCTTCTCAATGAATGGCTTTTTCTACATGTTTCCTAAGACAAGCATTCAAT
260 TATAAGTGGACTTTTCTTCTCAATGAATGACTTTTTCTACACGTTTCCTAAGACAAGCATTCAAT
* * ***
3057 TATTATCTATTTTAANNN
325 TATAACCTATTTTAATGA
******* * * *
3075 NNNNNNNAAAAAAATTAAACTTAAAATCAATTATGAGATTATAAAACCATTCAAAGCGCGTAATA
1 AAAATATAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATA
* * * ** *
3140 AGGCTTTTGAAGGAATGAGTGATTATAAATGGACTTTTTCTGCCA-CA-GAATTCCTTTTTCTTC
66 AGGCTTTTGAAGGAATGAGTGACTATAAATAGA-TTTTT-TGCCATAATGAATGACTTTTTCTAC
* *
3203 A-CATTTCCTAGGGC-AGTCATTCAATTATACTCTATTTTAACT-AAAAATACAAAATAATTCAA
129 ATCATTTCCTA-GGCAAG-CATTCAATTATACTATATTTT-ACTGAAAAATACAAAAAAATTCAA
* *********
3265 CTTAAAATTAATTATGAG-GTTATAAAACCATTTAAAGCTAGTAATAAGGCTTTNNNNNNNNNNA
191 CTTAAAATTAATTATGAGAG-TATAAAACCATTTAAAGCGAGTAATAAGGCTTT-TGAAAGAATA
* * * *
3329 -GTGACTATAAGTGGACTTTTTTTCTCAATGAATGACTTTTTCTACACGTTT-CTCGAGGCAAGC
254 GGCGACTATAAGTGGACTTTTCTTCTCAATGAATGACTTTTTCTACACGTTTCCT-AAGACAAGC
* *
3392 ATTCATTTATAACCTATTTTATTGA
318 ATTCAATTATAACCTATTTTAATGA
* * *
3417 AAAATGTAATAAAATTCAACTTAAAATCAATTATGAGATTATAAAACAATTTAAAG
1 AAAATATAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAG
3473 NNNNNNNNNN
Statistics
Matches: 1584, Mismatches: 423, Indels: 197
0.72 0.19 0.09
Matches are distributed among these distances:
338 4 0.00
339 92 0.06
340 274 0.17
341 482 0.30
342 459 0.29
343 37 0.02
344 58 0.04
345 167 0.11
346 9 0.01
347 2 0.00
ACGTcount: A:0.37, C:0.12, G:0.14, T:0.35
Consensus pattern (342 bp):
AAAATATAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATA
AGGCTTTTGAAGGAATGAGTGACTATAAATAGATTTTTTGCCATAATGAATGACTTTTTCTACAT
CATTTCCTAGGCAAGCATTCAATTATACTATATTTTACTGAAAAATACAAAAAAATTCAACTTAA
AATTAATTATGAGAGTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAAGAATAGGCGACT
ATAAGTGGACTTTTCTTCTCAATGAATGACTTTTTCTACACGTTTCCTAAGACAAGCATTCAATT
ATAACCTATTTTAATGA
Done.