Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018399756.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_3.0, 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: 12855
ACGTcount: A:0.32, C:0.14, G:0.14, T:0.29
Warning! 1373 characters in sequence are not A, C, G, or T
Found at i:527 original size:170 final size:170
Alignment explanation
Indices: 16--1450 Score: 952
Period size: 171 Copynumber: 8.4 Consensus size: 170
6 CTACAAACAG
* * * ** * * * *
16 ACTTTTCTTACCAATGGATGACTTTTGCTTCATATTTTCTGAGGCAGACATTCAATTATCATATA
1 ACTTTTCTTACCAATGAATGACTTTTGCTTCATGTTTCCCAAGGTAGACATTCAATTATAATCTG
* * * * **
81 TTTTAAGAAAAAATTTTAAAATAACT-AACTCAAAATCAATTATGAGATTATAAAACTGTTTAAA
66 TTTTAACAAAAAA-TATAAAA-AATTCAACTTAAAATCAATTATGAGATTATAAAACCATTTAAA
* * ** * *
145 GCAAGTAGTAAAACTTACGAAGGTATAGGTGA-TATAGAT-A
129 GCGAGTAATAAGGCTTTCGAAGGCATAGGTGACTATAGATGA
*** * * * * *
185 TACTTTTCTCGTCAATGAATGACTTTTTCTTCACGTTTCTCTAGGTAGAGATTCAA--ATACATC
1 -ACTTTTCTTACCAATGAATGACTTTTGCTTCATGTTTCCCAAGGTAGACATTCAATTATA-ATC
** * * *
248 TGTTTTAACCGAACATGTAAAAAGTTCAACTTAAAATCAATTATGAGATTATAAAACCATTTAAA
64 TGTTTTAACAAAAAATATAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACCATTTAAA
* * * * * * ** * *
313 TCAAGTAATTAGGCTTTCGAAGACTTAAGCCATTATAAATGA
129 GCGAGTAATAAGGCTTTCGAAGGCATAGGTGACTATAGATGA
* * * * * * *
355 ACTTTTCTTGCCAATGGATGACTTTTGCATCACGTTTCCCAATGCAGACATTCAATTATAATAT-
1 ACTTTTCTTACCAATGAATGACTTTTGCTTCATGTTTCCCAAGGTAGACATTCAATTATAATCTG
* * * **
419 ATTTAATAAAAAATATAAAAAAATTCAACTTAAAATCATTTATGAGATTATAAAATTATTTAAAG
66 TTTTAACAAAAAATAT-AAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAG
* * ** *
484 TGAGTAGTGGGGCTTTCGAAGGCATGGGTGACTATAGATGA
130 CGAGTAATAAGGCTTTCGAAGGCATAGGTGACTATAGATGA
* * * * * ** * * *
525 ACTTTTCTTACTAATGAATAACTTTTTCCTCACGTTTTCTGAA-ATAAACATTCAAATACT-ATC
1 ACTTTTCTTACCAATGAATGACTTTTGCTTCATG-TTTCCCAAGGTAGACATTCAATTA-TAATC
* * * * **
588 TGTTTTAA-AAAGAATTGTAAAAAAATTTAACTTAAAATTAATTATGAGATTATAAAACCACGTA
64 TGTTTTAACAAA-AAATAT-AAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACCATTTA
* * * *
652 AAGCGAGTAGTAAGGCTTTCGAAGGAAT-GAGTGTCTATAGATGG
127 AAGCGAGTAATAAGGCTTTCGAAGGCATAG-GTGACTATAGATGA
** * ** * * *
696 ACTTTTCTTACCGGTGAATGGCAC-TTT-CTTTATGTTT-TTAGAGGTAGCCATTCAAATATTAT
1 ACTTTTCTTACCAATGAAT-G-ACTTTTGCTTCATGTTTCCCA-AGGTAGACATTCAATTATAAT
** * * *
758 CTGTTTTAATGAAAAATGCTAAAAAATTCAACTTAAAATCAATTATAAGATTATAAAATCATTTA
63 CTGTTTTAACAAAAAAT-ATAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACCATTTA
* * * * * * *
823 AAGCCAGTAATAAGGCTCTCAAAGCCATGGGTGACAATATAT-A
127 AAGCGAGTAATAAGGCTTTCGAAGGCATAGGTGACTATAGATGA
* * ** *
866 GACTTTTCTGT-CCAATGGATGGCTTTTGCTTCATGTTTCTTAAGG-AAAGCATTCAATTATAAT
1 -ACTTTTCT-TACCAATGAATGACTTTTGCTTCATGTTTCCCAAGGTAGA-CATTCAATTATAAT
* * * * *
929 CTGTTTTAACCAACACTATAGAAAATATCAACTTAAAATCAATTATGAGATTATAAAACCCTTTA
63 CTGTTTTAACAAAAAATATAAAAAAT-TCAACTTAAAATCAATTATGAGATTATAAAACCATTTA
* *
994 AAGCGAATAATAAGGCTTTCGAAGGCATAGGTGACTATAAATGGA
127 AAGCGAGTAATAAGGCTTTCGAAGGCATAGGTGACTATAGAT-GA
* * * * * * **
1039 A-TTTTTTTACCAATGAATG-TTTTTTCTTCATGTTTTCCAATGTAGACATTCAAATATTTTCTG
1 ACTTTTCTTACCAATGAATGACTTTTGCTTCATGTTTCCCAAGGTAGACATTCAATTATAATCTG
* * * * ** *
1102 TTTTAACTAAAAGTGTAAAACAATTTAAGGTAAAATCAATTATGAGATTCTAAAACCATTTAAAG
66 TTTTAACAAAAAATATAAAA-AATTCAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAG
* * * * ** * * * *
1167 CGAGTAATAAATGCTTTTGAAGACTTCA-ACGACTACAAACGG
130 CGAGTAAT-AAGGCTTTCGAAGGCAT-AGGTGACTATAGATGA
* * * * * ** * * * *
1209 ATTTTTCTTACCAATGGATGACTTTTGCTTCATTTTTTCCTAGACAAACATTCAATTATCATATA
1 ACTTTTCTTACCAATGAATGACTTTTGCTTCATGTTTCCCAAGGTAGACATTCAATTATAATCTG
* * * **
1274 TTTTAACAAAAAATTTTAAGAAAACT-AACTCAAAATCAATTATGAGATTAT-AAACTGTTTAAA
66 TTTTAACAAAAAA-TATAA-AAAATTCAACTTAAAATCAATTATGAGATTATAAAACCATTTAAA
* * * * * *
1337 ACAAGTAATAAGGCTTTCGAAGGTATGGGTGACTATAGACGT
129 GCGAGTAATAAGGCTTTCGAAGGCATAGGTGACTATAGATGA
*** * * ** ** * *
1379 ACTTTTCTCGTCAATGAATGGCTTTTTCTTCCCGTTTTTCTAGGTAGACATTCAAATACT-ATCT
1 ACTTTTCTTACCAATGAATGACTTTTGCTTCATGTTTCCCAAGGTAGACATTCAATTA-TAATCT
1443 GTTTTAAC
65 GTTTTAAC
1451 CGAACATGTG
Statistics
Matches: 979, Mismatches: 246, Indels: 80
0.75 0.19 0.06
Matches are distributed among these distances:
167 2 0.00
168 63 0.06
169 76 0.08
170 346 0.35
171 404 0.41
172 76 0.08
173 10 0.01
174 2 0.00
ACGTcount: A:0.37, C:0.14, G:0.14, T:0.35
Consensus pattern (170 bp):
ACTTTTCTTACCAATGAATGACTTTTGCTTCATGTTTCCCAAGGTAGACATTCAATTATAATCTG
TTTTAACAAAAAATATAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGC
GAGTAATAAGGCTTTCGAAGGCATAGGTGACTATAGATGA
Found at i:10908 original size:171 final size:168
Alignment explanation
Indices: 10050--11523 Score: 726
Period size: 171 Copynumber: 8.6 Consensus size: 168
10040 NNNNNNNNNN
* * * *
10050 AAAACCATTTAAAGCAAGTAATAAGGCTTTCGAAGGCA-TGAGTGACTATAGATGTATTTTTCTT
1 AAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGCATTG-GTGACTATACATGGATTTTTCTT
* * * * * * * *
10114 ATCAATGAATGGCTTTTTCCTCATGTTTCCCAATGTACATATTCAAAGATTATT-T-GTTTAATT
65 GTCAATGAATAGCTTTTTCTTCATGTTT-CCAATGTAGACATTCAAATATT-TTCTATTTTAA-C
* * *
10177 AAAAAACTAAAACAATTCAAATTAACATCAATTATGATATTAT
127 AAAAAA-TAAAACAATTCAACTTAAAATCAATTATGAGATTAT
********** * * *
10220 AAAACCATTTAAAGCGAGTAATAAGGNNNNNNNNNNC-TTAAGTGACTATAAATGGACTTTTCTT
1 AAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGCATT-GGTGACTATACATGGATTTTTCTT
* * * * * * * * ** *
10284 G-CTAAT-AGTTGGCTTTTTCTTTATGTTTCATAAGGCAGAGATTCAATTATAATATATTTTAAC
65 GTC-AATGA-ATAGCTTTTTCTTCATGTTTC-CAATGTAGACATTCAAATATTTTCTATTTTAAC
* * * *
10347 AAAAAATATAATAAAATTCAACGTAAAATCAATTTTGAAATTAT
127 AAAAAATA-AA-ACAATTCAACTTAAAATCAATTATGAGATTAT
* ********** * * *
10391 AAAATCATNNNNNNNNNNTAATAAGGCTTTCGAAGGCA-TGGTTGACTATAGATGGACTTTTCTT
1 AAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGCATTGG-TGACTATACATGGATTTTTCTT
* * ** * ** * * *
10455 GCCAATGAATGGC-TTTTCTTCATGTTTTATAATGTAGACATTCAACTATCATCTCTTTGAACCA
65 GTCAATGAATAGCTTTTTCTTCATG-TTTCCAATGTAGACATTCAAATATTTTCTATTTTAACAA
*
10519 AAAATATAAACAAATGCAACTTAAAATCAATTATGAGATTAT
129 AAAATA-AAAC-AATTCAACTTAAAATCAATTATGAGATTAT
********** ** * * * * *
10561 AAAACNNNNNNNNNNGAGTAATAAGGCTTTCAAAGGCA-TGAGTGACTATAGACGAACTTTTATT
1 AAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGCATTG-GTGACTATACATGGATTTTTCTT
* * * * * **
10625 G-CTAATGAATGGATTTTTCTTCATGTTTCCCAATGTAGACATTGAAATATTATCTATATTAATG
65 GTC-AATGAATAGCTTTTTCTTCATGTTT-CCAATGTAGACATTCAAATATTTTCTATTTTAACA
* * **********
10689 AAAAATGTAAACAAATTCAACTTAAAATTAATNNNNNNNNNNT
128 AAAAAT-AAAAC-AATTCAACTTAAAATCAATTATGAGATTAT
* * * * * *
10732 AAAACCATTTAAAGCAAGTGATAAGGCTTTTAAAGGTATTGGTGGCTGTACATGGATTTTTCTTG
1 AAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGCATTGGTGACTATACATGGATTTTTCTTG
*
10797 TCAATAAATAGCTTTTTCTTCATGTTTTCCAATGTAGACATTCAAATATTTTCTATTTTAACCAA
66 TCAATGAATAGCTTTTTCTTCATG-TTTCCAATGTAGACATTCAAATATTTTCTATTTTAA-CAA
*
10862 AAAAGTAAAACAATTCAACTTAACATCAATTATGAGATTAT
129 AAAA-TAAAACAATTCAACTTAAAATCAATTATGAGATTAT
* * * * * *
10903 AAAACCATTGAGAGCGAGTAATAAAGCTTTTAAAGAC-TTAAGG-GACTATAAATGGACTTTTT-
1 AAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGCATT--GGTGACTATACATGGA-TTTTTC
* * * * * ** *
10965 TTG-CGAAT-AGAT-GACTTTTCCTTCTTAT-TTTCTAAGGCAGACATTCAATTATAATATATTT
63 TTGTC-AATGA-ATAG-CTTTTTCTTC--ATGTTTCCAATGTAGACATTCAAATATTTTCTATTT
*
11026 TTACAAGAAATATAATAA-AATTCAACTTAAAATTC-ATTATGAGATTAT
123 TAACAA-AAA-ATAA-AACAATTCAACTTAAAA-TCAATTATGAGATTAT
* * ********** * * * * * * *
11074 AAAATCATTTAAAGTGANNNNNNNNNNTTTCGAAGGTATGGGTGACTATAGATAGACTTTTCTTA
1 AAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGCATTGGTGACTATACATGGATTTTTCTTG
* * *
11139 TCGATGAAT-GACTTTTTCTTCGTGTTTCCTAATGTAGACATTCAAATATTTTCTATTTTGACAA
66 TCAATGAATAG-CTTTTTCTTCATGTTTCC-AATGTAGACATTCAAATATTTTCTATTTTAACAA
* * *
11203 AAAAGGTAAAAAAATTCAATTTAAAATCAATTATGAGATCAT
129 AAAA--TAAAACAATTCAACTTAAAATCAATTATGAGATTAT
* * * * * * * *
11245 AGAACTATTGAAAGTGAGTAATAAGGCTTTCGAAGGCATGGGTTACTATAGC-TGAACTTTTT-T
1 AAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGCATTGGTGACTATA-CATGGA-TTTTTCT
* ** * *
11308 TGCCAATGAATAAATTTTTCTTCACGTTTCCTAATATAGACATTCAAATATTATT-TATTTTAAC
64 TGTCAATGAATAGCTTTTTCTTCATGTTTCC-AATGTAGACATTCAAATATT-TTCTATTTTAAC
* **********
11372 TAAAAATATAAACAAATTCAANNNNNNNNNNATTATGAGATTAT
127 AAAAAATA-AAAC-AATTCAACTTAAAATCAATTATGAGATTAT
* * * * * *
11416 AAAACCATTTCAAGCTAGTAATAAGGCTTTTGAAGGCATGGGGGACTATAGATCGATTTTTCTTG
1 AAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGCATTGGTGACTATACATGGATTTTTCTTG
* *
11481 TCAATGAATAACTTTTTCTTCATGTTTCCTATGTAGACATTCA
66 TCAATGAATAGCTTTTTCTTCATGTTTCCAATGTAGACATTCA
11524 GAGATTATAG
Statistics
Matches: 980, Mismatches: 268, Indels: 112
0.72 0.20 0.08
Matches are distributed among these distances:
169 12 0.01
170 270 0.28
171 657 0.67
172 38 0.04
173 3 0.00
ACGTcount: A:0.36, C:0.12, G:0.13, T:0.35
Consensus pattern (168 bp):
AAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGCATTGGTGACTATACATGGATTTTTCTTG
TCAATGAATAGCTTTTTCTTCATGTTTCCAATGTAGACATTCAAATATTTTCTATTTTAACAAAA
AATAAAACAATTCAACTTAAAATCAATTATGAGATTAT
Found at i:10924 original size:342 final size:339
Alignment explanation
Indices: 10050--11523 Score: 958
Period size: 342 Copynumber: 4.3 Consensus size: 339
10040 NNNNNNNNNN
* * * * * * * *
10050 AAAACCATTTAAAGCAAGTAATAAGGCTTTCGAAGGCATGAGTGACTATAGATGTATTTTTCTTA
1 AAAACCATTTAAAGCAAGTGATAAGGCTTTCAAAGGTATGGGTGACTATACATGGACTTTTCTTG
* * * * * * **
10115 TCAATGAATGGCTTTTTCCTCATGTTTCCCAATGTACATATTCAAAGATTATT-T-GTTTAATTA
66 TCAATGAAT-GCTTTTTCTTCATGTTTTCCAATGTAGACATTCAAATATT-TTCTATTTTAACCA
* * * * *
10178 AAAAACTAAAACAATTCAAATTAACATCAATTATGATATTATAAAACCATTTAAAGCGAGTAATA
129 AAAAAGTAAAACAATTCAACTTAAAATCAATTATGAGATTATAAAACCATTGAAAGCGAGTAATA
********** * * * * * * * * * *
10243 AGGNNNNNNNNNNCTTAAGTGACTATAAATGGACTTTTCTTGCTAAT-AGTTGGCTTTTTCTTTA
194 AGGCTTTCAAAGGCATGAGTGACTATAGACGAACTTTTTTTGCCAATGA-AT-GATTTTTCTTCA
* * * * * * * *
10307 TGTTTCATAAGGCAGAGATTCAATTATAATATATTTTAACAAAAAATATAATA-AAATTCAACGT
257 TGTTTCCTAATGTAGACATTCAAATATTATATATTTTAA-TAAAAATATAA-ACAAATTCAACTT
* * *
10371 AAAATCAATTTTGAAATTAT
320 AAAATTAATTATGAGATTAT
* ********** * * * * *
10391 AAAATCATNNNNNNNNNNTAATAAGGCTTTCGAAGGCATGGTTGACTATAGATGGACTTTTCTTG
1 AAAACCATTTAAAGCAAGTGATAAGGCTTTCAAAGGTATGGGTGACTATACATGGACTTTTCTTG
* ** * ** * *
10456 CCAATGAATGGC-TTTTCTTCATGTTTTATAATGTAGACATTCAACTATCATCTCTTTGAACC-A
66 TCAATGAAT-GCTTTTTCTTCATGTTTTCCAATGTAGACATTCAAATATTTTCTATTTTAACCAA
* **********
10519 AAAA-TATAAACAAATGCAACTTAAAATCAATTATGAGATTATAAAACNNNNNNNNNNGAGTAAT
130 AAAAGTA-AAAC-AATTCAACTTAAAATCAATTATGAGATTATAAAACCATTGAAAGCGAGTAAT
* *
10583 AAGGCTTTCAAAGGCATGAGTGACTATAGACGAACTTTTATTGCTAATGAATGGATTTTTCTTCA
193 AAGGCTTTCAAAGGCATGAGTGACTATAGACGAACTTTTTTTGCCAATGAAT-GATTTTTCTTCA
* * * * *
10648 TGTTTCCCAATGTAGACATTGAAATATTATCTATATTAATGAAAAATGTAAACAAATTCAACTTA
257 TGTTTCCTAATGTAGACATTCAAATATTATATATTTTAAT-AAAAATATAAACAAATTCAACTTA
**********
10713 AAATTAATNNNNNNNNNNT
321 AAATTAATTATGAGATTAT
* * * * *
10732 AAAACCATTTAAAGCAAGTGATAAGGCTTTTAAAGGTATTGGTGGCTGTACATGGATTTTTCTTG
1 AAAACCATTTAAAGCAAGTGATAAGGCTTTCAAAGGTATGGGTGACTATACATGGACTTTTCTTG
*
10797 TCAATAAATAGCTTTTTCTTCATGTTTTCCAATGTAGACATTCAAATATTTTCTATTTTAACCAA
66 TCAATGAAT-GCTTTTTCTTCATGTTTTCCAATGTAGACATTCAAATATTTTCTATTTTAACCAA
* *
10862 AAAAGTAAAACAATTCAACTTAACATCAATTATGAGATTATAAAACCATTGAGAGCGAGTAATAA
130 AAAAGTAAAACAATTCAACTTAAAATCAATTATGAGATTATAAAACCATTGAAAGCGAGTAATAA
* * * * * * * * * * * *
10927 AGCTTTTAAAGACTTAAGGGACTATAAATGGACTTTTTTTGCGAAT-AGATGACTTTTCCTTCTT
195 GGCTTTCAAAGGCATGAGTGACTATAGACGAACTTTTTTTGCCAATGA-ATGA-TTTTTCTTCAT
* * * * * * * *
10991 ATTTTCTAAGGCAGACATTCAATTATAATATATTTTTACAAGAAATATAATA-AAATTCAACTTA
258 GTTTCCTAATGTAGACATTCAAATATTATATATTTTAATAA-AAATATAA-ACAAATTCAACTTA
*
11055 AAATTCATTATGAGATTAT
321 AAATTAATTATGAGATTAT
* ** ********** * * * *
11074 AAAATCATTTAAAGTGANNNNNNNNNNTTTCGAAGGTATGGGTGACTATAGATAGACTTTTCTTA
1 AAAACCATTTAAAGCAAGTGATAAGGCTTTCAAAGGTATGGGTGACTATACATGGACTTTTCTTG
* * *
11139 TCGATGAATGACTTTTTCTTCGTG-TTTCCTAATGTAGACATTCAAATATTTTCTATTTTGA-CA
66 TCAATGAATG-CTTTTTCTTCATGTTTTCC-AATGTAGACATTCAAATATTTTCTATTTTAACCA
* * * * * *
11202 AAAAAGGTAAAAAAATTCAATTTAAAATCAATTATGAGATCATAGAACTATTGAAAGTGAGTAAT
129 AAAAA-GTAAAACAATTCAACTTAAAATCAATTATGAGATTATAAAACCATTGAAAGCGAGTAAT
* * * *
11267 AAGGCTTTCGAAGGCATGGGTTACTATAG-CTGAACTTTTTTTGCCAATGAATAAATTTTTCTTC
193 AAGGCTTTCAAAGGCATGAGTGACTATAGAC-GAACTTTTTTTGCCAATGAAT-GATTTTTCTTC
* * * ***
11331 ACGTTTCCTAATATAGACATTCAAATATTATTTATTTTAACTAAAAATATAAACAAATTCAANNN
256 ATGTTTCCTAATGTAGACATTCAAATATTATATATTTTAA-TAAAAATATAAACAAATTCAACTT
*******
11396 NNNNNNNATTATGAGATTAT
320 AAAATTAATTATGAGATTAT
* * * ** * * * * *
11416 AAAACCATTTCAAGCTAGTAATAAGGCTTTTGAAGGCATGGGGGACTATAGATCGATTTTTCTTG
1 AAAACCATTTAAAGCAAGTGATAAGGCTTTCAAAGGTATGGGTGACTATACATGGACTTTTCTTG
* *
11481 TCAATGAATAACTTTTTCTTCATG-TTTCCTATGTAGACATTCA
66 TCAATGAAT-GCTTTTTCTTCATGTTTTCCAATGTAGACATTCA
11524 GAGATTATAG
Statistics
Matches: 847, Mismatches: 263, Indels: 46
0.73 0.23 0.04
Matches are distributed among these distances:
339 3 0.00
340 39 0.05
341 288 0.34
342 501 0.59
343 14 0.02
344 2 0.00
ACGTcount: A:0.36, C:0.12, G:0.13, T:0.35
Consensus pattern (339 bp):
AAAACCATTTAAAGCAAGTGATAAGGCTTTCAAAGGTATGGGTGACTATACATGGACTTTTCTTG
TCAATGAATGCTTTTTCTTCATGTTTTCCAATGTAGACATTCAAATATTTTCTATTTTAACCAAA
AAAGTAAAACAATTCAACTTAAAATCAATTATGAGATTATAAAACCATTGAAAGCGAGTAATAAG
GCTTTCAAAGGCATGAGTGACTATAGACGAACTTTTTTTGCCAATGAATGATTTTTCTTCATGTT
TCCTAATGTAGACATTCAAATATTATATATTTTAATAAAAATATAAACAAATTCAACTTAAAATT
AATTATGAGATTAT
Found at i:11612 original size:116 final size:117
Alignment explanation
Indices: 11408--11641 Score: 260
Period size: 116 Copynumber: 2.0 Consensus size: 117
11398 NNNNNATTAT
* * * * ** * * *
11408 GAGATTATAAAACCATTTCAAGCTAGTAATAAGGCTTTTGAAGGCATGGGGGACTATAGATCGAT
1 GAGATTATAAAACCATTTAAAGCGAGTAATAAGACTTTTGAAGACATAAGCGACTATAAATCGAC
* * *
11473 TTTTCTTGTCAATGAATAACTTTT-TCTTCATGTTTCCT-ATGTAGACATTCA
66 TTTTCTTGTCAATGAATAACTTTTGAC-TCATGTTTCCTAAGGCAGACATTCA
* * * *
11524 GAGATTATAGAACCATTTAAAGCGAGTAATAAGATTTTTGAAGACTTAAGCGACTATAAATGGAC
1 GAGATTATAAAACCATTTAAAGCGAGTAATAAGACTTTTGAAGACATAAGCGACTATAAATCGAC
*
11589 TTTTCTTG-CTAAT-AGATGACTTTTGACTCATGTTTCCTAAGGCAGACATTCA
66 TTTTCTTGTC-AATGA-ATAACTTTTGACTCATGTTTCCTAAGGCAGACATTCA
11641 G
1 G
11642 TTAAAATATA
Statistics
Matches: 97, Mismatches: 17, Indels: 7
0.80 0.14 0.06
Matches are distributed among these distances:
115 2 0.02
116 82 0.85
117 13 0.13
ACGTcount: A:0.32, C:0.15, G:0.18, T:0.35
Consensus pattern (117 bp):
GAGATTATAAAACCATTTAAAGCGAGTAATAAGACTTTTGAAGACATAAGCGACTATAAATCGAC
TTTTCTTGTCAATGAATAACTTTTGACTCATGTTTCCTAAGGCAGACATTCA
Found at i:12151 original size:340 final size:340
Alignment explanation
Indices: 11524--12398 Score: 962
Period size: 340 Copynumber: 2.6 Consensus size: 340
11514 TAGACATTCA
* ** * ** ** *
11524 GAGATTATAGAACCATTTAAAGCGAGTAATAAGATTTTTGAAGACTTAAGCGACTATAAATGGAC
1 GAGATTATAAAATGATTTAAAGTGAGTAATAAGGCTTTCAAAGACTTAAGAGACTATAAATGGAC
* * * * * *
11589 TTTTCTTGCTAATAGATGACTTTTGAC-TCATGTTTC-CTAAGGC-AGACATTCAGTTAAAATAT
66 TTTTCTTGCTAATAGATAAC-TTTCACTTCACGTTTCTC-AA-GCTAGACTTTCAATTATAATAT
* * * * *
11651 ATTTTAACAAAAAATGCAAAACAATTCAGCTTAAAATCGATTATGAAATTATAAAATCATTTAAA
128 ATTTTAACAAAAAATG-AAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAATTA-TTAAA
* * *
11716 GTGAGATATAAGACTTTCAAAAATATGGGTGACTATAGATGGACTTTTCTTGCCAATGAATGATT
191 GTGAGATATAACACTTTCAAAAACATGGGTGACTATAGATGGACTTTTCTTGCCAATGAATGACT
* *
11781 TTTTCTTCAAATTTCCTGATGTACACATTCAAATATTATCTGTTGTAGCCAGATA-TGCAA-AAA
256 TTTTCTTCAAATTTCCTGATGTAAACATTCAAATATTATCTGTTGTAGCCA-AAAGTGCAAGAAA
* * *
11844 CATTTAAGTTAAAGTTAATTAT
320 -ATTTAACTTAAAATGAATTAT
********* *
11866 GAGATTATAAAANNNNNNNNNNG-GAGTAATAAGGCTTTCAAAGACTTAAGAGAATATAAATGGA
1 GAGATTATAAAA-TGATTTAAAGTGAGTAATAAGGCTTTCAAAGACTTAAGAGACTATAAATGGA
* *
11930 CTTTTCTTGCTAATCGATAACTTTCACTTCACGTTTCTCAAGCTAGACTTTCAATTATATTATAT
65 CTTTTCTTGCTAATAGATAACTTTCACTTCACGTTTCTCAAGCTAGACTTTCAATTATAATATAT
* * *
11995 CTGAATAAAAAAT-AAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAATTATTAAATGTG
130 TTTAACAAAAAATGAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAATTATTAAA-GTG
** * *
12059 AG-TGATAACACTTTCAAATGCATGGGTGACTATAGATGGACTTTTGTTGCCCATGAATGACTTT
194 AGAT-ATAACACTTTCAAAAACATGGGTGACTATAGATGGACTTTTCTTGCCAATGAATGACTTT
* * * *
12123 TTCTTCACATTT-TTGAATGTAAACATTCAAATATTATCTGTTTTAGCCAAAAGTGTAAGAAAAT
258 TTCTTCAAATTTCCTG-ATGTAAACATTCAAATATTATCTGTTGTAGCCAAAAGTGCAAGAAAAT
12187 TTAACTTAAAATGAATTAT
322 TTAACTTAAAATGAATTAT
* * *
12206 GAGATTATAAAATGATTTAAAGTGAGTAATAAGGCTTTTAAAGACTTAAGTGACTATAAATAGAC
1 GAGATTATAAAATGATTTAAAGTGAGTAATAAGGCTTTCAAAGACTTAAGAGACTATAAATGGAC
* * * ** * *
12271 TTTTCTTGCCAATGGATGTA-TTTTGCTTCACGTTTCTCGAGGTAGACATTT-AATTATAATATA
66 TTTTCTTGCTAATAGAT-AACTTTCACTTCACGTTTCTCAAGCTAGAC-TTTCAATTATAATATA
* * *
12334 TTTTAACAAGAAATGAAATAAAATTTAACTTAAAATCAATTATGAGATTATAAAACTATTTAAAG
129 TTTTAACAAAAAATGAAA-AAAATTCAACTTAAAATCAATTATGAGATTATAAAATTA-TTAAAG
12399 NNNNNNNNNN
Statistics
Matches: 443, Mismatches: 75, Indels: 30
0.81 0.14 0.05
Matches are distributed among these distances:
339 11 0.02
340 268 0.60
341 17 0.04
342 140 0.32
343 7 0.02
ACGTcount: A:0.39, C:0.11, G:0.14, T:0.35
Consensus pattern (340 bp):
GAGATTATAAAATGATTTAAAGTGAGTAATAAGGCTTTCAAAGACTTAAGAGACTATAAATGGAC
TTTTCTTGCTAATAGATAACTTTCACTTCACGTTTCTCAAGCTAGACTTTCAATTATAATATATT
TTAACAAAAAATGAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAATTATTAAAGTGAG
ATATAACACTTTCAAAAACATGGGTGACTATAGATGGACTTTTCTTGCCAATGAATGACTTTTTC
TTCAAATTTCCTGATGTAAACATTCAAATATTATCTGTTGTAGCCAAAAGTGCAAGAAAATTTAA
CTTAAAATGAATTAT
Found at i:12215 original size:171 final size:170
Alignment explanation
Indices: 11646--12398 Score: 463
Period size: 171 Copynumber: 4.4 Consensus size: 170
11636 ATTCAGTTAA
* * * * * * *
11646 AATATATTTTAACAAAAAATGCAAA-ACAATTCAGCTTAAAATCGATTATGAAATTATAAAATCA
1 AATATATTTTAACAAGAAATG-AAAGAAAATTTAACTTAAAATCAATTATGAGATTATAAAATTA
* * * ** * *
11710 TTTAAAGTGAG-ATATAAGACTTTCAAAAATATGGGTGACTATAGATGGACTTTTCTTGCCAATG
65 -TTAAAGTGAGTA-ATAACACTTTCAAAGACATAAGTGACTATAAATAGACTTTTCTTGCCAATG
* * * *
11774 AATG-ATTTTTTCTTCAAATTTC-CTGATGTACACATTCAAATAT
128 AATGTA-TTTTGCTTCACATTTCTC-GAGGTAAACATTCAAATAT
* * * * * * * * * * * *
11817 TATCTGTTGTAGCCAGATATGCAAA-AACATTTAAGTTAAAGTTAATTATGAGATTATAAAANNN
1 AATATATTTTAACAAGAAATG-AAAGAAAATTTAACTTAAAATCAATTATGAGATTATAAAA--T
******* ** * * * * *
11881 NNNNNNNG-GAGTAATAAGGCTTTCAAAGACTTAAGAGAATATAAATGGACTTTTCTTGCTAATC
63 TATTAAAGTGAGTAATAACACTTTCAAAGACATAAGTGACTATAAATAGACTTTTCTTGCCAAT-
* ** * * * * * *
11945 G-AT-AACTTTCACTTCACGTTTCTCAAGCTAGACTTTCAATTAT
127 GAATGTA-TTTTGCTTCACATTTCTCGAGGTAAACATTCAAATAT
* * * * * *
11988 ATTATATCTGAATAAAAAAT-AAA-AAAATTCAACTTAAAATCAATTATGAGATTATAAAATTAT
1 AATATATTTTAACAAGAAATGAAAGAAAATTTAACTTAAAATCAATTATGAGATTATAAAATTAT
* ** * * * *
12051 TAAATGTGAGTGATAACACTTTCAAATG-CATGGGTGACTATAGATGGACTTTTGTTGCCCATGA
66 TAAA-GTGAGTAATAACACTTTCAAA-GACATAAGTGACTATAAATAGACTTTTCTTGCCAATGA
* * *
12115 ATG-ACTTTTTCTTCACATTT-TTGAATGTAAACATTCAAATAT
129 ATGTA-TTTTGCTTCACATTTCTCG-AGGTAAACATTCAAATAT
* * * * * * * *
12157 TATCTGTTTTAGCCAA-AAGTGTAAGAAAATTTAACTTAAAATGAATTATGAGATTATAAAATGA
1 AATATATTTTA-ACAAGAAATGAAAGAAAATTTAACTTAAAATCAATTATGAGATTATAAAATTA
** * * *
12221 TTTAAAGTGAGTAATAAGGCTTTTAAAGACTTAAGTGACTATAAATAGACTTTTCTTGCCAATGG
65 -TTAAAGTGAGTAATAACACTTTCAAAGACATAAGTGACTATAAATAGACTTTTCTTGCCAATGA
* * * *
12286 ATGTATTTTGCTTCACGTTTCTCGAGGTAGACATTTAATTAT
129 ATGTATTTTGCTTCACATTTCTCGAGGTAAACATTCAAATAT
* *
12328 AATATATTTTAACAAGAAATGAAATAAAATTTAACTTAAAATCAATTATGAGATTATAAAACTAT
1 AATATATTTTAACAAGAAATGAAAGAAAATTTAACTTAAAATCAATTATGAGATTATAAAATTA-
12393 TTAAAG
65 TTAAAG
12399 NNNNNNNNNN
Statistics
Matches: 427, Mismatches: 135, Indels: 40
0.71 0.22 0.07
Matches are distributed among these distances:
168 3 0.01
169 112 0.26
170 9 0.02
171 291 0.68
172 12 0.03
ACGTcount: A:0.39, C:0.11, G:0.13, T:0.35
Consensus pattern (170 bp):
AATATATTTTAACAAGAAATGAAAGAAAATTTAACTTAAAATCAATTATGAGATTATAAAATTAT
TAAAGTGAGTAATAACACTTTCAAAGACATAAGTGACTATAAATAGACTTTTCTTGCCAATGAAT
GTATTTTGCTTCACATTTCTCGAGGTAAACATTCAAATAT
Done.