Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018398886.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_2168.0, 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: 3226
ACGTcount: A:0.27, C:0.07, G:0.10, T:0.24
Warning! 1030 characters in sequence are not A, C, G, or T
Found at i:1094 original size:170 final size:168
Alignment explanation
Indices: 694--1605 Score: 690
Period size: 171 Copynumber: 5.3 Consensus size: 168
684 NNNNAATTTC
* * *
694 ACTTAAAATCAATTATGAGATTATAAAACTATTTAAAGCGAGTAATAAAGGCTTTTAAAGAAATG
1 ACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAAT-AAGGCTTTTGAAGGAATG
* * * * * ** * * **
759 AGAGGCTATAAGTGGATTTTTTTTCCAAATAAATGATTTTTTCTA-CACATTTCCTGAGGCAAAC
65 AGAGACTATAAATGGACTTTTCTTCAAAATAAATGGGTTTTTCTATCAC-TTTTCT-AGGTAGGC
* * * *
823 ATTCAATTAT-TTACTGTTTTAACCATAAATGTAAAAAAATTCA
128 ATTCAATTATAGT-CTGTTTTAA-GAAAAATAT-AAAAAATTCA
********** * * * *
866 ACTTAAAATCNNNNNNNNNNTTATAAAACCATTTAAAGCGAGTAATAAAGATTTTGAAGGGATGG
1 ACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGA
* * * *
931 GCGAGTATAAATGGACTTTTCTTCAAAATAAATGAGTTTTTCTATGCA-TTTTCTGAGGCAGGCA
66 GAGACTATAAATGGACTTTTCTTCAAAATAAATGGGTTTTTCTAT-CACTTTTCT-AGGTAGGCA
*
995 TTTAATTATAGTCTGTTTTAATGAAAAATATAAAAAATTTC-
129 TTCAATTATAGTCTGTTTTAA-GAAAAATATAAAAAA-TTCA
* * * * * * *
1036 ACTTAAAATTAATTATGAGATTATAAAATCATTTAAAGTGAGTCACAAGGCTTTTGAAGAAATGG
1 ACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGA
* * * ** * * *
1101 GTGACTATAAATGGACTTTTCTT-ACGAATGAATGCTTTTTTCT-TCATGTTTTTTAAGGTAGAC
66 GAGACTATAAATGGACTTTTCTTCA-AAATAAATGGGTTTTTCTATCA-CTTTTCT-AGGTAGGC
* *
1164 ATTCAATTATAGTTTGTTTTTACA-AAAAATATTAAAAAATACA
128 ATTCAATTATAGTCTG-TTTTA-AGAAAAATA-TAAAAAATTCA
* * **********
1207 ACTTAAAATCAATTATGAGGTTATAAAACTATTNNNNNNNNNNAATAAGGCTTTTGAAGGAATGA
1 ACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGA
* * * * *
1272 GAGACTATAAATGTATTTTTTTTCCAAATAAATGGGTTTTTCTA-CACATTTCTAGTAGTAGGCA
66 GAGACTATAAATGGACTTTTCTTCAAAATAAATGGGTTTTTCTATCACTTTTCTAG--GTAGGCA
*
1336 TTCAATTATAGTCTATTTTAAAGAAAAATATAAAACAATTCA
129 TTCAATTATAGTCTGTTTT-AAGAAAAATATAAAA-AATTCA
*********** * *
1378 ACTTAAAATCAATTATGAGANNNNNNNNNNTTTTAAAGCGAGTAACAAAGCTTTTGAAGGAATGA
1 ACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGA
* * * *
1443 GAGACTAGAAATGGACTTTTCTTCAAAATAAATGGGTTTTTCTA-CACGTTTCCCATGGTAAGCA
66 GAGACTATAAATGGACTTTTCTTCAAAATAAATGGGTTTTTCTATCAC-TTTTCTA-GGTAGGCA
* * * *
1507 TTCAATGATAGTCAGTTTTAACAAAGAATGTAAAAAATTCA
129 TTCAATTATAGTCTGTTTTAAGAAA-AATATAAAAAATTCA
* * *
1548 ACTAAAAATCAATAATGAGATTATAAAACCATTTAAAACGAGTAATAAGGCTTTTGAA
1 ACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAA
1606 NNNNNNNNNN
Statistics
Matches: 565, Mismatches: 154, Indels: 44
0.74 0.20 0.06
Matches are distributed among these distances:
168 2 0.00
169 4 0.01
170 188 0.33
171 327 0.58
172 41 0.07
173 3 0.01
ACGTcount: A:0.39, C:0.10, G:0.14, T:0.34
Consensus pattern (168 bp):
ACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGA
GAGACTATAAATGGACTTTTCTTCAAAATAAATGGGTTTTTCTATCACTTTTCTAGGTAGGCATT
CAATTATAGTCTGTTTTAAGAAAAATATAAAAAATTCA
Found at i:1597 original size:341 final size:341
Alignment explanation
Indices: 688--1605 Score: 783
Period size: 341 Copynumber: 2.7 Consensus size: 341
678 NNNNNNNNNN
* *
688 AATTTCACTTAAAATCAATTATGAGATTATAAAA-CTATTTAAAGCGAGTAATAAAGGCTTTTAA
1 AATTTCACTTAAAATCAATTATGAGATTATAAAATC-ATTTAAAGCGAGTAACAAA-GCTTTTGA
* * * * * * ** * **
752 AGAAATGAGAGGCTATAAGTGGATTTTTTTTCCAAATAAATGATTTTTTCTACACATTTCCTGAG
64 AGAAATGAGAGACTAGAAATGGACTTTTCTTACAAATAAATGCGTTTTTCTACACGTTTCCCAAG
* * * * * * * * * ****
817 GCAAACATTCAATTAT-TTACTGTTTTAACCATAAAT-GTAAAAAAATTCAACTTAAAATCNNNN
129 GTAGACATTCAATGATAGT-CAGTTTTAACAAAAAATAGT-AAAAAATACAACTAAAAATCAATA
****** * * * * * * *
880 NNNNNNTTATAAAACCATTTAAAGCGAGTAATAAAGATTTTGAAGGGATGGGCGAGTATAAATGG
192 ATGAGATTATAAAACCATTTAAAACGAGTAATAAGGCTTTTGAAGGAATGAGAGACTATAAATGG
** * *
945 ACTTTTCTTCAAAATAAATGAGTTTTTCTATGCATTTTCTGAGGCAGGCATTTAATTATAGTCTG
257 ACTTTTCTTCAAAATAAATGAGTTTTTCTACACATTTTCTGAGGCAGGCATTCAATTATAGTCTA
*
1010 TTTTAATGAAAAATATAAAA
322 TTTTAAAGAAAAATATAAAA
* * * *
1030 AATTTCACTTAAAATTAATTATGAGATTATAAAATCATTTAAAGTGAGTCACAAGGCTTTTGAAG
1 AATTTCACTTAAAATCAATTATGAGATTATAAAATCATTTAAAGCGAGTAACAAAGCTTTTGAAG
* * * * * * * * ***
1095 AAATGGGTGACTATAAATGGACTTTTCTTACGAATGAATGCTTTTTTCTTCATGTTTTTTAAGGT
66 AAATGAGAGACTAGAAATGGACTTTTCTTACAAATAAATGCGTTTTTCTACACGTTTCCCAAGGT
* ** * * * *
1160 AGACATTCAATTATAGTTTGTTTTTACAAAAAATATTAAAAAATACAACTTAAAATCAATTATGA
131 AGACATTCAATGATAGTCAGTTTTAACAAAAAATAGTAAAAAATACAACTAAAAATCAATAATGA
* * ********** * *
1225 GGTTATAAAACTATTNNNNNNNNNNAATAAGGCTTTTGAAGGAATGAGAGACTATAAATGTATTT
196 GATTATAAAACCATTTAAAACGAGTAATAAGGCTTTTGAAGGAATGAGAGACTATAAATGGACTT
* * * *
1290 TTTTTCCAAATAAATGGGTTTTTCTACACA-TTTCT-AGTAGTAGGCATTCAATTATAGTCTATT
261 TTCTTCAAAATAAATGAGTTTTTCTACACATTTTCTGAG--GCAGGCATTCAATTATAGTCTATT
1353 TTAAAGAAAAATATAAAA
324 TTAAAGAAAAATATAAAA
***********
1371 CAA-TTCAACTTAAAATCAATTATGAGANNNNNNNNNNTTTTAAAGCGAGTAACAAAGCTTTTGA
1 -AATTTC-ACTTAAAATCAATTATGAGATTATAAAATCATTTAAAGCGAGTAACAAAGCTTTTGA
* * *
1435 AGGAATGAGAGACTAGAAATGGACTTTTCTT-CAAAATAAATGGGTTTTTCTACACGTTTCCCAT
64 AGAAATGAGAGACTAGAAATGGACTTTTCTTAC-AAATAAATGCGTTTTTCTACACGTTTCCCAA
* *
1499 GGTA-AGCATTCAATGATAGTCAGTTTTAACAAAGAAT-GTAAAAAATTCAACTAAAAATCAATA
128 GGTAGA-CATTCAATGATAGTCAGTTTTAACAAAAAATAGTAAAAAATACAACTAAAAATCAATA
1562 ATGAGATTATAAAACCATTTAAAACGAGTAATAAGGCTTTTGAA
192 ATGAGATTATAAAACCATTTAAAACGAGTAATAAGGCTTTTGAA
1606 NNNNNNNNNN
Statistics
Matches: 448, Mismatches: 119, Indels: 19
0.76 0.20 0.03
Matches are distributed among these distances:
339 2 0.00
340 5 0.01
341 268 0.60
342 172 0.38
343 1 0.00
ACGTcount: A:0.39, C:0.10, G:0.14, T:0.34
Consensus pattern (341 bp):
AATTTCACTTAAAATCAATTATGAGATTATAAAATCATTTAAAGCGAGTAACAAAGCTTTTGAAG
AAATGAGAGACTAGAAATGGACTTTTCTTACAAATAAATGCGTTTTTCTACACGTTTCCCAAGGT
AGACATTCAATGATAGTCAGTTTTAACAAAAAATAGTAAAAAATACAACTAAAAATCAATAATGA
GATTATAAAACCATTTAAAACGAGTAATAAGGCTTTTGAAGGAATGAGAGACTATAAATGGACTT
TTCTTCAAAATAAATGAGTTTTTCTACACATTTTCTGAGGCAGGCATTCAATTATAGTCTATTTT
AAAGAAAAATATAAAA
Found at i:2482 original size:169 final size:168
Alignment explanation
Indices: 2034--2482 Score: 447
Period size: 171 Copynumber: 2.6 Consensus size: 168
2024 ATGAGGTATG
*
2034 CATTCAATTAAAATCTGTTTTAACAAAAAATGTAAAAAATTTAA-TTTAAAATCAATTATGACAT
1 CATTCAATTATAATCTGTTTTAAC-AAAAATGTAAAAAATTTAACTTT-AAATCAATTATGACAT
** * * * *
2098 TATGTAACCATTTAAAGCCAGTAATAAGGCTTTTGAATAAATGGGTGACTATAAATAGACTTTTT
64 TATAAAACCATTTAAAGCAAGTAATAAGGCTTTTGAATGAATGGGAGACTATAAATAGACTTTTC
* * * * *
2163 TTGTCAATGAATGCCTTTTTTCTCAAATTTCATGAAGTAGA
129 TTGCCAATAAAAG-CGTTTTTCTCAAATTTCATGAAGAAGA
* * * * * * *
2204 CATTCAATTATAATCTGTTTGATATAAAAATTTAAAAAAATTTAACTTAAAATTAATTATGATAG
1 CATTCAATTATAATCTGTTTTA-ACAAAAATGT-AAAAAATTTAACTTTAAATCAATTATGACAT
* * ** *
2269 TATAAAACCATTTAAAGCGAGTAATGAGGCTTTTGGTTGAATGGGAGACTATAAATGGACTTTTC
64 TATAAAACCATTTAAAGCAAGTAATAAGGCTTTTGAATGAATGGGAGACTATAAATAGACTTTTC
** * *
2334 TT-CCAAATAAAAG-GTTTTTCTACATGTTTCTTGAGGCAAG-
129 TTGCC-AATAAAAGCGTTTTTCT-CAAATTTCATGAAG-AAGA
* * * * * * *
2374 CATTTAATTGTAGTCTGTTTTAACAACAAATGTAAAAAATTCAACTTTAAAGCAATCATGAGATT
1 CATTCAATTATAATCTGTTTTAACAA-AAATGTAAAAAATTTAACTTTAAATCAATTATGACATT
** *
2439 ATAAAACCATTTAAAATAAGTAATAAGGCTTTTGAAGGAATGGG
65 ATAAAACCATTTAAAGCAAGTAATAAGGCTTTTGAATGAATGGG
2483 TGNNNNNNNN
Statistics
Matches: 225, Mismatches: 47, Indels: 15
0.78 0.16 0.05
Matches are distributed among these distances:
169 72 0.32
170 61 0.27
171 90 0.40
172 2 0.01
ACGTcount: A:0.40, C:0.10, G:0.14, T:0.36
Consensus pattern (168 bp):
CATTCAATTATAATCTGTTTTAACAAAAATGTAAAAAATTTAACTTTAAATCAATTATGACATTA
TAAAACCATTTAAAGCAAGTAATAAGGCTTTTGAATGAATGGGAGACTATAAATAGACTTTTCTT
GCCAATAAAAGCGTTTTTCTCAAATTTCATGAAGAAGA
Done.