Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018398807.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_2091.0, 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: 3243
ACGTcount: A:0.27, C:0.12, G:0.10, T:0.29
Warning! 712 characters in sequence are not A, C, G, or T
Found at i:3065 original size:172 final size:172
Alignment explanation
Indices: 2522--3243 Score: 766
Period size: 171 Copynumber: 4.2 Consensus size: 172
2512 NNNNNNNNNN
2522 TTATAGTCACCCATTCCTTCAAAAGCCTTATTACTCACTTTAAATGGTTTTATAATCTCAAAATT
1 TTATAGTCACCCATTCCTTCAAAAGCCTTATTACTCACTTTAAATGGTTTTATAATCTCAAAATT
* ** * * * *
2587 GATTTTAAGTTGAA-TTATTTTTATATTTTCAGCTAAAATAGATTATAATTGAATGTCAACCTCA
66 GATTTTAAGTTGAACTTATTTTTATATTTTTAATTAAAACAGACTATAATTGAATGTCAGCTTCA
* *
2651 AAAAACATGAAGAGAAAGGCATTTATTAGCAAGAAATA-TCCAT
131 AAAAACATGAA-AAAAAGGCATTCATTAGCAAGAAA-AGTCCAT
* * * *
2694 TTATAGTCACCCATCCCTTCAAAAGCCTTATTACTCATTTTAAATGGTTTTATAATCCCATAATT
1 TTATAGTCACCCATTCCTTCAAAAGCCTTATTACTCACTTTAAATGGTTTTATAATCTCAAAATT
* * * * *
2759 GATTTTAAGGTT-AACTT-TTTCT-CATTTTTAATTAAAACAGACTATAATTGAATATATACCTT
66 GATTTTAA-GTTGAACTTATTTTTATATTTTTAATTAAAACAGACTATAATTGAATGT-CAGCTT
* * *
2821 -AAGAAACATGAAGAAAAAGGCATTCAATGGCAAGAAAAGTCCAT
129 CAAAAAACATGAA-AAAAAGGCATTCATTAGCAAGAAAAGTCCAT
* * *
2865 TTATTA-CCACCCATTTCTTCAAAAGCCTTATTACTCATTTTAAATGGTTTTATAATCTCAAAAT
1 TTA-TAGTCACCCATTCCTTCAAAAGCCTTATTACTCACTTTAAATGGTTTTATAATCTCAAAAT
** * * **
2929 TGATTTTAAGTTGAA-TTATTTTTATATTTTTTGTTAAAATAGATTATAATTGAATGTTTGCTTC
65 TGATTTTAAGTTGAACTTATTTTTATATTTTTAATTAAAACAGACTATAATTGAATGTCAGCTTC
* *
2993 AAAAAACATGAAAAGAAAGGCATTCATTAGTAAGAAAAGTCCGT
130 AAAAAACATGAAAA-AAAGGCATTCATTAGCAAGAAAAGTCCAT
** * * * * ** *
3037 TTATAGTCACTTATTCTTTCAAAAGCCTTGTTACTCGCTTTAAATAGAATTATAATCTCATAATT
1 TTATAGTCACCCATTCCTTCAAAAGCCTTATTACTCACTTTAAATGGTTTTATAATCTCAAAATT
* * * * * *
3102 GATTTTAAGTTGAACTTA--TTTATATTTCTCATTAAAACAAACTATAATTGAATGCCTGCATCA
66 GATTTTAAGTTGAACTTATTTTTATATTTTTAATTAAAACAGACTATAATTGAATGTCAGCTTCA
* * * * *
3165 AGAAACGA-GTACAAAAAA-CCATTCATTAGGAAAAAAAGTCTAT
131 AAAAAC-ATG-A-AAAAAAGGCATTCATTAGCAAGAAAAGTCCAT
* * * *
3208 TTATAGTCTCTCATTCCTTCAAGAGCCTAATTACTC
1 TTATAGTCACCCATTCCTTCAAAAGCCTTATTACTC
Statistics
Matches: 463, Mismatches: 72, Indels: 31
0.82 0.13 0.05
Matches are distributed among these distances:
170 6 0.01
171 234 0.51
172 212 0.46
173 11 0.02
ACGTcount: A:0.37, C:0.15, G:0.10, T:0.37
Consensus pattern (172 bp):
TTATAGTCACCCATTCCTTCAAAAGCCTTATTACTCACTTTAAATGGTTTTATAATCTCAAAATT
GATTTTAAGTTGAACTTATTTTTATATTTTTAATTAAAACAGACTATAATTGAATGTCAGCTTCA
AAAAACATGAAAAAAAGGCATTCATTAGCAAGAAAAGTCCAT
Found at i:3170 original size:343 final size:343
Alignment explanation
Indices: 2529--3170 Score: 930
Period size: 343 Copynumber: 1.9 Consensus size: 343
2519 NNNTTATAGT
2529 CACCCATTCCTTCAAAAGCCTTATTACTCACTTTAAATGGTTTTATAATCTCAAAATTGATTTTA
1 CACCCATTCCTTCAAAAGCCTTATTACTCACTTTAAATGGTTTTATAATCTCAAAATTGATTTTA
2594 AGTTGAATTATTTTTATATTTTCAGCTAAAATAGATTATAATTGAATGTCAACCTCAAAAAACAT
66 AGTTGAATTATTTTTATATTTTCAGCTAAAATAGATTATAATTGAATGTCAACCTCAAAAAACAT
* *
2659 GAAGAGAAAGGCATTTATTAGCAAGAAATATCCATTTATAGTCACCCATCCCTTCAAAAGCCTTA
131 GAAAAGAAAGGCATTCATTAGCAAGAAATATCCATTTATAGTCACCCATCCCTTCAAAAGCCTTA
* * ** * *
2724 TTACTCATTTTAAATGGTTTTATAATCCCATAATTGATTTTAAGGTTAACTTTTTCTCATTTTTA
196 TTACTCACTTTAAATAGAATTATAATCCCATAATTGATTTTAAGGTTAACTTTTTATCATTTCTA
* * * *
2789 ATTAAAACAGACTATAATTGAATATATACCTTAAGAAACATGAAGAAAAAGGCATTCAATGGCAA
261 ATTAAAACAAACTATAATTGAATACATACATCAAGAAACATGAAGAAAAAGGCATTCAATGGCAA
2854 GAAAAGTCCATTTATTAC
326 GAAAAGTCCATTTATTAC
* *
2872 CACCCATTTCTTCAAAAGCCTTATTACTCATTTTAAATGGTTTTATAATCTCAAAATTGATTTTA
1 CACCCATTCCTTCAAAAGCCTTATTACTCACTTTAAATGGTTTTATAATCTCAAAATTGATTTTA
** * *** *
2937 AGTTGAATTATTTTTATATTTTTTGTTAAAATAGATTATAATTGAATGTTTGCTTCAAAAAACAT
66 AGTTGAATTATTTTTATATTTTCAGCTAAAATAGATTATAATTGAATGTCAACCTCAAAAAACAT
* * ** * *
3002 GAAAAGAAAGGCATTCATTAGTAAGAAA-AGTCCGTTTATAGTCACTTATTCTTTCAAAAGCCTT
131 GAAAAGAAAGGCATTCATTAGCAAGAAATA-TCCATTTATAGTCACCCATCCCTTCAAAAGCCTT
* * *
3066 GTTACTCGCTTTAAATAGAATTATAATCTCATAATTGATTTTAA-GTTGAACTTATTTAT-ATTT
195 ATTACTCACTTTAAATAGAATTATAATCCCATAATTGATTTTAAGGTT-AACTT-TTTATCATTT
* * * *
3129 CTCATTAAAACAAACTATAATTGAATGCCTGCATCAAGAAAC
258 CTAATTAAAACAAACTATAATTGAATACATACATCAAGAAAC
3171 GAGTACAAAA
Statistics
Matches: 262, Mismatches: 34, Indels: 6
0.87 0.11 0.02
Matches are distributed among these distances:
342 4 0.02
343 254 0.97
344 4 0.02
ACGTcount: A:0.37, C:0.15, G:0.10, T:0.38
Consensus pattern (343 bp):
CACCCATTCCTTCAAAAGCCTTATTACTCACTTTAAATGGTTTTATAATCTCAAAATTGATTTTA
AGTTGAATTATTTTTATATTTTCAGCTAAAATAGATTATAATTGAATGTCAACCTCAAAAAACAT
GAAAAGAAAGGCATTCATTAGCAAGAAATATCCATTTATAGTCACCCATCCCTTCAAAAGCCTTA
TTACTCACTTTAAATAGAATTATAATCCCATAATTGATTTTAAGGTTAACTTTTTATCATTTCTA
ATTAAAACAAACTATAATTGAATACATACATCAAGAAACATGAAGAAAAAGGCATTCAATGGCAA
GAAAAGTCCATTTATTAC
Found at i:3204 original size:343 final size:343
Alignment explanation
Indices: 2529--3243 Score: 920
Period size: 343 Copynumber: 2.1 Consensus size: 343
2519 NNNTTATAGT
2529 CACCCATTCCTTCAAAAGCCTTATTACTCACTTTAAATGGTTTTATAATCTCAAAATTGATTTTA
1 CACCCATTCCTTCAAAAGCCTTATTACTCACTTTAAATGGTTTTATAATCTCAAAATTGATTTTA
2594 AGTTGAATTATTTTTATATTTTCAGCTAAAATAGATTATAATTGAATGTCAACCTCAAAAAACAT
66 AGTTGAATTATTTTTATATTTTCAGCTAAAATAGATTATAATTGAATGTCAACCTCAAAAAACAT
* *
2659 GAAGAGAAAGGCATTTATTAGCAAGAAATATCCATTTATAGTCACCCATCCCTTCAAAAGCCTTA
131 GAAAAGAAAGGCATTCATTAGCAAGAAATATCCATTTATAGTCACCCATCCCTTCAAAAGCCTTA
* * ** * *
2724 TTACTCATTTTAAATGGTTTTATAATCCCATAATTGATTTTAAGGTTAACTTTTTCTCATTTTTA
196 TTACTCACTTTAAATAGAATTATAATCCCATAATTGATTTTAAGGTTAACTTTTTATCATTTCTA
* * * * * **
2789 ATTAAAACAGACTATAATTGAATATATACCTTAAGAAACATGAAGAAAAAGGCATTCAATGGCAA
261 ATTAAAACAAACTATAATTGAATACATACATCAAGAAACATGAACAAAAAACCATTCAATGGCAA
*
2854 GAAAAGTCCATTTATTAC
326 AAAAAGTCCATTTATTAC
* *
2872 CACCCATTTCTTCAAAAGCCTTATTACTCATTTTAAATGGTTTTATAATCTCAAAATTGATTTTA
1 CACCCATTCCTTCAAAAGCCTTATTACTCACTTTAAATGGTTTTATAATCTCAAAATTGATTTTA
** * *** *
2937 AGTTGAATTATTTTTATATTTTTTGTTAAAATAGATTATAATTGAATGTTTGCTTCAAAAAACAT
66 AGTTGAATTATTTTTATATTTTCAGCTAAAATAGATTATAATTGAATGTCAACCTCAAAAAACAT
* * ** * *
3002 GAAAAGAAAGGCATTCATTAGTAAGAAA-AGTCCGTTTATAGTCACTTATTCTTTCAAAAGCCTT
131 GAAAAGAAAGGCATTCATTAGCAAGAAATA-TCCATTTATAGTCACCCATCCCTTCAAAAGCCTT
* * *
3066 GTTACTCGCTTTAAATAGAATTATAATCTCATAATTGATTTTAA-GTTGAACTTATTTAT-ATTT
195 ATTACTCACTTTAAATAGAATTATAATCCCATAATTGATTTTAAGGTT-AACTT-TTTATCATTT
* * * * * *
3129 CTCATTAAAACAAACTATAATTGAATGCCTGCATCAAGAAACGA-GTACAAAAAACCATTCATTA
258 CTAATTAAAACAAACTATAATTGAATACATACATCAAGAAAC-ATGAACAAAAAACCATTCAAT-
* *
3193 GG-AAAAAAAGTCTATTTA-TAGT
321 GGCAAAAAAAGTCCATTTATTA-C
* * * *
3215 CTCTCATTCCTTCAAGAGCCTAATTACTC
1 CACCCATTCCTTCAAAAGCCTTATTACTC
Statistics
Matches: 319, Mismatches: 47, Indels: 12
0.84 0.12 0.03
Matches are distributed among these distances:
342 6 0.02
343 306 0.96
344 7 0.02
ACGTcount: A:0.37, C:0.15, G:0.10, T:0.37
Consensus pattern (343 bp):
CACCCATTCCTTCAAAAGCCTTATTACTCACTTTAAATGGTTTTATAATCTCAAAATTGATTTTA
AGTTGAATTATTTTTATATTTTCAGCTAAAATAGATTATAATTGAATGTCAACCTCAAAAAACAT
GAAAAGAAAGGCATTCATTAGCAAGAAATATCCATTTATAGTCACCCATCCCTTCAAAAGCCTTA
TTACTCACTTTAAATAGAATTATAATCCCATAATTGATTTTAAGGTTAACTTTTTATCATTTCTA
ATTAAAACAAACTATAATTGAATACATACATCAAGAAACATGAACAAAAAACCATTCAATGGCAA
AAAAAGTCCATTTATTAC
Done.