Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018397976.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_1281.0, 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, 892
Length: 1487
ACGTcount: A:0.32, C:0.11, G:0.12, T:0.28
Warning! 261 characters in sequence are not A, C, G, or T
Found at i:1061 original size:343 final size:332
Alignment explanation
Indices: 416--1307 Score: 948
Period size: 343 Copynumber: 2.6 Consensus size: 332
406 NNNNNNNNNT
*
416 CAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCGGGTAATAAGACCTTTGAAGGAAT
1 CAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCAGGTAATAAGACCTTTGAAGGAAT
* * *
481 GAGGGACTATAAATGGACTTTTCTTTTGAATGAATGGCTTTTTTTGCATGTTTCCCA-AGGCAAG
66 GAGGGACTATAAATGGACTTTTCTTCTCAATGAATGGCTTTTTTTGCACGTTT-CCAGAGGCAAG
********** * *
545 CATTCANNNNNNNNNNGTTTTAACAAAAAATGCAAAAAAATTCAACTTAAAATCAATTTTGAGAT
130 CATTCAATTATAGTCTGTTTTAATAAAAAATGTAAAAAAATTCAACTTAAAATCAATTTTGAGAT
********** *
610 TATAAAACGATTTGAAGCAAATAATAAGCTTTTNNNNNNNNNNGGTGACTCTACATGGCCTTTTC
195 TATAAAACGATTTGAAGCAAATAATAAGCTTTTTGAAGGAATGGGTGACTCTACATGCCCTTTTC
* * * *
675 TCGTTACTGAATGCTTATTTTGTCACATTTCTCAAGGTAGACATTCAATTATAGTATGTTTTAAT
260 TCATTAATAAATGCTTATTTTCTCACATTTCTCAAGGTAGACATTCAATTATAGTATGTTTTAAT
740 CAAAAATG
325 CAAAAATG
* * *
748 NNNNNNNNNNCAACTGAAAATCAATTATGAGATTATAAAACCATTTAAAGCAGGCAATAAGGCCT
1 ----------CAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCAGGTAATAAGACCT
*
813 TTGAAGGAATGAGGGACTATAAATGGACTTTTCTTCCCAATGAATGGCTTTTTTTGCACGTTTCC
56 TTGAAGGAATGAGGGACTATAAATGGACTTTTCTTCTCAATGAATGGCTTTTTTTGCACGTTTCC
* *
878 AGAGGCAAGCATTCAATTATAGTCTGTTTTAATAAAAAAATTTAAAAAAAATCAACTTAAAATCA
121 AGAGGCAAGCATTCAATTATAGTCTGTTTTAAT-AAAAAATGTAAAAAAATTCAACTTAAAATCA
* **********
943 ATTTTGAGATTATAAAACTATTNNNNNNNNNNAATAAGCTTTTTGAAGGAATGGGTGACTCTACA
185 ATTTTGAGATTATAAAACGATTTGAAGCAAATAATAAGCTTTTTGAAGGAATGGGTGACTCTACA
*
1008 TGCCCTTTTCTCATTAATAAATGCTTATTTTCTCACATTTCTCGAGGTAGACATTCAATTATAGT
250 TGCCCTTTTCTCATTAATAAATGCTTATTTTCTCACATTTCTCAAGGTAGACATTCAATTATAGT
1073 ATGTTTTAATCAAAAATG
315 ATGTTTTAATCAAAAATG
* *
1091 NNNNNNNNNNCAACTTAAAATCAATTATGAGATTATAAAGCCATTTAAAGCAAGTAATAA-ACCT
1 ----------CAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCAGGTAATAAGACC-
* * *
1155 TTTGAAGGAATG-GGTGACTGTAAATGGACTTTTCTGCTCAATGAAAGGCTTTTTTTGCACGTTT
55 TTTGAAGGAATGAGG-GACTATAAATGGACTTTTCTTCTCAATGAATGGCTTTTTTTGCACGTTT
* * * * * *
1219 CTTAG-GGCAGGCATTTAATTATAGTCTGTTTTAACT-AAAAATGTAAAAACATTTAAGTTAAAA
119 C-CAGAGGCAAGCATTCAATTATAGTCTGTTTTAA-TAAAAAATGTAAAAAAATTCAACTTAAAA
* * *
1282 TCAATTATGAGAGTATAAAACCATTT
182 TCAATTTTGAGATTATAAAACGATTT
1308 AAATTGAGTA
Statistics
Matches: 474, Mismatches: 70, Indels: 12
0.85 0.13 0.02
Matches are distributed among these distances:
341 3 0.01
342 178 0.38
343 290 0.61
344 3 0.01
ACGTcount: A:0.35, C:0.13, G:0.14, T:0.33
Consensus pattern (332 bp):
CAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCAGGTAATAAGACCTTTGAAGGAAT
GAGGGACTATAAATGGACTTTTCTTCTCAATGAATGGCTTTTTTTGCACGTTTCCAGAGGCAAGC
ATTCAATTATAGTCTGTTTTAATAAAAAATGTAAAAAAATTCAACTTAAAATCAATTTTGAGATT
ATAAAACGATTTGAAGCAAATAATAAGCTTTTTGAAGGAATGGGTGACTCTACATGCCCTTTTCT
CATTAATAAATGCTTATTTTCTCACATTTCTCAAGGTAGACATTCAATTATAGTATGTTTTAATC
AAAAATG
Found at i:1167 original size:171 final size:169
Alignment explanation
Indices: 415--1310 Score: 515
Period size: 171 Copynumber: 5.2 Consensus size: 169
405 NNNNNNNNNN
** *
415 TCAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCGGGTAATAAGACC-TTTGAAGGA
1 TCAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCAAGCAATAAG-CCTTTTGAAGGA
* * * * ** * * *
479 ATGAGG-GACTATAAATGGACTTTTCTTTTGAATGAATGGCTT-TTTTTGCATGTTTCCCAAGGC
65 ATG-GGTGACTCTACATGGCCTTTTCTCTT-AATGAAT-GCTTATTTTT-CACATTTCTCGAGGT
********** * *
542 A-AGCATTCANNNNNNNNNNGTTTTAA-CAAAAAATGCAAAAAAAT
126 AGA-CATTCAATTATAGTATGTTTTAATC-AAAAATGTAAAAAAAA
* * * ** ******
586 TCAACTTAAAATCAATTTTGAGATTATAAAACGATTTGAAGCAAATAATAAG-CTTTTNNNNNNN
1 TCAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCAAGCAATAAGCCTTTT-GAAGGA
*** * *
650 NNNGGTGACTCTACATGGCCTTTTCTCGTTACTGAATGCTTATTTTGTCACATTTCTCAAGGTAG
65 ATGGGTGACTCTACATGGCCTTTTCTC-TTAATGAATGCTTATTTT-TCACATTTCTCGAGGTAG
*********
715 ACATTCAATTATAGTATGTTTTAATCAAAAATGNNNNNNNNN
128 ACATTCAATTATAGTATGTTTTAATCAAAAATGTAAAAAAAA
* * *
757 NCAACTGAAAATCAATTATGAGATTATAAAACCATTTAAAGCAGGCAATAAGGCC-TTTGAAGGA
1 TCAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCAAGCAATAA-GCCTTTTGAAGGA
* * * ** *
821 ATGAGG-GACTATAAATGGACTTTTCTTCCCAATGAATGGCTT-TTTTTGCACGTTTC-CAGAGG
65 ATG-GGTGACTCTACATGGCCTTTTC-TCTTAATGAAT-GCTTATTTTT-CACATTTCTC-GAGG
* * * *
883 CA-AGCATTCAATTATAGTCTGTTTTAATAAAAAAATTTAAAAAAAA
125 TAGA-CATTCAATTATAGTATGTTTTAAT-CAAAAATGTAAAAAAAA
* * ********** *
929 TCAACTTAAAATCAATTTTGAGATTATAAAACTATTNNNNNNNNNNAATAAGCTTTTTGAAGGAA
1 TCAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCAAGCAATAAGCCTTTTGAAGGAA
* *
994 TGGGTGACTCTACATGCCCTTTTCTCATTAATAAATGCTTATTTTCTCACATTTCTCGAGGTAGA
66 TGGGTGACTCTACATGGCCTTTTCTC-TTAATGAATGCTTATTTT-TCACATTTCTCGAGGTAGA
*********
1059 CATTCAATTATAGTATGTTTTAATCAAAAATGNNNNNNNNN
129 CATTCAATTATAGTATGTTTTAATCAAAAATGTAAAAAAAA
* * * *
1100 NCAACTTAAAATCAATTATGAGATTATAAAGCCATTTAAAGCAAGTAATAAACCTTTTGAAGGAA
1 TCAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCAAGCAATAAGCCTTTTGAAGGAA
* * * * * * * *
1165 TGGGTGACTGTAAATGGACTTTTCTGCTCAATGAAAGGCTT-TTTTTGCACGTTTCT-TAGGGCA
66 TGGGTGACTCTACATGGCCTTTTCT-CTTAATG-AATGCTTATTTTT-CACATTTCTCGA-GGTA
* * * * *
1228 GGCATTTAATTATAGTCTGTTTTAA-CTAAAAATGTAAAAACAT
127 GACATTCAATTATAGTATGTTTTAATC-AAAAATGTAAAAAAAA
* * *
1271 TTAAGTTAAAATCAATTATGAGAGTATAAAACCATTTAAA
1 TCAACTTAAAATCAATTATGAGATTATAAAACCATTTAAA
1311 TTGAGTAATN
Statistics
Matches: 536, Mismatches: 160, Indels: 58
0.71 0.21 0.08
Matches are distributed among these distances:
169 1 0.00
170 15 0.03
171 377 0.70
172 139 0.26
173 4 0.01
ACGTcount: A:0.35, C:0.13, G:0.14, T:0.32
Consensus pattern (169 bp):
TCAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCAAGCAATAAGCCTTTTGAAGGAA
TGGGTGACTCTACATGGCCTTTTCTCTTAATGAATGCTTATTTTTCACATTTCTCGAGGTAGACA
TTCAATTATAGTATGTTTTAATCAAAAATGTAAAAAAAA
Done.