Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018397767.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_1065.0, 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: 4111
ACGTcount: A:0.18, C:0.06, G:0.07, T:0.17
Warning! 2110 characters in sequence are not A, C, G, or T
Found at i:3049 original size:171 final size:161
Alignment explanation
Indices: 2911--3384 Score: 245
Period size: 172 Copynumber: 2.8 Consensus size: 161
2901 NNNNNNNNNN
* *
2911 AAAAAATGTAACAATATTCAACTTAAAATCAATTATGGGATTATAAAACCACT-TAAAGCGAGCA
1 AAAAAATGTAACAATATTCAAATTAAAATCAATTATGAGATTATAAAACC-CTGTAAAGCGAGCA
* * *
2975 ATATGGCTTTCGAAAGAATGGGAGACTGTAAATGGACTTTTCTCGCCAATGAATGCTTTTTTCTT
65 ATAAGGCTTTCAAAAGAATGGGAGACTGTAAATGGACTTTTCTCGCAAATGAATGCTTTTTTCTT
* * **
3040 GATGTTTCTCAAGGTAGACATTCAATTANNNNNNNNNNTAAC
130 CACGTTTCTCAAGGTAGACATTCAATTA----------TAGT
* * * * * * *
3082 CAAAAATGT-ACAAATAATTCAAATTAAAATCAATTTTGAGATTATGAAACCATTTAAAGAGAGT
1 AAAAAATGTAAC-AAT-ATTCAAATTAAAATCAATTATGAGATTATAAAACCCTGTAAAGCGAGC
* * * * ** * * * * *
3146 ATTAAGGCTTTTAAAGGAATGAGAGACCATAAATTGACTTTTCTTGCCAATGAATACCTTTTTCT
64 AATAAGGCTTTCAAAAGAATGGGAGACTGTAAATGGACTTTTCTCGCAAATGAATGCTTTTTTCT
* * * *
3211 TTATGTTTC-CTAAGGTAGGCATTCAGTTATAGTCTGTTT
129 TCACGTTTCTC-AAGGTAGACATTCAATTATA----G--T
* * * * * * * *
3250 AATCAAAAATGTAAAAAAGATTCAACTTAAAACCAATTATAAGATTATAAAACCATTTAAAGAGA
1 -A--AAAAATGT-AACAATATTCAAATTAAAATCAATTATGAGATTATAAAACCCTGTAAAGCGA
* * ** * * ** * * *
3315 GTAATAAGGCTCTT-GAAAGAATGAAAAACTATAAATGGTGTTTTTTTGCCAATGAATGCTTTTT
62 GCAATAAGGCT-TTCAAAAGAATGGGAGACTGTAAATGGACTTTTCTCGCAAATGAATGCTTTTT
3379 TCTTCA
126 TCTTCA
3385 NNNNNNNNNN
Statistics
Matches: 241, Mismatches: 46, Indels: 32
0.76 0.14 0.10
Matches are distributed among these distances:
162 2 0.01
170 2 0.01
171 116 0.48
172 120 0.50
173 1 0.00
ACGTcount: A:0.38, C:0.13, G:0.14, T:0.33
Consensus pattern (161 bp):
AAAAAATGTAACAATATTCAAATTAAAATCAATTATGAGATTATAAAACCCTGTAAAGCGAGCAA
TAAGGCTTTCAAAAGAATGGGAGACTGTAAATGGACTTTTCTCGCAAATGAATGCTTTTTTCTTC
ACGTTTCTCAAGGTAGACATTCAATTATAGT
Found at i:3210 original size:172 final size:169
Alignment explanation
Indices: 2741--3384 Score: 608
Period size: 171 Copynumber: 3.8 Consensus size: 169
2731 NNNNNNNNNN
* * * * * *
2741 AAAATGTACAAAGAATTCAAATTAAAATCAATTTTGAGATTATAAAACCGTGTACAGTGAGTAAT
1 AAAATGTA-AAATAATTCAAATTAAAATCAATTATGAGATTATAAAACCATTTAAAGAGAGTAAT
* * * *
2806 AAGGCTTTTAAAAGAATGGGAGACTGTAAATGGACTTTTCTTGCAAATGAATGCTTTTTTCTTCA
65 AAGGC-TTTGAAAGAATGAGAGACTATAAATGGACTTTTCTTGCCAATGAATGCTTTTTTCTTCA
* * **********
2871 CGTTTCTCAAGGTAGACATTCAATTATAGTNNNNNNNNNNAA
129 TGTTTCTCAAGGTAGACATTCAATTAAAGT-CTGTTTAACCA
* * * * *
2913 AAAATGTAACAAT-ATTCAACTTAAAATCAATTATGGGATTATAAAACCACTTAAAGCGAGCAAT
1 AAAATGTAA-AATAATTCAAATTAAAATCAATTATGAGATTATAAAACCATTTAAAGAGAGTAAT
* * * * *
2977 ATGGCTTTCGAAAGAATGGGAGACTGTAAATGGACTTTTCTCGCCAATGAATGCTTTTTTCTTGA
65 AAGGCTTT-GAAAGAATGAGAGACTATAAATGGACTTTTCTTGCCAATGAATGCTTTTTTCTTCA
*********
3042 TGTTTCTCAAGGTAGACATTCAATTANNNNNNNNNNTAACCA
129 TGTTTCTCAAGGTAGACATTCAATTA-AAGTCTGTTTAACCA
* * *
3084 AAAATGTACAAATAATTCAAATTAAAATCAATTTTGAGATTATGAAACCATTTAAAGAGAGTATT
1 AAAATGTA-AAATAATTCAAATTAAAATCAATTATGAGATTATAAAACCATTTAAAGAGAGTAAT
* * * * * *
3149 AAGGCTTTTAAAGGAATGAGAGACCATAAATTGACTTTTCTTGCCAATGAATACCTTTTTCTTTA
65 AAGGCTTTGAAA-GAATGAGAGACTATAAATGGACTTTTCTTGCCAATGAATGCTTTTTTCTTCA
* * * *
3214 TGTTTC-CTAAGGTAGGCATTCAGTTATAGTCTGTTTAATCA
129 TGTTTCTC-AAGGTAGACATTCAATTAAAGTCTGTTTAACCA
* * * *
3255 AAAATGTAAAAAAGATTCAACTTAAAACCAATTATAAGATTATAAAACCATTTAAAGAGAGTAAT
1 AAAATGTAAAATA-ATTCAAATTAAAATCAATTATGAGATTATAAAACCATTTAAAGAGAGTAAT
* * ** *
3320 AAGGCTCTTGAAAGAATGAAAAACTATAAATGGTGTTTTTTTGCCAATGAATGCTTTTTTCTTCA
65 AAGGCT-TTGAAAGAATGAGAGACTATAAATGGACTTTTCTTGCCAATGAATGCTTTTTTCTTCA
3385 NNNNNNNNNN
Statistics
Matches: 390, Mismatches: 73, Indels: 19
0.81 0.15 0.04
Matches are distributed among these distances:
170 7 0.02
171 251 0.64
172 132 0.34
ACGTcount: A:0.37, C:0.12, G:0.15, T:0.32
Consensus pattern (169 bp):
AAAATGTAAAATAATTCAAATTAAAATCAATTATGAGATTATAAAACCATTTAAAGAGAGTAATA
AGGCTTTGAAAGAATGAGAGACTATAAATGGACTTTTCTTGCCAATGAATGCTTTTTTCTTCATG
TTTCTCAAGGTAGACATTCAATTAAAGTCTGTTTAACCA
Found at i:3368 original size:343 final size:333
Alignment explanation
Indices: 2741--3382 Score: 723
Period size: 343 Copynumber: 1.9 Consensus size: 333
2731 NNNNNNNNNN
* * *
2741 AAAATGTACAAAGAATTCAAATTAAAATCAATTTTGAGATTATAAAACCGTGTACAGTGAGTAAT
1 AAAATGTACAAAGAATTCAAATTAAAATCAATTTTGAGATTATAAAACCATGTAAAGAGAGTAAT
* ** * *
2806 AAGGCTTTTAAAAGAATGGGAGACTGTAAATGGACTTTTCTTGCAAATGAATGCTTTTTTCTTCA
66 AAGGCTTTTAAAAGAATGAGAGACCATAAATGGACTTTTCTTGCAAATGAATACCTTTTTCTTCA
********** * *
2871 CGTTTCTCAAGGTAGACATTCAATTATAGTNNNNNNNNNNAAAAAATGTAACAATATTCAACTTA
131 CGTTTCTCAAGGTAGACATTCAATTATAGTACTGTTTAATAAAAAATGTAAAAAGATTCAACTTA
* ** * * ** *
2936 AAATCAATTATGGGATTATAAAACCACTTAAAGCGAGCAATATGGCTTTCGAAAGAATGGGAGAC
196 AAACCAATTATAAGATTATAAAACCACTTAAAGAGAGCAATAAGGCTTTCGAAAGAATGAAAAAC
*
3001 TGTAAATGGACTTTTCTCGCCAATGAATGCTTTTTTCTTGATGTTTCTCAAGGTAGACATTCAAT
261 TATAAATGGACTTTTCTCGCCAATGAATGCTTTTTTCTTGATGTTTCTCAAGGTAGACATTCAAT
3066 TANNNNNNNNNNTAACCA
326 TA----------TAACCA
* * * *
3084 AAAATGTACAAATAATTCAAATTAAAATCAATTTTGAGATTATGAAACCATTTAAAGAGAGTATT
1 AAAATGTACAAAGAATTCAAATTAAAATCAATTTTGAGATTATAAAACCATGTAAAGAGAGTAAT
* * * *
3149 AAGGCTTTTAAAGGAATGAGAGACCATAAATTGACTTTTCTTGCCAATGAATACCTTTTTCTTTA
66 AAGGCTTTTAAAAGAATGAGAGACCATAAATGGACTTTTCTTGCAAATGAATACCTTTTTCTTCA
* * * *
3214 TGTTTC-CTAAGGTAGGCATTCAGTTATAGT-CTGTTTAATCAAAAATGTAAAAAAGATTCAACT
131 CGTTTCTC-AAGGTAGACATTCAATTATAGTACTGTTTAATAAAAAATGT-AAAAAGATTCAACT
* *
3277 TAAAACCAATTATAAGATTATAAAACCATTTAAAGAGAGTAATAAGGCTCTT-GAAAGAATGAAA
194 TAAAACCAATTATAAGATTATAAAACCACTTAAAGAGAGCAATAAGGCT-TTCGAAAGAATGAAA
** * *
3341 AACTATAAATGGTGTTTTTTTGCCAATGAATGCTTTTTTCTT
258 AACTATAAATGGACTTTTCTCGCCAATGAATGCTTTTTTCTT
3383 CANNNNNNNN
Statistics
Matches: 250, Mismatches: 46, Indels: 6
0.83 0.15 0.02
Matches are distributed among these distances:
342 9 0.04
343 239 0.96
344 2 0.01
ACGTcount: A:0.37, C:0.12, G:0.15, T:0.33
Consensus pattern (333 bp):
AAAATGTACAAAGAATTCAAATTAAAATCAATTTTGAGATTATAAAACCATGTAAAGAGAGTAAT
AAGGCTTTTAAAAGAATGAGAGACCATAAATGGACTTTTCTTGCAAATGAATACCTTTTTCTTCA
CGTTTCTCAAGGTAGACATTCAATTATAGTACTGTTTAATAAAAAATGTAAAAAGATTCAACTTA
AAACCAATTATAAGATTATAAAACCACTTAAAGAGAGCAATAAGGCTTTCGAAAGAATGAAAAAC
TATAAATGGACTTTTCTCGCCAATGAATGCTTTTTTCTTGATGTTTCTCAAGGTAGACATTCAAT
TATAACCA
Done.