Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018401708.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_4822.0, 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: 2210
ACGTcount: A:0.32, C:0.11, G:0.12, T:0.31
Warning! 295 characters in sequence are not A, C, G, or T
Found at i:288 original size:172 final size:170
Alignment explanation
Indices: 2--734 Score: 497
Period size: 172 Copynumber: 4.3 Consensus size: 170
1 G
* * * * *
2 AGTGACTATAAATGGACTTTTCTTGCCAATGAATGCTTTTTTCTTTATGTTTCACAATATAGATA
1 AGTGACTATAAATGAACTTTTCTTACCAATGAATGCTTTTTTCTTCATGTTTCACAAGATAGACA
* * * *
67 TTCAATTATAGTTTATTTCAGCAAAAAATGTAAAACAATTCAACTTAAAATTAATTA-TGGCATT
66 TTCAATTATAGTCTATTTCAACAAAAAATGTAAAACAATTCAACTTAAAATCAATTATTAG-ATT
* * *
131 ATAAAACCATTTGAAGCATGTAATAAGGCTTTTTGAAGG-TATA
130 ATAAAACCATTTAAAGCAAGTAATAAGG--TTTCGAAGGCT-TA
* * * *
174 AGTGACTATAAATGAACTTTTCTTATCAATGAACT-CTTTTTTCTTCATGTTTCTCAAGGTTGAC
1 AGTGACTATAAATGAACTTTTCTTACCAATGAA-TGCTTTTTTCTTCATGTTTCACAAGATAGAC
* * * ** *
238 ATTCAATTCTAGTCTGTTTTAACCGAAAATGTAAAA-ACATTCAACTTAAAATCAATTATTAGTT
65 ATTCAATTATAGTCTATTTCAACAAAAAATGTAAAACA-ATTCAACTTAAAATCAATTATTAGAT
*
302 TATAAAACCATTTAAAGCAAGTAATAAGGTTTCGAAGGCTTG
129 TATAAAACCATTTAAAGCAAGTAATAAGGTTTCGAAGGCTTA
* * * ** * * *
344 AGTGACTATAAATGGACCTTTT-GTGCCAATGGTTGGC-TTTTGCTTCACG-TTCCCTATA-ATA
1 AGTGACTATAAAT-GAACTTTTCTTACCAATGAAT-GCTTTTTTCTTCATGTTTCAC-A-AGATA
* * * * * * * *
405 GGA-ACTCAATTATTGCCTTTTTTAACCAAAAATGTAAAAAAAAATTTAACTTAAAATCAATT-T
62 -GACATTCAATTATAGTCTATTTCAACAAAAAATGT--AAAACAATTCAACTTAAAATCAATTAT
* **** * *
468 TGAGATTATAAAGCCATTTAATTTGAGTAATAAGGCTTTTGAAGGCTTG
124 T-AGATTATAAAACCATTTAAAGCAAGTAATAAGG-TTTCGAAGGCTTA
** * * * * * * *
517 AGCCACTATAAAT-AGACTTTTCTTACTAATGAGTACCTTTTTCTTGATGTTTGC-CAAGGTAAA
1 AGTGACTATAAATGA-ACTTTTCTTACCAATGAATGCTTTTTTCTTCATGTTT-CACAAGATAGA
* * * ** *
580 CAATCAATTATAATCTA-TTCTAACCAAAAACCTCAAAA-AATTCAA-TCTAAAATCAATTATGA
64 CATTCAATTATAGTCTATTTC-AACAAAAAATGT-AAAACAATTCAACT-TAAAATCAATTATTA
* ** * * ** *
642 GATTATAAAAACATTTAAAGTGAGTAATAAGGCTTTTGAAAGAATG
126 GATTATAAAACCATTTAAAGCAAGTAATAAGG-TTTCGAAGGCTTA
* * * * * *
688 GGTGACTATAAATGGACTTCTCTTGCCAATGAATTCCTTTTTCTTCA
1 AGTGACTATAAATGAACTTTTCTTACCAATGAATGCTTTTTTCTTCA
735 CTTTTGCCAT
Statistics
Matches: 445, Mismatches: 90, Indels: 53
0.76 0.15 0.09
Matches are distributed among these distances:
169 5 0.01
170 67 0.15
171 109 0.24
172 193 0.43
173 67 0.15
174 3 0.01
175 1 0.00
ACGTcount: A:0.36, C:0.14, G:0.13, T:0.37
Consensus pattern (170 bp):
AGTGACTATAAATGAACTTTTCTTACCAATGAATGCTTTTTTCTTCATGTTTCACAAGATAGACA
TTCAATTATAGTCTATTTCAACAAAAAATGTAAAACAATTCAACTTAAAATCAATTATTAGATTA
TAAAACCATTTAAAGCAAGTAATAAGGTTTCGAAGGCTTA
Found at i:743 original size:171 final size:171
Alignment explanation
Indices: 98--766 Score: 403
Period size: 171 Copynumber: 3.9 Consensus size: 171
88 CAAAAAATGT
* * * *
98 AAAACAATTCAACTTAAAATTAATTATG-GCATTATAAAACCATTTGAAG-CATGTAATAAGGCT
1 AAAA-AATTCAACTTAAAATCAATTATGAG-ATTATAAAAACATTTAAAGTGA-GTAATAAGGC-
* * * ** * * *
161 TTTTGAAGGTATAAGTGACTATAAAT-GAACTTTTCTTATCAATGAACT-CTTTTTTCTTCATGT
62 TTTTGAAAGAATGAGCCACTATAAATAG-ACTTCTCTTACCAATGAA-TACCTTTTTCTTCATGT
** * * * * * * **
224 TT-CTCAAGGTTGACATTCAATTCTAGTCTGTTTTAACCGAAAATGT-
125 TTGC-CAAGGTAAACAATCAATTATAATCTATTCTAACCAAAAACCTC
* * * **
270 AAAAACATTCAACTTAAAATCAATTATTAGTTTATAAAACCATTTAAAGCAAGTAATAAGG-TTT
1 AAAAA-ATTCAACTTAAAATCAATTATGAGATTATAAAAACATTTAAAGTGAGTAATAAGGCTTT
* * ** ** * * ** ** * * *
334 CGAAGGCTTGAGTGACTATAAATGGACCTT-T-TGTGCCAATGGTTGGCTTTTGCTTCACG-TTC
65 TGAAAGAATGAGCCACTATAAATAGA-CTTCTCT-TACCAATGAATACCTTTTTCTTCATGTTTG
* * *** * * ** *
396 CCTA--TAATAGGAACTCAATTATTGCCTTTTTTAACCAAAAATGTAAA
128 CCAAGGTAA-A-CAA-TCAATTATAATCTATTCTAACCAAAAACCT--C
* * ** **
443 AAAAAATTTAACTTAAAATCAATTTTGAGATTATAAAGCCATTTAATTTGAGTAATAAGGCTTTT
1 AAAAAATTCAACTTAAAATCAATTATGAGATTATAAAAACATTTAAAGTGAGTAATAAGGCTTTT
* ** * * * *
508 GAAGGCTTGAGCCACTATAAATAGACTTTTCTTACTAATGAGTACCTTTTTCTTGATGTTTGCCA
66 GAAAGAATGAGCCACTATAAATAGACTTCTCTTACCAATGAATACCTTTTTCTTCATGTTTGCCA
573 AGGTAAACAATCAATTATAATCTATTCTAACCAAAAACCTC
131 AGGTAAACAATCAATTATAATCTATTCTAACCAAAAACCTC
614 AAAAAATTCAA-TCTAAAATCAATTATGAGATTATAAAAACATTTAAAGTGAGTAATAAGGCTTT
1 AAAAAATTCAACT-TAAAATCAATTATGAGATTATAAAAACATTTAAAGTGAGTAATAAGGCTTT
* ** * * *
678 TGAAAGAATGGGTGACTATAAATGGACTTCTCTTGCCAATGAATTCCTTTTTCTTCACT-TTTGC
65 TGAAAGAATGAGCCACTATAAATAGACTTCTCTTACCAATGAATACCTTTTTCTTCA-TGTTTGC
* ** * *
742 CATGGTGGACATTCTATTATAATCT
129 CAAGGTAAACAATCAATTATAATCT
767 GTTTTAATGA
Statistics
Matches: 391, Mismatches: 84, Indels: 45
0.75 0.16 0.09
Matches are distributed among these distances:
167 1 0.00
168 1 0.00
169 7 0.02
170 67 0.17
171 130 0.33
172 100 0.26
173 73 0.19
174 8 0.02
175 1 0.00
176 3 0.01
ACGTcount: A:0.36, C:0.15, G:0.13, T:0.36
Consensus pattern (171 bp):
AAAAAATTCAACTTAAAATCAATTATGAGATTATAAAAACATTTAAAGTGAGTAATAAGGCTTTT
GAAAGAATGAGCCACTATAAATAGACTTCTCTTACCAATGAATACCTTTTTCTTCATGTTTGCCA
AGGTAAACAATCAATTATAATCTATTCTAACCAAAAACCTC
Done.