Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018402021.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_5116.0, 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: 1938
ACGTcount: A:0.28, C:0.10, G:0.10, T:0.26
Warning! 494 characters in sequence are not A, C, G, or T
Found at i:1190 original size:171 final size:170
Alignment explanation
Indices: 723--1275 Score: 434
Period size: 171 Copynumber: 3.2 Consensus size: 170
713 NNAAAAAGGT
** * ** * * *
723 TAAAA-AATTCAACCAAAAATCAATTATGAGATTATAAAATTATTTAGAGTGAGTAATAAAGCTT
1 TAAAAGAATTCAACTTAAAATCAATTTTGAGATTATAAAAACATTTAAAATGAGTAATAAGGCTT
* ********** * * * **
787 TTGAAGAAATGGGTGACTANNNNNNNNNNTTTCTTTCGAATGAA-ACACTTTTTCTTCACATTTC
66 TTGAAGGAATGGGTGACTAAAAATGGACTTTTCTTACCAATAAATAC-CTTTTTCTTCATGTTTC
* * *
851 TCAAGGTAGACATTTAATTATATTCTG-TTTACACCAAAAATG
130 TCAAGCTAGACATTCAATTATAATCTGTTTTA-A-CAAAAATG
* * * * * ******
893 CACAAAGAGTTCAAATTTAAATCAATTTTGAGATTATAAAACCATTTAAAATGAGTAATNNNNNN
1 TA-AAAGAATTCAACTTAAAATCAATTTTGAGATTATAAAAACATTTAAAATGAGTAATAAGGCT
**** * * *
958 NNNNAAGGAATGGGTGACTATAAATGGGCTTTTCTTACCAATAAATACCTTTTTTTTCATGTTTC
65 TTTGAAGGAATGGGTGACTAAAAATGGACTTTTCTTACCAATAAATACCTTTTTCTTCATGTTTC
*
1023 TCAAGCTAAACATTCAATTATAATCTGTTTTAACAAAAAATG
130 TCAAGCTAGACATTCAATTATAATCTGTTTTAAC-AAAAATG
* * *
1065 TAAAAGAATTCAACTTAAAATCAATTTTGAGATTATAAAAACTTTTACAGTGAGTAATAAGGCTT
1 TAAAAGAATTCAACTTAAAATCAATTTTGAGATTATAAAAACATTTAAAATGAGTAATAAGGCTT
* * * *
1130 TTGAAGGATTGGGTGACTAAAAATGGACTTTTGTTGCCAATGAATATCC-TTTTCTTCATGTTTC
66 TTGAAGGAATGGGTGACTAAAAATGGACTTTTCTTACCAATAAATA-CCTTTTTCTTCATGTTT-
* ** *
1194 CTCAGGC-AGATGTTCAATTATAATCTGTTTTAAGCAAAAAGG
129 CTCAAGCTAGACATTCAATTATAATCTGTTTTAA-CAAAAATG
* * * *
1236 TCAAAA-AATTCTACCTAAAATTAATTATGAGATTATAAAA
1 T-AAAAGAATTCAACTTAAAATCAATTTTGAGATTATAAAA
1276 CCNNNNNNNN
Statistics
Matches: 298, Mismatches: 76, Indels: 17
0.76 0.19 0.04
Matches are distributed among these distances:
170 1 0.00
171 163 0.55
172 128 0.43
173 6 0.02
ACGTcount: A:0.38, C:0.12, G:0.13, T:0.34
Consensus pattern (170 bp):
TAAAAGAATTCAACTTAAAATCAATTTTGAGATTATAAAAACATTTAAAATGAGTAATAAGGCTT
TTGAAGGAATGGGTGACTAAAAATGGACTTTTCTTACCAATAAATACCTTTTTCTTCATGTTTCT
CAAGCTAGACATTCAATTATAATCTGTTTTAACAAAAATG
Found at i:1873 original size:171 final size:162
Alignment explanation
Indices: 1620--1930 Score: 315
Period size: 171 Copynumber: 1.9 Consensus size: 162
1610 TATAAAAACT
* * * * *
1620 TTTACAGCGAGTAATAAGGCTTTTAAAGGATTGGGTGACTATAAATGGACTTTTGTTGCCAATGA
1 TTTAAAGCAAGTAATAAGCCTTTTAAAGGAATGGGTGACTATAAATAGACTTTTGTTGCCAATGA
* * * *
1685 ATATCCTTTTCTTCATGTTTC-CTAAGACAGATGTTCAATTATAATCTGTTCTAAGCAAAAAGGT
66 ATAACCTTTTCTTCATGTTTCTC-AAGACAGATGTTCAATCATAATCTATTCTAACCAAAAAGGT
1749 -CAAAAAATTCTACCTAAAATTAATTATGANNNNNNNNNNCCA
130 ACAAAAAATTCTACCTAAAATTAATTATGA----------CCA
* *
1791 TTTAAAGCAAGTAATAAGCCTTTTGAAGGAATGGGTGA-TAATAAATAGACTTTTTTTGCCAATG
1 TTTAAAGCAAGTAATAAGCCTTTTAAAGGAATGGGTGACT-ATAAATAGACTTTTGTTGCCAATG
* * ** * *
1855 AA-AGACTTTTTGTTCATGTTTCTCAAGGTAGATGTTCAATCATAATCTATTTTAACCAAAAATG
65 AATA-ACCTTTTCTTCATGTTTCTCAAGACAGATGTTCAATCATAATCTATTCTAACCAAAAAGG
*
1919 TACAAAGAATTC
129 TACAAAAAATTC
1931 AAATTTAA
Statistics
Matches: 118, Mismatches: 18, Indels: 7
0.83 0.13 0.05
Matches are distributed among these distances:
170 2 0.02
171 106 0.90
172 10 0.08
ACGTcount: A:0.34, C:0.13, G:0.15, T:0.34
Consensus pattern (162 bp):
TTTAAAGCAAGTAATAAGCCTTTTAAAGGAATGGGTGACTATAAATAGACTTTTGTTGCCAATGA
ATAACCTTTTCTTCATGTTTCTCAAGACAGATGTTCAATCATAATCTATTCTAACCAAAAAGGTA
CAAAAAATTCTACCTAAAATTAATTATGACCA
Done.