Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018400986.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_4148.0, 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: 2580
ACGTcount: A:0.31, C:0.12, G:0.12, T:0.31
Warning! 354 characters in sequence are not A, C, G, or T
Found at i:1418 original size:171 final size:170
Alignment explanation
Indices: 1126--2580 Score: 1212
Period size: 171 Copynumber: 8.6 Consensus size: 170
1116 NNNNNNNNNN
* * * *
1126 AGTTATGAGATTATAAAACCATTTAAAGCAAGTAATAAGCCTTTTGAAGGAAT-GAATGACTGTA
1 AGTTATGAGATTATAAAACTATTTAAAGCGAGTAATAAGCCTTTTGAAGGAATAG-GTGACTATA
* * * *
1190 AATGGAGTTTTCTT-CTCAATGAATGCCTTTTTCTTCACGTTTCTCAAGGTGCACATTCAATTAT
65 AATGGACTTTTCTTGC-CAATGAATG-CTTTTTCTTCACGTTTCCCTAGGTACACATTCAATTAT
* *
1254 AGTCTATTTTAACCAAAAATATGAAAACATTCAACTTAAAATA
128 AGTCTGTTTTAACCAAAAATGTGAAAACATTCAACTTAAAATA
* * * *
1297 AGTTATGAGATTATAAAACTAATTAAAGTGAGTAATAA-CCATTTTGAAGGAATCGGTGACTGTA
1 AGTTATGAGATTATAAAACTATTTAAAGCGAGTAATAAGCC-TTTTGAAGGAATAGGTGACTATA
* *
1361 AATGAACTTTTCTTGCCAATGAATGCTTGTTTCTTCACGTTTCCCTAGGTACACATTCAATTATT
65 AATGGACTTTTCTTGCCAATGAATGCTT-TTTCTTCACGTTTCCCTAGGTACACATTCAATTATA
* * * *
1426 GTTTGTTGTAACCAAAAATG-CAAAACAATTCAACTTAAAATC
129 GTCTGTTTTAACCAAAAATGTGAAAAC-ATTCAACTTAAAATA
* * * * *
1468 AGTTATGAGATTATAAAACCATTTAAAGCAAGTAATAAACTTTTTGAATGAATAGGTGACTATAA
1 AGTTATGAGATTATAAAACTATTTAAAGCGAGTAATAAGCCTTTTGAAGGAATAGGTGACTATAA
* * * * *
1533 ATGGACTTTTCTTACCAATGAATGGGTTTTTCTTCACATTT-CCTAAG-ACACATTCAATTGTAG
66 ATGGACTTTTCTTGCCAATGAAT-GCTTTTTCTTCACGTTTCCCTAGGTACACATTCAATTATAG
* ** *
1596 TTTGTTTTAATGAAAAATGT-AAAATAATTCAACTTAAAATCA
130 TCTGTTTTAACCAAAAATGTGAAAA-CATTCAACTTAAAAT-A
* * ** * * * *
1638 A-TTAGGAGATTATAAAACCATTT-CGGACGATTAAGAAGGCTTTTGAAGGAATGGGTGACTATA
1 AGTTATGAGATTATAAAACTATTTAAAG-CGAGTAATAAGCCTTTTGAAGGAATAGGTGACTATA
* * ** * * * *
1701 AATAGACGTTTCTTATCAATGAATGCTATCTTCTTCACATTT--CTGATGGTAGACATTTAATTA
65 AATGGACTTTTCTTGCCAATGAATGCT-TTTTCTTCACGTTTCCCT-A-GGTACACATTCAATTA
* * *
1764 TAGACTGTTTTAACCAAAAATG-GAAAA-A---AA-TTAAAGTC
127 TAGTCTGTTTTAACCAAAAATGTGAAAACATTCAACTTAAAATA
* * * *
1802 TGTTATGAGATTATAAAACCATTTAAAGCAAGTAATAAGCCTTCTT-AAGGAATGGGTGACTATA
1 AGTTATGAGATTATAAAACTATTTAAAGCGAGTAATAAGCCTT-TTGAAGGAATAGGTGACTATA
* ** * * * *
1866 AATGGACTTTTGTTTTCAATGAATGCCCTTTGT-TTCATGTTT-CTTGAGGTAGACATTCAATTA
65 AATGGACTTTTCTTGCCAATGAATG--CTTTTTCTTCACGTTTCCCT-AGGTACACATTCAATTA
* * * * *
1929 TTGTCTGTTTTAA-CAAGAAATTTAAAAAAATTCAACTTAAAATCT
127 TAGTCTGTTTTAACCAA-AAATGTGAAAACATTCAACTTAAAAT-A
* * *
1974 A-TTATGAGATTATAAAACTATTTAATGCGAGTAATAAGCCTTTTGAAGGAATCA-GTGGCTATG
1 AGTTATGAGATTATAAAACTATTTAAAGCGAGTAATAAGCCTTTTGAAGGAAT-AGGTGACTATA
* * * * * * * * **
2037 AATGGA-TTGTTCTTGCAAATAAATCCCCTTTTCTTTATGTTTCTCAAGGTAGGCATTCAATTAT
65 AATGGACTT-TTCTTGCCAATGAAT-GCTTTTTCTTCACGTTTCCCTAGGTACACATTCAATTAT
** *
2101 AGTCTGTTTTAATAAAAAATGTAGAAAA-ATTCAACTTAAAATT
128 AGTCTGTTTTAACCAAAAATGT-GAAAACATTCAACTTAAAATA
** ** * * * *
2144 AGAAATGAGATTATAAAA-TCAGATAAAGCGAGGAATAAGCCTTTTTAAGGAATGGGTGATTATA
1 AGTTATGAGATTATAAAACT-ATTTAAAGCGAGTAATAAGCCTTTTGAAGGAATAGGTGACTATA
* * ** * *
2208 AATGGACTGTTTTTTGCCAATGAATGCTTGGTTACTT-TTGTTTCTCTAGGTACACGTTCAATTA
65 AATGGACT-TTTCTTGCCAATGAATGCTT--TTTCTTCACGTTTCCCTAGGTACACATTCAATTA
* * * * * *
2272 TTGTTTGTTGTAACCAAAAGTGT-AAACCAATTCAACTTAAAATC
127 TAGTCTGTTTTAACCAAAAATGTGAAAAC-ATTCAACTTAAAATA
* * * *
2316 AGTTATGGGATTATAAAACTATTTAAAGCAAGTCATAAACCTTTTGAAGGAATAGGTGAGC-ATA
1 AGTTATGAGATTATAAAACTATTTAAAGCGAGTAATAAGCCTTTTGAAGGAATAGGTGA-CTATA
* * * ** * *
2380 AATGGACTTTTTTTCCCTATGAATGCTTTTTTCTTCACGTTTCCC-A-ACACACATTCACTTGTA
65 AATGGACTTTTCTTGCCAATGAATGC-TTTTTCTTCACGTTTCCCTAGGTACACATTCAATTATA
* * * ** *
2443 GTTTCTTTGAATGACAAATGT-AAAACAATTCAACTTAAAATCA
129 GTCTGTTTTAACCAAAAATGTGAAAAC-ATTCAACTTAAAAT-A
* * * * * * *
2486 A-TTAGGAGATTATAAAACGATTTCAAGTGAGTAATAAGGCATTTGATGGAATAGGTGACTATAA
1 AGTTATGAGATTATAAAACTATTTAAAGCGAGTAATAAGCCTTTTGAAGGAATAGGTGACTATAA
*
2550 ATGGACTTTTCTTGTCAATGAATGCCTTTTT
66 ATGGACTTTTCTTGCCAATGAATG-CTTTTT
Statistics
Matches: 1041, Mismatches: 189, Indels: 110
0.78 0.14 0.08
Matches are distributed among these distances:
164 3 0.00
165 114 0.11
166 14 0.01
167 3 0.00
168 6 0.01
169 252 0.24
170 41 0.04
171 464 0.45
172 137 0.13
173 7 0.01
ACGTcount: A:0.36, C:0.13, G:0.16, T:0.35
Consensus pattern (170 bp):
AGTTATGAGATTATAAAACTATTTAAAGCGAGTAATAAGCCTTTTGAAGGAATAGGTGACTATAA
ATGGACTTTTCTTGCCAATGAATGCTTTTTCTTCACGTTTCCCTAGGTACACATTCAATTATAGT
CTGTTTTAACCAAAAATGTGAAAACATTCAACTTAAAATA
Done.