Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018400934.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_4096.0, 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, 786
Length: 1310
ACGTcount: A:0.26, C:0.10, G:0.11, T:0.23
Warning! 385 characters in sequence are not A, C, G, or T
Found at i:475 original size:168 final size:170
Alignment explanation
Indices: 245--851 Score: 561
Period size: 171 Copynumber: 3.6 Consensus size: 170
235 NNNNNNNNNN
* * * * *
245 ATCAATTATGAGATTATAAAACCATTTAAAGTGAGTAATAAGGTTTTTGGAGGCATGGGTGACTC
1 ATCAATTATGAGATTATAAAGCCATTTAAAGCGAGTAATAAGGCTTTAGAAGGCATGGGTGACTC
* ********** * *
310 TATATAGGCTTTTCTTGCCAATGAATGGCTCTTGNNNNNNNNNNT-TTGAGGTAGACATTCAATT
66 TAAATAGGCTTTTCTTGCCAATGAATGGCTCTT-TCTTCATGTTTCTTCAGGTAAACATTCAATT
*
374 ATTATC-TATTTAACCAAAAATG-AAAAAATTCAACTTAAG
130 ATTATCTTATTTAACCAAAAATGAAAAAAATTCAACTTAAA
* * * *
413 GTCAATTATGAGATTATAAAGCCATTTAAAGCGACTAATAAAGCTTTCGAAGGCATGGGTGACTA
1 ATCAATTATGAGATTATAAAGCCATTTAAAGCGAGTAATAAGGCTTTAGAAGGCATGGGTGACT-
*
478 C-AAACAGGCCTTTCTCTT--CAATGAATGGCTCTTTCTTCATGTTTCTTCAGGTAAACATTCAA
65 CTAAATAGG-CTTT-TCTTGCCAATGAATGGCTCTTTCTTCATGTTTCTTCAGGTAAACATTCAA
*
540 TTATTATCTTTTTTAACCAAAAATGCAAAAAAATTCAACTTAAA
128 TTATTATCTTATTTAACCAAAAATG-AAAAAAATTCAACTTAAA
* * * * *
584 ATCAATTATGAGGTTATACAGCCATTTAAAACGAGTAATAAGGCTTTAGAAGGCGTGGGTGACTG
1 ATCAATTATGAGATTATAAAGCCATTTAAAGCGAGTAATAAGGCTTTAGAAGGCATGGGTGACTC
* * * * * ********
649 TAAAT-GAACTTTTCCTGCCAATGAATGGCTTTTTCATCACGTTTC-TCANNNNNNNNNNTT-AA
66 TAAATAG-GCTTTTCTTGCCAATGAATGGCTCTTTCTTCATGTTTCTTCA--GGTAAACATTCAA
*
711 TTATAATCTGT-TTTAACCAAAAATGTAAAACAAATTCAGA-TTAAA
128 TTATTATCT-TATTTAACCAAAAATG-AAAA-AAATTCA-ACTTAAA
* * * * * * *
756 ACCAATTATGAGGTTATAAATCCATTTAAAGCGAGTAATAAAGCTTTCGAAGGCTTGGGTGACTA
1 ATCAATTATGAGATTATAAAGCCATTTAAAGCGAGTAATAAGGCTTTAGAAGGCATGGGTGACTC
*
821 TAAATAGGCTTTTCTTGTCAATGAATGGCTC
66 TAAATAGGCTTTTCTTGCCAATGAATGGCTC
852 NNNNNNNNNN
Statistics
Matches: 361, Mismatches: 61, Indels: 30
0.80 0.13 0.07
Matches are distributed among these distances:
167 1 0.00
168 99 0.27
169 23 0.06
170 12 0.03
171 127 0.35
172 97 0.27
173 2 0.01
ACGTcount: A:0.34, C:0.14, G:0.16, T:0.32
Consensus pattern (170 bp):
ATCAATTATGAGATTATAAAGCCATTTAAAGCGAGTAATAAGGCTTTAGAAGGCATGGGTGACTC
TAAATAGGCTTTTCTTGCCAATGAATGGCTCTTTCTTCATGTTTCTTCAGGTAAACATTCAATTA
TTATCTTATTTAACCAAAAATGAAAAAAATTCAACTTAAA
Found at i:793 original size:172 final size:161
Alignment explanation
Indices: 533--850 Score: 370
Period size: 172 Copynumber: 1.9 Consensus size: 161
523 TTCAGGTAAA
* * *
533 CATTCAATTATTATCTTTTTTAACCAAAAATGCAAAAAAATTCAACTTAAAATCAATTATGAGGT
1 CATT-AATTATAATCTGTTTTAACCAAAAATGCAAAAAAATTCAACTTAAAACCAATTATGAGGT
* * *
598 TATACAGCCATTTAAAACGAGTAATAAGGCTTTAGAAGGCGTGGGTGACTGTAAAT-GAACTTTT
65 TATAAAGCCATTTAAAACGAGTAATAAAGCTTTAGAAGGCGTGGGTGACTATAAATAG-ACTTTT
662 CCTGCCAATGAATGGCTTTTTCATCACGTTTCT
129 CCTGCCAATGAATGGCTTTTTCATCACGTTTCT
*
695 CANNNNNNNNNNTTAATTATAATCTGTTTTAACCAAAAATGTAAAACAAATTCAGA-TTAAAACC
1 CA----------TTAATTATAATCTGTTTTAACCAAAAATGCAAAA-AAATTCA-ACTTAAAACC
* * * *
759 AATTATGAGGTTATAAATCCATTTAAAGCGAGTAATAAAGCTTTCGAAGGCTTGGGTGACTATAA
54 AATTATGAGGTTATAAAGCCATTTAAAACGAGTAATAAAGCTTTAGAAGGCGTGGGTGACTATAA
* * *
824 ATAGGCTTTTCTTGTCAATGAATGGCT
119 ATAGACTTTTCCTGCCAATGAATGGCT
851 CNNNNNNNNN
Statistics
Matches: 129, Mismatches: 14, Indels: 16
0.81 0.09 0.10
Matches are distributed among these distances:
162 2 0.02
171 29 0.22
172 96 0.74
173 2 0.02
ACGTcount: A:0.36, C:0.14, G:0.15, T:0.32
Consensus pattern (161 bp):
CATTAATTATAATCTGTTTTAACCAAAAATGCAAAAAAATTCAACTTAAAACCAATTATGAGGTT
ATAAAGCCATTTAAAACGAGTAATAAAGCTTTAGAAGGCGTGGGTGACTATAAATAGACTTTTCC
TGCCAATGAATGGCTTTTTCATCACGTTTCT
Done.