Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018400931.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_4093.0, 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: 3255
ACGTcount: A:0.33, C:0.11, G:0.12, T:0.31
Warning! 388 characters in sequence are not A, C, G, or T
Found at i:1556 original size:38 final size:38
Alignment explanation
Indices: 1509--1588 Score: 124
Period size: 38 Copynumber: 2.1 Consensus size: 38
1499 TTCTCTAGGT
1509 AAAAATTCAATTATAGTCTGTTTAAACAAAAAATGTAA
1 AAAAATTCAATTATAGTCTGTTTAAACAAAAAATGTAA
* * **
1547 AAAAATTCAATTATAGTGTGTTTGAATGAAAAATGTAA
1 AAAAATTCAATTATAGTCTGTTTAAACAAAAAATGTAA
1585 AAAA
1 AAAA
1589 TTTAAGTGAA
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
38 38 1.00
ACGTcount: A:0.53, C:0.05, G:0.11, T:0.31
Consensus pattern (38 bp):
AAAAATTCAATTATAGTCTGTTTAAACAAAAAATGTAA
Found at i:2143 original size:171 final size:168
Alignment explanation
Indices: 1767--3248 Score: 631
Period size: 171 Copynumber: 8.7 Consensus size: 168
1757 TTAAAATCAA
* * * * *
1767 TTTTGAAGGAATGAGTGATTATAAATAGACTTTTCTTGCTAAT-AAGTGCCTTTTCCTTCAAGTT
1 TTTTGAA-GAATGAGAGACTATAAATAGACTTTTCTTGCCAATGAA-TGCCTTTTTCTTCACG-T
* * *
1831 TTTCAAGGTAGACATTCAATTATAGTCTGTTTTAACAAAAAAATATAAACAAATTCAA-CTTAAT
63 TTTCAAGGTAGACATTCAATTATAATCTGTTTTAAC-AAAAAATGTAAA-AAATTTAATCTTAA-
* * * * * *
1895 ATCACTTTTGAAATTATAATACCATTTAAAGCGAGTAATAAGGG
125 ATCAATTATGAGATTATAAAACCATTTAAAGCAAGTAATAAGGC
* * * * *
1939 TTTTCAAAGAATGGGTGAGTATAAATGGACTTTTCTTGCCAATGAATGCCTTTTTCTTCACGTTT
1 TTTT-GAAGAATGAGAGACTATAAATAGACTTTTCTTGCCAATGAATGCCTTTTTCTTCACGTTT
* * * * ** *
2004 CCAGAGGTAGACAATCACTTATAATCTGCTTTAACAAAAAATGTAAAAAATTTTGTCTGAAAGTC
65 TCA-AGGTAGACATTCAATTATAATCTGTTTTAACAAAAAATGTAAAAAATTTAATCTTAAA-TC
* *
2069 AATTATGTGATTATAAAACCTTTTAAAGCAAGTAATAAGGC
128 AATTATGAGATTATAAAACCATTTAAAGCAAGTAATAAGGC
* * * * ** * * *
2110 TTTTGAAGCACTGACAGACTATAAATAGACTTTTCTTCCCAATGACTAACATTTTCTACATGTTT
1 TTTTGAAG-AATGAGAGACTATAAATAGACTTTTCTTGCCAATGAATGCCTTTTTCTTCACGTTT
** ** * *
2175 ATCAAGGTAGGTATTCAATTATCGTCTGTTTTAGCAACAAATGTAAAAAATTTAAT-TTAAAATC
65 -TCAAGGTAGACATTCAATTATAATCTGTTTTAACAAAAAATGTAAAAAATTTAATCTT-AAATC
* **********
2239 AATTATGAGGTTATAAAACCATTTANNNNNNNNNNTAAGGC
128 AATTATGAGATTATAAAACCATTTAAAGCAAGTAATAAGGC
* * * * * *
2280 TTTTGAAGGAATAAGGGACTATAAATAGATTTTTGTTGCCAATGAAAGCCTTTTTCTTCACCTTG
1 TTTTGAA-GAATGAGAGACTATAAATAGACTTTTCTTGCCAATGAATGCCTTTTTCTTCACGTT-
* * * *
2345 TTTAGGGTAGACATTCAATTATAATCTGTTTTAACCAAAAGTGTAAAAAAAATTTAA-CTTAAAA
64 TTCAAGGTAGACATTCAATTATAATCTGTTTTAACAAAAAATGT--AAAAAATTTAATCTT-AAA
********** ** *
2409 TCAATTATGAGATNNNNNNNNNNTTTAAAGTGAGTAATAGGGC
126 TCAATTATGAGATTATAAAACCATTTAAAGCAAGTAATAAGGC
* * * **
2452 TTTTGAAGGAATGAGTGTCTATAAATACACTTTTCTTGCCAATGAATGCCTTTTT-TTCATATTT
1 TTTTGAA-GAATGAGAGACTATAAATAGACTTTTCTTGCCAATGAATGCCTTTTTCTTCACGTTT
** * ** * * * * *
2516 CTTGACGTAGATGTTCAATTATAATTTGCTTTAACTAAAAATGTACAACAAATTGAA-CATAAAA
65 -TCAAGGTAGACATTCAATTATAATCTGTTTTAACAAAAAATGTA-AA-AAATTTAATC-TTAAA
** *********
2580 TCAAGTT-TGAGATTATAAAACCATTTAAAGTGAGNNNNNNNNN
126 TCAA-TTATGAGATTATAAAACCATTTAAAGCAAGTAATAAGGC
* * * * * * * ** *
2623 NTTTGAAGGAATGGGTGACTATAAAT-GAACTTTTCATGCTAATGGATGGCTTTTAATTCATGTT
1 TTTTGAA-GAATGAGAGACTATAAATAG-ACTTTTCTTGCCAATGAATGCCTTTTTCTTCACGTT
** *** * ** * * * *
2687 CCCTAAAACAAACATTCAATTATAGCCTTTTTTAAC-CAAAATGTAAAAAACTTCAA-CTCAAAA
64 TTC-AAGGTAGACATTCAATTATAATCTGTTTTAACAAAAAATGTAAAAAA-TTTAATCT-TAAA
* * ** * *
2750 TCAATTTTGAGATTATAAAACTATTTAAAGTGAGCAGTAAGGC
126 TCAATTATGAGATTATAAAACCATTTAAAGCAAGTAATAAGGC
* * * * ********* * *
2793 TTTTAAAAAAATGGGTGACTATAAAT-GNNNNNNNNNNGCCAATGAATGCATTTTTCTTCATGTT
1 TTTT-GAAGAATGAGAGACTATAAATAG-ACTTTTCTTGCCAATGAATGCCTTTTTCTTCACG-T
* * * * * * * * *
2857 TCTTGAA-TTAAACATTTAAATATAATCGGTTTTAACTAAAAATGTAAAACAA-TTCAGCTTAAA
63 T-TTCAAGGTAGACATTCAATTATAATCTGTTTTAACAAAAAATGTAAAA-AATTTAATCTTAAA
* * ** * **
2920 TTTAATTATGAGATTATAAAACCTTTTAAAGTGAGCAATAATAC
126 -TCAATTATGAGATTATAAAACCATTTAAAGCAAGTAATAAGGC
* * * *
2964 TTTTAAAGGAATGACAGACTATAAATGGACTTTTCTT-CCAATGAATGGCTTTTTCTAT-ACGTT
1 TTTTGAA-GAATGAGAGACTATAAATAGACTTTTCTTGCCAATGAATGCCTTTTTCT-TCACGTT
** * * ** * **********
3027 TAGT-AAGACAAGA-ATTCAATAATACTCTGTTTTAATGAAAAATATAAAAAAANNNNNNNNNNA
64 T--TCAAG-GTAGACATTCAATTATAATCTGTTTTAACAAAAAATGT-AAAAAATTTAATCTTAA
* * * * *
3090 ATTAATTATGAGATTATAAAACCATGTAACGCGAGTAATGAGGC
125 ATCAATTATGAGATTATAAAACCATTTAAAGCAAGTAATAAGGC
* * * * * * * * ** * *
3134 ATTTAAAGAAATGGGTGATTATAAATGGGCTTTTCTTGCTAATGAATAACTTTCTCTTCATGTTT
1 TTTTGAAG-AATGAGAGACTATAAATAGACTTTTCTTGCCAATGAATGCCTTTTTCTTCACGTTT
* * * *
3199 CTCAAGGTAGACATTCAATTATAATCTATTTTAACCAACAATATAAAAAA
65 -TCAAGGTAGACATTCAATTATAATCTGTTTTAACAAAAAATGTAAAAAA
3249 ATTCAAC
Statistics
Matches: 972, Mismatches: 293, Indels: 92
0.72 0.22 0.07
Matches are distributed among these distances:
168 1 0.00
169 12 0.01
170 354 0.36
171 404 0.42
172 197 0.20
173 4 0.00
ACGTcount: A:0.37, C:0.12, G:0.13, T:0.34
Consensus pattern (168 bp):
TTTTGAAGAATGAGAGACTATAAATAGACTTTTCTTGCCAATGAATGCCTTTTTCTTCACGTTTT
CAAGGTAGACATTCAATTATAATCTGTTTTAACAAAAAATGTAAAAAATTTAATCTTAAATCAAT
TATGAGATTATAAAACCATTTAAAGCAAGTAATAAGGC
Done.