Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018399781.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_3022.0, 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: 1959
ACGTcount: A:0.29, C:0.10, G:0.12, T:0.30
Warning! 381 characters in sequence are not A, C, G, or T
Found at i:1229 original size:171 final size:170
Alignment explanation
Indices: 854--1245 Score: 373
Period size: 171 Copynumber: 2.3 Consensus size: 170
844 NNNNNNNNNT
* * * **
854 GAGATTATAAAACCATTTAAAGCGAGTAATAAAGCTTTCGAAGGTATGGGTGATTATTCATGGAC
1 GAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGCATGGGTGATTATGAATGGAC
* * * *
919 TTTTCTTAAAAATGGAAATCTTTTCCTTCATGTTTCCCAGAGTAGACATTCAATTATTATTCGTT
66 TTTTCTTAAAAAT-GAAATCTTTTCCTTCAAGTTTCCCAGAGCAAACATTCAATTAATATTCGTT
* * * *
984 TTAGCAAAAAATATATAAAAATTCAAGTTAAAGTGAATTAC
130 TTAACAAAAAATATAAAAAAATTCAAGTTAAAATCAATTAC
* * * *
1025 GAGATTCTAAAAACA-TTATAG-GCACGAAATAAGGCTTTTGAAGGCATGGGTGATTATGAATGG
1 GAGATTATAAAACCATTTAAAGCG-A-GTAATAAGGCTTTTGAAGGCATGGGTGATTATGAATGG
* ** * * *
1088 ATTTTTCTTGCAAAT-AAATGGCTTTTTCTTTAAGTTTCCCTA-AGCAAACATTCAGTTAATATT
64 ACTTTTCTTAAAAATGAAAT--CTTTTCCTTCAAGTTTCCC-AGAGCAAACATTCAATTAATATT
** *** * **
1151 TTTTTTAATTGAAAATGTAAAAAAATT-TTGTTTAAAATCAATTAC
126 CGTTTTAACAAAAAATATAAAAAAATTCAAG-TTAAAATCAATTAC
* *
1196 GAGAATATAAAACCATTTAAAGCGAGTAATAAGG-TTTTCAAAGGCATGGG
1 GAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTT-GAAGGCATGGG
1246 NNNNNNNNNN
Statistics
Matches: 175, Mismatches: 37, Indels: 18
0.76 0.16 0.08
Matches are distributed among these distances:
169 5 0.03
170 11 0.06
171 151 0.86
172 7 0.04
173 1 0.01
ACGTcount: A:0.38, C:0.11, G:0.16, T:0.35
Consensus pattern (170 bp):
GAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGCATGGGTGATTATGAATGGAC
TTTTCTTAAAAATGAAATCTTTTCCTTCAAGTTTCCCAGAGCAAACATTCAATTAATATTCGTTT
TAACAAAAAATATAAAAAAATTCAAGTTAAAATCAATTAC
Found at i:1630 original size:170 final size:161
Alignment explanation
Indices: 1453--1764 Score: 321
Period size: 171 Copynumber: 1.9 Consensus size: 161
1443 NNNNNNNNNN
* *
1453 TTTTCTTCACGTTTCTCGAGGTAGACATTCAATTA-TATTCTGTT-TGAATAAAAAATGTAAAAA
1 TTTTCTTCACGTTTATCGAGGTAGACATTCAATTATTA-TCTGTTCT-AACAAAAAATGTAAAAA
* *
1516 -ATTTAACTTAAAA-CTAATTATGAGATAATAAAA-TTATTTAAAGA-GAGTAATAAGGCTTTCG
64 CATTCAACTTAAAATC-AATTATGAGACAATAAAACTT-TTTAAA-ATGAGTAATAAGGCTTTCG
* * *
1577 AATGCATGGGTGACTATNNNNNNNNNNTTCCTAGCAATGAATGGCT
126 AAGGCATGAGTAACTAT----------TTCCTAGCAATGAATGGCT
* * * *
1623 TTTTCTTCATGTTTATTGAGGTAGACATTCAATTATTATCTGTTCTACCCAAAAATGTAAAAACA
1 TTTTCTTCACGTTTATCGAGGTAGACATTCAATTATTATCTGTTCTAACAAAAAATGTAAAAACA
* * *
1688 TTCAACTTAAAATCATTTATGAGACCATAAAACTTTTTAAAATGAGTAATAAGGCTTTTGAAGGC
66 TTCAACTTAAAATCAATTATGAGACAATAAAACTTTTTAAAATGAGTAATAAGGCTTTCGAAGGC
1753 ATGAGTAACTAT
131 ATGAGTAACTAT
1765 AAGTAGACTT
Statistics
Matches: 122, Mismatches: 14, Indels: 11
0.83 0.10 0.07
Matches are distributed among these distances:
170 53 0.43
171 66 0.54
172 3 0.02
ACGTcount: A:0.36, C:0.12, G:0.14, T:0.35
Consensus pattern (161 bp):
TTTTCTTCACGTTTATCGAGGTAGACATTCAATTATTATCTGTTCTAACAAAAAATGTAAAAACA
TTCAACTTAAAATCAATTATGAGACAATAAAACTTTTTAAAATGAGTAATAAGGCTTTCGAAGGC
ATGAGTAACTATTTCCTAGCAATGAATGGCT
Done.