Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018401956.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_5055.0, 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: 3581
ACGTcount: A:0.20, C:0.07, G:0.08, T:0.21
Warning! 1562 characters in sequence are not A, C, G, or T
Found at i:2606 original size:171 final size:170
Alignment explanation
Indices: 2104--2828 Score: 491
Period size: 172 Copynumber: 4.2 Consensus size: 170
2094 NNNNNNNNNN
* * * * * * *
2104 ATGTATAAAGAATTCAAATTTAAATCAATTTTGATATTATAAAACCATTTAAAGCGAATAATGAG
1 ATGTACAAAGAATTAAAATTAAAATCAATTTTGGTATTATAAAACCATTTAAATCGACTAATAAG
* * * * * *
2169 GCTATTGAAGGTATGGGTGACAATAAATAGACTTTACTTGCTAATGAATAGTTTTTTCTTCATGT
66 GCTTTTGAAGGTATGGGTGACTATAAATGGA-TTTTCTTGCCAATGAATACTTTTTTCTTCATGT
* * * *
2234 TTCTGAAGGTCGACATTCAATTTTAGTTTTTTTTAACTAAAA
130 TTCTGAAGGTAGACATTCAATTATAG-TCTGTTTAACTAAAA
* *
2276 ATGTACAAAGAATTAAAATTGAAATCAATTTTGAG-CTTATAAAACCATTTAAAGT-G-CGTAAT
1 ATGTACAAAGAATTAAAATTAAAATCAATTTTG-GTATTATAAAACCATTTAAA-TCGAC-TAAT
* * * * * *
2338 AAGGCTTTTAAAAG-AGTGGGTGACTATAAATGGGATTTTCTTGCCAAAGAATGCCTTTTTCTTT
63 AAGGCTTTTGAAGGTA-TGGGTGACTATAAAT-GGATTTTCTTGCCAATGAATACTTTTTTCTTC
**********
2402 ATGTTTCTTG-AGGTNNNNNNNNNNTTATAGTCTGTTTAACTAAAA
126 ATGTTTC-TGAAGGTAGACATTCAATTATAGTCTGTTTAACTAAAA
* ** * * * *
2447 ATATA-AAAGAAGTTCGACTTAAAATCAATTATGGTATTACAAAACTATTTAAATCGACTAATAA
1 ATGTACAAAGAA-TTAAAATTAAAATCAATTTTGGTATTATAAAACCATTTAAATCGACTAATAA
*
2511 GGCTTTTGAAGGTATAGGTGACTATAAATGGATTTTTCTTGCCAATGAATACTTTTTTCTTCATG
65 GGCTTTTGAAGGTATGGGTGACTATAAATGGA-TTTTCTTGCCAATGAATACTTTTTTCTTCATG
* * ** *
2576 TCTCTGAAGGTAGACATTCCATCCTAGTCTGTTTGAACCAAAA
129 TTTCTGAAGGTAGACATTCAATTATAGTCTGTTT-AACTAAAA
* *********** * *
2619 ATGTACAAAGAATTCAAATTTAANNNNNNNNNNAG-ATTATAAAACCATTTAAAGT-GAGTACTA
1 ATGTACAAAGAATT-AAAATTAAAATCAATTTTGGTATTATAAAACCATTTAAA-TCGACTAATA
* * * * * * * * * *
2682 AGGCTTTTGAAAGAATGAGTTACTATAATTGGACTTCTT-TTGCCAATAAATGCCTTTTTATTTA
64 AGGCTTTTGAAGGTATGGGTGACTATAAATGGA-TT-TTCTTGCCAATGAATACTTTTTTCTTCA
* * *
2746 CGTTTCTTG-AGGTAGACATTCAATTATAGTTTGTTTAACCAAAA
127 TGTTTC-TGAAGGTAGACATTCAATTATAGTCTGTTTAACTAAAA
* * * * * *
2790 ATATA-AAACAAATTCAACTTAAAATCAATTATGGCATTA
1 ATGTACAAA-GAATTAAAATTAAAATCAATTTTGGTATTA
2829 CANNNNNNNN
Statistics
Matches: 417, Mismatches: 115, Indels: 43
0.73 0.20 0.07
Matches are distributed among these distances:
170 23 0.06
171 146 0.35
172 227 0.54
173 21 0.05
ACGTcount: A:0.36, C:0.11, G:0.14, T:0.36
Consensus pattern (170 bp):
ATGTACAAAGAATTAAAATTAAAATCAATTTTGGTATTATAAAACCATTTAAATCGACTAATAAG
GCTTTTGAAGGTATGGGTGACTATAAATGGATTTTCTTGCCAATGAATACTTTTTTCTTCATGTT
TCTGAAGGTAGACATTCAATTATAGTCTGTTTAACTAAAA
Found at i:2753 original size:343 final size:343
Alignment explanation
Indices: 2114--2830 Score: 810
Period size: 343 Copynumber: 2.1 Consensus size: 343
2104 ATGTATAAAG
* * * * * *
2114 AATTCAAATTTAAATCAATTTTGATATTATAAAACCATTTAAAGCGAATAATGAGGCTATTGAAG
1 AATTCAACTTAAAATCAATTATGGTATTACAAAACCATTTAAAGCGAATAATAAGGCTATTGAAG
* * * *
2179 GTATGGGTGACAATAAATAGACTTTACTTGCTAATGAATAGTTTTTTCTTCATGTTTCTGAAGGT
66 GTATAGGTGACAATAAATAGACTTTACTTGCCAATGAATACTTTTTTCTTCATGTCTCTGAAGGT
* ** * * * *
2244 CGACATTCAATTTTAGTTTTTTTTAACTAAAAATGTACAAAGAATTAAAATTGAAATCAATTTTG
131 AGACATTCAATCCTAGTCTGTTTGAACCAAAAATGTACAAAGAATTAAAATTGAAATCAATTTTG
* * * *
2309 AGCTTATAAAACCATTTAAAGTGCGTAATAAGGCTTTTAAAAGAGTGGGTGACTATAAATGGGAT
196 AGATTATAAAACCATTTAAAGTGAGTAATAAGGCTTTTAAAAGAATGAGTGACTATAAATGGGAT
* * **********
2374 TTTCTTGCCAAAGAATGCCTTTTTCTTTATGTTTCTTGAGGTNNNNNNNNNNTTATAGTCTGTTT
261 TTTCTTGCCAAAGAATGCCTTTTTATTTACGTTTCTTGAGGTAGACATTCAATTATAGTCTGTTT
* *
2439 AACTAAAAATATAAAAGA
326 AACCAAAAATATAAAACA
* * * * * *
2457 AGTTCGACTTAAAATCAATTATGGTATTACAAAACTATTTAAATCGACTAATAAGGCTTTTGAAG
1 AATTCAACTTAAAATCAATTATGGTATTACAAAACCATTTAAAGCGAATAATAAGGCTATTGAAG
* * * *
2522 GTATAGGTGACTATAAATGGATTTTTCTTGCCAATGAATACTTTTTTCTTCATGTCTCTGAAGGT
66 GTATAGGTGACAATAAATAGACTTTACTTGCCAATGAATACTTTTTTCTTCATGTCTCTGAAGGT
* * * **********
2587 AGACATTCCATCCTAGTCTGTTTGAACCAAAAATGTACAAAGAATTCAAATTTAANNNNNNNNNN
131 AGACATTCAATCCTAGTCTGTTTGAACCAAAAATGTACAAAGAATTAAAATTGAAATCAATTTTG
* * * *
2652 AGATTATAAAACCATTTAAAGTGAGTACTAAGGCTTTTGAAAGAATGAGTTACTAT-AATTGGAC
196 AGATTATAAAACCATTTAAAGTGAGTAATAAGGCTTTTAAAAGAATGAGTGACTATAAATGGGA-
*
2716 TTCTT-TTGCCAATA-AATGCCTTTTTATTTACGTTTCTTGAGGTAGACATTCAATTATAGTTTG
260 TT-TTCTTGCCAA-AGAATGCCTTTTTATTTACGTTTCTTGAGGTAGACATTCAATTATAGTCTG
2779 TTTAACCAAAAATATAAAACA
323 TTTAACCAAAAATATAAAACA
*
2800 AATTCAACTTAAAATCAATTATGGCATTACA
1 AATTCAACTTAAAATCAATTATGGTATTACA
2831 NNNNNNNNNN
Statistics
Matches: 305, Mismatches: 66, Indels: 6
0.81 0.18 0.02
Matches are distributed among these distances:
342 6 0.02
343 296 0.97
344 3 0.01
ACGTcount: A:0.35, C:0.12, G:0.14, T:0.36
Consensus pattern (343 bp):
AATTCAACTTAAAATCAATTATGGTATTACAAAACCATTTAAAGCGAATAATAAGGCTATTGAAG
GTATAGGTGACAATAAATAGACTTTACTTGCCAATGAATACTTTTTTCTTCATGTCTCTGAAGGT
AGACATTCAATCCTAGTCTGTTTGAACCAAAAATGTACAAAGAATTAAAATTGAAATCAATTTTG
AGATTATAAAACCATTTAAAGTGAGTAATAAGGCTTTTAAAAGAATGAGTGACTATAAATGGGAT
TTTCTTGCCAAAGAATGCCTTTTTATTTACGTTTCTTGAGGTAGACATTCAATTATAGTCTGTTT
AACCAAAAATATAAAACA
Done.