Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018398292.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_1596.0, 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: 2470
ACGTcount: A:0.20, C:0.07, G:0.08, T:0.20
Warning! 1114 characters in sequence are not A, C, G, or T
Found at i:1453 original size:171 final size:172
Alignment explanation
Indices: 1079--1878 Score: 924
Period size: 171 Copynumber: 4.7 Consensus size: 172
1069 AATTATAATA
* * * * * *
1079 TGTTTTAACCAGAAAA-GTA-AAAAAATTTGAACTTAAAATCAACTTTGAGATTATAAAACCATT
1 TGTTTTAACCA-AAAATGTACAAAGAA-TTCAAATTTAAATCAATTTTGAGATTAGAAAACCATT
* * ** * * * *
1142 TAGAGTGATTAATAAGGCTTTTGAACCAATGGGTGACTATAAATAGACTTTTTTTACTAATGAAT
64 TAAAGTGAGTAATAAGGCTTTTGAAGGAATGGGTGACTATAAATGGACTTTTCTTGCCAATGAAT
* * * * * *
1207 ACTTTTGTGTTCATGTTTCTCATGGTATAGATTCAATTCC-AGTC
129 ACTTTTTTCTTCATGTTTCTGAAGGTAAACATTCAA-TCCTAGTC
* * *
1251 CGTTTTAACAAAAAATGTACAAA-ACATTCAAATTTAAATCAATTTTGAGATTAGAAAATCATTT
1 TGTTTTAACCAAAAATGTACAAAGA-ATTCAAATTTAAATCAATTTTGAGATTAGAAAACCATTT
* ** * *
1315 AAACTGAGTAATAAGGCTCATGAAGGTATGGGTGACTATAAATGGACTTTT-TTGCTAATGAATA
65 AAAGTGAGTAATAAGGCTTTTGAAGGAATGGGTGACTATAAATGGACTTTTCTTGCCAATGAATA
* *
1379 CTTTTTTCTTCATGTTTCTGAAGGTAGACACTCAATCCTAGTC
130 CTTTTTTCTTCATGTTTCTGAAGGTAAACATTCAATCCTAGTC
* * *
1422 TGTTTTAACCAAAAATGTACAAAGAATTCAAACTTAAATAAATTTTGAGATTATAAAACCATTTA
1 TGTTTTAACCAAAAATGTACAAAGAATTCAAATTTAAATCAATTTTGAGATTAGAAAACCATTTA
* * ** *
1487 AAGTGAGTAAGAAGGCTTTTGAAGGAATTGGTGACTATAAATGGACTTTTCTTGCCAAAAAACAC
66 AAGTGAGTAATAAGGCTTTTGAAGGAATGGGTGACTATAAATGGACTTTTCTTGCCAATGAATAC
* * * **
1552 -CTTTTCTTTACGTTTCTCG-AGGTAAACAATT-AATTATAGTC
131 TTTTTTCTTCATGTTTCT-GAAGGTAAAC-ATTCAATCCTAGTC
* * * * *
1593 TG-TTTAACCAAAAATATA-AAAGAATTCAACTTAAAATCAATTATG-GCATTACAAAACCATTT
1 TGTTTTAACCAAAAATGTACAAAGAATTCAAATTTAAATCAATTTTGAG-ATTAGAAAACCATTT
* *
1655 AAA-TCGAGTAATAAGGCTTTTGAACGTATGGGTGACTATAAATGGACTTTTCTTGCCAATGAAT
65 AAAGT-GAGTAATAAGGCTTTTGAAGGAATGGGTGACTATAAATGGACTTTTCTTGCCAATGAAT
* * * *
1719 AATTTTTTCTTGATGTTGCTGAAAGTAAACATTCAATCCTAGTC
129 ACTTTTTTCTTCATGTTTCTGAAGGTAAACATTCAATCCTAGTC
*
1763 TGTTTTAACAAAAAATGTACAAAGAATTCAAATTTAAATCAATTTTGAGATTATG-AAACCATTT
1 TGTTTTAACCAAAAATGTACAAAGAATTCAAATTTAAATCAATTTTGAGATTA-GAAAACCATTT
*
1827 AAAGTGAGTAATAAGGCTTTTGAAGGAATGGGTGACTATAATTGGACTTTTC
65 AAAGTGAGTAATAAGGCTTTTGAAGGAATGGGTGACTATAAATGGACTTTTC
1879 ATCCTAAAGA
Statistics
Matches: 531, Mismatches: 79, Indels: 36
0.82 0.12 0.06
Matches are distributed among these distances:
168 2 0.00
169 96 0.18
170 48 0.09
171 194 0.37
172 185 0.35
173 6 0.01
ACGTcount: A:0.38, C:0.12, G:0.15, T:0.35
Consensus pattern (172 bp):
TGTTTTAACCAAAAATGTACAAAGAATTCAAATTTAAATCAATTTTGAGATTAGAAAACCATTTA
AAGTGAGTAATAAGGCTTTTGAAGGAATGGGTGACTATAAATGGACTTTTCTTGCCAATGAATAC
TTTTTTCTTCATGTTTCTGAAGGTAAACATTCAATCCTAGTC
Done.