Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018397715.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_1014.0, 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: 1699
ACGTcount: A:0.34, C:0.10, G:0.09, T:0.31
Warning! 282 characters in sequence are not A, C, G, or T
Found at i:1409 original size:174 final size:172
Alignment explanation
Indices: 851--1612 Score: 679
Period size: 173 Copynumber: 4.4 Consensus size: 172
841 CTAAAGTAAG
* * * * * *
851 TAATAAGGTTTTCGAAGG-TATAAGTGACCATAAATAGACTTTTCGTGTTAATGGGTGG-TTTTG
1 TAATAAAGCTTTCGAAGGCT-TGAGTGACTATAAATTGACTTTTC-TGTTAATGGATGGCTTTT-
* * *
914 GCTTCACATTTCTTAAGGTAGACATTCAATTATACTATGTTTTAACCAAAAATGT-AAAAA-AAT
63 GCTTCACATTTCTCAAGGCAGACATTCAATTATAATATGTTTTAACCAAAAATGTAAAAAACAAT
*
977 T-CTAAAAAAATCAATTATGAGATTACAAAATCATTTAAAGCGAC
128 TACTTAAAAAATCAATTATGAGATTACAAAATCATTTAAAGCGAC
* * * * * *
1021 TAATAAAGCTTTCGAAGGCTTAAGTGACTATAAATGGACTTTTATTGCTAATGAATGGCTTTTGT
1 TAATAAAGCTTTCGAAGGCTTGAGTGACTATAAATTGACTTTT-CTGTTAATGGATGGCTTTTGC
* ** *
1086 TTTATGTTT-TCTAAGGCAGACATTCAATTATAATATGTTTTAACCAAAAATGTAGAAAAC--TT
65 TTCACATTTCTC-AAGGCAGACATTCAATTATAATATGTTTTAACCAAAAATGTAAAAAACAATT
* ** *
1148 CACATTAAAAAATCAATTATGATATTACAAAGCCATTTAAAGTGAC
129 -AC-TTAAAAAATCAATTATGAGATTACAAAATCATTTAAAGCGAC
* * * * * *
1194 AAATAAAGCTTTTGAAGGCTTGAGCGACTATAAGTTGACTTTTTCTGTTAATGGATGGTTTTTGT
1 TAATAAAGCTTTCGAAGGCTTGAGTGACTATAAATTGAC-TTTTCTGTTAATGGATGGCTTTTGC
* * * * *
1259 TTTACGTTTCTCGAGGCAGACATTCAAATATAATATGTTTTAACTAAAAATGTAAAAAACAATTA
65 TTCACATTTCTCAAGGCAGACATTCAATTATAATATGTTTTAACCAAAAATGTAAAAAACAATT-
*
1324 ACTTAAAAAATCAATTATGAGATTACAAAATAATTTAAAGCGAC
129 ACTTAAAAAATCAATTATGAGATTACAAAATCATTTAAAGCGAC
* * * *
1368 TAATAAAGCTTTCAAAGGCATGAGTGACAATAAATTGACTTTTCT-TATCAATGGATGACTTTTG
1 TAATAAAGCTTTCGAAGGCTTGAGTGACTATAAATTGACTTTTCTGT-T-AATGGATGGCTTTTG
* * * * * * ** * *
1432 CTTCACATTTCACGAGGTAGACATTCAGTAATAATTTACTTTAATCGAAAATGT--AAAACAATT
64 CTTCACATTTCTCAAGGCAGACATTCAATTATAATATGTTTTAACCAAAAATGTAAAAAACAA-T
** * * * *
1495 TAACTT--AAAATCAACCATG-GATTTATAAAATCATTTTAAGTGAG
128 T-ACTTAAAAAATCAATTATGAGA-TTACAAAATCATTTAAAGCGAC
** * * * * * * * * *
1539 TAATAGGGCTTTGGAAGGCATGATTGACTGTAAATCGACTTTCCATATTAACGGATGGCTTTTGT
1 TAATAAAGCTTTCGAAGGCTTGAGTGACTATAAATTGACTTTTC-TGTTAATGGATGGCTTTTGC
*
1604 TTCATATTT
65 TTCACATTT
1613 TTTGAGGCAA
Statistics
Matches: 488, Mismatches: 85, Indels: 37
0.80 0.14 0.06
Matches are distributed among these distances:
169 1 0.00
170 97 0.20
171 93 0.19
172 11 0.02
173 154 0.32
174 128 0.26
175 4 0.01
ACGTcount: A:0.37, C:0.12, G:0.15, T:0.35
Consensus pattern (172 bp):
TAATAAAGCTTTCGAAGGCTTGAGTGACTATAAATTGACTTTTCTGTTAATGGATGGCTTTTGCT
TCACATTTCTCAAGGCAGACATTCAATTATAATATGTTTTAACCAAAAATGTAAAAAACAATTAC
TTAAAAAATCAATTATGAGATTACAAAATCATTTAAAGCGAC
Done.