Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018398067.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_1376.0, 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, 984
Length: 1641
ACGTcount: A:0.29, C:0.10, G:0.11, T:0.28
Warning! 369 characters in sequence are not A, C, G, or T
Found at i:1343 original size:172 final size:168
Alignment explanation
Indices: 621--1633 Score: 709
Period size: 170 Copynumber: 6.0 Consensus size: 168
611 ACAGTGAATC
* * * * * * **
621 TAAAATCAATTTTGAGACTACAAAATCATTTAAAGCGAGTAATAAGGCTTTTGAAGAAATAGGAA
1 TAAAATCAATTATGAGATTATAAAATCATTTAAAACGAGTAATAAGGCTTTTGAAGGAATGGGTG
* * * * * * * * *
686 ATTATAAATGGACTTTTCTTGCCTATGAAAGCTTTTTTCTTCACGTTTCTTGAGGTAGACAGTCA
66 ACTATAAATGAACTTTTTTTGCCAATGAATGCCTTTTTCTT-ATGTTTTTTGAGGTAGACATTCA
** * *
751 ATTATAACCTGTTTTAACCAAAAATATAAAAAATTCAACT
130 ATTATAGTCTGTTTTAACC-AAAATGTAAAAAATTCGACT
* * ********** ** * * * *
791 TAAAATCAATGATGAGCA-CATNNNNNNNNNNAAAGTGAGTAATAAGCCCTTTGAAGAAACGGGT
1 TAAAATCAATTATGAG-ATTATAAAATCATTTAAAACGAGTAATAAGGCTTTTGAAGGAATGGGT
* * * * * * * * *
855 GACTATAAATGGACTTTTCTTACCAATGAATGCATGTTTCTTCACGTTTCTCGAGGTAGATAGTT
65 GACTATAAATGAACTTTTTTTGCCAATGAATGCCTTTTTCTT-ATGTTTTTTGAGGTAGACA-TT
* * *
920 -AATTATAGTCTGTTTTAATCAAAAATATAAAAAATTCAACT
128 CAATTATAGTCTGTTTTAA-CCAAAATGTAAAAAATTCGACT
********** ** * **
961 NNNNNNNNNNTATGAGAATT-TAAAA-CTATTTAAAGTGAGTAATAAGGCTTTTAAAGGAATCAG
1 TAAAATCAATTATGAG-ATTATAAAATC-ATTTAAAACGAGTAATAAGGCTTTTGAAGGAATGGG
* * * * * * *
1024 -AAGCTATAAAT-AGAC-TTTTCTCCTCAATGAATGGCTTTTTCTATATGTTTTCTGAGGTAAAT
64 TGA-CTATAAATGA-ACTTTTTTTGC-CAATGAATGCCTTTTTCT-TATGTTTTTTGAGGTAGAC
* * * *
1086 ATTTAATTATAGTCTATTTTAA-AAAAATGTAATAAAATTCAACT
125 ATTCAATTATAGTCTGTTTTAACCAAAATGTAA-AAAATTCGACT
* * * * *
1130 TAAAATCAGTTATGAGATTATAAAATCATTCAAAGCGAGTAATAAGGCTTTTGAAAGAATGAGTG
1 TAAAATCAATTATGAGATTATAAAATCATTTAAAACGAGTAATAAGGCTTTTGAAGGAATGGGTG
* * * * *
1195 ACTATATATGAACTTTTTTTTGCCAATGAATGCCTTTTTCTTCTCGTTTTTTAAGATAGATATTC
66 ACTATAAATGAAC-TTTTTTTGCCAATGAATGCCTTTTTCTTAT-GTTTTTTGAGGTAGACATTC
*
1260 AATTATAGTCTGTTTTAACCGAAATTGTAAAAGAATTCGACT
129 AATTATAGTCTGTTTTAACC-AAAATGTAAAA-AATTCGACT
* *
1302 TAAAATCAATTATGAGATTATAAAACCATTTAAAACGAGTAACAAGGCTTTTGAAGGAATGGGTG
1 TAAAATCAATTATGAGATTATAAAATCATTTAAAACGAGTAATAAGGCTTTTGAAGGAATGGGTG
* * * * * * * *
1367 ACTATAAATGGACTTGTCTTGCCAATGAATACCTTTCTCTTCATGTTTTTTGTGGGAGACAATCA
66 ACTATAAATGAACTTTTTTTGCCAATGAATGCCTTTTTCTT-ATGTTTTTTGAGGTAGACATTCA
* * *
1432 ATTATA-ACATGTTTTAACCAATAATCTAAAAAATT-GAAT
130 ATTATAGTC-TGTTTTAACCAA-AATGTAAAAAATTCGACT
* ** *
1471 CTAAAATCAATTTTGAGATTATAAAATCATTTAAAAAAAGTAATAAGGTTTTTGAAGGAATGGGT
1 -TAAAATCAATTATGAGATTATAAAATCATTTAAAACGAGTAATAAGGCTTTTGAAGGAATGGGT
* * * * *
1536 GTCTATAAAT-ACACTTTTTCTACCAATGAATGCCTTTCCTT-TTATCTTTCTTGAGGTAGACAT
65 GACTATAAATGA-ACTTTTTTTGCCAATGAATGCCTTT--TTCTTATGTTTTTTGAGGTAGACAT
**
1599 TCAATTATAACCTGTTTTAACCAATAATGTAAAAA
127 TCAATTATAGTCTGTTTTAACCAA-AATGTAAAAA
1634 GACATTGA
Statistics
Matches: 662, Mismatches: 152, Indels: 58
0.76 0.17 0.07
Matches are distributed among these distances:
168 12 0.02
169 75 0.11
170 411 0.62
171 77 0.12
172 87 0.13
ACGTcount: A:0.37, C:0.12, G:0.14, T:0.35
Consensus pattern (168 bp):
TAAAATCAATTATGAGATTATAAAATCATTTAAAACGAGTAATAAGGCTTTTGAAGGAATGGGTG
ACTATAAATGAACTTTTTTTGCCAATGAATGCCTTTTTCTTATGTTTTTTGAGGTAGACATTCAA
TTATAGTCTGTTTTAACCAAAATGTAAAAAATTCGACT
Found at i:1415 original size:341 final size:339
Alignment explanation
Indices: 971--1620 Score: 706
Period size: 341 Copynumber: 1.9 Consensus size: 339
961 NNNNNNNNNN
* ** *
971 TATGAGAATTTAAAACTATTTAAAGTGAGTAATAAGGCTTTTAAAGGAATCAGAAGCTATAAATA
1 TATGAGAATTTAAAACCATTTAAAACGAGTAACAAGGCTTTTAAAGGAATCAGAAGCTATAAATA
* ** * * * * * *
1036 GACTTTTCTCCTCAATGAATGGCTTTTTCTATATGTTTTCTGAGGTAAATATTTAATTATAGTC-
66 GACTTGTCTCCTCAATGAATACCTTTCTCTATATGTTTTCTGAGGGAAACAATCAATTATA-ACA
* *
1100 TATTTTAA-AAAAATGTAATAAAATTCAA-CTTAAAATCAGTTATGAGATTATAAAATCATTCAA
130 TATTTTAACAAAAATCTAA-AAAATTCAATC-TAAAATCAATTATGAGATTATAAAATCATTCAA
*** * * *
1163 AGCGAGTAATAAGGCTTTTGAAAGAATGAGTGACTATATATGA-ACTTTTTTTTGCCAATGAATG
193 AAAAAGTAATAAGGCTTTTGAAAGAATGAGTGACTATAAAT-ACAC-TTTTTCTACCAATGAATG
* * * **
1227 CCTTT-TTCTTCTCGTTTTTTAAGATAGATATTCAATTATAGTCTGTTTTAACCGAAATTGTAAA
256 CCTTTCTT-TTATC-TTTCTTAAGATAGACATTCAATTATAACCTGTTTTAACCGAAATTGTAAA
1291 AGAATTCGACTTAAAATCAAT
319 AGAATTCGACTTAAAATCAAT
* * **
1312 TATGAG-ATTATAAAACCATTTAAAACGAGTAACAAGGCTTTTGAAGGAAT-GGGTGACTATAAA
1 TATGAGAATT-TAAAACCATTTAAAACGAGTAACAAGGCTTTTAAAGGAATCAGAAG-CTATAAA
* * * * *
1375 TGGACTTGTCTTGC-CAATGAATACCTTTCTCT-TCATGTTTTTTGTGGGAGACAATCAATTATA
64 TAGACTTGTC-TCCTCAATGAATACCTTTCTCTAT-ATGTTTTCTGAGGGAAACAATCAATTATA
* * * * *
1438 ACATGTTTTAACCAATAATCTAAAAAATTGAATCTAAAATCAATTTTGAGATTATAAAATCATTT
127 ACATATTTTAA-CAAAAATCTAAAAAATTCAATCTAAAATCAATTATGAGATTATAAAATCATTC
* * * *
1503 AAAAAAAGTAATAAGGTTTTTGAAGGAATGGGTGTCTATAAATACACTTTTTCTACCAATGAATG
191 AAAAAAAGTAATAAGGCTTTTGAAAGAATGAGTGACTATAAATACACTTTTTCTACCAATGAATG
* *
1568 CCTTTCCTTTTATCTTTCTTGAGGTAGACATTCAATTATAACCTGTTTTAACC
256 CCTTT-CTTTTATCTTTCTTAAGATAGACATTCAATTATAACCTGTTTTAACC
1621 AATAATGTAA
Statistics
Matches: 252, Mismatches: 46, Indels: 22
0.79 0.14 0.07
Matches are distributed among these distances:
340 7 0.03
341 155 0.62
342 79 0.31
343 11 0.04
ACGTcount: A:0.37, C:0.12, G:0.14, T:0.37
Consensus pattern (339 bp):
TATGAGAATTTAAAACCATTTAAAACGAGTAACAAGGCTTTTAAAGGAATCAGAAGCTATAAATA
GACTTGTCTCCTCAATGAATACCTTTCTCTATATGTTTTCTGAGGGAAACAATCAATTATAACAT
ATTTTAACAAAAATCTAAAAAATTCAATCTAAAATCAATTATGAGATTATAAAATCATTCAAAAA
AAGTAATAAGGCTTTTGAAAGAATGAGTGACTATAAATACACTTTTTCTACCAATGAATGCCTTT
CTTTTATCTTTCTTAAGATAGACATTCAATTATAACCTGTTTTAACCGAAATTGTAAAAGAATTC
GACTTAAAATCAAT
Done.