Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018398967.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_2249.0, 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: 2539
ACGTcount: A:0.32, C:0.13, G:0.13, T:0.31
Warning! 305 characters in sequence are not A, C, G, or T
Found at i:806 original size:171 final size:168
Alignment explanation
Indices: 455--1050 Score: 531
Period size: 171 Copynumber: 3.5 Consensus size: 168
445 CTATTAGCAC
* * * * * *
455 AAAAGGTCCATTTATAGTCA-CTAAAGCCTTCGAAAGCTTTATTACTTGCTCTAAATCGTTTTAT
1 AAAA-GTCCATTTATAGTCACCT--ATCCTTCAAAAGCCTTATTACTCGCTTTAAATGGTTTTAT
* * * * * *
519 AA-ACTAATAATTAATTTTAAGTT-AAATTTTATTAAATTTTTGATTAAAAAAGACAAGAATTGA
63 AATGC-CATAATTAATTTTAAGTTGAAATTTT-TTACATTTTTGGTTAAAACAGACTAGAATTG-
* * * *
582 ATGTCTACCTTGAGAAACATGAGAAAAAAAGCATTCGTTAGG-AAG
125 ATGTCTACCTCGAGAAACATAAG-AAAAAGGCATTCATT-GGCAAG
* ** *
627 AAAAGTCCATTTATAGCCACCTATACCTTCAAAAAGCCTTATTACTCGCTTTACGTGGTTCTATA
1 AAAAGTCCATTTATAGTCACCTAT-CCTTC-AAAAGCCTTATTACTCGCTTTAAATGGTTTTATA
* * * * * *
692 ATGGCATAATTGATTTTATGTTGAACTTTTTTACATTTTTGGTTAAAACAGGCTAGAATAGATGT
64 ATGCCATAATTAATTTTAAGTTGAAATTTTTTACATTTTTGGTTAAAACAGACTAGAATTGATGT
757 CTACCTCGAGAAACATAATGAAAAAGGCATTCATTGGCAAG
129 CTACCTCGAGAAACATAA-GAAAAAGGCATTCATTGGCAAG
* * * * * **
798 AGAAGTCCATTTATAGTCACCATTTCCTTCAAAAGCCTTTTTGCTCACTTTATTTGGTTTTATAA
1 AAAAGTCCATTTATAGTCACC-TATCCTTCAAAAGCCTTATTACTCGCTTTAAATGGTTTTATAA
* * * * * * * *
863 T-CTCAAAATTGA-TATAAATTGAAATTCTTTGCACA-TTTTAGTTAAAACAGATTATAATTGAG
65 TGC-CATAATTAATTTTAAGTTGAAATT-TTT-TACATTTTTGGTTAAAACAGACTAGAATTGA-
* * * * *
925 TGTCAACTTCAAGAAACGTGAAGAAAAAGGCATACATTGGCAAG
126 TGTCTACCTCGAGAAACAT-AAGAAAAAGGCATTCATTGGCAAG
* * * *
969 AAAAATCCATTTATAGTCGCCTATTCTGTCAAAAGCCTCATTACTCGCTTTAAATGGTTTTATAA
1 AAAAGTCCATTTATAGTCACCTATCCT-TCAAAAGCCTTATTACTCGCTTTAAATGGTTTTATAA
1034 TGCCATAATTAATTTTA
65 TGCCATAATTAATTTTA
1051 NNNNNNNNNN
Statistics
Matches: 342, Mismatches: 66, Indels: 32
0.78 0.15 0.07
Matches are distributed among these distances:
169 10 0.03
170 69 0.20
171 175 0.51
172 82 0.24
173 6 0.02
ACGTcount: A:0.36, C:0.15, G:0.14, T:0.35
Consensus pattern (168 bp):
AAAAGTCCATTTATAGTCACCTATCCTTCAAAAGCCTTATTACTCGCTTTAAATGGTTTTATAAT
GCCATAATTAATTTTAAGTTGAAATTTTTTACATTTTTGGTTAAAACAGACTAGAATTGATGTCT
ACCTCGAGAAACATAAGAAAAAGGCATTCATTGGCAAG
Found at i:1730 original size:171 final size:168
Alignment explanation
Indices: 1151--2539 Score: 1163
Period size: 171 Copynumber: 8.1 Consensus size: 168
1141 NNNNNNNNNN
1151 GACTATAAATGGACTTTTCTTGCCAATGAATGCCTTTTTCATT-ATGTTTCTCGAA-GTAGAC-A
1 GACTATAAATGGACTTTTCTTGCCAATGAATGCCTTTTTC-TTCATGTTTCTC-AAGGTAGACAA
* * * * * * * *
1213 TCAATTCTAGCCTGCTTTAACTACAAATATAAAAAAGTTCAACATAAAATCAATTATGGCATTAT
64 TCAATTATAG-C-GTTTTAACCAAAAATGTAAAAAAATTCAACTTAAAATCAATTTTGG-ATTAT
* * * * * *
1278 AGAACCATGTAAAGCGAGTAATAAGGTTTTTTGAAGGTATAGGT
126 AAAACCATTTAAAGTGAGTAATAAGG-CTTTTGAAGGAATGGGT
* * * * * * *
1322 GGCTAGAAATGGACATTTCTTGCCAATGAATGCTTTTTTCCTCATGTTCCTCAAGGTAGACATTC
1 GACTATAAATGGACTTTTCTTGCCAATGAATGCCTTTTTCTTCATGTTTCTCAAGGTAGACAATC
* * * * *
1387 AATTCTAGTCTCTTTTAACCAAAAATGTAAAAAAATTCAACTTAAAATTAATTATTAGTTTATAA
66 AATTATAG-C-GTTTTAACCAAAAATGTAAAAAAATTCAACTTAAAATCAATT-TTGGATTATAA
** * ** *
1452 AACCATTTAAAGAAAGTAATAAGGCTTTCGAAGGCTTGAGT
128 AACCATTTAAAGTGAGTAATAAGGCTTTTGAAGGAATGGGT
* * * ** * * * *
1493 GACAATAAATGAACTTTT-TGTGCTAATGGTTGGCC-TTTGCTTCACGTTTCCCAAGGCA-ATCA
1 GACTATAAATGGACTTTTCT-TGCCAATGAAT-GCCTTTTTCTTCATGTTTCTCAAGGTAGA-CA
* *
1555 ATCAATTATAGCAATTTTAAACCAATAATGTAAAAAAATTCAACTTAAAATCAATTTTGAGATTA
63 ATCAATTATAGC-GTTTT-AACCAAAAATGTAAAAAAATTCAACTTAAAATCAATTTTG-GATTA
* * *
1620 TAAAGCCATTTAAAATGAGTAATAAGGCTTTTAAAGGAATGGGT
125 TAAAACCATTTAAAGTGAGTAATAAGGCTTTTGAAGGAATGGGT
* * *
1664 GACTATAATTGGACTTTTCTTGCCAATGATTGCCTTTTTCTTCATGTTTCTCAAGCTAGACAATC
1 GACTATAAATGGACTTTTCTTGCCAATGAATGCCTTTTTCTTCATGTTTCTCAAGGTAGACAATC
** * * * * *
1729 AATTATAAAATGTTTTAATCAAAAATTTAAAAAAGTTCAACTTAAAATCAATTATGGCATTGTAA
66 AATTAT--AGCGTTTTAACCAAAAATGTAAAAAAATTCAACTTAAAATCAATTTTGG-ATTATAA
* * **
1794 AGCCATGTAAA-CCATGTAATAAGGCTTTTTGAAGGAATGGGT
128 AACCATTTAAAGTGA-GTAATAAGGC-TTTTGAAGGAATGGGT
* * ** * ** * *
1836 GACTACT-AATAGACTTTTCTTTCCAATGAATGCCTTTACCTTCATATTTCTTGAGGTTGACATT
1 GACTA-TAAATGGACTTTTCTTGCCAATGAATGCCTTTTTCTTCATGTTTCTCAAGGTAGACAAT
* * * * * * * * * ** *
1900 GAATTGTAATCTTTTTTTACCAAAAATGCATAAAGAATTTAAATTTCAATCAATTTTGAGATTAC
65 CAATTAT-AGC-GTTTTAACCAAAAATGTA-AAAAAATTCAACTTAAAATCAATTTTG-GATTAT
* *
1965 AAAACCATTTAAAGTGAGTAATAAGCCTTTTGGAGGAATGGGT
126 AAAACCATTTAAAGTGAGTAATAAGGCTTTTGAAGGAATGGGT
* ** ** ** * *
2008 GACTGTAAATGGACTTTTCTTAACAATGAA--AATTTTTCTTCATGTTTCTTGAGGTTGACATTC
1 GACTATAAATGGACTTTTCTTGCCAATGAATGCCTTTTTCTTCATGTTTCTCAAGGTAGACAATC
* * * * * *
2071 AATTATAATCTGTTTTAACTAAAAACGCACAAAGAATTCAAATTTAAAA-CAATTTTGAGATTAT
66 AATTAT-AGC-GTTTTAACCAAAAATGTA-AAAAAATTC-AACTTAAAATCAATTTTG-GATTAT
*
2135 AAAACCATTTAAAGTGAGTAATAAAAG-TTTTGAAGGAATGGGCT
126 AAAACCATTTAAAGTGAGTAAT-AAGGCTTTTGAAGGAATGGG-T
* * * * *
2179 -ACTATAAATGGACTTTTCTTGTCAATGAATGCCTTGTTCTTTATGTTTC-CTGAGCTAGAC-AT
1 GACTATAAATGGACTTTTCTTGCCAATGAATGCCTTTTTCTTCATGTTTCTC-AAGGTAGACAAT
* * *
2241 CCAATTACAGTTCGTTTTAACCAAAAATGTAAAACAAA-TCAACTTAAAATAAATTATTGCATTA
65 -CAATTATAG--CGTTTTAACCAAAAATGTAAAA-AAATTCAACTTAAAATCAATT-TTGGATTA
* * *
2305 TAAAACCATTTAAAGCGAGTAATGAGGCTTTTGAAGGTATGGGT
125 TAAAACCATTTAAAGTGAGTAATAAGGCTTTTGAAGGAATGGGT
* * * ** * *
2349 GACTATAATTGGACTTTTCCTGCCAATGAATGCCTTTTTCTTTATGTTTCTTGAGGTACACATTC
1 GACTATAAATGGACTTTTCTTGCCAATGAATGCCTTTTTCTTCATGTTTCTCAAGGTAGACAATC
* * * * *
2414 AATTACAGTCTGTTTTAACCAAAAATGTAAAAAATTTCAATTTAAAATCAATTATGGCATTGTAA
66 AATTATAG-C-GTTTTAACCAAAAATGTAAAAAAATTCAACTTAAAATCAATTTTGG-ATTATAA
* * * *
2479 AACCATTTAAAGTGAGCAATGAGGCTTCTGAAGGTATGGGT
128 AACCATTTAAAGTGAGTAATAAGGCTTTTGAAGGAATGGGT
2520 GACTATAAATGGACTTTTCT
1 GACTATAAATGGACTTTTCT
Statistics
Matches: 989, Mismatches: 187, Indels: 84
0.78 0.15 0.07
Matches are distributed among these distances:
170 169 0.17
171 520 0.53
172 250 0.25
173 48 0.05
174 2 0.00
ACGTcount: A:0.36, C:0.14, G:0.15, T:0.35
Consensus pattern (168 bp):
GACTATAAATGGACTTTTCTTGCCAATGAATGCCTTTTTCTTCATGTTTCTCAAGGTAGACAATC
AATTATAGCGTTTTAACCAAAAATGTAAAAAAATTCAACTTAAAATCAATTTTGGATTATAAAAC
CATTTAAAGTGAGTAATAAGGCTTTTGAAGGAATGGGT
Done.