Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018402858.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_591.0, 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: 19328
ACGTcount: A:0.25, C:0.08, G:0.09, T:0.24
Warning! 6391 characters in sequence are not A, C, G, or T
Found at i:2256 original size:171 final size:169
Alignment explanation
Indices: 1872--2758 Score: 576
Period size: 171 Copynumber: 5.2 Consensus size: 169
1862 NNNNTTAATC
* ** * * *
1872 AAAAAAGTAAAAAAGATTAAACTTAAAATCAATT-TGAGATTGTAAAACTATTTAAAATGAGTAA
1 AAAAATGTAAAAAA-ATTCTACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGTGAGTAA
** * * * * *
1936 TAAATCTTTTGAAGGAATGGAAGTCTATAAAT-AGACTTTCTTGCCAATAAATACTTTTTTCTTC
65 TAAA-CTTTTGAAGGAATGGGTGACTATAAATGA-ACTTTTTTGCCAATGAATGCCTTTTTCTTC
** * *
2000 ACGTTTCTTAAGGTAGACATTCAATTA-TAGCCTGTTTTAA-T
128 ACGTTTCTCGAGGTAGACATTCAATTATTA-TCTATTTTAACT
* * * * **
2041 AAAAAATGTAAGAAAATTCAACTTCAAATCAACTATGAGATTATAAAACCATTTAAAGCAAGTAA
1 -AAAAATGTAAAAAAATTCTACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGTGAGTAA
*
2106 TAATACTTTTGTAGGAATGGGTGACTATAAATGAACTTTTTTAGCCAATGAATGCCTTTTTCTTC
65 TAA-ACTTTTGAAGGAATGGGTGACTATAAATGAACTTTTTT-GCCAATGAATGCCTTTTTCTTC
* *
2171 ACGTTTCTCGAGGTCA-ACATTAAATTATTTTCTATTTTAACT
128 ACGTTTCTCGAGGT-AGACATTCAATTATTATCTATTTTAACT
* * *****
2213 AAAAATATAAAAAAATTCTACTTAAAATCAATTATGTGATTATAAAACCATTTAAAGTGNNNNNN
1 AAAAATGTAAAAAAATTCTACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGTG-AGTAA
***** * ** * *
2278 NNNNGTTTTAAAGGAATGGGTGACTATAAATGGGCTTTTCTT-CTCAATGAACGGCTTTTTCTTC
65 TAAACTTTTGAAGGAATGGGTGACTATAAATGAACTTTT-TTGC-CAATGAATGCCTTTTTCTTC
* * *
2342 ATGTTTCTCGAGGTAGACATTCAATTATTATCTTTTTTAACA
128 ACGTTTCTCGAGGTAGACATTCAATTATTATCTATTTTAACT
* * ** **********
2384 AAAAATGTAAAAGAATT-TAACTTAAAATCAATTATAAGATTATAAAATAATNNNNNNNNNNTAA
1 AAAAATGTAAAAAAATTCT-ACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGTGAGTAA
* * * * * *
2448 TAAGGCTTTTGAAGGAATGGGTGACAATAAATAAACTTTTCTTGCCAGTGAATACCTTTTTGTTC
65 TAA-ACTTTTGAAGGAATGGGTGACTATAAATGAACTTTT-TTGCCAATGAATGCCTTTTTCTTC
* * * * * * * *
2513 ACGTTCCTCGATGTAAACATGCAATTATAATCTGTTTGAACCA
128 ACGTTTCTCGAGGTAGACATTCAATTATTATCTATTTTAA-CT
******** * * *
2556 AAAAANNNNNNNNNNAATT-GAGCTTAAAATCAATTTTGAGATTACAAAACCATTTAAAGTGAGT
1 AAAAA--TGTAAAAAAATTCTA-CTTAAAATCAATTATGAGATTATAAAACCATTTAAAGTGAGT
* * ** * * * *
2620 AGTAAGGCTTTTGAACAAAT-GGAGAGCTATAAATGATCTTTTCTTGCCAATAAATGGCTTTTTC
63 AATAA-ACTTTTGAAGGAATGGGTGA-CTATAAATGAACTTTT-TTGCCAATGAATGCCTTTTTC
* ** *
2684 TACACGTTTCAT-GAGGTAGGTACTCAATTA-TAGTCTATTTTAA-T
125 TTCACGTTTC-TCGAGGTAGACATTCAATTATTA-TCTATTTTAACT
* *
2728 AAAAAATATAAAAAAA-TCAACTTAAAATCAA
1 -AAAAATGTAAAAAAATTCTACTTAAAATCAA
2759 NNNNNNNNNN
Statistics
Matches: 544, Mismatches: 150, Indels: 46
0.74 0.20 0.06
Matches are distributed among these distances:
169 16 0.03
170 87 0.16
171 310 0.57
172 13 0.02
173 11 0.02
174 106 0.19
175 1 0.00
ACGTcount: A:0.38, C:0.12, G:0.13, T:0.34
Consensus pattern (169 bp):
AAAAATGTAAAAAAATTCTACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGTGAGTAAT
AAACTTTTGAAGGAATGGGTGACTATAAATGAACTTTTTTGCCAATGAATGCCTTTTTCTTCACG
TTTCTCGAGGTAGACATTCAATTATTATCTATTTTAACT
Found at i:4696 original size:170 final size:170
Alignment explanation
Indices: 4400--4818 Score: 517
Period size: 170 Copynumber: 2.5 Consensus size: 170
4390 NNNNNAATCT
* * *
4400 CATAATTGATTTTAAGTTAAATTCTT-TTACATTTTTTGTTAAAACAGACAATAATTGCATGTCT
1 CATAATTGATTTTAAGTTGAATT-TTCTTACATTTTTGGTTAAAACAGACAATAATTG-AAGTCT
* * *
4464 ACCTCGA-AAAGCATAAAGAAAAAGCCATTCATTGAGAAGAAAAGCTCATTTATAGTCACCCATT
64 ACCTCGAGAAA-CATAAAAAAAAAGCAATTCATTGAGAAAAAAAGCTCATTTATAGTCACCCATT
**
4528 CCTTTAAAACTCTTATTACTCGCTTTAAAT-AGTTTTATAACCA
128 CCTGCAAAACTCTTATTACTCGCTTTAAATGA-TTTTATAACCA
* * * * *
4571 CATAATTGATTTTAAGTTGGATTTTCTTATATTTTTGGTTAAAATAGAAAATAATTGAAGTGTAC
1 CATAATTGATTTTAAGTTGAATTTTCTTACATTTTTGGTTAAAACAGACAATAATTGAAGTCTAC
*
4636 CTCGAGAAACATAAAAAAAAAAG-AATTCATTG-GCTAAAAAAATC-CATTTATAGTCACCCATT
66 CTCGAGAAACAT-AAAAAAAAAGCAATTCATTGAG--AAAAAAAGCTCATTTATAGTCACCCATT
* * * *
4698 CCTGCAAAAGTCTTATTACTTGCTTTAAATGATTTTATAATCT
128 CCTGCAAAACTCTTATTACTCGCTTTAAATGATTTTATAACCA
* * * *
4741 CATAATTAATTTAAAGTTGAATTTTCTTACATTTTTGGTTAAAACAGGCTATAATTGAATGTCTA
1 CATAATTGATTTTAAGTTGAATTTTCTTACATTTTTGGTTAAAACAGACAATAATTGAA-GTCTA
*
4806 CCTTGAGAAACAT
65 CCTCGAGAAACAT
4819 GAAGAANNNN
Statistics
Matches: 213, Mismatches: 28, Indels: 14
0.84 0.11 0.05
Matches are distributed among these distances:
169 1 0.00
170 128 0.60
171 84 0.39
ACGTcount: A:0.38, C:0.14, G:0.11, T:0.37
Consensus pattern (170 bp):
CATAATTGATTTTAAGTTGAATTTTCTTACATTTTTGGTTAAAACAGACAATAATTGAAGTCTAC
CTCGAGAAACATAAAAAAAAAGCAATTCATTGAGAAAAAAAGCTCATTTATAGTCACCCATTCCT
GCAAAACTCTTATTACTCGCTTTAAATGATTTTATAACCA
Found at i:15586 original size:171 final size:170
Alignment explanation
Indices: 14888--15979 Score: 1112
Period size: 171 Copynumber: 6.4 Consensus size: 170
14878 NNNNNNNNNN
* * *
14888 ATAAAACAATTTAAAGTGAGTAATAAGGCTTTTGAAAGAATGGGTGACTATAAA-AGGAC-TTTC
1 ATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAAT-GGTGACTATAAATA-GACTTTTC
** * * * * * * *
14951 TT-CTCAATTAATGGCTTTTTCTACATGTTTCTTGAGGTAGGTATACAATTATAGTCTGATTTAA
64 TTGC-CAACGAATGGCTTTTTCTACATGTTTCCTGAGGCAAGCATTCAATTATAATCTGTTTTAA
* * **
15015 TGAAAAATTTAAAGAAATTTGACTTAAAATCAATTATGAGATT
128 TGAAAAATGTAAAAAAATTCAACTTAAAATCAATTATGAGATT
*
15058 ATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGGATGACAATAAATAGACTTTTCT
1 ATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGG-TGACTATAAATAGACTTTTCT
* * * * * *
15123 TGCCAACGAATGCCTTTTTCTTCAT-ATTCCTCAATGTATA-CATTCAATTATAATCTGTTTTAA
65 TGCCAACGAATGGCTTTTTCTACATGTTTCCT-GAGGCA-AGCATTCAATTATAATCTGTTTTAA
* * * * *
15186 CTAAAAAAGTGAAAAAAAAATTGAACTTAAAATCAATTTTGAAATT
128 -TGAAAAA-TG-TAAAAAAATTCAACTTAAAATCAATTATGAGATT
* * * * * ** *
15232 ATAAAAGCATTTAAAGTGAGTAGTAAGGCTTTTGAAGGAACAGGGGACTGCAAATAGACGTTTCT
1 ATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAA-TGGTGACTATAAATAGACTTTTCT
* * * * * * *
15297 TACCAACGAATGGCTTTTTCTACACGTTTCCTAAGGTAGGTATTCAATTATAGTCTG-TTTAATG
65 TGCCAACGAATGGCTTTTTCTACATGTTTCCTGAGGCAAGCATTCAATTATAATCTGTTTTAATG
* * *
15361 AAAAATAT-AAAAAATTCATCTTAAAATCAATTGTGAGATT
130 AAAAATGTAAAAAAATTCAACTTAAAATCAATTATGAGATT
* *
15401 ATAAAACCATTTAAAGCGAGTAATAAGGTTTTTGAAGGAATGGATGACTATAAATGGACTTTTCT
1 ATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGG-TGACTATAAATAGACTTTTCT
* * * * * * * * *
15466 T-CTTAATGAATGGCTCTTTCTATAGGTTTCCTGAGGCAAGCATTCAGTCATAGTCTATTTTAAT
65 TGC-CAACGAATGGCTTTTTCTACATGTTTCCTGAGGCAAGCATTCAATTATAATCTGTTTTAAT
*
15530 GAAAAATGTAAAAGAATTCAACTTAAAATCAATTATGAGATT
129 GAAAAATGTAAAAAAATTCAACTTAAAATCAATTATGAGATT
* *
15572 ATAAAACTATTTAAAGCGAGTAATAAGGCTTTTG-AGAGAATGGGTGACAATAAATAGACTTTTC
1 ATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAG-GAAT-GGTGACTATAAATAGACTTTTC
* * * * * *
15636 TTGCTAGCGAATGCCTTTTTCTTCATG-TTCCTTGA--CATAGACTTTCTATTATAATCTGTTTT
64 TTGCCAACGAATGGCTTTTTCTACATGTTTCC-TGAGGCA-AG-CATTCAATTATAATCTGTTTT
* * *
15698 AACT-AAAAAAGTAAAAACAAAAAATTGAACTTAAAATCAATTTTGAGATT
126 AA-TGAAAAATGT----A-AAAAAATTCAACTTAAAATCAATTATGAGATT
* * * * *
15748 ACAAAACCATTTAAAGCCAGTAGTAAGGCTTTTGAAGGAATGGGGAGTATAAATAGACTTTTCTT
1 ATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGGTGACTATAAATAGACTTTTCTT
* * * * *
15813 GCCAATGAATGGCTTTTTCTACATGTTTCTTGAGTCAAGCATTCAATTATAATTTGTTTTAATAA
66 GCCAACGAATGGCTTTTTCTACATGTTTCCTGAGGCAAGCATTCAATTATAATCTGTTTTAATGA
* * *
15878 AAAATATAAAAAAATTTAACTTAAAATCAATTATGAGATG
131 AAAATGTAAAAAAATTCAACTTAAAATCAATTATGAGATT
* * *
15918 GTAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGTGTGACTACAAATGGACTTT
1 ATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATG-GTGACTATAAATAGACTTT
15980 NNNNNNNNNN
Statistics
Matches: 762, Mismatches: 126, Indels: 67
0.80 0.13 0.07
Matches are distributed among these distances:
168 3 0.00
169 127 0.17
170 143 0.19
171 193 0.25
172 17 0.02
173 6 0.01
174 123 0.16
175 78 0.10
176 68 0.09
177 4 0.01
ACGTcount: A:0.38, C:0.12, G:0.16, T:0.34
Consensus pattern (170 bp):
ATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGGTGACTATAAATAGACTTTTCTT
GCCAACGAATGGCTTTTTCTACATGTTTCCTGAGGCAAGCATTCAATTATAATCTGTTTTAATGA
AAAATGTAAAAAAATTCAACTTAAAATCAATTATGAGATT
Done.