Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018399534.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_2793.0, 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: 7400
ACGTcount: A:0.32, C:0.09, G:0.10, T:0.30
Warning! 1359 characters in sequence are not A, C, G, or T
Found at i:2060 original size:172 final size:167
Alignment explanation
Indices: 1621--3518 Score: 685
Period size: 171 Copynumber: 11.1 Consensus size: 167
1611 NNNNNNNNTT
1621 AACTTAAAATCAATTTTAAAAATATAAAACCTTTTAAAGCGAGTAATAAAGCTTTTAAGGGAATG
1 AACTTAAAATCAATTTTAAAAATATAAAA-CTTTTAAAGCGAGTAATAAAGCTTTTAA-GGAATG
* * * *
1686 GGTGACTATAAATGGAGTATACATACCAATGAATCCTTTTTTCCTTATGTTTCTTAAGGTAGACA
64 GGTGACTATAAATGGAGTATACTTATCAATGAAT-CTTTTTTCTTTAT-TTTTTTAAGGTAGACA
* * *
1751 GTCAATTATAATCTGTTTTATATGAAAATGTAAAAAAATTT
127 GTCAATTATAATCTATTTTATATGAAAATATAAAAAAATTG
* * **********
1792 AAGTTAACATCAATTTTAAAAATATAAAACGTTTTAAAGCGAGTAATAAAGCCTTNNNNNNNNNN
1 AACTTAAAATCAATTTTAAAAATATAAAAC-TTTTAAAGCGAGTAATAAAG-CTTTTAAGGAATG
* *
1857 GGTGACTATAAATGGAGTATACTTGTCAATGAATGCTTTTTTCTTTATATTTTTTAAGGTACACA
64 GGTGACTATAAATGGAGTATACTTATCAATGAAT-CTTTTTTCTTTAT-TTTTTTAAGGTAGACA
**********
1922 GTCAATTATAATCTATTTNNNNNNNNNNTATAAAAAAAATTG
127 GTCAATTATAATCTATTTTATATGAAAATAT-AAAAAAATTG
* * * *
1964 AACTTAAAAACAATTTTGAGAATATAAAATCTTTTAAAGCGAGTAGTAAAGCTTTTGAAGGAATG
1 AACTTAAAATCAATTTTAAAAATATAAAA-CTTTTAAAGCGAGTAATAAAGCTTTT-AAGGAATG
* * * * ** *
2029 GGTGACTATAAATGGA-CATTTCTTATCAATGAATATCTTTTTCTTCATTTTTGTCGAGGAAGAC
64 GGTGACTATAAATGGAGTA-TACTTATCAATGAATCT-TTTTTCTTTATTTTT-TTAAGGTAGAC
* ** *
2093 ATTCAATTATAATCTATTTTA-ACAAAAAATATAAAAAAATTT
126 AGTCAATTATAATCTATTTTATA-TGAAAATATAAAAAAATTG
* * * * * ************* * *
2135 ATCTTAAAATCAATTATGATATTATAAAACCTTTTAAAGNNNNNNNNNNNNNNTTTGAAAGAATG
1 AACTTAAAATCAATTTTAAAAATATAAAA-CTTTTAAAG-CGAGTAATAAAGCTTTTAAGGAATG
* * * * * * * * *
2200 AGTGACTATAAATGGACTTTTCTTGTCAATGAATACTATTTTT-TTTACGTTTCTCAAGATAGAC
64 GGTGACTATAAATGGAGTATACTTATCAATGAAT-CT-TTTTTCTTTA-TTTTTTTAAGGTAGAC
* * * * * *
2264 ATTCAATTTTAATCTATTTTA-A-CAAAAAATGTAAAAAATTC
126 AGTCAATTATAATCTATTTTATATGAAAATAT-AAAAAAATTG
*********** * *
2305 AACTTAAAATCNNNNNNNNNNTTATAAAACTTTTTAAAGCTAGTAATAAGGCTTTTGAAGGAATG
1 AACTTAAAATCAATTTTAAAAATATAAAAC-TTTTAAAGCGAGTAATAAAGCTTTT-AAGGAATG
* * * * * * * * * *
2370 GGTGACTATAAATAGACTTTACCTGTCAATGAATTCCTTTTTCTTCATGTTTCTCATGGTAGACA
64 GGTGACTATAAATGGAGTATACTTATCAATGAA-TCTTTTTTCTTTAT-TTTTTTAAGGTAGACA
* * * *
2435 TTCAATTATAATCTGTTTTGACTA--AAAATATACAAAGAATTCC
127 GTCAATTATAATCTATTTT-A-TATGAAAATATA-AAAAAATT-G
* * * * * * * * *****
2478 AA-TCAAAATCAAATTTGAGATTACAACACCATTTAAAGCGAGTAAT-AAGACTTTTAAANNNNN
1 AACTTAAAATCAATTTTAAAAATATAA-AACTTTTAAAGCGAGTAATAAAG-CTTTT-AAGGAAT
***** * * * * ** * * * *
2541 NNNNNACTATAAACGGACTTTTCTTGCCAATGAATGCCTTTTTCTTTATGTTTCTTAAGATATAC
63 GGGTGACTATAAATGGAGTATACTTATCAATGAAT-CTTTTTTCTTTAT-TTTTTTAAGGTAGAC
* * * **
2606 AGTCAATTATAATCTTTTTTACACGAAAATGGAAAGAAAATTG
126 AGTCAATTATAATCTATTTTATATGAAAATATAAA-AAAATTG
* * * * ** * ** *
2649 AACTTAAAATCAATTTTGAGAATATAAAATTTTTTAAAACGAGTAGGAAGGCTTTTGAAAAAATA
1 AACTTAAAATCAATTTTAAAAATATAAAA-CTTTTAAAGCGAGTAATAAAGCTTTT-AAGGAATG
* * * * * * * * * * *
2714 GGTGATTATAAAT-GAGCATTTCTTACCAATAAATGTATTTTT-TTCATGTTTCTCAAGGTAAAT
64 GGTGACTATAAATGGAGTA-TACTTATCAATGAATCT-TTTTTCTTTAT-TTTTTTAAGGTAGAC
* * ** *
2777 AGTCAATTATAATCTGTTTTAAATGAAAATGCAAAAACAATTT
126 AGTCAATTATAATCTATTTTATATGAAAATATAAAAA-AATTG
* * * * * *********
2820 ATCTTCAAATCAATTTTGAGAATATAAAACTATTTAAAGCGAGTAATAAGGNNNNNNNNNNAATG
1 AACTTAAAATCAATTTTAAAAATATAAAACT-TTTAAAGCGAGTAATAAAG-CTTTTAAGGAATG
* * * * * * ** **
2885 GGTGACTATAAATGGACTTTTCTTATCAATGAATACCTTTTTCTTTACATTTCTCGAGACAGACA
64 GGTGACTATAAATGGAGTATACTTATCAATGAAT-CTTTTTTCTTTA-TTTTTTTAAGGTAGACA
* * * ** * ****
2950 TTCAATTATAATATGTTTTA-ACAAAAAATGTAAAAAANNNN
127 GTCAATTATAATCTATTTTATA-TGAAAATATAAAAAAATTG
****** * * * * * * ** *
2991 NNNNNNAAATCAATTATGAGATTATGAAACCTTTTAAAGCGAGTAATAAGGCTTTTAAAAAATAG
1 AACTTAAAATCAATTTTAAAAATAT-AAAACTTTTAAAGCGAGTAATAAAGCTTTTAAGGAATGG
* * * * * * * * *
3056 GTGACTACAAATAGATTTTTCTT-TGCAATAAATGCCTTTTTCTTTATGTTTCTTGAGGTAGACA
65 GTGACTATAAATGGAGTATACTTAT-CAATGAAT-CTTTTTTCTTTAT-TTTTTTAAGGTAGACA
* * * * *
3120 GTCAATTATAAGCTGTTTTACATGAAAATGTAAAAAAATTT
127 GTCAATTATAATCTATTTTATATGAAAATATAAAAAAATTG
********** * * *
3161 AACTTAANNNNNNNNNNAAAAATATAAAACCTTTTAAAGCGAGTAATAAAGCCTCTGAGGGAATG
1 AACTTAAAATCAATTTTAAAAATATAAAA-CTTTTAAAGCGAGTAATAAAG-CTTTTAAGGAATG
* ** * * * *
3226 GATGACTATAAATGGAGTATACTTGCCAATGAATGCTTTTTTCTTCATATTTCTTATGGTAGATA
64 GGTGACTATAAATGGAGTATACTTATCAATGAAT-CTTTTTTCTTTAT-TTTTTTAAGGTAGACA
* * *
3291 GTCAATTATAATCTGTTTTATACGAAAATGTAAAAAAAATTG
127 GTCAATTATAATCTATTTTATATGAAAATAT-AAAAAAATTG
* * * * * *
3333 AACTTAAAATTAATTTTGAGAATATAAAACATTTTAAAGCGAGGAGTAAAGCTTTTGAAGGAATA
1 AACTTAAAATCAATTTTAAAAATATAAAAC-TTTTAAAGCGAGTAATAAAGCTTTT-AAGGAATG
* * * * * ** *
3398 AGTGACTGTAAATGGA-TATTTCTTATCAATGAATATATTTTTCTTAATTTTTGTCGAGGAAGAC
64 GGTGACTATAAATGGAGTA-TACTTATCAATGAATCT-TTTTTCTTTATTTTT-TTAAGGTAGAC
* * * ** *
3462 ATTCAATTATAACCTGTTTTA-ACAAAAAATATAAAAAAATTT
126 AGTCAATTATAATCTATTTTATA-TGAAAATATAAAAAAATTG
3504 AACTTAAAATCAATT
1 AACTTAAAATCAATT
3519 ATGANNNNNN
Statistics
Matches: 1277, Mismatches: 393, Indels: 114
0.72 0.22 0.06
Matches are distributed among these distances:
169 19 0.01
170 222 0.17
171 540 0.42
172 487 0.38
173 9 0.01
ACGTcount: A:0.38, C:0.10, G:0.12, T:0.35
Consensus pattern (167 bp):
AACTTAAAATCAATTTTAAAAATATAAAACTTTTAAAGCGAGTAATAAAGCTTTTAAGGAATGGG
TGACTATAAATGGAGTATACTTATCAATGAATCTTTTTTCTTTATTTTTTTAAGGTAGACAGTCA
ATTATAATCTATTTTATATGAAAATATAAAAAAATTG
Found at i:4911 original size:173 final size:171
Alignment explanation
Indices: 4504--4923 Score: 518
Period size: 172 Copynumber: 2.4 Consensus size: 171
4494 NNNNNNNNNN
* ** * *
4504 AAAGCGAGTAATAAGGCTTTTAAAAGAATAAGTGACTATAAATGGACTTTTCTTTACAATAAATG
1 AAAGCGAGTAATAAGGCTTTTGAAAGAATGGGTGACTATAAATGGACATTT-TTTACAATGAATG
* * * * * *
4569 CCTTTTTCTTTATGTTTCTCAAGGTAGACAGTTAATTATATTCTGTTTTACATGAAAATGTAAAA
65 CCTTTTTCTTTATATTTCTCAAGGTAGACAATCAATTATAATCTATTTTACACGAAAATGTAAAA
* * *
4634 AAAATTTAACTTAACATCAATTTTAAAAATATAAAACCTTTT
130 AAAATTGAACTTAAAATCAATTTTAAAAATATAAAAACTTTT
* * * * ** **
4676 AAAGTGAGTAATAAAGGC-TTTGAGAGAATGGGTGATTATAAATGGAGTATAGTTGCCAATGAAT
1 AAAGCGAGTAAT-AAGGCTTTTGAAAGAATGGGTGACTATAAATGGA-CATTTTTTACAATGAAT
* *
4740 GCTTTTTTCTTTATATTTCTTAAGGTAGACAATCAATTATAATCTATTTTACACGAAAATGTAAA
64 GCCTTTTTCTTTATATTTCTCAAGGTAGACAATCAATTATAATCTATTTTACACGAAAATGT-AA
*
4805 AAAAAATTGAACTTAAAATCAATTTTAAGAATATAAAAACTTTT
128 AAAAAATTGAACTTAAAATCAATTTTAAAAATATAAAAACTTTT
* ** *
4849 AAAGCGAGTAGTAAGGCTTTTGAAAGAATGGGCAACTATAAATGGACATTTTTTATCAATGAATA
1 AAAGCGAGTAATAAGGCTTTTGAAAGAATGGGTGACTATAAATGGACATTTTTTA-CAATGAATG
*
4914 TCTTTTTCTT
65 CCTTTTTCTT
4924 CACGTTTGTA
Statistics
Matches: 204, Mismatches: 39, Indels: 9
0.81 0.15 0.04
Matches are distributed among these distances:
172 106 0.52
173 98 0.48
ACGTcount: A:0.40, C:0.10, G:0.14, T:0.36
Consensus pattern (171 bp):
AAAGCGAGTAATAAGGCTTTTGAAAGAATGGGTGACTATAAATGGACATTTTTTACAATGAATGC
CTTTTTCTTTATATTTCTCAAGGTAGACAATCAATTATAATCTATTTTACACGAAAATGTAAAAA
AAATTGAACTTAAAATCAATTTTAAAAATATAAAAACTTTT
Found at i:6731 original size:171 final size:170
Alignment explanation
Indices: 6407--7399 Score: 667
Period size: 172 Copynumber: 5.8 Consensus size: 170
6397 NNNNNNNNNN
* * * **
6407 GTGACTGTAAATGGACATTTCTTATCAATGAATAT-CTTTTTCTTCATTTTTCTCAAGACAGACA
1 GTGACTATAAATGGACTTTTCTTATCAATGAAT-TCCTTTTTCTTCATGTTTCTCAAGGTAGACA
* * * * **********
6471 TTCAATTTTAATCTCTTTGAACAAAAAATGTAAAAA-AATTCAACTTAAAATCAANNNNNNNNNN
65 TTCAATTATAATCTTTTTTAAC-TAAAATGTAAAAAGAATTCAACTTAAAATCAATTTTGAGAAT
* * *
6535 ATAAAACCTTTTAAAGCAAGTAATAAGGCTTTTCAAGGAATGG
129 ATAAAACCATTTAAAGC-AGTAATAAGGCTTTTGAAGGAATAG
* * * * * *
6578 GTAACTATAAATAGACTTTACTTGTTAATGAATTCC-TTTTCTTCATGTTTCTCATGGTAGACAT
1 GTGACTATAAATGGACTTTTCTTATCAATGAATTCCTTTTTCTTCATGTTTCTCAAGGTAGACAT
*
6642 TCAATTATAATCTTTTTTGACTAAAAT-TATACAAAGAATTCCAA-TTAAAATCGAA-TTTGAGA
66 TCAATTATAATCTTTTTTAACTAAAATGTA-A-AAAGAATT-CAACTTAAAATC-AATTTTGAGA
* * * * * *
6704 TTAGAACACCATTTAAAGCATGTAATAAGACTTTTAAATGAATAG
127 ATATAAAACCATTTAAAGCA-GTAATAAGGCTTTTGAAGGAATAG
* ********** * * * * *
6749 GTGACTATAAACGGACTTTTNNNNNNNNNNAATGCCTTTTTCTTTATGTTTCTTAAGGTATACAA
1 GTGACTATAAATGGACTTTTCTTATCAATGAATTCCTTTTTCTTCATGTTTCTCAAGGTAGACAT
* * * * *
6814 TCAATTATAATATGTTTTACACGAAAATGTAAAGAGAATTGAACTTAAAATCAATTTTGAGAATA
66 TCAATTATAATCTTTTTTA-ACTAAAATGTAAAAAGAATTCAACTTAAAATCAATTTTGAGAATA
* * *
6879 TAAAACCTTTTAAAGTGAGTAGTAAGGCTTTTGAAGGAATAG
130 TAAAACCATTTAAAG-CAGTAATAAGGCTTTTGAAGGAATAG
* * * * * *
6921 GTGACTATAAATGAACTTTTCTTATCAATAAATGT-GTTTTTCTTCACGTTTCTCGAGGTAGATA
1 GTGACTATAAATGGACTTTTCTTATCAATGAAT-TCCTTTTTCTTCATGTTTCTCAAGGTAGACA
* * * * * *
6985 GTCAATTATAATCTGTTCTAAATGAAAATGTAAAAAAAATTTAACTTAAAATCAATTTTGAGAAT
65 TTCAATTATAATCTTTTTTAACT-AAAATGTAAAAAGAATTCAACTTAAAATCAATTTTGAGAAT
** **
7050 ATAAAAGTATTTAAAGCGAGTAATAAGGCTTTTGAAAAAAT-G
129 ATAAAACCATTTAAAGC-AGTAATAAGGCTTTTGAAGGAATAG
* *
7092 AGTGACTATAACTGGACTTTTCTTATCAATGAATACCTTTTTCTTCATGTTTCTCAAGGTAGACA
1 -GTGACTATAAATGGACTTTTCTTATCAATGAATTCCTTTTTCTTCATGTTTCTCAAGGTAGACA
* * * ********** * *
7157 TTCAATTATAATATATTTTAACAAAAAATGT-AAAANNNNNNNNNNTAAAATCAATTATGAGATT
65 TTCAATTATAATCTTTTTTAAC-TAAAATGTAAAAAGAATTCAACTTAAAATCAATTTTGAGAAT
* * * * * * *
7221 ATGAAATCTTTTAAAGCGAGCAATAAGGCTTTTAAAAGAATAA
129 ATAAAACCATTTAAAGC-AGTAATAAGGCTTTTGAAGGAATAG
** ********** * * * *
7264 GTGACTATAAATGGACTTTTCTTGGCAATNNNNNNNNNNTTCTTTACGTTTCTCAAGGTCGACAA
1 GTGACTATAAATGGACTTTTCTTATCAATGAATTCCTTTTTCTTCATGTTTCTCAAGGTAGACAT
* * * * *
7329 TCAATTATAATCTGTTTT-ACATGAAAATGTAAAAA-ACTTTAACTTAAAATCAATTTTAAAAAT
66 TCAATTATAATCTTTTTTAAC-T-AAAATGTAAAAAGAATTCAACTTAAAATCAATTTTGAGAAT
7392 ATAAAACC
129 ATAAAACC
7400 T
Statistics
Matches: 629, Mismatches: 171, Indels: 44
0.75 0.20 0.05
Matches are distributed among these distances:
168 2 0.00
169 6 0.01
170 49 0.08
171 247 0.39
172 314 0.50
173 9 0.01
174 2 0.00
ACGTcount: A:0.38, C:0.11, G:0.12, T:0.35
Consensus pattern (170 bp):
GTGACTATAAATGGACTTTTCTTATCAATGAATTCCTTTTTCTTCATGTTTCTCAAGGTAGACAT
TCAATTATAATCTTTTTTAACTAAAATGTAAAAAGAATTCAACTTAAAATCAATTTTGAGAATAT
AAAACCATTTAAAGCAGTAATAAGGCTTTTGAAGGAATAG
Done.