Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018400066.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_3285.0, 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: 5856
ACGTcount: A:0.27, C:0.09, G:0.10, T:0.25
Warning! 1696 characters in sequence are not A, C, G, or T
Found at i:2170 original size:170 final size:172
Alignment explanation
Indices: 1988--2361 Score: 387
Period size: 170 Copynumber: 2.2 Consensus size: 172
1978 NNNNNNNNNN
* *
1988 AATTATGAGATTATAAAACCATTTAAAGTGAGTAGTAAAGCTTTTGAAGGAATGGGTGA-TGATA
1 AATTATGAGATTATAAAACCATTTAAAGTGAGTAATAAAGCTTTTAAAGGAATGGGTGACT-ATA
* * * * * * *
2052 AATGGACTTTTCTTACCAATAAATGATTTTT-CTTCACGTTTCTTGAAGTAAACATTTATTTATT
65 AATGAACTTTTCCTACCAACAAATCATTTTTCCTTCACGTTTCTTGAAGTAAACATTCAATTATC
* * * *
2116 GTCTGTTTTGA-CTAAAAATGT-AAAACAATTCAACTTAAAATC
130 GTCTGTTTTAATC-AAAAATGTAAAAAAAAATCAACCTAAAATC
* *********** * *
2158 AATTACGAGATTANNNNNNNNNNGAAAGCGAGTAATAAGGCTTTTAAAGGAATGGGTGACTATAA
1 AATTATGAGATTATAAAACCATTTAAAGTGAGTAATAAAGCTTTTAAAGGAATGGGTGACTATAA
* * * * **
2223 ATGAACTTTTCCTGCCAACAAATCCTTTTTCCTTCATGTTTCTTGAGGTGGACATTCAATTATCG
66 ATGAACTTTTCCTACCAACAAATCATTTTTCCTTCACGTTTCTTGAAGTAAACATTCAATTATCG
2288 TCTGTTTTAATCAAAAATGTAAAAAAAAAAATCAACCTAAAATC
131 TCTGTTTTAATCAAAAATGT--AAAAAAAAATCAACCTAAAATC
2332 AATTATGAGATTATAAAACCATTTAAAGTG
1 AATTATGAGATTATAAAACCATTTAAAGTG
2362 TGTANNNNNN
Statistics
Matches: 152, Mismatches: 46, Indels: 8
0.74 0.22 0.04
Matches are distributed among these distances:
170 71 0.47
171 45 0.30
172 1 0.01
174 35 0.23
ACGTcount: A:0.37, C:0.12, G:0.14, T:0.34
Consensus pattern (172 bp):
AATTATGAGATTATAAAACCATTTAAAGTGAGTAATAAAGCTTTTAAAGGAATGGGTGACTATAA
ATGAACTTTTCCTACCAACAAATCATTTTTCCTTCACGTTTCTTGAAGTAAACATTCAATTATCG
TCTGTTTTAATCAAAAATGTAAAAAAAAATCAACCTAAAATC
Found at i:3063 original size:171 final size:171
Alignment explanation
Indices: 2886--3556 Score: 434
Period size: 171 Copynumber: 3.9 Consensus size: 171
2876 TGAAGGGATG
* ** * * *
2886 AGTGACTATAAATGGACTTTTCTTGCTAATGGATGGCTT-TTTCTACACGTTTCTCAAGGGAGGC
1 AGTGACTATAAATGGACTTTTCTTGCTAATGAATCCCTTGTTCCT-CACATTTCTCAAGGGAGAC
* * * * *
2950 ATTCAATTATAGTCTGTTTCAATGAAGAATGTAAAAAAATTTAACTTAAAAACAATTATGAGGTT
65 ATTCAATTATAGTATGTTTCAATAAAAAATGTAAAAAAATTCAACTTAAAAACAATTATGAGATT
*
3015 ATAAAACCATTTA-ACGCGAGCAATAAGGCCATTGAAGA-AATA
130 ATAAAACCATTTATA-GCGAGCAATAAGG-CATTGAAAAGAATA
* * * ** *
3057 AGTGACTATAAATGAACTCTT-TTGCTAATGAATCCCTTGTTCCTCACATTTTTTGAGGTAGACA
1 AGTGACTATAAATGGACTTTTCTTGCTAATGAATCCCTTGTTCCTCACATTTCTCAAGGGAGACA
* ** ** * *
3121 TTCAATTATAGTATGTTTTAATAAAAAATGTAAAACCATTCAACTTAAAATTACTTATGAGATTC
66 TTCAATTATAGTATGTTTCAATAAAAAATGTAAAAAAATTCAACTTAAAAACAATTATGAGATTA
* * * *
3186 TAAAACCATTTATAGCGAGTAATAAGGCTTTTAAAAGAATG
131 TAAAACCATTTATAGCGAGCAATAAGGCATTGAAAAGAATA
* * * ********** * * ** * *
3227 GGTGACAATAAATGGACTTTTCTTGCCAATNNNNNNNNNNTTCTTCACGTTTCTTGAGGTAGATA
1 AGTGACTATAAATGGACTTTTCTTGCTAATGAATCCCTTGTTCCTCACATTTCTCAAGGGAGACA
* * * ** * * *
3292 TTCAATTATAGTTTATTTTAACGAAAATTATAAAAAAATTCAACTTAAAATCAATTATGAGATTA
66 TTCAATTATAGTATGTTTCAATAAAAAATGTAAAAAAATTCAACTTAAAAACAATTATGAGATTA
********** * * *
3357 TAAAACCNNNNNNNNNNAGTAATAAGGCTTTTG-AAAGAATG
131 TAAAACCATTTATAGCGAGCAATAAGGC-ATTGAAAAGAATA
* * * * * * * *
3398 AGTGACTATAAATAGACTTTTTTTTGTTAATGAATGCCTTTTTCATAACATTTCTCAAGGTAGAC
1 AGTGACTATAAATGGAC-TTTTCTTGCTAATGAATCCCTTGTTCCTCACATTTCTCAAGGGAGAC
* * * * * *** * *
3463 ATTCCATTATGGTCTCTTTTTAATAAAAAAATGTAAAAAAATTGGGCTTACAATCAATTATGAGA
65 ATTCAATTATAGTAT-GTTTCAAT-AAAAAATGTAAAAAAATTCAACTTAAAAACAATTATGAGA
* * *
3528 TTATAAAACCATTTAAATCGAGTAATAAG
128 TTATAAAACCATTTATAGCGAGCAATAAG
3557 ACTTTTGANN
Statistics
Matches: 378, Mismatches: 114, Indels: 13
0.75 0.23 0.03
Matches are distributed among these distances:
169 6 0.02
170 125 0.33
171 146 0.39
172 43 0.11
173 6 0.02
174 52 0.14
ACGTcount: A:0.37, C:0.12, G:0.14, T:0.34
Consensus pattern (171 bp):
AGTGACTATAAATGGACTTTTCTTGCTAATGAATCCCTTGTTCCTCACATTTCTCAAGGGAGACA
TTCAATTATAGTATGTTTCAATAAAAAATGTAAAAAAATTCAACTTAAAAACAATTATGAGATTA
TAAAACCATTTATAGCGAGCAATAAGGCATTGAAAAGAATA
Found at i:4669 original size:171 final size:171
Alignment explanation
Indices: 4371--5704 Score: 1255
Period size: 171 Copynumber: 7.8 Consensus size: 171
4361 NNNNNNNNNN
* * * * * *
4371 TCTTGCCAATGAAT-GCTTTTTCTTCACGTTTCTTGAGG-TAGACATTCAATTATACTCTATTTT
1 TCTTGCTAATGAATGGCTTTTT-TACATGTTTCTTAAGGCAAG-CATTCAATTATAGTCTATTTT
** * *
4434 AA--CCAAATGTGAAAAAATTCAACTTAAAATCAATTATCAGATTATAAAACCATTTAAAGCAAG
64 AATGAAAAATGTAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCAAG
*
4497 TAATAAGGCTTTTGAAGAG-ATGAGTGACTATAAATGGAGTTT
129 TAATAAGGCTTTTGAAGAGAATGAGTGACTATAAATGGACTTT
* ** * *
4539 TCTTGCTAATGGATGGCTTTTTTGACATGTTTCACAAGGGAAGCATTCAATTATAGTCTGTTTTA
1 TCTTGCTAATGAATGGCTTTTTT-ACATGTTTCTTAAGGCAAGCATTCAATTATAGTCTATTTTA
* * * * * *
4604 ATGAAGAATGCAAAAAAATTCAATTTAAAATCAATTATGAGTTTATAAAATCATTTAACGCAAGT
65 ATGAAAAATGTAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCAAGT
** * * *
4669 AATAAGGCCATTGAAG-GAATGGGTGATTATAAATAGACTTT
130 AATAAGGCTTTTGAAGAGAATGAGTGACTATAAATGGACTTT
* ** * * * *
4710 TTTTGCTAATGAATCCCTTGTTCTT-CAGGTTTCTTGAGGCAAACATTCAATTATAGTCTGTTTT
1 TCTTGCTAATGAATGGCTT-TT-TTACATGTTTCTTAAGGCAAGCATTCAATTATAGTCTATTTT
** * ** * * * *
4774 AACAAAAAATATAAAACCATTCAACTTAAAATTACTTATGAGATTCTAAAACCATTTAAAGCGAG
64 AATGAAAAATGTAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCAAG
* *
4839 TAATAAGGCTTTT-AAAAGAATGAGTGACTATAAATGGATTTT
129 TAATAAGGCTTTTGAAGAGAATGAGTGACTATAAATGGACTTT
* * * * *
4881 TCTTGCCAATGAAT-GCTTTTTTTTCATGTTTCTTAAGG-TAGATATTCAATTATAGTTTATTTT
1 TCTTGCTAATGAATGGC-TTTTTTACATGTTTCTTAAGGCAAG-CATTCAATTATAGTCTATTTT
* * *
4944 AATGAAAATTATAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCGAG
64 AATGAAAAATGTAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCAAG
**
5009 TAATAAGGCTTTTGAA-AGAATGAGTGACTATAAACAGACTTT
129 TAATAAGGCTTTTGAAGAGAATGAGTGACTATAAATGGACTTT
* * * * *
5051 TTTTG-TCAATGAATGCCTTTTTCATAACA--TTTCTTAAGG-TAGACATTCCATTATAGTCTCT
1 TCTTGCT-AATGAATGGCTTTTT--T-ACATGTTTCTTAAGGCAAG-CATTCAATTATAGTCTAT
* *** * *
5112 TTTAATAGAAAAAAGTAAAAAAATTGGGCTTACAATCAATTATAAGATTATAAAACCATTTAAAG
61 TTTAAT-GAAAAATGTAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAG
* * * *
5177 CGAGTAAAAAGGCTTTTGAAG-GAATGGGTGACTATAAATAGACTTT
125 CAAGTAATAAGGCTTTTGAAGAGAATGAGTGACTATAAATGGACTTT
* * * *
5223 TCTT-CTCAATGAATGGCTTTTTTTACACGTTTCTTAAGGCAAACATTCAATTATAATTTATTTT
1 TCTTGCT-AATGAATGGC-TTTTTTACATGTTTCTTAAGGCAAGCATTCAATTATAGTCTATTTT
* * *
5287 AATAAAAAATGT-AAAAAATTCAACTTAAAATCAATTATGAAATTATAAAATCATTTAAAGCAAG
64 AATGAAAAATGTAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCAAG
*
5351 TAATAAGGCTTTTGAA-AGAATCG-CTGACTATAAATGGACTTT
129 TAATAAGGCTTTTGAAGAGAAT-GAGTGACTATAAATGGACTTT
* * * * * * *
5393 CCTT-CTGAATGAATGGCTTTTTCTACATGTTT-TCCAAGGTAGGCATTTAGTTATAG-CGCATT
1 TCTTGCT-AATGAATGGCTTTTT-TACATGTTTCT-TAAGGCAAGCATTCAATTATAGTC-TATT
* * ********** *
5455 TTAATGAAAAATGTAAGAAAATTGAACTTAAAATCANNNNNNNNNNTATAAAACCATTTAAAGTA
62 TTAATGAAAAATGTAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCA
* * * *
5520 CGTAATAAGGCTTTTAAAG-GAAT-AGGTTACTATAAATGAACTTT
127 AGTAATAAGGCTTTTGAAGAGAATGA-GTGACTATAAATGGACTTT
** * * *
5564 TCTT-CTTAATGAATAACTTTTTATACATGTTTCCTGAGGCAAGCATTCAATTATAGTTTATTTT
1 TCTTGC-TAATGAATGGCTTTTT-TACATGTTTCTTAAGGCAAGCATTCAATTATAGTCTATTTT
* * * **
5628 AATGAAAAATGTGAAAAAATTTC-ACTTAAAATCAATTATTAGATTATAAAACCATTAAAAGTGA
64 AATGAAAAATGT-AAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCAA
5692 GTAATAAGGCTTT
128 GTAATAAGGCTTT
5705 NNNNNNNNNN
Statistics
Matches: 948, Mismatches: 180, Indels: 73
0.79 0.15 0.06
Matches are distributed among these distances:
168 13 0.01
169 47 0.05
170 284 0.30
171 447 0.47
172 147 0.16
173 10 0.01
ACGTcount: A:0.38, C:0.12, G:0.14, T:0.36
Consensus pattern (171 bp):
TCTTGCTAATGAATGGCTTTTTTACATGTTTCTTAAGGCAAGCATTCAATTATAGTCTATTTTAA
TGAAAAATGTAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCAAGTA
ATAAGGCTTTTGAAGAGAATGAGTGACTATAAATGGACTTT
Found at i:5308 original size:342 final size:342
Alignment explanation
Indices: 4377--5704 Score: 1398
Period size: 342 Copynumber: 3.9 Consensus size: 342
4367 NNNNTCTTGC
* * * * **
4377 CAATGAATG-CTTTTTCTTCACGTTTCTTGAGGTAGACATTCAATTATACTCTATTTT-A-ACCA
1 CAATGAATGCCTTTTTCTTCACATTTCTTAAGGTAGACATTCAATTATAGTCTCTTTTAATAAAA
* * * *
4439 AATGTGAAAAAATTCAACTTAAAATCAATTATCAGATTATAAAACCATTTAAAGCAAGTAATAAG
66 AAAGTAAAAAAATTCAACTTAAAATCAATTATAAGATTATAAAACCATTTAAAGCGAGTAATAAG
* * * *
4504 GCTTTTGAA-GAGATGAGTGACTATAAATGGAGTTTTCTTGCT-AATGGATGGCTTTTTTGACAT
131 GCTTTTAAAGGA-ATGAGTGACTATAAATGGACTTTTCTTGCTCAATGAATGGCTTTTTTTACAT
** * * * * * * *
4567 GTTTCACAAGGGAAGCATTCAATTATAGTCTGTTTTAATGAAGAATGCAAAAAAATTCAATTTAA
195 GTTTCTTAAGGCAAACATTCAATTATAGTTTATTTTAATGAAAAATGTAAAAAAATTCAACTTAA
* * * ** * *
4632 AATCAATTATGAGTTTATAAAATCATTTAACGCAAGTAATAAGGCCATTGAAGGAATGGGTGATT
260 AATCAATTATGAGATTATAAAACCATTTAAAGCAAGTAATAAGGCTTTTGAAAGAAT-GGTGACT
4697 ATAAATAGACTTTTTTTG-
324 ATAAATAGACTTTTTTTGT
* * ** * * * * *
4715 CTAATGAATCCCTTGTTCTTCAGGTTTCTTGAGGCAAACATTCAATTATAGTCTGTTTTAACAAA
1 C-AATGAATGCCTTTTTCTTCACATTTCTTAAGGTAGACATTCAATTATAGTCTCTTTTAATAAA
** * * * *
4780 AAATA-TAAAACCATTCAACTTAAAATTACTTATGAGATTCTAAAACCATTTAAAGCGAGTAATA
65 AAA-AGTAAAAAAATTCAACTTAAAATCAATTATAAGATTATAAAACCATTTAAAGCGAGTAATA
* * *
4844 AGGCTTTTAAAAGAATGAGTGACTATAAATGGATTTTTCTTGC-CAATGAAT-GCTTTTTTTTCA
129 AGGCTTTTAAAGGAATGAGTGACTATAAATGGACTTTTCTTGCTCAATGAATGGCTTTTTTTACA
* * * * *
4907 TGTTTCTTAAGGTAGATATTCAATTATAGTTTATTTTAATGAAAATTATAAAAAAATTCAACTTA
194 TGTTTCTTAAGGCAAACATTCAATTATAGTTTATTTTAATGAAAAATGTAAAAAAATTCAACTTA
*
4972 AAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAAGAATGAGTGAC
259 AAATCAATTATGAGATTATAAAACCATTTAAAGCAAGTAATAAGGCTTTTGAAAGAATG-GTGAC
*
5037 TATAAACAGACTTTTTTTGT
323 TATAAATAGACTTTTTTTGT
* * *
5057 CAATGAATGCCTTTTTCATAACATTTCTTAAGGTAGACATTCCATTATAGTCTCTTTTAATAGAA
1 CAATGAATGCCTTTTTCTTCACATTTCTTAAGGTAGACATTCAATTATAGTCTCTTTTAATA-AA
*** * *
5122 AAAAGTAAAAAAATTGGGCTTACAATCAATTATAAGATTATAAAACCATTTAAAGCGAGTAAAAA
65 AAAAGTAAAAAAATTCAACTTAAAATCAATTATAAGATTATAAAACCATTTAAAGCGAGTAATAA
* * * *
5187 GGCTTTTGAAGGAATGGGTGACTATAAATAGACTTTTCTT-CTCAATGAATGGCTTTTTTTACAC
130 GGCTTTTAAAGGAATGAGTGACTATAAATGGACTTTTCTTGCTCAATGAATGGCTTTTTTTACAT
* *
5251 GTTTCTTAAGGCAAACATTCAATTATAATTTATTTTAATAAAAAATGT-AAAAAATTCAACTTAA
195 GTTTCTTAAGGCAAACATTCAATTATAGTTTATTTTAATGAAAAATGTAAAAAAATTCAACTTAA
* * *
5315 AATCAATTATGAAATTATAAAATCATTTAAAGCAAGTAATAAGGCTTTTGAAAGAATCGCTGACT
260 AATCAATTATGAGATTATAAAACCATTTAAAGCAAGTAATAAGGCTTTTGAAAGAAT-GGTGACT
* ** *
5380 ATAAATGGACTTTCCTTCT
324 ATAAATAGACTTTTTTTGT
* * * * * *
5399 GAATGAATGGCTTTTTC-T-ACATGTT-TTCCAAGGTAGGCATTTAGTTATAG-CGCATTTTAAT
1 CAATGAATGCCTTTTTCTTCACAT-TTCTT--AAGGTAGACATTCAATTATAGTCTC-TTTTAAT
* * * * ********** *
5460 GAAAAATGTAAGAAAATTGAACTTAAAATCANNNNNNNNNNTATAAAACCATTTAAAG-TACGTA
62 AAAAAAAGTAAAAAAATTCAACTTAAAATCAATTATAAGATTATAAAACCATTTAAAGCGA-GTA
* * * ** *
5524 ATAAGGCTTTTAAAGGAAT-AGGTTACTATAAATGAACTTTTCTT-CTTAATGAATAACTTTTTA
126 ATAAGGCTTTTAAAGGAATGA-GTGACTATAAATGGACTTTTCTTGCTCAATGAATGGCTTTTTT
* * * *
5587 TACATGTTTCCTGAGGCAAGCATTCAATTATAGTTTATTTTAATGAAAAATGTGAAAAAATTTC-
190 TACATGTTTCTTAAGGCAAACATTCAATTATAGTTTATTTTAATGAAAAATGT-AAAAAAATTCA
* * **
5651 ACTTAAAATCAATTATTAGATTATAAAACCATTAAAAGTGAGTAATAAGGCTTT
254 ACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCAAGTAATAAGGCTTT
5705 NNNNNNNNNN
Statistics
Matches: 830, Mismatches: 138, Indels: 40
0.82 0.14 0.04
Matches are distributed among these distances:
338 1 0.00
339 7 0.01
340 50 0.06
341 336 0.40
342 373 0.45
343 63 0.08
ACGTcount: A:0.38, C:0.12, G:0.14, T:0.35
Consensus pattern (342 bp):
CAATGAATGCCTTTTTCTTCACATTTCTTAAGGTAGACATTCAATTATAGTCTCTTTTAATAAAA
AAAGTAAAAAAATTCAACTTAAAATCAATTATAAGATTATAAAACCATTTAAAGCGAGTAATAAG
GCTTTTAAAGGAATGAGTGACTATAAATGGACTTTTCTTGCTCAATGAATGGCTTTTTTTACATG
TTTCTTAAGGCAAACATTCAATTATAGTTTATTTTAATGAAAAATGTAAAAAAATTCAACTTAAA
ATCAATTATGAGATTATAAAACCATTTAAAGCAAGTAATAAGGCTTTTGAAAGAATGGTGACTAT
AAATAGACTTTTTTTGT
Done.