Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018398908.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_2189.0, 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: 7470
ACGTcount: A:0.28, C:0.09, G:0.10, T:0.25
Warning! 2057 characters in sequence are not A, C, G, or T
Found at i:4237 original size:171 final size:169
Alignment explanation
Indices: 3955--5042 Score: 630
Period size: 171 Copynumber: 6.4 Consensus size: 169
3945 CTTGTCATGT
* * * *
3955 TAATGAATGGCTTTTTCTTCATGTTTCCTGAAG-TAGACACTCAATTATAATATATTTTAACTAA
1 TAATGAATGGCCTTTTCTTCATGTTTCCT-AAGATAGACAATCAATTATAATCTATTTTAACCAA
* * * * *
4019 AAATATAAGAAAATTCAACCTAAAATTAATTTTGAGATTATAAAACCATTTAAAGTGAGTAATAA
65 AAATGTAA-AAAATTCAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAA
**
4084 GGCTTTTAAAGGAATGGACGAATATAAATAGACTTTTCTTAC
129 GGCTTTCGAAGGAATGGA-GAATATAAATAGACTTTTCTTAC
* ** * * *
4126 TAATAAATGGCCTTTTCTTCACATTTCCTAAGATTGACAATCAATTATAATCTGTTTTACCCAAA
1 TAATGAATGGCCTTTTCTTCATGTTTCCTAAGATAGACAATCAATTATAATCTATTTTAACCAAA
* * * *
4191 AATGTAAAATAATTCAACTTAAAATCAATTATAAGATTAAAAAACCATTTAAAGCAAGTAATAAA
66 AATGTAAAA-AATTCAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAG
* * *
4256 GCTTTCGAAGG-CTTGAGTAATTTATAAAT-GAACTTTTCATA-
130 GCTTTCGAAGGAATGGAG-AA--TATAAATAG-ACTTTTCTTAC
* * * * *
4297 TCAATTG-ATGG-CTTTTGCTTCATGTTT-CTCAAGGTAGAGATTCAATTACAA-CATATTTGAA
1 T-AA-TGAATGGCCTTTT-CTTCATGTTTCCT-AAGATAGACAATCAATTATAATC-TATTTTAA
* * * * * * * * **
4358 TCGAAAAA-GTAGGAAAATACAACTTAAAAGCAATTATGAGATTCTAAAATCACTTAAAGTGAAC
61 -CCAAAAATGTA-AAAAATTCAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCGAGT
* * * ** *
4422 AATAAGGCTTTCGAA-GACTTGGGTGACTATAAATAGGTTTTTCTTGC
124 AATAAGGCTTTCGAAGGA-AT-GGAGAATATAAATAGACTTTTCTTAC
* * * * * * * * *
4469 AAAGGAATGACTTTTTCATCATGTTTCATAGAGCA-A-ACATTTAATTATAATCTGTTTTAACCA
1 TAATGAATGGCCTTTTCTTCATGTTTCCTA-AG-ATAGACAATCAATTATAATCTATTTTAACCA
* *
4532 AAAATGTAAATGAATTCAACTTAAAATCAATTATGAGATTATAAAACTATTTAAAGCGAGTAATA
64 AAAATGTAAA-AAATTCAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATA
* * ** * * * * **
4597 AGGCTTTTGAAGGCATAAAAGACTACAATTGGACTTTTCTTGT
128 AGGCTTTCGAAGGAAT-GGAGAATATAAATAGACTTTTCTTAC
* * * ** * *
4640 TAATGAAT-GACTCTTTCTTCACGTTGACC-AAGGCAGCCAATCAATTATAATCTATTCTAACCA
1 TAATGAATGGCCT-TTTCTTCATGTT-TCCTAAGATAGACAATCAATTATAATCTATTTTAACCA
* *
4703 AAAATGTAAAAAGTTCAA-TGTAAAATGAATTATGAGATTATAAAACCA-TT--------T-A-A
64 AAAATGTAAAAAATTCAACT-TAAAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATA
* * * * *********
4756 A-GCTTT-GAAGGCATGGGTGACTATAAATGGACNNNNNNNNN
128 AGGCTTTCGAAGGAAT-GGAGAATATAAATAGACTTTTCTTAC
***** * * * * * ** **
4797 NNNNNAATGGCTTTTTCTTCACGTTTCCTAAGGTAGTCACTCAATTATAATCTATTTCGATAAAA
1 TAATGAATGGCCTTTTCTTCATGTTTCCTAAGATAGACAATCAATTATAATCTATTTTAACCAAA
* ** * *
4862 AATGTAAGAAAATTTAACCCAAAATCAATTATGAGATTATAAAACTATTTAAAGTGAGTAATAAG
66 AATGTAA-AAAATTCAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAG
* * * *
4927 GCTTTTGAAGGAATAGACGACTATAAATGGACTTTTCTTAC
130 GCTTTCGAAGGAATGGA-GAATATAAATAGACTTTTCTTAC
* ** * ** * * * * * *
4968 TAGTGAATAACCTTTTCTTTATGTTTTTTGAGGTAGACATTCAATTATAATCTGTATTAACTAAA
1 TAATGAATGGCCTTTTCTTCATGTTTCCTAAGATAGACAATCAATTATAATCTATTTTAACCAAA
5033 AATGTAAAAA
66 AATGTAAAAA
5043 NNNNNNNNNN
Statistics
Matches: 684, Mismatches: 183, Indels: 101
0.71 0.19 0.10
Matches are distributed among these distances:
156 2 0.00
157 70 0.10
158 39 0.06
159 4 0.01
160 1 0.00
161 1 0.00
167 1 0.00
168 1 0.00
169 6 0.01
170 63 0.09
171 365 0.53
172 118 0.17
173 11 0.02
174 2 0.00
ACGTcount: A:0.39, C:0.13, G:0.13, T:0.34
Consensus pattern (169 bp):
TAATGAATGGCCTTTTCTTCATGTTTCCTAAGATAGACAATCAATTATAATCTATTTTAACCAAA
AATGTAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGG
CTTTCGAAGGAATGGAGAATATAAATAGACTTTTCTTAC
Found at i:6089 original size:170 final size:168
Alignment explanation
Indices: 5636--6162 Score: 551
Period size: 170 Copynumber: 3.1 Consensus size: 168
5626 NNNNNNNNNN
* * * ** *
5636 ACTTAAAATCAATTATGAGATTCTAAAACCATTTAAGGTGAGTAATAAGGCTTTTGAACTAAT-A
1 ACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGACTGA
* * * *
5700 GGTAACTATAATTGGACTTTTTTTGTCAATGAATAGATTTTCCTTCACGTTTCCCAAGGTAAACA
66 -GTGACTATAAAT-GACTTTTTTTGTCAATGAAT-GGTTTT-CTTCACGTTTCTCAAGGTAAACA
* * * *
5765 TTCAAATATAATTTGTTTTAACTAAAAATATAAAAACAAATCA
127 TTCAATTATAATATGTTTTAACTAAAAATGT-AAAACAATTCA
* * * *
5808 AGTTAAGATCAATTATGAGATTATAAAACCATTTGAAGCGAATAATAAGGCTTTTGAAGG-CTTG
1 ACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAC-TG
* * * * * * *
5872 GGTGATTTTAAATGAGCTTTTCTT-ACAAATGAATGAGTTTTTCTTCACGTTTCTCTAGGAAAAC
65 AGTGACTATAAATGA-CTTTTTTTGTC-AATGAATG-G-TTTTCTTCACGTTTCTCAAGGTAAAC
*
5936 ATTGAATTATAATATGTTTTAACCT-AAAATGTAAAACAATTCA
126 ATTCAATTATAATATGTTTTAA-CTAAAAATGTAAAACAATTCA
* * * *
5979 ACCTAAAATCAA-CATGAGATTATAAAACCATTTAAAGCGAGTAATAAGACTTTCGAAGGACTGA
1 ACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGACTGA
* * * * *
6043 GTGACTATAAATGTACTTTTTTTGTCATTGAATGGCTTTGTCTTCACATTTCTCAAGGTAGATAG
66 GTGACTATAAATG-ACTTTTTTTGTCAATGAATGG-TTT-TCTTCACGTTTCTCAAGGTAAACAT
* * *
6108 CCAATTATAATCTGTTTTAACTAAAAATGTAAAACAATTTA
128 TCAATTATAATATGTTTTAACTAAAAATGTAAAACAATTCA
6149 ACTTAAAATCAATT
1 ACTTAAAATCAATT
6163 NNNNNNNNNN
Statistics
Matches: 289, Mismatches: 53, Indels: 27
0.78 0.14 0.07
Matches are distributed among these distances:
169 6 0.02
170 133 0.46
171 26 0.09
172 118 0.41
173 6 0.02
ACGTcount: A:0.39, C:0.13, G:0.13, T:0.35
Consensus pattern (168 bp):
ACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGACTGA
GTGACTATAAATGACTTTTTTTGTCAATGAATGGTTTTCTTCACGTTTCTCAAGGTAAACATTCA
ATTATAATATGTTTTAACTAAAAATGTAAAACAATTCA
Found at i:6544 original size:343 final size:340
Alignment explanation
Indices: 5636--6609 Score: 905
Period size: 343 Copynumber: 2.8 Consensus size: 340
5626 NNNNNNNNNN
* *
5636 ACTTAAAATCAATTATGAGATTCTAAAACCATTTAAGGTGAGTAATAAGGCTTTTGAACTAATAG
1 ACTTAAAATCAATTATGAGATTCTAAAACCATTTAAGGCGAGTAATAAGACTTTTGAACTAATAG
* * * * * *
5701 GTAACTATAATTGGACTTTTTTTGTCAATGAATAGATTTTCCTTCACGTTTCCCAAGGTAAACAT
66 GTGACTATAATTGGACTTTTTTTGTCAATGAATGGCTTTTCCTACATGTTT-TCAAGGTAAACAT
* *
5766 TCAAATATAATTTGTTTTAACTAAAAATATAAAAACAAATCAAGTTAAGATCAATTATGAGATTA
130 TCAAATATAATCTGTTTTAACTAAAAATGT-AAAACAAATCAAGTTAAGATCAATTATGAGATTA
* * *
5831 TAAAACCATTTGAAGCGAATAATAAGGCTTTTGAAGGCTTGGGTGATTTTAAATGAGCTTTTCTT
194 TAAAACCATTTAAAGCGAATAATAAGGCTTTTGAAGGCTTGGGTGACTATAAATGA-CTTTTCTT
* * *
5896 ACAAATGAATGAGTTTTTCTTCACGTTTCTCTAGGAAAACATTGAATTATAATATGTTTTAACCT
258 ACCAATGAATGGGTTTTTCTTCACGTTTCTCTAGGAAAACATTAAATTATAATATGTTTTAACCT
*
5961 AAAATGTAAAACAATTCA
323 AAAATGTAAAAAAATTCA
* * * * * ** *
5979 ACCTAAAATCAA-CATGAGATTATAAAACCATTTAAAGCGAGTAATAAGACTTTCGAAGGACT-G
1 ACTTAAAATCAATTATGAGATTCTAAAACCATTTAAGGCGAGTAATAAGACTTTTGAACTAATAG
* * * * * * *
6042 AGTGACTATAAATGTACTTTTTTTGTCATTGAATGGCTTTGTCTTCACAT-TTCTCAAGGTAGAT
66 -GTGACTATAATTGGACTTTTTTTGTCAATGAATGGCTTT-TCCT-ACATGTTTTCAAGGTAAAC
** * * * * * ********
6106 AGCCAATTATAATCTGTTTTAACTAAAAATGTAAAACAATTTAACTTAAAATCAATTNNNNNNNN
128 ATTCAAATATAATCTGTTTTAACTAAAAATGTAAAACAAATCAAGTTAAGATCAATTATGAGATT
************************ *
6171 NNNNNNNNNNNNNNNNNNNNNNNNAAGGCTTTCGAAGGCTTGGGTGACTATAAATGCACTTTTCT
193 ATAAAACCATTTAAAGCGAATAATAAGGCTTTTGAAGGCTTGGGTGACTATAAATG-ACTTTTCT
* * * * ****
6236 TACCAATGAATGGGTTTTTCTTCACTTTTGT-TGATGCAAACATTAAATTATAAT-TGGTTNNNN
257 TACCAATGAATGGGTTTTTCTTCACGTTTCTCT-AGGAAAACATTAAATTATAATAT-GTTTTAA
******
6299 NNNNNNATGTAAAAAACATTCA
320 CCTAAAATGTAAAAAA-ATTCA
* * * **
6321 ACTTAAAACCAATTATGAGATTCCAAAACCATTTAAGGCGCGTAATAATTCTTTTGAACTAATAG
1 ACTTAAAATCAATTATGAGATTCTAAAACCATTTAAGGCGAGTAATAAGACTTTTGAACTAATAG
* *
6386 GTGACTATAATTGGACTTTTTTTGTCAATGAATGGCTTTTCCTACGTGTTTTCTAAGCTAAACAT
66 GTGACTATAATTGGACTTTTTTTGTCAATGAATGGCTTTTCCTACATGTTTTC-AAGGTAAACAT
*
6451 TCAAATATAATCTGTTTTAACCAAAAATGTAAAACAAATCAAGTTAAGATCAATTATGAGATTAT
130 TCAAATATAATCTGTTTTAACTAAAAATGTAAAACAAATCAAGTTAAGATCAATTATGAGATTAT
* * *
6516 AAAACCATTTAAAGCGAATAATAAGGCTTTTAAAGGCTTAGGTGACTATAAATGGGCTTTTCTTA
195 AAAACCATTTAAAGCGAATAATAAGGCTTTTGAAGGCTTGGGTGACTATAAAT-GACTTTTCTTA
* * *
6581 TCAATGAATGGATTTTGCTTCACGTTTCT
259 CCAATGAATGGGTTTTTCTTCACGTTTCT
6610 NNNNNNNNNN
Statistics
Matches: 463, Mismatches: 156, Indels: 24
0.72 0.24 0.04
Matches are distributed among these distances:
340 2 0.00
341 118 0.25
342 132 0.29
343 207 0.45
344 4 0.01
ACGTcount: A:0.35, C:0.13, G:0.14, T:0.34
Consensus pattern (340 bp):
ACTTAAAATCAATTATGAGATTCTAAAACCATTTAAGGCGAGTAATAAGACTTTTGAACTAATAG
GTGACTATAATTGGACTTTTTTTGTCAATGAATGGCTTTTCCTACATGTTTTCAAGGTAAACATT
CAAATATAATCTGTTTTAACTAAAAATGTAAAACAAATCAAGTTAAGATCAATTATGAGATTATA
AAACCATTTAAAGCGAATAATAAGGCTTTTGAAGGCTTGGGTGACTATAAATGACTTTTCTTACC
AATGAATGGGTTTTTCTTCACGTTTCTCTAGGAAAACATTAAATTATAATATGTTTTAACCTAAA
ATGTAAAAAAATTCA
Found at i:6564 original size:171 final size:171
Alignment explanation
Indices: 5636--6603 Score: 584
Period size: 172 Copynumber: 5.6 Consensus size: 171
5626 NNNNNNNNNN
* * *
5636 ACTTAAAATCAATTATGAGATTCTAAAACCATTTAAGGTGAGTAATAAGGCTTTTGAA--CTAAT
1 ACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGCT--T
* * * * * * *
5699 AGGTAACTATAATTGGACTTTTTTTGTCAATGAATAGATTTTCCTTCAC-GTTTCCCAAGGTAAA
64 AGGTGACTATAAATGGACTTTTCTTGTCAATGAATGGATTTT-CTTCACATTTTTCTAAGGTAAA
* * *
5763 CATTCAAATATAATTTGTTTTAACTAAAAATATAAAAACAAATCA
128 CATTCAAATATAATCTGTTTTAACCAAAAATGT-AAAACAAATCA
* * * * *
5808 AGTTAAGATCAATTATGAGATTATAAAACCATTTGAAGCGAATAATAAGGCTTTTGAAGGCTTGG
1 ACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGCTTAG
* * * * * * *
5873 GTGATTTTAAAT-GAGCTTTTCTT-ACAAATGAATGAGTTTTTCTTCACGTTTCTCT-AGGAAAA
66 GTGACTATAAATGGA-CTTTTCTTGTC-AATGAATG-GATTTTCTTCACATTTTTCTAAGGTAAA
* * * * *
5935 CATTGAATTATAATATGTTTTAACCTAAAATGTAAAACAATTCA
128 CATTCAAATATAATCTGTTTTAACCAAAAATGTAAAACAAATCA
* * * * *
5979 ACCTAAAATCAA-CATGAGATTATAAAACCATTTAAAGCGAGTAATAAGACTTTCGAAGGACTGA
1 ACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGG-CTTA
* * * * * * *
6043 -GTGACTATAAATGTACTTTTTTTGTCATTGAATGGCTTTGTCTTCACATTTCTC-AAGGTAGAT
65 GGTGACTATAAATGGACTTTTCTTGTCAATGAATGGATTT-TCTTCACATTTTTCTAAGGTAAAC
** * * * *
6106 AGCCAATTATAATCTGTTTTAACTAAAAATGTAAAACAATTTA
129 ATTCAAATATAATCTGTTTTAACCAAAAATGTAAAACAAATCA
******************************** * *
6149 ACTTAAAATCAATTNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNAAGGCTTTCGAAGGCTTGG
1 ACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGCTTAG
* ** * * * *
6214 GTGACTATAAATGCACTTTTCTTACCAATGAATGGGTTTTTCTTCAC-TTTTGT-TGATGCAAAC
66 GTGACTATAAATGGACTTTTCTTGTCAATGAAT-GGATTTTCTTCACATTTT-TCTAAGGTAAAC
**********
6277 ATT-AAATTATAAT-TGGTTNNNNNNNNNNATGTAAAA-AACATTCA
129 ATTCAAA-TATAATCT-GTTTTAACCAAAAATGTAAAACAA-A-TCA
* ** * * **
6321 ACTTAAAACCAATTATGAGATTCCAAAACCATTTAAGGCGCGTAATAATTCTTTTGAA--CTAAT
1 ACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGCT--T
* * * * * *
6384 AGGTGACTATAATTGGACTTTTTTTGTCAATGAATGGCTTTTCCT-ACGTGTTTTCTAAGCTAAA
64 AGGTGACTATAAATGGACTTTTCTTGTCAATGAATGGATTTTCTTCACAT-TTTTCTAAGGTAAA
6448 CATTCAAATATAATCTGTTTTAACCAAAAATGTAAAACAAATCA
128 CATTCAAATATAATCTGTTTTAACCAAAAATGTAAAACAAATCA
* * * *
6492 AGTTAAGATCAATTATGAGATTATAAAACCATTTAAAGCGAATAATAAGGCTTTTAAAGGCTTAG
1 ACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGCTTAG
* *
6557 GTGACTATAAATGGGCTTTTCTTATCAATGAATGGATTTTGCTTCAC
66 GTGACTATAAATGGACTTTTCTTGTCAATGAATGGATTTT-CTTCAC
6604 GTTTCTNNNN
Statistics
Matches: 569, Mismatches: 195, Indels: 63
0.69 0.24 0.08
Matches are distributed among these distances:
169 4 0.01
170 145 0.25
171 195 0.34
172 205 0.36
173 18 0.03
174 2 0.00
ACGTcount: A:0.35, C:0.13, G:0.14, T:0.34
Consensus pattern (171 bp):
ACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGCTTAG
GTGACTATAAATGGACTTTTCTTGTCAATGAATGGATTTTCTTCACATTTTTCTAAGGTAAACAT
TCAAATATAATCTGTTTTAACCAAAAATGTAAAACAAATCA
Found at i:7338 original size:171 final size:171
Alignment explanation
Indices: 7029--7339 Score: 360
Period size: 171 Copynumber: 1.8 Consensus size: 171
7019 NNNNNGAGTG
* * * *
7029 ACTATAAATGGACTTTTCTTATCAATGAATGACTTTTTCTTCATGTTTTACAAGGTAGACATTTA
1 ACTATAAATGGACTTTTCTTAGCAATGAATGACTTTTTCTTCACGTTTTACAAGGTAAACATTCA
* * * *********
7094 ATTATAATTTGTTTTAATCAAAAAGGTAAAAAAATTCAACTTAAAATTAATTATGANNNNNNNNN
66 ATTACAATTCGTTTTAATCAAAAAGGTAAAAAAATTCAACTTAAAATCAATTATGAGATTACAAA
*
7159 NCCATTTAAAACGAGTAATAAGGCTTTTGAAAGAATAAGTA
131 ACCATTTAAAACGAGTAATAAGGCTTTTGAAAGAATAAGTA
*
7200 ACTATAAATTGACTTTTCTTAGCAATGAATAGA-TTTTTCTTCACGTTTCT-CAAGGTAAACATT
1 ACTATAAATGGACTTTTCTTAGCAATGAAT-GACTTTTTCTTCACGTTT-TACAAGGTAAACATT
* * *
7263 CAATTACAA-TCGATTTTAA-CAAAAAATGTCAAAGAATTCAACTTAAAATCAATTATGAGATTA
64 CAATTACAATTCG-TTTTAATC-AAAAAGGTAAAAAAATTCAACTTAAAATCAATTATGAGATTA
*
7326 CAAAATCATTTAAA
127 CAAAACCATTTAAA
7340 GNNNNNNNNN
Statistics
Matches: 114, Mismatches: 22, Indels: 8
0.79 0.15 0.06
Matches are distributed among these distances:
170 3 0.03
171 108 0.95
172 3 0.03
ACGTcount: A:0.40, C:0.12, G:0.10, T:0.35
Consensus pattern (171 bp):
ACTATAAATGGACTTTTCTTAGCAATGAATGACTTTTTCTTCACGTTTTACAAGGTAAACATTCA
ATTACAATTCGTTTTAATCAAAAAGGTAAAAAAATTCAACTTAAAATCAATTATGAGATTACAAA
ACCATTTAAAACGAGTAATAAGGCTTTTGAAAGAATAAGTA
Done.