Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018402988.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_653.0, 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: 53153
ACGTcount: A:0.19, C:0.07, G:0.07, T:0.19
Warning! 26157 characters in sequence are not A, C, G, or T
Found at i:5394 original size:171 final size:170
Alignment explanation
Indices: 5091--5514 Score: 422
Period size: 171 Copynumber: 2.5 Consensus size: 170
5081 NNNTGAACCT
* * * * * * * * * *
5091 AAAATCAATTTTAAGATTAGAAATCCATTTAAAGAGAGTAATAAGGCCTTTGAAGGAATAGGAGA
1 AAAATCAATTATGAGATTATAAAACCATTTAAAGAAAGTAGTAAGGCTTTTAAAGGAATGGGTGA
* * *
5156 CTATAAATGAGCTTTTCTTGTCAATGAATGCTTTTTTCATCACGTTTCTCAAGGTAGACATTCAG
66 CTATAAATGA-CTTTTCATGTCAATGAATGCTTTTTTCATCACGTTTCTCAAGGTAAACAATCAG
5221 TTACAGCCTAGTTTAATCAAAAATATTAAAAAA-ATCAACTC
130 TTACAGCCT-GTTTAATCAAAAATATTAAAAAATATCAACTC
* ** *
5262 AAAATCAATTATGAGATTATAAAACTATTTAAAGCTAGTAGTAAGGGTTTTAAAGGAATGGGTGA
1 AAAATCAATTATGAGATTATAAAACCATTTAAAGAAAGTAGTAAGGCTTTTAAAGGAATGGGTGA
* * **
5327 CTATAAATAGACTTTTCATG-CTAATGAATTCTTTTTTCTTCACGTTTCTTGAGGTAAACAATCA
66 CTATAAAT-GACTTTTCATGTC-AATGAATGCTTTTTTCATCACGTTTCTCAAGGTAAACAATCA
* * * ********** * * *
5391 GTTATAGTCTGTTTTANNNNNNNNNNTAAAAAATTTTAACTT
129 GTTACAGCCTGTTTAATCAAAAATATTAAAAAATATCAACTC
* *
5433 AAAATTAATTATGAGATTATAAAACCATTTAAAGAAAGT-GATAAAGCTTTTAAAGGAATGGGTG
1 AAAATCAATTATGAGATTATAAAACCATTTAAAGAAAGTAG-TAAGGCTTTTAAAGGAATGGGTG
5497 ACTATAAATGGACTTTTC
65 ACTATAAAT-GACTTTTC
5515 TTGCCAANNN
Statistics
Matches: 206, Mismatches: 43, Indels: 8
0.80 0.17 0.03
Matches are distributed among these distances:
170 14 0.07
171 190 0.92
172 2 0.01
ACGTcount: A:0.38, C:0.11, G:0.15, T:0.34
Consensus pattern (170 bp):
AAAATCAATTATGAGATTATAAAACCATTTAAAGAAAGTAGTAAGGCTTTTAAAGGAATGGGTGA
CTATAAATGACTTTTCATGTCAATGAATGCTTTTTTCATCACGTTTCTCAAGGTAAACAATCAGT
TACAGCCTGTTTAATCAAAAATATTAAAAAATATCAACTC
Found at i:11962 original size:171 final size:171
Alignment explanation
Indices: 11839--12402 Score: 449
Period size: 171 Copynumber: 3.3 Consensus size: 171
11829 AGTTTGCTTT
* * * * * **
11839 AACCAAAAATATTAAAAAATTTAACTTAGAATCAATTATGAGATTATAAAGCCATTTAAAGCGTG
1 AACCAAAAATATAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACCAGTTAAAGCAAG
* * *
11904 TAATAAGCCTTTGAAAGGAATGGGTGACTATAAATGGACTTTTCTT-ACTAATGAATGCTTTTTT
66 TAATAAACCTTTGAAAGGAATGGGTGACTATAAATGGACTTTTCTTGA-GAATGAATACTTTTTT
*
11968 CCTCATGTTTCTTGAGGTAGACTTTCAGTTATAGACTGTTTG
130 CCTCACGTTTCTTGAGGTAGACTTTCAGTTATAGACTGTTTG
* * * *
12010 AATCAAAAATGTAAAAAAATTCAACTTAAAATCAATTGTGAGATTATAAAACTAGTTAAAGCAAG
1 AACCAAAAATATAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACCAGTTAAAGCAAG
* * *
12075 TAATAAACCTTTTAAAGGAATGTGTGACTATAAATTGACTTTTCTTGAGAATGAATACTTTTTTC
66 TAATAAACCTTTGAAAGGAATGGGTGACTATAAATGGACTTTTCTTGAGAATGAATACTTTTTTC
* ** * * *
12140 TTCACGTTTCTCAAGGTAGTCCTTCAATTATA-ATCTGTTTTG
131 CTCACGTTTCTTGAGGTAGACTTTCAGTTATAGA-CTG-TTTG
* * * * * * * * * * *
12182 -GCCAACAATGTAAAAGAACTTGAACCTAAAATCAATT-TTAGGATTAGAAATCCATTTCAAGCA
1 AACCAAAAATATAAAA-AAATTCAACTTAAAATCAATTATGA-GATTATAAAACCAGTTAAAGCA
* * * * ********* ** * *
12245 AGTAATAAGGCTTTTG-AAGGAATAGGAGNNNNNNNNNNGG-CTTTTCTTGCCAATTAATGCTTT
64 AGTAATAA-ACCTTTGAAAGGAATGGGTG-ACTATAAATGGACTTTTCTTGAGAATGAATACTTT
* * ** * * * *
12308 TTTCTTCACGTTTCTCGAGGTAGACAATCAATTGTAGTCTAATTT-
127 TTTCCTCACGTTTCTTGAGGTAGACTTTCAGTTATAGACT-GTTTG
* *
12353 AACCAAAAATATTAAAAAATACAACTTAAAATCAATTATGAGATTATAAA
1 AACCAAAAATATAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAA
12403 NNNNNNNNNN
Statistics
Matches: 309, Mismatches: 73, Indels: 22
0.76 0.18 0.05
Matches are distributed among these distances:
170 1 0.00
171 178 0.58
172 125 0.40
173 5 0.02
ACGTcount: A:0.37, C:0.13, G:0.14, T:0.34
Consensus pattern (171 bp):
AACCAAAAATATAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACCAGTTAAAGCAAG
TAATAAACCTTTGAAAGGAATGGGTGACTATAAATGGACTTTTCTTGAGAATGAATACTTTTTTC
CTCACGTTTCTTGAGGTAGACTTTCAGTTATAGACTGTTTG
Found at i:13470 original size:170 final size:171
Alignment explanation
Indices: 13006--13475 Score: 498
Period size: 172 Copynumber: 2.7 Consensus size: 171
12996 NNNNNNNNNN
* * ** *
13006 ATAATCTCATAATTGATTTTAAGTTGAATTTTTTAATATTTTTGGTTAAAGCAGTCTACAACTAA
1 ATAATCTCATAATTGATTTTAAGTTAAAGTTTTTAATATTTTTGGTTAAAGCAGAGTACAACTGA
* * * * *
13071 ATGTCTACCTTGAGAAACGTGAAGAAAAAACCATTCATTTGTAAGAAAAGCTCATTTATAGTCTC
66 ATGTCTACCTTGAGAAACGTGAAGAAAAAAGCATTCATTGGCAAGAAAAGCCCATTTATAGTCAC
* *********
13136 CTCTTCCTTCAAAAGCCTTATTACTCACTTTANNNNNNNNN
131 CTATTCCTTCAAAAGCCTTATTACTCACTTTAAACGGTTTT
* * * * * * * * * * *
13177 NTAATCAT-AAAATTGATTTTAGGTTCAAGTTTTTTTACATTATTGGTTAAAACAGAGAATAATT
1 ATAATC-TCATAATTGATTTTAAGTTAAAG-TTTTTAATATTTTTGGTTAAAGCAGAGTACAACT
* *
13241 GAATGTCTACCTTGAGAAACTTGAAGAAAAAAG-ATTTCATTGGCAAGAAAAGTCCATTTATAGT
64 GAATGTCTACCTTGAGAAACGTGAAGAAAAAAGCA-TTCATTGGCAAGAAAAGCCCATTTATAGT
* * * *
13305 CACCTATTTCTTTAAAAGCCTTATTGCTCGCTTTAAACGGTTTT
128 CACCTATTCCTTCAAAAGCCTTATTACTCACTTTAAACGGTTTT
**
13349 ATAATCTCATAATTGATTTTAAG-TAAAGTTTTTAATATTTTTTATTAAAGCAGAGTACAACTGA
1 ATAATCTCATAATTGATTTTAAGTTAAAGTTTTTAATATTTTTGGTTAAAGCAGAGTACAACTGA
* **
13413 TTGTCTACCTCAAGAAACGTGAAGAAAAAAGCATTCATTGGCAA-AAAAGGCCCATTTATAGTC
66 ATGTCTACCTTGAGAAACGTGAAGAAAAAAGCATTCATTGGCAAGAAAA-GCCCATTTATAGTC
13476 TNNNNNNNNN
Statistics
Matches: 239, Mismatches: 54, Indels: 13
0.78 0.18 0.04
Matches are distributed among these distances:
169 4 0.02
170 78 0.33
171 29 0.12
172 128 0.54
ACGTcount: A:0.35, C:0.14, G:0.13, T:0.36
Consensus pattern (171 bp):
ATAATCTCATAATTGATTTTAAGTTAAAGTTTTTAATATTTTTGGTTAAAGCAGAGTACAACTGA
ATGTCTACCTTGAGAAACGTGAAGAAAAAAGCATTCATTGGCAAGAAAAGCCCATTTATAGTCAC
CTATTCCTTCAAAAGCCTTATTACTCACTTTAAACGGTTTT
Found at i:20259 original size:171 final size:171
Alignment explanation
Indices: 19972--20360 Score: 453
Period size: 171 Copynumber: 2.3 Consensus size: 171
19962 NNNNNNNNNN
**
19972 GCAAGAAAAGTCCATTTATAGTCACCCATTCCTTTAAAAGGTTTATTACATGCTGTAAATAGTTT
1 GCAAGAAAAGTCCATTTATAGTCACCCATTCCTTTAAAAGCCTTATTACATGCTGTAAATAGTTT
* * * * * * *
20037 TATAATCTCAAAATTGATTTTCAGTTGATTTTTTTTACATTTTTGGTTAAAATAAACTACAACTG
66 TATAATATCAAAATTGATTTTAAGTTAAATTTTTTAACATTTTTAGTTAAAACAAACTACAACTG
* *
20102 AATGTCAACCTTGAA-AAACGTGAAGAAAAAAAC-TTTCATTG
131 AATGTCAACC-TAAAGAAACGTGAAGAAAAAAACATTT-ATTA
* * * * *
20143 GCAAGAAAAGCCCATTTATAGTC-CTCTATTCCTTCAAAAGCCTTATTACTTGCTTTAAAT-GAT
1 GCAAGAAAAGTCCATTTATAGTCAC-CCATTCCTTTAAAAGCCTTATTACATGCTGTAAATAG-T
** * * *
20206 TTTATAATATCATTATTGATTTTAAGTTAAATTTTTTAATATTTTTAGTTAAAACAGACTATAAC
64 TTTATAATATCAAAATTGATTTTAAGTTAAATTTTTTAACATTTTTAGTTAAAACAAACTACAAC
* * * **
20271 TGATTGTCTACCTAAAGAAAGGTGAAGAAAAAGGCATTTATTA
129 TGAATGTCAACCTAAAGAAACGTGAAGAAAAAAACATTTATTA
* * *
20314 CCAAGAAAAGTCCACTTATAGTCACCCATTCCTTTAAATGCCTTATT
1 GCAAGAAAAGTCCATTTATAGTCACCCATTCCTTTAAAAGCCTTATT
20361 NNNNNNNNNN
Statistics
Matches: 181, Mismatches: 32, Indels: 10
0.81 0.14 0.04
Matches are distributed among these distances:
170 5 0.03
171 172 0.95
172 4 0.02
ACGTcount: A:0.36, C:0.15, G:0.12, T:0.37
Consensus pattern (171 bp):
GCAAGAAAAGTCCATTTATAGTCACCCATTCCTTTAAAAGCCTTATTACATGCTGTAAATAGTTT
TATAATATCAAAATTGATTTTAAGTTAAATTTTTTAACATTTTTAGTTAAAACAAACTACAACTG
AATGTCAACCTAAAGAAACGTGAAGAAAAAAACATTTATTA
Found at i:23845 original size:21 final size:21
Alignment explanation
Indices: 23820--23860 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
23810 TAAATTATGA
23820 GAGTATAAAAG-CATTTAAAGC
1 GAGTA-AAAAGTCATTTAAAGC
*
23841 GAGTAATAAGTCATTTAAAG
1 GAGTAAAAAGTCATTTAAAG
23861 GAATGGGTGA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.46, C:0.07, G:0.20, T:0.27
Consensus pattern (21 bp):
GAGTAAAAAGTCATTTAAAGC
Found at i:40244 original size:173 final size:172
Alignment explanation
Indices: 39877--40208 Score: 486
Period size: 173 Copynumber: 1.9 Consensus size: 172
39867 CAAACACAAC
*
39877 TGAATGTCTACCCCGAGAAACATGTAGTAAAAAAGCATTCGTTGACAAGAAAAGTCCATTTATAG
1 TGAATGTCTACCCCGAGAAACATGTAGAAAAAAAGCATTCGTTGACAAGAAAAGTCCATTTATAG
39942 TCTCCTATTCCTTCAAAAGACCTATTACACGCTTTAAATAAATTTCTAACATTAAAATTGATTTT
66 TCTCCTATTCCTTCAAAAGACCTATTACACGCTTTAAATAAATTTCTAACATTAAAATTGATTTT
*********
40007 AGGTTCAAGTTTTTTTACATNNNNNNNNNNAATAGATTATAAT
131 AGGTTCAAGTTTTTTTACAT-TATTTTTTAAATAGATTATAAT
** * *
40050 TGAATGTCTACCTTGAGAAACATGTAGAAAAAAAGCATTCGTTGATAAGAAAAGTCCATTTTTAG
1 TGAATGTCTACCCCGAGAAACATGTAGAAAAAAAGCATTCGTTGACAAGAAAAGTCCATTTATAG
* *
40115 TCTCTTATTCCTTCAAAAG-CCTTATTACTCGCTTTAAATAAATTTCTAACATTAAAATTGATTT
66 TCTCCTATTCCTTCAAAAGACC-TATTACACGCTTTAAATAAATTTCTAACATTAAAATTGATTT
*
40179 TAGGTTTAAGTTTTTTTACATTATTTTTTA
130 TAGGTTCAAGTTTTTTTACATTATTTTTTA
40209 NNNNNNNNNN
Statistics
Matches: 141, Mismatches: 17, Indels: 3
0.88 0.11 0.02
Matches are distributed among these distances:
172 2 0.01
173 139 0.99
ACGTcount: A:0.35, C:0.14, G:0.11, T:0.37
Consensus pattern (172 bp):
TGAATGTCTACCCCGAGAAACATGTAGAAAAAAAGCATTCGTTGACAAGAAAAGTCCATTTATAG
TCTCCTATTCCTTCAAAAGACCTATTACACGCTTTAAATAAATTTCTAACATTAAAATTGATTTT
AGGTTCAAGTTTTTTTACATTATTTTTTAAATAGATTATAAT
Found at i:51101 original size:172 final size:172
Alignment explanation
Indices: 50583--51104 Score: 527
Period size: 172 Copynumber: 3.1 Consensus size: 172
50573 NNNNNNNNNN
* ** *
50583 AAGTAATAAACCTTTTAAAGGAATGGGTGACTATAAATGGACTTTTCTTGCCAAGGAATGCTTTT
1 AAGTAATAAACCTTTTAAAGGAATAGGACACTATAAATGGACTTTTCTTGCCAATGAATGCTTTT
* * * * *
50648 CTCGTCACATTTCTCAAGGTCA-ACCTTTAATTATAATCTGTTTTAAGCAACAATGTAAAAAAAC
66 CTCTTCACGTTTCTCAAGGT-ATACCTTCAATTATAATCTGTTTTAACCAACAATTTAAAAAAAC
*
50712 TTGAACCTAAAATCAATTTTAAG-TTAAGAAATCCATTTAAATC
130 TTGAACCTAAAATCAATTTTAAGATT-AGAAATCCATTTAAAGC
** ** * * *
50755 GTGTAATAAGGCTTTTCAAGGAATAGGACACTATAAATGGGCTTTTCCTGCCAATGAATGCTTTT
1 AAGTAATAAACCTTTTAAAGGAATAGGACACTATAAATGGACTTTTCTTGCCAATGAATGCTTTT
* ** * * * * * * *
50820 -T-TTCATGTTTCTTGAGAT-TGACATTCAGTTGTAGTCTATTTTAACCAAAAATGTT-AAAAAA
66 CTCTTCACGTTTCTCAAGGTAT-ACCTTCAATTATAATCTGTTTTAACCAACAAT-TTAAAAAAA
* * * * * *
50881 -TTCAACTTAAAAACAATTATAAGATTATAAAACCATTTAAAGC
129 CTTGAACCTAAAATCAATTTTAAGATTAGAAATCCATTTAAAGC
********** *
50924 AAGTAATAAACCTTTTAAAGGAANNNNNNNNNNTAAATGGACTTTTCTTGCAAATGAATGCTTTT
1 AAGTAATAAACCTTTTAAAGGAATAGGACACTATAAATGGACTTTTCTTGCCAATGAATGCTTTT
* *
50989 CTCTTCACGTTTCCCAAGGTATACCTTCAATTATAATCTGTTTTAATCAACAATTTAAAAAAACT
66 CTCTTCACGTTTCTCAAGGTATACCTTCAATTATAATCTGTTTTAACCAACAATTTAAAAAAACT
* *
51054 TGAACGTAAAATCAATTTTAAGATTGGAAATCCATTTAAAGC
131 TGAACCTAAAATCAATTTTAAGATTAGAAATCCATTTAAAGC
51096 AAGTAATAA
1 AAGTAATAA
51105 GGCTTTTGNN
Statistics
Matches: 271, Mismatches: 70, Indels: 18
0.75 0.19 0.05
Matches are distributed among these distances:
169 80 0.30
170 46 0.17
171 45 0.17
172 100 0.37
ACGTcount: A:0.37, C:0.14, G:0.12, T:0.34
Consensus pattern (172 bp):
AAGTAATAAACCTTTTAAAGGAATAGGACACTATAAATGGACTTTTCTTGCCAATGAATGCTTTT
CTCTTCACGTTTCTCAAGGTATACCTTCAATTATAATCTGTTTTAACCAACAATTTAAAAAAACT
TGAACCTAAAATCAATTTTAAGATTAGAAATCCATTTAAAGC
Done.