Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018400764.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_3942.0, 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: 4486
ACGTcount: A:0.33, C:0.10, G:0.11, T:0.30
Warning! 692 characters in sequence are not A, C, G, or T
Found at i:1079 original size:170 final size:170
Alignment explanation
Indices: 857--1357 Score: 429
Period size: 170 Copynumber: 2.9 Consensus size: 170
847 TCAACTTCTT
* * * * *
857 TTACCAATGGATATCTTTTTCTTTACAT-TTCCT-GAGGCAGACATTTAATTATAATATATTTTA
1 TTACCAATGGATATC-TTTTC-TTA-ATGTTTCTCGAGGTAAACATTCAATTATAATATATTTCA
* * * **
920 ACAAAAAATAT-AACACAATTCAACTTAGAATCAATTATGAGATTATAAAAATATATAAAGCGTG
63 ACAAAAAATATAAAAAC-ATTCAACTTAAAATCAATTATGAGATTATAAAAACATATAAAGCAAG
* *
984 TAACAAGGCTTTCGAAGTCATGGGTGTCTATAAATGGAGTTTTC
127 TAACAAGGCTTTCGAAGGCATGGGTGTCTATAAATGGACTTTTC
* * *
1028 TTATCAATGGATATCTTTTCTTAATGTTTCTCGAGGTAAACATTCAATTATAATCTATTTCAATA
1 TTACCAATGGATATCTTTTCTTAATGTTTCTCGAGGTAAACATTCAATTATAATATATTTCAACA
* * * * *
1093 AAAAATGTAAAAACATTTAACTTAAAATCAATTATGAGATTATAAAAACATTTAGAGCAAGTAAT
66 AAAAATATAAAAACATTCAACTTAAAATCAATTATGAGATTATAAAAACATATAAAGCAAGTAAC
**********
1158 AAGGCTTTCGAAGGCANNNNNNNNNNTAAATGGACTTTTC
131 AAGGCTTTCGAAGGCATGGGTGTCTATAAATGGACTTTTC
* * * * ** * *
1198 TTGCCAATGGATATAATTTTCTTCATGTTTCTCAAGGTAAACATTCAATTATAACCTCTTTAAAT
1 TTACCAATGGATAT-CTTTTCTTAATGTTTCTCGAGGTAAACATTCAATTATAATATATTTCAA-
* ** * ** * ** *
1263 GAAAACCT-TAAAAAAAATTCAACCAAAAATCACA-TATGAGATGATAAAGCCATTTAAAGCAAG
64 CAAAAAATAT-AAAAACATTCAACTTAAAATCA-ATTATGAGATTATAAAAACATATAAAGCAAG
* *
1326 TAA-AATGGCTTTCGAAGGCATGAGTGACTATA
127 TAACAA-GGCTTTCGAAGGCATGGGTGTCTATA
1358 NNNNNNNNNN
Statistics
Matches: 263, Mismatches: 59, Indels: 15
0.78 0.18 0.04
Matches are distributed among these distances:
168 2 0.01
169 7 0.03
170 122 0.46
171 64 0.24
172 67 0.25
173 1 0.00
ACGTcount: A:0.39, C:0.13, G:0.13, T:0.33
Consensus pattern (170 bp):
TTACCAATGGATATCTTTTCTTAATGTTTCTCGAGGTAAACATTCAATTATAATATATTTCAACA
AAAAATATAAAAACATTCAACTTAAAATCAATTATGAGATTATAAAAACATATAAAGCAAGTAAC
AAGGCTTTCGAAGGCATGGGTGTCTATAAATGGACTTTTC
Found at i:2503 original size:172 final size:169
Alignment explanation
Indices: 2135--2886 Score: 564
Period size: 171 Copynumber: 4.4 Consensus size: 169
2125 NNNNNNNNNN
* * * *
2135 TTATGAGATTAT-AAAATCATTTAAAGCGAGTAATAAGGCTTTCGAAGGCATAGGAGACTATTAA
1 TTATGAGATTATAAAAAT-ATTTAAAGCGAGTAATAAGGCTTTCGAAGGAATGGGTGACTATAAA
* * * * *
2199 TGGACTTTTCTTGCCAATGCATATCTTTTTTTTCACGTAT-CTCG-TGCTAGACATTTAATTATA
65 TGGACTTTTCTTG-CAATGGATATCTTTTTCTTCACGTTTCCT-GATG-TAGACATTCAATTATT
* * * **********
2262 ATCTATTTTAATAAAAAATATAAAAAAANNNNNNNNNNAATCAA
127 ATCTGTTTTAA-CAAAAATGTAAAAAAATTAAACTTAAAATCAA
* ** * * * *
2306 TTATGAGATTATAAAATTATTTAAAGCTTGTAATAAGGCTTCCAAAGGTATGGGTAACTATAAAT
1 TTATGAGATTATAAAAATATTTAAAGCGAGTAATAAGGCTTTCGAAGGAATGGGTGACTATAAAT
* * *
2371 GGACTTTTCTTGTCAATGGATATCCTTTTT-TTCACGTTTCTTGATGTAAAACATTCATTTATTA
66 GGACTTTTCTTG-CAATGGATAT-CTTTTTCTTCACGTTTCCTGATGT-AGACATTCAATTATTA
*
2435 TCTGTTTTAACTAAAAATGTAAAAAAATTAAACTTAAAATCCA
128 TCTGTTTTAAC-AAAAATGTAAAAAAATTAAACTTAAAATCAA
* * * * *
2478 TTATGAGGTTATAAAAATATTTAAAGCGAGTAATAAGACTTTTGAAGGCATGTGTGACTATAAAT
1 TTATGAGATTATAAAAATATTTAAAGCGAGTAATAAGGCTTTCGAAGGAATGGGTGACTATAAAT
********* * *
2543 GGACTTNNNNNNNNNNTGAATATCTTTTTCTTCATGTTTCCT-ATGGTAGACATTCAATTATTAT
66 GGACTT-TTCTTGCAATGGATATCTTTTTCTTCACGTTTCCTGAT-GTAGACATTCAATTATTAT
* * *
2607 CTGTTTTAAACAACAATGTATAAAAATTTAACTTAAAATCAA
129 CTGTTTT-AACAAAAATGTAAAAAAATTAAACTTAAAATCAA
********** *
2649 TTATGAGATTATAAAACA-NNNNNNNNNNAGTAATAAGGCTTTCGAAGGAATGGGTGTCTATAAA
1 TTATGAGATTATAAAA-ATATTTAAAGCGAGTAATAAGGCTTTCGAAGGAATGGGTGACTATAAA
* * * *
2713 TAGACTTTTCTTGCAAATAGATATCTTTTTCTTCACGTTTCCTGAGGTAGACACTCAATTATTAT
65 TGGACTTTTCTTGC-AATGGATATCTTTTTCTTCACGTTTCCTGATGTAGACATTCAATTATTAT
**********
2778 CTGTTTTAACCAAAAATGTAAAAANNNNNNNNNNAAAATCAA
129 CTGTTTTAA-CAAAAATGTAAAAAAATTAAACTTAAAATCAA
* * * * * *
2820 TTATGAGATTAT-GAAATCAATTAAAGCGAGTAACAAGGCTTTCGAAAGCATGGGTGCCTATAAA
1 TTATGAGATTATAAAAAT-ATTTAAAGCGAGTAATAAGGCTTTCGAAGGAATGGGTGACTATAAA
2884 TGG
65 TGG
2887 TAGACATTCA
Statistics
Matches: 445, Mismatches: 120, Indels: 32
0.75 0.20 0.05
Matches are distributed among these distances:
169 1 0.00
170 4 0.01
171 304 0.68
172 136 0.31
ACGTcount: A:0.36, C:0.11, G:0.14, T:0.34
Consensus pattern (169 bp):
TTATGAGATTATAAAAATATTTAAAGCGAGTAATAAGGCTTTCGAAGGAATGGGTGACTATAAAT
GGACTTTTCTTGCAATGGATATCTTTTTCTTCACGTTTCCTGATGTAGACATTCAATTATTATCT
GTTTTAACAAAAATGTAAAAAAATTAAACTTAAAATCAA
Found at i:3841 original size:170 final size:171
Alignment explanation
Indices: 2885--4486 Score: 1029
Period size: 171 Copynumber: 9.4 Consensus size: 171
2875 GCCTATAAAT
* * *
2885 GGTAGACATTCAATTATAATCTG-TTT-ATAAGAAAATGTAAAAAAATTCAACTT-AAATCAATT
1 GGTAGACATTCAATTATAATATGTTTTAATAA-AAAATATAAAAAAATTTAACTTAAAATCAATT
* ********** * *
2947 ATGAGATTATAAAACCATTTANNNNNNNNNNTAAGGCTTTTGAAGGCATAGGTGACTATAAATGG
65 ATGAGATTATAAAAACATTTAAAGCGAGTAATAAGGCTTTCGAAGGCATGGGTGACTATAAATGG
* * *
3012 ACTTTTCTTGCCAATGGAGATCATTTTCTTCATATTTTCCAA
130 ACTTTTCTTGCCAATGGATATCTTTTTCTTCATGTTTTCCAA
* * * * *
3054 GGCAGACATTCAA--AT-A-AGGTTTTAATCATAAATATAAAAAAACTTAACTTAAAATCAATTA
1 GGTAGACATTCAATTATAATATGTTTTAATAAAAAATATAAAAAAATTTAACTTAAAATCAATTA
* * * ********** *
3115 TGAGATTATAAAAATATTTAGAGCGAGTAATAAGGCTTTCAAAGGCATGNNNNNNNNNNAATTGA
66 TGAGATTATAAAAACATTTAAAGCGAGTAATAAGGCTTTCGAAGGCATGGGTGACTATAAATGGA
* * * *
3180 CTTTTCTTACCAATGGATATCTTTTTCTTCCT-ATTTCCTGA
131 CTTTTCTTGCCAATGGATATCTTTTTCTTCATGTTTTCC-AA
* * * *
3221 GTTAGACATTCAATTATAATATGTTTT--TACAAAAATATAAAAAAAATAAACTTAGAATCAATT
1 GGTAGACATTCAATTATAATATGTTTTAATA-AAAAATATAAAAAAATTTAACTTAAAATCAATT
* ********** * * *
3284 ATGAGATTATAAAAATATTNNNNNNNNNNAATAAAGCTTTCGAAGGCATGAGTGACTATAAATAG
65 ATGAGATTATAAAAACATTTAAAGCGAGTAATAAGGCTTTCGAAGGCATGGGTGACTATAAATGG
* * * * **
3349 ACTTTTCGTGTCAATGGATATATTTTTCTTTATG-TTTCTTGA
130 ACTTTTCTTGCCAATGGATATCTTTTTCTTCATGTTTTC-CAA
* * * * * ********** *
3391 GCTAGACAAAT-AATTATAATCTATTTTAATAAAAAATATAAAAAAATTCAACNNNNNNNNNNTC
1 GGTAGAC-ATTCAATTATAATATGTTTTAATAAAAAATATAAAAAAATTTAACTTAAAATCAATT
* * * * * *
3455 ATGAGATTATAAAACCATTTAAAGAGAGTAACAAGGCTTTCGAAGGTATGGGTGACTAGAAATAG
65 ATGAGATTATAAAAACATTTAAAGCGAGTAATAAGGCTTTCGAAGGCATGGGTGACTATAAATGG
* * * * *
3520 ACTTTTCTTACTAATGGATATCTTTTTCCTCATGTGTTCCAT
130 ACTTTTCTTGCCAATGGATATCTTTTTCTTCATGTTTTCCAA
* * * *
3562 GGTAGACATTCAATTATAATATGCTTTAATAAAAAATGTAAAAAATTTTAACATAAAATCAATTA
1 GGTAGACATTCAATTATAATATGTTTTAATAAAAAATATAAAAAAATTTAACTTAAAATCAATTA
* *********
3627 TGAGATTATAAAACCATTTAAAGCGAGTNNNNNNNNNNTT-GAAGGCATGGGTGACTATAAATGG
66 TGAGATTATAAAAACATTTAAAGCGAGT-AATAAGGCTTTCGAAGGCATGGGTGACTATAAATGG
*
3691 AC-TTTCTTGCCAATGGATATCGTTTTCTTCATGTTTTCCAA
130 ACTTTTCTTGCCAATGGATATCTTTTTCTTCATGTTTTCCAA
* * * * * * ** * * * *
3732 AGCAAAAATTCAATTATTATTTGTTTTAACCAAAAATGTAAGAAAATTCAATTTAAAATCAATTA
1 GGTAGACATTCAATTATAATATGTTTTAATAAAAAATATAAAAAAATTTAACTTAAAATCAATTA
* * * *
3797 TGAGATTATAAAAATATTTAAAGCGAGTAACAAGGCTTTTGAAGGCATGGGTGACTATAAATTGA
66 TGAGATTATAAAAACATTTAAAGCGAGTAATAAGGCTTTCGAAGGCATGGGTGACTATAAATGGA
********** **
3862 CNNNNNNNNNNAATGGATATCTTTTTCTTCACATTTT-CAGA
131 CTTTTCTTGCCAATGGATATCTTTTTCTTCATGTTTTCCA-A
* * * * *
3903 GGTAGATATTTAATTATAATAT-TTTTTAT-AAAAATATAAAAGAAA-TCAACTTAGAATCAATT
1 GGTAGACATTCAATTATAATATGTTTTAATAAAAAATATAAAA-AAATTTAACTTAAAATCAATT
** * *** *
3965 ATGAGATTATAAAAACATTTAAAATGAGTAATAAAGCTTTCGAATATATGAGTGACTATAAATGG
65 ATGAGATTATAAAAACATTTAAAGCGAGTAATAAGGCTTTCGAAGGCATGGGTGACTATAAATGG
* * * * *
4030 ACTTTTGTT-CCAATTGATTTATTTTTCTTCATG-TTTCTCGA
130 ACTTTTCTTGCCAATGGATATCTTTTTCTTCATGTTTTC-CAA
********** * *
4071 GGTAGACATTCAATTANNNNNNNNNNTAATAAAAAAATATAAAAATATTTAACTTAAAATCAGTT
1 GGTAGACATTCAATTATAATATGTTTTAAT-AAAAAATATAAAAAAATTTAACTTAAAATCAATT
* * * * * *
4136 ACGAGATTAT-AAAACTATTTAAAGCTAGTAACAAGGCTTTCAAAGGCATGGGTGACTACAAATA
65 ATGAGATTATAAAAAC-ATTTAAAGCGAGTAATAAGGCTTTCGAAGGCATGGGTGACTATAAATG
* * ** *
4200 GACTTTTATTGCTAATGGATATCTTTTTCCTT-ATGTGCTCCAT
129 GACTTTTCTTGCCAATGGATATCTTTTT-CTTCATGTTTTCCAA
* * ** * * * *
4243 GGTAAACATTCAATTATAATCTCATTTGATAAAAAATGTAAAAAAATTTAACTTAAAATTATTTA
1 GGTAGACATTCAATTATAATATGTTTTAATAAAAAATATAAAAAAATTTAACTTAAAATCAATTA
* * * *********** *
4308 CGAGATTATAAAACCATTTAAAGCGAGTAGTAAANNNNNNNNNNGTATGGGTGACTATAAATGGA
66 TGAGATTATAAAAACATTTAAAGCGAGTAATAAGGCTTTCGAAGGCATGGGTGACTATAAATGGA
* * *
4373 C-TTTCTTGCCAATGGGTATCATTTTCTTCATGTTTCCCAA
131 CTTTTCTTGCCAATGGATATCTTTTTCTTCATGTTTTCCAA
** * ** * *
4413 GCCAGACATTCAATTATTACCTATTTTAACT-AAAAATGTAAAAAAATTTAACTTAAAATCAATT
1 GGTAGACATTCAATTATAATATGTTTTAA-TAAAAAATATAAAAAAATTTAACTTAAAATCAATT
*
4477 ATGCGATTAT
65 ATGAGATTAT
Statistics
Matches: 1069, Mismatches: 330, Indels: 67
0.73 0.23 0.05
Matches are distributed among these distances:
165 1 0.00
166 27 0.03
167 97 0.09
168 32 0.03
169 105 0.10
170 366 0.34
171 390 0.36
172 46 0.04
173 5 0.00
ACGTcount: A:0.38, C:0.11, G:0.12, T:0.34
Consensus pattern (171 bp):
GGTAGACATTCAATTATAATATGTTTTAATAAAAAATATAAAAAAATTTAACTTAAAATCAATTA
TGAGATTATAAAAACATTTAAAGCGAGTAATAAGGCTTTCGAAGGCATGGGTGACTATAAATGGA
CTTTTCTTGCCAATGGATATCTTTTTCTTCATGTTTTCCAA
Done.