Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018401379.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_451.0, 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: 4989
ACGTcount: A:0.29, C:0.12, G:0.09, T:0.31
Warning! 961 characters in sequence are not A, C, G, or T
Found at i:2624 original size:172 final size:170
Alignment explanation
Indices: 2105--2740 Score: 621
Period size: 172 Copynumber: 3.7 Consensus size: 170
2095 NNNNNNNNNN
* * * * *
2105 ATCTTATAATTAATTTTAAGTTGAA-TTTTTTACATTT-TTAGTTAAAACATATTACAATTGAAA
1 ATCTCATAATTGATTTTAAGTTGAATTTTTTTACATTTATT-GTTAAAACATACTATAATTGAAT
* * * * *
2168 GTCTACT-TTAAGAAACGTGAAGGGAAAGGTGTTCATTTGTAAGAAAGGTCCATTTATAGTCACC
65 GTCTACTCATAA-AAACGTGAA-GAAAAGCTATTCATTTGTAAGAAAAGTCCATTTATAGTCACC
* ** *
2232 CATTCGTTT-AAAATCCTTATTACGAGCTTCAAATGGTTTTATA
128 CATTC-TTTCAAAAGCCTTATTACTCGCTTCAAATTGTTTTATA
* ** * * * *
2275 AACTCATAATTCTTTTTAACTTGAATTTTTTTATATTT-TCTATTAAAACAGACTATAATTGAAT
1 ATCTCATAATTGATTTTAAGTTGAATTTTTTTACATTTAT-TGTTAAAACATACTATAATTGAAT
* * * * * *
2339 GTCTGTA-TCA-AAAAACATGTAGAAAAAGCCATTCATTGAGAAAAAAAAAGTCCATTTATAGTC
65 GTC--TACTCATAAAAACGTGAAG-AAAAGCTATTCATT-TG-TAAGAAAAGTCCATTTATAGTC
* *
2402 ACCCATT-TCTTCAAAAGCCTTATTACTCCCTTGAAATTGTTTTATA
125 ACCCATTCT-TTCAAAAGCCTTATTACTCGCTTCAAATTGTTTTATA
* *
2448 ATCTCATAATTGATTTTAAGTTCAATTTTTTTACATTTATGGTTAAAACATACTATAATTGAATG
1 ATCTCATAATTGATTTTAAGTTGAATTTTTTTACATTTATTGTTAAAACATACTATAATTGAATG
* * *
2513 TCTACCTCATAAAAACGTGAAGAAAAGCATATTCATTTGTAAGAAAAGTCTATTTATAGTTACCT
66 TCTA-CTCATAAAAACGTGAAGAAAAGC-TATTCATTTGTAAGAAAAGTCCATTTATAGTCACCC
* * *
2578 ATTCTTTCAAAAGCCTTATTATTCGCTTTAAATTGTTTTGTA
129 ATTCTTTCAAAAGCCTTATTACTCGCTTCAAATTGTTTTATA
* *
2620 ATCTCATAATTGATTTTAAGTT-ATAGTTTTTTACATTTATTGATAAAACATACTATAATTGAAT
1 ATCTCATAATTGATTTTAAGTTGA-ATTTTTTTACATTTATTGTTAAAACATACTATAATTGAAT
* * * * * *
2684 G-CATGC-CTTGAGAAACATGAAGAAAAAGCCATTCA-TTGAGAAGAAAAGTCCATTTAT
65 GTC-TACTCAT-AAAAACGTGAAG-AAAAGCTATTCATTTG-TAAGAAAAGTCCATTTAT
2741 NNNNNNNNNN
Statistics
Matches: 385, Mismatches: 60, Indels: 41
0.79 0.12 0.08
Matches are distributed among these distances:
170 26 0.07
171 87 0.23
172 131 0.34
173 123 0.32
174 18 0.05
ACGTcount: A:0.36, C:0.13, G:0.11, T:0.39
Consensus pattern (170 bp):
ATCTCATAATTGATTTTAAGTTGAATTTTTTTACATTTATTGTTAAAACATACTATAATTGAATG
TCTACTCATAAAAACGTGAAGAAAAGCTATTCATTTGTAAGAAAAGTCCATTTATAGTCACCCAT
TCTTTCAAAAGCCTTATTACTCGCTTCAAATTGTTTTATA
Found at i:3169 original size:170 final size:169
Alignment explanation
Indices: 2795--3542 Score: 563
Period size: 170 Copynumber: 4.4 Consensus size: 169
2785 NNNNNNNNNN
*
2795 TTTATAATCTCATAATTAATTTTAAGTTGAATTTTTTTACATTTTTGA-TCAAAACAGATTATAA
1 TTTATAATCTCATAATTAATTTTAAGTTGAATTTTTTTACATTTTTGACT-AAAACAGACTATAA
* * * * *** * * * *
2859 TTCAATGTTTAC-TTAGGGAAACGCAAAGAAAAACACATTCGTTGGTAAG-AAAGTTCCCTTTAT
65 TTGAATGTCTACATCA-AGAAACATGAA-AAAAAGACATTC-ATGGCAAGAAAAGTT-CATTTAT
* * * ** * *
2922 AGTCACCCAATCCTTCAAACGCCTTATTTTTAGCTTTAAATTGT
126 AGTCACCCATTCCTTCAAAAGTCTTATTACTCGCTTTAAATTAT
********** * * * *
2966 TTTATAATCTCANNNNNNNNNNTAAGCTGAATTTTTTTACATTTTTGGCTAAATCAGACTATGAT
1 TTTATAATCTCATAATTAATTTTAAGTTGAATTTTTTTACATTTTTGACTAAAACAGACTATAAT
** ** * * * *
3031 TGAATGTCTATGTTGAGAAACATGAACCAAAAGGCATTCATGGGAAAAAAAGTTCATTTATAGTC
66 TGAATGTCTACATCAAGAAACATGAA-AAAAAGACATTCATGGCAAGAAAAGTTCATTTATAGTC
* * * * *
3096 ACCCATTCATTTAAGAGTTTTATTGCTCGCTTTAAATTAT
130 ACCCATTCCTTCAAAAGTCTTATTACTCGCTTTAAATTAT
* * * * * * * * *
3136 TTTATAATCTCATAATTGATTTTGAGTTGAATTTTTGTGCTTTTTTCATTAAAATAGGCTATAAT
1 TTTATAATCTCATAATTAATTTTAAGTTGAATTTTTTTACATTTTTGACTAAAACAGACTATAAT
* * * * * ***
3201 TAAATGTATACCTCAAGAAACATGAAGAAAAAGACATTCATTGGTAAGAAAAGTCCATTTATNNN
66 TGAATGTCTACATCAAGAAACATGAA-AAAAAGACATTCA-TGGCAAGAAAAGTTCATTTATAGT
******* * **
3266 NNNNNNNTCCTTCAAAAGCCTTATTACTCGCTTTAAATGGT
129 CACCCATTCCTTCAAAAGTCTTATTACTCGCTTTAAATTAT
* *
3307 TTTATAATCTCATAATTAATATTAAGTTGAATTGTTTTACATTTTT-ACTTAAAACAGA-TAATA
1 TTTATAATCTCATAATTAATTTTAAGTTGAATTTTTTTACATTTTTGAC-TAAAACAGACT-ATA
* * * * *
3370 ATTGAATGTCTACATCAAGAAATATGAAGAAAATACATTCGTTGGCAAGAAAAG-TCTTTTTATA
64 ATTGAATGTCTACATCAAGAAACATGAAAAAAAGACATTC-ATGGCAAGAAAAGTTC-ATTTATA
* * *
3434 GTTACCCATTCCTTCAAAAGTCCTATTACTCGCTTTAAATTAG
127 GTCACCCATTCCTTCAAAAGTCTTATTACTCGCTTTAAATTAT
* ** *
3477 TTTATAATATCATAATTAATTTTAAGTTGAATTTTTTTACATTTTTGTTTAAAACAGACTACAAT
1 TTTATAATCTCATAATTAATTTTAAGTTGAATTTTTTTACATTTTTGACTAAAACAGACTATAAT
3542 T
66 T
3543 AAATACCTAC
Statistics
Matches: 432, Mismatches: 135, Indels: 21
0.73 0.23 0.04
Matches are distributed among these distances:
169 1 0.00
170 232 0.54
171 196 0.45
172 3 0.01
ACGTcount: A:0.34, C:0.13, G:0.11, T:0.39
Consensus pattern (169 bp):
TTTATAATCTCATAATTAATTTTAAGTTGAATTTTTTTACATTTTTGACTAAAACAGACTATAAT
TGAATGTCTACATCAAGAAACATGAAAAAAAGACATTCATGGCAAGAAAAGTTCATTTATAGTCA
CCCATTCCTTCAAAAGTCTTATTACTCGCTTTAAATTAT
Found at i:4508 original size:170 final size:171
Alignment explanation
Indices: 3707--4989 Score: 913
Period size: 171 Copynumber: 7.5 Consensus size: 171
3697 NNNNTTTCAC
* * * * *
3707 ATTTTTGGTTAAAATAGACTATAATTGAATGTCTACCTCGAGAAACATAATGAAAAAGCCATTCA
1 ATTTTTGGTTAAAACAGACTATAATTGAAAGTCTACTTCGAGAAACATAAAGAAAAAGGCATTCA
* *
3772 TATAG-AAGAAAAGTCCATTTATAGTCACCCATTCCTTTAAAAGCCTTATT-TTCGCTTTAAATT
66 T-TAGCAAGAAAAGTCCATTTATAGTCACCCATTCCTTCAAAAGCCTTATTACTCGCTTTAAATT
* * *
3835 ATTTTATAATCTCATCATTGATTTTAAGTTGAATTTTTTGAC
130 ATTTTATAATCTCATAATTGATTTTAAGTTGAATTTTTTTAT
* ** * * * * * * ** * *
3877 AATTTTACTTAAAACA-AATATAATTGAATGACT-GTCTCAAGAAACGTGTAGAAAAAGCCATTA
1 ATTTTTGGTTAAAACAGACTATAATTGAAAGTCTACT-TCGAGAAACATAAAGAAAAAGGCATTC
** * * * * *
3940 ATTAATAACAAAAAATCTATTTAAAGTCACCCATTCCTTCAAAAGCCTTATTACTCACTTTAAAT
65 ATTAGCAA-GAAAAGTCCATTTATAGTCACCCATTCCTTCAAAAGCCTTATTACTCGCTTTAAAT
**********
4005 TATTTTATNNNNNNNNNNTTGATTTTAAGTTGAATTTTTTTAT
129 TATTTTATAATCTCATAATTGATTTTAAGTTGAATTTTTTTAT
* * * ** * * *
4048 ATTTTTGGTTAAAA-AAACTATAATTCAATGTCTACTTTAAGAAACGTAAAG-AAAACGCATTCG
1 ATTTTTGGTTAAAACAGACTATAATTGAAAGTCTACTTCGAGAAACATAAAGAAAAAGGCATTCA
* * * * * * * * * * *
4111 TTGGTAAGAAAAGGCCCTTTATATTCACCTATTCCTTCGAAAGCCTT-TAACTTGTTTTAAATTG
66 TTAGCAAGAAAAGTCCATTTATAGTCACCCATTCCTTCAAAAGCCTTATTACTCGCTTTAAATTA
**********
4175 TTTTATAATCTNNNNNNNNNNTTTAAGTTGAATTTTTTTAT
131 TTTTATAATCTCATAATTGATTTTAAGTTGAATTTTTTTAT
* * * * * *
4216 A-TTGTGGCTAAAACAGACTATAATT-AAATGTCT-GTATAGAGAAACATGAAGAAAAACGCATT
1 ATTTTTGGTTAAAACAGACTATAATTGAAA-GTCTACT-TCGAGAAACATAAAGAAAAAGGCATT
* ********** *
4278 CGTT-GACAAGAAAAGTCNNNNNNNNNNCACCCATTCCTTCAAAAGCTTTATTACTCGCTTTAAA
64 CATTAG-CAAGAAAAGTCCATTTATAGTCACCCATTCCTTCAAAAGCCTTATTACTCGCTTTAAA
* * * *
4342 TTGTTCTATAATCTCATAAATGATTTTAAGTTGAATTTGTTTAT
128 TTATTTTATAATCTCATAATTGATTTTAAGTTGAATTTTTTTAT
*
4386 ATTTTTGGTTAAAACAGACTATAATTGAAAGTCTACTTCGAGAAACGTAAAGAAAAAGGCATTCA
1 ATTTTTGGTTAAAACAGACTATAATTGAAAGTCTACTTCGAGAAACATAAAGAAAAAGGCATTCA
* * * * * * * *
4451 TTAGCATGAAAAGTCCGTTTATAGTCACCTATT-CGTAAAAAACCTTATTATTCGCTTTAAATCA
66 TTAGCAAGAAAAGTCCATTTATAGTCACCCATTCCTTCAAAAGCCTTATTACTCGCTTTAAATTA
* *
4515 TTTTATAATCTCATAATTAATTTTAAATT---TTTTTTT-T
131 TTTTATAATCTCATAATTGATTTTAAGTTGAATTTTTTTAT
* * * * * *
4552 ATTTTTGGTTAAAACAGACTATAATT-AAATGTC--CATCTATAATCTCATAATAGGTTAAAATG
1 ATTTTTGGTTAAAACAGACTATAATTGAAA-GTCTACTTCGAGAA--ACATAA-A-G-AAAAAGG
* * * * * * *
4614 CATTCCTTTGGAAGAAACGTCCATTTATAATCACCCATTCCTTTAAAAGCCTTATTACTAGCTTT
60 CATTCATTAGCAAGAAAAGTCCATTTATAGTCACCCATTCCTTCAAAAGCCTTATTACTCGCTTT
* * * * *
4679 AAATTGTTTTATAATCTCATAATTTATTTTAGGTTGAATTGTTTTAC
125 AAATTATTTTATAATCTCATAATTGATTTTAAGTTGAATTTTTTTAT
* * * * * * *
4726 ATTTTTAGTTAAAACA-AATAATAATTGAATGTCTACATAGAGAAACATGAAGAAAAATGCATTC
1 ATTTTTGGTTAAAACAGACT-ATAATTGAAAGTCTACTTCGAGAAACATAAAGAAAAAGGCATTC
* *
4790 ATT-GACAAGAAAAGTCCCTTTAT-GTTCACCCATTCCTTCAAAAGCCCTATTACTCGCTTTAAA
65 ATTAG-CAAGAAAAGTCCATTTATAG-TCACCCATTCCTTCAAAAGCCTTATTACTCGCTTTAAA
***********
4853 TTATTTTATAATGNNNNNNNNNNTTTTAAGTTGAATTTTTTTAT
128 TTATTTTATAATCTCATAATTGATTTTAAGTTGAATTTTTTTAT
* * * * ** *
4897 ATTTTTGCTTAAAACAGACTACAATT-AAATGCCTACCTCGAGAAACATGTAGAAAAAGCCATTC
1 ATTTTTGGTTAAAACAGACTATAATTGAAA-GTCTACTTCGAGAAACATAAAGAAAAAGGCATTC
*
4961 ATATAG-AAGAAAAGTCTATTTATAGTCAC
65 AT-TAGCAAGAAAAGTCCATTTATAGTCAC
Statistics
Matches: 858, Mismatches: 217, Indels: 75
0.75 0.19 0.07
Matches are distributed among these distances:
164 6 0.01
165 3 0.00
166 34 0.04
167 20 0.02
168 73 0.09
169 149 0.17
170 210 0.24
171 306 0.36
172 11 0.01
173 10 0.01
174 28 0.03
175 2 0.00
176 6 0.01
ACGTcount: A:0.35, C:0.14, G:0.11, T:0.37
Consensus pattern (171 bp):
ATTTTTGGTTAAAACAGACTATAATTGAAAGTCTACTTCGAGAAACATAAAGAAAAAGGCATTCA
TTAGCAAGAAAAGTCCATTTATAGTCACCCATTCCTTCAAAAGCCTTATTACTCGCTTTAAATTA
TTTTATAATCTCATAATTGATTTTAAGTTGAATTTTTTTAT
Done.