Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018399351.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_2619.0, 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: 5860
ACGTcount: A:0.23, C:0.09, G:0.08, T:0.24
Warning! 2109 characters in sequence are not A, C, G, or T
Found at i:2410 original size:169 final size:170
Alignment explanation
Indices: 2235--2881 Score: 870
Period size: 172 Copynumber: 3.8 Consensus size: 170
2225 NNNNNNNNNN
* * * ** * * *
2235 AAGTCTATTTATAGTCACCCATTCCTTC-GAAATCCATATTACACACTTTCAAA-GGTTTTATAA
1 AAGTCTATTTATAGTAACCCATTCCTTCAG-AAGCCTTATTATTCA-TTTTAAATAGTTTTCTAA
* * * * * ** * * **
2298 TCTCAAAATTGATTTAAATTTGAA-TTCTGTCATTTT-TGGTTAAAACAGACTAGGATTGAATGT
64 TCTCAAAATTGATTTTAAGTTCAATTTTTTTGTTTTTCTGGTTAAAACATATTATAATTGAATGT
2361 CTACCATCAAAAACATGAAGAAAAAAGTATTCATTGGCAAGAA
129 CTACCAT-AAAAACATGAAGAAAAAAGTATTCATTGGCAAGAA
* *
2404 AAGTCTATTTATAGTAACGCATTGCTTCAGAAGCCTTATTATTCATTTTAAATAGTTTTCTAATC
1 AAGTCTATTTATAGTAACCCATTCCTTCAGAAGCCTTATTATTCATTTTAAATAGTTTTCTAATC
2469 TCAAAATTGATTTTAAGTTCAATTTTTTTTGTTTTTCTGGTTAAAACATATTATAATTGAATGTC
66 TCAAAATTGATTTTAAGTTCAA-TTTTTTTGTTTTTCTGGTTAAAACATATTATAATTGAATGTC
* * * * * * * *
2534 TACCCTAAGAAACATAAAGAAGAGAGCAGTAATTGGCAAGAT
130 TACCATAA-AAACATGAAGAAAAAAGTATTCATTGGCAAGAA
* * *
2576 AAGTCCATTTATAGTTATCCATTCCTTCAGAAGCCTTATTATTCATTTTAAATAGTTTTCTAATC
1 AAGTCTATTTATAGTAACCCATTCCTTCAGAAGCCTTATTATTCATTTTAAATAGTTTTCTAATC
2641 TCAAAATTGATTTTAAGTTCAATTTTTTTTGTTTTTCTGGTTAAAACATATTATAATTGAATGTC
66 TCAAAATTGATTTTAAGTTCAA-TTTTTTTGTTTTTCTGGTTAAAACATATTATAATTGAATGTC
* *
2706 TACTATGAGAAACATGAAGAAAAAAGTATTCATTGGCAAGAA
130 TACCAT-AAAAACATGAAGAAAAAAGTATTCATTGGCAAGAA
* *
2748 AAGTCTATTTATAGTAACGCATTGCTTCAGAAGCCTTATTATTCATTTTAAATAGTTTTCTAATC
1 AAGTCTATTTATAGTAACCCATTCCTTCAGAAGCCTTATTATTCATTTTAAATAGTTTTCTAATC
2813 TCAAAATTGATTTTAAGTTCAATTTTTTTTGTTTTTCTGGTTAAAACATATTATAATTGAATGTC
66 TCAAAATTGATTTTAAGTTCAA-TTTTTTTGTTTTTCTGGTTAAAACATATTATAATTGAATGTC
2878 TACC
130 TACC
2882 CNNNNNNNNN
Statistics
Matches: 421, Mismatches: 50, Indels: 11
0.87 0.10 0.02
Matches are distributed among these distances:
168 6 0.01
169 65 0.15
170 1 0.00
171 10 0.02
172 338 0.80
173 1 0.00
ACGTcount: A:0.35, C:0.13, G:0.12, T:0.40
Consensus pattern (170 bp):
AAGTCTATTTATAGTAACCCATTCCTTCAGAAGCCTTATTATTCATTTTAAATAGTTTTCTAATC
TCAAAATTGATTTTAAGTTCAATTTTTTTGTTTTTCTGGTTAAAACATATTATAATTGAATGTCT
ACCATAAAAACATGAAGAAAAAAGTATTCATTGGCAAGAA
Found at i:2526 original size:341 final size:342
Alignment explanation
Indices: 1987--2882 Score: 1020
Period size: 341 Copynumber: 2.6 Consensus size: 342
1977 NNNNNNNNNN
* *
1987 CATTTTTGGTTAAAACAGACTAGAATTGAATGTCTA-CATTAAGAAACAT-AACGGAAAAAGTAT
1 CATTTTTGGTTAAAACAGACTAGAATTGAATGTCTACCATCAA-AAACATGAA-GAAAAAAGTAT
* * ********** *
2050 TCATTGACAAGAAAAGTCCATTTATAGNNNNNNNNNNCTTCAAAAGCCTTATTACTTGC--TTTA
64 TCATTGGCAAGAAAAGTCTATTTATAGTAACGCATTGCTTCAGAAGCCTTATTA-TT-CATTTTA
* * * *** * * *
2113 AATAGTTTTGTCATGTTGTAATTGATTTTAAGTTGAATTGTTTTTTATATTTT-TAGTT-AAACA
127 AATAGTTTTCTAATCTCAAAATTGATTTTAAGTTCAATT-TTTTTTGT-TTTTCTGGTTAAAACA
* * * * * * * * **********
2176 GACTATAATTGAAAGTCTAGCTTGAGAAACATAAAGAAAA-AGGCATTCANNNNNNNNNNAAGTC
190 TATTATAATTGAATGTCTACCCTAAGAAACATAAAGAAAAGA-GCAGTAATTGGCAAGATAAGTC
* * *
2240 TATTTATAGTCACCCATTCCTTC-GAAATCCATATTACACACTTTCAAA-GGTTTTATAATCTCA
254 CATTTATAGTCACCCATTCCTTCAG-AAGCCATATTACACA-TTTCAAATAGTTTTATAATCTCA
* *
2303 AAATTGATTTAAATTTGAA-TTCTGT
317 AAATTGATTTAAAGTTCAATTTCTGT
*
2328 CATTTTTGGTTAAAACAGACTAGGATTGAATGTCTACCATCAAAAACATGAAGAAAAAAGTATTC
1 CATTTTTGGTTAAAACAGACTAGAATTGAATGTCTACCATCAAAAACATGAAGAAAAAAGTATTC
2393 ATTGGCAAGAAAAGTCTATTTATAGTAACGCATTGCTTCAGAAGCCTTATTATTCATTTTAAATA
66 ATTGGCAAGAAAAGTCTATTTATAGTAACGCATTGCTTCAGAAGCCTTATTATTCATTTTAAATA
2458 GTTTTCTAATCTCAAAATTGATTTTAAGTTCAATTTTTTTTGTTTTTCTGGTTAAAACATATTAT
131 GTTTTCTAATCTCAAAATTGATTTTAAGTTCAATTTTTTTTGTTTTTCTGGTTAAAACATATTAT
*
2523 AATTGAATGTCTACCCTAAGAAACATAAAGAAGAGAGCAGTAATTGGCAAGATAAGTCCATTTAT
196 AATTGAATGTCTACCCTAAGAAACATAAAGAAAAGAGCAGTAATTGGCAAGATAAGTCCATTTAT
* * * ** * *
2588 AGTTATCCATTCCTTCAGAAGCCTTATTATTCATTTTAAATAGTTTTCTAATCTCAAAATTGATT
261 AGTCACCCATTCCTTCAGAAGCCATATTACACATTTCAAATAGTTTTATAATCTCAAAATTGATT
* * *
2653 TTAAGTTCAATTTTTTTT
326 TAAAGTTCAA-TTTCTGT
** * * * * * *
2671 GTTTTTCTGGTTAAAACATATTATAATTGAATGTCTACTATGAGAAACATGAAGAAAAAAGTATT
1 CATTTT-TGGTTAAAACAGACTAGAATTGAATGTCTACCATCAAAAACATGAAGAAAAAAGTATT
2736 CATTGGCAAGAAAAGTCTATTTATAGTAACGCATTGCTTCAGAAGCCTTATTATTCATTTTAAAT
65 CATTGGCAAGAAAAGTCTATTTATAGTAACGCATTGCTTCAGAAGCCTTATTATTCATTTTAAAT
2801 AGTTTTCTAATCTCAAAATTGATTTTAAGTTCAATTTTTTTTGTTTTTCTGGTTAAAACATATTA
130 AGTTTTCTAATCTCAAAATTGATTTTAAGTTCAATTTTTTTTGTTTTTCTGGTTAAAACATATTA
2866 TAATTGAATGTCTACCC
195 TAATTGAATGTCTACCC
2883 NNNNNNNNNN
Statistics
Matches: 475, Mismatches: 68, Indels: 21
0.84 0.12 0.04
Matches are distributed among these distances:
339 5 0.01
340 19 0.04
341 236 0.50
342 9 0.02
343 8 0.02
344 198 0.42
ACGTcount: A:0.35, C:0.12, G:0.12, T:0.38
Consensus pattern (342 bp):
CATTTTTGGTTAAAACAGACTAGAATTGAATGTCTACCATCAAAAACATGAAGAAAAAAGTATTC
ATTGGCAAGAAAAGTCTATTTATAGTAACGCATTGCTTCAGAAGCCTTATTATTCATTTTAAATA
GTTTTCTAATCTCAAAATTGATTTTAAGTTCAATTTTTTTTGTTTTTCTGGTTAAAACATATTAT
AATTGAATGTCTACCCTAAGAAACATAAAGAAAAGAGCAGTAATTGGCAAGATAAGTCCATTTAT
AGTCACCCATTCCTTCAGAAGCCATATTACACATTTCAAATAGTTTTATAATCTCAAAATTGATT
TAAAGTTCAATTTCTGT
Found at i:2572 original size:172 final size:172
Alignment explanation
Indices: 2330--2881 Score: 912
Period size: 172 Copynumber: 3.2 Consensus size: 172
2320 AATTCTGTCA
* * **
2330 TTTT-TGGTTAAAACAGACTAGGATTGAATGTCTACCATCAA-AAACATGAAGAAAAAAGTATTC
1 TTTTCTGGTTAAAACATATTATAATTGAATGTCTACCAT-AAGAAACATGAAGAAAAAAGTATTC
2393 ATTGGCAAGAAAAGTCTATTTATAGTAACGCATTGCTTCAGAAGCCTTATTATTCATTTTAAATA
65 ATTGGCAAGAAAAGTCTATTTATAGTAACGCATTGCTTCAGAAGCCTTATTATTCATTTTAAATA
2458 GTTTTCTAATCTCAAAATTGATTTTAAGTTCAATTTTTTTTGT
130 GTTTTCTAATCTCAAAATTGATTTTAAGTTCAATTTTTTTTGT
* * * * * * *
2501 TTTTCTGGTTAAAACATATTATAATTGAATGTCTACCCTAAGAAACATAAAGAAGAGAGCAGTAA
1 TTTTCTGGTTAAAACATATTATAATTGAATGTCTACCATAAGAAACATGAAGAAAAAAGTATTCA
* * * *
2566 TTGGCAAGATAAGTCCATTTATAGTTATC-CATTCCTTCAGAAGCCTTATTATTCATTTTAAATA
66 TTGGCAAGAAAAGTCTATTTATAG-TAACGCATTGCTTCAGAAGCCTTATTATTCATTTTAAATA
2630 GTTTTCTAATCTCAAAATTGATTTTAAGTTCAATTTTTTTTGT
130 GTTTTCTAATCTCAAAATTGATTTTAAGTTCAATTTTTTTTGT
* *
2673 TTTTCTGGTTAAAACATATTATAATTGAATGTCTACTATGAGAAACATGAAGAAAAAAGTATTCA
1 TTTTCTGGTTAAAACATATTATAATTGAATGTCTACCATAAGAAACATGAAGAAAAAAGTATTCA
2738 TTGGCAAGAAAAGTCTATTTATAGTAACGCATTGCTTCAGAAGCCTTATTATTCATTTTAAATAG
66 TTGGCAAGAAAAGTCTATTTATAGTAACGCATTGCTTCAGAAGCCTTATTATTCATTTTAAATAG
2803 TTTTCTAATCTCAAAATTGATTTTAAGTTCAATTTTTTTTGT
131 TTTTCTAATCTCAAAATTGATTTTAAGTTCAATTTTTTTTGT
2845 TTTTCTGGTTAAAACATATTATAATTGAATGTCTACC
1 TTTTCTGGTTAAAACATATTATAATTGAATGTCTACC
2882 CNNNNNNNNN
Statistics
Matches: 348, Mismatches: 29, Indels: 7
0.91 0.08 0.02
Matches are distributed among these distances:
171 9 0.03
172 336 0.97
173 3 0.01
ACGTcount: A:0.35, C:0.12, G:0.13, T:0.40
Consensus pattern (172 bp):
TTTTCTGGTTAAAACATATTATAATTGAATGTCTACCATAAGAAACATGAAGAAAAAAGTATTCA
TTGGCAAGAAAAGTCTATTTATAGTAACGCATTGCTTCAGAAGCCTTATTATTCATTTTAAATAG
TTTTCTAATCTCAAAATTGATTTTAAGTTCAATTTTTTTTGT
Found at i:3531 original size:63 final size:63
Alignment explanation
Indices: 3453--3577 Score: 189
Period size: 63 Copynumber: 2.0 Consensus size: 63
3443 GTTTACCATG
* *
3453 AGAAACATGAAGAAAAAAGCATTCTTTGGCAAGAAAAGATC-ATTTATAGTCACCCATACCTTT
1 AGAAACATGAAGAAAAAAGCATTCATTGGCAAGAAAAG-TCTATTCATAGTCACCCATACCTTT
* * *
3516 AGAAACATGAAGAAAAAAGTATTCATTGGCAAGAAAAGTCTATTCGTAGTCACCCATTCCTT
1 AGAAACATGAAGAAAAAAGCATTCATTGGCAAGAAAAGTCTATTCATAGTCACCCATACCTT
3578 CAAGAGCATT
Statistics
Matches: 56, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
62 2 0.04
63 54 0.96
ACGTcount: A:0.42, C:0.18, G:0.15, T:0.26
Consensus pattern (63 bp):
AGAAACATGAAGAAAAAAGCATTCATTGGCAAGAAAAGTCTATTCATAGTCACCCATACCTTT
Done.