Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018400680.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_3865.0, 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: 4286
ACGTcount: A:0.31, C:0.10, G:0.11, T:0.31
Warning! 739 characters in sequence are not A, C, G, or T
Found at i:584 original size:172 final size:162
Alignment explanation
Indices: 184--651 Score: 349
Period size: 172 Copynumber: 2.8 Consensus size: 162
174 AGAAAAAAGC
* * * * *
184 CATTGATTGGGAAGAGAAGTCCATTTATAGTC-TCTCATTCCTTCAAAAGTC-TTATTACTCACT
1 CATTCATTGGTAAGAAAAGTCCATTTATAGTCATC-CATTCCTTCAAAAG-CATCATTACTCGCT
* * * *
247 TTAAA-AGGTTTTATAATCTCATAATTGATTTTAAGTTG-ATTTTT-TTACATTTTCATTAAAAC
64 TCAAATA-GTTTTATAATCTCATAATTAACTTTAAGTTGAATTTTTCTCACA-TTT--TT-----
** * * *
309 ATATTATAATTGAATGTCTACCTTGAGAAACATGAAGATAAAAA
120 -GGTTAAAATTGAATGTCTACCTCGAGAAACATGAAGAGAAAAA
* * * *
353 GATTCATTGGTAAGAAAAGTCCATTTATTGTCATTCATTCCTTCAAAAGCCTCATTACTCGCTTC
1 CATTCATTGGTAAGAAAAGTCCATTTATAGTCATCCATTCCTTCAAAAGCATCATTACTCGCTTC
* *
418 AAATAGTTTTATAATCTCATAATTAATTTTCAGTTGAATTTTT-TCACATTTTTGGTTAANNNNN
66 AAATAGTTTTATAATCTCATAATTAACTTTAAGTTGAATTTTTCTCACATTTTTGGTTAA-----
* * *
482 NNNNNAATTGAATGTCTACCTCGAGAAAACGTGAATAGAAAGA
126 -----AATTGAATGTCTACCTCGAG-AAACATGAAGAGAAAAA
* * * * * *
525 CATTCATT-TTCAAGAAAAGTCCATTTATAGTCA-CCAATTCTTTTAAAAGTATTATTACTCTCT
1 CATTCATTGGT-AAGAAAAGTCCATTTATAGTCATCC-ATTCCTTCAAAAGCATCATTACTCGCT
* * * * *
588 TTAAATGGTTTTATAATCTCATAATTAACTTTAAGTTGACTTTTTCTTATATTTTTGGTTAAAA
64 TCAAATAGTTTTATAATCTCATAATTAACTTTAAGTTGAATTTTTCTCACATTTTTGGTTAAAA
652 CAGATTATAA
Statistics
Matches: 244, Mismatches: 37, Indels: 42
0.76 0.11 0.13
Matches are distributed among these distances:
161 3 0.01
163 2 0.01
167 2 0.01
168 1 0.00
169 87 0.36
170 12 0.05
171 21 0.09
172 102 0.42
173 14 0.06
ACGTcount: A:0.33, C:0.14, G:0.11, T:0.40
Consensus pattern (162 bp):
CATTCATTGGTAAGAAAAGTCCATTTATAGTCATCCATTCCTTCAAAAGCATCATTACTCGCTTC
AAATAGTTTTATAATCTCATAATTAACTTTAAGTTGAATTTTTCTCACATTTTTGGTTAAAATTG
AATGTCTACCTCGAGAAACATGAAGAGAAAAA
Found at i:686 original size:172 final size:169
Alignment explanation
Indices: 1--756 Score: 644
Period size: 171 Copynumber: 4.4 Consensus size: 169
* * * * * * * *
1 TGAAGAAAAAGACTTTCATTGGTATGAAAAGTCCATTTATAGTCGTCAATTTCTTTAAAAGCCTG
1 TGAAGAAAAAGACATTCATTGGTAAGAAAAGTCCATTTATAGTC-ACCATTCCTTCAAAAGTCTT
** * * * * *
66 ATTACTCTTTTTAAATGCTTTTATAAACTAATAA-TAGATTTTATGTTAATTTTTTTTACATTTT
65 ATTACTCACTTTAAATGGTTTTATAATCTCATAATTA-ATTTTAAGTTGA-TTTTTTTACATTTT
** * ** ** * * *
130 T-CATAAAACAG-TCTTTAATTGAATACCTGTCTCGATAAATG
128 TGGTTAAAACAGAT-TATAATTGAATGTCTACCTTGAGAAACG
* * * * * *
171 TGTAGAAAAAAGCCATTGATTGGGAAGAGAAGTCCATTTATAGTCTCTCATTCCTTCAAAAGTCT
1 TGAAG-AAAAAGACATTCATTGGTAAGAAAAGTCCATTTATAGTCAC-CATTCCTTCAAAAGTCT
* *
236 TATTACTCACTTTAAAAGGTTTTATAATCTCATAATTGATTTTAAGTTGATTTTTTTACA-TTTT
64 TATTACTCACTTTAAATGGTTTTATAATCTCATAATTAATTTTAAGTTGATTTTTTTACATTTTT
** * *
300 CATTAAAACATATTATAATTGAATGTCTACCTTGAGAAACA
129 GGTTAAAACAGATTATAATTGAATGTCTACCTTGAGAAACG
* * * *
341 TGAAGATAAAA-AGATTCATTGGTAAGAAAAGTCCATTTATTGTCATTCATTCCTTCAAAAGCCT
1 TGAAGA-AAAAGACATTCATTGGTAAGAAAAGTCCATTTATAGTCA-CCATTCCTTCAAAAGTCT
* * * * * *
405 CATTACTCGCTTCAAATAGTTTTATAATCTCATAATTAATTTTCAGTTGAATTTTTTCACATTTT
64 TATTACTCACTTTAAATGGTTTTATAATCTCATAATTAATTTTAAGTTG-ATTTTTTTACATTTT
********** *
470 TGGTTAANNNNNNNNNNAATTGAATGTCTACCTCGAGAAAACG
128 TGGTTAAAACAGATTATAATTGAATGTCTACCTTGAG-AAACG
* * * * * *
513 TGAATAGAAAGACATTCATT-TTCAAGAAAAGTCCATTTATAGTCACCAATTCTTTTAAAAGTAT
1 TGAAGAAAAAGACATTCATTGGT-AAGAAAAGTCCATTTATAGTCACC-ATTCCTTCAAAAGTCT
* * *
577 TATTACTCTCTTTAAATGGTTTTATAATCTCATAATTAACTTTAAGTTGACTTTTTCTTATATTT
64 TATTACTCACTTTAAATGGTTTTATAATCTCATAATTAATTTTAAGTTGA-TTTTT-TTACATTT
* *
642 TTGGTTAAAACAGATTATAATTGAATGTCCACCTTAAGAAACG
127 TTGGTTAAAACAGATTATAATTGAATGTCTACCTTGAGAAACG
* * * *
685 TGAAGAAAAAGACATTTAATTGGTATA-AAAAGTCTATTTATAGTTACTCATTCCTTCAAAAGCC
1 TGAAGAAAAAGACA-TTCATTGGTA-AGAAAAGTCCATTTATAGTCAC-CATTCCTTCAAAAGTC
*
749 TGATTACT
63 TTATTACT
757 NNNNNNNNNN
Statistics
Matches: 460, Mismatches: 107, Indels: 35
0.76 0.18 0.06
Matches are distributed among these distances:
169 90 0.20
170 60 0.13
171 118 0.26
172 116 0.25
173 73 0.16
174 3 0.01
ACGTcount: A:0.35, C:0.13, G:0.12, T:0.39
Consensus pattern (169 bp):
TGAAGAAAAAGACATTCATTGGTAAGAAAAGTCCATTTATAGTCACCATTCCTTCAAAAGTCTTA
TTACTCACTTTAAATGGTTTTATAATCTCATAATTAATTTTAAGTTGATTTTTTTACATTTTTGG
TTAAAACAGATTATAATTGAATGTCTACCTTGAGAAACG
Found at i:2501 original size:172 final size:169
Alignment explanation
Indices: 2321--2792 Score: 517
Period size: 172 Copynumber: 2.8 Consensus size: 169
2311 NNNNNNNNNA
* * * *
2321 ACTATAAATAGACTTTT-TATACCAATGAAAGTCTTTTTCTTTACGTTTCTTAAGGT-GAACATT
1 ACTATAAATAGACTTTTCT-TACCAATGAATGTCTTTATCTTCACGTTTCTCAAGGTAG-ACATT
* *
2384 CAATTATAATCTGTTGTAACCAAAAATGTATGAAAAAGTCAACTTAAAGTTAATTATGAGATTAT
64 CAATTATAATCTGTTTTAA-AAAAAATGTATGAAAAA-TCAACTTAAA-TTAATTATGAGATTAT
* * * * *
2449 AAAACCATTTAAAGAGAGTAGTAATGCTTTTAAAAGAATTGGTG
126 AAAACCATTTAAAGAGAGTAATAAGGCTTCTAAAAGAATAGATG
* * * * * *
2493 ACTATAAATAGACTTTTCTTGA-AAATGAATGCCTTTCTATTCACATTTTCTCGAGGTAGACATT
1 ACTATAAATAGACTTTTCTT-ACCAATGAATGTCTTTATCTTCAC-GTTTCTCAAGGTAGACATT
2557 CAATTATAATCTGTTTTAATAAAAAATG--TGAACAAATTCAACTGTAAATTAATTATGAGATTA
64 CAATTATAATCTGTTTTAA-AAAAAATGTATGAA-AAA-TCAACT-TAAATTAATTATGAGATTA
* * * *
2620 TAAAACCATTTGAAGCGAGTAATAAGGCTTCTGAAGGAATAGATG
125 TAAAACCATTTAAAGAGAGTAATAAGGCTTCTAAAAGAATAGATG
* * * *
2665 ACAATAAATGGACTTTTCTTACCAATGAATCTCTTTATCTTCATGTTTCTCAAGGTAGACATTCA
1 ACTATAAATAGACTTTTCTTACCAATGAATGTCTTTATCTTCACGTTTCTCAAGGTAGACATTCA
* * * *
2730 ATTATAATATATTTTAATAAAAATGTA--AAAAATACAACTTAAAATCAATTATGAGATTATAAA
66 ATTATAATCTGTTTTAAAAAAAATGTATGAAAAAT-CAACTT-AAATTAATTATGAGATTATAAA
2793 NNNNNNNNNN
Statistics
Matches: 253, Mismatches: 36, Indels: 25
0.81 0.11 0.08
Matches are distributed among these distances:
168 2 0.01
169 29 0.11
170 9 0.04
171 39 0.15
172 128 0.51
173 45 0.18
174 1 0.00
ACGTcount: A:0.40, C:0.12, G:0.12, T:0.36
Consensus pattern (169 bp):
ACTATAAATAGACTTTTCTTACCAATGAATGTCTTTATCTTCACGTTTCTCAAGGTAGACATTCA
ATTATAATCTGTTTTAAAAAAAATGTATGAAAAATCAACTTAAATTAATTATGAGATTATAAAAC
CATTTAAAGAGAGTAATAAGGCTTCTAAAAGAATAGATG
Done.