Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018399848.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_3083.0, 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: 11629
ACGTcount: A:0.22, C:0.08, G:0.07, T:0.23
Warning! 4561 characters in sequence are not A, C, G, or T
Found at i:3904 original size:171 final size:170
Alignment explanation
Indices: 3346--3906 Score: 604
Period size: 171 Copynumber: 3.3 Consensus size: 170
3336 NNNNNNNTAT
* * * *
3346 ATTTTTTACTAAAATAGACTATAATTCAATGTCTATTTAGAGAAACGTGAAGAAAAACGCATTCG
1 ATTTTTGACTAAAACAGACTATAATTCAATGTCTACTTAGAGAAACATGAAGAAAAACGCATTCG
* *
3411 TTGTCAA-AAAAAGTCCCTTTATAGTCATCCATTCCTTCAAAAGCCTTATTATTCGCTTTAAATT
66 TTGTCAAGAAAAA-TCCCTTTATAGTCACCCATTCCTTCAAAAGCCTTATTACTCGCTTTAAATT
* * *
3475 ATTTTTTAAACTCATAATTGATTTTAAGCTATATTTTTTTAC
130 ATTTTATAATCTCATAATTGATTTTAAGATA-ATTTTTTTAC
* * * * *
3517 TTTTTTTACTAAAACAGACTATAATTCAGTGTCTACTTAGAGAAACGT-AGAGAAAAATGCATTC
1 ATTTTTGACTAAAACAGACTATAATTCAATGTCTACTTAGAGAAACATGA-AGAAAAACGCATTC
* ********** **
3581 GTTGTCAAGAAAAGTNNNNNNNNNNTCACCCATTCCTTCAAAAGCCTTATTACTAACTTTAAATT
65 GTTGTCAAGAAAAATCCCTTTATAGTCACCCATTCCTTCAAAAGCCTTATTACTCGCTTTAAATT
* * *
3646 GTTTTACAATCTCATAATTGATTTTAAAATAAATTTTTTTAC
130 ATTTTATAATCTCATAATTGATTTTAAGAT-AATTTTTTTAC
** * *
3688 ATTTTTGGTTAAAACAGACTATAATTCAAAGTCTACTTAGAGAAACATGAACAAAAACGCATTCG
1 ATTTTTGACTAAAACAGACTATAATTCAATGTCTACTTAGAGAAACATGAAGAAAAACGCATTCG
* * ** *
3753 TTGGCAAGAAAAATCTCTTTATAGTCACCCATTCCTTCAAAAGTATTATTACTCGCTATAAATTA
66 TTGTCAAGAAAAATCCCTTTATAGTCACCCATTCCTTCAAAAGCCTTATTACTCGCTTTAAATTA
* * * * *
3818 TTTTATAATCTCTTAATTAATTTTAAGTTGAATTCTTTTAA
131 TTTTATAATCTCATAATTGATTTTAAGAT-AATTTTTTTAC
* * ** * * *
3859 ATTTTTGATTAAAATAGACTATAATGGAATGTTTACCTCGAGAAACAT
1 ATTTTTGACTAAAACAGACTATAATTCAATGTCTACTTAGAGAAACAT
3907 NNNNNNNNNN
Statistics
Matches: 317, Mismatches: 69, Indels: 8
0.80 0.18 0.02
Matches are distributed among these distances:
170 1 0.00
171 310 0.98
172 6 0.02
ACGTcount: A:0.36, C:0.15, G:0.10, T:0.38
Consensus pattern (170 bp):
ATTTTTGACTAAAACAGACTATAATTCAATGTCTACTTAGAGAAACATGAAGAAAAACGCATTCG
TTGTCAAGAAAAATCCCTTTATAGTCACCCATTCCTTCAAAAGCCTTATTACTCGCTTTAAATTA
TTTTATAATCTCATAATTGATTTTAAGATAATTTTTTTAC
Found at i:9085 original size:171 final size:171
Alignment explanation
Indices: 8689--9404 Score: 501
Period size: 170 Copynumber: 4.2 Consensus size: 171
8679 NNNNAAATGA
* * * * * **
8689 TTTTATAAACTCATAATTAATTTTAAGTTGAGTTTTTTTAAATTTTTCTTTAAAACCA-ACTATA
1 TTTTATAAACTCACAAGTGATTTTAAGTTGAATTTTTTTATATTTTTAGTTAAAA-CAGACTATA
** * ** * * * * * * *
8753 ATTGAATGTTTGTCTTAGA-AAACATGTAGAAAGAGGTATTTATTGGCAAGAAAAG-CTCATTTA
65 ATTGAAAATCTACCTTAGAGAAA-TTGAAGAAAAATGCATTCATTGGCAAAAAAAGTC-CATTTA
* * *
8816 GAGTCAC-CTACTCCTTCGAAAA-CTTTATTACTCGCTTTAAATTG
128 TAGTCACTC-ATTCCTTC-AAAAGCCTTATTACTCGCTTTAAATTG
********** * * *
8860 TTTTATANNNNNNNNNNTGATTTTAAGGTGAATTTTTTTATATTTTAAGTTAAAATAGACTATAA
1 TTTTATAAACTCACAAGTGATTTTAAGTTGAATTTTTTTATATTTTTAGTTAAAACAGACTATAA
**
8925 TTGAAAATCTA-CTTAGAGAAACTTGAAGAAAAATGCATTTGTTGGCAAGAAAAA-TCCATTTAT
66 TTGAAAATCTACCTTAGAGAAA-TTGAAGAAAAATGCATTCATTGGCAA-AAAAAGTCCATTTAT
* *
8988 AGTCACTCATTCCTTGAAAAGCCTTATTACTCGTTTTAAATTG
129 AGTCACTCATTCCTTCAAAAGCCTTATTACTCGCTTTAAATTG
********** * * * *
9031 TTTTATAAANNNNNNNNNNATTTTAAGTTGAATTTTTTTACATTTTTTGTTAAAACAGACAATAT
1 TTTTATAAACTCACAAGTGATTTTAAGTTGAATTTTTTTATATTTTTAGTTAAAACAGACTATAA
** * * *
9096 TTGAATGTCTACCATAG-GAAAATTGTA-TAAAA-GCCATTCATTGAG-AAAAAAAGTCCATTTA
66 TTGAAAATCTACCTTAGAG-AAATTGAAGAAAAATG-CATTCATTG-GCAAAAAAAGTCCATTTA
* * *
9157 TAGTCA-TCCAGTCCTTCAAAAGCCTTATTACTCACTCTAAATTG
128 TAGTCACT-CATTCCTTCAAAAGCCTTATTACTCGCTTTAAATTG
* * * * *
9201 TTTTATAATCTCACAAGTGATTTTAATTTGAAATTTTTTATATTTTTGGATAAAACAGACTATAA
1 TTTTATAAACTCACAAGTGATTTTAAGTTGAATTTTTTTATATTTTTAGTTAAAACAGACTATAA
* * *
9266 TTG--AATGCTTACCTT-GACAAAATGAAGAAAAATGCATTCATTGACAAAAAAAGTCCATTTAT
66 TTGAAAAT-C-TACCTTAGAGAAATTGAAGAAAAATGCATTCATTGGCAAAAAAAGTCCATTTAT
* ** *
9328 AGTCAGC-CATTCCTTCATAAGTGTTATTACTCGCTTTAAATTA
129 AGTCA-CTCATTCCTTCAAAAGCCTTATTACTCGCTTTAAATTG
* * * *
9371 TTTTATAATCTCATAATTGATTTTATGTTGAATT
1 TTTTATAAACTCACAAGTGATTTTAAGTTGAATT
9405 NNNNNNNNNN
Statistics
Matches: 430, Mismatches: 95, Indels: 41
0.76 0.17 0.07
Matches are distributed among these distances:
168 1 0.00
169 15 0.03
170 217 0.50
171 184 0.43
172 13 0.03
ACGTcount: A:0.35, C:0.12, G:0.11, T:0.39
Consensus pattern (171 bp):
TTTTATAAACTCACAAGTGATTTTAAGTTGAATTTTTTTATATTTTTAGTTAAAACAGACTATAA
TTGAAAATCTACCTTAGAGAAATTGAAGAAAAATGCATTCATTGGCAAAAAAAGTCCATTTATAG
TCACTCATTCCTTCAAAAGCCTTATTACTCGCTTTAAATTG
Found at i:10619 original size:171 final size:171
Alignment explanation
Indices: 10343--10656 Score: 371
Period size: 171 Copynumber: 1.8 Consensus size: 171
10333 NNNNNNTCGC
* *
10343 TTTAAATTATTTTATAATCTCACAATTAATTTTAAATTGAATTTTTTAAAATTTTTGGTTAAAAC
1 TTTAAATTATTTTATAATCTCACAATGAATTTTAAATTGAATTTTTTAAAATTTTTGATTAAAAC
* * * * ********** *
10408 AGACTATAATTCAATGTCTNNNNNNNNNNACATGAAGAAAAA-CGCATTCGTTGACAAGAAAAAT
66 AAAATATAATACAACGTCTACCTTGAGTAACATGAAGAAAAAGC-CATTCATTGACAAGAAAAAT
10472 CTC-TTTATAGTCACTCATTCCTTCAAAAGTGTTATTACTCGT
130 C-CATTTATAGTCACTCATTCCTTCAAAAGTGTTATTACTCGT
* * *
10514 TTTAAATTATTTTATAATCTCATAATGAATTTTAAGTTGAATTTTTTTAAATTTTTGATTAAAAC
1 TTTAAATTATTTTATAATCTCACAATGAATTTTAAATTGAATTTTTTAAAATTTTTGATTAAAAC
* * ** *
10579 AAAATATAATAGAACGTCTACCTTGAGTAACATTAAGAAAAAGCCATTCATTGTTAAGAAAAGTC
66 AAAATATAATACAACGTCTACCTTGAGTAACATGAAGAAAAAGCCATTCATTGACAAGAAAAATC
10644 CATTTATAGTCAC
131 CATTTATAGTCAC
10657 NNNNNNNNNN
Statistics
Matches: 116, Mismatches: 25, Indels: 4
0.80 0.17 0.03
Matches are distributed among these distances:
170 1 0.01
171 114 0.98
172 1 0.01
ACGTcount: A:0.38, C:0.12, G:0.09, T:0.38
Consensus pattern (171 bp):
TTTAAATTATTTTATAATCTCACAATGAATTTTAAATTGAATTTTTTAAAATTTTTGATTAAAAC
AAAATATAATACAACGTCTACCTTGAGTAACATGAAGAAAAAGCCATTCATTGACAAGAAAAATC
CATTTATAGTCACTCATTCCTTCAAAAGTGTTATTACTCGT
Done.