Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018403318.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_990.0, 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: 15014
ACGTcount: A:0.24, C:0.10, G:0.10, T:0.24
Warning! 4680 characters in sequence are not A, C, G, or T
Found at i:4010 original size:172 final size:169
Alignment explanation
Indices: 3832--4330 Score: 479
Period size: 171 Copynumber: 2.9 Consensus size: 169
3822 NNNNNNNNAA
** *
3832 GTAATAAGGCTTTTGGAAGGCATGAGTGACTATAAATAGGCTTTTCTTGTCATAGAATGGCTCTT
1 GTAATAA-GCTTTT-GAAGGCATGAGTGACTATAAATAGGCTTTTCTTGTCATAGAATAACTTTT
* *
3897 TCTTCACATTTCTCAAGGTAAATATTCAATTATTATTTATTTTAACCAAAAATGGAAGAAAATTT
64 TCTTCACATTTCTCAAGGTAAATATTCAATTATTATTTATTTTAACCAAAAAT-GAAAAAAATTA
** *
3962 AACTTAAAATCAATTATAAGGTTATGCAATCATTTAAAGCGG
128 AACTTAAAATCAATTATAAGGTTATAAAACCATTTAAAGCGG
* *** * ** *
4004 GTAATAAAGCTTTCGAAGGTGGGGGTGACTATAAAT-GGACTTTT-TCTACCA-ATGAATATCTT
1 GTAAT-AAGCTTTTGAAGGCATGAGTGACTATAAATAGG-CTTTTCT-TGTCATA-GAATAACTT
* * * * *
4066 TTTCTTCACGTTTGTGAAGGTAGACATA-T-AATTATAATTTGTTTTAACCAAAAATGTAAAAAA
62 TTTCTTCACATTTCTCAAGGTA-A-ATATTCAATTATTATTTATTTTAACCAAAAATG--AAAAA
* * * **
4129 AATTAAACTTAAAACCAATGATGAGGTTATAAAACCATTTAAAGCTT
123 AATTAAACTTAAAATCAATTATAAGGTTATAAAACCATTTAAAGCGG
* ** *
4176 GTAATAAGCTTTTAAAGGCATGAACGACTATAAATAAGGCTTTTCTTGCTAATA-AATAACTTTT
1 GTAATAAGCTTTTGAAGGCATGAGTGACTATAAAT-AGGCTTTTCTTG-TCATAGAATAACTTTT
*** * * * *
4240 TCTTCACATTTCTCAAGGTAGGCATTCAATTGTTACTTATTTTAACCAAAAATGTAAAACAATTC
64 TCTTCACATTTCTCAAGGTAAATATTCAATTATTATTTATTTTAACCAAAAATG-AAAAAAATTA
* *
4305 AACTTAAAATCAATTATGATGTTATA
128 AACTTAAAATCAATTATAAGGTTATA
4331 NNNNNNNNNN
Statistics
Matches: 259, Mismatches: 53, Indels: 31
0.76 0.15 0.09
Matches are distributed among these distances:
170 6 0.02
171 129 0.50
172 114 0.44
173 9 0.03
174 1 0.00
ACGTcount: A:0.37, C:0.13, G:0.14, T:0.36
Consensus pattern (169 bp):
GTAATAAGCTTTTGAAGGCATGAGTGACTATAAATAGGCTTTTCTTGTCATAGAATAACTTTTTC
TTCACATTTCTCAAGGTAAATATTCAATTATTATTTATTTTAACCAAAAATGAAAAAAATTAAAC
TTAAAATCAATTATAAGGTTATAAAACCATTTAAAGCGG
Found at i:4733 original size:171 final size:168
Alignment explanation
Indices: 4385--4849 Score: 506
Period size: 171 Copynumber: 2.7 Consensus size: 168
4375 NNNNNNNGCG
* * *
4385 TGGGTGACTGTAAATGGACTTTTCTTGCCAATGAATGGCTTTTTCTTCATGGTTCTCAAGA-CAG
1 TGGGTGACTATAAATGAACTTTTCTTGCCAATGAATGGC-TTTTCTTCAT-GTT-TCGAGAGCAG
* * *
4449 ACATTCAATTATTATTTATTTTAACAAAAAATGAAAAAAATTCAACTTAACGTCAATTATTAGAT
63 ACATTCAATTATTATTTGTTTTAACAAAAAATGAAAAAAATTCAACTTAAAGTCAATTATGAGAT
* **
4514 TATAAAACCATCTCAAGCAAGTAATATGGCTATTAAAGGCA
128 TATAAAACCATCTCAAGCAAGCAATAAAGCTATTAAAGGCA
* *
4555 TGGGTGACTATAAATGAACTTTTCTTGCCAAAGAATGGCTTTCTCTTCATGTTTCGAGAGGATGA
1 TGGGTGACTATAAATGAACTTTTCTTGCCAATGAATGGCTTT-TCTTCATGTTTCGAGAGCA-GA
* * * * * * * *
4620 CATTTAATTATAATTTGTTTTAGCAAAAAATGTTAAACAATTCAAGTTAAAATCAATTATGAGTT
64 CATTCAATTATTATTTGTTTTAACAAAAAATG-AAAAAAATTCAACTTAAAGTCAATTATGAGAT
* ** * *
4685 TATAAAACCAT-TTACAGTGAGCAATAAAGCTTTTGAAGGCA
128 TATAAAACCATCTCA-AGCAAGCAATAAAGCTATTAAAGGCA
* ** * * *
4726 TGGGTGACTCTAAAT-AGGTTTTTCTTACCAATGAATGGCTCTTGCTTCATGTTTTTCGAG-GTA
1 TGGGTGACTATAAATGA-ACTTTTCTTGCCAATGAATGGCT-TTTCTTCATG--TTTCGAGAGCA
* * *
4789 GACACTGAATTATTATTTGTTTTAACAAAAAATGAAAAAAATTCAACTTAAGGTCAATTAT
62 GACATTCAATTATTATTTGTTTTAACAAAAAATGAAAAAAATTCAACTTAAAGTCAATTAT
4850 AGGTAACAAA
Statistics
Matches: 246, Mismatches: 40, Indels: 18
0.81 0.13 0.06
Matches are distributed among these distances:
168 5 0.02
169 7 0.03
170 98 0.40
171 125 0.51
172 4 0.02
173 7 0.03
ACGTcount: A:0.36, C:0.13, G:0.15, T:0.35
Consensus pattern (168 bp):
TGGGTGACTATAAATGAACTTTTCTTGCCAATGAATGGCTTTTCTTCATGTTTCGAGAGCAGACA
TTCAATTATTATTTGTTTTAACAAAAAATGAAAAAAATTCAACTTAAAGTCAATTATGAGATTAT
AAAACCATCTCAAGCAAGCAATAAAGCTATTAAAGGCA
Found at i:11053 original size:171 final size:171
Alignment explanation
Indices: 10546--11432 Score: 585
Period size: 171 Copynumber: 5.2 Consensus size: 171
10536 NNNNNNNAGT
* * *
10546 GAGTAATAAGGCTTTTGAAGGCATGGGTGTCTCTAAATAGG-CTTTTCTTG-CAAATAAATAGCT
1 GAGTAATAAGGCTTTTCAAGGCATGGGTGACTATAAA-AGGACTTTTCTTGTC-AATAAATAGCT
* * * *
10609 CTTGCATCATGTCTT-TCGAA-GTAGACATTCAATAATTATCTATTTTAA-ATAAAAA--CATAA
64 CTTTCTTCATGT-TTCTC-AAGGTAGACATTCAATTATTATCTATTTCAACA-AAAAATGCA-AA
* ** *
10669 AACAATTAAACTTAAAATCAATTATGAGGTTATAAAACCAATTAAAGC
125 AAC-ATTCAACTTAAAATCAATTATGAAATTATAAAACCATTTAAAGC
* * * * * * *
10717 GAGTAATAGGGCTTTTGAAGGCATGGGTGACTATAAATGGACTTTTTCTCGTCAATGAATGGCTT
1 GAGTAATAAGGCTTTTCAAGGCATGGGTGACTATAAAAGGAC-TTTTCTTGTCAATAAATAGCTC
* * *** * * * * *
10782 TTTCTTCACGTTTCTCAAGTTAGACATTTGGTTGTCATATGTTTCATCAAAAAATGCAAAAACAT
65 TTTCTTCATGTTTCTCAAGGTAGACATTCAATTATTATCTATTTCAACAAAAAATGCAAAAACAT
**********
10847 TCAACTTAAAATCAATTATNNNNNNNNNNAACCATTTAAAGC
130 TCAACTTAAAATCAATTATGAAATTATAAAACCATTTAAAGC
* * * *
10889 AAGTAATAAGGCTTTTCAAGGCATTGGTGACTATAAACAGG-CTTTTCTTGTCAATGAATGGCTC
1 GAGTAATAAGGCTTTTCAAGGCATGGGTGACTATAAA-AGGACTTTTCTTGTCAATAAATAGCTC
* ** * *
10953 ATTCTTCATGTTTCTTGAGGTAAACATTCAATTATTATCTATTTCAACCAAAAATGCAAAAACAT
65 TTTCTTCATGTTTCTCAAGGTAGACATTCAATTATTATCTATTTCAACAAAAAATGCAAAAACAT
*
11018 TCAACTTAAAATCAATTATGAAATTATATAACCATTTAAAGC
130 TCAACTTAAAATCAATTATGAAATTATAAAACCATTTAAAGC
* * * * * *
11060 GAGTAATAAGAC-TTTCGAAGGCATGGGAGACTATCAATGGACTTTTCCTGTCAATAAATAGCTT
1 GAGTAATAAGGCTTTTC-AAGGCATGGGTGACTATAAAAGGACTTTTCTTGTCAATAAATAGCTC
* * * *********** *
11124 TTTCTTCAAGTTTCTCAAGGTAGACATTTAATTATAATCT-NNNNNNNNNNNAATGCAAAAAAAT
65 TTTCTTCATGTTTCTCAAGGTAGACATTCAATTATTATCTATTTCAACAAAAAATGCAAAAACAT
** * *
11188 TCAACTTAAAATCAATTATGAGGTTATACAACCATTTAAAGT
130 TCAACTTAAAATCAATTATGAAATTATAAAACCATTTAAAGC
* * ** * ********** * *
11230 GAATAATAAGAC-TTTCAAAGGTGTGGGTGACTATAAATGGACTTTTNNNNNNNNNNAATGGCTT
1 GAGTAATAAGGCTTTTC-AAGGCATGGGTGACTATAAAAGGACTTTTCTTGTCAATAAATAGCTC
** * * * * * * * * *
11294 TTTCTTCACATTTCTCAATGTCGACATTTAATTATAATCTGTTTTAACCAACAATGTAAACAA-A
65 TTTCTTCATGTTTCTCAAGGTAGACATTCAATTATTATCTATTTCAACAAAAAATGCAAA-AACA
* * ** * **
11358 TTCAACTTAAAATCAATTGTTAGGTTATAAATCCATTTAAAAA
129 TTCAACTTAAAATCAATTATGAAATTATAAAACCATTTAAAGC
*
11401 GAGTAATAAGGC-TTTCGAAGGCTTGGGTGACT
1 GAGTAATAAGGCTTTTC-AAGGCATGGGTGACT
11433 CTGAATAGGC
Statistics
Matches: 560, Mismatches: 143, Indels: 26
0.77 0.20 0.04
Matches are distributed among these distances:
170 141 0.25
171 292 0.52
172 116 0.21
173 9 0.02
174 2 0.00
ACGTcount: A:0.35, C:0.14, G:0.14, T:0.33
Consensus pattern (171 bp):
GAGTAATAAGGCTTTTCAAGGCATGGGTGACTATAAAAGGACTTTTCTTGTCAATAAATAGCTCT
TTCTTCATGTTTCTCAAGGTAGACATTCAATTATTATCTATTTCAACAAAAAATGCAAAAACATT
CAACTTAAAATCAATTATGAAATTATAAAACCATTTAAAGC
Done.