Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018398900.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_2181.1, 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: 4851
ACGTcount: A:0.35, C:0.12, G:0.13, T:0.32
Warning! 405 characters in sequence are not A, C, G, or T
Found at i:2601 original size:171 final size:171
Alignment explanation
Indices: 1883--2651 Score: 397
Period size: 171 Copynumber: 4.5 Consensus size: 171
1873 CTCACTCTGG
* * * * *
1883 CTTAAAATCAATTATGAGATTATAAAATTC-TTTAAAGTGAGTAATTAGACTTTTGAAGGAATAG
1 CTTAAAATCAATTATGAGATTATAAAA-CCATTTAAAGCGAGTAATAAGGCTTTTGAAAGAAT-G
* * * * * * * * *
1947 G-TGACTATAAATGGACTTCTCTTGCCAGTGAATGCCTTTTTCTTCACATTT-CTTGAGGCAGAT
64 GCTAACTATAAATGGACTTTTCTTACCAATAAATGCCTTTGTCTTCACGTTTCCTT-AAGCAGAC
* * * * * *
2010 ATTCAATTATAGTCTGTTTTAACTAAAAATGTAAAAAAATTTAA
128 ATTCAATTATAATCTATTCTAACCAAAAATGTAAAAATATTCAA
********** * * * * *
2054 CNNNNNNNNNNTTATGAGATTATAAAACTATTTAAAGCAAATAATAAGTC-TTTCAAAGGAATGG
1 CTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAA-GAATGG
* * ********** * * * *
2118 GTGACTATAAATGGACTTTTCNNNNNNNNNNATCCCTTTTTCTTCACGTTT-CTCAAAGTAGACA
65 CTAACTATAAATGGACTTTTCTTACCAATAAATGCCTTTGTCTTCACGTTTCCT-TAAGCAGACA
* * ** *
2182 TTCAATTATAACCTATTTTAAATAAAAATGTAAAAAAATTCAA
129 TTCAATTATAATCTATTCTAACCAAAAATGTAAAAATATTCAA
*********** * * * *
2225 CTCNNNNNNNNNNACGAGATTATAAAACTATTTACAGCGAGTAATAAGGCTTTTGAAGGAATGGC
1 CTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAAGAATGGC
** ** *
2290 TAACTATAAATGGACTTTTCTTGTCAATAAATTTCTTTTTCTTCACGTTTCCTTAAGCAGACATT
66 TAACTATAAATGGACTTTTCTTACCAATAAATGCCTTTGTCTTCACGTTTCCTTAAGCAGACATT
2355 CAATTATAATCTATTCTAACCAAAAATGTAAAAATATTCAA
131 CAATTATAATCTATTCTAACCAAAAATGTAAAAATATTCAA
********** * * * * *
2396 CTNNNNNNNNNNTATGCGAGTATAAAAACATTTAAAGTGAGTGATAAGGCTTTTGAAAGAATCGG
1 CTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAAGAAT-GG
* * *
2461 -TAACTGTAAATGGACTTTTCTTACCAATGAATGCCTTTGTC-TCTACGTTT-CTTAAGGTAGAC
65 CTAACTATAAATGGACTTTTCTTACCAATAAATGCCTTTGTCTTC-ACGTTTCCTTAA-GCAGAC
* * * * *
2523 ATTTAATTATAATCTGTTTTGACCAAAAATGTTAAAAA-ATTTAA
128 ATTCAATTATAATCTATTCTAACCAAAAATG-TAAAAATATTCAA
* * * * * * *
2567 CTTAAAATCAATTATGAGATTTTAAAACCATTTAAAACAAGTAAAAAAGTTTTTGAAGGAATAGG
1 CTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAAGAAT-GG
* *
2632 -TGACTATAAATAGACCTTTT
65 CTAACTATAAATGGA-CTTTT
2652 TCTTCACGTT
Statistics
Matches: 464, Mismatches: 123, Indels: 21
0.76 0.20 0.03
Matches are distributed among these distances:
170 14 0.03
171 430 0.93
172 20 0.04
ACGTcount: A:0.36, C:0.12, G:0.13, T:0.34
Consensus pattern (171 bp):
CTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAAGAATGGC
TAACTATAAATGGACTTTTCTTACCAATAAATGCCTTTGTCTTCACGTTTCCTTAAGCAGACATT
CAATTATAATCTATTCTAACCAAAAATGTAAAAATATTCAA
Found at i:4536 original size:171 final size:169
Alignment explanation
Indices: 2648--4851 Score: 650
Period size: 171 Copynumber: 12.9 Consensus size: 169
2638 TAAATAGACC
* * ** * * * * * *
2648 TTTTTCTTCACGTTTCTTGAGCCAAACATTCAACTATAATCTGTTTTAACTAAAAATGTTAAAGA
1 TTTTTCTTCATGTTTCTCGAGGTAGACATTCAATTATAGTCTGTTTTATC-AAAAATGTAAAATA
* * *** * * *
2713 ATTCAACTTAAAATCAATTTTGAGATTATAAAA-TCATTTATAGTGAGTAATAAGGCTTTTAAAG
65 ATTCAACTTAAAATCAATTATGAGATTATAAAACT-ATTTAAAACAAATAATAAGCCTTTTGAA-
* * * * * *
2777 GAATGAGTAACTATAGATGGACTTTTCATATCAATGAATGC-
128 GAATGGGTGACTATAAATGAACTTTTCTTGTCAATGAATGCT
* * * * * * * * * *
2818 CTTTACTTTACGTTTCTTGAGGCAGACATTCAGTTATAGTCTGTTTTAATAAAAAAATATAAAAA
1 TTTTTCTTCATGTTTCTCGAGGTAGACATTCAATTATAGTCTGTTTT-AT-CAAAAATGTAAAAT
** ********** * * * *
2883 AATTCAACTTAAAATCTGTTATGAGATTANNNNNNNNNNTAAAGCGAGTAATAAGGCTTTTGAAG
64 AATTCAACTTAAAATCAATTATGAGATTATAAAACTATTTAAAACAAATAATAAGCCTTTTGAA-
** *
2948 GAATAAGTGACTATAAA-AAGACTTTTCTTAGT-AATGAATG-T
128 GAATGGGTGACTATAAATGA-ACTTTTCTT-GTCAATGAATGCT
* * ** * * *
2989 CTTTTTCTTCACGTTTCTTGAGGTAGACATTCAATTATAACCTATTTTAACTAAAAATATAAAA-
1 -TTTTTCTTCATGTTTCTCGAGGTAGACATTCAATTATAGTCTGTTTTATC-AAAAATGTAAAAT
********* * * * * * * *
3053 AANNNNNNNNNNAAATCAATTACGAGATTATAAAACCATTTACAGCGAGTAATAAGACTTTTGAA
64 AA-TTCAACTTAAAATCAATTATGAGATTATAAAACTATTTAAAACAAATAATAAGCCTTTTG-A
* * * * *
3118 AAAATGGCTGACTATAAATGAACTTTTCTTGTCAATAAATTCC
127 AGAATGGGTGACTATAAATGAACTTTTCTTGTCAATGAATGCT
* * * * * * * * * * * * *
3161 TTTTCCTTCAATGTTTCCCTAAGTAGACATCCGATTATAATATATTTTAACGAAAACTATAAAAA
1 TTTTTCTTC-ATGTTTCTCGAGGTAGACATTCAATTATAGTCTGTTTTATC-AAAAATGTAAAAT
* * ************ * *
3226 AATTCAACCTAAAATCAATTATGAGATTATAAGANNNNNNNNNNTGAGTAATAAGGCTTTTGAAG
64 AATTCAACTTAAAATCAATTATGAGATTATAAAACTATTTAAAACAAATAATAAGCCTTTTGAA-
** ** ** *
3291 GAATAAGTGACTATAAACAAACTTTTCTTACCAATGAATACCT
128 GAATGGGTGACTATAAATGAACTTTTCTTGTCAATGAAT-GCT
** * * * * * *
3334 TTTTTC-TCACATTTCTTGAGGCAGACATTCAATTATAGTCTGTTTTAACCGAAAATGGAAAAAA
1 TTTTTCTTCATGTTTCTCGAGGTAGACATTCAATTATAGTCTGTTTT-ATCAAAAATGTAAAATA
* ********** * * * * * *
3398 ATTTAACTTAAAATCAATNNNNNNNNNNTAAAACCATTTAAAGCGAGTAGTAAAG-CTTTTAAAG
65 ATTCAACTTAAAATCAATTATGAGATTATAAAACTATTTAAAACAAATAAT-AAGCCTTTTGAAG
* * * * *
3462 AAATAGATGACTATAAATGGACTTTTCTTGCCAATGACT-CT
129 -AATGGGTGACTATAAATGAACTTTTCTTGTCAATGAATGCT
* * * * * * * *
3503 CTTTTTCTTTATGTTTCTTGAGATAGACATTCAATTATAATTTGTTTTAATCAAAAAGGCAAAAA
1 -TTTTTCTTCATGTTTCTCGAGGTAGACATTCAATTATAGTCTGTTTT-ATCAAAAATGTAAAAT
* ** * * ********** *** * *
3568 AAATGTACCTAAAATCAATTATGAGATTACAANNNNNNNNNNAGTGAGTAATAAGGCTTTTGAAG
64 AATTCAACTTAAAATCAATTATGAGATTATAAAACTATTTAAAACAAATAATAAGCCTTTTGAA-
* ** * *
3633 GGATAAGTGACTATAAACGGACTTTTCTTGTCAATGAATGCCT
128 GAATGGGTGACTATAAATGAACTTTTCTTGTCAATGAATG-CT
* ** * ** * * *
3676 TTTTT-TT-ATGTTTCTAGAGACAGATATTTGATTATAATATGTTTTAATCAAAAATATAAAA-A
1 TTTTTCTTCATGTTTCTCGAGGTAGACATTCAATTATAGTCTGTTTT-ATCAAAAATGTAAAATA
* ** * * * * *
3738 TATTCAAATTAAAATCAATTATTTGGTTATAAAACTATTTAAAGCGAGTAATAAAG-CTTTCGAA
65 -ATTCAACTTAAAATCAATTATGAGATTATAAAACTATTTAAAACAAATAAT-AAGCCTTTTGAA
** * * * **** *
3802 GGCTTGAGTAACTATAAATGCACTTTTCACACCAATGGATGAC-
128 -GAATGGGTGACTATAAATGAACTTTTCTTGTCAATGAATG-CT
* * * * * * * * * * *
3845 CTTTGCTTCATGTTTCCCCATGAAGACATTCAATCATAATATATTTTAATCAAAAATGTAAAANN
1 TTTTTCTTCATGTTTCTCGAGGTAGACATTCAATTATAGTCTGTTTT-ATCAAAAATGTAAAA-T
******** * * * * *** * *
3910 NNNNNNNNTTAAAATCAATTATGAGATTATACAACCATTCATAGTGAGTAATAAGGCTTTTGAAT
64 AATTCAACTTAAAATCAATTATGAGATTATAAAACTATTTAAAACAAATAATAAGCCTTTTGAA-
* * * **
3975 GAATAGGTGACTATAATTGGACTTTTCTTACCAATGAATGGCT
128 GAATGGGTGACTATAAATGAACTTTTCTTGTCAATGAAT-GCT
* * * ** * * * * * *
4018 TTTTTC-TAATGTTTTTCAAGACAGAGATTGAATTATAGCCTTTTTTAACCAAAAATGTAAAAAA
1 TTTTTCTTCATGTTTCTCGAGGTAGACATTCAATTATAGTCTGTTTT-ATCAAAAATGTAAAATA
* * * * * * ** **
4082 ACTCAACTTAAAATTAGTTATTAGTTTATAAAACCATTTAAAGA-AAGCAATAATG-CTTTCAAA
65 ATTCAACTTAAAATCAATTATGAGATTATAAAACTATTTAAA-ACAAATAATAA-GCCTTTTGAA
** * * * * * *
4145 GGCTTGAGTGATTATAAATGGACTTTT-TACGCCTAT-AGATGGC-
128 -GAATGGGTGACTATAAATGAACTTTTCT-TGTCAATGA-AT-GCT
* ** * * * * * ** * * *
4188 TTTTACTTCACATTCCCCAAGGCAAACATTCAACAATAGGT-T-TTTTAACCAAAATGTCAAAAA
1 TTTTTCTTCATGTTTCTCGAGGTAGACATTCAATTATA-GTCTGTTTTATCAAAAATGT-AAAAT
* *** * **********
4251 AATTCAACTTAAAATTAATT-TGGAGATTATAAAA-TCATTTAAAGTGAGTAANNNNNNNNNNGA
64 AATTCAACTTAAAATCAATTAT-GAGATTATAAAACT-ATTTAAAACAAATAATAAGCCTTTTGA
* *
4314 AGGAATGGGTGACTATAAATGAACTTTTCTCGTCAATGAAT-AT
127 A-GAATGGGTGACTATAAATGAACTTTTCTTGTCAATGAATGCT
* * * *
4357 ATTTTTCTTCATGTTTCTCGAGGCAGAGATTCAATTATAGTCTGTTTTAGTTAAAAATGTGAAAT
1 -TTTTTCTTCATGTTTCTCGAGGTAGACATTCAATTATAGTCTGTTTTA-TCAAAAATGTAAAAT
********** * *
4422 AATTCAACTTAAAATCAATTATGAGATNNNNNNNNNNTTTAAAGA-GAATAATAAGGCTTTTGAA
64 AATTCAACTTAAAATCAATTATGAGATTATAAAACTATTTAAA-ACAAATAATAAGCCTTTTGAA
* *
4486 GCAATGGGTAACTATAAATGAACTTTTCTTGCCAATGAATGCT
128 G-AATGGGTGACTATAAATGAACTTTTCTTGTCAATGAATGCT
* * * * * * *
4529 TTTTTCTTAACGTTTC-CTAGGGTAGACATTCAATTATAGTCTGTGTTAATCACAAATGCAAAAA
1 TTTTTCTTCATGTTTCTCGA-GGTAGACATTCAATTATAGTCTGT-TTTATCAAAAATGTAAAAT
** *
4593 AATTCAACTTAAAATCGGTTATGAGATTATAAAACTATTTAAAACAAATAATAAGCCTTTTAAAG
64 AATTCAACTTAAAATCAATTATGAGATTATAAAACTATTTAAAACAAATAATAAGCCTTTTGAAG
* * * *
4658 AATAGGTGACTATAAATGGACTTTTCTTGTCAATAAATGCA
129 AATGGGTGACTATAAATGAACTTTTCTTGTCAATGAATGCT
* * * * *
4699 TTTTTCTTCATG-TTCTCGAGGTAGACATTGAATTGTAATTTGTTTTACCAAAAATGTAAAATAA
1 TTTTTCTTCATGTTTCTCGAGGTAGACATTCAATTATAGTCTGTTTTATCAAAAATGTAAAAT-A
*** * *
4763 ATTCAACTTAAAATCAATT-TGGAGATTATAAAACTATTTAAAGTTAGTAATAAGGCTTTTGAAT
65 ATTCAACTTAAAATCAATTAT-GAGATTATAAAACTATTTAAAACAAATAATAAGCCTTTTGAA-
*
4827 GAATGGGTGACTATAAATGGACTTT
128 GAATGGGTGACTATAAATGAACTTT
Statistics
Matches: 1482, Mismatches: 487, Indels: 130
0.71 0.23 0.06
Matches are distributed among these distances:
168 15 0.01
169 95 0.06
170 359 0.24
171 704 0.48
172 294 0.20
173 15 0.01
ACGTcount: A:0.37, C:0.12, G:0.13, T:0.34
Consensus pattern (169 bp):
TTTTTCTTCATGTTTCTCGAGGTAGACATTCAATTATAGTCTGTTTTATCAAAAATGTAAAATAA
TTCAACTTAAAATCAATTATGAGATTATAAAACTATTTAAAACAAATAATAAGCCTTTTGAAGAA
TGGGTGACTATAAATGAACTTTTCTTGTCAATGAATGCT
Done.