Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018400674.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_386.0, 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: 16861
ACGTcount: A:0.23, C:0.08, G:0.08, T:0.23
Warning! 6318 characters in sequence are not A, C, G, or T
Found at i:8284 original size:171 final size:171
Alignment explanation
Indices: 7901--8298 Score: 419
Period size: 171 Copynumber: 2.3 Consensus size: 171
7891 AAAGCCTTAT
* * *
7901 TACTCGCTTTAAATGATTTTATAATCTGATAATTGATTTT-AGTTAAAATTTTTTTATATTTTTT
1 TACTCGCTTTAAATGATTTTATAATCTCATAATTAATTTTAAGTT-GAATTTTTTTATATTTTTT
* * * *
7965 ATTAAACCAGATTAAAATTGAATGTCTAACTTGAGAAACGAGAAGAAATAGATATCCATTGGCAA
65 ATTAAACCAGATTAAAATTGAATGTCTAACTAGAGAAACAAGAAGAAAAAGATATCCATTGACAA
********** * * *
8030 GAAAANNNNNNNNNNAGTCATCCATGCCTTCAAAAGCCTTAT
130 GAAAAGTCCATTTATAGTCATCCATGCCTTCAAAAGCATCAA
* *
8072 TACTCGGC-TTAAATGTTTTTATAGA-CTCATAATTAATTTTAAGTTGAATTTGTTTATATTTTT
1 TACTC-GCTTTAAATGATTTTATA-ATCTCATAATTAATTTTAAGTTGAATTTTTTTATATTTTT
* * * * * * *
8135 TATTCAAA-CAGATTATAATTGAATGTTTACCTAGAGAAATAAGAAGAAAAAGATATTCATTTAT
64 TATT-AAACCAGATTAAAATTGAATGTCTAACTAGAGAAACAAGAAGAAAAAGATATCCATTGAC
* *
8199 AAGAAAAGTCCATTTATAGTCA-CCTATTCCTTCGAAAGCATCAA
128 AAGAAAAGTCCATTTATAGTCATCC-ATGCCTTCAAAAGCATCAA
* *
8243 TACTCGCTTTAAATGATTTTATAATCTCATAATTAATTTTAATTTGAGTTTTTTTA
1 TACTCGCTTTAAATGATTTTATAATCTCATAATTAATTTTAAGTTGAATTTTTTTA
8299 NNNNNNNNNN
Statistics
Matches: 185, Mismatches: 35, Indels: 14
0.79 0.15 0.06
Matches are distributed among these distances:
170 5 0.03
171 170 0.92
172 10 0.05
ACGTcount: A:0.36, C:0.11, G:0.11, T:0.39
Consensus pattern (171 bp):
TACTCGCTTTAAATGATTTTATAATCTCATAATTAATTTTAAGTTGAATTTTTTTATATTTTTTA
TTAAACCAGATTAAAATTGAATGTCTAACTAGAGAAACAAGAAGAAAAAGATATCCATTGACAAG
AAAAGTCCATTTATAGTCATCCATGCCTTCAAAAGCATCAA
Found at i:12359 original size:170 final size:160
Alignment explanation
Indices: 12165--12492 Score: 383
Period size: 170 Copynumber: 2.0 Consensus size: 160
12155 AAAGCTTTCG
**
12165 AAGGCATGAATGACAATAAATGGACTTCTCTTACCAATGGATATCATTTTCTTTACAT-TTT-TG
1 AAGGCATGGGTGACAATAAATGGACTTCTCTTACCAATGGATATCATTTTC-TT-CATCTTTCTG
*
12228 GAGGCACACATTTAATTATAATCTATTTTAATAAAAA-AATAAATAAAATAAAATTAAAATCAAT
64 GAGGCACACATTCAATTATAATCTATTTTAATAAAAATAATAAA-AAAATAAAATTAAAATCAAT
* *
12292 TATGAGGTTCTAAAATCATTTAAAGCGAGTAAT
128 TATGAGGTTATAAAATCATTTAAACCGAGTAAT
* * *
12325 AAGGNNNNNNNNNNCATGGGTGACTATAAATGGACTTTTCTTGCCAATGGATATCATTTTCTTCA
1 AAGG----------CATGGGTGACAATAAATGGACTTCTCTTACCAATGGATATCATTTTCTTCA
* * * * * * *
12390 TCTTTCTTGAGGCAGACATTCAATTATAATCTTTTTTAATAAAAATTATAAAAAATTTAAATTAC
56 TCTTTCTGGAGGCACACATTCAATTATAATCTATTTTAATAAAAATAATAAAAAAATAAAATTAA
12455 AATCAATTATGAGGTTATAAAATCATTTAAACCGAGTA
121 AATCAATTATGAGGTTATAAAATCATTTAAACCGAGTA
12493 NNNNNNNNNN
Statistics
Matches: 140, Mismatches: 15, Indels: 16
0.82 0.09 0.09
Matches are distributed among these distances:
160 4 0.03
168 3 0.02
169 5 0.04
170 123 0.88
171 5 0.04
ACGTcount: A:0.39, C:0.12, G:0.12, T:0.35
Consensus pattern (160 bp):
AAGGCATGGGTGACAATAAATGGACTTCTCTTACCAATGGATATCATTTTCTTCATCTTTCTGGA
GGCACACATTCAATTATAATCTATTTTAATAAAAATAATAAAAAAATAAAATTAAAATCAATTAT
GAGGTTATAAAATCATTTAAACCGAGTAAT
Found at i:12921 original size:74 final size:74
Alignment explanation
Indices: 12800--12950 Score: 293
Period size: 74 Copynumber: 2.0 Consensus size: 74
12790 GGTAACAATA
*
12800 AATGGATTTCTCTTGCTAGTGGATATAATTTTCTTTACATTTTTTGTGGCACACATTCAATTATA
1 AATGGATTTCTCTTGCTAGTGGATATAATTTTCTTTACACTTTTTGTGGCACACATTCAATTATA
12865 ATCTGTTTT
66 ATCTGTTTT
12874 AATGGATTTCTCTTGCTAGTGGATATAATTTTCTTTACACTTTTTGTGGCACACATTCAATTATA
1 AATGGATTTCTCTTGCTAGTGGATATAATTTTCTTTACACTTTTTGTGGCACACATTCAATTATA
12939 ATCTGTTTT
66 ATCTGTTTT
12948 AAT
1 AAT
12951 AAAAAAATAA
Statistics
Matches: 76, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
74 76 1.00
ACGTcount: A:0.25, C:0.14, G:0.13, T:0.48
Consensus pattern (74 bp):
AATGGATTTCTCTTGCTAGTGGATATAATTTTCTTTACACTTTTTGTGGCACACATTCAATTATA
ATCTGTTTT
Found at i:15087 original size:171 final size:172
Alignment explanation
Indices: 14802--15775 Score: 790
Period size: 171 Copynumber: 5.7 Consensus size: 172
14792 NNNNNNNNNN
* * *
14802 TTTTGAAGGCGTGGGTGACTATAAATAGACTTTTCTTGCCAATGGATATC-TTTTCGTTTCGGTT
1 TTTTGAAGGCATGGGTGACTATAAATGGACTTTTCTTGCCAATGGATATCTTTTTC-TTTCAGTT
* * *
14866 TCTTGAGGCAGACGTTCT-ATTATAATCTATTTTTATAAAAATTATAAAAAAATTCAAACTTAAA
65 TCTTAAGGCAGACGTT-TAATTATAATCTATTTTAATAAAAAATATAAAAAAATTCAAACTTAAA
*
14930 ACTAATTATGAGGTTATATAATCATTTAAAGCGAGTAATAAGG-
129 ACTAATTATGAGGTTATAAAATCATTTAAAGCGAGTAATAAGGC
* * *
14973 TTTTGAAGGCGTGGGTGACTATAAATGGACTTTCCTTGCCAATGGATATCTTTTTATTTCAGTTT
1 TTTTGAAGGCATGGGTGACTATAAATGGACTTTTCTTGCCAATGGATATCTTTTTCTTTCAGTTT
** * * * *
15038 CTTAAGATAGACGTTTAATTATAATCTATTTTCATAAAAATTGTAAAAAAATTC-AACTGAAAAC
66 CTTAAGGCAGACGTTTAATTATAATCTATTTTAATAAAAAATATAAAAAAATTCAAACTTAAAAC
* * *
15102 TAATTATAAGGTTATACAATCATTTAAAGTGAGTAATAAGGC
131 TAATTATGAGGTTATAAAATCATTTAAAGCGAGTAATAAGGC
* * * * *******
15144 TTTTCAAGGCATGGGTGACAATAAATGGACTTTTTTTGCTAATGGATATCTTTTTCTTNNNNNNN
1 TTTTGAAGGCATGGGTGACTATAAATGGACTTTTCTTGCCAATGGATATCTTTTTCTTTCAGTTT
*** * * * * * * *
15209 NNNAAAGCAGACATTTAATTTTGATCAATTTTAATAAAAAATATAAAAAATTTC-AAGTTAAAAC
66 CTTAAGGCAGACGTTTAATTATAATCTATTTTAATAAAAAATATAAAAAAATTCAAACTTAAAAC
* * * *
15273 TAATTATGGGGTTAAAAAAACATTTAAAGCGAGTAATAAGAC
131 TAATTATGAGGTTATAAAATCATTTAAAGCGAGTAATAAGGC
* * **********
15315 TTTCGAAGGCATAGGTGNNNNNNNNNNGACTTTTCTTGCCAATGGATATCTTTTTC-TTCAAGTT
1 TTTTGAAGGCATGGGTGACTATAAATGGACTTTTCTTGCCAATGGATATCTTTTTCTTTC-AGTT
** * * * ********** *
15379 TCTCGAGGTAGAC-ATCAATTATAATCTATTTT-ANNNNNNNNNNAAAAAAATTCAAA-TTCAAA
65 TCTTAAGGCAGACGTTTAATTATAATCTATTTTAATAAAAAATATAAAAAAATTCAAACTTAAAA
* * * *
15441 -TCAATTATAAGGTTATAAAATCA-TTAGAAACGAGTGATGAGGC
130 CT-AATTATGAGGTTATAAAATCATTTA-AAGCGAGTAATAAGGC
* ************* * **
15484 TTTTGAAGGCGTGGGTGACTATAAATGGACTTTTCTTGNNNNNNNNNNNNNTTTTGTTTTGGTTT
1 TTTTGAAGGCATGGGTGACTATAAATGGACTTTTCTTGCCAATGGATATCTTTTTCTTTCAGTTT
* * * * * *
15549 CTTGAGGCAGACGTTCAATTTTAATCTATTTTTATAAAAAATATAAAAAAATT-TAACTTAACAC
66 CTTAAGGCAGACGTTTAATTATAATCTATTTTAATAAAAAATATAAAAAAATTCAAACTTAAAAC
*
15613 TAATTATGAGGTTATACAATCATTTAAAGCGAGTAATAAGGC
131 TAATTATGAGGTTATAAAATCATTTAAAGCGAGTAATAAGGC
* * * ** *
15655 TTTTGAATGCATGGGTGA-TAATAAATGGCCTTTTTTTAACAACGGATATCTTTTTCTTT-ACGT
1 TTTTGAAGGCATGGGTGACT-ATAAATGGACTTTTCTTGCCAATGGATATCTTTTTCTTTCA-GT
* * *
15718 TTCTTGAA-GCAGACATTTAATTATAATCTGTTTTAATAAAAAATATAAAAAAGTTCAA
64 TTCTT-AAGGCAGACGTTTAATTATAATCTATTTTAATAAAAAATATAAAAAAATTCAA
15776 CNNNNNNNNN
Statistics
Matches: 604, Mismatches: 182, Indels: 33
0.74 0.22 0.04
Matches are distributed among these distances:
168 4 0.01
169 87 0.14
170 87 0.14
171 416 0.69
172 10 0.02
ACGTcount: A:0.34, C:0.10, G:0.15, T:0.36
Consensus pattern (172 bp):
TTTTGAAGGCATGGGTGACTATAAATGGACTTTTCTTGCCAATGGATATCTTTTTCTTTCAGTTT
CTTAAGGCAGACGTTTAATTATAATCTATTTTAATAAAAAATATAAAAAAATTCAAACTTAAAAC
TAATTATGAGGTTATAAAATCATTTAAAGCGAGTAATAAGGC
Found at i:16377 original size:170 final size:161
Alignment explanation
Indices: 16196--16511 Score: 357
Period size: 170 Copynumber: 1.9 Consensus size: 161
16186 AAGGCATGGG
* * * * * *
16196 TGACAATAAATGGACTTCTT-TTGCAAATAGATTTGATTTTCTTTACGTTTTTTGTGGCACACAT
1 TGACAATAAATGGACTT-TTCTTGCAAATAGATATCATTTTCTTCACGTTTCTCGAGGCACACAT
* *
16260 TCAATTATAACTTTTTTTAATAAAAAA-TTAAAAAAATTTAAATTAAAATTAAATATGAGGTTAT
65 TCAATTATAACTTTTTTTAATAAAAAACATAAAAAAATTTAAATTAAAATCAAATATGAGGTTAT
*
16324 AAAACCATTTAAAGCGAGCAATAAGGCTTNNNNNNNNNNGAT
130 AAAACCATTAAAAGCGAGCAATAAGGCTT----------GAT
* * * * *
16366 TGACTATAAATGGACTTTTCTTGCCAATCGATATCATTTTCTTCATGTTTCTCGAGGCAGACATT
1 TGACAATAAATGGACTTTTCTTGCAAATAGATATCATTTTCTTCACGTTTCTCGAGGCACACATT
* * *
16431 CAATTATAATTTTTTTTAATAAAAAACATAAAAAAATTTAAATTAAAATCAATTTTGAGGTTATA
66 CAATTATAACTTTTTTTAATAAAAAACATAAAAAAATTTAAATTAAAATCAAATATGAGGTTATA
*
16496 AAATCATTAAAAGCGA
131 AAACCATTAAAAGCGA
16512 NNNNNNNNNN
Statistics
Matches: 126, Mismatches: 18, Indels: 3
0.86 0.12 0.02
Matches are distributed among these distances:
169 2 0.02
170 76 0.60
171 48 0.38
ACGTcount: A:0.39, C:0.11, G:0.11, T:0.37
Consensus pattern (161 bp):
TGACAATAAATGGACTTTTCTTGCAAATAGATATCATTTTCTTCACGTTTCTCGAGGCACACATT
CAATTATAACTTTTTTTAATAAAAAACATAAAAAAATTTAAATTAAAATCAAATATGAGGTTATA
AAACCATTAAAAGCGAGCAATAAGGCTTGAT
Done.