Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018403084.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_751.0, 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: 14459
ACGTcount: A:0.24, C:0.08, G:0.09, T:0.23
Warning! 5295 characters in sequence are not A, C, G, or T
Found at i:3900 original size:169 final size:169
Alignment explanation
Indices: 3205--4034 Score: 468
Period size: 171 Copynumber: 4.9 Consensus size: 169
3195 NTAAAATCAT
* * * * * *
3205 TTAAAGCGAGTAATAAGGCCTTT-GAAGGAATGGGTGACTATAAATACAGTTTTCTTG-CTAATG
1 TTAAAGCGAGTAATAAAGCTTTTAG-AGGAAT-GGTGACTATAAATAGACTTTTATAGTC-AATG
* ** ** * *
3268 AATGCCTTTTTCTTCACGTTTCTAGGTGTAAACTTTCAATTATAGTCTGTTTTAACTAAAAATAT
63 AATGCCTTTTTTTTCACGTTTCGCGAAGTAAACATTCAATTATAATCTGTTTTAACTAAAAATAT
* ********* *
3333 AAAAAAATTAAACTTAAAATCAANNNNNNNNNNNTA-AAACCAT
128 AAAAAAATTGAACTTAAAATCAA--TTATGAGATTATAAACCAA
* * * * * * * *
3376 TTAAAGCGAGTAATAAGGCTTTT-GAAAGAATGAGTGACAATAAATATACTTTTCTTGCCAATCA
1 TTAAAGCGAGTAATAAAGCTTTTAG-AGGAATG-GTGACTATAAATAGACTTTTATAGTCAATGA
* * * ** * * *
3440 ATCCCTTTTTCTTCATGTTTCTTGACA-TGAACATTCAATTACAATATGTTTTAA-TCAAAAA-A
64 ATGCCTTTTTTTTCACGTTTCGCGA-AGTAAACATTCAATTATAATCTGTTTTAACT-AAAAATA
* * * *******
3502 GTAAAAAAATTGGACTTAAAATCAATTTTGAGATTGTNNNNNNNN
127 -TAAAAAAATTGAACTTAAAATCAATTATGAGATTAT-AAACCAA
** * * * * * * *
3547 NNAAAGTGGGTAATAAGGCTTTT-GAAGGAATGGTAAACTATAAATGGACTTTTCT-TTCCAATG
1 TTAAAGCGAGTAATAAAGCTTTTAG-AGGAATGGT-GACTATAAATAGACTTTTATAGT-CAATG
* * ** * * **
3610 AATG-CTTTTTTCCTCACATTTTCTTGAGGTAGACATTCAATTATAGCCTGTTTTAA-TCAAAAA
63 AATGCCTTTTTT-TTCAC-GTTTCGCGAAGTAAACATTCAATTATAATCTGTTTTAACT-AAAAA
* ********** *
3673 TGTAAAAAAATNNNNNNNNNNATCAATTATGAGATTATAAACCAT
125 TATAAAAAAATTGAACTTAAAATCAATTATGAGATTATAAACCAA
* *
3718 TTAAAGTGAGTAAT-AAGACTTTT-GAAGGAATGGGTGAGTATAAATAGAC-TTTATAGTCAATG
1 TTAAAGCGAGTAATAAAG-CTTTTAG-AGGAAT-GGTGACTATAAATAGACTTTTATAGTCAATG
** * ** *
3780 AATG-CTTTTTTCTTCACGTTTTTCGAAGTAAATATTCAATTATTGTCTGTTTTAACTAAAAATG
63 AATGCCTTTTTT-TTCACGTTTCGCGAAGTAAACATTCAATTATAATCTGTTTTAACTAAAAATA
* * *
3844 T-ATAAAATTTAACTTAAAATCAATTATGAGATTATAAAATCAA
127 TAAAAAAATTGAACTTAAAATCAATTATGAGATTAT-AAACCAA
* * * *
3887 TTAGAGCGAGTAATAAAGCTTTTAGAGGAATGGTGACTATAAATGGACTTTTCTTGTCAATGAAT
1 TTAAAGCGAGTAATAAAGCTTTTAGAGGAATGGTGACTATAAATAGACTTTTATAGTCAATGAAT
* * * *
3952 GCCTTTTTTTTCATGTTTCGCGAGGTAGACATTCAATTATAATCTGTTTTGACTAAAAATATAAA
66 GCCTTTTTTTTCACGTTTCGCGAAGTAAACATTCAATTATAATCTGTTTTAACTAAAAATATAAA
4017 AAAATTGAACTTAAAATC
131 AAAATTGAACTTAAAATC
4035 NNNNNNNNNN
Statistics
Matches: 508, Mismatches: 128, Indels: 47
0.74 0.19 0.07
Matches are distributed among these distances:
168 38 0.07
169 125 0.25
170 68 0.13
171 213 0.42
172 64 0.13
ACGTcount: A:0.36, C:0.11, G:0.14, T:0.35
Consensus pattern (169 bp):
TTAAAGCGAGTAATAAAGCTTTTAGAGGAATGGTGACTATAAATAGACTTTTATAGTCAATGAAT
GCCTTTTTTTTCACGTTTCGCGAAGTAAACATTCAATTATAATCTGTTTTAACTAAAAATATAAA
AAAATTGAACTTAAAATCAATTATGAGATTATAAACCAA
Found at i:5610 original size:171 final size:167
Alignment explanation
Indices: 5222--5860 Score: 541
Period size: 171 Copynumber: 3.8 Consensus size: 167
5212 NNNNNNNNNT
* *
5222 AATCTCATAATTGATTTTAAGTTAAATTTTTTACATTTTTAGTTAAAACAGACAATAATTGAATA
1 AATCTCATAATTGATTTTAAGTTAATTTTTTTACATTTTTA-TTAAAACAGACTATAATTGAAT-
* * * * * *
5287 TTTACTTCGAGAAACGTGAAGAAAAAAGCATTCATTGGCTA-TAAAGTCTATTTATACTCACCTA
64 GTTACCTCAAGAAACGTGAAGAAAAAAGCATTCATTGGCAAGAAAAGTCTATTTATAGTCACC-A
* *
5351 TTCCTTCAAAAGTCTTATTA-CTCACTTTAAATGGTTTAAT
128 TTCCTTCAAAAGCCTTATTACCT-ACTTTAAATGGTTTAAC
* ******** *
5391 AATCTCATAATTGATTTTAAGTTGATTTTNNNNNNNNNNTTGATTAAAACAGACTATAATTGAAT
1 AATCTCATAATTGATTTTAAGTTAATTTT--TTTACATTTTTATTAAAACAGACTATAATTGAAT
* * * * * *
5456 GTCTACCTCAAGAAATGTGAGGAAAAATGCATTCATTGGAAAGAAAAGTCCATTTATAGTTTACC
64 GT-TACCTCAAGAAACGTGAAGAAAAAAGCATTCATTGGCAAGAAAAGTCTATTTATAG-TCACC
* *
5521 ATTCCTTGAAAAGCCTTATTACCTACTTTAAATGGTTTTAC
127 ATTCCTTCAAAAGCCTTATTACCTACTTTAAATGGTTTAAC
* * * * *
5562 AATCTCAAAATTGATTTTAAGTCCAATTTTTTTACTCTTTTTATTAAAACAGATTGTAATTGAAT
1 AATCTCATAATTGATTTTAAGT-TAATTTTTTTAC-ATTTTTATTAAAACAGACTATAATTGAAT
** * * * * *
5627 GTTCATGTCAAGAAACATGAAGAAAAAGGGATTCATTGGCAAGAAAAGTATATTTATTGTCACTC
64 GTT-ACCTCAAGAAACGTGAAGAAAAAAGCATTCATTGGCAAGAAAAGTCTATTTATAGTCAC-C
* * * ********
5692 ATTCTTTCAAAAGCCTTATTACTTGCTTTAAATNNNNNNNN
127 ATTCCTTCAAAAGCCTTATTACCTACTTTAAATGGTTTAAC
** * * *
5733 NNTCTCATAATTGATTTTAAGTTTAA-TTTTTTATATTTTTAGTTAAAACATACTATAATTGAAA
1 AATCTCATAATTGATTTTAAG-TTAATTTTTTTACATTTTTA-TTAAAACAGACTATAATTGAAT
* * * * *
5797 GTTTACAC-CTAGAAACATGAAGAAAAAGGCATTCATTAGCAAGAAAACTGC-ATTTATAGTCAC
64 G-TTAC-CTCAAGAAACGTGAAGAAAAAAGCATTCATTGGCAAGAAAAGT-CTATTTATAGTCAC
5860 C
126 C
5861 CANNNNNNNN
Statistics
Matches: 371, Mismatches: 84, Indels: 30
0.76 0.17 0.06
Matches are distributed among these distances:
169 35 0.09
170 132 0.36
171 192 0.52
172 12 0.03
ACGTcount: A:0.36, C:0.13, G:0.11, T:0.37
Consensus pattern (167 bp):
AATCTCATAATTGATTTTAAGTTAATTTTTTTACATTTTTATTAAAACAGACTATAATTGAATGT
TACCTCAAGAAACGTGAAGAAAAAAGCATTCATTGGCAAGAAAAGTCTATTTATAGTCACCATTC
CTTCAAAAGCCTTATTACCTACTTTAAATGGTTTAAC
Found at i:6280 original size:171 final size:171
Alignment explanation
Indices: 5988--6309 Score: 425
Period size: 171 Copynumber: 1.9 Consensus size: 171
5978 NNNNNNNNNN
* *
5988 TTATTAAAACAAACTATAATTGAATACCTGCCTCCAGAAACCTGTAGAAAAAGTCATTCGTTGAC
1 TTATTAAAACAAACTATAATTGAATACCTGCCTCCAGAAACATATAGAAAAAGTCATTCGTTGAC
**
6053 AAGAAAAGTCCATTTATAGTCATCCATTCCTTCAAAAGTCTTATTACTAGCTTTAAATGATTTTA
66 AAGAAAAGTCCATTTATAGTCATCCATTCCTTCAAAAACCTTATTACTAGCTTTAAATGATTTTA
* * *
6118 TCATCTCACAATTGATTTTAAGTTTAATTTTTTTATATTTT
131 TAATCTCAAAATTAATTTTAAGTTTAATTTTTTTATATTTT
* * * * * * * * **
6159 TTATTAAAATAGATTATAATTGAATACCTGCTTTCGGAAACATATAGAAAAATTCATTTGTTGGT
1 TTATTAAAACAAACTATAATTGAATACCTGCCTCCAGAAACATATAGAAAAAGTCATTCGTTGAC
* *
6224 AAGAAAAGTCTATTTATAGTCCTCCATTCCTAT-AAAAACCTTACTT-CTCA-CTTTAAATGATT
66 AAGAAAAGTCCATTTATAGTCATCCATTCCT-TCAAAAACCTTA-TTACT-AGCTTTAAATGATT
6286 TTATAATCTCAAAATTAATTTTAA
128 TTATAATCTCAAAATTAATTTTAA
6310 ANNNNNNNNN
Statistics
Matches: 129, Mismatches: 19, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
171 125 0.97
172 4 0.03
ACGTcount: A:0.37, C:0.15, G:0.09, T:0.39
Consensus pattern (171 bp):
TTATTAAAACAAACTATAATTGAATACCTGCCTCCAGAAACATATAGAAAAAGTCATTCGTTGAC
AAGAAAAGTCCATTTATAGTCATCCATTCCTTCAAAAACCTTATTACTAGCTTTAAATGATTTTA
TAATCTCAAAATTAATTTTAAGTTTAATTTTTTTATATTTT
Done.