Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018403039.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_706.0, 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: 10883
ACGTcount: A:0.20, C:0.07, G:0.07, T:0.20
Warning! 5111 characters in sequence are not A, C, G, or T
Found at i:1982 original size:171 final size:169
Alignment explanation
Indices: 1679--2081 Score: 470
Period size: 171 Copynumber: 2.4 Consensus size: 169
1669 TTTTTAATCC
* * * * * * *
1679 CATAATTAGTTTTAAGTTGAAATGTTTTATATTTATATTAAATAGATTATAATTAAATGTTTGCT
1 CATAATTAGTTTTAAGTTGAAATTTTTTATATTTTTATAAAATAGATTATAATTGAATGTCTACC
** ** * * * **
1744 TCGGGAAACGTGAAGAAAAAGATATCCATTAGCAAAAAAAGTCTATTTATTGTCGCCAATGCCTT
66 TCAAGAAACCAGAACAAAAAGATATCCATTAGCAAAAAAAGTCCATTTATAGTCGCCAACCCCTT
* * *
1809 CAAAAGCATTATTACTCGCTTTAAATGATTGTATAACCT
131 CAAAAGCATCATCACTCGCTTTAAATAATTGTATAACCT
* *
1848 CATAATTAGTTTTAAGTTGAAATTTTTTACAATTTTTATAAAAATAGATTATAGTTGAATGTCTA
1 CATAATTAGTTTTAAGTTGAAATTTTTTA-TATTTTTAT-AAAATAGATTATAATTGAATGTCTA
* * * *
1913 CCTCAAGAAACCAGAACAAAAAGTTATCCATTGGCAAGAAAAGTCCATTTATAGTCTCTC-ACCC
64 CCTCAAGAAACCAGAACAAAAAGATATCCATTAGCAAAAAAAGTCCATTTATAGTCGC-CAACCC
* * *
1977 CTTCAAAAGCCTCATCACTCGCTTTCAATAATTTTATAACCT
128 CTTCAAAAGCATCATCACTCGCTTTAAATAATTGTATAACCT
*
2019 CATAATTGAG-TTTAA-TTTAAATTTTTTTATATTTTTATTAAAATAGATTATAATTGAATGTCT
1 CATAATT-AGTTTTAAGTTGAAA-TTTTTTATATTTTTA-TAAAATAGATTATAATTGAATGTCT
2082 GNNNNNNNNN
Statistics
Matches: 197, Mismatches: 31, Indels: 11
0.82 0.13 0.05
Matches are distributed among these distances:
169 28 0.14
170 42 0.21
171 124 0.63
172 3 0.02
ACGTcount: A:0.37, C:0.13, G:0.11, T:0.38
Consensus pattern (169 bp):
CATAATTAGTTTTAAGTTGAAATTTTTTATATTTTTATAAAATAGATTATAATTGAATGTCTACC
TCAAGAAACCAGAACAAAAAGATATCCATTAGCAAAAAAAGTCCATTTATAGTCGCCAACCCCTT
CAAAAGCATCATCACTCGCTTTAAATAATTGTATAACCT
Found at i:5300 original size:170 final size:162
Alignment explanation
Indices: 5070--5540 Score: 380
Period size: 170 Copynumber: 2.8 Consensus size: 162
5060 NNNNNNNNNN
* * * * *
5070 TTAAAAAATTCAACTTAAAACCAATTATGAGG-TTATACAATCATTTAAAGAGAGTAATAAGGCT
1 TTAAAAATTTCAACTTAAAACTAATTATG-GGATTAAAAAAGCATTTAAAGAGAGTAATAAGGCT
* * * *
5134 TTTGAAGGCATGAGCGACAATAAATAGACTTTTTTTGCTAATGGGTATCTTTTTCTTCACGTTTC
65 TTTGAAGGCATGAGTGACTATAAATAGACTTTTTTTGC-AATAGATATCTTTTTCTTCACGTTTC
***
5199 TCGANNNNNNNNNNTAATTATAATCTATTTTAAT-AAAAATA
129 TC-A-------AGGTAATTATAATCTATTTTAATAAAAAATA
* * * *
5240 -TAAAGCATTTCAACTTAAAGCTAATTATGGGATTAAAAAAGCATTTAAAGCGAGTAATAAGTCT
1 TTAAA-AATTTCAACTTAAAACTAATTATGGGATTAAAAAAGCATTTAAAGAGAGTAATAAGGCT
** * * *
5304 TTCAAAGGCATTG-GTGACTATAAATGGACTTTTCTTAT-CAATTA-ATATCTTTTTCTTTATGT
65 TTTGAAGGCA-TGAGTGACTATAAATAGACTTTT-TT-TGCAA-TAGATATCTTTTTCTTCACGT
* ** *
5366 TTCTTAAGGNNNNNNNNNNATTATAATCTGTTTTAATAAAAAATA
126 TTCTCAAGG--------TAATTATAATCTATTTTAATAAAAAATA
** * *
5411 TTAAAAATTTCAACTTAAAACTAATTATAAGATTAAAAAAGCATTTAAAGTGAGTAATAA-GATT
1 TTAAAAATTTCAACTTAAAACTAATTATGGGATTAAAAAAGCATTTAAAGAGAGTAATAAGGCTT
* * *
5475 TTCGAAGGCATGAGTTACTATAAATAGACTGTTTTTGCCAATAGATATATTTTTCTTCACGTTTC
66 TT-GAAGGCATGAGTGACTATAAATAGACTTTTTTTG-CAATAGATATCTTTTTCTTCACGTTTC
5540 T
129 T
5541 TGAGGCAGAC
Statistics
Matches: 240, Mismatches: 40, Indels: 41
0.75 0.12 0.13
Matches are distributed among these distances:
169 8 0.03
170 119 0.50
171 108 0.45
172 5 0.02
ACGTcount: A:0.37, C:0.11, G:0.12, T:0.36
Consensus pattern (162 bp):
TTAAAAATTTCAACTTAAAACTAATTATGGGATTAAAAAAGCATTTAAAGAGAGTAATAAGGCTT
TTGAAGGCATGAGTGACTATAAATAGACTTTTTTTGCAATAGATATCTTTTTCTTCACGTTTCTC
AAGGTAATTATAATCTATTTTAATAAAAAATA
Found at i:5562 original size:171 final size:169
Alignment explanation
Indices: 4810--5841 Score: 576
Period size: 171 Copynumber: 6.0 Consensus size: 169
4800 NNNNNNNNNN
* * ** * * *
4810 CTATAAATGGACTTTTCTTGCCAATAGATATCTTTTTCTTCATGTTTCTCAAGACAGGCATTCAA
1 CTATAAATAGACTTTT-TTGCCAATAGATATCTTTTTCTTCACGTTTCTTGAGGCAGACATACAA
* * * * * * ********
4875 TTATAATATATTTTGAT-AAAAATATAAAAAAATTTAAATT-AAACTCAATTATGAGGNNNNNNN
65 TTATAATCTGTTTTAATAAAAAATATTAAAAAATTCAACTTAAAACT-AATTATGAGATTAAAAA
*** * * * * * * *
4938 NNNATTGAAAGCGAGTGATGAGGCTTTTGAAGGCGTGAGAGA
129 AGCATTTAAAGTGAGTAAT-AAGCTTTTAAAGGCATGAGTGA
* * * * * * *
4980 CTATAAATGGACTTTTCTTGTCAATGGATACCTTTTTGTTCTA-GTTTCTTGAGGTAGACATTCA
1 CTATAAATAGACTTTT-TTGCCAATAGATATCTTTTTCTTC-ACGTTTCTTGAGGCAGACATACA
* *********** * * * *
5044 ATTATAATCTATTTTTNNNNNNNNNNTTAAAAAATTCAACTTAAAACCAATTATGAGGTTATACA
64 ATTATAATCTGTTTTAATAAAAAATATTAAAAAATTCAACTTAAAACTAATTATGAGATTAAAAA
* * * *
5109 ATCATTTAAAGAGAGTAATAAGGCTTTTGAAGGCATGAGCGA
129 AGCATTTAAAGTGAGTAATAA-GCTTTTAAAGGCATGAGTGA
* * * * * ***********
5151 CAATAAATAGACTTTTTTTGCTAATGGGTATCTTTTTCTTCACGTTTCTCGANNNNNNNNNNTAA
1 CTATAAATAGAC-TTTTTTGCCAATAGATATCTTTTTCTTCACGTTTCTTGAGGCAGACATACAA
* * * * *
5216 TTATAATCTATTTTAAT-AAAAATA-TAAAGCATTTCAACTTAAAGCTAATTATGGGATTAAAAA
65 TTATAATCTGTTTTAATAAAAAATATTAAA-AAATTCAACTTAAAACTAATTATGAGATTAAAAA
* *
5279 AGCATTTAAAGCGAGTAATAAGTCTTTCAAAGGCATTG-GTGA
129 AGCATTTAAAGTGAGTAATAAG-CTTTTAAAGGCA-TGAGTGA
* ** * * * **********
5321 CTATAAATGGACTTTTCTTATCAATTA-ATATCTTTTTCTTTATGTTTCTTAAGGNNNNNNNNNN
1 CTATAAATAGACTTTT-TTGCCAA-TAGATATCTTTTTCTTCACGTTTCTTGAGGCAGACATACA
* *
5385 ATTATAATCTGTTTTAATAAAAAATATTAAAAATTTCAACTTAAAACTAATTATAAGATTAAAAA
64 ATTATAATCTGTTTTAATAAAAAATATTAAAAAATTCAACTTAAAACTAATTATGAGATTAAAAA
* * *
5450 AGCATTTAAAGTGAGTAATAAGATTTTCGAAGGCATGAGTTA
129 AGCATTTAAAGTGAGTAATAAGCTTTT-AAAGGCATGAGTGA
*
5492 CTATAAATAGACTGTTTTTGCCAATAGATATATTTTTCTTCACGTTTCTTGAGGCAGACATACAA
1 CTATAAATAGACT-TTTTTGCCAATAGATATCTTTTTCTTCACGTTTCTTGAGGCAGACATACAA
* *********** * *
5557 TTATAATCTGTTTTAATATAAAATA-TAAGAAAATTCAAANNNNNNNNNNTTATGAGGTTATAAA
65 TTATAATCTGTTTTAATAAAAAATATTAA-AAAATTCAACTTAAAACTAATTATGAGATTAAAAA
* * *
5621 ATCATTTAAGGCT-AGTAATAAAGCTTTTAAAGGCATGGGTGA
129 AGCATTTAAAG-TGAGTAAT-AAGCTTTTAAAGGCATGAGTGA
** * *
5663 CTATAAATAGACATTTCGTGCCAATGGATATCTTTTTCTTCACGTTTCTTGAGGCAGACATCCAA
1 CTATAAATAGAC-TTTTTTGCCAATAGATATCTTTTTCTTCACGTTTCTTGAGGCAGACATACAA
* * * * *
5728 TTATAATCTGTTTTAATAAGAAATATAAAAAAATTCAAATTAAAA-TCAATTATGAGGTCT-TAA
65 TTATAATCTGTTTTAATAAAAAATATTAAAAAATTCAACTTAAAACT-AATTATGAGAT-TAAAA
* * * * *
5791 AATCCTTTAGAGCGAGTAATAAAGCTTTTGAAA-GCATGGGTGA
128 AAGCATTTAAAGTGAGTAAT-AAGCTTTT-AAAGGCATGAGTGA
5834 CTATAAAT
1 CTATAAAT
5842 NNNNNNNNNN
Statistics
Matches: 669, Mismatches: 167, Indels: 51
0.75 0.19 0.06
Matches are distributed among these distances:
169 9 0.01
170 196 0.29
171 434 0.65
172 30 0.04
ACGTcount: A:0.36, C:0.11, G:0.14, T:0.35
Consensus pattern (169 bp):
CTATAAATAGACTTTTTTGCCAATAGATATCTTTTTCTTCACGTTTCTTGAGGCAGACATACAAT
TATAATCTGTTTTAATAAAAAATATTAAAAAATTCAACTTAAAACTAATTATGAGATTAAAAAAG
CATTTAAAGTGAGTAATAAGCTTTTAAAGGCATGAGTGA
Done.