Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018400973.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_4133.0, 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: 3770
ACGTcount: A:0.24, C:0.10, G:0.08, T:0.26
Warning! 1205 characters in sequence are not A, C, G, or T
Found at i:2092 original size:171 final size:171
Alignment explanation
Indices: 1732--2820 Score: 667
Period size: 171 Copynumber: 6.3 Consensus size: 171
1722 NNNNNNNNNN
* * ** * * * * *
1732 TTAAGTTGAATTTTTTTACATTTTTCTTTAAAACAGACAATAGTTGAATGTCTAACTCGACAAAC
1 TTAAGTTAAATTTTTTTATATTTTTGATTAAAACATACTATAATTGAATGTCTACCT-GAGAAAC
* * * *
1797 GTG-TA-AAA-AAGTCATTGATTGAGAAGAAAAGTCCATTTATAGTAGTCACCCATTCCTTCAAA
65 ATGAAAGAAACAAG-CATTCATTGACAAGAAAAGTCCA-TT-TA-TAGTCACCCATTCCTTCAAA
* ** * *
1859 AGGCTTATTACTTGCTTTAAATGGCCTTATAATCTCATAATTGAAT
126 AGGCTTATTACTCGCTTTAAATGGTTTTCTAATCTCATAATTGATT
********** * * * *
1905 NNNNNNNNNNTTTTTTTACATTTTTGATTAAAACAGACTATAATTAAATGCCTACCCTGAGAAAC
1 TTAAGTTAAATTTTTTTATATTTTTGATTAAAACATACTATAATTGAATGTCTA-CCTGAGAAAC
* * * ** * *
1970 ATGCAA-AAA-GAGCCATTCATTGAGAAGAAAAGTTTATTTATAGTCACCCATTCTTTCGAAAGG
65 ATGAAAGAAACAAG-CATTCATTGACAAGAAAAGTCCATTTATAGTCACCCATTCCTTCAAAAGG
* *
2033 TTTATTACTCGCTTTAAACGGTTTTCTAATCTCATAATTGATT
129 CTTATTACTCGCTTTAAATGGTTTTCTAATCTCATAATTGATT
* *
2076 TCAAGTTAAATTTTTTTTTTATATTTTTGATTAAAACATACTATAATTGAATATCTACCT-AGAT
1 TTAAGTTAAA---TTTTTTTATATTTTTGATTAAAACATACTATAATTGAATGTCTACCTGAGA-
* ********** *
2140 AA-ATGTAAAGAAACAAGCACTCATTGACAAGAAAAGTNNNNNNNNNNTCACTCATTCCTTCAAA
62 AACATG-AAAGAAACAAGCATTCATTGACAAGAAAAGTCCATTTATAGTCACCCATTCCTTCAAA
* * * *
2204 AAGCTTATTACTCTCTTTAAATGGTTTTATAATCTCATATTTGATT
126 AGGCTTATTACTCGCTTTAAATGGTTTTCTAATCTCATAATTGATT
********** *
2250 TTAAGTTAAATTTTTTTTATATTTTTGANNNNNNNNNNCTATAATTGAATATCTACCTTGAGAAA
1 TTAAGTTAAA-TTTTTTTATATTTTTGATTAAAACATACTATAATTGAATGTCTACC-TGAGAAA
* * * * *
2315 C-TTAAAGAAACAAGCATTCATTGACAAGAAAAGTCCATTCAGAGTCACACATTCCTTCAAAAAG
64 CATGAAAGAAACAAGCATTCATTGACAAGAAAAGTCCATTTATAGTCACCCATTCCTTCAAAAGG
** ********** *
2379 CTTATTACTCATTTTAAATGGTTTTNNNNNNNNNNATTTGATT
129 CTTATTACTCGCTTTAAATGGTTTTCTAATCTCATAATTGATT
* * * *
2422 TTAAGTTGAATTTTTTTATAGTTTTGATTAAAA-ATACTATAATTGAATGTTTACCTCGAGAAAT
1 TTAAGTTAAATTTTTTTATATTTTTGATTAAAACATACTATAATTGAATGTCTACCT-GAGAAAC
* * * * * **********
2486 GTG-AAGAAACAAGCATTCATTCACAAGAAAAGTCTATTTAGAGTCACCAANNNNNNNNNNAGGC
65 ATGAAAGAAACAAGCATTCATTGACAAGAAAAGTCCATTTATAGTCACCCATTCCTTCAAAAGGC
* *
2550 TTATTACTCGCTTTAAATAG-TTTCATAATCTAATAATTGATT
130 TTATTACTCGCTTTAAATGGTTTTC-TAATCTCATAATTGATT
* ********** * * * **
2592 TTAAGTTGAATGNNNNNNNNNNTTTTG-TTAAAACATACTATAATTAAATGCCCACCCCAAGAAA
1 TTAAGTTAAAT-TTTTTTATATTTTTGATTAAAACATACTATAATTGAATGTCTA-CCTGAGAAA
* * * * * *
2656 CATGCAA-AAA-AAGCCATTCATTTAGAAGAAAAGTTCATTTATAGTCAGCCATTCCTTCAAAAC
64 CATGAAAGAAACAAG-CATTCATTGACAAGAAAAGTCCATTTATAGTCACCCATTCCTTCAAAAG
2719 GCTTATTACTCGCTTTAAATGGTTTTCTAATCTCATAATTGATT
128 GCTTATTACTCGCTTTAAATGGTTTTCTAATCTCATAATTGATT
* ** * * *
2763 TCAAGTTGAGTTTTTTTTATATTTTTAATTAAAACATACTATACTTGAATGTATACCT
1 TTAAGTT-AAATTTTTTTATATTTTTGATTAAAACATACTATAATTGAATGTCTACCT
2821 CAAGACANNN
Statistics
Matches: 681, Mismatches: 212, Indels: 48
0.72 0.23 0.05
Matches are distributed among these distances:
169 4 0.01
170 112 0.16
171 185 0.27
172 165 0.24
173 59 0.09
174 154 0.23
175 2 0.00
ACGTcount: A:0.34, C:0.14, G:0.11, T:0.36
Consensus pattern (171 bp):
TTAAGTTAAATTTTTTTATATTTTTGATTAAAACATACTATAATTGAATGTCTACCTGAGAAACA
TGAAAGAAACAAGCATTCATTGACAAGAAAAGTCCATTTATAGTCACCCATTCCTTCAAAAGGCT
TATTACTCGCTTTAAATGGTTTTCTAATCTCATAATTGATT
Found at i:2340 original size:172 final size:163
Alignment explanation
Indices: 2187--2518 Score: 170
Period size: 172 Copynumber: 2.0 Consensus size: 163
2177 NNNNNNNNNN
* * * *
2187 TCACTCATTCCTTCAAAAAGCTTATTACTCTCTTTAAATGGTTTTATAATCTCATATTTGATTTT
1 TCACTCATTCCTTCAAAAAGCTTATTACTCGCTTTAAACGGTTTTATAATCTCATAATTGATTTC
********** *
2252 AAGTTAAA-TTTTTTTTATATTTTTGANNNNNNNNNNCTATAATTGAATATCTACCTTGAGAAAC
66 AAGTTAAATTTTTTTTTATATTTTTGATTAAAACATACTATAATTGAATATCTACCTAGAGAAA-
*
2316 T-TAAAGAAACAAGCATTCATTGACAAGAAAAGTCCATT
130 TGTAAAGAAACAAGCACTCATTGACAAGAAAAG-----T
* ** * ********** *
2354 CAGAGTCACACATTCCTTCAAAAAGCTTATTACTCATTTTAAATGGTTTTNNNNNNNNNNATTTG
1 -----TCACTCATTCCTTCAAAAAGCTTATTACTCGCTTTAAACGGTTTTATAATCTCATAATTG
* * * * * *
2419 ATTTTAAGTTGAA--TTTTTTTATAGTTTTGATTAAAA-ATACTATAATTGAATGTTTACCTCGA
61 ATTTCAAGTTAAATTTTTTTTTATATTTTTGATTAAAACATACTATAATTGAATATCTACCTAGA
* * *
2481 GAAATGTGAAGAAACAAGCATTCATTCACAAGAAAAGT
126 GAAATGTAAAGAAACAAGCACTCATTGACAAGAAAAGT
2519 CTATTTAGAG
Statistics
Matches: 130, Mismatches: 29, Indels: 9
0.77 0.17 0.05
Matches are distributed among these distances:
165 1 0.01
169 1 0.01
170 53 0.41
171 16 0.12
172 59 0.45
ACGTcount: A:0.34, C:0.13, G:0.10, T:0.37
Consensus pattern (163 bp):
TCACTCATTCCTTCAAAAAGCTTATTACTCGCTTTAAACGGTTTTATAATCTCATAATTGATTTC
AAGTTAAATTTTTTTTTATATTTTTGATTAAAACATACTATAATTGAATATCTACCTAGAGAAAT
GTAAAGAAACAAGCACTCATTGACAAGAAAAGT
Done.