Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018401230.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_4376.0, 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: 2718
ACGTcount: A:0.27, C:0.08, G:0.10, T:0.24
Warning! 857 characters in sequence are not A, C, G, or T
Found at i:615 original size:170 final size:167
Alignment explanation
Indices: 319--907 Score: 474
Period size: 170 Copynumber: 3.5 Consensus size: 167
309 NNNNNNNNNT
* * * * *
319 GAGTAATAAAGCTTTTGAAGGAAT-ATGTGACTAT-AATGAACTTTTCTTGCC-AATGAATG-GA
1 GAGTAATAAGGCTTTT-AAAGAATGA-GAGACTATAAATGGACTTTTCTT-CCAAATAAATGCG-
* * * * *
380 TTTTACTTCATGCTTCTCAAGGTAGACACTCAATTATAGTCTGTTTTAAAAAATATATAAAAAAA
62 TTTTTCTACATGTTTCTCAAGGCAGACATTCAATTATAGTCTGTTTTAAAAAA-ATATAAAAAAA
* * *
445 TTGAACTTAAAATAAGTTATGAGATTATAAAACTAGTTAAAGC
126 TTAAACTTAAAATAA-TTATGAGATTATAAAACCACTTAAAGC
* * *
488 GAGTAATATGGCTTTTAAAGAAATAAGAGACTATAAATGGACTTTTCTTCCAAATCAATGCGTTT
1 GAGTAATAAGGCTTTTAAAG-AATGAGAGACTATAAATGGACTTTTCTTCCAAATAAATGCGTTT
* * * *
553 TT-TAACATGTTTCTTAAGGCAGACATTCAATTATAATATGTTTTAAGGAAAAATGT-AAAAAAT
65 TTCT-ACATGTTTCTCAAGGCAGACATTCAATTATAGTCTGTTTTAA--AAAAATATAAAAAAAT
* * * ****************
616 TCAACTGAAACTCAATTATGNNNNNNNNNNNNNNNNTAAAGC
127 TAAACTTAAAAT-AATTATGAGATTATAAAACCACTTAAAGC
* * * * *
658 GAGTAATAAGGCTTTTAAATGAATGGGTGACTATAAATGGACTTTTC-TCAACAATGAATGCATT
1 GAGTAATAAGGCTTTTAAA-GAATGAGAGACTATAAATGGACTTTTCTTCCA-AATAAATGCGTT
* * *
722 TTTCTTCAAGTTTCTCAAGGCAGACATTCAATTATAGTCCGTTTTAAATAAAAATATAAAAAAAT
64 TTTCTACATGTTTCTCAAGGCAGACATTCAATTATAGTCTGTTTT-AA-AAAAATATAAAAAAAT
* * * *
787 TAAACTTAAAATCATTATGAGATTATAAAACCACTGAGAGT
127 TAAACTTAAAATAATTATGAGATTATAAAACCACTTAAAGC
* **
828 GAGTAATAAGGCTTCTTGAAGGAATGAGAGACTATAAATAAACTTTTCTTCCAAATAAATAG-GT
1 GAGTAATAAGGCTT-TT-AAAGAATGAGAGACTATAAATGGACTTTTCTTCCAAATAAAT-GCGT
892 TTTTCTACATGTTTCT
63 TTTTCTACATGTTTCT
908 TAAAAGAGGC
Statistics
Matches: 320, Mismatches: 82, Indels: 34
0.73 0.19 0.08
Matches are distributed among these distances:
168 3 0.01
169 30 0.09
170 205 0.64
171 72 0.22
172 10 0.03
ACGTcount: A:0.39, C:0.11, G:0.14, T:0.33
Consensus pattern (167 bp):
GAGTAATAAGGCTTTTAAAGAATGAGAGACTATAAATGGACTTTTCTTCCAAATAAATGCGTTTT
TCTACATGTTTCTCAAGGCAGACATTCAATTATAGTCTGTTTTAAAAAAATATAAAAAAATTAAA
CTTAAAATAATTATGAGATTATAAAACCACTTAAAGC
Found at i:1823 original size:170 final size:169
Alignment explanation
Indices: 1647--2153 Score: 579
Period size: 170 Copynumber: 3.0 Consensus size: 169
1637 NNNNNNNNNN
* *
1647 TTATAAAACTATTTAAAGCGAGTAATAAGGCTTTTGAAGAAATAAAAGACTATAAATGGACTTTT
1 TTATAAAACTATTTAAAGCGAGTAATAAGGCTTTTGAAG-AATGAGAGACTATAAATGGACTTTT
* * * *
1712 CTTTCAAATCAATGGGTTTTTTAACATGTTTCTTAAGGCAGACATTCAATTATAATCTATTTTAA
65 CTTTCAAATAAATGGGTTTTTTAACATGTTTCTCAAGGCAGACATTCAATTATAGTCTGTTTTAA
*
1777 GGAAAAATATAAAAAATTCAAC-GAAAACTCAATTATGAGA
130 AGAAAAATATAAAAAATTCAACTGAAAA-TCAATTATGAGA
* * * * *
1817 TTATAAAACCATTTAAAGCGAGTAATAAGGTTTTTAAATGAATGGGTGACTATAAATGGACTTTT
1 TTATAAAACTATTTAAAGCGAGTAATAAGGCTTTTGAA-GAATGAGAGACTATAAATGGACTTTT
* ** * *** * * * *
1882 CTCTGTAATGAATACATTTTTCT-TCAAGTTTCTCAAGGCAGACATTGAATTATAGTCCGTTTTA
65 CTTTCAAATAAATGGGTTTTT-TAACATGTTTCTCAAGGCAGACATTCAATTATAGTCTGTTTTA
* * *
1946 AATAAAAATATAAACAAATTAAACTTAAAATCAATTATGAGA
129 AAGAAAAATATAAA-AAATTCAACTGAAAATCAATTATGAGA
** *
1988 TTATAAAA-TCACCTAAAGTGAGTAATAAGGCTTCTTGAAGGAATGAGAGACTATAAATGGACTT
1 TTATAAAACT-ATTTAAAGCGAGTAATAAGGCTT-TTGAA-GAATGAGAGACTATAAATGGAC-T
* * *
2052 TTGTTTTTCAAATAAATGGGTTTTTTAACATGTTTCTCAAGGGAGGCATTCAATTATAGTCTGTT
62 TT-TCTTTCAAATAAATGGGTTTTTTAACATGTTTCTCAAGGCAGACATTCAATTATAGTCTGTT
* * * *
2117 TTAATGACAAATGTAAAAAATTCAGCTGAAAATCAAT
126 TTAAAGAAAAATATAAAAAATTCAACTGAAAATCAAT
2154 NNNNNNNNNN
Statistics
Matches: 273, Mismatches: 55, Indels: 15
0.80 0.16 0.04
Matches are distributed among these distances:
170 116 0.42
171 49 0.18
172 28 0.10
173 21 0.08
174 59 0.22
ACGTcount: A:0.40, C:0.11, G:0.15, T:0.34
Consensus pattern (169 bp):
TTATAAAACTATTTAAAGCGAGTAATAAGGCTTTTGAAGAATGAGAGACTATAAATGGACTTTTC
TTTCAAATAAATGGGTTTTTTAACATGTTTCTCAAGGCAGACATTCAATTATAGTCTGTTTTAAA
GAAAAATATAAAAAATTCAACTGAAAATCAATTATGAGA
Found at i:2214 original size:344 final size:341
Alignment explanation
Indices: 1660--2340 Score: 798
Period size: 344 Copynumber: 2.0 Consensus size: 341
1650 TAAAACTATT
*
1660 TAAAGCGAGTAATAAGGCTTTTGAAGAAATAAAAGACTATAAATGGACTTTTCTTTCAAATCAAT
1 TAAAGCGAGTAATAAGGCTTTTGAAGAAATAAAAGACTATAAATGGACTTTTCTTTCAAATAAAT
*
1725 GGGTTTTTTAACATGTTTCTTAAGGCAGACATTCAATTATAATCTATTTTAAGGAAAAATATAAA
66 GGGTTTTTTAACATGTTTCTCAAGGCAGACATTCAATTATAATCTATTTTAAGGAAAAATATAAA
* * *
1790 AAATTCAACGAAAACTCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGGTTTTTAAA
131 AAATTCAACGAAAACTCAATTATGAGATTATAAAACAATTTAAAGCGAGTAATAAGGCTTTGAAA
* * *
1855 TGAATGGGTGACTATAAATGGACTTTTCTCTG-TAATGAATACATTTTTCTTCAAGTTTCTCAAG
196 TGAATGGGTGACTATAAATGAACTTTTCT-TGCCAATGAATACATTTTTCTTCAACTTTCTCAAG
* * * * *
1919 GCAGACATTGAATTATAGTCCGTTTTAA-ATAAAAA-TATAAACAAATTAAACTTAAAATCAATT
260 ACAGACATTGAATTATAATCCGTCTCAACA-AAAAAGTA-AAAAAAATTAAACTTAAAATCAATT
1982 ATGAGATTATAAAATCACC
323 ATGAGATTATAAAATCACC
* * * * *
2001 TAAAGTGAGTAATAAGGCTTCTTGAAGGAATGAGAGACTATAAATGGACTTTTGTTTTTCAAATA
1 TAAAGCGAGTAATAAGGCTT-TTGAAGAAATAAAAGACTATAAATGGAC-TTT-TCTTTCAAATA
* * * * * * *
2066 AATGGGTTTTTTAACATGTTTCTCAAGGGAGGCATTCAATTATAGTCTGTTTTAATGACAAATGT
63 AATGGGTTTTTTAACATGTTTCTCAAGGCAGACATTCAATTATAATCTATTTTAAGGAAAAATAT
* ********** *
2131 AAAAAATTCAGCTGAAAA-TCAATNNNNNNNNNNTAAAACAATTTAAAGCGAGTAATAGGGCCTT
128 AAAAAATTCAAC-GAAAACTCAATTATGAGATTATAAAACAATTTAAAGCGAGTAATAAGG-CTT
* * *
2195 TGAAA-GAATAGGG-GACTATAAATGAACTTTTCTTGCCAATGAATGCCTTTTTCTTCATCTTTC
191 TGAAATGAAT-GGGTGACTATAAATGAACTTTTCTTGCCAATGAATACATTTTTCTTCAACTTTC
* * * * * *
2258 TCGATATAGACATTTAATTATAATCTGTCTCAAGCAAAAAAGTAAAAAAAATTGAACTTAAAATC
255 TCAAGACAGACATTGAATTATAATCCGTCTCAA-CAAAAAAGTAAAAAAAATTAAACTTAAAATC
* *
2323 AATTTTGAGGTTATAAAA
319 AATTATGAGATTATAAAA
2341 CCATTTNNNN
Statistics
Matches: 282, Mismatches: 48, Indels: 16
0.82 0.14 0.05
Matches are distributed among these distances:
341 19 0.07
342 25 0.09
343 5 0.02
344 176 0.62
345 54 0.19
346 3 0.01
ACGTcount: A:0.40, C:0.11, G:0.15, T:0.33
Consensus pattern (341 bp):
TAAAGCGAGTAATAAGGCTTTTGAAGAAATAAAAGACTATAAATGGACTTTTCTTTCAAATAAAT
GGGTTTTTTAACATGTTTCTCAAGGCAGACATTCAATTATAATCTATTTTAAGGAAAAATATAAA
AAATTCAACGAAAACTCAATTATGAGATTATAAAACAATTTAAAGCGAGTAATAAGGCTTTGAAA
TGAATGGGTGACTATAAATGAACTTTTCTTGCCAATGAATACATTTTTCTTCAACTTTCTCAAGA
CAGACATTGAATTATAATCCGTCTCAACAAAAAAGTAAAAAAAATTAAACTTAAAATCAATTATG
AGATTATAAAATCACC
Found at i:2217 original size:172 final size:169
Alignment explanation
Indices: 1647--2225 Score: 553
Period size: 170 Copynumber: 3.4 Consensus size: 169
1637 NNNNNNNNNN
**
1647 TTATAAAACTATTTAAAGCGAGTAATAAGGCTTTTG-AAGAAATAAAAGACTATAAATGGAC-TT
1 TTATAAAAC-ATTTAAAGCGAGTAATAAGGCTTTTGAAAG-AAT-GGAGACTATAAATGGACTTT
* * * *
1710 TTCTTTCAAATCAATGGGTTTTTTAACATGTTTCTTAAGGCAGACATTCAATTATAATCTATTTT
63 TTCTTTCAAATAAATGGGTTTTTTAACATGTTTCTCAAGGCAGACATTCAATTATAGTCTGTTTT
*
1775 AAGGAAAAATATAAAAAATTCAAC-GAAAACTCAATTATGAGA
128 AATGAAAAATATAAAAAATTCAACTGAAAA-TCAATTATGAGA
* *
1817 TTATAAAACCATTTAAAGCGAGTAATAAGG-TTTTTAAATGAATGGGTGACTATAAATGGACTTT
1 TTATAAAA-CATTTAAAGCGAGTAATAAGGCTTTTGAAA-GAAT-GGAGACTATAAATGGACTTT
* * *** * * * *
1881 TCTCTGT--AATGAATACATTTTTCT-TCAAGTTTCTCAAGGCAGACATTGAATTATAGTCCGTT
63 T-TCTTTCAAATAAATGGGTTTTT-TAACATGTTTCTCAAGGCAGACATTCAATTATAGTCTGTT
* *
1943 TTAAAT-AAAAATATAAACAAATTAAACTTAAAATCAATTATGAGA
126 TT-AATGAAAAATATAAA-AAATTCAACTGAAAATCAATTATGAGA
** * *
1988 TTATAAAATCACCTAAAGTGAGTAATAAGGCTTCTTGAAGGAATGAGAGACTATAAATGGACTTT
1 TTATAAAA-CATTTAAAGCGAGTAATAAGGCTT-TTGAAAGAATG-GAGACTATAAATGGACTTT
* * *
2053 TGTTTTTCAAATAAATGGGTTTTTTAACATGTTTCTCAAGGGAGGCATTCAATTATAGTCTGTTT
63 T-TCTTTCAAATAAATGGGTTTTTTAACATGTTTCTCAAGGCAGACATTCAATTATAGTCTGTTT
* * * *******
2118 TAATGACAAATGTAAAAAATTCAGCTGAAAATCAATNNNNNNN
127 TAATGAAAAATATAAAAAATTCAACTGAAAATCAATTATGAGA
*** * * * *
2161 NNNTAAAACAATTTAAAGCGAGTAATAGGGCCTTTGAAAGAATAGGGGACTATAAATGAACTTTT
1 TTATAAAAC-ATTTAAAGCGAGTAATAAGGCTTTTGAAAGAAT-GGAGACTATAAATGGACTTTT
2226 CTTGCCAATG
Statistics
Matches: 328, Mismatches: 63, Indels: 34
0.77 0.15 0.08
Matches are distributed among these distances:
169 4 0.01
170 102 0.31
171 55 0.17
172 64 0.20
173 49 0.15
174 54 0.16
ACGTcount: A:0.40, C:0.11, G:0.15, T:0.33
Consensus pattern (169 bp):
TTATAAAACATTTAAAGCGAGTAATAAGGCTTTTGAAAGAATGGAGACTATAAATGGACTTTTTC
TTTCAAATAAATGGGTTTTTTAACATGTTTCTCAAGGCAGACATTCAATTATAGTCTGTTTTAAT
GAAAAATATAAAAAATTCAACTGAAAATCAATTATGAGA
Done.