Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018398348.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_1647.1, 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: 3399
ACGTcount: A:0.26, C:0.12, G:0.10, T:0.28
Warning! 826 characters in sequence are not A, C, G, or T
Found at i:877 original size:21 final size:21
Alignment explanation
Indices: 853--892 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
843 GAGAAACATG
*
853 AAGAAAAATGCATTTATTAGT
1 AAGAAAAATCCATTTATTAGT
* *
874 AAGAGAAGTCCATTTATTA
1 AAGAAAAATCCATTTATTA
893 TTACCGTTTC
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.45, C:0.07, G:0.15, T:0.33
Consensus pattern (21 bp):
AAGAAAAATCCATTTATTAGT
Found at i:1007 original size:172 final size:167
Alignment explanation
Indices: 1--2121 Score: 1208
Period size: 170 Copynumber: 12.4 Consensus size: 167
* * * *
1 AGAAAAAGACATTCATTGGCAAGAAAAGTCTATTTATAGTCACTTATTCTTTCAAAAGCTTTATT
1 AGAAAAAG-CATTCATT-GCAAGAAAAGTCCATTTATAGTCAC-CATTCCTTCAAAAGCCTTATT
* ********** * * *
66 ACTCGCTTTAAATGATTTTNNNNNNNNNNAATTGATTTTAAGTTGAA-TTTTTTTACATATTGGT
63 ACTCGCTTTAAATGGTTTTATAATCTCATAATTGATTTTAAGTTCAATTTTTTTTACTTTTTGGT
* **
130 TAAAATAGACTATAATTGAATGTCTACATCAAGAAAC-TAGA
128 TAAAACA-ACTATAATTGAATGTCTACATTGAGAAACAT-GA
* * **
171 AGAAAAAGACATTCATTGCCAAGAAAAGTCCATTTATAGTCACTCGTTCTTTTGAAAGCCTTATT
1 AGAAAAAG-CATTCATTG-CAAGAAAAGTCCATTTATAGTCAC-CATTCCTTCAAAAGCCTTATT
* * ********** * *
236 GCTCGCTTTAAATGATTTTATAANNNNNNNNNNGATTTTAAGTTGAATTTTTCTATA-TTTTTGG
63 ACTCGCTTTAAATGGTTTTATAATCTCATAATTGATTTTAAGTTCAATTTTT-TTTACTTTTTGG
** * *
300 TTAAAACAAACTATTGTTGAATGTTTACCTTGAGAAACATGA
127 TTAAAAC-AACTATAATTGAATGTCTACATTGAGAAACATGA
* * * * *
342 AGAAAAGGCATTAATTGGCAAGAAAAATCTATTTATAGTCATCCATTCTTTCAAAAGCCTTATTA
1 AGAAAAAGCATTCATT-GCAAGAAAAGTCCATTTATAGTCA-CCATTCCTTCAAAAGCCTTATTA
********** * * * * *
407 CTCNNNNNNNNNNGTTTTATAATCTAATAATTGATTTTAAGCTGAA-TGTTTTTACGTTTTTTGT
64 CTCGCTTTAAATGGTTTTATAATCTCATAATTGATTTTAAGTTCAATTTTTTTTAC-TTTTTGGT
* * * * * * *
471 TAACACAGACTACT-GTTGAGTGGCTACCTTGAGGAACATAA
128 TAAAACA-ACTA-TAATTGAATGTCTACATTGAGAAACATGA
* *
512 AGAAAAAGCATTCATTAGCAAGAAAAATCTATTTATAGTCACGCATTCCTTCAAAAGCCTTATTA
1 AGAAAAAGCATTCATT-GCAAGAAAAGTCCATTTATAGTCAC-CATTCCTTCAAAAGCCTTATTA
********** * * * **
577 CTCGCTTTAAATNNNNNNNNNNTCTCATAATTAATTTTAAGTTGAA-TTTGTTTACATTTTTTAT
64 CTCGCTTTAAATGGTTTTATAATCTCATAATTGATTTTAAGTTCAATTTTTTTTAC-TTTTTGGT
* * * * *
641 TAAAACAGGCTATAATTAAATATCCAGC-TTAAGAAACATGA
128 TAAAACA-ACTATAATTGAATGTCTA-CATTGAGAAACATGA
*********
682 AGAAAGAAGCATTCATTGCCAAGAAAAGTCCATNNNNNNNNNNCCATTCCTTCAAAAGCCTTATT
1 AGAAA-AAGCATTCATTG-CAAGAAAAGTCCAT-TTATAGTCACCATTCCTTCAAAAGCCTTATT
* * * *
747 ACTC-CATTTAAATGGTTTTATATTCTCAAAATTGATTTTAAGTTTAATTTTTTTTACTTTTTTA
63 ACTCGC-TTTAAATGGTTTTATAATCTCATAATTGATTTTAAGTTCAATTTTTTTTAC-TTTTTG
********* * *
811 GTNNNNNNNNNNTATAACTGAATGTCGACATTGAGAAACATGA
126 GT-TAAAACAACTATAATTGAATGTCTACATTGAGAAACATGA
* * * * *
854 AGAAAAATGCATTTATTAGTAAGAGAAGTCCATTTATTA-TTACCGTTTCCTTCAAAAGCCTTAT
1 AGAAAAA-GCATTCATT-GCAAGAAAAGTCCATTTA-TAGTCACC-ATTCCTTCAAAAGCCTTAT
* * *
918 TACTCGCTTTAAATTGTTTTAAAATCTCAAAATTGATTTTAAGTTCAATTTTTTTTACTTGTTTG
62 TACTCGCTTTAAATGGTTTTATAATCTCATAATTGATTTTAAGTTCAATTTTTTTTACTT-TTTG
*
983 GTTAAAACCAATTATAATTGAATGTCTACATTGAGAAACATGA
126 GTTAAAA-CAACTATAATTGAATGTCTACATTGAGAAACATGA
********* * * *
1026 AGANNNNNNNNNNCATTGGCAAGAAAAGTCCATTTATTGTCACCCATTGCTTTAAAAGCCTTATT
1 AGA-AAAAGCATTCATT-GCAAGAAAAGTCCATTTATAGTCA-CCATTCCTTCAAAAGCCTTATT
** * * * * ** * **
1091 ACTCGCTTTAAATGCCTTTGTAATTTCATAACTGATTATAAGTAGAA-ATTTTTTACATTTTTCT
63 ACTCGCTTTAAATGGTTTTATAATCTCATAATTGATTTTAAGTTCAATTTTTTTTAC-TTTTTGG
* *
1155 TTAAAACAGACTATAACTGAATGTCTACTTTGAGAAACATGA
127 TTAAAACA-ACTATAATTGAATGTCTACATTGAGAAACATGA
* * * * ** * * *
1197 AGAAAAAGAAATTTATTGGTAAGAAAATTCTTTTTATAGTCACCCTTTTCTTCAAAATCCTTATT
1 AGAAAAAG-CATTCATT-GCAAGAAAAGTCCATTTATAGTCA-CCATTCCTTCAAAAGCCTTATT
* * ********** *
1262 ATTCACTTTAAATGGTTTTATAATCTCATANNNNNNNNNNAGTT-AA-ATTTTTTACATTTTTGG
63 ACTCGCTTTAAATGGTTTTATAATCTCATAATTGATTTTAAGTTCAATTTTTTTTAC-TTTTTGG
* * * * *
1325 TTAAAACAAACTATAGTTGAATGTCTACCTCG-GTAAACGTTA
127 TTAAAAC-AACTATAATTGAATGTCTACATTGAG-AAACATGA
* * * *
1367 AGAAAAAAGCGTTCATTGACAAGAAAAGTCAATTTATACTCACTCATTCTTTCAAAAGCCTTATT
1 AG-AAAAAGCATTCATTG-CAAGAAAAGTCCATTTATAGTCAC-CATTCCTTCAAAAGCCTTATT
* * ** *
1432 ACTCGCTATAAATGGTTTGATAATCTCATAATTGATTTTAAGTTGTATTGTTTTTACATTTTTGG
63 ACTCGCTTTAAATGGTTTTATAATCTCATAATTGATTTTAAGTTCAATTTTTTTTAC-TTTTTGG
* * **
1497 TTAAAA-ATGACTGTAATTGAATGCCTATC-TCAAGAAAC-TAGA
127 TTAAAACA--ACTATAATTGAATGTCTA-CATTGAGAAACAT-GA
* *
1539 AG-AAAAGACATTCATTG-AAAAGAAAGTCCATTTATAGTCACTCATTCTTTCAAAAGCCTTATT
1 AGAAAAAG-CATTCATTGCAAGA-AAAGTCCATTTATAGTCAC-CATTCCTTCAAAAGCCTTATT
* * *
1602 GCTCGATTTAAATGGTTTTATAATCTCATAATTCATTTTAAGTTCAATTTTTTTTTACTTTTTTG
63 ACTCGCTTTAAATGGTTTTATAATCTCATAATTGATTTTAAGTTCAA-TTTTTTTTAC-TTTTTG
* * * * *
1667 TTTAAAACATATTATAACTAAATGT-TGACATTGAGAAAGATGAA
126 GTTAAAACA-ACTATAATTGAATGTCT-ACATTGAGAAACATG-A
* * *
1711 AAAAAAATGCATTCATTAGCAAGAAAAGTCCATTTATTA-TCACCCATTCCTTTAAAAGCCGTAT
1 AGAAAAA-GCATTCATT-GCAAGAAAAGTCCATTTA-TAGTCA-CCATTCCTTCAAAAGCCTTAT
********** * * *
1775 TACTCGCTTNNNNNNNNNNTATAATCTCAAAATTGATTTTAAGTTTAATTTTTTTTACTTGTTTA
62 TACTCGCTTTAAATGGTTTTATAATCTCATAATTGATTTTAAGTTCAATTTTTTTTACTT-TTTG
* * ** *
1840 GTTAAAACAGATTATAATTGAATGTCTACGTCAAGAAACGTGA
126 GTTAAAACA-ACTATAATTGAATGTCTACATTGAGAAACATGA
* *
1883 AGAAAAAAGCATTCATTTGCAAAAAAAGTCCATTTATAGTCACTCATTCTTTCAAAAGCCTTATT
1 AG-AAAAAGCATTCA-TTGCAAGAAAAGTCCATTTATAGTCAC-CATTCCTTCAAAAGCCTTATT
* * ********** * * **
1948 ACTCCCTTTAAACGGTTTTATNNNNNNNNNNTTGATTTTAAGTTGAATTTTTTATA-TTTTTTAT
63 ACTCGCTTTAAATGGTTTTATAATCTCATAATTGATTTTAAGTTCAATTTTTTTTACTTTTTGGT
* * * *
2012 TAAAACAAACTATAGTTGAAT-TCGTACCTTGAAAAACTTGA
128 TAAAAC-AACTATAATTGAATGTC-TACATTGAGAAACATGA
* * * *
2053 AGAAAAAAGAATTCATTGGTAAGAAAAGTCCATTTATACTCACTCATTCTTTCAAAAGCCTTATT
1 AG-AAAAAGCATTCATT-GCAAGAAAAGTCCATTTATAGTCAC-CATTCCTTCAAAAGCCTTATT
2118 ACTC
63 ACTC
2122 ACTGTNNNNN
Statistics
Matches: 1501, Mismatches: 381, Indels: 138
0.74 0.19 0.07
Matches are distributed among these distances:
168 3 0.00
169 17 0.01
170 639 0.43
171 316 0.21
172 383 0.26
173 69 0.05
174 68 0.05
175 6 0.00
ACGTcount: A:0.34, C:0.13, G:0.11, T:0.37
Consensus pattern (167 bp):
AGAAAAAGCATTCATTGCAAGAAAAGTCCATTTATAGTCACCATTCCTTCAAAAGCCTTATTACT
CGCTTTAAATGGTTTTATAATCTCATAATTGATTTTAAGTTCAATTTTTTTTACTTTTTGGTTAA
AACAACTATAATTGAATGTCTACATTGAGAAACATGA
Done.