Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018397817.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_1119.0, 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: 10063
ACGTcount: A:0.23, C:0.08, G:0.08, T:0.24
Warning! 3671 characters in sequence are not A, C, G, or T
Found at i:6096 original size:9 final size:10
Alignment explanation
Indices: 6070--6095 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
6060 TTTAAGTTGA
6070 ATTTTTTAAT
1 ATTTTTTAAT
6080 ATTTTTTAAT
1 ATTTTTTAAT
6090 ATTTTT
1 ATTTTT
6096 AGTTAAAACA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (10 bp):
ATTTTTTAAT
Found at i:7943 original size:170 final size:169
Alignment explanation
Indices: 7271--7954 Score: 550
Period size: 170 Copynumber: 4.0 Consensus size: 169
7261 NNNNNNNNNN
* * * *
7271 TGAGATTATAAAACCATTTAAAGCGAGTAATAATGCTTTTGAAGGAATGGGTGATTATAAATAGA
1 TGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATAGGTGACTATAAATAAA
* * * * *
7336 CTCTTCTTGTCAATGAATGCCTTTTTATTCACGTTTCT-TAAGGAAGACATTCATTTGTAGTCTG
66 CTTTTCTTG-CAATGAATG-CTTTTTCTTCATGTTTCTCT-AGGAAGACATTCAATTATAGTCTG
7400 TTTTAACTAAAAATATAAAAAAATTCAACTGT-AAATCAATTA
128 TTTTAACTAAAAATATAAAAAAATTCAACT-TAAAATCAATTA
* * ********** * *
7442 TCAGATTATAAAACCATTTAAAGTGNNNNNNNNNNCTTTTGAAGGAGT-GTGTGACTATAAATGA
1 TGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATAG-GTGACTATAAATAA
* * * * * * * * *
7506 ACTTTTCTTGCTAGTAAATACCTTTTTCTTCATGTCTCTCGAGGTACACATTAAATTATAATCTG
65 ACTTTTCTTGC-AATGAAT-GCTTTTTCTTCATGTTTCTCTAGGAAGACATTCAATTATAGTCTG
*********** * * *
7571 TTTTAACCNNNNNNNNNNAAAACTTCAGCTTGAAATCAATTA
128 TTTTAACTAAAAATATAAAAAAATTCAACTTAAAATCAATTA
* * * * * * **
7613 TAAGATTATAAAACCATTTAAAGCGAGTAACAAGCCTTTTAAAGGAAAAGGTGGCTAT-AATGGA
1 TGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATAGGTGACTATAAATAAA
* * *
7677 CTTTTCTTGCCAATGAATGCATTTTGT-TTCATGTTTCTCAAGGTAGACATTCAATTATAGTCTA
66 CTTTTCTTG-CAATGAATGC-TTTT-TCTTCATGTTTCTCTAGGAAGACATTCAATTATAGTCTG
* ********** * *
7741 TCTTAACNNNNNNNNNNAAAACATTCAACTTAAAATCAATTG
128 TTTTAACTAAAAATATAAAAAAATTCAACTTAAAATCAATTA
* * * *
7783 TGAGATTCTCAAATCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATAGATGACTATAAATAAA
1 TGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATAGGTGACTATAAATAAA
*
7848 CTTTTCTTGCGAATGAATGCTTTTTCTTCATGTTTCTCTAGGAAGACATTCATTTATAGTCTGTT
66 CTTTTCTTGC-AATGAATGCTTTTTCTTCATGTTTCTCTAGGAAGACATTCAATTATAGTCTGTT
*
7913 TTAACTAAAAATATAAAAAAATTTAACTTAAAATCAATTA
130 TTAACTAAAAATATAAAAAAATTCAACTTAAAATCAATTA
7953 TG
1 TG
7955 NNNNNNNNNN
Statistics
Matches: 394, Mismatches: 107, Indels: 25
0.75 0.20 0.05
Matches are distributed among these distances:
169 2 0.01
170 207 0.53
171 184 0.47
172 1 0.00
ACGTcount: A:0.35, C:0.13, G:0.13, T:0.35
Consensus pattern (169 bp):
TGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATAGGTGACTATAAATAAA
CTTTTCTTGCAATGAATGCTTTTTCTTCATGTTTCTCTAGGAAGACATTCAATTATAGTCTGTTT
TAACTAAAAATATAAAAAAATTCAACTTAAAATCAATTA
Done.