Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018402242.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_5327.0, 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, 736
Length: 1227
ACGTcount: A:0.35, C:0.12, G:0.11, T:0.37
Warning! 50 characters in sequence are not A, C, G, or T
Found at i:391 original size:170 final size:171
Alignment explanation
Indices: 10--1046 Score: 524
Period size: 171 Copynumber: 6.1 Consensus size: 171
1 TTTAAATAG
* * *
10 TTTTATAATCTCATAATTGATTTTAAGTTAAATTTTTTTGCATTTCTCCTTAAAACACACTATAA
1 TTTTATAATCTCATAATTGATTTTAAGTTGAATTTTTTTACATTTCTCATTAAAACACACTATAA
* * * *
75 TTGAATGTCTGTCTTGAGAAACGTGAAGAAAAAGGCATTCATTGACAAAAAAAGTCTATTTATAG
66 TTGAATGTCTGTCTTGAGAAACATGAAGAAAAAGCCATTCATTGACAAAAAAAGGCCATTTATAG
** **********
140 TCATTTATTCCTTCAAAAGCCTTATTACTCGNNNNNNNNNN
131 TCATCCATTCCTTCAAAAGCCTTATTACTCGCTTCAAATTA
* * * * * *
181 TTTTATAATCTCATAATTGATTTTATGTTGAGTTTTTTTACATTTTTTATTAAAATAGACTATAA
1 TTTTATAATCTCATAATTGATTTTAAGTTGAATTTTTTTACATTTCTCATTAAAACACACTATAA
* * *
246 TTGAATG-CT-TGCTTTG-GAAAATATGTAGAAAAAGCCATTCATT-A-AGAAGAAAGGCCATTT
66 TTGAATGTCTGT-C-TTGAG-AAACATGAAGAAAAAGCCATTCATTGACA-AAAAAAGGCCATTT
*
306 ATAGTCATCCATTCCTTCAAATGCCTTATTACTCGCTTCAAATTA
127 ATAGTCATCCATTCCTTCAAAAGCCTTATTACTCGCTTCAAATTA
* * ********** *
351 TTTTATAATCTAATAATTGATTTTAAGTTGAATATTTTTACNNNNNNNNNNAAAACAGACTATAA
1 TTTTATAATCTCATAATTGATTTTAAGTTGAATTTTTTTACATTTCTCATTAAAACACACTATAA
* * * *** ** * *
416 TTGAATGTCTATCTTGAGAAACAT-AAAAAAAAGTCATTCATTGGTGAGTAAAGTCAATTTATAG
66 TTGAATGTCTGTCTTGAGAAACATGAAGAAAAAGCCATTCATTGACAAAAAAAGGCCATTTATAG
* * * **
480 TCA-CTCATT-CTATCAAAAGCTTTATTACTCACTTTAAATGGG
131 TCATC-CATTCCT-TCAAAAGCCTTATTACTCGCTTCAAAT-TA
* ********** * * * * *
522 GTNNNNNNNNNNA-AATTGATTTTAAGTTCAATTTATTTCATATTTC-CAGTTAAAACAGAATAT
1 TTTTATAATCTCATAATTGATTTTAAGTTGAATTT-TTTTACATTTCTCA-TTAAAACACACTAT
* * ** ** *
585 AATTGAATCTGTGTCTCAAGAAACATGAAGAAAAAGGAATTCATTGGA-AAAAGAAA-TCCATTT
64 AATTGAATGTCTGTCTTGAGAAACATGAAGAAAAAGCCATTCATT-GACAAAA-AAAGGCCATTT
* * * ****
648 ATAGTCA-CTTATTCCTTCAAAAGCCTTATTATTCGCTTTAANNNN
127 ATAGTCATC-CATTCCTTCAAAAGCCTTATTACTCGCTTCAAATTA
****** * * * *
693 NNNNNNAATCTCATAATTGATTTTAAGTTGAATTTTTTTATATTTTTCCTTAAAACAAACTATAA
1 TTTTATAATCTCATAATTGATTTTAAGTTGAATTTTTTTACATTTCTCATTAAAACACACTATAA
* ** * ** * *
758 TTGAATGTCT-ACGTTGAGAAATGTAAAGAAAAAGGAATTCATTGACAAAAAAAAGTCGATTTAT
66 TTGAATGTCTGTC-TTGAGAAACATGAAGAAAAAGCCATTCATTGAC-AAAAAAAGGCCATTTAT
* * * ** * * **
822 AGTCA-CCTATTCTTTCAAAAGTCTCACAACTTGCTTTAAATGG
129 AGTCATCC-ATTCCTTCAAAAGCCTTATTACTCGCTTCAAATTA
* ** * * * ****
865 CTTTATAATCTCATAATTGATTTTAAGTTGAATTTTTTTTTATTTTTGATGAAAATTGTCTATAA
1 TTTTATAATCTCATAATTGATTTTAAGTTGAATTTTTTTACATTTCTCATTAAAACACACTATAA
* ** * * * * * *
930 ATGAATGTCTACCATGAGAAATATGAAAAAAAAAAGACATTCATT-AGCAAGAAAAGTCCATTTA
66 TTGAATGTCTGTCTTGAGAAACATG--AAGAAAAAGCCATTCATTGA-CAAAAAAAGGCCATTTA
* * * * * **
994 TAGTCATGCATT-TTATCAAAAGCCTTATTATTTGCTTTAAATGG
128 TAGTCATCCATTCCT-TCAAAAGCCTTATTACTCGCTTCAAATTA
1038 TTTTATAAT
1 TTTTATAAT
1047 NNNNNNNNNN
Statistics
Matches: 663, Mismatches: 172, Indels: 60
0.74 0.19 0.07
Matches are distributed among these distances:
169 20 0.03
170 179 0.27
171 193 0.29
172 191 0.29
173 63 0.10
174 17 0.03
ACGTcount: A:0.35, C:0.12, G:0.11, T:0.37
Consensus pattern (171 bp):
TTTTATAATCTCATAATTGATTTTAAGTTGAATTTTTTTACATTTCTCATTAAAACACACTATAA
TTGAATGTCTGTCTTGAGAAACATGAAGAAAAAGCCATTCATTGACAAAAAAAGGCCATTTATAG
TCATCCATTCCTTCAAAAGCCTTATTACTCGCTTCAAATTA
Found at i:1045 original size:173 final size:172
Alignment explanation
Indices: 699--1046 Score: 416
Period size: 172 Copynumber: 2.0 Consensus size: 172
689 NNNNNNNNNN
* * *
699 AATCTCATAATTGATTTTAAGTTGAATTTTTTTATATTTTTCCTTAAAACAAACTATAATTGAAT
1 AATCTCATAATTGATTTTAAGTTGAATTTTTTTATATTTTTCATGAAAACAAACTATAAATGAAT
** * * * *
764 GTCTACGTTGAGAAATGTAAAGAAAAAGGAATTCATTGACAAAAAAAAGTCGATTTATAGTCACC
66 GTCTACCATGAGAAATATAAAAAAAAAAGAATTCATTGACAAAAAAAAGTCCATTTATAGTCACC
*
829 TATTCTTTCAAAAGTCTCACAACTTGCTTTAAATGGCTTTAT
131 TATTCTTTCAAAAGCCTCACAACTTGCTTTAAATGGCTTTAT
* * ****
871 AATCTCATAATTGATTTTAAGTTGAATTTTTTTTTATTTTTGATGAAAATTGTCTATAAATGAAT
1 AATCTCATAATTGATTTTAAGTTGAATTTTTTTATATTTTTCATGAAAACAAACTATAAATGAAT
*
936 GTCTACCATGAGAAATATGAAAAAAAAAAGACATTCATT-AGC-AAGAAAAGTCCATTTATAGTC
66 GTCTACCATGAGAAATAT-AAAAAAAAAAGA-ATTCATTGA-CAAAAAAAAGTCCATTTATAGTC
* * ** * *
999 ATGC-ATT-TTATCAAAAGCCTTATTATTTGCTTTAAATGGTTTTAT
128 A-CCTATTCTT-TCAAAAGCCTCACAACTTGCTTTAAATGGCTTTAT
1044 AAT
1 AAT
1047 NNNNNNNNNN
Statistics
Matches: 148, Mismatches: 23, Indels: 9
0.82 0.13 0.05
Matches are distributed among these distances:
172 73 0.49
173 66 0.45
174 9 0.06
ACGTcount: A:0.38, C:0.11, G:0.12, T:0.39
Consensus pattern (172 bp):
AATCTCATAATTGATTTTAAGTTGAATTTTTTTATATTTTTCATGAAAACAAACTATAAATGAAT
GTCTACCATGAGAAATATAAAAAAAAAAGAATTCATTGACAAAAAAAAGTCCATTTATAGTCACC
TATTCTTTCAAAAGCCTCACAACTTGCTTTAAATGGCTTTAT
Done.