Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018397851.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_1155.0, 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: 3483
ACGTcount: A:0.28, C:0.11, G:0.09, T:0.30
Warning! 754 characters in sequence are not A, C, G, or T
Found at i:1496 original size:170 final size:169
Alignment explanation
Indices: 783--1812 Score: 667
Period size: 170 Copynumber: 6.0 Consensus size: 169
773 NNNNNNNNNN
* * * * * *
783 TTTATAATCTCATAATGGATTTTAAGTTCAATTTTTTTACATTTTTTGTTAAAACAAATAATAAT
1 TTTATAATCTCATAATTGATTTTAAGTTGAA-TTTTTTATATTTTTTATTAAAACAGATTATAAT
** ** *
848 TGAATGTCTGTCTCAGTAA-ATGGGAAGAAAAAGATAAT-TATTGGCAAGAAAAGTCCATTTATA
65 TGAATGTCTACCTCAAAAACAT--GAAGAAAAAGAT-ATCCATTGGCAAGAAAAGTCCATTTATA
* * * * *
911 GTCA--CATACTCTTACCAAAGTCTT-TTCACTCGCTTTAAATGTT
127 ATCACCCATGC-CTT-CGAAAGCCTTATT-ACTCGCTTTAAATGAT
* **********
954 TTTATAATCTTATAATTGATTNNNNNNNNNNTTTTTT-TATATTTTTATTAAAACAGATTATAAT
1 TTTATAATCTCATAATTGATTTTAAGTTGAATTTTTTATAT-TTTTTATTAAAACAGATTATAAT
* * * * * * * *
1018 TAAATATCTACCTTGATAAACGTGAAAAAAAAGATATCCATTGGCAAAAAAAGTCCATTTATAGT
65 TGAATGTCTACC-TCAAAAACATGAAGAAAAAGATATCCATTGGCAAGAAAAGTCCATTTATAAT
* * *
1083 CACCTATGCCTTCGTAAGCCTTATTACTCGTTTTAAATGAT
129 CACCCATGCCTTCGAAAGCCTTATTACTCGCTTTAAATGAT
* ********* *
1124 TTTATAATCTTATAATTGATTTTANNNNNNNNNNTTTTATATTTTTTATTAAAACAGATTAGAAT
1 TTTATAATCTCATAATTGATTTTA-AGTTGAATTTTTTATATTTTTTATTAAAACAGATTATAAT
* * ** * *
1189 TGAATGTTTACATCAAAAAACATGAAGAAAAAGATATCCACCGGTAAGAAAAGTCCATTTATATT
65 TGAATGTCTACCTC-AAAAACATGAAGAAAAAGATATCCATTGGCAAGAAAAGTCCATTTATAAT
* *
1254 CACCCATGCCTTC-AAATGGCTTATTACTCGCTTTAAATGGT
129 CACCCATGCCTTCGAAA-GCCTTATTACTCGCTTTAAATGAT
********** *
1295 TTTATAATCTCATAANNNNNNNNNNGTTGAATTTTTTATATTTTTTATTAAAACAGATAATAATT
1 TTTATAATCTCATAATTGATTTTAAGTTGAATTTTTTATATTTTTTATTAAAACAGATTATAATT
1360 GAATGTCTACCTCAAAAACTATGAAGAAAAAGATATCCATTGGCAAGAAAAGTCCATTTATAATC
66 GAATGTCTACCTCAAAAAC-ATGAAGAAAAAGATATCCATTGGCAAGAAAAGTCCATTTATAATC
* *
1425 ACCCATGACTTCGAAAGCCTTATTATTCGCTTTAAATGAT
130 ACCCATGCCTTCGAAAGCCTTATTACTCGCTTTAAATGAT
********** * *
1465 TNNNNNNNNNNATAATTGATTTTAAGTTGAATTTTTT-TATCTTTTT-TTAAAACATATTGTAAT
1 TTTATAATCTCATAATTGATTTTAAGTTGAATTTTTTATAT-TTTTTATTAAAACAGATTATAAT
* * ********** * *
1528 TGAATGTCTACCTTGAGAANNNNNNNNNNAAAGATATCAATTGGCAAGAAAAGGT-CATTTATAG
65 TGAATGTCTACC-TCAAAAACATGAAGAAAAAGATATCCATTGGCAAGAAAA-GTCCATTTATAA
* * **
1592 TCACCCACGCCTTCGAAAGCCTTATTACTTGCTTTAAATGGC
128 TCACCCATGCCTTCGAAAGCCTTATTACTCGCTTTAAATGAT
* ********** * *
1634 TTTATAATCTCATATTTNNNNNNNNNNTGAATTTGTTTATGTTCTTTTGTTAAAACAGATTATAA
1 TTTATAATCTCATAATTGATTTTAAGTTGAATTT-TTTATATT-TTTTATTAAAACAGATTATAA
* * * * * * * * * * *
1699 TTGAATGTTTACCTTGAGAAATATAAAGAAAAAGGTATTCATTGGCAAAAAAAGCCCATATATAG
64 TTGAATGTCTACC-TCAAAAACATGAAGAAAAAGATATCCATTGGCAAGAAAAGTCCATTTATAA
* * * *
1764 TCACTCATGCCTTTGAAAGACTTATTACTCGCTTTAAATGGT
128 TCACCCATGCCTTCGAAAGCCTTATTACTCGCTTTAAATGAT
1806 TTTATAA
1 TTTATAA
1813 NNNNNNNNNN
Statistics
Matches: 660, Mismatches: 178, Indels: 41
0.75 0.20 0.05
Matches are distributed among these distances:
169 118 0.18
170 264 0.40
171 168 0.25
172 110 0.17
ACGTcount: A:0.34, C:0.13, G:0.11, T:0.37
Consensus pattern (169 bp):
TTTATAATCTCATAATTGATTTTAAGTTGAATTTTTTATATTTTTTATTAAAACAGATTATAATT
GAATGTCTACCTCAAAAACATGAAGAAAAAGATATCCATTGGCAAGAAAAGTCCATTTATAATCA
CCCATGCCTTCGAAAGCCTTATTACTCGCTTTAAATGAT
Found at i:2690 original size:171 final size:170
Alignment explanation
Indices: 2500--2948 Score: 486
Period size: 171 Copynumber: 2.6 Consensus size: 170
2490 TACATTTTTT
* * * * * *
2500 ATTAAAACAGATTATAATTGAATGTCTACCTTGGGCAACGTGAACAAAAAGATATTCATTGGTAA
1 ATTAAAACAGATAATAATTGAATGTCTGCCTTGGGAAACATGAAGAAAAAGATATCCATTGGTAA
* * * * *
2565 AAAAAGTCCATTTATAGTCACCCACGCCTTCAAAAGCCTTTTTATTAGCTTTAAATATTTTTTTA
66 GAAAAGTCCATTTATAGCCACCCATGCCTTCAAAAGCCTTTTTACTAGCTTTAAATATTTTTATA
* * ********
2630 ATCTCATAATGGATTTTAAGTTGAATTTTTTTANNNNNNNN
131 ATCTCATAATGGATTTTAAATTGAA-CTTTTTACGTGTTTC
** * * * * * *
2671 NNTAAAACATATAATAATTGAATGTTTGCCCTGAGAAACATGAAGAAAAAAATATCCAGT-GTCA
1 ATTAAAACAGATAATAATTGAATGTCTGCCTTGGGAAACATGAAGAAAAAGATATCCATTGGT-A
* * * * * *
2735 AGAAAAGTCCATTTACAGCCACTCATGCCTTCAAAAACCTTATTACTCGCTTTACATATTTTTAT
65 AGAAAAGTCCATTTATAGCCACCCATGCCTTCAAAAGCCTTTTTACTAGCTTTAAATATTTTTAT
**
2800 AATCTCATAATTTATTTTAAATTGAACTTTTTACGTGTTTC
130 AATCTCATAATGGATTTTAAATTGAACTTTTTACGTGTTTC
* * **
2841 ATTAAAACAGATAATTATTTAATGTCTGCCTCAGGAAACATGAAGAAAAAGATATCCATTGGTAA
1 ATTAAAACAGATAATAATTGAATGTCTGCCTTGGGAAACATGAAGAAAAAGATATCCATTGGTAA
* *
2906 GAAAAGTCCGTTTATAGCCACCCATGCCTTCAAAAGCTTTTTT
66 GAAAAGTCCATTTATAGCCACCCATGCCTTCAAAAGCCTTTTT
2949 GATTTTAAGC
Statistics
Matches: 221, Mismatches: 55, Indels: 5
0.79 0.20 0.02
Matches are distributed among these distances:
170 95 0.43
171 126 0.57
ACGTcount: A:0.36, C:0.16, G:0.12, T:0.34
Consensus pattern (170 bp):
ATTAAAACAGATAATAATTGAATGTCTGCCTTGGGAAACATGAAGAAAAAGATATCCATTGGTAA
GAAAAGTCCATTTATAGCCACCCATGCCTTCAAAAGCCTTTTTACTAGCTTTAAATATTTTTATA
ATCTCATAATGGATTTTAAATTGAACTTTTTACGTGTTTC
Done.