Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018397785.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_1085.0, 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: 2217
ACGTcount: A:0.28, C:0.10, G:0.10, T:0.29
Warning! 524 characters in sequence are not A, C, G, or T
Found at i:682 original size:171 final size:170
Alignment explanation
Indices: 351--1425 Score: 967
Period size: 171 Copynumber: 6.3 Consensus size: 170
341 NNNNNNNNNN
* * * * * * *
351 GCAAGATAAGTCCATTTATAGTCTCCTATTCCTTT-AAAAGCCTTATTACTTGCTTTATATAG-T
1 GCAAGAAAAGTCCATTTATAGTCACCCATT-CTTTCAAAAGCCATATTACTCGCTTTAAATGGTT
* * * * * * * * *
414 TTATAATCACAAAATTGATTTTAGGTTCAATTTTTTATTACATTATTT-GCTGAAATAGATTATA
65 TTATAATCTCATAATTGATTTTAAGTTGAA-TTTTT-TTATATT-TTTAGTTAAAACAGACTATA
* * * *
478 ATTG-GTGTCTAGCACAAGTAAA-AT-AATGAAAAAGCTATTCATAG
127 ATTGAATGTCTACCTCAAG-AAACATGAA-GAAAAAGC-ATTCATTG
*
522 TG-AAGAAAAGTCCATTTATTGTCACCCATTCTTTCAAAAGCCATATTACTCGCTTTAAATGGTT
1 -GCAAGAAAAGTCCATTTATAGTCACCCATTCTTTCAAAAGCCATATTACTCGCTTTAAATGGTT
* * * *
586 TTGTAATCTCGTAATTGATTTTAAGTTGAATTTTTTTATATTTTTTGTTAAAACAGACTATAGTT
65 TTATAATCTCATAATTGATTTTAAGTTGAATTTTTTTATATTTTTAGTTAAAACAGACTATAATT
* *
651 GAACGTCTACCTCAAGAAACATGTAGAAAAAGCCATTCATTG
130 GAATGTCTACCTCAAGAAACATGAAGAAAAAG-CATTCATTG
* * * * * * **
693 GTAA-AAAAATTCATTTTATAGTCACCCATACTTTCAAAAACCATATTACTCACTTTAAATTATT
1 GCAAGAAAAGTCCA-TTTATAGTCACCCATTCTTTCAAAAGCCATATTACTCGCTTTAAATGGTT
* * * * *
757 TTATAATCTCATAATTGATTTTGAGTTG-AGTTTTTCACT-TTTTTAGTTAAAACATACTAGAAT
65 TTATAATCTCATAATTGATTTTAAGTTGAATTTTTTTA-TATTTTTAGTTAAAACAGACTATAAT
* * * *
820 TGAATGTCTACCTCGAGAAATATGAAGAAAAACTCATTAATTG
129 TGAATGTCTACCTCAAGAAACATGAAGAAAAA-GCATTCATTG
* * ** * *
863 GTAAGAAAAGTCCAATTATAGTCACGTATTCTTTCAAAAGCCTTATTACTCGCTTTAAATGGTAT
1 GCAAGAAAAGTCCATTTATAGTCACCCATTCTTTCAAAAGCCATATTACTCGCTTTAAATGGTTT
* *
928 TATAATCTCATAATTGATTTTAAGTTGAATTTTTTAATATTTTTTGTTAAAACAGACTATAATT-
66 TATAATCTCATAATTGATTTTAAGTTGAATTTTTTTATATTTTTAGTTAAAACAGACTATAATTG
* * *
992 AATTGTATAGCTTGAA-AAACATGAAGAAACAAGCATTCATTG
131 AA-TGTCTA-CCTCAAGAAACATGAAGAAA-AAGCATTCATTG
* * * * * * * *
1034 GAAAGACAAGTCTATTTATAGTCTCCTATT-TCTTCAAAAGCCTTATTACTCGATTTAAATAGTT
1 GCAAGAAAAGTCCATTTATAGTCACCCATTCT-TTCAAAAGCCATATTACTCGCTTTAAATGGTT
* * * * * * * *
1098 TTATAATCTCAAAATTGATTTTAGGTTCAATTTTTTTTACATTATTGGTTAAAGA-ATATTATAA
65 TTATAATCTCATAATTGATTTTAAGTTGAA-TTTTTTTATATTTTTAGTTAAA-ACAGACTATAA
* ** * ** *
1162 TTGAATGTCTAGCTTGAGTAATGTAAAGAAAAAGACATTCATTG
128 TTGAATGTCTACCTCAAGAAACATGAAGAAAAAG-CATTCATTG
* * * * *
1206 GCAGGAAAAGGT-CATTTATAGTAACCTATTCCTTCAAAAGCCATATTACTGGCTTTAAATGGTT
1 GCAAGAAAA-GTCCATTTATAGTCACCCATTCTTTCAAAAGCCATATTACTCGCTTTAAATGGTT
* * * *
1270 CTATAATCTCATAATTGATTTTAAGTTGATTTTTTTTACA-TTTTAGTTAAAACAGACTATAATG
65 TTATAATCTCATAATTGATTTTAAGTTGAATTTTTTTATATTTTTAGTTAAAACAGACTATAATT
* * * * ** *
1334 GAAGGTCTACTTTAAGAAACATAAAGAAAAAGACATAAACTG
130 GAATGTCTACCTCAAGAAACATGAAGAAAAAG-CATTCATTG
* * * *
1376 GCAAAAAAAGTCCATTTAAAGTCACCCATTCCTTCAAAAGCCTTATTACT
1 GCAAGAAAAGTCCATTTATAGTCACCCATTCTTTCAAAAGCCATATTACT
1426 NNNNNNNNNN
Statistics
Matches: 738, Mismatches: 138, Indels: 56
0.79 0.15 0.06
Matches are distributed among these distances:
169 6 0.01
170 264 0.36
171 306 0.41
172 157 0.21
173 5 0.01
ACGTcount: A:0.36, C:0.14, G:0.12, T:0.38
Consensus pattern (170 bp):
GCAAGAAAAGTCCATTTATAGTCACCCATTCTTTCAAAAGCCATATTACTCGCTTTAAATGGTTT
TATAATCTCATAATTGATTTTAAGTTGAATTTTTTTATATTTTTAGTTAAAACAGACTATAATTG
AATGTCTACCTCAAGAAACATGAAGAAAAAGCATTCATTG
Done.