Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018401410.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_4538.0, 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: 2425
ACGTcount: A:0.32, C:0.12, G:0.10, T:0.34
Warning! 284 characters in sequence are not A, C, G, or T
Found at i:1066 original size:171 final size:169
Alignment explanation
Indices: 751--1177 Score: 470
Period size: 171 Copynumber: 2.5 Consensus size: 169
741 NNNNNNNNNN
* *
751 TTTATTAAAACATATTATAATTGAATGTCTACCTCAAGAAACGTAAAGAAAAAT-ATATCCATGG
1 TTTATTAAAACAGATTATAATTGAATGTCTACCTCAA-AAAAGTAAAG-AAAATGATATCCAT-G
* * * * * * *
815 GCAAAACAGGTCCATTTGTAGTCACCCATACTTTCGAAAGCCTTATTGCTCGCTTTAAATAGTTT
63 GCAAAAAAAGTCCATTTATAGTCACCCATACCTTCGAAAGCCTTATTACTCACATTAAATAGTTT
* * *
880 TTTAATCTAATAATTGGTTTTAA-GTTGAACTTT-TTTGCATTT
128 TATAATCTAATAATTGATTTTAATG-TGAA-TTTCTTTACATTT
* * *
922 TTTCTTAAAACAGATTATGATTAAATGTCTACCTCAAAAAAGGTAAAGAAAATGATATCCACTGG
1 TTTATTAAAACAGATTATAATTGAATGTCTACCTCAAAAAA-GTAAAGAAAATGATATCCA-TGG
* * *
987 CAATATAAGTCTATTTATAGTCACCCATACCTTCGAGAA-CCTTATTACTCACATTAAAT-GATT
64 CAAAAAAAGTCCATTTATAGTCACCCATACCTTCGA-AAGCCTTATTACTCACATTAAATAG-TT
* *
1050 TTATAATCTCATAATTGATTTTAATGTGAATTTCTTTATATTT
127 TTATAATCTAATAATTGATTTTAATGTGAATTTCTTTACATTT
* * * *
1093 TTTATTAAAAAAGATTATAATTGAATGTCTGCCTTCAGAAACA-TAAAGAAAAAGATATCCATTG
1 TTTATTAAAACAGATTATAATTGAATGTCTACC-TCA-AAAAAGTAAAGAAAATGATATCCA-TG
* *
1157 GTAAGAAAAGTCCATTTATAG
63 GCAAAAAAAGTCCATTTATAG
1178 NNNNNNNNNN
Statistics
Matches: 216, Mismatches: 31, Indels: 18
0.82 0.12 0.07
Matches are distributed among these distances:
170 12 0.06
171 193 0.89
172 7 0.03
173 4 0.02
ACGTcount: A:0.37, C:0.14, G:0.12, T:0.37
Consensus pattern (169 bp):
TTTATTAAAACAGATTATAATTGAATGTCTACCTCAAAAAAGTAAAGAAAATGATATCCATGGCA
AAAAAAGTCCATTTATAGTCACCCATACCTTCGAAAGCCTTATTACTCACATTAAATAGTTTTAT
AATCTAATAATTGATTTTAATGTGAATTTCTTTACATTT
Found at i:1801 original size:170 final size:169
Alignment explanation
Indices: 1309--2425 Score: 753
Period size: 170 Copynumber: 6.6 Consensus size: 169
1299 GGGAAGTGTG
* * *
1309 AAGAAAAAGATATCCATTAGTAAAAAAAGTCCATTTATTGTCAAC-CATGCCTTCAAAAGCCTTA
1 AAGAAAAAGATATCCATTAGCAAGAAAAGTCCATTTATAGTC-ACGCATGCCTTCAAAAGCCTTA
* * * *
1373 TTACTCGTTTTAAATGATTGTATAACCTCATAAATT-GTTTTAAGTTGAATTGTTTTACAATTTT
65 TTACTCGCTTTAAATGATTTTATAATCTCAT-AATTAGTTTTAAGTTGAATT-TTTTA-TATTTT
* * ** * * *
1437 TATAAAAATAGATTATAATTGAACATTTGCCTCAAGAAACCA-G
127 TATTAAAACAGATTATAATTGAATGTCTGCCTCGAGAAA-CATA
* * * * * *
1480 AACAAAAAGATATCCATTAGCAAGAAAAGTCCATTTGTAGTCACTCAAGCCTTCAAAAGTCTCAT
1 AAGAAAAAGATATCCATTAGCAAGAAAAGTCCATTTATAGTCACGCATGCCTTCAAAAGCCTTAT
* * * ********** * *
1545 CACTCGCTTTTAATGATTTTATAACCTCATNNNNNNNNNNAATTTAAATTTTTTTTATATTTTTA
66 TACTCGCTTTAAATGATTTTATAATCTCATAATTAGTTTTAAGTTGAA--TTTTTTATATTTTTA
* * *
1610 TTAAAATAGATTATAATTGAATATCTGCCTCGAGAAACATT
129 TTAAAACAGATTATAATTGAATGTCTGCCTCGAGAAACATA
* * * *
1651 AAGAAAAAGATATCCATTGGCAAGAAAAGTCTATTTATAATCACGCATGCCTTCGAAAGCCTTAT
1 AAGAAAAAGATATCCATTAGCAAGAAAAGTCCATTTATAGTCACGCATGCCTTCAAAAGCCTTAT
* * *
1716 TACTCTCTTTAAAT-ACTTTTTTAATCTCATACTTAGTTTTAAGTTGAAATTTTTTATATTTTTA
66 TACTCGCTTTAAATGA-TTTTATAATCTCATAATTAGTTTTAAGTTG-AATTTTTTATATTTTTA
* * ********** **
1780 CTAAAACATATTATAATTGAATGTNNNNNNNNNNAAATGTA
129 TTAAAACAGATTATAATTGAATGTCTGCCTCGAGAAACATA
* * * * * * * *
1821 AAGAGAATGATATCCAATT-GCAAGAGAACTCCATTTATAATCACTCATACCTTCAAAAACCTTA
1 AAGAAAAAGATATCC-ATTAGCAAGAAAAGTCCATTTATAGTCACGCATGCCTTCAAAAGCCTTA
* ********** * * *
1885 TTACTCGGTTTAAATGATTTTATNNNNNNNNNNTT-GATTTTGATTTGAATTTTTTTTATATTTT
65 TTACTCGCTTTAAATGATTTTATAATCTCATAATTAG-TTTTAAGTTGAATTTTTTATAT-TTTT
* * * * * *
1949 ATTAAAATAGAATATAATTGAATGTCTGTCTCAAGAAATATT
128 ATTAAAACAGATTATAATTGAATGTCTGCCTCGAGAAACATA
* * ********** *
1991 GAGAAATAGATATCCATT-GACAAGAAAAGTCCATTTATAGNNNNNNNNNNCTTCGAAAGCCTTA
1 AAGAAAAAGATATCCATTAG-CAAGAAAAGTCCATTTATAGTCACGCATGCCTTCAAAAGCCTTA
* *
2055 TTACTCGCTTTAAATGCTTTTCTAATCTCATAATTAGTTTTAAGTTGAAGTTTTTTATATTTGTT
65 TTACTCGCTTTAAATGATTTTATAATCTCATAATTAGTTTTAAGTTGAA-TTTTTTATATTT-TT
* * * * **
2120 ATTAAAAGAGATTATAATTTAATGTCTACCTAGAGAAATGTA
128 ATTAAAACAGATTATAATTGAATGTCTGCCTCGAGAAACATA
* * * * * * *
2162 AAGATAAAGATATCCATTGGTAAG-AGAGTCCATTTATTGTCACCCATGCCTTCGAAAGCCTTAT
1 AAGAAAAAGATATCCATTAGCAAGAAAAGTCCATTTATAGTCACGCATGCCTTCAAAAGCCTTAT
********* * *
2226 TACTCGCNNNNNNNNNNTTTT-TAATCTCATAATTACTTTTAAGTTGAACTTTTTATATTTATTA
66 TACTCGC-TTTAAATGATTTTATAATCTCATAATTAGTTTTAAGTTGAATTTTTTATATTT-TTA
* * * * *
2290 TTAAAACATATTATAATT-ATATGTTTACCTTGAGAAACATG
129 TTAAAACAGATTATAATTGA-ATGTCTGCCTCGAGAAACATA
* * * * *
2331 AAGAAAATGATATCCATTAGTAAGAAAAGTCTATTTATTGTCACTG-ATGCCTTCAAAAGTCTTA
1 AAGAAAAAGATATCCATTAGCAAGAAAAGTCCATTTATAGTCAC-GCATGCCTTCAAAAGCCTTA
*
2395 TTACTCGCTTTAAATGATTTTATAACCTCAT
65 TTACTCGCTTTAAATGATTTTATAATCTCAT
Statistics
Matches: 714, Mismatches: 211, Indels: 43
0.74 0.22 0.04
Matches are distributed among these distances:
168 1 0.00
169 87 0.12
170 337 0.47
171 279 0.39
172 8 0.01
173 2 0.00
ACGTcount: A:0.35, C:0.13, G:0.11, T:0.37
Consensus pattern (169 bp):
AAGAAAAAGATATCCATTAGCAAGAAAAGTCCATTTATAGTCACGCATGCCTTCAAAAGCCTTAT
TACTCGCTTTAAATGATTTTATAATCTCATAATTAGTTTTAAGTTGAATTTTTTATATTTTTATT
AAAACAGATTATAATTGAATGTCTGCCTCGAGAAACATA
Done.