Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018402294.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_5376.0, 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: 2110
ACGTcount: A:0.30, C:0.11, G:0.09, T:0.32
Warning! 369 characters in sequence are not A, C, G, or T
Found at i:433 original size:171 final size:170
Alignment explanation
Indices: 256--1354 Score: 522
Period size: 171 Copynumber: 6.4 Consensus size: 170
246 NNNNNNNNAT
*
256 AGATTATAATTGAATGTCTGCCTTCAGAAACTTAAAGAAAAAGATATCAATTGGCAAGAAAAGTC
1 AGATTATAATTGAATGTCTGCCTTCAGAAACTTGAAGAAAAAGATATCAATTGGCAAGAAAAGTC
* ********** * *
321 CATTTATAGTCACCGATGCCTTCAAAAGCATTATTACTCGNNNNNNNNNNTTTTATGATCTCATA
66 CATTTATAGTCACC-ATACCTTCAAAAGCATTATTACTCGCTCTAAAGTATTTAATAATCTCATA
* *
386 ATTGATTTTAATTTGAATTTTTTTATATTTTTTAAGAAAAC
130 ATTGATTTTAATTTAAAGTTTTTTATATTTTTTAAGAAAAC
* ********** *
427 AGATTATAATTGAATG-CTTGCC-TCAAGAAACGTGAAGAAANNNNNNNNNNTTGGCAAGGAAAG
1 AGATTATAATTGAATGTC-TGCCTTC-AGAAACTTGAAGAAAAAGATATCAATTGGCAAGAAAAG
* * * *
490 TCTATTTATCA-TCACCCATACTTTCAAAAGCTTTATTACTCGCTCTAAAGTATTTAATAATGTC
64 TCCATTTAT-AGTCA-CCATACCTTCAAAAGCATTATTACTCGCTCTAAAGTATTTAATAATCTC
** *
554 ATAATTGATTTTAATTTAAAGTTTTTTATATTTTTTATTAAGAC
127 ATAATTGATTTTAATTTAAAGTTTTTTATATTTTTTAAGAAAAC
* * * * * *
598 AGACTATAATTAAATGTCTACCTTGAGAAA-TGTGAAGAAAAAGATATCCATTGGCAAAAAAAGT
1 AGATTATAATTGAATGTCTGCCTTCAGAAACT-TGAAGAAAAAGATATCAATTGGCAAGAAAAGT
* * * * ** *
662 CCATTTATAGTAATCCATACCTTCGAAAGCGTTATTACTCGCTTTAAA-TACTTTTTTAATCTTA
65 CCATTTATAGTCA-CCATACCTTCAAAAGCATTATTACTCGCTCTAAAGTA-TTTAATAATCTCA
* * **
726 TAATT-AGTTTT-ATGTTGAACTTTTTTATATTTTTTATTAAAAC
128 TAATTGA-TTTTAAT-TTAAAGTTTTTTATATTTTTTAAGAAAAC
********** * * * * *
769 ANNNNNNNNNNGAATGTCTGCCTTGAGAAACATAAAGAAAAAAATATCAATTGGCAAAAAAAGTC
1 AGATTATAATTGAATGTCTGCCTTCAGAAACTTGAAGAAAAAGATATCAATTGGCAAGAAAAGTC
* * ** * * *
834 CATTTATGGTCACTAATACCTTTGAAAGCTTTATTACTCGCTTTAAA-TAGTTT-TTAATCTCAT
66 CATTTATAGTCAC-CATACCTTCAAAAGCATTATTACTCGCTCTAAAGTA-TTTAATAATCTCAT
* * * ********** * * **
897 AGTT-ACTTTTAAGTTGANNNNNNNNNNATTTATCATTAAAAC
129 AATTGA-TTTTAATTTAAAGTTTTTTATATTTTTTAAGAAAAC
* * * * ** * *
939 ATATTATAATT-ACACGTTTACC-TCGAGAAACGAGAAGAAAAAGATATCTATTAGCAA-AAAAG
1 AGATTATAATTGA-ATGTCTGCCTTC-AGAAACTTGAAGAAAAAGATATCAATTGGCAAGAAAAG
* ** * ********** *
1001 TCTATTTATAGTCACCGATACCTTCAAAAGCCCTATTACTCGCTTTNNNNNNNNNNATAACCTCA
64 TCCATTTATAGTCACC-ATACCTTCAAAAGCATTATTACTCGCTCTAAAGTATTTAATAATCTCA
* * ** *
1066 TAATT-AGTTTTAATTTGAATTTTTTTATATTTTTTATTAAAAT
128 TAATTGA-TTTTAATTTAAAGTTTTTTATATTTTTTAAGAAAAC
* * ** * * ******
1109 AGATTATAACTGAATGTTTTTC-TCGAGAAACTTGAAGAAAAAGATATCCATTGGTAAGNNNNNN
1 AGATTATAATTGAATGTCTGCCTTC-AGAAACTTGAAGAAAAAGATATCAATTGGCAAGAAAAGT
**** * * * *
1173 NNNNTTATAGTCACCCATACCTTCAAAAGCTTTATTACTCG-TCAGAAAAG-ATTTTATAACCTC
65 CCATTTATAGTCA-CCATACCTTCAAAAGCATTATTACTCGCTC--TAAAGTATTTAATAATCTC
* * * **
1236 ATAATAGATTTTAATTTGAATTTTTTTATATTTTTTATTAAAAC
127 ATAATTGATTTTAATTTAAAGTTTTTTATATTTTTTAAGAAAAC
* * * * * * * *
1280 AAACTATAATTGAATGTCTACCTTGAGAAACATGAAGAAAAAGGTATCCATTGGCAAAAAAAGTC
1 AGATTATAATTGAATGTCTGCCTTCAGAAACTTGAAGAAAAAGATATCAATTGGCAAGAAAAGTC
1345 CATTTATAGT
66 CATTTATAGT
1355 AACNNNNNNN
Statistics
Matches: 689, Mismatches: 213, Indels: 52
0.72 0.22 0.05
Matches are distributed among these distances:
169 45 0.07
170 157 0.23
171 478 0.69
172 9 0.01
ACGTcount: A:0.35, C:0.13, G:0.11, T:0.35
Consensus pattern (170 bp):
AGATTATAATTGAATGTCTGCCTTCAGAAACTTGAAGAAAAAGATATCAATTGGCAAGAAAAGTC
CATTTATAGTCACCATACCTTCAAAAGCATTATTACTCGCTCTAAAGTATTTAATAATCTCATAA
TTGATTTTAATTTAAAGTTTTTTATATTTTTTAAGAAAAC
Found at i:1915 original size:170 final size:170
Alignment explanation
Indices: 1627--2110 Score: 522
Period size: 171 Copynumber: 2.8 Consensus size: 170
1617 NNNNNNNNNN
* * * * * **
1627 AAGCCTTATTACTCGCTTTAAAAGATTTTATAACCTTATAATT-GATTTTAATTTGAGTTTTTTT
1 AAGCCTTATTACTCGATTTAAAA-CTTTTTTAATCTTATAATTAG-TTTTAAGTTGAACTTTTTT
* * * *
1691 ATATTTTTTCTTAAAATAGATTATAATTGAATGTCTGCTTTGAGAAACATAAAGAAAAAGATATT
64 ATATTTTTTATTAAAAAAGATTATAATTGAATGTCTGCCTTGAGAAACATAAAGAAAAAGATATA
**********
1756 CATTGGCAAGAAAAGTCCATNNNNNNNNNNCCATGCCTTCGA
129 CATTGGCAAGAAAAGTCCATTTATAGTAACCCATGCCTTCGA
*
1798 AAGCCTTCTTACTCGATTTAAAACTTTTTTAATCTTATAATTAGTTTTAAGTTGAACTTTTTTAT
1 AAGCCTTATTACTCGATTTAAAACTTTTTTAATCTTATAATTAGTTTTAAGTTGAACTTTTTTAT
* * * * * *
1863 ATTTTTTATTTAAACAGATTATAATTGAATGTCTACCCTGAGAAATATAAAGAAAATA-ATATCC
66 ATTTTTTATTAAAAAAGATTATAATTGAATGTCTGCCTTGAGAAACATAAAGAAAA-AGATATAC
*
1927 ATTGGCAAGAAAAGTCTATTTATAGTAACCCATGCCTTCGA
130 ATTGGCAAGAAAAGTCCATTTATAGTAACCCATGCCTTCGA
*********** * * *
1968 AAGCCTTGNNNNNNNNNNTAAATGCTTTTTTAATCTTATAATTAGTTTTAAGTTAAACCTTTTTA
1 AAGCCTTATTACTCGATTTAAA-ACTTTTTTAATCTTATAATTAGTTTTAAGTTGAACTTTTTTA
*
2033 TATTTTTTATTAAAAAAGATTATGATTGAATGTCTGCCTTGAGAAACATAAAGAAAAAGATATAC
65 TATTTTTTATTAAAAAAGATTATAATTGAATGTCTGCCTTGAGAAACATAAAGAAAAAGATATAC
2098 ATTGGCAAGAAAA
130 ATTGGCAAGAAAA
Statistics
Matches: 261, Mismatches: 48, Indels: 8
0.82 0.15 0.03
Matches are distributed among these distances:
170 130 0.50
171 131 0.50
ACGTcount: A:0.35, C:0.11, G:0.11, T:0.38
Consensus pattern (170 bp):
AAGCCTTATTACTCGATTTAAAACTTTTTTAATCTTATAATTAGTTTTAAGTTGAACTTTTTTAT
ATTTTTTATTAAAAAAGATTATAATTGAATGTCTGCCTTGAGAAACATAAAGAAAAAGATATACA
TTGGCAAGAAAAGTCCATTTATAGTAACCCATGCCTTCGA
Done.