Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018397955.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_126.0, 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: 3742
ACGTcount: A:0.30, C:0.11, G:0.09, T:0.30
Warning! 761 characters in sequence are not A, C, G, or T
Found at i:488 original size:170 final size:169
Alignment explanation
Indices: 240--1010 Score: 650
Period size: 170 Copynumber: 4.5 Consensus size: 169
230 AAAAAAAACC
* * * * * *
240 TATCCATTGAG-AGGAAAAGTCCATTTATAGTCAGCCATGCATTCGAAAGCCTTATCACTCGCTT
1 TATCCATTG-GCAAGAAAAGTCCATTTATAGTCA-CCATGCTTTTGAAAGCATTATTACTCACTT
* * *
304 TAAATGATTTTATAACCTCATAATT-AGCTTTAAGTTCAA-TTTTTTATATTTTTTATTAAATCA
64 TAAA-GATTTTATAATCTCATAATTGA-TTTTAAGTTGAAGTTTTTTATATTTTTTATTAAATCA
* * ** * *
367 GATTATATTTGAATGTGTGTCTCAAGAAACATGAAGGAAAAGA
127 GATTATAATTGAATGTCTACCTCGAGAAACATGAAGAAAAAGA
* * *
410 TATCAATTGGCAAGAAAAGTCCATTTATAGTCACCTATGCTTTTAAAAGCATTATTACTCACCTT
1 TATCCATTGGCAAGAAAAGTCCATTTATAGTCACC-ATGCTTTTGAAAGCATTATTACTCACTTT
* * * *
475 GAAGATATTTATAATCTTATAATTGA-TTTAAGTTAAATTTTTTTATATTTTTTATTAAAAT-AG
65 AAAGAT-TTTATAATCTCATAATTGATTTTAAGTTGAAGTTTTTTATATTTTTTATT-AAATCAG
********** * *
538 ANNNNNNNNNNATGTCTACCTTGAGAAACGTGAAGAAAAAGA
128 ATTATAATTGAATGTCTACCTCGAGAAACATGAAGAAAAAGA
* * *
580 TATCTATTGGCAAGAGAAGGT-CATTTATAGGT-ACTCATGCTTTCGAAAGCATTATTACT-AGC
1 TATCCATTGGCAAGA-AAAGTCCATTTATA-GTCAC-CATGCTTTTGAAAGCATTATTACTCA-C
* * ********** *
642 TTTAAATATTTTTATAATCTTATAATTGATTTTAAGTTGAAGTTTTTTANNNNNNNNNNTAAAAC
62 TTTAAAGA-TTTTATAATCTCATAATTGATTTTAAGTTGAAGTTTTTTATATTTTTTATTAAATC
*
707 AGATTATAATTGAATGTCTACCTCGAGAAACATGAAAAAAAAAGA
126 AGATTATAATTGAATGTCTACCTCGAGAAACATG-AAGAAAAAGA
* * * *
752 TATCCATTGGCAAGAAAAGTCCATTTATAGTCATCCATACTTTTAAAAGC-TAAATTACTCGCTT
1 TATCCATTGGCAAGAAAAGTCCATTTATAGTCA-CCATGCTTTTGAAAGCAT-TATTACTCACTT
* * *
816 TAAATGATTTTATAAGCTCATAATTGATTTTAAGTTGAA-TGTTTTTACATTTTTTTATAAAATC
64 TAAA-GATTTTATAATCTCATAATTGATTTTAAGTTGAAGT-TTTTTATA-TTTTTTATTAAATC
*
880 AGATTATAATTGAATGTCTACCT-TAGAAA-ATGTGAAGAAAAA-A
126 AGATTATAATTGAATGTCTACCTCGAGAAACA--TGAAGAAAAAGA
* * * * * *
923 GTATCCATTGGTAAGAAAAGTCTATTTATAGTCACCCATACCTTTGAAAGCTTTTTTACTCACTT
1 -TATCCATTGGCAAGAAAAGTCCATTTATAGTCA-CCATGCTTTTGAAAGCATTATTACTCACTT
*
988 TAAATATTTTTATAATCTCATAA
64 TAAAGA-TTTTATAATCTCATAA
1011 NNNNNNNNNN
Statistics
Matches: 477, Mismatches: 97, Indels: 52
0.76 0.15 0.08
Matches are distributed among these distances:
169 17 0.04
170 186 0.39
171 64 0.13
172 178 0.37
173 32 0.07
ACGTcount: A:0.36, C:0.12, G:0.12, T:0.37
Consensus pattern (169 bp):
TATCCATTGGCAAGAAAAGTCCATTTATAGTCACCATGCTTTTGAAAGCATTATTACTCACTTTA
AAGATTTTATAATCTCATAATTGATTTTAAGTTGAAGTTTTTTATATTTTTTATTAAATCAGATT
ATAATTGAATGTCTACCTCGAGAAACATGAAGAAAAAGA
Found at i:2178 original size:171 final size:171
Alignment explanation
Indices: 1640--2612 Score: 739
Period size: 171 Copynumber: 5.7 Consensus size: 171
1630 NNNNAACATG
*
1640 AAGAAAAAGATATCCATTGGCAAG-AAAGTTCCATTTATAGTCACCCATACC-TTCGAAAGCCTT
1 AAGAAAAAGATATCCATTGACAAGAAAAG-TCCATTTATAGTCACCCAT-CCTTTCGAAAGCCTT
* * * * * *
1703 -TCTACTCACTTTCAATACTTTTATAATTTCATAATTGATTTTGAGTT-AACTTTTTTTACATAT
64 AT-TACTCGCTTTAAATATTTTTATAATCTCATAATTGATTTTAAGTTGAA-TTTTTTTACATTT
* *
1766 TT--TTAAAAGAGATAATAATTGAATGTCTGCCTCAAGAAATA-G-GA
127 TTAGTTAAAACAGATAATAATTGAATGTCTACCT--AGAAA-ACGTGA
* * ********** * *
1810 AA-AAAAAGATATCTATTGGCAAGAANNNNNNNNNNATAGTCACCCATGCCTTT-AAAAGCCTTT
1 AAGAAAAAGATATCCATTGACAAGAAAAGTCCATTTATAGTCACCCAT-CCTTTCGAAAGCCTTA
* * * *
1873 TTACTCGCTTTAAATAGTTTTATAATCTCATAATAGATGTTAAGTTAAATTTTTTTACATTTTTC
65 TTACTCGCTTTAAATATTTTTATAATCTCATAATTGATTTTAAGTTGAATTTTTTTACATTTTT-
* * * * ******
1938 A-TTACAGCAGATAATAATTGAATGTCTACCTCGAGANNNNNN
129 AGTTAAAACAGATAATAATTGAATGTCTACCTAGAAAACGTGA
**** ** * * *
1980 NNNNAAAAGATATCCATTGACAAGAAAAGTTTATTTCTAGTCACCCATTCTTTCGAAAGCATTAT
1 AAGAAAAAGATATCCATTGACAAGAAAAGTCCATTTATAGTCACCCATCCTTTCGAAAGCCTTAT
* * *
2045 TACTCGCTCTAAATATTTTTATAATCTTATAATTGATTTTAAGTTGAATTTTTTTACATTTTTCG
66 TACTCGCTTTAAATATTTTTATAATCTCATAATTGATTTTAAGTTGAATTTTTTTACATTTTTAG
* *
2110 TAAAAACAGATTATAATTGAATGTCTACCTTAGAAAACGTGA
131 TTAAAACAGATAATAATTGAATGTCTACC-TAGAAAACGTGA
* * ** * * * *
2152 AAAAAAAAG-TATTCATTGGTAAGAAAAGTCTATTTATAGTCGCCCATACCTTT-GAAAGCTTTT
1 AAGAAAAAGATATCCATTGACAAGAAAAGTCCATTTATAGTCACCCAT-CCTTTCGAAAGCCTTA
* **********
2215 TTACTCACTTTAAATATTTTTATAATCTCATNNNNNNNNNNAAGTTGAATTTTTTTACATTTTTA
65 TTACTCGCTTTAAATATTTTTATAATCTCATAATTGATTTTAAGTTGAATTTTTTTACATTTTTA
* * * *
2280 GTTCAAATAGATAATAATTGAATGTCTGCCTTAGGAAA--TGA
130 GTTAAAACAGATAATAATTGAATGTCTACC-TAGAAAACGTGA
* * * *
2321 GAAGAAAAAGATATCCATTGCCAAGAAAAGTTCATTTATAGTCAACTATACC-TTCGAAAGCCTT
1 -AAGAAAAAGATATCCATTGACAAGAAAAGTCCATTTATAGTCACCCAT-CCTTTCGAAAGCCTT
********** * *
2385 ATTACTCGCTTTAAATATTTTTATANNNNNNNNNNTAATTTTAAGTTGAATTTTTTTATATTTTT
64 ATTACTCGCTTTAAATATTTTTATAATCTCATAATTGATTTTAAGTTGAATTTTTTTACATTTTT
*
2450 AGTTAAAACAGATACTAATTGAATGTCTACCTAGAGAAACGTG-
129 AGTTAAAACAGATAATAATTGAATGTCTACCTAGA-AAACGTGA
** *
2493 AAGAAAAAG-TATCCATTGACAA-AAAAGGTCCATTTATAACCACCCA-CGCCTTCGAAAGCCTT
1 AAGAAAAAGATATCCATTGACAAGAAAA-GTCCATTTATAGTCACCCATC-CTTTCGAAAGCCTT
* * * *
2555 GTTACTCACTTTAAATGA-TTTTATAACCTTC-TAATTGATTTTAAGTTAAATTTTTTTA
64 ATTACTCGCTTTAAAT-ATTTTTATAATC-TCATAATTGATTTTAAGTTGAATTTTTTTA
2613 TNNNNNNNNN
Statistics
Matches: 625, Mismatches: 154, Indels: 48
0.76 0.19 0.06
Matches are distributed among these distances:
168 1 0.00
169 105 0.17
170 105 0.17
171 399 0.64
172 13 0.02
173 2 0.00
ACGTcount: A:0.35, C:0.14, G:0.11, T:0.36
Consensus pattern (171 bp):
AAGAAAAAGATATCCATTGACAAGAAAAGTCCATTTATAGTCACCCATCCTTTCGAAAGCCTTAT
TACTCGCTTTAAATATTTTTATAATCTCATAATTGATTTTAAGTTGAATTTTTTTACATTTTTAG
TTAAAACAGATAATAATTGAATGTCTACCTAGAAAACGTGA
Done.