Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018397800.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_110.0, 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: 16200
ACGTcount: A:0.19, C:0.07, G:0.06, T:0.19
Warning! 8020 characters in sequence are not A, C, G, or T
Found at i:11829 original size:171 final size:162
Alignment explanation
Indices: 11565--11873 Score: 274
Period size: 171 Copynumber: 1.9 Consensus size: 162
11555 ATTATCTCAA
* *
11565 AATTGATTTTAAGTTTACTTTTTTTTACATTTTAGGTTAAAACAAACAATAATCGAATGTCTATC
1 AATTGATTTTAAGTTTAATTATTTTTACATTTTAGGTTAAAACAAACAATAATCGAATGTCTATC
*
11630 TCATGAAACATGAAGAGAAAAGCATTCATTGAG-AAGAAAAGTCT-ATTTATAATCA-CCACTCG
66 TCATGAAACATGAAGAGAAAAGCATTCA-TGAGCAAGAAAA-TCTCATTTATAATCACCCACTCC
11692 TTCAAAAGCCATATTACTCACTTTAAATGGTTTT
129 TTCAAAAGCCATATTACTCACTTTAAATGGTTTT
* * * ** *
11726 NNNNNNNNNNAATTGATTTTAAGTTTAATTATTTTTACTTTTTTGGTTAAAACATATTATAATTG
1 ----------AATTGATTTTAAGTTTAATTATTTTTACATTTTAGGTTAAAACAAACAATAATCG
* * * *
11791 AGTGTCTA-CATC-T-AGAA-ATGTAATGA-AAACGACATTCATGGGCAAGAAAATTTCATTTAT
56 AATGTCTATC-TCATGA-AACATG-AA-GAGAAAAG-CATTCATGAGCAAGAAAATCTCATTTAT
* *
11851 AGTCACCCATTCCTTCAAAAGCC
116 AATCACCCACTCCTTCAAAAGCC
11874 TNNNNNNNNN
Statistics
Matches: 115, Mismatches: 15, Indels: 15
0.79 0.10 0.10
Matches are distributed among these distances:
169 4 0.03
170 15 0.13
171 81 0.70
172 15 0.13
ACGTcount: A:0.36, C:0.14, G:0.12, T:0.36
Consensus pattern (162 bp):
AATTGATTTTAAGTTTAATTATTTTTACATTTTAGGTTAAAACAAACAATAATCGAATGTCTATC
TCATGAAACATGAAGAGAAAAGCATTCATGAGCAAGAAAATCTCATTTATAATCACCCACTCCTT
CAAAAGCCATATTACTCACTTTAAATGGTTTT
Found at i:12667 original size:169 final size:170
Alignment explanation
Indices: 12323--12667 Score: 417
Period size: 170 Copynumber: 2.0 Consensus size: 170
12313 NNNNNNNNNN
* * * ** *
12323 ATGGTTTTATAATCTCATAATTGATTTTAAGTTTAATTTTTTATATTTTTTGTTCAAACAAACTA
1 ATGGTTCTATAATCTCATAATTGATTTTAAGTTGAATTTTCTATATTTTTCATTAAAACAAACTA
*
12388 TAATTGAATGCATGCCTCAAAAAACGTGTAAAAAAACCTAGTTATTTGTAAAAAAAGTCCATTTA
66 TAATTGAATGCATGCCTCAAAAAACGTGTAAAAAAACCTAGTTATTTGAAAAAAAAGTCCATTTA
**********
12453 TAGTCTCTCATTCCTTCAAAAGCNNNNNNNNNNACTTTAA
131 TAGTCTCTCATTCCTTCAAAAGCCTTATTAGTCACTTTAA
* *
12493 ATGGTTCTCTAATCTCATAATTGATTTTAAGTTGAATTTTCTATATTTTTCATTAAAACAGACTA
1 ATGGTTCTATAATCTCATAATTGATTTTAAGTTGAATTTTCTATATTTTTCATTAAAACAAACTA
**** *
12558 TAATTGAATGC-T-CAGCTTGGGAAACGTGT-AAAAAACCTAGTTATTTGAAAAAAAAGTCTATT
66 TAATTGAATGCATGC--CTCAAAAAACGTGTAAAAAAACCTAGTTATTTGAAAAAAAAGTCCATT
* *
12620 TATAGTCTCTCATTCCTTCGAAAGCCTTATTAGTCGCTTTAA
129 TATAGTCTCTCATTCCTTCAAAAGCCTTATTAGTCACTTTAA
12662 ATGGTT
1 ATGGTT
12668 TNNNNNNNNN
Statistics
Matches: 147, Mismatches: 26, Indels: 5
0.83 0.15 0.03
Matches are distributed among these distances:
168 1 0.01
169 68 0.46
170 78 0.53
ACGTcount: A:0.34, C:0.14, G:0.11, T:0.39
Consensus pattern (170 bp):
ATGGTTCTATAATCTCATAATTGATTTTAAGTTGAATTTTCTATATTTTTCATTAAAACAAACTA
TAATTGAATGCATGCCTCAAAAAACGTGTAAAAAAACCTAGTTATTTGAAAAAAAAGTCCATTTA
TAGTCTCTCATTCCTTCAAAAGCCTTATTAGTCACTTTAA
Found at i:14091 original size:170 final size:171
Alignment explanation
Indices: 13915--14232 Score: 376
Period size: 171 Copynumber: 1.9 Consensus size: 171
13905 TAGGACTCTT
*
13915 TTTAAATGGTTTTAC-AATCTTATAATTAATTTTAAGT-TGAATTTGTTATATTTTTCATTAAAA
1 TTTAAATGGTTTT-CTAATCTCATAATTAATTTTAAGTATGAATTTGTTATATTTTTCATTAAAA
* *
13978 -AGGACTATAATTGAATG-TCAGCCTTAGGAAACATGTAGAAAAACCCATTTATTTAG-AAGAAA
65 CA-GACTATAATTGAATGCT-AGCCTTAGGAAACATGTA-AAAAACCCAGTTATTTAGAAAAAAA
*
14040 AGTCTATTTATAGTTTCTCATTTCTTCAAAAACCTTATTAGTCGG
127 AGTCTATTTATAGTCTCTCATTTCTTCAAAAACCTTATTAGTCGG
* **********
14085 TTTAAATGGTTTTCTAATCTCATAATTGATTTTAAGTNNNNNNNNNNTATATTTTTCATTAAAAC
1 TTTAAATGGTTTTCTAATCTCATAATTAATTTTAAGTATGAATTTGTTATATTTTTCATTAAAAC
* * ** * *
14150 AGACTATAATTGAATGCTTGCCTTGGGAAATGTGTAAAAAACCTAGTTATTTGGAAAAAAAAGTC
66 AGACTATAATTGAATGCTAGCCTTAGGAAACATGTAAAAAACCCAGTTATTTAGAAAAAAAAGTC
14215 TATTTATAGTCTCTCATT
131 TATTTATAGTCTCTCATT
14233 CCNNNNNNNN
Statistics
Matches: 123, Mismatches: 20, Indels: 9
0.81 0.13 0.06
Matches are distributed among these distances:
169 1 0.01
170 48 0.39
171 72 0.59
172 2 0.02
ACGTcount: A:0.34, C:0.11, G:0.12, T:0.40
Consensus pattern (171 bp):
TTTAAATGGTTTTCTAATCTCATAATTAATTTTAAGTATGAATTTGTTATATTTTTCATTAAAAC
AGACTATAATTGAATGCTAGCCTTAGGAAACATGTAAAAAACCCAGTTATTTAGAAAAAAAAGTC
TATTTATAGTCTCTCATTTCTTCAAAAACCTTATTAGTCGG
Done.