Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018400202.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_3415.0, 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: 2451
ACGTcount: A:0.27, C:0.11, G:0.09, T:0.29
Warning! 588 characters in sequence are not A, C, G, or T
Found at i:1112 original size:171 final size:170
Alignment explanation
Indices: 821--1134 Score: 436
Period size: 171 Copynumber: 1.8 Consensus size: 170
811 TTATATTTGT
* * * *
821 TATTAAAACAGATTATAATTGAATGTTTGCCTTAGGAAACTTGAAGAAAAAGATATGCACTGGCA
1 TATTAAAACAGATTATAATTGAATGTTTACCTTAGGAAACGTGAAGAAAAAGATATCCACTAGCA
* * *
886 AGAAAAGTCTATTTGTACTCACCTATGCCTTCGAAAACATTATTACTCACTTTAAAGTG-TTTTG
66 AGAAAAGTCCATTTATACTCACCTATGCCTTCGAAAACATTATTACTCACTTTAAA-TGATTTTA
* *
950 TAATCTCGTAATTGGTTTTAAGCTAAATTGTTTTTAATTCA
130 TAACCTCATAATTGGTTTTAAGCTAAATTGTTTTTAATTCA
* *
991 TATTAAAACAGATTATAATTGAATGTTTACCTTTGAGAAACGTGAAGAAAAAGATATCCATTAGC
1 TATTAAAACAGATTATAATTGAATGTTTACCTTAG-GAAACGTGAAGAAAAAGATATCCACTAGC
* * * *
1056 TAGAAAAGTCCATTTATAGTCATCCT-TGCCTTC-AACAGCATTATTACTCGCTTTAAATGATTT
65 AAGAAAAGTCCATTTATACTCA-CCTATGCCTTCGAA-AACATTATTACTCACTTTAAATGATTT
1119 TATAACCTCATAATTG
128 TATAACCTCATAATTG
1135 ATTTNNNNNN
Statistics
Matches: 125, Mismatches: 15, Indels: 7
0.85 0.10 0.05
Matches are distributed among these distances:
170 37 0.30
171 85 0.68
172 3 0.02
ACGTcount: A:0.36, C:0.15, G:0.14, T:0.36
Consensus pattern (170 bp):
TATTAAAACAGATTATAATTGAATGTTTACCTTAGGAAACGTGAAGAAAAAGATATCCACTAGCA
AGAAAAGTCCATTTATACTCACCTATGCCTTCGAAAACATTATTACTCACTTTAAATGATTTTAT
AACCTCATAATTGGTTTTAAGCTAAATTGTTTTTAATTCA
Found at i:1901 original size:170 final size:170
Alignment explanation
Indices: 1617--2451 Score: 734
Period size: 170 Copynumber: 4.9 Consensus size: 170
1607 ACCTCAAAAA
* *
1617 ATTACTCGCCTTAAAT-ATTTTTATAACCTCATAATTGATTTTAAGTTGAATTTATTTATAATTT
1 ATTACTCGCTTTAAATGATTTTT-TAACCTCATAATTGATTTTAAGTTGAATTTTTTTAT-ATTT
* * * * *
1681 TTATTAAAATAGATTATAATTAAATGTCTACCTCGATAAACGTAAAGAAAAAGATATCCATTGTC
64 TTATTAAAACAGATTATAATTGAATGTCTACCTCGAGAAACGTGAAGAAAAAGATATCCATTGGC
* *
1746 AAGAAAAGTCCATCTATAGTCACCTATGCCTTCGAAAGTCTT
129 AAGAAAAGTCCATTTATAGTCACCTATGCCTTCGAAAGCCTT
* * *
1788 ATTACTCACTTTAAATGATTTTTTAATCTCATAATTGATTTTAATTTGAATTTTTTTATATTTTT
1 ATTACTCGCTTTAAATGATTTTTTAACCTCATAATTGATTTTAAGTTGAATTTTTTTATATTTTT
* * * * *
1853 ATCAAAACAGATTATAATTGAATGTCTACATCGAGAAACATGAAGAAAAAGATATGCATTCGCAA
66 ATTAAAACAGATTATAATTGAATGTCTACCTCGAGAAACGTGAAGAAAAAGATATCCATTGGCAA
* * *
1918 GAAAAGTTCATTTGTAGTCATCC-ATACCTTCGAAAGCCTT
131 GAAAAGTCCATTTATAGTCA-CCTATGCCTTCGAAAGCCTT
* * * ******************* *
1958 ATTACTCGCTTTAAATGGTTTTATAATCNNNNNNNNNNNNNNNNNNNGAATTTTTTTACATTTTT
1 ATTACTCGCTTTAAATGATTTTTTAACCTCATAATTGATTTTAAGTTGAATTTTTTTATATTTTT
* * * ** *
2023 ATTAACACAGATTATAGTTGAATGTCTACCTC-AGCATACACGAAGAAAAAGATATTCATTGGCA
66 ATTAAAACAGATTATAATTGAATGTCTACCTCGAG-AAACGTGAAGAAAAAGATATCCATTGGCA
* * * *
2087 AGAATAGCCCATTTATAGTCATCTACT-CCTTCAAAAGCCTT
130 AGAAAAGTCCATTTATAGTCACCTA-TGCCTTCGAAAGCCTT
* * * * * *
2128 GTTACTCGCTTAAAATGATTTTATAACCTCATAATTAATTTTAATTTGAATTTTTTTAAAATTTT
1 ATTACTCGCTTTAAATGATTTTTTAACCTCATAATTGATTTTAAGTTGAATTTTTTT-ATATTTT
* * * * *
2193 TATTTAAAA-AAATTATAATTGAATGTTTTCCT-TAGGAAACGTGAAGAAAAAGATATCCATTAG
65 TA-TTAAAACAGATTATAATTGAATGTCTACCTCGA-GAAACGTGAAGAAAAAGATATCCATTGG
* * *
2256 TAAGAAAAGTCCATATATAGTCA-ATCATGCCTTCGAAAGCCTT
128 CAAGAAAAGTCCATTTATAGTCACCT-ATGCCTTCGAAAGCCTT
* ********** *
2299 ATTACTCGCTTTAAAT-AGTTTTTTAAACTCATANNNNNNNNNNAGTTGAACTTTTTTATATTTG
1 ATTACTCGCTTTAAATGA-TTTTTTAACCTCATAATTGATTTTAAGTTGAATTTTTTTATATTT-
* * * *
2363 TTATTAAAACATATTATAATTGAATGTCTACTTCTG-GAAACGTGAAGAAAAAAATATCCACTGG
64 TTATTAAAACAGATTATAATTGAATGTCTACCTC-GAGAAACGTGAAGAAAAAGATATCCATTGG
* *
2427 CAAGAAAAGTCCATTTGTACTCACC
128 CAAGAAAAGTCCATTTATAGTCACC
Statistics
Matches: 520, Mismatches: 127, Indels: 33
0.76 0.19 0.05
Matches are distributed among these distances:
169 3 0.01
170 267 0.51
171 238 0.46
172 12 0.02
ACGTcount: A:0.35, C:0.14, G:0.11, T:0.37
Consensus pattern (170 bp):
ATTACTCGCTTTAAATGATTTTTTAACCTCATAATTGATTTTAAGTTGAATTTTTTTATATTTTT
ATTAAAACAGATTATAATTGAATGTCTACCTCGAGAAACGTGAAGAAAAAGATATCCATTGGCAA
GAAAAGTCCATTTATAGTCACCTATGCCTTCGAAAGCCTT
Done.