Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018400784.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_3960.0, 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: 2181
ACGTcount: A:0.21, C:0.10, G:0.08, T:0.23
Warning! 839 characters in sequence are not A, C, G, or T
Found at i:1502 original size:169 final size:167
Alignment explanation
Indices: 1124--1714 Score: 671
Period size: 173 Copynumber: 3.5 Consensus size: 167
1114 NNNNNNNNNN
* *
1124 TCACCCAAGCCTTCAAAAGCCTTATTACTCTCTTTAAATGGTTTTATAATCCCAAAATCGATTTT
1 TCACCCAAGCCTTCAAAAGCCTTATTACTCTCTTTAAATGGTTTTATAATCCCATAATTGATTTT
* *
1189 AAGTTGAATTTTGTTATATTTTTTGTTAAAACATATTATAATTGAATTTTTGCCTTGGAAACATG
66 AAGTTGAATTTT-TTATA-TTTTTGTTAAAACAGATTATAATTGAATGTTTGCCTTGGAAACATG
*
1254 AACAAAAACCCATTCATTGGCAAGAAAAGCCCATTTATAG
129 AAGAAAAA-CCATTCATTGGCAAGAAAAGCCCATTTATAG
*********** * *
1294 TCACCCAAGCCTTCNNNNNNNNNNNTACTCTCTTTAAATGGTTTTATAATCTCAGAATTGATTTT
1 TCACCCAAGCCTTCAAAAGCCTTATTACTCTCTTTAAATGGTTTTATAATCCCATAATTGATTTT
* *
1359 AAGTTGAATTTTTTATATTTTTGTTAAAACAGATTACAATTGAATGTTTACCTTTGGAAACATGA
66 AAGTTGAATTTTTTATATTTTTGTTAAAACAGATTATAATTGAATGTTTGCC-TTGGAAACATGA
*
1424 AGAAAAACACATTCATTGGCAAGAAAAGCTCATTTATAG
130 AGAAAAAC-CATTCATTGGCAAGAAAAGCCCATTTATAG
* * * * * * *
1463 TCAGCCGAGCCTCCAAAAGCCATATTACTCGCGTTAAATGGTTTTGTAATCCCATAATTGATTTT
1 TCACCCAAGCCTTCAAAAGCCTTATTACTCTCTTTAAATGGTTTTATAATCCCATAATTGATTTT
*** * * * * *
1528 AAACCGAATGGTTTTTAAATTTTTTTGTTAAAACAGAATATAATGGAATGTTTGCCTCGAGAAAT
66 AAGTTGAAT--TTTTT--ATATTTTTGTTAAAACAGATTATAATTGAATGTTTGCCTTG-GAAAC
1593 ATGAAGAAAAAGCCATTCATTGGCAAG-AAAGTCCCATTTATAG
126 ATGAAGAAAAA-CCATTCATTGGCAAGAAAAG-CCCATTTATAG
* * * * * * * *
1636 TCATCCAAGCCTTGAAAAGCCTTATTATTCTCTATAAATGGTTGTCTAGTCTCATAATTGATTTT
1 TCACCCAAGCCTTCAAAAGCCTTATTACTCTCTTTAAATGGTTTTATAATCCCATAATTGATTTT
1701 AAGTTGAATTTTTT
66 AAGTTGAATTTTTT
1715 TCATGGGAAA
Statistics
Matches: 346, Mismatches: 66, Indels: 17
0.81 0.15 0.04
Matches are distributed among these distances:
168 32 0.09
169 104 0.30
170 63 0.18
171 10 0.03
172 6 0.02
173 130 0.38
174 1 0.00
ACGTcount: A:0.33, C:0.16, G:0.13, T:0.36
Consensus pattern (167 bp):
TCACCCAAGCCTTCAAAAGCCTTATTACTCTCTTTAAATGGTTTTATAATCCCATAATTGATTTT
AAGTTGAATTTTTTATATTTTTGTTAAAACAGATTATAATTGAATGTTTGCCTTGGAAACATGAA
GAAAAACCATTCATTGGCAAGAAAAGCCCATTTATAG
Found at i:1832 original size:133 final size:133
Alignment explanation
Indices: 1594--1848 Score: 386
Period size: 133 Copynumber: 1.9 Consensus size: 133
1584 TCGAGAAATA
*
1594 TGAAGAAAAAGCCATTCATTGGCAAGAAAGTCCCATTTATAGTCATCCAAGCCTTGAAAAGCCTT
1 TGAAGAAAAAGCCATTCATTGGCAAGAAAGTCCCATTTATAGTCACCCAAGCCTTGAAAAGCCTT
* * ** *
1659 ATTATTCTCTATAAATGGTTGTCTAGTCTCATAATTGATTTTAAGTTGAATTTTTTTCATGGGAA
66 ATTACTCTCTATAAATGGTTGTATAACCTCAAAATTGATTTTAAGTTGAATTTTTTTCATGGGAA
1724 ACC
131 ACC
* *
1727 TGAAGAAAAAGCCATTCATTGGCAAGAAAAG-CTCATTTATAGTCACCCAAGCCTTTAAAAGCCT
1 TGAAGAAAAAGCCATTCATTGGCAAG-AAAGTCCCATTTATAGTCACCCAAGCCTTGAAAAGCCT
* * * *
1791 TATTACTCTCTTTAAATGGTTTTATAACCTCAAAATTGATTTTGAGTTTAATTTTTTT
65 TATTACTCTCTATAAATGGTTGTATAACCTCAAAATTGATTTTAAGTTGAATTTTTTT
1849 TACATTTTTG
Statistics
Matches: 109, Mismatches: 12, Indels: 2
0.89 0.10 0.02
Matches are distributed among these distances:
133 105 0.96
134 4 0.04
ACGTcount: A:0.33, C:0.16, G:0.14, T:0.36
Consensus pattern (133 bp):
TGAAGAAAAAGCCATTCATTGGCAAGAAAGTCCCATTTATAGTCACCCAAGCCTTGAAAAGCCTT
ATTACTCTCTATAAATGGTTGTATAACCTCAAAATTGATTTTAAGTTGAATTTTTTTCATGGGAA
ACC
Found at i:2018 original size:172 final size:168
Alignment explanation
Indices: 1718--2179 Score: 536
Period size: 172 Copynumber: 2.7 Consensus size: 168
1708 ATTTTTTTCA
* * *
1718 TGGGAAACCTGAAGAAAAAGCCATTCATTGGCAAGAAAAGCTCATTTATAGTCACCCAAGCCTTT
1 TGGGAAA-CTGAAGAAAAA-CCATTCATTGGCAAGAAAAGCCCATTTATAGTCACCCAACCCTTC
* * * *
1783 AAAAGCCTTATTACTCTCTTTAAATGGTTTTATAACCTCAAAATTGATTTTGAGTTTAATTTTTT
64 AAAAGCCTCATTACTCTCTTTAAATGATTTTATAACCTCAAAATTGATTTTAAG-TTAA-ATTTT
* *
1848 TTACATTTTTGGTTAAAGA-AGATTGTAATTGAATGTTTACCT
127 TTACATTTTTGGTTAAA-ACAGATTATAATTGAATATTTACCT
* * *
1890 TGGGAAACATGAAGAAAAACCAATTCATTGGTAAGGAAAGCCCATTTATTGTCACCCAACCCTTC
1 TGGGAAAC-TGAAGAAAAACC-ATTCATTGGCAAGAAAAGCCCATTTATAGTCACCCAACCCTTC
*
1955 AAAAGCCTCATTACTCTCTTTAAATGATTTTATAACCTCAAAATCGATTTTAAGTTAAATTTTTT
64 AAAAGCCTCATTACTCTCTTTAAATGATTTTATAACCTCAAAATTGATTTTAAGTTAAATTTTTT
* *
2020 ATATTTTTGGTTAAAACAGATTATAATTGAATATTTGCCT
129 ACATTTTTGGTTAAAACAGATTATAATTGAATATTTACCT
* ** * * * * * * *
2060 TAGGAAACCCAAGTAAACATCGTTCATTGACAAGAAAAGTCCATTTATAGTCACCTAGGCCC-TC
1 TGGGAAACTGAAG-AAAAACCATTCATTGGCAAGAAAAGCCCATTTATAGTCACCCA-ACCCTTC
* * * *
2124 AAAAGCCTTC-TTACTCTTTTTAAAT-AGTTTTGTAATCTCATAATTGATTTTAAGTT
64 AAAAGCC-TCATTACTCTCTTTAAATGA-TTTTATAACCTCAAAATTGATTTTAAGTT
2180 GA
Statistics
Matches: 250, Mismatches: 33, Indels: 17
0.83 0.11 0.06
Matches are distributed among these distances:
168 1 0.00
169 81 0.32
170 57 0.23
171 7 0.03
172 104 0.42
ACGTcount: A:0.34, C:0.16, G:0.13, T:0.36
Consensus pattern (168 bp):
TGGGAAACTGAAGAAAAACCATTCATTGGCAAGAAAAGCCCATTTATAGTCACCCAACCCTTCAA
AAGCCTCATTACTCTCTTTAAATGATTTTATAACCTCAAAATTGATTTTAAGTTAAATTTTTTAC
ATTTTTGGTTAAAACAGATTATAATTGAATATTTACCT
Done.