Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018398027.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_1333.0, 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: 5312
ACGTcount: A:0.21, C:0.07, G:0.07, T:0.21
Warning! 2362 characters in sequence are not A, C, G, or T
Found at i:1638 original size:18 final size:18
Alignment explanation
Indices: 1607--1641 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
1597 GAGAAATGTC
**
1607 AGAAAAAACCATTCATTG
1 AGAAAAAAAAATTCATTG
1625 AGAAAAAAAAATTCATT
1 AGAAAAAAAAATTCATT
1642 TATAGTCACC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.57, C:0.11, G:0.09, T:0.23
Consensus pattern (18 bp):
AGAAAAAAAAATTCATTG
Found at i:1867 original size:170 final size:171
Alignment explanation
Indices: 1539--2114 Score: 552
Period size: 171 Copynumber: 3.4 Consensus size: 171
1529 NNNNNNNNNN
* * * * * ** * *
1539 TTAAGCTGAATTTTTTCACATTTTTGGTTAAAACAGACTATAATTGAATGTTTGGCTCGAGAAAT
1 TTAAGTTGAATTTTTTTACATTTTT-ATTAAAATAGACTATAATTAAATGTTTATCTCAAGAAAC
* * * * * *
1604 GTCAGAAAAAA-CCATTCATTGAGAAAAAAAAATTCATTTATAGTCACCTATTCCTTCAAAAACC
65 GTGAAAAAAAAGACATTCATTGAGAAAAAAAAGTTCATTTATAGTCACCCATTCCTTCAAAAGCC
* *
1668 TTATTACTCGCTTTAAA-TGATTCTATAATCTCATAATTGATT
130 TTACTACTCGCTTTAAATTGATT-TATAATCTTATAATTGATT
* * * *
1710 TTAAGTTGTATTTTTTTATATTTTTCATTAAAATAGATTATAATTAAATGTTTATCTTAAGAAAC
1 TTAAGTTGAATTTTTTTACATTTTT-ATTAAAATAGACTATAATTAAATGTTTATCTCAAGAAAC
* * *
1775 GTG-TAAAAAAGACATTCATTGAG-AAAAAAAGTTCATTTATAATCGCCCATTCCTTCAAAAGCC
65 GTGAAAAAAAAGACATTCATTGAGAAAAAAAAGTTCATTTATAGTCACCCATTCCTTCAAAAGCC
* * *
1838 TTACTACTCACTTTAAATTGCTTTATAATCTTATAATTAATT
130 TTACTACTCGCTTTAAATTGATTTATAATCTTATAATTGATT
* * * ********** *
1880 TTAAGTTAAATTGTTTTACATATTTTGTTAAAATAGNNNNNNNNNNAATGTTTATCTCGAGAAAC
1 TTAAGTTGAATTTTTTTACAT-TTTTATTAAAATAGACTATAATTAAATGTTTATCTCAAGAAAC
* * * *
1945 GTGAAAAAAAAGACATTCATTG-GCAAAAAATGTTCATTTATAGTCACTCATTCTTTCAAAAGCC
65 GTGAAAAAAAAGACATTCATTGAGAAAAAAAAGTTCATTTATAGTCACCCATTCCTTCAAAAGCC
* * * * *
2009 TTAGTACTGGGTTTAAATAGTTTTATAATCTTATAATTTG-TT
130 TTACTACTCGCTTTAAATTGATTTATAATCTTATAA-TTGATT
* * * * * *
2051 TTAAGTTGAATATGTTTAGATTTTTAATTAAAACAGACTATAATTGAATCTTTATCTCAAGAAA
1 TTAAGTTGAATTTTTTTACATTTTT-ATTAAAATAGACTATAATTAAATGTTTATCTCAAGAAA
2115 TATANNNNNN
Statistics
Matches: 322, Mismatches: 76, Indels: 14
0.78 0.18 0.03
Matches are distributed among these distances:
170 124 0.39
171 196 0.61
172 2 0.01
ACGTcount: A:0.37, C:0.12, G:0.11, T:0.39
Consensus pattern (171 bp):
TTAAGTTGAATTTTTTTACATTTTTATTAAAATAGACTATAATTAAATGTTTATCTCAAGAAACG
TGAAAAAAAAGACATTCATTGAGAAAAAAAAGTTCATTTATAGTCACCCATTCCTTCAAAAGCCT
TACTACTCGCTTTAAATTGATTTATAATCTTATAATTGATT
Found at i:2026 original size:171 final size:161
Alignment explanation
Indices: 1616--2067 Score: 365
Period size: 170 Copynumber: 2.7 Consensus size: 161
1606 CAGAAAAAAC
* * * * * *
1616 CATTCATTGAGAAAAAAAAATTCATTTATAGTCACCTATTCCTTCAAAAACCTTATTACTCGCTT
1 CATTCATTGAG-AAAAAAAGTTCATTTATAATCACCCATTCCTTCAAAAGCCTTACTACTCACTT
* * * ** * * *
1681 TAAAT-GATTCTATAATCTCATAATTGATTTTAAGTTGTAT-TTTTTTATAT-TTTTCATTAAAA
65 TAAATAGCTT-TATAATCTTATAATTAATTTTAAGTTAAATATGTTTTACATATTTT-GTTAAAA
* *
1743 TAGATTATAATTAAATGTTTATCTTAAGAAACGTGTAAAAAAGA
128 TAG----------AATGTTTATCTCAAGAAACGTGAAAAAAAGA
*
1787 CATTCATTGAGAAAAAAAGTTCATTTATAATCGCCCATTCCTTCAAAAGCCTTACTACTCACTTT
1 CATTCATTGAGAAAAAAAGTTCATTTATAATCACCCATTCCTTCAAAAGCCTTACTACTCACTTT
*
1852 AAATTGCTTTATAATCTTATAATTAATTTTAAGTTAAAT-TGTTTTACATATTTTGTTAAAATAG
66 AAATAGCTTTATAATCTTATAATTAATTTTAAGTTAAATATGTTTTACATATTTTGTTAAAATAG
*
1916 NNNNNNNNNNAATGTTTATCTCGAGAAACGTGAAAAAAAAGA
131 ----------AATGTTTATCTCAAGAAACGTG-AAAAAAAGA
* * * * * ***
1958 CATTCATTG-GCAAAAAATGTTCATTTATAGTCACTCATTCTTTCAAAAGCCTTAGTACTGGGTT
1 CATTCATTGAG-AAAAAAAGTTCATTTATAATCACCCATTCCTTCAAAAGCCTTACTACTCACTT
* ** *
2022 TAAATAGTTTTATAATCTTATAATTTGTTTTAAGTTGAATATGTTT
65 TAAATAGCTTTATAATCTTATAATTAATTTTAAGTTAAATATGTTT
2068 AGATTTTTAA
Statistics
Matches: 234, Mismatches: 42, Indels: 9
0.82 0.15 0.03
Matches are distributed among these distances:
170 115 0.49
171 114 0.49
172 5 0.02
ACGTcount: A:0.36, C:0.12, G:0.10, T:0.40
Consensus pattern (161 bp):
CATTCATTGAGAAAAAAAGTTCATTTATAATCACCCATTCCTTCAAAAGCCTTACTACTCACTTT
AAATAGCTTTATAATCTTATAATTAATTTTAAGTTAAATATGTTTTACATATTTTGTTAAAATAG
AATGTTTATCTCAAGAAACGTGAAAAAAAGA
Found at i:4398 original size:167 final size:169
Alignment explanation
Indices: 4015--4548 Score: 547
Period size: 171 Copynumber: 3.1 Consensus size: 169
4005 NNNNNNNNNN
* ** * * * * * *
4015 TTGGGAAGAAAAGTTTATTTATAATCACCCATTCCTTCAAAATCTTTACTACTCTCTTTAAATTA
1 TTGGCAAGAAAAGTCCATTTATAGTCACCCATTCCTTCAAAAGCCTTAGTACTCGCTTTAAATGA
* * * * * * * * ** *
4080 CTTTATAATCTCATAATTAATTTTAAATTGAATTTTTTTACATTTATGGTTAAAATAGACTATAA
66 TTTTATAATCTAATAATTGATTTTAAGTTGAATTCTTTAATATTTTTAATTAAAACAGACTATAA
* * * *
4145 TTGAATGTTTATCTCAAGAAACGTGAAGAAAAAGATATTCA
131 TTGAATATTTATCTCGAGAAACATGAA-AAAAA-ACATTCA
* * * * *
4186 TTGGCAAAAAAAGTCCATTTATAGTCACTCATTCCTTCAAAAGCCTTAGTATTGGGTTTAAAT-A
1 TTGGCAAGAAAAGTCCATTTATAGTCACCCATTCCTTCAAAAGCCTTAGTACTCGCTTTAAATGA
* * * *
4250 GTTTTATAATTTTATAATTTG-TTTTAAGTTGAATATTTTTAGT-TTTTTAATTAAAACAGACTA
66 -TTTTATAATCTAATAA-TTGATTTTAAGTTGAAT-TCTTTAATATTTTTAATTAAAACAGACTA
* * *
4313 TAATTGAATCTTTATCTTGAGAAATAT-AAAAAAAA-ATTCA
128 TAATTGAATATTTATCTCGAGAAACATGAAAAAAAACATTCA
* * * * *
4353 TTGGCGAGAAAAGTGCATTTATAGTCACCCGTTCCTTCAAAAGCCTTATTACTCTCTTTAAATGA
1 TTGGCAAGAAAAGTCCATTTATAGTCACCCATTCCTTCAAAAGCCTTAGTACTCGCTTTAAATGA
* **
4418 TTTTGTAATCTAATAATTGATTTTAAGTTGAATTCTTTAATATTTTTGGTTAAAACAGACTATAA
66 TTTTATAATCTAATAATTGATTTTAAGTTGAATTCTTTAATATTTTTAATTAAAACAGACTATAA
* *
4483 TTAAATATTTATCTCGAGAAACATGAAAAAACAAGCATTTA
131 TTGAATATTTATCTCGAGAAACATGAAAAAA-AA-CATTCA
*
4524 TTGGCAAGACAAGTCCATTTATAGT
1 TTGGCAAGAAAAGTCCATTTATAGT
4549 NNNNNNNNNN
Statistics
Matches: 298, Mismatches: 55, Indels: 20
0.80 0.15 0.05
Matches are distributed among these distances:
166 9 0.03
167 125 0.42
168 8 0.03
169 7 0.02
170 3 0.01
171 139 0.47
172 7 0.02
ACGTcount: A:0.37, C:0.12, G:0.11, T:0.40
Consensus pattern (169 bp):
TTGGCAAGAAAAGTCCATTTATAGTCACCCATTCCTTCAAAAGCCTTAGTACTCGCTTTAAATGA
TTTTATAATCTAATAATTGATTTTAAGTTGAATTCTTTAATATTTTTAATTAAAACAGACTATAA
TTGAATATTTATCTCGAGAAACATGAAAAAAAACATTCA
Done.