Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018398493.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_1788.0, 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: 5859
ACGTcount: A:0.24, C:0.07, G:0.09, T:0.23
Warning! 2133 characters in sequence are not A, C, G, or T
Found at i:526 original size:162 final size:165
Alignment explanation
Indices: 125--526 Score: 415
Period size: 172 Copynumber: 2.4 Consensus size: 165
115 NGCAAGTAAT
* * * * *
125 AAGACTTTTGAAAGAATGAGAGGCTATAAATTGACTTTTGTTGCTAATGAATTCTTTTTTCTTCA
1 AAGACTTTT-AAAGAATGAG-TGCTATAAATGGACTTTTCTTGCCAATGAA-TGTTTTTTCTTCA
190 CT-TTTCTCAAGGCAAACATTCAATTATAACCTGTTTTAATGAAAAATGTAAAACAAATTACACT
63 -TGTTTCTCAAGGCAAACATTCAATTATAACCTGTTTTAATGAAAAATGTAAAACAAATTACACT
*
254 TAAAATTAATTATGACATTATAAAACTATTTAGAATGAGTAAA
127 TAAAATCAATTATGACATTATAAAACTATTTA-AA-GAG--AA
* * * ** *
297 AAGGCTATTAACGGAATGAGATGCTATAAATGGACTTTTCTTATCAATAAATGCTTTTTTCTTCA
1 AAGACTTTTAA-AGAATGAG-TGCTATAAATGGACTTTTCTTGCCAATGAATG-TTTTTTCTTCA
* * * * * * *
362 TGTTTGTCATGGTAGACGTTCAATTATAATCTGTTTTAATGAAAAATGT--AA-AAATTTCAACT
63 TGTTTCTCAAGGCAAACATTCAATTATAACCTGTTTTAATGAAAAATGTAAAACAAATTAC-ACT
* * *
424 TAAAATCAATTATTAGATTAT-AAACTATTT-AA-AG-C
127 TAAAATCAATTATGACATTATAAAACTATTTAAAGAGAA
459 AAGACTTTTAAAGAAATGAGTGACTATAAATGGACTTTTCTTGCCAATGAATGTGTTTTTCTTCA
1 AAGACTTTTAAAG-AATGAGTG-CTATAAATGGACTTTTCTTGCCAATGAATGT-TTTTTCTTCA
524 TGT
63 TGT
527 NNNNNNNNNN
Statistics
Matches: 195, Mismatches: 28, Indels: 24
0.79 0.11 0.10
Matches are distributed among these distances:
161 4 0.02
162 55 0.28
165 2 0.01
167 2 0.01
169 15 0.08
170 23 0.12
171 4 0.02
172 90 0.46
ACGTcount: A:0.37, C:0.11, G:0.13, T:0.38
Consensus pattern (165 bp):
AAGACTTTTAAAGAATGAGTGCTATAAATGGACTTTTCTTGCCAATGAATGTTTTTTCTTCATGT
TTCTCAAGGCAAACATTCAATTATAACCTGTTTTAATGAAAAATGTAAAACAAATTACACTTAAA
ATCAATTATGACATTATAAAACTATTTAAAGAGAA
Found at i:1330 original size:171 final size:171
Alignment explanation
Indices: 1116--1536 Score: 412
Period size: 171 Copynumber: 2.5 Consensus size: 171
1106 NNNNNNNGAG
* * * * *
1116 ATTATAAAATCATTTAGAA-CGAGTAAAAAGACTATTAAAGGAATGAGAGGCCATAAATTGACTT
1 ATTATAAAATCATTTA-AAGCGAGTAATAAGACTTTTGAAGGAATGAGAGGCTATAAATAGACTT
* * *
1180 TTCTTATCAATGAATGCTTTTT-TCTT-AGCGATTGTCAAGGCAGACATTCAATTA-TAGTATGT
65 TTCTTATCAATGAATACTTTTTCT-TTCA-CGATTCTCAAGACAGACATTCAATTATTA-TATGT
* * * *
1242 TTTAA-CTAAAATTGTTAAAAA-ATTCAATTTAAAATTAATTATGAC
127 TTTAATC-AAAAAT-ATAAAAATATTCAACTTAAAATTAATTACGAC
* * * *
1287 ATTATAAAATCATTCAAAGCGTGTAATAATACTTTTGAAGGAAT-AG-GTGACTATAAATGGACT
1 ATTATAAAATCATTTAAAGCGAGTAATAAGACTTTTGAAGGAATGAGAG-G-CTATAAATAGACT
* * * * * *
1350 TTTCTTAAT-AATAAATACTTTTTCTTTCACGTTTCTCGAGATAGACTTTCAATTATTATTTGTT
64 TTTCTT-ATCAATGAATACTTTTTCTTTCACGATTCTCAAGACAGACATTCAATTATTATATGTT
*
1414 TTAATCAAAAATATAAAAATATTCAACTTAAAATTAATTACGAG
128 TTAATCAAAAATATAAAAATATTCAACTTAAAATTAATTACGAC
* * * * *
1458 ATTATAAAA-CTATTTAAAGTGAGTGATAAGGCTTTTGAAGGAGTGGGAGGCTATAAATAGACTT
1 ATTATAAAATC-ATTTAAAGCGAGTAATAAGACTTTTGAAGGAATGAGAGGCTATAAATAGACTT
**
1522 TTCTTGCCAATGAAT
65 TTCTTATCAATGAAT
1537 NNNNNNNNNN
Statistics
Matches: 203, Mismatches: 34, Indels: 26
0.77 0.13 0.10
Matches are distributed among these distances:
169 1 0.00
170 12 0.06
171 180 0.89
172 9 0.04
173 1 0.00
ACGTcount: A:0.39, C:0.10, G:0.14, T:0.37
Consensus pattern (171 bp):
ATTATAAAATCATTTAAAGCGAGTAATAAGACTTTTGAAGGAATGAGAGGCTATAAATAGACTTT
TCTTATCAATGAATACTTTTTCTTTCACGATTCTCAAGACAGACATTCAATTATTATATGTTTTA
ATCAAAAATATAAAAATATTCAACTTAAAATTAATTACGAC
Found at i:2888 original size:171 final size:171
Alignment explanation
Indices: 2531--3111 Score: 393
Period size: 171 Copynumber: 3.4 Consensus size: 171
2521 NNNNNNNNNN
* * * * *
2531 ATAAGGCTTTTAAAGGAATG-AGAGGCTGTAAATAGACTTTTCTTACCAATGAATACTTTTTTCT
1 ATAAGGCTTTTGAAGGAATGTA-AGGCTATAAATACACTTTTCTTATCAATGAATGCTTTTTTCT
* ** * ** * * * *
2595 TTACGTTTCTCAATGCAGACATTCAATTATAT-TCTGTTTTAATAAAAAAT-ATAAAAAAATTGA
65 TCACAATTCTCGACACAGACAGTCAATTAT-TGTCTGTCTTAATCAAAAATGA-AAAAAAATTCA
********** * * * * *
2658 ACTNNNNNNNNNNTATGAGATTATAAAACTATTTAGAA-CGAGTA
128 ACTTAAAATCAATTATGAGACTAAAAAACCATCTA-AAGCAAGTA
* * * * *
2702 AAAAGGCTGTTGAAGGACTAG-AAGGCTATAAATATACTTTTGTTATCAATGAATGCTTTTTTCT
1 ATAAGGCTTTTGAAGGAAT-GTAAGGCTATAAATACACTTTTCTTATCAATGAATGCTTTTTTCT
* ** * *
2766 TCACAATTCTCTAGGCAGACATTCAATTATTG-CTGTTTTAA-CAAAAATTGAAAAAACAATTCA
65 TCACAATTCTCGACACAGACAGTCAATTATTGTCTGTCTTAATCAAAAA-TGAAAAAA-AATTCA
* ** *
2829 ACTTAAAATCAATTATGAGACTAAAAAATCATCTAAAGTGATTA
128 ACTTAAAATCAATTATGAGACTAAAAAACCATCTAAAGCAAGTA
********** ** * *
2873 ATAAGGCTTTTGAAGGAATGNNNNNNNNNNAATGGACTTTTCTTATCAATGAATACTTTTATCTT
1 ATAAGGCTTTTGAAGGAATGTAAGGCTATAAATACACTTTTCTTATCAATGAATGCTTTTTTCTT
* * * * *
2938 CACATTTCTCGACATAGACAGTCAATTATTGTTTGTCTTAATCAAAAATGTAAAAAAATTTAACT
66 CACAATTCTCGACACAGACAGTCAATTATTGTCTGTCTTAATCAAAAATGAAAAAAAATTCAACT
* * * * * *
3003 TCAAATCAGTTATTAGATTATAAAACCATTTAAAGCAAGTA
131 TAAAATCAATTATGAGACTAAAAAACCATCTAAAGCAAGTA
* * **
3044 ATAAGGCTTTTGAGGGAATGTGAGGCTATAAATACACTTTTCTTGCCAATGAATGCTTTTTTCTT
1 ATAAGGCTTTTGAAGGAATGTAAGGCTATAAATACACTTTTCTTATCAATGAATGCTTTTTTCTT
3109 CAC
66 CAC
3112 TTTTCTCNNN
Statistics
Matches: 314, Mismatches: 87, Indels: 18
0.75 0.21 0.04
Matches are distributed among these distances:
169 5 0.02
170 19 0.06
171 268 0.85
172 16 0.05
173 6 0.02
ACGTcount: A:0.36, C:0.13, G:0.13, T:0.35
Consensus pattern (171 bp):
ATAAGGCTTTTGAAGGAATGTAAGGCTATAAATACACTTTTCTTATCAATGAATGCTTTTTTCTT
CACAATTCTCGACACAGACAGTCAATTATTGTCTGTCTTAATCAAAAATGAAAAAAAATTCAACT
TAAAATCAATTATGAGACTAAAAAACCATCTAAAGCAAGTA
Found at i:4113 original size:170 final size:162
Alignment explanation
Indices: 3898--4219 Score: 348
Period size: 170 Copynumber: 1.9 Consensus size: 162
3888 GAATAAGAGG
* * * * **
3898 CTATAAATGGACTTTTTTTACCAATGAATGCTTTTTTCATCACGTTTGTCAAGACAAACGTTCAA
1 CTATAAATGCACTTTTCTTACCAATGAATACTTTTTTCATCACGTTTCTCAAGACAAACAATCAA
* *
3963 TTATAGTCTGTTTTGAA-GAAAAATATAAAA-AATTTCAACTTAAAATT-GATTATTAGAGTAT-
66 TTATAGTCTGTTTT-AATAAAAAATATAAAACAATTT-AACTTAAAATTCAATTATTAGAGTATA
*
4024 AAACTATTTAAAGCGAGTAATAAGANNNNNNNNNNAATGGGTGA
129 AAACCATTTAAAGCGAGTAATAAGA----------AATGGGTGA
* * ** *
4068 CTATAAATGCACTTTTCTTGCCAATGAATACTTTTGTT-TTCACGTTTCTTGAGAGAAACAATCA
1 CTATAAATGCACTTTTCTTACCAATGAATACTTTT-TTCATCACGTTTCTCAAGACAAACAATCA
* *
4132 ATTATTGTCTGTTTTAATAAAAAATATAAAACAATTTAACTTAAAATTCAATTATTAGATTATAA
65 ATTATAGTCTGTTTTAATAAAAAATATAAAACAATTTAACTTAAAATTCAATTATTAGAGTATAA
4197 AACCATTTAAAGCGAGTAATAAG
130 AACCATTTAAAGCGAGTAATAAG
4220 GCTTTTAAAG
Statistics
Matches: 131, Mismatches: 16, Indels: 8
0.85 0.10 0.05
Matches are distributed among these distances:
169 2 0.02
170 87 0.66
171 19 0.15
172 23 0.18
ACGTcount: A:0.39, C:0.11, G:0.12, T:0.35
Consensus pattern (162 bp):
CTATAAATGCACTTTTCTTACCAATGAATACTTTTTTCATCACGTTTCTCAAGACAAACAATCAA
TTATAGTCTGTTTTAATAAAAAATATAAAACAATTTAACTTAAAATTCAATTATTAGAGTATAAA
ACCATTTAAAGCGAGTAATAAGAAATGGGTGA
Found at i:5317 original size:171 final size:170
Alignment explanation
Indices: 5013--5346 Score: 449
Period size: 171 Copynumber: 2.0 Consensus size: 170
5003 NNNNNNNNNT
*
5013 TTCAACTTAAAATCAATTATCAGATTATAAACTATTTAAAGCGAGTAATAAGAGTTTTGAAGGAA
1 TTCAACTTAAAATCAATTATCACATTATAAACTATTTAAAGCGAGTAATAAGAGTTTTGAAGGAA
* * * ** *
5078 TGGTTGACTATAAATGGACTATTCTTCCCAATGAATGTGTTTTCCTTCACGTTTCTTGAGGTAGA
66 TAGTAGACTATAAATAGACTATTCTTCCCAATGAATGTGTTTTCCTTCACGTTTCTCAAGGCAGA
* *
5143 CATTCAATTATAGTTTTTTTTAATGAAAAATGTAAGAAAA
131 CATTCAATTATAGTCTGTTTTAATGAAAAATGTAAGAAAA
* * *
5183 TTCAATTTAAAATCAATTATGACATTATAAACCTATTTAAAGTGAGTAATAAG-GCTTTTGAAGG
1 TTCAACTTAAAATCAATTATCACATTATAAA-CTATTTAAAGCGAGTAATAAGAG-TTTTGAAGG
** * * * *
5247 AATAAG-AGGTTATAAATAGACTTTTCTTGCCAATGAATGCT-TTTTGCTTCACTTTTCTCAAGG
64 AAT-AGTAGACTATAAATAGACTATTCTTCCCAATGAATG-TGTTTTCCTTCACGTTTCTCAAGG
5310 CAGACATTCAATTATAGTCTGTTTTAATGAAAAATGT
127 CAGACATTCAATTATAGTCTGTTTTAATGAAAAATGT
5347 NNNNNNNNNN
Statistics
Matches: 142, Mismatches: 18, Indels: 7
0.85 0.11 0.04
Matches are distributed among these distances:
170 29 0.20
171 111 0.78
172 2 0.01
ACGTcount: A:0.36, C:0.12, G:0.15, T:0.37
Consensus pattern (170 bp):
TTCAACTTAAAATCAATTATCACATTATAAACTATTTAAAGCGAGTAATAAGAGTTTTGAAGGAA
TAGTAGACTATAAATAGACTATTCTTCCCAATGAATGTGTTTTCCTTCACGTTTCTCAAGGCAGA
CATTCAATTATAGTCTGTTTTAATGAAAAATGTAAGAAAA
Done.