Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018401214.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_4361.0, 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: 3332
ACGTcount: A:0.30, C:0.09, G:0.10, T:0.28
Warning! 729 characters in sequence are not A, C, G, or T
Found at i:878 original size:171 final size:171
Alignment explanation
Indices: 582--1929 Score: 993
Period size: 172 Copynumber: 7.9 Consensus size: 171
572 NNNNNNNNNN
* * *
582 AGTAATAAGGCTTTTG-AAGAAATAGGAGACTATAAATGGACTTTTCTT-CTCAATAAATAG-CT
1 AGTAATAAGGCTTTTGAAAG-AATGGGTGACTATAAATGGACTTTTCTTAC-CAATGAAT-GCCT
* * * * * * *
644 TTTTCTTCATATTTC-CTGAGGCAAGCTTTCAATTATAGTCTGTTTTAA-TGAAAAATCTAAAAA
63 TTTTCTTCATGTTTCTC-AAGGTAAACATTCAATTATAATCTGTTTTAACT-AAAAATGTAAAAA
* * * *
707 AGTTCAACTTAAAATCAATTATGAGATTATAAGACCATTTATAGCG
126 AATTCAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGTG
* * **
753 AGTAATAAGGCTTTTGAAAGAATGGGTGACTATAAATGGACTTTACTTATCAATGAATGTGTTTT
1 AGTAATAAGGCTTTTGAAAGAATGGGTGACTATAAATGGACTTTTCTTACCAATGAATGCCTTTT
* * * *
818 TGTTTATGTTTCACAAGGTAAACATTCAATTATAATCTGTTTGT-ACCAAAAATGTAAAAAAAAT
66 TCTTCATGTTTCTCAAGGTAAACATTCAATTATAATCTGTTT-TAACTAAAAATGT-AAAAAAAT
********* * * *
882 T-AANNNNNNNNNNAATTTTGAGATTATAAAACCATTCAAAGTT
129 TCAA-CTTAAAATCAATTATGAGATTATAAAACCATTTAAAGTG
* * ********** **
925 AGTAATAAGGCTTTTAAAAGAATGAGTGACTATNNNNNNNNNNTTCTTGTCAATGAATGCCTTTT
1 AGTAATAAGGCTTTTGAAAGAATGGGTGACTATAAATGGACTTTTCTTACCAATGAATGCCTTTT
* * * * * *
990 TCTTCACGTTTCTCTAGGTAGACATTCAAATATAGTCTGTTTTAACTAAAAATATAAAAAAAATT
66 TCTTCATGTTTCTCAAGGTAAACATTCAATTATAATCTGTTTTAACTAAAAATGT-AAAAAAATT
* * * * * *
1055 GAACATAAATTTAATTTTGAGATAATAAAACCATTTAAAGTG
130 CAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGTG
* * * * *
1097 AATAATAAGGCTTTTG-AAGAAATTGGTGACTATAAATAGACTTTTCTTACCCATGAATGCATTT
1 AGTAATAAGGCTTTTGAAAG-AATGGGTGACTATAAATGGACTTTTCTTACCAATGAATGCCTTT
* *
1161 TTC-TCTATGTTTCTCATGGTAAACATTAAATTATAATCTGTTTTAACTAAAAA--TAAAAAACA
65 TTCTTC-ATGTTTCTCAAGGTAAACATTCAATTATAATCTGTTTTAACTAAAAATGTAAAAAA-A
* * * *
1223 TTCACCTTAAAATCAATTATGAGACTATAAAATCATTTAAAGCG
128 TTCAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGTG
********** * * * * *
1267 AGTAATAAGGCTNNNNNNNNNNTGAGTGACTATAAATAGACTTTTCTTGCTAATGAATACCTTTT
1 AGTAATAAGGCTTTTGAAAGAATGGGTGACTATAAATGGACTTTTCTTACCAATGAATGCCTTTT
* * * * * *
1332 TCTTCACGTATC-CTAAGGTAGACATTCAATTATAATCTGTTCTAAATAAAAATGTAAAACAATT
66 TCTTCATGTTTCTC-AAGGTAAACATTCAATTATAATCTGTTTTAACTAAAAATGTAAAAAAATT
** *
1396 CAACCAAAAATCAATTATGAGATTATAAAACCATTTGAAGTG
130 CAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGTG
********** * * **
1438 ANNNNNNNNNNTTTTGAAAGAATAGGCGACTATAAATGGACTTTTCTTACCAATGAATATCTTTT
1 AGTAATAAGGCTTTTGAAAGAATGGGTGACTATAAATGGACTTTTCTTACCAATGAATGCCTTTT
* * * * * *
1503 TCATCACGTTTCTCAATGTACAA-AATCAATTATAATTTGTATTAAGC-AAAAATGTACAAAAAA
66 TCTTCATGTTTCTCAAGGTA-AACATTCAATTATAATCTGTTTTAA-CTAAAAATGTA-AAAAAA
* * * * **
1566 TTCAAATTAAAATTAATTTTGAGAATATAAAACC-TTTCAAAGCA
128 TTCAACTTAAAATCAATTATGAGATTATAAAACCATTT-AAAGTG
* * * * *
1610 AATAATAA-GCATTTTGAAGGAATGGGTGACTATAAATAGACTTTTCTTGCCAGTGAATGCCTTT
1 AGTAATAAGGC-TTTTGAAAGAATGGGTGACTATAAATGGACTTTTCTTACCAATGAATGCCTTT
* * * * * * ** *
1674 TGCTTCATGTTTCTCAGGGTAGACTTTCAACTATAACCTGTTCAAACTAAAAATGTATAAAGAAT
65 TTCTTCATGTTTCTCAAGGTAAACATTCAATTATAATCTGTTTTAACTAAAAATGTA-AAAAAAT
* * * *
1739 TCAAATTAGAATCAATTTTAAGATTATAAAACCATTTAAAGTG
129 TCAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGTG
********* * *
1782 AGTAATAAGGCTTTT-AAAGNNNNNNNNNNCTATAAATGGACTTTTCTTGCTAATGAATGCCTTT
1 AGTAATAAGGCTTTTGAAAG-AATGGGTGACTATAAATGGACTTTTCTTACCAATGAATGCCTTT
** * * *
1846 TTCTTCATGTTTCTTGAGTTAGACATTCAATTATAATCTGTTTTAACAAAAAATGTAAAAAAATT
65 TTCTTCATGTTTCTCAAGGTAAACATTCAATTATAATCTGTTTTAACTAAAAATGTAAAAAAATT
*
1911 CAACTTTAAATCAATTATG
130 CAACTTAAAATCAATTATG
1930 NNNNNNNNNN
Statistics
Matches: 895, Mismatches: 253, Indels: 58
0.74 0.21 0.05
Matches are distributed among these distances:
169 7 0.01
170 124 0.14
171 249 0.28
172 508 0.57
173 7 0.01
ACGTcount: A:0.38, C:0.12, G:0.12, T:0.34
Consensus pattern (171 bp):
AGTAATAAGGCTTTTGAAAGAATGGGTGACTATAAATGGACTTTTCTTACCAATGAATGCCTTTT
TCTTCATGTTTCTCAAGGTAAACATTCAATTATAATCTGTTTTAACTAAAAATGTAAAAAAATTC
AACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGTG
Found at i:1305 original size:170 final size:161
Alignment explanation
Indices: 1122--1431 Score: 322
Period size: 170 Copynumber: 1.9 Consensus size: 161
1112 GAAGAAATTG
* * * * *
1122 GTGACTATAAATAGACTTTTCTTACCCATGAATGCATTTTTC-TCTATGT-TTCTCATGGTAAAC
1 GTGACTATAAATAGACTTTTCTTACCAATGAATACATTTTTCTTC-ACGTATCCT-AAGGTAAAC
* * *
1185 ATTAAATTATAATCTGTTTTAACTAAAAATAAAAAAC-ATTC-ACCTTAAAATCAATTATGAGAC
64 ATTAAATTATAATCTGTTCTAAATAAAAATAAAAAACAATTCAACC-AAAAATCAATTATGAGAC
*
1248 TATAAAATCATTTAAAGCGAGTAATAAGGCTNNNNNNNNNNTGA
128 TATAAAACCATTTAAAGCGAGTAATAAGGCT----------TGA
* * * *
1292 GTGACTATAAATAGACTTTTCTTGCTAATGAATACCTTTTTCTTCACGTATCCTAAGGTAGACAT
1 GTGACTATAAATAGACTTTTCTTACCAATGAATACATTTTTCTTCACGTATCCTAAGGTAAACAT
* ** *
1357 TCAATTATAATCTGTTCTAAATAAAAATGTAAAACAATTCAACCAAAAATCAATTATGAGATTAT
66 TAAATTATAATCTGTTCTAAATAAAAATAAAAAACAATTCAACCAAAAATCAATTATGAGACTAT
1422 AAAACCATTT
131 AAAACCATTT
1432 GAAGTGANNN
Statistics
Matches: 119, Mismatches: 17, Indels: 7
0.83 0.12 0.05
Matches are distributed among these distances:
170 79 0.66
171 37 0.31
172 3 0.03
ACGTcount: A:0.38, C:0.15, G:0.10, T:0.34
Consensus pattern (161 bp):
GTGACTATAAATAGACTTTTCTTACCAATGAATACATTTTTCTTCACGTATCCTAAGGTAAACAT
TAAATTATAATCTGTTCTAAATAAAAATAAAAAACAATTCAACCAAAAATCAATTATGAGACTAT
AAAACCATTTAAAGCGAGTAATAAGGCTTGA
Found at i:3105 original size:172 final size:172
Alignment explanation
Indices: 2786--3211 Score: 410
Period size: 172 Copynumber: 2.5 Consensus size: 172
2776 NNNNNCTTGT
** *
2786 CAATGAATACCTTTTTCTTCATATTTCTTGAGGTAGACATTCAATTATAATATGTTTTAACTAAA
1 CAATGAATACCTTTTTCTTCATATTTCTCAAGGTAGACATTCAATTATAATATGTTTTAACCAAA
* * * *
2851 AATATACAAATAATTCAAATTAAAATCAATTTTGAGATTATCAAACCATTTAAATTGAATAATAA
66 AATATACAAAAAATTCAAATTAAAATCAATTATGAGATTATAAAACCATATAAATTGAATAATAA
** **
2916 GCCTTTTCATGGAATGGGTGACTATAAATGGACTTTTTTTAC
131 AACTTTTCAAAGAATGGGTGACTATAAATGGACTTTTTTTAC
* * * * * *
2958 CAATGAATGCCTTTTTTCTTTA-ACTTTCTCAAGGTAGACATTTAATTATAGTCTTTTTTAACCA
1 CAATGAATACC-TTTTTCTTCATA-TTTCTCAAGGTAGACATTCAATTATAATATGTTTTAACCA
* * * * *
3022 AAAATGTA-AAAAAATTCAATTTAAAATCTATTATGAGATTATAAAACTATATAAAGTT-AGTAA
64 AAAATATACAAAAAATTCAAATTAAAATCAATTATGAGATTATAAAACCATATAAA-TTGAATAA
* ********** * *
3085 TAAAACTTTTGAAAGAATGGGTGACNNNNNNNNNNCTTTTCTTGC
128 TAAAACTTTTCAAAGAATGGGTGACTATAAATGGACTTTTTTTAC
* * ** * *
3130 TAATGAATGCCTTTTTCTTCAGGTTTCTCGAGGTAGACATTCAATTATAATATGTTTTAACTAAA
1 CAATGAATACCTTTTTCTTCATATTTCTCAAGGTAGACATTCAATTATAATATGTTTTAACCAAA
* *
3195 AATGTA-AAAATATTCAA
66 AATATACAAAAAATTCAA
3212 CTNNNNNNNN
Statistics
Matches: 205, Mismatches: 45, Indels: 9
0.79 0.17 0.03
Matches are distributed among these distances:
171 61 0.30
172 93 0.45
173 51 0.25
ACGTcount: A:0.37, C:0.12, G:0.11, T:0.38
Consensus pattern (172 bp):
CAATGAATACCTTTTTCTTCATATTTCTCAAGGTAGACATTCAATTATAATATGTTTTAACCAAA
AATATACAAAAAATTCAAATTAAAATCAATTATGAGATTATAAAACCATATAAATTGAATAATAA
AACTTTTCAAAGAATGGGTGACTATAAATGGACTTTTTTTAC
Done.