Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018402678.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_5741.0, 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: 2715
ACGTcount: A:0.31, C:0.09, G:0.11, T:0.30
Warning! 514 characters in sequence are not A, C, G, or T
Found at i:317 original size:173 final size:170
Alignment explanation
Indices: 1--756 Score: 583
Period size: 171 Copynumber: 4.4 Consensus size: 170
* * * * * *
1 TTTCTTCATGTTTCTCAAGGTAGACATTCAATTATAGTCTATTTTAA-TGAAAAAAG-AAACAAA
1 TTTCTTTATATTTCTCGAGGTAGACATTTAATTATAGTCTATTTTAACT-AAAAATGTAAAAAAA
* * ********** * * **
64 TTAAACTTAAAATCAATTATGAGATTANNNNNNNNNNTAAAGTGAGTAAGAAGACTTTTGAAGGT
65 TTAAACTTAAAATCAATTTTGACATTATAAAACTATTTAAAGTGAGTAATAAGGCTTTTGAAGAA
* * *
129 ATGGGAGGCTATAAATGAACTTTTTTTTGTCATTGAATACTTT
130 ATGGGAGACTATAAATGAACTTTTTTTT-ACAATGAATA-TTT
* *
172 TTTCTTTATATTTCTCGAGGTAAACATTTAATTATAGTCTATTTTAACTAAACATGTAAAGAAAA
1 TTTCTTTATATTTCTCGAGGTAGACATTTAATTATAGTCTATTTTAACTAAAAATGTAAA-AAAA
* * * * * * *
237 TTAAACATAAAATCAATTTTGAGATAACAAGACCATTTAAAGTGGGTAATAAGGCTTTTGAAGAA
65 TTAAACTTAAAATCAATTTTGACATTATAAAACTATTTAAAGTGAGTAATAAGGCTTTTGAAGAA
* * * *
302 ATTGGTGACTATAAATGGACTTTTTTTTACTAGTGAATATCTT
130 ATGGGAGACTATAAATGAACTTTTTTTTAC-AATGAATAT-TT
** * * * * *
345 TTTCTTTACGTTTCTCAATGTAGACATTTAATTATAATCTGTTTTAA-TAAAAAAGTAAAAAAAT
1 TTTCTTTATATTTCTCGAGGTAGACATTTAATTATAGTCTATTTTAACTAAAAATGTAAAAAAAT
* * * *
409 TGAACTTAAAATCAATTTTGACATTATAAAACTAGTTAAAGCGAGTAATAAGGCTTTTGAAGGAA
66 TAAACTTAAAATCAATTTTGACATTATAAAACTATTTAAAGTGAGTAATAAGGCTTTTGAAGAAA
** * * *
474 T-GGATGACCGT-AATGAAATTTTCTTTCCAATGAATGTATTT
131 TGGGA-GACTATAAATGAACTTTTTTTTACAATGAA--TATTT
* * * * * * *
515 TTT-ATCATATTTCTCGAGGTAGACAATTAATTATTGTCTATTTTAACCAAAGATGAAAAAAAAT
1 TTTCTTTATATTTCTCGAGGTAGACATTTAATTATAGTCTATTTTAACTAAAAATGTAAAAAAAT
* * * *
579 TCAACTTAAAATCAATTATT-ATATTATAAAACTATTTAAAGTGAGTAATAAGGTTTTTCAA-AG
66 TAAACTTAAAATCAATT-TTGACATTATAAAACTATTTAAAGTGAGTAATAAGGCTTTTGAAGA-
* * ** *********
642 AATGGGAGACTATAAATGGACTTTTCTTGCCNNNNNNNNNNTT
129 AATGGGAGACTATAAATGAACTTTTTTTTAC-AATGAATATTT
* * * * *
685 TTTCTTCATATTTCTCGAGGTAGACATTCAATTTTAGTCCATTTTAACAAAAAAATGTAAAAAAA
1 TTTCTTTATATTTCTCGAGGTAGACATTTAATTATAGTCTATTTTAAC-TAAAAATGTAAAAAAA
*
750 TTCAACT
65 TTAAACT
757 NNNNNNNNNN
Statistics
Matches: 465, Mismatches: 104, Indels: 31
0.77 0.17 0.05
Matches are distributed among these distances:
169 38 0.08
170 97 0.21
171 171 0.37
172 36 0.08
173 123 0.26
ACGTcount: A:0.38, C:0.10, G:0.13, T:0.37
Consensus pattern (170 bp):
TTTCTTTATATTTCTCGAGGTAGACATTTAATTATAGTCTATTTTAACTAAAAATGTAAAAAAAT
TAAACTTAAAATCAATTTTGACATTATAAAACTATTTAAAGTGAGTAATAAGGCTTTTGAAGAAA
TGGGAGACTATAAATGAACTTTTTTTTACAATGAATATTT
Found at i:1525 original size:170 final size:168
Alignment explanation
Indices: 1010--2171 Score: 699
Period size: 170 Copynumber: 6.8 Consensus size: 168
1000 NNNNNNNNNN
* *
1010 GAATGAGAGACTATAAATGGACTTTTCTTGTCAATGAATGCTTTTTTCTTCATGCTTCTTGAGGT
1 GAATGAGAGACTATAAAT-GACTTTTCTTGTCAATGAATGC-TTTTTCTTCACGTTTCTTGA-GT
* * * * *
1075 AAACATTCAATTATAGTCTATTTTAACTAATAATGTAAAAAAAATTGATCCA-AAAATCAATTTT
63 AGATATTCAATTATAGTCTATTTTAACTAAAAAAGT-AAAAAAATTGA-ACATAAAATCAATTTT
* * * *
1139 GAGGTTATAAAATTATTTAAAGCTAGTAAT-AGTGCTTTTGAAG
126 GAGATAATAAAATTATTTAAAGCGAGTAATAAG-ACTTTTGAAG
* *
1182 GAATG-GAAGACTTTAAATGAACTTTTCTTGTCAATGAATGCTTTTTGCTTCACGTTTCTCTTAG
1 GAATGAG-AGACTATAAATG-ACTTTTCTTGTCAATGAATGCTTTTT-CTTCACGTTTCT-TGAG
* * * * * *
1246 TAGATATTTAATTATAGTTTGTTTTAACCAAAATA-TTAAAAAA-TGAACATAAAATCAATTTTG
62 TAGATATTCAATTATAGTCTATTTTAACTAAAAAAGTAAAAAAATTGAACATAAAATCAATTTTG
* * * *
1309 GGATAACAAAATTATTTAAA-CTTG-GCAATAAGGA-TTTTAAAG
127 AGATAATAAAATTATTTAAAGC--GAGTAATAA-GACTTTTGAAG
* * * *
1351 GAATGAGCGACTATAAATAGACTTGTT-TTCTCAATGAATG-TGTTTTCTTCACATTTCTTGACA
1 GAATGAGAGACTATAAAT-GACTT-TTCTTGTCAATGAATGCT-TTTTCTTCACGTTTCTTGA-G
* * *
1414 TAGATATTCAATTATAATCTATTTTAACTAAAAAAGTAAAAAAATTGAACTTAAAATCAATTTTA
62 TAGATATTCAATTATAGTCTATTTTAACTAAAAAAGTAAAAAAATTGAACATAAAATCAATTTTG
* * * *
1479 ACATGATAAAACTATTTAAAGCGAATAATAAGACTTTTGAAG
127 AGATAATAAAATTATTTAAAGCGAGTAATAAGACTTTTGAAG
* * * ** *
1521 GAATG-GATGACTAT-AATGAAATTTTCTTGCCAATGAATGCATTTTTCATCATATTTCTCGAAG
1 GAATGAGA-GACTATAAATG-ACTTTTCTTGTCAATGAATGC-TTTTTCTTCACGTTTCTTG-AG
* * * * * * *
1584 TAGACATTCAATTATTA-TTTGTTTTAA-TCAAAGA-TGAAAACAAATT-TACTTAAAATCAATT
62 TAGATATTCAATTA-TAGTCTATTTTAACTAAAAAAGT-AAAA-AAATTGAACATAAAATCAATT
* * ********** * * *
1645 ATGAGATTATAANNNNNNNNNNAGTGAGTAAGAAGGCTTTTGAAG
124 TTGAGATAATAAAATTATTTAAAGCGAGTAATAAGACTTTTGAAG
* * * * * *
1690 GAAT-AGGAGACTATAAATGAACGTTTCTTGCCAATGAATACTTTTTTCTTCATGTTTCTTAATA
1 GAATGA-GAGACTATAAATG-ACTTTTCTTGTCAATGAATGC-TTTTTCTTCACGTTTCTTGA-G
* * * * * ** *
1754 TAGACATTCAATTATAGTCTATTTTAGCTAAAAATGTAAAAAAATTCAACTTGTAATCAATTATG
62 TAGATATTCAATTATAGTCTATTTTAACTAAAAAAGTAAAAAAATTGAACATAAAATCAATTTTG
* ********** *
1819 AGATTATAAAANNNNNNNNNNCGAGTAATAAGGCTTTTGAAG
127 AGATAATAAAATTATTTAAAGCGAGTAATAAGACTTTTGAAG
* * * **
1861 GATTGAGAGACTATAAATGAACTTTTCTTGCCAATGAATACTTTTT-TCTCTACGTTTCTCAAGG
1 GAATGAGAGACTATAAATG-ACTTTTCTTGTCAATGAATGCTTTTTCT-TC-ACGTTTCTTGA-G
* * * ** * * * **
1925 TAAACATTCAATTATAGTATGCTTTAACTAGAAATGCAAAAAAAAAAAGAACATAAAATCAATTT
62 TAGATATTCAATTATAGTCTATTTTAACTAAAAAAG--TAAAAAAATTGAACATAAAATCAATTT
* * ** * ** *
1990 TGGGACT-ACAAAACCATTTAAAGTG-GTTAATAAGGTTTTTGATG
125 TGAGA-TAATAAAATTATTTAAAGCGAG-TAATAAGACTTTTGAAG
* * ** * ** *
2034 GAATGAGTGACTATAATTGGACTTTTCTTACCAATGAATGCCTTTTTCTTCATGTTTCTCAACAT
1 GAATGAGAGACTATAAAT-GACTTTTCTTGTCAATGAATG-CTTTTTCTTCACGTTTCTTGA-GT
* * * * * *
2099 AGATATTCAATTATAATATGTTTTAACCAAAAAGGTAAAAAAATTGAACTTAAAATCAATTTTGA
63 AGATATTCAATTATAGTCTATTTTAACTAAAAAAGTAAAAAAATTGAACATAAAATCAATTTTGA
*
2164 GATTATAA
128 GATAATAA
2172 NNNNNNNNNN
Statistics
Matches: 785, Mismatches: 158, Indels: 95
0.76 0.15 0.09
Matches are distributed among these distances:
167 2 0.00
168 48 0.06
169 169 0.22
170 182 0.23
171 179 0.23
172 76 0.10
173 118 0.15
174 10 0.01
175 1 0.00
ACGTcount: A:0.38, C:0.11, G:0.13, T:0.36
Consensus pattern (168 bp):
GAATGAGAGACTATAAATGACTTTTCTTGTCAATGAATGCTTTTTCTTCACGTTTCTTGAGTAGA
TATTCAATTATAGTCTATTTTAACTAAAAAAGTAAAAAAATTGAACATAAAATCAATTTTGAGAT
AATAAAATTATTTAAAGCGAGTAATAAGACTTTTGAAG
Found at i:1640 original size:339 final size:340
Alignment explanation
Indices: 1010--2161 Score: 791
Period size: 340 Copynumber: 3.4 Consensus size: 340
1000 NNNNNNNNNN
* * * ** **
1010 GAATGAGAGACTATAAATGGACTTTTCTTGTCAATGAATGCTTTTTTCTTCATGCTTCTTGAGGT
1 GAATGAGAGACTATAAATAGACTTTTCTTCTCAATGAATGCTGTTTTCTTCACACTTCTTGACAT
* * * * *
1075 AAACATTCAATTATAGTCTATTTTAACTAATAATGTAAAAAAAATTGATCCAAAAATCAATTTTG
66 AAACATTCAATTATAATCTATTTTAACTAAAAAAGTAAAAAAAATTGAACCAAAAATCAATTTTA
** * * * * * * *
1140 AGGTTATAAAATTATTTAAAGCTAGTAATAGTGCTTTTGAAGGAATGGAAGACTTTAAATGAACT
131 ACATGATAAAACTATTTAAAGCGAATAATAGTACTTTTGAAGGAATGGAAGACTATAAATGAAAT
* * * ** * *
1205 TTTCTTGTCAATGAATGCTTTTTGCTTCACGTTTCTCTTAGTAGATATTTAATTATAGTTTGTTT
196 TTTCTTGCCAATGAATGCTTTTTGCATCACATTTCTCGAAGTAGACATTCAATTATAGTTTGTTT
1270 TAACCAAAATATTAAAAAATGAACATAAAATCAATTTTGGGATAACAAAATTATTTAAACTTGGC
261 TAACCAAAATA-TAAAAAATGAACATAAAATCAATTTTGGGATAACAAAATTATTTAAACTTGGC
1335 AATAAGGATTTTAAAG
325 AATAAGGATTTTAAAG
* *
1351 GAATGAGCGACTATAAATAGACTTGTT-TTCTCAATGAATG-TGTTTTCTTCACATTTCTTGACA
1 GAATGAGAGACTATAAATAGACTT-TTCTTCTCAATGAATGCTGTTTTCTTCACACTTCTTGACA
* * **
1414 TAGATATTCAATTATAATCTATTTTAACTAAAAAAGT-AAAAAAATTGAACTTAAAATCAATTTT
65 TAAACATTCAATTATAATCTATTTTAACTAAAAAAGTAAAAAAAATTGAACCAAAAATCAATTTT
*
1478 AACATGATAAAACTATTTAAAGCGAATAATAAG-ACTTTTGAAGGAATGGATGACTAT-AATGAA
130 AACATGATAAAACTATTTAAAGCGAATAAT-AGTACTTTTGAAGGAATGGAAGACTATAAATGAA
*
1541 ATTTTCTTGCCAATGAATGCATTTTT-CATCATATTTCTCGAAGTAGACATTCAATTATTA-TTT
194 ATTTTCTTGCCAATGAATGC-TTTTTGCATCACATTTCTCGAAGTAGACATTCAATTA-TAGTTT
* ** * * * * * **********
1604 GTTTTAATCAAAGATGA-AAACAAATTTACTTAAAATCAATTATGAGATTATAANNNNNNNNNNA
257 GTTTTAACCAAA-AT-ATAAA-AAATGAACATAAAATCAATTTTGGGATAACAAAATTATTTAAA
* * * * *
1668 -GTGAGTAAGAAGGCTTTTGAAG
319 CTTG-GCAATAAGGATTTTAAAG
* * * *** *
1690 GAAT-AGGAGACTATAAAT-GAACGTTTCTTGC-CAATGAATACTTTTTTCTTCATGTTTCTTAA
1 GAATGA-GAGACTATAAATAG-ACTTTTCTT-CTCAATGAATGCTGTTTTCTTCACACTTCTTGA
* * * * * * ****
1752 TATAGACATTCAATTATAGTCTATTTTAGCTAAAAATGT-AAAAAAATTCAACTTGTAATCAATT
63 CATAAACATTCAATTATAATCTATTTTAACTAAAAAAGTAAAAAAAATTGAACCAAAAATCAATT
* * * * ********** * * *
1816 ATGAGATTATAAAANNNNNNNNNNCGAGTAATAAG-GCTTTTGAAGG-ATTGAGAGACTATAAAT
128 TTAACATGATAAAACTATTTAAAGCGAATAAT-AGTACTTTTGAAGGAATGGA-AGACTATAAAT
* * * * *
1879 GAACTTTTCTTGCCAATGAATACTTTTTTC-TCTACGTTTCTC-AAGGTAAACATTCAATTATAG
191 GAAATTTTCTTGCCAATGAATGCTTTTTGCATC-ACATTTCTCGAA-GTAGACATTCAATTATAG
* * * * * **
1942 TATGCTTTAACTAGAAATGCAAAAAAAAAAAGAACATAAAATCAATTTTGGGACT-ACAAAACCA
254 TTTGTTTTAACCA-AAAT----ATAAAAAATGAACATAAAATCAATTTTGGGA-TAACAAAATTA
* * * * *
2006 TTTAAA-GTGGTTAATAAGGTTTTTGATG
313 TTTAAACTTGG-CAATAAGGATTTTAAAG
* * * *** **
2034 GAATGAGTGACTATAATTGGACTTTTCTTAC-CAATGAATGCCT-TTTTCTTCATGTTTCTCAAC
1 GAATGAGAGACTATAAATAGACTTTTCTT-CTCAATGAATG-CTGTTTTCTTCACACTTCTTGAC
* * * * * * **
2097 ATAGATATTCAATTATAATATGTTTTAACCAAAAAGGT-AAAAAAATTGAACTTAAAATCAATTT
64 ATAAACATTCAATTATAATCTATTTTAACTAAAAAAGTAAAAAAAATTGAACCAAAAATCAATTT
2161 T
129 T
2162 GAGATTATAA
Statistics
Matches: 642, Mismatches: 140, Indels: 55
0.77 0.17 0.07
Matches are distributed among these distances:
338 71 0.11
339 149 0.23
340 173 0.27
341 91 0.14
342 4 0.01
343 1 0.00
344 145 0.23
345 8 0.01
ACGTcount: A:0.38, C:0.11, G:0.13, T:0.36
Consensus pattern (340 bp):
GAATGAGAGACTATAAATAGACTTTTCTTCTCAATGAATGCTGTTTTCTTCACACTTCTTGACAT
AAACATTCAATTATAATCTATTTTAACTAAAAAAGTAAAAAAAATTGAACCAAAAATCAATTTTA
ACATGATAAAACTATTTAAAGCGAATAATAGTACTTTTGAAGGAATGGAAGACTATAAATGAAAT
TTTCTTGCCAATGAATGCTTTTTGCATCACATTTCTCGAAGTAGACATTCAATTATAGTTTGTTT
TAACCAAAATATAAAAAATGAACATAAAATCAATTTTGGGATAACAAAATTATTTAAACTTGGCA
ATAAGGATTTTAAAG
Found at i:2141 original size:173 final size:171
Alignment explanation
Indices: 1844--2162 Score: 397
Period size: 173 Copynumber: 1.9 Consensus size: 171
1834 NNNNNNCGAG
* * *
1844 TAATAAGGCTTTTGAAGGATTGAGAGACTATAAATGAACTTTTCTTGCCAATGAATACTTTTTTC
1 TAATAAGGCTTTTGAAGGAATGAGAGACTATAAATGAACTTTTCTTACCAATGAATACCTTTTTC
** * * * *
1909 TCTACGTTTCTCAAGGTAAACATTCAATTATAGTATGCTTTAACTAGAAATGCAAAAAAAAAAAG
66 TCTACGTTTCTCAACATAAACATTCAATTATAATATGCTTTAACCAAAAAGGC--AAAAAAAAAG
1974 AACATAAAATCAATTTTGGGACTACAAAACCATTTAAAGTGGT
129 AACATAAAATCAATTTTGGGACTACAAAACCATTTAAAGTGGT
* * * * * *
2017 TAATAAGGTTTTTGATGGAATGAGTGACTATAATTGGACTTTTCTTACCAATGAATGCCTTTTTC
1 TAATAAGGCTTTTGAAGGAATGAGAGACTATAAATGAACTTTTCTTACCAATGAATACCTTTTTC
* * * * * **
2082 T-TCATGTTTCTCAACATAGATATTCAATTATAATATGTTTTAACCAAAAAGGTAAAAAAATTGA
66 TCT-ACGTTTCTCAACATAAACATTCAATTATAATATGCTTTAACCAAAAAGGCAAAAAAAAAGA
*
2146 ACTTAAAATCAATTTTG
130 ACATAAAATCAATTTTG
2163 AGATTATAAN
Statistics
Matches: 122, Mismatches: 23, Indels: 4
0.82 0.15 0.03
Matches are distributed among these distances:
171 25 0.20
172 1 0.01
173 96 0.79
ACGTcount: A:0.38, C:0.13, G:0.14, T:0.35
Consensus pattern (171 bp):
TAATAAGGCTTTTGAAGGAATGAGAGACTATAAATGAACTTTTCTTACCAATGAATACCTTTTTC
TCTACGTTTCTCAACATAAACATTCAATTATAATATGCTTTAACCAAAAAGGCAAAAAAAAAGAA
CATAAAATCAATTTTGGGACTACAAAACCATTTAAAGTGGT
Done.