Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018399828.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_3066.0, 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: 6367
ACGTcount: A:0.28, C:0.08, G:0.11, T:0.27
Warning! 1624 characters in sequence are not A, C, G, or T
Found at i:1437 original size:170 final size:170
Alignment explanation
Indices: 809--1982 Score: 807
Period size: 171 Copynumber: 6.9 Consensus size: 170
799 NNNNNNNNTC
* * * * * *
809 TATTTTAATAAAAAATATAAAAAAATTCAACTTAAAATCAATAATGAGGTTATAAAATCTTTTAA
1 TATTTTACTAATAAATATAAAAAAATTCAACTTAAAATCAATTATGAGATTAAAAAAT-ATTTAA
* * * * * * * * * * *
874 AGCGAGTAACATGACTTCCGAATGTATGGGTGGCTAGAAATGAAATTTTCTTGCAAATGGATATC
65 AGCGAGTAATAAGGCTTTCGAAGGCATGGGTGGCAATAAATGGACTTTTCTTGCCAATGGATATC
* * * ** * *
939 TTTCTCTTTACGTTTCTTGAGGTAGACATTCAATTAAAATC
130 TTTTTCTTCAGGTTTCTCAAGGTAGACATTCAATTATAATA
* * ********* * * *
980 TGTTTTAATAA-AAANNNNNNNNNNATTCAACTTAAAATCAATTCTGAGATTATAATATCATTTA
1 TATTTTACTAATAAA-TATAAAAAAATTCAACTTAAAATCAATTATGAGATTAAAAAAT-ATTTA
* * * ** * * ** *
1044 AAGCGAGTTATAAGGCTATT-GAAGGCATGGATGACTGTAAATAGACTTTTCCTATCAATGGATG
64 AAGCGAGTAATAAGGCT-TTCGAAGGCATGGGTGGCAATAAATGGACTTTTCTTGCCAATGGATA
* * * *
1108 TTTTTTTCTTCATGTTTCTCAAGGCAAACATTCAATTATAATA
128 TCTTTTTCTTCAGGTTTCTCAAGGTAGACATTCAATTATAATA
* ********** *
1151 TGTTTTANNNNNNNNNNTAAAAAAATTCAACTTAAAATCAATTATGAAATTAGAAAAATATTTAA
1 TATTTTACTAATAAATATAAAAAAATTCAACTTAAAATCAATTATGAGATTA-AAAAATATTTAA
* * ** ** *
1216 AGCTAGTAATAAGGCTTTTGAAGGTGTGGGTGATAATAAATGGACTTTTCTTGCCAATAGATATC
65 AGCGAGTAATAAGGCTTTCGAAGGCATGGGTGGCAATAAATGGACTTTTCTTGCCAATGGATATC
********** *
1281 TTTTTCTNNNNNNNNNNCAAGGTAGACATTCAATTATAATC
130 TTTTTCTTCAGGTTTCTCAAGGTAGACATTCAATTATAATA
* * * *
1322 TATTTTAATTAA-AAA-ATAAAAAAATTCAATTTAAAAACAATTATGAGACTACAAAAATATTTA
1 TATTTT-ACTAATAAATATAAAAAAATTCAACTTAAAATCAATTATGAGATTA-AAAAATATTTA
* * * * ** *
1385 AAGCGAGTAGTAAGGCTTTCGAAGGCATGAGTGGCCAGAAATAAAATTTTCTTGCCAATGGATAT
64 AAGCGAGTAATAAGGCTTTCGAAGGCATGGGTGGCAATAAATGGACTTTTCTTGCCAATGGATAT
* * *
1450 CGTTTTCTTCAGGTTTCTCATGGTCGACATTCAATTATAATA
129 CTTTTTCTTCAGGTTTCTCAAGGTAGACATTCAATTATAATA
* * * *
1492 TGTTTTACTAATAAATATAAAAAAATTCAACTTAAAATTAATTATGAGGTTATAAAATCATTTAA
1 TATTTTACTAATAAATATAAAAAAATTCAACTTAAAATCAATTATGAGATTAAAAAAT-ATTTAA
* * * *
1557 AACGAGTAATAAGGCTTTCAAAGACATGGGTGGCTATAAATGGACTTTTCTTGCCAATGGATATC
65 AGCGAGTAATAAGGCTTTCGAAGGCATGGGTGGCAATAAATGGACTTTTCTTGCCAATGGATATC
* * ********** *
1622 TTTCTCTTCACGTTTCTNNNNNNNNNNATTCAATTATAATC
130 TTTTTCTTCAGGTTTCTCAAGGTAGACATTCAATTATAATA
* * * * * * *
1663 TGTTTTAAC-AAAAAATGTAAAAAAATTTAACTTAGAATCAATTATGAGGTTATAAAATTATTTA
1 TATTTT-ACTAATAAATATAAAAAAATTCAACTTAAAATCAATTATGAGATTA-AAAAATATTTA
* ** * *
1727 AAGCGAGTAATAAGGCTTCCGAAGATATGGGTGGCTATAAATGGACTTTTCTTGCTAATGGATAT
64 AAGCGAGTAATAAGGCTTTCGAAGGCATGGGTGGCAATAAATGGACTTTTCTTGCCAATGGATAT
* ** * * * *
1792 CTTTTTTTTCATATTTC-CTGAGGTAGACATTCAAATATTATC
129 CTTTTTCTTCAGGTTTCTC-AAGGTAGACATTCAATTATAATA
* ** * * *
1834 TATTTTAATAGA-AAACGTAACAAAATTCAA-TTGAAAATCCATTATGAGATTATAAAAACATTT
1 TATTTTACTA-ATAAATATAAAAAAATTCAACTT-AAAATCAATTATGAGATTA-AAAAATATTT
* * * * * *
1897 AAAGTGAGTAATAAGGCTTTCAAAGGCTTGGATGACTATAAATGGACTTTTCTTGCCAATGGATA
63 AAAGCGAGTAATAAGGCTTTCGAAGGCATGGGTGGCAATAAATGGACTTTTCTTGCCAATGGATA
* **
1962 TCTTTCTCTTCACATTTCTCA
128 TCTTTTTCTTCAGGTTTCTCA
1983 NNNNNNNNNN
Statistics
Matches: 772, Mismatches: 215, Indels: 32
0.76 0.21 0.03
Matches are distributed among these distances:
169 4 0.01
170 142 0.18
171 612 0.79
172 14 0.02
ACGTcount: A:0.37, C:0.12, G:0.14, T:0.35
Consensus pattern (170 bp):
TATTTTACTAATAAATATAAAAAAATTCAACTTAAAATCAATTATGAGATTAAAAAATATTTAAA
GCGAGTAATAAGGCTTTCGAAGGCATGGGTGGCAATAAATGGACTTTTCTTGCCAATGGATATCT
TTTTCTTCAGGTTTCTCAAGGTAGACATTCAATTATAATA
Found at i:2655 original size:171 final size:171
Alignment explanation
Indices: 2502--3268 Score: 492
Period size: 171 Copynumber: 4.5 Consensus size: 171
2492 NNNNNNNNTT
* * * * * * *
2502 TCTTCATGTTTCTTGAGGTAGACATTTAATTTTAATTTGTTTTAATAAAAAATATAAAAAAATTT
1 TCTTCACGTTTCCTGAGGTAAACATTCAATTATAATCTGTTTTAATAAAAAATATAAAAAAATTC
* * *
2567 AACTTAAAACCAATTAT-TGCGTTATAAAATTTTTTAAAGCGAGTAAT-AAGACTTTTGAAGGTA
66 AACTTAAAACCAATTATGTG-GTTATAAAATTATTTAAAGCGAGTAATAAAG-CTTTCGAAGGGA
* *
2630 TGGGTGGCTATAGATAGACTTTTCTTGCCAATAGATATATTTC
129 TAGGTGGCTATAAATAGACTTTTCTTGCCAATAGATATATTTC
* * ** * *
2673 TCTTTACGTTTCCTGAGGTAAACATTCACTTATAATCTGTTTTAATCCAAAATGTAAAATAATTC
1 TCTTCACGTTTCCTGAGGTAAACATTCAATTATAATCTGTTTTAATAAAAAATATAAAAAAATTC
*
2738 AACTTAAAATCAATTATGTGGTTATAAAATTATTTAAAGCGAGTAATAAAGCTTTCGAAGGGATA
66 AACTTAAAACCAATTATGTGGTTATAAAATTATTTAAAGCGAGTAATAAAGCTTTCGAAGGGATA
******** * * *
2803 GGTGGCTATAAATAGA-TAGATTTNNNNNNNNNNTGGATATCTTTT
131 GGTGGCTATAAATAGACT---TTT--CTTGCCAATAGATATATTTC
* * * * * **********
2848 TCTTCATGTTTCTTGAGGTACACATTTAATTATAATCTGTTTTAATAGAAAANNNNNNNNNNTTC
1 TCTTCACGTTTCCTGAGGTAAACATTCAATTATAATCTGTTTTAATAAAAAATATAAAAAAATTC
* ** * * * * * * * * *
2913 AACTTAAAATCAATTATAAGATTTTAAAAATATTTAAAGTGAGAAATAAGGCTTTTGAAGGCATG
66 AACTTAAAACCAATTATGTGGTTATAAAATTATTTAAAGCGAGTAATAAAGCTTTCGAAGGGATA
* * * * * *
2978 GGTGACTATTAATAGACTTTTCTTGCTAGTGGATATCTATT-
131 GGTGGCTATAAATAGACTTTTCTTGCCAATAGATATAT-TTC
* * **
3019 TCTTCACGTTT-CTCGAGGTAGACATTCAATTACT-ATATGTTTTAACCAAAAATATAAAAAAAT
1 TCTTCACGTTTCCT-GAGGTAAACATTCAATTA-TAATCTGTTTTAATAAAAAATATAAAAAAAT
* * ** * * * * * * * * *
3082 TTAATTTAAAATTAATTATGAGATTACAAAAATATTTACAGCGAGTAATAAGGTTTTTGAAGGCA
64 TCAACTTAAAACCAATTATGTGGTTATAAAATTATTTAAAGCGAGTAATAAAGCTTTCGAAGGGA
* * * * * *
3147 TGGGTGACTATAAATAGACTTTTCCTGGCAATGGATATATTTT
129 TAGGTGGCTATAAATAGACTTTTCTTGCCAATAGATATATTTC
* * * * * * *
3190 TCTTCACATTTTC-AAAG-ACAA-ATTAAATTATTATCTATTTTAGCA-AAAAAATATAAAAAAA
1 TCTTCACGTTTCCTGAGGTA-AACATTCAATTATAATCTGTTTTA--ATAAAAAATATAAAAAAA
* *
3251 TTTAACTTAAAATCAATT
63 TTCAACTTAAAACCAATT
3269 NNNNNNNNNN
Statistics
Matches: 466, Mismatches: 113, Indels: 35
0.76 0.18 0.06
Matches are distributed among these distances:
168 1 0.00
169 17 0.04
170 38 0.08
171 270 0.58
172 9 0.02
173 6 0.01
175 124 0.27
176 1 0.00
ACGTcount: A:0.37, C:0.10, G:0.13, T:0.37
Consensus pattern (171 bp):
TCTTCACGTTTCCTGAGGTAAACATTCAATTATAATCTGTTTTAATAAAAAATATAAAAAAATTC
AACTTAAAACCAATTATGTGGTTATAAAATTATTTAAAGCGAGTAATAAAGCTTTCGAAGGGATA
GGTGGCTATAAATAGACTTTTCTTGCCAATAGATATATTTC
Found at i:5661 original size:171 final size:169
Alignment explanation
Indices: 5115--5744 Score: 581
Period size: 171 Copynumber: 3.7 Consensus size: 169
5105 NNNNNNNNNN
5115 AATTCAACTTAAAATCAATTATGAGGTTATAAAATTATTTAAAGCGAGTAATAATG-CTTTCGAA
1 AATTCAACTTAAAATCAATTATGAGGTTATAAAATTATTTAAAGCGAGTAATAA-GACTTTCGAA
* * *********
5179 -GCGATGGGTGGCTATGAATGGACTTTT-TCTGCCAATGGATATCTTTTTCTTCNNNNNNNNNNA
65 GGC-ATGGGTGGCTATAAATGGACTTTTCT-TACCAATGGATATC-TTTTCTTC-TAGTTTCTGA
* *
5242 GGTAGACATTCAATTATAATCTCTTCTAATAAGAAAATATAAAAA
126 GGTAGACATTCAATTATAATCTGTTTTAAT-AGAAAATATAAAAA
* * * *
5287 AATTTAACTTAAAATCAAGTATTG-CGTTATAAAATCT-TTTAAAGCGAGTAATAAGACTTTTGA
1 AATTCAACTTAAAATCAATTA-TGAGGTTATAAAAT-TATTTAAAGCGAGTAATAAGACTTTCGA
* * * * * *
5350 AGGCATAGGTGGCTATAAATGGACTTTTCTTGCCAATAGATATATTTCTCTTTATATTTTCTGAG
64 AGGCATGGGTGGCTATAAATGGACTTTTCTTACCAATGGATATCTTT-TC-TTCTAGTTTCTGAG
* * * *
5415 GTAAACATTCAATTATAATCTGTTTTAATACAAAATGTAAAAT
127 GTAGACATTCAATTATAATCTGTTTTAATAGAAAATATAAAAA
********** * *
5458 AATTCAACTTAANNNNNNNNNNGAGGTTATAAAATTATTTAAAGCGAGTAACAAAACTTTCGAAT
1 AATTCAACTTAAAATCAATTATGAGGTTATAAAATTATTTAAAGCGAGTAATAAGACTTTCGAA-
* *
5523 GG-ATGGGTGGCTATAAATAGACTTTTCTTACCAATGGATATCCTTTTCTTCTCGTTTCTCGAGG
65 GGCATGGGTGGCTATAAATGGACTTTTCTTACCAATGGATAT-CTTTTCTTCTAGTTTCT-GAGG
* *
5587 TAGACATTCAATTATAATATGTTTTAATAGAAAATATAAAAG
128 TAGACATTCAATTATAATCTGTTTTAATAGAAAATATAAAAA
* * * * * * * *
5629 AATTCAACTTAAAATGAATTATAAGATTATAAAAATACTTAAAGTGAGTAATAAGGCTTTTGAAG
1 AATTCAACTTAAAATCAATTATGAGGTTATAAAATTATTTAAAGCGAGTAATAAGACTTTCGAAG
* * * *
5694 GTATGGGTGACTATTAATGGACTTTTC-TAGTCAATGGATATCTATTTCTTC
66 GCATGGGTGGCTATAAATGGACTTTTCTTA-CCAATGGATATCT-TTTCTTC
5745 ANNNNNNNNN
Statistics
Matches: 368, Mismatches: 75, Indels: 31
0.78 0.16 0.07
Matches are distributed among these distances:
170 16 0.04
171 222 0.60
172 122 0.33
173 8 0.02
ACGTcount: A:0.36, C:0.11, G:0.15, T:0.35
Consensus pattern (169 bp):
AATTCAACTTAAAATCAATTATGAGGTTATAAAATTATTTAAAGCGAGTAATAAGACTTTCGAAG
GCATGGGTGGCTATAAATGGACTTTTCTTACCAATGGATATCTTTTCTTCTAGTTTCTGAGGTAG
ACATTCAATTATAATCTGTTTTAATAGAAAATATAAAAA
Done.