Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018402268.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_5351.0, 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: 2975
ACGTcount: A:0.27, C:0.08, G:0.08, T:0.23
Warning! 1001 characters in sequence are not A, C, G, or T
Found at i:294 original size:171 final size:170
Alignment explanation
Indices: 1--653 Score: 676
Period size: 171 Copynumber: 3.8 Consensus size: 170
* * ** * * * *
1 TTCTTCACGTTTCTCGAGACAGACATTCAATTATA-ATATGTTTTAACAAAAAATATAAAAGAAT
1 TTCTTCACATTTCTCAAGGTAGACATTCAATT-TAGATTTGTTTTAACAAAAAATGTAAAAAAAA
* ** * * * *
65 TAAACTTAAATTAATTATGGGATTTTAAAACCGTTTAAAGCGAGTAATAAGACTTTTAAAAGAAT
65 TAAACTTAAATCAATTATAAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAAGAAT
* * * *
130 AGGTGACTATAAATAGACTTTTTTTGTGAATAAATGTCTTT
130 AGGTGACTATAAATAGACTTTTCTTGTCAATGAATATCTTT
* * ** * *
171 TTCTTCACATTCCCCAAGGTAGACATTCAATTCTAGCCTT-CTTTAACGAAAAATGTAAAAAAAA
1 TTCTTCACATTTCTCAAGGTAGACATTCAATT-TAGATTTGTTTTAACAAAAAATGTAAAAAAAA
*
235 TCAACTTAAAATCAATTATAAGATTATAAAACC-TTTAAAAGCGAGTAATAAGGCTTTT-AAAGC
65 TAAACTT-AAATCAATTATAAGATTATAAAACCATTT-AAAGCGAGTAATAAGGCTTTTGAAAG-
* * *
298 AATTGGTGACTATAAATGGACTTTTCTTGCCAATGAATATCTTT
127 AATAGGTGACTATAAATAGACTTTTCTTGTCAATGAATATCTTT
* * * ** *
342 TTATTCACGTTTTTCAAGGTAGACAACCAA-TTAGAATTTGTTTTAA-AGGAAAATGTAAAAAAC
1 TTCTTCACATTTCTCAAGGTAGACATTCAATTTAG-ATTTGTTTTAACA-AAAAATGTAAAAAA-
* * * * * * * * *
405 ATTAAACTTAAAATAAATTTTGAGAATATAAAACCATTTAAAGTGAATTATAAGGCTTTTGAAGG
63 AATAAACTT-AAATCAATTATAAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAAG
* *
470 AAT-GGATGACTATAAATTGACTTTTCTTGTCAATGAATACCTTT
127 AATAGG-TGACTATAAATAGACTTTTCTTGTCAATGAATATCTTT
* *
514 TTCTTTACATTTCTTAAGGTAGACATTCAATTATA-ATTTGTTTTAACAAAAAATGT-AAAAAAA
1 TTCTTCACATTTCTCAAGGTAGACATTCAATT-TAGATTTGTTTTAACAAAAAATGTAAAAAAAA
* *
577 TACAACTTAAATCAATTATAAGGTTATAAAACCTTTTAAAGCGAGTAATAAGGCTTTTGAAAGAA
65 TA-AACTTAAATCAATTATAAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAAGAA
*
642 TAAGTGACTATA
129 TAGGTGACTATA
654 NNNNNNNNNN
Statistics
Matches: 394, Mismatches: 73, Indels: 32
0.79 0.15 0.06
Matches are distributed among these distances:
169 3 0.01
170 122 0.31
171 133 0.34
172 126 0.32
173 8 0.02
174 2 0.01
ACGTcount: A:0.41, C:0.12, G:0.13, T:0.35
Consensus pattern (170 bp):
TTCTTCACATTTCTCAAGGTAGACATTCAATTTAGATTTGTTTTAACAAAAAATGTAAAAAAAAT
AAACTTAAATCAATTATAAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAAGAATA
GGTGACTATAAATAGACTTTTCTTGTCAATGAATATCTTT
Found at i:485 original size:172 final size:168
Alignment explanation
Indices: 28--653 Score: 598
Period size: 172 Copynumber: 3.7 Consensus size: 168
18 GACAGACATT
* * * * * ** *
28 CAATTATAATATGTTTTAACAAAAAATATAAAAGAATTAAACTT-AAATTAATTATGGGATTTTA
1 CAATTAGAATTTGTTTTAACAAAAAATGTAAAA-AAATAAACTTAAAATCAATTATAAGATTATA
* * * * * *
92 AAACCGTTTAAAGCGAGTAATAAGACTTTTAAAAGAATAGGTGACTATAAATAGACTTTTTTTGT
65 AAACC-TTTAAAGCGAGTAATAAGGCTTTTGAAGGAAT-GGTGACTATAAATGGACTTTTCTTGC
* * ** * * ** **
157 GAATAAATGTCTTTTTCTTCACATTCCCCAAGGTAGACATT
128 CAATGAATACCTTTTTATTCACATTTCTTAAGGTAGACAAC
** * * *
198 CAATTCTAG-CCTT-CTTTAACGAAAAATGTAAAAAAAATCAACTTAAAATCAATTATAAGATTA
1 CAA-T-TAGAATTTGTTTTAACAAAAAATGT-AAAAAAATAAACTTAAAATCAATTATAAGATTA
* *
261 TAAAACCTTTAAAAGCGAGTAATAAGGCTTTTAAAGCAATTGGTGACTATAAATGGACTTTTCTT
63 TAAAACCTTT-AAAGCGAGTAATAAGGCTTTTGAAGGAA-TGGTGACTATAAATGGACTTTTCTT
* *
326 GCCAATGAATATCTTTTTATTCACGTTT-TTCAAGGTAGACAAC
126 GCCAATGAATACCTTTTTATTCACATTTCTT-AAGGTAGACAAC
* * * * *
369 CAATTAGAATTTGTTTTAA-AGGAAAATGTAAAAAACATTAAACTTAAAATAAATTTTGAGAATA
1 CAATTAGAATTTGTTTTAACA-AAAAATGTAAAAAA-A-TAAACTTAAAATCAATTATAAGATTA
* * * *
433 TAAAACCATTTAAAGTGAATTATAAGGCTTTTGAAGGAATGGATGACTATAAATTGACTTTTCTT
63 TAAAACC-TTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGG-TGACTATAAATGGACTTTTCTT
* * * **
498 GTCAATGAATACCTTTTTCTTTACATTTCTTAAGGTAGACATT
126 GCCAATGAATACCTTTTTATTCACATTTCTTAAGGTAGACAAC
* *
541 CAATTATAATTTGTTTTAACAAAAAATGTAAAAAAATACAACTT-AAATCAATTATAAGGTTATA
1 CAATTAGAATTTGTTTTAACAAAAAATGTAAAAAAATA-AACTTAAAATCAATTATAAGATTATA
* *
605 AAACCTTTTAAAGCGAGTAATAAGGCTTTTGAAAGAATAAGTGACTATA
65 AAACC-TTTAAAGCGAGTAATAAGGCTTTTGAAGGAAT-GGTGACTATA
654 NNNNNNNNNN
Statistics
Matches: 373, Mismatches: 65, Indels: 36
0.79 0.14 0.08
Matches are distributed among these distances:
169 3 0.01
170 94 0.25
171 131 0.35
172 139 0.37
173 6 0.02
ACGTcount: A:0.42, C:0.11, G:0.12, T:0.35
Consensus pattern (168 bp):
CAATTAGAATTTGTTTTAACAAAAAATGTAAAAAAATAAACTTAAAATCAATTATAAGATTATAA
AACCTTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGGTGACTATAAATGGACTTTTCTTGCCAA
TGAATACCTTTTTATTCACATTTCTTAAGGTAGACAAC
Found at i:2044 original size:172 final size:172
Alignment explanation
Indices: 1729--2112 Score: 439
Period size: 172 Copynumber: 2.2 Consensus size: 172
1719 CAAAAAATGT
* * *
1729 AAAAACATTCAACTTAAAATTAATTATGAGATTATAAAACCTTTTAAAGTGAATAATAAAGCTTT
1 AAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACCGTTTAAAGTGAATAATAAAGCTTT
* * * * * *
1794 TGAAGAAATGGGTGACAATAAATTGACGTTTCTTGCCAATAAATACCTTTTTCTTGAGGTTTCTC
66 TAAAGAAATAGGTGACAATAAATGGACGTTTCATGCCAATAAATACCTTTTTCTTCAGATTTCTC
* ** * * *
1859 GAGGTAAACATTCAATTATAATCTGT-TTTAACCAAAAATATA
131 AAGACAAACATTCAATGATAACCT-TCTTTAACCAAAAACATA
* * * * * * * *
1901 TAAAGAATTCAAATTAAAATCAATTTTGACATTATAAATCCGTTTAAAGTGAGTAATAAGGCTTT
1 AAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACCGTTTAAAGTGAATAATAAAGCTTT
* * * * ** *
1966 TAAAGGAATAGGTGACAGTAACTGGACTTTTCATGCCAATAAATGTCTTTTTCTTCATATTTCTC
66 TAAAGAAATAGGTGACAATAAATGGACGTTTCATGCCAATAAATACCTTTTTCTTCAGATTTCTC
* * *
2031 AAGACAGACATTCAATGATAGCCTTCTTTAACCAAAAACGTA
131 AAGACAAACATTCAATGATAACCTTCTTTAACCAAAAACATA
*
2073 AAAAAAATT-AACTTAAAATCAATTATGAGATTACAAAACC
1 AAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACC
2113 TTTTNNNNNN
Statistics
Matches: 171, Mismatches: 40, Indels: 3
0.80 0.19 0.01
Matches are distributed among these distances:
171 27 0.16
172 144 0.84
ACGTcount: A:0.41, C:0.14, G:0.12, T:0.33
Consensus pattern (172 bp):
AAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACCGTTTAAAGTGAATAATAAAGCTTT
TAAAGAAATAGGTGACAATAAATGGACGTTTCATGCCAATAAATACCTTTTTCTTCAGATTTCTC
AAGACAAACATTCAATGATAACCTTCTTTAACCAAAAACATA
Found at i:2772 original size:171 final size:171
Alignment explanation
Indices: 1716--2975 Score: 797
Period size: 171 Copynumber: 7.4 Consensus size: 171
1706 NNNNNNNNNN
* * * *
1716 TAACAAAAAATGT-AAAAACATTCAACTTAAAATTAATTATGAGATTATAAAACCTTTTAAAGTG
1 TAACAAAAAATGTAAAAAAAATT-AACTTAAAATCAATTATGACATTATAAAACCTTTTAAAGAG
* * * * * * * *
1780 AATAATAAAGCTTTTG-AAGAAATGGGTGACAATAAATTGACGTTTCTTGCCAATAAATACCTTT
65 AGTAATAAGGCTTTTGAAAG-AATAGGTGACTATAAATGGACTTTTCTTGTCAATAAATATCTTT
* * * * *
1844 TTCTTGAGGTTTCTCGAGGTAAACATTCAATTATAATCTGTTT
129 TTCTTCACGTTTCTCAAGATAGACATTCAATTATAATCTGTTT
* * * * * * * * *
1887 TAACCAAAAATATATAAAGAATTCAAATTAAAATCAATTTTGACATTATAAATCCGTTTAAAGTG
1 TAACAAAAAATGTAAAAAAAATT-AACTTAAAATCAATTATGACATTATAAAACCTTTTAAAGAG
* * * *
1952 AGTAATAAGGCTTTT-AAAGGAATAGGTGAC-AGTAACTGGACTTTTCATGCCAATAAATGTCTT
65 AGTAATAAGGCTTTTGAAA-GAATAGGTGACTA-TAAATGGACTTTTCTTGTCAATAAATATCTT
** * * **
2015 TTTCTTCATATTTCTCAAGACAGACATTCAATGATAGCCT-TCTT
128 TTTCTTCACGTTTCTCAAGATAGACATTCAATTATAATCTGT-TT
* * * * *******
2059 TAACCAAAAACGTAAAAAAAATTAACTTAAAATCAATTATGAGATTACAAAACCTTTTNNNNNNN
1 TAACAAAAAATGTAAAAAAAATTAACTTAAAATCAATTATGACATTATAAAACCTTTTAAAGAGA
*** * * * * *
2124 NNNATAAAGCTTTTGAAAGAATGGGTAACTATAAATAGACTTTTCTTATCAATAAATATCTTTTT
66 GTAATAAGGCTTTTGAAAGAATAGGTGACTATAAATGGACTTTTCTTGTCAATAAATATCTTTTT
* * ** *
2189 -TTCCACATTTCTCAAGGTAGACAGACAATTATAATCTATTT
131 CTT-CACGTTTCTCAAGATAGACATTCAATTATAATCTGTTT
* * ********** * * **
2230 TAAATGAAAAAATATATAAAAAAATTAACTTANNNNNNNNNNTGAGAATATAAAACAATTTAAA-
1 T-AA-CAAAAAATGTA-AAAAAAATTAACTTAAAATCAATTATGACATTATAAAACCTTTTAAAG
* * * * ********** *
2294 ACGAGCAATAATGCTTTTGAAAGAATAGATGACTATAAATGGATTTTTCNNNNNNNNNNATACCT
63 A-GAGTAATAAGGCTTTTGAAAGAATAGGTGACTATAAATGGACTTTTCTTGTCAATAAATATCT
* * *
2359 TTTTTTTCACGTTTCTCGAGGTAGACATTCAATTATAATCTGTTT
127 TTTTCTTCACGTTTCTCAAGATAGACATTCAATTATAATCTGTTT
* * ******
2404 TAACAAAAAATGT--GAAAAATTGAACTTAAAATCAATTATGACATTATAAAATCTTTTNNNNNN
1 TAACAAAAAATGTAAAAAAAATT-AACTTAAAATCAATTATGACATTATAAAACCTTTTAAAGAG
**** * * *
2467 NNNNATAAGGCTTTTGAAAGAATAAGTGACTATAAATGGACTTTTTTTGTCAATCAATA-CTTTT
65 AGTAATAAGGCTTTTGAAAGAATAGGTGACTATAAATGGACTTTTCTTGTCAATAAATATCTTTT
** * * *
2531 TCCTTCATATTTCTTC-AGGTAGACATTCACTTATAATCTCTTT
130 T-CTTCACGTTTC-TCAAGATAGACATTCAATTATAATCTGTTT
* * * * * *
2574 TAATAAAAAATATACAAAAATTTAACTTAAAATCAAATATGACATTATAAAACCGTTTAAAGAGA
1 TAACAAAAAATGTAAAAAAAATTAACTTAAAATCAATTATGACATTATAAAACCTTTTAAAGAGA
* * * *
2639 GTAATAAGGCTTTTAAAAAAATAGGTGCCTATAAATGGACTTTTTTTGTCAATAAATATCTTTTT
66 GTAATAAGGCTTTTGAAAGAATAGGTGACTATAAATGGACTTTTCTTGTCAATAAATATCTTTTT
* * **
2704 CTTCACG-TTCTCCAAGACATACATTCAATTATAGCCT-TCTT
131 CTTCACGTTTCT-CAAGATAGACATTCAATTATAATCTGT-TT
* *********** * *
2745 TAACCAAAAATGTAAAAAAAATTAACTT-AAATTNNNNNNNNNNTTATAATACCTTTTAAAGCGA
1 TAACAAAAAATGTAAAAAAAATTAACTTAAAATCAATTATGACATTATAAAACCTTTTAAAGAGA
* * * * * * *
2809 GTAATAAGGCGTTTGTAAA-AATGGGTAACAATAAATAGACTTTTCTTGTCAATGAATGTCTTTT
66 GTAATAAGGCTTTTG-AAAGAATAGGTGACTATAAATGGACTTTTCTTGTCAATAAATATCTTTT
* * * * * *
2873 TCTTCATGTTTGTCAAGGTAAACAGTCAATTATCATCTGTTT
130 TCTTCACGTTTCTCAAGATAGACATTCAATTATAATCTGTTT
* * * * *
2915 TAA-ATAGAAATGTAAAAAAAATTAAACTTAAAATCAATTTTGAGAATATAAAACCATTTAA
1 TAACA-AAAAATGTAAAAAAAATT-AACTTAAAATCAATTATGACATTATAAAACCTTTTAA
Statistics
Matches: 812, Mismatches: 247, Indels: 59
0.73 0.22 0.05
Matches are distributed among these distances:
169 14 0.02
170 230 0.28
171 261 0.32
172 186 0.23
173 10 0.01
174 109 0.13
175 2 0.00
ACGTcount: A:0.39, C:0.12, G:0.11, T:0.34
Consensus pattern (171 bp):
TAACAAAAAATGTAAAAAAAATTAACTTAAAATCAATTATGACATTATAAAACCTTTTAAAGAGA
GTAATAAGGCTTTTGAAAGAATAGGTGACTATAAATGGACTTTTCTTGTCAATAAATATCTTTTT
CTTCACGTTTCTCAAGATAGACATTCAATTATAATCTGTTT
Done.