Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018399838.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_3075.0, 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: 4430
ACGTcount: A:0.27, C:0.11, G:0.11, T:0.24
Warning! 1212 characters in sequence are not A, C, G, or T
Found at i:328 original size:172 final size:168
Alignment explanation
Indices: 5--865 Score: 611
Period size: 170 Copynumber: 5.0 Consensus size: 168
1 TTCA
* * * ** *
5 AAGGCTTGAGTGACTATAAATAGACTTTTTTCTCTC-ATGGATGGCTTTTGAGTCACGTTT-CCA
1 AAGGCTTAAGTGACTATAAATGGA-TTTTCTCTC-CAATGGATGGCTTTTGCTTCATGTTTCCCA
* * * * * * *
68 GAGGCAAAAATTCAACTATAGCATGTTTTAACGAGAAATGTAAAAAAAT-TGAACTTAAAATCAA
64 -AGGTAGAAATTCAATTATAGCATATTTTAACCAAAAATAT-AAAAAATCT-AACTTAAAATCAA
* **********
132 TTATGANNNNNNNNNNCCATTTAAAGTGAGTAATAAGGCTTTC
126 TTACGAGAATATAAAACCATTTAAAGTGAGTAATAAGGCTTTC
*
175 AAGGGCTTAAGTGACTATAAATGGAACTTTTCTTTCCAATGGATGGCTTTTGCTTCATGTTTCCC
1 AA-GGCTTAAGTGACTATAAATGG-A-TTTTCTCTCCAATGGATGGCTTTTGCTTCATGTTTCCC
* ** ********** * * * *
240 AAGGTAGATATTTGATTATAGCNNNNNNNNNNCAAAAATGTAAAAACTTTCAACTTAGAATCAAT
63 AAGGTAGAAATTCAATTATAGCATATTTTAACCAAAAATATAAAAAATCT-AACTTAAAATCAAT
* * *
305 TATGAGAATATAAAACTATTTAAAGCGAGTAATAAGGCTTTC
127 TACGAGAATATAAAACCATTTAAAGTGAGTAATAAGGCTTTC
* * * * * * * *
347 TAAAGCTTGAGTAACTATAAATGCATATTTCTCTCCCATAGATGGCTTTTACTTCATGTTTCCCT
1 -AAGGCTTAAGTGACTATAAATGGAT-TTTCTCTCCAATGGATGGCTTTTGCTTCATGTTTCCCA
* * * * *
412 AGGAAAAAATTCAATTATGGCATATTTTAACCAAAAATATAAAAAATCTAATTTAAAATCAATTG
64 AGGTAGAAATTCAATTATAGCATATTTTAACCAAAAATATAAAAAATCTAACTTAAAATCAATTA
** * *
477 CGAGAATATAAAACCATCGAAAGTGAGTAATAATGCTCTC
129 CGAGAATATAAAACCATTTAAAGTGAGTAATAAGGCTTTC
** *
517 AAAGGCTTATA-TGACTATAAATGGATTTTTCTCTCCGTTGGATGGCTTTTGCTTCATGTTTCCT
1 -AAGGCTTA-AGTGACTATAAATGGA-TTTTCTCTCCAATGGATGGCTTTTGCTTCATGTTTCCC
** * * *
581 AAGGTAGTCATTCAATTATAACATATTTGAACCAAAAATGTAAACAAATCTAACTTAAAATCAAT
63 AAGGTAGAAATTCAATTATAGCATATTTTAACCAAAAATATAAA-AAATCTAACTTAAAATCAAT
* **********
646 TATGAGAATATAAAACCNNNNNNNNNNAGTAATAAGGCTTTC
127 TACGAGAATATAAAACCATTTAAAGTGAGTAATAAGGCTTTC
** * **
688 AAAGGCTTAAGTGACTATAAATAAAGTTTTCTCTCTAATGGATGGC-TTTGCTTCACATTTCCCA
1 -AAGGCTTAAGTGACTATAAATGGA-TTTTCTCTCCAATGGATGGCTTTTGCTTCATGTTTCCCA
* * * * ** * *
752 AAGTAGATATTCAATTGTAACATATTTT-ATTAAAAAGTGCA-AAAAAATCTAGCTTAAAACCAA
64 AGGTAGAAATTCAATTATAGCATATTTTAACCAAAAA-T--ATAAAAAATCTAACTTAAAATCAA
* * *
815 TTATGAGAATATAAAATCATTTAAAGCGAGTAATAAGGCTTTC
126 TTACGAGAATATAAAACCATTTAAAGTGAGTAATAAGGCTTTC
858 AAAGGCTT
1 -AAGGCTT
866 NNNNNNNNNN
Statistics
Matches: 535, Mismatches: 142, Indels: 28
0.76 0.20 0.04
Matches are distributed among these distances:
169 6 0.01
170 231 0.43
171 180 0.34
172 113 0.21
173 5 0.01
ACGTcount: A:0.36, C:0.14, G:0.14, T:0.32
Consensus pattern (168 bp):
AAGGCTTAAGTGACTATAAATGGATTTTCTCTCCAATGGATGGCTTTTGCTTCATGTTTCCCAAG
GTAGAAATTCAATTATAGCATATTTTAACCAAAAATATAAAAAATCTAACTTAAAATCAATTACG
AGAATATAAAACCATTTAAAGTGAGTAATAAGGCTTTC
Found at i:709 original size:171 final size:169
Alignment explanation
Indices: 154--865 Score: 649
Period size: 170 Copynumber: 4.2 Consensus size: 169
144 NNNNCCATTT
* * * *
154 AAAGTGAGTAATAAGGCTTTCAAGGGCTTAAGTGACTATAAATGGAACTTTTCTTTCCAATGGAT
1 AAAGCGAGTAATAAGGCTTTCAAAGGCTTAAGTGACTATAAATGG-ATTTTTCTCTCCAATGGAT
** * *********
219 GGCTTTTGCTTCATGTTTCCCAAGGTAGATATTTGATTATAGCNNNNNNNNNNCAAAAATGTAAA
65 GGCTTTTGCTTCATGTTTCCCAAGGTAGATATTCAATTATAAC-ATATTTAACCAAAAATGTAAA
* * * * **
284 AACTTTCAACTTAGAATCAATTATGAGAATATAAAACTATTT
129 AAATCT-AACTTAAAATCAATTATGAGAATATAAAACCATCG
* * * * * *
326 AAAGCGAGTAATAAGGCTTTCTAAA-GCTTGAGTAACTATAAATGCATATTTCTCTCCCATAGAT
1 AAAGCGAGTAATAAGGCTTTC-AAAGGCTTAAGTGACTATAAATGGATTTTTCTCTCCAATGGAT
* * * * * ** *
390 GGCTTTTACTTCATGTTTCCCTAGGAAAAAATTCAATTATGGCATATTTTAACCAAAAATATAAA
65 GGCTTTTGCTTCATGTTTCCCAAGGTAGATATTCAATTATAACATA-TTTAACCAAAAATGTAAA
* **
455 AAATCTAATTTAAAATCAATTGCGAGAATATAAAACCATCG
129 AAATCTAACTTAAAATCAATTATGAGAATATAAAACCATCG
* * * **
496 AAAGTGAGTAATAATGCTCTCAAAGGCTTATA-TGACTATAAATGGATTTTTCTCTCCGTTGGAT
1 AAAGCGAGTAATAAGGCTTTCAAAGGCTTA-AGTGACTATAAATGGATTTTTCTCTCCAATGGAT
*
560 GGCTTTTGCTTCATGTTTCCTAAGGTAG-TCATTCAATTATAACATATTTGAACCAAAAATGTAA
65 GGCTTTTGCTTCATGTTTCCCAAGGTAGAT-ATTCAATTATAACATATTT-AACCAAAAATGTAA
****
624 ACAAATCTAACTTAAAATCAATTATGAGAATATAAAACCNNNN
128 A-AAATCTAACTTAAAATCAATTATGAGAATATAAAACCATCG
****** ** * *
667 NNNNNNAGTAATAAGGCTTTCAAAGGCTTAAGTGACTATAAATAAAGTTTTCTCTCTAATGGATG
1 AAAGCGAGTAATAAGGCTTTCAAAGGCTTAAGTGACTATAAATGGATTTTTCTCTCCAATGGATG
** * * * ** *
732 GC-TTTGCTTCACATTTCCCAAAGTAGATATTCAATTGTAACATATTTTATTAAAAAGTGCAAAA
66 GCTTTTGCTTCATGTTTCCCAAGGTAGATATTCAATTATAACATATTTAACCAAAAA-TG-TAAA
* * * **
796 AAATCTAGCTTAAAACCAATTATGAGAATATAAAATCATTT
129 AAATCTAACTTAAAATCAATTATGAGAATATAAAACCATCG
837 AAAGCGAGTAATAAGGCTTTCAAAGGCTT
1 AAAGCGAGTAATAAGGCTTTCAAAGGCTT
866 NNNNNNNNNN
Statistics
Matches: 430, Mismatches: 99, Indels: 24
0.78 0.18 0.04
Matches are distributed among these distances:
169 12 0.03
170 225 0.52
171 154 0.36
172 37 0.09
173 2 0.00
ACGTcount: A:0.37, C:0.14, G:0.14, T:0.32
Consensus pattern (169 bp):
AAAGCGAGTAATAAGGCTTTCAAAGGCTTAAGTGACTATAAATGGATTTTTCTCTCCAATGGATG
GCTTTTGCTTCATGTTTCCCAAGGTAGATATTCAATTATAACATATTTAACCAAAAATGTAAAAA
ATCTAACTTAAAATCAATTATGAGAATATAAAACCATCG
Found at i:3460 original size:172 final size:172
Alignment explanation
Indices: 3172--4430 Score: 1252
Period size: 171 Copynumber: 7.4 Consensus size: 172
3162 AGGTAGACAT
* * **
3172 TCAATTATGAGAATATAAAACCATTGAAAGCGAGTAATAAGGCTTTCAAAGGCTTAAGTGGTTAT
1 TCAATTATGAGAATATAAAACCATTTAAAGCGAGTAATAAGGCTTTCAAAGGCTTGAGTGACTAT
* * * * * * *
3237 AAATAGACTTTTCTCACCAATAGATGGCTTTTGCATCACGTTTCCCAAGGCAGACATTCAACTAT
66 AAATGGACTTTTCTCTCCCATGGATGGCTTTTGCTTCATGTTTCCCAAGGCAGACATTCAATTAT
* * * *
3302 AGCTTATTTTAGCGAGAAATGTAAAAAAAATCCAACTTAAAA
131 AGCATATTTTAACCAAAAATGTAAAAAAAATCCAACTTAAAA
* * * *
3344 TAAATTATGAGAATATAAAACAATTTAAAGCGGGTAATAAGGCTTTCAAAGGCTTGAGTGACAAT
1 TCAATTATGAGAATATAAAACCATTTAAAGCGAGTAATAAGGCTTTCAAAGGCTTGAGTGACTAT
*
3409 AAATGGACTTTTCTCTCCCATGGATGGCATTTT-CTTCATGTTTCCCAAGGCAGTCATTCAATTA
66 AAATGGACTTTTCTCTCCCATGGATGGC-TTTTGCTTCATGTTTCCCAAGGCAGACATTCAATTA
** * *
3473 TAATATATTTTAACCAAAAATGTAAAAAAAGT-AAACTTAAAA
130 TAGCATATTTTAACCAAAAATGTAAAAAAAATCCAACTTAAAA
* *
3515 TCAATTATGTGAATATAAAACCATTTAAAGCGAGTAATAAGGCTTTC-AAGGACTTAAGTGACTA
1 TCAATTATGAGAATATAAAACCATTTAAAGCGAGTAATAAGGCTTTCAAAGG-CTTGAGTGACTA
** * * * ** * *** * * *
3579 TAAATATAGTTTTATC-CCTAATGGATCACTTTTGGTTTGCGGTTCCTATGGCAGACATTCAATT
65 TAAATGGACTTTTCTCTCC-CATGGATGGCTTTTGCTTCATGTTTCCCAAGGCAGACATTCAATT
** * * *
3643 ATAATATATTTTAA-TAAAAA-GTATAAAAAAAGCCAACTTAAAC
129 ATAGCATATTTTAACCAAAAATGTA-AAAAAAATCCAACTTAAAA
* * ** * * * * *
3686 CCAATTATGAGAATATAAAACTATTTAAAATGAATAATAAGACTTTCAAAGGCTTGAGTCATTAG
1 TCAATTATGAGAATATAAAACCATTTAAAGCGAGTAATAAGGCTTTCAAAGGCTTGAGTGACTAT
** * * ** * * *
3751 AACCGGACTTTTCTCTCCCATGGAT-GCTTTTACATCACATTTCCCAAAGCCGACA-TCAACTAT
66 AAATGGACTTTTCTCTCCCATGGATGGCTTTTGCTTCATGTTTCCCAAGGCAGACATTCAATTAT
* *
3814 AGCATATTTTAGA-GAAAAATGT-AAAAAAATTCAACTTAAAA
131 AGCATATTTTA-ACCAAAAATGTAAAAAAAATCCAACTTAAAA
* * * * * * * *
3855 TCAATTATGGGGATATAAAACTATTTAAAGTGAGTAATAAGGCTTTTAAGGGCTTAACTGACTAT
1 TCAATTATGAGAATATAAAACCATTTAAAGCGAGTAATAAGGCTTTCAAAGGCTTGAGTGACTAT
* ** * * * * **
3920 AAATGGGCTTTTCTCTCCCATGGATCACTTTTGCTTCATGTTTTCCAAGGAAAATATTTTATTAT
66 AAATGGACTTTTCTCTCCCATGGATGGCTTTTGCTTCATGTTTCCCAAGGCAGACATTCAATTAT
* ** * * * * *
3985 AGCATATTTTAA-TAAAAAAATATGAAAGAATCTAATTTAGAA
131 AGCATATTTTAACCAAAAATGTA-AAAAAAATCCAACTTAAAA
* * *
4027 TCAATTATGAGAATATAAAACCATTTAAAGCGAGTAGTAAAGCTTTCTAAGGCTTGAGTGACTAT
1 TCAATTATGAGAATATAAAACCATTTAAAGCGAGTAATAAGGCTTTCAAAGGCTTGAGTGACTAT
* * * * * * *
4092 AAATGGACATTTCTCTCCAATGAATGGCTTTTACTTCATGTTTGCCAAGGTAGACATTCTATTAT
66 AAATGGACTTTTCTCTCCCATGGATGGCTTTTGCTTCATGTTTCCCAAGGCAGACATTCAATTAT
*
4157 AGCATATTTTAACAAAAAATGT-AAAAAAATCCAACTTAAAA
131 AGCATATTTTAACCAAAAATGTAAAAAAAATCCAACTTAAAA
* *
4198 TCAATTATGAGAACATAAAACCATTTAAAGCGAGTAATAAGGCTTTCAAAGGCTTGAGTGAATAT
1 TCAATTATGAGAATATAAAACCATTTAAAGCGAGTAATAAGGCTTTCAAAGGCTTGAGTGACTAT
* * * * ** *
4263 AAATGTACTTTTCTCT-TCATTGGATGGCTTTTGCTTTATGTTTTCTGAGG-TGAACATTCAATT
66 AAATGGACTTTTCTCTCCCA-TGGATGGCTTTTGCTTCATGTTTCCCAAGGCAG-ACATTCAATT
* * * * **
4326 ATAACATCTTTTAACCAAAAATGT-AAACAAATCCGACTTGGAA
129 ATAGCATATTTTAACCAAAAATGTAAAAAAAATCCAACTTAAAA
* * * * *
4369 TCAATTACGAAAATATAAAACCATTTAAAGCAAGTAACAAGGCTTTCTAAGGCTTGAGTGAC
1 TCAATTATGAGAATATAAAACCATTTAAAGCGAGTAATAAGGCTTTCAAAGGCTTGAGTGAC
Statistics
Matches: 882, Mismatches: 188, Indels: 35
0.80 0.17 0.03
Matches are distributed among these distances:
169 109 0.12
170 73 0.08
171 419 0.48
172 271 0.31
173 10 0.01
ACGTcount: A:0.39, C:0.15, G:0.15, T:0.32
Consensus pattern (172 bp):
TCAATTATGAGAATATAAAACCATTTAAAGCGAGTAATAAGGCTTTCAAAGGCTTGAGTGACTAT
AAATGGACTTTTCTCTCCCATGGATGGCTTTTGCTTCATGTTTCCCAAGGCAGACATTCAATTAT
AGCATATTTTAACCAAAAATGTAAAAAAAATCCAACTTAAAA
Done.