Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018398507.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_1800.0, 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: 3444
ACGTcount: A:0.31, C:0.10, G:0.11, T:0.29
Warning! 669 characters in sequence are not A, C, G, or T
Found at i:420 original size:170 final size:171
Alignment explanation
Indices: 1--729 Score: 754
Period size: 171 Copynumber: 4.3 Consensus size: 171
* * * *
1 ATCTGTTTTAATAAAAAATGTAAAAAAATTTAACTTAAAATCAATTATGAGATTGTAAAACAT-T
1 ATCTATTTTAATAAAAAATATAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAA-ATAT
* ** * * **********
65 TTAAAGCGAGTAATAA-GATTTTCGAAGGTATGGATGACTATAANNNNNNNNNNCTTGCCAATGG
65 TTAAAGCGAGTAATAAGGCTTTT-GAAGACATGGGTAACTATAAATGGACTTTTCTTGCCAATGG
* *
129 ATATCTTTTTC-TCTAGGTTTCTTAAGGTAGACATTCAATTATA
129 ATATCTTTTTCTTC-ATGTTTCCTAAGGTAGACATTCAATTATA
* * * *
172 ATCTATATGAATAAAAAATATAAAAAAATTTAACTTAAAATCAATTATGAGAGTATAAAAATATT
1 ATCTATTTTAATAAAAAATATAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAAATATT
* * * *
237 GAAAGCGAGTAATAAGGCTTTTGAAGACATGGGTGAGTATAAATGGACTTTTCCTGCCAATGGAT
66 TAAAGCGAGTAATAAGGCTTTTGAAGACATGGGTAACTATAAATGGACTTTTCTTGCCAATGGAT
* * * * *
302 ATGTTTTTCTTCATGTTTCCTATGGCAGACAATCAATTATT
131 ATCTTTTTCTTCATGTTTCCTAAGGTAGACATTCAATTATA
* * * * *
343 ATCTGTTTTAAT-CAAAATGTAAAAAAATTCAAATTAAAATCAATTATGAGATTATAAAAATGTT
1 ATCTATTTTAATAAAAAATATAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAAATATT
* ** * * *
407 TAAAGCAAGTAATAATACTTTTGAA-AGCATGAGTAACTACAAATGGACTTTTCTTGCCAATAGA
66 TAAAGCGAGTAATAAGGCTTTTGAAGA-CATGGGTAACTATAAATGGACTTTTCTTGCCAATGGA
* * *
471 TATCTTTTTCTTCATGTTTCCTAAGGTAAACATTCAATTGTT
130 TATCTTTTTCTTCATGTTTCCTAAGGTAGACATTCAATTATA
** * * *
513 ATCTATTTTAACCAAAAATACT-TAAAAATTCAACGTAAAATCAATTATGAGATTATAAAACTAT
1 ATCTATTTTAATAAAAAATA-TAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAAATAT
** * ** * * *
577 TTAATTCGAGTAATAAGGTTTTTGAAGGTATGGGTAACTATCAATGGACTTTTCTTGTCAATGAA
65 TTAAAGCGAGTAATAAGGCTTTTGAAGACATGGGTAACTATAAATGGACTTTTCTTGCCAATGGA
* * * *
642 TATCTTTTT-TATCAAGTTTCTCT-AGTTTGACATTCAAATATA
130 TATCTTTTTCT-TCATGTTTC-CTAAGGTAGACATTCAATTATA
684 ATCTATTTTAATAAAAAATATAAAAAAATTCAACTTAAAATCAATT
1 ATCTATTTTAATAAAAAATATAAAAAAATTCAACTTAAAATCAATT
730 NNNNNNNNNN
Statistics
Matches: 459, Mismatches: 89, Indels: 20
0.81 0.16 0.04
Matches are distributed among these distances:
169 1 0.00
170 148 0.32
171 300 0.65
172 10 0.02
ACGTcount: A:0.40, C:0.11, G:0.12, T:0.36
Consensus pattern (171 bp):
ATCTATTTTAATAAAAAATATAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAAATATT
TAAAGCGAGTAATAAGGCTTTTGAAGACATGGGTAACTATAAATGGACTTTTCTTGCCAATGGAT
ATCTTTTTCTTCATGTTTCCTAAGGTAGACATTCAATTATA
Found at i:1462 original size:172 final size:165
Alignment explanation
Indices: 1214--1710 Score: 433
Period size: 171 Copynumber: 2.9 Consensus size: 165
1204 TTAACCTAAT
* * * * * ** ** * *
1214 TCAAATATTAGATTATAAAGCCATTTAAAGCAAGTAATAAGACTTTCGAAGGCATGAGTGAAAAT
1 TCAATTATGAGATTATAAAACTATTTAAAGCGAGTAATAAGACTTTTAAAGATATGGGTGAATAT
* *
1279 AAATAGACTTTTCTTGCCAATGGATATCTTTTTTTGTATGTTTTTTGAGGTAGACATTCAATTAT
66 AAATAGACTTTTCTTGCCAATGGATATCTTTTTTT-CATGTTTTCTGAGGTAGACATTCAATTAT
* *****
1344 AATCTATTTTAATAAAAAAANNNNNNNNNNTTCAACTTAAAA
130 AATCTGTTTTAAT-AAAAAA-----TGTAATTCAACTTAAAA
* *
1386 TTAATTATGAGATTATAAAA-TCATTTAACA-CGAGTAATAAG-GTTTCTAAAGATATGGGTGAA
1 TCAATTATGAGATTATAAAACT-ATTTAA-AGCGAGTAATAAGACTTT-TAAAGATATGGGTGAA
* * * * ** *
1448 TATAAATTGACTTTTCTTGCCAAGGGATATCTTTTTCCTCACGTTTTCCAAGGTAAACATTCAAT
63 TATAAATAGACTTTTCTTGCCAATGGATATCTTTTT-TTCATGTTTTCTGAGGTAGACATTCAAT
*****
1513 TATAATCTGTTTTAATAAAAAATGTAANNNNNNNNNNCTTAAAA
127 TATAATCTGTTTTAATAAAAAATGTAA-----TTCAACTTAAAA
* ***
1557 TCAATTATTAGATTATAAAACTATTTAAAGCGAGTAATAAGACTTTTAAAGATATGGGTTCCTAT
1 TCAATTATGAGATTATAAAACTATTTAAAGCGAGTAATAAGACTTTTAAAGATATGGGTGAATAT
* * *
1622 AAATGGACTTTTCTTGCCAATGGATATCTTCTTCTTCATGTTTTCTGAGATAGACATTCAATTAT
66 AAATAGACTTTTCTTGCCAATGGATATCTT-TTTTTCATGTTTTCTGAGGTAGACATTCAATTAT
* **
1687 TATCTGTTTTAACCAAAAATGTAA
130 AATCTGTTTTAATAAAAAATGTAA
1711 AAAAANNNNN
Statistics
Matches: 261, Mismatches: 51, Indels: 27
0.77 0.15 0.08
Matches are distributed among these distances:
170 1 0.00
171 141 0.54
172 117 0.45
173 2 0.01
ACGTcount: A:0.36, C:0.11, G:0.12, T:0.36
Consensus pattern (165 bp):
TCAATTATGAGATTATAAAACTATTTAAAGCGAGTAATAAGACTTTTAAAGATATGGGTGAATAT
AAATAGACTTTTCTTGCCAATGGATATCTTTTTTTCATGTTTTCTGAGGTAGACATTCAATTATA
ATCTGTTTTAATAAAAAATGTAATTCAACTTAAAA
Found at i:2105 original size:172 final size:168
Alignment explanation
Indices: 1779--2256 Score: 493
Period size: 172 Copynumber: 2.8 Consensus size: 168
1769 TTTTCTAGCT
* * * *
1779 AATGGATACCTTTTTG-TCCATGTTTCTCAAGGTAGATAATCAATTATAATCTGTTATAATAAAC
1 AATGGATACC-TTTTGCTTCATGTTTCT-AAGGTAGACATTCAATTATAATCTGTTTTAATAAAC
* * * * * *
1843 AATGTAAAACAATTCAAGTTAAAATTAACTGTGAGATTATAAAACTATTTAAAGCGAGTATTAAG
64 AATGTAAAACAATTCAAG-TAAAATCAACTATAAGATTATAAAACCATTTAAA-AGAGTAATAAG
* * * * * *
1908 GTTTTTAAGAGAGTGGGTGACTATAAATGGACTTTTCTTT-TC
127 GCTTTCAAAAGAGTGAGTGACTATAAATAGACTTTT-TTTACC
*
1950 AATGGATACCTTTTGCTTCATGTTTCTAGAGGTAGACATTCAATTATAATCTATTTTAATAAAAC
1 AATGGATACCTTTTGCTTCATGTTTCTA-AGGTAGACATTCAATTATAATCTGTTTTAAT-AAAC
* * *
2015 AATATAAAACAATTCAAGTAATAATCAATTATAAGATTATAAAACCATTTAAAATGAGTAATCAG
64 AATGTAAAACAATTCAAGTAA-AATCAACTATAAGATTATAAAACCATTTAAAA-GAGTAATAAG
2080 GCTTTCAAAAGCA-TGAGTGACTATAAATAGACTTTTTTTACC
127 GCTTTCAAAAG-AGTGAGTGACTATAAATAGACTTTTTTTACC
* * **
2122 AATGGATACCTTTAT-CCTCATGTTTCTTAAGGTAGACATTCAATTATTATCTGTTTTACCCAAA
1 AATGGATACCTTT-TGCTTCATGTTTC-TAAGGTAGACATTCAATTATAATCTGTTTTA-ATAAA
* * * *
2186 -AATGTTAAA-AATTCAATTTAAAATC-AGTACTAAGATTATAAAATCATTTAAAAGCAAGTAAT
63 CAATGTAAAACAATTCAA-GTAAAATCAACTA-TAAGATTATAAAACCATTTAAAAG--AGTAAT
*
2248 GAGGCTTTC
124 AAGGCTTTC
2257 GAAGGCATNN
Statistics
Matches: 262, Mismatches: 31, Indels: 28
0.82 0.10 0.09
Matches are distributed among these distances:
169 4 0.02
170 39 0.15
171 77 0.29
172 138 0.53
173 4 0.02
ACGTcount: A:0.39, C:0.12, G:0.13, T:0.36
Consensus pattern (168 bp):
AATGGATACCTTTTGCTTCATGTTTCTAAGGTAGACATTCAATTATAATCTGTTTTAATAAACAA
TGTAAAACAATTCAAGTAAAATCAACTATAAGATTATAAAACCATTTAAAAGAGTAATAAGGCTT
TCAAAAGAGTGAGTGACTATAAATAGACTTTTTTTACC
Found at i:3048 original size:171 final size:171
Alignment explanation
Indices: 2871--3232 Score: 384
Period size: 171 Copynumber: 2.1 Consensus size: 171
2861 AGAGACATCT
* *
2871 AATTATAATCTGTTTTAATAAAAAAAATAAAGAAATTTAACTCAAAAT-AAGTTATGAGATTGTA
1 AATTATAATCTGTTTTAATAAAAAAAATAAAAAAATTCAACTCAAAATCAA-TTATGAGATTGTA
* * * * * *
2935 AAACCATTTAAAGTGTGTAACAAGGCTTTCGAGGGCATGGGTGACTATAAATTAACTTTTCTTGC
65 AAACCATTTAAAGCGAGTAACAAGGCTTTCGAAGGCATGGGTAACTATAAATCAACTTCTCTTGC
* *
3000 CAATGGATATCATTTTCTTCACGTTCCCCAAAGCAAACATTC
130 CAATGCATACCATTTTCTTCACGTTCCCCAAAGCAAACATTC
* * * * * *******
3042 AATTATAATCAGTTTGAATAAAAAATATAAAAAAATTCAAGTTAAAATCAATTATGAGNNNNNNN
1 AATTATAATCTGTTTTAATAAAAAAAATAAAAAAATTCAACTCAAAATCAATTATGAGATTGTAA
*** * * * *
3107 NNNCATTTAAAGCGAGTAATAAGGCTTTTGAAGGTATGGGTAACTATAAATCGACTTCTCTTGCC
66 AACCATTTAAAGCGAGTAACAAGGCTTTCGAAGGCATGGGTAACTATAAATCAACTTCTCTTGCC
* * * * * *
3172 AATGCATACCTTTTTCTTTACGTTTCCCTAGGCACACATTC
131 AATGCATACCATTTTCTTCACGTTCCCCAAAGCAAACATTC
*
3213 AATTATAATCTCTTTTAATA
1 AATTATAATCTGTTTTAATA
3233 NNNNNNNNNN
Statistics
Matches: 152, Mismatches: 38, Indels: 2
0.79 0.20 0.01
Matches are distributed among these distances:
171 150 0.99
172 2 0.01
ACGTcount: A:0.37, C:0.14, G:0.13, T:0.33
Consensus pattern (171 bp):
AATTATAATCTGTTTTAATAAAAAAAATAAAAAAATTCAACTCAAAATCAATTATGAGATTGTAA
AACCATTTAAAGCGAGTAACAAGGCTTTCGAAGGCATGGGTAACTATAAATCAACTTCTCTTGCC
AATGCATACCATTTTCTTCACGTTCCCCAAAGCAAACATTC
Done.