Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018401821.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_4929.0, 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: 2615
ACGTcount: A:0.32, C:0.10, G:0.13, T:0.30
Warning! 413 characters in sequence are not A, C, G, or T
Found at i:1431 original size:170 final size:169
Alignment explanation
Indices: 1125--1515 Score: 407
Period size: 170 Copynumber: 2.3 Consensus size: 169
1115 NNNNNNNNNN
* *
1125 TTAAAGTGAGTAATAAGGCTTTTGAAGGAATGAGAGATTATAAATGGACTTTTCATGGCAATGAA
1 TTAAAGCGAGTAATAAGGCTTTTGAAGGAATGAGAGACTATAAAT-GACTTTTCATGGCAATGAA
* * * * * * * * *
1190 TGCTTTTTTCTTGACATTTCTCAGGATAAACGCTCCATTATGGTTTGTTTTAACCAAAACTGTAA
65 TGCTTTTTTCTTGACAGTTCTCAGAACAAACGCTCAATTATAGTCTATTTTAACAAAAAATGTAA
* *
1255 AAAATTCAACTTAAGAT-CAGTTATGAGATTATAAAATAAT
130 AAAATTCAACTTAA-ATACAATTATGAGATTATAAAACAAT
* * *
1295 TTAAAGCGAGTAATAAGGCTTTTGAAGGAATGAGAGACTATAAATAGACTTTTCTTGTCAGTGAA
1 TTAAAGCGAGTAATAAGGCTTTTGAAGGAATGAGAGACTATAAAT-GACTTTTCATGGCAATGAA
* ** * **
1360 TGGTTTTTTC-T-ACACGTTCTCCTAACCAA-GCATTCAATTATAGTCTATTTTATTAAAAAATG
65 TGCTTTTTTCTTGACA-GTTCTCAGAACAAACGC--TCAATTATAGTCTATTTTAACAAAAAATG
* *
1422 -AATAAAATTCAACTTAAATACAATTATGATATTATAAAACCAT
127 TAA-AAAATTCAACTTAAATACAATTATGAGATTATAAAACAAT
* * * * *
1465 TTAAGGCTAGTAATAAGGTTTTTGAAGGTAAGGA-AGACTGTAAATGACTTT
1 TTAAAGCGAGTAATAAGGCTTTTGAAGG-AATGAGAGACTATAAATGACTTT
1516 CTCTACATGT
Statistics
Matches: 185, Mismatches: 30, Indels: 13
0.81 0.13 0.06
Matches are distributed among these distances:
168 5 0.03
169 19 0.10
170 157 0.85
171 4 0.02
ACGTcount: A:0.37, C:0.11, G:0.16, T:0.35
Consensus pattern (169 bp):
TTAAAGCGAGTAATAAGGCTTTTGAAGGAATGAGAGACTATAAATGACTTTTCATGGCAATGAAT
GCTTTTTTCTTGACAGTTCTCAGAACAAACGCTCAATTATAGTCTATTTTAACAAAAAATGTAAA
AAATTCAACTTAAATACAATTATGAGATTATAAAACAAT
Found at i:1658 original size:149 final size:150
Alignment explanation
Indices: 1393--1665 Score: 367
Period size: 149 Copynumber: 1.8 Consensus size: 150
1383 AACCAAGCAT
* *
1393 TCAATTATAGTCTATTTTATTAAAAAATGAATAAAATTCAACTTAAATACAATTATGATATTATA
1 TCAATTATAGTCTATTTTAATAAAAAATGAATAAAATTCAACTTAAATACAATTATGAGATTATA
* * *
1458 AAACCATTTAAGGCTAGTAATAAGGTTTTTGAAGGTAAGGAAGACTGTAAATG-ACTTTCTCTAC
66 AAACCATTTAAAGCTAGTAATAAGGCTTTTGAAGGTAAGGAAGACTATAAATGAACTTTCTCTAC
1522 ATGTTTCCTAAGGTAGCCAA
131 ATGTTTCCTAAGGTAGCCAA
* * * * *
1542 TCAATTATAGTTTGTTTTAATGAAAAATGTAA-ATAATTCAACTTAAA-AGTAATTATGAGATTA
1 TCAATTATAGTCTATTTTAATAAAAAATG-AATAAAATTCAACTTAAATA-CAATTATGAGATTA
* *
1605 TAAAACCATTTAAAG-TGAGTAATAAGGCTTTTGAAGG-AATGAGAGATTATAAATGAACTTT
64 TAAAACCATTTAAAGCT-AGTAATAAGGCTTTTGAAGGTAAGGA-AGACTATAAATGAACTTT
1666 TCTTGACAAT
Statistics
Matches: 107, Mismatches: 12, Indels: 9
0.84 0.09 0.07
Matches are distributed among these distances:
148 6 0.06
149 94 0.88
150 7 0.07
ACGTcount: A:0.42, C:0.09, G:0.14, T:0.35
Consensus pattern (150 bp):
TCAATTATAGTCTATTTTAATAAAAAATGAATAAAATTCAACTTAAATACAATTATGAGATTATA
AAACCATTTAAAGCTAGTAATAAGGCTTTTGAAGGTAAGGAAGACTATAAATGAACTTTCTCTAC
ATGTTTCCTAAGGTAGCCAA
Found at i:1809 original size:172 final size:173
Alignment explanation
Indices: 1542--2218 Score: 748
Period size: 172 Copynumber: 3.9 Consensus size: 173
1532 AGGTAGCCAA
* * *
1542 TCAATTATAGTTTGTTTTAATGAAAAATGT--AAATAATTCAACTTAAAAGT-AATTATGAGATT
1 TCAATTATAGTCTGTTTTAATGAAAAATATAAAAAAAATTCAACTTAAAA-TCAATTATGAGATT
* * * * *
1604 ATAAAACCATTTAAAGTGAGTAATAAGGCTTTTGAAGGAATGAGAGATTATAAAT-GAACTTTTC
65 ATAAAACCATTTAAAGCGAGTAATAAAGCTTTTGAAAGAATGAGTGACTATAAATAG-ACTTTTC
* * *
1668 TTGA-CAATGAATGCTTTTTTCTTCATGTTTCTTGAGTTAGACGT
129 TTGATCAATGAATGCTTTTTTCTTCACGTTTCTTGAGATAGACAT
* * ** * *
1712 TCAATTATGGTTTGTTTTAACCAAAAGTGTAAAAAAAATTCAACTTAAAATCAATTATGAGATTA
1 TCAATTATAGTCTGTTTTAATGAAAAATATAAAAAAAATTCAACTTAAAATCAATTATGAGATTA
* * *
1777 TAAAAGCATTTAAAGCGAGTAATAAAGCTTTTGAAGGAATGTA-TGACTATAAATGGAC-TTTCT
66 TAAAACCATTTAAAGCGAGTAATAAAGCTTTTGAAAGAATG-AGTGACTATAAATAGACTTTTC-
* * * ** *
1840 TTTATCAATGAATGGTTTTTTCTACACGTTTCTTGAGGCAAACAT
129 TTGATCAATGAATGCTTTTTTCTTCACGTTTCTTGAGATAGACAT
** * * * *
1885 GAAACTATAGCCTATTTTAATGAAAAATATAAAAAAAA-GCAACTTAAAATCAATTATGAGATTA
1 TCAATTATAGTCTGTTTTAATGAAAAATATAAAAAAAATTCAACTTAAAATCAATTATGAGATTA
* * *
1949 TAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAAGAACGGGTGACTATAAATAGACTTTTCTT
66 TAAAACCATTTAAAGCGAGTAATAAAGCTTTTGAAAGAATGAGTGACTATAAATAGACTTTTCTT
* * *
2014 G-CCAATGAATGCTTTTTTTTTCACGTTTCTTGAGATAGACTT
131 GATCAATGAATGCTTTTTTCTTCACGTTTCTTGAGATAGACAT
* ** *
2056 TCAATTATAGTCTGTTTTAATAAAAAATATAAATAAAAATT-AAGCAGAAAATCAATTTTTGA-A
1 TCAATTATAGTCTGTTTTAATGAAAAATATAAA-AAAAATTCAA-CTTAAAATCAA-TTATGAGA
* * * * * *
2119 TAATAAAACGATTAAAAGTGAGTAATAAAGCTTTTGAAAGATTGGGTGACTATAAATAGACTTTT
63 TTATAAAACCATTTAAAGCGAGTAATAAAGCTTTTGAAAGAATGAGTGACTATAAATAGACTTTT
* * *
2184 CTT-ATCAATAAATGCATTTTTCTTCACATTTCTTG
128 CTTGATCAATGAATGCTTTTTTCTTCACGTTTCTTG
2219 NNNNNNNNNN
Statistics
Matches: 426, Mismatches: 67, Indels: 25
0.82 0.13 0.05
Matches are distributed among these distances:
170 26 0.06
171 65 0.15
172 167 0.39
173 163 0.38
174 5 0.01
ACGTcount: A:0.39, C:0.10, G:0.14, T:0.36
Consensus pattern (173 bp):
TCAATTATAGTCTGTTTTAATGAAAAATATAAAAAAAATTCAACTTAAAATCAATTATGAGATTA
TAAAACCATTTAAAGCGAGTAATAAAGCTTTTGAAAGAATGAGTGACTATAAATAGACTTTTCTT
GATCAATGAATGCTTTTTTCTTCACGTTTCTTGAGATAGACAT
Found at i:2218 original size:344 final size:343
Alignment explanation
Indices: 1556--2218 Score: 879
Period size: 344 Copynumber: 1.9 Consensus size: 343
1546 TTATAGTTTG
* * ** *
1556 TTTTAATGAAAAATGTAAATAATTCAACTTAAAAGTAATTATGAGATTATAAAACCATTTAAAGT
1 TTTTAATGAAAAATATAAAAAAAGCAACTTAAAAGTAATTATGAGATTATAAAACCATTTAAAGC
* * *
1621 GAGTAATAAGGCTTTTGAAGGAATGAGAGATTATAAATGAACTTTTCTTGACAATGAATGCTTTT
66 GAGTAATAAGGCTTTTGAAAGAACGAGAGACTATAAATGAACTTTTCTTGACAATGAATGCTTTT
* * * * * * *
1686 TTCTTCATGTTTCTTGAGTTAGACGTTCAATTATGGTTTGTTTTAACCAAAAGTGTAAAAAAAAT
131 TTCTTCACGTTTCTTGAGATAGACGTTCAATTATAGTCTGTTTTAACAAAAAATATAAAAAAAAT
** * * *
1751 TCAACTTAAAATCAATTATGAGATTATAAAAGCATTTAAAGCGAGTAATAAAGCTTTTGAAGGAA
196 TCAACAGAAAATCAATTATGAGATAATAAAAGCATTAAAAGCGAGTAATAAAGCTTTTGAAAGAA
* * * * ** *
1816 TGTATGACTATAAATGGACTTTCTTTTATCAATGAATGGTTTTTTCTACACGTTTCTTGAGGCAA
261 TGGATGACTATAAATAGACTTTCTCTTATCAATAAATGCATTTTTCTACACATTTCTTGAGGCAA
1881 ACATGAAACTATAGCCTA
326 ACATGAAACTATAGCCTA
1899 TTTTAATGAAAAATATAAAAAAAAGCAACTTAAAA-TCAATTATGAGATTATAAAACCATTTAAA
1 TTTTAATGAAAAATAT-AAAAAAAGCAACTTAAAAGT-AATTATGAGATTATAAAACCATTTAAA
* * *
1963 GCGAGTAATAAGGCTTTTGAAAGAACGGGTGACTATAAAT-AGACTTTTCTTGCCAATGAATGCT
64 GCGAGTAATAAGGCTTTTGAAAGAACGAGAGACTATAAATGA-ACTTTTCTTGACAATGAATGCT
* * *
2027 TTTTTTTTCACGTTTCTTGAGATAGACTTTCAATTATAGTCTGTTTTAATAAAAAATATAAATAA
128 TTTTTCTTCACGTTTCTTGAGATAGACGTTCAATTATAGTCTGTTTTAACAAAAAATATAAA-AA
* *
2092 AAATT-AAGCAGAAAATCAATTTTTGA-ATAATAAAA-CGATTAAAAGTGAGTAATAAAGCTTTT
192 AAATTCAA-CAGAAAATCAA-TTATGAGATAATAAAAGC-ATTAAAAGCGAGTAATAAAGCTTTT
* * *
2154 GAAAGATTGGGTGACTATAAATAGACTTT-TCTTATCAATAAATGCATTTTTCTTCACATTTCTT
254 GAAAGAATGGATGACTATAAATAGACTTTCTCTTATCAATAAATGCATTTTTCTACACATTTCTT
2218 G
319 G
2219 NNNNNNNNNN
Statistics
Matches: 275, Mismatches: 38, Indels: 13
0.84 0.12 0.04
Matches are distributed among these distances:
343 17 0.06
344 182 0.66
345 71 0.26
346 5 0.02
ACGTcount: A:0.40, C:0.10, G:0.14, T:0.36
Consensus pattern (343 bp):
TTTTAATGAAAAATATAAAAAAAGCAACTTAAAAGTAATTATGAGATTATAAAACCATTTAAAGC
GAGTAATAAGGCTTTTGAAAGAACGAGAGACTATAAATGAACTTTTCTTGACAATGAATGCTTTT
TTCTTCACGTTTCTTGAGATAGACGTTCAATTATAGTCTGTTTTAACAAAAAATATAAAAAAAAT
TCAACAGAAAATCAATTATGAGATAATAAAAGCATTAAAAGCGAGTAATAAAGCTTTTGAAAGAA
TGGATGACTATAAATAGACTTTCTCTTATCAATAAATGCATTTTTCTACACATTTCTTGAGGCAA
ACATGAAACTATAGCCTA
Done.