Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018399653.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_2900.0, 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: 3522
ACGTcount: A:0.30, C:0.11, G:0.10, T:0.31
Warning! 645 characters in sequence are not A, C, G, or T
Found at i:790 original size:170 final size:171
Alignment explanation
Indices: 596--949 Score: 455
Period size: 170 Copynumber: 2.1 Consensus size: 171
586 NNNNNNNNNN
**
596 CATTTATAGTCACCAATTCCTTCGAAAGCCTTATTACT-AGCCTTAAATGGTTTTATAATCTCAA
1 CATTTATAGTCACCAATTCCTTCGAAAGCCTTATTACTGA-CCTTAAATAATTTTATAATCTCAA
* * * **
660 AATTGACTTTAAG-TAGAATGTTTTTACATTTTT-AGTTAAAACAGATTATAATTGAAAGTTTAC
65 AATTCACTTTAAGCT-CAATGTTTTTACATTTTTGA-TAAAAACAGATTATAATTGAAAGCCTAC
* * * *
723 CTTGAGAAAC-TAAAGATAAAGGCATTCCTTGGCAATAAAAGTC
128 CTTAAGAAACGTAAAGAGAAAGGCATTCATTGGCAAGAAAAGTC
* * * *
766 CATTTATAGTCACCTATTCCTTCGAAAGCCTTATTACTGACTTTAAATAATTTTATTATCTCAAG
1 CATTTATAGTCACCAATTCCTTCGAAAGCCTTATTACTGACCTTAAATAATTTTATAATCTCAAA
* * * * * *
831 GTTCATTTTATGCTCAATTTTTTTACATTTTTGATAAAAACAGCTTATAATTGAATGCCTACCTT
66 ATTCACTTTAAGCTCAATGTTTTTACATTTTTGATAAAAACAGATTATAATTGAAAGCCTACCTT
*
896 AAGAAACGTGAAGAGAAAGGCATTCATTGGCAAGAAAAGTC
131 AAGAAACGTAAAGAGAAAGGCATTCATTGGCAAGAAAAGTC
937 CATTTATAGTCAC
1 CATTTATAGTCAC
950 NNNNNNNNNN
Statistics
Matches: 158, Mismatches: 22, Indels: 7
0.84 0.12 0.04
Matches are distributed among these distances:
170 113 0.72
171 45 0.28
ACGTcount: A:0.35, C:0.16, G:0.13, T:0.36
Consensus pattern (171 bp):
CATTTATAGTCACCAATTCCTTCGAAAGCCTTATTACTGACCTTAAATAATTTTATAATCTCAAA
ATTCACTTTAAGCTCAATGTTTTTACATTTTTGATAAAAACAGATTATAATTGAAAGCCTACCTT
AAGAAACGTAAAGAGAAAGGCATTCATTGGCAAGAAAAGTC
Found at i:1355 original size:170 final size:161
Alignment explanation
Indices: 1169--1477 Score: 293
Period size: 170 Copynumber: 1.9 Consensus size: 161
1159 TATAGTTTTC
** * ** * *
1169 CATTCCTTTCAAAGCCTTATTACTTTCTTTAAATAGTTTTATAATTTTATAATTAATTTTAAG-T
1 CATTCCTTTCAAAGCCTTATTACTCGCTTCAAATAGTTTTATAAGCTCAAAATTAATTTTAAGTT
* * **
1233 CAATTTTTTTTA-TATTTTTGGTTAAAACAGACTA-AATTGAATGTCTACCTTGAGAAATGTAAA
66 CAA-TGTTTTTACT-TTTTTGATTAAAACAGACTATAATTGAATGTCTACCTCAAGAAATGTAAA
1296 GAAAAAGGCATTCATTGGCAAGAANNNNNNNNNNATAGTCACT
129 GAAAAAGGCATTCATTGGCAAGAA----------ATAGTCACT
* *
1339 CATTCC-TTCAAAAGCCTTATTACTCGCTTCAAATGGTTTTATAAGCTCAAAATTGATTTTAAGT
1 CATTCCTTTC-AAAGCCTTATTACTCGCTTCAAATAGTTTTATAAGCTCAAAATTAATTTTAAGT
* ** * * * *
1403 TGAATGTTTTTACTTTTTTGATTAAAATGGATTATAATTGAATGTTTATCTCAAGAAATGTGAAG
65 TCAATGTTTTTACTTTTTTGATTAAAACAGACTATAATTGAATGTCTACCTCAAGAAATGTAAAG
1468 AAAAAGGCAT
130 AAAAAGGCAT
1478 NNNNNNNNNN
Statistics
Matches: 115, Mismatches: 20, Indels: 7
0.81 0.14 0.05
Matches are distributed among these distances:
169 3 0.03
170 73 0.63
171 39 0.34
ACGTcount: A:0.34, C:0.11, G:0.12, T:0.39
Consensus pattern (161 bp):
CATTCCTTTCAAAGCCTTATTACTCGCTTCAAATAGTTTTATAAGCTCAAAATTAATTTTAAGTT
CAATGTTTTTACTTTTTTGATTAAAACAGACTATAATTGAATGTCTACCTCAAGAAATGTAAAGA
AAAAGGCATTCATTGGCAAGAAATAGTCACT
Found at i:1509 original size:171 final size:162
Alignment explanation
Indices: 1488--1967 Score: 320
Period size: 172 Copynumber: 2.8 Consensus size: 162
1478 NNNNNNNNNN
* * *
1488 GAAAAGTTTATTTATAGTCACTCATTCCTTCAAAAGCCTTATTACTTACTTTAAATACTTTTATT
1 GAAAAGTTTATTTATAGTCACTCATTCCTTCAAAAGCCTTATTACTCACTTCAAATACTTTTATA
* * *
1553 ATCCCAAAATTGATTTTATGTTCAACTTTTGGTACATTTTTGGTTAAAACAGATTATAATTGAAT
66 AGCCCAAAATTGATTTTAAGTTCAACTTTTGGTACATTTTTGATTAAAACAGATTATAATTGAAT
*
1618 GTCTACTTCAAGAAACGTGAAGAGAAAGGCAT
131 GTCTACTTCAAGAAACGTGAAGAAAAAGGCAT
********** * *
1650 NNNNNNNNNNNNNNNNNNNNTTTATAGTCACCCATTCCTTCAAAAGCCTTATTACTCACTTTAAA
1 ----------GAAAAGTTTATTTATAGTCACTCATTCCTTCAAAAGCCTTATTACTCACTTCAAA
*** * * * * * *
1715 TAGC-TTTATTTTCACAAAATTGATTTTATGTTCAA-TTTTGTTTATATTTTT-AGGTAAAACAT
56 TA-CTTTTATAAGCCCAAAATTGATTTTAAGTTCAACTTTTG-GTACATTTTTGA-TTAAAACAG
* * *
1777 ATTATAATTGAATGTTTACCTCAAGAAACATGAAGAAAAAGGCATT
118 ATTATAATTGAATGTCTACTTCAAGAAACGTGAAGAAAAAGGCA-T
*** * * *
1823 NNNNNNNNNNNNAAGTCTATTTATATTCAC-CTATTCCTTCAAAAGCCTTATTACTCACTTTAAA
1 ---------GAAAAGTTTATTTATAGTCACTC-ATTCCTTCAAAAGCCTTATTACTCACTTCAAA
* * * * * *
1887 TGCTTTTATGATCCCAAAATTGATTTTATGTTCAACTTTTTGTACATTTTTGGTTAAAACAGATT
56 TACTTTTATAAGCCCAAAATTGATTTTAAGTTCAACTTTTGGTACATTTTTGATTAAAACAGATT
*
1952 ATAATTGCATGTCTAC
121 ATAATTGAATGTCTAC
1968 CTCNNNNNNN
Statistics
Matches: 257, Mismatches: 43, Indels: 16
0.81 0.14 0.05
Matches are distributed among these distances:
171 7 0.03
172 244 0.95
173 6 0.02
ACGTcount: A:0.31, C:0.14, G:0.10, T:0.38
Consensus pattern (162 bp):
GAAAAGTTTATTTATAGTCACTCATTCCTTCAAAAGCCTTATTACTCACTTCAAATACTTTTATA
AGCCCAAAATTGATTTTAAGTTCAACTTTTGGTACATTTTTGATTAAAACAGATTATAATTGAAT
GTCTACTTCAAGAAACGTGAAGAAAAAGGCAT
Found at i:1677 original size:172 final size:159
Alignment explanation
Indices: 1670--1970 Score: 329
Period size: 172 Copynumber: 1.8 Consensus size: 159
1660 NNNNNNNNNN
* *
1670 TTTATAGTCACCCATTCCTTCAAAAGCCTTATTACTCACTTTAAATAGC-TTTATTTTCACAAAA
1 TTTATAGTCA-CCATTCCTTCAAAAGCCTTATTACTCACTTTAAATA-CTTTTATTATCCCAAAA
* * * *
1734 TTGATTTTATGTTCAA-TTTTGTTTATATTTTTAGG-TAAAACATATTATAATTGAATGTTTACC
64 TTGATTTTATGTTCAACTTTTG-GTACATTTTT-GGTTAAAACAGATTATAATTGAATGTCTACC
1797 TCAAGAAACATGAAGAAAAAGGCATTNNNNNNNNNNNNAAGTCTA
127 TCAAGAAACATGAAGAAAAAGGCATT------------AAGTCTA
* * *
1842 TTTATATTCACCTATTCCTTCAAAAGCCTTATTACTCACTTTAAATGCTTTTATGATCCCAAAAT
1 TTTATAGTCACC-ATTCCTTCAAAAGCCTTATTACTCACTTTAAATACTTTTATTATCCCAAAAT
* *
1907 TGATTTTATGTTCAACTTTTTGTACATTTTTGGTTAAAACAGATTATAATTGCATGTCTACCTC
65 TGATTTTATGTTCAACTTTTGGTACATTTTTGGTTAAAACAGATTATAATTGAATGTCTACCTC
1971 NNNNNNNNNN
Statistics
Matches: 114, Mismatches: 11, Indels: 8
0.86 0.08 0.06
Matches are distributed among these distances:
171 5 0.04
172 105 0.92
173 4 0.04
ACGTcount: A:0.31, C:0.16, G:0.09, T:0.40
Consensus pattern (159 bp):
TTTATAGTCACCATTCCTTCAAAAGCCTTATTACTCACTTTAAATACTTTTATTATCCCAAAATT
GATTTTATGTTCAACTTTTGGTACATTTTTGGTTAAAACAGATTATAATTGAATGTCTACCTCAA
GAAACATGAAGAAAAAGGCATTAAGTCTA
Done.