Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018398532.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_1825.0, 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: 2292
ACGTcount: A:0.35, C:0.12, G:0.12, T:0.34
Warning! 150 characters in sequence are not A, C, G, or T
Found at i:976 original size:172 final size:172
Alignment explanation
Indices: 255--1131 Score: 604
Period size: 172 Copynumber: 5.1 Consensus size: 172
245 TTTATTTAAT
* * * ** * ** *
255 AGAAAAATCCATTTATAGTCTCTCATTTATTCAAAAGCCTTATTAATTTCTTTAAATGATTTTAT
1 AGAAAAGTCCATTTATAGTCACCCATTCCTTCAAAAGCCTTATTACTCACTTCAAATGATTTTAT
* **********
320 AATTTCATAAATGATTTTAAGTTGAA-TTTTTTTACATTTTTGGTTAAAACAGACNNNNNNNNNN
66 AATCTCATAAATGATTTTAAGTTGAATTTTTTTTACATTTTTGGTTAAAACAGACTATAATTGAA
* *
384 TGTCTACCTCAAGAAACGTGAAGAAAAAAACATTCATTGGCA
131 TGTCTACCTCGAGAAACGTGAAGAAAAAAACATTCATTGACA
* * * * * *
426 AGAAAAGTCTATTTATAGCCACCCGTTCCTCCAAAAGCCTTATTACTCGCTT-TAATG-TTTTAT
1 AGAAAAGTCCATTTATAGTCACCCATTCCTTCAAAAGCCTTATTACTCACTTCAAATGATTTTAT
* * * * * *
489 AATCTCATAAATGATTTTAAGTTCAATTTATTTTTACATTTTTAGTTAAAACAGATTTTATTTGT
66 AATCTCATAAATGATTTTAAGTTGAATTT-TTTTTACATTTTTGGTTAAAACAGACTATAATTGA
* * *** *
554 ATGTTTACCTCGAGAAAAGTGAAGAAAATGCCATCCATTGACA
130 ATGTCTACCTCGAGAAACGTGAAGAAAAAAACATTCATTGACA
* * * * * * *
597 ATAAAAGTCCATTTATAGTAACTCATTCTTTCAAAA-CCTTATTGCTCGC-TCTAAATGGTTTTA
1 AGAAAAGTCCATTTATAGTCACCCATTCCTTCAAAAGCCTTATTACTCACTTC-AAATGATTTTA
* *********** ** *
660 TAATCTCATAATTGA-TTTNNNNNNNNNNGTTTTTACATTTTTTATTAAAACAGATTATAATTGA
65 TAATCTCATAAATGATTTTAAGTTGAATTTTTTTTACATTTTTGGTTAAAACAGACTATAATTGA
* * * * * * *
724 ATGCCTACTTCTAGAAACATG-TGCAAAAAGACATTCATTGATA
130 ATGTCTACCTCGAGAAACGTGAAG-AAAAAAACATTCATTGACA
********** *
767 AGAAAAGTCCATTNNNNNNNNNNCATTCCTTCAAAAGCCTTATTACTCAATTCAAATGATTTTAT
1 AGAAAAGTCCATTTATAGTCACCCATTCCTTCAAAAGCCTTATTACTCACTTCAAATGATTTTAT
* *
832 AATCTCATAATTGATTTTCAA-TTGAATTTTTTTTACACTTTTGGTTAAAACAGACTATAATTGA
66 AATCTCATAAATGATTTT-AAGTTGAATTTTTTTTACATTTTTGGTTAAAACAGACTATAATTGA
* * * *
896 ATGTCTACCTTGAGGAACGTGAAGAAAAAAATATTCATTGGCA
130 ATGTCTACCTCGAGAAACGTGAAGAAAAAAACATTCATTGACA
* * ** * *
939 AGAAAAGTTCATTTATAGTCTCCCATTCCACCAAAAGCCTTATTACTCACTTTAAATGGTTTTAT
1 AGAAAAGTCCATTTATAGTCACCCATTCCTTCAAAAGCCTTATTACTCACTTCAAATGATTTTAT
********* * * * * * * * *
1004 AATCTCATAANNNNNNNNNNA-TTCAAATTCTTTAACATTATTAGTTAAAACAAATTATAATTGA
66 AATCTCATAA-ATGATTTTAAGTTGAATTTTTTTTACATTTTTGGTTAAAACAGACTATAATTGA
* * * * * *
1068 ATGTCTACCTCGAAAAACGTAAAGAAAAAGATATTCATTGGCT
130 ATGTCTACCTCGAGAAACGTGAAGAAAAAAACATTCATTGACA
1111 AGAAAAGTCCA-TTATAGTCAC
1 AGAAAAGTCCATTTATAGTCAC
1132 NNNNNNNNNN
Statistics
Matches: 538, Mismatches: 156, Indels: 24
0.75 0.22 0.03
Matches are distributed among these distances:
169 32 0.06
170 102 0.19
171 177 0.33
172 226 0.42
173 1 0.00
ACGTcount: A:0.35, C:0.15, G:0.10, T:0.36
Consensus pattern (172 bp):
AGAAAAGTCCATTTATAGTCACCCATTCCTTCAAAAGCCTTATTACTCACTTCAAATGATTTTAT
AATCTCATAAATGATTTTAAGTTGAATTTTTTTTACATTTTTGGTTAAAACAGACTATAATTGAA
TGTCTACCTCGAGAAACGTGAAGAAAAAAACATTCATTGACA
Found at i:1576 original size:171 final size:169
Alignment explanation
Indices: 1232--2292 Score: 1025
Period size: 171 Copynumber: 6.2 Consensus size: 169
1222 NNNNNNNNNN
*
1232 GTAATAAGGCTTTTGAAGGAATGAGTGACTAT-AATGGACTTTTCTTGCCAATGAATGTTTTTTT
1 GTAATAAGGCTTTTGAAGGAATGGGTGACTATAAATGGACTTTTCTTGCCAATGAATG-TTTTTT
* * * ** * * * * * * *
1296 CTTCACGTTCCACGAGGTATACATTCAATTATAATTTGTTTTAACTAATAATGTTAAAGAATTTG
65 CTTCACGTTTCTCGAGGTAGATGTTCAATTATAGTCTGTTTTAACGAAAAATG-TAAAAAAATTC
* *
1361 AA-TCTAAAATCAATTACGAGATTATAAAACCATTTAAGGTGA
129 AACT-TAAAATCAATTATGAGATTATAAAA-CATTTAAAGTGA
* *
1403 GTAATAAGGCTTTT-AGTGGAATGGGAGACTATAAATGGACTTTTCTTGCCAATGAATGCTTTTT
1 GTAATAAGGCTTTTGA-AGGAATGGGTGACTATAAATGGACTTTTCTTGCCAATGAATG-TTTTT
* * *
1467 TTTTCACG-TTCATCGAGGTAGATGTTCAATTATAGTCTGTTTTAACCAAAAGTGTAAAAAAATT
64 TCTTCACGTTTC-TCGAGGTAGATGTTCAATTATAGTCTGTTTTAACGAAAAATGTAAAAAAATT
* *
1531 CAACTGAAAATTAATTATGAGATTATAAAATCATTTAAAGTGA
128 CAACTTAAAATCAATTATGAGATTATAAAA-CATTTAAAGTGA
* ** * *
1574 GTAATGAGGCTTTTGAAGGAATGGGTGACTATAAATGGACTTTTCTTATCAATAAATATCTTTTT
1 GTAATAAGGCTTTTGAAGGAATGGGTGACTATAAATGGACTTTTCTTGCCAATGAATGT-TTTTT
* * * * * * * *
1639 GC-ACATGTTTCCCGAAGTCGGTGTTCAATTATTGTCTGTTTTAAAGAAAAATGTAAAAACAA-T
65 -CTTCACGTTTCTCGAGGTAGATGTTCAATTATAGTCTGTTTTAACGAAAAATGTAAAAA-AATT
*
1702 CAACTTAAAATCAATTATAAGATTATAAAACCATTTAAAGTGA
128 CAACTTAAAATCAATTATGAGATTATAAAA-CATTTAAAGTGA
* * * **
1745 GCAATAAGG-TTTT-AAGAGAATGGGTTACTATAAATAGACTTTTCTTGCCAATGAATAGCATTT
1 GTAATAAGGCTTTTGAAG-GAATGGGTGACTATAAATGGACTTTTCTTGCCAATGAAT-GTTTTT
* * * ** * * * * * *
1808 TCTTCACTTTTCTCAAGGTAAACATACAATTAAAATCTGCTTTAACTAAAAATATAAAAAAAATT
64 TCTTCACGTTTCTCGAGGTAGATGTTCAATTATAGTCTGTTTTAACGAAAAATGT-AAAAAAATT
* * *
1873 GAACTTAAAATCATTTATGAGATTATAAAACTATTTAAAGCGA
128 CAACTTAAAATCAATTATGAGATTATAAAAC-ATTTAAAGTGA
* * * * * *
1916 GTAATAAGGCTTTTGAAGGAACGAGTGGCTATAAATAGACTTTTCTTGCCAATGAATGCCTCTTT
1 GTAATAAGGCTTTTGAAGGAATGGGTGACTATAAATGGACTTTTCTTGCCAATGAATG-TTTTTT
* * * *
1981 CTTCATGTTTCTTGAGGTAGACAGTT-AATTATAGTCTGTTTTAACAAAAAATGTAAAAAAATTC
65 CTTCACGTTTCTCGAGGTAGA-TGTTCAATTATAGTCTGTTTTAACGAAAAATGTAAAAAAATTC
* * * **
2045 AACTTAAAATTATTTATGAAATTATAAAATCATTTAAAGCAA
129 AACTTAAAATCAATTATGAGATTATAAAA-CATTTAAAGTGA
** * *
2087 GTAATAAGGCTTTTGAATAAATGGGTGACTATAAATGGATTTTTCTACTG--AATAAATGTGTTT
1 GTAATAAGGCTTTTGAAGGAATGGGTGACTATAAATGGACTTTTCT--TGCCAATGAATGT-TTT
* * * * * * *
2150 TTCTACATGTTTCTTGAGGCAACCAT-TT-AATCATAGTCTGTTTTAAAGAAAAATGT-AAAAAA
63 TTCTTCACGTTTCTCGAGG-TA-GATGTTCAATTATAGTCTGTTTTAACGAAAAATGTAAAAAAA
* *
2212 TTCAACTTAAAATCAATTAGGAGATTATAAAACTATTTAAAGTAA
126 TTCAACTTAAAATCAATTATGAGATTATAAAAC-ATTTAAAGTGA
* * *
2257 GTAGTAAGGCTTTTGAAGGAATGAGAGACTATAAAT
1 GTAATAAGGCTTTTGAAGGAATGGGTGACTATAAAT
Statistics
Matches: 735, Mismatches: 129, Indels: 53
0.80 0.14 0.06
Matches are distributed among these distances:
169 5 0.01
170 155 0.21
171 407 0.55
172 161 0.22
173 7 0.01
ACGTcount: A:0.38, C:0.11, G:0.15, T:0.36
Consensus pattern (169 bp):
GTAATAAGGCTTTTGAAGGAATGGGTGACTATAAATGGACTTTTCTTGCCAATGAATGTTTTTTC
TTCACGTTTCTCGAGGTAGATGTTCAATTATAGTCTGTTTTAACGAAAAATGTAAAAAAATTCAA
CTTAAAATCAATTATGAGATTATAAAACATTTAAAGTGA
Found at i:2291 original size:513 final size:514
Alignment explanation
Indices: 1234--2292 Score: 1343
Period size: 513 Copynumber: 2.1 Consensus size: 514
1224 NNNNNNNNGT
* **
1234 AATAAGGCTTTTGAAGGAATGAGTGACTAT-AATGGACTTTTCTTGCCAATGAATGTTTTTTTCT
1 AATAAGGCTTTTGAAGGAATGAGTGACTATAAATAGACTTTTCTTGCCAATGAATGTCATTTTCT
* * * * * * * * * * *
1298 TCACGTTCCACGAGGTATACATTCAATTATAATTTGTTTTAACTAATAATGTTAAAGAATTTGAA
66 TCACGTTCCACAAGGTAAACATACAATTAAAATCTGCTTTAACTAAAAATATAAAAAAAATTGAA
* * * * *
1363 TCTAAAATCAATTACGAGATTATAAAACCATTTAAGGTGAGTAATAAGGCTTTTAGTGGAATGGG
131 TCTAAAATCAATTACGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTAGAGGAACGAG
* * * * *
1428 AGACTATAAATGGACTTTTCTTGCCAATGAATGCTTTTTTTTTCACGTTCATCGAGGTAGATGTT
196 AGACTATAAATAGACTTTTCTTGCCAATGAATGCCTCTTTCTTCACGTTCATCGAGGTAGAAGTT
* * *
1493 CAATTATAGTCTGTTTTAACCAAAAGTGTAAAAAAATTCAACTGAAAATTAATTATGAGATTATA
261 CAATTATAGTCTGTTTTAACAAAAAATGTAAAAAAATTCAACTGAAAATTAATTATGAAATTATA
** * *
1558 AAATCATTTAAAGTGAGTAATGAGGCTTTTGAAGGAATGGGTGACTATAAATGGACTTTTCTTAT
326 AAATCATTTAAAGCAAGTAATAAGGCTTTTGAAGAAATGGGTGACTATAAATGGACTTTTCTTAT
* ** * *
1623 CAATAAATATCTTTTTGCACATGTTTCCCGAAGTCGGTGTTCAATTATTGTCTGTTTTAAAGAAA
391 CAATAAATATCTTTTTGCACATGTTTCCCGAAGACCATGTTCAATCATAGTCTGTTTTAAAGAAA
* *
1688 AATGTAAAAACAATCAACTTAAAATCAATTATAAGATTATAAAACCATTTAAAGTGAGC
456 AATGTAAAAACAATCAACTTAAAATCAATTAGAAGATTATAAAACCATTTAAAGTAAGC
* *
1747 AATAAGG-TTTT-AAGAGAATGGGTTACTATAAATAGACTTTTCTTGCCAATGAATAG-CATTTT
1 AATAAGGCTTTTGAAG-GAATGAGTGACTATAAATAGACTTTTCTTGCCAATGAAT-GTCATTTT
* * *
1809 CTTCACTTTTCTCAAGGTAAACATACAATTAAAATCTGCTTTAACTAAAAATATAAAAAAAATTG
64 CTTCACGTTCCACAAGGTAAACATACAATTAAAATCTGCTTTAACTAAAAATATAAAAAAAATTG
* * *
1874 AA-CTTAAAATCATTTATGAGATTATAAAACTATTTAAAGCGAGTAATAAGGCTTTT-GAAGGAA
129 AATC-TAAAATCAATTACGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTAG-AGGAA
* * * *
1937 CGAGTGGCTATAAATAGACTTTTCTTGCCAATGAATGCCTCTTTCTTCATGTTTC-TTGAGGTAG
192 CGAGAGACTATAAATAGACTTTTCTTGCCAATGAATGCCTCTTTCTTCACG-TTCATCGAGGTAG
* *
2001 ACAGTT-AATTATAGTCTGTTTTAACAAAAAATGTAAAAAAATTCAACTTAAAATTATTTATGAA
256 A-AGTTCAATTATAGTCTGTTTTAACAAAAAATGTAAAAAAATTCAACTGAAAATTAATTATGAA
* *
2065 ATTATAAAATCATTTAAAGCAAGTAATAAGGCTTTTGAATAAATGGGTGACTATAAATGGATTTT
320 ATTATAAAATCATTTAAAGCAAGTAATAAGGCTTTTGAAGAAATGGGTGACTATAAATGGACTTT
* * * ** *
2130 TC-TACTGAATAAATGTGTTTTT-CTACATGTTTCTTGAGGCAACCAT-TT-AATCATAGTCTGT
385 TCTTA-TCAATAAATATCTTTTTGC-ACATGTTTCCCGAAG--ACCATGTTCAATCATAGTCTGT
* * *
2191 TTTAAAGAAAAATGTAAAAA-ATTCAACTTAAAATCAATTAGGAGATTATAAAACTATTTAAAGT
446 TTTAAAGAAAAATGTAAAAACAATCAACTTAAAATCAATTAGAAGATTATAAAACCATTTAAAGT
*
2255 AAGT
511 AAGC
* *
2259 AGTAAGGCTTTTGAAGGAATGAGAGACTATAAAT
1 AATAAGGCTTTTGAAGGAATGAGTGACTATAAAT
Statistics
Matches: 465, Mismatches: 68, Indels: 26
0.83 0.12 0.05
Matches are distributed among these distances:
511 3 0.01
512 69 0.15
513 379 0.82
514 12 0.03
515 2 0.00
ACGTcount: A:0.38, C:0.11, G:0.15, T:0.36
Consensus pattern (514 bp):
AATAAGGCTTTTGAAGGAATGAGTGACTATAAATAGACTTTTCTTGCCAATGAATGTCATTTTCT
TCACGTTCCACAAGGTAAACATACAATTAAAATCTGCTTTAACTAAAAATATAAAAAAAATTGAA
TCTAAAATCAATTACGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTAGAGGAACGAG
AGACTATAAATAGACTTTTCTTGCCAATGAATGCCTCTTTCTTCACGTTCATCGAGGTAGAAGTT
CAATTATAGTCTGTTTTAACAAAAAATGTAAAAAAATTCAACTGAAAATTAATTATGAAATTATA
AAATCATTTAAAGCAAGTAATAAGGCTTTTGAAGAAATGGGTGACTATAAATGGACTTTTCTTAT
CAATAAATATCTTTTTGCACATGTTTCCCGAAGACCATGTTCAATCATAGTCTGTTTTAAAGAAA
AATGTAAAAACAATCAACTTAAAATCAATTAGAAGATTATAAAACCATTTAAAGTAAGC
Done.