Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018399841.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_3077.1, 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: 2821
ACGTcount: A:0.32, C:0.13, G:0.12, T:0.33
Warning! 310 characters in sequence are not A, C, G, or T
Found at i:539 original size:172 final size:172
Alignment explanation
Indices: 5--990 Score: 792
Period size: 172 Copynumber: 5.8 Consensus size: 172
1 CTTA
* * * * * * * * *
5 AGAAACATGAAGGAAAAGTCATTGATTGATAAGCAAAGCCCATTTATGGTTACCCA-AGTCTTCG
1 AGAAACATAAAGAAAAAGCCATTCATTGATAAGAAAAGCCCATTTATAGTCACCCATA-CCTTCA
* * * * ** * ** * * * *
69 GAAGCCTTATTGCTCGCTTTAAATAACTTTATAATTTCATAATTGATTTTAAGTTGAATTTGTTT
65 AAAGACTTATTACTCACTTTAAATAGTTTTACAACCTCATAACTGATTTTAGGATGAATTTTTTT
* ** * *
134 TATATATTTAGTTAAAACGGATTATAATTGAATGTCTACCTTG
130 TATATTTTTAGTTAAAATAGATTATAATTGACTGTCTGCCTTG
* * * * * * * ** *
177 A-AAATAGTGAAGAAAAAGGCATTCATTGGTAAGAAAAGTCCGTTTATGGTCACTTATTCCCTT-
1 AGAAACA-TAAAGAAAAAGCCATTCATTGATAAGAAAAGCCCATTTATAGTCACCCA-TACCTTC
** * * ** * ********** *
240 AAAATCCTTATTACTCGCTTTAAATGGTTTTGTAATCTCATAANNNNNNNNNNGTTGAA-TTTTT
64 AAAAGACTTATTACTCACTTTAAATAGTTTTACAACCTCATAACTGATTTTAGGATGAATTTTTT
* * * *
304 TTACATTTTTAGTTAAAACATATTATAATTGACTGTCTACCTTG
129 TTATATTTTTAGTTAAAATAGATTATAATTGACTGTCTGCCTTG
* * * * * *
348 AGAAATATAAAGGAAAAGCCATTGATTGATAAGAGAAGCCCATTTATAGTCACTCATACCTTCGA
1 AGAAACATAAAGAAAAAGCCATTCATTGATAAGAAAAGCCCATTTATAGTCACCCATACCTTCAA
* *
413 AAGACTTATTACTCATTTTAAAT-GATTTTACAACCTCAAAACTGATTTTAGGATGAATTTTTTT
66 AAGACTTATTACTCACTTTAAATAG-TTTTACAACCTCATAACTGATTTTAGGATGAATTTTTTT
*
477 TATATTTTTAGTTAAAATAGATTATAATTGACTATCTGCCTTG
130 TATATTTTTAGTTAAAATAGATTATAATTGACTGTCTGCCTTG
* * **
520 AGAAACACAAAGAAAAAGCCATTGATTGGGAAGAAAAGCCCATTTATAGTCACCCATACCTTCAA
1 AGAAACATAAAGAAAAAGCCATTCATTGATAAGAAAAGCCCATTTATAGTCACCCATACCTTCAA
* * * *
585 AA-ACCTAATTACTCGCTTTAAATAGTTTTACAACCTCATAATTGATTTTAGGATAAATTTTTAT
66 AAGA-CTTATTACTCACTTTAAATAGTTTTACAACCTCATAACTGATTTTAGGATGAATTTTT-T
** * *
649 GCA-A--TTTGGTTAAAATAGATTATAATTAACTGTCTGCCTTG
129 TTATATTTTTAGTTAAAATAGATTATAATTGACTGTCTGCCTTG
* * * * * ** *
690 AAAAACATGAAGAAAAAGTCATTCATTGACAAGAAAAGCCCATTTATACTCAATCATGCCTTCAA
1 AGAAACATAAAGAAAAAGCCATTCATTGATAAGAAAAGCCCATTTATAGTCACCCATACCTTCAA
* * * * * * *
755 AAG-CTTTTTTACTCGCTTTAAATAGTTTTATAATCTCATAACTGATTTTAGGTTAAAATTTTTT
66 AAGAC-TTATTACTCACTTTAAATAGTTTTACAACCTCATAACTGATTTTAGGATGAATTTTTTT
* * * * * * **
819 TATAATTTTCA-TTAAAATAAATTACAATTGAATGTTTGTCAAG
130 TAT-ATTTTTAGTTAAAATAGATTATAATTGACTGTCTGCCTTG
* * ** *
862 GGAAACATGAAGAAAAAGTTATTCATTTG-TAAGAAAAGCCCATTTATAGTCACCCAAACCTTCA
1 AGAAACATAAAGAAAAAGCCATTCA-TTGATAAGAAAAGCCCATTTATAGTCACCCATACCTTCA
* * *
926 AAAGCCTTATTACT-AGCTTTAAATAGTTTTACAACCTCATAATTGATTTTATGATGAATTTTTT
65 AAAGACTTATTACTCA-CTTTAAATAGTTTTACAACCTCATAACTGATTTTAGGATGAATTTTTT
990 T
129 T
991 ACATTTNNNN
Statistics
Matches: 654, Mismatches: 141, Indels: 38
0.79 0.17 0.05
Matches are distributed among these distances:
169 3 0.00
170 146 0.22
171 126 0.19
172 367 0.56
173 12 0.02
ACGTcount: A:0.36, C:0.14, G:0.13, T:0.36
Consensus pattern (172 bp):
AGAAACATAAAGAAAAAGCCATTCATTGATAAGAAAAGCCCATTTATAGTCACCCATACCTTCAA
AAGACTTATTACTCACTTTAAATAGTTTTACAACCTCATAACTGATTTTAGGATGAATTTTTTTT
ATATTTTTAGTTAAAATAGATTATAATTGACTGTCTGCCTTG
Found at i:836 original size:342 final size:342
Alignment explanation
Indices: 315--988 Score: 868
Period size: 342 Copynumber: 2.0 Consensus size: 342
305 TACATTTTTA
* * * * * * *
315 GTTAAAACATATTATAATTGACTGTCTACCTTGAGAAATATAAAGGAAAAGCCATTGATTGATAA
1 GTTAAAACAGATTATAATTAACTGTCTACCTTGAAAAACATAAAGAAAAAGCCATTCATTGACAA
* * * * *
380 GAGAAGCCCATTTATAGTCACTCATACCTTCGAAAGACTTATTACTCATTTTAAATGATTTTACA
66 GAAAAGCCCATTTATACTCAATCATACCTTCAAAAGACTTATTACTCACTTTAAATGATTTTACA
* * * * * *
445 ACCTCAAAACTGATTTTAGGATGAATTTTTTTTATATTTTTAGTTAAAATAGATTATAATTGACT
131 ACCTCAAAACTGATTTTAGGATAAAATTTTTTTATATTTTCAGTTAAAATAAATTACAATTGAAT
** *
510 ATCTGCCTTGAGAAACACAAAGAAAAAGCCATTGATTGGGAAGAAAAGCCCATTTATAGTCACCC
196 ATCTGCCAAGAGAAACACAAAGAAAAAGCCATTCATTGGGAAGAAAAGCCCATTTATAGTCACCC
* *
575 ATACCTTCAAAAACCTAATTACTCGCTTTAAATAGTTTTACAACCTCATAATTGATTTTAGGATA
261 AAACCTTCAAAAACCTAATTACTAGCTTTAAATAGTTTTACAACCTCATAATTGATTTTAGGATA
640 AATTTTTATGCAATTTG
326 AATTTTTATGCAATTTG
* * * *
657 GTTAAAATAGATTATAATTAACTGTCTGCCTTGAAAAACATGAAGAAAAAGTCATTCATTGACAA
1 GTTAAAACAGATTATAATTAACTGTCTACCTTGAAAAACATAAAGAAAAAGCCATTCATTGACAA
* * *
722 GAAAAGCCCATTTATACTCAATCATGCCTTCAAAAG-CTTTTTTACTCGCTTTAAAT-AGTTTTA
66 GAAAAGCCCATTTATACTCAATCATACCTTCAAAAGAC-TTATTACTCACTTTAAATGA-TTTTA
* * * *
785 TAATCTCATAACTGATTTTAGGTTAAAATTTTTTTATAATTTTCA-TTAAAATAAATTACAATTG
129 CAACCTCAAAACTGATTTTAGGATAAAATTTTTTTAT-ATTTTCAGTTAAAATAAATTACAATTG
* * * * ** ** * *
849 AATGTTTGTCAAGGGAAACATGAAGAAAAAGTTATTCATTTGTAAGAAAAGCCCATTTATAGTCA
193 AATATCTGCCAAGAGAAACACAAAGAAAAAGCCATTCATTGGGAAGAAAAGCCCATTTATAGTCA
* * *
914 CCCAAACCTTCAAAAGCCTTATTACTAGCTTTAAATAGTTTTACAACCTCATAATTGATTTTATG
258 CCCAAACCTTCAAAAACCTAATTACTAGCTTTAAATAGTTTTACAACCTCATAATTGATTTTAGG
*
979 ATGAATTTTT
323 ATAAATTTTT
989 TTACATTTNN
Statistics
Matches: 281, Mismatches: 48, Indels: 6
0.84 0.14 0.02
Matches are distributed among these distances:
341 2 0.01
342 273 0.97
343 6 0.02
ACGTcount: A:0.38, C:0.15, G:0.12, T:0.36
Consensus pattern (342 bp):
GTTAAAACAGATTATAATTAACTGTCTACCTTGAAAAACATAAAGAAAAAGCCATTCATTGACAA
GAAAAGCCCATTTATACTCAATCATACCTTCAAAAGACTTATTACTCACTTTAAATGATTTTACA
ACCTCAAAACTGATTTTAGGATAAAATTTTTTTATATTTTCAGTTAAAATAAATTACAATTGAAT
ATCTGCCAAGAGAAACACAAAGAAAAAGCCATTCATTGGGAAGAAAAGCCCATTTATAGTCACCC
AAACCTTCAAAAACCTAATTACTAGCTTTAAATAGTTTTACAACCTCATAATTGATTTTAGGATA
AATTTTTATGCAATTTG
Found at i:1897 original size:171 final size:171
Alignment explanation
Indices: 1317--2086 Score: 706
Period size: 171 Copynumber: 4.5 Consensus size: 171
1307 TAAGTTAAAT
* ** * * * * *
1317 TTTTTTTATATTTTTGATTAAAAC-GAATTATAATTGAATGTCTGCATT-AGAAAAAATGAAGAA
1 TTTTTTTACATTTTTGGCTAAAACAG-ATTATAATTGACTGTCTACCTTGAG-AAACATGAAGGA
* * ** * * * * * *
1380 AAAGGCATTCATTGGCAAAAAAAGTCTATTTATAGTCACTCATTCCCTCAAAAGCCTTATTATTC
64 AAAGCCATTGATTGATAAGAAAAGCCCATTTATAGTCACTCATACCTTCAAAAGCCTTATTACTC
* ** * * * *
1445 GCTTTAAATAGTTTTGTAATCTGATAATTGATTTTA-AATTAAA
129 GTTTTAAATAGTTTTACAACCTCATAATTGATTTTAGGA-TGAA
* * * * ** **
1488 TTTTTTTACATTTTTGGTTAAAATAAATT-TAATTGATTGTCTACCTTGAGAAATGTGAACAAAA
1 TTTTTTTACATTTTTGGCTAAAACAGATTATAATTGACTGTCTACCTTGAGAAACATGAAGGAAA
* * * * *
1552 AGCCATTCATTGACAAAAAAAACCCATTTATAGTCACTCATGCCTTCAAAAGCCTTATTACTCGT
66 AGCCATTGATTGATAAGAAAAGCCCATTTATAGTCACTCATACCTTCAAAAGCCTTATTACTCGT
* * * * *
1617 TTTAAATAGTTTTATAACCTCATAATTAATTTTATGCT-ATT
131 TTTAAATAGTTTTACAACCTCATAATTGATTTTAGGATGA-A
* * * *
1658 TGTTTTTTACATTTTGGGCTAAAACAGATTATAATCGACTATCTACCTTAAGAAACATGAAGGAA
1 T-TTTTTTACATTTTTGGCTAAAACAGATTATAATTGACTGTCTACCTTGAGAAACATGAAGGAA
* ********** ** * *
1723 AAGCTANNNNNNNNNNAGAAAAGCCCATTTATAGTCACTCATACCTTTGAAGGACTTATTACTCG
65 AAGCCATTGATTGATAAGAAAAGCCCATTTATAGTCACTCATACCTTCAAAAGCCTTATTACTCG
* * * *
1788 TTTTAAATGGTTTTGCAGCCTCAAAATTGATTTTAGGATGAA
130 TTTTAAATAGTTTTACAACCTCATAATTGATTTTAGGATGAA
* * * * * *
1830 TTTTTTTACATTTTTGGTTAAAACAGATTATAATTGGCCGTCTACCTTGTGAAACGTGAATGAAA
1 TTTTTTTACATTTTTGGCTAAAACAGATTATAATTGACTGTCTACCTTGAGAAACATGAAGGAAA
* * *
1895 AGCCATTGATTGATAAGAAAAGCGCATTTATAGTCACCCATACCTTCAAAAGCCCTATTACTCGC
66 AGCCATTGATTGATAAGAAAAGCCCATTTATAGTCACTCATACCTTCAAAAGCCTTATTACTCG-
* *
1960 TTTT-AATAATTTTACAACCACATAATTGATTTTAGGATGAA
130 TTTTAAATAGTTTTACAACCTCATAATTGATTTTAGGATGAA
* * * *
2001 TTTTTGTACATTTTTAGCTAAAACAGATTATAATTGACTGTCTACCTTGAAAAATATGAAGGAAA
1 TTTTTTTACATTTTTGGCTAAAACAGATTATAATTGACTGTCTACCTTGAGAAACATGAAGGAAA
*
2066 AGCCATTTATTGATAAGAAAA
66 AGCCATTGATTGATAAGAAAA
2087 AACTATTTNN
Statistics
Matches: 481, Mismatches: 110, Indels: 16
0.79 0.18 0.03
Matches are distributed among these distances:
169 1 0.00
170 114 0.24
171 256 0.53
172 109 0.23
173 1 0.00
ACGTcount: A:0.36, C:0.14, G:0.13, T:0.36
Consensus pattern (171 bp):
TTTTTTTACATTTTTGGCTAAAACAGATTATAATTGACTGTCTACCTTGAGAAACATGAAGGAAA
AGCCATTGATTGATAAGAAAAGCCCATTTATAGTCACTCATACCTTCAAAAGCCTTATTACTCGT
TTTAAATAGTTTTACAACCTCATAATTGATTTTAGGATGAA
Found at i:2771 original size:172 final size:171
Alignment explanation
Indices: 2178--2821 Score: 780
Period size: 171 Copynumber: 3.8 Consensus size: 171
2168 NNNNNNNNNC
* * * *
2178 ATTTTTAGTTAAAACAGATTATAATTGATTGTTTGCCTT-AGGAAATATGAAGACAAA-CTCATT
1 ATTTTTAGTTAAAACAGATTATAATTGACTGTCTGCCTTGA-GAAATGTGAAGAAAAAGC-CATT
* * * * * *
2241 CATTTGCAG--GAAATGCCCATTTATAGTCACCCA-AGCCTTTAAAAGACTTATTACTCGCTTTG
64 GA-TTG-AGAAGAAAAGCCCATTTATAGTCACTCATA-CCTTCAAAAGCCTTATTACTCGCTTTA
* * * * *
2303 AA-AGACTTTACAACCTTATAATTGATTTTAGGATGAATGTTTTTAC
126 AATAG-TTTTACAATCTCATAATTGATTTTAGGATGAATTTTTTTAT
* * * *
2349 ATTTTTGGTTAAAACAGATTATAATTGACTGTCTGCCTTCAGAAATGTGAAGGAAAAGTCATTGA
1 ATTTTTAGTTAAAACAGATTATAATTGACTGTCTGCCTTGAGAAATGTGAAGAAAAAGCCATTGA
* * * *
2414 TTGATAAGAAAAGGCCATTTATAGTCACCCATACCTTCAGAAGCCTTATTACTCGCTTTAAATAG
66 TTGAGAAGAAAAGCCCATTTATAGTCACTCATACCTTCAAAAGCCTTATTACTCGCTTTAAATAG
* *
2479 TTTTACAATCTCATAATGGATTTAAGGATGAATTTTTTTAT
131 TTTTACAATCTCATAATTGATTTTAGGATGAATTTTTTTAT
* * *
2520 ATTTTTAGTTAAAGCATATTATAATTGACTGTCTGCCTTGAAAAATGTGAAGAAAAAGCCATTGA
1 ATTTTTAGTTAAAACAGATTATAATTGACTGTCTGCCTTGAGAAATGTGAAGAAAAAGCCATTGA
* * * * *
2585 TTGATG-AGAAAAGCCCATTTGTAGTCATTCATATCTTCAAAAGCCTTATTATTTGCTTTAAATA
66 TTGA-GAAGAAAAGCCCATTTATAGTCACTCATACCTTCAAAAGCCTTATTACTCGCTTTAAATA
* * *
2649 TTTTTATAATCTCATAATTGATTTTAGGTTGAATTTGTTTTAT
130 GTTTTACAATCTCATAATTGATTTTAGGATGAATTT-TTTTAT
* * * *
2692 ATTTTTTGTTAAAACAGATTATAATTAACTGTATGCCTTGAGAAACGTGAAGAAAAAGCCATTGA
1 ATTTTTAGTTAAAACAGATTATAATTGACTGTCTGCCTTGAGAAATGTGAAGAAAAAGCCATTGA
* * *
2757 GTGAGAAAAAAAGCCTATTTATAGTCACTCATACCTTCAAAAGCCTTATTACTCGCTTTAAATAG
66 TTGAGAAGAAAAGCCCATTTATAGTCACTCATACCTTCAAAAGCCTTATTACTCGCTTTAAATAG
Statistics
Matches: 405, Mismatches: 59, Indels: 17
0.84 0.12 0.04
Matches are distributed among these distances:
169 1 0.00
170 3 0.01
171 279 0.69
172 122 0.30
ACGTcount: A:0.35, C:0.14, G:0.15, T:0.37
Consensus pattern (171 bp):
ATTTTTAGTTAAAACAGATTATAATTGACTGTCTGCCTTGAGAAATGTGAAGAAAAAGCCATTGA
TTGAGAAGAAAAGCCCATTTATAGTCACTCATACCTTCAAAAGCCTTATTACTCGCTTTAAATAG
TTTTACAATCTCATAATTGATTTTAGGATGAATTTTTTTAT
Done.