Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018402966.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_627.0, 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: 19299
ACGTcount: A:0.23, C:0.08, G:0.08, T:0.23
Warning! 7432 characters in sequence are not A, C, G, or T
Found at i:7623 original size:172 final size:172
Alignment explanation
Indices: 7319--7645 Score: 442
Period size: 172 Copynumber: 1.9 Consensus size: 172
7309 NNNNNNNNNN
* * * *
7319 AGTGAGTAATAAGGCTTTTGAAAGAATAGGTGACTATAAATAGACTTTTCTTACGAATAAATGTC
1 AGTGAGTAATAAGGCTTTTGAAAGAATAGGAGACAATAAATAGACTTTTCTTACCAATAAATGCC
* *
7384 TTTTTCTTCATGTTTCAAGAAGTAGACATTCAATTATAATCTGTTTTAACCAAAATTATATAAAA
66 TTGTTCTTCATGTTTCAAGAAGTAAACATTCAATTATAATCTGTTTTAACCAAAATTATATAAAA
** *
7449 AATTGAATTTAAAATCAATTTTGAGTTTGTAAAACTATTTAA
131 AATTGAACCTAAAATCAATTATGAGTTTGTAAAACTATTTAA
* * * * *
7491 AGTGAGTAATAAGGCTTTTGAAAGAATGGGAGACAATAAATGGATTTTTCTTGCCAATGAATGCC
1 AGTGAGTAATAAGGCTTTTGAAAGAATAGGAGACAATAAATAGACTTTTCTTACCAATAAATGCC
***** *
7556 TTGTTCTTCATGTTTCTCTTGGTAAACATTCAATTATAATCTGTTTTAATCAATAATGTA-A-AA
66 TTGTTCTTCATGTTTCAAGAAGTAAACATTCAATTATAATCTGTTTTAACCAA-AAT-TATATAA
7619 AAAATTGAACCTAAAATCAATTATGAG
129 AAAATTGAACCTAAAATCAATTATGAG
7646 AATATAAAAC
Statistics
Matches: 133, Mismatches: 20, Indels: 4
0.85 0.13 0.03
Matches are distributed among these distances:
172 127 0.95
173 4 0.03
174 2 0.02
ACGTcount: A:0.38, C:0.10, G:0.14, T:0.37
Consensus pattern (172 bp):
AGTGAGTAATAAGGCTTTTGAAAGAATAGGAGACAATAAATAGACTTTTCTTACCAATAAATGCC
TTGTTCTTCATGTTTCAAGAAGTAAACATTCAATTATAATCTGTTTTAACCAAAATTATATAAAA
AATTGAACCTAAAATCAATTATGAGTTTGTAAAACTATTTAA
Found at i:8432 original size:173 final size:172
Alignment explanation
Indices: 8194--8505 Score: 405
Period size: 173 Copynumber: 1.8 Consensus size: 172
8184 NNNNNNNTCG
* * * * *
8194 CTTTAAATGATTTTATAATCTCATAATTGATTTTAAGTTCAATTATTTTTATATTATTTGTTAAA
1 CTTTAAATGATTTCATAACCTCAAAATCGATTTTAAGTTCAATTATTTTTAAATTATTTGTTAAA
* * *
8259 ACATATTATAATTGAATGTCTACC-TCAAAGAAAAGTGAAGAACAAGGCATTTATTGACAAGAAA
66 ACAGATTATAATTGAATGTCTACCGT-AAAGAAAA-TGAAGAAAAAGGCATTCATTGACAAGAAA
8323 AGTCCATTTATTGTCTCTCATTCCTTCGAAAGCCTTATTACTAA
129 AGTCCATTTATTGTCTCTCATTCCTTCGAAAGCCTTATTACTAA
* *
8367 CTTTAAAT-AGTTTCATAACCTCAAAATCGATTTTAAGTTTAATTTTTTTTAAATT-TTTGGTTA
1 CTTTAAATGA-TTTCATAACCTCAAAATCGATTTTAAGTTCAATTATTTTTAAATTATTT-GTTA
* * * * * * * *
8430 AAACAGGTTATAATTGAATGTCTGCCGTGAATAACATGGAGAAAAAGTCATTCATTGAGAAGAAA
64 AAACAGATTATAATTGAATGTCTACCGTAAAGAAAATGAAGAAAAAGGCATTCATTGACAAGAAA
8495 AGTCCATTTAT
129 AGTCCATTTAT
8506 ACTTACCCAT
Statistics
Matches: 118, Mismatches: 18, Indels: 7
0.83 0.13 0.05
Matches are distributed among these distances:
172 39 0.33
173 78 0.66
174 1 0.01
ACGTcount: A:0.37, C:0.12, G:0.12, T:0.39
Consensus pattern (172 bp):
CTTTAAATGATTTCATAACCTCAAAATCGATTTTAAGTTCAATTATTTTTAAATTATTTGTTAAA
ACAGATTATAATTGAATGTCTACCGTAAAGAAAATGAAGAAAAAGGCATTCATTGACAAGAAAAG
TCCATTTATTGTCTCTCATTCCTTCGAAAGCCTTATTACTAA
Found at i:12812 original size:172 final size:170
Alignment explanation
Indices: 12432--13271 Score: 848
Period size: 172 Copynumber: 4.9 Consensus size: 170
12422 NNNNNNNNNN
* * * **
12432 TAAGGCTTTTGAAAGAATGGGTGGCTATAAATAGACTTTTCTTGCCAATGAATGTTTTTTTCTTC
1 TAAGGCTTTTGAAAGAATGAGTGACTATAAATAGACTTTTCTTACCAATGAATACTTTTTTCTTC
** * * * * * * *
12497 ACATTTCTTGAAGTAGACATTTAATTATAGTCTATTTTAACCAAAAATGTAAATAAATTGAACTT
66 ATGTTTCTAGAGGTAGACATTCAATTATAGTCTGTTTTAATC-AAAATATAAAAAAATTGAACTT
* * * *
12562 AAAATCAATTATGAGATTATAAAATCATTTAGAGTGAGTAA
130 AAAATAAATTATGAGATTATAAAACCATTTAAAGCGAGTAA
* * *
12603 TAAGGCTTTTGAAGGAATGAGTGACTATAAATAGACTTTCCTTACCAATGAATACCTTTTTCTTC
1 TAAGGCTTTTGAAAGAATGAGTGACTATAAATAGACTTTTCTTACCAATGAATACTTTTTTCTTC
* * * *
12668 ATGTTTCAAGAGGTAGACATTCAATTATAATCTGTTTTAATGAAAATTATATAAAAAATTGAATT
66 ATGTTTCTAGAGGTAGACATTCAATTATAGTCTGTTTTAATCAAAA-TATA-AAAAAATTGAACT
* * * * * *
12733 TAAAATGAATTTTGAGCTTGTAAAACCATTTAAAGTGGGTAA
129 TAAAATAAATTATGAGATTATAAAACCATTTAAAGCGAGTAA
* * * * * *
12775 TAAGGCTTTTGAAAGAATAAGAGACTATAAATAGACTTTTCTTGCCAATGAATGCGTTGTTCTTC
1 TAAGGCTTTTGAAAGAATGAGTGACTATAAATAGACTTTTCTTACCAATGAATACTTTTTTCTTC
*** * * * *
12840 ATGTTTCTCTTGGTAAACATTGAATTATAATCTGTTTTGAA-CAATAATGTAAAAACAATTGAAC
66 ATGTTTCTAGAGGTAGACATTCAATTATAGTCTGTTTT-AATCAA-AATATAAAAA-AATTGAAC
* * *
12904 CTAAAATTAATTATGAGATTATAAAATCATTTAAAGCGAGTAA
128 TTAAAATAAATTATGAGATTATAAAACCATTTAAAGCGAGTAA
* * * * *
12947 TAAGACTTTTGAAGGAATGAGAGACTAAAAATAGACTTTTCTTACAAATGAATACTTTTTTCTTC
1 TAAGGCTTTTGAAAGAATGAGTGACTATAAATAGACTTTTCTTACCAATGAATACTTTTTTCTTC
* * * * *
13012 ATGTTTCTTGAGGTAGACATTTAATTATAGTCTGTTTACTAA--AAAATGTAAAAAAATTCAGCT
66 ATGTTTCTAGAGGTAGACATTCAATTATAGTCTGTTT--TAATCAAAATATAAAAAAATTGAACT
* * * * * *
13075 TAAAATAAACTATGAGGTTACATAACCTTTTAAAGC-AGGTAC
129 TAAAATAAATTATGAGATTATAAAACCATTTAAAGCGA-GTAA
* * *
13117 TAAGGCTTTTGAAAGAATGGGTGACTATAAAT-GCATTTTTCTTACCAATGATTA-TATTTTTCT
1 TAAGGCTTTTGAAAGAATGAGTGACTATAAATAG-ACTTTTCTTACCAATGAATACT-TTTTTCT
* * * * * *
13180 TCACGTTTCTCA-AAGTAGACATTCAATTATAGTCTGTGTTAATGAAGAATATAAAAAAATTCAT
64 TCATGTTTCT-AGAGGTAGACATTCAATTATAGTCTGTTTTAATCAA-AATATAAAAAAATTGAA
* *
13244 CTTAAAATCAATTATGAGAATATAAAAC
127 CTTAAAATAAATTATGAGATTATAAAAC
13272 TTTTTATTCG
Statistics
Matches: 555, Mismatches: 100, Indels: 28
0.81 0.15 0.04
Matches are distributed among these distances:
168 3 0.01
169 3 0.01
170 128 0.23
171 143 0.26
172 271 0.49
173 6 0.01
174 1 0.00
ACGTcount: A:0.38, C:0.11, G:0.14, T:0.36
Consensus pattern (170 bp):
TAAGGCTTTTGAAAGAATGAGTGACTATAAATAGACTTTTCTTACCAATGAATACTTTTTTCTTC
ATGTTTCTAGAGGTAGACATTCAATTATAGTCTGTTTTAATCAAAATATAAAAAAATTGAACTTA
AAATAAATTATGAGATTATAAAACCATTTAAAGCGAGTAA
Found at i:13641 original size:171 final size:171
Alignment explanation
Indices: 13283--14009 Score: 815
Period size: 171 Copynumber: 4.3 Consensus size: 171
13273 TTTTATTCGT
* * *
13283 AAGAAAAGTCTC-TTTATAATCACCCATTCCTTCAAAAGCCTTATTACTCGCTTTAAATGGTTCT
1 AAGAAAAGTC-CATTTATAGTCACCCATTCCTTCAAAAGCCTTATTACTCACTTTAAATGGTTTT
* * *
13347 ATAATCTCATAAATAATTTTAAGTTAAATTTTTTTACATTTTTTATTAAAACAGACTATAATTGA
65 ATAATCTCATAATTGATTTTAAGTTTAATTTTTTTACATTTTTTATTAAAACAGACTATAATTGA
* *
13412 ATG-CTTGCCTCAGGAAACGA-GTAGAAAAAAGTATTCATTGGC
130 ATGTC-TACCTCAGGAAAC-ATGAAGAAAAAAGTATTCATTGGC
* * * **
13454 AAGAAATGTCCATTTATAGTCTCCCATTCCTTCATAAGCCTTATTACTCGTTTTAAATGGTTTTA
1 AAGAAAAGTCCATTTATAGTCACCCATTCCTTCAAAAGCCTTATTACTCACTTTAAATGGTTTTA
* *
13519 TAATCTCATAATTGATTTTAAGTTTAACTTTTTTAC-TTTATTGT-TTAAAACAGACTGTAATTG
66 TAATCTCATAATTGATTTTAAGTTTAATTTTTTTACATTT-TT-TATTAAAACAGACTATAATTG
* * * *
13582 AATGTCTACCTC-GAGAAACATGAACAAAAAGGTATTTATTGGT
129 AATGTCTACCTCAG-GAAACATGAAGAAAAAAGTATTCATTGGC
* * *
13625 AAGAAAAGTTCATTTATAGTCACCCATTCTTTCAAAAGCCTTATTACTCACTTTAACTGGTTTTA
1 AAGAAAAGTCCATTTATAGTCACCCATTCCTTCAAAAGCCTTATTACTCACTTTAAATGGTTTTA
* * * * *
13690 TAATCTCAAAATTGACTTTAA-TTTCAATTTTTTTAAAATTTTTTATTAAAACAAATTATAATTG
66 TAATCTCATAATTGATTTTAAGTTT-AATTTTTTT-ACATTTTTTATTAAAACAGACTATAATTG
* *
13754 AATGTCTACCTCATGAAACATGAAGAAAAAAGCATTCATTGGC
129 AATGTCTACCTCAGGAAACATGAAGAAAAAAGTATTCATTGGC
* * * * * * *
13797 AAGAAATGTCCATTTATAGTCTCCTATTCTTTCAAAAGACTTATTACTCACTTTAAATGCTTTTG
1 AAGAAAAGTCCATTTATAGTCACCCATTCCTTCAAAAGCCTTATTACTCACTTTAAATGGTTTTA
* * * *
13862 TAATCTCATAATTGATTTTAAGTTCAA-TTTTTTACATTTTTTGTTAAAATAGACTATAATTGAT
66 TAATCTCATAATTGATTTTAAGTTTAATTTTTTTACATTTTTTATTAAAACAGACTATAATTGAA
*** * * ** * *** *
13926 TGTCTGTATTAGAAAATGTGCAGAAAAACCCATTTATTTGG-
131 TGTCTACCTCAGGAAACATGAAGAAAAAAGTATTCA-TTGGC
* * *
13967 AAGAAAAGTCCATTTATAGTCTCTCATTCATTCAAAAGCCTTA
1 AAGAAAAGTCCATTTATAGTCACCCATTCCTTCAAAAGCCTTA
14010 NNNNNNNNNN
Statistics
Matches: 471, Mismatches: 72, Indels: 27
0.83 0.13 0.05
Matches are distributed among these distances:
170 96 0.20
171 235 0.50
172 135 0.29
173 5 0.01
ACGTcount: A:0.35, C:0.15, G:0.11, T:0.39
Consensus pattern (171 bp):
AAGAAAAGTCCATTTATAGTCACCCATTCCTTCAAAAGCCTTATTACTCACTTTAAATGGTTTTA
TAATCTCATAATTGATTTTAAGTTTAATTTTTTTACATTTTTTATTAAAACAGACTATAATTGAA
TGTCTACCTCAGGAAACATGAAGAAAAAAGTATTCATTGGC
Found at i:14583 original size:172 final size:172
Alignment explanation
Indices: 14314--14690 Score: 406
Period size: 172 Copynumber: 2.2 Consensus size: 172
14304 TCATTGGTAG
* * *
14314 GAAAAGTCCATTTATAGTCATCCACTT-CTTCAAAAGCCTTATTACTCATTTTAAATATTTTTAT
1 GAAAAGTCCATTTATAGTCA-CCAATTCCTTCAAAAGCCTTATTACTCAGTTTAAATACTTTTAT
* * * * * * * * *
14378 AATCTTAAATTTTACTTTAAGGTTAATTTTTTTTTCATTTTTGGTTAAAACATATTACAATTGAA
65 AATCTCAAATTTGACTTTAAGGTTAAATTTTTTTACATTATTAGTTAAAACAGATCACAATGGAA
* *
14443 TGTTTA-CATCGAGAAACGA-GAAAAAAAAGGCACTCA-TCGACAA
130 TATCTACCAT-GAGAAAC-ATGAAAAAAAAGGCACTCATTCG-CAA
* * * * *
14486 GAAAAGTGCATTTATAGCCACCAATTCCTTCAAAAGTCTTATTACTCGGTTTAAATGCTTTTATA
1 GAAAAGTCCATTTATAGTCACCAATTCCTTCAAAAGCCTTATTACTCAGTTTAAATACTTTTATA
* * *
14551 ATCTCATAA-TTGA-TTTTAGGTTCAAATTTTTTTACATTATTAGTTCAAACAGATCATAATGGA
66 ATCTCA-AATTTGACTTTAAGGTT-AAATTTTTTTACATTATTAGTTAAAACAGATCACAATGGA
** * * *
14614 ATATCTACCATGAGAAACATGAGGAAAAAGGTATTCATTTGCAA
129 ATATCTACCATGAGAAACATGAAAAAAAAGGCACTCATTCGCAA
*
14658 GAAAAGTCCATTTATAGTCACCCATTCCTTCAA
1 GAAAAGTCCATTTATAGTCACCAATTCCTTCAA
14691 NNNNNNNNNN
Statistics
Matches: 169, Mismatches: 30, Indels: 12
0.80 0.14 0.06
Matches are distributed among these distances:
171 14 0.08
172 148 0.88
173 7 0.04
ACGTcount: A:0.36, C:0.16, G:0.11, T:0.37
Consensus pattern (172 bp):
GAAAAGTCCATTTATAGTCACCAATTCCTTCAAAAGCCTTATTACTCAGTTTAAATACTTTTATA
ATCTCAAATTTGACTTTAAGGTTAAATTTTTTTACATTATTAGTTAAAACAGATCACAATGGAAT
ATCTACCATGAGAAACATGAAAAAAAAGGCACTCATTCGCAA
Done.