Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018399788.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_303.0, 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: 11070
ACGTcount: A:0.22, C:0.08, G:0.09, T:0.23
Warning! 4196 characters in sequence are not A, C, G, or T
Found at i:2218 original size:171 final size:168
Alignment explanation
Indices: 1649--2265 Score: 548
Period size: 171 Copynumber: 3.6 Consensus size: 168
1639 NNNNNNNNTG
* * * *
1649 AAGAAAAAAGCATTCATTGG-AAAGAAAAGTCCGTTTATAGTCACCCATACCTTTAAAAACCTCA
1 AAGAAAAAAGCATTCATTGGCAAA-AAAAGTCCATTTATAGTCACCCATTCC-TTCAAAAGCTCA
********** * *
1713 TTACTCGCTTTAAATGGTTTTNNNNNNNNNNAATTGATTTTAAGTTGAATTTTTTATATTTTTTG
64 TTACTCGCTTTAAATGGTTTTATAATGCCTTAATTGATTTTAAGTTGAATTTTTTATAATTTTAG
** * * *
1778 TTAAAATGGACTATAATTGGATGTCTACCTCA-AGAAACGTA
129 TTAAAACAGACTATAATTGAATGTATA--TCATAGAAACGCA
* * * *******
1819 AAG-AAAAAGACATTAATTGGCAAGAAAAGTCTATTTATAGTCACCCATTCCTTCAANNNNNNNN
1 AAGAAAAAAG-CATTCATTGGCAAAAAAAGTCCATTTATAGTCACCCATTCCTTCAA-AAGCTCA
** * * * * * *
1883 NNACTCACTTTAAATGGTTTTATAAT-CTCTAAATTGATTTAAATTTGAAATCTTTGTACAATTT
64 TTACTCGCTTTAAATGGTTTTATAATGC-CTTAATTGATTTTAAGTTG-AAT-TTTTTATAATTT
* * * * *
1947 TAGTTAAAACATATTATAATTGAATGTCA-ACCTTAGAAA-ACA
126 TAGTTAAAACAGACTATAATTGAATGT-ATATCATAGAAACGCA
** * * *
1989 TGAAGAACTAGGCATACATTGGCAAGAAAAA-TCCATTTATAGTCACACATTCCTTCAAAAGTCT
1 --AAGAAAAAAGCATTCATTGGCAA-AAAAAGTCCATTTATAGTCACCCATTCCTTCAAAAG-CT
*
2053 CATTACTCGCTTTAAATAGTTTTATAATGCCTTAATTGATTTTAAGTTGAAGTTTTTTATAATTT
62 CATTACTCGCTTTAAATGGTTTTATAATGCCTTAATTGATTTTAAGTTGAA-TTTTTTATAATTT
2118 TAGTTAAAACAGACTATAATTGAATGTATATCATGAGAAACGCA
126 TAGTTAAAACAGACTATAATTGAATGTATATCAT-AGAAACGCA
*
2162 AAGAAAAAAGCATTCATTGGCAAAAAAAGTCCATTTATATTCACCCATAT-CTTCAAAAGCTTCA
1 AAGAAAAAAGCATTCATTGGCAAAAAAAGTCCATTTATAGTCACCCAT-TCCTTCAAAAGC-TCA
*
2226 TTACTCGCTTTAAATGGTTTTATAATGCCATAATTGATTT
64 TTACTCGCTTTAAATGGTTTTATAATGCCTTAATTGATTT
2266 NNNNNNNNNN
Statistics
Matches: 348, Mismatches: 78, Indels: 41
0.75 0.17 0.09
Matches are distributed among these distances:
169 10 0.03
170 77 0.22
171 136 0.39
172 115 0.33
173 10 0.03
ACGTcount: A:0.36, C:0.14, G:0.12, T:0.35
Consensus pattern (168 bp):
AAGAAAAAAGCATTCATTGGCAAAAAAAGTCCATTTATAGTCACCCATTCCTTCAAAAGCTCATT
ACTCGCTTTAAATGGTTTTATAATGCCTTAATTGATTTTAAGTTGAATTTTTTATAATTTTAGTT
AAAACAGACTATAATTGAATGTATATCATAGAAACGCA
Found at i:7000 original size:171 final size:170
Alignment explanation
Indices: 6609--7600 Score: 951
Period size: 171 Copynumber: 5.8 Consensus size: 170
6599 NNNNNNNAAG
* * *
6609 GCTTTTGAAGGAATGGGTGACTGTTAATGGACTTTTCTTGCCAATGAATGCTTTTTAT-TTCACG
1 GCTTTTGAAGGAATGGGTGACTATAAATGGACTTTTCTTGCCAATGAATGCTTTTT-TCTTTACG
* * * * * * **
6673 TTTCTTAAGGTTGACATTCAATTATAATCTTTTTTAACCAAAAATATACGAAGAATTCAAATTTC
65 TTTCTTAAGGTAGACATTCAATTATAGTCTGTTTTAACCAAAAATGTA-AAAAAATTCAAATTAA
* * * * * * *
6738 AATCAATTTTGAG-GTTAGAAAAACATGTAAAGTAAGTATTAA
129 AATCAATTATG-GCATTATAAAACCATTTAAAGTGAGTATCAA
* *
6780 GGCTTTTGAAGGAATGGGTGACTATAAATGGACTTTTCTTGCAAATGAATGCTTTTTTCTTTGCG
1 -GCTTTTGAAGGAATGGGTGACTATAAATGGACTTTTCTTGCCAATGAATGCTTTTTTCTTTACG
* * * * *
6845 TTTCTTGAGGTAGACATCCAATTATGGTTTGTTTTAACCAAAAATGTAAAAAAATTCAACTTAAA
65 TTTCTTAAGGTAGACATTCAATTATAGTCTGTTTTAACCAAAAATGTAAAAAAATTCAAATTAAA
* * * ** *
6910 ATCAATTATCGTATTATAAAACCTTTTAAAGCAAGTAGTGAA
130 ATCAATTATGGCATTATAAAACCATTTAAAGTGAGTA-TCAA
* ** * ** *
6952 GCTTTTGAA-GATTTGGGTGACTATAAATAAACTTTTCTTGCCAATGAATGC-CTTTTCCATGCG
1 GCTTTTGAAGGA-ATGGGTGACTATAAATGGACTTTTCTTGCCAATGAATGCTTTTTTCTTTACG
* * * *
7015 TTTCTCAAGATAGACATGCAATTATAGTCTGTTTTAACCAAAAA-GATAAAAAATTTCAAATTAA
65 TTTCTTAAGGTAGACATTCAATTATAGTCTGTTTTAACCAAAAATG-TAAAAAAATTCAAATTAA
* * *
7079 AATTAATTATGGCATTATAAAACCATTTAAAGCGAGTAATCAG
129 AATCAATTATGGCATTATAAAACCATTTAAAGTGAGT-ATCAA
* * * * * * *
7122 GCTTTTGAACGAATGGGTGACTATAAATGGATTTTTCTTGTCGATGTATGCCTTGTTT-TTTATG
1 GCTTTTGAAGGAATGGGTGACTATAAATGGACTTTTCTTGCCAATGAATG-CTTTTTTCTTTACG
* * * * * * * * *
7186 TTTGC-TAAGATTGACATTCAATTATAATCTGTGTTAACAAAAAATGTGCAAAGAATTTAAATTT
65 TTT-CTTAAGGTAGACATTCAATTATAGTCTGTTTTAACCAAAAATGT-AAAAAAATTCAAATTA
* * *
7250 AAATCGATTTTGAG-ATTATAAAACCATTTAAAGTGAGTAACAA
128 AAATCAATTATG-GCATTATAAAACCATTTAAAGTGAGTATCAA
* * * *
7293 GGCTTTTAAAGGAAAT-GGTGACTATAATTGGACTTTTCTTGCCAATGAGTGCCTTTTTCTTTAC
1 -GCTTTTGAAGG-AATGGGTGACTATAAATGGACTTTTCTTGCCAATGAATGCTTTTTTCTTTAC
* * * ** * * *
7357 GTTTCTTGAGGTAGACATTCAATTGTAGTCGGTTTTAGTCAAAAATATAAAGAAATTCAACTTAA
64 GTTTCTTAAGGTAGACATTCAATTATAGTCTGTTTTAACCAAAAATGTAAAAAAATTCAAATTAA
* *
7422 AATCAATTATGGCGTTATAAAACCATTTAAAGTGAGTAATGAA
129 AATCAATTATGGCATTATAAAACCATTTAAAGTGAGT-ATCAA
* * * * * *
7465 GTTTTTGAAGGTATGGGTGACTGTAAATGGACTTTTCTTGCAAATGAATGGTTTTTTCTTTATGT
1 GCTTTTGAAGGAATGGGTGACTATAAATGGACTTTTCTTGCCAATGAATGCTTTTTTCTTTACGT
* * * * * * *
7530 TTCTCAAGGTAGGCATTCAATT-TAGTTTGTTTTATCTAAAAATGTACAAAGAATTCAAATTTAA
66 TTCTTAAGGTAGACATTCAATTATAGTCTGTTTTAACCAAAAATGTA-AAAAAATTCAAATTAAA
7594 ATCAATT
130 ATCAATT
7601 TTGAGATTAT
Statistics
Matches: 664, Mismatches: 135, Indels: 43
0.79 0.16 0.05
Matches are distributed among these distances:
169 1 0.00
170 161 0.24
171 270 0.41
172 228 0.34
173 4 0.01
ACGTcount: A:0.34, C:0.12, G:0.17, T:0.38
Consensus pattern (170 bp):
GCTTTTGAAGGAATGGGTGACTATAAATGGACTTTTCTTGCCAATGAATGCTTTTTTCTTTACGT
TTCTTAAGGTAGACATTCAATTATAGTCTGTTTTAACCAAAAATGTAAAAAAATTCAAATTAAAA
TCAATTATGGCATTATAAAACCATTTAAAGTGAGTATCAA
Found at i:8517 original size:171 final size:170
Alignment explanation
Indices: 8273--8667 Score: 445
Period size: 171 Copynumber: 2.3 Consensus size: 170
8263 NNNNNNTTAC
* * * *
8273 AAAACCATTTAGAGTAAG-AATTAAGGCTTTTGAAGGAAT-GAGTGACTATAAATAAACTTTTCT
1 AAAACCATTTAAAGCAAGTAATGAA-GCTTTTGAA-GATTAG-GTGACTATAAATAAACTTTTCT
* *
8336 TGCAAATGAATGCCTTTTTCTTTACGTTTTTCCAAG-TAGACATCCAATTATGGTCTGTTTTAAC
63 TGCAAATGAATGCCTTTTTCTTTACGTTTCT-CAAGATAGACATCCAATTATAGTCTGTTTTAAC
********** *
8400 CAAAAANNNNNNNNNNTTCAACTTAAAATCAATTATGGCATTAA
127 CAAAAATGTAAAAAACTTCAACTCAAAATCAATTATGGCATTAA
** *
8444 AAAACCATTTAAAGCAAGTAATGAAGCTTTTGAAGATTTAGGTGACTATAAATGTACTTTTTTTG
1 AAAACCATTTAAAGCAAGTAATGAAGCTTTTGAAGA-TTAGGTGACTATAAATAAACTTTTCTTG
* * * *
8509 CCAATGAATGCCTTTTTCTTTGCGTTTCTCAAGATAGACATGCAATTATAGTTTGTTTTAACCAA
65 CAAATGAATGCCTTTTTCTTTACGTTTCTCAAGATAGACATCCAATTATAGTCTGTTTTAACCAA
*
8574 AAATGTAAAAAACTTCAACTCAAAATCAATTATGGCATTAT
130 AAATGTAAAAAACTTCAACTCAAAATCAATTATGGCATTAA
* * * * *
8615 AAAACCATTTAAGGCGAGTAATGAGGCTTTTGAAAGAATGGGTGACTATAAAT
1 AAAACCATTTAAAGCAAGTAATGAAGCTTTTG-AAGATTAGGTGACTATAAAT
8668 NNNNNNNNNN
Statistics
Matches: 189, Mismatches: 30, Indels: 10
0.83 0.13 0.04
Matches are distributed among these distances:
170 6 0.03
171 173 0.92
172 10 0.05
ACGTcount: A:0.36, C:0.13, G:0.15, T:0.34
Consensus pattern (170 bp):
AAAACCATTTAAAGCAAGTAATGAAGCTTTTGAAGATTAGGTGACTATAAATAAACTTTTCTTGC
AAATGAATGCCTTTTTCTTTACGTTTCTCAAGATAGACATCCAATTATAGTCTGTTTTAACCAAA
AATGTAAAAAACTTCAACTCAAAATCAATTATGGCATTAA
Found at i:10091 original size:171 final size:170
Alignment explanation
Indices: 9715--10103 Score: 450
Period size: 172 Copynumber: 2.3 Consensus size: 170
9705 NNNNNNNNNN
* * * * * *
9715 TTTAAAGTGTGTAATAAGGCTTTTGAAGGAATGGGTGACTATTAATGGACTTCTGTTGCCAATAA
1 TTTAAAGTGAGTAATAAGGCTTTTGAAGGAATAGGTGACTATAAATAGACTTCTCTTGCCAACAA
* * * *
9780 ATGACTTTTCTTTCATGTTTCTTGACGTTGACATTCAATTATAATCTTTTTTTACCAAAAATGTA
66 ATGAATTTTCTTTCATGTTTCTCGACGTTGACATTCAACTATAATCTTTTTTAACCAAAAATGTA
*
9845 TAAAGAATTCAAATTTCAAACAATTTTGATATTACAAAACCA
131 TAAAGAATTCAAA--TCAAAAAATTTTGATATTACAAAACCA
* * * *
9887 TTTAAAGTGAGTATTAAGGTTTTTGAAGGAATAGGTGATTATAAATAGACTTTTCTTGCCAACAA
1 TTTAAAGTGAGTAATAAGGCTTTTGAAGGAATAGGTGACTATAAATAGACTTCTCTTGCCAACAA
* *
9952 AT-ATATATTTCTTT-TTGTTTCTCGA-GATTGACATTCAACTATAGTCTTTTTTAACCAAAAAT
66 ATGA-AT-TTTCTTTCATGTTTCTCGACG-TTGACATTCAACTATAATCTTTTTTAACCAAAAAT
* * *
10014 GTA-AAATACTTC-AA-CAAAAAATTAATT-ACGTCTTTACAAAACCA
128 GTATAAAGAATTCAAATCAAAAAATT--TTGA--T-ATTACAAAACCA
*
10058 TTTAAAGTGAGTAATGAGGCTTTTGAAGGAATAGGTGACTATAAAT
1 TTTAAAGTGAGTAATAAGGCTTTTGAAGGAATAGGTGACTATAAAT
10104 GNNNNNNNNN
Statistics
Matches: 185, Mismatches: 24, Indels: 17
0.82 0.11 0.08
Matches are distributed among these distances:
167 8 0.04
168 1 0.01
169 2 0.01
170 3 0.02
171 62 0.34
172 102 0.55
173 7 0.04
ACGTcount: A:0.36, C:0.12, G:0.14, T:0.38
Consensus pattern (170 bp):
TTTAAAGTGAGTAATAAGGCTTTTGAAGGAATAGGTGACTATAAATAGACTTCTCTTGCCAACAA
ATGAATTTTCTTTCATGTTTCTCGACGTTGACATTCAACTATAATCTTTTTTAACCAAAAATGTA
TAAAGAATTCAAATCAAAAAATTTTGATATTACAAAACCA
Done.