Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018403282.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_957.0, 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: 30538
ACGTcount: A:0.19, C:0.06, G:0.06, T:0.19
Warning! 15278 characters in sequence are not A, C, G, or T
Found at i:5084 original size:171 final size:169
Alignment explanation
Indices: 4812--5137 Score: 415
Period size: 171 Copynumber: 1.9 Consensus size: 169
4802 TTATAACCTC
* * * **
4812 ATAATTGATTTTAATTTGAATTTTTTATATATTTTTTAAAACATATTATAATTGAATGTTTGCCT
1 ATAATTGATTTTAAGTTGAATTTTTTATATATTTTTTAAAACAGATTATAATTAAATGTCCGCCT
* *
4877 TGAGAAATGTCAAGAAAAAGATATCCATTAGCAAGAAAAGTCCATTTATAGCCACGCAA-GCCTT
66 TGAGAAACGTCAAGAAAAAGATATCCATTAGCAAGAAAAGTCCATATATAGCCAC-CAATGCCTT
*
4941 CAAAAGCCTTACTACTCGCTTTAAATATTTTTTTAATCCT
130 CAAAAGCCTTACTACTCACTTTAAATATTTTTTTAATCCT
* *
4981 ATAATTAGA-TTTAAGTTGAATGTTTTTATATTTTTTTATTAAAACCGATTATAATTAAATGTCC
1 ATAATT-GATTTTAAGTTGAAT-TTTTTATA-TATTTT-TTAAAACAGATTATAATTAAATGTCC
* * * * * **
5045 GCTTTG-GCAACGTGAAGAAAAAGATATCCATTGGCAAGAAAAGTCCATATATTGTTACCAATGC
62 GCCTTGAGAAACGTCAAGAAAAAGATATCCATTAGCAAGAAAAGTCCATATATAGCCACCAATGC
* *
5109 CTTCGAAAGCCTTATTACTCACTTTAAAT
127 CTTCAAAAGCCTTACTACTCACTTTAAAT
5138 GCTTTTGTAA
Statistics
Matches: 133, Mismatches: 19, Indels: 8
0.83 0.12 0.05
Matches are distributed among these distances:
169 17 0.13
170 13 0.10
171 77 0.58
172 26 0.20
ACGTcount: A:0.36, C:0.14, G:0.12, T:0.38
Consensus pattern (169 bp):
ATAATTGATTTTAAGTTGAATTTTTTATATATTTTTTAAAACAGATTATAATTAAATGTCCGCCT
TGAGAAACGTCAAGAAAAAGATATCCATTAGCAAGAAAAGTCCATATATAGCCACCAATGCCTTC
AAAAGCCTTACTACTCACTTTAAATATTTTTTTAATCCT
Found at i:7641 original size:171 final size:161
Alignment explanation
Indices: 7408--7736 Score: 354
Period size: 171 Copynumber: 2.0 Consensus size: 161
7398 ATATCCATCA
* * * *
7408 GCAAGAAATGTCCATTTATACTCACTGATGCCTTCAAAAGCCTTATTACTCGTTTTAAATGATTT
1 GCAAGAAAAGTCCATTTATACTCACTGATGCCTTCAAAAGCATTATTACTCGCTTCAAATGATTT
********** * *
7473 TANNNNNNNNNNATTGATTTTAATTTAAATTTTTTTATATTTTTTAATAAAATAGATTATAATTG
66 TATAACATCATAATTGATTTTAATTT-AAGTTTTTTATATTTTTTAATAAAATAGATTACAATTG
7538 AATCTTTGCCTCGAGAAACGTGA-AGAAAAANNNNNNNNNNG
130 AATCTTTGCCTCGAGAAACGTGAGAGAAAAA----------G
* * *
7579 GCAAGAAAAGTCCATTTATATTCACTTATGCCTTCAAAAGTATTATTACTCGCTTCAAATGATTT
1 GCAAGAAAAGTCCATTTATACTCACTGATGCCTTCAAAAGCATTATTACTCGCTTCAAATGATTT
* *
7644 TATAACATCATAATTGATTTTAATTTGAGTTTTTTATATTTTTTATTAAAATAGATTACAATTGA
66 TATAACATCATAATTGATTTTAATTTAAGTTTTTTATATTTTTTAATAAAATAGATTACAATTGA
*
7709 ATGTTTGCCTCGAGAAACGTGAGAGAAA
131 ATCTTTGCCTCGAGAAACGTGAGAGAAA
7737 GATATCCATT
Statistics
Matches: 135, Mismatches: 22, Indels: 2
0.85 0.14 0.01
Matches are distributed among these distances:
170 56 0.41
171 79 0.59
ACGTcount: A:0.33, C:0.11, G:0.12, T:0.38
Consensus pattern (161 bp):
GCAAGAAAAGTCCATTTATACTCACTGATGCCTTCAAAAGCATTATTACTCGCTTCAAATGATTT
TATAACATCATAATTGATTTTAATTTAAGTTTTTTATATTTTTTAATAAAATAGATTACAATTGA
ATCTTTGCCTCGAGAAACGTGAGAGAAAAAG
Found at i:8909 original size:172 final size:171
Alignment explanation
Indices: 8527--8944 Score: 466
Period size: 172 Copynumber: 2.4 Consensus size: 171
8517 NNNNNNNNNN
* * * *
8527 ATTGGCAAGAAAAGTCCATTTAGAGTCACCCATGCTTTTGAAAGCCTTATTACTTGTATTAAATA
1 ATTGGCAAGAAAAGTCCATTTTGAGTCACCCATGCTTTCGAAAGCCTTATTACTCGCATTAAATA
8592 ATTTTATAACCTCATAATTGATTTTGATTTGAATTTTTTTATATATTTTTTTAAAACAGATTATA
66 ATTTTATAACCTCATAATTGATTTTGATTTGAATTTTTTTATATATTTTTTTAAAACAGATTATA
** * **********
8657 ATTGAATGTCTACTTTGAGAAACNNNNNNNNNNAAGTATCC
131 ATCAAATGTCTACTTTAAGAAACAGTGAAGAAAAAGTATCC
* * *
8698 ATTGGTAAGAAAAGTCCATTTAT-AGTCACTCAGGCTTTCGAAAGCCTTATTACTCGCATTAAAT
1 ATTGGCAAGAAAAGTCCATTT-TGAGTCACCCATGCTTTCGAAAGCCTTATTACTCGCATTAAAT
********** * *
8762 AATTTTATAANNNNNNNNNNGATTTTGATTTGAATTTTTTT-TATATTTTTTATTAAAATAGGTT
65 AATTTTATAACCTCATAATTGATTTTGATTTGAATTTTTTTATATA-TTTTT-TTAAAACAGATT
*
8826 ATAATCAAATGTCT-TTCTTAAGAAAC-GTGAAGAAAAAGATATCC
128 ATAATCAAATGTCTACT-TTAAGAAACAGTGAAGAAAAAG-TATCC
8870 ATTGGCAAGAAAAGTCCATTTTGAGTCACCCATGCTTTCGAAAGCCTTATTACTCGCATTAAATA
1 ATTGGCAAGAAAAGTCCATTTTGAGTCACCCATGCTTTCGAAAGCCTTATTACTCGCATTAAATA
8935 ATTTTATAAC
66 ATTTTATAAC
8945 ANNNNNNNNN
Statistics
Matches: 205, Mismatches: 36, Indels: 11
0.81 0.14 0.04
Matches are distributed among these distances:
170 4 0.02
171 97 0.47
172 104 0.51
ACGTcount: A:0.33, C:0.13, G:0.12, T:0.38
Consensus pattern (171 bp):
ATTGGCAAGAAAAGTCCATTTTGAGTCACCCATGCTTTCGAAAGCCTTATTACTCGCATTAAATA
ATTTTATAACCTCATAATTGATTTTGATTTGAATTTTTTTATATATTTTTTTAAAACAGATTATA
ATCAAATGTCTACTTTAAGAAACAGTGAAGAAAAAGTATCC
Found at i:10143 original size:171 final size:160
Alignment explanation
Indices: 9921--10314 Score: 441
Period size: 171 Copynumber: 2.3 Consensus size: 160
9911 GAAGGGAAAG
* *
9921 ATATCCATTGGCAAGAAAAGTCTATTTAGAGTCACCCATGCTTTTGAAAGCCTTATTATTCGCAT
1 ATATCCATTGGCAAGAAAAGTCAATTTAGAGTCACCCATGCTTTTGAAAGCCTTATTACTCGCAT
* * *
9986 TAAATATATTTATAACCTCATAATTGATTTTAATTTGATTTTTTTTATATTTTTTATTAAAATAA
66 TAAATATATTTATAACCTCATAAGTGATTTTAATTTGAATTTTTTTATATATTTT-TTAAAATAA
10051 ATTATAATTAAATGTCTACTTTANNNNNNNNNNAGAAAAAT
130 ATTATAATTAAATGTCTACTTTA----------AGAAAAAT
* * *
10092 ATATCCATTGGTAAGAAAAGTCAATTTATAGTCGCCCATG-TTTTCGAAAGCCTTATTACTCGCA
1 ATATCCATTGGCAAGAAAAGTCAATTTAGAGTCACCCATGCTTTT-GAAAGCCTTATTACTCGCA
* * *
10156 TTAAATGTTTTTATAACCTCATAAGTGATTTTAATTTGAATTTTTTTATATATTTTTTAAAATAG
65 TTAAATATATTTATAACCTCATAAGTGATTTTAATTTGAATTTTTTTATATATTTTTTAAAATAA
* *
10221 ATTATAATTGAATATCAGTCTTGAGAAACGTGAAG-AAAAT
130 ATTATAATT-AA-AT--GTC-T-----ACTTTAAGAAAAAT
*
10261 GATATCCATTGGCAAGAAAAGTCCATTTAGAGTCACCCATGCTTTTGAAAGCCT
1 -ATATCCATTGGCAAGAAAAGTCAATTTAGAGTCACCCATGCTTTTGAAAGCCT
10315 NNNNNNNNNN
Statistics
Matches: 193, Mismatches: 17, Indels: 27
0.81 0.07 0.11
Matches are distributed among these distances:
169 5 0.03
170 67 0.35
171 111 0.58
172 2 0.01
174 3 0.02
175 1 0.01
180 4 0.02
ACGTcount: A:0.35, C:0.12, G:0.12, T:0.39
Consensus pattern (160 bp):
ATATCCATTGGCAAGAAAAGTCAATTTAGAGTCACCCATGCTTTTGAAAGCCTTATTACTCGCAT
TAAATATATTTATAACCTCATAAGTGATTTTAATTTGAATTTTTTTATATATTTTTTAAAATAAA
TTATAATTAAATGTCTACTTTAAGAAAAAT
Found at i:18314 original size:170 final size:171
Alignment explanation
Indices: 17988--18323 Score: 406
Period size: 170 Copynumber: 2.0 Consensus size: 171
17978 GGTCGCATTA
* *
17988 AATGTTTTTATAACCTCATAATTGATTTTAATTTGAAAGTTTTTATATTTTCTATTAAAACAGAT
1 AATGATTTTATAACCTCATAATTCATTTTAATTTGAAAGTTTTTATATTTTCTATTAAAACAGAT
* * * *
18053 TATAATTGAATGTTTACCTCAAGACACGTGAAGAAAAAGATATCCATTGGCAAGAAAAGTTCATT
66 TATAATTGAATGTCTACCTCAAGAAACGTGAAGAAAAAGATATCCATGGGCAAGAAAAGTCCATT
**********
18118 TATAGTCNNNNNNNNNNTCAAAAGCCTTATCACTCGGTTTT
131 TATAGTCAGCAATGCCTTCAAAAGCCTTATCACTCGGTTTT
** * *
18159 AATGATTTTATAACCTCATAATTCATTTTAATTTGAATTTTTTTATATTTT-TATTAAAGCATAT
1 AATGATTTTATAACCTCATAATTCATTTTAATTTGAAAGTTTTTATATTTTCTATTAAAACAGAT
* * * *
18223 TATAATTGGATGTCTACCTTAAGAAACGTGAAGAAAAAGATATCCATGGGTAA-AACAGGTCCAT
66 TATAATTGAATGTCTACCTCAAGAAACGTGAAGAAAAAGATATCCATGGGCAAGAA-AAGTCCAT
* * *
18287 TTGTAGTCAGCAATGCCTTCGAAAGCCTTATTACTCG
130 TTATAGTCAGCAATGCCTTCAAAAGCCTTATCACTCG
18324 CNNNNNNNNN
Statistics
Matches: 137, Mismatches: 27, Indels: 3
0.82 0.16 0.02
Matches are distributed among these distances:
169 2 0.01
170 88 0.64
171 47 0.34
ACGTcount: A:0.34, C:0.13, G:0.13, T:0.37
Consensus pattern (171 bp):
AATGATTTTATAACCTCATAATTCATTTTAATTTGAAAGTTTTTATATTTTCTATTAAAACAGAT
TATAATTGAATGTCTACCTCAAGAAACGTGAAGAAAAAGATATCCATGGGCAAGAAAAGTCCATT
TATAGTCAGCAATGCCTTCAAAAGCCTTATCACTCGGTTTT
Found at i:20371 original size:172 final size:171
Alignment explanation
Indices: 20063--20383 Score: 382
Period size: 172 Copynumber: 1.9 Consensus size: 171
20053 GTAAACGTTC
* * * *
20063 AATTATAATCTATTTTTATAAAAATTGGAAAAAATTTCAACTTAAAACCAATTATGAAGGTTATA
1 AATTATAATCTATTTTAATAAAAAATAGAAAAAAGTTCAACTTAAAACCAATTATG-AGGTTATA
* * * * * * * * * *
20128 CAATCATTTAAAGTGAGTAATAAGGCTTTTAAATGCATGGGTGGTAATGAATGGACTTTTTTTGT
65 AAAACATTTAAAGTGAGTAATAAGACTTTTAAAGGCATGGGTGCTAATAAATAGACCTTTCTTGC
20193 CAATGGATATCTTTTTCTTCACATTTCTCAAAGTAAATATTT
130 CAATGGATATCTTTTTCTTCACATTTCTCAAAGTAAATATTT
* *
20235 AATTATAATCTATTTTAATAAAAAAATATAAAAAAGGTT-AACTTAAAACTAATTATG-GGATTG
1 AATTATAATCTATTTTAAT-AAAAAATAGAAAAAA-GTTCAACTTAAAACCAATTATGAGG-TT-
* *
20298 A-AAAAACATTTAAAGTGAGTAATAAGAC-TTTATAAGGTATGGGTGACT-ATAAATATACCTTT
62 ATAAAAACATTTAAAGTGAGTAATAAGACTTTTA-AAGGCATGGGTG-CTAATAAATAGACCTTT
20360 CTTGCCAATGGATATCTTTTTCTT
125 CTTGCCAATGGATATCTTTTTCTT
20384 TNNNNNNNNN
Statistics
Matches: 125, Mismatches: 18, Indels: 12
0.81 0.12 0.08
Matches are distributed among these distances:
171 6 0.05
172 86 0.69
173 31 0.25
174 2 0.02
ACGTcount: A:0.40, C:0.09, G:0.13, T:0.38
Consensus pattern (171 bp):
AATTATAATCTATTTTAATAAAAAATAGAAAAAAGTTCAACTTAAAACCAATTATGAGGTTATAA
AAACATTTAAAGTGAGTAATAAGACTTTTAAAGGCATGGGTGCTAATAAATAGACCTTTCTTGCC
AATGGATATCTTTTTCTTCACATTTCTCAAAGTAAATATTT
Found at i:28783 original size:170 final size:161
Alignment explanation
Indices: 28518--28841 Score: 339
Period size: 170 Copynumber: 2.0 Consensus size: 161
28508 ATCAATTATG
* * * * * *
28518 AGGTTATAAAATTATTAAAAGCGAGTGATAAGATTTTTGAAGGCGTGGGTGACTATAAATTGACT
1 AGGTTATAAAATTATTAAAACCGAGTAATAAGATTTTCGAAAGCATGGGTGACTATAAATAGACT
* * * *
28583 TTTCTTGCCAATGGATAGAGTTTGCTTCACGTTTCTTAA-AGTAGACATTCAATTATAATTTG-T
66 TTTCTTGCCAATAGATAGAGTTTCCTTCACGTTTCTTAAGA-CAGACATTCAATTATAATCTGTT
*
28646 TTAATAAAAAATATGAAAAAATTTAATTTAAA
130 TTAATAAAAAATATAAAAAAATTTAATTTAAA
* *
28678 NNNNNNNNNNAGGTTATAAAATTATTTAATCCGAGTAATAAGGA-TTTCGAAAGCATGGGTGACT
1 ----------AGGTTATAAAATTATTAAAACCGAGTAATAA-GATTTTCGAAAGCATGGGTGACT
* * *** *
28742 CTAAATAGACTTTTCTTGCCAGTAGATATCTTTTCCTTCACGTTTCTTAAGACAGACATTTAATT
55 ATAAATAGACTTTTCTTGCCAATAGATAGAGTTTCCTTCACGTTTCTTAAGACAGACATTCAATT
*
28807 TTAATCTGTTTTAATAAAAAATATAAAAAAATTTA
120 ATAATCTGTTTTAATAAAAAATATAAAAAAATTTA
28842 NNNNNNNNNN
Statistics
Matches: 131, Mismatches: 20, Indels: 5
0.84 0.13 0.03
Matches are distributed among these distances:
170 103 0.79
171 28 0.21
ACGTcount: A:0.36, C:0.10, G:0.15, T:0.36
Consensus pattern (161 bp):
AGGTTATAAAATTATTAAAACCGAGTAATAAGATTTTCGAAAGCATGGGTGACTATAAATAGACT
TTTCTTGCCAATAGATAGAGTTTCCTTCACGTTTCTTAAGACAGACATTCAATTATAATCTGTTT
TAATAAAAAATATAAAAAAATTTAATTTAAA
Done.