Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018402118.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_5211.0, 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: 3467
ACGTcount: A:0.31, C:0.09, G:0.11, T:0.30
Warning! 677 characters in sequence are not A, C, G, or T
Found at i:379 original size:171 final size:169
Alignment explanation
Indices: 2--672 Score: 593
Period size: 171 Copynumber: 3.9 Consensus size: 169
1 A
* * *
2 GCTTTTGAAGGAAT-AGGTGACTATAAATGGACTTTTCTTACCAATGAATGCCTATTTCTTCACG
1 GCTTTTGAAGGAATGA-GAGACTATAAATAGACTTTTCTTGCCAATGAATG-CTATTTCTTCACG
** * * *
66 TTTCTTGATATCGACATTCAATTATAATCTGTTTTAAGCAAAAATGTAAAGAAAA-TGAACATAA
64 TTTCTTGAGGTAGACATTCAATTATAGTCTGTTTTAACCAAAAATGTAAA-AAAATTGAACATAA
* **
130 AATCAATTTTGAGATAATAAAGCCATTTAAAGCGGGTAATAAG
128 AATCAATTTTGAGATAATAAAACCATTTAAAG-TAGTAATAAG
* * ** * * * *
173 GCTTTTGAAGAAATGGGAGGTTAGAAGTAGACTTTTCTTGCCAATGAATGCTTTCTTTTTCACGT
1 GCTTTTGAAGGAATGAGAGACTATAAATAGACTTTTCTTGCCAATGAATGCTAT-TTCTTCACGT
* *
238 TTCTTGAGGTAAACATTCAATTATAGTCTGTTTTAACCAAGAATGTAAAAAACATTGAACAT-AA
65 TTCTTGAGGTAGACATTCAATTATAGTCTGTTTTAACCAAAAATGTAAAAAA-ATTGAACATAAA
302 ATCAATTTTGAGATAATAAAACCATTTAAAGATAGTAATAAG
129 ATCAATTTTGAGATAATAAAACCATTTAAAG-TAGTAATAAG
* * * *********
344 CCTTTTGAAGGAATGAAAGACTATAAATGGACTTTTCTTGCCAATNNNNNNNNNNTTCTTCACGT
1 GCTTTTGAAGGAATGAGAGACTATAAATAGACTTTTCTTGCCAAT-GAATGCTATTTCTTCACGT
** * * * * * *
409 TTCTCAAGGTAGACATTTAATTATAGTATGTTTTAACTAAAAATGTAAAAAAATTCATCCTAAAA
65 TTCTTGAGGTAGACATTCAATTATAGTCTGTTTTAACCAAAAATGTAAAAAAATTGAACATAAAA
* * * * *
474 TCAATTATAAGATTAT-AAACCATTAAAAGTGTGTAATAAG
130 TCAATTTTGAGATAATAAAACCATTTAAAGT-AGTAATAAG
* * * * * *
514 GTTTTTGAAGGAATGAGAGACTATAAATAGACTTTTGTT-CTTAATTAATGCCTTTTTC-TCTAT
1 GCTTTTGAAGGAATGAGAGACTATAAATAGACTTTTCTTGC-CAATGAATG-CTATTTCTTC-AC
** * * * ** *
577 GTTT-TCACAAGTAGGCATTCAATTATAGTTTGTTTTAATGAAAAATGT-AAAAAATTGAACTTA
63 GTTTCT-TGAGGTAGACATTCAATTATAGTCTGTTTTAACCAAAAATGTAAAAAAATTGAACATA
* * * *
640 AAAGCAATTATGAGATTATAAAACTATTTAAAG
127 AAATCAATTTTGAGATAATAAAACCATTTAAAG
673 CGNNNNNNNN
Statistics
Matches: 401, Mismatches: 87, Indels: 25
0.78 0.17 0.05
Matches are distributed among these distances:
169 34 0.08
170 122 0.30
171 238 0.59
172 7 0.02
ACGTcount: A:0.38, C:0.11, G:0.15, T:0.35
Consensus pattern (169 bp):
GCTTTTGAAGGAATGAGAGACTATAAATAGACTTTTCTTGCCAATGAATGCTATTTCTTCACGTT
TCTTGAGGTAGACATTCAATTATAGTCTGTTTTAACCAAAAATGTAAAAAAATTGAACATAAAAT
CAATTTTGAGATAATAAAACCATTTAAAGTAGTAATAAG
Found at i:2208 original size:170 final size:162
Alignment explanation
Indices: 1892--2486 Score: 362
Period size: 170 Copynumber: 3.5 Consensus size: 162
1882 GTTTCTTGAG
* *
1892 GTAGACATTCAATTATAGTCTGGTTTAATGAAAAATGTAAAAAAATTAAATTTAAAATCAATTAT
1 GTAGACATTCAATTATAGTCTGGTTTAATGAAAAATATAAAAAAATTAAACTTAAAATCAATTAT
* * ** *
1957 GAGATAATAAAACTATTTAAAGCGAGTGATAAGGCTTTTGAAGGAATGAGTGAATACAAGTAGAC
66 GAGACAATAAAACCATTTAAAGCGAGCAATAAGGCTTTTGAAGGAATGAGTGAATACAAATAGAC
* *
2022 TTTTCTTGCCAATGAATG-CTTTTTTNNNNNNNNNNCTCAAT
131 TTTTCTTACAAATGAATGTCTTTTTT----------CTCAAT
* * * * *
2063 GTAGACATTCAATTATAGTCTGTTTTAAT-CAAAATATAAAAAAATTCAACTTAAATTCAATTTT
1 GTAGACATTCAATTATAGTCTGGTTTAATGAAAAATATAAAAAAATTAAACTTAAAATCAATTAT
* * * * * * *
2127 GAGGCAATAAGACCATTTAAAGTGGGCAATAAGGCTTTTGAATGAATTG-GTGACTATAAATAGA
66 GAGACAATAAAACCATTTAAAGCGAGCAATAAGGCTTTTGAAGGAA-TGAGTGAATACAAATAGA
* * *
2191 TTTTTTTTACAAATGAATGTCTTTTTCTTCATGTTTCTCAAC
130 CTTTTCTTACAAATGAATG------TCTT--T-TTTCTCAAT
* * * * * *
2233 ATAGATATTTAATTATAATCT-GTTTAACTAAAAAAGTA-AAAAAAACTTGAACTTAAAATCAAT
1 GTAGACATTCAATTATAGTCTGGTTTAA-TGAAAAA-TATAAAAAAA-TTAAACTTAAAATCAAT
* ** * * * * * *
2296 TTTGAGATTATGAAACCATTTAAAGTGAGCAATAAGGCTTTTGAAGAAATGGGTGACTA-TAATA
63 TATGAGACAATAAAACCATTTAAAGCGAGCAATAAGGCTTTTGAAGGAATGAGTGAATACAAATA
2360 GACTTTTCCTGT-C-AATGAATATGTTTTACTTCATGTTTCTC-AT
128 GACTTTT-CT-TACAAATG-A-ATG---T-CTT--T-TTTCTCAAT
* * * * * * * *
2403 GGTAAACATTCAATTATTGTCTGTTTTAATAAAAAATACAAAAAACTTCAACTTAAAATTAATTA
1 -GTAGACATTCAATTATAGTCTGGTTTAATGAAAAATATAAAAAAATTAAACTTAAAATCAATTA
* **
2468 TTAGATTATAAAACCATTT
65 TGAGACAATAAAACCATTT
2487 NNNNNNNNNN
Statistics
Matches: 343, Mismatches: 57, Indels: 49
0.76 0.13 0.11
Matches are distributed among these distances:
169 5 0.01
170 156 0.45
171 98 0.29
172 73 0.21
173 4 0.01
177 3 0.01
179 1 0.00
180 3 0.01
ACGTcount: A:0.39, C:0.10, G:0.13, T:0.36
Consensus pattern (162 bp):
GTAGACATTCAATTATAGTCTGGTTTAATGAAAAATATAAAAAAATTAAACTTAAAATCAATTAT
GAGACAATAAAACCATTTAAAGCGAGCAATAAGGCTTTTGAAGGAATGAGTGAATACAAATAGAC
TTTTCTTACAAATGAATGTCTTTTTTCTCAAT
Found at i:2569 original size:171 final size:171
Alignment explanation
Indices: 1862--3156 Score: 753
Period size: 171 Copynumber: 7.6 Consensus size: 171
1852 NNNNNNNNNN
* ** *
1862 ATGAATACCTTTTTCTTCATGTTTCTTGAGGTAGACATTCAATTATAGTCTGGTTTAA-TGAAAA
1 ATGAATATCTTTTTCTTCATGTTTCTCAAGGTAGACATTCAATTATAGTCTGTTTTAACT-AAAA
* * * * * * * **
1926 ATGTAAAAAAA-TTAAATTTAAAATCAATTATGAGATAATAAAACTATTTAAAGCGAGTGATAAG
65 A-ATAAAAAAACTTCAACTTAAAATCAATTATTAGATTATAAAACCATTTAAAGTGAGCAATAAG
* * * * *
1990 GCTTTTGAAGGAAT-GAGTGAATACAAGTAGACTTTTCTTGCCA
129 GCTTTTGAAGGAATAG-GTGACTATAAATAGATTTTTCTTGCTA
* ******** *
2033 ATGAAT-GCTTTTT-TNNNNNNNNNNCTCAATGTAGACATTCAATTATAGTCTGTTTTAA-TCAA
1 ATGAATATCTTTTTCT--TCATGTTTCTCAAGGTAGACATTCAATTATAGTCTGTTTTAACT-AA
* * *** * *
2095 AATATAAAAAAA-TTCAACTTAAATTCAATT-TTGAGGCAATAAGACCATTTAAAGTGGGCAATA
63 AAAATAAAAAAACTTCAACTTAAAATCAATTATT-AGATTATAAAACCATTTAAAGTGAGCAATA
* * * * *
2158 AGGCTTTTGAATGAATTGGTGACTATAAATAGATTTTTTTTACAA
127 AGGCTTTTGAAGGAATAGGTGACTATAAATAGATTTTTCTTGCTA
* ** * * *
2203 ATGAATGTCTTTTTCTTCATGTTTCTCAACATAGATATTTAATTATAATCTG-TTTAACTAAAAA
1 ATGAATATCTTTTTCTTCATGTTTCTCAAGGTAGACATTCAATTATAGTCTGTTTTAACTAAAAA
* *
2267 AGTAAAAAAAACTTGAACTTAAAATCAATT-TTGAGATTATGAAACCATTTAAAGTGAGCAATAA
66 A-T-AAAAAAACTTCAACTTAAAATCAATTATT-AGATTATAAAACCATTTAAAGTGAGCAATAA
* * * *
2331 GGCTTTTGAAGAAATGGGTGACTAT-AATAGACTTTTCCTG-TCA
128 GGCTTTTGAAGGAATAGGTGACTATAAATAGATTTTTCTTGCT-A
* * * * *
2374 ATGAATATGTTTTACTTCATGTTTCTCATGGTAAACATTCAATTATTGTCTGTTTTAA-TAAAAA
1 ATGAATATCTTTTTCTTCATGTTTCTCAAGGTAGACATTCAATTATAGTCTGTTTTAACTAAAAA
* **********
2438 ATACAAAAAACTTCAACTTAAAATTAATTATTAGATTATAAAACCATTTNNNNNNNNNNATAAGG
66 ATA-AAAAAACTTCAACTTAAAATCAATTATTAGATTATAAAACCATTTAAAGTGAGCAATAAGG
* *
2503 CTTTTGAAGGAATAGGAGACTATAAATGGATTTTTCTTGCTA
130 CTTTTGAAGGAATAGGTGACTATAAATAGATTTTTCTTGCTA
*
2545 ATGAATA-CTTTTTTCTTCATGTTTCTCAAGGTAGACATTTC-ATTATAGTCTGTTTGAACTAAA
1 ATGAATATC-TTTTTCTTCATGTTTCTCAAGGTAGACA-TTCAATTATAGTCTGTTTTAACTAAA
** * * ******
2608 AATATAAAAAAA-TTCAACTTAAAATCGGTTATGAGATTATAAAACTATTTAAAGTGAGNNNNNN
64 AA-ATAAAAAAACTTCAACTTAAAATCAATTATTAGATTATAAAACCATTTAAAGTGAGCAATAA
**************** * *
2672 NNNNNNNNNNNNNNNGGGTGACTATAAATGGACTTTTCTT-CTCA
128 GGCTTTTGAAGGAATAGGTGACTATAAATAGATTTTTCTTGCT-A
** * * * *
2716 ATGAATGGCTTTTTCTATGCAT-TTCCT-GAGGTAGGA-ATTCAATTATAGTCTGTTTTGACGAA
1 ATGAATATCTTTTTCT-T-CATGTTTCTCAAGGTA-GACATTCAATTATAGTCTGTTTTAACTAA
* * * * * * *
2778 AAACGT-AAAAAA-TTCAACTTAAAATCATTTATGAGATTTTTAAACCATTTAAAG-CATGTAAT
63 AAA-ATAAAAAAACTTCAACTTAAAATCAATTATTAGATTATAAAACCATTTAAAGTGA-GCAAT
* * * * * *
2840 AAGGCTTTTGAGGGAAT-GAGTGACTCTAAATGGACTTTTCTTCCAA
126 AAGGCTTTTGAAGGAATAG-GTGACTATAAATAGATTTTTCTTGCTA
* ** * * ** * * * *
2886 ATAAATAGGTTTTTCTGT-ATATTTTTTGAGGTAGGCATTC-ATGTATAGTTTCTTTTAAC-CAA
1 ATGAATATCTTTTTCT-TCATGTTTCTCAAGGTAGACATTCAAT-TATAGTCTGTTTTAACTAAA
* * * * ** *
2948 AAATGTAAAAAACTTCAATTTAAAATCAATTATTAGATTATTAAACTATTTAAAGCAAGTAATAA
64 AAAT-AAAAAAACTTCAACTTAAAATCAATTATTAGATTATAAAACCATTTAAAGTGAGCAATAA
* ** * * * *
3013 GCCTTTCAAAAGAATAGGAGAC-ATAAAT-GTACTTTTCTTGCCA
128 GGCTTTTGAAGGAATAGGTGACTATAAATAG-ATTTTTCTTGCTA
* * * * **
3056 ATGAAT-TTTTTTTCTTCATTTTTTTCGAGGTAGACATTCAATTATAGAATGTTTTAACTAAATA
1 ATGAATATCTTTTTCTTCATGTTTCTCAAGGTAGACATTCAATTATAGTCTGTTTTAACTAAA-A
** * *
3120 TGTAAACAAA-TTCAACTTAAAATCAATTATGAGATTA
65 AATAAAAAAACTTCAACTTAAAATCAATTATTAGATTA
3157 NNNNNNNNNN
Statistics
Matches: 863, Mismatches: 218, Indels: 88
0.74 0.19 0.08
Matches are distributed among these distances:
168 4 0.00
169 90 0.10
170 328 0.38
171 337 0.39
172 98 0.11
173 6 0.01
ACGTcount: A:0.36, C:0.11, G:0.13, T:0.36
Consensus pattern (171 bp):
ATGAATATCTTTTTCTTCATGTTTCTCAAGGTAGACATTCAATTATAGTCTGTTTTAACTAAAAA
ATAAAAAAACTTCAACTTAAAATCAATTATTAGATTATAAAACCATTTAAAGTGAGCAATAAGGC
TTTTGAAGGAATAGGTGACTATAAATAGATTTTTCTTGCTA
Found at i:2874 original size:170 final size:166
Alignment explanation
Indices: 2688--3156 Score: 496
Period size: 170 Copynumber: 2.8 Consensus size: 166
2678 NNNNNNNNNG
**
2688 GGTGACTATAAATGGACTTTTCTTCTCAATGAATGGCTTTTTCTATGCATTTCCTGAGGTAGGAA
1 GGTGACTATAAATGGACTTTTCTTC-CAATGAATGG-TTTTTCT-T-CATTTTTTGAGGTAGGAA
* * * * * *
2753 TTCAATTATAGTCTGTTTTGACGAAAAACGTAAAAAATTCAACTTAAAATCATTTATGAGATTTT
62 TTCAATTATAGTATGTTTTAACCAAAAATGTAAAAAATTCAACTTAAAATCAATTATGAGATTAT
* * ** **
2818 TAAACCATTTAAAGCATGTAATAAGGCTTTTGAGGGAAT-
127 TAAACCATTTAAAGCAAGTAATAAGCCTTTCAAAAGAATA
* * * *
2857 GAGTGACTCTAAATGGACTTTTCTTCCAAATAAATAGGTTTTTCTGTATATTTTTTGAGGTAGGC
1 G-GTGACTATAAATGGACTTTTCTTCC-AATGAAT-GGTTTTTCT-T-CATTTTTTGAGGTAGGA
* * * *
2922 ATTC-ATGTATAGTTTCTTTTAACCAAAAATGTAAAAAACTTCAATTTAAAATCAATTATTAGAT
61 ATTCAAT-TATAGTATGTTTTAACCAAAAATGTAAAAAA-TTCAACTTAAAATCAATTATGAGAT
*
2986 TATTAAACTATTTAAAGCAAGTAATAAGCCTTTCAAAAGAATA
124 TATTAAACCATTTAAAGCAAGTAATAAGCCTTTCAAAAGAATA
* * **
3029 GGAGAC-ATAAATGTACTTTTCTTGCCAATGAATTTTTTTTCTTCATTTTTTTCGAGGTA-GACA
1 GGTGACTATAAATGGACTTTTCTT-CCAATGAATGGTTTTTCTTCA-TTTTTT-GAGGTAGGA-A
* * *
3092 TTCAATTATAGAATGTTTTAACTAAATATGTAAACAAATTCAACTTAAAATCAATTATGAGATTA
62 TTCAATTATAGTATGTTTTAACCAAAAATGTAAA-AAATTCAACTTAAAATCAATTATGAGATTA
3157 NNNNNNNNNN
Statistics
Matches: 249, Mismatches: 39, Indels: 24
0.80 0.12 0.08
Matches are distributed among these distances:
167 1 0.00
168 8 0.03
169 69 0.28
170 106 0.43
171 64 0.26
172 1 0.00
ACGTcount: A:0.36, C:0.12, G:0.14, T:0.38
Consensus pattern (166 bp):
GGTGACTATAAATGGACTTTTCTTCCAATGAATGGTTTTTCTTCATTTTTTGAGGTAGGAATTCA
ATTATAGTATGTTTTAACCAAAAATGTAAAAAATTCAACTTAAAATCAATTATGAGATTATTAAA
CCATTTAAAGCAAGTAATAAGCCTTTCAAAAGAATA
Done.