Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018397917.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_1222.0, 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: 3715
ACGTcount: A:0.29, C:0.10, G:0.11, T:0.27
Warning! 888 characters in sequence are not A, C, G, or T
Found at i:388 original size:170 final size:171
Alignment explanation
Indices: 177--501 Score: 451
Period size: 170 Copynumber: 1.9 Consensus size: 171
167 NNNNNNNNNN
* * *
177 ATTATGAGATTGTAAAACTATTCAAAGCAAGTAATAAGGCTTTCGAAGGCATGGGAGACTATAAA
1 ATTATGAGATTATAAAACCATTCAAAGCAAGTAATAAGGCTTCCGAAGGCATGGGAGACTATAAA
* * * *
242 TGGACTTTTCATGCCAATAGATATCT-TT-TTCTACATGTTTCTTGAGGTAGGCATTTAATTATA
66 TGAACTTTTCATGCCAATAGATATCTCTTCTT-TACA-GTTTCTCGAGGTAGACATTCAATTATA
305 ATCTGTTTTAATAAAAAATATAAAAAATATCTATCTAAAATCA
129 ATCTGTTTTAATAAAAAATATAAAAAATATCTATCTAAAATCA
* * * *
348 ATTATTAGATTATAAAACCATTTAAAG-AGAGTAA-AAGGCTTCCGAAGGTATGGGTGACTATAA
1 ATTATGAGATTATAAAACCATTCAAAGCA-AGTAATAAGGCTTCCGAAGGCATGGGAGACTATAA
** ** *
411 ATGAACTTTTGTTGCCAATAGATATCTCTTCTTTTGAGTTTCTCGAGGTAGATATTCAATTATAA
65 ATGAACTTTTCATGCCAATAGATATCTCTTCTTTACAGTTTCTCGAGGTAGACATTCAATTATAA
476 TCTGTTTTAATAAAAAATATAAAAAA
130 TCTGTTTTAATAAAAAATATAAAAAA
502 NNNNNNNNNN
Statistics
Matches: 135, Mismatches: 16, Indels: 7
0.85 0.10 0.04
Matches are distributed among these distances:
170 101 0.75
171 32 0.24
172 2 0.01
ACGTcount: A:0.38, C:0.11, G:0.15, T:0.35
Consensus pattern (171 bp):
ATTATGAGATTATAAAACCATTCAAAGCAAGTAATAAGGCTTCCGAAGGCATGGGAGACTATAAA
TGAACTTTTCATGCCAATAGATATCTCTTCTTTACAGTTTCTCGAGGTAGACATTCAATTATAAT
CTGTTTTAATAAAAAATATAAAAAATATCTATCTAAAATCA
Found at i:833 original size:170 final size:170
Alignment explanation
Indices: 537--846 Score: 414
Period size: 170 Copynumber: 1.8 Consensus size: 170
527 NNNNNNNNNN
* * *
537 ATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTCGAAGGCAATGGTGACTATAAA
1 ATTATGAGATTATAAAAACATTTAAACCGAGTAATAAGGCTTTCGAAGGCAATGGTGACTACAAA
* * * * * *
602 TGGGCTTTCCTTACCAGTGGACATCTTTTTCTTTATGTTTTCTAAGGTAGATATTAATTATAATC
66 TGGGATTTCCTTACCAATGGACATCTTTTTCTTCATCTTTTCTAAGGTAAACATTAATTATAATC
667 TGTTTTAATAAAAACTATAAAAAAATTCAGCTTAAAATCT
131 TGTTTTAATAAAAACTATAAAAAAATTCAGCTTAAAATCT
* * *
707 ATTATTAGGTTATAAAAACATTTAAACCGAGTAATAAGGCTTTCGAAGGC-ATGGGTGAGTACAA
1 ATTATGAGATTATAAAAACATTTAAACCGAGTAATAAGGCTTTCGAAGGCAAT-GGTGACTACAA
* *
771 AT-GGATTGTTCTTACCAATGG-CTATC-TTTTCTTCA-CTTTTCTCGAGGTAAACATTCAATTA
65 ATGGGATT-TCCTTACCAATGGAC-ATCTTTTTCTTCATCTTTTCT-AAGGTAAACATT-AATTA
832 TAATCTGTTTTAATA
126 TAATCTGTTTTAATA
847 NNNNNNNNNN
Statistics
Matches: 121, Mismatches: 14, Indels: 10
0.83 0.10 0.07
Matches are distributed among these distances:
168 6 0.05
169 24 0.20
170 91 0.75
ACGTcount: A:0.35, C:0.13, G:0.15, T:0.37
Consensus pattern (170 bp):
ATTATGAGATTATAAAAACATTTAAACCGAGTAATAAGGCTTTCGAAGGCAATGGTGACTACAAA
TGGGATTTCCTTACCAATGGACATCTTTTTCTTCATCTTTTCTAAGGTAAACATTAATTATAATC
TGTTTTAATAAAAACTATAAAAAAATTCAGCTTAAAATCT
Found at i:1287 original size:171 final size:171
Alignment explanation
Indices: 994--1329 Score: 394
Period size: 171 Copynumber: 2.0 Consensus size: 171
984 NNNNNNNNNN
* * * * *
994 TGACTATAAATGGACTTTTCTTGCCAATGGATATCTTTTTCTTTACGTTTCTCATGGTAAACATT
1 TGACTATAAATAGACTTTTCTTACCAATGGATATCTTTTTCTTCACATTTCTCAAGGTAAACATT
* *
1059 CAATTATAATTTATTTTAATAAAAATATAAAAAAAAATTAACTTAAAATCAATTATGAAATGAT-
66 AAATTATAATTTATTTGAATAAAAATATAAAAAAAAATTAACTTAAAATCAATTATGAAATGATA
* *
1123 AAAACTATTTAAAACGAGTAATAAGGGTTTCAAAGGTATGTG
131 AAAAC-ATTCAAAACGAGTAATAAGGCTTTCAAAGGTATGTG
* * *
1165 TGACTATAAGTAGA-TTTGTCTTACCAATGGATATCTTTTTCTTCATATTTCT-AGAGGTAGACA
1 TGACTATAAATAGACTTT-TCTTACCAATGGATATCTTTTTCTTCACATTTCTCA-AGGTAAACA
* ** * * *
1228 TTAAATTATAATTTGTTTGAATAAAAA-ATGTAAAAAAA-TACAGCTTGAAATCTATTATGAGAT
64 TTAAATTATAATTTATTTGAATAAAAATATAAAAAAAAATTA-A-CTTAAAATCAATTATGAAAT
** * *
1291 TTTAAAAACATTCACAACGAGTAATAAGGCTTTCGAAGG
127 GATAAAAACATTCAAAACGAGTAATAAGGCTTTCAAAGG
1330 CATGGGNNNN
Statistics
Matches: 138, Mismatches: 22, Indels: 10
0.81 0.13 0.06
Matches are distributed among these distances:
169 2 0.01
170 14 0.10
171 117 0.85
172 5 0.04
ACGTcount: A:0.40, C:0.10, G:0.13, T:0.37
Consensus pattern (171 bp):
TGACTATAAATAGACTTTTCTTACCAATGGATATCTTTTTCTTCACATTTCTCAAGGTAAACATT
AAATTATAATTTATTTGAATAAAAATATAAAAAAAAATTAACTTAAAATCAATTATGAAATGATA
AAAACATTCAAAACGAGTAATAAGGCTTTCAAAGGTATGTG
Found at i:2186 original size:179 final size:179
Alignment explanation
Indices: 1854--2267 Score: 402
Period size: 179 Copynumber: 2.4 Consensus size: 179
1844 TTCCTGAGGC
* * *
1854 AGACATTCAATTATTATCTGTTTTAACAAAAAAAACTAAAAAATTTAACGTAAAATCAATAATGA
1 AGACATTCAACTATAATCTGTTTTAACAAAAAAAACTAAAAAATTCAACGTAAAATCAATAATGA
* * ** * *
1919 GATTATAAAACCATTTAAAGTGAGTAATGAGGCTTTTAAAGGCATAGGTTACTATAAATAGACCT
66 GATTATAAAACCATTTAAAGCGAGTAATAAGGCTTCCAAAGACATAGGTGACTATAAATAGACCT
* * *
1984 TTCTTGTCAATTGATACCTTTTTCTTCACATTTCTATGTTTCTCAAGGT
131 TTCATGCCAATGGATACCTTTTTCTTCACATTTCTATGTTTCTCAAGGT
* * *** * *
2033 AGACATTTAACTATAATCTGTTTT-ACTAAAAAGTGTAAAACAATTCAACTTAAAATCAATTATG
1 AGACATTCAACTATAATCTGTTTTAACAAAAAAAACTAAAA-AATTCAACGTAAAATCAATAATG
* * * * * *
2097 AGATTATAAAACTA-TTAAACGCGAGTAATAAGGCTTCCGAAGACTTGGGTGACTATCAATCGAC
65 AGATTATAAAACCATTTAAA-GCGAGTAATAAGGCTTCCAAAGACATAGGTGACTATAAATAGAC
* * **
2161 TTTTCATGCCAATGGATA--TCTTT-TT--CA--TC-ATGTTTCTCAAAAT
129 CTTTCATGCCAATGGATACCTTTTTCTTCACATTTCTATGTTTCTCAAGGT
* * * * * *
2204 AGACATTCAAATATAATCTATTGTAA-AAAAAATAC-ATAAAAATTCAACTTAAAATCAATTATG
1 AGACATTCAACTATAATCTGTTTTAACAAAAAAAACTA-AAAAATTCAACGTAAAATCAATAATG
2267 A
65 A
2268 NNNNNNNNNN
Statistics
Matches: 194, Mismatches: 37, Indels: 17
0.78 0.15 0.07
Matches are distributed among these distances:
170 25 0.13
171 40 0.21
172 3 0.02
174 2 0.01
176 2 0.01
177 4 0.02
178 17 0.09
179 101 0.52
ACGTcount: A:0.41, C:0.14, G:0.11, T:0.34
Consensus pattern (179 bp):
AGACATTCAACTATAATCTGTTTTAACAAAAAAAACTAAAAAATTCAACGTAAAATCAATAATGA
GATTATAAAACCATTTAAAGCGAGTAATAAGGCTTCCAAAGACATAGGTGACTATAAATAGACCT
TTCATGCCAATGGATACCTTTTTCTTCACATTTCTATGTTTCTCAAGGT
Found at i:2849 original size:171 final size:170
Alignment explanation
Indices: 1785--2863 Score: 708
Period size: 171 Copynumber: 6.3 Consensus size: 170
1775 AAGGCTTTTA
* * ** * * *
1785 AAGGCATGGATGACTATAAATGGACTTTTCATGGGAATGGATATCCTTTTT-TTTCACGGTTC-C
1 AAGGCATGGGTGACTATAAATGGACTTTTCTTGCCAATGGATAT-CTTTTTCTTCCATGTTTCTC
* * ** * *
1848 TGAGGCAGACATTCAATTATTATCTGTTTTAACAAAAAAAACTAAAAAATTTAACGTAAAATCAA
65 -GAGGTAGACATTCAATTATAATCTGTTTT-A-AAAAAAATGTAAAAAATTCAACTTAAAATCAA
* * * * ***
1913 TAATGAGATTATAAAACCATTTAAAGTGAGTAATGAGGCTTTTA
127 TTATGAGATTATAAAACCATTTAAAGCGAGCAATAAGGCTTCCG
* * * * * * *
1957 AAGGCATAGGTTACTATAAATAGACCTTTCTTGTCAATTGATACCTTTTTCTTCACATTTCTATG
1 AAGGCATGGGTGACTATAAATGGACTTTTCTTGCCAATGGATATCTTTTTCTT--C----C-ATG
* * * * *
2022 TTTCTCAAGGTAGACATTTAACTATAATCTGTTTTACTAAAAAGTGTAAAACAATTCAACTTAAA
59 TTTCTCGAGGTAGACATTCAATTATAATCTGTTTTA-AAAAAAATGTAAAA-AATTCAACTTAAA
* *
2087 ATCAATTATGAGATTATAAAACTA-TTAAACGCGAGTAATAAGGCTTCCG
122 ATCAATTATGAGATTATAAAACCATTTAAA-GCGAGCAATAAGGCTTCCG
* * * * * * *
2136 AAGACTTGGGTGACTATCAATCGACTTTTCATGCCAATGGATATCTTTTTCAT-CATGTTTCTCA
1 AAGGCATGGGTGACTATAAATGGACTTTTCTTGCCAATGGATATCTTTTTCTTCCATGTTTCTCG
** * * * **
2200 AAATAGACATTCAAATATAATCTATTGTAAAAAAAATACATAAAAATTCAACTTAAAATCAATTA
66 AGGTAGACATTCAATTATAATCTGTTTTAAAAAAAATGTA-AAAAATTCAACTTAAAATCAATTA
********** * * * *
2265 TGANNNNNNNNNNCCATTTAAAAC-AACTAATAAGGCTCCCA
130 TGAGATTATAAAACCATTTAAAGCGAGC-AATAAGGCTTCCG
* * ** * * ** *
2306 AAGGCATGGGAGACTATAAATGGGCTTTTCTTTTCAATGAATAAT-TTTTT-TTTCACCTTTCAC
1 AAGGCATGGGTGACTATAAATGGACTTTTCTTGCCAATGGAT-ATCTTTTTCTTCCATGTTTCTC
* * * * * *
2369 GAGGTAAACATTCAATTATAATTTGTTTTAACAAAAAA-GAAAAAAAAATCCAACCTAAAATTAA
65 GAGGTAGACATTCAATTATAATCTGTTTTAA-AAAAAATG--TAAAAAATTCAACTTAAAATCAA
* * ** * * *
2433 ATATGGGATTATAATGCAATTT-AAGCCAAGTAATAAGGCTTCCG
127 TTATGAGATTATAAAACCATTTAAAG-CGAGCAATAAGGCTTCCG
* * * *
2477 AAGTCATGGGTGACTATAAATGGACTTTTTTTGCCAATAGATATCTTTCTCTT-CATGTTTCTCG
1 AAGGCATGGGTGACTATAAATGGACTTTTCTTGCCAATGGATATCTTTTTCTTCCATGTTTCTCG
* * * *********
2541 AGGTAGAGATGCAATTATAATTTGTTTTAATAAAAAANNNNNNNNNNTT-AACTTAAAATCAATT
66 AGGTAGACATTCAATTATAATCTGTTTTAA-AAAAAA-TGTAAAAAATTCAACTTAAAATCAATT
* * *
2605 ATGAGATTATTAAACCATTTAAAGCAAGCAATAAGGCTTTCG
129 ATGAGATTATAAAACCATTTAAAGCGAGCAATAAGGCTTCCG
* ********** *
2647 AAGGCATGGATGACTNNNNNNNNNNTTTTCTTGTCAATGGATATCTTTTTCTTCGCAT-TTTC-C
1 AAGGCATGGGTGACTATAAATGGACTTTTCTTGCCAATGGATATCTTTTTCTTC-CATGTTTCTC
* * *
2710 GAGGTTGACATTCAATTATAATCTATTTTAATTAAAAATGTAAAAAAGTTCAACTTAAAATCAAT
65 GAGGTAGACATTCAATTATAATCTGTTTTAA-AAAAAATGTAAAAAA-TTCAACTTAAAATCAAT
* * * *
2775 TATGAGATTGTAAAATCATTTAAAGCGAGCAATACGGCTTTCG
128 TATGAGATTATAAAACCATTTAAAGCGAGCAATAAGGCTTCCG
* * *
2818 AAGGTATGGGTGACTATAAATAGACTTTTCTTACCAATGGATATCT
1 AAGGCATGGGTGACTATAAATGGACTTTTCTTGCCAATGGATATCT
2864 NNNNNNNNNN
Statistics
Matches: 678, Mismatches: 199, Indels: 61
0.72 0.21 0.07
Matches are distributed among these distances:
169 2 0.00
170 231 0.34
171 265 0.39
172 44 0.06
178 18 0.03
179 117 0.17
180 1 0.00
ACGTcount: A:0.36, C:0.14, G:0.14, T:0.34
Consensus pattern (170 bp):
AAGGCATGGGTGACTATAAATGGACTTTTCTTGCCAATGGATATCTTTTTCTTCCATGTTTCTCG
AGGTAGACATTCAATTATAATCTGTTTTAAAAAAAATGTAAAAAATTCAACTTAAAATCAATTAT
GAGATTATAAAACCATTTAAAGCGAGCAATAAGGCTTCCG
Found at i:3495 original size:171 final size:168
Alignment explanation
Indices: 3201--3709 Score: 507
Period size: 171 Copynumber: 3.0 Consensus size: 168
3191 NNTTTCGAAG
* *
3201 GCATGGGTGACTATAAATAGACTTTTCTTACTAATGGATATC-TTTTCTTTATGTTTCTCGAGG-
1 GCAT-GGTGACTATAAATGGACTTTTCTTAC-AATGGATATCTTTTTCTTTACGTTTCT-GAGGT
* * * *
3264 AAACATTCAATTATAATATGTTTTAATAAAAAATATAAAAAAATTCAAT-GCAGAATCAATTATG
63 AGACATTCAATTATAATATGTTTTAA-AAAAAATGTAAAAAAATTCAATCTCAAAATCAATTATG
* ** *
3328 AGATTGTAAAACTATTCGAAGTGAATAATAGGGCTTTCAAAA
127 AGATTATAAAACTATTTAAAGTGAATAATAAGGCTTTCAAAA
*
3370 GCATGGCTGATTATAAATGGACTTTTCTTATCAATGGATATCTTTTTCTTTACGTTTCATGAGGT
1 GCATGG-TGACTATAAATGGACTTTTCTTA-CAATGGATATCTTTTTCTTTACGTTTC-TGAGGT
* * *
3435 AGACATTCAATTATTATATGTTTCAACCAAAAATGTAAAAAAATTC-ATCTCAAAATCAATTATG
63 AGACATTCAATTATAATATGTTTTAA-AAAAAATGTAAAAAAATTCAATCTCAAAATCAATTATG
* * * *
3499 AGATTAT-AAAGTCATTTAAAG-CAAGTAATAAGGCTTCCGAAA
127 AGATTATAAAACT-ATTTAAAGTGAA-TAATAAGGCTTTCAAAA
* * * * *
3541 G-ATTGAGTGACTATAAATGGACTTTTCTTGCCAATAGATATTTTTTTCTTTGCATTTCCTGAGG
1 GCA-TG-GTGACTATAAATGGACTTTTCTT-ACAATGGATATCTTTTTCTTTACGTTT-CTGAGG
* * * * * * * * *
3605 TAGACATTTAGTTATAATCTATTTTAATAAAAA-GTATAAAAAAATCGA-CTTAAAATTAATTAT
62 TAGACATTCAATTATAATATGTTTTAAAAAAAATGTA-AAAAAATTCAATCTCAAAATCAATTAT
*
3668 GAGATTATAAAAAC-ATTTAAAGTGAGTAATAAGGCTTTCAAA
126 GAGATTAT-AAAACTATTTAAAGTGAATAATAAGGCTTTCAAA
3710 GGTATG
Statistics
Matches: 283, Mismatches: 40, Indels: 33
0.79 0.11 0.09
Matches are distributed among these distances:
168 2 0.01
169 38 0.13
170 84 0.30
171 154 0.54
172 5 0.02
ACGTcount: A:0.39, C:0.11, G:0.14, T:0.36
Consensus pattern (168 bp):
GCATGGTGACTATAAATGGACTTTTCTTACAATGGATATCTTTTTCTTTACGTTTCTGAGGTAGA
CATTCAATTATAATATGTTTTAAAAAAAATGTAAAAAAATTCAATCTCAAAATCAATTATGAGAT
TATAAAACTATTTAAAGTGAATAATAAGGCTTTCAAAA
Done.