Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018402705.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_5768.0, 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, 862
Length: 1437
ACGTcount: A:0.37, C:0.15, G:0.15, T:0.33
Found at i:387 original size:170 final size:170
Alignment explanation
Indices: 1--1436 Score: 662
Period size: 171 Copynumber: 8.3 Consensus size: 170
* *
1 CAATTATGAGAATATAAAACCATTTAAAGCAAGTAATAAGGCTTTCGAAGGCTTAAGTGATTATA
1 CAATTATGAGAATATAAAACCATTTAAAGCGAGTAATAAGGCTTTCGAAGGCTTAAGTGACTATA
* * ** * *
66 AATGGACTTTTCTCT-CCCATTGATGGCTTTTGCTTCACGTTTCTTGAGGTAGACTTTCGATTAT
66 AA-GG-CTTTTCT-TGCCAATGGATGGCTTTTGCTTCACGTTTCCCGAGGTAGACATTCAATTAT
* *
130 AACATATTTTAACCAAAAGTGTAAAAAAAATCCATCTTAAAAT
128 AACATATTTTAACCAAAAATGTAAAAAAAATCCAACTTAAAAT
* * *
173 GAATTATGAGAATATAAAACCTTTTAAAGCGAGTAATAAGGCTTTCAAAGGCTTAAGTGACTATC
1 CAATTATGAGAATATAAAACCATTTAAAGCGAGTAATAAGGCTTTCGAAGGCTTAAGTGACTAT-
* * * *
238 AAAAGCTTTTCTTGCTAATGGATGGGTTTTGCTTCAGGTTTCCCGAGGCTAG-CATTCAATTATA
65 AAAGGCTTTTCTTGCCAATGGATGGCTTTTGCTTCACGTTTCCCGAGG-TAGACATTCAATTATA
* *
302 ACATATTTTAACCAAAAATGT-AAAAAATTCTAACTTAAAAT
129 ACATATTTTAACCAAAAATGTAAAAAAAATCCAACTTAAAAT
* * *
343 CAATTATGAGAATGTAAAACCATTTAAAGTGAGTAATAAGGCTTTTGAAGGCTTAAGTGACTATA
1 CAATTATGAGAATATAAAACCATTTAAAGCGAGTAATAAGGCTTTCGAAGGCTTAAGTGACTATA
* * **** *
408 ATGGCTTTTCTTGCCAATGGATGGCTTTTG-TT-A-----CCC-ATGG-ATGGC-TTTTGCT-TC
66 AAGGCTTTTCTTGCCAATGGATGGCTTTTGCTTCACGTTTCCCGA-GGTA-GACATTCAATTATA
** * * * ** * * **
462 ACAT-TTCCCAAGGCAGACAT-TCAATTATAA--CATCTTTTAAT
129 ACATATT-TTAA-CCAAAAATGT-AAAAAAAATCCAACTTAAAAT
* ** * * * * ** ** * **
503 CAATAATTTGAA-A-AAATCCAACTTCAAATCAATTATGAGAATATAAAATCTTTTAAAACGAGT
1 CAATTATGAGAATATAAAACC-A-TTTAAAGC------GAGTA-AT-AAGGC-TTTCGAAGGCTT
* * * *** * * * * * * * * *
566 AAGAAGGCTTTCAAAGGC-TTGAGTGGCTATCGAAAGCGTTTCTTGTTAATGGATGGCTTTTGCT
55 AAG-TGACTAT-AAAGGCTTTTCTTGCCAAT-GGATG-GCTT-TTGCT--T-CA---CGTTT-CC
** ** * * * * * *
630 TTAGGTTTCTAGAGGTTGGC-ATTCAATTATA-ACATATTTTAACCAAAACTCT-AAAAATATCC
108 CGAGG----TAGACATT--CAATT--A-TA-ACATAT-TTTAACCAAAAA-TGTAAAAAAAATCC
*
692 AACTTCAAAT
161 AACTTAAAAT
* * * * * *
702 CAATTATAAGAGTATAAAACCA-TTAAAACGAGTAATAAGGCTTTCAAAGGCCTGAGTGACTATA
1 CAATTATGAGAATATAAAACCATTTAAAGCGAGTAATAAGGCTTTCGAAGGCTTAAGTGACTATA
* * * * * * *
766 AATGAACATTTCTCT-CTAATGGATGGCTTTTGCTTCATGTTTCCCAAGGTAAACATTTAATTAT
66 AA-G-GCTTTTCT-TGCCAATGGATGGCTTTTGCTTCACGTTTCCCGAGGTAGACATTCAATTAT
*
830 AACATATTTTAACCAAAAATGT-AAAAAAATCTAACTTAAAAT
128 AACATATTTTAACCAAAAATGTAAAAAAAATCCAACTTAAAAT
* * * * * * *
872 CAGTTACGACAATATAAAACCATTTAAATCGAGTAGTAAGGGTTTCAAAGGCTTGAA-TGACTAT
1 CAATTATGAGAATATAAAACCATTTAAAGCGAGTAATAAGGCTTTCGAAGGCTT-AAGTGACTAT
* * * * *
936 AAAAGGACTTGTT-TCT-CCCATGGATGGCTTTTGCTTCACGTTTCCTGAAGCAGACATTTAATT
65 -AAAGG-CTT-TTCT-TGCCAATGGATGGCTTTTGCTTCACGTTTCCCGAGGTAGACATTCAATT
* * * * *
999 ATAACATTTTTTAACTAACAATGT-AAAACAATCCAGCTTAAAAT
126 ATAACATATTTTAACCAAAAATGTAAAAAAAATCCAACTTAAAAT
* * * * * * **
1043 CAATTATGTA-TATATAAATCCATTTAAAGCGAGTAATAAAGCTTTCAAAAGCTTGAGTGACCGT
1 CAATTATG-AGAATATAAAACCATTTAAAGCGAGTAATAAGGCTTTCGAAGGCTTAAGTGACTAT
** * * ** * * * *
1107 AAATGTATTTTCTTGCCAATGGATGACATTTGCTTCATC-TTTCCTTAGGCAAACAATCAATTAC
65 AAA-GGCTTTTCTTGCCAATGGATGGCTTTTGCTTCA-CGTTTCCCGAGGTAGACATTCAATTAT
* * * *** *
1171 AATATA-TTTAATCAGAAAA-GT-AAAAATATTTGACTTAAATT
128 AACATATTTTAACCA-AAAATGTAAAAAAAATCCAACTTAAAAT
* * * *
1212 CAATTATGAGAATATAAAACCATTTAAAGCGAGTAATAAGGCTTTCAAAGGCCTGAGTGACTCTA
1 CAATTATGAGAATATAAAACCATTTAAAGCGAGTAATAAGGCTTTCGAAGGCTTAAGTGACTATA
* * * * ** **
1277 AATGGACTTTTCTCT-CTAACGGATGACTTTTGCTTCATGTTTCCTAAGACAGACATTCAATTAT
66 AA-GG-CTTTTCT-TGCCAATGGATGGCTTTTGCTTCACGTTTCCCGAGGTAGACATTCAATTAT
* * * * *
1341 AATATATTTTATCTAAAAATGT-AAAAAAATCAAACTTGAAAT
128 AACATATTTTAACCAAAAATGTAAAAAAAATCCAACTTAAAAT
* * *
1383 TAGTTATGAGAATATAAAACCATTTAAAGCGAGTAATAAGGCTTTCAAAGGCTT
1 CAATTATGAGAATATAAAACCATTTAAAGCGAGTAATAAGGCTTTCGAAGGCTT
1437 G
Statistics
Matches: 942, Mismatches: 236, Indels: 173
0.70 0.17 0.13
Matches are distributed among these distances:
158 5 0.01
159 3 0.00
160 30 0.03
161 10 0.01
162 9 0.01
166 4 0.00
167 3 0.00
168 6 0.01
169 121 0.13
170 230 0.24
171 322 0.34
172 78 0.08
173 7 0.01
174 1 0.00
175 3 0.00
176 6 0.01
178 1 0.00
180 4 0.00
181 3 0.00
184 1 0.00
185 1 0.00
187 10 0.01
188 9 0.01
189 14 0.01
190 7 0.01
191 4 0.00
192 7 0.01
193 1 0.00
197 8 0.01
198 9 0.01
199 18 0.02
200 2 0.00
201 5 0.01
ACGTcount: A:0.37, C:0.15, G:0.15, T:0.33
Consensus pattern (170 bp):
CAATTATGAGAATATAAAACCATTTAAAGCGAGTAATAAGGCTTTCGAAGGCTTAAGTGACTATA
AAGGCTTTTCTTGCCAATGGATGGCTTTTGCTTCACGTTTCCCGAGGTAGACATTCAATTATAAC
ATATTTTAACCAAAAATGTAAAAAAAATCCAACTTAAAAT
Found at i:457 original size:20 final size:20
Alignment explanation
Indices: 408--457 Score: 73
Period size: 20 Copynumber: 2.5 Consensus size: 20
398 AGTGACTATA
* *
408 ATGGCTTTTCTTGCCAATGG
1 ATGGCTTTTGTTACCAATGG
*
428 ATGGCTTTTGTTACCCATGG
1 ATGGCTTTTGTTACCAATGG
448 ATGGCTTTTG
1 ATGGCTTTTG
458 CTTCACATTT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.14, C:0.18, G:0.26, T:0.42
Consensus pattern (20 bp):
ATGGCTTTTGTTACCAATGG
Found at i:575 original size:189 final size:189
Alignment explanation
Indices: 255--627 Score: 473
Period size: 189 Copynumber: 2.0 Consensus size: 189
245 TTTCTTGCTA
* ** *
255 ATGGATGGGTTTTGCTTCAGGTTTCCCGAGGCTAGCATTCAATTATAACATATTTTAACCAAAAA
1 ATGGATGGCTTTTGCTTCACATTTCCCAAGGCTAGCATTCAATTATAACATATTTTAACCAAAAA
* * ** *
320 TGTAAAAAATTCTAACTTAAAATCAATTATGAGAATGTAAAACCATTTAAAGTGAGTAATAAGGC
66 TGTAAAAAATTCCAACTTAAAATCAATTATGAGAATATAAAACCATTTAAAACGAGTAAGAAGGC
** * *
385 TTTTGAAGGCTTAAGTGACTAT-AATGGCTTTTCTTGCCAATGGATGGCTTTTGTTACCC
131 TTTCAAAGGCTTAAGTGACTATCAA-AGCGTTTCTTGCCAATGGATGGCTTTTGTTACCC
* * *
444 ATGGATGGCTTTTGCTTCACATTTCCCAAGGC-AGACATTCAATTATAACATCTTTTAATCAATA
1 ATGGATGGCTTTTGCTTCACATTTCCCAAGGCTAG-CATTCAATTATAACATATTTTAACCAAAA
* * * *
508 ATTTGAAAAAA-TCCAACTTCAAATCAATTATGAGAATATAAAATCTTTTAAAACGAGTAAGAAG
65 ATGT-AAAAAATTCCAACTTAAAATCAATTATGAGAATATAAAACCATTTAAAACGAGTAAGAAG
* * **
572 GCTTTCAAAGGCTTGAGTGGCTATCGAAAGCGTTTCTTGTTAATGGATGGCTTTTG
129 GCTTTCAAAGGCTTAAGTGACTATC-AAAGCGTTTCTTGCCAATGGATGGCTTTTG
628 CTTTAGGTTT
Statistics
Matches: 156, Mismatches: 24, Indels: 7
0.83 0.13 0.04
Matches are distributed among these distances:
188 2 0.01
189 122 0.78
190 30 0.19
191 2 0.01
ACGTcount: A:0.34, C:0.15, G:0.17, T:0.34
Consensus pattern (189 bp):
ATGGATGGCTTTTGCTTCACATTTCCCAAGGCTAGCATTCAATTATAACATATTTTAACCAAAAA
TGTAAAAAATTCCAACTTAAAATCAATTATGAGAATATAAAACCATTTAAAACGAGTAAGAAGGC
TTTCAAAGGCTTAAGTGACTATCAAAGCGTTTCTTGCCAATGGATGGCTTTTGTTACCC
Found at i:1312 original size:340 final size:337
Alignment explanation
Indices: 444--1437 Score: 997
Period size: 340 Copynumber: 2.9 Consensus size: 337
434 TTTGTTACCC
* * * * * * * *
444 ATGGATGGCTTTTGCTTCA-CATTTCCCAAGGCAGACATTCAATTATAACATCTTTTAATCAATA
1 ATGGATGACATTTGCTTCATC-TTTCCCAAGGCAAACAATCAATTACAACATATTTTAACCAAAA
* * * * * *
508 ATTTGAAAAAATCCAACTTCAAATCAATTATGAGAATATAAAATCTTTTAAAACGAGTAAGAAGG
65 ATGTAAAAAAATCTAACTT-AAATCAATTATGAGAATATAAAACCATTTAAAACGAGTAATAAGG
* * * * * *
573 CTTTCAAAGGCTTGAGTGGCTATCGAAA-G-CGTTTCT-TGTTAATGGATGGCTTTTGCTTTAGG
129 CTTTCAAAGGCTTGAGTGAC--TCTAAAGGACTTTTCTCT-CTAATGGATGGCTTTTGCTTCACG
* ** * * * *
635 TTT-CTAGAGGTTGGCATTCAATTATAACATATTTTAACCAAAACTCTAAAAATATCCAACTTCA
191 TTTCCT-GAAGCAGACATTCAATTATAACATATTTTAACTAAAA-TGTAAAAA-ATCCAACTTAA
* *
699 AATCAATTAT-AAGAGTATAAAACCA-TTAAAACGAGTAATAAGGCTTTCAAAGGCCTGAGTGAC
253 AATCAATTATGAA-A-TATAAAACCATTTAAAGCGAGTAATAAGGCTTTCAAAGGCTTGAGTGAC
* *
762 TATAAATGAACATTTCTCTCTA
316 CATAAATGAACATTTCTCTCCA
* * * * * * *
784 ATGGATGGCTTTTGCTTCATGTTTCCCAAGGTAAACATTTAATTATAACATATTTTAACCAAAAA
1 ATGGATGACATTTGCTTCATCTTTCCCAAGGCAAACAATCAATTACAACATATTTTAACCAAAAA
* * * * * *
849 TGTAAAAAAATCTAACTTAAAATCAGTTACGACAATATAAAACCATTTAAATCGAGTAGTAAGGG
66 TGTAAAAAAATCTAACTT-AAATCAATTATGAGAATATAAAACCATTTAAAACGAGTAATAAGGC
* * **
914 TTTCAAAGGCTTGAATGACTATAAAAGGACTTGTT-TCTCCCATGGATGGCTTTTGCTTCACGTT
130 TTTCAAAGGCTTGAGTGACTCT-AAAGGACTT-TTCTCTCTAATGGATGGCTTTTGCTTCACGTT
* * *
978 TCCTGAAGCAGACATTTAATTATAACATTTTTTAACTAACAATGTAAAACAATCCAGCTTAAAAT
193 TCCTGAAGCAGACATTCAATTATAACATATTTTAACTAA-AATGTAAAA-AATCCAACTTAAAAT
* * * * *
1043 CAATTATGTATATATAAATCCATTTAAAGCGAGTAATAAAGCTTTCAAAAGCTTGAGTGACCGTA
256 CAATTATG-AAATATAAAACCATTTAAAGCGAGTAATAAGGCTTTCAAAGGCTTGAGTGACCATA
* *
1108 AATGTA-TTTTCT-TGCCA
320 AATGAACATTTCTCT-CCA
** * *
1125 ATGGATGACATTTGCTTCATCTTTCCTTAGGCAAACAATCAATTACAATATA-TTTAATCAGAAA
1 ATGGATGACATTTGCTTCATCTTTCCCAAGGCAAACAATCAATTACAACATATTTTAACCA-AAA
* * * *
1189 A-GTAAAAATATTTGACTTAAATTCAATTATGAGAATATAAAACCATTTAAAGCGAGTAATAAGG
65 ATGTAAAAAAATCTAACTTAAA-TCAATTATGAGAATATAAAACCATTTAAAACGAGTAATAAGG
* * * *
1253 CTTTCAAAGGCCTGAGTGACTCTAAATGGACTTTTCTCTCTAACGGATGACTTTTGCTTCATGTT
129 CTTTCAAAGGCTTGAGTGACTCTAAA-GGACTTTTCTCTCTAATGGATGGCTTTTGCTTCACGTT
* * * *
1318 TCCT-AAGACAGACATTCAATTATAATATATTTTATCTAAAAATGTAAAAAAATCAAACTTGAAA
193 TCCTGAAG-CAGACATTCAATTATAACATATTTTAACT-AAAATGT-AAAAAATCCAACTTAAAA
* *
1382 TTAGTTATGAGAATATAAAACCATTTAAAGCGAGTAATAAGGCTTTCAAAGGCTTG
255 TCAATTATGA-AATATAAAACCATTTAAAGCGAGTAATAAGGCTTTCAAAGGCTTG
Statistics
Matches: 541, Mismatches: 92, Indels: 42
0.80 0.14 0.06
Matches are distributed among these distances:
338 1 0.00
339 15 0.03
340 328 0.61
341 146 0.27
342 50 0.09
343 1 0.00
ACGTcount: A:0.38, C:0.15, G:0.14, T:0.33
Consensus pattern (337 bp):
ATGGATGACATTTGCTTCATCTTTCCCAAGGCAAACAATCAATTACAACATATTTTAACCAAAAA
TGTAAAAAAATCTAACTTAAATCAATTATGAGAATATAAAACCATTTAAAACGAGTAATAAGGCT
TTCAAAGGCTTGAGTGACTCTAAAGGACTTTTCTCTCTAATGGATGGCTTTTGCTTCACGTTTCC
TGAAGCAGACATTCAATTATAACATATTTTAACTAAAATGTAAAAAATCCAACTTAAAATCAATT
ATGAAATATAAAACCATTTAAAGCGAGTAATAAGGCTTTCAAAGGCTTGAGTGACCATAAATGAA
CATTTCTCTCCA
Done.