Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018402692.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_5754.0, 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, 973
Length: 1622
ACGTcount: A:0.34, C:0.13, G:0.11, T:0.39
Warning! 60 characters in sequence are not A, C, G, or T
Found at i:610 original size:171 final size:162
Alignment explanation
Indices: 433--1349 Score: 361
Period size: 172 Copynumber: 5.4 Consensus size: 162
423 TGGTTTTATT
*
433 ATCTCAAAATTGATTTT-TGTTCAATTCT-TTATTACATTTTTGGTTAAAACAGACTATAATTGA
1 ATCTCAAAATTGATTTTAAGTTCAATT-TGTT-TTACATTTTTGGTTAAAACAGACTATAATTGA
* * * * * * *
496 ATGTCTTCTTTGAGA-AGCATGAAGAAAAATG-TATTTATTGGCAA-GAAAGTCTATTTATTGTC
64 ATGTCTACCTCGAGATA-CATGAAGAAAAAGGCT-TTCATTGGCAAGGAAAGTCCATTTATAGTC
*
558 ACTCATTCTTTCAAAAGCCTTATTACTCACTTCNNNNNNNNNNATA
127 ACACATTCTTTCAAAAGCCTTATTACTCACTTC----------ATA
* * * *
604 ATCTCAAAATTGATTTTAAGTTCAATTTGTTTTAGATTTTTGGTTAAGACATATTATAATTGAAT
1 ATCTCAAAATTGATTTTAAGTTCAATTTGTTTTACATTTTTGGTTAAAACAGACTATAATTGAAT
*
669 GTCTACCTCGAGATATATGAAGAAAAAGGCTTTCATTGGCAAGGAAAGTCCATTTATAGTCACAC
66 GTCTACCTCGAGATACATGAAGAAAAAGGCTTTCATTGGCAAGGAAAGTCCATTTATAGTCACAC
* * * *
734 ATTCTTTCAAAAGCCTTANNNNNNNNNNTAAAT-ATTTTTATA
131 ATTCTTTCAAAAGCCTTA----------TTACTCA-CTTCATA
* * * * * ** *
776 ATCTCATAATTCATTTTAACTTGAA-TT-TTCTACATTTTTTATTAAAACATACTATAATTGAAT
1 ATCTCAAAATTGATTTTAAGTTCAATTTGTTTTACATTTTTGGTTAAAACAGACTATAATTGAAT
* * ** * * ** * * * *
839 GTCTACCT-TATGAAAGGTGAAGAAAAAGACATTCATTTACAAGAAAAGTCTATTTATAGTAACT
66 GTCTACCTCGA-GATACATGAAGAAAAAGGCTTTCATTGGCAAGGAAAGTCCATTTATAGTCACA
* * *
903 GATTCTTTTAAAAGCCTTATTACTCACTTTTAATTGTTTTATA
130 CATTCTTTCAAAAGCCTTATTACTCAC----------TTCATA
* * * * * * *
946 ATATCAAAATTGATATTAAGTTTAATTT-TTTTA-TTTTTCTAGTTAAAACATATTATAATTGAA
1 ATCTCAAAATTGATTTTAAGTTCAATTTGTTTTACATTTT-TGGTTAAAACAGACTATAATTGAA
* * * * * * * * * * *
1009 TGTCAACATTGAGAAACGTGTAGAAAAA-CCTATTTATTTGG-AAGAAAAGCCCATTTATAGTCT
65 TGTCTACCTCGAGATACATGAAGAAAAAGGCT-TTCA-TTGGCAAGGAAAGTCCATTTATAGTCA
* * * * * * **
1072 CTCATTCCTTCAAAAGCCTTATNNNNNNNNNNAAATGATTTTGTA
128 CACATTCTTTCAAAAGCCTTAT----------TACTCACTTCATA
* * ** * *
1117 ATCTCATAATTGATTTTAAGTT-AATTTTTTTTTACATTTTTTATTAAAACAAATTATAATTGAA
1 ATCTCAAAATTGATTTTAAGTTCAA-TTTGTTTTACATTTTTGGTTAAAACAGACTATAATTGAA
* * * * ** * * * * *
1181 TATCTGCCTCAAGAAACATGAAGAAAAATACATTCATTGAC-AGCAAAAGTCTATTTATTGTCAC
65 TGTCTACCTCGAGATACATGAAGAAAAAGGCTTTCATTGGCAAG-GAAAGTCCATTTATAGTCAC
* * *
1245 CCATTCCTTCAAAAGCCTTATTACTCACNNNNNNNNNNTTTATA
129 ACATTCTTTCAAAAGCCTTATTACTCAC----------TTCATA
* * * *
1289 ATCTCAAAATTGATATTAAGTTCAATTTTTTTTACTTTTTTGGTTAAAACAGATTATAATT
1 ATCTCAAAATTGATTTTAAGTTCAATTTGTTTTACATTTTTGGTTAAAACAGACTATAATT
1350 CAAATGTTTG
Statistics
Matches: 573, Mismatches: 113, Indels: 119
0.71 0.14 0.15
Matches are distributed among these distances:
160 3 0.01
161 1 0.00
162 3 0.01
169 1 0.00
170 129 0.23
171 202 0.35
172 218 0.38
173 7 0.01
181 4 0.01
182 5 0.01
ACGTcount: A:0.34, C:0.13, G:0.10, T:0.39
Consensus pattern (162 bp):
ATCTCAAAATTGATTTTAAGTTCAATTTGTTTTACATTTTTGGTTAAAACAGACTATAATTGAAT
GTCTACCTCGAGATACATGAAGAAAAAGGCTTTCATTGGCAAGGAAAGTCCATTTATAGTCACAC
ATTCTTTCAAAAGCCTTATTACTCACTTCATA
Found at i:1483 original size:173 final size:169
Alignment explanation
Indices: 23--1622 Score: 746
Period size: 171 Copynumber: 9.3 Consensus size: 169
13 ATTCATTGAC
* * * * *
23 AAGAAAAGTCAATTTATAGTCTCTCATTTCTTCAAAAGACTTATTACT-AGTTTGAAATAGTTTT
1 AAGAAAAGTCTATTTATAGTCACTCATTCCTTCAAAAGCCTTATTACTCACTTT-AAAT-GTTTT
* * * * * *
87 ATAATCTCATAATTGAT-TTTAGCTTGAA-TTTTTTTACATTTTTGGTTAAAATAGACTATAATT
64 ATAATCTCAAAATTGATATTAAG-TT-AATTTTTTTTAC-TTTTTTGTTAAAACAAATTATAATT
** * *
150 GAATGTCTGC-TCAAGAAACATGAAGAAAAA-TGTATTCA-TTGG
126 GAATGTCTGCATTGAGAAACATGTAGAAAAACT-TATTTATTTGG
* * * * * ** *
192 CAATAAAAGTTTATTTATAGTTACCCATTCTTTCAAAAGCCTTAGCACTCACCTTAAATGATTTT
1 -AAGAAAAGTCTATTTATAGTCACTCATTCCTTCAAAAGCCTTATTACTCACTTTAAATG-TTTT
* * * * * * **
257 ATTATCTCAAAATTGATATTATGTTTGATTTTTTTTTACTTTTTTGCATCAAATAGGTTATAATT
64 ATAATCTCAAAATTGATATTAAG-TT-AATTTTTTTTACTTTTTTG-TTAAAACAAATTATAATT
* * * * ** * *** * *
322 GAATGTTTACCTTTAGAAGTATGAAGAAAAAGGCATTCATTGGG
126 GAATGTCTGCATTGAGAAACATGTAGAAAAACTTATTTATTTGG
********** * * * *
366 AAGAAAANNNNNNNNNNAGTCACCCATTCCTTCAAAAGTCTTATTACTTACCTTAAATGGTTTTA
1 AAGAAAAGTCTATTTATAGTCACTCATTCCTTCAAAAGCCTTATTACTCACTTTAAAT-GTTTTA
* ** * * * *
431 TTATCTCAAAATTGAT-TTTTGTTCAATTCTTTATTACATTTTTGGTTAAAACAGACTATAATTG
65 TAATCTCAAAATTGATATTAAGTT-AATT-TTTTTTAC-TTTTTTGTTAAAACAAATTATAATTG
* * * *
495 AATGTCTTCTTTGAGAAGCATGAAGAAAAA-TGTATTTA-TTGG
127 AATGTCTGCATTGAGAAACATGTAGAAAAACT-TATTTATTTGG
* * **********
537 CAAG-AAAGTCTATTTATTGTCACTCATTCTTTCAAAAGCCTTATTACTCACTTCNNNNNNNNNN
1 -AAGAAAAGTCTATTTATAGTCACTCATTCCTTCAAAAGCCTTATTACTCACTT-TAAATGTTTT
* * * * * *
601 ATAATCTCAAAATTGATTTTAAGTTCAATTTGTTTTAGATTTTTGGTTAAGACATATTATAATTG
64 ATAATCTCAAAATTGATATTAAGTT-AATTTTTTTTA-CTTTTTTGTTAAAACAAATTATAATTG
* * * * * * *
666 AATGTCTACCTCGAGATATATGAAGAAAAAGGC-T-TTCA-TTGG
127 AATGTCTGCATTGAGAAACATGTAGAAAAA--CTTATTTATTTGG
* * * * ********** *
708 CAAGGAAAGTCCATTTATAGTCACACATTCTTTCAAAAGCCTTANNNNNNNNNNTAAATATTTTT
1 -AAGAAAAGTCTATTTATAGTCACTCATTCCTTCAAAAGCCTTATTACTCACTTTAAAT-GTTTT
* * * * * * * *
773 ATAATCTCATAATTCATTTTAACTTGAA--TTTTCTACATTTTTTATTAAAACATACTATAATTG
64 ATAATCTCAAAATTGATATTAAGTT-AATTTTTTTTAC-TTTTTTGTTAAAACAAATTATAATTG
* * ** * *** * **
836 AATGTCTACCTT-ATGAAAGGTGAAGAAAAAGACATTCATTTAC
127 AATGTCTGCATTGA-GAAACATGTAGAAAAACTTATTTATTTGG
* * * * *
879 AAGAAAAGTCTATTTATAGTAACTGATTCTTTTAAAAGCCTTATTACTCACTTTTAATTGTTTTA
1 AAGAAAAGTCTATTTATAGTCACTCATTCCTTCAAAAGCCTTATTACTCAC-TTTAAATGTTTTA
* *
944 TAATATCAAAATTGATATTAAGTTTAA-TTTTTTTA-TTTTTCTAGTTAAAACATATTATAATTG
65 TAATCTCAAAATTGATATTAAG-TTAATTTTTTTTACTTTTT-T-GTTAAAACAAATTATAATTG
** * *
1007 AATGTCAACATTGAGAAACGTGTAGAAAAACCTATTTATTTGG
127 AATGTCTGCATTGAGAAACATGTAGAAAAACTTATTTATTTGG
* * * ********** *
1050 AAGAAAAGCCCATTTATAGTCTCTCATTCCTTCAAAAGCCTTATNNNNNNNNNNAAATGATTTTG
1 AAGAAAAGTCTATTTATAGTCACTCATTCCTTCAAAAGCCTTATTACTCACTTTAAATG-TTTTA
* * *
1115 TAATCTCATAATTGATTTTAAGTTAATTTTTTTTTACATTTTTTATTAAAACAAATTATAATTGA
65 TAATCTCAAAATTGATATTAAGTTAA-TTTTTTTTAC-TTTTTTGTTAAAACAAATTATAATTGA
* * ** * * *
1180 ATATCTGCCTCAAGAAACATGAAGAAAAA-TACATTCA-TT-G
128 ATGTCTGCATTGAGAAACATGTAGAAAAACT-TATTTATTTGG
* * *********
1220 ACAGCAAAAGTCTATTTATTGTCACCCATTCCTTCAAAAGCCTTATTACTCACNNNNNNNNNNTT
1 A-AG-AAAAGTCTATTTATAGTCACTCATTCCTTCAAAAGCCTTATTACTCAC-TTTAAATGTTT
*
1285 TATAATCTCAAAATTGATATTAAGTTCAATTTTTTTTACTTTTTTGGTTAAAACAGATTATAATT
63 TATAATCTCAAAATTGATATTAAGTT-AATTTTTTTTACTTTTTT-GTTAAAACAAATTATAATT
* * *
1350 CAAATGTTTGCATTGAGAAATATGTAGAAAAACTTATTTATTTGG
126 -GAATGTCTGCATTGAGAAACATGTAGAAAAACTTATTTATTTGG
* * * * *
1395 AAGAAAAG-CTCATTTATAGTCTCTCATTCTTTTAAAAGTCTTATTACTCGCTTTAAATAGTTTT
1 AAGAAAAGTCT-ATTTATAGTCACTCATTCCTTCAAAAGCCTTATTACTCACTTTAAAT-GTTTT
** ** * ********** * *
1459 ATAATCTCGTAATCAATTTTAAGTTGAATTTTTTTNNNNNNNNNNTTAAAACAGACTATAATTGA
64 ATAATCTCAAAATTGATATTAAGTT-AATTTTTTTTACTTTTTTGTTAAAACAAATTATAATTGA
* * * * * * *
1524 ATATCTGCCTTAAGAAACATGAAGAGAAA-TGCATTTATTTGT
128 ATGTCTGCATTGAGAAACATGTAGAAAAACT-TATTTATTTGG
* *
1566 AATAAAAGTCTATTTATAGTCAC-CTATTGCTTCAAAAGCCTTATTACTCACTTTAAA
1 AAGAAAAGTCTATTTATAGTCACTC-ATTCCTTCAAAAGCCTTATTACTCACTTTAAA
Statistics
Matches: 1071, Mismatches: 307, Indels: 103
0.72 0.21 0.07
Matches are distributed among these distances:
169 7 0.01
170 189 0.18
171 346 0.32
172 321 0.30
173 192 0.18
174 14 0.01
175 2 0.00
ACGTcount: A:0.34, C:0.12, G:0.11, T:0.39
Consensus pattern (169 bp):
AAGAAAAGTCTATTTATAGTCACTCATTCCTTCAAAAGCCTTATTACTCACTTTAAATGTTTTAT
AATCTCAAAATTGATATTAAGTTAATTTTTTTTACTTTTTTGTTAAAACAAATTATAATTGAATG
TCTGCATTGAGAAACATGTAGAAAAACTTATTTATTTGG
Found at i:1578 original size:344 final size:332
Alignment explanation
Indices: 23--1620 Score: 832
Period size: 343 Copynumber: 4.7 Consensus size: 332
13 ATTCATTGAC
* * * * *
23 AAGAAAAGTCAATTTATAGTCTCTCATTTCTTCAAAAGACTTATTACTAG-TTTGAAAT-AGTTT
1 AAGAAAAGCCCATTTATAGTCTCTCATTCCTTCAAAAGCCTTATTACTCGCTTT-AAATGA-TTT
** ** * *
86 TATAATCTCATAATTGATTTT-AGCTTGAA-TTTTTTTACATTTTTGGTTAAAATAGACTATAAT
64 TATAATCTCATAATCAATTTTAAG-TT-AATTTTTTTTACATTTTTTATTAAAACAAACTATAAT
* ** * ** *
149 TGAATGTCTG-CTCAAGAAACATGAAGAAAAATGTATTCATTGGCAATAAAAGTTTATTTATAGT
127 TGAATATCTGCCTCAAGAAACATGAAGAAAAATACATTCATTGACAGCAAAAGTCTATTTATAGT
* * ** *
213 TACCCATTCTTTCAAAAGCCTTAGCACTCACCTTAAATGATTTTATTATCTCAAAATTGATATTA
192 CACCCATTCCTTCAAAAGCCTTATTACTCA-CTT---T-A---TA--ATATCAAAATTGATATTA
* * * * * * * * ** * * *
278 TGTTTGATTTTTTTTTACTTTTT-T-GCATCAAATAGGTTATAATTGAATGTTTACCTTTAGAAG
247 AG-TTCA-ATTTTTTTA-TTTTTCTAG-TTAAAACAGATTATAATTAAATGTCAACATTGAGAAA
* * * * *
341 TATGAAGAAAAAGGC-ATTCATTGGG
308 CATGTAGAAAAA-CCTATTTATTTGG
********** * * * ** * *
366 AAGAAAANNNNNNNNNNAGTCACCCATTCCTTCAAAAGTCTTATTACTTACCTTAAATGGTTTTA
1 AAGAAAAGCCCATTTATAGTCTCTCATTCCTTCAAAAGCCTTATTACTCGCTTTAAATGATTTTA
* * ** * * ** *
431 TTATCTCAAAATTGATTTT-TGTTCAATTCTTTATTACATTTTTGGTTAAAACAGACTATAATTG
66 TAATCTCATAATCAATTTTAAGTT-AATT-TTTTTTACATTTTTTATTAAAACAAACTATAATTG
* * * ** * ** * * *
495 AATGTCTTCTTTGAGAAGCATGAAGAAAAATGTATTTATTGGCA--AGAAAGTCTATTTATTGTC
129 AATATCTGCCTCAAGAAACATGAAGAAAAATACATTCATTGACAGCA-AAAGTCTATTTATAGTC
* * * * *
558 ACTCATTCTTTCAAAAGCCTTATTACTCACTTCNNNNNNNNNNATAATCTCAAAATTGATTTTAA
193 ACCCATTCCTTCAAAAGCCTTATTACTCACTT----------TATAATATCAAAATTGATATTAA
* * * * * * * * * *
623 GTTCAATTTGTTTTAGATTTT-TGGTTAAGACATATTATAATTGAATGTCTACCTCGAGATATAT
248 GTTCAATTT-TTTTA-TTTTTCTAGTTAAAACAGATTATAATTAAATGTCAACATTGAGAAACAT
* * *
687 GAAGAAAAAGGCT-TTCA-TTGG
311 GTAGAAAAA-CCTATTTATTTGG
* * * * * **********
708 CAAGGAAAGTCCATTTATAGTCACACATTCTTTCAAAAGCCTTANNNNNNNNNNTAAAT-ATTTT
1 -AAGAAAAGCCCATTTATAGTCTCTCATTCCTTCAAAAGCCTTATTACTCGCTTTAAATGA-TTT
* * *
772 TATAATCTCATAATTC-ATTTTAACTTGAA--TTTTCTACATTTTTTATTAAAACATACTATAAT
64 TATAATCTCATAA-TCAATTTTAAGTT-AATTTTTTTTACATTTTTTATTAAAACAAACTATAAT
* * * * ** * *
834 TGAATGTCTACCTTATGAAAGGTGAAGAAAAAGACATTCATTTACAAG-AAAAGTCTATTTATAG
127 TGAATATCTGCCTCAAGAAACATGAAGAAAAATACATTCATTGAC-AGCAAAAGTCTATTTATAG
* ** * *
898 TAACTGATTCTTTTAAAAGCCTTATTACTCACTTTTAATTGTTTTATAATATCAAAATTGATATT
191 TCACCCATTCCTTCAAAAGCCTTATTACTCAC----------TTTATAATATCAAAATTGATATT
* * * *
963 AAGTTTAATTTTTTTATTTTTCTAGTTAAAACATATTATAATTGAATGTCAACATTGAGAAACGT
246 AAGTTCAATTTTTTTATTTTTCTAGTTAAAACAGATTATAATTAAATGTCAACATTGAGAAACAT
1028 GTAGAAAAACCTATTTATTTGG
311 GTAGAAAAACCTATTTATTTGG
********** *
1050 AAGAAAAGCCCATTTATAGTCTCTCATTCCTTCAAAAGCCTTATNNNNNNNNNNAAATGATTTTG
1 AAGAAAAGCCCATTTATAGTCTCTCATTCCTTCAAAAGCCTTATTACTCGCTTTAAATGATTTTA
** *
1115 TAATCTCATAATTGATTTTAAGTTAATTTTTTTTTACATTTTTTATTAAAACAAATTATAATTGA
66 TAATCTCATAATCAATTTTAAGTTAA-TTTTTTTTACATTTTTTATTAAAACAAACTATAATTGA
*
1180 ATATCTGCCTCAAGAAACATGAAGAAAAATACATTCATTGACAGCAAAAGTCTATTTATTGTCAC
130 ATATCTGCCTCAAGAAACATGAAGAAAAATACATTCATTGACAGCAAAAGTCTATTTATAGTCAC
*
1245 CCATTCCTTCAAAAGCCTTATTACTCACNNNNNNNNNNTTTATAATCTCAAAATTGATATTAAGT
195 CCATTCCTTCAAAAGCCTTATTACTCAC----------TTTATAATATCAAAATTGATATTAAGT
* *** *
1310 TCAATTTTTTTTACTTTTT-TGGTTAAAACAGATTATAATTCAAATGTTTGCATTGAGAAATATG
250 TCAA-TTTTTTTA-TTTTTCTAGTTAAAACAGATTATAATT-AAATGTCAACATTGAGAAACATG
*
1374 TAGAAAAACTTATTTATTTGG
312 TAGAAAAACCTATTTATTTGG
* * * *
1395 AAGAAAAGCTCATTTATAGTCTCTCATTCTTTTAAAAGTCTTATTACTCGCTTTAAAT-AGTTTT
1 AAGAAAAGCCCATTTATAGTCTCTCATTCCTTCAAAAGCCTTATTACTCGCTTTAAATGA-TTTT
* ********** *
1459 ATAATCTCGTAATCAATTTTAAGTTGAA-TTTTTTTNNNNNNNNNNTTAAAACAGACTATAATTG
65 ATAATCTCATAATCAATTTTAAGTT-AATTTTTTTTACATTTTTTATTAAAACAAACTATAATTG
* * * * *
1523 AATATCTGCCTTAAGAAACATGAAGAGAAATGCATTTATTTGTA-A-TAAAAGTCTATTTATAGT
129 AATATCTGCCTCAAGAAACATGAAGAAAAATACATTCA-TTG-ACAGCAAAAGTCTATTTATAGT
* *
1586 CACCTATTGCTTCAAAAGCCTTATTACTCACTTTA
192 CACCCATTCCTTCAAAAGCCTTATTACTCACTTTA
1621 AA
Statistics
Matches: 994, Mismatches: 213, Indels: 105
0.76 0.16 0.08
Matches are distributed among these distances:
334 4 0.00
340 9 0.01
341 186 0.19
342 89 0.09
343 316 0.32
344 237 0.24
345 145 0.15
346 5 0.01
349 1 0.00
352 2 0.00
ACGTcount: A:0.34, C:0.13, G:0.11, T:0.39
Consensus pattern (332 bp):
AAGAAAAGCCCATTTATAGTCTCTCATTCCTTCAAAAGCCTTATTACTCGCTTTAAATGATTTTA
TAATCTCATAATCAATTTTAAGTTAATTTTTTTTACATTTTTTATTAAAACAAACTATAATTGAA
TATCTGCCTCAAGAAACATGAAGAAAAATACATTCATTGACAGCAAAAGTCTATTTATAGTCACC
CATTCCTTCAAAAGCCTTATTACTCACTTTATAATATCAAAATTGATATTAAGTTCAATTTTTTT
ATTTTTCTAGTTAAAACAGATTATAATTAAATGTCAACATTGAGAAACATGTAGAAAAACCTATT
TATTTGG
Done.