Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018401726.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_4840.0, 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: 6218
ACGTcount: A:0.24, C:0.09, G:0.08, T:0.24
Warning! 2176 characters in sequence are not A, C, G, or T
Found at i:935 original size:171 final size:168
Alignment explanation
Indices: 246--1197 Score: 653
Period size: 171 Copynumber: 5.6 Consensus size: 168
236 NNNNNNNCTT
* * * * * * *
246 AAACAGATTATAATTGACTGTCTACCT-TAGAAAATATAAATAAAAAAATATTCATTGGTAAGAA
1 AAACAGATAATAATTGAATGTCTGCCTCGAG-AAATATAAAGAAAAAGATATTCATTGGCAAGAA
* * * * * * * * ***
310 TAGTCCATTTATAATCACCCATACCTTCAAAAGCTTTATTACTTGCTTTAAAGGTTTTTATAATC
65 AAGTCCGTTTATAGTCACCCATGCCTTCAAAAACCTTATTACTCGCATTAAATAATTTTATAATC
* ** * *
375 TCATAATTGACTTTAAGTAAAATGTTTTTACATTTTTTTTTA
130 TCATAATT-ATTTTAAGTTGAATTTTTTTA-A-TTTTTGTTA
* * * *
417 AAACAGATTAA-AATTGAATG-CTTTCCT-TAGGAAATATGAAA-AACAAGATATTCATTGGAAA
1 AAACAGA-TAATAATTGAATGTC-TGCCTCGA-GAAATAT-AAAGAAAAAGATATTCATTGGCAA
*** * * *
478 GAAAAGTCTACTTATAGTCACCCATGCCTTCAAAAACCCTTATTACTCGCTTTAAATAGTTTTAA
62 GAAAAGTCCGTTTATAGTCACCCATGCCTTCAAAAA-CCTTATTACTCGCATTAAATAATTTTAT
* * *
543 AATCTCATAAATAGTTTTGAGTTGAATATTTTTTAATTTTTAGGTA
126 AATCTCATAATTA-TTTTAAGTTGAAT-TTTTTTAATTTTT-GTTA
* * * * * * *
589 AAACAGATAATAATTGAACGTTTGACTCGACAAATGTCAAGAAAAAGACATTCATTGGCAAGAAA
1 AAACAGATAATAATTGAATGTCTGCCTCGAGAAATATAAAGAAAAAGATATTCATTGGCAAGAAA
* * ** * *
654 AGTCCGTTTATAGTCACCCATGCATTTAAAGGCCTTATTACTCGGATTAAATAATTTTATAACCT
66 AGTCCGTTTATAGTCACCCATGCCTTCAAAAACCTTATTACTCGCATTAAATAATTTTATAATCT
******** *
719 CATAATTGATTTTAAGTTGAATTNNNNNNNNNNTTTTATTA
131 CATAATT-ATTTTAAGTTGAATT--TTTTTAATTTTTGTTA
* * * * ***
760 AAACAGATTATAATTGAATATCTGCCTCAAGAAATATAAAGAAAAAGATATCCATTGGCAAGNNN
1 AAACAGATAATAATTGAATGTCTGCCTCGAGAAATATAAAGAAAAAGATATTCATTGGCAAGAAA
******* * * *
825 NNNNNNNTTATAGTCACCCATGCCTTCGAAAACCTTATTACTCGCCTTAAATATTTTTATAATCT
66 AGTCCGTTTATAGTCACCCATGCCTTCAAAAACCTTATTACTCGCATTAAATAATTTTATAATCT
890 CATAATTCATTTTAAGTT-AGATTTTTTTATATTTTTGTCTA
131 CATAATT-ATTTTAAGTTGA-ATTTTTTTA-ATTTTTGT-TA
* * * *
931 AAACAGATAATAATTGAATGTCTACCTTGAGAAAGATGAAG-AAAAGAATATTCATTGGCAAGAA
1 AAACAGATAATAATTGAATGTCTGCCTCGAGAAATATAAAGAAAAAG-ATATTCATTGGCAAGAA
* * * * * ** * * * * * * *
995 AAGCCCATTTGTAGTCACCGATGCTTTTGAAAGCCTTATTAATTGCTTTAGATATTTTTATAGTC
65 AAGTCCGTTTATAGTCACCCATGCCTTCAAAAACCTTATTACTCGCATTAAATAATTTTATAATC
* * *
1060 TCATAATTGATTTCAAGTAGAATTTTTTTACATTTTTTATTA
130 TCATAATT-ATTTTAAGTTGAATTTTTTTA-A-TTTTTGTTA
* * * * * *
1102 AAACAAATTAA-AATTGAATG-CATTCCTCTAGAAACATGAAGAAAATGATATTCATTGGCAAGA
1 AAACAGA-TAATAATTGAATGTC-TGCCTCGAGAAATATAAAGAAAAAGATATTCATTGGCAAGA
*** * *
1165 AAAGTCTACTTATACTCACCCATACCTTCAAAA
64 AAAGTCCGTTTATAGTCACCCATGCCTTCAAAA
1198 CCCTNNNNNN
Statistics
Matches: 607, Mismatches: 150, Indels: 48
0.75 0.19 0.06
Matches are distributed among these distances:
170 14 0.02
171 447 0.74
172 139 0.23
173 7 0.01
ACGTcount: A:0.37, C:0.14, G:0.11, T:0.36
Consensus pattern (168 bp):
AAACAGATAATAATTGAATGTCTGCCTCGAGAAATATAAAGAAAAAGATATTCATTGGCAAGAAA
AGTCCGTTTATAGTCACCCATGCCTTCAAAAACCTTATTACTCGCATTAAATAATTTTATAATCT
CATAATTATTTTAAGTTGAATTTTTTTAATTTTTGTTA
Found at i:1100 original size:342 final size:339
Alignment explanation
Indices: 246--1201 Score: 935
Period size: 342 Copynumber: 2.8 Consensus size: 339
236 NNNNNNNCTT
* * * * *
246 AAACAGATTATAATTGACTGTCTACCTT-AGAAAATATAAATAAAAAAATATTCATTGGTAAGAA
1 AAACAGATAATAATTGAATGTCTACCTTGAG-AAAGATAAA-GAAAAAATATTCATTGGCAAGAA
* * * * * * **
310 TAGTCCATTTATAATCACCCATACCTTCAAAAGCTTTATTACTTGCTTTAAAGGTTTTTATAATC
64 AAGTCCATTTATAGTCACCCATGCATT-TAAAGCCTTATTACTTGCTTTAAATATTTTTATAATC
* * * * *
375 TCATAATTGACTTTAAGTAAAATGTTTTTACATTTTTTTTTAAAACAGATTAAAATTGAATGCTT
128 TCATAATTGA-TTTAAGTAGAATTTTTTTACATTTTTTATTAAAACAGATTAAAATTGAAT-ATC
* * * *
440 TCCTTAGGAAATATGAAA-AACAAGATATTCATTGGAAAGAAAAGTCTACTTATAGTCACCCATG
191 TCCTCAAGAAATAT-AAAGAAAAAGATATTCATTGGCAAGAAAAGTCTACTTATAGTCACCCATG
* *
504 CCTTCAAAAACCCTTATTACTCGCTTTAAATAGTTTTAAAATCTCATAAATAGTTTTGAGTTGAA
255 CCTTCAAAAACCCTTATTACTCGCCTTAAATAGTTTTAAAATCTCATAAATAGTTTTAAGTTGAA
*
569 TATTTTTTAATTTTTAGGTA
320 TATTTTTTAATTTTTAGCTA
* * * * * *
589 AAACAGATAATAATTGAACGTTTGA-CTCGACAAATG-TCAAGAAAAAGACATTCATTGGCAAGA
1 AAACAGATAATAATTGAATGTCT-ACCTTGAGAAA-GATAAAGAAAAA-ATATTCATTGGCAAGA
* * ** * *
652 AAAGTCCGTTTATAGTCACCCATGCATTTAAAGGCCTTATTACTCGGATTAAATAATTTTATAAC
63 AAAGTCCATTTATAGTCACCCATGCATTTAAA-GCCTTATTACTTGCTTTAAATATTTTTATAAT
* ********** *
717 CTCATAATTGATTTTAAGTTGAATTNNNNNNNNNNTTTTATTAAAACAGATTATAATTGAATATC
127 CTCATAATTGA-TTTAAGTAGAATTTTTTTACATTTTTTATTAAAACAGATTAAAATTGAATATC
* **********
782 TGCCTCAAGAAATATAAAGAAAAAGATATCCATTGGCAAGNNNNNNNNNNTTATAGTCACCCATG
191 T-CCTCAAGAAATATAAAGAAAAAGATATTCATTGGCAAGAAAAGTCTACTTATAGTCACCCATG
* * * *
847 CCTTCGAAAA-CCTTATTACTCGCCTTAAATATTTTTATAATCTCATAATTCA-TTTTAAGTT-A
255 CCTTCAAAAACCCTTATTACTCGCCTTAAATAGTTTTAAAATCTCATAAAT-AGTTTTAAGTTGA
909 GAT-TTTTTTATATTTTT-GTCTA
319 -ATATTTTTTA-ATTTTTAG-CTA
*
931 AAACAGATAATAATTGAATGTCTACCTTGAGAAAGATGAAGAAAAGAATATTCATTGGCAAGAAA
1 AAACAGATAATAATTGAATGTCTACCTTGAGAAAGATAAAGAAAA-AATATTCATTGGCAAGAAA
* * * * * * *
996 AGCCCATTTGTAGTCACCGATGCTTTTGAAAGCCTTATTAATTGCTTTAGATATTTTTATAGTCT
65 AGTCCATTTATAGTCACCCATGCATTT-AAAGCCTTATTACTTGCTTTAAATATTTTTATAATCT
*
1061 CATAATTGATTTCAAGTAGAATTTTTTTACATTTTTTATTAAAACAAATTAAAATTGAATGCAT-
129 CATAATTGATTT-AAGTAGAATTTTTTTACATTTTTTATTAAAACAGATTAAAATTGAAT--ATC
* * * * * *
1125 TCCTCTAGAAACATGAAGAAAATGATATTCATTGGCAAGAAAAGTCTACTTATACTCACCCATAC
191 TCCTCAAGAAATATAAAGAAAAAGATATTCATTGGCAAGAAAAGTCTACTTATAGTCACCCATGC
1190 CTTC-AAAACCCT
256 CTTCAAAAACCCT
1202 NNNNNNNNNN
Statistics
Matches: 480, Mismatches: 114, Indels: 39
0.76 0.18 0.06
Matches are distributed among these distances:
341 18 0.04
342 265 0.55
343 193 0.40
344 4 0.01
ACGTcount: A:0.37, C:0.14, G:0.11, T:0.35
Consensus pattern (339 bp):
AAACAGATAATAATTGAATGTCTACCTTGAGAAAGATAAAGAAAAAATATTCATTGGCAAGAAAA
GTCCATTTATAGTCACCCATGCATTTAAAGCCTTATTACTTGCTTTAAATATTTTTATAATCTCA
TAATTGATTTAAGTAGAATTTTTTTACATTTTTTATTAAAACAGATTAAAATTGAATATCTCCTC
AAGAAATATAAAGAAAAAGATATTCATTGGCAAGAAAAGTCTACTTATAGTCACCCATGCCTTCA
AAAACCCTTATTACTCGCCTTAAATAGTTTTAAAATCTCATAAATAGTTTTAAGTTGAATATTTT
TTAATTTTTAGCTA
Found at i:1815 original size:171 final size:170
Alignment explanation
Indices: 1523--2505 Score: 760
Period size: 171 Copynumber: 5.8 Consensus size: 170
1513 NNNNCAGATT
* * * **
1523 ATAATTGAATGTTTACCTCGAGAAACATGAAAAAAAAGATATCCATTGATAAGAAAAGTCCATTT
1 ATAATTGAATGTTTACCTTGAGAAACGTGAAGAAAAAGATATCCATTGGCAAGAAAAGTCCATTT
* * * * *
1588 ATAGTCTCTCATGCCTTCGAAAGCCTTATTACTCGCCCTAAATGTGTTTATAATCTCATAATGGA
66 ATAGTCAC-CATGCCTTCGAAAGCCTTATTACTCACCTTAAATGTTTTTATAATCTCATAATTGA
* * *
1653 TTTTAAGTTAAGTTTTTTTATATTTTTTATTAAAACATATT
130 TTTTAAGTTAAATTTTTTTACATTTTTTATTAAAACATATA
* * * * *
1694 ATAATTGATTTTTTACCTTTAGAAACGTGAAGAAAAAGATATACAGTGGCAAGAAAAGTCCATTT
1 ATAATTGAATGTTTACCTTGAGAAACGTGAAGAAAAAGATATCCATTGGCAAGAAAAGTCCATTT
* * *
1759 ATAGTCACTCATACATTCGAAAGCCTTATTACTCACCTTAAATGTTTTTTTAATCTCATAATTGA
66 ATAGTCAC-CATGCCTTCGAAAGCCTTATTACTCACCTTAAATGTTTTTATAATCTCATAATTGA
***********
1824 TTTTAAGTTAAATTTTTTNNNNNNNNNNGTTAAAACATATA
130 TTTTAAGTTAAATTTTTTTACATTTTTTATTAAAACATATA
* ** * * * ** * * * *
1865 ATAATTGAATGTCTGTCTTGTGAAATGTAAAGAAAAAGATATTTATTAGTAGGAAAAGCCCATTT
1 ATAATTGAATGTTTACCTTGAGAAACGTGAAGAAAAAGATATCCATTGGCAAGAAAAGTCCATTT
* * * * * * *
1930 GTAGTCACCGATGCCTT-AAAAGCCTTATTACTCGCTTTAAATATTTTTACAATCTCATAATTAA
66 ATAGTCACC-ATGCCTTCGAAAGCCTTATTACTCACCTTAAATGTTTTTATAATCTCATAATTGA
* * * * *
1994 TTTTCA-TCAGAAATGTTTTACATTTTTAATTAAAA-ATAATA
130 TTTTAAGTTA-AATTTTTTTACATTTTTTATTAAAACAT-ATA
* * * * ** * * *
2035 ATAACTT-AATGTTT-GCTTAGGGAAACCTAAAGAAAAAGCCA-CTCAATGGCAAGAGAAGTTCA
1 ATAA-TTGAATGTTTACCTT-GAGAAACGTGAAGAAAAAGATATC-CATTGGCAAGAAAAGTCCA
* ********* * * *
2097 TTTATTGTCACCCATGCCTTC-AANNNNNNNNNNACGT-AACTAAAATGTTTTTAGAATCTCATA
63 TTTATAGTCA-CCATGCCTTCGAA-AGCCTTATTAC-TCACCTTAAATGTTTTTATAATCTCATA
* * * *
2160 ATTGATTTTAATTTAAATTTTTGTACATTTTTTGTTAAAACAGATA
125 ATTGATTTTAAGTTAAATTTTTTTACATTTTTTATTAAAACATATA
* * * * * * *
2206 ATAATTGAATGCTTGCC-TGGGAAAACTTGAAGCAAAAGATATCCTTTGGCAAGAAAAGTCTATT
1 ATAATTGAATGTTTACCTTGAG-AAACGTGAAGAAAAAGATATCCATTGGCAAGAAAAGTCCATT
* * * * * * * *
2270 TATAGTCACCCTTACCTTCGGAAGCCTTATTGCTCACTTTAAATGATTTTATAACCTCATAATCG
65 TATAGTCA-CCATGCCTTCGAAAGCCTTATTACTCACCTTAAATGTTTTTATAATCTCATAATTG
* * * * * * * *
2335 ATTTTAAGTTGAATTTATTTATATTTTCTCTTAAAAGAGATT
129 ATTTTAAGTTAAATTTTTTTACATTTTTTATTAAAACATATA
* * * * *
2377 ATAATTGAATGTTTACCTTGAGAAATGTGAAGAAAAAAATATTCATTGACAAGAAAAATCCATTT
1 ATAATTGAATGTTTACCTTGAGAAACGTGAAGAAAAAGATATCCATTGGCAAGAAAAGTCCATTT
* * *
2442 ATAGTCACCGATGCCTTCGAAAGTCTTATTACTCACTTTAAATGGTTTTATAATCTCATAATTG
66 ATAGTCACC-ATGCCTTCGAAAGCCTTATTACTCACCTTAAATGTTTTTATAATCTCATAATTG
2506 NNNNNNNNNN
Statistics
Matches: 616, Mismatches: 176, Indels: 40
0.74 0.21 0.05
Matches are distributed among these distances:
169 7 0.01
170 124 0.20
171 475 0.77
172 10 0.02
ACGTcount: A:0.36, C:0.14, G:0.12, T:0.37
Consensus pattern (170 bp):
ATAATTGAATGTTTACCTTGAGAAACGTGAAGAAAAAGATATCCATTGGCAAGAAAAGTCCATTT
ATAGTCACCATGCCTTCGAAAGCCTTATTACTCACCTTAAATGTTTTTATAATCTCATAATTGAT
TTTAAGTTAAATTTTTTTACATTTTTTATTAAAACATATA
Done.