Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018398986.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_2267.0, 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: 1941
ACGTcount: A:0.35, C:0.12, G:0.13, T:0.33
Warning! 151 characters in sequence are not A, C, G, or T
Found at i:367 original size:170 final size:169
Alignment explanation
Indices: 186--754 Score: 507
Period size: 171 Copynumber: 3.3 Consensus size: 169
176 NNNNNNAAAG
186 CGAGTAATAAGGCTTTCAAAGGCATGAGTGACTATAAATGGACTTTTTATGTCAATGGATGGCTT
1 CGAGTAATAAGGCTTTCAAAGGCATGAGTGACTATAAATGGACTTTTTATGTCAATGGATGGCTT
* * *
251 TCACTTCATGTTTCCTATGATAAACATTCAATTATAATCTATTTATGCCCAAAATATGAAAAATT
66 TCGCTTCATGTTTCTTATGATAGACATTCAATTATAATCTATTTATGCCCAAAATATGAAAAATT
*
316 CAACTTAAAATCAGTTATGAGATTACAAAACCATTTTATA
131 CAACTTAAAATCAG-TATGAGATTATAAAACCATTTTATA
* * * * *
356 CGAGTAATAAGGCTTTCGAAA-GCATGAGTAACTTTAAATAGACTTTTTTTATCAATAGG-TGGC
1 CGAGTAATAAGGCTTTC-AAAGGCATGAGTGACTATAAATGGACTTTTTATGTCAAT-GGATGGC
* ** * * *
419 TTTTGCTTCATGCATCTTAGGACAGACATTCAATTATAATCT-TTT-TGACCCAAAATAGTAAAA
64 TTTCGCTTCATGTTTCTTATGATAGACATTCAATTATAATCTATTTATG-CCCAAAATA-T-GAA
* * * *
482 AAATTCAACTTATAATCAACTATGA-ATTTGTAAAACCA-TTTAAA
126 AAATTCAACTTAAAATC-AGTATGAGA-TTATAAAACCATTTTATA
* * * * * * *
526 GGGAGTAATAGGGCTTTCGAAGGTATGATTGACTATAAATTGACTTTTCT-TGTCAGTGGATGGC
1 -CGAGTAATAAGGCTTTCAAAGGCATGAGTGACTATAAATGGACTTTT-TATGTCAATGGATGGC
* * * *
590 TTTCGCTTCACGTTT-TTCATGGTAGACATTCAATTATAATCTAGTTTA--ACC-TAATATGCAA
64 TTTCGCTTCATGTTTCTT-ATGATAGACATTCAATTATAATCTA-TTTATGCCCAAAATATG---
* * * *
651 AAACAATTTAGCTTACAATCAAGTATGAGATTATAAAACCATTTAAATA
124 AAA-AATTCAACTTAAAATC-AGTATGAGATTATAAAACCATTT-TATA
* * * * * * * *
700 -GTGTAATAAGACTTTCGAATGCATAAGAGACTATAAATGAAC-TTTCATGTCAATG
1 CGAGTAATAAGGCTTTCAAAGGCATGAGTGACTATAAATGGACTTTTTATGTCAATG
755 CATAAGTTTT
Statistics
Matches: 318, Mismatches: 58, Indels: 45
0.76 0.14 0.11
Matches are distributed among these distances:
168 2 0.01
169 13 0.04
170 102 0.32
171 129 0.41
172 64 0.20
173 6 0.02
174 2 0.01
ACGTcount: A:0.36, C:0.14, G:0.15, T:0.35
Consensus pattern (169 bp):
CGAGTAATAAGGCTTTCAAAGGCATGAGTGACTATAAATGGACTTTTTATGTCAATGGATGGCTT
TCGCTTCATGTTTCTTATGATAGACATTCAATTATAATCTATTTATGCCCAAAATATGAAAAATT
CAACTTAAAATCAGTATGAGATTATAAAACCATTTTATA
Found at i:573 original size:171 final size:171
Alignment explanation
Indices: 182--933 Score: 504
Period size: 171 Copynumber: 4.4 Consensus size: 171
172 NNNNNNNNNN
* * *
182 AAAGCGAGTAATAAGGCTTTCAAAGGCATGAGTGACTATAAATGGACTTTTTATGTCAATGGATG
1 AAAGCGAGTAATAAGGCTTTCGAAGGCATGAGTGACTATAAATAGACTTTTTTTGTCAATGGATG
* ** * * *
247 GCTTTCACTTCATGTTTCCTATGATAAACATTCAATTATAATCTATTTATGCCCAAAATATGAAA
66 GCTTTCGCTTCATGCATCCTAGGACAAACATTCAATTATAATCTATTTATGCCCAAAATATAAAA
**
312 AATTCAACTTAAAATCAGTTATGAGATTACAAAACCATTTT
131 AATTCAACTTAAAATCAACTATGAGATTACAAAACCATTTT
* * * * *
353 ATA-CGAGTAATAAGGCTTTCGAAAGCATGAGTAACTTTAAATAGACTTTTTTTATCAATAGG-T
1 AAAGCGAGTAATAAGGCTTTCGAAGGCATGAGTGACTATAAATAGACTTTTTTTGTCAAT-GGAT
* * *
416 GGCTTTTGCTTCATGCATCTTAGGACAGACATTCAATTATAATCT-TTT-TGACCCAAAATAGTA
65 GGCTTTCGCTTCATGCATCCTAGGACAAACATTCAATTATAATCTATTTATG-CCCAAAATA-T-
* **
479 AAAAAATTCAACTTATAATCAACTATGA-ATTTGTAAAACCA-TTT
127 AAAAAATTCAACTTAAAATCAACTATGAGA-TTACAAAACCATTTT
* * * * * * *
523 AAAGGGAGTAATAGGGCTTTCGAAGGTATGATTGACTATAAATTGACTTTTCTTGTCAGTGGATG
1 AAAGCGAGTAATAAGGCTTTCGAAGGCATGAGTGACTATAAATAGACTTTTTTTGTCAATGGATG
* * ** * * * * *
588 GCTTTCGCTTCACG-TTTTTCATGG-TAGACATTCAATTATAATCTAGTTTA-ACCTAATATGCA
66 GCTTTCGCTTCATGCATCCT-A-GGACAAACATTCAATTATAATCTA-TTTATGCCCAAAAT--A
* * * * *
650 -AAAACAATTTAGCTTACAATCAAGTATGAGATTATAAAACCA-TTT
126 TAAAA-AATTCAACTTAAAATCAACTATGAGATTACAAAACCATTTT
** * * * * * ** *
695 AAATAGTGTAATAAGACTTTCGAATGCATAAGAGACTATAAAT-GAAC-TTTCATGTCAATGCAT
1 AAAGCGAGTAATAAGGCTTTCGAAGGCATGAGTGACTATAAATAG-ACTTTTTTTGTCAATGGAT
* * * * * * * * * **
758 AAG-TTTTGCTTTACG-ATTCCCAAGGA-AAATAATCAATTATAATTTTTTTTAAT--AAAAAAT
65 -GGCTTTCGCTTCATGCA-T-CCTAGGACAAACATTCAATTATAA-TCTATTT-ATGCCCAAAAT
* * * * * * *
818 GTAAAAAAATT-TAGTTTAAATCAATTATGACATTATAAAACCA-TTT
125 AT-AAAAAATTCAACTTAAAATCAACTATGAGATTACAAAACCATTTT
* * *
864 AAAGC-ATGCAATAAGGCTTTCGAAGGAATGAGTGACTATAAATAGACTTTTCTTG-CTAATGGA
1 AAAGCGA-GTAATAAGGCTTTCGAAGGCATGAGTGACTATAAATAGACTTTTTTTGTC-AATGGA
927 TGGCTTT
64 TGGCTTT
934 TTCTTTACGT
Statistics
Matches: 455, Mismatches: 95, Indels: 63
0.74 0.15 0.10
Matches are distributed among these distances:
168 2 0.00
169 77 0.17
170 119 0.26
171 170 0.37
172 82 0.18
173 4 0.01
174 1 0.00
ACGTcount: A:0.37, C:0.13, G:0.15, T:0.35
Consensus pattern (171 bp):
AAAGCGAGTAATAAGGCTTTCGAAGGCATGAGTGACTATAAATAGACTTTTTTTGTCAATGGATG
GCTTTCGCTTCATGCATCCTAGGACAAACATTCAATTATAATCTATTTATGCCCAAAATATAAAA
AATTCAACTTAAAATCAACTATGAGATTACAAAACCATTTT
Found at i:1406 original size:171 final size:171
Alignment explanation
Indices: 1116--1854 Score: 502
Period size: 171 Copynumber: 4.3 Consensus size: 171
1106 NNNNNNNNNN
* *
1116 ATAATCTTTTTTAACCAAGAATATAAAAAAATTCACCTTAAAATCAATTATGAGAATACAAAACC
1 ATAATCTATTTTAACCAAGAATATAAAAAAATTCAACTTAAAATCAATTATGAGAATACAAAACC
* * *
1181 ATTTAAAGCAAGTAATAATGCTTCCAGAGGAATAAGTGACTATAAATAGACTTTTCATGTTAATG
66 ATTCAAAGAAAGTAATAATGCTTCCAGAGGAATAAGTGACTATAAATAGACTTTTCATGTCAATG
*
1246 GGTGGCTTTTGCTTCATATTTCTTTGAACAGGCATTCAATT
131 GATGGCTTTTGCTTCATATTTCTTTGAACAGGCATTCAATT
* * * *
1287 ATAATCTATTTTAACC-ATAATAATAAAAAAATTCAACTTAAAATTAATTATGA-ATTTATAAAA
1 ATAATCTATTTTAACCAAGAAT-ATAAAAAAATTCAACTTAAAATCAATTATGAGA-ATACAAAA
* * * * * * * * *
1350 CCATTCAAA-AAGAGTGATAGTGCTTTC-GAAGGCATAATTGACTGTCAATGGACTTTTCTTGTC
64 CCATTCAAAGAA-AGTAATAATGCTTCCAG-AGGAATAAGTGACTATAAATAGACTTTTCATGTC
* * ** *
1413 AATGGATGGCTTTTACTTAACGTTTCTCATAGTAA-A--CATTCAACTT
127 AATGGATGGCTTTTGCTTCATATTTCT--TTG-AACAGGCATTCAA-TT
* * * * * * * *
1459 AAAATCTGTTTTAAGCAAAAATTTAAAACAAATTCAACTTGAAATCAATTACGAGATTACAAAAC
1 ATAATCTATTTTAACCAAGAATATAAAA-AAATTCAACTTAAAATCAATTATGAGAATACAAAAC
** * * * * ** ** * * * ** **
1524 CATTTTATGCATGTAATAAGGCTT-TTGAAGTCATGAGTGATTATAAATAGGCTTTTTTTACCAA
65 CATTCAAAGAAAGTAATAATGCTTCCAG-AGGAATAAGTGACTATAAATAGACTTTTCATGTCAA
* * * ** *
1588 TGGATAGCTTTTCCTTCATGTTTC-TT-AAGGCAAACATACAATT
129 TGGATGGCTTTTGCTTCATATTTCTTTGAA--CAGGCATTCAATT
* ** * * * * * *
1631 ATAATCTATTTAAATAAAGAATATAAAAAAGTTTAATTTAAAATCAATTATGAGATTATAAAACT
1 ATAATCTATTTTAACCAAGAATATAAAAAAATTCAACTTAAAATCAATTATGAGAATACAAAACC
* * * * * *
1696 A-TCTAAAGAAAGGAATAATTCTAT-CAAAGGCATAAGTGACTATAAATGGACTTTTCTTGTCAA
66 ATTC-AAAGAAAGTAATAATGCT-TCCAGAGGAATAAGTGACTATAAATAGACTTTTCATGTCAA
* ** *
1759 TAGG-TGGCTTTTGCATT-ACT-TTTCTTGGGGCAGACATTCAATT
129 T-GGATGGCTTTTGC-TTCA-TATTTCTTTGAACAGGCATTCAATT
* * * *
1802 ATAATCTGTTTTATCCAA-AATAGTAAACAAATTAAACTTAAAATCAATTATGA
1 ATAATCTATTTTAACCAAGAATA-TAAAAAAATTCAACTTAAAATCAATTATGA
1855 ATTTATAAAA
Statistics
Matches: 434, Mismatches: 108, Indels: 52
0.73 0.18 0.09
Matches are distributed among these distances:
168 2 0.00
170 13 0.03
171 261 0.60
172 50 0.12
173 104 0.24
174 4 0.01
ACGTcount: A:0.40, C:0.13, G:0.12, T:0.35
Consensus pattern (171 bp):
ATAATCTATTTTAACCAAGAATATAAAAAAATTCAACTTAAAATCAATTATGAGAATACAAAACC
ATTCAAAGAAAGTAATAATGCTTCCAGAGGAATAAGTGACTATAAATAGACTTTTCATGTCAATG
GATGGCTTTTGCTTCATATTTCTTTGAACAGGCATTCAATT
Done.