Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018401845.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_4951.0, 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: 1820
ACGTcount: A:0.38, C:0.11, G:0.14, T:0.36
Warning! 10 characters in sequence are not A, C, G, or T
Found at i:310 original size:170 final size:169
Alignment explanation
Indices: 1--1125 Score: 918
Period size: 171 Copynumber: 6.6 Consensus size: 169
* * * * *
1 TCTTCATGTTTCTTGAGGTAGACATTCAATTATAGTTTGTTTTAACAAAAAATGCAAAAACATTG
1 TCTTCATGTTTCTTGAGGTAGACATTCAATTATAGTCTGTTTTAACTAAAAATGTAAAAAAATTC
* * ********** * *
66 AACTTAAAATCAATTATGAGATTATAAAATCATTTAAAGCAAGNNNNNNNNNNTTTGAAGGAATA
66 AACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAAGAATG
* *
131 AGAGACTATAAATGGACTTTTCTTGCCAATGACTACTTGTT
131 GGTGACTATAAATGGACTTTTCTTGCCAATGACTA-TT-TT
* * * * *
172 TCTTCATGTTTCTTGAGCTAGACATTCCATTATTGTCTGTTTTAAC-CAAAATGTAAAACAATTC
1 TCTTCATGTTTCTTGAGGTAGACATTCAATTATAGTCTGTTTTAACTAAAAATGTAAAAAAATTC
* * * * * **
236 AGCTTAAAATCAATTTTGAGATTATAAAACCATTTAAAACGAATAATAAGGTTTTTGATGGAATG
66 AACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAAGAATG
*
301 GGTGACTATAAATGGACTTTTCTTGCCAATGAATTGCATTTT
131 GGTGACTATAAATGGACTTTTCTTGCCAATG-ACT--ATTTT
* ** * * *
343 T-TACATGTTTCTTGAGACAAGTA-A-TCAATTATAGCCTGTTTTGACTAAAAATATAAAAAAAT
1 TCTTCATGTTTCTTGAG-GTAG-ACATTCAATTATAGTCTGTTTTAACTAAAAATGTAAAAAAAT
* * * *
405 TCAACTTAAAATCAATTATAAGATTATAGAACCATTTAAAGCGTGTAATAAAG-TTTTGAAAGAA
64 TCAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAAGAA
* * ** * * *
469 TAGGTAACTATAAATGGACTTTTCTTATCAAAGAGTGCCTTTT
129 TGGGTGACTATAAATGGACTTTTCTTGCCAATGACT--ATTTT
* * * * * *
512 TTTTCACT-TTTCTCGAGGTAAACATTGAATTATAATCTATTTTAACTAAAAATGTAAAAAAAAT
1 TCTTCA-TGTTTCTTGAGGTAGACATTCAATTATAGTCTGTTTTAACTAAAAATGT-AAAAAAAT
* * * * * *
576 TGAACTTGAAATCAATTTTGAGATTATAAAACTATTTCAAGTGAGTAATAAGGCTTTTGAAAGAA
64 TCAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAAGAA
* * *
641 TGGGTGACTATAAATGCACTTTGCTTGCTAATGAATCTATTTT
129 TGGGTGACTATAAATGGACTTTTCTTGCCAATG-A-CTATTTT
* * * * * * *
684 T-TTTACGTTTCTCGAGGTAAACATTGAATTATTA-TATTTTTTAACTAAAAATGTATAAAAAAT
1 TCTTCATGTTTCTTGAGGTAGACATTCAATTA-TAGTCTGTTTTAACTAAAAATGTA-AAAAAAT
* * * *
747 TAAACTGAAAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTG-ATGAG
64 TCAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAAGAA
* * * *
811 TGGGAGACTATAAATGGACTTTTCTT-CTAAATAAATGTATTTT
129 TGGGTGACTATAAATGGACTTTTCTTGC-CAAT-GA-CTATTTT
* ** * * * * * *
854 TGTATACA--TTTCCCGAGGCAGACATGT-AATCAAAGTTTTTTTTAA-TGAAAAATAT-AAAAA
1 TCT-T-CATGTTTCTTGAGGTAGACAT-TCAATTATAGTCTGTTTTAACT-AAAAATGTAAAAAA
* * * * *
914 ATTTAATTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCTAGTAATAAGGCTTCTGAAGG
62 ATTCAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAAG
* ** * * * *
979 AATGAGACACTATAAATGGACTTTTTTTGTCAATGAATGGCTTTT
127 AATGGGTGACTATAAATGGACTTTTCTTGCCAATGACT--ATTTT
* * * *
1024 T-TTACATATTTCTTGAGGTAGCCATTCAATTATAGTCTGTTTTAA-TGAAAAATGTAATAGAAT
1 TCTT-CATGTTTCTTGAGGTAGACATTCAATTATAGTCTGTTTTAACT-AAAAATGTAAAAAAAT
*
1087 TCAACTT-AAATACAATTATGAGATTATAATACCATTTAA
64 TCAACTTAAAAT-CAATTATGAGATTATAAAACCATTTAA
1126 GGCCACTAAT
Statistics
Matches: 777, Mismatches: 143, Indels: 68
0.79 0.14 0.07
Matches are distributed among these distances:
168 6 0.01
169 76 0.10
170 307 0.40
171 336 0.43
172 48 0.06
173 3 0.00
174 1 0.00
ACGTcount: A:0.38, C:0.11, G:0.14, T:0.36
Consensus pattern (169 bp):
TCTTCATGTTTCTTGAGGTAGACATTCAATTATAGTCTGTTTTAACTAAAAATGTAAAAAAATTC
AACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAAGAATG
GGTGACTATAAATGGACTTTTCTTGCCAATGACTATTTT
Found at i:1430 original size:306 final size:306
Alignment explanation
Indices: 894--1448 Score: 728
Period size: 306 Copynumber: 1.8 Consensus size: 306
884 CAAAGTTTTT
* * *
894 TTTAATGAAAAATATAAAAAATTTAATTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCT
1 TTTAATGAAAAATATAAAAAATTCAAATTAAAATCAATTATGAGATTATAAAACCATTTAAAGCG
* * * **
959 AGTAATAAGGCTTCTGAAGGAATGAGACACTATAAATGGACTTTTTTTGTCAATGAATGGCTTTT
66 AGTAATAAGGCTTCTGAAGGAATGAGACACTATAAATAGACTTTTCTTGCCAATGAATACCTTTT
** * * * *
1024 TTTACATATTTCTTGAGGTAGCCATTCAATTATAGTCTGTTTTAATGAAAAATGTAATAGAATTC
131 TTTACATATTTCTTGAGGTAAACATTCAATTATAATCTATTTTAATGAAAAATGTAAAACAATTC
* * *
1089 AACTTAAATACAATTATGAGATTATAATACCATTTAAGGCCACTAATATGGCTTATCAATAAATG
196 AACTAAAATACAATTATGAGATAATAATACCATTTAAAGCCACTAATATGGCTTATCAATAAATG
1154 GCTTTTTTTACACGTTTTCGAAGGCAAGGAATCAATTATAGTCTAC
261 GCTTTTTTTACACGTTTTCGAAGGCAAGGAATCAATTATAGTCTAC
* * *
1200 TTTAATGAAAAA-AGTAAACAATTCAAATTAAAATCAATTATGAGATTATAGAACCATTTTAAGC
1 TTTAATGAAAAATA-TAAAAAATTCAAATTAAAATCAATTATGAGATTATAAAACCATTTAAAGC
* ** *
1264 GAGTAATAAGGCTTTTGAAGGAATCG-GTGATTATAAATAGACTTTTCTTGCCAATGAATACCTT
65 GAGTAATAAGGCTTCTGAAGGAAT-GAGACACTATAAATAGACTTTTCTTGCCAATGAATACCTT
* *
1328 TTTCTT-TATGTTTCTTGA-GTAAACATTCAATTATAATCTATTTTAA-GTAAAAATGTAAAAAC
129 TTT-TTACATATTTCTTGAGGTAAACATTCAATTATAATCTATTTTAATG-AAAAATGT-AAAAC
* * * *
1390 AATTGAACATAAAAT-CAATTTTGAGATAATAA-AGCCATTTAAAGCGAGTAATATGGCTT
191 AATTCAAC-TAAAATACAATTATGAGATAATAATA-CCATTTAAAGCCACTAATATGGCTT
1449 TCGAAGGAAT
Statistics
Matches: 212, Mismatches: 30, Indels: 14
0.83 0.12 0.05
Matches are distributed among these distances:
304 1 0.00
305 34 0.16
306 169 0.80
307 8 0.04
ACGTcount: A:0.40, C:0.11, G:0.14, T:0.36
Consensus pattern (306 bp):
TTTAATGAAAAATATAAAAAATTCAAATTAAAATCAATTATGAGATTATAAAACCATTTAAAGCG
AGTAATAAGGCTTCTGAAGGAATGAGACACTATAAATAGACTTTTCTTGCCAATGAATACCTTTT
TTTACATATTTCTTGAGGTAAACATTCAATTATAATCTATTTTAATGAAAAATGTAAAACAATTC
AACTAAAATACAATTATGAGATAATAATACCATTTAAAGCCACTAATATGGCTTATCAATAAATG
GCTTTTTTTACACGTTTTCGAAGGCAAGGAATCAATTATAGTCTAC
Found at i:1503 original size:171 final size:167
Alignment explanation
Indices: 1185--1817 Score: 669
Period size: 171 Copynumber: 3.8 Consensus size: 167
1175 AGGCAAGGAA
* * * *
1185 TCAATTATAGTCTACTTTAATGAAAAAAGT-AAACAATTCAA-ATTAAAATCAATTATGAGATTA
1 TCAATTATAGTCTATTTTAAT-AAAAATGTAAAACAATTCAACA-TAAAATCAATTTTGAGATAA
* * *
1248 TAGAACCATTTTAAGCGAGTAATAAGGCTTTTGAAGGAATCGGTGATTATAAATAGACTTTTCTT
64 TA-AACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAAT-GGAGACTATAAAT-GACTTTTCTT
* *
1313 GCCAATGAATACCTTTTTCTTTATGTTTCTTGA-GTAAACAT
126 GCCAATGAATACTTTTTTCTTTATGTTTCTCGACGTAAACAT
* *
1354 TCAATTATAATCTATTTTAAGTAAAAATGTAAAAACAATTGAACATAAAATCAATTTTGAGATAA
1 TCAATTATAGTCTATTTTAA-TAAAAATGT-AAAACAATTCAACATAAAATCAATTTTGAGATAA
* *
1419 TAAAGCCATTTAAAGCGAGTAATATGGCTTTCGAAGGAATGAGAGACTATAAATGGACTTTTCTT
64 TAAA-CCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATG-GAGACTATAAAT-GACTTTTCTT
* *
1484 GCCAATGAATACTTTTTTCTTCACGTTTCTCGACGTAAACAT
126 GCCAATGAATACTTTTTTCTTTATGTTTCTCGACGTAAACAT
* * * * * * * *
1526 TCAATTATGGTCTGTTGTAACCAAAAATGCACAAAAAATTGAACATAAAATCAATTTTAAGATAA
1 TCAATTATAGTCTATTTTAA-TAAAAATGTA-AAACAATTCAACATAAAATCAATTTTGAGATAA
* *
1591 CAAAACCATTTAAAGTGAGTAATAAGGCTTTTGAAGGAATGGGAGACTATAAATGACTTTTCTTG
64 -TAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAAT-GGAGACTATAAATGACTTTTCTTG
* * * *
1656 CCAATGAATGCTTTTTT-TTTCATATTTCTCGATGTACACAT
127 CCAATGAATACTTTTTTCTTT-ATGTTTCTCGACGTAAACAT
* * * *
1697 TCAATTATAGTCTGTTTTAAAAAAAATGTAAAACAATT---C----AA-CAATTATGAGATTATA
1 TCAATTATAGTCTATTTTAATAAAAATGTAAAACAATTCAACATAAAATCAATTTTGAGATAATA
* ** * * * *
1754 AATCATTTAGTGTGAGTAATAAGGCTTTTGAAGGAATGGGTGATTATAAATGGACTTTGCTTGC
66 AACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAAT-GGAGACTATAAAT-GACTTTTCTTGC
1818 TAA
Statistics
Matches: 402, Mismatches: 50, Indels: 32
0.83 0.10 0.07
Matches are distributed among these distances:
160 47 0.12
161 22 0.05
162 2 0.00
166 1 0.00
169 32 0.08
170 14 0.03
171 173 0.43
172 107 0.27
173 4 0.01
ACGTcount: A:0.38, C:0.12, G:0.15, T:0.35
Consensus pattern (167 bp):
TCAATTATAGTCTATTTTAATAAAAATGTAAAACAATTCAACATAAAATCAATTTTGAGATAATA
AACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGGAGACTATAAATGACTTTTCTTGCCAA
TGAATACTTTTTTCTTTATGTTTCTCGACGTAAACAT
Done.