Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018401848.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_4954.0, 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: 2519
ACGTcount: A:0.31, C:0.10, G:0.11, T:0.30
Warning! 449 characters in sequence are not A, C, G, or T
Found at i:284 original size:170 final size:160
Alignment explanation
Indices: 1--498 Score: 438
Period size: 170 Copynumber: 3.0 Consensus size: 160
** * * ** *
1 TTATAAAATCATTTAAAGCGAGTAATAAACCTTTTGAAGGAATGGGTGACTATATGTTGACTTTA
1 TTATAAAATCATTTAAAGCGAGTAAT-AAGGTTTTGAAGGAATAGGAGACTATAAATGGACTTT-
* * * * * *
66 CTTACCAATGAATGCATTGTTCTTCATGTTTCTCAGGCTAGACATTCAATTATAATCTGTTTTAA
64 TTTGCCAATGAATACATT-TTCTTTACGTTTCTCAGGC-AAACATTCAATTATAATCTGTTTTAA
* ***
131 CAAAAAATGTAAAAAAATNNNNNNNNNNATTAATTATGAGA
127 CAAAAAATATAAAAAAAT-------TCAATTAATTATGAGA
*
172 TTATAAAATCATTTAAAGCGAGTAATAAGGTTTTGATGGAATAGGAGACTATAAATGGACTTCTT
1 TTATAAAATCATTTAAAGCGAGTAATAAGGTTTTGAAGGAATAGGAGACTATAAATGGACTT-TT
* * *
237 TTGCCAATGAATATATATTTCTTTACGTTTCTCAAGGCAAACATTCAATTATAGTCTGTTTCAAC
65 TTGCCAATGAATACAT-TTTCTTTACGTTTCTC-AGGCAAACATTCAATTATAATCTGTTTTAAC
* ***
302 CAAAAATATAAAAAAATTCANNNNNNNNNNAATTATGAGA
128 AAAAAATATAAAAAAATTCA-------ATTAATTATGAGA
* * * * *
342 TTATAAAACCATTTAAAGCAAGTAATAAGGCTTCTGAAAGAATAGGAGACTATAAATGAACTTTT
1 TTATAAAATCATTTAAAGCGAGTAATAAGG-TTTTGAAGGAATAGGAGACTATAAATGGACTTTT
* * * *
407 CTTGCCAATGAATACATTTTTCTTTACGTTTCTCGAGGTAAGCATTCAATTATAATATGTTTTCA
65 -TTGCCAATGAATACA-TTTTCTTTACGTTTCTC-AGGCAAACATTCAATTATAATCTGTTTTAA
**
472 CTGAAAATATAAAAAAATTCAACTTAA
127 CAAAAAATATAAAAAAATTCAA-TTAA
499 AATCAATTAT
Statistics
Matches: 269, Mismatches: 44, Indels: 34
0.78 0.13 0.10
Matches are distributed among these distances:
165 2 0.01
170 133 0.49
171 133 0.49
172 1 0.00
ACGTcount: A:0.38, C:0.12, G:0.13, T:0.34
Consensus pattern (160 bp):
TTATAAAATCATTTAAAGCGAGTAATAAGGTTTTGAAGGAATAGGAGACTATAAATGGACTTTTT
TGCCAATGAATACATTTTCTTTACGTTTCTCAGGCAAACATTCAATTATAATCTGTTTTAACAAA
AAATATAAAAAAATTCAATTAATTATGAGA
Found at i:509 original size:171 final size:170
Alignment explanation
Indices: 1--1169 Score: 724
Period size: 171 Copynumber: 6.8 Consensus size: 170
* ** * * **
1 TTATAAAATCATTTAAAGCGAGTAATAAACCTTTTGAAGGAATGGGTGACTATATGTTG-ACTTT
1 TTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATAGGAGACTATA-AATGAACTTT
* * * * * *
65 ACTTACCAATGAATGCATTGTTCTTCATGTTTCTC-AGGCTAGACATTCAATTATAATCTGTTTT
65 TCTTGCCAATGAATAC-TTTTTCTTCACGTTTCTCGAGG-TAGACATTCAATTATAGTCTGTTTT
* * ********** *
129 AACAAAAAATGTAAAAAAATNNNNNNNNNNATTAATTATGAGA
128 AACTAAAAATATAAAAAAATTCAACTTAAAATCAATTATGAGA
* * *
172 TTATAAAATCATTTAAAGCGAGTAATAAGG-TTTTGATGGAATAGGAGACTATAAATGGACTTCT
1 TTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATAGGAGACTATAAATGAACTT-T
* * * * *
236 T-TTGCCAATGAATA-TATATTTCTTTACGTTTCTCAAGGCAAACATTCAATTATAGTCTGTTTC
65 TCTTGCCAATGAATACT-T-TTTCTTCACGTTTCTCGAGGTAGACATTCAATTATAGTCTGTTTT
* **********
299 AACCAAAAATATAAAAAAATTCANNNNNNNNNNAATTATGAGA
128 AACTAAAAATATAAAAAAATTCAACTTAAAATCAATTATGAGA
* * *
342 TTATAAAACCATTTAAAGCAAGTAATAAGGCTTCTGAAAGAATAGGAGACTATAAATGAACTTTT
1 TTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATAGGAGACTATAAATGAACTTTT
* * * *
407 CTTGCCAATGAATACATTTTTCTTTACGTTTCTCGAGGTA-AGCATTCAATTATAATATGTTTTC
66 CTTGCCAATGAATAC-TTTTTCTTCACGTTTCTCGAGGTAGA-CATTCAATTATAGTCTGTTTTA
* **
471 ACTGAAAATATAAAAAAATTCAACTTAAAATCAATTATGANN
129 ACTAAAAATATAAAAAAATTCAACTTAAAATCAATTATGAGA
********* * * * * *
513 NNNNNNNNTCATTTAAAGTGAGTAATAAGGCTTTTGAAGGAACATGAGACTATGAATGGACTTTT
1 TTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATAGGAGACTATAAATGAACTTTT
******** * * * * * *
578 CTTGCCAATGAATNNNNNNNNNNTT-ATGTTTCTTGAGGTAGATATTTAATTATAGTTTTTTTTA
66 CTTGCCAATGAAT--ACTTTTTCTTCACGTTTCTCGAGGTAGACATTCAATTATAGTCTGTTTTA
* **********
642 A-TCAAAAATGTAAAAAAATTCAANNNNNNNNNNATTATGAGA
129 ACT-AAAAATATAAAAAAATTCAACTTAAAATCAATTATGAGA
* * * * * *
684 TTATAAAACTATTTAAAGAGAGTAATAA-GCTTTTTGAAGGGATGGGTGACTAT-AATGGACTTT
1 TTATAAAACCATTTAAAGCGAGTAATAAGGC-TTTTGAAGGAATAGGAGACTATAAATGAACTTT
* * * * * ** * *
747 TTTTGCTACTGAATGCCTTTTTCTTCACGTTTCTCAAGGTAGATGTTCAATTATAGTCTATTCTA
65 TCTTGCCAATGAAT-ACTTTTTCTTCACGTTTCTCGAGGTAGACATTCAATTATAGTCTGTTTTA
** * * *
812 A-TGAAAAATGCAAAAATATTTACCTTAAAATCAATTATGAGA
129 ACT-AAAAATATAAAAAAATTCAACTTAAAATCAATTATGAGA
********** * * *
854 TTATAAAACCATTTAAAGCGAGNNNNNNNNNNTTTAAAGGAATGGGTGACTATAAAT-AGACTTT
1 TTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATAGGAGACTATAAATGA-ACTTT
* * * * * ** * *
918 TCTTGCTAATGAATGTCTTTCTCTTCACATTTCTCAAGCCAGACATTCAATTATAATCTATTTTA
65 TCTTGCCAATGAAT-ACTTTTTCTTCACGTTTCTCGAGGTAGACATTCAATTATAGTCTGTTTTA
* * * * * *
983 ACTGATAATATAAAAAAAATTAAACCTAAAATCATTTTTGAGA
129 ACTAAAAATAT-AAAAAAATTCAACTTAAAATCAATTATGAGA
* * * * *
1026 TTATACAACCATTTAAAGCGACTAATAAGACTTTTGAAGGAATAGAAGACTATAAATAAACTTTT
1 TTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATAGGAGACTATAAATGAACTTTT
* * * * *
1091 CTTGCCAATGAATGCTTGTTTCTTCGCGTTTCTTGATGTAGACATTCAATTATAGTTTGTTTTAA
66 CTTGCCAATGAATACTT-TTTCTTCACGTTTCTCGAGGTAGACATTCAATTATAGTCTGTTTTAA
1156 CTAAAAATATAAAA
130 CTAAAAATATAAAA
1170 NNNNNNNNNN
Statistics
Matches: 760, Mismatches: 215, Indels: 46
0.74 0.21 0.05
Matches are distributed among these distances:
168 1 0.00
169 5 0.01
170 256 0.34
171 363 0.48
172 133 0.17
173 2 0.00
ACGTcount: A:0.36, C:0.11, G:0.13, T:0.34
Consensus pattern (170 bp):
TTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATAGGAGACTATAAATGAACTTTT
CTTGCCAATGAATACTTTTTCTTCACGTTTCTCGAGGTAGACATTCAATTATAGTCTGTTTTAAC
TAAAAATATAAAAAAATTCAACTTAAAATCAATTATGAGA
Found at i:1068 original size:172 final size:170
Alignment explanation
Indices: 675--1105 Score: 445
Period size: 172 Copynumber: 2.5 Consensus size: 170
665 NNNNNNNNNN
* * *
675 ATTATGAGATTATAAAACTATTTAAAGAGAGTAATAAGCTTTTTGAAGGGATGGGTGACTAT-AA
1 ATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGC-TTTTGAAGGAATGGGTGACTATAAA
* * * * * ** ** *
739 TGGACTTTTTTTGCTACTGAATGCCTTTTTCTTCACGTTTCTCAAGGTAGATGTTCAATTATAGT
65 TAGACTTTTCTTGCTAATGAATGCCTTTCTCTTCACATTTCTCAAGCCAGACATTCAATTATAAT
* * *
804 CTATTCTAATGAAAAATGCAAAAATATTTACCTTAAAATCA
130 CTATTCTAATGAAAAATGAAAAAAAATTAACCTTAAAATCA
********* *
845 ATTATGAGATTATAAAACCATTTAAAGCGAGNNNNNNNNNNTTTAAAGGAATGGGTGACTATAAA
1 ATTATGAGATTATAAAACCATTTAAAGCGAG-TAATAAGCTTTTGAAGGAATGGGTGACTATAAA
*
910 TAGACTTTTCTTGCTAATGAATGTCTTTCTCTTCACATTTCTCAAGCCAGACATTCAATTATAAT
65 TAGACTTTTCTTGCTAATGAATGCCTTTCTCTTCACATTTCTCAAGCCAGACATTCAATTATAAT
* *
975 CTATTTTAACTGATAATAT-AAAAAAAATTAAACC-TAAAATCA
130 CTATTCTAA-TGA-AAAATGAAAAAAAATT-AACCTTAAAATCA
* * * * * **
1017 TTTTTGAGATTATACAACCATTTAAAGCGACTAATAAGACTTTTGAAGGAATAGAAGACTATAAA
1 ATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAG-CTTTTGAAGGAATGGGTGACTATAAA
* *
1082 TAAACTTTTCTTGCCAATGAATGC
65 TAGACTTTTCTTGCTAATGAATGC
1106 TTGTTTCTTC
Statistics
Matches: 206, Mismatches: 49, Indels: 10
0.78 0.18 0.04
Matches are distributed among these distances:
170 48 0.23
171 64 0.31
172 87 0.42
173 7 0.03
ACGTcount: A:0.37, C:0.13, G:0.13, T:0.35
Consensus pattern (170 bp):
ATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGCTTTTGAAGGAATGGGTGACTATAAAT
AGACTTTTCTTGCTAATGAATGCCTTTCTCTTCACATTTCTCAAGCCAGACATTCAATTATAATC
TATTCTAATGAAAAATGAAAAAAAATTAACCTTAAAATCA
Found at i:2096 original size:171 final size:170
Alignment explanation
Indices: 1685--2161 Score: 396
Period size: 171 Copynumber: 2.8 Consensus size: 170
1675 NNNNNNNNNN
* * **
1685 AAATCAATTATGAGATTATAAAACCATTTAAGGCA-AGTAATAAGGCTTTTG-AAGAAATAGGAG
1 AAATCAATTTTGAGATTATAAAACTATTTAAATCATA-TAATAAGGC-TTTGAAAG-AATAGGAG
* * *
1748 ATTATATAT-AGACTTTTATTGCTAATGAATGTCTTTTTCTTCACATTTCTCAAGGTAAATATTC
63 ACTATA-ATGA-ACTTTTATTGCTAATGAATGTATTTTTCTTCACATTTCTCAAGGTAAACATTC
* * * *
1812 AATTATAATCTGTTTTAGCAAAAAATGTAAGGAAAATTAAACTTA
126 AATTATAATCTATTTGAACAAAAAATGTAAAGAAAATTAAACTTA
* ********** * *
1857 AAATCAATTTTGAGATTATAAAA-TCATTTAAAGTGAGTA-NNNNNNNNNNTGAAGGAAT-GAGT
1 AAATCAATTTTGAGATTATAAAACT-ATTTAAA-TCA-TATAATAAGGCTTTGAAAGAATAG-GA
* ** * * *
1919 GACTATAATGAACTTTTGTTGGC-AATGAATGTATTTTTCTTCATGTTTCTCGAGGTAGACATTT
62 GACTATAATGAACTTTTATT-GCTAATGAATGTATTTTTCTTCACATTTCTCAAGGTAAACATTC
* * * *
1983 AATTATAATCTATTTGAACCAATAATGTAAAGCAAATTAAGCTTA
126 AATTATAATCTATTTGAACAAAAAATGTAAAGAAAATTAAACTTA
2028 AAATCAATTTTGAGATTATAAAACTATTTAAATCATATAATAAGGCTTTCGAAAGAATAGGAGAC
1 AAATCAATTTTGAGATTATAAAACTATTTAAATCATATAATAAGGCTTT-GAAAGAATAGGAGAC
** * * * * *
2093 TATAAATGAACTTTTCGTGTTAATGAATGCT-TGTTTCTTCACATTT-TGTAAGGCAAACTTTCA
65 TAT-AATGAACTTTTATTGCTAATGAATG-TATTTTTCTTCACATTTCT-CAAGGTAAACATTCA
2156 ATTATA
127 ATTATA
2162 GTCTGTTTTA
Statistics
Matches: 230, Mismatches: 59, Indels: 32
0.72 0.18 0.10
Matches are distributed among these distances:
169 2 0.01
170 3 0.01
171 128 0.56
172 92 0.40
173 4 0.02
175 1 0.00
ACGTcount: A:0.38, C:0.10, G:0.14, T:0.36
Consensus pattern (170 bp):
AAATCAATTTTGAGATTATAAAACTATTTAAATCATATAATAAGGCTTTGAAAGAATAGGAGACT
ATAATGAACTTTTATTGCTAATGAATGTATTTTTCTTCACATTTCTCAAGGTAAACATTCAATTA
TAATCTATTTGAACAAAAAATGTAAAGAAAATTAAACTTA
Done.