Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018397742.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_104.0, 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: 13019
ACGTcount: A:0.24, C:0.09, G:0.09, T:0.25
Warning! 4474 characters in sequence are not A, C, G, or T
Found at i:8676 original size:171 final size:171
Alignment explanation
Indices: 8378--8897 Score: 433
Period size: 171 Copynumber: 3.0 Consensus size: 171
8368 NNNNNNNNNN
* * * * * * *
8378 CTTTAAATGGTTTTATAATCTCATAATTTATTTT-AAATTGAATTTTTTAACA-TTTGAGTTAAA
1 CTTTAAATGATTTTATAGTCTCATAA-TTATTTTCAAGTTAAATTGTTTCACATTTTTAGTTAAA
* * * ** * * * * ** *
8441 ACAGACTA-TAATAGAATGTCAATATCTAAAAATGTGAAGAAAAAGGTATTTATTGA-TGAGAAA
65 ACAAATTACAAAT-GAATGTCTGTCTCGAGAAACGTGAAGAAAAAGCCATTCATTGACT-AGAAA
* * * * * *
8504 AGTCCATTTGTAGTCACGCATTTCTTCCAAAGCCTTATTACTCG
128 AGTCTATTTGTAGTCACTCATTCCTTCAAAAACCTTATTACTCA
********** *
8548 CTTTAAATGATTTTATCA-TCTCATAATTNNNNNNNNNNTGAATTGTTTCACATTTTTAGTTAAA
1 CTTTAAATGATTTTAT-AGTCTCATAATTATTTTCAAGTTAAATTGTTTCACATTTTTAGTTAAA
* * *
8612 ATAGATTACAAATGAATGTCTG-CTTCGGGAAACGTGAAGAAAAAGCCATTCATTGACTAGAAAA
65 ACAAATTACAAATGAATGTCTGTC-TCGAGAAACGTGAAGAAAAAGCCATTCATTGACTAGAAAA
* * ** *
8676 GTCTATTTATAGTCACTCATACCTTTGAAAACCTTATTACTCT
129 GTCTATTTGTAGTCACTCATTCCTTCAAAAACCTTATTACTCA
* * * * * *
8719 TTTTAAATGGTTTTATAGTCTCGTAATTATTTTCAAGTTAAATTTTTTTACATTTTTGGTTAAAA
1 CTTTAAATGATTTTATAGTCTCATAATTATTTTCAAGTTAAATTGTTTCACATTTTTAGTTAAAA
* * * *
8784 CAAATTATAAATGATTGTCTGTCTCGAGAAACGTGAAGAAAAAGCCCTTCATTGACAAGAAAAGT
66 CAAATTACAAATGAATGTCTGTCTCGAGAAACGTGAAGAAAAAGCCATTCATTGACTAGAAAAGT
* *
8849 CTATTTAG-AGTCACTCATTCCTTCAAAAACTTTGTTACTCA
131 CTATTT-GTAGTCACTCATTCCTTCAAAAACCTTATTACTCA
8890 CTTTAAAT
1 CTTTAAAT
8898 AGTTTTTTNN
Statistics
Matches: 274, Mismatches: 67, Indels: 17
0.77 0.19 0.05
Matches are distributed among these distances:
169 2 0.01
170 36 0.13
171 231 0.84
172 5 0.02
ACGTcount: A:0.35, C:0.13, G:0.12, T:0.38
Consensus pattern (171 bp):
CTTTAAATGATTTTATAGTCTCATAATTATTTTCAAGTTAAATTGTTTCACATTTTTAGTTAAAA
CAAATTACAAATGAATGTCTGTCTCGAGAAACGTGAAGAAAAAGCCATTCATTGACTAGAAAAGT
CTATTTGTAGTCACTCATTCCTTCAAAAACCTTATTACTCA
Found at i:8937 original size:171 final size:171
Alignment explanation
Indices: 8588--8903 Score: 445
Period size: 171 Copynumber: 1.8 Consensus size: 171
8578 NNNNNNNNTG
* * *
8588 AATTGTTTCACATTTTTAGTTAAAATAGATTACAAATGAATGTCTGCTTCGGGAAACGTGAAGAA
1 AATTGTTTCACATTTTTAGTTAAAACAAATTACAAATGAATGTCTGCTTCGAGAAACGTGAAGAA
* * **
8653 AAAGCCATTCATTGACTAGAAAAGTCTATTTATAGTCACTCATACCTTTGAAAACCTTATTACTC
66 AAAGCCATTCATTGACAAGAAAAGTCTATTTAGAGTCACTCATACCTTCAAAAACCTTATTACTC
** *
8718 TTTTTAAATGGTTTTATAGTCTCGTAATTATTTTCAAGTTA
131 ACTTTAAATAGTTTTATAGTCTCGTAATTATTTTCAAGTTA
* * * * *
8759 AATTTTTTTACATTTTTGGTTAAAACAAATTATAAATGATTGTCTG-TCTCGAGAAACGTGAAGA
1 AATTGTTTCACATTTTTAGTTAAAACAAATTACAAATGAATGTCTGCT-TCGAGAAACGTGAAGA
* * * *
8823 AAAAGCCCTTCATTGACAAGAAAAGTCTATTTAGAGTCACTCATTCCTTCAAAAACTTTGTTACT
65 AAAAGCCATTCATTGACAAGAAAAGTCTATTTAGAGTCACTCATACCTTCAAAAACCTTATTACT
8888 CACTTTAAATAGTTTT
130 CACTTTAAATAGTTTT
8904 TTNNNNNNNN
Statistics
Matches: 125, Mismatches: 19, Indels: 2
0.86 0.13 0.01
Matches are distributed among these distances:
170 1 0.01
171 124 0.99
ACGTcount: A:0.34, C:0.15, G:0.13, T:0.38
Consensus pattern (171 bp):
AATTGTTTCACATTTTTAGTTAAAACAAATTACAAATGAATGTCTGCTTCGAGAAACGTGAAGAA
AAAGCCATTCATTGACAAGAAAAGTCTATTTAGAGTCACTCATACCTTCAAAAACCTTATTACTC
ACTTTAAATAGTTTTATAGTCTCGTAATTATTTTCAAGTTA
Found at i:9428 original size:171 final size:171
Alignment explanation
Indices: 9134--10998 Score: 1783
Period size: 171 Copynumber: 10.9 Consensus size: 171
9124 NNNNNNNNNN
* * * * * *
9134 ATAAGGCTTTCGAAGGTATGGGTGACTATAAATAGACTTTTCTAGTCAATGAATAGC-TTTTCTT
1 ATAAGGCTTTTGAAGGAATAGGTGACTATAAATGGACTTTTCTTGTCAATGAATGGCTTTTTCTT
* * * * * *
9198 CACGTTTTTTGAGGCAAACATTCAATTATAATCTGTTTTAACCAAAAATATGAAAAAATTCAACC
66 CATGTTTCTTGAGGCAGACATTCAATTATAATCTGTTTTAACCAAAAATGTAAAAAAATTCAACT
* * * **
9263 TAAAATCAATAATGAGATTAGAATACCATTTGCAGTGAGTA
131 TAAAATCAATTATGAGATTATAAAACCATTTAAAGTGAGTA
* * * * * * *
9304 ATAAGGCTTTTGATA-GAATAGGTGGCTATAAATAGACTTATCTTGCCAATGAAGGGTTTTTTTT
1 ATAAGGCTTTTGA-AGGAATAGGTGACTATAAATGGACTTTTCTTGTCAATGAATGGCTTTTTCT
* ** * * * * * * * *
9368 TCACGTTTCCAGAGGTAAACAATCAATTATATTTTATTTTAACAAAAAATGTAGAAAAATTCAAC
65 TCATGTTTCTTGAGGCAGACATTCAATTATAATCTGTTTTAACCAAAAATGTAAAAAAATTCAAC
* * *
9433 TGAAAATCAATTACGAGATTATAAAACCATTTAAAGCGAGTA
130 TTAAAATCAATTATGAGATTATAAAACCATTTAAAGTGAGTA
* ** * * * *
9475 ATAAAGCTTTCAAAGGCATGGGTGACTATAAATGGACATTTT-TGGTCAATGAATAGCTTTTTCT
1 ATAAGGCTTTTGAAGGAATAGGTGACTATAAATGGAC-TTTTCTTGTCAATGAATGGCTTTTTCT
** ** * * * * * * * *
9539 TCACATTTCTTGAGATAGATATTCAATTATAGTTTGTTCTAACCCAAAAGGTAAAAATATTGAAC
65 TCATGTTTCTTGAGGCAGACATTCAATTATAATCTGTTTTAACCAAAAATGTAAAAAAATTCAAC
* **
9604 TTAAAATTAATTATCCGATTATAAAACCATTTAAAGAT-AGTA
130 TTAAAATCAATTATGAGATTATAAAACCATTTAAAG-TGAGTA
* * * * *
9646 ATAAGGCTGTTGAAGGAATCGGTGACTATAAATAGACTTTGCTTATCAATGAATGG-TATTTTCT
1 ATAAGGCTTTTGAAGGAATAGGTGACTATAAATGGACTTTTCTTGTCAATGAATGGCT-TTTTCT
* * ** ** *
9710 TCACGTTT-TTTAGGACAGACATTCAATTATAGCCTGTTTTAATAAAAAATGTAAAAAAAATCAA
65 TCATGTTTCTTGAGG-CAGACATTCAATTATAATCTGTTTTAACCAAAAATGTAAAAAAATTCAA
* * * *
9774 TTTAAACTCAATTATGAGATTAGAAAATCATTTAAAGTGAGTA
129 CTTAAAATCAATTATGAGATTATAAAACCATTTAAAGTGAGTA
* * * * * * * * *
9817 ATAATGCTTTTAAAGGAATGGGTGGCTATAAATAGACTCTTCTTATCAGTGAA-GAGGTTTTTCT
1 ATAAGGCTTTTGAAGGAATAGGTGACTATAAATGGACTTTTCTTGTCAATGAATG-GCTTTTTCT
* * * * * *
9881 TCATGTTTCCTGAGGTAGACAATCATTTATAATTTATTTTAACCAAAAATGTAAAAACAATT-AA
65 TCATGTTTCTTGAGGCAGACATTCAATTATAATCTGTTTTAACCAAAAATGTAAAAA-AATTCAA
**
9945 CTTCAAAA-CAATTACAAGATTATAAAACCATTTAAAGTGAGTA
129 CTT-AAAATCAATTATGAGATTATAAAACCATTTAAAGTGAGTA
* * * * * * *
9988 ATAAGACTTTCGAAGGCATAGGTGACTCTAAATGGATTTTTTTTGTCAATGAATAGCTTTTTCTT
1 ATAAGGCTTTTGAAGGAATAGGTGACTATAAATGGACTTTTCTTGTCAATGAATGGCTTTTTCTT
* * * ** *
10053 CATGTTTCTTGATGCAGAGATTCAATTATAGTCTGTTTTAACTGAAAATGTAAAAACATTCAACT
66 CATGTTTCTTGAGGCAGACATTCAATTATAATCTGTTTTAACCAAAAATGTAAAAAAATTCAACT
* *
10118 TAAAATCAATTACT-AGATTATAAAACTATTTAAAGCGAGTA
131 TAAAATCAATTA-TGAGATTATAAAACCATTTAAAGTGAGTA
* * * *
10159 ATAAGGCTTTCGAAGGCATAGGTGACTATAAATGGGCTTTT-TTAGTTAATGACA-GGCTTTTTC
1 ATAAGGCTTTTGAAGGAATAGGTGACTATAAATGGACTTTTCTT-GTCAATGA-ATGGCTTTTTC
* * *
10222 TTCATGTTTCTTGAGGCAGACAATT-AATAATAATATGCTTTAACCAAAAATGTAAAAAAAAAAT
64 TTCATGTTTCTTGAGGCAGAC-ATTCAATTATAATCTGTTTTAACCAAAAATGT---AAAAAAAT
* * * *
10286 TCAACTAAAAATGAATTATGAGATTATAAAACTATTTAAAGTGAGTC
125 TCAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGTGAGTA
* * * * ** *
10333 ATAAGGCTTTGGAAAGAATAGGTGAATACAAATGGACTTTTC-TCACTAATGAATGCCTTTTTCT
1 ATAAGGCTTTTGAAGGAATAGGTGACTATAAATGGACTTTTCTTGTC-AATGAATGGCTTTTTCT
** * * ** * * *
10397 TCACATTTCTTGAGACTGAC-TATCTGTTATAGTCTGTTTTTATCAAAAATGTAAAAAAATTCAA
65 TCATGTTTCTTGAGGCAGACAT-TCAATTATAATCTGTTTTAACCAAAAATGTAAAAAAATTCAA
* * * * *
10461 CTCAAAGTGAATTATGAGATTACAAAACCATTTAAAGCGAGTA
129 CTTAAAATCAATTATGAGATTATAAAACCATTTAAAGTGAGTA
** * *
10504 ATAAGAATTTTGAAGGAAT-GAGTGACTATAAATGGACTTTTCTAGTCAATGAATGGCTATTTCT
1 ATAAGGCTTTTGAAGGAATAG-GTGACTATAAATGGACTTTTCTTGTCAATGAATGGCTTTTTCT
** * * * * *
10568 TCATGTTTCACGTGACA-ACCATTCAATTATAATATGTTTTAACCAAAAATGTGAAAACATTCAA
65 TCATGTTTCTTGAGGCAGA-CATTCAATTATAATCTGTTTTAACCAAAAATGTAAAAAAATTCAA
* * *
10632 CCTAAAATTAATTATGAGATTATAAAGCCATTTAAAGTGAGTA
129 CTTAAAATCAATTATGAGATTATAAAACCATTTAAAGTGAGTA
* * * * * *
10675 CTATGGCTTTTAAAGAAATGGGTGACTATAAATGGACTTTTCTTATCAATGAATGGCTTTTT-TT
1 ATAAGGCTTTTGAAGGAATAGGTGACTATAAATGGACTTTTCTTGTCAATGAATGGCTTTTTCTT
** * * * * *
10739 CATGTTTCTTGAGATAGACATTTAATTATAATTTGTTTTAACTAAAAATGTAAAAAAGTTCAATT
66 CATGTTTCTTGAGGCAGACATTCAATTATAATCTGTTTTAACCAAAAATGTAAAAAAATTCAACT
* * *
10804 TAAAATCAATTATGAGATTATAAAACCTTTTAAGGTAAGTA
131 TAAAATCAATTATGAGATTATAAAACCATTTAAAGTGAGTA
* * **
10845 ATAAGGCTTTTGAAGGTATGGGTGACTATAAATAGG-CTTTTCTAATCAATGAATGG-TTTTTCT
1 ATAAGGCTTTTGAAGGAATAGGTGACTATAAAT-GGACTTTTCTTGTCAATGAATGGCTTTTTCT
* ** * *
10908 TCATATTTCTTGAGGCAGACATTCAATTATAATCTACTTTAACTAAAAATATAAAAAAATTCAAC
65 TCATGTTTCTTGAGGCAGACATTCAATTATAATCTGTTTTAACCAAAAATGTAAAAAAATTCAAC
10973 TTAAAATCAATTACT-AGATTATAAAA
130 TTAAAATCAATTA-TGAGATTATAAAA
10999 NNNNNNNNNN
Statistics
Matches: 1376, Mismatches: 280, Indels: 78
0.79 0.16 0.04
Matches are distributed among these distances:
169 5 0.00
170 283 0.21
171 929 0.68
172 22 0.02
173 3 0.00
174 134 0.10
ACGTcount: A:0.38, C:0.12, G:0.15, T:0.35
Consensus pattern (171 bp):
ATAAGGCTTTTGAAGGAATAGGTGACTATAAATGGACTTTTCTTGTCAATGAATGGCTTTTTCTT
CATGTTTCTTGAGGCAGACATTCAATTATAATCTGTTTTAACCAAAAATGTAAAAAAATTCAACT
TAAAATCAATTATGAGATTATAAAACCATTTAAAGTGAGTA
Done.