Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018398126.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_1429.0, 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: 3856
ACGTcount: A:0.25, C:0.10, G:0.11, T:0.23
Warning! 1225 characters in sequence are not A, C, G, or T
Found at i:1141 original size:22 final size:22
Alignment explanation
Indices: 1113--1159 Score: 85
Period size: 22 Copynumber: 2.1 Consensus size: 22
1103 TATCTATTTT
1113 AACCAAAAATCCACAAAAATTC
1 AACCAAAAATCCACAAAAATTC
*
1135 AACCAAAATTCCACAAAAATTC
1 AACCAAAAATCCACAAAAATTC
1157 AAC
1 AAC
1160 TTAAAATCAA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.57, C:0.28, G:0.00, T:0.15
Consensus pattern (22 bp):
AACCAAAAATCCACAAAAATTC
Found at i:1142 original size:11 final size:11
Alignment explanation
Indices: 1116--1159 Score: 54
Period size: 11 Copynumber: 4.1 Consensus size: 11
1106 CTATTTTAAC
*
1116 CAAAAA-TCCA
1 CAAAAATTCAA
1126 CAAAAATTCAA
1 CAAAAATTCAA
* *
1137 CCAAAATTCCA
1 CAAAAATTCAA
1148 CAAAAATTCAA
1 CAAAAATTCAA
1159 C
1 C
1160 TTAAAATCAA
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
10 6 0.21
11 22 0.79
ACGTcount: A:0.57, C:0.27, G:0.00, T:0.16
Consensus pattern (11 bp):
CAAAAATTCAA
Found at i:2478 original size:171 final size:168
Alignment explanation
Indices: 2056--3007 Score: 693
Period size: 171 Copynumber: 5.6 Consensus size: 168
2046 NNNNNNNNNN
*
2056 ACTATAAATGGACTTTACTTGCCAATGAATGGCTTTTTCTTCACGTTTCTCAAGATAGACATTTA
1 ACTATAAATGGACTTTTCTTGCCAATGAATGGCTTTTTCTTCACGTTTCTCAAGATAGACATTTA
* * * * *
2121 ATTATAATTTGTTTGAACCAAAAATGTAAAGAAATTCAACTTAAAACCAATGATGAGGTTATAAA
66 ATTATAATTTATTTTAACCAAAAATGTAAAAAAATTCAACTT-AAATCAATTATGA-GTTATAAA
* * * * *
2186 ACCATTTAAAGCTAGAAATAA-GCTTTAAAAGGCATGAGAG
129 ACCATTCAAAGCGAGTAATAAGGCTTT-AAAGGCATGGGTG
********** * ** * * * *
2226 ACTATAAATANNNNNNNNNNTGCCAATAAATAACTTTTTCTTCACATTTCTCGATG-TGGGCATT
1 ACTATAAAT-GGACTTTTCTTGCCAATGAATGGCTTTTTCTTCACGTTTCTC-AAGATAGACATT
* * * * * *
2290 CAATTGTTATCTATTTTAACCAAAAATGTAAAACAATTCAACTTGAAATCAATTATGATGTCATA
64 TAATTATAATTTATTTTAACCAAAAATGTAAAAAAATTCAACTT-AAATCAATTATGA-GTTATA
* * *
2355 AAACCATTCAAAGCGAGTAATAAGGCTTTCGAAGGCGTGGTTG
127 AAACCATTCAAAGCGAGTAATAAGGCTTT-AAAGGCATGGGTG
* * * * *
2398 ATTGTAAATGGACTTTTGTTGCCAATGAATGGCTTTTTCTTCATGTTTC-CTAAGACAGACATTT
1 ACTATAAATGGACTTTTCTTGCCAATGAATGGCTTTTTCTTCACGTTTCTC-AAGATAGACATTT
* * * * *
2462 AATTATTATTTATTTTAACAAAAAAT-AAAAAAAAGTCAACTTAAAGTCAATTATTAGATTATAA
65 AATTATAATTTATTTTAACCAAAAATGTAAAAAAATTCAACTTAAA-TCAATTATGAG-TTATAA
* * * *
2526 TACCATCCCAAGCGAGTAATATGGCTGTTAAAGGCATGGGTG
128 AACCATTCAAAGCGAGTAATAAGGCT-TTAAAGGCATGGGTG
* * * * *
2568 ACTATAAATGAACTTTTCTTGTCAAAGAATGGCTTTCTATTCACGTTTCT-AGAGGAT-GACATT
1 ACTATAAATGGACTTTTCTTGCCAATGAATGGCTTTTTCTTCACGTTTCTCA-A-GATAGACATT
* * * * ***********
2631 TAATTATAATATGTTTTAGCAAAAAATGTAAAACNNNNNNNNNNAAAATCAATTATGAGTTTATA
64 TAATTATAATTTATTTTAACCAAAAATGTAAAA-AAATTCAACTTAAATCAATTATGAG-TTATA
* * *
2696 AAACCATTTAAGGTGAGTAATAAGGCTTTTAAAGGCATGGGTG
127 AAACCATTCAAAGCGAGTAATAAGGC-TTTAAAGGCATGGGTG
* * * * * * * * * *
2739 ACTCTAAAAAGG-CTTCTCTTGCAAATGAATGGCTCTTGCTTTATGTTTTTCAAGGTAGACATTC
1 ACTAT-AAATGGACTTTTCTTGCCAATGAATGGCTTTTTCTTCACGTTTCTCAAGATAGACATT-
* * * * * *
2803 T-ATTATTA-TTAGTTTTAACCGAAAATG-AAAAAAATTCAACTTAAGGTCAATTATTAGATAAC
64 TAATTATAATTTA-TTTTAACCAAAAATGTAAAAAAATTCAACTTAA-ATCAATTATGAG-TTAT
* *
2865 AAAACCATCTC-AAGCGAGTAATAAGGCTGTTGAAGGCATGGCTG
126 AAAACCAT-TCAAAGCGAGTAATAAGGCT-TTAAAGGCATGGGTG
* * * * * * *
2909 ACTATAAATGGACTTGTCTTGCAAATGAATGGGTTGTTCTTCACGTTTTTCAAGGTAGAGATTTA
1 ACTATAAATGGACTTTTCTTGCCAATGAATGGCTTTTTCTTCACGTTTCTCAAGATAGACATTTA
* * *
2974 ATTATAATCTATTTGAACCAAAAATGCAAAAAAA
66 ATTATAATTTATTTTAACCAAAAATGTAAAAAAA
3008 AATCAACNNN
Statistics
Matches: 589, Mismatches: 168, Indels: 49
0.73 0.21 0.06
Matches are distributed among these distances:
169 14 0.02
170 261 0.44
171 282 0.48
172 32 0.05
ACGTcount: A:0.36, C:0.13, G:0.15, T:0.33
Consensus pattern (168 bp):
ACTATAAATGGACTTTTCTTGCCAATGAATGGCTTTTTCTTCACGTTTCTCAAGATAGACATTTA
ATTATAATTTATTTTAACCAAAAATGTAAAAAAATTCAACTTAAATCAATTATGAGTTATAAAAC
CATTCAAAGCGAGTAATAAGGCTTTAAAGGCATGGGTG
Found at i:2954 original size:341 final size:331
Alignment explanation
Indices: 2335--3013 Score: 719
Period size: 341 Copynumber: 2.0 Consensus size: 331
2325 ATTCAACTTG
* * * *
2335 AAATCAATTATGATGTCATAAAACCATTCAAAGCGAGTAATAAGGCTTTCGAAGGCGTGGTTGAT
1 AAATCAATTATGATGTCATAAAACCATTCAAAGCGAGTAATAAGGCTTTCAAAGGCATGGGTGAC
* * * * * * *
2400 TGTAAATGGACTTTTGTTGCCAATGAATGGCTTTTTCTTCATGTTTCCTAAGACAGACATTTAAT
66 TCTAAAAGGACTTCTCTTGCAAATGAATGGCTCTTGCTTCATGTTTCCTAAGACAGACATTTAAT
* * *
2465 TATTATTTATTTTAACAAAAAATAAAAAAAAGTCAACTTAAAGTCAATTATTAGATTATAATACC
131 TATTATTTATTTTAACAAAAAATAAAAAAAAGTCAACTTAAAGTCAATTATTAGATAACAAAACC
* * *
2530 ATCCCAAGCGAGTAATATGGCTGTTAAAGGCATGGGTGACTATAAATGAACTTTTCTTGTCAAAG
196 ATCCCAAGCGAGTAATAAGGCTGTTAAAGGCATGGCTGACTATAAATGAACTTGTCTTGTCAAAG
2595 AATGGCTTTCTATTCACGTTTCT-AGAGG-ATGACATTTAATTATAATATGTTTTAGCAAAAAAT
261 AATGGCTTTCTATTCACGTTTCTCA-AGGTA-GACATTTAATTATAATATGTTTTAGCAAAAAAT
2658 GTAAAACNNNNNNNNNNA
324 GTAAAAC----------A
* * * * *
2676 AAATCAATTATGA-GTTTATAAAACCATTTAAGGTGAGTAATAAGGCTTTTAAAGGCATGGGTGA
1 AAATCAATTATGATG-TCATAAAACCATTCAAAGCGAGTAATAAGGCTTTCAAAGGCATGGGTGA
* * **
2740 CTCTAAAAAGG-CTTCTCTTGCAAATGAATGGCTCTTGCTTTATGTTT-TTCAAGGTAGACATTC
65 CTCT-AAAAGGACTTCTCTTGCAAATGAATGGCTCTTGCTTCATGTTTCCT-AAGACAGACATT-
** * * *
2803 T-ATTATTA-TTAGTTTTAACCGAAAATGAAAAAAATTCAACTTAAGGTCAATTATTAGATAACA
127 TAATTATTATTTA-TTTTAACAAAAAATAAAAAAAAGTCAACTTAAAGTCAATTATTAGATAACA
* * *
2866 AAACCATCTCAAGCGAGTAATAAGGCTGTTGAAGGCATGGCTGACTATAAATGGACTTGTCTTG-
191 AAACCATCCCAAGCGAGTAATAAGGCTGTTAAAGGCATGGCTGACTATAAATGAACTTGTCTTGT
* * * * * * * * *
2930 CAAATGAATGGGTTGT-TCTTCACGTTTTTCAAGGTAGAGATTTAATTATAATCTATTTGAACCA
256 CAAA-GAATGGCTT-TCTATTCACGTTTCTCAAGGTAGACATTTAATTATAATATGTTTTAGCAA
* *
2994 AAAATGCAAAAAA
319 AAAATGTAAAACA
3007 AAATCAA
1 AAATCAA
3014 CNNNNNNNNN
Statistics
Matches: 284, Mismatches: 45, Indels: 28
0.80 0.13 0.08
Matches are distributed among these distances:
331 8 0.03
340 9 0.03
341 258 0.91
342 9 0.03
ACGTcount: A:0.36, C:0.13, G:0.16, T:0.33
Consensus pattern (331 bp):
AAATCAATTATGATGTCATAAAACCATTCAAAGCGAGTAATAAGGCTTTCAAAGGCATGGGTGAC
TCTAAAAGGACTTCTCTTGCAAATGAATGGCTCTTGCTTCATGTTTCCTAAGACAGACATTTAAT
TATTATTTATTTTAACAAAAAATAAAAAAAAGTCAACTTAAAGTCAATTATTAGATAACAAAACC
ATCCCAAGCGAGTAATAAGGCTGTTAAAGGCATGGCTGACTATAAATGAACTTGTCTTGTCAAAG
AATGGCTTTCTATTCACGTTTCTCAAGGTAGACATTTAATTATAATATGTTTTAGCAAAAAATGT
AAAACA
Done.