Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018397629.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_5117.0, 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: 3692
ACGTcount: A:0.33, C:0.12, G:0.09, T:0.34
Warning! 424 characters in sequence are not A, C, G, or T
Found at i:449 original size:117 final size:117
Alignment explanation
Indices: 243--465 Score: 365
Period size: 117 Copynumber: 1.9 Consensus size: 117
233 ATGAGAAACG
* * *
243 TGTAAAAAAAACCATTCATTGAGGAAAAAAGTCCATTTATAGTCACCCATTCCTTCAAAAGCCTT
1 TGTAAAAAAAACCATTCATTGAGAAAAAAAATCCATTTATAGTCACCCACTCCTTCAAAAGCCTT
*
308 ATTACTCACTTTAAATTATTTTATAATCTCATAATTGATTTTAAGTTGAATT
66 ATTACTCACTTTAAATTATTTTATAATCTCATAATTCATTTTAAGTTGAATT
* * *
360 TGTAAAAAACATCATTCATTGAGAAAAAAAATCCATTTATAGTCACCCACTCCTTCAAAATCCTT
1 TGTAAAAAAAACCATTCATTGAGAAAAAAAATCCATTTATAGTCACCCACTCCTTCAAAAGCCTT
* *
425 ATTGCTCACTTTAAATTGTTTTATAATCTCATAATTCATTT
66 ATTACTCACTTTAAATTATTTTATAATCTCATAATTCATTT
466 NNNNNNNNNN
Statistics
Matches: 97, Mismatches: 9, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
117 97 1.00
ACGTcount: A:0.37, C:0.18, G:0.07, T:0.38
Consensus pattern (117 bp):
TGTAAAAAAAACCATTCATTGAGAAAAAAAATCCATTTATAGTCACCCACTCCTTCAAAAGCCTT
ATTACTCACTTTAAATTATTTTATAATCTCATAATTCATTTTAAGTTGAATT
Found at i:2172 original size:170 final size:161
Alignment explanation
Indices: 1976--2309 Score: 320
Period size: 171 Copynumber: 2.0 Consensus size: 161
1966 CTTCAAAAGT
* * *
1976 CTTATTACTCGCTTTAAAAGGTTTTAT-ATACTCATAATTAATTTTAAGTTAAGTTTTTTTACAG
1 CTTATTACTCGCTTTAAAAGGTTTTATAAT-CCCAAAATTAATTTTAAGTTAAATTTTTTTACA-
* * * * * *
2040 TTT-TGGTT-AGACAGACAATAACTGAATATTTACCTTGAGAAACATGAAAAGAAAAGC-ATTCA
64 TTTACGATTAAAACAGACAATAACTCAATATCTACCTTAAGAAACATGAAAA-AAAAGCTATTCA
2102 TT-AGCAAGAAAAGTCCATTTATAGTCACCT-ATTC
128 TTGAG-AAGAAAAGTCCATTTATAGTCA-CTAATTC
** *
2136 CTNNNNNNNNNNTATTACTCGCTTTAAATTGTTTTATAATCCCAAAATTAATTTTTAGTTAAATT
1 CT----------TATTACTCGCTTTAAAAGGTTTTATAATCCCAAAATTAATTTTAAGTTAAATT
* * * * * * *
2201 TTTTTACATTTACGATTAAAACAGACTATAATTCAATGTCTGCCTTAAGAAACGTGCAAAAAAAT
56 TTTTTACATTTACGATTAAAACAGACAATAACTCAATATCTACCTTAAGAAACATGAAAAAAAAG
2266 CTATTCATTGAGAAGAAAAGTCCATTTATAGTCACTAATTC
121 CTATTCATTGAGAAGAAAAGTCCATTTATAGTCACTAATTC
2307 CTT
1 CTT
2310 CAAAAGCTTT
Statistics
Matches: 139, Mismatches: 19, Indels: 31
0.74 0.10 0.16
Matches are distributed among these distances:
160 2 0.01
161 1 0.01
169 3 0.02
170 62 0.45
171 69 0.50
172 2 0.01
ACGTcount: A:0.36, C:0.14, G:0.10, T:0.37
Consensus pattern (161 bp):
CTTATTACTCGCTTTAAAAGGTTTTATAATCCCAAAATTAATTTTAAGTTAAATTTTTTTACATT
TACGATTAAAACAGACAATAACTCAATATCTACCTTAAGAAACATGAAAAAAAAGCTATTCATTG
AGAAGAAAAGTCCATTTATAGTCACTAATTC
Found at i:2332 original size:171 final size:170
Alignment explanation
Indices: 1962--2555 Score: 465
Period size: 172 Copynumber: 3.5 Consensus size: 170
1952 NNNNNNNNNN
** * *
1962 ATTCCTTCAAAAG-TCTTATTACTCGCTTTAAAAGGTTTTAT-ATACTCATAATTAATTTTAAGT
1 ATTCCTTCAAAAGCT-TTATTACTCGCTTTAAATTGTTTTATAAT-CCCAAAATTAATTTTAAGT
* * * * * * * * * * * *
2025 TAAGTTTTTTTACAGTTT-TGGTT-AGACAGACAATAACTGAATATTTACCTTGAGAAACATGAA
64 TAAATTTTTTTACAGTTTACGATTAAAACAGACTATAATTCAATGTCT-CCTTAAGAAACGTGCA
2088 AAGAAAAGCATTCATT-AGCAAGAAAAGTCCATTTATAGTCACCT
128 AA-AAAAGCATTCATTGAG-AAGAAAAGTCCATTTATAGTCACCT
********** *
2132 ATTCCTNNNNNNNNNNTATTACTCGCTTTAAATTGTTTTATAATCCCAAAATTAATTTTTAGTTA
1 ATTCCTTCAAAAGCTTTATTACTCGCTTTAAATTGTTTTATAATCCCAAAATTAATTTTAAGTTA
2197 AATTTTTTTACA-TTTACGATTAAAACAGACTATAATTCAATGTCTGCCTTAAGAAACGTGCAAA
66 AATTTTTTTACAGTTTACGATTAAAACAGACTATAATTCAATGTCT-CCTTAAGAAACGTGCAAA
*
2261 AAAATCTATTCATTGAGAAGAAAAGTCCATTTATAGTCA-CT
130 AAAAGC-ATTCATTGAGAAGAAAAGTCCATTTATAGTCACCT
********** * *
2302 AATTCCTTCAAAAGCTTTATTACTCGCTTTATANNNNNNNNNNAA-CTCATAATTAATTTTAAGT
1 -ATTCCTTCAAAAGCTTTATTACTCGCTTTA-AATTGTTTTATAATCCCAAAATTAATTTTAAGT
* * * * * * ** *
2366 TGAATTTTTTTTTCATTTTTC-ATTAAAATAGCCTATAATTCAATG-CTTATCTCAGAAAACGTG
64 T-AAATTTTTTTACAGTTTACGATTAAAACAGACTATAATTCAATGTCTCCT-TAAG-AAACGTG
* * *
2429 TC-GAAAAAGCCATTCATTGAGAAGAAAAGTACGTTTATAGTCACCT
126 -CAAAAAAAG-CATTCATTGAGAAGAAAAGTCCATTTATAGTCACCT
* * * * *
2475 ATTCCTTTAAAAGCCTTATTACTCGCTTTAGATTGTTTTATAATCCCAAAATTGATTTTAAGTTG
1 ATTCCTTCAAAAGCTTTATTACTCGCTTTAAATTGTTTTATAATCCCAAAATTAATTTTAAGTTA
2540 AATTTTTTTACA-TTTA
66 AATTTTTTTACAGTTTA
2556 TGATNNNNNN
Statistics
Matches: 325, Mismatches: 83, Indels: 32
0.74 0.19 0.07
Matches are distributed among these distances:
169 3 0.01
170 72 0.22
171 117 0.36
172 125 0.38
173 8 0.02
ACGTcount: A:0.34, C:0.14, G:0.10, T:0.38
Consensus pattern (170 bp):
ATTCCTTCAAAAGCTTTATTACTCGCTTTAAATTGTTTTATAATCCCAAAATTAATTTTAAGTTA
AATTTTTTTACAGTTTACGATTAAAACAGACTATAATTCAATGTCTCCTTAAGAAACGTGCAAAA
AAAGCATTCATTGAGAAGAAAAGTCCATTTATAGTCACCT
Found at i:3027 original size:171 final size:170
Alignment explanation
Indices: 2686--2995 Score: 442
Period size: 172 Copynumber: 1.8 Consensus size: 170
2676 NNNNNNNNAT
* *
2686 GTGTAAAAAACACCATTCATTGAGAAAAAAGTCCATTTATAGTCATCCATTCCTTTAAAAGTCTT
1 GTGTAAAAAAAACCATTCATTGAGAAAAAAGTCCATTTATAGTCACCCATTCCTTTAAAAGTCTT
* * * * *
2751 ATTACTCTCTTTAAATTGTTTTATAATCTCAAAATTGATTTGAAGTAAATTTTTTTTTCAATTTG
66 ATTACTCACTTTAAATGGTTTTATAAACTCAAAATTAATTTGAAGTAAATTTTTTTAT-AATTTG
2816 AAGTTAAAACAGACTATAATTGAATGCATACCCTGAGAAAC
130 AAGTTAAAACAGACTATAATTGAATGCATACCCTGAGAAAC
* * *
2857 GTGTAAAAAAAATCATTCATTGAGAAAAAAGGTTCATTTATAGTCACCCATTCTTTTAAAAGTCT
1 GTGTAAAAAAAACCATTCATTGAGAAAAAA-GTCCATTTATAGTCACCCATTCCTTTAAAAGTCT
* * * *
2922 TATTACTCACTTTATATGGTTTTATAAACTCATAATTAATTTTAAGTGTAATTTTTTTAT-ATTT
65 TATTACTCACTTTAAATGGTTTTATAAACTCAAAATTAATTTGAAGT-AAATTTTTTTATAATTT
**
2986 TTAGTTAAAA
129 GAAGTTAAAA
2996 TAGANNNNNN
Statistics
Matches: 121, Mismatches: 16, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
171 40 0.33
172 71 0.59
173 10 0.08
ACGTcount: A:0.37, C:0.13, G:0.10, T:0.40
Consensus pattern (170 bp):
GTGTAAAAAAAACCATTCATTGAGAAAAAAGTCCATTTATAGTCACCCATTCCTTTAAAAGTCTT
ATTACTCACTTTAAATGGTTTTATAAACTCAAAATTAATTTGAAGTAAATTTTTTTATAATTTGA
AGTTAAAACAGACTATAATTGAATGCATACCCTGAGAAAC
Found at i:3587 original size:170 final size:169
Alignment explanation
Indices: 2699--3589 Score: 629
Period size: 170 Copynumber: 5.2 Consensus size: 169
2689 TAAAAAACAC
* * *
2699 CATTCATTGAGAA-AAAAGTCCATTTATAGTCATCCATTCCTTTAAAAGTCTTATTACTCTCTTT
1 CATTCATTG-GAAGAAAAGTCCATTTATAGTCACCCATT-CTTTAAAAGCCTTATTACTCGCTTT
* * * * * *
2763 AAATTGTTTTATAATCTCAAAATTGATTTGAAG-TAAATTTTTTTTTCA-ATTTGAAGTTAAAAC
64 AAATTATTTTATAATCTCATAATTAATTTTAAGTTAAA-TTTTTTTACATTTTTG--GTTAAAAC
** *
2826 AGACTATAATTGAATGCATACC-CTGAGAAACGTGTAAAAAAAA-T
126 AGACTATAATTGAATGTTTACCTC-GAGAAACGTG-AAAAAAAAGG
* * *
2870 CATTCATTGAGAA-AAAAGGTTCATTTATAGTCACCCATTCTTTTAAAAGTCTTATTACTCACTT
1 CATTCATTG-GAAGAAAA-GTCCATTTATAGTCACCCATTC-TTTAAAAGCCTTATTACTCGCTT
* ** * * * *
2934 TATATGGTTTTATAAACTCATAATTAATTTTAAGTGT-AATTTTTTTATATTTTTAGTTAAAATA
63 TAAATTATTTTATAATCTCATAATTAATTTTAAGT-TAAATTTTTTTACATTTTTGGTTAAAACA
********** * *
2998 GANNNNNNNNNNATGTTTACCTTGAGAAACATG-AAAAAAAGG
127 GACTATAATTGAATGTTTACCTCGAGAAACGTGAAAAAAAAGG
* * *******
3040 CATTCATGGGCAAGAAAAGTCCATTTATAGTCACTCATTTCTTTAAAAGCCTTATTACNNNNNNN
1 CATTCATTGG-AAGAAAAGTCCATTTATAGTCACCCA-TTCTTTAAAAGCCTTATTACTCGCTTT
*** * * * *
3105 NNNTTATTTTATAAT-TCCAAAATTAATTTTAACTT-GATATTTTTTACATTTATGGTTAAAACA
64 AAATTATTTTATAATCT-CATAATTAATTTTAAGTTAAAT-TTTTTTACATTTTTGGTTAAAACA
* * *
3168 GACTATAATTGAATGCTTACCAT-TAGAAACGTGCAAAAAAA-G
127 GACTATAATTGAATGTTTACC-TCGAGAAACGTGAAAAAAAAGG
* ********** * *
3210 CTATTCATTGAGAAGAAAAATNNNNNNNNNNTCACCCATTCCTTCAAAAGCTTTATTACTCGCTT
1 C-ATTCATTG-GAAGAAAAGTCCATTTATAGTCACCCATT-CTTTAAAAGCCTTATTACTCGCTT
* * * * ** * *
3275 TATATGATTTTATAAACTCATAATTAATTTTAAGTTAAATTGTTTTACATTTTTTATTAGAACAA
63 TAAATTATTTTATAATCTCATAATTAATTTTAAGTTAAATTTTTTTACATTTTTGGTTAAAACAG
* * * * *
3340 ACAATAATTGAATGTCTA-CTAGAAGAAAAGTGAAGAAAAAGG
128 ACTATAATTGAATGTTTACCTCG-AGAAACGTGAAAAAAAAGG
**********
3382 CATTCATTGGTAAGAAAAGNNNNNNNNNNGTCACCCATTCTTTAAAAGCCTTATTACTCGCTTTA
1 CATTCATTGG-AAGAAAAGTCCATTTATAGTCACCCATTCTTTAAAAGCCTTATTACTCGCTTTA
* * *
3447 AATTATTTTATGATCTCATAATTAATTTTAAGTTAAATTTTTTTACATTTTTGGCTAAAACATAC
65 AATTATTTTATAATCTCATAATTAATTTTAAGTTAAATTTTTTTACATTTTTGGTTAAAACAGAC
* * *
3512 TATAATTAAATTTTTACCTCGAGAAACGTGAAAAAAAATG
130 TATAATTGAATGTTTACCTCGAGAAACGTGAAAAAAAAGG
*
3552 CATTCGTTGGCAAGAAAAGTCCATTTATAGTCACCCAT
1 CATTCATTGG-AAGAAAAGTCCATTTATAGTCACCCAT
3590 NNNNNNNNNN
Statistics
Matches: 552, Mismatches: 144, Indels: 49
0.74 0.19 0.07
Matches are distributed among these distances:
169 13 0.02
170 244 0.44
171 206 0.37
172 83 0.15
173 5 0.01
174 1 0.00
ACGTcount: A:0.36, C:0.13, G:0.10, T:0.36
Consensus pattern (169 bp):
CATTCATTGGAAGAAAAGTCCATTTATAGTCACCCATTCTTTAAAAGCCTTATTACTCGCTTTAA
ATTATTTTATAATCTCATAATTAATTTTAAGTTAAATTTTTTTACATTTTTGGTTAAAACAGACT
ATAATTGAATGTTTACCTCGAGAAACGTGAAAAAAAAGG
Done.