Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018402861.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_5912.0, 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, 642
Length: 1070
ACGTcount: A:0.36, C:0.15, G:0.12, T:0.37
Found at i:477 original size:171 final size:169
Alignment explanation
Indices: 1--478 Score: 511
Period size: 171 Copynumber: 2.8 Consensus size: 169
* * *
1 AAATGGTTTTATAATGTCATAATCGATTTTAAGTTGAATTTTTTTACATTTTTGGTTAAAATAGA
1 AAATGGTTTTATAATCTCATAATTGATTTTAAGTTGAA-TTTTTTACATTTTTGGTTAAAATATA
* * * * *
66 TTATAACTCAATGTCTACCTTAAGAAACGTGAAGCAAAAGCCAACCA-TTGACAACAAAAGTCCA
65 TTATAACTAAATGTCTACCTTAGGAAACGTGAAGCAAAA-ACATCCATTTG-CAAGAAAAGTCCA
* * * *
130 CTTATAGTCACTCATACCTTTAAAAGCATTATTATTCGCTTT
128 TTTATAGCCACTCATACCTTGAAAAGCATTATTACTCGCTTT
* * * *
172 AAATAGTTTTATAATCTCATAATTGATTTTAAGTTCAATTTTTTAATATTTTTGATTAAAATATA
1 AAATGGTTTTATAATCTCATAATTGATTTTAAGTTGAATTTTTT-ACATTTTTGGTTAAAATATA
* * * * * * * * *
237 TTATACCTAAATGTTTTCTTTGGGAAACATGTAGCAAAAGCAAAT-CATTAGTG-ACG-AAAG-C
65 TTATAACTAAATGTCTACCTTAGGAAACGTGAAGCAAAA--ACATCCATT--TGCAAGAAAAGTC
* *
298 TTATTTATAGCCACTCA-AGCCTTCGAAAA-CCTTATTACTCGCTTT
126 -CATTTATAGCCACTCATA-CCTT-GAAAAGCATTATTACTCGCTTT
* * *
343 AAATGGTTTTAAAATCTCATAATTGATTTTAAGTTGAATTCTTTTACATTATTGGTTCAAATATA
1 AAATGGTTTTATAATCTCATAATTGATTTTAAGTTGAATT-TTTTACATTTTTGGTTAAAATATA
*
408 TTATAATTAAATGTCTACCTTAGGAAACGTGAAGCAAAAATCATCCATTTGCAAGAAAAGTCCAT
65 TTATAACTAAATGTCTACCTTAGGAAACGTGAAGCAAAAA-CATCCATTTGCAAGAAAAGTCCAT
473 TTATAG
129 TTATAG
479 TCATTCAAAC
Statistics
Matches: 247, Mismatches: 46, Indels: 28
0.77 0.14 0.09
Matches are distributed among these distances:
169 3 0.01
170 12 0.05
171 218 0.88
172 12 0.05
174 2 0.01
ACGTcount: A:0.36, C:0.14, G:0.12, T:0.38
Consensus pattern (169 bp):
AAATGGTTTTATAATCTCATAATTGATTTTAAGTTGAATTTTTTACATTTTTGGTTAAAATATAT
TATAACTAAATGTCTACCTTAGGAAACGTGAAGCAAAAACATCCATTTGCAAGAAAAGTCCATTT
ATAGCCACTCATACCTTGAAAAGCATTATTACTCGCTTT
Found at i:909 original size:169 final size:170
Alignment explanation
Indices: 695--1070 Score: 424
Period size: 169 Copynumber: 2.2 Consensus size: 170
685 AAAAAAAATT
* *
695 CATTTATAGTCACGC-ATGCCTTCAAAAGTCTTATTACTAGCTTTAAATGGTTCTATAAT-TGCA
1 CATTTATAGTCAC-CTATGCCTTCAAAAGCCTTATTACTAGCTTTAAATAGTTCTATAATCT-CA
* * * * *
758 TAATTAATTTTAAGTCAAATTTTTACATTTTTTA-TTAAAATATACTATAATTGAATGTTTG-CT
64 TAATTAATTTTAAGTCAAATTTTTACATATTTTAGTTAAAAAAGACTATAATTAAATGTCTGCCT
*
821 TCGAGG-AACGTGAA-ACAAAAGCCACCCATTGGCAAGAAAAGTA
129 T--AGGAAAAGTGAAGA-AAAAGCCACCCATTGGCAAGAAAAGTA
* * * * *
864 CATTTATATTCACCTATTCCTTCCAAAGCCTTATTACTCGCTTTAAATAGTTTTATAATCTCATA
1 CATTTATAGTCACCTATGCCTTCAAAAGCCTTATTACTAGCTTTAAATAGTTCTATAATCTCATA
* * * ** *
929 ATTGATTTTAAGTTAACTTTTTTTATATTTTAGTTAAAAAAGATTATAATTAAATGTCTGCCTTA
66 ATTAATTTTAAGTCAAATTTTTACATATTTTAGTTAAAAAAGACTATAATTAAATGTCTGCCTTA
* ** *
994 GGAAAAGTGAAGAAAAAGCTAGTCATTGGCAAGAAAAGTC
131 GGAAAAGTGAAGAAAAAGCCACCCATTGGCAAGAAAAGTA
**
1034 CATTTATAGTCA-CTCATGCCTTCGGAAGCCTTATTAC
1 CATTTATAGTCACCT-ATGCCTTCAAAAGCCTTATTAC
Statistics
Matches: 173, Mismatches: 27, Indels: 13
0.81 0.13 0.06
Matches are distributed among these distances:
168 1 0.01
169 85 0.49
170 83 0.48
171 4 0.02
ACGTcount: A:0.35, C:0.15, G:0.12, T:0.37
Consensus pattern (170 bp):
CATTTATAGTCACCTATGCCTTCAAAAGCCTTATTACTAGCTTTAAATAGTTCTATAATCTCATA
ATTAATTTTAAGTCAAATTTTTACATATTTTAGTTAAAAAAGACTATAATTAAATGTCTGCCTTA
GGAAAAGTGAAGAAAAAGCCACCCATTGGCAAGAAAAGTA
Found at i:1065 original size:170 final size:167
Alignment explanation
Indices: 546--1070 Score: 481
Period size: 170 Copynumber: 3.1 Consensus size: 167
536 ACTCAAGCCA
* * * *
546 TCAAAACCCTTATGACTCTCCTTAAATGGTTTTATAATCTCATAATTGATTTTACA-TTGAATTT
1 TCAAAAGCCTTATTACTCGCTTTAAATGGTTTTATAATCTCATAATTGATTTTA-AGTT-AATTT
* * * * * *
610 TTTTATAATTTGGTTTAAAACAGATTATATTTAAATGTCAAT-CTCAAGAAACA-TGAAG-AAAA
64 TTTTATATTTTAG-TTAAAAAAGATTATAATTAAATGTC--TGCTTAGGAAA-AGTGAAGAAAAA
* * ** * * *
672 GCTATTTATTGATAAAAAAAATTCATTTATAGTCACGCATGCCT
125 GCTACTCATTGGCAAGAAAAGTACATTTATAGTCAC-CATGCCT
* * * * *
716 TCAAAAGTCTTATTACTAGCTTTAAATGGTTCTATAAT-TGCATAATTAATTTTAAGTCAAATTT
1 TCAAAAGCCTTATTACTCGCTTTAAATGGTTTTATAATCT-CATAATTGATTTTAAGT-TAATTT
** * * * * * * *
780 TTACATTTTTTA-TTAAAATATACTATAATTGAATGTTTGCTTCGAGG-AACGTGAA-ACAAAAG
64 TTTTATATTTTAGTTAAAAAAGATTATAATTAAATGTCTGCTT--AGGAAAAGTGAAGA-AAAAG
* * * *
842 CCACCCATTGGCAAGAAAAGTACATTTATATTCACCTATTCCT
126 CTACTCATTGGCAAGAAAAGTACATTTATAGTCACC-ATGCCT
* *
885 TCCAAAGCCTTATTACTCGCTTTAAATAGTTTTATAATCTCATAATTGATTTTAAGTTAACTTTT
1 TCAAAAGCCTTATTACTCGCTTTAAATGGTTTTATAATCTCATAATTGATTTTAAGTTAA-TTTT
950 TTTATATTTTAGTTAAAAAAGATTATAATTAAATGTCTGCCTTAGGAAAAGTGAAGAAAAAGCTA
65 TTTATATTTTAGTTAAAAAAGATTATAATTAAATGTCTG-CTTAGGAAAAGTGAAGAAAAAGCTA
* *
1015 GTCATTGGCAAGAAAAGTCCATTTATAGTCACTCATGCCT
129 CTCATTGGCAAGAAAAGTACATTTATAGTCAC-CATGCCT
**
1055 TCGGAAGCCTTATTAC
1 TCAAAAGCCTTATTAC
Statistics
Matches: 280, Mismatches: 58, Indels: 34
0.75 0.16 0.09
Matches are distributed among these distances:
166 1 0.00
167 2 0.01
168 28 0.10
169 103 0.37
170 141 0.50
171 5 0.02
ACGTcount: A:0.36, C:0.14, G:0.12, T:0.38
Consensus pattern (167 bp):
TCAAAAGCCTTATTACTCGCTTTAAATGGTTTTATAATCTCATAATTGATTTTAAGTTAATTTTT
TTATATTTTAGTTAAAAAAGATTATAATTAAATGTCTGCTTAGGAAAAGTGAAGAAAAAGCTACT
CATTGGCAAGAAAAGTACATTTATAGTCACCATGCCT
Done.