Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018398457.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_1755.0, 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: 2873
ACGTcount: A:0.29, C:0.10, G:0.09, T:0.30
Warning! 660 characters in sequence are not A, C, G, or T
Found at i:1573 original size:170 final size:170
Alignment explanation
Indices: 1417--1745 Score: 441
Period size: 170 Copynumber: 1.9 Consensus size: 170
1407 NNNNNNNNNN
* *
1417 AAAAGCCTTATTACTCGCTTTAAATGGTTTTATAATATCATAATTGATTT-TAGATTGAATTTT-
1 AAAAGCCTTATTACTCGCTTTAAATGGTTTTATAATATCATAATTGATTTGAAG-TTAAATTTTA
* * * * *
1480 TTAGATTTTTGGTTAAAACAAATTATAATTGAATGTTTGCCTTGAGAAACATAAAGAAAAAAG-C
65 TTACATTTTTGGTTAAAACAAACTATAA-TGAATGTCTACCTTGAAAAACATAAA-AAAAAAGCC
* *
1544 ATTC-ATTAGCAAGAAAAGTCCAGTTATAGTCTTCTTTTCTTTC
128 ATTCAATAAG-AAGAAAAGTCCAGTTATAGTCATCTTTTCTTTC
* * * *
1587 AAAAGCCTTATTACTTGCTTTAAATTGTTTTATAGTCTCATAATTGATTTGAAGTTAAATTTTAT
1 AAAAGCCTTATTACTCGCTTTAAATGGTTTTATAATATCATAATTGATTTGAAGTTAAATTTTAT
* *
1652 TACATTTTTTGTTAAAACAAACTATAATGAATGTCTACCTTGAAAAACATACAAAAAAAGCCATT
66 TACATTTTTGGTTAAAACAAACTATAATGAATGTCTACCTTGAAAAACATAAAAAAAAAGCCATT
* *
1717 CAATAAGAAGAAAAGTCTATTTATAGTCA
131 CAATAAGAAGAAAAGTCCAGTTATAGTCA
1746 CCATTCTTNN
Statistics
Matches: 138, Mismatches: 17, Indels: 8
0.85 0.10 0.05
Matches are distributed among these distances:
169 7 0.05
170 100 0.72
171 31 0.22
ACGTcount: A:0.38, C:0.12, G:0.12, T:0.39
Consensus pattern (170 bp):
AAAAGCCTTATTACTCGCTTTAAATGGTTTTATAATATCATAATTGATTTGAAGTTAAATTTTAT
TACATTTTTGGTTAAAACAAACTATAATGAATGTCTACCTTGAAAAACATAAAAAAAAAGCCATT
CAATAAGAAGAAAAGTCCAGTTATAGTCATCTTTTCTTTC
Found at i:2100 original size:170 final size:169
Alignment explanation
Indices: 1882--2358 Score: 392
Period size: 171 Copynumber: 2.8 Consensus size: 169
1872 AAACATGTAA
** * * * *
1882 AAAAAGCCTTTCATAGAGAAGAAAAGTCCATTTATAGTCGTCCATTCCTTGAAAAGACTTATTAC
1 AAAAAGCCAATCATTGAGAAGAAAAGTCTATTTATAGTC-ACCATTCCTTCAAAA-ACTTATTAC
* *
1947 TCGCTTTAAATTGTTTTATAATTTAATAATTGATTTTAAG-TCAATTTTTTTAACATTATT-GTT
64 TCGCTTTAAATTGTTTTATAATTTAATAATTGATTTTAAGTTCAATATTTTT-ACATTATTCATT
* **
2010 TAAACAGATTATAATTGAATATTTACCTCAAAAAACAT-GAAG
128 AAAACAGATTATAATTGAATACCTACCTCAAAAAACATCG-AG
** ********
2052 AAAAAGGTAATCATTG-GCAAGAAAAGTCTATTTATAGTCACACATTCCTTCAAAANNNNNNNNN
1 AAAAAGCCAATCATTGAG-AAGAAAAGTCTATTTATAGTCAC-CATTCCTTCAAAA-ACTTATTA
* * * * * * ** *
2116 NTCGCTTTAAATAGTTTTATTATCTCAA-AATTTATTTTAAGTTGAATATTTTTATGTTTTTCAT
63 CTCGCTTTAAATTGTTTTATAAT-TTAATAATTGATTTTAAGTTCAATATTTTTACATTATTCAT
* * ***
2180 TAAAACATATTATAATTGAATACCTGCCTCATGTAACATCGAG
127 TAAAACAGATTATAATTGAATACCTACCTCAAAAAACATCGAG
* * * *
2223 AAAAATCCATTCATTGAGAAAAAAAGTCTATTTATAGTCACCCTTTCCTTCAAAAACTTTATTAC
1 AAAAAGCCAATCATTGAGAAGAAAAGTCTATTTATAGTCA-CCATTCCTTCAAAAAC-TTATTAC
* * * * * * *
2288 TCGCTTTAAATTGTCTTATAATCTCATAATTGATTTTAAATTGAAT-TTTTTCCATT-TTTAGTT
64 TCGCTTTAAATTGTTTTATAATTTAATAATTGATTTTAAGTTCAATATTTTTACATTATTCA-TT
2351 AAAACAGA
128 AAAACAGA
2359 NNNNNNNNNN
Statistics
Matches: 232, Mismatches: 64, Indels: 22
0.73 0.20 0.07
Matches are distributed among these distances:
169 5 0.02
170 97 0.42
171 127 0.55
172 3 0.01
ACGTcount: A:0.36, C:0.13, G:0.09, T:0.39
Consensus pattern (169 bp):
AAAAAGCCAATCATTGAGAAGAAAAGTCTATTTATAGTCACCATTCCTTCAAAAACTTATTACTC
GCTTTAAATTGTTTTATAATTTAATAATTGATTTTAAGTTCAATATTTTTACATTATTCATTAAA
ACAGATTATAATTGAATACCTACCTCAAAAAACATCGAG
Done.