Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018399347.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_2615.0, 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: 3229
ACGTcount: A:0.27, C:0.11, G:0.09, T:0.26
Warning! 894 characters in sequence are not A, C, G, or T
Found at i:836 original size:172 final size:171
Alignment explanation
Indices: 16--1112 Score: 961
Period size: 171 Copynumber: 6.4 Consensus size: 171
6 ATCAACATCA
* * * * ** *
16 AGAAACATGAAGGAAAAGGCATTGATTGGTAAGAAAAGTTGATTAATAGTCACCCATTCCTTCAA
1 AGAAACATGAAGAAAAAAGCATTCATTGGCAAGAAAAGTCCATTTATAGTCACCCATTCCTTCAA
* * * * * *
81 AAGCCTTATTACACACTTTAAATGGTCTTACAATCTTAAAATTGA-TTTAAATTTTATTTCTTTG
66 AAGCCTTATTACTCACTTTAAATGGTTTTATAATCTCAAAATTGATTTTAAA-TTGAATTCTTT-
** * * *
145 TACATTTTTACTTAAAACATG-TTATAATTGAATGTCTACCTCG
129 TACATTTTTGGTTAAAA-AAGACTATAATTGAATGTCTACCTTG
* * * * *
188 AGAAACATGAAG-AAAAAGACATTAATTGGTAAGAAAACTCCGTTTATAGTCACCCATTCTTTCA
1 AGAAACATGAAGAAAAAAG-CATTCATTGGCAAGAAAAGTCCATTTATAGTCACCCATTCCTTCA
* * * ** *
252 AAAGCCTTATTACTCACTTTAAATGGTTTTGTAACCTCATAATTGATTTTAGGTTAAATT-TTTT
65 AAAGCCTTATTACTCACTTTAAATGGTTTTATAATCTCAAAATTGATTTTAAATTGAATTCTTTT
* * ** * **
316 GACATTTTTGGTTAGAACAGGTTGTAATTGAATGTCTGTCTTG
130 -ACATTTTTGGTTAAAAAAGACTATAATTGAATGTCTACCTTG
* * * ** * *
359 GGAAACATG-AGAAAAAAGGTATTCATTGGCAAGAAAAGTCTATTTATAGTCATTCATTTCTTCG
1 AGAAACATGAAGAAAAAA-GCATTCATTGGCAAGAAAAGTCCATTTATAGTCACCCATTCCTTCA
** * *
423 AAAGCCTTATTACTCACTTTAAATGACTTTATAATCTCAAAATTGATTTTAAATTGATTTTTTTT
65 AAAGCCTTATTACTCACTTTAAATGGTTTTATAATCTCAAAATTGATTTTAAATTGAATTCTTTT
* * *
488 ACATTTTCGGTGT-AAAAAGGCTATAATTGAATGTCTTCCATTG
130 ACATTTTTGGT-TAAAAAAGACTATAATTGAATGTCTACC-TTG
* * ** ** * * ** *
531 AG-AACACGAAG-CAAAAGCTAACCATTCACACA-AAAAGTCCATTTACAGTCACTCAAGCCTTG
1 AGAAACATGAAGAAAAAAGC-ATTCATTGGCA-AGAAAAGTCCATTTATAGTCACCCATTCCTTC
* ** * *
593 GAAAGCCTTATTACTTGCTTTAAATGGTTTTATAAACT-AATAATTAATTTTAAGA-TGAATTCT
64 AAAAGCCTTATTACTCACTTTAAATGGTTTTATAATCTCAA-AATTGATTTTAA-ATTGAATTCT
* * *
656 TTTACATTTTTGGCTAAAAAAGACTAGAATTGAATGTCTATCTTG
127 TTTACATTTTTGGTTAAAAAAGACTATAATTGAATGTCTACCTTG
* * * * * *
701 AGAAACGTGAAGAAAAAAACATTCATTGGTAAGAAAAGTCCATTTATAGTAACCCCTTACTTCAA
1 AGAAACATGAAGAAAAAAGCATTCATTGGCAAGAAAAGTCCATTTATAGTCACCCATTCCTTC-A
* * * * * *
766 AAAGCCTTATTACTCACTTTCAATAGTTTTATAATGTCATAATTGACTTTAAATTAAACTT-TTT
65 AAAGCCTTATTACTCACTTTAAATGGTTTTATAATCTCAAAATTGATTTTAAATTGAA-TTCTTT
* * *
830 TACATTTTTAGTTAAAACAA-ACAAAAATTG-ATGTCTACCTTG
129 TACATTTTTGGTTAAAA-AAGACTATAATTGAATGTCTACCTTG
* * * * *
872 AGAAACGT-AATGAAAAATGCAGTCATTGGCAAGAAAAGTCCATTTATAGTCACTCATTCCTTCC
1 AGAAACATGAA-GAAAAAAGCATTCATTGGCAAGAAAAGTCCATTTATAGTCACCCATTCCTTCA
*
936 AAAGCCTTTTTACTCACTTTAAATAGAG-TTTATAATCTCAAAATTGA-TTTAAATTTGAATTCT
65 AAAGCCTTATTACTCACTTTAAAT-G-GTTTTATAATCTCAAAATTGATTTTAAA-TTGAATTCT
* * * * **
999 TTGTACATTTTTTGTTAAAACAGATTATAATTGAATGTCAACCTCA
127 TT-TACATTTTTGGTTAAAAAAGACTATAATTGAATGTCTACCTTG
** * * * *
1045 AGAAATGTGAA-AACAAAGGCATACATTGGCAAGAAAAATCCATTTATAGTCATCCATTCCTTCA
1 AGAAACATGAAGAA-AAAAGCATTCATTGGCAAGAAAAGTCCATTTATAGTCACCCATTCCTTCA
1109 AAAG
65 AAAG
1113 NNNNNNNNNN
Statistics
Matches: 743, Mismatches: 149, Indels: 65
0.78 0.16 0.07
Matches are distributed among these distances:
170 46 0.06
171 414 0.56
172 209 0.28
173 72 0.10
174 2 0.00
ACGTcount: A:0.37, C:0.15, G:0.13, T:0.36
Consensus pattern (171 bp):
AGAAACATGAAGAAAAAAGCATTCATTGGCAAGAAAAGTCCATTTATAGTCACCCATTCCTTCAA
AAGCCTTATTACTCACTTTAAATGGTTTTATAATCTCAAAATTGATTTTAAATTGAATTCTTTTA
CATTTTTGGTTAAAAAAGACTATAATTGAATGTCTACCTTG
Found at i:3210 original size:171 final size:171
Alignment explanation
Indices: 2852--3229 Score: 409
Period size: 171 Copynumber: 2.2 Consensus size: 171
2842 NNNAAAAAGT
* * * *
2852 ATTCATTGGTAAGAAAAGTCTATTTATAATGACCCATACCTTCAAAAGCCTGTTTACTCGTTTTA
1 ATTCATTGGTAAGAAAAGTCCATTTATAGTCACCCATACCTTCAAAAGCCTCTTTACTCGTTTTA
* * * *
2917 AATAGTTTTATAATGCCATAATTAGTTTTAAGTTGAATGTTTTTAGATTTTTGGTTAAAATGGAC
66 AATAGTTTTATAATGCCATAATGAGTTTTAAGTTGAATGTTTTTACATTTTTGGTTAAAACGAAC
* **
2982 TATAATTGAATGTCTACCTCAAGAAACATAAAGAAAAAGNN
131 TATAATTGAATGTCTACCTCAAAAAACATAAAGAAAAAGAC
******** ***
3023 NNNNNNNNGTAAGAAAAGTCCATTTATAGTCACCCATTTTTTCAAAAGCCTCTTTACTCGTTTTA
1 ATTCATTGGTAAGAAAAGTCCATTTATAGTCACCCATACCTTCAAAAGCCTCTTTACTCGTTTTA
********* * *
3088 AATAGTTTTATANNNNNNNNNNTGA-TTTTAAGTTGAATTTTTTTACTTTTTTGGTTAAAACGAA
66 AATAGTTTTATA-ATGCCATAATGAGTTTTAAGTTGAATGTTTTTACATTTTTGGTTAAAACGAA
*
3152 CTATAATTGAATGTCTACCTCAAAAAATATAAAGAAAAATG-C
130 CTATAATTGAATGTCTACCTCAAAAAACATAAAGAAAAA-GAC
*
3194 ATTCATTGGCAAGAAAAGTCCATTTATAGTCACCCA
1 ATTCATTGGTAAGAAAAGTCCATTTATAGTCACCCA
Statistics
Matches: 163, Mismatches: 42, Indels: 4
0.78 0.20 0.02
Matches are distributed among these distances:
171 160 0.98
172 3 0.02
ACGTcount: A:0.34, C:0.13, G:0.12, T:0.35
Consensus pattern (171 bp):
ATTCATTGGTAAGAAAAGTCCATTTATAGTCACCCATACCTTCAAAAGCCTCTTTACTCGTTTTA
AATAGTTTTATAATGCCATAATGAGTTTTAAGTTGAATGTTTTTACATTTTTGGTTAAAACGAAC
TATAATTGAATGTCTACCTCAAAAAACATAAAGAAAAAGAC
Done.