Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018398834.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_2116.0, 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, 972
Length: 1620
ACGTcount: A:0.30, C:0.12, G:0.11, T:0.33
Warning! 213 characters in sequence are not A, C, G, or T
Found at i:671 original size:171 final size:171
Alignment explanation
Indices: 383--702 Score: 417
Period size: 171 Copynumber: 1.9 Consensus size: 171
373 TGAATTTCTC
* * * * **
383 TATATTTTTGGTTAAAACAAATTATTATTGAATTTTTACCTTGTGAAACACGAAGAAAAAGTCAT
1 TATATTTTTAGTTAAAACAAATTATAATTGAATGTCTACCTTGAAAAACACGAAGAAAAAGTCAT
* * * * * * * *
448 TCATTGGCTAAAAAAGTCCATTTATAGTTACCTAGGCCTTTAAAATCCTAATTACTCACTTTAAA
66 TCATTAGCTAAAAAAGTCAAATTATAATCACCCAGGCCTTCAAAAGCCTAATTACTCACTTTAAA
513 TGGTTTTATAATCTCATAATTAATTCTAGGTTAAATTATTT
131 TGGTTTTATAATCTCATAATTAATTCTAGGTTAAATTATTT
* * *
554 TATATTTTTAGTTAAAACAGATTATAATTGAATGTCTGCCTTGAAAAACATGAAGAAAAAGTCAT
1 TATATTTTTAGTTAAAACAAATTATAATTGAATGTCTACCTTGAAAAACACGAAGAAAAAGTCAT
* * * * *
619 TCATTAGC-AAGAAATGTCAAATTATAATCACCCATGCCTTCGAAGGCCTAATTACTTACTTTAA
66 TCATTAGCTAA-AAAAGTCAAATTATAATCACCCAGGCCTTCAAAAGCCTAATTACTCACTTTAA
*
683 ATGGTTTTATTATCTCATAA
130 ATGGTTTTATAATCTCATAA
703 CTGATNNNNN
Statistics
Matches: 125, Mismatches: 23, Indels: 2
0.83 0.15 0.01
Matches are distributed among these distances:
170 2 0.02
171 123 0.98
ACGTcount: A:0.37, C:0.14, G:0.11, T:0.38
Consensus pattern (171 bp):
TATATTTTTAGTTAAAACAAATTATAATTGAATGTCTACCTTGAAAAACACGAAGAAAAAGTCAT
TCATTAGCTAAAAAAGTCAAATTATAATCACCCAGGCCTTCAAAAGCCTAATTACTCACTTTAAA
TGGTTTTATAATCTCATAATTAATTCTAGGTTAAATTATTT
Found at i:1153 original size:171 final size:170
Alignment explanation
Indices: 847--1620 Score: 652
Period size: 171 Copynumber: 4.5 Consensus size: 170
837 TCTAGCCTCT
* * * * *
847 CAAGCCTTCGAAAGCCTAATTAGTTGCTTTAAATGGTTTTA-AATTCTCATAATTGATTTTAGGT
1 CAAGCCTTCGAAAACCTTATTACTCGCTTTAAATAGTTTTATAATTC-C-TAATTGATTTTAGGT
* * **
911 TTAATTTTTTTACATTTTT-GCTTAAAACATATTATAATTGAATGTCTGCCTCAGGAAACATGAA
64 TGAATTTTTTTACATTTTTAG-TTAAAACAGATTATAATTGAATGTCTGCC-CAAAAAACATGAA
* * * * *
975 GAAAAAGGCTA-TAATCGGCAA-AAAAATCTATTTATAGTCACC
127 AAAAAAGGCCATTCATCGGCAAGAAAAGTCCATTTATAGTCACC
** * *
1017 CAAGCCTTCGAAAATGTTATTACTCGCTTTAAATAGTTTTATAATGTCCTAATTAATTTTAAGAT
1 CAAGCCTTCGAAAACCTTATTACTCGCTTTAAATAGTTTTATAAT-TCCTAATTGATTTT-AGGT
* * * * * *
1082 TGAATTTTTTTATATTTTTAGTGAAAGCGGATTATAATTGAATGTTTGTCCCAAAAAACGTGAAA
64 TGAATTTTTTTACATTTTTAGTTAAAACAGATTATAATTGAATGTCTG-CCCAAAAAACATGAAA
* *
1147 AAAAAGGCTA-TCATTGGCAAGAAAAGTCCATTTATAGTCA-C
128 AAAAAGGCCATTCATCGGCAAGAAAAGTCCATTTATAGTCACC
* * * * * * * **
1188 CAATTCCTTTGAAAGCCTAATTACTCGCTTTCAATAGTTTTATAATTCCATAATCGATGTTATTT
1 CAA-GCCTTCGAAAACCTTATTACTCGCTTTAAATAGTTTTATAATTCC-TAATTGATTTTAGGT
* * * ** * **
1253 TGAATTTTTTTACATTTTTTGTTAAAACAGACTATAATTGAATGTCTATCTTAAAAAACCTGAGG
64 TGAATTTTTTTACATTTTTAGTTAAAACAGATTATAATTGAATGTCT-GCCCAAAAAACATGAAA
**********
1318 AAAAA-GCCATTNNNNNNNNNNAAAAGTCCATTTATAGTCACC
128 AAAAAGGCCATTCATCGGCAAGAAAAGTCCATTTATAGTCACC
* * * * *
1360 CAAGCATTCGAAAACCTTATTACTCGCTTTAAATGGTTTTATAAACTCATAATTGAATTTAGGTT
1 CAAGCCTTCGAAAACCTTATTACTCGCTTTAAATAGTTTTAT-AATTCCTAATTGATTTTAGGTT
* * ** * *
1425 GAATTTTTTTACGTTTTTAGTTAAAACATATTATAATTGAATGTCTGCATTAAGAAACATG-AAG
65 GAATTTTTTTACATTTTTAGTTAAAACAGATTATAATTGAATGTCTGC-CCAAAAAACATGAAAA
* **
1489 AGAAGGCCATTCATCGATAAGAAAAGTCCATTTATAGTCACC
129 AAAAGGCCATTCATCGGCAAGAAAAGTCCATTTATAGTCACC
* * * * *
1531 CATGACTTC-AAAA-TTATAATTACTCGCTTTAAGTCA-TTTTATAATCTCATAATTGATTTTAG
1 CAAGCCTTCGAAAACCT-T-ATTACTCGCTTTAAAT-AGTTTTATAAT-TCCTAATTGATTTTAG
* * *
1593 GTTAAATTTTTTTATATTTTTGGTTAAA
62 GTTGAATTTTTTTACATTTTTAGTTAAA
Statistics
Matches: 479, Mismatches: 107, Indels: 35
0.77 0.17 0.06
Matches are distributed among these distances:
169 1 0.00
170 58 0.12
171 347 0.72
172 73 0.15
ACGTcount: A:0.35, C:0.13, G:0.13, T:0.38
Consensus pattern (170 bp):
CAAGCCTTCGAAAACCTTATTACTCGCTTTAAATAGTTTTATAATTCCTAATTGATTTTAGGTTG
AATTTTTTTACATTTTTAGTTAAAACAGATTATAATTGAATGTCTGCCCAAAAAACATGAAAAAA
AAGGCCATTCATCGGCAAGAAAAGTCCATTTATAGTCACC
Done.