Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018398086.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_1393.0, 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: 5888
ACGTcount: A:0.25, C:0.10, G:0.08, T:0.27
Warning! 1757 characters in sequence are not A, C, G, or T
Found at i:2308 original size:170 final size:170
Alignment explanation
Indices: 1755--2309 Score: 492
Period size: 170 Copynumber: 3.3 Consensus size: 170
1745 NNNNNNNNNN
* * *
1755 TTATAGTCACCCATTCCTTTAAAAGCCTTATTACTCGCTTTATATGGTTTTATAGTCTCATAATT
1 TTATAGTCACCCATTCCTTCAAAAGCCTTATTACTCGCTTTAAATGGTTTTATAATCTCATAATT
* ** * * *
1820 GATTTGAAGTTGAATTTTTTTATATTTTTGGTTAAAACAGAGTGTAATTGAATGTCTA-C-CGTA
66 GATTTTAAGTT-AATTTTTTTATATTTTTTATTAAAACAGATTATAATTGAATGTTTACCTCGTA
* * * * *
1883 AGAACCATGAAGAAAAAGGAATTCAATGGCAAGC-AAAGTCCAT
130 A-AA-CGTGAAGAAAAAGGCATTCATTGACAA-CAAAAGTCTAT
**********
1926 TTATAGTCACCCATTCCTTCAAAANNNNNNNNNNTCGCTTTAAATGGTTTTATAATCTCATAATT
1 TTATAGTCACCCATTCCTTCAAAAGCCTTATTACTCGCTTTAAATGGTTTTATAATCTCATAATT
* * * *
1991 GATTTTAAGTT-TTTTTATTTTTA-TTTTTAGTTAAAACAGATTATAATTGAATGTTTACTTTAG
66 GATTTTAAGTTAATTTT-TTTATATTTTTTA-TTAAAACAGATTATAATTGAATGTTTAC-CTCG
* *
2054 -AAAATGGGAAGAAAAAGGCATTCATTGACAACAAAAGTCTAT
128 TAAAACGTGAAGAAAAAGGCATTCATTGACAACAAAAGTCTAT
* ******************* *
2096 TTTTAGTCACCNNNNNNNNNNNNNNNNNNNTTACTCGCTTTAAATGGTTTTATAATCTCATCATT
1 TTATAGTCACCCATTCCTTCAAAAGCCTTATTACTCGCTTTAAATGGTTTTATAATCTCATAATT
*
2161 GATTTTAAGTTAATATTTTTATATTTTTTATTAAAACAGATTATAATTGAATGTTTACCTCGTAA
66 GATTTTAAGTTAATTTTTTTATATTTTTTATTAAAACAGATTATAATTGAATGTTTACCTCGTAA
* *
2226 AACGTGAAGAAAAAGGCATTTATTGTCAACAAAAGTCTAT
131 AACGTGAAGAAAAAGGCATTCATTGACAACAAAAGTCTAT
* * *
2266 TTATTGTCTCCCATTCCTTCAAAAGCCTTATTACTTGCTTTAAA
1 TTATAGTCACCCATTCCTTCAAAAGCCTTATTACTCGCTTTAAA
2310 NNNNNNNNNN
Statistics
Matches: 294, Mismatches: 81, Indels: 19
0.75 0.21 0.05
Matches are distributed among these distances:
169 11 0.04
170 207 0.70
171 73 0.25
172 2 0.01
173 1 0.00
ACGTcount: A:0.32, C:0.13, G:0.12, T:0.38
Consensus pattern (170 bp):
TTATAGTCACCCATTCCTTCAAAAGCCTTATTACTCGCTTTAAATGGTTTTATAATCTCATAATT
GATTTTAAGTTAATTTTTTTATATTTTTTATTAAAACAGATTATAATTGAATGTTTACCTCGTAA
AACGTGAAGAAAAAGGCATTCATTGACAACAAAAGTCTAT
Found at i:3585 original size:173 final size:172
Alignment explanation
Indices: 3356--3794 Score: 494
Period size: 174 Copynumber: 2.6 Consensus size: 172
3346 NNNNNNNNNN
* * * *
3356 CATTTTTGGTTAAAACAGATTATAATTGAAAGTCTACCTTAAGAAACATGAAGAAAAAGGTATTC
1 CATTTTTTGTTAAAATAGACTATAATTGAATGTCTACCTTAAGAAACATGAAGAAAAAGGTATTC
* *
3421 ATT-ATCAAGAAAAGTCCATTTATAGTCACCCATTCCTTCAAAAGCCTTATTAGTCGCTTTAAAT
66 ATTGATCAAGAAAAGTCCATTTATAGTCACCCATTCCTTCAAAAGCCTTATTACTCACTTTAAAT
* *
3485 AGTTTTACAAGCTCATAATTGATTTTAAGTTGAATTTTTTTTA
131 AGTTTTACAAGCTCATAATTGATTTTAAATTG-ATTATTTTTA
* * * *
3528 TATTTTTTTGTTAAAATAGACTATAATTGAATGCCTA-CTTGAAGAAACATAAAGAAAAAGGCAC
1 CA-TTTTTTGTTAAAATAGACTATAATTGAATGTCTACCTT-AAGAAACATGAAGAAAAAGGTA-
* * * * **
3592 TT-ATTGGTAAAAAAAAGGT-CATTCATAGTCACCCATTCCTTCAAAAGCCTTATTACTCACTNN
63 TTCATTGATCAAGAAAA-GTCCATTTATAGTCACCCATTCCTTCAAAAGCCTTATTACTCACTTT
******** * *
3655 NNNNNNNNTTATAATCTCATAATTGATTTTAAATTGATTATTTTTA
127 AAATAGTTTTACAAGCTCATAATTGATTTTAAATTGATTATTTTTA
* * * *
3701 CATTTTTTGTTAAAATA-AGCAATAAGTGAATGTCTATCTTATGAAACATGAAGAAAAAGGTATT
1 CATTTTTTGTTAAAATAGA-CTATAATTGAATGTCTACCTTAAGAAACATGAAGAAAAAGGTATT
3765 CATTGA-CAAGAAAAGTCCATTTATAGTCAC
65 CATTGATCAAGAAAAGTCCATTTATAGTCAC
3795 NNNNNNNNNN
Statistics
Matches: 219, Mismatches: 39, Indels: 19
0.79 0.14 0.07
Matches are distributed among these distances:
170 2 0.01
171 21 0.10
172 56 0.26
173 65 0.30
174 73 0.33
175 2 0.01
ACGTcount: A:0.37, C:0.13, G:0.12, T:0.35
Consensus pattern (172 bp):
CATTTTTTGTTAAAATAGACTATAATTGAATGTCTACCTTAAGAAACATGAAGAAAAAGGTATTC
ATTGATCAAGAAAAGTCCATTTATAGTCACCCATTCCTTCAAAAGCCTTATTACTCACTTTAAAT
AGTTTTACAAGCTCATAATTGATTTTAAATTGATTATTTTTA
Done.