Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018398448.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_1747.0, 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: 4409
ACGTcount: A:0.26, C:0.10, G:0.08, T:0.27
Warning! 1219 characters in sequence are not A, C, G, or T
Found at i:969 original size:171 final size:170
Alignment explanation
Indices: 424--1219 Score: 632
Period size: 171 Copynumber: 4.7 Consensus size: 170
414 NNNTGACAAA
* * ** *
424 AAAAGTCCATTTATAGTCACTCATTCCTTCAAAAGCCTTATTACTCATTCTAAATGGTTTTCTAA
1 AAAAGTCCATTTATAGTCACCCATTCCTTCAAAACCCTTATTACTCGCTATAAATGGTTTTCTAA
* * * * * **
489 TCTCATAATTGATTTTAAGTT-GATTTTTTTACATATTTTATTAAAACTAACT-ATAATTGAANN
66 TCTCGTAATTGATTTTAAGTTCAATTTTTTTATATTTTTTATTAAAAC-AAATAATAATTGAATG
******** ** * *
552 NNNNNNNNGAGAAATGTGAAGAAAAAGTATTCATTGGCAAG
130 TCTATCTTGAGAAACATGAAGAAAAAGCATTCATTGGAAAG
* * ** * *
593 AAAAGTCAATTTATTA-TCACCCATTCCTTCAAAAGCCTTATTACTCATTCTAAATGGTTTTATA
1 AAAAGTCCATTTA-TAGTCACCCATTCCTTCAAAACCCTTATTACTCGCTATAAATGGTTTTCTA
********** *
657 ATCTCNNNNNNNNNNTTAAGTTCAATTTATTTTATATTTTTTATTAAAACAGACT-ATAATTGAA
65 ATCTCGTAATTGATTTTAAGTTCAATTT-TTTTATATTTTTTATTAAAACA-AATAATAATTGAA
* * *
721 TGTCTGTCTTGAGAAGCATGAAGAAAAAAGCATTCATTGGTAAG
128 TGTCTATCTTGAGAAACATGAAG-AAAAAGCATTCATTGGAAAG
** * * * * * ***
765 AAATA-TCTGTTTACAGCCTCCCATTCTTTCAAAACCCTTATTACTCGCTTTAAATGGTTTTNNN
1 AAA-AGTCCATTTATAGTCACCCATTCCTTCAAAACCCTTATTACTCGCTATAAATGGTTTTCTA
******* * * * *
829 NNNNNNNAATTGATTTTAAGTTCAATTTTTTTACATTTTTCAATAATACAAATAATAATTGAATG
65 ATCTCGTAATTGATTTTAAGTTCAATTTTTTTATATTTTTTATTAAAACAAATAATAATTGAATG
* *
894 TCTATCTCGAGAAACATGAAGAGAAAAGCATTCATTGGGAAG
130 TCTATCTTGAGAAACATGAAGA-AAAAGCATTCATTGGAAAG
* *
936 AAAAGTCCATTTATAGTCACCTATTCCTTCAAAACTCTTATTACTCGCTATAAATGGTTTTCTAA
1 AAAAGTCCATTTATAGTCACCCATTCCTTCAAAACCCTTATTACTCGCTATAAATGGTTTTCTAA
* * * *
1001 TCTCGTAATTGATTTTAGGTT-GATTTTTTTATATTTTTTATTAAAACAGATAATAATTGACTGT
66 TCTCGTAATTGATTTTAAGTTCAATTTTTTTATATTTTTTATTAAAACAAATAATAATTGAATGT
* *
1065 CTATCTTGAGAAACGTGAAGAAAAAGTATTCATTGGAAAG
131 CTATCTTGAGAAACATGAAGAAAAAGCATTCATTGGAAAG
* ********** * *** * *
1105 AAAAGTCCATTTATAGTCACTCNNNNNNNNNNAAGCCTTATTACTAATTTTAAATGGTTTTATAA
1 AAAAGTCCATTTATAGTCACCCATTCCTTCAAAACCCTTATTACTCGCTATAAATGGTTTTCTAA
* *
1170 TCTCATTATTGATTTTAAGTTCAATTTGTTTTATATTTTTTATTAAAACA
66 TCTCGTAATTGATTTTAAGTTCAATTT-TTTTATATTTTTTATTAAAACA
1220 GACTNNNNNN
Statistics
Matches: 495, Mismatches: 120, Indels: 22
0.78 0.19 0.03
Matches are distributed among these distances:
169 151 0.31
170 70 0.14
171 193 0.39
172 80 0.16
173 1 0.00
ACGTcount: A:0.33, C:0.13, G:0.11, T:0.38
Consensus pattern (170 bp):
AAAAGTCCATTTATAGTCACCCATTCCTTCAAAACCCTTATTACTCGCTATAAATGGTTTTCTAA
TCTCGTAATTGATTTTAAGTTCAATTTTTTTATATTTTTTATTAAAACAAATAATAATTGAATGT
CTATCTTGAGAAACATGAAGAAAAAGCATTCATTGGAAAG
Found at i:1361 original size:110 final size:110
Alignment explanation
Indices: 1168--1500 Score: 513
Period size: 110 Copynumber: 3.0 Consensus size: 110
1158 ATGGTTTTAT
* * *********
1168 AATCTCATTATTGATTTTAAGTTCAATTTGTTTTATATTTTTTATTAAAACAGACTNNNNNNNNN
1 AATCTCATTATTGATTTTAAATTCAATTTATTTTATATTTTTTATTAAAACAGACTATAATTGAA
* *
1233 NGTCTGCCTTGAGAAGCATGAAGAAAAAAGCATTCATTGGCAAGA
66 TGTCGGCCTTGAGAAGCATGAAGAAAAAAGCATTCATTGGCAAGA
* *
1278 AATCTCATTATTGATTTTAAATTCAATTTATTTTTTATTTTTTATTAAAACAAACTATAATTGAA
1 AATCTCATTATTGATTTTAAATTCAATTTATTTTATATTTTTTATTAAAACAGACTATAATTGAA
*
1343 TGTCGGCCTTGAGAAGCATGAAGAAAAAAGTATTCATTGGCAAGA
66 TGTCGGCCTTGAGAAGCATGAAGAAAAAAGCATTCATTGGCAAGA
*
1388 AATCTCATTATTGATTTTAAATTCAATTTATTTTATATTTTTTATAAAAACAGACTATAATTGAA
1 AATCTCATTATTGATTTTAAATTCAATTTATTTTATATTTTTTATTAAAACAGACTATAATTGAA
1453 TGTCGGCCTTGAGAAGCATGAAGAAAAAAGCATTCATTGGCAAGA
66 TGTCGGCCTTGAGAAGCATGAAGAAAAAAGCATTCATTGGCAAGA
1498 AAT
1 AAT
1501 GTNNNNNNNN
Statistics
Matches: 203, Mismatches: 20, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
110 203 1.00
ACGTcount: A:0.37, C:0.11, G:0.13, T:0.37
Consensus pattern (110 bp):
AATCTCATTATTGATTTTAAATTCAATTTATTTTATATTTTTTATTAAAACAGACTATAATTGAA
TGTCGGCCTTGAGAAGCATGAAGAAAAAAGCATTCATTGGCAAGA
Found at i:2182 original size:108 final size:110
Alignment explanation
Indices: 1992--2212 Score: 358
Period size: 109 Copynumber: 2.0 Consensus size: 110
1982 ATAGTTTTAT
* *
1992 AATCTCATTATTGATTTAAAGTTCAATTTGTTTTATATTTTTTATTAAAACAGACTATAATTTAA
1 AATCTCATTATTGATTTAAAGTTCAATTTATTTTATATTTTTTATTAAAACAGACTATAATTGAA
* *
2057 TGTCTGCCTTGAGAAGCATG-AAAAAAAAACATTCCTTGGCAAGA
66 TGTCTGCCTTGAGAAGCATGTAAAAAAAAACATTCATTGACAAGA
2101 AATCTCATTATTGATTTTAAA-TTCAATTTATTTTATA-TTTTTATTAAAACAGACTATAATTGA
1 AATCTCATTATTGA-TTTAAAGTTCAATTTATTTTATATTTTTTATTAAAACAGACTATAATTGA
* *
2164 ATGTCTGCCTTGAGAAGCATGTAGAAAAAAGCATTCATTGACAAGA
65 ATGTCTGCCTTGAGAAGCATGTAAAAAAAAACATTCATTGACAAGA
2210 AAT
1 AAT
2213 GTCTGTTTAC
Statistics
Matches: 104, Mismatches: 6, Indels: 4
0.91 0.05 0.04
Matches are distributed among these distances:
108 46 0.44
109 52 0.50
110 6 0.06
ACGTcount: A:0.38, C:0.11, G:0.12, T:0.38
Consensus pattern (110 bp):
AATCTCATTATTGATTTAAAGTTCAATTTATTTTATATTTTTTATTAAAACAGACTATAATTGAA
TGTCTGCCTTGAGAAGCATGTAAAAAAAAACATTCATTGACAAGA
Done.