Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018402611.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_5682.0, 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: 1968
ACGTcount: A:0.29, C:0.11, G:0.09, T:0.30
Warning! 412 characters in sequence are not A, C, G, or T
Found at i:828 original size:17 final size:17
Alignment explanation
Indices: 775--820 Score: 92
Period size: 17 Copynumber: 2.7 Consensus size: 17
765 ATAGTCACCC
775 ATTCCTTCAAAAGGCTT
1 ATTCCTTCAAAAGGCTT
792 ATTCCTTCAAAAGGCTT
1 ATTCCTTCAAAAGGCTT
809 ATTCCTTCAAAA
1 ATTCCTTCAAAA
821 AGATTATTAC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 29 1.00
ACGTcount: A:0.33, C:0.24, G:0.09, T:0.35
Consensus pattern (17 bp):
ATTCCTTCAAAAGGCTT
Found at i:986 original size:17 final size:17
Alignment explanation
Indices: 946--987 Score: 75
Period size: 17 Copynumber: 2.5 Consensus size: 17
936 AAAAAAATGA
*
946 TTCATTCAGAAGAAAAG
1 TTCATTTAGAAGAAAAG
963 TTCATTTAGAAGAAAAG
1 TTCATTTAGAAGAAAAG
980 TTCATTTA
1 TTCATTTA
988 TAGTCACCCC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 24 1.00
ACGTcount: A:0.43, C:0.10, G:0.14, T:0.33
Consensus pattern (17 bp):
TTCATTTAGAAGAAAAG
Found at i:1257 original size:171 final size:170
Alignment explanation
Indices: 963--1446 Score: 616
Period size: 171 Copynumber: 2.8 Consensus size: 170
953 AGAAGAAAAG
* * * *
963 TTCATTTAGAAGAAAAGT-TCATTTATAGTCACCCCTTCCATCAAAA-CGTATATTACTCGATTT
1 TTCATTGAGAAGAAAAGTCT-ATTTAGAGTCACCCATTCCTTCAAAAGCGT-TATTACTCG-TTT
*
1026 AAATAGTTTTATAATCTCATAATTGATTTTAAGTTGAATTTTTTTACATTTTTGATTAAAACATA
63 AAATAGTTTTATAATCTCATAATTGATTTTAAGTTGAATTTTTTTACATTTTTGATTAAAACAGA
*
1091 CTATAATTGAATGTCTACCTCA-AGAAACGTGAAGAAACAAG-TA
128 CTATAATTGAATGTCTACCTCACA-AAACGTGAAGAAA-AAGCCA
* *
1134 TTCATTGACAAGAAAAGTCTATTTAGAGTCACCCATTCCTTCAAAAGGGTTATTACTCGCTTTAA
1 TTCATTGAGAAGAAAAGTCTATTTAGAGTCACCCATTCCTTCAAAAGCGTTATTACTCG-TTTAA
* *
1199 ATAATTTTATAATCTCATAATTGATTTTAAGTTGAATTTTTTTACATTTTTTATTAAAACAGACT
65 ATAGTTTTATAATCTCATAATTGATTTTAAGTTGAATTTTTTTACATTTTTGATTAAAACAGACT
* *
1264 ATAATTGAATGTCTACCTTACAAAACGTGCAGAAAAAGCCA
130 ATAATTGAATGTCTACCTCACAAAACGTGAAGAAAAAGCCA
* * * * *
1305 TTCATTGAGAACAAAAGTCTATTTAGAGTAACTCATTCCTTCAAAAGCCTTATTACCCGTTGTAA
1 TTCATTGAGAAGAAAAGTCTATTTAGAGTCACCCATTCCTTCAAAAGCGTTATTACTCGTT-TAA
* * * ** * * ***
1370 ATGGTTTTATAATTTCATAAGTGATTTTAAGTCAAATTTTTTTTAAATTTTTGGTTAAATTTGAC
65 ATAGTTTTATAATCTCATAATTGATTTTAAGTTGAA-TTTTTTTACATTTTTGATTAAAACAGAC
*
1435 TATAATTAAATG
129 TATAATTGAATG
1447 CTTGCCCTAA
Statistics
Matches: 274, Mismatches: 33, Indels: 11
0.86 0.10 0.03
Matches are distributed among these distances:
170 5 0.02
171 232 0.85
172 37 0.14
ACGTcount: A:0.36, C:0.14, G:0.11, T:0.39
Consensus pattern (170 bp):
TTCATTGAGAAGAAAAGTCTATTTAGAGTCACCCATTCCTTCAAAAGCGTTATTACTCGTTTAAA
TAGTTTTATAATCTCATAATTGATTTTAAGTTGAATTTTTTTACATTTTTGATTAAAACAGACTA
TAATTGAATGTCTACCTCACAAAACGTGAAGAAAAAGCCA
Done.