Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018403260.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_934.0, 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: 25370
ACGTcount: A:0.29, C:0.14, G:0.13, T:0.29
Warning! 3955 characters in sequence are not A, C, G, or T
Found at i:17677 original size:12 final size:12
Alignment explanation
Indices: 17660--17690 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
17650 TAGAATGAAG
17660 AATCTATTAAAA
1 AATCTATTAAAA
*
17672 AATCTATTAAAG
1 AATCTATTAAAA
17684 AATCTAT
1 AATCTAT
17691 CACTAATAGC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.52, C:0.10, G:0.03, T:0.35
Consensus pattern (12 bp):
AATCTATTAAAA
Found at i:21723 original size:17 final size:17
Alignment explanation
Indices: 21703--21736 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
21693 CAAACTATTT
21703 TAACCGAAATAACCGAA
1 TAACCGAAATAACCGAA
*
21720 TAACCGAACTAACCGAA
1 TAACCGAAATAACCGAA
21737 CTGAAAAAAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.50, C:0.26, G:0.12, T:0.12
Consensus pattern (17 bp):
TAACCGAAATAACCGAA
Found at i:21737 original size:9 final size:9
Alignment explanation
Indices: 21703--21738 Score: 56
Period size: 9 Copynumber: 4.1 Consensus size: 9
21693 CAAACTATTT
*
21703 TAACCGAAA
1 TAACCGAAC
21712 TAACCGAA-
1 TAACCGAAC
21720 TAACCGAAC
1 TAACCGAAC
21729 TAACCGAAC
1 TAACCGAAC
21738 T
1 T
21739 GAAAAAACTG
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
8 8 0.31
9 18 0.69
ACGTcount: A:0.47, C:0.28, G:0.11, T:0.14
Consensus pattern (9 bp):
TAACCGAAC
Found at i:22881 original size:39 final size:40
Alignment explanation
Indices: 22832--22919 Score: 133
Period size: 40 Copynumber: 2.2 Consensus size: 40
22822 TTGGTTATTT
* * *
22832 TTCACTTTAGTGGG-TTTTCAACCTTGCCAAGATTGGTGA
1 TTCACCTTAGTGGGCTTTTCAACCTTACCAAGATGGGTGA
22871 TTCACCTTAGTGGGCTTTTCAACCTTACCAAGATGGGTGA
1 TTCACCTTAGTGGGCTTTTCAACCTTACCAAGATGGGTGA
*
22911 TTCATCTTA
1 TTCACCTTA
22920 ATAAGGTTTC
Statistics
Matches: 44, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
39 13 0.30
40 31 0.70
ACGTcount: A:0.22, C:0.20, G:0.20, T:0.38
Consensus pattern (40 bp):
TTCACCTTAGTGGGCTTTTCAACCTTACCAAGATGGGTGA
Found at i:23370 original size:17 final size:17
Alignment explanation
Indices: 23341--23374 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
23331 CAAATTATTC
23341 TAACCGAAATAACCGAA
1 TAACCGAAATAACCGAA
23358 TAACC-AAACTAACCGAA
1 TAACCGAAA-TAACCGAA
23375 CCAAAAAAAC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 3 0.19
17 13 0.81
ACGTcount: A:0.53, C:0.26, G:0.09, T:0.12
Consensus pattern (17 bp):
TAACCGAAATAACCGAA
Found at i:24732 original size:39 final size:40
Alignment explanation
Indices: 24687--24776 Score: 146
Period size: 40 Copynumber: 2.3 Consensus size: 40
24677 TTGATTATTT
*
24687 TTCACTTTAGTGGG-TTTTCAACTTTGCCAAGATTAGTGA
1 TTCACTTTAGTGGGCTTTTCAACCTTGCCAAGATTAGTGA
*
24726 TTCACTTTAGTGGGCTTTTCAACCTTGCCAAGATTGGTGA
1 TTCACTTTAGTGGGCTTTTCAACCTTGCCAAGATTAGTGA
*
24766 TTCACCTTAGT
1 TTCACTTTAGT
24777 AAGGTTTCTA
Statistics
Matches: 47, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
39 14 0.30
40 33 0.70
ACGTcount: A:0.21, C:0.19, G:0.20, T:0.40
Consensus pattern (40 bp):
TTCACTTTAGTGGGCTTTTCAACCTTGCCAAGATTAGTGA
Done.