Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01021204.1 Corchorus olitorius cultivar O-4 contig21237, 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: 13119
ACGTcount: A:0.30, C:0.18, G:0.22, T:0.30
Found at i:2407 original size:22 final size:22
Alignment explanation
Indices: 2366--2407 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
2356 GACCCGTTGC
**
2366 ACTGGGGTAGTTTTTCGTTTAT
1 ACTGGGGTAGTTTTGAGTTTAT
2388 ACTGGGGTAGTTTTGAGTTT
1 ACTGGGGTAGTTTTGAGTTT
2408 TTGTGAATTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.14, C:0.07, G:0.31, T:0.48
Consensus pattern (22 bp):
ACTGGGGTAGTTTTGAGTTTAT
Found at i:11936 original size:9 final size:9
Alignment explanation
Indices: 11922--11972 Score: 102
Period size: 9 Copynumber: 5.7 Consensus size: 9
11912 ATTAATTCAA
11922 AGACTTCTT
1 AGACTTCTT
11931 AGACTTCTT
1 AGACTTCTT
11940 AGACTTCTT
1 AGACTTCTT
11949 AGACTTCTT
1 AGACTTCTT
11958 AGACTTCTT
1 AGACTTCTT
11967 AGACTT
1 AGACTT
11973 TAATTTACTT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 42 1.00
ACGTcount: A:0.24, C:0.22, G:0.12, T:0.43
Consensus pattern (9 bp):
AGACTTCTT
Found at i:11992 original size:7 final size:7
Alignment explanation
Indices: 11979--12018 Score: 55
Period size: 7 Copynumber: 5.9 Consensus size: 7
11969 ACTTTAATTT
11979 ACTTTAG
1 ACTTTAG
*
11986 GCTTTAG
1 ACTTTAG
11993 ACTTTAG
1 ACTTTAG
12000 ACTTTA-
1 ACTTTAG
*
12006 TCTTTAG
1 ACTTTAG
12013 ACTTTA
1 ACTTTA
12019 TCAACACCTT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
6 5 0.18
7 23 0.82
ACGTcount: A:0.25, C:0.15, G:0.12, T:0.47
Consensus pattern (7 bp):
ACTTTAG
Found at i:12012 original size:13 final size:13
Alignment explanation
Indices: 11976--12020 Score: 56
Period size: 13 Copynumber: 3.5 Consensus size: 13
11966 TAGACTTTAA
*
11976 TTTA-CTTTAGGC
1 TTTATCTTTAGAC
*
11988 TTTAGACTTTAGAC
1 TTTA-TCTTTAGAC
12002 TTTATCTTTAGAC
1 TTTATCTTTAGAC
12015 TTTATC
1 TTTATC
12021 AACACCTTCC
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
12 4 0.14
13 14 0.48
14 11 0.38
ACGTcount: A:0.22, C:0.16, G:0.11, T:0.51
Consensus pattern (13 bp):
TTTATCTTTAGAC
Found at i:12399 original size:33 final size:32
Alignment explanation
Indices: 12327--12406 Score: 90
Period size: 33 Copynumber: 2.4 Consensus size: 32
12317 TTTCTATGCA
*
12327 TTTGTAGTAACTTAATACATGACTTTTCTAATC
1 TTTGTAGTAACTTAATACATGACTTTACT-ATC
* *
12360 TCTGTAGTAACTTAATACATAGACTTTAACT-TT
1 TTTGTAGTAACTTAATACAT-GACTTT-ACTATC
*
12393 TTTGTAGTGACTTA
1 TTTGTAGTAACTTA
12407 GCGATATTTT
Statistics
Matches: 40, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
33 32 0.80
34 6 0.15
35 2 0.05
ACGTcount: A:0.30, C:0.14, G:0.11, T:0.45
Consensus pattern (32 bp):
TTTGTAGTAACTTAATACATGACTTTACTATC
Found at i:12707 original size:33 final size:33
Alignment explanation
Indices: 12665--12742 Score: 102
Period size: 33 Copynumber: 2.4 Consensus size: 33
12655 AACTTTGATC
**
12665 AAGTTACTACAAACCCTCATTAATCAATGTATT
1 AAGTTACTACAAACCCTCATTAATCAATACATT
* **
12698 AAGTTACTACAAACCTTCATTTTTCAATACATT
1 AAGTTACTACAAACCCTCATTAATCAATACATT
*
12731 AGGTTACTACAA
1 AAGTTACTACAA
12743 TCCTATGTAA
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
33 39 1.00
ACGTcount: A:0.38, C:0.21, G:0.06, T:0.35
Consensus pattern (33 bp):
AAGTTACTACAAACCCTCATTAATCAATACATT
Done.