Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020748.1 Corchorus olitorius cultivar O-4 contig20781, 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: 47201
ACGTcount: A:0.35, C:0.17, G:0.17, T:0.32
Found at i:1085 original size:5 final size:5
Alignment explanation
Indices: 1077--1129 Score: 60
Period size: 5 Copynumber: 11.4 Consensus size: 5
1067 ATTATACATC
* *
1077 AAGAT AAGAT AAAAT AAGAT AAGAT AAGAT -AG-T AAAAT -AG-T AAGAT
1 AAGAT AAGAT AAGAT AAGAT AAGAT AAGAT AAGAT AAGAT AAGAT AAGAT
1123 AAGAT AA
1 AAGAT AA
1130 AGAATTATCC
Statistics
Matches: 40, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
3 2 0.05
4 6 0.15
5 32 0.80
ACGTcount: A:0.62, C:0.00, G:0.17, T:0.21
Consensus pattern (5 bp):
AAGAT
Found at i:8325 original size:19 final size:19
Alignment explanation
Indices: 8301--8337 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
8291 TTTGATCCCA
*
8301 AAACGATGGTGAAACAGTC
1 AAACGATAGTGAAACAGTC
8320 AAACGATAGTGAAACAGT
1 AAACGATAGTGAAACAGT
8338 AGTGAAACAG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.46, C:0.14, G:0.24, T:0.16
Consensus pattern (19 bp):
AAACGATAGTGAAACAGTC
Found at i:18031 original size:2 final size:2
Alignment explanation
Indices: 18024--18066 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
18014 GATATCCCTA
18024 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
18066 T
1 T
18067 TATTTATTGG
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:30674 original size:17 final size:18
Alignment explanation
Indices: 30638--30676 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
30628 AGTCTGATGA
30638 AGAAGAAGTTGATCCTTG
1 AGAAGAAGTTGATCCTTG
* *
30656 AGAAGTAGTTG-TTCTTG
1 AGAAGAAGTTGATCCTTG
30673 AGAA
1 AGAA
30677 TTCCCCCATG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 9 0.47
18 10 0.53
ACGTcount: A:0.33, C:0.08, G:0.28, T:0.31
Consensus pattern (18 bp):
AGAAGAAGTTGATCCTTG
Found at i:34022 original size:20 final size:20
Alignment explanation
Indices: 33997--34036 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
33987 AAATAGCTAA
33997 GGTATGACCATCTACCTGAT
1 GGTATGACCATCTACCTGAT
34017 GGTATGACCATCTACCTGAT
1 GGTATGACCATCTACCTGAT
34037 TAAGTTCAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.25, C:0.25, G:0.20, T:0.30
Consensus pattern (20 bp):
GGTATGACCATCTACCTGAT
Found at i:41673 original size:36 final size:36
Alignment explanation
Indices: 41624--41692 Score: 129
Period size: 36 Copynumber: 1.9 Consensus size: 36
41614 CTAACGTTTA
41624 TTTTTTCCATTTTTAAGACATGAACTCTTACTAAAG
1 TTTTTTCCATTTTTAAGACATGAACTCTTACTAAAG
*
41660 TTTTTTCCTTTTTTAAGACATGAACTCTTACTA
1 TTTTTTCCATTTTTAAGACATGAACTCTTACTA
41693 TAGGAAGATC
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 32 1.00
ACGTcount: A:0.28, C:0.17, G:0.07, T:0.48
Consensus pattern (36 bp):
TTTTTTCCATTTTTAAGACATGAACTCTTACTAAAG
Found at i:43960 original size:2 final size:2
Alignment explanation
Indices: 43953--43979 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
43943 TTTTAATTAA
43953 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
43980 ATCAAATTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Done.