Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01021229.1 Corchorus olitorius cultivar O-4 contig21262, 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: 28565
ACGTcount: A:0.30, C:0.19, G:0.19, T:0.31
Found at i:263 original size:8 final size:8
Alignment explanation
Indices: 252--285 Score: 52
Period size: 8 Copynumber: 4.4 Consensus size: 8
242 AAATTATAAA
252 AGTAAAAT
1 AGTAAAAT
260 AGTAAAAT
1 AGTAAAAT
268 AGTAAAA-
1 AGTAAAAT
*
275 AATAAAAT
1 AGTAAAAT
283 AGT
1 AGT
286 TATAAGGATA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
7 6 0.26
8 17 0.74
ACGTcount: A:0.65, C:0.00, G:0.12, T:0.24
Consensus pattern (8 bp):
AGTAAAAT
Found at i:282 original size:15 final size:16
Alignment explanation
Indices: 238--285 Score: 57
Period size: 15 Copynumber: 3.2 Consensus size: 16
228 TTTTTAGTTG
*
238 AGTAAAATTAT-AAA-
1 AGTAAAATAATAAAAT
*
252 AGTAAAATAGTAAAAT
1 AGTAAAATAATAAAAT
268 AGTAAAA-AATAAAAT
1 AGTAAAATAATAAAAT
283 AGT
1 AGT
286 TATAAGGATA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
14 9 0.31
15 13 0.45
16 7 0.24
ACGTcount: A:0.65, C:0.00, G:0.10, T:0.25
Consensus pattern (16 bp):
AGTAAAATAATAAAAT
Found at i:7791 original size:19 final size:19
Alignment explanation
Indices: 7767--7853 Score: 67
Period size: 19 Copynumber: 4.7 Consensus size: 19
7757 TCCACTGTTA
7767 TGTGCTGACGTGGCCACTT
1 TGTGCTGACGTGGCCACTT
* * *
7786 TGTGCTGACGTGGCGAATC
1 TGTGCTGACGTGGCCACTT
*
7805 TGT-C-AAC-T--CCACTGTT
1 TGTGCTGACGTGGCCAC--TT
*
7821 ATGTGCTGATGTGGCCACTT
1 -TGTGCTGACGTGGCCACTT
7841 TGTGCTGACGTGG
1 TGTGCTGACGTGG
7854 ATTTTCCACG
Statistics
Matches: 50, Mismatches: 10, Indels: 16
0.66 0.13 0.21
Matches are distributed among these distances:
14 2 0.04
16 2 0.04
17 5 0.10
18 2 0.04
19 32 0.64
20 3 0.06
22 4 0.08
ACGTcount: A:0.14, C:0.23, G:0.31, T:0.32
Consensus pattern (19 bp):
TGTGCTGACGTGGCCACTT
Found at i:7835 original size:55 final size:55
Alignment explanation
Indices: 7748--7853 Score: 203
Period size: 55 Copynumber: 1.9 Consensus size: 55
7738 GACTAACGAT
7748 TCTGTCAACTCCACTGTTATGTGCTGACGTGGCCACTTTGTGCTGACGTGGCGAA
1 TCTGTCAACTCCACTGTTATGTGCTGACGTGGCCACTTTGTGCTGACGTGGCGAA
*
7803 TCTGTCAACTCCACTGTTATGTGCTGATGTGGCCACTTTGTGCTGACGTGG
1 TCTGTCAACTCCACTGTTATGTGCTGACGTGGCCACTTTGTGCTGACGTGG
7854 ATTTTCCACG
Statistics
Matches: 50, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
55 50 1.00
ACGTcount: A:0.15, C:0.25, G:0.27, T:0.33
Consensus pattern (55 bp):
TCTGTCAACTCCACTGTTATGTGCTGACGTGGCCACTTTGTGCTGACGTGGCGAA
Found at i:24315 original size:27 final size:27
Alignment explanation
Indices: 24277--24333 Score: 105
Period size: 27 Copynumber: 2.1 Consensus size: 27
24267 ATCTTGTTTG
24277 TGTCCCACCGGGCGTGCCAAAAAGAGA
1 TGTCCCACCGGGCGTGCCAAAAAGAGA
*
24304 TGTCCCATCGGGCGTGCCAAAAAGAGA
1 TGTCCCACCGGGCGTGCCAAAAAGAGA
24331 TGT
1 TGT
24334 TGCGCCAAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.28, C:0.26, G:0.30, T:0.16
Consensus pattern (27 bp):
TGTCCCACCGGGCGTGCCAAAAAGAGA
Found at i:28376 original size:18 final size:19
Alignment explanation
Indices: 28343--28379 Score: 67
Period size: 18 Copynumber: 2.0 Consensus size: 19
28333 TTAATGATTA
28343 GCCAACTTATTTTAACTTT
1 GCCAACTTATTTTAACTTT
28362 GCCAACTTA-TTTAACTTT
1 GCCAACTTATTTTAACTTT
28380 TAAACTTGAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 9 0.50
19 9 0.50
ACGTcount: A:0.27, C:0.22, G:0.05, T:0.46
Consensus pattern (19 bp):
GCCAACTTATTTTAACTTT
Done.