Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012307.1 Corchorus olitorius cultivar O-4 contig12340, 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: 23895
ACGTcount: A:0.31, C:0.17, G:0.19, T:0.32
Found at i:8115 original size:32 final size:32
Alignment explanation
Indices: 8074--8139 Score: 123
Period size: 32 Copynumber: 2.1 Consensus size: 32
8064 AAGAAAAAAG
8074 TTAAACCGACCATGCAAGCTTCTAACTAATTT
1 TTAAACCGACCATGCAAGCTTCTAACTAATTT
*
8106 TTAAACCGACCATGCAAGCTTCTAATTAATTT
1 TTAAACCGACCATGCAAGCTTCTAACTAATTT
8138 TT
1 TT
8140 TTTAGATAAG
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.33, C:0.23, G:0.09, T:0.35
Consensus pattern (32 bp):
TTAAACCGACCATGCAAGCTTCTAACTAATTT
Found at i:12001 original size:27 final size:27
Alignment explanation
Indices: 11913--11993 Score: 144
Period size: 27 Copynumber: 3.0 Consensus size: 27
11903 TTAGCATTGG
*
11913 GGTCATTTGCACGTCCAGGGGCATTTT
1 GGTCATTTGCACATCCAGGGGCATTTT
11940 GGTCATTTGCACATCCAGGGGCATTTT
1 GGTCATTTGCACATCCAGGGGCATTTT
*
11967 GGTCATTTGCACATCCAAGGGCATTTT
1 GGTCATTTGCACATCCAGGGGCATTTT
11994 AGCCATTTTA
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 52 1.00
ACGTcount: A:0.19, C:0.22, G:0.26, T:0.33
Consensus pattern (27 bp):
GGTCATTTGCACATCCAGGGGCATTTT
Found at i:13069 original size:50 final size:50
Alignment explanation
Indices: 12994--13117 Score: 203
Period size: 50 Copynumber: 2.5 Consensus size: 50
12984 TGGCACCAAA
* * *
12994 GCAGCAAGCCAAGATTATGAGCATATCAAGTCACAAGGAAATTCCACATT
1 GCAGCAAGCCAAGATGATGAGCATATCAAGTCACAAAGAAATCCCACATT
*
13044 GCAGCAAGCCAAGATGATGAGCATATCTAGTCACAAAGAAATCCCACATT
1 GCAGCAAGCCAAGATGATGAGCATATCAAGTCACAAAGAAATCCCACATT
*
13094 GCAGCAAGACAAGATGATGAGCAT
1 GCAGCAAGCCAAGATGATGAGCAT
13118 GGTCGAGCCA
Statistics
Matches: 69, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
50 69 1.00
ACGTcount: A:0.40, C:0.22, G:0.20, T:0.18
Consensus pattern (50 bp):
GCAGCAAGCCAAGATGATGAGCATATCAAGTCACAAAGAAATCCCACATT
Found at i:14617 original size:31 final size:29
Alignment explanation
Indices: 14548--14621 Score: 85
Period size: 29 Copynumber: 2.5 Consensus size: 29
14538 CTTTAGGGAA
** *
14548 AAGGTCATTTAAGGTCCTAGCCTTTCAAT
1 AAGGTCAAATAAGGTCCTAACCTTTCAAT
14577 AAGGTCAAATAAGGTCCTAACCTTTACGAAT
1 AAGGTCAAATAAGGTCCTAACCTTT-C-AAT
**
14608 TGGGTCAAATAAGG
1 AAGGTCAAATAAGG
14622 ACAAAAGGGG
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
29 22 0.58
30 1 0.03
31 15 0.39
ACGTcount: A:0.34, C:0.18, G:0.20, T:0.28
Consensus pattern (29 bp):
AAGGTCAAATAAGGTCCTAACCTTTCAAT
Found at i:15550 original size:28 final size:28
Alignment explanation
Indices: 15510--15572 Score: 99
Period size: 28 Copynumber: 2.2 Consensus size: 28
15500 ATTTACTTTT
*
15510 ATTTTGGTCATTTTGTACATCCAGGGGC
1 ATTTTGGTCATTTTGCACATCCAGGGGC
**
15538 ATTTTGGTCATTTTGCATGTCCAGGGGC
1 ATTTTGGTCATTTTGCACATCCAGGGGC
15566 ATTTTGG
1 ATTTTGG
15573 GGTCATTTCA
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
28 32 1.00
ACGTcount: A:0.16, C:0.16, G:0.27, T:0.41
Consensus pattern (28 bp):
ATTTTGGTCATTTTGCACATCCAGGGGC
Found at i:15853 original size:24 final size:24
Alignment explanation
Indices: 15826--15875 Score: 64
Period size: 24 Copynumber: 2.1 Consensus size: 24
15816 TTCCCATTGA
*
15826 TCATGTCAATTATGCGCATGGTCT
1 TCATATCAATTATGCGCATGGTCT
* **
15850 TCATATCAATTGTGTTCATGGTCT
1 TCATATCAATTATGCGCATGGTCT
15874 TC
1 TC
15876 TTATACTTGT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.20, C:0.20, G:0.18, T:0.42
Consensus pattern (24 bp):
TCATATCAATTATGCGCATGGTCT
Done.