Locus 7420

Sequence ID	2L_DroMel_CAF1
Location	20,603,503 – 20,603,633
Length	130
Max. P	0.994185

overview

Window 1

Location	20,603,503 – 20,603,601
Length	98
Sequences	3
Columns	98
Reading direction	forward
Mean pairwise identity	97.96
Mean single sequence MFE	-18.90
Consensus MFE	-18.90
Energy contribution	-18.90
Covariance contribution	0.00
Combinations/Pair	1.00
Mean z-score	-2.96
Structure conservation index	1.00
SVM decision value	2.24
SVM RNA-class probability	0.990975
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 20603503 98 + 22407834
CAUCCAUCUGCGCACCCACACUUUCGCACACUUACCAACACACUCACAACGCCCAUUCAGCAGAGCAACAAAAGCUGCGCACUGGGCAUUGUAAAUCA
........((((............)))).................((((.(((((....((((...........))))....))))).))))...... ( -18.90)
>DroSec_CAF1 122741 98 + 1
CAUCCAUCUGCGCACCCACACUCUCGCACACUUACCAAUACACUCACAACGCCCAUUCAGCAGAACAACAAAAGCUGCGCACUGGGCAUUGUAAAUCA
........((((............)))).................((((.(((((....((((...........))))....))))).))))...... ( -18.90)
>DroSim_CAF1 118700 98 + 1
CAUCCAUCUGCGCACCCACACUCUCGCACACUUACCAACACACUCACAACGCCCAUUCAGCAGAGCAACAAAAGCUGCGCACUGGGCAUUGUAAAUCA
........((((............)))).................((((.(((((....((((...........))))....))))).))))...... ( -18.90)
>consensus
CAUCCAUCUGCGCACCCACACUCUCGCACACUUACCAACACACUCACAACGCCCAUUCAGCAGAGCAACAAAAGCUGCGCACUGGGCAUUGUAAAUCA
........((((............)))).................((((.(((((....((((...........))))....))))).))))...... (-18.90 = -18.90 +   0.00)

alignment

secondary structure

dotplot

Window 2

Location	20,603,503 – 20,603,601
Length	98
Sequences	3
Columns	98
Reading direction	reverse
Mean pairwise identity	97.96
Mean single sequence MFE	-35.77
Consensus MFE	-35.97
Energy contribution	-35.53
Covariance contribution	-0.44
Combinations/Pair	1.07
Mean z-score	-3.33
Structure conservation index	1.01
SVM decision value	2.46
SVM RNA-class probability	0.994185
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 20603503 98 - 22407834
UGAUUUACAAUGCCCAGUGCGCAGCUUUUGUUGCUCUGCUGAAUGGGCGUUGUGAGUGUGUUGGUAAGUGUGCGAAAGUGUGGGUGCGCAGAUGGAUG
..((((((((((((((..(((((((....)))))...))....))))))))))))))...((((((..((..(....)..))..))).)))....... ( -36.50)
>DroSec_CAF1 122741 98 - 1
UGAUUUACAAUGCCCAGUGCGCAGCUUUUGUUGUUCUGCUGAAUGGGCGUUGUGAGUGUAUUGGUAAGUGUGCGAGAGUGUGGGUGCGCAGAUGGAUG
..((((((((((((((..(((((((....)))))...))....)))))))))))))).((((.((..(((..(..........)..)))..)).)))) ( -34.70)
>DroSim_CAF1 118700 98 - 1
UGAUUUACAAUGCCCAGUGCGCAGCUUUUGUUGCUCUGCUGAAUGGGCGUUGUGAGUGUGUUGGUAAGUGUGCGAGAGUGUGGGUGCGCAGAUGGAUG
..((((((((((((((..(((((((....)))))...))....))))))))))))))..(((.((..(((..(..........)..)))..)).))). ( -36.10)
>consensus
UGAUUUACAAUGCCCAGUGCGCAGCUUUUGUUGCUCUGCUGAAUGGGCGUUGUGAGUGUGUUGGUAAGUGUGCGAGAGUGUGGGUGCGCAGAUGGAUG
..((((((((((((((..(((((((....)))))...))....))))))))))))))..(((.((..(((..(..........)..)))..)).))). (-35.97 = -35.53 +  -0.44)

alignment

secondary structure

dotplot

Window 3

Location	20,603,526 – 20,603,633
Length	107
Sequences	3
Columns	107
Reading direction	forward
Mean pairwise identity	98.13
Mean single sequence MFE	-18.81
Consensus MFE	-18.81
Energy contribution	-18.81
Covariance contribution	0.00
Combinations/Pair	1.00
Mean z-score	-2.02
Structure conservation index	1.00
SVM decision value	1.13
SVM RNA-class probability	0.919481
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 20603526 107 + 22407834
UCGCACACUUACCAACACACUCACAACGCCCAUUCAGCAGAGCAACAAAAGCUGCGCACUGGGCAUUGUAAAUCAUAAUCAAAACAAUAGAACAAAUGAAGCUAAUG
..((..................((((.(((((....((((...........))))....))))).))))...((((...................)))).))..... ( -18.81)
>DroSec_CAF1 122764 107 + 1
UCGCACACUUACCAAUACACUCACAACGCCCAUUCAGCAGAACAACAAAAGCUGCGCACUGGGCAUUGUAAAUCAUAAUCAAAACAAUAGAAGAAAUGAAGCUAAUG
..((..................((((.(((((....((((...........))))....))))).))))...((((...................)))).))..... ( -18.81)
>DroSim_CAF1 118723 107 + 1
UCGCACACUUACCAACACACUCACAACGCCCAUUCAGCAGAGCAACAAAAGCUGCGCACUGGGCAUUGUAAAUCAUAAUCAAAACAAUAGAACAAAUGAAGCUAAUG
..((..................((((.(((((....((((...........))))....))))).))))...((((...................)))).))..... ( -18.81)
>consensus
UCGCACACUUACCAACACACUCACAACGCCCAUUCAGCAGAGCAACAAAAGCUGCGCACUGGGCAUUGUAAAUCAUAAUCAAAACAAUAGAACAAAUGAAGCUAAUG
..((..................((((.(((((....((((...........))))....))))).))))...((((...................)))).))..... (-18.81 = -18.81 +   0.00)

alignment

secondary structure

dotplot

Window 4

Location	20,603,526 – 20,603,633
Length	107
Sequences	3
Columns	107
Reading direction	reverse
Mean pairwise identity	98.13
Mean single sequence MFE	-32.00
Consensus MFE	-31.71
Energy contribution	-31.60
Covariance contribution	-0.11
Combinations/Pair	1.06
Mean z-score	-2.66
Structure conservation index	0.99
SVM decision value	1.89
SVM RNA-class probability	0.981607
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 20603526 107 - 22407834
CAUUAGCUUCAUUUGUUCUAUUGUUUUGAUUAUGAUUUACAAUGCCCAGUGCGCAGCUUUUGUUGCUCUGCUGAAUGGGCGUUGUGAGUGUGUUGGUAAGUGUGCGA
.....((..((((((..........(..((....((((((((((((((..(((((((....)))))...))....))))))))))))))..))..))))))).)).. ( -32.50)
>DroSec_CAF1 122764 107 - 1
CAUUAGCUUCAUUUCUUCUAUUGUUUUGAUUAUGAUUUACAAUGCCCAGUGCGCAGCUUUUGUUGUUCUGCUGAAUGGGCGUUGUGAGUGUAUUGGUAAGUGUGCGA
.....((..(((((((..(((.............((((((((((((((..(((((((....)))))...))....)))))))))))))))))..)).))))).)).. ( -31.01)
>DroSim_CAF1 118723 107 - 1
CAUUAGCUUCAUUUGUUCUAUUGUUUUGAUUAUGAUUUACAAUGCCCAGUGCGCAGCUUUUGUUGCUCUGCUGAAUGGGCGUUGUGAGUGUGUUGGUAAGUGUGCGA
.....((..((((((..........(..((....((((((((((((((..(((((((....)))))...))....))))))))))))))..))..))))))).)).. ( -32.50)
>consensus
CAUUAGCUUCAUUUGUUCUAUUGUUUUGAUUAUGAUUUACAAUGCCCAGUGCGCAGCUUUUGUUGCUCUGCUGAAUGGGCGUUGUGAGUGUGUUGGUAAGUGUGCGA
.....((..((((((..........(..((....((((((((((((((..(((((((....)))))...))....))))))))))))))..))..))))))).)).. (-31.71 = -31.60 +  -0.11)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:36:23 2006