Locus 3143

Sequence ID	X_DroMel_CAF1
Location	8,363,861 – 8,364,052
Length	191
Max. P	0.906771

overview

Window 8

Location	8,363,861 – 8,363,981
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	91.89
Mean single sequence MFE	-28.44
Consensus MFE	-25.98
Energy contribution	-25.70
Covariance contribution	-0.28
Combinations/Pair	1.07
Mean z-score	-1.34
Structure conservation index	0.91
SVM decision value	0.77
SVM RNA-class probability	0.844982
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 8363861 120 - 22224390
UAGGAACGUGGAAAGUACAUGUGAAAAUGCGAGAAGAGCGCCAAAGUGGCGACGAACGAGGGAGAGGGCAAAAAACGUAAAAAGAGCUCAAAAAGUGAUCUCUUGAAGCUGCCCCACCUU
.....(((((.......)))))...............(((((.....)))).)....((((..(.(((((......((...(((((.(((.....))).)))))...)))))))).)))) ( -29.10)
>DroSec_CAF1 29029 119 - 1
UAGGAACGUGGAAAAUACAUGUGAAAAUACGAGAAGAGCGCCAAAGUGGCGACGAACUAUGGAGAGGGCGAAAAACGUAAAAAGAGCUCAA-AAGUGAUCUCUUGAAGCUGCCCCACCUU
.(((..(((((......(.(((....))).)......(((((.....)))).)...)))))..(.(((((......((...(((((.(((.-...))).)))))...)))))))).))). ( -27.60)
>DroSim_CAF1 32238 119 - 1
UAGGAACGUGGAAAAUACAUGUGAAAAUACGAGAAGAGCGCCAAAGUGGCGACGAACUAUGGAGAGGGCGAAAAACGUAAAAAGAGCUCAA-AAGUGAUCUCUUGAAGCUGCCCCACCUU
.(((..(((((......(.(((....))).)......(((((.....)))).)...)))))..(.(((((......((...(((((.(((.-...))).)))))...)))))))).))). ( -27.60)
>DroEre_CAF1 26203 117 - 1
UUUGAACAUGGAAAAUACAUGUGAAAAUGCGAGAAGAGCGCCAAAGUGGCGACGAAUGAGGGAGAAGGCAA---AUGUAAAAAGAGCUCAAAAAGUGAUCUCUUAAAGCUGCCCCACCUU
(((..(((((.......)))))..)))..........(((((.....)))).)....((((..(..((((.---..((...(((((.(((.....))).)))))...)))))))..)))) ( -26.10)
>DroYak_CAF1 27959 117 - 1
UAUGAACAUGGAAAAUACAUGUGAAAAUGCGAGAAGAGCGCCAAAGUGGCGACGAGCGAGGGAGAGGGCGA---AUGUGAAAAGAGCUCAAAAAGUGAUCUCUUCAAGCUGCCCCACCUU
.....(((((.......))))).....(((..(.....((((.....)))).)..)))((((.(.(((((.---...(((..((((.(((.....))).)))))))...)))))).)))) ( -31.80)
>consensus
UAGGAACGUGGAAAAUACAUGUGAAAAUGCGAGAAGAGCGCCAAAGUGGCGACGAACGAGGGAGAGGGCGAAAAACGUAAAAAGAGCUCAAAAAGUGAUCUCUUGAAGCUGCCCCACCUU
.....(((((.......)))))...............(((((.....)))).).......((.(.(((((......((...(((((.(((.....))).)))))...)))))))).)).. (-25.98 = -25.70 +  -0.28)

alignment

secondary structure

dotplot

Window 9

Location	8,363,901 – 8,364,020
Length	119
Sequences	5
Columns	119
Reading direction	reverse
Mean pairwise identity	91.49
Mean single sequence MFE	-23.20
Consensus MFE	-18.74
Energy contribution	-18.34
Covariance contribution	-0.40
Combinations/Pair	1.17
Mean z-score	-1.84
Structure conservation index	0.81
SVM decision value	1.05
SVM RNA-class probability	0.906771
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 8363901 119 - 22224390
CUUGAGGUAUGAAAUCGAAAGAAUUUAGAGAGAAAUCGCUAGGAACGUGGAAAGUACAUGUGAAAAUGCGAGAAGAGCGCCAAAGUGGCGACGAACGAGGGAGAGGGCAAAAAACGUAA
((((.....((((.((....)).))))........((((.....(((((.......)))))......)))).....(((((.....)))).)...)))).................... ( -24.00)
>DroSec_CAF1 29068 119 - 1
CUUGAGGUAUCAAAUCAAAAGAAUUUAGAGAGAAAUCGCUAGGAACGUGGAAAAUACAUGUGAAAAUACGAGAAGAGCGCCAAAGUGGCGACGAACUAUGGAGAGGGCGAAAAACGUAA
.((((....)))).((.......(((((.((....)).))))).(((((.......)))))))...((((.......((((.....)))).((..((......))..)).....)))). ( -23.90)
>DroSim_CAF1 32277 119 - 1
CUUGAGGUAUCAAAUCAAAAGAAUUUAGAGAGAAAUCGCUAGGAACGUGGAAAAUACAUGUGAAAAUACGAGAAGAGCGCCAAAGUGGCGACGAACUAUGGAGAGGGCGAAAAACGUAA
.((((....)))).((.......(((((.((....)).))))).(((((.......)))))))...((((.......((((.....)))).((..((......))..)).....)))). ( -23.90)
>DroEre_CAF1 26243 116 - 1
CUUGAGGUAUUAAAACGAAAGAAUUUAGAGAGAAAUCGCUUUGAACAUGGAAAAUACAUGUGAAAAUGCGAGAAGAGCGCCAAAGUGGCGACGAAUGAGGGAGAAGGCAA---AUGUAA
(((............(....).((((.........(((((((..(((((.......)))))..))).)))).....(((((.....)))).))))))))...........---...... ( -20.40)
>DroYak_CAF1 27999 116 - 1
CUUGAGGUAUCAAAUCGAAAGAAUUUAGAGAGAAAUCGCUAUGAACAUGGAAAAUACAUGUGAAAAUGCGAGAAGAGCGCCAAAGUGGCGACGAGCGAGGGAGAGGGCGA---AUGUGA
.((((....)))).((....)).............(((((....(((((.......))))).....(((..(.....((((.....)))).)..)))........)))))---...... ( -23.80)
>consensus
CUUGAGGUAUCAAAUCGAAAGAAUUUAGAGAGAAAUCGCUAGGAACGUGGAAAAUACAUGUGAAAAUGCGAGAAGAGCGCCAAAGUGGCGACGAACGAGGGAGAGGGCGAAAAACGUAA
(((..(((.....)))..)))..(((((.((....)).))))).(((((.......))))).....((((......(((((.....)))).)(..(........)..)......)))). (-18.74 = -18.34 +  -0.40)

alignment

secondary structure

dotplot

Window 0

Location	8,363,941 – 8,364,052
Length	111
Sequences	5
Columns	113
Reading direction	reverse
Mean pairwise identity	94.19
Mean single sequence MFE	-20.82
Consensus MFE	-16.96
Energy contribution	-17.28
Covariance contribution	0.32
Combinations/Pair	1.07
Mean z-score	-1.54
Structure conservation index	0.81
SVM decision value	0.34
SVM RNA-class probability	0.697902
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 8363941 111 - 22224390
AA--AUUGUAAAUGGAAAACCCGUUAUCUCUGUACUUGAGGUAUGAAAUCGAAAGAAUUUAGAGAGAAAUCGCUAGGAACGUGGAAAGUACAUGUGAAAAUGCGAGAAGAGCG
..--......(((((.....))))).(((((((((.....))))(((.((....)).)))..)))))..((((.....(((((.......)))))......))))........ ( -23.80)
>DroSec_CAF1 29108 111 - 1
AA--AAUGUAAUUGGAAAACCCGUUAUCUCAGUACUUGAGGUAUCAAAUCAAAAGAAUUUAGAGAGAAAUCGCUAGGAACGUGGAAAAUACAUGUGAAAAUACGAGAAGAGCG
..--.........((.....))(((.((((.(((.((((....)))).((.......(((((.((....)).))))).(((((.......)))))))...)))))))..))). ( -18.20)
>DroSim_CAF1 32317 111 - 1
AA--AAUGUAAUUGGAAAACCCGUUAUCUCAGUACUUGAGGUAUCAAAUCAAAAGAAUUUAGAGAGAAAUCGCUAGGAACGUGGAAAAUACAUGUGAAAAUACGAGAAGAGCG
..--.........((.....))(((.((((.(((.((((....)))).((.......(((((.((....)).))))).(((((.......)))))))...)))))))..))). ( -18.20)
>DroEre_CAF1 26280 113 - 1
AAAAAAUGUAAUUGGAAAACCCGUUAUCUCAGUACUUGAGGUAUUAAAACGAAAGAAUUUAGAGAGAAAUCGCUUUGAACAUGGAAAAUACAUGUGAAAAUGCGAGAAGAGCG
.............((.....))(((.(((((((((.....)))))....(....)......))))....(((((((..(((((.......)))))..))).))))....))). ( -22.40)
>DroYak_CAF1 28036 111 - 1
AA--AUUGUAAUUGGAAAACCCGUUAUCUCAGUACUUGAGGUAUCAAAUCGAAAGAAUUUAGAGAGAAAUCGCUAUGAACAUGGAAAAUACAUGUGAAAAUGCGAGAAGAGCG
..--.........((.....))(((.((((.....((((....)))).((....)).....))))....((((.....(((((.......)))))......))))....))). ( -21.50)
>consensus
AA__AAUGUAAUUGGAAAACCCGUUAUCUCAGUACUUGAGGUAUCAAAUCGAAAGAAUUUAGAGAGAAAUCGCUAGGAACGUGGAAAAUACAUGUGAAAAUGCGAGAAGAGCG
.............((.....))(((.((((.((((((..(((.....)))..)))..(((((.((....)).))))).(((((.......))))).....)))))))..))). (-16.96 = -17.28 +   0.32)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:51:59 2006