Locus 3671

Sequence ID	X_DroMel_CAF1
Location	9,816,207 – 9,816,337
Length	130
Max. P	0.998455

overview

Window 6

Location	9,816,207 – 9,816,302
Length	95
Sequences	5
Columns	96
Reading direction	forward
Mean pairwise identity	97.69
Mean single sequence MFE	-30.76
Consensus MFE	-29.74
Energy contribution	-29.42
Covariance contribution	-0.32
Combinations/Pair	1.08
Mean z-score	-1.76
Structure conservation index	0.97
SVM decision value	2.28
SVM RNA-class probability	0.991589
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 9816207 95 + 22224390
CGUUGGCAGCGAUUCGAGCGGAACGCCGGCGCAAA-AAACACGUUUUUGAGCGGUUUUGAGCGCAAAUUCGAACGGAAAGCGCUCAAUAAAGUGCA
.........((.(((((((((....)))((((..(-((((.((((....)))))))))..))))...))))))))....(((((......))))). ( -30.40)
>DroSec_CAF1 11502 95 + 1
CGUUGGCAGCGAUUCGAGCGGAACGCCGGCGCAAA-AAACACGUUUUUGAGCGGGUUUGAGCGCAAAUUCGAACGGAAAGCGCUCAAUAAAGUGCA
.((((((.((.......)).....))))))(((..-((((.((((....)))).))))((((((...(((....)))..)))))).......))). ( -29.40)
>DroSim_CAF1 7293 95 + 1
CGUUGGCAGCGAUUCGAGCGGAACGCCGGCGCAAA-AAACACGUUUUUGAGCGGGUUUGAGCGCAAAUUCGAACGGAAAGCGCUCAAUAAAGUGCA
.((((((.((.......)).....))))))(((..-((((.((((....)))).))))((((((...(((....)))..)))))).......))). ( -29.40)
>DroEre_CAF1 7437 95 + 1
CGUCGGCAGCGAUUCGAGCGGAACGCCGGCGCAAA-AAACACGUUUUUGAGCGGUUUUGAGCGCAAAUUCGAAUGGAAAGCGCUCAAUAAAGUGCA
.((((((.((.......)).....))))))(((.(-((((.((((....)))))))))((((((...(((.....))).)))))).......))). ( -31.90)
>DroYak_CAF1 9389 96 + 1
CGCUGGCAGCGAUUCGAGCGGAACGCCGGCGCAAAAAAACACGUUUUUGAGCGGUUUUGAGCGCAAAUUCGAACGGAAAGCGCUCAAUAAAGUGCA
.((((((.((.......)).....))))))(((..(((((.((((....)))))))))((((((...(((....)))..)))))).......))). ( -32.70)
>consensus
CGUUGGCAGCGAUUCGAGCGGAACGCCGGCGCAAA_AAACACGUUUUUGAGCGGUUUUGAGCGCAAAUUCGAACGGAAAGCGCUCAAUAAAGUGCA
.((((((.((.......)).....))))))(((........((((....))))...((((((((...(((....)))..)))))))).....))). (-29.74 = -29.42 +  -0.32)

alignment

secondary structure

dotplot

Window 7

Location	9,816,233 – 9,816,337
Length	104
Sequences	5
Columns	105
Reading direction	forward
Mean pairwise identity	98.28
Mean single sequence MFE	-33.20
Consensus MFE	-31.68
Energy contribution	-31.68
Covariance contribution	-0.00
Combinations/Pair	1.00
Mean z-score	-2.21
Structure conservation index	0.95
SVM decision value	3.11
SVM RNA-class probability	0.998455
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 9816233 104 + 22224390
CGGCGCAAA-AAACACGUUUUUGAGCGGUUUUGAGCGCAAAUUCGAACGGAAAGCGCUCAAUAAAGUGCAAAACCAGCCGCUGGAGAUGUUAAGUCACCGGUGUU
..((((..(-((((.((((....)))))))))((((((...(((....)))..))))))......)))).........((((((.(((.....))).)))))).. ( -33.40)
>DroSec_CAF1 11528 104 + 1
CGGCGCAAA-AAACACGUUUUUGAGCGGGUUUGAGCGCAAAUUCGAACGGAAAGCGCUCAAUAAAGUGCAAAACCAGCCGCUGGAGAUGUUAAGUCACCGGUGUU
..((((...-((((.((((....)))).))))((((((...(((....)))..))))))......)))).........((((((.(((.....))).)))))).. ( -32.60)
>DroSim_CAF1 7319 104 + 1
CGGCGCAAA-AAACACGUUUUUGAGCGGGUUUGAGCGCAAAUUCGAACGGAAAGCGCUCAAUAAAGUGCAAAACCAGCCGCUGGAGAUGUUAAGUCACCGGUGUU
..((((...-((((.((((....)))).))))((((((...(((....)))..))))))......)))).........((((((.(((.....))).)))))).. ( -32.60)
>DroEre_CAF1 7463 104 + 1
CGGCGCAAA-AAACACGUUUUUGAGCGGUUUUGAGCGCAAAUUCGAAUGGAAAGCGCUCAAUAAAGUGCAAAACCAGCCGCUGGAGAUGUUAAGUCACCGGUGCU
..((((..(-((((.((((....)))))))))((((((...(((.....))).))))))......))))......(((.(((((.(((.....))).)))))))) ( -33.70)
>DroYak_CAF1 9415 105 + 1
CGGCGCAAAAAAACACGUUUUUGAGCGGUUUUGAGCGCAAAUUCGAACGGAAAGCGCUCAAUAAAGUGCAAAACCAGCCGCUGGAGAUGUUAAGUCACCGGUGUU
.(((((..(((((....)))))..))((((((((((((...(((....)))..)))))))..........))))).)))(((((.(((.....))).)))))... ( -33.70)
>consensus
CGGCGCAAA_AAACACGUUUUUGAGCGGUUUUGAGCGCAAAUUCGAACGGAAAGCGCUCAAUAAAGUGCAAAACCAGCCGCUGGAGAUGUUAAGUCACCGGUGUU
..((((.........((((....))))...((((((((...(((....)))..))))))))....)))).........((((((.(((.....))).)))))).. (-31.68 = -31.68 +  -0.00)

alignment

secondary structure

dotplot

Window 8

Location	9,816,233 – 9,816,337
Length	104
Sequences	5
Columns	105
Reading direction	reverse
Mean pairwise identity	98.28
Mean single sequence MFE	-29.08
Consensus MFE	-28.60
Energy contribution	-28.60
Covariance contribution	-0.00
Combinations/Pair	1.00
Mean z-score	-1.67
Structure conservation index	0.98
SVM decision value	1.93
SVM RNA-class probability	0.982966
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 9816233 104 - 22224390
AACACCGGUGACUUAACAUCUCCAGCGGCUGGUUUUGCACUUUAUUGAGCGCUUUCCGUUCGAAUUUGCGCUCAAAACCGCUCAAAAACGUGUUU-UUUGCGCCG
.....(((((....(((((....(((((..(((.....)))...((((((((.(((.....)))...))))))))..))))).......))))).-....))))) ( -29.20)
>DroSec_CAF1 11528 104 - 1
AACACCGGUGACUUAACAUCUCCAGCGGCUGGUUUUGCACUUUAUUGAGCGCUUUCCGUUCGAAUUUGCGCUCAAACCCGCUCAAAAACGUGUUU-UUUGCGCCG
.....(((((....(((((....((((((.......))......((((((((.(((.....)))...))))))))...)))).......))))).-....))))) ( -29.20)
>DroSim_CAF1 7319 104 - 1
AACACCGGUGACUUAACAUCUCCAGCGGCUGGUUUUGCACUUUAUUGAGCGCUUUCCGUUCGAAUUUGCGCUCAAACCCGCUCAAAAACGUGUUU-UUUGCGCCG
.....(((((....(((((....((((((.......))......((((((((.(((.....)))...))))))))...)))).......))))).-....))))) ( -29.20)
>DroEre_CAF1 7463 104 - 1
AGCACCGGUGACUUAACAUCUCCAGCGGCUGGUUUUGCACUUUAUUGAGCGCUUUCCAUUCGAAUUUGCGCUCAAAACCGCUCAAAAACGUGUUU-UUUGCGCCG
.....(((((....(((((....(((((..(((.....)))...((((((((.(((.....)))...))))))))..))))).......))))).-....))))) ( -29.20)
>DroYak_CAF1 9415 105 - 1
AACACCGGUGACUUAACAUCUCCAGCGGCUGGUUUUGCACUUUAUUGAGCGCUUUCCGUUCGAAUUUGCGCUCAAAACCGCUCAAAAACGUGUUUUUUUGCGCCG
.....(((((....(((((....(((((..(((.....)))...((((((((.(((.....)))...))))))))..))))).......)))))......))))) ( -28.60)
>consensus
AACACCGGUGACUUAACAUCUCCAGCGGCUGGUUUUGCACUUUAUUGAGCGCUUUCCGUUCGAAUUUGCGCUCAAAACCGCUCAAAAACGUGUUU_UUUGCGCCG
.....(((((....(((((....((((((.......))......((((((((.(((.....)))...))))))))...)))).......)))))......))))) (-28.60 = -28.60 +  -0.00)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:05:20 2006