Locus 1009

Sequence ID	2R_DroMel_CAF1
Location	4,212,067 – 4,212,183
Length	116
Max. P	0.808025

overview

Window 4

Location	4,212,067 – 4,212,183
Length	116
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	91.66
Mean single sequence MFE	-37.82
Consensus MFE	-28.70
Energy contribution	-29.70
Covariance contribution	1.00
Combinations/Pair	1.07
Mean z-score	-1.91
Structure conservation index	0.76
SVM decision value	0.52
SVM RNA-class probability	0.768468
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 4212067 116 + 20766785
UUCUCCGAACUUCUGCUCACACACGGAAAUCGCAAAAAAGCCAG----CCGGGCCAACCUGGCGUAUGAGCAAUGAAAUGCAUCUGCUCUGAGGUUGGCACAUAUGUGCCUGCUUUCGCC
.....((((.(((((........)))))...(((....((((.(----(((((....))))))....((((((((.....))).)))))...))))(((((....)))))))).)))).. ( -38.20)
>DroSec_CAF1 23760 116 + 1
UUCCCGGAACUUCUGCUCACACACGGAAAUCGCAAAAAAGGCAA----CCGGGCCAACCUGGCGUAUGAGCAAUGAAAUGCAUCUGCUCCGAGGUUGGCCCAUAUGUGCCUGCCUUCGCC
....((((..(((((........)))))..........(((((.----..((((((((((((.(((.(((((......))).))))).)).)))))))))).....)))))...)))).. ( -41.30)
>DroSim_CAF1 55665 116 + 1
UUCCCCAAACUUUUGCUCACACACGGAAAUCGCAAAAAAGCCAG----CCGGGCCAACCUGGCGUAUGAGCAAUGAAAUGCAUCUGCUCCGAGGUUGGCCCAUAUGUGCCUGCCUUCGCC
..............((...((((.((.....((......))...----))((((((((((((.(((.(((((......))).))))).)).))))))))))...))))...))....... ( -38.00)
>DroEre_CAF1 25672 115 + 1
UUCCCCGAGCUUCUGCUCACACACGGAAAUCGCAAAAAAGCCAG----CCGGCCC-ACCUGGCGUAUGAGCAAUAAAACGCAUCUGCUGCGAGGUUGGCCCAUAUGUGCCUGCUUUCGUC
......((((....))))....((((((...(((.....((((.----..((((.-((((.(((((.((((........)).))))).)).)))).))))....)).)).))))))))). ( -35.60)
>DroYak_CAF1 26385 119 + 1
UUCCCCGAACUUCUGCUCACACACGGAAAUCGCAAAAAAGCCAGCCAGCCGGGCC-ACCUGGCGUAUGAGCAAUAAAAUGCAUCUGCUCUGGGGUUGGCCCAUAUGUGCCUGCUUUCAUC
.....(((..(((((........))))).)))....(((((..((((...(((((-(((..(.(((.(((((......))).))))).)..))..))))))...)).))..))))).... ( -36.00)
>consensus
UUCCCCGAACUUCUGCUCACACACGGAAAUCGCAAAAAAGCCAG____CCGGGCCAACCUGGCGUAUGAGCAAUGAAAUGCAUCUGCUCCGAGGUUGGCCCAUAUGUGCCUGCUUUCGCC
..............((...((((.((.....((......)).......))((((((((((((.(((.(((((......))).))))).)).))))))))))...))))...))....... (-28.70 = -29.70 +   1.00)

alignment

secondary structure

dotplot

Window 5

Location	4,212,067 – 4,212,183
Length	116
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	91.66
Mean single sequence MFE	-44.49
Consensus MFE	-34.50
Energy contribution	-33.98
Covariance contribution	-0.52
Combinations/Pair	1.25
Mean z-score	-1.85
Structure conservation index	0.78
SVM decision value	0.64
SVM RNA-class probability	0.808025
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 4212067 116 - 20766785
GGCGAAAGCAGGCACAUAUGUGCCAACCUCAGAGCAGAUGCAUUUCAUUGCUCAUACGCCAGGUUGGCCCGG----CUGGCUUUUUUGCGAUUUCCGUGUGUGAGCAGAAGUUCGGAGAA
.((....)).(((((....)))))...(((.((((.((......)).(((((((((((((.((....)).))----)..((......)).........))))))))))..)))).))).. ( -46.50)
>DroSec_CAF1 23760 116 - 1
GGCGAAGGCAGGCACAUAUGGGCCAACCUCGGAGCAGAUGCAUUUCAUUGCUCAUACGCCAGGUUGGCCCGG----UUGCCUUUUUUGCGAUUUCCGUGUGUGAGCAGAAGUUCCGGGAA
.(((((((.(((((....(((((((((((.((.......(((......))).......))))))))))))).----.))))))))))))..((((((.....((((....)))))))))) ( -48.54)
>DroSim_CAF1 55665 116 - 1
GGCGAAGGCAGGCACAUAUGGGCCAACCUCGGAGCAGAUGCAUUUCAUUGCUCAUACGCCAGGUUGGCCCGG----CUGGCUUUUUUGCGAUUUCCGUGUGUGAGCAAAAGUUUGGGGAA
.((....)).(((........)))..(((((((((....))......(((((((((((((.((....)).))----)..((......)).........))))))))))...))))))).. ( -41.80)
>DroEre_CAF1 25672 115 - 1
GACGAAAGCAGGCACAUAUGGGCCAACCUCGCAGCAGAUGCGUUUUAUUGCUCAUACGCCAGGU-GGGCCGG----CUGGCUUUUUUGCGAUUUCCGUGUGUGAGCAGAAGCUCGGGGAA
(.(....)).(((........)))..(((((((.....)))(((((..((((((((((((((.(-(...)).----)))))......(((.....)))))))))))))))))..)))).. ( -41.30)
>DroYak_CAF1 26385 119 - 1
GAUGAAAGCAGGCACAUAUGGGCCAACCCCAGAGCAGAUGCAUUUUAUUGCUCAUACGCCAGGU-GGCCCGGCUGGCUGGCUUUUUUGCGAUUUCCGUGUGUGAGCAGAAGUUCGGGGAA
..........(((........)))..((((.(((((((.....))).(((((((((((((((.(-(((...)))).)))))......(((.....)))))))))))))..)))))))).. ( -44.30)
>consensus
GGCGAAAGCAGGCACAUAUGGGCCAACCUCGGAGCAGAUGCAUUUCAUUGCUCAUACGCCAGGUUGGCCCGG____CUGGCUUUUUUGCGAUUUCCGUGUGUGAGCAGAAGUUCGGGGAA
.((....)).(((........)))...(((.((((.((......)).(((((((((((((((..............)))))......(((.....)))))))))))))..)))).))).. (-34.50 = -33.98 +  -0.52)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:53:59 2006