Locus 4189

Sequence ID	X_DroMel_CAF1
Location	10,996,566 – 10,996,681
Length	115
Max. P	0.976522

overview

Window 4

Location	10,996,566 – 10,996,681
Length	115
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	87.48
Mean single sequence MFE	-41.14
Consensus MFE	-33.28
Energy contribution	-34.40
Covariance contribution	1.12
Combinations/Pair	1.10
Mean z-score	-2.31
Structure conservation index	0.81
SVM decision value	1.77
SVM RNA-class probability	0.976522
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 10996566 115 + 22224390
GGAGGACCUGGAGAUCACCAGUUUGCAGAACGAUCGCAACAAGAACAGAACCAGCGAUGGCAAGGGGACACCGCCAUCGCUGGAGCCAACGAAUGCUGCCGCCAAUCAGGCAGCC-----
(..((..((((......)))).((((.((....))))))...........(((((((((((..(....)...)))))))))))..))..)....((((((........)))))).----- ( -44.40)
>DroSec_CAF1 8795 115 + 1
GGAGGACCUGGAGAUCACCAGUUUGCAGAACGGUCGCAACAAGAACAAGACGAGCGAUGGCAAGGGAACACCGCCAUCGCUGGAGCCAACGAAUGCUGCCGCCAAUCAGGCAGCC-----
((..(((((((......)))((((...))))))))...............(.(((((((((..((.....))))))))))).)..)).......((((((........)))))).----- ( -41.60)
>DroSim_CAF1 10814 115 + 1
GGAGGAACUGGAGAUCACCAGUUUGCAGAACGGUCGCAACAAGAACAAGACGAGCGAUGGCAAGGGAACACCGCCAUCGCUGGAGCCAACGAAUGCUGCCGCCAAUCAGGCAGCC-----
((..(((((((......)))))))((.((....)))).............(.(((((((((..((.....))))))))))).)..)).......((((((........)))))).----- ( -42.10)
>DroEre_CAF1 7969 117 + 1
GGAGGAUAUGGAGAUCACCAGUUUGGAGAACAGUCGCA---AGAACAAGACCAGCGAGGGCAGGAAGACACCGCCAUCGCUGGAGCUUACAAAUGCUGCCACCAAUCAGGCAGCCAAUGC
((..(((......))).)).((((((((.....((...---.))......(((((((.(((.((......))))).)))))))..))).)))))((((((........))))))...... ( -40.20)
>DroYak_CAF1 8822 117 + 1
GGAGGAUAUGGAGAUCACCAGUUUGGAGAACAGUCGCA---AGAACAAGACCAGCGAGGGCAGGAAGACACCGCCAUCGCUGGAGCUAACAAAUGCUGCUACCAAUCAGGCAGCCAAUGC
((..(((......))).)).(((((........((...---.))......(((((((.(((.((......))))).)))))))......)))))((((((........))))))...... ( -37.40)
>consensus
GGAGGACCUGGAGAUCACCAGUUUGCAGAACGGUCGCAACAAGAACAAGACCAGCGAUGGCAAGGGGACACCGCCAUCGCUGGAGCCAACGAAUGCUGCCGCCAAUCAGGCAGCC_____
((..(((((((......)))((((...))))))))...............(((((((((((..(....)...)))))))))))..)).......((((((........))))))...... (-33.28 = -34.40 +   1.12)

alignment

secondary structure

dotplot

Window 5

Location	10,996,566 – 10,996,681
Length	115
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	87.48
Mean single sequence MFE	-41.65
Consensus MFE	-38.22
Energy contribution	-38.54
Covariance contribution	0.32
Combinations/Pair	1.14
Mean z-score	-1.68
Structure conservation index	0.92
SVM decision value	1.17
SVM RNA-class probability	0.926088
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 10996566 115 - 22224390
-----GGCUGCCUGAUUGGCGGCAGCAUUCGUUGGCUCCAGCGAUGGCGGUGUCCCCUUGCCAUCGCUGGUUCUGUUCUUGUUGCGAUCGUUCUGCAAACUGGUGAUCUCCAGGUCCUCC
-----.((((((.....)))))).(((..((..(((.(((((((((((((.......)))))))))))))....)))..)).)))..............((((......))))....... ( -45.50)
>DroSec_CAF1 8795 115 - 1
-----GGCUGCCUGAUUGGCGGCAGCAUUCGUUGGCUCCAGCGAUGGCGGUGUUCCCUUGCCAUCGCUCGUCUUGUUCUUGUUGCGACCGUUCUGCAAACUGGUGAUCUCCAGGUCCUCC
-----((((((..((.(((..((((((......(((...(((((((((((.......))))))))))).))).......))))))..))).)).)))..((((......))))))).... ( -41.12)
>DroSim_CAF1 10814 115 - 1
-----GGCUGCCUGAUUGGCGGCAGCAUUCGUUGGCUCCAGCGAUGGCGGUGUUCCCUUGCCAUCGCUCGUCUUGUUCUUGUUGCGACCGUUCUGCAAACUGGUGAUCUCCAGUUCCUCC
-----((.(((..((.(((..((((((......(((...(((((((((((.......))))))))))).))).......))))))..))).)).)))((((((......))))))))... ( -41.32)
>DroEre_CAF1 7969 117 - 1
GCAUUGGCUGCCUGAUUGGUGGCAGCAUUUGUAAGCUCCAGCGAUGGCGGUGUCUUCCUGCCCUCGCUGGUCUUGUUCU---UGCGACUGUUCUCCAAACUGGUGAUCUCCAUAUCCUCC
(((...((((((........)))))).....((((..(((((((.(((((.(....)))))).))))))).))))....---)))......((.((.....)).)).............. ( -41.00)
>DroYak_CAF1 8822 117 - 1
GCAUUGGCUGCCUGAUUGGUAGCAGCAUUUGUUAGCUCCAGCGAUGGCGGUGUCUUCCUGCCCUCGCUGGUCUUGUUCU---UGCGACUGUUCUCCAAACUGGUGAUCUCCAUAUCCUCC
...(((((((((.....))))))((((.((((.(((.(((((((.(((((.(....)))))).)))))))....)))..---.)))).))))...)))..(((......)))........ ( -39.30)
>consensus
_____GGCUGCCUGAUUGGCGGCAGCAUUCGUUGGCUCCAGCGAUGGCGGUGUCCCCUUGCCAUCGCUGGUCUUGUUCUUGUUGCGACCGUUCUGCAAACUGGUGAUCUCCAGAUCCUCC
......((((((.....)))))).(((......(((.(((((((((((((.......)))))))))))))....))).....)))..............((((......))))....... (-38.22 = -38.54 +   0.32)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:18:42 2006