Locus 3031

Sequence ID	3R_DroMel_CAF1
Location	8,080,136 – 8,080,290
Length	154
Max. P	0.870178

overview

Window 5

Location	8,080,136 – 8,080,256
Length	120
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	82.44
Mean single sequence MFE	-40.82
Consensus MFE	-26.09
Energy contribution	-25.43
Covariance contribution	-0.66
Combinations/Pair	1.47
Mean z-score	-2.00
Structure conservation index	0.64
SVM decision value	0.17
SVM RNA-class probability	0.619154
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 8080136 120 - 27905053
GUACACCUCCUUGGGAUCCCAGUUUCCAAGAGAGGGACAGUUGCCACUAAUGGCAACAUACUCAUUACCGUUUAGUGAACUGUGAAAGACUACACAGAAGGGCCACUCAGUAGUCGGAAC
((...(((((((((((.......))))))).)))).)).(((((((....)))))))..........(((.(((.(((.(((((........)))))..(.....)))).))).)))... ( -39.40)
>DroVir_CAF1 15511 120 - 1
GUACACCUGCUUCGGGUCCCAGUUGCCCAGCUCGUCGCAGUUGCCGCUGAUCGCCAUAUGCUCGUUGCCCUGCAGCGGCAUCUUGAUCCGCACACAAAAUGGCCAAUCCGUAUAGACAAU
((((..((((..(((((............)))))..))))..(((((.(((((....((((.((((((...))))))))))..))))).)).........)))......))))....... ( -32.60)
>DroSec_CAF1 5056 120 - 1
GUACACCUCCUUGGGAUCCCAGUUUCCGAGAGAGGGACAGUUGCCACUAAUGGCAACAUACUCAUUUCCGUUGAGUGAACUGUGGAACACCACACAGAAUGGCCACUCGGUAGUCGGAAC
((...(((((((((((.......))))))).)))).)).(((((((....)))))))........((((((((((((..((((((....)))))......)..)))))))....))))). ( -43.40)
>DroSim_CAF1 3504 120 - 1
GUACACCUCCUUGGGAUCCCAGUUUCCGAGAGAGGGACAGUUGCCACUAAUGGCAACAUACUCAUUUCCGUUGAGUGAACUGUGGAACACCACACAGAAGGGCCACUCGGUAGUCGGAAC
((...(((((((((((.......))))))).)))).)).(((((((....)))))))........((((((((((((..((((((....))))......))..)))))))....))))). ( -43.40)
>DroEre_CAF1 6754 120 - 1
GUACACCUUCUUGGGAUCCCAGUUCCCGAGAGACGGACAGUUGCCACUAAUGGCCACAUACUCAUUCCCUUUGAGUGGAUGGUGGAACACCACACAGAAGGGCCACUCUGUAGUCGGCAC
.....(((((((((((.......)))))))))..)).....((((((((.(((((...((((((.......))))))..((((((....)))).))....))))).....)))).)))). ( -42.30)
>DroYak_CAF1 109 120 - 1
GAACACCUUCUUGGGAUCCCAGUUCCCGAGAGAGGGACAGUUGCCACUUAUGGCCACAUACUCAUUCCCUUUGAGUGGAUGGUGGUACACCACACAGAAGGGCCACUCUGUGGUCGGAAC
.....(((((((((((.......)))))))).))).......(((((...(((((...((((((.......))))))..((((((....)))).))....)))))....)))))...... ( -43.80)
>consensus
GUACACCUCCUUGGGAUCCCAGUUUCCGAGAGAGGGACAGUUGCCACUAAUGGCAACAUACUCAUUCCCGUUGAGUGAACUGUGGAACACCACACAGAAGGGCCACUCGGUAGUCGGAAC
.....(((((((((((.......))))))).))))(((.((.((((....)))).)).(((((((((.....)))))).(((((........)))))............))))))..... (-26.09 = -25.43 +  -0.66)

alignment

secondary structure

dotplot

Window 6

Location	8,080,176 – 8,080,290
Length	114
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	79.25
Mean single sequence MFE	-37.68
Consensus MFE	-23.35
Energy contribution	-23.08
Covariance contribution	-0.27
Combinations/Pair	1.52
Mean z-score	-2.03
Structure conservation index	0.62
SVM decision value	0.87
SVM RNA-class probability	0.870178
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 8080176 114 - 27905053
AUA------GGCAGCUAAUGCAGUCAUUCUUGGCCAAAAUGUACACCUCCUUGGGAUCCCAGUUUCCAAGAGAGGGACAGUUGCCACUAAUGGCAACAUACUCAUUACCGUUUAGUGAAC
...------(((.((....))...((....)))))....(((...(((((((((((.......))))))).)))).)))(((((((....)))))))....((((((.....)))))).. ( -37.00)
>DroVir_CAF1 15551 117 - 1
ACUGGCCCGCACAGG---UGCAGUUCGCCGGAUCCAUAAUGUACACCUGCUUCGGGUCCCAGUUGCCCAGCUCGUCGCAGUUGCCGCUGAUCGCCAUAUGCUCGUUGCCCUGCAGCGGCA
(((((((((..((((---((..(((....(....)..)))...))))))...))))..)))))......((.....))...((((((((...((.((......)).))....)))))))) ( -35.60)
>DroSec_CAF1 5096 114 - 1
AUA------GGCAGUUCAUGCAGUCAUGCUUUGCCAAAAUGUACACCUCCUUGGGAUCCCAGUUUCCGAGAGAGGGACAGUUGCCACUAAUGGCAACAUACUCAUUUCCGUUGAGUGAAC
...------(((((..((((....))))..)))))....(((...(((((((((((.......))))))).)))).)))(((((((....))))))).((((((.......))))))... ( -43.80)
>DroSim_CAF1 3544 114 - 1
AUA------GGCAGUUCAUGCAGUCAUGCUUGGCCAAAAUGUACACCUCCUUGGGAUCCCAGUUUCCGAGAGAGGGACAGUUGCCACUAAUGGCAACAUACUCAUUUCCGUUGAGUGAAC
...------(((....((((....))))....)))....(((...(((((((((((.......))))))).)))).)))(((((((....))))))).((((((.......))))))... ( -40.70)
>DroEre_CAF1 6794 114 - 1
AUA------GGCAGUUGAUGCAGUCGUUCCUUUCCAAGAUGUACACCUUCUUGGGAUCCCAGUUCCCGAGAGACGGACAGUUGCCACUAAUGGCCACAUACUCAUUCCCUUUGAGUGGAU
...------(((.((((..((((..((((((.....)).........(((((((((.......)))))))))..))))..))))...)))).)))...((((((.......))))))... ( -31.60)
>DroYak_CAF1 149 114 - 1
AUA------GGCAGUUGAUGCACUCGUGCUUUGCCAGGAUGAACACCUUCUUGGGAUCCCAGUUCCCGAGAGAGGGACAGUUGCCACUUAUGGCCACAUACUCAUUCCCUUUGAGUGGAU
...------(((((.....(((....))).))))).((((((...(((((((((((.......)))))))).)))....((.((((....)))).))....))))))((.......)).. ( -37.40)
>consensus
AUA______GGCAGUUCAUGCAGUCAUGCUUUGCCAAAAUGUACACCUCCUUGGGAUCCCAGUUUCCGAGAGAGGGACAGUUGCCACUAAUGGCAACAUACUCAUUCCCGUUGAGUGAAC
.........(((....((((....))))....)))....(((...(((((((((((.......))))))).)))).)))((.((((....)))).))....((((((.....)))))).. (-23.35 = -23.08 +  -0.27)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:50:37 2006