Locus 3088

Sequence ID	3L_DroMel_CAF1
Location	8,947,376 – 8,947,474
Length	98
Max. P	0.662197

overview

Window 2

Location	8,947,376 – 8,947,474
Length	98
Sequences	6
Columns	105
Reading direction	forward
Mean pairwise identity	84.39
Mean single sequence MFE	-29.66
Consensus MFE	-22.23
Energy contribution	-22.45
Covariance contribution	0.22
Combinations/Pair	1.11
Mean z-score	-2.16
Structure conservation index	0.75
SVM decision value	0.27
SVM RNA-class probability	0.662197
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 8947376 98 + 23771897
UUAAACAA-------UGGCACAUUAUUCAUCAACUUACUUGGUGGGAUGCAGGAGUGAUCGAAUGGUCAAGGCAGCGUUCAGACGCUGCUUAACAUCCAAAUACG
........-------............((((((.....))))))(((((......(((((....)))))(((((((((....)))))))))..)))))....... ( -28.00)
>DroPse_CAF1 16739 97 + 1
--AAGCGGAGUUCUUUCCCAGAUC------UUACUUACUUUGUGGGAUGCAGCAGCGAACGGAUGGUCAAAGCAGCAUUCAGGCGCUGCUUAACAUCCAGAUACG
--..((((((....))))...(((------((((.......)))))))...)).......(((((....(((((((........)))))))..)))))....... ( -29.70)
>DroSec_CAF1 4534 98 + 1
UAAAGCAA-------UGCCACAUUAUUCAUCAACUUACUUGGUGGGAUGCAGGAGUGAUCGAAUGGUCAAGGCAGCGUUCAGACGCUGCUUAACAUCCAAAUACG
....(((.-------(.((((....................)))).)))).(((.(((((....)))))(((((((((....)))))))))....)))....... ( -28.15)
>DroSim_CAF1 4583 98 + 1
UAAAGCAA-------UGCCACAUUAUUCAUCAACUUACUUGGUGGGAUGGAGGAGUGAUCGAAUGGUCAAGGCAGCGUUCAGACGCUGCUUAACAUCCAAAUACG
........-------............((((((.....))))))(((((......(((((....)))))(((((((((....)))))))))..)))))....... ( -28.90)
>DroEre_CAF1 5104 98 + 1
UUAAGCGC-------UGCCAUAAAACUCUUCAACCUACUUAGUGGGAUGCAGCAGUGAUCGAAUGGUCAAGGCAGCGUUCAGACGCUGCUUAACAUCCAAAUACG
((((((((-------((((.....(((((.((.(((((...))))).)).)).)))((((....))))..))))))((....))...))))))............ ( -29.20)
>DroYak_CAF1 4570 98 + 1
UAAAGCAU-------UGCCACAAAAGUGUUCAACUUACUUAGUGGGAUGCAGGAGUGAUCGAAUGGUCAAGGCAGCGUUCAGACGCUGCUUAACAUCCAAAUACG
....((((-------(.((((..(((((.......))))).))))))))).(((.(((((....)))))(((((((((....)))))))))....)))....... ( -34.00)
>consensus
UAAAGCAA_______UGCCACAUUAUUCAUCAACUUACUUGGUGGGAUGCAGGAGUGAUCGAAUGGUCAAGGCAGCGUUCAGACGCUGCUUAACAUCCAAAUACG
............................................(((((......(((((....)))))(((((((((....)))))))))..)))))....... (-22.23 = -22.45 +   0.22)

alignment

secondary structure

dotplot

Window 3

Location	8,947,376 – 8,947,474
Length	98
Sequences	6
Columns	105
Reading direction	reverse
Mean pairwise identity	84.39
Mean single sequence MFE	-27.92
Consensus MFE	-20.35
Energy contribution	-20.27
Covariance contribution	-0.08
Combinations/Pair	1.15
Mean z-score	-1.86
Structure conservation index	0.73
SVM decision value	-0.02
SVM RNA-class probability	0.523921
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 8947376 98 - 23771897
CGUAUUUGGAUGUUAAGCAGCGUCUGAACGCUGCCUUGACCAUUCGAUCACUCCUGCAUCCCACCAAGUAAGUUGAUGAAUAAUGUGCCA-------UUGUUUAA
..(((((((..((((((((((((....)))))).)))))).....(((((....)).)))...)))))))......(((((((((...))-------))))))). ( -26.30)
>DroPse_CAF1 16739 97 - 1
CGUAUCUGGAUGUUAAGCAGCGCCUGAAUGCUGCUUUGACCAUCCGUUCGCUGCUGCAUCCCACAAAGUAAGUAA------GAUCUGGGAAAGAACUCCGCUU--
.......(((((..((((((((......))))))))....)))))((((((....)).(((((............------....)))))..)))).......-- ( -28.69)
>DroSec_CAF1 4534 98 - 1
CGUAUUUGGAUGUUAAGCAGCGUCUGAACGCUGCCUUGACCAUUCGAUCACUCCUGCAUCCCACCAAGUAAGUUGAUGAAUAAUGUGGCA-------UUGCUUUA
.((..((((((((((((((((((....)))))).))))).)))))))..))....(((..((((....................))))..-------.))).... ( -26.35)
>DroSim_CAF1 4583 98 - 1
CGUAUUUGGAUGUUAAGCAGCGUCUGAACGCUGCCUUGACCAUUCGAUCACUCCUCCAUCCCACCAAGUAAGUUGAUGAAUAAUGUGGCA-------UUGCUUUA
.((..((((((((((((((((((....)))))).))))).)))))))..))..............((((((((((((.....)).)))).-------)))))).. ( -23.50)
>DroEre_CAF1 5104 98 - 1
CGUAUUUGGAUGUUAAGCAGCGUCUGAACGCUGCCUUGACCAUUCGAUCACUGCUGCAUCCCACUAAGUAGGUUGAAGAGUUUUAUGGCA-------GCGCUUAA
....((..((((((....))))))..))(((((((..(((..((((((..(((((...........)))))))))))..)))....))))-------)))..... ( -32.40)
>DroYak_CAF1 4570 98 - 1
CGUAUUUGGAUGUUAAGCAGCGUCUGAACGCUGCCUUGACCAUUCGAUCACUCCUGCAUCCCACUAAGUAAGUUGAACACUUUUGUGGCA-------AUGCUUUA
.((..((((((((((((((((((....)))))).))))).)))))))..))....((((.((((.((((.........))))..))))..-------)))).... ( -30.30)
>consensus
CGUAUUUGGAUGUUAAGCAGCGUCUGAACGCUGCCUUGACCAUUCGAUCACUCCUGCAUCCCACCAAGUAAGUUGAUGAAUAAUGUGGCA_______UUGCUUUA
.((..((((((((((((((((((....))))))).)))).)))))))..))...................................................... (-20.35 = -20.27 +  -0.08)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:49:11 2006