Locus 3133

Sequence ID	X_DroMel_CAF1
Location	8,348,991 – 8,349,096
Length	105
Max. P	0.739304

overview

Window 2

Location	8,348,991 – 8,349,096
Length	105
Sequences	5
Columns	107
Reading direction	forward
Mean pairwise identity	86.18
Mean single sequence MFE	-32.98
Consensus MFE	-22.74
Energy contribution	-23.86
Covariance contribution	1.12
Combinations/Pair	1.07
Mean z-score	-2.08
Structure conservation index	0.69
SVM decision value	0.45
SVM RNA-class probability	0.739304
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 8348991 105 + 22224390
UAAUGAGCUUCGUUGGGUCCUCCAAUCUGAUUUCUAGCGAGCCAGUUAGCUACUGCUGCCAUUCACUCGAUUU--GGUUUCGCUAACUUGGCCGGCUGCAGAUUGCA
....(((..((....))..)))(((((((.....((((..((((((((((.......((((.((....))..)--)))...)))))).))))..))))))))))).. ( -30.50)
>DroSec_CAF1 14415 104 + 1
UAAUGGGCUUCGUUGGGG-CUCCAGUCUGAUUUCUAGCCAGCCAGUUAGCUACUGCUGCCGUUCACUCGAUUU--GGUUUCGCUAACUUGGCCGGCUGCAGAUUGCA
....((((((.....)))-)))(((((((.....(((((.((((((((((.......((((.((....))..)--)))...)))))).)))).)))))))))))).. ( -38.10)
>DroSim_CAF1 17387 104 + 1
UAAUGAGCUUCGUUGGGG-CUCCAAUCUGAUUUCUAGCCAGCCAGUUAGCUACUGCUGCCGUUCACUCGAUUU--GGUUUCGCUAACUUGGCCGGCUGCAGAUUGCA
....((((((.....)))-)))(((((((.....(((((.((((((((((.......((((.((....))..)--)))...)))))).)))).)))))))))))).. ( -39.00)
>DroEre_CAF1 11560 101 + 1
UAAUGAGCUUUGGUCGGA-CGCGAAUCUGACUUCUAGCCACCCAGUGAGCUACU---GCCAUUCACUUGAUUU--GGUUUUGCUAACUUGGCCGGCUGCAGAUUGCA
......((((((((((((-......))))))...(((((.((.(((.(((....---((((.((....))..)--)))...))).))).))..)))))))))..)). ( -29.60)
>DroYak_CAF1 12236 93 + 1
UAAUGAGCUUG-----------CAAUCUGAUUUCUAGCUAACCAGUGAGCUACU---GCCAUUCACUCGAUUUCAGUUUUCGCUAACUUGGCCGGCUGCAGAUUGCA
.........((-----------(((((((....(..(((((..((((((..(((---(....((....))...)))).))))))...)))))..)...))))))))) ( -27.70)
>consensus
UAAUGAGCUUCGUUGGGG_CUCCAAUCUGAUUUCUAGCCAGCCAGUUAGCUACUGCUGCCAUUCACUCGAUUU__GGUUUCGCUAACUUGGCCGGCUGCAGAUUGCA
......................(((((((.....(((((.((((((((((.(((........((....)).....)))...)))))).)))).)))))))))))).. (-22.74 = -23.86 +   1.12)

alignment

secondary structure

dotplot

Window 3

Location	8,348,991 – 8,349,096
Length	105
Sequences	5
Columns	107
Reading direction	reverse
Mean pairwise identity	86.18
Mean single sequence MFE	-29.83
Consensus MFE	-23.54
Energy contribution	-24.42
Covariance contribution	0.88
Combinations/Pair	1.11
Mean z-score	-1.66
Structure conservation index	0.79
SVM decision value	0.32
SVM RNA-class probability	0.687236
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 8348991 105 - 22224390
UGCAAUCUGCAGCCGGCCAAGUUAGCGAAACC--AAAUCGAGUGAAUGGCAGCAGUAGCUAACUGGCUCGCUAGAAAUCAGAUUGGAGGACCCAACGAAGCUCAUUA
..(((((((((((.(((((.((((((....((--(..((....)).)))........))))))))))).))).)....)))))))(((............))).... ( -27.10)
>DroSec_CAF1 14415 104 - 1
UGCAAUCUGCAGCCGGCCAAGUUAGCGAAACC--AAAUCGAGUGAACGGCAGCAGUAGCUAACUGGCUGGCUAGAAAUCAGACUGGAG-CCCCAACGAAGCCCAUUA
.((.....))(((((((((.((((((......--...(((......)))........)))))))))))))))...........(((.(-(.........)))))... ( -30.63)
>DroSim_CAF1 17387 104 - 1
UGCAAUCUGCAGCCGGCCAAGUUAGCGAAACC--AAAUCGAGUGAACGGCAGCAGUAGCUAACUGGCUGGCUAGAAAUCAGAUUGGAG-CCCCAACGAAGCUCAUUA
..(((((((((((((((((.((((((......--...(((......)))........))))))))))))))).)....)))))))(((-(.........)))).... ( -36.83)
>DroEre_CAF1 11560 101 - 1
UGCAAUCUGCAGCCGGCCAAGUUAGCAAAACC--AAAUCAAGUGAAUGGC---AGUAGCUCACUGGGUGGCUAGAAGUCAGAUUCGCG-UCCGACCAAAGCUCAUUA
.((((((((((((((.(((.((.(((....((--(..((....)).))).---....))).))))).)))))....).)))))).)).-.................. ( -25.60)
>DroYak_CAF1 12236 93 - 1
UGCAAUCUGCAGCCGGCCAAGUUAGCGAAAACUGAAAUCGAGUGAAUGGC---AGUAGCUCACUGGUUAGCUAGAAAUCAGAUUG-----------CAAGCUCAUUA
(((((((((((((..((((.((.(((....((((..((.......))..)---))).))).))))))..))).)....)))))))-----------))......... ( -29.00)
>consensus
UGCAAUCUGCAGCCGGCCAAGUUAGCGAAACC__AAAUCGAGUGAAUGGCAGCAGUAGCUAACUGGCUGGCUAGAAAUCAGAUUGGAG_CCCCAACGAAGCUCAUUA
..(((((((((((((((((.((((((............((......))((....)).))))))))))))))).)....)))))))...................... (-23.54 = -24.42 +   0.88)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:51:44 2006