Locus 8762

Sequence ID	3R_DroMel_CAF1
Location	23,394,769 – 23,394,921
Length	152
Max. P	0.999758

overview

Window 3

Location	23,394,769 – 23,394,889
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	92.33
Mean single sequence MFE	-48.24
Consensus MFE	-42.96
Energy contribution	-43.00
Covariance contribution	0.04
Combinations/Pair	1.14
Mean z-score	-2.69
Structure conservation index	0.89
SVM decision value	4.02
SVM RNA-class probability	0.999758
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 23394769 120 - 27905053
AAGUUGGCCAAAAGCUGGGCUUUGCGGUUGGUGGUGUCCAACUGGCGAAGUCCAUUUGGGCCUCUCGGUUAACGUGGACUGCCGGAGAAAGUUCAGCUGGCGGGAACGGAAUUCAGGACU
.....((((...((.((((((((((((((((......)))))).)))))))))).)).))))((..((....(((...(((((((.((....))..)))))))..)))....))..)).. ( -48.10)
>DroSec_CAF1 9408 120 - 1
AAGUUGGCCAAAAUCUGGGCUUUGCGGUUGGUAGUGUCCAGCUGGCGAAGUCCAUUUGGGCCUCUCGGUUAUCGCGGUCUGCCAGAGAAAGUUCAGCUGGCGGGAAUGGAAUUCAGGAUU
.....((((...(..((((((((((((((((......)))))).))))))))))..).))))(((..(((.(((...((((((((.((....))..))))))))..))))))..)))... ( -45.40)
>DroSim_CAF1 9441 120 - 1
AAGUUGGCCAAAAUCUGGGCUUUGCGGUUGGUAGUGUCCAGCUGGCGAAGUCCAUUUGGGCCUCUCGGUUAACGCGGUCUGCCAGAGAAAGUUCAGCUGGCGGGAAUGGAAUUCAGGAUU
.....((((...(..((((((((((((((((......)))))).))))))))))..).))))((..((....((...((((((((.((....))..))))))))..))....))..)).. ( -45.10)
>DroEre_CAF1 12505 120 - 1
AAGUUGGCCAAAUUCUGGGCUUUGCGGUUGGUAGUGUCCAGCUGGCGAAGUCCAUUUUGGCCUCUUGAUUUUCGUGGUCUGCCGGAGAAAGUUCAGCUGGCGGGAACGGAAUUCAGGAUU
.....(((((((...((((((((((((((((......)))))).)))))))))).)))))))((((((.((((((..((((((((.((....))..)))))))).)))))).)))))).. ( -59.70)
>DroYak_CAF1 9571 120 - 1
AAGUUGGCCAAAUUCUGGGCUCUGCGGUUGGCAUUGUCCAGCUGGCAAUGUCCAUUUGGGCCUCUCGGUUUUCGUGGUCAGCCGGAGAAAGUUCAGCUGGCGGGAACGGAAUUCAGGAUU
.....((((......(((((..(((((((((......)))))).)))..)))))....))))((..(..((((((.((((((.(((.....))).))))))....))))))..)..)).. ( -42.90)
>consensus
AAGUUGGCCAAAAUCUGGGCUUUGCGGUUGGUAGUGUCCAGCUGGCGAAGUCCAUUUGGGCCUCUCGGUUAUCGUGGUCUGCCGGAGAAAGUUCAGCUGGCGGGAACGGAAUUCAGGAUU
.....((((......((((((((((((((((......)))))).))))))))))....))))(((.((....(((...(((((((.((....))..)))))))..)))....)).))).. (-42.96 = -43.00 +   0.04)

alignment

secondary structure

dotplot

Window 4

Location	23,394,809 – 23,394,921
Length	112
Sequences	5
Columns	113
Reading direction	reverse
Mean pairwise identity	85.79
Mean single sequence MFE	-39.46
Consensus MFE	-30.20
Energy contribution	-30.28
Covariance contribution	0.08
Combinations/Pair	1.16
Mean z-score	-2.09
Structure conservation index	0.77
SVM decision value	0.97
SVM RNA-class probability	0.892122
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 23394809 112 - 27905053
UAACAGUCAGUUACAACUCGCAAACCGAACAC-AAGUUGGCCAAAAGCUGGGCUUUGCGGUUGGUGGUGUCCAACUGGCGAAGUCCAUUUGGGCCUCUCGGUUAACGUGGACU
....(((((((....)))(((.((((((((..-..)).((((...((.((((((((((((((((......)))))).)))))))))).)).))))..))))))...))))))) ( -41.10)
>DroSec_CAF1 9448 111 - 1
UAACAGUCAGUUACAAUUCGCA-GCCGAACAC-AAGUUGGCCAAAAUCUGGGCUUUGCGGUUGGUAGUGUCCAGCUGGCGAAGUCCAUUUGGGCCUCUCGGUUAUCGCGGUCU
((((.....))))....(((((-(((((((..-..)).((((...(..((((((((((((((((......)))))).))))))))))..).))))..))))))...))))... ( -40.60)
>DroSim_CAF1 9481 111 - 1
UAACAGUCAGUUACAAUUCGCA-GCCGAACAC-AAGUUGGCCAAAAUCUGGGCUUUGCGGUUGGUAGUGUCCAGCUGGCGAAGUCCAUUUGGGCCUCUCGGUUAACGCGGUCU
((((.....))))....(((((-(((((((..-..)).((((...(..((((((((((((((((......)))))).))))))))))..).))))..))))))...))))... ( -40.60)
>DroEre_CAF1 12545 106 - 1
UAACAGUCAGUUACAGCUCG-------CAAGCGAAGUUGGCCAAAUUCUGGGCUUUGCGGUUGGUAGUGUCCAGCUGGCGAAGUCCAUUUUGGCCUCUUGAUUUUCGUGGUCU
.....((.(((....))).)-------)..((((((..(((((((...((((((((((((((((......)))))).)))))))))).))))))).......))))))..... ( -40.70)
>DroYak_CAF1 9611 104 - 1
UAACAG-CAGUCACAAGCCG-------AACAC-AAGUUGGCCAAAUUCUGGGCUCUGCGGUUGGCAUUGUCCAGCUGGCAAUGUCCAUUUGGGCCUCUCGGUUUUCGUGGUCA
......-..(((((((((((-------(((..-..)).((((......(((((..(((((((((......)))))).)))..)))))....))))..)))))))..)))).). ( -34.30)
>consensus
UAACAGUCAGUUACAACUCGCA__CCGAACAC_AAGUUGGCCAAAAUCUGGGCUUUGCGGUUGGUAGUGUCCAGCUGGCGAAGUCCAUUUGGGCCUCUCGGUUAUCGUGGUCU
.................((((.................((((......((((((((((((((((......)))))).))))))))))....))))....(.....)))))... (-30.20 = -30.28 +   0.08)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:19:08 2006