Locus 4380

Sequence ID	3L_DroMel_CAF1
Location	12,854,390 – 12,854,533
Length	143
Max. P	0.995247

overview

Window 8

Location	12,854,390 – 12,854,493
Length	103
Sequences	5
Columns	103
Reading direction	forward
Mean pairwise identity	93.57
Mean single sequence MFE	-23.72
Consensus MFE	-20.22
Energy contribution	-19.50
Covariance contribution	-0.72
Combinations/Pair	1.12
Mean z-score	-2.26
Structure conservation index	0.85
SVM decision value	2.56
SVM RNA-class probability	0.995247
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 12854390 103 + 23771897
AAAUGUUAAAACGAGGAUGGAAAAUUCUCAAGAAUCCUUAUCAAGCGGAGGGAAACAAAAGCCACUCCAGUGCUUCAGAAAACUGAAUGAAAAUAAGCAUGGG
............((((((.....))))))......((.........((((((.........)).)))).(((((((((....))))((....)).))))))). ( -21.30)
>DroSec_CAF1 92740 103 + 1
AAAUGUUAAAACGAGGAUGGAAAAUUCUCAAGAAUCCUUAUCGAACGGAGGGAAACAAAAGCCACUCCAGUGCUCCAGAAAACUGAAUGAAAAUGAGCAUGGG
....(((.....((((((.((......))....))))))....)))((((((.........)).)))).(((((((((....))).((....))))))))... ( -23.10)
>DroSim_CAF1 93413 103 + 1
AAAUGUUAAAACGAGGAUGGAAAAUUCUCAAGAAUCCUUAUCGAGCGGAGGGAAACAAAAGCCACUCCAGUGCUCCAGAAAACUGAAUGAAAAUGAGCAUGGG
............((((((.....))))))......((.....(((.((..(....).....)).)))..(((((((((....))).((....)))))))))). ( -23.20)
>DroEre_CAF1 97946 100 + 1
AAAUGUUAAAACGAGGAUGGGAAAUUCUCAAGAAUCCUUAUCGACCGGAGGGAAACAAAAGUCGCU---GUGCUCCAGAAAACUGAAUGAAAAUGAGCACGGG
............(((((((((.....))))....)))))..((((.....(....)....))))((---(((((((((....))).((....)))))))))). ( -26.10)
>DroYak_CAF1 103994 100 + 1
AAAUGUUAAAACGAGGAUGGAAAAUUCUCAAGAAUCCUUAUCGACCGAAGGGAAACAAAAGCCGCU---GUGCUCCAGAAAACUGAAUAAAAAUGAGCACGGG
...((((.....((((((.....)))))).....(((((.((....))))))))))).......((---(((((((((....))).........)))))))). ( -24.90)
>consensus
AAAUGUUAAAACGAGGAUGGAAAAUUCUCAAGAAUCCUUAUCGACCGGAGGGAAACAAAAGCCACUCCAGUGCUCCAGAAAACUGAAUGAAAAUGAGCAUGGG
...((((.....((((((.....)))))).....(((((.((....)))))))))))............(((((((((....))).........))))))... (-20.22 = -19.50 +  -0.72)

alignment

secondary structure

dotplot

Window 9

Location	12,854,413 – 12,854,533
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	90.97
Mean single sequence MFE	-29.34
Consensus MFE	-22.38
Energy contribution	-22.22
Covariance contribution	-0.16
Combinations/Pair	1.23
Mean z-score	-1.97
Structure conservation index	0.76
SVM decision value	0.71
SVM RNA-class probability	0.829496
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 12854413 120 - 23771897
UUAAGAGUCCCAGUUUUUAAUAAUUCACUUUAUUGAGAUGCCCAUGCUUAUUUUCAUUCAGUUUUCUGAAGCACUGGAGUGGCUUUUGUUUCCCUCCGCUUGAUAAGGAUUCUUGAGAAU
((((((((((....(((((((((......)))))))))....((.((.........(((((....))))).....((((.((.........)))))))).))....)))))))))).... ( -29.60)
>DroSec_CAF1 92763 120 - 1
UUAAGAGUCCCAGUUUUUUAUAAUUCAAUUUAUUGAGAUGCCCAUGCUCAUUUUCAUUCAGUUUUCUGGAGCACUGGAGUGGCUUUUGUUUCCCUCCGUUCGAUAAGGAUUCUUGAGAAU
((((((((((.((((......))))....((((((((.......(((((.........(((....))))))))..((((.((.........)))))).)))))))))))))))))).... ( -27.70)
>DroSim_CAF1 93436 120 - 1
UUAAGAGUCCCAGUUUUUAAUAAUUCAAUUUAUUGAGAUGCCCAUGCUCAUUUUCAUUCAGUUUUCUGGAGCACUGGAGUGGCUUUUGUUUCCCUCCGCUCGAUAAGGAUUCUUGAGAAU
(((((((((((((((((((((((......))))))))).......((((.........(((....)))))))))))((((((.............)))))).....)))))))))).... ( -31.82)
>DroEre_CAF1 97969 116 - 1
UUGCGAGUCCCAGUUCUUAAUAAUUCAAUUUAUUGAGA-ACCCGUGCUCAUUUUCAUUCAGUUUUCUGGAGCAC---AGCGACUUUUGUUUCCCUCCGGUCGAUAAGGAUUCUUGAGAAU
....((((((..(((((((((((......)))))))))-))..((((((.........(((....)))))))))---..(((((...(.....)...)))))....))))))........ ( -31.70)
>DroYak_CAF1 104017 116 - 1
UUGAGAGACCCAGUUCUUUAUAAUUCAAUUUAUUGGGA-ACCCGUGCUCAUUUUUAUUCAGUUUUCUGGAGCAC---AGCGGCUUUUGUUUCCCUUCGGUCGAUAAGGAUUCUUGAGAAU
(..((((.((..(((((..((((......))))..)))-))..((((((.........(((....)))))))))---..(((((...(.....)...)))))....)).))))..).... ( -25.90)
>consensus
UUAAGAGUCCCAGUUUUUAAUAAUUCAAUUUAUUGAGAUGCCCAUGCUCAUUUUCAUUCAGUUUUCUGGAGCACUGGAGUGGCUUUUGUUUCCCUCCGCUCGAUAAGGAUUCUUGAGAAU
((((((((((..(((((((((((......))))))))).))...(((((.......(((((....)))))......))))).........................)))))))))).... (-22.38 = -22.22 +  -0.16)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:21:01 2006