Locus 1454

Sequence ID	X_DroMel_CAF1
Location	4,379,116 – 4,379,245
Length	129
Max. P	0.994324

overview

Window 1

Location	4,379,116 – 4,379,215
Length	99
Sequences	5
Columns	105
Reading direction	reverse
Mean pairwise identity	95.66
Mean single sequence MFE	-15.07
Consensus MFE	-13.09
Energy contribution	-12.77
Covariance contribution	-0.32
Combinations/Pair	1.12
Mean z-score	-1.42
Structure conservation index	0.87
SVM decision value	0.53
SVM RNA-class probability	0.771545
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 4379116 99 - 22224390
AAUUAACUAUUAUGGUGUUAUAUCCUAGUUAUCCCUUGGAAAUCUGGGCUUCCACAGUUUACCUCCUUUCACCGAUCUUUCACU--CUUUCUUGUGAUU----UU
............(((((.....(((.((......)).)))...(((((...)).)))............))))).....((((.--.......))))..----.. ( -14.00)
>DroSec_CAF1 164403 99 - 1
AAUUAACUAUUACGGUGUUAUAUCCUAGUUAUCCCUUGGAAAUCUGGGCUUCCACAGUUUACCUCCUUUCACCGAUCUUUCACU--CUUUCUUGUGAUU----UU
............(((((.....(((.((......)).)))...(((((...)).)))............))))).....((((.--.......))))..----.. ( -16.00)
>DroSim_CAF1 151852 103 - 1
AAUUAACUAUUACGGUGUUAUAUCCUAGUUAUCCCUUGGAAAUCUGGGCUUCCACAGUUUACCUCCUUUCACCGAUCUUUCACU--CUUUCUUGUGAUUUAAUUU
((((((......(((((.....(((.((......)).)))...(((((...)).)))............))))).....((((.--.......)))).)))))). ( -16.30)
>DroEre_CAF1 175190 99 - 1
AAUUAACUAUUACGGUGUUAUAUCCUAGUUAUCCGUUAGAAAUCUGGGCUUCCACAGUUUACCUCCUUUCACCGAUCUUUCACU--CUUUCUUGUGAUU----UU
............(((((......(((((...((.....))...))))).....................))))).....((((.--.......))))..----.. ( -13.43)
>DroYak_CAF1 167653 101 - 1
AAUUAACUAUUACGGUGUUAUAUUCUAGUUAUCCGUUAGAAAUCUGGGCUUCCACAGUUUACCUCCUUUCACCGAUCUUUCACUCACUUUCUUGUGAUU----UU
............(((((.....((((((.......))))))..(((((...)).)))............))))).........((((......))))..----.. ( -15.60)
>consensus
AAUUAACUAUUACGGUGUUAUAUCCUAGUUAUCCCUUGGAAAUCUGGGCUUCCACAGUUUACCUCCUUUCACCGAUCUUUCACU__CUUUCUUGUGAUU____UU
............(((((......(((((...((.....))...))))).....................))))).....((((..........))))........ (-13.09 = -12.77 +  -0.32)

alignment

secondary structure

dotplot

Window 2

Location	4,379,135 – 4,379,245
Length	110
Sequences	5
Columns	110
Reading direction	forward
Mean pairwise identity	97.82
Mean single sequence MFE	-28.38
Consensus MFE	-26.38
Energy contribution	-26.38
Covariance contribution	0.00
Combinations/Pair	1.06
Mean z-score	-2.00
Structure conservation index	0.93
SVM decision value	2.47
SVM RNA-class probability	0.994324
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 4379135 110 + 22224390
AAAGAUCGGUGAAAGGAGGUAAACUGUGGAAGCCCAGAUUUCCAAGGGAUAACUAGGAUAUAACACCAUAAUAGUUAAUUGCUCUAGACCUCACAACUGAUCUCGAUUCG
..((((((((.....(((((......((((((......))))))((((.((((((..((........))..))))))....))))..)))))...))))))))....... ( -28.70)
>DroSec_CAF1 164422 110 + 1
AAAGAUCGGUGAAAGGAGGUAAACUGUGGAAGCCCAGAUUUCCAAGGGAUAACUAGGAUAUAACACCGUAAUAGUUAAUUGCUCUAGACCUCACAACUGAUCUCGAUUCG
..((((((((.....(((((......((((((......))))))((((.((((((..((........))..))))))....))))..)))))...))))))))....... ( -29.00)
>DroSim_CAF1 151875 110 + 1
AAAGAUCGGUGAAAGGAGGUAAACUGUGGAAGCCCAGAUUUCCAAGGGAUAACUAGGAUAUAACACCGUAAUAGUUAAUUGCUCUAGACCUCACAACUGAUCUCGAUUCG
..((((((((.....(((((......((((((......))))))((((.((((((..((........))..))))))....))))..)))))...))))))))....... ( -29.00)
>DroEre_CAF1 175209 110 + 1
AAAGAUCGGUGAAAGGAGGUAAACUGUGGAAGCCCAGAUUUCUAACGGAUAACUAGGAUAUAACACCGUAAUAGUUAAUUGCUCUAGACCUCACAACUGAUCUCGAUUCG
..((((((((.....(((((...(((((((((......))))).))))....((((..((((((.........))))..))..)))))))))...))))))))....... ( -27.70)
>DroYak_CAF1 167674 110 + 1
AAAGAUCGGUGAAAGGAGGUAAACUGUGGAAGCCCAGAUUUCUAACGGAUAACUAGAAUAUAACACCGUAAUAGUUAAUUGCUCUAGACCUCACAACUGAUCUCGAUUCA
..((((((((.....(((((...(((((((((......))))).))))....(((((.((((((.........))))..)).))))))))))...))))))))....... ( -27.50)
>consensus
AAAGAUCGGUGAAAGGAGGUAAACUGUGGAAGCCCAGAUUUCCAAGGGAUAACUAGGAUAUAACACCGUAAUAGUUAAUUGCUCUAGACCUCACAACUGAUCUCGAUUCG
..((((((((.....(((((......((((((......))))))((((.((((((..((........))..))))))....))))..)))))...))))))))....... (-26.38 = -26.38 +   0.00)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:09:50 2006