Locus 580

Sequence ID	3R_DroMel_CAF1
Location	2,169,315 – 2,169,419
Length	104
Max. P	0.868223

overview

Window 5

Location	2,169,315 – 2,169,419
Length	104
Sequences	6
Columns	108
Reading direction	forward
Mean pairwise identity	76.10
Mean single sequence MFE	-30.02
Consensus MFE	-17.83
Energy contribution	-17.30
Covariance contribution	-0.53
Combinations/Pair	1.43
Mean z-score	-1.66
Structure conservation index	0.59
SVM decision value	0.62
SVM RNA-class probability	0.802437
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 2169315 104 + 27905053
AAGCUGGGAGAUCCCAUUGCCGGAAACUUUUUUCAGGCACAGUGGGACGACUAUGUGCCCAAGUUAUACAAGCAACUAUCUGGCAAGAAGUAGUAU----CUUUCUCC
......(((((((((((((((.((((....)))).))))..))))))..(((((.((((..((((........))))....))))....)))))..----...))))) ( -32.20)
>DroVir_CAF1 412145 97 + 1
CAGCUGGGCAAUCCCAUUGCCGGCAAUUUCUACCAGGCACAGUGGGACAAUUAUGUGCCCAAGUUGUACAAACAGCUGUCGGGCAAAUGAUA-------UUAUU----
...........((((((((((((.........)).))))..))))))..(((((.(((((.((((((....))))))...))))).))))).-------.....---- ( -31.90)
>DroEre_CAF1 314999 102 + 1
AAGCUGGGGGAUCCCAUUGCUGGGAACUUUUUUCAGGCACAGUGGGACGAAUAUGUGCCCAAGUUAUACAAACAAUUAUCUGGCAAGAAAUAGUAU----UUUUC--U
..((..((((.(((((((((((..(.....)..)))...))))))))..........)))..(((.....)))......)..)).(((((......----.))))--) ( -25.00)
>DroYak_CAF1 315735 106 + 1
AAGCUGGGGGAUCCCAUUGCUGGGAACUUUUUCCAGGCACAGUGGGACGACUAUGUGCCCAAGUUAUACAAACAACUAUCUGGCAAGAAGUAGUAGUAGCUUCCU--U
.....(((((.((((((((((((((.....))))))...))))))))..(((((.((((..((((........))))....))))....))))).....))))).--. ( -32.70)
>DroMoj_CAF1 338308 108 + 1
CAGCUGGGCAAUCCCAUUGCCGGCAACUUCUACCAGGCACAGUGGGACGAUUAUGUGCCCAAGUUGUACAAACAGCUGUCGGGCAAGUGAUAAGAGUUAUUAUUAUUA
..((((((((.((((((((((((.........)).))))..))))))........))))).((((((....))))))....))).((((((((......)))))))). ( -34.30)
>DroAna_CAF1 284701 106 + 1
AGUCUGGGAGAUCCUAUUGCCGGGAACUUCUAUCAGGCCCAAUGGGAUGAUUAUGUCCCAAAGCUGUACAAACAACUCUCGGGAAAAUAGUAGAAUGAAAAUUAU--U
..((((((((.((((......))))..........(((....((((((......))))))..)))..........))))))))......................--. ( -24.00)
>consensus
AAGCUGGGAGAUCCCAUUGCCGGGAACUUCUACCAGGCACAGUGGGACGAUUAUGUGCCCAAGUUAUACAAACAACUAUCGGGCAAGAAAUAGUAU____UUUUC__U
...........((((((((((.((........)).))))..))))))..(((...((((..((((........))))....))))...)))................. (-17.83 = -17.30 +  -0.53)

alignment

secondary structure

dotplot

Window 6

Location	2,169,315 – 2,169,419
Length	104
Sequences	6
Columns	108
Reading direction	reverse
Mean pairwise identity	76.10
Mean single sequence MFE	-28.92
Consensus MFE	-17.08
Energy contribution	-18.17
Covariance contribution	1.08
Combinations/Pair	1.14
Mean z-score	-1.79
Structure conservation index	0.59
SVM decision value	0.86
SVM RNA-class probability	0.868223
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 2169315 104 - 27905053
GGAGAAAG----AUACUACUUCUUGCCAGAUAGUUGCUUGUAUAACUUGGGCACAUAGUCGUCCCACUGUGCCUGAAAAAAGUUUCCGGCAAUGGGAUCUCCCAGCUU
(((((...----...(.(((...((((....(((((......)))))..))))...))).)(((((...((((.((((....)))).)))).))))))))))...... ( -32.10)
>DroVir_CAF1 412145 97 - 1
----AAUAA-------UAUCAUUUGCCCGACAGCUGUUUGUACAACUUGGGCACAUAAUUGUCCCACUGUGCCUGGUAGAAAUUGCCGGCAAUGGGAUUGCCCAGCUG
----.....-------..............(((((((....)))...((((((.......((((((...((((.(((((...))))))))).)))))))))))))))) ( -32.01)
>DroEre_CAF1 314999 102 - 1
A--GAAAA----AUACUAUUUCUUGCCAGAUAAUUGUUUGUAUAACUUGGGCACAUAUUCGUCCCACUGUGCCUGAAAAAAGUUCCCAGCAAUGGGAUCCCCCAGCUU
.--.....----......((((..(((((......(((.....))).((((.((......))))))))).))..)))).....(((((....)))))........... ( -22.10)
>DroYak_CAF1 315735 106 - 1
A--AGGAAGCUACUACUACUUCUUGCCAGAUAGUUGUUUGUAUAACUUGGGCACAUAGUCGUCCCACUGUGCCUGGAAAAAGUUCCCAGCAAUGGGAUCCCCCAGCUU
.--...(((((......(((...((((....((((((....))))))..))))...))).((((((...(((..((((....))))..))).)))))).....))))) ( -30.40)
>DroMoj_CAF1 338308 108 - 1
UAAUAAUAAUAACUCUUAUCACUUGCCCGACAGCUGUUUGUACAACUUGGGCACAUAAUCGUCCCACUGUGCCUGGUAGAAGUUGCCGGCAAUGGGAUUGCCCAGCUG
..............................(((((((....)))...((((((.......((((((...((((.(((((...))))))))).)))))))))))))))) ( -32.01)
>DroAna_CAF1 284701 106 - 1
A--AUAAUUUUCAUUCUACUAUUUUCCCGAGAGUUGUUUGUACAGCUUUGGGACAUAAUCAUCCCAUUGGGCCUGAUAGAAGUUCCCGGCAAUAGGAUCUCCCAGACU
.--...........(((.(((((..((((((((((((....)))))))(((((........))))))))))...))))).((.(((........))).))...))).. ( -24.90)
>consensus
A__AAAAA____AUACUACUACUUGCCAGAUAGUUGUUUGUACAACUUGGGCACAUAAUCGUCCCACUGUGCCUGAAAAAAGUUCCCGGCAAUGGGAUCCCCCAGCUU
......................(((((.....(((((....)))))(..((((((............))))))..)...........)))))((((....)))).... (-17.08 = -18.17 +   1.08)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:46:38 2006