Locus 5100

Sequence ID	X_DroMel_CAF1
Location	13,321,286 – 13,321,474
Length	188
Max. P	0.999874

overview

Window 5

Location	13,321,286 – 13,321,395
Length	109
Sequences	5
Columns	110
Reading direction	forward
Mean pairwise identity	94.62
Mean single sequence MFE	-31.42
Consensus MFE	-29.25
Energy contribution	-29.89
Covariance contribution	0.64
Combinations/Pair	1.04
Mean z-score	-2.53
Structure conservation index	0.93
SVM decision value	4.34
SVM RNA-class probability	0.999874
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 13321286 109 + 22224390
-CCUUUCUGCCUUUCAGCCAGGAUGUGAGCUCUGCUCGGUGUCCUUUUAUUUCCCUUUCAAGAGCUAUAAGCUUAUGUCUCUGGCUUUGUGGUUUGGUAAACAUACUGCA
-..............((((((((((((((((..((((..((.................)).))))....)))))))))).)))))).((..((.((.....)).))..)) ( -33.23)
>DroSec_CAF1 34022 108 + 1
--CUUUCUGCCUUUCAGCCAGGAUGUGAGCUCUGCUCGGUGUCCUUUUAUUUCCCUUUCAAGAGCUACACGCUUAUGUCUCUGACUUUGUGGUUUGGUAAACAUACUGCA
--.............((.((((((((((((...((((..((.................)).)))).....))))))))).))).)).((..((.((.....)).))..)) ( -24.43)
>DroSim_CAF1 26810 109 + 1
-CCUUUCUGCCUUUCAGCCAGGAUGUGAGCUCUGCUCGGUGUCCUUUUAUUUCCCUUUCAAGAGCUAUAAGCUUAUGUCUCUGGCUUUGUGGUUUCGUAAACAUACUGCA
-.......(((....((((((((((((((((..((((..((.................)).))))....)))))))))).))))))....)))...(((.......))). ( -30.93)
>DroEre_CAF1 25625 110 + 1
GCCCCUCAGCCUUUCAGCCAAGAUGUGAGCUCUGCUCGGUGUCCUUUUAUUUCCCCUUCAAGAGCUAUAAGCUCAUGUCUCUGGCUUUGUGGUUUGGUAAACAUACUGCA
(((....((((....((((((((((((((((..((((..((.................)).))))....))))))))))).)))))....)))).)))............ ( -33.43)
>DroYak_CAF1 25287 110 + 1
ACCUCUCAGCCUUUCAGCCAGGAUGUGAGCUCUGCUCGGUGUCCUUUUAUUUCGCUUUCAAGAGCUAUAAGCUUAUGUCUCUGGCUUUGUGGUUUGGUAAACAUACUGCA
(((....((((....((((((((((((((((..((((((((...........)))).....))))....)))))))))).))))))....)))).)))............ ( -35.10)
>consensus
_CCUUUCUGCCUUUCAGCCAGGAUGUGAGCUCUGCUCGGUGUCCUUUUAUUUCCCUUUCAAGAGCUAUAAGCUUAUGUCUCUGGCUUUGUGGUUUGGUAAACAUACUGCA
...............((((((((((((((((..((((..((.................)).))))....)))))))))).)))))).((..((.((.....)).))..)) (-29.25 = -29.89 +   0.64)

alignment

secondary structure

dotplot

Window 6

Location	13,321,355 – 13,321,474
Length	119
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	94.24
Mean single sequence MFE	-29.32
Consensus MFE	-24.08
Energy contribution	-23.92
Covariance contribution	-0.16
Combinations/Pair	1.10
Mean z-score	-1.82
Structure conservation index	0.82
SVM decision value	1.06
SVM RNA-class probability	0.908753
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 13321355 119 + 22224390
GCUUAUGUCUCUGGCUUUGUGGUUUGGUAAACAUACUGCACAAAAUUAUAUUCUGCAAAUAUUUUCACAAGCUGAAUGAAAAUGUUUGCAAUAC-UUGCGAAAAGUUUCUGCGGAACCAA
(((.........)))....((((((.(((........................((((((((((((((.........))))))))))))))..((-((.....))))...))).)))))). ( -26.70)
>DroSec_CAF1 34090 119 + 1
GCUUAUGUCUCUGACUUUGUGGUUUGGUAAACAUACUGCACAAAAUUAUAUUCUGCAAAUAUUUUCGCAAGCCGAAUGAAAAUGUUUGCAUUAC-UUGCGAAAAGUUUCUGCGGAUAUAA
((.(((((.((.((((....)))).))...)))))..))......((((((.(((((....((((((((((...((((..........)))).)-))))))))).....))))))))))) ( -29.30)
>DroSim_CAF1 26879 119 + 1
GCUUAUGUCUCUGGCUUUGUGGUUUCGUAAACAUACUGCACAAAAUUAUAUUCUGCAAAUAUUUUCGCAAGCCGAAUGAAAAUGUUUGCAUUAC-UUGCGAAAAGUUUCUGCGGAUAUAA
((.(((((....((((....))))......)))))..))......((((((.(((((....((((((((((...((((..........)))).)-))))))))).....))))))))))) ( -28.30)
>DroEre_CAF1 25695 120 + 1
GCUCAUGUCUCUGGCUUUGUGGUUUGGUAAACAUACUGCACAAAAUUAUAGUCUGCAAAUAUUUUCGCAAGCCGAAUGAAAAUGUUUGCAUUAGCUUGCGAAAAGUUGCUGCGGAUACAA
.....(((.((((....((..((.((.....)).))..))..............((((...(((((((((((..((((..........)))).))))))))))).))))..)))).))). ( -33.90)
>DroYak_CAF1 25357 120 + 1
GCUUAUGUCUCUGGCUUUGUGGUUUGGUAAACAUACUGCACAAAAUUAUAGUCUGCAAAUAUUUUCGCAAGCCAAAUGAAAAUGUUUGCAUUACUUUGCAAAAAGUUGCUGCGGAUACAA
.....(((.((((....((..((.((.....)).))..))........((((.((((((((((((((.........))))))))))))))..(((((....))))).)))))))).))). ( -28.40)
>consensus
GCUUAUGUCUCUGGCUUUGUGGUUUGGUAAACAUACUGCACAAAAUUAUAUUCUGCAAAUAUUUUCGCAAGCCGAAUGAAAAUGUUUGCAUUAC_UUGCGAAAAGUUUCUGCGGAUACAA
.....(((.((((((((((..((.((.....)).))..)..............((((((((((((((.........))))))))))))))...........))))).....)))).))). (-24.08 = -23.92 +  -0.16)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:40:08 2006