Locus 4409

Sequence ID	X_DroMel_CAF1
Location	11,633,318 – 11,633,475
Length	157
Max. P	0.995878

overview

Window 5

Location	11,633,318 – 11,633,436
Length	118
Sequences	5
Columns	118
Reading direction	reverse
Mean pairwise identity	94.75
Mean single sequence MFE	-34.20
Consensus MFE	-33.44
Energy contribution	-32.92
Covariance contribution	-0.52
Combinations/Pair	1.13
Mean z-score	-1.68
Structure conservation index	0.98
SVM decision value	2.63
SVM RNA-class probability	0.995878
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 11633318 118 - 22224390
GGAUAUUGAUCUGAACCGUGAAUGUCUAUACCAAAUGAGUUGGCCGAGCCAACGGAAAAGUUCCAUGGAAAAUCCGGGAAAACGGAGCGGUGAUAUGAGUGUCCUUCUAAAUCUCCAA
(((((((.((....(((((...........(((.....((((((...))))))(((.....))).)))....((((......)))))))))...)).))))))).............. ( -35.30)
>DroSec_CAF1 6594 118 - 1
GGAUAUUGAUCUGAACCGUGAAUGUCUAUACCAAAUGAGUUGGCCGAGCCAACGGAAAAGUUCCAUGGGAAAUCCGGGAAAACGGAGCGGUGAUAUGAGUGUCCUUCUAAAUCUCCAA
(((((((.((....(((((...........(((.....((((((...))))))(((.....))).)))....((((......)))))))))...)).))))))).............. ( -35.50)
>DroSim_CAF1 5903 118 - 1
GGAUAUUGAUCUGAACCGUGAAUGUCUAUACCAAAUGAGUUGGCCGAGCCAACGGAAAAGUUCCAUGGGAAAUCCGGGAAAACGGAGCGGUGAUAUGAGUGUCCUUCUAAAUCUCCAA
(((((((.((....(((((...........(((.....((((((...))))))(((.....))).)))....((((......)))))))))...)).))))))).............. ( -35.50)
>DroEre_CAF1 7145 118 - 1
GGAUAUUAGUCUGAACCGUGAAUAACUAUACCAAAUGAGUUGGCCGAGUCAAUGAAAAAGUUCCAUGGGAUAUCCGGGGGAACGGAGCGGUGUUAUGAAUGUCCUUCAAAAUCUCCAA
(((((((.......(((((.....(((...((((.....))))...)))..........(((((.(.((....)).).)))))...)))))......))))))).............. ( -29.12)
>DroYak_CAF1 5933 118 - 1
GGAUAUUGAUCUGAACCGUGAAUGUCUAUACCAAAUGAGUUGGCCGAGCCAACGGAAAAGUUCCAUGGGAAAUCCGGGGGAACGGAGCGGUGAUAUGAAUGUCCUUCUAAAUCUCCAA
(((((((.((....(((((...(((((...((......((((((...))))))(((....((((...)))).))))).)).)))..)))))...)).))))))).............. ( -35.60)
>consensus
GGAUAUUGAUCUGAACCGUGAAUGUCUAUACCAAAUGAGUUGGCCGAGCCAACGGAAAAGUUCCAUGGGAAAUCCGGGAAAACGGAGCGGUGAUAUGAGUGUCCUUCUAAAUCUCCAA
(((((((.((....(((((...........(((.....((((((...))))))(((.....))).)))....((((......)))))))))...)).))))))).............. (-33.44 = -32.92 +  -0.52)

alignment

secondary structure

dotplot

Window 6

Location	11,633,356 – 11,633,475
Length	119
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	90.79
Mean single sequence MFE	-22.86
Consensus MFE	-19.42
Energy contribution	-19.46
Covariance contribution	0.04
Combinations/Pair	1.12
Mean z-score	-1.29
Structure conservation index	0.85
SVM decision value	0.10
SVM RNA-class probability	0.581493
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 11633356 119 + 22224390
UUCCCGGAUUUUCCAUGGAACUUUUCCGUUGGCUCGGCCAACUCAUUUGGUAUAGACAUUCACGGUUCAGAUCAAUAUCCUGAUGCCAU-UCCAUGCCAUUAUAAUCUCAACCCGUUUUC
....(((.........(((.....)))((((((...)))))).....((((((.(.....)..(((((((.........)))).)))..-...)))))).............)))..... ( -23.70)
>DroSec_CAF1 6632 119 + 1
UUCCCGGAUUUCCCAUGGAACUUUUCCGUUGGCUCGGCCAACUCAUUUGGUAUAGACAUUCACGGUUCAGAUCAAUAUCCUGAUGCCAU-UCCAUGCCAUUAUAAUCUCAACCCGUUUUC
....(((.........(((.....)))((((((...)))))).....((((((.(.....)..(((((((.........)))).)))..-...)))))).............)))..... ( -23.70)
>DroSim_CAF1 5941 119 + 1
UUCCCGGAUUUCCCAUGGAACUUUUCCGUUGGCUCGGCCAACUCAUUUGGUAUAGACAUUCACGGUUCAGAUCAAUAUCCUGAUGCCAU-UCCAUGCCAUUAUAAUCUCAACCCGUUUUC
....(((.........(((.....)))((((((...)))))).....((((((.(.....)..(((((((.........)))).)))..-...)))))).............)))..... ( -23.70)
>DroEre_CAF1 7183 116 + 1
CCCCCGGAUAUCCCAUGGAACUUUUUCAUUGACUCGGCCAACUCAUUUGGUAUAGUUAUUCACGGUUCAGACUAAUAUCCAGAAGCCAU-UCCAUACCAUUUUCAACUCAAACCGCC---
.....((((((......(((((.......(((((..(((((.....)))))..))))).....)))))......)))))).........-...........................--- ( -19.70)
>DroYak_CAF1 5971 120 + 1
CCCCCGGAUUUCCCAUGGAACUUUUCCGUUGGCUCGGCCAACUCAUUUGGUAUAGACAUUCACGGUUCAGAUCAAUAUCCUGAAGCCAUUUCCAUACCAUUAUAAUCUCAAAUCGUUUUC
.....(((.((((...))))....)))((((((...)))))).....((((((.((.((....(((((((.........))).)))))).)).))))))..................... ( -23.50)
>consensus
UUCCCGGAUUUCCCAUGGAACUUUUCCGUUGGCUCGGCCAACUCAUUUGGUAUAGACAUUCACGGUUCAGAUCAAUAUCCUGAUGCCAU_UCCAUGCCAUUAUAAUCUCAACCCGUUUUC
....(((.........(((.....)))((((((...)))))).....((((((.(.....)..(((((((.........)))).)))......)))))).............)))..... (-19.42 = -19.46 +   0.04)

alignment

secondary structure

dotplot

Window 7

Location	11,633,356 – 11,633,475
Length	119
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	90.79
Mean single sequence MFE	-31.72
Consensus MFE	-24.10
Energy contribution	-24.22
Covariance contribution	0.12
Combinations/Pair	1.15
Mean z-score	-1.62
Structure conservation index	0.76
SVM decision value	0.14
SVM RNA-class probability	0.602094
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 11633356 119 - 22224390
GAAAACGGGUUGAGAUUAUAAUGGCAUGGA-AUGGCAUCAGGAUAUUGAUCUGAACCGUGAAUGUCUAUACCAAAUGAGUUGGCCGAGCCAACGGAAAAGUUCCAUGGAAAAUCCGGGAA
.....((((((...........(((((...-((((..(((((.......))))).))))..)))))....(((.....((((((...))))))(((.....))).)))..)))))).... ( -32.80)
>DroSec_CAF1 6632 119 - 1
GAAAACGGGUUGAGAUUAUAAUGGCAUGGA-AUGGCAUCAGGAUAUUGAUCUGAACCGUGAAUGUCUAUACCAAAUGAGUUGGCCGAGCCAACGGAAAAGUUCCAUGGGAAAUCCGGGAA
.....((((((...........(((((...-((((..(((((.......))))).))))..)))))....(((.....((((((...))))))(((.....))).)))..)))))).... ( -33.00)
>DroSim_CAF1 5941 119 - 1
GAAAACGGGUUGAGAUUAUAAUGGCAUGGA-AUGGCAUCAGGAUAUUGAUCUGAACCGUGAAUGUCUAUACCAAAUGAGUUGGCCGAGCCAACGGAAAAGUUCCAUGGGAAAUCCGGGAA
.....((((((...........(((((...-((((..(((((.......))))).))))..)))))....(((.....((((((...))))))(((.....))).)))..)))))).... ( -33.00)
>DroEre_CAF1 7183 116 - 1
---GGCGGUUUGAGUUGAAAAUGGUAUGGA-AUGGCUUCUGGAUAUUAGUCUGAACCGUGAAUAACUAUACCAAAUGAGUUGGCCGAGUCAAUGAAAAAGUUCCAUGGGAUAUCCGGGGG
---...(..(((.((..(...((((((((.-((((.(((.((((....)))))))))))......))))))))......)..)))))..)............((.(((.....))).)). ( -26.40)
>DroYak_CAF1 5971 120 - 1
GAAAACGAUUUGAGAUUAUAAUGGUAUGGAAAUGGCUUCAGGAUAUUGAUCUGAACCGUGAAUGUCUAUACCAAAUGAGUUGGCCGAGCCAACGGAAAAGUUCCAUGGGAAAUCCGGGGG
.....................(((((((((.((((.((((((.......)))))))))).....))))))))).....((((((...))))))(((....((((...)))).)))..... ( -33.40)
>consensus
GAAAACGGGUUGAGAUUAUAAUGGCAUGGA_AUGGCAUCAGGAUAUUGAUCUGAACCGUGAAUGUCUAUACCAAAUGAGUUGGCCGAGCCAACGGAAAAGUUCCAUGGGAAAUCCGGGAA
.....((((((.........(((((((....((((.....((((....))))...))))..))).)))).(((.....((((((...))))))(((.....))).)))..)))))).... (-24.10 = -24.22 +   0.12)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:24:22 2006