Locus 6800

Sequence ID	3R_DroMel_CAF1
Location	17,963,477 – 17,963,618
Length	141
Max. P	0.974276

overview

Window 9

Location	17,963,477 – 17,963,583
Length	106
Sequences	5
Columns	111
Reading direction	forward
Mean pairwise identity	72.76
Mean single sequence MFE	-29.50
Consensus MFE	-19.00
Energy contribution	-20.72
Covariance contribution	1.72
Combinations/Pair	1.19
Mean z-score	-1.52
Structure conservation index	0.64
SVM decision value	0.57
SVM RNA-class probability	0.786773
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 17963477 106 + 27905053
GCGCGGUUUUCGUACCCGAGAUCCUCGUGGAUUAUGCGGAUAUACUGCGUUUGACCAUCAAAAUGUAAUGGUCAAAAGGAACAACUUUUAUUUGC-----UCAAGCUUUAA
(((((((.((((((((((((...)))).))....))))))...)))))))..((((((.........))))))(((((......)))))....((-----....))..... ( -29.10)
>DroSim_CAF1 7855 111 + 1
GCGCGGUUUUCGUACCCGAGAUCCUCGUGGAUUAUGCGGAUAUACCGCGUUUGACCAUCAAAAUGUAAUGGUCAAAAGGUACAACUUUUAUUUGUUUGUUUCCAGCUUAAA
(((((((.((((((((((((...)))).))....))))))...)))))))((((((((.........))))))))..((.(((((........).))))..))........ ( -33.30)
>DroEre_CAF1 7104 111 + 1
GCGCGGUUUUCGUACCCGAGAUCCUCGUGGAUUAUGGGGGUAUGCUGGGUUUGACCAUCAAAAUGUAAUGGUCAAAAGGAACAACUUUCAUUUGCUUGCUUCAAGCCUUAA
....(((((.....((((.(((((....))))).))))((((.((....(((((((((.........))))))))).((((....))))....)).))))..))))).... ( -30.70)
>DroYak_CAF1 7400 111 + 1
GCGCGGUUUUCGUACCCGAGAUCCUCGUGGAUUAUGGGGGUAUACGGCGUUUGACCAUCAAAAUGUAAUGGUCAAAAGGAACAACUUUUGUUUGCUUGCUUAAAGCUUUAA
((((.((.......((((.(((((....))))).)))).....)).))))((((((((.........))))))))...(((((.....)))))((((.....))))..... ( -33.30)
>DroAna_CAF1 6682 80 + 1
GCGCGCUUUUAUUACCCG--GUCCUUUUGGAUCGCAGGGGUAUAUUGUAUUAAAGCCGCAAAAUGACACGAUUGCAGAGUGC-----------------------------
(((.((((((((((((((--((((....)))))....)))))....)))..)))))))).......(((.........))).----------------------------- ( -21.10)
>consensus
GCGCGGUUUUCGUACCCGAGAUCCUCGUGGAUUAUGGGGGUAUACUGCGUUUGACCAUCAAAAUGUAAUGGUCAAAAGGAACAACUUUUAUUUGCUUG_UUCAAGCUUUAA
(((((((....((((((..(((((....)))))....)))))))))))))((((((((.........)))))))).................................... (-19.00 = -20.72 +   1.72)

alignment

secondary structure

dotplot

Window 0

Location	17,963,477 – 17,963,583
Length	106
Sequences	5
Columns	111
Reading direction	reverse
Mean pairwise identity	72.76
Mean single sequence MFE	-26.74
Consensus MFE	-15.98
Energy contribution	-16.86
Covariance contribution	0.88
Combinations/Pair	1.14
Mean z-score	-1.90
Structure conservation index	0.60
SVM decision value	1.33
SVM RNA-class probability	0.942879
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 17963477 106 - 27905053
UUAAAGCUUGA-----GCAAAUAAAAGUUGUUCCUUUUGACCAUUACAUUUUGAUGGUCAAACGCAGUAUAUCCGCAUAAUCCACGAGGAUCUCGGGUACGAAAACCGCGC
.........((-----((((.......))))))..(((((((((((.....)))))))))))(((.((.((((((....((((....))))..)))))).....)).))). ( -27.80)
>DroSim_CAF1 7855 111 - 1
UUUAAGCUGGAAACAAACAAAUAAAAGUUGUACCUUUUGACCAUUACAUUUUGAUGGUCAAACGCGGUAUAUCCGCAUAAUCCACGAGGAUCUCGGGUACGAAAACCGCGC
.....((((....))............(((((((((((((((((((.....))))))))))).((((.....))))...((((....))))...)))))))).....)).. ( -35.40)
>DroEre_CAF1 7104 111 - 1
UUAAGGCUUGAAGCAAGCAAAUGAAAGUUGUUCCUUUUGACCAUUACAUUUUGAUGGUCAAACCCAGCAUACCCCCAUAAUCCACGAGGAUCUCGGGUACGAAAACCGCGC
.....(((((...)))))........((((.....(((((((((((.....)))))))))))..)))).(((((.....((((....))))...)))))............ ( -28.20)
>DroYak_CAF1 7400 111 - 1
UUAAAGCUUUAAGCAAGCAAACAAAAGUUGUUCCUUUUGACCAUUACAUUUUGAUGGUCAAACGCCGUAUACCCCCAUAAUCCACGAGGAUCUCGGGUACGAAAACCGCGC
.....((((.....)))).................(((((((((((.....)))))))))))(((.((.(((((.....((((....))))...))))).....)).))). ( -26.80)
>DroAna_CAF1 6682 80 - 1
-----------------------------GCACUCUGCAAUCGUGUCAUUUUGCGGCUUUAAUACAAUAUACCCCUGCGAUCCAAAAGGAC--CGGGUAAUAAAAGCGCGC
-----------------------------((.((((((((..........)))))).............(((((....(.(((....))).--)))))).....)).)).. ( -15.50)
>consensus
UUAAAGCUUGAA_CAAGCAAAUAAAAGUUGUUCCUUUUGACCAUUACAUUUUGAUGGUCAAACGCAGUAUACCCCCAUAAUCCACGAGGAUCUCGGGUACGAAAACCGCGC
.............................((....(((((((((((.....))))))))))).......(((((.....((((....))))...)))))........)).. (-15.98 = -16.86 +   0.88)

alignment

secondary structure

dotplot

Window 1

Location	17,963,517 – 17,963,618
Length	101
Sequences	4
Columns	111
Reading direction	reverse
Mean pairwise identity	76.70
Mean single sequence MFE	-23.75
Consensus MFE	-12.60
Energy contribution	-12.35
Covariance contribution	-0.25
Combinations/Pair	1.17
Mean z-score	-2.63
Structure conservation index	0.53
SVM decision value	1.73
SVM RNA-class probability	0.974276
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 17963517 101 - 27905053
UAAA----UUGUA-AAAAUCUAAAAACUCCUUUAUUUCGCUUAAAGCUUGA-----GCAAAUAAAAGUUGUUCCUUUUGACCAUUACAUUUUGAUGGUCAAACGCAGUAUA
...(----((((.-..........((((..(((((((.(((((.....)))-----)))))))))))))......(((((((((((.....))))))))))).)))))... ( -23.80)
>DroSim_CAF1 7895 106 - 1
UAUA----AUGUU-GAAAUCUAAAAACUCCUUUAUUUCGCUUUAAGCUGGAAACAAACAAAUAAAAGUUGUACCUUUUGACCAUUACAUUUUGAUGGUCAAACGCGGUAUA
....----.....-..........((((..(((((((.((.....))((....))...)))))))))))(((((.(((((((((((.....)))))))))))...))))). ( -23.60)
>DroEre_CAF1 7144 111 - 1
CUCAGUUUCCGUUUGAAGAUGAAAAACUCUUUUUGUAAUCUUAAGGCUUGAAGCAAGCAAAUGAAAGUUGUUCCUUUUGACCAUUACAUUUUGAUGGUCAAACCCAGCAUA
....(((((.((((.(((((..((((....))))...))))).))))..)))))..((.(((....)))......(((((((((((.....)))))))))))....))... ( -25.00)
>DroYak_CAF1 7440 110 - 1
CUUAGUUUCUGUUUAAAGAUAUACUACUCAUAUU-UCCGCUUAAAGCUUUAAGCAAGCAAACAAAAGUUGUUCCUUUUGACCAUUACAUUUUGAUGGUCAAACGCCGUAUA
..((((.(((......)))...))))........-...((((((....))))))..((.((((.....))))...(((((((((((.....))))))))))).))...... ( -22.60)
>consensus
CAUA____CUGUU_AAAAACUAAAAACUCCUUUAUUUCGCUUAAAGCUUGAAGCAAGCAAAUAAAAGUUGUUCCUUUUGACCAUUACAUUUUGAUGGUCAAACGCAGUAUA
.............................................(((........((((.......))))....(((((((((((.....)))))))))))...)))... (-12.60 = -12.35 +  -0.25)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:30:17 2006