Locus 5952

Sequence ID 3R_DroMel_CAF1
Location 15,699,546 – 15,699,636
Length 90
Max. P 0.838245
window9709 window9710

overview

Window 9

Location 15,699,546 – 15,699,636
Length 90
Sequences 5
Columns 90
Reading direction forward
Mean pairwise identity 83.28
Mean single sequence MFE -21.58
Consensus MFE -16.29
Energy contribution -16.69
Covariance contribution 0.40
Combinations/Pair 1.00
Mean z-score -1.73
Structure conservation index 0.75
SVM decision value 0.37
SVM RNA-class probability 0.707442
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 15699546 90 + 27905053
AAGGAAUGGAAUUGGCCUGGCCAUUGUGUAAAGCACUUUUACUAGCUGACUAAUAGAUAAUAAAUACAUGGUCAGAUGUGGUCACCUAGU
.(((...((......))(((((((.(((.....))).........(((((((................)))))))..))))))))))... ( -20.09)
>DroSec_CAF1 9013 86 + 1
AAGGAAUGGAACUGGCCUGUCCAUGGUGUAAAGCACUUUUACUAGGUGACUAAUAGAUAA----UACAUGGCCAGAUGUGGUCACCUAGU
..(((..((......))..)))..((((.....))))...(((((((((((.........----.((((......))))))))))))))) ( -24.30)
>DroSim_CAF1 9048 86 + 1
AAGGAAUGGAACUGGCCUGUCCAUGGUGUAAAGCACUUUUACUAGGUGACUAAUAGAUAA----UACAUGGCCAGAUGUGGUCACCUAGU
..(((..((......))..)))..((((.....))))...(((((((((((.........----.((((......))))))))))))))) ( -24.30)
>DroEre_CAF1 9234 71 + 1
UGGGAAUGGAACUGG-----GCAUGGUGUAAAGCACUUUUACUAGGUGACUAAUAGAUG-----------GC---AUGUGGUCACCUAGU
...............-----....((((.....))))...((((((((((((...(...-----------.)---...)))))))))))) ( -19.60)
>DroYak_CAF1 9214 71 + 1
AAGGAAUGGAACUGG-----GCAUGGUGUAAAGCACUUUUACUAGGUGACUAAUAGAUG-----------GC---AUGUGGUCACCUAGU
...............-----....((((.....))))...((((((((((((...(...-----------.)---...)))))))))))) ( -19.60)
>consensus
AAGGAAUGGAACUGGCCUG_CCAUGGUGUAAAGCACUUUUACUAGGUGACUAAUAGAUAA____UACAUGGCCAGAUGUGGUCACCUAGU
........................((((.....))))...((((((((((((..........................)))))))))))) (-16.29 = -16.69 +   0.40)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 0

Location 15,699,546 – 15,699,636
Length 90
Sequences 5
Columns 90
Reading direction reverse
Mean pairwise identity 83.28
Mean single sequence MFE -16.53
Consensus MFE -13.09
Energy contribution -13.29
Covariance contribution 0.20
Combinations/Pair 1.00
Mean z-score -1.88
Structure conservation index 0.79
SVM decision value 0.74
SVM RNA-class probability 0.838245
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 15699546 90 - 27905053
ACUAGGUGACCACAUCUGACCAUGUAUUUAUUAUCUAUUAGUCAGCUAGUAAAAGUGCUUUACACAAUGGCCAGGCCAAUUCCAUUCCUU
(((((.((((.......((..(((....)))..)).....)))).)))))....(((.....)))..((((...))))............ ( -15.50)
>DroSec_CAF1 9013 86 - 1
ACUAGGUGACCACAUCUGGCCAUGUA----UUAUCUAUUAGUCACCUAGUAAAAGUGCUUUACACCAUGGACAGGCCAGUUCCAUUCCUU
...(((.........((((((.(((.----.....((((((....))))))...(((.....))).....))))))))).......))). ( -18.69)
>DroSim_CAF1 9048 86 - 1
ACUAGGUGACCACAUCUGGCCAUGUA----UUAUCUAUUAGUCACCUAGUAAAAGUGCUUUACACCAUGGACAGGCCAGUUCCAUUCCUU
...(((.........((((((.(((.----.....((((((....))))))...(((.....))).....))))))))).......))). ( -18.69)
>DroEre_CAF1 9234 71 - 1
ACUAGGUGACCACAU---GC-----------CAUCUAUUAGUCACCUAGUAAAAGUGCUUUACACCAUGC-----CCAGUUCCAUUCCCA
((((((((((.....---..-----------.........))))))))))....(((.....))).....-----............... ( -14.89)
>DroYak_CAF1 9214 71 - 1
ACUAGGUGACCACAU---GC-----------CAUCUAUUAGUCACCUAGUAAAAGUGCUUUACACCAUGC-----CCAGUUCCAUUCCUU
((((((((((.....---..-----------.........))))))))))....(((.....))).....-----............... ( -14.89)
>consensus
ACUAGGUGACCACAUCUGGCCAUGUA____UUAUCUAUUAGUCACCUAGUAAAAGUGCUUUACACCAUGG_CAGGCCAGUUCCAUUCCUU
((((((((((..............................))))))))))....(((.....)))......................... (-13.09 = -13.29 +   0.20)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:08:45 2006