Locus 8650

Sequence ID 3R_DroMel_CAF1
Location 23,141,673 – 23,141,799
Length 126
Max. P 0.999952
window13892 window13893

overview

Window 2

Location 23,141,673 – 23,141,775
Length 102
Sequences 4
Columns 119
Reading direction forward
Mean pairwise identity 63.06
Mean single sequence MFE -19.83
Consensus MFE -9.07
Energy contribution -10.08
Covariance contribution 1.00
Combinations/Pair 1.00
Mean z-score -2.19
Structure conservation index 0.46
SVM decision value 1.55
SVM RNA-class probability 0.962860
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 23141673 102 + 27905053
CAACUUAUGCACAUUAACUUAUCGGUAAUUUAUUGA-------AUAUA------AAAGGGGAACCAAAUAUACG----GAAGUAUAGAUAUGCCCUAAGAUAGGGUAAAUCGCAAUGCG
.......(((...........((((((...))))))-------.....------...((....))...(((((.----...)))))(((.(((((((...))))))).))))))..... ( -24.70)
>DroSec_CAF1 19299 102 + 1
UAACUCAUAAAAAUAAACUUAUCAAUAAUUUAUUGA-------AUAUA------AAAGGGGAACAAAAUAUACG----GAAGUAUAGAUAUGCCCUGAAAAAGGGUAUAUCGCAAUGCG
...(((.(((........)))((((((...))))))-------.....------...)))........(((((.----...)))))((((((((((.....))))))))))........ ( -24.30)
>DroEre_CAF1 19064 99 + 1
CAGAUUUUAAAAA---GCUUAUGA-U-----ACGAA-------AUAUGACAAAAUCAGGGGGACACAAAAUACG----AAAAAAUAUAUAUGCCCCAAGAAAGGGUAUAUCACAAUGCG
.............---((((.(((-.-----.((..-------...(((.....))).(....)........))----..........(((((((.......)))))))))).)).)). ( -13.20)
>DroYak_CAF1 20956 110 + 1
UAGAUUUUAAAAA---GCUUAUAA-U-----AUGAAGUUUUGUAUUUGAGGUAAUCAGUAAUCAACAUAAAAGGGAACAAUAAAUAUAUAUGCCCCAAGAAAGGGUAUACCACAAUGCG
..........(((---((((....-.-----...)))))))(((((.(.((((...................(....)............(((((.......))))))))).)))))). ( -17.10)
>consensus
CAAAUUAUAAAAA___ACUUAUCA_U_____AUGAA_______AUAUA______AAAGGGGAACAAAAAAUACG____AAAAAAUAGAUAUGCCCCAAGAAAGGGUAUAUCACAAUGCG
......................................................................................(((((((((.......)))))))))........ ( -9.07 = -10.08 +   1.00)

alignment

Postscript

secondary structure

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dotplot

Postscript

Window 3

Location 23,141,709 – 23,141,799
Length 90
Sequences 4
Columns 104
Reading direction forward
Mean pairwise identity 72.05
Mean single sequence MFE -24.82
Consensus MFE -17.29
Energy contribution -18.10
Covariance contribution 0.81
Combinations/Pair 1.06
Mean z-score -2.94
Structure conservation index 0.70
SVM decision value 4.81
SVM RNA-class probability 0.999952
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 23141709 90 + 27905053
----AUAUA------AAAGGGGAACCAAAUAUACG----GAAGUAUAGAUAUGCCCUAAGAUAGGGUAAAUCGCAAUGCGACCACUUAUUGGGGUGGCGAAAUC
----.....------...((....))...(((((.----...)))))(((.(((((((...))))))).)))....(((.(((.((....))))).)))..... ( -29.30)
>DroSec_CAF1 19335 90 + 1
----AUAUA------AAAGGGGAACAAAAUAUACG----GAAGUAUAGAUAUGCCCUGAAAAAGGGUAUAUCGCAAUGCGACCACUUAUCGGGGUGGCGAAAUC
----.....------..............(((((.----...)))))((((((((((.....))))))))))......((.((((((....))))))))..... ( -30.40)
>DroEre_CAF1 19091 96 + 1
----AUAUGACAAAAUCAGGGGGACACAAAAUACG----AAAAAAUAUAUAUGCCCCAAGAAAGGGUAUAUCACAAUGCGACCACUUAUCGGGGUGGUGAAUUC
----...............(....)........((----.........((((((((.......)))))))).......))(((((((....)))))))...... ( -18.59)
>DroYak_CAF1 20986 104 + 1
UUGUAUUUGAGGUAAUCAGUAAUCAACAUAAAAGGGAACAAUAAAUAUAUAUGCCCCAAGAAAGGGUAUACCACAAUGCGCCCACUUAGCGGGGUGGCGAAAUA
.((((((((.(((........))).........(....)..))))))))(((((((.......)))))))((((..(((.........)))..))))....... ( -21.00)
>consensus
____AUAUA______AAAGGGGAACAAAAAAUACG____AAAAAAUAGAUAUGCCCCAAGAAAGGGUAUAUCACAAUGCGACCACUUAUCGGGGUGGCGAAAUC
...............................................(((((((((.......)))))))))......((.((((((....))))))))..... (-17.29 = -18.10 +   0.81)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:16:20 2006