Locus 6704

Sequence ID	X_DroMel_CAF1
Location	16,728,511 – 16,728,671
Length	160
Max. P	0.801804

overview

Window 6

Location	16,728,511 – 16,728,631
Length	120
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	80.06
Mean single sequence MFE	-33.23
Consensus MFE	-22.54
Energy contribution	-24.35
Covariance contribution	1.81
Combinations/Pair	1.03
Mean z-score	-1.87
Structure conservation index	0.68
SVM decision value	0.62
SVM RNA-class probability	0.801804
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 16728511 120 - 22224390
AUCGCCACUGAGGCAUGAUCGCAUCCAGUGAUCUAAAUGAUCAGCGAUCGGAUUGCAGCAUCGACUUCCCUCACAGCCGCUGUAUCGUUUACACAAUGAUAGCCAUAUAGCCCACAGGCA
...(((.....(((..((((((......(((((.....)))))))))))(((...(......)...)))......)))(((((((.(((...........))).))))))).....))). ( -34.40)
>DroSec_CAF1 9308 100 - 1
AUCGCC--------AUGAUCGCGUCCAGUGAUCUAAAUGAUCAGCGAUCGGAUUGCAGCAUCU---------GUAGCCGCUGUAUCGUUUACACAAUGAUAGCCAUA---GCCGUGGGCA
...(((--------..((((((.....))))))(((((((((((((..(((((......))))---------)....))))).))))))))(((.(((.....))).---...)))))). ( -31.70)
>DroEre_CAF1 7921 110 - 1
AUCUCCACUGAGGCAUGAUCGCAUCUAAUGACCUAAAUGAUCAGCGAUCGGAUGGCAGCUUCGGCUUCCC-CACAGCCGCUGUAUCGUUUACACAAUGAUACUCAU---------AGGCA
....((..((((((..(((((((((.............)))..))))))((..((.(((....))).)))-)...)))...((((((((.....))))))))))).---------.)).. ( -32.32)
>DroYak_CAF1 8374 110 - 1
AUCUCCACUGGGGCAUGAUCGCAUCUAAUGAUCCAAAUGAUCAGCGAUCGGAUUGCAGCUUCGGCUUCCC-CACAGCCGCUGUAUCGUUUACACAAUGAUAGCCGU---------AGGCA
........((((((((((((((......(((((.....))))))))))))...)))(((....)))..))-))..(((((.((((((((.....)))))).)).))---------.))). ( -34.50)
>consensus
AUCGCCACUGAGGCAUGAUCGCAUCCAAUGAUCUAAAUGAUCAGCGAUCGGAUUGCAGCAUCGGCUUCCC_CACAGCCGCUGUAUCGUUUACACAAUGAUAGCCAU_________AGGCA
...(((..........((((((......(((((.....)))))))))))((...(((((...((((........)))))))))((((((.....))))))..))............))). (-22.54 = -24.35 +   1.81)

alignment

secondary structure

dotplot

Window 7

Location	16,728,551 – 16,728,671
Length	120
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	87.17
Mean single sequence MFE	-36.08
Consensus MFE	-24.32
Energy contribution	-25.32
Covariance contribution	1.00
Combinations/Pair	1.00
Mean z-score	-2.06
Structure conservation index	0.67
SVM decision value	0.42
SVM RNA-class probability	0.729738
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 16728551 120 - 22224390
UGAGGGAUCCCUGCACUUCCUAAUUACUCAAUCAACUGGGAUCGCCACUGAGGCAUGAUCGCAUCCAGUGAUCUAAAUGAUCAGCGAUCGGAUUGCAGCAUCGACUUCCCUCACAGCCGC
(((((((((.(((((..(((......((((......))))...(((.....)))..((((((......(((((.....)))))))))))))).)))))....))..)))))))....... ( -39.90)
>DroSec_CAF1 9345 103 - 1
UGAGGGAUCCCUGCACUUCCUAAUUACUCAAUCAACUGGGAUCGCC--------AUGAUCGCGUCCAGUGAUCUAAAUGAUCAGCGAUCGGAUUGCAGCAUCU---------GUAGCCGC
...((((((((..........................)))))).))--------..((((((......(((((.....)))))))))))((.((((((...))---------)))))).. ( -31.17)
>DroEre_CAF1 7952 119 - 1
UGAGGGAUCCCUGCACUUCCUAAUUACUCAAUCAACUGGGAUCUCCACUGAGGCAUGAUCGCAUCUAAUGACCUAAAUGAUCAGCGAUCGGAUGGCAGCUUCGGCUUCCC-CACAGCCGC
((.((((((((..........................))))))))))....(((..(((((((((.............)))..))))))((..((.(((....))).)))-)...))).. ( -36.29)
>DroYak_CAF1 8405 119 - 1
UGAGGGAUCCCUGCACUUCCUAAUUACUCAAUCAACUGGGAUCUCCACUGGGGCAUGAUCGCAUCUAAUGAUCCAAAUGAUCAGCGAUCGGAUUGCAGCUUCGGCUUCCC-CACAGCCGC
((.((((((((..........................)))))))))).((((((((((((((......(((((.....))))))))))))...)))(((....)))..))-))....... ( -36.97)
>consensus
UGAGGGAUCCCUGCACUUCCUAAUUACUCAAUCAACUGGGAUCGCCACUGAGGCAUGAUCGCAUCCAAUGAUCUAAAUGAUCAGCGAUCGGAUUGCAGCAUCGGCUUCCC_CACAGCCGC
...((((((((..........................)))))).)).....(((.(((((((......(((((.....))))))))))))((........)).............))).. (-24.32 = -25.32 +   1.00)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:20:19 2006