Locus 1607

Sequence ID 3R_DroMel_CAF1
Location 4,624,208 – 4,624,312
Length 104
Max. P 0.555624
window2650 window2651

overview

Window 0

Location 4,624,208 – 4,624,312
Length 104
Sequences 3
Columns 104
Reading direction forward
Mean pairwise identity 79.32
Mean single sequence MFE -25.60
Consensus MFE -18.24
Energy contribution -20.14
Covariance contribution 1.89
Combinations/Pair 1.07
Mean z-score -1.44
Structure conservation index 0.71
SVM decision value 0.04
SVM RNA-class probability 0.555624
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 4624208 104 + 27905053
CUUAAUGACGUCAUGUGGCGCGCCUUUUGGAAUAGAACAGAAUAUGUACGUACAUUCAUAUGUACAUGUGUUUUUUUUGUUUUGUGAGGUUCCCCACUGGGGCG
........((((..((((.(.(((((.(..(((((((.((((((((((((((......))))))))))).))).)))))))..).))))).).))))...)))) ( -35.00)
>DroEre_CAF1 24189 86 + 1
CUUAAUGACGUCAUGAGGCGCGCCUU-UGGAAUAGAACAGAAUAUGUAC--------AUAUGUACAUGUGUUUUU---------UGAGGUUCCCCUCUGGGGCU
.........(((..((((.(.(((((-......((((((...(((((((--------....))))))))))))).---------.))))).).))))...))). ( -25.10)
>DroYak_CAF1 24053 79 + 1
CUUAAUGACGUCAUGUGGCGCGCCUUGUGGAAUAGAACAGAAUAUG----------------UACAUGUGUUUUU---------UGAGGUUUCCCUCUGGGGCU
......(.((((....)))))(((((............(((((((.----------------.....))))))).---------.((((....)))).))))). ( -16.70)
>consensus
CUUAAUGACGUCAUGUGGCGCGCCUU_UGGAAUAGAACAGAAUAUGUAC________AUAUGUACAUGUGUUUUU_________UGAGGUUCCCCUCUGGGGCU
.........(((..((((.(.(((((.......((((((...((((((((((......))))))))))))))))...........))))).).))))...))). (-18.24 = -20.14 +   1.89)

alignment

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secondary structure

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dotplot

Postscript

Window 1

Location 4,624,208 – 4,624,312
Length 104
Sequences 3
Columns 104
Reading direction reverse
Mean pairwise identity 79.32
Mean single sequence MFE -18.53
Consensus MFE -13.22
Energy contribution -14.30
Covariance contribution 1.08
Combinations/Pair 1.00
Mean z-score -1.42
Structure conservation index 0.71
SVM decision value 0.01
SVM RNA-class probability 0.538531
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 4624208 104 - 27905053
CGCCCCAGUGGGGAACCUCACAAAACAAAAAAAACACAUGUACAUAUGAAUGUACGUACAUAUUCUGUUCUAUUCCAAAAGGCGCGCCACAUGACGUCAUUAAG
(((.((.(((((....)))))................((((((((....)))))))).......................)).))).................. ( -20.50)
>DroEre_CAF1 24189 86 - 1
AGCCCCAGAGGGGAACCUCA---------AAAAACACAUGUACAUAU--------GUACAUAUUCUGUUCUAUUCCA-AAGGCGCGCCUCAUGACGUCAUUAAG
.(((...((((....)))).---------........((((((....--------))))))................-..)))(((.(....).)))....... ( -19.40)
>DroYak_CAF1 24053 79 - 1
AGCCCCAGAGGGAAACCUCA---------AAAAACACAUGUA----------------CAUAUUCUGUUCUAUUCCACAAGGCGCGCCACAUGACGUCAUUAAG
.......((((....)))).---------.......(((((.----------------.......(((........))).((....)))))))........... ( -15.70)
>consensus
AGCCCCAGAGGGGAACCUCA_________AAAAACACAUGUACAUAU________GUACAUAUUCUGUUCUAUUCCA_AAGGCGCGCCACAUGACGUCAUUAAG
.(((...((((....))))..................((((((............))))))...................)))(((.(....).)))....... (-13.22 = -14.30 +   1.08)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:14:44 2006