Locus 4395

Sequence ID 3L_DroMel_CAF1
Location 12,873,625 – 12,873,719
Length 94
Max. P 0.992393
window6814 window6815

overview

Window 4

Location 12,873,625 – 12,873,719
Length 94
Sequences 3
Columns 113
Reading direction forward
Mean pairwise identity 78.62
Mean single sequence MFE -31.61
Consensus MFE -25.47
Energy contribution -25.81
Covariance contribution 0.34
Combinations/Pair 1.12
Mean z-score -2.30
Structure conservation index 0.81
SVM decision value 2.33
SVM RNA-class probability 0.992393
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 12873625 94 + 23771897
GGAUGGGGGCAUUUUGGGUUUCUGCGUUUCCGAAGUGACAAAAUGGGAAAAGCAUUUGCCCGAGACACUUGAAGUGUAAAUUUCAUGGCCUCA-------------------A
...(((((.((((((((((...(((.(((((.(..(....)..).))))).)))...))))))))....((((((....)))))))).)))))-------------------. ( -31.60)
>DroSim_CAF1 7087 89 + 1
G-----GGGCACUUUGGGUUUCUGCGUUUCCGAAGUGACAAAAUAGGAAAAGCAUUUGCCCGAGACACUUGAAGUGUAAAUUUCAUGGCCUCA-------------------A
(-----((((..(((((((...(((.(((((..............))))).)))...)))))))...(.((((((....)))))).)))))).-------------------. ( -30.34)
>DroYak_CAF1 7119 110 + 1
---UGGGGGGACAUUGGGCUUCUGGGUUUCCGCAGUGACAAAAUAGGAAAAGCAUUUGCCCGAGACACUUGAAGUGUAAACUUUAUGGCCUCAAGGCGUUCGUACAAGUGCAA
---((.((..((.(..(....)..)))..)).)).................(((((((..((((.(.(.((((((....)))))).)(((....))))))))..))))))).. ( -32.90)
>consensus
G__UGGGGGCACUUUGGGUUUCUGCGUUUCCGAAGUGACAAAAUAGGAAAAGCAUUUGCCCGAGACACUUGAAGUGUAAAUUUCAUGGCCUCA___________________A
.....(((((...((((((...(((.(((((..............))))).)))...))))))....(.((((((....)))))).))))))..................... (-25.47 = -25.81 +   0.34)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 5

Location 12,873,625 – 12,873,719
Length 94
Sequences 3
Columns 113
Reading direction reverse
Mean pairwise identity 78.62
Mean single sequence MFE -23.41
Consensus MFE -18.61
Energy contribution -19.27
Covariance contribution 0.67
Combinations/Pair 1.00
Mean z-score -1.63
Structure conservation index 0.79
SVM decision value 0.92
SVM RNA-class probability 0.882618
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 12873625 94 - 23771897
U-------------------UGAGGCCAUGAAAUUUACACUUCAAGUGUCUCGGGCAAAUGCUUUUCCCAUUUUGUCACUUCGGAAACGCAGAAACCCAAAAUGCCCCCAUCC
.-------------------.((((((.((((........)))).).)))))(((((..(((.(((((..............))))).)))(.....)....)))))...... ( -22.44)
>DroSim_CAF1 7087 89 - 1
U-------------------UGAGGCCAUGAAAUUUACACUUCAAGUGUCUCGGGCAAAUGCUUUUCCUAUUUUGUCACUUCGGAAACGCAGAAACCCAAAGUGCCC-----C
.-------------------.((((((.((((........)))).).)))))(((((..(((.(((((..............))))).)))...........)))))-----. ( -23.56)
>DroYak_CAF1 7119 110 - 1
UUGCACUUGUACGAACGCCUUGAGGCCAUAAAGUUUACACUUCAAGUGUCUCGGGCAAAUGCUUUUCCUAUUUUGUCACUGCGGAAACCCAGAAGCCCAAUGUCCCCCCA---
..(((((((.......(((....)))....((((....)))))))))))...((((...((..(((((..............)))))..))...))))............--- ( -24.24)
>consensus
U___________________UGAGGCCAUGAAAUUUACACUUCAAGUGUCUCGGGCAAAUGCUUUUCCUAUUUUGUCACUUCGGAAACGCAGAAACCCAAAGUGCCCCCA__C
.....................((((((.((((........)))).).)))))(((....(((.(((((..............))))).)))....)))............... (-18.61 = -19.27 +   0.67)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:21:35 2006