Locus 2025

Sequence ID 3L_DroMel_CAF1
Location 5,577,917 – 5,578,019
Length 102
Max. P 0.969315
window3165 window3166

overview

Window 5

Location 5,577,917 – 5,578,019
Length 102
Sequences 3
Columns 112
Reading direction forward
Mean pairwise identity 83.04
Mean single sequence MFE -28.71
Consensus MFE -23.36
Energy contribution -24.03
Covariance contribution 0.67
Combinations/Pair 1.10
Mean z-score -2.60
Structure conservation index 0.81
SVM decision value 1.64
SVM RNA-class probability 0.969315
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 5577917 102 + 23771897
UCGAUGCCAACAUCGAUGUCAUCGAUGUUUUCGAAAAAUCAAAAACGUCGAUGUUUUUCGAGGAAUCGUCGAUGUUU----------UCAGCGCAUAGAAACAGCAAAGUGU
((.(((((((((((((((.((((((((((((.((....)).)))))))))))).............)))))))))).----------...).)))).))............. ( -29.54)
>DroSec_CAF1 2185 112 + 1
UCGAUGCCAACAUCGAAGUCAUCGAUGUUUUCGAAAAACAAAAAACCUCCAUGUUUUUCGAGGGAUCAUCGUUGUUUAACCAUCUCUACUGCGCAUCGGAACAAAAAAGAGU
((((((((((((((((.....)))))))).((((((((((...........))))))))))(((((....(((....))).)))))....).)))))))............. ( -29.00)
>DroSim_CAF1 2535 111 + 1
UCGAUGCCAACAUCGAAGUCAUCGAUGUUUUCGAAAAAUAAAAAACCUCGAUGUU-UUCGAGGGAUCAUCAAUGUUUACCCAUCUCUACUGCGCAUUGGAACAAAAAAGCGU
(((((((((...((((((.((((((.(((((..........))))).)))))).)-)))))(((..((....))....)))........)).)))))))............. ( -27.60)
>consensus
UCGAUGCCAACAUCGAAGUCAUCGAUGUUUUCGAAAAAUAAAAAACCUCGAUGUUUUUCGAGGGAUCAUCGAUGUUUA_CCAUCUCUACUGCGCAUAGGAACAAAAAAGAGU
..(((.((((((((((.....)))))))).((((((((((...........)))))))))))).))).(((((((.................)))))))............. (-23.36 = -24.03 +   0.67)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 6

Location 5,577,917 – 5,578,019
Length 102
Sequences 3
Columns 112
Reading direction reverse
Mean pairwise identity 83.04
Mean single sequence MFE -30.13
Consensus MFE -18.89
Energy contribution -20.00
Covariance contribution 1.11
Combinations/Pair 1.04
Mean z-score -2.32
Structure conservation index 0.63
SVM decision value 0.40
SVM RNA-class probability 0.721254
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 5577917 102 - 23771897
ACACUUUGCUGUUUCUAUGCGCUGA----------AAACAUCGACGAUUCCUCGAAAAACAUCGACGUUUUUGAUUUUUCGAAAACAUCGAUGACAUCGAUGUUGGCAUCGA
...................((.((.----------.(((((((((((....))).....((((((.((((((((....)))))))).))))))...))))))))..)).)). ( -31.70)
>DroSec_CAF1 2185 112 - 1
ACUCUUUUUUGUUCCGAUGCGCAGUAGAGAUGGUUAAACAACGAUGAUCCCUCGAAAAACAUGGAGGUUUUUUGUUUUUCGAAAACAUCGAUGACUUCGAUGUUGGCAUCGA
..............((((((......(.(((.(((.......))).))).)((((((((((...........)))))))))).((((((((.....)))))))).)))))). ( -31.10)
>DroSim_CAF1 2535 111 - 1
ACGCUUUUUUGUUCCAAUGCGCAGUAGAGAUGGGUAAACAUUGAUGAUCCCUCGAA-AACAUCGAGGUUUUUUAUUUUUCGAAAACAUCGAUGACUUCGAUGUUGGCAUCGA
.((((((.((((........)))).)))).))......((((((((...((((((.-....))))))(((((........)))))))))))))...((((((....)))))) ( -27.60)
>consensus
ACACUUUUUUGUUCCAAUGCGCAGUAGAGAUGG_UAAACAUCGAUGAUCCCUCGAAAAACAUCGAGGUUUUUUAUUUUUCGAAAACAUCGAUGACUUCGAUGUUGGCAUCGA
......................................((((((((...((((((......))))))(((((........)))))))))))))...((((((....)))))) (-18.89 = -20.00 +   1.11)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:22:43 2006