Locus 1952

Sequence ID 3L_DroMel_CAF1
Location 5,404,718 – 5,404,831
Length 113
Max. P 0.998689
window3055 window3056

overview

Window 5

Location 5,404,718 – 5,404,831
Length 113
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 80.11
Mean single sequence MFE -35.67
Consensus MFE -30.40
Energy contribution -30.40
Covariance contribution -0.00
Combinations/Pair 1.00
Mean z-score -4.04
Structure conservation index 0.85
SVM decision value 3.19
SVM RNA-class probability 0.998689
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 5404718 113 + 23771897
AAACGGAGACAAAAGUGGCAUCAGGCAGCCUCAACAGGCAGCAGCUACGUGCUGCCACU-UUGCCCCACC------CACCAUGCCACUUCCACAUUGCACUCCCCGCUCUCCCCCCCCCC
....(((((...(((((((((..((((((((....)))).(((((.....)))))....-.)))).....------....))))))))).......((.......)))))))........ ( -36.10)
>DroSim_CAF1 50550 112 + 1
AAACGGAGACAAAAGUGGCAUCAGGCAGCCUCAACAGGCAGCAGCUACGUGCUGCCACU-UUGCCCCACCGCCCGCCAACAUGCCACUUUCCCAUUGCACUCCCCACUG-------CCCC
....((((.((((((((((((..(((.((((....)))).(((((.....)))))....-..............)))...))))))))).....)))..))))......-------.... ( -36.70)
>DroYak_CAF1 53748 113 + 1
AAACGGAGACAAAAGUGGCAUCAGGCAGCCUCAACAGGCAGCAGCUACGUGCUGCCACUGCUGCCCCACCGCU--CCAUCAUGCCACUUCCAUGCCCCAAC-----ACCACCCCCACCCC
....((.(.((.(((((((((..((((((.......(((((((......)))))))...)))))).....(..--....))))))))))...))).))...-----.............. ( -34.20)
>consensus
AAACGGAGACAAAAGUGGCAUCAGGCAGCCUCAACAGGCAGCAGCUACGUGCUGCCACU_UUGCCCCACCGC___CCAACAUGCCACUUCCACAUUGCACUCCCC_CUC_CCCCC_CCCC
....(....)..(((((((((..((((((((....)))).(((((.....)))))......))))...............)))))))))............................... (-30.40 = -30.40 +  -0.00)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 6

Location 5,404,718 – 5,404,831
Length 113
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 80.11
Mean single sequence MFE -48.17
Consensus MFE -37.57
Energy contribution -36.91
Covariance contribution -0.66
Combinations/Pair 1.12
Mean z-score -2.66
Structure conservation index 0.78
SVM decision value 2.38
SVM RNA-class probability 0.993207
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 5404718 113 - 23771897
GGGGGGGGGGAGAGCGGGGAGUGCAAUGUGGAAGUGGCAUGGUG------GGUGGGGCAA-AGUGGCAGCACGUAGCUGCUGCCUGUUGAGGCUGCCUGAUGCCACUUUUGUCUCCGUUU
...........((((((((........(..((((((((((((..------(.(..((((.-.(..(((((.....)))))..).))))..).)..))..))))))))))..))))))))) ( -46.90)
>DroSim_CAF1 50550 112 - 1
GGGG-------CAGUGGGGAGUGCAAUGGGAAAGUGGCAUGUUGGCGGGCGGUGGGGCAA-AGUGGCAGCACGUAGCUGCUGCCUGUUGAGGCUGCCUGAUGCCACUUUUGUCUCCGUUU
((((-------((.(....).))).....(((((((((((.....((((((((....(((-...(((((((......)))))))..)))..)))))))))))))))))))...))).... ( -47.10)
>DroYak_CAF1 53748 113 - 1
GGGGUGGGGGUGGU-----GUUGGGGCAUGGAAGUGGCAUGAUGG--AGCGGUGGGGCAGCAGUGGCAGCACGUAGCUGCUGCCUGUUGAGGCUGCCUGAUGCCACUUUUGUCUCCGUUU
((((..((((((((-----((..((.(((....))).).......--.(((((....((((((..(((((.....)))))..).)))))..))))))..))))))))))..)).)).... ( -50.50)
>consensus
GGGG_GGGGG_GAG_GGGGAGUGCAAUGUGGAAGUGGCAUGAUGG___GCGGUGGGGCAA_AGUGGCAGCACGUAGCUGCUGCCUGUUGAGGCUGCCUGAUGCCACUUUUGUCUCCGUUU
((((.........((.......))...(..(((((((((.............(.(((((.....((((((.....))))))((((....))))))))).))))))))))..))))).... (-37.57 = -36.91 +  -0.66)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:20:57 2006