Locus 4121

Sequence ID 3L_DroMel_CAF1
Location 12,025,505 – 12,025,602
Length 97
Max. P 0.999985
window6408 window6409

overview

Window 8

Location 12,025,505 – 12,025,602
Length 97
Sequences 4
Columns 100
Reading direction forward
Mean pairwise identity 73.43
Mean single sequence MFE -37.26
Consensus MFE -23.35
Energy contribution -24.66
Covariance contribution 1.31
Combinations/Pair 1.16
Mean z-score -3.81
Structure conservation index 0.63
SVM decision value 5.37
SVM RNA-class probability 0.999985
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 12025505 97 + 23771897
UCUGCAACAUGUGCAACACCGGCAGCAGCAACAUCC--AUGCAUUUACUGCUGGCGGUGCAGGCAACUUGUCAGGUUGCAGA-AACUUCUGCAACACGUU
.((((((....(((..(((((.((((((........--.........)))))).)))))...)))..))).)))((((((((-....))))))))..... ( -38.73)
>DroSim_CAF1 42526 89 + 1
UCUGCAACAUGUGCAACACCGGCAGCAGCAACAUUU----------GCUGCUGGCGGUGCAGGCAACUUGUCAGGUUGCAGA-AACUUUUGCAACACGUU
.((((((....(((..(((((.((((((((.....)----------))))))).)))))...)))..))).)))((((((((-....))))))))..... ( -42.30)
>DroEre_CAF1 45587 95 + 1
UCUGCAACAACUGCUUCACCGGCAGCAGCAACAUC---AUGCAUUUGCUGCUGGUG-AGCAGGCGACUUGUCAGGUUGCAGA-AACUUCUGCAACACGUU
.((((((...(((((.((((((((((((((.....---.)))...)))))))))))-))))).....))).)))((((((((-....))))))))..... ( -46.10)
>DroWil_CAF1 49146 98 + 1
AAGGAAAGUUGUGCAA--GCGACAGCAUUUAAGUGUGUGUGUGUGUCCCUCUGUGUGUGCAGUCAAGUUGUCAGGCGGCAGAAAACUUCUGCAACAUGUU
..(((..(((((....--))))).((((......)))).......)))....((((.(((((.....(((((....))))).......)))))))))... ( -21.90)
>consensus
UCUGCAACAUGUGCAACACCGGCAGCAGCAACAUCU__AUGCAUUUGCUGCUGGCGGUGCAGGCAACUUGUCAGGUUGCAGA_AACUUCUGCAACACGUU
...........((((...((((((((((................))))))))))...))))(((.....)))..((((((((.....))))))))..... (-23.35 = -24.66 +   1.31)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 9

Location 12,025,505 – 12,025,602
Length 97
Sequences 4
Columns 100
Reading direction reverse
Mean pairwise identity 73.43
Mean single sequence MFE -34.59
Consensus MFE -23.25
Energy contribution -23.87
Covariance contribution 0.62
Combinations/Pair 1.29
Mean z-score -3.25
Structure conservation index 0.67
SVM decision value 5.05
SVM RNA-class probability 0.999970
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 12025505 97 - 23771897
AACGUGUUGCAGAAGUU-UCUGCAACCUGACAAGUUGCCUGCACCGCCAGCAGUAAAUGCAU--GGAUGUUGCUGCUGCCGGUGUUGCACAUGUUGCAGA
.....((((((((....-))))))))((((((.((.((..((((((.((((((((...(((.--...))))))))))).)))))).)))).)))..))). ( -40.50)
>DroSim_CAF1 42526 89 - 1
AACGUGUUGCAAAAGUU-UCUGCAACCUGACAAGUUGCCUGCACCGCCAGCAGC----------AAAUGUUGCUGCUGCCGGUGUUGCACAUGUUGCAGA
(((((((.(((......-...(((((.......)))))..((((((.(((((((----------(.....)))))))).))))))))))))))))..... ( -38.50)
>DroEre_CAF1 45587 95 - 1
AACGUGUUGCAGAAGUU-UCUGCAACCUGACAAGUCGCCUGCU-CACCAGCAGCAAAUGCAU---GAUGUUGCUGCUGCCGGUGAAGCAGUUGUUGCAGA
.....((((((((....-))))))))(((.(((..((.(((((-((((.((((((...(((.---.....))))))))).)))).))))).)))))))). ( -42.00)
>DroWil_CAF1 49146 98 - 1
AACAUGUUGCAGAAGUUUUCUGCCGCCUGACAACUUGACUGCACACACAGAGGGACACACACACACACUUAAAUGCUGUCGC--UUGCACAACUUUCCUU
....(((((((((((((.((........)).)))))..))))).)))..(((.((((((..............)).)))).)--)).............. ( -17.34)
>consensus
AACGUGUUGCAGAAGUU_UCUGCAACCUGACAAGUUGCCUGCACCGCCAGCAGCAAAUGCAU__AGAUGUUGCUGCUGCCGGUGUUGCACAUGUUGCAGA
..((.((((((((.....)))))))).))..........((((.((((.((((((..................)))))).)))).))))........... (-23.25 = -23.87 +   0.62)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:14:58 2006