Locus 1040

Sequence ID X_DroMel_CAF1
Location 3,024,185 – 3,024,345
Length 160
Max. P 0.958118
window1688 window1689

overview

Window 8

Location 3,024,185 – 3,024,305
Length 120
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 92.22
Mean single sequence MFE -50.08
Consensus MFE -42.35
Energy contribution -42.73
Covariance contribution 0.38
Combinations/Pair 1.15
Mean z-score -1.41
Structure conservation index 0.85
SVM decision value -0.04
SVM RNA-class probability 0.514416
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 3024185 120 - 22224390
CGGAAACGGGAUCACUGCGCUGUCGCUUGGGCAACGGCAUAUCCGAUUCAUCGUCGGACCAAUGAGCACCUGGCUGGCCAACACCCUGCGAUUGCAUGGCCACCUGCUUGUUGAGAUUCC
.(....)((((((.....(((((.((....)).)))))...((((((.....)))))).(((..((((...((.((((((......(((....)))))))))))))))..))).)))))) ( -47.20)
>DroSec_CAF1 4604 120 - 1
CGGAAACGGGAUCGCUGCGCUGGCGCUUGGGCAACGGCAUAUCCGAUUCAUCGUCGGACCAAUGAGCACCCGGCUGGCCAACACCUUGCGACUGCAGGGCCACCUGCUUGUUGAGGUUCC
.(....)((((((((((.(((((.((((((((....))...((((((.....)))))))))...)))..)))))))))..........((((.(((((....)))))..)))).)))))) ( -45.20)
>DroEre_CAF1 4622 120 - 1
CGGAAACGGGAUCACUGCGCUGCCGCUUGGGCAGCGGCAUAUCCGAUUCAUCGUCGGACCAAUGGGCACCCGGCUGGCCGACACCCUGCGACUGCAGGGCCACCUGUUUGUUGAGGUUAC
((....))((((...(((((((((.....)))))).))).))))........(((((.(((.(((....)))..))))))))..(((.((((.(((((....)))))..))))))).... ( -54.10)
>DroYak_CAF1 4550 120 - 1
CGGAAACGGGAUCACUGCGCUGCCUUUUGGGCAGCGGCAUAUCCGAUUCAUCGUCGGACCAAUGGGCGCCCGGCUGGCCGACUCCCUGCGACUGCAGGGCCACCUGUUUGUUGAGGUUGC
((....))((((...(((((((((.....)))))).))).))))........(((((.(((.(((....)))..))))))))..(((.((((.(((((....)))))..))))))).... ( -53.80)
>consensus
CGGAAACGGGAUCACUGCGCUGCCGCUUGGGCAACGGCAUAUCCGAUUCAUCGUCGGACCAAUGAGCACCCGGCUGGCCAACACCCUGCGACUGCAGGGCCACCUGCUUGUUGAGGUUCC
.(....)((((((..(((((((((.....)))))).)))..((((((.....)))))).(((..((((...((.(((((......((((....)))))))))))))))..))).)))))) (-42.35 = -42.73 +   0.38)

alignment

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secondary structure

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dotplot

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Window 9

Location 3,024,225 – 3,024,345
Length 120
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 93.89
Mean single sequence MFE -50.08
Consensus MFE -44.94
Energy contribution -44.75
Covariance contribution -0.19
Combinations/Pair 1.06
Mean z-score -2.24
Structure conservation index 0.90
SVM decision value 1.49
SVM RNA-class probability 0.958118
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 3024225 120 - 22224390
UGAUCACUGGCAUAGCCACCAUUGUUGCCCAGACCGACACCGGAAACGGGAUCACUGCGCUGUCGCUUGGGCAACGGCAUAUCCGAUUCAUCGUCGGACCAAUGAGCACCUGGCUGGCCA
........(((.((((((.....(((((((((...((..(((....)))..))...(((....))))))))))))((....((((((.....))))))))..........))))))))). ( -49.00)
>DroSec_CAF1 4644 120 - 1
UGAUCACUGGCGUAGCCACCAUUGUUGCCCAGACCCACACCGGAAACGGGAUCGCUGCGCUGGCGCUUGGGCAACGGCAUAUCCGAUUCAUCGUCGGACCAAUGAGCACCCGGCUGGCCA
........(((.(((((......(((((((((.......(((....))).......(((....))))))))))))((....((((((.....))))))))...........)))))))). ( -48.00)
>DroEre_CAF1 4662 120 - 1
UGAUCACUGGCAUAGCCACCAUUGUUGCCCAGGCCCACACCGGAAACGGGAUCACUGCGCUGCCGCUUGGGCAGCGGCAUAUCCGAUUCAUCGUCGGACCAAUGGGCACCCGGCUGGCCG
........(((.(((((((....))((((((.(((....(((....))).........((((((.....)))))))))...((((((.....))))))....))))))...)))))))). ( -52.80)
>DroYak_CAF1 4590 120 - 1
UGAUCACUGGCAUAGCCACCAUUGUUGCCCAGACCCACGCCGGAAACGGGAUCACUGCGCUGCCUUUUGGGCAGCGGCAUAUCCGAUUCAUCGUCGGACCAAUGGGCGCCCGGCUGGCCG
........(((.(((((.((((((.((((..........(((....))).........((((((.....))))))))))..((((((.....)))))).))))))......)))))))). ( -50.50)
>consensus
UGAUCACUGGCAUAGCCACCAUUGUUGCCCAGACCCACACCGGAAACGGGAUCACUGCGCUGCCGCUUGGGCAACGGCAUAUCCGAUUCAUCGUCGGACCAAUGAGCACCCGGCUGGCCA
........(((.(((((......(((((((((.......(((....))).......(((....))))))))))))((....((((((.....))))))))...........)))))))). (-44.94 = -44.75 +  -0.19)

alignment

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secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:00:07 2006