Locus 706

Sequence ID X_DroMel_CAF1
Location 1,941,077 – 1,941,210
Length 133
Max. P 0.993984
window1132 window1133 window1134

overview

Window 2

Location 1,941,077 – 1,941,172
Length 95
Sequences 4
Columns 116
Reading direction forward
Mean pairwise identity 76.61
Mean single sequence MFE -35.15
Consensus MFE -21.24
Energy contribution -22.55
Covariance contribution 1.31
Combinations/Pair 1.14
Mean z-score -1.74
Structure conservation index 0.60
SVM decision value 0.14
SVM RNA-class probability 0.602461
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 1941077 95 + 22224390
CCGAAACUCGUUCGCAU----CCAUUUGCGGCAAAUGCCAGAAGCUGCUUCGCCUGGCCAAGCUGGUCGU--------CUGAUCGCGUUUCGCGAUCUAAGCGAUC---------U
............((((.----.....))))((....(((((..((......)))))))...)).((((((--------..(((((((...)))))))...))))))---------. ( -31.90)
>DroSec_CAF1 3641 93 + 1
-CGAAACCCGUUCGCAU----CCAUUUGCGGCAAAUGCCAAAAGCUGCUCCGCCUGGCCAAGCUGCUAGU--------CUGAUCGCGUUUCGCGAUCUAAGCGAUC----------
-..........((((..----......(((((....((((...((......)).))))...)))))....--------..(((((((...)))))))...))))..---------- ( -29.00)
>DroEre_CAF1 4200 112 + 1
CCGAAACUCGUUCGCAGCCAGCCAUUUGCGGCAAAUGCCAAAAGCCGCUUCGCGUGGCCAAGCUGAUCGGCUGAUCGGCUGAUC----UUGGCGAUCUUAGCGAUCUCAGCGAUCU
.........(.((((.(((((((((..(((((...........))))).....)))))......((((((((....))))))))----.))))((((.....))))...)))).). ( -42.40)
>DroYak_CAF1 3908 111 + 1
CCGAAACUUGUUCGCAG----CCAUUUGUGGCAAAUGCCAAAAGCUGCUUCGCUUGGCCAAG-UGCUCUGCUGCUUCGCUGAUCGCGUUUCGUGAUCUAAGCGAUCUUAGCGAUCU
..((.(((((..(((((----(......((((....))))...))))).......)..))))-)..))(((((..((((((((((((...)))))))..)))))...))))).... ( -37.31)
>consensus
CCGAAACUCGUUCGCAG____CCAUUUGCGGCAAAUGCCAAAAGCUGCUUCGCCUGGCCAAGCUGCUCGG________CUGAUCGCGUUUCGCGAUCUAAGCGAUC_________U
...........((((............(((((....(((((..((......)))))))...)))))..............((((((.....))))))...))))............ (-21.24 = -22.55 +   1.31) 

alignment

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secondary structure

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dotplot

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Window 3

Location 1,941,113 – 1,941,210
Length 97
Sequences 4
Columns 114
Reading direction forward
Mean pairwise identity 77.96
Mean single sequence MFE -38.38
Consensus MFE -20.94
Energy contribution -22.38
Covariance contribution 1.44
Combinations/Pair 1.08
Mean z-score -2.51
Structure conservation index 0.55
SVM decision value 1.35
SVM RNA-class probability 0.945384
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 1941113 97 + 22224390
GAAGCUGCUUCGCCUGGCCAAGCUGGUCGU--------CUGAUCGCGUUUCGCGAUCUAAGCGAUC---------UUAGCGUUCUGCAGUCAGAUCGAUUAAAUCACUCGGCUA
..((((((((.((...)).))))(((((((--------(((((.(((...(((((((.....))))---------...)))...))).)))))).))))))........)))). ( -31.10)
>DroSec_CAF1 3676 96 + 1
AAAGCUGCUCCGCCUGGCCAAGCUGCUAGU--------CUGAUCGCGUUUCGCGAUCUAAGCGAUC----------UAGCGAUCUGCAGUAAGAUCGAUUAAAUCACUCGGCUA
..(((((....(((((((......))))).--------..(((((((...)))))))...))(((.----------(((((((((......)))))).))).)))...))))). ( -32.50)
>DroEre_CAF1 4240 109 + 1
AAAGCCGCUUCGCGUGGCCAAGCUGAUCGGCUGAUCGGCUGAUC----UUGGCGAUCUUAGCGAUCUCAGCGAUCUUAGCGAGCUGCAGUCAGAUCGAUUA-AGCACUCGGCUA
..(((((((((((...(((((...((((((((....))))))))----)))))((((.....))))...))))....)))(((.(((((((.....)))).-.)))))))))). ( -43.90)
>DroYak_CAF1 3944 113 + 1
AAAGCUGCUUCGCUUGGCCAAG-UGCUCUGCUGCUUCGCUGAUCGCGUUUCGUGAUCUAAGCGAUCUUAGCGAUCUUGGCGAUCUGCAGUCAGAUCGAUUAAAGCACUCGGCUA
.((((......))))((((.((-(((((((((((.(((((((((((...((((.......)))).....))))))..)))))...)))).)))).........))))).)))). ( -46.00)
>consensus
AAAGCUGCUUCGCCUGGCCAAGCUGCUCGG________CUGAUCGCGUUUCGCGAUCUAAGCGAUC_________UUAGCGAUCUGCAGUCAGAUCGAUUAAAGCACUCGGCUA
..(((((..((((..(((...)))................((((((.....))))))...))))...............(((((((....)))))))...........))))). (-20.94 = -22.38 +   1.44) 

alignment

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secondary structure

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dotplot

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Window 4

Location 1,941,113 – 1,941,210
Length 97
Sequences 4
Columns 114
Reading direction reverse
Mean pairwise identity 77.96
Mean single sequence MFE -38.38
Consensus MFE -22.90
Energy contribution -24.78
Covariance contribution 1.88
Combinations/Pair 1.04
Mean z-score -2.75
Structure conservation index 0.60
SVM decision value 2.44
SVM RNA-class probability 0.993984
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 1941113 97 - 22224390
UAGCCGAGUGAUUUAAUCGAUCUGACUGCAGAACGCUAA---------GAUCGCUUAGAUCGCGAAACGCGAUCAG--------ACGACCAGCUUGGCCAGGCGAAGCAGCUUC
..(((((((....(((.((((((....((.....))..)---------))))).)))(((((((...)))))))..--------.......))))))).((((......)))). ( -33.40)
>DroSec_CAF1 3676 96 - 1
UAGCCGAGUGAUUUAAUCGAUCUUACUGCAGAUCGCUA----------GAUCGCUUAGAUCGCGAAACGCGAUCAG--------ACUAGCAGCUUGGCCAGGCGGAGCAGCUUU
(((.(((((((((((..((((((......)))))).))----------)))))))).(((((((...))))))).)--------.)))((.((((.((...)).)))).))... ( -36.70)
>DroEre_CAF1 4240 109 - 1
UAGCCGAGUGCU-UAAUCGAUCUGACUGCAGCUCGCUAAGAUCGCUGAGAUCGCUAAGAUCGCCAA----GAUCAGCCGAUCAGCCGAUCAGCUUGGCCACGCGAAGCGGCUUU
((((.((...((-((..((((((....((.....))..)))))).)))).)))))).((((.....----))))((((((((....)))).((((.((...)).)))))))).. ( -37.40)
>DroYak_CAF1 3944 113 - 1
UAGCCGAGUGCUUUAAUCGAUCUGACUGCAGAUCGCCAAGAUCGCUAAGAUCGCUUAGAUCACGAAACGCGAUCAGCGAAGCAGCAGAGCA-CUUGGCCAAGCGAAGCAGCUUU
..((((((((((((....((((((....))))))((.....(((((..((((((..............)))))))))))....))))))))-)))))).((((......)))). ( -46.04)
>consensus
UAGCCGAGUGAUUUAAUCGAUCUGACUGCAGAUCGCUAA_________GAUCGCUUAGAUCGCGAAACGCGAUCAG________ACGAGCAGCUUGGCCAGGCGAAGCAGCUUU
..(((((((........(((((((....)))))))......................((((((.....)))))).................))))))).((((......)))). (-22.90 = -24.78 +   1.88) 

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 09:51:39 2006