Locus 1729

Sequence ID 2L_DroMel_CAF1
Location 4,750,411 – 4,750,505
Length 94
Max. P 0.883010
window2775 window2776

overview

Window 5

Location 4,750,411 – 4,750,505
Length 94
Sequences 6
Columns 117
Reading direction forward
Mean pairwise identity 78.65
Mean single sequence MFE -31.58
Consensus MFE -18.93
Energy contribution -19.46
Covariance contribution 0.53
Combinations/Pair 1.12
Mean z-score -1.99
Structure conservation index 0.60
SVM decision value 0.84
SVM RNA-class probability 0.863066
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 4750411 94 + 22407834
------------GUGGCAAGAGUAAAAGCAAUUUAGUUUACUGCAAAUGCUGG-CCGGCGGGCCUUUGUUCUGUUC----------UGCUGCCUUCAGCAUUUUGGCUGAUUCAUGG
------------(..(((((((((((((((.(((((....))).)).))))((-((....))))))))))))....----------)))..)..(((((......)))))....... ( -26.20)
>DroPse_CAF1 216621 102 + 1
GCAUAAGCAGUAGCAGCAGCAGUAAAAGCAAUUUAGUUUACUGCAAAUGUUAG-CCGGCGGC----UACAAUGUUC----------UGCUGCCCUCAGCAUUUUAGCUGAUUCAUGG
.(((..(((((((.(((((((((((..((......)))))))))...(((.((-((...)))----)))).)))))----------))))))..(((((......)))))...))). ( -35.10)
>DroEre_CAF1 187412 94 + 1
------------GUGGCAAGAGUAAAAGCAAUUUAGUUUACUGCAAAUGCUGG-CCGGCGGCUCUUUGUUCUGUUC----------UGCUGCCUUCAGCAUUUUGGCUGAUUCAUGG
------------....((.((((...(((....(((....))).(((((((((-..((((((..............----------.)))))).)))))))))..))).)))).)). ( -26.86)
>DroYak_CAF1 185448 104 + 1
------------GUGGCAAGAGUAAAAGCAAUUUAGUUUACUGCAAAUGCUGG-CCGGCGGCCCUUUGUUCUGCUCUGUACUGUUGUGCUGCCUUCAGCAUUUUGGCUGAUUCAUGG
------------..((((((((((..((((.(((((....))).)).))))((-((...))))........))))))((((....)))))))).(((((......)))))....... ( -31.10)
>DroAna_CAF1 198023 95 + 1
------------GAGGCGGCAGUAAAAGCAAUUUAGUUUACUGCAAAUGUUGGGCUGGCCUGGCGGUGCAUUGUUC----------UGCUGCCUUCAGCAUUUUAGCUGAUUCAUGG
------------.(((((((((...((((......))))..((((..(((..((....))..))).)))).....)----------))))))))(((((......)))))....... ( -35.10)
>DroPer_CAF1 224337 102 + 1
GCAUAAGCAGUAGCAGCAGCAGUAAAAGCAAUUUAGUUUACUGCAAAUGUUAG-CCGGCGGC----UACAAUGUUC----------UGCUGCCCUCAGCAUUUUAGCUGAUUCAUGG
.(((..(((((((.(((((((((((..((......)))))))))...(((.((-((...)))----)))).)))))----------))))))..(((((......)))))...))). ( -35.10)
>consensus
____________GUGGCAACAGUAAAAGCAAUUUAGUUUACUGCAAAUGCUGG_CCGGCGGC_CUUUGCACUGUUC__________UGCUGCCUUCAGCAUUUUAGCUGAUUCAUGG
.............((((...(((((..((......)))))))..(((((((((...((((((.........................)))))).)))))))))..))))........ (-18.93 = -19.46 +   0.53)

alignment

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secondary structure

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dotplot

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Window 6

Location 4,750,411 – 4,750,505
Length 94
Sequences 6
Columns 117
Reading direction reverse
Mean pairwise identity 78.65
Mean single sequence MFE -27.76
Consensus MFE -13.90
Energy contribution -13.77
Covariance contribution -0.14
Combinations/Pair 1.12
Mean z-score -2.43
Structure conservation index 0.50
SVM decision value 0.92
SVM RNA-class probability 0.883010
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 4750411 94 - 22407834
CCAUGAAUCAGCCAAAAUGCUGAAGGCAGCA----------GAACAGAACAAAGGCCCGCCGG-CCAGCAUUUGCAGUAAACUAAAUUGCUUUUACUCUUGCCAC------------
.......(((((......))))).(((((.(----------(...........((((....))-))((((.((..((....)).)).))))....)).)))))..------------ ( -25.40)
>DroPse_CAF1 216621 102 - 1
CCAUGAAUCAGCUAAAAUGCUGAGGGCAGCA----------GAACAUUGUA----GCCGCCGG-CUAACAUUUGCAGUAAACUAAAUUGCUUUUACUGCUGCUGCUACUGCUUAUGC
.(((((.(((((......))))).(((((((----------......((((----(((...))-)).)))...((((((((..........))))))))))))))).....))))). ( -33.80)
>DroEre_CAF1 187412 94 - 1
CCAUGAAUCAGCCAAAAUGCUGAAGGCAGCA----------GAACAGAACAAAGAGCCGCCGG-CCAGCAUUUGCAGUAAACUAAAUUGCUUUUACUCUUGCCAC------------
.......(((((......))))).(((.((.----------..............)).)))((-(.((.....(((((.......))))).......)).)))..------------ ( -20.96)
>DroYak_CAF1 185448 104 - 1
CCAUGAAUCAGCCAAAAUGCUGAAGGCAGCACAACAGUACAGAGCAGAACAAAGGGCCGCCGG-CCAGCAUUUGCAGUAAACUAAAUUGCUUUUACUCUUGCCAC------------
.......(((((......))))).(((((......((((.(((((((.......((((...))-)).((....))...........))))))))))).)))))..------------ ( -27.50)
>DroAna_CAF1 198023 95 - 1
CCAUGAAUCAGCUAAAAUGCUGAAGGCAGCA----------GAACAAUGCACCGCCAGGCCAGCCCAACAUUUGCAGUAAACUAAAUUGCUUUUACUGCCGCCUC------------
.......(((((......)))))((((.(((----------(.....((((......((....)).......))))((((......)))).....)))).)))).------------ ( -25.12)
>DroPer_CAF1 224337 102 - 1
CCAUGAAUCAGCUAAAAUGCUGAGGGCAGCA----------GAACAUUGUA----GCCGCCGG-CUAACAUUUGCAGUAAACUAAAUUGCUUUUACUGCUGCUGCUACUGCUUAUGC
.(((((.(((((......))))).(((((((----------......((((----(((...))-)).)))...((((((((..........))))))))))))))).....))))). ( -33.80)
>consensus
CCAUGAAUCAGCCAAAAUGCUGAAGGCAGCA__________GAACAGAACAAAG_GCCGCCGG_CCAACAUUUGCAGUAAACUAAAUUGCUUUUACUCCUGCCAC____________
.......(((((......))))).(((((................................(......)....(((((.......)))))........))))).............. (-13.90 = -13.77 +  -0.14)

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 10:09:38 2006