Locus 9064

Sequence ID 3R_DroMel_CAF1
Location 24,218,432 – 24,218,569
Length 137
Max. P 0.954007
window14513 window14514 window14515

overview

Window 3

Location 24,218,432 – 24,218,535
Length 103
Sequences 6
Columns 103
Reading direction forward
Mean pairwise identity 82.26
Mean single sequence MFE -27.13
Consensus MFE -18.75
Energy contribution -19.73
Covariance contribution 0.97
Combinations/Pair 1.11
Mean z-score -2.94
Structure conservation index 0.69
SVM decision value 0.98
SVM RNA-class probability 0.895052
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 24218432 103 + 27905053
UUGUGUGUGUGUGGGUGAGAAUUUGUUUGGCUUGUUGUUUUUGCCGUUUUGCUAAUUUCUCGGCAUAAUUAUGGCAAUUGCCGUAAAACGUUGGGUACAUAUA
.....(((((((((.((((((.((((.((((...........))))....)).)).)))))).)....(((((((....))))))).........)))))))) ( -26.80)
>DroSec_CAF1 41083 102 + 1
UUGUGUGUGUGUGGGCGAGAAUUUGUUUGGUUUGUUGUUUUUGCCGU-UUGCUAAUUUCUCGGCAUAAUUAUGGCAAUUGCCGUAAAAUGUUGGGUACAUAUA
.....(((((((((((((((((..............)))))))))..-..........((((((((..(((((((....))))))).)))))))))))))))) ( -30.84)
>DroSim_CAF1 45072 102 + 1
UUGUGUGUGUGUGGGCGAGAAUUUGUUUGGUUUGUUGUUUUUGCCGU-UUGCUAAUUUCUCGGCAUAAUUAUGGCAAUUGCCGUAAAAUGUUGGGUACAUAUA
.....(((((((((((((((((..............)))))))))..-..........((((((((..(((((((....))))))).)))))))))))))))) ( -30.84)
>DroEre_CAF1 45854 98 + 1
GUGCGUGUGUG----UGAGAGGUUGUUUGGCUUGUUGUUUUUGCAGU-UUGCUAAUUUCUCGGCAUAAUUAUGGCAAUUGCCGUAAAAUGUUGGGUACAUAUA
((((.(((((.----((((((((....((((..(((((....)))))-..))))))))))))))))).(((((((....)))))))........))))..... ( -28.70)
>DroYak_CAF1 43638 81 + 1
---------------------GAAGUUUGGUUUGUUGUUUUUGCCGU-UUGCUAAUUUCUCGGCAUAAUUAUGGCAAUUGCCGUAAAAUGUUGGGUACAUAUA
---------------------..(((.((((..(.....)..)))).-..))).....((((((((..(((((((....))))))).))))))))........ ( -19.90)
>DroAna_CAF1 38812 80 + 1
-UGCGUGUGCG---------------UUGGCCUGUUGUU------GU-UUGCUAAUUUCUCAGCAUAAUUACGGCAAUUGCCGUAAAAUGUUGGGUACAUAUA
-...(((((((---------------(((((........------..-..))))))...(((((((..(((((((....))))))).)))))))))))))... ( -25.70)
>consensus
UUGUGUGUGUG_____GAGAAUUUGUUUGGCUUGUUGUUUUUGCCGU_UUGCUAAUUUCUCGGCAUAAUUAUGGCAAUUGCCGUAAAAUGUUGGGUACAUAUA
....(((((((...............(((((...................)))))...((((((((..(((((((....))))))).))))))))))))))). (-18.75 = -19.73 +   0.97)

alignment

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secondary structure

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dotplot

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Window 4

Location 24,218,432 – 24,218,535
Length 103
Sequences 6
Columns 103
Reading direction reverse
Mean pairwise identity 82.26
Mean single sequence MFE -13.83
Consensus MFE -9.72
Energy contribution -9.72
Covariance contribution 0.00
Combinations/Pair 1.00
Mean z-score -2.22
Structure conservation index 0.70
SVM decision value 0.61
SVM RNA-class probability 0.798404
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 24218432 103 - 27905053
UAUAUGUACCCAACGUUUUACGGCAAUUGCCAUAAUUAUGCCGAGAAAUUAGCAAAACGGCAAAAACAACAAGCCAAACAAAUUCUCACCCACACACACACAA
....(((.......(((((..(((....)))........((..(....)..)))))))(((...........)))..)))....................... ( -15.60)
>DroSec_CAF1 41083 102 - 1
UAUAUGUACCCAACAUUUUACGGCAAUUGCCAUAAUUAUGCCGAGAAAUUAGCAA-ACGGCAAAAACAACAAACCAAACAAAUUCUCGCCCACACACACACAA
....(((..............(((....))).......(((((............-.)))))...)))................................... ( -11.82)
>DroSim_CAF1 45072 102 - 1
UAUAUGUACCCAACAUUUUACGGCAAUUGCCAUAAUUAUGCCGAGAAAUUAGCAA-ACGGCAAAAACAACAAACCAAACAAAUUCUCGCCCACACACACACAA
....(((..............(((....))).......(((((............-.)))))...)))................................... ( -11.82)
>DroEre_CAF1 45854 98 - 1
UAUAUGUACCCAACAUUUUACGGCAAUUGCCAUAAUUAUGCCGAGAAAUUAGCAA-ACUGCAAAAACAACAAGCCAAACAACCUCUCA----CACACACGCAC
....((((.............(((....))).......(((..(....)..))).-..))))..........................----........... ( -11.10)
>DroYak_CAF1 43638 81 - 1
UAUAUGUACCCAACAUUUUACGGCAAUUGCCAUAAUUAUGCCGAGAAAUUAGCAA-ACGGCAAAAACAACAAACCAAACUUC---------------------
....(((..............(((....))).......(((((............-.)))))...)))..............--------------------- ( -11.82)
>DroAna_CAF1 38812 80 - 1
UAUAUGUACCCAACAUUUUACGGCAAUUGCCGUAAUUAUGCUGAGAAAUUAGCAA-AC------AACAACAGGCCAA---------------CGCACACGCA-
.....((..((......(((((((....)))))))...((((((....)))))).-..------.......))...)---------------)((....)).- ( -20.80)
>consensus
UAUAUGUACCCAACAUUUUACGGCAAUUGCCAUAAUUAUGCCGAGAAAUUAGCAA_ACGGCAAAAACAACAAACCAAACAAAUUCUC_____CACACACACAA
....(((..............(((....))).......(((..(....)..)))...........)))................................... ( -9.72 =  -9.72 +   0.00)

alignment

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secondary structure

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dotplot

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Window 5

Location 24,218,465 – 24,218,569
Length 104
Sequences 6
Columns 104
Reading direction forward
Mean pairwise identity 94.19
Mean single sequence MFE -24.77
Consensus MFE -21.88
Energy contribution -21.93
Covariance contribution 0.06
Combinations/Pair 1.07
Mean z-score -1.90
Structure conservation index 0.88
SVM decision value 1.44
SVM RNA-class probability 0.954007
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 24218465 104 + 27905053
GUUGUUUUUGCCGUUUUGCUAAUUUCUCGGCAUAAUUAUGGCAAUUGCCGUAAAACGUUGGGUACAUAUAAAUUGGAAAUUAGUUAAUUUGCCGUUGCAUUGCU
..(((..(.((......((((((((((((((....(((((((....)))))))...)))))...((.......)))))))))))......)).)..)))..... ( -22.30)
>DroSec_CAF1 41116 103 + 1
GUUGUUUUUGCCGU-UUGCUAAUUUCUCGGCAUAAUUAUGGCAAUUGCCGUAAAAUGUUGGGUACAUAUAAAUUGGAAAUUAGUUAAUUUGCCGUUGCAUUGCU
..(((..(.((.((-(.((((((((((((((((..(((((((....))))))).)))))))...((.......))))))))))).)))..)).)..)))..... ( -25.30)
>DroSim_CAF1 45105 103 + 1
GUUGUUUUUGCCGU-UUGCUAAUUUCUCGGCAUAAUUAUGGCAAUUGCCGUAAAAUGUUGGGUACAUAUAAAUUGGAAAUUAGUUAAUUUACCGUUGCAUUGCU
..(((....((.((-..((((((((((((((((..(((((((....))))))).)))))))...((.......)))))))))))......)).)).)))..... ( -22.90)
>DroEre_CAF1 45883 103 + 1
GUUGUUUUUGCAGU-UUGCUAAUUUCUCGGCAUAAUUAUGGCAAUUGCCGUAAAAUGUUGGGUACAUAUAAAUUGGAAAUUAGUUAAUUUUCUGUUGCAUCGCU
(.(((....((((.-..((((((((((((((((..(((((((....))))))).)))))))...((.......))))))))))).......)))).))).)... ( -26.20)
>DroYak_CAF1 43650 103 + 1
GUUGUUUUUGCCGU-UUGCUAAUUUCUCGGCAUAAUUAUGGCAAUUGCCGUAAAAUGUUGGGUACAUAUAAAUUGGAAAUUAGUUAAUUUGCCGUUGCAUCGCU
(.(((..(.((.((-(.((((((((((((((((..(((((((....))))))).)))))))...((.......))))))))))).)))..)).)..))).)... ( -25.70)
>DroAna_CAF1 38829 97 + 1
GUUGUU------GU-UUGCUAAUUUCUCAGCAUAAUUACGGCAAUUGCCGUAAAAUGUUGGGUACAUAUAAAUUGAAAAUUAGUUAAUUUGCAGUUGCAUUGCC
((..((------((-..((((((((((((((((..(((((((....))))))).))))))))..((.......)).))))))))......))))..))...... ( -26.20)
>consensus
GUUGUUUUUGCCGU_UUGCUAAUUUCUCGGCAUAAUUAUGGCAAUUGCCGUAAAAUGUUGGGUACAUAUAAAUUGGAAAUUAGUUAAUUUGCCGUUGCAUUGCU
..(((............((((((((((((((((..(((((((....))))))).)))))))...((.......)))))))))))............)))..... (-21.88 = -21.93 +   0.06)

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 13:25:52 2006