Locus 4696

Sequence ID 3R_DroMel_CAF1
Location 12,347,138 – 12,347,276
Length 138
Max. P 0.827971
window7719 window7720 window7721

overview

Window 9

Location 12,347,138 – 12,347,237
Length 99
Sequences 5
Columns 102
Reading direction forward
Mean pairwise identity 96.01
Mean single sequence MFE -24.54
Consensus MFE -19.08
Energy contribution -19.32
Covariance contribution 0.24
Combinations/Pair 1.04
Mean z-score -2.30
Structure conservation index 0.78
SVM decision value 0.70
SVM RNA-class probability 0.827971
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 12347138 99 + 27905053
CCAAAAGAGAUCUGUAUGCAUAAAAGCCGAAAAUGUCAUCAUU---UUCUUUUUUUAUGCCCGUUGAAGCGCAAAAUAUCACUCAUACGCCCCAUGGCGAGG
((....(((........(((((((((..(((((((....))))---)))..))))))))).(((....)))..........)))...((((....)))).)) ( -24.90)
>DroSec_CAF1 15911 99 + 1
CCAAAAGAGAUCAGUAUGCAUAAAAGCCGAAAAUGUCAUCAUU---UUCUUUUUUUAUGCUCGUUGAAGCGCAAAAUAUCACUCAUACGCCCCAUGGCGAGG
((....(((........(((((((((..(((((((....))))---)))..))))))))).(((....)))..........)))...((((....)))).)) ( -25.10)
>DroSim_CAF1 15041 99 + 1
CCAAAAGAGAUCAGUAUGCAUAAAAGCCGAAAAUGUCAUCAUU---UUCUUUUUUUAUGCUCGUUGAAGCGCAAAAUAUCACUCAUACGCCCCAUGGCGAGG
((....(((........(((((((((..(((((((....))))---)))..))))))))).(((....)))..........)))...((((....)))).)) ( -25.10)
>DroEre_CAF1 15809 99 + 1
CCAAAAGAGAUCUGUAUGCAUAAAAGCCGAAAAUGUCAUCAUU---UUCUUUUUUUAUGCUCGUUGAAGCGCAAAAUAUCACUCAUACGCCCCAUGGCGAGG
((....(((........(((((((((..(((((((....))))---)))..))))))))).(((....)))..........)))...((((....)))).)) ( -25.10)
>DroYak_CAF1 11913 102 + 1
CCAAACGAUAUCAGUAUGCAUAAAAGCCGAAAAUGUCAUCAUCAAAUUCUUUUUUUAUGCCCGCUGAAGCGCAAAAUAUCACUCAUACGCCCCAUGGCGAGG
((...((...(((((..(((((((((..(((..((.......))..)))..)))))))))..)))))..))................((((....)))).)) ( -22.50)
>consensus
CCAAAAGAGAUCAGUAUGCAUAAAAGCCGAAAAUGUCAUCAUU___UUCUUUUUUUAUGCUCGUUGAAGCGCAAAAUAUCACUCAUACGCCCCAUGGCGAGG
((....(((........(((((((((..(((((((....))))...)))..))))))))).(((....)))..........)))...((((....)))).)) (-19.08 = -19.32 +   0.24)

alignment

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secondary structure

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dotplot

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Window 0

Location 12,347,138 – 12,347,237
Length 99
Sequences 5
Columns 102
Reading direction reverse
Mean pairwise identity 96.01
Mean single sequence MFE -27.54
Consensus MFE -22.46
Energy contribution -22.06
Covariance contribution -0.40
Combinations/Pair 1.07
Mean z-score -1.79
Structure conservation index 0.82
SVM decision value 0.62
SVM RNA-class probability 0.802515
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 12347138 99 - 27905053
CCUCGCCAUGGGGCGUAUGAGUGAUAUUUUGCGCUUCAACGGGCAUAAAAAAAGAA---AAUGAUGACAUUUUCGGCUUUUAUGCAUACAGAUCUCUUUUGG
.....((.(((((((((.((......)).)))))))))..))((((((((...(((---((((....)))))))...))))))))...((((.....)))). ( -28.40)
>DroSec_CAF1 15911 99 - 1
CCUCGCCAUGGGGCGUAUGAGUGAUAUUUUGCGCUUCAACGAGCAUAAAAAAAGAA---AAUGAUGACAUUUUCGGCUUUUAUGCAUACUGAUCUCUUUUGG
.....((((((((((((.((......)).)))))))))....((((((((...(((---((((....)))))))...))))))))..............))) ( -27.40)
>DroSim_CAF1 15041 99 - 1
CCUCGCCAUGGGGCGUAUGAGUGAUAUUUUGCGCUUCAACGAGCAUAAAAAAAGAA---AAUGAUGACAUUUUCGGCUUUUAUGCAUACUGAUCUCUUUUGG
.....((((((((((((.((......)).)))))))))....((((((((...(((---((((....)))))))...))))))))..............))) ( -27.40)
>DroEre_CAF1 15809 99 - 1
CCUCGCCAUGGGGCGUAUGAGUGAUAUUUUGCGCUUCAACGAGCAUAAAAAAAGAA---AAUGAUGACAUUUUCGGCUUUUAUGCAUACAGAUCUCUUUUGG
..(((...(((((((((.((......)).))))))))).)))((((((((...(((---((((....)))))))...))))))))...((((.....)))). ( -28.60)
>DroYak_CAF1 11913 102 - 1
CCUCGCCAUGGGGCGUAUGAGUGAUAUUUUGCGCUUCAGCGGGCAUAAAAAAAGAAUUUGAUGAUGACAUUUUCGGCUUUUAUGCAUACUGAUAUCGUUUGG
..((((..(((((((((.((......)).)))))))))))))((((((((...(((..((.......))..)))...))))))))................. ( -25.90)
>consensus
CCUCGCCAUGGGGCGUAUGAGUGAUAUUUUGCGCUUCAACGAGCAUAAAAAAAGAA___AAUGAUGACAUUUUCGGCUUUUAUGCAUACUGAUCUCUUUUGG
..(((...(((((((((.((......)).))))))))).)))((((((((...(((...((((....)))))))...))))))))................. (-22.46 = -22.06 +  -0.40)

alignment

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secondary structure

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dotplot

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Window 1

Location 12,347,162 – 12,347,276
Length 114
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 78.87
Mean single sequence MFE -34.38
Consensus MFE -21.54
Energy contribution -23.40
Covariance contribution 1.86
Combinations/Pair 1.14
Mean z-score -1.53
Structure conservation index 0.63
SVM decision value 0.28
SVM RNA-class probability 0.664020
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 12347162 114 - 27905053
GCGUGGAAAUCUCUUGCGGCCUAAUGAGCCGUACUUGGG---CCUCGCCAUGGGGCGUAUGAGUGAUAUUUUGCGCUUCAACGGGCAUAAAAAAAGAA---AAUGAUGACAUUUUCGGCU
..............(((((((....).))))))....((---((..(((.(((((((((.((......)).)))))))))...))).........(((---((((....))))))))))) ( -37.20)
>DroPse_CAF1 17062 92 - 1
GAG--------CCA--UGGCCUAAUGAGCCGUACUUGGGAGCCAGCGCCAUGGGGCGUAUGGGUGAUAUUUUUCGCUUCAGCGGGCAACAAAU--AAA---AAUGA-------------U
..(--------(((--(((((....).)))))..(((((..((((((((....))))).)))((((......)))))))))..))).......--...---.....-------------. ( -26.50)
>DroSec_CAF1 15935 114 - 1
GCGUGGAAAUCUCAUGCGGCCUAAUGAGCCGUACUUGGG---CCUCGCCAUGGGGCGUAUGAGUGAUAUUUUGCGCUUCAACGAGCAUAAAAAAAGAA---AAUGAUGACAUUUUCGGCU
((((((.....))))))(((((((..........)))))---))..(((.(((((((((.((......)).)))))))))...............(((---((((....)))))))))). ( -38.40)
>DroSim_CAF1 15065 114 - 1
GCGUGGAAAUCUCAUGCGGCCUAAUGAGCCGUACUUGGG---CCUCGCCAUGGGGCGUAUGAGUGAUAUUUUGCGCUUCAACGAGCAUAAAAAAAGAA---AAUGAUGACAUUUUCGGCU
((((((.....))))))(((((((..........)))))---))..(((.(((((((((.((......)).)))))))))...............(((---((((....)))))))))). ( -38.40)
>DroYak_CAF1 11937 117 - 1
GCGUGGAAAUCUCUUGCGGCCUAAUGAGCCGUACUCGGG---CCUCGCCAUGGGGCGUAUGAGUGAUAUUUUGCGCUUCAGCGGGCAUAAAAAAAGAAUUUGAUGAUGACAUUUUCGGCU
((.(((((((.((.(((((((....).)))))).....(---((.(((..(((((((((.((......)).))))))))))))))).....................)).))))))))). ( -37.20)
>DroPer_CAF1 12877 92 - 1
GAG--------CCA--UGGCCUAAUGAGCCAUACUUGGGAGCCCACGCCAUGGGGCGUAUGGGUGAUAUUUUUCGCUUCAGCGGGCAACAAAU--AAA---AAUGA-------------U
...--------...--..((((..((((((((((.(((....))).(((....)))))))))((((......))))))))..)))).......--...---.....-------------. ( -28.60)
>consensus
GCGUGGAAAUCUCAUGCGGCCUAAUGAGCCGUACUUGGG___CCUCGCCAUGGGGCGUAUGAGUGAUAUUUUGCGCUUCAACGGGCAUAAAAAAAGAA___AAUGAUGACAUUUUCGGCU
..(.((....(((((((((((....).))))))..))))...)).)(((.(((((((((.((......)).)))))))))...))).................................. (-21.54 = -23.40 +   1.86)

alignment

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secondary structure

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dotplot

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Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:36:50 2006