Locus 1792

Sequence ID 3R_DroMel_CAF1
Location 5,118,541 – 5,118,688
Length 147
Max. P 0.780005
window2952 window2953 window2954

overview

Window 2

Location 5,118,541 – 5,118,648
Length 107
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 84.58
Mean single sequence MFE -36.55
Consensus MFE -24.18
Energy contribution -24.55
Covariance contribution 0.37
Combinations/Pair 1.07
Mean z-score -1.68
Structure conservation index 0.66
SVM decision value 0.13
SVM RNA-class probability 0.598341
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 5118541 107 + 27905053
CACGCCCCUUCGCCU--ACAACCAC-----UGAUGGCUGACAGGG------AAAAGGGAAAAAAGUUGUGUUUGUCGCAGCGAUAUGUAAAACGCGUGGCUUAUCCGGAUUACCGGAUGC
((((((((((..(((--.((.(((.-----...))).))...)))------..)))))......((((((.....))))))............)))))...(((((((....))))))). ( -37.60)
>DroSim_CAF1 20721 107 + 1
CACGCCCCUUCGCCU--ACACCCAC-----UGAUGGCUGACAGGG------AAAAGGGAAAAAAGUUGUGUUUGUCGCAGCGAUAUGUAAAAUGCGUGGCUUAUCCGGAUUACCGGAUGC
((((((((((..(((--.((.(((.-----...))).))...)))------..)))))......((((((.....))))))............)))))...(((((((....))))))). ( -37.30)
>DroEre_CAF1 21567 111 + 1
CAUGCCCCUUCGCCCCAACGCCUCCC-----GUUGGCUGACAAG---CAAAAAAAGGGAAAAAACUUCUGUUUGUCGCAGCGAUAUGUAAAAUGCGUGGCUUAUCCGGAUUACCGGAUG-
...(((...((((.((((((.....)-----)))))..((((((---((....(((........))).))))))))...)))).((((.....))))))).(((((((....)))))))- ( -34.60)
>DroYak_CAF1 21596 119 + 1
CACGCCCCUUCGUCCUGCCGCCGCCCCUUCUGAUGGCUGACAAGGGACAAAAAAAGGGAAUAAAGUUCUGUUUGUCGCAGCGAUAUGUAAAAUGCGUGGCUUAUCCGGAUUACCGGAUG-
((((((((((.(((..((((.((.......)).)))).))))))))(((...(((.(((((...))))).)))((((...)))).))).....)))))...(((((((....)))))))- ( -36.70)
>consensus
CACGCCCCUUCGCCC__ACACCCAC_____UGAUGGCUGACAAGG______AAAAGGGAAAAAAGUUCUGUUUGUCGCAGCGAUAUGUAAAAUGCGUGGCUUAUCCGGAUUACCGGAUG_
((((((((((((((....................))).))..............))))......((((((.....))))))............)))))...(((((((....))))))). (-24.18 = -24.55 +   0.37)

alignment

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secondary structure

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Window 3

Location 5,118,574 – 5,118,688
Length 114
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 89.62
Mean single sequence MFE -31.77
Consensus MFE -27.83
Energy contribution -28.58
Covariance contribution 0.75
Combinations/Pair 1.00
Mean z-score -1.62
Structure conservation index 0.88
SVM decision value 0.55
SVM RNA-class probability 0.780005
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 5118574 114 + 27905053
CAGGG------AAAAGGGAAAAAAGUUGUGUUUGUCGCAGCGAUAUGUAAAACGCGUGGCUUAUCCGGAUUACCGGAUGCUGGAUGCUGGAGCGCACAAACAUUAGCACAACUCUCUAUU
.....------...(((((.....(((((((((((....(((..........)))(((((((((((((....))))))((.....))..)))).)))..)))..)))))))))))))... ( -32.80)
>DroSim_CAF1 20754 114 + 1
CAGGG------AAAAGGGAAAAAAGUUGUGUUUGUCGCAGCGAUAUGUAAAAUGCGUGGCUUAUCCGGAUUACCGGAUGCUGGAUGCUGGAGCGCACAAACAUUAGCACAACUCUCUAUU
.....------...(((((.....(((((((((((.((.(((.(((.....)))))).((((((((((....))))))((.....))..))))))))))))).)))).....)))))... ( -32.50)
>DroEre_CAF1 21602 110 + 1
CAAG---CAAAAAAAGGGAAAAAACUUCUGUUUGUCGCAGCGAUAUGUAAAAUGCGUGGCUUAUCCGGAUUACCGGAUG-------CUGGAGCGCACAAACAUUAGCACAACUCUCUAUU
....---.......(((((.....((..((((((((((.(((.(((.....))))))(((..((((((....)))))))-------))...))).)))))))..))......)))))... ( -30.00)
>DroYak_CAF1 21636 113 + 1
CAAGGGACAAAAAAAGGGAAUAAAGUUCUGUUUGUCGCAGCGAUAUGUAAAAUGCGUGGCUUAUCCGGAUUACCGGAUG-------CUGGAGCGCACAAACAUUAGCACAACCCUCUAUU
..(((((((((....((((......)))).))))))...((...((((....(((((..(.(((((((....)))))))-------..)..)))))...))))..)).....)))..... ( -31.80)
>consensus
CAAGG______AAAAGGGAAAAAAGUUCUGUUUGUCGCAGCGAUAUGUAAAAUGCGUGGCUUAUCCGGAUUACCGGAUG_______CUGGAGCGCACAAACAUUAGCACAACUCUCUAUU
..............(((((........((((((((((((((..(((((.....))))))))(((((((....)))))))............))).)))))))).........)))))... (-27.83 = -28.58 +   0.75)

alignment

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secondary structure

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Window 4

Location 5,118,574 – 5,118,688
Length 114
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 89.62
Mean single sequence MFE -29.95
Consensus MFE -22.81
Energy contribution -22.75
Covariance contribution -0.06
Combinations/Pair 1.04
Mean z-score -1.84
Structure conservation index 0.76
SVM decision value 0.45
SVM RNA-class probability 0.741023
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 5118574 114 - 27905053
AAUAGAGAGUUGUGCUAAUGUUUGUGCGCUCCAGCAUCCAGCAUCCGGUAAUCCGGAUAAGCCACGCGUUUUACAUAUCGCUGCGACAAACACAACUUUUUUCCCUUUU------CCCUG
...(((((((((((....((((.(((.(((...((.....))((((((....)))))).))))))(((..........)))...))))..)))))))))))........------..... ( -31.10)
>DroSim_CAF1 20754 114 - 1
AAUAGAGAGUUGUGCUAAUGUUUGUGCGCUCCAGCAUCCAGCAUCCGGUAAUCCGGAUAAGCCACGCAUUUUACAUAUCGCUGCGACAAACACAACUUUUUUCCCUUUU------CCCUG
...(((((((((((...((((..(((((.....((.....))((((((....))))))......)))))...)))).(((...)))....)))))))))))........------..... ( -30.20)
>DroEre_CAF1 21602 110 - 1
AAUAGAGAGUUGUGCUAAUGUUUGUGCGCUCCAG-------CAUCCGGUAAUCCGGAUAAGCCACGCAUUUUACAUAUCGCUGCGACAAACAGAAGUUUUUUCCCUUUUUUUG---CUUG
....(((((....(((..(((((((.(((...((-------(((((((....))))))..((...))............)))))))))))))..))).)))))..........---.... ( -28.20)
>DroYak_CAF1 21636 113 - 1
AAUAGAGGGUUGUGCUAAUGUUUGUGCGCUCCAG-------CAUCCGGUAAUCCGGAUAAGCCACGCAUUUUACAUAUCGCUGCGACAAACAGAACUUUAUUCCCUUUUUUUGUCCCUUG
...((((((.........(((((((.(((...((-------(((((((....))))))..((...))............)))))))))))))..........))))))............ ( -30.31)
>consensus
AAUAGAGAGUUGUGCUAAUGUUUGUGCGCUCCAG_______CAUCCGGUAAUCCGGAUAAGCCACGCAUUUUACAUAUCGCUGCGACAAACACAACUUUUUUCCCUUUU______CCCUG
........(((((((..((((..(((((.....((.....))((((((....))))))......)))))...))))...)).)))))................................. (-22.81 = -22.75 +  -0.06)

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 10:19:40 2006