Locus 2308

Sequence ID 2L_DroMel_CAF1
Location 6,260,944 – 6,261,065
Length 121
Max. P 0.951668
window3707 window3708 window3709

overview

Window 7

Location 6,260,944 – 6,261,034
Length 90
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 79.70
Mean single sequence MFE -19.62
Consensus MFE -13.16
Energy contribution -13.16
Covariance contribution 0.00
Combinations/Pair 1.00
Mean z-score -1.33
Structure conservation index 0.67
SVM decision value 0.14
SVM RNA-class probability 0.603056
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 6260944 90 + 22407834
AAAUGG---CAGA----------------------AACGGGAUUUUCAAACAUAUCGCAUAUACAAAAUGCAAACAUGUCUGGCAAACACAAAUCCCAUAAAUGUUU-UGUGC----CCC
....((---((((----------------------(((((((((((((.((((...((((.......))))....)))).))).......)))))))......))))-).)))----).. ( -18.71)
>DroVir_CAF1 122262 91 + 1
CAAUG------GA----------------------AAUGGGAUUUUCAAACAUAUCGCAUAUACAAAAUGCAAACAUGUCUGGCAAACACAAAUCCCAUAAAUGUUU-UGUGUGGUGCUG
....(------((----------------------.(((.(((..........)))((((.......))))...))).)))((((.(((((((............))-)))))..)))). ( -17.20)
>DroPse_CAF1 172378 115 + 1
AAAUGGCAGCAGAAACACACAAAACGAGUGGAACGGAGGGGAUUUUCAAACAUAUCGCAUAUACAAAAUGCAAACAUGUCUGGCAAACACAAAUCCCAUAAAUGUUU-UGUGC----CCC
....((((...(((((((((.......)))........((((((((((.((((...((((.......))))....)))).))).......))))))).....)))))-).)))----).. ( -24.51)
>DroGri_CAF1 105118 90 + 1
CAGUGG---CAGA----------------------AAUGGGAUUUUCAAACAUAUCGCAUAUACAAAAUGCAAACAUGUCUGGCAAACACAAAUCCCAUAAAUGUUU-UGAGU----CCC
(((.((---((..----------------------.((((((((((((.((((...((((.......))))....)))).))).......)))))))))...)))))-))...----... ( -17.91)
>DroMoj_CAF1 154596 95 + 1
CAAUGG---GAGA----------------------AAUGGGAUUUUCAAACAUAUCGCAUAUACAAAAUGCAAACAUGUCUGGCAAACACAAAUCCCAUAAAUGUCUGUGUGUGUGUCUG
..((((---(...----------------------.((((((((((((.((((...((((.......))))....)))).))).......))))))))).....)))))........... ( -16.61)
>DroPer_CAF1 172835 115 + 1
AAAUGGCAGCAGAAACACACAAAACGAGGGGAACGGAGGGGAUUUUCAAACAUAUCGCAUAUACAAAAUGCAAACAUGUCUGGCAAACACAAAUCCCAUAAAUGUUU-UGUGC----CCC
....((((...((((((...........(....)....((((((((((.((((...((((.......))))....)))).))).......))))))).....)))))-).)))----).. ( -22.81)
>consensus
AAAUGG___CAGA______________________AAUGGGAUUUUCAAACAUAUCGCAUAUACAAAAUGCAAACAUGUCUGGCAAACACAAAUCCCAUAAAUGUUU_UGUGC____CCC
......................................((((((((((.((((...((((.......))))....)))).))).......)))))))....................... (-13.16 = -13.16 +   0.00)

alignment

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secondary structure

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Window 8

Location 6,260,944 – 6,261,034
Length 90
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 79.70
Mean single sequence MFE -26.37
Consensus MFE -21.42
Energy contribution -21.67
Covariance contribution 0.25
Combinations/Pair 1.04
Mean z-score -2.32
Structure conservation index 0.81
SVM decision value 1.41
SVM RNA-class probability 0.951668
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 6260944 90 - 22407834
GGG----GCACA-AAACAUUUAUGGGAUUUGUGUUUGCCAGACAUGUUUGCAUUUUGUAUAUGCGAUAUGUUUGAAAAUCCCGUU----------------------UCUG---CCAUUU
..(----(((.(-(.......(((((((((((....))((((((((((.((((.......)))))))))))))).))))))))))----------------------).))---)).... ( -26.71)
>DroVir_CAF1 122262 91 - 1
CAGCACCACACA-AAACAUUUAUGGGAUUUGUGUUUGCCAGACAUGUUUGCAUUUUGUAUAUGCGAUAUGUUUGAAAAUCCCAUU----------------------UC------CAUUG
............-........(((((((((((....))((((((((((.((((.......)))))))))))))).))))))))).----------------------..------..... ( -22.80)
>DroPse_CAF1 172378 115 - 1
GGG----GCACA-AAACAUUUAUGGGAUUUGUGUUUGCCAGACAUGUUUGCAUUUUGUAUAUGCGAUAUGUUUGAAAAUCCCCUCCGUUCCACUCGUUUUGUGUGUUUCUGCUGCCAUUU
..(----(((((-(((((.....(((((((((....))((((((((((.((((.......)))))))))))))).)))))))........(((.......)))))))).)).)))).... ( -31.80)
>DroGri_CAF1 105118 90 - 1
GGG----ACUCA-AAACAUUUAUGGGAUUUGUGUUUGCCAGACAUGUUUGCAUUUUGUAUAUGCGAUAUGUUUGAAAAUCCCAUU----------------------UCUG---CCACUG
...----.....-...((...(((((((((((....))((((((((((.((((.......)))))))))))))).))))))))).----------------------..))---...... ( -23.30)
>DroMoj_CAF1 154596 95 - 1
CAGACACACACACAGACAUUUAUGGGAUUUGUGUUUGCCAGACAUGUUUGCAUUUUGUAUAUGCGAUAUGUUUGAAAAUCCCAUU----------------------UCUC---CCAUUG
.....................(((((((((((....))((((((((((.((((.......)))))))))))))).))))))))).----------------------....---...... ( -22.80)
>DroPer_CAF1 172835 115 - 1
GGG----GCACA-AAACAUUUAUGGGAUUUGUGUUUGCCAGACAUGUUUGCAUUUUGUAUAUGCGAUAUGUUUGAAAAUCCCCUCCGUUCCCCUCGUUUUGUGUGUUUCUGCUGCCAUUU
.((----(((((-((((......(((((((((....))((((((((((.((((.......)))))))))))))).)))))))....(.......))))))))))((....))..)).... ( -30.80)
>consensus
GGG____ACACA_AAACAUUUAUGGGAUUUGUGUUUGCCAGACAUGUUUGCAUUUUGUAUAUGCGAUAUGUUUGAAAAUCCCAUU______________________UCUG___CCAUUG
.....................(((((((((((....))((((((((((.((((.......)))))))))))))).))))))))).................................... (-21.42 = -21.67 +   0.25)

alignment

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secondary structure

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dotplot

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Window 9

Location 6,260,959 – 6,261,065
Length 106
Sequences 6
Columns 109
Reading direction reverse
Mean pairwise identity 79.81
Mean single sequence MFE -25.37
Consensus MFE -19.94
Energy contribution -19.97
Covariance contribution 0.03
Combinations/Pair 1.04
Mean z-score -1.55
Structure conservation index 0.79
SVM decision value 0.72
SVM RNA-class probability 0.832527
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 6260959 106 - 22407834
CCUCUAACUUCCCUUCGUGG---UUGUUGGGUGGGGGGCACAAAACAUUUAUGGGAUUUGUGUUUGCCAGACAUGUUUGCAUUUUGUAUAUGCGAUAUGUUUGAAAAUC
((((((((..((......))---..)))))).)).(((((((((.(........).)))))))))..((((((((((.((((.......))))))))))))))...... ( -29.30)
>DroPse_CAF1 172418 96 - 1
CCGCCCAUUC-------------CCAUUGAGAGAGGGGCACAAAACAUUUAUGGGAUUUGUGUUUGCCAGACAUGUUUGCAUUUUGUAUAUGCGAUAUGUUUGAAAAUC
..((.....(-------------((.((....)))))(((((((.(........).)))))))..))((((((((((.((((.......))))))))))))))...... ( -25.00)
>DroGri_CAF1 105133 90 - 1
-----------------AGGGAG--GCAGGUUGGGGGACUCAAAACAUUUAUGGGAUUUGUGUUUGCCAGACAUGUUUGCAUUUUGUAUAUGCGAUAUGUUUGAAAAUC
-----------------..(((.--(((((((((....)).....((....)).))))))).)))..((((((((((.((((.......))))))))))))))...... ( -21.10)
>DroYak_CAF1 109644 97 - 1
CCUCCAACUUCCCUUCCAGG------------GGGGGGCACAAAACAUUUAUGGGAUUUGUGUUUGCCAGACAUGUUUGCAUUUUGUAUAUGCGAUAUGUUUGAAAAUC
.......(((((((....))------------)))))(((((((.(........).)))))))....((((((((((.((((.......))))))))))))))...... ( -28.60)
>DroAna_CAF1 56891 92 - 1
CCCCUAACACCC-----ACG------------AUGGGGCACAAAACAUUUAUGGGAUUUGUGUUUGCCAGACAUGUUUGCAUUUUGUAUAUGCGAUAUGUUUGAAAAUC
.........(((-----...------------..)))(((((((.(........).)))))))....((((((((((.((((.......))))))))))))))...... ( -23.60)
>DroPer_CAF1 172875 95 - 1
CCGCCCAUUC--------------CAUUGAGAGAGGGGCACAAAACAUUUAUGGGAUUUGUGUUUGCCAGACAUGUUUGCAUUUUGUAUAUGCGAUAUGUUUGAAAAUC
...(((.(((--------------......))).)))(((((((.(........).)))))))....((((((((((.((((.......))))))))))))))...... ( -24.60)
>consensus
CCGCCAACUC_______AGG______UUG_G_GGGGGGCACAAAACAUUUAUGGGAUUUGUGUUUGCCAGACAUGUUUGCAUUUUGUAUAUGCGAUAUGUUUGAAAAUC
...................................(((((((((.(........).)))))))))..((((((((((.((((.......))))))))))))))...... (-19.94 = -19.97 +   0.03)

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 10:24:41 2006