Locus 4363

Sequence ID 2L_DroMel_CAF1
Location 12,550,478 – 12,550,630
Length 152
Max. P 0.987195
window6872 window6873 window6874

overview

Window 2

Location 12,550,478 – 12,550,591
Length 113
Sequences 6
Columns 115
Reading direction forward
Mean pairwise identity 77.59
Mean single sequence MFE -38.02
Consensus MFE -26.02
Energy contribution -26.33
Covariance contribution 0.31
Combinations/Pair 1.17
Mean z-score -2.87
Structure conservation index 0.68
SVM decision value 2.07
SVM RNA-class probability 0.987195
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 12550478 113 + 22407834
UUUACGGGGGCGUAGGCCUU--UUGGGGAUCCAGCGAUAGCUUUUUUAUGGCCAAAUCCAGGCUGACAAAUGGCCAAAGGACUUGGCCAUUAGAGGCUGUUCAAUCGCAUUCGAA
....((((.((((.(((((.--...)))..)).))((((((((((..((((((((.(((.((((.......))))...))).)))))))).)))))))))).....)).)))).. ( -42.10)
>DroSec_CAF1 122564 101 + 1
------------UAGGCCUU--UUGGGGCAAUAUCAGUUGCUUUUUUAUGGCCGAAUCCAGGCUGACAAAUGGCCAAAGGACUUGGCCAUUAGAGGCUGUUCAAUCGAAUUCGAA
------------..((((((--(.((((((((....))))))))...((((((((.(((.((((.......))))...))).)))))))).)))))))......(((....))). ( -36.60)
>DroSim_CAF1 125402 101 + 1
------------UAGGCCUU--UUGGGGCAAUAUCAGUUGCUUUUUUAUGGCCAAAUCCAGGCUGACAAAUGGCCAAAGGACUUGGCCAUUAGAGGCUGUUCAAUCGAAUUCGAA
------------..((((((--(.((((((((....))))))))...((((((((.(((.((((.......))))...))).)))))))).)))))))......(((....))). ( -36.90)
>DroEre_CAF1 121605 113 + 1
UUUUCCGGGACGUAGGCCUU--UUGGGGCUACAGCGGUUGCUUUUUUAUGGCCAAAUCCAGGCUGACAAAUGGCCAAGGGACUUGGCCAUUAGAGGCUGUUCAAUCGAAUUCGAA
.......((((((((.((..--...)).)))).......((((((..((((((((.(((.((((.......))))...))).)))))))).)))))).))))..(((....))). ( -43.60)
>DroYak_CAF1 126166 93 + 1
UUUUCCGGGGCGUAGGCCUU----------------------UUUUUAUGGCCAAAUCCAGGCUGACAAAUGGCCAAAGGACUUGGCCAUUAGAGGCUGUUCAAUCGAAUUCGAA
.......((((...((((((----------------------(....((((((((.(((.((((.......))))...))).)))))))).)))))))))))..(((....))). ( -35.00)
>DroAna_CAF1 122936 103 + 1
------------UAGGCUAUAACCGGGGGUGCAGCGGUAGCUUUUUUAUGGCCACAUCCUUGCUGACAAAUGGCCCGAGGAGUCCGCCAUUAGAGGCCUCUGAAUCGGAUUCGGA
------------..((((((...((((((((..((.((((.....)))).))..)))))))).......))))))....(((((((...(((((....)))))..)))))))... ( -33.90)
>consensus
____________UAGGCCUU__UUGGGGCUACAGCGGUUGCUUUUUUAUGGCCAAAUCCAGGCUGACAAAUGGCCAAAGGACUUGGCCAUUAGAGGCUGUUCAAUCGAAUUCGAA
..............((((((...........................((((((((.(((.((((.......))))...))).))))))))..))))))......(((....))). (-26.02 = -26.33 +   0.31)

alignment

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secondary structure

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dotplot

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Window 3

Location 12,550,478 – 12,550,591
Length 113
Sequences 6
Columns 115
Reading direction reverse
Mean pairwise identity 77.59
Mean single sequence MFE -31.73
Consensus MFE -21.50
Energy contribution -22.77
Covariance contribution 1.26
Combinations/Pair 1.04
Mean z-score -2.45
Structure conservation index 0.68
SVM decision value 1.83
SVM RNA-class probability 0.978996
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 12550478 113 - 22407834
UUCGAAUGCGAUUGAACAGCCUCUAAUGGCCAAGUCCUUUGGCCAUUUGUCAGCCUGGAUUUGGCCAUAAAAAAGCUAUCGCUGGAUCCCCAA--AAGGCCUACGCCCCCGUAAA
.......(((((.....(((.....((((((((((((...(((.........))).))))))))))))......))))))))(((....))).--..(((....)))........ ( -35.80)
>DroSec_CAF1 122564 101 - 1
UUCGAAUUCGAUUGAACAGCCUCUAAUGGCCAAGUCCUUUGGCCAUUUGUCAGCCUGGAUUCGGCCAUAAAAAAGCAACUGAUAUUGCCCCAA--AAGGCCUA------------
.(((....))).......((((...((((((.(((((...(((.........))).))))).))))))......((((......)))).....--.))))...------------ ( -29.10)
>DroSim_CAF1 125402 101 - 1
UUCGAAUUCGAUUGAACAGCCUCUAAUGGCCAAGUCCUUUGGCCAUUUGUCAGCCUGGAUUUGGCCAUAAAAAAGCAACUGAUAUUGCCCCAA--AAGGCCUA------------
.(((....))).......((((...((((((((((((...(((.........))).))))))))))))......((((......)))).....--.))))...------------ ( -33.20)
>DroEre_CAF1 121605 113 - 1
UUCGAAUUCGAUUGAACAGCCUCUAAUGGCCAAGUCCCUUGGCCAUUUGUCAGCCUGGAUUUGGCCAUAAAAAAGCAACCGCUGUAGCCCCAA--AAGGCCUACGUCCCGGAAAA
.(((....))).......((.....((((((((((((...(((.........))).))))))))))))......))..(((.(((((((....--..)).)))))...))).... ( -35.70)
>DroYak_CAF1 126166 93 - 1
UUCGAAUUCGAUUGAACAGCCUCUAAUGGCCAAGUCCUUUGGCCAUUUGUCAGCCUGGAUUUGGCCAUAAAAA----------------------AAGGCCUACGCCCCGGAAAA
.(((....)))........((....((((((((((((...(((.........))).)))))))))))).....----------------------..(((....)))..)).... ( -30.50)
>DroAna_CAF1 122936 103 - 1
UCCGAAUCCGAUUCAGAGGCCUCUAAUGGCGGACUCCUCGGGCCAUUUGUCAGCAAGGAUGUGGCCAUAAAAAAGCUACCGCUGCACCCCCGGUUAUAGCCUA------------
(((((((...))))....(((......)))))).......((((((..(((......)))))))))........((((..((((......))))..))))...------------ ( -26.10)
>consensus
UUCGAAUUCGAUUGAACAGCCUCUAAUGGCCAAGUCCUUUGGCCAUUUGUCAGCCUGGAUUUGGCCAUAAAAAAGCAACCGCUGUAGCCCCAA__AAGGCCUA____________
.(((....))).......((((...((((((((((((...(((.........))).)))))))))))).......(....)...............))))............... (-21.50 = -22.77 +   1.26)

alignment

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secondary structure

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dotplot

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Window 4

Location 12,550,516 – 12,550,630
Length 114
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 87.07
Mean single sequence MFE -30.05
Consensus MFE -23.47
Energy contribution -24.92
Covariance contribution 1.45
Combinations/Pair 1.10
Mean z-score -2.11
Structure conservation index 0.78
SVM decision value 0.02
SVM RNA-class probability 0.542074
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 12550516 114 - 22407834
AG-UCAUAAAUUAUGGGCAAUUAAUAUGUAACACGUUAGA--UUCGAAUGCGAUU-GAACAGCCUCUAAUGGCCAAGUCCUU--UGGCCAUUUGUCAGCCUGGAUUUGGCCAUAAAAAAG
..-......((((.((((..(((((.((((...((.....--..))..)))))))-))...)))).))))((((((((((..--.(((.........))).))))))))))......... ( -32.00)
>DroSec_CAF1 122590 114 - 1
AG-UCAUAAAUUAUGGGCAAUUAAUAUGUAACACGUUAGA--UUCGAAUUCGAUU-GAACAGCCUCUAAUGGCCAAGUCCUU--UGGCCAUUUGUCAGCCUGGAUUCGGCCAUAAAAAAG
..-......((((.((((.........(.....)(((...--.(((....)))..-.))).)))).))))((((.(((((..--.(((.........))).))))).))))......... ( -28.60)
>DroEre_CAF1 121643 114 - 1
AG-UCAUAAAUUAUGGGCAAUUAAUAUGUAACACGUUAGA--UUCGAAUUCGAUU-GAACAGCCUCUAAUGGCCAAGUCCCU--UGGCCAUUUGUCAGCCUGGAUUUGGCCAUAAAAAAG
..-......((((.((((.........(.....)(((...--.(((....)))..-.))).)))).))))((((((((((..--.(((.........))).))))))))))......... ( -32.00)
>DroWil_CAF1 185014 119 - 1
AU-CCAUAAAUAAUGGGCAAUUAAUAUGUAACACGUUAGUCUUUCGAUUUCGAUUUGGGCAACUCUAAAUGGCCAAUUCUUUUCUAGCCAUUUGUCAAUUUUGAUGUGGCCAUAAAAAAC
.(-((((.....))))).......((((...(((((((((((.(((....)))...)))).....((((((((.............)))))))).......)))))))..))))...... ( -26.12)
>DroYak_CAF1 126186 112 - 1
AG-UCAUAAAUUAUGGGCAAUUAAUAUGUAACACGUUAGA--UUCGAAUUCGAUU-GAACAGCCUCUAAUGGCCAAGUCCUU--UGGCCAUUUGUCAGCCUGGAUUUGGCCAUAAAAA--
..-......((((.((((.........(.....)(((...--.(((....)))..-.))).)))).))))((((((((((..--.(((.........))).)))))))))).......-- ( -32.70)
>DroAna_CAF1 122964 115 - 1
AGGCCAUAAAUUAUGGGCAAUUAAUAUGUAACACGUUAGA--UCCGAAUCCGAUU-CAGAGGCCUCUAAUGGCGGACUCCUC--GGGCCAUUUGUCAGCAAGGAUGUGGCCAUAAAAAAG
.(((((((.......(((..((((..((...))..)))).--.((((.((((...-.(((....))).....))))....))--))))).((((....))))..)))))))......... ( -28.90)
>consensus
AG_UCAUAAAUUAUGGGCAAUUAAUAUGUAACACGUUAGA__UUCGAAUUCGAUU_GAACAGCCUCUAAUGGCCAAGUCCUU__UGGCCAUUUGUCAGCCUGGAUUUGGCCAUAAAAAAG
..............((((..((((..((...))..))))....(((....)))........))))...((((((((((((....((((.....))))....))))))))))))....... (-23.47 = -24.92 +   1.45)

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 11:16:01 2006