Locus 8768

Sequence ID 3R_DroMel_CAF1
Location 23,405,046 – 23,405,163
Length 117
Max. P 0.960941
window14086 window14087 window14088 window14089

overview

Window 6

Location 23,405,046 – 23,405,139
Length 93
Sequences 5
Columns 96
Reading direction forward
Mean pairwise identity 90.47
Mean single sequence MFE -29.38
Consensus MFE -24.34
Energy contribution -23.54
Covariance contribution -0.80
Combinations/Pair 1.15
Mean z-score -1.96
Structure conservation index 0.83
SVM decision value 1.52
SVM RNA-class probability 0.960941
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 23405046 93 + 27905053
A--GUGAUCUUUUUUUCAUCGCCACUUAAUUGCACCCUAGUCACGUUCGGUUUGGGAACUUUACGC-UGGGCGUGCUUGGGUUGCCUUGUGGAUUA
.--((((........))))..((((......((((((.((.((((((((((..(....).....))-)))))))))).))).)))...)))).... ( -29.90)
>DroSec_CAF1 19514 93 + 1
A--GUGAUCUUGUUUUCAUCGUCACUUAAUUGCAACCUAGUCACGUUCGAUUUGGGAACUUUACGC-UGGGCGUGCUUGGGUUGCCUUGUGGGCUA
(--(((((..((....))..)))))).....(((((((((.((((((((....(....).......-)))))))).)))))))))........... ( -28.20)
>DroSim_CAF1 19735 93 + 1
A--GUGAUCUUGUUUUCAUCGCCACUUAAUUGCAACCUAGUCACGUUCGAUUUGGGAACUUUACGC-UGGGCGUGCUUGGGUUGCCUUGUGGGCUA
.--((((........))))..((((......(((((((((.((((((((....(....).......-)))))))).)))))))))...)))).... ( -28.50)
>DroEre_CAF1 22888 91 + 1
AUGAUGAUCUUGUUUUCAUCGCCACUUAAUUGCACCCUAGUCACGUUCGAUUUGGGAACCUAACGC-UGGGCGUGCUUAGGUUGCCUUGUGG----
..(((((........))))).((((......(((.(((((.((((((((..((((....))))...-)))))))).))))).)))...))))---- ( -30.60)
>DroYak_CAF1 20862 92 + 1
AUGAUGAUCUGGUUUUCAUCGCCACUUAAUUGCACCCUAGUCACGUUCGAUUUGGGAACUUUACGCCUGGGCGUGCCUAGGUUGCCUUGUGG----
..(((((........))))).((((......(((.(((((.(((((((.......)))).....((....))))).))))).)))...))))---- ( -29.70)
>consensus
A__GUGAUCUUGUUUUCAUCGCCACUUAAUUGCACCCUAGUCACGUUCGAUUUGGGAACUUUACGC_UGGGCGUGCUUGGGUUGCCUUGUGG__UA
...((((........))))..((((......(((.(((((.((((((((...((.........))..)))))))).))))).)))...)))).... (-24.34 = -23.54 +  -0.80)

alignment

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secondary structure

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dotplot

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Window 7

Location 23,405,046 – 23,405,139
Length 93
Sequences 5
Columns 96
Reading direction reverse
Mean pairwise identity 90.47
Mean single sequence MFE -23.06
Consensus MFE -17.58
Energy contribution -17.78
Covariance contribution 0.20
Combinations/Pair 1.10
Mean z-score -1.69
Structure conservation index 0.76
SVM decision value 0.29
SVM RNA-class probability 0.671421
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 23405046 93 - 27905053
UAAUCCACAAGGCAACCCAAGCACGCCCA-GCGUAAAGUUCCCAAACCGAACGUGACUAGGGUGCAAUUAAGUGGCGAUGAAAAAAAGAUCAC--U
....((((...(((.(((.(((((((...-)).....((((.......))))))).)).))))))......))))..................--. ( -20.20)
>DroSec_CAF1 19514 93 - 1
UAGCCCACAAGGCAACCCAAGCACGCCCA-GCGUAAAGUUCCCAAAUCGAACGUGACUAGGUUGCAAUUAAGUGACGAUGAAAACAAGAUCAC--U
...........((((((..(((((((...-)).....((((.......))))))).)).)))))).....((((((..((....)).).))))--) ( -19.00)
>DroSim_CAF1 19735 93 - 1
UAGCCCACAAGGCAACCCAAGCACGCCCA-GCGUAAAGUUCCCAAAUCGAACGUGACUAGGUUGCAAUUAAGUGGCGAUGAAAACAAGAUCAC--U
..(((.((...((((((..(((((((...-)).....((((.......))))))).)).))))))......))))).................--. ( -20.80)
>DroEre_CAF1 22888 91 - 1
----CCACAAGGCAACCUAAGCACGCCCA-GCGUUAGGUUCCCAAAUCGAACGUGACUAGGGUGCAAUUAAGUGGCGAUGAAAACAAGAUCAUCAU
----((((...((.......)).(((((.-..((((.((((.......)))).))))..))))).......)))).(((((........))))).. ( -25.80)
>DroYak_CAF1 20862 92 - 1
----CCACAAGGCAACCUAGGCACGCCCAGGCGUAAAGUUCCCAAAUCGAACGUGACUAGGGUGCAAUUAAGUGGCGAUGAAAACCAGAUCAUCAU
----((((...(((.(((((.(((((....)).....((((.......))))))).))))).)))......)))).(((((........))))).. ( -29.50)
>consensus
UA__CCACAAGGCAACCCAAGCACGCCCA_GCGUAAAGUUCCCAAAUCGAACGUGACUAGGGUGCAAUUAAGUGGCGAUGAAAACAAGAUCAC__U
....((((...(((.(((.(((((((....)).....((((.......))))))).)).))))))......))))..................... (-17.58 = -17.78 +   0.20)

alignment

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secondary structure

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dotplot

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Window 8

Location 23,405,070 – 23,405,163
Length 93
Sequences 5
Columns 94
Reading direction forward
Mean pairwise identity 84.80
Mean single sequence MFE -26.02
Consensus MFE -18.92
Energy contribution -18.52
Covariance contribution -0.40
Combinations/Pair 1.11
Mean z-score -1.67
Structure conservation index 0.73
SVM decision value 0.13
SVM RNA-class probability 0.600048
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 23405070 93 + 27905053
UAAUUGCACCCUAGUCACGUUCGGUUUGGGAACUUUACGC-UGGGCGUGCUUGGGUUGCCUUGUGGAUUACAUGGAUUAUGGAUUAUAAUUAAA
(((((((((((.((.((((((((((..(....).....))-)))))))))).))).))).(..((.....))..)......)))))........ ( -26.20)
>DroSec_CAF1 19538 93 + 1
UAAUUGCAACCUAGUCACGUUCGAUUUGGGAACUUUACGC-UGGGCGUGCUUGGGUUGCCUUGUGGGCUAUAUGGAUUAUGGAUUAUAAUUAAA
.....(((((((((.((((((((....(....).......-)))))))).))))))))).((((((.(((((.....))))).))))))..... ( -27.00)
>DroSim_CAF1 19759 93 + 1
UAAUUGCAACCUAGUCACGUUCGAUUUGGGAACUUUACGC-UGGGCGUGCUUGGGUUGCCUUGUGGGCUAUAUGGAUUAUGGAUUAUAAUUAAA
.....(((((((((.((((((((....(....).......-)))))))).))))))))).((((((.(((((.....))))).))))))..... ( -27.00)
>DroEre_CAF1 22914 80 + 1
UAAUUGCACCCUAGUCACGUUCGAUUUGGGAACCUAACGC-UGGGCGUGCUUAGGUUGCCUUGUGG---------AUUAUGG----CAAUAGUG
.....((((((((((...((((.......)))).....))-)))).))))....((((((......---------.....))----)))).... ( -23.70)
>DroYak_CAF1 20888 81 + 1
UAAUUGCACCCUAGUCACGUUCGAUUUGGGAACUUUACGCCUGGGCGUGCCUAGGUUGCCUUGUGG---------AUUAUGG----CAAUUGAA
(((((((.......(((((..(((((((((.....(((((....))))))))))))))...)))))---------......)----)))))).. ( -26.22)
>consensus
UAAUUGCACCCUAGUCACGUUCGAUUUGGGAACUUUACGC_UGGGCGUGCUUGGGUUGCCUUGUGG__UA_AUGGAUUAUGGAUUAUAAUUAAA
.....(((.(((((.((((((((...((.........))..)))))))).))))).)))................................... (-18.92 = -18.52 +  -0.40)

alignment

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secondary structure

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dotplot

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Window 9

Location 23,405,070 – 23,405,163
Length 93
Sequences 5
Columns 94
Reading direction reverse
Mean pairwise identity 84.80
Mean single sequence MFE -18.30
Consensus MFE -15.04
Energy contribution -15.04
Covariance contribution 0.00
Combinations/Pair 1.12
Mean z-score -1.63
Structure conservation index 0.82
SVM decision value 0.31
SVM RNA-class probability 0.685000
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 23405070 93 - 27905053
UUUAAUUAUAAUCCAUAAUCCAUGUAAUCCACAAGGCAACCCAAGCACGCCCA-GCGUAAAGUUCCCAAACCGAACGUGACUAGGGUGCAAUUA
...................................(((.(((.(((((((...-)).....((((.......))))))).)).))))))..... ( -16.60)
>DroSec_CAF1 19538 93 - 1
UUUAAUUAUAAUCCAUAAUCCAUAUAGCCCACAAGGCAACCCAAGCACGCCCA-GCGUAAAGUUCCCAAAUCGAACGUGACUAGGUUGCAAUUA
...................................((((((..(((((((...-)).....((((.......))))))).)).))))))..... ( -16.20)
>DroSim_CAF1 19759 93 - 1
UUUAAUUAUAAUCCAUAAUCCAUAUAGCCCACAAGGCAACCCAAGCACGCCCA-GCGUAAAGUUCCCAAAUCGAACGUGACUAGGUUGCAAUUA
...................................((((((..(((((((...-)).....((((.......))))))).)).))))))..... ( -16.20)
>DroEre_CAF1 22914 80 - 1
CACUAUUG----CCAUAAU---------CCACAAGGCAACCUAAGCACGCCCA-GCGUUAGGUUCCCAAAUCGAACGUGACUAGGGUGCAAUUA
.....(((----((.....---------......))))).....((((.((..-..((((.((((.......)))).))))..))))))..... ( -20.30)
>DroYak_CAF1 20888 81 - 1
UUCAAUUG----CCAUAAU---------CCACAAGGCAACCUAGGCACGCCCAGGCGUAAAGUUCCCAAAUCGAACGUGACUAGGGUGCAAUUA
...(((((----((.....---------((....))...(((((.(((((....)).....((((.......))))))).)))))).)))))). ( -22.20)
>consensus
UUUAAUUAUAAUCCAUAAUCCAU_UA__CCACAAGGCAACCCAAGCACGCCCA_GCGUAAAGUUCCCAAAUCGAACGUGACUAGGGUGCAAUUA
...................................(((.(((.(((((((....)).....((((.......))))))).)).))))))..... (-15.04 = -15.04 +   0.00)

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 13:19:22 2006