Locus 5468

Sequence ID 3L_DroMel_CAF1
Location 14,944,626 – 14,944,903
Length 277
Max. P 0.977153
window8651 window8652 window8653 window8654

overview

Window 1

Location 14,944,626 – 14,944,746
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 95.82
Mean single sequence MFE -35.32
Consensus MFE -31.08
Energy contribution -31.76
Covariance contribution 0.68
Combinations/Pair 1.06
Mean z-score -1.35
Structure conservation index 0.88
SVM decision value 0.44
SVM RNA-class probability 0.736453
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 14944626 120 + 23771897
UCAUUUCCUUUUCGCCGUGACUCCUUUCGAGAACCCUCCUCCUUAUAAAAUCAUGGGAACGUACGUUAUGCGUGCGCUCCUCACGCGCAGGACACGUACGGAAGAAACCGUGGGAAUCGA
((((((((.((((.((((((........(((.......))).........))))))...(((((((....(.(((((.......))))).)..)))))))...))))....)))))).)) ( -34.13)
>DroSec_CAF1 125002 120 + 1
UCAUUUCCUUUUUGCCGUGACUCCUUUCGAGAACCCUCCUCCUUAUAAAAUCAUGGGAACGUACGUUAGGCGUGCGCUCCUCAAGCGCAGGACACGUACGGAAGAAACCGUGGUAUUCGA
....((((...((.((((((........(((.......))).........)))))).)).((((((....(.((((((.....)))))).)..))))))))))(((((....)).))).. ( -33.03)
>DroSim_CAF1 122710 120 + 1
UCAUUUCCUUUUUGCCGUGACUCCUUUCGAGAACCCUCCUCCUUAUAAAAUCAUGGGAACGUACGUUAUGCGUGCGCUCCUCACGCGCAGGACACGUACGGAAGAAACCGUGGGAAUCGA
((((((((.(((((((((((........(((....))).................(((.((((((.....)))))).)))))))).)))))).....((((......)))))))))).)) ( -35.50)
>DroEre_CAF1 119731 117 + 1
UCAUUUCCUUUCUGCCGUGACUCCUUUCGAGAACCCU---CCUUAUAAAAUCAUGGGAACGUACGUUAUGCGUGCGCUCCUCACGCGCAGGACACGUACGGAAGAAAUCGUGGGAAUCGA
((..((((.(((((((((((........(((....))---)..............(((.((((((.....)))))).)))))))).))))))((((..(....)....))))))))..)) ( -38.70)
>DroYak_CAF1 120720 117 + 1
UCAUUUCCUUUUUUCCGUGACUCCUUUCGAGAACCCU---CCUUAUAAAAUCAUGGGAACGUACGUUAUGCGUGCGCUCCUCACGCGCAGGACACGUACGGAAGAAACCGUGGGAAUCGA
((((((((...(((((((((........(((....))---).........)))))))))(((((((....(.(((((.......))))).)..)))))))...........)))))).)) ( -35.23)
>consensus
UCAUUUCCUUUUUGCCGUGACUCCUUUCGAGAACCCUCCUCCUUAUAAAAUCAUGGGAACGUACGUUAUGCGUGCGCUCCUCACGCGCAGGACACGUACGGAAGAAACCGUGGGAAUCGA
((((((((.((((((((((((((.....)))........................(((.((((((.....)))))).)))))))).)))))).....((((......)))))))))).)) (-31.08 = -31.76 +   0.68)

alignment

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secondary structure

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Window 2

Location 14,944,666 – 14,944,786
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 96.16
Mean single sequence MFE -29.92
Consensus MFE -28.12
Energy contribution -27.64
Covariance contribution -0.48
Combinations/Pair 1.11
Mean z-score -1.41
Structure conservation index 0.94
SVM decision value 1.19
SVM RNA-class probability 0.928968
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 14944666 120 + 23771897
CCUUAUAAAAUCAUGGGAACGUACGUUAUGCGUGCGCUCCUCACGCGCAGGACACGUACGGAAGAAACCGUGGGAAUCGAAACCGAAAAUGCACCUAAACAAAAAUAAAUGCACCAGACC
...........(((((...(((((((....(.(((((.......))))).)..))))))).......)))))((..(((....)))...((((..((........))..))))))..... ( -30.00)
>DroSec_CAF1 125042 120 + 1
CCUUAUAAAAUCAUGGGAACGUACGUUAGGCGUGCGCUCCUCAAGCGCAGGACACGUACGGAAGAAACCGUGGUAUUCGAAACCGAAAAUGCGCCUGAACAAAGAUAAAUGCACCAGACC
.........(((...(((.((((((.....)))))).)))(((.(((((....((.(((((......))))))).((((....))))..))))).))).....))).............. ( -33.10)
>DroSim_CAF1 122750 120 + 1
CCUUAUAAAAUCAUGGGAACGUACGUUAUGCGUGCGCUCCUCACGCGCAGGACACGUACGGAAGAAACCGUGGGAAUCGAAACCGAAAAUGCACCUAAACAAAAAUAAAUGCACCAGACC
...........(((((...(((((((....(.(((((.......))))).)..))))))).......)))))((..(((....)))...((((..((........))..))))))..... ( -30.00)
>DroEre_CAF1 119768 119 + 1
CCUUAUAAAAUCAUGGGAACGUACGUUAUGCGUGCGCUCCUCACGCGCAGGACACGUACGGAAGAAAUCGUGGGAAUCGAAACCGA-AAUGCACCUAAACAAAAAUAAAUGCAGUAGACC
..........((((((...(((((((....(.(((((.......))))).)..))))))).......))))))...(((....)))-..((((..((........))..))))....... ( -26.50)
>DroYak_CAF1 120757 119 + 1
CCUUAUAAAAUCAUGGGAACGUACGUUAUGCGUGCGCUCCUCACGCGCAGGACACGUACGGAAGAAACCGUGGGAAUCGAAACCGA-AAUGCACCUAAACAAAAAUAAAUGCACCAGACC
...........(((((...(((((((....(.(((((.......))))).)..))))))).......)))))((..(((....)))-..((((..((........))..))))))..... ( -30.00)
>consensus
CCUUAUAAAAUCAUGGGAACGUACGUUAUGCGUGCGCUCCUCACGCGCAGGACACGUACGGAAGAAACCGUGGGAAUCGAAACCGAAAAUGCACCUAAACAAAAAUAAAUGCACCAGACC
..........((((((...(((((((....(.(((((.......))))).)..))))))).......))))))...(((....)))...((((..((........))..))))....... (-28.12 = -27.64 +  -0.48)

alignment

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secondary structure

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Window 3

Location 14,944,746 – 14,944,864
Length 118
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 94.27
Mean single sequence MFE -35.56
Consensus MFE -31.16
Energy contribution -31.64
Covariance contribution 0.48
Combinations/Pair 1.06
Mean z-score -1.77
Structure conservation index 0.88
SVM decision value 1.79
SVM RNA-class probability 0.977153
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 14944746 118 - 23771897
CCACCUGGGCAACCUUUUCUAAUUCCAUUCGAAAUGGCCCGGGUGCGGA--GGGACCUGUCUAUUGUUACCCUCUUCUAGGGUCUGGUGCAUUUAUUUUUGUUUAGGUGCAUUUUCGGUU
.(((((((((.....((((...........))))..)))))))))((((--(((((((.......(.....).......)))))).(((((((((........))))))))))))))... ( -36.04)
>DroSec_CAF1 125122 115 - 1
CCACCUGGGCAACCUUUUCUAAUUCCAUUCGAAAUGGCCCGGGUGCGGA--GGGACCUGUCUAUG--U-ACCUCUUCUAAGGUCUGGUGCAUUUAUCUUUGUUCAGGCGCAUUUUCGGUU
((((((((((.....((((...........))))..))))))))(((((--((.((........)--)-.)))))......((((((.(((........)))))))))))......)).. ( -34.00)
>DroSim_CAF1 122830 118 - 1
CCACCUGGGCAACCUUUUCUAAUUCCAUUCGAAAUGGCCCGGGUGCGGA--GGGACCUGUCUAUUGUUACCCUCUUCUAGGGUCUGGUGCAUUUAUUUUUGUUUAGGUGCAUUUUCGGUU
.(((((((((.....((((...........))))..)))))))))((((--(((((((.......(.....).......)))))).(((((((((........))))))))))))))... ( -36.04)
>DroEre_CAF1 119848 117 - 1
CCACCUGGGCAACCUUUUCUAAUUCAAUUCGAAAUGGCCCGGCUGCGGA--GGGACCUGUCUAUUGUUACCCUCUUCUAGGGUCUACUGCAUUUAUUUUUGUUUAGGUGCAUU-UCGGUU
..(((.((....))................((((((((((....(.(((--(((...............)))))).)..)))))....(((((((........))))))))))-))))). ( -32.66)
>DroYak_CAF1 120837 119 - 1
CCACCUGGGCAACCUUUUCUAAUUCAAUUCGAAAUGGCCCGGGUGCGGAGAGGGACCUGUCUAUUGUUACCCUCUUCUAGGGUCUGGUGCAUUUAUUUUUGUUUAGGUGCAUU-UCGGUU
.(((((((((.....((((...........))))..))))))))).((((((((...............))))))))......((((((((((((........))))))))).-.))).. ( -39.06)
>consensus
CCACCUGGGCAACCUUUUCUAAUUCCAUUCGAAAUGGCCCGGGUGCGGA__GGGACCUGUCUAUUGUUACCCUCUUCUAGGGUCUGGUGCAUUUAUUUUUGUUUAGGUGCAUUUUCGGUU
.(((((((((.....((((...........))))..)))))))))(((....((((((.....................))))))((((((((((........)))))))))).)))... (-31.16 = -31.64 +   0.48)

alignment

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secondary structure

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dotplot

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Window 4

Location 14,944,786 – 14,944,903
Length 117
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 94.08
Mean single sequence MFE -30.23
Consensus MFE -23.48
Energy contribution -23.68
Covariance contribution 0.20
Combinations/Pair 1.00
Mean z-score -1.71
Structure conservation index 0.78
SVM decision value 0.18
SVM RNA-class probability 0.619845
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 14944786 117 - 23771897
CUUUCAUUCUUCGG-GACCCAUUAAAAUCGACCCCCAACUCCACCUGGGCAACCUUUUCUAAUUCCAUUCGAAAUGGCCCGGGUGCGGA--GGGACCUGUCUAUUGUUACCCUCUUCUAG
....((.....(((-(.(((.........(.....)..((.(((((((((.....((((...........))))..))))))))).)).--))).)))).....)).............. ( -28.90)
>DroSec_CAF1 125162 115 - 1
CUUUCAUUCUUCGGGGGCCCAUUAAAAUCGACCCCCAACUCCACCUGGGCAACCUUUUCUAAUUCCAUUCGAAAUGGCCCGGGUGCGGA--GGGACCUGUCUAUG--U-ACCUCUUCUAA
............(((((.(.((....)).).))))).....(((((((((.....((((...........))))..))))))))).(((--((.((........)--)-.)))))..... ( -33.80)
>DroSim_CAF1 122870 117 - 1
CUUUCAUUCUUCGG-GGCCCAUUAAAAUCGACCCCCAACUCCACCUGGGCAACCUUUUCUAAUUCCAUUCGAAAUGGCCCGGGUGCGGA--GGGACCUGUCUAUUGUUACCCUCUUCUAG
............((-((..(.........)..)))).....(((((((((.....((((...........))))..))))))))).(((--(((...............))))))..... ( -31.56)
>DroEre_CAF1 119887 117 - 1
CUUUCAUUCUGCGG-GACCCAUUAAGAUCUACCCCCAACUCCACCUGGGCAACCUUUUCUAAUUCAAUUCGAAAUGGCCCGGCUGCGGA--GGGACCUGUCUAUUGUUACCCUCUUCUAG
............((-(...((...((((...(((((.....((.((((((.....((((...........))))..)))))).)).)).--)))....))))..))...)))........ ( -24.00)
>DroYak_CAF1 120876 119 - 1
CUUUCAUUCUUCGG-GACCCAUUACAAUCUACCCCCAACUCCACCUGGGCAACCUUUUCUAAUUCAAUUCGAAAUGGCCCGGGUGCGGAGAGGGACCUGUCUAUUGUUACCCUCUUCUAG
............((-(.................))).....(((((((((.....((((...........))))..))))))))).((((((((...............))))))))... ( -32.89)
>consensus
CUUUCAUUCUUCGG_GACCCAUUAAAAUCGACCCCCAACUCCACCUGGGCAACCUUUUCUAAUUCCAUUCGAAAUGGCCCGGGUGCGGA__GGGACCUGUCUAUUGUUACCCUCUUCUAG
............((....))............(((...((.(((((((((.....((((...........))))..))))))))).))...))).......................... (-23.48 = -23.68 +   0.20)

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 11:51:09 2006