Locus 599

Sequence ID 3L_DroMel_CAF1
Location 1,719,230 – 1,719,343
Length 113
Max. P 0.999868
window913 window914 window915 window916

overview

Window 3

Location 1,719,230 – 1,719,326
Length 96
Sequences 5
Columns 113
Reading direction forward
Mean pairwise identity 85.37
Mean single sequence MFE -37.44
Consensus MFE -31.44
Energy contribution -30.84
Covariance contribution -0.60
Combinations/Pair 1.12
Mean z-score -1.71
Structure conservation index 0.84
SVM decision value 0.57
SVM RNA-class probability 0.784426
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 1719230 96 + 23771897
-----------------UCAGCUGGCCAAAGACCCAAGCCUGUUUUGGGCCCAAAAAGUGGUUCAAUUGGUAUUGGUGGCAAGUGGCAGUGAAGCACCUGCUGCCACCUGUUG
-----------------.((((.(((((.....(((((((....((((((((.....).)))))))..))).))))))))..((((((((.........))))))))).)))) ( -33.70)
>DroSec_CAF1 1155 95 + 1
-----------------UCAGCUGGCCAA-AACCCAAGCCUGUUUUGGGCCCAAAAGGUGGUUCAAUUGGUAUUGGUGGCAAGUGGCAGUGAGGCACCUGCUGCCACCUGUUG
-----------------.((((.(((((.-...(((((((....((((((((.....).)))))))..))).))))))))..((((((((.((....))))))))))).)))) ( -36.30)
>DroSim_CAF1 1124 95 + 1
-----------------UCAGCUGGCCAA-GACCCAAGCCUGUUUUGGGUCCAAAAGGUGGUUCAAUUGGUAUUGGUGGCAAGUGGCAGUGAGGCACCUGCUGCCACCUGUUG
-----------------.(((.((((...-((((((((.....))))))))....(((((.((((.(((.((((.......)))).))))))).)))))...)))).)))... ( -35.30)
>DroEre_CAF1 1180 112 + 1
UCAUGGCCACGCAGCGCUCAGCUGGCUAA-AACCCAAGCCUGUUUUGGGCCCAUAAAGUGGCUUAAUUGGUAUUGGUGGCAAGUGGCAGGGAAGCACCUGCUGCCACCUGUUG
(((.((((((.((((.....)))).....-..((((((.....))))))........))))))....)))....(((((((....(((((......))))))))))))..... ( -43.60)
>DroYak_CAF1 1032 112 + 1
UUACGGCCACGCAGCUCUCAGCUGGCUAA-AACCCAAGCCUGUUUUGGGCCCAUAAAGUGGUUUAAUUGGUAUUGGUGGCAAGUGGCAGUGAAGCACCUGCUGCCACCUGUUG
.....(((((.((((.....))))(((((-..((((((.....)))))).((((...)))).....)))))....)))))..((((((((.........))))))))...... ( -38.30)
>consensus
_________________UCAGCUGGCCAA_AACCCAAGCCUGUUUUGGGCCCAAAAAGUGGUUCAAUUGGUAUUGGUGGCAAGUGGCAGUGAAGCACCUGCUGCCACCUGUUG
..................((((.(((((.....(((((((....((((((((.....).)))))))..))).))))))))..(((((((((.......)))))))))).)))) (-31.44 = -30.84 +  -0.60)

alignment

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secondary structure

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dotplot

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Window 4

Location 1,719,230 – 1,719,326
Length 96
Sequences 5
Columns 113
Reading direction reverse
Mean pairwise identity 85.37
Mean single sequence MFE -35.52
Consensus MFE -30.30
Energy contribution -29.90
Covariance contribution -0.40
Combinations/Pair 1.09
Mean z-score -2.29
Structure conservation index 0.85
SVM decision value 1.93
SVM RNA-class probability 0.982873
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 1719230 96 - 23771897
CAACAGGUGGCAGCAGGUGCUUCACUGCCACUUGCCACCAAUACCAAUUGAACCACUUUUUGGGCCCAAAACAGGCUUGGGUCUUUGGCCAGCUGA-----------------
...(((.((((.((((((((......).)))))))..........................((((((((.......))))))))...)))).))).----------------- ( -32.50)
>DroSec_CAF1 1155 95 - 1
CAACAGGUGGCAGCAGGUGCCUCACUGCCACUUGCCACCAAUACCAAUUGAACCACCUUUUGGGCCCAAAACAGGCUUGGGUU-UUGGCCAGCUGA-----------------
...(((.((((.(((((((.(.....).)))))))...(((..((((..(......)..))))((((((.......)))))).-))))))).))).----------------- ( -33.30)
>DroSim_CAF1 1124 95 - 1
CAACAGGUGGCAGCAGGUGCCUCACUGCCACUUGCCACCAAUACCAAUUGAACCACCUUUUGGACCCAAAACAGGCUUGGGUC-UUGGCCAGCUGA-----------------
...(((.((((.(((((((.(.....).)))))))...(((...(((..(......)..)))(((((((.......)))))))-))))))).))).----------------- ( -33.00)
>DroEre_CAF1 1180 112 - 1
CAACAGGUGGCAGCAGGUGCUUCCCUGCCACUUGCCACCAAUACCAAUUAAGCCACUUUAUGGGCCCAAAACAGGCUUGGGUU-UUAGCCAGCUGAGCGCUGCGUGGCCAUGA
.....((((((((((((......)))))....)))))))............(((((.....((((((((.......)))))))-)..((.(((.....))))))))))..... ( -42.00)
>DroYak_CAF1 1032 112 - 1
CAACAGGUGGCAGCAGGUGCUUCACUGCCACUUGCCACCAAUACCAAUUAAACCACUUUAUGGGCCCAAAACAGGCUUGGGUU-UUAGCCAGCUGAGAGCUGCGUGGCCGUAA
..((.(((((((((((........))))....))))))).............((((.....((((((((.......)))))))-)..((.(((.....)))))))))..)).. ( -36.80)
>consensus
CAACAGGUGGCAGCAGGUGCUUCACUGCCACUUGCCACCAAUACCAAUUGAACCACUUUUUGGGCCCAAAACAGGCUUGGGUU_UUGGCCAGCUGA_________________
...(((.((((.((((((((......).)))))))...........................(((((((.......)))))))....)))).))).................. (-30.30 = -29.90 +  -0.40)

alignment

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secondary structure

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dotplot

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Window 5

Location 1,719,253 – 1,719,343
Length 90
Sequences 5
Columns 90
Reading direction forward
Mean pairwise identity 94.89
Mean single sequence MFE -34.88
Consensus MFE -30.92
Energy contribution -30.56
Covariance contribution -0.36
Combinations/Pair 1.10
Mean z-score -2.85
Structure conservation index 0.89
SVM decision value 3.98
SVM RNA-class probability 0.999739
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 1719253 90 + 23771897
UGUUUUGGGCCCAAAAAGUGGUUCAAUUGGUAUUGGUGGCAAGUGGCAGUGAAGCACCUGCUGCCACCUGUUGCUAUCGAAGCACCUGUG
....((((((((.....).)))))))..(((.((((((((((((((((((.........))))))))...))))))))))...))).... ( -32.50)
>DroSec_CAF1 1177 90 + 1
UGUUUUGGGCCCAAAAGGUGGUUCAAUUGGUAUUGGUGGCAAGUGGCAGUGAGGCACCUGCUGCCACCUGUUGCUAUCGAUGCACCUGUG
....((((((((.....).)))))))...(((((((((((((((((((((.((....))))))))))...)))))))))))))....... ( -38.40)
>DroSim_CAF1 1146 90 + 1
UGUUUUGGGUCCAAAAGGUGGUUCAAUUGGUAUUGGUGGCAAGUGGCAGUGAGGCACCUGCUGCCACCUGUUGCUAUCGAUGCACCUGUG
....(((((.(((.....))))))))...(((((((((((((((((((((.((....))))))))))...)))))))))))))....... ( -36.10)
>DroEre_CAF1 1219 90 + 1
UGUUUUGGGCCCAUAAAGUGGCUUAAUUGGUAUUGGUGGCAAGUGGCAGGGAAGCACCUGCUGCCACCUGUUGCUAUCGAAGCACCUGUG
((((((((((((.....).))))....(((((..(((((((....(((((......))))))))))))...))))).)))))))...... ( -35.30)
>DroYak_CAF1 1071 90 + 1
UGUUUUGGGCCCAUAAAGUGGUUUAAUUGGUAUUGGUGGCAAGUGGCAGUGAAGCACCUGCUGCCACCUGUUGCUAUCGAAGUACCUGUG
....((((((((.....).)))))))..((((((((((((((((((((((.........))))))))...)))))))))..))))).... ( -32.10)
>consensus
UGUUUUGGGCCCAAAAAGUGGUUCAAUUGGUAUUGGUGGCAAGUGGCAGUGAAGCACCUGCUGCCACCUGUUGCUAUCGAAGCACCUGUG
....((((((((.....).)))))))..(((.(((((((((((((((((((.......)))))))))...))))))))))...))).... (-30.92 = -30.56 +  -0.36)

alignment

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secondary structure

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dotplot

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Window 6

Location 1,719,253 – 1,719,343
Length 90
Sequences 5
Columns 90
Reading direction reverse
Mean pairwise identity 94.89
Mean single sequence MFE -27.40
Consensus MFE -24.64
Energy contribution -25.72
Covariance contribution 1.08
Combinations/Pair 1.08
Mean z-score -2.93
Structure conservation index 0.90
SVM decision value 4.31
SVM RNA-class probability 0.999868
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 1719253 90 - 23771897
CACAGGUGCUUCGAUAGCAACAGGUGGCAGCAGGUGCUUCACUGCCACUUGCCACCAAUACCAAUUGAACCACUUUUUGGGCCCAAAACA
...(((((.((((((.......(((((((((((........))))....))))))).......)))))).)))))((((....))))... ( -27.74)
>DroSec_CAF1 1177 90 - 1
CACAGGUGCAUCGAUAGCAACAGGUGGCAGCAGGUGCCUCACUGCCACUUGCCACCAAUACCAAUUGAACCACCUUUUGGGCCCAAAACA
...(((((..(((((.......(((((((((((........))))....))))))).......)))))..)))))((((....))))... ( -28.14)
>DroSim_CAF1 1146 90 - 1
CACAGGUGCAUCGAUAGCAACAGGUGGCAGCAGGUGCCUCACUGCCACUUGCCACCAAUACCAAUUGAACCACCUUUUGGACCCAAAACA
...(((((..(((((.......(((((((((((........))))....))))))).......)))))..)))))((((....))))... ( -28.14)
>DroEre_CAF1 1219 90 - 1
CACAGGUGCUUCGAUAGCAACAGGUGGCAGCAGGUGCUUCCCUGCCACUUGCCACCAAUACCAAUUAAGCCACUUUAUGGGCCCAAAACA
....((((((.....)))....((((((((((((......)))))....)))))))...)))......(((.(.....))))........ ( -29.90)
>DroYak_CAF1 1071 90 - 1
CACAGGUACUUCGAUAGCAACAGGUGGCAGCAGGUGCUUCACUGCCACUUGCCACCAAUACCAAUUAAACCACUUUAUGGGCCCAAAACA
....(((...............(((((((((((........))))....))))))).............(((.....))))))....... ( -23.10)
>consensus
CACAGGUGCUUCGAUAGCAACAGGUGGCAGCAGGUGCUUCACUGCCACUUGCCACCAAUACCAAUUGAACCACUUUUUGGGCCCAAAACA
...(((((.((((((.......(((((((((((........))))....))))))).......)))))).)))))((((....))))... (-24.64 = -25.72 +   1.08)

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 09:46:18 2006