Locus 4740

Sequence ID X_DroMel_CAF1
Location 12,317,036 – 12,317,204
Length 168
Max. P 0.997195
window7774 window7775 window7776

overview

Window 4

Location 12,317,036 – 12,317,131
Length 95
Sequences 4
Columns 117
Reading direction reverse
Mean pairwise identity 84.67
Mean single sequence MFE -26.58
Consensus MFE -21.20
Energy contribution -21.26
Covariance contribution 0.06
Combinations/Pair 1.04
Mean z-score -1.43
Structure conservation index 0.80
SVM decision value -0.00
SVM RNA-class probability 0.532759
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 12317036 95 - 22224390
UUU------U----------AAUUUUGGCAAUAGCUGGUUGUCAUUAGUGGAGCAUGUCCAGGGCGUGAUUGAAUCUGAAUGGUAUAUUA------AGAAUCAGUUAUGGCUGCACG
...------.----------.....(((((((.....)))))))...(((.(((..((.....))((((((((.(((.((((...)))).------))).)))))))).))).))). ( -24.50)
>DroSim_CAF1 19666 100 - 1
UUU------UUUU-----UUUUUUUUGGCAAUAGCUGGUUGUCAUUAGUGGAGCAUGUCCAGGGCGUGAUUGAAUCUGAAUGGAAUAUUA------AGAAUCAGUUAUGGCUGCACG
...------....-----.......(((((((.....)))))))...(((.(((..((.....))((((((((.(((.((((...)))).------))).)))))))).))).))). ( -24.50)
>DroEre_CAF1 19598 117 - 1
UUGGCCACUUUUUUGGCCACUUUUUUGGCAAUAGCUGGUUGUCAUUAGUGGAGCAUGUCCAGGGCGUGAUUGAAUCUGAAUGGAAUAUUAAUAUUAGGAAUCAGUUAUGGCUGCACG
.((((((......))))))......(((((((.....)))))))...(((.(((..((.....))((((((((.(((.((((.........)))).))).)))))))).))).))). ( -34.40)
>DroYak_CAF1 18731 93 - 1
UU------------------UUAUUUGGCAAUAGCUGGUUGUCAUUAGUGGAGCAUGUCCAGGGCGUGAUUGAAUCUGAAUGGAAUAUUA------AGAAUCAGUUAUGGCUGCAGG
..------------------.....(((((((.....)))))))....((((.....))))((.(((((((((.(((.((((...)))).------))).))))))))).))..... ( -22.90)
>consensus
UUU______U__________UUUUUUGGCAAUAGCUGGUUGUCAUUAGUGGAGCAUGUCCAGGGCGUGAUUGAAUCUGAAUGGAAUAUUA______AGAAUCAGUUAUGGCUGCACG
.........................(((((((.....)))))))...(((.(((..((.....))((((((((.(((...................))).)))))))).))).))). (-21.20 = -21.26 +   0.06)

alignment

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secondary structure

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Window 5

Location 12,317,107 – 12,317,204
Length 97
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 70.76
Mean single sequence MFE -26.91
Consensus MFE -16.91
Energy contribution -17.13
Covariance contribution 0.22
Combinations/Pair 1.05
Mean z-score -2.00
Structure conservation index 0.63
SVM decision value 2.81
SVM RNA-class probability 0.997195
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 12317107 97 + 22224390
AACCAGCUAUUGCCAAAAUU----------A------AAAAUAAGGGGCGUUGUUCGGCCACCUACAAGAAUAAUUAUAAUAAUAUUCCAGGAACGGGAAGGGUGGAGGGG--UA-----
.(((..((.(..((......----------.------......((((((........))).))).....................((((......))))..))..))).))--).----- ( -20.00)
>DroSim_CAF1 19737 92 + 1
AACCAGCUAUUGCCAAAAAAAA-----AAAA------AAAAUUAGGGGCGUUGUUCGGCCACCUACAAGAAUAAUUAUAAUAUUAUUCCAGGAGCGGGGGG------------UA-----
.(((.(((.(((..........-----....------.....(((((((........))).))))...(((((((......)))))))))).)))....))------------).----- ( -20.70)
>DroEre_CAF1 19675 120 + 1
AACCAGCUAUUGCCAAAAAAGUGGCCAAAAAAGUGGCCAAAUGAGGGGCGUUGUUCGGCCACCUACAAGCAUAAUUAUAAUAUUAUGCCAGGGCUGGGAGGGGCGGACGAUUCGAUAUGA
...........(((.......((((((......)))))).......)))((((((((.((.(((((..(((((((......)))))))....).))))..)).))))))))......... ( -40.04)
>consensus
AACCAGCUAUUGCCAAAAAA_______AAAA______AAAAUAAGGGGCGUUGUUCGGCCACCUACAAGAAUAAUUAUAAUAUUAUUCCAGGAACGGGAGGGG_GGA_G____UA_____
..((..((....((.............................((((((........))).)))....(((((((......)))))))..))....))..)).................. (-16.91 = -17.13 +   0.22)

alignment

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secondary structure

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dotplot

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Window 6

Location 12,317,107 – 12,317,204
Length 97
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 70.76
Mean single sequence MFE -22.08
Consensus MFE -14.88
Energy contribution -14.77
Covariance contribution -0.11
Combinations/Pair 1.06
Mean z-score -1.37
Structure conservation index 0.67
SVM decision value 0.98
SVM RNA-class probability 0.893704
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 12317107 97 - 22224390
-----UA--CCCCUCCACCCUUCCCGUUCCUGGAAUAUUAUUAUAAUUAUUCUUGUAGGUGGCCGAACAACGCCCCUUAUUUU------U----------AAUUUUGGCAAUAGCUGGUU
-----.(--((....((((.((((.......))))......(((((......)))))))))((((((................------.----------...)))))).......))). ( -13.75)
>DroSim_CAF1 19737 92 - 1
-----UA------------CCCCCCGCUCCUGGAAUAAUAUUAUAAUUAUUCUUGUAGGUGGCCGAACAACGCCCCUAAUUUU------UUUU-----UUUUUUUUGGCAAUAGCUGGUU
-----..------------...((.(((..(((((((((......)))))))...((((.(((........))))))).....------....-----..........))..))).)).. ( -18.70)
>DroEre_CAF1 19675 120 - 1
UCAUAUCGAAUCGUCCGCCCCUCCCAGCCCUGGCAUAAUAUUAUAAUUAUGCUUGUAGGUGGCCGAACAACGCCCCUCAUUUGGCCACUUUUUUGGCCACUUUUUUGGCAAUAGCUGGUU
.......................(((((...((((((((......))))))))...(((((((((((............))))))))))).....((((......))))....))))).. ( -33.80)
>consensus
_____UA____C_UCC_CCCCUCCCGCUCCUGGAAUAAUAUUAUAAUUAUUCUUGUAGGUGGCCGAACAACGCCCCUAAUUUU______UUUU_______UUUUUUGGCAAUAGCUGGUU
...............................((((((((......))))))))...(((.(((........))))))...........................(..((....))..).. (-14.88 = -14.77 +  -0.11)

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 11:32:15 2006