Locus 2431

Sequence ID X_DroMel_CAF1
Location 6,527,196 – 6,527,344
Length 148
Max. P 0.983349
window3951 window3952 window3953

overview

Window 1

Location 6,527,196 – 6,527,304
Length 108
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 68.85
Mean single sequence MFE -32.21
Consensus MFE -20.12
Energy contribution -19.57
Covariance contribution -0.55
Combinations/Pair 1.22
Mean z-score -1.97
Structure conservation index 0.62
SVM decision value 1.94
SVM RNA-class probability 0.983349
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 6527196 108 + 22224390
UCUUUGC------------AGUGCGACAGUGGCGGUAAGGGCGGCAAGGGCAAGGAGAAUGGCAAGUUUCGUACGGAGAAGGACACCUUCGGGGAGCUAAAGGUGCCGGCGGACAAGCUG
(((((((------------...((....)).((.((....)).))....)))))))....(((..(((.(((........((.((((((..(....)..)))))))).))))))..))). ( -31.10)
>DroPse_CAF1 527 88 + 1
U-CAGGC------------A----AAAAAGGGCAAUUC------------CAAGGAG---GGAAAGUUCCGGAUGGAGAAGGACACCUUUGGGGAGCUAAAGGUGCCUGCCGAAAUGUUG
.-..(((------------.----...........(((------------((.((((---......))))...))))).(((.(((((((((....)))))))))))))))......... ( -31.00)
>DroSim_CAF1 476 96 + 1
UCUUUGC------------AGUGUGACAAGGGCGGUAAGGGCGGCAAGGGC------------AAGUUCCGCACGGAGAAGGACACCUUCGGGGAGCUAAAGGUGCCGGCGGACAAGCUG
.((((((------------.....).)))))((.((....)).))...(((------------..((.((((.(((.......((((((..(....)..)))))))))))))))..))). ( -31.21)
>DroEre_CAF1 529 90 + 1
UAUUUGC---------------------AGGGCGACA---------AGGGCAAGGAGACUGGAAAGUUUCGCACGGAGAAGGACACCUUUGGGGAGCUAAAGGUGCCGGCGGACAAGAUG
..(((((---------------------..(....).---------...)))))((((((....))))))((.(((.......(((((((((....)))))))))))))).......... ( -30.61)
>DroYak_CAF1 541 111 + 1
UAUUUGCAUUUGCAUUCGCAGUGCGACAAGGGCGGCA---------AGGGAAAGGAGAAUGCCAAGUUCCGCAUGGAGAAGGACACCUUUGGGGAGCUGAGGGUGCCGGCGGACAAGCUG
...(((((((.((....)))))))))....(((((((---------.............))))..((.((((........((.((((((..(....)..)))))))).))))))..))). ( -38.32)
>DroPer_CAF1 524 88 + 1
U-CAGGC------------A----AAAAAGGGCAAUUC------------CAAGGAG---GGAAAGUUCCGGAUGGAGAAGGACACCUUUGGGGAGCUAAAGGUGCCUGCCGAAAUGUUG
.-..(((------------.----...........(((------------((.((((---......))))...))))).(((.(((((((((....)))))))))))))))......... ( -31.00)
>consensus
U_UUUGC____________A____GACAAGGGCGAUA_________AGGGCAAGGAG___GGAAAGUUCCGCACGGAGAAGGACACCUUUGGGGAGCUAAAGGUGCCGGCGGACAAGCUG
....(((...........................................................((((....))))..((.(((((((((....))))))))))).)))......... (-20.12 = -19.57 +  -0.55)

alignment

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secondary structure

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dotplot

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Window 2

Location 6,527,224 – 6,527,344
Length 120
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 80.91
Mean single sequence MFE -45.30
Consensus MFE -26.33
Energy contribution -26.67
Covariance contribution 0.33
Combinations/Pair 1.20
Mean z-score -3.15
Structure conservation index 0.58
SVM decision value 1.32
SVM RNA-class probability 0.942006
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 6527224 120 + 22224390
GCGGCAAGGGCAAGGAGAAUGGCAAGUUUCGUACGGAGAAGGACACCUUCGGGGAGCUAAAGGUGCCGGCGGACAAGCUGUACGGCGCACAGACGAUGCGCUCCAAAUUGAAUUUUCCCA
...((....))..(((((((..(((....(((((......((.((((((..(....)..))))))))(((......))))))))((((((....).)))))......))).))))))).. ( -39.30)
>DroPse_CAF1 548 107 + 1
----------CAAGGAG---GGAAAGUUCCGGAUGGAGAAGGACACCUUUGGGGAGCUAAAGGUGCCUGCCGAAAUGUUGUUCGGCGCACAGACGAUGCGCUCCAAGAUCAACUUUCCCA
----------......(---((((((((.....(((((.(((.(((((((((....))))))))))))((((((......))))))((((....).))).))))).....))))))))). ( -48.40)
>DroGri_CAF1 933 107 + 1
----------CCAGG---AUGGCAAGUUUCGCAUGGAGCGGGACACAUUUGGCGAGCUGAAGGUGCCAGCGGAUAAACUGUUUGGCGCACAGACGAUGCGCUCCGUGAUCAAUUUCCCCA
----------...((---..((.(((((...(((((((((.(.(...((..(....)..)).((((((((((.....))).)))))))......).).)))))))))...))))))))). ( -36.80)
>DroEre_CAF1 545 114 + 1
------AGGGCAAGGAGACUGGAAAGUUUCGCACGGAGAAGGACACCUUUGGGGAGCUAAAGGUGCCGGCGGACAAGAUGUACGGUGCGCAGACGAUGCGCUCCAAGCUAAAUUUUCCCA
------...((...((((((....))))))))..((((((((.(((((((((....)))))))))))((((.((.....)).)((.(((((.....))))).))..)))...)))))).. ( -45.10)
>DroYak_CAF1 578 114 + 1
------AGGGAAAGGAGAAUGCCAAGUUCCGCAUGGAGAAGGACACCUUUGGGGAGCUGAGGGUGCCGGCGGACAAGCUGUACGGAGCGCAGACGAUGCGCUCCAAGCUGAAUUUUCCCA
------.(((((((..(..((((...((((....))))..((.((((((..(....)..))))))))))))..).((((....((((((((.....)))))))).))))...))))))). ( -53.80)
>DroPer_CAF1 545 107 + 1
----------CAAGGAG---GGAAAGUUCCGGAUGGAGAAGGACACCUUUGGGGAGCUAAAGGUGCCUGCCGAAAUGUUGUUCGGCGCACAGACGAUGCGCUCCAAGAUCAACUUUCCCA
----------......(---((((((((.....(((((.(((.(((((((((....))))))))))))((((((......))))))((((....).))).))))).....))))))))). ( -48.40)
>consensus
__________CAAGGAG_AUGGAAAGUUCCGCAUGGAGAAGGACACCUUUGGGGAGCUAAAGGUGCCGGCGGACAAGCUGUACGGCGCACAGACGAUGCGCUCCAAGAUCAAUUUUCCCA
....................((.(((((.....(((((..((.(((((((((....))))))))))).(((......((((.......))))....))).))))).....))))).)).. (-26.33 = -26.67 +   0.33)

alignment

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secondary structure

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dotplot

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Window 3

Location 6,527,224 – 6,527,344
Length 120
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 80.91
Mean single sequence MFE -36.91
Consensus MFE -22.03
Energy contribution -22.25
Covariance contribution 0.22
Combinations/Pair 1.16
Mean z-score -2.04
Structure conservation index 0.60
SVM decision value 0.38
SVM RNA-class probability 0.711699
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 6527224 120 - 22224390
UGGGAAAAUUCAAUUUGGAGCGCAUCGUCUGUGCGCCGUACAGCUUGUCCGCCGGCACCUUUAGCUCCCCGAAGGUGUCCUUCUCCGUACGAAACUUGCCAUUCUCCUUGCCCUUGCCGC
.(((...........(((.((((((.....))))))(((((.((......)).(((((((((........))))))))).......))))).......))).........)))....... ( -33.85)
>DroPse_CAF1 548 107 - 1
UGGGAAAGUUGAUCUUGGAGCGCAUCGUCUGUGCGCCGAACAACAUUUCGGCAGGCACCUUUAGCUCCCCAAAGGUGUCCUUCUCCAUCCGGAACUUUCC---CUCCUUG----------
.(((((((((.....(((((((((.....)))))((((((......)))))).(((((((((........)))))))))....)))).....))))))))---)......---------- ( -43.60)
>DroGri_CAF1 933 107 - 1
UGGGGAAAUUGAUCACGGAGCGCAUCGUCUGUGCGCCAAACAGUUUAUCCGCUGGCACCUUCAGCUCGCCAAAUGUGUCCCGCUCCAUGCGAAACUUGCCAU---CCUGG----------
.((..((((((.....((.(((((.....))))).))...))))))..))(((((.....)))))...(((.(((.((..(((.....)))..))....)))---..)))---------- ( -26.20)
>DroEre_CAF1 545 114 - 1
UGGGAAAAUUUAGCUUGGAGCGCAUCGUCUGCGCACCGUACAUCUUGUCCGCCGGCACCUUUAGCUCCCCAAAGGUGUCCUUCUCCGUGCGAAACUUUCCAGUCUCCUUGCCCU------
.(((.......((.((((((((((.....)))))..(((((.....(....).(((((((((........))))))))).......)))))......))))).)).....))).------ ( -33.30)
>DroYak_CAF1 578 114 - 1
UGGGAAAAUUCAGCUUGGAGCGCAUCGUCUGCGCUCCGUACAGCUUGUCCGCCGGCACCCUCAGCUCCCCAAAGGUGUCCUUCUCCAUGCGGAACUUGGCAUUCUCCUUUCCCU------
.((((((....(((((((((((((.....)))))))))...)))).....(((((((((..............))))))....(((....)))....))).......)))))).------ ( -40.94)
>DroPer_CAF1 545 107 - 1
UGGGAAAGUUGAUCUUGGAGCGCAUCGUCUGUGCGCCGAACAACAUUUCGGCAGGCACCUUUAGCUCCCCAAAGGUGUCCUUCUCCAUCCGGAACUUUCC---CUCCUUG----------
.(((((((((.....(((((((((.....)))))((((((......)))))).(((((((((........)))))))))....)))).....))))))))---)......---------- ( -43.60)
>consensus
UGGGAAAAUUGAUCUUGGAGCGCAUCGUCUGUGCGCCGAACAGCUUGUCCGCCGGCACCUUUAGCUCCCCAAAGGUGUCCUUCUCCAUGCGAAACUUGCCAU_CUCCUUG__________
..(((...........((.(((((.....))))).))................(((((((((........)))))))))....))).................................. (-22.03 = -22.25 +   0.22)

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 10:34:18 2006