Locus 8145

Sequence ID X_DroMel_CAF1
Location 20,265,318 – 20,265,468
Length 150
Max. P 0.999899
window13386 window13387 window13388 window13389

overview

Window 6

Location 20,265,318 – 20,265,437
Length 119
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 79.33
Mean single sequence MFE -33.73
Consensus MFE -23.17
Energy contribution -23.09
Covariance contribution -0.08
Combinations/Pair 1.10
Mean z-score -1.83
Structure conservation index 0.69
SVM decision value 0.69
SVM RNA-class probability 0.824453
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 20265318 119 + 22224390
AAAUUUUUAAUUGCAAACACCAACAAAUUGCAUUUGCCAGCGGCGUGGGCGAGCAACUGCAGCAGAUCCAGCUCCAGCUCCAGAUCCAGCUCCAGAUUCUCGGAAA-GCCGCGCGGCUUA
...........(((((...........)))))...(((.(((((.....((((...(((.(((.((((.(((....)))...))))..))).)))...))))....-)))))..)))... ( -36.00)
>DroEre_CAF1 11551 101 + 1
UAAUU-UUAAUUGCAAACACCAACAAAUUGCAUUUGCCAGCGGCGUGGCCCAGUAACUGCAGU------------------AUCUCCAGCUGCAGAUCCUCGGAAAAACCACGCGGCUUA
.....-.(((.(((((...........))))).)))..(((.((((((((.((...(((((((------------------.......)))))))...)).)).....)))))).))).. ( -30.50)
>DroYak_CAF1 12051 118 + 1
UAAUU-UUAAUUGCAAACACCAACAAAUUGCAUUUGCCAGCGGCGUGGGCGAGCAACUGCAGCCGCUUCAGCUUCAGCUUGAGCUUCAGCUCCAGAUCCUCGGAAA-GUCGCGCGGCUCA
.....-.....(((((...........)))))...(((.(((((.....((((...(((.(((.((((.(((....))).))))....))).)))...))))....-)))))..)))... ( -34.70)
>consensus
UAAUU_UUAAUUGCAAACACCAACAAAUUGCAUUUGCCAGCGGCGUGGGCGAGCAACUGCAGC_G_U_CAGCU_CAGCU__AGCUCCAGCUCCAGAUCCUCGGAAA_GCCGCGCGGCUUA
.......(((.(((((...........))))).)))..(((.((((((.((((...(((.(((......(((....))).........))).)))...))))......)))))).))).. (-23.17 = -23.09 +  -0.08)

alignment

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secondary structure

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dotplot

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Window 7

Location 20,265,318 – 20,265,437
Length 119
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 79.33
Mean single sequence MFE -39.20
Consensus MFE -25.58
Energy contribution -26.39
Covariance contribution 0.81
Combinations/Pair 1.07
Mean z-score -1.67
Structure conservation index 0.65
SVM decision value 0.18
SVM RNA-class probability 0.622530
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 20265318 119 - 22224390
UAAGCCGCGCGGC-UUUCCGAGAAUCUGGAGCUGGAUCUGGAGCUGGAGCUGGAUCUGCUGCAGUUGCUCGCCCACGCCGCUGGCAAAUGCAAUUUGUUGGUGUUUGCAAUUAAAAAUUU
...((((.(((((-....((((...(((.(((.((((((..(((....)))))))))))).)))...)))).....)))))))))...(((((...........)))))........... ( -44.40)
>DroEre_CAF1 11551 101 - 1
UAAGCCGCGUGGUUUUUCCGAGGAUCUGCAGCUGGAGAU------------------ACUGCAGUUACUGGGCCACGCCGCUGGCAAAUGCAAUUUGUUGGUGUUUGCAAUUAA-AAUUA
..(((.((((((.....((.((...((((((........------------------.))))))...)).)))))))).))).((((((((.........))))))))......-..... ( -35.30)
>DroYak_CAF1 12051 118 - 1
UGAGCCGCGCGAC-UUUCCGAGGAUCUGGAGCUGAAGCUCAAGCUGAAGCUGAAGCGGCUGCAGUUGCUCGCCCACGCCGCUGGCAAAUGCAAUUUGUUGGUGUUUGCAAUUAA-AAUUA
..((((((.....-..((((......))))(((..(((....)))..)))....))))))..((((((..((....))(((..((((((...))))))..)))...))))))..-..... ( -37.90)
>consensus
UAAGCCGCGCGGC_UUUCCGAGGAUCUGGAGCUGGAGCU__AGCUG_AGCUG_A_C_GCUGCAGUUGCUCGCCCACGCCGCUGGCAAAUGCAAUUUGUUGGUGUUUGCAAUUAA_AAUUA
...((((.(((((.....((((...(((.(((.........(((....)))......))).)))...)))).....)))))))))...(((((...........)))))........... (-25.58 = -26.39 +   0.81)

alignment

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secondary structure

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dotplot

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Window 8

Location 20,265,358 – 20,265,468
Length 110
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 72.14
Mean single sequence MFE -45.23
Consensus MFE -33.79
Energy contribution -33.83
Covariance contribution 0.03
Combinations/Pair 1.10
Mean z-score -2.31
Structure conservation index 0.75
SVM decision value 4.44
SVM RNA-class probability 0.999899
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 20265358 110 + 22224390
CGGCGUGGGCGAGCAACUGCAGCAGAUCCAGCUCCAGCUCCAGAUCCAGCUCCAGAUUCUCGGAAA-GCCGCGCGGCUUAGCUGCGCGCAUUUCCAUGCCUGCGAUUUUCU---------
...((..((((((...(((.(((.((((.(((....)))...))))..))).)))...)))(((((-..((((((((...))))))))..)))))..)))..)).......--------- ( -47.70)
>DroEre_CAF1 11590 102 + 1
CGGCGUGGCCCAGUAACUGCAGU------------------AUCUCCAGCUGCAGAUCCUCGGAAAAACCACGCGGCUUAGCUGCGCGCAUUUCCAUGGCUGCGAUUUUCCUGAGGGAAA
...((..(((......(((((((------------------.......)))))))......(((((...(.((((((...)))))).)..)))))..)))..))..(((((....))))) ( -38.80)
>DroYak_CAF1 12090 119 + 1
CGGCGUGGGCGAGCAACUGCAGCCGCUUCAGCUUCAGCUUGAGCUUCAGCUCCAGAUCCUCGGAAA-GUCGCGCGGCUCAGCUGCGCGCUUUUCCAUGCCUGUGAUUUUGUGGAGGAAAA
.(((((((.((((...(((.(((.((((.(((....))).))))....))).)))...))))((((-(.((((((((...)))))))))))))))))))).................... ( -49.20)
>consensus
CGGCGUGGGCGAGCAACUGCAGC_G_U_CAGCU_CAGCU__AGCUCCAGCUCCAGAUCCUCGGAAA_GCCGCGCGGCUUAGCUGCGCGCAUUUCCAUGCCUGCGAUUUUCU_GAGG_AAA
...((..((((((...(((.(((......(((....))).........))).)))...)))(((((...((((((((...))))))))..)))))..)))..))................ (-33.79 = -33.83 +   0.03)

alignment

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secondary structure

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dotplot

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Window 9

Location 20,265,358 – 20,265,468
Length 110
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 72.14
Mean single sequence MFE -43.27
Consensus MFE -27.89
Energy contribution -27.93
Covariance contribution 0.03
Combinations/Pair 1.11
Mean z-score -1.59
Structure conservation index 0.64
SVM decision value 1.19
SVM RNA-class probability 0.928244
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 20265358 110 - 22224390
---------AGAAAAUCGCAGGCAUGGAAAUGCGCGCAGCUAAGCCGCGCGGC-UUUCCGAGAAUCUGGAGCUGGAUCUGGAGCUGGAGCUGGAUCUGCUGCAGUUGCUCGCCCACGCCG
---------.......((..(((..(((((.((((((.((...)).)))).))-)))))(((...(((.(((.((((((..(((....)))))))))))).)))...))))))..))... ( -44.50)
>DroEre_CAF1 11590 102 - 1
UUUCCCUCAGGAAAAUCGCAGCCAUGGAAAUGCGCGCAGCUAAGCCGCGUGGUUUUUCCGAGGAUCUGCAGCUGGAGAU------------------ACUGCAGUUACUGGGCCACGCCG
....((((.((((((((((.(((((....))).))((.((...)).)))))))))))).))))..((((((........------------------.))))))......(((...))). ( -36.40)
>DroYak_CAF1 12090 119 - 1
UUUUCCUCCACAAAAUCACAGGCAUGGAAAAGCGCGCAGCUGAGCCGCGCGAC-UUUCCGAGGAUCUGGAGCUGAAGCUCAAGCUGAAGCUGAAGCGGCUGCAGUUGCUCGCCCACGCCG
....................(((.(((....(((.(((((((((((((.....-..((((......))))(((..(((....)))..)))....)))))).))))))).)))))).))). ( -48.90)
>consensus
UUU_CCUC_AGAAAAUCGCAGGCAUGGAAAUGCGCGCAGCUAAGCCGCGCGGC_UUUCCGAGGAUCUGGAGCUGGAGCU__AGCUG_AGCUG_A_C_GCUGCAGUUGCUCGCCCACGCCG
....................(((..(((((.((((((.((...)).))))).).)))))(((...(((.(((.........(((....)))......))).)))...))))))....... (-27.89 = -27.93 +   0.03)

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 12:56:58 2006