Locus 2037

Sequence ID X_DroMel_CAF1
Location 5,595,963 – 5,596,094
Length 131
Max. P 0.991932
window3313 window3314 window3315 window3316

overview

Window 3

Location 5,595,963 – 5,596,065
Length 102
Sequences 5
Columns 102
Reading direction forward
Mean pairwise identity 83.73
Mean single sequence MFE -24.02
Consensus MFE -18.06
Energy contribution -16.58
Covariance contribution -1.48
Combinations/Pair 1.52
Mean z-score -2.02
Structure conservation index 0.75
SVM decision value 0.85
SVM RNA-class probability 0.866772
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 5595963 102 + 22224390
AAAGUGAAAUGCUGUAAGCCAUUUCCAGUGGCCUUUUGUCAUCACUGCCAGGGUAAAUAAACUUUCGUUUGCCUUUCUCCUGGUAUUGACACUUUGAAAUAU
((((((...........(((((.....))))).........(((.(((((((..((((((((....)))))..)))..))))))).)))))))))....... ( -27.70)
>DroSec_CAF1 2834 102 + 1
AAAGUGAAAUGCUGUAAGCCAUUUCCUGUGACGUUUUGUCAUUUCUGCCAGGGUAAAUAAACUUUUGUUUACCCCUUCCCUGGUAUUGACUCUUUGAGAUAU
..((.(((((((.....).))))))))....((....((((....((((((((....(((((....)))))......)))))))).))))....))...... ( -25.10)
>DroSim_CAF1 4642 102 + 1
AAAGUAAAAUGCUGUAAGACAUUUCCUGUGACCUUUUGUCAUCACUGCCAGGGUAAAUAAACUUACGUUUACCUCUUCCCUGGUAUUGACUCUUUGAAAUAU
....................(((((...((((.....))))(((.((((((((....(((((....)))))......)))))))).)))......))))).. ( -22.50)
>DroEre_CAF1 2877 102 + 1
AAAGUGAAAAGUUAUAAGCCAUUCCCAUUGGCCUUUUGUCAUCACUGCAGGGGUAAACAAACUCUUGUUUGCCAUUCCACUCGUGUUGACUCUUUGAAAUAU
.......((((......((((.......)))).....((((.(((....(((((((((((....)))))))))...))....))).)))).))))....... ( -23.20)
>DroYak_CAF1 4857 102 + 1
UAAGUGAAAAGUUUUAAGCCAUUUUCAGUGGUCAUUUGCCAUCACUGCAAGGGUAAAUAAACUUUUGUUUGUCUUUCCUCUUGUAUUGACUCUUUGAAAUAU
..........((((((((((((.....))))).........(((.((((((((...((((((....))))))....)).)))))).)))....))))))).. ( -21.60)
>consensus
AAAGUGAAAUGCUGUAAGCCAUUUCCAGUGGCCUUUUGUCAUCACUGCCAGGGUAAAUAAACUUUUGUUUGCCUUUCCCCUGGUAUUGACUCUUUGAAAUAU
....................(((((...((((.....))))(((.((((((((....(((((....)))))......)))))))).)))......))))).. (-18.06 = -16.58 +  -1.48)

alignment

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secondary structure

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dotplot

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Window 4

Location 5,595,963 – 5,596,065
Length 102
Sequences 5
Columns 102
Reading direction reverse
Mean pairwise identity 83.73
Mean single sequence MFE -24.48
Consensus MFE -17.46
Energy contribution -18.14
Covariance contribution 0.68
Combinations/Pair 1.33
Mean z-score -2.21
Structure conservation index 0.71
SVM decision value 1.00
SVM RNA-class probability 0.898229
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 5595963 102 - 22224390
AUAUUUCAAAGUGUCAAUACCAGGAGAAAGGCAAACGAAAGUUUAUUUACCCUGGCAGUGAUGACAAAAGGCCACUGGAAAUGGCUUACAGCAUUUCACUUU
.......(((((((((...(((((..(((...((((....)))).)))..)))))...))).......((((((.(....))))))).........)))))) ( -26.30)
>DroSec_CAF1 2834 102 - 1
AUAUCUCAAAGAGUCAAUACCAGGGAAGGGGUAAACAAAAGUUUAUUUACCCUGGCAGAAAUGACAAAACGUCACAGGAAAUGGCUUACAGCAUUUCACUUU
..........((((((...((((((...((((((((....)))))))).))))))......((((.....)))).......))))))............... ( -25.20)
>DroSim_CAF1 4642 102 - 1
AUAUUUCAAAGAGUCAAUACCAGGGAAGAGGUAAACGUAAGUUUAUUUACCCUGGCAGUGAUGACAAAAGGUCACAGGAAAUGUCUUACAGCAUUUUACUUU
.......((((.((((...((((((...((((((((....)))))))).))))))...))))(((.....)))....(((((((......))))))).)))) ( -29.60)
>DroEre_CAF1 2877 102 - 1
AUAUUUCAAAGAGUCAACACGAGUGGAAUGGCAAACAAGAGUUUGUUUACCCCUGCAGUGAUGACAAAAGGCCAAUGGGAAUGGCUUAUAACUUUUCACUUU
.......((((.((((.(((.((.((...(((((((....)))))))...))))...))).))))...((((((.......))))))....))))....... ( -24.60)
>DroYak_CAF1 4857 102 - 1
AUAUUUCAAAGAGUCAAUACAAGAGGAAAGACAAACAAAAGUUUAUUUACCCUUGCAGUGAUGGCAAAUGACCACUGAAAAUGGCUUAAAACUUUUCACUUA
..........((((((...((((.(((((...((((....)))).))).))))))(((((............)))))....))))))............... ( -16.70)
>consensus
AUAUUUCAAAGAGUCAAUACCAGGGGAAAGGCAAACAAAAGUUUAUUUACCCUGGCAGUGAUGACAAAAGGCCACUGGAAAUGGCUUACAGCAUUUCACUUU
.......((((.((((.((((((((...((((((((....)))))))).))))))...)).))))............((((((........)))))).)))) (-17.46 = -18.14 +   0.68)

alignment

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secondary structure

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dotplot

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Window 5

Location 5,596,003 – 5,596,094
Length 91
Sequences 5
Columns 91
Reading direction forward
Mean pairwise identity 88.02
Mean single sequence MFE -22.96
Consensus MFE -17.96
Energy contribution -17.16
Covariance contribution -0.80
Combinations/Pair 1.32
Mean z-score -2.86
Structure conservation index 0.78
SVM decision value 2.30
SVM RNA-class probability 0.991932
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 5596003 91 + 22224390
AUCACUGCCAGGGUAAAUAAACUUUCGUUUGCCUUUCUCCUGGUAUUGACACUUUGAAAUAUUUAUUAUUUUUCUUUGUAGCAAAGUGGAG
.(((.(((((((..((((((((....)))))..)))..))))))).)))(((((((..(((...............)))..)))))))... ( -24.06)
>DroSec_CAF1 2874 91 + 1
AUUUCUGCCAGGGUAAAUAAACUUUUGUUUACCCCUUCCCUGGUAUUGACUCUUUGAGAUAUUUAUUAUUUCUCUUUGUAGCAAAGUGGAG
.....((((((((....(((((....)))))......))))))))....((((..((((((.....)))))).(((((...))))).)))) ( -22.70)
>DroSim_CAF1 4682 91 + 1
AUCACUGCCAGGGUAAAUAAACUUACGUUUACCUCUUCCCUGGUAUUGACUCUUUGAAAUAUUUAUUAUUUCUCUUUGCAGCAAAGUGGAG
.(((.((((((((....(((((....)))))......)))))))).)))......((((((.....)))))).(((..(......)..))) ( -25.10)
>DroEre_CAF1 2917 91 + 1
AUCACUGCAGGGGUAAACAAACUCUUGUUUGCCAUUCCACUCGUGUUGACUCUUUGAAAUAUUUAUUAUUUUUCUUCGUAGCAAAGUGGAG
...........(((((((((....)))))))))..((((((..(((((.......((((((.....))))))......))))).)))))). ( -24.22)
>DroYak_CAF1 4897 91 + 1
AUCACUGCAAGGGUAAAUAAACUUUUGUUUGUCUUUCCUCUUGUAUUGACUCUUUGAAAUAUUUAUUAUUUUUCUUUGUAGCAAAGUGGAG
.(((.((((((((...((((((....))))))....)).)))))).)))((((..((((((.....)))))).(((((...))))).)))) ( -18.70)
>consensus
AUCACUGCCAGGGUAAAUAAACUUUUGUUUGCCUUUCCCCUGGUAUUGACUCUUUGAAAUAUUUAUUAUUUUUCUUUGUAGCAAAGUGGAG
.(((.((((((((....(((((....)))))......)))))))).)))((((..((((((.....)))))).(((((...))))).)))) (-17.96 = -17.16 +  -0.80)

alignment

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secondary structure

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dotplot

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Window 6

Location 5,596,003 – 5,596,094
Length 91
Sequences 5
Columns 91
Reading direction reverse
Mean pairwise identity 88.02
Mean single sequence MFE -19.06
Consensus MFE -14.96
Energy contribution -15.64
Covariance contribution 0.68
Combinations/Pair 1.26
Mean z-score -2.27
Structure conservation index 0.78
SVM decision value 1.47
SVM RNA-class probability 0.956453
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 5596003 91 - 22224390
CUCCACUUUGCUACAAAGAAAAAUAAUAAAUAUUUCAAAGUGUCAAUACCAGGAGAAAGGCAAACGAAAGUUUAUUUACCCUGGCAGUGAU
...(((((((..........(((((.....))))))))))))(((...(((((..(((...((((....)))).)))..)))))...))). ( -20.30)
>DroSec_CAF1 2874 91 - 1
CUCCACUUUGCUACAAAGAGAAAUAAUAAAUAUCUCAAAGAGUCAAUACCAGGGAAGGGGUAAACAAAAGUUUAUUUACCCUGGCAGAAAU
......(((((......((((.((.....)).)))).............(((((...((((((((....)))))))).))))))))))... ( -21.20)
>DroSim_CAF1 4682 91 - 1
CUCCACUUUGCUGCAAAGAGAAAUAAUAAAUAUUUCAAAGAGUCAAUACCAGGGAAGAGGUAAACGUAAGUUUAUUUACCCUGGCAGUGAU
.......(..((((.....((((((.....)))))).............(((((...((((((((....)))))))).)))))))))..). ( -28.60)
>DroEre_CAF1 2917 91 - 1
CUCCACUUUGCUACGAAGAAAAAUAAUAAAUAUUUCAAAGAGUCAACACGAGUGGAAUGGCAAACAAGAGUUUGUUUACCCCUGCAGUGAU
.(((((((((((.(...((((.((.....)).))))...))).))....)))))))..(((((((....)))))))............... ( -14.00)
>DroYak_CAF1 4897 91 - 1
CUCCACUUUGCUACAAAGAAAAAUAAUAAAUAUUUCAAAGAGUCAAUACAAGAGGAAAGACAAACAAAAGUUUAUUUACCCUUGCAGUGAU
.....(((((...))))).......................((((...((((.(((((...((((....)))).))).))))))...)))) ( -11.20)
>consensus
CUCCACUUUGCUACAAAGAAAAAUAAUAAAUAUUUCAAAGAGUCAAUACCAGGGGAAAGGCAAACAAAAGUUUAUUUACCCUGGCAGUGAU
.....(((((...))))).......................((((...((((((...((((((((....)))))))).))))))...)))) (-14.96 = -15.64 +   0.68)

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 10:24:45 2006