Locus 3862

Sequence ID 2R_DroMel_CAF1
Location 12,769,214 – 12,769,309
Length 95
Max. P 0.978904
window6241 window6242

overview

Window 1

Location 12,769,214 – 12,769,309
Length 95
Sequences 6
Columns 104
Reading direction forward
Mean pairwise identity 77.25
Mean single sequence MFE -19.38
Consensus MFE -13.97
Energy contribution -14.17
Covariance contribution 0.20
Combinations/Pair 1.22
Mean z-score -1.69
Structure conservation index 0.72
SVM decision value 1.22
SVM RNA-class probability 0.932663
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 12769214 95 + 20766785
UUGGCUGUCUCACUUUGGCCCGGCAAAGUUUU--ACCAACUU-UCGUCCACUUUGGCAUUGAAA-UUGCC-----UUAGCCACUUCUCAAUAGAUUUUCAGUUU
.((((((..............(((((((((..--...)))))-).)))......((((......-.))))-----.))))))...................... ( -17.90)
>DroSec_CAF1 110849 95 + 1
UUGGCUGUCUCACUUUGGCCCGGCAAAGUUUU--ACCAACUU-UCGCCCACUUUGGCAUUGAAU-UUGCC-----UUAGCCACUUCUCAAUAGAUUUUCAGUUU
.((((((..............(((((((((..--...)))))-).)))......((((......-.))))-----.))))))...................... ( -20.60)
>DroSim_CAF1 118736 95 + 1
UUGGCUGUCUCACUUUGGCCCGGCAAAGUUUU--ACCAACUU-UCGCCCACUUUGGCAUUGAAU-UUGCC-----UUAGCCACUUCUCAAUAGAUUUUCAGUUU
.((((((..............(((((((((..--...)))))-).)))......((((......-.))))-----.))))))...................... ( -20.60)
>DroEre_CAF1 114231 80 + 1
UUGGC--------------CCGGCAAAGUUUU--ACCAACUU-UCGCCCACUUUGGCAUUGCAU-UUGCC-----UGAGCCACUUGUCAAUAGAUUUC-AGCUA
.((((--------------.((((((((((..--...)))))-).)))......((((......-.))))-----.).))))................-..... ( -18.60)
>DroYak_CAF1 118962 83 + 1
UUGGC-------------CCCGGCAAAGUUUUCUCCCAACUU-UCGCCCACUUUGGCAUUGCAU-UUGCC-----UUGGCCACUUCUCAAUAGAUUUU-AGCUA
.((((-------------(..(((((((((.......)))))-).)))......((((......-.))))-----..)))))................-..... ( -21.00)
>DroAna_CAF1 103077 97 + 1
UUUUUUGU-----UUUUGUUUGGCAAAGUUUU--UACAACUUAUCGCCCACUUCGGCAUUGAAUAUUGCCAUGUUUUGGCAAGACUGGAAUGAAUUUACAAUUA
...((..(-----((..(((((((((((((..--...)))))...(((......))).........)))).(((....)))))))..)))..)).......... ( -17.60)
>consensus
UUGGCUGU_____UUUGGCCCGGCAAAGUUUU__ACCAACUU_UCGCCCACUUUGGCAUUGAAU_UUGCC_____UUAGCCACUUCUCAAUAGAUUUUCAGUUA
.((((((..............(((.(((((.......)))))...)))......((((........))))......))))))...................... (-13.97 = -14.17 +   0.20)

alignment

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secondary structure

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dotplot

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Window 2

Location 12,769,214 – 12,769,309
Length 95
Sequences 6
Columns 104
Reading direction reverse
Mean pairwise identity 77.25
Mean single sequence MFE -23.10
Consensus MFE -16.18
Energy contribution -16.40
Covariance contribution 0.22
Combinations/Pair 1.06
Mean z-score -2.33
Structure conservation index 0.70
SVM decision value 1.82
SVM RNA-class probability 0.978904
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 12769214 95 - 20766785
AAACUGAAAAUCUAUUGAGAAGUGGCUAA-----GGCAA-UUUCAAUGCCAAAGUGGACGA-AAGUUGGU--AAAACUUUGCCGGGCCAAAGUGAGACAGCCAA
...........(((((....)))))....-----(((..-(((((..(((......(((..-..)))(((--((....))))).))).....)))))..))).. ( -22.90)
>DroSec_CAF1 110849 95 - 1
AAACUGAAAAUCUAUUGAGAAGUGGCUAA-----GGCAA-AUUCAAUGCCAAAGUGGGCGA-AAGUUGGU--AAAACUUUGCCGGGCCAAAGUGAGACAGCCAA
...(((....(((....)))..(((((..-----((((.-......))))......(((.(-(((((...--..))))))))).)))))........))).... ( -24.20)
>DroSim_CAF1 118736 95 - 1
AAACUGAAAAUCUAUUGAGAAGUGGCUAA-----GGCAA-AUUCAAUGCCAAAGUGGGCGA-AAGUUGGU--AAAACUUUGCCGGGCCAAAGUGAGACAGCCAA
...(((....(((....)))..(((((..-----((((.-......))))......(((.(-(((((...--..))))))))).)))))........))).... ( -24.20)
>DroEre_CAF1 114231 80 - 1
UAGCU-GAAAUCUAUUGACAAGUGGCUCA-----GGCAA-AUGCAAUGCCAAAGUGGGCGA-AAGUUGGU--AAAACUUUGCCGG--------------GCCAA
.....-................((((((.-----((((.-......))))......(((.(-(((((...--..)))))))))))--------------)))). ( -24.90)
>DroYak_CAF1 118962 83 - 1
UAGCU-AAAAUCUAUUGAGAAGUGGCCAA-----GGCAA-AUGCAAUGCCAAAGUGGGCGA-AAGUUGGGAGAAAACUUUGCCGGG-------------GCCAA
.....-....(((....)))..(((((..-----(((..-......((((......))))(-(((((.......)))))))))..)-------------)))). ( -25.00)
>DroAna_CAF1 103077 97 - 1
UAAUUGUAAAUUCAUUCCAGUCUUGCCAAAACAUGGCAAUAUUCAAUGCCGAAGUGGGCGAUAAGUUGUA--AAAACUUUGCCAAACAAAA-----ACAAAAAA
...((((.....((((..(((.((((((.....)))))).))).))))........(((((..((((...--..)))))))))..))))..-----........ ( -17.40)
>consensus
AAACUGAAAAUCUAUUGAGAAGUGGCUAA_____GGCAA_AUUCAAUGCCAAAGUGGGCGA_AAGUUGGU__AAAACUUUGCCGGGCCAAA_____ACAGCCAA
......................((((........((((........))))......(((((..((((.......)))))))))................)))). (-16.18 = -16.40 +   0.22)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:05:55 2006