Locus 4339

Sequence ID 2R_DroMel_CAF1
Location 14,266,350 – 14,266,449
Length 99
Max. P 0.553349
window6952 window6953

overview

Window 2

Location 14,266,350 – 14,266,449
Length 99
Sequences 6
Columns 112
Reading direction forward
Mean pairwise identity 83.33
Mean single sequence MFE -36.35
Consensus MFE -22.48
Energy contribution -22.53
Covariance contribution 0.06
Combinations/Pair 1.10
Mean z-score -2.19
Structure conservation index 0.62
SVM decision value -0.04
SVM RNA-class probability 0.512759
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 14266350 99 + 20766785
-AAAGGAGCCAAGGACUC---UGUUUAACAUGGUCGUAGAGCUGGCUGAAGU--------GGGGAGCUG-GGAGCUGCUCAUUUGCAGCUGCUGGCAAUUCAAUUUGCCAUC
-.....((((.(.((((.---((.....)).)))).).).)))(((.....(--------(((..((..-(.((((((......)))))).)..))..))))....)))... ( -37.10)
>DroSec_CAF1 3626 98 + 1
-AAAGGAGCCAAGGACUC---UGUUUAACAUGGUCGUGGAGCUGGCUGGAGU--------GGGUAG-UG-GGAGCUGCUCAUUUGCAGCUGCUGGCAAUUCAAUUUGCCAUC
-.......(((..((((.---((.....)).)))).)))(((.(((((((((--------((((((-(.-...))))))))))).))))))))(((((......)))))... ( -39.00)
>DroSim_CAF1 3731 98 + 1
-AAAGGAGCCAAGGACUC---UGUUUAACAUGGUCGUGGAGCUGGCUGGAGU--------GGGUAG-UG-GGAGCUGCUCAUUUGCAGCUGCUGGCAAUUCAAUUUGCCAUC
-.......(((..((((.---((.....)).)))).)))(((.(((((((((--------((((((-(.-...))))))))))).))))))))(((((......)))))... ( -39.00)
>DroEre_CAF1 3574 104 + 1
-AACGGAGCCAAGGACUC---UGUUUAACAUGGUCGUCG-GCGAGCUGGAGUAGG-GAAAGGGAAG-UG-GGAGCUGCUCAUUUGCAGCUGCUGGCAAUUCAAUUUGCCAUC
-..(((.(((.(.((((.---((.....)).)))).).)-))...))).....((-.(((..((((-(.-((((((((......)))))).)).))..)))..))).))... ( -36.30)
>DroYak_CAF1 3650 103 + 1
-AAAGGAGCCAAGGACUC---UGUUUAACAUGGUCGUC----CAGCUGGAGUGGGAGUGAGGGGAG-UGGGGAGCUGCUCAUUUGCAGCUGCUGGCAAUUCAAUUUGCCAUC
-..((.(((....((((.---((.....)).)))).((----(.((....)).)))(..((..(((-..(....)..))).))..).))).))(((((......)))))... ( -32.40)
>DroAna_CAF1 4097 94 + 1
AAAAGGAGCCAAGGACCUGAAGGCUUGACAUGGCCGUGAAG--GGCUGA--------------CAG-GA-GGAGCUGCUCAUUUGCAGCUGUUGGCCAUUCAAUUUGCCAUC
.....(((((...........)))))...(((((..((((.--(((..(--------------((.-..-...(((((......))))))))..))).))))....))))). ( -34.30)
>consensus
_AAAGGAGCCAAGGACUC___UGUUUAACAUGGUCGUGGAGCUGGCUGGAGU________GGGGAG_UG_GGAGCUGCUCAUUUGCAGCUGCUGGCAAUUCAAUUUGCCAUC
.......((((.((((......))))....))))....................................(.((((((......)))))).)((((((......)))))).. (-22.48 = -22.53 +   0.06)

alignment

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secondary structure

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dotplot

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Window 3

Location 14,266,350 – 14,266,449
Length 99
Sequences 6
Columns 112
Reading direction reverse
Mean pairwise identity 83.33
Mean single sequence MFE -26.62
Consensus MFE -18.99
Energy contribution -19.18
Covariance contribution 0.20
Combinations/Pair 1.06
Mean z-score -1.69
Structure conservation index 0.71
SVM decision value 0.04
SVM RNA-class probability 0.553349
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 14266350 99 - 20766785
GAUGGCAAAUUGAAUUGCCAGCAGCUGCAAAUGAGCAGCUCC-CAGCUCCCC--------ACUUCAGCCAGCUCUACGACCAUGUUAAACA---GAGUCCUUGGCUCCUUU-
..((((((......))))))((((((((......))))))..-..)).....--------.....((((((((((..(((...)))....)---))))...))))).....- ( -26.30)
>DroSec_CAF1 3626 98 - 1
GAUGGCAAAUUGAAUUGCCAGCAGCUGCAAAUGAGCAGCUCC-CA-CUACCC--------ACUCCAGCCAGCUCCACGACCAUGUUAAACA---GAGUCCUUGGCUCCUUU-
..((((((......))))))..((((((......))))))..-..-......--------.....((((((......(((..((.....))---..))).)))))).....- ( -24.70)
>DroSim_CAF1 3731 98 - 1
GAUGGCAAAUUGAAUUGCCAGCAGCUGCAAAUGAGCAGCUCC-CA-CUACCC--------ACUCCAGCCAGCUCCACGACCAUGUUAAACA---GAGUCCUUGGCUCCUUU-
..((((((......))))))..((((((......))))))..-..-......--------.....((((((......(((..((.....))---..))).)))))).....- ( -24.70)
>DroEre_CAF1 3574 104 - 1
GAUGGCAAAUUGAAUUGCCAGCAGCUGCAAAUGAGCAGCUCC-CA-CUUCCCUUUC-CCUACUCCAGCUCGC-CGACGACCAUGUUAAACA---GAGUCCUUGGCUCCGUU-
..((((((......))))))..((((((......))))))..-..-..........-.............((-(((.(((..((.....))---..))).)))))......- ( -28.50)
>DroYak_CAF1 3650 103 - 1
GAUGGCAAAUUGAAUUGCCAGCAGCUGCAAAUGAGCAGCUCCCCA-CUCCCCUCACUCCCACUCCAGCUG----GACGACCAUGUUAAACA---GAGUCCUUGGCUCCUUU-
..((((((......))))))..((((((......)))))).....-...................(((((----(((.....((.....))---..))))..)))).....- ( -24.70)
>DroAna_CAF1 4097 94 - 1
GAUGGCAAAUUGAAUGGCCAACAGCUGCAAAUGAGCAGCUCC-UC-CUG--------------UCAGCC--CUUCACGGCCAUGUCAAGCCUUCAGGUCCUUGGCUCCUUUU
.(((((....((((.(((..((((((((......)))))...-..-.))--------------)..)))--.))))..)))))((((((((....))..))))))....... ( -30.80)
>consensus
GAUGGCAAAUUGAAUUGCCAGCAGCUGCAAAUGAGCAGCUCC_CA_CUACCC________ACUCCAGCCAGCUCCACGACCAUGUUAAACA___GAGUCCUUGGCUCCUUU_
..((((((......))))))..((((((......))))))......................................................((((.....))))..... (-18.99 = -19.18 +   0.20)

alignment

Postscript

secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:17:22 2006