Locus 2531

Sequence ID X_DroMel_CAF1
Location 6,739,556 – 6,739,703
Length 147
Max. P 0.997750
window4133 window4134

overview

Window 3

Location 6,739,556 – 6,739,665
Length 109
Sequences 5
Columns 116
Reading direction reverse
Mean pairwise identity 77.53
Mean single sequence MFE -19.52
Consensus MFE -7.82
Energy contribution -8.58
Covariance contribution 0.76
Combinations/Pair 1.15
Mean z-score -2.14
Structure conservation index 0.40
SVM decision value 0.82
SVM RNA-class probability 0.858057
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 6739556 109 - 22224390
A--AAACAUUUU----CCUUUUUUUUUGCCGCUCGCACUUUGAUAUCUAUUACAAUCAAAUUGCAAAUUAAAUCACAAAACCAGAGUUGGGCGAA-CGAAGGAAAAGCGGAAAAAU
.--.....((((----((((((((((((.((((((((.((((((..........)))))).)))..............(((....))))))))..-))))))))))).)))))... ( -25.90)
>DroSim_CAF1 28478 102 - 1
A--AAACAUUUU----CCUU-----UUGCCGCUCGCACUUUGAUAUCUAUUACAAUCAAAUUGCAAAUUAAAUCACAA-ACCAGAGUUGGGUGAA-CGGAGGAAAAGCGGAAAAA-
.--.....((((----((((-----((.(((...(((.((((((..........)))))).)))........((((.(-((....)))..)))).-)))....)))).)))))).- ( -21.70)
>DroEre_CAF1 29780 104 - 1
A--AAACAUUUU----CCUU-----UUGCCACUCGCACUUUGAUAUCUAUUACAAUCAAAUUGCAAAUUAAAUCACAA-GCCAGAGUUGGAUGAAAAGUAGGAAAAGCGGAACAAA
.--......(((----((((-----((.(((((.(((.((((((..........)))))).)))........(((...-.((......)).)))..))).))))))).)))).... ( -17.10)
>DroAna_CAF1 29974 100 - 1
UACAGAAAUUGUGAACCUUU-----UUCCCACUCGCACUUUGAUAUCUAUUACAAUCAAAUUGCAAAUUAAAUCACAA-ACCAGAGUUAAGCGAA-G---GGAAAAGUU------A
.................(((-----(((((....(((.((((((..........)))))).)))...((((.((....-....)).)))).....-)---)))))))..------. ( -17.30)
>DroPer_CAF1 81840 95 - 1
A--AAAG------AAACCUU-----UUACCACUCGCACUUUGAUAUCUAUUGCAAUCAAAUUGCAAAUUAAAUCACAA-AACAGAGUUAAGCGAU-G----GCAAACCCCAAAA--
(--((((------....)))-----)).(((.((((((((((.......(((((((...))))))).((........)-).))))))...)))))-)----)............-- ( -15.60)
>consensus
A__AAACAUUUU____CCUU_____UUGCCACUCGCACUUUGAUAUCUAUUACAAUCAAAUUGCAAAUUAAAUCACAA_ACCAGAGUUGGGCGAA_CG_AGGAAAAGCGGAAAAA_
............................(((((.(((.((((((..........)))))).)))...((((.((.........)).))))...............)))))...... ( -7.82 =  -8.58 +   0.76)

alignment

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secondary structure

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dotplot

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Window 4

Location 6,739,591 – 6,739,703
Length 112
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 74.93
Mean single sequence MFE -21.41
Consensus MFE -8.57
Energy contribution -8.21
Covariance contribution -0.36
Combinations/Pair 1.22
Mean z-score -2.71
Structure conservation index 0.40
SVM decision value 2.92
SVM RNA-class probability 0.997750
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 6739591 112 - 22224390
AGGGAAAAUG--CGGCACAGAAGGGAGAGAGAGAAAAAAAA--AAACAUUUU----CCUUUUUUUUUGCCGCUCGCACUUUGAUAUCUAUUACAAUCAAAUUGCAAAUUAAAUCACAAAA
...((....(--(((((.(((((((((((.(..........--...).))))----)))))))...))))))..(((.((((((..........)))))).)))........))...... ( -25.92)
>DroSim_CAF1 28512 96 - 1
AGGGAAAAUG--CGGCACAGAAGGGAGAGG----------A--AAACAUUUU----CCUU-----UUGCCGCUCGCACUUUGAUAUCUAUUACAAUCAAAUUGCAAAUUAAAUCACAA-A
...((....(--(((((..(((((((((..----------.--.....))))----))))-----)))))))..(((.((((((..........)))))).)))........))....-. ( -27.10)
>DroEre_CAF1 29816 96 - 1
AGCGAAAGUA--CGGCACAGAAGGGAGAGG----------A--AAACAUUUU----CCUU-----UUGCCACUCGCACUUUGAUAUCUAUUACAAUCAAAUUGCAAAUUAAAUCACAA-G
.((....)).--.((((..(((((((((..----------.--.....))))----))))-----)))))....(((.((((((..........)))))).)))..............-. ( -24.60)
>DroAna_CAF1 30000 100 - 1
AGCGAAAAGG----ACAAAAAAAAAAAAAG----------UACAGAAAUUGUGAACCUUU-----UUCCCACUCGCACUUUGAUAUCUAUUACAAUCAAAUUGCAAAUUAAAUCACAA-A
...(((((((----((((............----------........))))...)))))-----)).......(((.((((((..........)))))).)))..............-. ( -11.05)
>DroPer_CAF1 81869 94 - 1
--UGAAAUGGAGAGGUACAGAGAGAGCAGA----------A--AAAG------AAACCUU-----UUACCACUCGCACUUUGAUAUCUAUUGCAAUCAAAUUGCAAAUUAAAUCACAA-A
--.....((((.((((((((((.(((..(.----------(--((((------....)))-----)).)..)))...))))).))))).(((((((...)))))))......)).)).-. ( -18.40)
>consensus
AGCGAAAAUG__CGGCACAGAAGGGAGAGG__________A__AAACAUUUU____CCUU_____UUGCCACUCGCACUUUGAUAUCUAUUACAAUCAAAUUGCAAAUUAAAUCACAA_A
...((........((((....(((.................................)))......))))....(((.((((((..........)))))).)))........))...... ( -8.57 =  -8.21 +  -0.36)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:37:01 2006