Locus 1648

Sequence ID 2R_DroMel_CAF1
Location 6,220,605 – 6,220,699
Length 94
Max. P 0.959152
window2753 window2754

overview

Window 3

Location 6,220,605 – 6,220,699
Length 94
Sequences 6
Columns 100
Reading direction forward
Mean pairwise identity 70.63
Mean single sequence MFE -17.58
Consensus MFE -7.80
Energy contribution -6.92
Covariance contribution -0.89
Combinations/Pair 1.30
Mean z-score -2.15
Structure conservation index 0.44
SVM decision value 1.50
SVM RNA-class probability 0.959152
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 6220605 94 + 20766785
UUAACACUGCAAUUAACGCGGCGACAAGCGUCUC-----ACACGCAACUGCAGUCUGGGGAAUUUCUCCAAAAAUAUA-CAAAAAAAGCAAAACACACGA
.....((((((........(....)..((((...-----..))))...)))))).(((((.....)))))........-..................... ( -18.20)
>DroPse_CAF1 45793 80 + 1
UUAACACUGCAAUUAACAGAAAGUUAAGCGACUGCCACGACAUGUAAUUGCAGUCUUCAGACUUUCUCCCCGAAAAAC-AC-------------------
.................((((((((....((((((....(....)....))))))....))))))))...........-..------------------- ( -15.00)
>DroSec_CAF1 51683 92 + 1
UUAACACUGCAAUUAACACGGCGACAAGCGCCUC-----ACACGCAACUGCAGUCUAGGGGAUUUCUCCCAAAAAAAU-AACAAAAAG--AAACACCCGA
.....((((((........((((.....))))..-----.........))))))...(((..(((((...........-.......))--)))..))).. ( -19.18)
>DroSim_CAF1 53142 92 + 1
UUAACACUGCAAUUAACAUGGCGACAAGCGCCUC-----ACACGCAACUGCAGUCUAGGGGAUUUCUCCAAAAAAAAU-AACAAAAAG--AAACACACGA
.....((((((........((((.....))))..-----.........))))))...((((....)))).........-.........--.......... ( -17.21)
>DroEre_CAF1 53989 92 + 1
UUAACACUGCAAUUAACACGGCGACAAGCGACUC-----ACACGCAACUGCAGUCUGGGGGAUUUCUCCAAAAA-AAUAACAAAAAUG--GAACCCAGGA
.....((((((........(....)..(((....-----...)))...))))))((((((((....))).....-.....((....))--...))))).. ( -20.90)
>DroPer_CAF1 45441 80 + 1
UUAACACUGCAAUUAACAGAAAGUUAAGCGACUGCCACGACAUGUAAUUGCAGUCUUCAGACUUUCUCCCCGAAAAAC-AC-------------------
.................((((((((....((((((....(....)....))))))....))))))))...........-..------------------- ( -15.00)
>consensus
UUAACACUGCAAUUAACACGGCGACAAGCGACUC_____ACACGCAACUGCAGUCUAGGGAAUUUCUCCAAAAAAAAU_AA_AAAAAG__AAACACACGA
.....((((((........(....)..(((............)))...)))))).............................................. ( -7.80 =  -6.92 +  -0.89)

alignment

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secondary structure

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dotplot

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Window 4

Location 6,220,605 – 6,220,699
Length 94
Sequences 6
Columns 100
Reading direction reverse
Mean pairwise identity 70.63
Mean single sequence MFE -23.47
Consensus MFE -13.86
Energy contribution -13.17
Covariance contribution -0.69
Combinations/Pair 1.41
Mean z-score -1.45
Structure conservation index 0.59
SVM decision value 0.63
SVM RNA-class probability 0.805378
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 6220605 94 - 20766785
UCGUGUGUUUUGCUUUUUUUG-UAUAUUUUUGGAGAAAUUCCCCAGACUGCAGUUGCGUGU-----GAGACGCUUGUCGCCGCGUUAAUUGCAGUGUUAA
.....................-.......((((.(.....).))))((((((((((((((.-----(.(((....))).))))).))))))))))..... ( -23.80)
>DroPse_CAF1 45793 80 - 1
-------------------GU-GUUUUUCGGGGAGAAAGUCUGAAGACUGCAAUUACAUGUCGUGGCAGUCGCUUAACUUUCUGUUAAUUGCAGUGUUAA
-------------------.(-((......((.(((((((.(((.((((((...(((.....)))))))))..)))))))))).))....)))....... ( -19.10)
>DroSec_CAF1 51683 92 - 1
UCGGGUGUUU--CUUUUUGUU-AUUUUUUUGGGAGAAAUCCCCUAGACUGCAGUUGCGUGU-----GAGGCGCUUGUCGCCGUGUUAAUUGCAGUGUUAA
..(((..(((--(((((....-........))))))))..)))...((((((((((((...-----..((((.....)))).)).))))))))))..... ( -28.20)
>DroSim_CAF1 53142 92 - 1
UCGUGUGUUU--CUUUUUGUU-AUUUUUUUUGGAGAAAUCCCCUAGACUGCAGUUGCGUGU-----GAGGCGCUUGUCGCCAUGUUAAUUGCAGUGUUAA
..........--.........-.........(((....))).....((((((((((((((.-----(.(((....))).))))).))))))))))..... ( -23.10)
>DroEre_CAF1 53989 92 - 1
UCCUGGGUUC--CAUUUUUGUUAUU-UUUUUGGAGAAAUCCCCCAGACUGCAGUUGCGUGU-----GAGUCGCUUGUCGCCGUGUUAAUUGCAGUGUUAA
..(((((...--((....)).....-.....(((....))))))))((((((((((((.((-----((........)))))))...)))))))))..... ( -27.50)
>DroPer_CAF1 45441 80 - 1
-------------------GU-GUUUUUCGGGGAGAAAGUCUGAAGACUGCAAUUACAUGUCGUGGCAGUCGCUUAACUUUCUGUUAAUUGCAGUGUUAA
-------------------.(-((......((.(((((((.(((.((((((...(((.....)))))))))..)))))))))).))....)))....... ( -19.10)
>consensus
UCGUGUGUUU__CUUUUU_GU_AUUUUUUUGGGAGAAAUCCCCAAGACUGCAGUUGCGUGU_____GAGUCGCUUGUCGCCGUGUUAAUUGCAGUGUUAA
...............................(((....))).....((((((((((((((....................)))).))))))))))..... (-13.86 = -13.17 +  -0.69)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:09:40 2006