Locus 3655

Sequence ID 3L_DroMel_CAF1
Location 10,712,316 – 10,712,457
Length 141
Max. P 0.991822
window5697 window5698 window5699

overview

Window 7

Location 10,712,316 – 10,712,429
Length 113
Sequences 3
Columns 113
Reading direction forward
Mean pairwise identity 97.64
Mean single sequence MFE -20.34
Consensus MFE -17.79
Energy contribution -17.57
Covariance contribution -0.22
Combinations/Pair 1.03
Mean z-score -1.86
Structure conservation index 0.87
SVM decision value -0.03
SVM RNA-class probability 0.516106
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 10712316 113 + 23771897
AAAGCAAGAAAUAAACAAAGGCACAGACAAAAGCAAAGGCAAACAAACACAGCACAAAUAUUAAAGUCAAUUUGCGAAAUGAGAAUGCUGCGAAUGUUUCGCCUUUGGAUUUG
...........................((((..((((((((((((..(.(((((....((((...((......))..))))....))))).)..))))).)))))))..)))) ( -22.20)
>DroSec_CAF1 46508 113 + 1
AAAGCAAGAAAUAAACAAAGGCACAGACAAAAGCAAAGGCAAACAAACACAACACAAAUAUUAAAGUCAAUUUGGGAAAUGAGAACGCCGCGAAUGUUUCGCCUUUGGAUUUG
........((((...(((((((..(((((...((...(((..............(((((..........)))))(..........))))))...))))).))))))).)))). ( -19.30)
>DroSim_CAF1 48250 113 + 1
AAAGCAAGAAAUAAACAAAGGCACAGACAAAAGCAAAGGCAAACAAACACAACACAAAUAUUAAAGUCAAUUUGCGAAAUGAGAACGCUGCGAAUGUUUCGCCUUUGGAUUUG
........((((...(((((((..(((((...(((..(((.........................))).....(((.........))))))...))))).))))))).)))). ( -19.51)
>consensus
AAAGCAAGAAAUAAACAAAGGCACAGACAAAAGCAAAGGCAAACAAACACAACACAAAUAUUAAAGUCAAUUUGCGAAAUGAGAACGCUGCGAAUGUUUCGCCUUUGGAUUUG
........((((...(((((((..(((((...((...(((.......((...(.(((((..........))))).)...)).....)))))...))))).))))))).)))). (-17.79 = -17.57 +  -0.22)

alignment

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secondary structure

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dotplot

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Window 8

Location 10,712,316 – 10,712,429
Length 113
Sequences 3
Columns 113
Reading direction reverse
Mean pairwise identity 97.64
Mean single sequence MFE -26.82
Consensus MFE -26.53
Energy contribution -25.87
Covariance contribution -0.66
Combinations/Pair 1.11
Mean z-score -3.17
Structure conservation index 0.99
SVM decision value 2.29
SVM RNA-class probability 0.991822
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 10712316 113 - 23771897
CAAAUCCAAAGGCGAAACAUUCGCAGCAUUCUCAUUUCGCAAAUUGACUUUAAUAUUUGUGCUGUGUUUGUUUGCCUUUGCUUUUGUCUGUGCCUUUGUUUAUUUCUUGCUUU
((((..(((((((.(((((..((((((((.............................))))))))..))))))))))))..))))........................... ( -28.95)
>DroSec_CAF1 46508 113 - 1
CAAAUCCAAAGGCGAAACAUUCGCGGCGUUCUCAUUUCCCAAAUUGACUUUAAUAUUUGUGUUGUGUUUGUUUGCCUUUGCUUUUGUCUGUGCCUUUGUUUAUUUCUUGCUUU
((((..(((((((.(((((..(((((((...........(((((..........))))))))))))..))))))))))))..))))........................... ( -24.30)
>DroSim_CAF1 48250 113 - 1
CAAAUCCAAAGGCGAAACAUUCGCAGCGUUCUCAUUUCGCAAAUUGACUUUAAUAUUUGUGUUGUGUUUGUUUGCCUUUGCUUUUGUCUGUGCCUUUGUUUAUUUCUUGCUUU
((((..(((((((.(((((..(((((((....).....((((((..........))))))))))))..))))))))))))..))))........................... ( -27.20)
>consensus
CAAAUCCAAAGGCGAAACAUUCGCAGCGUUCUCAUUUCGCAAAUUGACUUUAAUAUUUGUGUUGUGUUUGUUUGCCUUUGCUUUUGUCUGUGCCUUUGUUUAUUUCUUGCUUU
((((..(((((((.(((((..(((((((...........(((((..........))))))))))))..))))))))))))..))))........................... (-26.53 = -25.87 +  -0.66)

alignment

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secondary structure

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dotplot

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Window 9

Location 10,712,349 – 10,712,457
Length 108
Sequences 3
Columns 108
Reading direction reverse
Mean pairwise identity 95.00
Mean single sequence MFE -25.15
Consensus MFE -24.73
Energy contribution -24.07
Covariance contribution -0.66
Combinations/Pair 1.11
Mean z-score -2.19
Structure conservation index 0.98
SVM decision value 1.44
SVM RNA-class probability 0.954277
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 10712349 108 - 23771897
GCACACAAUUGCAUAGGCAUUAACAUAUCAAAUCCAAAGGCGAAACAUUCGCAGCAUUCUCAUUUCGCAAAUUGACUUUAAUAUUUGUGCUGUGUUUGUUUGCCUUUG
(((......)))......................(((((((.(((((..((((((((.............................))))))))..)))))))))))) ( -27.55)
>DroSec_CAF1 46541 104 - 1
----ACAAUUGCAUAGGCAUUAACAUAUCAAAUCCAAAGGCGAAACAUUCGCGGCGUUCUCAUUUCCCAAAUUGACUUUAAUAUUUGUGUUGUGUUUGUUUGCCUUUG
----.....(((....)))...............(((((((.(((((..(((((((...........(((((..........))))))))))))..)))))))))))) ( -22.50)
>DroSim_CAF1 48283 104 - 1
----ACAAUUGCAUAGGCAUUAACAUAUCAAAUCCAAAGGCGAAACAUUCGCAGCGUUCUCAUUUCGCAAAUUGACUUUAAUAUUUGUGUUGUGUUUGUUUGCCUUUG
----.....(((....)))...............(((((((.(((((..(((((((....).....((((((..........))))))))))))..)))))))))))) ( -25.40)
>consensus
____ACAAUUGCAUAGGCAUUAACAUAUCAAAUCCAAAGGCGAAACAUUCGCAGCGUUCUCAUUUCGCAAAUUGACUUUAAUAUUUGUGUUGUGUUUGUUUGCCUUUG
.........(((....)))...............(((((((.(((((..(((((((...........(((((..........))))))))))))..)))))))))))) (-24.73 = -24.07 +  -0.66)

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 11:03:20 2006