Locus 4046

Sequence ID 3L_DroMel_CAF1
Location 11,795,881 – 11,796,023
Length 142
Max. P 0.943557
window6300 window6301 window6302

overview

Window 0

Location 11,795,881 – 11,795,984
Length 103
Sequences 3
Columns 103
Reading direction reverse
Mean pairwise identity 96.09
Mean single sequence MFE -27.47
Consensus MFE -25.50
Energy contribution -25.50
Covariance contribution 0.00
Combinations/Pair 1.00
Mean z-score -2.02
Structure conservation index 0.93
SVM decision value 0.64
SVM RNA-class probability 0.808354
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 11795881 103 - 23771897
UUAAAACGGAGAGUGCGUGGAAAUGAAAACAUUGCUUUCACCAUCUCGCCGAUUAGUCUGCAUAUCAGUGUUUAGUCGGCUUUUCGCUUUCGUUAGAUAAAAA
....(((((((((((.((((((..((.....))..)))))))).)))(((((((((.(((.....)))...)))))))))........))))))......... ( -28.00)
>DroSec_CAF1 5182 101 - 1
CCAACACAGAGAGUGCGUGGAAAUGAAAACAUUGCUUUCACCAUCUCGCCGAUUAGUCUGCAUAUCAG--UUUAGUCGGCUUUUCGCUUUCGUUAGAUAAAAA
........(((((((.((((((..((.....))..))))))......(((((((((.(((.....)))--.)))))))))....)))))))............ ( -27.00)
>DroSim_CAF1 4790 101 - 1
CCAACACGGAGAGUGCGUGGAAAUGAAAACAUUGCUUUCACCAUCUCGCCGAUUAGUCUGCAUAUCAG--UUUAGUCGGCUUUUCGCUUUCGUUAGAUAAAAA
.....((((((((((.((((((..((.....))..)))))))).)))(((((((((.(((.....)))--.)))))))))........))))).......... ( -27.40)
>consensus
CCAACACGGAGAGUGCGUGGAAAUGAAAACAUUGCUUUCACCAUCUCGCCGAUUAGUCUGCAUAUCAG__UUUAGUCGGCUUUUCGCUUUCGUUAGAUAAAAA
........(((((((.((((((..((.....))..))))))......(((((((((.(((.....)))...)))))))))....)))))))............ (-25.50 = -25.50 +   0.00)

alignment

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secondary structure

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dotplot

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Window 1

Location 11,795,916 – 11,796,023
Length 107
Sequences 3
Columns 107
Reading direction forward
Mean pairwise identity 97.51
Mean single sequence MFE -35.73
Consensus MFE -34.04
Energy contribution -34.27
Covariance contribution 0.23
Combinations/Pair 1.05
Mean z-score -2.43
Structure conservation index 0.95
SVM decision value 1.34
SVM RNA-class probability 0.943557
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 11795916 107 + 23771897
CUGAUAUGCAGACUAAUCGGCGAGAUGGUGAAAGCAAUGUUUUCAUUUCCACGCACUCUCCGUUUUAAGGAGAGAGCGCAAGAGAGUUUCUCUUUGCCUCUCUUGAA
.......((..........(((.(..(((((((((...)))))))))..).))).((((((.......)))))).)).((((((((...........)))))))).. ( -34.10)
>DroSec_CAF1 5215 107 + 1
CUGAUAUGCAGACUAAUCGGCGAGAUGGUGAAAGCAAUGUUUUCAUUUCCACGCACUCUCUGUGUUGGGGAGAGAGCGCAAGAGAGUUUCUCUUUGCCUCUCUUGAA
(..((..(((((.......(((.(..(((((((((...)))))))))..).)))....)))))))..).(((((((.(((((((.....))).)))))))))))... ( -36.00)
>DroSim_CAF1 4823 107 + 1
CUGAUAUGCAGACUAAUCGGCGAGAUGGUGAAAGCAAUGUUUUCAUUUCCACGCACUCUCCGUGUUGGGGAGAGAGCGCAAGAGAGUUUCUCUUUGCCUCUCUUGAA
(..(((((.(((.......(((.(..(((((((((...)))))))))..).)))..))).)))))..).(((((((.(((((((.....))).)))))))))))... ( -37.10)
>consensus
CUGAUAUGCAGACUAAUCGGCGAGAUGGUGAAAGCAAUGUUUUCAUUUCCACGCACUCUCCGUGUUGGGGAGAGAGCGCAAGAGAGUUUCUCUUUGCCUCUCUUGAA
((((((((.(((.......(((.(..(((((((((...)))))))))..).)))..))).)))))))).(((((((.(((((((.....))).)))))))))))... (-34.04 = -34.27 +   0.23)

alignment

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secondary structure

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dotplot

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Window 2

Location 11,795,916 – 11,796,023
Length 107
Sequences 3
Columns 107
Reading direction reverse
Mean pairwise identity 97.51
Mean single sequence MFE -30.70
Consensus MFE -29.63
Energy contribution -29.97
Covariance contribution 0.33
Combinations/Pair 1.00
Mean z-score -2.11
Structure conservation index 0.97
SVM decision value 1.02
SVM RNA-class probability 0.901878
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 11795916 107 - 23771897
UUCAAGAGAGGCAAAGAGAAACUCUCUUGCGCUCUCUCCUUAAAACGGAGAGUGCGUGGAAAUGAAAACAUUGCUUUCACCAUCUCGCCGAUUAGUCUGCAUAUCAG
.....((((.((((.(((.....)))))))((.((((((.......)))))).))((((((..((.....))..))))))..))))((.((....)).))....... ( -31.70)
>DroSec_CAF1 5215 107 - 1
UUCAAGAGAGGCAAAGAGAAACUCUCUUGCGCUCUCUCCCCAACACAGAGAGUGCGUGGAAAUGAAAACAUUGCUUUCACCAUCUCGCCGAUUAGUCUGCAUAUCAG
....((((((((((.(((.....))))))).))))))..........((((.((.((((((..((.....))..))))))))))))((.((....)).))....... ( -29.20)
>DroSim_CAF1 4823 107 - 1
UUCAAGAGAGGCAAAGAGAAACUCUCUUGCGCUCUCUCCCCAACACGGAGAGUGCGUGGAAAUGAAAACAUUGCUUUCACCAUCUCGCCGAUUAGUCUGCAUAUCAG
.....((((.((((.(((.....)))))))((.((((((.......)))))).))((((((..((.....))..))))))..))))((.((....)).))....... ( -31.20)
>consensus
UUCAAGAGAGGCAAAGAGAAACUCUCUUGCGCUCUCUCCCCAACACGGAGAGUGCGUGGAAAUGAAAACAUUGCUUUCACCAUCUCGCCGAUUAGUCUGCAUAUCAG
.....((((.((((.(((.....)))))))((.((((((.......)))))).))((((((..((.....))..))))))..))))((.((....)).))....... (-29.63 = -29.97 +   0.33)

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 11:13:13 2006