Locus 7299

Sequence ID 3L_DroMel_CAF1
Location 19,532,265 – 19,532,534
Length 269
Max. P 0.693766
window11862 window11863 window11864

overview

Window 2

Location 19,532,265 – 19,532,377
Length 112
Sequences 3
Columns 112
Reading direction reverse
Mean pairwise identity 96.43
Mean single sequence MFE -22.41
Consensus MFE -21.12
Energy contribution -21.12
Covariance contribution -0.00
Combinations/Pair 1.00
Mean z-score -1.63
Structure conservation index 0.94
SVM decision value 0.13
SVM RNA-class probability 0.600371
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 19532265 112 - 23771897
AAAUUUGGUUACUUAAACCAACUCUUGUAGCGAUAUUCUAAAAGAAAACCAAAACUAUCAGAUAAACGAAAGUCGGGGUCGAAACCCAAAUCCGAUGGAGGAAGACGACAUU
....((((((.....)))))).(((.((((.....(((.....)))........)))).))).........((((((((....))))...(((......)))...))))... ( -21.02)
>DroSec_CAF1 2506 112 - 1
AAAUUUGGUUACUAAAACCAACUCUUGUAGCGAUAUUCUAAAAGAAAACCAAAACUAUCAGAUUAACGAAAGUCGGGGUCGAAACCCAAAUCCGAUGGAGGAAGACGACAUU
....((((((.....)))))).((((.(((.......))).)))).........(((((.((((.((....))..((((....)))).)))).))))).............. ( -21.50)
>DroYak_CAF1 15977 111 - 1
AAAUUUGGUUACUAAAACCAACUCUUGUAGCGAUAUUCUAAAAGAAAACCA-AUCUAUCAGAUAAACGAAAGUCGGGGUAGAAACCCAUAUCCGAUGGAGGAAGACGACAUU
....((((((.....)))))).((((.(((.......))).))))...((.-.((((((.((((.((....))..((((....)))).)))).))))))))........... ( -24.70)
>consensus
AAAUUUGGUUACUAAAACCAACUCUUGUAGCGAUAUUCUAAAAGAAAACCAAAACUAUCAGAUAAACGAAAGUCGGGGUCGAAACCCAAAUCCGAUGGAGGAAGACGACAUU
....((((((.....)))))).(((.((((.....(((.....)))........)))).))).........((((((((....))))...(((......)))...))))... (-21.12 = -21.12 +  -0.00)

alignment

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secondary structure

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dotplot

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Window 3

Location 19,532,377 – 19,532,494
Length 117
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 85.99
Mean single sequence MFE -21.64
Consensus MFE -16.86
Energy contribution -17.53
Covariance contribution 0.67
Combinations/Pair 1.11
Mean z-score -1.99
Structure conservation index 0.78
SVM decision value 0.27
SVM RNA-class probability 0.661423
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 19532377 117 - 23771897
CUAAACUAACAAAACUCACAGCUUUUGUUUAUCAAAACGAAGUUGUGCAUAAAACGCUUAAGAUGCGAU-UAUGAUUAGAUCGGAGAUUUACGAAAACCACAUCAAGAAGACAAACUA--
.....((((.......(((((((((.((((....)))))))))))))(((((..(((.......))).)-)))).)))).(((........)))........................-- ( -20.00)
>DroSec_CAF1 2618 120 - 1
CUAAACAAACAAAACUAACAGCUUUUGUUUAUCAAAACGAAGUUGUGCAUAAAGCGCUUAAGAGGCGAUUUAUGAUUAGAUCGGAGAUUUACGAAAACCACAUCACGAUAACAAACAAAG
((((.............((((((((.((((....)))))))))))).((((((.((((.....)))).)))))).))))((((..(((.............))).))))........... ( -22.02)
>DroYak_CAF1 16088 117 - 1
CUAAACUUACAAAAAUCACAGCUGUCGUUAAUCAAAACGAAGCUGUGAGUAAAACGCUAAAGAGGCGAU-UAUGAUUAGAUCGGAAAUAUACAAAAAUCACAUCAAGAAGACAAGCAA--
((((...........((((((((.(((((......)))))))))))))......((((.....))))..-.....)))).......................................-- ( -22.90)
>consensus
CUAAACUAACAAAACUCACAGCUUUUGUUUAUCAAAACGAAGUUGUGCAUAAAACGCUUAAGAGGCGAU_UAUGAUUAGAUCGGAGAUUUACGAAAACCACAUCAAGAAGACAAACAA__
((((............(((((((.((((((....)))))))))))))((((...(((.......)))...)))).)))).(((........))).......................... (-16.86 = -17.53 +   0.67)

alignment

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secondary structure

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dotplot

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Window 4

Location 19,532,415 – 19,532,534
Length 119
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 89.69
Mean single sequence MFE -23.41
Consensus MFE -17.99
Energy contribution -18.33
Covariance contribution 0.34
Combinations/Pair 1.12
Mean z-score -2.41
Structure conservation index 0.77
SVM decision value 0.33
SVM RNA-class probability 0.693766
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 19532415 119 - 23771897
ACUCUCUAAGUUGCCUAAUAAUUUCCCAAAAGAUAACAAGCUAAACUAACAAAACUCACAGCUUUUGUUUAUCAAAACGAAGUUGUGCAUAAAACGCUUAAGAUGCGAU-UAUGAUUAGA
..............(((((.....................................(((((((((.((((....)))))))))))))(((((..(((.......))).)-))))))))). ( -19.00)
>DroSec_CAF1 2658 120 - 1
ACUCUCUAAGUUGCCUAAUAAUUUCCCAAAACAAAACAAGCUAAACAAACAAAACUAACAGCUUUUGUUUAUCAAAACGAAGUUGUGCAUAAAGCGCUUAAGAGGCGAUUUAUGAUUAGA
....((((((((((((...((((((........(((((((((.................))))..)))))........))))))((((.....)))).....)))))))))).))..... ( -23.02)
>DroYak_CAF1 16126 117 - 1
ACUUUCUAAGUUGCCUAAUAAUUUCCCAAAAG--AACAAGCUAAACUUACAAAAAUCACAGCUGUCGUUAAUCAAAACGAAGCUGUGAGUAAAACGCUAAAGAGGCGAU-UAUGAUUAGA
.((.((..((((((((......(((......)--))..(((.....((((.....((((((((.(((((......)))))))))))))))))...)))....)))))))-)..))..)). ( -28.20)
>consensus
ACUCUCUAAGUUGCCUAAUAAUUUCCCAAAAGA_AACAAGCUAAACUAACAAAACUCACAGCUUUUGUUUAUCAAAACGAAGUUGUGCAUAAAACGCUUAAGAGGCGAU_UAUGAUUAGA
..............(((((.....................................(((((((.((((((....)))))))))))))((((...(((.......)))...))))))))). (-17.99 = -18.33 +   0.34)

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 12:43:27 2006