Locus 1953

Sequence ID 2L_DroMel_CAF1
Location 5,273,165 – 5,273,325
Length 160
Max. P 0.830835
window3161 window3162

overview

Window 1

Location 5,273,165 – 5,273,285
Length 120
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 85.44
Mean single sequence MFE -42.73
Consensus MFE -35.71
Energy contribution -35.85
Covariance contribution 0.14
Combinations/Pair 1.31
Mean z-score -2.14
Structure conservation index 0.84
SVM decision value 0.71
SVM RNA-class probability 0.830835
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 5273165 120 - 22407834
GCCUUAAGUUCUUCGAGCUCUCCCUCAAGGAGCAAAUCAAGGAUCUGAGUCUGCAGCGGGACGGUCUGGUCAUGGAACUGCAGCAGUUGCAGGAGGCGCGACCCGUGCUCGAGAAGGCCU
(((((......(((((((..(((.....)))(((..(((......)))...))).(((((.((((((..((.((.(((((...))))).)))))))).)).))))))))))))))))).. ( -40.40)
>DroVir_CAF1 3214 120 - 1
GUCUUAAGUUCUUUGAGCUUUCACUCAAGGAGCAGAUAAAGGAUCUGAGUCUGCAACGUGACGGUUUGGUCAUGGAAUUGCAACAGUUGCAGGAAGCACGUCCUGUUCUUCAGAAAGCAU
.(((...((((((((((......))))))))))(((...(((((.((..((((((((.((.((((((.......))))))))...))))))))...)).)))))..)))..)))...... ( -39.60)
>DroGri_CAF1 524 120 - 1
GCCUCAAAUUCUUUGAGCUCUCACUCAGAGAGCAGAUCAAGGAUUUGAGCCUGCAACGUGAUGGUUUAGUAAUGGAACUGCAACAGUUGCAGGAAGCGCGUCCAGUUCUCGAGAAGGCCU
(((((((((.((((((((((((.....))))))...)))))))))))))((((((((.((.((((((.......))))))))...))))))))..))((.((..(....)..))..)).. ( -41.90)
>DroWil_CAF1 2974 120 - 1
GCCUUAAAUUCUUUGAAUUGUCACUAAAGGAACACAUCAAAGAUUUGAGCCUGCAACGUGACGGUUUGGUCAUGGAACUGCAACAGUUGCAGGAGGCGCGUCCAGUACUUGAAAAGGCCU
(((((....(((((((..(((..(....)..)))..)))))))((..((((((((((.((.((((((.......))))))))...)))))))).((.....))....))..))))))).. ( -38.20)
>DroMoj_CAF1 498 120 - 1
GUCUCAAGUUCUUUGAGCUUUCGCUCAAGGAGCAGAUCAAGGAUUUGAGCCUGCAACGUGACGGUUUAGUCAUGGAACUGCAACAGUUGCAGGAAGCACGUCCCGUUCUCGAGAAGGCAU
.((((..(((((((((((....)))))))))))(((....((((.((..((((((((.((.((((((.......))))))))...))))))))...)).))))...))).))))...... ( -49.90)
>DroAna_CAF1 28907 120 - 1
GCCUCAAGUUCUUCGAGCUGUCGCUCAAGGAGCAGAUCAAGGACUUGAGCCUGCAACGCGACGGUUUGGUCAUGGAACUGCAGCAGUUGCAGGAGGCGCGACCCGUAUUAGAGAAGGCCU
..(((((((((((.((.((((..(....)..)))).)))))))))))))((((((((((..((((((.......))))))..)).))))))))((((.(..(.(......).)..))))) ( -46.40)
>consensus
GCCUCAAGUUCUUUGAGCUCUCACUCAAGGAGCAGAUCAAGGAUUUGAGCCUGCAACGUGACGGUUUGGUCAUGGAACUGCAACAGUUGCAGGAAGCGCGUCCCGUUCUCGAGAAGGCCU
((((...((((((((((......)))))))))).......((((.((..((((((((((..((((((.......))))))..)).))))))))...)).))))...........)))).. (-35.71 = -35.85 +   0.14)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 2

Location 5,273,205 – 5,273,325
Length 120
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 82.33
Mean single sequence MFE -32.93
Consensus MFE -22.15
Energy contribution -21.18
Covariance contribution -0.96
Combinations/Pair 1.50
Mean z-score -1.51
Structure conservation index 0.67
SVM decision value -0.03
SVM RNA-class probability 0.516645
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 5273205 120 + 22407834
CAGUUCCAUGACCAGACCGUCCCGCUGCAGACUCAGAUCCUUGAUUUGCUCCUUGAGGGAGAGCUCGAAGAACUUAAGGCGCUUCAGUUCCUCCUUCAGUGCCGACGGACUGCUGCACUU
........((..(((.(((((.(((((((((.((((....))))))))).....(((((((((((.((((..(.....)..)))))))).)))))))))))..))))).)))...))... ( -38.60)
>DroVir_CAF1 3254 120 + 1
CAAUUCCAUGACCAAACCGUCACGUUGCAGACUCAGAUCCUUUAUCUGCUCCUUGAGUGAAAGCUCAAAGAACUUAAGACGUUUCAGUUCCUCCUUCAGAGCACUUGGACUACUGCACUU
........((((......))))...(((((....((.(((......(((((.((((((....)))))).(((((.(((...))).)))))........)))))...))))).)))))... ( -26.90)
>DroGri_CAF1 564 120 + 1
CAGUUCCAUUACUAAACCAUCACGUUGCAGGCUCAAAUCCUUGAUCUGCUCUCUGAGUGAGAGCUCAAAGAAUUUGAGGCGCUUCAGUUCUUCCUUUAAAAGAUUCGGACUACUGCACUU
(((((((................(..((.(.(((((((.(((.....((((((.....))))))...))).))))))).)))..)...((((.......))))...)))..))))..... ( -29.60)
>DroWil_CAF1 3014 120 + 1
CAGUUCCAUGACCAAACCGUCACGUUGCAGGCUCAAAUCUUUGAUGUGUUCCUUUAGUGACAAUUCAAAGAAUUUAAGGCGUUUCAGUUCCUCCUUCAGUAUGCUUGGGCUGCUGCAUUU
........((((......)))).((.((((.(((((.(((((((..(((..(....)..)))..)))))))(((.((((.(.........).)))).)))....))))))))).)).... ( -27.70)
>DroMoj_CAF1 538 120 + 1
CAGUUCCAUGACUAAACCGUCACGUUGCAGGCUCAAAUCCUUGAUCUGCUCCUUGAGCGAAAGCUCAAAGAACUUGAGACGCUUUAAUUCCUCCUUAAGGACACUUGGGCUAUUACAUUU
.(((.(((.(..((((.((((.....(((((.((((....)))))))))((.((((((....)))))).))......)))).))))..((((.....))))..).))))))......... ( -33.80)
>DroAna_CAF1 28947 120 + 1
CAGUUCCAUGACCAAACCGUCGCGUUGCAGGCUCAAGUCCUUGAUCUGCUCCUUGAGCGACAGCUCGAAGAACUUGAGGCGCUUCAGCUCCUCCUUGAGGACCGAGGGACUGCUGCACUU
(((((((..(((......)))((((((((((.((((....)))))))))((.((((((....)))))).))......))))).((.(.(((((...)))))).)))))))))........ ( -41.00)
>consensus
CAGUUCCAUGACCAAACCGUCACGUUGCAGGCUCAAAUCCUUGAUCUGCUCCUUGAGUGAAAGCUCAAAGAACUUAAGGCGCUUCAGUUCCUCCUUCAGAACACUUGGACUACUGCACUU
.................((((.....(((((.((((....)))))))))((.((((((....)))))).))......))))...((((...(((............)))..))))..... (-22.15 = -21.18 +  -0.96)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:15:51 2006