Locus 1914

Sequence ID X_DroMel_CAF1
Location 5,289,854 – 5,290,029
Length 175
Max. P 0.849117
window3112 window3113 window3114

overview

Window 2

Location 5,289,854 – 5,289,954
Length 100
Sequences 4
Columns 109
Reading direction reverse
Mean pairwise identity 83.89
Mean single sequence MFE -34.33
Consensus MFE -26.29
Energy contribution -27.35
Covariance contribution 1.06
Combinations/Pair 1.12
Mean z-score -1.41
Structure conservation index 0.77
SVM decision value -0.08
SVM RNA-class probability 0.500000
Prediction OTHER

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 5289854 100 - 22224390
UAAUUGCAUUUUUGCGCUCCUGCCUGGGGCGUGGGCAGAACGGUCCGGACCGGAAGUCCUGUCCAGGACA---------ACGAAAGCCACAGAAACAAAAACGAGCUGA
..........((..((((((.....))))))..))(((..((((((((((.((....)).)))).)))).---------.(....)...............))..))). ( -34.70)
>DroSec_CAF1 27192 100 - 1
UAAUUGCAUUUUUGCGCUCCUGCCUGCGGCGUGGGCAGAACGGUCCGGACCGGAAGUCCUCCUCAGGACA---------CCGAAUGGCGCAGAAACAAAAAGGAGCUGA
.....(((....)))((((((..(((((.(((((((......))))....(((..(((((....))))).---------))).))).)))))........))))))... ( -37.50)
>DroSim_CAF1 18012 100 - 1
UAAUUGCAUUUUUGCGCUCCUGCCUGCGGCGUGUGCAGAAUGGUCCGGACCGGAAGUCCUCCUCAGGACA---------CCGAAAGGCGCAGAAACAAAAAGGAGCUGA
.....(((....)))(((((((((...))).(((((....(((((((...)))).(((((....))))).---------)))....))))).........))))))... ( -34.60)
>DroEre_CAF1 28423 105 - 1
UAAUUGCAUUUUUGCGCUCU-UCCUGGGGCACGGGCAGAACAGA--AGUCCGGAAGUCCUU-CCAGGACACCACGCGCGCCGAAAGCCACAGAAACAAAAAGGAGCUGA
.....((.((((.(((((((-.((((.....)))).))).....--.((((((((....))-)).)))).......)))).))))))..(((...(.....)...))). ( -30.50)
>consensus
UAAUUGCAUUUUUGCGCUCCUGCCUGCGGCGUGGGCAGAACGGUCCGGACCGGAAGUCCUCCCCAGGACA_________CCGAAAGCCACAGAAACAAAAAGGAGCUGA
.....(((....)))((((((..(((((((..........((((....))))...(((((....)))))................)))))))........))))))... (-26.29 = -27.35 +   1.06)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 3

Location 5,289,914 – 5,290,029
Length 115
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 81.35
Mean single sequence MFE -39.88
Consensus MFE -25.42
Energy contribution -27.54
Covariance contribution 2.12
Combinations/Pair 1.10
Mean z-score -2.08
Structure conservation index 0.64
SVM decision value 0.73
SVM RNA-class probability 0.836452
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 5289914 115 + 22224390
UUCUGCCCACGCCCCAGGCAGGAGCGCAAAAAUGCAAUUAUAAUCCCAG-----UGGCAGCAGGCGGCAACUGGCAGUGCAACUGCAUUGAAAAUUGCGCCUGCAAGUGCAACUUUGCAU
(((((((.........)))))))..(((((..((((........((...-----.))..(((((((.(((.(..((((((....))))))..).))))))))))...))))..))))).. ( -43.40)
>DroSec_CAF1 27252 115 + 1
UUCUGCCCACGCCGCAGGCAGGAGCGCAAAAAUGCAAUUAUAAUCCUAG-----AGGCAGCAGGCGGCGACGGGCAAUGCACCUGCAUUGGAUAUUGCGCCUGCAAGUGCAACUUUGCAU
(((((((.........)))))))..(((((..((((........((...-----.))..(((((((.(((.(..((((((....))))))..).))))))))))...))))..))))).. ( -43.20)
>DroSim_CAF1 18072 115 + 1
UUCUGCACACGCCGCAGGCAGGAGCGCAAAAAUGCAAUUAUAAUCCUAG-----AGGCAGCAGGCGGCGACGGGCAAUGCAACUGCAUUGGAUAUUGCGCCUGCAAGUGCAACUUUGCAU
...(((((..(((.((((...((..(((....)))..)).....))).)-----.))).(((((((.(((.(..((((((....))))))..).))))))))))..)))))......... ( -42.00)
>DroEre_CAF1 28489 105 + 1
UUCUGCCCGUGCCCCAGGA-AGAGCGCAAAAAUGCAAUUAUAAUCUCAGGCAGCAGGCGG--------------CAGUGCAACUGCAUUGGAAAUUGCCGCUGCAAGUGCAACUUUGCAU
((((..((........)).-)))).(((((..((((.............(((((.(((((--------------((((((....))))))....))))))))))...))))..))))).. ( -33.29)
>DroYak_CAF1 28303 112 + 1
--------AUGCCCCAGGCAGGAGCGCAAAAAUGCAAUUAUAAUCCCAGGCAGCAGGCGGCAGGCGGCGACUGGCAGUGCAACUGCAUUGGAAAUUGCAGCUGGCCGUGCAACUUUGCAU
--------..((.((.....)).))(((((..((((.........((........))((((.(((.((((.(..((((((....))))))..).)))).))).))))))))..))))).. ( -37.50)
>consensus
UUCUGCCCACGCCCCAGGCAGGAGCGCAAAAAUGCAAUUAUAAUCCCAG_____AGGCAGCAGGCGGCGACGGGCAGUGCAACUGCAUUGGAAAUUGCGCCUGCAAGUGCAACUUUGCAU
..........(((....((....))(((....)))....................))).(((((((.(((.(..((((((....))))))..).))))))))))..(((((....))))) (-25.42 = -27.54 +   2.12)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 4

Location 5,289,914 – 5,290,029
Length 115
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 81.35
Mean single sequence MFE -41.37
Consensus MFE -25.26
Energy contribution -27.22
Covariance contribution 1.96
Combinations/Pair 1.10
Mean z-score -2.17
Structure conservation index 0.61
SVM decision value 0.78
SVM RNA-class probability 0.849117
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 5289914 115 - 22224390
AUGCAAAGUUGCACUUGCAGGCGCAAUUUUCAAUGCAGUUGCACUGCCAGUUGCCGCCUGCUGCCA-----CUGGGAUUAUAAUUGCAUUUUUGCGCUCCUGCCUGGGGCGUGGGCAGAA
..((((((.((((...((((((((((((..((.(((....))).))..))))).)))))))..((.-----...))........)))).))))))((((.((((...)))).)))).... ( -44.50)
>DroSec_CAF1 27252 115 - 1
AUGCAAAGUUGCACUUGCAGGCGCAAUAUCCAAUGCAGGUGCAUUGCCCGUCGCCGCCUGCUGCCU-----CUAGGAUUAUAAUUGCAUUUUUGCGCUCCUGCCUGCGGCGUGGGCAGAA
.........((((((((((((........))..))))))))))(((((((.((((((..((..((.-----...)).........(((....)))......))..))))))))))))).. ( -45.60)
>DroSim_CAF1 18072 115 - 1
AUGCAAAGUUGCACUUGCAGGCGCAAUAUCCAAUGCAGUUGCAUUGCCCGUCGCCGCCUGCUGCCU-----CUAGGAUUAUAAUUGCAUUUUUGCGCUCCUGCCUGCGGCGUGUGCAGAA
..((((((.((((...((((((((.((...((((((....))))))...)).).)))))))..((.-----...))........)))).))))))((.(.((((...)))).).)).... ( -39.70)
>DroEre_CAF1 28489 105 - 1
AUGCAAAGUUGCACUUGCAGCGGCAAUUUCCAAUGCAGUUGCACUG--------------CCGCCUGCUGCCUGAGAUUAUAAUUGCAUUUUUGCGCUCU-UCCUGGGGCACGGGCAGAA
.(((...(((((....))))).))).........((((.....)))--------------).(((((.(((((.((........((((....))))....-..)).)))))))))).... ( -36.94)
>DroYak_CAF1 28303 112 - 1
AUGCAAAGUUGCACGGCCAGCUGCAAUUUCCAAUGCAGUUGCACUGCCAGUCGCCGCCUGCCGCCUGCUGCCUGGGAUUAUAAUUGCAUUUUUGCGCUCCUGCCUGGGGCAU--------
..((((((.((((.(((((((((((........))))))))....)))((((.((((..((.....)).))..)))))).....)))).))))))(((((.....)))))..-------- ( -40.10)
>consensus
AUGCAAAGUUGCACUUGCAGGCGCAAUUUCCAAUGCAGUUGCACUGCCAGUCGCCGCCUGCUGCCU_____CUGGGAUUAUAAUUGCAUUUUUGCGCUCCUGCCUGGGGCGUGGGCAGAA
..((((((.((((...(((((((.......((.(((....))).))........)))))))..(((.......)))........)))).))))))(((((.....))))).......... (-25.26 = -27.22 +   1.96)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:21:46 2006