Locus 3017

Sequence ID 2R_DroMel_CAF1
Location 10,415,703 – 10,415,823
Length 120
Max. P 0.960579
window4975 window4976

overview

Window 5

Location 10,415,703 – 10,415,823
Length 120
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 76.50
Mean single sequence MFE -46.88
Consensus MFE -22.35
Energy contribution -24.72
Covariance contribution 2.37
Combinations/Pair 1.44
Mean z-score -2.52
Structure conservation index 0.48
SVM decision value 1.52
SVM RNA-class probability 0.960579
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 10415703 120 + 20766785
CACUUGGUUUGGAUUCGGCGUGGGUGCUCGCAGUUGCAUUGGUAUACAAUUCGCACAGCUGCAACUGCGAUUGGCAUUGGCUCUGCUUCUAUCCGAGUAUGAAUUCUCCUUGAAUACCAG
.((((((..((((..(((.((.(((((((((((((((((((((.........)).))).)))))))))))...))))).)).)))..)))).))))))....((((.....))))..... ( -44.20)
>DroVir_CAF1 27072 120 + 1
CACAUGGUUUGGCUUUGGCUCCGGCGUCCGCAAUUGCAUUGGCAUGCAAUUCGCCCAGCUCCAACUGCGUCUCGCACUGGCGCUACUUCUGCUGGAGUUCGAGUUCACUUUGAACUCCAA
..((.((.....)).))(((((((((..((.((((((((....))))))))))..)(((.(((..((((...)))).))).)))......))))))))..((((((.....))))))... ( -41.50)
>DroPse_CAF1 18038 120 + 1
CACCUGGUUCGGCUUUGGGGUGGGCGCCCGCAGCUGCAUAGGCAUACAGUUUGCCCAGCUGCAACUGCGCCUGGCUCUGGCCUUGCUCCUUAUGGAGUACGAAUUUACACUAAACUCGAG
.....(((((((((..(((.(((((((..(((((((....((((.......)))))))))))....))))))).))).)))).((((((....)))))).)))))............... ( -50.10)
>DroWil_CAF1 35764 120 + 1
CACUUGGUUUGGCUUCGGUGUGGGGGCUCGCAAUUGCAUUGGCAUACAUUUUGCCCAAUUGCAAAUACGUCUGGCCCUUGCCCUGCUUCUAAUGGAGUAUGAAUUCACAUUGAAUUCGCG
.((((.(((.(((...((.(..((((((((...(((((..((((.......))))....)))))...))...))))))..))).)))...))).))))..((((((.....))))))... ( -41.60)
>DroMoj_CAF1 24972 120 + 1
CACCUGGUUCGGCUUUGGCUCCGGGGUGCGGAACUGCAUUGGCAUGCAAUUCGCAGAGCUGCAGCUGCGCGUGGCACUCGCUCUGCUGCUGCUGGAGUUCGAGUUCAGUUUGAACUCGAG
..(((((...(((....)))))))).((((((..(((((....))))).))))))(((((.((((.(((((.(((....))).))).)).)))).)))))((((((.....))))))... ( -53.00)
>DroPer_CAF1 24115 120 + 1
CACCUGGUUCGGCUUUGGGGUGGGCGCCCGCAGCUGCAUAGGCAUACAGUUUGCCCAGCUGCAACUGCGCCUGGCUCUGGCCUUGCUCCUUAUGGAGUACGAAUUUACUCUAAACUCGAG
........(((..((((((((((((((..(((((((....((((.......)))))))))))....))))))(((....))).((((((....)))))).......))))))))..))). ( -50.90)
>consensus
CACCUGGUUCGGCUUUGGCGUGGGCGCCCGCAACUGCAUUGGCAUACAAUUCGCCCAGCUGCAACUGCGCCUGGCACUGGCCCUGCUUCUAAUGGAGUACGAAUUCACUUUGAACUCGAG
..........((((...((.(((((((..(((((((....(((.........))))))))))....)))))))))...)))).((((((....))))))(((((((.....))))))).. (-22.35 = -24.72 +   2.37)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 6

Location 10,415,703 – 10,415,823
Length 120
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 76.50
Mean single sequence MFE -41.48
Consensus MFE -25.02
Energy contribution -24.50
Covariance contribution -0.52
Combinations/Pair 1.40
Mean z-score -1.89
Structure conservation index 0.60
SVM decision value 1.09
SVM RNA-class probability 0.913102
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 10415703 120 - 20766785
CUGGUAUUCAAGGAGAAUUCAUACUCGGAUAGAAGCAGAGCCAAUGCCAAUCGCAGUUGCAGCUGUGCGAAUUGUAUACCAAUGCAACUGCGAGCACCCACGCCGAAUCCAAACCAAGUG
.((((.......(((........)))((((....(((.......)))...(((((((((((..(((((.....)))))....)))))))))))((......))...))))..)))).... ( -33.90)
>DroVir_CAF1 27072 120 - 1
UUGGAGUUCAAAGUGAACUCGAACUCCAGCAGAAGUAGCGCCAGUGCGAGACGCAGUUGGAGCUGGGCGAAUUGCAUGCCAAUGCAAUUGCGGACGCCGGAGCCAAAGCCAAACCAUGUG
.((((((((..((....)).))))))))((.....((((.((((((((...)))).)))).))))(((.((((((((....)))))))).(((...)))..)))...))........... ( -42.50)
>DroPse_CAF1 18038 120 - 1
CUCGAGUUUAGUGUAAAUUCGUACUCCAUAAGGAGCAAGGCCAGAGCCAGGCGCAGUUGCAGCUGGGCAAACUGUAUGCCUAUGCAGCUGCGGGCGCCCACCCCAAAGCCGAACCAGGUG
..((((((((...))))))))..((((....))))...(((....))).((((((((((((..((((((.......)))))))))))))))(((.(....))))...))).......... ( -45.30)
>DroWil_CAF1 35764 120 - 1
CGCGAAUUCAAUGUGAAUUCAUACUCCAUUAGAAGCAGGGCAAGGGCCAGACGUAUUUGCAAUUGGGCAAAAUGUAUGCCAAUGCAAUUGCGAGCCCCCACACCGAAGCCAAACCAAGUG
(((((((((.....))))))..............((.((....((((....((((.(((((....((((.......))))..))))).)))).)))).....))...))........))) ( -31.90)
>DroMoj_CAF1 24972 120 - 1
CUCGAGUUCAAACUGAACUCGAACUCCAGCAGCAGCAGAGCGAGUGCCACGCGCAGCUGCAGCUCUGCGAAUUGCAUGCCAAUGCAGUUCCGCACCCCGGAGCCAAAGCCGAACCAGGUG
.((((((((.....)))))))).(((((((.(((((...(((.......)))...))))).))).((((((((((((....)))))))).))))....)))).....(((......))). ( -50.00)
>DroPer_CAF1 24115 120 - 1
CUCGAGUUUAGAGUAAAUUCGUACUCCAUAAGGAGCAAGGCCAGAGCCAGGCGCAGUUGCAGCUGGGCAAACUGUAUGCCUAUGCAGCUGCGGGCGCCCACCCCAAAGCCGAACCAGGUG
..((((((((...))))))))..((((....))))...(((....))).((((((((((((..((((((.......)))))))))))))))(((.(....))))...))).......... ( -45.30)
>consensus
CUCGAGUUCAAAGUGAAUUCGUACUCCAUAAGAAGCAGGGCCAGUGCCAGGCGCAGUUGCAGCUGGGCAAAUUGUAUGCCAAUGCAACUGCGGGCGCCCACGCCAAAGCCAAACCAGGUG
...((((((.....))))))..............((..(((....)))...((((((((((....((((.......))))..)))))))))).))......................... (-25.02 = -24.50 +  -0.52)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:45:18 2006