Locus 4222

Sequence ID 3R_DroMel_CAF1
Location 11,365,061 – 11,365,261
Length 200
Max. P 0.802197
window6826 window6827 window6828

overview

Window 6

Location 11,365,061 – 11,365,181
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 92.67
Mean single sequence MFE -30.27
Consensus MFE -25.02
Energy contribution -24.94
Covariance contribution -0.08
Combinations/Pair 1.10
Mean z-score -1.52
Structure conservation index 0.83
SVM decision value 0.55
SVM RNA-class probability 0.779637
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11365061 120 + 27905053
AGCUUUGAAGCCACCAAAGCCGUGGCGCAAGCAACUAUAUUGCCUCUAGUGACCUUUGCACCAUACGCUCCACCCACUCGUCUAACUUGGAGCUGAAUGGAGUUCACACUAACUUUCAAC
....((((((((((.......)))))((((.........))))...(((((......((.((((.(((((((...............)))))).).)))).))...)))))...))))). ( -28.96)
>DroSec_CAF1 112692 120 + 1
AGCUUUGAAGCCACCAAAGCCGUGACGCAAGCAACUAUAUUGCCCCUAGUGACCUUUGCACCAUACGCUCCACCCACUCGUCUAACUUGGAGCUGAAUGGAGUUCACACUAACACUCAAC
.((((((.......)))))).(((..((((.........))))...(((((......((.((((.(((((((...............)))))).).)))).))...))))).)))..... ( -27.86)
>DroSim_CAF1 103726 120 + 1
AGCUUUGAAGCCACCAAAGCCGUGGCGCAAGCAACUAUAUUGCCCCUAGUGACCUUUGCACCAUACGCUCCACCCACUCGUCUAACUUGGAGCUGAAUGGAGUUCACACUAACACUCAAC
.((((((.......)))))).(((((....))..............(((((......((.((((.(((((((...............)))))).).)))).))...))))).)))..... ( -30.56)
>DroEre_CAF1 100043 120 + 1
AGCUUCGAAGCAACCAAGGCCGUGGCGCAAGCCACUAAAUUGCCCCUAGUGACCUUUGCGCCGUAUGCCCCACCCACUCGUCUAACUUGGAGCUGAAUGGAGUUCACACUAACCCUCAGC
.(((....)))..(((((...(((((....)))))............((((......(((.....)))......)))).......))))).(((((..((.(((......)))))))))) ( -31.60)
>DroYak_CAF1 102773 120 + 1
AGCUUUGAAGCCACCAAAGCCGUGGCGCAAGCCACUAAAUUGCACCUAGUAACCUUUGCGCCAUAUGCUCCACCCACUCGUCUAACUUGGAGCUGAAUGGAGUUCACAGUGACCCCCAAC
.((((((.......)))))).((((((((((..((((.........))))....))))))))))..((((((...............))))))....(((.(.((.....)).).))).. ( -32.36)
>consensus
AGCUUUGAAGCCACCAAAGCCGUGGCGCAAGCAACUAUAUUGCCCCUAGUGACCUUUGCACCAUACGCUCCACCCACUCGUCUAACUUGGAGCUGAAUGGAGUUCACACUAACACUCAAC
.((((((.......)))))).((((((((((..((((.........))))....))))).((((..((((((...............))))))...)))).).))))............. (-25.02 = -24.94 +  -0.08)

alignment

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secondary structure

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dotplot

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Window 7

Location 11,365,061 – 11,365,181
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 92.67
Mean single sequence MFE -41.70
Consensus MFE -35.92
Energy contribution -35.24
Covariance contribution -0.68
Combinations/Pair 1.14
Mean z-score -1.41
Structure conservation index 0.86
SVM decision value 0.62
SVM RNA-class probability 0.802197
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11365061 120 - 27905053
GUUGAAAGUUAGUGUGAACUCCAUUCAGCUCCAAGUUAGACGAGUGGGUGGAGCGUAUGGUGCAAAGGUCACUAGAGGCAAUAUAGUUGCUUGCGCCACGGCUUUGGUGGCUUCAAAGCU
.............(((..(((((((((.(((..........))))))))))))..)))((((((..(((.((((.........)))).)))))))))..((((((((.....)))))))) ( -37.00)
>DroSec_CAF1 112692 120 - 1
GUUGAGUGUUAGUGUGAACUCCAUUCAGCUCCAAGUUAGACGAGUGGGUGGAGCGUAUGGUGCAAAGGUCACUAGGGGCAAUAUAGUUGCUUGCGUCACGGCUUUGGUGGCUUCAAAGCU
((((((((..(((....))).)))))))).(((.(.....)...)))(((..((...((((((....).))))).(((((((...)))))))))..)))((((((((.....)))))))) ( -36.20)
>DroSim_CAF1 103726 120 - 1
GUUGAGUGUUAGUGUGAACUCCAUUCAGCUCCAAGUUAGACGAGUGGGUGGAGCGUAUGGUGCAAAGGUCACUAGGGGCAAUAUAGUUGCUUGCGCCACGGCUUUGGUGGCUUCAAAGCU
((((((((..(((....))).)))))))).(((.(.....)...)))((((.((...((((((....).))))).(((((((...))))))))).))))((((((((.....)))))))) ( -38.30)
>DroEre_CAF1 100043 120 - 1
GCUGAGGGUUAGUGUGAACUCCAUUCAGCUCCAAGUUAGACGAGUGGGUGGGGCAUACGGCGCAAAGGUCACUAGGGGCAAUUUAGUGGCUUGCGCCACGGCCUUGGUUGCUUCGAAGCU
((..(((....(((((..(((((((((.(((..........)))))))))))))))))((((((..((((((((((.....))))))))))))))))....)))..)).(((....))). ( -49.90)
>DroYak_CAF1 102773 120 - 1
GUUGGGGGUCACUGUGAACUCCAUUCAGCUCCAAGUUAGACGAGUGGGUGGAGCAUAUGGCGCAAAGGUUACUAGGUGCAAUUUAGUGGCUUGCGCCACGGCUUUGGUGGCUUCAAAGCU
(((.((((((((((((..(((((((((.(((..........))))))))))))))).(((((((..(((((((((((...)))))))))))))))))).......)))))))))..))). ( -47.10)
>consensus
GUUGAGGGUUAGUGUGAACUCCAUUCAGCUCCAAGUUAGACGAGUGGGUGGAGCGUAUGGUGCAAAGGUCACUAGGGGCAAUAUAGUUGCUUGCGCCACGGCUUUGGUGGCUUCAAAGCU
.............(((..(((((((((.(((..........))))))))))))..)))((((((..(((.((((.........)))).)))))))))..((((((((.....)))))))) (-35.92 = -35.24 +  -0.68)

alignment

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secondary structure

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dotplot

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Window 8

Location 11,365,141 – 11,365,261
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 92.50
Mean single sequence MFE -39.21
Consensus MFE -35.06
Energy contribution -35.42
Covariance contribution 0.36
Combinations/Pair 1.03
Mean z-score -1.13
Structure conservation index 0.89
SVM decision value -0.04
SVM RNA-class probability 0.510682
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11365141 120 + 27905053
UCUAACUUGGAGCUGAAUGGAGUUCACACUAACUUUCAACAUGUGGGCAAUCGCUCCUUGGGUGGCGUCCAUCCAUUGGGUGGCGCAGUAUACCUGCAGAAUGUUAUCAAGCGGCACCAC
.......(((.((((..(((.(((((((.............)))))))..((((((..(((((((...)))))))..)))))).((((.....)))).........)))..)))).))). ( -38.02)
>DroSec_CAF1 112772 120 + 1
UCUAACUUGGAGCUGAAUGGAGUUCACACUAACACUCAACAUGUGGGCAAUCGCUCCUUGGGUGGCGUCCAUCCAUUGGGUGGCGCAGUAUACCUGCAGAAUGUUAUCCAGCGGCACCAC
.......(((.((((..(((((((((((.............)))))))..((((((..(((((((...)))))))..)))))).((((.....)))).........)))).)))).))). ( -40.42)
>DroSim_CAF1 103806 120 + 1
UCUAACUUGGAGCUGAAUGGAGUUCACACUAACACUCAACAUGUGGGCAAUCGCUCCUUGGGUGGCGUCCAUCCAUUGGGUGGCGCAGUAUACCUGCAGAAUGUUAUCCAGCGGCACCAC
.......(((.((((..(((((((((((.............)))))))..((((((..(((((((...)))))))..)))))).((((.....)))).........)))).)))).))). ( -40.42)
>DroEre_CAF1 100123 120 + 1
UCUAACUUGGAGCUGAAUGGAGUUCACACUAACCCUCAGCAUGCGGGCGAUCGCUCCUUGGGUGGAGUUCAUCCAUUGGGUGGCACAGUAUACCUGUAGAAUGUCAUCCAACGGCACCAC
.......(((.(((((..((.(((......)))))))))).(((((..((..(((((......)))))))..)).(((((((((((((.....)))).....)))))))))..)))))). ( -38.90)
>DroYak_CAF1 102853 120 + 1
UCUAACUUGGAGCUGAAUGGAGUUCACAGUGACCCCCAACAUGUGGGCAAUCGCUCCCUGGGUGCAAUCCAUCCAUUGGGUGGCACAGUAUACCUGCAGGAUGUUGUCCAACGGCACCAC
.......(((.((((..(((((((((((((........)).)))))))....((..((((.((((.(((((.....))))).))))((.....)).))))..))..)))).)))).))). ( -38.30)
>consensus
UCUAACUUGGAGCUGAAUGGAGUUCACACUAACACUCAACAUGUGGGCAAUCGCUCCUUGGGUGGCGUCCAUCCAUUGGGUGGCGCAGUAUACCUGCAGAAUGUUAUCCAGCGGCACCAC
.......(((.((((..(((((((((((.............)))))))..((((((..((((((.....))))))..)))))).((((.....)))).........)))).)))).))). (-35.06 = -35.42 +   0.36)

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 11:22:20 2006