Locus 6287

Sequence ID 3L_DroMel_CAF1
Location 16,746,081 – 16,746,278
Length 197
Max. P 0.739744
window10083 window10084 window10085

overview

Window 3

Location 16,746,081 – 16,746,199
Length 118
Sequences 5
Columns 118
Reading direction forward
Mean pairwise identity 85.15
Mean single sequence MFE -30.20
Consensus MFE -21.63
Energy contribution -22.31
Covariance contribution 0.68
Combinations/Pair 1.10
Mean z-score -1.91
Structure conservation index 0.72
SVM decision value 0.45
SVM RNA-class probability 0.739744
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 16746081 118 + 23771897
CCAGCAAAACCACCCACCCACUACUGGCCCCACACACACUUGACCCCAAGGGGAACUUGGCCCCUAUGCAGAGCCUUUAUGGGGCCAAAUAGGCGCCGAAAGUUCACAUUAUUUCACA
...................(((..((((.((............(((....)))...((((((((.(((.((...)).)))))))))))...)).))))..)))............... ( -30.40)
>DroSec_CAF1 152 114 + 1
-CUGCCCUG---CCCACCCACUACUUGUCCCACACACACUUGACCCCAAGGGGAACUUGGCCCCUAUGCAGAGCCUUUAUGGGGCCAAAUAGGCGCCGAAAGUUCACAUUAUUUCACA
-..((((((---....(((......(((.....)))..((((....)))))))...((((((((.(((.((...)).))))))))))).)))).)).((((..........))))... ( -28.80)
>DroSim_CAF1 158 115 + 1
CCAGCAAAA---CCCACCCACUACUGGCCCCACACACACUUGACCCCAAGGGGAACUUGGCCCCUAUGCAGAGCCUUAAUGGGGCCAAAUAGGCGCCGAAAGUUCACAUUAUUUCACA
.........---.......(((..((((.((............(((....)))...((((((((................))))))))...)).))))..)))............... ( -30.29)
>DroEre_CAF1 376 113 + 1
CCACCAAAACCACCCACCC---ACUGGCCUCA--AACACUUGACCCCAAAGGGAACUUGGCCCGUAUGUAGAGCCUUUACGGAGCCAAACGGGCGCCGAAAGUUCAUAUUAUUUCGCA
............(((.(((---..(((..(((--(....))))..)))..)))...((((((((((...........))))).)))))..))).((.((((..........)))))). ( -31.40)
>DroYak_CAF1 173 113 + 1
CGACCCAGUAAUUCCACCC---ACUGGCCCCA--CACACUUGACCCCAAAGGGAACUUGGCCCCUAUGCAGAGCCUUUACGGGGCCAAAUGAGCGCGGAAAGUUCAUAUUAUUUCGCA
(((...((((((.......---..(((((((.--.........(((....))).....(((..((....)).))).....))))))).((((((.......))))))))))))))).. ( -30.10)
>consensus
CCAGCAAAA___CCCACCCACUACUGGCCCCACACACACUUGACCCCAAGGGGAACUUGGCCCCUAUGCAGAGCCUUUAUGGGGCCAAAUAGGCGCCGAAAGUUCACAUUAUUUCACA
.........................(((.((............(((....)))...((((((((................))))))))...)).)))((((..........))))... (-21.63 = -22.31 +   0.68)

alignment

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secondary structure

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dotplot

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Window 4

Location 16,746,081 – 16,746,199
Length 118
Sequences 5
Columns 118
Reading direction reverse
Mean pairwise identity 85.15
Mean single sequence MFE -42.36
Consensus MFE -33.50
Energy contribution -34.70
Covariance contribution 1.20
Combinations/Pair 1.15
Mean z-score -1.67
Structure conservation index 0.79
SVM decision value 0.32
SVM RNA-class probability 0.685063
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 16746081 118 - 23771897
UGUGAAAUAAUGUGAACUUUCGGCGCCUAUUUGGCCCCAUAAAGGCUCUGCAUAGGGGCCAAGUUCCCCUUGGGGUCAAGUGUGUGUGGGGCCAGUAGUGGGUGGGUGGUUUUGCUGG
.(..((((...(....)......((((((((((((((((((..((((((.....)))))).....(((....))).........))))))))))..))))))))....))))..)... ( -46.50)
>DroSec_CAF1 152 114 - 1
UGUGAAAUAAUGUGAACUUUCGGCGCCUAUUUGGCCCCAUAAAGGCUCUGCAUAGGGGCCAAGUUCCCCUUGGGGUCAAGUGUGUGUGGGACAAGUAGUGGGUGGG---CAGGGCAG-
............((..((.((.((.((((((((..((((((..((((((.....)))))).....(((....))).........)))))).))))))).).)).))---.))..)).- ( -40.00)
>DroSim_CAF1 158 115 - 1
UGUGAAAUAAUGUGAACUUUCGGCGCCUAUUUGGCCCCAUUAAGGCUCUGCAUAGGGGCCAAGUUCCCCUUGGGGUCAAGUGUGUGUGGGGCCAGUAGUGGGUGGG---UUUUGCUGG
.(..((((...(....)......(((((((((((((((((...((((((.....)))))).....(((....)))..........)))))))))..)))))))).)---)))..)... ( -44.80)
>DroEre_CAF1 376 113 - 1
UGCGAAAUAAUAUGAACUUUCGGCGCCCGUUUGGCUCCGUAAAGGCUCUACAUACGGGCCAAGUUCCCUUUGGGGUCAAGUGUU--UGAGGCCAGU---GGGUGGGUGGUUUUGGUGG
..((((((........(((((((.(((.....))).))).))))((.((((.(((.((((.....(((....)))((((....)--))))))).))---).)))))).)))))).... ( -35.80)
>DroYak_CAF1 173 113 - 1
UGCGAAAUAAUAUGAACUUUCCGCGCUCAUUUGGCCCCGUAAAGGCUCUGCAUAGGGGCCAAGUUCCCUUUGGGGUCAAGUGUG--UGGGGCCAGU---GGGUGGAAUUACUGGGUCG
..(((...............((.(((.((((((((((((....((((((.....))))))(((....))))))))))))))).)--)).))(((((---((......))))))).))) ( -44.70)
>consensus
UGUGAAAUAAUGUGAACUUUCGGCGCCUAUUUGGCCCCAUAAAGGCUCUGCAUAGGGGCCAAGUUCCCCUUGGGGUCAAGUGUGUGUGGGGCCAGUAGUGGGUGGG___UUUUGCUGG
.......................(((((((((((((((((...((((((.....)))))).....(((....)))..........))))))))))..))))))).............. (-33.50 = -34.70 +   1.20)

alignment

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secondary structure

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dotplot

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Window 5

Location 16,746,159 – 16,746,278
Length 119
Sequences 5
Columns 119
Reading direction forward
Mean pairwise identity 86.80
Mean single sequence MFE -29.23
Consensus MFE -19.66
Energy contribution -20.18
Covariance contribution 0.52
Combinations/Pair 1.07
Mean z-score -2.10
Structure conservation index 0.67
SVM decision value 0.27
SVM RNA-class probability 0.661648
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 16746159 119 + 23771897
AUGGGGCCAAAUAGGCGCCGAAAGUUCACAUUAUUUCACAAGGUUCGCUCUUUUGUAUGAAAACCAAAUACAACCUUUUGAAAUAGUAAAAGAAUAGCAUGGAAGCUUGUAAUUUCUAA
..((.(((.....))).))((((((((..(((((((((.(((((.........(((((.........)))))))))).)))))))))....))))(((......))).....))))... ( -27.30)
>DroSec_CAF1 226 119 + 1
AUGGGGCCAAAUAGGCGCCGAAAGUUCACAUUAUUUCACAAGGUUCGCUCUUUUGUACAAAAACCAAAUACAACCUUUUGAAAUAGUAAAAGAAAAGCGUGGGGCCAUGUAAUUUCUAA
.(((.(((.....))).))).........(((((((((.((((((......((((.........))))...)))))).)))))))))...(((((.(((((....)))))..))))).. ( -30.00)
>DroSim_CAF1 233 119 + 1
AUGGGGCCAAAUAGGCGCCGAAAGUUCACAUUAUUUCACAAGGUUCGCUCUUUUGUACAAAAACCAAAUACCACCUUUUGAAAUAGAACAAGAAUAGCGUGGGGCCAUGUAAUUUCUAA
.(((.(((.....))).)))...((((....(((((((.(((((.......((((.........))))....))))).))))))))))).((((..(((((....)))))...)))).. ( -29.70)
>DroEre_CAF1 449 118 + 1
ACGGAGCCAAACGGGCGCCGAAAGUUCAUAUUAUUUCGCAAGGUUUGCUCUUUUGUAUACAAACCAAAUACAACCUUUUGAAAUAGUAAUCGAAU-GUUUAGGCUCUUGUGAAUUAUAA
(((((((((((((..((.(....)....((((((((((.((((((......((((....))))........)))))).))))))))))..))..)-)))).))))).)))......... ( -30.84)
>DroYak_CAF1 246 118 + 1
ACGGGGCCAAAUGAGCGCGGAAAGUUCAUAUUAUUUCGCAAGGUUCGCUCUUUUGUAUGAAAACCAAAUACAACCUUUUGAAAUAGUAAACGAAU-GUUUAGGGGCUUCUGAAUUCUAA
..((((((...(((((.((((....)).((((((((((.(((((.........(((((.........)))))))))).))))))))))..))...-)))))..)))))).......... ( -28.30)
>consensus
AUGGGGCCAAAUAGGCGCCGAAAGUUCACAUUAUUUCACAAGGUUCGCUCUUUUGUAUAAAAACCAAAUACAACCUUUUGAAAUAGUAAAAGAAUAGCGUGGGGCCUUGUAAUUUCUAA
.(((.(((.....))).)))...((((..(((((((((.((((((......((((.........))))...)))))).)))))))))....))))........................ (-19.66 = -20.18 +   0.52)

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 12:14:45 2006