Locus 5611

Sequence ID 2R_DroMel_CAF1
Location 17,875,774 – 17,876,009
Length 235
Max. P 0.988571
window8989 window8990 window8991 window8992

overview

Window 9

Location 17,875,774 – 17,875,864
Length 90
Sequences 5
Columns 90
Reading direction forward
Mean pairwise identity 95.56
Mean single sequence MFE -22.22
Consensus MFE -18.58
Energy contribution -18.10
Covariance contribution -0.48
Combinations/Pair 1.17
Mean z-score -1.43
Structure conservation index 0.84
SVM decision value 0.18
SVM RNA-class probability 0.619964
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 17875774 90 + 20766785
UAGCCUGAAUCUGUAAGCAUUAGAUGUUUUUUAUAGCCAACAACAUCCGCGUUGUCAUGGGGGUUAUGACAAUUUCCCCACAGAUGUCAU
.....(((((((((..((..((((.....))))..))..(((((......)))))....((((..((....))..)))))))))).))). ( -20.00)
>DroSec_CAF1 40629 90 + 1
UAGCCCAAAUCUGUAAGCAUUAGAUGUUUUUUAUAGCCAACAACAUCCGCGUUGUCAUGGGGGUUAUGACAAUUUCCCCACAGAUGUCAU
((((((....((((((((((...))))...))))))((((((((......)))))..)))))))))(((((.(((......)))))))). ( -20.40)
>DroSim_CAF1 41089 90 + 1
UAGCCCAAAUCUGUAAGCAUUAGAUGUUUUUUAUAGCCAACAACAUCCGCGUUGUCAUGGGGGUUAUGACAAUUUCCCCACAGAUGUCAU
((((((....((((((((((...))))...))))))((((((((......)))))..)))))))))(((((.(((......)))))))). ( -20.40)
>DroEre_CAF1 43040 90 + 1
UAGCCCAAAUCUGUAGGCAUUAGAGGUUUUUUAUGGCCAACAACAUCCGCGUUGCCAUGGGGGCUAUGACAAUUUCCCCACAGAUGUCAU
((((((((((((.(((...))).)))))).(((((((.(((.........))))))))))))))))(((((.(((......)))))))). ( -24.90)
>DroYak_CAF1 39776 90 + 1
UAGCCCAAAUCUUUGGGCAUUAGAGGUUUUUUAUAGCCAACAACAUCCGCGUUGUCAUGGGGGUUAUGACAAUUUCCCCACAGAUGUCAU
..((((((....))))))......((((......)))).(((((......)))))..((((((..((....))..)))).))........ ( -25.40)
>consensus
UAGCCCAAAUCUGUAAGCAUUAGAUGUUUUUUAUAGCCAACAACAUCCGCGUUGUCAUGGGGGUUAUGACAAUUUCCCCACAGAUGUCAU
((((((....(((((((.(........).)))))))((((((((......)))))..)))))))))(((((.(((......)))))))). (-18.58 = -18.10 +  -0.48)

alignment

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secondary structure

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dotplot

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Window 0

Location 17,875,774 – 17,875,864
Length 90
Sequences 5
Columns 90
Reading direction reverse
Mean pairwise identity 95.56
Mean single sequence MFE -23.88
Consensus MFE -22.38
Energy contribution -21.86
Covariance contribution -0.52
Combinations/Pair 1.18
Mean z-score -1.67
Structure conservation index 0.94
SVM decision value 2.13
SVM RNA-class probability 0.988571
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 17875774 90 - 20766785
AUGACAUCUGUGGGGAAAUUGUCAUAACCCCCAUGACAACGCGGAUGUUGUUGGCUAUAAAAAACAUCUAAUGCUUACAGAUUCAGGCUA
.(((.(((((((((.(..(((((((.......)))))))...(((((((.((.......)).)))))))..).))))))))))))..... ( -24.20)
>DroSec_CAF1 40629 90 - 1
AUGACAUCUGUGGGGAAAUUGUCAUAACCCCCAUGACAACGCGGAUGUUGUUGGCUAUAAAAAACAUCUAAUGCUUACAGAUUUGGGCUA
.....(((((((((.(..(((((((.......)))))))...(((((((.((.......)).)))))))..).)))))))))........ ( -21.90)
>DroSim_CAF1 41089 90 - 1
AUGACAUCUGUGGGGAAAUUGUCAUAACCCCCAUGACAACGCGGAUGUUGUUGGCUAUAAAAAACAUCUAAUGCUUACAGAUUUGGGCUA
.....(((((((((.(..(((((((.......)))))))...(((((((.((.......)).)))))))..).)))))))))........ ( -21.90)
>DroEre_CAF1 43040 90 - 1
AUGACAUCUGUGGGGAAAUUGUCAUAGCCCCCAUGGCAACGCGGAUGUUGUUGGCCAUAAAAAACCUCUAAUGCCUACAGAUUUGGGCUA
(..((((((((((((.............))))..(....)))))))))..).....................(((((......))))).. ( -24.92)
>DroYak_CAF1 39776 90 - 1
AUGACAUCUGUGGGGAAAUUGUCAUAACCCCCAUGACAACGCGGAUGUUGUUGGCUAUAAAAAACCUCUAAUGCCCAAAGAUUUGGGCUA
(..(((((((((......(((((((.......))))))))))))))))..).....................((((((....)))))).. ( -26.50)
>consensus
AUGACAUCUGUGGGGAAAUUGUCAUAACCCCCAUGACAACGCGGAUGUUGUUGGCUAUAAAAAACAUCUAAUGCUUACAGAUUUGGGCUA
(..(((((((((......(((((((.......))))))))))))))))..).....................(((((......))))).. (-22.38 = -21.86 +  -0.52)

alignment

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secondary structure

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dotplot

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Window 1

Location 17,875,864 – 17,875,970
Length 106
Sequences 5
Columns 106
Reading direction reverse
Mean pairwise identity 95.28
Mean single sequence MFE -25.28
Consensus MFE -23.10
Energy contribution -22.74
Covariance contribution -0.36
Combinations/Pair 1.12
Mean z-score -1.15
Structure conservation index 0.91
SVM decision value 0.14
SVM RNA-class probability 0.604939
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 17875864 106 - 20766785
UGCCUUAAUGGGCCUGGCAGAUGUCACCGAGUUCAUGGCUGCCAAAUCCGGCGCUGUACAGAAAUGUAAUUAAACUUUUAAUUAAAUGAAUUAAAAUACCAUCUCG
.((((....))))...(.(((((......((((((((((.(((......)))))).((((....)))).................))))))).......)))))). ( -25.22)
>DroSec_CAF1 40719 106 - 1
UGCCUUAAUGGGCCUGGCAGAUGUCACGGAGUUCAUGGCUGCCAAAUCCGGCGCUGUACAGAAAUGUAAUUAAACUUUUAACUAAAUGAAUUAAAAUACCAUCUCG
.((((....))))...(.(((((......((((((((((.(((......)))))).((((....)))).................))))))).......)))))). ( -25.22)
>DroSim_CAF1 41179 106 - 1
UGCCCUAAUGGGCCUGGCAGAUGUCACGGAGUUCAUGGCUGCCAAAUCCGGCGCUGUACAGAAAUGUAAUUAAACUUUUAAUUAAAUGAAUUAAAAUACCAUCUCG
.((((....))))...(.(((((......((((((((((.(((......)))))).((((....)))).................))))))).......)))))). ( -27.62)
>DroEre_CAF1 43130 106 - 1
UGCCCUAAUGGGCCUGGCAGAUGUCACGGAGUUCAUGGCCGCCAAAUCUGGCGCAGUGUUGAAAUGUAAUUAAACUUUUAAUUAAAUGAAUUAAAAUACCAUCUCG
.((((....))))...(.(((((......(((((((.((.((((....))))))...(((((((.((......)))))))))...))))))).......)))))). ( -25.92)
>DroYak_CAF1 39866 106 - 1
UGCCUUAAUGGGCCUGGCAGAUGUCACGGAGUUCAUGGCCGCCAAAACCGGCGCAGUACACAAAUGUAAUUAAACUUUUAAUUAAAUGAAUUAAAAUACCAUCUCG
.((((....))))...(.(((((......(((((((.((.(((......)))))............(((((((....))))))).))))))).......)))))). ( -22.42)
>consensus
UGCCUUAAUGGGCCUGGCAGAUGUCACGGAGUUCAUGGCUGCCAAAUCCGGCGCUGUACAGAAAUGUAAUUAAACUUUUAAUUAAAUGAAUUAAAAUACCAUCUCG
.((((....))))...(.(((((......(((((((.((.(((......)))))..((((....)))).................))))))).......)))))). (-23.10 = -22.74 +  -0.36)

alignment

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secondary structure

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dotplot

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Window 2

Location 17,875,890 – 17,876,009
Length 119
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 88.02
Mean single sequence MFE -36.18
Consensus MFE -26.46
Energy contribution -26.94
Covariance contribution 0.48
Combinations/Pair 1.11
Mean z-score -1.88
Structure conservation index 0.73
SVM decision value 0.38
SVM RNA-class probability 0.713270
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 17875890 119 - 20766785
AUGCUGCGAUAUUCGC-UGCUGGCAUUUUGAAAUCCGUAUUGCCUUAAUGGGCCUGGCAGAUGUCACCGAGUUCAUGGCUGCCAAAUCCGGCGCUGUACAGAAAUGUAAUUAAACUUUUA
..((.(((.....)))-.))..(((((((((.(((.((...((((....))))...)).))).)).........(((((.(((......))))))))...)))))))............. ( -30.70)
>DroSec_CAF1 40745 119 - 1
AUGCUGCGAUAGUCGC-UGCUGGCAUUUUGAAAUCCGUAUUGCCUUAAUGGGCCUGGCAGAUGUCACGGAGUUCAUGGCUGCCAAAUCCGGCGCUGUACAGAAAUGUAAUUAAACUUUUA
...(((..((((.(((-((.((((((..((((.(((((...((((....))))..(((....)))))))).))))..).)))))....))))))))).)))................... ( -36.90)
>DroSim_CAF1 41205 119 - 1
AUGCUGCGAUAGUCGC-UGCUGGCAUUUUGAAAUCCGUAUUGCCCUAAUGGGCCUGGCAGAUGUCACGGAGUUCAUGGCUGCCAAAUCCGGCGCUGUACAGAAAUGUAAUUAAACUUUUA
...(((..((((.(((-((.((((((..((((.(((((...((((....))))..(((....)))))))).))))..).)))))....))))))))).)))................... ( -39.30)
>DroEre_CAF1 43156 98 - 1
AUGCUGC----------------------GAAAUCCGUAUUGCCCUAAUGGGCCUGGCAGAUGUCACGGAGUUCAUGGCCGCCAAAUCUGGCGCAGUGUUGAAAUGUAAUUAAACUUUUA
(((((((----------------------(((.(((((...((((....))))..(((....)))))))).)))......((((....)))))))))))..................... ( -32.80)
>DroYak_CAF1 39892 120 - 1
AUGCUGCGUUAGUCGUUUGCUGGCAUUUUGAAAUCCGUAUUGCCUUAAUGGGCCUGGCAGAUGUCACGGAGUUCAUGGCCGCCAAAACCGGCGCAGUACACAAAUGUAAUUAAACUUUUA
.((((((((..((..((((.((((....((((.(((((...((((....))))..(((....)))))))).))))..)))).))))))..))))))))...................... ( -41.20)
>consensus
AUGCUGCGAUAGUCGC_UGCUGGCAUUUUGAAAUCCGUAUUGCCUUAAUGGGCCUGGCAGAUGUCACGGAGUUCAUGGCUGCCAAAUCCGGCGCUGUACAGAAAUGUAAUUAAACUUUUA
.(((.((..............(((....((((.(((((...((((....))))..(((....)))))))).))))..)))(((......))))).)))...................... (-26.46 = -26.94 +   0.48)

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 11:49:57 2006