Locus 6258

Sequence ID 2L_DroMel_CAF1
Location 17,377,315 – 17,377,424
Length 109
Max. P 0.999912
window9998 window9999 window10000 window10001

overview

Window 8

Location 17,377,315 – 17,377,406
Length 91
Sequences 5
Columns 91
Reading direction forward
Mean pairwise identity 98.02
Mean single sequence MFE -28.14
Consensus MFE -26.70
Energy contribution -26.90
Covariance contribution 0.20
Combinations/Pair 1.00
Mean z-score -1.21
Structure conservation index 0.95
SVM decision value 0.20
SVM RNA-class probability 0.628930
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 17377315 91 + 22407834
UUGUGGUUGCAAGCCAUUAAGGCUAAGAGCCGUUGCCACCUCUUAAAGUCCACCGCCCCCACUUGCGAAAACCCUUCGCCGAGGGUGGCUU
..((((..((..(((.....)))((((((..........))))))..)))))).((((((.(..(((((.....))))).).))).))).. ( -28.00)
>DroSec_CAF1 13474 91 + 1
UUGUGGUUGCAAGCCAUUAAGGCUAAGAGCCGUUGCCACCUCUUAAAGUCCACCGCCCCCACUUGCGAAAACCCUUCGCCGAGGGUGGCUU
..((((..((..(((.....)))((((((..........))))))..)))))).((((((.(..(((((.....))))).).))).))).. ( -28.00)
>DroSim_CAF1 13749 91 + 1
UUGUGGUUGCAAGCCAUUAAGGCUAAGAGCCGUUGCCACCUCUUAAAGUCCACCGCCCCCACAUGCGAAAACCCUUCGCCGAGGGUGGCUU
..((((..((..(((.....)))((((((..........))))))..)))))).((((((.(..(((((.....))))).).))).))).. ( -28.00)
>DroEre_CAF1 12996 91 + 1
UUGUGGUUGCAAGCCAUUAAGGCUAAGAGCCGUUGCCACCUCUUAAGGUCCACCGCCCCCACAUGCGAAAACCCUUCGCCGAGGGUGGCUU
....((((...((((.....))))...))))...((((((.(((..((....))..........(((((.....))))).))))))))).. ( -30.00)
>DroYak_CAF1 13413 90 + 1
UUGUGGUUGCAAGCCAUUAAGGCUAAGAGCCGUUGCCACCUCUUAAAGUCCACCGCCCCCACAUGC-AAAACCCUUCGCAGAGGGUGGCUU
.(((((..((..(((.....)))((((((..........)))))).........))..))))).((-...((((((....)))))).)).. ( -26.70)
>consensus
UUGUGGUUGCAAGCCAUUAAGGCUAAGAGCCGUUGCCACCUCUUAAAGUCCACCGCCCCCACAUGCGAAAACCCUUCGCCGAGGGUGGCUU
..((((..((..(((.....)))((((((..........))))))..)))))).((((((....(((((.....)))))...))).))).. (-26.70 = -26.90 +   0.20)

alignment

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secondary structure

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dotplot

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Window 9

Location 17,377,315 – 17,377,406
Length 91
Sequences 5
Columns 91
Reading direction reverse
Mean pairwise identity 98.02
Mean single sequence MFE -39.32
Consensus MFE -37.72
Energy contribution -37.92
Covariance contribution 0.20
Combinations/Pair 1.00
Mean z-score -3.30
Structure conservation index 0.96
SVM decision value 4.51
SVM RNA-class probability 0.999912
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 17377315 91 - 22407834
AAGCCACCCUCGGCGAAGGGUUUUCGCAAGUGGGGGCGGUGGACUUUAAGAGGUGGCAACGGCUCUUAGCCUUAAUGGCUUGCAACCACAA
..(((.(((...((((((...))))))....)))))).((((....((((((.((....)).))))))(((.....)))......)))).. ( -39.10)
>DroSec_CAF1 13474 91 - 1
AAGCCACCCUCGGCGAAGGGUUUUCGCAAGUGGGGGCGGUGGACUUUAAGAGGUGGCAACGGCUCUUAGCCUUAAUGGCUUGCAACCACAA
..(((.(((...((((((...))))))....)))))).((((....((((((.((....)).))))))(((.....)))......)))).. ( -39.10)
>DroSim_CAF1 13749 91 - 1
AAGCCACCCUCGGCGAAGGGUUUUCGCAUGUGGGGGCGGUGGACUUUAAGAGGUGGCAACGGCUCUUAGCCUUAAUGGCUUGCAACCACAA
..(((.(((.((((((((...)))))).)).)))))).((((....((((((.((....)).))))))(((.....)))......)))).. ( -40.00)
>DroEre_CAF1 12996 91 - 1
AAGCCACCCUCGGCGAAGGGUUUUCGCAUGUGGGGGCGGUGGACCUUAAGAGGUGGCAACGGCUCUUAGCCUUAAUGGCUUGCAACCACAA
..(((.(((.((((((((...)))))).)).)))))).((((....((((((.((....)).))))))(((.....)))......)))).. ( -40.00)
>DroYak_CAF1 13413 90 - 1
AAGCCACCCUCUGCGAAGGGUUUU-GCAUGUGGGGGCGGUGGACUUUAAGAGGUGGCAACGGCUCUUAGCCUUAAUGGCUUGCAACCACAA
..(((.(((.(((((((....)))-))).).)))))).((((....((((((.((....)).))))))(((.....)))......)))).. ( -38.40)
>consensus
AAGCCACCCUCGGCGAAGGGUUUUCGCAUGUGGGGGCGGUGGACUUUAAGAGGUGGCAACGGCUCUUAGCCUUAAUGGCUUGCAACCACAA
..(((.(((...((((((...))))))....)))))).((((....((((((.((....)).))))))(((.....)))......)))).. (-37.72 = -37.92 +   0.20)

alignment

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secondary structure

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dotplot

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Window 0

Location 17,377,332 – 17,377,424
Length 92
Sequences 5
Columns 97
Reading direction forward
Mean pairwise identity 95.96
Mean single sequence MFE -29.20
Consensus MFE -27.70
Energy contribution -27.74
Covariance contribution 0.04
Combinations/Pair 1.04
Mean z-score -1.52
Structure conservation index 0.95
SVM decision value 1.68
SVM RNA-class probability 0.971966
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 17377332 92 + 22407834
UAAGGCUAAGAGCCGUUGCCACCUCUUAAAGUCCACCGCCCCCACUUGCGAAAACCCUUCGCCGAGGGUGGCUU-----CAUUGUUCUCGAAGAGGC
...(((.....))).......((((((..((..((..((((((.(..(((((.....))))).).))).)))..-----...))..))..)))))). ( -29.80)
>DroSec_CAF1 13491 92 + 1
UAAGGCUAAGAGCCGUUGCCACCUCUUAAAGUCCACCGCCCCCACUUGCGAAAACCCUUCGCCGAGGGUGGCUU-----CAUUGUUCUCGAAGAGGC
...(((.....))).......((((((..((..((..((((((.(..(((((.....))))).).))).)))..-----...))..))..)))))). ( -29.80)
>DroSim_CAF1 13766 92 + 1
UAAGGCUAAGAGCCGUUGCCACCUCUUAAAGUCCACCGCCCCCACAUGCGAAAACCCUUCGCCGAGGGUGGCUU-----CAUUGUUCUCGAAGAGGC
...(((.....))).......((((((..((..((..((((((.(..(((((.....))))).).))).)))..-----...))..))..)))))). ( -29.80)
>DroEre_CAF1 13013 97 + 1
UAAGGCUAAGAGCCGUUGCCACCUCUUAAGGUCCACCGCCCCCACAUGCGAAAACCCUUCGCCGAGGGUGGCUUCACUUCAUUGUUCUCGAAGAGGC
...(((.....))).......((((((..((....))((((((.(..(((((.....))))).).))).)))..................)))))). ( -29.60)
>DroYak_CAF1 13430 91 + 1
UAAGGCUAAGAGCCGUUGCCACCUCUUAAAGUCCACCGCCCCCACAUGC-AAAACCCUUCGCAGAGGGUGGCUU-----CAUUGUUCUCGAAGAGGC
...(((.....))).......((((((..((..((..((((((...(((-..........)))..))).)))..-----...))..))..)))))). ( -27.00)
>consensus
UAAGGCUAAGAGCCGUUGCCACCUCUUAAAGUCCACCGCCCCCACAUGCGAAAACCCUUCGCCGAGGGUGGCUU_____CAUUGUUCUCGAAGAGGC
...(((.....))).......((((((..((..((((((((.(....(((((.....))))).).))))))...........))..))..)))))). (-27.70 = -27.74 +   0.04)

alignment

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secondary structure

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dotplot

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Window 1

Location 17,377,332 – 17,377,424
Length 92
Sequences 5
Columns 97
Reading direction reverse
Mean pairwise identity 95.96
Mean single sequence MFE -36.02
Consensus MFE -32.04
Energy contribution -32.44
Covariance contribution 0.40
Combinations/Pair 1.00
Mean z-score -1.93
Structure conservation index 0.89
SVM decision value 2.20
SVM RNA-class probability 0.990119
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 17377332 92 - 22407834
GCCUCUUCGAGAACAAUG-----AAGCCACCCUCGGCGAAGGGUUUUCGCAAGUGGGGGCGGUGGACUUUAAGAGGUGGCAACGGCUCUUAGCCUUA
(((((((.(((..((...-----..(((.(((...((((((...))))))....))))))..))..))).)))))))(....)(((.....)))... ( -36.30)
>DroSec_CAF1 13491 92 - 1
GCCUCUUCGAGAACAAUG-----AAGCCACCCUCGGCGAAGGGUUUUCGCAAGUGGGGGCGGUGGACUUUAAGAGGUGGCAACGGCUCUUAGCCUUA
(((((((.(((..((...-----..(((.(((...((((((...))))))....))))))..))..))).)))))))(....)(((.....)))... ( -36.30)
>DroSim_CAF1 13766 92 - 1
GCCUCUUCGAGAACAAUG-----AAGCCACCCUCGGCGAAGGGUUUUCGCAUGUGGGGGCGGUGGACUUUAAGAGGUGGCAACGGCUCUUAGCCUUA
(((((((.(((..((...-----..(((.(((.((((((((...)))))).)).))))))..))..))).)))))))(....)(((.....)))... ( -37.20)
>DroEre_CAF1 13013 97 - 1
GCCUCUUCGAGAACAAUGAAGUGAAGCCACCCUCGGCGAAGGGUUUUCGCAUGUGGGGGCGGUGGACCUUAAGAGGUGGCAACGGCUCUUAGCCUUA
(((.((((.................(((.(((.((((((((...)))))).)).))))))((....))....)))).)))...(((.....)))... ( -34.70)
>DroYak_CAF1 13430 91 - 1
GCCUCUUCGAGAACAAUG-----AAGCCACCCUCUGCGAAGGGUUUU-GCAUGUGGGGGCGGUGGACUUUAAGAGGUGGCAACGGCUCUUAGCCUUA
(((((((.(((..((...-----..(((.(((.(((((((....)))-))).).))))))..))..))).)))))))(....)(((.....)))... ( -35.60)
>consensus
GCCUCUUCGAGAACAAUG_____AAGCCACCCUCGGCGAAGGGUUUUCGCAUGUGGGGGCGGUGGACUUUAAGAGGUGGCAACGGCUCUUAGCCUUA
(((((((.(((..((..........(((.(((...((((((...))))))....))))))..))..))).)))))))(....)(((.....)))... (-32.04 = -32.44 +   0.40)

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 12:06:35 2006