Locus 5614

Sequence ID 2R_DroMel_CAF1
Location 17,879,534 – 17,879,718
Length 184
Max. P 0.999856
window8995 window8996 window8997 window8998 window8999 window9000

overview

Window 5

Location 17,879,534 – 17,879,647
Length 113
Sequences 5
Columns 113
Reading direction forward
Mean pairwise identity 97.17
Mean single sequence MFE -29.52
Consensus MFE -27.10
Energy contribution -27.94
Covariance contribution 0.84
Combinations/Pair 1.03
Mean z-score -2.61
Structure conservation index 0.92
SVM decision value 3.70
SVM RNA-class probability 0.999540
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 17879534 113 + 20766785
ACCACUAAUUGUGCAAAUUAUUUGGAGUAAUUUCCUAAUUUGUAUUCUCUGCUGACCGAGAUAGUUGGCAGCCAUUCAUUUCAGUCAGCACCACCGAACCAGGCCAAUUAAUA
.....(((((((((((((((...((((....))))))))))))).....(((((((.(((((...(((...)))...))))).)))))))...((......)).))))))... ( -29.10)
>DroSec_CAF1 44443 113 + 1
ACCACUAAUUGCGCAAAUUAUUUGGAGUAAUUUCCUAAUUUGUAUUCUCUGCUGACCGAGAUAGUUGGCAGCCAUUCAUUUCAGUCAGCAGCGCCGAACCAGGCCAAUUAAUA
.....((((((.((((((((...((((....)))))))))))).....((((((((.(((((...(((...)))...))))).)))))))).(((......)))))))))... ( -34.20)
>DroSim_CAF1 44921 113 + 1
ACCACUAAUUGCGCAAAUUAUUUGGAGUUAUUUCCUAAUUUGUAUUCUCUGCUGACCGAGAUAGUUGGCAGCCAUUCAUUUCAGUCAGCAGCACCGAACCAGGCCAAUUAAUA
.....(((((((((((((((...((((....)))))))))))).....((((((((.(((((...(((...)))...))))).))))))))...........).))))))... ( -30.60)
>DroEre_CAF1 46852 112 + 1
ACCACUAAUUGCGCA-AUUAUUUGGAGUAAUUUCCUAAUUUGUAUUCUCUGCUGACCGAGAUAGUUGGCAGCCUUUCAUUUCAGUCAGCAGCACCGAACCAGGCCAAUUAAUA
.....((((((.((.-.......((((....)))).............((((((((.(((((.(..((...))..).))))).))))))))...........))))))))... ( -27.40)
>DroYak_CAF1 44077 112 + 1
ACCACUAAUUGCGCA-AUUAUUUGGAGUAAUUUCCUAAUUUGUAUUCUCUGCUGACCGAGAUAGUUGGCAGCCUUUCAUUUUAGUCAGCAGCACCGAACCAGGCCAAUUAAUA
.....((((((.((.-.......((((....)))).............((((((((..((((.(..((...))..).))))..))))))))...........))))))))... ( -26.30)
>consensus
ACCACUAAUUGCGCAAAUUAUUUGGAGUAAUUUCCUAAUUUGUAUUCUCUGCUGACCGAGAUAGUUGGCAGCCAUUCAUUUCAGUCAGCAGCACCGAACCAGGCCAAUUAAUA
.....((((((.((((((((...((((....)))))))))))).....((((((((.(((((...(((...)))...))))).))))))))..((......)).))))))... (-27.10 = -27.94 +   0.84)

alignment

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secondary structure

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dotplot

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Window 6

Location 17,879,534 – 17,879,647
Length 113
Sequences 5
Columns 113
Reading direction reverse
Mean pairwise identity 97.17
Mean single sequence MFE -33.70
Consensus MFE -31.86
Energy contribution -32.66
Covariance contribution 0.80
Combinations/Pair 1.00
Mean z-score -2.73
Structure conservation index 0.95
SVM decision value 4.27
SVM RNA-class probability 0.999856
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 17879534 113 - 20766785
UAUUAAUUGGCCUGGUUCGGUGGUGCUGACUGAAAUGAAUGGCUGCCAACUAUCUCGGUCAGCAGAGAAUACAAAUUAGGAAAUUACUCCAAAUAAUUUGCACAAUUAGUGGU
((((((((((((......)))..((((((((((.(((..(((...)))..))).)))))))))).......((((((((((......)))...)))))))..))))))))).. ( -32.20)
>DroSec_CAF1 44443 113 - 1
UAUUAAUUGGCCUGGUUCGGCGCUGCUGACUGAAAUGAAUGGCUGCCAACUAUCUCGGUCAGCAGAGAAUACAAAUUAGGAAAUUACUCCAAAUAAUUUGCGCAAUUAGUGGU
((((((((((((......))).(((((((((((.(((..(((...)))..))).)))))))))))......((((((((((......)))...)))))))..))))))))).. ( -36.80)
>DroSim_CAF1 44921 113 - 1
UAUUAAUUGGCCUGGUUCGGUGCUGCUGACUGAAAUGAAUGGCUGCCAACUAUCUCGGUCAGCAGAGAAUACAAAUUAGGAAAUAACUCCAAAUAAUUUGCGCAAUUAGUGGU
(((((((((.....((((....(((((((((((.(((..(((...)))..))).))))))))))).)))).((((((((((......)))...)))))))..))))))))).. ( -35.70)
>DroEre_CAF1 46852 112 - 1
UAUUAAUUGGCCUGGUUCGGUGCUGCUGACUGAAAUGAAAGGCUGCCAACUAUCUCGGUCAGCAGAGAAUACAAAUUAGGAAAUUACUCCAAAUAAU-UGCGCAAUUAGUGGU
(((((((((((...((((....(((((((((((...((.((........)).))))))))))))).))))........(((......))).......-.)).))))))))).. ( -33.80)
>DroYak_CAF1 44077 112 - 1
UAUUAAUUGGCCUGGUUCGGUGCUGCUGACUAAAAUGAAAGGCUGCCAACUAUCUCGGUCAGCAGAGAAUACAAAUUAGGAAAUUACUCCAAAUAAU-UGCGCAAUUAGUGGU
(((((((((((...((((....(((((((((.....((.((........)).))..))))))))).))))........(((......))).......-.)).))))))))).. ( -30.00)
>consensus
UAUUAAUUGGCCUGGUUCGGUGCUGCUGACUGAAAUGAAUGGCUGCCAACUAUCUCGGUCAGCAGAGAAUACAAAUUAGGAAAUUACUCCAAAUAAUUUGCGCAAUUAGUGGU
(((((((((((...((((....(((((((((((.(((..(((...)))..))).))))))))))).))))........(((......))).........)).))))))))).. (-31.86 = -32.66 +   0.80)

alignment

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secondary structure

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dotplot

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Window 7

Location 17,879,568 – 17,879,684
Length 116
Sequences 5
Columns 119
Reading direction forward
Mean pairwise identity 96.08
Mean single sequence MFE -27.29
Consensus MFE -24.34
Energy contribution -24.98
Covariance contribution 0.64
Combinations/Pair 1.04
Mean z-score -2.46
Structure conservation index 0.89
SVM decision value 3.31
SVM RNA-class probability 0.998977
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 17879568 116 + 20766785
CUAAUUUGUAUUCUCUGCUGACCGAGAUAGUUGGCAGCCAUUCAUUUCAGUCAGCACCACCGAACCAGGCCAAUUAAUAUUCAUUUGGCCCAAACUCACCC---GCUGAACACUUUCCA
.......((.(((..(((((((.(((((...(((...)))...))))).)))))))...........((((((...........))))))...........---...))).))...... ( -26.50)
>DroSec_CAF1 44477 119 + 1
CUAAUUUGUAUUCUCUGCUGACCGAGAUAGUUGGCAGCCAUUCAUUUCAGUCAGCAGCGCCGAACCAGGCCAAUUAAUAUUCAUUUGGCCCAAACUCACCCGCCGCUCAACACUUUCCA
......(((......(((((((.(((((...(((...)))...))))).)))))))(((.((.....((((((...........))))))..........)).)))...)))....... ( -28.36)
>DroSim_CAF1 44955 116 + 1
CUAAUUUGUAUUCUCUGCUGACCGAGAUAGUUGGCAGCCAUUCAUUUCAGUCAGCAGCACCGAACCAGGCCAAUUAAUAUUCAUUUGGCCCAAACUCACCC---GCUCAACACUUUCUA
....((((......((((((((.(((((...(((...)))...))))).))))))))..........((((((...........)))))))))).......---............... ( -27.90)
>DroEre_CAF1 46885 116 + 1
CUAAUUUGUAUUCUCUGCUGACCGAGAUAGUUGGCAGCCUUUCAUUUCAGUCAGCAGCACCGAACCAGGCCAAUUAAUAUUCAUUUGGCCCAAACUCACCC---GCUCAACACUUUCCA
....((((......((((((((.(((((.(..((...))..).))))).))))))))..........((((((...........)))))))))).......---............... ( -26.70)
>DroYak_CAF1 44110 115 + 1
CUAAUUUGUAUUCUCUGCUGACCGAGAUAGUUGGCAGCCUUUCAUUUUAGUCAGCAGCACCGAACCAGGCCAAUUAAUAUUCAUUUGGC-CAAACUCACCC---GCUCAACACUUUGCA
......((((....((((((((..((((.(..((...))..).))))..))))))))..........((((((...........)))))-)..........---...........)))) ( -27.00)
>consensus
CUAAUUUGUAUUCUCUGCUGACCGAGAUAGUUGGCAGCCAUUCAUUUCAGUCAGCAGCACCGAACCAGGCCAAUUAAUAUUCAUUUGGCCCAAACUCACCC___GCUCAACACUUUCCA
....((((......((((((((.(((((...(((...)))...))))).))))))))..........((((((...........))))))))))......................... (-24.34 = -24.98 +   0.64)

alignment

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secondary structure

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dotplot

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Window 8

Location 17,879,568 – 17,879,684
Length 116
Sequences 5
Columns 119
Reading direction reverse
Mean pairwise identity 96.08
Mean single sequence MFE -36.80
Consensus MFE -31.30
Energy contribution -32.14
Covariance contribution 0.84
Combinations/Pair 1.03
Mean z-score -2.33
Structure conservation index 0.85
SVM decision value 2.29
SVM RNA-class probability 0.991802
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 17879568 116 - 20766785
UGGAAAGUGUUCAGC---GGGUGAGUUUGGGCCAAAUGAAUAUUAAUUGGCCUGGUUCGGUGGUGCUGACUGAAAUGAAUGGCUGCCAACUAUCUCGGUCAGCAGAGAAUACAAAUUAG
......((((((.((---.(.((((.(..((((((.(((...))).))))))..))))).).))(((((((((.(((..(((...)))..))).)))))))))...))))))....... ( -39.00)
>DroSec_CAF1 44477 119 - 1
UGGAAAGUGUUGAGCGGCGGGUGAGUUUGGGCCAAAUGAAUAUUAAUUGGCCUGGUUCGGCGCUGCUGACUGAAAUGAAUGGCUGCCAACUAUCUCGGUCAGCAGAGAAUACAAAUUAG
......(((((.((((.((((.....(..((((((.(((...))).))))))..))))).))))(((((((((.(((..(((...)))..))).)))))))))....)))))....... ( -41.60)
>DroSim_CAF1 44955 116 - 1
UAGAAAGUGUUGAGC---GGGUGAGUUUGGGCCAAAUGAAUAUUAAUUGGCCUGGUUCGGUGCUGCUGACUGAAAUGAAUGGCUGCCAACUAUCUCGGUCAGCAGAGAAUACAAAUUAG
......(((((..((---.((.....(..((((((.(((...))).))))))..).)).)).(((((((((((.(((..(((...)))..))).)))))))))))..)))))....... ( -37.30)
>DroEre_CAF1 46885 116 - 1
UGGAAAGUGUUGAGC---GGGUGAGUUUGGGCCAAAUGAAUAUUAAUUGGCCUGGUUCGGUGCUGCUGACUGAAAUGAAAGGCUGCCAACUAUCUCGGUCAGCAGAGAAUACAAAUUAG
......(((((..((---.((.....(..((((((.(((...))).))))))..).)).)).(((((((((((...((.((........)).)))))))))))))..)))))....... ( -35.70)
>DroYak_CAF1 44110 115 - 1
UGCAAAGUGUUGAGC---GGGUGAGUUUG-GCCAAAUGAAUAUUAAUUGGCCUGGUUCGGUGCUGCUGACUAAAAUGAAAGGCUGCCAACUAUCUCGGUCAGCAGAGAAUACAAAUUAG
......(((((....---.(.(((((..(-(((((.(((...))).))))))..))))).).(((((((((.....((.((........)).))..)))))))))..)))))....... ( -30.40)
>consensus
UGGAAAGUGUUGAGC___GGGUGAGUUUGGGCCAAAUGAAUAUUAAUUGGCCUGGUUCGGUGCUGCUGACUGAAAUGAAUGGCUGCCAACUAUCUCGGUCAGCAGAGAAUACAAAUUAG
......(((((........(.((((...(((((((.(((...))).)))))))..)))).).(((((((((((.(((..(((...)))..))).)))))))))))..)))))....... (-31.30 = -32.14 +   0.84)

alignment

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secondary structure

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dotplot

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Window 9

Location 17,879,607 – 17,879,718
Length 111
Sequences 5
Columns 114
Reading direction forward
Mean pairwise identity 95.19
Mean single sequence MFE -25.14
Consensus MFE -20.18
Energy contribution -20.42
Covariance contribution 0.24
Combinations/Pair 1.05
Mean z-score -1.96
Structure conservation index 0.80
SVM decision value 0.88
SVM RNA-class probability 0.874026
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 17879607 111 + 20766785
AUUCAUUUCAGUCAGCACCACCGAACCAGGCCAAUUAAUAUUCAUUUGGCCCAAACUCACCC---GCUGAACACUUUCCAGCUGGGUGGAAAAUCCUUUAUUUAGCGAGCAACU
..........((..((............((((((...........)))))).....((((((---((((.........)))).))))))...............))..)).... ( -27.10)
>DroSec_CAF1 44516 114 + 1
AUUCAUUUCAGUCAGCAGCGCCGAACCAGGCCAAUUAAUAUUCAUUUGGCCCAAACUCACCCGCCGCUCAACACUUUCCAGCUGGGUGGAAAAUCCUUUAUUUAGCGAGCAACU
..............((..(((..((...((((((...........)))))).....(((((((..(((...........))))))))))...........))..))).)).... ( -24.90)
>DroSim_CAF1 44994 111 + 1
AUUCAUUUCAGUCAGCAGCACCGAACCAGGCCAAUUAAUAUUCAUUUGGCCCAAACUCACCC---GCUCAACACUUUCUAGCUGGGUGGAAAAUCCUUUAUUUAGCGAGCAACU
..............((.((.........((((((...........)))))).....((((((---(((...........))).))))))...............))..)).... ( -23.80)
>DroEre_CAF1 46924 111 + 1
UUUCAUUUCAGUCAGCAGCACCGAACCAGGCCAAUUAAUAUUCAUUUGGCCCAAACUCACCC---GCUCAACACUUUCCAGCUGGGUGGAAAAUCCUUUAUUUAGCGAGCAACU
..............((.((.........((((((...........)))))).....((((((---(((...........))).))))))...............))..)).... ( -23.90)
>DroYak_CAF1 44149 110 + 1
UUUCAUUUUAGUCAGCAGCACCGAACCAGGCCAAUUAAUAUUCAUUUGGC-CAAACUCACCC---GCUCAACACUUUGCAGCUGGCUGAAAAAUCCUUUAUUUAGCGAGCAACU
.....(((((((((((............((((((...........)))))-)..........---((..........)).)))))))))))....................... ( -26.00)
>consensus
AUUCAUUUCAGUCAGCAGCACCGAACCAGGCCAAUUAAUAUUCAUUUGGCCCAAACUCACCC___GCUCAACACUUUCCAGCUGGGUGGAAAAUCCUUUAUUUAGCGAGCAACU
..........((..((............((((((...........)))))).....((((((...(((...........))).))))))...............))..)).... (-20.18 = -20.42 +   0.24)

alignment

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secondary structure

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dotplot

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Window 0

Location 17,879,607 – 17,879,718
Length 111
Sequences 5
Columns 114
Reading direction reverse
Mean pairwise identity 95.19
Mean single sequence MFE -33.48
Consensus MFE -26.66
Energy contribution -27.10
Covariance contribution 0.44
Combinations/Pair 1.03
Mean z-score -1.67
Structure conservation index 0.80
SVM decision value 0.23
SVM RNA-class probability 0.645495
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 17879607 111 - 20766785
AGUUGCUCGCUAAAUAAAGGAUUUUCCACCCAGCUGGAAAGUGUUCAGC---GGGUGAGUUUGGGCCAAAUGAAUAUUAAUUGGCCUGGUUCGGUGGUGCUGACUGAAAUGAAU
((((((((((..(((...........(((((.((((((.....))))))---))))).....(((((((.(((...))).))))))).)))..)))).)).))))......... ( -35.80)
>DroSec_CAF1 44516 114 - 1
AGUUGCUCGCUAAAUAAAGGAUUUUCCACCCAGCUGGAAAGUGUUGAGCGGCGGGUGAGUUUGGGCCAAAUGAAUAUUAAUUGGCCUGGUUCGGCGCUGCUGACUGAAAUGAAU
..(..((((((......((.((((((((......)))))))).))....))))))..)..(..((((((.(((...))).))))))..).(((((...)))))........... ( -34.50)
>DroSim_CAF1 44994 111 - 1
AGUUGCUCGCUAAAUAAAGGAUUUUCCACCCAGCUAGAAAGUGUUGAGC---GGGUGAGUUUGGGCCAAAUGAAUAUUAAUUGGCCUGGUUCGGUGCUGCUGACUGAAAUGAAU
..(..((((((.......((.....))...((((........)))))))---)))..)..(..((((((.(((...))).))))))..)((((((.(....)))))))...... ( -32.30)
>DroEre_CAF1 46924 111 - 1
AGUUGCUCGCUAAAUAAAGGAUUUUCCACCCAGCUGGAAAGUGUUGAGC---GGGUGAGUUUGGGCCAAAUGAAUAUUAAUUGGCCUGGUUCGGUGCUGCUGACUGAAAUGAAA
..(..((((((......((.((((((((......)))))))).)).)))---)))..)..(..((((((.(((...))).))))))..)((((((.(....)))))))...... ( -35.10)
>DroYak_CAF1 44149 110 - 1
AGUUGCUCGCUAAAUAAAGGAUUUUUCAGCCAGCUGCAAAGUGUUGAGC---GGGUGAGUUUG-GCCAAAUGAAUAUUAAUUGGCCUGGUUCGGUGCUGCUGACUAAAAUGAAA
..(..((((((......((.(((((.(((....))).))))).)).)))---)))..)....(-(((((.(((...))).))))))((((.(((.....)))))))........ ( -29.70)
>consensus
AGUUGCUCGCUAAAUAAAGGAUUUUCCACCCAGCUGGAAAGUGUUGAGC___GGGUGAGUUUGGGCCAAAUGAAUAUUAAUUGGCCUGGUUCGGUGCUGCUGACUGAAAUGAAU
....(((((((......((.((((((((......)))))))).))........)))))))..(((((((.(((...))).)))))))(((.((((...)))))))......... (-26.66 = -27.10 +   0.44)

alignment

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secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:50:05 2006