Locus 8701

Sequence ID 3R_DroMel_CAF1
Location 23,243,690 – 23,243,822
Length 132
Max. P 0.999659
window13969 window13970 window13971 window13972

overview

Window 9

Location 23,243,690 – 23,243,791
Length 101
Sequences 6
Columns 106
Reading direction forward
Mean pairwise identity 81.09
Mean single sequence MFE -30.78
Consensus MFE -22.04
Energy contribution -24.85
Covariance contribution 2.81
Combinations/Pair 1.03
Mean z-score -3.40
Structure conservation index 0.72
SVM decision value 1.48
SVM RNA-class probability 0.957516
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 23243690 101 + 27905053
UUGUCUGGGCAAAUCCUAAUGACGAGCGCAGACCAUAACGAGCAAGACUUCCCUUCAAAAAU----UUGAGGGGAAACCAGCAGCUCGUUACAGCUGCA-AAUAAC
(((((((((.....))))..)))))..((((.(..((((((((.....((((((((((....----)))))))))).......))))))))..))))).-...... ( -36.10)
>DroSec_CAF1 41387 101 + 1
UUGUCUGGGCAAAUCCUAAUGACGAGCGCAGACCAUAACGAGCAAGACUUCCCUUCAAUAAU----UUGAGGGGAAACCAGCAGCUCGCUACAGCUGCA-AAUAAC
..(((((.((...((.....))...)).)))))...............((((((((((....----))))))))))....((((((......)))))).-...... ( -33.20)
>DroSim_CAF1 41277 101 + 1
UUGUCUGGGCAAAUCCUAAUGACGAGCGCAGACCAUAACGAGCAAGACUUCCCUUCAAUAAU----UUGAGGGGAAAGCAGCAGCUCGUUACAGCUGCA-AAUAAC
(((((((((.....))))..)))))..((((.(..((((((((..(..((((((((((....----))))))))))..)....))))))))..))))).-...... ( -37.70)
>DroEre_CAF1 46192 99 + 1
UUGUCUG-GCAAAUCCUAAUGACGAGUGCAGACCAUAACGAGCAAGACUUCCCUUCAAUAAU----UCGAGGG-AAACCAGCAGCUCGUUACCGCUGCA-AAUAAC
(((((.(-(.....))....))))).(((((....((((((((.....(((((((.......----..)))))-)).......))))))))...)))))-...... ( -29.10)
>DroYak_CAF1 41012 101 + 1
UUGUCUGGGCAAAUCCUAAUGACGAGCGCAGACCAUAACGAGCAAGAGUUCCCUUCAAUAAU----UUGAGGGUAAACCAGCAGCUCGUUACUGCUGCA-AAUAAC
(((((((((.....))))..)))))..((((.(..((((((((....(((.(((((((....----)))))))..))).....))))))))..))))).-...... ( -31.50)
>DroAna_CAF1 35672 85 + 1
---------CAAAUACU----------CUAACCCGUAACUAGGACCU-GUCCCACCAAUAAUAAUUUUUUGGGGAAACCA-CUGCUCGUUAUUGCAACGGAGUAAC
---------....((((----------((............(((...-.)))...(((((((.........((....)).-......)))))))....)))))).. ( -17.09)
>consensus
UUGUCUGGGCAAAUCCUAAUGACGAGCGCAGACCAUAACGAGCAAGACUUCCCUUCAAUAAU____UUGAGGGGAAACCAGCAGCUCGUUACAGCUGCA_AAUAAC
(((((((((.....))))..)))))..((((.(..((((((((.....((((((((((........)))))))))).......))))))))..)))))........ (-22.04 = -24.85 +   2.81)

alignment

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secondary structure

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dotplot

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Window 0

Location 23,243,690 – 23,243,791
Length 101
Sequences 6
Columns 106
Reading direction reverse
Mean pairwise identity 81.09
Mean single sequence MFE -34.27
Consensus MFE -24.83
Energy contribution -25.80
Covariance contribution 0.97
Combinations/Pair 1.17
Mean z-score -3.07
Structure conservation index 0.72
SVM decision value 1.38
SVM RNA-class probability 0.947874
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 23243690 101 - 27905053
GUUAUU-UGCAGCUGUAACGAGCUGCUGGUUUCCCCUCAA----AUUUUUGAAGGGAAGUCUUGCUCGUUAUGGUCUGCGCUCGUCAUUAGGAUUUGCCCAGACAA
(((...-.(((((((((((((((....(..(((((.((((----....)))).)))))..)..))))))))))).))))((..(((.....)))..))...))).. ( -40.20)
>DroSec_CAF1 41387 101 - 1
GUUAUU-UGCAGCUGUAGCGAGCUGCUGGUUUCCCCUCAA----AUUAUUGAAGGGAAGUCUUGCUCGUUAUGGUCUGCGCUCGUCAUUAGGAUUUGCCCAGACAA
(((...-.(((((((((((((((....(..(((((.((((----....)))).)))))..)..))))))))))).))))((..(((.....)))..))...))).. ( -40.20)
>DroSim_CAF1 41277 101 - 1
GUUAUU-UGCAGCUGUAACGAGCUGCUGCUUUCCCCUCAA----AUUAUUGAAGGGAAGUCUUGCUCGUUAUGGUCUGCGCUCGUCAUUAGGAUUUGCCCAGACAA
(((...-.(((((((((((((((....((((.(((.((((----....)))).)))))))...))))))))))).))))((..(((.....)))..))...))).. ( -37.80)
>DroEre_CAF1 46192 99 - 1
GUUAUU-UGCAGCGGUAACGAGCUGCUGGUUU-CCCUCGA----AUUAUUGAAGGGAAGUCUUGCUCGUUAUGGUCUGCACUCGUCAUUAGGAUUUGC-CAGACAA
......-((((((.(((((((((....(..((-(((((((----....))).))))))..)..))))))))).).)))))...(((....((.....)-).))).. ( -37.40)
>DroYak_CAF1 41012 101 - 1
GUUAUU-UGCAGCAGUAACGAGCUGCUGGUUUACCCUCAA----AUUAUUGAAGGGAACUCUUGCUCGUUAUGGUCUGCGCUCGUCAUUAGGAUUUGCCCAGACAA
......-.......(((((((((....((((..(((((((----....))).))))))))...))))))))).(((((.((..(((.....)))..)).))))).. ( -32.60)
>DroAna_CAF1 35672 85 - 1
GUUACUCCGUUGCAAUAACGAGCAG-UGGUUUCCCCAAAAAAUUAUUAUUGGUGGGAC-AGGUCCUAGUUACGGGUUAG----------AGUAUUUG---------
.(((..((((..((((((..(....-(((.....))).....)..)))))).(((((.-...)))))...))))..)))----------........--------- ( -17.40)
>consensus
GUUAUU_UGCAGCUGUAACGAGCUGCUGGUUUCCCCUCAA____AUUAUUGAAGGGAAGUCUUGCUCGUUAUGGUCUGCGCUCGUCAUUAGGAUUUGCCCAGACAA
........(((((..((((((((....(..(((((.((((........)))).)))))..)..))))))))..).))))........................... (-24.83 = -25.80 +   0.97)

alignment

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secondary structure

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dotplot

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Window 1

Location 23,243,730 – 23,243,822
Length 92
Sequences 5
Columns 101
Reading direction forward
Mean pairwise identity 89.93
Mean single sequence MFE -27.76
Consensus MFE -24.22
Energy contribution -24.86
Covariance contribution 0.64
Combinations/Pair 1.04
Mean z-score -2.91
Structure conservation index 0.87
SVM decision value 3.85
SVM RNA-class probability 0.999659
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 23243730 92 + 27905053
AGCAAGACUUCCCUUCAAAAAUUUGAGGGGAAACCAGCAGCUCGUUACAGCUGCAAAUAACUGAGUUUGAUGCUGACUUUCUUUUCAGUUUU---------
........((((((((((....))))))))))....((((((......))))))....(((((((...((.........))..)))))))..--------- ( -28.40)
>DroSec_CAF1 41427 92 + 1
AGCAAGACUUCCCUUCAAUAAUUUGAGGGGAAACCAGCAGCUCGCUACAGCUGCAAAUAACUGAGUUUGAUGCUGACUUUCUUUUCAGUUUU---------
........((((((((((....))))))))))....((((((......))))))....(((((((...((.........))..)))))))..--------- ( -29.20)
>DroSim_CAF1 41317 92 + 1
AGCAAGACUUCCCUUCAAUAAUUUGAGGGGAAAGCAGCAGCUCGUUACAGCUGCAAAUAACUGAGUUUGAUGCUGACUUUCUUUUCAGUUUU---------
.....(..((((((((((....))))))))))..).((((((......))))))....(((((((...((.........))..)))))))..--------- ( -30.10)
>DroEre_CAF1 46231 100 + 1
AGCAAGACUUCCCUUCAAUAAUUCGAGGG-AAACCAGCAGCUCGUUACCGCUGCAAAUAACUGAGUUUGCUGCUGACUUUCUUUUCGGUUUUCGGUUUUCG
((((((..(((((((.........)))))-))....(((((........)))))...........))))))(((((........)))))............ ( -24.10)
>DroYak_CAF1 41052 101 + 1
AGCAAGAGUUCCCUUCAAUAAUUUGAGGGUAAACCAGCAGCUCGUUACUGCUGCAAAUAACUGAGUUUGAUGCUGACUUUCUUUUCAGUUUUUCGUUUUCA
......((((.(((((((....))))))).......(((((........)))))....))))(((..(((.(((((........)))))...)))..))). ( -27.00)
>consensus
AGCAAGACUUCCCUUCAAUAAUUUGAGGGGAAACCAGCAGCUCGUUACAGCUGCAAAUAACUGAGUUUGAUGCUGACUUUCUUUUCAGUUUU_________
.....(..((((((((((....))))))))))..).(((((........)))))....(((((((...((.........))..)))))))........... (-24.22 = -24.86 +   0.64)

alignment

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secondary structure

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dotplot

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Window 2

Location 23,243,730 – 23,243,822
Length 92
Sequences 5
Columns 101
Reading direction reverse
Mean pairwise identity 89.93
Mean single sequence MFE -24.77
Consensus MFE -19.96
Energy contribution -20.20
Covariance contribution 0.24
Combinations/Pair 1.05
Mean z-score -2.02
Structure conservation index 0.81
SVM decision value 1.34
SVM RNA-class probability 0.944343
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 23243730 92 - 27905053
---------AAAACUGAAAAGAAAGUCAGCAUCAAACUCAGUUAUUUGCAGCUGUAACGAGCUGCUGGUUUCCCCUCAAAUUUUUGAAGGGAAGUCUUGCU
---------....((....))......((((................((((((......)))))).(..(((((.((((....)))).)))))..).)))) ( -25.90)
>DroSec_CAF1 41427 92 - 1
---------AAAACUGAAAAGAAAGUCAGCAUCAAACUCAGUUAUUUGCAGCUGUAGCGAGCUGCUGGUUUCCCCUCAAAUUAUUGAAGGGAAGUCUUGCU
---------....((....))......((((................((((((......)))))).(..(((((.((((....)))).)))))..).)))) ( -25.90)
>DroSim_CAF1 41317 92 - 1
---------AAAACUGAAAAGAAAGUCAGCAUCAAACUCAGUUAUUUGCAGCUGUAACGAGCUGCUGCUUUCCCCUCAAAUUAUUGAAGGGAAGUCUUGCU
---------....((....))......((((................((((((......))))))...((((((.((((....)))).))))))...)))) ( -23.40)
>DroEre_CAF1 46231 100 - 1
CGAAAACCGAAAACCGAAAAGAAAGUCAGCAGCAAACUCAGUUAUUUGCAGCGGUAACGAGCUGCUGGUUU-CCCUCGAAUUAUUGAAGGGAAGUCUUGCU
..................((((...((((((((....((.((((((......))))))))))))))))(((-(((((((....))).)))))))))))... ( -25.60)
>DroYak_CAF1 41052 101 - 1
UGAAAACGAAAAACUGAAAAGAAAGUCAGCAUCAAACUCAGUUAUUUGCAGCAGUAACGAGCUGCUGGUUUACCCUCAAAUUAUUGAAGGGAACUCUUGCU
......((((.((((((....................)))))).))))(((((((.....))))))).....(((((((....))).)))).......... ( -23.05)
>consensus
_________AAAACUGAAAAGAAAGUCAGCAUCAAACUCAGUUAUUUGCAGCUGUAACGAGCUGCUGGUUUCCCCUCAAAUUAUUGAAGGGAAGUCUUGCU
...........................((((................(((((........))))).(..(((((.((((....)))).)))))..).)))) (-19.96 = -20.20 +   0.24)

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 13:17:34 2006