Locus 6584

Sequence ID 3R_DroMel_CAF1
Location 17,334,329 – 17,334,563
Length 234
Max. P 0.990777
window10718 window10719 window10720 window10721

overview

Window 8

Location 17,334,329 – 17,334,429
Length 100
Sequences 6
Columns 113
Reading direction forward
Mean pairwise identity 73.23
Mean single sequence MFE -32.88
Consensus MFE -12.84
Energy contribution -13.57
Covariance contribution 0.72
Combinations/Pair 1.12
Mean z-score -2.60
Structure conservation index 0.39
SVM decision value 1.92
SVM RNA-class probability 0.982732
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 17334329 100 + 27905053
AGUGGCCGUCAUAAAGACGAUGGCAAAUGGCGGCUAAAUGGCCGAAGUUUCCCACUUU-CCCAGG-----AAAGGGAGCAGGGAAAGCGGCA-------AGUCGGGAAAGCAG
.((.((((((........))))))......(((((.....((((...((((((...((-(((...-----...)))))..)))))).)))).-------))))).....)).. ( -36.50)
>DroPse_CAF1 17816 87 + 1
ACCGACGAUCAUAAGGCUGAUGGCAAAUGGCGGCUAAAUGGGCAAAGUUUCCUACUUUUCUCAGGCCGGCAACGGGAACGGG------AACG-------G-------------
.(((.(.((((......)))).)....((.(((((...((((.(((((.....))))).))))))))).)).)))...((..------..))-------.------------- ( -27.10)
>DroSec_CAF1 10291 96 + 1
AGUGGCCGUCAUAAAGACGAUGGCAAAUGGCGGCUAAAUGACCGAAGUUUCCCACUUU-CCCAGG-----AAAGGGAGCAGGGAAAGCGGCA-------AGUCGGGAAA----
....((((((........))))))......(((((...((.(((...((((((...((-(((...-----...)))))..)))))).)))))-------))))).....---- ( -33.90)
>DroSim_CAF1 15899 96 + 1
AGUGGCCGUCAUAAAGACGAUGGCAAAUGGCGGCUAAAUGGCCGAAGUUUCCCACUUU-CCCAGG-----AAAGGGAGCAGGGAAAGCGGCA-------AGUCGGGAAA----
....((((((........))))))......(((((.....((((...((((((...((-(((...-----...)))))..)))))).)))).-------))))).....---- ( -36.20)
>DroYak_CAF1 13848 107 + 1
AGGGGCCGUCAUAAAGACGAUGGCAAAUGGCGGCUAAAUGGCCGAAGUUUCCCACUUU-CCCAGG-----AAAGGGAGCAGGAAAAGCGGGAUGCGAGAAGGCGGGAAAGUAG
.(((((((((........))))))((((..(((((....)))))..)))))))(((((-(((...-----.......((.......)).....((......)))))))))).. ( -39.50)
>DroPer_CAF1 18841 86 + 1
ACCGACGAUCAUAAGGCUGAUGGCAAAUGGCGGCUAAAUGGGCAAAGUUUCCAACUUUUCUCAGGCCGGCAACGGGAACG-C------AACG-------A-------------
.(((.(.((((......)))).)....((.(((((...((((.(((((.....))))).))))))))).)).))).....-.------....-------.------------- ( -24.10)
>consensus
AGUGGCCGUCAUAAAGACGAUGGCAAAUGGCGGCUAAAUGGCCGAAGUUUCCCACUUU_CCCAGG_____AAAGGGAGCAGGGAAAGCGGCA_______AGUCGGGAAA____
....((((((........)))))).......((((....))))...((((((.....................)))))).................................. (-12.84 = -13.57 +   0.72)

alignment

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secondary structure

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dotplot

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Window 9

Location 17,334,366 – 17,334,469
Length 103
Sequences 4
Columns 110
Reading direction reverse
Mean pairwise identity 82.34
Mean single sequence MFE -30.54
Consensus MFE -22.30
Energy contribution -21.92
Covariance contribution -0.38
Combinations/Pair 1.11
Mean z-score -2.27
Structure conservation index 0.73
SVM decision value 1.41
SVM RNA-class probability 0.951705
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 17334366 103 - 27905053
AACGCGACUUAAGCGCCGUCCCGCCAGCUUUCCCGCCUUGCUGCUUUCCCGACU-------UGCCGCUUUCCCUGCUCCCUUUCCUGGGAAAGUGGGAAACUUCGGCCAU
...((.......))((((....((.(((...........))))).........(-------(.((((((((((.............)))))))))).))....))))... ( -29.72)
>DroSec_CAF1 10328 87 - 1
AACGCGGCUUAAGCGCCCUCCCGCCCGC----------------UUUCCCGACU-------UGCCGCUUUCCCUGCUCCCUUUCCUGGGAAAGUGGGAAACUUCGGUCAU
...((((.....(((......)))))))----------------....((((.(-------(.((((((((((.............)))))))))).))...)))).... ( -29.82)
>DroSim_CAF1 15936 87 - 1
AACGCGGCUUAAGCGCCCUCCCGCCCGC----------------UUUCCCGACU-------UGCCGCUUUCCCUGCUCCCUUUCCUGGGAAAGUGGGAAACUUCGGCCAU
...((((.....(((......)))))))----------------....((((.(-------(.((((((((((.............)))))))))).))...)))).... ( -29.62)
>DroYak_CAF1 13885 110 - 1
AACGCGACUUAAGCGCCGUCCCGCCCGCUUUCCCGCCUUCCUACUUUCCCGCCUUCUCGCAUCCCGCUUUUCCUGCUCCCUUUCCUGGGAAAGUGGGAAACUUCGGCCAU
...((.......))((((.....(((((((((((................((......)).....((.......))..........)))))))))))......))))... ( -33.00)
>consensus
AACGCGACUUAAGCGCCCUCCCGCCCGC________________UUUCCCGACU_______UGCCGCUUUCCCUGCUCCCUUUCCUGGGAAAGUGGGAAACUUCGGCCAU
..(((.......))).......(((......................................((((((((((.............))))))))))((....)))))... (-22.30 = -21.92 +  -0.38)

alignment

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secondary structure

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dotplot

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Window 0

Location 17,334,469 – 17,334,563
Length 94
Sequences 6
Columns 113
Reading direction forward
Mean pairwise identity 73.65
Mean single sequence MFE -30.35
Consensus MFE -16.78
Energy contribution -18.28
Covariance contribution 1.50
Combinations/Pair 1.00
Mean z-score -2.30
Structure conservation index 0.55
SVM decision value 2.01
SVM RNA-class probability 0.985386
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 17334469 94 + 27905053
AAUUGCCGCUUAGCAGGCGGCGUUUUC-AGGC----------AU-UUCAGACAUUUUUAGAGCCCAGUCCUCCU-------GGCUUAUCAGCCAUUUUGGGCCUAUUCCAGCU
....((((((.....))))))......-....----------..-............(((.((((((......(-------((((....)))))..)))))))))........ ( -27.60)
>DroSec_CAF1 10415 75 + 1
AAUUGCCGCUUAGCAGGCGGCGUU-------------------------------UUUAGAGCCCAGUCAUCCU-------GGCUUAUCAGCCAUUUUGGGCCUAUUCCAACU
....((((((.....))))))(((-------------------------------..(((.((((((......(-------((((....)))))..)))))))))....))). ( -28.20)
>DroSim_CAF1 16023 75 + 1
AAUUGCCGCUUAGCAGGCGGCGUU-------------------------------UUUAGAGCCCAGUCCUCCU-------GGCUUAUCAGCCAUUUUGGGCCUAUUCCAGCU
....((((((.....))))))(((-------------------------------..(((.((((((......(-------((((....)))))..)))))))))....))). ( -28.20)
>DroEre_CAF1 15581 109 + 1
AAUUGCCGCUUAGCAGGCGGCCUUUUC-AGGCGUGUUCAGGCAU-UUCAGUCGUUUUUAGAGCCCAGUCCUCCUGG--ACUGGCUUAUCAGCCAUUUUGGGCCUAUUCCAGCU
....((((((.....))))))......-.(((.......(((..-....))).....(((.(((((((((....))--))(((((....)))))...)))))))).....))) ( -37.50)
>DroYak_CAF1 13995 104 + 1
AAUUGCCGCUUAGCAGGCGGACUUUUC-AGGCGU-UUCAGUCGUUUUCAGACGUUUUCAGAGCCCAGUCCUCCU-------GGCUUAUCAGCCAUUUUGGGCCUAUUCCAGCU
.....(((((.....))))).......-.(((..-....(((.......)))......((.((((((......(-------((((....)))))..))))))))......))) ( -28.10)
>DroAna_CAF1 14441 89 + 1
AAUUGCCGCUUAGCAGGCCCAGUUGUCGAGGC----------A------A--------ACGGGGCAGUCCUCUCGGCAGUCGGCUUAUCAGCCAUUUUGGGCCUAUUCCAGCU
.......(((....(((((((((((((((((.----------.------.--------((......))..)))))))))..((((....))))...)))))))).....))). ( -32.50)
>consensus
AAUUGCCGCUUAGCAGGCGGCGUUUUC_AGGC__________A______G_____UUUAGAGCCCAGUCCUCCU_______GGCUUAUCAGCCAUUUUGGGCCUAUUCCAGCU
....((((((.....))))))....................................(((.((((((....).........((((....))))....))))))))........ (-16.78 = -18.28 +   1.50)

alignment

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secondary structure

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dotplot

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Window 1

Location 17,334,469 – 17,334,563
Length 94
Sequences 6
Columns 113
Reading direction reverse
Mean pairwise identity 73.65
Mean single sequence MFE -30.80
Consensus MFE -17.33
Energy contribution -18.22
Covariance contribution 0.89
Combinations/Pair 1.12
Mean z-score -2.41
Structure conservation index 0.56
SVM decision value 2.23
SVM RNA-class probability 0.990777
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 17334469 94 - 27905053
AGCUGGAAUAGGCCCAAAAUGGCUGAUAAGCC-------AGGAGGACUGGGCUCUAAAAAUGUCUGAA-AU----------GCCU-GAAAACGCCGCCUGCUAAGCGGCAAUU
........(((((((....(((((....))))-------)...))...((((.........))))...-..----------))))-).....(((((.......))))).... ( -27.40)
>DroSec_CAF1 10415 75 - 1
AGUUGGAAUAGGCCCAAAAUGGCUGAUAAGCC-------AGGAUGACUGGGCUCUAAA-------------------------------AACGCCGCCUGCUAAGCGGCAAUU
.(((....((((((((...(((((....))))-------).......))))).)))..-------------------------------)))(((((.......))))).... ( -28.20)
>DroSim_CAF1 16023 75 - 1
AGCUGGAAUAGGCCCAAAAUGGCUGAUAAGCC-------AGGAGGACUGGGCUCUAAA-------------------------------AACGCCGCCUGCUAAGCGGCAAUU
........((((((((...(((((....))))-------).......))))).)))..-------------------------------...(((((.......))))).... ( -27.10)
>DroEre_CAF1 15581 109 - 1
AGCUGGAAUAGGCCCAAAAUGGCUGAUAAGCCAGU--CCAGGAGGACUGGGCUCUAAAAACGACUGAA-AUGCCUGAACACGCCU-GAAAAGGCCGCCUGCUAAGCGGCAAUU
........((((((((...(((((....)))))((--((....))))))))).)))............-.((((.......((((-....)))).((.......))))))... ( -37.90)
>DroYak_CAF1 13995 104 - 1
AGCUGGAAUAGGCCCAAAAUGGCUGAUAAGCC-------AGGAGGACUGGGCUCUGAAAACGUCUGAAAACGACUGAA-ACGCCU-GAAAAGUCCGCCUGCUAAGCGGCAAUU
.((((.(.(((((......(((((....))))-------)...(((((((((........(((......)))......-..))))-....)))))))))).)...)))).... ( -30.89)
>DroAna_CAF1 14441 89 - 1
AGCUGGAAUAGGCCCAAAAUGGCUGAUAAGCCGACUGCCGAGAGGACUGCCCCGU--------U------U----------GCCUCGACAACUGGGCCUGCUAAGCGGCAAUU
.((((.(.((((((((...(((((....)))))..((.((((.((((......))--------)------)----------..)))).))..)))))))).)...)))).... ( -33.30)
>consensus
AGCUGGAAUAGGCCCAAAAUGGCUGAUAAGCC_______AGGAGGACUGGGCUCUAAA_____C______U__________GCCU_GAAAACGCCGCCUGCUAAGCGGCAAUU
..........(((((.....((((....)))).......((.....))))))).......................................(((((.......))))).... (-17.33 = -18.22 +   0.89)

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 12:25:10 2006