Locus 966

Sequence ID 3R_DroMel_CAF1
Location 3,154,077 – 3,154,346
Length 269
Max. P 0.984307
window1544 window1545 window1546 window1547 window1548 window1549

overview

Window 4

Location 3,154,077 – 3,154,197
Length 120
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 93.19
Mean single sequence MFE -34.97
Consensus MFE -31.48
Energy contribution -31.16
Covariance contribution -0.31
Combinations/Pair 1.09
Mean z-score -1.37
Structure conservation index 0.90
SVM decision value 0.02
SVM RNA-class probability 0.542141
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 3154077 120 + 27905053
GGGGCCAACGGCAAAUGGCAACAAAUUAGCCAAAGUGAUGAUGCGUUAAGUGGCAUAGUGGGGAAAUCGCCAGUGAGGAAAUUAGUUUUGGCGGUUUGCGAACCUAACGCACAGGGUGUU
(((..(..(.((...((....)).....((((...(((((...)))))..))))...)).)(.((((((((((..............)))))))))).))..)))(((((.....))))) ( -32.94)
>DroSec_CAF1 1965 120 + 1
GGGGCCAACGGCAAAUGGCAACAAAUUAGCCAAAGUGAUGAUGCGUUAAGUGGCAAAGUGGGGAAAUCGCCAGUGAGGAAAUUAGUUUUGGCGGUUGGCGGCGCAAGCACACAGGGUGUU
...((((((.((...((....))(((((((((...(((((...)))))..))))..(.(((.(....).))).)........)))))...)).)))))).((....))((((...)))). ( -36.00)
>DroSim_CAF1 4135 120 + 1
GGGGCCAACGGCAAAUGGCAACAAAUUAGCCAAAGUGAUGAUGCGUUAAGUGGCAAAGUGGGGAAAUCGCCAGUAAGGAAAUUAGUUUUGGCGGUUGGCGGCGCAAGCACACAGGGUGUU
...((((((.((...((....))(((((((((...(((((...)))))..))))..(.(((.(....).))).)........)))))...)).)))))).((....))((((...)))). ( -36.00)
>DroYak_CAF1 1265 118 + 1
GGGGCCAACGGCAAAUGGCAACAAAUUAGCCAAAGUGAUGAUGCGUUAAGUGGCAAAGUGGUGCAAUCGCCAGUGAGGAAAUUAGUUUUGGCGGUUGGCAGGG--AGCACACUUGGUGUU
...((((((.(((..((....)).....((((...(((((...)))))..)))).......)))...((((((..............))))))))))))....--(((((.....))))) ( -34.94)
>consensus
GGGGCCAACGGCAAAUGGCAACAAAUUAGCCAAAGUGAUGAUGCGUUAAGUGGCAAAGUGGGGAAAUCGCCAGUGAGGAAAUUAGUUUUGGCGGUUGGCGGCGCAAGCACACAGGGUGUU
...((((((......((....)).....(((((((((((....(.(((..((((..............)))).))).)..)))).))))))).))))))......(((((.....))))) (-31.48 = -31.16 +  -0.31)

alignment

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secondary structure

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Window 5

Location 3,154,077 – 3,154,197
Length 120
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 93.19
Mean single sequence MFE -25.64
Consensus MFE -20.83
Energy contribution -21.57
Covariance contribution 0.75
Combinations/Pair 1.00
Mean z-score -1.66
Structure conservation index 0.81
SVM decision value 0.10
SVM RNA-class probability 0.585688
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 3154077 120 - 27905053
AACACCCUGUGCGUUAGGUUCGCAAACCGCCAAAACUAAUUUCCUCACUGGCGAUUUCCCCACUAUGCCACUUAACGCAUCAUCACUUUGGCUAAUUUGUUGCCAUUUGCCGUUGGCCCC
........(((((((((((..(((((.(((((................))))).)).........))).))))))))))).........(((((((..((........)).))))))).. ( -27.49)
>DroSec_CAF1 1965 120 - 1
AACACCCUGUGUGCUUGCGCCGCCAACCGCCAAAACUAAUUUCCUCACUGGCGAUUUCCCCACUUUGCCACUUAACGCAUCAUCACUUUGGCUAAUUUGUUGCCAUUUGCCGUUGGCCCC
........((((....)))).((((((.((..................((((((..........))))))..................((((.........))))...)).))))))... ( -25.40)
>DroSim_CAF1 4135 120 - 1
AACACCCUGUGUGCUUGCGCCGCCAACCGCCAAAACUAAUUUCCUUACUGGCGAUUUCCCCACUUUGCCACUUAACGCAUCAUCACUUUGGCUAAUUUGUUGCCAUUUGCCGUUGGCCCC
........((((....)))).((((((.((..................((((((..........))))))..................((((.........))))...)).))))))... ( -25.40)
>DroYak_CAF1 1265 118 - 1
AACACCAAGUGUGCU--CCCUGCCAACCGCCAAAACUAAUUUCCUCACUGGCGAUUGCACCACUUUGCCACUUAACGCAUCAUCACUUUGGCUAAUUUGUUGCCAUUUGCCGUUGGCCCC
.((((...))))...--....(((((((((((................)))))...(((......(((........))).........((((.........))))..))).))))))... ( -24.29)
>consensus
AACACCCUGUGUGCUUGCGCCGCCAACCGCCAAAACUAAUUUCCUCACUGGCGAUUUCCCCACUUUGCCACUUAACGCAUCAUCACUUUGGCUAAUUUGUUGCCAUUUGCCGUUGGCCCC
.((((...)))).........((((((.((..................((((((..........))))))..................((((.........))))...)).))))))... (-20.83 = -21.57 +   0.75)

alignment

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secondary structure

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Window 6

Location 3,154,197 – 3,154,307
Length 110
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 87.61
Mean single sequence MFE -26.12
Consensus MFE -23.02
Energy contribution -23.90
Covariance contribution 0.88
Combinations/Pair 1.04
Mean z-score -1.78
Structure conservation index 0.88
SVM decision value 0.86
SVM RNA-class probability 0.867985
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 3154197 110 + 27905053
AGGUCUUUCAAGGGAACGA--CACUCGUCACAUUGCUGUGACAGCUGCCCACACUCCUGGCCACUUUGUCUUUGGCCAAUUAAAAUCAAAUUUCAAAAUU--------UCAAAAUGUUCC
............((((((.--.....((((((....))))))...............((((((.........))))))......................--------......)))))) ( -22.30)
>DroSec_CAF1 2085 104 + 1
AGGUCUUUCAAGGGAACGGCGCACUCGUCACAUUGCUGUGACAGCUGCCCACACUCCUGGCCACUUUGUCUUUGGCCAAUUAAAAUCAAAUUU----------------CAAAAUGUUCC
............(((((((.(((((.((((((....)))))))).))))).......((((((.........))))))...............----------------......))))) ( -29.10)
>DroSim_CAF1 4255 104 + 1
AGGUCUUUCAAGGGAACGGCGCACUCGUCACAUUGCUGUGACAGCUGCCCACACUCCUGGCCACUUUGUCUUUGGCCAAUUAAAAUCAAAUUU----------------CAAAAUGUUCC
............(((((((.(((((.((((((....)))))))).))))).......((((((.........))))))...............----------------......))))) ( -29.10)
>DroYak_CAF1 1383 118 + 1
AGGUCUUUCAGAGGAACGG--CACUCGUCACAUUGCUGUGACAGCACCCCACACUCCUGGGCACUUUGUCUUUGCCCAAUUAAAAUCAAAUUUCAAAAUUUCAGCAUUUCAAAAUGUUCC
............(((((((--..((.((((((....))))))))..)).........((((((.........)))))).....................................))))) ( -24.00)
>consensus
AGGUCUUUCAAGGGAACGG__CACUCGUCACAUUGCUGUGACAGCUGCCCACACUCCUGGCCACUUUGUCUUUGGCCAAUUAAAAUCAAAUUU________________CAAAAUGUUCC
............(((((((.(((((.((((((....)))))))).))))).......((((((.........)))))).....................................))))) (-23.02 = -23.90 +   0.88)

alignment

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secondary structure

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dotplot

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Window 7

Location 3,154,197 – 3,154,307
Length 110
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 87.61
Mean single sequence MFE -35.23
Consensus MFE -30.54
Energy contribution -29.98
Covariance contribution -0.56
Combinations/Pair 1.09
Mean z-score -2.49
Structure conservation index 0.87
SVM decision value 1.97
SVM RNA-class probability 0.984307
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 3154197 110 - 27905053
GGAACAUUUUGA--------AAUUUUGAAAUUUGAUUUUAAUUGGCCAAAGACAAAGUGGCCAGGAGUGUGGGCAGCUGUCACAGCAAUGUGACGAGUG--UCGUUCCCUUGAAAGACCU
(((((...((((--------((((.........))))))))(((((((.........))))))).......((((..(((((((....)))))))..))--)))))))............ ( -33.30)
>DroSec_CAF1 2085 104 - 1
GGAACAUUUUG----------------AAAUUUGAUUUUAAUUGGCCAAAGACAAAGUGGCCAGGAGUGUGGGCAGCUGUCACAGCAAUGUGACGAGUGCGCCGUUCCCUUGAAAGACCU
(((((......----------------..............(((((((.........))))))).......(((.(((((((((....)))))).)))..))))))))............ ( -34.20)
>DroSim_CAF1 4255 104 - 1
GGAACAUUUUG----------------AAAUUUGAUUUUAAUUGGCCAAAGACAAAGUGGCCAGGAGUGUGGGCAGCUGUCACAGCAAUGUGACGAGUGCGCCGUUCCCUUGAAAGACCU
(((((......----------------..............(((((((.........))))))).......(((.(((((((((....)))))).)))..))))))))............ ( -34.20)
>DroYak_CAF1 1383 118 - 1
GGAACAUUUUGAAAUGCUGAAAUUUUGAAAUUUGAUUUUAAUUGGGCAAAGACAAAGUGCCCAGGAGUGUGGGGUGCUGUCACAGCAAUGUGACGAGUG--CCGUUCCUCUGAAAGACCU
(((((((((..((((......))))..))))..........(((((((.........)))))))........((..((((((((....)))))).))..--)))))))............ ( -39.20)
>consensus
GGAACAUUUUG________________AAAUUUGAUUUUAAUUGGCCAAAGACAAAGUGGCCAGGAGUGUGGGCAGCUGUCACAGCAAUGUGACGAGUG__CCGUUCCCUUGAAAGACCU
(((((....................................(((((((.........)))))))......((...(((((((((....)))))).)))...)))))))............ (-30.54 = -29.98 +  -0.56)

alignment

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secondary structure

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dotplot

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Window 8

Location 3,154,235 – 3,154,346
Length 111
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 88.65
Mean single sequence MFE -22.75
Consensus MFE -19.12
Energy contribution -19.00
Covariance contribution -0.12
Combinations/Pair 1.05
Mean z-score -2.11
Structure conservation index 0.84
SVM decision value 1.24
SVM RNA-class probability 0.935271
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 3154235 111 + 27905053
ACAGCUGCCCACACUCCUGGCCACUUUGUCUUUGGCCAAUUAAAAUCAAAUUUCAAAAUU--------UCAAAAUGUUCCAAAUUUUGUGCA-ACUGAUGACAGUUUAAUUGCUGUCCUG
.(((.(((.........((((((.........))))))......................--------.((((((.......)))))).)))-.)))..((((((......))))))... ( -24.40)
>DroSec_CAF1 2125 104 + 1
ACAGCUGCCCACACUCCUGGCCACUUUGUCUUUGGCCAAUUAAAAUCAAAUUU----------------CAAAAUGUUCCAAAUUUUGUGCAAACUGAUGACAGUUUAAUUGCUGUCCUG
.(((.(((.........((((((.........))))))...............----------------((((((.......)))))).)))..)))..((((((......))))))... ( -22.40)
>DroSim_CAF1 4295 104 + 1
ACAGCUGCCCACACUCCUGGCCACUUUGUCUUUGGCCAAUUAAAAUCAAAUUU----------------CAAAAUGUUCCAAAUUUUGUGCAAACUGAUGACAGUUUAAUUGCUGUCCUG
.(((.(((.........((((((.........))))))...............----------------((((((.......)))))).)))..)))..((((((......))))))... ( -22.40)
>DroYak_CAF1 1421 119 + 1
ACAGCACCCCACACUCCUGGGCACUUUGUCUUUGCCCAAUUAAAAUCAAAUUUCAAAAUUUCAGCAUUUCAAAAUGUUCCUAAUUUUGUGCA-ACUGAUGACAGUUUAAUUGCCGUCCUG
...((((..........((((((.........))))))................((((((..((((((....))))))...)))))))))).-...((((.((((...)))).))))... ( -21.80)
>consensus
ACAGCUGCCCACACUCCUGGCCACUUUGUCUUUGGCCAAUUAAAAUCAAAUUU________________CAAAAUGUUCCAAAUUUUGUGCA_ACUGAUGACAGUUUAAUUGCUGUCCUG
.(((.............((((((.........))))))...............................((((((.......))))))......)))..((((((......))))))... (-19.12 = -19.00 +  -0.12)

alignment

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secondary structure

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dotplot

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Window 9

Location 3,154,235 – 3,154,346
Length 111
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 88.65
Mean single sequence MFE -30.35
Consensus MFE -23.58
Energy contribution -23.77
Covariance contribution 0.19
Combinations/Pair 1.06
Mean z-score -2.49
Structure conservation index 0.78
SVM decision value 1.32
SVM RNA-class probability 0.941583
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 3154235 111 - 27905053
CAGGACAGCAAUUAAACUGUCAUCAGU-UGCACAAAAUUUGGAACAUUUUGA--------AAUUUUGAAAUUUGAUUUUAAUUGGCCAAAGACAAAGUGGCCAGGAGUGUGGGCAGCUGU
...(((((........)))))..((((-(((.((((((((.((.....)).)--------)))))))..............(((((((.........)))))))........))))))). ( -31.60)
>DroSec_CAF1 2125 104 - 1
CAGGACAGCAAUUAAACUGUCAUCAGUUUGCACAAAAUUUGGAACAUUUUG----------------AAAUUUGAUUUUAAUUGGCCAAAGACAAAGUGGCCAGGAGUGUGGGCAGCUGU
((((((((........)))))....(((..(((.((((((.((.....)).----------------))))))........(((((((.........)))))))..)))..)))..))). ( -29.00)
>DroSim_CAF1 4295 104 - 1
CAGGACAGCAAUUAAACUGUCAUCAGUUUGCACAAAAUUUGGAACAUUUUG----------------AAAUUUGAUUUUAAUUGGCCAAAGACAAAGUGGCCAGGAGUGUGGGCAGCUGU
((((((((........)))))....(((..(((.((((((.((.....)).----------------))))))........(((((((.........)))))))..)))..)))..))). ( -29.00)
>DroYak_CAF1 1421 119 - 1
CAGGACGGCAAUUAAACUGUCAUCAGU-UGCACAAAAUUAGGAACAUUUUGAAAUGCUGAAAUUUUGAAAUUUGAUUUUAAUUGGGCAAAGACAAAGUGCCCAGGAGUGUGGGGUGCUGU
....((((((....(((((....))))-)((((((((((((....((((..((((......))))..))))))))))))..(((((((.........)))))))..))))....)))))) ( -31.80)
>consensus
CAGGACAGCAAUUAAACUGUCAUCAGU_UGCACAAAAUUUGGAACAUUUUG________________AAAUUUGAUUUUAAUUGGCCAAAGACAAAGUGGCCAGGAGUGUGGGCAGCUGU
....(((((...(((((((....)))))))((((....((((((((..((..................))..)).))))))(((((((.........)))))))...))))....))))) (-23.58 = -23.77 +   0.19)

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 09:56:51 2006