Locus 3033

Sequence ID 2L_DroMel_CAF1
Location 8,638,303 – 8,638,428
Length 125
Max. P 0.855476
window4826 window4827 window4828 window4829

overview

Window 6

Location 8,638,303 – 8,638,405
Length 102
Sequences 6
Columns 108
Reading direction forward
Mean pairwise identity 83.97
Mean single sequence MFE -27.15
Consensus MFE -22.35
Energy contribution -23.22
Covariance contribution 0.86
Combinations/Pair 1.16
Mean z-score -1.91
Structure conservation index 0.82
SVM decision value 0.52
SVM RNA-class probability 0.766763
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 8638303 102 + 22407834
UAAAUGUGCAACUGCAACAAGGAUGGCAAGA------AGAACAACAACAGGGCCAGGAUAAUACGAGCCAAAGCAGUGGAAAUCCUGGCGUAAUCGUUGCGUUCACUG
.....(((.(((.(((((...(((.((....------.......(....).((((((((..(((..((....)).)))...)))))))))).)))))))))))))).. ( -28.40)
>DroPse_CAF1 16663 78 + 1
UAAAUGUGCAAUGGCAGCAGC-AUCCU----------------------------ACCAAACACGAG-GAAAGCAGUGAAAAUCCUUGCGUAAUCGUUGCGUUCGCUG
.......((((((((....))-.....----------------------------.....((.((((-((............)))))).))...))))))........ ( -15.90)
>DroSec_CAF1 7134 102 + 1
UAAAUGUGCAACUGCAACAAGGAUGGCAAGA------AGAACAACAACAGCGCCAGGAUAAUACGAGCCAAAGCAGUGGAAAUCCUGGCGUAAUCGUUGCGUUCACUG
.....(((.(((.(((((.....((......------....))......((((((((((..(((..((....)).)))...))))))))))....))))))))))).. ( -31.90)
>DroSim_CAF1 7249 102 + 1
UAAAUGUGCAACUGCAACAAGGAUGGCAAGA------AGAACAACAACAGGGCCAGGAUAAUACGAGCCAAAGCAGUGGAAAUCCUGGCGUAAUCGUUGCGUUCACUG
.....(((.(((.(((((...(((.((....------.......(....).((((((((..(((..((....)).)))...)))))))))).)))))))))))))).. ( -28.40)
>DroEre_CAF1 9735 108 + 1
UAAAUGUGCAACUGCAGCAAGGAUGGCAAGAAGAAGAAGAACAACAACAGGGCCAGGAUAAUACGAGCCAAAGCAGUGGAAAUCCUGGCGUAAUCGUUGCGUUCACUG
......(((....)))((((.(((.((.................(....).((((((((..(((..((....)).)))...)))))))))).))).))))........ ( -28.70)
>DroYak_CAF1 7707 102 + 1
UAAAUGUGCAACUGCAACAAGGAUGGCAAGA------GGAACAACAACAUGGCCAGGAUAAUACGAGCCAAAGCAGUGGAAAUCCUGGCGUAAUCGUUGCGUUCACUG
.....(((.(((.(((((...(((.((....------(......)......((((((((..(((..((....)).)))...)))))))))).)))))))))))))).. ( -29.60)
>consensus
UAAAUGUGCAACUGCAACAAGGAUGGCAAGA______AGAACAACAACAGGGCCAGGAUAAUACGAGCCAAAGCAGUGGAAAUCCUGGCGUAAUCGUUGCGUUCACUG
.....(((.(((.(((((.................................((((((((..(((..((....)).)))...))))))))(....)))))))))))).. (-22.35 = -23.22 +   0.86)

alignment

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secondary structure

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dotplot

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Window 7

Location 8,638,303 – 8,638,405
Length 102
Sequences 6
Columns 108
Reading direction reverse
Mean pairwise identity 83.97
Mean single sequence MFE -29.50
Consensus MFE -18.44
Energy contribution -20.97
Covariance contribution 2.53
Combinations/Pair 1.04
Mean z-score -2.78
Structure conservation index 0.63
SVM decision value 0.14
SVM RNA-class probability 0.600871
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 8638303 102 - 22407834
CAGUGAACGCAACGAUUACGCCAGGAUUUCCACUGCUUUGGCUCGUAUUAUCCUGGCCCUGUUGUUGUUCU------UCUUGCCAUCCUUGUUGCAGUUGCACAUUUA
..((((((((((((((...((((((((.......((....)).......))))))))...))))))))...------...(((((....))..)))))).)))..... ( -30.84)
>DroPse_CAF1 16663 78 - 1
CAGCGAACGCAACGAUUACGCAAGGAUUUUCACUGCUUUC-CUCGUGUUUGGU----------------------------AGGAU-GCUGCUGCCAUUGCACAUUUA
.((.(((.(((..((...(....).....))..))).)))-)).((((.((((----------------------------((...-....))))))..))))..... ( -19.40)
>DroSec_CAF1 7134 102 - 1
CAGUGAACGCAACGAUUACGCCAGGAUUUCCACUGCUUUGGCUCGUAUUAUCCUGGCGCUGUUGUUGUUCU------UCUUGCCAUCCUUGUUGCAGUUGCACAUUUA
..((((((((((((((..(((((((((.......((....)).......)))))))))..))))))))...------...(((((....))..)))))).)))..... ( -34.24)
>DroSim_CAF1 7249 102 - 1
CAGUGAACGCAACGAUUACGCCAGGAUUUCCACUGCUUUGGCUCGUAUUAUCCUGGCCCUGUUGUUGUUCU------UCUUGCCAUCCUUGUUGCAGUUGCACAUUUA
..((((((((((((((...((((((((.......((....)).......))))))))...))))))))...------...(((((....))..)))))).)))..... ( -30.84)
>DroEre_CAF1 9735 108 - 1
CAGUGAACGCAACGAUUACGCCAGGAUUUCCACUGCUUUGGCUCGUAUUAUCCUGGCCCUGUUGUUGUUCUUCUUCUUCUUGCCAUCCUUGCUGCAGUUGCACAUUUA
..((((((((((((((...((((((((.......((....)).......))))))))...))))))))............(((((....))..)))))).)))..... ( -30.84)
>DroYak_CAF1 7707 102 - 1
CAGUGAACGCAACGAUUACGCCAGGAUUUCCACUGCUUUGGCUCGUAUUAUCCUGGCCAUGUUGUUGUUCC------UCUUGCCAUCCUUGUUGCAGUUGCACAUUUA
..((((((((((((((...((((((((.......((....)).......))))))))...))))))))...------...(((((....))..)))))).)))..... ( -30.84)
>consensus
CAGUGAACGCAACGAUUACGCCAGGAUUUCCACUGCUUUGGCUCGUAUUAUCCUGGCCCUGUUGUUGUUCU______UCUUGCCAUCCUUGUUGCAGUUGCACAUUUA
........((((((((...((((((((.......((....)).......))))))))...)))))))).....................((.(((....))))).... (-18.44 = -20.97 +   2.53)

alignment

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secondary structure

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dotplot

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Window 8

Location 8,638,337 – 8,638,428
Length 91
Sequences 6
Columns 103
Reading direction forward
Mean pairwise identity 81.35
Mean single sequence MFE -27.56
Consensus MFE -17.56
Energy contribution -17.95
Covariance contribution 0.39
Combinations/Pair 1.12
Mean z-score -2.45
Structure conservation index 0.64
SVM decision value 0.81
SVM RNA-class probability 0.855476
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 8638337 91 + 22407834
ACAACAACAGGGCCAGGAUAAUACGAGCCAAAGCAGUGGAAAUCCUGGCGUAAUCGUUGCGUUCACUGCUGGCAGGCAACAACAAC------------AGCAA
.((((....(.((((((((..(((..((....)).)))...)))))))).)....)))).......(((((...(....).....)------------)))). ( -27.40)
>DroPse_CAF1 16689 76 + 1
---------------ACCAAACACGAG-GAAAGCAGUGAAAAUCCUUGCGUAAUCGUUGCGUUCGCUGCUGC-GGGGAA-AACUACUGC---------AACAC
---------------.((........)-)...((((((....((((((((.....((.((....)).)))))-))))).-...))))))---------..... ( -21.00)
>DroSec_CAF1 7168 94 + 1
ACAACAACAGCGCCAGGAUAAUACGAGCCAAAGCAGUGGAAAUCCUGGCGUAAUCGUUGCGUUCACUGCUGGCAGGCAACAACAACUGG---------AACAA
.((((....((((((((((..(((..((....)).)))...))))))))))....)))).((((..((((....)))).((.....)))---------))).. ( -30.70)
>DroSim_CAF1 7283 94 + 1
ACAACAACAGGGCCAGGAUAAUACGAGCCAAAGCAGUGGAAAUCCUGGCGUAAUCGUUGCGUUCACUGCUGGCAGGCAACAACAACUGG---------AACAA
.........(..((((..........((((..((((((((......((((....))))...)))))))))))).(....).....))))---------..).. ( -28.90)
>DroEre_CAF1 9775 103 + 1
ACAACAACAGGGCCAGGAUAAUACGAGCCAAAGCAGUGGAAAUCCUGGCGUAAUCGUUGCGUUCACUGCUGGCAGGCAACAACAACUGCAACAACUGGAACAA
.......(((.((((((((..(((..((....)).)))...))))))))......((((((((...((((....)))).....))).)))))..)))...... ( -31.40)
>DroYak_CAF1 7741 103 + 1
ACAACAACAUGGCCAGGAUAAUACGAGCCAAAGCAGUGGAAAUCCUGGCGUAAUCGUUGCGUUCACUGCUCGCUGGCAACAACAACUGGAACCACUACAACAA
.........(((((((..........((((.(((((((((......((((....))))...)))))))))...))))........))))..)))......... ( -25.97)
>consensus
ACAACAACAGGGCCAGGAUAAUACGAGCCAAAGCAGUGGAAAUCCUGGCGUAAUCGUUGCGUUCACUGCUGGCAGGCAACAACAACUGG_________AACAA
..........................(((..(((((((((......((((....))))...)))))))))....))).......................... (-17.56 = -17.95 +   0.39)

alignment

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secondary structure

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dotplot

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Window 9

Location 8,638,337 – 8,638,428
Length 91
Sequences 6
Columns 103
Reading direction reverse
Mean pairwise identity 81.35
Mean single sequence MFE -30.85
Consensus MFE -19.09
Energy contribution -22.12
Covariance contribution 3.03
Combinations/Pair 1.04
Mean z-score -2.24
Structure conservation index 0.62
SVM decision value 0.56
SVM RNA-class probability 0.782696
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 8638337 91 - 22407834
UUGCU------------GUUGUUGUUGCCUGCCAGCAGUGAACGCAACGAUUACGCCAGGAUUUCCACUGCUUUGGCUCGUAUUAUCCUGGCCCUGUUGUUGU
(..((------------((((..((.....))))))))..)..((((((((...((((((((.......((....)).......))))))))...)))))))) ( -33.24)
>DroPse_CAF1 16689 76 - 1
GUGUU---------GCAGUAGUU-UUCCCC-GCAGCAGCGAACGCAACGAUUACGCAAGGAUUUUCACUGCUUUC-CUCGUGUUUGGU---------------
.((((---------((.......-......-)))))).(((((((...((....(((..(.....)..)))..))-...)))))))..--------------- ( -15.62)
>DroSec_CAF1 7168 94 - 1
UUGUU---------CCAGUUGUUGUUGCCUGCCAGCAGUGAACGCAACGAUUACGCCAGGAUUUCCACUGCUUUGGCUCGUAUUAUCCUGGCGCUGUUGUUGU
..(((---------(...((((((........)))))).))))((((((((..(((((((((.......((....)).......)))))))))..)))))))) ( -35.24)
>DroSim_CAF1 7283 94 - 1
UUGUU---------CCAGUUGUUGUUGCCUGCCAGCAGUGAACGCAACGAUUACGCCAGGAUUUCCACUGCUUUGGCUCGUAUUAUCCUGGCCCUGUUGUUGU
..(((---------(...((((((........)))))).))))((((((((...((((((((.......((....)).......))))))))...)))))))) ( -31.84)
>DroEre_CAF1 9775 103 - 1
UUGUUCCAGUUGUUGCAGUUGUUGUUGCCUGCCAGCAGUGAACGCAACGAUUACGCCAGGAUUUCCACUGCUUUGGCUCGUAUUAUCCUGGCCCUGUUGUUGU
..(((((.((((..((((..(....)..)))))))).).))))((((((((...((((((((.......((....)).......))))))))...)))))))) ( -35.44)
>DroYak_CAF1 7741 103 - 1
UUGUUGUAGUGGUUCCAGUUGUUGUUGCCAGCGAGCAGUGAACGCAACGAUUACGCCAGGAUUUCCACUGCUUUGGCUCGUAUUAUCCUGGCCAUGUUGUUGU
(..((((.(((((..(((...)))..)))).)..))))..)..((((((((...((((((((.......((....)).......))))))))...)))))))) ( -33.74)
>consensus
UUGUU_________CCAGUUGUUGUUGCCUGCCAGCAGUGAACGCAACGAUUACGCCAGGAUUUCCACUGCUUUGGCUCGUAUUAUCCUGGCCCUGUUGUUGU
..................(..((((((.....))))))..)..((((((((...((((((((.......((....)).......))))))))...)))))))) (-19.09 = -22.12 +   3.03)

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 10:42:42 2006