Locus 6933

Sequence ID 3R_DroMel_CAF1
Location 18,282,082 – 18,282,219
Length 137
Max. P 0.999941
window11246 window11247 window11248 window11249

overview

Window 6

Location 18,282,082 – 18,282,193
Length 111
Sequences 5
Columns 111
Reading direction forward
Mean pairwise identity 83.41
Mean single sequence MFE -24.07
Consensus MFE -15.02
Energy contribution -15.74
Covariance contribution 0.72
Combinations/Pair 1.26
Mean z-score -2.59
Structure conservation index 0.62
SVM decision value 1.11
SVM RNA-class probability 0.916674
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 18282082 111 + 27905053
AGUCUGGAAUCAUUUAAAAAAUCCCCUUUGGUUUUAAACGCAAUUCGAAUAUUCUUUGCCUUGUUGAUAAACACGUUUUUGGAUUUUUCCAAAAAUGUUGUUUGCUACUUA
.((.((((((((................)))))))).))((((............))))...((.(.((((((((((((((((....)))))))))).))))))).))... ( -23.29)
>DroSec_CAF1 7639 110 + 1
AGUCCUGAAACAUUUAAAA-AUUCCAUUUAGGUUUAAACGCAUUUCAAAUAUUCUUUGCGUUGUUGACAAACAUGUUUUUGGAUUUUUCCAAAAAUGUUGUUUGUUACUUA
...((((((..........-......))))))....((((((..............))))))..(((((((((((((((((((....)))))))))).))))))))).... ( -26.83)
>DroSim_CAF1 8423 110 + 1
AGUCUGGAAACAUUUAAAA-AUUCCCUUUGGGUUUAAACGCAUUUCAAAUAUUCUUUGCGUUGUUGACAAACAUGUUUUUGGAUUUUUCCAAAAAUUUUGUUUGUUACUUA
....((....)).......-...(((...)))....((((((..............))))))..(((((((((.(((((((((....)))))))))..))))))))).... ( -27.94)
>DroEre_CAF1 13713 109 + 1
AGUCUGGAAACAUUUUCAA-AUCCCCU-UAGUUUUAAACGCUUUUAAAAUGCUCACUGACCUGUUGACAAACACUUUUUCGGAUUUUUCCAAAAAUGUUCGUUUUUACUCA
.(((((....)).......-.......-..((((((((....)))))))).......)))..((.(((.((((.(((((.(((....)))))))))))).)))...))... ( -15.30)
>DroYak_CAF1 7731 109 + 1
AGUCUGGAAACAUUUCAAA-AUCCCCU-UAAGUUUAAACGUUUUUAAAACAAUCACUGGGCUGUUGACAAGCACGUUUUUGGAUUUUUCCAGGAAUGUUGUUUGUUACUUA
((((..(((((........-.......-...))))....(((.....))).....)..))))..(((((((((((((((((((....)))))))))).))))))))).... ( -26.97)
>consensus
AGUCUGGAAACAUUUAAAA_AUCCCCUUUAGGUUUAAACGCAUUUCAAAUAUUCUUUGCGUUGUUGACAAACACGUUUUUGGAUUUUUCCAAAAAUGUUGUUUGUUACUUA
................................................................(((((((((((((((((((....)))))))))).))))))))).... (-15.02 = -15.74 +   0.72)

alignment

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secondary structure

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dotplot

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Window 7

Location 18,282,082 – 18,282,193
Length 111
Sequences 5
Columns 111
Reading direction reverse
Mean pairwise identity 83.41
Mean single sequence MFE -21.43
Consensus MFE -13.24
Energy contribution -14.16
Covariance contribution 0.92
Combinations/Pair 1.24
Mean z-score -2.00
Structure conservation index 0.62
SVM decision value 0.23
SVM RNA-class probability 0.646564
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 18282082 111 - 27905053
UAAGUAGCAAACAACAUUUUUGGAAAAAUCCAAAAACGUGUUUAUCAACAAGGCAAAGAAUAUUCGAAUUGCGUUUAAAACCAAAGGGGAUUUUUUAAAUGAUUCCAGACU
..(((((((((((...((((((((....))))))))..))))).........((((.((....))...)))))))...........((((((........))))))..))) ( -18.80)
>DroSec_CAF1 7639 110 - 1
UAAGUAACAAACAACAUUUUUGGAAAAAUCCAAAAACAUGUUUGUCAACAACGCAAAGAAUAUUUGAAAUGCGUUUAAACCUAAAUGGAAU-UUUUAAAUGUUUCAGGACU
...((.(((((((...((((((((....))))))))..)))))))..))........(((((((((((((.((((((....)))))).)..-))))))))))))....... ( -22.80)
>DroSim_CAF1 8423 110 - 1
UAAGUAACAAACAAAAUUUUUGGAAAAAUCCAAAAACAUGUUUGUCAACAACGCAAAGAAUAUUUGAAAUGCGUUUAAACCCAAAGGGAAU-UUUUAAAUGUUUCCAGACU
...((.(((((((...((((((((....))))))))..)))))))..))((((((..............))))))..........((((((-........))))))..... ( -23.14)
>DroEre_CAF1 13713 109 - 1
UGAGUAAAAACGAACAUUUUUGGAAAAAUCCGAAAAAGUGUUUGUCAACAGGUCAGUGAGCAUUUUAAAAGCGUUUAAAACUA-AGGGGAU-UUGAAAAUGUUUCCAGACU
.........(((((((((((((((....)))))))..)))))))).....((((.(..((((((((.(((.(.((((....))-)).)..)-)).))))))))..).)))) ( -25.00)
>DroYak_CAF1 7731 109 - 1
UAAGUAACAAACAACAUUCCUGGAAAAAUCCAAAAACGUGCUUGUCAACAGCCCAGUGAUUGUUUUAAAAACGUUUAAACUUA-AGGGGAU-UUUGAAAUGUUUCCAGACU
(((((...............((((....)))).((((((..(((..(((((........))))).)))..))))))..)))))-.((..((-........))..))..... ( -17.40)
>consensus
UAAGUAACAAACAACAUUUUUGGAAAAAUCCAAAAACGUGUUUGUCAACAACGCAAAGAAUAUUUGAAAUGCGUUUAAACCUAAAGGGGAU_UUUUAAAUGUUUCCAGACU
...((.(((((((...((((((((....))))))))..)))))))..))........((((((((((((...((((...........)))).))))))))))))....... (-13.24 = -14.16 +   0.92)

alignment

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secondary structure

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dotplot

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Window 8

Location 18,282,113 – 18,282,219
Length 106
Sequences 4
Columns 119
Reading direction forward
Mean pairwise identity 69.80
Mean single sequence MFE -20.75
Consensus MFE -13.11
Energy contribution -15.86
Covariance contribution 2.75
Combinations/Pair 1.08
Mean z-score -2.90
Structure conservation index 0.63
SVM decision value 4.71
SVM RNA-class probability 0.999941
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 18282113 106 + 27905053
UUUUAAACGCAAUUCGAAUAUUCUUUGCCUUGUUGAUAAACACGUUUUUGGAUUUUUCCAAAAAUGUUGUUUGCUACUUA-------------UCUUAAAAAAAAUACCCUGUCUAAUA
((((((..((((............))))...((.(.((((((((((((((((....)))))))))).))))))).))...-------------..)))))).................. ( -19.10)
>DroSec_CAF1 7669 92 + 1
GUUUAAACGCAUUUCAAAUAUUCUUUGCGUUGUUGACAAACAUGUUUUUGGAUUUUUCCAAAAAUGUUGUUUGUUACUUA-------------UCUU--------------AAAAAGAA
.....((((((..............))))))..(((((((((((((((((((....)))))))))).)))))))))....-------------....--------------........ ( -24.24)
>DroSim_CAF1 8453 92 + 1
GUUUAAACGCAUUUCAAAUAUUCUUUGCGUUGUUGACAAACAUGUUUUUGGAUUUUUCCAAAAAUUUUGUUUGUUACUUA-------------CCCU--------------GCCUAAUA
.....((((((..............))))))..(((((((((.(((((((((....)))))))))..)))))))))....-------------....--------------........ ( -24.24)
>DroEre_CAF1 13742 118 + 1
UUUUAAACGCUUUUAAAAUGCUCACUGACCUGUUGACAAACACUUUUUCGGAUUUUUCCAAAAAUGUUCGUUUUUACUCAAAAGGUGUACUUAUCUCAUA-AAAAUUCCCGGCAUAAUC
........(((.......((.((((......).))))).(((((((((.(((....)))((((((....))))))....)))))))))............-.........)))...... ( -15.40)
>consensus
GUUUAAACGCAUUUCAAAUAUUCUUUGCCUUGUUGACAAACACGUUUUUGGAUUUUUCCAAAAAUGUUGUUUGUUACUUA_____________UCUU______________GCAUAAUA
.....((((((..............))))))..(((((((((((((((((((....)))))))))).)))))))))........................................... (-13.11 = -15.86 +   2.75)

alignment

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secondary structure

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dotplot

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Window 9

Location 18,282,113 – 18,282,219
Length 106
Sequences 4
Columns 119
Reading direction reverse
Mean pairwise identity 69.80
Mean single sequence MFE -19.04
Consensus MFE -9.70
Energy contribution -10.32
Covariance contribution 0.63
Combinations/Pair 1.12
Mean z-score -1.93
Structure conservation index 0.51
SVM decision value 0.92
SVM RNA-class probability 0.881865
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 18282113 106 - 27905053
UAUUAGACAGGGUAUUUUUUUUAAGA-------------UAAGUAGCAAACAACAUUUUUGGAAAAAUCCAAAAACGUGUUUAUCAACAAGGCAAAGAAUAUUCGAAUUGCGUUUAAAA
..((((((..(.(((((.((....))-------------.))))).)(((((...((((((((....))))))))..))))).........((((.((....))...)))))))))).. ( -18.60)
>DroSec_CAF1 7669 92 - 1
UUCUUUUU--------------AAGA-------------UAAGUAACAAACAACAUUUUUGGAAAAAUCCAAAAACAUGUUUGUCAACAACGCAAAGAAUAUUUGAAAUGCGUUUAAAC
........--------------....-------------...((.(((((((...((((((((....))))))))..)))))))..))((((((..............))))))..... ( -17.64)
>DroSim_CAF1 8453 92 - 1
UAUUAGGC--------------AGGG-------------UAAGUAACAAACAAAAUUUUUGGAAAAAUCCAAAAACAUGUUUGUCAACAACGCAAAGAAUAUUUGAAAUGCGUUUAAAC
......((--------------(...-------------(((((((((((((...((((((((....))))))))..)))))))......(.....)..))))))...)))........ ( -18.10)
>DroEre_CAF1 13742 118 - 1
GAUUAUGCCGGGAAUUUU-UAUGAGAUAAGUACACCUUUUGAGUAAAAACGAACAUUUUUGGAAAAAUCCGAAAAAGUGUUUGUCAACAGGUCAGUGAGCAUUUUAAAAGCGUUUAAAA
...........((((.((-(.((((((...(((((((.((((.......((((((((((((((....)))))))..))))))))))).))))..)))...)))))).))).)))).... ( -21.81)
>consensus
UAUUAGGC______________AAGA_____________UAAGUAACAAACAACAUUUUUGGAAAAAUCCAAAAACAUGUUUGUCAACAACGCAAAGAAUAUUUGAAAUGCGUUUAAAA
..........................................((.(((((((...((((((((....))))))))..)))))))..))............................... ( -9.70 = -10.32 +   0.63)

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 12:33:36 2006