Locus 5938

Sequence ID 3R_DroMel_CAF1
Location 15,652,935 – 15,653,076
Length 141
Max. P 0.714542
window9691 window9692 window9693

overview

Window 1

Location 15,652,935 – 15,653,040
Length 105
Sequences 4
Columns 106
Reading direction forward
Mean pairwise identity 88.10
Mean single sequence MFE -24.48
Consensus MFE -20.31
Energy contribution -20.88
Covariance contribution 0.56
Combinations/Pair 1.08
Mean z-score -1.37
Structure conservation index 0.83
SVM decision value -0.02
SVM RNA-class probability 0.521228
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 15652935 105 + 27905053
UUUCAUAUGGCCAUUGGCAUUAGUUUAUUUGGUUGUUCAUGCAGUCCAAGUGGAAUGGGUGGUUCGAAGUUCGAAACAAAAAAACCAAACAAA-GAACCCCCAAAG
.........(((...))).....(((((((((((((....)))).))))))))).((((.(((((...(((.(............).)))...-)))))))))... ( -26.90)
>DroSim_CAF1 175855 105 + 1
UUUCAUAUGGCCAUUGGCAUUAGUUUAUUUGGUUGUUCAUGCAGUCCAAGUGGAAUGGGUGGUUCGAACUUCGAAACAAA-AAACCAAACAAAGGAACCCCCAAAG
.........(((...))).....(((((((((((((....)))).))))))))).((((.((((((.....)))......-...((.......)).)))))))... ( -25.30)
>DroEre_CAF1 158728 91 + 1
UUUCAUAUGGCCAUUGGCAUUAGUUUAUUUGGCUCUUCAUGCAGUCCAA-UGGAAUGGGUGGUUCGAA----------AA-AAACCAAACAA---AACCCCCGAAG
.(((......((((((((..(((.....)))((.......)).).))))-)))...(((.((((....----------..-...........---)))))))))). ( -18.33)
>DroYak_CAF1 183023 95 + 1
UUUCAUAUGGCCAUUGGCAUUAGUUUAUUUGGUUGUUCAUGCAGUCCAAGUGGAAUGGGUGGUUCGAA----------AA-AAACCAAACCAAAGAACCACCGAAG
.(((.....(((...))).....(((((((((((((....)))).)))))))))...((((((((...----------..-.............))))))))))). ( -27.37)
>consensus
UUUCAUAUGGCCAUUGGCAUUAGUUUAUUUGGUUGUUCAUGCAGUCCAAGUGGAAUGGGUGGUUCGAA__________AA_AAACCAAACAAA_GAACCCCCAAAG
.........(((...))).....(((((((((((((....)))).))))))))).((((.(((((.............................)))))))))... (-20.31 = -20.88 +   0.56)

alignment

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secondary structure

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dotplot

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Window 2

Location 15,652,965 – 15,653,076
Length 111
Sequences 3
Columns 112
Reading direction forward
Mean pairwise identity 87.13
Mean single sequence MFE -19.10
Consensus MFE -15.90
Energy contribution -16.35
Covariance contribution 0.45
Combinations/Pair 1.06
Mean z-score -1.87
Structure conservation index 0.83
SVM decision value 0.25
SVM RNA-class probability 0.655109
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 15652965 111 + 27905053
GGUUGUUCAUGCAGUCCAAGUGGAAUGGGUGGUUCGAAGUUCGAAACAAAAAAACCAAACAAA-GAACCCCCAAAGAAAUUGAACAUAAAACAUAUUCAAACCGAAAUACAA
(((((((((.....(((....))).((((.(((((...(((.(............).)))...-))))))))).......))))))..............)))......... ( -22.23)
>DroSim_CAF1 175885 111 + 1
GGUUGUUCAUGCAGUCCAAGUGGAAUGGGUGGUUCGAACUUCGAAACAAA-AAACCAAACAAAGGAACCCCCAAAGAAAUUGAACAUAAAACAUAUUCAAACCGAAAUAAAA
(((((((((.....(((....))).((((.((((((.....)))......-...((.......)).))))))).......))))))..............)))......... ( -20.63)
>DroEre_CAF1 158758 97 + 1
GGCUCUUCAUGCAGUCCAA-UGGAAUGGGUGGUUCGAA----------AA-AAACCAAACAA---AACCCCCGAAGAAACUGAACAUUAAACAUAUUCAAACCGAAAUACAA
((.(((((......(((..-.)))..(((.((((....----------..-...........---))))))))))))...((((.((.....)).))))..))......... ( -14.43)
>consensus
GGUUGUUCAUGCAGUCCAAGUGGAAUGGGUGGUUCGAA_UUCGAAACAAA_AAACCAAACAAA_GAACCCCCAAAGAAAUUGAACAUAAAACAUAUUCAAACCGAAAUACAA
...((((((.....(((....))).((((.(((((.............................))))))))).......)))))).......................... (-15.90 = -16.35 +   0.45)

alignment

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secondary structure

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dotplot

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Window 3

Location 15,652,965 – 15,653,076
Length 111
Sequences 3
Columns 112
Reading direction reverse
Mean pairwise identity 87.13
Mean single sequence MFE -25.79
Consensus MFE -18.59
Energy contribution -18.82
Covariance contribution 0.23
Combinations/Pair 1.08
Mean z-score -2.40
Structure conservation index 0.72
SVM decision value 0.38
SVM RNA-class probability 0.714542
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 15652965 111 - 27905053
UUGUAUUUCGGUUUGAAUAUGUUUUAUGUUCAAUUUCUUUGGGGGUUC-UUUGUUUGGUUUUUUUGUUUCGAACUUCGAACCACCCAUUCCACUUGGACUGCAUGAACAACC
.........((((.(..(((((.....((((((......(((((((((-...((((((..........))))))...))))).))))......)))))).)))))..))))) ( -28.50)
>DroSim_CAF1 175885 111 - 1
UUUUAUUUCGGUUUGAAUAUGUUUUAUGUUCAAUUUCUUUGGGGGUUCCUUUGUUUGGUUU-UUUGUUUCGAAGUUCGAACCACCCAUUCCACUUGGACUGCAUGAACAACC
.........((((.(..(((((.....((((((......((((((((((((((........-.......)))))...))))).))))......)))))).)))))..))))) ( -24.96)
>DroEre_CAF1 158758 97 - 1
UUGUAUUUCGGUUUGAAUAUGUUUAAUGUUCAGUUUCUUCGGGGGUU---UUGUUUGGUUU-UU----------UUCGAACCACCCAUUCCA-UUGGACUGCAUGAAGAGCC
.........(((((...(((((.....(((((((..(....)((((.---..((((((...-..----------.)))))).)))).....)-)))))).)))))..))))) ( -23.90)
>consensus
UUGUAUUUCGGUUUGAAUAUGUUUUAUGUUCAAUUUCUUUGGGGGUUC_UUUGUUUGGUUU_UUUGUUUCGAA_UUCGAACCACCCAUUCCACUUGGACUGCAUGAACAACC
.........((((....(((((.....((((((......(((((((((.............................))))).))))......)))))).)))))...)))) (-18.59 = -18.82 +   0.23)

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 12:08:28 2006