Locus 1755

Sequence ID 3L_DroMel_CAF1
Location 5,046,476 – 5,046,699
Length 223
Max. P 0.992949
window2711 window2712 window2713

overview

Window 1

Location 5,046,476 – 5,046,589
Length 113
Sequences 5
Columns 114
Reading direction forward
Mean pairwise identity 90.64
Mean single sequence MFE -24.59
Consensus MFE -21.20
Energy contribution -21.88
Covariance contribution 0.68
Combinations/Pair 1.05
Mean z-score -2.13
Structure conservation index 0.86
SVM decision value 2.36
SVM RNA-class probability 0.992949
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 5046476 113 + 23771897
ACCCUAAUCAGAGCUCGGCGAAAUGUAAUUUUAAUUUCGCAGCAAUUUGCAAUGCAGAUUGCGUUU-UUUUUUUUUUUUUUUUGUCAUUACAAAAUUUGAGCAUUAUGCAUACA
............((((((((((((.........))))))).(((((((((...)))))))))....-............((((((....))))))..)))))............ ( -27.30)
>DroSec_CAF1 252997 102 + 1
GCCCUAAUCAGAGCUCGGCGAAAUGUAAUUUUAAUUUCGGAGCAAUUUGCAAUGCAGAUUGCGUUU-U-----------UUCUGGCAUUACAAAAUUUGAGCAUUAUGCAUACA
(((......(((((....((((((.........))))))..(((((((((...)))))))))))))-)-----------....)))..............((.....))..... ( -22.90)
>DroSim_CAF1 274285 102 + 1
GCCCUAAUCAGAGCUCGGCGAAAUGUAAUUUUAAUUUCGCAGCAAUUUGCAAUGCAGAUUGCGUUU-U-----------UUCUGGCAUUACAAAAUUUGAGCAUUAUGCAUACA
(((......(((((...(((((((.........))))))).(((((((((...)))))))))))))-)-----------....)))..............((.....))..... ( -26.50)
>DroEre_CAF1 259788 102 + 1
GCACUAAUCAGAGCUCGGUGAAAUAUAAUUUUAAUUUCGCAGCAAUUUGCAAUGCAGAUUGCGUUU-U-----------UUCUGGCAUUACAAAAUUUGAGCAUUAUGCAUACA
(((.((((....((((((((((((.........))))))).(((((((((...)))))))))....-.-----------..................))))))))))))..... ( -25.00)
>DroYak_CAF1 262931 103 + 1
GCACUAAUCAGAGCUCGGCGAAAUGUAAUUUUAAUUUCACAGCAAUUUGCCAUGCAGAUCUCGUUUUU-----------UUCUGUCAUUACCAAAUUUGAGCAUUAUGCAUACA
(((.((((....((((((((((.(((...............))).))))))(((((((..........-----------.)))).)))..........)))))))))))..... ( -21.26)
>consensus
GCCCUAAUCAGAGCUCGGCGAAAUGUAAUUUUAAUUUCGCAGCAAUUUGCAAUGCAGAUUGCGUUU_U___________UUCUGGCAUUACAAAAUUUGAGCAUUAUGCAUACA
............((((((((((((.........))))))).(((((((((...)))))))))...................................)))))............ (-21.20 = -21.88 +   0.68)

alignment

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secondary structure

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dotplot

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Window 2

Location 5,046,476 – 5,046,589
Length 113
Sequences 5
Columns 114
Reading direction reverse
Mean pairwise identity 90.64
Mean single sequence MFE -22.02
Consensus MFE -17.95
Energy contribution -18.83
Covariance contribution 0.88
Combinations/Pair 1.04
Mean z-score -1.53
Structure conservation index 0.82
SVM decision value 0.44
SVM RNA-class probability 0.738174
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 5046476 113 - 23771897
UGUAUGCAUAAUGCUCAAAUUUUGUAAUGACAAAAAAAAAAAAAAAA-AAACGCAAUCUGCAUUGCAAAUUGCUGCGAAAUUAAAAUUACAUUUCGCCGAGCUCUGAUUAGGGU
............((((...((((((....))))))............-....(((((.(((...))).))))).(((((((.........))))))).))))............ ( -21.40)
>DroSec_CAF1 252997 102 - 1
UGUAUGCAUAAUGCUCAAAUUUUGUAAUGCCAGAA-----------A-AAACGCAAUCUGCAUUGCAAAUUGCUCCGAAAUUAAAAUUACAUUUCGCCGAGCUCUGAUUAGGGC
............((((....((((((((((.(((.-----------.-........)))))))))))))..((((((((((.........))))))..))))........)))) ( -23.80)
>DroSim_CAF1 274285 102 - 1
UGUAUGCAUAAUGCUCAAAUUUUGUAAUGCCAGAA-----------A-AAACGCAAUCUGCAUUGCAAAUUGCUGCGAAAUUAAAAUUACAUUUCGCCGAGCUCUGAUUAGGGC
............((((....((((((((((.(((.-----------.-........)))))))))))))..((((((((((.........)))))))..)))........)))) ( -24.30)
>DroEre_CAF1 259788 102 - 1
UGUAUGCAUAAUGCUCAAAUUUUGUAAUGCCAGAA-----------A-AAACGCAAUCUGCAUUGCAAAUUGCUGCGAAAUUAAAAUUAUAUUUCACCGAGCUCUGAUUAGUGC
.((((.......((((....((((((((((.(((.-----------.-........))))))))))))).......(((((.........)))))...))))........)))) ( -21.36)
>DroYak_CAF1 262931 103 - 1
UGUAUGCAUAAUGCUCAAAUUUGGUAAUGACAGAA-----------AAAAACGAGAUCUGCAUGGCAAAUUGCUGUGAAAUUAAAAUUACAUUUCGCCGAGCUCUGAUUAGUGC
.((((.......((((.((((((.((.((.((((.-----------..........)))))))).))))))...(((((((.........))))))).))))........)))) ( -19.26)
>consensus
UGUAUGCAUAAUGCUCAAAUUUUGUAAUGCCAGAA___________A_AAACGCAAUCUGCAUUGCAAAUUGCUGCGAAAUUAAAAUUACAUUUCGCCGAGCUCUGAUUAGGGC
............((((....(((((((((.((((......................))))))))))))).....(((((((.........))))))).))))............ (-17.95 = -18.83 +   0.88)

alignment

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secondary structure

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dotplot

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Window 3

Location 5,046,589 – 5,046,699
Length 110
Sequences 5
Columns 114
Reading direction forward
Mean pairwise identity 93.37
Mean single sequence MFE -26.41
Consensus MFE -21.16
Energy contribution -21.00
Covariance contribution -0.16
Combinations/Pair 1.13
Mean z-score -1.49
Structure conservation index 0.80
SVM decision value 0.16
SVM RNA-class probability 0.614631
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 5046589 110 + 23771897
GUAUUCAUAUGGAUCAUCACAACGGCUGUCAUAAGUGACGUGAUUGAUUGAUGAUGUCACUUAAAGCGACCAACGAAAUAACAGC---AGCAGCAGUUACAACAGAAAU-GUUC
(.((((....))))).....(((.(((((..((((((((((.(((....))).))))))))))..((................))---.))))).)))..((((....)-))). ( -26.59)
>DroSec_CAF1 253099 110 + 1
GUAUUCAUAUGGAUCAUCACAACGGCUGUCAUAAGUGACGUGAUUGAUUGAUGAUGUCACUUAAAGCGACCAACGAAAUAACAGC---AGCAGCAGUUACAACAGAAAU-GUUC
(.((((....))))).....(((.(((((..((((((((((.(((....))).))))))))))..((................))---.))))).)))..((((....)-))). ( -26.59)
>DroSim_CAF1 274387 110 + 1
GUAUUCAUAUGGAUCAUCACAACGGCUGUCAUAAGUGACGUGAUUGAUUGAUGAUGUCACUUAAAGCGACCAACGAAAUAACAGC---AGCAGCAGUUACAACAGAAAU-GUUC
(.((((....))))).....(((.(((((..((((((((((.(((....))).))))))))))..((................))---.))))).)))..((((....)-))). ( -26.59)
>DroEre_CAF1 259890 110 + 1
GUAUUCAUAUAGAGCACCACGCUGGCUGUCAAAAGUGACGUGAUUGAUUGAUGAUGUCACUUAAAGCGACCAACGAAAUAACAGC---AGCGGCAGUUACAAAAAAAAU-GUUC
...........(((((...((.(((.(((...(((((((((.(((....))).)))))))))...))).))).))...((((.((---....)).)))).........)-)))) ( -26.60)
>DroYak_CAF1 263034 114 + 1
GUAUUCAUAUAGAGCACCACGACGGCUGUCAUAAGUGACGUGAUUGAUUGAUGAUGUCACUUAAAGCGACCAACGAAAUAUCAGCAGCAGCAGCAGUUACAACAAAAACGGUUC
...............(((.((..((.(((..((((((((((.(((....))).))))))))))..))).))..)).......(((.((....)).)))...........))).. ( -25.70)
>consensus
GUAUUCAUAUGGAUCAUCACAACGGCUGUCAUAAGUGACGUGAUUGAUUGAUGAUGUCACUUAAAGCGACCAACGAAAUAACAGC___AGCAGCAGUUACAACAGAAAU_GUUC
....................(((.(((((..((((((((((.(((....))).))))))))))...((.....))..............))))).)))................ (-21.16 = -21.00 +  -0.16)

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 10:15:27 2006