Locus 5650

Sequence ID 3R_DroMel_CAF1
Location 14,835,067 – 14,835,347
Length 280
Max. P 0.901075
window9225 window9226 window9227

overview

Window 5

Location 14,835,067 – 14,835,187
Length 120
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 98.33
Mean single sequence MFE -40.00
Consensus MFE -40.24
Energy contribution -39.80
Covariance contribution -0.44
Combinations/Pair 1.05
Mean z-score -1.49
Structure conservation index 1.01
SVM decision value 0.28
SVM RNA-class probability 0.664228
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 14835067 120 - 27905053
ACGACUGCAUCAUAGUUUGCCAAGCGACGAUGGCGUGGGUCGUCAGUUGGGCAAUUAAAACGAGUCAACUAACUCGAAAUGAUUUGCAGCGCCGUUGAUGGAGUCAUGCCAUGAGCUGCU
..(.(((((((((...(((((.(((((((((.......)))))).))).)))))......(((((......)))))..))))..))))))((.(((.((((.......)))).))).)). ( -40.20)
>DroSec_CAF1 13254 120 - 1
ACGACUGCAUCAUAGCUUGCCAAGCAACGAUGGCGUGGGUCGUCAGUUGGGCAAUUAAAACGAGUCAACUAACUCGAAAUGAUUUGCAGCGCCGUUGAUGGAGUCAUGCCAUGAGCUGCU
..(.(((((((((...(((((...((((((((((....)))))).)))))))))......(((((......)))))..))))..))))))((.(((.((((.......)))).))).)). ( -40.10)
>DroSim_CAF1 13412 120 - 1
ACGACUGCAUCGUAGCUUGCCAAGCGACGAUGGCGUGGGUCGUCAGUUGGGCAAUUAAAACGAGUCAACUAACUCGAAAUGAUUUGCAGCGCCGUUGAUGGAGUCAUGCCAUGAGCUGCU
..(.(((((((((...(((((.(((((((((.......)))))).))).)))))......(((((......)))))..))))..))))))((.(((.((((.......)))).))).)). ( -39.70)
>consensus
ACGACUGCAUCAUAGCUUGCCAAGCGACGAUGGCGUGGGUCGUCAGUUGGGCAAUUAAAACGAGUCAACUAACUCGAAAUGAUUUGCAGCGCCGUUGAUGGAGUCAUGCCAUGAGCUGCU
..(.(((((((((...(((((...((((((((((....)))))).)))))))))......(((((......)))))..))))..))))))((.(((.((((.......)))).))).)). (-40.24 = -39.80 +  -0.44)

alignment

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secondary structure

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dotplot

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Window 6

Location 14,835,187 – 14,835,307
Length 120
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 97.78
Mean single sequence MFE -34.27
Consensus MFE -34.90
Energy contribution -34.23
Covariance contribution -0.66
Combinations/Pair 1.05
Mean z-score -1.86
Structure conservation index 1.02
SVM decision value 1.02
SVM RNA-class probability 0.901075
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 14835187 120 + 27905053
UAGGGAAGAUUUUGCAGUCUGCGCUUGGGCUGGACAAAUCCAUUGAAUCUUGGCAGUUUAAUUGGGGCAUCUUAAUUAGACACUGCUGGGGUAAUUAUGUAAGACAGUGGGAAACUAUAU
.........((((((((((((.((....)))))))...........((((..((((((((((((((....)))))))))..)))))..)))).....)))))))..((((....)))).. ( -34.70)
>DroSec_CAF1 13374 120 + 1
UAGGGAAGAUUUUGCAGUCUGCGCUUGGGCUGGACAAAUUCAUUGAAUCAUGGCAGUUUAAUUGGGGCAUCUUAAUUAGACACUGCUGUGGUAAUUAUGUAAGGCAGUGGGAAACUAUAU
.......(.((((((((((((.((....)))))))...........((((((((((((((((((((....)))))))))..))))))))))).....)))))))).((((....)))).. ( -33.90)
>DroSim_CAF1 13532 120 + 1
UAGGGAAGAUUUUGCAGUCUGCGCUUGGGCUGGACAAAUCCAUUGAAUCUUGGCAGUUUAAUUGGGGCAUCUUAAUUAGACACUGCUGGGGUAAUUAUGUAAGGCAGUGGGAAACUAUAU
.......(.((((((((((((.((....)))))))...........((((..((((((((((((((....)))))))))..)))))..)))).....)))))))).((((....)))).. ( -34.20)
>consensus
UAGGGAAGAUUUUGCAGUCUGCGCUUGGGCUGGACAAAUCCAUUGAAUCUUGGCAGUUUAAUUGGGGCAUCUUAAUUAGACACUGCUGGGGUAAUUAUGUAAGGCAGUGGGAAACUAUAU
.......(.((((((((((((.((....)))))))...........((((..((((((((((((((....)))))))))..)))))..)))).....)))))))).((((....)))).. (-34.90 = -34.23 +  -0.66)

alignment

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secondary structure

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dotplot

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Window 7

Location 14,835,227 – 14,835,347
Length 120
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 97.22
Mean single sequence MFE -28.43
Consensus MFE -28.76
Energy contribution -28.10
Covariance contribution -0.66
Combinations/Pair 1.06
Mean z-score -1.42
Structure conservation index 1.01
SVM decision value 0.22
SVM RNA-class probability 0.640488
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 14835227 120 + 27905053
CAUUGAAUCUUGGCAGUUUAAUUGGGGCAUCUUAAUUAGACACUGCUGGGGUAAUUAUGUAAGACAGUGGGAAACUAUAUUAAAUUGGCAAUCAGUCUUGGUACUAAAAACCAGAAAGCU
.(((((((((..((((((((((((((....)))))))))..)))))..))))..............((((....)))).............))))).(((((.......)))))...... ( -29.40)
>DroSec_CAF1 13414 120 + 1
CAUUGAAUCAUGGCAGUUUAAUUGGGGCAUCUUAAUUAGACACUGCUGUGGUAAUUAUGUAAGGCAGUGGGAAACUAUAUUAAAUUGGCAAUCAGUCUUGGUACUAAAAAACAGAAACCU
..(((.((((((((((((((((((((....)))))))))..))))))))))).......((((((.((((....)))).......((.....))))))))...........)))...... ( -27.80)
>DroSim_CAF1 13572 120 + 1
CAUUGAAUCUUGGCAGUUUAAUUGGGGCAUCUUAAUUAGACACUGCUGGGGUAAUUAUGUAAGGCAGUGGGAAACUAUAUUAAAUUGGCAAUCAGUCUUGGUACUAAAAAACAGAAACCU
..(((.((((..((((((((((((((....)))))))))..)))))..)))).......((((((.((((....)))).......((.....))))))))...........)))...... ( -28.10)
>consensus
CAUUGAAUCUUGGCAGUUUAAUUGGGGCAUCUUAAUUAGACACUGCUGGGGUAAUUAUGUAAGGCAGUGGGAAACUAUAUUAAAUUGGCAAUCAGUCUUGGUACUAAAAAACAGAAACCU
..(((.((((..((((((((((((((....)))))))))..)))))..)))).......((((((.((((....)))).......((.....))))))))...........)))...... (-28.76 = -28.10 +  -0.66)

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 12:00:39 2006