Locus 98

Sequence ID 3R_DroMel_CAF1
Location 606,356 – 606,480
Length 124
Max. P 0.993041
window164 window165 window166

overview

Window 4

Location 606,356 – 606,451
Length 95
Sequences 3
Columns 96
Reading direction reverse
Mean pairwise identity 90.88
Mean single sequence MFE -19.43
Consensus MFE -18.23
Energy contribution -18.90
Covariance contribution 0.67
Combinations/Pair 1.07
Mean z-score -1.40
Structure conservation index 0.94
SVM decision value 0.06
SVM RNA-class probability 0.565587
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 606356 95 - 27905053
CAAUAAGAGUACAUAUUAAUGUGUUUACUUUUUAUGGAGUGCUUAAA-AAAUGGAGCGACAAUUGCAGUAACCAACCAUAUUCCAAUUGGAUAUUG
((..(((((((.((((....)))).)))))))..))...(((((...-.....))))).((((((.((((........)))).))))))....... ( -15.70)
>DroSec_CAF1 22434 93 - 1
CAAUAAGAGUAGAUUUUAGUGAGUUUACUCUUAAUGGAGUGCUUAAAAAAAUGGAGCUACAAUUGCAGUAACC---CAUAUUCCAAUUGGAUAUUG
((.(((((((((((((....))))))))))))).))....((((.........))))..((((((.((((...---..)))).))))))....... ( -22.40)
>DroSim_CAF1 21591 93 - 1
CAAUAAGAGUAGAUUUUAGUGAGUUUACUCGUAAUGGAGUGCUUAAAAAAAUGGAGCUACAAUUGCAGUAACC---CAUUUUCCAAUUGGAUAUUG
(((((.((((((((((....))))))))))(((((...((((((.........)))).)).))))).......---.....(((....)))))))) ( -20.20)
>consensus
CAAUAAGAGUAGAUUUUAGUGAGUUUACUCUUAAUGGAGUGCUUAAAAAAAUGGAGCUACAAUUGCAGUAACC___CAUAUUCCAAUUGGAUAUUG
((.(((((((((((((....))))))))))))).))....((((.........))))..((((((.((((........)))).))))))....... (-18.23 = -18.90 +   0.67)

alignment

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secondary structure

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dotplot

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Window 5

Location 606,390 – 606,480
Length 90
Sequences 3
Columns 91
Reading direction forward
Mean pairwise identity 87.78
Mean single sequence MFE -14.53
Consensus MFE -13.11
Energy contribution -14.11
Covariance contribution 1.00
Combinations/Pair 1.00
Mean z-score -1.64
Structure conservation index 0.90
SVM decision value 0.41
SVM RNA-class probability 0.724423
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 606390 90 + 27905053
UUGUCGCUCCAUUU-UUUAAGCACUCCAUAAAAAGUAAACACAUUAAUAUGUACUCUUAUUGGAGAUUUCUUCUUUCGAUUUUAGUUUCGG
.....(((......-....))).(((((.....(((....((((....))))))).....)))))...........(((........))). ( -11.50)
>DroSec_CAF1 22465 87 + 1
UUGUAGCUCCAUUUUUUUAAGCACUCCAUUAAGAGUAAACUCACUAAAAUCUACUCUUAUUGGAGAUUUC---UUUUGAUUUUGGUUUCG-
........(((...((..(((..(((((.((((((((..............)))))))).)))))....)---))..))...))).....- ( -18.94)
>DroSim_CAF1 21622 88 + 1
UUGUAGCUCCAUUUUUUUAAGCACUCCAUUACGAGUAAACUCACUAAAAUCUACUCUUAUUGGAGAUUUC---UUUCUAUUUUAGUUUCGU
.....(((...........))).(((((.((.(((((..............))))).)).))))).....---.................. ( -13.14)
>consensus
UUGUAGCUCCAUUUUUUUAAGCACUCCAUUAAGAGUAAACUCACUAAAAUCUACUCUUAUUGGAGAUUUC___UUUCGAUUUUAGUUUCG_
.....(((...........))).(((((.((((((((..............)))))))).))))).......................... (-13.11 = -14.11 +   1.00)

alignment

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secondary structure

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dotplot

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Window 6

Location 606,390 – 606,480
Length 90
Sequences 3
Columns 91
Reading direction reverse
Mean pairwise identity 87.78
Mean single sequence MFE -21.61
Consensus MFE -20.86
Energy contribution -21.20
Covariance contribution 0.34
Combinations/Pair 1.09
Mean z-score -4.06
Structure conservation index 0.97
SVM decision value 2.37
SVM RNA-class probability 0.993041
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 606390 90 - 27905053
CCGAAACUAAAAUCGAAAGAAGAAAUCUCCAAUAAGAGUACAUAUUAAUGUGUUUACUUUUUAUGGAGUGCUUAAA-AAAUGGAGCGACAA
............((....))......(((((..(((((((.((((....)))).)))))))..)))))(((((...-.....))))).... ( -19.70)
>DroSec_CAF1 22465 87 - 1
-CGAAACCAAAAUCAAAA---GAAAUCUCCAAUAAGAGUAGAUUUUAGUGAGUUUACUCUUAAUGGAGUGCUUAAAAAAAUGGAGCUACAA
-.....(((.......((---(....(((((.(((((((((((((....))))))))))))).)))))..))).......)))........ ( -25.44)
>DroSim_CAF1 21622 88 - 1
ACGAAACUAAAAUAGAAA---GAAAUCUCCAAUAAGAGUAGAUUUUAGUGAGUUUACUCGUAAUGGAGUGCUUAAAAAAAUGGAGCUACAA
..................---.....(((((.((.((((((((((....)))))))))).)).))))).((((.........))))..... ( -19.70)
>consensus
_CGAAACUAAAAUCGAAA___GAAAUCUCCAAUAAGAGUAGAUUUUAGUGAGUUUACUCUUAAUGGAGUGCUUAAAAAAAUGGAGCUACAA
..........................(((((.(((((((((((((....))))))))))))).))))).((((.........))))..... (-20.86 = -21.20 +   0.34)

alignment

Postscript

secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:33:02 2006