Locus 6231

Sequence ID 2L_DroMel_CAF1
Location 17,322,066 – 17,322,205
Length 139
Max. P 0.977720
window9957 window9958 window9959

overview

Window 7

Location 17,322,066 – 17,322,186
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 87.31
Mean single sequence MFE -39.68
Consensus MFE -29.98
Energy contribution -32.78
Covariance contribution 2.80
Combinations/Pair 1.08
Mean z-score -2.72
Structure conservation index 0.76
SVM decision value 1.80
SVM RNA-class probability 0.977720
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 17322066 120 - 22407834
GAUGGCAAGGUGGCAUGUUUGCCAUCGUUAUGAGGGCCAGAAGAUACGAACUAAACGAGAUUGCCAUUUCGAAGUUUGUACUUCUCUUAAAGUCCUUGAGCAGCUUGAGAGGGCUCUUGC
....(((((((((((....)))))))(((.(((((((.(((((.((((((((...((((((....)))))).)))))))))))))......))))))))))(((((....))))).)))) ( -42.50)
>DroSec_CAF1 19723 118 - 1
GACGGCAAGGUGGCAUGUUUGCCAUCGUUACGA--GCCAGAAGAUACAAACUAAACGAGAUUGCCAUUUCGAAGUUUGUACUUCUCUUAAAGUCCUUGAGCAGCUUGAGAGGGCUCUUGC
....(((((((((((....))))))).....((--((((((((.((((((((...((((((....)))))).))))))))))))).........((..((...))..))..))))))))) ( -42.40)
>DroSim_CAF1 22071 120 - 1
GAUGGUAAGGUGGCAUGUUUGCCAUCGUUACGAGGGCCAGAAGAUACAAACUAAACGAGAUUGCCAUUUCGAAGUUUGUACUUCUCUUAAAGUCCUUGAGCAGCUUGAGAGGGCUCUUGC
....(((((((((((....))))))).))))((((((.(((((.((((((((...((((((....)))))).)))))))))))))......))))))(((.(((((....)))))))).. ( -44.20)
>DroEre_CAF1 21634 93 - 1
-----------GGCAUGUUUGCCAUCGUUACG----------------AACUAAACGAGAUUGCCAUUUCGAAGUUUGUACUGCGCUUAAAGUCCUUGAGCAGCUUGAGCGGGCUCUUGC
-----------((((....))))...((((((----------------((((...((((((....)))))).))))))))..))((((((.....)))))).((..(((....)))..)) ( -27.90)
>DroYak_CAF1 14698 120 - 1
GAUGGCAAGGUGGCAUGUUUGCCAUCGUUACGAGGGCCAGAAGACACAAACUAAACGAGAUUGCUAUUUCGAAGUUUGCACUUCUCUUAAAGUCCUUAAGCAGCUUGAGAGGGCUCUUGC
(((((((((........)))))))))....(((((((((((((...((((((...((((((....)))))).))))))..))))).........((((((...))))))..)))))))). ( -41.40)
>consensus
GAUGGCAAGGUGGCAUGUUUGCCAUCGUUACGAGGGCCAGAAGAUACAAACUAAACGAGAUUGCCAUUUCGAAGUUUGUACUUCUCUUAAAGUCCUUGAGCAGCUUGAGAGGGCUCUUGC
........(((((((....)))))))....((((((((......((((((((...((((((....)))))).))))))))...(((((((.((.........))))))))))))))))). (-29.98 = -32.78 +   2.80)

alignment

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secondary structure

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dotplot

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Window 8

Location 17,322,106 – 17,322,205
Length 99
Sequences 4
Columns 99
Reading direction forward
Mean pairwise identity 95.45
Mean single sequence MFE -19.38
Consensus MFE -18.39
Energy contribution -18.33
Covariance contribution -0.06
Combinations/Pair 1.14
Mean z-score -2.22
Structure conservation index 0.95
SVM decision value 1.59
SVM RNA-class probability 0.965808
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 17322106 99 + 22407834
UACAAACUUCGAAAUGGCAAUCUCGUUUAGUUCGUAUCUUCUGGCCCUCAUAACGAUGGCAAACAUGCCACCUUGCCAUCACUCCCCUAUACUCAAUCU
.............(((((((..(((((......((........))......)))))(((((....)))))..))))))).................... ( -17.20)
>DroSec_CAF1 19763 97 + 1
UACAAACUUCGAAAUGGCAAUCUCGUUUAGUUUGUAUCUUCUGGC--UCGUAACGAUGGCAAACAUGCCACCUUGCCGUCACUCCCCUAUACUCAAUCU
((((((((.(((.((....)).)))...)))))))).....((((--..((((.(.(((((....)))))).)))).)))).................. ( -21.40)
>DroSim_CAF1 22111 99 + 1
UACAAACUUCGAAAUGGCAAUCUCGUUUAGUUUGUAUCUUCUGGCCCUCGUAACGAUGGCAAACAUGCCACCUUACCAUCACUCCCCUAUACUCAAUCU
((((((((.(((.((....)).)))...)))))))).............((((.(.(((((....)))))).))))....................... ( -18.20)
>DroYak_CAF1 14738 99 + 1
UGCAAACUUCGAAAUAGCAAUCUCGUUUAGUUUGUGUCUUCUGGCCCUCGUAACGAUGGCAAACAUGCCACCUUGCCAUCACUCCCCUAUACUCAAUCU
.(((((((.(((.((....)).)))...)))))))(((....))).........((((((((..........))))))))................... ( -20.70)
>consensus
UACAAACUUCGAAAUGGCAAUCUCGUUUAGUUUGUAUCUUCUGGCCCUCGUAACGAUGGCAAACAUGCCACCUUGCCAUCACUCCCCUAUACUCAAUCU
((((((((.(((.((....)).)))...))))))))..................((((((((..........))))))))................... (-18.39 = -18.33 +  -0.06)

alignment

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secondary structure

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dotplot

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Window 9

Location 17,322,106 – 17,322,205
Length 99
Sequences 4
Columns 99
Reading direction reverse
Mean pairwise identity 95.45
Mean single sequence MFE -25.88
Consensus MFE -23.49
Energy contribution -23.42
Covariance contribution -0.06
Combinations/Pair 1.11
Mean z-score -1.46
Structure conservation index 0.91
SVM decision value -0.01
SVM RNA-class probability 0.526914
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 17322106 99 - 22407834
AGAUUGAGUAUAGGGGAGUGAUGGCAAGGUGGCAUGUUUGCCAUCGUUAUGAGGGCCAGAAGAUACGAACUAAACGAGAUUGCCAUUUCGAAGUUUGUA
.....................((((..(((((((....))))))).........)))).....((((((((...((((((....)))))).)))))))) ( -25.40)
>DroSec_CAF1 19763 97 - 1
AGAUUGAGUAUAGGGGAGUGACGGCAAGGUGGCAUGUUUGCCAUCGUUACGA--GCCAGAAGAUACAAACUAAACGAGAUUGCCAUUUCGAAGUUUGUA
..............((.((((((.....((((((....))))))))))))..--.))......((((((((...((((((....)))))).)))))))) ( -27.30)
>DroSim_CAF1 22111 99 - 1
AGAUUGAGUAUAGGGGAGUGAUGGUAAGGUGGCAUGUUUGCCAUCGUUACGAGGGCCAGAAGAUACAAACUAAACGAGAUUGCCAUUUCGAAGUUUGUA
..............((.....(.(((((((((((....))))))).)))).)...))......((((((((...((((((....)))))).)))))))) ( -26.60)
>DroYak_CAF1 14738 99 - 1
AGAUUGAGUAUAGGGGAGUGAUGGCAAGGUGGCAUGUUUGCCAUCGUUACGAGGGCCAGAAGACACAAACUAAACGAGAUUGCUAUUUCGAAGUUUGCA
.................((..((((..(((((((....))))))).........))))....)).((((((...((((((....)))))).)))))).. ( -24.20)
>consensus
AGAUUGAGUAUAGGGGAGUGAUGGCAAGGUGGCAUGUUUGCCAUCGUUACGAGGGCCAGAAGAUACAAACUAAACGAGAUUGCCAUUUCGAAGUUUGUA
..............((.((((((.....((((((....)))))))))))).....))......((((((((...((((((....)))))).)))))))) (-23.49 = -23.42 +  -0.06)

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 12:05:54 2006