Locus 3191

Sequence ID 2L_DroMel_CAF1
Location 9,110,033 – 9,110,220
Length 187
Max. P 0.999884
window5069 window5070 window5071 window5072

overview

Window 9

Location 9,110,033 – 9,110,142
Length 109
Sequences 5
Columns 110
Reading direction forward
Mean pairwise identity 94.70
Mean single sequence MFE -20.94
Consensus MFE -16.44
Energy contribution -16.88
Covariance contribution 0.44
Combinations/Pair 1.04
Mean z-score -2.43
Structure conservation index 0.79
SVM decision value 1.31
SVM RNA-class probability 0.940985
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 9110033 109 + 22407834
GAACAGAAUUUAAUAAAACCUAUUUCCAUUUAUUAAAUUCUUCUCUUCAUCGUCGCCUCUAAUU-UUGCUUUGCCACAAACUUUGGCCGGUUUUCCCGACAGCCGUGGCA
((..(((((((((((((...........)))))))))))))..)).........(((.......-.......((((.......))))(((((........))))).))). ( -22.80)
>DroSec_CAF1 12149 109 + 1
GAACAGAAUUUAAUAAAACCUUCUUCCAUUUAUUAAAUUCUUCUCUUCAUCGUCGCCUCUAAUU-UUGUUUUGCCACAAACUUUUGCCGGUUUCCCCGACAGCCGUGGCA
((..(((((((((((((...........)))))))))))))..))...................-......((((((......(((.(((.....))).)))..)))))) ( -20.60)
>DroSim_CAF1 12269 110 + 1
GAACAGAAUUUAAUAAAACCUAUUUCCAUUUAUUAAAUUCUUCUCUUCAUCGUCGCCUCUAAUUUUUGUUUUGCCACAAACUUUUGCCGGUUUCCCUGACAGCCGUGGCA
((..(((((((((((((...........)))))))))))))..)).........(((.......(((((......))))).......(((((........))))).))). ( -19.90)
>DroEre_CAF1 12246 108 + 1
GAACAGAAUUUAAUAAAACCUAUUUCCAUUUAUUAAAUUCUUCUGCUCAUCGUCGCCUCUAAUU-UUGUUUUGCCACAAACUUUGGCCGCUUUU-CCGGCAGCCGUGGCA
(((((((((((((((((...........))))))))))))....((........))........-.)))))((((((.......(((.(((...-..))).))))))))) ( -24.21)
>DroYak_CAF1 17208 109 + 1
GAACAGAAUUUAAUAAAACCUAUUUCCAUUUAUUAAAUUCUUCUCUUCAUCGUCGCCUCUAAUU-UUGUUUUGCCACAAACUUUUGCCGCCUUUCCCGACAGCCGUGGCA
((..(((((((((((((...........)))))))))))))..))...................-......((((((...((.(((..........))).))..)))))) ( -17.20)
>consensus
GAACAGAAUUUAAUAAAACCUAUUUCCAUUUAUUAAAUUCUUCUCUUCAUCGUCGCCUCUAAUU_UUGUUUUGCCACAAACUUUUGCCGGUUUUCCCGACAGCCGUGGCA
((..(((((((((((((...........)))))))))))))..))..........................((((((...(....)..((((........)))))))))) (-16.44 = -16.88 +   0.44)

alignment

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secondary structure

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dotplot

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Window 0

Location 9,110,033 – 9,110,142
Length 109
Sequences 5
Columns 110
Reading direction reverse
Mean pairwise identity 94.70
Mean single sequence MFE -30.48
Consensus MFE -26.94
Energy contribution -27.22
Covariance contribution 0.28
Combinations/Pair 1.06
Mean z-score -3.49
Structure conservation index 0.88
SVM decision value 4.38
SVM RNA-class probability 0.999884
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 9110033 109 - 22407834
UGCCACGGCUGUCGGGAAAACCGGCCAAAGUUUGUGGCAAAGCAA-AAUUAGAGGCGACGAUGAAGAGAAGAAUUUAAUAAAUGGAAAUAGGUUUUAUUAAAUUCUGUUC
(((((((((((((((.....)))))...)).))))))))......-..(((..(....)..))).(((.(((((((((((((...........))))))))))))).))) ( -31.00)
>DroSec_CAF1 12149 109 - 1
UGCCACGGCUGUCGGGGAAACCGGCAAAAGUUUGUGGCAAAACAA-AAUUAGAGGCGACGAUGAAGAGAAGAAUUUAAUAAAUGGAAGAAGGUUUUAUUAAAUUCUGUUC
(((((((((((((((.....)))))...)).))))))))......-..(((..(....)..))).(((.(((((((((((((...........))))))))))))).))) ( -31.00)
>DroSim_CAF1 12269 110 - 1
UGCCACGGCUGUCAGGGAAACCGGCAAAAGUUUGUGGCAAAACAAAAAUUAGAGGCGACGAUGAAGAGAAGAAUUUAAUAAAUGGAAAUAGGUUUUAUUAAAUUCUGUUC
(((((((((((((.((....)))))...)).)))))))).........(((..(....)..))).(((.(((((((((((((...........))))))))))))).))) ( -30.20)
>DroEre_CAF1 12246 108 - 1
UGCCACGGCUGCCGG-AAAAGCGGCCAAAGUUUGUGGCAAAACAA-AAUUAGAGGCGACGAUGAGCAGAAGAAUUUAAUAAAUGGAAAUAGGUUUUAUUAAAUUCUGUUC
.(((..((((((...-....))))))....(((((......))))-)......)))......(((((((...((((((((((...........))))))))))))))))) ( -30.70)
>DroYak_CAF1 17208 109 - 1
UGCCACGGCUGUCGGGAAAGGCGGCAAAAGUUUGUGGCAAAACAA-AAUUAGAGGCGACGAUGAAGAGAAGAAUUUAAUAAAUGGAAAUAGGUUUUAUUAAAUUCUGUUC
(((((((((((((......)))))).......)))))))......-..(((..(....)..))).(((.(((((((((((((...........))))))))))))).))) ( -29.51)
>consensus
UGCCACGGCUGUCGGGAAAACCGGCAAAAGUUUGUGGCAAAACAA_AAUUAGAGGCGACGAUGAAGAGAAGAAUUUAAUAAAUGGAAAUAGGUUUUAUUAAAUUCUGUUC
(((((((((((((((.....)))))...)).)))))))).(((.....(((..(....)..))).....(((((((((((((...........)))))))))))))))). (-26.94 = -27.22 +   0.28)

alignment

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secondary structure

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dotplot

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Window 1

Location 9,110,065 – 9,110,182
Length 117
Sequences 5
Columns 118
Reading direction reverse
Mean pairwise identity 91.65
Mean single sequence MFE -33.42
Consensus MFE -26.66
Energy contribution -27.86
Covariance contribution 1.20
Combinations/Pair 1.10
Mean z-score -2.86
Structure conservation index 0.80
SVM decision value 2.47
SVM RNA-class probability 0.994321
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 9110065 117 - 22407834
UGAAUUGCGCCAGUAGUCGUGGAUGCGCAAGAUAAACAUUUGCCACGGCUGUCGGGAAAACCGGCCAAAGUUUGUGGCAAAGCAA-AAUUAGAGGCGACGAUGAAGAGAAGAAUUUAA
...((((((((..((((..((....(....).......(((((((((((((((((.....)))))...)).)))))))))).)).-.))))..)))).))))................ ( -34.80)
>DroSec_CAF1 12181 111 - 1
UGAAUUGCGCCAGUAU------AUGUGCAAGAUAAACAUUUGCCACGGCUGUCGGGGAAACCGGCAAAAGUUUGUGGCAAAACAA-AAUUAGAGGCGACGAUGAAGAGAAGAAUUUAA
...((((((((.(((.------...)))..........(((((((((((((((((.....)))))...)).))))))))))....-.......)))).))))................ ( -31.70)
>DroSim_CAF1 12301 118 - 1
UGAAUUGCGCCAGUAAUCGUGGAUGCCCAAGAUAAACAUUUGCCACGGCUGUCAGGGAAACCGGCAAAAGUUUGUGGCAAAACAAAAAUUAGAGGCGACGAUGAAGAGAAGAAUUUAA
...((((((((....(((.(((....))).))).....(((((((((((((((.((....)))))...)).))))))))))............)))).))))................ ( -34.70)
>DroEre_CAF1 12278 116 - 1
UGAAUUGCGCCAGUAGUCGUGGAUGUGCAAGAUAAACAUUUGCCACGGCUGCCGG-AAAAGCGGCCAAAGUUUGUGGCAAAACAA-AAUUAGAGGCGACGAUGAGCAGAAGAAUUUAA
((.((((((((.((((((((((..(((.........)))...))))))))))...-.......((((.......)))).......-.......)))).))))...))........... ( -33.50)
>DroYak_CAF1 17240 117 - 1
UGAAUUGCGCCAGUGGUUGUGGAUGUGCAAGAUAAACAUUUGCCACGGCUGUCGGGAAAGGCGGCAAAAGUUUGUGGCAAAACAA-AAUUAGAGGCGACGAUGAAGAGAAGAAUUUAA
...((((((((..(((((.(((((((.........)))))(((((((((((((......)))))).......)))))))...)).-)))))..)))).))))................ ( -32.41)
>consensus
UGAAUUGCGCCAGUAGUCGUGGAUGUGCAAGAUAAACAUUUGCCACGGCUGUCGGGAAAACCGGCAAAAGUUUGUGGCAAAACAA_AAUUAGAGGCGACGAUGAAGAGAAGAAUUUAA
...((((((((....(((.((......)).))).....(((((((((((((((((.....)))))...)).))))))))))............)))).))))................ (-26.66 = -27.86 +   1.20)

alignment

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secondary structure

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dotplot

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Window 2

Location 9,110,102 – 9,110,220
Length 118
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 92.42
Mean single sequence MFE -37.03
Consensus MFE -29.48
Energy contribution -31.60
Covariance contribution 2.12
Combinations/Pair 1.05
Mean z-score -2.25
Structure conservation index 0.80
SVM decision value 1.58
SVM RNA-class probability 0.965398
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 9110102 118 - 22407834
-CCAACUACAGAUAUUUGCAUUUCUUGAGGU-UUGCUUUAUGAAUUGCGCCAGUAGUCGUGGAUGCGCAAGAUAAACAUUUGCCACGGCUGUCGGGAAAACCGGCCAAAGUUUGUGGCAA
-....((((((((....(((.(((.(((((.-...))))).))).)))(((.((((((((((...(....)...........))))))))).)((.....)))))....))))))))... ( -38.24)
>DroSec_CAF1 12218 112 - 1
-CCAACUACAGAUAUUUGCAUUUCUUGAGGU-UUGCUUUAUGAAUUGCGCCAGUAU------AUGUGCAAGAUAAACAUUUGCCACGGCUGUCGGGGAAACCGGCAAAAGUUUGUGGCAA
-................(((.(((.(((((.-...))))).))).)))(((.(((.------...)))...((((((.((((((.((.....))((....)))))))).))))))))).. ( -34.50)
>DroSim_CAF1 12339 119 - 1
-CCAACUACAGAUAUUUGCAUUUCUUGAGGUUUUGCUUUAUGAAUUGCGCCAGUAAUCGUGGAUGCCCAAGAUAAACAUUUGCCACGGCUGUCAGGGAAACCGGCAAAAGUUUGUGGCAA
-....((((((((.(((((...(((((.(((.....(((((((.((((....))))))))))).)))))))).........((....)).....((....)).))))).))))))))... ( -35.50)
>DroEre_CAF1 12315 117 - 1
-CCAACUACAGAUAUUUGCAUUUCUUGAGGU-UUGCUUUAUGAAUUGCGCCAGUAGUCGUGGAUGUGCAAGAUAAACAUUUGCCACGGCUGCCGG-AAAAGCGGCCAAAGUUUGUGGCAA
-....((((((((....(((.(((.(((((.-...))))).))).))).((.((((((((((..(((.........)))...)))))))))).))-.............))))))))... ( -38.10)
>DroYak_CAF1 17277 119 - 1
ACCAACUACAGAUAUUUGCAUUUCUUGAGGU-UUGCUUUAUGAAUUGCGCCAGUGGUUGUGGAUGUGCAAGAUAAACAUUUGCCACGGCUGUCGGGAAAGGCGGCAAAAGUUUGUGGCAA
.....((((((((.((((((.(((.(((((.-...))))).))).)))((((((.((.(..(((((.........)))))..).)).)))(((......))))))))).))))))))... ( -38.80)
>consensus
_CCAACUACAGAUAUUUGCAUUUCUUGAGGU_UUGCUUUAUGAAUUGCGCCAGUAGUCGUGGAUGUGCAAGAUAAACAUUUGCCACGGCUGUCGGGAAAACCGGCAAAAGUUUGUGGCAA
.....((((((((....(((.(((.(((((.....))))).))).)))(((.((((((((((((((.........))))...))))))))).).((....)))))....))))))))... (-29.48 = -31.60 +   2.12)

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 10:46:34 2006