Locus 5725

Sequence ID X_DroMel_CAF1
Location 14,813,341 – 14,813,483
Length 142
Max. P 0.959978
window9290 window9291 window9292

overview

Window 0

Location 14,813,341 – 14,813,443
Length 102
Sequences 3
Columns 104
Reading direction forward
Mean pairwise identity 81.61
Mean single sequence MFE -31.87
Consensus MFE -17.28
Energy contribution -17.53
Covariance contribution 0.25
Combinations/Pair 1.00
Mean z-score -3.14
Structure conservation index 0.54
SVM decision value 0.67
SVM RNA-class probability 0.818766
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 14813341 102 + 22224390
AGUGUGACAGUGUGCGUGUGCGUCUAAAUGUGUGUGUUUGUGAGAGUUGGUCAACCCACUAACACUUGCACACACUCGCA--CAAAAAGAAAGUGCCAAGAAUU
.........(.(..(.((((((.......((((((((..(((..(((.((....)).)))..)))..)))))))).))))--))........)..))....... ( -31.80)
>DroSec_CAF1 7352 104 + 1
AGUGUGCCAGUGUGCGUGUGCGUCUGAAUUUGUGUGUUUGUGAGUGUUGGUCAACCCACUAACACUUGCACACACUCGCACACAAAAAGAAAGUGCCAAGAAUU
.((((((.((((((.(..((((........))))..).((..(((((((((......)))))))))..)))))))).))))))..................... ( -36.60)
>DroYak_CAF1 141 78 + 1
AGUGUG----------UG--------------UGUGUUUGUGAGAGUUGGUCAACCCACUAACACUUGCACACACUCGCA--CAAAAAGAAAGUGCCAAGAAUU
.(((.(----------((--------------(((((..(((..(((.((....)).)))..)))..)))))))).))).--...................... ( -27.20)
>consensus
AGUGUG_CAGUGUGCGUGUGCGUCU_AAU_UGUGUGUUUGUGAGAGUUGGUCAACCCACUAACACUUGCACACACUCGCA__CAAAAAGAAAGUGCCAAGAAUU
.(((.........(((....)))..........((((.((..((.((((((......)))))).))..)).)))).)))......................... (-17.28 = -17.53 +   0.25)

alignment

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secondary structure

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dotplot

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Window 1

Location 14,813,341 – 14,813,443
Length 102
Sequences 3
Columns 104
Reading direction reverse
Mean pairwise identity 81.61
Mean single sequence MFE -30.17
Consensus MFE -17.52
Energy contribution -17.69
Covariance contribution 0.17
Combinations/Pair 1.00
Mean z-score -3.38
Structure conservation index 0.58
SVM decision value 1.51
SVM RNA-class probability 0.959978
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 14813341 102 - 22224390
AAUUCUUGGCACUUUCUUUUUG--UGCGAGUGUGUGCAAGUGUUAGUGGGUUGACCAACUCUCACAAACACACACAUUUAGACGCACACGCACACUGUCACACU
........((((.........)--)))..((((((((..(((((.(((((..........))))).)))))...(.....)..))))))))............. ( -28.80)
>DroSec_CAF1 7352 104 - 1
AAUUCUUGGCACUUUCUUUUUGUGUGCGAGUGUGUGCAAGUGUUAGUGGGUUGACCAACACUCACAAACACACAAAUUCAGACGCACACGCACACUGGCACACU
.....................((((((.((((((((...(((((.((((((........)))))).))))).........(.....).)))))))).)))))). ( -35.30)
>DroYak_CAF1 141 78 - 1
AAUUCUUGGCACUUUCUUUUUG--UGCGAGUGUGUGCAAGUGUUAGUGGGUUGACCAACUCUCACAAACACA--------------CA----------CACACU
........((((.........)--))).((((((((...(((((.(((((..........))))).))))).--------------))----------)))))) ( -26.40)
>consensus
AAUUCUUGGCACUUUCUUUUUG__UGCGAGUGUGUGCAAGUGUUAGUGGGUUGACCAACUCUCACAAACACACA_AUU_AGACGCACACGCACACUG_CACACU
........(((.............))).((((((.....(((((.(((((..........))))).)))))............((....)).......)))))) (-17.52 = -17.69 +   0.17)

alignment

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secondary structure

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dotplot

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Window 2

Location 14,813,367 – 14,813,483
Length 116
Sequences 3
Columns 118
Reading direction forward
Mean pairwise identity 91.76
Mean single sequence MFE -33.70
Consensus MFE -24.97
Energy contribution -25.30
Covariance contribution 0.33
Combinations/Pair 1.00
Mean z-score -3.13
Structure conservation index 0.74
SVM decision value 0.50
SVM RNA-class probability 0.760427
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 14813367 116 + 22224390
AAUGUGUGUGUUUGUGAGAGUUGGUCAACCCACUAACACUUGCACACACUCGCA--CAAAAAGAAAGUGCCAAGAAUUGGCAAGCAAUCGGUAGUUAAUUCAAUAUGGCCGUAAAACG
...((((((((..(((..(((.((....)).)))..)))..)))))))).....--..........(.((((.((((((((.(.(....).).))))))))....)))))........ ( -33.60)
>DroSec_CAF1 7378 118 + 1
AAUUUGUGUGUUUGUGAGUGUUGGUCAACCCACUAACACUUGCACACACUCGCACACAAAAAGAAAGUGCCAAGAAUUGGCAAGCAAUCGGUAGUUAAUUCAAUAUGGCCGUAAAACG
..(((((((((.((..(((((((((......)))))))))..)).......)))))))))......(.((((.((((((((.(.(....).).))))))))....)))))........ ( -35.70)
>DroYak_CAF1 149 110 + 1
------UGUGUUUGUGAGAGUUGGUCAACCCACUAACACUUGCACACACUCGCA--CAAAAAGAAAGUGCCAAGAAUUGGCAAGCAAUCGUUAGUUAAUUCAAUAUCGCAUUAAAGCG
------.((((.((..((.((((((......)))))).))..)).))))..(((--(.........))))...((((((((.(((....))).)))))))).....(((......))) ( -31.80)
>consensus
AAU_UGUGUGUUUGUGAGAGUUGGUCAACCCACUAACACUUGCACACACUCGCA__CAAAAAGAAAGUGCCAAGAAUUGGCAAGCAAUCGGUAGUUAAUUCAAUAUGGCCGUAAAACG
.......((((.((..((.((((((......)))))).))..)).))))...................((((.((((((((.(.(....).).))))))))....))))......... (-24.97 = -25.30 +   0.33)

alignment

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secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:54:54 2006