Locus 6727

Sequence ID X_DroMel_CAF1
Location 16,749,414 – 16,749,586
Length 172
Max. P 0.999952
window10980 window10981 window10982 window10983 window10984

overview

Window 0

Location 16,749,414 – 16,749,534
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 92.33
Mean single sequence MFE -32.19
Consensus MFE -26.76
Energy contribution -26.68
Covariance contribution -0.08
Combinations/Pair 1.18
Mean z-score -1.95
Structure conservation index 0.83
SVM decision value 1.61
SVM RNA-class probability 0.967705
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 16749414 120 + 22224390
GGUCGCCAAAAGAUUUUAAAUCAUUAUUCACUCGAAUUCCCUAACGUACCCGCAAUUUUGAUGUCGGAUAAUUUGGCACAAAUGGGGUUUUGUGGGUGGUCCACACCCACACGCCCAUCU
.((.((((((.(((.....))).(((((((((((((....................))))).)).)))))))))))))).....((((..((((((((.....)))))))).)))).... ( -35.25)
>DroSec_CAF1 36630 120 + 1
GGUCGCCAAAAGAUUUUAAAUCAUUAUUCACUCGAAUUCCCUAACGUACCCGUAAUUUUUAUGUCGGAUAAUUUGGCACAAAUGGGGUUUUGUGGGUGGUCCACACCCACACGCCCAUCU
.((.((((((.(((.....))).((((((((..(((.......(((....)))....)))..)).)))))))))))))).....((((..((((((((.....)))))))).)))).... ( -33.30)
>DroSim_CAF1 34982 120 + 1
GGUCGCCAAAAGAUUUUAAAUCAUUAUUCACUCGAAUUCCCUAACGUACCCGCAAUUUUUAUGUCGGAUAAUUUGGCGCAAAUGGGGUUUUGUGGGUGGUCCACACCCACACGCCCAUCU
.(.(((((((.(((.....)))...........................(((((.......)).)))....)))))))).....((((..((((((((.....)))))))).)))).... ( -34.80)
>DroEre_CAF1 28278 120 + 1
GGUCGCUUACAGAUUUUAAAUCAUUAUUCACUUGAGUUCCCUUACGUACCUGCAAUUUUUAUGUCGGAUAAUUUGGCACAAAUGGCAUUUUGUGGGUGGUCCACACCCACACACCCAUCU
(((((......(((.....)))...((((....)))).......)).)))(((....(((.(((((((...))))))).)))..)))...((((((((.....))))))))......... ( -25.80)
>DroYak_CAF1 28144 120 + 1
GGUGGCUUGUAGAUUUGAAAUCAUUAUUCACUUGACUUUCCUUACGUACCCGCAAUUUUGAUGUCGGCUAAUUUGGCACAAAUGGCAUUUUGUGGGUGGUCCACACCCACACGCCCAUCU
.((((..(((((....(((((((.........))).)))).)))))...))))......((((..(((.....((.((....)).))...((((((((.....)))))))).))))))). ( -31.80)
>consensus
GGUCGCCAAAAGAUUUUAAAUCAUUAUUCACUCGAAUUCCCUAACGUACCCGCAAUUUUUAUGUCGGAUAAUUUGGCACAAAUGGGGUUUUGUGGGUGGUCCACACCCACACGCCCAUCU
.((.(((((..(((.....)))...........................(((((.......)).))).....)))))))..(((((....((((((((.....))))))))..))))).. (-26.76 = -26.68 +  -0.08)

alignment

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secondary structure

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dotplot

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Window 1

Location 16,749,414 – 16,749,534
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 92.33
Mean single sequence MFE -34.70
Consensus MFE -26.94
Energy contribution -29.50
Covariance contribution 2.56
Combinations/Pair 1.06
Mean z-score -1.88
Structure conservation index 0.78
SVM decision value 0.67
SVM RNA-class probability 0.816929
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 16749414 120 - 22224390
AGAUGGGCGUGUGGGUGUGGACCACCCACAAAACCCCAUUUGUGCCAAAUUAUCCGACAUCAAAAUUGCGGGUACGUUAGGGAAUUCGAGUGAAUAAUGAUUUAAAAUCUUUUGGCGACC
(((((((..((((((((.....))))))))....))))))).(((((((.((((((.((.......)))))))).............((.(((((....)))))...)).)))))))... ( -38.50)
>DroSec_CAF1 36630 120 - 1
AGAUGGGCGUGUGGGUGUGGACCACCCACAAAACCCCAUUUGUGCCAAAUUAUCCGACAUAAAAAUUACGGGUACGUUAGGGAAUUCGAGUGAAUAAUGAUUUAAAAUCUUUUGGCGACC
(((((((..((((((((.....))))))))....))))))).(((((((.((((((............)))))).............((.(((((....)))))...)).)))))))... ( -36.00)
>DroSim_CAF1 34982 120 - 1
AGAUGGGCGUGUGGGUGUGGACCACCCACAAAACCCCAUUUGCGCCAAAUUAUCCGACAUAAAAAUUGCGGGUACGUUAGGGAAUUCGAGUGAAUAAUGAUUUAAAAUCUUUUGGCGACC
(((((((..((((((((.....))))))))....))))))).(((((((.((((((.((.......)))))))).............((.(((((....)))))...)).)))))))... ( -40.30)
>DroEre_CAF1 28278 120 - 1
AGAUGGGUGUGUGGGUGUGGACCACCCACAAAAUGCCAUUUGUGCCAAAUUAUCCGACAUAAAAAUUGCAGGUACGUAAGGGAACUCAAGUGAAUAAUGAUUUAAAAUCUGUAAGCGACC
((((((...((((((((.....)))))))).....)))))).(((....((((.....))))...((((((((.(....)..........(((((....)))))..)))))))))))... ( -26.70)
>DroYak_CAF1 28144 120 - 1
AGAUGGGCGUGUGGGUGUGGACCACCCACAAAAUGCCAUUUGUGCCAAAUUAGCCGACAUCAAAAUUGCGGGUACGUAAGGAAAGUCAAGUGAAUAAUGAUUUCAAAUCUACAAGCCACC
.((((((((((((((((.....))))))))...))))..(((.((.......)))))))))....(((((....)))))((...((....((((.......)))).....))...))... ( -32.00)
>consensus
AGAUGGGCGUGUGGGUGUGGACCACCCACAAAACCCCAUUUGUGCCAAAUUAUCCGACAUAAAAAUUGCGGGUACGUUAGGGAAUUCGAGUGAAUAAUGAUUUAAAAUCUUUUGGCGACC
(((((((..((((((((.....))))))))....))))))).((((((..((((((.((.......))))))))(((((....((....))...)))))............))))))... (-26.94 = -29.50 +   2.56)

alignment

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secondary structure

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dotplot

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Window 2

Location 16,749,454 – 16,749,574
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 95.67
Mean single sequence MFE -36.68
Consensus MFE -32.98
Energy contribution -33.06
Covariance contribution 0.08
Combinations/Pair 1.07
Mean z-score -1.26
Structure conservation index 0.90
SVM decision value 0.37
SVM RNA-class probability 0.708515
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 16749454 120 + 22224390
CUAACGUACCCGCAAUUUUGAUGUCGGAUAAUUUGGCACAAAUGGGGUUUUGUGGGUGGUCCACACCCACACGCCCAUCUAUGGCCAUGUGACGUGCUGUAUCUGAUGGAUACUUUUUGG
.....((((.((((..((((....)))).....((((.......((((..((((((((.....)))))))).)))).......))))))))..)))).(((((.....)))))....... ( -39.34)
>DroSec_CAF1 36670 120 + 1
CUAACGUACCCGUAAUUUUUAUGUCGGAUAAUUUGGCACAAAUGGGGUUUUGUGGGUGGUCCACACCCACACGCCCAUCUAUGGCCAUGUGACGCGCUGUAUCUGAUGGAUACUUUUUGG
.....(((.(((((.....)))((((((((...((((.......((((..((((((((.....)))))))).)))).......)))).(((...)))..)))))))))).)))....... ( -37.94)
>DroSim_CAF1 35022 120 + 1
CUAACGUACCCGCAAUUUUUAUGUCGGAUAAUUUGGCGCAAAUGGGGUUUUGUGGGUGGUCCACACCCACACGCCCAUCUAUGGCCAUGUGACGCGCUGUAUCUGAUGGAUACUUUUUGG
.....(((.((...........((((((((....(((((.....((((..((((((((.....)))))))).)))).(((((....))).)).))))).)))))))))).)))....... ( -38.80)
>DroEre_CAF1 28318 120 + 1
CUUACGUACCUGCAAUUUUUAUGUCGGAUAAUUUGGCACAAAUGGCAUUUUGUGGGUGGUCCACACCCACACACCCAUCUAAGGCCAUGUGACGCGCUGUAUCUGAUGGAUACUUUUUGG
.((((((.((.(((.......))).)).......(((....((((.....((((((((.....))))))))...)))).....)))))))))......(((((.....)))))....... ( -33.00)
>DroYak_CAF1 28184 120 + 1
CUUACGUACCCGCAAUUUUGAUGUCGGCUAAUUUGGCACAAAUGGCAUUUUGUGGGUGGUCCACACCCACACGCCCAUCUAUGGCCAUGUGACGCGCUGUAUCUGAUGGAUACUUUUUGG
.....(((.(((((.....((((.((((..((.((((.((.((((.....((((((((.....))))))))...))))...)))))).)).....)))))))))).))).)))....... ( -34.30)
>consensus
CUAACGUACCCGCAAUUUUUAUGUCGGAUAAUUUGGCACAAAUGGGGUUUUGUGGGUGGUCCACACCCACACGCCCAUCUAUGGCCAUGUGACGCGCUGUAUCUGAUGGAUACUUUUUGG
....(((..(((((.......)).)))......((((....(((((....((((((((.....))))))))..))))).....))))....)))....(((((.....)))))....... (-32.98 = -33.06 +   0.08)

alignment

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secondary structure

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dotplot

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Window 3

Location 16,749,454 – 16,749,574
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 95.67
Mean single sequence MFE -41.28
Consensus MFE -37.98
Energy contribution -39.02
Covariance contribution 1.04
Combinations/Pair 1.03
Mean z-score -3.48
Structure conservation index 0.92
SVM decision value 4.81
SVM RNA-class probability 0.999952
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 16749454 120 - 22224390
CCAAAAAGUAUCCAUCAGAUACAGCACGUCACAUGGCCAUAGAUGGGCGUGUGGGUGUGGACCACCCACAAAACCCCAUUUGUGCCAAAUUAUCCGACAUCAAAAUUGCGGGUACGUUAG
.......(((((.....)))))...(((.....((((.(((((((((..((((((((.....))))))))....)))))))))))))...((((((.((.......)))))))))))... ( -44.20)
>DroSec_CAF1 36670 120 - 1
CCAAAAAGUAUCCAUCAGAUACAGCGCGUCACAUGGCCAUAGAUGGGCGUGUGGGUGUGGACCACCCACAAAACCCCAUUUGUGCCAAAUUAUCCGACAUAAAAAUUACGGGUACGUUAG
.......(((((.....)))))((((.......((((.(((((((((..((((((((.....))))))))....)))))))))))))...((((((............)))))))))).. ( -43.00)
>DroSim_CAF1 35022 120 - 1
CCAAAAAGUAUCCAUCAGAUACAGCGCGUCACAUGGCCAUAGAUGGGCGUGUGGGUGUGGACCACCCACAAAACCCCAUUUGCGCCAAAUUAUCCGACAUAAAAAUUGCGGGUACGUUAG
.......(((((.....)))))((((.......((((..((((((((..((((((((.....))))))))....)))))))).))))...((((((.((.......)))))))))))).. ( -42.80)
>DroEre_CAF1 28318 120 - 1
CCAAAAAGUAUCCAUCAGAUACAGCGCGUCACAUGGCCUUAGAUGGGUGUGUGGGUGUGGACCACCCACAAAAUGCCAUUUGUGCCAAAUUAUCCGACAUAAAAAUUGCAGGUACGUAAG
.......(((((.....)))))...((((....((((..(((((((...((((((((.....)))))))).....))))))).))))......((..((.......))..)).))))... ( -35.30)
>DroYak_CAF1 28184 120 - 1
CCAAAAAGUAUCCAUCAGAUACAGCGCGUCACAUGGCCAUAGAUGGGCGUGUGGGUGUGGACCACCCACAAAAUGCCAUUUGUGCCAAAUUAGCCGACAUCAAAAUUGCGGGUACGUAAG
.......(((((.....)))))...((((.((.((((.((((((((...((((((((.....)))))))).....))))))))))))......(((.((.......)))))))))))... ( -41.10)
>consensus
CCAAAAAGUAUCCAUCAGAUACAGCGCGUCACAUGGCCAUAGAUGGGCGUGUGGGUGUGGACCACCCACAAAACCCCAUUUGUGCCAAAUUAUCCGACAUAAAAAUUGCGGGUACGUUAG
.......(((((.....)))))...((((.((.((((.(((((((((..((((((((.....))))))))....)))))))))))))......(((.((.......)))))))))))... (-37.98 = -39.02 +   1.04)

alignment

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secondary structure

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dotplot

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Window 4

Location 16,749,494 – 16,749,586
Length 92
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 84.85
Mean single sequence MFE -28.74
Consensus MFE -25.34
Energy contribution -25.02
Covariance contribution -0.32
Combinations/Pair 1.09
Mean z-score -1.90
Structure conservation index 0.88
SVM decision value 1.15
SVM RNA-class probability 0.922764
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 16749494 92 - 22224390
----------------------------CAAUUCCAAAUCCCAAAAAGUAUCCAUCAGAUACAGCACGUCACAUGGCCAUAGAUGGGCGUGUGGGUGUGGACCACCCACAAAACCCCAUU
----------------------------...................(((((.....))))).....(((....)))....((((((..((((((((.....))))))))....)))))) ( -26.60)
>DroSec_CAF1 36710 113 - 1
GUUCCCCUGUUCCGCAAGC-------CUCAAUCCCAAAUCCCAAAAAGUAUCCAUCAGAUACAGCGCGUCACAUGGCCAUAGAUGGGCGUGUGGGUGUGGACCACCCACAAAACCCCAUU
....((.(((..(((..(.-------..)..................(((((.....)))))...)))..))).)).....((((((..((((((((.....))))))))....)))))) ( -31.00)
>DroSim_CAF1 35062 113 - 1
UUUCCCCUGUUCCGCAAAC-------CUCAAUCCCAAAUCCCAAAAAGUAUCCAUCAGAUACAGCGCGUCACAUGGCCAUAGAUGGGCGUGUGGGUGUGGACCACCCACAAAACCCCAUU
....((.(((..(((....-------....((.....))........(((((.....)))))...)))..))).)).....((((((..((((((((.....))))))))....)))))) ( -30.40)
>DroEre_CAF1 28358 112 - 1
GU-CGCCUGUUCCCCAAUC-------CGCAAUCCCAAAUCCCAAAAAGUAUCCAUCAGAUACAGCGCGUCACAUGGCCUUAGAUGGGUGUGUGGGUGUGGACCACCCACAAAAUGCCAUU
..-.((..........(((-------((((..((((...........(((((.....))))).....(((....)))......))))..)))))))((((.....)))).....)).... ( -27.20)
>DroYak_CAF1 28224 119 - 1
GU-UUCCCAAUCCCCAAUCCACAAACCGCAAUCCCAAAUCCCAAAAAGUAUCCAUCAGAUACAGCGCGUCACAUGGCCAUAGAUGGGCGUGUGGGUGUGGACCACCCACAAAAUGCCAUU
..-........................(((.........(((.....(((((.....))))).(((((((.(((........)))))))))))))(((((.....)))))...))).... ( -28.50)
>consensus
GU_CCCCUGUUCCCCAAUC_______CGCAAUCCCAAAUCCCAAAAAGUAUCCAUCAGAUACAGCGCGUCACAUGGCCAUAGAUGGGCGUGUGGGUGUGGACCACCCACAAAACCCCAUU
.......................................(((.....(((((.....))))).(((((((.(((........)))))))))))))(((((.....))))).......... (-25.34 = -25.02 +  -0.32)

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 12:21:02 2006