Locus 5292

Sequence ID 2R_DroMel_CAF1
Location 17,181,216 – 17,181,378
Length 162
Max. P 0.876004
window8461 window8462

overview

Window 1

Location 17,181,216 – 17,181,310
Length 94
Sequences 6
Columns 110
Reading direction forward
Mean pairwise identity 79.15
Mean single sequence MFE -36.85
Consensus MFE -23.56
Energy contribution -24.95
Covariance contribution 1.39
Combinations/Pair 1.26
Mean z-score -1.43
Structure conservation index 0.64
SVM decision value 0.16
SVM RNA-class probability 0.612876
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 17181216 94 + 20766785
UGUCUCUAGGAAUUCCCC-GACUUGUGACUCCGUGUGACUCCA------------CUGGGGGUUCGAGUUGGACCCCAC-AA--GGGGCGGGUUUUUGGGGGCUAACACG
.((((((((((((((.((-((((((.((((((..(((....))------------)..)))))))))))))).((((..-..--)))).))))))))))))))....... ( -43.30)
>DroSec_CAF1 6040 93 + 1
UGUCUCUAGGAAUUCCCC-GACUUGUGACUCCGUGUGGCUCCA------------CUGGGGGUUCGAGUUGGACCCCAC-AA--GGGGCG-GUUUUUGGGGGCUAACACG
.(((((((((((((..((-((((((.((((((..(((....))------------)..)))))))))))))).((((..-..--)))).)-))))))))))))....... ( -42.00)
>DroSim_CAF1 6034 93 + 1
UGUCUCUAGGAAUUCCCC-GACUUGUGACUCCGUGUGACUCCA------------CUGGGGGUUCGAGUUGGACCCCAC-AA--GGGGCG-GUUUUUGGGGGCUAACACG
.(((((((((((((..((-((((((.((((((..(((....))------------)..)))))))))))))).((((..-..--)))).)-))))))))))))....... ( -40.60)
>DroEre_CAF1 6087 106 + 1
UGUCUUUAGGAAUUCCCC-GAGUUGUGACUCCGUGUGACUCCGCUUU-UGCUGGACUUGGGGUGCGAGUUGGACCCCUAAAA-GGGGGCG-GUUUUUGGGGGCUAACACG
.((((((((((((..(((-((.((((.((((((......(((((...-.)).)))..)))))))))).)))).((((.....-)))))..-))))))))))))....... ( -37.70)
>DroYak_CAF1 5902 107 + 1
UGUCUUUAGGAAUUCCCC-GACUUGUGACUCCGUGUGACUCCACUUUCUGCUGGACUUGUGGUGCGAGUUGUACCCCCCCAA-GGGGGCG-GUGUUUGGGGGCUAACACG
.....((((....(((((-((...(..((((.(..(.(((((((.....).))))...)).)..)))))..)(((((((...-.)))).)-))..))))))))))).... ( -35.90)
>DroAna_CAF1 6923 89 + 1
UGUCUCUUGGAAUUCCCCUGACUUUGGACUCCGU--GACUCCA------------CUUUUUUGUUGAACUGAGCUGACC-AAGUUGGGCG-GU-----GGGGCUAUCACG
.(((....((....))...))).........(((--(((((((------------((.....(((.((((.........-.)))).))))-))-----))))...))))) ( -21.60)
>consensus
UGUCUCUAGGAAUUCCCC_GACUUGUGACUCCGUGUGACUCCA____________CUGGGGGUUCGAGUUGGACCCCAC_AA__GGGGCG_GUUUUUGGGGGCUAACACG
.((((((((((((.((((......((.((.....)).))...................(((((((.....))))))).......))))...))))))))))))....... (-23.56 = -24.95 +   1.39)

alignment

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secondary structure

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dotplot

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Window 2

Location 17,181,273 – 17,181,378
Length 105
Sequences 6
Columns 110
Reading direction reverse
Mean pairwise identity 80.93
Mean single sequence MFE -36.54
Consensus MFE -30.03
Energy contribution -30.28
Covariance contribution 0.25
Combinations/Pair 1.08
Mean z-score -1.87
Structure conservation index 0.82
SVM decision value 0.89
SVM RNA-class probability 0.876004
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 17181273 105 - 20766785
AAAG--CCACGAAUCCCUCGGAACGGGGGGACUUUUAAGUGGCAGUGCCGGAGAAAUCCUUGGCUAAUGUCGUGUUAGCCCCCAAAAACCCGCCCC--UU-GUGGGGUCC
...(--((((...((((((......)))))).......)))))......(((....)))..(((((((.....)))))))...........(((((--..-..))))).. ( -39.30)
>DroSec_CAF1 6097 103 - 1
AAAG--CCACGAAAACCUCGGAACGGG-GGACUUUUAAGUGGCAGUGCCGGAGAAAUCCUUGGCUAAUGUCGUGUUAGCCCCCAAAAAC-CGCCCC--UU-GUGGGGUCC
....--...(((.....)))....(((-((.((..((...((((..((((((....)))..)))...)))).))..)))))))......-.(((((--..-..))))).. ( -37.00)
>DroSim_CAF1 6091 104 - 1
AAAG--CCACGAAACCCUCGGAACGGGGGGACUUUUAAGUGGCAGUGCCGGAGAAAUCCUUGGCUAAUGUCGUGUUAGCCCCCAAAAAC-CGCCCC--UU-GUGGGGUCC
...(--((((....((((((...)))))).........)))))......(((....)))..(((((((.....))))))).........-.(((((--..-..))))).. ( -38.42)
>DroEre_CAF1 6155 96 - 1
AAAA--CCACCA---------GUG-GGGGGACUUUUAAGUGGCAGUGCCGGAGAAAUCCUUGGCUAAUGUCGUGUUAGCCCCCAAAAAC-CGCCCCC-UUUUAGGGGUCC
....--......---------...-(((((.((..((...((((..((((((....)))..)))...)))).))..)))))))......-.(((((.-.....))))).. ( -34.40)
>DroYak_CAF1 5971 99 - 1
AAAAACCCACCA---------GAGAGGGGGACUUUUAAGUGGCAGUGCCGGAGAAAUCCUUGGCUAAUGUCGUGUUAGCCCCCAAACAC-CGCCCCC-UUGGGGGGGUAC
....((((.((.---------..(((((((..........((((..((((((....)))..)))...))))(((((........)))))-..)))))-))..)))))).. ( -41.70)
>DroAna_CAF1 6979 86 - 1
-------CAUUU---------GAG-GGGGGACUUUUAAGUGGCAGUGCCGGAGAAAUCCUUGGCUAAUGUCGUGAUAGCCCC-----AC-CGCCCAACUU-GGUCAGCUC
-------...((---------(((-(((((.((.(((...((((..((((((....)))..)))...)))).))).))))))-----.)-)..((.....-))))))... ( -28.40)
>consensus
AAAG__CCACGA_________AACGGGGGGACUUUUAAGUGGCAGUGCCGGAGAAAUCCUUGGCUAAUGUCGUGUUAGCCCCCAAAAAC_CGCCCC__UU_GUGGGGUCC
.........................(((((.((..((...((((..((((((....)))..)))...)))).))..)))))))........(((((.......))))).. (-30.03 = -30.28 +   0.25)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:41:25 2006