Locus 1104

Sequence ID 3R_DroMel_CAF1
Location 3,343,884 – 3,344,072
Length 188
Max. P 0.993355
window1806 window1807 window1808

overview

Window 6

Location 3,343,884 – 3,343,996
Length 112
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 74.15
Mean single sequence MFE -28.03
Consensus MFE -20.17
Energy contribution -20.73
Covariance contribution 0.56
Combinations/Pair 1.07
Mean z-score -1.20
Structure conservation index 0.72
SVM decision value 0.18
SVM RNA-class probability 0.623492
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 3343884 112 + 27905053
AUCG-------GCAGCAGACUUUUAUUAUCGUGUAUAUAUGAAAGUAUGUUAUUAUCCUUCGCAGACGCUACUGGUACGCUUCGUCACUACGUGGACUACCUG-ACGUCCAAAGUGAUGA
...(-------((((((.((((((((............)))))))).))))...........(((......)))....)))((((((((...(((((......-..))))).)))))))) ( -28.30)
>DroSec_CAF1 37327 97 + 1
AUGGUUAAAUAACAGCAGACUUUUAUUAUCGUGUGUAUAUGGAAGUAUGUUAUUAGCCUU----------------------CGUCACUACGUGGAAUGCCUG-CCGUCCACAGUGAUGA
..((((((.(((((....(((((((((((.....))).)))))))).))))))))))).(----------------------(((((((..(((((..(....-)..))))))))))))) ( -29.80)
>DroSim_CAF1 31511 112 + 1
UUUG--------GAGCAGACUUUUAUUAUCGUGUAUAUAUGAAAGUAUGUUAUUAGCCUUCGCAGACGCUACUGGUGCGCUUCGUCACUACGUGGACUGACUGACUGUCCACACUGAUGA
...(--------((((.(((...((((.(((((....))))).)))).)))....(((...((....))....)))..)))))((((....((((((.........))))))..)))).. ( -26.00)
>consensus
AUCG________CAGCAGACUUUUAUUAUCGUGUAUAUAUGAAAGUAUGUUAUUAGCCUUCGCAGACGCUACUGGU_CGCUUCGUCACUACGUGGACUGCCUG_CCGUCCACAGUGAUGA
.............((((.(((((((((((.....))).)))))))).))))...............................(((((((..((((((.........))))))))))))). (-20.17 = -20.73 +   0.56) 

alignment

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secondary structure

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dotplot

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Window 7

Location 3,343,917 – 3,344,033
Length 116
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 75.00
Mean single sequence MFE -30.83
Consensus MFE -18.27
Energy contribution -19.17
Covariance contribution 0.89
Combinations/Pair 1.07
Mean z-score -1.76
Structure conservation index 0.59
SVM decision value 0.51
SVM RNA-class probability 0.762428
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 3343917 116 + 27905053
GAAAGUAUGUUAUUAUCCUUCGCAGACGCUACUGGUACGCUUCGUCACUACGUGGACUACCUG-ACGUCCAAAGUGAUGAAUGUGGUCAAUAUUUGAUAGCUUAUGCGUAUAUGUGU---
....................((((.((((....(((.((((((((((((...(((((......-..))))).))))))))).)))((((.....)))).)))...))))...)))).--- ( -34.20)
>DroSec_CAF1 37367 90 + 1
GGAAGUAUGUUAUUAGCCUU----------------------CGUCACUACGUGGAAUGCCUG-CCGUCCACAGUGAUGAAUGUGGUCAAUAUUUAUUGGCUUAUGCUAAUAU-------
..........(((((((.((----------------------(((((((..(((((..(....-)..))))))))))))))...(((((((....)))))))...))))))).------- ( -28.30)
>DroSim_CAF1 31543 120 + 1
GAAAGUAUGUUAUUAGCCUUCGCAGACGCUACUGGUGCGCUUCGUCACUACGUGGACUGACUGACUGUCCACACUGAUGAAUGUGGUCAAUAUUUAAUAGCUUAUGCUAAUAUGUGUAUG
....(((..((((((((.(..((...(((.....)))((((((((((....((((((.........))))))..))))))).)))..............))..).))))))).)..))). ( -30.00)
>consensus
GAAAGUAUGUUAUUAGCCUUCGCAGACGCUACUGGU_CGCUUCGUCACUACGUGGACUGCCUG_CCGUCCACAGUGAUGAAUGUGGUCAAUAUUUAAUAGCUUAUGCUAAUAUGUGU___
....(((((((((((...........................(((((((..((((((.........)))))))))))))(((((.....))))))))))))..))))............. (-18.27 = -19.17 +   0.89) 

alignment

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secondary structure

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dotplot

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Window 8

Location 3,343,957 – 3,344,072
Length 115
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 77.46
Mean single sequence MFE -29.73
Consensus MFE -20.99
Energy contribution -22.44
Covariance contribution 1.45
Combinations/Pair 1.10
Mean z-score -2.33
Structure conservation index 0.71
SVM decision value 2.39
SVM RNA-class probability 0.993355
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 3343957 115 + 27905053
UUCGUCACUACGUGGACUACCUG-ACGUCCAAAGUGAUGAAUGUGGUCAAUAUUUGAUAGCUUAUGCGUAUAUGUGU----AACUGUAUUAGGUAAAUAUGAUUGCUAUAAUUACCAAUA
(((((((((...(((((......-..))))).))))))))).(..((((.(((((((((..(((((((....)))))----))...)))))))))....))))..).............. ( -30.80)
>DroSec_CAF1 37387 99 + 1
--CGUCACUACGUGGAAUGCCUG-CCGUCCACAGUGAUGAAUGUGGUCAAUAUUUAUUGGCUUAUGCUAAUAU------------------GGUGAAUAUGAUUGCUACACUUACCUUUA
--(((((((..(((((..(....-)..))))))))))))...(..((((.(((((((((((....))))....------------------.)))))))))))..).............. ( -27.60)
>DroSim_CAF1 31583 120 + 1
UUCGUCACUACGUGGACUGACUGACUGUCCACACUGAUGAAUGUGGUCAAUAUUUAAUAGCUUAUGCUAAUAUGUGUAUGUAAAAGCAUUAGGUGAAUAUGAUUGCUAUAGUUACCUAUA
(((((((....((((((.........))))))..))))))).(..((((.((((((....((.(((((..(((......)))..))))).)).))))))))))..)(((((....))))) ( -30.80)
>consensus
UUCGUCACUACGUGGACUGCCUG_CCGUCCACAGUGAUGAAUGUGGUCAAUAUUUAAUAGCUUAUGCUAAUAUGUGU____AA__G_AUUAGGUGAAUAUGAUUGCUAUAAUUACCUAUA
.((((((((..((((((.........))))))))))))))..(..((((.((((((.((((....))))........................))))))))))..).............. (-20.99 = -22.44 +   1.45) 

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 10:01:00 2006