Locus 2413

Sequence ID 3R_DroMel_CAF1
Location 6,759,671 – 6,759,775
Length 104
Max. P 0.598719
window3923 window3924

overview

Window 3

Location 6,759,671 – 6,759,775
Length 104
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 79.67
Mean single sequence MFE -27.03
Consensus MFE -16.58
Energy contribution -15.98
Covariance contribution -0.60
Combinations/Pair 1.37
Mean z-score -1.73
Structure conservation index 0.61
SVM decision value 0.13
SVM RNA-class probability 0.598719
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 6759671 104 + 27905053
GUGG--CCCACCACCCUUCGACAUUCGUAUGCAUUCUACCCCCUAUUUGCAAGGGUGGCCAUAUUAAUGUGCCAACAGCUCUCUCGGCUUCGUGAACACACAC--------------UAC
((((--((....(((((.((.....))..((((..............))))))))))))))).....((((...((((((.....))))..))...))))...--------------... ( -23.94)
>DroSec_CAF1 23893 99 + 1
GUGG--CCCACC---CCUCGACCAUCGUAUGCAUUCCACCUCCUAUUUGCGGGGGUGGCCAUAUUAAUGUGCCAACAGCUCUCUCGGCUUCGUGAACA--CAC--------------UAC
((((--((.(((---(((((.....))...(((..............))))))))))))))).....((((...((((((.....))))..))...))--)).--------------... ( -28.64)
>DroSim_CAF1 28268 92 + 1
GUGG--CCCACC---CCU-------CGUAUGCAUUCCACCCCCUAUUUGCGGGGGUGGCCAUAUUAAUGUGCCAACAGCUCUCUCGGCUUCGUGAACA--CAC--------------UAC
((((--((.(((---((.-------((((..................))))))))))))))).....((((...((((((.....))))..))...))--)).--------------... ( -29.57)
>DroEre_CAF1 8431 99 + 1
GUU--CCCCACC---CUUCGCACCCCAUAUGCAUUUAGCCCCCUAUUUGCGGGGGUGGCCGUAUUAAUGGGCCAACAGCUCUCUCGGCCCCAUGAACA--CAC--------------UAC
(((--(.(((((---((.((((........((.....))........)))))))))))..........(((((............)))))...)))).--...--------------... ( -30.49)
>DroYak_CAF1 20378 115 + 1
GUUGCCCCCACC---CUUCGCCCCACAUAUGCAUGUCGCCCACUAUUUGCGGGGGUGGCCAUAUUAAUGUGCCAACAGCUCUCUCGGCUCCAUGAACA--CACUACACACUACACACUAC
((..(((((...---.........((((....)))).((.........)))))))..))........((((.((..((((.....))))...))..))--)).................. ( -22.50)
>consensus
GUGG__CCCACC___CUUCGACCCUCGUAUGCAUUCCACCCCCUAUUUGCGGGGGUGGCCAUAUUAAUGUGCCAACAGCUCUCUCGGCUUCGUGAACA__CAC______________UAC
..........................(((((....((((((((.......)))))))).)))))..(((.(((............)))..)))........................... (-16.58 = -15.98 +  -0.60)

alignment

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secondary structure

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dotplot

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Window 4

Location 6,759,671 – 6,759,775
Length 104
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 79.67
Mean single sequence MFE -36.40
Consensus MFE -19.54
Energy contribution -19.46
Covariance contribution -0.08
Combinations/Pair 1.19
Mean z-score -1.87
Structure conservation index 0.54
SVM decision value 0.06
SVM RNA-class probability 0.565416
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 6759671 104 - 27905053
GUA--------------GUGUGUGUUCACGAAGCCGAGAGAGCUGUUGGCACAUUAAUAUGGCCACCCUUGCAAAUAGGGGGUAGAAUGCAUACGAAUGUCGAAGGGUGGUGGG--CCAC
...--------------((((((((((((..((((....).)))..((((.(((....)))))))((((((....)))))))).))))))))))............((((....--)))) ( -34.50)
>DroSec_CAF1 23893 99 - 1
GUA--------------GUG--UGUUCACGAAGCCGAGAGAGCUGUUGGCACAUUAAUAUGGCCACCCCCGCAAAUAGGAGGUGGAAUGCAUACGAUGGUCGAGG---GGUGGG--CCAC
.((--------------(((--(((..((..((((....).)))))..))))))))...(((((((((((((.....(...(((.....))).)....).)).))---))).))--))). ( -35.90)
>DroSim_CAF1 28268 92 - 1
GUA--------------GUG--UGUUCACGAAGCCGAGAGAGCUGUUGGCACAUUAAUAUGGCCACCCCCGCAAAUAGGGGGUGGAAUGCAUACG-------AGG---GGUGGG--CCAC
...--------------(((--.((((((...(((((.(....).))))).......((((.((((((((.......))))))))....))))..-------...---.)))))--)))) ( -36.90)
>DroEre_CAF1 8431 99 - 1
GUA--------------GUG--UGUUCAUGGGGCCGAGAGAGCUGUUGGCCCAUUAAUACGGCCACCCCCGCAAAUAGGGGGCUAAAUGCAUAUGGGGUGCGAAG---GGUGGGG--AAC
...--------------.((--((((.(((((.((((.(....).))))))))).)))))).((((((.((((..(.....((.....)).....)..))))..)---)))))..--... ( -36.90)
>DroYak_CAF1 20378 115 - 1
GUAGUGUGUAGUGUGUAGUG--UGUUCAUGGAGCCGAGAGAGCUGUUGGCACAUUAAUAUGGCCACCCCCGCAAAUAGUGGGCGACAUGCAUAUGUGGGGCGAAG---GGUGGGGGCAAC
....(((.(.((((.(((((--((((...(.((((....).))).).)))))))))))))..((((((((((.....))))((..(((......)))..))...)---)))))).))).. ( -37.80)
>consensus
GUA______________GUG__UGUUCACGAAGCCGAGAGAGCUGUUGGCACAUUAAUAUGGCCACCCCCGCAAAUAGGGGGUGGAAUGCAUACGAGGGGCGAAG___GGUGGG__CCAC
........................(((((..((((....).)))..((((.(((....)))))))(((((.......)))))...........................)))))...... (-19.54 = -19.46 +  -0.08)

alignment

Postscript

secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:35:12 2006