Locus 1120

Sequence ID 3R_DroMel_CAF1
Location 3,380,713 – 3,380,867
Length 154
Max. P 0.823017
window1834 window1835

overview

Window 4

Location 3,380,713 – 3,380,827
Length 114
Sequences 3
Columns 114
Reading direction reverse
Mean pairwise identity 96.49
Mean single sequence MFE -41.30
Consensus MFE -37.83
Energy contribution -38.17
Covariance contribution 0.33
Combinations/Pair 1.00
Mean z-score -2.14
Structure conservation index 0.92
SVM decision value 0.69
SVM RNA-class probability 0.823017
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 3380713 114 - 27905053
GGCAGGAUUCUCGGGGGAGAGGUUCUGCCCCAAAUUAGAUGAUAAAUCUCUGCGGGCGCAUCAGAAUGUAGAGAGGACCAAGAGGACCGCGUUGGGGAGACCUUAAGUCUCCAU
((((((((((((....)))).))))))))((((.............((((((((..(......)..))))))))((.((....)).))...))))((((((.....)))))).. ( -44.30)
>DroSec_CAF1 9057 114 - 1
GCCAGGAUUCUCGGGGGAGAGGUCCUGCCCCAAAUUAGAUGAUAAAUCUCUGCGGGCGCAUCAGAAUGUAGAGAGAACCAGGAGGACCGCGUUGGGGAUACCUUAAGUCUCCAA
((..((.(((((((((.((.....)).))))...............((((((((..(......)..)))))))).......))))))))).((((((((.......)))))))) ( -39.10)
>DroSim_CAF1 9891 114 - 1
GGCAGGAUUCUCGGGGGAGAGGUCCUGCCCCAAAUUAGAUGAUAAAUCUCUGCGGGCGCAUCAGAAUGUAGAGAGAACCAGGAGGACCGCGUUGGGGAUACCUUAAGUCUCCAA
.((.((.(((((((((.((.....)).))))...............((((((((..(......)..)))))))).......))))))))).((((((((.......)))))))) ( -40.50)
>consensus
GGCAGGAUUCUCGGGGGAGAGGUCCUGCCCCAAAUUAGAUGAUAAAUCUCUGCGGGCGCAUCAGAAUGUAGAGAGAACCAGGAGGACCGCGUUGGGGAUACCUUAAGUCUCCAA
....((.(((((((((.((.....)).))))...............((((((((..(......)..)))))))).......)))))))....(((((((.......))))))). (-37.83 = -38.17 +   0.33)

alignment

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secondary structure

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dotplot

Postscript

Window 5

Location 3,380,753 – 3,380,867
Length 114
Sequences 4
Columns 114
Reading direction reverse
Mean pairwise identity 86.70
Mean single sequence MFE -35.00
Consensus MFE -27.01
Energy contribution -29.70
Covariance contribution 2.69
Combinations/Pair 1.03
Mean z-score -1.87
Structure conservation index 0.77
SVM decision value 0.65
SVM RNA-class probability 0.812864
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 3380753 114 - 27905053
AGCACAUUAUGUUGUUGCUAAUUAGCGAUGUCUUCAGACGGGCAGGAUUCUCGGGGGAGAGGUUCUGCCCCAAAUUAGAUGAUAAAUCUCUGCGGGCGCAUCAGAAUGUAGAGA
....((((.....((((((....))))))(((....)))(((((((((((((....)))).))))))))).......)))).....((((((((..(......)..)))))))) ( -39.10)
>DroSec_CAF1 9097 101 - 1
AGCACAUUAUGUUGUUGCUAAUUAGC-------------GGCCAGGAUUCUCGGGGGAGAGGUCCUGCCCCAAAUUAGAUGAUAAAUCUCUGCGGGCGCAUCAGAAUGUAGAGA
...........((((((((((((.(.-------------((.((((((((((....)))).)))))).))).)))))).)))))).((((((((..(......)..)))))))) ( -33.10)
>DroSim_CAF1 9931 114 - 1
AGCACAUUAUGUUGUUGCUAAUUAGCGAUGUCUUCAGACGGGCAGGAUUCUCGGGGGAGAGGUCCUGCCCCAAAUUAGAUGAUAAAUCUCUGCGGGCGCAUCAGAAUGUAGAGA
....((((.....((((((....))))))(((....)))(((((((((((((....)))).))))))))).......)))).....((((((((..(......)..)))))))) ( -42.00)
>DroEre_CAF1 9470 105 - 1
AGCACAUUAGGUUGUUGCUAAUUAGCGAUGUCUUCAGACGGGAAGGAUUCUCGGAGGAG---CUCUGCCCCAAAUUAGAUGAUAAAUCUCUGCGGGCAUAUCAGAAUG------
(((..........((((((....)))))).(((((...(((((.....)))))))))))---)).(((((((....((((.....)))).)).)))))..........------ ( -25.80)
>consensus
AGCACAUUAUGUUGUUGCUAAUUAGCGAUGUCUUCAGACGGGCAGGAUUCUCGGGGGAGAGGUCCUGCCCCAAAUUAGAUGAUAAAUCUCUGCGGGCGCAUCAGAAUGUAGAGA
...........((((((((((((......(((....)))(((((((((((((....)))).)))))))))..)))))).)))))).((((((((..(......)..)))))))) (-27.01 = -29.70 +   2.69)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:01:26 2006