Locus 4284

Sequence ID 2L_DroMel_CAF1
Location 12,242,876 – 12,242,996
Length 120
Max. P 0.997960
window6754 window6755 window6756

overview

Window 4

Location 12,242,876 – 12,242,973
Length 97
Sequences 5
Columns 102
Reading direction reverse
Mean pairwise identity 84.68
Mean single sequence MFE -28.04
Consensus MFE -16.29
Energy contribution -18.05
Covariance contribution 1.76
Combinations/Pair 1.04
Mean z-score -2.26
Structure conservation index 0.58
SVM decision value 0.10
SVM RNA-class probability 0.585300
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 12242876 97 - 22407834
GUGAGUA-----AAGGAAAGAGUACGGUUUCGUGUCGAGCAUGUGCUCGGAAAACUCGAUUUUCCUCACACCUACGACAACAAACUCACUUAAGUUAACCUA
((((((.-----.(((...(((((((..((((...))))..)))))))((((((.....)))))).....)))..(....)..))))))............. ( -23.90)
>DroSec_CAF1 66227 102 - 1
GUGAGGAAGGGAAAGGAAAGAGCACGGUUUCGUGUCGAGCAUGUGCUCGGAAAACUCGAUUUUCCUCACACCUACACCUUCGAACUCACUUAAGUUAACCUA
((((((((((...(((...(((((((..((((...))))..)))))))((((((.....)))))).....)))...)))))...)))))............. ( -33.70)
>DroSim_CAF1 67669 102 - 1
GUGAGAAAAGGAAAGGAAAGAGCACGGUUUCGUGUCGAGCAUGUGCUCGGAAAACUCGAUUUUCCUCACACCUACACCUUCGAACUCACUUAAGUUAACCUA
(((((..((((..(((...(((((((..((((...))))..)))))))((((((.....)))))).....)))...))))....)))))............. ( -29.40)
>DroEre_CAF1 64118 99 - 1
GUACGG--GUGUAAGGAAGGAGU-AGGUUUCGUGUCGAGCAUGUGCUCGGAAAACUCGAUUUUCCUUACACCUACACCUCCGAACACACUUAACUUAACCUA
......--((((..(((.((.((-((((........((((....))))((((((.....))))))....)))))).)))))..))))............... ( -31.00)
>DroYak_CAF1 65270 90 - 1
G----------UAAGGAA-AAGC-CGUUUUCGUGUCGAGCAUGUGCUCGGAAAACUCGAUUUUCCUUAUACCUACACCUCCGAACCCACUUAACUUAACGUA
(----------(((((((-((..-.((((((....(((((....)))))))))))....))))))))))................................. ( -22.20)
>consensus
GUGAGGA___GAAAGGAAAGAGCACGGUUUCGUGUCGAGCAUGUGCUCGGAAAACUCGAUUUUCCUCACACCUACACCUCCGAACUCACUUAAGUUAACCUA
(((((........(((...(((((((..((((...))))..)))))))((((((.....)))))).....)))...........)))))............. (-16.29 = -18.05 +   1.76)

alignment

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secondary structure

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Window 5

Location 12,242,904 – 12,242,996
Length 92
Sequences 5
Columns 97
Reading direction forward
Mean pairwise identity 85.26
Mean single sequence MFE -27.92
Consensus MFE -20.10
Energy contribution -20.46
Covariance contribution 0.36
Combinations/Pair 1.12
Mean z-score -4.64
Structure conservation index 0.72
SVM decision value 2.97
SVM RNA-class probability 0.997960
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 12242904 92 + 22407834
UAGGUGUGAGGAAAAUCGAGUUUUCCGAGCACAUGCUCGACACGAAACCGUACUCUUUCCUU-----UACUCACACCCAAACACACCCCCACAGACA
..((((((((((((...((((....(((((....)))))..(((....))))))))))))..-----...))))))).................... ( -25.40)
>DroSec_CAF1 66255 95 + 1
UAGGUGUGAGGAAAAUCGAGUUUUCCGAGCACAUGCUCGACACGAAACCGUGCUCUUUCCUUUCCCUUCCUCACACCCAAAU--AUCCCCGCAGACA
..(((((((((((....(((.....(((((....))))).((((....)))).......)))....))))))))))).....--............. ( -31.40)
>DroSim_CAF1 67697 95 + 1
UAGGUGUGAGGAAAAUCGAGUUUUCCGAGCACAUGCUCGACACGAAACCGUGCUCUUUCCUUUCCUUUUCUCACACCCAAAC--AUCCCCGCAGACA
..((((((((((((...(((.....(((((....))))).((((....)))).......)))...)))))))))))).....--............. ( -29.70)
>DroEre_CAF1 64146 92 + 1
UAGGUGUAAGGAAAAUCGAGUUUUCCGAGCACAUGCUCGACACGAAACCU-ACUCCUUCCUUACAC--CCGUACACCCAAAC--AUCCCCGCAAACA
..(((((((((((....(((((((((((((....)))))....))))...-)))).))))))))))--).............--............. ( -27.30)
>DroYak_CAF1 65298 83 + 1
UAGGUAUAAGGAAAAUCGAGUUUUCCGAGCACAUGCUCGACACGAAAACG-GCUU-UUCCUUA----------CACCCAAAC--ACCCCCGCAGACA
..(((.(((((((((.(..(((((((((((....)))))....)))))).-).))-)))))))----------.))).....--............. ( -25.80)
>consensus
UAGGUGUGAGGAAAAUCGAGUUUUCCGAGCACAUGCUCGACACGAAACCGUGCUCUUUCCUUAC___UCCUCACACCCAAAC__AUCCCCGCAGACA
..((((((((((((...(((((((((((((....)))))....))))....))))))))))..........)))))).................... (-20.10 = -20.46 +   0.36)

alignment

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secondary structure

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dotplot

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Window 6

Location 12,242,904 – 12,242,996
Length 92
Sequences 5
Columns 97
Reading direction reverse
Mean pairwise identity 85.26
Mean single sequence MFE -32.72
Consensus MFE -23.24
Energy contribution -24.20
Covariance contribution 0.96
Combinations/Pair 1.12
Mean z-score -2.82
Structure conservation index 0.71
SVM decision value 1.66
SVM RNA-class probability 0.970567
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 12242904 92 - 22407834
UGUCUGUGGGGGUGUGUUUGGGUGUGAGUA-----AAGGAAAGAGUACGGUUUCGUGUCGAGCAUGUGCUCGGAAAACUCGAUUUUCCUCACACCUA
..................((((((((((.(-----(((....(((((((....))).((((((....))))))...))))..)))).)))))))))) ( -30.70)
>DroSec_CAF1 66255 95 - 1
UGUCUGCGGGGAU--AUUUGGGUGUGAGGAAGGGAAAGGAAAGAGCACGGUUUCGUGUCGAGCAUGUGCUCGGAAAACUCGAUUUUCCUCACACCUA
(((((....))))--)..(((((((((((((((...((....(((((((..((((...))))..)))))))......))...))))))))))))))) ( -38.20)
>DroSim_CAF1 67697 95 - 1
UGUCUGCGGGGAU--GUUUGGGUGUGAGAAAAGGAAAGGAAAGAGCACGGUUUCGUGUCGAGCAUGUGCUCGGAAAACUCGAUUUUCCUCACACCUA
.((((....))))--...(((((((((.....((((((....(((((((....))))((((((....))))))....)))..))))))))))))))) ( -32.60)
>DroEre_CAF1 64146 92 - 1
UGUUUGCGGGGAU--GUUUGGGUGUACGG--GUGUAAGGAAGGAGU-AGGUUUCGUGUCGAGCAUGUGCUCGGAAAACUCGAUUUUCCUUACACCUA
.............--............((--((((((((((((...-.(((((....((((((....)))))).)))))...)))))))))))))). ( -30.80)
>DroYak_CAF1 65298 83 - 1
UGUCUGCGGGGGU--GUUUGGGUG----------UAAGGAA-AAGC-CGUUUUCGUGUCGAGCAUGUGCUCGGAAAACUCGAUUUUCCUUAUACCUA
.............--...((((((----------(((((((-((..-.((((((....(((((....)))))))))))....))))))))))))))) ( -31.30)
>consensus
UGUCUGCGGGGAU__GUUUGGGUGUGAGGA___GAAAGGAAAGAGCACGGUUUCGUGUCGAGCAUGUGCUCGGAAAACUCGAUUUUCCUCACACCUA
..................(((((((((...............(((((((..((((...))))..)))))))((((((.....))))))))))))))) (-23.24 = -24.20 +   0.96)

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 11:14:09 2006