Locus 2418

Sequence ID 2R_DroMel_CAF1
Location 8,699,603 – 8,699,721
Length 118
Max. P 0.994074
window4002 window4003 window4004

overview

Window 2

Location 8,699,603 – 8,699,701
Length 98
Sequences 6
Columns 112
Reading direction reverse
Mean pairwise identity 65.75
Mean single sequence MFE -31.13
Consensus MFE -8.16
Energy contribution -6.99
Covariance contribution -1.16
Combinations/Pair 1.45
Mean z-score -3.55
Structure conservation index 0.26
SVM decision value 2.45
SVM RNA-class probability 0.994074
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 8699603 98 - 20766785
CACAACACAA-ACACAAUCCGUUGCCAGCUCCUCCUGCUCCGCCCCAAGCGAUGGAGGAGGAGGAGGAGUCUACACAAAGUUGG-------------CACCAGUUUCAUCCU
..........-.........(.((((((((((((((.((((...(((.....))).)))).)))))))((....))...)))))-------------)).)........... ( -33.60)
>DroPse_CAF1 9890 93 - 1
C----CAAAG-ACACUAUCCGUUGGCAACACUGCACUAUCCCUCCCC---UU-AGAAGGGGUGGGGGAUA--CUCCAACUUUGGCCA---A----UUCACAAAUUUUACUU-
(----(((((-....(((((....(((....))).....(((.((((---(.-...))))).))))))))--......))))))...---.----................- ( -27.80)
>DroSec_CAF1 6010 104 - 1
CAGAACACAA-ACACAAUCCGUUGCCAGCUCCUCCUGCUCCCCCGCAAGCAA---AGGAGAAGGAGGAGUCUGUCCAACGUUGGCCACACA----CACACCAGUUUCAUCCU
..(((.((..-........(((((.(((((((((((.((((..(....)...---.)))).)))))))).)))..))))).(((.......----....))))))))..... ( -33.60)
>DroSim_CAF1 6053 104 - 1
CUCAACACAA-ACACAAUCCGUUGGCAGCUCCUCCUGCUCCCCCGCAAACAA---AGGAGGAGGAGGAGUUUGUCCAACGUUGGCCACACA----CACACCAGUUUCAUCCU
........((-((......(((((((((((((((((.((((...........---.)))).)))))))).))).)))))).(((.......----....)))))))...... ( -35.20)
>DroYak_CAF1 6334 106 - 1
CACCACACAAAACCCAAUCCGUUCCCAGCUCC---UGCUCCUUCGCAAAAG---GUGUAGGAGGAGGAGUCUGACCAACGUUGGCCACACACACACACACCAGUUUCAUCCU
.............((((..((((..(((((((---(.(((((.(((.....---))).))))).))))).)))...))))))))............................ ( -29.40)
>DroPer_CAF1 10427 93 - 1
C----CAAAG-ACACUAUCCGUUGGCAACACUGCACUAUCCCUCCCC---UU-AGAAGGGGUGGGGGGUA--CUCCAACUUUGGCCA---A----UUCACAAAUUUUACUU-
(----(((((-....(((((....(((....))).....(((.((((---(.-...))))).))))))))--......))))))...---.----................- ( -27.20)
>consensus
CACAACACAA_ACACAAUCCGUUGCCAGCUCCUCCUGCUCCCCCCCAA_CAA__GAGGAGGAGGAGGAGUCUGUCCAACGUUGGCCA___A____CACACCAGUUUCAUCCU
.........................((((.......(((((.((..................)).))))).........))))............................. ( -8.16 =  -6.99 +  -1.16)

alignment

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secondary structure

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dotplot

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Window 3

Location 8,699,625 – 8,699,721
Length 96
Sequences 6
Columns 103
Reading direction forward
Mean pairwise identity 67.26
Mean single sequence MFE -34.27
Consensus MFE -7.27
Energy contribution -6.97
Covariance contribution -0.30
Combinations/Pair 1.54
Mean z-score -2.53
Structure conservation index 0.21
SVM decision value 0.81
SVM RNA-class probability 0.856107
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 8699625 96 + 20766785
UGUGUAGACUCCUCCUCCUCCUCCAUCGCUUGGGGCGGAGCAGGAGGAGCUGGCAACGGAUUGUGU-UUGUGUUGUGUCCAA------AGAGUGGGAAACAAU
(((.(((.((((((((.((((((((.....))))..)))).))))))))))))))((((((...))-))))(((((.(((..------......))).))))) ( -35.00)
>DroPse_CAF1 9917 85 + 1
UGGAG--UAUCCCCCACCCCUUCU-AA---GGGGAGGGAUAGUGCAGUGUUGCCAACGGAUAGUGU-CUUUG----GUUCAC------AGA-UAAGAAACAAG
((.(.--((((((...(((((...-.)---)))).)))))).).))(((..(((((.((((...))-)))))----)).)))------...-........... ( -28.70)
>DroSec_CAF1 6041 93 + 1
UGGACAGACUCCUCCUUCUCCU---UUGCUUGCGGGGGAGCAGGAGGAGCUGGCAACGGAUUGUGU-UUGUGUUCUGUCCAA------AGAGUGGGAAACAAU
((((((((((((((((.(((((---(((....)))))))).))))))))(((....))).......-......)))))))).------......(....)... ( -44.70)
>DroSim_CAF1 6084 93 + 1
UGGACAAACUCCUCCUCCUCCU---UUGUUUGCGGGGGAGCAGGAGGAGCUGCCAACGGAUUGUGU-UUGUGUUGAGUCCAA------AGAGUGGGAAACAAU
(((((...((((((((.(((((---(((....)))))))).))))))))....(((((.(......-.).))))).))))).------......(....)... ( -39.10)
>DroYak_CAF1 6369 97 + 1
UGGUCAGACUCCUCCUCCUACAC---CUUUUGCGAAGGAGCA---GGAGCUGGGAACGGAUUGGGUUUUGUGUGGUGUCCAGUGUGGUGGAGUGGGAAACAAU
.........(((..((((..(((---(((((((......)))---))))(((((..((.((........)).))...))))).)))..))))..)))...... ( -30.40)
>DroPer_CAF1 10454 85 + 1
UGGAG--UACCCCCCACCCCUUCU-AA---GGGGAGGGAUAGUGCAGUGUUGCCAACGGAUAGUGU-CUUUG----GUUCAC------AGA-UAAGAAACAAG
....(--(((..(((.(((((...-.)---)))).)))...)))).(((..(((((.((((...))-)))))----)).)))------...-........... ( -27.70)
>consensus
UGGACAGACUCCUCCUCCUCCUC__UAG_UUGCGAGGGAGCAGGAGGAGCUGCCAACGGAUUGUGU_UUGUGUUGUGUCCAA______AGAGUGGGAAACAAU
(((((...(((((......................))))).........(((....))).................)))))...................... ( -7.27 =  -6.97 +  -0.30)

alignment

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secondary structure

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dotplot

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Window 4

Location 8,699,625 – 8,699,721
Length 96
Sequences 6
Columns 103
Reading direction reverse
Mean pairwise identity 67.26
Mean single sequence MFE -28.91
Consensus MFE -6.64
Energy contribution -5.37
Covariance contribution -1.27
Combinations/Pair 1.57
Mean z-score -2.97
Structure conservation index 0.23
SVM decision value 1.73
SVM RNA-class probability 0.974518
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 8699625 96 - 20766785
AUUGUUUCCCACUCU------UUGGACACAACACAA-ACACAAUCCGUUGCCAGCUCCUCCUGCUCCGCCCCAAGCGAUGGAGGAGGAGGAGGAGUCUACACA
.((((.(((......------..))).)))).....-................(((((((((.((((...(((.....))).)))).)))))))))....... ( -32.10)
>DroPse_CAF1 9917 85 - 1
CUUGUUUCUUA-UCU------GUGAAC----CAAAG-ACACUAUCCGUUGGCAACACUGCACUAUCCCUCCCC---UU-AGAAGGGGUGGGGGAUA--CUCCA
.(((.(((...-...------..))).----)))..-....(((((....(((....))).....(((.((((---(.-...))))).))))))))--..... ( -24.40)
>DroSec_CAF1 6041 93 - 1
AUUGUUUCCCACUCU------UUGGACAGAACACAA-ACACAAUCCGUUGCCAGCUCCUCCUGCUCCCCCGCAAGCAA---AGGAGAAGGAGGAGUCUGUCCA
...............------.((((((((.....(-((.......))).....((((((((.((((..(....)...---.)))).)))))))))))))))) ( -33.20)
>DroSim_CAF1 6084 93 - 1
AUUGUUUCCCACUCU------UUGGACUCAACACAA-ACACAAUCCGUUGGCAGCUCCUCCUGCUCCCCCGCAAACAA---AGGAGGAGGAGGAGUUUGUCCA
...............------.((((((((((....-.........))))).((((((((((.((((...........---.)))).)))))))))).))))) ( -31.62)
>DroYak_CAF1 6369 97 - 1
AUUGUUUCCCACUCCACCACACUGGACACCACACAAAACCCAAUCCGUUCCCAGCUCC---UGCUCCUUCGCAAAAG---GUGUAGGAGGAGGAGUCUGACCA
.((((.......((((......))))......))))...............(((((((---(.(((((.(((.....---))).))))).))))).))).... ( -28.32)
>DroPer_CAF1 10454 85 - 1
CUUGUUUCUUA-UCU------GUGAAC----CAAAG-ACACUAUCCGUUGGCAACACUGCACUAUCCCUCCCC---UU-AGAAGGGGUGGGGGGUA--CUCCA
.(((.(((...-...------..))).----)))..-....(((((....(((....))).....(((.((((---(.-...))))).))))))))--..... ( -23.80)
>consensus
AUUGUUUCCCACUCU______UUGGACACAACACAA_ACACAAUCCGUUGCCAGCUCCUCCUGCUCCCCCCCAA_CAA__GAGGAGGAGGAGGAGUCUGUCCA
..............................................................(((((.((..................)).)))))....... ( -6.64 =  -5.37 +  -1.27)

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 10:29:40 2006