Locus 137

Sequence ID 2L_DroMel_CAF1
Location 426,906 – 427,129
Length 223
Max. P 0.994311
window213 window214 window215

overview

Window 3

Location 426,906 – 427,011
Length 105
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 76.56
Mean single sequence MFE -23.45
Consensus MFE -9.38
Energy contribution -10.35
Covariance contribution 0.98
Combinations/Pair 1.26
Mean z-score -2.74
Structure conservation index 0.40
SVM decision value 1.42
SVM RNA-class probability 0.951768
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 426906 105 - 22407834
ACCGCAGG-------AAAAACACUUGUUCAAACAGAGGCGUGUGAAGUGUGCGGAAU---GUAUGCACAUAUACAAUUUCACACAUGACACAC-----AAAACAAUUUACUUAAAAUCAU
.(((((((-------.......)))))((.....)))).(((((..(((((.(((((---(((((....))))).))))).)))))..)))))-----...................... ( -23.60)
>DroSec_CAF1 4381 110 - 1
ACCGCAGG-------AAAAACACUUGUUCAAACAGAGGCGUGUGAAGUGUGCGGAAU---GUAUGCACAUAUACAAUUUCACACAUGACACACAUCUCAAAACAAUUUACUUAAAAUCAA
...(((((-------.......))))).......(((..(((((..(((((.(((((---(((((....))))).))))).)))))..)))))..)))...................... ( -28.30)
>DroSim_CAF1 3366 110 - 1
ACCGCAGG-------AAAAACACUUGUUCAAACAGAGGCGUGUGAAGUGUGCGGAAU---GUAUGCACAUAUACAAUUUCACACAUGACACACAUCUCAAAACAAUUUACUUAAAAUCAA
...(((((-------.......))))).......(((..(((((..(((((.(((((---(((((....))))).))))).)))))..)))))..)))...................... ( -28.30)
>DroEre_CAF1 3979 103 - 1
ACCGCAG--------G-AAACACUUGUUCAAACAGAGGCGUGUGAAGUGUGCGG-------AAUGUGCAUA-ACAAUUUCACACAUGACACACAUCUCAAAACAAUUUACUUUAAAUCAA
...((((--------(-.....))))).......(((..(((((..(((((.((-------(((((.....-)).))))).)))))..)))))..)))...................... ( -26.50)
>DroYak_CAF1 3610 112 - 1
ACCGCAGG-------G-AAACACUUGUUCAAACAGAGGCGUGUGAAGUGUGCGGAACUUGGAAUGUACAUAUACAAUUUCACACAUGACACACAUCUCAAAACAAUUUACUUUAAAUCAA
...(((((-------.-.....))))).......(((..(((((..(((((.((((.(((.............))))))).)))))..)))))..)))...................... ( -26.52)
>DroAna_CAF1 4243 110 - 1
ACCACAGGGACAAAAAAAAACACUUGUCAAAAUAACAGACUAUGGGAUAUGAGAGUU---AAAAAACAAUAUAGAGUUAAAGACUAA--AAAA-----AAAGGGGUUUAAAGAUAAUUAU
.((.....(((((..........))))).........((((.....((((....(((---....))).))))..)))).........--....-----...))................. (  -7.50)
>consensus
ACCGCAGG_______AAAAACACUUGUUCAAACAGAGGCGUGUGAAGUGUGCGGAAU___GAAUGCACAUAUACAAUUUCACACAUGACACACAUCUCAAAACAAUUUACUUAAAAUCAA
...(((((..............)))))............((((((((((((((..........))))))).......))))))).................................... ( -9.38 = -10.35 +   0.98)

alignment

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secondary structure

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Window 4

Location 426,978 – 427,091
Length 113
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 82.19
Mean single sequence MFE -26.06
Consensus MFE -16.58
Energy contribution -17.17
Covariance contribution 0.59
Combinations/Pair 1.33
Mean z-score -1.82
Structure conservation index 0.64
SVM decision value 0.09
SVM RNA-class probability 0.577756
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 426978 113 - 22407834
CGGCAAAGAGAAGGAGCGGGGGGGGGGGGCUGGUUGCCAUAUUAUUAUGGUAACACAGUUUUAGGCAGAAAUAGAAAUAAACCGCAGG-------AAAAACACUUGUUCAAACAGAGGCG
..((.........(((((((.(.((((((((((((((((((....))))))))).))))))).........((....))..)).).(.-------.....).)))))))........)). ( -30.83)
>DroSec_CAF1 4458 108 - 1
CGGGAAAGAGAAGGAGCUGG-----GGGGCUGGUUGCCAUAUUAUUAUGGUAACACAGUUUUAGGCAGAAAUAGAAAUAAACCGCAGG-------AAAAACACUUGUUCAAACAGAGGCG
.((............(((..-----((((((((((((((((....))))))))).))))))).))).....((....))..))(((((-------.......)))))............. ( -27.40)
>DroSim_CAF1 3443 108 - 1
CGGGAAAGAGAAGGAGCUGG-----GGGGCUGGUUGCCAUAUUAUUAUGGUAACACAGUUUUAGGCAGAAAUAGAAAGAAACCGCAGG-------AAAAACACUUGUUCAAACAGAGGCG
.((............(((..-----((((((((((((((((....))))))))).))))))).)))(....).........))(((((-------.......)))))............. ( -26.00)
>DroEre_CAF1 4051 106 - 1
CAGGAAAGAAGAGGAGCUCA-----GGGACUGGUUGCCAUAUUAUUAUGGUAACACAGUUUUAGGCAGAAAUAGAAAUAAACCGCAG--------G-AAACACUUGUUCAAACAGAGGCG
.......(((.(((.((.(.-----.(((((((((((((((....))))))))).))))))..)))....................(--------.-...).))).)))........... ( -29.20)
>DroYak_CAF1 3690 107 - 1
CGGGAAGGAAAAGGAGCCGA-----GGGGCUGGUUGCCAUGUUAUUAUGGUAACACAGUUUUAGGCAGAAAUAGAAAUAAACCGCAGG-------G-AAACACUUGUUCAAACAGAGGCG
.((............(((..-----((((((((((((((((....))))))))).))))))).))).....((....))..))(((((-------.-.....)))))............. ( -30.20)
>DroAna_CAF1 4313 106 - 1
-----AAGAUUGGGGGGUGG-----GGG-AGGGUAAU--GAUUAUUAUGGUAACACAGUUUUGGGCAAAAAUAGAAACA-ACCACAGGGACAAAAAAAAACACUUGUCAAAAUAACAGAC
-----....((((.(((((.-----(..-(..(((((--....)))))..)..)...(((((.((..............-.))...))))).........))))).)))).......... ( -12.76)
>consensus
CGGGAAAGAGAAGGAGCUGG_____GGGGCUGGUUGCCAUAUUAUUAUGGUAACACAGUUUUAGGCAGAAAUAGAAAUAAACCGCAGG_______AAAAACACUUGUUCAAACAGAGGCG
.........(((.(((.........((((((((((((((((....))))))))).))))))).((................))...................))).)))........... (-16.58 = -17.17 +   0.59)

alignment

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secondary structure

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Window 5

Location 427,011 – 427,129
Length 118
Sequences 5
Columns 118
Reading direction reverse
Mean pairwise identity 92.26
Mean single sequence MFE -33.66
Consensus MFE -27.96
Energy contribution -27.84
Covariance contribution -0.12
Combinations/Pair 1.17
Mean z-score -2.41
Structure conservation index 0.83
SVM decision value 2.47
SVM RNA-class probability 0.994311
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 427011 118 - 22407834
CAAUGGAUUCACGGUAAUGCAAUUGGUUCCCAUGGGCUCGGCAAAGAGAAGGAGCGGGGGGGGGGGGCUGGUUGCCAUAUUAUUAUGGUAACACAGUUUUAGGCAGAAAUAGAAAUAA
.......(((.......(((......(((((....((((............))))...)))))((((((((((((((((....))))))))).)))))))..)))......))).... ( -32.12)
>DroSec_CAF1 4491 113 - 1
CAAUGGAUUCACGGUAAUGUAUUUGGUUCCCAUGGGCUCGGGAAAGAGAAGGAGCUGG-----GGGGCUGGUUGCCAUAUUAUUAUGGUAACACAGUUUUAGGCAGAAAUAGAAAUAA
.......(((...........(((..(((((........)))))..)))....(((..-----((((((((((((((((....))))))))).))))))).))).))).......... ( -31.70)
>DroSim_CAF1 3476 113 - 1
CAAUGGAUUCACGGUAAUGUAUUUGGUUCCCAUGGGCUCGGGAAAGAGAAGGAGCUGG-----GGGGCUGGUUGCCAUAUUAUUAUGGUAACACAGUUUUAGGCAGAAAUAGAAAGAA
.......(((...........(((..(((((........)))))..)))....(((..-----((((((((((((((((....))))))))).))))))).))).))).......... ( -31.70)
>DroEre_CAF1 4082 113 - 1
CAAUGGAUGCACGGUAAUGCAUUUGGUUCCCAUGGGCUCAGGAAAGAAGAGGAGCUCA-----GGGACUGGUUGCCAUAUUAUUAUGGUAACACAGUUUUAGGCAGAAAUAGAAAUAA
....(((((((......)))))))...((((.(((((((............)))))))-----))))((((((((((((....))))))))).)))(((((........))))).... ( -36.20)
>DroYak_CAF1 3722 113 - 1
CAAUGGAUUCCCGGUAAUGCAUUUGGUUCCCAUGGGCUCGGGAAGGAAAAGGAGCCGA-----GGGGCUGGUUGCCAUGUUAUUAUGGUAACACAGUUUUAGGCAGAAAUAGAAAUAA
.......(((((((....((...(((...)))...))))))))).........(((..-----((((((((((((((((....))))))))).))))))).))).............. ( -36.60)
>consensus
CAAUGGAUUCACGGUAAUGCAUUUGGUUCCCAUGGGCUCGGGAAAGAGAAGGAGCUGG_____GGGGCUGGUUGCCAUAUUAUUAUGGUAACACAGUUUUAGGCAGAAAUAGAAAUAA
.................(((..((((((((......(((......)))..)))))))).....((((((((((((((((....))))))))).)))))))..)))............. (-27.96 = -27.84 +  -0.12)

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 09:27:10 2006