Locus 6387

Sequence ID 2L_DroMel_CAF1
Location 17,903,290 – 17,903,497
Length 207
Max. P 0.994057
window10195 window10196 window10197 window10198 window10199

overview

Window 5

Location 17,903,290 – 17,903,385
Length 95
Sequences 5
Columns 96
Reading direction forward
Mean pairwise identity 93.92
Mean single sequence MFE -25.22
Consensus MFE -20.40
Energy contribution -20.44
Covariance contribution 0.04
Combinations/Pair 1.06
Mean z-score -1.82
Structure conservation index 0.81
SVM decision value 0.89
SVM RNA-class probability 0.876246
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 17903290 95 + 22407834
AAAGGCUGCUGUUUGGGCCAACGGCAGUUGCAGUGCAAGCG-AAAAAAUUGGCCAGCAGAAGGGCACAAAAAUCAGUGAAUAAGUUUUUUUUUUUU
(((((((.((((...((((((......((((.......)))-).....)))))).)))).....(((........)))....)))))))....... ( -21.50)
>DroSec_CAF1 123143 90 + 1
AAAGGCUGCUGUUUGGGCCAACGGCAGUCGCAGUGCAAGCGGAAAAAAUUGGCCAGCAGAAGGGCACAAAAAUCAGUGGAUAAGUUUU------UU
((((((((((.(((.((((((......((((.......))))......))))))....))).)))......(((....))).))))))------). ( -23.70)
>DroSim_CAF1 100867 90 + 1
AAAGGCUGCUGUUUGGGCCAACGGCAGUCGCAGUGCAAGCGGAAAAAAUUGGCCAGCAGAAGGGCACAAAAAUCAGUGGAUAAGUUUU------UU
((((((((((.(((.((((((......((((.......))))......))))))....))).)))......(((....))).))))))------). ( -23.70)
>DroEre_CAF1 112887 89 + 1
AAAGGCUGCUCUUUGGGCCAAUGGCAGUCGCAGUGGAAGCG-AAAAAAUUGGCCAGCAGAAGGGCACAAAAAUCAGUGGAUAAGUUUU------UU
((((((((((((((.(((((((.....((((.......)))-)....)))))))....)))))))......(((....))).))))))------). ( -29.80)
>DroYak_CAF1 120437 89 + 1
AAAGGCUGCUGUUUGGGCCAACGGCAGUCGCAGUGGAAGCG-AAAAAAUUGGCCCGCAGAAGGGCACAAAAAUCAGUGGAUAAGUUUU------UU
...((((((((((......)))))))))).....((((((.-......(((((((......)))).)))..(((....)))..)))))------). ( -27.40)
>consensus
AAAGGCUGCUGUUUGGGCCAACGGCAGUCGCAGUGCAAGCG_AAAAAAUUGGCCAGCAGAAGGGCACAAAAAUCAGUGGAUAAGUUUU______UU
...((((((((((......))))))))))((.......))........((((((........))).)))........................... (-20.40 = -20.44 +   0.04)

alignment

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secondary structure

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dotplot

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Window 6

Location 17,903,290 – 17,903,385
Length 95
Sequences 5
Columns 96
Reading direction reverse
Mean pairwise identity 93.92
Mean single sequence MFE -20.34
Consensus MFE -18.58
Energy contribution -18.82
Covariance contribution 0.24
Combinations/Pair 1.06
Mean z-score -1.83
Structure conservation index 0.91
SVM decision value 2.45
SVM RNA-class probability 0.994057
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 17903290 95 - 22407834
AAAAAAAAAAAACUUAUUCACUGAUUUUUGUGCCCUUCUGCUGGCCAAUUUUUU-CGCUUGCACUGCAACUGCCGUUGGCCCAAACAGCAGCCUUU
..................(((........))).....((((((((((((.....-((.((((...)))).))..))))))).....)))))..... ( -17.30)
>DroSec_CAF1 123143 90 - 1
AA------AAAACUUAUCCACUGAUUUUUGUGCCCUUCUGCUGGCCAAUUUUUUCCGCUUGCACUGCGACUGCCGUUGGCCCAAACAGCAGCCUUU
..------..........(((........))).....((((((((((((......(((.......)))......))))))).....)))))..... ( -20.00)
>DroSim_CAF1 100867 90 - 1
AA------AAAACUUAUCCACUGAUUUUUGUGCCCUUCUGCUGGCCAAUUUUUUCCGCUUGCACUGCGACUGCCGUUGGCCCAAACAGCAGCCUUU
..------..........(((........))).....((((((((((((......(((.......)))......))))))).....)))))..... ( -20.00)
>DroEre_CAF1 112887 89 - 1
AA------AAAACUUAUCCACUGAUUUUUGUGCCCUUCUGCUGGCCAAUUUUUU-CGCUUCCACUGCGACUGCCAUUGGCCCAAAGAGCAGCCUUU
..------..........(((........))).....((((((((((((....(-(((.......)))).....))))))).....)))))..... ( -21.20)
>DroYak_CAF1 120437 89 - 1
AA------AAAACUUAUCCACUGAUUUUUGUGCCCUUCUGCGGGCCAAUUUUUU-CGCUUCCACUGCGACUGCCGUUGGCCCAAACAGCAGCCUUU
..------..........(((........))).....((((((((((((....(-(((.......)))).....)))))))).....))))..... ( -23.20)
>consensus
AA______AAAACUUAUCCACUGAUUUUUGUGCCCUUCUGCUGGCCAAUUUUUU_CGCUUGCACUGCGACUGCCGUUGGCCCAAACAGCAGCCUUU
..................(((........))).....((((((((((((......(((.......)))......))))))).....)))))..... (-18.58 = -18.82 +   0.24)

alignment

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secondary structure

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dotplot

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Window 7

Location 17,903,350 – 17,903,459
Length 109
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 76.29
Mean single sequence MFE -29.20
Consensus MFE -12.91
Energy contribution -12.99
Covariance contribution 0.08
Combinations/Pair 1.14
Mean z-score -2.63
Structure conservation index 0.44
SVM decision value 1.57
SVM RNA-class probability 0.964808
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 17903350 109 + 22407834
GGGCACAAAAAUCAGUGAAUAAGUU-----UUUUUUUUUUUGUCGUUCAGGCAAGUU-AC-----CAAAAAGCAGCGCCAAAAAUUGUGCUACAAAAAUUGCAUUUAAGGUAUGCAAUAA
.(((((((......(((.....(((-----((((....((((((.....))))))..-..-----.)))))))..)))......)))))))......(((((((.......))))))).. ( -24.70)
>DroPse_CAF1 194820 103 + 1
AGGCACAAAAAUCAGUGGGCAGGGG-----GC------AGC-----CCUGGAGGGGA-ACCCGGGCAGGAGCCAGCGCCAAAAAUUGUGCUACAAAAAUUGCAUUUAAGGUAUGCAAUAA
.(((((((.......(((((..(((-----..------..(-----((.....))).-.))).(((....))).)).)))....)))))))......(((((((.......))))))).. ( -35.20)
>DroSim_CAF1 100928 103 + 1
GGGCACAAAAAUCAGUGGAUAAGUU-----UU------UUCGCCAUUCAGGCAAGUU-AC-----CAAAAAGCAGCGCCAAAAAUUGUGUUACAAAAAUUGCAUUUAAGGUAUGCAAUAA
.(((((((.......(((....(((-----((------((.(((.....)))..(..-..-----))))))))....)))....)))))))......(((((((.......))))))).. ( -20.70)
>DroEre_CAF1 112947 103 + 1
GGGCACAAAAAUCAGUGGAUAAGUU-----UU------UUUCCCGCUCAGGCAAGUU-AC-----CAAAAAGCAGCGCCAAAAAUUGUGCUACAAAAAUUGCAUUUAAGGUAUGCAAUAA
.(((((((.....(((((.......-----..------....)))))..(((..(((-..-----.....)))...))).....)))))))......(((((((.......))))))).. ( -23.42)
>DroAna_CAF1 116873 109 + 1
AGGCACAAAAAUCAGUGGCCAGAGCCAGGGCC------AGGGCCGAGGGAGCAAGUUUCC-----CAAAAAGCAGCGCCAAAAAUUGUGCUGCAAAAAUUGCAUUUAAGGUAUGCAAUAA
.(((((........))((((........))))------...)))..(((((.....))))-----).....(((((((........)))))))....(((((((.......))))))).. ( -36.00)
>DroPer_CAF1 195930 103 + 1
AGGCACAAAAAUCAGUGGGCAGGGG-----GC------AGC-----CCUGGAGGGGA-ACCCGGGCAGGAGCCAGCGCCAAAAAUUGUGCUACAAAAAUUGCAUUUAAGGUAUGCAAUAA
.(((((((.......(((((..(((-----..------..(-----((.....))).-.))).(((....))).)).)))....)))))))......(((((((.......))))))).. ( -35.20)
>consensus
AGGCACAAAAAUCAGUGGACAAGGU_____UC______AGCGCCG_UCAGGCAAGUU_AC_____CAAAAAGCAGCGCCAAAAAUUGUGCUACAAAAAUUGCAUUUAAGGUAUGCAAUAA
.(((((((...((....))..............................(((..((...............))...))).....)))))))......(((((((.......))))))).. (-12.91 = -12.99 +   0.08)

alignment

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secondary structure

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dotplot

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Window 8

Location 17,903,350 – 17,903,459
Length 109
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 76.29
Mean single sequence MFE -26.79
Consensus MFE -10.52
Energy contribution -10.88
Covariance contribution 0.36
Combinations/Pair 1.06
Mean z-score -2.20
Structure conservation index 0.39
SVM decision value 0.23
SVM RNA-class probability 0.645332
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 17903350 109 - 22407834
UUAUUGCAUACCUUAAAUGCAAUUUUUGUAGCACAAUUUUUGGCGCUGCUUUUUG-----GU-AACUUGCCUGAACGACAAAAAAAAAAA-----AACUUAUUCACUGAUUUUUGUGCCC
..(((((((.......))))))).......((((((.....((((.((((....)-----))-)...))))((((..(............-----...)..)))).......)))))).. ( -17.56)
>DroPse_CAF1 194820 103 - 1
UUAUUGCAUACCUUAAAUGCAAUUUUUGUAGCACAAUUUUUGGCGCUGGCUCCUGCCCGGGU-UCCCCUCCAGG-----GCU------GC-----CCCCUGCCCACUGAUUUUUGUGCCU
..(((((((.......))))))).......((((((.((.(((.((.(((....))).((((-..(((....))-----)..------))-----))...)))))..))...)))))).. ( -33.30)
>DroSim_CAF1 100928 103 - 1
UUAUUGCAUACCUUAAAUGCAAUUUUUGUAACACAAUUUUUGGCGCUGCUUUUUG-----GU-AACUUGCCUGAAUGGCGAA------AA-----AACUUAUCCACUGAUUUUUGUGCCC
..(((((((.......)))))))..................(((((((((....)-----))-)..(((((.....))))).------..-----...................))))). ( -20.50)
>DroEre_CAF1 112947 103 - 1
UUAUUGCAUACCUUAAAUGCAAUUUUUGUAGCACAAUUUUUGGCGCUGCUUUUUG-----GU-AACUUGCCUGAGCGGGAAA------AA-----AACUUAUCCACUGAUUUUUGUGCCC
..(((((((.......))))))).......(((((((((((..(.((((((...(-----((-.....))).)))))))..)------))-----))...(((....)))..)))))).. ( -23.70)
>DroAna_CAF1 116873 109 - 1
UUAUUGCAUACCUUAAAUGCAAUUUUUGCAGCACAAUUUUUGGCGCUGCUUUUUG-----GGAAACUUGCUCCCUCGGCCCU------GGCCCUGGCUCUGGCCACUGAUUUUUGUGCCU
..(((((((.......))))))).......((((((...(..(...........(-----(((.......))))..((((..------(((....)))..)))).)..)...)))))).. ( -32.40)
>DroPer_CAF1 195930 103 - 1
UUAUUGCAUACCUUAAAUGCAAUUUUUGUAGCACAAUUUUUGGCGCUGGCUCCUGCCCGGGU-UCCCCUCCAGG-----GCU------GC-----CCCCUGCCCACUGAUUUUUGUGCCU
..(((((((.......))))))).......((((((.((.(((.((.(((....))).((((-..(((....))-----)..------))-----))...)))))..))...)))))).. ( -33.30)
>consensus
UUAUUGCAUACCUUAAAUGCAAUUUUUGUAGCACAAUUUUUGGCGCUGCUUUUUG_____GU_AACUUGCCUGA_CGGCGAA______AA_____AACCUAUCCACUGAUUUUUGUGCCC
..(((((((.......)))))))....(((((.(........).)))))......................................................(((........)))... (-10.52 = -10.88 +   0.36)

alignment

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secondary structure

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dotplot

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Window 9

Location 17,903,385 – 17,903,497
Length 112
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 82.52
Mean single sequence MFE -32.50
Consensus MFE -19.03
Energy contribution -20.12
Covariance contribution 1.09
Combinations/Pair 1.11
Mean z-score -3.10
Structure conservation index 0.59
SVM decision value 0.72
SVM RNA-class probability 0.832704
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 17903385 112 + 22407834
UGUCGUUCAGGCAAGUU-AC-----CAAAAAGCAGCGCCAAAAAUUGUGCUACAAAAAUUGCAUUUAAGGUAUGCAAUAAAAUGCCAUGCAUA--UUUGGCUCUUGCUGUGCUUUUUGCA
((((.....))))....-..-----(((((((((((((........)))))(((...(((((((.......))))))).....((((......--..))))......))))))))))).. ( -29.20)
>DroSim_CAF1 100957 112 + 1
CGCCAUUCAGGCAAGUU-AC-----CAAAAAGCAGCGCCAAAAAUUGUGUUACAAAAAUUGCAUUUAAGGUAUGCAAUAAAAUGCCAUGCAUA--UUUGGCUCUUGCUGUGCUUUUUGCA
.(((.....))).....-..-----(((((((((((((((((..(((.....)))....(((((....(((((........))))))))))..--))))))....))..))))))))).. ( -30.20)
>DroEre_CAF1 112976 112 + 1
UCCCGCUCAGGCAAGUU-AC-----CAAAAAGCAGCGCCAAAAAUUGUGCUACAAAAAUUGCAUUUAAGGUAUGCAAUAAAAUGCCAUGCAUA--UUUUGGUCUUGCUGGGCUUUUUGCC
....((((((.((((..-((-----(((((.(.(((((........))))).)......(((((....(((((........))))))))))..--)))))))))))))))))........ ( -34.40)
>DroYak_CAF1 120526 111 + 1
UCCCGUUCAUGCAAGUU-AC-----CAAAAAGCAGCGCCAAAAAUUGUGCUACAAAAAUUGCAUUUAAGGUAUGCAAUAAAAUGCCAUGCAUA--UU-UGGUCUUGCUGGGCUUUUUGCA
....(((((.(((((..-((-----((((..(.(((((........))))).)......(((((....(((((........))))))))))..--))-))))))))))))))........ ( -31.00)
>DroAna_CAF1 116907 115 + 1
GGCCGAGGGAGCAAGUUUCC-----CAAAAAGCAGCGCCAAAAAUUGUGCUGCAAAAAUUGCAUUUAAGGUAUGCAAUAAAAUGCCAUGCAUACAUUUUGCUCUUCUUGCUCUUUUUGCC
(((.(((((((((((.....-----(((((.(((((((........)))))))......(((((....(((((........))))))))))....))))).....))))))))))).))) ( -42.70)
>DroPer_CAF1 195959 104 + 1
C-----CCUGGAGGGGA-ACCCGGGCAGGAGCCAGCGCCAAAAAUUGUGCUACAAAAAUUGCAUUUAAGGUAUGCAAUAAAAUGCCAUGCAUACAUUUUGCUCUU-------UUU---UU
.-----(((((.(....-.)))))).((((((.(((((........)))))........(((((....(((((........))))))))))........))))))-------...---.. ( -27.50)
>consensus
UGCCGUUCAGGCAAGUU_AC_____CAAAAAGCAGCGCCAAAAAUUGUGCUACAAAAAUUGCAUUUAAGGUAUGCAAUAAAAUGCCAUGCAUA__UUUUGCUCUUGCUGGGCUUUUUGCA
.........................(((((((((((((........))))).(((((..(((((....(((((........))))))))))....)))))..........)))))))).. (-19.03 = -20.12 +   1.09)

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 12:09:48 2006