Locus 2509

Sequence ID 2R_DroMel_CAF1
Location 8,946,577 – 8,946,749
Length 172
Max. P 0.832990
window4141 window4142 window4143

overview

Window 1

Location 8,946,577 – 8,946,671
Length 94
Sequences 6
Columns 113
Reading direction reverse
Mean pairwise identity 82.57
Mean single sequence MFE -24.63
Consensus MFE -19.32
Energy contribution -19.18
Covariance contribution -0.14
Combinations/Pair 1.06
Mean z-score -1.33
Structure conservation index 0.78
SVM decision value -0.01
SVM RNA-class probability 0.528093
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 8946577 94 - 20766785
CUUUCUGAACGAAAGCG-UAUGAGCGUUCUGGUCCUCUCUGAGGGCGUGGGUUCGAAUCCCACUUCUGACAAAAUUUUUUUUA-G------------UGGU-UUUGUUU----
..........(((.((.-.....)).)))..((((((...))))))(((((.......)))))....(((((((((.......-.------------.)))-)))))).---- ( -24.10)
>DroPse_CAF1 13077 104 - 1
CUUUCUGAACGAAAGUG-U-UGAGCGUUCUGGUCCUCUCUGAGGGCGUGGGUUCGAAUCCCACUUCUGACAAACUUUUUUUUUCUGUUUUUUG----AUGU-UUUUUUU--UA
(((((.....)))))..-.-.(((((((...((((((...))))))(((((.......))))).............................)----))))-)).....--.. ( -22.00)
>DroSim_CAF1 15079 103 - 1
CUUUCCGAACGAAAGUGUUAUGAGCGUUCUGGUCCUCUCUGAGGGCGUGGGUUCGAAUCCCACUUCUGACAAAAUUUUUUUUA-U--------GCUCUUGU-UUUGUUUAGUA
......((((((((.......((((((....((((((...))))))(((((.......)))))...................)-)--------))))...)-))))))).... ( -26.60)
>DroEre_CAF1 20165 100 - 1
CUUUCUGAACGAAAGUG-UAUGAGCGUUCUGGUCCUCUCUGAGGGCGUGGGUUCGAAUCCCACUUCUGACAAAACUUUUUUUG-UUU------AUUG-----UUUUUGUAAUC
........((((((..(-.(((((((.....((((((...))))))(((((.......)))))..................))-)))------))).-----.)))))).... ( -24.30)
>DroYak_CAF1 15877 106 - 1
CUUUCUGAAUGAAAGUG-UAUGGGCGUUCUGGUCCUCUCUGAGGGCGUGGGUUCGAAUCCCACUUCUGACAAAUCUUUUUUUCAUAU------AUUAUUACUUUUUUGUGGUC
(((((.....)))))((-((((((.......((((((...))))))(((((.......))))).................)))))))------)..(((((......))))). ( -25.40)
>DroPer_CAF1 13162 96 - 1
CUUUCUGAACGAAAGUG-U-UGAGCGUUCUGGUCCUCUCUGAGGGCGUGGGUUCGAAUCCCACUUCUGACAAACCUUUUU-UGCUG-----------UUGU-UUUUUUU--UA
......((((((.((((-.-.(((.(((.((((((((...))))))(((((.......)))))......))))))))...-)))).-----------))))-)).....--.. ( -25.40)
>consensus
CUUUCUGAACGAAAGUG_UAUGAGCGUUCUGGUCCUCUCUGAGGGCGUGGGUUCGAAUCCCACUUCUGACAAAACUUUUUUUA_U____________UUGU_UUUUUUU__UA
......(((((..(......)...)))))..((((((...))))))(((((.......))))).................................................. (-19.32 = -19.18 +  -0.14)

alignment

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secondary structure

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dotplot

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Window 2

Location 8,946,592 – 8,946,709
Length 117
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 93.40
Mean single sequence MFE -34.78
Consensus MFE -32.96
Energy contribution -32.60
Covariance contribution -0.36
Combinations/Pair 1.09
Mean z-score -1.10
Structure conservation index 0.95
SVM decision value 0.72
SVM RNA-class probability 0.832990
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 8946592 117 - 20766785
AGCGGUCUAAGGCGCCAGACUCAAGAUU--UAAAAUCUUACUUUCUGAACGAAAGCG-UAUGAGCGUUCUGGUCCUCUCUGAGGGCGUGGGUUCGAAUCCCACUUCUGACAAAAUUUUUU
....(((((..((((((.((..(((((.--....))))).(((((.....))))).)-).)).))))..))((((((...))))))(((((.......)))))....))).......... ( -31.90)
>DroPse_CAF1 13103 117 - 1
AGCGGUCUAAGGCGCCAGACUCAAGGUGU-UGAAAUCUUGCUUUCUGAACGAAAGUG-U-UGAGCGUUCUGGUCCUCUCUGAGGGCGUGGGUUCGAAUCCCACUUCUGACAAACUUUUUU
....(((((..((((((((..((((((..-....))))))...)))).((....)).-.-...))))..))((((((...))))))(((((.......)))))....))).......... ( -35.90)
>DroSim_CAF1 15102 118 - 1
AGCGGUCUAAGGCGCCAGACUCAAGAUU--GUAAAUCUUACUUUCCGAACGAAAGUGUUAUGAGCGUUCUGGUCCUCUCUGAGGGCGUGGGUUCGAAUCCCACUUCUGACAAAAUUUUUU
....(((....((((((((((((((((.--....))))(((((((.....)))))))...))))...))))))((((...))))))(((((.......)))))....))).......... ( -33.10)
>DroYak_CAF1 15904 117 - 1
AGCGGUCUAAGGCGCCAGACUCAAGAUU--UAAAAUCUUACUUUCUGAAUGAAAGUG-UAUGGGCGUUCUGGUCCUCUCUGAGGGCGUGGGUUCGAAUCCCACUUCUGACAAAUCUUUUU
....(((((..(((((..((..(((((.--....)))))((((((.....)))))))-)...)))))..))((((((...))))))(((((.......)))))....))).......... ( -36.50)
>DroAna_CAF1 17798 117 - 1
AGCGGUCUAAGGCGCCAGACUCAAGAUA--UAGAAUCUUGCUUUCUGAACGAAAGUG-UGUGAGCGUUCUGGUCCUCUCUGAGGGCGUGGGUUCGAAUCCCACUUCUGACAAAAUUUUUU
....(((((..((((((.((..(((((.--....)))))((((((.....)))))))-).)).))))..))((((((...))))))(((((.......)))))....))).......... ( -35.90)
>DroPer_CAF1 13180 118 - 1
AGCGGUCUAAGGCGCCAGACUCAAGGUGUUUGAAAUCUUGCUUUCUGAACGAAAGUG-U-UGAGCGUUCUGGUCCUCUCUGAGGGCGUGGGUUCGAAUCCCACUUCUGACAAACCUUUUU
....(((((..((((((((..((((((.......))))))...)))).((....)).-.-...))))..))((((((...))))))(((((.......)))))....))).......... ( -35.40)
>consensus
AGCGGUCUAAGGCGCCAGACUCAAGAUU__UAAAAUCUUACUUUCUGAACGAAAGUG_UAUGAGCGUUCUGGUCCUCUCUGAGGGCGUGGGUUCGAAUCCCACUUCUGACAAAAUUUUUU
....(((....((((((((((((((((.......)))))((((((.....)))))).....)))...))))))((((...))))))(((((.......)))))....))).......... (-32.96 = -32.60 +  -0.36)

alignment

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secondary structure

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dotplot

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Window 3

Location 8,946,632 – 8,946,749
Length 117
Sequences 6
Columns 119
Reading direction reverse
Mean pairwise identity 86.82
Mean single sequence MFE -39.72
Consensus MFE -32.34
Energy contribution -32.37
Covariance contribution 0.03
Combinations/Pair 1.11
Mean z-score -1.76
Structure conservation index 0.81
SVM decision value 0.02
SVM RNA-class probability 0.543875
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 8946632 117 - 20766785
ACGGAAUCGGACACGAGUUUGGCAUAUGUCAGGAUGGCCGAGCGGUCUAAGGCGCCAGACUCAAGAUU--UAAAAUCUUACUUUCUGAACGAAAGCGUAUGAGCGUUCUGGUCCUCUCU
..(((.(((((.(((((((((((....(((.((((.((...)).))))..))))))))))))(((((.--....))))).(((((.....))))).........))))))))))..... ( -34.40)
>DroPse_CAF1 13143 117 - 1
GCGGUUUGUGACACGGAAUCAGCAUGUGUCAGGAUGGCCGAGCGGUCUAAGGCGCCAGACUCAAGGUGU-UGAAAUCUUGCUUUCUGAACGAAAGUGU-UGAGCGUUCUGGUCCUCUCU
..(((((.(((((((.........))))))).))..)))(((.((.(((..((((((((..((((((..-....))))))...)))).((....))..-...))))..))).)).))). ( -41.90)
>DroEre_CAF1 20226 117 - 1
AGCGAAUCUGACACAAGCAUGCCAUGUGUCAGGAUGGCCGAGCGGUCUAAGGCGCCAGACUCAAGAUG--UCAAAUCUUGCUUUCUGAACGAAAGUGUAUGAGCGUUCUGGUCCUCUCU
.((.(.(((((((((.(.....).))))))))).).)).(((.((.(((..((((((((..((((((.--....))))))...)))).((....))......))))..))).)).))). ( -44.10)
>DroYak_CAF1 15944 117 - 1
AGCGAAUCGGACACUAGUAUAUCAUGUGUCAGGAUGGCCGAGCGGUCUAAGGCGCCAGACUCAAGAUU--UAAAAUCUUACUUUCUGAAUGAAAGUGUAUGGGCGUUCUGGUCCUCUCU
.((..(((.(((((...........)))))..))).)).(((.((.(((..(((((..((..(((((.--....)))))((((((.....))))))))...)))))..))).)).))). ( -39.70)
>DroAna_CAF1 17838 117 - 1
AGCGCUUCGGACGCACAACUAACAUAUGUCAGGAUGGCCGAGCGGUCUAAGGCGCCAGACUCAAGAUA--UAGAAUCUUGCUUUCUGAACGAAAGUGUGUGAGCGUUCUGGUCCUCUCU
.((((....).))).............(((.....))).(((.((.(((..((((((.((..(((((.--....)))))((((((.....)))))))).)).))))..))).)).))). ( -36.80)
>DroPer_CAF1 13220 118 - 1
ACGGUUUGUGACACGGAAUUAGCAUGUGUCAGGAUGGCCGAGCGGUCUAAGGCGCCAGACUCAAGGUGUUUGAAAUCUUGCUUUCUGAACGAAAGUGU-UGAGCGUUCUGGUCCUCUCU
..(((((.(((((((.........))))))).))..)))(((.((.(((..((((((((..((((((.......))))))...)))).((....))..-...))))..))).)).))). ( -41.40)
>consensus
ACCGAAUCGGACACGAAAUUAGCAUGUGUCAGGAUGGCCGAGCGGUCUAAGGCGCCAGACUCAAGAUG__UAAAAUCUUGCUUUCUGAACGAAAGUGUAUGAGCGUUCUGGUCCUCUCU
.........((((((.........)))))).((....))(((.((.(((..((((((.((..(((((.......)))))((((((.....)))))))).)).))))..))).)).))). (-32.34 = -32.37 +   0.03)

alignment

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secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:31:53 2006