Locus 3466

Sequence ID 3L_DroMel_CAF1
Location 10,190,747 – 10,190,870
Length 123
Max. P 0.970758
window5409 window5410 window5411

overview

Window 9

Location 10,190,747 – 10,190,846
Length 99
Sequences 6
Columns 111
Reading direction forward
Mean pairwise identity 80.35
Mean single sequence MFE -27.18
Consensus MFE -17.39
Energy contribution -17.42
Covariance contribution 0.03
Combinations/Pair 1.23
Mean z-score -3.36
Structure conservation index 0.64
SVM decision value 1.66
SVM RNA-class probability 0.970758
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 10190747 99 + 23771897
ACACAA---UGAUCGGGCUAAUUGUGCAAAAAUGU--------UUUUGCAAAUAUUUUGUUAACAAAUUUUGCGGCAUUUUAAGCCACAGAAAUGCAAUUAGC-CGUGAAC
......---...(((((((((((((((((((.(((--------(...((((.....)))).))))..))))))(((.......)))........)))))))))-).))).. ( -29.10)
>DroVir_CAF1 95204 106 + 1
AUACAA---UUGUCAUGCUAAUUGUAUAAAAAUGA-UAAAGAGUUUUGCAAAUAUUUUGUUAACAAAUUGUGUGGCAAUUUAGGCCACAAAAAUGCAAUUAGC-UGUACAC
......---.(((((.(((((((((((.....(((-(((((.(((.....))).))))))))........((((((.......))))))...)))))))))))-)).))). ( -27.90)
>DroPse_CAF1 76843 107 + 1
AUACAA---UGACCGAGCUAAUUGUGCAAAAAUGUGUGUGUUUUUCUGCAAAUAUUUUGUUAACAAAUUUUGCGGCCAUUUAAACCACAGAAAUGCAAUUAGC-CAUGAAC
......---.....(.((((((((((((....)))(((.((((..(((((((...((((....)))).)))))))......)))))))......)))))))))-)...... ( -24.80)
>DroWil_CAF1 97216 99 + 1
GCACAA---UGACCAAACUAAUUGCGCAAAAAUGU--------U-UGGCAAAUAUUUUGUUAACAAAUUGUGUGGCAAUUUAAGCCACAGAAAUGCAAUUAGCCCAUAAGC
......---........(((((((((......(((--------(-.(((((.....)))))))))..((.((((((.......)))))).)).)))))))))......... ( -24.10)
>DroAna_CAF1 65247 102 + 1
AUACAUUCCUGUGCUGGCUAGUUGUGCAAACAUGU--------UAUUGCAAAUAUUUUGUUAACAAAUUUUGUGGCCUUUUAAGCCACAGAAACGCAAUUAGC-CGUGAAC
.((((....))))..(((((((((((......(((--------((..((((.....)))))))))..(((((((((.......))))))))).))))))))))-)...... ( -32.40)
>DroPer_CAF1 77081 107 + 1
AUACAA---UGACCGAGCUAAUUGUGCAAAAAUGUGUGUGUUUUUCUGCAAAUAUUUUGUUAACAAAUUUUGCGGCCAUUUAAACCACAGAAAUGCAAUUAGC-CAUGAAC
......---.....(.((((((((((((....)))(((.((((..(((((((...((((....)))).)))))))......)))))))......)))))))))-)...... ( -24.80)
>consensus
AUACAA___UGACCGAGCUAAUUGUGCAAAAAUGU________UUUUGCAAAUAUUUUGUUAACAAAUUUUGCGGCAAUUUAAGCCACAGAAAUGCAAUUAGC_CAUGAAC
................((((((((((.....................(((((...((((....)))).)))))(((.......))).......))))))))))........ (-17.39 = -17.42 +   0.03)

alignment

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secondary structure

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Window 0

Location 10,190,747 – 10,190,846
Length 99
Sequences 6
Columns 111
Reading direction reverse
Mean pairwise identity 80.35
Mean single sequence MFE -24.25
Consensus MFE -19.35
Energy contribution -18.88
Covariance contribution -0.47
Combinations/Pair 1.33
Mean z-score -2.39
Structure conservation index 0.80
SVM decision value 1.33
SVM RNA-class probability 0.943106
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 10190747 99 - 23771897
GUUCACG-GCUAAUUGCAUUUCUGUGGCUUAAAAUGCCGCAAAAUUUGUUAACAAAAUAUUUGCAAAA--------ACAUUUUUGCACAAUUAGCCCGAUCA---UUGUGU
......(-((((((((......((((((.......))))))...((((....)))).....(((((((--------....))))))))))))))))......---...... ( -27.30)
>DroVir_CAF1 95204 106 - 1
GUGUACA-GCUAAUUGCAUUUUUGUGGCCUAAAUUGCCACACAAUUUGUUAACAAAAUAUUUGCAAAACUCUUUA-UCAUUUUUAUACAAUUAGCAUGACAA---UUGUAU
.(((.((-((((((((......((((((.......))))))...(((((.............)))))........-...........)))))))).))))).---...... ( -21.12)
>DroPse_CAF1 76843 107 - 1
GUUCAUG-GCUAAUUGCAUUUCUGUGGUUUAAAUGGCCGCAAAAUUUGUUAACAAAAUAUUUGCAGAAAAACACACACAUUUUUGCACAAUUAGCUCGGUCA---UUGUAU
......(-((((((((......(((((((.....)))))))...((((....)))).....((((((((..........)))))))))))))))))......---...... ( -23.60)
>DroWil_CAF1 97216 99 - 1
GCUUAUGGGCUAAUUGCAUUUCUGUGGCUUAAAUUGCCACACAAUUUGUUAACAAAAUAUUUGCCA-A--------ACAUUUUUGCGCAAUUAGUUUGGUCA---UUGUGC
.....(..(((((((((.....((((((.......))))))(((..((((..(((.....)))...-)--------)))...))).)))))))))..)....---...... ( -24.70)
>DroAna_CAF1 65247 102 - 1
GUUCACG-GCUAAUUGCGUUUCUGUGGCUUAAAAGGCCACAAAAUUUGUUAACAAAAUAUUUGCAAUA--------ACAUGUUUGCACAACUAGCCAGCACAGGAAUGUAU
......(-((((.(((.((...(((((((.....)))))))((((.(((((.(((.....)))...))--------))).)))))).))).)))))...(((....))).. ( -25.20)
>DroPer_CAF1 77081 107 - 1
GUUCAUG-GCUAAUUGCAUUUCUGUGGUUUAAAUGGCCGCAAAAUUUGUUAACAAAAUAUUUGCAGAAAAACACACACAUUUUUGCACAAUUAGCUCGGUCA---UUGUAU
......(-((((((((......(((((((.....)))))))...((((....)))).....((((((((..........)))))))))))))))))......---...... ( -23.60)
>consensus
GUUCACG_GCUAAUUGCAUUUCUGUGGCUUAAAUGGCCACAAAAUUUGUUAACAAAAUAUUUGCAAAA________ACAUUUUUGCACAAUUAGCUCGGUCA___UUGUAU
.....((.((((((((......((((((.......))))))...((((....)))).....(((((((............))))))))))))))).))............. (-19.35 = -18.88 +  -0.47)

alignment

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secondary structure

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Window 1

Location 10,190,777 – 10,190,870
Length 93
Sequences 6
Columns 104
Reading direction reverse
Mean pairwise identity 81.22
Mean single sequence MFE -17.48
Consensus MFE -14.00
Energy contribution -13.37
Covariance contribution -0.64
Combinations/Pair 1.27
Mean z-score -1.12
Structure conservation index 0.80
SVM decision value -0.06
SVM RNA-class probability 0.500000
Prediction OTHER

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 10190777 93 - 23771897
-ACU-AAAAUUUUG-UCGGUUAAUUACGUUCACGGCUAAUUGCAUUUCUGUGGCUUAAAAUGCCGCAAAAUUUGUUAACAAAAUAUUUGCAAAA--------AC
-...-........(-(((..............))))...(((((....((((((.......))))))...((((....)))).....)))))..--------.. ( -17.94)
>DroVir_CAF1 95234 99 - 1
-AUA-CUCAUAU--UUCAGUUAAUUGCGUGUACAGCUAAUUGCAUUUUUGUGGCCUAAAUUGCCACACAAUUUGUUAACAAAAUAUUUGCAAAACUCUUUA-UC
-...-...((((--((..((((((....(((...((.....))......(((((.......))))))))....)))))).))))))...............-.. ( -16.60)
>DroPse_CAF1 76873 104 - 1
CAUUCCUCAUUUUGUUCGGUUAAUUACGUUCAUGGCUAAUUGCAUUUCUGUGGUUUAAAUGGCCGCAAAAUUUGUUAACAAAAUAUUUGCAGAAAAACACACAC
..(((..((...((((..((((((....((..((((((((..((....))..)).....))))))..))....))))))..))))..))..))).......... ( -17.20)
>DroEre_CAF1 71449 93 - 1
-ACU-CACAUUUUG-UCGGUUAAUUACAUUCACGGCUAAUUGCAUUUUUGUGGCUUCAAAUGCCGCAAAAUUUGUUAACAUAAUAUUUGCAAAA--------AC
-...-........(-(((..............))))...(((((.(((((((((.......)))))))))..((....)).......)))))..--------.. ( -18.44)
>DroAna_CAF1 65280 95 - 1
CAUU-CUCAUUUUAUUUGGUUAAUUACGUUCACGGCUAAUUGCGUUUCUGUGGCUUAAAAGGCCACAAAAUUUGUUAACAAAAUAUUUGCAAUA--------AC
....-.......(((((.((((((..((....))((.....)).....(((((((.....)))))))......)))))).))))).........--------.. ( -17.50)
>DroPer_CAF1 77111 104 - 1
CAUUCCUCAUUUUGUUCGGUUAAUUACGUUCAUGGCUAAUUGCAUUUCUGUGGUUUAAAUGGCCGCAAAAUUUGUUAACAAAAUAUUUGCAGAAAAACACACAC
..(((..((...((((..((((((....((..((((((((..((....))..)).....))))))..))....))))))..))))..))..))).......... ( -17.20)
>consensus
_AUU_CUCAUUUUGUUCGGUUAAUUACGUUCACGGCUAAUUGCAUUUCUGUGGCUUAAAAGGCCGCAAAAUUUGUUAACAAAAUAUUUGCAAAA________AC
.......................................(((((....((((((.......))))))...((((....)))).....)))))............ (-14.00 = -13.37 +  -0.64)

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 10:58:47 2006