Locus 7443

Sequence ID 3L_DroMel_CAF1
Location 19,997,844 – 19,997,966
Length 122
Max. P 0.825602
window12092 window12093 window12094

overview

Window 2

Location 19,997,844 – 19,997,937
Length 93
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 84.18
Mean single sequence MFE -18.62
Consensus MFE -17.51
Energy contribution -17.52
Covariance contribution 0.00
Combinations/Pair 1.17
Mean z-score -1.44
Structure conservation index 0.94
SVM decision value 0.48
SVM RNA-class probability 0.754682
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 19997844 93 + 23771897
UACAAA------------AAAUUAUUCAAUGUAUGCAUGGA--ACAUGGGAACAUUUAACGCUAUGAAAUUUAAUGAGCCCAAAAUGGCGCAUUAAAUGACACGACG-------------
......------------...........(((...(((((.--..(((....)))......)))))..((((((((.(((......))).)))))))).))).....------------- ( -17.20)
>DroSec_CAF1 87706 93 + 1
UACAAA------------AAAUUACUCAAUGUAUGCAUGGA--ACAUGGGAACAUUUAACGCUAUGAAAUUUAAUGAGCCCAAAAUGGCGCAUUAAAUGACAGGACG-------------
......------------.........(((((.(.((((..--.)))).).)))))...((((.((..((((((((.(((......))).))))))))..)))).))------------- ( -18.00)
>DroSim_CAF1 46596 93 + 1
UACAAA------------AAAUUACUCAAUGUAUGCAUGGA--ACAUGGGAACAUUUAACGCUAUGAAAUUUAAUGAGCCCAAAAUGGCGCAUUAAAUGACAGGACG-------------
......------------.........(((((.(.((((..--.)))).).)))))...((((.((..((((((((.(((......))).))))))))..)))).))------------- ( -18.00)
>DroEre_CAF1 38736 93 + 1
UACAAA------------AAAUUACUCCAUGCAUGCAUGGA--ACUUGGGAGCAUUUAACGCUAUGAAAUUUAAUGAGCCCAAAAUGGCGCAUUAAAUGACAGGACG-------------
......------------.......((((((....))))))--.((((..(((.......))).....((((((((.(((......))).))))))))..))))...------------- ( -24.50)
>DroYak_CAF1 39744 105 + 1
UACAAAAAAUUGUACAAAAAAUUACUCAAUGUAUGCAUGGG--ACAUGGGAACAUUUAACGCUAUGAAAUUUAAUGAGCCCAAAAUGGCGCAUUAAAUGCCAGGACG-------------
(((((....))))).............(((((.(.((((..--.)))).).)))))...((((.((..((((((((.(((......))).))))))))..)))).))------------- ( -19.50)
>DroAna_CAF1 40510 108 + 1
AAAUAA------------AAAUUACACAACGUAUGUAUGCAUGACGUGAAAACAUUUAACGCAAUGAAAUUUAAUGAGCCCAAAAUGGCGCAUUAACUGCCAGGACCAGGACCACAACCA
......------------..........(((((((....))).)))).....((((......))))....((((((.(((......))).))))))(((.......)))........... ( -14.50)
>consensus
UACAAA____________AAAUUACUCAAUGUAUGCAUGGA__ACAUGGGAACAUUUAACGCUAUGAAAUUUAAUGAGCCCAAAAUGGCGCAUUAAAUGACAGGACG_____________
...........................(((((.(.((((.....)))).).)))))........((..((((((((.(((......))).))))))))..)).................. (-17.51 = -17.52 +   0.00)

alignment

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secondary structure

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dotplot

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Window 3

Location 19,997,844 – 19,997,937
Length 93
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 84.18
Mean single sequence MFE -21.52
Consensus MFE -18.61
Energy contribution -19.20
Covariance contribution 0.59
Combinations/Pair 1.08
Mean z-score -1.87
Structure conservation index 0.87
SVM decision value 0.70
SVM RNA-class probability 0.825602
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 19997844 93 - 23771897
-------------CGUCGUGUCAUUUAAUGCGCCAUUUUGGGCUCAUUAAAUUUCAUAGCGUUAAAUGUUCCCAUGU--UCCAUGCAUACAUUGAAUAAUUU------------UUUGUA
-------------(((..((..((((((((.(((......))).))))))))..))..)))...(((((...((((.--..))))...))))).........------------...... ( -22.00)
>DroSec_CAF1 87706 93 - 1
-------------CGUCCUGUCAUUUAAUGCGCCAUUUUGGGCUCAUUAAAUUUCAUAGCGUUAAAUGUUCCCAUGU--UCCAUGCAUACAUUGAGUAAUUU------------UUUGUA
-------------(((..((..((((((((.(((......))).))))))))..))..)))...(((((...((((.--..))))...))))).........------------...... ( -19.90)
>DroSim_CAF1 46596 93 - 1
-------------CGUCCUGUCAUUUAAUGCGCCAUUUUGGGCUCAUUAAAUUUCAUAGCGUUAAAUGUUCCCAUGU--UCCAUGCAUACAUUGAGUAAUUU------------UUUGUA
-------------(((..((..((((((((.(((......))).))))))))..))..)))...(((((...((((.--..))))...))))).........------------...... ( -19.90)
>DroEre_CAF1 38736 93 - 1
-------------CGUCCUGUCAUUUAAUGCGCCAUUUUGGGCUCAUUAAAUUUCAUAGCGUUAAAUGCUCCCAAGU--UCCAUGCAUGCAUGGAGUAAUUU------------UUUGUA
-------------(((..((..((((((((.(((......))).))))))))..))..)))...............(--((((((....)))))))......------------...... ( -24.20)
>DroYak_CAF1 39744 105 - 1
-------------CGUCCUGGCAUUUAAUGCGCCAUUUUGGGCUCAUUAAAUUUCAUAGCGUUAAAUGUUCCCAUGU--CCCAUGCAUACAUUGAGUAAUUUUUUGUACAAUUUUUUGUA
-------------(((..(((.((((((((.(((......))).)))))))).)))..)))...(((((...((((.--..))))...))))).............(((((....))))) ( -22.50)
>DroAna_CAF1 40510 108 - 1
UGGUUGUGGUCCUGGUCCUGGCAGUUAAUGCGCCAUUUUGGGCUCAUUAAAUUUCAUUGCGUUAAAUGUUUUCACGUCAUGCAUACAUACGUUGUGUAAUUU------------UUAUUU
.....(((..((..(...((((.((....))))))..)..))..))).(((((.(((.((((...((((...........))))....)))).))).)))))------------...... ( -20.60)
>consensus
_____________CGUCCUGUCAUUUAAUGCGCCAUUUUGGGCUCAUUAAAUUUCAUAGCGUUAAAUGUUCCCAUGU__UCCAUGCAUACAUUGAGUAAUUU____________UUUGUA
.............(((..((..((((((((.(((......))).))))))))..))..)))...(((((...((((.....))))...)))))........................... (-18.61 = -19.20 +   0.59)

alignment

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secondary structure

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dotplot

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Window 4

Location 19,997,872 – 19,997,966
Length 94
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 84.16
Mean single sequence MFE -23.70
Consensus MFE -16.51
Energy contribution -16.93
Covariance contribution 0.42
Combinations/Pair 1.12
Mean z-score -1.94
Structure conservation index 0.70
SVM decision value -0.05
SVM RNA-class probability 0.507966
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 19997872 94 - 23771897
CAGCAUUCACUUCCUGGGCCUAC-------GUCCUU-----------------CGUCGUGUCAUUUAAUGCGCCAUUUUGGGCUCAUUAAAUUUCAUAGCGUUAAAUGUUCCCAUGU--U
..............((((...((-------((....-----------------(((..((..((((((((.(((......))).))))))))..))..)))....)))).))))...--. ( -25.90)
>DroSec_CAF1 87734 94 - 1
CAGCAUCCACUUCCUGCGCCUUC-------GUCCUU-----------------CGUCCUGUCAUUUAAUGCGCCAUUUUGGGCUCAUUAAAUUUCAUAGCGUUAAAUGUUCCCAUGU--U
.(((((..((.....((((...(-------(.....-----------------))...((..((((((((.(((......))).))))))))..))..)))).....))....))))--) ( -18.00)
>DroSim_CAF1 46624 94 - 1
CAGCAUCCACUUCCUGCGCCUUC-------GUCCUU-----------------CGUCCUGUCAUUUAAUGCGCCAUUUUGGGCUCAUUAAAUUUCAUAGCGUUAAAUGUUCCCAUGU--U
.(((((..((.....((((...(-------(.....-----------------))...((..((((((((.(((......))).))))))))..))..)))).....))....))))--) ( -18.00)
>DroEre_CAF1 38764 101 - 1
CAGCAUCCACUUCUUGGGCCUGCGUCCUGCGUCCUU-----------------CGUCCUGUCAUUUAAUGCGCCAUUUUGGGCUCAUUAAAUUUCAUAGCGUUAAAUGCUCCCAAGU--U
............((((((...((((...((((....-----------------.....((..((((((((.(((......))).))))))))..))..))))...)))).)))))).--. ( -26.30)
>DroYak_CAF1 39784 94 - 1
CAGCAUCCACUUCCUGGGCCUUC-------GUCCUU-----------------CGUCCUGGCAUUUAAUGCGCCAUUUUGGGCUCAUUAAAUUUCAUAGCGUUAAAUGUUCCCAUGU--C
..............((((....(-------((....-----------------(((..(((.((((((((.(((......))).)))))))).)))..)))....)))..))))...--. ( -22.90)
>DroAna_CAF1 40538 113 - 1
CAGAGACAGCUUCCUGGGCCUUG-------GUCCUUGUCCUGGUUGUGGUCCUGGUCCUGGCAGUUAAUGCGCCAUUUUGGGCUCAUUAAAUUUCAUUGCGUUAAAUGUUUUCACGUCAU
....(((.(((.((.(((((..(-------(.((.............)).)).))))).)).)))(((((.(((......))).))))).....((((......)))).......))).. ( -31.12)
>consensus
CAGCAUCCACUUCCUGGGCCUUC_______GUCCUU_________________CGUCCUGUCAUUUAAUGCGCCAUUUUGGGCUCAUUAAAUUUCAUAGCGUUAAAUGUUCCCAUGU__U
.(((((..((.....((((...........))))....................((..((..((((((((.(((......))).))))))))..))..))))...))))).......... (-16.51 = -16.93 +   0.42)

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 12:47:13 2006