Locus 9254

Sequence ID 3R_DroMel_CAF1
Location 24,673,308 – 24,673,533
Length 225
Max. P 0.636234
window14795 window14796 window14797

overview

Window 5

Location 24,673,308 – 24,673,413
Length 105
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 77.00
Mean single sequence MFE -40.77
Consensus MFE -28.23
Energy contribution -27.97
Covariance contribution -0.25
Combinations/Pair 1.05
Mean z-score -1.51
Structure conservation index 0.69
SVM decision value 0.03
SVM RNA-class probability 0.549021
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 24673308 105 - 27905053
GUCCAAAGUGU----------GCGCAAGGAGGCGGGACUGGGCAUUGUGCAAGGUUAGGGCGUUGGCUUGCCAGCGCCUCGU-----AUCGCUAAUGAUGCUAAACCAGCCUGGAUCGCU
((((...((.(----------.(....).).))(((.((((((((..(....(((..(((((((((....)))))))))...-----)))....)..))))....))))))))))).... ( -43.30)
>DroSim_CAF1 14330 105 - 1
GUCCAAAGUGG----------GCGCAAGAAGGCGGGUCUGGGCAUUGUGCAAGGUUAGGGCGUUGGCUGGGCAGCGCCUCGA-----AUCGCUAAUGAUGCUAAACCAGCCUAGAUCGCU
((((.....))----------))((....((((.(((...(((((..(....((((.((((((((......))))))))..)-----)))....)..)))))..))).)))).....)). ( -41.30)
>DroEre_CAF1 15870 83 - 1
---------------------GCGCAAG-GGGCGGGGCUGGGCAUUGUGCAAGGUUAGGGCGUUGGCUUGACAGCGCCUCGA-----AUCGCUAAUGAUGCUAAGCCAGC----------
---------------------.(((...-..))).((((.(((((..(....((((.((((((((......))))))))..)-----)))....)..))))).))))...---------- ( -36.40)
>DroYak_CAF1 14658 119 - 1
GUUUGGAGUGGGCGCAAGGGGGCGCAAGGGGGCGGGGCCGGGCAUUGUGCAAGGUUAGGGCGUUGGCUUGACAGCGCCUCGAAUCGAAUCGCUAAUGAUGCUAAGCCAGC-UGGAUGGCU
......(((.(((((......)))).....(((..(((..(((((..(((..((((.((((((((......))))))))..)))).....))..)..)))))..))).))-)...).))) ( -42.10)
>consensus
GUCCAAAGUGG__________GCGCAAGGAGGCGGGGCUGGGCAUUGUGCAAGGUUAGGGCGUUGGCUUGACAGCGCCUCGA_____AUCGCUAAUGAUGCUAAACCAGC_UGGAUCGCU
.....................((((((....((........)).))))))..((((.((((((((......))))))))...........((.......))..))))............. (-28.23 = -27.97 +  -0.25)

alignment

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secondary structure

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dotplot

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Window 6

Location 24,673,343 – 24,673,453
Length 110
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 76.46
Mean single sequence MFE -36.18
Consensus MFE -23.58
Energy contribution -25.78
Covariance contribution 2.20
Combinations/Pair 1.11
Mean z-score -1.49
Structure conservation index 0.65
SVM decision value 0.10
SVM RNA-class probability 0.581077
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 24673343 110 - 27905053
CGACAGGAGGAGGACAGUGGGCCGGGAACCAAGGAAGUAGGUCCAAAGUGU----------GCGCAAGGAGGCGGGACUGGGCAUUGUGCAAGGUUAGGGCGUUGGCUUGCCAGCGCCUC
...........(.(((((.(.((((...((..(((......)))...((.(----------.(....).).))))..)))).)))))).).......(((((((((....))))))))). ( -41.30)
>DroSec_CAF1 14343 91 - 1
----AGGAGGAGGACAGUGGGCCGGGAACCAAGGAAGUGGGUCCAAAGUGG----------GCGCAAGAAGGCGGGGCUGGGCAUUGUGCAAGGUUAGGGCAUUG---------------
----.......(.(((((..(((.((..((.......((.((((.....))----------)).)).......))..)).)))))))).)...............--------------- ( -25.74)
>DroSim_CAF1 14365 106 - 1
----AGGAGGAGGACAGUGGGCCGGGAACCAAGGAAGUGGGUCCAAAGUGG----------GCGCAAGAAGGCGGGUCUGGGCAUUGUGCAAGGUUAGGGCGUUGGCUGGGCAGCGCCUC
----.......(.(((((..(((.(((.((.......((.((((.....))----------)).))........))))).)))))))).).......((((((((......)))))))). ( -37.46)
>DroEre_CAF1 15895 91 - 1
----AG---GAGGACAGUGAGCCGGUACCCAAGGAAGUGG---------------------GCGCAAG-GGGCGGGGCUGGGCAUUGUGCAAGGUUAGGGCGUUGGCUUGACAGCGCCUC
----..---..(.((((((..(((((.((((......)))---------------------)(((...-..)))..))))).)))))).).......((((((((......)))))))). ( -36.70)
>DroYak_CAF1 14697 113 - 1
----AG---GAGGACAGUGAGCCGACAGGCAAGGAAGUGGGUUUGGAGUGGGCGCAAGGGGGCGCAAGGGGGCGGGGCCGGGCAUUGUGCAAGGUUAGGGCGUUGGCUUGACAGCGCCUC
----..---..(.((((((.(((....))).........(((((.(.....((((......)))).......).)))))...)))))).).......((((((((......)))))))). ( -39.70)
>consensus
____AGGAGGAGGACAGUGGGCCGGGAACCAAGGAAGUGGGUCCAAAGUGG__________GCGCAAGAAGGCGGGGCUGGGCAUUGUGCAAGGUUAGGGCGUUGGCUUGACAGCGCCUC
...........(.((((((..((((...((..(((......)))..................(((......))))).)))).)))))).).......((((((((......)))))))). (-23.58 = -25.78 +   2.20)

alignment

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secondary structure

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dotplot

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Window 7

Location 24,673,413 – 24,673,533
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 91.30
Mean single sequence MFE -31.04
Consensus MFE -25.62
Energy contribution -25.70
Covariance contribution 0.08
Combinations/Pair 1.12
Mean z-score -1.39
Structure conservation index 0.83
SVM decision value 0.21
SVM RNA-class probability 0.636234
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 24673413 120 + 27905053
CUACUUCCUUGGUUCCCGGCCCACUGUCCUCCUCCUGUCGUUCUGUCCUUUCAUCUGGGAGCGCCACGUGCUGGCCAACUGCAACUGCUGGGCAAUGACUUCAUUACCAGCGCGUUCUUU
...........((((((((......(..(...............)..)......))))))))...(((((((((((....((....))..)))((((....))))..))))))))..... ( -32.26)
>DroSec_CAF1 14398 112 + 1
CCACUUCCUUGGUUCCCGGCCCACUGUCCUCCUCCU--------GUCCUUUCAUCUGGGAGCGCCACGUGCUGGCCAACUGCAACUGCUGGGCAAUGACUUCAUUACCAGCGCACUCUUU
...........((((((((......(..(.......--------)..)......)))))))).....(((((((((....((....))..)))((((....))))..))))))....... ( -30.80)
>DroSim_CAF1 14435 112 + 1
CCACUUCCUUGGUUCCCGGCCCACUGUCCUCCUCCU--------GUCCUUUCAUCUGGGAGCGCCACGUGCUGGCCAACUGCAACUGCUGGGCAAUGACUUCAUUACCAGCGCGCUCUUU
...........((((((((......(..(.......--------)..)......))))))))....((((((((((....((....))..)))((((....))))..)))))))...... ( -32.10)
>DroEre_CAF1 15953 109 + 1
CCACUUCCUUGGGUACCGGCUCACUGUCCUC---CU--------GCCCUUUCAUCUGGGAGCGCCACGUGCUGGCCAACUGCAACUGCUGGGCAAUGACUUCAUUACCAGCGCACUCUUU
(((.......(((((..(((.....)))...---.)--------)))).......)))(((.((....(((.(.....).)))...(((((..((((....)))).))))))).)))... ( -30.84)
>DroYak_CAF1 14777 109 + 1
CCACUUCCUUGCCUGUCGGCUCACUGUCCUC---CU--------GUCCUUUCAUCUGGCAGCGCCACGUGCUGGCCAACUGCAACUGCUGGGCAAUGACUUCAUUACCAGCGCACUCUUU
........((((..((.(((((((.((....---((--------(.((........)))))....)))))..)))).)).))))..(((((..((((....)))).)))))......... ( -29.20)
>consensus
CCACUUCCUUGGUUCCCGGCCCACUGUCCUCCUCCU________GUCCUUUCAUCUGGGAGCGCCACGUGCUGGCCAACUGCAACUGCUGGGCAAUGACUUCAUUACCAGCGCACUCUUU
...........((((((((......(..(...............)..)......)))))))).....(((((((((....((....))..)))((((....))))..))))))....... (-25.62 = -25.70 +   0.08)

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 13:30:00 2006