Locus 168

Sequence ID 3R_DroMel_CAF1
Location 824,916 – 825,076
Length 160
Max. P 0.998547
window279 window280 window281

overview

Window 9

Location 824,916 – 825,036
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 89.58
Mean single sequence MFE -36.82
Consensus MFE -30.02
Energy contribution -30.94
Covariance contribution 0.92
Combinations/Pair 1.06
Mean z-score -3.14
Structure conservation index 0.82
SVM decision value 3.14
SVM RNA-class probability 0.998547
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 824916 120 + 27905053
GGAGUGCUUUUCCGGUGACCCACUGGAGACGCUUCUACCCACUUAAGCUCCAAGAAUACCAAUAUUUUCCUUGGCCGUUUUUUUGGCCAAUAAAUCAUGUGGCACAUUGUGUCAGCUCUU
(((((.....(((((((...)))))))(((((......((((..........((((((....))))))..(((((((......)))))))........))))......))))).))))). ( -35.40)
>DroSec_CAF1 7223 120 + 1
GGAGUGCUUUUCCGGUGACCCACUGGAGACGCUUCUACCCACUCAAGCUGCAAGAAUACCAAUAUUUUCCUUGGCCGUUUUUUUGGCCAAUAAAUCAUGUGGCACAUUGUGUGUGCUCUU
(((((((.(((((((((...))))))))).)).......(((.(((((..((((((((....))))))..(((((((......))))))).......))..))...))).))).))))). ( -38.30)
>DroSim_CAF1 4396 120 + 1
GGAGUGCUUUUCCGGUGACCCACUGGAGACGCUUCUACCCACUCAAGCUGCAAGAAUACCAAUAUUUUCCUUGGCCGUUUUUUUGGCCAAUAAAUCAUGUGGCACAUUGUGUGUGCUCUU
(((((((.(((((((((...))))))))).)).......(((.(((((..((((((((....))))))..(((((((......))))))).......))..))...))).))).))))). ( -38.30)
>DroEre_CAF1 7677 120 + 1
GGAGUGUUUUUCCGGUGACCCACUGGAGAUGCUCCAACCCACUUAGGCUGCAAGAAUACCAAUAUUUUCCUUGGCCUUUUUUUUGGCCAAUAAAUCUUGUGGCACAUUGUGUAUGCUCUU
((((((((..(((((((...)))))))))))))))....(((....((..((((((((....))).....((((((........))))))....)))))..)).....)))......... ( -40.20)
>DroYak_CAF1 7317 109 + 1
GGAGUGUUUUUC--------UACCGGAGAUGCUCCAACCCACUUAAGCUGCAAGAAUACCAAUUUUUUCC-UGGCCUUU--UUUGGCCAAUAAAUCUUGUGGCACAUUGUGUACCCUCUU
(((((((((((.--------....)))))))))))....(((....((..(((((..........(((..-(((((...--...)))))..))))))))..)).....)))......... ( -31.90)
>consensus
GGAGUGCUUUUCCGGUGACCCACUGGAGACGCUUCUACCCACUUAAGCUGCAAGAAUACCAAUAUUUUCCUUGGCCGUUUUUUUGGCCAAUAAAUCAUGUGGCACAUUGUGUAUGCUCUU
((((((..(((((((((...)))))))))))))))....(((....((..((((((((....))))))..((((((........)))))).......))..)).....)))......... (-30.02 = -30.94 +   0.92) 

alignment

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secondary structure

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dotplot

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Window 0

Location 824,956 – 825,076
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 88.50
Mean single sequence MFE -25.63
Consensus MFE -17.57
Energy contribution -17.57
Covariance contribution 0.00
Combinations/Pair 1.09
Mean z-score -2.52
Structure conservation index 0.69
SVM decision value 0.57
SVM RNA-class probability 0.783979
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 824956 120 + 27905053
ACUUAAGCUCCAAGAAUACCAAUAUUUUCCUUGGCCGUUUUUUUGGCCAAUAAAUCAUGUGGCACAUUGUGUCAGCUCUUUUCUUGUCUUUUCUUUGAGAUUCUGUUGUUUGUUCUCUGU
...(((((..((((((..............(((((((......))))))).........((((((...))))))......))))))((((......)))).......)))))........ ( -23.90)
>DroSec_CAF1 7263 120 + 1
ACUCAAGCUGCAAGAAUACCAAUAUUUUCCUUGGCCGUUUUUUUGGCCAAUAAAUCAUGUGGCACAUUGUGUGUGCUCUUUUCUUGUCUUUUCUUCGGGAUUCUUUUGUUUGUCCUCUGU
...(((((.(((((((..............(((((((......)))))))..........(((((((...)))))))...)))))))...(((....))).......)))))........ ( -29.30)
>DroSim_CAF1 4436 120 + 1
ACUCAAGCUGCAAGAAUACCAAUAUUUUCCUUGGCCGUUUUUUUGGCCAAUAAAUCAUGUGGCACAUUGUGUGUGCUCUUUUCUUGUCUGUUCUUCGGGAUUCUUUUGUUUGUCCUCUGU
...(((((.(((((((..............(((((((......)))))))..........(((((((...)))))))...)))))))..((((....))))......)))))........ ( -30.20)
>DroEre_CAF1 7717 120 + 1
ACUUAGGCUGCAAGAAUACCAAUAUUUUCCUUGGCCUUUUUUUUGGCCAAUAAAUCUUGUGGCACAUUGUGUAUGCUCUUUUAUUUUCUUUUCUUUGAGAUUCUUUUGUUUGCCCUCAGU
(((.((((..((((((((....))).....((((((........))))))....)))))..)).......(((.((........((((........)))).......)).))).)).))) ( -23.66)
>DroYak_CAF1 7349 112 + 1
ACUUAAGCUGCAAGAAUACCAAUUUUUUCC-UGGCCUUU--UUUGGCCAAUAAAUCUUGUGGCACAUUGUGUACCCUCUU-----UUCCUUUCUUUAAGAUUCUUUUGUUUGCCCUCAUU
.(((((((..(((((..........(((..-(((((...--...)))))..))))))))..))((.....))........-----.........)))))..................... ( -21.10)
>consensus
ACUUAAGCUGCAAGAAUACCAAUAUUUUCCUUGGCCGUUUUUUUGGCCAAUAAAUCAUGUGGCACAUUGUGUAUGCUCUUUUCUUGUCUUUUCUUUGAGAUUCUUUUGUUUGUCCUCUGU
...(((((...((((((.(((.........((((((........)))))).........)))(((...)))............................))))))..)))))........ (-17.57 = -17.57 +   0.00) 

alignment

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secondary structure

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dotplot

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Window 1

Location 824,956 – 825,076
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 88.50
Mean single sequence MFE -25.92
Consensus MFE -18.50
Energy contribution -18.58
Covariance contribution 0.08
Combinations/Pair 1.20
Mean z-score -2.94
Structure conservation index 0.71
SVM decision value 1.36
SVM RNA-class probability 0.946484
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 824956 120 - 27905053
ACAGAGAACAAACAACAGAAUCUCAAAGAAAAGACAAGAAAAGAGCUGACACAAUGUGCCACAUGAUUUAUUGGCCAAAAAAACGGCCAAGGAAAAUAUUGGUAUUCUUGGAGCUUAAGU
...((((.............))))..................(((((..((....((((((.(((.(((.((((((........))))))..))).)))))))))...)).))))).... ( -25.42)
>DroSec_CAF1 7263 120 - 1
ACAGAGGACAAACAAAAGAAUCCCGAAGAAAAGACAAGAAAAGAGCACACACAAUGUGCCACAUGAUUUAUUGGCCAAAAAAACGGCCAAGGAAAAUAUUGGUAUUCUUGCAGCUUGAGU
........(((.(..((((((.((((................(.(((((.....))))))......(((.((((((........)))))).)))....)))).))))))...).)))... ( -25.60)
>DroSim_CAF1 4436 120 - 1
ACAGAGGACAAACAAAAGAAUCCCGAAGAACAGACAAGAAAAGAGCACACACAAUGUGCCACAUGAUUUAUUGGCCAAAAAAACGGCCAAGGAAAAUAUUGGUAUUCUUGCAGCUUGAGU
........(((.(..((((((.((((................(.(((((.....))))))......(((.((((((........)))))).)))....)))).))))))...).)))... ( -25.60)
>DroEre_CAF1 7717 120 - 1
ACUGAGGGCAAACAAAAGAAUCUCAAAGAAAAGAAAAUAAAAGAGCAUACACAAUGUGCCACAAGAUUUAUUGGCCAAAAAAAAGGCCAAGGAAAAUAUUGGUAUUCUUGCAGCCUAAGU
(((..((((......((((((..(((................(.(((((.....))))))......(((.((((((........)))))).)))....)))..))))))...)))).))) ( -26.70)
>DroYak_CAF1 7349 112 - 1
AAUGAGGGCAAACAAAAGAAUCUUAAAGAAAGGAA-----AAGAGGGUACACAAUGUGCCACAAGAUUUAUUGGCCAAA--AAAGGCCA-GGAAAAAAUUGGUAUUCUUGCAGCUUAAGU
..((((.((...........((((......)))).-----((((((((((.....))))).(((..(((.((((((...--...)))))-)..)))..)))...)))))))..))))... ( -26.30)
>consensus
ACAGAGGACAAACAAAAGAAUCUCAAAGAAAAGACAAGAAAAGAGCACACACAAUGUGCCACAUGAUUUAUUGGCCAAAAAAACGGCCAAGGAAAAUAUUGGUAUUCUUGCAGCUUAAGU
...............((((((.((((................(.(((((.....))))))......(((.((((((........)))))).)))....)))).))))))........... (-18.50 = -18.58 +   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 09:35:41 2006