Locus 3665

Sequence ID 3L_DroMel_CAF1
Location 10,725,268 – 10,725,395
Length 127
Max. P 0.999923
window5722 window5723 window5724 window5725

overview

Window 2

Location 10,725,268 – 10,725,363
Length 95
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 91.94
Mean single sequence MFE -22.15
Consensus MFE -19.80
Energy contribution -19.80
Covariance contribution 0.00
Combinations/Pair 1.00
Mean z-score -2.40
Structure conservation index 0.89
SVM decision value 2.38
SVM RNA-class probability 0.993237
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 10725268 95 + 23771897
--------------------GGAUGGGU-----ACAUAUAUUUAUAUUUAGCCAAUUUUCAACGCUUGUUGACAAAACUGUCAACAAAAUGCAAUGCAAAGCGUAAUAAAAUUGUACAAG
--------------------...(((.(-----(.((((....)))).)).))).......(((((((((((((....)))))))....(((...)))))))))................ ( -21.30)
>DroSec_CAF1 59131 95 + 1
--------------------GGAUGGGU-----ACAUAUAUUUAUAUUUAGCCAAUUUUCAACGCUUGUUGACAAAACUGUCAACAAAAUGCAAUGCAAAGCGUAAUAAAAUUGUACAAG
--------------------...(((.(-----(.((((....)))).)).))).......(((((((((((((....)))))))....(((...)))))))))................ ( -21.30)
>DroSim_CAF1 61303 95 + 1
--------------------GGAUGGGU-----ACAUAUAUUUAUAUUUAGCCAAUUUUCAACGCUUGUUGACAAAACUGUCAACAAAAUGCAAUGCAAAGCGUAAUAAAAUUGUACAAG
--------------------...(((.(-----(.((((....)))).)).))).......(((((((((((((....)))))))....(((...)))))))))................ ( -21.30)
>DroEre_CAF1 63941 95 + 1
--------------------GGAUGGGU-----ACAUAUAUUUAUAUUUAGCCAAUUUUCAACGCUUGUUGACAAAACUGUCAACAAAAUGCAAUGCAAAGCGUAAUAAAAUUGUACAAG
--------------------...(((.(-----(.((((....)))).)).))).......(((((((((((((....)))))))....(((...)))))))))................ ( -21.30)
>DroYak_CAF1 73697 95 + 1
--------------------GGAUGGGU-----ACAUAUAUUUAUAUUUAGCCAAUUUUCAACGCUUGUUGACAAAACUGUCAACAAAAUGCAAUGCAAAGCGUAAUAAAAUUGUACAAG
--------------------...(((.(-----(.((((....)))).)).))).......(((((((((((((....)))))))....(((...)))))))))................ ( -21.30)
>DroAna_CAF1 61190 120 + 1
AUGGACGGGGGGAGAUGGAUGGAUGGGUACAGUACAUAUAUUUAUAUUUAGCCAAUUUUCAACGCUUGUUGACAAAACUGUCAACAAAAUGCAAUGCAAAGCGUAAUAAAAUUGUACAAG
.((.((((..(((.(((((((.(((.........))).))))))).)))..))((((((..(((((((((((((....)))))))....(((...)))))))))...)))))))).)).. ( -26.40)
>consensus
____________________GGAUGGGU_____ACAUAUAUUUAUAUUUAGCCAAUUUUCAACGCUUGUUGACAAAACUGUCAACAAAAUGCAAUGCAAAGCGUAAUAAAAUUGUACAAG
....................................................(((((((..(((((((((((((....)))))))....(((...)))))))))...)))))))...... (-19.80 = -19.80 +   0.00)

alignment

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secondary structure

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dotplot

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Window 3

Location 10,725,268 – 10,725,363
Length 95
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 91.94
Mean single sequence MFE -21.40
Consensus MFE -21.30
Energy contribution -21.30
Covariance contribution 0.00
Combinations/Pair 1.00
Mean z-score -2.39
Structure conservation index 1.00
SVM decision value 4.58
SVM RNA-class probability 0.999923
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 10725268 95 - 23771897
CUUGUACAAUUUUAUUACGCUUUGCAUUGCAUUUUGUUGACAGUUUUGUCAACAAGCGUUGAAAAUUGGCUAAAUAUAAAUAUAUGU-----ACCCAUCC--------------------
......(((((((...((((..(((...)))..((((((((......))))))))))))..)))))))...................-----........-------------------- ( -21.30)
>DroSec_CAF1 59131 95 - 1
CUUGUACAAUUUUAUUACGCUUUGCAUUGCAUUUUGUUGACAGUUUUGUCAACAAGCGUUGAAAAUUGGCUAAAUAUAAAUAUAUGU-----ACCCAUCC--------------------
......(((((((...((((..(((...)))..((((((((......))))))))))))..)))))))...................-----........-------------------- ( -21.30)
>DroSim_CAF1 61303 95 - 1
CUUGUACAAUUUUAUUACGCUUUGCAUUGCAUUUUGUUGACAGUUUUGUCAACAAGCGUUGAAAAUUGGCUAAAUAUAAAUAUAUGU-----ACCCAUCC--------------------
......(((((((...((((..(((...)))..((((((((......))))))))))))..)))))))...................-----........-------------------- ( -21.30)
>DroEre_CAF1 63941 95 - 1
CUUGUACAAUUUUAUUACGCUUUGCAUUGCAUUUUGUUGACAGUUUUGUCAACAAGCGUUGAAAAUUGGCUAAAUAUAAAUAUAUGU-----ACCCAUCC--------------------
......(((((((...((((..(((...)))..((((((((......))))))))))))..)))))))...................-----........-------------------- ( -21.30)
>DroYak_CAF1 73697 95 - 1
CUUGUACAAUUUUAUUACGCUUUGCAUUGCAUUUUGUUGACAGUUUUGUCAACAAGCGUUGAAAAUUGGCUAAAUAUAAAUAUAUGU-----ACCCAUCC--------------------
......(((((((...((((..(((...)))..((((((((......))))))))))))..)))))))...................-----........-------------------- ( -21.30)
>DroAna_CAF1 61190 120 - 1
CUUGUACAAUUUUAUUACGCUUUGCAUUGCAUUUUGUUGACAGUUUUGUCAACAAGCGUUGAAAAUUGGCUAAAUAUAAAUAUAUGUACUGUACCCAUCCAUCCAUCUCCCCCCGUCCAU
......(((((((...((((..(((...)))..((((((((......))))))))))))..)))))))((...(((((....)))))...))............................ ( -21.90)
>consensus
CUUGUACAAUUUUAUUACGCUUUGCAUUGCAUUUUGUUGACAGUUUUGUCAACAAGCGUUGAAAAUUGGCUAAAUAUAAAUAUAUGU_____ACCCAUCC____________________
......(((((((...((((..(((...)))..((((((((......))))))))))))..))))))).................................................... (-21.30 = -21.30 +   0.00)

alignment

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secondary structure

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Window 4

Location 10,725,283 – 10,725,395
Length 112
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 92.71
Mean single sequence MFE -26.22
Consensus MFE -23.46
Energy contribution -23.35
Covariance contribution -0.11
Combinations/Pair 1.07
Mean z-score -1.30
Structure conservation index 0.89
SVM decision value 0.33
SVM RNA-class probability 0.692375
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 10725283 112 + 23771897
UUUAUAUUUAGCCAAUUUUCAACGCUUGUUGACAAAACUGUCAACAAAAUGCAAUGCAAAGCGUAAUAAAAUUGUACAAGAUGUUCCGU-------UGGGCGGCGGGGG-CAGGAGUGAG
....(((((.(((((((((..(((((((((((((....)))))))....(((...)))))))))...))))))...........(((((-------(....))))))))-)..))))).. ( -29.90)
>DroSec_CAF1 59146 110 + 1
UUUAUAUUUAGCCAAUUUUCAACGCUUGUUGACAAAACUGUCAACAAAAUGCAAUGCAAAGCGUAAUAAAAUUGUACAAGAUGUUCCGA-------UGGGAGGCG--GG-CAGGAGUGAG
....(((((.(((((((((..(((((((((((((....)))))))....(((...)))))))))...))))))........((((((..-------..))).)))--))-)..))))).. ( -26.60)
>DroSim_CAF1 61318 110 + 1
UUUAUAUUUAGCCAAUUUUCAACGCUUGUUGACAAAACUGUCAACAAAAUGCAAUGCAAAGCGUAAUAAAAUUGUACAAGAUGUUCCGA-------UGGGCGGCG--GG-CAGGAGUGAG
....(((((.(((((((((..(((((((((((((....)))))))....(((...)))))))))...))))))........((((((..-------..)).))))--))-)..))))).. ( -25.60)
>DroEre_CAF1 63956 110 + 1
UUUAUAUUUAGCCAAUUUUCAACGCUUGUUGACAAAACUGUCAACAAAAUGCAAUGCAAAGCGUAAUAAAAUUGUACAAGAUGUUCCGA-------UGGGCGGCG--GG-AAGGAGCGAG
............(((((((..(((((((((((((....)))))))....(((...)))))))))...))))))).......((((((..-------(.(....).--).-..)))))).. ( -26.60)
>DroYak_CAF1 73712 111 + 1
UUUAUAUUUAGCCAAUUUUCAACGCUUGUUGACAAAACUGUCAACAAAAUGCAAUGCAAAGCGUAAUAAAAUUGUACAAGAUGUUCCGA-------UGGGCGGCG--GUAAAGGAGUGAG
(((((.....(((((((((..(((((((((((((....)))))))....(((...)))))))))...)))))).........((((...-------.))))))).--)))))........ ( -25.10)
>DroAna_CAF1 61230 117 + 1
UUUAUAUUUAGCCAAUUUUCAACGCUUGUUGACAAAACUGUCAACAAAAUGCAAUGCAAAGCGUAAUAAAAUUGUACAAGAUGUUCUGAGAAAAAAAGGGAGGUG--AG-UAGCAGUAGC
..........(((((((((..(((((((((((((....)))))))....(((...)))))))))...)))))))(((...((.((((..........)))).)).--.)-))))...... ( -23.50)
>consensus
UUUAUAUUUAGCCAAUUUUCAACGCUUGUUGACAAAACUGUCAACAAAAUGCAAUGCAAAGCGUAAUAAAAUUGUACAAGAUGUUCCGA_______UGGGCGGCG__GG_CAGGAGUGAG
..........(((((((((..(((((((((((((....)))))))....(((...)))))))))...))))))...........((((........)))).)))................ (-23.46 = -23.35 +  -0.11)

alignment

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secondary structure

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dotplot

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Window 5

Location 10,725,283 – 10,725,395
Length 112
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 92.71
Mean single sequence MFE -23.92
Consensus MFE -21.30
Energy contribution -21.30
Covariance contribution 0.00
Combinations/Pair 1.00
Mean z-score -1.92
Structure conservation index 0.89
SVM decision value 1.56
SVM RNA-class probability 0.963660
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 10725283 112 - 23771897
CUCACUCCUG-CCCCCGCCGCCCA-------ACGGAACAUCUUGUACAAUUUUAUUACGCUUUGCAUUGCAUUUUGUUGACAGUUUUGUCAACAAGCGUUGAAAAUUGGCUAAAUAUAAA
.........(-(..(((.......-------.)))...........(((((((...((((..(((...)))..((((((((......))))))))))))..))))))))).......... ( -24.70)
>DroSec_CAF1 59146 110 - 1
CUCACUCCUG-CC--CGCCUCCCA-------UCGGAACAUCUUGUACAAUUUUAUUACGCUUUGCAUUGCAUUUUGUUGACAGUUUUGUCAACAAGCGUUGAAAAUUGGCUAAAUAUAAA
..........-..--.((((((..-------..)))...........((((((...((((..(((...)))..((((((((......))))))))))))..))))))))).......... ( -24.10)
>DroSim_CAF1 61318 110 - 1
CUCACUCCUG-CC--CGCCGCCCA-------UCGGAACAUCUUGUACAAUUUUAUUACGCUUUGCAUUGCAUUUUGUUGACAGUUUUGUCAACAAGCGUUGAAAAUUGGCUAAAUAUAAA
.........(-((--((.......-------.)))...........(((((((...((((..(((...)))..((((((((......))))))))))))..))))))))).......... ( -24.10)
>DroEre_CAF1 63956 110 - 1
CUCGCUCCUU-CC--CGCCGCCCA-------UCGGAACAUCUUGUACAAUUUUAUUACGCUUUGCAUUGCAUUUUGUUGACAGUUUUGUCAACAAGCGUUGAAAAUUGGCUAAAUAUAAA
...((.....-.(--((.......-------.)))...........(((((((...((((..(((...)))..((((((((......))))))))))))..))))))))).......... ( -24.80)
>DroYak_CAF1 73712 111 - 1
CUCACUCCUUUAC--CGCCGCCCA-------UCGGAACAUCUUGUACAAUUUUAUUACGCUUUGCAUUGCAUUUUGUUGACAGUUUUGUCAACAAGCGUUGAAAAUUGGCUAAAUAUAAA
............(--((.......-------.)))...........(((((((...((((..(((...)))..((((((((......))))))))))))..)))))))............ ( -23.50)
>DroAna_CAF1 61230 117 - 1
GCUACUGCUA-CU--CACCUCCCUUUUUUUCUCAGAACAUCUUGUACAAUUUUAUUACGCUUUGCAUUGCAUUUUGUUGACAGUUUUGUCAACAAGCGUUGAAAAUUGGCUAAAUAUAAA
((....))..-..--...............................(((((((...((((..(((...)))..((((((((......))))))))))))..)))))))............ ( -22.30)
>consensus
CUCACUCCUG_CC__CGCCGCCCA_______UCGGAACAUCUUGUACAAUUUUAUUACGCUUUGCAUUGCAUUUUGUUGACAGUUUUGUCAACAAGCGUUGAAAAUUGGCUAAAUAUAAA
..............................................(((((((...((((..(((...)))..((((((((......))))))))))))..)))))))............ (-21.30 = -21.30 +   0.00)

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 11:03:45 2006