Locus 5449

Sequence ID 2R_DroMel_CAF1
Location 17,536,078 – 17,536,204
Length 126
Max. P 0.919841
window8696 window8697 window8698 window8699

overview

Window 6

Location 17,536,078 – 17,536,186
Length 108
Sequences 6
Columns 112
Reading direction forward
Mean pairwise identity 81.61
Mean single sequence MFE -23.73
Consensus MFE -16.85
Energy contribution -16.38
Covariance contribution -0.47
Combinations/Pair 1.12
Mean z-score -2.78
Structure conservation index 0.71
SVM decision value 1.11
SVM RNA-class probability 0.916706
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 17536078 108 + 20766785
----UGCUGUGUAUAAAAUUACAAUAAAUCCUUGCAUUUUAGCUGCAAAUAAACAAAGAUUUGCAGCGCCGAAAACGAAGUCUGAGCGCGCUAAAACAAAACAGAAGGAAUC
----.....((((......)))).....(((((...((((((((((((((........)))))))(((((((........)).).)))))))))))(......))))))... ( -23.70)
>DroPse_CAF1 54509 92 + 1
UUUGGCUUGUGUAUAAAAUUACAAUAAAUCGUUGCAUUUUAGCUGCAAAUAAACAAAGAUUUGCAGCGCCGAAAACGA--------------------AAGCAGAAGGAACA
....((((.((((......)))).....(((((........(((((((((........)))))))))......)))))--------------------)))).......... ( -22.94)
>DroEre_CAF1 50243 108 + 1
----UGCUGUGUAUAAAAUUACAAUAAAUCCUUGCAUUUUAGCUGCAAAUAAACAAAGAUUUGCAGCGCAGAAAACGAAGUCUGAGCGCGCUAAAACAAAACAGAAGGAAUC
----.....((((......)))).....(((((...((((((((((((((........)))))))(((((((........)))..)))))))))))(......))))))... ( -24.40)
>DroYak_CAF1 45195 107 + 1
-----GCUGUGUAUAAAAUUACAAUAAAUCCUUGCAUUUUAGCUGCAAAUAAACAAAGAUUUGCAGCGCAGAAAACGAAGUCUGAGCGCGCUAAAACAAAACAGAAGGAAUC
-----....((((......)))).....(((((...((((((((((((((........)))))))(((((((........)))..)))))))))))(......))))))... ( -24.40)
>DroAna_CAF1 46119 84 + 1
----GGCUGUGUAUAAAAUUACUAUAAAUCCUUGCAUUUUAGCUGCAAAUAAACAAAGAUUUGCAGC--CGAAA-C---------------------AAAGCAGAAGGAGGC
----.(((..(((......)))......(((((((.(((..(((((((((........)))))))))--..)))-.---------------------...)))..))))))) ( -21.60)
>DroPer_CAF1 59320 112 + 1
UUUGGCUUGUGUAUAAAAUUACAAUAAAUCGUUGCAUUUUAGCUGCAAAUAAACAAAGAUUUGCAGCGCCGAAAACGAACACUGAGCGCGCUAAAACAAAGCAGAAGGAACA
((((((.((((((......)))......(((((........(((((((((........)))))))))......))))).......))).))))))................. ( -25.34)
>consensus
____GGCUGUGUAUAAAAUUACAAUAAAUCCUUGCAUUUUAGCUGCAAAUAAACAAAGAUUUGCAGCGCCGAAAACGAAGUCUGAGCGCGCUAAAACAAAACAGAAGGAAUC
......(((((((......)))...................(((((((((........))))))))).................................))))........ (-16.85 = -16.38 +  -0.47)

alignment

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secondary structure

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Window 7

Location 17,536,078 – 17,536,186
Length 108
Sequences 6
Columns 112
Reading direction reverse
Mean pairwise identity 81.61
Mean single sequence MFE -24.02
Consensus MFE -14.05
Energy contribution -14.22
Covariance contribution 0.17
Combinations/Pair 1.00
Mean z-score -2.38
Structure conservation index 0.59
SVM decision value 0.46
SVM RNA-class probability 0.745066
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 17536078 108 - 20766785
GAUUCCUUCUGUUUUGUUUUAGCGCGCUCAGACUUCGUUUUCGGCGCUGCAAAUCUUUGUUUAUUUGCAGCUAAAAUGCAAGGAUUUAUUGUAAUUUUAUACACAGCA----
...((((..(((...(((((((((((((.(((......))).)))))(((((((........)))))))))))))))))))))).....((((......)))).....---- ( -26.70)
>DroPse_CAF1 54509 92 - 1
UGUUCCUUCUGCUU--------------------UCGUUUUCGGCGCUGCAAAUCUUUGUUUAUUUGCAGCUAAAAUGCAACGAUUUAUUGUAAUUUUAUACACAAGCCAAA
..............--------------------........((((((((((((........)))))))))((((((((((.......)))).)))))).......)))... ( -20.10)
>DroEre_CAF1 50243 108 - 1
GAUUCCUUCUGUUUUGUUUUAGCGCGCUCAGACUUCGUUUUCUGCGCUGCAAAUCUUUGUUUAUUUGCAGCUAAAAUGCAAGGAUUUAUUGUAAUUUUAUACACAGCA----
...((((..(((...((((((((((((..((((...))))...))))(((((((........)))))))))))))))))))))).....((((......)))).....---- ( -25.70)
>DroYak_CAF1 45195 107 - 1
GAUUCCUUCUGUUUUGUUUUAGCGCGCUCAGACUUCGUUUUCUGCGCUGCAAAUCUUUGUUUAUUUGCAGCUAAAAUGCAAGGAUUUAUUGUAAUUUUAUACACAGC-----
...((((..(((...((((((((((((..((((...))))...))))(((((((........)))))))))))))))))))))).....((((......))))....----- ( -25.70)
>DroAna_CAF1 46119 84 - 1
GCCUCCUUCUGCUUU---------------------G-UUUCG--GCUGCAAAUCUUUGUUUAUUUGCAGCUAAAAUGCAAGGAUUUAUAGUAAUUUUAUACACAGCC----
((.((((..(((...---------------------(-(((..--(((((((((........)))))))))..)))))))))))......(((......)))...)).---- ( -21.60)
>DroPer_CAF1 59320 112 - 1
UGUUCCUUCUGCUUUGUUUUAGCGCGCUCAGUGUUCGUUUUCGGCGCUGCAAAUCUUUGUUUAUUUGCAGCUAAAAUGCAACGAUUUAUUGUAAUUUUAUACACAAGCCAAA
..........((((.(((((((((((((.((........)).)))))(((((((........)))))))))))))))............((((......)))).)))).... ( -24.30)
>consensus
GAUUCCUUCUGCUUUGUUUUAGCGCGCUCAGACUUCGUUUUCGGCGCUGCAAAUCUUUGUUUAUUUGCAGCUAAAAUGCAAGGAUUUAUUGUAAUUUUAUACACAGCC____
.............................................(((((((((........)))))))))((((((((((.......)))).))))))............. (-14.05 = -14.22 +   0.17)

alignment

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secondary structure

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Window 8

Location 17,536,107 – 17,536,204
Length 97
Sequences 6
Columns 119
Reading direction forward
Mean pairwise identity 86.90
Mean single sequence MFE -25.11
Consensus MFE -18.73
Energy contribution -18.92
Covariance contribution 0.20
Combinations/Pair 1.05
Mean z-score -2.54
Structure conservation index 0.75
SVM decision value 0.01
SVM RNA-class probability 0.536562
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 17536107 97 + 20766785
GCAUUUUAGCUGCAAAUAAACAAAGAUUUGCAGCGCCGAAAACGAAGUCUGAGCGCGCUAAAACAAAACAGAAGGAAUCGGAAGGCCAAAGUGUAUG----------------------
(((((((.(((((((((........)))))))))(((.....(((..((((.................)))).....)))...))).)))))))...---------------------- ( -25.53)
>DroSec_CAF1 42650 97 + 1
GCAUUUUAGCUGCAAAUAAACAAAGAUUUGCAGCGCCGAAAACGAAGUCUGAGCGCGCUAAAACAAAACAGAAGGAAUCGGAAGGCCAAAGUGUAUG----------------------
(((((((.(((((((((........)))))))))(((.....(((..((((.................)))).....)))...))).)))))))...---------------------- ( -25.53)
>DroSim_CAF1 43984 97 + 1
GCAUUUUAGCUGCAAAUAAACAAAGAUUUGCAGCGCCGAAAACGAAGUCUGAGCGCGCUAAAACAAAACAGAAGGAAUCGGAAGGCCAAAGUGUAUG----------------------
(((((((.(((((((((........)))))))))(((.....(((..((((.................)))).....)))...))).)))))))...---------------------- ( -25.53)
>DroEre_CAF1 50272 97 + 1
GCAUUUUAGCUGCAAAUAAACAAAGAUUUGCAGCGCAGAAAACGAAGUCUGAGCGCGCUAAAACAAAACAGAAGGAAUCGGAAGGCCGAAGUAUGUG----------------------
(((((((((((((((((........)))))))(((((((........)))..)))))))))))..............((((....))))....))).---------------------- ( -24.60)
>DroYak_CAF1 45223 97 + 1
GCAUUUUAGCUGCAAAUAAACAAAGAUUUGCAGCGCAGAAAACGAAGUCUGAGCGCGCUAAAACAAAACAGAAGGAAUCGGAAGGCCGAAGUAUAUG----------------------
...((((((((((((((........)))))))(((((((........)))..)))))))))))..............((((....))))........---------------------- ( -24.00)
>DroPer_CAF1 59353 116 + 1
GCAUUUUAGCUGCAAAUAAACAAAGAUUUGCAGCGCCGAAAACGAACACUGAGCGCGCUAAAACAAAGCAGAAGGAACAGGGA---UAUAGGAUAUAAACGAUUCGAGGCACUAAGCAC
((......(((((((((........)))))))))(((...........(((..(.((((.......))).)...)..)))(((---(...(........).))))..))).....)).. ( -25.50)
>consensus
GCAUUUUAGCUGCAAAUAAACAAAGAUUUGCAGCGCCGAAAACGAAGUCUGAGCGCGCUAAAACAAAACAGAAGGAAUCGGAAGGCCAAAGUAUAUG______________________
...((((((((((((((........)))))))((((................)))))))))))..........((...(....).))................................ (-18.73 = -18.92 +   0.20)

alignment

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secondary structure

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Window 9

Location 17,536,107 – 17,536,204
Length 97
Sequences 6
Columns 119
Reading direction reverse
Mean pairwise identity 86.90
Mean single sequence MFE -23.52
Consensus MFE -20.47
Energy contribution -21.13
Covariance contribution 0.67
Combinations/Pair 1.04
Mean z-score -2.17
Structure conservation index 0.87
SVM decision value 1.13
SVM RNA-class probability 0.919841
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 17536107 97 - 20766785
----------------------CAUACACUUUGGCCUUCCGAUUCCUUCUGUUUUGUUUUAGCGCGCUCAGACUUCGUUUUCGGCGCUGCAAAUCUUUGUUUAUUUGCAGCUAAAAUGC
----------------------........((((....)))).............(((((((((((((.(((......))).)))))(((((((........))))))))))))))).. ( -22.90)
>DroSec_CAF1 42650 97 - 1
----------------------CAUACACUUUGGCCUUCCGAUUCCUUCUGUUUUGUUUUAGCGCGCUCAGACUUCGUUUUCGGCGCUGCAAAUCUUUGUUUAUUUGCAGCUAAAAUGC
----------------------........((((....)))).............(((((((((((((.(((......))).)))))(((((((........))))))))))))))).. ( -22.90)
>DroSim_CAF1 43984 97 - 1
----------------------CAUACACUUUGGCCUUCCGAUUCCUUCUGUUUUGUUUUAGCGCGCUCAGACUUCGUUUUCGGCGCUGCAAAUCUUUGUUUAUUUGCAGCUAAAAUGC
----------------------........((((....)))).............(((((((((((((.(((......))).)))))(((((((........))))))))))))))).. ( -22.90)
>DroEre_CAF1 50272 97 - 1
----------------------CACAUACUUCGGCCUUCCGAUUCCUUCUGUUUUGUUUUAGCGCGCUCAGACUUCGUUUUCUGCGCUGCAAAUCUUUGUUUAUUUGCAGCUAAAAUGC
----------------------........((((....)))).............((((((((((((..((((...))))...))))(((((((........))))))))))))))).. ( -24.00)
>DroYak_CAF1 45223 97 - 1
----------------------CAUAUACUUCGGCCUUCCGAUUCCUUCUGUUUUGUUUUAGCGCGCUCAGACUUCGUUUUCUGCGCUGCAAAUCUUUGUUUAUUUGCAGCUAAAAUGC
----------------------........((((....)))).............((((((((((((..((((...))))...))))(((((((........))))))))))))))).. ( -24.00)
>DroPer_CAF1 59353 116 - 1
GUGCUUAGUGCCUCGAAUCGUUUAUAUCCUAUA---UCCCUGUUCCUUCUGCUUUGUUUUAGCGCGCUCAGUGUUCGUUUUCGGCGCUGCAAAUCUUUGUUUAUUUGCAGCUAAAAUGC
(..((.(((((...((((.(..((((...))))---..)..)))).....(((.......)))))))).))..).((((((....(((((((((........))))))))).)))))). ( -24.40)
>consensus
______________________CAUACACUUUGGCCUUCCGAUUCCUUCUGUUUUGUUUUAGCGCGCUCAGACUUCGUUUUCGGCGCUGCAAAUCUUUGUUUAUUUGCAGCUAAAAUGC
..............................((((....)))).............((((((((((((..(((......)))..))))(((((((........))))))))))))))).. (-20.47 = -21.13 +   0.67)

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 11:45:13 2006