Locus 2678

Sequence ID X_DroMel_CAF1
Location 7,180,493 – 7,180,647
Length 154
Max. P 0.984158
window4386 window4387 window4388 window4389

overview

Window 6

Location 7,180,493 – 7,180,589
Length 96
Sequences 4
Columns 108
Reading direction forward
Mean pairwise identity 61.41
Mean single sequence MFE -25.40
Consensus MFE -9.47
Energy contribution -9.40
Covariance contribution -0.06
Combinations/Pair 1.33
Mean z-score -2.65
Structure conservation index 0.37
SVM decision value 0.79
SVM RNA-class probability 0.850447
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 7180493 96 + 22224390
-------UGUUUAUUUGUUUGCAGGUGCAGCAGCAAAUAGAUUA-----UAAUUUAUGUAUUUGUAGCGGGCGCAUGCUAAACUGCACACACUCUACACCUACAUAUG
-------.((((((((((((((....)))..)))))))))))..-----.....((((((..(((((.(.(.(((........))).)...).)))))..)))))).. ( -24.30)
>DroSec_CAF1 5954 86 + 1
-------UGUUUAUUUGUUUGCAGGUGCAGCAGCAAAUAGAUUA-----UAAUUUAUGUAUUUGUAGCGGGCGCAUGCUAAACUACACACACUCUA----------UA
-------.........(((((((.((((.((.(((((((.((..-----......)).))))))).))..)))).))).)))).............----------.. ( -22.60)
>DroEre_CAF1 7662 105 + 1
CACCUUCUGUUUGGU--UUUGCAGGUGCAGCAGCAAAUAGAUUGUAUGUAAUUGUGUGUAUUUGUAGCGGGCGCAUGCUAAACUGCAUACACCCUAUACAUACAUAC-
.((..((((((((.(--.((((....)))).).))))))))..))........((((((((.(((((.((..(.((((......)))).).))))))).))))))))- ( -33.80)
>DroAna_CAF1 12296 74 + 1
-------UGUGU------CUUGAGAUACA-------------CA-----GGGCUGCUGUAUUUUUAGCAGCCAUAUGUUAAA-UGCAC-CACCCCAGAAAUCCAUAC-
-------.((((------(....)))))(-------------((-----.((((((((......))))))))...)))....-.....-..................- ( -20.90)
>consensus
_______UGUUUAUU__UUUGCAGGUGCAGCAGCAAAUAGAUUA_____UAAUUUAUGUAUUUGUAGCGGGCGCAUGCUAAACUGCACACACCCUA_ACAUACAUAC_
..................(((((((((((...........................))))))))))).(((.(..(((......)))..).))).............. ( -9.47 =  -9.40 +  -0.06)

alignment

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secondary structure

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Window 7

Location 7,180,493 – 7,180,589
Length 96
Sequences 4
Columns 108
Reading direction reverse
Mean pairwise identity 61.41
Mean single sequence MFE -25.18
Consensus MFE -9.24
Energy contribution -9.80
Covariance contribution 0.56
Combinations/Pair 1.40
Mean z-score -2.85
Structure conservation index 0.37
SVM decision value 0.93
SVM RNA-class probability 0.883663
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 7180493 96 - 22224390
CAUAUGUAGGUGUAGAGUGUGUGCAGUUUAGCAUGCGCCCGCUACAAAUACAUAAAUUA-----UAAUCUAUUUGCUGCUGCACCUGCAAACAAAUAAACA-------
....(((((((((((.((((((((......)))))))).)((..((((((.((......-----..)).))))))..))))))))))))............------- ( -31.10)
>DroSec_CAF1 5954 86 - 1
UA----------UAGAGUGUGUGUAGUUUAGCAUGCGCCCGCUACAAAUACAUAAAUUA-----UAAUCUAUUUGCUGCUGCACCUGCAAACAAAUAAACA-------
..----------....((((.((((((...((....))..)))))).))))........-----.....((((((.(((.......)))..))))))....------- ( -16.50)
>DroEre_CAF1 7662 105 - 1
-GUAUGUAUGUAUAGGGUGUAUGCAGUUUAGCAUGCGCCCGCUACAAAUACACACAAUUACAUACAAUCUAUUUGCUGCUGCACCUGCAAA--ACCAAACAGAAGGUG
-(((((((((((..((((((((((......))))))))))..))))............)))))))..(((.((((.(..(((....)))..--).)))).)))..... ( -32.70)
>DroAna_CAF1 12296 74 - 1
-GUAUGGAUUUCUGGGGUG-GUGCA-UUUAACAUAUGGCUGCUAAAAAUACAGCAGCCC-----UG-------------UGUAUCUCAAG------ACACA-------
-...((..(((.((((((.-.....-....(((((.(((((((........))))))).-----))-------------)))))))))))------)..))------- ( -20.40)
>consensus
_AUAUGUAUGU_UAGAGUGUGUGCAGUUUAGCAUGCGCCCGCUACAAAUACAUAAAUUA_____UAAUCUAUUUGCUGCUGCACCUGCAAA__AAUAAACA_______
..............((((((((((......)))))))))).................................................................... ( -9.24 =  -9.80 +   0.56)

alignment

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secondary structure

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Window 8

Location 7,180,522 – 7,180,626
Length 104
Sequences 4
Columns 112
Reading direction reverse
Mean pairwise identity 57.68
Mean single sequence MFE -28.35
Consensus MFE -9.24
Energy contribution -9.80
Covariance contribution 0.56
Combinations/Pair 1.40
Mean z-score -3.80
Structure conservation index 0.33
SVM decision value 0.86
SVM RNA-class probability 0.868547
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 7180522 104 - 22224390
UCUCCAACCAUGUAGUAUAU---ACAUACAUAUGUAUGUACAUAUGUAGGUGUAGAGUGUGUGCAGUUUAGCAUGCGCCCGCUACAAAUACAUAAAUUA-----UAAUCUAU
..........((((((((((---((((....)))))))))).((((((..(((((.((((((((......))))))))...)))))..))))))...))-----))...... ( -34.20)
>DroSec_CAF1 5983 85 - 1
UCUC-AACCAUGUAGUAUAU-----------AUGUAUGUAUA----------UAGAGUGUGUGUAGUUUAGCAUGCGCCCGCUACAAAUACAUAAAUUA-----UAAUCUAU
....-......((((..(((-----------(..(((((((.----------...((((.(((((........))))).))))....)))))))...))-----))..)))) ( -19.10)
>DroEre_CAF1 7696 105 - 1
UCGC-UACCACAUAGUAUAUCGCACAUACAAGUGU------GUAUGUAUGUAUAGGGUGUAUGCAGUUUAGCAUGCGCCCGCUACAAAUACACACAAUUACAUACAAUCUAU
..((-((.....))))...............((((------((((...((((..((((((((((......))))))))))..)))).))))))))................. ( -33.60)
>DroAna_CAF1 12312 78 - 1
UCUU-GGCCC--------------CAUGCAAGUCU------GUAUGGAUUUCUGGGGUG-GUGCA-UUUAACAUAUGGCUGCUAAAAAUACAGCAGCCC-----UG------
...(-.((((--------------((.(.((((((------....))))))))))))).-)....-..........(((((((........))))))).-----..------ ( -26.50)
>consensus
UCUC_AACCAUGUAGUAUAU____CAUACAAAUGU______AUAUGUAUGU_UAGAGUGUGUGCAGUUUAGCAUGCGCCCGCUACAAAUACAUAAAUUA_____UAAUCUAU
......................................................((((((((((......))))))))))................................ ( -9.24 =  -9.80 +   0.56)

alignment

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secondary structure

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dotplot

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Window 9

Location 7,180,551 – 7,180,647
Length 96
Sequences 3
Columns 99
Reading direction reverse
Mean pairwise identity 73.38
Mean single sequence MFE -23.53
Consensus MFE -15.68
Energy contribution -17.13
Covariance contribution 1.45
Combinations/Pair 1.21
Mean z-score -1.83
Structure conservation index 0.67
SVM decision value 1.97
SVM RNA-class probability 0.984158
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 7180551 96 - 22224390
CAUAUGACCACCAAAACAGGGUCUCCAACCAUGUAGUAUAU---ACAUACAUAUGUAUGUACAUAUGUAGGUGUAGAGUGUGUGCAGUUUAGCAUGCGC
........((((...(((.(((.....))).))).((((((---((((....)))))))))).......))))....((((((((......)))))))) ( -29.40)
>DroSec_CAF1 6012 77 - 1
CAUAUGACCACCAAAACAGGGUCUC-AACCAUGUAGUAUAU-----------AUGUAUGUAUA----------UAGAGUGUGUGUAGUUUAGCAUGCGC
.....((((..........))))..-..........(((((-----------((....)))))----------))..((((((((......)))))))) ( -14.50)
>DroEre_CAF1 7730 92 - 1
CAUAUGACCACCAAAACAGGGUCGC-UACCACAUAGUAUAUCGCACAUACAAGUGU------GUAUGUAUGUAUAGGGUGUAUGCAGUUUAGCAUGCGC
.....((((..........)))).(-((..(((((.((((.(((((......))))------)))))))))).))).((((((((......)))))))) ( -26.70)
>consensus
CAUAUGACCACCAAAACAGGGUCUC_AACCAUGUAGUAUAU___ACAUACA_AUGUAUGUA_AUAUGUA_GU_UAGAGUGUGUGCAGUUUAGCAUGCGC
.....((((..........)))).....................((((((((((((....)))))))))))).....((((((((......)))))))) (-15.68 = -17.13 +   1.45)

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 10:40:47 2006