Locus 2783

Sequence ID 2R_DroMel_CAF1
Location 9,725,181 – 9,725,314
Length 133
Max. P 0.999735
window4605 window4606 window4607 window4608

overview

Window 5

Location 9,725,181 – 9,725,294
Length 113
Sequences 6
Columns 114
Reading direction forward
Mean pairwise identity 94.38
Mean single sequence MFE -24.86
Consensus MFE -20.73
Energy contribution -21.07
Covariance contribution 0.33
Combinations/Pair 1.00
Mean z-score -2.10
Structure conservation index 0.83
SVM decision value 0.61
SVM RNA-class probability 0.797432
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 9725181 113 + 20766785
GUGUGCGGACUUAUCAGAGC-UUUUCAUCUGUACUUAAUUUAAUUUCAUGGCUUCAUUUCCAUUCAUAAUUCCAGCCAAUUUGUAGACGGGAAUUUCCCGUCGGAAACUACGAA
.((.(((((.((((((((..-......))))................((((........))))..)))).))).)))).((((((((((((.....))))))(....))))))) ( -26.80)
>DroSec_CAF1 43312 105 + 1
--------ACUUAUCAGAGC-UUUUCAUCUGUACUUAGUUUAAUUUCAUGGCUUCAUUUCCAUUCAUAAUUCCAGCCAAUUUGUAGACGGGAAUUUCCCGUCGGAAACUACGAA
--------(((...((((..-......)))).....))).........(((((....................))))).((((((((((((.....))))))(....))))))) ( -23.75)
>DroSim_CAF1 34585 105 + 1
--------ACUUAUCAGAGC-UUUUCAUCUGUACUUAAUUUAAUUUCAUGGCUUCAUUUCCAUUCAUAAUUCCAGCCAAUUUGUAGACGGGAAUUUCCCGUCGGAAACUACGAA
--------......((((..-......)))).................(((((....................))))).((((((((((((.....))))))(....))))))) ( -23.15)
>DroEre_CAF1 36065 111 + 1
G--UGCGGACUUAUCAGAGC-UUUUCAUCUGUACUUAAUUUAAUUUCAUGGCUUCAUUUCCAUUCAUAAUUUCAGCCAAUUUGUAGACGGGAAUUUCCCGUCGGAAACUACGAA
(--(((((((((....))).-......)))))))..............(((((....................))))).((((((((((((.....))))))(....))))))) ( -26.36)
>DroYak_CAF1 42229 111 + 1
G--UGCGGACUUAUCAGAGC-UUUUCAUCUGUACUUAAUUUAAUUUCACGGCUUCAUUUCCAUUCAUAAUUUCAGCCAAUUUGUAGACGGGAAUUUCCCGUCGGAAACUACGAA
(--(((((((((....))).-......)))))))...............((((....................))))..((((((((((((.....))))))(....))))))) ( -25.66)
>DroAna_CAF1 40586 112 + 1
G--UUCGGAUUUAUCAAAGCGUUUUCAUCUGUACUUAAUUUAAUUUCAUGGCUUCAUUUCCAUUCAUAAUUCCAGCCAAUUUGUAGACGGGAAUUUCCCGUCGGAAACUACGAA
.--((((((....)).....((((((......................(((((....................))))).......((((((.....))))))))))))..)))) ( -23.45)
>consensus
G__UGCGGACUUAUCAGAGC_UUUUCAUCUGUACUUAAUUUAAUUUCAUGGCUUCAUUUCCAUUCAUAAUUCCAGCCAAUUUGUAGACGGGAAUUUCCCGUCGGAAACUACGAA
..............((((.........)))).................(((((....................))))).((((((((((((.....))))))(....))))))) (-20.73 = -21.07 +   0.33)

alignment

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secondary structure

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Window 6

Location 9,725,181 – 9,725,294
Length 113
Sequences 6
Columns 114
Reading direction reverse
Mean pairwise identity 94.38
Mean single sequence MFE -24.65
Consensus MFE -23.76
Energy contribution -23.27
Covariance contribution -0.50
Combinations/Pair 1.12
Mean z-score -1.36
Structure conservation index 0.96
SVM decision value 1.86
SVM RNA-class probability 0.980278
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 9725181 113 - 20766785
UUCGUAGUUUCCGACGGGAAAUUCCCGUCUACAAAUUGGCUGGAAUUAUGAAUGGAAAUGAAGCCAUGAAAUUAAAUUAAGUACAGAUGAAAA-GCUCUGAUAAGUCCGCACAC
....((((((..((((((.....))))))...))))))((.(((.((((..((((........))))................((((......-..)))))))).))))).... ( -25.00)
>DroSec_CAF1 43312 105 - 1
UUCGUAGUUUCCGACGGGAAAUUCCCGUCUACAAAUUGGCUGGAAUUAUGAAUGGAAAUGAAGCCAUGAAAUUAAACUAAGUACAGAUGAAAA-GCUCUGAUAAGU--------
....(((((((.((((((.....)))))).......(((((...(((.........)))..))))).))))))).........((((......-..))))......-------- ( -24.50)
>DroSim_CAF1 34585 105 - 1
UUCGUAGUUUCCGACGGGAAAUUCCCGUCUACAAAUUGGCUGGAAUUAUGAAUGGAAAUGAAGCCAUGAAAUUAAAUUAAGUACAGAUGAAAA-GCUCUGAUAAGU--------
....(((((((.((((((.....)))))).......(((((...(((.........)))..))))).))))))).........((((......-..))))......-------- ( -24.50)
>DroEre_CAF1 36065 111 - 1
UUCGUAGUUUCCGACGGGAAAUUCCCGUCUACAAAUUGGCUGAAAUUAUGAAUGGAAAUGAAGCCAUGAAAUUAAAUUAAGUACAGAUGAAAA-GCUCUGAUAAGUCCGCA--C
(((((((((((.((((((.....))))))..(.....)...))))))))))).(((.(((....)))................((((......-..)))).....)))...--. ( -25.30)
>DroYak_CAF1 42229 111 - 1
UUCGUAGUUUCCGACGGGAAAUUCCCGUCUACAAAUUGGCUGAAAUUAUGAAUGGAAAUGAAGCCGUGAAAUUAAAUUAAGUACAGAUGAAAA-GCUCUGAUAAGUCCGCA--C
(((((((((((.((((((.....))))))..(.....)...))))))))))).(((.(((....)))................((((......-..)))).....)))...--. ( -24.90)
>DroAna_CAF1 40586 112 - 1
UUCGUAGUUUCCGACGGGAAAUUCCCGUCUACAAAUUGGCUGGAAUUAUGAAUGGAAAUGAAGCCAUGAAAUUAAAUUAAGUACAGAUGAAAACGCUUUGAUAAAUCCGAA--C
(((((((((((.((((((.....)))))).......(((((...(((.........)))..))))).))))))).........((((((....)).)))).......))))--. ( -23.70)
>consensus
UUCGUAGUUUCCGACGGGAAAUUCCCGUCUACAAAUUGGCUGGAAUUAUGAAUGGAAAUGAAGCCAUGAAAUUAAAUUAAGUACAGAUGAAAA_GCUCUGAUAAGUCCGCA__C
.((((((((((.((((((.....))))))..(.....)...))))))))))((((........))))................((((.(......))))).............. (-23.76 = -23.27 +  -0.50)

alignment

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secondary structure

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dotplot

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Window 7

Location 9,725,220 – 9,725,314
Length 94
Sequences 6
Columns 94
Reading direction forward
Mean pairwise identity 95.74
Mean single sequence MFE -24.46
Consensus MFE -21.65
Energy contribution -22.32
Covariance contribution 0.67
Combinations/Pair 1.00
Mean z-score -2.87
Structure conservation index 0.89
SVM decision value 3.09
SVM RNA-class probability 0.998408
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 9725220 94 + 20766785
UAAUUUCAUGGCUUCAUUUCCAUUCAUAAUUCCAGCCAAUUUGUAGACGGGAAUUUCCCGUCGGAAACUACGAAAGUCAGUCAGCUGAAAUGGC
.......((((........))))...........((((.((((((((((((.....))))))(....)))))))..((((....))))..)))) ( -26.80)
>DroSec_CAF1 43343 89 + 1
UAAUUUCAUGGCUUCAUUUCCAUUCAUAAUUCCAGCCAAUUUGUAGACGGGAAUUUCCCGUCGGAAACUACGAAAGUCAGUCAGCUGAA-----
........(((((....................))))).((((((((((((.....))))))(....)))))))..((((....)))).----- ( -24.85)
>DroSim_CAF1 34616 89 + 1
UAAUUUCAUGGCUUCAUUUCCAUUCAUAAUUCCAGCCAAUUUGUAGACGGGAAUUUCCCGUCGGAAACUACGAAAGUCAGUCAGCUGAA-----
........(((((....................))))).((((((((((((.....))))))(....)))))))..((((....)))).----- ( -24.85)
>DroEre_CAF1 36102 89 + 1
UAAUUUCAUGGCUUCAUUUCCAUUCAUAAUUUCAGCCAAUUUGUAGACGGGAAUUUCCCGUCGGAAACUACGAAAGUCAGUCAGCUGAA-----
........(((((....................))))).((((((((((((.....))))))(....)))))))..((((....)))).----- ( -24.85)
>DroYak_CAF1 42266 89 + 1
UAAUUUCACGGCUUCAUUUCCAUUCAUAAUUUCAGCCAAUUUGUAGACGGGAAUUUCCCGUCGGAAACUACGAAAGUCAUUCAGCUGAA-----
........(((((...(((((.............((......)).((((((.....)))))))))))..((....)).....)))))..----- ( -23.10)
>DroAna_CAF1 40624 89 + 1
UAAUUUCAUGGCUUCAUUUCCAUUCAUAAUUCCAGCCAAUUUGUAGACGGGAAUUUCCCGUCGGAAACUACGAAAGUCAGUCGGGUGUA-----
....................(((((....((((.((......)).((((((.....))))))))))(((((....)).))).)))))..----- ( -22.30)
>consensus
UAAUUUCAUGGCUUCAUUUCCAUUCAUAAUUCCAGCCAAUUUGUAGACGGGAAUUUCCCGUCGGAAACUACGAAAGUCAGUCAGCUGAA_____
........(((((....................))))).((((((((((((.....))))))(....)))))))..((((....))))...... (-21.65 = -22.32 +   0.67)

alignment

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secondary structure

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dotplot

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Window 8

Location 9,725,220 – 9,725,314
Length 94
Sequences 6
Columns 94
Reading direction reverse
Mean pairwise identity 95.74
Mean single sequence MFE -24.72
Consensus MFE -23.79
Energy contribution -23.68
Covariance contribution -0.11
Combinations/Pair 1.13
Mean z-score -2.21
Structure conservation index 0.96
SVM decision value 3.97
SVM RNA-class probability 0.999735
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 9725220 94 - 20766785
GCCAUUUCAGCUGACUGACUUUCGUAGUUUCCGACGGGAAAUUCCCGUCUACAAAUUGGCUGGAAUUAUGAAUGGAAAUGAAGCCAUGAAAUUA
...((((((((..(..((((.....))))...((((((.....))))))......)..)))))))).....((((........))))....... ( -26.40)
>DroSec_CAF1 43343 89 - 1
-----UUCAGCUGACUGACUUUCGUAGUUUCCGACGGGAAAUUCCCGUCUACAAAUUGGCUGGAAUUAUGAAUGGAAAUGAAGCCAUGAAAUUA
-----((((((..(..((((.....))))...((((((.....))))))......)..)))))).......((((........))))....... ( -24.80)
>DroSim_CAF1 34616 89 - 1
-----UUCAGCUGACUGACUUUCGUAGUUUCCGACGGGAAAUUCCCGUCUACAAAUUGGCUGGAAUUAUGAAUGGAAAUGAAGCCAUGAAAUUA
-----((((((..(..((((.....))))...((((((.....))))))......)..)))))).......((((........))))....... ( -24.80)
>DroEre_CAF1 36102 89 - 1
-----UUCAGCUGACUGACUUUCGUAGUUUCCGACGGGAAAUUCCCGUCUACAAAUUGGCUGAAAUUAUGAAUGGAAAUGAAGCCAUGAAAUUA
-----((((((..(..((((.....))))...((((((.....))))))......)..)))))).......((((........))))....... ( -25.30)
>DroYak_CAF1 42266 89 - 1
-----UUCAGCUGAAUGACUUUCGUAGUUUCCGACGGGAAAUUCCCGUCUACAAAUUGGCUGAAAUUAUGAAUGGAAAUGAAGCCGUGAAAUUA
-----(((((((..((..(.(((((((((((.((((((.....))))))..(.....)...))))))))))).)...))..)))..)))).... ( -25.80)
>DroAna_CAF1 40624 89 - 1
-----UACACCCGACUGACUUUCGUAGUUUCCGACGGGAAAUUCCCGUCUACAAAUUGGCUGGAAUUAUGAAUGGAAAUGAAGCCAUGAAAUUA
-----................((((((((((.((((((.....))))))..(.....)...))))))))))((((........))))....... ( -21.20)
>consensus
_____UUCAGCUGACUGACUUUCGUAGUUUCCGACGGGAAAUUCCCGUCUACAAAUUGGCUGGAAUUAUGAAUGGAAAUGAAGCCAUGAAAUUA
.....(((((((((..((((.....))))...((((((.....))))))......))))))))).......((((........))))....... (-23.79 = -23.68 +  -0.11)

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 10:39:23 2006