Locus 4929

Sequence ID	3L_DroMel_CAF1
Location	13,681,549 – 13,681,683
Length	134
Max. P	0.964153

overview

Window 5

Location	13,681,549 – 13,681,646
Length	97
Sequences	6
Columns	116
Reading direction	forward
Mean pairwise identity	81.04
Mean single sequence MFE	-34.03
Consensus MFE	-24.75
Energy contribution	-27.78
Covariance contribution	3.03
Combinations/Pair	1.17
Mean z-score	-3.72
Structure conservation index	0.73
SVM decision value	1.56
SVM RNA-class probability	0.964153
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13681549 97 + 23771897
UACCCCGGGGAGUUAAUAAUAACGCGUAAGCAAAUAAUAAAUAAACCCCUUGUUGCGCAAAAAAGUGCAAUAAAGUUUUUCGGGUC------UG-----------GGGGCUGG--G
..((((((((.((((....))))((....))..............))))(((((((((......))))))))).............------.)-----------))).....--. ( -32.30)
>DroSec_CAF1 88798 100 + 1
UGCCCCGGGGAGUUAAUAAUAACGCGUAAGCAAAUAAUAAAUAAACCCCUUGUUGCGCAAAAAAGUGCAAUAAAGUUUUUCGGUUG------UG----------AGGGGCUGGGGG
..((((((((.((((....))))((....))..............))))(((((((((......)))))))))(((((((((....------))----------))))))))))). ( -37.30)
>DroSim_CAF1 99410 100 + 1
UGCCCCGGGGAGUUAAUAAUAACGCGUAAGCAAAUAAUAAAUAAACCCCUUGUUGCGCAAAAAAGUGCAAUAAAGUUUUUCGGUUG------UG----------AGGGGCUGGGUG
.(((((((((.((((....))))((....))..............))))(((((((((......))))))))).............------..----------.)))))...... ( -35.30)
>DroEre_CAF1 94205 115 + 1
UGCCCCGGGGAGUUAAUAAUAACGCGUAAGCAAAUAAUAAAUAAACCCCUUGUUGCGCAAAAAAGUGCAAUAAAGUUUUUCGGAGCUCUGGAUGGGGAUGGGGCAGGGGCUG-GGG
.(((((((((.((((....))))((....))..............))))(((((((((......)))))))))...........((((((........)))))).)))))..-... ( -40.90)
>DroYak_CAF1 97852 105 + 1
UGCCCCGGGGAGUUAAUAAUAACGCGUAAGCAAAUAAUAAAUAAACCCCUUGUUGCGCAAAAAAGUGCAAUAAAGUUUUUCGGGGC------UGGGAAUGGGAGAGA----G-GGG
.(((((((((.((((....))))((....))..............))))(((((((((......)))))))))........)))))------...............----.-... ( -35.40)
>DroAna_CAF1 134205 96 + 1
UGCCCCGGGGAGUUAAUAAUAGCGCGUAAGCCAAUGAUAAAUAAAGUCCUGGUUGCG-AAAAAAGUGCAAUCCACAACUAGGGG---------G----------AGGUCUUGGAAA
..((((.((((((((....))))((....))...............))))(((((((-.......)))))))........))))---------.----------............ ( -23.00)
>consensus
UGCCCCGGGGAGUUAAUAAUAACGCGUAAGCAAAUAAUAAAUAAACCCCUUGUUGCGCAAAAAAGUGCAAUAAAGUUUUUCGGGUC______UG__________AGGGGCUGGGGG
.(((((((((.((((....))))((....))..............))))(((((((((......)))))))))................................)))))...... (-24.75 = -27.78 +   3.03)

alignment

secondary structure

dotplot

Window 6

Location	13,681,549 – 13,681,646
Length	97
Sequences	6
Columns	116
Reading direction	reverse
Mean pairwise identity	81.04
Mean single sequence MFE	-24.92
Consensus MFE	-17.14
Energy contribution	-18.58
Covariance contribution	1.44
Combinations/Pair	1.10
Mean z-score	-2.70
Structure conservation index	0.69
SVM decision value	1.18
SVM RNA-class probability	0.926871
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13681549 97 - 23771897
C--CCAGCCCC-----------CA------GACCCGAAAAACUUUAUUGCACUUUUUUGCGCAACAAGGGGUUUAUUUAUUAUUUGCUUACGCGUUAUUAUUAACUCCCCGGGGUA
.--...(((((-----------..------................((((.(......).))))...((((..............((....))((((....)))).))))))))). ( -23.30)
>DroSec_CAF1 88798 100 - 1
CCCCCAGCCCCU----------CA------CAACCGAAAAACUUUAUUGCACUUUUUUGCGCAACAAGGGGUUUAUUUAUUAUUUGCUUACGCGUUAUUAUUAACUCCCCGGGGCA
......(((((.----------..------................((((.(......).))))...((((..............((....))((((....)))).))))))))). ( -26.00)
>DroSim_CAF1 99410 100 - 1
CACCCAGCCCCU----------CA------CAACCGAAAAACUUUAUUGCACUUUUUUGCGCAACAAGGGGUUUAUUUAUUAUUUGCUUACGCGUUAUUAUUAACUCCCCGGGGCA
......(((((.----------..------................((((.(......).))))...((((..............((....))((((....)))).))))))))). ( -26.00)
>DroEre_CAF1 94205 115 - 1
CCC-CAGCCCCUGCCCCAUCCCCAUCCAGAGCUCCGAAAAACUUUAUUGCACUUUUUUGCGCAACAAGGGGUUUAUUUAUUAUUUGCUUACGCGUUAUUAUUAACUCCCCGGGGCA
...-........(((((.............................((((.(......).))))...((((..............((....))((((....)))).))))))))). ( -26.30)
>DroYak_CAF1 97852 105 - 1
CCC-C----UCUCUCCCAUUCCCA------GCCCCGAAAAACUUUAUUGCACUUUUUUGCGCAACAAGGGGUUUAUUUAUUAUUUGCUUACGCGUUAUUAUUAACUCCCCGGGGCA
...-.----...............------(((((...........((((.(......).))))...((((..............((....))((((....)))).))))))))). ( -26.50)
>DroAna_CAF1 134205 96 - 1
UUUCCAAGACCU----------C---------CCCCUAGUUGUGGAUUGCACUUUUUU-CGCAACCAGGACUUUAUUUAUCAUUGGCUUACGCGCUAUUAUUAACUCCCCGGGGCA
............----------.---------((((.((((.(((.((((........-.))))))).))))...........((((......)))).............)))).. ( -21.40)
>consensus
CCCCCAGCCCCU__________CA______GACCCGAAAAACUUUAUUGCACUUUUUUGCGCAACAAGGGGUUUAUUUAUUAUUUGCUUACGCGUUAUUAUUAACUCCCCGGGGCA
......(((((...................................((((.(......).))))...((((..............((....))((((....)))).))))))))). (-17.14 = -18.58 +   1.44)

alignment

secondary structure

dotplot

Window 7

Location	13,681,589 – 13,681,683
Length	94
Sequences	6
Columns	116
Reading direction	forward
Mean pairwise identity	78.79
Mean single sequence MFE	-25.01
Consensus MFE	-14.42
Energy contribution	-14.37
Covariance contribution	-0.05
Combinations/Pair	1.19
Mean z-score	-1.79
Structure conservation index	0.58
SVM decision value	0.35
SVM RNA-class probability	0.698143
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13681589 94 + 23771897
AUAAACCCCUUGUUGCGCAAAAAAGUGCAAUAAAGUUUUUCGGGUC------UG-----------GGGGCUGG--GGG---AUAUGCAGAGAUAUAAGUAAAUAUUGGCCGAACAA
(((..(((((((((((((......))))))))).........((((------..-----------..))))))--)).---.)))((...(((((......))))).))....... ( -24.90)
>DroSec_CAF1 88838 97 + 1
AUAAACCCCUUGUUGCGCAAAAAAGUGCAAUAAAGUUUUUCGGUUG------UG----------AGGGGCUGGGGGGG---AUAUGCAGAGAUAUAAGUAAAUAUUGGCCGAACAA
(((..(((((((((((((......)))))))).(((((((((....------))----------))))))).))))).---.)))((...(((((......))))).))....... ( -27.80)
>DroSim_CAF1 99450 97 + 1
AUAAACCCCUUGUUGCGCAAAAAAGUGCAAUAAAGUUUUUCGGUUG------UG----------AGGGGCUGGGUGGG---AUAUGCAGAGAUAUAAGUAAAUAUUGGCCGAACAA
....((((.(((((((((......)))))))))(((((((((....------))----------)))))))))))...---....((...(((((......))))).))....... ( -24.20)
>DroEre_CAF1 94245 112 + 1
AUAAACCCCUUGUUGCGCAAAAAAGUGCAAUAAAGUUUUUCGGAGCUCUGGAUGGGGAUGGGGCAGGGGCUG-GGGGG---AUAUGCAGAGAUAUAAGUAAAUAUUGGCCGAACAA
(((..(((((((((((((......)))))))))(((((((....((((((........))))))))))))).-)))).---.)))((...(((((......))))).))....... ( -29.20)
>DroYak_CAF1 97892 102 + 1
AUAAACCCCUUGUUGCGCAAAAAAGUGCAAUAAAGUUUUUCGGGGC------UGGGAAUGGGAGAGA----G-GGGGG---AUGUGCAGAGAUAUAAGUAAAUAUUGGCCGAACAA
.....(((((((((((((......)))))))....(((..((....------......))..)))))----)-)))(.---.((.((...(((((......))))).))))..).. ( -25.50)
>DroAna_CAF1 134245 96 + 1
AUAAAGUCCUGGUUGCG-AAAAAAGUGCAAUCCACAACUAGGGG---------G----------AGGUCUUGGAAAGGGUCGAACACAGAGAUAUGAGUAAAUAUUGGUCGAACAA
......(((((((((.(-..............).))))))))).---------.----------.(..(((....)))..)....((...(((((......))))).))....... ( -18.44)
>consensus
AUAAACCCCUUGUUGCGCAAAAAAGUGCAAUAAAGUUUUUCGGGUC______UG__________AGGGGCUGGGGGGG___AUAUGCAGAGAUAUAAGUAAAUAUUGGCCGAACAA
.....(((((((((((((......))))))))).(.....)........................))))................((...(((((......))))).))....... (-14.42 = -14.37 +  -0.05)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:37:19 2006