Locus 6978

Sequence ID	2L_DroMel_CAF1
Location	19,384,179 – 19,384,274
Length	95
Max. P	0.627925

overview

Window 1

Location	19,384,179 – 19,384,274
Length	95
Sequences	6
Columns	110
Reading direction	forward
Mean pairwise identity	79.52
Mean single sequence MFE	-32.85
Consensus MFE	-19.17
Energy contribution	-21.03
Covariance contribution	1.87
Combinations/Pair	1.15
Mean z-score	-1.72
Structure conservation index	0.58
SVM decision value	0.16
SVM RNA-class probability	0.609990
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 19384179 95 + 22407834
UGGCAUACCCUCCGGCGUAACCGCCGGCAUAUGCUCGUCGUCUGCGGGUCGGAGCCGUUUUUGCU---GAAAUGGAA-AACAUCAU--GUGGAUGAUAAAA---------
.((((((....((((((....))))))..)))))).((((((..(((((.....(((((((....---)))))))..-...))).)--)..))))))....--------- ( -35.10)
>DroSec_CAF1 17997 94 + 1
UGGCAUACCCUCCAGCGUAACCGCCGGCAUAUGCUCGUCGUCUGCGGGUCGGACCCGUUUUUGCU---GAAAUCGAA-AAUAUCAU--GUGGAUGAUAAA----------
.((((((....((.(((....))).))..)))))).((((((..((((.....)))(((((((..---.....))))-))).....--)..))))))...---------- ( -28.00)
>DroSim_CAF1 18310 94 + 1
UGGCAUACCCUCCGGCGUAACCGCCGGCAUAUGCUCGUCGUCUGCGGGUCGGACCCGUUUUUGCU---GAAAUGGAA-AACAUCAU--GUGGAUAAUAAA----------
.((((((....((((((....))))))..)))))).((..((..((((.....)))((((((.(.---.....))))-))).....--)..))..))...---------- ( -29.60)
>DroEre_CAF1 18236 105 + 1
UGGCAUACCCUCCGGCGUAUCCGCCGGCGUAUGCUCGUCGUCUGCGGGUCGGACCCGUUUUUGCU---GAAAUAAAGGAAAAUCAU--GUGGAUGAUAAAAAAAUUAUUU
.(((((((...((((((....)))))).))))))).((((((..((((.....)))(.((((.((---.......)).)))).)..--)..))))))............. ( -37.70)
>DroYak_CAF1 18666 93 + 1
UGGCAUACCCUCCGGCGUAUCCGCCGGCGUAUGCUCGUCGUCUCCGGGUCGGACCCGUUUUUGCU---GAAAUAAAA-AAAAUCAU--GUGGAUGAUAC-----------
.(((((((...((((((....)))))).))))))).((((((..((((.....)))(((((....---)))))....-........--)..))))))..----------- ( -32.80)
>DroAna_CAF1 25016 99 + 1
UGGCAUAGCCUCCAGCAUAUCCUCCGGCGUAGGCACGACGUUUACGGGGCAGCUGGCGGUUGGCUAUGGGGAUUUAU-UAGUUCGUUAAUGGAUGAUCCA----------
((((.(((((.(((((....(((....(((((((.....))))))))))..))))).)))))))))((((.((((((-(((....)))))))))..))))---------- ( -33.90)
>consensus
UGGCAUACCCUCCGGCGUAACCGCCGGCAUAUGCUCGUCGUCUGCGGGUCGGACCCGUUUUUGCU___GAAAUAGAA_AAAAUCAU__GUGGAUGAUAAA__________
.((((((....((((((....))))))..)))))).(((((((((((((...))))((....))........................)))))))))............. (-19.17 = -21.03 +   1.87)

alignment

secondary structure

dotplot

Window 2

Location	19,384,179 – 19,384,274
Length	95
Sequences	6
Columns	110
Reading direction	reverse
Mean pairwise identity	79.52
Mean single sequence MFE	-28.52
Consensus MFE	-21.15
Energy contribution	-22.27
Covariance contribution	1.11
Combinations/Pair	1.26
Mean z-score	-1.15
Structure conservation index	0.74
SVM decision value	0.19
SVM RNA-class probability	0.627925
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 19384179 95 - 22407834
---------UUUUAUCAUCCAC--AUGAUGUU-UUCCAUUUC---AGCAAAAACGGCUCCGACCCGCAGACGACGAGCAUAUGCCGGCGGUUACGCCGGAGGGUAUGCCA
---------...((((((....--))))))..-.........---.........(((....((((((.........)).....((((((....)))))).))))..))). ( -28.80)
>DroSec_CAF1 17997 94 - 1
----------UUUAUCAUCCAC--AUGAUAUU-UUCGAUUUC---AGCAAAAACGGGUCCGACCCGCAGACGACGAGCAUAUGCCGGCGGUUACGCUGGAGGGUAUGCCA
----------..((((((....--))))))..-.........---........((((.....))))........(.((((((.((((((....))))))...))))))). ( -26.90)
>DroSim_CAF1 18310 94 - 1
----------UUUAUUAUCCAC--AUGAUGUU-UUCCAUUUC---AGCAAAAACGGGUCCGACCCGCAGACGACGAGCAUAUGCCGGCGGUUACGCCGGAGGGUAUGCCA
----------..((((((....--))))))..-.........---........((((.....))))........(.((((((.((((((....))))))...))))))). ( -26.60)
>DroEre_CAF1 18236 105 - 1
AAAUAAUUUUUUUAUCAUCCAC--AUGAUUUUCCUUUAUUUC---AGCAAAAACGGGUCCGACCCGCAGACGACGAGCAUACGCCGGCGGAUACGCCGGAGGGUAUGCCA
((((((.......(((((....--)))))......)))))).---........((((.....))))........(.((((((.((((((....))))))...))))))). ( -30.42)
>DroYak_CAF1 18666 93 - 1
-----------GUAUCAUCCAC--AUGAUUUU-UUUUAUUUC---AGCAAAAACGGGUCCGACCCGGAGACGACGAGCAUACGCCGGCGGAUACGCCGGAGGGUAUGCCA
-----------((....(((..--.(((..(.-....)..))---)........(((.....))))))....))(.((((((.((((((....))))))...))))))). ( -31.70)
>DroAna_CAF1 25016 99 - 1
----------UGGAUCAUCCAUUAACGAACUA-AUAAAUCCCCAUAGCCAACCGCCAGCUGCCCCGUAAACGUCGUGCCUACGCCGGAGGAUAUGCUGGAGGCUAUGCCA
----------(((.....)))...........-.........(((((((.....(((((..(((((....(((.......))).))).))....))))).)))))))... ( -26.70)
>consensus
__________UUUAUCAUCCAC__AUGAUGUU_UUCCAUUUC___AGCAAAAACGGGUCCGACCCGCAGACGACGAGCAUACGCCGGCGGAUACGCCGGAGGGUAUGCCA
............((((((......)))))).......................((((.....))))........(.((((((.((((((....))))))...))))))). (-21.15 = -22.27 +   1.11)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:24:26 2006