Locus 1442

Sequence ID	3L_DroMel_CAF1
Location	4,172,807 – 4,172,964
Length	157
Max. P	0.954054

overview

Window 7

Location	4,172,807 – 4,172,906
Length	99
Sequences	5
Columns	112
Reading direction	reverse
Mean pairwise identity	84.83
Mean single sequence MFE	-19.43
Consensus MFE	-15.08
Energy contribution	-14.44
Covariance contribution	-0.64
Combinations/Pair	1.23
Mean z-score	-2.31
Structure conservation index	0.78
SVM decision value	1.44
SVM RNA-class probability	0.954054
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 4172807 99 - 23771897
CACAUACCAACUCACACGAACUGGAAACAGACUGUGCACAUGCAAGUAGG----C-UCUCCCCCUCCCA------CUUACCCACACACACACACAUUGAC--ACACAGAGUC
.........((((.((((..(((....)))..)))).......((((.((----.-.........)).)------)))......................--.....)))). ( -14.40)
>DroSec_CAF1 18471 102 - 1
CACAUACCAGCUCACACGAACUGGAAACAGACUGUGCACAUGCAAGUGGAGAGCCUACUCUCCCUCCCC------CUUAC--ACACACACACACAUUGGC--ACACAGAGUC
.........((((.......(((....)))..(((((.......((.((((((....))))))))....------.....--.......((.....))))--)))..)))). ( -24.60)
>DroSim_CAF1 22995 97 - 1
CACAUACCAGCUCACACGAACUGGAAACAGACUGUGCACAUGCAAGUAGG----C-UCUCCCCCUCCCC------CUUAC--ACACACACACACAUUGAC--ACAGAGAGUC
....(((..((...((((..(((....)))..)))).....))..)))((----(-((((.........------.....--..................--...))))))) ( -17.75)
>DroEre_CAF1 18914 105 - 1
CACAUACCAGCUCACACGAACUGGAAACAGGCUGUGCACAUGCAAGUAGG----C-UCUCCCCUCCCCCUUCCUUCUUAC--ACACACACACACACUGACAUACACAGAGCC
.........((((.((((..(((....)))..))))....((.(((.(((----.-...............))).))).)--)........................)))). ( -18.89)
>DroYak_CAF1 22877 103 - 1
CACAUACCAGCUCACACGAACUGGAAACAGGCUGUGCACAUGCAAGUAGG----C-UCUCCCCCUACCCCUCC--CCAAC--CCCCUUACACACACUGACAUACACAGAGCC
.........((((.((((..(((....)))..)))).........(((((----.-......)))))......--.....--.........................)))). ( -21.50)
>consensus
CACAUACCAGCUCACACGAACUGGAAACAGACUGUGCACAUGCAAGUAGG____C_UCUCCCCCUCCCC______CUUAC__ACACACACACACAUUGAC__ACACAGAGUC
.........((((.......(((....)))(((.(((....))))))............................................................)))). (-15.08 = -14.44 +  -0.64)

alignment

secondary structure

dotplot

Window 8

Location	4,172,868 – 4,172,964
Length	96
Sequences	6
Columns	97
Reading direction	reverse
Mean pairwise identity	94.53
Mean single sequence MFE	-26.22
Consensus MFE	-22.10
Energy contribution	-21.85
Covariance contribution	-0.25
Combinations/Pair	1.12
Mean z-score	-1.86
Structure conservation index	0.84
SVM decision value	0.43
SVM RNA-class probability	0.734238
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 4172868 96 - 23771897
GGGAGACAGAGUGGAGCCACAUGUAAUUUUCAAUUCAUUUGGCACGCUUUCACUCACACACAUACCAACUCACACGAACUGGA-AACAGACUGUGCA
..(((..((((((..((((.(((.(((.....)))))).)))).))))))..))).................((((..(((..-..)))..)))).. ( -24.80)
>DroSec_CAF1 18535 96 - 1
GGGAGACAGAGUGGAGCCACAUGUAAUUUUCAAUUCAUUUGGCACGCUUUCACUCACACACAUACCAGCUCACACGAACUGGA-AACAGACUGUGCA
..(((..((((((..((((.(((.(((.....)))))).)))).))))))..))).................((((..(((..-..)))..)))).. ( -24.80)
>DroSim_CAF1 23054 96 - 1
GGGAGACAGAGUGGAGCCACAUGUAAUUUUCAAUUCAUUUGGCACGCUUUCACUCACACACAUACCAGCUCACACGAACUGGA-AACAGACUGUGCA
..(((..((((((..((((.(((.(((.....)))))).)))).))))))..))).................((((..(((..-..)))..)))).. ( -24.80)
>DroEre_CAF1 18981 96 - 1
GGGAGACAGAGUGGAGCCACAUGUAAUUUUCAAUUCAUUUGGCACGCUUUCACUCACACACAUACCAGCUCACACGAACUGGA-AACAGGCUGUGCA
..(((..((((((..((((.(((.(((.....)))))).)))).))))))..))).................((((..(((..-..)))..)))).. ( -26.80)
>DroYak_CAF1 22942 96 - 1
GUGAGACAGAGUGGAGCCACAUGUAAUUUUCAAUUCAUUUGGCACGCUUUCACUCACACACAUACCAGCUCACACGAACUGGA-AACAGGCUGUGCA
(((((..((((((..((((.(((.(((.....)))))).)))).))))))..)))))...............((((..(((..-..)))..)))).. ( -31.10)
>DroAna_CAF1 19222 93 - 1
GGGAGACAGAGCGGAGCCACAUGUAAUUUUCAAUUCAUUUGGCACGCUCGGACACACACACACAC--GCUCACACG--CUGGAAAACAGGCCGUGCA
..(((.(.(((((..((((.(((.(((.....)))))).)))).)))))(......)........--)))).((((--(((.....)))..)))).. ( -25.00)
>consensus
GGGAGACAGAGUGGAGCCACAUGUAAUUUUCAAUUCAUUUGGCACGCUUUCACUCACACACAUACCAGCUCACACGAACUGGA_AACAGACUGUGCA
..(((...(((((..((((.(((.(((.....)))))).)))).)))))...))).................((((..(((.....)))..)))).. (-22.10 = -21.85 +  -0.25)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:07:47 2006