Locus 722

Sequence ID	2R_DroMel_CAF1
Location	3,541,803 – 3,541,901
Length	98
Max. P	0.999867

overview

Window 4

Location	3,541,803 – 3,541,901
Length	98
Sequences	5
Columns	113
Reading direction	forward
Mean pairwise identity	72.86
Mean single sequence MFE	-34.50
Consensus MFE	-12.65
Energy contribution	-14.86
Covariance contribution	2.21
Combinations/Pair	1.27
Mean z-score	-3.33
Structure conservation index	0.37
SVM decision value	4.31
SVM RNA-class probability	0.999867
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 3541803 98 + 20766785
------CCUUUGCCAAAAUGAAAACGUG-AUUUUCUCCUUGGUCAUAUAUAUGUGCAUAUAAAUGG--------CGGAUGAGAGGGCUGGAGGUUCGUCCUGGCACAAGGAUA
------(((((((((..(((((..((.(-.(((((((.((.(((((.(((((....))))).))))--------).)).))))))))))....)))))..))))).))))... ( -31.80)
>DroGri_CAF1 18499 102 + 1
UUUUUGCCUUUGCCAAAAUGAAAC-CUAAAUUUCGUA-UUCUGUAUGGA--------UUUUAGGGGUUAGCUGUGCUGGCAAG-GGCUGGAAGCUAUGAUUUCCUUAGCGGUC
(((..((((((((((...(((..(-(((((.((((((-(...)))))))--------.))))))..)))((...)))))))))-)))..)))((((.(.....).)))).... ( -35.30)
>DroSec_CAF1 16255 97 + 1
------CCUUUGCCAAAAUGAAAACGUG-AUUUUCUCCUUGGUCAUAUAUAUGUGCAUAUAAAUGG--------CAGGGGAGG-GGCUGGAGGUUCGUCCUGGCUCAAGGAUA
------((((.((((..(((((....(.-(.(..(((((..(((((.(((((....))))).))))--------)..))))).-.).).)...)))))..))))..))))... ( -33.70)
>DroSim_CAF1 11970 98 + 1
------CCUUUGCCAAAAUGAAAACGUG-AUUUUCUCCUUGGUCAUAUAUAUGUGCAUAUAAAUGG--------CAGGGGAGGGGGCUGGAGGUUCGUCCUGGCACAAGGAUA
------(((((((((..(((((..((.(-.((..(((((..(((((.(((((....))))).))))--------)..)))))..)))))....)))))..))))).))))... ( -36.00)
>DroEre_CAF1 9246 98 + 1
------CCUUUGCCAAAAUGGAAACGUG-AUUUUCUCCUUGGUCAUAUAUAUGUGCAUAUAAAUGC--------CAGGGGAGAGGGCUGGAUGUUCGUCCUGGCAUAAGGAUA
------(((((((((..(((....))).-.(((((.((((((.(((.(((((....))))).))))--------))))))))))....((((....))))))))).))))... ( -35.70)
>consensus
______CCUUUGCCAAAAUGAAAACGUG_AUUUUCUCCUUGGUCAUAUAUAUGUGCAUAUAAAUGG________CAGGGGAGGGGGCUGGAGGUUCGUCCUGGCACAAGGAUA
......(((((((((..(((((........(((((((((..(((((.(((((....))))).))))........)..))))))))).......)))))..))))).))))... (-12.65 = -14.86 +   2.21)

alignment

secondary structure

dotplot

Window 5

Location	3,541,803 – 3,541,901
Length	98
Sequences	5
Columns	113
Reading direction	reverse
Mean pairwise identity	72.86
Mean single sequence MFE	-22.72
Consensus MFE	-6.59
Energy contribution	-9.96
Covariance contribution	3.37
Combinations/Pair	1.08
Mean z-score	-1.93
Structure conservation index	0.29
SVM decision value	0.89
SVM RNA-class probability	0.874686
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 3541803 98 - 20766785
UAUCCUUGUGCCAGGACGAACCUCCAGCCCUCUCAUCCG--------CCAUUUAUAUGCACAUAUAUAUGACCAAGGAGAAAAU-CACGUUUUCAUUUUGGCAAAGG------
...((((.((((((((.(((..........((((....(--------.(((.(((((....))))).))).)....))))....-......))).))))))))))))------ ( -21.75)
>DroGri_CAF1 18499 102 - 1
GACCGCUAAGGAAAUCAUAGCUUCCAGCC-CUUGCCAGCACAGCUAACCCCUAAAA--------UCCAUACAGAA-UACGAAAUUUAG-GUUUCAUUUUGGCAAAGGCAAAAA
.........((((........)))).(((-.((((((((...)))...........--------...........-...(((((....-))))).....))))).)))..... ( -20.60)
>DroSec_CAF1 16255 97 - 1
UAUCCUUGAGCCAGGACGAACCUCCAGCC-CCUCCCCUG--------CCAUUUAUAUGCACAUAUAUAUGACCAAGGAGAAAAU-CACGUUUUCAUUUUGGCAAAGG------
...((((..(((((((.(((.........-.((((...(--------.(((.(((((....))))).))).)...)))).....-......))).))))))).))))------ ( -21.00)
>DroSim_CAF1 11970 98 - 1
UAUCCUUGUGCCAGGACGAACCUCCAGCCCCCUCCCCUG--------CCAUUUAUAUGCACAUAUAUAUGACCAAGGAGAAAAU-CACGUUUUCAUUUUGGCAAAGG------
...((((.((((((((.(((...........((((...(--------.(((.(((((....))))).))).)...)))).....-......))).))))))))))))------ ( -22.45)
>DroEre_CAF1 9246 98 - 1
UAUCCUUAUGCCAGGACGAACAUCCAGCCCUCUCCCCUG--------GCAUUUAUAUGCACAUAUAUAUGACCAAGGAGAAAAU-CACGUUUCCAUUUUGGCAAAGG------
...((((.((((((((......))).....(((((..((--------((((.(((((....))))).))).))).)))))....-.............)))))))))------ ( -27.80)
>consensus
UAUCCUUGUGCCAGGACGAACCUCCAGCCCCCUCCCCUG________CCAUUUAUAUGCACAUAUAUAUGACCAAGGAGAAAAU_CACGUUUUCAUUUUGGCAAAGG______
...((((.((((((((................................(((.(((((....))))).)))........((((((....)))))).))))))))))))...... ( -6.59 =  -9.96 +   3.37)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:45:39 2006