Locus 1758

Sequence ID	3L_DroMel_CAF1
Location	5,050,459 – 5,050,611
Length	152
Max. P	0.996313

overview

Window 6

Location	5,050,459 – 5,050,571
Length	112
Sequences	5
Columns	114
Reading direction	forward
Mean pairwise identity	92.64
Mean single sequence MFE	-39.54
Consensus MFE	-33.78
Energy contribution	-35.66
Covariance contribution	1.88
Combinations/Pair	1.05
Mean z-score	-2.29
Structure conservation index	0.85
SVM decision value	2.68
SVM RNA-class probability	0.996313
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 5050459 112 + 23771897
--UGGCCAUGGCAACAUGGCAGCACGUGUGUGCGUGCGGGUUUGCUAGCUGGAAAAGUUUCAAUAGCCAAAUGCCUAUUGACGUCGCAGAAGAAGUUACCCUAAAGCGAACCGA
--..((((((....)))))).((((((....)))))).((((((((....((.......(((((((.(....).)))))))..((......))......))...)))))))).. ( -41.90)
>DroSec_CAF1 256878 112 + 1
--UGGCCAUGGCAACAUGGCAGCACGUGUGUGCGUGCGGGUUUGCUAGCUGGAAAAGUUUCAAUAGCCAAAUGCCUAUUGACGGCGCAGAAGAAGUGACCCGAAAGCGAACCGA
--..((((((....)))))).((((((....)))))).((((((((((((.....))))(((((((.(....).)))))))((((((.......)))..)))..)))))))).. ( -45.10)
>DroSim_CAF1 278187 112 + 1
--UGGCCAUGGCAACAUGGCAGCACGUGUGUGCGUGCGGGUUUGCUAGCUGGAAAAGUUUCAAUAGCCAAAUGCCUAUUGACGGCGCAGAAGAAGUGACCCGAAAGCGAACCGA
--..((((((....)))))).((((((....)))))).((((((((((((.....))))(((((((.(....).)))))))((((((.......)))..)))..)))))))).. ( -45.10)
>DroEre_CAF1 263600 104 + 1
----------GCAACAUGGCAGCACGUGUGUGCGUGCGGGUUUCCUAGCUGGAAAAGUUUCAAUAGCCAAAUGUCUAUUGACGGCGCAGAAGAAGUGACCCGAAAGCGGGCCGA
----------......((((.((((....))))((((.(.(((((.....)))))....(((((((.(....).)))))))).))))...........(((....).)))))). ( -32.90)
>DroYak_CAF1 266792 114 + 1
CAUGGCCAUAGCAACAUGGCAGCACGUGUGUGCGUGCGGGUUUCCUAGCUGCAAAAGUUUCAAUAGCCAAAUGUCUAUUGACGGCGCAAAAGAAGUGACCCGAAAGCGAACCGA
....(((((......))))).((((((....)))))).(((((.((((((.....))))(((((((.(....).)))))))((((((.......)))..)))..)).))))).. ( -32.70)
>consensus
__UGGCCAUGGCAACAUGGCAGCACGUGUGUGCGUGCGGGUUUGCUAGCUGGAAAAGUUUCAAUAGCCAAAUGCCUAUUGACGGCGCAGAAGAAGUGACCCGAAAGCGAACCGA
....((((((....)))))).((((((....)))))).((((((((((((.....))))(((((((.(....).))))))).(((((.......))).))....)))))))).. (-33.78 = -35.66 +   1.88)

alignment

secondary structure

dotplot

Window 7

Location	5,050,495 – 5,050,611
Length	116
Sequences	5
Columns	116
Reading direction	reverse
Mean pairwise identity	95.86
Mean single sequence MFE	-26.04
Consensus MFE	-23.37
Energy contribution	-23.17
Covariance contribution	-0.20
Combinations/Pair	1.08
Mean z-score	-1.28
Structure conservation index	0.90
SVM decision value	0.37
SVM RNA-class probability	0.709357
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 5050495 116 - 23771897
UGCUUUUCCUUUUCCCAGCCAGCAGCAUCUCAUUUCCCGUUCGGUUCGCUUUAGGGUAACUUCUUCUGCGACGUCAAUAGGCAUUUGGCUAUUGAAACUUUUCCAGCUAGCAAACC
.................((.(((.(((........(((....((....))...)))..........)))....(((((((.(....).)))))))..........))).))..... ( -21.97)
>DroSec_CAF1 256914 116 - 1
CGCUUUUCCUUUUCCCAGCCAGCAGCAUCUCAUUUCCCGUUCGGUUCGCUUUCGGGUCACUUCUUCUGCGCCGUCAAUAGGCAUUUGGCUAUUGAAACUUUUCCAGCUAGCAAACC
.(((......((((..(((((((((..........((((...((....))..)))).........))))(((.......)))...)))))...)))).......)))......... ( -27.23)
>DroSim_CAF1 278223 116 - 1
CGCUUUUCCUUUUCCCAGCCAGCAGCAUCUCAUUUCCCGUUCGGUUCGCUUUCGGGUCACUUCUUCUGCGCCGUCAAUAGGCAUUUGGCUAUUGAAACUUUUCCAGCUAGCAAACC
.(((......((((..(((((((((..........((((...((....))..)))).........))))(((.......)))...)))))...)))).......)))......... ( -27.23)
>DroEre_CAF1 263628 116 - 1
UGCUUUUCCUUUUCCCAGCCAGCAGCAUCUCAUUUCCCGUUCGGCCCGCUUUCGGGUCACUUCUUCUGCGCCGUCAAUAGACAUUUGGCUAUUGAAACUUUUCCAGCUAGGAAACC
..........(((((.(((..((((..........((((...((....))..)))).........))))....(((((((.(....).)))))))..........))).))))).. ( -26.81)
>DroYak_CAF1 266830 116 - 1
AGCUUUUCCUUUUCCCAGCCAGCAGCAUCUCAUUUCCCGUUCGGUUCGCUUUCGGGUCACUUCUUUUGCGCCGUCAAUAGACAUUUGGCUAUUGAAACUUUUGCAGCUAGGAAACC
..........(((((.(((..((((((........((((...((....))..))))..........)))....(((((((.(....).)))))))......))).))).))))).. ( -26.97)
>consensus
CGCUUUUCCUUUUCCCAGCCAGCAGCAUCUCAUUUCCCGUUCGGUUCGCUUUCGGGUCACUUCUUCUGCGCCGUCAAUAGGCAUUUGGCUAUUGAAACUUUUCCAGCUAGCAAACC
.(((......((((..(((((((((..........((((...((....))..)))).........))))...(((....)))...)))))...)))).......)))......... (-23.37 = -23.17 +  -0.20)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:15:31 2006