Locus 2566

Sequence ID	X_DroMel_CAF1
Location	6,889,636 – 6,889,785
Length	149
Max. P	0.963959

overview

Window 2

Location	6,889,636 – 6,889,752
Length	116
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	87.24
Mean single sequence MFE	-36.37
Consensus MFE	-29.20
Energy contribution	-29.80
Covariance contribution	0.60
Combinations/Pair	1.00
Mean z-score	-2.18
Structure conservation index	0.80
SVM decision value	1.46
SVM RNA-class probability	0.955904
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 6889636 116 - 22224390
CAAGUGCCGCGUUGGAGUCAGACAAACACUUGCGGCUGUCAAACGGCAGCAAAGUCCCUUGGCUUCAUCCGCACCUCGUACAUAUCCAUAGCCGCAUAGCCUUGUC----CCAGGACACA
...((((((((.(((((((((......((((...((((((....)))))).))))...)))))))))..)))..............((..((......))..))..----...)).))). ( -32.80)
>DroSec_CAF1 14066 114 - 1
CAAGUGCCGCGUUGGAGUCAGCCAAACACUUGCGGCUGUCAAACGGCAGCAAAGUCCCUUGGCUUCCUCCGCACCUCGACCACAUCCAUAGCCGCUU--CCUUGUC----CCAGGACACA
...(((.((.(((((((..((((((..((((...((((((....)))))).))))...))))))..))))).))..))..)))..............--...((((----....)))).. ( -36.00)
>DroSim_CAF1 14769 114 - 1
CAAGUGCCGCGUUGGAGUCAGCCAAACACUUGCGGCUGUCAAACGGCAGCAAAGUCCCUUGGCUUCCUCCGCACCUCGACCACAUCCAUAGCCGAUU--CCUUGUC----CCAGGACACA
...(((.((.(((((((..((((((..((((...((((((....)))))).))))...))))))..))))).))..))..)))..............--...((((----....)))).. ( -36.00)
>DroEre_CAF1 13385 102 - 1
CAAGUGCCGCGUUGGAGUCAGCCAAACACUUGCGGCUGUCAAACGGCAGCAAAGUCCCUUGGCUUCCUCCGCACCUCGUCCAUGUCC--------------UUGUC----CCAGGACACA
...((((......((((..((((((..((((...((((((....)))))).))))...))))))..))))))))........(((((--------------(....----..)))))).. ( -37.90)
>DroYak_CAF1 16353 106 - 1
CAAGUGCCGCGUUGGAGUCAGCCAAACACUUGCGGCUGUCAAACGGCAGCAAAGUCCCUUGGCUUCCUCGGCACCUCCUUCACAUCC--------------UUGCCAGGCACAGGACACA
...(((((......(((..((((((..((((...((((((....)))))).))))...))))))..)))((((..............--------------.)))).)))))........ ( -39.16)
>consensus
CAAGUGCCGCGUUGGAGUCAGCCAAACACUUGCGGCUGUCAAACGGCAGCAAAGUCCCUUGGCUUCCUCCGCACCUCGUCCACAUCCAUAGCCG__U__CCUUGUC____CCAGGACACA
...(((((((...((((..((((((..((((...((((((....)))))).))))...))))))..))))))..............................((.......)))).))). (-29.20 = -29.80 +   0.60)

alignment

secondary structure

dotplot

Window 3

Location	6,889,672 – 6,889,785
Length	113
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	94.73
Mean single sequence MFE	-41.82
Consensus MFE	-34.04
Energy contribution	-34.84
Covariance contribution	0.80
Combinations/Pair	1.00
Mean z-score	-2.18
Structure conservation index	0.81
SVM decision value	1.56
SVM RNA-class probability	0.963959
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 6889672 113 - 22224390
----CGGACCACUUUGCUUUGUCCGCCACUCG---AGGCUCAAGUGCCGCGUUGGAGUCAGACAAACACUUGCGGCUGUCAAACGGCAGCAAAGUCCCUUGGCUUCAUCCGCACCUCGUA
----(((((...........))))).....((---((((......)))(((.(((((((((......((((...((((((....)))))).))))...)))))))))..)))...))).. ( -36.60)
>DroSec_CAF1 14100 113 - 1
----CGGACCACUUUGCUUUGUCCGCCACUCG---AGGCUCAAGUGCCGCGUUGGAGUCAGCCAAACACUUGCGGCUGUCAAACGGCAGCAAAGUCCCUUGGCUUCCUCCGCACCUCGAC
----(((((...........)))))....(((---((((......)))(((..(((...((((((..((((...((((((....)))))).))))...)))))))))..)))...)))). ( -42.00)
>DroSim_CAF1 14803 113 - 1
----CGGACCACUUUGCUUUGUCCGCCACUCG---AGGCUCAAGUGCCGCGUUGGAGUCAGCCAAACACUUGCGGCUGUCAAACGGCAGCAAAGUCCCUUGGCUUCCUCCGCACCUCGAC
----(((((...........)))))....(((---((((......)))(((..(((...((((((..((((...((((((....)))))).))))...)))))))))..)))...)))). ( -42.00)
>DroEre_CAF1 13407 116 - 1
----CGUACCACUUUGCUUUGUCCGCCACUCGACGAGGCUCAAGUGCCGCGUUGGAGUCAGCCAAACACUUGCGGCUGUCAAACGGCAGCAAAGUCCCUUGGCUUCCUCCGCACCUCGUC
----(((..(((((.((((((((........))))))))..)))))..)))..((((..((((((..((((...((((((....)))))).))))...))))))..)))).......... ( -45.30)
>DroYak_CAF1 16379 117 - 1
GCCACGGACCACUUUGCUUUGUCCGCCACUCG---AGGCUCAAGUGCCGCGUUGGAGUCAGCCAAACACUUGCGGCUGUCAAACGGCAGCAAAGUCCCUUGGCUUCCUCGGCACCUCCUU
(((.(((..(((((.((((((.........))---))))..)))))))).....(((..((((((..((((...((((((....)))))).))))...))))))..))))))........ ( -43.20)
>consensus
____CGGACCACUUUGCUUUGUCCGCCACUCG___AGGCUCAAGUGCCGCGUUGGAGUCAGCCAAACACUUGCGGCUGUCAAACGGCAGCAAAGUCCCUUGGCUUCCUCCGCACCUCGUC
.....((((...........))))((..........(((......))).....((((..((((((..((((...((((((....)))))).))))...))))))..))))))........ (-34.04 = -34.84 +   0.80)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:37:54 2006