Locus 4037

Sequence ID	X_DroMel_CAF1
Location	10,672,384 – 10,672,519
Length	135
Max. P	0.914040

overview

Window 6

Location	10,672,384 – 10,672,493
Length	109
Sequences	3
Columns	118
Reading direction	forward
Mean pairwise identity	75.22
Mean single sequence MFE	-38.63
Consensus MFE	-21.24
Energy contribution	-23.47
Covariance contribution	2.23
Combinations/Pair	1.12
Mean z-score	-2.06
Structure conservation index	0.55
SVM decision value	0.58
SVM RNA-class probability	0.788842
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 10672384 109 + 22224390
GAUUGCAUUUCA-AGGGGCAGCGAGAAGUUCGGUCGCGUGGCAA------CGGCAACCCCUGCAGCCAA--CUGCAACUUCCACGUUGCAUCGCUGCAACUCGGCCCUGUUUGCAGCC
..(((((.....-.(((((..((((......(((.((.((....------)))).)))..((((((...--.((((((......))))))..)))))).)))))))))...))))).. ( -42.60)
>DroEre_CAF1 2709 112 + 1
GAUUGCAUUUCAAAGGGGCAGCGGGAUGUUCGGUCGCGUGGCAAUGGCAAUGGCAA-CCCUCCAGCCAU----GCAACUUCCACGUUGCAUCGUUGCAUCUCUGCCUUGU-UGCAGCC
..(((((.......(((((((..((((((.(((((((((((.....(((.((((..-.......)))))----)).....))))).)).))))..)))))))))))))..-))))).. ( -41.70)
>DroYak_CAF1 3733 90 + 1
GAUUGCAUUUCA--------------------GUCGCGUGGCAA------UGGCAA-CCCUCCAGCCAUGCAUGCAACUGCCACGUUGCAUCGUUGCAUCUCUGCCUUGC-UGCAGCC
(((((.....))--------------------)))(((((((..------(((...-....))))))))))(((((((......))))))).((((((.(........).-)))))). ( -31.60)
>consensus
GAUUGCAUUUCA_AGGGGCAGCG_GA_GUUCGGUCGCGUGGCAA______UGGCAA_CCCUCCAGCCAU___UGCAACUUCCACGUUGCAUCGUUGCAUCUCUGCCUUGU_UGCAGCC
..(((((...((...((((.((((.........))))(..((.........(((..........)))......(((((......)))))...))..)......))))))..))))).. (-21.24 = -23.47 +   2.23)

alignment

secondary structure

dotplot

Window 7

Location	10,672,423 – 10,672,519
Length	96
Sequences	3
Columns	117
Reading direction	forward
Mean pairwise identity	75.30
Mean single sequence MFE	-27.33
Consensus MFE	-18.25
Energy contribution	-18.03
Covariance contribution	-0.22
Combinations/Pair	1.06
Mean z-score	-1.70
Structure conservation index	0.67
SVM decision value	1.09
SVM RNA-class probability	0.914040
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 10672423 96 + 22224390
GCAA------CGGCAACCCCUGCAGCCAA--CUGCAACUUCCACGUUGCAUCGCUGCAACUCGGCCCUGUUUGCAGCCUCCUCUUG--UCUUUCCCAUCCGUGUGC-----------
((((------(((.......((((((...--.((((((......))))))..))))))....(((..((....)))))........--..........)))).)))----------- ( -26.50)
>DroEre_CAF1 2749 98 + 1
GCAAUGGCAAUGGCAA-CCCUCCAGCCAU----GCAACUUCCACGUUGCAUCGUUGCAUCUCUGCCUUGU-UGCAGCCUCCUCUUG--UCCUCCGCGCCCAUGUGC-----------
(((...((((.((((.-.....((((.((----(((((......))))))).))))......))))))))-)))............--......((((....))))----------- ( -26.90)
>DroYak_CAF1 3753 109 + 1
GCAA------UGGCAA-CCCUCCAGCCAUGCAUGCAACUGCCACGUUGCAUCGUUGCAUCUCUGCCUUGC-UGCAGCCUCCUCUUGUGUCUUCCCCACCCGUGUGCUCAUGUGCCUC
(((.------((((..-.......)))))))..(((...(((((((((((.((..(((....)))..)).-))))))........(((.......)))..))).)).....)))... ( -28.60)
>consensus
GCAA______UGGCAA_CCCUCCAGCCAU___UGCAACUUCCACGUUGCAUCGUUGCAUCUCUGCCUUGU_UGCAGCCUCCUCUUG__UCUUCCCCACCCGUGUGC___________
(((........(((..........)))......(((((......)))))...((((((...(......)..))))))..........................)))........... (-18.25 = -18.03 +  -0.22)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:14:50 2006