Locus 174

Sequence ID	3L_DroMel_CAF1
Location	528,058 – 528,188
Length	130
Max. P	0.994344

overview

Window 8

Location	528,058 – 528,159
Length	101
Sequences	5
Columns	108
Reading direction	forward
Mean pairwise identity	85.93
Mean single sequence MFE	-22.69
Consensus MFE	-21.28
Energy contribution	-20.88
Covariance contribution	-0.40
Combinations/Pair	1.10
Mean z-score	-1.95
Structure conservation index	0.94
SVM decision value	1.77
SVM RNA-class probability	0.976233
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 528058 101 + 23771897
-------CAUUCCCCCAACCCACUCGCCCACUUUGGCAGCUGUCAAUUAGAGCUUACAGGGAGAAAAAAUGAAAACCCGAAGCUUCCAUAUGUUAGCUGUCCCUCCCA
-------...........................((((((((.((((..((((((...(((..............))).))))))..)).)).))))))))....... ( -21.84)
>DroSec_CAF1 2289 102 + 1
C-CUUCCCAUCUU-CCAA----CCCGCCCACUUUGGCAGCUGUCAAUUAGAGCUUACGGGGAGAAAAAAUGAAAACCCGAAGCUUCCAUAUGUUAGCUGUCCCUCCCA
.-...........-....----............((((((((.((((..((((((.((((...............))))))))))..)).)).))))))))....... ( -25.26)
>DroSim_CAF1 3099 103 + 1
A-CUUCUCAUCAUCCCAA----CCCGCCCACUUUGGCAGCUGUCAAUUAGAGCUUACGGGGAAAGAAAAUGAAAACCCGAAGCUUCCAUAUGUUAGCUGUCCCUCCCA
.-................----............((((((((.((((..((((((.((((...............))))))))))..)).)).))))))))....... ( -25.26)
>DroEre_CAF1 2309 100 + 1
---CUCCCUCCAC-CCCA----CUCGCCCACUUUGGCAGCUGUCAAUUAAAGCUUACAGGGCGAAAAAAUGAAAACCCCGAGCUUCCAUAUGCUAGCUGUCCCUCCCA
---..........-....----............((((((((.((((..((((((...(((..............))).))))))..)).)).))))))))....... ( -19.64)
>DroYak_CAF1 2396 102 + 1
UCCCUCCCUCCAC-CCCA----C-CGCCCACUUUGGCAGCUGUCAAUUAAAGCUUACAGGGAGAAAAAAUGAAAACCCGAAGCUUCCAUAUGUUAGCUGUCCCGCCCA
.............-....----.-..........((((((((.((((..((((((...(((..............))).))))))..)).)).))))))))....... ( -21.44)
>consensus
__CCUCCCAUCAC_CCAA____CCCGCCCACUUUGGCAGCUGUCAAUUAGAGCUUACAGGGAGAAAAAAUGAAAACCCGAAGCUUCCAUAUGUUAGCUGUCCCUCCCA
..................................((((((((.((((..((((((...(((..............))).))))))..)).)).))))))))....... (-21.28 = -20.88 +  -0.40)

alignment

secondary structure

dotplot

Window 9

Location	528,079 – 528,188
Length	109
Sequences	5
Columns	112
Reading direction	forward
Mean pairwise identity	94.03
Mean single sequence MFE	-31.68
Consensus MFE	-28.70
Energy contribution	-28.30
Covariance contribution	-0.40
Combinations/Pair	1.07
Mean z-score	-1.87
Structure conservation index	0.91
SVM decision value	2.47
SVM RNA-class probability	0.994344
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 528079 109 + 23771897
CACUUUGGCAGCUGUCAAUUAGAGCUUACAGGGAGAAAAAAUGAAAACCCGAAGCUUCCAUAUGUUAGCUGUCCCUCCCACAGGUC--UCCGCC-CCCAACAGCUGUUGGAA
...((..((((((((......((((((...(((((......((......)).((((..(....)..))))....)))))..))).)--))....-....))))))))..)). ( -30.64)
>DroSec_CAF1 2311 108 + 1
CACUUUGGCAGCUGUCAAUUAGAGCUUACGGGGAGAAAAAAUGAAAACCCGAAGCUUCCAUAUGUUAGCUGUCCCUCCCACAGGUC--UCCGCC--CCAACAGCUGUUGGAA
......((((((((.((((..((((((.((((...............))))))))))..)).)).)))))))).........(((.--...)))--(((((....))))).. ( -32.66)
>DroSim_CAF1 3122 109 + 1
CACUUUGGCAGCUGUCAAUUAGAGCUUACGGGGAAAGAAAAUGAAAACCCGAAGCUUCCAUAUGUUAGCUGUCCCUCCCACAGGUC--UCCGCC-CCCAACAGCUGUUGGAA
......((((((((.((((..((((((.((((...............))))))))))..)).)).)))))))).........(((.--...)))-.(((((....))))).. ( -32.66)
>DroEre_CAF1 2329 110 + 1
CACUUUGGCAGCUGUCAAUUAAAGCUUACAGGGCGAAAAAAUGAAAACCCCGAGCUUCCAUAUGCUAGCUGUCCCUCCCACAGGUC--UCCGCCCCCCAACAGCUGUUGGAA
...((..((((((((........(....).(((((.................(((........)))..((((.......))))...--..)))))....))))))))..)). ( -28.60)
>DroYak_CAF1 2418 112 + 1
CACUUUGGCAGCUGUCAAUUAAAGCUUACAGGGAGAAAAAAUGAAAACCCGAAGCUUCCAUAUGUUAGCUGUCCCGCCCACAGGGCCCCCCGCCCCCCAACAGCUGUUGGAA
......((((((((.((((..((((((...(((..............))).))))))..)).)).)))))))).........((((.....)))).(((((....))))).. ( -33.84)
>consensus
CACUUUGGCAGCUGUCAAUUAGAGCUUACAGGGAGAAAAAAUGAAAACCCGAAGCUUCCAUAUGUUAGCUGUCCCUCCCACAGGUC__UCCGCC_CCCAACAGCUGUUGGAA
......((((((((.((((..((((((...(((..............))).))))))..)).)).)))))))).........((.....)).....(((((....))))).. (-28.70 = -28.30 +  -0.40)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:34:30 2006