Locus 8668

Sequence ID	3L_DroMel_CAF1
Location	22,497,164 – 22,497,263
Length	99
Max. P	0.998404

overview

Window 5

Location	22,497,164 – 22,497,263
Length	99
Sequences	4
Columns	101
Reading direction	forward
Mean pairwise identity	89.59
Mean single sequence MFE	-34.23
Consensus MFE	-28.14
Energy contribution	-28.20
Covariance contribution	0.06
Combinations/Pair	1.05
Mean z-score	-3.33
Structure conservation index	0.82
SVM decision value	2.10
SVM RNA-class probability	0.988077
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 22497164 99 + 23771897
CGGGGCAAACAGGAUCU-UGUUAAAGGGGG-GUAGGGCAGGAUCCUGCGGAAAGGAGACAGGAGACAGAUGGGGAAGUAUUUUCAUUGUCUUGUUUGCCAA
...((((((((((((((-((((........-....)))))))))))........(((((.(....).((((..((....))..)))))))))))))))).. ( -37.00)
>DroSec_CAF1 5567 101 + 1
CGGGGCAAACAGGAACUGCGUUGAACGGGGGGUGGGGCAGGAUCCUGCGGAAUGGAGAAAGGAGACAGAUGGGAAAGUAUUUUCAUUGUCUUGUUUGCCAA
...(((((((((((.((.((((...((.(((((........))))).)).)))).))...(....).((((..((....))..)))).))))))))))).. ( -35.90)
>DroSim_CAF1 5589 100 + 1
CGGGGCAAACAGGAACUGUGUUGAACGGGGGGUG-GGCAGGAUCCUGCGGAAUGGAGACCGGAGACAGAUGGGGAAGUAUUUUCAUUGUCUUGUUUGCCAA
...(((((((((((.((((.((...((.(((((.-......))))).))....(....)..)).))))(((..((....))..)))..))))))))))).. ( -34.90)
>DroEre_CAF1 7648 97 + 1
CGGGACAAACAGGAAUUGCGUUG---GGGG-AUGGGGCAGGAUCCUGCGGAAGGGGAACAGGAGACAGAUGGGGAAGUAUUUUCAUUGUCUUGUUUGCCAA
.........(((((.((((.(((---....-.))).))))..))))).....((.((((((((....((((..((....))..)))).)))))))).)).. ( -29.10)
>consensus
CGGGGCAAACAGGAACUGCGUUGAACGGGG_GUGGGGCAGGAUCCUGCGGAAUGGAGACAGGAGACAGAUGGGGAAGUAUUUUCAUUGUCUUGUUUGCCAA
...(((((((((((......................((((....))))............(....).((((..((....))..)))).))))))))))).. (-28.14 = -28.20 +   0.06)

alignment

secondary structure

dotplot

Window 6

Location	22,497,164 – 22,497,263
Length	99
Sequences	4
Columns	101
Reading direction	reverse
Mean pairwise identity	89.59
Mean single sequence MFE	-21.09
Consensus MFE	-20.81
Energy contribution	-20.62
Covariance contribution	-0.19
Combinations/Pair	1.05
Mean z-score	-2.76
Structure conservation index	0.99
SVM decision value	3.09
SVM RNA-class probability	0.998404
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 22497164 99 - 23771897
UUGGCAAACAAGACAAUGAAAAUACUUCCCCAUCUGUCUCCUGUCUCCUUUCCGCAGGAUCCUGCCCUAC-CCCCCUUUAACA-AGAUCCUGUUUGCCCCG
..((((((((((((((((............))).)))))..))).........((((((((.((......-..........))-.)))))))))))))... ( -21.59)
>DroSec_CAF1 5567 101 - 1
UUGGCAAACAAGACAAUGAAAAUACUUUCCCAUCUGUCUCCUUUCUCCAUUCCGCAGGAUCCUGCCCCACCCCCCGUUCAACGCAGUUCCUGUUUGCCCCG
..(((((((.((((((((..((....))..))).)))))................((((..((((.................)))).)))))))))))... ( -21.93)
>DroSim_CAF1 5589 100 - 1
UUGGCAAACAAGACAAUGAAAAUACUUCCCCAUCUGUCUCCGGUCUCCAUUCCGCAGGAUCCUGCC-CACCCCCCGUUCAACACAGUUCCUGUUUGCCCCG
..((((((((((((((((............))).))))).(((..........((((....)))).-......)))..............))))))))... ( -22.23)
>DroEre_CAF1 7648 97 - 1
UUGGCAAACAAGACAAUGAAAAUACUUCCCCAUCUGUCUCCUGUUCCCCUUCCGCAGGAUCCUGCCCCAU-CCCC---CAACGCAAUUCCUGUUUGUCCCG
..((((((((((((((((............))).)))))..............((((....)))).....-....---............))))))))... ( -18.60)
>consensus
UUGGCAAACAAGACAAUGAAAAUACUUCCCCAUCUGUCUCCUGUCUCCAUUCCGCAGGAUCCUGCCCCAC_CCCCGUUCAACACAGUUCCUGUUUGCCCCG
..((((((((((((((((............))).)))))..............((((....)))).........................))))))))... (-20.81 = -20.62 +  -0.19)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:21:50 2006