Locus 8173

Sequence ID	3R_DroMel_CAF1
Location	21,979,277 – 21,979,422
Length	145
Max. P	0.958577

overview

Window 2

Location	21,979,277 – 21,979,395
Length	118
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	79.89
Mean single sequence MFE	-26.53
Consensus MFE	-17.36
Energy contribution	-17.55
Covariance contribution	0.19
Combinations/Pair	1.23
Mean z-score	-1.28
Structure conservation index	0.65
SVM decision value	-0.04
SVM RNA-class probability	0.514358
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 21979277 118 - 27905053
AUUUUAUGCUAAACAAAUACAAUUGGUUCAAG--UCGAGCUUUGUAGCAAUUUCAUGCCAUUUUGACAGCCGCCCGGCAGAAUGCAAAUCCAAUAGUUGCAAGCUCUCAGGCAAGCAAAG
......((((.......(((((..(((((...--..)))))))))).........((((.........(((....)))((..(((((.........)))))..))....))))))))... ( -26.30)
>DroSec_CAF1 18822 118 - 1
AUUUCAUGCUAAACAAAUACAAUUGGUUCAAC--UCGAGCUUUGUAGCAAUUUCAUGCCAUUUUGACAGCCGCCCGGCAAAAUGCAAAUCCAAUAGUUGCAAGCUCCCAGGCAAGCAAAG
......((((.......(((((..(((((...--..)))))))))).........((((.........(((....)))....(((((.........)))))........))))))))... ( -25.60)
>DroSim_CAF1 22956 118 - 1
AUUUCAUGCUAAACAAAUACAAUUGAUUCAAG--UCGAGCUUUGUAGCAAUUUCAUGCCAUUUUGACAGCCGCCCGGCAGAAUGCAAAUCCAAUAGUUGCAAGCUCCCAGGCAAGCAAAG
......((((...((((((((((((((....)--))))...)))))(((......)))...))))......(((.((.((..(((((.........)))))..)).)).))).))))... ( -25.40)
>DroEre_CAF1 20428 118 - 1
AUUUCAUGCUAAACAAAUACAAUUGGUUUAAG--CCGAGCCUUGUAGCAAUUUCAUGCCAUUUUGACAGCACCCUGCCAGAAUGCAAAUCCAAUAGUUGCAAGCUCUCAGGCAAGCAAAU
......((((...(((......)))......(--(((((.((((((((.(((...(((.((((((.(((....))).))))))))).....))).))))))))..))).))).))))... ( -29.90)
>DroYak_CAF1 19709 118 - 1
AUUUCAUGCUAAGCAAAUACAAUUGGUUUAAG--CCGAGCCCUGCAGCAAUUUCAUGCCAUUUUGACAGUCGCCUGGCAAAAUGCAAAUCCAAUAGUUGCAAGCUUACAGGCAAGCAAAU
......((((((.(((......))).))...(--((((((..((((((.(((...(((.((((((.(((....))).))))))))).....))).)))))).))))...))).))))... ( -28.70)
>DroAna_CAF1 26838 101 - 1
UUUGCACGCUAAGCACU---GAGUGGAGUAAUUUCCGAAGCAUCCAGCCAAGUCAUGGUAUUU----------------AAAUGAAAAUCCAAUAGUUGCAGGCAGUGGGGCGAGCCAAA
...((.((((...((((---(..(((((....)))))..(((....((((.....))))....----------------...((......)).....)))...))))).)))).)).... ( -23.30)
>consensus
AUUUCAUGCUAAACAAAUACAAUUGGUUCAAG__CCGAGCCUUGUAGCAAUUUCAUGCCAUUUUGACAGCCGCCCGGCAAAAUGCAAAUCCAAUAGUUGCAAGCUCUCAGGCAAGCAAAG
......((((...(((......)))...........(((((.((((((.(((..((..(((((((.(........).)))))))...))..))).)))))))))))...))))....... (-17.36 = -17.55 +   0.19)

alignment

secondary structure

dotplot

Window 3

Location	21,979,317 – 21,979,422
Length	105
Sequences	5
Columns	112
Reading direction	forward
Mean pairwise identity	89.64
Mean single sequence MFE	-31.82
Consensus MFE	-25.62
Energy contribution	-26.98
Covariance contribution	1.36
Combinations/Pair	1.14
Mean z-score	-2.11
Structure conservation index	0.81
SVM decision value	1.49
SVM RNA-class probability	0.958577
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 21979317 105 + 27905053
CUGCCGGGCGGCUGUCAAAAUGGCAUGAAAUUGCUACAAAGCUCGACUUGAACCAAUUGUAUUUGUUUAGCAUAAAAUAUAUUUAUUCGAG-------CUGCACUUAUUGGC
..(((....))).(((((..(((((......)))))...(((((((..((((.....(((((((..........))))))))))).)))))-------)).......))))) ( -24.10)
>DroSec_CAF1 18862 112 + 1
UUGCCGGGCGGCUGUCAAAAUGGCAUGAAAUUGCUACAAAGCUCGAGUUGAACCAAUUGUAUUUGUUUAGCAUGAAAUAUAUUUAUUCGAGCUGACAGCUGCACUUAUUGGC
..((((((((((((((....(((((......)))))...((((((((((((((.((......)))))))))(((((.....))))))))))))))))))))).))....))) ( -40.40)
>DroSim_CAF1 22996 112 + 1
CUGCCGGGCGGCUGUCAAAAUGGCAUGAAAUUGCUACAAAGCUCGACUUGAAUCAAUUGUAUUUGUUUAGCAUGAAAUAUAUUUAUUCGAGCUGACAGCUGCACUUAUUGGC
..((((((((((((((....(((((......)))))...(((((((..(((((.....((((((..........))))))))))).)))))))))))))))).))....))) ( -36.60)
>DroEre_CAF1 20468 112 + 1
CUGGCAGGGUGCUGUCAAAAUGGCAUGAAAUUGCUACAAGGCUCGGCUUAAACCAAUUGUAUUUGUUUAGCAUGAAAUAUAUUUAUUCGAGCUGACAGCUGCACUUAAAGGC
...(((....((((((....(((((......)))))...(((((((((.((((.((......)))))))))(((((.....))))).))))))))))))))).......... ( -29.20)
>DroYak_CAF1 19749 112 + 1
UUGCCAGGCGACUGUCAAAAUGGCAUGAAAUUGCUGCAGGGCUCGGCUUAAACCAAUUGUAUUUGCUUAGCAUGAAAUAAAUUUAUUCGAGCUGACAGCUGCACUCAUAGGC
..((((((((.(((((.....((((......))))....(((((((((.....(((......)))...)))(((((.....))))).))))))))))).))).))....))) ( -28.80)
>consensus
CUGCCGGGCGGCUGUCAAAAUGGCAUGAAAUUGCUACAAAGCUCGACUUGAACCAAUUGUAUUUGUUUAGCAUGAAAUAUAUUUAUUCGAGCUGACAGCUGCACUUAUUGGC
..((((((((((((((....(((((......)))))...(((((((..((((.....(((((((..........))))))))))).)))))))))))))))).))....))) (-25.62 = -26.98 +   1.36)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:04:17 2006