Locus 1409

Sequence ID	2R_DroMel_CAF1
Location	5,444,780 – 5,444,873
Length	93
Max. P	0.997352

overview

Window 6

Location	5,444,780 – 5,444,873
Length	93
Sequences	5
Columns	95
Reading direction	forward
Mean pairwise identity	82.01
Mean single sequence MFE	-17.64
Consensus MFE	-16.32
Energy contribution	-16.20
Covariance contribution	-0.12
Combinations/Pair	1.13
Mean z-score	-2.78
Structure conservation index	0.93
SVM decision value	2.84
SVM RNA-class probability	0.997352
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 5444780 93 + 20766785
CGUUGACCAUUUUCCCUUGUUACCAAAUUGUUUUUUUUUUUUAUCUCUUUACUCCUCACACUUUUCCUUUCGAGCUGGU--UUGGGAAAAUGGCA
...((.((((((((((.....((((..(((........................................)))..))))--..)))))))))))) ( -19.00)
>DroSec_CAF1 33232 84 + 1
CGUCGACCAUUUUCCCUUGUUACCAAACUGUUUUU--UUUU-------CAACUCCUCACACUUUUCCUUUCGAGCUGGU--UUGGGAAAAUGGCA
....(.((((((((((.....((((....(((...--....-------.)))..(((..............))).))))--..))))))))))). ( -18.84)
>DroSim_CAF1 33346 84 + 1
CGUCGACCAUUUUCCCUUGUUACCAAACUGUUUUUUUUUUU-------CUACUCCUC--ACUUUUCCUUUCGAGCUGGU--UUGGGAAAAUGGCA
....(.((((((((((.....((((....((..........-------..))..(((--............))).))))--..))))))))))). ( -17.70)
>DroEre_CAF1 33807 80 + 1
CGUCGACCAUUUUCCCUUGUUACCAAACGUUUU---------------UUACUUCUCACACUUUUCCUUUUCAGCUGAUUUUUGGGAAAGUGGCA
....(.((((((((((..(((....)))((...---------------..))...............................))))))))))). ( -15.00)
>DroYak_CAF1 34078 78 + 1
CGUCGACCAUUUUCCCUUGUUACCAAGCAUUUU---------------UUACUUCUCACACUUUUCCUUUUGAUCUGGU--UUGGGGAAAUGGCA
....(.((((((((((.....((((..((....---------------......................))...))))--..))))))))))). ( -17.67)
>consensus
CGUCGACCAUUUUCCCUUGUUACCAAACUGUUUUU__UUUU_______UUACUCCUCACACUUUUCCUUUCGAGCUGGU__UUGGGAAAAUGGCA
....(.((((((((((.....((((..................................................))))....))))))))))). (-16.32 = -16.20 +  -0.12)

alignment

secondary structure

dotplot

Window 7

Location	5,444,780 – 5,444,873
Length	93
Sequences	5
Columns	95
Reading direction	reverse
Mean pairwise identity	82.01
Mean single sequence MFE	-19.49
Consensus MFE	-16.22
Energy contribution	-16.46
Covariance contribution	0.24
Combinations/Pair	1.06
Mean z-score	-2.75
Structure conservation index	0.83
SVM decision value	2.51
SVM RNA-class probability	0.994804
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 5444780 93 - 20766785
UGCCAUUUUCCCAA--ACCAGCUCGAAAGGAAAAGUGUGAGGAGUAAAGAGAUAAAAAAAAAAAACAAUUUGGUAACAAGGGAAAAUGGUCAACG
.(((((((((((..--.((.((((....)....)))....))...........................(((....))))))))))))))..... ( -20.20)
>DroSec_CAF1 33232 84 - 1
UGCCAUUUUCCCAA--ACCAGCUCGAAAGGAAAAGUGUGAGGAGUUG-------AAAA--AAAAACAGUUUGGUAACAAGGGAAAAUGGUCGACG
.(((((((((((..--..((((((.................))))))-------....--.........(((....))))))))))))))..... ( -23.73)
>DroSim_CAF1 33346 84 - 1
UGCCAUUUUCCCAA--ACCAGCUCGAAAGGAAAAGU--GAGGAGUAG-------AAAAAAAAAAACAGUUUGGUAACAAGGGAAAAUGGUCGACG
.(((((((((((..--.((.((((....)....)))--..)).....-------...............(((....))))))))))))))..... ( -21.30)
>DroEre_CAF1 33807 80 - 1
UGCCACUUUCCCAAAAAUCAGCUGAAAAGGAAAAGUGUGAGAAGUAA---------------AAAACGUUUGGUAACAAGGGAAAAUGGUCGACG
.((((.((((((.....((((((..........))).))).......---------------.....(((....)))..)))))).))))..... ( -15.80)
>DroYak_CAF1 34078 78 - 1
UGCCAUUUCCCCAA--ACCAGAUCAAAAGGAAAAGUGUGAGAAGUAA---------------AAAAUGCUUGGUAACAAGGGAAAAUGGUCGACG
.(((((((.(((..--.((.........)).....(((...(((((.---------------....)))))....))).))).)))))))..... ( -16.40)
>consensus
UGCCAUUUUCCCAA__ACCAGCUCGAAAGGAAAAGUGUGAGGAGUAA_______AAAA__AAAAACAGUUUGGUAACAAGGGAAAAUGGUCGACG
.(((((((((((.....((.........)).......................................(((....))))))))))))))..... (-16.22 = -16.46 +   0.24)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:04:11 2006