Locus 476

Sequence ID	X_DroMel_CAF1
Location	1,397,551 – 1,397,673
Length	122
Max. P	0.993790

overview

Window 4

Location	1,397,551 – 1,397,655
Length	104
Sequences	4
Columns	117
Reading direction	reverse
Mean pairwise identity	68.84
Mean single sequence MFE	-27.93
Consensus MFE	-14.58
Energy contribution	-15.83
Covariance contribution	1.25
Combinations/Pair	1.00
Mean z-score	-1.99
Structure conservation index	0.52
SVM decision value	1.41
SVM RNA-class probability	0.951161
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 1397551 104 - 22224390
UUGCAUUUG--CCACUUGAC-GCUUUUGUGUGUAAUUGAUUUUCAACGCUU--AUUGUCAAGUGGCAAGCAGAACAGCAAGCGCAACAAAGCGGUCCCA-------ACCCAG-CCAG
((((..(((--(((((((((-(.....((((..............))))..--..)))))))))))))))))....((..((........))(((....-------)))..)-)... ( -30.74)
>DroGri_CAF1 41657 89 - 1
UUGCGUUUGAAGCACUCGACGCCUUUUGUGUGUA-AUUAUU--CAACGCUUUGACUGUCAAGUGG---------UUGGAACAACAUUCAU----------------AACAACAACAA
....((((.((.((((.((((......((((...-......--..))))......)))).)))).---------)).)))).........----------------........... ( -18.20)
>DroEre_CAF1 32230 92 - 1
UUGCAUUUG--CCACUUGAC-GCUUUUGUGUGUAAUUGAUUUCCAACGCUU--AUUGUCAAGUGGCAAGCAAAACAGCAAGCGCAACAAAGCGGCCC--------------------
((((..(((--(((((((((-(.....((((..............))))..--..))))))))))))))))).........(((......)))....-------------------- ( -29.64)
>DroYak_CAF1 11483 111 - 1
UUGCAUUUG--CCACUUGAC-GCUUUUGUGUGUAAUUGAUUUCCAACGCUU--AUUGUCAAGUGGCAAGCAAAACAGCAAGCGCAACAAAGCGGCCCCCCAGUUUCUGCCAU-CCAG
((((..(((--(((((((((-(.....((((..............))))..--..)))))))))))))))))..(((.((((((......))((....)).)))))))....-.... ( -33.14)
>consensus
UUGCAUUUG__CCACUUGAC_GCUUUUGUGUGUAAUUGAUUUCCAACGCUU__AUUGUCAAGUGGCAAGCAAAACAGCAAGCGCAACAAAGCGGCCC_________A_CCA__CCAG
.(((.......(((((((((.......((((..............)))).......)))))))))...((......))....)))................................ (-14.58 = -15.83 +   1.25)

alignment

secondary structure

dotplot

Window 5

Location	1,397,583 – 1,397,673
Length	90
Sequences	3
Columns	90
Reading direction	forward
Mean pairwise identity	98.52
Mean single sequence MFE	-24.84
Consensus MFE	-24.69
Energy contribution	-25.03
Covariance contribution	0.33
Combinations/Pair	1.00
Mean z-score	-3.36
Structure conservation index	0.99
SVM decision value	2.31
SVM RNA-class probability	0.992110
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 1397583 90 + 22224390
CUGUUCUGCUUGCCACUUGACAAUAAGCGUUGAAAAUCAAUUACACACAAAAGCGUCAAGUGGCAAAUGCAAAUGUUUGAAAAGCAAAGC
..(((.(((((((((((((((.......((((.....))))....(......).))))))))))((((......))))...))))).))) ( -22.40)
>DroEre_CAF1 32250 90 + 1
CUGUUUUGCUUGCCACUUGACAAUAAGCGUUGGAAAUCAAUUACACACAAAAGCGUCAAGUGGCAAAUGCAAAUGUUUGAAAAGCAAAGC
..(((((((((((((((((((.....((.(((...............)))..))))))))))))((((......))))...))))))))) ( -26.06)
>DroYak_CAF1 11522 90 + 1
CUGUUUUGCUUGCCACUUGACAAUAAGCGUUGGAAAUCAAUUACACACAAAAGCGUCAAGUGGCAAAUGCAAAUGUUUGAAAAGCAAAGC
..(((((((((((((((((((.....((.(((...............)))..))))))))))))((((......))))...))))))))) ( -26.06)
>consensus
CUGUUUUGCUUGCCACUUGACAAUAAGCGUUGGAAAUCAAUUACACACAAAAGCGUCAAGUGGCAAAUGCAAAUGUUUGAAAAGCAAAGC
..(((((((((((((((((((.....((.(((...............)))..))))))))))))((((......))))...))))))))) (-24.69 = -25.03 +   0.33)

alignment

secondary structure

dotplot

Window 6

Location	1,397,583 – 1,397,673
Length	90
Sequences	3
Columns	90
Reading direction	reverse
Mean pairwise identity	98.52
Mean single sequence MFE	-27.47
Consensus MFE	-27.69
Energy contribution	-27.47
Covariance contribution	-0.22
Combinations/Pair	1.05
Mean z-score	-3.71
Structure conservation index	1.01
SVM decision value	2.43
SVM RNA-class probability	0.993790
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 1397583 90 - 22224390
GCUUUGCUUUUCAAACAUUUGCAUUUGCCACUUGACGCUUUUGUGUGUAAUUGAUUUUCAACGCUUAUUGUCAAGUGGCAAGCAGAACAG
.................(((((..(((((((((((((.....((((..............))))....)))))))))))))))))).... ( -27.54)
>DroEre_CAF1 32250 90 - 1
GCUUUGCUUUUCAAACAUUUGCAUUUGCCACUUGACGCUUUUGUGUGUAAUUGAUUUCCAACGCUUAUUGUCAAGUGGCAAGCAAAACAG
.................(((((..(((((((((((((.....((((..............))))....)))))))))))))))))).... ( -27.44)
>DroYak_CAF1 11522 90 - 1
GCUUUGCUUUUCAAACAUUUGCAUUUGCCACUUGACGCUUUUGUGUGUAAUUGAUUUCCAACGCUUAUUGUCAAGUGGCAAGCAAAACAG
.................(((((..(((((((((((((.....((((..............))))....)))))))))))))))))).... ( -27.44)
>consensus
GCUUUGCUUUUCAAACAUUUGCAUUUGCCACUUGACGCUUUUGUGUGUAAUUGAUUUCCAACGCUUAUUGUCAAGUGGCAAGCAAAACAG
.................(((((..(((((((((((((.....((((..............))))....)))))))))))))))))).... (-27.69 = -27.47 +  -0.22)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:45:33 2006