Locus 5185

Sequence ID	3L_DroMel_CAF1
Location	14,271,927 – 14,272,021
Length	94
Max. P	0.997880

overview

Window 9

Location	14,271,927 – 14,272,021
Length	94
Sequences	6
Columns	105
Reading direction	forward
Mean pairwise identity	73.24
Mean single sequence MFE	-33.72
Consensus MFE	-15.86
Energy contribution	-16.05
Covariance contribution	0.19
Combinations/Pair	1.36
Mean z-score	-2.99
Structure conservation index	0.47
SVM decision value	2.95
SVM RNA-class probability	0.997880
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 14271927 94 + 23771897
AGGA--------CCUUC-AUUUGGGUGGAUGGC--GGUCCUGUUGUCUGGGGGGUGGAAUUCACCCCUUGAGAACAUUGUCACUCAUAUGGGGACAUGUUUUGCA
((((--------((.((-((((....)))))).--))))))(((.((.((((((((.....)))))))))).)))..((((.(((....)))))))......... ( -37.90)
>DroSec_CAF1 101891 93 + 1
AGGA--------CCUUU-UUUGGGGGGGAUGGG--UGUCCUGUUGUCUGGG-GGUGCAAUUCACCCCUUGAGAACAUUGUCACUCAUAUGGGGAUAUGUUUUGCA
....--------((((.-..((((.(((((...--.)))))(((.((.(((-((((.....))))))).)).))).......))))...))))............ ( -31.00)
>DroSim_CAF1 101973 94 + 1
AGGA--------CCUUUUUUUGGGGGGGAUUGG--GGUCCUGUUGUCUGGG-GGUGGAAUUCACCCCUUGAGAACAUUGUCACUCAUAUGGGGACAUGUUUUGCA
((((--------((((..(((.....)))..))--))))))(((.((.(((-((((.....))))))).)).)))..((((.(((....)))))))......... ( -36.50)
>DroEre_CAF1 101665 92 + 1
AGCA--------UCUUUUUUUG-GG-GGAUGGG--GGCUCUGUUAUCUGGG-GGUGAAAUUCACCCCUUGAGAACAUUGUCACUCAUAUGGGGACAUGUUUUGCA
.(((--------(((((.....-))-))))(((--(((..((((.((.(((-((((.....))))))).)).))))..))).)))(((((....)))))...)). ( -34.90)
>DroYak_CAF1 105442 78 + 1
AGGA--------CCUCUUUUUUGGG-AGG-----------------UUGGG-GGUGAGAUUCACCCCCUGAGAACAUUGUCACUCAUAUGGGGACAUGUUUUGCA
..((--------((((((....)))-)))-----------------))(((-((((.....)))))))..(((((((.(((.(((....)))))))))))))... ( -35.90)
>DroAna_CAF1 96908 102 + 1
GGGGUAGUUCUAUUUUUUUUUUUGUUGGAUGGGAGGAUCCUGUU--CGGAA-GGUGGCAGGCAGCCUCGGGGAAAAAUUUCACUCACAGGACUUGAUGUUUUGCA
(((((.(((((((((((........((((((((.....))))))--)))))-)))))..))).)))))((((((....))).))).((((((.....)))))).. ( -26.10)
>consensus
AGGA________CCUUUUUUUGGGG_GGAUGGG__GGUCCUGUUGUCUGGG_GGUGGAAUUCACCCCUUGAGAACAUUGUCACUCAUAUGGGGACAUGUUUUGCA
..........................((((......))))......(.(((.((((.....))))))).)((((((.((((.(((....)))))))))))))... (-15.86 = -16.05 +   0.19)

alignment

secondary structure

dotplot

Window 0

Location	14,271,927 – 14,272,021
Length	94
Sequences	6
Columns	105
Reading direction	reverse
Mean pairwise identity	73.24
Mean single sequence MFE	-22.50
Consensus MFE	-7.15
Energy contribution	-8.32
Covariance contribution	1.17
Combinations/Pair	1.24
Mean z-score	-2.74
Structure conservation index	0.32
SVM decision value	1.69
SVM RNA-class probability	0.972155
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 14271927 94 - 23771897
UGCAAAACAUGUCCCCAUAUGAGUGACAAUGUUCUCAAGGGGUGAAUUCCACCCCCCAGACAACAGGACC--GCCAUCCACCCAAAU-GAAGG--------UCCU
.........((((......((((.(((...))))))).((((((.....))))))...))))..((((((--..(((........))-)..))--------)))) ( -27.70)
>DroSec_CAF1 101891 93 - 1
UGCAAAACAUAUCCCCAUAUGAGUGACAAUGUUCUCAAGGGGUGAAUUGCACC-CCCAGACAACAGGACA--CCCAUCCCCCCCAAA-AAAGG--------UCCU
.......(((((....)))))((.(((..((((.((..((((((.....))))-))..)).))))(((..--....)))........-....)--------)))) ( -21.50)
>DroSim_CAF1 101973 94 - 1
UGCAAAACAUGUCCCCAUAUGAGUGACAAUGUUCUCAAGGGGUGAAUUCCACC-CCCAGACAACAGGACC--CCAAUCCCCCCCAAAAAAAGG--------UCCU
.........(((((.(....).).)))).((((.((..((((((.....))))-))..)).))))(((((--...................))--------))). ( -24.51)
>DroEre_CAF1 101665 92 - 1
UGCAAAACAUGUCCCCAUAUGAGUGACAAUGUUCUCAAGGGGUGAAUUUCACC-CCCAGAUAACAGAGCC--CCCAUCC-CC-CAAAAAAAGA--------UGCU
.(((.....(((((.(....).).)))).((((.((..((((((.....))))-))..)).)))).....--.......-..-..........--------))). ( -21.40)
>DroYak_CAF1 105442 78 - 1
UGCAAAACAUGUCCCCAUAUGAGUGACAAUGUUCUCAGGGGGUGAAUCUCACC-CCCAA-----------------CCU-CCCAAAAAAGAGG--------UCCU
.....(((((((((.(....).).))).)))))....(((((((.....))))-))).(-----------------(((-(........))))--------)... ( -25.70)
>DroAna_CAF1 96908 102 - 1
UGCAAAACAUCAAGUCCUGUGAGUGAAAUUUUUCCCCGAGGCUGCCUGCCACC-UUCCG--AACAGGAUCCUCCCAUCCAACAAAAAAAAAAAUAGAACUACCCC
.............(((((((..(.(((.....((...))(((.....)))...-)))).--.))))))).................................... ( -14.20)
>consensus
UGCAAAACAUGUCCCCAUAUGAGUGACAAUGUUCUCAAGGGGUGAAUUCCACC_CCCAGACAACAGGACC__CCCAUCC_CCCAAAAAAAAGG________UCCU
.......(((((....)))))........((((.((..((((((.....)))).))..)).))))........................................ ( -7.15 =  -8.32 +   1.17)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:44:03 2006