Locus 4318

Sequence ID	3L_DroMel_CAF1
Location	12,696,407 – 12,696,534
Length	127
Max. P	0.980036

overview

Window 9

Location	12,696,407 – 12,696,500
Length	93
Sequences	6
Columns	98
Reading direction	forward
Mean pairwise identity	76.73
Mean single sequence MFE	-29.65
Consensus MFE	-18.97
Energy contribution	-19.58
Covariance contribution	0.61
Combinations/Pair	1.18
Mean z-score	-1.67
Structure conservation index	0.64
SVM decision value	0.88
SVM RNA-class probability	0.874148
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 12696407 93 + 23771897
ACAGGCUGAAGGCUCAUUAAGGCGCUCGACGGUGGCGUGGG----CGCGGGGCGU-UUACCGCGAUUCGGUUGCAAUUUCCAUAUGGAAAUUGAAUUU
...(((((((.((((((...(.((((....)))).))))))----)((((.....-...))))..))))))).((((((((....))))))))..... ( -34.40)
>DroSec_CAF1 60127 95 + 1
ACAGGCUGAAGGCUCAUUAAGGCGUUCGAUGGUGGGGUGGGG---GGCGGGGCCUGUUACCGCGAUUCGGUUGCAAUUUCCAUAUGGAAAUUGAAUUU
...(((((((.(((......))).)))((...((.(((((.(---(((...)))).))))).))..)))))).((((((((....))))))))..... ( -33.00)
>DroSim_CAF1 58857 95 + 1
ACAGGCUGAAGGCUCAUUAAGGCGUUCGAUGGUGGGGUGGGG---GGCGGGGCCUGUUACCGCGAUUCGGUUGCAAUUUCCAUAUGGAAAUUGAAUUU
...(((((((.(((......))).)))((...((.(((((.(---(((...)))).))))).))..)))))).((((((((....))))))))..... ( -33.00)
>DroEre_CAF1 62435 80 + 1
ACAGGCUGAAGGCUCAUUAGGGCGAUCG------------------GCGGAGGCGGGAACCGCGAUUCGGUUGCAAUUUCCAUAUGGAAAUUGAAUUU
....(((((..((((....))))..)))------------------))(((.((((...))))..))).....((((((((....))))))))..... ( -27.80)
>DroYak_CAF1 62573 98 + 1
ACAGGCUGAAGGCUCAUUAAGGCGAUCGGUGGCGGAGGAGGAGGCGGCGGAGGCGGGAACCGCGAUUCGGUUGCAAUUUCCAUAUGGAAAUUGAAUUU
...(((((((.(((......)))..((.((.((..........)).)).)).((((...))))..))))))).((((((((....))))))))..... ( -28.50)
>DroPer_CAF1 55689 77 + 1
AU-GGCA-GAGUCUCAUUAAAGUGUU-GGCGCAC-------A---GGCGG--------AUCCAGGCUCGACUGCAAUUUCCAUAUGGAAAUUGAAUUU
..-((..-((((((.......((((.-...))))-------.---((...--------..))))))))..)).((((((((....))))))))..... ( -21.20)
>consensus
ACAGGCUGAAGGCUCAUUAAGGCGUUCGAUGGUGG_GUGGG____GGCGGGGCCUGUUACCGCGAUUCGGUUGCAAUUUCCAUAUGGAAAUUGAAUUU
...(((((((.(((......))).......................((((.........))))..))))))).((((((((....))))))))..... (-18.97 = -19.58 +   0.61)

alignment

secondary structure

dotplot

Window 0

Location	12,696,427 – 12,696,534
Length	107
Sequences	6
Columns	114
Reading direction	reverse
Mean pairwise identity	76.90
Mean single sequence MFE	-31.25
Consensus MFE	-18.36
Energy contribution	-18.70
Covariance contribution	0.34
Combinations/Pair	1.33
Mean z-score	-2.48
Structure conservation index	0.59
SVM decision value	1.85
SVM RNA-class probability	0.980036
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 12696427 107 - 23771897
GCAUCAAUUGG--GAAAACCACAUCAAGGCCGGUGGAAAUUCAAUUUCCAUAUGGAAAUUGCAACCGAAUCGCGGUAA-ACGCCCCGCG----CCCACGCCACCGUCGAGCGCC
((.((...(((--.....)))......(((.(((((.....((((((((....)))))))).........(((((...-.....)))))----......))))))))))))... ( -33.40)
>DroSec_CAF1 60147 108 - 1
GCAUCA-UUGG--GAAAACCACAUCAAGGCCGAUGGAAAUUCAAUUUCCAUAUGGAAAUUGCAACCGAAUCGCGGUAACAGGCCCCGCC---CCCCACCCCACCAUCGAACGCC
((....-.(((--.....)))......(..((((((.....((((((((....))))))))..((((.....))))....(((...)))---..........))))))..))). ( -29.00)
>DroSim_CAF1 58877 108 - 1
GCAUCA-UUGG--GAAAACCACAUCAAGGCCGAUGGAAAUUCAAUUUCCAUAUGGAAAUUGCAACCGAAUCGCGGUAACAGGCCCCGCC---CCCCACCCCACCAUCGAACGCC
((....-.(((--.....)))......(..((((((.....((((((((....))))))))..((((.....))))....(((...)))---..........))))))..))). ( -29.00)
>DroEre_CAF1 62455 93 - 1
ACAUCA-UUGG--GAAAACCACAUCAAGGCCGGUGGAAAUUCAAUUUCCAUAUGGAAAUUGCAACCGAAUCGCGGUUCCCGCCUCCGC------------------CGAUCGCC
......-.(((--.....)))......((((((((((....((((((((....))))))))..........((((...)))).)))))------------------))...))) ( -30.00)
>DroYak_CAF1 62593 111 - 1
ACAUCA-UUGG--GCAAACCACAUCAAGGCCGGUGGAAAUUCAAUUUCCAUAUGGAAAUUGCAACCGAAUCGCGGUUCCCGCCUCCGCCGCCUCCUCCUCCGCCACCGAUCGCC
.....(-((((--.............((((.((((((....((((((((....))))))))..........((((...)))).))))))))))............))))).... ( -32.31)
>DroPer_CAF1 55707 94 - 1
GGUGCU-GUGGCAGAAAACCGCAUCAAGGCCAGCGAAAAUUCAAUUUCCAUAUGGAAAUUGCAGUCGAGCCUGGAU--------CCGCC---U-------GUGCGCC-AACACU
(((((.-..(((.(.....)(.(((.((((...(((.....((((((((....))))))))...))).)))).)))--------.))))---.-------..)))))-...... ( -33.80)
>consensus
GCAUCA_UUGG__GAAAACCACAUCAAGGCCGGUGGAAAUUCAAUUUCCAUAUGGAAAUUGCAACCGAAUCGCGGUAACAGGCCCCGCC____CCCAC_CCACCAUCGAACGCC
...........................(((((((((.....((((((((....))))))))..((((.....))))..........................))))))...))) (-18.36 = -18.70 +   0.34)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:19:24 2006