Locus 7331

Sequence ID	X_DroMel_CAF1
Location	18,290,748 – 18,290,851
Length	103
Max. P	0.992854

overview

Window 4

Location	18,290,748 – 18,290,851
Length	103
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	71.04
Mean single sequence MFE	-28.48
Consensus MFE	-6.70
Energy contribution	-7.02
Covariance contribution	0.32
Combinations/Pair	1.11
Mean z-score	-1.67
Structure conservation index	0.24
SVM decision value	0.02
SVM RNA-class probability	0.545894
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 18290748 103 + 22224390
AAGGGAAGCCGCUGCCAG-----GAGGUGGCAAGGUGGAAUCUGCCACCAGAA-----------ACGAGGGGCAU-GCGUAGAAAUAUGGAAAAUUUCAAUUUGCUUGGUAUGGAGAAAA
........(((.((((((-----(.(((((((.(((...))))))))))....-----------..((((....(-.((((....)))).)...))))......))))))))))...... ( -30.30)
>DroPse_CAF1 1229 98 + 1
AAGGGAAGCCGAAGCCGCGUCUGGCAGUGCCACAGGGACAGUUGC----AGA--------------GUGGGGCACAGCGCAGAAAUAUGGAAAAUUUCAAUUUGUUUUGU----GGAAAA
..((....))...(((.((((((.(((((((....)).)).))))----)))--------------.)).)))....(((((((...((((....)))).....))))))----)..... ( -25.40)
>DroSec_CAF1 3731 103 + 1
AAGGGAAGCCGCUGCCAG-----GAGGUGGCAAGGUGGAACCUGCCACCAGAA-----------UCGAGGGGCAU-GCGUAGAAAUAUGGAAAAUUUCAAUUUGCUUGGUAUGGAGAAAA
........(((.((((((-----(.(((((((.((.....))))))))).(((-----------(.((((....(-.((((....)))).)...)))).)))).))))))))))...... ( -33.90)
>DroYak_CAF1 4016 103 + 1
AAGGGAAGCCGCUGCCAG----------------GUGGAACUUGCCACCAGACGACGCACGACGAGGAGGGGCAU-GCGUAGAAAUAUGGAAAAUUUCAAAUUGCUUGGUGUGGUGAAAA
.......(((((.(((((----------------(..(....((((.((...(..((.....)).)..))))))(-.((((....)))).)..........)..)))))))))))..... ( -28.90)
>DroPer_CAF1 1281 98 + 1
AAGGGAAGCCGAAGCCGCGUCUGGCAGUGCCACAGGGACAGUUGC----AGA--------------GUUGGGCACAGCGCAGAAAUAUGGAAAAUUUCAAUUUGUUUUGU----GGAAAA
..((....))...((((....))))....(((((((.((((.(((----...--------------((((....)))))))(((((.......)))))...)))))))))----)).... ( -23.90)
>consensus
AAGGGAAGCCGCUGCCAG_____GAAGUGCCAAAGUGGAACUUGCCACCAGA______________GAGGGGCAU_GCGUAGAAAUAUGGAAAAUUUCAAUUUGCUUGGU_UGGAGAAAA
..((....))...((((.........................((((........................))))..(((..(((((.......)))))....))).)))).......... ( -6.70 =  -7.02 +   0.32)

alignment

secondary structure

dotplot

Window 5

Location	18,290,748 – 18,290,851
Length	103
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	71.04
Mean single sequence MFE	-24.27
Consensus MFE	-4.91
Energy contribution	-6.11
Covariance contribution	1.20
Combinations/Pair	1.00
Mean z-score	-2.56
Structure conservation index	0.20
SVM decision value	2.36
SVM RNA-class probability	0.992854
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 18290748 103 - 22224390
UUUUCUCCAUACCAAGCAAAUUGAAAUUUUCCAUAUUUCUACGC-AUGCCCCUCGU-----------UUCUGGUGGCAGAUUCCACCUUGCCACCUC-----CUGGCAGCGGCUUCCCUU
.............((((.....(((((.......)))))..(((-.((((......-----------....((((((((........))))))))..-----..)))))))))))..... ( -26.24)
>DroPse_CAF1 1229 98 - 1
UUUUCC----ACAAAACAAAUUGAAAUUUUCCAUAUUUCUGCGCUGUGCCCCAC--------------UCU----GCAACUGUCCCUGUGGCACUGCCAGACGCGGCUUCGGCUUCCCUU
......----...........................((((.((.(((((.((.--------------...----((....))...)).))))).)))))).(.(((....))).).... ( -21.20)
>DroSec_CAF1 3731 103 - 1
UUUUCUCCAUACCAAGCAAAUUGAAAUUUUCCAUAUUUCUACGC-AUGCCCCUCGA-----------UUCUGGUGGCAGGUUCCACCUUGCCACCUC-----CUGGCAGCGGCUUCCCUU
.............((((.....(((((.......)))))..(((-.((((....((-----------....(((((((((......)))))))))))-----..)))))))))))..... ( -29.50)
>DroYak_CAF1 4016 103 - 1
UUUUCACCACACCAAGCAAUUUGAAAUUUUCCAUAUUUCUACGC-AUGCCCCUCCUCGUCGUGCGUCGUCUGGUGGCAAGUUCCAC----------------CUGGCAGCGGCUUCCCUU
......((.(((((..(.....(((((.......))))).((((-((((........).))))))).)..)))))....(((((..----------------..)).)))))........ ( -23.80)
>DroPer_CAF1 1281 98 - 1
UUUUCC----ACAAAACAAAUUGAAAUUUUCCAUAUUUCUGCGCUGUGCCCAAC--------------UCU----GCAACUGUCCCUGUGGCACUGCCAGACGCGGCUUCGGCUUCCCUU
......----...........................((((.((.(((((((..--------------...----((....))...)).))))).)))))).(.(((....))).).... ( -20.60)
>consensus
UUUUCCCCA_ACCAAGCAAAUUGAAAUUUUCCAUAUUUCUACGC_AUGCCCCUC______________UCUGGUGGCAACUUCCACCGUGCCACCGC_____CUGGCAGCGGCUUCCCUU
......................(((((.......))))).......((((((...................)).))))..........................(((....)))...... ( -4.91 =  -6.11 +   1.20)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:36:16 2006