Locus 6251

Sequence ID	3R_DroMel_CAF1
Location	16,306,085 – 16,306,223
Length	138
Max. P	0.989857

overview

Window 7

Location	16,306,085 – 16,306,183
Length	98
Sequences	5
Columns	113
Reading direction	forward
Mean pairwise identity	75.61
Mean single sequence MFE	-23.96
Consensus MFE	-11.50
Energy contribution	-11.90
Covariance contribution	0.40
Combinations/Pair	1.13
Mean z-score	-2.46
Structure conservation index	0.48
SVM decision value	2.18
SVM RNA-class probability	0.989857
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 16306085 98 + 27905053
AACUGUAUCCAU---UUUCAGAAUGAAUUUUCCUGUUC------------AAAAACUAUCCAGUUUUCUUGCAAUUAAGCAAGGAAAAUUGGUCGAACUGCUUUUACCACAAC
............---...(((..(((((......))))------------)........(((((((((((((......)))).))))))))).....)))............. ( -18.50)
>DroSec_CAF1 3721 95 + 1
AGCUGUAUUCAU---UUUCAGUAUGAAUUUUCCUGUGG------------AAAAACUAUCAAGUUUUCUUGCAAUUAAGCAAGGAAAAUUGGUCGAAAGCA---ACCCACAAC
......((((((---.......)))))).....(((((------------.......(((((.(((((((((......))))))))).)))))(....)..---..))))).. ( -22.50)
>DroSim_CAF1 8859 95 + 1
AACUGUAUCCAU---UUUCAGUAUGAAUUUUCCUGUGC------------AAAAACUAUCAAGUUUUCUUGCAAUUAAGCAAGGAAAAUUGGUCGAAAGCC---ACCCACAAC
.((((.......---...))))...(((((((((.(((------------(((((((....)))))..)))))........)))))))))((.(....)))---......... ( -20.30)
>DroEre_CAF1 6873 108 + 1
AACGGUAUCCAUGUCGUUCAGAAUGAAUUUU-CUGUGCAGUGGGUGAUGGGAAAACUAUCAAGUUUUCUUGCAAUUAGGCAAGGAAAAUUGAACGAAAUAA---AU-AACCAC
...(((((((((...((.(((((......))-))).)).))))))(((((.....)))))...(((((((((......)))))))))..............---..-.))).. ( -30.10)
>DroYak_CAF1 15691 109 + 1
UACUGUAUCCAUGGCUUUUGGCAUGAAUUUUCCUGUGCAGUGGCUGAUGGAAAAACAAUUAAGUUUUCUUGCAAUGAGGCAAAGAAAUUUGAACGACAGAA---AU-AAGCAC
..((((.(((((((((....(((((........)))))...)))).))))).......((((((((..((((......))))..))))))))...))))..---..-...... ( -28.40)
>consensus
AACUGUAUCCAU___UUUCAGAAUGAAUUUUCCUGUGC____________AAAAACUAUCAAGUUUUCUUGCAAUUAAGCAAGGAAAAUUGGUCGAAAGAA___ACCCACAAC
.......................................................(.(((((.(((((((((......))))))))).))))).).................. (-11.50 = -11.90 +   0.40)

alignment

secondary structure

dotplot

Window 8

Location	16,306,115 – 16,306,223
Length	108
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	76.42
Mean single sequence MFE	-20.79
Consensus MFE	-11.50
Energy contribution	-11.90
Covariance contribution	0.40
Combinations/Pair	1.13
Mean z-score	-1.70
Structure conservation index	0.55
SVM decision value	0.04
SVM RNA-class probability	0.553544
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 16306115 108 + 27905053
UGUUC------------AAAAACUAUCCAGUUUUCUUGCAAUUAAGCAAGGAAAAUUGGUCGAACUGCUUUUACCACAACUGCUUUUCCUGUACUGAUAUAAAUUCAUUUUCUCUACUUA
...((------------(........(((((((((((((......)))).)))))))))..(((..((.............))..)))......)))....................... ( -16.72)
>DroSec_CAF1 3751 105 + 1
UGUGG------------AAAAACUAUCAAGUUUUCUUGCAAUUAAGCAAGGAAAAUUGGUCGAAAGCA---ACCCACAACUCAUUUUCCUGUACUGAUAUAAAUCCAUUUCCUCUACUUA
(((((------------.......(((((.(((((((((......))))))))).)))))(....)..---..))))).......................................... ( -20.10)
>DroSim_CAF1 8889 105 + 1
UGUGC------------AAAAACUAUCAAGUUUUCUUGCAAUUAAGCAAGGAAAAUUGGUCGAAAGCC---ACCCACAACUCAUUUUCCUGUACUGAUAUAAAUCCAUUUCCUCUACUUA
.((((------------(............(((((((((......)))))))))..(((.(....)))---).................))))).......................... ( -19.30)
>DroEre_CAF1 6905 116 + 1
UGUGCAGUGGGUGAUGGGAAAACUAUCAAGUUUUCUUGCAAUUAGGCAAGGAAAAUUGAACGAAAUAA---AU-AACCACCUCCUCCCAUGUACUCAUAUAAAUCCUUUUCCUCAACUUA
......(((((((((((((......((((.(((((((((......))))))))).))))..((.....---..-.......)).)))))).)))))))...................... ( -26.84)
>DroYak_CAF1 15724 116 + 1
UGUGCAGUGGCUGAUGGAAAAACAAUUAAGUUUUCUUGCAAUGAGGCAAAGAAAUUUGAACGACAGAA---AU-AAGCACUCCUUUGCCUGUAUUCAUAUAAAUUCCUUUCCUCAACUUA
..(((((.((((..((......))....))))...))))).(((((.((((.((((((((..((((..---..-..(((......))))))).))))....)))).)))))))))..... ( -21.00)
>consensus
UGUGC____________AAAAACUAUCAAGUUUUCUUGCAAUUAAGCAAGGAAAAUUGGUCGAAAGAA___ACCCACAACUCCUUUUCCUGUACUGAUAUAAAUCCAUUUCCUCUACUUA
......................(.(((((.(((((((((......))))))))).))))).).......................................................... (-11.50 = -11.90 +   0.40)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:16:46 2006