Locus 1814

Sequence ID	3L_DroMel_CAF1
Location	5,099,354 – 5,099,468
Length	114
Max. P	0.625305

overview

Window 7

Location	5,099,354 – 5,099,468
Length	114
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	89.06
Mean single sequence MFE	-26.37
Consensus MFE	-17.90
Energy contribution	-18.15
Covariance contribution	0.25
Combinations/Pair	1.00
Mean z-score	-2.04
Structure conservation index	0.68
SVM decision value	0.19
SVM RNA-class probability	0.625305
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 5099354 114 + 23771897
CUAGAUGGCGCCAGCACGUGCUCCGAGUCGGGGGAUUCCCCUCUCUAUUUUCCACCCCC------CUCUACUCUACGCACCCAAUCAAUACUUGAAUUGGUUUCGGUUUACCAAACUUUU
.....(((.(((.....((((...((((.(((((.....................))))------)...))))...))))(((((((.....)).)))))....)))...)))....... ( -27.00)
>DroSec_CAF1 292423 119 + 1
CUAGAUGGCGUCAGCACGUGCUCCGGGUCGGGGGAUUCCCCUCUCUUUUUUUCACCCCCCUCCCCCUCUACUC-ACGCACCCAAUCAAUAUUUGAAUUGGUUUCGGUUUACCAACCUUUU
.......((((.(((....)))..(((..(((((.....................)))))..)))........-))))..(((((((.....)).)))))....((((....)))).... ( -27.60)
>DroSim_CAF1 314067 118 + 1
CUAGAUGGCGUCAGCACGUGCUCCCAGUCGGGGGAUUCCCC-CUCUUUUUUCCACCCCCCUCCCCCUCUACUC-ACGCACCCAAUCAAUAUUUGAAUUGGUUUCGGUUUACCAACCUUUU
.((((.((((..(((....)))..).)))((((((......-..................))))))))))...-......(((((((.....)).)))))....((((....)))).... ( -22.66)
>DroYak_CAF1 304711 115 + 1
CUAGAUGGCGCCAGCACGUGCUCCCUGUCAGGGGAUUCCCC-CUCUUUUCUACACCCCC---UCCCUCUAUUC-GUGAAACCAAUCAAUAUUUGAAUUGGUUUCGGUUUACCAACCUUUU
.(((((((((..(((....)))...)))))((((....)))-).....)))).......---...........-..(((((((((((.....)).)))))))))((((....)))).... ( -28.20)
>consensus
CUAGAUGGCGCCAGCACGUGCUCCCAGUCGGGGGAUUCCCC_CUCUUUUUUCCACCCCC___CCCCUCUACUC_ACGCACCCAAUCAAUAUUUGAAUUGGUUUCGGUUUACCAACCUUUU
.((((.(((...(((....)))....)))(((((....................))))).......))))..........(((((((.....)).)))))....((....))........ (-17.90 = -18.15 +   0.25)

alignment

secondary structure

dotplot

Window 8

Location	5,099,354 – 5,099,468
Length	114
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	89.06
Mean single sequence MFE	-36.51
Consensus MFE	-23.26
Energy contribution	-23.07
Covariance contribution	-0.19
Combinations/Pair	1.04
Mean z-score	-2.51
Structure conservation index	0.64
SVM decision value	0.05
SVM RNA-class probability	0.558346
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 5099354 114 - 23771897
AAAAGUUUGGUAAACCGAAACCAAUUCAAGUAUUGAUUGGGUGCGUAGAGUAGAG------GGGGGUGGAAAAUAGAGAGGGGAAUCCCCCGACUCGGAGCACGUGCUGGCGCCAUCUAG
...((..((((...(((...((((((........))))))((((...((((...(------((((((.................))))))).))))...))))....))).)))).)).. ( -36.03)
>DroSec_CAF1 292423 119 - 1
AAAAGGUUGGUAAACCGAAACCAAUUCAAAUAUUGAUUGGGUGCGU-GAGUAGAGGGGGAGGGGGGUGAAAAAAAGAGAGGGGAAUCCCCCGACCCGGAGCACGUGCUGACGCCAUCUAG
...((((.(((.........((((((........))))))(..(((-(..(....(((..(((((((.................)))))))..))).)..))))..)....))))))).. ( -39.53)
>DroSim_CAF1 314067 118 - 1
AAAAGGUUGGUAAACCGAAACCAAUUCAAAUAUUGAUUGGGUGCGU-GAGUAGAGGGGGAGGGGGGUGGAAAAAAGAG-GGGGAAUCCCCCGACUGGGAGCACGUGCUGACGCCAUCUAG
...((((.(((...((....((((((........)))))).(((..-..)))..))((..(((((((...........-.....)))))))..))(..(((....)))..)))))))).. ( -34.79)
>DroYak_CAF1 304711 115 - 1
AAAAGGUUGGUAAACCGAAACCAAUUCAAAUAUUGAUUGGUUUCAC-GAAUAGAGGGA---GGGGGUGUAGAAAAGAG-GGGGAAUCCCCUGACAGGGAGCACGUGCUGGCGCCAUCUAG
....((((....))))((((((((((........))))))))))..-........(((---...(((((.......((-(((....))))).......(((....))).))))).))).. ( -35.70)
>consensus
AAAAGGUUGGUAAACCGAAACCAAUUCAAAUAUUGAUUGGGUGCGU_GAGUAGAGGGG___GGGGGUGGAAAAAAGAG_GGGGAAUCCCCCGACUCGGAGCACGUGCUGACGCCAUCUAG
......((((....))))..((((((........)))))).....................(((((((...........((((....)))).......(((....)))..)))).))).. (-23.26 = -23.07 +  -0.19)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:17:22 2006