Locus 3292

Sequence ID	3L_DroMel_CAF1
Location	9,652,017 – 9,652,170
Length	153
Max. P	0.952811

overview

Window 1

Location	9,652,017 – 9,652,134
Length	117
Sequences	4
Columns	119
Reading direction	forward
Mean pairwise identity	91.24
Mean single sequence MFE	-24.55
Consensus MFE	-20.84
Energy contribution	-20.77
Covariance contribution	-0.06
Combinations/Pair	1.11
Mean z-score	-2.29
Structure conservation index	0.85
SVM decision value	1.43
SVM RNA-class probability	0.952811
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 9652017 117 + 23771897
CCCAAAAUUAGAAUGAAAAUCCCACUUUGAUCU--AAAUCAAGAGCAGAGGUAAAUAUUUUCAUAGACGCCCAAACUUACCGGCGACUCUCUGUGAAGAUAUUGUACAUACAUAUAAGC
............(((.........(((((.(((--......))).)))))(((((((((((((((((((((..........))))....)))))))))))))).)))...)))...... ( -27.40)
>DroSec_CAF1 47591 113 + 1
CCCAAAAUUAGAAUGAAAAUCUCACUUUGAUCU--AAAUCGAGAGAAGAGGUAAAUAUUUUCAUAGACGUCCAAACACACCGGCGACUCUCUGUGAAGAUAUCGUAC----AUAUAAAC
..........(.((((..(((((.(((((((..--..))).))))..)))))...((((((((((((((((..........))))....)))))))))))))))).)----........ ( -21.70)
>DroSim_CAF1 50182 113 + 1
CCCAAAAUUAGAAUGAAAAUCUCACUUUGAUCU--AAAUCGAGAGAAGAGGUAAAUAUUUUCAUAGACGCCCAAACACACCGGCGACUCUCUGUGAAGAUAUCGUAC----AUAUAAAC
..........(.((((..(((((.(((((((..--..))).))))..)))))...((((((((((((((((..........))))....)))))))))))))))).)----........ ( -24.40)
>DroYak_CAF1 47773 115 + 1
GCCCAAAUUAGAAUGAAAAUCCUACUUUGAUCUAUAAAUCGGGAGGAGAGGUAAAUAUUUUUAUAGACGCCCAAACACACCGGCGACUCUCUGUGAAGAUAUUGUAC----AUAUAAAC
.((((((.(((.((....)).))).)))(((......)))))).......(((((((((((((((((((((..........))))....)))))))))))))).)))----........ ( -24.70)
>consensus
CCCAAAAUUAGAAUGAAAAUCCCACUUUGAUCU__AAAUCGAGAGAAGAGGUAAAUAUUUUCAUAGACGCCCAAACACACCGGCGACUCUCUGUGAAGAUAUCGUAC____AUAUAAAC
........................((((..(((........)))..))))(((((((((((((((((((((..........))))....)))))))))))))).)))............ (-20.84 = -20.77 +  -0.06)

alignment

secondary structure

dotplot

Window 2

Location	9,652,055 – 9,652,170
Length	115
Sequences	4
Columns	115
Reading direction	forward
Mean pairwise identity	91.45
Mean single sequence MFE	-25.75
Consensus MFE	-22.61
Energy contribution	-22.30
Covariance contribution	-0.31
Combinations/Pair	1.12
Mean z-score	-1.49
Structure conservation index	0.88
SVM decision value	0.28
SVM RNA-class probability	0.667352
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 9652055 115 + 23771897
AAGAGCAGAGGUAAAUAUUUUCAUAGACGCCCAAACUUACCGGCGACUCUCUGUGAAGAUAUUGUACAUACAUAUAAGCACUUAGAAGCCCUUAAGAUAGAAGUUUUUCAAAGUA
..........(((((((((((((((((((((..........))))....)))))))))))))).)))............((((.((((..(((.......)))..)))).)))). ( -25.90)
>DroSec_CAF1 47629 111 + 1
GAGAGAAGAGGUAAAUAUUUUCAUAGACGUCCAAACACACCGGCGACUCUCUGUGAAGAUAUCGUAC----AUAUAAACACUUAGGAGCCCUUAGGAUAGAAGUUUUUCAAAGUA
((((((....(((.(((((((((((((((((..........))))....)))))))))))))..)))----.........((((((....)))))).......))))))...... ( -24.50)
>DroSim_CAF1 50220 111 + 1
GAGAGAAGAGGUAAAUAUUUUCAUAGACGCCCAAACACACCGGCGACUCUCUGUGAAGAUAUCGUAC----AUAUAAACACUUAGAAGCCCUUAGGAUAGAAGUUUUUCAAAGUA
..........(((.(((((((((((((((((..........))))....)))))))))))))..)))----........((((.((((..(((.......)))..)))).)))). ( -24.80)
>DroYak_CAF1 47813 111 + 1
GGGAGGAGAGGUAAAUAUUUUUAUAGACGCCCAAACACACCGGCGACUCUCUGUGAAGAUAUUGUAC----AUAUAAACACUUAGGAGCUCUUAGGUUAGGAGUUUUUCAAAGUA
..........(((((((((((((((((((((..........))))....)))))))))))))).)))----........(((((((((((((((...)))))))))))..)))). ( -27.80)
>consensus
GAGAGAAGAGGUAAAUAUUUUCAUAGACGCCCAAACACACCGGCGACUCUCUGUGAAGAUAUCGUAC____AUAUAAACACUUAGAAGCCCUUAGGAUAGAAGUUUUUCAAAGUA
..........(((((((((((((((((((((..........))))....)))))))))))))).)))............((((.((((..(((.......)))..)))).)))). (-22.61 = -22.30 +  -0.31)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:54:07 2006