Locus 1741

Sequence ID	3L_DroMel_CAF1
Location	5,039,715 – 5,039,844
Length	129
Max. P	0.999797

overview

Window 3

Location	5,039,715 – 5,039,818
Length	103
Sequences	5
Columns	105
Reading direction	forward
Mean pairwise identity	97.11
Mean single sequence MFE	-27.27
Consensus MFE	-24.44
Energy contribution	-24.64
Covariance contribution	0.20
Combinations/Pair	1.00
Mean z-score	-3.30
Structure conservation index	0.90
SVM decision value	3.90
SVM RNA-class probability	0.999696
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 5039715 103 + 23771897
GCGACACACUAAACUC-AACUUAAAUAUAAAUUAUGAGCAUCUUAAAAAGCCACAGCGAAAGGAUAAUUUUCAUAAAUAUUCGAGCCAUGUGGCUGUGUGUCUG-
..(((((((....(((-(................))))..........(((((((((....(((((.((.....)).)))))..))..))))))))))))))..- ( -26.69)
>DroSec_CAF1 246240 103 + 1
GCGACACACUAAACUC-AACUUAAAUAUAAAUUAUGAGCAUCUUAAAAAGCCACAGCGAAAGGAUAAUUUUCAUAAAUAUUCGAGCCAUGUGGCUGUGUGUCUG-
..(((((((....(((-(................))))..........(((((((((....(((((.((.....)).)))))..))..))))))))))))))..- ( -26.69)
>DroSim_CAF1 267099 103 + 1
GCGACACACUAAACUC-AACUUAAAUAUAAAUUAUGAGCAUCUUAAAAAGCCACAGCGAAAGGAUAAUUUUCAUAAAUAUUCGAGCCAUGUGGCUGUGUGUCUG-
..(((((((....(((-(................))))..........(((((((((....(((((.((.....)).)))))..))..))))))))))))))..- ( -26.69)
>DroEre_CAF1 249650 105 + 1
GCGACACACUAAACUCUAACUUAAAGAUAAAUUAUGAGCAUCUUAAAAAGCCACAGCGAAAGGAUAAUUUUCAUAAAUAUUCGAGCCAUGUGGCCGUGUGUCUGU
..(((((((....((((((.(((....))).))).)))...........((((((((....(((((.((.....)).)))))..))..)))))).)))))))... ( -25.70)
>DroYak_CAF1 255994 103 + 1
GCGACACACUAAACUC-AGUUUUAAGAUAAAUUAUGAGCAUCUUAAAAAGCCACAGCGAAAGGAUAAUUUUCAUAAAUAUUCGAGCCAUGUGGCUGUGUGUCUG-
..(((((((.......-..(((((((((...........)))))))))(((((((((....(((((.((.....)).)))))..))..))))))))))))))..- ( -30.60)
>consensus
GCGACACACUAAACUC_AACUUAAAUAUAAAUUAUGAGCAUCUUAAAAAGCCACAGCGAAAGGAUAAUUUUCAUAAAUAUUCGAGCCAUGUGGCUGUGUGUCUG_
..(((((((.........................((((...))))...(((((((((....(((((.((.....)).)))))..))..))))))))))))))... (-24.44 = -24.64 +   0.20)

alignment

secondary structure

dotplot

Window 4

Location	5,039,715 – 5,039,818
Length	103
Sequences	5
Columns	105
Reading direction	reverse
Mean pairwise identity	97.11
Mean single sequence MFE	-29.18
Consensus MFE	-26.48
Energy contribution	-26.56
Covariance contribution	0.08
Combinations/Pair	1.07
Mean z-score	-3.27
Structure conservation index	0.91
SVM decision value	4.10
SVM RNA-class probability	0.999797
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 5039715 103 - 23771897
-CAGACACACAGCCACAUGGCUCGAAUAUUUAUGAAAAUUAUCCUUUCGCUGUGGCUUUUUAAGAUGCUCAUAAUUUAUAUUUAAGUU-GAGUUUAGUGUGUCGC
-..((((((((((((((.....((((.....((....))......)))).))))))).........(((((..(((((....))))))-))))...))))))).. ( -28.60)
>DroSec_CAF1 246240 103 - 1
-CAGACACACAGCCACAUGGCUCGAAUAUUUAUGAAAAUUAUCCUUUCGCUGUGGCUUUUUAAGAUGCUCAUAAUUUAUAUUUAAGUU-GAGUUUAGUGUGUCGC
-..((((((((((((((.....((((.....((....))......)))).))))))).........(((((..(((((....))))))-))))...))))))).. ( -28.60)
>DroSim_CAF1 267099 103 - 1
-CAGACACACAGCCACAUGGCUCGAAUAUUUAUGAAAAUUAUCCUUUCGCUGUGGCUUUUUAAGAUGCUCAUAAUUUAUAUUUAAGUU-GAGUUUAGUGUGUCGC
-..((((((((((((((.....((((.....((....))......)))).))))))).........(((((..(((((....))))))-))))...))))))).. ( -28.60)
>DroEre_CAF1 249650 105 - 1
ACAGACACACGGCCACAUGGCUCGAAUAUUUAUGAAAAUUAUCCUUUCGCUGUGGCUUUUUAAGAUGCUCAUAAUUUAUCUUUAAGUUAGAGUUUAGUGUGUCGC
...((((((((((((((.....((((.....((....))......)))).))))))).........((((.(((((((....)))))))))))...))))))).. ( -30.80)
>DroYak_CAF1 255994 103 - 1
-CAGACACACAGCCACAUGGCUCGAAUAUUUAUGAAAAUUAUCCUUUCGCUGUGGCUUUUUAAGAUGCUCAUAAUUUAUCUUAAAACU-GAGUUUAGUGUGUCGC
-..((((((((((((((.....((((.....((....))......)))).)))))))((((((((((.........))))))))))..-.......))))))).. ( -29.30)
>consensus
_CAGACACACAGCCACAUGGCUCGAAUAUUUAUGAAAAUUAUCCUUUCGCUGUGGCUUUUUAAGAUGCUCAUAAUUUAUAUUUAAGUU_GAGUUUAGUGUGUCGC
...((((((((((((((.....((((.....((....))......)))).))))))).........((((...(((((....)))))..))))...))))))).. (-26.48 = -26.56 +   0.08)

alignment

secondary structure

dotplot

Window 5

Location	5,039,754 – 5,039,844
Length	90
Sequences	5
Columns	104
Reading direction	reverse
Mean pairwise identity	92.47
Mean single sequence MFE	-16.74
Consensus MFE	-15.10
Energy contribution	-15.14
Covariance contribution	0.04
Combinations/Pair	1.05
Mean z-score	-1.30
Structure conservation index	0.90
SVM decision value	0.59
SVM RNA-class probability	0.791438
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 5039754 90 - 23771897
CCAAGCAGCCACCAGAU------AUAUAAACA--------CAGACACACAGCCACAUGGCUCGAAUAUUUAUGAAAAUUAUCCUUUCGCUGUGGCUUUUUAAGA
..(((.((((((.((..------.........--------.........((((....))))((((.....((....))......)))))))))))).))).... ( -16.90)
>DroSec_CAF1 246279 90 - 1
CCAAGCAGCCACCAGAU------AUCUAAACA--------CAGACACACAGCCACAUGGCUCGAAUAUUUAUGAAAAUUAUCCUUUCGCUGUGGCUUUUUAAGA
..(((.((((((.((..------.........--------.........((((....))))((((.....((....))......)))))))))))).))).... ( -16.90)
>DroSim_CAF1 267138 90 - 1
CCAAGCAGCCACCAGAU------AUAUAAACA--------CAGACACACAGCCACAUGGCUCGAAUAUUUAUGAAAAUUAUCCUUUCGCUGUGGCUUUUUAAGA
..(((.((((((.((..------.........--------.........((((....))))((((.....((....))......)))))))))))).))).... ( -16.90)
>DroEre_CAF1 249690 98 - 1
CCAAGCAGCCACCAGAU------AUAUAAACACACCCAUACAGACACACGGCCACAUGGCUCGAAUAUUUAUGAAAAUUAUCCUUUCGCUGUGGCUUUUUAAGA
..(((.((((((.((..------.........................(((((....))).)).........((((.......)))).)))))))).))).... ( -17.40)
>DroYak_CAF1 256033 96 - 1
CCAAGCAGCCUCCAAAUACUCGUAUAUAAACA--------CAGACACACAGCCACAUGGCUCGAAUAUUUAUGAAAAUUAUCCUUUCGCUGUGGCUUUUUAAGA
..((((.........(((....))).....((--------(((......((((....))))((((.....((....))......)))))))))))))....... ( -15.60)
>consensus
CCAAGCAGCCACCAGAU______AUAUAAACA________CAGACACACAGCCACAUGGCUCGAAUAUUUAUGAAAAUUAUCCUUUCGCUGUGGCUUUUUAAGA
..(((.((((((.....................................((((....))))((((.....((....))......))))..)))))).))).... (-15.10 = -15.14 +   0.04)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:15:00 2006