Locus 4440

Sequence ID	2L_DroMel_CAF1
Location	12,763,588 – 12,763,762
Length	174
Max. P	0.999371

overview

Window 3

Location	12,763,588 – 12,763,682
Length	94
Sequences	5
Columns	97
Reading direction	forward
Mean pairwise identity	94.59
Mean single sequence MFE	-30.90
Consensus MFE	-26.70
Energy contribution	-26.54
Covariance contribution	-0.16
Combinations/Pair	1.12
Mean z-score	-2.82
Structure conservation index	0.86
SVM decision value	3.55
SVM RNA-class probability	0.999371
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 12763588 94 + 22407834
UUGAUGCCGGGCGGAUCAAUGGCCCCGGGAGAA-AGGUGAAAGUGCUU--UUCCCAAAGAAAUCAUAUUUACCUGUGCGUCGGACAUAAAAAUGUCA
.((((((((((..(((..((((...(.((.(((-((((......))))--)))))...)...)))))))..)))).))))))(((((....))))). ( -29.70)
>DroSec_CAF1 40744 96 + 1
UUGAUGCAGGGCGGAUCAAUGGCCCCGGGAGAA-AGGUGAAAGUGCUUUUUUCCCAAAGAAAUCAUAUUUAUCUGUGCGGCGGACAUAAAAAUGUCA
....(((.(.((((((.((((.....(((((((-((((......)))))))))))...(....).)))).)))))).).)))(((((....))))). ( -30.80)
>DroSim_CAF1 40996 96 + 1
UUGAUGCAGGGCGGAUCAAUGGCCCCGGGAGAA-AGGUGAAAGUGCUUUUUUCCCAAAGAAAUCAUAUUUACCUGUGCGUCGGACAUAAAAAUGUCA
.(((((((((((.........)))).(((((((-((((......)))))))))))....................)))))))(((((....))))). ( -34.30)
>DroEre_CAF1 41565 95 + 1
UUGAUGCAGGGCGGAUCAAUGGCCCCGGGAGAA-AGGUUAAAGUGCUUU-UUCCCAAAGAAAUCAUAUUUGCCUGUGCAUUCGACAUAAAAAUGUCA
..((((((((((((((....(....)(((((((-((.........))))-)))))...........)))))))).)))))).(((((....))))). ( -30.40)
>DroYak_CAF1 41851 96 + 1
UUGAUGCAGGGCGGAUCAAUGGCCCCGGGAGAAAAGGUGAAAGUGCCUU-UUCCCAAAGAAAUCAUAUUUACCUGUGCGUUGGACAUAAAAAUGUCA
..((((((((((.........))))..((.((((((((......)))))-)))))....................)))))).(((((....))))). ( -29.30)
>consensus
UUGAUGCAGGGCGGAUCAAUGGCCCCGGGAGAA_AGGUGAAAGUGCUUU_UUCCCAAAGAAAUCAUAUUUACCUGUGCGUCGGACAUAAAAAUGUCA
..((((((((((.........)))).(((((...((((......))))..)))))....................)))))).(((((....))))). (-26.70 = -26.54 +  -0.16)

alignment

secondary structure

dotplot

Window 4

Location	12,763,611 – 12,763,722
Length	111
Sequences	5
Columns	114
Reading direction	forward
Mean pairwise identity	91.10
Mean single sequence MFE	-30.40
Consensus MFE	-22.40
Energy contribution	-22.12
Covariance contribution	-0.28
Combinations/Pair	1.12
Mean z-score	-2.18
Structure conservation index	0.74
SVM decision value	0.60
SVM RNA-class probability	0.794437
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 12763611 111 + 22407834
CCCGGGAGAA-AGGUGAAAGUGCUU--UUCCCAAAGAAAUCAUAUUUACCUGUGCGUCGGACAUAAAAAUGUCAGGAAAAAAUGGCAGGGCGAGGAAGGAGGAAUCAGGUGUAU
....((.(((-((((......))))--)))))..............((((((..(.((.(((((....)))))...........((...)).......)).)...))))))... ( -24.00)
>DroSec_CAF1 40767 112 + 1
CCCGGGAGAA-AGGUGAAAGUGCUUUUUUCCCAAAGAAAUCAUAUUUAUCUGUGCGGCGGACAUAAAAAUGUCAG-AAAAAAUGGCAGGGCGAGGAAGCAGGAAUCAGGUGGAU
...(((((((-((((......)))))))))))...........(((((((((..(.((...........(((((.-......)))))..........))..)...))))))))) ( -29.10)
>DroSim_CAF1 41019 112 + 1
CCCGGGAGAA-AGGUGAAAGUGCUUUUUUCCCAAAGAAAUCAUAUUUACCUGUGCGUCGGACAUAAAAAUGUCAG-AAAAAAUGGCAGGGCGAGGAAGCAGGAAUCAGGUGGAU
...(((((((-((((......)))))))))))...........(((((((((....((.(((((....)))))..-.............((......))..))..))))))))) ( -32.40)
>DroEre_CAF1 41588 109 + 1
CCCGGGAGAA-AGGUUAAAGUGCUUU-UUCCCAAAGAAAUCAUAUUUGCCUGUGCAUUCGACAUAAAAAUGUCAG--GAAAAU-GCAGGGCGAGUAAGCGGCAAUCAGGUGGAU
.(((((((((-((.........))))-)))))..........(((((((((.((((((.(((((....)))))..--...)))-))))))))))))..............)).. ( -33.40)
>DroYak_CAF1 41874 111 + 1
CCCGGGAGAAAAGGUGAAAGUGCCUU-UUCCCAAAGAAAUCAUAUUUACCUGUGCGUUGGACAUAAAAAUGUCAG-GGAAAAU-GCAGGGCGAGGAAACGGAAAUCAGGUGGAU
....((.((((((((......)))))-)))))...........(((((((((((((((.(((((....)))))..-....)))-)))......(....)......))))))))) ( -33.10)
>consensus
CCCGGGAGAA_AGGUGAAAGUGCUUU_UUCCCAAAGAAAUCAUAUUUACCUGUGCGUCGGACAUAAAAAUGUCAG_AAAAAAUGGCAGGGCGAGGAAGCAGGAAUCAGGUGGAU
...(((((...((((......))))..)))))...........(((((((((.......(((((....)))))...........((...))..............))))))))) (-22.40 = -22.12 +  -0.28)

alignment

secondary structure

dotplot

Window 5

Location	12,763,642 – 12,763,762
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	88.26
Mean single sequence MFE	-28.22
Consensus MFE	-20.84
Energy contribution	-20.92
Covariance contribution	0.08
Combinations/Pair	1.08
Mean z-score	-2.42
Structure conservation index	0.74
SVM decision value	1.14
SVM RNA-class probability	0.921729
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 12763642 120 + 22407834
AGAAAUCAUAUUUACCUGUGCGUCGGACAUAAAAAUGUCAGGAAAAAAUGGCAGGGCGAGGAAGGAGGAAUCAGGUGUAUAGAGUUUCGUAAAGCAAAAGUCAGCUGAAAAUACGGACUA
.(((((..(((.((((((..(.((.(((((....)))))...........((...)).......)).)...)))))).)))..)))))(((.(((........))).....)))...... ( -24.20)
>DroSec_CAF1 40800 119 + 1
AGAAAUCAUAUUUAUCUGUGCGGCGGACAUAAAAAUGUCAG-AAAAAAUGGCAGGGCGAGGAAGCAGGAAUCAGGUGGAUAGAGUUUCGUAAAGCAAAAGUCAGCUGAAAAUACGGACUA
..............((((((((((.(((.......(((((.-......)))))..((.(.(((((....(((.....)))...))))).)...))....))).))))....))))))... ( -24.90)
>DroSim_CAF1 41052 119 + 1
AGAAAUCAUAUUUACCUGUGCGUCGGACAUAAAAAUGUCAG-AAAAAAUGGCAGGGCGAGGAAGCAGGAAUCAGGUGGAUAGAGUUUCGUAAAGCAAAAGUCAGCUGAAAAUACGGACUA
.(((((..((((((((((....((.(((((....)))))..-.............((......))..))..))))))))))..)))))(((.(((........))).....)))...... ( -27.80)
>DroEre_CAF1 41620 117 + 1
AGAAAUCAUAUUUGCCUGUGCAUUCGACAUAAAAAUGUCAG--GAAAAU-GCAGGGCGAGUAAGCGGCAAUCAGGUGGAUAGGGUUUCAUAAAGGAAGAGUCAGCUGACAAGACAAAAUA
.((((((.((((..((((((((((.(((((....)))))..--...)))-))).(.((......)).)...))))..)))).))))))...........(((....)))........... ( -32.00)
>DroYak_CAF1 41907 117 + 1
AGAAAUCAUAUUUACCUGUGCGUUGGACAUAAAAAUGUCAG-GGAAAAU-GCAGGGCGAGGAAACGGAAAUCAGGUGGAUAGAGUUUCAUAAAGCAAGACUCAGCUGAAAAGG-AGUAUA
.(((((..((((((((((((((((.(((((....)))))..-....)))-)))......(....)......))))))))))..)))))..........((((..((....)))-)))... ( -32.20)
>consensus
AGAAAUCAUAUUUACCUGUGCGUCGGACAUAAAAAUGUCAG_AAAAAAUGGCAGGGCGAGGAAGCAGGAAUCAGGUGGAUAGAGUUUCGUAAAGCAAAAGUCAGCUGAAAAUACGGACUA
.(((((..((((((((((.......(((((....)))))...........((...))..............))))))))))..)))))....(((........))).............. (-20.84 = -20.92 +   0.08)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:17:48 2006