Locus 1985

Sequence ID	X_DroMel_CAF1
Location	5,451,630 – 5,451,728
Length	98
Max. P	0.993377

overview

Window 5

Location	5,451,630 – 5,451,728
Length	98
Sequences	6
Columns	105
Reading direction	forward
Mean pairwise identity	77.40
Mean single sequence MFE	-47.57
Consensus MFE	-27.43
Energy contribution	-27.52
Covariance contribution	0.08
Combinations/Pair	1.15
Mean z-score	-3.17
Structure conservation index	0.58
SVM decision value	2.39
SVM RNA-class probability	0.993377
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 5451630 98 + 22224390
CCGCUGGU-------CCGCAUCACUCGGCCGCACUGGCUGCCCAUCAGCAUGCAGCGGCUGCUGCGGCCGCCGCUCAUCAUCAUGCCGCUGCCGCUGCUGCCGCC
..((((((-------..(((.......(((.....))))))..)))))).....(((((.((.(((((.((.((..........)).)).))))).)).))))). ( -43.01)
>DroVir_CAF1 135722 99 + 1
------ACGACGGCAGCCCAUCAUCAUGCCGCUCUGGCGGCACAUCAGCAUGCUGCGGCAGCGGCAGCGGCGGCACAUCAUCAUGCCGCUGCCGCGGCAGCCGCC
------....((((.(((........((((((...((((((......)).))))))))))((((((((((((...........))))))))))))))).)))).. ( -55.10)
>DroGri_CAF1 113735 93 + 1
------ACG------GCUCAUCAUCAUGCCGCACUCGCCGCCCAUCAGCAUGCGGCGGCAGCGGCUGCGGCGGCACAUCAUCAUGCCGCUGCCGCCGCAGCUGUU
------.((------((..........)))).....(((((((((....))).))))))(((((((((((((((((((....)))....)))))))))))))))) ( -51.80)
>DroEre_CAF1 70205 98 + 1
CAGCUGGU-------CCGCAUCAUUCGGCCGCGCUGGCCGCCCAUCAGCAUGCAGCGGCUGCUGCGGCCGCCGCUCAUCAUCAUGCCGCUGCCGCUGCCGCCGCC
..((((((-------..((.......((((.....))))))..)))))).....(((((.((.(((((.((.((..........)).)).))))).)).))))). ( -44.61)
>DroYak_CAF1 60107 98 + 1
CCGCUGGU-------CCGCAUCACUCGGCCGCUCUGGCCGCCCAUCAGCAUGCAGCGGCUGCUGCGGCCGCCGCUCAUCAUCAUGCCGCUGCCGCUGCCGCCGCC
..((((((-------..((.......((((.....))))))..)))))).....(((((.((.(((((.((.((..........)).)).))))).)).))))). ( -44.71)
>DroMoj_CAF1 141976 87 + 1
------------------CAUCAUCAUGCCGCUUUGGCCGCCCAUCAGCAUGCGGCAGCGGCUGCAGCAGCGGCACACCAUCAUGCCGCUGCCGCAGCGGCCGCU
------------------........((((((....((.........))..))))))((((((((.(((((((((........)))))))))....)))))))). ( -46.20)
>consensus
______GU_______CCGCAUCAUCAGGCCGCUCUGGCCGCCCAUCAGCAUGCAGCGGCUGCUGCGGCCGCCGCACAUCAUCAUGCCGCUGCCGCUGCAGCCGCC
..........................(((.((....)).)))............(((((.((.((.((.((.((..........)).)).)).)).)).))))). (-27.43 = -27.52 +   0.08)

alignment

secondary structure

dotplot

Window 6

Location	5,451,630 – 5,451,728
Length	98
Sequences	6
Columns	105
Reading direction	reverse
Mean pairwise identity	77.40
Mean single sequence MFE	-51.80
Consensus MFE	-33.25
Energy contribution	-33.37
Covariance contribution	0.11
Combinations/Pair	1.17
Mean z-score	-2.55
Structure conservation index	0.64
SVM decision value	1.92
SVM RNA-class probability	0.982668
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 5451630 98 - 22224390
GGCGGCAGCAGCGGCAGCGGCAUGAUGAUGAGCGGCGGCCGCAGCAGCCGCUGCAUGCUGAUGGGCAGCCAGUGCGGCCGAGUGAUGCGG-------ACCAGCGG
(((.((..(((((((((((((.((.((.((.((....)))))).)))))))))).)))))....)).)))..(((((((((....).)))-------.)).))). ( -46.50)
>DroVir_CAF1 135722 99 - 1
GGCGGCUGCCGCGGCAGCGGCAUGAUGAUGUGCCGCCGCUGCCGCUGCCGCAGCAUGCUGAUGUGCCGCCAGAGCGGCAUGAUGAUGGGCUGCCGUCGU------
((((((.(((((((((((((((((.((......)).)).))))))))))))..(((.(...((((((((....))))))))..))))))).))))))..------ ( -59.00)
>DroGri_CAF1 113735 93 - 1
AACAGCUGCGGCGGCAGCGGCAUGAUGAUGUGCCGCCGCAGCCGCUGCCGCCGCAUGCUGAUGGGCGGCGAGUGCGGCAUGAUGAUGAGC------CGU------
..(((((((((((((((((((.......((((....))))))))))))))))))).))))....(((((..((.((......))))..))------)))------ ( -52.31)
>DroEre_CAF1 70205 98 - 1
GGCGGCGGCAGCGGCAGCGGCAUGAUGAUGAGCGGCGGCCGCAGCAGCCGCUGCAUGCUGAUGGGCGGCCAGCGCGGCCGAAUGAUGCGG-------ACCAGCUG
(((.((..(((((((((((((.((.((.((.((....)))))).)))))))))).)))))....)).)))(((..(((((.......)))-------.)).))). ( -48.50)
>DroYak_CAF1 60107 98 - 1
GGCGGCGGCAGCGGCAGCGGCAUGAUGAUGAGCGGCGGCCGCAGCAGCCGCUGCAUGCUGAUGGGCGGCCAGAGCGGCCGAGUGAUGCGG-------ACCAGCGG
.((((((((.(((((.((.((..........)).)).)))))....)))))))).(((((.....(((((.....))))).(.....)..-------..))))). ( -47.60)
>DroMoj_CAF1 141976 87 - 1
AGCGGCCGCUGCGGCAGCGGCAUGAUGGUGUGCCGCUGCUGCAGCCGCUGCCGCAUGCUGAUGGGCGGCCAAAGCGGCAUGAUGAUG------------------
.(((((.((((((((((((((((......)))))))))))))))).)))))(((((((((.(((....)))...))))))).))...------------------ ( -56.90)
>consensus
GGCGGCGGCAGCGGCAGCGGCAUGAUGAUGAGCCGCGGCCGCAGCAGCCGCUGCAUGCUGAUGGGCGGCCAGAGCGGCAGAAUGAUGCGG_______AC______
...(((.((.(((((.((.((..........)).)).))))).)).)))(((((..((((.....))))....)))))........................... (-33.25 = -33.37 +   0.11)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:23:34 2006