Locus 2256

Sequence ID	3R_DroMel_CAF1
Location	6,401,441 – 6,401,537
Length	96
Max. P	0.724165

overview

Window 6

Location	6,401,441 – 6,401,537
Length	96
Sequences	5
Columns	102
Reading direction	forward
Mean pairwise identity	89.74
Mean single sequence MFE	-23.74
Consensus MFE	-17.54
Energy contribution	-17.54
Covariance contribution	-0.00
Combinations/Pair	1.10
Mean z-score	-1.74
Structure conservation index	0.74
SVM decision value	0.18
SVM RNA-class probability	0.622660
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 6401441 96 + 27905053
------GCAGCAACAACUAAGCUGACAGCAAGUUAUGAUACUUUAUAAGUUGCAGCAUUAGCAGCAUCUUGAAUACCAGCAGAACUAGAAUUAUUAAAGACA
------..............((((...((((.((((((....)))))).)))).((....))..............))))...................... ( -17.30)
>DroSec_CAF1 165250 96 + 1
------GCAGCAGCAACUAAGCUGACAGCAAGUUAUGAUACUUUAUAAGUUGCAGCAUUAGCAGCAUCUUGGCUACCAGCAGAACUAGAAUUAUUAAAGACA
------((.(((((......)))).).((((.((((((....)))))).)))).))....(((((......)))....))...................... ( -20.10)
>DroSim_CAF1 189059 96 + 1
------GCAGCAGCAACUAAGCUGACAGCAAGUUAUGAUACUUUAUAAGUUGCAGCAUUAGCAGCAUCUUGGCUACCAGCAGAACUAGAAUUAUUAGAGACA
------((.(((((......)))).).((((.((((((....)))))).)))).))....(((((......)))....))...................... ( -20.10)
>DroEre_CAF1 176447 96 + 1
------GCAGCAACAACUAAGCUGCCAGCAAGUUAUGAUACCUUAUAAGCUGCGGCAUUAGCGGCAUCUUCGCUGCCAGCAGCACUAGAAUUGCUAAAGACA
------(((((.........))))).(((((.((((((....))))))(((((((((...((((.....)))))))).))))).......)))))....... ( -31.20)
>DroYak_CAF1 169291 102 + 1
GCAGCAGCAGCCACAACUAAGCUGGCAGCAAGUUAUGAUACUUUAUAAGCUGCUGCAUUAGCAGCAUCUUGGCUUCCAGCAGCACUAGAAUUAUUAGAGACA
((.((....)).........(((((.(((((((......))))..((((.((((((....)))))).))))))).))))).))................... ( -30.00)
>consensus
______GCAGCAACAACUAAGCUGACAGCAAGUUAUGAUACUUUAUAAGUUGCAGCAUUAGCAGCAUCUUGGCUACCAGCAGAACUAGAAUUAUUAAAGACA
....................((((..((((((((((((....))))))(((((.......)))))..))).)))..))))...................... (-17.54 = -17.54 +  -0.00)

alignment

secondary structure

dotplot

Window 7

Location	6,401,441 – 6,401,537
Length	96
Sequences	5
Columns	102
Reading direction	reverse
Mean pairwise identity	89.74
Mean single sequence MFE	-26.30
Consensus MFE	-20.16
Energy contribution	-20.20
Covariance contribution	0.04
Combinations/Pair	1.16
Mean z-score	-1.73
Structure conservation index	0.77
SVM decision value	0.41
SVM RNA-class probability	0.724165
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 6401441 96 - 27905053
UGUCUUUAAUAAUUCUAGUUCUGCUGGUAUUCAAGAUGCUGCUAAUGCUGCAACUUAUAAAGUAUCAUAACUUGCUGUCAGCUUAGUUGUUGCUGC------
.(((((.((((...((((.....)))))))).)))))((.((....)).)).........((((..((((((.((.....))..))))))))))..------ ( -18.80)
>DroSec_CAF1 165250 96 - 1
UGUCUUUAAUAAUUCUAGUUCUGCUGGUAGCCAAGAUGCUGCUAAUGCUGCAACUUAUAAAGUAUCAUAACUUGCUGUCAGCUUAGUUGCUGCUGC------
...............((((.((((((..(((.(((.(((.((....)).))).)))...((((......)))))))..))))..))..))))....------ ( -22.10)
>DroSim_CAF1 189059 96 - 1
UGUCUCUAAUAAUUCUAGUUCUGCUGGUAGCCAAGAUGCUGCUAAUGCUGCAACUUAUAAAGUAUCAUAACUUGCUGUCAGCUUAGUUGCUGCUGC------
...............((((.((((((..(((.(((.(((.((....)).))).)))...((((......)))))))..))))..))..))))....------ ( -22.10)
>DroEre_CAF1 176447 96 - 1
UGUCUUUAGCAAUUCUAGUGCUGCUGGCAGCGAAGAUGCCGCUAAUGCCGCAGCUUAUAAGGUAUCAUAACUUGCUGGCAGCUUAGUUGUUGCUGC------
......(((((((.((((.(((((..((((....((((((......((....))......)))))).....))))..)))))))))..))))))).------ ( -37.30)
>DroYak_CAF1 169291 102 - 1
UGUCUCUAAUAAUUCUAGUGCUGCUGGAAGCCAAGAUGCUGCUAAUGCAGCAGCUUAUAAAGUAUCAUAACUUGCUGCCAGCUUAGUUGUGGCUGCUGCUGC
.............(((((.....)))))(((.(((.((((((....)))))).)))....((((((((((((.((.....))..)))))))).))))))).. ( -31.20)
>consensus
UGUCUUUAAUAAUUCUAGUUCUGCUGGUAGCCAAGAUGCUGCUAAUGCUGCAACUUAUAAAGUAUCAUAACUUGCUGUCAGCUUAGUUGUUGCUGC______
......................(((((((((.(((.(((.((....)).))).)))...((((......))))))))))))).((((....))))....... (-20.16 = -20.20 +   0.04)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:30:59 2006