Locus 5906

Sequence ID	2R_DroMel_CAF1
Location	18,631,110 – 18,631,210
Length	100
Max. P	0.987868

overview

Window 1

Location	18,631,110 – 18,631,210
Length	100
Sequences	5
Columns	100
Reading direction	forward
Mean pairwise identity	91.81
Mean single sequence MFE	-36.76
Consensus MFE	-28.68
Energy contribution	-28.72
Covariance contribution	0.04
Combinations/Pair	1.04
Mean z-score	-2.86
Structure conservation index	0.78
SVM decision value	2.10
SVM RNA-class probability	0.987868
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 18631110 100 + 20766785
UAGUCGCACACUGAGCCCACUGCUACGUGUGCUGGUUGAAGGACACGAAAGUGGGCCACGGCAUAAGCCAGGGAAGCAGGGCAGGUUGACGACACACAAA
..((((((.(((..((((..((((.(.((.(((.((((..((.(((....)))..)).))))...))))).)..)))))))).))))).))))....... ( -38.50)
>DroSec_CAF1 41738 97 + 1
UAGUCGCACACUGAGCCCACUGCUACGUGUGCUGGUUGAAGGACACGAAAGUGGGCCAGGACAUAAGCCAGGGAAGCAGGGCAGGUUGG---CACACAAA
..((((.((.(((.(((((((....(((((.((......)).)))))..)))))))))).......(((..(....)..)))..)))))---)....... ( -38.00)
>DroSim_CAF1 38140 96 + 1
UAGUCGCACACUGAGCCCACUGCUACGUGUGCUGGUUGAAGGACACGAAAGUGGGCCAGGACAUAAGCCAGGG-AGCAGGGCAGGUUGG---CACACAAA
..((((.((.(((.(((((((....(((((.((......)).)))))..)))))))))).......(((.(..-..)..)))..)))))---)....... ( -35.70)
>DroEre_CAF1 43900 92 + 1
UAGUCGCACACUGAGCCCACUGCUACGUGUGCUGCUUGAAGGACACGAAAGUGGGCCAGGACAUAAGCCAGGCAAA-----CAGGUUGG---CACACAAA
..(((.....(((.(((((((....(((((.((......)).)))))..)))))))))))))....(((((.(...-----..).))))---)....... ( -36.20)
>DroYak_CAF1 40676 92 + 1
UAGUCGCACACUGAGCCCACUGCUACGUGUGCUGGCUGAAGGACACGAAAGUGGGCCAGGACCUAAGCCAGGGAAA-----CAGGUUGG---CACACAAA
..(((.....(((.(((((((....(((((.((......)).)))))..))))))))))......((((..(....-----).))))))---)....... ( -35.40)
>consensus
UAGUCGCACACUGAGCCCACUGCUACGUGUGCUGGUUGAAGGACACGAAAGUGGGCCAGGACAUAAGCCAGGGAAGCAGGGCAGGUUGG___CACACAAA
..(((.....(((.(((((((....(((((.((......)).)))))..)))))))))))))...((((..............))))............. (-28.68 = -28.72 +   0.04)

alignment

secondary structure

dotplot

Window 2

Location	18,631,110 – 18,631,210
Length	100
Sequences	5
Columns	100
Reading direction	reverse
Mean pairwise identity	91.81
Mean single sequence MFE	-30.52
Consensus MFE	-25.94
Energy contribution	-25.98
Covariance contribution	0.04
Combinations/Pair	1.04
Mean z-score	-1.30
Structure conservation index	0.85
SVM decision value	0.18
SVM RNA-class probability	0.621682
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 18631110 100 - 20766785
UUUGUGUGUCGUCAACCUGCCCUGCUUCCCUGGCUUAUGCCGUGGCCCACUUUCGUGUCCUUCAACCAGCACACGUAGCAGUGGGCUCAGUGUGCGACUA
.......((((.((..(((............(((....)))..((((((((..(((((.((......)).)))))....)))))))))))..)))))).. ( -34.00)
>DroSec_CAF1 41738 97 - 1
UUUGUGUG---CCAACCUGCCCUGCUUCCCUGGCUUAUGUCCUGGCCCACUUUCGUGUCCUUCAACCAGCACACGUAGCAGUGGGCUCAGUGUGCGACUA
.(((..((---(((....((...)).....)))).......((((((((((..(((((.((......)).)))))....))))))).))).)..)))... ( -29.60)
>DroSim_CAF1 38140 96 - 1
UUUGUGUG---CCAACCUGCCCUGCU-CCCUGGCUUAUGUCCUGGCCCACUUUCGUGUCCUUCAACCAGCACACGUAGCAGUGGGCUCAGUGUGCGACUA
.(((..((---(((....((...)).-...)))).......((((((((((..(((((.((......)).)))))....))))))).))).)..)))... ( -30.20)
>DroEre_CAF1 43900 92 - 1
UUUGUGUG---CCAACCUG-----UUUGCCUGGCUUAUGUCCUGGCCCACUUUCGUGUCCUUCAAGCAGCACACGUAGCAGUGGGCUCAGUGUGCGACUA
.(((..((---(((..(..-----...)..)))).......((((((((((..(((((.((......)).)))))....))))))).))).)..)))... ( -29.50)
>DroYak_CAF1 40676 92 - 1
UUUGUGUG---CCAACCUG-----UUUCCCUGGCUUAGGUCCUGGCCCACUUUCGUGUCCUUCAGCCAGCACACGUAGCAGUGGGCUCAGUGUGCGACUA
...((.((---((((((((-----...(....)..))))).((((((((((..(((((.((......)).)))))....))))))).))))).))))).. ( -29.30)
>consensus
UUUGUGUG___CCAACCUGCCCUGCUUCCCUGGCUUAUGUCCUGGCCCACUUUCGUGUCCUUCAACCAGCACACGUAGCAGUGGGCUCAGUGUGCGACUA
.(((..(........................(((....)))((((((((((..(((((.((......)).)))))....))))))).))).)..)))... (-25.94 = -25.98 +   0.04)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:57:48 2006