Locus 181

Sequence ID	4_DroMel_CAF1
Location	1,106,838 – 1,106,984
Length	146
Max. P	0.909450

overview

Window 2

Location	1,106,838 – 1,106,944
Length	106
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	86.93
Mean single sequence MFE	-26.40
Consensus MFE	-26.39
Energy contribution	-26.32
Covariance contribution	-0.06
Combinations/Pair	1.12
Mean z-score	-1.48
Structure conservation index	1.00
SVM decision value	0.95
SVM RNA-class probability	0.888378
Prediction	RNA

Download alignment: ClustalW | MAF

>4_DroMel_CAF1 1106838 106 - 1281640
UGCAAGCCAACCGAGACAGCUUUUCCGCCGUUUCUUUUGGUUGUUUUUGGCUGCU------AGGUACUGGAAAUGCUACUGCUGUAUAUAUUAUGUUAUGUACUAUU--------UAUUU
.(((((((((..(((((.((......)).)))))..)))))).....((((..((------((...))))....)))).))).(((((((......)))))))....--------..... ( -26.30)
>DroSec_CAF1 19682 112 - 1
UGCAAGCCAACCGAGACUGCUUUUCCGCCGUUUCUUUUGGUUGUUUUUGGCUGCUAACUCUAGGUACUGAAAAUGCCACUGCUGUAUAUAUUAUGUUUUGUGCUAUA--------UAUUU
.(((((((((..(((((.((......)).)))))..))))))(((((..(.((((.......)))))..))))).....))).(((((((.(((.....))).))))--------))).. ( -25.80)
>DroEre_CAF1 19996 120 - 1
UGCAAGCCAACCGAGACAGCUUUUCCGCCGUUUCUUUUGGUUGUUUUUGGCUACUAGCUCUAGGUACUGGAAAUGCCAUUGCUGUAUUUAUUAUGUUAUAUACUGUAACUAUCUUUGUUA
.((.((((((..(((((.((......)).)))))..))))))(((((..(.((((.......)))))..)))))))..((((.((((.((......)).)))).))))............ ( -26.30)
>DroYak_CAF1 11022 112 - 1
UGCAAGCCAACCGAGACAGCUUUUCCGCCGUUUCUUUUGGUUGUUUUUGGCUGCUAGCUCUAGGUACUGGAAAUGCCAUUGCUGUAUCUAUUAUGUUAUAUACUGCA--------UAUUU
.((.((((((..(((((.((......)).)))))..))))))(((((..(.((((.......)))))..)))))))...(((.((((.((......)).)))).)))--------..... ( -27.20)
>consensus
UGCAAGCCAACCGAGACAGCUUUUCCGCCGUUUCUUUUGGUUGUUUUUGGCUGCUAGCUCUAGGUACUGGAAAUGCCACUGCUGUAUAUAUUAUGUUAUAUACUAUA________UAUUU
.(((((((((..(((((.((......)).)))))..))))))(((((..(.((((.......)))))..))))).....))).(((((((......)))))))................. (-26.39 = -26.32 +  -0.06)

alignment

secondary structure

dotplot

Window 3

Location	1,106,870 – 1,106,984
Length	114
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	95.00
Mean single sequence MFE	-36.08
Consensus MFE	-33.38
Energy contribution	-33.25
Covariance contribution	-0.12
Combinations/Pair	1.06
Mean z-score	-1.94
Structure conservation index	0.93
SVM decision value	1.06
SVM RNA-class probability	0.909450
Prediction	RNA

Download alignment: ClustalW | MAF

>4_DroMel_CAF1 1106870 114 - 1281640
AAUUCGGUAUUUCAAUCGUGGCUCGUGGCUUUUCACGGUCUGCAAGCCAACCGAGACAGCUUUUCCGCCGUUUCUUUUGGUUGUUUUUGGCUGCU------AGGUACUGGAAAUGCUACU
.....((((((((...(.((((.(((((....)))))(((.((((.((((..(((((.((......)).)))))..))))))))....))).)))------).).....))))))))... ( -34.70)
>DroSec_CAF1 19714 120 - 1
AAUUCGGUAUUUCAAUCGUGGCUCGUGGCUUUUCACGGUCUGCAAGCCAACCGAGACUGCUUUUCCGCCGUUUCUUUUGGUUGUUUUUGGCUGCUAACUCUAGGUACUGAAAAUGCCACU
....((((......))))......((((((((((((((((.((((.((((..(((((.((......)).)))))..))))))))....)))))(((....)))....)))))).))))). ( -34.10)
>DroEre_CAF1 20036 120 - 1
AAUUCGGUAUUUCAAUCGUGGCUCGUGGCUUUUCACGGUCUGCAAGCCAACCGAGACAGCUUUUCCGCCGUUUCUUUUGGUUGUUUUUGGCUACUAGCUCUAGGUACUGGAAAUGCCAUU
.....((((((((.(((..((((.((((((....((.(....).((((((..(((((.((......)).)))))..))))))))....)))))).))))...)))....))))))))... ( -37.70)
>DroYak_CAF1 11054 120 - 1
AAUUCGGUAUUUCAAUCGUGGCUCGUGGCUUUUCACGGUCUGCAAGCCAACCGAGACAGCUUUUCCGCCGUUUCUUUUGGUUGUUUUUGGCUGCUAGCUCUAGGUACUGGAAAUGCCAUU
.....((((((((....(((.((.(.((((.....(((((.((((.((((..(((((.((......)).)))))..))))))))....)))))..))))).)).)))..))))))))... ( -37.80)
>consensus
AAUUCGGUAUUUCAAUCGUGGCUCGUGGCUUUUCACGGUCUGCAAGCCAACCGAGACAGCUUUUCCGCCGUUUCUUUUGGUUGUUUUUGGCUGCUAGCUCUAGGUACUGGAAAUGCCACU
.....((((((((....(..(..(((((....)))))..)..).((((((..(((((.((......)).)))))..))))))......((.((((.......)))))).))))))))... (-33.38 = -33.25 +  -0.12)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:38:29 2006