Locus 5796

Sequence ID	2R_DroMel_CAF1
Location	18,352,825 – 18,353,022
Length	197
Max. P	0.874656

overview

Window 1

Location	18,352,825 – 18,352,942
Length	117
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	90.72
Mean single sequence MFE	-31.47
Consensus MFE	-25.64
Energy contribution	-26.70
Covariance contribution	1.06
Combinations/Pair	1.12
Mean z-score	-1.50
Structure conservation index	0.81
SVM decision value	0.11
SVM RNA-class probability	0.587585
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 18352825 117 - 20766785
AUCAGAGGCUAAAUAAAGCGCCGGCAGUUAGCCAGGUGCUUUAUAUCAAUCGCCAGAGCCAAUUACAAUCACUUAGUUCCGGGCACUAGAUUGCUAUU---UUAUCAAAUGGCGAGGCGA
............(((((((((((((.....))).)))))))))).....(((((((.(((....((.........))....))).))...((((((((---(....)))))))))))))) ( -39.40)
>DroSim_CAF1 2676 117 - 1
AUCAGAGGCUAAAUAAAGCGCCGGCAGUCGGCCAGGUACUUUAUAUCAAUCGCCAGAGCCAAUUACAAUCACUUAGUUCCGGGCACUAGACUGCUAUU---UUAUCAAAUGGCGAAGCGA
.......(((..((((((..(((((.....))).))..)))))).....((((((..(((....((.........))....)))..(((....)))..---........))))))))).. ( -30.40)
>DroEre_CAF1 2521 117 - 1
AUCAGAGGCUAAAUAAAGCGCCGGCACUCAGCUGGGCACUUUAUAUCAAUCGCCAGAGCCAAUUACAAUCACUUGCUUCCGGGCACUAGACUGCCUUU---UUAUCAAAUGGCAAAGCGA
.......(((..((((((.((((((.....))).))).)))))).......((((((((...............))))..(((((......)))))..---........))))..))).. ( -28.96)
>DroYak_CAF1 2881 120 - 1
AUCAGAGGCUAAAUAAACCGCCGGCAGUCAGCUAGACACUUUAUAUCAAUCGCCAGUGCCAAUUACAAUCACUUGGUUCCGGGCACUAGACUGCCUUUUUUUUAUCAAAUGGCAAAGCGA
....(((((..........)))(((((((.((...................)).((((((.....(((....)))......)))))).))))))).........)).............. ( -27.11)
>consensus
AUCAGAGGCUAAAUAAAGCGCCGGCAGUCAGCCAGGCACUUUAUAUCAAUCGCCAGAGCCAAUUACAAUCACUUAGUUCCGGGCACUAGACUGCCAUU___UUAUCAAAUGGCAAAGCGA
.......(((..((((((.((((((.....))).))).)))))).....(((((((((((((..........)))))))..((((......))))..............))))))))).. (-25.64 = -26.70 +   1.06)

alignment

secondary structure

dotplot

Window 2

Location	18,352,902 – 18,353,022
Length	120
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	90.00
Mean single sequence MFE	-33.45
Consensus MFE	-25.76
Energy contribution	-27.32
Covariance contribution	1.56
Combinations/Pair	1.09
Mean z-score	-2.24
Structure conservation index	0.77
SVM decision value	0.89
SVM RNA-class probability	0.874656
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 18352902 120 - 20766785
AAUAACUCACAGUCUCGUGGGAGCAAUAGUUGUGUACAAAUACAAACAAUAACAAUGACGGGUGCGAAUCGUUUGCUCUUAUCAGAGGCUAAAUAAAGCGCCGGCAGUUAGCCAGGUGCU
..........(((((((((((((((....((((((....))))))...........(((((.......))))))))))))))..))))))......(((((((((.....))).)))))) ( -37.60)
>DroSim_CAF1 2753 115 - 1
AAUAACUCACAGCCUCGUGCGAGCAAUAG-----UAUAAAUACAAACAAUAACAAUGACGGGUGCAAAUCGUUUGCUCUUAUCAGAGGCUAAAUAAAGCGCCGGCAGUCGGCCAGGUACU
..........((((((((((........)-----)))..................(((..((.((((.....)))).))..)))))))))......((..(((((.....))).))..)) ( -30.20)
>DroEre_CAF1 2598 120 - 1
AAUAAUUCACAGCCUCGUGGGAGCAAUAGUUGAGUAUAAAUACAAACAAUAACAAUGACAGGUGCGAAUCGUUUGCUCUUAUCAGAGGCUAAAUAAAGCGCCGGCACUCAGCUGGGCACU
..........((((((((((((((((..(((..(((....))).))).............(((....)))..))))))))))..)))))).......((.(((((.....)))))))... ( -35.00)
>DroYak_CAF1 2961 120 - 1
AAUAAUUCACAGCCUCGUGGGAGCAAUAGUUGUGUGCAAAUACAAACAAUAACAAUGACGGUUGCGAAUCGUUUGCUCUUAUCAGAGGCUAAAUAAACCGCCGGCAGUCAGCUAGACACU
..........(((((((((((((((....((((((....))))))...........((((((.....)))))))))))))))..))))))................(((.....)))... ( -31.00)
>consensus
AAUAACUCACAGCCUCGUGGGAGCAAUAGUUGUGUACAAAUACAAACAAUAACAAUGACGGGUGCGAAUCGUUUGCUCUUAUCAGAGGCUAAAUAAAGCGCCGGCAGUCAGCCAGGCACU
..........(((((((((((((((....((((((....))))))...........(((((.......))))))))))))))..)))))).........((((((.....))).)))... (-25.76 = -27.32 +   1.56)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:54:35 2006