Locus 1808

Sequence ID	3R_DroMel_CAF1
Location	5,165,635 – 5,165,766
Length	131
Max. P	0.999980

overview

Window 7

Location	5,165,635 – 5,165,733
Length	98
Sequences	5
Columns	98
Reading direction	forward
Mean pairwise identity	92.65
Mean single sequence MFE	-24.22
Consensus MFE	-23.88
Energy contribution	-24.08
Covariance contribution	0.20
Combinations/Pair	1.00
Mean z-score	-2.61
Structure conservation index	0.99
SVM decision value	5.24
SVM RNA-class probability	0.999980
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 5165635 98 + 27905053
GCAGCCGUCGCUGUUGCGUGUCUGAUAUUUUAUUUUUAACGCUCAGCGACUUUAUACUACGUAGUAUUUAGUAUCGCUCGCUUUUAAGUUUGCCUUUG
(((((.(((((((..((((....((((...))))....)))).)))))))...((((((.........)))))).))).))................. ( -25.00)
>DroSec_CAF1 4238 98 + 1
GCAGCCGUCGCUGUUGCGUGUCUGAUAUUUUAUUUUUAACGCUCAGCGACUUUAUACUACGUAGUAUUUAGUAUCGCUCGCUUUUAAGUUUGCCCUUU
(((((.(((((((..((((....((((...))))....)))).)))))))...((((((.........)))))).))).))................. ( -25.00)
>DroSim_CAF1 4217 98 + 1
GCAGCCGUCGCUGUUGCGUGUCUGAUAUUUUAUUUUUAACGCUCAGCGACUUUAUACUACGUAGUAUUUAGUAUCGCUCGCUUUUAAGUUUGCCUUUU
(((((.(((((((..((((....((((...))))....)))).)))))))...((((((.........)))))).))).))................. ( -25.00)
>DroEre_CAF1 3897 84 + 1
GCAGCCGUCGCUGUUGCGUGUCUGAUAUUUUAUUUUUAACGCUCAGCGCCUUUAUACUACGUUGUAUUUAGUAUCGCUCGCUUU--------------
(((((.(.(((((..((((....((((...))))....)))).))))))((..((((......))))..))....))).))...-------------- ( -21.10)
>DroYak_CAF1 4266 98 + 1
GCAGCCGUCGCUGUUGCGUGUCUGAUAUUUUAUUUUUAACGCUCAGCGACUUUAUACUACGUUGUAUUUAGUAUCGCUCGCUUUUAAGUUUGCCUUUU
(((((.(((((((..((((....((((...))))....)))).)))))))...((((((.........)))))).))).))................. ( -25.00)
>consensus
GCAGCCGUCGCUGUUGCGUGUCUGAUAUUUUAUUUUUAACGCUCAGCGACUUUAUACUACGUAGUAUUUAGUAUCGCUCGCUUUUAAGUUUGCCUUUU
(((((.(((((((..((((....((((...))))....)))).)))))))...((((((.........)))))).))).))................. (-23.88 = -24.08 +   0.20)

alignment

secondary structure

dotplot

Window 8

Location	5,165,635 – 5,165,733
Length	98
Sequences	5
Columns	98
Reading direction	reverse
Mean pairwise identity	92.65
Mean single sequence MFE	-21.19
Consensus MFE	-20.79
Energy contribution	-20.99
Covariance contribution	0.20
Combinations/Pair	1.00
Mean z-score	-2.37
Structure conservation index	0.98
SVM decision value	4.68
SVM RNA-class probability	0.999938
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 5165635 98 - 27905053
CAAAGGCAAACUUAAAAGCGAGCGAUACUAAAUACUACGUAGUAUAAAGUCGCUGAGCGUUAAAAAUAAAAUAUCAGACACGCAACAGCGACGGCUGC
..(((.....)))....((.(((.((((((.........))))))...(((((((.((((...................))))..))))))).))))) ( -22.21)
>DroSec_CAF1 4238 98 - 1
AAAGGGCAAACUUAAAAGCGAGCGAUACUAAAUACUACGUAGUAUAAAGUCGCUGAGCGUUAAAAAUAAAAUAUCAGACACGCAACAGCGACGGCUGC
.(((......)))....((.(((.((((((.........))))))...(((((((.((((...................))))..))))))).))))) ( -22.41)
>DroSim_CAF1 4217 98 - 1
AAAAGGCAAACUUAAAAGCGAGCGAUACUAAAUACUACGUAGUAUAAAGUCGCUGAGCGUUAAAAAUAAAAUAUCAGACACGCAACAGCGACGGCUGC
..(((.....)))....((.(((.((((((.........))))))...(((((((.((((...................))))..))))))).))))) ( -22.21)
>DroEre_CAF1 3897 84 - 1
--------------AAAGCGAGCGAUACUAAAUACAACGUAGUAUAAAGGCGCUGAGCGUUAAAAAUAAAAUAUCAGACACGCAACAGCGACGGCUGC
--------------...((.(((.((((((.........))))))...(.(((((.((((...................))))..))))).).))))) ( -16.91)
>DroYak_CAF1 4266 98 - 1
AAAAGGCAAACUUAAAAGCGAGCGAUACUAAAUACAACGUAGUAUAAAGUCGCUGAGCGUUAAAAAUAAAAUAUCAGACACGCAACAGCGACGGCUGC
..(((.....)))....((.(((.((((((.........))))))...(((((((.((((...................))))..))))))).))))) ( -22.21)
>consensus
AAAAGGCAAACUUAAAAGCGAGCGAUACUAAAUACUACGUAGUAUAAAGUCGCUGAGCGUUAAAAAUAAAAUAUCAGACACGCAACAGCGACGGCUGC
.................((.(((.((((((.........))))))...(((((((.((((...................))))..))))))).))))) (-20.79 = -20.99 +   0.20)

alignment

secondary structure

dotplot

Window 9

Location	5,165,662 – 5,165,766
Length	104
Sequences	5
Columns	104
Reading direction	reverse
Mean pairwise identity	92.31
Mean single sequence MFE	-17.41
Consensus MFE	-14.14
Energy contribution	-14.37
Covariance contribution	0.23
Combinations/Pair	1.05
Mean z-score	-1.95
Structure conservation index	0.81
SVM decision value	1.33
SVM RNA-class probability	0.942892
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 5165662 104 - 27905053
AAGCAGAAAAGCUCCAAAAUUAUGCGAGACGUACAAAGGCAAACUUAAAAGCGAGCGAUACUAAAUACUACGUAGUAUAAAGUCGCUGAGCGUUAAAAAUAAAA
..........((((...............(((...(((.....)))....)))((((((.....(((((....)))))...))))))))))............. ( -17.40)
>DroSec_CAF1 4265 104 - 1
AAGCAGAAAAGCUCCAAAAUUAUGCGAGACGUAAAAGGGCAAACUUAAAAGCGAGCGAUACUAAAUACUACGUAGUAUAAAGUCGCUGAGCGUUAAAAAUAAAA
.(((......((((.....(((((.....)))))..))))..........((.((((((.....(((((....)))))...))))))..))))).......... ( -18.30)
>DroSim_CAF1 4244 104 - 1
AAGCAGAAAAGCUUCAAAAUUAUGCGAGACGUAAAAAGGCAAACUUAAAAGCGAGCGAUACUAAAUACUACGUAGUAUAAAGUCGCUGAGCGUUAAAAAUAAAA
((((......)))).....((((....(((((...(((.....)))...(((((.(.((((((.........))))))...))))))..)))))....)))).. ( -17.90)
>DroEre_CAF1 3924 90 - 1
AAGCAGAAAAUCUCCAAAAUUAUGCGAGACGUA--------------AAAGCGAGCGAUACUAAAUACAACGUAGUAUAAAGGCGCUGAGCGUUAAAAAUAAAA
..(((.................)))..(((((.--------------..((((....((((((.........)))))).....))))..))))).......... ( -16.13)
>DroYak_CAF1 4293 104 - 1
AAGCAGAAAAGCUCCAAAAUUAUGCGAGACGUAAAAAGGCAAACUUAAAAGCGAGCGAUACUAAAUACAACGUAGUAUAAAGUCGCUGAGCGUUAAAAAUAAAA
.(((......)))......((((....(((((...(((.....)))...(((((.(.((((((.........))))))...))))))..)))))....)))).. ( -17.30)
>consensus
AAGCAGAAAAGCUCCAAAAUUAUGCGAGACGUAAAAAGGCAAACUUAAAAGCGAGCGAUACUAAAUACUACGUAGUAUAAAGUCGCUGAGCGUUAAAAAUAAAA
..(((.................)))..(((((...(((.....)))...(((((...((((((.........))))))....)))))..))))).......... (-14.14 = -14.37 +   0.23)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:20:03 2006