Locus 1299

Sequence ID	2R_DroMel_CAF1
Location	5,059,021 – 5,059,184
Length	163
Max. P	0.999758

overview

Window 6

Location	5,059,021 – 5,059,112
Length	91
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	78.04
Mean single sequence MFE	-27.47
Consensus MFE	-20.10
Energy contribution	-20.85
Covariance contribution	0.75
Combinations/Pair	1.11
Mean z-score	-3.19
Structure conservation index	0.73
SVM decision value	4.02
SVM RNA-class probability	0.999758
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 5059021 91 - 20766785
AGGUAUGAAUGUCU----ACAUACGCGUACAUACCAUGGACGUAGUCUUGAUUACAUUUGUA-------------------------AUAAUUACAACUGAUUACACGCCCAAACCAAAU
.((((((.((((..----......)))).)))))).(((.(((.((...(((((...(((((-------------------------.....))))).)))))))))).)))........ ( -18.90)
>DroSec_CAF1 1876 91 - 1
AGGUAUGAAUGUGU----ACAUACGCGUACAUACCAUGGGCGUAGUCUUGAUUACAUUUGUA-------------------------AUAAUUACAUCUGAUUGCACGUCCAAAGCAAAU
.((((((.((((((----....)))))).)))))).(((((((((((.(((((((....)))-------------------------)).....))...))))..)))))))........ ( -27.10)
>DroSim_CAF1 1888 91 - 1
AGGUAUGAAUGUGU----ACAUACGCGUACAUACCAUGGGCGUAGUCUUGAUUACAUUUGUA-------------------------AUAAUUACAACUGAUUGCACGUCCAAAGCAAAU
.((((((.((((((----....)))))).)))))).(((((((.((...(((((...(((((-------------------------.....))))).))))))))))))))........ ( -27.60)
>DroEre_CAF1 1893 120 - 1
AGGUAUGAAUGUGUACGUACAUACGCGUACAUACCAUGGGCGUAGUAGUGAUUAGAUUGGUGGGUAUUAUGUACAUAUUUGUGUGGUACAAGUACAACUGAUUGCGUGCCAAAAGAAAAU
.((((((.(((((((......))))))).))))))...((((.....(..(((((.(((....((((((..((......))..)))))).....))))))))..).)))).......... ( -36.30)
>consensus
AGGUAUGAAUGUGU____ACAUACGCGUACAUACCAUGGGCGUAGUCUUGAUUACAUUUGUA_________________________AUAAUUACAACUGAUUGCACGCCCAAAGCAAAU
.((((((.((((((........)))))).)))))).((((((((((....))))).................................((((((....))))))...)))))........ (-20.10 = -20.85 +   0.75)

alignment

secondary structure

dotplot

Window 7

Location	5,059,054 – 5,059,152
Length	98
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	84.40
Mean single sequence MFE	-28.08
Consensus MFE	-23.73
Energy contribution	-24.35
Covariance contribution	0.62
Combinations/Pair	1.03
Mean z-score	-2.20
Structure conservation index	0.85
SVM decision value	1.48
SVM RNA-class probability	0.957320
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 5059054 98 - 20766785
AUGAAAACAGUACAACGCUGCAUUACACACAUGCCAGCUCAGGUAUGAAUGUCU----ACAUACGCGUACAUACCAUGGACGUAGUCUUGAUUACAUUUGUA------------------
......(((((.((..(((((((.......))).))))...((((((.((((..----......)))).)))))).)).))(((((....)))))...))).------------------ ( -21.60)
>DroSec_CAF1 1909 98 - 1
AUGAAAACAGUACAACGCUGCAUUACACACACGCCAGCUCAGGUAUGAAUGUGU----ACAUACGCGUACAUACCAUGGGCGUAGUCUUGAUUACAUUUGUA------------------
.......((((.....))))...((((.........(((((((((((.((((((----....)))))).)))))).)))))(((((....)))))...))))------------------ ( -28.30)
>DroSim_CAF1 1921 98 - 1
AUGAAAACAGUACAACGCUGCAUUACACACACGCCAGCUCAGGUAUGAAUGUGU----ACAUACGCGUACAUACCAUGGGCGUAGUCUUGAUUACAUUUGUA------------------
.......((((.....))))...((((.........(((((((((((.((((((----....)))))).)))))).)))))(((((....)))))...))))------------------ ( -28.30)
>DroEre_CAF1 1933 120 - 1
ACGAAAGCACUAAAACGCUGCAUUACACACACGCCAGCUCAGGUAUGAAUGUGUACGUACAUACGCGUACAUACCAUGGGCGUAGUAGUGAUUAGAUUGGUGGGUAUUAUGUACAUAUUU
.....(((........)))((((...((...((((((((((((((((.(((((((......))))))).)))))).))))).((((....))))...))))).))...))))........ ( -34.10)
>consensus
AUGAAAACAGUACAACGCUGCAUUACACACACGCCAGCUCAGGUAUGAAUGUGU____ACAUACGCGUACAUACCAUGGGCGUAGUCUUGAUUACAUUUGUA__________________
.........((((((.(((((....(......)...(((((((((((.((((((........)))))).)))))).)))))))))).)))..)))......................... (-23.73 = -24.35 +   0.62)

alignment

secondary structure

dotplot

Window 8

Location	5,059,076 – 5,059,184
Length	108
Sequences	3
Columns	108
Reading direction	reverse
Mean pairwise identity	96.30
Mean single sequence MFE	-22.92
Consensus MFE	-21.90
Energy contribution	-22.23
Covariance contribution	0.33
Combinations/Pair	1.00
Mean z-score	-2.16
Structure conservation index	0.96
SVM decision value	1.06
SVM RNA-class probability	0.909302
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 5059076 108 - 20766785
ACGUGCAGCCACAGAAGAACACACAAAAAUAAAUGAAAACAGUACAACGCUGCAUUACACACAUGCCAGCUCAGGUAUGAAUGUCUACAUACGCGUACAUACCAUGGA
..(((((((..............((........))......(.....))))))))..........(((.....((((((.((((........)))).)))))).))). ( -19.30)
>DroSec_CAF1 1931 108 - 1
ACGUGCAGCCACAUAAAAACACACAAAAAUAAAUGAAAACAGUACAACGCUGCAUUACACACACGCCAGCUCAGGUAUGAAUGUGUACAUACGCGUACAUACCAUGGG
..(((((((..............((........))......(.....))))))))..............((((((((((.((((((....)))))).)))))).)))) ( -24.40)
>DroSim_CAF1 1943 108 - 1
ACGUGCAGCCACAUGAAAACACACAAAAAUAAAUGAAAACAGUACAACGCUGCAUUACACACACGCCAGCUCAGGUAUGAAUGUGUACAUACGCGUACAUACCAUGGG
..(((((((..(((..................)))......(.....))))))))..............((((((((((.((((((....)))))).)))))).)))) ( -25.07)
>consensus
ACGUGCAGCCACAUAAAAACACACAAAAAUAAAUGAAAACAGUACAACGCUGCAUUACACACACGCCAGCUCAGGUAUGAAUGUGUACAUACGCGUACAUACCAUGGG
..(((((((..............((........))......(.....))))))))..........(((.....((((((.((((((....)))))).)))))).))). (-21.90 = -22.23 +   0.33)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:01:37 2006