Locus 904

Sequence ID	3L_DroMel_CAF1
Location	2,730,423 – 2,730,538
Length	115
Max. P	0.998630

overview

Window 0

Location	2,730,423 – 2,730,538
Length	115
Sequences	5
Columns	115
Reading direction	forward
Mean pairwise identity	93.91
Mean single sequence MFE	-33.40
Consensus MFE	-31.02
Energy contribution	-30.46
Covariance contribution	-0.56
Combinations/Pair	1.11
Mean z-score	-2.01
Structure conservation index	0.93
SVM decision value	3.17
SVM RNA-class probability	0.998630
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 2730423 115 + 23771897
AUUCUCGAUGUGGUCAGCCGCAGAUGUAUAGAAAGCAAUGCCAAAUAAAGAUUCAACUAGAGAAGGACUUUUGCGGCUGGCCUGUAGCCUGUAAAUUAAUUACAUUUGGGCAAGG
...........(((((((((((((.((((........))))..........(((.....))).......)))))))))))))....((((((((.....))))....)))).... ( -30.40)
>DroSec_CAF1 90331 115 + 1
AUUCUCAACGUGGUCAGCCGCAGAUGUAUAGAAGGCAAUGCCAAAUAAAGAUUCAACUAGAGAAGGACUUUUGCGGCUGGCCUGUAGCCUGUAGAUUAAUUACAUUCGGGCAAGG
.......(((.(((((((((((((.((......(((...))).........(((.....)))....)).)))))))))))))))).(((((...............))))).... ( -36.56)
>DroSim_CAF1 88690 115 + 1
AUUUUCGACGUGGUCAGCCGCAGAUGUAUAGAAGGCAAUGCCAAAUAAAGAUUCAACUAGAGAAGGACUUUUGCGGCUGGCCUGUAGCCUGUAAAUUAAUUACAUUCGGGCCAGG
.......(((.(((((((((((((.((......(((...))).........(((.....)))....)).)))))))))))))))).(((((...............))))).... ( -35.76)
>DroEre_CAF1 98957 111 + 1
AUUCUCGACGUGGUCAGCCGCAGAUGUAUA----GCAAUGCCAAAUAAAGAUUCAACUAUAGAAGGACUUUUGCGGCUGGCCUGUAGCCUGUAAAUUAAUUACAUUUGGGCUAUG
...........(((((((((((((.((.((----....))((...((.((......)).))...)))).))))))))))))).(((((((((((.....))))....))))))). ( -34.00)
>DroYak_CAF1 92290 115 + 1
AUUCUCGACGUGGUCAGCCGCAGAUGUAUAGAAAGCAAUGCCAAAUAAAGAUUCAACUAUAGAAGGACUUUUGCGGCUGGCUUGUAGCCUGUAAAUUAAUUACAUUCGGGCAAAA
.......(((.((((((((((((((((.......)))...((...((.((......)).))...))...)))))))))))))))).(((((...............))))).... ( -30.26)
>consensus
AUUCUCGACGUGGUCAGCCGCAGAUGUAUAGAAAGCAAUGCCAAAUAAAGAUUCAACUAGAGAAGGACUUUUGCGGCUGGCCUGUAGCCUGUAAAUUAAUUACAUUCGGGCAAGG
.......(((.(((((((((((((.((((........))))..........(((.......))).....)))))))))))))))).(((((...............))))).... (-31.02 = -30.46 +  -0.56)

alignment

secondary structure

dotplot

Window 1

Location	2,730,423 – 2,730,538
Length	115
Sequences	5
Columns	115
Reading direction	reverse
Mean pairwise identity	93.91
Mean single sequence MFE	-27.94
Consensus MFE	-25.14
Energy contribution	-25.54
Covariance contribution	0.40
Combinations/Pair	1.00
Mean z-score	-1.58
Structure conservation index	0.90
SVM decision value	1.53
SVM RNA-class probability	0.962038
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 2730423 115 - 23771897
CCUUGCCCAAAUGUAAUUAAUUUACAGGCUACAGGCCAGCCGCAAAAGUCCUUCUCUAGUUGAAUCUUUAUUUGGCAUUGCUUUCUAUACAUCUGCGGCUGACCACAUCGAGAAU
.((((((....(((((.....))))))))....((.((((((((..((.......)).((..(((....)))..)).................)))))))).)).....)))... ( -27.80)
>DroSec_CAF1 90331 115 - 1
CCUUGCCCGAAUGUAAUUAAUCUACAGGCUACAGGCCAGCCGCAAAAGUCCUUCUCUAGUUGAAUCUUUAUUUGGCAUUGCCUUCUAUACAUCUGCGGCUGACCACGUUGAGAAU
.((((((....((((.......)))))))....((.((((((((((((...(((.......))).))))....(((...)))...........)))))))).)).....)))... ( -27.30)
>DroSim_CAF1 88690 115 - 1
CCUGGCCCGAAUGUAAUUAAUUUACAGGCUACAGGCCAGCCGCAAAAGUCCUUCUCUAGUUGAAUCUUUAUUUGGCAUUGCCUUCUAUACAUCUGCGGCUGACCACGUCGAAAAU
..(((((....(((((.....))))))))))..((.((((((((((((...(((.......))).))))....(((...)))...........)))))))).))........... ( -30.50)
>DroEre_CAF1 98957 111 - 1
CAUAGCCCAAAUGUAAUUAAUUUACAGGCUACAGGCCAGCCGCAAAAGUCCUUCUAUAGUUGAAUCUUUAUUUGGCAUUGC----UAUACAUCUGCGGCUGACCACGUCGAGAAU
..(((((....(((((.....))))))))))..((.((((((((..((.....))...((..(((....)))..)).....----........)))))))).))........... ( -29.90)
>DroYak_CAF1 92290 115 - 1
UUUUGCCCGAAUGUAAUUAAUUUACAGGCUACAAGCCAGCCGCAAAAGUCCUUCUAUAGUUGAAUCUUUAUUUGGCAUUGCUUUCUAUACAUCUGCGGCUGACCACGUCGAGAAU
.......(((.(((((.....)))))(((.....)))(((((((..((.....))...((..(((....)))..)).................))))))).......)))..... ( -24.20)
>consensus
CCUUGCCCGAAUGUAAUUAAUUUACAGGCUACAGGCCAGCCGCAAAAGUCCUUCUCUAGUUGAAUCUUUAUUUGGCAUUGCCUUCUAUACAUCUGCGGCUGACCACGUCGAGAAU
....(((....(((((.....))))))))....((.((((((((..((.....))...((..(((....)))..)).................)))))))).))........... (-25.14 = -25.54 +   0.40)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:54:03 2006