Locus 10134

Sequence ID	3R_DroMel_CAF1
Location	27,186,550 – 27,186,680
Length	130
Max. P	0.835813

overview

Window 1

Location	27,186,550 – 27,186,640
Length	90
Sequences	6
Columns	91
Reading direction	forward
Mean pairwise identity	80.73
Mean single sequence MFE	-25.13
Consensus MFE	-16.51
Energy contribution	-16.10
Covariance contribution	-0.41
Combinations/Pair	1.18
Mean z-score	-2.07
Structure conservation index	0.66
SVM decision value	0.73
SVM RNA-class probability	0.835813
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 27186550 90 + 27905053
AAUUUUGGAAUAUGAAUGUGGAUUUCCGAACU-UCAGAAUGAUGUCCAGCAUGAGCAUGGGUGACUUUAUCUCGCCCACUGGCUCCAAUCU
....(((((...((((..(((....)))...)-)))........)))))...((((.(((((((.......)))))))...))))...... ( -24.00)
>DroPse_CAF1 156 87 + 1
GGAUUCGAAGUAAGAGUAUCACUUUCU---UU-AUAGAAUGAUGUCUAGCAUGAGCAUGGGUGACUUCAUCUCGCCCACUGGUUCGAAUCU
(((((((((((.(((.(((((..((((---..-..)))))))))))).)).....(((((((((.......))))))).)).))))))))) ( -28.40)
>DroSec_CAF1 162 89 + 1
AAUUUGGG-AAAUUAAUGUAAAUUUCUCAACU-UCAGAAUGAUGUCCAGCAUGAGCAUGGGUGACUUUAUCUCGCCCACUGGCUCCAAUCU
...(((((-(((((......))))))))))..-..(((.(((((.....)))((((.(((((((.......)))))))...)))))).))) ( -25.70)
>DroSim_CAF1 174 89 + 1
AAUUUGGG-AGAUGAAUGUGGAUUUUCCAACU-UCAGAAUGAUGUCCAGCAUGAGCAUGGGUGACUUUAUCUCGCCCACUGGCUCCAAUCU
...(((((-((((........)))))))))..-..(((.(((((.....)))((((.(((((((.......)))))))...)))))).))) ( -25.00)
>DroEre_CAF1 171 89 + 1
AAUGUGGG-AAAUGUAUGUGGAUUAUCCAACU-UCAGAAUGAUGUCCAGCAUGAGCAUGGGUGACUUUAUCUCGCCCACUGGCUCCAAUCU
.((((.((-(..((....(((.....)))...-.))........))).))))((((.(((((((.......)))))))...))))...... ( -24.60)
>DroWil_CAF1 193 88 + 1
--UGUGGA-GACUAUAUAUGCAUUUUUCGUUUGCCAGAAUGAUGUCAAGCAUGAGUAUGGGUGAUUUUAUCUCACCCACUGGCUCAAAUCU
--((((..-..).......(((((.(((........))).)))))...)))(((((.(((((((.......)))))))...)))))..... ( -23.10)
>consensus
AAUUUGGG_AAAUGAAUGUGGAUUUCCCAACU_UCAGAAUGAUGUCCAGCAUGAGCAUGGGUGACUUUAUCUCGCCCACUGGCUCCAAUCU
...................................(((...(((.....)))((((.(((((((.......)))))))...))))...))) (-16.51 = -16.10 +  -0.41)

alignment

secondary structure

dotplot

Window 2

Location	27,186,572 – 27,186,680
Length	108
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	76.05
Mean single sequence MFE	-35.45
Consensus MFE	-21.38
Energy contribution	-21.52
Covariance contribution	0.14
Combinations/Pair	1.23
Mean z-score	-1.67
Structure conservation index	0.60
SVM decision value	0.71
SVM RNA-class probability	0.829761
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 27186572 108 - 27905053
CUCGUGGGACACCCGCAGAGCUGAGUUUUCCAAAGGACUCAGAUUGGAGCCAGUGGGCGAGAUAAAGUCACCCAUGCUCAUGCUGGACAUCAUUCUGA-AGUUCG----------GAAA-
((((((((...))))).)))((((((((......))))))))....((((..(((((.((.......)).)))))))))...((((((.((.....))-.)))))----------)...- ( -38.30)
>DroVir_CAF1 203 119 - 1
CUCGUGCGAAACGCGUAACGCUGAAUUCUCCAAGGGACUCAGAUUGGAGCCCGUAGGUGAGAUAAAGUCGCCCAUGCUCAUGCUGGACAUCAUGCUGC-AGAAGAUAAAACAUGGGAGAG
..((((((.....))).)))......(((((..(((.(((......))))))(((((((((((...)))(.(((.((....))))).).)))).))))-...............))))). ( -31.10)
>DroGri_CAF1 290 118 - 1
CUCGUGGGAAACGCGCAAUGCUGAGUUCUCCAAUGGACUUAGAUUGGAGCCAGUGGGUGAGAUAAAAUCGCCCAUGCUCAUGCUAGACAUCAUGCUGG-GAAUAAUAAGAGAUGAAAGA-
((((((.....))).((((.((((((((......))))))))))))((((..((((((((.......)))))))))))).(.((((.(.....)))))-.).......)))........- ( -37.60)
>DroWil_CAF1 212 109 - 1
CUCAUGCGAUACACGUAACGCUGAGUUCUCCAAUGGACUCAGAUUUGAGCCAGUGGGUGAGAUAAAAUCACCCAUACUCAUGCUUGACAUCAUUCUGGCAAACGA----------AAAA-
.(((((((.....))))...((((((((......))))))))...)))((((((((((((.......)))))))...(((....))).......)))))......----------....- ( -34.10)
>DroMoj_CAF1 202 119 - 1
CUCAUGCGAAACGCGCAGCGUCGAGUUCUCCAAGGGGCUCAGAUUGGAGCCGGUGGGCGAGAUAAAGUCACCCAUGCUCAUGCUAGACAUCAUGCUGC-GAGCGAUCAAAGAAACGAGAU
(((..(((...)))(((((((.(((((((....)))))))((....((((..(((((.((.......)).)))))))))...)).......)))))))-................))).. ( -37.50)
>DroAna_CAF1 13 102 - 1
CUCAUGGGAAACUCUCAGAGCGGAGUUCUCCAAGGGACUUAGAUUGGAGCCCGUGGGCGAAAUAAAGUCACCCAUGCUCAUGCUGGACAUCAUUCUA---G---G-----------CGA-
(((.(((..((((((......))))))..))).))).((((((.((..(.(((((((.((.......)).)))))((....)).)).)..)).))))---)---)-----------...- ( -34.10)
>consensus
CUCAUGCGAAACGCGCAACGCUGAGUUCUCCAAGGGACUCAGAUUGGAGCCAGUGGGCGAGAUAAAGUCACCCAUGCUCAUGCUGGACAUCAUGCUGC_AAACGA__________GAGA_
..............(((...((((((((......))))))))....((((..(((((.((.......)).))))))))).)))..................................... (-21.38 = -21.52 +   0.14)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:49:38 2006