Locus 3293

Sequence ID	2L_DroMel_CAF1
Location	9,532,628 – 9,532,740
Length	112
Max. P	0.850863

overview

Window 3

Location	9,532,628 – 9,532,740
Length	112
Sequences	5
Columns	119
Reading direction	forward
Mean pairwise identity	87.68
Mean single sequence MFE	-36.12
Consensus MFE	-27.51
Energy contribution	-28.22
Covariance contribution	0.71
Combinations/Pair	1.03
Mean z-score	-1.99
Structure conservation index	0.76
SVM decision value	0.79
SVM RNA-class probability	0.850863
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 9532628 112 + 22407834
AAGUGAGCAACUGUUACUGCUCUCACCCGGAUGGUUAUUGCGAUGACGA------CGAUGGCGACGCCAUCG-AAUCUUUUUUGCAUCUUGACGAGGGCAUAGCAGUUUCAUUAGCCCU
.(((((..((((((((.(((((((..(.((((((((((....)))))..------(((((((...)))))))-...........))))).)..))))))))))))))))))))...... ( -41.00)
>DroSec_CAF1 40014 110 + 1
AAGUGAGCAACUGUUACUGCUCUCACCCGGAUGGUUAUUGCGAUGA---------CGAUGGCGACGCCAUCGGAAUCUUUUUUGCAUCUUGACGAGGACAUAGCAGUUUCAUUAGCCCU
.(((((..((((((((.((..(((..(.(((((((....))(((..---------(((((((...)))))))..))).......))))).)..)))..)))))))))))))))...... ( -37.00)
>DroSim_CAF1 43162 98 + 1
AAGUGAGCAACUGUUACUACUCUCACCCGGAUGGUUA---------------------UGGCGACGCCAUCGGAAUCUUUUUUGCAUCUUGACGAGGGCAUAGCAGUUUCAUUAGCCCU
.(((((..((((((((...(((((..(.(((((...(---------------------((((...)))))(((((....)))))))))).)..)))))..)))))))))))))...... ( -26.50)
>DroEre_CAF1 43904 118 + 1
AAGUGAGCAACUGUUACUGCUCUCACCCGGAUGGUUAUUGUGAUGAUGACGAUGACGAUGACGACGCCAUUGGAAUCUU-UUUGCAUCUUGACGAGGGCAUAGCAGUUUCAUUAGCCCU
.(((((..((((((((.(((((((..(.(((((((((((.....))))))(((..(((((.......)))))..)))..-....))))).)..))))))))))))))))))))...... ( -39.30)
>DroYak_CAF1 47978 119 + 1
AAGUGAGCAACUGUUACUGCUCUCACCCGGAUGGUUAUUGCGAUGACGAUGAUGACGACGACGACGCCAUUGGAAUCUUUUUUGCAUCUUGACGAGGGCAUAGCAGUUUCAUUAACCCU
.(((((..((((((((.(((((((..(.(((((((....))(((..(((((.((.((....)).)).)))))..))).......))))).)..))))))))))))))))))))...... ( -36.80)
>consensus
AAGUGAGCAACUGUUACUGCUCUCACCCGGAUGGUUAUUGCGAUGA_GA______CGAUGGCGACGCCAUCGGAAUCUUUUUUGCAUCUUGACGAGGGCAUAGCAGUUUCAUUAGCCCU
.(((((..((((((((.(((((((..(.((((((((((((...............)))))))((..((...))..)).......))))).)..))))))))))))))))))))...... (-27.51 = -28.22 +   0.71)

alignment

secondary structure

dotplot

Window 4

Location	9,532,628 – 9,532,740
Length	112
Sequences	5
Columns	119
Reading direction	reverse
Mean pairwise identity	87.68
Mean single sequence MFE	-32.21
Consensus MFE	-24.02
Energy contribution	-23.34
Covariance contribution	-0.68
Combinations/Pair	1.22
Mean z-score	-1.52
Structure conservation index	0.75
SVM decision value	-0.04
SVM RNA-class probability	0.514962
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 9532628 112 - 22407834
AGGGCUAAUGAAACUGCUAUGCCCUCGUCAAGAUGCAAAAAAGAUU-CGAUGGCGUCGCCAUCG------UCGUCAUCGCAAUAACCAUCCGGGUGAGAGCAGUAACAGUUGCUCACUU
.((((...((..((((((..((((((.....))..........(((-((((((((.((....))------.)))))))).)))........))))...))))))..))...)))).... ( -36.10)
>DroSec_CAF1 40014 110 - 1
AGGGCUAAUGAAACUGCUAUGUCCUCGUCAAGAUGCAAAAAAGAUUCCGAUGGCGUCGCCAUCG---------UCAUCGCAAUAACCAUCCGGGUGAGAGCAGUAACAGUUGCUCACUU
.((((...((..((((((.....(((..(..((((.......(((..(((((((...)))))))---------..)))........))))..)..)))))))))..))...)))).... ( -36.96)
>DroSim_CAF1 43162 98 - 1
AGGGCUAAUGAAACUGCUAUGCCCUCGUCAAGAUGCAAAAAAGAUUCCGAUGGCGUCGCCA---------------------UAACCAUCCGGGUGAGAGUAGUAACAGUUGCUCACUU
.((((...((..((((((..((((((.....)).........(((....(((((...))))---------------------)....))).))))...))))))..))...)))).... ( -26.60)
>DroEre_CAF1 43904 118 - 1
AGGGCUAAUGAAACUGCUAUGCCCUCGUCAAGAUGCAAA-AAGAUUCCAAUGGCGUCGUCAUCGUCAUCGUCAUCAUCACAAUAACCAUCCGGGUGAGAGCAGUAACAGUUGCUCACUU
.((((...((..((((((..((((((.....))......-..(((..(.((((((.......)))))).)..)))................))))...))))))..))...)))).... ( -31.10)
>DroYak_CAF1 47978 119 - 1
AGGGUUAAUGAAACUGCUAUGCCCUCGUCAAGAUGCAAAAAAGAUUCCAAUGGCGUCGUCGUCGUCAUCAUCGUCAUCGCAAUAACCAUCCGGGUGAGAGCAGUAACAGUUGCUCACUU
.((((...((..((((((..((((((.....))(((......(((....((((((....))))))....)))......)))..........))))...))))))..))...)))).... ( -30.30)
>consensus
AGGGCUAAUGAAACUGCUAUGCCCUCGUCAAGAUGCAAAAAAGAUUCCGAUGGCGUCGCCAUCG______UC_UCAUCGCAAUAACCAUCCGGGUGAGAGCAGUAACAGUUGCUCACUU
.((((...((..((((((..((((((.....))................(((((...))))).............................))))...))))))..))...)))).... (-24.02 = -23.34 +  -0.68)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:49:07 2006