Locus 6137

Sequence ID	3L_DroMel_CAF1
Location	16,253,804 – 16,253,948
Length	144
Max. P	0.989568

overview

Window 8

Location	16,253,804 – 16,253,910
Length	106
Sequences	6
Columns	116
Reading direction	reverse
Mean pairwise identity	87.05
Mean single sequence MFE	-25.50
Consensus MFE	-21.69
Energy contribution	-22.00
Covariance contribution	0.31
Combinations/Pair	1.14
Mean z-score	-1.81
Structure conservation index	0.85
SVM decision value	0.42
SVM RNA-class probability	0.728181
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 16253804 106 - 23771897
AAACAAAGGCAGCUACAAAUGCCAAAAAAGCUUCGUCUUGGCCUGCACUCAAAGUGUUGGCCCAAAGCCGUUCACCAAGAGCCAAAAGAAGACCUGAACAGAG----------UGG
.......((((........)))).......(((((..((((((.((((.....)))).)).))))..).((((.....)))).....))))............----------... ( -26.00)
>DroSec_CAF1 5299 105 - 1
AAACAAAGGCAGCCACAAAUGCCAAAAAAGCUUCGUCUUGGCCUGCACUCA-AGUGUUGGCCCAAAGCCGUUCACAAAGAGCCAAAAGAAGACCUGAACAGAG----------UGG
.......((((........)))).......(((((..((((((.((((...-.)))).)).))))..).((((.....)))).....))))............----------... ( -26.00)
>DroSim_CAF1 3708 105 - 1
AAACAAAGGCAGCCACAAAUGCCAAAAAAGCUUCGUCUUGGCCUGCACUCA-AGUGUUGGCCCAAAGCCGUUCACAAAGAGCCAAAAGAAGACCUGAACAGAG----------UGG
.......((((........)))).......(((((..((((((.((((...-.)))).)).))))..).((((.....)))).....))))............----------... ( -26.00)
>DroEre_CAF1 5257 102 - 1
AAACAAAGGCAGCA--AAAUGCCAA-AAAGCUUCGUCUUGGCCUGCACUCA-AGUGUUGGCUCAAAGCCGUUCACAAAGAGCCAAAAGAAGACCUGAAAAGAG----------UGG
.......((((...--...))))..-....(((((..((((((.((((...-.)))).))).)))..).((((.....)))).....))))((((....)).)----------).. ( -27.90)
>DroYak_CAF1 7111 102 - 1
AAACAAAGGCAGCU--AAAUGCCAA-AAAGCUUCGUCUUGGCCUGCACUCA-AGUGUUGGCUCAAAGCCGUUCACAAAGAGCCAAAAGAAGACCUAAAAAGAG----------UGG
.......((((...--...))))..-....(((((..((((((.((((...-.)))).))).)))..).((((.....)))).....))))............----------... ( -26.20)
>DroAna_CAF1 3918 106 - 1
AAACAAAGGCAACA--AAAUGCCAA-AAAGCUUCGUCUUGGCCUGCACUCA-AGCGUUGGCUUAAA--CAUUCAC----AGCCAAAAAGUAGCAUCAAAAGAGACAGAAAUAGGGG
.......((((...--...))))..-.....((((((((....((((((..-....((((((....--.......----))))))..))).)))......))))).)))....... ( -20.90)
>consensus
AAACAAAGGCAGCA__AAAUGCCAA_AAAGCUUCGUCUUGGCCUGCACUCA_AGUGUUGGCCCAAAGCCGUUCACAAAGAGCCAAAAGAAGACCUGAAAAGAG__________UGG
.......((((........))))...........(((((((((.((((.....)))).)))).......((((.....))))......)))))....................... (-21.69 = -22.00 +   0.31)

alignment

secondary structure

dotplot

Window 9

Location	16,253,830 – 16,253,948
Length	118
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	90.69
Mean single sequence MFE	-27.18
Consensus MFE	-23.74
Energy contribution	-23.71
Covariance contribution	-0.03
Combinations/Pair	1.12
Mean z-score	-2.68
Structure conservation index	0.87
SVM decision value	2.17
SVM RNA-class probability	0.989568
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 16253830 118 - 23771897
ACCGCUUUGUUAAGCCACCAG--AAAUAAACAAAGUAAAUAAACAAAGGCAGCUACAAAUGCCAAAAAAGCUUCGUCUUGGCCUGCACUCAAAGUGUUGGCCCAAAGCCGUUCACCAAGA
((.((((((..((((......--...........((......))...((((........))))......))))......((((.((((.....)))).)))))))))).))......... ( -27.70)
>DroSec_CAF1 5325 117 - 1
ACCGCUUUGUUAAGCCACCAG--AAAUAAACAAAGUAAAUAAACAAAGGCAGCCACAAAUGCCAAAAAAGCUUCGUCUUGGCCUGCACUCA-AGUGUUGGCCCAAAGCCGUUCACAAAGA
((.((((((..((((......--...........((......))...((((........))))......))))......((((.((((...-.)))).)))))))))).))......... ( -27.70)
>DroSim_CAF1 3734 117 - 1
ACCGCUUUGUUAAGCCACCAG--AAAUAAACAAAGUAAAUAAACAAAGGCAGCCACAAAUGCCAAAAAAGCUUCGUCUUGGCCUGCACUCA-AGUGUUGGCCCAAAGCCGUUCACAAAGA
((.((((((..((((......--...........((......))...((((........))))......))))......((((.((((...-.)))).)))))))))).))......... ( -27.70)
>DroEre_CAF1 5283 114 - 1
ACCGCUUUGUUAAGCCAUCAG--AAACAAACAAAGUAAACAAACAAAGGCAGCA--AAAUGCCAA-AAAGCUUCGUCUUGGCCUGCACUCA-AGUGUUGGCUCAAAGCCGUUCACAAAGA
....((((((.((((......--...........((......))...((((...--...))))..-...)))).(..((((((.((((...-.)))).))).)))..).....)))))). ( -26.30)
>DroYak_CAF1 7137 114 - 1
ACCGCUUUGUUAAGCCACCAG--AAAUAAACAAAGUAAAUAAACAAAGGCAGCU--AAAUGCCAA-AAAGCUUCGUCUUGGCCUGCACUCA-AGUGUUGGCUCAAAGCCGUUCACAAAGA
....((((((.((((......--...........((......))...((((...--...))))..-...)))).(..((((((.((((...-.)))).))).)))..).....)))))). ( -26.30)
>DroAna_CAF1 3954 110 - 1
ACAGCUUUGUUGAGUCAACUGACAAACAAACAAAGCAAAUAAACAAAGGCAACA--AAAUGCCAA-AAAGCUUCGUCUUGGCCUGCACUCA-AGCGUUGGCUUAAA--CAUUCAC----A
...((((((((..(((....))).....))))))))...........((((...--...))))..-.(((((.((.(((((.......)))-))))..)))))...--.......----. ( -27.40)
>consensus
ACCGCUUUGUUAAGCCACCAG__AAAUAAACAAAGUAAAUAAACAAAGGCAGCA__AAAUGCCAA_AAAGCUUCGUCUUGGCCUGCACUCA_AGUGUUGGCCCAAAGCCGUUCACAAAGA
...((((((((.................))))))))...........((((........))))......((((.(....((((.((((.....)))).))))).))))............ (-23.74 = -23.71 +  -0.03)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:11:02 2006