Locus 6464

Sequence ID	3L_DroMel_CAF1
Location	17,238,061 – 17,238,170
Length	109
Max. P	0.999528

overview

Window 4

Location	17,238,061 – 17,238,170
Length	109
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	94.23
Mean single sequence MFE	-42.44
Consensus MFE	-39.60
Energy contribution	-39.60
Covariance contribution	0.00
Combinations/Pair	1.00
Mean z-score	-2.16
Structure conservation index	0.93
SVM decision value	3.60
SVM RNA-class probability	0.999438
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 17238061 109 + 23771897
-----------GUGGUUCCUGGUGCCCAGGAUCCCGGAGCAGUAGGUAGCCUGAUGCUUGGUUCUGUUGUGGCUUAUAGUCGCGUCUGAUUAAUGAACCGUGGCUAUGUAGCCGGAUUAA
-----------..((.((((((...)))))).))(.(((((.((((...)))).))))).)......(.(((((((((((((((((........))..)))))))))).))))).).... ( -40.10)
>DroSec_CAF1 122058 109 + 1
-----------GUGGCUCCUGGUGCCCAGGAUCCCGGAGCAGUAGGUAGCCUGAUGCUUGGUUUUGUUGUGGCUUAUAGUCGCGUCUGAUUAAUGAACCGUGGCUAUGUAGCCGGAUUAA
-----------..((((((((.(((((.(....).)).))).)))).))))................(.(((((((((((((((((........))..)))))))))).))))).).... ( -40.30)
>DroSim_CAF1 115936 109 + 1
-----------GUGGCUCCUGGUGCCCAGGAUCCCGGAGCAGUAGGUAGCCUGAUGCUUGGUUUUGUUGUGGCUUAUAGUCGCGUCUGAUUAAUGAACCGUGGCUAUGUAGCCGGAUUAA
-----------..((((((((.(((((.(....).)).))).)))).))))................(.(((((((((((((((((........))..)))))))))).))))).).... ( -40.30)
>DroEre_CAF1 125285 112 + 1
--------CUGGUGGCUCCUGGUGCCCAGGAUCCCGGAGCACUAGGUAGCCUGAUGCUUGGUUUUGUUGUGGCUUAUAGUCGCGUCUGAUUAAUGAACCGUGGCUAUGUAGCCGGAUUAA
--------.....((((((((((((((.(....).)).)))))))).))))................(.(((((((((((((((((........))..)))))))))).))))).).... ( -44.20)
>DroYak_CAF1 128507 120 + 1
GGCUGCUGCUGGUGGCUCCUGGUGCCCAGGAUCCCAGAGCAGUAGGUAGCCUGAUGCUUGGUUUUGUUGUGGCUUAUAGUCGCGUCUGAUUAAUGAACCGUGGCUAUGUAGCCGGAUUAA
.((((((.((((.((.((((((...))))))))))))))))))....((((........))))....(.(((((((((((((((((........))..)))))))))).))))).).... ( -47.30)
>consensus
___________GUGGCUCCUGGUGCCCAGGAUCCCGGAGCAGUAGGUAGCCUGAUGCUUGGUUUUGUUGUGGCUUAUAGUCGCGUCUGAUUAAUGAACCGUGGCUAUGUAGCCGGAUUAA
.............((.((((((...)))))).))(.(((((.((((...)))).))))).)......(.(((((((((((((((((........))..)))))))))).))))).).... (-39.60 = -39.60 +   0.00)

alignment

secondary structure

dotplot

Window 5

Location	17,238,061 – 17,238,170
Length	109
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	94.23
Mean single sequence MFE	-31.60
Consensus MFE	-29.22
Energy contribution	-29.26
Covariance contribution	0.04
Combinations/Pair	1.04
Mean z-score	-2.24
Structure conservation index	0.92
SVM decision value	3.69
SVM RNA-class probability	0.999528
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 17238061 109 - 23771897
UUAAUCCGGCUACAUAGCCACGGUUCAUUAAUCAGACGCGACUAUAAGCCACAACAGAACCAAGCAUCAGGCUACCUACUGCUCCGGGAUCCUGGGCACCAGGAACCAC-----------
.......((((....))))..(((((....................((((...................))))..((..(((.((((....)))))))..)))))))..----------- ( -27.51)
>DroSec_CAF1 122058 109 - 1
UUAAUCCGGCUACAUAGCCACGGUUCAUUAAUCAGACGCGACUAUAAGCCACAACAAAACCAAGCAUCAGGCUACCUACUGCUCCGGGAUCCUGGGCACCAGGAGCCAC-----------
.......((((..((((.(.((..............)).).)))).))))...................((((.(((..(((.((((....)))))))..)))))))..----------- ( -30.84)
>DroSim_CAF1 115936 109 - 1
UUAAUCCGGCUACAUAGCCACGGUUCAUUAAUCAGACGCGACUAUAAGCCACAACAAAACCAAGCAUCAGGCUACCUACUGCUCCGGGAUCCUGGGCACCAGGAGCCAC-----------
.......((((..((((.(.((..............)).).)))).))))...................((((.(((..(((.((((....)))))))..)))))))..----------- ( -30.84)
>DroEre_CAF1 125285 112 - 1
UUAAUCCGGCUACAUAGCCACGGUUCAUUAAUCAGACGCGACUAUAAGCCACAACAAAACCAAGCAUCAGGCUACCUAGUGCUCCGGGAUCCUGGGCACCAGGAGCCACCAG--------
.......((((....))))..(((..........((.((........................)).)).((((.(((.((((.((((....)))))))).))))))))))..-------- ( -34.76)
>DroYak_CAF1 128507 120 - 1
UUAAUCCGGCUACAUAGCCACGGUUCAUUAAUCAGACGCGACUAUAAGCCACAACAAAACCAAGCAUCAGGCUACCUACUGCUCUGGGAUCCUGGGCACCAGGAGCCACCAGCAGCAGCC
.......((((..((((.(.((..............)).).)))).))))............(((.....))).....(((((((((..((((((...))))))....)))).))))).. ( -34.04)
>consensus
UUAAUCCGGCUACAUAGCCACGGUUCAUUAAUCAGACGCGACUAUAAGCCACAACAAAACCAAGCAUCAGGCUACCUACUGCUCCGGGAUCCUGGGCACCAGGAGCCAC___________
.......((((..((((.(.((..............)).).)))).))))...................((((.(((..(((.((((....)))))))..)))))))............. (-29.22 = -29.26 +   0.04)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:19:58 2006