Locus 4750

Sequence ID	3L_DroMel_CAF1
Location	13,362,909 – 13,363,016
Length	107
Max. P	0.620631

overview

Window 7

Location	13,362,909 – 13,363,016
Length	107
Sequences	6
Columns	107
Reading direction	forward
Mean pairwise identity	80.86
Mean single sequence MFE	-30.32
Consensus MFE	-16.26
Energy contribution	-16.48
Covariance contribution	0.23
Combinations/Pair	1.33
Mean z-score	-2.19
Structure conservation index	0.54
SVM decision value	0.18
SVM RNA-class probability	0.620631
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13362909 107 + 23771897
UUCAUACCUUUAUUAAGAAACAGAAACUCACCUGGCGAUCACUGCCACCGGUAGCAAAUUUGUCGCCAUCGCGACUGAAUGCCACCGCAUUCACCGCAUCAGUGUGG
..(((((.........................(((((((..(((((...))))).......)))))))..(((..(((((((....))))))).)))....))))). ( -29.40)
>DroSec_CAF1 34403 107 + 1
UUCAUACCUUCAUAAAGAAACAGAAACUCACCUGGCGAUCACUACCACCGGUAGCAAACUUGUCGCCAUCGUGACUGAAUGCCACCGCAUUCACCGCAUCAGUGUGG
...........................((((.(((((((..(((((...))))).......)))))))..)))).(((((((....)))))))(((((....))))) ( -28.90)
>DroSim_CAF1 34328 107 + 1
UCCAUACCUUCAUAAAGAAACAGAAACUCACCUGGCGAUCACUACCACCGGUAGCAAACUUGUCGCCAUCGUGACUGAAUGCCACCGCAUUUACCGCAUCAGUGUGG
.((((((....................((((.(((((((..(((((...))))).......)))))))..)))).(((((((....)))))))........)))))) ( -28.40)
>DroEre_CAF1 34928 106 + 1
UGCGCACA-UUAUCAAGAGACAGAAACUCACCUGACGAUCACUACCACCGGUGGCAAACUUGUCGCCAUCGCGACUGAAUGCCACCGCAUUGACCGCAUCAGUGUGG
..(((((.-.......(((.......)))...((.((.(((.......((((((((.....(((((....)))))....))))))))...))).))))...))))). ( -32.70)
>DroYak_CAF1 35807 99 + 1
AA-------CAAUCAAGAAACA-AAACUCACCUGACGAUCACUGCCACCGGUGGCAAACUUGUCGCCAUCGCGACUGAAUGCCACCGCAUUGACCGCAUCAGUGUGG
..-------.............-.....(((((((((.(((.(((....(((((((.....(((((....)))))....)))))))))).))).))..)))).))). ( -33.70)
>DroPer_CAF1 9688 103 + 1
GCCAU----UGGAUGAGCCGCCCCAACUCACCUGGCGAUCGUUGCCACCAGUGGCAAACUUCUCUCCAUCCUGGGAAAAGCCCACAGCAUUUACAGCCGCCGUAUGG
(((((----(((.((((.........))))..((((((...))))))))))))))..........((((.(((((.....))))..((.......))....).)))) ( -28.80)
>consensus
UCCAUACC_UCAUAAAGAAACAGAAACUCACCUGGCGAUCACUACCACCGGUAGCAAACUUGUCGCCAUCGCGACUGAAUGCCACCGCAUUCACCGCAUCAGUGUGG
............................(((((((.......(((.....)))((......(((((....)))))(((((((....)))))))..)).)))).))). (-16.26 = -16.48 +   0.23)

alignment

secondary structure

dotplot

Window 8

Location	13,362,909 – 13,363,016
Length	107
Sequences	6
Columns	107
Reading direction	reverse
Mean pairwise identity	80.86
Mean single sequence MFE	-36.47
Consensus MFE	-24.93
Energy contribution	-23.38
Covariance contribution	-1.55
Combinations/Pair	1.40
Mean z-score	-1.38
Structure conservation index	0.68
SVM decision value	0.12
SVM RNA-class probability	0.592917
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13362909 107 - 23771897
CCACACUGAUGCGGUGAAUGCGGUGGCAUUCAGUCGCGAUGGCGACAAAUUUGCUACCGGUGGCAGUGAUCGCCAGGUGAGUUUCUGUUUCUUAAUAAAGGUAUGAA
...((((..((((((((((((....))))))).))))).((((((((...((((((....)))))))).))))))))))...(((....((((....))))...))) ( -34.80)
>DroSec_CAF1 34403 107 - 1
CCACACUGAUGCGGUGAAUGCGGUGGCAUUCAGUCACGAUGGCGACAAGUUUGCUACCGGUGGUAGUGAUCGCCAGGUGAGUUUCUGUUUCUUUAUGAAGGUAUGAA
.((.(((...(((((((((((....))))))).((((..((((((.....(..(((((...)))))..))))))).))))....))))(((.....)))))).)).. ( -33.90)
>DroSim_CAF1 34328 107 - 1
CCACACUGAUGCGGUAAAUGCGGUGGCAUUCAGUCACGAUGGCGACAAGUUUGCUACCGGUGGUAGUGAUCGCCAGGUGAGUUUCUGUUUCUUUAUGAAGGUAUGGA
(((.(((...((((..(((((....)))))...((((..((((((.....(..(((((...)))))..))))))).))))....))))(((.....)))))).))). ( -31.80)
>DroEre_CAF1 34928 106 - 1
CCACACUGAUGCGGUCAAUGCGGUGGCAUUCAGUCGCGAUGGCGACAAGUUUGCCACCGGUGGUAGUGAUCGUCAGGUGAGUUUCUGUCUCUUGAUAA-UGUGCGCA
.(((.(((..(((((((.((((((((((..(.(((((....)))))..)..))))))).)))....))))))))))))).((...((((....)))).-...))... ( -39.30)
>DroYak_CAF1 35807 99 - 1
CCACACUGAUGCGGUCAAUGCGGUGGCAUUCAGUCGCGAUGGCGACAAGUUUGCCACCGGUGGCAGUGAUCGUCAGGUGAGUUU-UGUUUCUUGAUUG-------UU
.(((.(((..(((((((.((((((((((..(.(((((....)))))..)..)))))))....))).))))))))))))).....-.............-------.. ( -39.00)
>DroPer_CAF1 9688 103 - 1
CCAUACGGCGGCUGUAAAUGCUGUGGGCUUUUCCCAGGAUGGAGAGAAGUUUGCCACUGGUGGCAACGAUCGCCAGGUGAGUUGGGGCGGCUCAUCCA----AUGGC
((((..((((..(((..........((((((((((.....)).))))))))(((((....))))))))..)))).(((((((((...)))))))))..----)))). ( -40.00)
>consensus
CCACACUGAUGCGGUAAAUGCGGUGGCAUUCAGUCACGAUGGCGACAAGUUUGCCACCGGUGGCAGUGAUCGCCAGGUGAGUUUCUGUUUCUUAAUAA_GGUAUGAA
.......((.((((.....((.(((((.....)))))..((((((.....((((((....))))))...)))))).....))..)))).))................ (-24.93 = -23.38 +  -1.55)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:32:15 2006