Locus 2631

Sequence ID	3R_DroMel_CAF1
Location	7,100,327 – 7,100,428
Length	101
Max. P	0.998607

overview

Window 2

Location	7,100,327 – 7,100,428
Length	101
Sequences	5
Columns	117
Reading direction	forward
Mean pairwise identity	78.49
Mean single sequence MFE	-44.46
Consensus MFE	-25.27
Energy contribution	-26.15
Covariance contribution	0.88
Combinations/Pair	1.08
Mean z-score	-2.54
Structure conservation index	0.57
SVM decision value	1.97
SVM RNA-class probability	0.984243
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 7100327 101 + 27905053
CCCGGCGCCCAGAUUCUGUGUUUCGGAUGCGUAUGCCGGGACAGGAUCCGGGUAUCUGGAGAUUCGUGGAGCCGGGUGGC----------------CGGGAGAGUCCGGCUUAUUAA
((((((..(((((.(((.(((..(((.........)))..))).).(((((....))))))).)).))).)))))).(((----------------((((....)))))))...... ( -44.90)
>DroSec_CAF1 33345 85 + 1
CCCGGCGCCCAGAUUCUGUGUUUCGGAUGCGUAUGCCGGGACAGGAUCCGGG----------------GAGCCGGGUAGC----------------CGGGACAGUCCGGCUUAUUAA
((((((.(((.((((((((..(((((.........))))))))))))).)))----------------..)))))).(((----------------((((....)))))))...... ( -43.70)
>DroSim_CAF1 37208 85 + 1
CCCGGCGCCCAGAUUCUGUGUUUCGGAUGCGUAUGCCCGGACAGGAUCCGGG----------------UGGCCGGGUAGC----------------CGGGACAGUCCGGCUUAUUAA
((((((((((.((((((((...((((..((....)))))))))))))).)))----------------).)))))).(((----------------((((....)))))))...... ( -44.90)
>DroEre_CAF1 34133 109 + 1
CCCGGCGCCCAGAUUCUGUGUUUCGGAUGCGUAUGCCGGGACAGGAUCCGGGGAUCCG--------GGGACCCAGGGAUCCAGUGAAUCGGGGAGCCAGGACAGUCCGGCUUAUUAA
.(((((.(((.(((((..(((..(((.........)))..)))((((((.(((.((..--------..)))))..))))))...))))).))).))).((.....))))........ ( -48.70)
>DroYak_CAF1 35512 93 + 1
CCCGGCGCCCAGAUUCAGUGUUUCGGAUGCGUAUGCCGGGACAGAGUCCGGUGAUUCG--------GGGCUCCGGGAAUC----------------CGGGACAGUCCGGCUUAUUAA
(((((.((((.(((((..(((..(((.........)))..))))))))(((....)))--------)))).)))))...(----------------((((....)))))........ ( -40.10)
>consensus
CCCGGCGCCCAGAUUCUGUGUUUCGGAUGCGUAUGCCGGGACAGGAUCCGGG_AU__G_________GGAGCCGGGUAGC________________CGGGACAGUCCGGCUUAUUAA
((((((.(((.(((((..((((((((.........))))))))))))).)))..................))))))....................((((....))))......... (-25.27 = -26.15 +   0.88)

alignment

secondary structure

dotplot

Window 3

Location	7,100,327 – 7,100,428
Length	101
Sequences	5
Columns	117
Reading direction	reverse
Mean pairwise identity	78.49
Mean single sequence MFE	-40.20
Consensus MFE	-21.51
Energy contribution	-22.39
Covariance contribution	0.88
Combinations/Pair	1.08
Mean z-score	-3.21
Structure conservation index	0.54
SVM decision value	3.16
SVM RNA-class probability	0.998607
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 7100327 101 - 27905053
UUAAUAAGCCGGACUCUCCCG----------------GCCACCCGGCUCCACGAAUCUCCAGAUACCCGGAUCCUGUCCCGGCAUACGCAUCCGAAACACAGAAUCUGGGCGCCGGG
.......(((((......)))----------------))..((((((.......(((....))).(((((((.((((..(((.((....)))))....)))).))))))).)))))) ( -38.90)
>DroSec_CAF1 33345 85 - 1
UUAAUAAGCCGGACUGUCCCG----------------GCUACCCGGCUC----------------CCCGGAUCCUGUCCCGGCAUACGCAUCCGAAACACAGAAUCUGGGCGCCGGG
......((((((......)))----------------))).((((((..----------------(((((((.((((..(((.((....)))))....)))).))))))).)))))) ( -40.70)
>DroSim_CAF1 37208 85 - 1
UUAAUAAGCCGGACUGUCCCG----------------GCUACCCGGCCA----------------CCCGGAUCCUGUCCGGGCAUACGCAUCCGAAACACAGAAUCUGGGCGCCGGG
......((((((......)))----------------))).((((((..----------------(((((((.((((.(((((....))..)))....)))).))))))).)))))) ( -42.20)
>DroEre_CAF1 34133 109 - 1
UUAAUAAGCCGGACUGUCCUGGCUCCCCGAUUCACUGGAUCCCUGGGUCCC--------CGGAUCCCCGGAUCCUGUCCCGGCAUACGCAUCCGAAACACAGAAUCUGGGCGCCGGG
.................((((((.(((.(((((...((((((..(((((..--------..)))))..))))))(((..(((.((....)))))..)))..))))).))).)))))) ( -45.10)
>DroYak_CAF1 35512 93 - 1
UUAAUAAGCCGGACUGUCCCG----------------GAUUCCCGGAGCCC--------CGAAUCACCGGACUCUGUCCCGGCAUACGCAUCCGAAACACUGAAUCUGGGCGCCGGG
........((((......)))----------------)...(((((.((((--------.((.(((((((........))))....((....))......))).)).)))).))))) ( -34.10)
>consensus
UUAAUAAGCCGGACUGUCCCG________________GCUACCCGGCUCC_________C__AU_CCCGGAUCCUGUCCCGGCAUACGCAUCCGAAACACAGAAUCUGGGCGCCGGG
.........(((......)))....................((((((..................(((((((.((((..(((.((....)))))....)))).))))))).)))))) (-21.51 = -22.39 +   0.88)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:41:00 2006