Locus 2521

Sequence ID	2L_DroMel_CAF1
Location	6,970,460 – 6,970,565
Length	105
Max. P	0.781003

overview

Window 3

Location	6,970,460 – 6,970,565
Length	105
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	80.21
Mean single sequence MFE	-36.96
Consensus MFE	-20.49
Energy contribution	-22.60
Covariance contribution	2.11
Combinations/Pair	1.08
Mean z-score	-1.85
Structure conservation index	0.55
SVM decision value	0.00
SVM RNA-class probability	0.535285
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 6970460 105 + 22407834
GGAUUCGCGUUCGCGAGACUUGGAGCGCUUCUUUUUCUUCUCACGCUCGCGAUC------------GCGAUCACGCUCGCGCUCCCUGUCCCGCCGAUCGCGGCG---GUCGAACUCGUC
.....((.(((((...(((..(((((((...............((....))...------------(((....)))..)))))))..)))((((((....)))))---).))))).)).. ( -40.90)
>DroPse_CAF1 10496 117 + 1
GGAAUCGCGCUCGCGCGACUUGGAACGCUUCUUCCUCUUCUCACGUUCACGAUCACGGUCGCGAUCGCGAUCUCUCUCACGGUCCCUCUCCCGCCUGUCGCGGCG---GUCGAACUCAUC
(..((((((....(((((((.((((......))))........((....)).....)))))))..))))))..)............((..(((((......))))---)..))....... ( -36.20)
>DroEre_CAF1 10911 105 + 1
GGAUUCGCGUUCGCGAGACUUGGAGCGCUUCUUUUUCUUCUCACGCUCGCGAUC------------GCGAUCCCGCUCGCGCUCCCUGUCUCGCCGAUCGCGGCG---GUCGAACUCGUC
.((((((((.(((((((((..(((((((...............((....))...------------(((....)))..)))))))..)))))).))).)))))..---)))......... ( -43.70)
>DroYak_CAF1 11056 105 + 1
GGAUUCUCGUUCGCGAGACUUGGAGCGCUUCUUUUUCUUCUCACGCUCACGAUC------------GCGAUCCCGCUCGCGCUCUCUGUCUCGCCGAUCGCGGCG---GUCGAACUCAUC
........(((((((((((..(((((((...............((....))...------------(((....)))..)))))))..))))))).(((((...))---)))))))..... ( -38.90)
>DroMoj_CAF1 11801 102 + 1
UGAUUCCCGUUCGCGUGACUUGGAGCGCUUCUUUUUCUUCUCACGCUCACGAUC------------GCGAU------CGCGGUCCCUGUCGCGCCUAUCCCGUCGUCCAUCGAAAUCGUC
.((((.......(((((((...(((((................)))))..((((------------((...------.))))))...)))))))........(((.....)))))))... ( -29.29)
>DroAna_CAF1 8238 117 + 1
GGACUCACGUUCGCGCGACUUGGAGCGCUUCUUUUUCUUCUCACGCUCGCGAUCACGAUCCCGAUCGCGAUCUCGCUCCCGUUCCCUGUCACGUCUGUCCCUUCG---AUCGAACUCUUC
((((..((((.((.(.(((..(((((((................))((((((((........))))))))....))))).))).).))..))))..)))).....---............ ( -32.79)
>consensus
GGAUUCGCGUUCGCGAGACUUGGAGCGCUUCUUUUUCUUCUCACGCUCACGAUC____________GCGAUCCCGCUCGCGCUCCCUGUCCCGCCGAUCGCGGCG___GUCGAACUCGUC
........(((((...(((..(((((((...............((....))...............(((....)))..)))))))..))).((((......)))).....)))))..... (-20.49 = -22.60 +   2.11)

alignment

secondary structure

dotplot

Window 4

Location	6,970,460 – 6,970,565
Length	105
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	80.21
Mean single sequence MFE	-42.20
Consensus MFE	-24.40
Energy contribution	-25.16
Covariance contribution	0.75
Combinations/Pair	1.21
Mean z-score	-2.14
Structure conservation index	0.58
SVM decision value	0.56
SVM RNA-class probability	0.781003
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 6970460 105 - 22407834
GACGAGUUCGAC---CGCCGCGAUCGGCGGGACAGGGAGCGCGAGCGUGAUCGC------------GAUCGCGAGCGUGAGAAGAAAAAGAAGCGCUCCAAGUCUCGCGAACGCGAAUCC
..((.(((((.(---(((((....))))))(((..(((((((...((((((...------------.))))))..(....)...........)))))))..)))...))))).))..... ( -47.60)
>DroPse_CAF1 10496 117 - 1
GAUGAGUUCGAC---CGCCGCGACAGGCGGGAGAGGGACCGUGAGAGAGAUCGCGAUCGCGACCGUGAUCGUGAACGUGAGAAGAGGAAGAAGCGUUCCAAGUCGCGCGAGCGCGAUUCC
.......((..(---((((......)))))..))((((.((((.......((((((((((....)))))))))).((((.((...((((......))))...)).))))..)))).)))) ( -47.70)
>DroEre_CAF1 10911 105 - 1
GACGAGUUCGAC---CGCCGCGAUCGGCGAGACAGGGAGCGCGAGCGGGAUCGC------------GAUCGCGAGCGUGAGAAGAAAAAGAAGCGCUCCAAGUCUCGCGAACGCGAAUCC
..((.(((((..---.((((....))))(((((..(((((((..(((....)))------------..((((....))))............)))))))..))))).))))).))..... ( -46.40)
>DroYak_CAF1 11056 105 - 1
GAUGAGUUCGAC---CGCCGCGAUCGGCGAGACAGAGAGCGCGAGCGGGAUCGC------------GAUCGUGAGCGUGAGAAGAAAAAGAAGCGCUCCAAGUCUCGCGAACGAGAAUCC
(((..(((((..---.((((....))))(((((...((.(((((......))))------------).))(.((((((..............)))))))..))))).)))))....))). ( -39.54)
>DroMoj_CAF1 11801 102 - 1
GACGAUUUCGAUGGACGACGGGAUAGGCGCGACAGGGACCGCG------AUCGC------------GAUCGUGAGCGUGAGAAGAAAAAGAAGCGCUCCAAGUCACGCGAACGGGAAUCA
...(((((((((..((((((.(((...((((........))))------))).)------------).))))((((((..............))))))...))).((....)))))))). ( -29.24)
>DroAna_CAF1 8238 117 - 1
GAAGAGUUCGAU---CGAAGGGACAGACGUGACAGGGAACGGGAGCGAGAUCGCGAUCGGGAUCGUGAUCGCGAGCGUGAGAAGAAAAAGAAGCGCUCCAAGUCGCGCGAACGUGAGUCC
.....(((((.(---(....)).....((((((.(....).((((((...(((((((((......))))))))).(....)............))))))..)))))))))))........ ( -42.70)
>consensus
GACGAGUUCGAC___CGCCGCGAUAGGCGAGACAGGGAGCGCGAGCGAGAUCGC____________GAUCGCGAGCGUGAGAAGAAAAAGAAGCGCUCCAAGUCUCGCGAACGCGAAUCC
.....(((((......(((......)))(((((.......((((......))))................(.((((((..............)))))))..))))).)))))........ (-24.40 = -25.16 +   0.75)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:29:52 2006