Locus 4251

Sequence ID	2L_DroMel_CAF1
Location	12,149,308 – 12,149,447
Length	139
Max. P	0.685802

overview

Window 1

Location	12,149,308 – 12,149,415
Length	107
Sequences	5
Columns	109
Reading direction	reverse
Mean pairwise identity	88.87
Mean single sequence MFE	-25.26
Consensus MFE	-19.00
Energy contribution	-18.48
Covariance contribution	-0.52
Combinations/Pair	1.26
Mean z-score	-1.74
Structure conservation index	0.75
SVM decision value	0.32
SVM RNA-class probability	0.685802
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 12149308 107 - 22407834
CAGAAAGUGUCGCAAAAACUGCAACGACAUC--AAAUGAGAUAGUGGCAACAGCUGGAAAAAGUCAUUUCGCCUCCAGCACUCAGAGCAACAUUAGAAACAGACGCACA
......((((((((.....))).........--...((((....((....))((((((....(......)...)))))).)))).................)))))... ( -25.20)
>DroSec_CAF1 34669 107 - 1
CAGAAAGUGUCGCAAAAACUGCAACGACAUC--AAAUGAGAUAGUGGCAACAGCUGGAAAAAGUCAUUUUGCCUCCAGCACUCAGAGCAACAUUAGAAACAGACGCACA
......((((((((.....))).........--...((((....((....))((((((..(((....)))...)))))).)))).................)))))... ( -25.80)
>DroSim_CAF1 31296 107 - 1
CAGAAAGUGUCGCAAAAACUGCAACGACAUC--AAAUGAGAUAGUGGCAACAGCUGGAAAAAGUCAUUUUGCCUCCAGCACUCAGAGCAACAUUAGAAACAGACGCACA
......((((((((.....))).........--...((((....((....))((((((..(((....)))...)))))).)))).................)))))... ( -25.80)
>DroEre_CAF1 30449 107 - 1
CAAAAAGUGUCGUAGAAACUGCAACGACAUC--AAAUGAGAUAGCGGCCACAGCUGGGAAAAGUCAUUUUGCUCCCGGCUCUAAGAGCCACAUUAGAAGCAGAUGCACA
......(((.(((.....((((...(..(((--......)))..)((((..((((((((.(((....)))..))))))))....).))).........)))))))))). ( -27.30)
>DroYak_CAF1 25024 109 - 1
CAGAAAGUGUCGUAGAAACUGCAACUGAAACUGCUAUGAGAUAGCGACAACAGCUGGGAAAAGUCAUUUCGCUUCGGGCACUAAGAGCCACAUUAGAAACAGAUGCACA
(((....((((((((...))))..........(((((...)))))))))....)))......(((((((.(.(((.(((.......)))......))).)))))).)). ( -22.20)
>consensus
CAGAAAGUGUCGCAAAAACUGCAACGACAUC__AAAUGAGAUAGUGGCAACAGCUGGAAAAAGUCAUUUUGCCUCCAGCACUCAGAGCAACAUUAGAAACAGACGCACA
......((((((((.....)))..............((((.....(....).((((((...............)))))).)))).................)))))... (-19.00 = -18.48 +  -0.52)

alignment

secondary structure

dotplot

Window 2

Location	12,149,348 – 12,149,447
Length	99
Sequences	6
Columns	104
Reading direction	reverse
Mean pairwise identity	80.20
Mean single sequence MFE	-24.33
Consensus MFE	-14.21
Energy contribution	-14.18
Covariance contribution	-0.02
Combinations/Pair	1.25
Mean z-score	-1.87
Structure conservation index	0.58
SVM decision value	0.26
SVM RNA-class probability	0.656318
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 12149348 99 - 22407834
GUGGCCUUAAAGGCGGAAAAGUCGAAAGGCAACAGAAAGUGUCGCAAAAACUGCAACGACAUC--AA---AUGAGAUAGUGGCAACAGCUGGAAAAAGUCAUUU
...(((((...(((......)))..)))))..(((....(((((((.....)))....(((((--..---....))).))))))....)))............. ( -21.80)
>DroSec_CAF1 34709 99 - 1
GUGUCCUUAAAGGCGGAAAAGUCGAAAGGCGACAGAAAGUGUCGCAAAAACUGCAACGACAUC--AA---AUGAGAUAGUGGCAACAGCUGGAAAAAGUCAUUU
(((((.......((((......(....)((((((.....)))))).....))))...))))).--((---((((..(((((....)).))).......)))))) ( -22.90)
>DroSim_CAF1 31336 99 - 1
GUGGCCUUAAAGGCGGAAAAGUCGAAAGGCGACAGAAAGUGUCGCAAAAACUGCAACGACAUC--AA---AUGAGAUAGUGGCAACAGCUGGAAAAAGUCAUUU
((.(((((...(((......)))..))))).)).....((((((((.....)))...))))).--((---((((..(((((....)).))).......)))))) ( -23.60)
>DroEre_CAF1 30489 99 - 1
GUGGCCUUAAAGGCGGAAAAGUCGAAAGGCGACAAAAAGUGUCGUAGAAACUGCAACGACAUC--AA---AUGAGAUAGCGGCCACAGCUGGGAAAAGUCAUUU
((((((......((((....(((....)))((((.....)))).......))))...(..(((--..---....)))..))))))).(((......)))..... ( -28.80)
>DroYak_CAF1 25064 101 - 1
GUGGCCUUAAAGGCGGAAAAGUCGAAAGGCGACAGAAAGUGUCGUAGAAACUGCAACUGAAACUGCU---AUGAGAUAGCGACAACAGCUGGGAAAAGUCAUUU
(((((((((..(((((....(((....)))((((.....))))((((...))))........)))))---.)))).((((.......))))......))))).. ( -25.10)
>DroAna_CAF1 29246 85 - 1
UUGGCCUUUAAGGCG-ACAGGUCGAAAGGCAACAGGAGCUGUCGCGUCACCUGCAAUGACACG--AAGGAAGGAAAUAUUGCAAACGA----------------
....(((((...(((-((((.((....(....)..)).)))))))((((.......))))...--...)))))...............---------------- ( -23.80)
>consensus
GUGGCCUUAAAGGCGGAAAAGUCGAAAGGCGACAGAAAGUGUCGCAAAAACUGCAACGACAUC__AA___AUGAGAUAGUGGCAACAGCUGGAAAAAGUCAUUU
((.(((((...(((......)))..))))).)).......((.(((.....))).))...................(((((....).))))............. (-14.21 = -14.18 +  -0.02)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:13:28 2006