Locus 4580

Sequence ID	3L_DroMel_CAF1
Location	13,125,708 – 13,125,819
Length	111
Max. P	0.883467

overview

Window 5

Location	13,125,708 – 13,125,819
Length	111
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	81.37
Mean single sequence MFE	-16.18
Consensus MFE	-14.04
Energy contribution	-13.64
Covariance contribution	-0.40
Combinations/Pair	1.10
Mean z-score	-1.82
Structure conservation index	0.87
SVM decision value	0.93
SVM RNA-class probability	0.883467
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13125708 111 + 23771897
CGCCAUCUGUUUGCUUUCUGCUUUGCUUUGCAGAAAUCCUUAAAGAAAUGACAAAUACCUCUUCUUCAGACACUCCGUUCUCCACAUUUCCCUCCCACU---------UUUGCCACUUUU
.......((((((.(((((((........)))))))......(((((..(........)..)))))))))))...........................---------............ ( -13.80)
>DroSec_CAF1 113569 107 + 1
CGCCAUCUGUUUGCUUUCUGCUUUGCUUUGCAGAAAUCCUUAAAGAAAUGACAAAUACCUCUUCUUCAGACACUCCGUCCUCCACAUUUC----CCACU---------CUGGCCACUUCU
.((((..((((((.(((((((........)))))))......(((((..(........)..)))))))))))....((.....)).....----.....---------.))))....... ( -18.00)
>DroSim_CAF1 111805 107 + 1
CGCCAUCUGUUUGCUUUCUGCUUUGCUUUGCAGAAAUCCUUAAAGAAAUGACAAAUACCUCUUCUUCAGACACUCCGUCCUCCAUAUUUC----CCACU---------UUGGCCACUUCU
.(((((((......(((((((........))))))).......)))......................(((.....)))...........----.....---------.))))....... ( -16.82)
>DroEre_CAF1 110558 91 + 1
CGCCAUCUGUUUGCUUUCUGCUUAGCUUUGCAGAAAUCCUUAAAGAAAUGACAAAUACCUCUUCUUCAGGCAUUCCGCCACU-----------------------------CCCACGUCC
.(((.(((((..(((........)))...)))))........(((((..(........)..)))))..)))...........-----------------------------......... ( -15.90)
>DroYak_CAF1 113856 116 + 1
CGCCAGUUGUUUGCUUUCUGCUUGGCUUUGCAGAAAUCCUUAAAGAAAUGACAAAUACCUUUUCUUCAGACACUCCGCCCAUCACUUCUC----CCACUUCCCCCCGUUUUUCCACGUCC
.((.(((.(((((.(((((((........)))))))......((((((.(........).))))))))))))))..))............----...........(((......)))... ( -16.40)
>consensus
CGCCAUCUGUUUGCUUUCUGCUUUGCUUUGCAGAAAUCCUUAAAGAAAUGACAAAUACCUCUUCUUCAGACACUCCGUCCUCCACAUUUC____CCACU_________UUGGCCACUUCU
.((....((((((.(((((((........)))))))......(((((..(........)..)))))))))))....)).......................................... (-14.04 = -13.64 +  -0.40)

alignment

secondary structure

dotplot

Window 6

Location	13,125,708 – 13,125,819
Length	111
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	81.37
Mean single sequence MFE	-24.16
Consensus MFE	-17.72
Energy contribution	-17.44
Covariance contribution	-0.28
Combinations/Pair	1.12
Mean z-score	-1.50
Structure conservation index	0.73
SVM decision value	0.02
SVM RNA-class probability	0.541986
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13125708 111 - 23771897
AAAAGUGGCAAA---------AGUGGGAGGGAAAUGUGGAGAACGGAGUGUCUGAAGAAGAGGUAUUUGUCAUUUCUUUAAGGAUUUCUGCAAAGCAAAGCAGAAAGCAAACAGAUGGCG
.......((...---------.............(((.....)))....(((((..((((((((.......)))))))).....(((((((........))))))).....))))).)). ( -20.00)
>DroSec_CAF1 113569 107 - 1
AGAAGUGGCCAG---------AGUGG----GAAAUGUGGAGGACGGAGUGUCUGAAGAAGAGGUAUUUGUCAUUUCUUUAAGGAUUUCUGCAAAGCAAAGCAGAAAGCAAACAGAUGGCG
.......((((.---------.((..----(......((((((((((...(((.....)))....)))))).))))........(((((((........))))))).)..))...)))). ( -23.80)
>DroSim_CAF1 111805 107 - 1
AGAAGUGGCCAA---------AGUGG----GAAAUAUGGAGGACGGAGUGUCUGAAGAAGAGGUAUUUGUCAUUUCUUUAAGGAUUUCUGCAAAGCAAAGCAGAAAGCAAACAGAUGGCG
.......(((((---------(((((----.((((((...((((.....)))).........)))))).)))))).........(((((((........))))))).........)))). ( -23.40)
>DroEre_CAF1 110558 91 - 1
GGACGUGGG-----------------------------AGUGGCGGAAUGCCUGAAGAAGAGGUAUUUGUCAUUUCUUUAAGGAUUUCUGCAAAGCUAAGCAGAAAGCAAACAGAUGGCG
...((((((-----------------------------(((((((.(((((((.......))))))))))))))))).......(((((((........)))))))...........))) ( -27.10)
>DroYak_CAF1 113856 116 - 1
GGACGUGGAAAAACGGGGGGAAGUGG----GAGAAGUGAUGGGCGGAGUGUCUGAAGAAAAGGUAUUUGUCAUUUCUUUAAGGAUUUCUGCAAAGCCAAGCAGAAAGCAAACAACUGGCG
.............(((..(...((.(----((((((((((.....((((..((.......))..))))))))))))))).....(((((((........)))))))))...)..)))... ( -26.50)
>consensus
AGAAGUGGCAAA_________AGUGG____GAAAUGUGGAGGACGGAGUGUCUGAAGAAGAGGUAUUUGUCAUUUCUUUAAGGAUUUCUGCAAAGCAAAGCAGAAAGCAAACAGAUGGCG
.............................................((((((((.......))))))))(((((((.(((.....(((((((........)))))))..))).))))))). (-17.72 = -17.44 +  -0.28)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:27:26 2006