Locus 7350

Sequence ID	3L_DroMel_CAF1
Location	19,716,281 – 19,716,479
Length	198
Max. P	0.741713

overview

Window 7

Location	19,716,281 – 19,716,399
Length	118
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	95.15
Mean single sequence MFE	-26.16
Consensus MFE	-23.06
Energy contribution	-23.50
Covariance contribution	0.44
Combinations/Pair	1.04
Mean z-score	-1.32
Structure conservation index	0.88
SVM decision value	0.45
SVM RNA-class probability	0.741713
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 19716281 118 + 23771897
CGUCGUUUUCUUCAAUCUACUCUACUUACAUUCUGUUUAUUAAACAAAAACACUCAAAUUGGGGCCACAGGCAAGCCC--AUAUAUUGCCCAUGACGAAAGGGCGCCGAGAAGAAAAGCG
(((..((((((((....................((((.....))))............((((.(((...(((((....--.....))))).....(....)))).))))))))))))))) ( -28.10)
>DroSec_CAF1 25431 120 + 1
CGUCGUUUUCUUCAAUCUACUCUACUUACAUUCUGUUUAUUAAACAAAAACACUCAAAUUGGGGCCACAGGCAAGCCCACAUAUAUUGCCCAUAACGAAAGGGCGCCGAGAAGAAAAGCG
(((..((((((((....................((((.....))))............((((.(((...(((((...........))))).....(....)))).))))))))))))))) ( -27.90)
>DroSim_CAF1 27656 120 + 1
CGUCGUUUUCUUCAAUCUACUCUACUUACAUUCUGUUUAUUAAACAAAAACACUCAAAUUGGGGCCACAGGCAAGCCCACAUAUAUUGCCCAUGACGAAAGGGCGCCGAGAAGAAAAGCG
(((..((((((((....................((((.....))))............((((.(((...(((((...........))))).....(....)))).))))))))))))))) ( -27.90)
>DroEre_CAF1 28181 117 + 1
CGUCAUUUUCUUCAAUCUACUCUACUUACAUUCUGUUUAUUAAACAAAAACACUCAAAUUGGGACCGCAGGCAAGCCCAC--AUAUUGCCCAUGACGA-AGGGCCCCGAGAAGAAAAGCG
(((..((((((((....................((((.....))))............(((((......((....))...--.....((((.......-.)))))))))))))))))))) ( -23.70)
>DroYak_CAF1 26378 117 + 1
CGUCGUUUUCUUCAAUCUACUCUACUUACAUUCUGUUUAUUAAACAAAAACACUCAAAUUGGGACCACAGGCAAGCCCAC--AUAUUGUCCAUGACGA-AGGGCCCCGAGAAGAAACGCG
((.(((((.((((....................((((.....))))............(((((.((...((....))...--...(((((...)))))-..)).)))))))))))))))) ( -23.20)
>consensus
CGUCGUUUUCUUCAAUCUACUCUACUUACAUUCUGUUUAUUAAACAAAAACACUCAAAUUGGGGCCACAGGCAAGCCCACAUAUAUUGCCCAUGACGAAAGGGCGCCGAGAAGAAAAGCG
(((..((((((((....................((((.....))))............((((.(((...(((((...........))))).....(....)))).))))))))))))))) (-23.06 = -23.50 +   0.44)

alignment

secondary structure

dotplot

Window 8

Location	19,716,359 – 19,716,479
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	89.22
Mean single sequence MFE	-34.16
Consensus MFE	-29.76
Energy contribution	-29.38
Covariance contribution	-0.38
Combinations/Pair	1.16
Mean z-score	-1.28
Structure conservation index	0.87
SVM decision value	0.02
SVM RNA-class probability	0.542421
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 19716359 120 + 23771897
AUAUAUUGCCCAUGACGAAAGGGCGCCGAGAAGAAAAGCGGAAAAUCAGUCGGCAGGGAAAACUGGCCGCCAGGUAGGCGGACACUGAUAACAGCGAUUUCCUUUCAUAUUUUCAUCGGA
.......((((.........)))).(((((((((...((.((.......)).))(((((((.....(((((.....))))).(.(((....))).).))))))).....))))).)))). ( -36.60)
>DroSec_CAF1 25511 120 + 1
AUAUAUUGCCCAUAACGAAAGGGCGCCGAGAAGAAAAGCGGAAAAUCAGUCGGCAGGGAAAACUGGCCGCCAGGUAGGCGGACAUUGAUAACAGCGAGUUCCUUUCAUAUUUUCAUCGGA
.......((((.........)))).(((((((((...((.((.......)).))((((((..(((.(((((.....)))))..........)))....)))))).....))))).)))). ( -34.90)
>DroSim_CAF1 27736 108 + 1
AUAUAUUGCCCAUGACGAAAGGGCGCCGAGAAGAAAAGCG------------GCAGGGAAAACUGGCCGCCAGGUAGGCGGACACUGAUAACAGCGAGUUCCUUUCAUAUUUUCAUCGGA
.......((((.........)))).((((...(((((...------------(.((((((......(((((.....))))).(.(((....))).)..)))))).)...))))).)))). ( -33.90)
>DroEre_CAF1 28261 117 + 1
--AUAUUGCCCAUGACGA-AGGGCCCCGAGAAGAAAAGCGGAAAAUAUGUCGGUAGGGAAAACUGCCCGCCAGGUAGGCGGACACUGAUAACGGAGAGUUCCUUUCAUAUUUUCAUCGAA
--.....((((.......-.))))..(((...(((((...((((...(((((((((......)))))((((.....))))))))........((......))))))...))))).))).. ( -34.40)
>DroYak_CAF1 26458 117 + 1
--AUAUUGUCCAUGACGA-AGGGCCCCGAGAAGAAACGCGGAAAAUCUGUCGGUAGGGAAAACUGCCCGCCAGGUAGGCGGACACUGAUAACAGCGAGUUCCUUUCAUAUUUUCAUUGAA
--.....((((.......-.))))...((((.(((.(((.....((((((((((((......)))))((((.....))))))))..)))....)))..))).)))).............. ( -31.00)
>consensus
AUAUAUUGCCCAUGACGAAAGGGCGCCGAGAAGAAAAGCGGAAAAUCAGUCGGCAGGGAAAACUGGCCGCCAGGUAGGCGGACACUGAUAACAGCGAGUUCCUUUCAUAUUUUCAUCGGA
.......((((.........)))).(((((((((...((.((.......)).))((((((......(((((.....))))).(.(((....))).)..)))))).....))))).)))). (-29.76 = -29.38 +  -0.38)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:44:41 2006