Locus 1540

Sequence ID	2R_DroMel_CAF1
Location	5,820,012 – 5,820,120
Length	108
Max. P	0.829198

overview

Window 4

Location	5,820,012 – 5,820,120
Length	108
Sequences	6
Columns	108
Reading direction	forward
Mean pairwise identity	75.86
Mean single sequence MFE	-35.58
Consensus MFE	-22.81
Energy contribution	-20.62
Covariance contribution	-2.19
Combinations/Pair	1.48
Mean z-score	-1.46
Structure conservation index	0.64
SVM decision value	0.61
SVM RNA-class probability	0.798336
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 5820012 108 + 20766785
UUAUUGGGAAUGCAGGAGCCUGUGCCCAAGAAAAUUAUCUUCGGGUAGCUAUCGGCAGAAUUGUCAGGGAAACUAUACUCUUCUUUGAAUUUGGCCAAUAGUUCCAGA
...(((((...((((....)))).)))))..............((.((((((.(((.((((..((((((((.........)))))))))))).))).))))))))... ( -32.20)
>DroPse_CAF1 18342 108 + 1
UUGUUGGGAAUGCAGGAGCCCGUGCCCAGGAAGAUGAUCCUUGGGUAGCUGCUGGCGGCGGACGAUGGGAAGUUGGUUUCGGCCUUUAGCUUAGCCAGCAGCUCCGUA
..............(((((((((((((((((......))).))))).((((....)))).....))))...(((((((..(((.....))).))))))).)))))... ( -40.50)
>DroSec_CAF1 17512 108 + 1
UUAUUGGGAAUGCAGGAGCCAGUGCCCAAGAAAAUGAUCUUUGGGUAGCUAUCGGCAGAAUUGUCAGGGAAACUAUACUCUUCUUUGAACUUGGCCAAUAGUUCCAGA
......(((((....(.((((((((((((((......)).)))))))....((((.((((..((..((....))..))..))))))))..))))))....)))))... ( -30.50)
>DroYak_CAF1 17710 108 + 1
UUAUUGGGAAUGCAGGAGCCUGUGCCCAGGAAAAUGAUUUUCGGGUAGCUAUCGGCAGUAUUGUCAGGGAAACUAUACUCAUCUUUAAAUUUGGUCAAUAGUUCCAUA
...(((((...((((....)))).)))))((((.....)))).((.((((((.((((((((.....((....)))))))((..........))))).))))))))... ( -25.00)
>DroAna_CAF1 15078 108 + 1
UUGUUGGGAAUACACGAGCCCGUUCCGAGAAAAAUAAUUUUGGGGUAGCUGUUGGUAGAGCUGGCCGGGAAGGAGUACUCUUCCUUAAACUUGGCCAGCAGUUCCGUG
......(((((.((..(((..(..((((((.......))))))..).)))..)).....((((((((((((((((.....))))))...)))))))))).)))))... ( -39.30)
>DroPer_CAF1 18855 108 + 1
UUGUUGGGAAUGCAGGAGCCCGUGCCCAGGAAGAUGAUCCUUGGGUAGCUGCUGGCGGCGGACGAUGGGAAGUCGGUUUCCGCCUUUAGCUUAGCCAGCAGCUCCGUA
..............(((.....(((((((((......))).))))))(((((((((((((((((((.....))))...)))))).........))))))))))))... ( -46.00)
>consensus
UUAUUGGGAAUGCAGGAGCCCGUGCCCAGGAAAAUGAUCUUUGGGUAGCUAUCGGCAGAAUUGGCAGGGAAACUAUACUCUUCCUUAAACUUGGCCAACAGUUCCAUA
......(((.............(((((((((......)))).)))))(((((.(((..........(((.............)))........))).))))))))... (-22.81 = -20.62 +  -2.19)

alignment

secondary structure

dotplot

Window 5

Location	5,820,012 – 5,820,120
Length	108
Sequences	6
Columns	108
Reading direction	reverse
Mean pairwise identity	75.86
Mean single sequence MFE	-28.19
Consensus MFE	-18.85
Energy contribution	-17.91
Covariance contribution	-0.94
Combinations/Pair	1.33
Mean z-score	-1.40
Structure conservation index	0.67
SVM decision value	0.71
SVM RNA-class probability	0.829198
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 5820012 108 - 20766785
UCUGGAACUAUUGGCCAAAUUCAAAGAAGAGUAUAGUUUCCCUGACAAUUCUGCCGAUAGCUACCCGAAGAUAAUUUUCUUGGGCACAGGCUCCUGCAUUCCCAAUAA
...((((((((((((...((((......))))...(((.....)))......))))))))...(((.((((......)))))))..(((....)))..))))...... ( -24.60)
>DroPse_CAF1 18342 108 - 1
UACGGAGCUGCUGGCUAAGCUAAAGGCCGAAACCAACUUCCCAUCGUCCGCCGCCAGCAGCUACCCAAGGAUCAUCUUCCUGGGCACGGGCUCCUGCAUUCCCAACAA
...((((((((((((...((....((.(((.............))).)))).)))))))))).((((.(((......)))))))..(((....))).....))..... ( -35.62)
>DroSec_CAF1 17512 108 - 1
UCUGGAACUAUUGGCCAAGUUCAAAGAAGAGUAUAGUUUCCCUGACAAUUCUGCCGAUAGCUACCCAAAGAUCAUUUUCUUGGGCACUGGCUCCUGCAUUCCCAAUAA
...((((((((((((..((((((..((((.......))))..)))..)))..))))))))...(((((.((......))))))).....((....)).))))...... ( -23.50)
>DroYak_CAF1 17710 108 - 1
UAUGGAACUAUUGACCAAAUUUAAAGAUGAGUAUAGUUUCCCUGACAAUACUGCCGAUAGCUACCCGAAAAUCAUUUUCCUGGGCACAGGCUCCUGCAUUCCCAAUAA
...((((((((((.....(((....))).(((((.(((.....))).)))))..))))))......(.....)...))))((((..(((....)))....)))).... ( -17.20)
>DroAna_CAF1 15078 108 - 1
CACGGAACUGCUGGCCAAGUUUAAGGAAGAGUACUCCUUCCCGGCCAGCUCUACCAACAGCUACCCCAAAAUUAUUUUUCUCGGAACGGGCUCGUGUAUUCCCAACAA
(((((....(((((((........(((((.......))))).)))))))....))...((((.((..((((....))))...))....)))).)))............ ( -25.60)
>DroPer_CAF1 18855 108 - 1
UACGGAGCUGCUGGCUAAGCUAAAGGCGGAAACCGACUUCCCAUCGUCCGCCGCCAGCAGCUACCCAAGGAUCAUCUUCCUGGGCACGGGCUCCUGCAUUCCCAACAA
...((((((((((((.........((((((...(((.......))))))))))))))))))).((((.(((......)))))))..(((....))).....))..... ( -42.60)
>consensus
UACGGAACUACUGGCCAAGUUAAAAGAAGAGUACAGCUUCCCUGACAACUCUGCCAACAGCUACCCAAAGAUCAUUUUCCUGGGCACGGGCUCCUGCAUUCCCAACAA
...((((((((((((.............(((......)))............))))))))...(((.((((......))))))).....((....)).))))...... (-18.85 = -17.91 +  -0.94)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:07:08 2006