Locus 2698

Sequence ID	2R_DroMel_CAF1
Location	9,509,466 – 9,509,659
Length	193
Max. P	0.988450

overview

Window 8

Location	9,509,466 – 9,509,586
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	95.83
Mean single sequence MFE	-34.96
Consensus MFE	-31.60
Energy contribution	-32.28
Covariance contribution	0.68
Combinations/Pair	1.05
Mean z-score	-1.68
Structure conservation index	0.90
SVM decision value	1.73
SVM RNA-class probability	0.974348
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 9509466 120 - 20766785
GUUCGCGAUACGGAGGCAAACCUGUAGCAGCCAACUGCAGCAGACGAAGCGAGGUGAGGCCAAGUAAACCUGUUUACAGUUCAAACUUCGCAUUCGAUAUAUUCGAUGUGAACUCUUUUU
(((((((...((((.......((((.((((....)))).)))).(((((((((((..(..(..(((((....))))).)..)..))))))).)))).....)))).)))))))....... ( -37.90)
>DroSec_CAF1 6474 120 - 1
GUUCGCGAUACAGAGGCAAACCUGUAGCAGCCAACUGCAGCAGACGAAGCGAGGUGAGGCCAAGUAAACCUGUUUACAGUUUAAACUUCGCAUUCGAUAUAUUCGAUGUGAACUCUUUUU
(((((((..............((((.((((....)))).)))).(((((((((((.((((...(((((....))))).))))..))))))).))))..........)))))))....... ( -35.70)
>DroSim_CAF1 6483 120 - 1
GUUCGCGAUACAGAGGCAAACCUGUAGCAGCCAACUGCAGCAGACGUAGCGAGGUGAGGCCAAGUAAACCUGUUUACAGUUCAAACUUCGCAUUCGAUAUAUUCGAUGUGAACUCUUUUU
(((((((..............((((.((((....)))).)))).....(((((((..(..(..(((((....))))).)..)..)))))))..((((.....)))))))))))....... ( -35.00)
>DroEre_CAF1 6486 120 - 1
GUUCGCGGUAAAGAGGAAAACCUGUAGCUACCAACUGCAGCAGACGAAGCGAGGUGAGGCCAAGUAAACCUGUUUACAGUUCAAACUUCGCAUUCGAUAUAUUCGAUGUGAACUCUUUUU
(((((((.....(((......((((.((........)).)))).(((((((((((..(..(..(((((....))))).)..)..))))))).)))).....)))..)))))))....... ( -33.60)
>DroYak_CAF1 6394 120 - 1
GUUCGCUAUACAGAGGAGUACCUGUAGCUACCAACUGCAGCAGACGAAGCGAGGUGAGGCCAAGUAAACCUGUUUACAGUUCAAACUUCGCAUUCGAUAUAUUCGAUGUGAACUCUUUUU
((((((.((...(((......((((.((........)).)))).(((((((((((..(..(..(((((....))))).)..)..))))))).)))).....))).))))))))....... ( -32.60)
>consensus
GUUCGCGAUACAGAGGCAAACCUGUAGCAGCCAACUGCAGCAGACGAAGCGAGGUGAGGCCAAGUAAACCUGUUUACAGUUCAAACUUCGCAUUCGAUAUAUUCGAUGUGAACUCUUUUU
((((((.((...(((......((((.((((....)))).)))).(((((((((((..(..(..(((((....))))).)..)..))))))).)))).....))).))))))))....... (-31.60 = -32.28 +   0.68)

alignment

secondary structure

dotplot

Window 9

Location	9,509,546 – 9,509,659
Length	113
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	75.32
Mean single sequence MFE	-30.16
Consensus MFE	-14.50
Energy contribution	-14.94
Covariance contribution	0.44
Combinations/Pair	1.07
Mean z-score	-2.41
Structure conservation index	0.48
SVM decision value	2.12
SVM RNA-class probability	0.988450
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 9509546 113 - 20766785
UAACUUAAGUGAAAUAAGGCUUAUGUUAUAUGGAUUCAAAA-AUGA-----AUGAAU-ACAGGAAAUUCCAUGGCGCGCAGUUCGCGAUACGGAGGCAAACCUGUAGCAGCCAACUGCAG
((((.(((((........))))).)))).....(((((...-.)))-----))...(-(((((...((((.((.((((.....)))).)).)))).....))))))((((....)))).. ( -28.60)
>DroSec_CAF1 6554 115 - 1
UAAUUUAAGUGGAUAAAGGCUUAAGUUAUAUGGGUUCAAAAAAUGA-----AUUCGUAACAGGAAAUUCCAUGGUGCGCAGUUCGCGAUACAGAGGCAAACCUGUAGCAGCCAACUGCAG
((((((((((........))))))))))((((((((((.....)))-----))))))).((((.....)).))....((((((.((..(((((.(.....))))))...)).)))))).. ( -35.10)
>DroSim_CAF1 6563 115 - 1
UAAUUUAAGUGAACAAAGGCUUAAGUUAUAUGGGUUCAAAAAAUGA-----AUUCGUAACAGGAAAUUCCAUGGUGCGCAGUUCGCGAUACAGAGGCAAACCUGUAGCAGCCAACUGCAG
((((((((((........))))))))))((((((((((.....)))-----))))))).((((.....)).))....((((((.((..(((((.(.....))))))...)).)))))).. ( -35.10)
>DroEre_CAF1 6566 105 - 1
UGUUUA-CGUAAACUACG--------------GGUUCAACAAAUGAAACAAAUUCGUUACAGAAAAUUCCACGGGCAGCAGUUCGCGGUAAAGAGGAAAACCUGUAGCUACCAACUGCAG
(((...-.(((..(((((--------------((((...(.((((((.....))))))..........((.(((((....))))).))......)...))))))))).))).....))). ( -23.00)
>DroYak_CAF1 6474 110 - 1
UGAUUU-AGUGAACUAGGACU--------AU-AGUUCCAAAAAUUAAACAUAUUUGUUACAGAAACUUCAAUGGUCCGCAGUUCGCUAUACAGAGGAGUACCUGUAGCUACCAACUGCAG
.....(-((((((((.(((((--------((-.((..((((.((.....)).))))..)).((....)).)))))))..)))))))))(((((.(.....))))))((........)).. ( -29.00)
>consensus
UAAUUUAAGUGAACUAAGGCUUA_GUUAUAUGGGUUCAAAAAAUGA_____AUUCGUAACAGGAAAUUCCAUGGUGCGCAGUUCGCGAUACAGAGGCAAACCUGUAGCAGCCAACUGCAG
.............................................................................((((((.((..(((((.(.....))))))...)).)))))).. (-14.50 = -14.94 +   0.44)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:36:48 2006