Locus 2649

Sequence ID	3L_DroMel_CAF1
Location	7,340,501 – 7,340,621
Length	120
Max. P	0.999874

overview

Window 3

Location	7,340,501 – 7,340,621
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	75.67
Mean single sequence MFE	-26.73
Consensus MFE	-16.06
Energy contribution	-16.62
Covariance contribution	0.56
Combinations/Pair	1.19
Mean z-score	-2.62
Structure conservation index	0.60
SVM decision value	2.82
SVM RNA-class probability	0.997225
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 7340501 120 + 23771897
UUACGAAACUGUUUCGAAAAAGUCGGUCUUUAAGGCAACAAAAUUGCUCAAGAAUAUUGAAAUUCACCAUAUUCCUGUACUUUUCGUGAAAAGUUUUUUUCGUCAAACCUAAAGACCAAC
...((((.....))))........((((((((.(((((.....)))))((.((((((((.....))..)))))).)).((((((....))))))...............))))))))... ( -21.10)
>DroSec_CAF1 5500 119 + 1
UUACGAAACUGUUUCGAAAAAGUCGGUCUUUAAGGCAAAGAAAUUGCUCAAGAAUAUGGAAAUUCACCAUAUUCCUGUACUUUUCGUGAAGAGCUC-UUUCGUCAAAACUAAAGACCAAC
...((((.....))))........((((((((.......((((..((((..((((((((.......))))))))...(((.....)))..))))..-))))........))))))))... ( -30.46)
>DroSim_CAF1 5561 119 + 1
UUACGAAACUGUUUCGAAAUAGUCGGUCUUUAAGGCAACGAAAUUGCUCAAGAAUAUGGAAAUUCACCAUAUUCCUGUACUUCUCGCGAAGAGCUC-UUUCGUCAAAACUAAAGACCAAC
.......((((((....)))))).((((((((.....((((((..((((..((((((((.......))))))))......(((....)))))))..-))))))......))))))))... ( -33.80)
>DroEre_CAF1 5628 111 + 1
UUACGAAACUGCUUCGAAAAAGCCGGUCUUUAGGGCAACAAAAGUGCUCAAGAAUAUUUCAGUUCAUAAUCUUUGUGCGCUAUUUGUAAAGAGCUA-CC------UAACUAAAGACCA--
...((((.....))))........(((((((((....((((((((((.(((((.(((........))).)).))).))))).)))))..((.....-.)------)..))))))))).-- ( -27.60)
>DroYak_CAF1 5599 93 + 1
UUACGAAACU--------AAAGUCGGUCUUUAGAGCAACAAACGUGCUCAAGAAUAUUGCAGUUCAUAAUCUUUC--------UUGCAAAGAGCUA-CC------U----AAAGACCAGC
..........--------......((((((((((((.......(.((((((.....))).))).)....(((((.--------....)))))))).-.)------)----)))))))... ( -20.70)
>consensus
UUACGAAACUGUUUCGAAAAAGUCGGUCUUUAAGGCAACAAAAUUGCUCAAGAAUAUUGAAAUUCACCAUAUUCCUGUACUUUUCGUGAAGAGCUA_UUUCGUCAAAACUAAAGACCAAC
........................((((((((.(((((.....)))))...((((((((.......))))))))...................................))))))))... (-16.06 = -16.62 +   0.56)

alignment

secondary structure

dotplot

Window 4

Location	7,340,501 – 7,340,621
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	75.67
Mean single sequence MFE	-34.43
Consensus MFE	-19.46
Energy contribution	-22.42
Covariance contribution	2.96
Combinations/Pair	1.07
Mean z-score	-3.60
Structure conservation index	0.57
SVM decision value	4.34
SVM RNA-class probability	0.999874
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 7340501 120 - 23771897
GUUGGUCUUUAGGUUUGACGAAAAAAACUUUUCACGAAAAGUACAGGAAUAUGGUGAAUUUCAAUAUUCUUGAGCAAUUUUGUUGCCUUAAAGACCGACUUUUUCGAAACAGUUUCGUAA
((((((((((((((..(((((((...((((((....)))))).(((((((((((......)).))))))))).....)))))))))).))))))))))).....((((.....))))... ( -36.40)
>DroSec_CAF1 5500 119 - 1
GUUGGUCUUUAGUUUUGACGAAA-GAGCUCUUCACGAAAAGUACAGGAAUAUGGUGAAUUUCCAUAUUCUUGAGCAAUUUCUUUGCCUUAAAGACCGACUUUUUCGAAACAGUUUCGUAA
((((((((((((....((.((((-..((((...((.....))..((((((((((.......))))))))))))))..))))))....)))))))))))).....((((.....))))... ( -35.70)
>DroSim_CAF1 5561 119 - 1
GUUGGUCUUUAGUUUUGACGAAA-GAGCUCUUCGCGAGAAGUACAGGAAUAUGGUGAAUUUCCAUAUUCUUGAGCAAUUUCGUUGCCUUAAAGACCGACUAUUUCGAAACAGUUUCGUAA
((((((((((((...((((((((-..(((((((....))))..(((((((((((.......))))))))))))))..))))))))..)))))))))))).....((((.....))))... ( -46.50)
>DroEre_CAF1 5628 111 - 1
--UGGUCUUUAGUUA------GG-UAGCUCUUUACAAAUAGCGCACAAAGAUUAUGAACUGAAAUAUUCUUGAGCACUUUUGUUGCCCUAAAGACCGGCUUUUUCGAAGCAGUUUCGUAA
--.(((((((((...------((-((((...........((.((...((((.(((........))).))))..)).))...))))))))))))))).(((((...))))).......... ( -28.04)
>DroYak_CAF1 5599 93 - 1
GCUGGUCUUU----A------GG-UAGCUCUUUGCAA--------GAAAGAUUAUGAACUGCAAUAUUCUUGAGCACGUUUGUUGCUCUAAAGACCGACUUU--------AGUUUCGUAA
..((((((((----(------((-((((....(((..--------..((((.(((........))).))))..))).....))))).)))))))))).....--------.......... ( -25.50)
>consensus
GUUGGUCUUUAGUUUUGACGAAA_GAGCUCUUCACGAAAAGUACAGGAAUAUGGUGAAUUUCAAUAUUCUUGAGCAAUUUUGUUGCCUUAAAGACCGACUUUUUCGAAACAGUUUCGUAA
((((((((((((...............................(((((((((((.......))))))))))).((((.....)))).))))))))))))..................... (-19.46 = -22.42 +   2.96)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:38:28 2006