Locus 8309

Sequence ID	3L_DroMel_CAF1
Location	21,753,064 – 21,753,184
Length	120
Max. P	0.833579

overview

Window 1

Location	21,753,064 – 21,753,184
Length	120
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	86.85
Mean single sequence MFE	-33.27
Consensus MFE	-25.30
Energy contribution	-27.80
Covariance contribution	2.50
Combinations/Pair	1.03
Mean z-score	-1.90
Structure conservation index	0.76
SVM decision value	0.66
SVM RNA-class probability	0.814099
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 21753064 120 + 23771897
UGUAGAUGCUUGUUGCAGAUACUUUCGCAAUGAGUUUUAUUGGUGUCGCUCCGUAGAGAUCGAUAGAGAUCUACGGAUCUCUGGAAAGCAUCUGGCAUGAAGGGAUAACGAUAAGGUAAA
.......(((..((((.((.....))))))..)))(((((((.((((.((.(((..(((((..((((((((....))))))))....).))))...))).)).)))).)))))))..... ( -37.30)
>DroSec_CAF1 38276 110 + 1
UGUAGAUGCUUGUUGCAGAUACUUUCGCAAUGAGUUUUAUUGGUGUCGCUCGAUA----------GAGAUCUACGGAUCUCGGGAAAGCGUCUGGCAUGAAGGGAUAACGAUAAGGUAAA
.......(((..((((.((.....))))))..)))(((((((.((((.((((...----------((((((....))))))......((.....)).)).)).)))).)))))))..... ( -32.70)
>DroSim_CAF1 40868 120 + 1
UGUAGAUGCUUGUUGCAGAUACUUUCGCAAUGAGUUUUAUUGGUGUCGCUCGAUAGAGAUCGAUAGAGAUCUACGGAUCUCGGGAAAGCGUCUGGCACGAAGGGAUAACGAUAAGGUAAA
........(((((((((((..(((((.(.........(((((((.((........)).)))))))((((((....))))))).)))))..))))...(....).....)))))))..... ( -39.10)
>DroEre_CAF1 20615 109 + 1
UGUAGAUGCUUGUUGCAGAUACUUUCGCAAUGAGUUUUAUUUGUGUCGC-----------CGAUAGAGCUCUACCGAUCAAAGAAAAGCCCCUGGCAUGAAGGGAUAAAGAUAAGGUAAA
.(((..(((.....)))..))).........((((((((((.(.....)-----------.))))))))))((((.(((...(.....)((((.......)))).....)))..)))).. ( -24.00)
>consensus
UGUAGAUGCUUGUUGCAGAUACUUUCGCAAUGAGUUUUAUUGGUGUCGCUCGAUA_____CGAUAGAGAUCUACGGAUCUCGGGAAAGCGUCUGGCAUGAAGGGAUAACGAUAAGGUAAA
.......(((..((((.((.....))))))..)))(((((((.((((.((...............((((((....))))))......((.....))....)).)))).)))))))..... (-25.30 = -27.80 +   2.50)

alignment

secondary structure

dotplot

Window 2

Location	21,753,064 – 21,753,184
Length	120
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	86.85
Mean single sequence MFE	-25.27
Consensus MFE	-17.27
Energy contribution	-17.46
Covariance contribution	0.19
Combinations/Pair	1.12
Mean z-score	-2.28
Structure conservation index	0.68
SVM decision value	0.72
SVM RNA-class probability	0.833579
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 21753064 120 - 23771897
UUUACCUUAUCGUUAUCCCUUCAUGCCAGAUGCUUUCCAGAGAUCCGUAGAUCUCUAUCGAUCUCUACGGAGCGACACCAAUAAAACUCAUUGCGAAAGUAUCUGCAACAAGCAUCUACA
...........((.....(((..(((.((((((((((.(((((((.((((....)))).))))))).....((((...............)))))))))))))))))..))).....)). ( -31.36)
>DroSec_CAF1 38276 110 - 1
UUUACCUUAUCGUUAUCCCUUCAUGCCAGACGCUUUCCCGAGAUCCGUAGAUCUC----------UAUCGAGCGACACCAAUAAAACUCAUUGCGAAAGUAUCUGCAACAAGCAUCUACA
...........((.....(((..(((.((((((((....((((((....))))))----------....))))).................(((....)))))))))..))).....)). ( -22.30)
>DroSim_CAF1 40868 120 - 1
UUUACCUUAUCGUUAUCCCUUCGUGCCAGACGCUUUCCCGAGAUCCGUAGAUCUCUAUCGAUCUCUAUCGAGCGACACCAAUAAAACUCAUUGCGAAAGUAUCUGCAACAAGCAUCUACA
...........((.....(((..(((.((((((((....((((((.((((....)))).))))))....))))).................(((....)))))))))..))).....)). ( -28.00)
>DroEre_CAF1 20615 109 - 1
UUUACCUUAUCUUUAUCCCUUCAUGCCAGGGGCUUUUCUUUGAUCGGUAGAGCUCUAUCG-----------GCGACACAAAUAAAACUCAUUGCGAAAGUAUCUGCAACAAGCAUCUACA
................((((.......))))((((....(((.(((((((....))))))-----------))))................(((....)))........))))....... ( -19.40)
>consensus
UUUACCUUAUCGUUAUCCCUUCAUGCCAGACGCUUUCCCGAGAUCCGUAGAUCUCUAUCG_____UAUCGAGCGACACCAAUAAAACUCAUUGCGAAAGUAUCUGCAACAAGCAUCUACA
......................((((((((.((((((..((((((....))))))................((((...............)))))))))).))))......))))..... (-17.27 = -17.46 +   0.19)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:12:16 2006