Locus 919

Sequence ID 3R_DroMel_CAF1
Location 3,109,485 – 3,109,604
Length 119
Max. P 0.927432
window1456 window1457

overview

Window 6

Location 3,109,485 – 3,109,604
Length 119
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 89.74
Mean single sequence MFE -23.84
Consensus MFE -22.61
Energy contribution -22.83
Covariance contribution 0.23
Combinations/Pair 1.08
Mean z-score -1.98
Structure conservation index 0.95
SVM decision value 1.18
SVM RNA-class probability 0.927432
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 3109485 119 + 27905053
CAUUUUGAACCCCCCCCCCCCCCGUUCGCAAAACACAAUCAUUU-UUUUGCAGUCAUUUCCCCACCGCUUUGGUGGUGUUGCUAUUGCUGUUGCAUUUGCAUCUGUGUUUUCGCUUUUAG
......((((.............))))((((((((((.......-....(((((.((.....((((((....)))))).....)).)))))(((....)))..)))))))).))...... ( -27.22)
>DroSim_CAF1 2399 112 + 1
CAUUUUGA--------CCCCCCCGUUCGCAAAACACAAUCAUUUUUUUUGCAGUCAUUUCCCCACCGCUUUGCUGGUGUUGCUAUUGCUGUUGCAUUUGCAUCUGUGUUUUCGCUUUUAG
........--------...........((((((((((............(((((.((.....((((((...)).)))).....)).)))))(((....)))..)))))))).))...... ( -22.10)
>DroYak_CAF1 98 110 + 1
CAUUUUGA--------CC-CCCCUUUUGCAAAACACAAUAAUUU-UUUUGCAGCCAUUUCCCCACUGCCUUGGUGCUGUUGCUAUUGCUGUUGCAUUUGCAUCUGUGUUUUCGCUUUUAG
........--------..-........((((((((((.......-....((((...........))))...(((((...(((..........)))...))))))))))))).))...... ( -22.20)
>consensus
CAUUUUGA________CCCCCCCGUUCGCAAAACACAAUCAUUU_UUUUGCAGUCAUUUCCCCACCGCUUUGGUGGUGUUGCUAUUGCUGUUGCAUUUGCAUCUGUGUUUUCGCUUUUAG
...........................((((((((((............(((((.((.....((((((....)))))).....)).)))))(((....)))..)))))))).))...... (-22.61 = -22.83 +   0.23)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 7

Location 3,109,485 – 3,109,604
Length 119
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 89.74
Mean single sequence MFE -25.16
Consensus MFE -23.71
Energy contribution -23.27
Covariance contribution -0.44
Combinations/Pair 1.09
Mean z-score -1.44
Structure conservation index 0.94
SVM decision value 0.29
SVM RNA-class probability 0.668453
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 3109485 119 - 27905053
CUAAAAGCGAAAACACAGAUGCAAAUGCAACAGCAAUAGCAACACCACCAAAGCGGUGGGGAAAUGACUGCAAAA-AAAUGAUUGUGUUUUGCGAACGGGGGGGGGGGGGGUUCAAAAUG
......((.(((((((((.(((....)))...(((.........(((((.....))))).........)))....-......)))))))))))((((.............))))...... ( -27.59)
>DroSim_CAF1 2399 112 - 1
CUAAAAGCGAAAACACAGAUGCAAAUGCAACAGCAAUAGCAACACCAGCAAAGCGGUGGGGAAAUGACUGCAAAAAAAAUGAUUGUGUUUUGCGAACGGGGGGG--------UCAAAAUG
((....((.(((((((((.(((....))).(((..((..(..((((.((...))))))..)..))..)))............))))))))))).....))....--------........ ( -24.10)
>DroYak_CAF1 98 110 - 1
CUAAAAGCGAAAACACAGAUGCAAAUGCAACAGCAAUAGCAACAGCACCAAGGCAGUGGGGAAAUGGCUGCAAAA-AAAUUAUUGUGUUUUGCAAAAGGGG-GG--------UCAAAAUG
......((.(((((((((.(((...(((....)))...)))...........(((((.(.....).)))))....-......)))))))))))........-..--------........ ( -23.80)
>consensus
CUAAAAGCGAAAACACAGAUGCAAAUGCAACAGCAAUAGCAACACCACCAAAGCGGUGGGGAAAUGACUGCAAAA_AAAUGAUUGUGUUUUGCGAACGGGGGGG________UCAAAAUG
......((.(((((((((.(((...(((....)))...)))...........(((((.(.....).)))))...........)))))))))))........................... (-23.71 = -23.27 +  -0.44)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:55:24 2006