Locus 6229

Sequence ID	3R_DroMel_CAF1
Location	16,279,946 – 16,280,106
Length	160
Max. P	0.809417

overview

Window 5

Location	16,279,946 – 16,280,066
Length	120
Sequences	3
Columns	120
Reading direction	forward
Mean pairwise identity	98.33
Mean single sequence MFE	-35.03
Consensus MFE	-32.70
Energy contribution	-33.37
Covariance contribution	0.67
Combinations/Pair	1.00
Mean z-score	-1.81
Structure conservation index	0.93
SVM decision value	0.31
SVM RNA-class probability	0.681345
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 16279946 120 + 27905053
CAUAUUUCAUGCAAGAGAGUAAAAAGCUAUUAGGGCUAGCCCUGGUGCUGGGAAAAACGGGAAAAGACAGCAGCUCCAACGACAGCUGUCUUCAACUGCAGCCCGAGUGCAUAAAUCUUG
........(((((...........(((.(((((((....))))))))))(((.....(((...((((((((.(.((....))).))))))))...)))...)))...)))))........ ( -36.00)
>DroSec_CAF1 626 120 + 1
CAUAUUUCAUGCAAGAGAGUAAAAAGCUAUUAGGACUAGCCCUGGUGCUGGGAAAAACGGGAAAAGACAGCAGCUCCAACGACAGCUGUCUUCAACUGCAGCCCGAGUGCAUAAAUCUUG
........(((((...........(((.((((((......)))))))))(((.....(((...((((((((.(.((....))).))))))))...)))...)))...)))))........ ( -32.00)
>DroYak_CAF1 1529 120 + 1
CAUAUUUCAUGCACGAGAGUAAAAAGCUAUUAGGGCUAGCCCUGCUGCUGGGAAAAACGGGAAAAGACAGCAGCUCCAACGACAGCUGUCUUCAACUGCAGCCCGAGUGCAUAAAUCUUG
........((((((..........(((...(((((....)))))..)))(((.....(((...((((((((.(.((....))).))))))))...)))...)))..))))))........ ( -37.10)
>consensus
CAUAUUUCAUGCAAGAGAGUAAAAAGCUAUUAGGGCUAGCCCUGGUGCUGGGAAAAACGGGAAAAGACAGCAGCUCCAACGACAGCUGUCUUCAACUGCAGCCCGAGUGCAUAAAUCUUG
........(((((...........(((.(((((((....))))))))))(((.....(((...((((((((.(.((....))).))))))))...)))...)))...)))))........ (-32.70 = -33.37 +   0.67)

alignment

secondary structure

dotplot

Window 6

Location	16,279,946 – 16,280,066
Length	120
Sequences	3
Columns	120
Reading direction	reverse
Mean pairwise identity	98.33
Mean single sequence MFE	-37.11
Consensus MFE	-35.52
Energy contribution	-35.30
Covariance contribution	-0.22
Combinations/Pair	1.03
Mean z-score	-1.92
Structure conservation index	0.96
SVM decision value	0.64
SVM RNA-class probability	0.809417
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 16279946 120 - 27905053
CAAGAUUUAUGCACUCGGGCUGCAGUUGAAGACAGCUGUCGUUGGAGCUGCUGUCUUUUCCCGUUUUUCCCAGCACCAGGGCUAGCCCUAAUAGCUUUUUACUCUCUUGCAUGAAAUAUG
.....((((((((...(((..((.(..(((((((((.((.......)).)))))))))..).))....)))(((...((((....))))....)))...........))))))))..... ( -36.20)
>DroSec_CAF1 626 120 - 1
CAAGAUUUAUGCACUCGGGCUGCAGUUGAAGACAGCUGUCGUUGGAGCUGCUGUCUUUUCCCGUUUUUCCCAGCACCAGGGCUAGUCCUAAUAGCUUUUUACUCUCUUGCAUGAAAUAUG
.....((((((((...(((..((.(..(((((((((.((.......)).)))))))))..).))....)))......(((((((.......))))))).........))))))))..... ( -33.80)
>DroYak_CAF1 1529 120 - 1
CAAGAUUUAUGCACUCGGGCUGCAGUUGAAGACAGCUGUCGUUGGAGCUGCUGUCUUUUCCCGUUUUUCCCAGCAGCAGGGCUAGCCCUAAUAGCUUUUUACUCUCGUGCAUGAAAUAUG
.....(((((((((((.(((.(((((((....))))))).))).))(((((((.................)))))))((((....)))).................)))))))))..... ( -41.33)
>consensus
CAAGAUUUAUGCACUCGGGCUGCAGUUGAAGACAGCUGUCGUUGGAGCUGCUGUCUUUUCCCGUUUUUCCCAGCACCAGGGCUAGCCCUAAUAGCUUUUUACUCUCUUGCAUGAAAUAUG
.....((((((((...(((..((.(..(((((((((.((.......)).)))))))))..).))....)))(((...((((....))))....)))...........))))))))..... (-35.52 = -35.30 +  -0.22)

alignment

secondary structure

dotplot

Window 7

Location	16,279,986 – 16,280,106
Length	120
Sequences	3
Columns	120
Reading direction	forward
Mean pairwise identity	98.89
Mean single sequence MFE	-39.73
Consensus MFE	-37.90
Energy contribution	-38.23
Covariance contribution	0.33
Combinations/Pair	1.00
Mean z-score	-1.78
Structure conservation index	0.95
SVM decision value	0.41
SVM RNA-class probability	0.725419
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 16279986 120 + 27905053
CCUGGUGCUGGGAAAAACGGGAAAAGACAGCAGCUCCAACGACAGCUGUCUUCAACUGCAGCCCGAGUGCAUAAAUCUUGCGCGGAAAUGUCAGCGCAGGACGUUCGACAAAAACGCGCC
....(..(((((.....(((...((((((((.(.((....))).))))))))...)))...))).))..).........(((((....((((((((.....)))).))))....))))). ( -40.00)
>DroSec_CAF1 666 120 + 1
CCUGGUGCUGGGAAAAACGGGAAAAGACAGCAGCUCCAACGACAGCUGUCUUCAACUGCAGCCCGAGUGCAUAAAUCUUGCGCGGAAAUGUCAGCGCAGAACGUUCGACAAAAACGCGCC
....(..(((((.....(((...((((((((.(.((....))).))))))))...)))...))).))..).........(((((....((((((((.....)))).))))....))))). ( -40.00)
>DroYak_CAF1 1569 120 + 1
CCUGCUGCUGGGAAAAACGGGAAAAGACAGCAGCUCCAACGACAGCUGUCUUCAACUGCAGCCCGAGUGCAUAAAUCUUGCGCGGAAAUGUCAGCGCAGGACGUUCGACAAAAACGCGCC
..(((.((((((.....(((...((((((((.(.((....))).))))))))...)))...))).))))))........(((((....((((((((.....)))).))))....))))). ( -39.20)
>consensus
CCUGGUGCUGGGAAAAACGGGAAAAGACAGCAGCUCCAACGACAGCUGUCUUCAACUGCAGCCCGAGUGCAUAAAUCUUGCGCGGAAAUGUCAGCGCAGGACGUUCGACAAAAACGCGCC
....((((((((.....(((...((((((((.(.((....))).))))))))...)))...))).))))).........(((((....((((((((.....)))).))))....))))). (-37.90 = -38.23 +   0.33)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:16:06 2006