Locus 3496

Sequence ID	3R_DroMel_CAF1
Location	9,443,253 – 9,443,402
Length	149
Max. P	0.999915

overview

Window 7

Location	9,443,253 – 9,443,362
Length	109
Sequences	5
Columns	109
Reading direction	forward
Mean pairwise identity	97.80
Mean single sequence MFE	-34.02
Consensus MFE	-32.38
Energy contribution	-32.30
Covariance contribution	-0.08
Combinations/Pair	1.08
Mean z-score	-3.55
Structure conservation index	0.95
SVM decision value	4.53
SVM RNA-class probability	0.999915
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 9443253 109 + 27905053
AAUAAAGUCAUCACUAUUUGCAUGCACCGCAUGUUGGGAAUCCUUAAUAAUUUACAAUGGCAUGCCGUCAACUAAUUGUGGUGUUUGGGCUUCUUAGUUGACUUUGUUA
((((((((((..((((...((..(((((((((((((((....))))))).......((((....))))........))))))))....))....)))))))))))))). ( -33.40)
>DroSec_CAF1 72833 109 + 1
AAUAAAGUCAUCACUAUUUGCAUGCACCGCAUGUUGGGAAUCCUUAAUAAUUCACAAUGGCAUGCCGUCAACUAAUUGUGGUGUUUGGGAUUCUUAGUUGACUUUGUAA
.(((((((((.(.......((((((...))))))((((((((((.((((..((((((((((.....)))).....)))))))))).))))))))))).))))))))).. ( -35.00)
>DroSim_CAF1 61692 109 + 1
AAUAAAGUCAUCACUAUUUGCAUGCGCCGCAUGUUGGGAAUCCUUAAUAAUUCACAAUGGCAUGCCGUCAACUAAUUGUGGUGUUUGGGCUUCUUAGUUGACUUUGUAA
.(((((((((..((((...((..((((((((.(((((((((........))))...((((....))))...)))))))))))))....))....))))))))))))).. ( -33.40)
>DroEre_CAF1 81026 109 + 1
AAUAAAGUCAUCACUAUUUGCAUGCACCGCAUGUGGGGAAUCCUUAAUAAUUCACAAUGGCAUGCCGUCAACUAAUUGCGGUGUUUGGGCUUCUUAGUUGACUUUGUAA
.(((((((((..((((...((..((((((((((((((..((.....))..))))))((((....))))........))))))))....))....))))))))))))).. ( -34.50)
>DroYak_CAF1 75233 109 + 1
AAUAAAGUCAUCACUAUUUGCAUGCACCGCAUGUUGGGAAUCCUUAAUAAUUCACAAUGGCAUGCCGUCAACUAAUUGUGGUGUUUGGGCUUCUUAGUUGACUUUGUAA
.(((((((((..((((...((..((((((((.(((((((((........))))...((((....))))...)))))))))))))....))....))))))))))))).. ( -33.80)
>consensus
AAUAAAGUCAUCACUAUUUGCAUGCACCGCAUGUUGGGAAUCCUUAAUAAUUCACAAUGGCAUGCCGUCAACUAAUUGUGGUGUUUGGGCUUCUUAGUUGACUUUGUAA
.(((((((((..((((...((..((((((((.(((((((((........))))...((((....))))...)))))))))))))....))....))))))))))))).. (-32.38 = -32.30 +  -0.08)

alignment

secondary structure

dotplot

Window 8

Location	9,443,253 – 9,443,362
Length	109
Sequences	5
Columns	109
Reading direction	reverse
Mean pairwise identity	97.80
Mean single sequence MFE	-25.13
Consensus MFE	-23.33
Energy contribution	-23.73
Covariance contribution	0.40
Combinations/Pair	1.00
Mean z-score	-1.89
Structure conservation index	0.93
SVM decision value	2.19
SVM RNA-class probability	0.989995
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 9443253 109 - 27905053
UAACAAAGUCAACUAAGAAGCCCAAACACCACAAUUAGUUGACGGCAUGCCAUUGUAAAUUAUUAAGGAUUCCCAACAUGCGGUGCAUGCAAAUAGUGAUGACUUUAUU
.......(((((((((..................))))))))).((((((.((((((.........((....))....))))))))))))................... ( -22.09)
>DroSec_CAF1 72833 109 - 1
UUACAAAGUCAACUAAGAAUCCCAAACACCACAAUUAGUUGACGGCAUGCCAUUGUGAAUUAUUAAGGAUUCCCAACAUGCGGUGCAUGCAAAUAGUGAUGACUUUAUU
((((...(((((((((..................))))))))).((((((.((((((((((......))))).......))))))))))).....)))).......... ( -25.58)
>DroSim_CAF1 61692 109 - 1
UUACAAAGUCAACUAAGAAGCCCAAACACCACAAUUAGUUGACGGCAUGCCAUUGUGAAUUAUUAAGGAUUCCCAACAUGCGGCGCAUGCAAAUAGUGAUGACUUUAUU
((((...(((((((((..................))))))))).(((((((..((((((((......)))))...)))....).)))))).....)))).......... ( -24.77)
>DroEre_CAF1 81026 109 - 1
UUACAAAGUCAACUAAGAAGCCCAAACACCGCAAUUAGUUGACGGCAUGCCAUUGUGAAUUAUUAAGGAUUCCCCACAUGCGGUGCAUGCAAAUAGUGAUGACUUUAUU
((((...(((((((((...((.........))..))))))))).((((((.((((((((((......))))).......))))))))))).....)))).......... ( -27.61)
>DroYak_CAF1 75233 109 - 1
UUACAAAGUCAACUAAGAAGCCCAAACACCACAAUUAGUUGACGGCAUGCCAUUGUGAAUUAUUAAGGAUUCCCAACAUGCGGUGCAUGCAAAUAGUGAUGACUUUAUU
((((...(((((((((..................))))))))).((((((.((((((((((......))))).......))))))))))).....)))).......... ( -25.58)
>consensus
UUACAAAGUCAACUAAGAAGCCCAAACACCACAAUUAGUUGACGGCAUGCCAUUGUGAAUUAUUAAGGAUUCCCAACAUGCGGUGCAUGCAAAUAGUGAUGACUUUAUU
((((...(((((((((..................))))))))).(((((((..((((((((......)))))...)))....).)))))).....)))).......... (-23.33 = -23.73 +   0.40)

alignment

secondary structure

dotplot

Window 9

Location	9,443,282 – 9,443,402
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	95.67
Mean single sequence MFE	-23.16
Consensus MFE	-19.99
Energy contribution	-19.83
Covariance contribution	-0.16
Combinations/Pair	1.03
Mean z-score	-1.65
Structure conservation index	0.86
SVM decision value	1.11
SVM RNA-class probability	0.916802
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 9443282 120 - 27905053
UAGGAGCAAAUGAUUAUUAAUUUAUGCUCAGUUACUGCAAUAACAAAGUCAACUAAGAAGCCCAAACACCACAAUUAGUUGACGGCAUGCCAUUGUAAAUUAUUAAGGAUUCCCAACAUG
...(((((...(((.....)))..))))).(((..((((((......(((((((((..................)))))))))((....)))))))).........((....)))))... ( -23.77)
>DroSec_CAF1 72862 120 - 1
UAGGACCAAAUGAUUAUUAAUUUAUGCUCAAUUACUGCAAUUACAAAGUCAACUAAGAAUCCCAAACACCACAAUUAGUUGACGGCAUGCCAUUGUGAAUUAUUAAGGAUUCCCAACAUG
..(((((.(((((((.........(((.........)))..(((((.(((((((((..................)))))))))((....)).))))))))))))..))..)))....... ( -22.27)
>DroSim_CAF1 61721 120 - 1
UAGGAGCAAAUGAUUAUUAAUUUAUGCUCAAUUACUGCAAUUACAAAGUCAACUAAGAAGCCCAAACACCACAAUUAGUUGACGGCAUGCCAUUGUGAAUUAUUAAGGAUUCCCAACAUG
...(((((...(((.....)))..)))))...........((((((.(((((((((..................)))))))))((....)).))))))........((....))...... ( -23.07)
>DroEre_CAF1 81055 116 - 1
----UGCUAAUGAUUAUUAAUUUAUGCUCAAUUACUGCAAUUACAAAGUCAACUAAGAAGCCCAAACACCGCAAUUAGUUGACGGCAUGCCAUUGUGAAUUAUUAAGGAUUCCCCACAUG
----...((((((((.........(((.........)))..(((((.(((((((((...((.........))..)))))))))((....)).))))))))))))).((.....))..... ( -23.60)
>DroYak_CAF1 75262 120 - 1
UAGGAGCAAAUGAUUAUUAAUUUAUGCUCAAUUACUGCAAUUACAAAGUCAACUAAGAAGCCCAAACACCACAAUUAGUUGACGGCAUGCCAUUGUGAAUUAUUAAGGAUUCCCAACAUG
...(((((...(((.....)))..)))))...........((((((.(((((((((..................)))))))))((....)).))))))........((....))...... ( -23.07)
>consensus
UAGGAGCAAAUGAUUAUUAAUUUAUGCUCAAUUACUGCAAUUACAAAGUCAACUAAGAAGCCCAAACACCACAAUUAGUUGACGGCAUGCCAUUGUGAAUUAUUAAGGAUUCCCAACAUG
.........(((.(((.((((((.(((.........)))...((((.(((((((((..................)))))))))((....)).)))))))))).)))((....))..))). (-19.99 = -19.83 +  -0.16)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:02:35 2006