Locus 4437

Sequence ID	3L_DroMel_CAF1
Location	12,944,370 – 12,944,648
Length	278
Max. P	0.997251

overview

Window 6

Location	12,944,370 – 12,944,490
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	96.50
Mean single sequence MFE	-37.12
Consensus MFE	-34.94
Energy contribution	-34.94
Covariance contribution	0.00
Combinations/Pair	1.00
Mean z-score	-1.94
Structure conservation index	0.94
SVM decision value	2.82
SVM RNA-class probability	0.997251
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 12944370 120 + 23771897
GCCACUUAACUGAGACACCUUUUUGGGGGCCAUGUUUUGUUAUUUGGAAAUACAUUUUCUGGCCAACAUGUUGCCCGAAAUGCCUGGGCUUAAUUUAUAUGUUGUCAGACCGGGUGGCAG
(((((((..((((....(((....)))(((((.....(((...........))).....)))))(((((((.(((((.......))))).......))))))).))))...))))))).. ( -36.50)
>DroSec_CAF1 61621 120 + 1
GCCACUUAACUGAGACACCUUUUUGGGGCCCAUGUUUUGUUAUUUGGAAAUACAUUUUCUGGCCAACAUGUUGCCCGAAAUGCCUGGGCUUAAUUUAUAUGUUGUCAGACCGGGUGGCAG
(((((((..((((((((((.....))(((((((((((((......(((((.....)))))(((.((....))))))))))))..)))))).........)))).))))...))))))).. ( -35.60)
>DroSim_CAF1 65967 120 + 1
GCCACUUAACUGAGACACCUUUUUGGGGCCCAUGUUUUGUUAUUUGGAAAUACAUUUUCUGGCCAACAUGUUGCCCGAAAUGCCUGGGCUUAAUUUAUAUGUUGUCAGACCGGGUGGCAG
(((((((..((((((((((.....))(((((((((((((......(((((.....)))))(((.((....))))))))))))..)))))).........)))).))))...))))))).. ( -35.60)
>DroEre_CAF1 67850 120 + 1
GCCACUUAACUGAGACACCUUCUUGGGAGCCGUGUUUUGUUAUUUGGAAAUACAUUCUCUGGACAACAUGUUGCCCGAAAUGCCUGGGCUUUAUUUAUAUGUUGUCAGACUGGGUGGCAG
((((((((.(.((((..(((....)))....(((((((........)))))))..)))).)((((((((((.(((((.......))))).......))))))))))....)))))))).. ( -41.10)
>DroYak_CAF1 65436 120 + 1
GCCACUUAACUGAGACACCUUUUUGGGACCCAUGUUUUGUUUUUUGGAAAUACAUUUUCUGGACAACAUGUUGCCCGAAAUGCCUGGGCUUAAUUUAUAUGUUGUCAGACCGGGUGGCAG
(((((((..((((((((...(((((((...(((((..(((((...(((((.....)))))))))))))))...))))))).((....))..........)))).))))...))))))).. ( -36.80)
>consensus
GCCACUUAACUGAGACACCUUUUUGGGGCCCAUGUUUUGUUAUUUGGAAAUACAUUUUCUGGCCAACAUGUUGCCCGAAAUGCCUGGGCUUAAUUUAUAUGUUGUCAGACCGGGUGGCAG
((((((((((.(((((((((....))).....)))))))))................(((((.((((((((.(((((.......))))).......)))))))))))))..))))))).. (-34.94 = -34.94 +   0.00)

alignment

secondary structure

dotplot

Window 7

Location	12,944,370 – 12,944,490
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	96.50
Mean single sequence MFE	-30.11
Consensus MFE	-25.54
Energy contribution	-25.74
Covariance contribution	0.20
Combinations/Pair	1.07
Mean z-score	-1.58
Structure conservation index	0.85
SVM decision value	0.57
SVM RNA-class probability	0.785201
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 12944370 120 - 23771897
CUGCCACCCGGUCUGACAACAUAUAAAUUAAGCCCAGGCAUUUCGGGCAACAUGUUGGCCAGAAAAUGUAUUUCCAAAUAACAAAACAUGGCCCCCAAAAAGGUGUCUCAGUUAAGUGGC
..(((((.....((((..((((.........((((.........))))....((..(((((.....((((((....))).))).....)))))..)).....)))).))))....))))) ( -29.20)
>DroSec_CAF1 61621 120 - 1
CUGCCACCCGGUCUGACAACAUAUAAAUUAAGCCCAGGCAUUUCGGGCAACAUGUUGGCCAGAAAAUGUAUUUCCAAAUAACAAAACAUGGGCCCCAAAAAGGUGUCUCAGUUAAGUGGC
..(((((.....((((..((((.........(((((.(((((((((.(((....))).)).).))))))...................))))).........)))).))))....))))) ( -30.32)
>DroSim_CAF1 65967 120 - 1
CUGCCACCCGGUCUGACAACAUAUAAAUUAAGCCCAGGCAUUUCGGGCAACAUGUUGGCCAGAAAAUGUAUUUCCAAAUAACAAAACAUGGGCCCCAAAAAGGUGUCUCAGUUAAGUGGC
..(((((.....((((..((((.........(((((.(((((((((.(((....))).)).).))))))...................))))).........)))).))))....))))) ( -30.32)
>DroEre_CAF1 67850 120 - 1
CUGCCACCCAGUCUGACAACAUAUAAAUAAAGCCCAGGCAUUUCGGGCAACAUGUUGUCCAGAGAAUGUAUUUCCAAAUAACAAAACACGGCUCCCAAGAAGGUGUCUCAGUUAAGUGGC
..(((((.....((((..((((.........((....)).((((((((((....)))))).))))))))....................(((.((......)).)))))))....))))) ( -29.70)
>DroYak_CAF1 65436 120 - 1
CUGCCACCCGGUCUGACAACAUAUAAAUUAAGCCCAGGCAUUUCGGGCAACAUGUUGUCCAGAAAAUGUAUUUCCAAAAAACAAAACAUGGGUCCCAAAAAGGUGUCUCAGUUAAGUGGC
..(((((..((....(((.............((....)).((((((((((....)))))).)))).)))....)).........(((.((((.(((.....)).).)))))))..))))) ( -31.00)
>consensus
CUGCCACCCGGUCUGACAACAUAUAAAUUAAGCCCAGGCAUUUCGGGCAACAUGUUGGCCAGAAAAUGUAUUUCCAAAUAACAAAACAUGGGCCCCAAAAAGGUGUCUCAGUUAAGUGGC
..(((((.....((((..((((.........(((((.(((((((((.(((....))).)).))).))))...................))))).........)))).))))....))))) (-25.54 = -25.74 +   0.20)

alignment

secondary structure

dotplot

Window 8

Location	12,944,410 – 12,944,528
Length	118
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	95.41
Mean single sequence MFE	-32.92
Consensus MFE	-26.92
Energy contribution	-27.12
Covariance contribution	0.20
Combinations/Pair	1.00
Mean z-score	-1.76
Structure conservation index	0.82
SVM decision value	0.71
SVM RNA-class probability	0.830053
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 12944410 118 + 23771897
UAUUUGGAAAUACAUUUUCUGGCCAACAUGUUGCCCGAAAUGCCUGGGCUUAAUUUAUAUGUUGUCAGACCGGGUGGCAGCAACAAAUGCAGC--CGCAAUAGUGGAAUUACUCAUACAC
............((((.((((((.(((((((.(((((.......))))).......)))))))))))))....(((((.(((.....))).))--)))...))))............... ( -31.70)
>DroSec_CAF1 61661 116 + 1
UAUUUGGAAAUACAUUUUCUGGCCAACAUGUUGCCCGAAAUGCCUGGGCUUAAUUUAUAUGUUGUCAGACCGGGUGGCAGCAACAAAUGCAGC--CGCAAUAGUGGAAUUACUCA--CAU
...((((..........((((((.(((((((.(((((.......))))).......)))))))))))))))))(((((.(((.....))).))--)))....((((......)))--).. ( -33.50)
>DroSim_CAF1 66007 116 + 1
UAUUUGGAAAUACAUUUUCUGGCCAACAUGUUGCCCGAAAUGCCUGGGCUUAAUUUAUAUGUUGUCAGACCGGGUGGCAGCAACAAAUGCAGC--CGCAAUAGUGGAAUUACUCA--CAC
...((((..........((((((.(((((((.(((((.......))))).......)))))))))))))))))(((((.(((.....))).))--)))....((((......)))--).. ( -33.50)
>DroEre_CAF1 67890 114 + 1
UAUUUGGAAAUACAUUCUCUGGACAACAUGUUGCCCGAAAUGCCUGGGCUUUAUUUAUAUGUUGUCAGACUGGGUGGCAGCAACAAAUGCAGC--CGCAAUAGUGGAAUUACUCA--C--
.............(((((...((((((((((.(((((.......))))).......))))))))))..((((.(((((.(((.....))).))--)))..)))))))))......--.-- ( -33.20)
>DroYak_CAF1 65476 118 + 1
UUUUUGGAAAUACAUUUUCUGGACAACAUGUUGCCCGAAAUGCCUGGGCUUAAUUUAUAUGUUGUCAGACCGGGUGGCAGCAACAAAUGCAGCACGGCAAUAGUGGAAUUACUCA--CAU
.....(((((.....))))).((((((((((.(((((.......))))).......)))))))))).(.(((.((.(((........))).)).))))....((((......)))--).. ( -32.70)
>consensus
UAUUUGGAAAUACAUUUUCUGGCCAACAUGUUGCCCGAAAUGCCUGGGCUUAAUUUAUAUGUUGUCAGACCGGGUGGCAGCAACAAAUGCAGC__CGCAAUAGUGGAAUUACUCA__CAC
.................(((((.((((((((.(((((.......))))).......)))))))))))))..(((((((.(((.....))).))..(((....)))....)))))...... (-26.92 = -27.12 +   0.20)

alignment

secondary structure

dotplot

Window 9

Location	12,944,528 – 12,944,648
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	92.78
Mean single sequence MFE	-37.70
Consensus MFE	-31.52
Energy contribution	-31.32
Covariance contribution	-0.20
Combinations/Pair	1.15
Mean z-score	-1.40
Structure conservation index	0.84
SVM decision value	0.33
SVM RNA-class probability	0.693451
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 12944528 120 + 23771897
ACACACGCUCAAUCUGAAACGUGGCCAGGUGAACUCCUGGCGAAAGUGAAACUGGGUCGCAAGAAAGUUGUCGGGCCACCACCCACUUUCCUUUUUGGCAAUGGGGGGGACAACAAGAUA
...((((.((.....))..))))((((((......))))))....((((.......))))......(((((((((......))).((..((...........))..))))))))...... ( -37.80)
>DroSec_CAF1 61777 119 + 1
ACACACGCUCAAUUCGAAACUUGGCCAGGUGAACUCCUGGCGAAAGUGAAACUGGGUCGCAAGAAAGUUGUCGGGCCACCACCCACUUUCCUUUUGGGCAAUGGG-GGGACAACAAGAUA
.......((((.((((....((.((((((......)))))).))..))))..))))((....))..((((((((....)).((((.(.(((....))).).))))-..))))))...... ( -38.10)
>DroSim_CAF1 66123 119 + 1
ACACACGCUCCAUCUGAAACUUGGCCAGGUGAACUCCUGGCGAAAGUGAAACUGGGUCGCAAGAAAGUUGUCGGGCCACCACCCACUUUCCUUUUGGGCAAUGGG-GGGACAACAAGAUA
........((((......((((.((((((......))))))..)))).....))))((....))..((((((((....)).((((.(.(((....))).).))))-..))))))...... ( -39.30)
>DroEre_CAF1 68004 114 + 1
--ACACGCUCAAUCUGAAACUUGGCCAGGUGAACUCCUGGCGAAAGUGAAACUGGGUCGCAAGAAAGUUUUCGGGCC---ACCCACUUUCCUUUUUGGCAAUGGG-GGGACAACGAGAUA
--.....(((..(((((.((((.((((((......))))))..)))).(((((...((....)).))))))))))((---.((((.((.((.....)).))))))-))......)))... ( -37.20)
>DroYak_CAF1 65594 116 + 1
ACACACGCCCAAUCUGAAACUUGGCCAGGUGAACUCUUGGUGAAAGUGAAACUGGGUCGCAAGAAAGUUUUCGGGCC---ACCCACUUUCUUUUUUGGCACUGGG-GGUACAACAAGAUA
....((.((((..(..((((((.((((((......))))))..))))((((.(((((.((..(((....)))..)).---))))).))))...))..)...))))-.))........... ( -36.10)
>consensus
ACACACGCUCAAUCUGAAACUUGGCCAGGUGAACUCCUGGCGAAAGUGAAACUGGGUCGCAAGAAAGUUGUCGGGCCACCACCCACUUUCCUUUUUGGCAAUGGG_GGGACAACAAGAUA
.....(.((((..((((((....((((((......))))))((((((((((((...((....)).)))).))(((......)))))))))..))))))...)))).)............. (-31.52 = -31.32 +  -0.20)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:22:46 2006