Locus 938

Sequence ID	3L_DroMel_CAF1
Location	2,813,162 – 2,813,309
Length	147
Max. P	0.898587

overview

Window 1

Location	2,813,162 – 2,813,282
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	98.33
Mean single sequence MFE	-22.54
Consensus MFE	-22.24
Energy contribution	-21.92
Covariance contribution	-0.32
Combinations/Pair	1.06
Mean z-score	-1.39
Structure conservation index	0.99
SVM decision value	1.00
SVM RNA-class probability	0.898587
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 2813162 120 + 23771897
UAUUCCAAUCAUUCUUUGAACACAAUAUGGAUUGGAUUGGCCUUAACUAAUUCCAAAAUGAGCCGAAUCAAAUCCCUUGGCCUCAACGUACAUCACGUCCAAAUGGAUAUGUUUUCACAC
...(((((((.....(((....)))....)))))))..((((.................).)))(((.((.((((.((((.....((((.....))))))))..)))).))..))).... ( -22.83)
>DroSec_CAF1 58210 120 + 1
UAUUCCAAUCAUUCUUUGAACACAAUAUGGAUUGGAUUGGCCUUAACUAAUUCCAAAAUGAGCCGAAUCAAAUCCCUUGGCCUCAACGUACAUCACGUCCAAAUGGAUAUGUUUUCACAC
...(((((((.....(((....)))....)))))))..((((.................).)))(((.((.((((.((((.....((((.....))))))))..)))).))..))).... ( -22.83)
>DroSim_CAF1 49502 120 + 1
UAUUCCAAUCAUUCUUUGAACACAAUAUGGAUUGGAUUGGCCUUAACUAAUUCCAAAAUGAGCCGAAUCAAAUCCCUUGGCCUCAACGUACAUCACGUCCAAAUGGAUAUGUUUUCACAC
...(((((((.....(((....)))....)))))))..((((.................).)))(((.((.((((.((((.....((((.....))))))))..)))).))..))).... ( -22.83)
>DroEre_CAF1 60818 120 + 1
UAUUUCAAUCAUUCUUUGAACACAAUAUGGAUUGGAUUGGCCUUAACUAAUUCCGAAAUGAGCCGAAUCAAAUCCCUUGGCCUCGACGUACAUCACGUCCAAAUGGAUAUGUUUUCACAC
...(((((((.....(((....)))....))))))).((.....(((....((((....(((((((..........)))).)))(((((.....)))))....))))...)))....)). ( -21.80)
>DroYak_CAF1 60218 120 + 1
UAUUCCAAUCAUUCUUUGAGCACAAUAUGGAUUGGAUUGGCCUUAACUAAUUCCAAAAUAAGCCGAAUCAAAUCCCUUGGCCUCAACGUACAUCACGUCCAAAUGGAUAUGUUUUCACAC
...(((((((.....(((....)))....)))))))..(((.(((.............))))))(((.((.((((.((((.....((((.....))))))))..)))).))..))).... ( -22.42)
>consensus
UAUUCCAAUCAUUCUUUGAACACAAUAUGGAUUGGAUUGGCCUUAACUAAUUCCAAAAUGAGCCGAAUCAAAUCCCUUGGCCUCAACGUACAUCACGUCCAAAUGGAUAUGUUUUCACAC
...(((((((.....(((....)))....)))))))..(((.(((.............))))))(((.((.((((.((((.....((((.....))))))))..)))).))..))).... (-22.24 = -21.92 +  -0.32)

alignment

secondary structure

dotplot

Window 2

Location	2,813,162 – 2,813,282
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	98.33
Mean single sequence MFE	-30.26
Consensus MFE	-27.88
Energy contribution	-27.76
Covariance contribution	-0.12
Combinations/Pair	1.05
Mean z-score	-1.28
Structure conservation index	0.92
SVM decision value	0.12
SVM RNA-class probability	0.594762
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 2813162 120 - 23771897
GUGUGAAAACAUAUCCAUUUGGACGUGAUGUACGUUGAGGCCAAGGGAUUUGAUUCGGCUCAUUUUGGAAUUAGUUAAGGCCAAUCCAAUCCAUAUUGUGUUCAAAGAAUGAUUGGAAUA
((((....)))).((((((((((((..((((...(((....))).(((((.((((.((((.(((........)))...)))))))).)))))))))..)))))))).......))))... ( -30.51)
>DroSec_CAF1 58210 120 - 1
GUGUGAAAACAUAUCCAUUUGGACGUGAUGUACGUUGAGGCCAAGGGAUUUGAUUCGGCUCAUUUUGGAAUUAGUUAAGGCCAAUCCAAUCCAUAUUGUGUUCAAAGAAUGAUUGGAAUA
((((....)))).((((((((((((..((((...(((....))).(((((.((((.((((.(((........)))...)))))))).)))))))))..)))))))).......))))... ( -30.51)
>DroSim_CAF1 49502 120 - 1
GUGUGAAAACAUAUCCAUUUGGACGUGAUGUACGUUGAGGCCAAGGGAUUUGAUUCGGCUCAUUUUGGAAUUAGUUAAGGCCAAUCCAAUCCAUAUUGUGUUCAAAGAAUGAUUGGAAUA
((((....)))).((((((((((((..((((...(((....))).(((((.((((.((((.(((........)))...)))))))).)))))))))..)))))))).......))))... ( -30.51)
>DroEre_CAF1 60818 120 - 1
GUGUGAAAACAUAUCCAUUUGGACGUGAUGUACGUCGAGGCCAAGGGAUUUGAUUCGGCUCAUUUCGGAAUUAGUUAAGGCCAAUCCAAUCCAUAUUGUGUUCAAAGAAUGAUUGAAAUA
((((....))))...(((((.((((((...))))))(((..(((.(((((.((((.((((.....(.......)....)))))))).)))))...)))..)))...)))))......... ( -29.10)
>DroYak_CAF1 60218 120 - 1
GUGUGAAAACAUAUCCAUUUGGACGUGAUGUACGUUGAGGCCAAGGGAUUUGAUUCGGCUUAUUUUGGAAUUAGUUAAGGCCAAUCCAAUCCAUAUUGUGCUCAAAGAAUGAUUGGAAUA
((((....)))).((((.((.((((((...))))))(((..(((.(((((.((((.(((((................))))))))).)))))...)))..))).......)).))))... ( -30.69)
>consensus
GUGUGAAAACAUAUCCAUUUGGACGUGAUGUACGUUGAGGCCAAGGGAUUUGAUUCGGCUCAUUUUGGAAUUAGUUAAGGCCAAUCCAAUCCAUAUUGUGUUCAAAGAAUGAUUGGAAUA
((((....)))).((((.((.((((((...))))))(((..(((.(((((.((((.((((.(((........)))...)))))))).)))))...)))..))).......)).))))... (-27.88 = -27.76 +  -0.12)

alignment

secondary structure

dotplot

Window 3

Location	2,813,202 – 2,813,309
Length	107
Sequences	5
Columns	113
Reading direction	forward
Mean pairwise identity	94.11
Mean single sequence MFE	-25.98
Consensus MFE	-22.48
Energy contribution	-22.24
Covariance contribution	-0.24
Combinations/Pair	1.12
Mean z-score	-1.31
Structure conservation index	0.87
SVM decision value	0.32
SVM RNA-class probability	0.688263
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 2813202 107 + 23771897
CCUUAACUAAUUCCAAAAUGAGCCGAAUCAAAUCCCUUGGCCUCAACGUACAUCACGUCCAAAUGGAUAUGUUUUCACACAUCAUUGGUUGGGGACUC---AAAAGGG---GC
(((((((((((((((...((((((((..........)))).))))((((.....)))).....)))).((((......)))).))))))))))).(((---....)))---.. ( -25.00)
>DroSec_CAF1 58250 107 + 1
CCUUAACUAAUUCCAAAAUGAGCCGAAUCAAAUCCCUUGGCCUCAACGUACAUCACGUCCAAAUGGAUAUGUUUUCACACAUCAUUGGUUGGGGACUC---AAAAGGG---GC
(((((((((((((((...((((((((..........)))).))))((((.....)))).....)))).((((......)))).))))))))))).(((---....)))---.. ( -25.00)
>DroSim_CAF1 49542 107 + 1
CCUUAACUAAUUCCAAAAUGAGCCGAAUCAAAUCCCUUGGCCUCAACGUACAUCACGUCCAAAUGGAUAUGUUUUCACACAUCAUUGGUUGGGGACUC---AAAAGGG---GC
(((((((((((((((...((((((((..........)))).))))((((.....)))).....)))).((((......)))).))))))))))).(((---....)))---.. ( -25.00)
>DroEre_CAF1 60858 110 + 1
CCUUAACUAAUUCCGAAAUGAGCCGAAUCAAAUCCCUUGGCCUCGACGUACAUCACGUCCAAAUGGAUAUGUUUUCACACAUCAUUGGUUGGGGACUC---AAAGGAGGAAGC
(((((((((((((((....(((((((..........)))).)))(((((.....)))))....)))).((((......)))).))))))))))).(((---....)))..... ( -27.70)
>DroYak_CAF1 60258 113 + 1
CCUUAACUAAUUCCAAAAUAAGCCGAAUCAAAUCCCUUGGCCUCAACGUACAUCACGUCCAAAUGGAUAUGUUUUCACACAUCAUAGGUUGGGGACCCCAAAAGGGGGGAUGC
...........(((....................(((..((((..((((.....)))).......(((.(((....))).)))..))))..))).((((....)))))))... ( -27.20)
>consensus
CCUUAACUAAUUCCAAAAUGAGCCGAAUCAAAUCCCUUGGCCUCAACGUACAUCACGUCCAAAUGGAUAUGUUUUCACACAUCAUUGGUUGGGGACUC___AAAAGGG___GC
(((((((((((((((...((((((((..........)))).))))((((.....)))).....)))).((((......)))).))))))))))).(((.......)))..... (-22.48 = -22.24 +  -0.24)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:54:53 2006