Locus 4470

Sequence ID	2L_DroMel_CAF1
Location	12,812,326 – 12,812,517
Length	191
Max. P	0.765701

overview

Window 1

Location	12,812,326 – 12,812,446
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	97.08
Mean single sequence MFE	-28.78
Consensus MFE	-25.78
Energy contribution	-25.98
Covariance contribution	0.20
Combinations/Pair	1.00
Mean z-score	-1.39
Structure conservation index	0.90
SVM decision value	0.51
SVM RNA-class probability	0.765701
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 12812326 120 - 22407834
AUACAAAUUCCAAUCCGAAACCAAAUCGAAUCGAAUUGCUGCCAAUCAAAUCGAUUCGUGUCCUCGUCUCUCUUAUUGAUUCAUUGAGUGUCGAGGCAGCCGGCUAGUUAACUUAAGUUC
..............(((.........((((((((.(((........))).))))))))((.(((((.(.(((.............))).).)))))))..)))................. ( -27.02)
>DroSec_CAF1 78297 120 - 1
AUACGAAUUCCAAUCCGAAACCAAAUCGAAUCGAAUUGCUGCCAAUCAAAUCGAUUCGUGUCCUCGUCUCUCUUAUUGAUUCAUUGAGUGUCGAGGCAGCCGGCUAGUUAACUUAAGUUC
..............(((.........((((((((.(((........))).))))))))((.(((((.(.(((.............))).).)))))))..)))................. ( -27.02)
>DroSim_CAF1 81608 120 - 1
AUACGAAUUCCAAUCCGAAACCAAAUCGAAUCGAAUUGCUGCCAAUCAAAUCGAUUCGUGUCCUCGUCUCUCUUAUUGAUUCAUUGAGUGUCGAGGCAGCCGGCUAGUUAACUUAAGUUC
..............(((.........((((((((.(((........))).))))))))((.(((((.(.(((.............))).).)))))))..)))................. ( -27.02)
>DroEre_CAF1 81634 120 - 1
AUCCAAAUUCCAAUCCGAAUCCAAAUCGAAUCGAAUUGCUGCCAAUCAAAUCGAUUCGUGUCCUCGUCGCUCUUAUUGAUUCAUUGAGUGUCGAGGCAGCCGGCUAGUUAACUUAAGUUC
..............(((.........((((((((.(((........))).))))))))((.(((((.(((((.............))))).)))))))..)))................. ( -30.62)
>DroYak_CAF1 82048 120 - 1
AUCCAAAUUCAAAUCCGAAGCCAAAUCGAAUCGAAUUGCUGCCAAUCAAAUCGAUUCGUGUCCUCGUCUCGCUUAUUGAUUCAUUGAGUGUCGAGGCAGCCGGCUAGUUAGCUUAAGUUC
..................((((....((((((((.(((........))).))))))))((.(((((...((((((.((...)).)))))).)))))))...))))............... ( -32.20)
>consensus
AUACAAAUUCCAAUCCGAAACCAAAUCGAAUCGAAUUGCUGCCAAUCAAAUCGAUUCGUGUCCUCGUCUCUCUUAUUGAUUCAUUGAGUGUCGAGGCAGCCGGCUAGUUAACUUAAGUUC
..............(((.........((((((((.(((........))).))))))))((.(((((.(.(((.............))).).)))))))..)))................. (-25.78 = -25.98 +   0.20)

alignment

secondary structure

dotplot

Window 2

Location	12,812,406 – 12,812,517
Length	111
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	91.36
Mean single sequence MFE	-34.74
Consensus MFE	-24.16
Energy contribution	-24.40
Covariance contribution	0.24
Combinations/Pair	1.10
Mean z-score	-2.47
Structure conservation index	0.70
SVM decision value	0.18
SVM RNA-class probability	0.619702
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 12812406 111 + 22407834
AGCAAUUCGAUUCGAUUUGGUUUCGGAUUGGAAUUUGUAUUGAGGAA--------UUGAGGAAUGCUA-UCUUCGGUGUGGUGACACACGUGCCCAAUUAUCCUUGGAUAUUGCUUUAAU
(((((((((((((((.......)))))))))).......(..((((.--------.((((((......-))))))(((((....)))))...........))))..)...)))))..... ( -35.60)
>DroSec_CAF1 78377 111 + 1
AGCAAUUCGAUUCGAUUUGGUUUCGGAUUGGAAUUCGUAUUGAGGAA--------UUGAGGAAUGCUU-UCUCCGGCGUGGUGACACACGUGCCCAAUUAUCCUUGGAUAUUGCUUUAAU
(((((((((((((((.......)))))))))).......(..(((((--------(((.(((......-..)))((((((....)))....)))))))..))))..)...)))))..... ( -33.10)
>DroSim_CAF1 81688 112 + 1
AGCAAUUCGAUUCGAUUUGGUUUCGGAUUGGAAUUCGUAUUGAGGAA--------UUGGGGAAUGCUAUGCUCCGGCGUGGUGACACACGUGCCCAAUUAUCCUUGGAUAUUGCUUUAAU
(((((((((((((((.......)))))))))).......(..(((((--------(((((..(((....((....))(((....))).))).))))))..))))..)...)))))..... ( -37.00)
>DroEre_CAF1 81714 119 + 1
AGCAAUUCGAUUCGAUUUGGAUUCGGAUUGGAAUUUGGAUUGAGGAAUUGAGGAAUUGAGGAAUGCCA-UCUCAGGUGUGGUGACACACGUGCCCAAUUAUCCUUGGAUAUUGCUUUAAU
((((((....(((((((..(((((......)))))..)))))))...(..((((((((.((....)).-...((.(((((....))))).))..))))..))))..)..))))))..... ( -39.20)
>DroYak_CAF1 82128 111 + 1
AGCAAUUCGAUUCGAUUUGGCUUCGGAUUUGAAUUUGGAUUGAGAAA--------UUGAGGAAUGCUA-UCUCAGCUGUGGUGACACACGUGCCCAAUUAUCCUUGGAUAUUGCUUUAAU
(((((((((((((((((..((....)..)..)).))))))))))...--------(..((((..(((.-....)))((((....))))............))))..)...)))))..... ( -28.80)
>consensus
AGCAAUUCGAUUCGAUUUGGUUUCGGAUUGGAAUUUGUAUUGAGGAA________UUGAGGAAUGCUA_UCUCCGGUGUGGUGACACACGUGCCCAAUUAUCCUUGGAUAUUGCUUUAAU
(((((((((((((((.......)))))))))).......(..((((...........((((........)))).((((((......)))..)))......))))..)...)))))..... (-24.16 = -24.40 +   0.24)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:18:35 2006