Locus 3881

Sequence ID	2R_DroMel_CAF1
Location	12,852,335 – 12,852,473
Length	138
Max. P	0.999902

overview

Window 6

Location	12,852,335 – 12,852,437
Length	102
Sequences	5
Columns	103
Reading direction	forward
Mean pairwise identity	94.73
Mean single sequence MFE	-29.20
Consensus MFE	-26.74
Energy contribution	-26.94
Covariance contribution	0.20
Combinations/Pair	1.08
Mean z-score	-2.78
Structure conservation index	0.92
SVM decision value	4.46
SVM RNA-class probability	0.999902
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 12852335 102 + 20766785
UAGACCAGAUAUUGAUUGAACUAU-CAUUUGUGGCUGGACAUGUCUCCGGCCACAAAACAAGGCACAAAACUUGGCAUAAUUGACCAUAAACCGUCCAUCGGG
....((.(((..((((......))-))((((((((((((......))))))))))))....((.((......(((((....)).)))......))))))))). ( -29.40)
>DroSec_CAF1 196091 102 + 1
UAGACCAGAUAUUGAUUGAACUAU-CAUUUGUGGCUGGACAUAUCUCCGGCCACAAAACAAGGCCCAAAACUUGGCAUAAUUGACCAUAAACCGUCCAUCGGG
............((((......))-))((((((((((((......)))))))))))).(((.(((........)))....)))........(((.....))). ( -28.90)
>DroSim_CAF1 204537 102 + 1
UAGACCAGAUAUUGAUUGAACUAU-CAUUUGUGGCCGGACAUAUUUCCUGCCACAAAACAAGGCCCAAAACUUGGCAUAAUUGACCAUAAACCGUCCAUCGGG
............((((......))-))((((((((.(((......))).)))))))).(((.(((........)))....)))........(((.....))). ( -25.00)
>DroEre_CAF1 199736 102 + 1
CAGACCAGAUAUUGAUUGAACUAU-CAUUUGUGGCUGGACAUAUCCCCGGCCACAAAACAAGGCCCAAAACAUGGCAUAAUUGACCAUAAACCGUCCAUCGGG
....((......((((......))-))(((((((((((........)))))))))))....))........((((((....)).))))...(((.....))). ( -28.60)
>DroYak_CAF1 204203 103 + 1
UAGACCAGAUAUUGAUUGAACUAUCCAUUUGUGGCUGGACAUAUCUCCGGCCACAAAACGUGGUCCAGAACAUGGCAUAAUUGACCAUAAACCGUCCAUCGGG
..(((((((((.(......).))))..((((((((((((......))))))))))))...)))))......((((((....)).))))...(((.....))). ( -34.10)
>consensus
UAGACCAGAUAUUGAUUGAACUAU_CAUUUGUGGCUGGACAUAUCUCCGGCCACAAAACAAGGCCCAAAACUUGGCAUAAUUGACCAUAAACCGUCCAUCGGG
...........(..((((.........((((((((((((......)))))))))))).((((........))))...))))..).......(((.....))). (-26.74 = -26.94 +   0.20)

alignment

secondary structure

dotplot

Window 7

Location	12,852,335 – 12,852,437
Length	102
Sequences	5
Columns	103
Reading direction	reverse
Mean pairwise identity	94.73
Mean single sequence MFE	-28.70
Consensus MFE	-27.68
Energy contribution	-27.56
Covariance contribution	-0.12
Combinations/Pair	1.07
Mean z-score	-1.15
Structure conservation index	0.96
SVM decision value	0.55
SVM RNA-class probability	0.778225
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 12852335 102 - 20766785
CCCGAUGGACGGUUUAUGGUCAAUUAUGCCAAGUUUUGUGCCUUGUUUUGUGGCCGGAGACAUGUCCAGCCACAAAUG-AUAGUUCAAUCAAUAUCUGGUCUA
((.(((((((((..(.((((.......)))).)..)))).))....((((((((.(((......))).))))))))((-((......))))..))).)).... ( -25.90)
>DroSec_CAF1 196091 102 - 1
CCCGAUGGACGGUUUAUGGUCAAUUAUGCCAAGUUUUGGGCCUUGUUUUGUGGCCGGAGAUAUGUCCAGCCACAAAUG-AUAGUUCAAUCAAUAUCUGGUCUA
.(((.....)))....((((.......)))).....((((((....((((((((.(((......))).))))))))((-((......))))......)))))) ( -28.00)
>DroSim_CAF1 204537 102 - 1
CCCGAUGGACGGUUUAUGGUCAAUUAUGCCAAGUUUUGGGCCUUGUUUUGUGGCAGGAAAUAUGUCCGGCCACAAAUG-AUAGUUCAAUCAAUAUCUGGUCUA
.(((.....)))....((((.......)))).....((((((....((((((((.(((......))).))))))))((-((......))))......)))))) ( -28.10)
>DroEre_CAF1 199736 102 - 1
CCCGAUGGACGGUUUAUGGUCAAUUAUGCCAUGUUUUGGGCCUUGUUUUGUGGCCGGGGAUAUGUCCAGCCACAAAUG-AUAGUUCAAUCAAUAUCUGGUCUG
.(((.....)))..((((((.......))))))....(((((....((((((((.(((......))).))))))))((-((......))))......))))). ( -28.70)
>DroYak_CAF1 204203 103 - 1
CCCGAUGGACGGUUUAUGGUCAAUUAUGCCAUGUUCUGGACCACGUUUUGUGGCCGGAGAUAUGUCCAGCCACAAAUGGAUAGUUCAAUCAAUAUCUGGUCUA
.........(((..((((((.......))))))..)))((((....((((((((.(((......))).)))))))).(((((..........))))))))).. ( -32.80)
>consensus
CCCGAUGGACGGUUUAUGGUCAAUUAUGCCAAGUUUUGGGCCUUGUUUUGUGGCCGGAGAUAUGUCCAGCCACAAAUG_AUAGUUCAAUCAAUAUCUGGUCUA
...(((((((((((((((((.......)))).....))))))....((((((((.(((......))).))))))))......)))).)))............. (-27.68 = -27.56 +  -0.12)

alignment

secondary structure

dotplot

Window 8

Location	12,852,374 – 12,852,473
Length	99
Sequences	5
Columns	99
Reading direction	forward
Mean pairwise identity	94.95
Mean single sequence MFE	-19.58
Consensus MFE	-15.52
Energy contribution	-16.40
Covariance contribution	0.88
Combinations/Pair	1.10
Mean z-score	-2.05
Structure conservation index	0.79
SVM decision value	0.88
SVM RNA-class probability	0.873773
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 12852374 99 + 20766785
AUGUCUCCGGCCACAAAACAAGGCACAAAACUUGGCAUAAUUGACCAUAAACCGUCCAUCGGGCAAUCAACUGCUAACCGCCUGCAGUUUUUAAUCAAC
.(((..((((((.........)))........(((((....)).)))............))))))...((((((.........)))))).......... ( -17.00)
>DroSec_CAF1 196130 99 + 1
AUAUCUCCGGCCACAAAACAAGGCCCAAAACUUGGCAUAAUUGACCAUAAACCGUCCAUCGGGCAAUCAACUGCUCACCGCCUGCAGUUUUUAAUCAAC
........((((.........)))).((((((.(((......(((........)))....(((((......)))))...)))...))))))........ ( -21.40)
>DroSim_CAF1 204576 99 + 1
AUAUUUCCUGCCACAAAACAAGGCCCAAAACUUGGCAUAAUUGACCAUAAACCGUCCAUCGGGCAAUCAACUGCUCACCGCCUGCACUUUUUAAUCAAC
....................((((........(((((....)).))).............(((((......)))))...))))................ ( -14.90)
>DroEre_CAF1 199775 99 + 1
AUAUCCCCGGCCACAAAACAAGGCCCAAAACAUGGCAUAAUUGACCAUAAACCGUCCAUCGGGCAAUCAACUGCUCACCGCCUGCAGUUUUUAAUCAAC
.....(((((((.........))))......((((((....)).))))............))).....((((((.........)))))).......... ( -21.30)
>DroYak_CAF1 204243 99 + 1
AUAUCUCCGGCCACAAAACGUGGUCCAGAACAUGGCAUAAUUGACCAUAAACCGUCCAUCGGGCAAUCAACUGCUCACCGCCUGCAGUUUUUAAUCAAC
...(((..((((((.....)))))).)))..((((((....)).)))).....((((...))))....((((((.........)))))).......... ( -23.30)
>consensus
AUAUCUCCGGCCACAAAACAAGGCCCAAAACUUGGCAUAAUUGACCAUAAACCGUCCAUCGGGCAAUCAACUGCUCACCGCCUGCAGUUUUUAAUCAAC
........((((.........)))).((((((.(((......(((........)))....(((((......)))))...)))...))))))........ (-15.52 = -16.40 +   0.88)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:06:20 2006