Locus 4579

Sequence ID	3L_DroMel_CAF1
Location	13,125,430 – 13,125,630
Length	200
Max. P	0.996806

overview

Window 2

Location	13,125,430 – 13,125,550
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	95.00
Mean single sequence MFE	-35.10
Consensus MFE	-30.64
Energy contribution	-32.56
Covariance contribution	1.92
Combinations/Pair	1.08
Mean z-score	-1.29
Structure conservation index	0.87
SVM decision value	0.28
SVM RNA-class probability	0.667824
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13125430 120 + 23771897
CAUACAGUAUCUUAAAGUCGGUCUUUCCAAUCCGUUUCGUAAUAAUGUUACGUGUUUCACCUUCAUCACGUAGCCAGGCGCCUAACGGGGCCAUCCUGGAGGCCGUUGGCACCCGCCCCU
..................(((((..((((.................((((((((............))))))))..(((.((....)).)))....)))))))))..(((....)))... ( -34.40)
>DroSec_CAF1 113291 120 + 1
CAUACAGUAUCUUAAAGUCGGUCUUUCCAAUCCGUUUCGUAACAAUGUUACGUGUUUCACCUUCAUCACGUAGCCAGGCGCCUAACGGGGCCAUCCUGGAGGCCGUUGGCACCCGCCCCU
..................(((((..((((.................((((((((............))))))))..(((.((....)).)))....)))))))))..(((....)))... ( -34.40)
>DroSim_CAF1 111526 120 + 1
CAUACAGUAUCUUAAAGUCGGUCUUUCCAAUCCGUUUCGUAACAAUGUUACGUGUUUCACCUUCAUCACGUAGCCAGGCGCCUAACGGGGCCAUCCUGGAGGCCGUUGGCACCCGCCCCU
..................(((((..((((.................((((((((............))))))))..(((.((....)).)))....)))))))))..(((....)))... ( -34.40)
>DroEre_CAF1 110282 120 + 1
CCUACAGUAUCUUAAAGUCGGCCCUUUCAAUCCGUUGCGUAAUAACAUUACGUGUUUCACCUUCAUCACGUAGCCGGGCGCCUAACGGGGCCAUCCUGGAGGCGGUAGGCACCCGCCCCU
..................((((...........((((.....))))..((((((............))))))))))(((.((....)).))).....((.(((((.......))))))). ( -35.70)
>DroYak_CAF1 113579 120 + 1
CAUACAGUAUCUUAAAGUCGGCCUUUUCAAUCCGUUUCGUAAUAACGUUACGUGUUCCACCUUCAUCACGUAGCCAGGCGCCUAACGGGGCCAUCCUGGAGGCCGUUGGCACCCGCCUCU
..................((((((((....................((((((((............))))))))..(((.((....)).))).....))))))))..(((....)))... ( -36.60)
>consensus
CAUACAGUAUCUUAAAGUCGGUCUUUCCAAUCCGUUUCGUAAUAAUGUUACGUGUUUCACCUUCAUCACGUAGCCAGGCGCCUAACGGGGCCAUCCUGGAGGCCGUUGGCACCCGCCCCU
..................(((((..((((.................((((((((............))))))))..(((.((....)).)))....)))))))))..(((....)))... (-30.64 = -32.56 +   1.92)

alignment

secondary structure

dotplot

Window 3

Location	13,125,470 – 13,125,590
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	97.00
Mean single sequence MFE	-39.86
Consensus MFE	-37.46
Energy contribution	-37.34
Covariance contribution	-0.12
Combinations/Pair	1.06
Mean z-score	-1.96
Structure conservation index	0.94
SVM decision value	2.75
SVM RNA-class probability	0.996806
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13125470 120 + 23771897
AAUAAUGUUACGUGUUUCACCUUCAUCACGUAGCCAGGCGCCUAACGGGGCCAUCCUGGAGGCCGUUGGCACCCGCCCCUUUCGGUUCCGUUAAAUUUGUUUAUUGCGGCACUUGAACAC
......((((((((............))))))))((((.(((((((((((((.....((.(((.(.......).)))))....)))))))))).....((.....))))).))))..... ( -38.80)
>DroSec_CAF1 113331 120 + 1
AACAAUGUUACGUGUUUCACCUUCAUCACGUAGCCAGGCGCCUAACGGGGCCAUCCUGGAGGCCGUUGGCACCCGCCCCUUUCGGUUCCGUUAAAUUUGUUUAUUGCGGCACUUGAACAC
......((((((((............))))))))((((.(((((((((((((.....((.(((.(.......).)))))....)))))))))).....((.....))))).))))..... ( -38.80)
>DroSim_CAF1 111566 120 + 1
AACAAUGUUACGUGUUUCACCUUCAUCACGUAGCCAGGCGCCUAACGGGGCCAUCCUGGAGGCCGUUGGCACCCGCCCCUUUCGGUUCCGUUAAAUUUGUUUAUUGCGGCACUUGAACAC
......((((((((............))))))))((((.(((((((((((((.....((.(((.(.......).)))))....)))))))))).....((.....))))).))))..... ( -38.80)
>DroEre_CAF1 110322 120 + 1
AAUAACAUUACGUGUUUCACCUUCAUCACGUAGCCGGGCGCCUAACGGGGCCAUCCUGGAGGCGGUAGGCACCCGCCCCUUUCGGUUCCGUUAAAUUUGUUUAUUGCGGCACUUGAACAC
.......(((((((............))))))).((((.(((((((((((((.....((.(((((.......)))))))....)))))))))).....((.....))))).))))..... ( -41.10)
>DroYak_CAF1 113619 120 + 1
AAUAACGUUACGUGUUCCACCUUCAUCACGUAGCCAGGCGCCUAACGGGGCCAUCCUGGAGGCCGUUGGCACCCGCCUCUUUCGGUUCCGUUAAAUUUGUUUAUUGCGGCACUUGAACAC
......((((((((............))))))))((((.(((((((((((((.....((((((.(.......).))))))...)))))))))).....((.....))))).))))..... ( -41.80)
>consensus
AAUAAUGUUACGUGUUUCACCUUCAUCACGUAGCCAGGCGCCUAACGGGGCCAUCCUGGAGGCCGUUGGCACCCGCCCCUUUCGGUUCCGUUAAAUUUGUUUAUUGCGGCACUUGAACAC
......((((((((............))))))))((((.(((((((((((((.....((.(((.(.......).)))))....)))))))))).....((.....))))).))))..... (-37.46 = -37.34 +  -0.12)

alignment

secondary structure

dotplot

Window 4

Location	13,125,510 – 13,125,630
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	97.49
Mean single sequence MFE	-34.16
Consensus MFE	-32.60
Energy contribution	-32.44
Covariance contribution	-0.16
Combinations/Pair	1.04
Mean z-score	-1.58
Structure conservation index	0.95
SVM decision value	1.64
SVM RNA-class probability	0.969595
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13125510 120 + 23771897
CCUAACGGGGCCAUCCUGGAGGCCGUUGGCACCCGCCCCUUUCGGUUCCGUUAAAUUUGUUUAUUGCGGCACUUGAACACAAGUGGCAUCAUCUUUAUAUCCCUUUCCCCCCGGAACUCC
......(((((......((..(((...)))..)))))))....(((((((........((.....))(.((((((....)))))).)........................))))))).. ( -33.60)
>DroSec_CAF1 113371 119 + 1
CCUAACGGGGCCAUCCUGGAGGCCGUUGGCACCCGCCCCUUUCGGUUCCGUUAAAUUUGUUUAUUGCGGCACUUGAACACAAGUGGCAUCAUCUUCAUAUCCCUUUCC-CCCGGAACUCC
......(((((......((..(((...)))..)))))))....(((((((........((.....))(.((((((....)))))).).....................-..))))))).. ( -33.60)
>DroSim_CAF1 111606 119 + 1
CCUAACGGGGCCAUCCUGGAGGCCGUUGGCACCCGCCCCUUUCGGUUCCGUUAAAUUUGUUUAUUGCGGCACUUGAACACAAGUGGCAUCAUCUUCAUAUCCCUUUCC-CCCGGAACUCC
......(((((......((..(((...)))..)))))))....(((((((........((.....))(.((((((....)))))).).....................-..))))))).. ( -33.60)
>DroEre_CAF1 110362 119 + 1
CCUAACGGGGCCAUCCUGGAGGCGGUAGGCACCCGCCCCUUUCGGUUCCGUUAAAUUUGUUUAUUGCGGCACUUGAACACAAGUGGCAUCAUCUUCAUAUCCCACUCC-CCCGGAACUCC
((((((((((((.....((.(((((.......)))))))....))))))))))..............(.((((((....)))))).).....................-...))...... ( -36.70)
>DroYak_CAF1 113659 119 + 1
CCUAACGGGGCCAUCCUGGAGGCCGUUGGCACCCGCCUCUUUCGGUUCCGUUAAAUUUGUUUAUUGCGGCACUUGAACACAAGUGGCAUCAUCUUCAUAUCCCAUUCC-CCCGGAACUCC
((((((((((((.....((((((.(.......).))))))...))))))))))..............(.((((((....)))))).).....................-...))...... ( -33.30)
>consensus
CCUAACGGGGCCAUCCUGGAGGCCGUUGGCACCCGCCCCUUUCGGUUCCGUUAAAUUUGUUUAUUGCGGCACUUGAACACAAGUGGCAUCAUCUUCAUAUCCCUUUCC_CCCGGAACUCC
......(((((......((..((.....))..)))))))....(((((((........((.....))(.((((((....)))))).)........................))))))).. (-32.60 = -32.44 +  -0.16)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:27:25 2006