Locus 6216

Sequence ID	3L_DroMel_CAF1
Location	16,525,537 – 16,525,657
Length	120
Max. P	0.937242

overview

Window 4

Location	16,525,537 – 16,525,657
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	82.87
Mean single sequence MFE	-42.31
Consensus MFE	-27.86
Energy contribution	-28.50
Covariance contribution	0.64
Combinations/Pair	1.12
Mean z-score	-2.48
Structure conservation index	0.66
SVM decision value	1.26
SVM RNA-class probability	0.937242
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 16525537 120 + 23771897
AAGUGGCAUCCUUAACCGAAGGAUGUGACUUUUGCAGGUGGCCCCCUUUCCCCCUCUCUCCCUCUCUCCAUUCUCAGUGAUCCACGACGGUGGAAUGUUCGGUUUUGGGGGAACCACUUU
((((.((((((((.....)))))))).))))....((((((......(((((((.....((..(..(((((..((.(((...)))))..)))))..)...))....))))))))))))). ( -43.70)
>DroSec_CAF1 138956 112 + 1
AGGUGGCAUCCUUAACCGAAGGAUGUGACUUUUGCAGGUGGCCGCCUAUCCCCCUC--------UUCCCAUUCCCGAUGAUCCACGACGUUGGGAUGUUCGGUUUUGGGGGAACCACUUU
(((((((..(((....((((((......)))))).)))..))))))).((((((..--------..((...((((((((........)))))))).....))....))))))........ ( -44.00)
>DroSim_CAF1 141952 111 + 1
AGGUGGCAUCCUUAACCGAAGGAUGUGACUUUUGCAGGUGGCGGCCUUUCCCCCUC--------UUUCCAUUCCCGAUGAUCCACGACGUUG-GAUGUUCGGUUUUGGGGGAACCACUUU
((((.((((((((.....)))))))).))))....((((((......(((((((..--------.........((((..(((((......))-)))..))))....))))))))))))). ( -40.66)
>DroEre_CAF1 136484 100 + 1
AGGUGGCAUCCUUAACCGAAGGAUGUGACUUUUGCAGGAGGU--CCUUUCC----------------CCUUUCCCGCUGAUGCACAGCGGGGGGAUGCUCGGUUUCGGG-G-ACCACUUU
((((((..(((..((((((.(((...((((((.....)))))--)...)))----------------..(..(((((((.....)))))))..)....))))))..)))-.-.)))))). ( -44.20)
>DroYak_CAF1 139409 110 + 1
AGGUGGCAUCCUUAACCGAAGGAUGUGACUUUUGCAGGAGGU--CCUUUCCCCCCCUUU-------CCCUUUCCCGGUGAUGCACAGCGGUGGGAUGUUCGGUUUCGGG-GAACCACUUU
((((((..((((.((((((((((...((((((.....)))))--)...))).......(-------(((....(((.((.....)).))).))))..)))))))..)))-)..)))))). ( -39.00)
>consensus
AGGUGGCAUCCUUAACCGAAGGAUGUGACUUUUGCAGGUGGC__CCUUUCCCCCUC________U_CCCAUUCCCGAUGAUCCACGACGGUGGGAUGUUCGGUUUUGGGGGAACCACUUU
((((((..(((..((((((((((((..(...)..))((......))..)))....................((((((((........))))))))..)))))))..)))....)))))). (-27.86 = -28.50 +   0.64)

alignment

secondary structure

dotplot

Window 5

Location	16,525,537 – 16,525,657
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	82.87
Mean single sequence MFE	-37.62
Consensus MFE	-22.50
Energy contribution	-23.18
Covariance contribution	0.68
Combinations/Pair	1.30
Mean z-score	-1.92
Structure conservation index	0.60
SVM decision value	0.08
SVM RNA-class probability	0.574353
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 16525537 120 - 23771897
AAAGUGGUUCCCCCAAAACCGAACAUUCCACCGUCGUGGAUCACUGAGAAUGGAGAGAGGGAGAGAGGGGGAAAGGGGGCCACCUGCAAAAGUCACAUCCUUCGGUUAAGGAUGCCACUU
.(((((((((((((....((......(((((....)))))((.((......)).))..))......)))))))(((......)))..........(((((((.....))))))))))))) ( -37.10)
>DroSec_CAF1 138956 112 - 1
AAAGUGGUUCCCCCAAAACCGAACAUCCCAACGUCGUGGAUCAUCGGGAAUGGGAA--------GAGGGGGAUAGGCGGCCACCUGCAAAAGUCACAUCCUUCGGUUAAGGAUGCCACCU
...((((((((((((...((((..(((((......).))))..))))...))))..--------..(((((((.(((.((.....))....)))..)))))))......))).))))).. ( -36.90)
>DroSim_CAF1 141952 111 - 1
AAAGUGGUUCCCCCAAAACCGAACAUC-CAACGUCGUGGAUCAUCGGGAAUGGAAA--------GAGGGGGAAAGGCCGCCACCUGCAAAAGUCACAUCCUUCGGUUAAGGAUGCCACCU
...(((((((((((....((((..(((-((......)))))..))))...(....)--------..)))))))(((......)))..........(((((((.....))))))))))).. ( -35.70)
>DroEre_CAF1 136484 100 - 1
AAAGUGGU-C-CCCGAAACCGAGCAUCCCCCCGCUGUGCAUCAGCGGGAAAGG----------------GGAAAGG--ACCUCCUGCAAAAGUCACAUCCUUCGGUUAAGGAUGCCACCU
...(((((-.-.((..(((((((..(((((((((((.....))))))....))----------------))).(((--....)))...............)))))))..))..))))).. ( -40.10)
>DroYak_CAF1 139409 110 - 1
AAAGUGGUUC-CCCGAAACCGAACAUCCCACCGCUGUGCAUCACCGGGAAAGGG-------AAAGGGGGGGAAAGG--ACCUCCUGCAAAAGUCACAUCCUUCGGUUAAGGAUGCCACCU
...(((((..-.((..(((((((..((((.(((.((.....)).)))....)))-------).((((((.......--.))))))...............)))))))..))..))))).. ( -38.30)
>consensus
AAAGUGGUUCCCCCAAAACCGAACAUCCCACCGUCGUGGAUCACCGGGAAUGGA_A________GAGGGGGAAAGG__GCCACCUGCAAAAGUCACAUCCUUCGGUUAAGGAUGCCACCU
...(((((....((..(((((((..(((((...(((........)))...)))))..........(((.((........)).)))...............)))))))..))..))))).. (-22.50 = -23.18 +   0.68)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:12:57 2006