Locus 2439

Sequence ID	3R_DroMel_CAF1
Location	6,773,196 – 6,773,353
Length	157
Max. P	0.821431

overview

Window 2

Location	6,773,196 – 6,773,313
Length	117
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	91.23
Mean single sequence MFE	-37.83
Consensus MFE	-29.71
Energy contribution	-31.03
Covariance contribution	1.31
Combinations/Pair	1.06
Mean z-score	-1.99
Structure conservation index	0.79
SVM decision value	0.60
SVM RNA-class probability	0.794565
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 6773196 117 - 27905053
GCAGCAAUUAAGCUCCGGGCCAGUUCUGACAUUGGGCCCAAAAGCAAGGCACACUUGUGGC---GGGCGGGAGGGGGAGGAGAGCAAAUAAUUUUUAAUUGUGCUGCACAAUGCUGUAAA
((((((......((((((((((((......))).)))))....((..(.(((....))).)---..)).))))..........(((.(((((.....)))))..)))....))))))... ( -38.10)
>DroSec_CAF1 37442 117 - 1
GCAGCAAUUAAGCUCCGGGCCAGUUCUGACAUUGGGCCCAAAAGCAAGGCACACUUGCGGA---GGGGCGGAGCGGGAGGAGAGCAAAUAAUUUUUAAUUGUGCUGCACAAUGCUGUAAA
((((((.....(((((...(((((......)))))((((....(((((.....)))))...---.))))))))).........(((.(((((.....)))))..)))....))))))... ( -43.80)
>DroEre_CAF1 22476 111 - 1
GCAGCAAUUAAGCUCCGGGCCAGUUCUGACAUUGGGCCCA-AAGCAAGGCAAAGU-ACGGC---GGGGCGG---GGG-GGAGAGCAAAUAAUUUUUAAUUGUGCUGCACAAUGCUGUAAA
((((((.....(((((((((((((......))).))))).-..((...((...))-...))---)))))..---...-.....(((.(((((.....)))))..)))....))))))... ( -34.30)
>DroYak_CAF1 34624 116 - 1
GCAGCAAUUAAGCUUCGGGCCAGUUCUGACAUUGGGCCCAAAAGCAAGGCAAAGU-GUUGCAAGGGGGCGG---GGGAGGAGAGCAAAUAAUUUUUAAUUGUGCUGCACAAUGCUGUAAA
((((((.....(((((((((((((......))).)))))....((((.((...))-.))))...)))))..---.........(((.(((((.....)))))..)))....))))))... ( -35.10)
>consensus
GCAGCAAUUAAGCUCCGGGCCAGUUCUGACAUUGGGCCCAAAAGCAAGGCAAACU_GCGGC___GGGGCGG___GGGAGGAGAGCAAAUAAUUUUUAAUUGUGCUGCACAAUGCUGUAAA
((((((.....(((((((((((((......))).)))))....(((((.....)))))......)))))..............(((.(((((.....)))))..)))....))))))... (-29.71 = -31.03 +   1.31)

alignment

secondary structure

dotplot

Window 3

Location	6,773,236 – 6,773,353
Length	117
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	88.40
Mean single sequence MFE	-45.12
Consensus MFE	-32.45
Energy contribution	-32.33
Covariance contribution	-0.13
Combinations/Pair	1.10
Mean z-score	-1.61
Structure conservation index	0.72
SVM decision value	0.13
SVM RNA-class probability	0.595795
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 6773236 117 + 27905053
CCUCCCCCUCCCGCCC---GCCACAAGUGUGCCUUGCUUUUGGGCCCAAUGUCAGAACUGGCCCGGAGCUUAAUUGCUGCAAAGUUGUUGUGGCUUAGCCGGUUGGGCGUGGCAGUAGGA
..(((..(((((((((---(((((((.(.(((...((..((((((((...((((....))))..)).))))))..)).))).).))))...(((...))))).)))))).)).))..))) ( -45.40)
>DroSec_CAF1 37482 112 + 1
CCUCCCGCUCCGCCCC---UCCGCAAGUGUGCCUUGCUUUUGGGCCCAAUGUCAGAACUGGCCCGGAGCUUAAUUGCUGCAAAGUUGUUGUGGCUUAGCCGGUUGGGCGUGGCAG-----
......((..(((((.---.(((((((.....))))).((((((((....((....)).))))))))(((.....((..(((.....)))..))..))).))..)))))..))..----- ( -45.10)
>DroEre_CAF1 22516 111 + 1
CC-CCC---CCGCCCC---GCCGU-ACUUUGCCUUGCUU-UGGGCCCAAUGUCAGAACUGGCCCGGAGCUUAAUUGCUGCAAAGUUGUUGUGGCUUAGCCGGUUGGGCGUGGCACUAGCA
..-..(---((((((.---((((.-.((..(((..((((-((((((....((....)).)))))))))).((((.(((....))).)))).)))..)).)))).))))).))........ ( -45.30)
>DroYak_CAF1 34664 116 + 1
CCUCCC---CCGCCCCCUUGCAAC-ACUUUGCCUUGCUUUUGGGCCCAAUGUCAGAACUGGCCCGAAGCUUAAUUGCUGCAAAGUUGUUGUGGCUUAGCCGGUUGGGCGUGGCAGUAGCA
.((.((---.(((((((..(((((-(((((((.......(((((((....((....)).)))))))(((......))))))))).))))))(((...)))))..))))).)).))..... ( -44.70)
>consensus
CCUCCC___CCGCCCC___GCCAC_ACUGUGCCUUGCUUUUGGGCCCAAUGUCAGAACUGGCCCGGAGCUUAAUUGCUGCAAAGUUGUUGUGGCUUAGCCGGUUGGGCGUGGCAGUAGCA
...................(((((......((((.......)))).....(((..(((((((...(((((((((.(((....))).)))).))))).))))))).))))))))....... (-32.45 = -32.33 +  -0.13)

alignment

secondary structure

dotplot

Window 4

Location	6,773,236 – 6,773,353
Length	117
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	88.40
Mean single sequence MFE	-45.23
Consensus MFE	-33.38
Energy contribution	-35.88
Covariance contribution	2.50
Combinations/Pair	1.00
Mean z-score	-2.07
Structure conservation index	0.74
SVM decision value	0.68
SVM RNA-class probability	0.821431
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 6773236 117 - 27905053
UCCUACUGCCACGCCCAACCGGCUAAGCCACAACAACUUUGCAGCAAUUAAGCUCCGGGCCAGUUCUGACAUUGGGCCCAAAAGCAAGGCACACUUGUGGC---GGGCGGGAGGGGGAGG
((((.(((((..(((.....)))...(((((((...(((((((((......)))..((((((((......))).)))))....)))))).....)))))))---.)))))....)))).. ( -47.20)
>DroSec_CAF1 37482 112 - 1
-----CUGCCACGCCCAACCGGCUAAGCCACAACAACUUUGCAGCAAUUAAGCUCCGGGCCAGUUCUGACAUUGGGCCCAAAAGCAAGGCACACUUGCGGA---GGGGCGGAGCGGGAGG
-----((((..(((((....(((...))).......................((((((((((((......))).)))))....(((((.....))))))))---))))))..)))).... ( -45.60)
>DroEre_CAF1 22516 111 - 1
UGCUAGUGCCACGCCCAACCGGCUAAGCCACAACAACUUUGCAGCAAUUAAGCUCCGGGCCAGUUCUGACAUUGGGCCCA-AAGCAAGGCAAAGU-ACGGC---GGGGCGG---GGG-GG
........((.(((((..(((((...)))......((((((((((......)))..((((((((......))).))))).-.......)))))))-..)).---.))))).---)).-.. ( -42.20)
>DroYak_CAF1 34664 116 - 1
UGCUACUGCCACGCCCAACCGGCUAAGCCACAACAACUUUGCAGCAAUUAAGCUUCGGGCCAGUUCUGACAUUGGGCCCAAAAGCAAGGCAAAGU-GUUGCAAGGGGGCGG---GGGAGG
.....((.((.(((((..(((((...))).(((((.(((((((((......)))..((((((((......))).))))).........)))))))-))))...))))))).---)).)). ( -45.90)
>consensus
UGCUACUGCCACGCCCAACCGGCUAAGCCACAACAACUUUGCAGCAAUUAAGCUCCGGGCCAGUUCUGACAUUGGGCCCAAAAGCAAGGCAAACU_GCGGC___GGGGCGG___GGGAGG
........((...(((..(((.((..((((((((..(((((((((......)))..((((((((......))).)))))....))))))....))))))))....)).)))...))).)) (-33.38 = -35.88 +   2.50)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:36:09 2006