Locus 3400

Sequence ID	3L_DroMel_CAF1
Location	9,978,787 – 9,978,897
Length	110
Max. P	0.798502

overview

Window 7

Location	9,978,787 – 9,978,897
Length	110
Sequences	4
Columns	115
Reading direction	forward
Mean pairwise identity	89.50
Mean single sequence MFE	-27.14
Consensus MFE	-19.76
Energy contribution	-20.76
Covariance contribution	1.00
Combinations/Pair	1.10
Mean z-score	-2.20
Structure conservation index	0.73
SVM decision value	0.61
SVM RNA-class probability	0.798502
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 9978787 110 + 23771897
--UGAGCCUAGGGCCCAUUUUUCCCCCAAAGCCCAGCUUAAAAUGCGACAUAAUAUUUUGCCUAAA--UAUUUUUCCACAACCGACCGAGUUUGGU-UGCAAAAUAUUUUAGCAG
--(((((...((((................)))).)))))..................(((..(((--((((((....(((((((......)))))-)).)))))))))..))). ( -24.29)
>DroSec_CAF1 31575 111 + 1
AUUGAGCCUAGGGCCCAUU-UUCCCCCAAAGCCCAGCUUAAAAUGCGACAUAAUAUUUUGCCUAUA--UAUUUUUCCACAACCGACCGAGUUUGGU-UGCAAAAUAUUUUAGCAG
.((((((...((((.....-..........)))).))))))..(((.....((((((((((.....--...........((((((......)))))-)))))))))))...))). ( -25.15)
>DroEre_CAF1 33771 112 + 1
UUUGAGCCUAGGGCCCAUU-UU--CCCAAAGGCCAGCUUAAAAUGCGGCAAAAUAUUUUGCCAAAACACAUUUUUCCACAACCGACCAAGUUAGGUUUGCAAAAUAUUUUAGCAG
(((((((....((((....-..--......)))).))))))).(((...((((((((((((.((((.....))))........((((......)))).)))))))))))).))). ( -26.40)
>DroYak_CAF1 31956 109 + 1
CUUGAGCCUAGGGCCCAUU-UU--CCCAAAGGCCAGCUUAAAAUGCGGCAAAAUAUUUUGCCAAAA--UAUUUUUCCACUGCCGGCCGUGUUCGGU-UGCAAAAUAUUUUAGCAG
.((((((....((((....-..--......)))).))))))..(((((((((....))))))((((--(((((......(((.(((((....))))-))))))))))))).))). ( -32.70)
>consensus
_UUGAGCCUAGGGCCCAUU_UU__CCCAAAGCCCAGCUUAAAAUGCGACAAAAUAUUUUGCCAAAA__UAUUUUUCCACAACCGACCGAGUUUGGU_UGCAAAAUAUUUUAGCAG
.((((((....((((...............)))).))))))..(((...((((((((((((...................(((((......)))))..)))))))))))).))). (-19.76 = -20.76 +   1.00)

alignment

secondary structure

dotplot

Window 8

Location	9,978,787 – 9,978,897
Length	110
Sequences	4
Columns	115
Reading direction	reverse
Mean pairwise identity	89.50
Mean single sequence MFE	-31.62
Consensus MFE	-21.83
Energy contribution	-23.07
Covariance contribution	1.25
Combinations/Pair	1.03
Mean z-score	-2.00
Structure conservation index	0.69
SVM decision value	0.18
SVM RNA-class probability	0.621587
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 9978787 110 - 23771897
CUGCUAAAAUAUUUUGCA-ACCAAACUCGGUCGGUUGUGGAAAAAUA--UUUAGGCAAAAUAUUAUGUCGCAUUUUAAGCUGGGCUUUGGGGGAAAAAUGGGCCCUAGGCUCA--
..((((((((.(((..((-(((..........)))))..))).....--....((((........))))..))))).))).((((((.((((..........)))))))))).-- ( -29.00)
>DroSec_CAF1 31575 111 - 1
CUGCUAAAAUAUUUUGCA-ACCAAACUCGGUCGGUUGUGGAAAAAUA--UAUAGGCAAAAUAUUAUGUCGCAUUUUAAGCUGGGCUUUGGGGGAA-AAUGGGCCCUAGGCUCAAU
..((((((((.(((..((-(((..........)))))..))).....--....((((........))))..))))).)))(((((((.((((...-......))))))))))).. ( -29.90)
>DroEre_CAF1 33771 112 - 1
CUGCUAAAAUAUUUUGCAAACCUAACUUGGUCGGUUGUGGAAAAAUGUGUUUUGGCAAAAUAUUUUGCCGCAUUUUAAGCUGGCCUUUGGG--AA-AAUGGGCCCUAGGCUCAAA
.(((...........)))..(((((...((((((((.....(((((((.....((((((....))))))))))))).)))))))).)))))--..-..((((((...)))))).. ( -33.60)
>DroYak_CAF1 31956 109 - 1
CUGCUAAAAUAUUUUGCA-ACCGAACACGGCCGGCAGUGGAAAAAUA--UUUUGGCAAAAUAUUUUGCCGCAUUUUAAGCUGGCCUUUGGG--AA-AAUGGGCCCUAGGCUCAAG
.(((...........)))-.(((((...(((((((.((((.((((((--(((.....))))))))).)))).......)))))))))))).--..-..((((((...)))))).. ( -34.00)
>consensus
CUGCUAAAAUAUUUUGCA_ACCAAACUCGGUCGGUUGUGGAAAAAUA__UUUAGGCAAAAUAUUAUGCCGCAUUUUAAGCUGGCCUUUGGG__AA_AAUGGGCCCUAGGCUCAA_
..((((((((.(((..((.(((......)))....))..)))...........((((((....))))))..))))).)))(((((((.(((...........))).))))))).. (-21.83 = -23.07 +   1.25)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:57:16 2006