Locus 2620

Sequence ID	3R_DroMel_CAF1
Location	7,082,647 – 7,082,782
Length	135
Max. P	0.889098

overview

Window 4

Location	7,082,647 – 7,082,749
Length	102
Sequences	6
Columns	104
Reading direction	reverse
Mean pairwise identity	92.05
Mean single sequence MFE	-21.80
Consensus MFE	-19.26
Energy contribution	-19.15
Covariance contribution	-0.11
Combinations/Pair	1.10
Mean z-score	-1.71
Structure conservation index	0.88
SVM decision value	0.95
SVM RNA-class probability	0.889098
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 7082647 102 - 27905053
AAACAAGGGUUAACAGCAAUUUAAAUAAUAAAAGUGCUCGGCUCCGGGAUUCGGGGAAACGGAAAAGUACAAAAA--AAAACAGCGGCGCAACCCUUAACUUGU
....(((((((....((..((((.....)))).(((((((.(((((.....)))))...))....))))).....--......)).....)))))))....... ( -22.20)
>DroSec_CAF1 15577 100 - 1
AAACAAGGGUUAACAGCAACUUAAAUAAUAAAAGUGCUCGGCUCCGGGAUUCGGGGAAACGGAAAAGUACAAA----AAAACAGCGGCGCAACCCUUAACUUGU
....(((((((..(((((.(((.........))))))).)((.(((...((((......))))...((.....----...))..))).)))))))))....... ( -21.80)
>DroSim_CAF1 18217 102 - 1
AAACAAGGGUUAACAGCAAUUUAAAUAAUAAAAGUGCUCGGCUCCGGGAUUCGGGGAAACGGAAAAGUACAAAAA--AAAACAGCGGCGCAACCCUUAACUUGU
....(((((((....((..((((.....)))).(((((((.(((((.....)))))...))....))))).....--......)).....)))))))....... ( -22.20)
>DroEre_CAF1 15814 98 - 1
AAACAAGGGUUAAAAGCAAUUUAAAUAAUAAAAGUGCUCGGCUCCGGGAUUCGGGGAAACGGAAAAGUACAAA------AAAAGCGGUGCAACCCUUAACUUGU
....(((((((.(..((..((((.....)))).(((((((.(((((.....)))))...))....)))))...------....))..)..)))))))....... ( -22.80)
>DroYak_CAF1 16797 104 - 1
AAACAAGGGUUAACAGCAAUUUAAAUAAUAAAAGUGCUCGGCUCCGGGAUUCGGGGAAACGGAAAAGUACAAAAAAAAAAAAAGCGGCGCAACCCUUAACUUGU
....(((((((....((..((((.....)))).(((((((.(((((.....)))))...))....))))).............)).....)))))))....... ( -22.20)
>DroAna_CAF1 17257 96 - 1
AAACAAGGGUUAACAGCAAUUUAAAUAAUAAAAGUGCUCGGCUCUGGGAUUCGGGGAAGCGAAACGG---AA-----AAAAAUUCAGCGCAACCCUUAACUUGU
....(((((((..(((((.(((........))).)))).).(((((.....)))))..(((.....(---((-----.....)))..))))))))))....... ( -19.60)
>consensus
AAACAAGGGUUAACAGCAAUUUAAAUAAUAAAAGUGCUCGGCUCCGGGAUUCGGGGAAACGGAAAAGUACAAA____AAAAAAGCGGCGCAACCCUUAACUUGU
....(((((((....(((.(((........))).)))(((.(((((.....)))))...)))............................)))))))....... (-19.26 = -19.15 +  -0.11)

alignment

secondary structure

dotplot

Window 5

Location	7,082,680 – 7,082,782
Length	102
Sequences	6
Columns	113
Reading direction	reverse
Mean pairwise identity	81.83
Mean single sequence MFE	-25.17
Consensus MFE	-18.27
Energy contribution	-18.88
Covariance contribution	0.61
Combinations/Pair	1.15
Mean z-score	-1.49
Structure conservation index	0.73
SVM decision value	0.19
SVM RNA-class probability	0.628327
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 7082680 102 - 27905053
CCUCUAACCCAAUGACCGGGACCA-------ACCUGGGCCAAACAAGGGUUAACAGCAAU-UUAAAU---AAUAAAAGUGCUCGGCUCCGGGAUUCGGGGAAACGGAAAAGUA
((.....((((((..((((..(((-------((((..(.....)..)))))...((((.(-((....---....))).)))).))..)))).))).))).....))....... ( -26.50)
>DroVir_CAF1 29339 90 - 1
CCUCUAACCCGUUAC------CCA-------ACCCGGGCCAAGCAGGGGUUAACGGCAACUUUAAAUAAUAAUAAACGUACGUGGCAAC------C----AAACAAAAAAAAA
(((((..((((....------...-------...))))...)).)))((((.(((...((((((........)))).)).)))...)))------)----............. ( -13.60)
>DroSec_CAF1 15608 102 - 1
CCUCUAACCCAAUGACCGGGACCA-------ACCCGGGCCAAACAAGGGUUAACAGCAAC-UUAAAU---AAUAAAAGUGCUCGGCUCCGGGAUUCGGGGAAACGGAAAAGUA
((.....((((((..((((..(((-------((((..(.....)..)))))...((((.(-((....---.....))))))).))..)))).))).))).....))....... ( -28.90)
>DroEre_CAF1 15843 102 - 1
CCUCUAACCCAAUGACCGGGACCA-------ACCCGGGCCAAACAAGGGUUAAAAGCAAU-UUAAAU---AAUAAAAGUGCUCGGCUCCGGGAUUCGGGGAAACGGAAAAGUA
((.....((((((..((((..(((-------((((..(.....)..)))))...((((.(-((....---....))).)))).))..)))).))).))).....))....... ( -28.40)
>DroYak_CAF1 16832 102 - 1
CCUCUAACCCAAUGACCGGGACCA-------ACCCGGGCCAAACAAGGGUUAACAGCAAU-UUAAAU---AAUAAAAGUGCUCGGCUCCGGGAUUCGGGGAAACGGAAAAGUA
((.....((((((..((((..(((-------((((..(.....)..)))))...((((.(-((....---....))).)))).))..)))).))).))).....))....... ( -28.40)
>DroAna_CAF1 17286 106 - 1
CCUCUAACCU-AUGACCAGGACCAAGGACCUACCCAGGCCAAACAAGGGUUAACAGCAAU-UUAAAU---AAUAAAAGUGCUCGGCUCUGGGAUUCGGGGAAGCGAAACGG--
((((......-......(((.(....).))).((((((((.(((....)))...((((.(-((....---....))).)))).))).)))))....))))...........-- ( -25.20)
>consensus
CCUCUAACCCAAUGACCGGGACCA_______ACCCGGGCCAAACAAGGGUUAACAGCAAU_UUAAAU___AAUAAAAGUGCUCGGCUCCGGGAUUCGGGGAAACGGAAAAGUA
.......(((.....((((..((........((((..(.....)..)))).....(((...(((........)))...)))..))..)))).....))).............. (-18.27 = -18.88 +   0.61)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:40:42 2006