Locus 7489

Sequence ID	2L_DroMel_CAF1
Location	20,793,993 – 20,794,088
Length	95
Max. P	0.714111

overview

Window 8

Location	20,793,993 – 20,794,088
Length	95
Sequences	5
Columns	99
Reading direction	forward
Mean pairwise identity	87.73
Mean single sequence MFE	-35.24
Consensus MFE	-28.70
Energy contribution	-27.78
Covariance contribution	-0.92
Combinations/Pair	1.26
Mean z-score	-1.59
Structure conservation index	0.81
SVM decision value	0.38
SVM RNA-class probability	0.714111
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 20793993 95 + 22407834
UAAUGCCCGGGGACGCCGAUUUCUCGGAAUCUUUCGCGGCUUGGGGCCAAACUGAGUUCCAGGGAAAGGUCAGUUUUUCAGGGUGUUA----GGGCGCU
....((((...(((((((((((....)))))......(((.....)))(((((((.(((....)))...))))))).....)))))).----))))... ( -34.20)
>DroSec_CAF1 17323 97 + 1
UAAUGCCCG--GACUCCGAUUUCUCGGAAUCGUUCGCCGCUUGGGGACAACCUGAGUUCCAGGGAAAGGUCAGUUUUCCAGGGAGUUAGUCAGGGCGCU
....((((.--((((.((((((....))))))......(((..((.....))..)))(((..((((((.....))))))..)))...)))).))))... ( -35.70)
>DroSim_CAF1 20885 97 + 1
UAAUGCCCG--GACUCCGAUUUCUCGGAAUCGUUCGCGGCUUGGGGCCAAACUGAGUUCCAGGGAAAGGUCAGUUUUCCAGGGAGUUAGUCAGGGCGCU
....(((((--((((((((....)))))...))))).)))..((.(((..(((((.((((.((((((......)))))).)))).)))))...))).)) ( -39.30)
>DroEre_CAF1 20723 95 + 1
UGAUGCCUG--GGCUCCGAUUUCUCGGAACUGUUCGCGGCUUGGGGCCAAA-UGGGUUCCAGGGAAAGGUCAGUUUUUCAGGGAGUU-GUCAGGGCGAU
...(((((.--(((...(((((((.(((((((..(....(((((((((...-..)))))))))....)..)))))))...)))))))-))).))))).. ( -34.20)
>DroYak_CAF1 18296 97 + 1
UGAUGCCUG--GGCUCCGUUUUCUCGGAAUUGUUCGUGGCUUGGGGCCAAACUGAGUUCCAGGAAAAGGUCAGUUUUUUAGGGAGUUAGUCAGGGUGAU
.....((((--(((((((...((.((((....)))).))..)))))))..(((((.((((..(((((......)))))..)))).)))))))))..... ( -32.80)
>consensus
UAAUGCCCG__GACUCCGAUUUCUCGGAAUCGUUCGCGGCUUGGGGCCAAACUGAGUUCCAGGGAAAGGUCAGUUUUUCAGGGAGUUAGUCAGGGCGCU
...(((((...((((((..(((((((((((.......(((.....))).......))))).))))))((........))..)))))).....))))).. (-28.70 = -27.78 +  -0.92)

alignment

secondary structure

dotplot

Window 9

Location	20,793,993 – 20,794,088
Length	95
Sequences	5
Columns	99
Reading direction	reverse
Mean pairwise identity	87.73
Mean single sequence MFE	-28.02
Consensus MFE	-19.72
Energy contribution	-21.92
Covariance contribution	2.20
Combinations/Pair	1.08
Mean z-score	-2.02
Structure conservation index	0.70
SVM decision value	0.34
SVM RNA-class probability	0.697578
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 20793993 95 - 22407834
AGCGCCC----UAACACCCUGAAAAACUGACCUUUCCCUGGAACUCAGUUUGGCCCCAAGCCGCGAAAGAUUCCGAGAAAUCGGCGUCCCCGGGCAUUA
...((((----............(((((((...(((....))).)))))))(((.....)))......(((.((((....)))).)))...)))).... ( -29.20)
>DroSec_CAF1 17323 97 - 1
AGCGCCCUGACUAACUCCCUGGAAAACUGACCUUUCCCUGGAACUCAGGUUGUCCCCAAGCGGCGAACGAUUCCGAGAAAUCGGAGUC--CGGGCAUUA
...((((.......(.(((((((...((((...(((....))).))))....)))...)).)).)...((((((((....))))))))--.)))).... ( -32.80)
>DroSim_CAF1 20885 97 - 1
AGCGCCCUGACUAACUCCCUGGAAAACUGACCUUUCCCUGGAACUCAGUUUGGCCCCAAGCCGCGAACGAUUCCGAGAAAUCGGAGUC--CGGGCAUUA
...((((........(((..(((((.......)))))..))).....(((((((.....)))..))))((((((((....))))))))--.)))).... ( -33.90)
>DroEre_CAF1 20723 95 - 1
AUCGCCCUGAC-AACUCCCUGAAAAACUGACCUUUCCCUGGAACCCA-UUUGGCCCCAAGCCGCGAACAGUUCCGAGAAAUCGGAGCC--CAGGCAUCA
...(((.((..-...(((..((((........))))...))).....-...(((.....))).......(((((((....))))))).--))))).... ( -24.30)
>DroYak_CAF1 18296 97 - 1
AUCACCCUGACUAACUCCCUAAAAAACUGACCUUUUCCUGGAACUCAGUUUGGCCCCAAGCCACGAACAAUUCCGAGAAAACGGAGCC--CAGGCAUCA
.....((((..............(((((((((.......))...)))))))(((.....)))........(((((......)))))..--))))..... ( -19.90)
>consensus
AGCGCCCUGACUAACUCCCUGAAAAACUGACCUUUCCCUGGAACUCAGUUUGGCCCCAAGCCGCGAACGAUUCCGAGAAAUCGGAGUC__CGGGCAUUA
...((((................(((((((...(((....))).)))))))(((.....)))......((((((((....))))))))...)))).... (-19.72 = -21.92 +   2.20)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:38:06 2006