Locus 3025

Sequence ID	3R_DroMel_CAF1
Location	8,076,308 – 8,076,440
Length	132
Max. P	0.959786

overview

Window 8

Location	8,076,308 – 8,076,405
Length	97
Sequences	5
Columns	103
Reading direction	forward
Mean pairwise identity	78.67
Mean single sequence MFE	-34.70
Consensus MFE	-20.64
Energy contribution	-22.00
Covariance contribution	1.36
Combinations/Pair	1.29
Mean z-score	-1.80
Structure conservation index	0.59
SVM decision value	0.29
SVM RNA-class probability	0.672293
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 8076308 97 + 27905053
GUGGGAAUUACAGAACCUUCGCCGGUAGCCCAGAUCUCUGGGUCUCUAAAGGUGGGC------AGAGCGGAAGUCCAAGUCGUGAUAAGAGUGGUUCCGAUGU
((.((((((((........((((..((((((((....)))))...)))..))))(((------.(..(....)..)..))).........)))))))).)).. ( -32.80)
>DroSim_CAF1 22354 97 + 1
GUGGGAACCGCAGAACCUUUGCUGGUAGCCCAGAUCUCUGGGUCUCUAAAGGUGGGC------AGAGCGGAAGUCCAAGUCGUGAUAAGAGUGGUUCCGAUGU
((.((((((((...(((((...(((..((((((....))))))..)))))))).(((------.(..(....)..)..))).........)))))))).)).. ( -37.80)
>DroEre_CAF1 20862 97 + 1
GUGGGAACCAAAGAACCUCUGCUAGUAGCCCACAUCUCUGGGACCCGAAAGGUGGGC------AGAGCGGAAGUCUAAGUCCUGAUAAGAGUGGUUCCGAUGU
((.(((((((.(((...((((((....((((((...((.(....).))...))))))------..))))))..))).....((....))..))))))).)).. ( -35.20)
>DroYak_CAF1 21275 103 + 1
GUGGGAACCACAGAACCUCUGCUGGUAGCCCAGAUCUCUGAGUCUCGGAAGGUGGGCAAAGUCAGAGCGGAAGUCCAAGUCCUGAUAAGAGUGGUUCCGAUGU
((.((((((((...(((......))).(((((..(.((((.....)))))..)))))...(((((..(((....))..)..)))))....)))))))).)).. ( -38.70)
>DroAna_CAF1 27722 90 + 1
GUGGGAAAC-CAGACCUCUUGCCGGAGGC---GAUCUCGAAGUUUCUUGGACUGG---------AAGCGGAAGUCGGGGGCUAGAUAAAGGUGGUUCCGAUGU
.(((....)-))..(((((....)))))(---((..((...((((((......))---------)))).))..)))(((((((........)))))))..... ( -29.00)
>consensus
GUGGGAACCACAGAACCUUUGCUGGUAGCCCAGAUCUCUGGGUCUCUAAAGGUGGGC______AGAGCGGAAGUCCAAGUCCUGAUAAGAGUGGUUCCGAUGU
((.((((((((....((.((...((..((((((....))))))..))...)).))...........((....))................)))))))).)).. (-20.64 = -22.00 +   1.36)

alignment

secondary structure

dotplot

Window 9

Location	8,076,347 – 8,076,440
Length	93
Sequences	5
Columns	101
Reading direction	forward
Mean pairwise identity	81.70
Mean single sequence MFE	-35.22
Consensus MFE	-24.98
Energy contribution	-27.12
Covariance contribution	2.14
Combinations/Pair	1.17
Mean z-score	-2.37
Structure conservation index	0.71
SVM decision value	1.51
SVM RNA-class probability	0.959786
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 8076347 93 + 27905053
GGGUCUCUAAAGGUGGGC------AGAGCGGAAGUCCAAGUCGUGAUAAGAGUGGUUCCGAUGUGGAAACAUCUGGGGCUUCGCUUUGAAU--AUCCCACC
...........(((((((------((((((.((((((..((((..((.......))..))))(((....)))...)))))))))))))...--..)))))) ( -35.10)
>DroSim_CAF1 22393 93 + 1
GGGUCUCUAAAGGUGGGC------AGAGCGGAAGUCCAAGUCGUGAUAAGAGUGGUUCCGAUGUGGAAACAUCUGGGGCUUCGCUUUGCAU--AUCCCACC
...........(((((((------((((((.((((((..((((..((.......))..))))(((....)))...))))))))))))))..--...))))) ( -35.20)
>DroEre_CAF1 20901 93 + 1
GGGACCCGAAAGGUGGGC------AGAGCGGAAGUCUAAGUCCUGAUAAGAGUGGUUCCGAUGUGGAAACAUCUGGGGCUUCGCUUUGCAU--AUCCCACC
(((((((....)).).((------((((((((.(((........))).......((((((((((....))))).)))))))))))))))..--.))))... ( -39.60)
>DroYak_CAF1 21314 99 + 1
GAGUCUCGGAAGGUGGGCAAAGUCAGAGCGGAAGUCCAAGUCCUGAUAAGAGUGGUUCCGAUGUGGAAACAUCUGGGGCUUCGCUUUGCAU--AUCCCACC
...........((((((....(.(((((((.((((((....((..........))....(((((....)))))..))))))))))))))..--..)))))) ( -35.70)
>DroAna_CAF1 27757 92 + 1
AAGUUUCUUGGACUGG---------AAGCGGAAGUCGGGGGCUAGAUAAAGGUGGUUCCGAUGUGGAAACAUCUGUGGCUUCGUCCGGAAUGGAUCUCUAC
..((((((......))---------)))).((((((((((((((........)))))))(((((....)))))..)))))))((((.....))))...... ( -30.50)
>consensus
GGGUCUCUAAAGGUGGGC______AGAGCGGAAGUCCAAGUCCUGAUAAGAGUGGUUCCGAUGUGGAAACAUCUGGGGCUUCGCUUUGCAU__AUCCCACC
...........((((((.......((((((.((((((................(....)(((((....)))))..))))))))))))........)))))) (-24.98 = -27.12 +   2.14)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:50:30 2006