Locus 6325

Sequence ID	2R_DroMel_CAF1
Location	19,827,211 – 19,827,370
Length	159
Max. P	0.814647

overview

Window 6

Location	19,827,211 – 19,827,302
Length	91
Sequences	4
Columns	99
Reading direction	forward
Mean pairwise identity	88.07
Mean single sequence MFE	-39.98
Consensus MFE	-31.79
Energy contribution	-31.16
Covariance contribution	-0.63
Combinations/Pair	1.12
Mean z-score	-1.84
Structure conservation index	0.80
SVM decision value	0.66
SVM RNA-class probability	0.814647
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 19827211 91 + 20766785
UCUGUGCAUGUCUUGGCCAUUGGAGGCUCCUAAGUCGGUCGGCUGGUCU--------AUUGGUGUGCUGGUCGGCUGGUCGGCUGGAGCGACUCCAGCC
..............(((...((((((((((..(((((..((((((..(.--------...........)..))))))..))))))))))..)))))))) ( -40.40)
>DroSim_CAF1 57507 83 + 1
UCUGUGCAUGUCUUGGCCAUUGGAGGCUCCUAAGUCGGUCGGCUGGUCU--------AUUGGUGUGCUGGU--------CGGCUGGAGCGACUCCAGCC
..............(((...((((((((((..(((((..((((...((.--------...))...))))..--------))))))))))..)))))))) ( -33.40)
>DroEre_CAF1 70952 99 + 1
GCUGUGCACGUCUUGGCCACUGGAGGCUCCUAAGUCGGUCGGCUGGCCUAUUGGACUAUUGGUGUGCUGGUCGGCUGGUCGGCUGGAGCGACUCCAGCC
..((.((........))))(((((((((((..(((((..(((((((((....(.((.......)).).)))))))))..))))))))))..)))))).. ( -46.60)
>DroYak_CAF1 67664 91 + 1
UCGGUGCAUGUCUUGGCCACUGGAGGCUCCUAAGUCGGUCGGCUGGUCU--------AUUGGUGUGCUGGUGUGCUGGUCGGCUGGAGCGACUCCAGCC
..(((.((.....))))).(((((((((((......(((((((..((.(--------((..(....)..))).))..))))))))))))..)))))).. ( -39.50)
>consensus
UCUGUGCAUGUCUUGGCCACUGGAGGCUCCUAAGUCGGUCGGCUGGUCU________AUUGGUGUGCUGGUCGGCUGGUCGGCUGGAGCGACUCCAGCC
.....((((..(..(((((((((.((((....))))..)))).)))))............)..)))).............((((((((...)))))))) (-31.79 = -31.16 +  -0.63)

alignment

secondary structure

dotplot

Window 7

Location	19,827,276 – 19,827,370
Length	94
Sequences	5
Columns	94
Reading direction	reverse
Mean pairwise identity	92.98
Mean single sequence MFE	-35.68
Consensus MFE	-28.06
Energy contribution	-28.90
Covariance contribution	0.84
Combinations/Pair	1.04
Mean z-score	-1.57
Structure conservation index	0.79
SVM decision value	0.19
SVM RNA-class probability	0.625588
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 19827276 94 - 20766785
GGGCCUGGUUAUAUCAUCGAGCACUCUUACGACGUGCCGCAGCCAAAUGGUCAACAGCUUGGUCGCUUGGCUGGAGUCGCUCCAGCCGACCAGC
....((((((........(.((((((....)).)))))((.(((((.((.....))..))))).))..((((((((...)))))))))))))). ( -37.00)
>DroSim_CAF1 57570 88 - 1
GGGCCUGGUUAUAUCAUCGAGCACUCUUACGACGUGCCGCAGCCAAAUGGUCAACAGCUUGGUCGCUUGGCUGGAGUCGCUCCAGCCG------
.(((.(((.....((..((.((((((....)).))))))(((((((.((..(((....)))..)).)))))))))......)))))).------ ( -33.00)
>DroEre_CAF1 71025 94 - 1
GGGCCUGGUUAUAUCAUCGAGCACUCUUACGACGUGCCGCAGCCAAAUGGUCAACAGCUUGGUCGCUUGGCUGGAGUCGCUCCAGCCGACCAGC
....((((((........(.((((((....)).)))))((.(((((.((.....))..))))).))..((((((((...)))))))))))))). ( -37.00)
>DroYak_CAF1 67729 94 - 1
GGGCCUGGUUAUAUCAUCGAGCACUCUUACGACGUGCCGCAGCCAAAUGGUCAACAGCUUGGUCGCUUGGCUGGAGUCGCUCCAGCCGACCAGC
....((((((........(.((((((....)).)))))((.(((((.((.....))..))))).))..((((((((...)))))))))))))). ( -37.00)
>DroAna_CAF1 65866 94 - 1
GGGCCUGGUUAUAUCAUCGAGCACUCUUACGACGUGCCGCAGCCAAAUGGUCAACAGCUUGGCCGCUUGGCUGGAGCCUCGAACGGCUAAGAGC
.((((.((((.......((.((((((....)).))))))(((((((.(((((((....))))))).))))))).))))......))))...... ( -34.40)
>consensus
GGGCCUGGUUAUAUCAUCGAGCACUCUUACGACGUGCCGCAGCCAAAUGGUCAACAGCUUGGUCGCUUGGCUGGAGUCGCUCCAGCCGACCAGC
.((((.((((.......((.((((((....)).))))))..(((....)))....)))).))))....((((((((...))))))))....... (-28.06 = -28.90 +   0.84)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:08:18 2006