Locus 3537

Sequence ID	3R_DroMel_CAF1
Location	9,557,722 – 9,557,816
Length	94
Max. P	0.974561

overview

Window 7

Location	9,557,722 – 9,557,816
Length	94
Sequences	5
Columns	105
Reading direction	forward
Mean pairwise identity	70.56
Mean single sequence MFE	-33.62
Consensus MFE	-17.06
Energy contribution	-17.66
Covariance contribution	0.60
Combinations/Pair	1.30
Mean z-score	-2.10
Structure conservation index	0.51
SVM decision value	1.73
SVM RNA-class probability	0.974561
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 9557722 94 + 27905053
CGUCUGCUGGUGAGCCCAGCU---CCACGGAGGAUGCA----UGUAUAUGCUCCUCCUG----UUGGCCAAACUGUCAAAGGUGGUCGCCGUAAUUGGCGAAAUA
.....(((((.....))))).---((((((((((.(((----(....))))))))))..----(((((......)))))..))))((((((....)))))).... ( -39.20)
>DroSec_CAF1 34373 79 + 1
---------------CCAGCU---CCACGGAGGAUGCA----UGUAUGUGCUCCUCCUG----UUGGCCAAACUGUCAAAGGUGGUCGCCGUAAUUGGCGAAAUA
---------------......---((((((((((.(((----(....))))))))))..----(((((......)))))..))))((((((....)))))).... ( -32.50)
>DroEre_CAF1 36016 95 + 1
CG---GUUGGCGAACCAACCU---CCAUGGAGGAUACCCAUGUAUAUGUGCCCCUCCUG----UUGGCCAAACUGUCAAAGGUGGUCGCCGUAAUUGGCGAAAUA
.(---(((((....)))))).---.(((((.(....))))))..........((.(((.----(((((......)))))))).))((((((....)))))).... ( -32.90)
>DroWil_CAF1 38713 101 + 1
CCGCUGCUCACAAAAGUACCUUGUCAGUGACGGGUGCU----GAUGCCGGUGGCUCCUGGUGACUGGUCUCGCUGUCAGAGUUGGUUCAUGUAAUUGGCAAAAUA
..((.((.......(((((((.(((...))))))))))----((.((((((.((.....)).)))))).)))).))....((..(((.....)))..))...... ( -29.50)
>DroYak_CAF1 34649 91 + 1
CG---GUUGGCGAACCCACCU---CCAUGGAGGAUGCC----UACAUGUGCUCCUCCUG----UUGGCCAAACUGUCAAAGGUGGUCGCCGUAAUUGGCGAAAUA
((---((((((((..((((((---.((.((((((.(((----.....).))))))))))----(((((......))))))))))))))))..)))))........ ( -34.00)
>consensus
CG___GCUGGCGAACCCACCU___CCAUGGAGGAUGCA____UAUAUGUGCUCCUCCUG____UUGGCCAAACUGUCAAAGGUGGUCGCCGUAAUUGGCGAAAUA
........................((((((((((.((............))))))))......(((((......)))))..))))((((((....)))))).... (-17.06 = -17.66 +   0.60)

alignment

secondary structure

dotplot

Window 8

Location	9,557,722 – 9,557,816
Length	94
Sequences	5
Columns	105
Reading direction	reverse
Mean pairwise identity	70.56
Mean single sequence MFE	-30.40
Consensus MFE	-12.40
Energy contribution	-13.08
Covariance contribution	0.68
Combinations/Pair	1.31
Mean z-score	-1.74
Structure conservation index	0.41
SVM decision value	0.18
SVM RNA-class probability	0.620571
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 9557722 94 - 27905053
UAUUUCGCCAAUUACGGCGACCACCUUUGACAGUUUGGCCAA----CAGGAGGAGCAUAUACA----UGCAUCCUCCGUGG---AGCUGGGCUCACCAGCAGACG
....(((((......)))))............((((..(((.----..((((((((((....)----))).)))))).)))---.(((((.....))))))))). ( -37.90)
>DroSec_CAF1 34373 79 - 1
UAUUUCGCCAAUUACGGCGACCACCUUUGACAGUUUGGCCAA----CAGGAGGAGCACAUACA----UGCAUCCUCCGUGG---AGCUGG---------------
....(((((......)))))..........((((....(((.----..(((((((((......----))).)))))).)))---.)))).--------------- ( -29.60)
>DroEre_CAF1 36016 95 - 1
UAUUUCGCCAAUUACGGCGACCACCUUUGACAGUUUGGCCAA----CAGGAGGGGCACAUAUACAUGGGUAUCCUCCAUGG---AGGUUGGUUCGCCAAC---CG
....(((((......)))))(((((...........))....----..((((((((.(((....))).)).)))))).)))---.((((((....)))))---). ( -31.60)
>DroWil_CAF1 38713 101 - 1
UAUUUUGCCAAUUACAUGAACCAACUCUGACAGCGAGACCAGUCACCAGGAGCCACCGGCAUC----AGCACCCGUCACUGACAAGGUACUUUUGUGAGCAGCGG
.....((((.......(((.....(((.......))).....)))...((.....))))))..----.....((((..((.(((((.....))))).))..)))) ( -19.70)
>DroYak_CAF1 34649 91 - 1
UAUUUCGCCAAUUACGGCGACCACCUUUGACAGUUUGGCCAA----CAGGAGGAGCACAUGUA----GGCAUCCUCCAUGG---AGGUGGGUUCGCCAAC---CG
...............(((((((((((((....(((.....))----).((((((((.......----.)).))))))..))---))))))..)))))...---.. ( -33.20)
>consensus
UAUUUCGCCAAUUACGGCGACCACCUUUGACAGUUUGGCCAA____CAGGAGGAGCACAUAUA____GGCAUCCUCCAUGG___AGGUGGGUUCGCCAAC___CG
....(((((......)))))............................((((((((............)).))))))............................ (-12.40 = -13.08 +   0.68)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:03:42 2006