Locus 5352

Sequence ID	3L_DroMel_CAF1
Location	14,764,912 – 14,765,036
Length	124
Max. P	0.638172

overview

Window 0

Location	14,764,912 – 14,765,022
Length	110
Sequences	5
Columns	119
Reading direction	reverse
Mean pairwise identity	82.39
Mean single sequence MFE	-46.02
Consensus MFE	-31.98
Energy contribution	-34.74
Covariance contribution	2.76
Combinations/Pair	1.03
Mean z-score	-1.71
Structure conservation index	0.69
SVM decision value	0.22
SVM RNA-class probability	0.638172
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 14764912 110 - 23771897
AGAGCAACCCGUUGGAUGCUGGG-AGCCACAUGGGCGGCGCCUGAGGCGCCCUUGGGGGCGUGGCAGAGGUGUAACAGGUGGAGCGGGGGAUGGCGCUGUUUGUGGGCAAG--------
..((((.((....)).))))...-.(((.(((..((((((((((..((((((....))))))..))....(((..(....)..)))......))))))))..))))))...-------- ( -47.90)
>DroSec_CAF1 7836 110 - 1
AGAGCAACCCGUUGGAUGCUGGGAAGCCACAUGGGCGGCGCCUGAGGCGCCCUUGGGGGCGUGGCAGAGGGGUGACAGGUGGAGCGGGAG-UCGCGCUGUUUGUGGGCAAG--------
..((((.((....)).)))).....(((.(((..((((((((((..((((((....))))))..)))...(....).....((.(....)-)))))))))..))))))...-------- ( -48.80)
>DroSim_CAF1 7972 110 - 1
AGAGCAACCCGUAGGAUGCUGGGAAGCCACAUGGGCGGCGCCUGAGGCGCCCUUGGGGGCGUGGCAGAGGGGUAACAGGUGGAGCGGGAG-UCGCGCUGCUUGUGGGCAAG--------
..((((.((....)).)))).....(((.((..(((((((((((..((((((....))))))..)))..............((.(....)-))))))))))..)))))...-------- ( -50.40)
>DroEre_CAF1 7735 106 - 1
AGAGCAACCCGUUGGAUGCUGGG-AGCCACGUGGGCGGCGCCUGAGGCGGCCUUGGGGGCGUGGCAGAGGGCUAACAGG--GGGCGGG----------GCUGGAGGGCAAGGGUAAAUG
...((..(((((....(.(((..-((((.(....((.((((((((((...))))..)))))).))...)))))..))).--).)))))----------(((....)))....))..... ( -40.90)
>DroYak_CAF1 7748 107 - 1
AGAGCAACCCGUUGGAUGCUGGG-AGCCACGUGGGCGACGCCUCUGGCGGCCUUGGGGGCGUGGCAGAUGGUUAACAGGG-GGGCGGG----------GCUGGAGGGCAAGGGUGAAAG
...((..((((((...(.(((..-((((((....((.(((((((..(.....)..))))))).)).).)))))..))).)-.))))))----------(((....)))....))..... ( -42.10)
>consensus
AGAGCAACCCGUUGGAUGCUGGG_AGCCACAUGGGCGGCGCCUGAGGCGCCCUUGGGGGCGUGGCAGAGGGGUAACAGGUGGAGCGGG_G_U_GCGCUGCUUGUGGGCAAG________
..((((.((....)).)))).....(((.(((..((((((((((..((((((....))))))..)))..(.....).................)))))))..))))))........... (-31.98 = -34.74 +   2.76)

alignment

secondary structure

dotplot

Window 1

Location	14,764,944 – 14,765,036
Length	92
Sequences	6
Columns	97
Reading direction	forward
Mean pairwise identity	84.46
Mean single sequence MFE	-31.59
Consensus MFE	-23.74
Energy contribution	-24.37
Covariance contribution	0.63
Combinations/Pair	1.16
Mean z-score	-1.72
Structure conservation index	0.75
SVM decision value	-0.04
SVM RNA-class probability	0.515071
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 14764944 92 + 23771897
CCUGUUACACCUCUGCCACGCCCCCAAGGGCGCCUCAGGCGCCGCCCAUGUGGCU-CCCAGCAUCCAACGGGUUGCUCUGAGCAGCCC----AGAAA
...........(((((..(((((....))))).....((.(((((....))))).-))..)).......(((((((.....)))))))----))).. ( -34.40)
>DroSec_CAF1 7867 93 + 1
CCUGUCACCCCUCUGCCACGCCCCCAAGGGCGCCUCAGGCGCCGCCCAUGUGGCUUCCCAGCAUCCAACGGGUUGCUCUGAGCAGCCC----AGAAA
.(((..........(((.(((((....))))).....)))(((((....)))))....)))........(((((((.....)))))))----..... ( -34.00)
>DroSim_CAF1 8003 93 + 1
CCUGUUACCCCUCUGCCACGCCCCCAAGGGCGCCUCAGGCGCCGCCCAUGUGGCUUCCCAGCAUCCUACGGGUUGCUCUGAGCAGCCC----AGAAA
..((((........(((.(((((....))))).....)))(((((....))))).....))))......(((((((.....)))))))----..... ( -34.10)
>DroEre_CAF1 7763 92 + 1
CCUGUUAGCCCUCUGCCACGCCCCCAAGGCCGCCUCAGGCGCCGCCCACGUGGCU-CCCAGCAUCCAACGGGUUGCUCUGAGCAGCCC----AGAAA
.......((.....((((((.......(((.(((...)))))).....)))))).-....)).......(((((((.....)))))))----..... ( -33.90)
>DroYak_CAF1 7777 92 + 1
CCUGUUAACCAUCUGCCACGCCCCCAAGGCCGCCAGAGGCGUCGCCCACGUGGCU-CCCAGCAUCCAACGGGUUGCUCUGAGCAGCCC----AGAAA
...........(((((((((((.....)))((((...))))........))))).-.............(((((((.....)))))))----))).. ( -31.40)
>DroPer_CAF1 11574 86 + 1
CCCGAUAGUC---------CCCUCCAAGUACGCCACAGGCGCCAUUUAU-CGGCU-CGCAGCAUCCAAAGGGUUGCUCUGAGCAGCCUUACAAAAAA
..((((((..---------...........((((...))))....))))-))(((-((.((((.((....)).)))).))))).............. ( -21.73)
>consensus
CCUGUUACCCCUCUGCCACGCCCCCAAGGGCGCCUCAGGCGCCGCCCAUGUGGCU_CCCAGCAUCCAACGGGUUGCUCUGAGCAGCCC____AGAAA
..............((((((.......((.((((...)))))).....))))))...............(((((((.....)))))))......... (-23.74 = -24.37 +   0.63)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:48:02 2006