Locus 2352

Sequence ID	X_DroMel_CAF1
Location	6,283,389 – 6,283,509
Length	120
Max. P	0.779610

overview

Window 8

Location	6,283,389 – 6,283,509
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	82.67
Mean single sequence MFE	-34.86
Consensus MFE	-26.72
Energy contribution	-27.00
Covariance contribution	0.28
Combinations/Pair	1.07
Mean z-score	-1.80
Structure conservation index	0.77
SVM decision value	0.55
SVM RNA-class probability	0.779610
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 6283389 120 + 22224390
AAAUGGUUGGAAAAAUGGGUGGAAAAUGCCCGUGUGCCGGGCGAAACACAAAUAUUAAAUCCCGCAAGGUGUACAGGCCGUGUUGAGGCUUCCGCAAAAAGGGGCAUAAAUUGUGUGCCA
.......(((....(((((((.....)))))))...)))(((...((((((...(((..((((.....(((...(((((.......))))).))).....))))..))).))))))))). ( -34.70)
>DroPse_CAF1 5139 98 + 1
-------------UGUGG-------CUGCUC--GUGCUGGGCGAAACACAAAUAUUAAAUGCCGCAAGGUGUACGGACCGUGUUGAGGCUCCGGCAAAAAGGGGCAUAAAUUGUGUGCCC
-------------((((.-------.(((((--.....)))))...))))........(((((....))))).((((((.......)).))))........(((((((.....))))))) ( -32.80)
>DroSec_CAF1 20375 120 + 1
AAAUGGUUGGAAAAAUGGGUGGAAAAUGCCCGUGUGCCGGGCGAAACACAAAUAUUAAAUGCCGCAAGGUGUACAGGCCGUGUUGAGGCUUCCGCAAAAAGGGGCAUAAAUUGUGUGCCA
.......(((....(((((((.....)))))))...)))(((...((((((.......(((((.(....(((..(((((.......)))))..)))....).)))))...))))))))). ( -36.40)
>DroPer_CAF1 5372 98 + 1
-------------UGUGG-------CUGCUC--GUGCUGGGCGAAACACAAAUAUUAAAUGCCGCAAGGUGUACGGACCGUGUUGAGGCUCCGGCAAAAGGGGGCAUAAAUUGUGUGCCC
-------------.....-------...((.--.((((((((..(((((.........(((((....))))).......)))))...)).))))))..)).(((((((.....))))))) ( -34.19)
>DroYak_CAF1 17476 108 + 1
A------------AAUGGGUGGAAAAUGCCCGUGUGCCGGGCGAAACACAAAUAUUAAAUGCCGCAAGGUGUACAGGCCGUGUUGAGGCUUCCGCAAAAAGGGGCAUAAAUUGUGUGCCA
.------------.....((((((..((((((.....))))))...............(((((....)))))....(((.......))))))))).......((((((.....)))))). ( -36.20)
>consensus
A____________AAUGGGUGGAAAAUGCCCGUGUGCCGGGCGAAACACAAAUAUUAAAUGCCGCAAGGUGUACAGGCCGUGUUGAGGCUUCCGCAAAAAGGGGCAUAAAUUGUGUGCCA
................((........((((((.....))))))..((((((.......(((((.(....(((..(((((.......)))))..)))....).)))))...)))))).)). (-26.72 = -27.00 +   0.28)

alignment

secondary structure

dotplot

Window 9

Location	6,283,389 – 6,283,509
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	82.67
Mean single sequence MFE	-28.40
Consensus MFE	-21.08
Energy contribution	-22.24
Covariance contribution	1.16
Combinations/Pair	1.04
Mean z-score	-1.71
Structure conservation index	0.74
SVM decision value	0.33
SVM RNA-class probability	0.693335
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 6283389 120 - 22224390
UGGCACACAAUUUAUGCCCCUUUUUGCGGAAGCCUCAACACGGCCUGUACACCUUGCGGGAUUUAAUAUUUGUGUUUCGCCCGGCACACGGGCAUUUUCCACCCAUUUUUCCAACCAUUU
(((.((((((.(((..((((....(((((..(((.......))))))))......).)))...)))...))))))...(((((.....))))).....................)))... ( -29.70)
>DroPse_CAF1 5139 98 - 1
GGGCACACAAUUUAUGCCCCUUUUUGCCGGAGCCUCAACACGGUCCGUACACCUUGCGGCAUUUAAUAUUUGUGUUUCGCCCAGCAC--GAGCAG-------CCACA-------------
((((((((((...(((((.(....((.((((.((.......))))))..))....).))))).......))))))...)))).((..--..))..-------.....------------- ( -26.20)
>DroSec_CAF1 20375 120 - 1
UGGCACACAAUUUAUGCCCCUUUUUGCGGAAGCCUCAACACGGCCUGUACACCUUGCGGCAUUUAAUAUUUGUGUUUCGCCCGGCACACGGGCAUUUUCCACCCAUUUUUCCAACCAUUU
(((.((((((...(((((.(....(((((..(((.......))))))))......).))))).......))))))...(((((.....))))).....................)))... ( -30.20)
>DroPer_CAF1 5372 98 - 1
GGGCACACAAUUUAUGCCCCCUUUUGCCGGAGCCUCAACACGGUCCGUACACCUUGCGGCAUUUAAUAUUUGUGUUUCGCCCAGCAC--GAGCAG-------CCACA-------------
((((((((((...((((((........((((.((.......))))))........).))))).......))))))...)))).((..--..))..-------.....------------- ( -25.89)
>DroYak_CAF1 17476 108 - 1
UGGCACACAAUUUAUGCCCCUUUUUGCGGAAGCCUCAACACGGCCUGUACACCUUGCGGCAUUUAAUAUUUGUGUUUCGCCCGGCACACGGGCAUUUUCCACCCAUU------------U
.((.((((((...(((((.(....(((((..(((.......))))))))......).))))).......)))))).))(((((.....)))))..............------------. ( -30.00)
>consensus
UGGCACACAAUUUAUGCCCCUUUUUGCGGAAGCCUCAACACGGCCUGUACACCUUGCGGCAUUUAAUAUUUGUGUUUCGCCCGGCACACGGGCAUUUUCCACCCAUU____________U
.((.((((((...(((((.(....(((((..(((.......))))))))......).))))).......)))))).))(((((.....)))))........................... (-21.08 = -22.24 +   1.16)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:32:30 2006