Locus 5847

Sequence ID	2L_DroMel_CAF1
Location	16,569,007 – 16,569,172
Length	165
Max. P	0.868952

overview

Window 8

Location	16,569,007 – 16,569,098
Length	91
Sequences	4
Columns	102
Reading direction	forward
Mean pairwise identity	80.31
Mean single sequence MFE	-29.15
Consensus MFE	-14.57
Energy contribution	-17.32
Covariance contribution	2.75
Combinations/Pair	1.00
Mean z-score	-2.70
Structure conservation index	0.50
SVM decision value	0.59
SVM RNA-class probability	0.792119
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 16569007 91 + 22407834
AGCAGCAACACCCAAGUGCAGCAGCAACAUCAA-CUAUAAUAAGUAC-------CAAGGGCUGGAUGAAGUUGAGAGGCUGCGAAUGGCGCUUGG---UGUU
......((((((.((((((.(((((....((((-((.((...(((.(-------....))))...)).))))))...))))).....))))))))---)))) ( -33.40)
>DroSec_CAF1 23985 91 + 1
AGCAGCAACACCCAAGUGCAGCAGCAACAUCAA-CUAUAAUAAGUAC-------CAAGGGCUGGAUGAAGUUGAGAGGCUGCGAAUGGCGCUUGG---UGUU
......((((((.((((((.(((((....((((-((.((...(((.(-------....))))...)).))))))...))))).....))))))))---)))) ( -33.40)
>DroSim_CAF1 22071 91 + 1
AGCAGCAACACCCAAGUGCAGCAGCAACAUCAA-CUAUAAUAAGUAC-------CAAGGGCUGGAUGAAGUUGAGAGGCUGCGAAUGGCGCUUGG---UGUU
......((((((.((((((.(((((....((((-((.((...(((.(-------....))))...)).))))))...))))).....))))))))---)))) ( -33.40)
>DroWil_CAF1 25722 100 + 1
AGCAGCAACAGACAACAACAACAACAGCAGCAAAGUAGUAUAAGCAGAAGAAUACAAAGUCGAGAGGGAACUGAG--ACUGCAACUGGCGCUUGGUGGUGUU
..........((((.((.((((..(((..((......((((..........))))..((((...((....))..)--)))))..)))..).))).)).)))) ( -16.40)
>consensus
AGCAGCAACACCCAAGUGCAGCAGCAACAUCAA_CUAUAAUAAGUAC_______CAAGGGCUGGAUGAAGUUGAGAGGCUGCGAAUGGCGCUUGG___UGUU
...((((....((((((((.(((((....((((.........(((..............)))........))))...))))).....))))))))...)))) (-14.57 = -17.32 +   2.75)

alignment

secondary structure

dotplot

Window 9

Location	16,569,061 – 16,569,172
Length	111
Sequences	6
Columns	117
Reading direction	reverse
Mean pairwise identity	78.43
Mean single sequence MFE	-30.83
Consensus MFE	-18.11
Energy contribution	-18.87
Covariance contribution	0.75
Combinations/Pair	1.12
Mean z-score	-2.02
Structure conservation index	0.59
SVM decision value	0.86
SVM RNA-class probability	0.868952
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 16569061 111 - 22407834
GGCGAA-----CCGAUGCACAACAGCAACAUGCAACAA-CAUCGCGAAUGGCAAGUGGUAGUCAUAACAACAAUGCCGUCAACACCAAGCGCCAUUCGCAGCCUCUCAACUUCAUCC
(((...-----..((((.......((.....)).....-))))(((((((((...((((.((...................))))))...))))))))).))).............. ( -29.21)
>DroPse_CAF1 30907 103 - 1
AUCGUG-----CUGGUGCUG---------GUGCUGUAGCUGUAGCUGGUGGCAAGUGGUAGUCAUAAUAACAAUGCCGUCAACACCAAGCGCCAGUCGCAGCCUCUCAGCUUCUUUC
...(((-----(((((((((---------(((....(((....)))(..((((..((.............)).))))..)..)))).)))))))).)))(((......)))...... ( -35.12)
>DroSim_CAF1 22125 111 - 1
GGCGAA-----CCGAUGCACAACAGCAACAUGCAACAA-CAUCGCGGAUGGCAAGUGGUAGUCAUAACAACAAUGCCGUCAACACCAAGCGCCAUUCGCAGCCUCUCAACUUCAUCC
(((...-----..((((.......((.....)).....-))))(((((((((...((((.((...................))))))...))))))))).))).............. ( -28.71)
>DroEre_CAF1 23379 116 - 1
GGCAAACCGAGCCGAGGCACACCAGCAACGUGCAACAA-CAUCGCGGAUGGCAAGUGGUAGUCAUAACAACAGUGCCGUCAACACCAAGCGCCAUUCGCAGCCUCUCAACUUCAUCC
(((.......)))(((((......((.....)).....-....(((((((((...((((.((....((....)).......))))))...))))))))).)))))............ ( -36.20)
>DroYak_CAF1 23384 116 - 1
GGCCAACCGAACCAAUGCACAACAGCAACAUGCAACAA-CAUCGCGGAUGGCAAGUGGUAGUCAUAACAACAAUGCCGCCAACACCAAGCGCCAUUCGCAGCCUCUCAACUUCAUCC
(((............(((......)))...........-....(((((((((....((((.............))))((.........))))))))))).))).............. ( -27.22)
>DroPer_CAF1 32474 91 - 1
AUCGUG-----CUGGUGC---------------------UGUAGCUGGUGGCAAGUGGUAGUCAUAAUAACAAUGCCGUCAACACCAAGCGCCAGUCGCAGCCUCUCAGCUUCUUUC
.....(-----((((.((---------------------((..(((((((.(...((((.((...................)))))).))))))))..))))..).))))....... ( -28.51)
>consensus
GGCGAA_____CCGAUGCACAACAGCAACAUGCAACAA_CAUCGCGGAUGGCAAGUGGUAGUCAUAACAACAAUGCCGUCAACACCAAGCGCCAUUCGCAGCCUCUCAACUUCAUCC
.............((.((......((.....))..........(((((((((...((((.(((((.......)))......))))))...))))))))).)).))............ (-18.11 = -18.87 +   0.75)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:54:29 2006