Locus 1809

Sequence ID	3L_DroMel_CAF1
Location	5,082,979 – 5,083,136
Length	157
Max. P	0.964004

overview

Window 4

Location	5,082,979 – 5,083,096
Length	117
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	87.52
Mean single sequence MFE	-24.73
Consensus MFE	-19.94
Energy contribution	-20.25
Covariance contribution	0.31
Combinations/Pair	1.05
Mean z-score	-2.45
Structure conservation index	0.81
SVM decision value	1.56
SVM RNA-class probability	0.964004
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 5082979 117 - 23771897
GGCAACACUUGUGGCAUUUGCCAUUUGCCGCAGAAGAAAGGCCGUCUGCUGCACUCGCCCUGCUUUCUCCUCCUUUCUCCUCCUUUCUCCACCGUUCUCCACCU---UCUUCGCCUUUCU
(((.....((((((((.........)))))))).(((((((......((.((....))...))........)))))))..........................---.....)))..... ( -24.94)
>DroSec_CAF1 289258 107 - 1
GGCAACUCUUGUGGCAUUUGCCAUUUGCCGCAGAAGAAAGGCCGUCUGCUGCACUCGCCCUGCUUUCUCCC----------CAUUUCCCCACCGUUCUGCACCU---UCUUCGCCUUUCU
(((((.....(((((....)))))))))).....((((((((.....(.((((..((..............----------...........))...)))).).---.....)))))))) ( -25.11)
>DroSim_CAF1 310604 107 - 1
GGCAACACUUGUGGCAUUUGCCAUUUGCCGCAGAAGAAAGGCCGUCUGCUGCACUCGCCCUGCUUUCUCCC----------CCUUUCUCCACCGUUCUCCACCU---UCUUCGCCUUUCU
(((......(((((((.........)))))))(.(((((((......((.((....))...))........----------))))))).)..............---.....)))..... ( -25.34)
>DroYak_CAF1 300738 110 - 1
GGCAACUCUUUUGGCAUUUAACAUUUGCCGUGGAAGAAAGGCCGUCUGCUGCACUCGCCCUGCUUUCUCCC----------CCUUUCUCCACAUUACUCCACCUUUCUCUUCACCUCUCU
((..........((((.........))))(((((.((((((......((.((....))...))........----------)))))))))))......)).................... ( -23.54)
>consensus
GGCAACACUUGUGGCAUUUGCCAUUUGCCGCAGAAGAAAGGCCGUCUGCUGCACUCGCCCUGCUUUCUCCC__________CCUUUCUCCACCGUUCUCCACCU___UCUUCGCCUUUCU
(((......(((((((.........)))))))(((((..(((.....)))(((.......)))............................................))))))))..... (-19.94 = -20.25 +   0.31)

alignment

secondary structure

dotplot

Window 5

Location	5,083,016 – 5,083,136
Length	120
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	89.67
Mean single sequence MFE	-30.80
Consensus MFE	-27.85
Energy contribution	-28.47
Covariance contribution	0.62
Combinations/Pair	1.07
Mean z-score	-1.69
Structure conservation index	0.90
SVM decision value	0.82
SVM RNA-class probability	0.858339
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 5083016 120 - 23771897
UCUAGUUCCAAGUUUGCGAACCCAUUUUAGCCCGAAAGUAGGCAACACUUGUGGCAUUUGCCAUUUGCCGCAGAAGAAAGGCCGUCUGCUGCACUCGCCCUGCUUUCUCCUCCUUUCUCC
....((((((....)).))))............((((((((((.......(((((....))))).(((.(((((.(......).))))).)))...).)))))))))............. ( -33.00)
>DroSec_CAF1 289294 109 - 1
UCUAGUUCCAA--UUGCGAACUCAUUUCAGCCCGAAAGUAGGCAACUCUUGUGGCAUUUGCCAUUUGCCGCAGAAGAAAGGCCGUCUGCUGCACUCGCCCUGCUUUCUCCC---------
...((((((..--..).)))))...........((((((((((.......(((((....))))).(((.(((((.(......).))))).)))...).)))))))))....--------- ( -33.30)
>DroSim_CAF1 310640 109 - 1
UCUAGUUCCAA--UUGCGAACUCAUUUUAGCCCGAAAGUAGGCAACACUUGUGGCAUUUGCCAUUUGCCGCAGAAGAAAGGCCGUCUGCUGCACUCGCCCUGCUUUCUCCC---------
...((((((..--..).)))))...........((((((((((.......(((((....))))).(((.(((((.(......).))))).)))...).)))))))))....--------- ( -33.30)
>DroYak_CAF1 300777 109 - 1
ACUAGUUCCUA--UUGCGAACUCAUUUCAGCCCAAAAGUAGGCAACUCUUUUGGCAUUUAACAUUUGCCGUGGAAGAAAGGCCGUCUGCUGCACUCGCCCUGCUUUCUCCC---------
...........--..((((..........(((.(((((.((....))))))))))..........(((.(..((.(......).))..).))).)))).............--------- ( -23.60)
>consensus
UCUAGUUCCAA__UUGCGAACUCAUUUCAGCCCGAAAGUAGGCAACACUUGUGGCAUUUGCCAUUUGCCGCAGAAGAAAGGCCGUCUGCUGCACUCGCCCUGCUUUCUCCC_________
....(((((......).))))............((((((((((.......(((((....))))).(((.(((((.(......).))))).)))...).)))))))))............. (-27.85 = -28.47 +   0.62)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:17:10 2006