Locus 7989

Sequence ID	3R_DroMel_CAF1
Location	21,417,356 – 21,417,476
Length	120
Max. P	0.558219

overview

Window 2

Location	21,417,356 – 21,417,466
Length	110
Sequences	5
Columns	110
Reading direction	forward
Mean pairwise identity	87.98
Mean single sequence MFE	-25.44
Consensus MFE	-16.98
Energy contribution	-18.58
Covariance contribution	1.60
Combinations/Pair	1.16
Mean z-score	-1.99
Structure conservation index	0.67
SVM decision value	-0.03
SVM RNA-class probability	0.519050
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 21417356 110 + 27905053
UACAUCCACCAUUUGCAUUCUACAUAGCUGUAGAACAUUUUACAUCGAGGACCUCUCUUUACUUUCCAUAUGAAAGAAGUAGCUACUCGGCACUUGGUGGCGCCUCUUAU
.....((((((..(((.(((((((....)))))))..........((((...((..(((..(((((.....)))))))).))...)))))))..)))))).......... ( -29.30)
>DroSec_CAF1 25281 101 + 1
UACAUCCUCCAUUUGCAUUCUACAUAGCUGUAGAAAAUUUUACAUCGAGGACCUCUCU---------AUACGAAAGGAGUAGCUACUCGCCACUUGGUGGCGCCUCUUAU
.................(((((((....)))))))...........((((.(((.((.---------....)).)))..........((((((...)))))))))).... ( -24.00)
>DroSim_CAF1 10084 110 + 1
UACAUCCACCAUUUGCAUUCUACAUUGCUGUAGAAAAUUUUACAUCGAGGACCUCUCUUUACUUUCCAUACGAAAGGAGUAGCUACUCGUCACUUGAGGGCGCCUCUUAU
.................(((((((....)))))))...........((((.((((......(((((.....)))))((((....)))).......))))...)))).... ( -26.20)
>DroEre_CAF1 25210 106 + 1
UACAUUCACAAUUUGCAUUCUACACAGCUGUGUAAAAUUUUACAUCGAGGACCUC--UUUACUUUCCA-AGGAAAGGAA-AGCUACUCGCCACUUGGGGGCGCCUCUUAU
....................(((((....)))))............((((....(--(((.(((((..-..))))).))-)).....((((.(....))))))))).... ( -22.60)
>DroYak_CAF1 10473 107 + 1
UACAUCCACCAUUUGCAUUCUACACAGC-GUAGAACAUUUUACAUCGAGGACCUC--UUUACUUUCCAUACGAAAGGAGUAGCUACUCGCCACUUGGGGGCGCCUCUAAU
.................((((((.....-))))))...........((((.((((--....(((((.....)))))((((.((.....)).))))))))...)))).... ( -25.10)
>consensus
UACAUCCACCAUUUGCAUUCUACAUAGCUGUAGAAAAUUUUACAUCGAGGACCUCUCUUUACUUUCCAUACGAAAGGAGUAGCUACUCGCCACUUGGGGGCGCCUCUUAU
.................((((((......))))))...........((((.((((......(((((.....)))))((((.((.....)).))))))))...)))).... (-16.98 = -18.58 +   1.60)

alignment

secondary structure

dotplot

Window 3

Location	21,417,386 – 21,417,476
Length	90
Sequences	5
Columns	90
Reading direction	reverse
Mean pairwise identity	85.41
Mean single sequence MFE	-23.22
Consensus MFE	-15.40
Energy contribution	-17.44
Covariance contribution	2.04
Combinations/Pair	1.04
Mean z-score	-1.82
Structure conservation index	0.66
SVM decision value	0.05
SVM RNA-class probability	0.558219
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 21417386 90 - 27905053
ACGCAAUUUUAUAAGAGGCGCCACCAAGUGCCGAGUAGCUACUUCUUUCAUAUGGAAAGUAAAGAGAGGUCCUCGAUGUAAAAUGUUCUA
..(((.(((((((...(((((......)))))(((.(.((.((((((((.....)))))....))))).).)))..)))))))))).... ( -20.80)
>DroSec_CAF1 25311 81 - 1
ACUCAAUUUUAUAAGAGGCGCCACCAAGUGGCGAGUAGCUACUCCUUUCGUAU---------AGAGAGGUCCUCGAUGUAAAAUUUUCUA
....(((((((((.((((((((((...))))))..........((((((....---------.)))))).))))..)))))))))..... ( -26.20)
>DroSim_CAF1 10114 90 - 1
ACGCAAUUUUAUAAGAGGCGCCCUCAAGUGACGAGUAGCUACUCCUUUCGUAUGGAAAGUAAAGAGAGGUCCUCGAUGUAAAAUUUUCUA
....(((((((((.((((.((((((.......((((....))))(((((.....)))))....))).)))))))..)))))))))..... ( -25.00)
>DroEre_CAF1 25240 82 - 1
AC----UUUCAUAAGAGGCGCCCCCAAGUGGCGAGUAGCU-UUCCUUUCCU-UGGAAAGUAAA--GAGGUCCUCGAUGUAAAAUUUUACA
..----........((((((((.......))))....(((-((((......-.)))))))...--.....))))..(((((....))))) ( -20.60)
>DroYak_CAF1 10502 88 - 1
ACGCAAUUUCAUUAGAGGCGCCCCCAAGUGGCGAGUAGCUACUCCUUUCGUAUGGAAAGUAAA--GAGGUCCUCGAUGUAAAAUGUUCUA
..(((.(((((((.((((.(((....((((((.....)))))).(((((.....)))))....--..))))))))))).))).))).... ( -23.50)
>consensus
ACGCAAUUUUAUAAGAGGCGCCCCCAAGUGGCGAGUAGCUACUCCUUUCGUAUGGAAAGUAAAGAGAGGUCCUCGAUGUAAAAUUUUCUA
.....(((((((..((((.(((....((((((.....)))))).(((((.....)))))........)))))))...)))))))...... (-15.40 = -17.44 +   2.04)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:59:43 2006