Locus 3001

Sequence ID	2R_DroMel_CAF1
Location	10,351,681 – 10,351,771
Length	90
Max. P	0.929537

overview

Window 4

Location	10,351,681 – 10,351,771
Length	90
Sequences	6
Columns	90
Reading direction	forward
Mean pairwise identity	83.45
Mean single sequence MFE	-24.15
Consensus MFE	-18.60
Energy contribution	-18.52
Covariance contribution	-0.08
Combinations/Pair	1.12
Mean z-score	-2.43
Structure conservation index	0.77
SVM decision value	0.73
SVM RNA-class probability	0.835326
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 10351681 90 + 20766785
AAGCUCAGAGGUCGAGUGCUGGGCCAUAGAUGGCCCAAUAAAUGCCAUUCGAUGCUGUUCGAGCCACAACAAUACACUCAAAGAAAAGUA
..((((.(((((((((((((((((((....)))))))......).))))))))....))))))).......................... ( -25.50)
>DroSec_CAF1 70594 90 + 1
AAGCUCAGAGGUCGAGUGCUGGGCCAUAGAUGGCCCAAUAAAUGCCAUUCGAUGCUGUUCGAGCCACAACAAUACACUUAAAGAAAAGUA
..((((.(((((((((((((((((((....)))))))......).))))))))....)))))))...........((((......)))). ( -26.30)
>DroSim_CAF1 66274 90 + 1
AAGCUCAGAGGUCGAGUGCUGGGCCAUAGAUGGCCCAAUAAAUGCCAUUCGAUGCUGUUCGAGCCACAACAAUACACUCAAAGAAAAGUA
..((((.(((((((((((((((((((....)))))))......).))))))))....))))))).......................... ( -25.50)
>DroEre_CAF1 66317 81 + 1
AGGCUCAGAGGUCGAGUGCUGGGCCAUAGAUGGCCCAAUAUAUGCCAUUCGAUGC---------CACAACAGUACACUCAAAGAAAAGGA
.(((((..(((.((.(((.(((((((....))))))).))).)))).)..)).))---------)......................... ( -23.50)
>DroYak_CAF1 67549 90 + 1
AAGCUCAGAGGUCGAGUGCUGGGCCAUAGAUGGCCCAAUAAAUGCCAUUCGAUGCUGCUCGAAUCGCAACAGUACACUCAAAGAAAAGUA
.............(((((.(((((((....))))))).....(((.((((((......)))))).)))......)))))........... ( -28.80)
>DroAna_CAF1 71182 68 + 1
AAACUCAGAGGUCGAGUACCAGGCCAUAGAUGGCCCAAUAAAUGCUAUUUGAUU-----------------AUACACUGAAAA-----UA
....((((.(((((((((.(((((((....))))).......)).)))))))))-----------------.....))))...-----.. ( -15.31)
>consensus
AAGCUCAGAGGUCGAGUGCUGGGCCAUAGAUGGCCCAAUAAAUGCCAUUCGAUGCUGUUCGAGCCACAACAAUACACUCAAAGAAAAGUA
..........((((((((((((((((....)))))))......).))))))))..................................... (-18.60 = -18.52 +  -0.08)

alignment

secondary structure

dotplot

Window 5

Location	10,351,681 – 10,351,771
Length	90
Sequences	6
Columns	90
Reading direction	reverse
Mean pairwise identity	83.45
Mean single sequence MFE	-26.67
Consensus MFE	-21.98
Energy contribution	-22.73
Covariance contribution	0.75
Combinations/Pair	1.19
Mean z-score	-2.67
Structure conservation index	0.82
SVM decision value	1.20
SVM RNA-class probability	0.929537
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 10351681 90 - 20766785
UACUUUUCUUUGAGUGUAUUGUUGUGGCUCGAACAGCAUCGAAUGGCAUUUAUUGGGCCAUCUAUGGCCCAGCACUCGACCUCUGAGCUU
..(((....((((((((.....(((.(.((((......)))).).))).....(((((((....))))))))))))))).....)))... ( -29.00)
>DroSec_CAF1 70594 90 - 1
UACUUUUCUUUAAGUGUAUUGUUGUGGCUCGAACAGCAUCGAAUGGCAUUUAUUGGGCCAUCUAUGGCCCAGCACUCGACCUCUGAGCUU
..........(((((((..((((((.......)))))).......)))))))((((((((....))))))))..((((.....))))... ( -24.40)
>DroSim_CAF1 66274 90 - 1
UACUUUUCUUUGAGUGUAUUGUUGUGGCUCGAACAGCAUCGAAUGGCAUUUAUUGGGCCAUCUAUGGCCCAGCACUCGACCUCUGAGCUU
..(((....((((((((.....(((.(.((((......)))).).))).....(((((((....))))))))))))))).....)))... ( -29.00)
>DroEre_CAF1 66317 81 - 1
UCCUUUUCUUUGAGUGUACUGUUGUG---------GCAUCGAAUGGCAUAUAUUGGGCCAUCUAUGGCCCAGCACUCGACCUCUGAGCCU
..(((....((((((((.....((((---------.(((...))).))))...(((((((....))))))))))))))).....)))... ( -27.00)
>DroYak_CAF1 67549 90 - 1
UACUUUUCUUUGAGUGUACUGUUGCGAUUCGAGCAGCAUCGAAUGGCAUUUAUUGGGCCAUCUAUGGCCCAGCACUCGACCUCUGAGCUU
..(((....((((((((.....(((.((((((......)))))).))).....(((((((....))))))))))))))).....)))... ( -35.00)
>DroAna_CAF1 71182 68 - 1
UA-----UUUUCAGUGUAU-----------------AAUCAAAUAGCAUUUAUUGGGCCAUCUAUGGCCUGGUACUCGACCUCUGAGUUU
..-----..((((((((..-----------------.........)))..(((..(((((....)))))..)))........)))))... ( -15.60)
>consensus
UACUUUUCUUUGAGUGUAUUGUUGUGGCUCGAACAGCAUCGAAUGGCAUUUAUUGGGCCAUCUAUGGCCCAGCACUCGACCUCUGAGCUU
.........((((((((..((((((.......))))))...............(((((((....)))))))))))))))........... (-21.98 = -22.73 +   0.75)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:44:57 2006