Locus 1122

Sequence ID	3R_DroMel_CAF1
Location	3,383,210 – 3,383,308
Length	98
Max. P	0.945930

overview

Window 8

Location	3,383,210 – 3,383,308
Length	98
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	83.15
Mean single sequence MFE	-27.72
Consensus MFE	-16.58
Energy contribution	-17.06
Covariance contribution	0.48
Combinations/Pair	1.08
Mean z-score	-2.01
Structure conservation index	0.60
SVM decision value	0.17
SVM RNA-class probability	0.616947
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 3383210 98 + 27905053
AAACGCUUUCUGCGUUUCG----------------------GGGCCAUUUCAUAAAUAUAACCAAAAGGCCAUCAGUACAAACGAUCCGGGCGAGCGCAGCCAAUGAAAUAACCCCGUCA
((((((.....))))))((----------------------(((..(((((((..............((..(((.((....))))))).(((.......))).)))))))..)))))... ( -27.10)
>DroSec_CAF1 11583 98 + 1
AAACGCUUUCUGCGUUUCG----------------------GGGCCAUUUCAUAAAUAUAACCAAAAGGCCAUCAGCCCAAACGAUCCGGGCGAGCGCAGCCAAUGAAAUAACCCCGUCA
((((((.....))))))((----------------------(((..(((((((..............(((.....)))...........(((.......))).)))))))..)))))... ( -29.10)
>DroAna_CAF1 19959 120 + 1
AAACGCUUUUUGCCUUUCGUGGACAUUUGAUAGUCCGAGUUGGGCAAUUUCAUAAAUAUAACGAGAAGGCCAUCAGAGGGAACGGUCCAGGCAAGCGAAACCAAUGGAAUGACCCCAUCG
...((((...(((((.((((((((........))))((....(((..((((...........))))..))).)).......))))...)))))))))......((((.......)))).. ( -29.80)
>DroSim_CAF1 12418 98 + 1
AAACGCUUUCUGCGUUUCG----------------------GGGCCAUUUCAUAAAUAUAACCAAAAGGCCAUCAGCCCAAACGAUCCGGGCGAGCGCAGCCAAUGAAAUAACCCCGUCA
((((((.....))))))((----------------------(((..(((((((..............(((.....)))...........(((.......))).)))))))..)))))... ( -29.10)
>DroEre_CAF1 11812 97 + 1
AAACGCUUUCUGCCUUUCG----------------------GGGCCAUUUCAUAAAUAUAACCAAAAGGCCAUCAGCCCAAACGAUCCG-GCGAGCGCAGCCAAUGAAAUAACCCGGACA
....((.....))..((((----------------------((...(((((((..............(((.....)))..........(-((.......))).)))))))..)))))).. ( -23.50)
>consensus
AAACGCUUUCUGCGUUUCG______________________GGGCCAUUUCAUAAAUAUAACCAAAAGGCCAUCAGCCCAAACGAUCCGGGCGAGCGCAGCCAAUGAAAUAACCCCGUCA
((((((.....))))))........................(((..(((((((..............((..(((.........))))).(((.......))).)))))))..)))..... (-16.58 = -17.06 +   0.48)

alignment

secondary structure

dotplot

Window 9

Location	3,383,210 – 3,383,308
Length	98
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	83.15
Mean single sequence MFE	-36.06
Consensus MFE	-23.50
Energy contribution	-24.18
Covariance contribution	0.68
Combinations/Pair	1.07
Mean z-score	-2.61
Structure conservation index	0.65
SVM decision value	1.36
SVM RNA-class probability	0.945930
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 3383210 98 - 27905053
UGACGGGGUUAUUUCAUUGGCUGCGCUCGCCCGGAUCGUUUGUACUGAUGGCCUUUUGGUUAUAUUUAUGAAAUGGCCC----------------------CGAAACGCAGAAAGCGUUU
...((((((((((((((..((.(((.((.....)).)))..))....((((((....))))))....))))))))))))----------------------))((((((.....)))))) ( -35.90)
>DroSec_CAF1 11583 98 - 1
UGACGGGGUUAUUUCAUUGGCUGCGCUCGCCCGGAUCGUUUGGGCUGAUGGCCUUUUGGUUAUAUUUAUGAAAUGGCCC----------------------CGAAACGCAGAAAGCGUUU
...((((((((((((((...........(((((((...)))))))..((((((....))))))....))))))))))))----------------------))((((((.....)))))) ( -41.10)
>DroAna_CAF1 19959 120 - 1
CGAUGGGGUCAUUCCAUUGGUUUCGCUUGCCUGGACCGUUCCCUCUGAUGGCCUUCUCGUUAUAUUUAUGAAAUUGCCCAACUCGGACUAUCAAAUGUCCACGAAAGGCAAAAAGCGUUU
(((((((.....)))))))....(((((((((((.(((((......)))))))...((((........((........))....((((........)))))))).)))))...))))... ( -31.30)
>DroSim_CAF1 12418 98 - 1
UGACGGGGUUAUUUCAUUGGCUGCGCUCGCCCGGAUCGUUUGGGCUGAUGGCCUUUUGGUUAUAUUUAUGAAAUGGCCC----------------------CGAAACGCAGAAAGCGUUU
...((((((((((((((...........(((((((...)))))))..((((((....))))))....))))))))))))----------------------))((((((.....)))))) ( -41.10)
>DroEre_CAF1 11812 97 - 1
UGUCCGGGUUAUUUCAUUGGCUGCGCUCGC-CGGAUCGUUUGGGCUGAUGGCCUUUUGGUUAUAUUUAUGAAAUGGCCC----------------------CGAAAGGCAGAAAGCGUUU
..((.((((((((((((((((.......))-))(((((...((((.....))))..)))))......))))))))))))----------------------.))((.((.....)).)). ( -30.90)
>consensus
UGACGGGGUUAUUUCAUUGGCUGCGCUCGCCCGGAUCGUUUGGGCUGAUGGCCUUUUGGUUAUAUUUAUGAAAUGGCCC______________________CGAAACGCAGAAAGCGUUU
.....((((((((((((.(((.......))).((.(((((......)))))))..............))))))))))))........................((((((.....)))))) (-23.50 = -24.18 +   0.68)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:01:30 2006