Locus 8525

Sequence ID	3R_DroMel_CAF1
Location	22,757,717 – 22,757,867
Length	150
Max. P	0.715645

overview

Window 2

Location	22,757,717 – 22,757,833
Length	116
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	85.09
Mean single sequence MFE	-36.27
Consensus MFE	-23.83
Energy contribution	-26.20
Covariance contribution	2.37
Combinations/Pair	1.06
Mean z-score	-1.65
Structure conservation index	0.66
SVM decision value	0.07
SVM RNA-class probability	0.570181
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 22757717 116 + 27905053
----UUGAUUGUUGUUGCAUGCGAAAUGCUUCGUUUUGCUUGGGCAUAAUGGUAAUCGUAUGGUAAUUGCCACAGUGAAGCGAAUUGCAUUUCAAGUUGCACGUCUGUUGCGGCAUGAAG
----.............(((((((((((((((((((..((..((((..((.(((....))).))...))))..))..)))))))..)))))))..((.(((....))).)).)))))... ( -37.20)
>DroSec_CAF1 47345 116 + 1
CCACUUGAUUG----UGCAUGCGAAAUGCUUCGUUUUGCUUGGGCGUAAUGGUAAUCGUAUGGUAAUUGCCGCACUGAAGCGAAUUGCAUUUCGAGUUGCACGUCUGUUGGGGCAUGAAG
(((...(((.(----((((..((((((((.....(((((((.((.((...((((((..(...)..)))))))).)).)))))))..))))))))...))))))))...)))......... ( -39.30)
>DroSim_CAF1 47469 117 + 1
CCACUUGAUUG---UUGCAUGCGAAAUGCUUCGUUUUGCUUGGGCGUAAUGGUAAUCGUAUGGUAAUUGCUGCAGUGAAGCGAAUUGCAUUUCGAGUUGCACGUCUGUUGGGGCAUGAAG
(((...(((.(---(.(((..(((((((((((((((..((..((((..((.(((....))).))...))))..))..)))))))..))))))))...))))))))...)))......... ( -36.90)
>DroAna_CAF1 48039 116 + 1
CCACUUGAUCU---GGGCAUGCAAAAUUGCUCGCUUUGCUUC-GCAUAAUGGUUAUCUUAUGGUAAUUGGUGGAGUGAAACGAAUUGCAUUUGGAGUUGCACGACUCAUGGGCCAUGAAG
........(((---((.(((((((......(((.((..((((-((.....(((((((....))))))).))))))..)).))).))))))...(((((....)))))...).))).)).. ( -31.70)
>consensus
CCACUUGAUUG___UUGCAUGCGAAAUGCUUCGUUUUGCUUGGGCAUAAUGGUAAUCGUAUGGUAAUUGCCGCAGUGAAGCGAAUUGCAUUUCGAGUUGCACGUCUGUUGGGGCAUGAAG
................(((..(((((((((((((((((((..((((..((.(((....))).))...))))..)))))))))))..))))))))...)))..(((......)))...... (-23.83 = -26.20 +   2.37)

alignment

secondary structure

dotplot

Window 3

Location	22,757,753 – 22,757,867
Length	114
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	84.62
Mean single sequence MFE	-31.90
Consensus MFE	-20.76
Energy contribution	-22.70
Covariance contribution	1.94
Combinations/Pair	1.08
Mean z-score	-1.95
Structure conservation index	0.65
SVM decision value	0.39
SVM RNA-class probability	0.715645
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 22757753 114 - 27905053
------AAGUGGGCGUGGCACCCGGCCAUUCGACAUGCCACUUCAUGCCGCAACAGACGUGCAACUUGAAAUGCAAUUCGCUUCACUGUGGCAAUUACCAUACGAUUACCAUUAUGCCCA
------...(((((((((((..(((....)))...))))))....(((((((...((..((((........))))..)).......)))))))......................))))) ( -32.80)
>DroSec_CAF1 47381 114 - 1
------UAGUGGGCGUGGCACCCGGCCAUUCGCCAUGCCACUUCAUGCCCCAACAGACGUGCAACUCGAAAUGCAAUUCGCUUCAGUGCGGCAAUUACCAUACGAUUACCAUUACGCCCA
------...(((((((((((...(((.....))).))))))....((((......((..((((........))))..))((......))))))......................))))) ( -34.70)
>DroSim_CAF1 47506 114 - 1
------UAGUGGGCGUGGCACCCGGCCAUUCGCCAUGCCACUUCAUGCCCCAACAGACGUGCAACUCGAAAUGCAAUUCGCUUCACUGCAGCAAUUACCAUACGAUUACCAUUACGCCCA
------...(((((((((((...(((.....))).))))))....(((.......((..((((........))))..))((......)).)))......................))))) ( -31.30)
>DroAna_CAF1 48076 118 - 1
AUUACCAAAGAGGCGUGGCAG-CGCACAUUGGCCAUGCCCCUUCAUGGCCCAUGAGUCGUGCAACUCCAAAUGCAAUUCGUUUCACUCCACCAAUUACCAUAAGAUAACCAUUAUGC-GA
...........((.((((.((-((..(((.(((((((......))))))).))).....((((........))))...)))))))).))........((((((........))))).-). ( -28.80)
>consensus
______AAGUGGGCGUGGCACCCGGCCAUUCGCCAUGCCACUUCAUGCCCCAACAGACGUGCAACUCGAAAUGCAAUUCGCUUCACUGCAGCAAUUACCAUACGAUUACCAUUACGCCCA
..........((((((((((...(((.....))).))))))....((((......((..((((........))))..))((......))))))......................)))). (-20.76 = -22.70 +   1.94)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:13:17 2006