Locus 873

Sequence ID	2R_DroMel_CAF1
Location	4,026,072 – 4,026,232
Length	160
Max. P	0.816936

overview

Window 1

Location	4,026,072 – 4,026,192
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	95.17
Mean single sequence MFE	-33.38
Consensus MFE	-27.33
Energy contribution	-27.41
Covariance contribution	0.08
Combinations/Pair	1.07
Mean z-score	-1.71
Structure conservation index	0.82
SVM decision value	0.67
SVM RNA-class probability	0.816936
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 4026072 120 - 20766785
CCGUUCAACGGGGCGUAUGCUCAAUAAUUAAAACGAAUUGGUGUCUACUAAUGAGCAUGCAAGCGGGCACUUUUCUAUUAAUUUAUUUAUGACCCGACAGAGCCAUAAAGGCGGAAACGU
(((.....)))((((((((((((.((......((......))......)).)))))))))..(((((((....................)).)))).)...)))......(((....))) ( -32.35)
>DroSec_CAF1 8883 120 - 1
CCGUUCAACGGGGCGUAUGCUCAAUAAUUAAAUCGAAUUAGUGUCUCCUAAUGAGCAUGCAAGCGGGCACUUUUCUAUUAAUUUAUUUAUGGCCCGACAGAGCCAUAAAGGCGGAAACGU
(((.....)))((((((((((((..............((((......)))))))))))))..((((((.(....................)))))).)...)))......(((....))) ( -34.08)
>DroSim_CAF1 10937 120 - 1
CCGUUCAACGGGGCGUAUGCUCAAUAAUUAAAACGAAUUAGUGUCUCCUAAUGAGCAUGCAAGCGGGCACUUUUCUAUUAAUUUAUUUAUGGCCCGACAGAGCCAUAAAGGCGGAAACGU
(((.....)))((((((((((((.((......((......))......)).)))))))))..((((((.(....................)))))).)...)))......(((....))) ( -36.05)
>DroEre_CAF1 8057 120 - 1
CCGUUCAACGGGGCGUAUGCUCAAUAAUUAAAACGAAUUAGCGUCUCCUAAUGAGCAUGCAGGCGCGCACUUUUCCAUUAAUUUAUUUAUGGCCCAGCAGCGCCAUAAAGGCGGAAACGU
(((.....)))...(((((((((.((......(((......)))....)).))))))))).(((((((......((((..........))))....)).)))))......(((....))) ( -35.50)
>DroYak_CAF1 10662 119 - 1
-CGUUCAACGGGGCGUAUGCUCAAUAAUUAAAACGAAUUAGCGUCUCCUAAUGAGCAUGCAAGCGCGCACUUUUCUAUUAAUUUAUUUAUGGUCCAACAGAGCCAUAAAGGCGGAAACGU
-.((((....))))(((((((((.((......(((......)))....)).))))))))).........................(((((((..(....)..))))))).(((....))) ( -28.90)
>consensus
CCGUUCAACGGGGCGUAUGCUCAAUAAUUAAAACGAAUUAGUGUCUCCUAAUGAGCAUGCAAGCGGGCACUUUUCUAUUAAUUUAUUUAUGGCCCGACAGAGCCAUAAAGGCGGAAACGU
(((.....))).(((((((((((..............((((......)))))))))))))..)).....................((((((((.(....).)))))))).(((....))) (-27.33 = -27.41 +   0.08)

alignment

secondary structure

dotplot

Window 2

Location	4,026,112 – 4,026,232
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	95.50
Mean single sequence MFE	-30.38
Consensus MFE	-25.42
Energy contribution	-26.22
Covariance contribution	0.80
Combinations/Pair	1.00
Mean z-score	-1.38
Structure conservation index	0.84
SVM decision value	0.07
SVM RNA-class probability	0.567029
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 4026112 120 + 20766785
UAAUAGAAAAGUGCCCGCUUGCAUGCUCAUUAGUAGACACCAAUUCGUUUUAAUUAUUGAGCAUACGCCCCGUUGAACGGCAGCAUGAUUAUUUAUGUUGACAUCUCCGCAGCAUUCAUA
.....(((((((....))))(((((((((.((((((((........))))..)))).)))))))..((.(((.....)))((((((((....))))))))........)).)).)))... ( -29.30)
>DroSec_CAF1 8923 120 + 1
UAAUAGAAAAGUGCCCGCUUGCAUGCUCAUUAGGAGACACUAAUUCGAUUUAAUUAUUGAGCAUACGCCCCGUUGAACGGCAGCAUGAUUAUUUAUGUUGACAUCUCCGCAGCAUUCAUA
.....(((((((....))))(((((((((...(....)..(((((......))))).)))))))..((.(((.....)))((((((((....))))))))........)).)).)))... ( -27.40)
>DroSim_CAF1 10977 120 + 1
UAAUAGAAAAGUGCCCGCUUGCAUGCUCAUUAGGAGACACUAAUUCGUUUUAAUUAUUGAGCAUACGCCCCGUUGAACGGCAGCAUGAUUAUUUAUGUUGACAUCUCCGCAGCAUUCAUA
.....(((((((....))))(((((((((.((.(((((........)))))...)).)))))))..((.(((.....)))((((((((....))))))))........)).)).)))... ( -29.40)
>DroEre_CAF1 8097 120 + 1
UAAUGGAAAAGUGCGCGCCUGCAUGCUCAUUAGGAGACGCUAAUUCGUUUUAAUUAUUGAGCAUACGCCCCGUUGAACGGCGGCAUGAUUAUUUAUGUGGACAUCUCCGCAGCAUUCAGU
.........(((((((....))(((((((.((.((((((......))))))...)).)))))))..((((((.....))).)))...........((((((....))))))))))).... ( -35.60)
>DroYak_CAF1 10702 119 + 1
UAAUAGAAAAGUGCGCGCUUGCAUGCUCAUUAGGAGACGCUAAUUCGUUUUAAUUAUUGAGCAUACGCCCCGUUGAACG-CAGCAUGAUUAUUUAUGUUGACAUCUCCGCAGCAUUCAUU
.........((((((((...(((((((((.((.((((((......))))))...)).)))))))..))......((...-((((((((....))))))))...))..))).))))).... ( -30.20)
>consensus
UAAUAGAAAAGUGCCCGCUUGCAUGCUCAUUAGGAGACACUAAUUCGUUUUAAUUAUUGAGCAUACGCCCCGUUGAACGGCAGCAUGAUUAUUUAUGUUGACAUCUCCGCAGCAUUCAUA
.........(((((..((..(((((((((.((((((((........)))))..))).)))))))..)).(((.....)))((((((((....))))))))........)).))))).... (-25.42 = -26.22 +   0.80)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:49:31 2006