Locus 1917

Sequence ID	2L_DroMel_CAF1
Location	5,226,987 – 5,227,180
Length	193
Max. P	0.983953

overview

Window 7

Location	5,226,987 – 5,227,107
Length	120
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	98.33
Mean single sequence MFE	-27.64
Consensus MFE	-26.51
Energy contribution	-26.32
Covariance contribution	-0.19
Combinations/Pair	1.03
Mean z-score	-1.73
Structure conservation index	0.96
SVM decision value	0.18
SVM RNA-class probability	0.620691
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 5226987 120 + 22407834
AAAUUCUUAAUAAAACGCGCUGCAGUCUCUCGAAAUAUUUGCAAGUGUCUCAACGUCGCAUGCGUUUUAAUUAAGUGUCGCAUAUUUUUAAUUAAAUCACAAACGCCCAGGCGACGCGAC
.....((((((((((((((.(((((.............))))).(((.(.....).))).)))))))).)))))).(((((..((((......))))......(((....)))..))))) ( -28.12)
>DroSec_CAF1 4437 120 + 1
AAAUUCUUAAUAAAACGCGCUGCAGUCUCUCGAAAUAUUUCCAAGUGUCUUAACGUCGCAUGCGUUUUAAUUAAGUGUCGCAUAUUUCUAAUUAAAUCACAAACGCCCAGGCGACGCGAC
.....((((((((((((((.(((........(((....)))...((......))...))))))))))).)))))).(((((.((........)).........(((....)))..))))) ( -26.20)
>DroSim_CAF1 5315 120 + 1
AAAUUCUUAAUAAAACGCGCUGCAGUCUCUCGAAAUAUUUGCAAGUGUCUCAACGUCGCAUGCGUUUUAAUUAAGUGUCGCAUAUUUUUAAUUAAAUCACAAACGCCCAGGCGACGCGAC
.....((((((((((((((.(((((.............))))).(((.(.....).))).)))))))).)))))).(((((..((((......))))......(((....)))..))))) ( -28.12)
>DroYak_CAF1 5511 120 + 1
AAAUUCUUAAUAAAACGCGCUGCAGUCUCUCGAAAUAUUUGCAAGUGUCUCUACGUCGCAUGCGUUUUAAUUAAGUGUCGCAUAUUUUUAAUUAAAUCACAAACGCCCAGGCGACGCGAC
.....((((((((((((((.(((((.............))))).(((.(.....).))).)))))))).)))))).(((((..((((......))))......(((....)))..))))) ( -28.12)
>consensus
AAAUUCUUAAUAAAACGCGCUGCAGUCUCUCGAAAUAUUUGCAAGUGUCUCAACGUCGCAUGCGUUUUAAUUAAGUGUCGCAUAUUUUUAAUUAAAUCACAAACGCCCAGGCGACGCGAC
.....((((((((((((((.(((.(.....)((.(((((....))))).))......))))))))))).)))))).(((((..((((......))))......(((....)))..))))) (-26.51 = -26.32 +  -0.19)

alignment

secondary structure

dotplot

Window 8

Location	5,227,027 – 5,227,141
Length	114
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	95.73
Mean single sequence MFE	-35.87
Consensus MFE	-33.41
Energy contribution	-33.47
Covariance contribution	0.06
Combinations/Pair	1.03
Mean z-score	-1.85
Structure conservation index	0.93
SVM decision value	0.83
SVM RNA-class probability	0.862074
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 5227027 114 - 22407834
CCUCCAG------AGCCCACGCGGCUUUUAUCGCCUAGAAGUCGCGUCGCCUGGGCGUUUGUGAUUUAAUUAAAAAUAUGCGACACUUAAUUAAAACGCAUGCGACGUUGAGACACUUGC
..(((((------.((..((((((((((((.....)))))))))))).)))))))(((.((((.(((((((((.............))))))))).)))).)))................ ( -35.32)
>DroSec_CAF1 4477 114 - 1
CCUCCAG------AGCCCACGCGGCUUUUAUCGCCUAGAAGUCGCGUCGCCUGGGCGUUUGUGAUUUAAUUAGAAAUAUGCGACACUUAAUUAAAACGCAUGCGACGUUAAGACACUUGG
..(((((------.((..((((((((((((.....)))))))))))).)))))))(((.((((.(((((((((.............))))))))).)))).)))................ ( -35.02)
>DroSim_CAF1 5355 114 - 1
CCUCCAG------AGCCCACGCGGCUUUUAUCGCCUAGAAGUCGCGUCGCCUGGGCGUUUGUGAUUUAAUUAAAAAUAUGCGACACUUAAUUAAAACGCAUGCGACGUUGAGACACUUGC
..(((((------.((..((((((((((((.....)))))))))))).)))))))(((.((((.(((((((((.............))))))))).)))).)))................ ( -35.32)
>DroYak_CAF1 5551 120 - 1
CCUCCAGAGCCAGAGCCCACGCGGCUUUUAUCGCCUAGAAGUCGCGUCGCCUGGGCGUUUGUGAUUUAAUUAAAAAUAUGCGACACUUAAUUAAAACGCAUGCGACGUAGAGACACUUGC
.(((.....((((.((..((((((((((((.....)))))))))))).))))))(((((((((.(((((((((.............))))))))).))))...))))).)))........ ( -37.82)
>consensus
CCUCCAG______AGCCCACGCGGCUUUUAUCGCCUAGAAGUCGCGUCGCCUGGGCGUUUGUGAUUUAAUUAAAAAUAUGCGACACUUAAUUAAAACGCAUGCGACGUUGAGACACUUGC
.(((..........((((((((((((((((.....)))))))))))).....))))((.((((.(((((((((.............))))))))).)))).))......)))........ (-33.41 = -33.47 +   0.06)

alignment

secondary structure

dotplot

Window 9

Location	5,227,067 – 5,227,180
Length	113
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	93.30
Mean single sequence MFE	-37.20
Consensus MFE	-32.28
Energy contribution	-32.53
Covariance contribution	0.25
Combinations/Pair	1.00
Mean z-score	-3.29
Structure conservation index	0.87
SVM decision value	1.96
SVM RNA-class probability	0.983953
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 5227067 113 - 22407834
AUUUGCUCGAUU-CAAAUCGCACUCCUCCCUUUUGGAUUCCCUCCAG------AGCCCACGCGGCUUUUAUCGCCUAGAAGUCGCGUCGCCUGGGCGUUUGUGAUUUAAUUAAAAAUAUG
........((((-.((((((((..(......((((((.....)))))------)((((((((((((((((.....)))))))))))).....)))))..))))))))))))......... ( -35.90)
>DroSec_CAF1 4517 110 - 1
AUUU----GAUUCCAAAUCGCACUCCUCCCUUUUGGAUUCCCUCCAG------AGCCCACGCGGCUUUUAUCGCCUAGAAGUCGCGUCGCCUGGGCGUUUGUGAUUUAAUUAGAAAUAUG
.(((----((((..((((((((..(......((((((.....)))))------)((((((((((((((((.....)))))))))))).....)))))..)))))))))))))))...... ( -37.60)
>DroSim_CAF1 5395 114 - 1
AUUUGCUCGAUUCCAAAUCGCACUCCUCCCUUUUGGAUUCCCUCCAG------AGCCCACGCGGCUUUUAUCGCCUAGAAGUCGCGUCGCCUGGGCGUUUGUGAUUUAAUUAAAAAUAUG
..............((((((((..(......((((((.....)))))------)((((((((((((((((.....)))))))))))).....)))))..))))))))............. ( -35.10)
>DroYak_CAF1 5591 119 - 1
AUUUGUGCGAUU-CAAAUCGCACUCCUCCCUUUUGGUUACCCUCCAGAGCCAGAGCCCACGCGGCUUUUAUCGCCUAGAAGUCGCGUCGCCUGGGCGUUUGUGAUUUAAUUAAAAAUAUG
....(((((((.-...))))))).......(((((((((...(((((((((((.((..((((((((((((.....)))))))))))).)))).))).)))).))..)))))))))..... ( -40.20)
>consensus
AUUUGCUCGAUU_CAAAUCGCACUCCUCCCUUUUGGAUUCCCUCCAG______AGCCCACGCGGCUUUUAUCGCCUAGAAGUCGCGUCGCCUGGGCGUUUGUGAUUUAAUUAAAAAUAUG
..............((((((((..(........((((.....))))........((((((((((((((((.....)))))))))))).....)))))..))))))))............. (-32.28 = -32.53 +   0.25)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:14:42 2006