Locus 5484

Sequence ID	3L_DroMel_CAF1
Location	14,990,720 – 14,990,851
Length	131
Max. P	0.994889

overview

Window 3

Location	14,990,720 – 14,990,818
Length	98
Sequences	5
Columns	99
Reading direction	forward
Mean pairwise identity	95.33
Mean single sequence MFE	-24.12
Consensus MFE	-21.42
Energy contribution	-22.10
Covariance contribution	0.68
Combinations/Pair	1.06
Mean z-score	-1.62
Structure conservation index	0.89
SVM decision value	1.43
SVM RNA-class probability	0.952904
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 14990720 98 + 23771897
UUAAAUGCUAAUUUGUUUAGUUUAAAGUUUGCCAACUGUGCCAGGUCUUUAGGGCAAACU-UUGCUAACUGACAUGUGUCCGUUAGUGGAAACUACUGA
.................((((((((((((((((.(((......)))......))))))))-))((((((.(((....))).))))))..)))))).... ( -25.90)
>DroSec_CAF1 9103 98 + 1
UUAAAUGCUAAUUUAUUUAAUUUAAAGUUUGCCAACUGUGCCAGGUCAUUAGGGCAAACU-UUGCUAACUGACAUGUGUCCGUUAGUGGAAACUACUGA
(((((((......)))))))...((((((((((....(((......)))...))))))))-))((((((.(((....))).))))))(....)...... ( -25.90)
>DroSim_CAF1 8015 98 + 1
UUAAAUGCUAAUUUAUUUAGUUUAAAGUUUGCCAACUGUGCCAGGUCUUUAGGGCAAACU-UUGCUAACUGACAUGUGUCCGUUAGUGGAAACUACUGA
.(((((....)))))..((((((((((((((((.(((......)))......))))))))-))((((((.(((....))).))))))..)))))).... ( -26.20)
>DroEre_CAF1 8071 98 + 1
UUAAAUGCUAAUUUAUUUAGUUUAAAACUUGCCAACUGCGCCAGGUCUUUAGGGCGAACU-UUGCUAACUGACAUGUGUCCGUUAGUGGAAACUACUGG
......(((((.....)))))..........(((....((((..(....)..))))...(-(..(((((.(((....))).)))))..))......))) ( -21.90)
>DroYak_CAF1 9629 99 + 1
UUAAAUGCAAAUUUAUUUAGUUUAAAACUUGCCAACUGCGCCAGGUCUUUAGGGCAAACUUUUGCUAACUGACAUGUGUCCGUUAGUGGAAACUACUGA
.(((((....)))))..((((((.....(((((.(((......)))......)))))....(..(((((.(((....))).)))))..))))))).... ( -20.70)
>consensus
UUAAAUGCUAAUUUAUUUAGUUUAAAGUUUGCCAACUGUGCCAGGUCUUUAGGGCAAACU_UUGCUAACUGACAUGUGUCCGUUAGUGGAAACUACUGA
.(((((....)))))..((((((..((((((((.(((......)))......)))))))).(..(((((.(((....))).)))))..))))))).... (-21.42 = -22.10 +   0.68)

alignment

secondary structure

dotplot

Window 4

Location	14,990,720 – 14,990,818
Length	98
Sequences	5
Columns	99
Reading direction	reverse
Mean pairwise identity	95.33
Mean single sequence MFE	-20.28
Consensus MFE	-17.12
Energy contribution	-16.68
Covariance contribution	-0.44
Combinations/Pair	1.12
Mean z-score	-1.48
Structure conservation index	0.84
SVM decision value	0.45
SVM RNA-class probability	0.739941
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 14990720 98 - 23771897
UCAGUAGUUUCCACUAACGGACACAUGUCAGUUAGCAA-AGUUUGCCCUAAAGACCUGGCACAGUUGGCAAACUUUAAACUAAACAAAUUAGCAUUUAA
....((((((...(((((.(((....))).))))).((-((((((((.....(((........)))))))))))))))))))................. ( -22.50)
>DroSec_CAF1 9103 98 - 1
UCAGUAGUUUCCACUAACGGACACAUGUCAGUUAGCAA-AGUUUGCCCUAAUGACCUGGCACAGUUGGCAAACUUUAAAUUAAAUAAAUUAGCAUUUAA
....((((((...(((((.(((....))).))))).((-((((((((....((........))...))))))))))))))))................. ( -21.10)
>DroSim_CAF1 8015 98 - 1
UCAGUAGUUUCCACUAACGGACACAUGUCAGUUAGCAA-AGUUUGCCCUAAAGACCUGGCACAGUUGGCAAACUUUAAACUAAAUAAAUUAGCAUUUAA
....((((((...(((((.(((....))).))))).((-((((((((.....(((........)))))))))))))))))))................. ( -22.50)
>DroEre_CAF1 8071 98 - 1
CCAGUAGUUUCCACUAACGGACACAUGUCAGUUAGCAA-AGUUCGCCCUAAAGACCUGGCGCAGUUGGCAAGUUUUAAACUAAAUAAAUUAGCAUUUAA
....((((((...(((((.(((....))).)))))(((-....((((..........))))...))).........))))))................. ( -16.50)
>DroYak_CAF1 9629 99 - 1
UCAGUAGUUUCCACUAACGGACACAUGUCAGUUAGCAAAAGUUUGCCCUAAAGACCUGGCGCAGUUGGCAAGUUUUAAACUAAAUAAAUUUGCAUUUAA
.............(((((.(((....))).))))).......((((((.........)).))))...((((((((..........))))))))...... ( -18.80)
>consensus
UCAGUAGUUUCCACUAACGGACACAUGUCAGUUAGCAA_AGUUUGCCCUAAAGACCUGGCACAGUUGGCAAACUUUAAACUAAAUAAAUUAGCAUUUAA
....((((((...(((((.(((....))).)))))....((((((((.....(((........)))))))))))..))))))................. (-17.12 = -16.68 +  -0.44)

alignment

secondary structure

dotplot

Window 5

Location	14,990,743 – 14,990,851
Length	108
Sequences	5
Columns	109
Reading direction	forward
Mean pairwise identity	94.19
Mean single sequence MFE	-35.56
Consensus MFE	-29.64
Energy contribution	-29.44
Covariance contribution	-0.20
Combinations/Pair	1.07
Mean z-score	-2.49
Structure conservation index	0.83
SVM decision value	2.52
SVM RNA-class probability	0.994889
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 14990743 108 + 23771897
AAAGUUUGCCAACUGUGCCAGGUCUUUAGGGCAAACU-UUGCUAACUGACAUGUGUCCGUUAGUGGAAACUACUGACAAACUCAUUAGGGGCUCAGACUCUGGGCCCAA
((((((((((.(((......)))......))))))))-))((((((.(((....))).)))))).....(((.(((.....))).)))((((((((...)))))))).. ( -38.50)
>DroSec_CAF1 9126 108 + 1
AAAGUUUGCCAACUGUGCCAGGUCAUUAGGGCAAACU-UUGCUAACUGACAUGUGUCCGUUAGUGGAAACUACUGACAAACUCAUUAGGGGCUCAGACUCCGGGCCCAA
((((((((((....(((......)))...))))))))-))((((((.(((....))).)))))).....(((.(((.....))).)))((((((.......)))))).. ( -37.20)
>DroSim_CAF1 8038 108 + 1
AAAGUUUGCCAACUGUGCCAGGUCUUUAGGGCAAACU-UUGCUAACUGACAUGUGUCCGUUAGUGGAAACUACUGACAAACUCAUUAGGGGCUCAGACUCCGGGCCCAA
((((((((((.(((......)))......))))))))-))((((((.(((....))).)))))).....(((.(((.....))).)))((((((.......)))))).. ( -35.60)
>DroEre_CAF1 8094 107 + 1
AAAACUUGCCAACUGCGCCAGGUCUUUAGGGCGAACU-UUGCUAACUGACAUGUGUCCGUUAGUGGAAACUACUGGCAAACUCAUUAGGUGCUCAGACCUUGGGC-CAA
.............((.(((((((((...(((((...(-(..(((((.(((....))).)))))..))..(((.(((.....))).))).)))))))))))..)))-)). ( -32.30)
>DroYak_CAF1 9652 109 + 1
AAAACUUGCCAACUGCGCCAGGUCUUUAGGGCAAACUUUUGCUAACUGACAUGUGUCCGUUAGUGGAAACUACUGACAAACUCAUUAGGCGCUCAGACCUUGGGCCCAA
.............((.(((((((((...((((....(((..(((((.(((....))).)))))..))).(((.(((.....))).)))..))))))))))..))).)). ( -34.20)
>consensus
AAAGUUUGCCAACUGUGCCAGGUCUUUAGGGCAAACU_UUGCUAACUGACAUGUGUCCGUUAGUGGAAACUACUGACAAACUCAUUAGGGGCUCAGACUCUGGGCCCAA
.............((.(((.(((((...((((......(..(((((.(((....))).)))))..)...(((.(((.....))).)))..)))))))))...))).)). (-29.64 = -29.44 +  -0.20)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:51:30 2006