Locus 565

Sequence ID	2R_DroMel_CAF1
Location	2,923,931 – 2,924,155
Length	224
Max. P	0.946313

overview

Window 8

Location	2,923,931 – 2,924,040
Length	109
Sequences	4
Columns	109
Reading direction	forward
Mean pairwise identity	89.51
Mean single sequence MFE	-36.88
Consensus MFE	-28.71
Energy contribution	-28.15
Covariance contribution	-0.56
Combinations/Pair	1.10
Mean z-score	-1.54
Structure conservation index	0.78
SVM decision value	0.14
SVM RNA-class probability	0.604304
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 2923931 109 + 20766785
AGUCUGUCCAGCUACAACAUCGAUUACAAGAUCCCAUGCGGAGAGCAGCCCAGUGAGCUGGGCACGAGUCGUGAUUGAGACUGGUCGAUAUGGGGAUUCGAAUGGGACU
.....((((..........((........))(((((((((.......((((((....))))))((.((((........)))).)))).))))))).........)))). ( -35.50)
>DroSec_CAF1 12523 107 + 1
AGUCUGUCCAGCUACAACAUCGAUUACAAGAUCCCAUGUGG--AGCAGCCCAGUGAGCUGGGCACGAGUCGUGAUUGAGACUGGUCGAUAUGGGGAGUCGAAUGGGAGU
..........(((....((((((((......((((((((.(--(.(.((((((....))))))...((((........))))).)).))))))))))))).)))..))) ( -37.90)
>DroSim_CAF1 15496 107 + 1
AGUCUGUCCAGCUACAACAUCGAUUACAAGAUCCCAUGUGG--AGCAGCCCAGUGAGCUGGGCACGAGUCGUGAUUGAGACUGGUCGAUAUGGGCAGUCGAAUGGGAGU
.(.((((((((((...((((.((((....))))..))))..--))).((((((....))))))((.((((........)))).)).....))))))).).......... ( -38.60)
>DroEre_CAF1 14093 95 + 1
AGCCUCUCCAGCUACAACAUCGAUUACAAGAUCCCAUGCGG--AGCAGCCCAGUGAGCUGGGCACGGGUCGUGAUUGAGACUGGGCGAUAUG------------GGAGC
...(((((..(((......((((((((..(((((..(((..--.)))((((((....))))))..))))))))))))).....))).....)------------)))). ( -35.50)
>consensus
AGUCUGUCCAGCUACAACAUCGAUUACAAGAUCCCAUGCGG__AGCAGCCCAGUGAGCUGGGCACGAGUCGUGAUUGAGACUGGUCGAUAUGGGGAGUCGAAUGGGAGU
.(((.(.((((((.(((((.(((((...........(((.....)))((((((....))))))...))))))).))))).))))).))).................... (-28.71 = -28.15 +  -0.56)

alignment

secondary structure

dotplot

Window 9

Location	2,924,040 – 2,924,155
Length	115
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	85.31
Mean single sequence MFE	-29.78
Consensus MFE	-21.71
Energy contribution	-22.47
Covariance contribution	0.76
Combinations/Pair	1.17
Mean z-score	-2.49
Structure conservation index	0.73
SVM decision value	1.36
SVM RNA-class probability	0.946313
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 2924040 115 + 20766785
CUUCGCAGCCGGAGUCUCCAUUUCCAUUACCAAUUCCAUUUCCGAUCUGAUCUG-----AUUAGGUCCAACGCCAUUCCCAGCAUGUCUGACCCACCUCCGAGGUCAGCAAUGCAAACAA
....((....((((.......))))..................((((((((...-----))))))))....))........((((..(((((((......).))))))..))))...... ( -25.40)
>DroSec_CAF1 12630 115 + 1
CAUCGCAGCCGGAGUCUCCAUUUCCAUUUGCAAUUCCAUUUCCGAUCUGAUCUG-----AUUAGGCCCAACGCCAUUCCCAGCGUGUCUGACCCUCCUCCGGGGUCAGCAAUGCAAACAA
....((((..((((.......))))..))))............((((......)-----))).(((.....))).......((((..((((((((.....))))))))..))))...... ( -31.50)
>DroSim_CAF1 15603 115 + 1
CAUCGCAGCCGGAGUCUCCAUUUCCAUUUCCAAUUCCAUUUCCGAUCUGAUCUG-----AUUAGGCCCAACGCCAUUCCCAGCGUGUCUGACCCUCCUCCGGGGUCAGCAAUGCAAACAA
....((((((((((.......))))..................((((......)-----))).)))...((((........))))(.((((((((.....)))))))))..)))...... ( -30.70)
>DroEre_CAF1 14188 109 + 1
CAUCGCAGCCGGAGUCUCCAUU------UCCAUUCCCAUUUCCGAUCUGAUCUG-----AUUAGGCCCACCGCCAUUCCCAGCGUGUCUGACCCUCCUCCGGGGUCAGCAAUGCAAACAA
....((((((((((.......)------)))............((((......)-----))).)))....(((........)))((.((((((((.....)))))))))).)))...... ( -29.80)
>DroYak_CAF1 13241 109 + 1
-----CCGUUUCCAUUUCCAUU------UCAAUUUCCAUUUCCGAUCUGAUCUGAUCCGAUUAGGCCCACUGCCAUUCCCAGCGUUGGUGACCCUCCUCCGGGGUCAGCAAUGCAAACAA
-----..((((...........------............((.((((......)))).))...(((.....))).......((((((.(((((((.....))))))).)))))))))).. ( -31.50)
>consensus
CAUCGCAGCCGGAGUCUCCAUUUCCAUUUCCAAUUCCAUUUCCGAUCUGAUCUG_____AUUAGGCCCAACGCCAUUCCCAGCGUGUCUGACCCUCCUCCGGGGUCAGCAAUGCAAACAA
.....(((.(((((.........................)))))..)))..............(((.....))).......((((..((((((((.....))))))))..))))...... (-21.71 = -22.47 +   0.76)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:41:47 2006