Locus 3673

Sequence ID	X_DroMel_CAF1
Location	9,818,517 – 9,818,622
Length	105
Max. P	0.862083

overview

Window 0

Location	9,818,517 – 9,818,622
Length	105
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	90.16
Mean single sequence MFE	-20.66
Consensus MFE	-16.72
Energy contribution	-16.76
Covariance contribution	0.04
Combinations/Pair	1.04
Mean z-score	-1.38
Structure conservation index	0.81
SVM decision value	0.05
SVM RNA-class probability	0.559332
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 9818517 105 + 22224390
---------UCCACAUCCACAUCUGUGUAUCUUUUUAUACACAUUUUUUUUUUUUUAACAGAUCGC------AGAACCUGUGCCCAGUGCAUGCUCGAGUGCCUCUUACUUUGUGGCCUU
---------.(((((..((((((((((.((((.((.....................)).)))))))------)))...))))...((.((((......)))))).......))))).... ( -20.00)
>DroSec_CAF1 20000 100 + 1
---------UCCACAUCCACAUCUGUGUAUCUUUUUAUACACAUUUUUUUUU-----ACAGAUCGC------AGAACCUGUGCCCAGUGCAUGCUCGAGUGCCUCUUACUUUGUGGCCUU
---------.(((((..((((((((((.((((....................-----..)))))))------)))...))))...((.((((......)))))).......))))).... ( -20.05)
>DroSim_CAF1 9985 100 + 1
---------UCCACAUCCACAUCUGUGUAUCUUUUUAUACACAUUUUUUUUU-----ACAGAUCGC------AGAACCUGUGCCCAGUGCAUGCUCGAGUGCCUCUUACUUUGUGGCCUU
---------.(((((..((((((((((.((((....................-----..)))))))------)))...))))...((.((((......)))))).......))))).... ( -20.05)
>DroEre_CAF1 11320 97 + 1
---------UCCACAUCCAUAUCUGUGUAUCUUUUUAUACACAUUUU---UU-----ACAGAUCGC------AGAACCUGUGCCCAGUGCAUGCUCGAGUGCCUCUUACUUUGUGGCCUU
---------.(((((......((((((.((((...............---..-----..)))))))------)))....(((...((.((((......))))))..)))..))))).... ( -18.71)
>DroYak_CAF1 11900 112 + 1
GCAGCCACAUCCACAUCCACAUCUGGGUAUCUUUUUAUACACAUUUU---UU-----ACAGAUCGCAGACGCAGAACCUGUGCCCAGUGCAUGCUCGAGUGCCUCUUACUUUGUGGCCUU
...((((((....(((.(((.((((.(.((((...............---..-----..))))).))))(((((...)))))....))).)))...(((((.....)))))))))))... ( -24.51)
>consensus
_________UCCACAUCCACAUCUGUGUAUCUUUUUAUACACAUUUUUUUUU_____ACAGAUCGC______AGAACCUGUGCCCAGUGCAUGCUCGAGUGCCUCUUACUUUGUGGCCUU
.............(((.(((...(((((((......)))))))..............((((.((.........))..)))).....))).)))...(((.(((.(.......).)))))) (-16.72 = -16.76 +   0.04)

alignment

secondary structure

dotplot

Window 1

Location	9,818,517 – 9,818,622
Length	105
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	90.16
Mean single sequence MFE	-26.02
Consensus MFE	-20.50
Energy contribution	-20.90
Covariance contribution	0.40
Combinations/Pair	1.00
Mean z-score	-1.85
Structure conservation index	0.79
SVM decision value	0.83
SVM RNA-class probability	0.862083
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 9818517 105 - 22224390
AAGGCCACAAAGUAAGAGGCACUCGAGCAUGCACUGGGCACAGGUUCU------GCGAUCUGUUAAAAAAAAAAAAAUGUGUAUAAAAAGAUACACAGAUGUGGAUGUGGA---------
....(((((.....(((.(((...((((.(((.....)))...)))))------))..)))................(((((((......)))))))..))))).......--------- ( -23.50)
>DroSec_CAF1 20000 100 - 1
AAGGCCACAAAGUAAGAGGCACUCGAGCAUGCACUGGGCACAGGUUCU------GCGAUCUGU-----AAAAAAAAAUGUGUAUAAAAAGAUACACAGAUGUGGAUGUGGA---------
...(((.(.......).)))......((((.(((.....(((((((..------..)))))))-----.........(((((((......)))))))...))).))))...--------- ( -24.10)
>DroSim_CAF1 9985 100 - 1
AAGGCCACAAAGUAAGAGGCACUCGAGCAUGCACUGGGCACAGGUUCU------GCGAUCUGU-----AAAAAAAAAUGUGUAUAAAAAGAUACACAGAUGUGGAUGUGGA---------
...(((.(.......).)))......((((.(((.....(((((((..------..)))))))-----.........(((((((......)))))))...))).))))...--------- ( -24.10)
>DroEre_CAF1 11320 97 - 1
AAGGCCACAAAGUAAGAGGCACUCGAGCAUGCACUGGGCACAGGUUCU------GCGAUCUGU-----AA---AAAAUGUGUAUAAAAAGAUACACAGAUAUGGAUGUGGA---------
....((((..........(((...((((.(((.....)))...)))))------)).((((((-----(.---....(((((((......)))))))..))))))))))).--------- ( -24.80)
>DroYak_CAF1 11900 112 - 1
AAGGCCACAAAGUAAGAGGCACUCGAGCAUGCACUGGGCACAGGUUCUGCGUCUGCGAUCUGU-----AA---AAAAUGUGUAUAAAAAGAUACCCAGAUGUGGAUGUGGAUGUGGCUGC
..(((((((..((..(((...)))..)).....(((....)))..((..((((..(.(((((.-----..---.....(.((((......)))))))))))..))))..))))))))).. ( -33.60)
>consensus
AAGGCCACAAAGUAAGAGGCACUCGAGCAUGCACUGGGCACAGGUUCU______GCGAUCUGU_____AAAAAAAAAUGUGUAUAAAAAGAUACACAGAUGUGGAUGUGGA_________
...(((.(.......).)))..((..((((.(((.....(((((((..........)))))))..............(((((((......)))))))...))).)))).))......... (-20.50 = -20.90 +   0.40)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:05:23 2006