Locus 8031

Sequence ID	X_DroMel_CAF1
Location	19,958,409 – 19,958,607
Length	198
Max. P	0.938088

overview

Window 9

Location	19,958,409 – 19,958,517
Length	108
Sequences	5
Columns	115
Reading direction	reverse
Mean pairwise identity	77.85
Mean single sequence MFE	-24.26
Consensus MFE	-8.22
Energy contribution	-7.82
Covariance contribution	-0.40
Combinations/Pair	1.12
Mean z-score	-2.34
Structure conservation index	0.34
SVM decision value	1.29
SVM RNA-class probability	0.938088
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 19958409 108 - 22224390
AAACAAAUUAUUAUAAAGAUAUACACGAAAAUAUGUAUGUAUAUUUUUAU------AUGUAAGCUGGG-GGAGUAUCUGCCAUCAAUGUGGAGCCUCUGCCUGCAUCCUGGAUUC
.......((((((((((((((((((............)))))))))))))------).))))((.((.-((((..((..(.......)..))..)))).)).))........... ( -27.70)
>DroSec_CAF1 70790 105 - 1
AAACAAAUUAUUAUAAAGAUAUACACGAAAAUAUG----UAUAUUUUUAU------AUGUAAGCCGGGGGGAGUAUCUGCCAUCAAUGUGGAGCCUCUGCCUGCAUCCUGGAUAC
.......((((((((((((((((((........))----)))))))))))------).))))((.(((.((((..((..(.......)..))..)))).)))))........... ( -28.90)
>DroSim_CAF1 60107 85 - 1
AAACAAAUUAUUAUAAAGAUAUACACGAAAAUAUG----UAUAUUUUUAU------AUGUAAGCCGGGGGGAGUAUCU--------------------GCCUGCAUCCUGGAUAC
.......((((((((((((((((((........))----)))))))))))------).)))).(((((((.((.....--------------------..)).).)))))).... ( -21.40)
>DroEre_CAF1 57101 83 - 1
AAACAAAUUAUUAUAAAGAUACACACGAAAAUAUG----UAUAUUUUUG-------AUGUUAGCCGGU-GGAGUAUCUACCAUCGAUGUG--------------------GAUUC
.....................((((((((((((..----..))))))))-------........((((-((........)))))).))))--------------------..... ( -15.60)
>DroYak_CAF1 60095 110 - 1
AAACAAAUUAUUAUAAAGAUAUACACGAAAAUAUG----UAUAUUUUUAUACGACUACCUAAGCUGGG-GGAGUAUCUGCCAUCGAUGUGGAGCCACUGCCUGCAUCCUGGAUUC
...........((((((((((((((........))----))))))))))))..(((.(((......))-).))).....(((..((((..(.((....)))..)))).))).... ( -27.70)
>consensus
AAACAAAUUAUUAUAAAGAUAUACACGAAAAUAUG____UAUAUUUUUAU______AUGUAAGCCGGG_GGAGUAUCUGCCAUCAAUGUGGAGCC_CUGCCUGCAUCCUGGAUUC
................((((((....(((((((((....)))))))))...............((....)).))))))..................................... ( -8.22 =  -7.82 +  -0.40)

alignment

secondary structure

dotplot

Window 0

Location	19,958,517 – 19,958,607
Length	90
Sequences	5
Columns	90
Reading direction	reverse
Mean pairwise identity	93.22
Mean single sequence MFE	-29.50
Consensus MFE	-26.04
Energy contribution	-26.52
Covariance contribution	0.48
Combinations/Pair	1.08
Mean z-score	-1.35
Structure conservation index	0.88
SVM decision value	0.62
SVM RNA-class probability	0.800700
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 19958517 90 - 22224390
CGGCAGGACCCUCCCAUCCUUCCACUUCUCCAUCAAUGCUGUCCUUGGCUGUGCCUUAGUUAAAUGUGCCCCGGGGAGAGUUUUGCUGGC
.((.((((........)))).))......(((.(((.(((.(((((((..(..(.((.....)).)..).))))))).))).))).))). ( -28.00)
>DroSec_CAF1 70895 90 - 1
CGGCAGGACCCUCCCAUCCUUCCAGCUCUCCAUCAAUGCUGUCCUUGGCUGUGCUUUAGUUAAAUGUGCCCCGGGGAGAGUUUUGCUGGC
(((((((((.(((((.......((((...........))))...(((((((.....)))))))..........))))).))))))))).. ( -30.60)
>DroSim_CAF1 60192 90 - 1
CGGCAGGACCCUCCCAUCCUUCCAGCUCUCCAUCAAUGCUGUCCUUGGCUGUGCUUUAGUUAAAUGUGCCCCGGGGAGAGUUUUGCUGGC
(((((((((.(((((.......((((...........))))...(((((((.....)))))))..........))))).))))))))).. ( -30.60)
>DroEre_CAF1 57184 90 - 1
CGGCAGGACCCUGCCACCCACCCACUUCUCCAUCAAUGCUGUCCUCGGCUGUGCUUUAGUUAAAUGUGCCCCGGGGAGAGUUUAGCUGGC
.(((((....)))))..............(((.(...(((.(((((((..(..(...........)..).))))))).)))...).))). ( -31.10)
>DroYak_CAF1 60205 90 - 1
CGGCAGGACUCGCCCAUCCCCUCACUUCACCAUCAAUGCUGUCCUUGGCUGUGCUUUAGUUAAAUGUGCCCCGGGGAGAGUUUUGCUGGC
(((((((((((.....(((((.(((..((.((....)).))...(((((((.....)))))))..)))....)))))))))))))))).. ( -27.20)
>consensus
CGGCAGGACCCUCCCAUCCUUCCACUUCUCCAUCAAUGCUGUCCUUGGCUGUGCUUUAGUUAAAUGUGCCCCGGGGAGAGUUUUGCUGGC
.((.((((........)))).))......(((.(((.(((.(((((((..(..(...........)..).))))))).))).))).))). (-26.04 = -26.52 +   0.48)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:53:40 2006