Locus 9556

Sequence ID	3R_DroMel_CAF1
Location	25,251,196 – 25,251,336
Length	140
Max. P	0.906269

overview

Window 3

Location	25,251,196 – 25,251,300
Length	104
Sequences	6
Columns	110
Reading direction	forward
Mean pairwise identity	74.23
Mean single sequence MFE	-21.95
Consensus MFE	-5.51
Energy contribution	-5.35
Covariance contribution	-0.16
Combinations/Pair	1.20
Mean z-score	-2.85
Structure conservation index	0.25
SVM decision value	1.05
SVM RNA-class probability	0.906269
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 25251196 104 + 27905053
ACAAUGAUUAAUCGUACGCCGCUGCGUGUUCCACAUGUA------GCAUAUACAUAUGUACAUAUGUAGCACCCCCACAUAUGUACAAUAUGUAUAAAUGGACUCCAAAA
...((((....))))...((((((((((.....))))))------)).(((((((((((((((((((.(.....).)))))))))).)))))))))...))......... ( -34.30)
>DroSec_CAF1 108496 100 + 1
ACAAUGAUUAAUCGUAAGCCGCUGCGUGUUCCACAUGUA------GCAUAU----ACAUAUGUAUGUAGCACCCCCACAUAUGUACAAUAUGUAUAAAUGGACUCCAAAA
...((((....)))).((((((((((((.....))))))------)).(((----(((((((((((((...........))))))).)))))))))...)).))...... ( -26.80)
>DroSim_CAF1 110640 104 + 1
ACAAUGAUUAAUCGUACGCCGCUGCGUGUUCCACAUGUA------GCAUAUAUGUACAUAUGUAUGUAGCACCCCCACAUAUGUACAAUAUGUAUAAAUGGACUCCAAAA
...((((....))))...((((((((((.....))))))------))((((((((((((((((.............)))))))))).))))))......))......... ( -28.12)
>DroEre_CAF1 125303 79 + 1
ACAAUGAUUAAUCGUGCGCCGCUGCGUGUUCCACAUACA------GCGAA----------------CAGCACCCGCACAUAU---------GCAUAAAUGGACUCCAAAA
.............((((..(((((..((.....))..))------)))..----------------..))))..(((....)---------)).....(((...)))... ( -18.10)
>DroYak_CAF1 112733 79 + 1
ACAAUGAUUAAUCGUACGCCGCUGCGUGUUUCACAUGUA------GUAUA----------------CAGCACCCCCACAUAU---------GCAUAAAUGGACUCCAAAA
...((((....))))...((((((((((.....))))))------))...----------------..(((..........)---------))......))......... ( -12.90)
>DroAna_CAF1 104570 93 + 1
ACAAUGAUUAAUCGUAUGACCGUGCGUGUCCCACAUGCGUACAUCCCAUAU----CCAUAUCCAU---CCGCCCCUACAUAC----------UAUAAAUGGACUCCAAAA
.............(((((...((((((((.....))))))))....)))))----.....(((((---..............----------.....)))))........ ( -11.51)
>consensus
ACAAUGAUUAAUCGUACGCCGCUGCGUGUUCCACAUGUA______GCAUAU____ACAUAU_UAU_UAGCACCCCCACAUAU_________GUAUAAAUGGACUCCAAAA
...((((....))))..((...((((((.....))))))......))...................................................(((...)))... ( -5.51 =  -5.35 +  -0.16)

alignment

secondary structure

dotplot

Window 4

Location	25,251,227 – 25,251,336
Length	109
Sequences	6
Columns	115
Reading direction	reverse
Mean pairwise identity	77.56
Mean single sequence MFE	-25.68
Consensus MFE	-16.43
Energy contribution	-16.52
Covariance contribution	0.08
Combinations/Pair	1.12
Mean z-score	-1.22
Structure conservation index	0.64
SVM decision value	-0.05
SVM RNA-class probability	0.510457
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 25251227 109 - 27905053
CUCGCGCUCUUAAAGCCUACGGAAAGUUUUGUGACUUUUUGGAGUCCAUUUAUACAUAUUGUACAUAUGUGGGGGUGCUACAUAUGUACAUAUGUAUAUGC------UACAUGUG
(((..(((.....)))...(((((((((....))))))))))))......(((((((((.((((((((((((.....)))))))))))))))))))))...------........ ( -35.60)
>DroSec_CAF1 108527 105 - 1
CUCGCGCUCUUAAAGCCUACGGAAAGUUUUGUGACUUUUUGGAGUCCAUUUAUACAUAUUGUACAUAUGUGGGGGUGCUACAUACAUAUGU----AUAUGC------UACAUGUG
...(((((((......((.(((((((((....))))))))).))........(((((((.....))))))))))))))......(((((((----(.....------)))))))) ( -27.90)
>DroSim_CAF1 110671 109 - 1
CUCGCGCUCUUAAAGCCUACGGAAAGUUUUGUGACUUUUUGGAGUCCAUUUAUACAUAUUGUACAUAUGUGGGGGUGCUACAUACAUAUGUACAUAUAUGC------UACAUGUG
(((..(((.....)))...(((((((((....))))))))))))..........(((((((((((((((((..(......).)))))))))))).))))).------........ ( -29.10)
>DroEre_CAF1 125334 84 - 1
CUCGCGCUCUUAAAGCCUACGGAAAGUUUUGUGACUUUUUGGAGUCCAUUUAUGC---------AUAUGUGCGGGUGCUG----------------UUCGC------UGUAUGUG
(((..(((.....)))...(((((((((....)))))))))))).........((---------(((((.(((..(...)----------------..)))------))))))). ( -20.50)
>DroYak_CAF1 112764 84 - 1
CUCGCGCUCUUAAAGCCUAUGGAAAGUUUUGUGACUUUUUGGAGUCCAUUUAUGC---------AUAUGUGGGGGUGCUG----------------UAUAC------UACAUGUG
...(((((((....((.((((.(.((...((.(((((....))))))).)).).)---------))).)).)))))))..----------------.....------........ ( -18.60)
>DroAna_CAF1 104601 98 - 1
CUCGCGCUCUUAAAGCCUACGGAAAGUUUUGUGACUUUUUGGAGUCCAUUUAUA----------GUAUGUAGGGGCGG---AUGGAUAUGG----AUAUGGGAUGUACGCAUGUG
...(((.(((((...((..(((((((((....)))))))))..(((((((....----------((........)).)---))))))..))----...)))))....)))..... ( -22.40)
>consensus
CUCGCGCUCUUAAAGCCUACGGAAAGUUUUGUGACUUUUUGGAGUCCAUUUAUAC_________AUAUGUGGGGGUGCUA_AUA_AUAUGU____AUAUGC______UACAUGUG
...((((((.......((.(((((((((....))))))))).)).((((.(((...........))).))))))))))..................................... (-16.43 = -16.52 +   0.08)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:37:06 2006