Locus 1033

Sequence ID	3L_DroMel_CAF1
Location	3,064,379 – 3,064,490
Length	111
Max. P	0.680664

overview

Window 5

Location	3,064,379 – 3,064,490
Length	111
Sequences	4
Columns	112
Reading direction	forward
Mean pairwise identity	87.44
Mean single sequence MFE	-28.85
Consensus MFE	-19.17
Energy contribution	-19.61
Covariance contribution	0.44
Combinations/Pair	1.24
Mean z-score	-2.04
Structure conservation index	0.66
SVM decision value	0.31
SVM RNA-class probability	0.680664
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 3064379 111 + 23771897
GAUUAGCUGGCCCAAACUACAAUCGUGGGAGUAUUAAACUAUACGCUUGAUAG-GCUAAUUAAUAGAAGAAUUGAGCAGUUGGGUAACAUUAUGGCUAGUCUUCGUAUUUAA
((((((((.((((((.((((....))))..((((......))))(((..((..-.(((.....)))....))..)))..))))))........))))))))........... ( -28.60)
>DroSec_CAF1 25132 111 + 1
GAUUAGCUGGCCCAAACUACAAUCGUGGGUGUAUUAAACUAUACGCUUGAUAG-GCUAAUUAAUAGAAAAAUUGAGCCGUUGGGUAACAUUAUGGCUAGCCUUCGUAUUUAA
((...(((((((....((((....))))(((((......)))))(((..((.(-(((((((........)))).))))))..)))........)))))))..))........ ( -29.50)
>DroSim_CAF1 25102 111 + 1
GAUUAGCUGGCCCAAACUACAAUCGUGGGAGUAUUAAACUAUACGCUUGAUAG-GCUAAUUAAUAGAAGAAUUGAGCCGUUGGGUAACAUUACGGCUAGUCUUCGUAUUUAA
(((((((((((((((....(((.((((..(((.....))).)))).)))...(-(((((((........)))).)))).)))))).......)))))))))........... ( -31.31)
>DroYak_CAF1 25390 111 + 1
GUUUGGGUAGCCCAAACUACAAUCAUGGGAAUAUUUAACUCUACGCUUAAUGGAGGGAAUUAAUAGAAGAAUUAAACCAUUGGGUAAUAUUAUGGUUAGUUCUCGUAUGGA-
(((((((...))))))).....(((((.((.((.((..(((((.......)))))..)).))......(((((((.((((...........))))))))))))).))))).- ( -26.00)
>consensus
GAUUAGCUGGCCCAAACUACAAUCGUGGGAGUAUUAAACUAUACGCUUGAUAG_GCUAAUUAAUAGAAGAAUUGAGCCGUUGGGUAACAUUAUGGCUAGUCUUCGUAUUUAA
(((((((((((((((.((((....))))................(((((((....(((.....)))....)))))))..)))))).......)))))))))........... (-19.17 = -19.61 +   0.44)

alignment

secondary structure

dotplot

Window 6

Location	3,064,379 – 3,064,490
Length	111
Sequences	4
Columns	112
Reading direction	reverse
Mean pairwise identity	87.44
Mean single sequence MFE	-21.25
Consensus MFE	-15.04
Energy contribution	-15.85
Covariance contribution	0.81
Combinations/Pair	1.21
Mean z-score	-1.41
Structure conservation index	0.71
SVM decision value	-0.06
SVM RNA-class probability	0.500000
Prediction	OTHER

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 3064379 111 - 23771897
UUAAAUACGAAGACUAGCCAUAAUGUUACCCAACUGCUCAAUUCUUCUAUUAAUUAGC-CUAUCAAGCGUAUAGUUUAAUACUCCCACGAUUGUAGUUUGGGCCAGCUAAUC
...((((.(((((..(((......(((....))).)))....))))))))).((((((-...((((((.(((((((............)))))))))))))....)))))). ( -17.50)
>DroSec_CAF1 25132 111 - 1
UUAAAUACGAAGGCUAGCCAUAAUGUUACCCAACGGCUCAAUUUUUCUAUUAAUUAGC-CUAUCAAGCGUAUAGUUUAAUACACCCACGAUUGUAGUUUGGGCCAGCUAAUC
...........((((.(((...............((((.((((........)))))))-)...(((((.(((((((............))))))))))))))).)))).... ( -22.90)
>DroSim_CAF1 25102 111 - 1
UUAAAUACGAAGACUAGCCGUAAUGUUACCCAACGGCUCAAUUCUUCUAUUAAUUAGC-CUAUCAAGCGUAUAGUUUAAUACUCCCACGAUUGUAGUUUGGGCCAGCUAAUC
...((((.(((((..((((((...........))))))....))))))))).((((((-...((((((.(((((((............)))))))))))))....)))))). ( -25.50)
>DroYak_CAF1 25390 111 - 1
-UCCAUACGAGAACUAACCAUAAUAUUACCCAAUGGUUUAAUUCUUCUAUUAAUUCCCUCCAUUAAGCGUAGAGUUAAAUAUUCCCAUGAUUGUAGUUUGGGCUACCCAAAC
-....(((((......(((((...........)))))((((((((....(((((.......)))))....))))))))............)))))(((((((...))))))) ( -19.10)
>consensus
UUAAAUACGAAGACUAGCCAUAAUGUUACCCAACGGCUCAAUUCUUCUAUUAAUUAGC_CUAUCAAGCGUAUAGUUUAAUACUCCCACGAUUGUAGUUUGGGCCAGCUAAUC
........(((((..((((((...........))))))....)))))......(((((....((((((.(((((((............)))))))))))))....))))).. (-15.04 = -15.85 +   0.81)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:57:20 2006