Locus 3960

Sequence ID 2L_DroMel_CAF1
Location 11,569,071 – 11,569,186
Length 115
Max. P 0.872201
window6244 window6245

overview

Window 4

Location 11,569,071 – 11,569,186
Length 115
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 78.88
Mean single sequence MFE -32.57
Consensus MFE -19.14
Energy contribution -19.87
Covariance contribution 0.72
Combinations/Pair 1.10
Mean z-score -1.69
Structure conservation index 0.59
SVM decision value 0.24
SVM RNA-class probability 0.648665
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 11569071 115 + 22407834
AUUAUGAAGCGUGGCCCUGAUGCGCAUUCGGUGUUUGUUU-----GGCACCCAGUCGCAGGUGCUACUGAGCGUAUACUUAAUAUGCCAUUUAUUUUGGGCGAAAAACUCAAGGCUAAGC
........((.(((((.((((((((....((((((.....-----))))))((((.((....)).)))).))))).........((((..........))))......))).))))).)) ( -35.10)
>DroPse_CAF1 25248 93 + 1
AUUAUGUGCCCUGGCCU-----------------UUG-CU-----GGCACCC-GUCACAGGUGCCACUGAGCGUAUACUUAAUAUGCCAUUUAUUUUGGC---ACAACUCAAGGCUAAGC
.......((..((((((-----------------(((-((-----((((((.-......))))))..((.((((((.....))))))))........)))---)......))))))).)) ( -28.10)
>DroSec_CAF1 23557 115 + 1
AUUAUGAAGCGUGGCCCUGAUGCGCAUUCGGUGUUUGUUU-----GGCACCCAGUCGCAGGUGCCACUGAGCGUAUACUUAAUAUGCCAUUUAUUUUGGGCGAAAAACUCAAGCCUAAGC
........((((((((((...(((.(((.((((((.....-----)))))).))))))))).)))))((.((((((.....))))))))......((((((...........)))))))) ( -37.40)
>DroEre_CAF1 54175 114 + 1
AUUAUUAGGCGUGGC-CUGAUGCGCAUUCGGUGUUAGUUU-----GGCACCCAGUCGCAGGUGCCACUGAGCGUAUACUUAAUAUGCCAUUUAUUUUGGGCGAAAAACUCAAGGCUAAGC
........((.((((-((.((((((....((((((.....-----))))))((((.((....)).)))).))))))........((((..........)))).........)))))).)) ( -34.90)
>DroAna_CAF1 35717 117 + 1
UUUAUUUAGCAUGGCCUCGAUUCGUAUUCAGUGUUUGUUUGCUUUGUCAUGGAGACGCAGGUGCCACUGAGCGUAUACUUAAUAUGCCAUUUAUUUCGGCCGA---ACUCAAGGCUAAGC
........((.((((((.((((((...((((((...(..(((...(((.....))))))..)..))))))((((((.....)))))).............)))---).)).)))))).)) ( -31.80)
>DroPer_CAF1 25416 93 + 1
AUUAUGUGCCCUGGCCU-----------------UUG-UU-----GGCACCC-GUCACAGGUGCCACUGAGCGUAUACUUAAUAUGCCAUUUAUUUUGGC---ACAACUCAAGGCUAAGC
.......((..((((((-----------------(..-.(-----((((((.-......)))))))..(((.((((.....))))((((.......))))---....)))))))))).)) ( -28.10)
>consensus
AUUAUGAAGCGUGGCCCUGAUGCGCAUUCGGUGUUUGUUU_____GGCACCCAGUCGCAGGUGCCACUGAGCGUAUACUUAAUAUGCCAUUUAUUUUGGCCGAAAAACUCAAGGCUAAGC
........((.(((((.............................((((((........))))))..((.((((((.....)))))))).......................))))).)) (-19.14 = -19.87 +   0.72)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 5

Location 11,569,071 – 11,569,186
Length 115
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 78.88
Mean single sequence MFE -32.62
Consensus MFE -16.61
Energy contribution -18.25
Covariance contribution 1.64
Combinations/Pair 1.20
Mean z-score -2.41
Structure conservation index 0.51
SVM decision value 0.88
SVM RNA-class probability 0.872201
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 11569071 115 - 22407834
GCUUAGCCUUGAGUUUUUCGCCCAAAAUAAAUGGCAUAUUAAGUAUACGCUCAGUAGCACCUGCGACUGGGUGCC-----AAACAAACACCGAAUGCGCAUCAGGGCCACGCUUCAUAAU
((...(((((((((..((((((..........)))............((((((((.((....)).))))))))..-----...........)))...)).)))))))...))........ ( -31.30)
>DroPse_CAF1 25248 93 - 1
GCUUAGCCUUGAGUUGU---GCCAAAAUAAAUGGCAUAUUAAGUAUACGCUCAGUGGCACCUGUGAC-GGGUGCC-----AG-CAA-----------------AGGCCAGGGCACAUAAU
((((.((((((((((((---((((.......)))))))..........))))..(((((((((...)-)))))))-----).-..)-----------------))))..))))....... ( -35.60)
>DroSec_CAF1 23557 115 - 1
GCUUAGGCUUGAGUUUUUCGCCCAAAAUAAAUGGCAUAUUAAGUAUACGCUCAGUGGCACCUGCGACUGGGUGCC-----AAACAAACACCGAAUGCGCAUCAGGGCCACGCUUCAUAAU
....((((.(((((.....(((..........))).......(....))))))(((((.((((((..(.((((..-----.......)))).)...)))...))))))))))))...... ( -30.20)
>DroEre_CAF1 54175 114 - 1
GCUUAGCCUUGAGUUUUUCGCCCAAAAUAAAUGGCAUAUUAAGUAUACGCUCAGUGGCACCUGCGACUGGGUGCC-----AAACUAACACCGAAUGCGCAUCAG-GCCACGCCUAAUAAU
((...((((.((((..((((((..........)))......(((...((((((((.((....)).))))))))..-----..)))......)))...)).))))-))...))........ ( -29.10)
>DroAna_CAF1 35717 117 - 1
GCUUAGCCUUGAGU---UCGGCCGAAAUAAAUGGCAUAUUAAGUAUACGCUCAGUGGCACCUGCGUCUCCAUGACAAAGCAAACAAACACUGAAUACGAAUCGAGGCCAUGCUAAAUAAA
((...(((((((.(---(((((((.......))))...............((((((((....))(((.....)))............))))))...)))))))))))...))........ ( -33.90)
>DroPer_CAF1 25416 93 - 1
GCUUAGCCUUGAGUUGU---GCCAAAAUAAAUGGCAUAUUAAGUAUACGCUCAGUGGCACCUGUGAC-GGGUGCC-----AA-CAA-----------------AGGCCAGGGCACAUAAU
((((.((((((((((((---((((.......)))))))..........))))..(((((((((...)-)))))))-----).-..)-----------------))))..))))....... ( -35.60)
>consensus
GCUUAGCCUUGAGUUUUUCGCCCAAAAUAAAUGGCAUAUUAAGUAUACGCUCAGUGGCACCUGCGACUGGGUGCC_____AAACAAACACCGAAUGCGCAUCAAGGCCACGCCACAUAAU
.....(((((((.........(((.......))).............((((((((.((....)).))))))))...........................)))))))............. (-16.61 = -18.25 +   1.64)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:05:49 2006