Locus 4881

Sequence ID	3L_DroMel_CAF1
Location	13,617,395 – 13,617,533
Length	138
Max. P	0.985907

overview

Window 5

Location	13,617,395 – 13,617,503
Length	108
Sequences	5
Columns	108
Reading direction	forward
Mean pairwise identity	93.98
Mean single sequence MFE	-20.27
Consensus MFE	-17.36
Energy contribution	-16.92
Covariance contribution	-0.44
Combinations/Pair	1.19
Mean z-score	-1.98
Structure conservation index	0.86
SVM decision value	2.02
SVM RNA-class probability	0.985907
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13617395 108 + 23771897
AGAGGGAAACACGCGGCAAGGCCAGAAAUUUAUGACAUUUUUAUUAUACAACGAAAUGUGUAAAAAAAAGAGAGAGAUAUGGAAAUGAAAGCGAAACUCCGUGUAGAC
.((((....).(((..((...(((...((((......(((((.(((((((......))))))).))))).....)))).)))...))...)))...)))......... ( -20.80)
>DroSec_CAF1 24367 106 + 1
AGAGGGAAACACGCGGCAAGGCCAGAAAUUUAUGACAUUUUUAUUAUACAACGAAAUGUAUAAAAAAAC--GAGAGAUAUGGAAAUGAAAGCGAAACUCCGUGUAGAC
.((((....).((((((...)))............(((((((((((((((......))))))).....(--....)...))))))))...)))...)))......... ( -21.70)
>DroSim_CAF1 33488 105 + 1
AGAGGGAAACACGCGGCAAGGCCAGAAAUUUAUGACAUUUUUAUUAUACAACGAAAUGUAUAAAAAAA---GAGAGAUAUGGAAAUGAAAGCGAAACUCCGUGUAGAC
.((((....).((((((...)))............(((((((((((((((......))))))......---.......)))))))))...)))...)))......... ( -19.11)
>DroEre_CAF1 27210 103 + 1
AGAGGGAAACACGCGGCAAGGCCAGAAAUUUAUGACAUUUUUAUUAUACAACGAAAUGUAUGAA-AAA----AAAGAUAUGGAAAUGAAAGCGAAACUCCAUGUAGAC
.((((....).((((((...))).....((((((.(.(((((.(((((((......))))))).-)))----)).).)))))).......)))...)))......... ( -21.00)
>DroYak_CAF1 31570 104 + 1
AGUGGGAAACACGCAGCAAGGCCGCAAAUUUAUGACAUUUUUAUUAUACAACGAAAUGUAUAAAGAAA----AAAGAUAUGGAAAUGAAAGCGAAACUCCAUGUAGAC
.((((....).))).((......))............(((((.(((((((......))))))).))))----)...(((((((..............))))))).... ( -18.74)
>consensus
AGAGGGAAACACGCGGCAAGGCCAGAAAUUUAUGACAUUUUUAUUAUACAACGAAAUGUAUAAAAAAA___GAGAGAUAUGGAAAUGAAAGCGAAACUCCGUGUAGAC
.((((....).(((..((...(((....(((......(((((.(((((((......))))))))))))....)))....)))...))...)))...)))......... (-17.36 = -16.92 +  -0.44)

alignment

secondary structure

dotplot

Window 6

Location	13,617,395 – 13,617,503
Length	108
Sequences	5
Columns	108
Reading direction	reverse
Mean pairwise identity	93.98
Mean single sequence MFE	-17.24
Consensus MFE	-15.02
Energy contribution	-15.66
Covariance contribution	0.64
Combinations/Pair	1.05
Mean z-score	-1.63
Structure conservation index	0.87
SVM decision value	1.35
SVM RNA-class probability	0.944767
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13617395 108 - 23771897
GUCUACACGGAGUUUCGCUUUCAUUUCCAUAUCUCUCUCUUUUUUUUACACAUUUCGUUGUAUAAUAAAAAUGUCAUAAAUUUCUGGCCUUGCCGCGUGUUUCCCUCU
........((((...(((.....................(((((.(((.(((......))).))).)))))..............(((...))))))...)))).... ( -14.30)
>DroSec_CAF1 24367 106 - 1
GUCUACACGGAGUUUCGCUUUCAUUUCCAUAUCUCUC--GUUUUUUUAUACAUUUCGUUGUAUAAUAAAAAUGUCAUAAAUUUCUGGCCUUGCCGCGUGUUUCCCUCU
........((((...(((..................(--(((((((((((((......))))))).)))))))............(((...))))))...)))).... ( -20.30)
>DroSim_CAF1 33488 105 - 1
GUCUACACGGAGUUUCGCUUUCAUUUCCAUAUCUCUC---UUUUUUUAUACAUUUCGUUGUAUAAUAAAAAUGUCAUAAAUUUCUGGCCUUGCCGCGUGUUUCCCUCU
........((((...(((...........(((..(..---((((.(((((((......))))))).))))..)..))).......(((...))))))...)))).... ( -18.20)
>DroEre_CAF1 27210 103 - 1
GUCUACAUGGAGUUUCGCUUUCAUUUCCAUAUCUUU----UUU-UUCAUACAUUUCGUUGUAUAAUAAAAAUGUCAUAAAUUUCUGGCCUUGCCGCGUGUUUCCCUCU
........((((...(((................((----(((-...(((((......)))))...)))))..............(((...))))))...)))).... ( -14.80)
>DroYak_CAF1 31570 104 - 1
GUCUACAUGGAGUUUCGCUUUCAUUUCCAUAUCUUU----UUUCUUUAUACAUUUCGUUGUAUAAUAAAAAUGUCAUAAAUUUGCGGCCUUGCUGCGUGUUUCCCACU
........((((...(((.................(----(((..(((((((......)))))))..))))............(((((...)))))))).)))).... ( -18.60)
>consensus
GUCUACACGGAGUUUCGCUUUCAUUUCCAUAUCUCUC___UUUUUUUAUACAUUUCGUUGUAUAAUAAAAAUGUCAUAAAUUUCUGGCCUUGCCGCGUGUUUCCCUCU
........((((...(((......................((((.(((((((......))))))).))))...............(((...))))))...)))).... (-15.02 = -15.66 +   0.64)

alignment

secondary structure

dotplot

Window 7

Location	13,617,424 – 13,617,533
Length	109
Sequences	5
Columns	109
Reading direction	forward
Mean pairwise identity	94.60
Mean single sequence MFE	-24.10
Consensus MFE	-21.40
Energy contribution	-21.28
Covariance contribution	-0.12
Combinations/Pair	1.15
Mean z-score	-1.68
Structure conservation index	0.89
SVM decision value	1.66
SVM RNA-class probability	0.970541
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13617424 109 + 23771897
UUAUGACAUUUUUAUUAUACAACGAAAUGUGUAAAAAAAAGAGAGAGAUAUGGAAAUGAAAGCGAAACUCCGUGUAGACCAUGUCCUUUCGCUGGCUUUCCCCGGUUUC
........(((((.(((((((......))))))).)))))(((((.(((((((...((...(((......))).))..))))))))))))(((((......)))))... ( -28.10)
>DroSec_CAF1 24396 107 + 1
UUAUGACAUUUUUAUUAUACAACGAAAUGUAUAAAAAAAC--GAGAGAUAUGGAAAUGAAAGCGAAACUCCGUGUAGACCAUGUCCUUUCACUGGCUUUCCCCGGUUUC
.........((((.(((((((......))))))).)))).--(((((((((((...((...(((......))).))..)))))).)))))(((((......)))))... ( -23.30)
>DroSim_CAF1 33517 106 + 1
UUAUGACAUUUUUAUUAUACAACGAAAUGUAUAAAAAAA---GAGAGAUAUGGAAAUGAAAGCGAAACUCCGUGUAGACCAUGUCCUUUCGCUGGCUUUCCCCGGUUUC
........(((((.(((((((......))))))).))))---).(((((..(((((.(..(((((((...((((.....))))...)))))))..))))))...))))) ( -25.80)
>DroEre_CAF1 27239 104 + 1
UUAUGACAUUUUUAUUAUACAACGAAAUGUAUGAA-AAA----AAAGAUAUGGAAAUGAAAGCGAAACUCCAUGUAGACCAUGUCCUUUCGUUGGCUUUCCCCGGUUUC
........(((((.(((((((......))))))).-)))----))((((..(((((.(..(((((((...((((.....))))...)))))))..))))))...)))). ( -21.50)
>DroYak_CAF1 31599 105 + 1
UUAUGACAUUUUUAUUAUACAACGAAAUGUAUAAAGAAA----AAAGAUAUGGAAAUGAAAGCGAAACUCCAUGUAGACCAUGUCCUUUCGUUGGCUUUCCCCGGUUUC
........(((((.(((((((......))))))).))))----).((((..(((((.(..(((((((...((((.....))))...)))))))..))))))...)))). ( -21.80)
>consensus
UUAUGACAUUUUUAUUAUACAACGAAAUGUAUAAAAAAA___GAGAGAUAUGGAAAUGAAAGCGAAACUCCGUGUAGACCAUGUCCUUUCGCUGGCUUUCCCCGGUUUC
.........((((.(((((((......))))))).)))).....(((((..(((((.(..(((((((...((((.....))))...)))))))..))))))...))))) (-21.40 = -21.28 +  -0.12)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:36:02 2006