Locus 1709

Sequence ID	X_DroMel_CAF1
Location	4,774,478 – 4,774,686
Length	208
Max. P	0.747493

overview

Window 5

Location	4,774,478 – 4,774,579
Length	101
Sequences	6
Columns	108
Reading direction	reverse
Mean pairwise identity	78.83
Mean single sequence MFE	-31.35
Consensus MFE	-25.17
Energy contribution	-25.83
Covariance contribution	0.67
Combinations/Pair	1.00
Mean z-score	-1.20
Structure conservation index	0.80
SVM decision value	0.47
SVM RNA-class probability	0.747493
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 4774478 101 - 22224390
AAAAUAGUAGCU-------UAUCGUUUUGCGCACAUUACAGGUGGUGGAUGCCCGUGCUGGACCCGGCACCAAGUCCAUGGCCAAACAGAAGAAGCGCGACAACGCAG
............-------...((((((((((........(((.((((((....((((((....))))))...)))))).)))...(....)..)))))).))))... ( -34.70)
>DroPse_CAF1 8662 97 - 1
ACUUUACUAACUCUCUGUUU-----------CCUGUAAAAGGUGGUGGAUGCCCGAGCUGGUCCCGGCACCAAGUCCCUGGCCAAACAGAAAAAGCGCGAGAACGCAG
...........(((((((((-----------.((((....(((.(.((((....(.((((....)))).)...)))).).)))..))))...))))).))))...... ( -24.00)
>DroSim_CAF1 9844 108 - 1
AAAAUACUAACCCGCUUUCUCUCGCUUUGCGCACAUUGCAGGUGGUGGAUGCCCGUGCUGGACCCGGCACCAAGUCCAUGGCCAAACAGAAGAAGCGCGACAACGCAG
.............((((..(((.((..((....))..)).(((.((((((....((((((....))))))...)))))).)))....)))..))))(((....))).. ( -39.50)
>DroEre_CAF1 7929 108 - 1
GCAAAACUAAUCCUCUGUUUUACCCUUUGCGCACAUAACAGGUGGUGGAUGCCCGUGCUGGACCCGGCACCAAGUCCAUGGCCAAACAAAAGAAGCGCGACAACGCAG
(((((((.........))))).....((((((........(((.((((((....((((((....))))))...)))))).)))...(....)..))))))....)).. ( -35.30)
>DroYak_CAF1 8679 97 - 1
GUAAAACUAAUCCUCUCUCU-----------CACAUGACAGGUGGUGGAUGCUCGUGCUGGACCCGGCACCAAGUCCAUGGCCAAACAAAAGAAGCGUGACAACGCAG
....................-----------.........(((.((((((....((((((....))))))...)))))).)))...........((((....)))).. ( -30.60)
>DroPer_CAF1 9158 97 - 1
ACUUUACUAACUCUCUGUUU-----------CCUGUAAAAGGUGGUGGAUGCCCGAGCUGGUCCCGGCACCAAGUCCCUGGCCAAACAGAAAAAGCGCGAGAACGCAG
...........(((((((((-----------.((((....(((.(.((((....(.((((....)))).)...)))).).)))..))))...))))).))))...... ( -24.00)
>consensus
ACAAUACUAACCCUCUGUUU___________CACAUAACAGGUGGUGGAUGCCCGUGCUGGACCCGGCACCAAGUCCAUGGCCAAACAGAAGAAGCGCGACAACGCAG
........................................(((.((((((....((((((....))))))...)))))).)))...........(((......))).. (-25.17 = -25.83 +   0.67)

alignment

secondary structure

dotplot

Window 6

Location	4,774,579 – 4,774,686
Length	107
Sequences	6
Columns	116
Reading direction	forward
Mean pairwise identity	79.03
Mean single sequence MFE	-31.68
Consensus MFE	-21.94
Energy contribution	-21.70
Covariance contribution	-0.24
Combinations/Pair	1.29
Mean z-score	-1.18
Structure conservation index	0.69
SVM decision value	0.12
SVM RNA-class probability	0.593169
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 4774579 107 + 22224390
UCU---------UUUUUUUUACAUAUGCCUUAAUACUUACAUGACCCCAGUGACGCUUACUACCUAUGGGUAGUCGCUUGUAGCGCUUGACCAAAAGGACGCAGGCGUUGCAGAUU
...---------........................((((.((....)))))).((..((((((....)))))).))((((((((((((.((....))...))))))))))))... ( -28.00)
>DroSec_CAF1 11172 105 + 1
U-----------UUUGUUUUACAUAGGCAUUAAUACUUACAUGACCCCAGUGACGCUUACUACCUAUGGGUAGUCUCUUGUAGCGCUUGACCAAAAGGACGCAGGCGUUGCAGAUU
.-----------...((.((((...(((((..........))).))...)))).))..((((((....))))))...((((((((((((.((....))...))))))))))))... ( -29.20)
>DroSim_CAF1 9952 105 + 1
U-----------UUUGUUUUACAUAGGCAUUAAUACUUACAUGACCCCAGUGACGCUUACUACCUAUGGGUAGUCGCUUGUAGCGCUUGACCAAAAGGACGCAGGCGUUGCAGAUU
.-----------......((((...(((((..........))).))...)))).((..((((((....)))))).))((((((((((((.((....))...))))))))))))... ( -29.50)
>DroEre_CAF1 8037 111 + 1
UGAUUGCUAC---AUGUUUUAUAUGUGGA--AGGACUUACAUGACCCCAGUGGCGCUUACUCCCUAUGGGCAGUCGUUUGUAGCGCUUGACCAGAAGAACGCAGGCGUUGCAGAUU
.(((((((((---((((...)))))))).--..............((((..((.(....).))...)))))))))((((((((((((((............)))))))))))))). ( -33.60)
>DroYak_CAF1 8776 113 + 1
UCAUUGCUACUAUAUGGUUUAUAUGUGGA--A-UACUUACAUGACCCCAGUGACGCUUGCUACCGACAGGCAGUCGCUUGUAGCGCUUGACCAGAAGGACGCAGGCGUUGCAGAUU
..............(((..(.(((((((.--.-...))))))))..)))(((((((((((....).))))).)))))((((((((((((.((....))...))))))))))))... ( -35.70)
>DroAna_CAF1 10729 109 + 1
UAAUUAGCA---AGUAUAUCACAUGAG----AGUACUUACGUGACCCCAGUGGCGUUUGCUGCCAGCCGGGAGGCGCUUGUAGCGUUUGACCAGCAAGACGCAGGCGUUGCAGAUC
.........---......((((.((((----....)))).)))).....(..((((((((..(..((.((.((((((.....))))))..)).))..)..))))))))..)..... ( -34.10)
>consensus
U_A_________UUUGUUUUACAUAUGCA__AAUACUUACAUGACCCCAGUGACGCUUACUACCUAUGGGUAGUCGCUUGUAGCGCUUGACCAAAAGGACGCAGGCGUUGCAGAUU
................................................(((((((((((.......))))).))))))(((((((((((.((....))...))))))))))).... (-21.94 = -21.70 +  -0.24)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:17:10 2006