Locus 2042

Sequence ID	2L_DroMel_CAF1
Location	5,515,536 – 5,515,708
Length	172
Max. P	0.845499

overview

Window 7

Location	5,515,536 – 5,515,654
Length	118
Sequences	3
Columns	118
Reading direction	reverse
Mean pairwise identity	84.01
Mean single sequence MFE	-29.92
Consensus MFE	-18.40
Energy contribution	-18.62
Covariance contribution	0.22
Combinations/Pair	1.04
Mean z-score	-2.58
Structure conservation index	0.61
SVM decision value	0.41
SVM RNA-class probability	0.723272
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 5515536 118 - 22407834
CUAAUUAGGACUAGUAACAAAAGGUGCUGGCAGUCUGGAAAAAUUGUAAUUCAGUUGAUAAGAAGUAAUUGGCACUCAGCACCUUACUUUAUCUAUUAUAUAUUCUGUUUAUAUUCCA
.......(((.((((((...((((((((((((((.(....).)))))......((..((........))..))...)))))))))...))).)))..(((((.......)))))))). ( -24.90)
>DroSim_CAF1 146004 108 - 1
CUAAUUAGGACUAGCACCAAAAGGUGCUGGCAGUCUGGAAAAAUUGUAAUUCAGCUGAUAAGAAGUAAGUGGCACUCAGCACCUUACCUUAUCUAG----------GCUGAUAUUCCA
.......(((((((((((....))))))))((((.(....).))))....((((((((((((..(((((..((.....))..)))))))))))..)----------)))))...))). ( -36.00)
>DroYak_CAF1 144760 105 - 1
CUAAUUAGGUUGUG---CAAAAGGUGCUGGGAGGCUGGAAAAAUUGUAAUUCAGUUGAUAAGAAGUAAGUGCCACUCAGCACCUUACAUUAUCUAU----------GCUGAUAUUCCA
.....(((((.(((---...(((((((((((.(((......(((((.....)))))..............))).))))))))))).))).))))).----------............ ( -28.85)
>consensus
CUAAUUAGGACUAG_A_CAAAAGGUGCUGGCAGUCUGGAAAAAUUGUAAUUCAGUUGAUAAGAAGUAAGUGGCACUCAGCACCUUACAUUAUCUAU__________GCUGAUAUUCCA
.......(((..........((((((((((..(((........((((..........)))).........)))..))))))))))....((((................)))).))). (-18.40 = -18.62 +   0.22)

alignment

secondary structure

dotplot

Window 8

Location	5,515,614 – 5,515,708
Length	94
Sequences	3
Columns	112
Reading direction	forward
Mean pairwise identity	76.10
Mean single sequence MFE	-24.88
Consensus MFE	-13.39
Energy contribution	-14.06
Covariance contribution	0.67
Combinations/Pair	1.00
Mean z-score	-2.32
Structure conservation index	0.54
SVM decision value	0.77
SVM RNA-class probability	0.845499
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 5515614 94 + 22407834
UUCCAGACUGCCAGCACCUUUUGUUACUAGUCCUAAUUAGCAGGACACUGCCAUGGAG---CCAUAUUCCCGCCUCCUGGCUGCUCCUUGCUU---------------CAAA
.....(((((..((((.....))))..)))))......(((((((....((((.((((---.(........).))))))))...))).)))).---------------.... ( -25.10)
>DroSim_CAF1 146072 94 + 1
UUCCAGACUGCCAGCACCUUUUGGUGCUAGUCCUAAUUAGCAGGACACUGCCAUGGAG---CCGUAUACCCACCUACUGGCUGCUCCUUGCUC---------------CAAA
.....((((...((((((....)))))))))).......((((....))))..(((((---(........((((....)).))......))))---------------)).. ( -28.64)
>DroYak_CAF1 144828 109 + 1
UUCCAGCCUCCCAGCACCUUUUG---CACAACCUAAUUAGCAGGACACUGCCAUGGAAUUCCCGAAUUCCCGCAUCCUGGCUCCUCCUUGCUCCUGUAUCCUCGCAGUCCAA
....((((.....(((.....))---)..............((((...(((...((((((....)))))).)))))))))))...........((((......))))..... ( -20.90)
>consensus
UUCCAGACUGCCAGCACCUUUUG_U_CUAGUCCUAAUUAGCAGGACACUGCCAUGGAG___CCGUAUUCCCGCCUCCUGGCUGCUCCUUGCUC_______________CAAA
......................................(((((((....((((.((((...............))))))))...))).)))).................... (-13.39 = -14.06 +   0.67)

alignment

secondary structure

dotplot

Window 9

Location	5,515,614 – 5,515,708
Length	94
Sequences	3
Columns	112
Reading direction	reverse
Mean pairwise identity	76.10
Mean single sequence MFE	-32.51
Consensus MFE	-18.38
Energy contribution	-19.50
Covariance contribution	1.12
Combinations/Pair	1.18
Mean z-score	-2.01
Structure conservation index	0.57
SVM decision value	0.52
SVM RNA-class probability	0.766893
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 5515614 94 - 22407834
UUUG---------------AAGCAAGGAGCAGCCAGGAGGCGGGAAUAUGG---CUCCAUGGCAGUGUCCUGCUAAUUAGGACUAGUAACAAAAGGUGCUGGCAGUCUGGAA
....---------------.((((.(((((.((((((((.((......)).---)))).)))).)).)))))))..(((((.((((((.(....).))))))...))))).. ( -31.10)
>DroSim_CAF1 146072 94 - 1
UUUG---------------GAGCAAGGAGCAGCCAGUAGGUGGGUAUACGG---CUCCAUGGCAGUGUCCUGCUAAUUAGGACUAGCACCAAAAGGUGCUGGCAGUCUGGAA
..((---------------((((.....((.(((....)))..)).....)---)))))((((((....)))))).(((((.((((((((....))))))))...))))).. ( -36.70)
>DroYak_CAF1 144828 109 - 1
UUGGACUGCGAGGAUACAGGAGCAAGGAGGAGCCAGGAUGCGGGAAUUCGGGAAUUCCAUGGCAGUGUCCUGCUAAUUAGGUUGUG---CAAAAGGUGCUGGGAGGCUGGAA
(..(.((.(.((.((......((((.((..(((.(((((((.((((((....))))))......))))))))))..))...)))).---......)).)).).)).)..).. ( -29.72)
>consensus
UUUG_______________GAGCAAGGAGCAGCCAGGAGGCGGGAAUACGG___CUCCAUGGCAGUGUCCUGCUAAUUAGGACUAG_A_CAAAAGGUGCUGGCAGUCUGGAA
....................((((.(((((.((((((((.(.(.....).)...)))).)))).)).))))))).....(((((((((........))))...))))).... (-18.38 = -19.50 +   1.12)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:17:52 2006