Locus 3576

Sequence ID	X_DroMel_CAF1
Location	9,596,359 – 9,596,454
Length	95
Max. P	0.755999

overview

Window 2

Location	9,596,359 – 9,596,454
Length	95
Sequences	6
Columns	113
Reading direction	forward
Mean pairwise identity	81.40
Mean single sequence MFE	-35.50
Consensus MFE	-24.54
Energy contribution	-25.27
Covariance contribution	0.72
Combinations/Pair	1.09
Mean z-score	-1.47
Structure conservation index	0.69
SVM decision value	0.15
SVM RNA-class probability	0.608359
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 9596359 95 + 22224390
GGUUAGGUGGGCGGUUGU---AAGGGGUAUUCCCCAAA-------G-----UUGCCUUUCCUCUC---AAUUUCUGGAGUGGCCAAUUACUGGCCAAAAUAGCAGCUUCCGCG
..........((((....---..((((....)))).((-------(-----((((..((((....---.......))))((((((.....)))))).....))))))))))). ( -34.10)
>DroSec_CAF1 55022 95 + 1
GGUUAGGUGGGCGGUUGU---AAGGGGGAUUCCCCAGA-------G-----UUGCCUUUCCUCUC---AAUUUCUGGAGUGGCCAAUUACUGGCCAAAAUAGCAGCUUCCGCG
..........((((....---..((((....)))).((-------(-----((((..((((....---.......))))((((((.....)))))).....))))))))))). ( -34.20)
>DroSim_CAF1 41522 95 + 1
GGUUAGGUGGGCGGUUGU---AAGGGGGAUUCCCCAGA-------G-----UUGCCUUUCCUCUC---AAUUUCUGGAGUGGCCAAUUACUGGCCAAAAUAGCAGCUUCCGCG
..........((((....---..((((....)))).((-------(-----((((..((((....---.......))))((((((.....)))))).....))))))))))). ( -34.20)
>DroEre_CAF1 59830 102 + 1
GGUUGGGUGGGCGGUAGU---ACGGGGGAUUCCCCAGAUACCCCAG-----UUGCCGUUCCUCUC---AAUUUCUGGAGUGGCCAAUUACUGGCCAAAAUAGCAGCUUCCGCG
(((((((.(((((((((.---..((((...((....))..))))..-----)))))).))).)))---)))).(((...((((((.....))))))...)))..((....)). ( -37.80)
>DroYak_CAF1 58299 107 + 1
GGUUAGGUGGGCGGUAGU---AAGGGAGAUUCCCCAGAUUCGCCAGCUUCGUUGCCUUUCCUCUC---AAUUUCUGGAGUGGCCAAUUACUGGCCAAAAUAGCAGCUUCCGCG
((..((((.(((((....---..(((.....))).....))))).)))).(((((..((((....---.......))))((((((.....)))))).....)))))..))... ( -33.70)
>DroAna_CAF1 69059 101 + 1
GGCUUGGUGGGCGGUUAAAGAGCGGGGGAUUCCCCCGC-------G-----AUUCAAGCCAACGGAAUACUCUCUGAUUUGGCCAAUUACCCGCUGAAAUAGCAGCUUCCGCA
.(((...(.(((((.(((...(((((((...)))))))-------.-----......(((((((((......))))..)))))...))).))))).)...))).((....)). ( -39.00)
>consensus
GGUUAGGUGGGCGGUUGU___AAGGGGGAUUCCCCAGA_______G_____UUGCCUUUCCUCUC___AAUUUCUGGAGUGGCCAAUUACUGGCCAAAAUAGCAGCUUCCGCG
......(((((.(((((......((((....))))......................................(((...((((((.....))))))...))))))))))))). (-24.54 = -25.27 +   0.72)

alignment

secondary structure

dotplot

Window 3

Location	9,596,359 – 9,596,454
Length	95
Sequences	6
Columns	113
Reading direction	reverse
Mean pairwise identity	81.40
Mean single sequence MFE	-32.37
Consensus MFE	-23.00
Energy contribution	-22.87
Covariance contribution	-0.13
Combinations/Pair	1.23
Mean z-score	-1.76
Structure conservation index	0.71
SVM decision value	0.49
SVM RNA-class probability	0.755999
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 9596359 95 - 22224390
CGCGGAAGCUGCUAUUUUGGCCAGUAAUUGGCCACUCCAGAAAUU---GAGAGGAAAGGCAA-----C-------UUUGGGGAAUACCCCUU---ACAACCGCCCACCUAACC
.(((((((.((((.((((((((((...)))))).(((.(....).---))).)))).)))).-----)-------)).((((....))))..---....)))).......... ( -30.90)
>DroSec_CAF1 55022 95 - 1
CGCGGAAGCUGCUAUUUUGGCCAGUAAUUGGCCACUCCAGAAAUU---GAGAGGAAAGGCAA-----C-------UCUGGGGAAUCCCCCUU---ACAACCGCCCACCUAACC
.((((.((.((((.((((((((((...)))))).(((.(....).---))).)))).)))).-----)-------)..((((....))))..---....)))).......... ( -30.30)
>DroSim_CAF1 41522 95 - 1
CGCGGAAGCUGCUAUUUUGGCCAGUAAUUGGCCACUCCAGAAAUU---GAGAGGAAAGGCAA-----C-------UCUGGGGAAUCCCCCUU---ACAACCGCCCACCUAACC
.((((.((.((((.((((((((((...)))))).(((.(....).---))).)))).)))).-----)-------)..((((....))))..---....)))).......... ( -30.30)
>DroEre_CAF1 59830 102 - 1
CGCGGAAGCUGCUAUUUUGGCCAGUAAUUGGCCACUCCAGAAAUU---GAGAGGAACGGCAA-----CUGGGGUAUCUGGGGAAUCCCCCGU---ACUACCGCCCACCCAACC
.((((.((.(((..((((((((((...)))))).(((.(....).---))).))))..))).-----))..(((((..((((....))))))---))).)))).......... ( -34.50)
>DroYak_CAF1 58299 107 - 1
CGCGGAAGCUGCUAUUUUGGCCAGUAAUUGGCCACUCCAGAAAUU---GAGAGGAAAGGCAACGAAGCUGGCGAAUCUGGGGAAUCUCCCUU---ACUACCGCCCACCUAACC
.((....))........(((((((...)))))))(((.(....).---)))(((...(((......)))((((.....((((.....)))).---.....))))..))).... ( -32.90)
>DroAna_CAF1 69059 101 - 1
UGCGGAAGCUGCUAUUUCAGCGGGUAAUUGGCCAAAUCAGAGAGUAUUCCGUUGGCUUGAAU-----C-------GCGGGGGAAUCCCCCGCUCUUUAACCGCCCACCAAGCC
...((..((((......))))((((....((((((....(((....)))..))))))((((.-----.-------(((((((...)))))))..))))...)))).))..... ( -35.30)
>consensus
CGCGGAAGCUGCUAUUUUGGCCAGUAAUUGGCCACUCCAGAAAUU___GAGAGGAAAGGCAA_____C_______UCUGGGGAAUCCCCCUU___ACAACCGCCCACCUAACC
.((((....((((....(((((((...)))))))(((.............)))....)))).................((((....)))).........)))).......... (-23.00 = -22.87 +  -0.13)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:02:50 2006