Locus 56

Sequence ID	2R_DroMel_CAF1
Location	1,311,657 – 1,311,816
Length	159
Max. P	0.960433

overview

Window 6

Location	1,311,657 – 1,311,776
Length	119
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	96.81
Mean single sequence MFE	-46.60
Consensus MFE	-46.31
Energy contribution	-46.62
Covariance contribution	0.31
Combinations/Pair	1.02
Mean z-score	-1.54
Structure conservation index	0.99
SVM decision value	0.26
SVM RNA-class probability	0.656958
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 1311657 119 + 20766785
AUUUGCGGGACACUGAUUCGCCAGU-UUACUUGCGAAGUGUGGGUGCCAAAAGAGGUCCGGCUGUUGGGGUCCUUCAGCAGCCAAACGCUCCGGCACGUGACAUUGGCAAAGUGAGUUCC
......(((((((((......))))-((((((((..(((((.((((((....(((((..((((((((((....))))))))))..)).))).))))).).))))).)).))))))))))) ( -47.00)
>DroSec_CAF1 30062 120 + 1
AUUUGCGGGACACUGAUUCGCCAGUUUUACUUGCGAAGUGUGGGUGCCAGAAGAGGUCCGGCUGUUGGGGUCCUUCAGCAGCCAAACGCUCCGGCACGUGACAUUGGCAAAGUGAGUUCC
......(((((((((......)))).((((((((..(((((.((((((....(((((..((((((((((....))))))))))..)).))).))))).).))))).)).))))))))))) ( -47.00)
>DroSim_CAF1 9007 120 + 1
AUUUGCGGGACACUGAUUCGCCAGUUUUACUUGCGAAGUGUGGGUGCCAGAAGAGGUCCGGCUGUUGGGGUCCUUCAGCAGCCAAACGCUCCGGCACGUGACAUUGGCAAAGUGAGUUCC
......(((((((((......)))).((((((((..(((((.((((((....(((((..((((((((((....))))))))))..)).))).))))).).))))).)).))))))))))) ( -47.00)
>DroEre_CAF1 12548 119 + 1
AUUUGCGGGACACUGAUUCGCCAGUUGUACUUGCGAAGUGUGGGCGCCAUAAGAGGUCCGGCUGUUGGGG-CCUCCAGCAGCCAAACGCUCCGGCACGUGACUUUGGCAAAGUGAGUUCC
......(((((.(...((.(((((...(((.((((.(((((.((.(((......)))))(((((((((..-...)))))))))..))))).).))).)))...))))).))..).))))) ( -45.40)
>consensus
AUUUGCGGGACACUGAUUCGCCAGUUUUACUUGCGAAGUGUGGGUGCCAGAAGAGGUCCGGCUGUUGGGGUCCUUCAGCAGCCAAACGCUCCGGCACGUGACAUUGGCAAAGUGAGUUCC
......(((((.(...((.((((((.((((.((((.(((((.((.(((......)))))((((((((((....))))))))))..))))).).))).)))).)))))).))..).))))) (-46.31 = -46.62 +   0.31)

alignment

secondary structure

dotplot

Window 7

Location	1,311,657 – 1,311,776
Length	119
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	96.81
Mean single sequence MFE	-42.58
Consensus MFE	-41.94
Energy contribution	-41.75
Covariance contribution	-0.19
Combinations/Pair	1.03
Mean z-score	-2.18
Structure conservation index	0.99
SVM decision value	1.43
SVM RNA-class probability	0.953216
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 1311657 119 - 20766785
GGAACUCACUUUGCCAAUGUCACGUGCCGGAGCGUUUGGCUGCUGAAGGACCCCAACAGCCGGACCUCUUUUGGCACCCACACUUCGCAAGUAA-ACUGGCGAAUCAGUGUCCCGCAAAU
.........(((((.........(((((((((.(((((((((.((........)).)))))))))))))...)))))..(((((((((.((...-.)).))))...)))))...))))). ( -41.50)
>DroSec_CAF1 30062 120 - 1
GGAACUCACUUUGCCAAUGUCACGUGCCGGAGCGUUUGGCUGCUGAAGGACCCCAACAGCCGGACCUCUUCUGGCACCCACACUUCGCAAGUAAAACUGGCGAAUCAGUGUCCCGCAAAU
.........(((((.........(((((((((.(((((((((.((........)).)))))))))...)))))))))..(((((((((.((.....)).))))...)))))...))))). ( -42.20)
>DroSim_CAF1 9007 120 - 1
GGAACUCACUUUGCCAAUGUCACGUGCCGGAGCGUUUGGCUGCUGAAGGACCCCAACAGCCGGACCUCUUCUGGCACCCACACUUCGCAAGUAAAACUGGCGAAUCAGUGUCCCGCAAAU
.........(((((.........(((((((((.(((((((((.((........)).)))))))))...)))))))))..(((((((((.((.....)).))))...)))))...))))). ( -42.20)
>DroEre_CAF1 12548 119 - 1
GGAACUCACUUUGCCAAAGUCACGUGCCGGAGCGUUUGGCUGCUGGAGG-CCCCAACAGCCGGACCUCUUAUGGCGCCCACACUUCGCAAGUACAACUGGCGAAUCAGUGUCCCGCAAAU
.........(((((.........(((((((((.(((((((((.(((...-..))).)))))))))))))...)))))..(((((((((.((.....)).))))...)))))...))))). ( -44.40)
>consensus
GGAACUCACUUUGCCAAUGUCACGUGCCGGAGCGUUUGGCUGCUGAAGGACCCCAACAGCCGGACCUCUUCUGGCACCCACACUUCGCAAGUAAAACUGGCGAAUCAGUGUCCCGCAAAU
.........(((((.........(((((((((.(((((((((.((........)).)))))))))))))...)))))..(((((((((.((.....)).))))...)))))...))))). (-41.94 = -41.75 +  -0.19)

alignment

secondary structure

dotplot

Window 8

Location	1,311,696 – 1,311,816
Length	120
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	97.22
Mean single sequence MFE	-43.38
Consensus MFE	-42.29
Energy contribution	-42.60
Covariance contribution	0.31
Combinations/Pair	1.02
Mean z-score	-2.37
Structure conservation index	0.97
SVM decision value	1.51
SVM RNA-class probability	0.960433
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 1311696 120 - 20766785
CUUGGUCCCAAGAUGACCAAAUUGUGUCACAUUUGCGAACGGAACUCACUUUGCCAAUGUCACGUGCCGGAGCGUUUGGCUGCUGAAGGACCCCAACAGCCGGACCUCUUUUGGCACCCA
.((((((.......))))))...(((..(((((.(((((.(.......)))))).))))))))(((((((((.(((((((((.((........)).)))))))))))))...)))))... ( -43.60)
>DroSec_CAF1 30102 120 - 1
CUUGGUCCCAAGAUGACCAAAUUGUGUCACAUUUGCGAACGGAACUCACUUUGCCAAUGUCACGUGCCGGAGCGUUUGGCUGCUGAAGGACCCCAACAGCCGGACCUCUUCUGGCACCCA
.((((((.......))))))...(((..(((((.(((((.(.......)))))).))))))))(((((((((.(((((((((.((........)).)))))))))...)))))))))... ( -44.30)
>DroSim_CAF1 9047 120 - 1
CUUGGUCCCAAGAUGACCAAAUUGUGUCACAUUUGCGAACGGAACUCACUUUGCCAAUGUCACGUGCCGGAGCGUUUGGCUGCUGAAGGACCCCAACAGCCGGACCUCUUCUGGCACCCA
.((((((.......))))))...(((..(((((.(((((.(.......)))))).))))))))(((((((((.(((((((((.((........)).)))))))))...)))))))))... ( -44.30)
>DroEre_CAF1 12588 119 - 1
CCUGGUCCCAAGAUGACCAAAUUGUGUCACAUUUGCGAACGGAACUCACUUUGCCAAAGUCACGUGCCGGAGCGUUUGGCUGCUGGAGG-CCCCAACAGCCGGACCUCUUAUGGCGCCCA
..(((((.......)))))....(((..((.((.(((((.(.......)))))).)).)))))(((((((((.(((((((((.(((...-..))).)))))))))))))...)))))... ( -41.30)
>consensus
CUUGGUCCCAAGAUGACCAAAUUGUGUCACAUUUGCGAACGGAACUCACUUUGCCAAUGUCACGUGCCGGAGCGUUUGGCUGCUGAAGGACCCCAACAGCCGGACCUCUUCUGGCACCCA
.((((((.......))))))...(((..(((((.(((((.(.......)))))).))))))))(((((((((.(((((((((.((........)).)))))))))))))...)))))... (-42.29 = -42.60 +   0.31)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:25:02 2006