Locus 8436

Sequence ID	3L_DroMel_CAF1
Location	22,155,171 – 22,155,267
Length	96
Max. P	0.958639

overview

Window 5

Location	22,155,171 – 22,155,267
Length	96
Sequences	5
Columns	96
Reading direction	forward
Mean pairwise identity	94.27
Mean single sequence MFE	-25.12
Consensus MFE	-22.78
Energy contribution	-22.58
Covariance contribution	-0.20
Combinations/Pair	1.16
Mean z-score	-1.14
Structure conservation index	0.91
SVM decision value	0.10
SVM RNA-class probability	0.581220
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 22155171 96 + 23771897
CCGGCUGGCCAGCUCUGCCCACAGGCAAACAUCCUUGCUUCCUUCCUGUCCUGUUGUUACCGGCUGCCCAACUCGCAAGCGCGAGCUUCUGCUUUU
.(((((((.((((.(((....)))((((......))))..............))))...)))))))........((((((....)))..))).... ( -25.10)
>DroSec_CAF1 14689 96 + 1
CCGGCUGGCCAGCUCUGCCCACAGGCAAACAUCCUUGCUUCCUUCCUGCCCUGUUGUUACCGGCUGCCCAACUCGCAAGCGCGAGCUUCUGCUUUU
..((((((.(((((.((((....))))((((.....((.........)).....))))...))))).))).(((((....))))).....)))... ( -26.30)
>DroSim_CAF1 14568 96 + 1
CCGGCUGGCCAGCUCUGCCCACAGGCAAACAUCCUUGCUUCCUUCCUGCCCUGUUGUUACCGGCUGCCCAACUCGCAAGCGCGAGCUUCUGCUUUU
..((((((.(((((.((((....))))((((.....((.........)).....))))...))))).))).(((((....))))).....)))... ( -26.30)
>DroEre_CAF1 14371 95 + 1
CCAACUGGCC-GCUCUGCCCACAGGCAAACAUCCUUGCUUCCUUCCUGCCCUGUUGUUACCGGUUGCCCAACUCGCAAGCGCGAGCUCCUGCCUUU
.(((((((..-((.(((....))))).((((.....((.........)).....)))).)))))))........((((((....)))..))).... ( -23.20)
>DroYak_CAF1 16106 93 + 1
CAAGCUGGCCAGCUCUGCCCACAGGCAAACAUCCUUGCUUCCUUCCUGC--UGUUUUUACCGGUUGCCCAACUCGCAAGCGCUAGCUUCUGC-UUU
.((((((((((((.(((....)))((((......)))).........))--))........(.((((.......)))).)))))))))....-... ( -24.70)
>consensus
CCGGCUGGCCAGCUCUGCCCACAGGCAAACAUCCUUGCUUCCUUCCUGCCCUGUUGUUACCGGCUGCCCAACUCGCAAGCGCGAGCUUCUGCUUUU
.(((((((.((((...((....((((((......)))))).......))...))))...)))))))........((((((....)))..))).... (-22.78 = -22.58 +  -0.20)

alignment

secondary structure

dotplot

Window 6

Location	22,155,171 – 22,155,267
Length	96
Sequences	5
Columns	96
Reading direction	reverse
Mean pairwise identity	94.27
Mean single sequence MFE	-33.36
Consensus MFE	-29.42
Energy contribution	-29.46
Covariance contribution	0.04
Combinations/Pair	1.11
Mean z-score	-1.64
Structure conservation index	0.88
SVM decision value	1.49
SVM RNA-class probability	0.958639
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 22155171 96 - 23771897
AAAAGCAGAAGCUCGCGCUUGCGAGUUGGGCAGCCGGUAACAACAGGACAGGAAGGAAGCAAGGAUGUUUGCCUGUGGGCAGAGCUGGCCAGCCGG
....((...(((((((....)))))))..))..(((((.........(((((....(((((....))))).)))))((.((....)).)).))))) ( -34.00)
>DroSec_CAF1 14689 96 - 1
AAAAGCAGAAGCUCGCGCUUGCGAGUUGGGCAGCCGGUAACAACAGGGCAGGAAGGAAGCAAGGAUGUUUGCCUGUGGGCAGAGCUGGCCAGCCGG
....((...(((((((....)))))))..))..(((((.........(((((....(((((....))))).)))))((.((....)).)).))))) ( -34.30)
>DroSim_CAF1 14568 96 - 1
AAAAGCAGAAGCUCGCGCUUGCGAGUUGGGCAGCCGGUAACAACAGGGCAGGAAGGAAGCAAGGAUGUUUGCCUGUGGGCAGAGCUGGCCAGCCGG
....((...(((((((....)))))))..))..(((((.........(((((....(((((....))))).)))))((.((....)).)).))))) ( -34.30)
>DroEre_CAF1 14371 95 - 1
AAAGGCAGGAGCUCGCGCUUGCGAGUUGGGCAACCGGUAACAACAGGGCAGGAAGGAAGCAAGGAUGUUUGCCUGUGGGCAGAGC-GGCCAGUUGG
...(((....((((..(((..((....((....))(((((((.(...((.........))...).)).)))))))..))).))))-.)))...... ( -33.00)
>DroYak_CAF1 16106 93 - 1
AAA-GCAGAAGCUAGCGCUUGCGAGUUGGGCAACCGGUAAAAACA--GCAGGAAGGAAGCAAGGAUGUUUGCCUGUGGGCAGAGCUGGCCAGCUUG
.((-((....((((((.(((((....(((....)))((....)).--...........)))))....((((((....))))))))))))..)))). ( -31.20)
>consensus
AAAAGCAGAAGCUCGCGCUUGCGAGUUGGGCAGCCGGUAACAACAGGGCAGGAAGGAAGCAAGGAUGUUUGCCUGUGGGCAGAGCUGGCCAGCCGG
....((...(((((((....)))))))..))..(((((.........(((((....(((((....))))).)))))((.((....)).)).))))) (-29.42 = -29.46 +   0.04)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:15:19 2006