Locus 6526

Sequence ID	2R_DroMel_CAF1
Location	20,395,735 – 20,395,890
Length	155
Max. P	0.801594

overview

Window 6

Location	20,395,735 – 20,395,825
Length	90
Sequences	6
Columns	97
Reading direction	reverse
Mean pairwise identity	82.21
Mean single sequence MFE	-32.35
Consensus MFE	-23.27
Energy contribution	-22.08
Covariance contribution	-1.19
Combinations/Pair	1.50
Mean z-score	-2.14
Structure conservation index	0.72
SVM decision value	0.62
SVM RNA-class probability	0.801594
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 20395735 90 - 20766785
GGAUCCAUUGGCGGCGGUGGAGGAUACUGCUGCUGUUGGUGCUG-CU------GUAGUUGCAUGGGAUGCUGUUGGUAGAGGGGUGGCGUACAAGGA
.....(((..(((((((..(......)..)))))))..)))((.-.(------(((((..(......(((.....))).....)..)).)))).)). ( -29.80)
>DroGri_CAF1 5806 87 - 1
GGUUCCGGCACAGGUGGUGGCAGAUAUUGUUGCUGCUGCUGCUGU----------UGAUGGAUGGGAUGCUGCUGGUAGAGCGGCGGUGUGCAGGGC
...(((.(((((((..(..((((.((....))))))..)..))..----------............(((((((.....))))))).))))).))). ( -34.00)
>DroSec_CAF1 5149 90 - 1
GGAUCCAUUGGCGGCGGCGGAGGAUACUGCUGCUGUUGGUGCUG-CU------GUAGUUGCAUGGGAUGCUGUUGGUAGAGGGGUGGCGUACAAGGA
.....(((..((((((((((......))))))))))..)))((.-.(------(((((..(......(((.....))).....)..)).)))).)). ( -32.30)
>DroSim_CAF1 5086 90 - 1
GGAUCCAUUGGCGGCGGCGGAGGAUACUGCUGCUGUUGAUGCUG-CU------GUAGUUGCAUGGGAUGCUGUUGGUAGAGGGGUGGCGUACAAGGA
.....(((..((((((((((......))))))))))..)))((.-.(------(((((..(......(((.....))).....)..)).)))).)). ( -32.00)
>DroEre_CAF1 5153 84 - 1
GGAUCCAUUGGCGGCGGUGGAGGAUACUGCUGCUGCUGCU-------------GCAGUUGCAUUGGAUGCUGUUGGUAGAGGGGUGGUGUGCAAGGA
...(((((((....)))))))(.((((..((.((.(((((-------------(((((..........)))).)))))))).))..)))).)..... ( -30.30)
>DroYak_CAF1 5039 96 - 1
GGAUCCAUUGGCGGCGGUGGAGGAUACUGCUGCUGCUGCUGUUG-UUGUAGUUGCAGUUGCAUGGGAUGCUGUUGGUAGAGGGGCGGCGUACAAGGA
...(((...((((((((..(......)..))))))))((((((.-((.((.(.(((((..........))))).).)).)).))))))......))) ( -35.70)
>consensus
GGAUCCAUUGGCGGCGGUGGAGGAUACUGCUGCUGCUGCUGCUG_CU______GUAGUUGCAUGGGAUGCUGUUGGUAGAGGGGUGGCGUACAAGGA
...(((((((((((((((((......))))))))))))))........................(.((((((((........)))))))).)..))) (-23.27 = -22.08 +  -1.19)

alignment

secondary structure

dotplot

Window 7

Location	20,395,785 – 20,395,890
Length	105
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	82.79
Mean single sequence MFE	-43.93
Consensus MFE	-32.58
Energy contribution	-31.25
Covariance contribution	-1.33
Combinations/Pair	1.53
Mean z-score	-1.63
Structure conservation index	0.74
SVM decision value	0.18
SVM RNA-class probability	0.621623
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 20395785 105 - 20766785
AGCGAAUGCUUUCCCGAGAGGCAGUUCUUUUGGAGAACGACAU---------------GGUGCUGACGUAAGCAGGCGCCGGAUCCAUUGGCGGCGGUGGAGGAUACUGCUGCUGUUGGU
.....((((.(((((((((((....)))))))).))).).)))---------------((((((..(....)..))))))....(((..((((((((((.....))))))))))..))). ( -41.90)
>DroGri_CAF1 5853 120 - 1
AGCGUAUGCUCUCCCGUGAGGCGGUGCGCUUUGAGAACGACAUAUGACCAUGCGACUGGGCACUGACAUAGCUGGGCGCCGGUUCCGGCACAGGUGGUGGCAGAUAUUGUUGCUGCUGCU
.((.((.(((...((....))((((((...(((....))).......(((......)))))))))....))))).))((((....))))...((..(..((((......))))..)..)) ( -40.10)
>DroSec_CAF1 5199 105 - 1
AGCGGAUGCUUUCCCGCGAAGCAGUUCUUUUGGAGAACGACAU---------------GGUGCUGACGUAAGCAGGCGCCGGAUCCAUUGGCGGCGGCGGAGGAUACUGCUGCUGUUGGU
.((((........))))......((((((...))))))((..(---------------((((((..(....)..)))))))..)).((..((((((((((......))))))))))..)) ( -45.20)
>DroSim_CAF1 5136 105 - 1
AGCGGAUGCUUUCCCGCGAAGCAGUUCUUUUGGAGAACGACAU---------------GGUGCUGACGUAAGCAGGCGCCGGAUCCAUUGGCGGCGGCGGAGGAUACUGCUGCUGUUGAU
.((((........))))......((((((...))))))((..(---------------((((((..(....)..)))))))..)).((..((((((((((......))))))))))..)) ( -44.90)
>DroEre_CAF1 5197 105 - 1
ACCGGAUGCUUUCCCGCGAGGCAGUCCUUUUGGAAAAGGACAU---------------GGUGCUAACGUAAGCAGGCGCCGGAUCCAUUGGCGGCGGUGGAGGAUACUGCUGCUGCUGCU
...((((.(....((....))..(((((((....)))))))..---------------((((((..(....)..))))))).))))...((((((((..(((....)).)..)))))))) ( -46.40)
>DroYak_CAF1 5095 105 - 1
AGCGGAUGCUUUCCCGCGAGGCAGUCCUUUUGGAGAAUGACAU---------------GGUGCUGACGUAAGCAGGCGCCGGAUCCAUUGGCGGCGGUGGAGGAUACUGCUGCUGCUGCU
(((((((.(.((((((.((((....)))).))).)))......---------------((((((..(....)..))))))).))))...((((((((..(......)..))))))))))) ( -45.10)
>consensus
AGCGGAUGCUUUCCCGCGAGGCAGUUCUUUUGGAGAACGACAU_______________GGUGCUGACGUAAGCAGGCGCCGGAUCCAUUGGCGGCGGUGGAGGAUACUGCUGCUGCUGCU
...(((((((((.....)))))).)))...............................((((((..(....)..))))))......((((((((((((((......)))))))))))))) (-32.58 = -31.25 +  -1.33)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:12:54 2006