Locus 6399

Sequence ID	3L_DroMel_CAF1
Location	17,145,747 – 17,145,847
Length	100
Max. P	0.976065

overview

Window 3

Location	17,145,747 – 17,145,847
Length	100
Sequences	5
Columns	103
Reading direction	forward
Mean pairwise identity	85.39
Mean single sequence MFE	-33.56
Consensus MFE	-24.84
Energy contribution	-26.52
Covariance contribution	1.68
Combinations/Pair	1.11
Mean z-score	-2.71
Structure conservation index	0.74
SVM decision value	1.76
SVM RNA-class probability	0.976065
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 17145747 100 + 23771897
GUGGCCAAGACGAUCCGGCCAUAAAUGCGGUGCGAGAAAUCGCACCAGGGAGCACCAGUUGCCCC---ACCACCACCUCCACCAGAGCACAACUACCCCAGCC
((((((..........))))))...((((((((((....))))))).(((.(((.....))))))---..................))).............. ( -35.20)
>DroSec_CAF1 30177 91 + 1
GUGGCCAAGACGAUCCGGCUAUAAAUGUGGUGCGAGAAAUCGCACCAGGGAGCACCAGUUGUCCC---ACCA---------CCAGUGCACCACUACCCCAGCC
((((....((((((..((((.....(.((((((((....)))))))).).))).)..))))))..---.)))---------).((((...))))......... ( -31.40)
>DroSim_CAF1 21942 91 + 1
GUGGCCAAGACGAUACGGCCAUAAAUGUGGUGCGAGAAAUCGCACCAGGGAGCACCAGUUGUCCC---ACCA---------CUAGUGCACCACUACCCCAGCC
((((((..........)))))).....((((((((....)))))))).((.((((.(((.(....---.).)---------)).)))).))............ ( -35.30)
>DroEre_CAF1 30747 92 + 1
GUGGCCAAGACGCUCCGGCCAUAAAUGUGGUGCGAGAAAUCGCACCAGGGA--ACCAGUAGCGGCAACACCA---------CCAUCGCACCACUACCCCGGCC
(..((......))..)((((.......((((((((....))))))))(((.--....((((.((........---------........)).))))))))))) ( -33.69)
>DroYak_CAF1 32543 92 + 1
GUGGCCAAGACGCUCCGGCCAUAAAUGUGGUGCGAGAAAUCGCACCAGGGA--ACCAGUAGCGCCAACACCA---------CCACCGCACCACUGCUCCAGCC
((((((..........)))))).....((((((((....)))))))).(((--..((((.(.((........---------.....)).).)))).))).... ( -32.22)
>consensus
GUGGCCAAGACGAUCCGGCCAUAAAUGUGGUGCGAGAAAUCGCACCAGGGAGCACCAGUUGCCCC___ACCA_________CCAGCGCACCACUACCCCAGCC
((((((..........))))))...((((((((((....))))))).((.....))..............................))).............. (-24.84 = -26.52 +   1.68)

alignment

secondary structure

dotplot

Window 4

Location	17,145,747 – 17,145,847
Length	100
Sequences	5
Columns	103
Reading direction	reverse
Mean pairwise identity	85.39
Mean single sequence MFE	-41.20
Consensus MFE	-28.23
Energy contribution	-30.35
Covariance contribution	2.12
Combinations/Pair	1.10
Mean z-score	-2.21
Structure conservation index	0.69
SVM decision value	0.65
SVM RNA-class probability	0.812361
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 17145747 100 - 23771897
GGCUGGGGUAGUUGUGCUCUGGUGGAGGUGGUGGU---GGGGCAACUGGUGCUCCCUGGUGCGAUUUCUCGCACCGCAUUUAUGGCCGGAUCGUCUUGGCCAC
(((..(((......((.((((((.((((((..((.---((((((.....))))))))(((((((....))))))).))))).).)))))).)))))..))).. ( -42.80)
>DroSec_CAF1 30177 91 - 1
GGCUGGGGUAGUGGUGCACUGG---------UGGU---GGGACAACUGGUGCUCCCUGGUGCGAUUUCUCGCACCACAUUUAUAGCCGGAUCGUCUUGGCCAC
(((..(((..((((.((((..(---------((..---....).))..)))).)).((((((((....)))))))).............))..)))..))).. ( -39.50)
>DroSim_CAF1 21942 91 - 1
GGCUGGGGUAGUGGUGCACUAG---------UGGU---GGGACAACUGGUGCUCCCUGGUGCGAUUUCUCGCACCACAUUUAUGGCCGUAUCGUCUUGGCCAC
(((..(((..((((.(((((((---------((..---....).)))))))).)).((((((((....)))))))).............))..)))..))).. ( -40.30)
>DroEre_CAF1 30747 92 - 1
GGCCGGGGUAGUGGUGCGAUGG---------UGGUGUUGCCGCUACUGGU--UCCCUGGUGCGAUUUCUCGCACCACAUUUAUGGCCGGAGCGUCUUGGCCAC
((((((((((((((((((((..---------....)))).))))))))((--(((.((((((((....))))))))((....))...))))).)))))))).. ( -43.00)
>DroYak_CAF1 32543 92 - 1
GGCUGGAGCAGUGGUGCGGUGG---------UGGUGUUGGCGCUACUGGU--UCCCUGGUGCGAUUUCUCGCACCACAUUUAUGGCCGGAGCGUCUUGGCCAC
....(((((((((((((.(...---------......).)))))))).))--))).((((((((....))))))))......(((((((......))))))). ( -40.40)
>consensus
GGCUGGGGUAGUGGUGCACUGG_________UGGU___GGGGCAACUGGUGCUCCCUGGUGCGAUUUCUCGCACCACAUUUAUGGCCGGAUCGUCUUGGCCAC
....((((((.(((((((((..................))))).)))).)))))).((((((((....))))))))......(((((((......))))))). (-28.23 = -30.35 +   2.12)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:17:32 2006