Locus 6027

Sequence ID	2R_DroMel_CAF1
Location	18,950,677 – 18,950,791
Length	114
Max. P	0.539095

overview

Window 2

Location	18,950,677 – 18,950,767
Length	90
Sequences	6
Columns	108
Reading direction	reverse
Mean pairwise identity	76.81
Mean single sequence MFE	-21.92
Consensus MFE	-11.91
Energy contribution	-12.05
Covariance contribution	0.14
Combinations/Pair	1.12
Mean z-score	-1.62
Structure conservation index	0.54
SVM decision value	0.01
SVM RNA-class probability	0.539095
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 18950677 90 - 20766785
AAAUGCGCAACGCUGCAGACGCAAUUAAUGCGCACCGUUUUACAAUUAGCGA-CCUGGCCCAAUUAUGCAGCU----GCCACCC-CCUGCA------C----C--CCU
...((.(((..(((((((.((((.....)))))..((((........)))).-.............)))))))----))))...-......------.----.--... ( -19.40)
>DroPse_CAF1 52560 93 - 1
AAAUGCGCAACGCUGCAGACGCAAUUAAUGCGCAACGUUUUACAAUUAGUGAAACUACCUCAAUUAUGCAGCU----GCAGUCC-CAGCCA------C----CAACCU
......(((..(((((((.((((.....)))))...(((((((.....)))))))...........)))))))----)).....-......------.----...... ( -23.30)
>DroYak_CAF1 51580 83 - 1
AAAUGCGCAACGCUGCAGACGCAAUUAAUGCGCACCGUUUUACAAUUAGCGA-CCUGGCCCAAUUAUGCAGCU----GCA--CC-CCUGCC-----------------
......(((..(((((((.((((.....)))))..((((........)))).-.............)))))))----)).--..-......----------------- ( -19.50)
>DroMoj_CAF1 72067 100 - 1
AAACGAGCUUCGUUACAGGCGCAAUUAAUGAGCUGCGUUCCACAAUUAGGGA-ACUGCCUCAAUUAUGCAGCCAACAACAGUCGCCGGCCACC----CCAGCC---CU
.((((.....))))...(((((......((.(((((((........(((...-.)))........)))))))))......).))))(((....----...)))---.. ( -25.69)
>DroAna_CAF1 58014 92 - 1
AAAUGCUAAACGCUGCAGACGCAAUUAAUGCGCACCGUUUUACAAUUAGCGA-ACUGGCCCAAUUAUGCAGCU----GCC--UU-CCUGCA--AAGCC----C--CCU
....(((....(((((((.((((.....)))))..((((........)))).-.............))))))(----((.--..-...)))--.))).----.--... ( -20.30)
>DroPer_CAF1 53572 93 - 1
AAAUGCGCAACGCUGCAGACGCAAUUAAUGCGCAACGUUUUACAAUUAGUGAAACUACCUCAAUUAUGCAGCU----GCAGUCC-CAGCCA------C----CAACCU
......(((..(((((((.((((.....)))))...(((((((.....)))))))...........)))))))----)).....-......------.----...... ( -23.30)
>consensus
AAAUGCGCAACGCUGCAGACGCAAUUAAUGCGCACCGUUUUACAAUUAGCGA_ACUGCCCCAAUUAUGCAGCU____GCAGUCC_CCGCCA______C____C__CCU
....((.....(((((((.((((.....))))).............(((.....))).........)))))).....))............................. (-11.91 = -12.05 +   0.14)

alignment

secondary structure

dotplot

Window 3

Location	18,950,695 – 18,950,791
Length	96
Sequences	6
Columns	107
Reading direction	forward
Mean pairwise identity	80.51
Mean single sequence MFE	-29.50
Consensus MFE	-22.00
Energy contribution	-21.50
Covariance contribution	-0.50
Combinations/Pair	1.23
Mean z-score	-1.08
Structure conservation index	0.75
SVM decision value	-0.04
SVM RNA-class probability	0.515265
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 18950695 96 + 20766785
AGCUGCAUAAUUGGGCCAGG-UCGCUAAUUGUAAAACGGUGCGCAUUAAUUGCGUCUGCAGCGUUGCGCAUUUUGCGGCAACCUUUUCGCCUC--GCC--------C
............((((.(((-(.(((.((((.....))))(((((.....)))))....)))(((((((.....)).)))))......)))).--)))--------) ( -29.20)
>DroPse_CAF1 52580 101 + 1
AGCUGCAUAAUUGAGGUAGUUUCACUAAUUGUAAAACGUUGCGCAUUAAUUGCGUCUGCAGCGUUGCGCAUUUUGUGGCUUGCC----ACUCGAGAG--UCGCCUCC
............((((((.((((......(((..(((((((((((.....)))....))))))))..)))....((((....))----))..)))).--).))))). ( -30.70)
>DroSec_CAF1 49256 102 + 1
AGCUGCAUAAUUGGGCCAGG-UCGCUAAUUGUAAAACGGUGCGCAUUAAUUGCGUCUGCAGCGUUGCGCAUUUUGUGGUAACCUUUCCGCCCC--CC--UCCCCUUC
............((((.(((-(..(((..(((..((((.((((((.....)))....))).))))..))).....)))..))))....)))).--..--........ ( -28.00)
>DroSim_CAF1 52577 104 + 1
AGCUGCAUAAUUGGGCCAGG-UCGCUAAUUGUAAAACGGUGCGCAUUAAUUGCGUCUGCAGCGUUGCGCAUUUUGCGGUAACCUUUCCGCCCC--CCCCACCCUUUC
............((((.(((-(..((....(((((...(((((((....((((....))))...))))))))))))))..))))....)))).--............ ( -28.00)
>DroYak_CAF1 51591 104 + 1
AGCUGCAUAAUUGGGCCAGG-UCGCUAAUUGUAAAACGGUGCGCAUUAAUUGCGUCUGCAGCGUUGCGCAUUUUGCGGUUACCCUUCCGACCU--UCCCACCGCACC
...(((.....((((..(((-(((.((((((((((...(((((((....((((....))))...)))))))))))))))))......))))))--.))))..))).. ( -33.50)
>DroAna_CAF1 58034 87 + 1
AGCUGCAUAAUUGGGCCAGU-UCGCUAAUUGUAAAACGGUGCGCAUUAAUUGCGUCUGCAGCGUUUAGCAUUUUGUGGUUUGCU----GGUC---------------
.............(((((((-..((((..(((.(((((.((((((.....)))....))).))))).))).....))))..)))----))))--------------- ( -27.60)
>consensus
AGCUGCAUAAUUGGGCCAGG_UCGCUAAUUGUAAAACGGUGCGCAUUAAUUGCGUCUGCAGCGUUGCGCAUUUUGCGGUAACCUUUCCGCCCC__CC___CCCCU_C
............((((.(((.((((.((.(((..((((.((((((.....)))....))).))))..))).)).))))...)))....))))............... (-22.00 = -21.50 +  -0.50)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:00:44 2006