Locus 1321

Sequence ID	2R_DroMel_CAF1
Location	5,123,533 – 5,123,663
Length	130
Max. P	0.549302

overview

Window 0

Location	5,123,533 – 5,123,624
Length	91
Sequences	6
Columns	94
Reading direction	forward
Mean pairwise identity	81.28
Mean single sequence MFE	-27.40
Consensus MFE	-20.50
Energy contribution	-20.33
Covariance contribution	-0.16
Combinations/Pair	1.12
Mean z-score	-1.17
Structure conservation index	0.75
SVM decision value	-0.03
SVM RNA-class probability	0.519026
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 5123533 91 + 20766785
AAAUCUAAGGAAAGGCCGCUCG-GUGUCGUCUUUGGGGGCAUUGAAGCGCCAGACUGUCACACAGCUGCGCUCUGCAGUUAAAAAUGC-AUUA-
...((((((((.(.(((....)-)).)..))))))))........(((((.((.(((.....)))))))))).((((........)))-)...- ( -25.70)
>DroPse_CAF1 28517 79 + 1
UAAUUCUAUAAAAGGCCGCUCGGGUGUCGUCUUUGGGGGCAAUCAAGCGCCAGACUGUCACACAGUUGCGCUCUGCUCA---------------
..........((((((.((......)).))))))..(((((....(((((..(((((.....)))))))))).))))).--------------- ( -24.50)
>DroSec_CAF1 32745 92 + 1
AAACCUAAGGAAAGGCCGCUCG-GUGUCGUCUUUGGGGGCAUUGAAGCGCCAGACUGUCACACAGUGGCGCUCUGCAGU-AUAGAUGCUAUUAA
...((((((((.(.(((....)-)).)..))))))))((((((..((((((..((((.....)))))))))).......-...))))))..... ( -32.30)
>DroSim_CAF1 52593 92 + 1
AAACCUAAGGAAAGGCCGCUCG-GUGUCGUCUUUGGGGGCAUUGAAGCGCCAGACUGUCACACAGUGGCGCUCUGCAGU-AUAGAUGCUAUUAA
...((((((((.(.(((....)-)).)..))))))))((((((..((((((..((((.....)))))))))).......-...))))))..... ( -32.30)
>DroYak_CAF1 30154 91 + 1
AAAUCUAAGGAAAGGCCGCUCG-GUGUCGUCUUUUGGGGCAUGGAAGCGCCAGACUGUCACACAGUUGCGCUCUGCAUU-AUAGAUCCUAUUA-
..(((((.((.....))((((.-(((((.((....))))))).))(((((..(((((.....))))))))))..))...-.))))).......- ( -25.10)
>DroPer_CAF1 27949 79 + 1
UAAUUCUAUAAAAGGCCGCUCGGGUGUCGUCUUUGGGGGCAAUCAAGCGCCAGACUGUCACACAGUUGCGCUCUGCUCA---------------
..........((((((.((......)).))))))..(((((....(((((..(((((.....)))))))))).))))).--------------- ( -24.50)
>consensus
AAAUCUAAGGAAAGGCCGCUCG_GUGUCGUCUUUGGGGGCAUUGAAGCGCCAGACUGUCACACAGUUGCGCUCUGCAGU_AUAGAUGC_AUUA_
...(((....((((((.((......)).)))))).)))(((....(((((..(((((.....)))))))))).))).................. (-20.50 = -20.33 +  -0.16)

alignment

secondary structure

dotplot

Window 1

Location	5,123,563 – 5,123,663
Length	100
Sequences	4
Columns	103
Reading direction	forward
Mean pairwise identity	90.05
Mean single sequence MFE	-26.62
Consensus MFE	-21.81
Energy contribution	-23.12
Covariance contribution	1.31
Combinations/Pair	1.04
Mean z-score	-1.42
Structure conservation index	0.82
SVM decision value	0.03
SVM RNA-class probability	0.549302
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 5123563 100 + 20766785
UUUGGGGGCAUUGAAGCGCCAGACUGUCACACAGCUGCGCUCUGCAGUUAAAAAUGC-AUUA--AAUCUGCUCAGGCCGCUACAAUUUACAACUCAAUCUUAA
..(((.(((.((((.(((((((.(((.....)))))).))..((((........)))-)...--.....))))))))).)))..................... ( -25.90)
>DroSec_CAF1 32775 102 + 1
UUUGGGGGCAUUGAAGCGCCAGACUGUCACACAGUGGCGCUCUGCAGU-AUAGAUGCUAUUAAAAAUCUGCUCAGGCCGCUACAAUUUACAACUAAAUCGUAA
..(((.(((.....((((((..((((.....))))))))))(((.(((-..((((..........))))))))))))).)))..................... ( -28.20)
>DroSim_CAF1 52623 102 + 1
UUUGGGGGCAUUGAAGCGCCAGACUGUCACACAGUGGCGCUCUGCAGU-AUAGAUGCUAUUAAAAAUCUGCUCAGGCCGCUACAAUUUACAACUAAAUCGUAA
..(((.(((.....((((((..((((.....))))))))))(((.(((-..((((..........))))))))))))).)))..................... ( -28.20)
>DroYak_CAF1 30184 100 + 1
UUUUGGGGCAUGGAAGCGCCAGACUGUCACACAGUUGCGCUCUGCAUU-AUAGAUCCUAUUA--AAUCUGCUCAAGCCGCUAGAAUUUACAGCAAAAUCUUGA
((((((((((((.((((((..(((((.....)))))))))).).))).-.(((((.......--.))))).....))).)))))).................. ( -24.20)
>consensus
UUUGGGGGCAUUGAAGCGCCAGACUGUCACACAGUGGCGCUCUGCAGU_AUAGAUGCUAUUA__AAUCUGCUCAGGCCGCUACAAUUUACAACUAAAUCGUAA
..(((.(((.((((((((((..((((.....))))))))))..((((....................))))))))))).)))..................... (-21.81 = -23.12 +   1.31)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:02:09 2006