Locus 5269

Sequence ID	3R_DroMel_CAF1
Location	13,739,788 – 13,739,889
Length	101
Max. P	0.961794

overview

Window 8

Location	13,739,788 – 13,739,889
Length	101
Sequences	6
Columns	110
Reading direction	forward
Mean pairwise identity	71.08
Mean single sequence MFE	-30.12
Consensus MFE	-11.47
Energy contribution	-11.22
Covariance contribution	-0.25
Combinations/Pair	1.38
Mean z-score	-2.32
Structure conservation index	0.38
SVM decision value	1.53
SVM RNA-class probability	0.961794
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 13739788 101 + 27905053
GGCCA-A--GGGGGUGAAAGUGGGAGAAGGGCGAGCGACGACAGCGAAGCAUAAAAAGCAAUUUCAUGCACCCAUUGACCCCCACAAAAUGUUGGUUACAUGG------G
..((.-.--((((((...((((((......((..((.......))...)).......(((......))).)))))).)))))).....((((.....))))))------. ( -32.00)
>DroPse_CAF1 17034 98 + 1
UUUUGCACUCGAGAAGAGAAUGUCAGAAGAG---GCAAUGACAUCGAAGCAUAAAAAGCAAUUUUAUGCACACAUUGACCCUCAAA--AGGGGGGCAGCG-GC------A
...(((.(((.....))).((((((......---....))))))((..((((((((.....)))))))).....(((.(((((...--.))))).)))))-))------) ( -25.40)
>DroSec_CAF1 13069 103 + 1
GGCCA-AGAGGGGGUGAAAGGGGCAGAAGGGCGAGCAACGACAGCGAAGCAUAAAAAGCAAUUUCAUGCACCCAUUGACCCCCACAAAAUGUUGGGGACAUGC------G
.((..-...((((((.((.((((((((((.((..((..((....))..)).......))..)))).))).))).)).)))))).........((....)).))------. ( -32.90)
>DroSim_CAF1 12756 103 + 1
GGCCA-AGAGGGGGUGAAAGUGGCAGAGGGGCGAGCAACGACAGCGAAGCAUAAAAAGCAAUUUCAUGCACCCAUUGACCCCCUCAAAAUGUUGGCGACAUGC------G
.((((-(((((((((...(((((.......((..((.......))...)).......(((......)))..))))).))))))))......))))).......------. ( -33.20)
>DroAna_CAF1 11563 92 + 1
UGC---AG--AGGGAAAAGGGCACAAAGAGGCGAGCAUUGACAUCGAAGCAUAA-AAGCAAUUUUAUGCACCCAUUGACCCUCACAAAAACG------AAUGG------A
...---.(--((((..(((((..........(((.........)))..((((((-((....)))))))).))).))..))))).........------.....------. ( -24.30)
>DroPer_CAF1 16131 104 + 1
UGCUGCACUCGAGAAGAGAAUGUCAGAAGAG---GCAAUGACAUCGAAGCAUAAAAAGCAAUUUUAUGCACACAUUGACCCUCAAA--AGGGGGGCAGCG-GCAGCGGCA
.(((((.(((.....))).((((((......---....))))))((..((((((((.....)))))))).....(((.(((((...--.))))).)))))-))))).... ( -32.90)
>consensus
GGCCA_AG_GGGGGAGAAAGUGGCAGAAGGGCGAGCAACGACAGCGAAGCAUAAAAAGCAAUUUCAUGCACCCAUUGACCCCCACAAAAUGGUGGCAACAUGC______A
..........((((....(((((...........((..((....))..)).......(((......)))..)))))...))))........................... (-11.47 = -11.22 +  -0.25)

alignment

secondary structure

dotplot

Window 9

Location	13,739,788 – 13,739,889
Length	101
Sequences	6
Columns	110
Reading direction	reverse
Mean pairwise identity	71.08
Mean single sequence MFE	-27.13
Consensus MFE	-13.07
Energy contribution	-12.93
Covariance contribution	-0.14
Combinations/Pair	1.32
Mean z-score	-1.74
Structure conservation index	0.48
SVM decision value	0.55
SVM RNA-class probability	0.776727
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 13739788 101 - 27905053
C------CCAUGUAACCAACAUUUUGUGGGGGUCAAUGGGUGCAUGAAAUUGCUUUUUAUGCUUCGCUGUCGUCGCUCGCCCUUCUCCCACUUUCACCCCC--U-UGGCC
.------((((((.....)))....(((((((.....((((((((((((.....))))))))...((.......))..))))..)))))))..........--.-))).. ( -27.60)
>DroPse_CAF1 17034 98 - 1
U------GC-CGCUGCCCCCCU--UUUGAGGGUCAAUGUGUGCAUAAAAUUGCUUUUUAUGCUUCGAUGUCAUUGC---CUCUUCUGACAUUCUCUUCUCGAGUGCAAAA
(------((-(((.....((((--....)))).....))).((((((((.....))))))))...(((((((....---......)))))))(((.....))).)))... ( -21.00)
>DroSec_CAF1 13069 103 - 1
C------GCAUGUCCCCAACAUUUUGUGGGGGUCAAUGGGUGCAUGAAAUUGCUUUUUAUGCUUCGCUGUCGUUGCUCGCCCUUCUGCCCCUUUCACCCCCUCU-UGGCC
.------((((((.....))))...(.((((((.((.((((((((((((.....))))))))...((.......))..........))))..)).)))))).).-..)). ( -28.80)
>DroSim_CAF1 12756 103 - 1
C------GCAUGUCGCCAACAUUUUGAGGGGGUCAAUGGGUGCAUGAAAUUGCUUUUUAUGCUUCGCUGUCGUUGCUCGCCCCUCUGCCACUUUCACCCCCUCU-UGGCC
.------.......(((((......((((((((.((..(((((((((((.....))))))))...((.......))..........)))...)).)))))))))-)))). ( -33.80)
>DroAna_CAF1 11563 92 - 1
U------CCAUU------CGUUUUUGUGAGGGUCAAUGGGUGCAUAAAAUUGCUU-UUAUGCUUCGAUGUCAAUGCUCGCCUCUUUGUGCCCUUUUCCCU--CU---GCA
.------.....------......((((((((.....((((((((((((....))-))))))..(((.((....))))).........))))....))))--).---))) ( -23.40)
>DroPer_CAF1 16131 104 - 1
UGCCGCUGC-CGCUGCCCCCCU--UUUGAGGGUCAAUGUGUGCAUAAAAUUGCUUUUUAUGCUUCGAUGUCAUUGC---CUCUUCUGACAUUCUCUUCUCGAGUGCAGCA
....(((((-(((.....((((--....)))).....))).((((((((.....))))))))...(((((((....---......)))))))(((.....))).))))). ( -28.20)
>consensus
C______GCAUGUCGCCAACAUUUUGUGAGGGUCAAUGGGUGCAUAAAAUUGCUUUUUAUGCUUCGAUGUCAUUGCUCGCCCUUCUGCCACUUUCACCCCC_CU_UGGCA
...........................(((((((((((...((((((((.....))))))))........)))))...)))))).......................... (-13.07 = -12.93 +  -0.14)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:50:42 2006