Locus 1167

Sequence ID	3R_DroMel_CAF1
Location	3,545,739 – 3,545,875
Length	136
Max. P	0.778777

overview

Window 4

Location	3,545,739 – 3,545,844
Length	105
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	85.61
Mean single sequence MFE	-25.52
Consensus MFE	-17.21
Energy contribution	-17.10
Covariance contribution	-0.11
Combinations/Pair	1.10
Mean z-score	-3.11
Structure conservation index	0.67
SVM decision value	0.10
SVM RNA-class probability	0.581136
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 3545739 105 + 27905053
AAGUGCUGUUAUUCUACAGUUUUACACCACAAUUACCAGUUCC-------------CUCACACUG--GCAACGUGUCAAAAUCGACACCGGCACAAGCUGCGUACCCGCGAACACCCCUU
..((((((...........................(((((...-------------.....))))--)....(((((......)))))))))))....((((....)))).......... ( -23.60)
>DroSec_CAF1 4638 99 + 1
AAGUGCUGUUAUUCUACAGUUUUACACCACAAUUACCAGUUCC-------------CCCACACUGGGGCAACGUGUCAAAAUCGACACCGGCACAAGCUGC---UCCGCGAACAC-----
..((((((..............................(((.(-------------(((.....)))).)))(((((......)))))))))))..((...---...))......----- ( -26.80)
>DroSim_CAF1 4901 104 + 1
AAGUGCUGUUAUUCUACAGUUUUACACCACAAUUACCAGUUCC-------------CCCACACUGGGGCAACGUGUCAAAAUCGACACCGGCACAAGCUGC---CCCGCGAACACCCCUU
..((((((..............................(((.(-------------(((.....)))).)))(((((......)))))))))))..((...---...))........... ( -26.80)
>DroEre_CAF1 4911 102 + 1
AAGUGCUGUUAUUCUACAGUUUUACACCACAAUUACCAGUUCC-------------CACACACUG--GCAACGUGUCAAAAUCGACACCGGCACAAGCUGC---CCCACGAACACCACCA
..(((.((((......((((((....((.......(((((...-------------.....))))--)....(((((......))))).))...)))))).---......)))).))).. ( -23.22)
>DroYak_CAF1 5400 102 + 1
AAGUGCUGUUAUUCUACAGUUUUACACCACAAUUACCAGUUCC-------------CACACACAG--GCAACGUGUCAAAAUCGACACCGGCACAAGCUGC---CCCGGGAACUCCCCCA
..(((((((......)))))...))............((((((-------------(.......(--....)(((((......))))).((((.....)))---)..)))))))...... ( -27.10)
>DroAna_CAF1 1564 118 + 1
AAGUGCUGUUAUUUUACAGUUUUACACCGCAAUUACCAGUUCCACCCACGCACACACACACACUG--GUAUCGUGUCAAAAUCGACACCAGCACAUGCUGUACUCCCCCGGCCACCCCUC
..((((((.........................(((((((.....................))))--)))..(((((......)))))))))))..((((........))))........ ( -25.60)
>consensus
AAGUGCUGUUAUUCUACAGUUUUACACCACAAUUACCAGUUCC_____________CACACACUG__GCAACGUGUCAAAAUCGACACCGGCACAAGCUGC___CCCGCGAACACCCCUA
..(((((((......)))))...)).............((((..............................(((((......)))))((((....)))).........))))....... (-17.21 = -17.10 +  -0.11)

alignment

secondary structure

dotplot

Window 5

Location	3,545,779 – 3,545,875
Length	96
Sequences	3
Columns	98
Reading direction	forward
Mean pairwise identity	82.13
Mean single sequence MFE	-22.20
Consensus MFE	-17.89
Energy contribution	-18.67
Covariance contribution	0.78
Combinations/Pair	1.06
Mean z-score	-1.75
Structure conservation index	0.81
SVM decision value	0.55
SVM RNA-class probability	0.778777
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 3545779 96 + 27905053
UCCCUCACACUG--GCAACGUGUCAAAAUCGACACCGGCACAAGCUGCGUACCCGCGAACACCCCUUAUCAGUCGCCCACCCCGCUGAAACAUCCCUU
...........(--((.(((((((......))))).(((....)))(((....)))...............)).)))..................... ( -16.40)
>DroSec_CAF1 4678 81 + 1
UCCCCCACACUGGGGCAACGUGUCAAAAUCGACACCGGCACAAGCUGC---UCCGCGAACAC--------------CCGCCCCACUGAAGCAUCUCUU
.......((.((((((...(((((......)))))((((....)))).---...........--------------..)))))).))........... ( -24.40)
>DroSim_CAF1 4941 95 + 1
UCCCCCACACUGGGGCAACGUGUCAAAAUCGACACCGGCACAAGCUGC---CCCGCGAACACCCCUUACCAGCCGCCCGCCCCGCUGAAGCAUCCCUU
.......((.((((((...(((((......))))).(((....((((.---..................)))).))).)))))).))........... ( -25.81)
>consensus
UCCCCCACACUGGGGCAACGUGUCAAAAUCGACACCGGCACAAGCUGC___CCCGCGAACACCCCUUA_CAG_CGCCCGCCCCGCUGAAGCAUCCCUU
.......((.((((((...(((((......)))))((((....))))...............................)))))).))........... (-17.89 = -18.67 +   0.78)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:02:41 2006