Locus 1222

Sequence ID	X_DroMel_CAF1
Location	3,645,177 – 3,645,337
Length	160
Max. P	0.654470

overview

Window 5

Location	3,645,177 – 3,645,297
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	88.83
Mean single sequence MFE	-42.76
Consensus MFE	-32.24
Energy contribution	-32.48
Covariance contribution	0.24
Combinations/Pair	1.21
Mean z-score	-1.69
Structure conservation index	0.75
SVM decision value	0.25
SVM RNA-class probability	0.654470
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 3645177 120 + 22224390
CGGCCUCCGCUUACGGCCAGCAGAAGUUCGACGAGGCCAUCGCCUUGUACACCAAGGCCAUUGAACUGAGCCCGGGUAAUGCCCUUUUCCACGCUAAGCGUGGUCAGGCCUUCCUCAAGC
.(((((..(((((.((((.(..(.....)..)..))))...((((((.....))))))........)))))..(((.....)))....((((((...))))))..))))).......... ( -42.20)
>DroSec_CAF1 15150 120 + 1
CGGCCUCCGCCUACGGCGAGCAGAAGUUCGACGAGGCCAUCGCCUUGUACACCAAGGCCAUUGAACUGAGCCCGGGUAAUGCCCUUUUCCACGCUAAGCGUGGUCAGGCAUUCCUCAAGC
(((.(((.((((.((.(((((....))))).))))))((..((((((.....))))))...))....))).)))((.((((((.....((((((...))))))...))))))))...... ( -49.00)
>DroSim_CAF1 7142 120 + 1
CGGCCUCCGCCUACGGCCAGCAGAAGUUCGACGAGGCCAUCGCCUUGUACACCAAGGCCAUUGAACUGAGCCCGGGUAAUGCCCUUUUCCACGCUAAGCGUGGUCAGGCCUUCCUCAAGC
.(((....)))...((((.(((........(((((((....)))))))..(((..(((((......)).)))..)))..)))......((((((...))))))...)))).......... ( -41.80)
>DroEre_CAF1 16076 120 + 1
CGGCCUCUGCCUACGGCCAGCAGAAGUUCGACGAGGCAAUCGCCUUCUACACCAAGGCCAUCGAACUAAACCCGGGCAAUGCCCUGUUCCACGCCAAGCGUGGCCAGGCCUUUCUCAAGC
.((((((((((....)...)))))(((((((.((.....))(((((.......)))))..)))))))......((((...))))....((((((...))))))...)))).......... ( -40.90)
>DroWil_CAF1 8875 120 + 1
CAGCUGCCGCCUACAGUGAGCAGAAAUUCGAUGAGGCCAUCGAAUUCUAUACCAAGGCCAUUGAGCUCAAUCCGGGCAAUGCUCUGUUCUACGCCAAGCGUGGUCAGGCUUUCCUUAAGC
..(((...((((....(((((((((.(((((((....)))))))))))....(((.....))).)))))....))))...((.(((..((((((...)))))).)))))........))) ( -39.90)
>consensus
CGGCCUCCGCCUACGGCCAGCAGAAGUUCGACGAGGCCAUCGCCUUGUACACCAAGGCCAUUGAACUGAGCCCGGGUAAUGCCCUUUUCCACGCUAAGCGUGGUCAGGCCUUCCUCAAGC
.((((.........)))).((.........(((((((....))))))).....((((((..............((((...))))....((((((...))))))...))))))......)) (-32.24 = -32.48 +   0.24)

alignment

secondary structure

dotplot

Window 6

Location	3,645,217 – 3,645,337
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	89.33
Mean single sequence MFE	-45.54
Consensus MFE	-36.64
Energy contribution	-37.56
Covariance contribution	0.92
Combinations/Pair	1.17
Mean z-score	-1.35
Structure conservation index	0.80
SVM decision value	-0.07
SVM RNA-class probability	0.500000
Prediction	OTHER

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 3645217 120 - 22224390
GCCACGUCGCAGUCCCGAAUGCAGGCAUUCGGCUUCUUCAGCUUGAGGAAGGCCUGACCACGCUUAGCGUGGAAAAGGGCAUUACCCGGGCUCAGUUCAAUGGCCUUGGUGUACAAGGCG
(((...........(((((((....)))))))(((((((.....)))))))((((..((((((...))))))....))))..((((.((((.((......)))))).)))).....))). ( -50.20)
>DroSec_CAF1 15190 120 - 1
GCCAUGUCGCAGUCCCGAAUGCAGGCAUUCGGCUUCUUCAGCUUGAGGAAUGCCUGACCACGCUUAGCGUGGAAAAGGGCAUUACCCGGGCUCAGUUCAAUGGCCUUGGUGUACAAGGCG
..(((...((....(((((((....))))))).......((((((.(((((((((..((((((...))))))....))))))).))))))))..))...)))((((((.....)))))). ( -51.10)
>DroSim_CAF1 7182 120 - 1
GCCAUGUCGCAGUCCCGAAUGCAGGCAUUCGGCUUCUUCAGCUUGAGGAAGGCCUGACCACGCUUAGCGUGGAAAAGGGCAUUACCCGGGCUCAGUUCAAUGGCCUUGGUGUACAAGGCG
(((.(((.((....(((((((....)))))))(((((((.....)))))))((((..((((((...))))))....))))...(((.((((.((......)))))).)))))))).))). ( -52.00)
>DroEre_CAF1 16116 120 - 1
GCCUUGUCGCAGUCCCGAAUGCAGGCAUUCGGUUUCUUCAGCUUGAGAAAGGCCUGGCCACGCUUGGCGUGGAACAGGGCAUUGCCCGGGUUUAGUUCGAUGGCCUUGGUGUAGAAGGCG
(((((.((((....(((((((....)))))))((((........))))((((((...((((((...))))))(((.((((...))))..))).........)))))).))).).))))). ( -48.20)
>DroWil_CAF1 8915 120 - 1
GCCUUAUCGCAGUCGCGUAUGCAUGCAUUUGGUUUCUUAAGCUUAAGGAAAGCCUGACCACGCUUGGCGUAGAACAGAGCAUUGCCCGGAUUGAGCUCAAUGGCCUUGGUAUAGAAUUCG
((..((.(((....))))).))((((....((((.....(((((((((((.(((((..(((((...)))).)..))).)).)).))....)))))))....))))...))))........ ( -26.20)
>consensus
GCCAUGUCGCAGUCCCGAAUGCAGGCAUUCGGCUUCUUCAGCUUGAGGAAGGCCUGACCACGCUUAGCGUGGAAAAGGGCAUUACCCGGGCUCAGUUCAAUGGCCUUGGUGUACAAGGCG
(((...........(((((((....)))))))(((((((.....)))))))((((..((((((...))))))....))))..((((.(((((.........))))).)))).....))). (-36.64 = -37.56 +   0.92)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:04:18 2006