Locus 6721

Sequence ID	X_DroMel_CAF1
Location	16,745,993 – 16,746,163
Length	170
Max. P	0.993720

overview

Window 5

Location	16,745,993 – 16,746,089
Length	96
Sequences	4
Columns	96
Reading direction	forward
Mean pairwise identity	85.30
Mean single sequence MFE	-21.75
Consensus MFE	-19.33
Energy contribution	-19.82
Covariance contribution	0.50
Combinations/Pair	1.00
Mean z-score	-2.07
Structure conservation index	0.89
SVM decision value	1.41
SVM RNA-class probability	0.951323
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 16745993 96 + 22224390
ACAAGCACAAGCACACACUCACACUCUUACACACGGAUCGGAUGCUCCACGAAAGUGGGCGUGGCAUCGGAUAAUUUCUAAUGAAAGUUGAAAAGC
....((....))........................(((.((((((((((....))))....)))))).)))..((((.(((....)))))))... ( -23.50)
>DroSec_CAF1 33345 85 + 1
AAAAGCAGA----------CACACUCUCACACAA-AAUCGGAUGCUCCACGAAAGUGGGCGUGGCAUCGGAUAAUUUCUAAUGAAAGUUGAAAAGC
....((...----------...............-.(((.((((((((((....))))....)))))).)))..((((.(((....))))))).)) ( -23.10)
>DroSim_CAF1 31679 85 + 1
ACAAGCACA----------CACACUCUCACACAC-AAUCGGAUGCUCCACGAAAGUGGGCGUGGCAUCGGAUAAUUUCUAAUGAAAGUUGAAAAGC
....((...----------...............-.(((.((((((((((....))))....)))))).)))..((((.(((....))))))).)) ( -23.10)
>DroEre_CAF1 25003 83 + 1
AUAAGCACA------CACUC------ACACACAC-AAUCGGAUACACCACGAAAGUGGGCGUGGCAUCGGAUAAUUUCUAAUGAAAGUUGAAAAGC
....((.((------(....------........-....(....).((((....))))..))))).((((....((((....)))).))))..... ( -17.30)
>consensus
ACAAGCACA__________CACACUCUCACACAC_AAUCGGAUGCUCCACGAAAGUGGGCGUGGCAUCGGAUAAUUUCUAAUGAAAGUUGAAAAGC
...(((..............................(((.((((((((((....))))....)))))).)))..((((....)))))))....... (-19.33 = -19.82 +   0.50)

alignment

secondary structure

dotplot

Window 6

Location	16,746,013 – 16,746,123
Length	110
Sequences	4
Columns	116
Reading direction	forward
Mean pairwise identity	91.11
Mean single sequence MFE	-38.38
Consensus MFE	-32.43
Energy contribution	-32.99
Covariance contribution	0.56
Combinations/Pair	1.04
Mean z-score	-2.39
Structure conservation index	0.85
SVM decision value	1.52
SVM RNA-class probability	0.961279
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 16746013 110 + 22224390
ACACUCUUACACACGGAUCGGAUGCUCCACGAAAGUGGGCGUGGCAUCGGAUAAUUUCUAAUGAAAGUUGAAAAGCGCCGCUGGAAGCG------AUUGGCUGGCGUGUGAAUCCC
.........(((((..(((.((((((((((....))))....)))))).)))..((((....))))(((....)))(((((..(.....------.)..)).))))))))...... ( -38.60)
>DroSec_CAF1 33355 115 + 1
ACACUCUCACACAA-AAUCGGAUGCUCCACGAAAGUGGGCGUGGCAUCGGAUAAUUUCUAAUGAAAGUUGAAAAGCGCCGCUGGAAGCGGUUUGGAUUGGCUGGCGUGUGAAUCCC
......((((((..-.(((.((((((((((....))))....)))))).)))..........(..(((..(.....(((((.....))))).....)..)))..)))))))..... ( -41.70)
>DroSim_CAF1 31689 109 + 1
ACACUCUCACACAC-AAUCGGAUGCUCCACGAAAGUGGGCGUGGCAUCGGAUAAUUUCUAAUGAAAGUUGAAAAGCGCCGCUGGAAGCG------AUUGGCUGGCGUGUGAAUCCC
......((((((..-.(((.((((((((((....))))....)))))).)))..((((....))))(((....)))(((((..(.....------.)..)).)))))))))..... ( -39.70)
>DroEre_CAF1 25017 103 + 1
------ACACACAC-AAUCGGAUACACCACGAAAGUGGGCGUGGCAUCGGAUAAUUUCUAAUGAAAGUUGAAAAGCACCGCUGGAAGCG------AUUGGCUGGCGUGUGAAUCCC
------.(((((.(-(((((......((((....))))..(((((((..((.....))..)))...(((....))).))))......))------))))(....))))))...... ( -33.50)
>consensus
ACACUCUCACACAC_AAUCGGAUGCUCCACGAAAGUGGGCGUGGCAUCGGAUAAUUUCUAAUGAAAGUUGAAAAGCGCCGCUGGAAGCG______AUUGGCUGGCGUGUGAAUCCC
......((((((....(((.((((((((((....))))....)))))).)))..........(..(((..(.......(((.....))).......)..)))..)))))))..... (-32.43 = -32.99 +   0.56)

alignment

secondary structure

dotplot

Window 7

Location	16,746,049 – 16,746,163
Length	114
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	96.39
Mean single sequence MFE	-50.70
Consensus MFE	-41.06
Energy contribution	-40.90
Covariance contribution	-0.16
Combinations/Pair	1.03
Mean z-score	-3.94
Structure conservation index	0.81
SVM decision value	2.42
SVM RNA-class probability	0.993720
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 16746049 114 + 22224390
GGGCGUGGCAUCGGAUAAUUUCUAAUGAAAGUUGAAAAGCGCCGCUGGAAGCG------AUUGGCUGGCGUGUGAAUCCCACAUGCUGCGCAGUCGACUUCCGCACAGUGGGCCCAAAUU
(((((((((.........((((....))))(((....)))))))).(((((((------((((((.((((((((.....)))))))))).)))))).))))).........))))..... ( -51.80)
>DroSec_CAF1 33390 120 + 1
GGGCGUGGCAUCGGAUAAUUUCUAAUGAAAGUUGAAAAGCGCCGCUGGAAGCGGUUUGGAUUGGCUGGCGUGUGAAUCCCACAUGCUGCGCAGUCGACUUCCGCACAGUGGGCCCAAAUU
((((....(((..((.....))..)))...(((....))).((((((...((((..(.(((((((.((((((((.....)))))))))).))))).)...)))).))))))))))..... ( -50.90)
>DroSim_CAF1 31724 114 + 1
GGGCGUGGCAUCGGAUAAUUUCUAAUGAAAGUUGAAAAGCGCCGCUGGAAGCG------AUUGGCUGGCGUGUGAAUCCCACAUGCUGCGCAGUCGACUUCCGCACAGUGGGCCCAAAUU
(((((((((.........((((....))))(((....)))))))).(((((((------((((((.((((((((.....)))))))))).)))))).))))).........))))..... ( -51.80)
>DroEre_CAF1 25046 114 + 1
GGGCGUGGCAUCGGAUAAUUUCUAAUGAAAGUUGAAAAGCACCGCUGGAAGCG------AUUGGCUGGCGUGUGAAUCCCACAUGCUGCGCAGUCGACUUCCGCACAGUGGGCCCAAGUU
(((((((((((..((.....))..)))...(((....))).)))).(((((((------((((((.((((((((.....)))))))))).)))))).))))).........))))..... ( -49.60)
>DroYak_CAF1 24843 114 + 1
GGGCGUGGCAUCAGAUAAUUUCUAAUGAAAGUUGAAAAGAGCCGCUGGAAGCG------AUUGGCUGGCGUGUGAAUCCCACAUGCUGCGCAGUCGACUUCCGCACAGUGGGCCCAAGUU
(((((((((.((((....((((....)))).)))).....))))).(((((((------((((((.((((((((.....)))))))))).)))))).))))).........))))..... ( -49.40)
>consensus
GGGCGUGGCAUCGGAUAAUUUCUAAUGAAAGUUGAAAAGCGCCGCUGGAAGCG______AUUGGCUGGCGUGUGAAUCCCACAUGCUGCGCAGUCGACUUCCGCACAGUGGGCCCAAAUU
((((......((((....((((....)))).))))......((((((...(((......((((((.((((((((.....)))))))))).)))).......))).))))))))))..... (-41.06 = -40.90 +  -0.16)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:20:47 2006