Locus 4393

Sequence ID	3R_DroMel_CAF1
Location	11,616,982 – 11,617,130
Length	148
Max. P	0.995670

overview

Window 7

Location	11,616,982 – 11,617,090
Length	108
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	83.54
Mean single sequence MFE	-38.26
Consensus MFE	-29.30
Energy contribution	-30.50
Covariance contribution	1.20
Combinations/Pair	1.26
Mean z-score	-3.08
Structure conservation index	0.77
SVM decision value	2.60
SVM RNA-class probability	0.995670
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11616982 108 + 27905053
CUAUUGGCAGCUGCUCAAUGCGAUCUUCAAGCUGGGCGCAGUCAAGCAUCUUUGCAUUUAAGUCGCUGCUUAAUUGUAAAAUGUUUGCCUGUGG---AGAACAUAAUGU---------UA
.(((((.(((((((.....))(.....).)))))..(((((.(((((((.((((((.((((((....)))))).))))))))))))).))))).---......))))).---------.. ( -31.20)
>DroSec_CAF1 6918 120 + 1
CUAUUGGUAGCUGCUCAAUGCGGUCUUCAAGCUCGGCGCAGGUAAGCAACUUUGCAUUUAAGUCGCUGCUUAAUUGUAAAAUGCUUGCCUGUGGAGGAGAACAUAAUGUCAAUAAUCUUA
...((((..(((((.....)))))..)))).(((..((((((((((((..((((((.((((((....)))))).)))))).))))))))))))...)))..................... ( -41.20)
>DroSim_CAF1 7046 120 + 1
CUAAUGGCAGCUGCUCAAUGCGAACUUCAAGCUCGGCGCAGGCAAGCAUCUUUGCAUUUAAGUCGCUGCUUAAUUGUAAAAUGUUUGCCUGUGGAGGAGAACAUAAUAUUAUUAAUCAUA
...(((....((.(((....(((.(.....).))).(((((((((((((.((((((.((((((....)))))).)))))))))))))))))))))).))..)))................ ( -39.90)
>DroEre_CAF1 4510 117 + 1
CUAUUGGCAUCUGCUCAAUGCGCUCUGCAAGCUCGGUGCAGGCAAGAAUCAUUGCAUUUAAGUCGGUGCUUAGUUGUAAGAUGUUUGCCUGUGG---AGAAAAUAAUGUUAGUAAUCCUA
.(((((((((..((.....)).(((..(..((.....))(((((((.(((.(((((.((((((....)))))).)))))))).))))))))..)---))......)))))))))...... ( -36.30)
>DroYak_CAF1 5006 117 + 1
CUAUUGUCACCUGCUCAUUGCGCUCUGCAAGCUCGUCGCAGGCUUGCAUCUUUGCAUUUAAGUCGGAGCUUAGUUGUAAGAUGUUUGCCUGUGG---AGACAGCAAUGUUAGUAAUCAUA
...........(((((((((((((.....)))((..(((((((..(((((((.(((.((((((....)))))).))))))))))..))))))).---.))..))))))..))))...... ( -42.70)
>consensus
CUAUUGGCAGCUGCUCAAUGCGAUCUUCAAGCUCGGCGCAGGCAAGCAUCUUUGCAUUUAAGUCGCUGCUUAAUUGUAAAAUGUUUGCCUGUGG___AGAACAUAAUGUUAGUAAUCAUA
.((((((((...((.....))...............(((((((((((((.((((((.((((((....)))))).))))))))))))))))))).............))))))))...... (-29.30 = -30.50 +   1.20)

alignment

secondary structure

dotplot

Window 8

Location	11,617,022 – 11,617,130
Length	108
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	78.00
Mean single sequence MFE	-27.92
Consensus MFE	-18.42
Energy contribution	-19.02
Covariance contribution	0.60
Combinations/Pair	1.24
Mean z-score	-1.98
Structure conservation index	0.66
SVM decision value	1.14
SVM RNA-class probability	0.920692
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11617022 108 + 27905053
GUCAAGCAUCUUUGCAUUUAAGUCGCUGCUUAAUUGUAAAAUGUUUGCCUGUGG---AGAACAUAAUGU---------UAUAAUCUAAUACAAGGAAAGCCAGUGUAACCCACCUCAAAC
(.(((((((.((((((.((((((....)))))).))))))))))))).).((((---..(((.....))---------).........((((.((....))..))))..))))....... ( -23.40)
>DroSec_CAF1 6958 120 + 1
GGUAAGCAACUUUGCAUUUAAGUCGCUGCUUAAUUGUAAAAUGCUUGCCUGUGGAGGAGAACAUAAUGUCAAUAAUCUUAUAACCUAAUACAAGGAAAGCCAGAGUAACACACCUCGCAA
((((((((..((((((.((((((....)))))).)))))).))))))))((((.(((.((........)).............(((......))).................))))))). ( -29.60)
>DroSim_CAF1 7086 120 + 1
GGCAAGCAUCUUUGCAUUUAAGUCGCUGCUUAAUUGUAAAAUGUUUGCCUGUGGAGGAGAACAUAAUAUUAUUAAUCAUAUAACCUAAUACAAGGAAAUCCAUUGUAACCCACCUCGCAA
(((((((((.((((((.((((((....)))))).)))))))))))))))((((.(((........((((........)))).......(((((((....)).))))).....))))))). ( -33.70)
>DroEre_CAF1 4550 106 + 1
GGCAAGAAUCAUUGCAUUUAAGUCGGUGCUUAGUUGUAAGAUGUUUGCCUGUGG---AGAAAAUAAUGUUAGUAAUCCUAUAAGU-----------AAACCCGUGUAACCCACCUCGAAA
((((((.(((.(((((.((((((....)))))).)))))))).))))))....(---((..........(((.....))).....-----------......(((.....)))))).... ( -21.10)
>DroYak_CAF1 5046 115 + 1
GGCUUGCAUCUUUGCAUUUAAGUCGGAGCUUAGUUGUAAGAUGUUUGCCUGUGG---AGACAGCAAUGUUAGUAAUCAUAUAAGUUGAUACAAGGAAAACC--AGUAACCCACCUCUUUU
(((..(((((((.(((.((((((....)))))).))))))))))..))).((((---.((((....)))).(((.(((.......))))))..((....))--......))))....... ( -31.80)
>consensus
GGCAAGCAUCUUUGCAUUUAAGUCGCUGCUUAAUUGUAAAAUGUUUGCCUGUGG___AGAACAUAAUGUUAGUAAUCAUAUAACCUAAUACAAGGAAAACCAGUGUAACCCACCUCGAAA
(((((((((.((((((.((((((....)))))).)))))))))))))))((((........))))....................................................... (-18.42 = -19.02 +   0.60)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:28:01 2006