Locus 686

Sequence ID	3R_DroMel_CAF1
Location	2,462,134 – 2,462,278
Length	144
Max. P	0.935264

overview

Window 7

Location	2,462,134 – 2,462,254
Length	120
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	96.06
Mean single sequence MFE	-49.43
Consensus MFE	-45.76
Energy contribution	-45.83
Covariance contribution	0.06
Combinations/Pair	1.06
Mean z-score	-2.12
Structure conservation index	0.93
SVM decision value	1.17
SVM RNA-class probability	0.925545
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 2462134 120 + 27905053
GGGGAUGAGGGCGCAAAAAUGGGGACGACGAAAAUGGUCUGGCAUGGGGUGAAAUGUCUGCUCCGGCUUCCUUGUUGCCACAGAAGGUGUCGCUGCACUGGCAGUGGCGCGCUGUUGUGG
((.((..((((.((.....(((((.((((.......))).(((((........))))).)))))))).))))..)).))((((.((((((((((((....)))))))))).)).)))).. ( -46.00)
>DroSec_CAF1 21120 117 + 1
GGGGAUGAGGGCGCAAAAAUGGGGAC---GCAAAUGGCCUGGCAAGGGGUGAAAUGUCUGCGCCGGCUUCCUUGUUGCCACAGAAGGUGUCGCUGCACUGGCAGUGGCGCGCUGUUGUGG
(((((.(..((((((.....(....)---(((..(.((((......)))).)..))).))))))..).)))))....((((((.((((((((((((....)))))))))).)).)))))) ( -50.00)
>DroSim_CAF1 17855 117 + 1
GAGGAUGAGGGCGCAAAAAUGGGGAC---GCAAAUGGCCUGGCAUGGGGUGAAAUGUCUGCGCCGGCUUCCUUGUUGCCACAGAAGGUGUCGCUGCACUGGCAGUGGCGCGCUGUUGUGG
(((((.(..((((((.....(....)---(((..(.((((......)))).)..))).))))))..).)))))....((((((.((((((((((((....)))))))))).)).)))))) ( -50.80)
>DroEre_CAF1 22594 117 + 1
GGGGAUGAGGGAGCAAAAAUGGGGAC---GCAAAUGGCCUGGCAUGGGGUGAAAUGUCUGCUCCGGCUUCCUUGUUGCCACAGAAGGUGUCGCUGCACUGGCAGUGGCGCGCUGUUGUGG
((.((..(((((((.....(((((..---(((..(.((((......)))).)..)))...))))))))))))..)).))((((.((((((((((((....)))))))))).)).)))).. ( -50.90)
>consensus
GGGGAUGAGGGCGCAAAAAUGGGGAC___GCAAAUGGCCUGGCAUGGGGUGAAAUGUCUGCGCCGGCUUCCUUGUUGCCACAGAAGGUGUCGCUGCACUGGCAGUGGCGCGCUGUUGUGG
(((((.(..((((((.....(....)..............(((((........)))))))))))..).)))))....((((((.((((((((((((....)))))))))).)).)))))) (-45.76 = -45.83 +   0.06)

alignment

secondary structure

dotplot

Window 8

Location	2,462,174 – 2,462,278
Length	104
Sequences	4
Columns	104
Reading direction	forward
Mean pairwise identity	98.88
Mean single sequence MFE	-48.38
Consensus MFE	-46.25
Energy contribution	-46.75
Covariance contribution	0.50
Combinations/Pair	1.00
Mean z-score	-2.92
Structure conservation index	0.96
SVM decision value	1.24
SVM RNA-class probability	0.935264
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 2462174 104 + 27905053
GGCAUGGGGUGAAAUGUCUGCUCCGGCUUCCUUGUUGCCACAGAAGGUGUCGCUGCACUGGCAGUGGCGCGCUGUUGUGGCAAAACACGAGCCCGCAUCAUCAG
.((..(((((((....)).)))))(((((.....(((((((((.((((((((((((....)))))))))).)).))))))))).....))))).))........ ( -48.50)
>DroSec_CAF1 21157 104 + 1
GGCAAGGGGUGAAAUGUCUGCGCCGGCUUCCUUGUUGCCACAGAAGGUGUCGCUGCACUGGCAGUGGCGCGCUGUUGUGGCAAAACACGAGCCCGCAUCAUCAG
.......(((((......((((..(((((.....(((((((((.((((((((((((....)))))))))).)).))))))))).....)))))))))))))).. ( -47.90)
>DroSim_CAF1 17892 104 + 1
GGCAUGGGGUGAAAUGUCUGCGCCGGCUUCCUUGUUGCCACAGAAGGUGUCGCUGCACUGGCAGUGGCGCGCUGUUGUGGCAAAACACGAGCCCGCAUCAUCAG
(((((........)))))((((..(((((.....(((((((((.((((((((((((....)))))))))).)).))))))))).....)))))))))....... ( -48.60)
>DroEre_CAF1 22631 104 + 1
GGCAUGGGGUGAAAUGUCUGCUCCGGCUUCCUUGUUGCCACAGAAGGUGUCGCUGCACUGGCAGUGGCGCGCUGUUGUGGCAAAACACGAGCCCGCAUCAUCAG
.((..(((((((....)).)))))(((((.....(((((((((.((((((((((((....)))))))))).)).))))))))).....))))).))........ ( -48.50)
>consensus
GGCAUGGGGUGAAAUGUCUGCGCCGGCUUCCUUGUUGCCACAGAAGGUGUCGCUGCACUGGCAGUGGCGCGCUGUUGUGGCAAAACACGAGCCCGCAUCAUCAG
.((..(((((((....)).)))))(((((.....(((((((((.((((((((((((....)))))))))).)).))))))))).....))))).))........ (-46.25 = -46.75 +   0.50)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:49:21 2006