Locus 1262

Sequence ID	3R_DroMel_CAF1
Location	3,778,029 – 3,778,179
Length	150
Max. P	0.847971

overview

Window 0

Location	3,778,029 – 3,778,139
Length	110
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	90.76
Mean single sequence MFE	-43.45
Consensus MFE	-36.39
Energy contribution	-36.83
Covariance contribution	0.44
Combinations/Pair	1.09
Mean z-score	-1.38
Structure conservation index	0.84
SVM decision value	-0.02
SVM RNA-class probability	0.522907
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 3778029 110 + 27905053
GGUCGCCCGAGAGCCGUGGGUUGCU---------GGCUUUGGCCGAAUAUGCAAAUUCACAUAUUAA-CUUAAUGGCCAUCGACAUGCUCGGCGUUGUCGGGGCUCCUGGCCAUGGCCUA
(((.(((((.......))))).)))---------((((.((((((((((((........))))))..-......((((.(((((((((...))).))))))))))..)))))).)))).. ( -42.40)
>DroSec_CAF1 7585 111 + 1
GGUCGCCCGAGAGCCGUGGGUUGCU---------GGCUUUGGCCGAAUAUGCAAAUUCACAUAUUUACCCUAAUGGCCAUCGACAUGCUCGGCGUUGUCGGGGCUCCUGGCCAUGGCCUA
(((.(((((.......))))).)))---------((((.((((((((((((........)))))))........((((.(((((((((...))).))))))))))...))))).)))).. ( -43.50)
>DroSim_CAF1 11258 111 + 1
GGUCGCCCGAGAGCCGUGGGUUGCU---------GGCUUUGGCCGAAUAUGCAAAUUCACAUAUUUACCCUAAUGGCCAUCGACAUGCUCGGCGUUGUCGGGGCUCCUGGCCAUGGCCUA
(((.(((((.......))))).)))---------((((.((((((((((((........)))))))........((((.(((((((((...))).))))))))))...))))).)))).. ( -43.50)
>DroYak_CAF1 9337 119 + 1
CGUCGC-CGAGAGACGUGGGUUGUUGGCAGUGGUGGCUGUGGCCGAAUAUGCAAAUUCACAUAUUUACCUUAAUGGCCAUCGACGCGCUCGGAGUUGUCGGUGCUCCUGGCCAUGGCCUA
((..((-(((..(((....))).)))))..))..(((((((((((((((((........)))))))........((.((((((((.((.....))))))))))..)).)))))))))).. ( -44.40)
>consensus
GGUCGCCCGAGAGCCGUGGGUUGCU_________GGCUUUGGCCGAAUAUGCAAAUUCACAUAUUUACCCUAAUGGCCAUCGACAUGCUCGGCGUUGUCGGGGCUCCUGGCCAUGGCCUA
.((.(((((.......))))).))..........(((..((((((((((((........)))))))........((((.(((((((((...))).))))))))))...)))))..))).. (-36.39 = -36.83 +   0.44)

alignment

secondary structure

dotplot

Window 1

Location	3,778,060 – 3,778,179
Length	119
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	95.28
Mean single sequence MFE	-36.48
Consensus MFE	-31.42
Energy contribution	-31.67
Covariance contribution	0.25
Combinations/Pair	1.11
Mean z-score	-2.11
Structure conservation index	0.86
SVM decision value	0.78
SVM RNA-class probability	0.847971
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 3778060 119 + 27905053
GGCCGAAUAUGCAAAUUCACAUAUUAA-CUUAAUGGCCAUCGACAUGCUCGGCGUUGUCGGGGCUCCUGGCCAUGGCCUAUCAAUCAUUGAAUUCUGGACAUUAAAGACCGUAUUCAAGA
((((.((((((........))))))..-....((((((..((((((((...))).)))))((....)))))))))))).........((((((..(((.(......).))).)))))).. ( -33.70)
>DroSec_CAF1 7616 120 + 1
GGCCGAAUAUGCAAAUUCACAUAUUUACCCUAAUGGCCAUCGACAUGCUCGGCGUUGUCGGGGCUCCUGGCCAUGGCCUAUCAAUCAUUGAAUUCUGGACAUUAAAGACCGUAUUCAAGA
(((((((((((........)))))))......((((((..((((((((...))).)))))((....)))))))))))).........((((((..(((.(......).))).)))))).. ( -34.90)
>DroSim_CAF1 11289 120 + 1
GGCCGAAUAUGCAAAUUCACAUAUUUACCCUAAUGGCCAUCGACAUGCUCGGCGUUGUCGGGGCUCCUGGCCAUGGCCUAUCAAUCAUUGAAUUCUGGACAUUAAAGACCGUAUUCAAGA
(((((((((((........)))))))......((((((..((((((((...))).)))))((....)))))))))))).........((((((..(((.(......).))).)))))).. ( -34.90)
>DroYak_CAF1 9376 120 + 1
GGCCGAAUAUGCAAAUUCACAUAUUUACCUUAAUGGCCAUCGACGCGCUCGGAGUUGUCGGUGCUCCUGGCCAUGGCCUAUCAAUCAUUGAAUUCUGGACAUUAAAGAGAGUGUUCAGGA
(((((((((((........)))))))......(((((((..((.((((.(((.....))))))))).)))))))))))..............(((((((((((......))))))))))) ( -42.40)
>consensus
GGCCGAAUAUGCAAAUUCACAUAUUUACCCUAAUGGCCAUCGACAUGCUCGGCGUUGUCGGGGCUCCUGGCCAUGGCCUAUCAAUCAUUGAAUUCUGGACAUUAAAGACCGUAUUCAAGA
(((((((((((........)))))))......((((((((((((((((...))).))))))......))))))))))).........((((((..(((.(......).))).)))))).. (-31.42 = -31.67 +   0.25)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:05:01 2006