Locus 445

Sequence ID	2R_DroMel_CAF1
Location	2,563,468 – 2,563,564
Length	96
Max. P	0.992742

overview

Window 2

Location	2,563,468 – 2,563,564
Length	96
Sequences	6
Columns	99
Reading direction	forward
Mean pairwise identity	75.89
Mean single sequence MFE	-23.65
Consensus MFE	-14.25
Energy contribution	-14.45
Covariance contribution	0.20
Combinations/Pair	1.27
Mean z-score	-1.81
Structure conservation index	0.60
SVM decision value	1.01
SVM RNA-class probability	0.900630
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 2563468 96 + 20766785
--AUUAACCGACUUUC-UUUCAGUUAAUCUGCUUCGCCUUGGCCGUGUUUCUGGCCAUUAGUUUUAAGAACAAGCAGCGACGGAUGGAGUUCUAGUUCU
--.......((..(((-(.((.(((...((((((.....((((((......))))))...((((...)))))))))).))).)).)))).))....... ( -21.30)
>DroPse_CAF1 620 89 + 1
CUUUUA----AUUUCCUUUGCAGUUGCUCUGCUUCGUCCUGGCCGUCUUUCUAGCCAUUAGCUUCCGCAACAAGCAGCGCCGCCUGCAGUU------CU
......----.......((((((..((.((((((.((..((((..........))))...((....)).)))))))).))...))))))..------.. ( -22.70)
>DroEre_CAF1 733 92 + 1
UUAUUACCCGACUUCC-UUUCAGUUGAUCUGCUGUGCCUUGGCCGUUUUUCUGGCCAUUAGCUUUAAGAACAAGCAGCGGCGGAUGGAGUU------CU
......(((((((...-....)))))(((((((((....((((((......))))))...((((.......)))).)))))))))))....------.. ( -27.80)
>DroWil_CAF1 1529 89 + 1
AAUUUA----AUUCAUUUUCCAGCUGAUUUGCUGUGCCUUGGCCGUAUUUUUGGCCAUCAGUUUUCGCAAUAAGCAACGGCGGAUGCAAUU------UU
......----........(((.((((..(((((.(((..((((((......))))))...(....))))...)))))))))))).......------.. ( -24.10)
>DroYak_CAF1 859 92 + 1
UUAUUAUCCGACUUCU-UUUCAGUUAAUCUGCUUCGCCUUGGCCGUAUUUCUGGCCAUUAGUUUUAAGAACAAGCAGCGGCGGAUGGAGUU------CU
.........((((((.-...(((.....))).((((((.((((((......))))))...((((...)))).......)))))).))))))------.. ( -23.30)
>DroPer_CAF1 620 89 + 1
CUUUUA----AUUUCCUUUGCAGUUGCUCUGCUUCGUCCUGGCCGUCUUUCUAGCCAUUAGCUUCCGCAACAAGCAGCGCCGCCUGCAGUU------CU
......----.......((((((..((.((((((.((..((((..........))))...((....)).)))))))).))...))))))..------.. ( -22.70)
>consensus
CUAUUA____ACUUCC_UUUCAGUUGAUCUGCUUCGCCUUGGCCGUAUUUCUGGCCAUUAGCUUUAACAACAAGCAGCGGCGGAUGCAGUU______CU
.................(((((.(((..((((((.((..((((((......))))))...)).........))))))...))).))))).......... (-14.25 = -14.45 +   0.20)

alignment

secondary structure

dotplot

Window 3

Location	2,563,468 – 2,563,564
Length	96
Sequences	6
Columns	99
Reading direction	reverse
Mean pairwise identity	75.89
Mean single sequence MFE	-26.35
Consensus MFE	-13.80
Energy contribution	-13.55
Covariance contribution	-0.25
Combinations/Pair	1.21
Mean z-score	-2.81
Structure conservation index	0.52
SVM decision value	2.35
SVM RNA-class probability	0.992742
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 2563468 96 - 20766785
AGAACUAGAACUCCAUCCGUCGCUGCUUGUUCUUAAAACUAAUGGCCAGAAACACGGCCAAGGCGAAGCAGAUUAACUGAAA-GAAAGUCGGUUAAU--
......................(((((((((.....)))...(((((........))))).....))))))(((((((((..-.....)))))))))-- ( -22.00)
>DroPse_CAF1 620 89 - 1
AG------AACUGCAGGCGGCGCUGCUUGUUGCGGAAGCUAAUGGCUAGAAAGACGGCCAGGACGAAGCAGAGCAACUGCAAAGGAAAU----UAAAAG
..------...(((((...((.(((((((((((....))...(((((........))))).))).)))))).))..)))))........----...... ( -32.30)
>DroEre_CAF1 733 92 - 1
AG------AACUCCAUCCGCCGCUGCUUGUUCUUAAAGCUAAUGGCCAGAAAAACGGCCAAGGCACAGCAGAUCAACUGAAA-GGAAGUCGGGUAAUAA
.(------(..(((....(((...((((.......))))...(((((........))))).))).(((........)))...-)))..))......... ( -24.90)
>DroWil_CAF1 1529 89 - 1
AA------AAUUGCAUCCGCCGUUGCUUAUUGCGAAAACUGAUGGCCAAAAAUACGGCCAAGGCACAGCAAAUCAGCUGGAAAAUGAAU----UAAAUU
..------((((.(((..(((.((((.....)))).......(((((........))))).))).((((......))))....))))))----)..... ( -23.60)
>DroYak_CAF1 859 92 - 1
AG------AACUCCAUCCGCCGCUGCUUGUUCUUAAAACUAAUGGCCAGAAAUACGGCCAAGGCGAAGCAGAUUAACUGAAA-AGAAGUCGGAUAAUAA
..------......(((((.(.(((((((((.....)))...(((((........))))).....)))))).....((....-))..).)))))..... ( -23.00)
>DroPer_CAF1 620 89 - 1
AG------AACUGCAGGCGGCGCUGCUUGUUGCGGAAGCUAAUGGCUAGAAAGACGGCCAGGACGAAGCAGAGCAACUGCAAAGGAAAU----UAAAAG
..------...(((((...((.(((((((((((....))...(((((........))))).))).)))))).))..)))))........----...... ( -32.30)
>consensus
AG______AACUCCAUCCGCCGCUGCUUGUUCCGAAAACUAAUGGCCAGAAAGACGGCCAAGGCGAAGCAGAUCAACUGAAA_GGAAAU____UAAAAA
......................(((((((((.....)))...(((((........))))).....))))))............................ (-13.80 = -13.55 +  -0.25)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:38:44 2006