Locus 5187

Sequence ID	X_DroMel_CAF1
Location	13,541,187 – 13,541,313
Length	126
Max. P	0.974013

overview

Window 0

Location	13,541,187 – 13,541,282
Length	95
Sequences	5
Columns	99
Reading direction	forward
Mean pairwise identity	88.31
Mean single sequence MFE	-23.78
Consensus MFE	-20.69
Energy contribution	-20.97
Covariance contribution	0.28
Combinations/Pair	1.05
Mean z-score	-1.52
Structure conservation index	0.87
SVM decision value	0.56
SVM RNA-class probability	0.783140
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 13541187 95 + 22224390
GUUUUUUUUUUCAA-GGGUCAAACAGAAAAUUGGCCAACUGAUUGAUUAAACAGACGGCCACAAGGGG---GAGGCGGGUGGCAAAUGAAUCAAUUGGA
..............-.((((((........))))))..(..(((((((...((....(((((..(...---....)..)))))...)))))))))..). ( -24.70)
>DroSec_CAF1 23198 91 + 1
GUUU----UUUCAG-GGGUCAAACAGAAAAUUGGCCAACUGAUUGAUUAAACAGACGGCCACAAGGGG---GAGGCGGGUGGCAAAUGAAGCAAUUGGA
((((----(.((((-.((((((........))))))..))))...............(((((..(...---....)..)))))....)))))....... ( -21.30)
>DroSim_CAF1 24125 91 + 1
GUUU----UUUCAG-GGGUCAAACAGAAAAUUGGCCAACUGAUUGAUUAAACAGACGGCCACCGGGGG---GAGGCGGGUGGCAAAUGAAGCAAUUGGA
((((----(.((((-.((((((........))))))..))))...............((((((.(...---....).))))))....)))))....... ( -25.30)
>DroEre_CAF1 23769 90 + 1
GCUU-----UGCAG-GGGUCAAGCAAGAGAUUGGCCAACUGAUUGAUUAAAUAGACGGCCACAAGGGG---GAGGCGGGUGGCAAAUAAAUCAAUUGGA
....-----.....-.((((((........))))))..(..(((((((...((....(((((..(...---....)..)))))...)))))))))..). ( -24.20)
>DroYak_CAF1 36059 94 + 1
GUUU-----UGAAGGGGGUCAAACAAGAGAUUGGCCAACUGAUUGAUUAAACAGACGGCCAGAGGGGGCGGCAGGCGGGUGGCAAAUGAAUCAAUUGGA
....-----.......((((((.(....).))))))..(..(((((((.......((.((.....)).)).((.((.....))...)))))))))..). ( -23.40)
>consensus
GUUU____UUUCAG_GGGUCAAACAGAAAAUUGGCCAACUGAUUGAUUAAACAGACGGCCACAAGGGG___GAGGCGGGUGGCAAAUGAAUCAAUUGGA
................((((((........))))))..(..(((((((...((....(((((................)))))...)))))))))..). (-20.69 = -20.97 +   0.28)

alignment

secondary structure

dotplot

Window 1

Location	13,541,206 – 13,541,313
Length	107
Sequences	5
Columns	110
Reading direction	forward
Mean pairwise identity	89.83
Mean single sequence MFE	-31.90
Consensus MFE	-24.03
Energy contribution	-24.27
Covariance contribution	0.24
Combinations/Pair	1.07
Mean z-score	-2.82
Structure conservation index	0.75
SVM decision value	1.72
SVM RNA-class probability	0.974013
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 13541206 107 + 22224390
AAACAGAAAAUUGGCCAACUGAUUGAUUAAACAGACGGCCACAAGGGG---GAGGCGGGUGGCAAAUGAAUCAAUUGGAGGUCAAUUGCUGAGCAAUUUGUGGCGCAAUU
...(((..((((((((..(..(((((((...((....(((((..(...---....)..)))))...)))))))))..).)))))))).))).((........))...... ( -30.60)
>DroSec_CAF1 23213 107 + 1
AAACAGAAAAUUGGCCAACUGAUUGAUUAAACAGACGGCCACAAGGGG---GAGGCGGGUGGCAAAUGAAGCAAUUGGAGGUCAAUUGCUGAGCAAUUUGUGGCGCAAUU
........(((((((((...(((((......((....(((((..(...---....)..)))))...)).((((((((.....))))))))...)))))..)))).))))) ( -31.70)
>DroSim_CAF1 24140 107 + 1
AAACAGAAAAUUGGCCAACUGAUUGAUUAAACAGACGGCCACCGGGGG---GAGGCGGGUGGCAAAUGAAGCAAUUGGAGGUCAAUUGCUGAGCAAUUUGUGGCGCAAUU
........(((((((((...(((((......((....((((((.(...---....).))))))...)).((((((((.....))))))))...)))))..)))).))))) ( -35.70)
>DroEre_CAF1 23783 96 + 1
AAGCAAGAGAUUGGCCAACUGAUUGAUUAAAUAGACGGCCACAAGGGG---GAGGCGGGUGGCAAAUAAAUCAAUUGGAGGUCAA-----------UUUGUGGCGCAAUU
..((.(.(((((((((..(..(((((((...((....(((((..(...---....)..)))))...)))))))))..).))))))-----------))).).))...... ( -30.50)
>DroYak_CAF1 36074 110 + 1
AAACAAGAGAUUGGCCAACUGAUUGAUUAAACAGACGGCCAGAGGGGGCGGCAGGCGGGUGGCAAAUGAAUCAAUUGGAGGUCAAUUGCUGAGCAAUUUGUGGCGCAAUU
..........((((((..(((.((.....)))))..))))))...(.((.(((.((...((((((.(((.((.....))..))).)))))).))....))).)).).... ( -31.00)
>consensus
AAACAGAAAAUUGGCCAACUGAUUGAUUAAACAGACGGCCACAAGGGG___GAGGCGGGUGGCAAAUGAAUCAAUUGGAGGUCAAUUGCUGAGCAAUUUGUGGCGCAAUU
........(((((((((.(..(((((((...((....(((((................)))))...)))))))))..).....((((((...))))))..)))).))))) (-24.03 = -24.27 +   0.24)

alignment

secondary structure

dotplot

Window 2

Location	13,541,206 – 13,541,313
Length	107
Sequences	5
Columns	110
Reading direction	reverse
Mean pairwise identity	89.83
Mean single sequence MFE	-22.45
Consensus MFE	-16.32
Energy contribution	-17.12
Covariance contribution	0.80
Combinations/Pair	1.00
Mean z-score	-2.05
Structure conservation index	0.73
SVM decision value	0.44
SVM RNA-class probability	0.738256
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 13541206 107 - 22224390
AAUUGCGCCACAAAUUGCUCAGCAAUUGACCUCCAAUUGAUUCAUUUGCCACCCGCCUC---CCCCUUGUGGCCGUCUGUUUAAUCAAUCAGUUGGCCAAUUUUCUGUUU
(((((.(((...((((((...)))))).......((((((((.(((...((..((((.(---......).)).))..))...))).))))))))))))))))........ ( -21.80)
>DroSec_CAF1 23213 107 - 1
AAUUGCGCCACAAAUUGCUCAGCAAUUGACCUCCAAUUGCUUCAUUUGCCACCCGCCUC---CCCCUUGUGGCCGUCUGUUUAAUCAAUCAGUUGGCCAAUUUUCUGUUU
(((((.(((((..((((...((((((((.....))))))))......(((((.......---......)))))............))))..).)))))))))........ ( -23.92)
>DroSim_CAF1 24140 107 - 1
AAUUGCGCCACAAAUUGCUCAGCAAUUGACCUCCAAUUGCUUCAUUUGCCACCCGCCUC---CCCCCGGUGGCCGUCUGUUUAAUCAAUCAGUUGGCCAAUUUUCUGUUU
(((((.(((((..((((...((((((((.....))))))))......((((((.(....---...).))))))............))))..).)))))))))........ ( -27.60)
>DroEre_CAF1 23783 96 - 1
AAUUGCGCCACAAA-----------UUGACCUCCAAUUGAUUUAUUUGCCACCCGCCUC---CCCCUUGUGGCCGUCUAUUUAAUCAAUCAGUUGGCCAAUCUCUUGCUU
......((.....(-----------(((....((((((((((.(((.(((((.......---......))))).........))).)))))))))).)))).....)).. ( -17.12)
>DroYak_CAF1 36074 110 - 1
AAUUGCGCCACAAAUUGCUCAGCAAUUGACCUCCAAUUGAUUCAUUUGCCACCCGCCUGCCGCCCCCUCUGGCCGUCUGUUUAAUCAAUCAGUUGGCCAAUCUCUUGUUU
.((((.(((...((((((...)))))).......((((((((.(((...((..((...((((.......))))))..))...))).)))))))))))))))......... ( -21.80)
>consensus
AAUUGCGCCACAAAUUGCUCAGCAAUUGACCUCCAAUUGAUUCAUUUGCCACCCGCCUC___CCCCUUGUGGCCGUCUGUUUAAUCAAUCAGUUGGCCAAUUUUCUGUUU
.((((.(((...((((((...)))))).......((((((((.(((...((..((((.............)).))..))...))).)))))))))))))))......... (-16.32 = -17.12 +   0.80)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:41:52 2006