Locus 4254

Sequence ID	2L_DroMel_CAF1
Location	12,152,834 – 12,153,046
Length	212
Max. P	0.966014

overview

Window 5

Location	12,152,834 – 12,152,954
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	89.83
Mean single sequence MFE	-23.63
Consensus MFE	-19.57
Energy contribution	-19.89
Covariance contribution	0.32
Combinations/Pair	1.10
Mean z-score	-1.78
Structure conservation index	0.83
SVM decision value	1.08
SVM RNA-class probability	0.911291
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 12152834 120 + 22407834
AAAUAAAUACUGAAAGCAUAAAUAAAAUAGGUGGGAGUGGGUGGAAAACACUUGCAGAACCGACCCAUUUCCACGUCAGCACAGUGAAAGCGAGCGAAAUGUAAAUAUCAAAUAAAACGC
...............((((...........((((((((((((((...............)).))))))))))))....((...((....))..))...)))).................. ( -26.66)
>DroSec_CAF1 38055 114 + 1
------UUACUGAAAGCAUAAAUAAAAUAGGUGGGAAUGGGUGGAAAACACUUGCAGAACCGACCCAUUUUCUCGUCAGCACAGUGAAAGCGAGCAAAAUGUAAAUAUCAAAUAAAACGC
------.........((............(((.((..((((((.....))))..))...)).)))(((((((((((...(.....)...))))).)))))).................)) ( -21.30)
>DroSim_CAF1 34705 120 + 1
AAAUAAAUACUGAAAGCAUAAAUAAAAUAGGUGGGAAUGGGUGGAAAGCACUUGCAGAACCGACCCAUUUCCACGUCAGCACAGUGAAAGCGAGCGAAAUGUAAAUAUCAAAUAAAACGC
...............((((...........((((((((((((((...((....))....)).))))))))))))....((...((....))..))...)))).................. ( -29.40)
>DroEre_CAF1 33908 111 + 1
AAAUAAAUACUGAAAGCAUAAAUAAAACAAGAGUGAAUGGGUGGAAAACACUUGCAGAAGCGACCCAUUUCCACGUCAGCGCAGUGAAAGCGAGCGAAAUGUAAAUAUCAA---------
.......(((.....((...............(((..((((((((((....((((....))))....))))))).))).))).((....))..)).....)))........--------- ( -21.00)
>DroYak_CAF1 28568 120 + 1
AAAUAAAUACUGAAGGCAUAAAUAAAAUAAGAGGGUAUGGGUGGAAAACACUUGCAGAAGCGACCCAUUUCCACGUCAGCACAGUGAAAGCGAGCGAAAUGUAAAUAUCAAAUAAAACGC
..........(((..((((.............(((.(((((((.....)))((((....)))).)))).))).(((..((.........))..)))..)))).....))).......... ( -19.80)
>consensus
AAAUAAAUACUGAAAGCAUAAAUAAAAUAGGUGGGAAUGGGUGGAAAACACUUGCAGAACCGACCCAUUUCCACGUCAGCACAGUGAAAGCGAGCGAAAUGUAAAUAUCAAAUAAAACGC
...............((((.............((((((((((.(................).)))))))))).(((..((.........))..)))..)))).................. (-19.57 = -19.89 +   0.32)

alignment

secondary structure

dotplot

Window 6

Location	12,152,954 – 12,153,046
Length	92
Sequences	5
Columns	94
Reading direction	forward
Mean pairwise identity	84.13
Mean single sequence MFE	-21.44
Consensus MFE	-15.80
Energy contribution	-16.60
Covariance contribution	0.80
Combinations/Pair	1.00
Mean z-score	-1.52
Structure conservation index	0.74
SVM decision value	-0.06
SVM RNA-class probability	0.500000
Prediction	OTHER

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 12152954 92 + 22407834
GUAGCAAAAA--AAAAAGGGAAAUGCUACACAUUUGCGUUUGAGCUGAACUGAAAGGCAUGGAAAGUAAGUUUUGGACUUGAUUUCCAGACCAC
((((((....--...........)))))).....(((.(((.((.....)).))).)))((((((.((((((...)))))).))))))...... ( -22.56)
>DroSec_CAF1 38169 94 + 1
GUAGCAAAAAGAAAGAAGGGAAAUGCUACACAUUUGCGUUUGAGCUGAACUGAAAGGCAUGGAAAGUAAGUUUUGGACUUGAUUUCCAGACCAC
((((((.................)))))).....(((.(((.((.....)).))).)))((((((.((((((...)))))).))))))...... ( -22.43)
>DroSim_CAF1 34825 94 + 1
GUAGCAAAGAAGAAAAAGGGAAAUGCUACACAUUUGCGUUUGAGCUGAACUGAAAGGCAUGGAAAGUAAGUUUUGGACUUGAUUUCCAGACCAC
((((((.................)))))).....(((.(((.((.....)).))).)))((((((.((((((...)))))).))))))...... ( -22.43)
>DroEre_CAF1 34019 71 + 1
----------------------AUGCUACACAUUUGCGUUUGAGCUGAGCUGAAAGGCAUGGA-AGUAAGUUUUGGACUUGAUUUCCACGCCAC
----------------------.(((.........)))(((.(((...))).)))(((.((((-((((((((...))))).))))))).))).. ( -19.30)
>DroYak_CAF1 28688 84 + 1
GUAGGGA---------AAGGAAAUGCCACACAUUUGCGUUUGAGCUGAGCUGAAAGGCAUGGA-AGUAAGUUUUGGACUUGAUUUCCACACCAC
...((..---------..((.....)).......(((.(((.(((...))).))).)))((((-((((((((...))))).)))))))..)).. ( -20.50)
>consensus
GUAGCAAA_A__AA_AAGGGAAAUGCUACACAUUUGCGUUUGAGCUGAACUGAAAGGCAUGGAAAGUAAGUUUUGGACUUGAUUUCCAGACCAC
..................((..............(((.(((.((.....)).))).)))((((((.((((((...)))))).))))))..)).. (-15.80 = -16.60 +   0.80)

alignment

secondary structure

dotplot

Window 7

Location	12,152,954 – 12,153,046
Length	92
Sequences	5
Columns	94
Reading direction	reverse
Mean pairwise identity	84.13
Mean single sequence MFE	-19.08
Consensus MFE	-17.20
Energy contribution	-17.28
Covariance contribution	0.08
Combinations/Pair	1.10
Mean z-score	-2.07
Structure conservation index	0.90
SVM decision value	1.59
SVM RNA-class probability	0.966014
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 12152954 92 - 22407834
GUGGUCUGGAAAUCAAGUCCAAAACUUACUUUCCAUGCCUUUCAGUUCAGCUCAAACGCAAAUGUGUAGCAUUUCCCUUUUU--UUUUUGCUAC
..(((.((((((..((((.....))))..)))))).)))..........((......))......((((((...........--....)))))) ( -18.76)
>DroSec_CAF1 38169 94 - 1
GUGGUCUGGAAAUCAAGUCCAAAACUUACUUUCCAUGCCUUUCAGUUCAGCUCAAACGCAAAUGUGUAGCAUUUCCCUUCUUUCUUUUUGCUAC
..(((.((((((..((((.....))))..)))))).)))..........((......))......((((((.................)))))) ( -18.63)
>DroSim_CAF1 34825 94 - 1
GUGGUCUGGAAAUCAAGUCCAAAACUUACUUUCCAUGCCUUUCAGUUCAGCUCAAACGCAAAUGUGUAGCAUUUCCCUUUUUCUUCUUUGCUAC
..(((.((((((..((((.....))))..)))))).)))..........((......))......((((((.................)))))) ( -18.63)
>DroEre_CAF1 34019 71 - 1
GUGGCGUGGAAAUCAAGUCCAAAACUUACU-UCCAUGCCUUUCAGCUCAGCUCAAACGCAAAUGUGUAGCAU----------------------
..(((((((((...((((.....))))..)-))))))))..........(((...((((....)))))))..---------------------- ( -21.00)
>DroYak_CAF1 28688 84 - 1
GUGGUGUGGAAAUCAAGUCCAAAACUUACU-UCCAUGCCUUUCAGCUCAGCUCAAACGCAAAUGUGUGGCAUUUCCUU---------UCCCUAC
..(((((((((...((((.....))))..)-))))))))..........(((...((((....)))))))........---------....... ( -18.40)
>consensus
GUGGUCUGGAAAUCAAGUCCAAAACUUACUUUCCAUGCCUUUCAGUUCAGCUCAAACGCAAAUGUGUAGCAUUUCCCUU_UU__U_UUUGCUAC
..(((.((((((..((((.....))))..)))))).)))..........(((...((((....)))))))........................ (-17.20 = -17.28 +   0.08)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:13:33 2006