Locus 5777

Sequence ID	2L_DroMel_CAF1
Location	16,393,635 – 16,393,798
Length	163
Max. P	0.999645

overview

Window 7

Location	16,393,635 – 16,393,729
Length	94
Sequences	3
Columns	108
Reading direction	forward
Mean pairwise identity	87.54
Mean single sequence MFE	-22.45
Consensus MFE	-21.68
Energy contribution	-21.79
Covariance contribution	0.11
Combinations/Pair	1.05
Mean z-score	-0.77
Structure conservation index	0.97
SVM decision value	-0.03
SVM RNA-class probability	0.517830
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 16393635 94 + 22407834
CCCCCCUCCAUCCAUCCAGACUUUUUUCCACUCCAGCUGUGCCAAGUUUGCAUGCCAAAAA--------------AAAGCGGCAAACAAGUUGGCUCAAUGGCUCGGG
...........................((...(((..((.(((((((((((.(((......--------------...)))))))))...))))).)).)))...)). ( -21.60)
>DroSec_CAF1 18183 105 + 1
--CCCUUCCAUCCAUCCAGACUUUUUUCCACUCCAGCUGGGCCAAGUUUGCAUGCCAAAAAAAGCGAAAAUAAA-AAAGAGGCAAAUAAGUUGGCUCAAUGGCUCGGG
--.........................((...(((..((((((((.((....((((..................-.....))))...)).)))))))).)))...)). ( -22.20)
>DroSim_CAF1 16688 106 + 1
--CCCUUCCAUCCAUCCAGACUUUUUUCCACUCCAGCUGGGCCAAGUUUGCAUGCCAAAAAAAGCGAAAAUAAAAAAAGAGGCAAACAAGUUGGCUCAAUGGCUCGGG
--.........................((...(((..((((((((.((((..((((........................))))..)))))))))))).)))...)). ( -23.56)
>consensus
__CCCUUCCAUCCAUCCAGACUUUUUUCCACUCCAGCUGGGCCAAGUUUGCAUGCCAAAAAAAGCGAAAAUAAA_AAAGAGGCAAACAAGUUGGCUCAAUGGCUCGGG
...........................((...(((..((((((((.((((..((((........................))))..)))))))))))).)))...)). (-21.68 = -21.79 +   0.11)

alignment

secondary structure

dotplot

Window 8

Location	16,393,673 – 16,393,768
Length	95
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	86.26
Mean single sequence MFE	-33.89
Consensus MFE	-32.26
Energy contribution	-32.30
Covariance contribution	0.04
Combinations/Pair	1.04
Mean z-score	-2.79
Structure conservation index	0.95
SVM decision value	3.83
SVM RNA-class probability	0.999645
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 16393673 95 + 22407834
GUGCCAAGUUUGCAUGCCAAAAA------------------------AAAGCGGCAAACAAGUUGGCUCAAUGGCUCGGGCCCACUUGAUUUACAACAGUCGCCACUUGGCCA-AAGUGC
(.(((((((..((.((((.....------------------------.....))))..(((((.(((((........))))).))))).............)).)))))))).-...... ( -31.40)
>DroSec_CAF1 18219 108 + 1
GGGCCAAGUUUGCAUGCCAAAAA----------AAGCGAAAAUAAA-AAAGAGGCAAAUAAGUUGGCUCAAUGGCUCGGGCCCACUUGAUUUACAACAGUCGCCACUUGGCCA-AAGUGC
.((((((((((((..........----------..)))).......-.....(((....((((.(((((........))))).))))((((......))))))))))))))).-...... ( -33.20)
>DroSim_CAF1 16724 109 + 1
GGGCCAAGUUUGCAUGCCAAAAA----------AAGCGAAAAUAAAAAAAGAGGCAAACAAGUUGGCUCAAUGGCUCGGGCCCACUUGAUUUACAACAGUCGCCACUUGGCCA-AAGUGC
.((((((((..((.((((.....----------...................))))..(((((.(((((........))))).))))).............)).)))))))).-...... ( -34.26)
>DroEre_CAF1 14848 116 + 1
GGGCCAAGUUUGCAUGCCAAAAAAGUGGGGAAAAAGGGAAAAUAAA--AUAAGGCAAGCAAGUUGGCUCAAUGGCUCGGGCCCACUUGAUUUACAACAGUCGCCACUUGGCCA--AGUGC
.((((((((.....(.(((......))).)................--....(((....((((.(((((........))))).))))((((......))))))))))))))).--..... ( -33.80)
>DroYak_CAF1 18665 107 + 1
GGGCCAAGUUUGCAUGCCAAAAAG-----------GCGAACAUAAA--AUAAGGCAAACAAGUUGGCUCAAUGGCGCGGGCCCACUUGAUUUACAACAGUCGCCACUUGGCCAAAAGUGC
.((((((((.....((((.....)-----------)))........--....(((...(((((.(((((........))))).)))))....((....)).)))))))))))........ ( -36.80)
>consensus
GGGCCAAGUUUGCAUGCCAAAAA__________AAGCGAAAAUAAA_AAAGAGGCAAACAAGUUGGCUCAAUGGCUCGGGCCCACUUGAUUUACAACAGUCGCCACUUGGCCA_AAGUGC
.((((((((..((.((((..................................))))..(((((.(((((........))))).))))).............)).))))))))........ (-32.26 = -32.30 +   0.04)

alignment

secondary structure

dotplot

Window 9

Location	16,393,673 – 16,393,768
Length	95
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	86.26
Mean single sequence MFE	-34.51
Consensus MFE	-31.00
Energy contribution	-31.24
Covariance contribution	0.24
Combinations/Pair	1.04
Mean z-score	-2.52
Structure conservation index	0.90
SVM decision value	2.87
SVM RNA-class probability	0.997479
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 16393673 95 - 22407834
GCACUU-UGGCCAAGUGGCGACUGUUGUAAAUCAAGUGGGCCCGAGCCAUUGAGCCAACUUGUUUGCCGCUUU------------------------UUUUUGGCAUGCAAACUUGGCAC
......-..((((((((((.((....))...((((...(((....))).)))))))...((((.(((((....------------------------....))))).))))))))))).. ( -32.40)
>DroSec_CAF1 18219 108 - 1
GCACUU-UGGCCAAGUGGCGACUGUUGUAAAUCAAGUGGGCCCGAGCCAUUGAGCCAACUUAUUUGCCUCUUU-UUUAUUUUCGCUU----------UUUUUGGCAUGCAAACUUGGCCC
......-.(((((((((((((..((((....((((...(((....))).))))..))))....))))).....-.........(((.----------.....)))......)))))))). ( -33.40)
>DroSim_CAF1 16724 109 - 1
GCACUU-UGGCCAAGUGGCGACUGUUGUAAAUCAAGUGGGCCCGAGCCAUUGAGCCAACUUGUUUGCCUCUUUUUUUAUUUUCGCUU----------UUUUUGGCAUGCAAACUUGGCCC
......-.((((((((.(((...(..(((((.(((((.(((.(((....))).))).))))))))))..).............(((.----------.....))).)))..)))))))). ( -34.80)
>DroEre_CAF1 14848 116 - 1
GCACU--UGGCCAAGUGGCGACUGUUGUAAAUCAAGUGGGCCCGAGCCAUUGAGCCAACUUGCUUGCCUUAU--UUUAUUUUCCCUUUUUCCCCACUUUUUUGGCAUGCAAACUUGGCCC
.....--.(((((((((((.((....))...((((...(((....))).)))))))...((((.((((....--............................)))).)))))))))))). ( -34.55)
>DroYak_CAF1 18665 107 - 1
GCACUUUUGGCCAAGUGGCGACUGUUGUAAAUCAAGUGGGCCCGCGCCAUUGAGCCAACUUGUUUGCCUUAU--UUUAUGUUCGC-----------CUUUUUGGCAUGCAAACUUGGCCC
........((((((((((((((.((((....((((...(((....))).))))..))))..).)))))....--....(((..((-----------(.....)))..))).)))))))). ( -37.40)
>consensus
GCACUU_UGGCCAAGUGGCGACUGUUGUAAAUCAAGUGGGCCCGAGCCAUUGAGCCAACUUGUUUGCCUCUUU_UUUAUUUUCGCUU__________UUUUUGGCAUGCAAACUUGGCCC
........(((((((((((.((....))...((((...(((....))).)))))))...((((.((((..................................)))).)))))))))))). (-31.00 = -31.24 +   0.24)

alignment

secondary structure

dotplot

Window 0

Location	16,393,696 – 16,393,798
Length	102
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	88.91
Mean single sequence MFE	-30.26
Consensus MFE	-26.94
Energy contribution	-27.18
Covariance contribution	0.24
Combinations/Pair	1.05
Mean z-score	-1.46
Structure conservation index	0.89
SVM decision value	0.58
SVM RNA-class probability	0.790304
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 16393696 102 - 22407834
----------ACACACACGAAAAAUCGGGCCCAUAACUCAGCACUU-UGGCCAAGUGGCGACUGUUGUAAAUCAAGUGGGCCCGAGCCAUUGAGCCAACUUGUUUGCCGCUUU-------
----------...((.((((....((((((((((....(((((...-(.(((....))).).)))))........))))))))))((......))....)))).)).......------- ( -29.90)
>DroSec_CAF1 18249 108 - 1
----------ACACACACGAAAAAUCGGGCCCAUAACUCAGCACUU-UGGCCAAGUGGCGACUGUUGUAAAUCAAGUGGGCCCGAGCCAUUGAGCCAACUUAUUUGCCUCUUU-UUUAUU
----------........((((((((((((((((....(((((...-(.(((....))).).)))))........))))))))))......(((.(((.....))).))))))-)))... ( -31.80)
>DroSim_CAF1 16754 109 - 1
----------ACACACACGAAAAAUCGGGCCCAUAACUCAGCACUU-UGGCCAAGUGGCGACUGUUGUAAAUCAAGUGGGCCCGAGCCAUUGAGCCAACUUGUUUGCCUCUUUUUUUAUU
----------........((((((((((((((((....(((((...-(.(((....))).).)))))........))))))))))......(((.(((.....))).))).))))))... ( -31.90)
>DroEre_CAF1 14888 116 - 1
ACACACACACACACACACGGGAAAUCGGGCCCAUAACUCAGCACU--UGGCCAAGUGGCGACUGUUGUAAAUCAAGUGGGCCCGAGCCAUUGAGCCAACUUGCUUGCCUUAU--UUUAUU
...................((...((((((((((....(((((..--(.(((....))).).)))))........)))))))))).))...((((......)))).......--...... ( -34.10)
>DroYak_CAF1 18694 108 - 1
----------ACACACACGAAAAAUCGAGCCCAUAACUCAGCACUUUUGGCCAAGUGGCGACUGUUGUAAAUCAAGUGGGCCCGCGCCAUUGAGCCAACUUGUUUGCCUUAU--UUUAUG
----------...((.((((......(((.......))).......(((((..(((((((.(..((........))..).....)))))))..))))).)))).))......--...... ( -23.60)
>consensus
__________ACACACACGAAAAAUCGGGCCCAUAACUCAGCACUU_UGGCCAAGUGGCGACUGUUGUAAAUCAAGUGGGCCCGAGCCAUUGAGCCAACUUGUUUGCCUCUUU_UUUAUU
.................(((....((((((((((....(((((....(.(((....))).).)))))........))))))))))....)))............................ (-26.94 = -27.18 +   0.24)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:52:28 2006