Locus 4500

Sequence ID	2L_DroMel_CAF1
Location	12,903,756 – 12,903,897
Length	141
Max. P	0.819570

overview

Window 8

Location	12,903,756 – 12,903,874
Length	118
Sequences	6
Columns	119
Reading direction	forward
Mean pairwise identity	88.68
Mean single sequence MFE	-31.82
Consensus MFE	-24.72
Energy contribution	-25.38
Covariance contribution	0.67
Combinations/Pair	1.11
Mean z-score	-3.10
Structure conservation index	0.78
SVM decision value	0.68
SVM RNA-class probability	0.819570
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 12903756 118 + 22407834
GCCAAAAAAAGAUUGCUGCUGGAAAUUGCGAAUGGAAAUGAAGGUGAAAAUAAAAAUUGGCAUAGGCACGUAAAUUAUGUGCUGCCAAUUAGCAGGCCACAA-AUUUCUGCACGCAAUU
..........(((((((((.(((((((.....(((...((...((....))...((((((((...(((((((...)))))))))))))))..))..)))..)-))))))))).)))))) ( -33.20)
>DroSec_CAF1 81383 118 + 1
GCCAAAAAAAGAUUGCUGCUGGAAAUUGCGAAUGGAAAUGAAGGUGAAAAUAAAAAUUGGCAUAGGCACGUAAAUUAUGUGCUGCCAAUUAGCAGGCCACAA-AUUUCUGCACGCAAUU
..........(((((((((.(((((((.....(((...((...((....))...((((((((...(((((((...)))))))))))))))..))..)))..)-))))))))).)))))) ( -33.20)
>DroSim_CAF1 86077 118 + 1
GCCAAAAAAAGAUUGCUGCUGGAAAUUGCGAAUGGAAAUGAAGGUGAAAAUAAAAAUUGGCAUAGGCACGUAAAUUAUGUGCUGCCAAUUAGCAGGCCACAA-AUUUCUGCACGCAAUU
..........(((((((((.(((((((.....(((...((...((....))...((((((((...(((((((...)))))))))))))))..))..)))..)-))))))))).)))))) ( -33.20)
>DroEre_CAF1 86791 114 + 1
GCCAAAAAAAC--UG--GCUGGAAAUUGCGAAUGGAAAUGAAGGUGAAAAUAAAAAUUGGCAUAGGCACGUAAAUUAUGUGCUGCCAAUUAGCAGGCCACAA-AUUCCUGCACGCAAUG
((((.......--))--)).....((((((........................((((((((...(((((((...))))))))))))))).(((((......-...))))).)))))). ( -35.10)
>DroYak_CAF1 83765 119 + 1
GCCAAAAAAAGAUUGCUCCUGGAAAUUGGGAAUGGAAAUGAAGGUGAAAAUAAAAAUUGGCAUAGGCACGUAAAUUAUGUGCUGCCAAUUAGCAGGCCACAAAAUUCCUGCACGCAAUU
..........(((((((((..(...)..)))............((.........((((((((...(((((((...))))))))))))))).(((((..........))))))))))))) ( -31.70)
>DroAna_CAF1 102957 111 + 1
------AAAGCACUGCAACUGGAAGUGGGCUAAGGGAAUAAGCACGAGAAAUAAAUUUGGCAUAAGCACCUAAAUUAUGUGCUGCCAAUUAGCAGGCCACAA-AA-UCUGCACGCAAUU
------..(((.(..(........)..))))..........((.............((((((...((((.........))))))))))...(((((......-..-)))))..)).... ( -24.50)
>consensus
GCCAAAAAAAGAUUGCUGCUGGAAAUUGCGAAUGGAAAUGAAGGUGAAAAUAAAAAUUGGCAUAGGCACGUAAAUUAUGUGCUGCCAAUUAGCAGGCCACAA_AUUUCUGCACGCAAUU
.......................(((((((........................(((((((...((((((((...))))))))))))))).(((((..........))))).))))))) (-24.72 = -25.38 +   0.67)

alignment

secondary structure

dotplot

Window 9

Location	12,903,795 – 12,903,897
Length	102
Sequences	6
Columns	104
Reading direction	forward
Mean pairwise identity	84.58
Mean single sequence MFE	-26.72
Consensus MFE	-18.81
Energy contribution	-18.70
Covariance contribution	-0.11
Combinations/Pair	1.11
Mean z-score	-2.46
Structure conservation index	0.70
SVM decision value	0.16
SVM RNA-class probability	0.610552
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 12903795 102 + 22407834
GAAGGUGAAAAUAAAAAUUGGCAUAGGCACGUAAAUUAUGUGCUGCCAAUUAGCAGGCCACAAAUUUCUGCACGCAAUUCUUCUCU--CGUCCUUUUGAAAAAA
((((((((.......((((((((...(((((((...))))))))))))))).(((((.........)))))..............)--)).)))))........ ( -26.50)
>DroPse_CAF1 96439 97 + 1
GCGAAUGAAAA-----UUUGGCAUAGGCACGUAAAUUAUGUGCUGCCAAUUAGCAGGCAACAAAUUUCUGCACGCCAUUCUUCUCGAAGGUCCUUUAG-A-AAA
..(((((....-----.((((((...(((((((...)))))))))))))...(((((.........)))))....)))))((((.((((...))))))-)-).. ( -25.20)
>DroSec_CAF1 81422 101 + 1
GAAGGUGAAAAUAAAAAUUGGCAUAGGCACGUAAAUUAUGUGCUGCCAAUUAGCAGGCCACAAAUUUCUGCACGCAAUUCUUCCCU--CGUCCUUUUGGA-AAA
((.((.(((......((((((((...(((((((...))))))))))))))).(((((.........)))))......)))..)).)--).(((....)))-... ( -28.00)
>DroEre_CAF1 86826 101 + 1
GAAGGUGAAAAUAAAAAUUGGCAUAGGCACGUAAAUUAUGUGCUGCCAAUUAGCAGGCCACAAAUUCCUGCACGCAAUGCUGCUCU--CGUCCUUUUGCG-AAA
((((((((.......((((((((...(((((((...))))))))))))))).(((((.........)))))..(((....)))..)--)).)))))....-... ( -30.10)
>DroAna_CAF1 102990 99 + 1
AAGCACGAGAAAUAAAUUUGGCAUAAGCACCUAAAUUAUGUGCUGCCAAUUAGCAGGCCACAAAA-UCUGCACGCAAUUCUUCUCU--AGUCCUUUGG-A-GAA
..((.............((((((...((((.........))))))))))...(((((........-)))))..))......(((((--((....))))-)-)). ( -25.30)
>DroPer_CAF1 116524 97 + 1
GCGAAUGAAAA-----UUUGGCAUAGGCACGUAAAUUAUGUGCUGCCAAUUAGCAGGCAACAAAUUUCUGCACGCCAUUCUUCUCGAAGGUCCUUUAG-A-AAA
..(((((....-----.((((((...(((((((...)))))))))))))...(((((.........)))))....)))))((((.((((...))))))-)-).. ( -25.20)
>consensus
GAAGAUGAAAAUAAAAAUUGGCAUAGGCACGUAAAUUAUGUGCUGCCAAUUAGCAGGCCACAAAUUUCUGCACGCAAUUCUUCUCU__CGUCCUUUUG_A_AAA
.................(((((...((((((((...)))))))))))))...(((((.........)))))................................. (-18.81 = -18.70 +  -0.11)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:19:19 2006