Locus 2638

Sequence ID	2R_DroMel_CAF1
Location	9,321,944 – 9,322,082
Length	138
Max. P	0.953436

overview

Window 6

Location	9,321,944 – 9,322,042
Length	98
Sequences	6
Columns	106
Reading direction	reverse
Mean pairwise identity	73.91
Mean single sequence MFE	-28.14
Consensus MFE	-19.38
Energy contribution	-19.85
Covariance contribution	0.48
Combinations/Pair	1.41
Mean z-score	-1.62
Structure conservation index	0.69
SVM decision value	1.43
SVM RNA-class probability	0.953436
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 9321944 98 - 20766785
CUCUUUUGCCCAACAUA--------CCUUAGCCGAAAAGGGACAACCCUUGUCUCUCGCUUUUGGCCAUUUGCCGCACUCUUCUUUCCACCCAGUGCGCUUGCCCU
.......((........--------.....((((((((((((((.....)))))))...))))))).....((.(((((.............)))))))..))... ( -21.82)
>DroSec_CAF1 206621 98 - 1
CUCUUUAACCCAACAUC--------CUUUGGCCGGAAAGGGACAACUCUCGUGUCUCCCUUUUGGCCAUUUGCCGCACUCUUCUGGCCGCUCAGUGCGCGUGCCCU
.................--------...((((((.(((((((..((....))...)))))))))))))...(((((.(....((((....)))).).))).))... ( -27.90)
>DroSim_CAF1 193922 98 - 1
CUCUUUAACCCAACAUC--------CUUUGGCCGGAAAGGGACAACUAUCGUGUCUCCCUUUUGGCCAUUUGCCGCACUCUUCUGGCCGCCCAGUGCGCGUGCCCU
.................--------...((((((.(((((((..((....))...)))))))))))))...(((((.(....((((....)))).).))).))... ( -30.20)
>DroEre_CAF1 191904 106 - 1
CUCUGUCGCCCAACAUCCCAAUCUCCCUUGGCCGGAAAGGGAUAACCCUCGAGUCCUCCUUUCGGCCAUUCGCCGCACUCUUCUGGGCGUCCAGUGCGCCUGCCCU
..(((.((((((............(...(((((((((.(((((.........)))))..)))))))))...)...........))))))..)))............ ( -29.40)
>DroYak_CAF1 191208 98 - 1
CUCUGUAGCCCCACAUC--------CCUUGGCCGAAAAGGGACAACCCUCGAGUCUCCCUUUCGGCCAUUCGCCGCACUCUUCUGGGCGCCAAGUGCGCCUGUCCU
...((..((........--------...(((((((((.((((..((......)).)))))))))))))...))..)).......((((((.....))))))..... ( -31.94)
>DroPer_CAF1 169312 97 - 1
UUCAU-CGCCUAGUUGC--------CACUAGCCAGAGCGAGACCACAGCCGGGUUCCAGCAUUAAGCUCUAGCUGCACUGCUCUGGGCUACCACUGCGCCUGCCCU
.((.(-(((((.((((.--------...)))).)).))))))........((((....(((...(((((.(((......)))..))))).....)))....)))). ( -27.60)
>consensus
CUCUUUAGCCCAACAUC________CCUUGGCCGGAAAGGGACAACCCUCGUGUCUCCCUUUUGGCCAUUUGCCGCACUCUUCUGGCCGCCCAGUGCGCCUGCCCU
............................(((((((((.((((((.......))))))..)))))))))...((.(((((.............)))))))....... (-19.38 = -19.85 +   0.48)

alignment

secondary structure

dotplot

Window 7

Location	9,321,984 – 9,322,082
Length	98
Sequences	6
Columns	98
Reading direction	forward
Mean pairwise identity	73.19
Mean single sequence MFE	-30.88
Consensus MFE	-8.86
Energy contribution	-8.03
Covariance contribution	-0.83
Combinations/Pair	1.45
Mean z-score	-2.17
Structure conservation index	0.29
SVM decision value	0.03
SVM RNA-class probability	0.551055
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 9321984 98 + 20766785
GCCAAAAGCGAGAGACAAGGGUUGUCCCUUUUCGGCUAAGGUAUGUUGGGCAAAAGAGCUUUAAGCUGGCCCAGAAACGUUAAAAGAAACGUCAAAAC
(((...(((..((((..((((....)))))))).)))..)))...((((((.....(((.....))).))))))..(((((......)))))...... ( -26.70)
>DroPse_CAF1 168918 96 + 1
CUUAAUGCUGGAACCCGGCUGUGGUCUCGCUCUGGCUAGUGGCAACUAGGCG-AUGAACUCAUCGCUGACACAGAAACGCCA-CAGAAACGUCAGAAC
.......((((....((.(((((((.....((((.(((((....)))))(((-(((....)))))).....))))...))))-)))...))))))... ( -32.30)
>DroSec_CAF1 206661 98 + 1
GCCAAAAGGGAGACACGAGAGUUGUCCCUUUCCGGCCAAAGGAUGUUGGGUUAAAGAGCUUUAAGCUGGCCCAGAAACGUCAAAAGAAACGUCAAAAC
(((.(((((((.(.((....))).)))))))..))).....(((((((((((....(((.....)))))))))...)))))................. ( -29.80)
>DroSim_CAF1 193962 98 + 1
GCCAAAAGGGAGACACGAUAGUUGUCCCUUUCCGGCCAAAGGAUGUUGGGUUAAAGAGCUUUAAGCUGGCCCAGAAACGUCAAAAGAAACGUCAAAAC
(((.((((((((((......))).)))))))..))).....(((((((((((....(((.....)))))))))...)))))................. ( -27.90)
>DroYak_CAF1 191248 97 + 1
GCCGAAAGGGAGACUCGAGGGUUGUCCCUUUUCGGCCAAGGGAUGUGGGGCUACAGAGCUUUAAGCUGGCCCAGAAACGUCA-AAGAAACGUCAAAAC
(((((((((((((((....)))).)))).))))))).....(((((.(((((....(((.....))))))))....))))).-............... ( -36.30)
>DroPer_CAF1 169352 96 + 1
CUUAAUGCUGGAACCCGGCUGUGGUCUCGCUCUGGCUAGUGGCAACUAGGCG-AUGAACUCAUCGCUGACACAGAAACGCCA-CAGAAACGUCAGAAC
.......((((....((.(((((((.....((((.(((((....)))))(((-(((....)))))).....))))...))))-)))...))))))... ( -32.30)
>consensus
GCCAAAAGGGAGACACGAGAGUUGUCCCUUUCCGGCCAAAGGAUGUUGGGCUAAAGAGCUUUAAGCUGGCCCAGAAACGUCA_AAGAAACGUCAAAAC
((((..((((.(((((....).)))).))))..(.((((......)))).)...............))))......((((........))))...... ( -8.86 =  -8.03 +  -0.83)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:35:09 2006