Locus 2312

Sequence ID	2R_DroMel_CAF1
Location	8,500,294 – 8,500,446
Length	152
Max. P	0.806356

overview

Window 7

Location	8,500,294 – 8,500,414
Length	120
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	90.97
Mean single sequence MFE	-39.35
Consensus MFE	-31.31
Energy contribution	-32.00
Covariance contribution	0.69
Combinations/Pair	1.12
Mean z-score	-1.81
Structure conservation index	0.80
SVM decision value	0.47
SVM RNA-class probability	0.749491
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 8500294 120 + 20766785
GACACUCUUUCGCUUUCGAGGAGAUCUAUCUCCUUAGAUCCAUUAGUUUGGACCUAUCGAGGCAUCACUGUAGUCUUGAGCCGCACAGUGAAAAGACGAUGGAGCCAAGCUAAAGUCGUG
(((........(..((..((((((....))))))..))..).(((((((((..((((((.....(((((((.((........))))))))).....))))))..))))))))).)))... ( -42.30)
>DroSec_CAF1 12859 120 + 1
GACACUCUUUCGCUUUGGAGGAGAUCUAUCUCCUUAGAUCCCAAGAUUUGAACCUAUCGAGGCUUCACUGUAGUCUUGAGCCGCUCAGUGAAAAGACGAUGGAGCCAAGCCAAAGUCGUG
..(((.((((.((((.((.((.((((((......))))))))...........((((((....(((((((.(((........))))))))))....))))))..)))))).))))..))) ( -37.20)
>DroSim_CAF1 12744 120 + 1
GACACUCUUUCGCUUUGGAGGAGAUCUAUCUCCUUAGAUCCCUAGGUUUGGACCUAGCGAGGCAUCACUGUAGUCUUGAGCCGCUCAGUGAAAAGACGAUGGAGCCAAGCCAAAGUCGUG
..(((......(((((((((((((....)))))))......((((((....)))))))))))).((((((.(((........)))))))))...(((..(((.......)))..)))))) ( -40.00)
>DroEre_CAF1 10452 120 + 1
GGCACUCUUUCGCCUUAGAAGGGACUUAGCUCCUAAGAUCCAUUAGCUUGGACCUAUCGAGGCAUCACUGUAGUCUUGAGCCGCUCAGUGAAAAGACGAUGGAGCCAAGCCAAAGUCGUG
(((.((((.(((((((.((.(((.(((((...))))).((((......))))))).))))))).((((((.(((........)))))))))......)).))))....)))......... ( -37.90)
>consensus
GACACUCUUUCGCUUUGGAGGAGAUCUAUCUCCUUAGAUCCAUAAGUUUGGACCUAUCGAGGCAUCACUGUAGUCUUGAGCCGCUCAGUGAAAAGACGAUGGAGCCAAGCCAAAGUCGUG
(((........(..((..(((((......)))))..))..)...(((((((..((((((.....((((((.(((........))))))))).....))))))..)))))))...)))... (-31.31 = -32.00 +   0.69)

alignment

secondary structure

dotplot

Window 8

Location	8,500,294 – 8,500,414
Length	120
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	90.97
Mean single sequence MFE	-39.48
Consensus MFE	-30.69
Energy contribution	-30.82
Covariance contribution	0.12
Combinations/Pair	1.06
Mean z-score	-2.04
Structure conservation index	0.78
SVM decision value	0.63
SVM RNA-class probability	0.806356
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 8500294 120 - 20766785
CACGACUUUAGCUUGGCUCCAUCGUCUUUUCACUGUGCGGCUCAAGACUACAGUGAUGCCUCGAUAGGUCCAAACUAAUGGAUCUAAGGAGAUAGAUCUCCUCGAAAGCGAAAGAGUGUC
(((..((((.(((((((............((((((((.(........))))))))).)))((((((((((((......)))))))).(((((....))))))))))))).)))).))).. ( -39.92)
>DroSec_CAF1 12859 120 - 1
CACGACUUUGGCUUGGCUCCAUCGUCUUUUCACUGAGCGGCUCAAGACUACAGUGAAGCCUCGAUAGGUUCAAAUCUUGGGAUCUAAGGAGAUAGAUCUCCUCCAAAGCGAAAGAGUGUC
(((..((((.((((((.....(((...(((((((((((.......).)).))))))))...)))(((((((........)))))))((((((....)))))))).)))).)))).))).. ( -36.70)
>DroSim_CAF1 12744 120 - 1
CACGACUUUGGCUUGGCUCCAUCGUCUUUUCACUGAGCGGCUCAAGACUACAGUGAUGCCUCGCUAGGUCCAAACCUAGGGAUCUAAGGAGAUAGAUCUCCUCCAAAGCGAAAGAGUGUC
(((..((((.((((((.(((..((.....(((((((((.......).)).)))))).....))((((((....)))))))))....((((((....)))))))).)))).)))).))).. ( -38.10)
>DroEre_CAF1 10452 120 - 1
CACGACUUUGGCUUGGCUCCAUCGUCUUUUCACUGAGCGGCUCAAGACUACAGUGAUGCCUCGAUAGGUCCAAGCUAAUGGAUCUUAGGAGCUAAGUCCCUUCUAAGGCGAAAGAGUGCC
(((..(((((((((((((((((((.....(((((((((.......).)).)))))).....))))(((((((......)))))))..)))))))))))(((....)))..)))).))).. ( -43.20)
>consensus
CACGACUUUGGCUUGGCUCCAUCGUCUUUUCACUGAGCGGCUCAAGACUACAGUGAUGCCUCGAUAGGUCCAAACCAAGGGAUCUAAGGAGAUAGAUCUCCUCCAAAGCGAAAGAGUGUC
(((..((((.((((..((((((((.....(((((((((.......).)).)))))).....))))((((((........))))))..))))..............)))).)))).))).. (-30.69 = -30.82 +   0.12)

alignment

secondary structure

dotplot

Window 9

Location	8,500,334 – 8,500,446
Length	112
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	78.55
Mean single sequence MFE	-32.50
Consensus MFE	-18.31
Energy contribution	-19.82
Covariance contribution	1.51
Combinations/Pair	1.32
Mean z-score	-1.98
Structure conservation index	0.56
SVM decision value	0.61
SVM RNA-class probability	0.800416
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 8500334 112 + 20766785
CAUUAGUUUGGACCUAUCGAGGCAUCACUGUAGUCUUGAGCCGCACAGUGAAAAGACGAUGGAGCCAAGCUAAAGUCGUGUCCACAGCGGCAACAAU------AACAACAACCUAAAC--
..(((((((((..((((((.....(((((((.((........))))))))).....))))))..))))))))).(((((.......)))))......------...............-- ( -34.40)
>DroSec_CAF1 12899 112 + 1
CCAAGAUUUGAACCUAUCGAGGCUUCACUGUAGUCUUGAGCCGCUCAGUGAAAAGACGAUGGAGCCAAGCCAAAGUCGUGUCCACAGCGGCAACAAC------AACAACAACCUAAAC--
.((((((((((((((....))).))))....))))))).((((((..(((....(((..(((.......)))..))).....)))))))))......------...............-- ( -30.60)
>DroSim_CAF1 12784 112 + 1
CCUAGGUUUGGACCUAGCGAGGCAUCACUGUAGUCUUGAGCCGCUCAGUGAAAAGACGAUGGAGCCAAGCCAAAGUCGUGUCCACAGCGGCAACAAC------AACAACAAUCUAAAC--
.((((((....))))))((((((.........)))))).((((((..(((....(((..(((.......)))..))).....)))))))))......------...............-- ( -31.90)
>DroEre_CAF1 10492 109 + 1
CAUUAGCUUGGACCUAUCGAGGCAUCACUGUAGUCUUGAGCCGCUCAGUGAAAAGACGAUGGAGCCAAGCCAAAGUCGUGUCCGCAGCGGCAA---C------AACAACAACUUAAAC--
.....((((((..((((((.....((((((.(((........))))))))).....))))))..))))))....(((((.......)))))..---.------...............-- ( -33.10)
>DroYak_CAF1 13458 112 + 1
CAUUAGUGUGGGCCUAUCGAGGCAUCACUGUAGUUUUGAGCCGCUCAGUGAAAAGACGAUGGAGCCAAGCCAAAGUCGUGUCCGCAGCGGCAAUAAC------AACAACAACUUAAAC--
...(((((...((((....))))..)))))..(((....((((((..(.((...(((..(((.......)))..)))...)))..))))))...)))------...............-- ( -31.70)
>DroAna_CAF1 9680 106 + 1
CU---GUUUG-GUUUAUGGACGCUCCACUGUAAUUUUGUGGCGCGGAUUGAACAUGCGA----------CUUAAGUCGUGUCCAAAGAUCCACUAGCCUGUGCUCCAACAACUCAAGCAA
.(---(((((-(((..(((((((.((((.........)))).))(((((....((((((----------(....))))))).....)))))..........).))))..))).)))))). ( -33.30)
>consensus
CAUUAGUUUGGACCUAUCGAGGCAUCACUGUAGUCUUGAGCCGCUCAGUGAAAAGACGAUGGAGCCAAGCCAAAGUCGUGUCCACAGCGGCAACAAC______AACAACAACCUAAAC__
.....((((((.....(((((((.........)))))))((((((..(((....(((..(((.......)))..))).....))))))))).....................)))))).. (-18.31 = -19.82 +   1.51)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:26:34 2006