Locus 5926

Sequence ID	3L_DroMel_CAF1
Location	15,909,915 – 15,910,062
Length	147
Max. P	0.703475

overview

Window 2

Location	15,909,915 – 15,910,023
Length	108
Sequences	5
Columns	109
Reading direction	forward
Mean pairwise identity	93.12
Mean single sequence MFE	-20.74
Consensus MFE	-17.84
Energy contribution	-17.92
Covariance contribution	0.08
Combinations/Pair	1.14
Mean z-score	-1.33
Structure conservation index	0.86
SVM decision value	0.36
SVM RNA-class probability	0.703475
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 15909915 108 + 23771897
GUUUCGUUUCAGUGCGGUUUUUGUUCAUAUUUUCUUGCCAUAUUGUUUUCAGCAUACACUGGCUUUUCCUCAAUUAUGGCGAU-AUGUUCACUUCUAUCCAUCGCCUCU
..........((.(((((...((..((((((.....(((((((((.....(((........)))......))).)))))))))-)))..)).........))))))).. ( -17.80)
>DroSec_CAF1 11632 109 + 1
GUUUCGUUUCAGUGCGGGUUUUGUUCAUAUUUUCUUGCCAUAUUGUUUUCAGCAUACACUGGCUUUUCCUCAAUUAUGGCGAUGAUGUUCACUUCUAUCCAUCGCCUGU
.........(((.((((((...((..(((((...(((((((((((.....(((........)))......))).)))))))).)))))..))....))))...))))). ( -22.00)
>DroSim_CAF1 11897 109 + 1
GUUUCGUUUCAGUGCGGGUUUUGUUCAUAUUUUCUUGCCAUAUUGUUUUCAGCAUACACUGGCUUUUCCUCAAUUAUGGCGAUGAUGUUCACUUCUAUCCAUCGCCUGU
.........(((.((((((...((..(((((...(((((((((((.....(((........)))......))).)))))))).)))))..))....))))...))))). ( -22.00)
>DroEre_CAF1 9414 109 + 1
GUUUGGCUUCAGAGCGCGUUUUCUUCAUAUUUUCUUGCCAUAUUGCUUUCAGCAUCCACUGGCUUUUCCUCAAUUUUGGCGAUGAUGCUCACUUCUAUCCAUCGCCCGU
.....(((....)))(((..................((((...(((.....))).....))))..............((((((((((........))).)))))))))) ( -21.50)
>DroYak_CAF1 9437 109 + 1
CUUUUGUUUUAGUGCGGGUUUUCUUCAUAUUCUCUUGCCAUAUUGCUUUCAGCAUCCACUGGCUUUUCCUCAAUUAUGGCGAUGAUGCUCACUUCUAUCCAUCGCCUGU
.............((((((.................(((((((((.....(((........)))......))).))))))(((((((........))).)))))))))) ( -20.40)
>consensus
GUUUCGUUUCAGUGCGGGUUUUGUUCAUAUUUUCUUGCCAUAUUGUUUUCAGCAUACACUGGCUUUUCCUCAAUUAUGGCGAUGAUGUUCACUUCUAUCCAUCGCCUGU
...((((......))))...................((((...(((.....))).....))))..............((((((((((........))).)))))))... (-17.84 = -17.92 +   0.08)

alignment

secondary structure

dotplot

Window 3

Location	15,909,915 – 15,910,023
Length	108
Sequences	5
Columns	109
Reading direction	reverse
Mean pairwise identity	93.12
Mean single sequence MFE	-20.77
Consensus MFE	-18.10
Energy contribution	-18.74
Covariance contribution	0.64
Combinations/Pair	1.04
Mean z-score	-1.28
Structure conservation index	0.87
SVM decision value	0.32
SVM RNA-class probability	0.685490
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 15909915 108 - 23771897
AGAGGCGAUGGAUAGAAGUGAACAU-AUCGCCAUAAUUGAGGAAAAGCCAGUGUAUGCUGAAAACAAUAUGGCAAGAAAAUAUGAACAAAAACCGCACUGAAACGAAAC
..(((((...((((...(....).)-)))((((((.(((.((.....))(((....))).....)))))))))....................))).)).......... ( -18.40)
>DroSec_CAF1 11632 109 - 1
ACAGGCGAUGGAUAGAAGUGAACAUCAUCGCCAUAAUUGAGGAAAAGCCAGUGUAUGCUGAAAACAAUAUGGCAAGAAAAUAUGAACAAAACCCGCACUGAAACGAAAC
.((((((...(((.((.(....).)))))((((((.(((.((.....))(((....))).....)))))))))....................))).)))......... ( -22.10)
>DroSim_CAF1 11897 109 - 1
ACAGGCGAUGGAUAGAAGUGAACAUCAUCGCCAUAAUUGAGGAAAAGCCAGUGUAUGCUGAAAACAAUAUGGCAAGAAAAUAUGAACAAAACCCGCACUGAAACGAAAC
.((((((...(((.((.(....).)))))((((((.(((.((.....))(((....))).....)))))))))....................))).)))......... ( -22.10)
>DroEre_CAF1 9414 109 - 1
ACGGGCGAUGGAUAGAAGUGAGCAUCAUCGCCAAAAUUGAGGAAAAGCCAGUGGAUGCUGAAAGCAAUAUGGCAAGAAAAUAUGAAGAAAACGCGCUCUGAAGCCAAAC
...((((((((.............))))))))........((....((((...(.(((.....))).).))))............(((........)))....)).... ( -21.42)
>DroYak_CAF1 9437 109 - 1
ACAGGCGAUGGAUAGAAGUGAGCAUCAUCGCCAUAAUUGAGGAAAAGCCAGUGGAUGCUGAAAGCAAUAUGGCAAGAGAAUAUGAAGAAAACCCGCACUAAAACAAAAG
...((((((((.............))))))))..............((((...(.(((.....))).).)))).................................... ( -19.82)
>consensus
ACAGGCGAUGGAUAGAAGUGAACAUCAUCGCCAUAAUUGAGGAAAAGCCAGUGUAUGCUGAAAACAAUAUGGCAAGAAAAUAUGAACAAAACCCGCACUGAAACGAAAC
.((((((...(((.((.(....).)))))((((((.(((......(((........))).....)))))))))....................))).)))......... (-18.10 = -18.74 +   0.64)

alignment

secondary structure

dotplot

Window 4

Location	15,909,944 – 15,910,062
Length	118
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	89.69
Mean single sequence MFE	-30.04
Consensus MFE	-21.22
Energy contribution	-21.18
Covariance contribution	-0.04
Combinations/Pair	1.04
Mean z-score	-1.81
Structure conservation index	0.71
SVM decision value	-0.03
SVM RNA-class probability	0.517618
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 15909944 118 + 23771897
UUUUCUUGCCAUAUUGUUUUCAGCAUACACUGGCUUUUCCUCAAUUAUGGCGAU-AUGUUCACUUCUAUCCAUCGCCUCUUAUUGUUAUUAUCGGC-AGGGGAAUGGGAUAAACUAGACC
((..((((((.........((((......))))........((((...((((((-..((........))..))))))....))))........)))-)))..))(((......))).... ( -25.20)
>DroSec_CAF1 11661 119 + 1
UUUUCUUGCCAUAUUGUUUUCAGCAUACACUGGCUUUUCCUCAAUUAUGGCGAUGAUGUUCACUUCUAUCCAUCGCCUGUUAGUGUUAUUAUCGGC-AGGGGAAUGGGGUAAAAUGGACC
...(((((((((((((.....(((........)))......))).)))))))).)).(((((.((.(((((.((.(((((..(((....)))..))-))).))...))))).))))))). ( -35.50)
>DroSim_CAF1 11926 119 + 1
UUUUCUUGCCAUAUUGUUUUCAGCAUACACUGGCUUUUCCUCAAUUAUGGCGAUGAUGUUCACUUCUAUCCAUCGCCUGUUAUUGUUAUUAUCGGC-AGGGGAUUGGGGUAAACUGGACC
...(((((((((((((.....(((........)))......))).)))))))).)).(((((.((.((((((((.((((((..((....))..)))-))).)))..))))))).))))). ( -32.30)
>DroEre_CAF1 9443 108 + 1
UUUUCUUGCCAUAUUGCUUUCAGCAUCCACUGGCUUUUCCUCAAUUUUGGCGAUGAUGCUCACUUCUAUCCAUCGCCCGUAAUUGUUAUUAUCGGA-AGGGGACUGG-GU----------
.......((((...(((.....))).....))))...(((((......((((((((((........))).)))))))((((((....)))).))..-.)))))....-..---------- ( -26.10)
>DroYak_CAF1 9466 119 + 1
UUCUCUUGCCAUAUUGCUUUCAGCAUCCACUGGCUUUUCCUCAAUUAUGGCGAUGAUGCUCACUUCUAUCCAUCGCCUGUAAUUGUUAUUAUCGGAAAGGGGAAUGG-GUAAAAUAGACC
.(((.(((((.((((.(..((((......))))(((((((.(((((((((((((((((........))).))))))).)))))))........)))))))).)))))-))))...))).. ( -31.10)
>consensus
UUUUCUUGCCAUAUUGUUUUCAGCAUACACUGGCUUUUCCUCAAUUAUGGCGAUGAUGUUCACUUCUAUCCAUCGCCUGUUAUUGUUAUUAUCGGC_AGGGGAAUGGGGUAAAAUAGACC
.......((((...(((.....))).....))))...(((((......((((((((((........))).)))))))......((.......))....)))))................. (-21.22 = -21.18 +  -0.04)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:04:16 2006