Locus 5351

Sequence ID	3R_DroMel_CAF1
Location	14,037,871 – 14,038,005
Length	134
Max. P	0.988731

overview

Window 4

Location	14,037,871 – 14,037,966
Length	95
Sequences	6
Columns	105
Reading direction	forward
Mean pairwise identity	75.91
Mean single sequence MFE	-25.92
Consensus MFE	-14.94
Energy contribution	-15.63
Covariance contribution	0.69
Combinations/Pair	1.14
Mean z-score	-2.56
Structure conservation index	0.58
SVM decision value	2.13
SVM RNA-class probability	0.988731
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 14037871 95 + 27905053
AAGUGAUGCAAGUUUUUACUCAGCAGCAUUGCAGUGGCUGACUUGCCACAGCGUCACACUGAUGAAAAAAACUAUGC----------UACUAUUUACAUUGUAAC
.((((..((((((((((..(((.(((...(((.(((((......))))).))).....))).))).))))))).)))----------)))).............. ( -24.90)
>DroSec_CAF1 25302 95 + 1
AAGUGAUGCAAGUUUUUACUCAGCAGCAUUGCAGUGGCUGACUUGCCACAGCGUCACACUGAUGAAAAAAACUAUGC----------UACUACUUACUUUCUAUC
(((((..((((((((((..(((.(((...(((.(((((......))))).))).....))).))).))))))).)))----------...))))).......... ( -26.50)
>DroSim_CAF1 23358 95 + 1
AAGUGAUGCAAGUUUUUACUCAGCAGCAUUGCAGUGGCUGACUUGCCACAGCGUCACACUGAUGAAAAAAACUAUGC----------UACUACUUACUUUCUAUC
(((((..((((((((((..(((.(((...(((.(((((......))))).))).....))).))).))))))).)))----------...))))).......... ( -26.50)
>DroEre_CAF1 23949 101 + 1
AAGUGAUGCAAGUUUUUACUCUGCAGCACUGCAGUGGCUGACUUGCCACAGC--UACACUGCUGAAAAU-ACUGUUCUGUGAAAGCAUACAAUA-CAAUUCUAUC
.((((.(((((((....))).)))).))))((((((((......))).((((--......)))).....-)))))..(((....))).......-.......... ( -27.30)
>DroYak_CAF1 29512 102 + 1
AAGUGAUGCAAGUUUUUACUCUGCAGCAUUGCAGUGGCUGUCUUGCCACAGC--UACACUGAUGAAAAU-ACUGUUGUGUGAAACCAUACUAUUUUCAUUCUAGC
..(..((((.((........))...))))..).(((((......))))).((--((....(((((((((-(.....(((((....))))))))))))))).)))) ( -30.00)
>DroAna_CAF1 22403 91 + 1
AAGUGAAGCAAGUUUUUCAUCUGCAACCCUGCAGUGGCUUACUUUCCACUUGCUGGCACUGAGAGAAUAAAGGAAGU---------UUAAUAUUUUGUUU-----
.((((.(((((((.......(((((....))))).((........)))))))))..))))........(((.(((((---------.....))))).)))----- ( -20.30)
>consensus
AAGUGAUGCAAGUUUUUACUCAGCAGCAUUGCAGUGGCUGACUUGCCACAGCGUCACACUGAUGAAAAAAACUAUGC__________UACUAUUUACAUUCUAUC
..((((.((.............(((....))).(((((......))))).)).))))................................................ (-14.94 = -15.63 +   0.69)

alignment

secondary structure

dotplot

Window 5

Location	14,037,871 – 14,037,966
Length	95
Sequences	6
Columns	105
Reading direction	reverse
Mean pairwise identity	75.91
Mean single sequence MFE	-27.68
Consensus MFE	-14.90
Energy contribution	-17.10
Covariance contribution	2.20
Combinations/Pair	1.17
Mean z-score	-2.62
Structure conservation index	0.54
SVM decision value	2.12
SVM RNA-class probability	0.988329
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 14037871 95 - 27905053
GUUACAAUGUAAAUAGUA----------GCAUAGUUUUUUUCAUCAGUGUGACGCUGUGGCAAGUCAGCCACUGCAAUGCUGCUGAGUAAAAACUUGCAUCACUU
..................----------(((.(((((((((((.((((((...((.(((((......))))).)).)))))).)))).))))))))))....... ( -29.50)
>DroSec_CAF1 25302 95 - 1
GAUAGAAAGUAAGUAGUA----------GCAUAGUUUUUUUCAUCAGUGUGACGCUGUGGCAAGUCAGCCACUGCAAUGCUGCUGAGUAAAAACUUGCAUCACUU
..........((((.((.----------(((.(((((((((((.((((((...((.(((((......))))).)).)))))).)))).)))))))))))).)))) ( -30.50)
>DroSim_CAF1 23358 95 - 1
GAUAGAAAGUAAGUAGUA----------GCAUAGUUUUUUUCAUCAGUGUGACGCUGUGGCAAGUCAGCCACUGCAAUGCUGCUGAGUAAAAACUUGCAUCACUU
..........((((.((.----------(((.(((((((((((.((((((...((.(((((......))))).)).)))))).)))).)))))))))))).)))) ( -30.50)
>DroEre_CAF1 23949 101 - 1
GAUAGAAUUG-UAUUGUAUGCUUUCACAGAACAGU-AUUUUCAGCAGUGUA--GCUGUGGCAAGUCAGCCACUGCAGUGCUGCAGAGUAAAAACUUGCAUCACUU
....(((..(-((((((.((......))..)))))-)).))).((((..(.--((.(((((......))))).)).)..)))).((((((....)))).)).... ( -30.70)
>DroYak_CAF1 29512 102 - 1
GCUAGAAUGAAAAUAGUAUGGUUUCACACAACAGU-AUUUUCAUCAGUGUA--GCUGUGGCAAGACAGCCACUGCAAUGCUGCAGAGUAAAAACUUGCAUCACUU
((.((.(((((((((.(.((........))..).)-))))))))((((((.--((.(((((......))))).)).))))))...........)).))....... ( -26.60)
>DroAna_CAF1 22403 91 - 1
-----AAACAAAAUAUUAA---------ACUUCCUUUAUUCUCUCAGUGCCAGCAAGUGGAAAGUAAGCCACUGCAGGGUUGCAGAUGAAAAACUUGCUUCACUU
-----..............---------.................((((..(((((((((........)).((((......)))).......))))))).)))). ( -18.30)
>consensus
GAUAGAAAGUAAAUAGUA__________GCAUAGUUUUUUUCAUCAGUGUGACGCUGUGGCAAGUCAGCCACUGCAAUGCUGCAGAGUAAAAACUUGCAUCACUU
............................(((.((((((((((..(((..(...((.(((((......))))).)).)..)))..))).))))))))))....... (-14.90 = -17.10 +   2.20)

alignment

secondary structure

dotplot

Window 6

Location	14,037,898 – 14,038,005
Length	107
Sequences	6
Columns	118
Reading direction	forward
Mean pairwise identity	65.23
Mean single sequence MFE	-20.07
Consensus MFE	-8.70
Energy contribution	-9.20
Covariance contribution	0.50
Combinations/Pair	1.00
Mean z-score	-1.81
Structure conservation index	0.43
SVM decision value	0.89
SVM RNA-class probability	0.876286
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 14037898 107 + 27905053
AUUGCAGUGGCUGACUUGCCACAGCGUCACACUGAUGAAAAAAACUAUGC----------UACUAUUUACAUUGUAACUUAUGAUAUAAUUUGUAUAUCAAAUAAACCUAUCCCAAA-
...((((((((......)))))..((((.....))))..........)))----------.....................(((((((.....))))))).................- ( -19.50)
>DroSec_CAF1 25329 107 + 1
AUUGCAGUGGCUGACUUGCCACAGCGUCACACUGAUGAAAAAAACUAUGC----------UACUACUUACUUUCUAUCUUAGGAUAUAAUUUGUAUUUCAAAUAAACCUACCCCAGC-
...((((((((......)))))..((((.....))))..........)))----------...................((((.....(((((.....)))))...)))).......- ( -18.70)
>DroSim_CAF1 23385 107 + 1
AUUGCAGUGGCUGACUUGCCACAGCGUCACACUGAUGAAAAAAACUAUGC----------UACUACUUACUUUCUAUCUCAGGAUAUACUUUGUAAUUCAAAUAAACCUACCCCAGC-
...((((((((......)))))..((((.....))))..........)))----------......((((....((((....))))......)))).....................- ( -17.00)
>DroEre_CAF1 23976 107 + 1
ACUGCAGUGGCUGACUUGCCACAGC--UACACUGCUGAAAAU-ACUGUUCUGUGAAAGCAUACAAUA-CAAUUCUAUCUUAA-AAAUAC---UUAUAUCAAAAAUUCUUGC--CAAC-
...((((((((......))).((((--......)))).....-)))))..(((....))).......-..............-......---...................--....- ( -17.30)
>DroYak_CAF1 29539 108 + 1
AUUGCAGUGGCUGUCUUGCCACAGC--UACACUGAUGAAAAU-ACUGUUGUGUGAAACCAUACUAUUUUCAUUCUAGCUUGA-AAAUAC---CUUUAUCAAAUAAACUUAU--CAUC-
......((((((((......)))))--)))..(((((((...-......(((((....)))))((((((((........)))-))))).---.)))))))...........--....- ( -25.70)
>DroAna_CAF1 22430 97 + 1
CCUGCAGUGGCUUACUUUCCACUUGCUGGCACUGAGAGAAUAAAGGAAGU---------UUAAUAUUUUGUUU---------AAUAUCUUUU---UUUCUCCUAAAUUAUCGGUAGUU
((.(((((((........)))).))).)).((((((((((.((((((.((---------(.(((.....))).---------))).))))))---.)))))........))))).... ( -22.20)
>consensus
AUUGCAGUGGCUGACUUGCCACAGCGUCACACUGAUGAAAAAAACUAUGC__________UACUAUUUACAUUCUAUCUUAAGAUAUACUUUGUAUAUCAAAUAAACCUACCCCAGC_
...((.(((((......))))).))............................................................................................. ( -8.70 =  -9.20 +   0.50)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:52:42 2006