Locus 2624

Sequence ID	3L_DroMel_CAF1
Location	7,235,322 – 7,235,544
Length	222
Max. P	0.875366

overview

Window 9

Location	7,235,322 – 7,235,424
Length	102
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	81.14
Mean single sequence MFE	-28.38
Consensus MFE	-14.12
Energy contribution	-13.88
Covariance contribution	-0.24
Combinations/Pair	1.21
Mean z-score	-2.09
Structure conservation index	0.50
SVM decision value	0.11
SVM RNA-class probability	0.589757
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 7235322 102 + 23771897
AACCGCAACAGCCGCA---------GCAGGAUUACGUAACUUUCCCUGUAUCUUGCGAAUUACGCUGCUGACCAUGAGCAUCGGUUUUUAGCUGAUAGCUGAAAAG---------CUAUC
....((..((((.((.---------(((((((.(((..........))))))))))(.....))).))))(((.........))).....)).(((((((....))---------))))) ( -28.10)
>DroSec_CAF1 16875 102 + 1
AACCGCAAGAGCCGCA---------GCAGCAUUACGUAACUUUCCCUGCAUCUUGCGAAUUACGCUGCUGACCAUGAGCAGUGGCUUUUUUCUUUUAGCUGAAAAG---------CUAUC
...(((((((...(((---------(...................)))).))))))).....(((((((.......)))))))............(((((....))---------))).. ( -30.21)
>DroSim_CAF1 16891 102 + 1
AACCGCAACAGCCGCA---------GCAGCAUUACGUAACUUUCCCUGCAUCUUGCGAAUUACGCUGCUGACCAUGAGCAGUGGCUUUUUUUCUUUAGCUAAAAAG---------CUAUC
....((..((....((---------((((((((.(((((.............))))))))...)))))))....)).)).((((((((((..(....)..))))))---------)))). ( -25.02)
>DroEre_CAF1 17390 105 + 1
AACCGCAGCAGCCACAGCCACUGCCGCAGCAUUACGUAACUUUCGCUGCAUCUUGCGAAUUACGCUGCUGACCAUGAGCAGUGGCUUUU------CAGCUGAAAAG---------UUAUC
(((..((((......((((((((((((((((...(((((..(((((........)))))))))).)))))....)).)))))))))...------..))))....)---------))... ( -37.50)
>DroYak_CAF1 18445 102 + 1
AACCGCAACAG------------CCGCAGCAUUACGUAACUUUCCCUGCAUCUUGCGAAUUACGCUGCUGACCAUGAGCACUGGCUUUU------CAGCUGCAAACUUACCAAACUUAUC
...(((((.(.------------..((((................)))).).)))))......((.(((((....((((....)))).)------)))).)).................. ( -21.09)
>consensus
AACCGCAACAGCCGCA_________GCAGCAUUACGUAACUUUCCCUGCAUCUUGCGAAUUACGCUGCUGACCAUGAGCAGUGGCUUUU______UAGCUGAAAAG_________CUAUC
...(((((.................((((................))))...))))).....(((((((.......)))))))(((..........)))..................... (-14.12 = -13.88 +  -0.24)

alignment

secondary structure

dotplot

Window 0

Location	7,235,353 – 7,235,464
Length	111
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	87.11
Mean single sequence MFE	-27.64
Consensus MFE	-18.56
Energy contribution	-18.52
Covariance contribution	-0.04
Combinations/Pair	1.20
Mean z-score	-2.02
Structure conservation index	0.67
SVM decision value	0.14
SVM RNA-class probability	0.602574
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 7235353 111 + 23771897
UUUCCCUGUAUCUUGCGAAUUACGCUGCUGACCAUGAGCAUCGGUUUUUAGCUGAUAGCUGAAAAG---------CUAUCUUUGCCAAAACUCUAAUUGUUACCGAAUUCGGCGCAAUCA
............((((((((((((.((((.......)))).))(((((..((.(((((((....))---------)))))...)).)))))..)))))....(((....))))))))... ( -29.20)
>DroSec_CAF1 16906 111 + 1
UUUCCCUGCAUCUUGCGAAUUACGCUGCUGACCAUGAGCAGUGGCUUUUUUCUUUUAGCUGAAAAG---------CUAUCAUCGCCAAAACUCUAAUUGUUACCGAAUUCGGCGCAAUCA
......(((.....((((....(((((((.......)))))))............(((((....))---------)))...)))).................(((....))).))).... ( -28.10)
>DroSim_CAF1 16922 111 + 1
UUUCCCUGCAUCUUGCGAAUUACGCUGCUGACCAUGAGCAGUGGCUUUUUUUCUUUAGCUAAAAAG---------CUAUCAUCGCCAAAACUCUAAUUGUUACCGAAUUCGGCGCAAUCA
......(((.....((((....(((((((.......)))))))(((((((..(....)..))))))---------).....)))).................(((....))).))).... ( -26.90)
>DroEre_CAF1 17430 105 + 1
UUUCGCUGCAUCUUGCGAAUUACGCUGCUGACCAUGAGCAGUGGCUUUU------CAGCUGAAAAG---------UUAUCAACGCCAAAACUCUAAUUGUUGCCGAAUUCGGCGCAAUCA
.(((((........)))))...(((((((.......)))))))((((((------(....))))))---------)...................(((((.((((....))))))))).. ( -31.60)
>DroYak_CAF1 18473 114 + 1
UUUCCCUGCAUCUUGCGAAUUACGCUGCUGACCAUGAGCACUGGCUUUU------CAGCUGCAAACUUACCAAACUUAUCAUCGCCAAAACUCUAAUUGUUACCGAAUUCGGCGCAAUCA
............(((((......((.(((((....((((....)))).)------)))).))........................................(((....))))))))... ( -22.40)
>consensus
UUUCCCUGCAUCUUGCGAAUUACGCUGCUGACCAUGAGCAGUGGCUUUU______UAGCUGAAAAG_________CUAUCAUCGCCAAAACUCUAAUUGUUACCGAAUUCGGCGCAAUCA
......(((.....((((....(((((((.......)))))))(((..........)))......................)))).................(((....))).))).... (-18.56 = -18.52 +  -0.04)

alignment

secondary structure

dotplot

Window 1

Location	7,235,424 – 7,235,544
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	80.03
Mean single sequence MFE	-15.88
Consensus MFE	-11.06
Energy contribution	-11.50
Covariance contribution	0.44
Combinations/Pair	1.06
Mean z-score	-1.94
Structure conservation index	0.70
SVM decision value	0.89
SVM RNA-class probability	0.875366
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 7235424 120 + 23771897
UUUGCCAAAACUCUAAUUGUUACCGAAUUCGGCGCAAUCACGAAACUCAUAACUUCAUGUUGACCCCAAACCAAAAAUAAAAAAUAAAAACGAAAAAAAAACCCCAGCACAAUAAGAGAC
..........((((.(((((..(((....))).((......(.....).((((.....))))............................................))))))).)))).. ( -13.50)
>DroSec_CAF1 16977 111 + 1
AUCGCCAAAACUCUAAUUGUUACCGAAUUCGGCGCAAUCACGAAACUCACAACUUCAUGUUGACCCCAAACCAAAAAUAAAAACC---------AGAAAAACCCCAGCACAAUAAGAGAC
..........((((.(((((..(((....))).((......(.....).((((.....)))).......................---------............))))))).)))).. ( -15.60)
>DroSim_CAF1 16993 98 + 1
AUCGCCAAAACUCUAAUUGUUACCGAAUUCGGCGCAAUCACGAAACUCACAACUUCAUGUUGACCCCAAA-------------CG---------AGAAAAACCCCAGCACAAUAAGAGAC
..........((((.(((((..(((....))).((......(.....).((((.....))))........-------------..---------............))))))).)))).. ( -15.60)
>DroEre_CAF1 17495 112 + 1
AACGCCAAAACUCUAAUUGUUGCCGAAUUCGGCGCAAUCACGACAAACACAACUCCAUGCUGACCCCAAAGCAAACGAAAA--------AUGUAAAAAAUACCCCGGCACAAUAAAAGAC
...(((.........(((((.((((....)))))))))...................((((........))))........--------................)))............ ( -19.80)
>DroYak_CAF1 18547 109 + 1
AUCGCCAAAACUCUAAUUGUUACCGAAUUCGGCGCAAUCACGACCAAAACAACUCUAUGUUGACCCCAACUGAAAAAAAAA-----------GGAAAAAUACCCCGGCACAAUAAAAGAC
...(((.........(((((..(((....))).))))).....((........((...((((....)))).))........-----------))...........)))............ ( -14.89)
>consensus
AUCGCCAAAACUCUAAUUGUUACCGAAUUCGGCGCAAUCACGAAACUCACAACUUCAUGUUGACCCCAAACCAAAAAAAAA_____________AAAAAAACCCCAGCACAAUAAGAGAC
..........((((.(((((..(((....))).................((((.....))))..............................................))))).)))).. (-11.06 = -11.50 +   0.44)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:37:57 2006