Locus 1192

Sequence ID	2L_DroMel_CAF1
Location	3,230,071 – 3,230,197
Length	126
Max. P	0.779046

overview

Window 3

Location	3,230,071 – 3,230,176
Length	105
Sequences	5
Columns	116
Reading direction	reverse
Mean pairwise identity	84.35
Mean single sequence MFE	-39.56
Consensus MFE	-25.66
Energy contribution	-26.06
Covariance contribution	0.40
Combinations/Pair	1.08
Mean z-score	-2.21
Structure conservation index	0.65
SVM decision value	0.55
SVM RNA-class probability	0.779046
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 3230071 105 - 22407834
GCCAGCGCACAGGCGAACGCCAUUGCCAGGUCCUUUUGGCCAUAAAUGAAAAUGGUAGUGGCGAGAAGAUGGCUAGCUU---------UUGGUCAUG--UCAGCGGCAUCUGGAAU
(((.((((....))...((((((((((.((.((....))))....((....)))))))))))).((..((((((((...---------)))))))).--)).)))))......... ( -37.30)
>DroSec_CAF1 64138 97 - 1
GCCAGCGCACAGGCGAACGCCAUCGCCAGGUCCUUUUGGCCAUAAAUGAAAAUGGUGGUGGCGAGAAGCUGGCUAGC-----------------AUG--UCAGAGGUUUCUGGAAU
((((((((....))...((((((((((.((.((....))))....((....))))))))))))....))))))....-----------------...--((((......))))... ( -40.30)
>DroSim_CAF1 62645 97 - 1
GCCAGCGCACAGGCGAACGCCAUCGCCAGGUCCUUUUGGCCAUAAAUGAAAAUGGUAGUGGCGAGAAGCUGGCUAGC-----------------AUG--UCAGAGGUUUCUGGAAU
((((((((....))...((((((..((.((.((....))))....((....))))..))))))....))))))....-----------------...--((((......))))... ( -36.40)
>DroEre_CAF1 60937 116 - 1
GCCAGCACACAGGCGAACGCCAUCGCCAGGUCCUUUUGGCCAUAAAUGAAACAGGUAGUGGGGAGAAGCUGGCUAGCAUGGGCAUAGCUUGGGCAUGUUUCGCCAGCUUCUGGCAU
(((....(((.(((((......))))).((.((....))))................)))...((((((((((.((((((..((.....))..))))))..))))))))))))).. ( -46.80)
>DroYak_CAF1 59607 105 - 1
GCCAGCACACAGGCGAACGCCAUCGCCAGGUCCUUUUGGCCAUAAAUGAAACAGGUAGUGGGGAGAAGCUGGCUAGCUU---------UUGGGCAUG--UCGGCAGUUUCUGGCAU
(((....(((.(((((......))))).((.((....))))................)))(((((..((((((..(((.---------...)))..)--)))))..)))))))).. ( -37.00)
>consensus
GCCAGCGCACAGGCGAACGCCAUCGCCAGGUCCUUUUGGCCAUAAAUGAAAAUGGUAGUGGCGAGAAGCUGGCUAGC_U_________UUGG_CAUG__UCAGCGGUUUCUGGAAU
((((((.....(((((......)))))......((((.(((((..............))))).))))))))))..........................((((......))))... (-25.66 = -26.06 +   0.40)

alignment

secondary structure

dotplot

Window 4

Location	3,230,100 – 3,230,197
Length	97
Sequences	5
Columns	97
Reading direction	reverse
Mean pairwise identity	96.29
Mean single sequence MFE	-32.48
Consensus MFE	-26.40
Energy contribution	-26.60
Covariance contribution	0.20
Combinations/Pair	1.08
Mean z-score	-1.56
Structure conservation index	0.81
SVM decision value	0.02
SVM RNA-class probability	0.545853
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 3230100 97 - 22407834
AUUUCCUUUUUGGCUGCAAUUGCCAGCGCACAGGCGAACGCCAUUGCCAGGUCCUUUUGGCCAUAAAUGAAAAUGGUAGUGGCGAGAAGAUGGCUAG
..........(((((....(((((........))))).((((((((((.((.((....))))....((....)))))))))))).......))))). ( -32.90)
>DroSec_CAF1 64159 97 - 1
AUUUCCUUUUUGGCUGCAAUUGCCAGCGCACAGGCGAACGCCAUCGCCAGGUCCUUUUGGCCAUAAAUGAAAAUGGUGGUGGCGAGAAGCUGGCUAG
....((.....))........((((((((....))...((((((((((.((.((....))))....((....))))))))))))....))))))... ( -37.60)
>DroSim_CAF1 62666 97 - 1
AUUUCCUUUUUGGCUGCAAUUGCCAGCGCACAGGCGAACGCCAUCGCCAGGUCCUUUUGGCCAUAAAUGAAAAUGGUAGUGGCGAGAAGCUGGCUAG
....((.....))........((((((((....))...((((((..((.((.((....))))....((....))))..))))))....))))))... ( -33.70)
>DroEre_CAF1 60977 97 - 1
AUUUCCUUUUUGGCUGCAAUUGCCAGCACACAGGCGAACGCCAUCGCCAGGUCCUUUUGGCCAUAAAUGAAACAGGUAGUGGGGAGAAGCUGGCUAG
....((.....))........((((((.....(((((......)))))...(((((...(((............)))...)))))...))))))... ( -29.10)
>DroYak_CAF1 59636 97 - 1
AUUUCCUUUUUGGCUGCAAUUGCCAGCACACAGGCGAACGCCAUCGCCAGGUCCUUUUGGCCAUAAAUGAAACAGGUAGUGGGGAGAAGCUGGCUAG
....((.....))........((((((.....(((((......)))))...(((((...(((............)))...)))))...))))))... ( -29.10)
>consensus
AUUUCCUUUUUGGCUGCAAUUGCCAGCGCACAGGCGAACGCCAUCGCCAGGUCCUUUUGGCCAUAAAUGAAAAUGGUAGUGGCGAGAAGCUGGCUAG
..........(((((((..((((((..((...(((((......))))).((.((....)))).............))..))))))...)).))))). (-26.40 = -26.60 +   0.20)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:55:56 2006