Locus 7099

Sequence ID	3L_DroMel_CAF1
Location	19,153,790 – 19,154,019
Length	229
Max. P	0.997782

overview

Window 3

Location	19,153,790 – 19,153,899
Length	109
Sequences	3
Columns	109
Reading direction	forward
Mean pairwise identity	86.98
Mean single sequence MFE	-18.97
Consensus MFE	-18.70
Energy contribution	-18.70
Covariance contribution	-0.00
Combinations/Pair	1.00
Mean z-score	-0.83
Structure conservation index	0.99
SVM decision value	0.44
SVM RNA-class probability	0.737945
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 19153790 109 + 23771897
GGCAACGGCAAAGCAAAUGCCGCUACGCGCUUUUCAACCCAGUCCCCUGCAUUUCUUCGGGACACCGCCCGCCCCAUAAGCCACCUCAUCCCCUCUCCCCCCCCUCAUC
(((..(((((.......)))))...................(((((............)))))................)))........................... ( -19.50)
>DroSec_CAF1 16669 97 + 1
GGCAACGGCAAAGCAAAUGCCGCUACGCGCUUUUCACCCCAGUCCCCUGCAUUUCUUCGGGACACCCCCCGCCCCAUAAGCC---------CCCCUCCCCA---ACCAG
(((..(((((.......)))))...................(((((............))))).......))).........---------..........---..... ( -18.70)
>DroSim_CAF1 16332 96 + 1
GGCAACGGCAAAGCAAAUGCCGCUACGCGCUUUUCACCCCAGUCCCCUGCAUUUCUUCGGGACACCCCCCGCCCCAUAAGCC---------CCCCUCCCC----ACCAG
(((..(((((.......)))))...................(((((............))))).......))).........---------.........----..... ( -18.70)
>consensus
GGCAACGGCAAAGCAAAUGCCGCUACGCGCUUUUCACCCCAGUCCCCUGCAUUUCUUCGGGACACCCCCCGCCCCAUAAGCC_________CCCCUCCCC____ACCAG
(((..(((((.......)))))...................(((((............))))).......))).................................... (-18.70 = -18.70 +  -0.00)

alignment

secondary structure

dotplot

Window 4

Location	19,153,790 – 19,153,899
Length	109
Sequences	3
Columns	109
Reading direction	reverse
Mean pairwise identity	86.98
Mean single sequence MFE	-34.67
Consensus MFE	-32.33
Energy contribution	-32.33
Covariance contribution	0.00
Combinations/Pair	1.00
Mean z-score	-1.06
Structure conservation index	0.93
SVM decision value	0.05
SVM RNA-class probability	0.558817
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 19153790 109 - 23771897
GAUGAGGGGGGGGAGAGGGGAUGAGGUGGCUUAUGGGGCGGGCGGUGUCCCGAAGAAAUGCAGGGGACUGGGUUGAAAAGCGCGUAGCGGCAUUUGCUUUGCCGUUGCC
.....((.((.((((((.(((((..((.((((.(((((((.....)))))))....(((.(((....))).)))...)))).....))..))))).)))).)).)).)) ( -35.80)
>DroSec_CAF1 16669 97 - 1
CUGGU---UGGGGAGGGG---------GGCUUAUGGGGCGGGGGGUGUCCCGAAGAAAUGCAGGGGACUGGGGUGAAAAGCGCGUAGCGGCAUUUGCUUUGCCGUUGCC
.....---.........(---------.((((.(((((((.....)))))))......(.(((....))).).....)))).)(((((((((.......))))))))). ( -34.10)
>DroSim_CAF1 16332 96 - 1
CUGGU----GGGGAGGGG---------GGCUUAUGGGGCGGGGGGUGUCCCGAAGAAAUGCAGGGGACUGGGGUGAAAAGCGCGUAGCGGCAUUUGCUUUGCCGUUGCC
.....----........(---------.((((.(((((((.....)))))))......(.(((....))).).....)))).)(((((((((.......))))))))). ( -34.10)
>consensus
CUGGU____GGGGAGGGG_________GGCUUAUGGGGCGGGGGGUGUCCCGAAGAAAUGCAGGGGACUGGGGUGAAAAGCGCGUAGCGGCAUUUGCUUUGCCGUUGCC
............................((((.(((((((.....)))))))......(.(((....))).).....))))..(((((((((.......))))))))). (-32.33 = -32.33 +   0.00)

alignment

secondary structure

dotplot

Window 5

Location	19,153,899 – 19,154,019
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	96.66
Mean single sequence MFE	-29.58
Consensus MFE	-28.76
Energy contribution	-28.60
Covariance contribution	-0.16
Combinations/Pair	1.03
Mean z-score	-1.87
Structure conservation index	0.97
SVM decision value	2.93
SVM RNA-class probability	0.997782
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 19153899 120 + 23771897
CAGACGCCCAUGAUGGCCAUGUUUAAAUACGCAAACAGCCGACAGAAGCUACGUGCUUGGAAAAUAAUUUAAAAGCUCAAAAGGUGAGCAAAAGCAAUGCACAUAGGCACGUCCUAGCAA
..........((.((((..(((((........))))))))).))...((((((((((((...............(((((.....)))))....((...))...)))))))))...))).. ( -28.60)
>DroSec_CAF1 16766 120 + 1
CAGACGCCCAUGAUGGCCAUGUUUAAAUACGCAAACAGCCGACAGAAGCUACGUGCUUGGAAAAUAAUUUAAAAGCUCAAAAGGUGAGCAAAAGCAAUGCACAUAGGCACGUCCUAGCAA
..........((.((((..(((((........))))))))).))...((((((((((((...............(((((.....)))))....((...))...)))))))))...))).. ( -28.60)
>DroAna_CAF1 9863 118 + 1
--UAGGUCCAUGUUGGCCAUGUUUAAAUACGCAAACAGCCGACAGAAGCUACGUGCUUGGAAAAUAAUUUAAAAGCUCAAAAGGUGAGCAAAAGCAAUGCACAUAGGCACGUCCUGGCAA
--........(((((((..(((((........))))))))))))...((((((((((((...............(((((.....)))))....((...))...)))))))))...))).. ( -33.20)
>DroSim_CAF1 16428 120 + 1
CAGACGCCCAUGAUGGCCAUGUUUAAAUACGCAAACAGCCGACAGAAGCUACGUGCUUGGAAAAUAAUUUAAAAGCUCAAAAGGUGAGCAAAAGCAAUGCACAUAGGCACGUCCUAGCAA
..........((.((((..(((((........))))))))).))...((((((((((((...............(((((.....)))))....((...))...)))))))))...))).. ( -28.60)
>DroEre_CAF1 17355 117 + 1
--GACGCCCAUGAUGGCCAUGUUUAAAUACGCAAACAGCCGACAGAAGCUACGUGCUUGGAAAAUAAUUUAAAAGCUCAAAAGGUGAGCAA-AGCAAUGCACAUAGGCACGUCCUAGCAC
--...((...((.((((..(((((........))))))))).))...))...(((((.(((.............(((((.....)))))..-.....(((......)))..))).))))) ( -28.90)
>consensus
CAGACGCCCAUGAUGGCCAUGUUUAAAUACGCAAACAGCCGACAGAAGCUACGUGCUUGGAAAAUAAUUUAAAAGCUCAAAAGGUGAGCAAAAGCAAUGCACAUAGGCACGUCCUAGCAA
..........((.((((..(((((........))))))))).))...((((((((((((...............(((((.....)))))....((...))...)))))))))...))).. (-28.76 = -28.60 +  -0.16)

alignment

secondary structure

dotplot

Window 6

Location	19,153,899 – 19,154,019
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	96.66
Mean single sequence MFE	-31.64
Consensus MFE	-29.14
Energy contribution	-29.38
Covariance contribution	0.24
Combinations/Pair	1.03
Mean z-score	-1.37
Structure conservation index	0.92
SVM decision value	0.79
SVM RNA-class probability	0.851237
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 19153899 120 - 23771897
UUGCUAGGACGUGCCUAUGUGCAUUGCUUUUGCUCACCUUUUGAGCUUUUAAAUUAUUUUCCAAGCACGUAGCUUCUGUCGGCUGUUUGCGUAUUUAAACAUGGCCAUCAUGGGCGUCUG
......((((((.(((((((((.(((.....(((((.....)))))...............)))))))))))....((..(((((((((......)))))..))))..)).).)))))). ( -31.85)
>DroSec_CAF1 16766 120 - 1
UUGCUAGGACGUGCCUAUGUGCAUUGCUUUUGCUCACCUUUUGAGCUUUUAAAUUAUUUUCCAAGCACGUAGCUUCUGUCGGCUGUUUGCGUAUUUAAACAUGGCCAUCAUGGGCGUCUG
......((((((.(((((((((.(((.....(((((.....)))))...............)))))))))))....((..(((((((((......)))))..))))..)).).)))))). ( -31.85)
>DroAna_CAF1 9863 118 - 1
UUGCCAGGACGUGCCUAUGUGCAUUGCUUUUGCUCACCUUUUGAGCUUUUAAAUUAUUUUCCAAGCACGUAGCUUCUGUCGGCUGUUUGCGUAUUUAAACAUGGCCAACAUGGACCUA--
...(((.((((.((.(((((((.(((.....(((((.....)))))...............))))))))))))...))))(((((((((......)))))..))))....))).....-- ( -28.85)
>DroSim_CAF1 16428 120 - 1
UUGCUAGGACGUGCCUAUGUGCAUUGCUUUUGCUCACCUUUUGAGCUUUUAAAUUAUUUUCCAAGCACGUAGCUUCUGUCGGCUGUUUGCGUAUUUAAACAUGGCCAUCAUGGGCGUCUG
......((((((.(((((((((.(((.....(((((.....)))))...............)))))))))))....((..(((((((((......)))))..))))..)).).)))))). ( -31.85)
>DroEre_CAF1 17355 117 - 1
GUGCUAGGACGUGCCUAUGUGCAUUGCU-UUGCUCACCUUUUGAGCUUUUAAAUUAUUUUCCAAGCACGUAGCUUCUGUCGGCUGUUUGCGUAUUUAAACAUGGCCAUCAUGGGCGUC--
(((((.(((.((((......))))....-..(((((.....))))).............))).)))))...(((..((..(((((((((......)))))..))))..))..)))...-- ( -33.80)
>consensus
UUGCUAGGACGUGCCUAUGUGCAUUGCUUUUGCUCACCUUUUGAGCUUUUAAAUUAUUUUCCAAGCACGUAGCUUCUGUCGGCUGUUUGCGUAUUUAAACAUGGCCAUCAUGGGCGUCUG
..(((..((.(.(((.((((....(((....(((((.....)))))..................(((..(((((......)))))..)))))).....)))))))).))...)))..... (-29.14 = -29.38 +   0.24)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:37:47 2006