Locus 6195

Sequence ID	3R_DroMel_CAF1
Location	16,189,858 – 16,190,126
Length	268
Max. P	0.967006

overview

Window 3

Location	16,189,858 – 16,189,973
Length	115
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	94.70
Mean single sequence MFE	-31.02
Consensus MFE	-28.80
Energy contribution	-28.60
Covariance contribution	-0.20
Combinations/Pair	1.07
Mean z-score	-1.52
Structure conservation index	0.93
SVM decision value	1.60
SVM RNA-class probability	0.967006
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 16189858 115 - 27905053
CCCGCUGCAUUGAUUUAUGCCAAUCACGAUUCGCUAAUAACUCAGCGGGUCCACCCAUGCCACUUCUCCACUUGGAUGCUACUGU-----UCCCGAUGCUGUCAUAAUGGCAGCAAUUUG
(((((((.....(((...((.(((....))).)).)))....)))))))......................((((..((....))-----..))))(((((((.....)))))))..... ( -29.20)
>DroSec_CAF1 19066 115 - 1
CCCGCUGCAUUGAUUUAUGCCAAUCACGAUUCGCUAAUAACUCAGCGGGUCCACCCAUGCCGCUCCUCCACUUGGAUGCUACUCU-----UCCCGAUGCUGUCAUAAUGACAGCAAUUUG
(((((((.....(((...((.(((....))).)).)))....)))))))............(((((.......))).))......-----......(((((((.....)))))))..... ( -30.70)
>DroSim_CAF1 12629 115 - 1
CCCGCUGCAUUGAUUUAUGCCAAUCACGAUUCGCUAAUAACUCAGCGGGUCCACCCAUGCCGCUCCUCCACUUGGAUGCUACUGU-----UCCCGAUGCUGUCAUAAUGGCAGCAAUUUG
...((.(((((((((......))))).((((((((........)))))))).....)))).))........((((..((....))-----..))))(((((((.....)))))))..... ( -31.90)
>DroEre_CAF1 18430 120 - 1
CCCGCUGCAUUGAUUUAUGCCAAUCACGAUUCGCUAAUAACUCAGCGGGUCCACCGAUGUCGCUCCUCCACUUGGAUGCUGCUGUUCCGUUCCUGAUGCUGUCAUAAUGGCAGCAAUUUG
(((((((.....(((...((.(((....))).)).)))....)))))))...((.((.((.(((((.......))).)).))...)).))......(((((((.....)))))))..... ( -32.10)
>DroYak_CAF1 19763 115 - 1
CCCGCUGCAUUGAUUUAUGCCAAUCACGAUUCGCUAAUAACUCAGCGGGUCCGCCGAUGUCGCUCCUCCACUUGGAUGCUACUGU-----UCCUGAUGCUGUCAUAAUGGCAGCAAUUUG
(((((((.....(((...((.(((....))).)).)))....)))))))......((.((.(((((.......))).)).))...-----))....(((((((.....)))))))..... ( -31.20)
>consensus
CCCGCUGCAUUGAUUUAUGCCAAUCACGAUUCGCUAAUAACUCAGCGGGUCCACCCAUGCCGCUCCUCCACUUGGAUGCUACUGU_____UCCCGAUGCUGUCAUAAUGGCAGCAAUUUG
...((.(((((((((......))))).((((((((........)))))))).....)))).))...(((....)))....................(((((((.....)))))))..... (-28.80 = -28.60 +  -0.20)

alignment

secondary structure

dotplot

Window 4

Location	16,189,933 – 16,190,046
Length	113
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	85.92
Mean single sequence MFE	-31.34
Consensus MFE	-22.38
Energy contribution	-22.78
Covariance contribution	0.40
Combinations/Pair	1.00
Mean z-score	-1.62
Structure conservation index	0.71
SVM decision value	0.01
SVM RNA-class probability	0.537271
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 16189933 113 - 27905053
CCAGUGAGUUGGCAAAGUGUCUUCGGCAGGUGCAUUCCCUGCCCCACCUGCCCCAC-CUGCCACACCCGCCUC------CCCCGCUGCAUUGAUUUAUGCCAAUCACGAUUCGCUAAUAA
..((((((((((((..(((.....((((((((((.....)))...))))))).)))-.))))...........------.......((((......)))).......))))))))..... ( -31.50)
>DroSec_CAF1 19141 104 - 1
CCAGUGAGUUGGCAAAGUGUCUGCGGCAGGUGCAUUCCCUGCCCC---------AC-CUGGCACACCCGACUC------CCCCGCUGCAUUGAUUUAUGCCAAUCACGAUUCGCUAAUAA
..((((((((((((..(((((((.((((((.......)))))).)---------).-..)))))...((....------...)).)))..(((((......))))))))))))))..... ( -31.30)
>DroSim_CAF1 12704 104 - 1
CCAGUGAGUUGGCAAAGUGUCUGCGGCAGGUGCAUUCCCUGCCCC---------AC-CUGGCACACCCGCCUC------CCCCGCUGCAUUGAUUUAUGCCAAUCACGAUUCGCUAAUAA
...((((.((((((....(((((((((.((.(((.....))).))---------..-..(((......)))..------....))))))..)))...))))))))))............. ( -33.50)
>DroEre_CAF1 18510 95 - 1
CCAGUGAGUUGGCAAAGUGUCUGCGGCAGGUGCAUUCCCUGCUCC---------GC----------CCGGCGC------CCCCGCUGCAUUGAUUUAUGCCAAUCACGAUUCGCUAAUAA
...((((.((((((....(((((((((.((.(((.....))).))---------))----------).((((.------...)))))))..)))...))))))))))............. ( -31.10)
>DroYak_CAF1 19838 108 - 1
CCAGUGAGUUGGCAAAGUGUCUGCGGCAGGUGCAUUCUCUACUCC---------GACCUC---CAUCCGCCGCCUACCGCCCCGCUGCAUUGAUUUAUGCCAAUCACGAUUCGCUAAUAA
..(((((((((((...(((...(((((.((((...((........---------))....---)))).)))))....)))...)).((((......))))......)))))))))..... ( -29.30)
>consensus
CCAGUGAGUUGGCAAAGUGUCUGCGGCAGGUGCAUUCCCUGCCCC_________AC_CUG_CACACCCGCCUC______CCCCGCUGCAUUGAUUUAUGCCAAUCACGAUUCGCUAAUAA
...((((.((((((....(((((((((.((.(((.....))).)).......................(.............)))))))..)))...))))))))))............. (-22.38 = -22.78 +   0.40)

alignment

secondary structure

dotplot

Window 5

Location	16,190,006 – 16,190,126
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	96.67
Mean single sequence MFE	-34.82
Consensus MFE	-33.00
Energy contribution	-33.08
Covariance contribution	0.08
Combinations/Pair	1.06
Mean z-score	-1.46
Structure conservation index	0.95
SVM decision value	1.36
SVM RNA-class probability	0.945943
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 16190006 120 + 27905053
AGGGAAUGCACCUGCCGAAGACACUUUGCCAACUCACUGGCCACUCUUUUAGCCUAAUGGGCUUGAAGCCAGUGCGGGAUUUAUGACUGCCAUCCGUCUGCCACUACCUUCUCCAUUCGC
.(.(((((..((((((((((...))))).......((((((...((....((((.....)))).)).)))))))))))......(((........)))...............))))).) ( -29.80)
>DroSec_CAF1 19205 120 + 1
AGGGAAUGCACCUGCCGCAGACACUUUGCCAACUCACUGGCCACUCUUUUAGCCUAAUGGGCUUGAAGCCAGUGCGGGAUUUAUGACUAUCAUCCGUCUGCCACAACCUUCUCCAUUCGC
.(((((.((....)).((((((..........(.(((((((...((....((((.....)))).)).))))))).)((((...........)))))))))).......))).))...... ( -35.10)
>DroSim_CAF1 12768 120 + 1
AGGGAAUGCACCUGCCGCAGACACUUUGCCAACUCACUGGCCACUCUUUUAGCCUAAUGGGCUUGAAGCCAGUGCGGGAUUUAUGACUACCAUCCGUCUGCCACAACCUUCUCCAUUCGC
.(((((.((....)).((((((..........(.(((((((...((....((((.....)))).)).))))))).)((((...........)))))))))).......))).))...... ( -35.10)
>DroEre_CAF1 18565 120 + 1
AGGGAAUGCACCUGCCGCAGACACUUUGCCAACUCACUGGCCACUCUUUUAGCCUAAUGGGCUUGAAGCCAGUGCGGGAUUUAUGACUGCCAUCCGUCUGCCACUGCCUUCUCCAUUCGC
.(((((.(((......((((((..........(.(((((((...((....((((.....)))).)).))))))).)((((...........))))))))))...))).))).))...... ( -37.80)
>DroYak_CAF1 19906 119 + 1
AGAGAAUGCACCUGCCGCAGACACUUUGCCAACUCACUGGCCACUCUUUUAGCCUAAUGGGC-UGAAGUCAGUGCGGGAUUUAUGACUGCCAUCCGUCUGCCACUAGCUUCUCCAUUCGC
.(((((.((...((..((((((..........(.(((((((......(((((((.....)))-))))))))))).)((((...........))))))))))))...)))))))....... ( -36.30)
>consensus
AGGGAAUGCACCUGCCGCAGACACUUUGCCAACUCACUGGCCACUCUUUUAGCCUAAUGGGCUUGAAGCCAGUGCGGGAUUUAUGACUGCCAUCCGUCUGCCACUACCUUCUCCAUUCGC
.(((((.((....)).((((((..........(.(((((((...((....((((.....)))).)).))))))).)((((...........)))))))))).......)))))....... (-33.00 = -33.08 +   0.08)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:15:05 2006