Locus 1172

Sequence ID	3L_DroMel_CAF1
Location	3,364,360 – 3,364,621
Length	261
Max. P	0.984225

overview

Window 3

Location	3,364,360 – 3,364,480
Length	120
Sequences	3
Columns	120
Reading direction	forward
Mean pairwise identity	92.61
Mean single sequence MFE	-41.27
Consensus MFE	-37.47
Energy contribution	-37.80
Covariance contribution	0.33
Combinations/Pair	1.00
Mean z-score	-1.57
Structure conservation index	0.91
SVM decision value	-0.04
SVM RNA-class probability	0.511169
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 3364360 120 + 23771897
CCCCGGGGACCAGCCCCCCAGCCCCCCAGCCCCCGCCUUCGGCCCACUCUUUCUCUACGUGCUCUCUAAUGUGCAUAUUUGGUGUGGGCUGCGUUUUGGGUUCGCCAUGUGGGCUGUCUC
....((((......))))(((((((...((.((((....((((((((.((........((((.(......).))))....)).)))))))).....))))...))...).)))))).... ( -43.40)
>DroSec_CAF1 31655 111 + 1
CUCCGGGGACCAGCC---------CCCAGCCCCCGCAUUCGGCCCACUCUUUCUCUACGUGCUCUCUAAUGUGCAUAUUUGGUGUGGGCUGCGUUUUGGGUUCGCCAUGUGGGCUGUCUC
.....(((((.((((---------(.((((.((((.((.((((((((.((........((((.(......).))))....)).)))))))).))..))))...))..)).)))))))))) ( -40.80)
>DroSim_CAF1 29348 112 + 1
CCCCGGGGAACAGCCC--------CCCAGUCCCCGCCUUCGGCCCACUCUUUCUCUACGUGCUCUCUAAUGUGCAUAUUUGGUGUGGGCUGCGUUUUGGGUUCGCCAUGUGGGCUGUCUC
.....((((.((((((--------(...(..((((....((((((((.((........((((.(......).))))....)).)))))))).....))))..).....).)))))))))) ( -39.60)
>consensus
CCCCGGGGACCAGCCC________CCCAGCCCCCGCCUUCGGCCCACUCUUUCUCUACGUGCUCUCUAAUGUGCAUAUUUGGUGUGGGCUGCGUUUUGGGUUCGCCAUGUGGGCUGUCUC
.....((((.((((((........(((((....(((....(((((((.((........((((.(......).))))....)).))))))))))..)))))..........)))))))))) (-37.47 = -37.80 +   0.33)

alignment

secondary structure

dotplot

Window 4

Location	3,364,440 – 3,364,543
Length	103
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	90.91
Mean single sequence MFE	-34.92
Consensus MFE	-25.94
Energy contribution	-28.02
Covariance contribution	2.08
Combinations/Pair	1.06
Mean z-score	-1.60
Structure conservation index	0.74
SVM decision value	-0.05
SVM RNA-class probability	0.505780
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 3364440 103 - 23771897
CAUAUUUUUCGAAAAGUGUGUG-----------------GUUGAAAGUGCUGCCAAAAUGCAGUUUAAUCACCUCCGGAGGAGACAGCCCACAUGGCGAACCCAAAACGCAGCCCACACC
...............(((((.(-----------------((((...(((((((......)))))....((..((((...))))...(((.....))))).......)).)))))))))). ( -28.20)
>DroSec_CAF1 31726 113 - 1
CAUAUUUUUCCAAAGGUGUGUGGUG-------GUGUGCGGUUGAAAGUGCUGCCAAAAUGCAGUUUAAUCACCUCCGGAGGAGACAGCCCACAUGGCGAACCCAAAACGCAGCCCACACC
..............((((((.(((.-------(((((.(((((.....(((((......)))))........((((...)))).)))))))))).(((.........))).))))))))) ( -37.70)
>DroSim_CAF1 29420 113 - 1
CAUAUUUUUCGAAAAGUGUGUGGUG-------GUGUGCGGUUGAAAGUGCUGCCAAAAUGCAGUUUAAUCACCUCCGGAGGAGACAGCCCACAUGGCGAACCCAAAACGCAGCCCACACC
...............(((((.(((.-------(((((.(((((.....(((((......)))))........((((...)))).)))))))))).(((.........))).)))))))). ( -35.20)
>DroEre_CAF1 30446 110 - 1
CAUAUUUUUCGAAAUGUGUGUGGU----------GUGCGGCUGAAAGUGCUGCCAAAAUGCAGUUUAAUCACCUCCGGAGCAGACGGCCCACAUGGCAAACCCAAAACGCAGCCCACACC
(((((((....)))))))...(((----------(((.(((((...(((((((......)))))............((.((.....))))...(((.....)))..)).))))))))))) ( -32.80)
>DroYak_CAF1 30309 120 - 1
CAUAUUUUUCGAAAUGUGUGUGGUGUGGUGUAGUGUGUGGUUGAAAGUGCUGCCAAAAUGCAGUUUAAUCACCUCCGGAGGAGACAGCCCACAUGGCGAACCCAAAACGCAGCCCACACC
(((((((....)))))))...(((((((.((.((((((((((((....(((((......)))))))))))))....((.(....).(((.....)))....))...)))).))))))))) ( -40.70)
>consensus
CAUAUUUUUCGAAAAGUGUGUGGUG_______GUGUGCGGUUGAAAGUGCUGCCAAAAUGCAGUUUAAUCACCUCCGGAGGAGACAGCCCACAUGGCGAACCCAAAACGCAGCCCACACC
...............(((((.(((........(((((.(((((.....(((((......)))))....((.(((....))).)))))))))))).(((.........))).)))))))). (-25.94 = -28.02 +   2.08)

alignment

secondary structure

dotplot

Window 5

Location	3,364,520 – 3,364,621
Length	101
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	89.35
Mean single sequence MFE	-24.28
Consensus MFE	-18.46
Energy contribution	-19.06
Covariance contribution	0.60
Combinations/Pair	1.00
Mean z-score	-2.03
Structure conservation index	0.76
SVM decision value	0.82
SVM RNA-class probability	0.858657
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 3364520 101 + 23771897
C-----------------CACACACUUUUCGAAAAAUAUGUGCC--CCAAGAGGGCGUGGCCAUUUCAACUUUAUGAUUUUUGUCAUAUUUCUCGAGACUUUGUGGCUUUUACAAUUCCA
(-----------------((((....((((((.((((((..(((--(.....))))..(((....(((......))).....))))))))).))))))...))))).............. ( -23.90)
>DroSec_CAF1 31806 110 + 1
CCGCACAC-------CACCACACACCUUUGGAAAAAUAUGUGCC--CCAAGAGGGCGUGGCCAUUUCAACUUUAUGAUUUUUGUCAUAUUUCUAGAGACUUUGUGGCU-UUACAAUUCCA
........-------..(((((...(((((((((.......(((--(.....))))(((((....(((......))).....))))).)))))))))....)))))..-........... ( -26.10)
>DroSim_CAF1 29500 111 + 1
CCGCACAC-------CACCACACACUUUUCGAAAAAUAUGUGCC--CCAAGAGGGCGUGGCCAUUUCAACUUUAUGAUUUUUGUCAUAUUUCUCGAGACUUUGUGGCUUUUACAAUUCCA
........-------..(((((....((((((.((((((..(((--(.....))))..(((....(((......))).....))))))))).))))))...))))).............. ( -24.40)
>DroEre_CAF1 30526 110 + 1
CCGCAC----------ACCACACACAUUUCGAAAAAUAUGUGCCCACCAAGAAGGCGUGGCCACUUCAACUUUAUGAUUUUUGUCAUAUUUCUCGAGACUUUGUGGCAUUUACAAUUCCA
......----------.(((((....((((((.(((((((((.(((((......).)))).)))...........(((....))))))))).))))))...))))).............. ( -24.00)
>DroYak_CAF1 30389 119 + 1
CCACACACUACACCACACCACACACAUUUCGAAAAAUAUGUGCC-UCCAAGAAGGCGUGGCCAUUUCAACUUUAUGAUUUUUGUCAUAUUUCUCGAGACUUUGUGGCUUUUACAAUUCCA
............((((((((((((.((((....)))).)))(((-(......))))))))...((((.....((((((....))))))......))))...))))).............. ( -23.00)
>consensus
CCGCACAC_______CACCACACACAUUUCGAAAAAUAUGUGCC__CCAAGAGGGCGUGGCCAUUUCAACUUUAUGAUUUUUGUCAUAUUUCUCGAGACUUUGUGGCUUUUACAAUUCCA
.................(((((....((((((.(((((((.(((..((.....))...)))....(((......))).......))))))).))))))...))))).............. (-18.46 = -19.06 +   0.60)

alignment

secondary structure

dotplot

Window 6

Location	3,364,520 – 3,364,621
Length	101
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	89.35
Mean single sequence MFE	-32.94
Consensus MFE	-25.36
Energy contribution	-26.16
Covariance contribution	0.80
Combinations/Pair	1.00
Mean z-score	-2.77
Structure conservation index	0.77
SVM decision value	1.97
SVM RNA-class probability	0.984225
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 3364520 101 - 23771897
UGGAAUUGUAAAAGCCACAAAGUCUCGAGAAAUAUGACAAAAAUCAUAAAGUUGAAAUGGCCACGCCCUCUUGG--GGCACAUAUUUUUCGAAAAGUGUGUG-----------------G
..............(((((.....((((((((((((.......(((......))).........((((.....)--))).))))))))))))......))))-----------------) ( -29.00)
>DroSec_CAF1 31806 110 - 1
UGGAAUUGUAA-AGCCACAAAGUCUCUAGAAAUAUGACAAAAAUCAUAAAGUUGAAAUGGCCACGCCCUCUUGG--GGCACAUAUUUUUCCAAAGGUGUGUGGUG-------GUGUGCGG
...........-.(((((...(((..((....)).))).....(((......)))....((((((((((.((((--((.........))))))))).))))))).-------))).)).. ( -28.10)
>DroSim_CAF1 29500 111 - 1
UGGAAUUGUAAAAGCCACAAAGUCUCGAGAAAUAUGACAAAAAUCAUAAAGUUGAAAUGGCCACGCCCUCUUGG--GGCACAUAUUUUUCGAAAAGUGUGUGGUG-------GUGUGCGG
......((((...((((((.....((((((((((((.......(((......))).........((((.....)--))).))))))))))))......)))))).-------...)))). ( -34.80)
>DroEre_CAF1 30526 110 - 1
UGGAAUUGUAAAUGCCACAAAGUCUCGAGAAAUAUGACAAAAAUCAUAAAGUUGAAGUGGCCACGCCUUCUUGGUGGGCACAUAUUUUUCGAAAUGUGUGUGGU----------GUGCGG
......((((...((((((..((.((((((((((((.......(((......)))....(((.((((.....))))))).)))))))))))).))...))))))----------.)))). ( -38.60)
>DroYak_CAF1 30389 119 - 1
UGGAAUUGUAAAAGCCACAAAGUCUCGAGAAAUAUGACAAAAAUCAUAAAGUUGAAAUGGCCACGCCUUCUUGGA-GGCACAUAUUUUUCGAAAUGUGUGUGGUGUGGUGUAGUGUGUGG
....((((((...((((((..((.((((((((((((.......(((......))).........(((((....))-))).)))))))))))).))...))))))....))))))...... ( -34.20)
>consensus
UGGAAUUGUAAAAGCCACAAAGUCUCGAGAAAUAUGACAAAAAUCAUAAAGUUGAAAUGGCCACGCCCUCUUGG__GGCACAUAUUUUUCGAAAAGUGUGUGGUG_______GUGUGCGG
.............((((((.....((((((((((((.......(((......)))....(((...((.....))..))).))))))))))))......))))))................ (-25.36 = -26.16 +   0.80)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:01:10 2006