Locus 5166

Sequence ID	X_DroMel_CAF1
Location	13,481,365 – 13,481,493
Length	128
Max. P	0.999999

overview

Window 2

Location	13,481,365 – 13,481,455
Length	90
Sequences	3
Columns	96
Reading direction	forward
Mean pairwise identity	86.46
Mean single sequence MFE	-33.13
Consensus MFE	-27.67
Energy contribution	-28.33
Covariance contribution	0.67
Combinations/Pair	1.00
Mean z-score	-1.97
Structure conservation index	0.84
SVM decision value	0.45
SVM RNA-class probability	0.742004
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 13481365 90 + 22224390
CGGAUCCCAACCCGUGUAUCUGCCUUAUCUGCAGCCGUGCCAGGUAAAGCCCAUUUGGCGGGAUCCGUUCUGCGGGUUCCCGCUUUUGUG------
((((((((.(((.(.((((((((.......))))..))))).)))...(((.....)))))))))))....((((....)))).......------ ( -36.80)
>DroSec_CAF1 14147 96 + 1
CCGAUCCCAAACCGUGUAUCUGCCUUAUCUGCAGCCGUGCCAGGUAAAGCCCAUUUGGCGGGAUCCGUUCUGCGGGUUCCCGCUUAUGUGGCUCUA
..........(((..((((((((.......))))..))))..)))..(((((((..(((((((((((.....)))).))))))).))).))))... ( -35.80)
>DroSim_CAF1 6757 96 + 1
CCGAUCCCAAACCGUGUAUCUGCCUUAUCUGCAGCCGUGCCAGGUAAAGCCCAUUUGGCGGGAUCCGUUCUGCGGGUUCCCGNNNNNNNNNNNNNN
..((((((..(((..((((((((.......))))..))))..)))...(((.....))))))))).......(((....))).............. ( -26.80)
>consensus
CCGAUCCCAAACCGUGUAUCUGCCUUAUCUGCAGCCGUGCCAGGUAAAGCCCAUUUGGCGGGAUCCGUUCUGCGGGUUCCCGCUU_UGUG______
..((((((..(((..((((((((.......))))..))))..)))...(((.....)))))))))......((((....))))............. (-27.67 = -28.33 +   0.67)

alignment

secondary structure

dotplot

Window 3

Location	13,481,365 – 13,481,455
Length	90
Sequences	3
Columns	96
Reading direction	reverse
Mean pairwise identity	86.46
Mean single sequence MFE	-34.30
Consensus MFE	-29.93
Energy contribution	-30.27
Covariance contribution	0.33
Combinations/Pair	1.00
Mean z-score	-2.18
Structure conservation index	0.87
SVM decision value	1.00
SVM RNA-class probability	0.897292
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 13481365 90 - 22224390
------CACAAAAGCGGGAACCCGCAGAACGGAUCCCGCCAAAUGGGCUUUACCUGGCACGGCUGCAGAUAAGGCAGAUACACGGGUUGGGAUCCG
------.......((((....))))....(((((((((((.....)))...(((((......((((.......)))).....))))).)))))))) ( -39.10)
>DroSec_CAF1 14147 96 - 1
UAGAGCCACAUAAGCGGGAACCCGCAGAACGGAUCCCGCCAAAUGGGCUUUACCUGGCACGGCUGCAGAUAAGGCAGAUACACGGUUUGGGAUCGG
(((((((.(((..((((((..(((.....))).))))))...))))))))))((..(..((.((((.......)))).....))..)..))..... ( -36.00)
>DroSim_CAF1 6757 96 - 1
NNNNNNNNNNNNNNCGGGAACCCGCAGAACGGAUCCCGCCAAAUGGGCUUUACCUGGCACGGCUGCAGAUAAGGCAGAUACACGGUUUGGGAUCGG
..............(((....))).....(.((((((((((...((......)))))).((.((((.......)))).....))....)))))).) ( -27.80)
>consensus
______CACA_AAGCGGGAACCCGCAGAACGGAUCCCGCCAAAUGGGCUUUACCUGGCACGGCUGCAGAUAAGGCAGAUACACGGUUUGGGAUCGG
.............((((....))))......((((((((((...((......)))))).((.((((.......)))).....))....)))))).. (-29.93 = -30.27 +   0.33)

alignment

secondary structure

dotplot

Window 4

Location	13,481,388 – 13,481,493
Length	105
Sequences	3
Columns	113
Reading direction	forward
Mean pairwise identity	65.09
Mean single sequence MFE	-39.47
Consensus MFE	-24.95
Energy contribution	-26.20
Covariance contribution	1.25
Combinations/Pair	1.00
Mean z-score	-2.85
Structure conservation index	0.63
SVM decision value	6.68
SVM RNA-class probability	0.999999
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 13481388 105 + 22224390
CUUAUCUGCAGCCGUGCCAGGUAAAGCCCAUUUGGCGGGAUCCGUUCUGCGGGUUCCCGCUUUUGUG--------UGCAGGUAGUUGGGCGCGUUCCGCAAGCCCAACAAUAA
..(((((((((((......)))......(((..(((((((((((.....)))).)))))))...)))--------))))))))((((((((((...)))..)))))))..... ( -48.20)
>DroSec_CAF1 14170 112 + 1
CUUAUCUGCAGCCGUGCCAGGUAAAGCCCAUUUGGCGGGAUCCGUUCUGCGGGUUCCCGCUUAUGUGGCUCUACUUGCAGGUAGU-AGGCGCGUUCCGCAAGCCCAACAAUAA
.....((((.(((.(((.(((((.(((((((..(((((((((((.....)))).))))))).))).)))).))))))))))).))-))(((.....))).............. ( -48.00)
>DroSim_CAF1 6780 112 + 1
CUUAUCUGCAGCCGUGCCAGGUAAAGCCCAUUUGGCGGGAUCCGUUCUGCGGGUUCCCGNNNNNNNNNNNNNNNNNNNNNNNNNN-NNNNNNNNNNNNNNNNNNNNNNNNNNN
.(((((((((....)).))))))).(((.....)))((((((((.....))))))))............................-........................... ( -22.20)
>consensus
CUUAUCUGCAGCCGUGCCAGGUAAAGCCCAUUUGGCGGGAUCCGUUCUGCGGGUUCCCGCUU_UGUG________UGCAGGUAGU__GGCGCGUUCCGCAAGCCCAACAAUAA
.(((((((((....)).))))))).(((.....)))((((((((.....))))))))..........................(((((((...........)))))))..... (-24.95 = -26.20 +   1.25)

alignment

secondary structure

dotplot

Window 5

Location	13,481,388 – 13,481,493
Length	105
Sequences	3
Columns	113
Reading direction	reverse
Mean pairwise identity	65.09
Mean single sequence MFE	-32.20
Consensus MFE	-20.73
Energy contribution	-23.03
Covariance contribution	2.31
Combinations/Pair	1.04
Mean z-score	-1.50
Structure conservation index	0.64
SVM decision value	2.24
SVM RNA-class probability	0.990982
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 13481388 105 - 22224390
UUAUUGUUGGGCUUGCGGAACGCGCCCAACUACCUGCA--------CACAAAAGCGGGAACCCGCAGAACGGAUCCCGCCAAAUGGGCUUUACCUGGCACGGCUGCAGAUAAG
.....(((((((..(((...))))))))))...(((((--------..(......((((..(((.....))).))))((((...((......))))))..)..)))))..... ( -38.00)
>DroSec_CAF1 14170 112 - 1
UUAUUGUUGGGCUUGCGGAACGCGCCU-ACUACCUGCAAGUAGAGCCACAUAAGCGGGAACCCGCAGAACGGAUCCCGCCAAAUGGGCUUUACCUGGCACGGCUGCAGAUAAG
...(((((((((..(((...)))))))-)...(((((..((((((((.(((..((((((..(((.....))).))))))...)))))))))))...))).))..))))..... ( -42.00)
>DroSim_CAF1 6780 112 - 1
NNNNNNNNNNNNNNNNNNNNNNNNNNN-NNNNNNNNNNNNNNNNNNNNNNNNNNCGGGAACCCGCAGAACGGAUCCCGCCAAAUGGGCUUUACCUGGCACGGCUGCAGAUAAG
...........................-...........................((((..(((.....))).))))((((...((......))))))............... ( -16.60)
>consensus
UUAUUGUUGGGCUUGCGGAACGCGCC__ACUACCUGCA________CACA_AAGCGGGAACCCGCAGAACGGAUCCCGCCAAAUGGGCUUUACCUGGCACGGCUGCAGAUAAG
.....(((((((..((.....)))))))))...((((..................((((..(((.....))).))))((((...((......))))))......))))..... (-20.73 = -23.03 +   2.31)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:41:27 2006