Locus 8597

Sequence ID	X_DroMel_CAF1
Location	21,325,495 – 21,325,634
Length	139
Max. P	0.843285

overview

Window 5

Location	21,325,495 – 21,325,599
Length	104
Sequences	3
Columns	120
Reading direction	reverse
Mean pairwise identity	86.08
Mean single sequence MFE	-36.43
Consensus MFE	-28.72
Energy contribution	-29.17
Covariance contribution	0.45
Combinations/Pair	1.03
Mean z-score	-2.37
Structure conservation index	0.79
SVM decision value	0.76
SVM RNA-class probability	0.843285
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 21325495 104 - 22224390
UGCCCUCUUUUCCAUUGUGAAAGGACAAAGGAGACGAAGGGCAGGCCAG----------------UAUUUGCAUCGGAUGAUCUGGCAAAUGUGAGGAAUAAUCCAGCGUAUUAUUCAAA
(((((((.(((((.((((......)))).))))).).)))))).(((((----------------((((((...))))))..)))))..((((..(((....))).)))).......... ( -32.30)
>DroEre_CAF1 64130 112 - 1
UGCCCUCUUUUCCAUUGUGACAGGACAAAGGAGUCGACGGGCAGCCCAGAGGCCGAG--------CAUUUGCAUCGGAUGAUCUGGCAAAUGUGAGGAGUAAUCCAGCGCAUUACUCAAA
(((((((..((((.((((......)))).))))..)).)))))(((.(((..(((((--------(....)).))))....)))))).((((((.(((....)))..))))))....... ( -42.80)
>DroYak_CAF1 67819 120 - 1
UGCCCUCUUUUCCAUUGUGAAAGGACAAAGGAGUCGAAGGGCAGCCCAGAGGCCAAGUAUAUAAGUAUUUGCAUCGGAUGAUCUGGCAAAUGUGAGGAAUAAUCCAGCGCAUUACUCAAA
(((((((..((((.((((......)))).))))..).))))))(((.(((.((.((((((....)))))))).........)))))).((((((.(((....)))..))))))....... ( -34.20)
>consensus
UGCCCUCUUUUCCAUUGUGAAAGGACAAAGGAGUCGAAGGGCAGCCCAGAGGCC_AG________UAUUUGCAUCGGAUGAUCUGGCAAAUGUGAGGAAUAAUCCAGCGCAUUACUCAAA
(((((((..((((.((((......)))).))))..)).))))).....(((..............(((((((..(((.....))))))))))...(((....))).........)))... (-28.72 = -29.17 +   0.45)

alignment

secondary structure

dotplot

Window 6

Location	21,325,535 – 21,325,634
Length	99
Sequences	3
Columns	115
Reading direction	forward
Mean pairwise identity	86.65
Mean single sequence MFE	-24.17
Consensus MFE	-19.80
Energy contribution	-20.80
Covariance contribution	1.00
Combinations/Pair	1.00
Mean z-score	-1.88
Structure conservation index	0.82
SVM decision value	0.24
SVM RNA-class probability	0.649143
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 21325535 99 + 22224390
CAUCCGAUGCAAAUA----------------CUGGCCUGCCCUUCGUCUCCUUUGUCCUUUCACAAUGGAAAAGAGGGCAUUUCAAAUCCAAUUUACUUAGUCAUCCCACUCAAA
.....(((((.....----------------.(((..(((((((..(.(((.((((......)))).))))..)))))))..)))((......)).....).))))......... ( -18.50)
>DroEre_CAF1 64170 107 + 1
CAUCCGAUGCAAAUG--------CUCGGCCUCUGGGCUGCCCGUCGACUCCUUUGUCCUGUCACAAUGGAAAAGAGGGCAUUUCAAAUCCAAUUUACUUAGUCAUCGCACUCAAA
....((((((....(--------(((((...))))))(((((.((...(((.((((......)))).)))...)))))))....................).)))))........ ( -27.50)
>DroYak_CAF1 67859 115 + 1
CAUCCGAUGCAAAUACUUAUAUACUUGGCCUCUGGGCUGCCCUUCGACUCCUUUGUCCUUUCACAAUGGAAAAGAGGGCAUUUCAAAUCCAAUUUACUUAGUCAUCGCACUCAAA
....((((((................((((....))))((((((....(((.((((......)))).)))...)))))).....................).)))))........ ( -26.50)
>consensus
CAUCCGAUGCAAAUA________CU_GGCCUCUGGGCUGCCCUUCGACUCCUUUGUCCUUUCACAAUGGAAAAGAGGGCAUUUCAAAUCCAAUUUACUUAGUCAUCGCACUCAAA
.....(((((.................(((....)))(((((.((...(((.((((......)))).)))...)))))))....................).))))......... (-19.80 = -20.80 +   1.00)

alignment

secondary structure

dotplot

Window 7

Location	21,325,535 – 21,325,634
Length	99
Sequences	3
Columns	115
Reading direction	reverse
Mean pairwise identity	86.65
Mean single sequence MFE	-31.81
Consensus MFE	-25.70
Energy contribution	-26.37
Covariance contribution	0.67
Combinations/Pair	1.00
Mean z-score	-1.83
Structure conservation index	0.81
SVM decision value	0.13
SVM RNA-class probability	0.597798
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 21325535 99 - 22224390
UUUGAGUGGGAUGACUAAGUAAAUUGGAUUUGAAAUGCCCUCUUUUCCAUUGUGAAAGGACAAAGGAGACGAAGGGCAGGCCAG----------------UAUUUGCAUCGGAUG
(((((.(((.....))).(((((((((........(((((((.(((((.((((......)))).))))).).))))))..))).----------------.)))))).))))).. ( -26.70)
>DroEre_CAF1 64170 107 - 1
UUUGAGUGCGAUGACUAAGUAAAUUGGAUUUGAAAUGCCCUCUUUUCCAUUGUGACAGGACAAAGGAGUCGACGGGCAGCCCAGAGGCCGAG--------CAUUUGCAUCGGAUG
.....((.(((((.(.((((...((((.((((...(((((((..((((.((((......)))).))))..)).)))))...))))..)))).--------.)))))))))).)). ( -33.80)
>DroYak_CAF1 67859 115 - 1
UUUGAGUGCGAUGACUAAGUAAAUUGGAUUUGAAAUGCCCUCUUUUCCAUUGUGAAAGGACAAAGGAGUCGAAGGGCAGCCCAGAGGCCAAGUAUAUAAGUAUUUGCAUCGGAUG
(((((.(((((..(((.......((((.((((...(((((((..((((.((((......)))).))))..).))))))...))))..)))).......)))..)))))))))).. ( -34.94)
>consensus
UUUGAGUGCGAUGACUAAGUAAAUUGGAUUUGAAAUGCCCUCUUUUCCAUUGUGAAAGGACAAAGGAGUCGAAGGGCAGCCCAGAGGCC_AG________UAUUUGCAUCGGAUG
.....((.(((((.((((.....)))).((((...(((((((..((((.((((......)))).))))..)).)))))...)))).....................))))).)). (-25.70 = -26.37 +   0.67)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:08:08 2006