Locus 8689

Sequence ID	3R_DroMel_CAF1
Location	23,203,151 – 23,203,247
Length	96
Max. P	0.891864

overview

Window 4

Location	23,203,151 – 23,203,247
Length	96
Sequences	6
Columns	108
Reading direction	forward
Mean pairwise identity	84.19
Mean single sequence MFE	-24.95
Consensus MFE	-21.56
Energy contribution	-21.87
Covariance contribution	0.31
Combinations/Pair	1.07
Mean z-score	-2.10
Structure conservation index	0.86
SVM decision value	0.97
SVM RNA-class probability	0.891864
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 23203151 96 + 27905053
-GUACUAUUUUAUUAUUAUCGCCUUUUAUGUCACAUUUGUGUGGCGUCUUUGGGCCAUAAAGGCGCACAAACUAAGGCAGCCCUC---UGGAGUUUC--------AAU
-...................(((((...(((((((....))))(((((((((.....))))))))))))....)))))(((((..---.)).)))..--------... ( -22.50)
>DroVir_CAF1 763 108 + 1
UGUUAUAUUUUAUUAUUAUCGCCCUUUAUGUCACAUUUGUGUGGCGUCUUUGAGUCAUAAAGACGCACAAACUAAAGCAACGUCCAAAUGGCGUCACACAUUGCGUAU
..........................((((.((....(((((((((((((((.(((.....)))((..........))......)))).))))))))))).)))))). ( -25.00)
>DroPse_CAF1 754 89 + 1
UGUGAUAUUUUAUUAUUAUCGCCUUUUAUGUCACAUUUGUGUGGCGUCUUUGAGUCAUAAAGACGCACAAACUAAGGCAGCCGU-----------AC--------UAU
.((((((......)))))).(((((...(((((((....))))(((((((((.....))))))))))))....)))))......-----------..--------... ( -23.50)
>DroSim_CAF1 839 96 + 1
-GUGAUAUUUUAUUAUUAUCGCCUUUUAUGUCACAUUUGUGUGGCGUCUUUGGGCCAUAAAGGCGCACAAACUAAGGCAGCCCUC---UGGUGUUUC--------UAU
-((((((......)))))).(((((...(((((((....))))(((((((((.....))))))))))))....))))).(((...---.))).....--------... ( -25.30)
>DroEre_CAF1 813 96 + 1
-GUGAUAUUUUAUUAUUAUCGCCUUUUAUGUCACAUUUGUGUGGCGUCUUUGGGCCAUAAAGGCGCACAAACUAAGGCAGCUCUC---UGGAGCUUC--------UAC
-((((((......)))))).(((((...(((((((....))))(((((((((.....))))))))))))....)))))(((((..---..)))))..--------... ( -29.90)
>DroPer_CAF1 778 89 + 1
UGUGAUAUUUUAUUAUUAUCGCCUUUUAUGUCACAUUUGUGUGGCGUCUUUGAGUCAUAAAGACGCACAAACUAAGGCAGCCCU-----------AC--------UAU
.((((((......)))))).(((((...(((((((....))))(((((((((.....))))))))))))....)))))......-----------..--------... ( -23.50)
>consensus
_GUGAUAUUUUAUUAUUAUCGCCUUUUAUGUCACAUUUGUGUGGCGUCUUUGAGCCAUAAAGACGCACAAACUAAGGCAGCCCUC___UGG_GUUAC________UAU
.((((((......)))))).(((((...(((((((....))))(((((((((.....))))))))))))....))))).............................. (-21.56 = -21.87 +   0.31)

alignment

secondary structure

dotplot

Window 5

Location	23,203,151 – 23,203,247
Length	96
Sequences	6
Columns	108
Reading direction	reverse
Mean pairwise identity	84.19
Mean single sequence MFE	-22.92
Consensus MFE	-18.38
Energy contribution	-17.60
Covariance contribution	-0.78
Combinations/Pair	1.15
Mean z-score	-2.03
Structure conservation index	0.80
SVM decision value	0.49
SVM RNA-class probability	0.755689
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 23203151 96 - 27905053
AUU--------GAAACUCCA---GAGGGCUGCCUUAGUUUGUGCGCCUUUAUGGCCCAAAGACGCCACACAAAUGUGACAUAAAAGGCGAUAAUAAUAAAAUAGUAC-
...--------.(((((...---((((....)))))))))...(((((((.((((........))))(((....))).....)))))))..................- ( -21.70)
>DroVir_CAF1 763 108 - 1
AUACGCAAUGUGUGACGCCAUUUGGACGUUGCUUUAGUUUGUGCGUCUUUAUGACUCAAAGACGCCACACAAAUGUGACAUAAAGGGCGAUAAUAAUAAAAUAUAACA
.(((((...))))).((((.((((...((..(.((.((.((.((((((((.......)))))))))).)).)).)..)).)))).))))................... ( -27.70)
>DroPse_CAF1 754 89 - 1
AUA--------GU-----------ACGGCUGCCUUAGUUUGUGCGUCUUUAUGACUCAAAGACGCCACACAAAUGUGACAUAAAAGGCGAUAAUAAUAAAAUAUCACA
...--------..-----------......(((((....(((((((((((.......))))))))((((....)))))))...)))))((((.........))))... ( -20.80)
>DroSim_CAF1 839 96 - 1
AUA--------GAAACACCA---GAGGGCUGCCUUAGUUUGUGCGCCUUUAUGGCCCAAAGACGCCACACAAAUGUGACAUAAAAGGCGAUAAUAAUAAAAUAUCAC-
...--------((.......---((((....))))...((((.(((((((.((((........))))(((....))).....)))))))...)))).......))..- ( -21.10)
>DroEre_CAF1 813 96 - 1
GUA--------GAAGCUCCA---GAGAGCUGCCUUAGUUUGUGCGCCUUUAUGGCCCAAAGACGCCACACAAAUGUGACAUAAAAGGCGAUAAUAAUAAAAUAUCAC-
...--------..(((((..---..)))))(((((.((((.((.(((.....))).)).))))(.((((....)))).)....)))))((((.........))))..- ( -25.40)
>DroPer_CAF1 778 89 - 1
AUA--------GU-----------AGGGCUGCCUUAGUUUGUGCGUCUUUAUGACUCAAAGACGCCACACAAAUGUGACAUAAAAGGCGAUAAUAAUAAAAUAUCACA
...--------..-----------......(((((....(((((((((((.......))))))))((((....)))))))...)))))((((.........))))... ( -20.80)
>consensus
AUA________GAAAC_CCA___GAGGGCUGCCUUAGUUUGUGCGCCUUUAUGACCCAAAGACGCCACACAAAUGUGACAUAAAAGGCGAUAAUAAUAAAAUAUCAC_
.............................((((((.((((.((.(((.....))).)).))))(.((((....)))).)....))))))................... (-18.38 = -17.60 +  -0.78)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:17:19 2006