Locus 612

Sequence ID	3R_DroMel_CAF1
Location	2,265,870 – 2,265,963
Length	93
Max. P	0.990119

overview

Window 2

Location	2,265,870 – 2,265,963
Length	93
Sequences	6
Columns	96
Reading direction	forward
Mean pairwise identity	74.93
Mean single sequence MFE	-41.27
Consensus MFE	-26.20
Energy contribution	-24.73
Covariance contribution	-1.47
Combinations/Pair	1.45
Mean z-score	-2.40
Structure conservation index	0.63
SVM decision value	2.20
SVM RNA-class probability	0.990119
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 2265870 93 + 27905053
UAGGAAGGCUGCGAUAGCCAGCAAAUCUGCUGCCGCUGCCCAAAGGGAA---GCGGAGGCGGCAGCGGCGGCGGCGGUAUCCGUACCAAGCAAGGA
......(((((...))))).((....(((((((((((((((....(...---.)....).)))))))))))))).((((....))))..))..... ( -41.80)
>DroPse_CAF1 28941 87 + 1
CCGCAAAGCGGCAAUUGCCAGCAAGUCGGCGGCAGCGGCCCAGAGGGAG---GCGGAGGCGGCCGCCGCCGUGGCUU------UGGCCAGCAAGGA
((.......(((....))).((....(((((((.((.((((...(....---.).).))).)).)))))))((((..------..))))))..)). ( -39.50)
>DroSim_CAF1 2422 93 + 1
AAGGAAGGCUGCGAUAGCCAGCAAAUCUGCUGCCGCUGCCCAAAGGGAA---GCGGAGGCGGCAGCGGCGGCGGCGUCAUCCGUACCAAGCAAGGA
..(((.((((((........)))...(((((((((((((((....(...---.)....).)))))))))))))).))).)))...((......)). ( -40.80)
>DroEre_CAF1 2525 93 + 1
UAGGAAAGCUGCGAUAGCCAGCAAAUCUGCUGCCGCUGCACAAAGGGAA---GCGGAGGCUGCAGCAGCGGCGGCGGCAACGGUGCCAAGCAAGGA
.......(((((..(((((((((....)))).(((((...(....)..)---)))).)))))..)))))((((.((....)).))))......... ( -42.50)
>DroWil_CAF1 2085 96 + 1
ACGCAAAGCAGCCAUUGCCAGUAAAUCAGCGGCUGCUGCCCAACGGGCUACUGCCGAGGCAGCGGCUGUUGCUGCUGCAGCAGCUACCAGCAAGGA
...........((.((((..(((....(((((((((((((.....(((....)))..)))))))))))))(((((....))))))))..)))))). ( -43.50)
>DroPer_CAF1 28900 87 + 1
CCGCAAAGCGGCAAUUGCCAGCAAGUCGGCGGCAGCGGCCCAGAGGGAG---GCGGAGGCGGCCGCCGCCGUGGCUU------UGGCCAGCAAGGA
((.......(((....))).((....(((((((.((.((((...(....---.).).))).)).)))))))((((..------..))))))..)). ( -39.50)
>consensus
AAGCAAAGCUGCGAUAGCCAGCAAAUCUGCGGCCGCUGCCCAAAGGGAA___GCGGAGGCGGCAGCCGCGGCGGCGGCA_C_GUGCCAAGCAAGGA
.......((.((........))....(((((((.(((((((....)......((....)))))))).)))))))...............))..... (-26.20 = -24.73 +  -1.47)

alignment

secondary structure

dotplot

Window 3

Location	2,265,870 – 2,265,963
Length	93
Sequences	6
Columns	96
Reading direction	reverse
Mean pairwise identity	74.93
Mean single sequence MFE	-38.08
Consensus MFE	-20.69
Energy contribution	-19.80
Covariance contribution	-0.89
Combinations/Pair	1.53
Mean z-score	-1.83
Structure conservation index	0.54
SVM decision value	0.77
SVM RNA-class probability	0.845842
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 2265870 93 - 27905053
UCCUUGCUUGGUACGGAUACCGCCGCCGCCGCUGCCGCCUCCGC---UUCCCUUUGGGCAGCGGCAGCAGAUUUGCUGGCUAUCGCAGCCUUCCUA
...((((..((((....))))...((((((((((((........---.........)))))))))(((......))))))....))))........ ( -33.73)
>DroPse_CAF1 28941 87 - 1
UCCUUGCUGGCCA------AAGCCACGGCGGCGGCCGCCUCCGC---CUCCCUCUGGGCCGCUGCCGCCGACUUGCUGGCAAUUGCCGCUUUGCGG
...((((..((..------(((...((((((((((.((((....---........)))).)))))))))).)))))..))))...((((...)))) ( -41.60)
>DroSim_CAF1 2422 93 - 1
UCCUUGCUUGGUACGGAUGACGCCGCCGCCGCUGCCGCCUCCGC---UUCCCUUUGGGCAGCGGCAGCAGAUUUGCUGGCUAUCGCAGCCUUCCUU
.....((((((((.((......))((((((((((((........---.........)))))))))(((......))))))))))).)))....... ( -33.73)
>DroEre_CAF1 2525 93 - 1
UCCUUGCUUGGCACCGUUGCCGCCGCCGCUGCUGCAGCCUCCGC---UUCCCUUUGUGCAGCGGCAGCAGAUUUGCUGGCUAUCGCAGCUUUCCUA
...((((..((((....))))(((((((((((.((((.......---......))))))))))))(((......))))))....))))........ ( -34.22)
>DroWil_CAF1 2085 96 - 1
UCCUUGCUGGUAGCUGCUGCAGCAGCAACAGCCGCUGCCUCGGCAGUAGCCCGUUGGGCAGCAGCCGCUGAUUUACUGGCAAUGGCUGCUUUGCGU
.((..((.(((.(((((((..(((((.......)))))..))))))).))).)).))((((((((((((........)))...))))))..))).. ( -43.60)
>DroPer_CAF1 28900 87 - 1
UCCUUGCUGGCCA------AAGCCACGGCGGCGGCCGCCUCCGC---CUCCCUCUGGGCCGCUGCCGCCGACUUGCUGGCAAUUGCCGCUUUGCGG
...((((..((..------(((...((((((((((.((((....---........)))).)))))))))).)))))..))))...((((...)))) ( -41.60)
>consensus
UCCUUGCUGGGCAC_G_UGAAGCCGCCGCCGCUGCCGCCUCCGC___UUCCCUUUGGGCAGCGGCAGCAGAUUUGCUGGCAAUCGCAGCUUUCCGA
.........((.............((.(((((((((....................))))))))).)).........((((.....))))..)).. (-20.69 = -19.80 +  -0.89)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:47:25 2006