Locus 414

Sequence ID	3R_DroMel_CAF1
Location	1,541,775 – 1,541,899
Length	124
Max. P	0.759460

overview

Window 7

Location	1,541,775 – 1,541,874
Length	99
Sequences	6
Columns	114
Reading direction	reverse
Mean pairwise identity	75.74
Mean single sequence MFE	-28.55
Consensus MFE	-11.14
Energy contribution	-12.28
Covariance contribution	1.14
Combinations/Pair	1.19
Mean z-score	-2.26
Structure conservation index	0.39
SVM decision value	0.50
SVM RNA-class probability	0.759460
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 1541775 99 - 27905053
CCAACCUUCUACUAACACCCACCCACACCCCCAGUUCGCUGGGCAAGCAGGAUCCAC---UGCAGCAUCCGUUGUUGCUGGGCCAGUUUGCCGGC---UCC---------GAAC
.................................(((((.(.(((((((.((.((((.---.((((((.....)))))))))))).))))))).).---..)---------)))) ( -29.20)
>DroPse_CAF1 42610 105 - 1
CGAACCUCCUACUAACACCCACCCACACGCCCAGCUCCCUG---AAGCAGGAGCAGC---UGCAACAAAACAUGAUGCUGGGCCAGUUCUCAAAC---GCAGUAAAUGUCGAAC
(((......((((...............(((((((((((((---...)))).((...---.))..........)).)))))))..(((....)))---..))))....)))... ( -23.50)
>DroEre_CAF1 42664 99 - 1
CCAACCUCCUACUAACACCCACCCACACCCCCAGUUCGCUGGGCAAGCAGGAGCCAC---UGCAGCAUCAGUUGCUGCUGGGCCAGCUUGCCGGC---UCC---------GAAC
.............................(((((....)))))......((((((.(---.((((((.....)))))).)(((......))))))---)))---------.... ( -35.70)
>DroYak_CAF1 38730 102 - 1
CCAACCUCCUACUAACACCCACCCAUACCCCCAGUUCGCUGGGCAAGCAGGAUCCAC---UGCAACAUCAGUUGCUGCUGGGCCAGUUCGCCACCUCCUCC---------GAAC
.....................(((.....(((((....)))))..(((((....)..---.(((((....))))))))))))...(((((..........)---------)))) ( -23.80)
>DroAna_CAF1 41230 111 - 1
CAAACCUUCUACUAACCCCCAACAAUACUCCCAACUCGAUGGGCAAGCAGGAGGCACAGUUGCAACAUCAGUUGCUCCUGGGCCAAUACGCCAGC---UCCCUGCAAUCGGAAC
..................((.........((((......))))...(((((..((.(((..(((((....)))))..)))(((......))).))---..)))))....))... ( -35.60)
>DroPer_CAF1 44130 105 - 1
CGAACCUCCUACUAACACCCACCCACACGCCCAGCUCCCUG---AAGCAGGAGCAGC---UGCAACAAAACAUGAUGCUGGGCCAGUUCUCAAAC---GCAGUAAAUGUCGAAC
(((......((((...............(((((((((((((---...)))).((...---.))..........)).)))))))..(((....)))---..))))....)))... ( -23.50)
>consensus
CCAACCUCCUACUAACACCCACCCACACCCCCAGCUCGCUGGGCAAGCAGGAGCCAC___UGCAACAUCAGUUGCUGCUGGGCCAGUUCGCCAGC___UCC_________GAAC
.............................((((((((.(((......))))).........(((((....))))).))))))................................ (-11.14 = -12.28 +   1.14)

alignment

secondary structure

dotplot

Window 8

Location	1,541,801 – 1,541,899
Length	98
Sequences	6
Columns	101
Reading direction	reverse
Mean pairwise identity	82.39
Mean single sequence MFE	-23.66
Consensus MFE	-11.31
Energy contribution	-13.00
Covariance contribution	1.70
Combinations/Pair	1.18
Mean z-score	-3.26
Structure conservation index	0.48
SVM decision value	0.46
SVM RNA-class probability	0.744164
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 1541801 98 - 27905053
CAGCAGCAACAUUUGCUGACCACCUCCAACCUUCUACUAACACCCACCCACACCCCCAGUUCGCUGGGCAAGCAGGAUCCAC---UGCAGCAUCCGUUGUU
....((((((...((((.....................................(((((....)))))...((((......)---)))))))...)))))) ( -24.20)
>DroPse_CAF1 42645 95 - 1
CAGCAGCAACACUUGUUAGCAACAUCGAACCUCCUACUAACACCCACCCACACGCCCAGCUCCCUG---AAGCAGGAGCAGC---UGCAACAAAACAUGAU
..(((((......((((((.................))))))................(((((...---.....))))).))---)))............. ( -21.53)
>DroEre_CAF1 42690 98 - 1
CACCAGCAACAUUUGCUGACCACCUCCAACCUCCUACUAACACCCACCCACACCCCCAGUUCGCUGGGCAAGCAGGAGCCAC---UGCAGCAUCAGUUGCU
....((((((...((((.....................................(((((....)))))...((((......)---)))))))...)))))) ( -26.60)
>DroYak_CAF1 38759 98 - 1
CAGCAGCAACAUUUGCUGACCACCUCCAACCUCCUACUAACACCCACCCAUACCCCCAGUUCGCUGGGCAAGCAGGAUCCAC---UGCAACAUCAGUUGCU
((((((......))))))........((((........................(((((....)))))...((((......)---))).......)))).. ( -23.10)
>DroAna_CAF1 41265 101 - 1
CAACAGCAACAUUUGCUGGCAACAUCAAACCUUCUACUAACCCCCAACAAUACUCCCAACUCGAUGGGCAAGCAGGAGGCACAGUUGCAACAUCAGUUGCU
....((((((...((...(((((......((((((.((....((((.(..............).))))..)).))))))....)))))..))...)))))) ( -24.34)
>DroPer_CAF1 44165 95 - 1
CAGCAGCAACACUUGUUGGCAACAUCGAACCUCCUACUAACACCCACCCACACGCCCAGCUCCCUG---AAGCAGGAGCAGC---UGCAACAAAACAUGAU
..(((((.....(((.((....)).)))..............................(((((...---.....))))).))---)))............. ( -22.20)
>consensus
CAGCAGCAACAUUUGCUGACAACAUCCAACCUCCUACUAACACCCACCCACACCCCCAGCUCGCUGGGCAAGCAGGAGCCAC___UGCAACAUCAGUUGCU
...(((((.....)))))............(((((.((................(((((....)))))..)).)))))........(((((....))))). (-11.31 = -13.00 +   1.70)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:42:37 2006