Locus 991

Sequence ID	3R_DroMel_CAF1
Location	3,169,788 – 3,169,948
Length	160
Max. P	0.898664

overview

Window 5

Location	3,169,788 – 3,169,908
Length	120
Sequences	3
Columns	120
Reading direction	forward
Mean pairwise identity	98.33
Mean single sequence MFE	-31.33
Consensus MFE	-29.55
Energy contribution	-29.67
Covariance contribution	0.11
Combinations/Pair	1.03
Mean z-score	-2.16
Structure conservation index	0.94
SVM decision value	0.87
SVM RNA-class probability	0.872039
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 3169788 120 + 27905053
CUAAACAUUUGAUGCAGGUCAUUUCGACACCGAAACGGUUGCCCCAUGACUCGGCAGCUUCCACUAACGAAUUAUGCGCUCUAGCGCCUCAUGUUCUCCGUCCAAAUCUUCUGUCAUCAU
.........(((((((((..((((.(((........(((((((.........))))))).........((((...((((....)))).....))))...))).))))..)))).))))). ( -32.00)
>DroSim_CAF1 928 120 + 1
CGAAACAUUUGAUGCAGGUCAUUUCGACACCGAAACGGUUGCCCCAUGACUCGGCAGCUUCCACUAACGAAUUAUGCGCUCUAGCGCCUCAUGUUCUCCGGCCAAAUCUUCUGUCAUCAU
.........(((((((((((.....))).(((....(((((((.........))))))).........((((...((((....)))).....))))..))).........))).))))). ( -30.80)
>DroYak_CAF1 1181 120 + 1
CGAAACAUUUGAUGCAGGUCAUUUCGACACCGAAACGGUUGCCCCAUGACUCGGCAGCUUCCACUAACGAAUUAUGCGCUCUAGCGCCUCAUGUUCUCCAGCCAAAUCUUCUGUCAUCAU
.........(((((((((...(((((....))))).(((((...(((((.(((..((......))..))).....((((....)))).))))).....)))))......)))).))))). ( -31.20)
>consensus
CGAAACAUUUGAUGCAGGUCAUUUCGACACCGAAACGGUUGCCCCAUGACUCGGCAGCUUCCACUAACGAAUUAUGCGCUCUAGCGCCUCAUGUUCUCCGGCCAAAUCUUCUGUCAUCAU
.........(((((((((...(((((....))))).(((((...(((((.(((..((......))..))).....((((....)))).))))).....)))))......)))).))))). (-29.55 = -29.67 +   0.11)

alignment

secondary structure

dotplot

Window 6

Location	3,169,788 – 3,169,908
Length	120
Sequences	3
Columns	120
Reading direction	reverse
Mean pairwise identity	98.33
Mean single sequence MFE	-39.53
Consensus MFE	-37.32
Energy contribution	-37.43
Covariance contribution	0.11
Combinations/Pair	1.03
Mean z-score	-1.92
Structure conservation index	0.94
SVM decision value	0.55
SVM RNA-class probability	0.778328
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 3169788 120 - 27905053
AUGAUGACAGAAGAUUUGGACGGAGAACAUGAGGCGCUAGAGCGCAUAAUUCGUUAGUGGAAGCUGCCGAGUCAUGGGGCAACCGUUUCGGUGUCGAAAUGACCUGCAUCAAAUGUUUAG
.(((((.(((...((((.((((..((((((((.((((....))))....((((.((((....)))).)))))))))((....))..)))..)))).))))...))))))))......... ( -40.10)
>DroSim_CAF1 928 120 - 1
AUGAUGACAGAAGAUUUGGCCGGAGAACAUGAGGCGCUAGAGCGCAUAAUUCGUUAGUGGAAGCUGCCGAGUCAUGGGGCAACCGUUUCGGUGUCGAAAUGACCUGCAUCAAAUGUUUCG
.(((((.(((........(((((((..(((((.((((....))))....((((.((((....)))).)))))))))((....)).)))))))(((.....)))))))))))......... ( -40.10)
>DroYak_CAF1 1181 120 - 1
AUGAUGACAGAAGAUUUGGCUGGAGAACAUGAGGCGCUAGAGCGCAUAAUUCGUUAGUGGAAGCUGCCGAGUCAUGGGGCAACCGUUUCGGUGUCGAAAUGACCUGCAUCAAAUGUUUCG
.........((((((((((.((.((..(((..(((((..((((.(((.(((((.((((....)))).))))).)))((....))))))..)))))...)))..)).)))))))).)))). ( -38.40)
>consensus
AUGAUGACAGAAGAUUUGGCCGGAGAACAUGAGGCGCUAGAGCGCAUAAUUCGUUAGUGGAAGCUGCCGAGUCAUGGGGCAACCGUUUCGGUGUCGAAAUGACCUGCAUCAAAUGUUUCG
.(((((.(((........(((((((..(((((.((((....))))....((((.((((....)))).)))))))))((....)).)))))))(((.....)))))))))))......... (-37.32 = -37.43 +   0.11)

alignment

secondary structure

dotplot

Window 7

Location	3,169,828 – 3,169,948
Length	120
Sequences	3
Columns	120
Reading direction	reverse
Mean pairwise identity	98.89
Mean single sequence MFE	-36.93
Consensus MFE	-36.50
Energy contribution	-36.50
Covariance contribution	0.00
Combinations/Pair	1.00
Mean z-score	-2.01
Structure conservation index	0.99
SVM decision value	1.00
SVM RNA-class probability	0.898664
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 3169828 120 - 27905053
GGCAAUUGCUAUUGAUUAAAUCGGCUUAAAGCUUUGACUAAUGAUGACAGAAGAUUUGGACGGAGAACAUGAGGCGCUAGAGCGCAUAAUUCGUUAGUGGAAGCUGCCGAGUCAUGGGGC
.......(((..((((....(((((....((((((.((((((((...((((...))))...............((((....)))).....)))))))).)))))))))))))))...))) ( -36.50)
>DroSim_CAF1 968 120 - 1
GGCAAUUGCUAUUGAUUAAAUCGGCUUAAAGCUUUGACUAAUGAUGACAGAAGAUUUGGCCGGAGAACAUGAGGCGCUAGAGCGCAUAAUUCGUUAGUGGAAGCUGCCGAGUCAUGGGGC
.......(((..((((....(((((....((((((.((((((((...((((...))))...............((((....)))).....)))))))).)))))))))))))))...))) ( -36.50)
>DroYak_CAF1 1221 120 - 1
GGCAAUUGCUAUUGAUUAAAUCGGCUUAAAGCUUUGACUAAUGAUGACAGAAGAUUUGGCUGGAGAACAUGAGGCGCUAGAGCGCAUAAUUCGUUAGUGGAAGCUGCCGAGUCAUGGGGC
.......(((..((((....(((((....((((((.((((((((...(((.........)))...........((((....)))).....)))))))).)))))))))))))))...))) ( -37.80)
>consensus
GGCAAUUGCUAUUGAUUAAAUCGGCUUAAAGCUUUGACUAAUGAUGACAGAAGAUUUGGCCGGAGAACAUGAGGCGCUAGAGCGCAUAAUUCGUUAGUGGAAGCUGCCGAGUCAUGGGGC
.......(((..((((....(((((....((((((.((((((((...((((...))))...............((((....)))).....)))))))).)))))))))))))))...))) (-36.50 = -36.50 +   0.00)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:57:49 2006