Locus 6060

Sequence ID	3L_DroMel_CAF1
Location	16,133,765 – 16,134,005
Length	240
Max. P	0.910157

overview

Window 7

Location	16,133,765 – 16,133,885
Length	120
Sequences	3
Columns	120
Reading direction	forward
Mean pairwise identity	98.32
Mean single sequence MFE	-37.07
Consensus MFE	-32.07
Energy contribution	-32.07
Covariance contribution	0.00
Combinations/Pair	1.00
Mean z-score	-2.44
Structure conservation index	0.87
SVM decision value	0.51
SVM RNA-class probability	0.762180
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 16133765 120 + 23771897
CCAAUACAAAGAGCCCUGUCUCGAAUCAUAACUCAUUGAACUUUUGCCGGCAGCAGCAGCCGCUGCUGAAACAUAAAAAGUGUCAAUCAGUGACUCUGCUGUGGCAACGAUGGCGACGCC
............((..(((((((..(((........)))....((((((.((((((.((.(((((.(((.((.......)).)))..))))).))))))))))))))))).))))..)). ( -36.20)
>DroSim_CAF1 9071 117 + 1
CCAAUACAAAGAGCCCUGUCUCGAAUCAUAACUCAUUGAACUUUUGCCGGCAGCAGCAGCCGC---UGAAACAUAAAAAGUGUCAAUCAGUGACUCUGCUGUGGCAACGAUGGCGACGCC
............((..(((((((..(((........)))....((((((.((((((.((.(((---(((.((((.....))))...)))))).))))))))))))))))).))))..)). ( -37.50)
>DroYak_CAF1 1958 117 + 1
CCAAUACAAAGAGCCCUGUCUCGAAUCAUAACUCAUUGAACUUUUGCCGGCAGCAGCAGCCGC---UGAAACAUAAAAAGUGUCAAUCAGUGACUCUGCUGUGGCAACGAUGGCGACGCC
............((..(((((((..(((........)))....((((((.((((((.((.(((---(((.((((.....))))...)))))).))))))))))))))))).))))..)). ( -37.50)
>consensus
CCAAUACAAAGAGCCCUGUCUCGAAUCAUAACUCAUUGAACUUUUGCCGGCAGCAGCAGCCGC___UGAAACAUAAAAAGUGUCAAUCAGUGACUCUGCUGUGGCAACGAUGGCGACGCC
............((..(((((((..(((........)))....((((((.((((((.((.(((...(((.((.......)).)))....))).))))))))))))))))).))))..)). (-32.07 = -32.07 +   0.00)

alignment

secondary structure

dotplot

Window 8

Location	16,133,805 – 16,133,925
Length	120
Sequences	3
Columns	120
Reading direction	forward
Mean pairwise identity	98.32
Mean single sequence MFE	-40.60
Consensus MFE	-35.57
Energy contribution	-35.57
Covariance contribution	0.00
Combinations/Pair	1.00
Mean z-score	-3.08
Structure conservation index	0.88
SVM decision value	1.07
SVM RNA-class probability	0.910157
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 16133805 120 + 23771897
CUUUUGCCGGCAGCAGCAGCCGCUGCUGAAACAUAAAAAGUGUCAAUCAGUGACUCUGCUGUGGCAACGAUGGCGACGCCUCCAAAGUCCCAUUACAAUGCCAUUUUUAUGGACACCGCU
.....((.(((((((((....)))))))...(((((((((.((((.....)))).))...((((((..(((((.(((.........))))))))....)))))))))))))....)))). ( -39.80)
>DroSim_CAF1 9111 117 + 1
CUUUUGCCGGCAGCAGCAGCCGC---UGAAACAUAAAAAGUGUCAAUCAGUGACUCUGCUGUGGCAACGAUGGCGACGCCUCCAAAGUCCCAUUACAAUGCCAUUUUUAUGGACACCGCU
...((((((.((((((.((.(((---(((.((((.....))))...)))))).)))))))))))))).(((((.(((.........))))))))....((((((....)))).))..... ( -41.00)
>DroYak_CAF1 1998 117 + 1
CUUUUGCCGGCAGCAGCAGCCGC---UGAAACAUAAAAAGUGUCAAUCAGUGACUCUGCUGUGGCAACGAUGGCGACGCCUCCAAAGUCCCAUUACAAUGCCAUUUUUAUGGACACCGCU
...((((((.((((((.((.(((---(((.((((.....))))...)))))).)))))))))))))).(((((.(((.........))))))))....((((((....)))).))..... ( -41.00)
>consensus
CUUUUGCCGGCAGCAGCAGCCGC___UGAAACAUAAAAAGUGUCAAUCAGUGACUCUGCUGUGGCAACGAUGGCGACGCCUCCAAAGUCCCAUUACAAUGCCAUUUUUAUGGACACCGCU
...((((((.((((((.((.(((...(((.((.......)).)))....))).)))))))))))))).(((((.(((.........))))))))....((((((....)))).))..... (-35.57 = -35.57 +   0.00)

alignment

secondary structure

dotplot

Window 9

Location	16,133,805 – 16,133,925
Length	120
Sequences	3
Columns	120
Reading direction	reverse
Mean pairwise identity	98.32
Mean single sequence MFE	-43.57
Consensus MFE	-38.47
Energy contribution	-38.47
Covariance contribution	-0.00
Combinations/Pair	1.00
Mean z-score	-2.43
Structure conservation index	0.88
SVM decision value	0.66
SVM RNA-class probability	0.814127
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 16133805 120 - 23771897
AGCGGUGUCCAUAAAAAUGGCAUUGUAAUGGGACUUUGGAGGCGUCGCCAUCGUUGCCACAGCAGAGUCACUGAUUGACACUUUUUAUGUUUCAGCAGCGGCUGCUGCUGCCGGCAAAAG
.((((((.((((....)))))))))).(((((((.........))).))))..(((((.((((((((((.(((.((((.((.......)).))))))).)))).))))))..)))))... ( -44.90)
>DroSim_CAF1 9111 117 - 1
AGCGGUGUCCAUAAAAAUGGCAUUGUAAUGGGACUUUGGAGGCGUCGCCAUCGUUGCCACAGCAGAGUCACUGAUUGACACUUUUUAUGUUUCA---GCGGCUGCUGCUGCCGGCAAAAG
.((((((.((((....)))))))))).(((((((.........))).))))..(((((.((((((((((.((((..((((.......)))))))---).)))).))))))..)))))... ( -42.90)
>DroYak_CAF1 1998 117 - 1
AGCGGUGUCCAUAAAAAUGGCAUUGUAAUGGGACUUUGGAGGCGUCGCCAUCGUUGCCACAGCAGAGUCACUGAUUGACACUUUUUAUGUUUCA---GCGGCUGCUGCUGCCGGCAAAAG
.((((((.((((....)))))))))).(((((((.........))).))))..(((((.((((((((((.((((..((((.......)))))))---).)))).))))))..)))))... ( -42.90)
>consensus
AGCGGUGUCCAUAAAAAUGGCAUUGUAAUGGGACUUUGGAGGCGUCGCCAUCGUUGCCACAGCAGAGUCACUGAUUGACACUUUUUAUGUUUCA___GCGGCUGCUGCUGCCGGCAAAAG
.((((((.((((....)))))))))).(((((((.........))).))))..(((((.((((((((((.(....(((.((.......)).)))...).)))).))))))..)))))... (-38.47 = -38.47 +  -0.00)

alignment

secondary structure

dotplot

Window 0

Location	16,133,845 – 16,133,965
Length	120
Sequences	3
Columns	120
Reading direction	reverse
Mean pairwise identity	98.33
Mean single sequence MFE	-42.83
Consensus MFE	-42.83
Energy contribution	-42.83
Covariance contribution	0.00
Combinations/Pair	1.00
Mean z-score	-1.41
Structure conservation index	1.00
SVM decision value	0.10
SVM RNA-class probability	0.584297
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 16133845 120 - 23771897
GAGCUGCUCACUCCGCUCCAGCUGGAGCAGCAUCCCCGCCAGCGGUGUCCAUAAAAAUGGCAUUGUAAUGGGACUUUGGAGGCGUCGCCAUCGUUGCCACAGCAGAGUCACUGAUUGACA
...(((((...((((((((....)))))......((((...((((((.((((....))))))))))..)))).....)))((((.((....)).))))..))))).((((.....)))). ( -42.90)
>DroSim_CAF1 9148 120 - 1
GAGCUGCUCACUCCGCUCCAGCUGGAGCAGCAUCCCCGCCAGCGGUGUCCAUAAAAAUGGCAUUGUAAUGGGACUUUGGAGGCGUCGCCAUCGUUGCCACAGCAGAGUCACUGAUUGACA
...(((((...((((((((....)))))......((((...((((((.((((....))))))))))..)))).....)))((((.((....)).))))..))))).((((.....)))). ( -42.90)
>DroYak_CAF1 2035 117 - 1
---CUGCUCACUCCGCUCCAGCUGGAGCAGCAUCCCCGCCAGCGGUGUCCAUAAAAAUGGCAUUGUAAUGGGACUUUGGAGGCGUCGCCAUCGUUGCCACAGCAGAGUCACUGAUUGACA
---(((((...((((((((....)))))......((((...((((((.((((....))))))))))..)))).....)))((((.((....)).))))..))))).((((.....)))). ( -42.70)
>consensus
GAGCUGCUCACUCCGCUCCAGCUGGAGCAGCAUCCCCGCCAGCGGUGUCCAUAAAAAUGGCAUUGUAAUGGGACUUUGGAGGCGUCGCCAUCGUUGCCACAGCAGAGUCACUGAUUGACA
...(((((...((((((((....)))))......((((...((((((.((((....))))))))))..)))).....)))((((.((....)).))))..))))).((((.....)))). (-42.83 = -42.83 +   0.00)

alignment

secondary structure

dotplot

Window 1

Location	16,133,885 – 16,134,005
Length	120
Sequences	3
Columns	120
Reading direction	reverse
Mean pairwise identity	82.22
Mean single sequence MFE	-34.83
Consensus MFE	-28.67
Energy contribution	-29.00
Covariance contribution	0.33
Combinations/Pair	1.00
Mean z-score	-1.91
Structure conservation index	0.82
SVM decision value	0.88
SVM RNA-class probability	0.872300
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 16133885 120 - 23771897
CUCCUGCUCCUUCUACUACUCCACUCCUCGUCUCCAGAUGGAGCUGCUCACUCCGCUCCAGCUGGAGCAGCAUCCCCGCCAGCGGUGUCCAUAAAAAUGGCAUUGUAAUGGGACUUUGGA
...................((((......(.((((((.((((((..........)))))).)))))))......((((...((((((.((((....))))))))))..))))....)))) ( -38.30)
>DroSim_CAF1 9188 120 - 1
CUCCUGCUCCUUCUACUCCUGCACUCCUCGUCUCCAGAUGGAGCUGCUCACUCCGCUCCAGCUGGAGCAGCAUCCCCGCCAGCGGUGUCCAUAAAAAUGGCAUUGUAAUGGGACUUUGGA
.(((((((............(((((((((.......)).)))).))).......(((((....)))))))))..((((...((((((.((((....))))))))))..)))).....))) ( -38.90)
>DroYak_CAF1 2075 92 - 1
GUCCUUCUCCUUCUU----------------------------CUGCUCACUCCGCUCCAGCUGGAGCAGCAUCCCCGCCAGCGGUGUCCAUAAAAAUGGCAUUGUAAUGGGACUUUGGA
.(((...........----------------------------.((((..((((((....)).)))).))))..((((...((((((.((((....))))))))))..)))).....))) ( -27.30)
>consensus
CUCCUGCUCCUUCUACU_CU_CACUCCUCGUCUCCAGAUGGAGCUGCUCACUCCGCUCCAGCUGGAGCAGCAUCCCCGCCAGCGGUGUCCAUAAAAAUGGCAUUGUAAUGGGACUUUGGA
.(((......................................(((((((.(...((....)).))))))))...((((...((((((.((((....))))))))))..)))).....))) (-28.67 = -29.00 +   0.33)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:08:44 2006