Locus 1332

Sequence ID	2L_DroMel_CAF1
Location	3,523,717 – 3,523,865
Length	148
Max. P	0.908492

overview

Window 5

Location	3,523,717 – 3,523,825
Length	108
Sequences	5
Columns	110
Reading direction	forward
Mean pairwise identity	86.02
Mean single sequence MFE	-22.92
Consensus MFE	-19.68
Energy contribution	-19.72
Covariance contribution	0.04
Combinations/Pair	1.13
Mean z-score	-1.40
Structure conservation index	0.86
SVM decision value	-0.07
SVM RNA-class probability	0.500000
Prediction	OTHER

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 3523717 108 + 22407834
AUAAUUAAAAUUGUUU--UCUUAUUUUGUACACCUACUGGCGCAAAAUGGUUUUUUCCCUCGAGGAAUACCGCGAUCGCAGGUGAACACUUUCGAUCCUUGUAGAAAGUA
.............(((--(((.(((((((...((....)).)))))))(((...((((.....)))).)))..(((((.((((....)))).))))).....)))))).. ( -22.40)
>DroSec_CAF1 32728 108 + 1
AUAAUUUAAAUUGUUU--UCUUAUUUUGUACACCUACUGGCGCAAAAUGGUUUUUUCCCUCGAGGAAUACCGCGAUCGCAGGUGAACACCUUCGAUCCUUGUAGAAAGUA
.............(((--(((.(((((((...((....)).)))))))(((...((((.....)))).)))..(((((.((((....)))).))))).....)))))).. ( -25.10)
>DroSim_CAF1 34421 108 + 1
AUAAUUUAAAUUGUUU--UCUUAUUUUGUACACCUACUGGCGCAAAAUGGUUUUUUCCCUCGAGGAAUACCGCGAUCGCAGGCGAACACCUUCGAUCCUUGUAGAAAGUA
.............(((--(((.(((((((...((....)).)))))))(((...((((.....)))).)))..(((((.(((......))).))))).....)))))).. ( -23.00)
>DroEre_CAF1 30654 109 + 1
AUAGU-AAAAUUGUUUAUUUUUGUUAUAUACACCUACUAGCACAAAAUGGUUUUUUCCCUCGCGGAAUACCGCGAUCGCAGGUGAACACCUUCGAUCCUUGUAAAGAAUA
.((((-(....(((.(((.......))).)))..)))))..........(((((((.....((((....))))(((((.((((....)))).))))).....))))))). ( -23.10)
>DroYak_CAF1 32112 95 + 1
AUUAC-AAA--------------UAAUAUUCACCUACUAGCACAAAAUGGUUUUUUCCCUCGAGGAAUUCCACGAUCGCAGGUGAACACCUUCGAUCCUUGUAGAAAAUA
.....-...--------------..........((((.((.......(((....((((.....))))..))).(((((.((((....)))).))))))).))))...... ( -21.00)
>consensus
AUAAUUAAAAUUGUUU__UCUUAUUUUGUACACCUACUGGCGCAAAAUGGUUUUUUCCCUCGAGGAAUACCGCGAUCGCAGGUGAACACCUUCGAUCCUUGUAGAAAGUA
.................................((((.((.......((((...((((.....)))).)))).(((((.((((....)))).))))))).))))...... (-19.68 = -19.72 +   0.04)

alignment

secondary structure

dotplot

Window 6

Location	3,523,717 – 3,523,825
Length	108
Sequences	5
Columns	110
Reading direction	reverse
Mean pairwise identity	86.02
Mean single sequence MFE	-26.92
Consensus MFE	-21.36
Energy contribution	-20.60
Covariance contribution	-0.76
Combinations/Pair	1.23
Mean z-score	-2.04
Structure conservation index	0.79
SVM decision value	1.06
SVM RNA-class probability	0.908492
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 3523717 108 - 22407834
UACUUUCUACAAGGAUCGAAAGUGUUCACCUGCGAUCGCGGUAUUCCUCGAGGGAAAAAACCAUUUUGCGCCAGUAGGUGUACAAAAUAAGA--AAACAAUUUUAAUUAU
.((((((..........))))))((.(((((((...((((((.((((.....))))...))).....)))...))))))).)).........--................ ( -24.90)
>DroSec_CAF1 32728 108 - 1
UACUUUCUACAAGGAUCGAAGGUGUUCACCUGCGAUCGCGGUAUUCCUCGAGGGAAAAAACCAUUUUGCGCCAGUAGGUGUACAAAAUAAGA--AAACAAUUUAAAUUAU
...(((((.....(((((.((((....)))).)))))..(((.((((.....))))...)))....((((((....)))))).......)))--)).............. ( -27.30)
>DroSim_CAF1 34421 108 - 1
UACUUUCUACAAGGAUCGAAGGUGUUCGCCUGCGAUCGCGGUAUUCCUCGAGGGAAAAAACCAUUUUGCGCCAGUAGGUGUACAAAAUAAGA--AAACAAUUUAAAUUAU
...(((((.....(((((.((((....)))).)))))..(((.((((.....))))...)))....((((((....)))))).......)))--)).............. ( -27.60)
>DroEre_CAF1 30654 109 - 1
UAUUCUUUACAAGGAUCGAAGGUGUUCACCUGCGAUCGCGGUAUUCCGCGAGGGAAAAAACCAUUUUGUGCUAGUAGGUGUAUAUAACAAAAAUAAACAAUUUU-ACUAU
.......(((((((((((.((((....)))).)))))((((....))))..((.......))..)))))).((((((.(((.(((.......))).)))...))-)))). ( -27.60)
>DroYak_CAF1 32112 95 - 1
UAUUUUCUACAAGGAUCGAAGGUGUUCACCUGCGAUCGUGGAAUUCCUCGAGGGAAAAAACCAUUUUGUGCUAGUAGGUGAAUAUUA--------------UUU-GUAAU
.......((((((.......(((((((((((((..(((.((....)).)))((.......))...........))))))))))))).--------------)))-))).. ( -27.20)
>consensus
UACUUUCUACAAGGAUCGAAGGUGUUCACCUGCGAUCGCGGUAUUCCUCGAGGGAAAAAACCAUUUUGCGCCAGUAGGUGUACAAAAUAAGA__AAACAAUUUUAAUUAU
.((((((..........))))))((.(((((((..(((.((....)).)))((.......))...........))))))).))........................... (-21.36 = -20.60 +  -0.76)

alignment

secondary structure

dotplot

Window 7

Location	3,523,745 – 3,523,865
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	92.75
Mean single sequence MFE	-33.10
Consensus MFE	-27.92
Energy contribution	-27.32
Covariance contribution	-0.60
Combinations/Pair	1.18
Mean z-score	-1.39
Structure conservation index	0.84
SVM decision value	0.39
SVM RNA-class probability	0.716748
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 3523745 120 - 22407834
AAUAGUAAAUGGAUCCAUUAUUUUUCAUUGCGAUCAAGGAUACUUUCUACAAGGAUCGAAAGUGUUCACCUGCGAUCGCGGUAUUCCUCGAGGGAAAAAACCAUUUUGCGCCAGUAGGUG
....((((((((..............(((((((((.(((((((((((..........))))))))...)))..))))))))).((((.....))))....))).)))))(((....))). ( -34.10)
>DroSec_CAF1 32756 120 - 1
AAUAGUUAAUGGAUCUAUUGUUUUCCAUUGCGAUCAAGGAUACUUUCUACAAGGAUCGAAGGUGUUCACCUGCGAUCGCGGUAUUCCUCGAGGGAAAAAACCAUUUUGCGCCAGUAGGUG
.......((((((..........))))))((((((.(((((((((((..........))))))))...)))..))))))(((.((((.....))))...)))......((((....)))) ( -33.50)
>DroSim_CAF1 34449 120 - 1
AAUAGUUAAUGGAUCUAUUGUUUUCCAUUGCGAUCAAGGAUACUUUCUACAAGGAUCGAAGGUGUUCGCCUGCGAUCGCGGUAUUCCUCGAGGGAAAAAACCAUUUUGCGCCAGUAGGUG
.......((((((..........))))))((((((..((((((((((..........))))))))))(....)))))))(((.((((.....))))...)))......((((....)))) ( -34.10)
>DroEre_CAF1 30683 120 - 1
AAAAUUAAAUGGAUCUAUACUUUUUCUUUGCGAUCAAGGAUAUUCUUUACAAGGAUCGAAGGUGUUCACCUGCGAUCGCGGUAUUCCGCGAGGGAAAAAACCAUUUUGUGCUAGUAGGUG
................((((((((((((((..(..((.....))..)..))))))..)))))))).(((((((..((((((....))))))((.......))...........))))))) ( -31.90)
>DroYak_CAF1 32127 120 - 1
AAUAGUUAAUGGAUCCAUUGUUUUUCAUUGCGAUCAAGGAUAUUUUCUACAAGGAUCGAAGGUGUUCACCUGCGAUCGUGGAAUUCCUCGAGGGAAAAAACCAUUUUGUGCUAGUAGGUG
..((((.((((((((((((((........)))))...))))...((((((...(((((.((((....)))).)))))))))))((((.....))))....)))))....))))....... ( -31.90)
>consensus
AAUAGUUAAUGGAUCUAUUGUUUUUCAUUGCGAUCAAGGAUACUUUCUACAAGGAUCGAAGGUGUUCACCUGCGAUCGCGGUAUUCCUCGAGGGAAAAAACCAUUUUGCGCCAGUAGGUG
.......(((((..............(((((((((.(((((((((((..........))))))))...)))..))))))))).((((....)))).....)))))...((((....)))) (-27.92 = -27.32 +  -0.60)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:59:52 2006