Locus 1424

Sequence ID	3R_DroMel_CAF1
Location	4,130,403 – 4,130,563
Length	160
Max. P	0.901734

overview

Window 1

Location	4,130,403 – 4,130,523
Length	120
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	85.56
Mean single sequence MFE	-43.96
Consensus MFE	-29.31
Energy contribution	-30.00
Covariance contribution	0.69
Combinations/Pair	1.22
Mean z-score	-2.01
Structure conservation index	0.67
SVM decision value	0.48
SVM RNA-class probability	0.753929
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 4130403 120 + 27905053
UCCGGACUCCGAGAAGGACUUGUUCAUGGCCUUUUGGACCUCGGGCGAGGAUGAGCUGUAGAUUUUCUUGAACAGGUUGGUGAGGGCCGCCUCGCCCUUGGCCUCCUUCUCGUCGAUCUU
...((((..(((((((((.........((((.....(((((.(..((((((....(....)...))))))..))))))(((((((....)))))))...)))))))))))))..).))). ( -45.30)
>DroSim_CAF1 634 120 + 1
UCCCGACUCCGAGAAGGACUUGUUCAUGGCCUUUUGGACCUCGGGCGAGGAUGAGCUGUAGAUUUUCUUGAACAGGUUGGUGAGUGCCGCCUCGCCCUUGGCCUCCUUCUCGGCGAUCUU
....(((.((((((((((.........((((.....(....)((((((((..((.((((((.....))...)))).))(((....))).))))))))..)))))))))))))).).)).. ( -47.60)
>DroWil_CAF1 1051 120 + 1
GCCGGACUCCGUAAAUGAUUUGUUCAUGGCCAUUUGCACCUCCGGUGUGGAGGUGCUGUAGAUCUUUUUGAAUAAUUGAUUGAGAGCCGCUUCACCUUUGGCUUCUUUUUCAUCGAUCUU
(((((...))....((((.....))))))).....((((((((.....))))))))...(((((............(((..((((((((.........)))).))))..)))..))))). ( -32.94)
>DroYak_CAF1 636 120 + 1
UCCGGAUUCCGAGAAGGACUUGUUCAUGGCCUUUUGGACCUCGGGCGAGGAUGUGCUGUAGAUCUUCUUGAACAGGUUGUUGAGGGCCGUCUCGCCCUUAGCCUCCUUCUCGUCGAUCUU
...(((((.(((((((((((((((((..((((..........))))((((((.((...)).)))))).))))))))..(((((((((......))))))))).)))))))))..))))). ( -50.00)
>consensus
UCCGGACUCCGAGAAGGACUUGUUCAUGGCCUUUUGGACCUCGGGCGAGGAUGAGCUGUAGAUCUUCUUGAACAGGUUGGUGAGGGCCGCCUCGCCCUUGGCCUCCUUCUCGUCGAUCUU
.........(((((((((...(((((........)))))...((((((((....(((.(.(((..(((.....)))..))).).)))..))))))))......)))))))))........ (-29.31 = -30.00 +   0.69)

alignment

secondary structure

dotplot

Window 2

Location	4,130,403 – 4,130,523
Length	120
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	85.56
Mean single sequence MFE	-38.70
Consensus MFE	-29.35
Energy contribution	-29.60
Covariance contribution	0.25
Combinations/Pair	1.18
Mean z-score	-2.12
Structure conservation index	0.76
SVM decision value	1.02
SVM RNA-class probability	0.901734
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 4130403 120 - 27905053
AAGAUCGACGAGAAGGAGGCCAAGGGCGAGGCGGCCCUCACCAACCUGUUCAAGAAAAUCUACAGCUCAUCCUCGCCCGAGGUCCAAAAGGCCAUGAACAAGUCCUUCUCGGAGUCCGGA
..((.(..(((((((((((((..((((((((.((......))...((((...((.....)))))).....))))))))..)))).....(........)...)))))))))..))).... ( -42.70)
>DroSim_CAF1 634 120 - 1
AAGAUCGCCGAGAAGGAGGCCAAGGGCGAGGCGGCACUCACCAACCUGUUCAAGAAAAUCUACAGCUCAUCCUCGCCCGAGGUCCAAAAGGCCAUGAACAAGUCCUUCUCGGAGUCGGGA
..(((..((((((((((((((..((((((((.((......))...((((...((.....)))))).....))))))))..)))).....(........)...)))))))))).))).... ( -45.80)
>DroWil_CAF1 1051 120 - 1
AAGAUCGAUGAAAAAGAAGCCAAAGGUGAAGCGGCUCUCAAUCAAUUAUUCAAAAAGAUCUACAGCACCUCCACACCGGAGGUGCAAAUGGCCAUGAACAAAUCAUUUACGGAGUCCGGC
.(((((..((((.((((((((...........)))).))......)).))))....)))))...((((((((.....)))))))).....(((((((.....))))....((...))))) ( -29.30)
>DroYak_CAF1 636 120 - 1
AAGAUCGACGAGAAGGAGGCUAAGGGCGAGACGGCCCUCAACAACCUGUUCAAGAAGAUCUACAGCACAUCCUCGCCCGAGGUCCAAAAGGCCAUGAACAAGUCCUUCUCGGAAUCCGGA
..(((...(((((((((......(((((((..(........)...((((...((.....))))))......)))))))..((((.....)))).........)))))))))..))).... ( -37.00)
>consensus
AAGAUCGACGAGAAGGAGGCCAAGGGCGAGGCGGCCCUCAACAACCUGUUCAAGAAAAUCUACAGCACAUCCUCGCCCGAGGUCCAAAAGGCCAUGAACAAGUCCUUCUCGGAGUCCGGA
..(((...(((((((((......((((((((..((..........((.....))..........))....))))))))..((((.....)))).........)))))))))..))).... (-29.35 = -29.60 +   0.25)

alignment

secondary structure

dotplot

Window 3

Location	4,130,443 – 4,130,563
Length	120
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	83.75
Mean single sequence MFE	-39.71
Consensus MFE	-29.76
Energy contribution	-30.82
Covariance contribution	1.06
Combinations/Pair	1.20
Mean z-score	-1.49
Structure conservation index	0.75
SVM decision value	0.04
SVM RNA-class probability	0.556138
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 4130443 120 + 27905053
UCGGGCGAGGAUGAGCUGUAGAUUUUCUUGAACAGGUUGGUGAGGGCCGCCUCGCCCUUGGCCUCCUUCUCGUCGAUCUUUUCCUCCUCGCUGACCAGCUGGUCCCAGUUCUUGGCCUUG
..(((((((((.(((....(((((..(..(((.((((((((((((....)))))))...)))))..)))..)..))))).))).)))))))...(((((((....))))...)))))... ( -43.00)
>DroSim_CAF1 674 120 + 1
UCGGGCGAGGAUGAGCUGUAGAUUUUCUUGAACAGGUUGGUGAGUGCCGCCUCGCCCUUGGCCUCCUUCUCGGCGAUCUUCUCCUCCUCGUUGACCAGCUGGUCCCAGUUUUUGGCCUUG
..((((((((..((.((((((.....))...)))).))(((....))).))))))))..((((......(((((((...........)))))))..(((((....)))))...))))... ( -42.20)
>DroWil_CAF1 1091 120 + 1
UCCGGUGUGGAGGUGCUGUAGAUCUUUUUGAAUAAUUGAUUGAGAGCCGCUUCACCUUUGGCUUCUUUUUCAUCGAUCUUUUCCUCCUCCUUGACCAAAAGGUCCCAGUUCUUUGUUUGC
...((...(((((.(....(((((............(((..((((((((.........)))).))))..)))..)))))....).)))))..((((....)))))).............. ( -28.34)
>DroYak_CAF1 676 120 + 1
UCGGGCGAGGAUGUGCUGUAGAUCUUCUUGAACAGGUUGUUGAGGGCCGUCUCGCCCUUAGCCUCCUUCUCGUCGAUCUUCUCCUCCUCGCUGACCAGCUGGUCCCAGUUCUUGGCCUUA
..(((((((((.(.(....(((((....(((..(((..(((((((((......)))))))))..)))..)))..))))).).).)))))))...(((((((....))))...)))))... ( -45.30)
>consensus
UCGGGCGAGGAUGAGCUGUAGAUCUUCUUGAACAGGUUGGUGAGGGCCGCCUCGCCCUUGGCCUCCUUCUCGUCGAUCUUCUCCUCCUCGCUGACCAGCUGGUCCCAGUUCUUGGCCUUG
...((((((((.(((....(((((....(((..(((..(((((((((......)))))))))..)))..)))..))))).))).))))))))((((....))))................ (-29.76 = -30.82 +   1.06)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:10:12 2006