Locus 2707

Sequence ID	3L_DroMel_CAF1
Location	7,545,800 – 7,545,938
Length	138
Max. P	0.995054

overview

Window 1

Location	7,545,800 – 7,545,904
Length	104
Sequences	5
Columns	104
Reading direction	forward
Mean pairwise identity	93.27
Mean single sequence MFE	-21.74
Consensus MFE	-20.86
Energy contribution	-20.54
Covariance contribution	-0.32
Combinations/Pair	1.08
Mean z-score	-1.70
Structure conservation index	0.96
SVM decision value	2.54
SVM RNA-class probability	0.995054
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 7545800 104 + 23771897
GUAUUUUCUACUAUUUCCAAACUGACCGAUAUUUGAUCUCUAUAAACCCGGUUCCGCUCCCACAUUUCGGAUUGAUUCCCAUCCAAAUCGGAGCGCUUGUCAGU
....................((((((.(((.....)))................((((((...((((.((((.(....).)))))))).))))))...)))))) ( -20.70)
>DroSec_CAF1 15258 104 + 1
AUAUUUCCGACUAUUUCCAAACUGACCGAUAUUUGAUCUCCAUAAACACGGUUCCGCUCCCACAUUUCGGAUUGAUUCCCAUCCAAAUCGGAGCGCCUGUCAGU
....................((((((.(((.....)))...........((...((((((...((((.((((.(....).)))))))).)))))))).)))))) ( -21.60)
>DroSim_CAF1 15176 104 + 1
AUAUUUUUGACUAUUUCCAAACUGACCGAUAUUUGAUCUCCAUAAACCCGGUUCCGCUCCCACAUUUCGGAUUGAUUCCCAUCCAAAUCGGAGCGCUUGUCAGU
......(((((............(((((.....((.....))......))))).((((((...((((.((((.(....).)))))))).))))))...))))). ( -21.80)
>DroEre_CAF1 15407 104 + 1
CCAUAUCCGACUAUUUCCGAACUGACCGAUAUUUGAUCUCCAUACACCCGGUUCCGCUCCCACAUUUCGGAUUGAUUCCCAUCCAAAUCGGAGCGCUUGUCAGU
....................((((((........((...((........)).))((((((...((((.((((.(....).)))))))).))))))...)))))) ( -21.10)
>DroYak_CAF1 15314 104 + 1
UUAUUUUCGACUAUUUCCCAGCUGACCGAUAUUUGAUGACCACAAACCCGGUUCCGCUCCCACAUUUCGGAUUGAUUCCCAUCCAAAUCGGAGCGCUUGUCAGU
....................((((((...........((((........)))).((((((...((((.((((.(....).)))))))).))))))...)))))) ( -23.50)
>consensus
AUAUUUUCGACUAUUUCCAAACUGACCGAUAUUUGAUCUCCAUAAACCCGGUUCCGCUCCCACAUUUCGGAUUGAUUCCCAUCCAAAUCGGAGCGCUUGUCAGU
....................((((((........((...((........)).))((((((...((((.((((.(....).)))))))).))))))...)))))) (-20.86 = -20.54 +  -0.32)

alignment

secondary structure

dotplot

Window 2

Location	7,545,800 – 7,545,904
Length	104
Sequences	5
Columns	104
Reading direction	reverse
Mean pairwise identity	93.27
Mean single sequence MFE	-29.96
Consensus MFE	-25.96
Energy contribution	-26.36
Covariance contribution	0.40
Combinations/Pair	1.00
Mean z-score	-1.99
Structure conservation index	0.87
SVM decision value	2.23
SVM RNA-class probability	0.990754
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 7545800 104 - 23771897
ACUGACAAGCGCUCCGAUUUGGAUGGGAAUCAAUCCGAAAUGUGGGAGCGGAACCGGGUUUAUAGAGAUCAAAUAUCGGUCAGUUUGGAAAUAGUAGAAAAUAC
((((((...((((((.((((((((........))))))...)).))))))......(((((....)))))........)))))).................... ( -27.80)
>DroSec_CAF1 15258 104 - 1
ACUGACAGGCGCUCCGAUUUGGAUGGGAAUCAAUCCGAAAUGUGGGAGCGGAACCGUGUUUAUGGAGAUCAAAUAUCGGUCAGUUUGGAAAUAGUCGGAAAUAU
.(((((...((((((.((((((((........))))))...)).))))))...((((....)))).((((.......))))............)))))...... ( -30.30)
>DroSim_CAF1 15176 104 - 1
ACUGACAAGCGCUCCGAUUUGGAUGGGAAUCAAUCCGAAAUGUGGGAGCGGAACCGGGUUUAUGGAGAUCAAAUAUCGGUCAGUUUGGAAAUAGUCAAAAAUAU
..((((...((((((.((((((((........))))))...)).))))))...(((..((.((.((.........)).)).))..))).....))))....... ( -28.80)
>DroEre_CAF1 15407 104 - 1
ACUGACAAGCGCUCCGAUUUGGAUGGGAAUCAAUCCGAAAUGUGGGAGCGGAACCGGGUGUAUGGAGAUCAAAUAUCGGUCAGUUCGGAAAUAGUCGGAUAUGG
.(((((...((((((.((((((((........))))))...)).))))))...(((..(..((.((.........)).))..)..))).....)))))...... ( -33.10)
>DroYak_CAF1 15314 104 - 1
ACUGACAAGCGCUCCGAUUUGGAUGGGAAUCAAUCCGAAAUGUGGGAGCGGAACCGGGUUUGUGGUCAUCAAAUAUCGGUCAGCUGGGAAAUAGUCGAAAAUAA
..((((...((((((.((((((((........))))))...)).))))))...((.(((...((..(..........)..))))).)).....))))....... ( -29.80)
>consensus
ACUGACAAGCGCUCCGAUUUGGAUGGGAAUCAAUCCGAAAUGUGGGAGCGGAACCGGGUUUAUGGAGAUCAAAUAUCGGUCAGUUUGGAAAUAGUCGAAAAUAU
((((((...((((((.((((((((........))))))...)).))))))...(((......))).............)))))).................... (-25.96 = -26.36 +   0.40)

alignment

secondary structure

dotplot

Window 3

Location	7,545,835 – 7,545,938
Length	103
Sequences	6
Columns	112
Reading direction	reverse
Mean pairwise identity	78.67
Mean single sequence MFE	-36.30
Consensus MFE	-20.00
Energy contribution	-21.78
Covariance contribution	1.78
Combinations/Pair	1.27
Mean z-score	-1.97
Structure conservation index	0.55
SVM decision value	0.48
SVM RNA-class probability	0.752970
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 7545835 103 - 23771897
AUGGACCCCGAAAGC-CAG----CGGCUAGAGAUGGCCGACUGACAAGCGCUCCGAUUUGGAUGGGAAUCAAUCCG---AAAUGUGGGAG-CGGAACCGGGUUUAUAGAGAU
((((((((.(...(.-(((----((((((....)))))).))).)...((((((.((((((((........)))))---)...)).))))-))...).))))))))...... ( -41.10)
>DroSec_CAF1 15293 102 - 1
AUGGACCCC-AAAGC-CAG----CGGCUAGAGAUGGCCAACUGACAGGCGCUCCGAUUUGGAUGGGAAUCAAUCCG---AAAUGUGGGAG-CGGAACCGUGUUUAUGGAGAU
.......((-(((((-(((----.(((((....)))))..)))...((((((((.((((((((........)))))---)...)).))))-))...))..)))).))).... ( -31.80)
>DroSim_CAF1 15211 102 - 1
AUGGACCCC-AAAGC-CAG----CGGCUAGAGAUGGCCAACUGACAAGCGCUCCGAUUUGGAUGGGAAUCAAUCCG---AAAUGUGGGAG-CGGAACCGGGUUUAUGGAGAU
((((((((.-...(.-(((----.(((((....)))))..))).)...((((((.((((((((........)))))---)...)).))))-)).....))))))))...... ( -36.70)
>DroEre_CAF1 15442 106 - 1
ACGGAUCCC-AAAGC-CAGCCGGCGGCUAGAGAUGGCCGACUGACAAGCGCUCCGAUUUGGAUGGGAAUCAAUCCG---AAAUGUGGGAG-CGGAACCGGGUGUAUGGAGAU
....(((((-(....-((.((((((((((....)))))).........((((((.((((((((........)))))---)...)).))))-))...)))).))..))).))) ( -40.60)
>DroYak_CAF1 15349 102 - 1
ACGGACCCC-AAAGC-CAG----CGGCUAGAGAUGGCCGACUGACAAGCGCUCCGAUUUGGAUGGGAAUCAAUCCG---AAAUGUGGGAG-CGGAACCGGGUUUGUGGUCAU
...((((.(-(((.(-(((----((((((....)))))).))......((((((.((((((((........)))))---)...)).))))-)).....)).)))).)))).. ( -43.20)
>DroPer_CAF1 9620 89 - 1
AUGGAUCUG-GGGCCCCAC----UGGCUAGAGAUGGACAAGUGACAGGCCGCGCGACUCUCAAGAGAUUGAAACAGCUUGAAUGUGGGCUAUGG------------------
.........-.((((((((----(..(((....)))...)))).(((((.(..((((((....))).)))...).))))).....)))))....------------------ ( -24.40)
>consensus
AUGGACCCC_AAAGC_CAG____CGGCUAGAGAUGGCCAACUGACAAGCGCUCCGAUUUGGAUGGGAAUCAAUCCG___AAAUGUGGGAG_CGGAACCGGGUUUAUGGAGAU
((((((((........(((....((((((....)))))).))).....((((((.((.(((((........))))).......)).)))).)).....))))))))...... (-20.00 = -21.78 +   1.78)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:39:55 2006