Locus 7688

Sequence ID	3L_DroMel_CAF1
Location	20,588,001 – 20,588,187
Length	186
Max. P	0.824098

overview

Window 2

Location	20,588,001 – 20,588,107
Length	106
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	79.76
Mean single sequence MFE	-25.44
Consensus MFE	-15.72
Energy contribution	-15.76
Covariance contribution	0.04
Combinations/Pair	1.38
Mean z-score	-1.99
Structure conservation index	0.62
SVM decision value	0.69
SVM RNA-class probability	0.824098
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 20588001 106 - 23771897
AUUAACUUCACAUCCUCCGGUACAAUUAAGUGCCCU-UCUGCCGU-CC------CACUCGCAC------CGAGUGGAUCAGUCUCGCUCCAUCUGCACACACACGGUUAUCAGGAACUUU
............((((..(((((......)))))..-...(((((-.(------((((((...------))))))).........((.......))......)))))....))))..... ( -27.10)
>DroSec_CAF1 32784 102 - 1
AUUAACUUCACAUCCUCCGGUACAAUUAAGUGCCCU-UCUGCCGU-CC------CACUCGCAC------CGAGUGGAUCUGUCUCGCUCCAUCUGCA----CACGGUUAUCAGGAACUUU
............((((..(((((......)))))..-...(((((-.(------((((((...------))))))).........((.......)).----.)))))....))))..... ( -27.10)
>DroAna_CAF1 54297 103 - 1
AUUAACGUCACAUCCUU----GCUGU---UCGCCCUGUCUUCCACACCCAUACUCCUUCGCGG------CGAGGGGAUCUGGCUCUUUCCAUCUGCA----UUUGGUUAUCAGGAACUUU
......((((.(((((.----....(---(((((.((.....................)).))------))))))))).))))((((.(((......----..))).....))))..... ( -18.80)
>DroSim_CAF1 26285 102 - 1
AUUAACUUCACAUCCUCCGGUACAAUUAAGUGCCCU-UCUGCCGU-CC------CACUCGCAC------CGAGUGGAGCUGUCUCGCUCCAUCUGCA----CACGGUUAUCAGGAACUUU
............((((..(((((......)))))..-...(((((-..------.(((((...------)))))(((((......))))).......----.)))))....))))..... ( -28.20)
>DroEre_CAF1 25917 108 - 1
AUUAACUUCACAUCCUCCGGCACAAUUAAGCGCCCU-UCUGCCGU-CC------CACUCGCACAUCCGACGGGUGCAUCUGCCCCGCUCCAUCUGCA----CGUGGUUAUCAGAAACUUU
..................(((.(......).))).(-((((....-.(------(((..(((.....((((((.((....)))))).))....))).----.))))....)))))..... ( -26.00)
>consensus
AUUAACUUCACAUCCUCCGGUACAAUUAAGUGCCCU_UCUGCCGU_CC______CACUCGCAC______CGAGUGGAUCUGUCUCGCUCCAUCUGCA____CACGGUUAUCAGGAACUUU
............((((..(((((......)))))......((((..........((((((.........))))))..........((.......)).......))))....))))..... (-15.72 = -15.76 +   0.04)

alignment

secondary structure

dotplot

Window 3

Location	20,588,041 – 20,588,147
Length	106
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	82.97
Mean single sequence MFE	-39.56
Consensus MFE	-23.82
Energy contribution	-24.82
Covariance contribution	1.00
Combinations/Pair	1.19
Mean z-score	-2.19
Structure conservation index	0.60
SVM decision value	0.49
SVM RNA-class probability	0.757029
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 20588041 106 + 23771897
UGAUCCACUCG------GUGCGAGUG------GG-ACGGCAGA-AGGGCACUUAAUUGUACCGGAGGAUGUGAAGUUAAUGCCGCCGAUUUGCAUUCAUUUCGGUGGCAUAAUGAGUCGC
..((((.(.((------((((((.((------((-...((...-...)).)))).))))))))).))))((((.((((.(((((((((..((....))..)))))))))))))...)))) ( -42.80)
>DroSec_CAF1 32820 106 + 1
AGAUCCACUCG------GUGCGAGUG------GG-ACGGCAGA-AGGGCACUUAAUUGUACCGGAGGAUGUGAAGUUAAUGCCGCCGAUUUGCAUUCAUUUCGGUGGCAUAAUGAGUCGC
..((((.(.((------((((((.((------((-...((...-...)).)))).))))))))).))))((((.((((.(((((((((..((....))..)))))))))))))...)))) ( -42.80)
>DroAna_CAF1 54333 107 + 1
AGAUCCCCUCG------CCGCGAAGGAGUAUGGGUGUGGAAGACAGGGCGA---ACAGC----AAGGAUGUGACGUUAAUGCCGCCGAUUUGCAUUCAUUUCGGUAGCAUAAUGAGCUCA
......((.((------((((......))...)))).))......((((..---(((..----.....)))..(((((.(((..((((..((....))..))))..)))))))).)))). ( -29.80)
>DroSim_CAF1 26321 106 + 1
AGCUCCACUCG------GUGCGAGUG------GG-ACGGCAGA-AGGGCACUUAAUUGUACCGGAGGAUGUGAAGUUAAUGCCGCCGAUUUGCAUUCAUUUCGGUGGCAUAAUGAGUCGC
...(((.(.((------((((((.((------((-...((...-...)).)))).))))))))).))).((((.((((.(((((((((..((....))..)))))))))))))...)))) ( -41.30)
>DroEre_CAF1 25953 112 + 1
AGAUGCACCCGUCGGAUGUGCGAGUG------GG-ACGGCAGA-AGGGCGCUUAAUUGUGCCGGAGGAUGUGAAGUUAAUGCCGCCGAUUUGCAUUCAUUUCGGUGGCAUAAUGAGUACC
..((((..(((...((.((((((((.------((-.(((((..-..(((((......)))))....(((.....)))..))))))).))))))))))....)))..)))).......... ( -41.10)
>consensus
AGAUCCACUCG______GUGCGAGUG______GG_ACGGCAGA_AGGGCACUUAAUUGUACCGGAGGAUGUGAAGUUAAUGCCGCCGAUUUGCAUUCAUUUCGGUGGCAUAAUGAGUCGC
.....((((((.........))))))..........((((......((.((......)).))................((((((((((..((....))..)))))))))).....)))). (-23.82 = -24.82 +   1.00)

alignment

secondary structure

dotplot

Window 4

Location	20,588,041 – 20,588,147
Length	106
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	82.97
Mean single sequence MFE	-30.04
Consensus MFE	-22.60
Energy contribution	-22.44
Covariance contribution	-0.16
Combinations/Pair	1.27
Mean z-score	-1.88
Structure conservation index	0.75
SVM decision value	0.64
SVM RNA-class probability	0.809013
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 20588041 106 - 23771897
GCGACUCAUUAUGCCACCGAAAUGAAUGCAAAUCGGCGGCAUUAACUUCACAUCCUCCGGUACAAUUAAGUGCCCU-UCUGCCGU-CC------CACUCGCAC------CGAGUGGAUCA
..(((.....(((((.((((..((....))..)))).)))))................(((((......)))))..-......))-)(------((((((...------))))))).... ( -32.20)
>DroSec_CAF1 32820 106 - 1
GCGACUCAUUAUGCCACCGAAAUGAAUGCAAAUCGGCGGCAUUAACUUCACAUCCUCCGGUACAAUUAAGUGCCCU-UCUGCCGU-CC------CACUCGCAC------CGAGUGGAUCU
..(((.....(((((.((((..((....))..)))).)))))................(((((......)))))..-......))-)(------((((((...------))))))).... ( -32.20)
>DroAna_CAF1 54333 107 - 1
UGAGCUCAUUAUGCUACCGAAAUGAAUGCAAAUCGGCGGCAUUAACGUCACAUCCUU----GCUGU---UCGCCCUGUCUUCCACACCCAUACUCCUUCGCGG------CGAGGGGAUCU
..((.((...((((..((((..((....))..))))..))))..........(((((----(((((---..............................))))------)))))))).)) ( -23.51)
>DroSim_CAF1 26321 106 - 1
GCGACUCAUUAUGCCACCGAAAUGAAUGCAAAUCGGCGGCAUUAACUUCACAUCCUCCGGUACAAUUAAGUGCCCU-UCUGCCGU-CC------CACUCGCAC------CGAGUGGAGCU
(((((.....(((((.((((..((....))..)))).)))))................(((((......)))))..-......))-)(------((((((...------))))))).)). ( -34.10)
>DroEre_CAF1 25953 112 - 1
GGUACUCAUUAUGCCACCGAAAUGAAUGCAAAUCGGCGGCAUUAACUUCACAUCCUCCGGCACAAUUAAGCGCCCU-UCUGCCGU-CC------CACUCGCACAUCCGACGGGUGCAUCU
((((......(((((.((((..((....))..)))).)))))................(((.(......).)))..-..))))..-..------(((((((......).))))))..... ( -28.20)
>consensus
GCGACUCAUUAUGCCACCGAAAUGAAUGCAAAUCGGCGGCAUUAACUUCACAUCCUCCGGUACAAUUAAGUGCCCU_UCUGCCGU_CC______CACUCGCAC______CGAGUGGAUCU
..........(((((.((((..((....))..)))).)))))................(((((......)))))....................((((((.........))))))..... (-22.60 = -22.44 +  -0.16)

alignment

secondary structure

dotplot

Window 5

Location	20,588,068 – 20,588,187
Length	119
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	87.35
Mean single sequence MFE	-41.04
Consensus MFE	-27.04
Energy contribution	-29.84
Covariance contribution	2.80
Combinations/Pair	1.12
Mean z-score	-2.07
Structure conservation index	0.66
SVM decision value	0.05
SVM RNA-class probability	0.560177
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 20588068 119 + 23771897
AGA-AGGGCACUUAAUUGUACCGGAGGAUGUGAAGUUAAUGCCGCCGAUUUGCAUUCAUUUCGGUGGCAUAAUGAGUCGCGGUCCCCAACUGCAAAGAGGUCGAGGUCAAUCUGCGAAGA
(((-..(((((((..(((((..((.((((((((.((((.(((((((((..((....))..)))))))))))))...)))).))))))...)))))..))))....)))..)))....... ( -40.30)
>DroSec_CAF1 32847 119 + 1
AGA-AGGGCACUUAAUUGUACCGGAGGAUGUGAAGUUAAUGCCGCCGAUUUGCAUUCAUUUCGGUGGCAUAAUGAGUCGCGGUCCCCCACUGCAAAGAGGUCGAGGUCAAUCUGCCAAGA
...-..((((....((((.(((((.((((((((.((((.(((((((((..((....))..)))))))))))))...)))).)))).)).((....)).......))))))).)))).... ( -43.00)
>DroAna_CAF1 54367 110 + 1
AGACAGGGCGA---ACAGC----AAGGAUGUGACGUUAAUGCCGCCGAUUUGCAUUCAUUUCGGUAGCAUAAUGAGCUCAGGC---CCACUGCAAAGAGGUCGAGGUCAAGCUGAGAGGA
...........---.((((----...............((((..((((..((....))..))))..))))..(((.(((.(((---(..((....)).))))))).))).))))...... ( -32.30)
>DroSim_CAF1 26348 119 + 1
AGA-AGGGCACUUAAUUGUACCGGAGGAUGUGAAGUUAAUGCCGCCGAUUUGCAUUCAUUUCGGUGGCAUAAUGAGUCGCGGUCCCCAACUGCAAAGAGGUCGAGGUCAAUCUGCGAAGA
(((-..(((((((..(((((..((.((((((((.((((.(((((((((..((....))..)))))))))))))...)))).))))))...)))))..))))....)))..)))....... ( -40.30)
>DroEre_CAF1 25986 119 + 1
AGA-AGGGCGCUUAAUUGUGCCGGAGGAUGUGAAGUUAAUGCCGCCGAUUUGCAUUCAUUUCGGUGGCAUAAUGAGUACCCGUCCCCAGCUGCAAGGAGGUCGAGGUCAAUUUGCGGCGA
...-..(((((......)))))((.(((((.(.(.(((((((((((((..((....))..))))))))))..))).).).))))))).((((((((..((......))..)))))))).. ( -49.30)
>consensus
AGA_AGGGCACUUAAUUGUACCGGAGGAUGUGAAGUUAAUGCCGCCGAUUUGCAUUCAUUUCGGUGGCAUAAUGAGUCGCGGUCCCCAACUGCAAAGAGGUCGAGGUCAAUCUGCGAAGA
(((...(((((((..(((((..((.((((((((.((((.(((((((((..((....))..)))))))))))))...)))).))))))...)))))..))))....)))..)))....... (-27.04 = -29.84 +   2.80)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:53:53 2006