Locus 3745

Sequence ID	2R_DroMel_CAF1
Location	12,365,212 – 12,365,412
Length	200
Max. P	0.994214

overview

Window 0

Location	12,365,212 – 12,365,332
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	79.48
Mean single sequence MFE	-35.22
Consensus MFE	-21.28
Energy contribution	-21.52
Covariance contribution	0.24
Combinations/Pair	1.20
Mean z-score	-2.86
Structure conservation index	0.60
SVM decision value	2.46
SVM RNA-class probability	0.994214
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 12365212 120 + 20766785
GAGUUGGCAGGGAUGUAUCGAUAACACAAAUCAAAUUAUUUGGCAAAUUUAUCGAAAUCAAAAGCGGACAGAAUCUAUCGCCCAUCGAUAGAUACAUCGAUUGUAUAGCCACAGCCAGCU
.(((((((...(((((((((((((..(((((......)))))......)))))))..................(((((((.....)))))))))))))...(((......)))))))))) ( -31.30)
>DroSec_CAF1 24058 118 + 1
GAGUUGGCAGGGCUG--UCAAUAACAGAAAUCAGAUUAUUUGGCACAAGUAUCGAAACCAAAAGCGGACAAAAUCUAUCGCCCGUCGAUAGAUAAAUCGAUUGUAUGGCCACAGCCAGCU
.(((((((.((.(((--(.....))))...))........((((......(((((..((......)).....((((((((.....))))))))...)))))......))))..))))))) ( -35.30)
>DroSim_CAF1 24506 118 + 1
GAGUUGGCAGGGCUG--UCGAUAACAGAAAACAGAUUAUUUGGCACAAGUAUCGAAACCAAAAGCGGACAAAAUCUAUCGCCCAUCGAUAGAUAAAUCGAUUGUAUGGCCACAGCCAGCU
.(((((((....(((--(.....)))).............((((......(((((..((......)).....((((((((.....))))))))...)))))......))))..))))))) ( -34.40)
>DroEre_CAF1 24251 109 + 1
GAGUUGGCAGGGCAG--UCGAUAACAUGG---CGAUUGACUGG--CAAAUAUCGGCAUCAGAAGCUGACGAAACAUAUCGCCAAUCGA----UUCAUCGAUUGCAAAGCCACAGCCAGCU
.(((((((..(.(((--(((((.......---..)))))))).--).......(((.((((...))))...........((.((((((----....))))))))...)))...))))))) ( -36.60)
>DroYak_CAF1 24999 114 + 1
GAGUUGGCAGGGCAG--UCGAUAACAUAAAUCCGAUGAAUGGGCGCUAGUAUCGGUAUCAGAAGGUGAUAGUACAUAUCGCCAAUCGA----UACAUCGAUUGAAAAGCCACAGCCAGCU
.(((((((..(((((--(((((..........(((((...(....)...)))))(((((.((.(((((((.....)))))))..))))----)))))))))).....)))...))))))) ( -38.50)
>consensus
GAGUUGGCAGGGCUG__UCGAUAACAGAAAUCAGAUUAUUUGGCACAAGUAUCGAAAUCAAAAGCGGACAAAAUCUAUCGCCCAUCGAUAGAUACAUCGAUUGUAUAGCCACAGCCAGCU
.(((((((..(((....((((((........(((.....))).......))))))............................((((((......))))))......)))...))))))) (-21.28 = -21.52 +   0.24)

alignment

secondary structure

dotplot

Window 1

Location	12,365,212 – 12,365,332
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	79.48
Mean single sequence MFE	-32.33
Consensus MFE	-19.51
Energy contribution	-20.11
Covariance contribution	0.60
Combinations/Pair	1.11
Mean z-score	-1.79
Structure conservation index	0.60
SVM decision value	0.21
SVM RNA-class probability	0.637621
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 12365212 120 - 20766785
AGCUGGCUGUGGCUAUACAAUCGAUGUAUCUAUCGAUGGGCGAUAGAUUCUGUCCGCUUUUGAUUUCGAUAAAUUUGCCAAAUAAUUUGAUUUGUGUUAUCGAUACAUCCCUGCCAACUC
((.((((((((....))))...((((((((((((((.(((((((((...)))).)))))......)))))).....(((((((......))))).))....))))))))...)))).)). ( -30.70)
>DroSec_CAF1 24058 118 - 1
AGCUGGCUGUGGCCAUACAAUCGAUUUAUCUAUCGACGGGCGAUAGAUUUUGUCCGCUUUUGGUUUCGAUACUUGUGCCAAAUAAUCUGAUUUCUGUUAUUGA--CAGCCCUGCCAACUC
.((.(((((((((((....(((((...(((....(.(((((((......))))))))....))).)))))...)).))).((((((..(....).)))))).)--)))))..))...... ( -33.90)
>DroSim_CAF1 24506 118 - 1
AGCUGGCUGUGGCCAUACAAUCGAUUUAUCUAUCGAUGGGCGAUAGAUUUUGUCCGCUUUUGGUUUCGAUACUUGUGCCAAAUAAUCUGUUUUCUGUUAUCGA--CAGCCCUGCCAACUC
.((.((((((.(((.....((((((......)))))).)))((((((...........((((((..(((...))).))))))..........))))))....)--)))))..))...... ( -32.00)
>DroEre_CAF1 24251 109 - 1
AGCUGGCUGUGGCUUUGCAAUCGAUGAA----UCGAUUGGCGAUAUGUUUCGUCAGCUUCUGAUGCCGAUAUUUG--CCAGUCAAUCG---CCAUGUUAUCGA--CUGCCCUGCCAACUC
.........((((...(((.(((((((.----..(((((((((.(((((.((((((...))))))..))))))))--)))))).....---.....)))))))--.)))...)))).... ( -35.52)
>DroYak_CAF1 24999 114 - 1
AGCUGGCUGUGGCUUUUCAAUCGAUGUA----UCGAUUGGCGAUAUGUACUAUCACCUUCUGAUACCGAUACUAGCGCCCAUUCAUCGGAUUUAUGUUAUCGA--CUGCCCUGCCAACUC
((.((((.(.(((...((((((((....----))))))))(((((.....(((((.....)))))(((((..............)))))........))))).--..)))).)))).)). ( -29.54)
>consensus
AGCUGGCUGUGGCUAUACAAUCGAUGUAUCUAUCGAUGGGCGAUAGAUUUUGUCCGCUUUUGAUUUCGAUACUUGUGCCAAAUAAUCUGAUUUAUGUUAUCGA__CAGCCCUGCCAACUC
((.((((.(.(((......((((((......))))))((((((......))))))...........(((((..........................))))).....)))).)))).)). (-19.51 = -20.11 +   0.60)

alignment

secondary structure

dotplot

Window 2

Location	12,365,292 – 12,365,412
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	92.22
Mean single sequence MFE	-31.98
Consensus MFE	-27.32
Energy contribution	-28.16
Covariance contribution	0.84
Combinations/Pair	1.03
Mean z-score	-1.40
Structure conservation index	0.85
SVM decision value	0.49
SVM RNA-class probability	0.757124
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 12365292 120 + 20766785
CCCAUCGAUAGAUACAUCGAUUGUAUAGCCACAGCCAGCUGGUCUCCCUUCGCCAUUCUUUAAUUUUUGUUUUGAUUGGUGAAUUUUGGCAGGGAUUAGCAUGGACGAUCCUCUUAAGCC
...((((....(((((.....)))))........(((((((((((((((((((((.((...(((....)))..)).)))))))....))..))))))))).))).))))........... ( -31.10)
>DroSec_CAF1 24136 120 + 1
CCCGUCGAUAGAUAAAUCGAUUGUAUGGCCACAGCCAGCUGGUCUCCCUUCGCCAUUCUUAAAUUUUUGUUUUGAUUGGUGAAUUUUGGCAGGGAUUAGCAUGGACGAUCCUCUUAAGCC
..((((.((................((((....))))((((((((((((((((((.((..((((....)))).)).)))))))....))..))))))))))).))))............. ( -34.10)
>DroSim_CAF1 24584 120 + 1
CCCAUCGAUAGAUAAAUCGAUUGUAUGGCCACAGCCAGCUGGUCUCCCUUCGCCAUUCUUUAAUUUUUGUUUUGAUUGGUGAAUUUUGGCAGGGAUUAGCAUGGACGAUCCUCUUAAGCC
...(((....))).....((((((.((((....))))((((((((((((((((((.((...(((....)))..)).)))))))....))..)))))))))....)))))).......... ( -33.30)
>DroEre_CAF1 24324 112 + 1
CCAAUCGA----UUCAUCGAUUGCAAAGCCACAGCCAGCUGGUCUCCCUUCGCC----UCUAAUUUUUGUUUUGAUUGGUGAAUUUUGGCAGGGAUUAGCAUGGACGAUCCUCUCAAGCC
.(((((((----....)))))))..........(((((((((((((((((((((----..(((........)))...))))))....))..))))))))).))).).............. ( -28.30)
>DroYak_CAF1 25077 116 + 1
CCAAUCGA----UACAUCGAUUGAAAAGCCACAGCCAGCUGGUCUCCCUUCGCCAUUCUUUAAUUUUUGUUUUGAUUGGUGAAUUUUGGCAGGGAUUAGCAUGGACGAUCCUCUCAAGCC
.(((((((----....)))))))..........((((((((((((((((((((((.((...(((....)))..)).)))))))....))..))))))))).))).).............. ( -33.10)
>consensus
CCCAUCGAUAGAUACAUCGAUUGUAUAGCCACAGCCAGCUGGUCUCCCUUCGCCAUUCUUUAAUUUUUGUUUUGAUUGGUGAAUUUUGGCAGGGAUUAGCAUGGACGAUCCUCUUAAGCC
...((((((......))))))............((((((((((((((((((((((.((...(((....)))..)).)))))))....))..))))))))).))).).............. (-27.32 = -28.16 +   0.84)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:03:18 2006