Locus 1813

Sequence ID	2R_DroMel_CAF1
Location	6,789,246 – 6,789,376
Length	130
Max. P	0.908688

overview

Window 7

Location	6,789,246 – 6,789,356
Length	110
Sequences	5
Columns	111
Reading direction	forward
Mean pairwise identity	90.24
Mean single sequence MFE	-17.82
Consensus MFE	-15.46
Energy contribution	-15.66
Covariance contribution	0.20
Combinations/Pair	1.00
Mean z-score	-1.61
Structure conservation index	0.87
SVM decision value	1.06
SVM RNA-class probability	0.908688
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 6789246 110 + 20766785
CUCCACUUGGUGGCAACAUCCAAACCCCAACCCAUCCACAUCGAUCUGCCCCAAGCCCCUUCUCCUUUUU-UUUCGCUAACUUUUCAGAAAGGGCAGUUGCUUCUUUUCGC
......((((.((((..(((......................))).))))))))((((.((((.......-...............)))).))))................ ( -17.30)
>DroSec_CAF1 39393 108 + 1
CUCCACUUGGUGGCAACAUCCAAACCCCAAC--AUCCACAUCGAUCUGCCCCCAGCCCCUUCUCCUUUUU-UUUUGCUAACUUUUCAGAAAGGGCAGUUGCUUCUUUUCGC
......((((((....)).))))....((((--(((......))).........((((.((((.......-...............)))).)))).))))........... ( -17.55)
>DroSim_CAF1 48307 108 + 1
CUCCACUUGGUGGCAACAUCCAAACCCCAAC--AUCCACAUCGAUCUGCC-CCAGCCCCUUCUCCUUUUUUUUUUCCUAACUUUUCAGAAAGGGCAGUUGCUUCUUUUCGC
......((((((....)).))))....((((--(((......))).....-...((((.((((.......................)))).)))).))))........... ( -17.50)
>DroEre_CAF1 41970 103 + 1
CUCCACUUGGUGGCAACAUCCAAACCCCAAC--AACC-CAUCGAUCUGCC-GCAGCCCCUUCUCCAU----UUUCGUAAACUUUUCAGAAAGGGCAGUUGCUUCUUUUCGC
......((((((....)).))))........--....-...(((...((.-((.((((.((((....----...............)))).)))).)).))......))). ( -19.51)
>DroYak_CAF1 47175 97 + 1
CUCCACUUGGUGGCAACAUCC-------AAC--AUCC-CAUCGAUCUGCC-CCAGCCCCUUCUCCUUU---UUUCGUAAACUUUUCAGAAAGGGCAGUUGCUUCUUUUCGC
.......(((.((((..(((.-------...--....-....))).))))-)))((((.((((.....---...............)))).))))................ ( -17.25)
>consensus
CUCCACUUGGUGGCAACAUCCAAACCCCAAC__AUCCACAUCGAUCUGCC_CCAGCCCCUUCUCCUUUUU_UUUCGCUAACUUUUCAGAAAGGGCAGUUGCUUCUUUUCGC
........((.((((((................(((......))).........((((.((((.......................)))).)))).)))))).))...... (-15.46 = -15.66 +   0.20)

alignment

secondary structure

dotplot

Window 8

Location	6,789,246 – 6,789,356
Length	110
Sequences	5
Columns	111
Reading direction	reverse
Mean pairwise identity	90.24
Mean single sequence MFE	-26.61
Consensus MFE	-22.49
Energy contribution	-22.89
Covariance contribution	0.40
Combinations/Pair	1.00
Mean z-score	-1.28
Structure conservation index	0.85
SVM decision value	-0.02
SVM RNA-class probability	0.525418
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 6789246 110 - 20766785
GCGAAAAGAAGCAACUGCCCUUUCUGAAAAGUUAGCGAAA-AAAAAGGAGAAGGGGCUUGGGGCAGAUCGAUGUGGAUGGGUUGGGGUUUGGAUGUUGCCACCAAGUGGAG
((........))....(((((((((...............-.......)))))))))(((((((((((((((.(.((....)).).)))..))).))))).))))...... ( -27.45)
>DroSec_CAF1 39393 108 - 1
GCGAAAAGAAGCAACUGCCCUUUCUGAAAAGUUAGCAAAA-AAAAAGGAGAAGGGGCUGGGGGCAGAUCGAUGUGGAU--GUUGGGGUUUGGAUGUUGCCACCAAGUGGAG
((........)).((((((((((((...............-.......)))))))))(((.(((((.(((((......--)))))..........))))).)))))).... ( -25.95)
>DroSim_CAF1 48307 108 - 1
GCGAAAAGAAGCAACUGCCCUUUCUGAAAAGUUAGGAAAAAAAAAAGGAGAAGGGGCUGG-GGCAGAUCGAUGUGGAU--GUUGGGGUUUGGAUGUUGCCACCAAGUGGAG
((........)).((((((((((((.......................)))))))))(((-(((((.(((((......--)))))..........))))).)))))).... ( -25.80)
>DroEre_CAF1 41970 103 - 1
GCGAAAAGAAGCAACUGCCCUUUCUGAAAAGUUUACGAAA----AUGGAGAAGGGGCUGC-GGCAGAUCGAUG-GGUU--GUUGGGGUUUGGAUGUUGCCACCAAGUGGAG
.((((....((((((((((((((((.....((((....))----))..)))))))))..(-((....)))...-))))--)))....)))).......((((...)))).. ( -26.30)
>DroYak_CAF1 47175 97 - 1
GCGAAAAGAAGCAACUGCCCUUUCUGAAAAGUUUACGAAA---AAAGGAGAAGGGGCUGG-GGCAGAUCGAUG-GGAU--GUU-------GGAUGUUGCCACCAAGUGGAG
((........)).((((((((((((...............---.....)))))))))(((-(((((.(((((.-....--)))-------))...))))).)))))).... ( -27.55)
>consensus
GCGAAAAGAAGCAACUGCCCUUUCUGAAAAGUUAGCGAAA_AAAAAGGAGAAGGGGCUGG_GGCAGAUCGAUGUGGAU__GUUGGGGUUUGGAUGUUGCCACCAAGUGGAG
((........)).((((((((((((.......................)))))))))(((.((((((((......................))).))))).)))))).... (-22.49 = -22.89 +   0.40)

alignment

secondary structure

dotplot

Window 9

Location	6,789,286 – 6,789,376
Length	90
Sequences	5
Columns	91
Reading direction	reverse
Mean pairwise identity	89.39
Mean single sequence MFE	-22.47
Consensus MFE	-16.10
Energy contribution	-17.30
Covariance contribution	1.20
Combinations/Pair	1.00
Mean z-score	-2.22
Structure conservation index	0.72
SVM decision value	0.55
SVM RNA-class probability	0.778101
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 6789286 90 - 20766785
AGUUUGUUUUCCCAAAUUCAGCGAAAAGAAGCAACUGCCCUUUCUGAAAAGUUAGCGAAA-AAAAAGGAGAAGGGGCUUGGGGCAGAUCGA
.((((((...(((((.....((........))....(((((((((...............-.......))))))))))))))))))))... ( -24.05)
>DroSec_CAF1 39431 90 - 1
AGUUUGUUUUCCCAAAAGCAGCGAAAAGAAGCAACUGCCCUUUCUGAAAAGUUAGCAAAA-AAAAAGGAGAAGGGGCUGGGGGCAGAUCGA
.((((((..(((((......((........))....(((((((((...............-.......))))))))))))))))))))... ( -24.55)
>DroSim_CAF1 48345 90 - 1
AGUUUGUUUUCCCAAAAGCAGCGAAAAGAAGCAACUGCCCUUUCUGAAAAGUUAGGAAAAAAAAAAGGAGAAGGGGCUGG-GGCAGAUCGA
.((((((...((((......((........))....(((((((((.......................))))))))))))-)))))))... ( -23.10)
>DroEre_CAF1 42007 82 - 1
AGU----UUUCCCAAAAGCAGCGAAAAGAAGCAACUGCCCUUUCUGAAAAGUUUACGAAA----AUGGAGAAGGGGCUGC-GGCAGAUCGA
.((----(((....)))))..(((...(..(((...(((((((((.....((((....))----))..))))))))))))-..)...))). ( -19.30)
>DroYak_CAF1 47205 82 - 1
AGU----UUUCCCAAAA-CAGCGAAAAGAAGCAACUGCCCUUUCUGAAAAGUUUACGAAA---AAAGGAGAAGGGGCUGG-GGCAGAUCGA
.((----(((((((...-..((........))....(((((((((...............---.....))))))))))))-)).))))... ( -21.35)
>consensus
AGUUUGUUUUCCCAAAAGCAGCGAAAAGAAGCAACUGCCCUUUCUGAAAAGUUAGCGAAA_AAAAAGGAGAAGGGGCUGG_GGCAGAUCGA
.((((.(((((.(.......).))))).))))....(((((((((.......................))))))))).............. (-16.10 = -17.30 +   1.20)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:13:45 2006