Locus 5040

Sequence ID 3L_DroMel_CAF1
Location 13,799,818 – 13,800,018
Length 200
Max. P 0.999823
window7993 window7994 window7995 window7996

overview

Window 3

Location 13,799,818 – 13,799,938
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 99.00
Mean single sequence MFE -29.44
Consensus MFE -28.30
Energy contribution -28.14
Covariance contribution -0.16
Combinations/Pair 1.03
Mean z-score -1.80
Structure conservation index 0.96
SVM decision value 1.87
SVM RNA-class probability 0.980592
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13799818 120 + 23771897
ACUCAAGUGAAUUAAAUUGGUUUCCAGCUGGUCUGUGCUAUUAGUUGUAAUUGAUUCUUGAAAUAAUUUAUUUUAUGGCUUUUUGUCGCCAACCGCCUCCGGCUGACGAUUGACUUCACU
.....((((((...(((((.....(((((((...(.((....................(((((((...)))))))((((........))))...))).))))))).)))))...)))))) ( -27.70)
>DroSec_CAF1 36648 120 + 1
ACUCAAGUGAAUUAAAUUGGUUUCCAGCUGGUCUGUGCUAUUAGUUGUAAUUGAUUCUUGAAAUAAUUUAUUUCAUGGCUUUUUGUCGCCAACCGCCUCCGGCUGACGAUUGCCUUCACU
.....((((((...(((..(((..((((((((.......)))))))).)))..)))..(((((((...))))))).(((...((((((((..........))).)))))..))))))))) ( -30.30)
>DroSim_CAF1 32834 120 + 1
ACUCAAGUGAAUUAAAUUGGUUUCCAGCUGGUCUGUGCUAUUAGUUGUAAUUGAUUCUUGAAAUAAUUUAUUUUAUGGCUUUUUGUCGCCAACCGCCUCCGGCUGACGAUUGCCUUCACU
.....((((((...(((..(((..((((((((.......)))))))).)))..)))..(((((((...))))))).(((...((((((((..........))).)))))..))))))))) ( -28.10)
>DroEre_CAF1 37523 120 + 1
ACUCAAGUGAAUUAAAUUGGUUUCCAGCUGGUCUGUGCUAUUAGUUGUAAUUGAUUCUUGAAAUAAUUUAUUUUAUGGCUUUUUGUCGCCAGCCGCCUCCGGCUGACGAUUGCCUUCACU
.....((((((...(((..(((..((((((((.......)))))))).)))..)))..(((((((...))))))).(((.....((((.((((((....)))))).)))).))))))))) ( -33.00)
>DroYak_CAF1 35355 120 + 1
ACUCAAGUGAAUUAAAUUGGUUUCCAGCUGGUCUGUGCUAUUAGUUGUAAUUGAUUCUUGAAAUAAUUUAUUUUAUGGCUUUUUGUCGCCAACCGCCUCCGGCUGACGAUUGCCUUCACU
.....((((((...(((..(((..((((((((.......)))))))).)))..)))..(((((((...))))))).(((...((((((((..........))).)))))..))))))))) ( -28.10)
>consensus
ACUCAAGUGAAUUAAAUUGGUUUCCAGCUGGUCUGUGCUAUUAGUUGUAAUUGAUUCUUGAAAUAAUUUAUUUUAUGGCUUUUUGUCGCCAACCGCCUCCGGCUGACGAUUGCCUUCACU
.....((((((...(((((.....(((((((...(.((....................(((((((...)))))))((((........))))...))).))))))).)))))...)))))) (-28.30 = -28.14 +  -0.16)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 4

Location 13,799,818 – 13,799,938
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 99.00
Mean single sequence MFE -28.56
Consensus MFE -27.50
Energy contribution -27.54
Covariance contribution 0.04
Combinations/Pair 1.03
Mean z-score -2.31
Structure conservation index 0.96
SVM decision value 3.09
SVM RNA-class probability 0.998388
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13799818 120 - 23771897
AGUGAAGUCAAUCGUCAGCCGGAGGCGGUUGGCGACAAAAAGCCAUAAAAUAAAUUAUUUCAAGAAUCAAUUACAACUAAUAGCACAGACCAGCUGGAAACCAAUUUAAUUCACUUGAGU
((((((.....((((((((((....))))))))))...............((((((.((((.........(((....)))((((........))))))))..)))))).))))))..... ( -25.10)
>DroSec_CAF1 36648 120 - 1
AGUGAAGGCAAUCGUCAGCCGGAGGCGGUUGGCGACAAAAAGCCAUGAAAUAAAUUAUUUCAAGAAUCAAUUACAACUAAUAGCACAGACCAGCUGGAAACCAAUUUAAUUCACUUGAGU
(((((((((..((((((((((....))))))))))......))).(((((((...)))))))..................((((........)))).............))))))..... ( -30.10)
>DroSim_CAF1 32834 120 - 1
AGUGAAGGCAAUCGUCAGCCGGAGGCGGUUGGCGACAAAAAGCCAUAAAAUAAAUUAUUUCAAGAAUCAAUUACAACUAAUAGCACAGACCAGCUGGAAACCAAUUUAAUUCACUUGAGU
(((((((((..((((((((((....))))))))))......)))......((((((.((((.........(((....)))((((........))))))))..)))))).))))))..... ( -28.40)
>DroEre_CAF1 37523 120 - 1
AGUGAAGGCAAUCGUCAGCCGGAGGCGGCUGGCGACAAAAAGCCAUAAAAUAAAUUAUUUCAAGAAUCAAUUACAACUAAUAGCACAGACCAGCUGGAAACCAAUUUAAUUCACUUGAGU
(((((((((..((((((((((....))))))))))......)))......((((((.((((.........(((....)))((((........))))))))..)))))).))))))..... ( -30.80)
>DroYak_CAF1 35355 120 - 1
AGUGAAGGCAAUCGUCAGCCGGAGGCGGUUGGCGACAAAAAGCCAUAAAAUAAAUUAUUUCAAGAAUCAAUUACAACUAAUAGCACAGACCAGCUGGAAACCAAUUUAAUUCACUUGAGU
(((((((((..((((((((((....))))))))))......)))......((((((.((((.........(((....)))((((........))))))))..)))))).))))))..... ( -28.40)
>consensus
AGUGAAGGCAAUCGUCAGCCGGAGGCGGUUGGCGACAAAAAGCCAUAAAAUAAAUUAUUUCAAGAAUCAAUUACAACUAAUAGCACAGACCAGCUGGAAACCAAUUUAAUUCACUUGAGU
(((((((((..((((((((((....))))))))))......)))......((((((.((((.........(((....)))((((........))))))))..)))))).))))))..... (-27.50 = -27.54 +   0.04)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 5

Location 13,799,858 – 13,799,978
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 97.00
Mean single sequence MFE -29.68
Consensus MFE -28.90
Energy contribution -28.94
Covariance contribution 0.04
Combinations/Pair 1.04
Mean z-score -2.41
Structure conservation index 0.97
SVM decision value 4.17
SVM RNA-class probability 0.999823
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13799858 120 - 23771897
GCAAUUUGCCGAACUUUCAACUCCACUCCAAGGAUCGUUAAGUGAAGUCAAUCGUCAGCCGGAGGCGGUUGGCGACAAAAAGCCAUAAAAUAAAUUAUUUCAAGAAUCAAUUACAACUAA
((...(((.(..((((.....(((.......))).....))))...).)))((((((((((....))))))))))......))..................................... ( -22.70)
>DroSec_CAF1 36688 120 - 1
GCAAUUUGCCGAACUUUCAACUCCACUCCUAGGAUCGUUAAGUGAAGGCAAUCGUCAGCCGGAGGCGGUUGGCGACAAAAAGCCAUGAAAUAAAUUAUUUCAAGAAUCAAUUACAACUAA
((...(((((..((((.....(((.......))).....))))...)))))((((((((((....))))))))))......))..(((((((...))))))).................. ( -32.90)
>DroSim_CAF1 32874 120 - 1
GCAAUUUGCCGAACUUUCAACUCCACUCCAAGGAUCGUUAAGUGAAGGCAAUCGUCAGCCGGAGGCGGUUGGCGACAAAAAGCCAUAAAAUAAAUUAUUUCAAGAAUCAAUUACAACUAA
((...(((((..((((.....(((.......))).....))))...)))))((((((((((....))))))))))......))..................................... ( -29.80)
>DroEre_CAF1 37563 119 - 1
GCAAUUUGCCGAACUUUCAACUCCACU-AAAGGAUCGUUAAGUGAAGGCAAUCGUCAGCCGGAGGCGGCUGGCGACAAAAAGCCAUAAAAUAAAUUAUUUCAAGAAUCAAUUACAACUAA
((...(((((..((((.....(((...-...))).....))))...)))))((((((((((....))))))))))......))..................................... ( -32.70)
>DroYak_CAF1 35395 119 - 1
GCAAUUUGCCGAACUUUCAACUCCACC-AAAGGACCGUUAAGUGAAGGCAAUCGUCAGCCGGAGGCGGUUGGCGACAAAAAGCCAUAAAAUAAAUUAUUUCAAGAAUCAAUUACAACUAA
((...(((((..((((.....(((...-...))).....))))...)))))((((((((((....))))))))))......))..................................... ( -30.30)
>consensus
GCAAUUUGCCGAACUUUCAACUCCACUCCAAGGAUCGUUAAGUGAAGGCAAUCGUCAGCCGGAGGCGGUUGGCGACAAAAAGCCAUAAAAUAAAUUAUUUCAAGAAUCAAUUACAACUAA
((...(((((..((((.....(((.......))).....))))...)))))((((((((((....))))))))))......))..................................... (-28.90 = -28.94 +   0.04)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 6

Location 13,799,898 – 13,800,018
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 95.83
Mean single sequence MFE -32.68
Consensus MFE -30.90
Energy contribution -30.90
Covariance contribution 0.00
Combinations/Pair 1.06
Mean z-score -1.49
Structure conservation index 0.95
SVM decision value 1.58
SVM RNA-class probability 0.965616
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13799898 120 - 23771897
AAUUCAAGCCAUUGACAUUGACAGGAAAUCCCGAUUAUAUGCAAUUUGCCGAACUUUCAACUCCACUCCAAGGAUCGUUAAGUGAAGUCAAUCGUCAGCCGGAGGCGGUUGGCGACAAAA
...((((....))))..(((((.((.....))...........(((((.(((.((((............)))).))).)))))...)))))((((((((((....))))))))))..... ( -27.30)
>DroSec_CAF1 36728 120 - 1
AAUUUAAGCCAUUGACAUUGACAGGAAAUCCCGAUUAUGUGCAAUUUGCCGAACUUUCAACUCCACUCCUAGGAUCGUUAAGUGAAGGCAAUCGUCAGCCGGAGGCGGUUGGCGACAAAA
..........((((((((...(.((....)).)...)))).))))(((((..((((.....(((.......))).....))))...)))))((((((((((....))))))))))..... ( -33.70)
>DroSim_CAF1 32914 120 - 1
AAUUUAAGCCAUUGAAAUUGACAGGAAAUCCCGAUUAUGUGCAAUUUGCCGAACUUUCAACUCCACUCCAAGGAUCGUUAAGUGAAGGCAAUCGUCAGCCGGAGGCGGUUGGCGACAAAA
.......(((((...(((((...((....)))))))))).))...(((((..((((.....(((.......))).....))))...)))))((((((((((....))))))))))..... ( -33.40)
>DroEre_CAF1 37603 119 - 1
AAUUUAAGCCAUUGACAUUGACAGGAAAUCCCGAUUAUAUGCAAUUUGCCGAACUUUCAACUCCACU-AAAGGAUCGUUAAGUGAAGGCAAUCGUCAGCCGGAGGCGGCUGGCGACAAAA
..........((((.((((((..((.....))..))).)))))))(((((..((((.....(((...-...))).....))))...)))))((((((((((....))))))))))..... ( -35.80)
>DroYak_CAF1 35435 119 - 1
AAUUUAAGCCAUUGACAUUGACAGGAAAUGCCGAUUAUAUGCAAUUUGCCGAACUUUCAACUCCACC-AAAGGACCGUUAAGUGAAGGCAAUCGUCAGCCGGAGGCGGUUGGCGACAAAA
..........((((.((((((..((.....))..))).)))))))(((((..((((.....(((...-...))).....))))...)))))((((((((((....))))))))))..... ( -33.20)
>consensus
AAUUUAAGCCAUUGACAUUGACAGGAAAUCCCGAUUAUAUGCAAUUUGCCGAACUUUCAACUCCACUCCAAGGAUCGUUAAGUGAAGGCAAUCGUCAGCCGGAGGCGGUUGGCGACAAAA
..........((((.((((((..((.....))..))).)))))))(((((..((((.....(((.......))).....))))...)))))((((((((((....))))))))))..... (-30.90 = -30.90 +   0.00)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:40:37 2006