Locus 4566

Sequence ID	3L_DroMel_CAF1
Location	13,117,347 – 13,117,615
Length	268
Max. P	0.999912

overview

Window 3

Location	13,117,347 – 13,117,467
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	95.73
Mean single sequence MFE	-24.30
Consensus MFE	-24.14
Energy contribution	-23.66
Covariance contribution	-0.48
Combinations/Pair	1.09
Mean z-score	-1.29
Structure conservation index	0.99
SVM decision value	1.19
SVM RNA-class probability	0.928144
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13117347 120 + 23771897
AACGUUUAAACAUAUUGAAUUACUUUAAAAAAGAUCUUACCCCCCAACCCGGCGGCCAACGUCGCAAUUUGUUAAUUUCUUGUCAACACGAGUCGAAAGACUAAUUGGCCCGAAGAACCC
...((((.((((.((((.....(((.....)))................(((((.....))))))))).))))...(((..(((((....((((....))))..)))))..))))))).. ( -24.40)
>DroSec_CAF1 105253 119 + 1
AACGUUUAAACAUAUUGAAUUACUUUAAAAAAGAUCUUACCC-CCAACCCGGCGGCCAACGUCGCAAUUUGUUAAUUUCUUGUCAACACGAGUCAAAAGACUAAUUGGCCCGAAGAACCC
...((((.((((.((((.....(((.....))).........-......(((((.....))))))))).))))...(((..(((((....((((....))))..)))))..))))))).. ( -20.70)
>DroSim_CAF1 103359 119 + 1
AACGUUUAAACAUAUUGAAUUACUUUAAAAAAGAUCUUACCC-CCAACCCGGCGGCCAACGUCGCAAUUUGUUAAUUUCUUGUCAACACGAGUCGAAAGACUAAUUGGCCCGAAGAACCC
...((((.((((.((((.....(((.....))).........-......(((((.....))))))))).))))...(((..(((((....((((....))))..)))))..))))))).. ( -24.40)
>DroEre_CAF1 101748 118 + 1
AGCGUUUAAACAUAUUGAAUUACUUUAAAAAAGAUAUUUGCC-CC-ACCCGGCGGCCAACGUCGCAAUUUGUUAAUUUCUUGUCAACACGAGUCGAAGGACUAAUUGGCCCGAGGAACCC
.((((((((.....))))))............((..((.(((-((-....)).))).))..))))..........(((((((((((....((((....))))..)))))..))))))... ( -25.20)
>DroYak_CAF1 105340 118 + 1
AACGUUUAAACAUAUUGAAUUACUUUAAAAGAGAUCUUUUCC-CC-ACCCGACGGCCAACGUCGCAAUUUGUUAAUUUCUUGUCAACACGAGUCGAAAGACUAAUUGGCCCGAAGAACCC
...((((.((((.((((.........(((((....)))))..-..-...(((((.....))))))))).))))...(((..(((((....((((....))))..)))))..))))))).. ( -26.80)
>consensus
AACGUUUAAACAUAUUGAAUUACUUUAAAAAAGAUCUUACCC_CCAACCCGGCGGCCAACGUCGCAAUUUGUUAAUUUCUUGUCAACACGAGUCGAAAGACUAAUUGGCCCGAAGAACCC
...((((.((((.((((.....(((.....)))................(((((.....))))))))).))))...(((..(((((....((((....))))..)))))..))))))).. (-24.14 = -23.66 +  -0.48)

alignment

secondary structure

dotplot

Window 4

Location	13,117,427 – 13,117,547
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	98.00
Mean single sequence MFE	-35.54
Consensus MFE	-34.54
Energy contribution	-34.30
Covariance contribution	-0.24
Combinations/Pair	1.10
Mean z-score	-1.79
Structure conservation index	0.97
SVM decision value	2.29
SVM RNA-class probability	0.991783
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13117427 120 - 23771897
CGUUAAAUGAAAAUAUUCAGAGUGGCAAGAGGCUAAAUAUGGCCAAGUGAUUUAAAGGGUAAGAGUGACGGGGCCGAAGCGGGUUCUUCGGGCCAAUUAGUCUUUCGACUCGUGUUGACA
.(((((.((((....))))((((.(..(((((((((...(((((..((.((((.........)))).))..))))).....(((.(....))))..)))))))))).))))...))))). ( -35.70)
>DroSec_CAF1 105332 120 - 1
CGUUAAAUGAAAAUAUUCAGAGUGGCAAGAGGCUAAAUAUGGCCAAGUGAUUUAAAGGGUAAGAGUGACGGGGCCGAAGCGGGUUCUUCGGGCCAAUUAGUCUUUUGACUCGUGUUGACA
.(((((.((((....))))((((..(((((((((((...(((((..((.((((.........)))).))..))))).....(((.(....))))..)))))))))))))))...))))). ( -37.70)
>DroSim_CAF1 103438 120 - 1
CGUUAAAUGAAAAUAUUCAGAGUGGCAAGAGGCUAAAUAUGGCCAAGUGAUUUAAAGGGUAAGAGUGACGGGGCCGAAGCGGGUUCUUCGGGCCAAUUAGUCUUUCGACUCGUGUUGACA
.(((((.((((....))))((((.(..(((((((((...(((((..((.((((.........)))).))..))))).....(((.(....))))..)))))))))).))))...))))). ( -35.70)
>DroEre_CAF1 101826 120 - 1
CGUUAAAUGAAAAUAUUCAGAGUGGCAAGAGGCUAAAUAUGGCCAAGUGAUUUAAAGGGUAAGAGUGACGGCACUGAAGCGGGUUCCUCGGGCCAAUUAGUCCUUCGACUCGUGUUGACA
.(((((.((((....))))((((.(.(((.((((((...(((((..((.((((.........)))).))((.(((......))).))...))))).)))))))))).))))...))))). ( -32.90)
>DroYak_CAF1 105418 120 - 1
CGUUAAAUGAAAAUAUUCAGAGUGGCAAGAGGCUAAAUAUGGCCAAGUGAUUUAAAGGGUAAGAGUGACGGGGCCGAAGCGGGUUCUUCGGGCCAAUUAGUCUUUCGACUCGUGUUGACA
.(((((.((((....))))((((.(..(((((((((...(((((..((.((((.........)))).))..))))).....(((.(....))))..)))))))))).))))...))))). ( -35.70)
>consensus
CGUUAAAUGAAAAUAUUCAGAGUGGCAAGAGGCUAAAUAUGGCCAAGUGAUUUAAAGGGUAAGAGUGACGGGGCCGAAGCGGGUUCUUCGGGCCAAUUAGUCUUUCGACUCGUGUUGACA
.(((((.((((....))))((((.(..(((((((((...(((((..((.((((.........)))).))((((((......))))))...))))).)))))))))).))))...))))). (-34.54 = -34.30 +  -0.24)

alignment

secondary structure

dotplot

Window 5

Location	13,117,467 – 13,117,575
Length	108
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	94.36
Mean single sequence MFE	-17.90
Consensus MFE	-17.38
Energy contribution	-17.06
Covariance contribution	-0.32
Combinations/Pair	1.08
Mean z-score	-1.81
Structure conservation index	0.97
SVM decision value	3.05
SVM RNA-class probability	0.998266
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13117467 108 - 23771897
AUGAUAAA------------AAACGAGGAAAAGUAAAUGACGUUAAAUGAAAAUAUUCAGAGUGGCAAGAGGCUAAAUAUGGCCAAGUGAUUUAAAGGGUAAGAGUGACGGGGCCGAAGC
........------------.............(((((.((((((..((((....))))...))))....(((((....)))))..)).)))))...(((..(.....)...)))..... ( -17.80)
>DroSec_CAF1 105372 108 - 1
AUGAUAAA------------AAACGAGGAAAAGUAAAUGACGUUAAAUGAAAAUAUUCAGAGUGGCAAGAGGCUAAAUAUGGCCAAGUGAUUUAAAGGGUAAGAGUGACGGGGCCGAAGC
........------------.............(((((.((((((..((((....))))...))))....(((((....)))))..)).)))))...(((..(.....)...)))..... ( -17.80)
>DroSim_CAF1 103478 108 - 1
AUGAUAAA------------AAACGAGGAAAAGUAAAUGACGUUAAAUGAAAAUAUUCAGAGUGGCAAGAGGCUAAAUAUGGCCAAGUGAUUUAAAGGGUAAGAGUGACGGGGCCGAAGC
........------------.............(((((.((((((..((((....))))...))))....(((((....)))))..)).)))))...(((..(.....)...)))..... ( -17.80)
>DroEre_CAF1 101866 120 - 1
AUGAUAAAAAAAAAGAAAAAAAACGAGGAAAAGUAAAUGACGUUAAAUGAAAAUAUUCAGAGUGGCAAGAGGCUAAAUAUGGCCAAGUGAUUUAAAGGGUAAGAGUGACGGCACUGAAGC
.................................(((((.((((((..((((....))))...))))....(((((....)))))..)).))))).........((((....))))..... ( -18.30)
>DroYak_CAF1 105458 110 - 1
AUGAUAAAA----------AAAACGAGGAAAAGUAAAUGACGUUAAAUGAAAAUAUUCAGAGUGGCAAGAGGCUAAAUAUGGCCAAGUGAUUUAAAGGGUAAGAGUGACGGGGCCGAAGC
.........----------..............(((((.((((((..((((....))))...))))....(((((....)))))..)).)))))...(((..(.....)...)))..... ( -17.80)
>consensus
AUGAUAAA____________AAACGAGGAAAAGUAAAUGACGUUAAAUGAAAAUAUUCAGAGUGGCAAGAGGCUAAAUAUGGCCAAGUGAUUUAAAGGGUAAGAGUGACGGGGCCGAAGC
.................................(((((.((((((..((((....))))...))))....(((((....)))))..)).)))))...(((..(.....)...)))..... (-17.38 = -17.06 +  -0.32)

alignment

secondary structure

dotplot

Window 6

Location	13,117,507 – 13,117,615
Length	108
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	92.77
Mean single sequence MFE	-13.96
Consensus MFE	-13.78
Energy contribution	-13.62
Covariance contribution	-0.16
Combinations/Pair	1.06
Mean z-score	-2.27
Structure conservation index	0.99
SVM decision value	4.51
SVM RNA-class probability	0.999912
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13117507 108 + 23771897
AUAUUUAGCCUCUUGCCACUCUGAAUAUUUUCAUUUAACGUCAUUUACUUUUCCUCGUUU------------UUUAUCAUUCUUCAUUAAACUUUGUGGCGAAUGCUUGCUCCGCCGCAC
......(((...(((((((..((((....))))...((((...............)))).------------.......................)))))))..)))(((......))). ( -15.26)
>DroSec_CAF1 105412 108 + 1
AUAUUUAGCCUCUUGCCACUCUGAAUAUUUUCAUUUAACGUCAUUUACUUUUCCUCGUUU------------UUUAUCAUUCUUCAUUAAACUUUGUGGCAAUUGCUUUCUCCACCGCAC
......(((...(((((((..((((....))))...((((...............)))).------------.......................)))))))..)))............. ( -13.86)
>DroSim_CAF1 103518 108 + 1
AUAUUUAGCCUCUUGCCACUCUGAAUAUUUUCAUUUAACGUCAUUUACUUUUCCUCGUUU------------UUUAUCAUUCUUCAUUAAACUUUGUGGCGAAUGCUUUCUCCACCGCAC
......(((...(((((((..((((....))))...((((...............)))).------------.......................)))))))..)))............. ( -13.56)
>DroEre_CAF1 101906 120 + 1
AUAUUUAGCCUCUUGCCACUCUGAAUAUUUUCAUUUAACGUCAUUUACUUUUCCUCGUUUUUUUUCUUUUUUUUUAUCAUUCUUCAUUAAACUUUGUGGCGAAUGCUUUCUCCACCGCAC
......(((...(((((((..((((....))))...((((...............))))....................................)))))))..)))............. ( -13.56)
>DroYak_CAF1 105498 110 + 1
AUAUUUAGCCUCUUGCCACUCUGAAUAUUUUCAUUUAACGUCAUUUACUUUUCCUCGUUUU----------UUUUAUCAUUCUUCAUUAAACUUUGUGGCGAUUGCUUUCCCCACCGCCA
......(((...(((((((..((((....))))...((((...............))))..----------........................)))))))..)))............. ( -13.56)
>consensus
AUAUUUAGCCUCUUGCCACUCUGAAUAUUUUCAUUUAACGUCAUUUACUUUUCCUCGUUU____________UUUAUCAUUCUUCAUUAAACUUUGUGGCGAAUGCUUUCUCCACCGCAC
......(((...(((((((..((((....))))...((((...............))))....................................)))))))..)))............. (-13.78 = -13.62 +  -0.16)

alignment

secondary structure

dotplot

Window 7

Location	13,117,507 – 13,117,615
Length	108
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	92.77
Mean single sequence MFE	-16.25
Consensus MFE	-13.90
Energy contribution	-13.90
Covariance contribution	0.00
Combinations/Pair	1.00
Mean z-score	-1.33
Structure conservation index	0.86
SVM decision value	0.32
SVM RNA-class probability	0.685784
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13117507 108 - 23771897
GUGCGGCGGAGCAAGCAUUCGCCACAAAGUUUAAUGAAGAAUGAUAAA------------AAACGAGGAAAAGUAAAUGACGUUAAAUGAAAAUAUUCAGAGUGGCAAGAGGCUAAAUAU
.(((......)))(((.((((((((...((((((((............------------....................))))))))(((....)))...)))))..))))))...... ( -17.35)
>DroSec_CAF1 105412 108 - 1
GUGCGGUGGAGAAAGCAAUUGCCACAAAGUUUAAUGAAGAAUGAUAAA------------AAACGAGGAAAAGUAAAUGACGUUAAAUGAAAAUAUUCAGAGUGGCAAGAGGCUAAAUAU
.............(((..(((((((...((((((((............------------....................))))))))(((....)))...)))))))...)))...... ( -18.25)
>DroSim_CAF1 103518 108 - 1
GUGCGGUGGAGAAAGCAUUCGCCACAAAGUUUAAUGAAGAAUGAUAAA------------AAACGAGGAAAAGUAAAUGACGUUAAAUGAAAAUAUUCAGAGUGGCAAGAGGCUAAAUAU
.............(((.((((((((...((((((((............------------....................))))))))(((....)))...)))))..))))))...... ( -14.55)
>DroEre_CAF1 101906 120 - 1
GUGCGGUGGAGAAAGCAUUCGCCACAAAGUUUAAUGAAGAAUGAUAAAAAAAAAGAAAAAAAACGAGGAAAAGUAAAUGACGUUAAAUGAAAAUAUUCAGAGUGGCAAGAGGCUAAAUAU
.((.((((((.......)))))).)).(((((..............................((........)).......((((..((((....))))...))))...)))))...... ( -14.30)
>DroYak_CAF1 105498 110 - 1
UGGCGGUGGGGAAAGCAAUCGCCACAAAGUUUAAUGAAGAAUGAUAAAA----------AAAACGAGGAAAAGUAAAUGACGUUAAAUGAAAAUAUUCAGAGUGGCAAGAGGCUAAAUAU
((((.((((.((......)).))))........................----------......................((((..((((....))))...)))).....))))..... ( -16.80)
>consensus
GUGCGGUGGAGAAAGCAUUCGCCACAAAGUUUAAUGAAGAAUGAUAAA____________AAACGAGGAAAAGUAAAUGACGUUAAAUGAAAAUAUUCAGAGUGGCAAGAGGCUAAAUAU
.............(((....(((((...((((((((............................................))))))))(((....)))...))))).....)))...... (-13.90 = -13.90 +   0.00)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:26:49 2006