Locus 6502

Sequence ID 2R_DroMel_CAF1
Location 20,323,025 – 20,323,136
Length 111
Max. P 0.899838
window10356 window10357

overview

Window 6

Location 20,323,025 – 20,323,136
Length 111
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 78.40
Mean single sequence MFE -43.52
Consensus MFE -23.96
Energy contribution -24.13
Covariance contribution 0.17
Combinations/Pair 1.33
Mean z-score -1.95
Structure conservation index 0.55
SVM decision value 0.49
SVM RNA-class probability 0.755011
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 20323025 111 + 20766785
CCCAGUCGGGCAUGGACGCCCCCGACGCCCCGCACACGCCCAAGUACAUGGACGGCGGGAACACGGCG---------GCCAGCGUCACGCCCGGCAUUAACAUCCCGGGAAAGUCCGCCU
....(((((((...((((((((((....(((((...((.(((......))).)))))))....))).)---------)...)))))..)))))))..........((((....))))... ( -44.60)
>DroVir_CAF1 52485 120 + 1
CACAAUCGGGCAUGGAUGCGCCGGACGCACCGCAUACGCCCAAAUAUAUGGACGGCGGCAGCACCGUGCCCGUCAGCGCCAGCAUCACGCCCGGCGUCAAUAUACCCGGCAAAUCAGCGU
......(((((((((.(((((((...((...))...((.(((......))).)).)))).))))))))))))...((((..((.....))((((.((......)))))).......)))) ( -44.40)
>DroGri_CAF1 51153 114 + 1
CACAAUCGGGCAUGGAUGCGCCGGACGCACCACAUACGCCCAAAUAUAUGGACGGUGGCAGCACCUCAGC------CGCCAGCAUCACGCCCGGCGUUCAAAUACCGGGCAAGUCCGCCU
.......((((.(((.((((.....))))))).....))))........((((((((((.........))------))))........((((((..(....)..))))))..)))).... ( -45.30)
>DroWil_CAF1 73151 111 + 1
CGCAAUCGGGCAUGGAUGCUCCGGAUGCCCCUCAUACGCCCAAAUAUAUGGAUGGAGGGAGUACGGCC---------AGUAGCAUAACGCCCGGUGUUAAUAUACCCGGCAAAUCGGCCU
.(((.(((((((....))).)))).)))(((((......(((......)))...))))).....((((---------.((......))(((.(((((....))))).))).....)))). ( -41.30)
>DroMoj_CAF1 62576 120 + 1
CACAGUCGGGCAUGGAUGCACCAGAUGCACCGCAUACGCCCAAAUAUAUGGACGGCGGUAGCACGGCAGCCGUUAGCGCCAGCAUAACACCUGGCGUUAAUAUACCUGGCAAAUCAGCAU
....((((((...((.(((....(.((((((((...((.(((......))).))))))).)))).))).))(((((((((((........)))))))))))...)))))).......... ( -45.50)
>DroPer_CAF1 47595 111 + 1
CCCAGUCGGGCAUGGACGCCCCCGAUGCCCCCCACACGCCCAAAUACAUGGACGGUGGCAACACCGCG---------GCCAGCGUCACGCCCGGCGUCAACAUACCCGGAAAGUCAGCCU
....(((((((...(((((..(((...............(((......))).(((((....)))))))---------)...)))))..)))))))............((........)). ( -40.00)
>consensus
CACAAUCGGGCAUGGAUGCCCCGGACGCACCGCAUACGCCCAAAUAUAUGGACGGCGGCAGCACCGCG_________GCCAGCAUCACGCCCGGCGUUAAUAUACCCGGCAAAUCAGCCU
....(((((((...(((((..........((((...((.(((......))).)))))).......((..........))..)))))..)))))))..........((((....))))... (-23.96 = -24.13 +   0.17)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 7

Location 20,323,025 – 20,323,136
Length 111
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 78.40
Mean single sequence MFE -52.03
Consensus MFE -34.65
Energy contribution -33.98
Covariance contribution -0.66
Combinations/Pair 1.41
Mean z-score -1.84
Structure conservation index 0.67
SVM decision value 1.01
SVM RNA-class probability 0.899838
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 20323025 111 - 20766785
AGGCGGACUUUCCCGGGAUGUUAAUGCCGGGCGUGACGCUGGC---------CGCCGUGUUCCCGCCGUCCAUGUACUUGGGCGUGUGCGGGGCGUCGGGGGCGUCCAUGCCCGACUGGG
...........(((((...((....))((((((((((((...(---------(.((((((((((((((((((......)))))).))).)))))).))))))))).)))))))).))))) ( -54.80)
>DroVir_CAF1 52485 120 - 1
ACGCUGAUUUGCCGGGUAUAUUGACGCCGGGCGUGAUGCUGGCGCUGACGGGCACGGUGCUGCCGCCGUCCAUAUAUUUGGGCGUAUGCGGUGCGUCCGGCGCAUCCAUGCCCGAUUGUG
..((......))(((((((..((.((((((((((......(((((((.......)))))))(((((((((((......))))))...)))))))))))))))))...)))))))...... ( -59.10)
>DroGri_CAF1 51153 114 - 1
AGGCGGACUUGCCCGGUAUUUGAACGCCGGGCGUGAUGCUGGCG------GCUGAGGUGCUGCCACCGUCCAUAUAUUUGGGCGUAUGUGGUGCGUCCGGCGCAUCCAUGCCCGAUUGUG
.(((((.(.((((((((........)))))))).)....(((((------((......))))))))))))((((...((((((..(((.((((((.....))))))))))))))).)))) ( -56.50)
>DroWil_CAF1 73151 111 - 1
AGGCCGAUUUGCCGGGUAUAUUAACACCGGGCGUUAUGCUACU---------GGCCGUACUCCCUCCAUCCAUAUAUUUGGGCGUAUGAGGGGCAUCCGGAGCAUCCAUGCCCGAUUGCG
.(((((....(((.(((........))).)))((......)))---------)))).....((((((..(((......)))..)...)))))(((..(((.(((....))))))..))). ( -41.10)
>DroMoj_CAF1 62576 120 - 1
AUGCUGAUUUGCCAGGUAUAUUAACGCCAGGUGUUAUGCUGGCGCUAACGGCUGCCGUGCUACCGCCGUCCAUAUAUUUGGGCGUAUGCGGUGCAUCUGGUGCAUCCAUGCCCGACUGUG
..((......))..(((((.....((((((((((...((((((((.....)).)))).)).(((((((((((......))))))...))))))))))))))).....)))))........ ( -45.80)
>DroPer_CAF1 47595 111 - 1
AGGCUGACUUUCCGGGUAUGUUGACGCCGGGCGUGACGCUGGC---------CGCGGUGUUGCCACCGUCCAUGUAUUUGGGCGUGUGGGGGGCAUCGGGGGCGUCCAUGCCCGACUGGG
.......((...((((((((..((((((.((((...))))..(---------(.(((((((.((((((((((......)))))).)).)).)))))))))))))))))))))))...)). ( -54.90)
>consensus
AGGCUGACUUGCCGGGUAUAUUAACGCCGGGCGUGAUGCUGGC_________CGCCGUGCUGCCGCCGUCCAUAUAUUUGGGCGUAUGCGGGGCAUCCGGCGCAUCCAUGCCCGACUGUG
.(((.(((.(((((((.........(((((........)))))..............(((.(((((((((((......))))))...))))))))))))))).)))...)))........ (-34.65 = -33.98 +  -0.66)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:12:25 2006