Locus 5165

Sequence ID 2R_DroMel_CAF1
Location 16,809,307 – 16,809,515
Length 208
Max. P 0.921235
window8256 window8257

overview

Window 6

Location 16,809,307 – 16,809,403
Length 96
Sequences 5
Columns 108
Reading direction reverse
Mean pairwise identity 83.43
Mean single sequence MFE -35.46
Consensus MFE -19.36
Energy contribution -19.16
Covariance contribution -0.20
Combinations/Pair 1.19
Mean z-score -2.19
Structure conservation index 0.55
SVM decision value 0.05
SVM RNA-class probability 0.560118
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 16809307 96 - 20766785
GGCCGAG-----AUACGU---UGGCCACUUAAGCGCUGGUUUAUUGC--UGGUGGUGGCCCGCGCUUCGUGCCGCAAAUGUGGUAAAUGUAAU--GUAAUUGGACACU
..(((((-----(..(((---.((((((.....(((..((.....))--..))))))))).)))..)).((((((....))))))........--....))))..... ( -34.10)
>DroSec_CAF1 3432 92 - 1
GGCCGAG-----AUACGU---UGGCCACUUAAGCGCUGGCUUAAUGC--UGGUGG---C-CGCGCUUCGUGCCGCAAAUGUGGUAAACGAAAU--GUAAUUGGACACU
..((((.-----.(((((---(((((((((((((....)))))....--.)))))---)-).....(((((((((....)))))..)))))))--))).))))..... ( -34.30)
>DroSim_CAF1 3445 93 - 1
GGCCGAG-----AUACGU---UGGCCACUUAAGCGCUGGCUUAUUGC--UGGUGG---CCCGCGCUUCGUGCCGCAAAUGUGGUAAACGAAUU--GUAAUUGGACACU
..((((.-----.(((((---.((((((((((((....)))))....--.)))))---)).))..((((((((((....)))))..)))))..--))).))))..... ( -34.10)
>DroEre_CAF1 3375 95 - 1
GGCCGAG-----AUACGU---UGGCCACUAAUAAGCUGGUUUGUUUU--UGGCGG---CCUGCGCUUCGUGCCGCAAAUGUGGUAAAUGUAAUUGGUAAUUGGCCACU
(((((((-----(..(((---.((((.((((.((((......)))))--))).))---)).)))..)).((((((....))))))..............))))))... ( -37.20)
>DroYak_CAF1 3328 105 - 1
GGCCGAGUACGGGUACGUUUUUGGCCACCAAUACGCUGGUUUGUUUUUCUGGCGG---GCUGCGCUUCGUGCCGCAAAUGUGGUAAAUGUAAUUGGUAAUUGGGCACU
(((((((.(((....))).)))))))((((((.(((.((((((((.....)))))---)))))).....((((((....))))))......))))))........... ( -37.60)
>consensus
GGCCGAG_____AUACGU___UGGCCACUUAAGCGCUGGUUUAUUGC__UGGUGG___CCCGCGCUUCGUGCCGCAAAUGUGGUAAAUGUAAU__GUAAUUGGACACU
(.((((.......(((((.....(((((......((.(((.....((....((((....)))))).....)))))....)))))..)))))........)))).)... (-19.36 = -19.16 +  -0.20)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 7

Location 16,809,403 – 16,809,515
Length 112
Sequences 5
Columns 112
Reading direction forward
Mean pairwise identity 93.24
Mean single sequence MFE -29.98
Consensus MFE -24.60
Energy contribution -24.96
Covariance contribution 0.36
Combinations/Pair 1.04
Mean z-score -1.82
Structure conservation index 0.82
SVM decision value 1.14
SVM RNA-class probability 0.921235
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 16809403 112 + 20766785
AAAAAAAAAGCACCCACAUCGAGCGUAAUCGGCCAGAAAACAGCGAUGCUCGCUUCGGGUCGCGUGUAAACCUAAAAUCGCACUGUCCGGCAGCAAAACGCUUGAUAACCCA
.................(((((((((.....(((.((.....(((((.(.......).)))))(((..(........)..)))..)).)))......)))))))))...... ( -28.70)
>DroSec_CAF1 3524 111 + 1
AAAA-AAAAGCACCCACAUCGAGCGUAAUCGGCCAGAAAACAGCGAUGCUCGCUUCGGGUCGCGUGUAAACCUAAAAUCGCACGGUCCGGCAGCAAAACGCUUGAUAACCCA
....-............(((((((((.....(((.......((((.....))))..((..((.(((............))).))..)))))......)))))))))...... ( -33.40)
>DroSim_CAF1 3538 111 + 1
AAAA-AAAAGCACCCACAUCGAGCGUAAUCGGCCAGAAAACAGCGAUGCUCGCUUCGGGUCGCGUGUAAACCUAAAAUCGCACUGUCCGGCAGCAAAACGCUUGAUAACCCA
....-............(((((((((.....(((.((.....(((((.(.......).)))))(((..(........)..)))..)).)))......)))))))))...... ( -28.70)
>DroEre_CAF1 3470 107 + 1
AA-----AAGCACCCACAUCGACUGUAAUCGGCCAGAAAACAGCGAUGCUUGCGUCGGGUCGCGUGUAAACUUAAUAUCGCACAGUCCGGCAGCAAAACGCUUGAUAACUCA
..-----((((.....(((((.((((..((.....))..))))))))).((((((((((..(.(((............))).)..)))))).))))...))))......... ( -31.10)
>DroYak_CAF1 3433 107 + 1
AA-----AAGCACCCACAUCGACUGUAAUCGGGCAGAAAACAGCGAUGCUCGCUUCGGGUCGCGUGUAAACUUAAUAUCGCACUGUCCGGCAGCAAAACGCUUGAUAACCCA
..-----((((.....(((((.((((..((.....))..)))))))))...((((((((.((.(((..(........)..)))))))))).))).....))))......... ( -28.00)
>consensus
AAAA_AAAAGCACCCACAUCGAGCGUAAUCGGCCAGAAAACAGCGAUGCUCGCUUCGGGUCGCGUGUAAACCUAAAAUCGCACUGUCCGGCAGCAAAACGCUUGAUAACCCA
.................(((((((((.....(((.((.....(((((.(.......).)))))(((..(........)..)))..)).)))......)))))))))...... (-24.60 = -24.96 +   0.36)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:38:08 2006