Locus 5702

Sequence ID 2L_DroMel_CAF1
Location 16,226,477 – 16,226,597
Length 120
Max. P 0.998574
window9034 window9035

overview

Window 4

Location 16,226,477 – 16,226,568
Length 91
Sequences 5
Columns 104
Reading direction forward
Mean pairwise identity 80.99
Mean single sequence MFE -33.36
Consensus MFE -17.41
Energy contribution -16.21
Covariance contribution -1.20
Combinations/Pair 1.32
Mean z-score -4.24
Structure conservation index 0.52
SVM decision value 3.15
SVM RNA-class probability 0.998574
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 16226477 91 + 22407834
CACGUCCUUGCCAGAGGUUCUAUGUGCAU--GUG--UUUGUGCUUAUAUAUGUACAUACAU--------AUACGGAUGGUU-UUCGGUGAGGAUAUACUACUGA
...(((((..((.((((..((((.((.((--(((--(.(((((........))))).))))--------)).)).)))).)-)))))..))))).......... ( -32.40)
>DroSec_CAF1 143640 92 + 1
CACGUCCUUGCCAGAGGUUCUAUGUGCAUAUGUGUGUGUGUGCUUAUA----UAGAUACAU--------AUACGGAUGGUUUUUCGGUGAGGAUAUGCUACUGA
((..((((..((.((((..((((.((.((((((((.(((((....)))----)).))))))--------)).)).))))..))))))..))))..))....... ( -34.40)
>DroSim_CAF1 145315 90 + 1
CACGUCCUUGCCAGAGGUUCUAUGUGCAU--GUGUGUGUGUGCUCAUA----UACAUACAU--------AUACGGAUGGUUUUUCGGUGAGGAUAUGCUACUGA
((..((((..((.((((..((((.((.((--(((((((((((....))----)))))))))--------)).)).))))..))))))..))))..))....... ( -36.80)
>DroEre_CAF1 147013 91 + 1
CACGUCCUUGCCAGAAGUUGUUUGU------GUG--UGUGUGCUUAUA----UGUACAUACAUACAUAUAUAAGCGUGGUU-UUCGGUGAGGAUAUGCUACUGA
((..((((..((.((((.(((((((------(((--(((((((.....----.)))))))))))))......))))....)-)))))..))))..))....... ( -33.50)
>DroYak_CAF1 154740 85 + 1
CACGUCCUUGCCAGAAGUUCUACGU------GUGUUUGUGUGCUUAUA----UGUACAUAU--------AUGCGGAUGGUU-UUCGGUGAGGAUAUGCUACUGG
((..((((..((.((((..(..(((------((((..((((((.....----.))))))))--------)))))...)..)-)))))..))))..))....... ( -29.70)
>consensus
CACGUCCUUGCCAGAGGUUCUAUGUGCAU__GUGU_UGUGUGCUUAUA____UACAUACAU________AUACGGAUGGUU_UUCGGUGAGGAUAUGCUACUGA
...(((((..((.(((..(((.(((...........((((((............)))))).........))).)))......)))))..))))).......... (-17.41 = -16.21 +  -1.20)

alignment

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secondary structure

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dotplot

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Window 5

Location 16,226,506 – 16,226,597
Length 91
Sequences 5
Columns 104
Reading direction forward
Mean pairwise identity 84.23
Mean single sequence MFE -28.58
Consensus MFE -17.26
Energy contribution -16.98
Covariance contribution -0.28
Combinations/Pair 1.17
Mean z-score -2.08
Structure conservation index 0.60
SVM decision value 0.13
SVM RNA-class probability 0.596860
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 16226506 91 + 22407834
--GUG--UUUGUGCUUAUAUAUGUACAUACAU--------AUACGGAUGGUU-UUCGGUGAGGAUAUACUACUGAUGUGCGGUAGGCGCGCUUGAACUUUGCCG
--(((--(.(((((........))))).))))--------...(((..((((-((((((.((......))))))).(((((.....)))))..)))))...))) ( -27.00)
>DroSec_CAF1 143669 92 + 1
AUGUGUGUGUGUGCUUAUA----UAGAUACAU--------AUACGGAUGGUUUUUCGGUGAGGAUAUGCUACUGAUGUGCGGUAGGCGCGCUUGAACUUUGCCG
..((((((((((.((....----.))))))))--------))))((..(((((.(((((.((......))))))).(((((.....)))))..)))))...)). ( -27.80)
>DroSim_CAF1 145344 90 + 1
--GUGUGUGUGUGCUCAUA----UACAUACAU--------AUACGGAUGGUUUUUCGGUGAGGAUAUGCUACUGAUGUGCGGUAGGCGCGCUUGAACUUUGCCG
--(((((((((((......----..)))))))--------))))((..(((((.(((((.((......))))))).(((((.....)))))..)))))...)). ( -29.50)
>DroEre_CAF1 147038 95 + 1
--GUG--UGUGUGCUUAUA----UGUACAUACAUACAUAUAUAAGCGUGGUU-UUCGGUGAGGAUAUGCUACUGAUGUGCGCUAGGCGCACUUAAACUUUGCCG
--(((--(((((((.....----.))))))))))..........(((.((((-((((((.((......))))))).((((((...))))))..))))).))).. ( -31.10)
>DroYak_CAF1 154765 89 + 1
--GUGUUUGUGUGCUUAUA----UGUACAUAU--------AUGCGGAUGGUU-UUCGGUGAGGAUAUGCUACUGGUGUGCGGUAGGCGCGCUUGAACUUUGCCG
--((((.(((((((.....----.))))))).--------))))((..((((-(.((((.((......))))))((((((.....))))))..)))))...)). ( -27.50)
>consensus
__GUGU_UGUGUGCUUAUA____UACAUACAU________AUACGGAUGGUU_UUCGGUGAGGAUAUGCUACUGAUGUGCGGUAGGCGCGCUUGAACUUUGCCG
..((....((((((((((...........(((..............)))((...(((((.((......)))))))...)).))))))))))....))....... (-17.26 = -16.98 +  -0.28)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:50:35 2006