Locus 1254

Sequence ID 3R_DroMel_CAF1
Location 3,764,615 – 3,764,716
Length 101
Max. P 0.999609
window2042 window2043

overview

Window 2

Location 3,764,615 – 3,764,716
Length 101
Sequences 4
Columns 114
Reading direction forward
Mean pairwise identity 73.67
Mean single sequence MFE -31.40
Consensus MFE -17.93
Energy contribution -20.00
Covariance contribution 2.06
Combinations/Pair 1.23
Mean z-score -3.00
Structure conservation index 0.57
SVM decision value 3.78
SVM RNA-class probability 0.999609
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 3764615 101 + 27905053
AACCCAUGUAUAUGGUGCAGCUAUAUGUAUGUGCAGGUUGCACGUGUACUGGUACUGUGUACU-------------GGUAUUGGUACUGGGUACUGGUGUUGUUAUUACUUUUA
.(((((.((((...((((((((...(((....)))))))))))..((((..((((...)))).-------------.))))..)))))))))...((((.......)))).... ( -31.80)
>DroSec_CAF1 18131 110 + 1
AAUCCAUGUACAUGGUCCAGCUAUA----UGUGCAGGUUGCACGUGUACUAGUACUGUGUACUGUGCAGUGGUAUUGGUACUGGUACUGGGUACUGGUGUUGUUAUUACUUUUA
....(((((((((((((.((.((((----(((((.....))))))))))).).))))))))).))).(((((((.(..(((..((((...))))..)))..).))))))).... ( -38.70)
>DroEre_CAF1 17829 83 + 1
ACCCCAUGUACAUGGUGCAGCUAUU----CGUGCAGGCUGCACUUGUACUGGUAC--------------------------UGCUGCUG-GUACUGGUGUUGUUAUUACUUUUA
(((....(((((.(((((((((...----......)))))))))))))).(((((--------------------------(......)-))))))))................ ( -26.90)
>DroYak_CAF1 20544 83 + 1
ACCCCAUGUACAUGAUGGAGCUCUU----UGUGCAGGCUGCACUGGUACUGGUGC--------------------------UAGUACUG-GUACUGGUGUUGUUAUUACUUUUA
......((((((.((......))..----))))))(((.((((..((((..(((.--------------------------...)))..-))))..)))).))).......... ( -28.20)
>consensus
AACCCAUGUACAUGGUGCAGCUAUA____UGUGCAGGCUGCACGUGUACUGGUAC__________________________UGGUACUG_GUACUGGUGUUGUUAUUACUUUUA
...(((.((((...((((((((.............))))))))..(((((((((((....................)))))))))))...)))))))................. (-17.93 = -20.00 +   2.06)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 3

Location 3,764,615 – 3,764,716
Length 101
Sequences 4
Columns 114
Reading direction reverse
Mean pairwise identity 73.67
Mean single sequence MFE -21.84
Consensus MFE -13.49
Energy contribution -14.05
Covariance contribution 0.56
Combinations/Pair 1.06
Mean z-score -2.72
Structure conservation index 0.62
SVM decision value 3.60
SVM RNA-class probability 0.999436
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 3764615 101 - 27905053
UAAAAGUAAUAACAACACCAGUACCCAGUACCAAUACC-------------AGUACACAGUACCAGUACACGUGCAACCUGCACAUACAUAUAGCUGCACCAUAUACAUGGGUU
......................((((((((.......(-------------(((.....(((....)))..((((.....)))).........)))).......))).))))). ( -18.74)
>DroSec_CAF1 18131 110 - 1
UAAAAGUAAUAACAACACCAGUACCCAGUACCAGUACCAAUACCACUGCACAGUACACAGUACUAGUACACGUGCAACCUGCACA----UAUAGCUGGACCAUGUACAUGGAUU
.................(((((.....((((.(((((.......(((....))).....))))).))))..((((.....)))).----....))))).((((....))))... ( -26.90)
>DroEre_CAF1 17829 83 - 1
UAAAAGUAAUAACAACACCAGUAC-CAGCAGCA--------------------------GUACCAGUACAAGUGCAGCCUGCACG----AAUAGCUGCACCAUGUACAUGGGGU
................(((.....-..(((((.--------------------------(((....)))..((((.....)))).----....))))).((((....))))))) ( -23.60)
>DroYak_CAF1 20544 83 - 1
UAAAAGUAAUAACAACACCAGUAC-CAGUACUA--------------------------GCACCAGUACCAGUGCAGCCUGCACA----AAGAGCUCCAUCAUGUACAUGGGGU
................(((((((.-...)))).--------------------------...(((((((..(((.(((((.....----.)).))).)))...)))).)))))) ( -18.10)
>consensus
UAAAAGUAAUAACAACACCAGUAC_CAGUACCA__________________________GUACCAGUACAAGUGCAACCUGCACA____AAUAGCUGCACCAUGUACAUGGGGU
.................(((((((.((((..............................(((....)))..((((.....)))).........))))......)))).)))... (-13.49 = -14.05 +   0.56)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:04:44 2006