Locus 7728

Sequence ID 3R_DroMel_CAF1
Location 20,740,564 – 20,740,683
Length 119
Max. P 0.993713
window12462 window12463

overview

Window 2

Location 20,740,564 – 20,740,683
Length 119
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 77.18
Mean single sequence MFE -34.20
Consensus MFE -26.01
Energy contribution -26.45
Covariance contribution 0.44
Combinations/Pair 1.42
Mean z-score -2.31
Structure conservation index 0.76
SVM decision value 2.42
SVM RNA-class probability 0.993713
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 20740564 119 + 27905053
GUAUAGUGGUUAGUAUCCCC-GCCUGUCACGCGGGAGACCGGGGUUCAAUUCCCCGUCGGGGAGACCGAUAAAAUAUAUAUUUCUUUUUAAAACCGCAUUAUCAUGUAAAUAAUAAAUUA
.....((((((.((.(((((-.((((.....)))).(((.((((.......)))))))))))).))...(((((...........))))).))))))....................... ( -33.70)
>DroSec_CAF1 36822 111 + 1
GUAUAGUGGUUAGUAUCCCCCCCCCGUCACGCGGGAGAUCGGGGUUCAAUUCCUUGUCGGGGAUACAG-CAGAGA--AUAU---UUUUUUGAACCACU-UUUCAUGUAAAUAA--AAUUA
(...(((((((.((((((((..((((.....)))).(((.((((......)))).)))))))))))..-((((((--....---.)))))))))))))-...)..........--..... ( -40.00)
>DroSim_CAF1 37837 114 + 1
GUAUAGUGGUUAGUAUCCCC-GCCUGUCACGCGGGAGACCGGGGUUCAAUUCCCCGUCGGGGAGAUGUGUAUUAG--UUUU---UUUUUUUUGUUACUAUUUCUUUUUAAUAGUCAAUUA
...(((((..((...(((((-.((((.....)))).(((.((((.......))))))))))))..))..))))).--....---......(((..((((((.......)))))))))... ( -29.90)
>DroEre_CAF1 41954 117 + 1
GUAUAGUGGUUAGUAUCCCC-GCCUGUCACGCGGGAGACCGGGGUUCAAUUCCCCGUCGGGGAGACGU-AAAGGGAUUUCUUUUUUUCUUAACUCUCU-UUUUAUGUGAAUAAUAAAAUA
........((((...(((((-.((((.....)))).(((.((((.......)))))))))))).((((-(((((((...................)))-))))))))...))))...... ( -33.21)
>consensus
GUAUAGUGGUUAGUAUCCCC_GCCUGUCACGCGGGAGACCGGGGUUCAAUUCCCCGUCGGGGAGACGG_UAAAAG__AUAU___UUUUUUAAACCACU_UUUCAUGUAAAUAAUAAAUUA
.....((((((.((.(((((..((((.....)))).((.(((((.......)))))))))))).))...(((((((........)))))))))))))....................... (-26.01 = -26.45 +   0.44)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 3

Location 20,740,564 – 20,740,683
Length 119
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 77.18
Mean single sequence MFE -29.69
Consensus MFE -17.98
Energy contribution -18.73
Covariance contribution 0.75
Combinations/Pair 1.00
Mean z-score -2.24
Structure conservation index 0.61
SVM decision value 1.44
SVM RNA-class probability 0.954115
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 20740564 119 - 27905053
UAAUUUAUUAUUUACAUGAUAAUGCGGUUUUAAAAAGAAAUAUAUAUUUUAUCGGUCUCCCCGACGGGGAAUUGAACCCCGGUCUCCCGCGUGACAGGC-GGGGAUACUAACCACUAUAC
.....(((((((.....))))))).((((.......(((((....)))))...(((.((((((.(((((.......)))))(((........)))...)-))))).)))))))....... ( -31.80)
>DroSec_CAF1 36822 111 - 1
UAAUU--UUAUUUACAUGAAA-AGUGGUUCAAAAAA---AUAU--UCUCUG-CUGUAUCCCCGACAAGGAAUUGAACCCCGAUCUCCCGCGUGACGGGGGGGGGAUACUAACCACUAUAC
...((--((((....))))))-(((((((.......---....--......-..((((((((..(((....)))..(((((.((........))))))).)))))))).))))))).... ( -32.75)
>DroSim_CAF1 37837 114 - 1
UAAUUGACUAUUAAAAAGAAAUAGUAACAAAAAAAA---AAAA--CUAAUACACAUCUCCCCGACGGGGAAUUGAACCCCGGUCUCCCGCGUGACAGGC-GGGGAUACUAACCACUAUAC
......((((((.......))))))...........---....--............((((((.(((((.......)))))(((........)))...)-)))))............... ( -26.40)
>DroEre_CAF1 41954 117 - 1
UAUUUUAUUAUUCACAUAAAA-AGAGAGUUAAGAAAAAAAGAAAUCCCUUU-ACGUCUCCCCGACGGGGAAUUGAACCCCGGUCUCCCGCGUGACAGGC-GGGGAUACUAACCACUAUAC
.....................-((.(.((((......((((......))))-..((.((((((.(((((.......)))))(((........)))...)-))))).))))))).)).... ( -27.80)
>consensus
UAAUUUAUUAUUUACAUGAAA_AGUGAUUUAAAAAA___AUAA__CCUUUA_ACGUCUCCCCGACGGGGAAUUGAACCCCGGUCUCCCGCGUGACAGGC_GGGGAUACUAACCACUAUAC
......................................................((.((((((((.(((........))).)))..((........))..))))).))............ (-17.98 = -18.73 +   0.75)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:53:06 2006