Locus 3461

Sequence ID	2R_DroMel_CAF1
Location	11,628,347 – 11,628,475
Length	128
Max. P	0.774836

overview

Window 7

Location	11,628,347 – 11,628,443
Length	96
Sequences	5
Columns	97
Reading direction	forward
Mean pairwise identity	82.17
Mean single sequence MFE	-20.52
Consensus MFE	-10.67
Energy contribution	-11.27
Covariance contribution	0.60
Combinations/Pair	1.17
Mean z-score	-2.40
Structure conservation index	0.52
SVM decision value	0.54
SVM RNA-class probability	0.774836
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 11628347 96 + 20766785
AUUCUCGUUGUAUUAACAAAACUAAAAACAAACUCUGGG-CAAUGACUUCUCUUUUUGGUUUCAUUAGAAUGAGAACUCAUUGGCCCUGUCUAAAUU
.......((((....)))).................(((-((((((.(((((.(((((((...))))))).))))).))))).)))).......... ( -21.10)
>DroSec_CAF1 896 94 + 1
AUUCUCGAUGUAUUAACAAAAACUAAAACAAACUCUGGG-CAAUGGCCUCUCUUUUUGGUUUCA--ACAAUGAGAAUCCAUGGGCCCAGUCCAAAUU
........(((.(((........))).)))....(((((-(.((((..((((...(((......--.))).))))..))))..))))))........ ( -23.10)
>DroSim_CAF1 899 94 + 1
AUUCUCGAUGUAUUAACAAAAACUAAAACAAACUCUGGG-CAAUGGCCUCUCUUUUUGGUUUCA--ACAAUGAGAAUCCAUGGGCCCAGUCCAAAUU
........(((.(((........))).)))....(((((-(.((((..((((...(((......--.))).))))..))))..))))))........ ( -23.10)
>DroEre_CAF1 879 90 + 1
AAAUCUGAUGUAUUAACAAA-ACUAAAACAAAGGCUGGG-CAAUGGCUUCUCUUU---GUUUUA--ACGAUGAGAAUCCAUGAAGCCUGUCUAAAUU
....................-..........((((.(((-(.((((.(((((.((---((....--)))).))))).))))...))))))))..... ( -22.40)
>DroYak_CAF1 895 91 + 1
AUUCUCGAUGUAUUAACCAA-ACUAAAACAAAGUCUGGGACAAUGACUUCUCUUU---GUUUCA--ACCCUGAGAAUCUUUGAACCCUGUAUAAAUU
(((((((..((.....(((.-(((.......))).)))(((((.((....)).))---)))...--))..))))))).................... ( -12.90)
>consensus
AUUCUCGAUGUAUUAACAAAAACUAAAACAAACUCUGGG_CAAUGGCUUCUCUUUUUGGUUUCA__ACAAUGAGAAUCCAUGGGCCCUGUCUAAAUU
....................................(((...((((.(((((...................))))).))))...))).......... (-10.67 = -11.27 +   0.60)

alignment

secondary structure

dotplot

Window 8

Location	11,628,373 – 11,628,475
Length	102
Sequences	5
Columns	103
Reading direction	reverse
Mean pairwise identity	87.81
Mean single sequence MFE	-22.90
Consensus MFE	-14.91
Energy contribution	-15.23
Covariance contribution	0.32
Combinations/Pair	1.17
Mean z-score	-2.15
Structure conservation index	0.65
SVM decision value	-0.03
SVM RNA-class probability	0.520628
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 11628373 102 - 20766785
UAAUCAAAAUAAGCUAACUGAAGAAAGUGCAAAAUUUAGACAGGGCCAAUGAGUUCUCAUUCUAAUGAAACCAAAAAGAGAAGUCAUUG-CCCAGAGUUUGUU
.......((((((((..(((((............)))))...((((.(((((.(((((...................))))).))))))-)))..)))))))) ( -25.71)
>DroSec_CAF1 922 100 - 1
UAAUCAAAAUAAGCUAACUGAAGAAAGUGCAAAAUUUGGACUGGGCCCAUGGAUUCUCAUUGU--UGAAACCAAAAAGAGAGGCCAUUG-CCCAGAGUUUGUU
.......((((((((.(((......)))............((((((..((((.(((((....(--((....)))...))))).)))).)-))))))))))))) ( -28.30)
>DroSim_CAF1 925 100 - 1
UAAUCAAAAUAAGCUAACUGAAGAAAGUGCAAAAUUUGGACUGGGCCCAUGGAUUCUCAUUGU--UGAAACCAAAAAGAGAGGCCAUUG-CCCAGAGUUUGUU
.......((((((((.(((......)))............((((((..((((.(((((....(--((....)))...))))).)))).)-))))))))))))) ( -28.30)
>DroEre_CAF1 904 97 - 1
UAAUCAAAAUAAGCUAACUGAAGAAAGUGCAAAAUUUAGACAGGCUUCAUGGAUUCUCAUCGU--UAAAAC---AAAGAGAAGCCAUUG-CCCAGCCUUUGUU
............(((..(((((............)))))...(((...((((.(((((...((--....))---...))))).)))).)-)).)))....... ( -16.80)
>DroYak_CAF1 920 98 - 1
UAAUCAAAAUAAGCUAACUGAAGAAAGUGCAAAAUUUAUACAGGGUUCAAAGAUUCUCAGGGU--UGAAAC---AAAGAGAAGUCAUUGUCCCAGACUUUGUU
....((((....((..(((......)))))............(((..(((.(((((((...((--....))---...))).)))).))).)))....)))).. ( -15.40)
>consensus
UAAUCAAAAUAAGCUAACUGAAGAAAGUGCAAAAUUUAGACAGGGCCCAUGGAUUCUCAUUGU__UGAAACCAAAAAGAGAAGCCAUUG_CCCAGAGUUUGUU
.......((((((((.(((......)))..............(((.(.((((.(((((...................))))).)))).).)))..)))))))) (-14.91 = -15.23 +   0.32)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:56:07 2006