Locus 3578

Sequence ID	3R_DroMel_CAF1
Location	9,673,930 – 9,674,077
Length	147
Max. P	0.860082

overview

Window 1

Location	9,673,930 – 9,674,050
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	92.49
Mean single sequence MFE	-33.56
Consensus MFE	-25.93
Energy contribution	-26.69
Covariance contribution	0.76
Combinations/Pair	1.13
Mean z-score	-1.84
Structure conservation index	0.77
SVM decision value	0.52
SVM RNA-class probability	0.769127
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 9673930 120 + 27905053
GCAUAUUAAAUCGUGUCUAGGAACAGGUGAAGAUGUUCACAUAAAUUACCACCUCUUCAUUAGCCUGGGCUUUCAGAGAGCCCACAACAGUGGGCUAAAUCUUAUUUGUUUUCUGAAGGG
..............(((((((....((((((((.((..............)).))))))))..)))))))(((((((((((((((....))))))(((((...))))).))))))))).. ( -35.44)
>DroSec_CAF1 65619 120 + 1
GCAUAUUAAAUCGUGUCUAGGAACAGGUGAAGAUGUUCACAUAAAUUACCACCUCUUCAUUAGCCUGGGCUUUCAGAGAGCCCAGAACAGUGGGCUAAAUCUUAUUUGUUUUCUGAAAAG
..............(((((((....((((((((.((..............)).))))))))..)))))))((((((((((((((......)))))(((((...))))).))))))))).. ( -32.44)
>DroSim_CAF1 68557 120 + 1
GCAUAUUAAAUCGUGUCUAGGAACAGGUGAAGAUGUUCACAUAAAUUACCACCUCUUCAUUAGCCUGGGCUUUCAGAGAGCCCACAACAGUGGGCUAAAUCUUGUUUGUUUUCUAAAAAG
..............(((((((....((((((((.((..............)).))))))))..)))))))....(((.(((((((....)))))))...))).................. ( -32.04)
>DroEre_CAF1 66816 119 + 1
GCAUAUUAAAUCGUGUCUAGGAACAGGUGAAGAUGUUCACAUAAAUUACCACCUCUUCAUUAGCC-GGGCUUACAGAGAGCGCGGCACAGUGGGCUAAAGGUUAUUUGCCCUCUGAAAAG
((((........))))....(((.(((((..(((..........)))..))))).)))....(((-(.((((.....)))).)))).(((.((((.(((.....))))))).)))..... ( -34.90)
>DroYak_CAF1 70668 119 + 1
GCAUAUUAAAUCGUGUCUAGGAACAGGUGAAGAUGUUCACAUAAAUUACCACCUCUUCAUUAGCC-GGGCUUACUGGGAGCCCAGAACAGUGGGCUUAAGGUUGUGUGCUUUCUGAAAAG
((((((..((((....(((((((.(((((..(((..........)))..))))).))).))))((-((.....))))(((((((......)))))))..))))))))))........... ( -33.00)
>consensus
GCAUAUUAAAUCGUGUCUAGGAACAGGUGAAGAUGUUCACAUAAAUUACCACCUCUUCAUUAGCCUGGGCUUUCAGAGAGCCCAGAACAGUGGGCUAAAUCUUAUUUGUUUUCUGAAAAG
..............(((((((....((((((((.((..............)).))))))))..)))))))((((((((((((((......))))))..............)))))))).. (-25.93 = -26.69 +   0.76)

alignment

secondary structure

dotplot

Window 2

Location	9,673,970 – 9,674,077
Length	107
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	81.11
Mean single sequence MFE	-26.68
Consensus MFE	-16.40
Energy contribution	-17.77
Covariance contribution	1.38
Combinations/Pair	1.16
Mean z-score	-1.92
Structure conservation index	0.61
SVM decision value	0.32
SVM RNA-class probability	0.686163
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 9673970 107 + 27905053
AUAAAUUACCACCUCUUCAUUAGCCUGGGCUUUCAGAGAGCCCACAACAGUGGGCUAAAUCUUAUUUGUUUUCUGAAGGGAAAU-UUGUCAU------------UAUUCUAUUAAAUAAA
............(((((((..(((....)))...(((.(((((((....)))))))...)))...........)))))))....-.......------------................ ( -25.50)
>DroSec_CAF1 65659 120 + 1
AUAAAUUACCACCUCUUCAUUAGCCUGGGCUUUCAGAGAGCCCAGAACAGUGGGCUAAAUCUUAUUUGUUUUCUGAAAAGGAAUUAUGUCAUUGUAAAUGCAUUUAUUCUAUUAAGUAAA
......................((((((((((.....)))))))).(((((((..(((.((((.(((.......))).)))).)))..)))))))....))(((((......)))))... ( -24.80)
>DroSim_CAF1 68597 120 + 1
AUAAAUUACCACCUCUUCAUUAGCCUGGGCUUUCAGAGAGCCCACAACAGUGGGCUAAAUCUUGUUUGUUUUCUAAAAAGGAAUUAUAUCAUUGUAAAUGCAUUUAUUCUACUAAGUAAA
.....((((...((((.....(((....)))...))))(((((((....))))))).......................(((((.....(((.....))).....))))).....)))). ( -23.10)
>DroEre_CAF1 66856 116 + 1
AUAAAUUACCACCUCUUCAUUAGCC-GGGCUUACAGAGAGCGCGGCACAGUGGGCUAAAGGUUAUUUGCCCUCUGAAAAGAAAUUUAGUUAAUGAACAUGGAUU---UUUACUGAGUUAA
...........((..((((((((((-(.((((.....)))).)))).(((.((((.(((.....))))))).)))..............)))))))...))...---............. ( -33.30)
>consensus
AUAAAUUACCACCUCUUCAUUAGCCUGGGCUUUCAGAGAGCCCACAACAGUGGGCUAAAUCUUAUUUGUUUUCUGAAAAGAAAUUAUGUCAUUGUAAAUGCAUUUAUUCUACUAAGUAAA
............((((.....(((....)))...))))(((((((....))))))).............(((((....)))))..................................... (-16.40 = -17.77 +   1.38)

alignment

secondary structure

dotplot

Window 3

Location	9,673,970 – 9,674,077
Length	107
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	81.11
Mean single sequence MFE	-27.10
Consensus MFE	-18.27
Energy contribution	-18.90
Covariance contribution	0.63
Combinations/Pair	1.17
Mean z-score	-2.01
Structure conservation index	0.67
SVM decision value	0.82
SVM RNA-class probability	0.860082
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 9673970 107 - 27905053
UUUAUUUAAUAGAAUA------------AUGACAA-AUUUCCCUUCAGAAAACAAAUAAGAUUUAGCCCACUGUUGUGGGCUCUCUGAAAGCCCAGGCUAAUGAAGAGGUGGUAAUUUAU
.((((((....)))))------------)....((-(((.((((((............(((...(((((((....))))))).)))...(((....)))......)))).)).))))).. ( -26.10)
>DroSec_CAF1 65659 120 - 1
UUUACUUAAUAGAAUAAAUGCAUUUACAAUGACAUAAUUCCUUUUCAGAAAACAAAUAAGAUUUAGCCCACUGUUCUGGGCUCUCUGAAAGCCCAGGCUAAUGAAGAGGUGGUAAUUUAU
.(((((...........((((((.....))).)))....((((((((...........(((...((((((......)))))).)))...(((....)))..)))))))).)))))..... ( -25.80)
>DroSim_CAF1 68597 120 - 1
UUUACUUAGUAGAAUAAAUGCAUUUACAAUGAUAUAAUUCCUUUUUAGAAAACAAACAAGAUUUAGCCCACUGUUGUGGGCUCUCUGAAAGCCCAGGCUAAUGAAGAGGUGGUAAUUUAU
.(((((..(((((.........)))))............((((((((...........(((...(((((((....))))))).)))...(((....)))..)))))))).)))))..... ( -27.40)
>DroEre_CAF1 66856 116 - 1
UUAACUCAGUAAA---AAUCCAUGUUCAUUAACUAAAUUUCUUUUCAGAGGGCAAAUAACCUUUAGCCCACUGUGCCGCGCUCUCUGUAAGCCC-GGCUAAUGAAGAGGUGGUAAUUUAU
........(((((---...((((.(((((((..............(((.((((.((......)).)))).))).((((.(((.......))).)-))))))))))...))))...))))) ( -29.10)
>consensus
UUUACUUAAUAGAAUAAAUGCAUUUACAAUGACAAAAUUCCUUUUCAGAAAACAAAUAAGAUUUAGCCCACUGUUCUGGGCUCUCUGAAAGCCCAGGCUAAUGAAGAGGUGGUAAUUUAU
.......................................((((((((.................(((((((....))))))).......(((....)))..))))))))........... (-18.27 = -18.90 +   0.63)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:04:54 2006