Locus 5529

Sequence ID	3L_DroMel_CAF1
Location	15,181,237 – 15,181,377
Length	140
Max. P	0.869102

overview

Window 5

Location	15,181,237 – 15,181,338
Length	101
Sequences	4
Columns	101
Reading direction	reverse
Mean pairwise identity	84.91
Mean single sequence MFE	-23.40
Consensus MFE	-18.50
Energy contribution	-18.12
Covariance contribution	-0.38
Combinations/Pair	1.10
Mean z-score	-1.47
Structure conservation index	0.79
SVM decision value	0.06
SVM RNA-class probability	0.564171
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 15181237 101 - 23771897
UUUUCAGUUACCAACUGGGGCUAUAUCCCCCCAUUCCCCCCGGCUGUCCAAUCCCCCCAGAUAUCGAUGGUAAUACCGCCGGGUAAUUUUCGUACCUACUG
....(((((((....(((((........))))).....((((((.(((..(((......)))...)))((.....))))))))........)))...)))) ( -24.70)
>DroSec_CAF1 70847 86 - 1
UUUUCAGUUACCAACUGGGGCUAUAUCCC---------------UGCCCGAUCCCCCCAGAUAUCGAUGGUAAUACCGCCGGGUAAUUUUCGUACCUGCUG
.....(((((((..((((((....(((..---------------.....)))..))))))....((.(((.....))).)))))))))............. ( -20.90)
>DroSim_CAF1 72254 86 - 1
UUUUCAGUUACCAACUGGGGCUAUAUCCC---------------UGCCCGAUCCCCCCAGAUAUCGAUGGUAAUACCGCCGGGUAAUUUUCGUACCUGCUG
.....(((((((..((((((....(((..---------------.....)))..))))))....((.(((.....))).)))))))))............. ( -20.90)
>DroYak_CAF1 73754 97 - 1
UUUUCAGUUACCAACUGGGGCUAUAUCCC--CAUUCCCCCUU--UACGAGGUUCCUCCAGAUAUCGGUGGUAAUACCGCCGGGUAAUUUUCGUACCUGCUG
.....(((((((...(((((......)))--)).........--...(((....))).......((((((.....)))))))))))))............. ( -27.10)
>consensus
UUUUCAGUUACCAACUGGGGCUAUAUCCC_______________UGCCCGAUCCCCCCAGAUAUCGAUGGUAAUACCGCCGGGUAAUUUUCGUACCUGCUG
.....(((((((..((((((..((..........................))..))))))....((.(((.....))).)))))))))............. (-18.50 = -18.12 +  -0.38)

alignment

secondary structure

dotplot

Window 6

Location	15,181,258 – 15,181,377
Length	119
Sequences	4
Columns	119
Reading direction	forward
Mean pairwise identity	86.83
Mean single sequence MFE	-30.60
Consensus MFE	-23.30
Energy contribution	-23.05
Covariance contribution	-0.25
Combinations/Pair	1.14
Mean z-score	-1.59
Structure conservation index	0.76
SVM decision value	0.24
SVM RNA-class probability	0.649244
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 15181258 119 + 23771897
GGCGGUAUUACCAUCGAUAUCUGGGGGGAUUGGACAGCCGGGGGGAAUGGGGGGAUAUAGCCCCAGUUGGUAACUGAAAAUAUGAGUAGGCUAAAGGUUUAUCAGCGCCAUAAAUAAGA
((((...((((((.(....(((((..(.......)..))))).....(((((........)))))).))))))((((((((...((....))....)))).)))))))).......... ( -32.50)
>DroSec_CAF1 70868 104 + 1
GGCGGUAUUACCAUCGAUAUCUGGGGGGAUCGGGCA---------------GGGAUAUAGCCCCAGUUGGUAACUGAAAAUAUGAGUAGGCUAAAGGUUUAUCAGCGCCAUAAAUAAGA
((((...((((((.......((((((..(((.....---------------..)))....)))))).))))))((((((((...((....))....)))).)))))))).......... ( -28.50)
>DroSim_CAF1 72275 104 + 1
GGCGGUAUUACCAUCGAUAUCUGGGGGGAUCGGGCA---------------GGGAUAUAGCCCCAGUUGGUAACUGAAAAUAUGAGUAGGCUAAAGGUUUAUCAGCGCCAUAAAUAAGA
((((...((((((.......((((((..(((.....---------------..)))....)))))).))))))((((((((...((....))....)))).)))))))).......... ( -28.50)
>DroYak_CAF1 73775 115 + 1
GGCGGUAUUACCACCGAUAUCUGGAGGAACCUCGUA--AAGGGGGAAUG--GGGAUAUAGCCCCAGUUGGUAACUGAAAAUAUGAGUAGGCUAAAGGUUUAUCAGUGCCAUAAAUAAAA
(((((.....))((((((...........((((...--..))))...((--(((......))))))))))).(((((((((...((....))....)))).)))))))).......... ( -32.90)
>consensus
GGCGGUAUUACCAUCGAUAUCUGGGGGGAUCGGGCA_______________GGGAUAUAGCCCCAGUUGGUAACUGAAAAUAUGAGUAGGCUAAAGGUUUAUCAGCGCCAUAAAUAAGA
((((...((((((.(....(((((.....))))).................(((.......))).).))))))((((((((...((....))....)))).)))))))).......... (-23.30 = -23.05 +  -0.25)

alignment

secondary structure

dotplot

Window 7

Location	15,181,258 – 15,181,377
Length	119
Sequences	4
Columns	119
Reading direction	reverse
Mean pairwise identity	86.83
Mean single sequence MFE	-23.62
Consensus MFE	-19.17
Energy contribution	-19.04
Covariance contribution	-0.13
Combinations/Pair	1.09
Mean z-score	-1.93
Structure conservation index	0.81
SVM decision value	0.86
SVM RNA-class probability	0.869102
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 15181258 119 - 23771897
UCUUAUUUAUGGCGCUGAUAAACCUUUAGCCUACUCAUAUUUUCAGUUACCAACUGGGGCUAUAUCCCCCCAUUCCCCCCGGCUGUCCAAUCCCCCCAGAUAUCGAUGGUAAUACCGCC
..........((((((((.......)))))...............(((((((..(((((........))))).......(((.((((...........))))))).)))))))...))) ( -25.30)
>DroSec_CAF1 70868 104 - 1
UCUUAUUUAUGGCGCUGAUAAACCUUUAGCCUACUCAUAUUUUCAGUUACCAACUGGGGCUAUAUCCC---------------UGCCCGAUCCCCCCAGAUAUCGAUGGUAAUACCGCC
..........((((((((.......)))))...............(((((((....((((........---------------.)))).(((......))).....)))))))...))) ( -22.90)
>DroSim_CAF1 72275 104 - 1
UCUUAUUUAUGGCGCUGAUAAACCUUUAGCCUACUCAUAUUUUCAGUUACCAACUGGGGCUAUAUCCC---------------UGCCCGAUCCCCCCAGAUAUCGAUGGUAAUACCGCC
..........((((((((.......)))))...............(((((((....((((........---------------.)))).(((......))).....)))))))...))) ( -22.90)
>DroYak_CAF1 73775 115 - 1
UUUUAUUUAUGGCACUGAUAAACCUUUAGCCUACUCAUAUUUUCAGUUACCAACUGGGGCUAUAUCCC--CAUUCCCCCUU--UACGAGGUUCCUCCAGAUAUCGGUGGUAAUACCGCC
..........(((.((((.......)))).(((((.((((((..((..(((...(((((......)))--)).((......--...)))))..))..)))))).))))).......))) ( -23.40)
>consensus
UCUUAUUUAUGGCGCUGAUAAACCUUUAGCCUACUCAUAUUUUCAGUUACCAACUGGGGCUAUAUCCC_______________UGCCCGAUCCCCCCAGAUAUCGAUGGUAAUACCGCC
..........((((((((.......)))))...............(((((((.((((((..((..........................))..)))))).......)))))))...))) (-19.17 = -19.04 +  -0.13)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:52:30 2006