Locus 4048

Sequence ID	2R_DroMel_CAF1
Location	13,365,147 – 13,365,256
Length	109
Max. P	0.999845

overview

Window 2

Location	13,365,147 – 13,365,256
Length	109
Sequences	5
Columns	113
Reading direction	forward
Mean pairwise identity	92.49
Mean single sequence MFE	-32.37
Consensus MFE	-29.56
Energy contribution	-29.04
Covariance contribution	-0.52
Combinations/Pair	1.12
Mean z-score	-2.59
Structure conservation index	0.91
SVM decision value	4.23
SVM RNA-class probability	0.999845
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 13365147 109 + 20766785
----ACUUGCGAAACUGUGGGUGUGAAUAUUAGAAGACUGACAGAGAAGGCGAAUAGCACAGUUAUGCGAGAACCAUACCGCACUCCUCGCACUCAUUCAAAAUUUGCAAGUU
----(((((((((...((((((((((.........(((((.(......)((.....)).))))).((((..........))))....))))))))))......))))))))). ( -30.80)
>DroSec_CAF1 63968 109 + 1
----ACUUGCGAAACUGUGGGUGUGAAUAUUAGAAGACUGACAGAGAGGGCGAAUAGCACAGUUAUGCGAGAACCAUACCGCACUCCUCGAACUCAUUCAAAAUUUGCAAGUU
----(((((((((.((((.(((.(..........).))).)))).(((..((((((((...)))))(((..........))).....)))..)))........))))))))). ( -29.60)
>DroSim_CAF1 66899 109 + 1
----ACUUGCGAAACUGUGGGUGUGAAUAUUAGAAGACUGACAGAGAGGGCGAAUAGCACAGUUAUGCGAGAACCAUACCGCACUCCUCGCACUCAUUCAAAAUUUGCAAGUU
----(((((((((...((((((((((...((((....))))....(((.(((....(((......)))(.....)....))).))).))))))))))......))))))))). ( -30.70)
>DroEre_CAF1 64864 113 + 1
AAACACUUGCGAAACAGUGGGUGUGAAUAUUAGAAGACUAAAAGAGAGGGCGAAAAGCCCAGUUAUGCGAAAACCAUUCCGCGCUCCUCACACUCAUUCAAAAUUUGCAAGUU
....(((((((((..(((((((((((...((((....))))..(((.((((.....))))......(((..........))).))).))))))))))).....))))))))). ( -37.20)
>DroYak_CAF1 66110 113 + 1
AAACACUUGCGAAACUGUGGGUGUGAAUAUUAGAAGAUUGACAGAGAGGGCGAAUAGCACAGUUAUGCGAGAACCAUUUCGCACUCGUCACACUCAUUCAAAAUUUGCAAGUU
....(((((((((...((((((((((...................(((.((.....)).......(((((((....)))))))))).))))))))))......))))))))). ( -33.55)
>consensus
____ACUUGCGAAACUGUGGGUGUGAAUAUUAGAAGACUGACAGAGAGGGCGAAUAGCACAGUUAUGCGAGAACCAUACCGCACUCCUCGCACUCAUUCAAAAUUUGCAAGUU
....(((((((((...((((((((((...((((....))))..(((...((.....)).......((((..........))))))).))))))))))......))))))))). (-29.56 = -29.04 +  -0.52)

alignment

secondary structure

dotplot

Window 3

Location	13,365,147 – 13,365,256
Length	109
Sequences	5
Columns	113
Reading direction	reverse
Mean pairwise identity	92.49
Mean single sequence MFE	-29.60
Consensus MFE	-24.14
Energy contribution	-25.02
Covariance contribution	0.88
Combinations/Pair	1.11
Mean z-score	-1.77
Structure conservation index	0.82
SVM decision value	1.00
SVM RNA-class probability	0.897384
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 13365147 109 - 20766785
AACUUGCAAAUUUUGAAUGAGUGCGAGGAGUGCGGUAUGGUUCUCGCAUAACUGUGCUAUUCGCCUUCUCUGUCAGUCUUCUAAUAUUCACACCCACAGUUUCGCAAGU----
.(((((((((((.((..((((((.(((((.(((((...(((....((((....)))).....)))....))).)).)))))...))))))....)).))))).))))))---- ( -29.20)
>DroSec_CAF1 63968 109 - 1
AACUUGCAAAUUUUGAAUGAGUUCGAGGAGUGCGGUAUGGUUCUCGCAUAACUGUGCUAUUCGCCCUCUCUGUCAGUCUUCUAAUAUUCACACCCACAGUUUCGCAAGU----
.(((((((((((.((..(((((..(((((.(((((...(((....((((....)))).....)))....))).)).)))))....)))))....)).))))).))))))---- ( -27.90)
>DroSim_CAF1 66899 109 - 1
AACUUGCAAAUUUUGAAUGAGUGCGAGGAGUGCGGUAUGGUUCUCGCAUAACUGUGCUAUUCGCCCUCUCUGUCAGUCUUCUAAUAUUCACACCCACAGUUUCGCAAGU----
.(((((((((((.((...(((.(((((.((..(((((((.......))).))))..)).))))).)))..(((.(((........))).)))..)).))))).))))))---- ( -30.10)
>DroEre_CAF1 64864 113 - 1
AACUUGCAAAUUUUGAAUGAGUGUGAGGAGCGCGGAAUGGUUUUCGCAUAACUGGGCUUUUCGCCCUCUCUUUUAGUCUUCUAAUAUUCACACCCACUGUUUCGCAAGUGUUU
.((((((((((..((..(((((((.((((((((((((....))))))......((((.....)))).........).))))).)))))))....))..)))).)))))).... ( -34.60)
>DroYak_CAF1 66110 113 - 1
AACUUGCAAAUUUUGAAUGAGUGUGACGAGUGCGAAAUGGUUCUCGCAUAACUGUGCUAUUCGCCCUCUCUGUCAAUCUUCUAAUAUUCACACCCACAGUUUCGCAAGUGUUU
.(((((((((((.((..(((((((((((((.(((((.((((....(((....))))))))))))...))).)))).........))))))....)).))))).)))))).... ( -26.20)
>consensus
AACUUGCAAAUUUUGAAUGAGUGCGAGGAGUGCGGUAUGGUUCUCGCAUAACUGUGCUAUUCGCCCUCUCUGUCAGUCUUCUAAUAUUCACACCCACAGUUUCGCAAGU____
.(((((((((((.((...(((.(((((.(((((((((((.......))).)))))))).))))).)))..(((.(((........))).)))..)).))))).)))))).... (-24.14 = -25.02 +   0.88)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:10:27 2006