Locus 7679

Sequence ID	3R_DroMel_CAF1
Location	20,594,761 – 20,594,892
Length	131
Max. P	0.855134

overview

Window 6

Location	20,594,761 – 20,594,854
Length	93
Sequences	3
Columns	103
Reading direction	forward
Mean pairwise identity	85.15
Mean single sequence MFE	-12.95
Consensus MFE	-9.32
Energy contribution	-9.10
Covariance contribution	-0.22
Combinations/Pair	1.06
Mean z-score	-1.90
Structure conservation index	0.72
SVM decision value	0.07
SVM RNA-class probability	0.570866
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 20594761 93 + 27905053
UAACGACAUCCGCACACUUUACAUAU--AUAUUUGGAACCU----CCAAUGGAUUCUGU-UCCUAAAAAUCCACACACAUAUGCUGGAAUUUUAUCU---UUU
........((((((............--....((((.....----))))((((((.(..-.....).))))))........))).))).........---... ( -13.10)
>DroSec_CAF1 19564 98 + 1
UAACGACAUCAGCACACCUUACAUAU--AUAUUCGGAACCUCCAUCCAAUGGAUCCCGUUUACUAAAAAUCCACACUAAUAUGCUGGACUUUUAUCU---UUU
........((((((............--......(((.......)))..(((((..............)))))........))))))..........---... ( -12.14)
>DroSim_CAF1 19678 102 + 1
UAACAACAUCAGUACAUUUUACAUAUAUAUAUUUGGAACCUCCCUCCAAUGGAUCCUGU-UACUAAAAAUCCACACACAUAUGCUGGACUUUUAUCUCUCUUU
(((((..(((.(((.....)))..........(((((.......)))))..)))..)))-)).(((((.((((((......)).)))).)))))......... ( -13.60)
>consensus
UAACGACAUCAGCACACUUUACAUAU__AUAUUUGGAACCUCC_UCCAAUGGAUCCUGU_UACUAAAAAUCCACACACAUAUGCUGGACUUUUAUCU___UUU
..................................(((.((..........)).))).......(((((.((((((......)).)))).)))))......... ( -9.32 =  -9.10 +  -0.22)

alignment

secondary structure

dotplot

Window 7

Location	20,594,761 – 20,594,854
Length	93
Sequences	3
Columns	103
Reading direction	reverse
Mean pairwise identity	85.15
Mean single sequence MFE	-23.20
Consensus MFE	-16.23
Energy contribution	-16.13
Covariance contribution	-0.10
Combinations/Pair	1.16
Mean z-score	-2.23
Structure conservation index	0.70
SVM decision value	0.38
SVM RNA-class probability	0.713029
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 20594761 93 - 27905053
AAA---AGAUAAAAUUCCAGCAUAUGUGUGUGGAUUUUUAGGA-ACAGAAUCCAUUGG----AGGUUCCAAAUAU--AUAUGUAAAGUGUGCGGAUGUCGUUA
...---.((((....(((.((((((((((.((((((((.....-..))))))))((((----.....))))))))--))))))...(....)))))))).... ( -22.60)
>DroSec_CAF1 19564 98 - 1
AAA---AGAUAAAAGUCCAGCAUAUUAGUGUGGAUUUUUAGUAAACGGGAUCCAUUGGAUGGAGGUUCCGAAUAU--AUAUGUAAGGUGUGCUGAUGUCGUUA
...---...((((((((((.(((....)))))))))))))...(((((.(((..(((((.......)))))...(--((((.....)))))..))).))))). ( -22.80)
>DroSim_CAF1 19678 102 - 1
AAAGAGAGAUAAAAGUCCAGCAUAUGUGUGUGGAUUUUUAGUA-ACAGGAUCCAUUGGAGGGAGGUUCCAAAUAUAUAUAUGUAAAAUGUACUGAUGUUGUUA
.......(((((.(((.(((((((((((((((((((((.....-..))))))).((((((.....))))))))))))))))))....)).)))....))))). ( -24.20)
>consensus
AAA___AGAUAAAAGUCCAGCAUAUGUGUGUGGAUUUUUAGUA_ACAGGAUCCAUUGGA_GGAGGUUCCAAAUAU__AUAUGUAAAGUGUGCUGAUGUCGUUA
.......((((..(((.((((((((..(((((((((((........))))))).(((((.......)))))))))..))))))....)).)))..)))).... (-16.23 = -16.13 +  -0.10)

alignment

secondary structure

dotplot

Window 8

Location	20,594,798 – 20,594,892
Length	94
Sequences	4
Columns	117
Reading direction	forward
Mean pairwise identity	76.12
Mean single sequence MFE	-17.38
Consensus MFE	-10.10
Energy contribution	-10.10
Covariance contribution	-0.00
Combinations/Pair	1.00
Mean z-score	-2.02
Structure conservation index	0.58
SVM decision value	0.80
SVM RNA-class probability	0.855134
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 20594798 94 + 27905053
CU-----CCAAUGGAUUCUGU-UCCU--------------AAAAAUCCACACACAUAUGCUGGAAUUUUAUCU---UUUUUUCGGUGUAGAGAAAUUUAUCAUUUCACUGCAGCACA
..-----.....(((......-)))(--------------((((.((((((......)).)))).)))))...---.......(.(((((.(((((.....))))).))))).)... ( -18.20)
>DroSec_CAF1 19601 99 + 1
CUCCA-UCCAAUGGAUCCCGUUUACU--------------AAAAAUCCACACUAAUAUGCUGGACUUUUAUCU---UUUUUUCGGUGUAGAGAAAUUUAUCAUUUCACUGCAGCACA
.((((-(...)))))..........(--------------((((.((((((......)).)))).)))))...---.......(.(((((.(((((.....))))).))))).)... ( -18.50)
>DroSim_CAF1 19717 101 + 1
CUCCC-UCCAAUGGAUCCUGU-UACU--------------AAAAAUCCACACACAUAUGCUGGACUUUUAUCUCUCUUUUUUCGGUGUAGAGAAAUUUAUCAUUUCACUGCAGCACA
...((-......)).......-...(--------------((((.((((((......)).)))).))))).............(.(((((.(((((.....))))).))))).)... ( -16.90)
>DroEre_CAF1 19523 104 + 1
CUCCAAA---------UCUGU-UACUUUUUAGUAAUAUUUAGUAACCCACCAACAUAUUUUGAAUUCUUCUCU---UUUUCUCGGUGUAGAGAAAUUUAUCAUUUCACUGCAGCACA
.......---------...((-((((...((....))...))))))...........................---.......(.(((((.(((((.....))))).))))).)... ( -15.90)
>consensus
CUCCA_UCCAAUGGAUCCUGU_UACU______________AAAAAUCCACACACAUAUGCUGGACUUUUAUCU___UUUUUUCGGUGUAGAGAAAUUUAUCAUUUCACUGCAGCACA
...................................................................................(.(((((.(((((.....))))).))))).)... (-10.10 = -10.10 +  -0.00)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:51:49 2006