Locus 6981

Sequence ID	3R_DroMel_CAF1
Location	18,418,254 – 18,418,392
Length	138
Max. P	0.805816

overview

Window 9

Location	18,418,254 – 18,418,368
Length	114
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	82.66
Mean single sequence MFE	-27.76
Consensus MFE	-14.20
Energy contribution	-14.96
Covariance contribution	0.76
Combinations/Pair	1.11
Mean z-score	-2.58
Structure conservation index	0.51
SVM decision value	0.63
SVM RNA-class probability	0.805816
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 18418254 114 - 27905053
AAGUAGCAUCACACCCUUGUGACUCACAUUAGUAUCUUUUAUCGAAU-AAGAUGUCUGCAUCUGAUAUUUUACAGAUACAGUAUCUUAAGUGUGGAUCUCUGCCA-----UAGCUUCAGA
..(.(((.(((((....))))).(((((((....((.......)).(-((((((.(((.(((((........))))).)))))))))))))))))..........-----..))).)... ( -26.40)
>DroSec_CAF1 3989 119 - 1
AAAUAGCAUCUCACACUUGUGACUCACAAAAGUAUCUUGUAUCGAAC-AAGAUAUCUCCGUCUGAUACUUUACAGAUACAGUAUCUUAAGUGUGCAUCUUCGCCAUCGGCUAGCUUCAGC
....(((....((((((((.((..(......(((((((((.....))-)))))))....(((((........)))))...)..)).)))))))).......(((...)))..)))..... ( -28.20)
>DroSim_CAF1 4426 120 - 1
AAAUAGCAUCUCACACUUCUGACUCACAAAAGUAUCUUUUAUCGAUUAAAGAUAUCUCCGUCUGAUACUUUACAGAUACAGUAUCUUAAGUGUGGAUCUCCGCCAUCGGAUAGCUUCAGC
....((((((.(((((((..((..(......((((((((........))))))))....(((((........)))))...)..))..)))))))))).((((....))))..)))..... ( -27.40)
>DroEre_CAF1 4393 109 - 1
--GUAGCAUCUCACACUUGUGACUCACAAAAGUGUCUUU---------AAGACAUUUCCGUCUGAUACGUUACAGAUACAGUAUCUUAACUGUGGAUCUCUGCCAUCAGAUAUCUUCAGA
--(((((...((((....)))).........(((((...---------.((((......))))))))))))))(((((...)))))...(((.((((.((((....)))).)))).))). ( -27.00)
>DroYak_CAF1 4357 118 - 1
AAGUAGCAUCUCACAGUUGGUACUCA-AAAAGUACCUUUUAUCACUC-AAGAUAUUUCCGUCUGAUAUGUUACAGAUACAGUAUCUUAAGUGUGGAUCUCCGCAAUCAGAUAUCUUCAGC
..(((((((.(((.....((((((..-...))))))...((((....-..))))........))).))))))).((....((((((....(((((....)))))...))))))..))... ( -29.80)
>consensus
AAGUAGCAUCUCACACUUGUGACUCACAAAAGUAUCUUUUAUCGAAC_AAGAUAUCUCCGUCUGAUACUUUACAGAUACAGUAUCUUAAGUGUGGAUCUCCGCCAUCAGAUAGCUUCAGC
....((.(((.((((((((.((..(......(((((((..........)))))))....(((((........)))))...)..)).)))))))))))))..................... (-14.20 = -14.96 +   0.76)

alignment

secondary structure

dotplot

Window 0

Location	18,418,289 – 18,418,392
Length	103
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	73.96
Mean single sequence MFE	-22.84
Consensus MFE	-9.38
Energy contribution	-10.14
Covariance contribution	0.76
Combinations/Pair	1.19
Mean z-score	-1.88
Structure conservation index	0.41
SVM decision value	0.53
SVM RNA-class probability	0.770733
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 18418289 103 + 27905053
UGUAUCUGUAAAAUAUCAGAUGCAGACAUCUU-AUUCGAUAAAAGAUACUAAUGUGAGUCACAAGGGUGUGAUGCUACUUUACUUU--------------U--AAAUAGUACUACAUAUU
((((((((........))))))))((((((..-....)))......(((....))).)))......(((((.(((((.((((....--------------)--)))))))).)))))... ( -21.00)
>DroSec_CAF1 4029 103 + 1
UGUAUCUGUAAAGUAUCAGACGGAGAUAUCUU-GUUCGAUACAAGAUACUUUUGUGAGUCACAAGUGUGAGAUGCUAUUUAACUUA--------------U--AAAUAGUACUACACAUU
.((((((.....(((((..(((((....)).)-))..))))).))))))..(((((...)))))(((((((.(((((((((.....--------------)--)))))))))).))))). ( -28.60)
>DroSim_CAF1 4466 104 + 1
UGUAUCUGUAAAGUAUCAGACGGAGAUAUCUUUAAUCGAUAAAAGAUACUUUUGUGAGUCAGAAGUGUGAGAUGCUAUUUAACUUA--------------U--AAAUAGUACUACAUAUU
..((((..(((((((((.......)))).)))))...))))....(((((((((.....))))))))).((.(((((((((.....--------------)--))))))))))....... ( -22.40)
>DroEre_CAF1 4433 93 + 1
UGUAUCUGUAACGUAUCAGACGGAAAUGUCUU---------AAAGACACUUUUGUGAGUCACAAGUGUGAGAUGCUAC-------------UAAAAGACUU--AAAUAGUACU--AUAU-
.(((.((((...(((((..((((((.((((..---------...)))).))))))...((((....)))))))))..(-------------.....)....--..))))))).--....- ( -18.40)
>DroYak_CAF1 4397 118 + 1
UGUAUCUGUAACAUAUCAGACGGAAAUAUCUU-GAGUGAUAAAAGGUACUUUU-UGAGUACCAACUGUGAGAUGCUACUUUACCUUUAAACUAAAAGACUUUAAAAUAGGAUUUCAUAUC
....((((........))))......((((..-....))))...(((((((..-.)))))))...((((((((.(((.((((.((((......))))....)))).))).)))))))).. ( -23.80)
>consensus
UGUAUCUGUAAAGUAUCAGACGGAGAUAUCUU_AAUCGAUAAAAGAUACUUUUGUGAGUCACAAGUGUGAGAUGCUACUUAACUUA______________U__AAAUAGUACUACAUAUU
.(((((.............((((((.((((((..........)))))).))))))...((((....)))))))))............................................. ( -9.38 = -10.14 +   0.76)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:34:45 2006