Locus 1726

Sequence ID	3R_DroMel_CAF1
Location	4,966,917 – 4,967,012
Length	95
Max. P	0.994154

overview

Window 8

Location	4,966,917 – 4,967,012
Length	95
Sequences	5
Columns	101
Reading direction	forward
Mean pairwise identity	74.95
Mean single sequence MFE	-27.92
Consensus MFE	-14.00
Energy contribution	-13.92
Covariance contribution	-0.08
Combinations/Pair	1.10
Mean z-score	-2.50
Structure conservation index	0.50
SVM decision value	2.45
SVM RNA-class probability	0.994154
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 4966917 95 + 27905053
-GAGCCAUCUGUAAAGAACUUUCAGUCAUAGAAGAAUAUAUGUGUGUACAUCACCCA-GGUGGCAAAGAGUUUUGGGGUUCAAAAGUGCAGAUG----GCC
-..((((((((((..((((.....((((((.(........).)))).))....((((-((..((.....)))))))))))).....))))))))----)). ( -28.30)
>DroSec_CAF1 73904 78 + 1
-GAGCCAUCUGU------------------GAAGAAUACAUGUGUGUACAUCACCCAUGGAGGCAAAGAGUUUUGGGCUUUGAAAGUGCAGAUG----GCC
-..(((((((((------------------........((((.(((.....))).))))(((((..((....))..)))))......)))))))----)). ( -25.90)
>DroSim_CAF1 74883 78 + 1
-GAGCCAUCUGU------------------GAAGAAUACAUGUGUGUACAUCACCCGUGGAGGCAAAGAGUUUUGGGAUUUGAAAGUGCAGAUG----GCC
-..(((((((((------------------(..((((.((((.(((.....))).))))(((((.....)))))...)))).....))))))))----)). ( -23.90)
>DroEre_CAF1 74549 89 + 1
-GAGCCAUCUGUGAAGAGUUUUCAGACAAG---GAAUACAU--GUGUAAUUCACCCU-GGAGGCAACCAGUU-UGGGGAUUGAAAGUGCAGAUG----GCC
-..((((((((((...((((..(((((..(---((.(((..--..))).)))....(-((......))))))-))..)))).....))))))))----)). ( -30.60)
>DroYak_CAF1 75471 95 + 1
GGAGCCAUCUGUGAAUAACUUUCAGACAGG---GAAUACAU--GUGUACAUCACCCA-GGAGGCAACCAGUUUUGGGGAUUGAAAGUGCAGAUGGUCGGCC
((.(((((((((.....(((((((((((.(---.....).)--)).....((.((((-((((....)...))))))))))))))))))))))))))...)) ( -30.90)
>consensus
_GAGCCAUCUGU_AA_A__UUUCAG_CA__GAAGAAUACAUGUGUGUACAUCACCCA_GGAGGCAAAGAGUUUUGGGGUUUGAAAGUGCAGAUG____GCC
...(((((((((........................((((....)))).....((((....(((.....))).))))..........)))))))....)). (-14.00 = -13.92 +  -0.08)

alignment

secondary structure

dotplot

Window 9

Location	4,966,917 – 4,967,012
Length	95
Sequences	5
Columns	101
Reading direction	reverse
Mean pairwise identity	74.95
Mean single sequence MFE	-22.18
Consensus MFE	-11.16
Energy contribution	-11.56
Covariance contribution	0.40
Combinations/Pair	1.00
Mean z-score	-2.41
Structure conservation index	0.50
SVM decision value	2.19
SVM RNA-class probability	0.990040
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 4966917 95 - 27905053
GGC----CAUCUGCACUUUUGAACCCCAAAACUCUUUGCCACC-UGGGUGAUGUACACACAUAUAUUCUUCUAUGACUGAAAGUUCUUUACAGAUGGCUC-
(((----((((((.......((((......((...(..((...-..))..).)).....((((........)))).......))))....))))))))).- ( -21.20)
>DroSec_CAF1 73904 78 - 1
GGC----CAUCUGCACUUUCAAAGCCCAAAACUCUUUGCCUCCAUGGGUGAUGUACACACAUGUAUUCUUC------------------ACAGAUGGCUC-
(((----((((((..........(((((................)))))((.(((((....)))))...))------------------.))))))))).- ( -22.39)
>DroSim_CAF1 74883 78 - 1
GGC----CAUCUGCACUUUCAAAUCCCAAAACUCUUUGCCUCCACGGGUGAUGUACACACAUGUAUUCUUC------------------ACAGAUGGCUC-
(((----((((((........................((((....))))((.(((((....)))))...))------------------.))))))))).- ( -20.20)
>DroEre_CAF1 74549 89 - 1
GGC----CAUCUGCACUUUCAAUCCCCA-AACUGGUUGCCUCC-AGGGUGAAUUACAC--AUGUAUUC---CUUGUCUGAAAACUCUUCACAGAUGGCUC-
(((----((((((.............((-..((((......))-))..))........--........---......((((.....))))))))))))).- ( -23.10)
>DroYak_CAF1 75471 95 - 1
GGCCGACCAUCUGCACUUUCAAUCCCCAAAACUGGUUGCCUCC-UGGGUGAUGUACAC--AUGUAUUC---CCUGUCUGAAAGUUAUUCACAGAUGGCUCC
....(((((((((.((((((((((((((.....((......))-)))).)))((((..--..))))..---......)))))))......))))))).)). ( -24.00)
>consensus
GGC____CAUCUGCACUUUCAAACCCCAAAACUCUUUGCCUCC_UGGGUGAUGUACACACAUGUAUUCUUC__UG_CUGAAA__U_UU_ACAGAUGGCUC_
(((....((((((......................(..((......))..).(((((....)))))........................))))))))).. (-11.16 = -11.56 +   0.40)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:17:48 2006