Locus 1986

Sequence ID	X_DroMel_CAF1
Location	5,453,087 – 5,453,214
Length	127
Max. P	0.973266

overview

Window 7

Location	5,453,087 – 5,453,178
Length	91
Sequences	6
Columns	91
Reading direction	forward
Mean pairwise identity	81.46
Mean single sequence MFE	-25.55
Consensus MFE	-11.99
Energy contribution	-15.02
Covariance contribution	3.03
Combinations/Pair	1.23
Mean z-score	-2.69
Structure conservation index	0.47
SVM decision value	0.14
SVM RNA-class probability	0.601339
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 5453087 91 + 22224390
UGUGUGUGUGUGUGUGUGGGAGUGAGUGCAUUUCGCUUUUUGCAUUUGUGUGCAAAAAUCAAAUUAACAAGCACAAUUGGCUGAAAGGCAA
..(((((.(((.....((((((((((.....)))))))(((((((....)))))))..))).....))).)))))....(((....))).. ( -26.60)
>DroPse_CAF1 86096 71 + 1
CGUGUGU----GUGUGCGCGCGUG----------------UGUGUUAAUGUUCAGAAAUCAAAUUAACAAACACAAUUGGCUGAAAAGUGA
.((((((----....))))))(((----------------(.(((((((.............))))))).)))).....(((....))).. ( -19.82)
>DroSec_CAF1 59882 89 + 1
UGUGUGUG--UGUUUGUGGGUGUGAGUGCAUUUCCCUUUUUGCAUUUGUGUGCAAAAAUCAAAUUAACAAGCACAAUUGGCUGAAAGGCAA
......((--((((((((((.(((....)))..)))(((((((((....)))))))))........)))))))))....(((....))).. ( -28.50)
>DroSim_CAF1 58275 89 + 1
UGUGUGUG--UGUUUGUGGGUGUGAGUGCAUUUCGCUUUUUGCAUUUGUGUGCGAAAAUCAAAUUAACAAGCACAAUUGGCUGAAAGGCAA
......((--(((((((..(((((((.....)))))(((((((((....)))))))))....))..)))))))))....(((....))).. ( -27.50)
>DroEre_CAF1 71663 85 + 1
UCUGUGU------GUGCGGGUGUGAGUACAAUUCGCUUUUUGCAUUUGUGUGCGAAAAUCAAAUUAACAAGCACAAUUGGCUGAAAGGCAA
......(------((((..((((((((...))))))(((((((((....)))))))))........))..)))))....(((....))).. ( -24.50)
>DroYak_CAF1 61566 89 + 1
UGUAAGUG--CGAGCGUGGGUGUGAGUGCAUUUCGCUUUUUGCAUUUGUGUGCGAAAAUCAAAUUAACAAGCACAAUUGGCUGAAAGGCAA
.....(((--((((((.((((((....)))))))))))(((((((....)))))))..............)))).....(((....))).. ( -26.40)
>consensus
UGUGUGUG__UGUGUGUGGGUGUGAGUGCAUUUCGCUUUUUGCAUUUGUGUGCAAAAAUCAAAUUAACAAGCACAAUUGGCUGAAAGGCAA
..(((((..............(((((.....)))))(((((((((....)))))))))............)))))....(((....))).. (-11.99 = -15.02 +   3.03)

alignment

secondary structure

dotplot

Window 8

Location	5,453,110 – 5,453,214
Length	104
Sequences	6
Columns	108
Reading direction	forward
Mean pairwise identity	82.51
Mean single sequence MFE	-24.67
Consensus MFE	-14.62
Energy contribution	-18.60
Covariance contribution	3.97
Combinations/Pair	1.22
Mean z-score	-4.77
Structure conservation index	0.59
SVM decision value	1.71
SVM RNA-class probability	0.973266
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 5453110 104 + 22224390
GAGUGCAUUUCGCUUUUUGCAUUUGUGUGCAAAAAUCAAAUUAACAAGCACAAUUGGCUGAAAGGCAACA---AAAAAAAAACAAGCAAA-AAGCGAAACAACAACAA
..((...(((((((((((((.....(((((.................)))))....(((....)))....---............)))))-))))))))..))..... ( -29.13)
>DroPse_CAF1 86115 89 + 1
G----------------UGUGUUAAUGUUCAGAAAUCAAAUUAACAAACACAAUUGGCUGAAAAGUGAAAAGUAAA--AGAAGAAGCAGA-AUCAGAAGCAAAAGCAA
(----------------(((((((((.............))))))..))))..((.(((....))).)).......--............-.......((....)).. ( -10.92)
>DroSec_CAF1 59903 102 + 1
GAGUGCAUUUCCCUUUUUGCAUUUGUGUGCAAAAAUCAAAUUAACAAGCACAAUUGGCUGAAAGGCAACA---AAA--AAAACAAGCAAA-AAGCGAAACAACAACAA
..((...((((.((((((((.....(((((.................)))))....(((....)))....---...--.......)))))-))).))))..))..... ( -22.83)
>DroSim_CAF1 58296 102 + 1
GAGUGCAUUUCGCUUUUUGCAUUUGUGUGCGAAAAUCAAAUUAACAAGCACAAUUGGCUGAAAGGCAACA---AAA--AAAACAAGCAAA-AAGCGAAACAACAACAA
..((...(((((((((((((.....(((((.................)))))....(((....)))....---...--.......)))))-))))))))..))..... ( -29.83)
>DroEre_CAF1 71680 105 + 1
GAGUACAAUUCGCUUUUUGCAUUUGUGUGCGAAAAUCAAAUUAACAAGCACAAUUGGCUGAAAGGCAACAACAAAA--UAAAAAAGCAAAAAAGUGAAAAAGCGA-AA
........((((((((((.(((((...(((..............(((......)))(((....)))..........--.......)))...))))))))))))))-). ( -25.50)
>DroYak_CAF1 61587 102 + 1
GAGUGCAUUUCGCUUUUUGCAUUUGUGUGCGAAAAUCAAAUUAACAAGCACAAUUGGCUGAAAGGCAACA---AAA--AAAACAAGCAAA-AAGCGAAACAACAACAA
..((...(((((((((((((.....(((((.................)))))....(((....)))....---...--.......)))))-))))))))..))..... ( -29.83)
>consensus
GAGUGCAUUUCGCUUUUUGCAUUUGUGUGCAAAAAUCAAAUUAACAAGCACAAUUGGCUGAAAGGCAACA___AAA__AAAACAAGCAAA_AAGCGAAACAACAACAA
..((...(((((((((((((.....(((((.................)))))....(((....)))...................))))).))))))))..))..... (-14.62 = -18.60 +   3.97)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:23:36 2006