Locus 5073

Sequence ID	2R_DroMel_CAF1
Location	16,473,743 – 16,473,841
Length	98
Max. P	0.635895

overview

Window 0

Location	16,473,743 – 16,473,841
Length	98
Sequences	5
Columns	102
Reading direction	forward
Mean pairwise identity	87.41
Mean single sequence MFE	-31.12
Consensus MFE	-20.32
Energy contribution	-19.80
Covariance contribution	-0.52
Combinations/Pair	1.29
Mean z-score	-2.12
Structure conservation index	0.65
SVM decision value	0.03
SVM RNA-class probability	0.548879
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 16473743 98 + 20766785
GAUUUUUU--UUUCAGUGCACCCCUUCCUCACCUCCUACUUUUCCGCCACUCGCGUUAUGAGUGCCAAAAUG--GGGCGGUGUGGGUGGAAACUUGUUCAAA
........--.....................((.(((((....((((((((((.....))))).((.....)--)))))).))))).))............. ( -25.50)
>DroSec_CAF1 148958 96 + 1
GGUU-UUU--UUUCAGUGCACCCCUUCCGCACCCCCUACUUUUCCACCACUCGCGUUAUGAGUGCCAAAAUG--GUG-GGUGUGGGUGGAAACUUGUUCAAA
....-...--............((.(((((((((((...((((....((((((.....))))))..)))).)--).)-)))))))).))............. ( -27.00)
>DroSim_CAF1 145714 97 + 1
GGUAAUUU--UUUCAGUGCACCCCUCCCACGCCCCCUACUUUUCCACCACUCGCGUUAUGAGCGCCAAAAUG--GGG-GGUGUGGGUGGAAACUUGUUCAAA
(((.(((.--....)))..)))((.(((((((((((((.((((....(.((((.....)))).)..))))))--)))-)))))))).))............. ( -33.90)
>DroEre_CAF1 150372 97 + 1
UGCU-UUU--UUUCAGUGCACCCCUCCCUUACCCCCUUCUUUUCCGCUACUCGCGUUAUGAGUGCCAAAA-GAGGGG-GGUGUGGGUGGAAACUUGUUCAAA
(((.-...--.......)))..((.(((.((((((((((((((..((.(((((.....))))))).))))-))))))-)))).))).))............. ( -38.70)
>DroYak_CAF1 150982 99 + 1
UGCC-UUUUCUUUGAGUGCACCCCUCCCUUACCCCCCACUUUUCC-CCACUCGCGUUAUGAGUGCCAAGAUGAGAGG-GGUGUGGGUGGAAACUUGUUCAAA
((((-((......))).)))..((.(((.((((((...(((.((.-.((((((.....))))))....)).))).))-)))).))).))............. ( -30.50)
>consensus
GGUU_UUU__UUUCAGUGCACCCCUCCCUCACCCCCUACUUUUCCACCACUCGCGUUAUGAGUGCCAAAAUG__GGG_GGUGUGGGUGGAAACUUGUUCAAA
......................((.(((.(((((((....(((....((((((.....))))))...)))....))).)))).))).))............. (-20.32 = -19.80 +  -0.52)

alignment

secondary structure

dotplot

Window 1

Location	16,473,743 – 16,473,841
Length	98
Sequences	5
Columns	102
Reading direction	reverse
Mean pairwise identity	87.41
Mean single sequence MFE	-31.58
Consensus MFE	-21.46
Energy contribution	-22.98
Covariance contribution	1.52
Combinations/Pair	1.12
Mean z-score	-2.06
Structure conservation index	0.68
SVM decision value	0.21
SVM RNA-class probability	0.635895
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 16473743 98 - 20766785
UUUGAACAAGUUUCCACCCACACCGCCC--CAUUUUGGCACUCAUAACGCGAGUGGCGGAAAAGUAGGAGGUGAGGAAGGGGUGCACUGAAA--AAAAAAUC
........(((...(((((.(..(((((--(.(((((.(((((.......))))).))))).....)).))))..)...))))).)))....--........ ( -27.60)
>DroSec_CAF1 148958 96 - 1
UUUGAACAAGUUUCCACCCACACC-CAC--CAUUUUGGCACUCAUAACGCGAGUGGUGGAAAAGUAGGGGGUGCGGAAGGGGUGCACUGAAA--AAA-AACC
........(((...(((((.((((-(.(--((((((..((((....((....))))))..))))).)))))))(....)))))).)))....--...-.... ( -29.60)
>DroSim_CAF1 145714 97 - 1
UUUGAACAAGUUUCCACCCACACC-CCC--CAUUUUGGCGCUCAUAACGCGAGUGGUGGAAAAGUAGGGGGCGUGGGAGGGGUGCACUGAAA--AAAUUACC
.........((.(((.(((((.((-(((--.(((((..((((....((....))))))..))))).))))).)))))..))).)).......--........ ( -35.60)
>DroEre_CAF1 150372 97 - 1
UUUGAACAAGUUUCCACCCACACC-CCCCUC-UUUUGGCACUCAUAACGCGAGUAGCGGAAAAGAAGGGGGUAAGGGAGGGGUGCACUGAAA--AAA-AGCA
.........((.(((.(((..(((-(((.((-((((.((((((.......)))).)).).))))).))))))..)))..))).)).......--...-.... ( -34.10)
>DroYak_CAF1 150982 99 - 1
UUUGAACAAGUUUCCACCCACACC-CCUCUCAUCUUGGCACUCAUAACGCGAGUGG-GGAAAAGUGGGGGGUAAGGGAGGGGUGCACUCAAAGAAAA-GGCA
(((((......((((.(((..(((-((((.(.((((..(((((.......))))))-)))...).)))))))..))).)))).....))))).....-.... ( -31.00)
>consensus
UUUGAACAAGUUUCCACCCACACC_CCC__CAUUUUGGCACUCAUAACGCGAGUGGCGGAAAAGUAGGGGGUGAGGGAGGGGUGCACUGAAA__AAA_AACC
.........((((((.(((.((((.(((....(((((.(((((.......))))).))))).....))))))).))).)))).))................. (-21.46 = -22.98 +   1.52)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:35:50 2006