Locus 6071

Sequence ID	3R_DroMel_CAF1
Location	15,949,027 – 15,949,122
Length	95
Max. P	0.902180

overview

Window 3

Location	15,949,027 – 15,949,122
Length	95
Sequences	5
Columns	102
Reading direction	forward
Mean pairwise identity	87.73
Mean single sequence MFE	-28.66
Consensus MFE	-22.68
Energy contribution	-23.40
Covariance contribution	0.72
Combinations/Pair	1.08
Mean z-score	-1.98
Structure conservation index	0.79
SVM decision value	1.02
SVM RNA-class probability	0.902180
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 15949027 95 + 27905053
AGCUGCAGCAGCAUCGGCAAUAGCAACAAAGGCACAUCAUGUUGAGAUGUUGCCAUUGCUGUCCUUAUCCCU-------CAUCCCUUUUCCUGGGUCCUGCG
....(((((((((..(((((((.(((((...........)))))...)))))))..)))))...........-------...(((.......)))..)))). ( -29.90)
>DroSec_CAF1 75386 95 + 1
AGCAGCAGAAGCAUUGGCAAUAGCAACAAAGGCACAUCAUGUUGAGAUGUUGCCAUUGCUGUCCUUAUCCCU-------CAUCCCUCUUCCUGGGUCCAGCG
....((...((((.((((((((.(((((...........)))))...)))))))).))))............-------...(((.......)))....)). ( -26.90)
>DroSim_CAF1 50730 95 + 1
AGCUGCAGCAGCAUUGGCAAUAGCAACAAAGGCACAUCAUGUUGAGAUGUUGCCAUUGCUGUCCUUAUCCCU-------CAUCCCUCUUCCUGGGUCCCGCG
....((.((((((.((((((((.(((((...........)))))...)))))))).))))))..........-------...(((.......)))....)). ( -30.80)
>DroEre_CAF1 50367 102 + 1
AGCUGCAGUAGCAUCGGCAAUAGCAACAAAGGCACAUCAUGUUGAGAUGUUGCCAUUGCUGUCCUCAUCCCUUAUUCCCCAUCCCUCUUCCUGGGAGCUGCG
....(((((((((..(((((((.(((((...........)))))...)))))))..)))).....................((((.......))))))))). ( -32.00)
>DroYak_CAF1 79130 88 + 1
AGCUGCAGCAUCAUCGGCAAAAGCAACAAAGGCACAUCAUGUUGAGAUGUUGCCAUUGCUGUCCUCAUC--------------CCUCUUUCAAGGACCUGCG
....((((((((.((((((...((.......))......))))))))))))))....((.(((((....--------------.........)))))..)). ( -23.72)
>consensus
AGCUGCAGCAGCAUCGGCAAUAGCAACAAAGGCACAUCAUGUUGAGAUGUUGCCAUUGCUGUCCUUAUCCCU_______CAUCCCUCUUCCUGGGUCCUGCG
....(((((((((..(((((((.(((((...........)))))...)))))))..)))))......................(((......)))..)))). (-22.68 = -23.40 +   0.72)

alignment

secondary structure

dotplot

Window 4

Location	15,949,027 – 15,949,122
Length	95
Sequences	5
Columns	102
Reading direction	reverse
Mean pairwise identity	87.73
Mean single sequence MFE	-31.36
Consensus MFE	-26.88
Energy contribution	-27.20
Covariance contribution	0.32
Combinations/Pair	1.08
Mean z-score	-1.58
Structure conservation index	0.86
SVM decision value	0.58
SVM RNA-class probability	0.790282
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 15949027 95 - 27905053
CGCAGGACCCAGGAAAAGGGAUG-------AGGGAUAAGGACAGCAAUGGCAACAUCUCAACAUGAUGUGCCUUUGUUGCUAUUGCCGAUGCUGCUGCAGCU
.((((..(((.......)))...-------.((.(...((.((((((.((((.((((.......)))))))).))))))))..).)).......)))).... ( -31.20)
>DroSec_CAF1 75386 95 - 1
CGCUGGACCCAGGAAGAGGGAUG-------AGGGAUAAGGACAGCAAUGGCAACAUCUCAACAUGAUGUGCCUUUGUUGCUAUUGCCAAUGCUUCUGCUGCU
..(((....)))..(((((.((.-------..((....((.((((((.((((.((((.......)))))))).))))))))....)).)).)))))...... ( -30.70)
>DroSim_CAF1 50730 95 - 1
CGCGGGACCCAGGAAGAGGGAUG-------AGGGAUAAGGACAGCAAUGGCAACAUCUCAACAUGAUGUGCCUUUGUUGCUAUUGCCAAUGCUGCUGCAGCU
.((((..(((.......)))...-------.((.(...((.((((((.((((.((((.......)))))))).))))))))..).)).......)))).... ( -30.50)
>DroEre_CAF1 50367 102 - 1
CGCAGCUCCCAGGAAGAGGGAUGGGGAAUAAGGGAUGAGGACAGCAAUGGCAACAUCUCAACAUGAUGUGCCUUUGUUGCUAUUGCCGAUGCUACUGCAGCU
.((((.(((((..........))))).....((.(...((.((((((.((((.((((.......)))))))).))))))))..).)).......)))).... ( -32.00)
>DroYak_CAF1 79130 88 - 1
CGCAGGUCCUUGAAAGAGG--------------GAUGAGGACAGCAAUGGCAACAUCUCAACAUGAUGUGCCUUUGUUGCUUUUGCCGAUGAUGCUGCAGCU
.((((((((((....)))(--------------(..((((.((((((.((((.((((.......)))))))).))))))))))..))...))).)))).... ( -32.40)
>consensus
CGCAGGACCCAGGAAGAGGGAUG_______AGGGAUAAGGACAGCAAUGGCAACAUCUCAACAUGAUGUGCCUUUGUUGCUAUUGCCGAUGCUGCUGCAGCU
.((((..(((.......)))............((....((.((((((.((((.((((.......)))))))).))))))))....)).......)))).... (-26.88 = -27.20 +   0.32)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:11:57 2006