Locus 1381

Sequence ID	2R_DroMel_CAF1
Location	5,324,385 – 5,324,517
Length	132
Max. P	0.827441

overview

Window 5

Location	5,324,385 – 5,324,498
Length	113
Sequences	6
Columns	119
Reading direction	reverse
Mean pairwise identity	78.05
Mean single sequence MFE	-36.45
Consensus MFE	-22.44
Energy contribution	-22.72
Covariance contribution	0.28
Combinations/Pair	1.30
Mean z-score	-1.77
Structure conservation index	0.62
SVM decision value	0.70
SVM RNA-class probability	0.827441
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 5324385 113 - 20766785
CACUCCUCAUUC--AAUCC-CC---AGCUUCCUUGAAGAACUUCGGUGACAAGACCGCCAACCUCUUCAGCAAGAAGAAGGAUGAGGCCGAGAAGCUGGCCAACGAGAAGGCUGCCGAG
............--..((.-.(---(((((.((((.......((((((.......))))..(((((((.....)))).)))..))(((((......)))))..)))).))))))..)). ( -32.80)
>DroVir_CAF1 643 115 - 1
UACUUGUUUUGCUAUUUCG-GC---AGCCUCCCUGAAGAGCUUUGGCGACAAGACCGUCAACUUGUUCAGCAAGAAGAAGGAUGAGGCCGAGAAGUUGGCCAGCGACAAGGCUGUCGAG
................(((-((---(((((.(((........((((((.......))))))((((.....))))....)))....((((((....)))))).......)))))))))). ( -38.00)
>DroGri_CAF1 972 103 - 1
CUAU------------UCG-AC---AGCGUCCCUGAAGAGCUUUGGCGACAAGACCGCCAAUCUGUUCAGCAGGAAGAAGGACGAGGCCGAGAAGUUGGCCAGCGACAAAUCUGUCGAG
....------------(((-((---((((((((((((.((..((((((.......)))))).)).))))).........))))).((((((....))))))..........))))))). ( -41.60)
>DroWil_CAF1 644 115 - 1
CUUUCAUUUUUCU-AAUCCUUU---AGCCUCUUUGAAGAACUUUGGCGACAAGACAGCCAAUCUGUUCAGCAAGAAGAAGGAUGAGGCUGAGAAAUUGGCCAACGAUAAGGCCACCGAG
...((...(((((-...((((.---..(((((((...((((.(((((.........)))))...)))).....)))).)))..))))...))))).(((((........)))))..)). ( -33.40)
>DroMoj_CAF1 672 115 - 1
CUAUUAUAUUUCUUUUCCG-AC---AGCCUCUCUGAAGAGCUUUGGCGACAAGACCGCCAACUUGUUCAGCAAGAAGAAGGAUGAGGCCGAGAAGCUGGCCAACGAAAAGGCAGCCGAG
..........(((((((..-.(---(.((((((((..((((.((((((.......))))))...))))..).)).)).))).)).(((((......)))))...)))))))........ ( -31.60)
>DroAna_CAF1 642 115 - 1
-CCUUUUCGUUU--AUUUC-UCGGUAGCAUCCUUGAAGAACUUUGGCGACAAGACGGCCAAUCUGUUCAGCAAGAAGAAGGAUGAGGCUGAGAAGCUGGCCAACGAGAAGGCUAACGAG
-(((((((((((--(((((-(((((..((((((((..((((.(((((.........)))))...))))..))......))))))..))))))))).))...))))))))))........ ( -41.30)
>consensus
CUCUUAUCUUUC__AUUCC_AC___AGCCUCCCUGAAGAACUUUGGCGACAAGACCGCCAACCUGUUCAGCAAGAAGAAGGAUGAGGCCGAGAAGCUGGCCAACGACAAGGCUGCCGAG
..........................((((.((((..((((.((((((.......))))))...))))..))))...........(((((......))))).......))))....... (-22.44 = -22.72 +   0.28)

alignment

secondary structure

dotplot

Window 6

Location	5,324,425 – 5,324,517
Length	92
Sequences	6
Columns	101
Reading direction	reverse
Mean pairwise identity	81.49
Mean single sequence MFE	-19.49
Consensus MFE	-13.89
Energy contribution	-14.12
Covariance contribution	0.22
Combinations/Pair	1.12
Mean z-score	-1.49
Structure conservation index	0.71
SVM decision value	0.22
SVM RNA-class probability	0.640725
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 5324425 92 - 20766785
ACAGUC-AGGAUCUAAAAU------GCACUCCUCAUUC--AAUCCCCAGCUUCCUUGAAGAACUUCGGUGACAAGACCGCCAACCUCUUCAGCAAGAAGAA
......-.((((....(((------(.......)))).--.))))....((((.(((((((..((.((((.......))))))..)))))))...)))).. ( -15.60)
>DroSec_CAF1 1097 92 - 1
CCAGUC-AGGAUCUAAAAU------GCUCUCCUCCUUC--AAUCCCCAGCUUCCUUGAAGAACUUCGGCGACAAGACCGCCAACCUCUUCAGCAAGAAGAA
......-((((........------....)))).....--.........((((.(((((((..((.((((.......))))))..)))))))...)))).. ( -16.70)
>DroSim_CAF1 1133 92 - 1
CCAGUC-AGGAUCUAAAAU------GAACUCCUCAUUC--AAUCCCCAGCUUCCUUGAAGAACUUCGGCGACAAGACCGCCAACCUCUUCAGCAAGAAGAA
......-.((((....(((------((.....))))).--.))))....((((.(((((((..((.((((.......))))))..)))))))...)))).. ( -20.20)
>DroEre_CAF1 1073 95 - 1
CUAGUC-AGGAUCCACAAUAAC---GCACUCCUUGUUC--AAUCCCCAGCCUCGUUGAAGAACUUCGGCGACAAGACCGCCAACCUCUUCAGCAAGAAGAA
....((-.((((..((((....---.......))))..--.)))).....((.((((((((..((.((((.......))))))..)))))))).))..)). ( -20.20)
>DroYak_CAF1 1183 91 - 1
UCAAGC-AGGAUCUACAAU------GCACUCCUC-UUU--AAUCCGCAGCUUCGUUGAAGAACUUCGGCGACAAGACCGCCAACCUCUUCAGCAAGAAGAA
....((-.((((.......------.........-...--.))))))..((((((((((((..((.((((.......))))))..))))))))..)))).. ( -22.15)
>DroMoj_CAF1 712 98 - 1
UGAA--UUGGAAGUAAAAUUGAUUU-CUAUUAUAUUUCUUUUCCGACAGCCUCUCUGAAGAGCUUUGGCGACAAGACCGCCAACUUGUUCAGCAAGAAGAA
....--(((((((..((((((((..-..)))).))))..)))))))....((..(((((.((..((((((.......)))))).)).)))))..))..... ( -22.10)
>consensus
CCAGUC_AGGAUCUAAAAU______GCACUCCUCAUUC__AAUCCCCAGCUUCCUUGAAGAACUUCGGCGACAAGACCGCCAACCUCUUCAGCAAGAAGAA
.................................................((((.(((((((..((.((((.......))))))..)))))))...)))).. (-13.89 = -14.12 +   0.22)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:03:31 2006