Locus 6453

Sequence ID	2R_DroMel_CAF1
Location	20,152,638 – 20,152,729
Length	91
Max. P	0.985272

overview

Window 1

Location	20,152,638 – 20,152,729
Length	91
Sequences	5
Columns	98
Reading direction	forward
Mean pairwise identity	88.81
Mean single sequence MFE	-30.86
Consensus MFE	-25.93
Energy contribution	-26.73
Covariance contribution	0.80
Combinations/Pair	1.09
Mean z-score	-2.05
Structure conservation index	0.84
SVM decision value	1.71
SVM RNA-class probability	0.973470
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 20152638 91 + 20766785
UUUUUAUAGCCAGCUCCACGAAAAAGGCAAUUUGCG-------GCAUGCAACUUUUGUUGCUCCACUGCCAACAUGCGAGAGCUGGCUGGAUCGGACU
......(((((((((((.((......((.....))(-------(((.(((((....))))).....))))....)).).))))))))))......... ( -32.90)
>DroSec_CAF1 37076 91 + 1
UUUUUAUAGCCAGCUCCACGAAAGAGGCAAUUUGCG-------GCAUGCAACUUUUGUUGCUCCACUGCCAACAUGCGAGGGCUGGCUGGACCGGACC
......(((((((((((.(....)..(((....(((-------(...(((((....)))))....)))).....)))).))))))))))......... ( -33.20)
>DroSim_CAF1 38557 91 + 1
UUUUUAUAGCCAGCUCCACGAAAAAGGCAAUUUGCG-------GCAUGCAACUUUUGUUGCUCCACUGCCAACAUGCGAGGGCUGGCUGGACCGGACC
......((((((((.((.((......((.....))(-------(((.(((((....))))).....))))......)).))))))))))......... ( -32.60)
>DroEre_CAF1 39356 90 + 1
UUUUUAUAGCCACCUCCACGAA-AAGGCAAUUUGCG-------GCAUGCACCUCUUGUUGCUCCACUGCCAACAUGCAGGAGCUGGCUGCACCGGACU
......((((((.((((.....-..((((((..(.(-------(......)).)..))))))....(((......))))))).))))))......... ( -26.00)
>DroYak_CAF1 38645 98 + 1
UUUUUAUGGCCAGCUCCACGAAAAAGGCAAUUUGCGGUCAUAGGCCUGCUCCUUUUGUUGCUCCACUGCCAACAUGCAGCAGCUGGCUGGCACGGACU
........(((((((......((((((......(((((.....))).)).))))))((((((.((.((....)))).)))))).)))))))....... ( -29.60)
>consensus
UUUUUAUAGCCAGCUCCACGAAAAAGGCAAUUUGCG_______GCAUGCAACUUUUGUUGCUCCACUGCCAACAUGCGAGAGCUGGCUGGACCGGACU
......((((((((((.........((((...(((........))).(((((....))))).....)))).........))))))))))......... (-25.93 = -26.73 +   0.80)

alignment

secondary structure

dotplot

Window 2

Location	20,152,638 – 20,152,729
Length	91
Sequences	5
Columns	98
Reading direction	reverse
Mean pairwise identity	88.81
Mean single sequence MFE	-33.82
Consensus MFE	-27.02
Energy contribution	-28.34
Covariance contribution	1.32
Combinations/Pair	1.08
Mean z-score	-2.48
Structure conservation index	0.80
SVM decision value	2.00
SVM RNA-class probability	0.985272
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 20152638 91 - 20766785
AGUCCGAUCCAGCCAGCUCUCGCAUGUUGGCAGUGGAGCAACAAAAGUUGCAUGC-------CGCAAAUUGCCUUUUUCGUGGAGCUGGCUAUAAAAA
..........(((((((((.(((..(..((((((((.(((((....)))))...)-------)))....))))..)...))))))))))))....... ( -37.20)
>DroSec_CAF1 37076 91 - 1
GGUCCGGUCCAGCCAGCCCUCGCAUGUUGGCAGUGGAGCAACAAAAGUUGCAUGC-------CGCAAAUUGCCUCUUUCGUGGAGCUGGCUAUAAAAA
((......))(((((((((.((......((((((((.(((((....)))))...)-------)))....)))).....)).)).)))))))....... ( -35.90)
>DroSim_CAF1 38557 91 - 1
GGUCCGGUCCAGCCAGCCCUCGCAUGUUGGCAGUGGAGCAACAAAAGUUGCAUGC-------CGCAAAUUGCCUUUUUCGUGGAGCUGGCUAUAAAAA
((......))(((((((((.((...(..((((((((.(((((....)))))...)-------)))....))))..)..)).)).)))))))....... ( -35.90)
>DroEre_CAF1 39356 90 - 1
AGUCCGGUGCAGCCAGCUCCUGCAUGUUGGCAGUGGAGCAACAAGAGGUGCAUGC-------CGCAAAUUGCCUU-UUCGUGGAGGUGGCUAUAAAAA
..........(((((.((((.((..(..((((((((.(((.(....).)))...)-------)))....))))..-)..)))))).)))))....... ( -29.30)
>DroYak_CAF1 38645 98 - 1
AGUCCGUGCCAGCCAGCUGCUGCAUGUUGGCAGUGGAGCAACAAAAGGAGCAGGCCUAUGACCGCAAAUUGCCUUUUUCGUGGAGCUGGCCAUAAAAA
..(((((((((((..((....))..))))))).))))((..(....)..)).((((.....(((((((.......))).))))....))))....... ( -30.80)
>consensus
AGUCCGGUCCAGCCAGCUCUCGCAUGUUGGCAGUGGAGCAACAAAAGUUGCAUGC_______CGCAAAUUGCCUUUUUCGUGGAGCUGGCUAUAAAAA
..........((((((((((((......((((((...(((((....))))).(((........))).)))))).....)).))))))))))....... (-27.02 = -28.34 +   1.32)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:11:21 2006