Locus 4043

Sequence ID	2R_DroMel_CAF1
Location	13,343,180 – 13,343,276
Length	96
Max. P	0.855834

overview

Window 3

Location	13,343,180 – 13,343,276
Length	96
Sequences	6
Columns	112
Reading direction	forward
Mean pairwise identity	77.81
Mean single sequence MFE	-26.83
Consensus MFE	-19.92
Energy contribution	-19.73
Covariance contribution	-0.19
Combinations/Pair	1.17
Mean z-score	-1.40
Structure conservation index	0.74
SVM decision value	0.81
SVM RNA-class probability	0.855834
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 13343180 96 + 20766785
--------------UCUCUA-CAAACAGUCCUUUGAUUAUACGGAAUUGUGCCAGCCGGGCACGCUGAUCGAUGCCAAUGGCAGCAUACCCGUCAGCGUGAACAGCAUCCA-
--------------......-((((......)))).......(((...(((((.....)))))((((.((.((((..((((........))))..)))))).)))).))).- ( -27.60)
>DroPse_CAF1 39679 94 + 1
---------------CCAUCU--UCCAGUCCUUCGAUUACACGGAACUGUGCCAGCCGGGCACCCUCAUCGAUGCCAAUGGCAGCAUACCCGUGUCCGUGAACAGCAUCCA-
---------------......--....((..((((...((((((...(((((..(((.((((.(......).))))...))).))))).))))))...))))..)).....- ( -27.70)
>DroWil_CAF1 54436 98 + 1
U-------------GCCUCU-UCUACAGUCAUUCGACUACACGGAAUUAUGCCAGCCGGGCACCUUGAUCGAUGCCAAUGGCAGCAUUCCCGUUUCGGUCAAUAGCCUUCAA
.-------------(((...-.....((((....))))....(((((..(((((....((((.(......).))))..)))))..)))))......)))............. ( -25.00)
>DroMoj_CAF1 50247 109 + 1
-CAUAUUUGCAACUUCUUUU-CGAACAGUCCUUCGACUAUACGGAACUGUGUCAGCCGGGCACCCUCAUCGAUGCCAAUGGCAGCAUACCCGUUUCAGUGAAUAGCAUACA-
-..((((..(.........(-((((......)))))....((((...(((((..(((.((((.(......).))))...))).))))).))))....)..)))).......- ( -24.90)
>DroAna_CAF1 42837 91 + 1
--------------UU------AUUUAGUCCUUCGAUUAUACGGAACUGUGCCAGCCGGGCACGCUGAUCGAUGCCAAUGGCAGCAUACCCGUCAGUGUGAACAGUAUCCA-
--------------..------...(((((....)))))...(((((((((((.....)))((((((((..((((........))))....))))))))..))))).))).- ( -28.10)
>DroPer_CAF1 39947 94 + 1
---------------CCAUCU--UCCAGUCCUUCGAUUACACGGAACUGUGCCAGCCGGGCACCCUCAUCGAUGCCAAUGGCAGCAUACCCGUGUCCGUGAACAGCAUCCA-
---------------......--....((..((((...((((((...(((((..(((.((((.(......).))))...))).))))).))))))...))))..)).....- ( -27.70)
>consensus
______________UCCAUC___UACAGUCCUUCGAUUACACGGAACUGUGCCAGCCGGGCACCCUCAUCGAUGCCAAUGGCAGCAUACCCGUCUCCGUGAACAGCAUCCA_
...........................((..((((.....((((...(((((..(((.(((((.......).))))...))).))))).)))).....))))..))...... (-19.92 = -19.73 +  -0.19)

alignment

secondary structure

dotplot

Window 4

Location	13,343,180 – 13,343,276
Length	96
Sequences	6
Columns	112
Reading direction	reverse
Mean pairwise identity	77.81
Mean single sequence MFE	-32.28
Consensus MFE	-21.08
Energy contribution	-21.58
Covariance contribution	0.50
Combinations/Pair	1.00
Mean z-score	-1.24
Structure conservation index	0.65
SVM decision value	0.09
SVM RNA-class probability	0.577618
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 13343180 96 - 20766785
-UGGAUGCUGUUCACGCUGACGGGUAUGCUGCCAUUGGCAUCGAUCAGCGUGCCCGGCUGGCACAAUUCCGUAUAAUCAAAGGACUGUUUG-UAGAGA--------------
-.....((((..((((((((((...(((((......))))))).))))))))..))))....((((.(((...........)))....)))-).....-------------- ( -28.90)
>DroPse_CAF1 39679 94 - 1
-UGGAUGCUGUUCACGGACACGGGUAUGCUGCCAUUGGCAUCGAUGAGGGUGCCCGGCUGGCACAGUUCCGUGUAAUCGAAGGACUGGA--AGAUGG---------------
-.......(.(((.((((((((((..((.(((((..((((((......))))))....)))))))..)))))))..((....)))))))--).)...--------------- ( -32.80)
>DroWil_CAF1 54436 98 - 1
UUGAAGGCUAUUGACCGAAACGGGAAUGCUGCCAUUGGCAUCGAUCAAGGUGCCCGGCUGGCAUAAUUCCGUGUAGUCGAAUGACUGUAGA-AGAGGC-------------A
......(((.(((((....((((((((((((((...((((((......)))))).))).)))))..))))))...)))))....((.....-)).)))-------------. ( -33.90)
>DroMoj_CAF1 50247 109 - 1
-UGUAUGCUAUUCACUGAAACGGGUAUGCUGCCAUUGGCAUCGAUGAGGGUGCCCGGCUGACACAGUUCCGUAUAGUCGAAGGACUGUUCG-AAAAGAAGUUGCAAAUAUG-
-(((.(((..(((((((...(((((((.((..(((((....))))))).))))))).......))))..((.((((((....)))))).))-....)))...))).)))..- ( -34.10)
>DroAna_CAF1 42837 91 - 1
-UGGAUACUGUUCACACUGACGGGUAUGCUGCCAUUGGCAUCGAUCAGCGUGCCCGGCUGGCACAGUUCCGUAUAAUCGAAGGACUAAAU------AA--------------
-.(((.(((((.(.((....(((((((((((..((((....)))))))))))))))..))).))))))))......((....))......------..-------------- ( -31.20)
>DroPer_CAF1 39947 94 - 1
-UGGAUGCUGUUCACGGACACGGGUAUGCUGCCAUUGGCAUCGAUGAGGGUGCCCGGCUGGCACAGUUCCGUGUAAUCGAAGGACUGGA--AGAUGG---------------
-.......(.(((.((((((((((..((.(((((..((((((......))))))....)))))))..)))))))..((....)))))))--).)...--------------- ( -32.80)
>consensus
_UGGAUGCUGUUCACGGAAACGGGUAUGCUGCCAUUGGCAUCGAUCAGGGUGCCCGGCUGGCACAGUUCCGUAUAAUCGAAGGACUGUA___AAAGGA______________
...................(((((..(((((((...((((((......)))))).))).))))....)))))....((....))............................ (-21.08 = -21.58 +   0.50)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:10:18 2006