Locus 8055

Sequence ID	X_DroMel_CAF1
Location	20,072,769 – 20,072,913
Length	144
Max. P	0.729063

overview

Window 8

Location	20,072,769 – 20,072,874
Length	105
Sequences	5
Columns	105
Reading direction	forward
Mean pairwise identity	87.52
Mean single sequence MFE	-29.18
Consensus MFE	-24.23
Energy contribution	-25.07
Covariance contribution	0.84
Combinations/Pair	1.04
Mean z-score	-1.56
Structure conservation index	0.83
SVM decision value	0.37
SVM RNA-class probability	0.707791
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 20072769 105 + 22224390
CAUCACCAAGACACCCAGUGCCGCCACUCGGGGCCACUACGGAUUUUCAUGGAAUCCGAUUCAGAACCGAGCGGCCCAACGAAAACCAACAUCCGUUGCUGUGUG
...........(((.(((....(((.(((((..(.....(((((((.....))))))).....)..))))).))).(((((............)))))))).))) ( -32.00)
>DroSec_CAF1 9571 101 + 1
CAUCACCAAGACACCCAGUCCCGCCGCUCGGG----CAACGGAUUUUCAUGGAAUCCGAUUCAGAACCGAGCGGCCCAACGAAAACCAACAUCCGUUGCUGUGUG
...........(((.(((....(((((((((.----...(((((((.....)))))))........))))))))).(((((............)))))))).))) ( -34.40)
>DroSim_CAF1 23799 101 + 1
CAUCACCAAGACACCCAGUCCCGCCGCUCGGG----CAACGGAUUUUCAUGGAAUCCGAUUCGGAACCGAGCGGCCCAACGAAAACCAACAUCCGUUGCUGUGUG
...........(((.(((....(((((((((.----...(((((((.....)))))))........))))))))).(((((............)))))))).))) ( -34.40)
>DroEre_CAF1 8701 101 + 1
CAGAACCAACACCCCCAGCCCCACCACUCGGA----CACCGGAUUUUCAUGGAAUCCGAUUCGGAAUCGAGCGGCCCAACGAAGACCAACAUCCGUUGCUGUGUG
........................(((.(((.----((.(((((((((.(((...(((.((((....))))))).)))..)))))......)))).))))).))) ( -22.00)
>DroYak_CAF1 9797 95 + 1
------CAAACCCCACAAACCCGCCACACGGA----CUCCGGAUUUUCAUGGAAUCCGAUUCAGAACCGAGCGGCCCAACGAAAACCAACAUCCGUUGCUGUGUG
------..................(((((((.----(..(((((((((.(((...(((.(((......)))))).)))..))))......)))))..)))))))) ( -23.10)
>consensus
CAUCACCAAGACACCCAGUCCCGCCACUCGGG____CAACGGAUUUUCAUGGAAUCCGAUUCAGAACCGAGCGGCCCAACGAAAACCAACAUCCGUUGCUGUGUG
...........(((.(((....(((.(((((........(((((((.....)))))))........))))).))).(((((............)))))))).))) (-24.23 = -25.07 +   0.84)

alignment

secondary structure

dotplot

Window 9

Location	20,072,794 – 20,072,913
Length	119
Sequences	5
Columns	119
Reading direction	reverse
Mean pairwise identity	93.83
Mean single sequence MFE	-40.94
Consensus MFE	-35.57
Energy contribution	-35.01
Covariance contribution	-0.56
Combinations/Pair	1.14
Mean z-score	-1.33
Structure conservation index	0.87
SVM decision value	0.42
SVM RNA-class probability	0.729063
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 20072794 119 - 22224390
CAGCGUCCGAAAUGGUCAGAAUCGUUUUGGUCAACCGUGCACACAGCAACGGAUGUUGGUUUUCGUUGGGCCGCUCGGUUCUGAAUCGGAUUCCAUGAAAAUCCGUAGUGGCCCCGAGU
(((((((((...((..((((.....))))..))....(((.....))).)))))))))...((((..((((((((((((((.((((...))))...)))...))).)))))))))))). ( -44.10)
>DroSec_CAF1 9596 115 - 1
CAGCGUCCGAAAUGGUCGGAAUCGUUUUGGUCAACCGUGCACACAGCAACGGAUGUUGGUUUUCGUUGGGCCGCUCGGUUCUGAAUCGGAUUCCAUGAAAAUCCGUUG----CCCGAGC
..(((.((((((((((....)))))))))).).............(((((((((..(((..((((..(((((....))))).....))))..))).....))))))))----)....)) ( -39.70)
>DroSim_CAF1 23824 115 - 1
CAGCGUCCGAAAUGGUCGGAAUCGUUUUGGUCAACCGUGCACACAGCAACGGAUGUUGGUUUUCGUUGGGCCGCUCGGUUCCGAAUCGGAUUCCAUGAAAAUCCGUUG----CCCGAGC
..(((.((((((((((....)))))))))).).............(((((((((..(((..(((((((((((....)).)))))..))))..))).....))))))))----)....)) ( -40.40)
>DroEre_CAF1 8726 115 - 1
CAGCGUCCGAAAUGGUCAGAAUCGUUUUGGUCAACCGUGCACACAGCAACGGAUGUUGGUCUUCGUUGGGCCGCUCGAUUCCGAAUCGGAUUCCAUGAAAAUCCGGUG----UCCGAGU
.((((((((...((..((((.....))))..))....(((.....))).))))))))(((((.....)))))(((((.......((((((((.......)))))))).----..))))) ( -37.60)
>DroYak_CAF1 9816 115 - 1
CAGCAUCCGAAAUGGCCAGAAUCGUUUUGGUCAACCGUGCACACAGCAACGGAUGUUGGUUUUCGUUGGGCCGCUCGGUUCUGAAUCGGAUUCCAUGAAAAUCCGGAG----UCCGUGU
(((((((((...((((((((.....))))))))....(((.....))).)))))))))...((((..(((((....))))))))).((((((((((....))..))))----))))... ( -42.90)
>consensus
CAGCGUCCGAAAUGGUCAGAAUCGUUUUGGUCAACCGUGCACACAGCAACGGAUGUUGGUUUUCGUUGGGCCGCUCGGUUCUGAAUCGGAUUCCAUGAAAAUCCGUUG____CCCGAGU
.((((((((...((((((((.....))))))))....(((.....))).))))))))(((((.....)))))((((((........((((((.......))))))........)))))) (-35.57 = -35.01 +  -0.56)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:54:20 2006