Locus 8377

Sequence ID	3R_DroMel_CAF1
Location	22,348,715 – 22,348,893
Length	178
Max. P	0.775221

overview

Window 5

Location	22,348,715 – 22,348,818
Length	103
Sequences	5
Columns	114
Reading direction	reverse
Mean pairwise identity	84.29
Mean single sequence MFE	-28.84
Consensus MFE	-21.89
Energy contribution	-21.33
Covariance contribution	-0.56
Combinations/Pair	1.18
Mean z-score	-1.84
Structure conservation index	0.76
SVM decision value	0.54
SVM RNA-class probability	0.775221
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 22348715 103 - 27905053
---GGAGCCAG--------AACCAAAACCAAGACCAAAAUCUCAUGAAUGAAGUGGGAUUGAAGUGGCCGACGGAAAAUGUUUCAUCGUUCGGCGGUGGUGCGGUUAACUAAAU
---..((((..--------.(((...(((...((...((((((((.......))))))))...)).((((((((((.....)))..)).)))))))))))..))))........ ( -26.60)
>DroSec_CAF1 56487 103 - 1
---GAAGCCAG--------AACCAAAACCAAGACCGAAAUCUCAUGAAUGAAAUGGGAUUGAAGUGGCCGACGGAAAAUGUUUCGUUGUUCGGCGGUGGUGCGGUUAACUAAAU
---........--------((((...((((.(.((((((((((((.......))))))))........((((((((....)))))))).)))))..))))..))))........ ( -28.90)
>DroSim_CAF1 55629 103 - 1
---GAAGCCAG--------AACCAAAACCGAGACCGAAAUCUCAUGAAUGAAGUGGGAUUGAAGUGGCCGACGGAAAAUGUUUCGUCGUUCGGCGGUGGUGCGGUUAACUAAAU
---..((((..--------.((((...(((((.(((.((((((((.......))))))))....))).((((((((....)))))))))))))...))))..))))........ ( -33.80)
>DroEre_CAF1 58691 103 - 1
---GAAUCUAA-AUCCAACAACCAACACCAAAACCGAGAUCCCAUGAAUGAAUUGGGAUUGAAGUGGCCGACGGGAAAUGUUU-------CGGCGAUGGUGCGGUUAACUAAAU
---........-.......((((..(((((..((...(((((((.........)))))))...)).(((((...........)-------))))..))))).))))........ ( -26.40)
>DroYak_CAF1 58159 105 - 1
CGUGAACCUAAAAUCCA--AACCAAAACCGAAACCAAAAUCCCAUGAAUGAAGUGGGAUUGAAGUGGCCGACGGAAAAUGUUU-------CGGCGGUGGUGCGGUUAACUAAAU
.................--......(((((..(((..((((((((.......))))))))......((((.(((((....)))-------)).))))))).)))))........ ( -28.50)
>consensus
___GAAGCCAG________AACCAAAACCAAGACCGAAAUCUCAUGAAUGAAGUGGGAUUGAAGUGGCCGACGGAAAAUGUUUC_U_GUUCGGCGGUGGUGCGGUUAACUAAAU
...................((((...((((..((...((((((((.......))))))))...)).((((....................))))..))))..))))........ (-21.89 = -21.33 +  -0.56)

alignment

secondary structure

dotplot

Window 6

Location	22,348,789 – 22,348,893
Length	104
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	81.84
Mean single sequence MFE	-42.30
Consensus MFE	-27.56
Energy contribution	-29.24
Covariance contribution	1.68
Combinations/Pair	1.09
Mean z-score	-1.81
Structure conservation index	0.65
SVM decision value	0.26
SVM RNA-class probability	0.658226
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 22348789 104 + 27905053
AUUUUGGUCUUGGUUUUGGUU--------CUGGCUCC-------UCGGGAGUGGUUCU-CCUAUCUGGGGCUCUGCCACUCCGACCGGGGCCCCUGGAAUCGGGACAAAGAUUCCGACGA
...((((((((.(((((((((--------((((((((-------((((.((((((.((-((.....))))....))))))))))..))))))...))))))))))).))))..))))... ( -46.90)
>DroSec_CAF1 56561 104 + 1
AUUUCGGUCUUGGUUUUGGUU--------CUGGCUUC-------UCGGGAGUGGUUCU-UCUAUCUGGGGCUCUGCCACUCCGACCGGGGCCCCUGGAAUCGGGACAAAGAUUCCGCCGA
...((((((((.(((((((((--------((((((((-------((((.((((((.((-((.....))))....))))))))))..))))))...))))))))))).))).....))))) ( -41.80)
>DroSim_CAF1 55703 105 + 1
AUUUCGGUCUCGGUUUUGGUU--------CUGGCUUC-------UCGGGAGUGGUUCUCUGGGUCUGGGGCUCUGCCACUCCGACCGGGGCCCCUGGAAUCGGGACAAAGAUUCCGCCGA
...(((((...((....((((--------((((....-------((((.((((((.....((((.....)))).)))))))))))))))))))).((((((........))))))))))) ( -43.50)
>DroEre_CAF1 58758 109 + 1
AUCUCGGUUUUGGUGUUGGUUGUUGGAU-UUAGAUUC-------UCGGGAGUGGUUCU-CCUAUCUGCGGUCUG-CGAAUCCGACUG-GGCCCCUGGAAUCGGGACAAAGAUUCCGCCGA
...(((((...((.(((.(..(((((((-((((((..-------..(((((.....))-)))))))((.....)-))))))))))).-))).)).((((((........))))))))))) ( -35.60)
>DroYak_CAF1 58226 116 + 1
AUUUUGGUUUCGGUUUUGGUU--UGGAUUUUAGGUUCACGGGAGUCGGGAGUGGUUCU-CCUAUCUGGGGUCUGGCGACUCCGACUG-GGCACCUGGAAUCGGGACAAAGAUUCCGCCGA
...((((...(((..((.(((--(.((((((((((((.(((.((..(((((.....))-)))..))((((((....))))))..)))-)).)))))))))).))))...))..))))))) ( -43.70)
>consensus
AUUUCGGUCUUGGUUUUGGUU________CUGGCUUC_______UCGGGAGUGGUUCU_CCUAUCUGGGGCUCUGCCACUCCGACCGGGGCCCCUGGAAUCGGGACAAAGAUUCCGCCGA
...(((((...((((((((((..........................((((((((....(((.....)))....))))))))))))))))))...((((((........))))))))))) (-27.56 = -29.24 +   1.68)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:10:04 2006