Locus 1137

Sequence ID	3R_DroMel_CAF1
Location	3,399,026 – 3,399,146
Length	120
Max. P	0.954256

overview

Window 7

Location	3,399,026 – 3,399,146
Length	120
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	90.56
Mean single sequence MFE	-40.73
Consensus MFE	-37.20
Energy contribution	-38.82
Covariance contribution	1.62
Combinations/Pair	1.09
Mean z-score	-1.98
Structure conservation index	0.91
SVM decision value	1.44
SVM RNA-class probability	0.954256
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 3399026 120 + 27905053
GCACAUUGUCGCCUCCUGGCUUAUGCAGAUCCGGUAUGAGAUUGAGCCAGAAGGAGAGGCGAUGUGCUCUAUAGUGAUUCUUGAGCUUCGGCUUGGUGUCUAUGGGAAACAUAUGAAAUA
((((((((((.(((.((((((((..((.........))....)))))))).)))...))))))))))(((((((......(..(((....)))..)...))))))).............. ( -46.00)
>DroSim_CAF1 7980 120 + 1
GCACAUUAUCACCUCCUGGCUUAUGCAGAUCCGGGAUAAGAUUUAGCCAGAAGGAGAGGCGAUGUGCUCUAUAGUGAUUCUUGAGCUUUGGCUUGGUGUCUAUGGGAAACAUGUGAAAUA
(((((((.((.(((.((((((.....(((((........))))))))))).))).))...)))))))(((((((......(..(((....)))..)...))))))).............. ( -35.70)
>DroEre_CAF1 6314 120 + 1
GCACAUUGUCGCCGCCUGGCUUAUGCAGAUCCGGGAUGAGAUUCAGCCAGAAGGACAGGCGGUGCGCUCUAUAGUGGUUUUUGAGCUUGGGCUUGGUGUCUAUAGGAAGCAUUUGAGAGG
.....((.((((((((((((....))...(((.((.((.....)).))....)))))))))))((..(((((((......(..(((....)))..)...)))))))..))....)).)). ( -40.10)
>DroYak_CAF1 11680 120 + 1
GCACAUUGUCGCCUCCUGGCUUAUGCAGAUCCGGGAUAAGAUUUAGCCAGAAGGAGAGGCGAUGCGCCCUAUAGUGGUUUUUGAGCUUUGGCUUGGUGUCUAUAGGAAACAUUUGAAAUA
((.(((((((.(((.((((((.....(((((........))))))))))).)))...))))))).))(((((((......(..(((....)))..)...))))))).............. ( -41.10)
>consensus
GCACAUUGUCGCCUCCUGGCUUAUGCAGAUCCGGGAUAAGAUUUAGCCAGAAGGAGAGGCGAUGCGCUCUAUAGUGAUUCUUGAGCUUUGGCUUGGUGUCUAUAGGAAACAUUUGAAAUA
((((((((((.(((.((((((.....(((((........))))))))))).)))...))))))))))(((((((......(..(((....)))..)...))))))).............. (-37.20 = -38.82 +   1.62)

alignment

secondary structure

dotplot

Window 8

Location	3,399,026 – 3,399,146
Length	120
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	90.56
Mean single sequence MFE	-29.18
Consensus MFE	-25.10
Energy contribution	-25.91
Covariance contribution	0.81
Combinations/Pair	1.06
Mean z-score	-1.60
Structure conservation index	0.86
SVM decision value	0.46
SVM RNA-class probability	0.743787
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 3399026 120 - 27905053
UAUUUCAUAUGUUUCCCAUAGACACCAAGCCGAAGCUCAAGAAUCACUAUAGAGCACAUCGCCUCUCCUUCUGGCUCAAUCUCAUACCGGAUCUGCAUAAGCCAGGAGGCGACAAUGUGC
...(((...(((((.....)))))...(((....)))...)))..........((((((((((((.....((((((((((((......)))).))....)))))))))))))...))))) ( -28.80)
>DroSim_CAF1 7980 120 - 1
UAUUUCACAUGUUUCCCAUAGACACCAAGCCAAAGCUCAAGAAUCACUAUAGAGCACAUCGCCUCUCCUUCUGGCUAAAUCUUAUCCCGGAUCUGCAUAAGCCAGGAGGUGAUAAUGUGC
...(((...(((((.....)))))...(((....)))...)))..........((((((....((.((((((((((..((((......)))).......)))))))))).))..)))))) ( -27.20)
>DroEre_CAF1 6314 120 - 1
CCUCUCAAAUGCUUCCUAUAGACACCAAGCCCAAGCUCAAAAACCACUAUAGAGCGCACCGCCUGUCCUUCUGGCUGAAUCUCAUCCCGGAUCUGCAUAAGCCAGGCGGCGACAAUGUGC
...............((((((......(((....))).........)))))).((((((((((((....(((((.((.....))..)))))...((....)))))))))......))))) ( -28.16)
>DroYak_CAF1 11680 120 - 1
UAUUUCAAAUGUUUCCUAUAGACACCAAGCCAAAGCUCAAAAACCACUAUAGGGCGCAUCGCCUCUCCUUCUGGCUAAAUCUUAUCCCGGAUCUGCAUAAGCCAGGAGGCGACAAUGUGC
..............(((((((......(((....))).........)))))))((((((((((((.....((((((..((((......)))).......)))))))))))))...))))) ( -32.56)
>consensus
UAUUUCAAAUGUUUCCCAUAGACACCAAGCCAAAGCUCAAAAACCACUAUAGAGCACAUCGCCUCUCCUUCUGGCUAAAUCUCAUCCCGGAUCUGCAUAAGCCAGGAGGCGACAAUGUGC
...............((((((......(((....))).........)))))).((((((((((((.....((((((..((((......)))).......)))))))))))))...))))) (-25.10 = -25.91 +   0.81)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:01:58 2006