Locus 3069

Sequence ID 3R_DroMel_CAF1
Location 8,103,685 – 8,103,775
Length 90
Max. P 0.911784
window4983 window4984

overview

Window 3

Location 8,103,685 – 8,103,775
Length 90
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 76.86
Mean single sequence MFE -28.24
Consensus MFE -11.98
Energy contribution -12.70
Covariance contribution 0.72
Combinations/Pair 1.20
Mean z-score -2.18
Structure conservation index 0.42
SVM decision value 1.08
SVM RNA-class probability 0.911784
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 8103685 90 + 27905053
UGGAACACAGAGCUCCGUGCAUCUGAGUGCAGCAGUGCAUCCACAUGUGGCAAACCAAGAU------------------------------GCAAAGCAAAAUUUUUCAUAAAACUGAAA
.......(((.(((...(((((((...(((.((((((....))).))).))).....))))------------------------------))).)))....((((....)))))))... ( -22.80)
>DroSec_CAF1 55375 120 + 1
UGGAACACAAAGCUCCGUGCAUCGGAGUACUGCAGUGCAUCCACAUAUGGCAAACUGAGCUGCAGUGCAUCCACAUAUGGCAAACUGAGCUGCAAAGCACAAUGUUGCAUAAAACUGAAA
((((.........((((.....))))((((((((((.((.(((....))).....)).)))))))))).))))......((((..((.(((....))).))...))))............ ( -34.80)
>DroSim_CAF1 27479 90 + 1
UGGAACACAGAGCUCUGUGCAUCGGAGUGCUGCAGUGCAUCCACAUGUGGCAAACUGAGCU------------------------------GCAAAGCAUAAUGUUGCAUAAAACUGAAA
((.((((....(((.(((((.((((..(((..(((((....))).))..)))..)))))).------------------------------))).)))....)))).))........... ( -27.80)
>DroEre_CAF1 30414 90 + 1
UGGAUCACAGAGCUCCGUGCAUUCGAGUGCAGCAGUGCAUCCACAUGUGGCACGCCGAGCU------------------------------GCAGAGCACAAUGUUGCACAUAAGUGAAA
....((((...((((..((((((((.((((.((((((....))).))).))))..)))).)------------------------------)))))))...(((.....)))..)))).. ( -30.00)
>DroYak_CAF1 23929 89 + 1
UGGAACACAGAACUCCGUGCAUUCGAGUGCAGCAGUGCAUCCACAUGUGGCAAACGGAGCU------------------------------GCA-AGAACAAUGCUGCACAUAAGUGAAA
.....(((.......((......)).(((((((((((....))).((..((.......)).------------------------------.))-.......))))))))....)))... ( -25.80)
>consensus
UGGAACACAGAGCUCCGUGCAUCCGAGUGCAGCAGUGCAUCCACAUGUGGCAAACCGAGCU______________________________GCAAAGCACAAUGUUGCAUAAAACUGAAA
.(((.(.....).)))(((((((((..(((.((((((....))).))).)))..)))).................................(((........)))))))).......... (-11.98 = -12.70 +   0.72)

alignment

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secondary structure

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dotplot

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Window 4

Location 8,103,685 – 8,103,775
Length 90
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 76.86
Mean single sequence MFE -29.12
Consensus MFE -16.04
Energy contribution -16.32
Covariance contribution 0.28
Combinations/Pair 1.22
Mean z-score -1.93
Structure conservation index 0.55
SVM decision value 0.65
SVM RNA-class probability 0.811217
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 8103685 90 - 27905053
UUUCAGUUUUAUGAAAAAUUUUGCUUUGC------------------------------AUCUUGGUUUGCCACAUGUGGAUGCACUGCUGCACUCAGAUGCACGGAGCUCUGUGUUCCA
(((((......)))))......((..(((------------------------------(((((((....))).....)))))))..))((((......)))).(((((.....))))). ( -25.80)
>DroSec_CAF1 55375 120 - 1
UUUCAGUUUUAUGCAACAUUGUGCUUUGCAGCUCAGUUUGCCAUAUGUGGAUGCACUGCAGCUCAGUUUGCCAUAUGUGGAUGCACUGCAGUACUCCGAUGCACGGAGCUUUGUGUUCCA
...........((((.(...(((((..((((..((.....((((((((((....((((.....))))...)))))))))).))..)))))))))...).)))).(((((.....))))). ( -39.10)
>DroSim_CAF1 27479 90 - 1
UUUCAGUUUUAUGCAACAUUAUGCUUUGC------------------------------AGCUCAGUUUGCCACAUGUGGAUGCACUGCAGCACUCCGAUGCACAGAGCUCUGUGUUCCA
...........(((((.........))))------------------------------)(((((((...(((....)))....)))).))).....(..((((((....))))))..). ( -22.80)
>DroEre_CAF1 30414 90 - 1
UUUCACUUAUGUGCAACAUUGUGCUCUGC------------------------------AGCUCGGCGUGCCACAUGUGGAUGCACUGCUGCACUCGAAUGCACGGAGCUCUGUGAUCCA
..((((...((((((.....((((...((------------------------------((....((((.(((....))))))).)))).)))).....)))))).......)))).... ( -30.20)
>DroYak_CAF1 23929 89 - 1
UUUCACUUAUGUGCAGCAUUGUUCU-UGC------------------------------AGCUCCGUUUGCCACAUGUGGAUGCACUGCUGCACUCGAAUGCACGGAGUUCUGUGUUCCA
..........((((((((.(((..(-..(------------------------------(((.......))....))..)..))).))))))))......((((((....)))))).... ( -27.70)
>consensus
UUUCAGUUUUAUGCAACAUUGUGCUUUGC______________________________AGCUCAGUUUGCCACAUGUGGAUGCACUGCUGCACUCCGAUGCACGGAGCUCUGUGUUCCA
...........((.(((((...((((((................................((...((...(((....)))..))...)).(((......))).))))))...))))).)) (-16.04 = -16.32 +   0.28)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:52:20 2006