Locus 4072

Sequence ID 2R_DroMel_CAF1
Location 13,444,844 – 13,444,937
Length 93
Max. P 0.999834
window6557 window6558

overview

Window 7

Location 13,444,844 – 13,444,937
Length 93
Sequences 5
Columns 93
Reading direction forward
Mean pairwise identity 89.76
Mean single sequence MFE -19.50
Consensus MFE -17.94
Energy contribution -17.94
Covariance contribution -0.00
Combinations/Pair 1.00
Mean z-score -2.71
Structure conservation index 0.92
SVM decision value 4.20
SVM RNA-class probability 0.999834
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 13444844 93 + 20766785
GCGGGCAAGUUUCACUCAGCUGCCGUUUUGUUUUUUUUUUUUUUACUCUAUGCUACCAACUUUUUGCAACUUUUGUGGCAACUUUUUGCCACA
...((((.(((......)))))))..........................(((............))).....((((((((....)))))))) ( -18.40)
>DroSec_CAF1 8762 90 + 1
GAGGGCAAGUUUCACUCAGCUGCCGCUUC---UUUUUUUUUUUUACUCUAUGCUACCAACUUUUUGCAACUUUUGUGGCAACUUUUUGCCACA
(((((((.(((......))))))).))).---..................(((............))).....((((((((....)))))))) ( -19.20)
>DroSim_CAF1 9414 87 + 1
GAGGGCAAGUUUCACUCAGCUGCCGUU------UUUUUUUUUUUACUCUAUGCUACCAACUUUUUGCAACUUUUGUGGCAACUUUUUGCCACA
((.((((.(((......))))))).))------.................(((............))).....((((((((....)))))))) ( -18.60)
>DroEre_CAF1 8840 82 + 1
GAGGGCAAGUUUCACUCAGCUGCCUUU-----------UUUUUUACUCUAUGCCACCAACUUUUUGCAACUUUUGUGGCAACUUUUUGCCACA
(((((((.(((......))))))))))-----------............(((............))).....((((((((....)))))))) ( -19.10)
>DroYak_CAF1 8879 93 + 1
GCGGGCAAGUUUCACUCAGCUGCCUGUUCUUUUUUUUUAUUUUUACGCUGUGCUACCAACUUUUUGCAACUUUUGUGGCAACUUUUUGCCACA
(((((((.(((......)))))))))).......................(((............))).....((((((((....)))))))) ( -22.20)
>consensus
GAGGGCAAGUUUCACUCAGCUGCCGUUU____UUUUUUUUUUUUACUCUAUGCUACCAACUUUUUGCAACUUUUGUGGCAACUUUUUGCCACA
...((((.(((......)))))))..........................(((............))).....((((((((....)))))))) (-17.94 = -17.94 +  -0.00)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 8

Location 13,444,844 – 13,444,937
Length 93
Sequences 5
Columns 93
Reading direction reverse
Mean pairwise identity 89.76
Mean single sequence MFE -20.04
Consensus MFE -18.74
Energy contribution -18.58
Covariance contribution -0.16
Combinations/Pair 1.05
Mean z-score -2.47
Structure conservation index 0.94
SVM decision value 3.93
SVM RNA-class probability 0.999710
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 13444844 93 - 20766785
UGUGGCAAAAAGUUGCCACAAAAGUUGCAAAAAGUUGGUAGCAUAGAGUAAAAAAAAAAAAAACAAAACGGCAGCUGAGUGAAACUUGCCCGC
((((((((....))))))))...(((((.........)))))..........................(((..((.(((.....)))))))). ( -19.10)
>DroSec_CAF1 8762 90 - 1
UGUGGCAAAAAGUUGCCACAAAAGUUGCAAAAAGUUGGUAGCAUAGAGUAAAAAAAAAAAA---GAAGCGGCAGCUGAGUGAAACUUGCCCUC
((((((((....)))))))).(((((.((...(((((...((...................---...))..)))))...)).)))))...... ( -21.15)
>DroSim_CAF1 9414 87 - 1
UGUGGCAAAAAGUUGCCACAAAAGUUGCAAAAAGUUGGUAGCAUAGAGUAAAAAAAAAAA------AACGGCAGCUGAGUGAAACUUGCCCUC
((((((((....))))))))...(((((.........)))))..................------...(((((.(.......).)))))... ( -18.90)
>DroEre_CAF1 8840 82 - 1
UGUGGCAAAAAGUUGCCACAAAAGUUGCAAAAAGUUGGUGGCAUAGAGUAAAAAA-----------AAAGGCAGCUGAGUGAAACUUGCCCUC
((((((((....)))))))).(((((.((...(((((.(.((.....))......-----------...).)))))...)).)))))...... ( -19.50)
>DroYak_CAF1 8879 93 - 1
UGUGGCAAAAAGUUGCCACAAAAGUUGCAAAAAGUUGGUAGCACAGCGUAAAAAUAAAAAAAAAGAACAGGCAGCUGAGUGAAACUUGCCCGC
.(.((((...((((..(((...((((((.....((((......))))((.................))..))))))..))).))))))))).. ( -21.53)
>consensus
UGUGGCAAAAAGUUGCCACAAAAGUUGCAAAAAGUUGGUAGCAUAGAGUAAAAAAAAAAAA____AAACGGCAGCUGAGUGAAACUUGCCCUC
((((((((....))))))))...(((((.........)))))...........................(((((.(.......).)))))... (-18.74 = -18.58 +  -0.16)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:11:04 2006