Locus 7150

Sequence ID 3L_DroMel_CAF1
Location 19,197,864 – 19,198,004
Length 140
Max. P 0.972559
window11609 window11610

overview

Window 9

Location 19,197,864 – 19,197,973
Length 109
Sequences 4
Columns 113
Reading direction forward
Mean pairwise identity 80.00
Mean single sequence MFE -22.03
Consensus MFE -16.64
Energy contribution -16.20
Covariance contribution -0.44
Combinations/Pair 1.11
Mean z-score -2.23
Structure conservation index 0.76
SVM decision value 1.69
SVM RNA-class probability 0.972559
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 19197864 109 + 23771897
CGUGCAAGUGGCUAAAACAGCUAUUAAAUAGAAAACAAAGGACUUGCAGGG-GGCAA---CCAAAACGCAGACGUGUAGUUUGCUGAAAAAAAAAUUGAAAAUAGAAAAACAC
(.(((((((((((.....))))........(....).....))))))).)(-(....---)).....((((((.....))))))............................. ( -23.20)
>DroSim_CAF1 30526 112 + 1
CGUGCAAGUGGCUAAAACAGCUAUUAAAUGGAAAACAAAGGACUUGCAGGG-GGCAAGGACCAAAACGCAGACGUGUAGUUUGCUGUAAAAAAAAAUGAAAAUAGAAAAACAC
(((...(((((((.....)))))))..)))....(((..((.(((((....-.)))))..)).....((((((.....))))))))).......................... ( -23.60)
>DroEre_CAF1 29403 85 + 1
CGUGCAAGUGGCGAAAACAGCUAUUAAAUAGAAAACAAAGGACUUGCAGAG-GGCAC---CCAAAACGCAGACGUGUUGUUUGCA------------------------ACAC
.(((..((((((.......))))))..................(((((((.-(((((---.............))))).))))))------------------------)))) ( -18.52)
>DroYak_CAF1 54344 104 + 1
CGUGCAAGUGGCAAAAACAGCUAUUAGAUGGAAAACAAAGAGCUUGCAGAGGGGCAA---CCAAAACGCAGACGUGUUGUUUGCA------AAAAAAUAAAAUAGAACAACAC
..((((((((((.......)))......((.....))....)))))))...((....---))...........(((((((((...------.............))))))))) ( -22.79)
>consensus
CGUGCAAGUGGCUAAAACAGCUAUUAAAUAGAAAACAAAGGACUUGCAGAG_GGCAA___CCAAAACGCAGACGUGUAGUUUGCA______AAAAAUGAAAAUAGAAAAACAC
..(((((((...........((((...))))..........)))))))....((......)).....((((((.....))))))............................. (-16.64 = -16.20 +  -0.44)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 0

Location 19,197,898 – 19,198,004
Length 106
Sequences 4
Columns 110
Reading direction forward
Mean pairwise identity 79.91
Mean single sequence MFE -23.31
Consensus MFE -15.73
Energy contribution -15.97
Covariance contribution 0.25
Combinations/Pair 1.00
Mean z-score -1.97
Structure conservation index 0.67
SVM decision value 0.84
SVM RNA-class probability 0.864506
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 19197898 106 + 23771897
ACAAAGGACUUGCAGGG-GGCAA---CCAAAACGCAGACGUGUAGUUUGCUGAAAAAAAAAUUGAAAAUAGAAAAACACAGACGACAGGUGUGAGUGAAAAGGUGUAACC
..............((.-.(((.---((...((.((.((.(((.(((((.((........................))))))).))).)).)).)).....)))))..)) ( -19.36)
>DroSim_CAF1 30560 109 + 1
ACAAAGGACUUGCAGGG-GGCAAGGACCAAAACGCAGACGUGUAGUUUGCUGUAAAAAAAAAUGAAAAUAGAAAAACACAGCCGACAGGUGUGAGUGAAAAGGUGUAACC
.....((.(((((....-.))))).(((.....((((((.....))))))..........................((((.((....))))))........)))....)) ( -24.00)
>DroEre_CAF1 29437 82 + 1
ACAAAGGACUUGCAGAG-GGCAC---CCAAAACGCAGACGUGUUGUUUGCA------------------------ACACAGCCGACAGGUGUGAGGGAAAAGGUGUAACC
.....(.((((((....-.)).(---((.....((((((.....)))))).------------------------.((((.((....)))))).)))...)))).).... ( -21.50)
>DroYak_CAF1 54378 101 + 1
ACAAAGAGCUUGCAGAGGGGCAA---CCAAAACGCAGACGUGUUGUUUGCA------AAAAAAUAAAAUAGAACAACACAGCCGACAGGUGUGAGUGAAAAGGUGUAAGC
.......(((((((...((....---))....(((..(((((((((((...------.............))))))))).(((....)))))..)))......))))))) ( -28.39)
>consensus
ACAAAGGACUUGCAGAG_GGCAA___CCAAAACGCAGACGUGUAGUUUGCA______AAAAAUGAAAAUAGAAAAACACAGCCGACAGGUGUGAGUGAAAAGGUGUAACC
(((.......(((......)))....((.....((((((.....))))))..........................((((.((....))))))........))))).... (-15.73 = -15.97 +   0.25)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:39:20 2006