Locus 3720

Sequence ID 2R_DroMel_CAF1
Location 12,327,273 – 12,327,408
Length 135
Max. P 0.969563
window6044 window6045

overview

Window 4

Location 12,327,273 – 12,327,368
Length 95
Sequences 5
Columns 110
Reading direction reverse
Mean pairwise identity 78.83
Mean single sequence MFE -18.88
Consensus MFE -13.40
Energy contribution -13.36
Covariance contribution -0.04
Combinations/Pair 1.19
Mean z-score -2.20
Structure conservation index 0.71
SVM decision value 1.64
SVM RNA-class probability 0.969563
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 12327273 95 - 20766785
AAAUGAACA---------AAAAACACAAACACACACACUGCAACAGCAACUUGUUGCACAAAUACAAGUACCAACUUAUGAAGUCCGGGUACAGUGGUACUUCG------
.........---------..............((.(((((((((((....)))))))..........(((((.(((.....)))...)))))))))))......------ ( -19.70)
>DroSec_CAF1 25993 101 - 1
AAAUGGAGAAAAAAACAA-AAA--ACACACACACACACUGCAACAGCAACUUGUUGCACAAAUACAAUUACCAACUUAUGAAGUCCGGGUACAGUGGUAAUUCG------
..................-...--........((.(((((((((((....)))))))...........((((.(((.....)))...)))).))))))......------ ( -15.80)
>DroSim_CAF1 24172 104 - 1
AAAUGAAGAAAAAAACCAAAAAACACACACACACACACUGCAACAGCAACUUGUUGCACAAAUACAAGUACCAACUUAUGAAGUCCGGGUACAGUGGUACUUCG------
....((((......((((....................((((((((....)))))))).........(((((.(((.....)))...)))))..)))).)))).------ ( -20.90)
>DroEre_CAF1 26267 91 - 1
AAAUGAAAAAA------C-AA------AACACACACACUGCCACAGCAACUUGUUGCACAAAUA------CCAAGGAAUGAAGUCCGGGUACAGUGGUGCUUCGAGCGAC
...........------.-..------....(((.(((((.....((((....)))).....((------((..(((......))).))))))))))))........... ( -19.70)
>DroYak_CAF1 25391 90 - 1
AAAUGAAAAAA---AUAA-AA------AACACACACACUGCGACAGCAACUUGUUGCACAAAUA------CCAGCGAAUGGAGUCCGGGUACAGUGGUACUUCG----AC
...........---....-..------...........((((((((....))))))))......------(((.....))).(((..(((((....)))))..)----)) ( -18.30)
>consensus
AAAUGAAAAAA___A__A_AAA__ACAAACACACACACUGCAACAGCAACUUGUUGCACAAAUACAA_UACCAACUUAUGAAGUCCGGGUACAGUGGUACUUCG______
......................................((((((((....)))))))).....................((((((((.......))).)))))....... (-13.40 = -13.36 +  -0.04)

alignment

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secondary structure

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dotplot

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Window 5

Location 12,327,297 – 12,327,408
Length 111
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 79.40
Mean single sequence MFE -14.78
Consensus MFE -10.06
Energy contribution -10.40
Covariance contribution 0.34
Combinations/Pair 1.20
Mean z-score -1.25
Structure conservation index 0.68
SVM decision value 0.12
SVM RNA-class probability 0.595226
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 12327297 111 - 20766785
AGUAUUAAAGUCAGCGCGACACAAUCUGCAUAUUAAAGGAAAAUGAACA---------AAAAACACAAACACACACACUGCAACAGCAACUUGUUGCACAAAUACAAGUACCAACUUAUG
.(((((...(((.....))).............................---------....................((((((((....))))))))..)))))((((....))))... ( -14.40)
>DroSec_CAF1 26017 117 - 1
AGUAUUAAAGUCAGCGCGACACAAUCUGCAUAUUAAAGGAAAAUGGAGAAAAAAACAA-AAA--ACACACACACACACUGCAACAGCAACUUGUUGCACAAAUACAAUUACCAACUUAUG
.(((((...(((.....)))....(((.(((.((.....)).))).))).........-...--..............((((((((....))))))))..)))))............... ( -16.90)
>DroSim_CAF1 24196 120 - 1
AGUAUUAAAGUCAGCGCGACACAAUCUGCAUAUUAAAGGAAAAUGAAGAAAAAAACCAAAAAACACACACACACACACUGCAACAGCAACUUGUUGCACAAAUACAAGUACCAACUUAUG
.(((((...(((.....)))....(((.(((.((.....)).))).))).............................((((((((....))))))))..)))))((((....))))... ( -15.40)
>DroEre_CAF1 26297 101 - 1
AGUAUUAAAGUCAGCGCGACACAAUCUGCAUAUUAAAGGAAAAUGAAAAAA------C-AA------AACACACACACUGCCACAGCAACUUGUUGCACAAAUA------CCAAGGAAUG
.(((((...(....)((((((...(((..........)))...........------.-..------...........(((....)))...))))))...))))------)......... (  -9.60)
>DroYak_CAF1 25417 104 - 1
AGUAUUAAAGUCAGCGCGACACAAUCUGCAUAUUAAAGGAAAAUGAAAAAA---AUAA-AA------AACACACACACUGCGACAGCAACUUGUUGCACAAAUA------CCAGCGAAUG
.(((((...(((.....)))...............................---....-..------...........((((((((....))))))))..))))------)......... ( -12.60)
>DroAna_CAF1 23840 95 - 1
AGUAUUAAAGUCAGCGCGACACAAUCUGCAUAUUAAAAGAAAACGAAAAAA---A----------------GAGAUGUGGCAACAACAACUUGUUGCACAAACAUCAGUAC------AGG
.(((((...(((.....)))...............................---.----------------..(((((.(((((((....)))))))....))))))))))------... ( -19.80)
>consensus
AGUAUUAAAGUCAGCGCGACACAAUCUGCAUAUUAAAGGAAAAUGAAAAAA___A__A_AA______AACACACACACUGCAACAGCAACUUGUUGCACAAAUACAAGUACCAACUUAUG
.(((((...(((.....)))...........................................................(((((((....)))))))...)))))............... (-10.06 = -10.40 +   0.34)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:02:42 2006