Locus 10237

Sequence ID 3R_DroMel_CAF1
Location 27,430,569 – 27,430,679
Length 110
Max. P 0.959751
window16314 window16315

overview

Window 4

Location 27,430,569 – 27,430,661
Length 92
Sequences 5
Columns 95
Reading direction forward
Mean pairwise identity 79.33
Mean single sequence MFE -20.40
Consensus MFE -11.27
Energy contribution -12.03
Covariance contribution 0.76
Combinations/Pair 1.06
Mean z-score -2.44
Structure conservation index 0.55
SVM decision value 1.51
SVM RNA-class probability 0.959751
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 27430569 92 + 27905053
CAAAGUUUUUGGCUCGAAAGCUGCUGAGCCAAGCAC--GAAAGAAAUAUGGAGAUCGCGGCUUGAAGAGAGCUUAAAAGUAAAUCAGAA-AAAAG
...(.((((.(((((..(((((((.((.(((....(--....).....)))...))))))))).....))))).)))).).........-..... ( -24.20)
>DroSec_CAF1 5529 81 + 1
CCAAGUUUUUGGCUCGAAAGCUGCUGAGC-AAGCAC--GAAAGAAA-----------CGGCUUGAAGAGAGCUUAAAAGCACAUCAGAAGAAAAG
....(((((((((((..((((((((....-.))).(--....)...-----------.))))).....)))).)))))))............... ( -21.30)
>DroSim_CAF1 11915 81 + 1
CAAAGUUUUUGGCUCGAAAGCUGCUGAGC-AAGCAC--GAAAGAAA-----------CGGCUUGAAGAGAGCUUAAAAGUAAAUCAGAAGAAAAG
...(.((((.(((((..((((((((....-.))).(--....)...-----------.))))).....))))).)))).)............... ( -18.30)
>DroEre_CAF1 5871 91 + 1
CAAAGUUUUCGGCU-CAAAGCUGCUGAGC-AAGCACGGAGAAGAAAUACUGAGAUCGCGGCUUAAA--GAGCUUUAAAGUAAAUUUAGAAAAAAG
.....(((((((((-(.(((((((.((..-...(.(((..........))).).)))))))))...--))))).((((.....)))))))))... ( -18.00)
>DroYak_CAF1 8484 90 + 1
CAGAGUUUUUGGCUACAAAGCUGCUGAGC-AAGCAC--AAAAGAAAUAGUGAGAUCGCGGCUUAAA--AAGCUUAAAAGCAAAAUCAGAGAAAAG
....((((((((((...(((((((.((..-...(((--..........)))...)))))))))...--.))).)))))))............... ( -20.20)
>consensus
CAAAGUUUUUGGCUCGAAAGCUGCUGAGC_AAGCAC__GAAAGAAAUA__GAGAUCGCGGCUUGAAGAGAGCUUAAAAGUAAAUCAGAAGAAAAG
....(((((((((((..(((((((................................))))))).....)))).)))))))............... (-11.27 = -12.03 +   0.76)

alignment

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secondary structure

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dotplot

Postscript

Window 5

Location 27,430,587 – 27,430,679
Length 92
Sequences 3
Columns 95
Reading direction forward
Mean pairwise identity 78.78
Mean single sequence MFE -19.54
Consensus MFE -13.51
Energy contribution -13.40
Covariance contribution -0.11
Combinations/Pair 1.13
Mean z-score -1.77
Structure conservation index 0.69
SVM decision value 0.70
SVM RNA-class probability 0.825346
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 27430587 92 + 27905053
AGCUGCUGAGCCAAGCAC--GAAAGAAAUAUGGAGAUCGCGGCUUGAAGAGAGCUUAAAAGUAAAUCAGAA-AAAAGCUUCCGUCGAGAAAAUAA
.(((((.((.(((....(--....).....)))...)))))))((((.(..(((((...............-..)))))..).))))........ ( -20.23)
>DroEre_CAF1 5888 90 + 1
AGCUGCUGAGC-AAGCACGGAGAAGAAAUACUGAGAUCGCGGCUUAAA--GAGCUUUAAAGUAAAUUUAGAAAAAAGCUUCUGCCGCA--AGGCA
.((((((....-.)))......................(((((.....--(((((((................)))))))..))))).--.))). ( -21.29)
>DroYak_CAF1 8502 88 + 1
AGCUGCUGAGC-AAGCAC--AAAAGAAAUAGUGAGAUCGCGGCUUAAA--AAGCUUAAAAGCAAAAUCAGAGAAAAGCUUCCGCCGCA--AGUAA
.((((((....-.)))..--..................(((((.....--..(((....))).......(.(((....))))))))).--))).. ( -17.10)
>consensus
AGCUGCUGAGC_AAGCAC__AAAAGAAAUACUGAGAUCGCGGCUUAAA__GAGCUUAAAAGUAAAUUAAGA_AAAAGCUUCCGCCGCA__AGUAA
...((((......)))).....................(((((.......((((((..................))))))..)))))........ (-13.51 = -13.40 +  -0.11)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:52:19 2006