Locus 652

Sequence ID 3R_DroMel_CAF1
Location 2,404,940 – 2,405,031
Length 91
Max. P 0.779015
window1032 window1033

overview

Window 2

Location 2,404,940 – 2,405,031
Length 91
Sequences 6
Columns 108
Reading direction forward
Mean pairwise identity 82.69
Mean single sequence MFE -40.93
Consensus MFE -27.42
Energy contribution -27.73
Covariance contribution 0.31
Combinations/Pair 1.19
Mean z-score -2.50
Structure conservation index 0.67
SVM decision value 0.55
SVM RNA-class probability 0.779015
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 2404940 91 + 27905053
-GUGGCGAUGGCAGGGGGCGUGGCAAGUC---GUCC-------UGCGAGUCAAGAGCUCGCUCGCUGCCAUUUCCCCC-UGUCAGGGACUCAAUGUGUCCGUA-----
-...((..((((((((((.((((((.(.(---(...-------.((((((.....)))))).)))))))))..)))))-))))).((((.......)))))).----- ( -45.40)
>DroSec_CAF1 118097 91 + 1
-GUGGCGAUGGCAGGGGGCGUGGCAAGUC---GUCC-------UGCGAGUCAAGAGCUCGCUCGCUGCCAUUUCCCCC-UGUCAAGGACUCAAUGUGUCCGUA-----
-...((..((((((((((.((((((.(.(---(...-------.((((((.....)))))).)))))))))..)))))-))))).((((.......)))))).----- ( -45.60)
>DroSim_CAF1 110170 91 + 1
-GUGGCGAUGGCAGGGGGCGUGGCAAGUC---GUCC-------UGCGAGUCAAGAGCUCGCUCGCUGCCAUUUCCCCC-UGUCAAGGACUCAAUGUGUCCGUA-----
-...((..((((((((((.((((((.(.(---(...-------.((((((.....)))))).)))))))))..)))))-))))).((((.......)))))).----- ( -45.60)
>DroEre_CAF1 111814 91 + 1
-AUGGCUAUGGCAGGGGGCGUGGCAAGCC---GUCC-------UGCGAGUCAAGAGCUCACUCGCUGCCAUUUCCCCC-UGUCAAGGACUCAAUGUGUCCAUA-----
-.......((((((((((.((((((....---....-------.((((((.........))))))))))))..)))))-))))).((((.......))))...----- ( -40.20)
>DroYak_CAF1 106303 91 + 1
-GUGGCUAUGGCGGCGGG-GUGGCAAAUU---GUCC-------UGCGAGUCAAGAGCUCACUCGCUGCCCUCUCCCCCAUGUCAAGGACUCAAUGUGUCCGUA-----
-.((((.((((.((.(((-(.((((....---....-------.((((((.........)))))))))))))).)))))))))).((((.......))))...----- ( -33.90)
>DroAna_CAF1 110081 107 + 1
UAGGGCCAGGGCUGGGGAGGUAGCAAAGAGAGGUUCAAAGGAUGGGAAGUCAAGAGCUCGUUCUCAGCCAUUUUCCCC-UGUCAAGGCCUCAAUGUGUCCGUGUCCGU
..(((((..(((.(((((((..((..((((.(((((....(((.....)))..)))))..))))..))...)))))))-.)))..))))).................. ( -34.90)
>consensus
_GUGGCGAUGGCAGGGGGCGUGGCAAGUC___GUCC_______UGCGAGUCAAGAGCUCGCUCGCUGCCAUUUCCCCC_UGUCAAGGACUCAAUGUGUCCGUA_____
........((((((((((.((((((...................((((((.........))))))))))))..))))).))))).((((.......))))........ (-27.42 = -27.73 +   0.31)

alignment

Postscript

secondary structure

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dotplot

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Window 3

Location 2,404,940 – 2,405,031
Length 91
Sequences 6
Columns 108
Reading direction reverse
Mean pairwise identity 82.69
Mean single sequence MFE -34.27
Consensus MFE -24.16
Energy contribution -24.17
Covariance contribution 0.00
Combinations/Pair 1.22
Mean z-score -1.56
Structure conservation index 0.71
SVM decision value 0.05
SVM RNA-class probability 0.557497
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 2404940 91 - 27905053
-----UACGGACACAUUGAGUCCCUGACA-GGGGGAAAUGGCAGCGAGCGAGCUCUUGACUCGCA-------GGAC---GACUUGCCACGCCCCCUGCCAUCGCCAC-
-----...((((.......)))).((.((-(((((...(((((((((((((....))).)))))(-------(...---..)))))))..))))))).)).......- ( -37.70)
>DroSec_CAF1 118097 91 - 1
-----UACGGACACAUUGAGUCCUUGACA-GGGGGAAAUGGCAGCGAGCGAGCUCUUGACUCGCA-------GGAC---GACUUGCCACGCCCCCUGCCAUCGCCAC-
-----...((((.......)))).((.((-(((((...(((((((((((((....))).)))))(-------(...---..)))))))..))))))).)).......- ( -38.20)
>DroSim_CAF1 110170 91 - 1
-----UACGGACACAUUGAGUCCUUGACA-GGGGGAAAUGGCAGCGAGCGAGCUCUUGACUCGCA-------GGAC---GACUUGCCACGCCCCCUGCCAUCGCCAC-
-----...((((.......)))).((.((-(((((...(((((((((((((....))).)))))(-------(...---..)))))))..))))))).)).......- ( -38.20)
>DroEre_CAF1 111814 91 - 1
-----UAUGGACACAUUGAGUCCUUGACA-GGGGGAAAUGGCAGCGAGUGAGCUCUUGACUCGCA-------GGAC---GGCUUGCCACGCCCCCUGCCAUAGCCAU-
-----...((((.......)))).((.((-(((((...((((.((((((.((...)).))))))(-------((..---..)))))))..))))))).)).......- ( -36.20)
>DroYak_CAF1 106303 91 - 1
-----UACGGACACAUUGAGUCCUUGACAUGGGGGAGAGGGCAGCGAGUGAGCUCUUGACUCGCA-------GGAC---AAUUUGCCAC-CCCGCCGCCAUAGCCAC-
-----...((((.......)))).....((((.((.(.(((..((((((....(((((.....))-------))).---.))))))..)-))).)).))))......- ( -29.90)
>DroAna_CAF1 110081 107 - 1
ACGGACACGGACACAUUGAGGCCUUGACA-GGGGAAAAUGGCUGAGAACGAGCUCUUGACUUCCCAUCCUUUGAACCUCUCUUUGCUACCUCCCCAGCCCUGGCCCUA
.((....))..........((((..(.(.-(((((...((((.((((.(((....)))......((.....))....))))...))))..))))).).)..))))... ( -25.40)
>consensus
_____UACGGACACAUUGAGUCCUUGACA_GGGGGAAAUGGCAGCGAGCGAGCUCUUGACUCGCA_______GGAC___GACUUGCCACGCCCCCUGCCAUCGCCAC_
........((((.......)))).......(((((...(((((((((((((....))).)))))........(........).)))))..)))))............. (-24.16 = -24.17 +   0.00)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:48:25 2006