Locus 541

Sequence ID 3R_DroMel_CAF1
Location 2,009,162 – 2,009,270
Length 108
Max. P 0.694511
window861 window862

overview

Window 1

Location 2,009,162 – 2,009,270
Length 108
Sequences 5
Columns 118
Reading direction forward
Mean pairwise identity 88.43
Mean single sequence MFE -30.59
Consensus MFE -23.94
Energy contribution -25.38
Covariance contribution 1.44
Combinations/Pair 1.04
Mean z-score -1.63
Structure conservation index 0.78
SVM decision value 0.34
SVM RNA-class probability 0.694511
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 2009162 108 + 27905053
CGCAGGCAAUUC------UUCUUC---UAGGCCCCAGCCGGGCCAAUAUAGAAAUUCUAUGUUCGGCGACCUUUAUGUUCCGAUGUUUACCAGCUUCUUAUCAG-GCCUGCCUUUGUG
.((((((.....------......---..(((((.....))))).((((((.....))))))((((.(((......))))))).....................-))))))....... ( -30.90)
>DroSec_CAF1 151260 114 + 1
CGCAGGCGAUUUUUCUUCUUCUUC---UAGGCCCCAGCCGGGCCAAUAUAGAAAUGCUAUGUUCGGCGUCCUUUAUGUUCCGAUGUUUACCAGCUUCUUAUCAG-GCCUGCCUUUGUU
.((((((.................---..(((((.....)))))((((((((.(((((......)))))..))))))))..((((.............))))..-))))))....... ( -30.92)
>DroSim_CAF1 156460 114 + 1
CGCAGGCGAUUCUUCUUCUUCUUC---UAGGCCCCAGCCGGGCCAAUAUAGAAAUGCUAUGUUCGGCGUCCUUUAUGUUCCGAUGUUUACCAGCUUCUUAUCAG-GCCUGCCUUUGUU
.((((((.................---..(((((.....)))))((((((((.(((((......)))))..))))))))..((((.............))))..-))))))....... ( -30.92)
>DroEre_CAF1 154937 110 + 1
CGCAGGCGAUUC------UUCUUCUGCUAGACCCCAGCUGGGCCAAUAUAGAAAUGCUAUGUUCGGCGUCCUUUU--UUCCGAUGUUUACCAGCUUCUUAUCAGGGCCUGCCUUUGUU
.((((((((...------.)).((((..(((....((((((((((((((((.....))))))).)))(((.....--....))).....)))))))))...))))))))))....... ( -34.90)
>DroYak_CAF1 157893 109 + 1
CGCAGGCAAUUC------UUUUUU---CAGGCUCCAGAUGGGCCAAUAUACAAAUGCUCUGUUCGGCGUCCUUUUUGUUCCGAUGUGUACCAGCUUCUUAUCAGGGCCUGCCUUUGUU
.((((((.....------......---..(((.((....))))).....(((((((((......))))).....)))).((((((.((....))....)))).))))))))....... ( -25.30)
>consensus
CGCAGGCGAUUC______UUCUUC___UAGGCCCCAGCCGGGCCAAUAUAGAAAUGCUAUGUUCGGCGUCCUUUAUGUUCCGAUGUUUACCAGCUUCUUAUCAG_GCCUGCCUUUGUU
.((((((......................(((((.....)))))((((((((.(((((......)))))..))))))))..((((.............))))...))))))....... (-23.94 = -25.38 +   1.44)

alignment

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secondary structure

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dotplot

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Window 2

Location 2,009,162 – 2,009,270
Length 108
Sequences 5
Columns 118
Reading direction reverse
Mean pairwise identity 88.43
Mean single sequence MFE -30.26
Consensus MFE -25.52
Energy contribution -26.16
Covariance contribution 0.64
Combinations/Pair 1.04
Mean z-score -1.42
Structure conservation index 0.84
SVM decision value 0.18
SVM RNA-class probability 0.619514
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 2009162 108 - 27905053
CACAAAGGCAGGC-CUGAUAAGAAGCUGGUAAACAUCGGAACAUAAAGGUCGCCGAACAUAGAAUUUCUAUAUUGGCCCGGCUGGGGCCUA---GAAGAA------GAAUUGCCUGCG
.....((((((((-((.........(((((....))))).......))))).............((((((....(((((.....)))))))---))))..------....)))))... ( -30.29)
>DroSec_CAF1 151260 114 - 1
AACAAAGGCAGGC-CUGAUAAGAAGCUGGUAAACAUCGGAACAUAAAGGACGCCGAACAUAGCAUUUCUAUAUUGGCCCGGCUGGGGCCUA---GAAGAAGAAGAAAAAUCGCCUGCG
.......((((((-..(((.....((((((.....((((..(.....)....)))))).)))).((((((....(((((.....)))))))---))))..........))))))))). ( -32.80)
>DroSim_CAF1 156460 114 - 1
AACAAAGGCAGGC-CUGAUAAGAAGCUGGUAAACAUCGGAACAUAAAGGACGCCGAACAUAGCAUUUCUAUAUUGGCCCGGCUGGGGCCUA---GAAGAAGAAGAAGAAUCGCCUGCG
.......((((((-..(((.....((((((.....((((..(.....)....)))))).)))).((((((....(((((.....)))))))---))))..........))))))))). ( -32.80)
>DroEre_CAF1 154937 110 - 1
AACAAAGGCAGGCCCUGAUAAGAAGCUGGUAAACAUCGGAA--AAAAGGACGCCGAACAUAGCAUUUCUAUAUUGGCCCAGCUGGGGUCUAGCAGAAGAA------GAAUCGCCUGCG
.........(((((((.......((((((......((....--....))..(((((..((((.....)))).)))))))))))))))))).((((..((.------...))..)))). ( -29.81)
>DroYak_CAF1 157893 109 - 1
AACAAAGGCAGGCCCUGAUAAGAAGCUGGUACACAUCGGAACAAAAAGGACGCCGAACAGAGCAUUUGUAUAUUGGCCCAUCUGGAGCCUG---AAAAAA------GAAUUGCCUGCG
.......(((((((((.........(((((....))))).......)))..(((.....).))...........(((((....)).)))..---......------.....)))))). ( -25.59)
>consensus
AACAAAGGCAGGC_CUGAUAAGAAGCUGGUAAACAUCGGAACAUAAAGGACGCCGAACAUAGCAUUUCUAUAUUGGCCCGGCUGGGGCCUA___GAAGAA______GAAUCGCCUGCG
.......((((((...((((((((((((.......((((.............))))...))))..)))).))))(((((.....)))))......................)))))). (-25.52 = -26.16 +   0.64)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:45:36 2006