Locus 4497

Sequence ID X_DroMel_CAF1
Location 11,884,079 – 11,884,189
Length 110
Max. P 0.968478
window7396 window7397

overview

Window 6

Location 11,884,079 – 11,884,189
Length 110
Sequences 4
Columns 115
Reading direction forward
Mean pairwise identity 81.90
Mean single sequence MFE -22.55
Consensus MFE -16.14
Energy contribution -16.95
Covariance contribution 0.81
Combinations/Pair 1.15
Mean z-score -2.27
Structure conservation index 0.72
SVM decision value 1.41
SVM RNA-class probability 0.951476
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 11884079 110 + 22224390
CCCUUCUUUUUUU-CGCAUUUUGUUUCCCGGUUUUUUU----UUUCUUUUGAGAUGUCUUAUCAAAUCACCUUUUGCCUCUUCGUGUUGGGGCAAUGGCAAUAAUAAAAGGAAUG
...((((((((..-......(((((.((.(((......----((((....))))......)))..........(((((((........))))))).)).))))).)))))))).. ( -19.00)
>DroSec_CAF1 15969 113 + 1
CCCUUCUAU-UUU-CGCAUUUUGGUUCCCCGUUUUAUUUUAUUUUUUUUUGAGAUGUCUUAUCAAAUCACCUUUUGCCUCUUCGUUUUGGGGCACUGGCAAUAAUAAAAGGAAUG
.((((.(((-(..-.((..((((((....(((((((.............)))))))....))))))........((((((........))))))...))...)))).)))).... ( -22.92)
>DroEre_CAF1 17486 105 + 1
CC-UUCUAU-UUUGUACGUUUUUUUUGU-----UUCU-CCACUUUUUGUUGAGAUGUCUUAUCAAAUCACCU-UUGCCUCUUCGU-UUGGGGCAAUGGCAAUAAUAAAAGGGACU
..-......-.......(((((((((((-----((((-(.((.....)).))))...............((.-(((((((.....-..))))))).))....)))))))))))). ( -25.00)
>DroYak_CAF1 20442 103 + 1
CUGUUCUAU-UUU-UGCAUUUCUUUUCC-----UUUU----UUUUUUGUUGAGAUGUCUUAUCAAAUCACCUUUUGCCUCUUCGU-UUGGGGCAAUGGCAAUAAUAAAAGAAAUG
.........-...-..((((((((((..-----....----...((((.((((....)))).))))...((..(((((((.....-..))))))).)).......)))))))))) ( -23.30)
>consensus
CCCUUCUAU_UUU_CGCAUUUUGUUUCC_____UUUU____UUUUUUGUUGAGAUGUCUUAUCAAAUCACCUUUUGCCUCUUCGU_UUGGGGCAAUGGCAAUAAUAAAAGGAAUG
................((((((((((..................((((.((((....)))).))))...((...((((((........))))))..)).......)))))))))) (-16.14 = -16.95 +   0.81)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 7

Location 11,884,079 – 11,884,189
Length 110
Sequences 4
Columns 115
Reading direction reverse
Mean pairwise identity 81.90
Mean single sequence MFE -21.25
Consensus MFE -14.32
Energy contribution -14.32
Covariance contribution 0.00
Combinations/Pair 1.15
Mean z-score -2.49
Structure conservation index 0.67
SVM decision value 1.63
SVM RNA-class probability 0.968478
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 11884079 110 - 22224390
CAUUCCUUUUAUUAUUGCCAUUGCCCCAACACGAAGAGGCAAAAGGUGAUUUGAUAAGACAUCUCAAAAGAAA----AAAAAAACCGGGAAACAAAAUGCG-AAAAAAAGAAGGG
....((((((....((((..(((((.(........).))))).(((((.(((....)))))))).........----..........(....).....)))-).....)))))). ( -17.70)
>DroSec_CAF1 15969 113 - 1
CAUUCCUUUUAUUAUUGCCAGUGCCCCAAAACGAAGAGGCAAAAGGUGAUUUGAUAAGACAUCUCAAAAAAAAAUAAAAUAAAACGGGGAACCAAAAUGCG-AAA-AUAGAAGGG
....(((((((((.((((...((((.(........).))))..(((((.(((....)))))))).....................((....)).....)))-).)-)))))))). ( -24.70)
>DroEre_CAF1 17486 105 - 1
AGUCCCUUUUAUUAUUGCCAUUGCCCCAA-ACGAAGAGGCAA-AGGUGAUUUGAUAAGACAUCUCAACAAAAAGUGG-AGAA-----ACAAAAAAAACGUACAAA-AUAGAA-GG
....(((((((((((..((.(((((.(..-.....).)))))-.))..))...........((((.((.....)).)-))).-----.................)-))))))-)) ( -24.20)
>DroYak_CAF1 20442 103 - 1
CAUUUCUUUUAUUAUUGCCAUUGCCCCAA-ACGAAGAGGCAAAAGGUGAUUUGAUAAGACAUCUCAACAAAAAA----AAAA-----GGAAAAGAAAUGCA-AAA-AUAGAACAG
((((((((((....(..((.(((((.(..-.....).)))))..))..)((((...((....))...))))...----....-----..))))))))))..-...-......... ( -18.40)
>consensus
CAUUCCUUUUAUUAUUGCCAUUGCCCCAA_ACGAAGAGGCAAAAGGUGAUUUGAUAAGACAUCUCAAAAAAAAA____AAAA_____GGAAAAAAAAUGCA_AAA_AUAGAAGGG
...(((((((((...(((..(((((.(........).))))).(((((.(((....))))))))..................................))).....))))))))) (-14.32 = -14.32 +   0.00)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:26:36 2006