Locus 4670

Sequence ID 3L_DroMel_CAF1
Location 13,213,613 – 13,213,754
Length 141
Max. P 0.912931
window7348 window7349 window7350

overview

Window 8

Location 13,213,613 – 13,213,720
Length 107
Sequences 4
Columns 107
Reading direction reverse
Mean pairwise identity 93.40
Mean single sequence MFE -41.48
Consensus MFE -35.88
Energy contribution -35.88
Covariance contribution -0.00
Combinations/Pair 1.00
Mean z-score -2.09
Structure conservation index 0.87
SVM decision value 1.09
SVM RNA-class probability 0.912931
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13213613 107 - 23771897
AUGGCGCACACGCCCCUUUGCUGGGCGUGGGGCAGGGGGCGUGGCAGGGAGGUGGUAAGCGAUAGCCCAGACAGAUACUUUAUGCCGUACGUGCCAAACAAAACUCC
.((((((..(((((((((.(((........))))))))))))((((..(((...((..((....))....)).....)))..))))....))))))........... ( -42.20)
>DroSec_CAF1 6954 100 - 1
AUGGCGCACACGCCCCUUUGCUGGCAG-------GGGGGCGUGGCAGGGAGGUGGUAAGCGAUAGCCCAGACAGAUACUUUAUGCCGUACGUGCCAAACAAAACUCC
.((((((..(((((((((((....)))-------))))))))((((..(((...((..((....))....)).....)))..))))....))))))........... ( -43.10)
>DroSim_CAF1 12027 100 - 1
AUGGCGCACACGCCCCUUUGCUGGCUG-------GGGGGCGUGGCAGGGAGGUGGUAAGCGAUAGCCCAGACAGAUACUUUAUGCCGUACGUGCCAAACAAAACUCC
.((((((..((((((((..(....)..-------))))))))((((..(((...((..((....))....)).....)))..))))....))))))........... ( -39.70)
>DroYak_CAF1 6863 98 - 1
AUGGCGCACACGCCCCU-UGCUGUCA--------GGGGGCGUGGCAGGGUGGUGGUAAGCGAUAGCCCAGACAGAUACUUUAUGCCGUACGUGCCAAACAAAACUCC
.((((((..((((((((-((....))--------))))))))((((((((.((.(....).)).)))).....((....)).))))....))))))........... ( -40.90)
>consensus
AUGGCGCACACGCCCCUUUGCUGGCAG_______GGGGGCGUGGCAGGGAGGUGGUAAGCGAUAGCCCAGACAGAUACUUUAUGCCGUACGUGCCAAACAAAACUCC
.((((((..((((((((.................))))))))(((((((..((.(....).))..))).....((....)).))))....))))))........... (-35.88 = -35.88 +  -0.00)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 9

Location 13,213,640 – 13,213,754
Length 114
Sequences 4
Columns 114
Reading direction forward
Mean pairwise identity 93.36
Mean single sequence MFE -33.15
Consensus MFE -30.31
Energy contribution -30.31
Covariance contribution 0.00
Combinations/Pair 1.00
Mean z-score -1.37
Structure conservation index 0.91
SVM decision value 0.05
SVM RNA-class probability 0.556429
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13213640 114 + 23771897
AAGUAUCUGUCUGGGCUAUCGCUUACCACCUCCCUGCCACGCCCCCUGCCCCACGCCCAGCAAAGGGGCGUGUGCGCCAUUUCUUUUGAGGCAGUGUCUGCAUAUAUUUGUUUA
((((((.(((.(((((....))))).(((......((((((((((.(((..........)))..)))))))).))(((...((....))))).)))...))).))))))..... ( -33.40)
>DroSec_CAF1 6981 107 + 1
AAGUAUCUGUCUGGGCUAUCGCUUACCACCUCCCUGCCACGCCCCC-------CUGCCAGCAAAGGGGCGUGUGCGCCAUUUCUUUUGAGGCAGUGUCUGCAUAUAUUUGUUUA
((((((.(((.(((((....))))).(((......((((((((((.-------.((....))..)))))))).))(((...((....))))).)))...))).))))))..... ( -33.60)
>DroSim_CAF1 12054 107 + 1
AAGUAUCUGUCUGGGCUAUCGCUUACCACCUCCCUGCCACGCCCCC-------CAGCCAGCAAAGGGGCGUGUGCGCCAUUUCUUUUGAGGCAGUGUCUGCAUAUAUUUGUUUA
((((((.(((.(((((....))))).(((......((((((((((.-------..(....)...)))))))).))(((...((....))))).)))...))).))))))..... ( -31.30)
>DroYak_CAF1 6890 105 + 1
AAGUAUCUGUCUGGGCUAUCGCUUACCACCACCCUGCCACGCCCCC--------UGACAGCA-AGGGGCGUGUGCGCCAUUUCUUUUGAGGCAGUGUCUGCAUAUAUUUGCUUA
(((((..(((....((...((((............((((((((((.--------((....))-.)))))))).))(((...((....)))))))))...))..)))..))))). ( -34.30)
>consensus
AAGUAUCUGUCUGGGCUAUCGCUUACCACCUCCCUGCCACGCCCCC_______CUGCCAGCAAAGGGGCGUGUGCGCCAUUUCUUUUGAGGCAGUGUCUGCAUAUAUUUGUUUA
((((((.(((.(((((....))))).(((......((((((((((...................)))))))).))(((...((....))))).)))...))).))))))..... (-30.31 = -30.31 +   0.00)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 0

Location 13,213,640 – 13,213,754
Length 114
Sequences 4
Columns 114
Reading direction reverse
Mean pairwise identity 93.36
Mean single sequence MFE -37.70
Consensus MFE -31.78
Energy contribution -31.78
Covariance contribution -0.00
Combinations/Pair 1.00
Mean z-score -2.00
Structure conservation index 0.84
SVM decision value 0.79
SVM RNA-class probability 0.851253
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13213640 114 - 23771897
UAAACAAAUAUAUGCAGACACUGCCUCAAAAGAAAUGGCGCACACGCCCCUUUGCUGGGCGUGGGGCAGGGGGCGUGGCAGGGAGGUGGUAAGCGAUAGCCCAGACAGAUACUU
............(((.......(((...........)))...((((((((((.(((........))))))))))))))))(((..((.(....).))..)))............ ( -37.80)
>DroSec_CAF1 6981 107 - 1
UAAACAAAUAUAUGCAGACACUGCCUCAAAAGAAAUGGCGCACACGCCCCUUUGCUGGCAG-------GGGGGCGUGGCAGGGAGGUGGUAAGCGAUAGCCCAGACAGAUACUU
............(((.......(((...........)))...((((((((((((....)))-------))))))))))))(((..((.(....).))..)))............ ( -38.70)
>DroSim_CAF1 12054 107 - 1
UAAACAAAUAUAUGCAGACACUGCCUCAAAAGAAAUGGCGCACACGCCCCUUUGCUGGCUG-------GGGGGCGUGGCAGGGAGGUGGUAAGCGAUAGCCCAGACAGAUACUU
............(((.......(((...........)))...(((((((((..(....)..-------))))))))))))(((..((.(....).))..)))............ ( -35.30)
>DroYak_CAF1 6890 105 - 1
UAAGCAAAUAUAUGCAGACACUGCCUCAAAAGAAAUGGCGCACACGCCCCU-UGCUGUCA--------GGGGGCGUGGCAGGGUGGUGGUAAGCGAUAGCCCAGACAGAUACUU
...(((......))).......(((...........)))((.(((((((((-((....))--------))))))))))).((((.((.(....).)).))))............ ( -39.00)
>consensus
UAAACAAAUAUAUGCAGACACUGCCUCAAAAGAAAUGGCGCACACGCCCCUUUGCUGGCAG_______GGGGGCGUGGCAGGGAGGUGGUAAGCGAUAGCCCAGACAGAUACUU
............(((.......(((...........)))...(((((((((.................))))))))))))(((..((.(....).))..)))............ (-31.78 = -31.78 +  -0.00)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:30:14 2006