Locus 7785

Sequence ID 3L_DroMel_CAF1
Location 20,776,239 – 20,776,359
Length 120
Max. P 0.914960
window12672 window12673

overview

Window 2

Location 20,776,239 – 20,776,359
Length 120
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 77.61
Mean single sequence MFE -40.83
Consensus MFE -26.16
Energy contribution -25.88
Covariance contribution -0.27
Combinations/Pair 1.38
Mean z-score -1.44
Structure conservation index 0.64
SVM decision value 0.37
SVM RNA-class probability 0.708978
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 20776239 120 + 23771897
AAAGGUGCUCCUUUGGAAAGGAAUGCCCCUUCAAGUUCCAAGAUGCUACCAAAAUGGAGCUCCACUGUAGUUGCCAUAAGGGUGGCAGUUUUUCCUGCUGCGAAUGUGGCAUGGAACUGC
.((((.(((((((....)))))..)).))))..(((((((....(((((.....(((....)))..)))))(((((((...(..((((......))))..)...)))))))))))))).. ( -42.60)
>DroPse_CAF1 37786 120 + 1
UUAGGUGUUCCGCGAGCAAGGAGUGCCUAUUUAAGUUCGAGGAUGCCAGCAAGAUGGAGGUGCAUCGUAGAUGCCACAAGGGUAGCAGUUUCGCCUGCUGCGAAUGCGGCUUGGAGAUGG
.((((..((((........))))..))))......(((((.((((((..(......)..).)))))......(((.((...(((((((......)))))))...)).))))))))..... ( -38.60)
>DroSim_CAF1 30633 120 + 1
AAAGGUGCUCCUUUGGAAAGGAAUGCCCCUUCAAGUUCCAAGAUGCUACCAGAAUGGAGCUUCACUCCAGUUGCCAUAAGGGUGGCAGCUUUUCCUGCUGCGAAUGUGGCAUGGAACUGC
.((((.(((((((....)))))..)).))))..(((((((...(((((((((..(((((.....)))))((((((((....))))))))........))).....))))))))))))).. ( -44.00)
>DroYak_CAF1 30105 120 + 1
AAAGGUGCUCCUUUGGGAAGGAAUGUCCCUUCAAGUUUCAAGAUGCUGCCAAAAUGAAGCUCCACUCCAGUUGCCACAAGGGCGGCAGCUUUUCCUGUUGCGAAUGUGGAAUGGAACUGC
...((.((((.((((((((((......))))).(((........))).)))))..).))).))..((((....(((((...(((((((......)))))))...)))))..))))..... ( -38.50)
>DroAna_CAF1 33305 120 + 1
UUAGGUGCUCCUUUGGCAAAGACUGUACAUUCAAGUUCCUGGAUGCCAAGAAAAUGGAACUGCACUCGAGGUGCCACAAGGACAGCAGCUUUGCUUGCUGUGAGUGUGGACUGGAGCUCC
...((.(((((.........((.((((..((((..(((.(((...))).)))..))))..)))).))..(((.(((((...((((((((...)).))))))...))))))))))))).)) ( -40.70)
>DroPer_CAF1 37502 120 + 1
UUAGGUGUUCCGCGAGCAAGGAGUGCCUAUUUAAGUUCGAGGAUGCCAGCAAGAUGGAGGUGCAUCGUAGAUGCCACAAGGGCAGCAGUUUCGCCUGCUGCGAAUGCGGCUUGGAGAUGG
.((((..((((........))))..))))......(((((.((((((..(......)..).)))))......(((.((...(((((((......)))))))...)).))))))))..... ( -40.60)
>consensus
AAAGGUGCUCCUUUGGCAAGGAAUGCCCAUUCAAGUUCCAAGAUGCCACCAAAAUGGAGCUGCACUCUAGUUGCCACAAGGGCAGCAGCUUUGCCUGCUGCGAAUGUGGCAUGGAACUGC
...(((..(((........)))..)))......(((((((.....(((......)))...............((((((...(((((((......)))))))...)))))).))))))).. (-26.16 = -25.88 +  -0.27)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 3

Location 20,776,239 – 20,776,359
Length 120
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 77.61
Mean single sequence MFE -38.36
Consensus MFE -18.29
Energy contribution -18.98
Covariance contribution 0.70
Combinations/Pair 1.21
Mean z-score -2.45
Structure conservation index 0.48
SVM decision value 1.10
SVM RNA-class probability 0.914960
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 20776239 120 - 23771897
GCAGUUCCAUGCCACAUUCGCAGCAGGAAAAACUGCCACCCUUAUGGCAACUACAGUGGAGCUCCAUUUUGGUAGCAUCUUGGAACUUGAAGGGGCAUUCCUUUCCAAAGGAGCACCUUU
..((((((((((((........((((......))))........)))))((((.(((((....))))).)))).......))))))).(((((.((..(((((....))))))).))))) ( -39.39)
>DroPse_CAF1 37786 120 - 1
CCAUCUCCAAGCCGCAUUCGCAGCAGGCGAAACUGCUACCCUUGUGGCAUCUACGAUGCACCUCCAUCUUGCUGGCAUCCUCGAACUUAAAUAGGCACUCCUUGCUCGCGGAACACCUAA
.....(((..((((((...(.(((((......))))).)...))))))......((((......))))..((.((((........((.....))........)))).)))))........ ( -30.69)
>DroSim_CAF1 30633 120 - 1
GCAGUUCCAUGCCACAUUCGCAGCAGGAAAAGCUGCCACCCUUAUGGCAACUGGAGUGAAGCUCCAUUCUGGUAGCAUCUUGGAACUUGAAGGGGCAUUCCUUUCCAAAGGAGCACCUUU
..((((((((((((.....(((((.......)))))........)))))((..(((((......)))))..)).......))))))).(((((.((..(((((....))))))).))))) ( -41.62)
>DroYak_CAF1 30105 120 - 1
GCAGUUCCAUUCCACAUUCGCAACAGGAAAAGCUGCCGCCCUUGUGGCAACUGGAGUGGAGCUUCAUUUUGGCAGCAUCUUGAAACUUGAAGGGACAUUCCUUCCCAAAGGAGCACCUUU
(((((((((((((...(((......)))..((.((((((....)))))).)))))))))))))((.(((((((((....)))......((((((....))))))))))))))))...... ( -39.10)
>DroAna_CAF1 33305 120 - 1
GGAGCUCCAGUCCACACUCACAGCAAGCAAAGCUGCUGUCCUUGUGGCACCUCGAGUGCAGUUCCAUUUUCUUGGCAUCCAGGAACUUGAAUGUACAGUCUUUGCCAAAGGAGCACCUAA
((.(((((.(((((((...((((((.((...))))))))...))))).)).....(((((....((..(((((((...)))))))..))..))))).............))))).))... ( -42.10)
>DroPer_CAF1 37502 120 - 1
CCAUCUCCAAGCCGCAUUCGCAGCAGGCGAAACUGCUGCCCUUGUGGCAUCUACGAUGCACCUCCAUCUUGCUGGCAUCCUCGAACUUAAAUAGGCACUCCUUGCUCGCGGAACACCUAA
.....(((..((((((...(((((((......)))))))...))))))......((((......))))..((.((((........((.....))........)))).)))))........ ( -37.29)
>consensus
GCAGCUCCAUGCCACAUUCGCAGCAGGAAAAACUGCCACCCUUGUGGCAACUACAGUGCAGCUCCAUUUUGGUAGCAUCCUGGAACUUGAAGGGGCAUUCCUUGCCAAAGGAGCACCUAA
...(((((..((((((......((((......))))......))))))......((((......)))).........................................)))))...... (-18.29 = -18.98 +   0.70)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:56:53 2006