Locus 2366

Sequence ID 2L_DroMel_CAF1
Location 6,410,672 – 6,410,772
Length 100
Max. P 0.871181
window3813 window3814

overview

Window 3

Location 6,410,672 – 6,410,772
Length 100
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 82.72
Mean single sequence MFE -33.56
Consensus MFE -20.00
Energy contribution -21.20
Covariance contribution 1.20
Combinations/Pair 1.15
Mean z-score -2.43
Structure conservation index 0.60
SVM decision value 0.87
SVM RNA-class probability 0.871181
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 6410672 100 + 22407834
CCCAGCAGAUGUAAACCAAU------UCGGAAGGAUCCU-UUGUAAAAGAUGCAGCUCCCUAAACAGGCCAUCCUGCGAACUCACUAU-------UCAAUGAUGCCCCAUCUG------C
....(((((((.......((------((....))))...-..........(((((...(((....))).....)))))..........-------............))))))------) ( -19.50)
>DroSec_CAF1 38960 99 + 1
CCCAGCAGAUGUAAACCAAU------UCGGAAGGAUCCG-UUGUGAGAGAUGCAGCUCCCUAAACAGGGCAUCCUGCGAACUCACUAU-------UCAAUGGUGC-CCAUCUG------C
....(((((((...((((..------.((((....))))-..(((((...(((((..((((....))))....)))))..)))))...-------....))))..-.))))))------) ( -35.30)
>DroSim_CAF1 39449 100 + 1
CCCAGCAGAUGUAAACCAAU------UCGGAAGGAUCCUUUUGUGAGAGAUGCAGCUCCCUAAACAGGGCAUCCUGCGAACUCACUAU-------UCAAUGGUGC-CCAUCUG------C
....(((((((...((((((------((....))))......(((((...(((((..((((....))))....)))))..)))))...-------....))))..-.))))))------) ( -35.20)
>DroEre_CAF1 37554 111 + 1
C-AAGCAGAGGUAAACCAAU------UCGGAAGGAUCCU-UUGUGGAAGGUGCAGCUCCAUAAACGGGGCAUCCUGUGAACUCACUAUUGUGCCGACAAUGGUGC-CCAUCUGCAACUGC
.-..(((((((...((((.(------((....)))(((.-....))).((..(((((((......))))).....(((....)))...))..)).....))))..-)).)))))...... ( -38.70)
>DroYak_CAF1 42978 111 + 1
C-AAGCAGAGGUAAGCCAAGAGGUAAACGGAAGGAUCCU-UUGUGGGAGGAGCAGCUCCAUAAACAGGGCAUCCUGUGAACUCACUAUAAUGCCCUCAAUGGUGC-CCAUCUG------C
.-..(((((((...(((((((((....(....)...)))-))((.((((......))))....))(((((((...(((....)))....)))))))...))))..-)).))))------) ( -39.10)
>consensus
CCCAGCAGAUGUAAACCAAU______UCGGAAGGAUCCU_UUGUGAGAGAUGCAGCUCCCUAAACAGGGCAUCCUGCGAACUCACUAU_______UCAAUGGUGC_CCAUCUG______C
.....((((((...((((..........(((....)))....(((((...(((((..((((....))))....)))))..)))))..............))))....))))))....... (-20.00 = -21.20 +   1.20)

alignment

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secondary structure

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dotplot

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Window 4

Location 6,410,672 – 6,410,772
Length 100
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 82.72
Mean single sequence MFE -35.69
Consensus MFE -21.62
Energy contribution -21.98
Covariance contribution 0.36
Combinations/Pair 1.12
Mean z-score -1.97
Structure conservation index 0.61
SVM decision value 0.21
SVM RNA-class probability 0.633868
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 6410672 100 - 22407834
G------CAGAUGGGGCAUCAUUGA-------AUAGUGAGUUCGCAGGAUGGCCUGUUUAGGGAGCUGCAUCUUUUACAA-AGGAUCCUUCCGA------AUUGGUUUACAUCUGCUGGG
(------((((((((.((((..(((-------((.....)))))...)))).))......(((((....((((((....)-))))).)))))..------.........))))))).... ( -30.80)
>DroSec_CAF1 38960 99 - 1
G------CAGAUGG-GCACCAUUGA-------AUAGUGAGUUCGCAGGAUGCCCUGUUUAGGGAGCUGCAUCUCUCACAA-CGGAUCCUUCCGA------AUUGGUUUACAUCUGCUGGG
(------((((((.-..((((....-------...(((((...((((....((((....))))..))))....)))))..-((((....)))).------..))))...))))))).... ( -39.00)
>DroSim_CAF1 39449 100 - 1
G------CAGAUGG-GCACCAUUGA-------AUAGUGAGUUCGCAGGAUGCCCUGUUUAGGGAGCUGCAUCUCUCACAAAAGGAUCCUUCCGA------AUUGGUUUACAUCUGCUGGG
(------((((((.-..((((....-------...(((((...((((....((((....))))..))))....)))))....(((....)))..------..))))...))))))).... ( -36.90)
>DroEre_CAF1 37554 111 - 1
GCAGUUGCAGAUGG-GCACCAUUGUCGGCACAAUAGUGAGUUCACAGGAUGCCCCGUUUAUGGAGCUGCACCUUCCACAA-AGGAUCCUUCCGA------AUUGGUUUACCUCUGCUU-G
......(((((.((-..((((...((((.......(((....)))(((((((.(((....))).))....((((.....)-)))))))).))))------..))))...)))))))..-. ( -34.30)
>DroYak_CAF1 42978 111 - 1
G------CAGAUGG-GCACCAUUGAGGGCAUUAUAGUGAGUUCACAGGAUGCCCUGUUUAUGGAGCUGCUCCUCCCACAA-AGGAUCCUUCCGUUUACCUCUUGGCUUACCUCUGCUU-G
(------((((.((-((.((((..((((((((...(((....)))..))))))))....)))).)).(((..........-.(((....)))...........)))...)))))))..-. ( -37.45)
>consensus
G______CAGAUGG_GCACCAUUGA_______AUAGUGAGUUCGCAGGAUGCCCUGUUUAGGGAGCUGCAUCUCUCACAA_AGGAUCCUUCCGA______AUUGGUUUACAUCUGCUGGG
.......((((((....((((..............(((((((((((((....))))).....))))).)))...........(((....)))..........))))...))))))..... (-21.62 = -21.98 +   0.36)

alignment

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secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:26:20 2006