Locus 3313

Sequence ID 2L_DroMel_CAF1
Location 9,578,828 – 9,578,976
Length 148
Max. P 0.994103
window5261 window5262 window5263

overview

Window 1

Location 9,578,828 – 9,578,920
Length 92
Sequences 4
Columns 109
Reading direction reverse
Mean pairwise identity 64.83
Mean single sequence MFE -24.82
Consensus MFE -16.27
Energy contribution -16.40
Covariance contribution 0.13
Combinations/Pair 1.13
Mean z-score -1.80
Structure conservation index 0.66
SVM decision value 2.45
SVM RNA-class probability 0.994103
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 9578828 92 - 22407834
UUCAACCGGCAGCUCAGGCAGCUGAUGAUGAUAACAAUAUGACAAAUUCAAAUCCGGAGGUUCCAGAUGUCGG--AGGCAAAU---------------CAGAAGGAUCA
(((..(((((((((.....)))))...............(((.....)))...)))).(.((((.......))--)).)....---------------..)))...... ( -17.40)
>DroSec_CAF1 6908 69 - 1
-----CCGGCAGCUCAGGCUGCUGAGGACAAUA------------------AUCCGGAGGUUCCAAAUGCCAA--AAGCAAAU---------------CAGGAGGAUCA
-----.(((((((....))))))).(((.....------------------.))).((..((((...(((...--..)))...---------------..))))..)). ( -20.90)
>DroSim_CAF1 6565 69 - 1
-----CCGGCAGCUCAGGCUGCUGAGGAUAAUA------------------AUCCGGAGGUUCCAGAUGCCAA--AAGCAAAU---------------CAGGAGGAUCA
-----.(((((((....))))))).((((....------------------)))).((..((((.(((((...--..)))..)---------------).))))..)). ( -23.70)
>DroEre_CAF1 7020 106 - 1
UUCAUCCGGCAGCUCAGGCUGCCGAUGAAAAUAACAAUGUGCAAAAUCAGAAUCCGCAGGCUCCAGAUGCCGAUGAUGCAAAUGGGCGGGUUGAAGUGCAGGAGGA---
((((((.((((((....))))))))))))........(.((((...(((..((((((.....(((..(((.......)))..))))))))))))..)))).)....--- ( -37.30)
>consensus
_____CCGGCAGCUCAGGCUGCUGAGGAUAAUA__________________AUCCGGAGGUUCCAGAUGCCAA__AAGCAAAU_______________CAGGAGGAUCA
......(((((((....)))))))............................(((((.....))...(((.......))).......................)))... (-16.27 = -16.40 +   0.13)

alignment

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secondary structure

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dotplot

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Window 2

Location 9,578,880 – 9,578,976
Length 96
Sequences 4
Columns 96
Reading direction forward
Mean pairwise identity 70.56
Mean single sequence MFE -25.62
Consensus MFE -12.00
Energy contribution -12.25
Covariance contribution 0.25
Combinations/Pair 1.11
Mean z-score -1.98
Structure conservation index 0.47
SVM decision value 0.38
SVM RNA-class probability 0.711211
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 9578880 96 + 22407834
AUAUUGUUAUCAUCAUCAGCUGCCUGAGCUGCCGGUUGAAGAUUCCGAUCAUUGCCGUCUUCGACCUGUUGGUUCUGACCAUUCCGACUGGGAUUU
...........(((..(((((.....)))))((((((((((((..(((...)))..)))))))))).(((((...........))))).))))).. ( -25.50)
>DroSec_CAF1 6949 77 + 1
-------UAUUGUCCUCAGCAGCCUGAGCUGCCGG------------AUCAUUGCCAUCUUGGACCUGUUGGUUCUGACCAUUCCCAAUGGGAUUU
-------....((((.(((((((....))))).((------------.(((..((((.(........).))))..)))))........)))))).. ( -21.80)
>DroSim_CAF1 6606 77 + 1
-------UAUUAUCCUCAGCAGCCUGAGCUGCCGG------------AUCAUUGCCAUCUUGGACCUGUUGGUUCUGACCAUUCCCAAUGGGAUUU
-------....((((.(((((((....))))).((------------.(((..((((.(........).))))..)))))........)))))).. ( -21.50)
>DroEre_CAF1 7086 84 + 1
ACAUUGUUAUUUUCAUCGGCAGCCUGAGCUGCCGGAUGAAGAUUCCGGUCAUUGCCGCCUUGAGCCUCUUGGUGCUGGCCAU------------UU
.....(..(((((((((((((((....)))))).)))))))))..)(((((..((.(((..(.....)..))))))))))..------------.. ( -33.70)
>consensus
_______UAUUAUCAUCAGCAGCCUGAGCUGCCGG____________AUCAUUGCCAUCUUGGACCUGUUGGUUCUGACCAUUCCCAAUGGGAUUU
...............((.(((((....))))).)).............(((..((((.(........).))))..)))....(((.....)))... (-12.00 = -12.25 +   0.25)

alignment

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secondary structure

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dotplot

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Window 3

Location 9,578,880 – 9,578,976
Length 96
Sequences 4
Columns 96
Reading direction reverse
Mean pairwise identity 70.56
Mean single sequence MFE -23.85
Consensus MFE -16.30
Energy contribution -16.18
Covariance contribution -0.12
Combinations/Pair 1.19
Mean z-score -1.76
Structure conservation index 0.68
SVM decision value 1.82
SVM RNA-class probability 0.978859
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 9578880 96 - 22407834
AAAUCCCAGUCGGAAUGGUCAGAACCAACAGGUCGAAGACGGCAAUGAUCGGAAUCUUCAACCGGCAGCUCAGGCAGCUGAUGAUGAUAACAAUAU
.....((.((((...((((....))))....((((....))))..)))).)).(((.(((..((((.((....)).)))).))).)))........ ( -21.00)
>DroSec_CAF1 6949 77 - 1
AAAUCCCAUUGGGAAUGGUCAGAACCAACAGGUCCAAGAUGGCAAUGAU------------CCGGCAGCUCAGGCUGCUGAGGACAAUA-------
...((((...)))).((((....))))....((((..(((.......))------------)(((((((....))))))).))))....------- ( -25.00)
>DroSim_CAF1 6606 77 - 1
AAAUCCCAUUGGGAAUGGUCAGAACCAACAGGUCCAAGAUGGCAAUGAU------------CCGGCAGCUCAGGCUGCUGAGGAUAAUA-------
...((((...)))).((((....))))....((((..(((.......))------------)(((((((....))))))).))))....------- ( -23.10)
>DroEre_CAF1 7086 84 - 1
AA------------AUGGCCAGCACCAAGAGGCUCAAGGCGGCAAUGACCGGAAUCUUCAUCCGGCAGCUCAGGCUGCCGAUGAAAAUAACAAUGU
..------------...((((((........)))...)))((......))(..((.((((((.((((((....)))))))))))).))..)..... ( -26.30)
>consensus
AAAUCCCAUUGGGAAUGGUCAGAACCAACAGGUCCAAGACGGCAAUGAU____________CCGGCAGCUCAGGCUGCUGAGGAUAAUA_______
...(((.....))).(((......)))....(((......)))...................(((((((....)))))))................ (-16.30 = -16.18 +  -0.12)

alignment

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secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:49:35 2006