Locus 5926

Sequence ID 2R_DroMel_CAF1
Location 18,683,122 – 18,683,219
Length 97
Max. P 0.928060
window9508 window9509

overview

Window 8

Location 18,683,122 – 18,683,219
Length 97
Sequences 5
Columns 98
Reading direction forward
Mean pairwise identity 81.82
Mean single sequence MFE -24.42
Consensus MFE -13.76
Energy contribution -16.72
Covariance contribution 2.96
Combinations/Pair 1.14
Mean z-score -2.53
Structure conservation index 0.56
SVM decision value 1.08
SVM RNA-class probability 0.912528
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 18683122 97 + 20766785
CACAUUUUUUUUUUCGAAGUGCUUAUAAAGCAAUGAAGAGGAGGGGCUGGGUCUU-UUUACCUUAACCCCACCUUCAUCGUUUUUUUAGCCCCCGCCC
..............((..(.(((...(((((.((((((.(..((((..((((...-...))))...)))).))))))).)))))...))))..))... ( -25.80)
>DroSec_CAF1 46663 93 + 1
CACAUUUU---UUUCCAAGUGCUAAUAAAGCAAUGAGGAGGAGGGGGUGGGUCUU-UUUACCUUAACCCCACCUUCAUCGCUU-UUUAGCCCCCUCCC
........---..(((...((((.....))))....)))((((((((((((....-...........))))))......(((.-...))).)))))). ( -30.06)
>DroSim_CAF1 47013 94 + 1
CACAUUUU---UUUCCAAGUGCUAAUAAAGCAAUGAGGAGGAGGGGGUGGGUCUUUUUUACCUUAACCCCACCUUCAUCGCUU-UUUAGCCCCCGCCC
........---.........(((((.(((((.((((((.(..((((..((((.......))))...)))).))))))).))))-))))))........ ( -29.20)
>DroEre_CAF1 47629 88 + 1
CACAUUUU---UUUCCAAGUGCUAAUAAAGCGAUGAAGA----GGGGAGGCGCUU-UUUACCUUAACCCCACCCUCAGCAUU--UUUAGCCCCCGCCC
........---.........(((((......((((..((----(((..((.(.((-........)))))..)))))..))))--.)))))........ ( -16.30)
>DroYak_CAF1 47049 79 + 1
CACAUU-----UUUCCAAGUGCUAAUAAG--------AG----GGGGCGGGGCUC-UCUACCUUAACCCCACCUUCAUAAUUU-UUUAGCCCCCGCCC
..((((-----(....)))))........--------.(----(((((((((...-..........)))).......(((...-.))))))))).... ( -20.72)
>consensus
CACAUUUU___UUUCCAAGUGCUAAUAAAGCAAUGAAGAGGAGGGGGUGGGUCUU_UUUACCUUAACCCCACCUUCAUCGUUU_UUUAGCCCCCGCCC
....................(((((...(((.((((..(((.((((..(((.........)))...)))).))))))).)))...)))))........ (-13.76 = -16.72 +   2.96)

alignment

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secondary structure

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dotplot

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Window 9

Location 18,683,122 – 18,683,219
Length 97
Sequences 5
Columns 98
Reading direction reverse
Mean pairwise identity 81.82
Mean single sequence MFE -30.00
Consensus MFE -13.60
Energy contribution -15.92
Covariance contribution 2.32
Combinations/Pair 1.20
Mean z-score -2.90
Structure conservation index 0.45
SVM decision value 1.19
SVM RNA-class probability 0.928060
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 18683122 97 - 20766785
GGGCGGGGGCUAAAAAAACGAUGAAGGUGGGGUUAAGGUAAA-AAGACCCAGCCCCUCCUCUUCAUUGCUUUAUAAGCACUUCGAAAAAAAAAAUGUG
...((((((((.(.(((.(((((((((.((((((..(((...-...))).)))))).)))..)))))).))).).))).))))).............. ( -30.90)
>DroSec_CAF1 46663 93 - 1
GGGAGGGGGCUAAA-AAGCGAUGAAGGUGGGGUUAAGGUAAA-AAGACCCACCCCCUCCUCCUCAUUGCUUUAUUAGCACUUGGAAA---AAAAUGUG
..(((...((((((-((((((((((((.((((....(((...-...)))...)))).)))..)))))))))).))))).))).....---........ ( -33.70)
>DroSim_CAF1 47013 94 - 1
GGGCGGGGGCUAAA-AAGCGAUGAAGGUGGGGUUAAGGUAAAAAAGACCCACCCCCUCCUCCUCAUUGCUUUAUUAGCACUUGGAAA---AAAAUGUG
...((((.((((((-((((((((((((.((((....(((.......)))...)))).)))..)))))))))).))))).))))....---........ ( -34.80)
>DroEre_CAF1 47629 88 - 1
GGGCGGGGGCUAAA--AAUGCUGAGGGUGGGGUUAAGGUAAA-AAGCGCCUCCCC----UCUUCAUCGCUUUAUUAGCACUUGGAAA---AAAAUGUG
...((((.(((((.--((.((((((((.((((...((((...-....))))))))----))))))..)).)).))))).))))....---........ ( -26.50)
>DroYak_CAF1 47049 79 - 1
GGGCGGGGGCUAAA-AAAUUAUGAAGGUGGGGUUAAGGUAGA-GAGCCCCGCCCC----CU--------CUUAUUAGCACUUGGAAA-----AAUGUG
(((.((((((....-..(((.....)))((((((........-.)))))))))))----).--------)))....(((.((....)-----).))). ( -24.10)
>consensus
GGGCGGGGGCUAAA_AAACGAUGAAGGUGGGGUUAAGGUAAA_AAGACCCACCCCCUCCUCCUCAUUGCUUUAUUAGCACUUGGAAA___AAAAUGUG
...((((.(((((.....((((((.((.(((((...(((.......))).)))))....)).)))))).....))))).))))............... (-13.60 = -15.92 +   2.32)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:58:15 2006