Locus 409

Sequence ID 2L_DroMel_CAF1
Location 1,232,321 – 1,232,477
Length 156
Max. P 0.933694
window653 window654 window655 window656

overview

Window 3

Location 1,232,321 – 1,232,437
Length 116
Sequences 4
Columns 117
Reading direction forward
Mean pairwise identity 93.69
Mean single sequence MFE -27.20
Consensus MFE -26.50
Energy contribution -26.50
Covariance contribution 0.00
Combinations/Pair 1.00
Mean z-score -1.26
Structure conservation index 0.97
SVM decision value -0.01
SVM RNA-class probability 0.529823
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 1232321 116 + 22407834
AUAUAUAUGUAUUUUUUUUUGGCUGCGAUGUUUGUGCAAUUGUAUGUGAAACAUUUCUGGACUU-UUAACCCUUUUUUAUGGGUCUGACUGGGGUCGGAGGUCUUGGACUGUCGCUU
((((((((((((......(((....))).....)))))..)))))))(..(((.(((.((((((-(..(((((...(((......)))..)))))..))))))).))).)))..).. ( -27.50)
>DroSec_CAF1 9695 110 + 1
AUAU------UCUUUUUUUUGGCUGCGAUGUUUGUGCAAUUGUAUGUGAAACAUUUCUGGACUU-UUAACCCUUUUUUAUGGGUCUGACUGGGGUCGGAGGUCUUGGACUGUCGCUU
....------..............(((((((((((((....))))...))))..(((.((((((-(..(((((...(((......)))..)))))..))))))).)))..))))).. ( -27.40)
>DroSim_CAF1 5477 110 + 1
AUAU------UCUUU-UUUUGGCUGCGAUGUUUGUGCAAUUGUAUGUGAAACAUUUCUGGACUUUUUAACCCUUUUUUAUGGGUCUGACUGGGGUCGGAGGUCUUGGACUGUCGCUU
....------.....-........(((((((((((((....))))...))))..(((.((((((....((((........))))(((((....))))))))))).)))..))))).. ( -26.50)
>DroYak_CAF1 5602 105 + 1
AU-----------UUUUUUUGGCUGCGAUGUUUGUGCAAUUGUAUGUGAAACAUUUCUGGACUU-UUAACCCUUUUUUAUGGGUCUGACUGGGGUCGGAGGUCUUGGACUGUCGCUU
..-----------...........(((((((((((((....))))...))))..(((.((((((-(..(((((...(((......)))..)))))..))))))).)))..))))).. ( -27.40)
>consensus
AUAU______UCUUUUUUUUGGCUGCGAUGUUUGUGCAAUUGUAUGUGAAACAUUUCUGGACUU_UUAACCCUUUUUUAUGGGUCUGACUGGGGUCGGAGGUCUUGGACUGUCGCUU
........................(((((((((((((....))))...))))..(((.(((((......(((........)))((((((....))))))))))).)))..))))).. (-26.50 = -26.50 +   0.00) 

alignment

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secondary structure

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dotplot

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Window 4

Location 1,232,321 – 1,232,437
Length 116
Sequences 4
Columns 117
Reading direction reverse
Mean pairwise identity 93.69
Mean single sequence MFE -17.60
Consensus MFE -17.60
Energy contribution -17.60
Covariance contribution -0.00
Combinations/Pair 1.00
Mean z-score -1.74
Structure conservation index 1.00
SVM decision value 1.23
SVM RNA-class probability 0.933694
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 1232321 116 - 22407834
AAGCGACAGUCCAAGACCUCCGACCCCAGUCAGACCCAUAAAAAAGGGUUAA-AAGUCCAGAAAUGUUUCACAUACAAUUGCACAAACAUCGCAGCCAAAAAAAAAUACAUAUAUAU
..((((........(((....(((....))).(((((........)))))..-..)))......(((((..((......))...)))))))))........................ ( -17.60)
>DroSec_CAF1 9695 110 - 1
AAGCGACAGUCCAAGACCUCCGACCCCAGUCAGACCCAUAAAAAAGGGUUAA-AAGUCCAGAAAUGUUUCACAUACAAUUGCACAAACAUCGCAGCCAAAAAAAAGA------AUAU
..((((........(((....(((....))).(((((........)))))..-..)))......(((((..((......))...)))))))))..............------.... ( -17.60)
>DroSim_CAF1 5477 110 - 1
AAGCGACAGUCCAAGACCUCCGACCCCAGUCAGACCCAUAAAAAAGGGUUAAAAAGUCCAGAAAUGUUUCACAUACAAUUGCACAAACAUCGCAGCCAAAA-AAAGA------AUAU
..((((........(((....(((....))).(((((........))))).....)))......(((((..((......))...)))))))))........-.....------.... ( -17.60)
>DroYak_CAF1 5602 105 - 1
AAGCGACAGUCCAAGACCUCCGACCCCAGUCAGACCCAUAAAAAAGGGUUAA-AAGUCCAGAAAUGUUUCACAUACAAUUGCACAAACAUCGCAGCCAAAAAAA-----------AU
..((((........(((....(((....))).(((((........)))))..-..)))......(((((..((......))...)))))))))...........-----------.. ( -17.60)
>consensus
AAGCGACAGUCCAAGACCUCCGACCCCAGUCAGACCCAUAAAAAAGGGUUAA_AAGUCCAGAAAUGUUUCACAUACAAUUGCACAAACAUCGCAGCCAAAAAAAAGA______AUAU
..((((........(((....(((....))).(((((........))))).....)))......(((((..((......))...)))))))))........................ (-17.60 = -17.60 +  -0.00) 

alignment

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secondary structure

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dotplot

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Window 5

Location 1,232,358 – 1,232,477
Length 119
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 99.16
Mean single sequence MFE -33.68
Consensus MFE -34.08
Energy contribution -34.08
Covariance contribution -0.00
Combinations/Pair 1.00
Mean z-score -1.69
Structure conservation index 1.01
SVM decision value 0.04
SVM RNA-class probability 0.551487
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 1232358 119 + 22407834
AAUUGUAUGUGAAACAUUUCUGGACUU-UUAACCCUUUUUUAUGGGUCUGACUGGGGUCGGAGGUCUUGGACUGUCGCUUGCAGUCCAUUUACCUGCACAAUUGAAUGAUUUCCUAAGCC
...((((.(((((........((((((-(..(((((...(((......)))..)))))..)))))))((((((((.....))))))))))))).))))...................... ( -33.60)
>DroSec_CAF1 9726 119 + 1
AAUUGUAUGUGAAACAUUUCUGGACUU-UUAACCCUUUUUUAUGGGUCUGACUGGGGUCGGAGGUCUUGGACUGUCGCUUGCAGUCCAUUUACCUGCACAAUUGAAUGAUUUCCUAAGCC
...((((.(((((........((((((-(..(((((...(((......)))..)))))..)))))))((((((((.....))))))))))))).))))...................... ( -33.60)
>DroSim_CAF1 5507 120 + 1
AAUUGUAUGUGAAACAUUUCUGGACUUUUUAACCCUUUUUUAUGGGUCUGACUGGGGUCGGAGGUCUUGGACUGUCGCUUGCAGUCCAUUUACCUGCACAAUUGAAUGAUUUCCUAAGCC
....((.((.(((((((((.(((((((((((((((........)))).)))..))))))(.((((..((((((((.....))))))))...)))).).))...))))).)))).)).)). ( -33.60)
>DroYak_CAF1 5628 119 + 1
AAUUGUAUGUGAAACAUUUCUGGACUU-UUAACCCUUUUUUAUGGGUCUGACUGGGGUCGGAGGUCUUGGACUGUCGCUUGCAGUCCAUUUACCUGCACAAUUGAAUGAUUUCCUAAGCG
....((.((.(((((((((.(((((((-(..((((........))))......))))))(.((((..((((((((.....))))))))...)))).).))...))))).)))).)).)). ( -33.90)
>consensus
AAUUGUAUGUGAAACAUUUCUGGACUU_UUAACCCUUUUUUAUGGGUCUGACUGGGGUCGGAGGUCUUGGACUGUCGCUUGCAGUCCAUUUACCUGCACAAUUGAAUGAUUUCCUAAGCC
....((.((.(((((((((.(((((((.(((((((........)))).)))...)))))(.((((..((((((((.....))))))))...)))).).))...))))).)))).)).)). (-34.08 = -34.08 +  -0.00) 

alignment

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secondary structure

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dotplot

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Window 6

Location 1,232,358 – 1,232,477
Length 119
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 99.16
Mean single sequence MFE -29.05
Consensus MFE -28.90
Energy contribution -28.90
Covariance contribution 0.00
Combinations/Pair 1.00
Mean z-score -1.93
Structure conservation index 0.99
SVM decision value 0.42
SVM RNA-class probability 0.729076
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 1232358 119 - 22407834
GGCUUAGGAAAUCAUUCAAUUGUGCAGGUAAAUGGACUGCAAGCGACAGUCCAAGACCUCCGACCCCAGUCAGACCCAUAAAAAAGGGUUAA-AAGUCCAGAAAUGUUUCACAUACAAUU
(((((.(((...(((......)))..(((...((((((((....).)))))))..))))))(((....))).(((((........)))))..-)))))((....)).............. ( -29.10)
>DroSec_CAF1 9726 119 - 1
GGCUUAGGAAAUCAUUCAAUUGUGCAGGUAAAUGGACUGCAAGCGACAGUCCAAGACCUCCGACCCCAGUCAGACCCAUAAAAAAGGGUUAA-AAGUCCAGAAAUGUUUCACAUACAAUU
(((((.(((...(((......)))..(((...((((((((....).)))))))..))))))(((....))).(((((........)))))..-)))))((....)).............. ( -29.10)
>DroSim_CAF1 5507 120 - 1
GGCUUAGGAAAUCAUUCAAUUGUGCAGGUAAAUGGACUGCAAGCGACAGUCCAAGACCUCCGACCCCAGUCAGACCCAUAAAAAAGGGUUAAAAAGUCCAGAAAUGUUUCACAUACAAUU
(((((.(((...(((......)))..(((...((((((((....).)))))))..))))))(((....))).(((((........)))))...)))))((....)).............. ( -29.10)
>DroYak_CAF1 5628 119 - 1
CGCUUAGGAAAUCAUUCAAUUGUGCAGGUAAAUGGACUGCAAGCGACAGUCCAAGACCUCCGACCCCAGUCAGACCCAUAAAAAAGGGUUAA-AAGUCCAGAAAUGUUUCACAUACAAUU
.......((((.((((...(((..(((((...((((((((....).)))))))..))))..(((....))).(((((........)))))..-..)..))).)))))))).......... ( -28.90)
>consensus
GGCUUAGGAAAUCAUUCAAUUGUGCAGGUAAAUGGACUGCAAGCGACAGUCCAAGACCUCCGACCCCAGUCAGACCCAUAAAAAAGGGUUAA_AAGUCCAGAAAUGUUUCACAUACAAUU
.......((((.((((...(((..(((((...((((((((....).)))))))..))))..(((....))).(((((........))))).....)..))).)))))))).......... (-28.90 = -28.90 +   0.00) 

alignment

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secondary structure

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dotplot

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Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:35:22 2006