Locus 6445

Sequence ID 2L_DroMel_CAF1
Location 18,107,751 – 18,107,919
Length 168
Max. P 0.918426
window10293 window10294 window10295 window10296

overview

Window 3

Location 18,107,751 – 18,107,856
Length 105
Sequences 6
Columns 115
Reading direction forward
Mean pairwise identity 79.87
Mean single sequence MFE -37.83
Consensus MFE -24.57
Energy contribution -25.07
Covariance contribution 0.50
Combinations/Pair 1.00
Mean z-score -1.60
Structure conservation index 0.65
SVM decision value 0.37
SVM RNA-class probability 0.707068
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 18107751 105 + 22407834
----AAU-GGGC---UGGGAAAAUCGAGCUGGUUUCAGCCACUUCAGUCACACUUUUGUGCUCGGCAGCCGUGUGCACUGACGCAAAGCGGAAGUGGCACUUUUCCC-AGUUGA-
----...-.(((---((((((((..(((.....))).((((((((((((((((..((((.....))))..))))).)))..(((...)))))))))))..)))))))-))))..- ( -42.10)
>DroPse_CAF1 34969 101 + 1
UACCGAUGGGGA---UGGAA-----------GCAGAAACCACUUCAGUCACACUUUUGUGCUCGGCAGCCGUGUGCACUGACGCAAAGCGGAAGUGGCACUUUUUCCGAGCUGAA
....(((((((.---(((..-----------.......)))))))).))..........((((((.((..((((.((((..(((...)))..))))))))..)).)))))).... ( -30.80)
>DroSec_CAF1 20657 105 + 1
----AAU-GGGC---UGGGAAAAUCGAGCUGGUUUCAGCCACUUCAGUCACACUCUUGUGCUCGGCAGCCGUGUGCACUGACGCAAAGCGGAAGUGGCACUUUUCCC-AGUUGA-
----...-.(((---((((((((..(((.....))).((((((((((((((((..((((.....))))..))))).)))..(((...)))))))))))..)))))))-))))..- ( -42.10)
>DroYak_CAF1 21008 105 + 1
----AAU-GGGC---UGGGAAAAUCGAGCUGGCUUUAGCCACUUCAGUCACACUUUUGUGCUCGGCAGCCGUGUGCACUGACGCAAAGCGGAAGUGGCACUUUUCCC-AGUUGA-
----...-.(((---((((((((..(((....)))..((((((((((((((((..((((.....))))..))))).)))..(((...)))))))))))..)))))))-))))..- ( -42.60)
>DroAna_CAF1 26505 99 + 1
----UGU-GGGUGGAUGGGGG----CAGGCGGCCGAGGCCACUUCAGUCACACUUUUGUGCUCGGCAUCCGUGUGCACUGACGCAAAGCGGAAGUGGCACUUUGCA------GG-
----(((-(((((..((((((----((((.(((....))).)))..))).(((....))))))).)))))((((.((((..(((...)))..))))))))...)))------..- ( -35.50)
>DroPer_CAF1 35207 101 + 1
UACCGAUGGGGC---UGGAA-----------GCAGAAACCACUUCAGUCACACUUUUGUGCUCGGCAGCCGUGUGCACUGACGCAAAGCGGAAGUGGCACUUUUUCCGAGCUGAA
.........(((---(((((-----------(.((...(((((((((((((((..((((.....))))..))))).)))..(((...))))))))))..)).))))).))))... ( -33.90)
>consensus
____AAU_GGGC___UGGGAA____GAGCUGGCUGAAGCCACUUCAGUCACACUUUUGUGCUCGGCAGCCGUGUGCACUGACGCAAAGCGGAAGUGGCACUUUUCCC_AGUUGA_
.....................................((((((((((((((((..((((.....))))..))))).)))..(((...)))))))))))................. (-24.57 = -25.07 +   0.50)

alignment

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secondary structure

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dotplot

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Window 4

Location 18,107,751 – 18,107,856
Length 105
Sequences 6
Columns 115
Reading direction reverse
Mean pairwise identity 79.87
Mean single sequence MFE -34.57
Consensus MFE -24.50
Energy contribution -24.33
Covariance contribution -0.16
Combinations/Pair 1.07
Mean z-score -1.67
Structure conservation index 0.71
SVM decision value 0.69
SVM RNA-class probability 0.822741
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 18107751 105 - 22407834
-UCAACU-GGGAAAAGUGCCACUUCCGCUUUGCGUCAGUGCACACGGCUGCCGAGCACAAAAGUGUGACUGAAGUGGCUGAAACCAGCUCGAUUUUCCCA---GCCC-AUU----
-....((-(((((((((((.(((..(((...)))..))))))).((((..(..((((((....)))).))...)..))))............))))))))---)...-...---- ( -36.90)
>DroPse_CAF1 34969 101 - 1
UUCAGCUCGGAAAAAGUGCCACUUCCGCUUUGCGUCAGUGCACACGGCUGCCGAGCACAAAAGUGUGACUGAAGUGGUUUCUGC-----------UUCCA---UCCCCAUCGGUA
........((((..((.((((((..(((...)))(((((.(((((.(((....)))......))))))))))))))))..))..-----------)))).---............ ( -30.20)
>DroSec_CAF1 20657 105 - 1
-UCAACU-GGGAAAAGUGCCACUUCCGCUUUGCGUCAGUGCACACGGCUGCCGAGCACAAGAGUGUGACUGAAGUGGCUGAAACCAGCUCGAUUUUCCCA---GCCC-AUU----
-....((-(((((((((((.(((..(((...)))..))))))).((((..(..((((((....)))).))...)..))))............))))))))---)...-...---- ( -36.90)
>DroYak_CAF1 21008 105 - 1
-UCAACU-GGGAAAAGUGCCACUUCCGCUUUGCGUCAGUGCACACGGCUGCCGAGCACAAAAGUGUGACUGAAGUGGCUAAAGCCAGCUCGAUUUUCCCA---GCCC-AUU----
-....((-(((((((((((.(((..(((...)))..)))))))........((((((((....)))........((((....))))))))).))))))))---)...-...---- ( -38.10)
>DroAna_CAF1 26505 99 - 1
-CC------UGCAAAGUGCCACUUCCGCUUUGCGUCAGUGCACACGGAUGCCGAGCACAAAAGUGUGACUGAAGUGGCCUCGGCCGCCUG----CCCCCAUCCACCC-ACA----
-..------.((((((((.......)))))))).(((((.(((((.(.(((...))))....)))))))))).(((((....)))))...----.............-...---- ( -32.30)
>DroPer_CAF1 35207 101 - 1
UUCAGCUCGGAAAAAGUGCCACUUCCGCUUUGCGUCAGUGCACACGGCUGCCGAGCACAAAAGUGUGACUGAAGUGGUUUCUGC-----------UUCCA---GCCCCAUCGGUA
....(((.((((..((.((((((..(((...)))(((((.(((((.(((....)))......))))))))))))))))..))..-----------)))))---)).......... ( -33.00)
>consensus
_UCAACU_GGGAAAAGUGCCACUUCCGCUUUGCGUCAGUGCACACGGCUGCCGAGCACAAAAGUGUGACUGAAGUGGCUUAAGCCAGCUC____UUCCCA___GCCC_AUU____
........((((.....((((((..(((...)))(((((.(((((.(.(((...))))....)))))))))))))))).................))))................ (-24.50 = -24.33 +  -0.16)

alignment

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secondary structure

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dotplot

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Window 5

Location 18,107,778 – 18,107,880
Length 102
Sequences 6
Columns 115
Reading direction forward
Mean pairwise identity 80.69
Mean single sequence MFE -36.03
Consensus MFE -25.08
Energy contribution -25.75
Covariance contribution 0.67
Combinations/Pair 1.00
Mean z-score -1.32
Structure conservation index 0.70
SVM decision value 0.12
SVM RNA-class probability 0.593069
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 18107778 102 + 22407834
CAGCCACUUCAGUCACACUUUUGUGCUCGGCAGCCGUGUGCACUGACGCAAAGCGGAAGUGGCACUUUUCCC-AGUUGA------------AGCUGGAGCGGAAUUUCAGAAUGG
..((((((((((((((((..((((.....))))..))))).)))..(((...))))))))))).......((-(((...------------.))))).................. ( -33.80)
>DroPse_CAF1 34990 107 + 1
AAACCACUUCAGUCACACUUUUGUGCUCGGCAGCCGUGUGCACUGACGCAAAGCGGAAGUGGCACUUUUUCCGAGCUGAAGCCCAACCUGAAGCUGGAGCUGGAG------CU--
...(((((((((.....((((...((((((.((..((((.((((..(((...)))..))))))))..)).)))))).))))......)))))).)))(((....)------))-- ( -38.90)
>DroSec_CAF1 20684 102 + 1
CAGCCACUUCAGUCACACUCUUGUGCUCGGCAGCCGUGUGCACUGACGCAAAGCGGAAGUGGCACUUUUCCC-AGUUGA------------AGCUGGAGCGGAAUUCCAGAAUGG
..((((((((((((((((..((((.....))))..))))).)))..(((...))))))))))).((.(((((-(((...------------.)))))...((....)).))).)) ( -36.20)
>DroEre_CAF1 28726 102 + 1
UAGCCACUUCAGUCACACUUUUGUGCUCGGCAGCCGUGUGCACUGACGCAAAGCGGAAGUGGCACUUUUCCC-AGUUGA------------AGCUGGAGCGGAAUUACAGAAUGG
..((((((((((((((((..((((.....))))..))))).)))..(((...))))))))))).......((-(((...------------.))))).................. ( -33.80)
>DroAna_CAF1 26531 93 + 1
AGGCCACUUCAGUCACACUUUUGUGCUCGGCAUCCGUGUGCACUGACGCAAAGCGGAAGUGGCACUUUGCA------GG------------GCCUGGAGCGGGAGCU----AUGU
(((((...((((((((((....((((...))))..))))).))))).((((((.(.......).)))))).------.)------------))))..(((....)))----.... ( -34.60)
>DroPer_CAF1 35228 107 + 1
AAACCACUUCAGUCACACUUUUGUGCUCGGCAGCCGUGUGCACUGACGCAAAGCGGAAGUGGCACUUUUUCCGAGCUGAAGCCCAACCUGAAGCUGGAGCUGGAG------CU--
...(((((((((.....((((...((((((.((..((((.((((..(((...)))..))))))))..)).)))))).))))......)))))).)))(((....)------))-- ( -38.90)
>consensus
AAGCCACUUCAGUCACACUUUUGUGCUCGGCAGCCGUGUGCACUGACGCAAAGCGGAAGUGGCACUUUUCCC_AGUUGA____________AGCUGGAGCGGAAGU_____AUGG
...((.((((((((((((..((((.....))))..)))))((((..(((...)))..))))...............................))))))).))............. (-25.08 = -25.75 +   0.67)

alignment

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secondary structure

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dotplot

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Window 6

Location 18,107,818 – 18,107,919
Length 101
Sequences 4
Columns 102
Reading direction forward
Mean pairwise identity 84.26
Mean single sequence MFE -25.88
Consensus MFE -24.64
Energy contribution -24.32
Covariance contribution -0.31
Combinations/Pair 1.12
Mean z-score -1.70
Structure conservation index 0.95
SVM decision value 1.12
SVM RNA-class probability 0.918426
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 18107818 101 + 22407834
CACUGACGCAAAGCGGAAGUGGCACUUUUCCCAGUUGAAGCUGGAGCGGAAUUUCAGAAUGGAUGGGGGGAUGGAAA-AUGGGAGCGGGGAAUAAGGAAUGG
((((..(((...)))..)))).((.((..((((.((.(..((((((.....))))))..).))))))..))))....-........................ ( -23.50)
>DroSim_CAF1 20881 81 + 1
CACUGACGCAAAGCGGAAGUGGCACUUUUCCCAGUUGAAGCUGGAGCGGAAUUCCAGAAUGGAUGGGGGGAUGG---------------------GGAAUGA
((((..(((...)))..))))...((..((((.(((.(..((((((.....))))))..).)))...))))..)---------------------)...... ( -27.10)
>DroEre_CAF1 28766 96 + 1
CACUGACGCAAAGCGGAAGUGGCACUUUUCCCAGUUGAAGCUGGAGCGGAAUUACAGAAUGGAUGGGGAGAUGGCGAGAU------GGGGAAUGGGGAAUGA
((((..(((...)))..))))((...((((((.(((.(..(((...........)))..).))).))))))..)).....------................ ( -24.80)
>DroYak_CAF1 21075 95 + 1
CACUGACGCAAAGCGGAAGUGGCACUUUUCCCAGUUGAAGCUGGAGCGGAAUUCCAGAAUGGACGGGGAGAUGGGGA-AU------GAGGAAUGGAGAAUGG
((((..(((...)))..))))...(.((((((.(((.(..((((((.....))))))..).))).)))))).)....-..------................ ( -28.10)
>consensus
CACUGACGCAAAGCGGAAGUGGCACUUUUCCCAGUUGAAGCUGGAGCGGAAUUCCAGAAUGGAUGGGGAGAUGG_GA_AU______GGGGAAUGGGGAAUGA
((((..(((...)))..))))...(.((((((.(((.(..((((((.....))))))..).))).)))))).)............................. (-24.64 = -24.32 +  -0.31)

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 12:11:26 2006