Locus 428

Sequence ID 2L_DroMel_CAF1
Location 1,256,548 – 1,256,767
Length 219
Max. P 0.816687
window696 window697 window698 window699

overview

Window 6

Location 1,256,548 – 1,256,643
Length 95
Sequences 6
Columns 101
Reading direction forward
Mean pairwise identity 85.88
Mean single sequence MFE -29.93
Consensus MFE -25.83
Energy contribution -25.17
Covariance contribution -0.66
Combinations/Pair 1.29
Mean z-score -1.89
Structure conservation index 0.86
SVM decision value 0.67
SVM RNA-class probability 0.816687
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 1256548 95 + 22407834
AAAUC--AGCUAAUUGACACAACGGACAUGCGAGGGCCAGACUUUGGCCAAAU----UUGGCCUGGCCAAAAAGGAAGCGGAAGUACUGCGGCCGCAAAAU
.....--.....................(((...(((((......(((((...----.)))))))))).....((..((((.....))))..))))).... ( -27.30)
>DroSec_CAF1 16240 94 + 1
AAAUC--AGCUAAUUGACACUACGGACAUGCGACGGCCAGACUUUGGCCAAAU----UUGGCCUGGCCAA-AAGGAAGCGGAAGCACUGCGUCCGCAAAAU
.....--...............(((((..(((..(((((......(((((...----.))))))))))..-......((....))..))))))))...... ( -29.90)
>DroSim_CAF1 16732 94 + 1
AAAUC--AGCUAAUUGACACUACGGACAUGCGACGGCCAGACUUUGGCCAAAU----UUGGCCUGGCCAA-AAGGAAGCGGAAGCACUGCGGCCGCAAAAU
.....--...............(((...((((..(((((......(((((...----.))))))))))..-......((....))..)))).)))...... ( -28.30)
>DroEre_CAF1 28965 94 + 1
AAAUC--AGCUAAUUGACACUGCGGACAUGCGACGGCCAGAUUUUGGCCAAAU----UUGGCCUGGCCAA-AAGGAAGCGGAAGCACUGUGGCCGCAACAU
...((--.((...........)).))..(((...((((((((((.....))))----)))))).(((((.-..((..((....)).)).)))))))).... ( -32.20)
>DroYak_CAF1 16971 96 + 1
AAAUCUAAGCUAAUUGACAUUACGGACAUGCGAGGGCCGGACUUUGGCCAAAU----UUGGCCUGGCCAA-AAGGAAGCGGAAGCAUUGUGGCCGCAACAU
........((...(((.(((.......)))))).((((((.((..(((((...----.))))).))))..-......((....)).....))))))..... ( -28.00)
>DroAna_CAF1 40041 97 + 1
AGGCC--UGCUAAUUGAUA-UACGAACAUGUGGCAGCUAGACUCUGGCCAGAAGUUCCUGGCCUGGCCGA-AAGGAAGCGGAAGCGUUUAAGCCGCACAAU
.((((--(((((..((...-......))..)))))).(((((...((((((......))))))...((..-..))..((....))))))).)))....... ( -33.90)
>consensus
AAAUC__AGCUAAUUGACACUACGGACAUGCGACGGCCAGACUUUGGCCAAAU____UUGGCCUGGCCAA_AAGGAAGCGGAAGCACUGCGGCCGCAAAAU
............................((((..(((((......((((((......))))))))))).........((....))........)))).... (-25.83 = -25.17 +  -0.66)

alignment

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secondary structure

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dotplot

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Window 7

Location 1,256,581 – 1,256,675
Length 94
Sequences 6
Columns 105
Reading direction forward
Mean pairwise identity 81.22
Mean single sequence MFE -29.23
Consensus MFE -21.36
Energy contribution -21.17
Covariance contribution -0.19
Combinations/Pair 1.26
Mean z-score -1.61
Structure conservation index 0.73
SVM decision value 0.43
SVM RNA-class probability 0.733936
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 1256581 94 + 22407834
GCCAGACUUUGGCCAAAU----UUGGCCUGGCCAAAAAGGAAGCGGAAGUACUGCGGCCGCAAAAUACAUUGUAAACU-------GCUAAACUGCAGGGGAAGUG
.....(((((((((...(----(((((...))))))......((((.....))))))))((((......))))...((-------((......))))..))))). ( -28.50)
>DroSec_CAF1 16273 100 + 1
GCCAGACUUUGGCCAAAU----UUGGCCUGGCCAA-AAGGAAGCGGAAGCACUGCGUCCGCAAAAUACAUUGUAAACUGCUAACUGCUAAACUGCAGGGGAAGUG
.....((((((((((...----.)))))((((...-..(((.((((.....)))).)))((((......)))).....)))).((((......))))..))))). ( -29.60)
>DroSim_CAF1 16765 100 + 1
GCCAGACUUUGGCCAAAU----UUGGCCUGGCCAA-AAGGAAGCGGAAGCACUGCGGCCGCAAAAUACAUUGUAAACUGCUAACUGCUAAACUGCAGGGGAAGUG
.....((((((((((...----.))))).((((..-.((...((....)).))..))))(((...(((...)))...)))...((((......))))..))))). ( -31.00)
>DroEre_CAF1 28998 93 + 1
GCCAGAUUUUGGCCAAAU----UUGGCCUGGCCAA-AAGGAAGCGGAAGCACUGUGGCCGCAACAUACAUUGUAAACU-------CCUAAACUGCAGGGGAAGUG
((........(((((...----.))))).(((((.-..((..((....)).)).))))))).(((.....)))...((-------(((.......)))))..... ( -29.60)
>DroYak_CAF1 17006 93 + 1
GCCGGACUUUGGCCAAAU----UUGGCCUGGCCAA-AAGGAAGCGGAAGCAUUGUGGCCGCAACAUACAUUGUAAACU-------CCUAAACUGCAGGCGAAGUG
(((((.((..(((((...----.))))).))))..-.((((.((((..((...))..)))).(((.....)))....)-------)))........)))...... ( -30.00)
>DroAna_CAF1 40073 86 + 1
GCUAGACUCUGGCCAGAAGUUCCUGGCCUGGCCGA-AAGGAAGCGGAAGCGUUUAAGCCGCACAAUGACGUACAAACUG-------C--AACU---------GUG
(((((((...((((((......))))))...((..-..))..((....)))))).))).(((...((.....))...))-------)--....---------... ( -26.70)
>consensus
GCCAGACUUUGGCCAAAU____UUGGCCUGGCCAA_AAGGAAGCGGAAGCACUGCGGCCGCAAAAUACAUUGUAAACU_______GCUAAACUGCAGGGGAAGUG
.....(((((((((((......)))))).((((....((...((....)).))..))))((((......))))..........................))))). (-21.36 = -21.17 +  -0.19)

alignment

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secondary structure

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dotplot

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Window 8

Location 1,256,675 – 1,256,767
Length 92
Sequences 3
Columns 100
Reading direction forward
Mean pairwise identity 94.00
Mean single sequence MFE -23.33
Consensus MFE -23.73
Energy contribution -23.90
Covariance contribution 0.17
Combinations/Pair 1.00
Mean z-score -1.20
Structure conservation index 1.02
SVM decision value 0.06
SVM RNA-class probability 0.565683
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 1256675 92 + 22407834
UAGCGAAUAGUGUGCGAAUGGAAGUCGAGUAAAAAUCAAGCAACUCGAAUAGAUAUA--------UAUAUCUUUAUAUCCCUGCGGGAGUCGCUCCCCUG
.(((((....(.((((...((...((((((............))))))...((((((--------........)))))))))))).)..)))))...... ( -20.40)
>DroSec_CAF1 16373 100 + 1
UAGCGAAUAGUGUGCGAAUGGAAGUCGAGUAAAAAUCAAGCAACUCGAAUAGAUAUAUAUACAUAUAUAUCUUUAUAUCCCUGCGGGAGUCGCUCCCCCG
.(((((....(.((((...(((..((((((............))))))..(((((((((....))))))))).....))).)))).)..)))))...... ( -24.80)
>DroSim_CAF1 16865 100 + 1
UAGCGAAUAGUGUGCGAAUGGAAGUCGAGUAAAAAUCAAGCAACUCGAAUAGAUAUAUAUACAUAUAUAUCUUUAUAUCCCUGCGGGAGUCGCUCCCCCG
.(((((....(.((((...(((..((((((............))))))..(((((((((....))))))))).....))).)))).)..)))))...... ( -24.80)
>consensus
UAGCGAAUAGUGUGCGAAUGGAAGUCGAGUAAAAAUCAAGCAACUCGAAUAGAUAUAUAUACAUAUAUAUCUUUAUAUCCCUGCGGGAGUCGCUCCCCCG
.(((((....(.((((...(((..((((((............))))))..(((((((((....))))))))).....))).)))).)..)))))...... (-23.73 = -23.90 +   0.17)

alignment

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secondary structure

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dotplot

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Window 9

Location 1,256,675 – 1,256,767
Length 92
Sequences 3
Columns 100
Reading direction reverse
Mean pairwise identity 94.00
Mean single sequence MFE -23.70
Consensus MFE -23.65
Energy contribution -23.60
Covariance contribution -0.05
Combinations/Pair 1.04
Mean z-score -1.38
Structure conservation index 1.00
SVM decision value 0.25
SVM RNA-class probability 0.651796
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 1256675 92 - 22407834
CAGGGGAGCGACUCCCGCAGGGAUAUAAAGAUAUA--------UAUAUCUAUUCGAGUUGCUUGAUUUUUACUCGACUUCCAUUCGCACACUAUUCGCUA
...(((((...)))))((..(((((((........--------)))))))..((((((............)))))).........))............. ( -20.30)
>DroSec_CAF1 16373 100 - 1
CGGGGGAGCGACUCCCGCAGGGAUAUAAAGAUAUAUAUGUAUAUAUAUCUAUUCGAGUUGCUUGAUUUUUACUCGACUUCCAUUCGCACACUAUUCGCUA
.(.(((((...))))).).((((.....(((((((((....)))))))))..((((((............)))))).))))................... ( -25.40)
>DroSim_CAF1 16865 100 - 1
CGGGGGAGCGACUCCCGCAGGGAUAUAAAGAUAUAUAUGUAUAUAUAUCUAUUCGAGUUGCUUGAUUUUUACUCGACUUCCAUUCGCACACUAUUCGCUA
.(.(((((...))))).).((((.....(((((((((....)))))))))..((((((............)))))).))))................... ( -25.40)
>consensus
CGGGGGAGCGACUCCCGCAGGGAUAUAAAGAUAUAUAUGUAUAUAUAUCUAUUCGAGUUGCUUGAUUUUUACUCGACUUCCAUUCGCACACUAUUCGCUA
.(((((((...)))))((..(((.....(((((((((....)))))))))..((((((............))))))..)))....))...))........ (-23.65 = -23.60 +  -0.05)

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 09:36:02 2006