Locus 4028

Sequence ID 3R_DroMel_CAF1
Location 11,004,740 – 11,004,867
Length 127
Max. P 0.976509
window6450 window6451 window6452

overview

Window 0

Location 11,004,740 – 11,004,832
Length 92
Sequences 6
Columns 116
Reading direction forward
Mean pairwise identity 80.52
Mean single sequence MFE -27.20
Consensus MFE -24.90
Energy contribution -25.07
Covariance contribution 0.17
Combinations/Pair 1.00
Mean z-score -1.59
Structure conservation index 0.92
SVM decision value 0.78
SVM RNA-class probability 0.850154
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11004740 92 + 27905053
C--------UUAU--------------UUAGUGA--AUGCUUACCCUUCAGGGACCUGAUGUAGGACUGCCAGAAUUUCGCCUUCUUGCUGGGGCUCUCAUUGCGCCCAAUCAUUU
.--------....--------------..(((((--...(((((...((((....)))).))))).(.((.((((.......)))).)).)((((.(.....).))))..))))). ( -22.20)
>DroVir_CAF1 107479 111 + 1
C---AUAUGUUAUAGGAAUUGUGAUAUGAUAUUU--AUGCUUACCCUUCAGGGAUCUGAUGUAGGAUUGCCAGAAUUUGGCCUUCUUGCUGGGGCUCUCGUUGCGCCCAAUCAUUU
.---.((((((((((...))))))))))......--.......(((....)))...((((((((((..(((((...)))))..))))))..((((.(.....).)))).))))... ( -30.30)
>DroGri_CAF1 80008 97 + 1
G---GUAUAUUAU--------------GUGGUUA--UUGCUUACCCUUCAGGGAUCUGAUGUAGGAUUGCCAGAAUUUGGCCUUCUUGCUGGGGCUCUCAUUGCGCCCAAUCAUUU
.---.........--------------((((((.--.......(((....))).......((((((..(((((...)))))..))))))..((((.(.....).)))))))))).. ( -27.00)
>DroWil_CAF1 75228 102 + 1
GUAGUAUUGUUAU--------------UUGAUUUUUAAACUUACCCUUCAGGGAUCUGAUGUAGGAUUGCCAGAAUUUGGCCUUCUUGCUGGGGCUCUCAUUGCGCCCAAUCAUUU
.............--------------................(((....)))...((((((((((..(((((...)))))..))))))..((((.(.....).)))).))))... ( -26.10)
>DroMoj_CAF1 89367 95 + 1
C---AUAUAUCAU----------------UCAGU--ACACUUACCCUUCAGGGAUCUGAUGUAGGAUUGCCAGAAUUUGGCCUUCUUGCUGGGGCUCUCAUUGCGCCCAAUCAUUU
.---.........----------------.....--.......(((....)))...((((((((((..(((((...)))))..))))))..((((.(.....).)))).))))... ( -26.10)
>DroAna_CAF1 89893 92 + 1
A--------UUGU--------------UGGGGCU--UUACUUACCCUUCAGGGACCUGAUGUAGGAUUGCCAGAACUUGGCCUUCUUGCUGGGGCUCUCGUUGCGCCCAAUCAUUU
.--------.((.--------------..((((.--.......(((.((((....)))).((((((..(((((...)))))..)))))).)))((.......))))))...))... ( -31.50)
>consensus
C____UAU_UUAU______________UUGGUUU__AUACUUACCCUUCAGGGAUCUGAUGUAGGAUUGCCAGAAUUUGGCCUUCUUGCUGGGGCUCUCAUUGCGCCCAAUCAUUU
...........................................(((....)))...((((((((((..(((((...)))))..))))))..((((.(.....).)))).))))... (-24.90 = -25.07 +   0.17)

alignment

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secondary structure

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dotplot

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Window 1

Location 11,004,740 – 11,004,832
Length 92
Sequences 6
Columns 116
Reading direction reverse
Mean pairwise identity 80.52
Mean single sequence MFE -23.49
Consensus MFE -20.89
Energy contribution -20.67
Covariance contribution -0.22
Combinations/Pair 1.10
Mean z-score -1.41
Structure conservation index 0.89
SVM decision value 0.50
SVM RNA-class probability 0.760574
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11004740 92 - 27905053
AAAUGAUUGGGCGCAAUGAGAGCCCCAGCAAGAAGGCGAAAUUCUGGCAGUCCUACAUCAGGUCCCUGAAGGGUAAGCAU--UCACUAA--------------AUAA--------G
...((.(((((.((.......))))))))).(((.((...(((((..(((.(((.....)))...))).)))))..)).)--)).....--------------....--------. ( -21.40)
>DroVir_CAF1 107479 111 - 1
AAAUGAUUGGGCGCAACGAGAGCCCCAGCAAGAAGGCCAAAUUCUGGCAAUCCUACAUCAGAUCCCUGAAGGGUAAGCAU--AAAUAUCAUAUCACAAUUCCUAUAACAUAU---G
..(((((((((.((.......))))))((......((((.....)))).(((((...((((....)))))))))..))..--....))))).....................---. ( -25.20)
>DroGri_CAF1 80008 97 - 1
AAAUGAUUGGGCGCAAUGAGAGCCCCAGCAAGAAGGCCAAAUUCUGGCAAUCCUACAUCAGAUCCCUGAAGGGUAAGCAA--UAACCAC--------------AUAAUAUAC---C
..(((..((((.((.......))))))((......((((.....)))).(((((...((((....)))))))))..))..--......)--------------)).......---. ( -23.50)
>DroWil_CAF1 75228 102 - 1
AAAUGAUUGGGCGCAAUGAGAGCCCCAGCAAGAAGGCCAAAUUCUGGCAAUCCUACAUCAGAUCCCUGAAGGGUAAGUUUAAAAAUCAA--------------AUAACAAUACUAC
...(((((((((.(.....).)))).(((......((((.....)))).(((((...((((....)))))))))..)))....))))).--------------............. ( -22.60)
>DroMoj_CAF1 89367 95 - 1
AAAUGAUUGGGCGCAAUGAGAGCCCCAGCAAGAAGGCCAAAUUCUGGCAAUCCUACAUCAGAUCCCUGAAGGGUAAGUGU--ACUGA----------------AUGAUAUAU---G
...((.(((((.((.......))))))))).....((((.....)))).(((((...((((....)))))))))..((((--((...----------------..).)))))---. ( -22.10)
>DroAna_CAF1 89893 92 - 1
AAAUGAUUGGGCGCAACGAGAGCCCCAGCAAGAAGGCCAAGUUCUGGCAAUCCUACAUCAGGUCCCUGAAGGGUAAGUAA--AGCCCCA--------------ACAA--------U
...((.(((((.((.......((((......((..((((.....))))..)).....((((....)))).))))......--.))))))--------------))).--------. ( -26.14)
>consensus
AAAUGAUUGGGCGCAAUGAGAGCCCCAGCAAGAAGGCCAAAUUCUGGCAAUCCUACAUCAGAUCCCUGAAGGGUAAGCAU__AAACCAA______________AUAA_AUA____G
.......((((.((.......))))))((......((((.....)))).(((((...((((....)))))))))..))...................................... (-20.89 = -20.67 +  -0.22)

alignment

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secondary structure

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dotplot

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Window 2

Location 11,004,752 – 11,004,867
Length 115
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 92.32
Mean single sequence MFE -29.85
Consensus MFE -28.53
Energy contribution -28.37
Covariance contribution -0.16
Combinations/Pair 1.12
Mean z-score -1.47
Structure conservation index 0.96
SVM decision value 1.77
SVM RNA-class probability 0.976509
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11004752 115 + 27905053
AUGCUUACCCUUCAGGGACCUGAUGUAGGACUGCCAGAAUUUCGCCUUCUUGCUGGGGCUCUCAUUGCGCCCAAUCAUUUCCAAGUGGUUUUUGAACAUUUUGAUCGAUUUGUUU-----
......((((((...(((..((((((((((..((.........))..))))))..((((.(.....).)))).))))..)))))).)))....(((((..((....))..)))))----- ( -25.60)
>DroPse_CAF1 81896 120 + 1
UUACUUACCCUUCAGGGAUCUAAUGUAAGACUGCCAGAACUUGGCCUUCUUGCUGGGGCUCUCAUUGCGCCCAAUCAUUUCCAAAUGGUUCUUGAACAUUUUGAUCGAUUUGUUUCUGUU
..........((((((((((....((((((..(((((...)))))..))))))..((((.(.....).))))..............))))))))))........................ ( -30.10)
>DroWil_CAF1 75250 115 + 1
AAACUUACCCUUCAGGGAUCUGAUGUAGGAUUGCCAGAAUUUGGCCUUCUUGCUGGGGCUCUCAUUGCGCCCAAUCAUUUCCAAAUGGCUCUUGAACAUUUUGAUCGAUUUGUUU-----
........((.....(((..((((((((((..(((((...)))))..))))))..((((.(.....).)))).))))..)))....)).....(((((..((....))..)))))----- ( -31.30)
>DroMoj_CAF1 89382 115 + 1
ACACUUACCCUUCAGGGAUCUGAUGUAGGAUUGCCAGAAUUUGGCCUUCUUGCUGGGGCUCUCAUUGCGCCCAAUCAUUUCCAAAUGGUUUUUGAACAUUUUGAUCGAUUUGUUU-----
.((...(((......(((..((((((((((..(((((...)))))..))))))..((((.(.....).)))).))))..)))....)))...))((((..((....))..)))).----- ( -31.50)
>DroAna_CAF1 89905 115 + 1
UUACUUACCCUUCAGGGACCUGAUGUAGGAUUGCCAGAACUUGGCCUUCUUGCUGGGGCUCUCGUUGCGCCCAAUCAUUUCCAAAUGGCUCUUGAACAUUUUGAUCGAUUUGUUU-----
........((.....(((..((((((((((..(((((...)))))..))))))..((((.(.....).)))).))))..)))....)).....(((((..((....))..)))))----- ( -30.50)
>DroPer_CAF1 79699 120 + 1
UUACUUACCCUUCAGGGAUCUAAUGUAAGACUGCCAGAACUUGGCCUUCUUGCUGGGGCUCUCAUUGCGCCCAAUCAUUUCCAAAUGGUUCUUGAACAUUUUGAUCGAUUUGUUUCUGUU
..........((((((((((....((((((..(((((...)))))..))))))..((((.(.....).))))..............))))))))))........................ ( -30.10)
>consensus
AUACUUACCCUUCAGGGAUCUGAUGUAGGACUGCCAGAACUUGGCCUUCUUGCUGGGGCUCUCAUUGCGCCCAAUCAUUUCCAAAUGGUUCUUGAACAUUUUGAUCGAUUUGUUU_____
..........((((((((((....((((((..(((((...)))))..))))))..((((.(.....).))))..............))))))))))........................ (-28.53 = -28.37 +  -0.16)

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 11:16:12 2006