Locus 8738

Sequence ID 3R_DroMel_CAF1
Location 23,325,882 – 23,326,012
Length 130
Max. P 0.857650
window14037 window14038 window14039

overview

Window 7

Location 23,325,882 – 23,325,973
Length 91
Sequences 5
Columns 117
Reading direction reverse
Mean pairwise identity 88.15
Mean single sequence MFE -25.80
Consensus MFE -21.58
Energy contribution -21.58
Covariance contribution 0.00
Combinations/Pair 1.00
Mean z-score -1.57
Structure conservation index 0.84
SVM decision value 0.48
SVM RNA-class probability 0.752911
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 23325882 91 - 27905053
UGUUGGCUAAAAUUAGAGCCAGACAAAUAUUGCGCAUACGCCUAGUAUGCCAGU--------AUGCCUAUAUGCCUAGUAUCCGCGUUAAAAGGAU------------------GUU
((((((((........))))).))).((((((.((((((.....))))))))))--------))..............(((((.........))))------------------).. ( -24.70)
>DroSec_CAF1 123188 91 - 1
UGUUGGCUAAAAUUAGAGCCAGACAAAUAUUGCGCAUACGCCUAGUAUGCCAGU--------AUGCCUAUAUGCCUAGUAUCCGCGUUAAAAGGAU------------------GUU
((((((((........))))).))).((((((.((((((.....))))))))))--------))..............(((((.........))))------------------).. ( -24.70)
>DroSim_CAF1 127549 91 - 1
UGUUGGCUAAAAUUAGAGCCAGACAAAUAUUGCGCAUACGCCUAGUAUGCCAGU--------AUGCCUAUAUGCCUAGUAUCCGCGUUAAAAGGAU------------------GUU
((((((((........))))).))).((((((.((((((.....))))))))))--------))..............(((((.........))))------------------).. ( -24.70)
>DroEre_CAF1 129518 99 - 1
UGUUGGCUAAAAUUAGAGCCAGACAAAUAUUGCGCAUACGCCUAGUAUGCCAGUAUGCCAGUAUGCCUAUAUGCCUAGUAUCCGCGUUAAAAGGAU------------------GUU
((((((((........))))).))).((((((.((((((.....))))))))))))....(((((....)))))....(((((.........))))------------------).. ( -25.80)
>DroYak_CAF1 134947 117 - 1
UGUUGGCUAAAAUUAGAGCCAGACAAAUAUUGCGCAUACGCCUAGUAUGCCAGUGUGCCUAUAUGCCUAUAUGCCUAGUAUCCGCGUUAAAAGGAUGUUCUUCAUGUUGUUGAUGUU
((((((((........))))).))).((((((.((((((.....))))))))))))((.((((....)))).)).........(((((((.((.(((.....))).)).))))))). ( -29.10)
>consensus
UGUUGGCUAAAAUUAGAGCCAGACAAAUAUUGCGCAUACGCCUAGUAUGCCAGU________AUGCCUAUAUGCCUAGUAUCCGCGUUAAAAGGAU__________________GUU
((((((((........))))).)))...((((.((((((.....))))))))))...........(((..((((.........))))....)))....................... (-21.58 = -21.58 +   0.00)

alignment

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secondary structure

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Window 8

Location 23,325,904 – 23,326,012
Length 108
Sequences 6
Columns 112
Reading direction forward
Mean pairwise identity 82.87
Mean single sequence MFE -23.15
Consensus MFE -18.56
Energy contribution -18.33
Covariance contribution -0.22
Combinations/Pair 1.04
Mean z-score -2.06
Structure conservation index 0.80
SVM decision value 0.70
SVM RNA-class probability 0.826737
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 23325904 108 + 27905053
UAGGCAUAUAGGCAUACUGGCAUACUAGGCGUAUGCGCAAUAUUUGUCUGGCUCUAA---UUUUAGCCAACAAUUUGCCAGCACUUACAUGAUUAAAUUGCAGCCUCGAAC-
.((((.....((((...((((((((.....)))))).))....((((.(((((....---....)))))))))..)))).(((.((.........)).))).)))).....- ( -28.80)
>DroPse_CAF1 125351 85 + 1
------------------------CUAGGCGUAUGCGCAAUAUUUGUCUGGCUCUAA---UUUUAGCCAGCAAUUUGCCAGCACUUACAUGAUUAAAUUGCAGCCCCGAUCC
------------------------...(((...((.((((...(((.((((((....---....))))))))).))))))(((.((.........)).))).)))....... ( -21.60)
>DroSec_CAF1 123210 108 + 1
UAGGCAUAUAGGCAUACUGGCAUACUAGGCGUAUGCGCAAUAUUUGUCUGGCUCUAA---UUUUAGCCAACAAUUUGCCAGCACUUACAUGAUUAAAUUGCAGCCCCGAAC-
..(((.....((((...((((((((.....)))))).))....((((.(((((....---....)))))))))..)))).(((.((.........)).))).)))......- ( -27.90)
>DroWil_CAF1 131752 87 + 1
----------------------UACUAGGCGUAUGCGCAAUAUUUGUCUGGCUCUAAAUUUUUUAGCCAACAAUUUGCCAGCACUUACAUGAUUAAAUUGCAGCCUCGA---
----------------------..(.((((...((.((((...((((.(((((...........))))))))).))))))(((.((.........)).))).)))).).--- ( -19.80)
>DroAna_CAF1 119470 83 + 1
------------------------CUAGGCGUAUGCGCAAUAUUUGUCUGGCUCUAA---UUUUAGCCAACAAUUUGCCAGCACUUACAUGAUUAAAUUGCAGCCCC-AAU-
------------------------...(((...((.((((...((((.(((((....---....))))))))).))))))(((.((.........)).))).)))..-...- ( -19.20)
>DroPer_CAF1 125811 85 + 1
------------------------CUAGGCGUAUGCGCAAUAUUUGUCUGGCUCUAA---UUUUAGCCAGCAAUUUGCCAGCACUUACAUGAUUAAAUUGCAGCCCCGAUCC
------------------------...(((...((.((((...(((.((((((....---....))))))))).))))))(((.((.........)).))).)))....... ( -21.60)
>consensus
________________________CUAGGCGUAUGCGCAAUAUUUGUCUGGCUCUAA___UUUUAGCCAACAAUUUGCCAGCACUUACAUGAUUAAAUUGCAGCCCCGAAC_
...........................(((...((.((((...((((.(((((...........))))))))).))))))(((.((.........)).))).)))....... (-18.56 = -18.33 +  -0.22)

alignment

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secondary structure

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Window 9

Location 23,325,904 – 23,326,012
Length 108
Sequences 6
Columns 112
Reading direction reverse
Mean pairwise identity 82.87
Mean single sequence MFE -26.50
Consensus MFE -21.54
Energy contribution -21.10
Covariance contribution -0.44
Combinations/Pair 1.08
Mean z-score -2.14
Structure conservation index 0.81
SVM decision value 0.81
SVM RNA-class probability 0.857650
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 23325904 108 - 27905053
-GUUCGAGGCUGCAAUUUAAUCAUGUAAGUGCUGGCAAAUUGUUGGCUAAAA---UUAGAGCCAGACAAAUAUUGCGCAUACGCCUAGUAUGCCAGUAUGCCUAUAUGCCUA
-.....((((.(((.((((......))))))).(((...(((((((((....---....))))).))))((((((.((((((.....))))))))))))))).....)))). ( -35.00)
>DroPse_CAF1 125351 85 - 1
GGAUCGGGGCUGCAAUUUAAUCAUGUAAGUGCUGGCAAAUUGCUGGCUAAAA---UUAGAGCCAGACAAAUAUUGCGCAUACGCCUAG------------------------
......((((((((.........)))).((((..((((.(((((((((....---....)))))).)))...))))))))..))))..------------------------ ( -23.70)
>DroSec_CAF1 123210 108 - 1
-GUUCGGGGCUGCAAUUUAAUCAUGUAAGUGCUGGCAAAUUGUUGGCUAAAA---UUAGAGCCAGACAAAUAUUGCGCAUACGCCUAGUAUGCCAGUAUGCCUAUAUGCCUA
-.....((((.(((.((((......))))))).(((...(((((((((....---....))))).))))((((((.((((((.....))))))))))))))).....)))). ( -35.00)
>DroWil_CAF1 131752 87 - 1
---UCGAGGCUGCAAUUUAAUCAUGUAAGUGCUGGCAAAUUGUUGGCUAAAAAAUUUAGAGCCAGACAAAUAUUGCGCAUACGCCUAGUA----------------------
---...((((((((.........)))).((((..((((.(((((((((...........))))).))))...))))))))..))))....---------------------- ( -20.30)
>DroAna_CAF1 119470 83 - 1
-AUU-GGGGCUGCAAUUUAAUCAUGUAAGUGCUGGCAAAUUGUUGGCUAAAA---UUAGAGCCAGACAAAUAUUGCGCAUACGCCUAG------------------------
-...-.((((((((.........)))).((((..((((.(((((((((....---....))))).))))...))))))))..))))..------------------------ ( -21.30)
>DroPer_CAF1 125811 85 - 1
GGAUCGGGGCUGCAAUUUAAUCAUGUAAGUGCUGGCAAAUUGCUGGCUAAAA---UUAGAGCCAGACAAAUAUUGCGCAUACGCCUAG------------------------
......((((((((.........)))).((((..((((.(((((((((....---....)))))).)))...))))))))..))))..------------------------ ( -23.70)
>consensus
_GUUCGGGGCUGCAAUUUAAUCAUGUAAGUGCUGGCAAAUUGUUGGCUAAAA___UUAGAGCCAGACAAAUAUUGCGCAUACGCCUAG________________________
......((((((((.........)))).((((..((((.(((((((((...........)))))).)))...))))))))..)))).......................... (-21.54 = -21.10 +  -0.44)

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 13:18:35 2006