Locus 4508

Sequence ID 2L_DroMel_CAF1
Location 12,925,284 – 12,925,427
Length 143
Max. P 0.998807
window7088 window7089 window7090 window7091

overview

Window 8

Location 12,925,284 – 12,925,389
Length 105
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 82.97
Mean single sequence MFE -36.24
Consensus MFE -23.52
Energy contribution -23.48
Covariance contribution -0.04
Combinations/Pair 1.15
Mean z-score -4.67
Structure conservation index 0.65
SVM decision value 3.02
SVM RNA-class probability 0.998157
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 12925284 105 + 22407834
AAUUCUUCUCAAUAUGGAAUUCGAAUCGCAAAUGCAUAUUGAAGGCUUCGUUUCUCAAAUUUUGAGAUCGUAG----UUCUUGUCUGUAAAAU-----------UUGAGAUGCGUAGCCU
........((((((((.(.((((...)).)).).))))))))(((((.(((.(((((((((((((((.((...----....))))).))))))-----------)))))).))).))))) ( -32.30)
>DroSec_CAF1 104461 105 + 1
AAAUCUUCAUAAUAUGGAGUUCGAAUGGCAAAUGCAUAUUGAAGGCUACGUUUCUCAAAUUUUGAGAUCGUAG----UUCUUGACUGUAAAAU-----------UUGAGAUGCGUAGCCU
....((((((...))))))(((((...((....))...)))))((((((((.((((((((((((((.(((...----....))))).))))))-----------)))))).)))))))). ( -36.60)
>DroSim_CAF1 108471 105 + 1
AAAUCUUCAUAAUAUGGAAUUAGAAUGGCAAAUGCAUAUUGAAGGCUACGUUUCUCAAAUUUUGAGAUCGUAG----UUCUUGACUGUAAAAU-----------UUGAGAUGCGUAGCCU
.........(((((((..(((.(.....).))).))))))).(((((((((.((((((((((((((.(((...----....))))).))))))-----------)))))).))))))))) ( -33.10)
>DroEre_CAF1 111231 105 + 1
AAUUAGUCACAAUAUGGAAAUUGAAUCGCAACUGCAUAUUGUUGGCUACGUCUCUCAGAUUUUGAGUUCGUAG----UUCUUGACUGAAAAAU-----------UUGAGAUGCGUAGCCA
........((((((((.(..(((.....))).).))))))))(((((((((.(((((((((((.(((.((...----....)))))..)))))-----------)))))).))))))))) ( -35.80)
>DroYak_CAF1 106513 118 + 1
--UUUAUCACAAUAUGGAAAUCGAAUCGCAAGUGCAUAUUGUUGGCUACGUCUCUCAGAUUUUGAGUUCGUAGUCAGUCCGUGGCUGAAAAAUUUGAGCAAAAUUUGAGAUGCGUAGCCA
--......((((((((.(...((...))....).))))))))(((((((((.((((((((((((...(((...(((((.....)))))......))).)))))))))))).))))))))) ( -43.40)
>consensus
AAUUCUUCACAAUAUGGAAUUCGAAUCGCAAAUGCAUAUUGAAGGCUACGUUUCUCAAAUUUUGAGAUCGUAG____UUCUUGACUGUAAAAU___________UUGAGAUGCGUAGCCU
........((((((((.(..............).))))))))(((((((((.((((((((((((...(((...........)))...))))))...........)))))).))))))))) (-23.52 = -23.48 +  -0.04)

alignment

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secondary structure

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dotplot

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Window 9

Location 12,925,284 – 12,925,389
Length 105
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 82.97
Mean single sequence MFE -29.46
Consensus MFE -19.65
Energy contribution -20.25
Covariance contribution 0.60
Combinations/Pair 1.15
Mean z-score -4.27
Structure conservation index 0.67
SVM decision value 3.06
SVM RNA-class probability 0.998291
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 12925284 105 - 22407834
AGGCUACGCAUCUCAA-----------AUUUUACAGACAAGAA----CUACGAUCUCAAAAUUUGAGAAACGAAGCCUUCAAUAUGCAUUUGCGAUUCGAAUUCCAUAUUGAGAAGAAUU
.((((.((..((((((-----------(((((..(((...(..----...)..))).)))))))))))..)).))))(((((((((.(((((.....)))))..)))))))))....... ( -27.50)
>DroSec_CAF1 104461 105 - 1
AGGCUACGCAUCUCAA-----------AUUUUACAGUCAAGAA----CUACGAUCUCAAAAUUUGAGAAACGUAGCCUUCAAUAUGCAUUUGCCAUUCGAACUCCAUAUUAUGAAGAUUU
.(((((((..((((((-----------(((((...(((.....----....)))...)))))))))))..)))))))(((((((((..((((.....))))...)))))..))))..... ( -27.40)
>DroSim_CAF1 108471 105 - 1
AGGCUACGCAUCUCAA-----------AUUUUACAGUCAAGAA----CUACGAUCUCAAAAUUUGAGAAACGUAGCCUUCAAUAUGCAUUUGCCAUUCUAAUUCCAUAUUAUGAAGAUUU
.(((((((..((((((-----------(((((...(((.....----....)))...)))))))))))..)))))))(((((((((...(((......)))...)))))..))))..... ( -26.60)
>DroEre_CAF1 111231 105 - 1
UGGCUACGCAUCUCAA-----------AUUUUUCAGUCAAGAA----CUACGAACUCAAAAUCUGAGAGACGUAGCCAACAAUAUGCAGUUGCGAUUCAAUUUCCAUAUUGUGACUAAUU
((((((((..(((((.-----------(((((....((.....----....))....))))).)))))..))))))))((((((((.(((((.....)))))..))))))))........ ( -31.00)
>DroYak_CAF1 106513 118 - 1
UGGCUACGCAUCUCAAAUUUUGCUCAAAUUUUUCAGCCACGGACUGACUACGAACUCAAAAUCUGAGAGACGUAGCCAACAAUAUGCACUUGCGAUUCGAUUUCCAUAUUGUGAUAAA--
((((((((..(((((.((((((..........(((((....).)))).........)))))).)))))..))))))))((((((((......((...)).....))))))))......-- ( -34.81)
>consensus
AGGCUACGCAUCUCAA___________AUUUUACAGUCAAGAA____CUACGAUCUCAAAAUUUGAGAAACGUAGCCUUCAAUAUGCAUUUGCGAUUCGAAUUCCAUAUUGUGAAGAAUU
((((((((..(((((................................................)))))..))))))))((((((((.(((((.....)))))..))))))))........ (-19.65 = -20.25 +   0.60)

alignment

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secondary structure

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dotplot

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Window 0

Location 12,925,324 – 12,925,427
Length 103
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 82.24
Mean single sequence MFE -33.12
Consensus MFE -19.94
Energy contribution -20.30
Covariance contribution 0.36
Combinations/Pair 1.12
Mean z-score -4.21
Structure conservation index 0.60
SVM decision value 2.97
SVM RNA-class probability 0.997951
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 12925324 103 + 22407834
GAAGGCUUCGUUUCUCAAAUUUUGAGAUCGUAG----UUCUUGUCUGUAAAAU-----------UUGAGAUGCGUAGCCUUACAAAAUGAUGUGG--ACUCAAAUCUUGUAAAAAUUAUG
.((((((.(((.(((((((((((((((.((...----....))))).))))))-----------)))))).))).))))))((((...(((.((.--...)).))))))).......... ( -28.50)
>DroSec_CAF1 104501 103 + 1
GAAGGCUACGUUUCUCAAAUUUUGAGAUCGUAG----UUCUUGACUGUAAAAU-----------UUGAGAUGCGUAGCCUUUCAAAAUGAUGUGG--ACUUAAAUCUUGUAAAAAUUAUU
(((((((((((.((((((((((((((.(((...----....))))).))))))-----------)))))).)))))))))))...((((((....--((.........))....)))))) ( -33.50)
>DroSim_CAF1 108511 103 + 1
GAAGGCUACGUUUCUCAAAUUUUGAGAUCGUAG----UUCUUGACUGUAAAAU-----------UUGAGAUGCGUAGCCUUACAAAAUGAUGUGG--ACUCAAAUCUUGUAAAAAUUAUG
.((((((((((.((((((((((((((.(((...----....))))).))))))-----------)))))).))))))))))((((...(((.((.--...)).))))))).......... ( -33.10)
>DroEre_CAF1 111271 105 + 1
GUUGGCUACGUCUCUCAGAUUUUGAGUUCGUAG----UUCUUGACUGAAAAAU-----------UUGAGAUGCGUAGCCAUACAAAAUGAUGUAAAAACUGGAACCUUGUAAAAAUUAGU
..(((((((((.(((((((((((.(((.((...----....)))))..)))))-----------)))))).)))))))))((((......)))).......................... ( -30.90)
>DroYak_CAF1 106551 112 + 1
GUUGGCUACGUCUCUCAGAUUUUGAGUUCGUAGUCAGUCCGUGGCUGAAAAAUUUGAGCAAAAUUUGAGAUGCGUAGCCAUACAAAAUGA--------CUUGAAUCUUGUACAAAUUAUU
..(((((((((.((((((((((((...(((...(((((.....)))))......))).)))))))))))).)))))))))(((((.((..--------.....)).)))))......... ( -39.60)
>consensus
GAAGGCUACGUUUCUCAAAUUUUGAGAUCGUAG____UUCUUGACUGUAAAAU___________UUGAGAUGCGUAGCCUUACAAAAUGAUGUGG__ACUCAAAUCUUGUAAAAAUUAUU
.((((((((((.((((((((((((...(((...........)))...))))))...........)))))).))))))))))....................................... (-19.94 = -20.30 +   0.36)

alignment

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secondary structure

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dotplot

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Window 1

Location 12,925,324 – 12,925,427
Length 103
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 82.24
Mean single sequence MFE -28.15
Consensus MFE -18.61
Energy contribution -18.37
Covariance contribution -0.24
Combinations/Pair 1.10
Mean z-score -4.60
Structure conservation index 0.66
SVM decision value 3.23
SVM RNA-class probability 0.998807
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 12925324 103 - 22407834
CAUAAUUUUUACAAGAUUUGAGU--CCACAUCAUUUUGUAAGGCUACGCAUCUCAA-----------AUUUUACAGACAAGAA----CUACGAUCUCAAAAUUUGAGAAACGAAGCCUUC
........((((((((..(((..--.....)))))))))))((((.((..((((((-----------(((((..(((...(..----...)..))).)))))))))))..)).))))... ( -24.30)
>DroSec_CAF1 104501 103 - 1
AAUAAUUUUUACAAGAUUUAAGU--CCACAUCAUUUUGAAAGGCUACGCAUCUCAA-----------AUUUUACAGUCAAGAA----CUACGAUCUCAAAAUUUGAGAAACGUAGCCUUC
...........((((((......--.......)))))).(((((((((..((((((-----------(((((...(((.....----....)))...)))))))))))..))))))))). ( -26.72)
>DroSim_CAF1 108511 103 - 1
CAUAAUUUUUACAAGAUUUGAGU--CCACAUCAUUUUGUAAGGCUACGCAUCUCAA-----------AUUUUACAGUCAAGAA----CUACGAUCUCAAAAUUUGAGAAACGUAGCCUUC
........((((((((..(((..--.....)))))))))))(((((((..((((((-----------(((((...(((.....----....)))...)))))))))))..)))))))... ( -30.00)
>DroEre_CAF1 111271 105 - 1
ACUAAUUUUUACAAGGUUCCAGUUUUUACAUCAUUUUGUAUGGCUACGCAUCUCAA-----------AUUUUUCAGUCAAGAA----CUACGAACUCAAAAUCUGAGAGACGUAGCCAAC
.........((((((((....((....))...))))))))((((((((..(((((.-----------(((((....((.....----....))....))))).)))))..)))))))).. ( -26.10)
>DroYak_CAF1 106551 112 - 1
AAUAAUUUGUACAAGAUUCAAG--------UCAUUUUGUAUGGCUACGCAUCUCAAAUUUUGCUCAAAUUUUUCAGCCACGGACUGACUACGAACUCAAAAUCUGAGAGACGUAGCCAAC
........(((((((((.....--------..)))))))))(((((((..(((((.((((((..........(((((....).)))).........)))))).)))))..)))))))... ( -33.61)
>consensus
AAUAAUUUUUACAAGAUUUAAGU__CCACAUCAUUUUGUAAGGCUACGCAUCUCAA___________AUUUUACAGUCAAGAA____CUACGAUCUCAAAAUUUGAGAAACGUAGCCUUC
.........((((((((...............))))))))((((((((..(((((................................................)))))..)))))))).. (-18.61 = -18.37 +  -0.24)

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 11:19:30 2006