Locus 6079

Sequence ID X_DroMel_CAF1
Location 15,607,058 – 15,607,320
Length 262
Max. P 0.831322
window9869 window9870 window9871 window9872

overview

Window 9

Location 15,607,058 – 15,607,178
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 89.08
Mean single sequence MFE -35.32
Consensus MFE -27.10
Energy contribution -26.74
Covariance contribution -0.36
Combinations/Pair 1.20
Mean z-score -1.75
Structure conservation index 0.77
SVM decision value 0.45
SVM RNA-class probability 0.742228
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 15607058 120 + 22224390
AUUCGCUCAUCGAGUGAUUCAAAUAUGAGAGACUACUCGAUACGAGCAGAAGCCGAACUUUUGGAGUUCAGCUGGAGCUCACUCAUUGGCAAAAUCCAAGAGAGACGCGCCAAAAUGGCA
.(((((((((((((((.(((........)))..))))))))..)))).)))(((((((((...))))))...(((.((((.(((.((((......))))))).)).)).)))....))). ( -40.10)
>DroSec_CAF1 5137 120 + 1
AUUCGCUCCUCGAGUGACUCAAAUAUGAGAGACUACUCGAUCCGAGCUGAAGCCGAACUUCUGGAGUUCAGCUGGAGCUCACUCAUUGACAAAAUCCACGAGAGACGCGCCAAAAUGGCA
....(((((((((((..((((....))))..)))..(((((..(((((..(((.((((((...)))))).)))..)))))....))))).........)))).)).))(((.....))). ( -38.40)
>DroSim_CAF1 5093 120 + 1
AUUCGCUCCUCGAGUGACUCAAAUAUGAGAGACUACUCGAUCCGAGCGGAAGCCGAACUUCUGGAGUUCAGCUGGAGCUCACUCAUUGACAAAAUCCACGAGAGACGCGCCAAAAUGACA
.(((((((.(((((((.(((........)))..)))))))...)))))))(((.((((((...)))))).)))((.((((.(((..((........)).))).)).)).))......... ( -36.80)
>DroEre_CAF1 5138 120 + 1
ACUCGCUCCUCAAGUGAUUUAAAUAUGAGAGACUACUCGAUACGAGCACAAGCGGAAAUUUUGGAGUUCAGUUGGAGCUCACUCAUAGACAAAAUCGGCGAGAGACGCGUUAAAAUGGCA
...(((..(((..(((((((...((((((......((((...)))).................((((((.....)))))).))))))....))))).))..)))..)))........... ( -27.60)
>DroYak_CAF1 5115 120 + 1
ACACGCUCCUCAAGUGAUUUUAAUAUGAGAGACUACUCGAUACGAGCGGAAGCCGAGCUUUUGGAGUUCAGUUGGAGCUCACUCAUUGACAAAGUCAACGAGCGACGCGCUAAAAUGGUC
...((((((((...(((((((...(((((......((((...))))(((((((...)))))))((((((.....)))))).)))))....)))))))..))).)).)))........... ( -33.70)
>consensus
AUUCGCUCCUCGAGUGAUUCAAAUAUGAGAGACUACUCGAUACGAGCAGAAGCCGAACUUUUGGAGUUCAGCUGGAGCUCACUCAUUGACAAAAUCCACGAGAGACGCGCCAAAAUGGCA
....((((.(((((((.(((........)))..)))))))...))))....(((((((((...))))))...(((.((((.(((...((.....))...))).)).)).)))....))). (-27.10 = -26.74 +  -0.36)

alignment

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secondary structure

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dotplot

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Window 0

Location 15,607,058 – 15,607,178
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 89.08
Mean single sequence MFE -38.82
Consensus MFE -28.40
Energy contribution -29.44
Covariance contribution 1.04
Combinations/Pair 1.09
Mean z-score -2.19
Structure conservation index 0.73
SVM decision value 0.72
SVM RNA-class probability 0.831322
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 15607058 120 - 22224390
UGCCAUUUUGGCGCGUCUCUCUUGGAUUUUGCCAAUGAGUGAGCUCCAGCUGAACUCCAAAAGUUCGGCUUCUGCUCGUAUCGAGUAGUCUCUCAUAUUUGAAUCACUCGAUGAGCGAAU
.(((.....)))((.((.(((((((......)))).))).))))...(((((((((.....)))))))))..(((((..(((((((.(..((........))..)))))))))))))... ( -41.70)
>DroSec_CAF1 5137 120 - 1
UGCCAUUUUGGCGCGUCUCUCGUGGAUUUUGUCAAUGAGUGAGCUCCAGCUGAACUCCAGAAGUUCGGCUUCAGCUCGGAUCGAGUAGUCUCUCAUAUUUGAGUCACUCGAGGAGCGAAU
.(((.....))).(((..((((.((((((.....(((((.(((((..(((((((((.....)))))))))..)))))((((......)))))))))....))))).).))))..)))... ( -45.20)
>DroSim_CAF1 5093 120 - 1
UGUCAUUUUGGCGCGUCUCUCGUGGAUUUUGUCAAUGAGUGAGCUCCAGCUGAACUCCAGAAGUUCGGCUUCCGCUCGGAUCGAGUAGUCUCUCAUAUUUGAGUCACUCGAGGAGCGAAU
........(((.((.((.(((((.(((...))).))))).)))).)))((((((((.....))))))))...(((((...((((((.(.(((........))).))))))).)))))... ( -45.40)
>DroEre_CAF1 5138 120 - 1
UGCCAUUUUAACGCGUCUCUCGCCGAUUUUGUCUAUGAGUGAGCUCCAACUGAACUCCAAAAUUUCCGCUUGUGCUCGUAUCGAGUAGUCUCUCAUAUUUAAAUCACUUGAGGAGCGAGU
...........(((..(((..(..(((((....((((((.(((.((.....)).)))...............((((((...))))))....))))))...))))).)..)))..)))... ( -25.00)
>DroYak_CAF1 5115 120 - 1
GACCAUUUUAGCGCGUCGCUCGUUGACUUUGUCAAUGAGUGAGCUCCAACUGAACUCCAAAAGCUCGGCUUCCGCUCGUAUCGAGUAGUCUCUCAUAUUAAAAUCACUUGAGGAGCGUGU
..........((((.((((((((((((...))))))))))))(((((....((.((.....)).))((((...(((((...))))))))).....................))))))))) ( -36.80)
>consensus
UGCCAUUUUGGCGCGUCUCUCGUGGAUUUUGUCAAUGAGUGAGCUCCAGCUGAACUCCAAAAGUUCGGCUUCCGCUCGUAUCGAGUAGUCUCUCAUAUUUGAAUCACUCGAGGAGCGAAU
...........(((.((.((((..(((((.....((((.(((((...(((((((((.....)))))))))...)))))....(((....)))))))....)))))...)))))))))... (-28.40 = -29.44 +   1.04)

alignment

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secondary structure

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Window 1

Location 15,607,178 – 15,607,280
Length 102
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 72.09
Mean single sequence MFE -24.76
Consensus MFE -14.86
Energy contribution -14.90
Covariance contribution 0.04
Combinations/Pair 1.14
Mean z-score -1.63
Structure conservation index 0.60
SVM decision value 0.60
SVM RNA-class probability 0.796238
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 15607178 102 - 22224390
ACGUUUGUUGUAAAACUACAAGUGGCGGAAAUGAAGUGAAUGAUAUGAGCCAUUUCAAUAUCUAAGAUAUUAG---U---------------ACGGUUCUACUUACUUUCGCUGCUUACU
..((((......))))...(((..((((((...(((((........(((((.....((((((...))))))..---.---------------..))))))))))..))))))..)))... ( -24.00)
>DroSec_CAF1 5257 105 - 1
ACGUUUGUUGUAAAACUACAAGUGGCGGAAAUGGAGUGAAUGAUAUGAGCCACUUCCAUAUCUAAGAUAUCAGAUAU---------------UAGGUUCUACUUACUUUCGCUGCUUACU
..((((......))))...(((..((((((...((((((((((((((.........))))))...(((((...))))---------------)..)))).))))..))))))..)))... ( -24.30)
>DroSim_CAF1 5213 105 - 1
ACGUUCGUUGUAAAACUACAAGUGGCGGAAAUGGAGUGAACGAUAUGAGCCAUUUCCAUAUCUAAGAUAUUAGAUAU---------------UAGGUUCUACUUACUUUCGCUGCUUACU
..((..(((....))).))(((..((((((...((((((((((.(((...))).)).((((((((....))))))))---------------...)))).))))..))))))..)))... ( -27.00)
>DroEre_CAF1 5258 102 - 1
ACGUUUGUUGUGAAACUGAAAGUAGCGGAAAUAAAGUGAA--------AUG------AAUUGAAAGUUAUGAG---UGGUA-UUGUAAUUACAGUGUUCUACUUACUUUCGCUGCUUAUU
..((((......))))...(((((((((((...(((((((--------...------.((((..(((((..(.---.....-)..))))).)))).))).))))..)))))))))))... ( -23.30)
>DroYak_CAF1 5235 114 - 1
ACGUUGGUUGUAAAACUGCAAGUAGCGUAAAUGAAGUGAACGAUAUUAAAG------AUAUGAAAGAUAUGAGAUAUGAUAGAUAUAAUUACAUUGUUCCACUCACUUUCGCUGCUUGUU
.....((((....))))((((((((((.((.(((.(((((((((.......------((((.....))))...((((.....))))......)))))).)))))).)).)))))))))). ( -25.20)
>consensus
ACGUUUGUUGUAAAACUACAAGUGGCGGAAAUGAAGUGAACGAUAUGAGCCA_UUC_AUAUCUAAGAUAUGAGAUAU_______________AAGGUUCUACUUACUUUCGCUGCUUACU
......(((....)))...(((((((((((...((((((((......................................................)))).))))..)))))))))))... (-14.86 = -14.90 +   0.04)

alignment

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secondary structure

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dotplot

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Window 2

Location 15,607,206 – 15,607,320
Length 114
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 85.51
Mean single sequence MFE -22.32
Consensus MFE -15.31
Energy contribution -15.88
Covariance contribution 0.56
Combinations/Pair 1.18
Mean z-score -2.10
Structure conservation index 0.69
SVM decision value 0.69
SVM RNA-class probability 0.823594
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 15607206 114 + 22224390
---A---CUAAUAUCUUAGAUAUUGAAAUGGCUCAUAUCAUUCACUUCAUUUCCGCCACUUGUAGUUUUACAACAAACGUAUUCAUUCCGGAUAUUCGAGUGGCAUUCGCACCCAACUCA
---.---..((((((...))))))(((((((...............))))))).((((((((..((((......))))((((((.....)))))).))))))))................ ( -21.36)
>DroSec_CAF1 5285 117 + 1
---AUAUCUGAUAUCUUAGAUAUGGAAGUGGCUCAUAUCAUUCACUCCAUUUCCGCCACUUGUAGUUUUACAACAAACGUAUUCAUUCCGGACAUUCGAGUGGCAUUCGCACCCAACUCA
---((((((((....))))))))((((((((...............))))))))((((((((..(((((((.......)))........))))...))))))))................ ( -28.06)
>DroSim_CAF1 5241 117 + 1
---AUAUCUAAUAUCUUAGAUAUGGAAAUGGCUCAUAUCGUUCACUCCAUUUCCGCCACUUGUAGUUUUACAACGAACGUAUUCAUUCCGGACAUUCGAGUGGCAUUCGCACCCAACUCA
---((((((((....))))))))((((((((...............))))))))((((((((..((((......(((....))).....))))...))))))))................ ( -28.56)
>DroYak_CAF1 5275 114 + 1
AUCAUAUCUCAUAUCUUUCAUAU------CUUUAAUAUCGUUCACUUCAUUUACGCUACUUGCAGUUUUACAACCAACGUAUUCAUACCGAACAUCCAAGUGGCAUUCGCGCCCAACUCA
.......................------.........................((((((((..(((((((.......)))........))))...))))))))................ ( -11.30)
>consensus
___AUAUCUAAUAUCUUAGAUAUGGAAAUGGCUCAUAUCAUUCACUCCAUUUCCGCCACUUGUAGUUUUACAACAAACGUAUUCAUUCCGGACAUUCGAGUGGCAUUCGCACCCAACUCA
..................(((((((.......)))))))...............((((((((..((((......))))...(((.....)))....))))))))................ (-15.31 = -15.88 +   0.56)

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 12:03:34 2006