Locus 6293

Sequence ID 2L_DroMel_CAF1
Location 17,529,630 – 17,529,771
Length 141
Max. P 0.964641
window10051 window10052 window10053

overview

Window 1

Location 17,529,630 – 17,529,738
Length 108
Sequences 5
Columns 116
Reading direction forward
Mean pairwise identity 77.33
Mean single sequence MFE -27.59
Consensus MFE -17.21
Energy contribution -18.21
Covariance contribution 1.00
Combinations/Pair 1.27
Mean z-score -2.19
Structure conservation index 0.62
SVM decision value 1.57
SVM RNA-class probability 0.964641
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 17529630 108 + 22407834
UUUGGA----AGGAGCAGCAGUCUAUCAUCGGUUUCCUUUGUUGGCUAA----CUCUUCUAGCCGAACUUUUUUCCAAAGUUCAUUAAAAUCGAAGAGGAAAGAAACCCUGCAAUC
......----....((((...(((.((.(((((((........(((((.----......)))))(((((((.....)))))))....)))))))....)).)))....)))).... ( -26.60)
>DroSec_CAF1 47213 107 + 1
-----A----AGAAGCAGCAGUCUAUCAUCGCUUUCCUUUGUUGGCUGGAAGCGUUUUUUAGUCGAACUUUUUUUCAAAGUUCAUUAAAAUCGAAGAGGAAAGAAACCCUGCAAUC
-----.----.......((((..........(((((((((...(((((((((...)))))))))(((((((.....)))))))...........))))))))).....)))).... ( -26.46)
>DroSim_CAF1 46024 107 + 1
-----A----AGGAGCAGCAGUCUAUCAUCGCUUUCCUUUGUUGGCUAGAAGCGUUUUCUAGUCGAACUUUUUUUAAAAGUUCAUUAAAAUCGAAGAGGAAAGAAACCCUGCAAUC
-----.----.......((((..........(((((((((...(((((((((...)))))))))(((((((.....)))))))...........))))))))).....)))).... ( -29.66)
>DroEre_CAF1 48006 104 + 1
UUAGGAAAUGGA-GGCAGU---CUAUCAACGGUUUCCUUUGUUGACUUG---C-GCCUCUACUUGAACUUUUUUUCAAAGUUCAUUAAAAUCUAAGAGGAAAG----CCUGCAAUC
(((((...((((-(((.((---...(((((((......)))))))...)---)-)))))))..((((((((.....))))))))......))))).(((....----)))...... ( -27.60)
>DroYak_CAF1 47811 108 + 1
UUUGAAAAAGAGGAGCAGCAG-CUAUCAUGGGUUUCCCUUGUUCGCUUA---C-GCUUCAUAUCGAACUUUUUCUUAAAGUUCAUUAAAAUCUAAGAGGAAAC---CCCUGCAAUC
.................((((-.......((((((((((((...((...---.-))........(((((((.....))))))).........)))).))))))---)))))).... ( -27.61)
>consensus
UU_G_A____AGGAGCAGCAGUCUAUCAUCGGUUUCCUUUGUUGGCUAG___C_UCUUCUAGUCGAACUUUUUUUCAAAGUUCAUUAAAAUCGAAGAGGAAAGAAACCCUGCAAUC
..............((((.............(((((((((...((((((.........))))))(((((((.....)))))))...........))))))))).....)))).... (-17.21 = -18.21 +   1.00)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 2

Location 17,529,630 – 17,529,738
Length 108
Sequences 5
Columns 116
Reading direction reverse
Mean pairwise identity 77.33
Mean single sequence MFE -26.18
Consensus MFE -14.58
Energy contribution -15.65
Covariance contribution 1.07
Combinations/Pair 1.12
Mean z-score -1.69
Structure conservation index 0.56
SVM decision value -0.06
SVM RNA-class probability 0.500000
Prediction OTHER

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 17529630 108 - 22407834
GAUUGCAGGGUUUCUUUCCUCUUCGAUUUUAAUGAACUUUGGAAAAAAGUUCGGCUAGAAGAG----UUAGCCAACAAAGGAAACCGAUGAUAGACUGCUGCUCCU----UCCAAA
....(((((((((((((................(((((((.....)))))))((((((.....----))))))....)))))))))(........)..))))....----...... ( -27.30)
>DroSec_CAF1 47213 107 - 1
GAUUGCAGGGUUUCUUUCCUCUUCGAUUUUAAUGAACUUUGAAAAAAAGUUCGACUAAAAAACGCUUCCAGCCAACAAAGGAAAGCGAUGAUAGACUGCUGCUUCU----U-----
((..((((((((((((((((......(((((.((((((((.....))))))))..)))))...((.....))......))))))).......))))).)))).)).----.----- ( -23.11)
>DroSim_CAF1 46024 107 - 1
GAUUGCAGGGUUUCUUUCCUCUUCGAUUUUAAUGAACUUUUAAAAAAAGUUCGACUAGAAAACGCUUCUAGCCAACAAAGGAAAGCGAUGAUAGACUGCUGCUCCU----U-----
....((((((((((((((((.............(((((((.....)))))))(.((((((.....)))))).).....))))))).......))))).))))....----.----- ( -25.71)
>DroEre_CAF1 48006 104 - 1
GAUUGCAGG----CUUUCCUCUUAGAUUUUAAUGAACUUUGAAAAAAAGUUCAAGUAGAGGC-G---CAAGUCAACAAAGGAAACCGUUGAUAG---ACUGCC-UCCAUUUCCUAA
((.((.(((----(((((((............((((((((.....))))))))......(((-.---...))).....))))))..(((....)---)).)))-).))..)).... ( -25.50)
>DroYak_CAF1 47811 108 - 1
GAUUGCAGGG---GUUUCCUCUUAGAUUUUAAUGAACUUUAAGAAAAAGUUCGAUAUGAAGC-G---UAAGCGAACAAGGGAAACCCAUGAUAG-CUGCUGCUCCUCUUUUUCAAA
((..((((((---((((((.(((.........((((((((.....)))))))).......((-.---...))....)))))))))))..(....-)..))))...))......... ( -29.30)
>consensus
GAUUGCAGGGUUUCUUUCCUCUUCGAUUUUAAUGAACUUUGAAAAAAAGUUCGACUAGAAGA_G___CAAGCCAACAAAGGAAACCGAUGAUAGACUGCUGCUCCU____U_C_AA
....((((((((((((((((............((((((((.....)))))))).................(....)..))))))).......))))).)))).............. (-14.58 = -15.65 +   1.07)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 3

Location 17,529,666 – 17,529,771
Length 105
Sequences 5
Columns 109
Reading direction reverse
Mean pairwise identity 85.33
Mean single sequence MFE -24.20
Consensus MFE -17.61
Energy contribution -17.89
Covariance contribution 0.28
Combinations/Pair 1.21
Mean z-score -1.60
Structure conservation index 0.73
SVM decision value 0.03
SVM RNA-class probability 0.547951
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 17529666 105 - 22407834
AAGCAAGCGUAGAACUAAUUUUAGUUAGCCAGAGAUUGCAGGGUUUCUUUCCUCUUCGAUUUUAAUGAACUUUGGAAAAAAGUUCGGCUAGAAGAG----UUAGCCAAC
..............((((((((..((((((.(((((((.((((........)))).)))))))...(((((((.....))))))))))))).))))----))))..... ( -28.50)
>DroSec_CAF1 47244 109 - 1
AAGCAAGCGUAGAACUAAUUUUAGUUAGCCAGAGAUUGCAGGGUUUCUUUCCUCUUCGAUUUUAAUGAACUUUGAAAAAAAGUUCGACUAAAAAACGCUUCCAGCCAAC
..(.((((((........((((((((.....(((((((.((((........)))).)))))))...(((((((.....))))))))))))))).)))))).)....... ( -24.90)
>DroSim_CAF1 46055 109 - 1
AAGCAAGCGUAGAACUAAUUUUAGUUAACCAGAGAUUGCAGGGUUUCUUUCCUCUUCGAUUUUAAUGAACUUUUAAAAAAAGUUCGACUAGAAAACGCUUCUAGCCAAC
.((.((((((........((((((((.....(((((((.((((........)))).)))))))...(((((((.....))))))))))))))).))))))))....... ( -24.30)
>DroEre_CAF1 48042 101 - 1
AAGCUCGCGUAGAACUAAUUUUAGUUAGCCAGAGAUUGCAGG----CUUUCCUCUUAGAUUUUAAUGAACUUUGAAAAAAAGUUCAAGUAGAGGC-G---CAAGUCAAC
..(((.((....(((((....))))).(((.((((((..(((----....)))....))))))..((((((((.....))))))))......)))-)---).))).... ( -22.90)
>DroYak_CAF1 47850 102 - 1
AAGCAAGCGUAGAACUUAUUUUAGUUAGCCAGAGAUUGCAGGG---GUUUCCUCUUAGAUUUUAAUGAACUUUAAGAAAAAGUUCGAUAUGAAGC-G---UAAGCGAAC
..((..((((..((((......)))).....((((((..((((---(...)))))..))))))..((((((((.....)))))))).......))-)---)..)).... ( -20.40)
>consensus
AAGCAAGCGUAGAACUAAUUUUAGUUAGCCAGAGAUUGCAGGGUUUCUUUCCUCUUCGAUUUUAAUGAACUUUGAAAAAAAGUUCGACUAGAAGA_G___CAAGCCAAC
......((..........((((((((.....(((((((.((((........)))).)))))))...(((((((.....)))))))))))))))..........)).... (-17.61 = -17.89 +   0.28)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:07:27 2006