Locus 1249

Sequence ID 2L_DroMel_CAF1
Location 3,305,551 – 3,305,697
Length 146
Max. P 0.998440
window2043 window2044 window2045

overview

Window 3

Location 3,305,551 – 3,305,661
Length 110
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 77.17
Mean single sequence MFE -18.24
Consensus MFE -9.50
Energy contribution -9.50
Covariance contribution 0.00
Combinations/Pair 1.00
Mean z-score -2.49
Structure conservation index 0.52
SVM decision value 2.02
SVM RNA-class probability 0.985863
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 3305551 110 + 22407834
AACAA-CACAAGUAU--------AGUAUCAAUAUAUGUAUAUAUACAUAUAUACGCUAUAUGCCCU-GCACAUGAUUAAGUAGCCCCAUUUAAUCUACUUAAACACGCGCCCCAAUUGAU
.....-..(((((((--------(((....(((((((((....)))))))))..))))))).....-((.(.((.((((((((...........)))))))).)).).)).....))).. ( -21.80)
>DroSim_CAF1 14604 105 + 1
AACAA-CACAAGUAC--------AGUAUCAAUAUAUAUAU------AUAUAUACGCUGCAGGGCAUAGCACAUGAUUAAGUAGCCCCAUUUAAUCUACUUAAACACGCGCCCCAAUUGAU
.....-..(((...(--------(((....((((((....------))))))..))))..((((...((...((.((((((((...........)))))))).)).))))))...))).. ( -18.10)
>DroEre_CAF1 22733 100 + 1
AACGA-CACAAGUAC--------AGUAUCAAUACA-------G--UAUAUAUACGCUAUAUAC-CA-GCACAUGAUUAAGUAGCCCCAUUUAAUCUACUUAAACACGCGCCCCAAUUGAU
.....-.........--------...((((((...-------(--((((((.....)))))))-..-((.(.((.((((((((...........)))))))).)).).))....)))))) ( -16.60)
>DroYak_CAF1 14738 108 + 1
AACCA-CACAAGUAC--------AGUAUCAAUAUAUAUACAUA--UACAUAUACGCUAUAUACCCA-GCACAUGAUUAAGUAGCCCCAUUUAAUCUACUUAAACACGCGCACCAAUUGAU
.....-.........--------...((((((.(((((((.((--(....))).).))))))....-((.(.((.((((((((...........)))))))).)).).))....)))))) ( -14.50)
>DroAna_CAF1 24654 107 + 1
UACAAAGGCCAAUACUUUCGAGGAGUAUCGAGCCG-------G--AAUAAA---AGUAUAUACCCU-GCACAUGAUUAAGUAGCCUCAUUUAAUCUACUUAAACACGCGCUAAAAUAAAU
......((((.((((((.....)))))).).)))(-------(--.(((..---....))).))..-((.(.((.((((((((...........)))))))).)).).)).......... ( -20.20)
>consensus
AACAA_CACAAGUAC________AGUAUCAAUAUAU_UA___A__UAUAUAUACGCUAUAUACCCU_GCACAUGAUUAAGUAGCCCCAUUUAAUCUACUUAAACACGCGCCCCAAUUGAU
...................................................................((.(.((.((((((((...........)))))))).)).).)).......... ( -9.50 =  -9.50 +   0.00)

alignment

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secondary structure

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Window 4

Location 3,305,551 – 3,305,661
Length 110
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 77.17
Mean single sequence MFE -29.70
Consensus MFE -17.74
Energy contribution -18.50
Covariance contribution 0.76
Combinations/Pair 1.15
Mean z-score -2.91
Structure conservation index 0.60
SVM decision value 3.10
SVM RNA-class probability 0.998440
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 3305551 110 - 22407834
AUCAAUUGGGGCGCGUGUUUAAGUAGAUUAAAUGGGGCUACUUAAUCAUGUGC-AGGGCAUAUAGCGUAUAUAUGUAUAUAUACAUAUAUUGAUACU--------AUACUUGUG-UUGUU
..........(((((((.((((((((...........)))))))).)))))))-((.((((((((..((((((((((....)))))))))..)..))--------)))..))).-))... ( -29.40)
>DroSim_CAF1 14604 105 - 1
AUCAAUUGGGGCGCGUGUUUAAGUAGAUUAAAUGGGGCUACUUAAUCAUGUGCUAUGCCCUGCAGCGUAUAUAU------AUAUAUAUAUUGAUACU--------GUACUUGUG-UUGUU
..((((.((((((((((.((((((((...........)))))))).)))))))....)))(((((.(((((((.------...))))))).....))--------))).....)-))).. ( -26.50)
>DroEre_CAF1 22733 100 - 1
AUCAAUUGGGGCGCGUGUUUAAGUAGAUUAAAUGGGGCUACUUAAUCAUGUGC-UG-GUAUAUAGCGUAUAUAUA--C-------UGUAUUGAUACU--------GUACUUGUG-UCGUU
.........((((((((.((((((((...........)))))))).)))))))-)(-(((((((.....))))))--)-------).....(((((.--------......)))-))... ( -30.50)
>DroYak_CAF1 14738 108 - 1
AUCAAUUGGUGCGCGUGUUUAAGUAGAUUAAAUGGGGCUACUUAAUCAUGUGC-UGGGUAUAUAGCGUAUAUGUA--UAUGUAUAUAUAUUGAUACU--------GUACUUGUG-UGGUU
((((((....(((((((.((((((((...........)))))))).)))))))-...(((((((.(((((....)--)))))))))))))))))((.--------.((....))-..)). ( -29.50)
>DroAna_CAF1 24654 107 - 1
AUUUAUUUUAGCGCGUGUUUAAGUAGAUUAAAUGAGGCUACUUAAUCAUGUGC-AGGGUAUAUACU---UUUAUU--C-------CGGCUCGAUACUCCUCGAAAGUAUUGGCCUUUGUA
..........(((((((.((((((((.((....))..)))))))).)))))))-.(((.(((....---..))))--)-------)(((.(((((((.......))))))))))...... ( -32.60)
>consensus
AUCAAUUGGGGCGCGUGUUUAAGUAGAUUAAAUGGGGCUACUUAAUCAUGUGC_AGGGUAUAUAGCGUAUAUAUA__C___UA_AUAUAUUGAUACU________GUACUUGUG_UUGUU
((((((....(((((((.((((((((...........)))))))).))))))).....((((((.....)))))).............)))))).......................... (-17.74 = -18.50 +   0.76)

alignment

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secondary structure

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Window 5

Location 3,305,582 – 3,305,697
Length 115
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 82.65
Mean single sequence MFE -29.54
Consensus MFE -20.62
Energy contribution -22.22
Covariance contribution 1.60
Combinations/Pair 1.10
Mean z-score -1.98
Structure conservation index 0.70
SVM decision value 0.66
SVM RNA-class probability 0.816034
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 3305582 115 - 22407834
CCCAGAAAUGUCGCUAUUUGGUCUUU----GCCAUUAUUUAUCAAUUGGGGCGCGUGUUUAAGUAGAUUAAAUGGGGCUACUUAAUCAUGUGC-AGGGCAUAUAGCGUAUAUAUGUAUAU
.......((((((((((...(((((.----.(((............))).(((((((.((((((((...........)))))))).)))))))-)))))..)))))).))))........ ( -33.40)
>DroSim_CAF1 14635 110 - 1
CCCAGAAAUGUCGCUGUUUAGUCUUU----GCCAUUAUUUAUCAAUUGGGGCGCGUGUUUAAGUAGAUUAAAUGGGGCUACUUAAUCAUGUGCUAUGCCCUGCAGCGUAUAUAU------
.......((((((((((...((....----.(((............)))((((((((.((((((((...........)))))))).))))))))..))...)))))).))))..------ ( -31.50)
>DroEre_CAF1 22759 114 - 1
CCCAGAAAUGUCGCUGUUUGGUCUUUGACUGCCAUUAUUUAUCAAUUGGGGCGCGUGUUUAAGUAGAUUAAAUGGGGCUACUUAAUCAUGUGC-UG-GUAUAUAGCGUAUAUAUA--C--
((((((((((..((.(((........))).))...))))).....)))))(((((((.((((((((...........)))))))).)))))))-..-(((((((.....))))))--)-- ( -30.60)
>DroYak_CAF1 14769 117 - 1
CCCAGAAAUGUCGCUGUUUGGUCUUUGACUGCCAUUAUUUAUCAAUUGGUGCGCGUGUUUAAGUAGAUUAAAUGGGGCUACUUAAUCAUGUGC-UGGGUAUAUAGCGUAUAUGUA--UAU
.......((((((((((.((.((.......((((............))))(((((((.((((((((...........)))))))).)))))))-.)).)).)))))).))))...--... ( -31.50)
>DroAna_CAF1 24689 107 - 1
UCCAAAAAUUUC-CUUUUUCUUUUCU----GCUAUUAUUUAUUUAUUUUAGCGCGUGUUUAAGUAGAUUAAAUGAGGCUACUUAAUCAUGUGC-AGGGUAUAUACU---UUUAUU--C--
............-.............----.........(((.((((((.(((((((.((((((((.((....))..)))))))).)))))))-)))))).)))..---......--.-- ( -20.70)
>consensus
CCCAGAAAUGUCGCUGUUUGGUCUUU____GCCAUUAUUUAUCAAUUGGGGCGCGUGUUUAAGUAGAUUAAAUGGGGCUACUUAAUCAUGUGC_AGGGUAUAUAGCGUAUAUAUA__C__
.......((((((((((.((((........))))................(((((((.((((((((...........)))))))).)))))))........)))))).))))........ (-20.62 = -22.22 +   1.60)

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 09:57:44 2006