Locus 1078

Sequence ID 3L_DroMel_CAF1
Location 3,150,561 – 3,150,742
Length 181
Max. P 0.951607
window1665 window1666 window1667 window1668 window1669

overview

Window 5

Location 3,150,561 – 3,150,676
Length 115
Sequences 3
Columns 115
Reading direction forward
Mean pairwise identity 92.46
Mean single sequence MFE -36.30
Consensus MFE -30.92
Energy contribution -32.03
Covariance contribution 1.11
Combinations/Pair 1.03
Mean z-score -1.98
Structure conservation index 0.85
SVM decision value 0.15
SVM RNA-class probability 0.609108
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 3150561 115 + 23771897
AAUGGUGAAAGUUGGCGCAGUUUGGAUUUGGAUGAGGGGCAGGUCAUUGUACACCAGCUCAAAAAGUUGAGCGCCUAUUGUCGUCUGAUAUUCAGACAUGUAAAGACAAUUGCUC
...((..(..(((...((((((((((((..(((((.((((.(((........))).((((((....))))))))))....)))))..).)))))))).)))...)))..)..)). ( -38.20)
>DroSec_CAF1 14350 115 + 1
AAUGGUGAAAGUUGGCGCAGUUUGGAUUUGGAUGAGGGGCAGGUCAUUGUACACCAGCUCCAAAAGUUGAGCGCCUGUCGUCGUCUGAUAUUCAGACAUGUAAAGACAAUUGCUC
................((((((.(..(((((((((.((((.(((........))).((((........)))))))).)))))(((((.....)))))...))))..))))))).. ( -38.10)
>DroEre_CAF1 14471 112 + 1
AAUGGUGAAAGUUGGCGCAGUUUGGAAUUGGAUGAGGGGCAGGUCAUUAUACUCCAGGUCCAAAAGUUGAGCGCCU---GUCGUCUGAUCGUCAGACAUGUAAAAACGAUUGCUC
...((..(..(((...(((((((((.((..(((((.((((.((..........))..(..((.....))..)))))---.)))))..))..)))))).)))...)))..)..)). ( -32.60)
>consensus
AAUGGUGAAAGUUGGCGCAGUUUGGAUUUGGAUGAGGGGCAGGUCAUUGUACACCAGCUCCAAAAGUUGAGCGCCU_U_GUCGUCUGAUAUUCAGACAUGUAAAGACAAUUGCUC
...((..(..(((...((((((((((((..(((((.((((.(((........))).((((........))))))))....)))))..).)))))))).)))...)))..)..)). (-30.92 = -32.03 +   1.11)

alignment

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secondary structure

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dotplot

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Window 6

Location 3,150,561 – 3,150,676
Length 115
Sequences 3
Columns 115
Reading direction reverse
Mean pairwise identity 92.46
Mean single sequence MFE -28.07
Consensus MFE -25.34
Energy contribution -26.01
Covariance contribution 0.67
Combinations/Pair 1.00
Mean z-score -2.03
Structure conservation index 0.90
SVM decision value 0.62
SVM RNA-class probability 0.801370
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 3150561 115 - 23771897
GAGCAAUUGUCUUUACAUGUCUGAAUAUCAGACGACAAUAGGCGCUCAACUUUUUGAGCUGGUGUACAAUGACCUGCCCCUCAUCCAAAUCCAAACUGCGCCAACUUUCACCAUU
..(((((((((.......(((((.....))))))))))).(((((((((....)))))).(((........))).)))..................)))................ ( -26.71)
>DroSec_CAF1 14350 115 - 1
GAGCAAUUGUCUUUACAUGUCUGAAUAUCAGACGACGACAGGCGCUCAACUUUUGGAGCUGGUGUACAAUGACCUGCCCCUCAUCCAAAUCCAAACUGCGCCAACUUUCACCAUU
(((....((((......((((((.....))))))..))))(((((......((((((...((.(((........))).))...))))))........)))))....)))...... ( -30.04)
>DroEre_CAF1 14471 112 - 1
GAGCAAUCGUUUUUACAUGUCUGACGAUCAGACGAC---AGGCGCUCAACUUUUGGACCUGGAGUAUAAUGACCUGCCCCUCAUCCAAUUCCAAACUGCGCCAACUUUCACCAUU
((....)).........((((((.....))))))..---.(((((......((((((..((((....................))))..))))))..)))))............. ( -27.45)
>consensus
GAGCAAUUGUCUUUACAUGUCUGAAUAUCAGACGAC_A_AGGCGCUCAACUUUUGGAGCUGGUGUACAAUGACCUGCCCCUCAUCCAAAUCCAAACUGCGCCAACUUUCACCAUU
(((..............((((((.....))))))......(((((......((((((...((.(((........))).))...))))))........)))))....)))...... (-25.34 = -26.01 +   0.67)

alignment

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secondary structure

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dotplot

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Window 7

Location 3,150,601 – 3,150,708
Length 107
Sequences 3
Columns 107
Reading direction forward
Mean pairwise identity 90.65
Mean single sequence MFE -29.20
Consensus MFE -24.85
Energy contribution -25.30
Covariance contribution 0.45
Combinations/Pair 1.04
Mean z-score -2.05
Structure conservation index 0.85
SVM decision value 0.34
SVM RNA-class probability 0.696153
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 3150601 107 + 23771897
AGGUCAUUGUACACCAGCUCAAAAAGUUGAGCGCCUAUUGUCGUCUGAUAUUCAGACAUGUAAAGACAAUUGCUCAAUUGCAUUAGCAGUUGUCGUCAUACGAAUAC
.(((........))).((((((....))))))((..(((((((((((.....))))).(....))))))).)).(((((((....)))))))(((.....))).... ( -30.60)
>DroSec_CAF1 14390 107 + 1
AGGUCAUUGUACACCAGCUCCAAAAGUUGAGCGCCUGUCGUCGUCUGAUAUUCAGACAUGUAAAGACAAUUGCUCAAUUGCUUUGGCAGUUGUCGUCAUACGAAUAC
......((((((..(((((((((((((((((((..((((...(((((.....))))).......))))..)))))))))..))))).)))))..))...)))).... ( -32.90)
>DroEre_CAF1 14511 104 + 1
AGGUCAUUAUACUCCAGGUCCAAAAGUUGAGCGCCU---GUCGUCUGAUCGUCAGACAUGUAAAAACGAUUGCUCAAUUGCUUUGGCAAUUGUCGUCAUACGAAUAC
..............(((..((((((((((((((...---((((((((.....)))))..((....))))))))))))))..)))))...)))(((.....))).... ( -24.10)
>consensus
AGGUCAUUGUACACCAGCUCCAAAAGUUGAGCGCCU_U_GUCGUCUGAUAUUCAGACAUGUAAAGACAAUUGCUCAAUUGCUUUGGCAGUUGUCGUCAUACGAAUAC
..............(((((((((.((((((((..........(((((.....))))).(((....)))...))))))))...)))).)))))(((.....))).... (-24.85 = -25.30 +   0.45)

alignment

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secondary structure

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dotplot

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Window 8

Location 3,150,636 – 3,150,742
Length 106
Sequences 3
Columns 106
Reading direction forward
Mean pairwise identity 91.19
Mean single sequence MFE -25.87
Consensus MFE -22.21
Energy contribution -23.10
Covariance contribution 0.89
Combinations/Pair 1.07
Mean z-score -2.54
Structure conservation index 0.86
SVM decision value 0.95
SVM RNA-class probability 0.887531
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 3150636 106 + 23771897
UAUUGUCGUCUGAUAUUCAGACAUGUAAAGACAAUUGCUCAAUUGCAUUAGCAGUUGUCGUCAUACGAAUACAAUUGCCAUAUCUUAUCUGAGUUUCCACCGAAAA
.....(((...((.(((((((...(((..(.((((((..(((((((....)))))))(((.....)))...)))))))..)))....))))))).))...)))... ( -23.60)
>DroSec_CAF1 14425 106 + 1
UGUCGUCGUCUGAUAUUCAGACAUGUAAAGACAAUUGCUCAAUUGCUUUGGCAGUUGUCGUCAUACGAAUACAAUUGCCAUAUCUUAUCUGAGUUUCUACCGAAAA
.....(((...((.(((((((.....((((.(((((....)))))))))(((((((((..((....))..)))))))))........))))))).))...)))... ( -29.90)
>DroEre_CAF1 14546 103 + 1
U---GUCGUCUGAUCGUCAGACAUGUAAAAACGAUUGCUCAAUUGCUUUGGCAAUUGUCGUCAUACGAAUACAAUUGCCAUAUCUUAUCCGAAUUUCCACCGAAAA
.---.(((((((.....))))).........((...((......))..((((((((((..((....))..)))))))))).........))..........))... ( -24.10)
>consensus
U_U_GUCGUCUGAUAUUCAGACAUGUAAAGACAAUUGCUCAAUUGCUUUGGCAGUUGUCGUCAUACGAAUACAAUUGCCAUAUCUUAUCUGAGUUUCCACCGAAAA
.....(((...((.(((((((..........(((((....)))))...((((((((((..((....))..)))))))))).......))))))).))...)))... (-22.21 = -23.10 +   0.89)

alignment

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secondary structure

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dotplot

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Window 9

Location 3,150,636 – 3,150,742
Length 106
Sequences 3
Columns 106
Reading direction reverse
Mean pairwise identity 91.19
Mean single sequence MFE -27.97
Consensus MFE -25.77
Energy contribution -25.67
Covariance contribution -0.11
Combinations/Pair 1.06
Mean z-score -2.45
Structure conservation index 0.92
SVM decision value 1.41
SVM RNA-class probability 0.951607
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 3150636 106 - 23771897
UUUUCGGUGGAAACUCAGAUAAGAUAUGGCAAUUGUAUUCGUAUGACGACAACUGCUAAUGCAAUUGAGCAAUUGUCUUUACAUGUCUGAAUAUCAGACGACAAUA
...(((...((.(.(((((((.(....(((((((((..(((.....)))(((.(((....))).))).)))))))))....).))))))).).))...)))..... ( -28.50)
>DroSec_CAF1 14425 106 - 1
UUUUCGGUAGAAACUCAGAUAAGAUAUGGCAAUUGUAUUCGUAUGACGACAACUGCCAAAGCAAUUGAGCAAUUGUCUUUACAUGUCUGAAUAUCAGACGACGACA
...((((((((...((......))...(((((((((..(((.....)))(((.(((....))).))).)))))))))))))).((((((.....)))))).))).. ( -26.90)
>DroEre_CAF1 14546 103 - 1
UUUUCGGUGGAAAUUCGGAUAAGAUAUGGCAAUUGUAUUCGUAUGACGACAAUUGCCAAAGCAAUUGAGCAAUCGUUUUUACAUGUCUGACGAUCAGACGAC---A
......((((((((...(((......((((((((((..((....))..))))))))))..((......)).))))))))))).((((((.....))))))..---. ( -28.50)
>consensus
UUUUCGGUGGAAACUCAGAUAAGAUAUGGCAAUUGUAUUCGUAUGACGACAACUGCCAAAGCAAUUGAGCAAUUGUCUUUACAUGUCUGAAUAUCAGACGAC_A_A
...(((...((...(((((((.(....(((((((((..(((.....)))(((.(((....))).))).)))))))))....).)))))))...))...)))..... (-25.77 = -25.67 +  -0.11)

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 09:58:29 2006