Locus 1533

Sequence ID 2L_DroMel_CAF1
Location 4,139,105 – 4,139,250
Length 145
Max. P 0.775881
window2480 window2481 window2482

overview

Window 0

Location 4,139,105 – 4,139,210
Length 105
Sequences 6
Columns 113
Reading direction forward
Mean pairwise identity 89.35
Mean single sequence MFE -32.17
Consensus MFE -26.59
Energy contribution -26.73
Covariance contribution 0.14
Combinations/Pair 1.10
Mean z-score -2.18
Structure conservation index 0.83
SVM decision value 0.54
SVM RNA-class probability 0.775881
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 4139105 105 + 22407834
CUCGAGGAGAUGCAGAUAAUGGAAUGCCAAUCAGGGGAUGCAUUUCCGAGCUCGAGUG-------CAGAGAAAGAGGAAUCGAAAUUGCAUUAUCC-UGCAGAGGGAUAAUGC
.(((((((((((((..(..(((........)))..)..)))))))))...(((.....-------..))).........))))....(((((((((-(.....)))))))))) ( -33.80)
>DroSec_CAF1 268558 105 + 1
CUCGAGGAGAUGCAGAUAAUGGAAUGCCAAUCAGGGGAUGCAUUUCCGAGCUCGAGUG-------CGGAGAAAGAGGAAUCGAAAUUGCAUUAUCC-UGCAGAGGGAUAAUGC
.(((((((((((((..(..(((........)))..)..)))))))))..((......)-------).............))))....(((((((((-(.....)))))))))) ( -33.60)
>DroSim_CAF1 272198 105 + 1
CUCGAGGAGAUGCAGAUAAUGGAAUGCCAAUCAGGGGAUGCAUUUCCGAGCUCGAGUG-------CGGAGAAAGAGGAAUCGAAAUUGCAUUAUCC-UGCAGAGGGAUAAUGC
.(((((((((((((..(..(((........)))..)..)))))))))..((......)-------).............))))....(((((((((-(.....)))))))))) ( -33.60)
>DroEre_CAF1 282543 105 + 1
CUCGAGGAGAUGCAGAUAAUGGAAUGCCAAUCAGGGAAUGCCUUUCCGAGCUCGAAUG-------CAGAGAAAGAGGAAUCGAAAUUGCAUUAUCC-UGCAGAGGGAUAAUGC
.(((((((((.(((.....(((........))).....))).)))))...(((.....-------..))).........))))....(((((((((-(.....)))))))))) ( -28.60)
>DroYak_CAF1 287133 105 + 1
CUCGAGGAGAUGCAGAUAAUGGAAUGCCAAUCAGGGGAUGCAUUUCCGAGCUCGAGUG-------CAGAGAAAGAGGAAUCGAAAUUGCAUUAUCC-UGCAGAGGGAUAAUGC
.(((((((((((((..(..(((........)))..)..)))))))))...(((.....-------..))).........))))....(((((((((-(.....)))))))))) ( -33.80)
>DroAna_CAF1 316205 113 + 1
CUCGCGGAGAUUCAGAUAAUGGGAUGCCAAUCAGGGGUUGCAUUUCCCGAUCCGUAUGCCUUAUCCGGUGAAAGGAAAAUCGAAACUGCAUUACCCCAGCAACGGGAUGAAGC
...((((.......(((((.((.((((..(((.((((.......)))))))..)))).)))))))((((.........))))...)))).(((.(((......))).)))... ( -29.60)
>consensus
CUCGAGGAGAUGCAGAUAAUGGAAUGCCAAUCAGGGGAUGCAUUUCCGAGCUCGAGUG_______CAGAGAAAGAGGAAUCGAAAUUGCAUUAUCC_UGCAGAGGGAUAAUGC
.(((((((((((((..(..(((........)))..)..)))))))))...(((....................)))...))))....(((((((((........))))))))) (-26.59 = -26.73 +   0.14)

alignment

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secondary structure

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dotplot

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Window 1

Location 4,139,105 – 4,139,210
Length 105
Sequences 6
Columns 113
Reading direction reverse
Mean pairwise identity 89.35
Mean single sequence MFE -26.25
Consensus MFE -21.98
Energy contribution -22.12
Covariance contribution 0.14
Combinations/Pair 1.10
Mean z-score -1.94
Structure conservation index 0.84
SVM decision value 0.40
SVM RNA-class probability 0.723208
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 4139105 105 - 22407834
GCAUUAUCCCUCUGCA-GGAUAAUGCAAUUUCGAUUCCUCUUUCUCUG-------CACUCGAGCUCGGAAAUGCAUCCCCUGAUUGGCAUUCCAUUAUCUGCAUCUCCUCGAG
(((((((((.......-)))))))))......................-------..(((((....(((.(((((......((((((....)))..)))))))).)))))))) ( -25.90)
>DroSec_CAF1 268558 105 - 1
GCAUUAUCCCUCUGCA-GGAUAAUGCAAUUUCGAUUCCUCUUUCUCCG-------CACUCGAGCUCGGAAAUGCAUCCCCUGAUUGGCAUUCCAUUAUCUGCAUCUCCUCGAG
(((((((((.......-)))))))))....((((.............(-------(......))..(((.(((((......((((((....)))..)))))))).))))))). ( -26.00)
>DroSim_CAF1 272198 105 - 1
GCAUUAUCCCUCUGCA-GGAUAAUGCAAUUUCGAUUCCUCUUUCUCCG-------CACUCGAGCUCGGAAAUGCAUCCCCUGAUUGGCAUUCCAUUAUCUGCAUCUCCUCGAG
(((((((((.......-)))))))))....((((.............(-------(......))..(((.(((((......((((((....)))..)))))))).))))))). ( -26.00)
>DroEre_CAF1 282543 105 - 1
GCAUUAUCCCUCUGCA-GGAUAAUGCAAUUUCGAUUCCUCUUUCUCUG-------CAUUCGAGCUCGGAAAGGCAUUCCCUGAUUGGCAUUCCAUUAUCUGCAUCUCCUCGAG
(((((((((.......-)))))))))....((((.....((((((..(-------(......))..))))))(((......((((((....)))..))))))......)))). ( -26.10)
>DroYak_CAF1 287133 105 - 1
GCAUUAUCCCUCUGCA-GGAUAAUGCAAUUUCGAUUCCUCUUUCUCUG-------CACUCGAGCUCGGAAAUGCAUCCCCUGAUUGGCAUUCCAUUAUCUGCAUCUCCUCGAG
(((((((((.......-)))))))))......................-------..(((((....(((.(((((......((((((....)))..)))))))).)))))))) ( -25.90)
>DroAna_CAF1 316205 113 - 1
GCUUCAUCCCGUUGCUGGGGUAAUGCAGUUUCGAUUUUCCUUUCACCGGAUAAGGCAUACGGAUCGGGAAAUGCAACCCCUGAUUGGCAUCCCAUUAUCUGAAUCUCCGCGAG
((...((((((....))))))...))....((((........))..(((((((((.((.(.(((((((..........))))))).).)).)).))))))).........)). ( -27.60)
>consensus
GCAUUAUCCCUCUGCA_GGAUAAUGCAAUUUCGAUUCCUCUUUCUCCG_______CACUCGAGCUCGGAAAUGCAUCCCCUGAUUGGCAUUCCAUUAUCUGCAUCUCCUCGAG
(((((((((........)))))))))....((((...(((....................)))...(((.(((((......((((((....)))..)))))))).))))))). (-21.98 = -22.12 +   0.14)

alignment

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secondary structure

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dotplot

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Window 2

Location 4,139,138 – 4,139,250
Length 112
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 83.14
Mean single sequence MFE -26.07
Consensus MFE -17.23
Energy contribution -17.15
Covariance contribution -0.08
Combinations/Pair 1.22
Mean z-score -1.83
Structure conservation index 0.66
SVM decision value -0.01
SVM RNA-class probability 0.528519
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 4139138 112 - 22407834
UUACAAAUAAAUAUAUCGAACAUCUUGCUUCGACUGAGGAGCAUUAUCCCUCUGCA-GGAUAAUGCAAUUUCGAUUCCUCUUUCUCUG-------CACUCGAGCUCGGAAAUGCAUCCCC
...............((((......(((...((..((((((((((((((.......-))))))))).........)))))..))...)-------)).))))((........))...... ( -24.70)
>DroSec_CAF1 268591 112 - 1
UUACAAAUAAAUAUGUCGAACAUCUCCCUUCGACUGGAGAGCAUUAUCCCUCUGCA-GGAUAAUGCAAUUUCGAUUCCUCUUUCUCCG-------CACUCGAGCUCGGAAAUGCAUCCCC
..............((((((........)))))).((((((((((((((.......-)))))))))......((....))..)))))(-------((.(((....)))...)))...... ( -28.90)
>DroSim_CAF1 272231 112 - 1
CUACAAAUAAAUAUAUCGAACAUCUCGCUUCGACUGGAGAGCAUUAUCCCUCUGCA-GGAUAAUGCAAUUUCGAUUCCUCUUUCUCCG-------CACUCGAGCUCGGAAAUGCAUCCCC
..........................(((.(((.(((((((((((((((.......-)))))))))......((....))..))))))-------...))))))..(((......))).. ( -26.70)
>DroEre_CAF1 282576 112 - 1
UUACAAAUAAAUAUAUUGAACAUCUCGGUACGACUGAAGAGCAUUAUCCCUCUGCA-GGAUAAUGCAAUUUCGAUUCCUCUUUCUCUG-------CAUUCGAGCUCGGAAAGGCAUUCCC
..............((((((..((((((.....))).)))(((((((((.......-)))))))))...))))))...(((((((..(-------(......))..)))))))....... ( -26.90)
>DroYak_CAF1 287166 112 - 1
UUACAAAUAAAUAUAUUGAACAUCUCGUUUCGACUGAAGAGCAUUAUCCCUCUGCA-GGAUAAUGCAAUUUCGAUUCCUCUUUCUCUG-------CACUCGAGCUCGGAAAUGCAUCCCC
......................((.((.(((((.((.((((((((((((.......-)))))))))......((........))))).-------)).)))))..))))........... ( -22.20)
>DroAna_CAF1 316238 119 - 1
AUAUACAUAUGUGUAUUGAAAAUGGCACU-CAAGGUAAAAGCUUCAUCCCGUUGCUGGGGUAAUGCAGUUUCGAUUUUCCUUUCACCGGAUAAGGCAUACGGAUCGGGAAAUGCAACCCC
((((((....))))))....(((((....-..((((....))))....)))))...(((((..((((.(..((((((.((((((....)).)))).....))))))..)..))))))))) ( -27.00)
>consensus
UUACAAAUAAAUAUAUCGAACAUCUCGCUUCGACUGAAGAGCAUUAUCCCUCUGCA_GGAUAAUGCAAUUUCGAUUCCUCUUUCUCCG_______CACUCGAGCUCGGAAAUGCAUCCCC
...............(((((........))))).......(((((((((........)))))))))..((((((...(((....................))).)))))).......... (-17.23 = -17.15 +  -0.08)

alignment

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secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:04:55 2006