Locus 1431

Sequence ID 2R_DroMel_CAF1
Location 5,499,255 – 5,499,449
Length 194
Max. P 0.919912
window2444 window2445 window2446 window2447

overview

Window 4

Location 5,499,255 – 5,499,372
Length 117
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 93.08
Mean single sequence MFE -37.65
Consensus MFE -33.31
Energy contribution -33.12
Covariance contribution -0.19
Combinations/Pair 1.03
Mean z-score -1.39
Structure conservation index 0.88
SVM decision value 0.01
SVM RNA-class probability 0.538719
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 5499255 117 + 20766785
GGAA---AGGGGGCGGGGGUUCAGCGGGUGAUAAAUGUGCGUGAUUUGGAAUGAAUGCGCAUCGAUUAAAACCGCAGGGCAAUCAAUUUAGCGCCUUUUACGCCAAAUUGGCUCGUACAC
....---...(..((((.((((.((((.((((..((((((((............))))))))..))))...)))).))))..(((((((.(((.......))).)))))))))))..).. ( -37.20)
>DroSec_CAF1 23899 112 + 1
GG--------GGGCGGAGGUUCAGCGGGUGAUAAAUGUGCGUGAUUUGGAAUGAAUGCGCAUCGAUUAAAACCGCAGGGCAAUCAAUUUAGCGCCUUUUACGCCAAAUUGGCUCGUACAC
..--------((((....((((.((((.((((..((((((((............))))))))..))))...)))).))))...((((((.(((.......))).))))))))))...... ( -36.10)
>DroEre_CAF1 921 120 + 1
GGGGUGUCGGUGGUGGGGGUUCAGCGGGUGAUAAAUGUGCGUGAUUUGGAAUGAAUGCGCAUCGAUUAAAACCGCAGGGCAAUCAAUUUAGCGCCUUUUACGCCAAAUUGGCUCGUACAC
(((((((..(...(((..((((.((((.((((..((((((((............))))))))..))))...)))).))))..)))..)..)))))))....(((.....)))........ ( -40.10)
>DroYak_CAF1 625 111 + 1
GGGG---------CGGGGGUUCAGCGGGUGAUAAAUGUGCGUGAUUUGGAAUGAAUGCGCAUCGAUUAAAACCGCAGGGCAAUCAAUUUAGCGCCUUUUACGCCAAAUUGGCUCGUACAC
.(..---------((((.((((.((((.((((..((((((((............))))))))..))))...)))).))))..(((((((.(((.......))).)))))))))))..).. ( -37.20)
>consensus
GGGG______GGGCGGGGGUUCAGCGGGUGAUAAAUGUGCGUGAUUUGGAAUGAAUGCGCAUCGAUUAAAACCGCAGGGCAAUCAAUUUAGCGCCUUUUACGCCAAAUUGGCUCGUACAC
...............(((((((.((((.((((..((((((((............))))))))..))))...)))).))))..(((((((.(((.......))).))))))))))...... (-33.31 = -33.12 +  -0.19)

alignment

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secondary structure

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dotplot

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Window 5

Location 5,499,292 – 5,499,412
Length 120
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 98.06
Mean single sequence MFE -40.12
Consensus MFE -39.29
Energy contribution -39.10
Covariance contribution -0.19
Combinations/Pair 1.03
Mean z-score -1.98
Structure conservation index 0.98
SVM decision value 0.76
SVM RNA-class probability 0.842912
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 5499292 120 - 20766785
UGGGCGAUGGUGUCAGUUCACCCGCUGACAUUAAUUGGUUGUGUACGAGCCAAUUUGGCGUAAAAGGCGCUAAAUUGAUUGCCCUGCGGUUUUAAUCGAUGCGCAUUCAUUCCAAAUCAC
((((...((((((((((......))))))))))..((..(((((((((..(((((((((((.....)))))))))))(((((...))))).....))).))))))..)).))))...... ( -40.10)
>DroSec_CAF1 23931 120 - 1
AGGGCGAGGGUGUCAGUUCACCCGCUGACAUUAAUUGGUUGUGUACGAGCCAAUUUGGCGUAAAAGGCGCUAAAUUGAUUGCCCUGCGGUUUUAAUCGAUGCGCAUUCAUUCCAAAUCAC
((((((((((((......)))))(((.((((.........))))...)))(((((((((((.....))))))))))).)))))))((((((......))).)))................ ( -39.50)
>DroEre_CAF1 961 120 - 1
CGGGCGGGGGUGUCAGCUCACCCGCUGACAUUAAUUGGUUGUGUACGAGCCAAUUUGGCGUAAAAGGCGCUAAAUUGAUUGCCCUGCGGUUUUAAUCGAUGCGCAUUCAUUCCAAAUCAC
.((...(((((((((((......)))))))))...((..(((((((((..(((((((((((.....)))))))))))(((((...))))).....))).))))))..))..))...)).. ( -41.60)
>DroYak_CAF1 656 120 - 1
CGGGCGAGGGUGUCAGUUCACCCGCUGACAUUAAUUGGUUGUGUACGAGCCAAUUUGGCGUAAAAGGCGCUAAAUUGAUUGCCCUGCGGUUUUAAUCGAUGCGCAUUCAUUCCAAAUCAC
.(((((((((((......)))))(((.((((.........))))...)))(((((((((((.....))))))))))).))))))(((((((......))).))))............... ( -39.30)
>consensus
CGGGCGAGGGUGUCAGUUCACCCGCUGACAUUAAUUGGUUGUGUACGAGCCAAUUUGGCGUAAAAGGCGCUAAAUUGAUUGCCCUGCGGUUUUAAUCGAUGCGCAUUCAUUCCAAAUCAC
.(((....(((((((((......)))))))))...((..(((((((((..(((((((((((.....)))))))))))(((((...))))).....))).))))))..)).)))....... (-39.29 = -39.10 +  -0.19)

alignment

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secondary structure

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dotplot

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Window 6

Location 5,499,332 – 5,499,449
Length 117
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 90.72
Mean single sequence MFE -25.38
Consensus MFE -22.02
Energy contribution -22.28
Covariance contribution 0.25
Combinations/Pair 1.04
Mean z-score -1.59
Structure conservation index 0.87
SVM decision value 0.46
SVM RNA-class probability 0.744033
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 5499332 117 + 20766785
AAUCAAUUUAGCGCCUUUUACGCCAAAUUGGCUCGUACACAACCAAUUAAUGUCAGCGGGUGAACUGACACCAUCGCCCACCACCGCAUCC---CCCUUUCCCCUGUUGGCCAUCCACCC
..(((((((.(((.......))).)))))))....................(((((((((.(((..((.....))((........))....---....))).)))))))))......... ( -22.10)
>DroSec_CAF1 23971 117 + 1
AAUCAAUUUAGCGCCUUUUACGCCAAAUUGGCUCGUACACAACCAAUUAAUGUCAGCGGGUGAACUGACACCCUCGCCCUCCACCGCAUCC---CCCUCUCCCCUGUUGGCCAUCCACCC
..(((((((.(((.......))).)))))))....................(((((((((((......)))))..((........))....---...........))))))......... ( -23.50)
>DroEre_CAF1 1001 120 + 1
AAUCAAUUUAGCGCCUUUUACGCCAAAUUGGCUCGUACACAACCAAUUAAUGUCAGCGGGUGAGCUGACACCCCCGCCCGCACCCGCACCCGCACCCCUCCGCCUGCUGGCCAUCCACCC
..(((((((.(((.......))).)))))))....................(((((((((((.((.(.(......).).))....((....)).......)))))))))))......... ( -29.40)
>DroYak_CAF1 696 115 + 1
AAUCAAUUUAGCGCCUUUUACGCCAAAUUGGCUCGUACACAACCAAUUAAUGUCAGCGGGUGAACUGACACCCUCGCCCGCACCCGCACC-----CCCUCCGCCAGCCGGCCAUCCACCC
..........(((........(((.....))).......................((((((((..........))))))))...)))...-----......(((....)))......... ( -26.50)
>consensus
AAUCAAUUUAGCGCCUUUUACGCCAAAUUGGCUCGUACACAACCAAUUAAUGUCAGCGGGUGAACUGACACCCUCGCCCGCAACCGCACCC___CCCCUCCCCCUGCUGGCCAUCCACCC
..(((((((.(((.......))).)))))))....................(((((((((((......)))))..((........))..................))))))......... (-22.02 = -22.28 +   0.25)

alignment

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secondary structure

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dotplot

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Window 7

Location 5,499,332 – 5,499,449
Length 117
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 90.72
Mean single sequence MFE -41.25
Consensus MFE -38.72
Energy contribution -38.10
Covariance contribution -0.62
Combinations/Pair 1.09
Mean z-score -1.75
Structure conservation index 0.94
SVM decision value 1.13
SVM RNA-class probability 0.919912
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 5499332 117 - 20766785
GGGUGGAUGGCCAACAGGGGAAAGGG---GGAUGCGGUGGUGGGCGAUGGUGUCAGUUCACCCGCUGACAUUAAUUGGUUGUGUACGAGCCAAUUUGGCGUAAAAGGCGCUAAAUUGAUU
..(((.(..((((((........)..---.((((((((((((((((((...))).))))).)))))).))))..)))))..).)))....(((((((((((.....)))))))))))... ( -40.30)
>DroSec_CAF1 23971 117 - 1
GGGUGGAUGGCCAACAGGGGAGAGGG---GGAUGCGGUGGAGGGCGAGGGUGUCAGUUCACCCGCUGACAUUAAUUGGUUGUGUACGAGCCAAUUUGGCGUAAAAGGCGCUAAAUUGAUU
..(((.(..(((((............---...(((........)))..(((((((((......)))))))))..)))))..).)))....(((((((((((.....)))))))))))... ( -38.00)
>DroEre_CAF1 1001 120 - 1
GGGUGGAUGGCCAGCAGGCGGAGGGGUGCGGGUGCGGGUGCGGGCGGGGGUGUCAGCUCACCCGCUGACAUUAAUUGGUUGUGUACGAGCCAAUUUGGCGUAAAAGGCGCUAAAUUGAUU
..(((.(..(((((((..((........))..))).((((..(((((((((....)).).))))))..))))...))))..).)))....(((((((((((.....)))))))))))... ( -44.40)
>DroYak_CAF1 696 115 - 1
GGGUGGAUGGCCGGCUGGCGGAGGG-----GGUGCGGGUGCGGGCGAGGGUGUCAGUUCACCCGCUGACAUUAAUUGGUUGUGUACGAGCCAAUUUGGCGUAAAAGGCGCUAAAUUGAUU
..(((.(..(((((((.(((..(..-----....)...))).)))...(((((((((......)))))))))...))))..).)))....(((((((((((.....)))))))))))... ( -42.30)
>consensus
GGGUGGAUGGCCAACAGGCGAAAGGG___GGAUGCGGGGGCGGGCGAGGGUGUCAGUUCACCCGCUGACAUUAAUUGGUUGUGUACGAGCCAAUUUGGCGUAAAAGGCGCUAAAUUGAUU
..(((.(..(((((..................(((........)))..(((((((((......)))))))))..)))))..).)))....(((((((((((.....)))))))))))... (-38.72 = -38.10 +  -0.62)

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 10:04:41 2006