Locus 6072

Sequence ID 3L_DroMel_CAF1
Location 16,148,856 – 16,148,997
Length 141
Max. P 0.902160
window9745 window9746 window9747 window9748

overview

Window 5

Location 16,148,856 – 16,148,957
Length 101
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 86.34
Mean single sequence MFE -42.59
Consensus MFE -27.67
Energy contribution -27.91
Covariance contribution 0.25
Combinations/Pair 1.00
Mean z-score -2.72
Structure conservation index 0.65
SVM decision value 0.90
SVM RNA-class probability 0.878044
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 16148856 101 + 23771897
----GAAGUGACUUUUGCACCCCUUUUAAGCGCUGCCUUGAAAGUCUGGCCAGAAAUCCAGACAGCCAGACAGACAG---------------GGGUGGGAGGGGGGUGAAAGGGUUCGCC
----...(((((((((.((((((((((...(((..(((((...(((((((..............)))))))...)))---------------))))).)))))))))).))))).)))). ( -41.94)
>DroSec_CAF1 10992 102 + 1
GCGAGAAGUGACUUUUGCACCCCUUUUAAGCGCUGCCUUGAAAGUCUGGCCAGAAAUCCAGACAGCCAGACAGACAG---------------GGGUGG---CGGGGAAAAAGGGUUCGCC
(((((..(((.(....))))(((((((...(((..((((....(((((((..............))))))).....)---------------)))..)---))....)))))))))))). ( -38.94)
>DroSim_CAF1 12373 102 + 1
GCGAGAAGUGACUUUUGCACCCCUUUUAAGCGCUGCCUUGAAAGUCUGGCCAGCAAUCCAGACAGCCAGACAGACAG---------------GGGUGG---CGGGGUAAAAGGGUUCGCC
(((((..(((.(....))))((((((((..(((..((((....(((((((...(......)...))))))).....)---------------)))..)---))...))))))))))))). ( -42.80)
>DroEre_CAF1 10693 116 + 1
CCGAGAAGUGACUUUUGCACCCCUUUUAAGCGCUGCCUUGAAAGUCUGGCCAGAAAUCCAGACAGCGAGACAGCCAGACAGCCAGACUGACAGGGCGG---CGGGG-AAAAGGGUUCGCC
.((((..(((.(....))))(((((((...((((((((((..((((((((..(.....).....((......))......))))))))..))))))))---))...-))))))))))).. ( -46.70)
>consensus
GCGAGAAGUGACUUUUGCACCCCUUUUAAGCGCUGCCUUGAAAGUCUGGCCAGAAAUCCAGACAGCCAGACAGACAG_______________GGGUGG___CGGGGUAAAAGGGUUCGCC
.......(((((((((...(((((((((((......)))))))(((((((..............)))))))...............................))))...))))).)))). (-27.67 = -27.91 +   0.25)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 6

Location 16,148,856 – 16,148,957
Length 101
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 86.34
Mean single sequence MFE -36.98
Consensus MFE -24.28
Energy contribution -24.78
Covariance contribution 0.50
Combinations/Pair 1.00
Mean z-score -1.85
Structure conservation index 0.66
SVM decision value 0.20
SVM RNA-class probability 0.632527
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 16148856 101 - 23771897
GGCGAACCCUUUCACCCCCCUCCCACCC---------------CUGUCUGUCUGGCUGUCUGGAUUUCUGGCCAGACUUUCAAGGCAGCGCUUAAAAGGGGUGCAAAAGUCACUUC----
((((((....)))..........(((((---------------((((((((((((..((((((........))))))..)).)))))).)).....))))))).....))).....---- ( -32.60)
>DroSec_CAF1 10992 102 - 1
GGCGAACCCUUUUUCCCCG---CCACCC---------------CUGUCUGUCUGGCUGUCUGGAUUUCUGGCCAGACUUUCAAGGCAGCGCUUAAAAGGGGUGCAAAAGUCACUUCUCGC
.((((.(((((((....((---(...((---------------.((...((((((((............))))))))...)).))..)))...)))))))((((....).)))...)))) ( -34.30)
>DroSim_CAF1 12373 102 - 1
GGCGAACCCUUUUACCCCG---CCACCC---------------CUGUCUGUCUGGCUGUCUGGAUUGCUGGCCAGACUUUCAAGGCAGCGCUUAAAAGGGGUGCAAAAGUCACUUCUCGC
.((((.((((((((...((---(...((---------------.((...(((((((((.(......).)))))))))...)).))..)))..))))))))((((....).)))...)))) ( -36.50)
>DroEre_CAF1 10693 116 - 1
GGCGAACCCUUUU-CCCCG---CCGCCCUGUCAGUCUGGCUGUCUGGCUGUCUCGCUGUCUGGAUUUCUGGCCAGACUUUCAAGGCAGCGCUUAAAAGGGGUGCAAAAGUCACUUCUCGG
..(((.(((((((-...((---(.(((.((..((((((((((((..((.(.....).).)..)))....)))))))))..)).))).)))...)))))))((((....).)))...))). ( -44.50)
>consensus
GGCGAACCCUUUUACCCCG___CCACCC_______________CUGUCUGUCUGGCUGUCUGGAUUUCUGGCCAGACUUUCAAGGCAGCGCUUAAAAGGGGUGCAAAAGUCACUUCUCGC
(((..((((((((....((............................((((((....((((((........)))))).....))))))))....))))))))......)))......... (-24.28 = -24.78 +   0.50)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 7

Location 16,148,892 – 16,148,997
Length 105
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 87.09
Mean single sequence MFE -46.78
Consensus MFE -29.77
Energy contribution -29.64
Covariance contribution -0.13
Combinations/Pair 1.08
Mean z-score -3.86
Structure conservation index 0.64
SVM decision value 1.02
SVM RNA-class probability 0.902160
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 16148892 105 + 23771897
AAAGUCUGGCCAGAAAUCCAGACAGCCAGACAGACAG---------------GGGUGGGAGGGGGGUGAAAGGGUUCGCCCCCGCUGCGCCCCUGUCCAUCAUUUCGAUUGAGAAAUACU
...(((((((..............))))))).(((((---------------(((((.(..(((((((((....)))))))))..).))))))))))....(((((......)))))... ( -52.24)
>DroSec_CAF1 11032 102 + 1
AAAGUCUGGCCAGAAAUCCAGACAGCCAGACAGACAG---------------GGGUGG---CGGGGAAAAAGGGUUCGCCCCCGCUGCGCCCCUGUCCAUCGUUUCGAUUGAGAAAUACU
...(((((((..............))))))).(((((---------------((((((---(((((.............))))))..))))))))))....(((((......)))))... ( -45.66)
>DroSim_CAF1 12413 102 + 1
AAAGUCUGGCCAGCAAUCCAGACAGCCAGACAGACAG---------------GGGUGG---CGGGGUAAAAGGGUUCGCCCCCGCUGCGCCCCUGUCCAUCAUUUCGAUUGAGAAAUACU
...(((((((...(......)...))))))).(((((---------------((((((---(((((.............))))))..))))))))))....(((((......)))))... ( -45.92)
>DroEre_CAF1 10733 116 + 1
AAAGUCUGGCCAGAAAUCCAGACAGCGAGACAGCCAGACAGCCAGACUGACAGGGCGG---CGGGG-AAAAGGGUUCGCCCCCGCUGCGCCCCUGUCCACGAUUUCGAUUGAGAAAUACU
..((((((((..(.....).....((......))......))))))))((((((((((---(((((-............)))))))))...))))))....(((((......)))))... ( -43.30)
>consensus
AAAGUCUGGCCAGAAAUCCAGACAGCCAGACAGACAG_______________GGGUGG___CGGGGUAAAAGGGUUCGCCCCCGCUGCGCCCCUGUCCAUCAUUUCGAUUGAGAAAUACU
...((((((........)))))).....(((((...................(((((....(((((.............)))))...))))))))))....(((((......)))))... (-29.77 = -29.64 +  -0.13)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 8

Location 16,148,892 – 16,148,997
Length 105
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 87.09
Mean single sequence MFE -46.98
Consensus MFE -29.06
Energy contribution -29.44
Covariance contribution 0.38
Combinations/Pair 1.06
Mean z-score -3.66
Structure conservation index 0.62
SVM decision value 0.81
SVM RNA-class probability 0.855761
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 16148892 105 - 23771897
AGUAUUUCUCAAUCGAAAUGAUGGACAGGGGCGCAGCGGGGGCGAACCCUUUCACCCCCCUCCCACCC---------------CUGUCUGUCUGGCUGUCUGGAUUUCUGGCCAGACUUU
((((((((......)))))((((((((((((.(.((.(((((.(((....))).)))))))..).)))---------------)))))))))..)))((((((........))))))... ( -47.20)
>DroSec_CAF1 11032 102 - 1
AGUAUUUCUCAAUCGAAACGAUGGACAGGGGCGCAGCGGGGGCGAACCCUUUUUCCCCG---CCACCC---------------CUGUCUGUCUGGCUGUCUGGAUUUCUGGCCAGACUUU
(((.((((......)))).((((((((((((.(..(((((((.((.....)).))))))---)).)))---------------)))))))))..)))((((((........))))))... ( -45.20)
>DroSim_CAF1 12413 102 - 1
AGUAUUUCUCAAUCGAAAUGAUGGACAGGGGCGCAGCGGGGGCGAACCCUUUUACCCCG---CCACCC---------------CUGUCUGUCUGGCUGUCUGGAUUGCUGGCCAGACUUU
..((((((......))))))..(((((((((.(..((((((.............)))))---)).)))---------------))))))(((((((((.(......).)))))))))... ( -46.92)
>DroEre_CAF1 10733 116 - 1
AGUAUUUCUCAAUCGAAAUCGUGGACAGGGGCGCAGCGGGGGCGAACCCUUUU-CCCCG---CCGCCCUGUCAGUCUGGCUGUCUGGCUGUCUCGCUGUCUGGAUUUCUGGCCAGACUUU
.(.(((((......))))))(((((((((((((..(((((((.((....)).)-)))))---)))))))(((((.(.....).))))))))).))).((((((........))))))... ( -48.60)
>consensus
AGUAUUUCUCAAUCGAAAUGAUGGACAGGGGCGCAGCGGGGGCGAACCCUUUUACCCCG___CCACCC_______________CUGUCUGUCUGGCUGUCUGGAUUUCUGGCCAGACUUU
((((((((......)))))((..((((((((.(.....((((.(((....))).)))).....).)))...............)))))..))..)))((((((........))))))... (-29.06 = -29.44 +   0.38)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:09:12 2006