Locus 3692

Sequence ID 3L_DroMel_CAF1
Location 10,758,449 – 10,758,640
Length 191
Max. P 0.976068
window5762 window5763 window5764

overview

Window 2

Location 10,758,449 – 10,758,566
Length 117
Sequences 5
Columns 117
Reading direction forward
Mean pairwise identity 88.21
Mean single sequence MFE -31.65
Consensus MFE -22.24
Energy contribution -25.04
Covariance contribution 2.80
Combinations/Pair 1.00
Mean z-score -1.81
Structure conservation index 0.70
SVM decision value 0.07
SVM RNA-class probability 0.567241
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 10758449 117 + 23771897
UAAAUAACUCAAAUGUGCACUGGAUGGUGAUGAUCAAGCAAAGCUUAAAACGGCAUGAUAAUAAUCGCGAACAAUUCAGUUCAGUGCAUGUGCGGGUGGAGUGAUCAUCGAGUGCGA
......((((..(((((((((((((.(((((.((((.((...(.......).)).))))....)))))((.....)).)))))))))))))...(((((.....))))))))).... ( -32.40)
>DroSec_CAF1 92182 117 + 1
UAAAUCACUCAAAUGUGCACUGGAUGGUGAUGAUCAAGCAAAGCUUAAAUCGGCAUGAUAAUAAUCGCGAACAAUUCAGUUCAGUGCAUGUGCGGGUGGAGUGAUCAUCGAGUGCGA
.....(((((..(((((((((((((.(((((.((((.((.............)).))))....)))))((.....)).)))))))))))))...(((((.....))))))))))... ( -34.42)
>DroSim_CAF1 94995 117 + 1
UAAAUCACUCAAAUGUGCACUGGAUGGUGAUGAUCAAGCAAAGCUUAAAACGGCAUGAUAAUAAUCGCGAACAAUUCAGUUCAGUGCAUGUGCGGGUGGAGUGAUCAUCGAGUGCGA
.....(((((..(((((((((((((.(((((.((((.((...(.......).)).))))....)))))((.....)).)))))))))))))...(((((.....))))))))))... ( -34.50)
>DroEre_CAF1 96899 91 + 1
UAAAUC--------------------------AUCAAGCAAAGCUUAAAACGGCAUGAUAGUAAUCGCGAACAAUUCAGUUCAGUGCAUGUGCGGGUGGAGUGAUCUGCGAGUGGGA
....((--------------------------((...(((..((((....(.(((((((....)))((((((......))))...))..)))).)...))))....)))..)))).. ( -18.60)
>DroYak_CAF1 107881 117 + 1
UAAAUCACUCAAAUGUGCACUGGAUGCUGAUGAUCAAGCAAAGCUUAAAACGGCAUGAUAGUAAUCGCGAACAAUUCAGUUCAGUGCAUGUGCGGGUGGAGUGAUCACCGAGUGGGA
....((((((..(((((((((((..(((((.......((...(((......)))..(((....))))).......))))))))))))))))...(((((.....))))))))))).. ( -38.34)
>consensus
UAAAUCACUCAAAUGUGCACUGGAUGGUGAUGAUCAAGCAAAGCUUAAAACGGCAUGAUAAUAAUCGCGAACAAUUCAGUUCAGUGCAUGUGCGGGUGGAGUGAUCAUCGAGUGCGA
...............((((((......(((((((((..(...((((...((((((((((....)))..((((......)))).)))).)))..)))).)..))))))))))))))). (-22.24 = -25.04 +   2.80)

alignment

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secondary structure

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dotplot

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Window 3

Location 10,758,526 – 10,758,640
Length 114
Sequences 4
Columns 116
Reading direction forward
Mean pairwise identity 88.24
Mean single sequence MFE -26.38
Consensus MFE -22.48
Energy contribution -22.98
Covariance contribution 0.50
Combinations/Pair 1.00
Mean z-score -2.42
Structure conservation index 0.85
SVM decision value 1.76
SVM RNA-class probability 0.976068
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 10758526 114 + 23771897
AGUUCAGUGCAUGUGCGGGUGGAGUGAUCAUCGAGUGCGAAUGAGAGGUAAGAUUAUGCACCAGUGAAGUACACUGAACAAAAA--AAUUAAUAACUUACGGGAGUAUAUUGUAAC
.((((((((.((..((.((((..((((((.(((....))).(....)....)))))).)))).))...)).)))))))).....--.....((((..(((....)))..))))... ( -29.60)
>DroSec_CAF1 92259 113 + 1
AGUUCAGUGCAUGUGCGGGUGGAGUGAUCAUCGAGUGCGAAUGAGAGGGAAGAUUAUGCACCAGUGAAGUACACUGAACAAA-A--AAUUAAUAUCUAAUAGAAGAAUAAUGUAAC
.((((((((.((..((.((((..((((((.(((....))).(....)....)))))).)))).))...)).))))))))...-.--........(((......))).......... ( -25.80)
>DroSim_CAF1 95072 113 + 1
AGUUCAGUGCAUGUGCGGGUGGAGUGAUCAUCGAGUGCGAAUGAGAGGGAAGAUUAUGCACCAGUGAAGUACACUGAACAAA-A--AAUUAAUAAGUUAUAGGAGUAUAAUGUAAC
.((((((((.((..((.((((..((((((.(((....))).(....)....)))))).)))).))...)).))))))))...-.--.........((((((.........)))))) ( -27.30)
>DroEre_CAF1 96950 116 + 1
AGUUCAGUGCAUGUGCGGGUGGAGUGAUCUGCGAGUGGGAAUGAGAGGGAAGAUUAUGCACGAGUGAAGUACACUGAACAAAAAUAAAAAAAUAAAGAAGUGAAAUAUUAUCAAAA
.((((((((.((..((..(((..(((((((.(..((....))..).....))))))).)))..))...)).))))))))..................................... ( -22.80)
>consensus
AGUUCAGUGCAUGUGCGGGUGGAGUGAUCAUCGAGUGCGAAUGAGAGGGAAGAUUAUGCACCAGUGAAGUACACUGAACAAA_A__AAUUAAUAACUAAUAGAAGUAUAAUGUAAC
.((((((((.((..((.((((..((((((.((..((....))..)).....)))))).)))).))...)).))))))))..................................... (-22.48 = -22.98 +   0.50)

alignment

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secondary structure

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dotplot

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Window 4

Location 10,758,526 – 10,758,640
Length 114
Sequences 4
Columns 116
Reading direction reverse
Mean pairwise identity 88.24
Mean single sequence MFE -17.70
Consensus MFE -15.52
Energy contribution -15.78
Covariance contribution 0.25
Combinations/Pair 1.00
Mean z-score -2.01
Structure conservation index 0.88
SVM decision value 1.27
SVM RNA-class probability 0.938141
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 10758526 114 - 23771897
GUUACAAUAUACUCCCGUAAGUUAUUAAUU--UUUUUGUUCAGUGUACUUCACUGGUGCAUAAUCUUACCUCUCAUUCGCACUCGAUGAUCACUCCACCCGCACAUGCACUGAACU
.....(((.(((....))).))).......--.....(((((((((((......)((((.............((((.((....))))))...........)))).)))))))))). ( -18.95)
>DroSec_CAF1 92259 113 - 1
GUUACAUUAUUCUUCUAUUAGAUAUUAAUU--U-UUUGUUCAGUGUACUUCACUGGUGCAUAAUCUUCCCUCUCAUUCGCACUCGAUGAUCACUCCACCCGCACAUGCACUGAACU
.....((((.(((......)))...)))).--.-...(((((((((((......)((((.............((((.((....))))))...........)))).)))))))))). ( -18.95)
>DroSim_CAF1 95072 113 - 1
GUUACAUUAUACUCCUAUAACUUAUUAAUU--U-UUUGUUCAGUGUACUUCACUGGUGCAUAAUCUUCCCUCUCAUUCGCACUCGAUGAUCACUCCACCCGCACAUGCACUGAACU
..............................--.-...(((((((((((......)((((.............((((.((....))))))...........)))).)))))))))). ( -18.55)
>DroEre_CAF1 96950 116 - 1
UUUUGAUAAUAUUUCACUUCUUUAUUUUUUUAUUUUUGUUCAGUGUACUUCACUCGUGCAUAAUCUUCCCUCUCAUUCCCACUCGCAGAUCACUCCACCCGCACAUGCACUGAACU
.....................................((((((((((........((((...........((((..........).)))...........)))).)))))))))). ( -14.35)
>consensus
GUUACAUUAUACUCCUAUAAGUUAUUAAUU__U_UUUGUUCAGUGUACUUCACUGGUGCAUAAUCUUCCCUCUCAUUCGCACUCGAUGAUCACUCCACCCGCACAUGCACUGAACU
.....................................((((((((((.....(.((((....(((......................))).....)))).)....)))))))))). (-15.52 = -15.78 +   0.25)

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 11:04:23 2006