Locus 2306

Sequence ID X_DroMel_CAF1
Location 6,236,415 – 6,236,526
Length 111
Max. P 0.949293
window3735 window3736

overview

Window 5

Location 6,236,415 – 6,236,526
Length 111
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 84.06
Mean single sequence MFE -24.70
Consensus MFE -22.66
Energy contribution -22.98
Covariance contribution 0.31
Combinations/Pair 1.05
Mean z-score -1.96
Structure conservation index 0.92
SVM decision value 1.39
SVM RNA-class probability 0.949293
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 6236415 111 + 22224390
---------UCUGAUUCUGAUUCUGAUUCCUAUUCCGGAUUCGGAAUCCGCUUCUUAUUCCGGCUGCCUUGAUUACGUGGCCAAAUCGAUUUCUUUAUCUGCCACCCCCCGCCCCCCUCG
---------...((..(.((((((((.(((......))).)))))))).)..)).......(((.(((.((....)).)))......(((......))).)))................. ( -24.60)
>DroSec_CAF1 9407 101 + 1
-----------CGAUUCCGAUUCUGAUUCCUAUUCCGGAUUCGGAAUCCGAUUCCUAUUCCGGCUGCCUUGAUUACGUGGCCAAAUCGAUUUCUUUAUCUGCC--------CCCCGCUCG
-----------.((.((.((((((((.(((......))).)))))))).)).)).......(((.(((.((....)).)))......(((......))).)))--------......... ( -25.60)
>DroEre_CAF1 4080 109 + 1
CAUGCCGAUUCCGAUUCCGAUUCAGAUUCCUAUUCCGGAUUCCGAAUCCGAUUCUUAUUCCGGCUGCCUUGAUUACGUGGCCAAAUCGAUUUCUUUAUCUGCC--------CC---CUCG
.....(((((..((.((.(((((.((.(((......))).)).))))).)).)).......(((..(.........)..))).)))))...............--------..---.... ( -25.10)
>DroYak_CAF1 17076 108 + 1
CAUUCACAUUGCGAUUCCGAUUCAGAUUCCUAUUCCGGAUUCGGAAUCCGAUUCUUAUUCCGGCUGCCUUGAUUACGUGGCCAAAUCGAUUUCUUUAUCUGCC--------CU---C-CG
.......((((.(((((((((((.((.......)).))).)))))))))))).........(((.(((.((....)).)))......(((......))).)))--------..---.-.. ( -23.50)
>consensus
_________UCCGAUUCCGAUUCAGAUUCCUAUUCCGGAUUCGGAAUCCGAUUCUUAUUCCGGCUGCCUUGAUUACGUGGCCAAAUCGAUUUCUUUAUCUGCC________CC___CUCG
...........(((((..((((((((.(((......))).)))))))).............(((..(.........)..))).)))))................................ (-22.66 = -22.98 +   0.31)

alignment

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secondary structure

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dotplot

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Window 6

Location 6,236,415 – 6,236,526
Length 111
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 84.06
Mean single sequence MFE -30.20
Consensus MFE -24.25
Energy contribution -24.50
Covariance contribution 0.25
Combinations/Pair 1.00
Mean z-score -2.01
Structure conservation index 0.80
SVM decision value 1.03
SVM RNA-class probability 0.902669
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 6236415 111 - 22224390
CGAGGGGGGCGGGGGGUGGCAGAUAAAGAAAUCGAUUUGGCCACGUAAUCAAGGCAGCCGGAAUAAGAAGCGGAUUCCGAAUCCGGAAUAGGAAUCAGAAUCAGAAUCAGA---------
.......(((.....(((((((((..(....)..)))).)))))((.......)).))).......((..(.(((((.((.(((......))).)).))))).)..))...--------- ( -27.90)
>DroSec_CAF1 9407 101 - 1
CGAGCGGGG--------GGCAGAUAAAGAAAUCGAUUUGGCCACGUAAUCAAGGCAGCCGGAAUAGGAAUCGGAUUCCGAAUCCGGAAUAGGAAUCAGAAUCGGAAUCG-----------
((((((..(--------(.(((((..(....)..))))).)).)))...........((......))..)))((((((((.((.((........)).)).)))))))).----------- ( -27.80)
>DroEre_CAF1 4080 109 - 1
CGAG---GG--------GGCAGAUAAAGAAAUCGAUUUGGCCACGUAAUCAAGGCAGCCGGAAUAAGAAUCGGAUUCGGAAUCCGGAAUAGGAAUCUGAAUCGGAAUCGGAAUCGGCAUG
....---.(--------(.(((((..(....)..))))).))..............(((((.....((.((.((((((((.(((......))).)))))))).)).))....)))))... ( -36.40)
>DroYak_CAF1 17076 108 - 1
CG-G---AG--------GGCAGAUAAAGAAAUCGAUUUGGCCACGUAAUCAAGGCAGCCGGAAUAAGAAUCGGAUUCCGAAUCCGGAAUAGGAAUCUGAAUCGGAAUCGCAAUGUGAAUG
((-.---.(--------(.(((((..(....)..))))).)).))...(((..((..((((....(((.((..((((((....))))))..)).)))...))))....))....)))... ( -28.70)
>consensus
CGAG___GG________GGCAGAUAAAGAAAUCGAUUUGGCCACGUAAUCAAGGCAGCCGGAAUAAGAAUCGGAUUCCGAAUCCGGAAUAGGAAUCAGAAUCGGAAUCGGA_________
.................(((.(((......)))......(((..........))).))).......((.((.(((((.((.(((......))).)).))))).)).))............ (-24.25 = -24.50 +   0.25)

alignment

Postscript

secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:31:07 2006