Locus 2612

Sequence ID X_DroMel_CAF1
Location 6,997,344 – 6,997,584
Length 240
Max. P 0.993006
window4279 window4280 window4281 window4282

overview

Window 9

Location 6,997,344 – 6,997,464
Length 120
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 95.45
Mean single sequence MFE -32.90
Consensus MFE -31.77
Energy contribution -31.77
Covariance contribution 0.00
Combinations/Pair 1.00
Mean z-score -3.80
Structure conservation index 0.97
SVM decision value 2.29
SVM RNA-class probability 0.991785
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 6997344 120 + 22224390
AGAUGGGUUGGAGAUGGUGAAGUGGAGAUGGAGAUGGAGAUGAAGCUGCGAAAGCAAGCGAAAGUUCAAAAUGUGCAAAAAGCGAGCACAGAAAGCUGAAAGCACAACUCCACACACGCA
................(((..((((((.........(((.....(((((....)).))).....)))....(((((....(((...........)))....))))).)))))).)))... ( -32.90)
>DroSec_CAF1 19664 112 + 1
AGAUGGGUUGGAGAUGGUGAAGUGGAGAU------GGAGAUGAAGCUGCGAAAGCAAGCGAAAGUUCAAAAUGUGCAAAAAGCGAGCACAGAAAGCUGAAAGCACAACUCCACACAC--A
................(((..((((((..------.(((.....(((((....)).))).....)))....(((((....(((...........)))....))))).)))))).)))--. ( -32.90)
>DroSim_CAF1 4805 112 + 1
AGAUGGGUUGGAGAUGGUGAAGUGGAGAU------GGAGAUGAAGCUGCGAAAGCAAGCGAAAGUUCAAAAUGUGCAAAAAGCGAGCACAGAAAGCUGAAAGCACAACUCCACACAC--A
................(((..((((((..------.(((.....(((((....)).))).....)))....(((((....(((...........)))....))))).)))))).)))--. ( -32.90)
>consensus
AGAUGGGUUGGAGAUGGUGAAGUGGAGAU______GGAGAUGAAGCUGCGAAAGCAAGCGAAAGUUCAAAAUGUGCAAAAAGCGAGCACAGAAAGCUGAAAGCACAACUCCACACAC__A
................(((..((((((.........(((.....(((((....)).))).....)))....(((((....(((...........)))....))))).)))))).)))... (-31.77 = -31.77 +   0.00)

alignment

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secondary structure

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Window 0

Location 6,997,344 – 6,997,464
Length 120
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 95.45
Mean single sequence MFE -25.00
Consensus MFE -24.80
Energy contribution -24.80
Covariance contribution 0.00
Combinations/Pair 1.00
Mean z-score -2.95
Structure conservation index 0.99
SVM decision value 2.37
SVM RNA-class probability 0.993006
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 6997344 120 - 22224390
UGCGUGUGUGGAGUUGUGCUUUCAGCUUUCUGUGCUCGCUUUUUGCACAUUUUGAACUUUCGCUUGCUUUCGCAGCUUCAUCUCCAUCUCCAUCUCCACUUCACCAUCUCCAACCCAUCU
((.(((.((((((.(((((....(((...........)))....)))))............(((.((....))))).................))))))..))))).............. ( -25.60)
>DroSec_CAF1 19664 112 - 1
U--GUGUGUGGAGUUGUGCUUUCAGCUUUCUGUGCUCGCUUUUUGCACAUUUUGAACUUUCGCUUGCUUUCGCAGCUUCAUCUCC------AUCUCCACUUCACCAUCUCCAACCCAUCU
.--(((.((((((.(((((....(((...........)))....)))))............(((.((....))))).........------..))))))..)))................ ( -24.70)
>DroSim_CAF1 4805 112 - 1
U--GUGUGUGGAGUUGUGCUUUCAGCUUUCUGUGCUCGCUUUUUGCACAUUUUGAACUUUCGCUUGCUUUCGCAGCUUCAUCUCC------AUCUCCACUUCACCAUCUCCAACCCAUCU
.--(((.((((((.(((((....(((...........)))....)))))............(((.((....))))).........------..))))))..)))................ ( -24.70)
>consensus
U__GUGUGUGGAGUUGUGCUUUCAGCUUUCUGUGCUCGCUUUUUGCACAUUUUGAACUUUCGCUUGCUUUCGCAGCUUCAUCUCC______AUCUCCACUUCACCAUCUCCAACCCAUCU
...(((.((((((.(((((....(((...........)))....)))))............(((.((....))))).................))))))..)))................ (-24.80 = -24.80 +   0.00)

alignment

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secondary structure

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dotplot

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Window 1

Location 6,997,464 – 6,997,584
Length 120
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 86.09
Mean single sequence MFE -25.00
Consensus MFE -22.20
Energy contribution -22.20
Covariance contribution -0.00
Combinations/Pair 1.00
Mean z-score -2.77
Structure conservation index 0.89
SVM decision value 1.78
SVM RNA-class probability 0.977006
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 6997464 120 + 22224390
CACCCACACACCCACACAUGUGAAAGCACACAGACUACCGUGCGCCCAAAUGCGUGCGAUAUAUGCAUAUGCAUGUACAGUCCAACUUCUAUAAGCCUCACUUUUGUGCAAAAAGGAAAA
...((.((((........))))...(((((..((((..((..(((......)))..)).(((((((....))))))).))))...(((....))).........))))).....)).... ( -30.40)
>DroSec_CAF1 19776 97 + 1
CAC--------CCACACAUGUGAAAGCACACAGACAACCGUGCGCCCAAAUGCGUGCGAUAUAUGCAUAUGCAUGUACAGUCCAACUUCUAUAAGCCUCACUUUU---------------
...--------.......((((......))))(((...((..(((......)))..)).(((((((....)))))))..))).......................--------------- ( -22.30)
>DroSim_CAF1 4917 105 + 1
CACCCACACACCCACACAUGUGAAAGCACACAGACAACCGUGCGCCCAAAUGCGUGCGAUAUAUGCAUAUGCAUGUACAGUCCAACUUCUAUAAGCCUCACUUUU---------------
..................((((......))))(((...((..(((......)))..)).(((((((....)))))))..))).......................--------------- ( -22.30)
>consensus
CACCCACACACCCACACAUGUGAAAGCACACAGACAACCGUGCGCCCAAAUGCGUGCGAUAUAUGCAUAUGCAUGUACAGUCCAACUUCUAUAAGCCUCACUUUU_______________
...................((((..((...........((..(((......)))..)).(((((((....))))))).................)).))))................... (-22.20 = -22.20 +  -0.00)

alignment

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secondary structure

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dotplot

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Window 2

Location 6,997,464 – 6,997,584
Length 120
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 86.09
Mean single sequence MFE -38.20
Consensus MFE -32.30
Energy contribution -34.63
Covariance contribution 2.33
Combinations/Pair 1.00
Mean z-score -3.06
Structure conservation index 0.85
SVM decision value 1.71
SVM RNA-class probability 0.973196
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 6997464 120 - 22224390
UUUUCCUUUUUGCACAAAAGUGAGGCUUAUAGAAGUUGGACUGUACAUGCAUAUGCAUAUAUCGCACGCAUUUGGGCGCACGGUAGUCUGUGUGCUUUCACAUGUGUGGGUGUGUGGGUG
..........((((....(((..(((((....)))))..))).....))))(((.((((((((.(((((((.(((((((((((....)))))))))..)).))))))))))))))).))) ( -43.00)
>DroSec_CAF1 19776 97 - 1
---------------AAAAGUGAGGCUUAUAGAAGUUGGACUGUACAUGCAUAUGCAUAUAUCGCACGCAUUUGGGCGCACGGUUGUCUGUGUGCUUUCACAUGUGUGG--------GUG
---------------...(((..(((((....)))))..)))....((((....)))).((((.(((((((.(((((((((((....)))))))))..)).))))))))--------))) ( -32.80)
>DroSim_CAF1 4917 105 - 1
---------------AAAAGUGAGGCUUAUAGAAGUUGGACUGUACAUGCAUAUGCAUAUAUCGCACGCAUUUGGGCGCACGGUUGUCUGUGUGCUUUCACAUGUGUGGGUGUGUGGGUG
---------------...(((..(((((....)))))..))).........(((.((((((((.(((((((.(((((((((((....)))))))))..)).))))))))))))))).))) ( -38.80)
>consensus
_______________AAAAGUGAGGCUUAUAGAAGUUGGACUGUACAUGCAUAUGCAUAUAUCGCACGCAUUUGGGCGCACGGUUGUCUGUGUGCUUUCACAUGUGUGGGUGUGUGGGUG
..................(((..(((((....)))))..))).........(((.((((((((.(((((((.(((((((((((....)))))))))..)).))))))))))))))).))) (-32.30 = -34.63 +   2.33)

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 10:39:12 2006