Locus 6396

Sequence ID 3R_DroMel_CAF1
Location 16,772,356 – 16,772,636
Length 280
Max. P 0.866184
window10425 window10426 window10427 window10428

overview

Window 5

Location 16,772,356 – 16,772,476
Length 120
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 93.67
Mean single sequence MFE -29.52
Consensus MFE -28.95
Energy contribution -29.20
Covariance contribution 0.25
Combinations/Pair 1.00
Mean z-score -1.41
Structure conservation index 0.98
SVM decision value 0.38
SVM RNA-class probability 0.712433
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 16772356 120 + 27905053
UCCAGGAGCCUGGCAGAGCAAACAUGAACGAAAAAACAUGAAACGUGCCCAGCCUGCUAAGGACAUUCAUUACGCAAGCUAUGAAGCUGCCUUCUCCGAACUGAAUCCAACCAUCGCAGC
....((((...(((((.(((..((((..........)))).....)))...((((....))).).(((((..(....)..))))).)))))..))))....................... ( -26.80)
>DroSec_CAF1 4437 117 + 1
UCCAGGAGCUUGGCAGAGCAAACAUGAACGAAAAAACAUGAAACGUGCCCUGCCUGCUAAGGACAUUCAUUACGCAAGCUAUGAAGCUGCCUUCUCCGAACUGAAUCCAACCAUCGC---
..(((.(((..(((((.(((..((((..........)))).....))).))))).)))((((...(((((..(....)..)))))....)))).......)))..............--- ( -30.40)
>DroSim_CAF1 5887 117 + 1
UCCAGGAGCUCGGCAGAGCAAACAUGAACGAAAAAACAUGAAACGUGCCCUGCCUGCUAAGGACAUUCAUUACGCAAGCUAUGAAGCUGCCUUCUCCGAACUGAAUCCAACCAUCGC---
..(((.(((..(((((.(((..((((..........)))).....))).))))).)))((((...(((((..(....)..)))))....)))).......)))..............--- ( -29.90)
>DroEre_CAF1 620 110 + 1
UCCAGGAGCUUGGCAGAGCAAACAUGAACGAA-AAACAUGAAACGUGCCCUGCCUGCUAAGGACAUUCAUUACGCAAGCUAUGAAGCUGCCUUUU-CGAACUGAAUCCAGCC--------
(((...(((..(((((.(((..((((......-...)))).....))).))))).)))..)))..(((((..(....)..)))))((((....((-(.....)))..)))).-------- ( -31.00)
>consensus
UCCAGGAGCUUGGCAGAGCAAACAUGAACGAAAAAACAUGAAACGUGCCCUGCCUGCUAAGGACAUUCAUUACGCAAGCUAUGAAGCUGCCUUCUCCGAACUGAAUCCAACCAUCGC___
..(((.(((..(((((.(((..((((..........)))).....))).))))).)))((((...(((((..(....)..)))))....)))).......)))................. (-28.95 = -29.20 +   0.25)

alignment

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secondary structure

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dotplot

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Window 6

Location 16,772,476 – 16,772,596
Length 120
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 85.10
Mean single sequence MFE -27.82
Consensus MFE -21.70
Energy contribution -22.82
Covariance contribution 1.12
Combinations/Pair 1.10
Mean z-score -1.96
Structure conservation index 0.78
SVM decision value 0.85
SVM RNA-class probability 0.866184
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 16772476 120 + 27905053
CAUACCCACACACCCCCCCCCCUCCACUUCCUACCCAUGGGCUUAGUGGGCUGGCCACGCCUCCUAUUGAAUUAUUCCAGUUUUAUUUCUCGCCAUUUGGCUUGGCACACACCGAGGCAU
..................((..((((((.((((....))))...))))))..))....(((((..((((........))))..........((((.......)))).......))))).. ( -27.10)
>DroSec_CAF1 4554 106 + 1
--------------CCCACCUUCCCCCUUUCUACCCAUGGGCUUAGUGGGCUGGCCACGCCUCCUAUUGAAUUAUUCCAGUUUUAUUUCUCGCCAUUUGGCUUGGCACACACCGAGGCAU
--------------(((((.....(((...........)))....)))))........(((((..((((........))))..........((((.......)))).......))))).. ( -25.90)
>DroSim_CAF1 6004 106 + 1
--------------CCCACCUUCCCCCUUCCUACCCAUGGGCUCAGGGGGCUGGCCACGCCUCCUAUUGAAUUAUUCCAGUUUUAUUUCUCGCCAUUUGGCUUGGCACACACCGAGGCAU
--------------....((..((((((.((((....))))...))))))..))....(((((..((((........))))..........((((.......)))).......))))).. ( -32.20)
>DroEre_CAF1 730 101 + 1
---------------CC-CCUUUACC--U-UUACCCAGGGACUUAGUGGGCUGGCCACGCCUCCUAUUGAAUUAUUCCACUUUUAUUUCUCGCCAUUUGGCUGGGCACACACCGAGGCAG
---------------..-((((....--.-...((((((((.((((((((..(((...))).))))))))....)))).............(((....)))))))........))))... ( -26.09)
>consensus
______________CCCACCUUCCCCCUUCCUACCCAUGGGCUUAGUGGGCUGGCCACGCCUCCUAUUGAAUUAUUCCAGUUUUAUUUCUCGCCAUUUGGCUUGGCACACACCGAGGCAU
..................((..((((((.....((....))...))))))..))....(((((............................(((....)))..((......))))))).. (-21.70 = -22.82 +   1.12)

alignment

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secondary structure

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dotplot

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Window 7

Location 16,772,476 – 16,772,596
Length 120
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 85.10
Mean single sequence MFE -33.48
Consensus MFE -24.74
Energy contribution -26.43
Covariance contribution 1.69
Combinations/Pair 1.08
Mean z-score -1.41
Structure conservation index 0.74
SVM decision value -0.05
SVM RNA-class probability 0.509245
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 16772476 120 - 27905053
AUGCCUCGGUGUGUGCCAAGCCAAAUGGCGAGAAAUAAAACUGGAAUAAUUCAAUAGGAGGCGUGGCCAGCCCACUAAGCCCAUGGGUAGGAAGUGGAGGGGGGGGGGUGUGUGGGUAUG
((((((((((....)))..(((....)))............................))))))).....((((((...((((.......................))))..))))))... ( -34.80)
>DroSec_CAF1 4554 106 - 1
AUGCCUCGGUGUGUGCCAAGCCAAAUGGCGAGAAAUAAAACUGGAAUAAUUCAAUAGGAGGCGUGGCCAGCCCACUAAGCCCAUGGGUAGAAAGGGGGAAGGUGGG--------------
((((((((((....)))..(((....)))............................))))))).(((..(((.((..(((....)))....)).)))..)))...-------------- ( -32.00)
>DroSim_CAF1 6004 106 - 1
AUGCCUCGGUGUGUGCCAAGCCAAAUGGCGAGAAAUAAAACUGGAAUAAUUCAAUAGGAGGCGUGGCCAGCCCCCUGAGCCCAUGGGUAGGAAGGGGGAAGGUGGG--------------
((((((((((....)))..(((....)))............................))))))).(((..((((((..(((....)))....))))))..)))...-------------- ( -40.10)
>DroEre_CAF1 730 101 - 1
CUGCCUCGGUGUGUGCCCAGCCAAAUGGCGAGAAAUAAAAGUGGAAUAAUUCAAUAGGAGGCGUGGCCAGCCCACUAAGUCCCUGGGUAA-A--GGUAAAGG-GG---------------
...((((..((..(((((((((....)))..........(((((.....(((....)))(((...)))...))))).......)))))).-.--..))..))-))--------------- ( -27.00)
>consensus
AUGCCUCGGUGUGUGCCAAGCCAAAUGGCGAGAAAUAAAACUGGAAUAAUUCAAUAGGAGGCGUGGCCAGCCCACUAAGCCCAUGGGUAGGAAGGGGAAAGGUGGG______________
((((((((((....)))..(((....)))............................)))))))..((..((((((..(((....)))....))))))..)).................. (-24.74 = -26.43 +   1.69)

alignment

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secondary structure

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dotplot

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Window 8

Location 16,772,516 – 16,772,636
Length 120
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 94.03
Mean single sequence MFE -42.58
Consensus MFE -36.83
Energy contribution -37.95
Covariance contribution 1.12
Combinations/Pair 1.04
Mean z-score -1.48
Structure conservation index 0.86
SVM decision value -0.00
SVM RNA-class probability 0.531515
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 16772516 120 - 27905053
GGCCACCGGCGGCAAGGAGUCAGCUUCACGGCCGAGUCGGAUGCCUCGGUGUGUGCCAAGCCAAAUGGCGAGAAAUAAAACUGGAAUAAUUCAAUAGGAGGCGUGGCCAGCCCACUAAGC
((((.((((((((..((((....))))...)))..)))))((((((((((....)))..(((....)))............................)))))))))))............ ( -43.70)
>DroSec_CAF1 4580 120 - 1
GGCCACCGACGGCAAGGAGUCAGCUUCACGGCAGAGUCGGAUGCCUCGGUGUGUGCCAAGCCAAAUGGCGAGAAAUAAAACUGGAAUAAUUCAAUAGGAGGCGUGGCCAGCCCACUAAGC
((((.(((((.((..((((....))))...))...)))))((((((((((....)))..(((....)))............................)))))))))))............ ( -43.30)
>DroSim_CAF1 6030 120 - 1
GGCCACCGACGGCAAGGAGUCAGCUUCACGGCAGAGUCGGAUGCCUCGGUGUGUGCCAAGCCAAAUGGCGAGAAAUAAAACUGGAAUAAUUCAAUAGGAGGCGUGGCCAGCCCCCUGAGC
((((.(((((.((..((((....))))...))...)))))((((((((((....)))..(((....)))............................)))))))))))............ ( -43.30)
>DroEre_CAF1 751 120 - 1
GGCCAGCGGCGGCAAGAAGUCAGCUCCACUGCAGAGGCAGCUGCCUCGGUGUGUGCCCAGCCAAAUGGCGAGAAAUAAAAGUGGAAUAAUUCAAUAGGAGGCGUGGCCAGCCCACUAAGU
(((((.((.((((.....)))...((((((...(((((....)))))(((....)))..(((....)))..........))))))..............).)))))))............ ( -40.00)
>consensus
GGCCACCGACGGCAAGGAGUCAGCUUCACGGCAGAGUCGGAUGCCUCGGUGUGUGCCAAGCCAAAUGGCGAGAAAUAAAACUGGAAUAAUUCAAUAGGAGGCGUGGCCAGCCCACUAAGC
((((.(((((.((..((((....))))...))...)))))((((((((((....)))..(((....)))............................)))))))))))............ (-36.83 = -37.95 +   1.12)

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 12:20:30 2006