Locus 38

Sequence ID 2R_DroMel_CAF1
Location 1,255,618 – 1,255,753
Length 135
Max. P 0.987314
window66 window67 window68 window69

overview

Window 6

Location 1,255,618 – 1,255,720
Length 102
Sequences 5
Columns 104
Reading direction forward
Mean pairwise identity 88.68
Mean single sequence MFE -32.44
Consensus MFE -25.82
Energy contribution -25.78
Covariance contribution -0.04
Combinations/Pair 1.04
Mean z-score -2.52
Structure conservation index 0.80
SVM decision value 2.03
SVM RNA-class probability 0.986037
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 1255618 102 + 20766785
CUGCAUCAGCUCCAAAGUGUGCUACUUAAUUACAAAUUGGCCCUGACUAGGCCAAUCACCCUUCUCACUGGCCAGUAACUCGAACCUGGCCUCGAGCAGGAG--
..((((..(((....))))))).............(((((((.......)))))))...(((.(((...((((((..........))))))..))).)))..-- ( -29.90)
>DroSec_CAF1 7335 104 + 1
CUGCCGCAGCUCCAAAGUGUGCUGCUUAAUUACAAAUUGGCCCUGACUAGGCCAAUCACCCUUCUCCCUGGCCAGUAACUCGAACCUGGCCUCGAGCAGGUGAA
.....(((((.(......).)))))...........((((((.......))))))(((((...(((...((((((..........))))))..)))..))))). ( -36.60)
>DroSim_CAF1 13161 104 + 1
CUGCCGCAGCUCCAAAGUGUGCUGCUUAAUUACAAAUUGGCCCUGACUAGGCCAAUCACCCUUCUCACUGGCCAGUAACUCGAACCUGGCCUCGAGCAGGUGGA
.....(((((.(......).)))))...........((((((.......))))))(((((...(((...((((((..........))))))..)))..))))). ( -35.70)
>DroEre_CAF1 11548 94 + 1
--------GUACCAAAGUGUGGUACUUAAUUACAAAUUGGCCCUGAGUAGGCCAAUAACCCUUCUCACUGGCCAGUAACUUGAACCUGGCCUCGAGCAGGAG--
--------((((((.....))))))..........(((((((.......)))))))...(((.(((...((((((..........))))))..))).)))..-- ( -34.00)
>DroYak_CAF1 10828 102 + 1
CUGCCGCAGUUUCAAAGUAUGGUACUUAAUUACAAAUUGGCCCUGACUAGGCCAAUAACCCUUCUCACUGACCAGUAUCUCGAACCUGGCCUCGAGAAGGAG--
.(((((.(.(.....).).)))))...........(((((((.......)))))))...(((((((...(.((((..........)))).)..)))))))..-- ( -26.00)
>consensus
CUGCCGCAGCUCCAAAGUGUGCUACUUAAUUACAAAUUGGCCCUGACUAGGCCAAUCACCCUUCUCACUGGCCAGUAACUCGAACCUGGCCUCGAGCAGGAG__
..............((((.....))))........(((((((.......)))))))...(((.(((...((((((..........))))))..))).))).... (-25.82 = -25.78 +  -0.04)

alignment

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secondary structure

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dotplot

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Window 7

Location 1,255,618 – 1,255,720
Length 102
Sequences 5
Columns 104
Reading direction reverse
Mean pairwise identity 88.68
Mean single sequence MFE -38.20
Consensus MFE -30.40
Energy contribution -31.96
Covariance contribution 1.56
Combinations/Pair 1.11
Mean z-score -2.56
Structure conservation index 0.80
SVM decision value 2.07
SVM RNA-class probability 0.987314
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 1255618 102 - 20766785
--CUCCUGCUCGAGGCCAGGUUCGAGUUACUGGCCAGUGAGAAGGGUGAUUGGCCUAGUCAGGGCCAAUUUGUAAUUAAGUAGCACACUUUGGAGCUGAUGCAG
--...((((((..((((((..........))))))(((..((((.(((..((((((.....))))))(((((....)))))..))).))))...))))).)))) ( -35.70)
>DroSec_CAF1 7335 104 - 1
UUCACCUGCUCGAGGCCAGGUUCGAGUUACUGGCCAGGGAGAAGGGUGAUUGGCCUAGUCAGGGCCAAUUUGUAAUUAAGCAGCACACUUUGGAGCUGCGGCAG
.((((((.(((..((((((..........)))))).)))....))))))(((((((.....)))))))...........(((((.(......).)))))..... ( -42.20)
>DroSim_CAF1 13161 104 - 1
UCCACCUGCUCGAGGCCAGGUUCGAGUUACUGGCCAGUGAGAAGGGUGAUUGGCCUAGUCAGGGCCAAUUUGUAAUUAAGCAGCACACUUUGGAGCUGCGGCAG
..(((((.((((.((((((..........))))))..))))..)))))((((((((.....))))))))..........(((((.(......).)))))..... ( -41.80)
>DroEre_CAF1 11548 94 - 1
--CUCCUGCUCGAGGCCAGGUUCAAGUUACUGGCCAGUGAGAAGGGUUAUUGGCCUACUCAGGGCCAAUUUGUAAUUAAGUACCACACUUUGGUAC--------
--.((((.((((.((((((..........))))))..)))).))))..((((((((.....))))))))..........((((((.....))))))-------- ( -36.40)
>DroYak_CAF1 10828 102 - 1
--CUCCUUCUCGAGGCCAGGUUCGAGAUACUGGUCAGUGAGAAGGGUUAUUGGCCUAGUCAGGGCCAAUUUGUAAUUAAGUACCAUACUUUGAAACUGCGGCAG
--.(((((((((.((((((..........))))))..)))))))))..((((((((.....)))))))).(((.....(((..((.....))..)))...))). ( -34.90)
>consensus
__CUCCUGCUCGAGGCCAGGUUCGAGUUACUGGCCAGUGAGAAGGGUGAUUGGCCUAGUCAGGGCCAAUUUGUAAUUAAGUAGCACACUUUGGAGCUGCGGCAG
....(((.((((.((((((..........))))))..)))).)))..(((((((((.....))))))))).........(((((.(......).)))))..... (-30.40 = -31.96 +   1.56)

alignment

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secondary structure

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dotplot

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Window 8

Location 1,255,655 – 1,255,753
Length 98
Sequences 5
Columns 100
Reading direction forward
Mean pairwise identity 89.54
Mean single sequence MFE -31.64
Consensus MFE -27.86
Energy contribution -27.74
Covariance contribution -0.12
Combinations/Pair 1.09
Mean z-score -1.66
Structure conservation index 0.88
SVM decision value 1.21
SVM RNA-class probability 0.930488
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 1255655 98 + 20766785
UGGCCCUGACUAGGCCAAUCACCCUUCUCACUGGCCAGUAACUCGAACCUGGCCUCGAGCAGGAG--CUUCACCGCAUUCGCAUCAAGUGUGACGCUUGU
(((((.......))))).....(((.(((...((((((..........))))))..))).)))((--(.((((.((...........)))))).)))... ( -30.90)
>DroSec_CAF1 7372 100 + 1
UGGCCCUGACUAGGCCAAUCACCCUUCUCCCUGGCCAGUAACUCGAACCUGGCCUCGAGCAGGUGAAGCUCACCACACUCGCAUCAAGUGUGACGCUUGC
(((((.......))))).(((((...(((...((((((..........))))))..)))..)))))(((....((((((.......))))))..)))... ( -34.80)
>DroSim_CAF1 13198 100 + 1
UGGCCCUGACUAGGCCAAUCACCCUUCUCACUGGCCAGUAACUCGAACCUGGCCUCGAGCAGGUGGAGCUCACCACAUUCGCAUCAAGUGUGACGCUUGC
(((((.......)))))..((((...(((...((((((..........))))))..)))..))))((((((((.((...........)))))).)))).. ( -33.60)
>DroEre_CAF1 11577 93 + 1
UGGCCCUGAGUAGGCCAAUAACCCUUCUCACUGGCCAGUAACUUGAACCUGGCCUCGAGCAGGAG--CUGCACCACAUUCGCAUCAAGUGUGACG-----
(((((.((((.(((........))).))))..)))))((.((((((.((((........))))..--.(((.........)))))))))...)).----- ( -29.00)
>DroYak_CAF1 10865 98 + 1
UGGCCCUGACUAGGCCAAUAACCCUUCUCACUGACCAGUAUCUCGAACCUGGCCUCGAGAAGGAG--UUGCACCACAUUCGGAUCAAGUGUGACGCUUGC
(((((.......)))))..((((((((((...(.((((..........)))).)..))))))).)--))((..((((((.......))))))..)).... ( -29.90)
>consensus
UGGCCCUGACUAGGCCAAUCACCCUUCUCACUGGCCAGUAACUCGAACCUGGCCUCGAGCAGGAG__CUUCACCACAUUCGCAUCAAGUGUGACGCUUGC
(((((.......))))).....(((.(((...((((((..........))))))..))).)))..........((((((.......))))))........ (-27.86 = -27.74 +  -0.12)

alignment

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secondary structure

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dotplot

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Window 9

Location 1,255,655 – 1,255,753
Length 98
Sequences 5
Columns 100
Reading direction reverse
Mean pairwise identity 89.54
Mean single sequence MFE -39.24
Consensus MFE -31.46
Energy contribution -31.90
Covariance contribution 0.44
Combinations/Pair 1.04
Mean z-score -2.13
Structure conservation index 0.80
SVM decision value 1.47
SVM RNA-class probability 0.956914
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 1255655 98 - 20766785
ACAAGCGUCACACUUGAUGCGAAUGCGGUGAAG--CUCCUGCUCGAGGCCAGGUUCGAGUUACUGGCCAGUGAGAAGGGUGAUUGGCCUAGUCAGGGCCA
....((((((....))))))....((......)--)((((.((((.((((((..........))))))..)))).))))....((((((.....)))))) ( -37.00)
>DroSec_CAF1 7372 100 - 1
GCAAGCGUCACACUUGAUGCGAGUGUGGUGAGCUUCACCUGCUCGAGGCCAGGUUCGAGUUACUGGCCAGGGAGAAGGGUGAUUGGCCUAGUCAGGGCCA
((...(..((((((((...))))))))..).)).((((((.(((..((((((..........)))))).)))....)))))).((((((.....)))))) ( -45.20)
>DroSim_CAF1 13198 100 - 1
GCAAGCGUCACACUUGAUGCGAAUGUGGUGAGCUCCACCUGCUCGAGGCCAGGUUCGAGUUACUGGCCAGUGAGAAGGGUGAUUGGCCUAGUCAGGGCCA
(((.((((((....))))))...))).........(((((.((((.((((((..........))))))..))))..)))))..((((((.....)))))) ( -38.80)
>DroEre_CAF1 11577 93 - 1
-----CGUCACACUUGAUGCGAAUGUGGUGCAG--CUCCUGCUCGAGGCCAGGUUCAAGUUACUGGCCAGUGAGAAGGGUUAUUGGCCUACUCAGGGCCA
-----(..((((.(((...))).))))..).((--(.(((.((((.((((((..........))))))..)))).))))))..((((((.....)))))) ( -34.30)
>DroYak_CAF1 10865 98 - 1
GCAAGCGUCACACUUGAUCCGAAUGUGGUGCAA--CUCCUUCUCGAGGCCAGGUUCGAGAUACUGGUCAGUGAGAAGGGUUAUUGGCCUAGUCAGGGCCA
....((..((((.(((...))).))))..))((--(.((((((((.((((((..........))))))..)))))))))))..((((((.....)))))) ( -40.90)
>consensus
GCAAGCGUCACACUUGAUGCGAAUGUGGUGAAC__CUCCUGCUCGAGGCCAGGUUCGAGUUACUGGCCAGUGAGAAGGGUGAUUGGCCUAGUCAGGGCCA
....((((((....)))))).................(((.((((.((((((..........))))))..)))).))).....((((((.....)))))) (-31.46 = -31.90 +   0.44)

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 09:24:20 2006