Locus 5693

Sequence ID 2R_DroMel_CAF1
Location 18,037,412 – 18,037,572
Length 160
Max. P 0.997205
window9114 window9115 window9116 window9117 window9118

overview

Window 4

Location 18,037,412 – 18,037,515
Length 103
Sequences 5
Columns 119
Reading direction forward
Mean pairwise identity 77.13
Mean single sequence MFE -21.57
Consensus MFE -13.28
Energy contribution -13.76
Covariance contribution 0.48
Combinations/Pair 1.11
Mean z-score -1.57
Structure conservation index 0.62
SVM decision value -0.03
SVM RNA-class probability 0.519164
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 18037412 103 + 20766785
AACCUUUUUUAUAGC----------------AACACCCCUUAUUUUUCCUUGUGCACCUCCUGCUUCACAAAUGUUAUUGUACGUCUGUUUCUGUUGCUGUUUCGCAGCAAGGAGCAAC
.............((----------------(.((...............)))))......(((((((((.((((......)))).))).....((((((.....)))))))))))).. ( -19.86)
>DroSec_CAF1 48041 101 + 1
UAGCUUU-UUUUAGC----------------AGCACCCCUU-UUUUUCCCUGUGCACCUCGUGCUUCACAAAUGUUAUUGUACGUCUGUUUCUGUUGCCGUUUCGCAGCAAGGAGCAAC
..(((..-....)))----------------.((((.....-.........))))......(((((((((.((((......)))).)))...((((((......)))))).)))))).. ( -24.04)
>DroSim_CAF1 47062 103 + 1
UAGCUUUUUUUUAGC----------------AGCACCCCUUAUUUUUCACUGUGCACCUCCUGCUUCACAAAUGUUAUUGUACGUCUGUUUCUGUUGCCGUUUCGCAGCAAGGAGCAAC
..(((.......)))----------------.((((...............))))......(((((((((.((((......)))).)))...((((((......)))))).)))))).. ( -23.36)
>DroEre_CAF1 49772 119 + 1
CGCCGCUUUUUUAUCAGAAAACAUCCCAUGGAACACCCAUUAUUUUUCCCAGUGCACCUCGUGCUUCACAAAUGUUAUUGUACCUCUGUUUCUAUUGCUGUUUCGCAGCAAGGAGCAAC
....(((((......(((((.......((((.....)))).........(((.((((...))))...((((......))))....)))))))).((((((.....)))))))))))... ( -22.40)
>DroYak_CAF1 48668 81 + 1
--------------------------------------UUUAUUUUUCGCUGUGCACCUCGUGCUUUACAAAUGUUAUUGUACCUCCGUCUUUGUUGCUGUUUCGCAGCAAGGAACAAC
--------------------------------------............(((((((...))))..(((((......)))))......((((((((((......))))))))))))).. ( -18.20)
>consensus
UACCUUUUUUUUAGC________________AACACCCCUUAUUUUUCCCUGUGCACCUCGUGCUUCACAAAUGUUAUUGUACGUCUGUUUCUGUUGCUGUUUCGCAGCAAGGAGCAAC
...................................................(((((...(((.........)))....)))))....(((((((((((......))))).))))))... (-13.28 = -13.76 +   0.48)

alignment

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secondary structure

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Window 5

Location 18,037,436 – 18,037,551
Length 115
Sequences 5
Columns 115
Reading direction forward
Mean pairwise identity 94.70
Mean single sequence MFE -28.69
Consensus MFE -22.90
Energy contribution -23.58
Covariance contribution 0.68
Combinations/Pair 1.07
Mean z-score -1.60
Structure conservation index 0.80
SVM decision value 0.20
SVM RNA-class probability 0.630507
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 18037436 115 + 20766785
UAUUUUUCCUUGUGCACCUCCUGCUUCACAAAUGUUAUUGUACGUCUGUUUCUGUUGCUGUUUCGCAGCAAGGAGCAACUGGCAAAUAUUUAAAUUCGUGCGCUAAGGCACACAA
.......((((((((((..........((((......))))..(((((((((((((((......))))).)))))))...)))..............)))))).))))....... ( -29.10)
>DroSec_CAF1 48064 114 + 1
U-UUUUUCCCUGUGCACCUCGUGCUUCACAAAUGUUAUUGUACGUCUGUUUCUGUUGCCGUUUCGCAGCAAGGAGCAACUGGCAAAUAUUUAAAUUCGUGCGCUAAGGCACACAA
.-......(((((((((...((((...((....))....))))(((((((((((((((......))))).)))))))...)))..............))))))..)))....... ( -29.10)
>DroSim_CAF1 47086 115 + 1
UAUUUUUCACUGUGCACCUCCUGCUUCACAAAUGUUAUUGUACGUCUGUUUCUGUUGCCGUUUCGCAGCAAGGAGCAACUGGCAAAUAUUUAAAUUCGUGCGCUAAGGCACACAA
............(((......(((((((((.((((......)))).)))...((((((......)))))).))))))....))).............(((.((....)).))).. ( -26.40)
>DroEre_CAF1 49812 115 + 1
UAUUUUUCCCAGUGCACCUCGUGCUUCACAAAUGUUAUUGUACCUCUGUUUCUAUUGCUGUUUCGCAGCAAGGAGCAACUGGCAAAUAUUUAAAUUCGUGCGCUAAGGCACACAA
....(((.(((((((((...))))...((((......)))).....(((((((..(((((.....))))))))))))))))).)))...........(((.((....)).))).. ( -29.30)
>DroYak_CAF1 48670 115 + 1
UAUUUUUCGCUGUGCACCUCGUGCUUUACAAAUGUUAUUGUACCUCCGUCUUUGUUGCUGUUUCGCAGCAAGGAACAACUGGCAAAUAUUUAAAUUCGUGCGCUAAGGCACACAA
........(.(((((....((..(.....(((((((..(((.......((((((((((......)))))))))).......))))))))))......)..)).....)))))).. ( -29.54)
>consensus
UAUUUUUCCCUGUGCACCUCGUGCUUCACAAAUGUUAUUGUACGUCUGUUUCUGUUGCUGUUUCGCAGCAAGGAGCAACUGGCAAAUAUUUAAAUUCGUGCGCUAAGGCACACAA
...........((((.....((((.....(((((((..(((.....((((((((((((......))))).)))))))....))))))))))........))))....)))).... (-22.90 = -23.58 +   0.68)

alignment

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secondary structure

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Window 6

Location 18,037,436 – 18,037,551
Length 115
Sequences 5
Columns 115
Reading direction reverse
Mean pairwise identity 94.70
Mean single sequence MFE -32.46
Consensus MFE -28.20
Energy contribution -27.68
Covariance contribution -0.52
Combinations/Pair 1.12
Mean z-score -2.29
Structure conservation index 0.87
SVM decision value 2.82
SVM RNA-class probability 0.997205
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 18037436 115 - 20766785
UUGUGUGCCUUAGCGCACGAAUUUAAAUAUUUGCCAGUUGCUCCUUGCUGCGAAACAGCAACAGAAACAGACGUACAAUAACAUUUGUGAAGCAGGAGGUGCACAAGGAAAAAUA
(((((..((((.((.(((((((..............(((.((..((((((.....)))))).)).)))....((......)))))))))..))..))))..)))))......... ( -30.20)
>DroSec_CAF1 48064 114 - 1
UUGUGUGCCUUAGCGCACGAAUUUAAAUAUUUGCCAGUUGCUCCUUGCUGCGAAACGGCAACAGAAACAGACGUACAAUAACAUUUGUGAAGCACGAGGUGCACAGGGAAAAA-A
((((((((....)))))))).........(((.((.((.((.(((((.(((.....(....)....(((((.((......)).)))))...)))))))).)))).)).)))..-. ( -33.30)
>DroSim_CAF1 47086 115 - 1
UUGUGUGCCUUAGCGCACGAAUUUAAAUAUUUGCCAGUUGCUCCUUGCUGCGAAACGGCAACAGAAACAGACGUACAAUAACAUUUGUGAAGCAGGAGGUGCACAGUGAAAAAUA
(((((..((((.((.(((((((........(((((..((((........))))...)))))...........((......)))))))))..))..))))..)))))......... ( -32.10)
>DroEre_CAF1 49812 115 - 1
UUGUGUGCCUUAGCGCACGAAUUUAAAUAUUUGCCAGUUGCUCCUUGCUGCGAAACAGCAAUAGAAACAGAGGUACAAUAACAUUUGUGAAGCACGAGGUGCACUGGGAAAAAUA
((((((((....)))))))).........(((.(((((.((.((((((((.....))))..........(...(((((......)))))...)..)))).))))))).))).... ( -35.80)
>DroYak_CAF1 48670 115 - 1
UUGUGUGCCUUAGCGCACGAAUUUAAAUAUUUGCCAGUUGUUCCUUGCUGCGAAACAGCAACAAAGACGGAGGUACAAUAACAUUUGUAAAGCACGAGGUGCACAGCGAAAAAUA
(((((..((((.((..((((((.....((((((((.(((.....((((((.....))))))....)))...)))).))))..))))))...))..))))..)))))......... ( -30.90)
>consensus
UUGUGUGCCUUAGCGCACGAAUUUAAAUAUUUGCCAGUUGCUCCUUGCUGCGAAACAGCAACAGAAACAGACGUACAAUAACAUUUGUGAAGCACGAGGUGCACAGGGAAAAAUA
(((((..(((((((...(((((......)))))...)))(((..((((((.....)))))).....(((((.((......)).)))))..)))..))))..)))))......... (-28.20 = -27.68 +  -0.52)

alignment

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secondary structure

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Window 7

Location 18,037,476 – 18,037,572
Length 96
Sequences 5
Columns 96
Reading direction forward
Mean pairwise identity 96.67
Mean single sequence MFE -22.32
Consensus MFE -18.28
Energy contribution -18.76
Covariance contribution 0.48
Combinations/Pair 1.10
Mean z-score -2.23
Structure conservation index 0.82
SVM decision value 1.33
SVM RNA-class probability 0.943102
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 18037476 96 + 20766785
UACGUCUGUUUCUGUUGCUGUUUCGCAGCAAGGAGCAACUGGCAAAUAUUUAAAUUCGUGCGCUAAGGCACACAAUAAAAACGUAAACAAAUACAA
(((((.((((((((((((......))))).)))))))....................(((.((....)).))).......)))))........... ( -23.40)
>DroSec_CAF1 48103 96 + 1
UACGUCUGUUUCUGUUGCCGUUUCGCAGCAAGGAGCAACUGGCAAAUAUUUAAAUUCGUGCGCUAAGGCACACAAUAAAAACGUAAACAAAUACAA
(((((.((((((((((((......))))).)))))))....................(((.((....)).))).......)))))........... ( -22.90)
>DroSim_CAF1 47126 96 + 1
UACGUCUGUUUCUGUUGCCGUUUCGCAGCAAGGAGCAACUGGCAAAUAUUUAAAUUCGUGCGCUAAGGCACACAAUAAAAACGUAAACAAAUACAA
(((((.((((((((((((......))))).)))))))....................(((.((....)).))).......)))))........... ( -22.90)
>DroEre_CAF1 49852 96 + 1
UACCUCUGUUUCUAUUGCUGUUUCGCAGCAAGGAGCAACUGGCAAAUAUUUAAAUUCGUGCGCUAAGGCACACAAUAAAAACGUAAACAAAUACAA
..((..(((((((..(((((.....))))))))))))...))...............(((.((....)).))).........(((......))).. ( -21.20)
>DroYak_CAF1 48710 96 + 1
UACCUCCGUCUUUGUUGCUGUUUCGCAGCAAGGAACAACUGGCAAAUAUUUAAAUUCGUGCGCUAAGGCACACAAUAAAAACGUAAACAAAUACAA
..((....((((((((((......))))))))))......))...............(((.((....)).))).........(((......))).. ( -21.20)
>consensus
UACGUCUGUUUCUGUUGCUGUUUCGCAGCAAGGAGCAACUGGCAAAUAUUUAAAUUCGUGCGCUAAGGCACACAAUAAAAACGUAAACAAAUACAA
(((((..(((((((((((......))))).)))))).....................(((.((....)).))).......)))))........... (-18.28 = -18.76 +   0.48)

alignment

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secondary structure

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dotplot

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Window 8

Location 18,037,476 – 18,037,572
Length 96
Sequences 5
Columns 96
Reading direction reverse
Mean pairwise identity 96.67
Mean single sequence MFE -24.22
Consensus MFE -21.92
Energy contribution -21.20
Covariance contribution -0.72
Combinations/Pair 1.10
Mean z-score -1.66
Structure conservation index 0.91
SVM decision value 1.54
SVM RNA-class probability 0.962107
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 18037476 96 - 20766785
UUGUAUUUGUUUACGUUUUUAUUGUGUGCCUUAGCGCACGAAUUUAAAUAUUUGCCAGUUGCUCCUUGCUGCGAAACAGCAACAGAAACAGACGUA
...........(((((((...((((((((....))))))))................(((.((..((((((.....)))))).)).)))))))))) ( -23.40)
>DroSec_CAF1 48103 96 - 1
UUGUAUUUGUUUACGUUUUUAUUGUGUGCCUUAGCGCACGAAUUUAAAUAUUUGCCAGUUGCUCCUUGCUGCGAAACGGCAACAGAAACAGACGUA
((((.((((((..((((((..((((((((....))))))))............((.(((........)))))))))))..)))))).))))..... ( -26.00)
>DroSim_CAF1 47126 96 - 1
UUGUAUUUGUUUACGUUUUUAUUGUGUGCCUUAGCGCACGAAUUUAAAUAUUUGCCAGUUGCUCCUUGCUGCGAAACGGCAACAGAAACAGACGUA
((((.((((((..((((((..((((((((....))))))))............((.(((........)))))))))))..)))))).))))..... ( -26.00)
>DroEre_CAF1 49852 96 - 1
UUGUAUUUGUUUACGUUUUUAUUGUGUGCCUUAGCGCACGAAUUUAAAUAUUUGCCAGUUGCUCCUUGCUGCGAAACAGCAAUAGAAACAGAGGUA
..(((......)))(((((((((((((((......))))...........(((((.(((........))))))))...)))))))))))....... ( -23.20)
>DroYak_CAF1 48710 96 - 1
UUGUAUUUGUUUACGUUUUUAUUGUGUGCCUUAGCGCACGAAUUUAAAUAUUUGCCAGUUGUUCCUUGCUGCGAAACAGCAACAAAGACGGAGGUA
.............(((((((.((((((((....))))))))........................((((((.....)))))).)))))))...... ( -22.50)
>consensus
UUGUAUUUGUUUACGUUUUUAUUGUGUGCCUUAGCGCACGAAUUUAAAUAUUUGCCAGUUGCUCCUUGCUGCGAAACAGCAACAGAAACAGACGUA
..(((..((((((.((((.....((((((....)))))))))).))))))..)))..(((.((..((((((.....)))))).)).)))....... (-21.92 = -21.20 +  -0.72)

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 11:52:00 2006