Locus 5630

Sequence ID 3R_DroMel_CAF1
Location 14,824,650 – 14,825,007
Length 357
Max. P 0.979265
window9172 window9173 window9174 window9175 window9176 window9177

overview

Window 2

Location 14,824,650 – 14,824,770
Length 120
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 98.89
Mean single sequence MFE -29.40
Consensus MFE -27.69
Energy contribution -27.80
Covariance contribution 0.11
Combinations/Pair 1.03
Mean z-score -1.74
Structure conservation index 0.94
SVM decision value 0.26
SVM RNA-class probability 0.657323
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 14824650 120 + 27905053
AGUUUUCCUAUGCAAAUCUGAGCCGCAUUCGCAUUCCCGACAAAUUUUUGGGAAAGUUGACACAAUUUGAACCCCUUCAACCAGCUUUGGCCAGUCAGGCAUUCAGAUGCUCUGAGACAA
.(((((.....(((..((((((((((....)).(((((((.......)))))))...((((.....(((((....)))))((......))...)))))))..))))))))...))))).. ( -30.00)
>DroSec_CAF1 2818 120 + 1
AGUUUUCCUAUGCAAAUCUGAGCCGCAUUCGCAUUCCCGACAAAUUUUUGGGAAAGUUGACACAAUUUGAACCCCUUCAACCAGCUUUGGCCAGUCAGCCAUUCAGAUGCUCUGAAACAA
.(((((.....(((..((((((..((....)).(((((((.......))))))).((((((.....(((((....)))))((......))...))))))..)))))))))...))))).. ( -29.10)
>DroSim_CAF1 2952 120 + 1
AGUUUUCCUAUGCAAAUCUGAGCCGCAUUCGCAUUCCCGACAAAUUUUUGGGAAAGUUGACACAAUUUGAACCCCUUCAACCAGCUUUGGCCAGUCAGCCAUUCAGAUGCUCUGAAACAA
.(((((.....(((..((((((..((....)).(((((((.......))))))).((((((.....(((((....)))))((......))...))))))..)))))))))...))))).. ( -29.10)
>consensus
AGUUUUCCUAUGCAAAUCUGAGCCGCAUUCGCAUUCCCGACAAAUUUUUGGGAAAGUUGACACAAUUUGAACCCCUUCAACCAGCUUUGGCCAGUCAGCCAUUCAGAUGCUCUGAAACAA
.(((((.....(((..((((((..((....)).(((((((.......))))))).((((((.....(((((....)))))((......))...))))))..)))))))))...))))).. (-27.69 = -27.80 +   0.11)

alignment

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secondary structure

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Window 3

Location 14,824,690 – 14,824,810
Length 120
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 95.28
Mean single sequence MFE -39.50
Consensus MFE -37.89
Energy contribution -37.57
Covariance contribution -0.33
Combinations/Pair 1.09
Mean z-score -2.69
Structure conservation index 0.96
SVM decision value 1.83
SVM RNA-class probability 0.979265
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 14824690 120 - 27905053
UGCUGCUCACGGUUUUAGCCCCAAAGACCGGCGAUGUUAUUUGUCUCAGAGCAUCUGAAUGCCUGACUGGCCAAAGCUGGUUGAAGGGGUUCAAAUUGUGUCAACUUUCCCAAAAAUUUG
...((..((((((((.((((((...(((((((((((((...........)))))).....(((.....)))....)))))))...)))))).)))))))).))................. ( -39.40)
>DroSec_CAF1 2858 117 - 1
---UGCUCACGGUUUUAGCCCCAAAGACCAGUGAUGUUAUUUGUUUCAGAGCAUCUGAAUGGCUGACUGGCCAAAGCUGGUUGAAGGGGUUCAAAUUGUGUCAACUUUCCCAAAAAUUUG
---((..((((((((.((((((...(((((((............(((((.....)))))(((((....)))))..)))))))...)))))).)))))))).))................. ( -40.50)
>DroSim_CAF1 2992 120 - 1
CGCUGCUCACGGUUUUAGUCCCAAAGACCAGCGAUGUUAUUUGUUUCAGAGCAUCUGAAUGGCUGACUGGCCAAAGCUGGUUGAAGGGGUUCAAAUUGUGUCAACUUUCCCAAAAAUUUG
...((..((((((((.(..(((...(((((((............(((((.....)))))(((((....)))))..)))))))...)))..).)))))))).))................. ( -38.60)
>consensus
_GCUGCUCACGGUUUUAGCCCCAAAGACCAGCGAUGUUAUUUGUUUCAGAGCAUCUGAAUGGCUGACUGGCCAAAGCUGGUUGAAGGGGUUCAAAUUGUGUCAACUUUCCCAAAAAUUUG
...((..((((((((.((((((...(((((((((((((...........))))))....(((((....)))))..)))))))...)))))).)))))))).))................. (-37.89 = -37.57 +  -0.33)

alignment

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secondary structure

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Window 4

Location 14,824,810 – 14,824,927
Length 117
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 96.92
Mean single sequence MFE -41.80
Consensus MFE -41.77
Energy contribution -41.77
Covariance contribution 0.00
Combinations/Pair 1.00
Mean z-score -2.06
Structure conservation index 1.00
SVM decision value 1.26
SVM RNA-class probability 0.937679
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 14824810 117 + 27905053
U---UGUGCCUUUCACUUGGCCAGGCUCUUAGCCCGGAGUCCCAAAUGGCCAACACCUUGCCAACACCAGACACACUCGGCUAAUCGCCGCCUGGCCAUCUGCGGAGGAGUCCUCGGCCA
.---((.(((...((..(((((((((..((((((.((.(((.....((((.........))))......)))...)).)))))).....)))))))))..))..((((...))))))))) ( -41.80)
>DroSec_CAF1 2975 115 + 1
-----GUGCCUUUCACUUGGCCAGGCUCUUAGCCCGGAGUCCCAAAUGGCCAACACCUUGCCAACACCAGACACACUCGGCUAAUCGCCGCCUGGCCAUCUGCGGAGGAGUCCUCGGCCA
-----(.(((...((..(((((((((..((((((.((.(((.....((((.........))))......)))...)).)))))).....)))))))))..))..((((...)))))))). ( -41.70)
>DroSim_CAF1 3112 120 + 1
UAGUAGUGCCUUUCACUUGGCCAGGCUCUUAGCCCGGAGUCCCAAAUGGCCAACACCUUGCCAACACCAGACACACUCGGCUAAUCGCCGCCUGGCCAUCUGCGGAGGAGUCCUCGGCCA
.....(.(((...((..(((((((((..((((((.((.(((.....((((.........))))......)))...)).)))))).....)))))))))..))..((((...)))))))). ( -41.90)
>consensus
U____GUGCCUUUCACUUGGCCAGGCUCUUAGCCCGGAGUCCCAAAUGGCCAACACCUUGCCAACACCAGACACACUCGGCUAAUCGCCGCCUGGCCAUCUGCGGAGGAGUCCUCGGCCA
.....(.(((...((..(((((((((..((((((.((.(((.....((((.........))))......)))...)).)))))).....)))))))))..))..((((...)))))))). (-41.77 = -41.77 +   0.00)

alignment

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secondary structure

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dotplot

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Window 5

Location 14,824,810 – 14,824,927
Length 117
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 96.92
Mean single sequence MFE -50.57
Consensus MFE -50.20
Energy contribution -50.20
Covariance contribution -0.00
Combinations/Pair 1.00
Mean z-score -1.77
Structure conservation index 0.99
SVM decision value 0.73
SVM RNA-class probability 0.834312
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 14824810 117 - 27905053
UGGCCGAGGACUCCUCCGCAGAUGGCCAGGCGGCGAUUAGCCGAGUGUGUCUGGUGUUGGCAAGGUGUUGGCCAUUUGGGACUCCGGGCUAAGAGCCUGGCCAAGUGAAAGGCACA---A
(((((..(((....(((.(((((((((((.((((.....))))....((((.......)))).....)))))))))))))).)))((((.....))))))))).(((.....))).---. ( -50.40)
>DroSec_CAF1 2975 115 - 1
UGGCCGAGGACUCCUCCGCAGAUGGCCAGGCGGCGAUUAGCCGAGUGUGUCUGGUGUUGGCAAGGUGUUGGCCAUUUGGGACUCCGGGCUAAGAGCCUGGCCAAGUGAAAGGCAC-----
..(((((((...))))(((...(((((((((.....((((((..(.(.((((.(...((((.........))))..).)))).)).))))))..))))))))).)))...)))..----- ( -50.20)
>DroSim_CAF1 3112 120 - 1
UGGCCGAGGACUCCUCCGCAGAUGGCCAGGCGGCGAUUAGCCGAGUGUGUCUGGUGUUGGCAAGGUGUUGGCCAUUUGGGACUCCGGGCUAAGAGCCUGGCCAAGUGAAAGGCACUACUA
(((((..(((....(((.(((((((((((.((((.....))))....((((.......)))).....)))))))))))))).)))((((.....)))))))))((((.....)))).... ( -51.10)
>consensus
UGGCCGAGGACUCCUCCGCAGAUGGCCAGGCGGCGAUUAGCCGAGUGUGUCUGGUGUUGGCAAGGUGUUGGCCAUUUGGGACUCCGGGCUAAGAGCCUGGCCAAGUGAAAGGCAC____A
..(((((((...))))(((...(((((((((.....((((((..(.(.((((.(...((((.........))))..).)))).)).))))))..))))))))).)))...)))....... (-50.20 = -50.20 +  -0.00)

alignment

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secondary structure

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dotplot

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Window 6

Location 14,824,887 – 14,825,007
Length 120
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 98.33
Mean single sequence MFE -36.20
Consensus MFE -34.59
Energy contribution -34.70
Covariance contribution 0.11
Combinations/Pair 1.03
Mean z-score -1.84
Structure conservation index 0.96
SVM decision value 0.51
SVM RNA-class probability 0.762616
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 14824887 120 + 27905053
CUAAUCGCCGCCUGGCCAUCUGCGGAGGAGUCCUCGGCCACAAUCUUGACAUUAUUCUCCAUGGAGAGCUCUUCGCGCGGCGACAAUGCGGAAAAACAACUUUCGCAAAUUCUUUCAAUU
....(((((((.(((((.......((((...)))))))))...............((((....))))((.....)))))))))...(((((((.......)))))))............. ( -36.01)
>DroSec_CAF1 3050 120 + 1
CUAAUCGCCGCCUGGCCAUCUGCGGAGGAGUCCUCGGCCACAAUUUUGACAUUAUUCUCCAUGGAGAGCUCCUCGCGCGGCGACAAUGCGGAAAAACAACUUUCGCAAAUUCUUUCAAUU
....(((((((...((.....)).((((((..((((....)........(((........))))))..))))))..)))))))...(((((((.......)))))))............. ( -37.10)
>DroSim_CAF1 3192 120 + 1
CUAAUCGCCGCCUGGCCAUCUGCGGAGGAGUCCUCGGCCACAAUCUUGACAUUAUUCUCCAUGGUGAGCUCCUCGCGCGGCGACAAUGCGGAAAAACAACUUUCGCAAAUUCUUUCAAUU
....(((((((...((.....)).((((((..((((.(((.......((......))....)))))))))))))..)))))))...(((((((.......)))))))............. ( -35.50)
>consensus
CUAAUCGCCGCCUGGCCAUCUGCGGAGGAGUCCUCGGCCACAAUCUUGACAUUAUUCUCCAUGGAGAGCUCCUCGCGCGGCGACAAUGCGGAAAAACAACUUUCGCAAAUUCUUUCAAUU
....(((((((...((.....)).((((((..((((....)........(((........))))))..))))))..)))))))...(((((((.......)))))))............. (-34.59 = -34.70 +   0.11)

alignment

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secondary structure

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dotplot

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Window 7

Location 14,824,887 – 14,825,007
Length 120
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 98.33
Mean single sequence MFE -40.80
Consensus MFE -39.37
Energy contribution -40.03
Covariance contribution 0.67
Combinations/Pair 1.00
Mean z-score -1.48
Structure conservation index 0.96
SVM decision value 0.01
SVM RNA-class probability 0.539679
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 14824887 120 - 27905053
AAUUGAAAGAAUUUGCGAAAGUUGUUUUUCCGCAUUGUCGCCGCGCGAAGAGCUCUCCAUGGAGAAUAAUGUCAAGAUUGUGGCCGAGGACUCCUCCGCAGAUGGCCAGGCGGCGAUUAG
....((((((....((....))..))))))......((((((((((.....))((((....))))...............((((((.(((....))).....)))))).))))))))... ( -38.40)
>DroSec_CAF1 3050 120 - 1
AAUUGAAAGAAUUUGCGAAAGUUGUUUUUCCGCAUUGUCGCCGCGCGAGGAGCUCUCCAUGGAGAAUAAUGUCAAAAUUGUGGCCGAGGACUCCUCCGCAGAUGGCCAGGCGGCGAUUAG
....((((((....((....))..))))))...((((((((((((.((((((..(((...((...(((((......)))))..)))))..))))))))).(.....).)))))))))... ( -43.60)
>DroSim_CAF1 3192 120 - 1
AAUUGAAAGAAUUUGCGAAAGUUGUUUUUCCGCAUUGUCGCCGCGCGAGGAGCUCACCAUGGAGAAUAAUGUCAAGAUUGUGGCCGAGGACUCCUCCGCAGAUGGCCAGGCGGCGAUUAG
....((((((....((....))..))))))...((((((((((((.((((((....((.(((...(((((......)))))..))).)).))))))))).(.....).)))))))))... ( -40.40)
>consensus
AAUUGAAAGAAUUUGCGAAAGUUGUUUUUCCGCAUUGUCGCCGCGCGAGGAGCUCUCCAUGGAGAAUAAUGUCAAGAUUGUGGCCGAGGACUCCUCCGCAGAUGGCCAGGCGGCGAUUAG
....((((((....((....))..))))))...((((((((((((.((((((...(((.(((...(((((......)))))..))).)))))))))))).(.....).)))))))))... (-39.37 = -40.03 +   0.67)

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 11:59:53 2006