Locus 419

Sequence ID 2L_DroMel_CAF1
Location 1,237,629 – 1,237,852
Length 223
Max. P 0.976263
window676 window677 window678 window679

overview

Window 6

Location 1,237,629 – 1,237,732
Length 103
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 83.86
Mean single sequence MFE -28.27
Consensus MFE -22.09
Energy contribution -22.37
Covariance contribution 0.28
Combinations/Pair 1.03
Mean z-score -1.74
Structure conservation index 0.78
SVM decision value 0.20
SVM RNA-class probability 0.631446
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 1237629 103 - 22407834
AUAUUAAUUAUAAAACAAUAAUUGAAUUGUGCUCUU------GCUCUUGGCAGCUG---AGUGAGCGUCGAAAGGUGAGCGAUUUUCCUCGCCCCCGAAUUUCCUCGCACAC--------
...((((((((......))))))))..(((((..((------((.....))))..(---((.(((..(((...((((((.(.....)))))))..)))..))))))))))).-------- ( -29.30)
>DroSec_CAF1 15074 107 - 1
AUAUUAAUUAUAAAACAAUAAUUGAAUUGUGCUCUU------GCUCUUGGCAGCUG---AGUGAGCGUCGAAAGGUGAGCGAUUUUCCUCGCCCCCGAUUUUCCUCUCACACAC----AC
...((((((((......))))))))..((((...((------((.....)))).((---((.(((.((((...((((((.(.....)))))))..)))).)))..)))))))).----.. ( -27.00)
>DroYak_CAF1 11132 117 - 1
AUAUUAAUUAUAAAACAAUAAUUGAAUUGUGCUCUUGCUCUUGCUCUUGGCAGCUUGGCAGUGAGCGUCGAAAGGUGAGCGAUU-UCCUCGCCCCCGGAAAA--UCACACACACACCACC
...((((((((......))))))))..((((....((((.((((.....))))...))))((((...(((...((((((.(...-.)))))))..)))....--)))).))))....... ( -28.50)
>consensus
AUAUUAAUUAUAAAACAAUAAUUGAAUUGUGCUCUU______GCUCUUGGCAGCUG___AGUGAGCGUCGAAAGGUGAGCGAUUUUCCUCGCCCCCGAAUUUCCUCACACACAC_____C
...((((((((......))))))))..((((((((((((...(((......)))..))))).)))).(((...((((((.(.....)))))))..)))..........)))......... (-22.09 = -22.37 +   0.28)

alignment

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secondary structure

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dotplot

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Window 7

Location 1,237,661 – 1,237,772
Length 111
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 95.24
Mean single sequence MFE -32.67
Consensus MFE -27.84
Energy contribution -28.09
Covariance contribution 0.25
Combinations/Pair 1.00
Mean z-score -1.72
Structure conservation index 0.85
SVM decision value 0.16
SVM RNA-class probability 0.612980
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 1237661 111 - 22407834
CAGCUUCCCAGCUGCUGCUGAUGCGAUUUUGAUGUGCAAAAUAUUAAUUAUAAAACAAUAAUUGAAUUGUGCUCUU------GCUCUUGGCAGCUG---AGUGAGCGUCGAAAGGUGAGC
..(((..(((((((((...((.((((....((.(..(((....((((((((......)))))))).)))..)))))------))))..))))))))---.)..))).((....))..... ( -33.50)
>DroSec_CAF1 15110 111 - 1
CAGCUUCCCAGCUGCUGCUGAUGCGAUUUUGAUGUGCAAAAUAUUAAUUAUAAAACAAUAAUUGAAUUGUGCUCUU------GCUCUUGGCAGCUG---AGUGAGCGUCGAAAGGUGAGC
..(((..(((((((((...((.((((....((.(..(((....((((((((......)))))))).)))..)))))------))))..))))))))---.)..))).((....))..... ( -33.50)
>DroSim_CAF1 11255 111 - 1
CAGCUUCCCAGCUGCUGCUGAUGCGAUUUUGAUGUGCAAAAUAUUAAUUAUAAAACAAUAAUUGAAUUGUGCUCUU------GCUCUUGGCAGCUG---AGUGAACGUCGAAAGGUGAGC
..((((((((((((((...((.((((....((.(..(((....((((((((......)))))))).)))..)))))------))))..))))))))---.).)).(..(....)..)))) ( -30.90)
>DroYak_CAF1 11169 120 - 1
CAGCUUCCCAGCUGCUGCUGAUGCGAUUUUGAUGUGCAAAAUAUUAAUUAUAAAACAAUAAUUGAAUUGUGCUCUUGCUCUUGCUCUUGGCAGCUUGGCAGUGAGCGUCGAAAGGUGAGC
..((((((((((....))))......((((((((((((.(((.((((((((......))))))))))).)))(((((((.((((.....))))...))))).))))))))))))).)))) ( -32.80)
>consensus
CAGCUUCCCAGCUGCUGCUGAUGCGAUUUUGAUGUGCAAAAUAUUAAUUAUAAAACAAUAAUUGAAUUGUGCUCUU______GCUCUUGGCAGCUG___AGUGAGCGUCGAAAGGUGAGC
..(((...((((((((...((.((......((.(..(((....((((((((......)))))))).)))..)))........))))..))))))))...)))...(..(....)..)... (-27.84 = -28.09 +   0.25)

alignment

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secondary structure

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dotplot

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Window 8

Location 1,237,696 – 1,237,812
Length 116
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 97.88
Mean single sequence MFE -38.50
Consensus MFE -38.28
Energy contribution -38.27
Covariance contribution -0.00
Combinations/Pair 1.00
Mean z-score -2.78
Structure conservation index 0.99
SVM decision value 1.77
SVM RNA-class probability 0.976263
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 1237696 116 - 22407834
CGCCCAUAAGUGCGUGGGAGGCGUUCGUGGAAAUUAGCGGCAGCUUCCCAGCUGCUGCUGAUGCGAUUUUGAUGUGCAAAAUAUUAAUUAUAAAACAAUAAUUGAAUUGUGCUCUU----
((((((..(((((.......)))))..)))..(((((((((((((....)))))))))))))))).....((.(..(((....((((((((......)))))))).)))..)))..---- ( -38.10)
>DroSec_CAF1 15145 116 - 1
CGCCCAUAAGUGCGUGGGAGGCGUUCGUGGAAAUUAGCGGCAGCUUCCCAGCUGCUGCUGAUGCGAUUUUGAUGUGCAAAAUAUUAAUUAUAAAACAAUAAUUGAAUUGUGCUCUU----
((((((..(((((.......)))))..)))..(((((((((((((....)))))))))))))))).....((.(..(((....((((((((......)))))))).)))..)))..---- ( -38.10)
>DroSim_CAF1 11290 116 - 1
CGCCCAUAAGUGCGUGGGAGGCGUUCGUGGAAAUUAGCGGCAGCUUCCCAGCUGCUGCUGAUGCGAUUUUGAUGUGCAAAAUAUUAAUUAUAAAACAAUAAUUGAAUUGUGCUCUU----
((((((..(((((.......)))))..)))..(((((((((((((....)))))))))))))))).....((.(..(((....((((((((......)))))))).)))..)))..---- ( -38.10)
>DroYak_CAF1 11209 120 - 1
CGCCCAUAAGUGCGUGGGAGGCGUUGGUGGAAAUUAGCGGCAGCUUCCCAGCUGCUGCUGAUGCGAUUUUGAUGUGCAAAAUAUUAAUUAUAAAACAAUAAUUGAAUUGUGCUCUUGCUC
.((.(....).))(..((((((((..(.....(((((((((((((....)))))))))))))......)..))))((((....((((((((......)))))))).)))).))))..).. ( -39.70)
>consensus
CGCCCAUAAGUGCGUGGGAGGCGUUCGUGGAAAUUAGCGGCAGCUUCCCAGCUGCUGCUGAUGCGAUUUUGAUGUGCAAAAUAUUAAUUAUAAAACAAUAAUUGAAUUGUGCUCUU____
(((((((....((((.....))))..))))..(((((((((((((....)))))))))))))))).....((.(..(((....((((((((......)))))))).)))..)))...... (-38.28 = -38.27 +  -0.00)

alignment

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secondary structure

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dotplot

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Window 9

Location 1,237,732 – 1,237,852
Length 120
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 94.86
Mean single sequence MFE -47.97
Consensus MFE -42.95
Energy contribution -43.83
Covariance contribution 0.87
Combinations/Pair 1.05
Mean z-score -2.29
Structure conservation index 0.90
SVM decision value 1.38
SVM RNA-class probability 0.948075
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 1237732 120 - 22407834
AACUCCCCCCCUCCAUCAACCAGUGAAUGUGCGUGUGCCACGCCCAUAAGUGCGUGGGAGGCGUUCGUGGAAAUUAGCGGCAGCUUCCCAGCUGCUGCUGAUGCGAUUUUGAUGUGCAAA
.............(((((((((.(((....((((.(.((((((.(....).)))))).).))))))))))..(((((((((((((....)))))))))))))......))))))...... ( -47.00)
>DroSec_CAF1 15181 120 - 1
AACUCCCCCCUUCCAUCAACCGGCGAAUGUGCGUGUGCCACGCCCAUAAGUGCGUGGGAGGCGUUCGUGGAAAUUAGCGGCAGCUUCCCAGCUGCUGCUGAUGCGAUUUUGAUGUGCAAA
.............(((((((((.(((....((((.(.((((((.(....).)))))).).))))))))))..(((((((((((((....)))))))))))))......))))))...... ( -48.40)
>DroSim_CAF1 11326 120 - 1
AGCUCCCCCUUUCCAUCAACCAGCGAAUGUGCGUGUGCCACGCCCAUAAGUGCGUGGGAGGCGUUCGUGGAAAUUAGCGGCAGCUUCCCAGCUGCUGCUGAUGCGAUUUUGAUGUGCAAA
.............(((((((((.(((....((((.(.((((((.(....).)))))).).))))))))))..(((((((((((((....)))))))))))))......))))))...... ( -48.80)
>DroYak_CAF1 11249 119 - 1
AACUGCCCCCCUCCCCC-ACCUUUGAAUGUGCGUGUGCCACGCCCAUAAGUGCGUGGGAGGCGUUGGUGGAAAUUAGCGGCAGCUUCCCAGCUGCUGCUGAUGCGAUUUUGAUGUGCAAA
...(((.........((-(((.........((((.(.((((((.(....).)))))).).)))).)))))..(((((((((((((....))))))))))))).............))).. ( -47.70)
>consensus
AACUCCCCCCCUCCAUCAACCAGCGAAUGUGCGUGUGCCACGCCCAUAAGUGCGUGGGAGGCGUUCGUGGAAAUUAGCGGCAGCUUCCCAGCUGCUGCUGAUGCGAUUUUGAUGUGCAAA
.............(((((((((.(((....((((.(.((((((.(....).)))))).).))))))))))..(((((((((((((....)))))))))))))......))))))...... (-42.95 = -43.83 +   0.87)

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 09:35:43 2006