Locus 2329

Sequence ID 2R_DroMel_CAF1
Location 8,539,288 – 8,539,460
Length 172
Max. P 0.997684
window3840 window3841 window3842 window3843

overview

Window 0

Location 8,539,288 – 8,539,380
Length 92
Sequences 5
Columns 113
Reading direction reverse
Mean pairwise identity 82.03
Mean single sequence MFE -35.58
Consensus MFE -25.34
Energy contribution -26.54
Covariance contribution 1.20
Combinations/Pair 1.12
Mean z-score -2.09
Structure conservation index 0.71
SVM decision value 0.97
SVM RNA-class probability 0.892063
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 8539288 92 - 20766785
AAUCGCGAUACCAAACGAGCGGCGAGAGCGACAAG---------------------CGGCAAGCGGCAAGAUACGAGAUUCGGUGCCGAAAGCCAGUUGCCAAUUGCGACGGC
..(((((((..(....)...(((((..((.....)---------------------)(((...(((((.((........))..)))))...)))..))))).))))))).... ( -30.40)
>DroSec_CAF1 14865 85 - 1
AAUCGCGAUACCAAACGAGUGGCGAGAGC----------------------------GGCGAGCGGCAAGAUUCGAGAUUCGGUGCCGAAAGCCAGUUGCCAAUUGCGACGGC
..(((((((....(((.....((....))----------------------------(((...(((((.((........))..)))))...))).)))....))))))).... ( -30.60)
>DroSim_CAF1 18391 92 - 1
AAUCGCGAUACCAAACGAGUGGCGAGAGCGGCAAG---------------------CGGCGAGCGGCAAGAUUCGAGAUUCGGUGCCGAAAGCCAGUUGCCAAUUGCGACGGC
..(((((((............((....))(((((.---------------------.(((...(((((.((........))..)))))...)))..))))).))))))).... ( -36.70)
>DroEre_CAF1 4158 98 - 1
AAUCGCGAUACCA-ACGAGCGGCAAGAGCAGCGAGC--------------UGCAAGCCGCAAGCGGCAAGAUUCGAGAUUCGGUGCCGAAAGCCAGUUGCCAAUUGCGACGGC
..(((((((..((-((..(((((....((((....)--------------)))..)))))...(((((.((........))..))))).......))))...))))))).... ( -36.80)
>DroYak_CAF1 18080 112 - 1
AAUCGCGAUACCA-GCGAGCGGCGAGAGCAGCAAGCAGCAAGUUGCAAGUUGCAAGCCGCAAGUCGCAAGAUUCAAGAUUCGGUGCCGAAAGCCAGUUGCCAAUUGCGACGGC
..((((.......-))))(((((....(((((..((((....))))..)))))..))))).((((....)))).....((((....)))).(((.(((((.....)))))))) ( -43.40)
>consensus
AAUCGCGAUACCAAACGAGCGGCGAGAGCAGCAAG_____________________CGGCAAGCGGCAAGAUUCGAGAUUCGGUGCCGAAAGCCAGUUGCCAAUUGCGACGGC
..(((((((....(((..((.((....)).)).........................(((...(((((.((........))..)))))...))).)))....))))))).... (-25.34 = -26.54 +   1.20)

alignment

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secondary structure

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dotplot

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Window 1

Location 8,539,328 – 8,539,420
Length 92
Sequences 5
Columns 113
Reading direction forward
Mean pairwise identity 82.42
Mean single sequence MFE -30.96
Consensus MFE -20.38
Energy contribution -20.18
Covariance contribution -0.20
Combinations/Pair 1.12
Mean z-score -3.23
Structure conservation index 0.66
SVM decision value 2.40
SVM RNA-class probability 0.993441
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 8539328 92 + 20766785
UAUCUUGCCGCUUGCCG---------------------CUUGUCGCUCUCGCCGCUCGUUUGGUAUCGCGAUUGAAAUCGCAAUUAAGUUUUAUUUUGUGGCGAGCAUUUUUU
.........((((((((---------------------(.((..(((...((((......))))...(((((....))))).....)))..))....)))))))))....... ( -25.90)
>DroSec_CAF1 14905 85 + 1
AAUCUUGCCGCUCGCC----------------------------GCUCUCGCCACUCGUUUGGUAUCGCGAUUGAAAUCGCAAUUAAGUUUUAUUUUGUGGCGAGCAUUUUUU
.........(((((((----------------------------((....((((......))))...(((((....)))))................)))))))))....... ( -28.70)
>DroSim_CAF1 18431 92 + 1
AAUCUUGCCGCUCGCCG---------------------CUUGCCGCUCUCGCCACUCGUUUGGUAUCGCGAUUGAAAUCGCAAUUAAGUUUUAUUUUGUGGCGAGCAUUUUUU
.........((((((((---------------------(...........((((......))))...(((((....)))))................)))))))))....... ( -28.70)
>DroEre_CAF1 4198 98 + 1
AAUCUUGCCGCUUGCGGCUUGCA--------------GCUCGCUGCUCUUGCCGCUCGU-UGGUAUCGCGAUUGAAAUCGCAAUUAAGUUUUAUUUUGUGGCGAGCAUUUUUU
...((((((((..(((((..(((--------------(....))))....)))))....-.......(((((....)))))................))))))))........ ( -35.00)
>DroYak_CAF1 18120 112 + 1
AAUCUUGCGACUUGCGGCUUGCAACUUGCAACUUGCUGCUUGCUGCUCUCGCCGCUCGC-UGGUAUCGCGAUUGAAAUCGCAAUUAAGUUUUAUUUUGUGGCGAGCAUUUUUU
......((((...(((((..(((....((.....)))))..)))))..)))).((((((-(......(((((....)))))...((((......)))).)))))))....... ( -36.50)
>consensus
AAUCUUGCCGCUUGCCG_____________________CUUGCCGCUCUCGCCGCUCGUUUGGUAUCGCGAUUGAAAUCGCAAUUAAGUUUUAUUUUGUGGCGAGCAUUUUUU
...((((((((.......................................((((......))))...(((((....)))))................))))))))........ (-20.38 = -20.18 +  -0.20)

alignment

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secondary structure

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dotplot

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Window 2

Location 8,539,328 – 8,539,420
Length 92
Sequences 5
Columns 113
Reading direction reverse
Mean pairwise identity 82.42
Mean single sequence MFE -30.56
Consensus MFE -19.14
Energy contribution -19.90
Covariance contribution 0.76
Combinations/Pair 1.11
Mean z-score -3.98
Structure conservation index 0.63
SVM decision value 2.91
SVM RNA-class probability 0.997684
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 8539328 92 - 20766785
AAAAAAUGCUCGCCACAAAAUAAAACUUAAUUGCGAUUUCAAUCGCGAUACCAAACGAGCGGCGAGAGCGACAAG---------------------CGGCAAGCGGCAAGAUA
......((((.(((...............((((((((....)))))))).........((.((....)).....)---------------------)))).))))........ ( -23.20)
>DroSec_CAF1 14905 85 - 1
AAAAAAUGCUCGCCACAAAAUAAAACUUAAUUGCGAUUUCAAUCGCGAUACCAAACGAGUGGCGAGAGC----------------------------GGCGAGCGGCAAGAUU
......((((((((...............((((((((....))))))))............((....))----------------------------))))))))........ ( -28.40)
>DroSim_CAF1 18431 92 - 1
AAAAAAUGCUCGCCACAAAAUAAAACUUAAUUGCGAUUUCAAUCGCGAUACCAAACGAGUGGCGAGAGCGGCAAG---------------------CGGCGAGCGGCAAGAUU
......((((((((.(.............((((((((....)))))))).........((.((....)).))..)---------------------.))))))))........ ( -32.40)
>DroEre_CAF1 4198 98 - 1
AAAAAAUGCUCGCCACAAAAUAAAACUUAAUUGCGAUUUCAAUCGCGAUACCA-ACGAGCGGCAAGAGCAGCGAGC--------------UGCAAGCCGCAAGCGGCAAGAUU
......(((.(((................((((((((....))))))))....-....(((((....((((....)--------------)))..)))))..))))))..... ( -31.90)
>DroYak_CAF1 18120 112 - 1
AAAAAAUGCUCGCCACAAAAUAAAACUUAAUUGCGAUUUCAAUCGCGAUACCA-GCGAGCGGCGAGAGCAGCAAGCAGCAAGUUGCAAGUUGCAAGCCGCAAGUCGCAAGAUU
..............................(((((((((...((((.......-))))(((((....(((((..((((....))))..)))))..)))))))))))))).... ( -36.90)
>consensus
AAAAAAUGCUCGCCACAAAAUAAAACUUAAUUGCGAUUUCAAUCGCGAUACCAAACGAGCGGCGAGAGCAGCAAG_____________________CGGCAAGCGGCAAGAUU
.......(((.(((...............((((((((....)))))))).........((.((....)).)).........................))).)))......... (-19.14 = -19.90 +   0.76)

alignment

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secondary structure

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dotplot

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Window 3

Location 8,539,347 – 8,539,460
Length 113
Sequences 5
Columns 113
Reading direction reverse
Mean pairwise identity 95.57
Mean single sequence MFE -32.46
Consensus MFE -28.04
Energy contribution -28.24
Covariance contribution 0.20
Combinations/Pair 1.07
Mean z-score -1.82
Structure conservation index 0.86
SVM decision value 1.57
SVM RNA-class probability 0.964334
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 8539347 113 - 20766785
AGCCGUUGCAAAUGGGGCAGUCGUCGCGUCGUUGCUAAUUAAAAAAUGCUCGCCACAAAAUAAAACUUAAUUGCGAUUUCAAUCGCGAUACCAAACGAGCGGCGAGAGCGACA
.(((.(.......).)))....(((((.((((((((..........((.......))............((((((((....))))))))........))))))))..))))). ( -32.20)
>DroSec_CAF1 14921 109 - 1
AGCCGUUGCAAAUGGGGCAGUCGUCGCGUCGUUGCUAAUUAAAAAAUGCUCGCCACAAAAUAAAACUUAAUUGCGAUUUCAAUCGCGAUACCAAACGAGUGGCGAGAGC----
..((((.....))))(((((.((......)))))))............((((((((.............((((((((....))))))))..(....).))))))))...---- ( -30.40)
>DroSim_CAF1 18450 113 - 1
AGCCGUUUCAAAUGGGGCAGUCGUCGCGUCGUUGCUAAUUAAAAAAUGCUCGCCACAAAAUAAAACUUAAUUGCGAUUUCAAUCGCGAUACCAAACGAGUGGCGAGAGCGGCA
.((((((........(((((.((......)))))))............((((((((.............((((((((....))))))))..(....).)))))))))))))). ( -37.60)
>DroEre_CAF1 4224 112 - 1
AGCCGUUGCAAAUGGGGCAGUCGUCGCGUCGUUGCUAAUUAAAAAAUGCUCGCCACAAAAUAAAACUUAAUUGCGAUUUCAAUCGCGAUACCA-ACGAGCGGCAAGAGCAGCG
...((((((.....((....))(((((.((((((............((.......))............((((((((....))))))))..))-)))))))))....)))))) ( -28.90)
>DroYak_CAF1 18160 112 - 1
AGCCGUUGCAAAUGGGGCAGUCGUCGCGUCGUUGCUAAUUAAAAAAUGCUCGCCACAAAAUAAAACUUAAUUGCGAUUUCAAUCGCGAUACCA-GCGAGCGGCGAGAGCAGCA
....(((((......(((((.((......)))))))............((((((...............((((((((....))))))))....-(....))))))).))))). ( -33.20)
>consensus
AGCCGUUGCAAAUGGGGCAGUCGUCGCGUCGUUGCUAAUUAAAAAAUGCUCGCCACAAAAUAAAACUUAAUUGCGAUUUCAAUCGCGAUACCAAACGAGCGGCGAGAGCAGCA
..((((.....)))).((..(((((((.(((((((............))....................((((((((....))))))))....))))))))))))..)).... (-28.04 = -28.24 +   0.20)

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 10:27:06 2006