Locus 4459

Sequence ID 2R_DroMel_CAF1
Location 14,665,536 – 14,665,760
Length 224
Max. P 0.994985
window7124 window7125 window7126 window7127 window7128

overview

Window 4

Location 14,665,536 – 14,665,628
Length 92
Sequences 4
Columns 119
Reading direction forward
Mean pairwise identity 81.51
Mean single sequence MFE -33.65
Consensus MFE -21.26
Energy contribution -21.07
Covariance contribution -0.19
Combinations/Pair 1.05
Mean z-score -1.94
Structure conservation index 0.63
SVM decision value 0.44
SVM RNA-class probability 0.737341
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 14665536 92 + 20766785
UUUAUUCUGGAUAAUUGCCCAGGGGCUUAAUUUUCGGUGGUGUGUGCUUUU---------------UUUUUGGCAGGGGGAAGCGGCACAUAUGCGCCUACCA------------CCCA
.........((.(((((((....)))..)))).))(((((((...((((((---------------(((......)))))))))(((.(....).))))))))------------)).. ( -28.40)
>DroSim_CAF1 20127 98 + 1
UUUAUUCUGGAUAAUUGCCCAGGGGCUUAAUUUUCGGUGGUGUGUGCUUUUCUUUU---------UUUUUGGACAGGGGGAAGCGGCACAUAUGCGCCUGCCA------------CCCA
.........((.(((((((....)))..)))).))((((((....((((..((((.---------((....)).))))..))))(((.(....).))).))))------------)).. ( -30.70)
>DroEre_CAF1 20380 110 + 1
UUUAUUCUGGAUAAUUGCCCAGGGGCUUAAUUUUCGGUGGUGUGUGCUUUU---------UUUUUGUUUUGGACAGGGGGAAGCGGCACAUAUGCGCCUACCACCCACCAUACCACCGA
....((((((........)))))).........(((((((((((.((((((---------((((.(((...)))))))))))))(((.(....).)))..........))))))))))) ( -36.80)
>DroYak_CAF1 20438 117 + 1
UUUAUUCUGGAUAAUUGCCCAGGGGCUUAAUUUUCGGUGGUGUGUGUUUUUU--UCUCUUUUUUUUUUUUGGACGGGGGGAAGCGGCACAUAUGCGCCUACCACCCACCACACCACCGA
....((((((........)))))).........(((((((((((.((((((.--.((.(((.........))).))..))))))(((.(....).)))..........))))))))))) ( -38.70)
>consensus
UUUAUUCUGGAUAAUUGCCCAGGGGCUUAAUUUUCGGUGGUGUGUGCUUUU______________UUUUUGGACAGGGGGAAGCGGCACAUAUGCGCCUACCA____________CCCA
.......(((......(((....))).........(((((((((((((....................................))))))))).))))..)))................ (-21.26 = -21.07 +  -0.19)

alignment

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secondary structure

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Window 5

Location 14,665,536 – 14,665,628
Length 92
Sequences 4
Columns 119
Reading direction reverse
Mean pairwise identity 81.51
Mean single sequence MFE -32.95
Consensus MFE -19.71
Energy contribution -20.78
Covariance contribution 1.06
Combinations/Pair 1.06
Mean z-score -3.49
Structure conservation index 0.60
SVM decision value 2.50
SVM RNA-class probability 0.994630
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 14665536 92 - 20766785
UGGG------------UGGUAGGCGCAUAUGUGCCGCUUCCCCCUGCCAAAAA---------------AAAAGCACACACCACCGAAAAUUAAGCCCCUGGGCAAUUAUCCAGAAUAAA
..((------------((((.(((((....)))))((((..............---------------..))))....)))))).........(((....)))................ ( -26.89)
>DroSim_CAF1 20127 98 - 1
UGGG------------UGGCAGGCGCAUAUGUGCCGCUUCCCCCUGUCCAAAAA---------AAAAGAAAAGCACACACCACCGAAAAUUAAGCCCCUGGGCAAUUAUCCAGAAUAAA
..((------------(((..(((((....)))))((((....((.........---------...))..)))).....))))).........(((....)))................ ( -25.00)
>DroEre_CAF1 20380 110 - 1
UCGGUGGUAUGGUGGGUGGUAGGCGCAUAUGUGCCGCUUCCCCCUGUCCAAAACAAAAA---------AAAAGCACACACCACCGAAAAUUAAGCCCCUGGGCAAUUAUCCAGAAUAAA
((((((((.(((((((.((..(((((....)))))....)))))(((.....)))....---------....)).)).)))))))).......(((....)))................ ( -37.90)
>DroYak_CAF1 20438 117 - 1
UCGGUGGUGUGGUGGGUGGUAGGCGCAUAUGUGCCGCUUCCCCCCGUCCAAAAAAAAAAAAGAGA--AAAAAACACACACCACCGAAAAUUAAGCCCCUGGGCAAUUAUCCAGAAUAAA
((((((((((((((((.((..(((((....)))))....)).))).(((............).))--.....)).))))))))))).......(((....)))................ ( -42.00)
>consensus
UCGG____________UGGUAGGCGCAUAUGUGCCGCUUCCCCCUGUCCAAAAA______________AAAAGCACACACCACCGAAAAUUAAGCCCCUGGGCAAUUAUCCAGAAUAAA
..((..........((((((.(((((....)))))((........))...............................)))))).........(((....)))......))........ (-19.71 = -20.78 +   1.06)

alignment

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secondary structure

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Window 6

Location 14,665,575 – 14,665,668
Length 93
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 77.13
Mean single sequence MFE -34.02
Consensus MFE -23.14
Energy contribution -24.89
Covariance contribution 1.75
Combinations/Pair 1.14
Mean z-score -2.35
Structure conservation index 0.68
SVM decision value 2.25
SVM RNA-class probability 0.991135
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 14665575 93 - 20766785
AAAGCCAUUGAAGGGCAACUUCAAGGUGUGGGCGGCAUUGUGGG------------UGGUAGGCGCAUAUGUGCCGCUUCCCCCUGCCAAAAA---------------AAAAGCACACAC
...(((.((((((.....)))))))))(((.((((((..(.(((------------.(((.(((((....)))))))).)))).)))).....---------------....)).))).. ( -33.80)
>DroSim_CAF1 20166 99 - 1
AAAGCCAUUGAAGGGCAACUUCAAGGUGUGGGCGGCAAAAUGGG------------UGGCAGGCGCAUAUGUGCCGCUUCCCCCUGUCCAAAAA---------AAAAGAAAAGCACACAC
...(((.((((((.....))))))))).(((((((......(((------------.(((.(((((....)))))))).))).)))))))....---------................. ( -34.90)
>DroEre_CAF1 20419 111 - 1
AAAGCCAUUGAAGGGCAACAUCGAGGUGUGGGCGGGAAAAUCGGUGGUAUGGUGGGUGGUAGGCGCAUAUGUGCCGCUUCCCCCUGUCCAAAACAAAAA---------AAAAGCACACAC
...(((.((((..(....).))))))).((((((((...((((......))))(((.(((.(((((....)))))))).))))))))))).........---------............ ( -35.70)
>DroYak_CAF1 20477 118 - 1
AAAGCCAUUGAAGGGCAACUUCAAGAAGUAAGCGGGAAAAUCGGUGGUGUGGUGGGUGGUAGGCGCAUAUGUGCCGCUUCCCCCCGUCCAAAAAAAAAAAAGAGA--AAAAAACACACAC
...((((((((((.....))))).........(((.....)))))))).(((((((.((..(((((....)))))....)).)))).)))...............--............. ( -31.70)
>consensus
AAAGCCAUUGAAGGGCAACUUCAAGGUGUGGGCGGCAAAAUCGG____________UGGUAGGCGCAUAUGUGCCGCUUCCCCCUGUCCAAAAA______________AAAAGCACACAC
...(((.((((((.....))))))))).((((((((.....(((.............(((.(((((....)))))))).))))))))))).............................. (-23.14 = -24.89 +   1.75)

alignment

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secondary structure

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dotplot

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Window 7

Location 14,665,668 – 14,665,760
Length 92
Sequences 5
Columns 92
Reading direction forward
Mean pairwise identity 94.23
Mean single sequence MFE -19.14
Consensus MFE -16.46
Energy contribution -16.90
Covariance contribution 0.44
Combinations/Pair 1.04
Mean z-score -1.21
Structure conservation index 0.86
SVM decision value -0.04
SVM RNA-class probability 0.514007
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 14665668 92 + 20766785
CUUUUGUUUUGGAAUAUGCGAAAAUUAACUGGUAAAAUGUUGGCCCAUCAACACGGGGGUAACUUCAACAUUUUCCAAUUAAAAAAGUCACC
(((((.(((((.......))))).((((.(((.(((((((((((((.((.....)))))).....)))))))))))).)))))))))..... ( -19.20)
>DroSec_CAF1 20226 92 + 1
CUUUUGUUUUGGAAUAUGCGAAAAUUAACUGGUAAAAUGUUGGCCCAUCAACACGGGGGUAAAUCCAACAUUUUCCAAUUAAAAAAGUCACC
(((((.(((((.......))))).((((.(((.(((((((((((((.((.....))))).....))))))))))))).)))))))))..... ( -20.50)
>DroSim_CAF1 20265 92 + 1
CUUUUGUUUUGGAAUAUGCGAAAAUUAACUGGUAAAAUGUUGGCCCAUCAACACGGGGGUAAAUCCAACAUUUUCCAAUUAAAAAAGUCACC
(((((.(((((.......))))).((((.(((.(((((((((((((.((.....))))).....))))))))))))).)))))))))..... ( -20.50)
>DroEre_CAF1 20530 91 + 1
CUGUUGUUUCGGAGUAUGCGAAAAUUAACUGGUAAAAUGUUGGCCCAUCAACACAGGGGUAACU-CAACAUUUUCCAAUUAAAAAAGUCACC
......(((((.......))))).((((.(((.(((((((((((((..........))))....-)))))))))))).)))).......... ( -19.60)
>DroYak_CAF1 20595 91 + 1
CCUUUGUUUGGGAGUAUGCGAAAAUUAACUGGUAAAAUGUUGGCCCAUCAACGCAGGGGUAACU-CUACGUUUUCCAAUUAAAAAAGUCACC
(((......))).......((...((((.(((.(((((((..((((..........))))....-..)))))))))).)))).....))... ( -15.90)
>consensus
CUUUUGUUUUGGAAUAUGCGAAAAUUAACUGGUAAAAUGUUGGCCCAUCAACACGGGGGUAACU_CAACAUUUUCCAAUUAAAAAAGUCACC
.((((((..........)))))).((((.(((.(((((((((((((..........)))).....)))))))))))).)))).......... (-16.46 = -16.90 +   0.44)

alignment

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secondary structure

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dotplot

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Window 8

Location 14,665,668 – 14,665,760
Length 92
Sequences 5
Columns 92
Reading direction reverse
Mean pairwise identity 94.23
Mean single sequence MFE -24.14
Consensus MFE -20.12
Energy contribution -20.48
Covariance contribution 0.36
Combinations/Pair 1.04
Mean z-score -2.50
Structure conservation index 0.83
SVM decision value 2.53
SVM RNA-class probability 0.994985
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 14665668 92 - 20766785
GGUGACUUUUUUAAUUGGAAAAUGUUGAAGUUACCCCCGUGUUGAUGGGCCAACAUUUUACCAGUUAAUUUUCGCAUAUUCCAAAACAAAAG
.((((.....(((((((((((((((((........(((((....))))).))))))))).))))))))...))))................. ( -23.30)
>DroSec_CAF1 20226 92 - 1
GGUGACUUUUUUAAUUGGAAAAUGUUGGAUUUACCCCCGUGUUGAUGGGCCAACAUUUUACCAGUUAAUUUUCGCAUAUUCCAAAACAAAAG
.((((.....((((((((((((((((((.......(((((....))))))))))))))).))))))))...))))................. ( -27.41)
>DroSim_CAF1 20265 92 - 1
GGUGACUUUUUUAAUUGGAAAAUGUUGGAUUUACCCCCGUGUUGAUGGGCCAACAUUUUACCAGUUAAUUUUCGCAUAUUCCAAAACAAAAG
.((((.....((((((((((((((((((.......(((((....))))))))))))))).))))))))...))))................. ( -27.41)
>DroEre_CAF1 20530 91 - 1
GGUGACUUUUUUAAUUGGAAAAUGUUG-AGUUACCCCUGUGUUGAUGGGCCAACAUUUUACCAGUUAAUUUUCGCAUACUCCGAAACAACAG
.((((.....(((((((((((((((((-.(....(((.........))))))))))))).))))))))...))))................. ( -22.30)
>DroYak_CAF1 20595 91 - 1
GGUGACUUUUUUAAUUGGAAAACGUAG-AGUUACCCCUGCGUUGAUGGGCCAACAUUUUACCAGUUAAUUUUCGCAUACUCCCAAACAAAGG
.((((.....((((((((..(((((((-........)))))))((((......))))...))))))))...))))................. ( -20.30)
>consensus
GGUGACUUUUUUAAUUGGAAAAUGUUG_AGUUACCCCCGUGUUGAUGGGCCAACAUUUUACCAGUUAAUUUUCGCAUAUUCCAAAACAAAAG
.((((.....(((((((((((((((((........(((((....))))).))))))))).))))))))...))))................. (-20.12 = -20.48 +   0.36)

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 11:20:12 2006