Locus 1668

Sequence ID X_DroMel_CAF1
Location 4,687,640 – 4,687,766
Length 126
Max. P 0.998373
window2744 window2745 window2746 window2747

overview

Window 4

Location 4,687,640 – 4,687,739
Length 99
Sequences 4
Columns 118
Reading direction forward
Mean pairwise identity 67.03
Mean single sequence MFE -22.95
Consensus MFE -11.48
Energy contribution -12.10
Covariance contribution 0.62
Combinations/Pair 1.15
Mean z-score -1.76
Structure conservation index 0.50
SVM decision value 0.75
SVM RNA-class probability 0.839504
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 4687640 99 + 22224390
UGAAAUUCCUUCACUG-UGGGGG-GGGGAGG-AAAUACUCCACCA--------AAAAAGCAUAAACAAAAAAAAAUGGCAAAAAUAUUCGCACACUUUGCGUGUGCG--------UGU
.......(((((....-.)))))-((((((.-.....)))).)).--------...................................(((((((.....)))))))--------... ( -25.20)
>DroSec_CAF1 41195 90 + 1
UGAAAUUCCUUCACUGCUGGAGU-GGGGAGC-AAAUACUCAUCCA--------AAAAAGCAUAAACAAAAAAAAA----------AUUCGCACACUUUGCGUGUGCG--------UGU
...........(((((((....(-((((((.-.....))).))))--------....))))..............----------....((((((.....)))))))--------)). ( -23.40)
>DroEre_CAF1 41581 79 + 1
UCAAAUUCUUUCGCUG---GAGG----GGGGAAAAAGUUCCACCA----------------------AAA--AAAUGGCAAAAAUAUUCGCACACUUUGGGUUUGCG--------UGU
............((((---....----((((((....)))).)).----------------------...--...)))).........((((.((.....)).))))--------... ( -14.00)
>DroYak_CAF1 38448 113 + 1
UGAAAUUCUUUCGCGG---GGGGGAAGGAGCAAAAAGCUCCACCAAACAAAAAAAAAAGUAUAAGCAAAA--AAAUGGCAAAAAUAUUCGCACACUUUGCGUGUGCGUGAGUGUGUGU
.....((((..(....---)..))))(((((.....))))).......................((....--.....)).........(((((((.(..((....))..)))))))). ( -29.20)
>consensus
UGAAAUUCCUUCACUG___GAGG_GGGGAGC_AAAAACUCCACCA________AAAAAGCAUAAACAAAA__AAAUGGCAAAAAUAUUCGCACACUUUGCGUGUGCG________UGU
.....................((...((((.......)))).))............................................(((((((.....)))))))........... (-11.48 = -12.10 +   0.62)

alignment

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secondary structure

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dotplot

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Window 5

Location 4,687,640 – 4,687,739
Length 99
Sequences 4
Columns 118
Reading direction reverse
Mean pairwise identity 67.03
Mean single sequence MFE -23.80
Consensus MFE -10.81
Energy contribution -12.50
Covariance contribution 1.69
Combinations/Pair 1.08
Mean z-score -2.49
Structure conservation index 0.45
SVM decision value 1.94
SVM RNA-class probability 0.983170
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 4687640 99 - 22224390
ACA--------CGCACACGCAAAGUGUGCGAAUAUUUUUGCCAUUUUUUUUUGUUUAUGCUUUUU--------UGGUGGAGUAUUU-CCUCCCC-CCCCCA-CAGUGAAGGAAUUUCA
...--------(((((((.....)))))))...................(((.(((((.......--------.((.((((.....-.))))))-......-..))))).)))..... ( -23.69)
>DroSec_CAF1 41195 90 - 1
ACA--------CGCACACGCAAAGUGUGCGAAU----------UUUUUUUUUGUUUAUGCUUUUU--------UGGAUGAGUAUUU-GCUCCCC-ACUCCAGCAGUGAAGGAAUUUCA
...--------(((((((.....)))))))...----------......(((.((((((((....--------(((..((((....-)))).))-)....)))).)))).)))..... ( -25.00)
>DroEre_CAF1 41581 79 - 1
ACA--------CGCAAACCCAAAGUGUGCGAAUAUUUUUGCCAUUU--UUU----------------------UGGUGGAACUUUUUCCCC----CCUC---CAGCGAAAGAAUUUGA
...--------(((......((((((.(((((....))))))))))--)..----------------------.((.((((....))))))----....---..)))........... ( -17.30)
>DroYak_CAF1 38448 113 - 1
ACACACACUCACGCACACGCAAAGUGUGCGAAUAUUUUUGCCAUUU--UUUUGCUUAUACUUUUUUUUUUGUUUGGUGGAGCUUUUUGCUCCUUCCCCC---CCGCGAAAGAAUUUCA
...........(((((((.....)))))))............((((--((((((....((..........))..((.(((((.....)))))..))...---..)))))))))).... ( -29.20)
>consensus
ACA________CGCACACGCAAAGUGUGCGAAUAUUUUUGCCAUUU__UUUUGUUUAUGCUUUUU________UGGUGGAGCAUUU_CCUCCCC_CCCC___CAGCGAAAGAAUUUCA
...........(((((((.....)))))))...............................................(((((.....))))).......................... (-10.81 = -12.50 +   1.69)

alignment

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secondary structure

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dotplot

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Window 6

Location 4,687,676 – 4,687,766
Length 90
Sequences 4
Columns 106
Reading direction forward
Mean pairwise identity 74.74
Mean single sequence MFE -19.56
Consensus MFE -16.17
Energy contribution -17.93
Covariance contribution 1.75
Combinations/Pair 1.00
Mean z-score -2.31
Structure conservation index 0.83
SVM decision value 3.08
SVM RNA-class probability 0.998373
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 4687676 90 + 22224390
CCACCA--------AAAAAGCAUAAACAAAAAAAAAUGGCAAAAAUAUUCGCACACUUUGCGUGUGCG--------UGUGUGGGGGAAAGUAAUUUACCAACACAG
.(((..--------.....((.................))..........((((((.....)))))))--------))((((..(((((....))).))..)))). ( -20.33)
>DroSec_CAF1 41232 80 + 1
CAUCCA--------AAAAAGCAUAAACAAAAAAAAA----------AUUCGCACACUUUGCGUGUGCG--------UGUGUGGGGGAAAGUAAUUUACCAACACAG
......--------......................----------...(((((((.....)))))))--------..((((..(((((....))).))..)))). ( -20.10)
>DroEre_CAF1 41613 74 + 1
CCACCA----------------------AAA--AAAUGGCAAAAAUAUUCGCACACUUUGGGUUUGCG--------UGUGUGAGGGAAAGUAAUUUACCAACACAG
...(((----------------------...--...)))..........((((.((.....)).))))--------(((((...(((((....))).)).))))). ( -15.10)
>DroYak_CAF1 38484 104 + 1
CCACCAAACAAAAAAAAAAGUAUAAGCAAAA--AAAUGGCAAAAAUAUUCGCACACUUUGCGUGUGCGUGAGUGUGUGUGUGAGGGAAAGUAAUUUACCAACACAG
.(((((..((...............((....--.....)).........(((((((.....)))))))))..)).)))((((..(((((....))).))..)))). ( -22.70)
>consensus
CCACCA________AAAAAGCAUAAACAAAA__AAAUGGCAAAAAUAUUCGCACACUUUGCGUGUGCG________UGUGUGAGGGAAAGUAAUUUACCAACACAG
.................................................(((((((.....)))))))........(((((..((.(((....))).)).))))). (-16.17 = -17.93 +   1.75)

alignment

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secondary structure

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dotplot

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Window 7

Location 4,687,676 – 4,687,766
Length 90
Sequences 4
Columns 106
Reading direction reverse
Mean pairwise identity 74.74
Mean single sequence MFE -20.16
Consensus MFE -16.48
Energy contribution -16.48
Covariance contribution -0.00
Combinations/Pair 1.06
Mean z-score -2.20
Structure conservation index 0.82
SVM decision value 2.81
SVM RNA-class probability 0.997183
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 4687676 90 - 22224390
CUGUGUUGGUAAAUUACUUUCCCCCACACA--------CGCACACGCAAAGUGUGCGAAUAUUUUUGCCAUUUUUUUUUGUUUAUGCUUUUU--------UGGUGG
.(((((.((..((.....))..)).)))))--------(((((((.....))))))).......(..(((......................--------)))..) ( -22.25)
>DroSec_CAF1 41232 80 - 1
CUGUGUUGGUAAAUUACUUUCCCCCACACA--------CGCACACGCAAAGUGUGCGAAU----------UUUUUUUUUGUUUAUGCUUUUU--------UGGAUG
.(((((.((..((.....))..)).)))))--------(((((((.....)))))))...----------.........(((((........--------))))). ( -19.60)
>DroEre_CAF1 41613 74 - 1
CUGUGUUGGUAAAUUACUUUCCCUCACACA--------CGCAAACCCAAAGUGUGCGAAUAUUUUUGCCAUUU--UUU----------------------UGGUGG
.((((..((.(((....)))))..))))((--------(.((((...((((((.(((((....))))))))))--)))----------------------))))). ( -17.90)
>DroYak_CAF1 38484 104 - 1
CUGUGUUGGUAAAUUACUUUCCCUCACACACACACUCACGCACACGCAAAGUGUGCGAAUAUUUUUGCCAUUU--UUUUGCUUAUACUUUUUUUUUUGUUUGGUGG
.((((..((.(((....)))))..))))(((.((..(((((((((.....))))))).........((.....--....))...............))..))))). ( -20.90)
>consensus
CUGUGUUGGUAAAUUACUUUCCCCCACACA________CGCACACGCAAAGUGUGCGAAUAUUUUUGCCAUUU__UUUUGUUUAUGCUUUUU________UGGUGG
.(((((.((..((.....))..)).)))))........(((((((.....)))))))................................................. (-16.48 = -16.48 +  -0.00)

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 10:16:17 2006