Locus 4712

Sequence ID 2L_DroMel_CAF1
Location 13,518,820 – 13,519,017
Length 197
Max. P 0.999467
window7456 window7457 window7458 window7459

overview

Window 6

Location 13,518,820 – 13,518,916
Length 96
Sequences 6
Columns 101
Reading direction forward
Mean pairwise identity 90.02
Mean single sequence MFE -33.38
Consensus MFE -28.75
Energy contribution -29.67
Covariance contribution 0.92
Combinations/Pair 1.07
Mean z-score -2.24
Structure conservation index 0.86
SVM decision value 1.27
SVM RNA-class probability 0.938042
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 13518820 96 + 22407834
GGUAGGGGUGGCGCCACAUCAGCAGCUGCUGUUGGCCCACAGUUAACAGUGCUAACUGU-----GUUGCCUGGCACUGCGAUUUAUUAACAGUUAGCCAAA
(((((..((((.((((...((((....)))).)))))))).....(((((....)))))-----.)))))((((((((..(.....)..))))..)))).. ( -35.10)
>DroSec_CAF1 10045 94 + 1
GGUAG--GUGGCGCCACAUCAGCAGCUGCUGUUGGCCCACAGUUAACUGUACUAACUGU-----GUUGCCUGGCACUGCGAUUUAUUAACAGUUAGCCAAA
...((--(..((((((...((((....)))).))))..(((((((.......)))))))-----))..)))(((((((..(.....)..))))..)))... ( -32.40)
>DroSim_CAF1 6669 94 + 1
GGAAG--GUGGCGCCACAUCAGCAGCUGCUGUUGGCCCACAGUUAACUGUGCUAACUGU-----GUUGCCUGGCACUGCGAUUUAUUAACAGUUAGCCAAA
.((..--((((.((((...((((....)))).))))))))..))...((.(((((((((-----(((((........)))))......))))))))))).. ( -34.70)
>DroEre_CAF1 10416 94 + 1
GGAAG--GUGGCGCCACAUCAGCAGCUGCUGUUGGGCCACAGUUAACUGUGCUAACUGU-----GUUGCCUGGCACUGCGAUUUAUUAACAGUUAGCCAAA
.((..--(((((.(((...((((....)))).))))))))..))...((.(((((((((-----(((((........)))))......))))))))))).. ( -34.70)
>DroYak_CAF1 10735 93 + 1
GGAAG--GUGGCGCCACAUCAGCAGCUGCUGUUG-CCCACAGUUAACUGUGCUAACUGU-----GUUGCCUGGCACUGCGAUUUAUUAACAGUUAGCCAAA
...((--(..((((.......(((((....))))-).(((((....)))))......))-----))..)))(((((((..(.....)..))))..)))... ( -30.10)
>DroAna_CAF1 9814 97 + 1
GAUGGGGCGGGAGCCACAUCAGCAGCUGCUUCUGGCCCAG----AACUGUGCUAACUGUUUGCUGAUAUCUGGCACUGCGAUUUAUUAACAGUUAGCCAAA
..((((.(((((((..(.......)..))))))).)))).----...((.(((((((((....(((((..(.((...)).)..)))))))))))))))).. ( -33.30)
>consensus
GGAAG__GUGGCGCCACAUCAGCAGCUGCUGUUGGCCCACAGUUAACUGUGCUAACUGU_____GUUGCCUGGCACUGCGAUUUAUUAACAGUUAGCCAAA
.......((((.((((...((((....)))).)))))))).......((.(((((((((.....(((((........)))))......))))))))))).. (-28.75 = -29.67 +   0.92)

alignment

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secondary structure

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dotplot

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Window 7

Location 13,518,820 – 13,518,916
Length 96
Sequences 6
Columns 101
Reading direction reverse
Mean pairwise identity 90.02
Mean single sequence MFE -36.00
Consensus MFE -26.50
Energy contribution -28.03
Covariance contribution 1.53
Combinations/Pair 1.03
Mean z-score -3.60
Structure conservation index 0.74
SVM decision value 0.48
SVM RNA-class probability 0.754061
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 13518820 96 - 22407834
UUUGGCUAACUGUUAAUAAAUCGCAGUGCCAGGCAAC-----ACAGUUAGCACUGUUAACUGUGGGCCAACAGCAGCUGCUGAUGUGGCGCCACCCCUACC
..((((..(((((.........)))))))))(((..(-----(((((((((...)))))))))).((((.((((....))))...)))))))......... ( -38.70)
>DroSec_CAF1 10045 94 - 1
UUUGGCUAACUGUUAAUAAAUCGCAGUGCCAGGCAAC-----ACAGUUAGUACAGUUAACUGUGGGCCAACAGCAGCUGCUGAUGUGGCGCCAC--CUACC
..((((..(((((.........)))))))))(((..(-----((((((((.....))))))))).((((.((((....))))...)))))))..--..... ( -36.70)
>DroSim_CAF1 6669 94 - 1
UUUGGCUAACUGUUAAUAAAUCGCAGUGCCAGGCAAC-----ACAGUUAGCACAGUUAACUGUGGGCCAACAGCAGCUGCUGAUGUGGCGCCAC--CUUCC
..((((..(((((.........)))))))))(((..(-----(((((((((...)))))))))).((((.((((....))))...)))))))..--..... ( -38.70)
>DroEre_CAF1 10416 94 - 1
UUUGGCUAACUGUUAAUAAAUCGCAGUGCCAGGCAAC-----ACAGUUAGCACAGUUAACUGUGGCCCAACAGCAGCUGCUGAUGUGGCGCCAC--CUUCC
..((((..(((((.........)))))))))(((..(-----(((((((((...))))))))))(((((.((((....)))).)).))))))..--..... ( -39.40)
>DroYak_CAF1 10735 93 - 1
UUUGGCUAACUGUUAAUAAAUCGCAGUGCCAGGCAAC-----ACAGUUAGCACAGUUAACUGUGGG-CAACAGCAGCUGCUGAUGUGGCGCCAC--CUUCC
..((((..(((((.........)))))))))(((..(-----(((((((((...)))))))))).(-((.((((....)))).)))...)))..--..... ( -34.60)
>DroAna_CAF1 9814 97 - 1
UUUGGCUAACUGUUAAUAAAUCGCAGUGCCAGAUAUCAGCAAACAGUUAGCACAGUU----CUGGGCCAGAAGCAGCUGCUGAUGUGGCUCCCGCCCCAUC
((((((..(((((.........))))).(((((.....((.........)).....)----))))))))))(((....)))((((.(((....))).)))) ( -27.90)
>consensus
UUUGGCUAACUGUUAAUAAAUCGCAGUGCCAGGCAAC_____ACAGUUAGCACAGUUAACUGUGGGCCAACAGCAGCUGCUGAUGUGGCGCCAC__CUACC
..((((..(((((.........)))))))))(((........(((((((((...)))))))))..((((.((((....))))...)))))))......... (-26.50 = -28.03 +   1.53)

alignment

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secondary structure

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dotplot

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Window 8

Location 13,518,916 – 13,519,017
Length 101
Sequences 4
Columns 105
Reading direction forward
Mean pairwise identity 71.43
Mean single sequence MFE -17.29
Consensus MFE -10.98
Energy contribution -11.97
Covariance contribution 1.00
Combinations/Pair 1.12
Mean z-score -2.52
Structure conservation index 0.63
SVM decision value 3.63
SVM RNA-class probability 0.999467
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 13518916 101 + 22407834
AGUCCGGAUAGCUAUAGCUACCUAC---CUACUACUCAAAUAACUUAGCUGCUACCUACAACUGCUACAAUUAUUGUAGUUAUUCUCUUACU-GGGCUCUACUGA
(((((((.((((...(((((.....---.................))))))))).........((((((.....))))))..........))-)))))....... ( -19.35)
>DroSec_CAF1 10139 84 + 1
AGCCCGGAUAGCU--AGCUACCUAC---CUAC---UCAA------------CUACCUACAACUGCUACAAUUAUUGUAGUUAUUCUUCUGCU-GGGCUCCACUGA
(((((((.(((.(--((....))).---))).---....------------............((((((.....))))))..........))-)))))....... ( -17.70)
>DroSim_CAF1 6763 84 + 1
AGCCCGGAUAGCU--AGCUACCUAC---CUAC---UCAA------------CUACCUACAACUGCUACAAUUAUUGUAGUUAUUCUUNNNNN-NNNNNNNNNNNN
.....(..(((.(--((....))).---))).---.)..------------............((((((.....))))))............-............ (  -8.40)
>DroEre_CAF1 10510 84 + 1
AGCCCGAAUAUCU--AUGUAGCUACUUCCUAC---CUAG------------CUACCUACAACUGCUACAAUUGUUGUAGUUAUUCUUCUACUUGGGC----CUAA
.((((((......--..(((((((........---.)))------------))))(((((((..........)))))))............))))))----.... ( -23.70)
>consensus
AGCCCGGAUAGCU__AGCUACCUAC___CUAC___UCAA____________CUACCUACAACUGCUACAAUUAUUGUAGUUAUUCUUCUACU_GGGC____CUGA
.((((((.((((....)))))).........................................((((((.....)))))).............))))........ (-10.98 = -11.97 +   1.00)

alignment

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secondary structure

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dotplot

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Window 9

Location 13,518,916 – 13,519,017
Length 101
Sequences 4
Columns 105
Reading direction reverse
Mean pairwise identity 71.43
Mean single sequence MFE -21.83
Consensus MFE -11.25
Energy contribution -12.88
Covariance contribution 1.62
Combinations/Pair 1.12
Mean z-score -1.80
Structure conservation index 0.52
SVM decision value 0.27
SVM RNA-class probability 0.662512
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 13518916 101 - 22407834
UCAGUAGAGCCC-AGUAAGAGAAUAACUACAAUAAUUGUAGCAGUUGUAGGUAGCAGCUAAGUUAUUUGAGUAGUAG---GUAGGUAGCUAUAGCUAUCCGGACU
..(((...(((.-(.((...(((((((((((.....))))..((((((.....))))))..)))))))...)).).)---)).((((((....))))))...))) ( -23.00)
>DroSec_CAF1 10139 84 - 1
UCAGUGGAGCCC-AGCAGAAGAAUAACUACAAUAAUUGUAGCAGUUGUAGGUAG------------UUGA---GUAG---GUAGGUAGCU--AGCUAUCCGGGCU
.......(((((-..........(((((((.(((((((...)))))))..))))------------))).---((((---.(((....))--).))))..))))) ( -23.90)
>DroSim_CAF1 6763 84 - 1
NNNNNNNNNNNN-NNNNNAAGAAUAACUACAAUAAUUGUAGCAGUUGUAGGUAG------------UUGA---GUAG---GUAGGUAGCU--AGCUAUCCGGGCU
............-..........(((((((.(((((((...)))))))..))))------------))).---...(---((.(((((..--..)))))...))) ( -14.80)
>DroEre_CAF1 10510 84 - 1
UUAG----GCCCAAGUAGAAGAAUAACUACAACAAUUGUAGCAGUUGUAGGUAG------------CUAG---GUAGGAAGUAGCUACAU--AGAUAUUCGGGCU
...(----((((.((((.........(((((((..........)))))))((((------------(((.---........)))))))..--...)))).))))) ( -25.60)
>consensus
UCAG____GCCC_AGUAGAAGAAUAACUACAAUAAUUGUAGCAGUUGUAGGUAG____________UUGA___GUAG___GUAGGUAGCU__AGCUAUCCGGGCU
........((((..............(((((((..........))))))).................................((((((....)))))).)))). (-11.25 = -12.88 +   1.62)

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 11:25:22 2006