Locus 6719

Sequence ID X_DroMel_CAF1
Location 16,744,646 – 16,744,797
Length 151
Max. P 0.998101
window10961 window10962 window10963

overview

Window 1

Location 16,744,646 – 16,744,758
Length 112
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 73.51
Mean single sequence MFE -18.51
Consensus MFE -3.73
Energy contribution -3.89
Covariance contribution 0.16
Combinations/Pair 1.11
Mean z-score -1.67
Structure conservation index 0.20
SVM decision value 0.35
SVM RNA-class probability 0.701663
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 16744646 112 + 22224390
AAUAAAUAAAUCGACAAUUAAGCGAGGGACA--GUCGGCGGGUACUGCCACCCCACUUCCCU-CGUUUCCAUCC----UAUCUAUGGAUAUGAAUAUACAUACAUAUAUUUAUCCA-CAU
...................((((((((((.(--((.((..((.....))..)).))))))))-)))))......----......((((((..((((((......))))))))))))-... ( -30.90)
>DroSec_CAF1 31996 91 + 1
AAUAAAUAAAUCGACAAUUAAGCGAGGGACA--GCA---CGGCACUGGCACCCCACUUCCCC--------CUCC----CAUCUAUAGAUAU------------AUGUAUAUAUCCACCAU
.....................(.(((((...--((.---..))..(((....))).....))--------))).----).......(((((------------(....))))))...... ( -12.40)
>DroSim_CAF1 30324 91 + 1
AAUAAAUAAAUCGACAAUUAAGCGAGGGACA--GCA---CGGCACUUGCACCCCACUUCCCC--------CUCC----CAUCUAUAGAUAU------------AUGUAUAUAUCCACCAU
.....................(.(((((..(--(..---..((....))......))...))--------))).----).......(((((------------(....))))))...... ( -11.70)
>DroEre_CAF1 23455 96 + 1
AAUAAAUAAGACGACAAUUAAACGAGGGACA--GCU---UGGAACUGCCACCCCACUCCUCC--GAUUCCUUCC----UAUCUAUGGAUGUGGAU--------AU----UUAUCCA-CAU
......................((..(((..--...---(((.....)))......)))..)--)......(((----.......)))(((((((--------..----..)))))-)). ( -18.50)
>DroYak_CAF1 23475 108 + 1
AAUAAAUAAAACGACAAUUAAACGAGGGACAACGCU---CGCUGCUGCCACCCCACUCCUCCCCAUUUCCCUUCAAUGUAUCUAUGGAUGUGGAU--------AUACAUAUAUCCA-CAU
.......................(((((........---.((....))........))))).((((.................))))((((((((--------((....)))))))-))) ( -19.06)
>consensus
AAUAAAUAAAUCGACAAUUAAGCGAGGGACA__GCA___CGGCACUGCCACCCCACUUCCCC____UUCCCUCC____UAUCUAUGGAUAUG_AU________AUAUAUAUAUCCA_CAU
.........................(((.......................)))..............................((((((....................)))))).... ( -3.73 =  -3.89 +   0.16)

alignment

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secondary structure

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Window 2

Location 16,744,646 – 16,744,758
Length 112
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 73.51
Mean single sequence MFE -31.32
Consensus MFE -12.66
Energy contribution -12.46
Covariance contribution -0.20
Combinations/Pair 1.19
Mean z-score -2.66
Structure conservation index 0.40
SVM decision value 3.01
SVM RNA-class probability 0.998101
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 16744646 112 - 22224390
AUG-UGGAUAAAUAUAUGUAUGUAUAUUCAUAUCCAUAGAUA----GGAUGGAAACG-AGGGAAGUGGGGUGGCAGUACCCGCCGAC--UGUCCCUCGCUUAAUUGUCGAUUUAUUUAUU
.((-(((((((((((((....)))))))..))))))))((((----(...((...((-((((((((.((.(((......))))).))--).)))))))))...)))))............ ( -36.50)
>DroSec_CAF1 31996 91 - 1
AUGGUGGAUAUAUACAU------------AUAUCUAUAGAUG----GGAG--------GGGGAAGUGGGGUGCCAGUGCCG---UGC--UGUCCCUCGCUUAAUUGUCGAUUUAUUUAUU
...(((((((((....)------------))))))))...((----((.(--------(((((((((.((((....)))).---)))--).)))))).)))).................. ( -27.70)
>DroSim_CAF1 30324 91 - 1
AUGGUGGAUAUAUACAU------------AUAUCUAUAGAUG----GGAG--------GGGGAAGUGGGGUGCAAGUGCCG---UGC--UGUCCCUCGCUUAAUUGUCGAUUUAUUUAUU
...(((((((((....)------------))))))))...((----((.(--------(((((((((.((((....)))).---)))--).)))))).)))).................. ( -27.70)
>DroEre_CAF1 23455 96 - 1
AUG-UGGAUAA----AU--------AUCCACAUCCAUAGAUA----GGAAGGAAUC--GGAGGAGUGGGGUGGCAGUUCCA---AGC--UGUCCCUCGUUUAAUUGUCGUCUUAUUUAUU
(((-(((((..----..--------))))))))..(((((((----(((.(((((.--.((.((..((((..((.......---.))--..)))))).))..))).)).)))))))))). ( -32.80)
>DroYak_CAF1 23475 108 - 1
AUG-UGGAUAUAUGUAU--------AUCCACAUCCAUAGAUACAUUGAAGGGAAAUGGGGAGGAGUGGGGUGGCAGCAGCG---AGCGUUGUCCCUCGUUUAAUUGUCGUUUUAUUUAUU
(((-(((((((....))--------))))))))............((((..(((((((.((.((((((((.((((((....---...))))))))))))))..)).))))))).)))).. ( -31.90)
>consensus
AUG_UGGAUAUAUACAU________AU_CAUAUCCAUAGAUA____GGAGGGAA____GGGGAAGUGGGGUGGCAGUACCG___AGC__UGUCCCUCGCUUAAUUGUCGAUUUAUUUAUU
......((((.....................(((....))).....................((((((((.((((((........))..))))))))))))...))))............ (-12.66 = -12.46 +  -0.20)

alignment

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secondary structure

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dotplot

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Window 3

Location 16,744,684 – 16,744,797
Length 113
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 78.06
Mean single sequence MFE -29.40
Consensus MFE -15.87
Energy contribution -16.39
Covariance contribution 0.52
Combinations/Pair 1.15
Mean z-score -1.79
Structure conservation index 0.54
SVM decision value 0.06
SVM RNA-class probability 0.565811
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 16744684 113 - 22224390
AAACAGUG-CGCUGUUAUCAAUCUCGUGUAUCUCGUGUAUAUG-UGGAUAAAUAUAUGUAUGUAUAUUCAUAUCCAUAGAUA----GGAUGGAAACG-AGGGAAGUGGGGUGGCAGUACC
........-.(((((((((..((((((...((((.(((...((-(((((((((((((....)))))))..)))))))).)))----.)).))..)))-))).......)))))))))... ( -33.40)
>DroSec_CAF1 32031 95 - 1
AAACAGUG-CGCUGUUAUCAAUCUCGUGUAUCUCGUGUAUAUGGUGGAUAUAUACAU------------AUAUCUAUAGAUG----GGAG--------GGGGAAGUGGGGUGCCAGUGCC
.......(-(((((.((((..((((.(...((((((.(((.....(((((((....)------------))))))))).)))----))))--------.)))).....)))).)))))). ( -25.20)
>DroSim_CAF1 30359 95 - 1
AAACAGUG-CGCUGUUAUCAAUCUCGUGUAUCUCGUGUAUAUGGUGGAUAUAUACAU------------AUAUCUAUAGAUG----GGAG--------GGGGAAGUGGGGUGCAAGUGCC
.....(..-(.(..((.((..((((((.(((...(((((((((.....)))))))))------------......))).)))----))).--------.))..))..).)..)....... ( -24.50)
>DroEre_CAF1 23490 101 - 1
AAACAGUGUCGCUGUUAUCAAUCUCGUGUAUCUCAUGUAUAUG-UGGAUAA----AU--------AUCCACAUCCAUAGAUA----GGAAGGAAUC--GGAGGAGUGGGGUGGCAGUUCC
..........(((((((((...(((...(((((.(((...(((-(((((..----..--------)))))))).))))))))----.((.....))--....)))...)))))))))... ( -27.60)
>DroYak_CAF1 23512 111 - 1
AAACAGUGUCGCUGUUAUCAAUCUCGUGUAUCUCAUGUAUAUG-UGGAUAUAUGUAU--------AUCCACAUCCAUAGAUACAUUGAAGGGAAAUGGGGAGGAGUGGGGUGGCAGCAGC
..........(((((((((...(((((((((((.(((...(((-(((((((....))--------)))))))).))))))))))).................)))...)))))))))... ( -36.32)
>consensus
AAACAGUG_CGCUGUUAUCAAUCUCGUGUAUCUCGUGUAUAUG_UGGAUAUAUACAU________AU_CAUAUCCAUAGAUA____GGAGGGAA____GGGGAAGUGGGGUGGCAGUACC
..........(((((((((..((((((((((.....))))))..(((((((..................))))))).......................)))).....)))))))))... (-15.87 = -16.39 +   0.52)

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 12:20:43 2006