Locus 2408

Sequence ID 3L_DroMel_CAF1
Location 6,775,349 – 6,775,471
Length 122
Max. P 0.971382
window3718 window3719 window3720 window3721

overview

Window 8

Location 6,775,349 – 6,775,439
Length 90
Sequences 6
Columns 111
Reading direction forward
Mean pairwise identity 80.77
Mean single sequence MFE -28.63
Consensus MFE -24.73
Energy contribution -24.37
Covariance contribution -0.36
Combinations/Pair 1.08
Mean z-score -3.07
Structure conservation index 0.86
SVM decision value 1.67
SVM RNA-class probability 0.971382
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 6775349 90 + 23771897
UA-----CAUACAUAUUUGGGCCAACUUAAAGCGCAGGAAAUUAAAUUUUAUGAUGCCGAGUC--G----------AGUCGAGUCGCAUUGGCAGCU----AAGUUGGCCA
..-----............(((((((((..(((.((.(((((...))))).)).((((((..(--(----------(......)))..)))))))))----))))))))). ( -28.60)
>DroSec_CAF1 36186 90 + 1
UAUGGUACAUACAUAUUUGGGCCAACUUAAAGCGCAGGAAAUUAAAUUUUAUGAUGCCGAGUC-----------------GAGUCGCAUUGGCAGCU----AAGUUGGCCA
((((.......))))....(((((((((..(((.((.(((((...))))).)).((((((((.-----------------.....)).)))))))))----))))))))). ( -27.30)
>DroSim_CAF1 36614 89 + 1
UAC-AUACAUACAUAUUUGGGCCAACUUAAAGCGCAGGAAAUUAAAUUUUAUGAUGCCGAGUC-----------------GAGUCGCAUUGGCAGCU----AAGUUGGCCA
...-...............(((((((((..(((.((.(((((...))))).)).((((((((.-----------------.....)).)))))))))----))))))))). ( -26.20)
>DroYak_CAF1 39721 102 + 1
UA---------CAUAUUUGGGCCAACUUAAAGCGCAGGAAAUUAAAUUUUAUGAUGCCGAGUCGCGAGUCGAGUCGAGUUGAGUCGCAUUGGCAGCUAUGUAAGUUGGCCA
..---------........((((((((((.(((.((.(((((...))))).)).((((((...((((.((((......)))).)))).)))))))))...)))))))))). ( -39.00)
>DroAna_CAF1 46418 72 + 1
-------------UAUUUGGGCCAGCUUAAAGCGCAGGAAAUUAAAUUUUAUGAUGCCGAG----------------------UCGCAUUGGCAGCU----AAGUUGGCCA
-------------......(((((((((..(((.((.(((((...))))).)).((((((.----------------------.....)))))))))----))))))))). ( -26.40)
>DroPer_CAF1 45974 79 + 1
--------GGGCAUAUUUGGGCCAGCUUAAAGUGCAGGAAAUUAAAUUUUAUGAUGCCGAG--------------------AGUCGCAUUGGCAGCU----AAGUUGGCCA
--------...........((((((((((.....((.(((((...))))).)).((((((.--------------------.......))))))..)----))))))))). ( -24.30)
>consensus
UA______AUACAUAUUUGGGCCAACUUAAAGCGCAGGAAAUUAAAUUUUAUGAUGCCGAGUC_________________GAGUCGCAUUGGCAGCU____AAGUUGGCCA
...................(((((((((..(((.((.(((((...))))).)).((((((............................)))))))))....))))))))). (-24.73 = -24.37 +  -0.36)

alignment

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secondary structure

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dotplot

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Window 9

Location 6,775,349 – 6,775,439
Length 90
Sequences 6
Columns 111
Reading direction reverse
Mean pairwise identity 80.77
Mean single sequence MFE -20.06
Consensus MFE -16.62
Energy contribution -17.12
Covariance contribution 0.50
Combinations/Pair 1.00
Mean z-score -1.66
Structure conservation index 0.83
SVM decision value 0.72
SVM RNA-class probability 0.831722
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 6775349 90 - 23771897
UGGCCAACUU----AGCUGCCAAUGCGACUCGACU----------C--GACUCGGCAUCAUAAAAUUUAAUUUCCUGCGCUUUAAGUUGGCCCAAAUAUGUAUG-----UA
.(((((((((----((..((.....(((.(((...----------)--)).)))(((..................))))).)))))))))))............-----.. ( -22.77)
>DroSec_CAF1 36186 90 - 1
UGGCCAACUU----AGCUGCCAAUGCGACUC-----------------GACUCGGCAUCAUAAAAUUUAAUUUCCUGCGCUUUAAGUUGGCCCAAAUAUGUAUGUACCAUA
.(((((((((----((..((.....(((...-----------------...)))(((..................))))).)))))))))))................... ( -20.17)
>DroSim_CAF1 36614 89 - 1
UGGCCAACUU----AGCUGCCAAUGCGACUC-----------------GACUCGGCAUCAUAAAAUUUAAUUUCCUGCGCUUUAAGUUGGCCCAAAUAUGUAUGUAU-GUA
.(((((((((----((..((.....(((...-----------------...)))(((..................))))).)))))))))))...............-... ( -20.17)
>DroYak_CAF1 39721 102 - 1
UGGCCAACUUACAUAGCUGCCAAUGCGACUCAACUCGACUCGACUCGCGACUCGGCAUCAUAAAAUUUAAUUUCCUGCGCUUUAAGUUGGCCCAAAUAUG---------UA
.((((((((((...(((((((..(((((.((..........)).)))))....)))).((..((((...))))..)).))).))))))))))........---------.. ( -27.20)
>DroAna_CAF1 46418 72 - 1
UGGCCAACUU----AGCUGCCAAUGCGA----------------------CUCGGCAUCAUAAAAUUUAAUUUCCUGCGCUUUAAGCUGGCCCAAAUA-------------
.(((((.(((----((..((((((((..----------------------....)))).................)).)).))))).)))))......------------- ( -15.92)
>DroPer_CAF1 45974 79 - 1
UGGCCAACUU----AGCUGCCAAUGCGACU--------------------CUCGGCAUCAUAAAAUUUAAUUUCCUGCACUUUAAGCUGGCCCAAAUAUGCCC--------
.(((((.(((----((.(((..((((....--------------------....))))..................)))..))))).)))))...........-------- ( -14.15)
>consensus
UGGCCAACUU____AGCUGCCAAUGCGACUC_________________GACUCGGCAUCAUAAAAUUUAAUUUCCUGCGCUUUAAGUUGGCCCAAAUAUGUAU______UA
.(((((((((....((((((....)))...........................(((..................))))))..)))))))))................... (-16.62 = -17.12 +   0.50)

alignment

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secondary structure

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dotplot

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Window 0

Location 6,775,380 – 6,775,471
Length 91
Sequences 6
Columns 107
Reading direction forward
Mean pairwise identity 79.47
Mean single sequence MFE -27.20
Consensus MFE -14.03
Energy contribution -15.03
Covariance contribution 1.00
Combinations/Pair 1.00
Mean z-score -2.07
Structure conservation index 0.52
SVM decision value 0.20
SVM RNA-class probability 0.632205
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 6775380 91 + 23771897
GGAAAUUAAAUUUUAUGAUGCCGAGUC--G----------AGUCGAGUCGCAUUGGCAGCU----AAGUUGGCCAUUUGGCCAUUUGGCCAUUCGACCAGGCCCAGA
((..((((.......))))(((..(((--(----------((((((......))))).(((----((((.((((....)))))))))))...)))))..)))))... ( -31.90)
>DroSec_CAF1 36222 78 + 1
GGAAAUUAAAUUUUAUGAUGCCGAGUC-----------------GAGUCGCAUUGGCAGCU----AAGUUGGCCAUU--------UGGCCAUUCGACCAGGCCCAGA
((..((((.......))))(((..(((-----------------((((.((..(((((((.----..))).))))..--------..)).)))))))..)))))... ( -23.70)
>DroSim_CAF1 36649 86 + 1
GGAAAUUAAAUUUUAUGAUGCCGAGUC-----------------GAGUCGCAUUGGCAGCU----AAGUUGGCCAUUUGGCCAUUUGGCCAUUCGACCAGGCCCAAA
((..((((.......))))(((..(((-----------------((((.((....)).(((----((((.((((....))))))))))).)))))))..)))))... ( -30.20)
>DroYak_CAF1 39748 99 + 1
GGAAAUUAAAUUUUAUGAUGCCGAGUCGCGAGUCGAGUCGAGUUGAGUCGCAUUGGCAGCUAUGUAAGUUGGCCAUU--------UGGCCAUUCGACCAGGCCCAGA
((................((((((...((((.((((......)))).)))).))))))(((..((....(((((...--------.)))))....))..)))))... ( -32.50)
>DroAna_CAF1 46441 73 + 1
GGAAAUUAAAUUUUAUGAUGCCGAG----------------------UCGCAUUGGCAGCU----AAGUUGGCCAUU--------UGGCCAUUUGGCCAGACCCAGA
((................((((((.----------------------.....))))))(((----((((.((((...--------.))))))))))).....))... ( -24.50)
>DroPer_CAF1 46002 72 + 1
GGAAAUUAAAUUUUAUGAUGCCGAG--------------------AGUCGCAUUGGCAGCU----AAGUUGGCCAUU--------UGU---GUUGGCCAGGCACAGG
...............((.((((...--------------------(((.((....)).)))----....((((((..--------...---..)))))))))))).. ( -20.40)
>consensus
GGAAAUUAAAUUUUAUGAUGCCGAGUC_________________GAGUCGCAUUGGCAGCU____AAGUUGGCCAUU________UGGCCAUUCGACCAGGCCCAGA
((................((((((............................))))))(((........((((((..........))))))........)))))... (-14.03 = -15.03 +   1.00)

alignment

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secondary structure

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dotplot

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Window 1

Location 6,775,380 – 6,775,471
Length 91
Sequences 6
Columns 107
Reading direction reverse
Mean pairwise identity 79.47
Mean single sequence MFE -24.28
Consensus MFE -14.84
Energy contribution -16.03
Covariance contribution 1.20
Combinations/Pair 1.07
Mean z-score -2.49
Structure conservation index 0.61
SVM decision value 1.29
SVM RNA-class probability 0.938113
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 6775380 91 - 23771897
UCUGGGCCUGGUCGAAUGGCCAAAUGGCCAAAUGGCCAACUU----AGCUGCCAAUGCGACUCGACU----------C--GACUCGGCAUCAUAAAAUUUAAUUUCC
..((((((.((((((.(((((....)))))..((((......----....))))............)----------)--)))).))).)))............... ( -27.60)
>DroSec_CAF1 36222 78 - 1
UCUGGGCCUGGUCGAAUGGCCA--------AAUGGCCAACUU----AGCUGCCAAUGCGACUC-----------------GACUCGGCAUCAUAAAAUUUAAUUUCC
..((((((.((((((.(((((.--------...)))))....----.((.......))...))-----------------)))).))).)))............... ( -25.30)
>DroSim_CAF1 36649 86 - 1
UUUGGGCCUGGUCGAAUGGCCAAAUGGCCAAAUGGCCAACUU----AGCUGCCAAUGCGACUC-----------------GACUCGGCAUCAUAAAAUUUAAUUUCC
..((((((.((((((.(((((....)))))..((((......----....)))).......))-----------------)))).))).)))............... ( -27.70)
>DroYak_CAF1 39748 99 - 1
UCUGGGCCUGGUCGAAUGGCCA--------AAUGGCCAACUUACAUAGCUGCCAAUGCGACUCAACUCGACUCGACUCGCGACUCGGCAUCAUAAAAUUUAAUUUCC
..((((((.((((...(((((.--------...)))))..................((((.((..........)).)))))))).))).)))............... ( -26.30)
>DroAna_CAF1 46441 73 - 1
UCUGGGUCUGGCCAAAUGGCCA--------AAUGGCCAACUU----AGCUGCCAAUGCGA----------------------CUCGGCAUCAUAAAAUUUAAUUUCC
.((((((((((((....)))))--------..((((......----....))))....))----------------------))))).................... ( -21.50)
>DroPer_CAF1 46002 72 - 1
CCUGUGCCUGGCCAAC---ACA--------AAUGGCCAACUU----AGCUGCCAAUGCGACU--------------------CUCGGCAUCAUAAAAUUUAAUUUCC
...(((((((((((..---...--------..))))))....----.((.......))....--------------------...)))))................. ( -17.30)
>consensus
UCUGGGCCUGGUCGAAUGGCCA________AAUGGCCAACUU____AGCUGCCAAUGCGACUC_________________GACUCGGCAUCAUAAAAUUUAAUUUCC
.....(((.((((...((((((..........)))))).........((.......))......................)))).)))................... (-14.84 = -16.03 +   1.20)

alignment

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secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:31:40 2006