Locus 4699

Sequence ID 2R_DroMel_CAF1
Location 15,390,506 – 15,390,620
Length 114
Max. P 0.953794
window7564 window7565 window7566

overview

Window 4

Location 15,390,506 – 15,390,596
Length 90
Sequences 6
Columns 90
Reading direction forward
Mean pairwise identity 82.96
Mean single sequence MFE -23.73
Consensus MFE -13.81
Energy contribution -16.32
Covariance contribution 2.50
Combinations/Pair 1.13
Mean z-score -2.52
Structure conservation index 0.58
SVM decision value 0.12
SVM RNA-class probability 0.593779
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 15390506 90 + 20766785
AACGCCACAAAAACAACAGAAAAAGGCUGCGAAGUGCAAGUACUUUGAGUACUACGAGUAUCUCGGCAUCGCACUCGCAACUGCAUUCGA
..................(((...((.(((((.((((.(((((.....))))).((((...)))).....))))))))).))...))).. ( -25.00)
>DroPse_CAF1 225044 69 + 1
UCCACCG-AAAAACUGCAGCCA-----------------CAACUGCGAG---UGCGAGUAUCUUGUCCUCGCACUCGCAACUGCAUCCGA
.......-......(((((...-----------------....((((((---((((((.........)))))))))))).)))))..... ( -25.50)
>DroSec_CAF1 196083 90 + 1
AACGCCACAAAAACAACAGAAAAAGGCUGCGAAGUGCAAGUACUUUGAGUACUACGAGUAUCUCGGCAUCGCACUCGCAACUGAAUUCGA
..................(((...((.(((((.((((.(((((.....))))).((((...)))).....))))))))).))...))).. ( -25.00)
>DroSim_CAF1 174355 90 + 1
AACGCCACAAAAACAACAGAAAAAGGCUGCGAAGUGCAAGUACUUUGAGUACUACGAGUAUCUCGGCAUCGCACUCGCAACUGCAUUCGA
..................(((...((.(((((.((((.(((((.....))))).((((...)))).....))))))))).))...))).. ( -25.00)
>DroEre_CAF1 183359 90 + 1
AACGCCACAAAAACAACAGAAAAAGGCUGCGAAGUGCAAGUACUUUGAGUACUGCGAGUAUUUCGGCAUCGCACUCGCAACUGCAUUCGA
...(((..................)))..((((.(((((((((.....)))))((((((....((....)).))))))...)))))))). ( -22.87)
>DroYak_CAF1 189485 89 + 1
AACGCCACAAAAACAAGAGAA-AAGGCUACGAAGUGCAAGUACUUUGAGUACUACGGGUAUUUCGGCAUCGCACUCGGAACUGCAUUCGA
...(((...............-..)))..((((.(((((((((.....))))).(((((....((....)).)))))....)))))))). ( -19.03)
>consensus
AACGCCACAAAAACAACAGAAAAAGGCUGCGAAGUGCAAGUACUUUGAGUACUACGAGUAUCUCGGCAUCGCACUCGCAACUGCAUUCGA
..................(((...((.(((((.((((.(((((.....))))).((((...)))).....))))))))).))...))).. (-13.81 = -16.32 +   2.50)

alignment

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secondary structure

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dotplot

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Window 5

Location 15,390,523 – 15,390,620
Length 97
Sequences 6
Columns 97
Reading direction forward
Mean pairwise identity 79.93
Mean single sequence MFE -25.82
Consensus MFE -12.12
Energy contribution -13.26
Covariance contribution 1.14
Combinations/Pair 1.12
Mean z-score -2.49
Structure conservation index 0.47
SVM decision value 0.41
SVM RNA-class probability 0.724380
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 15390523 97 + 20766785
AGAAAAAGGCUGCGAAGUGCAAGUACUUUGAGUACUACGAGUAUCUCGGCAUCGCACUCGCAACUGCAUUCGAUAGAUACUCGCAACCACAAACAAG
.......((.((((((((((.(((((.....))))).((((...)))).....))))).((....)).............))))).))......... ( -26.30)
>DroPse_CAF1 225060 77 + 1
AGCCA-----------------CAACUGCGAG---UGCGAGUAUCUUGUCCUCGCACUCGCAACUGCAUCCGAUAGAUACUCGCAACCGCAAACAAG
.....-----------------....((((..---(((((((((((.(((...(((........)))....))))))))))))))..))))...... ( -27.60)
>DroSec_CAF1 196100 97 + 1
AGAAAAAGGCUGCGAAGUGCAAGUACUUUGAGUACUACGAGUAUCUCGGCAUCGCACUCGCAACUGAAUUCGAUAGAUACUCGCAACCACAAACAAG
.......((.(((((((((....))))))(((((((((((((...((((....((....))..))))))))).))).)))))))).))......... ( -25.60)
>DroEre_CAF1 183376 97 + 1
AGAAAAAGGCUGCGAAGUGCAAGUACUUUGAGUACUGCGAGUAUUUCGGCAUCGCACUCGCAACUGCAUUCGAUAGAUACUCGCAACCACAAACAAG
........(((.(((((((....))))))))))..((((((((((((((((..((....))...)))...)))..))))))))))............ ( -26.90)
>DroYak_CAF1 189502 96 + 1
AGAA-AAGGCUACGAAGUGCAAGUACUUUGAGUACUACGGGUAUUUCGGCAUCGCACUCGGAACUGCAUUCGAUAGAUACUCGCAACCACAAACAAG
....-...(((.(((((((....))))))))))....((((((((((((.((.(((........)))))))))..)))))))).............. ( -20.90)
>DroPer_CAF1 184985 77 + 1
AGCCA-----------------CAACUGCGAG---UGCGAGUAUCUUGUCCUCGCACUCGCAACUGCAUCCGAUAGAUACUCGCAACCGCAAACAAG
.....-----------------....((((..---(((((((((((.(((...(((........)))....))))))))))))))..))))...... ( -27.60)
>consensus
AGAAAAAGGCUGCGAAGUGCAAGUACUUUGAGUACUACGAGUAUCUCGGCAUCGCACUCGCAACUGCAUUCGAUAGAUACUCGCAACCACAAACAAG
.....................(((((.....))))).(((((((((.......(((........))).......))))))))).............. (-12.12 = -13.26 +   1.14)

alignment

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secondary structure

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dotplot

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Window 6

Location 15,390,523 – 15,390,620
Length 97
Sequences 6
Columns 97
Reading direction reverse
Mean pairwise identity 79.93
Mean single sequence MFE -31.90
Consensus MFE -17.49
Energy contribution -18.02
Covariance contribution 0.53
Combinations/Pair 1.10
Mean z-score -2.98
Structure conservation index 0.55
SVM decision value 1.44
SVM RNA-class probability 0.953794
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 15390523 97 - 20766785
CUUGUUUGUGGUUGCGAGUAUCUAUCGAAUGCAGUUGCGAGUGCGAUGCCGAGAUACUCGUAGUACUCAAAGUACUUGCACUUCGCAGCCUUUUUCU
.........(((((((((((((..(((...(((.((((....)))))))))))))))))(((((((.....)))).))).....))))))....... ( -32.30)
>DroPse_CAF1 225060 77 - 1
CUUGUUUGCGGUUGCGAGUAUCUAUCGGAUGCAGUUGCGAGUGCGAGGACAAGAUACUCGCA---CUCGCAGUUG-----------------UGGCU
.........(((..((((((((.....)))))..(((((((((((((.........))))))---))))))))))-----------------..))) ( -35.90)
>DroSec_CAF1 196100 97 - 1
CUUGUUUGUGGUUGCGAGUAUCUAUCGAAUUCAGUUGCGAGUGCGAUGCCGAGAUACUCGUAGUACUCAAAGUACUUGCACUUCGCAGCCUUUUUCU
.........((((((((((((((((((.((((......)))).))))....))))))))(((((((.....)))).))).....))))))....... ( -32.40)
>DroEre_CAF1 183376 97 - 1
CUUGUUUGUGGUUGCGAGUAUCUAUCGAAUGCAGUUGCGAGUGCGAUGCCGAAAUACUCGCAGUACUCAAAGUACUUGCACUUCGCAGCCUUUUUCU
.........((((((((((((...(((...(((.((((....)))))))))).))))))(((((((.....)))).))).....))))))....... ( -31.10)
>DroYak_CAF1 189502 96 - 1
CUUGUUUGUGGUUGCGAGUAUCUAUCGAAUGCAGUUCCGAGUGCGAUGCCGAAAUACCCGUAGUACUCAAAGUACUUGCACUUCGUAGCCUU-UUCU
.........(((((((((((((....).)))).......((((((((((.(......).)))((((.....)))))))))))))))))))..-.... ( -23.80)
>DroPer_CAF1 184985 77 - 1
CUUGUUUGCGGUUGCGAGUAUCUAUCGGAUGCAGUUGCGAGUGCGAGGACAAGAUACUCGCA---CUCGCAGUUG-----------------UGGCU
.........(((..((((((((.....)))))..(((((((((((((.........))))))---))))))))))-----------------..))) ( -35.90)
>consensus
CUUGUUUGUGGUUGCGAGUAUCUAUCGAAUGCAGUUGCGAGUGCGAUGCCGAGAUACUCGCAGUACUCAAAGUACUUGCACUUCGCAGCCUUUUUCU
....((((.(..(((((((((((......((((.(....).))))......)))))))))))...).)))).......................... (-17.49 = -18.02 +   0.53)

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 11:27:10 2006