Locus 6107

Sequence ID 2L_DroMel_CAF1
Location 17,107,112 – 17,107,352
Length 240
Max. P 0.998605
window9719 window9720 window9721 window9722 window9723

overview

Window 9

Location 17,107,112 – 17,107,232
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 93.07
Mean single sequence MFE -24.79
Consensus MFE -21.10
Energy contribution -22.10
Covariance contribution 1.00
Combinations/Pair 1.00
Mean z-score -1.38
Structure conservation index 0.85
SVM decision value 0.42
SVM RNA-class probability 0.729375
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 17107112 120 + 22407834
CAACGGGUGCAGUCUGUAAUUGGAAACUCAUGUUAAUGACUUUCACUCUUUCGCCAAAGCCAAAUGAAGGUUAUGCUUUGGCCUUCCGCCCAUUACUUCCAUUUACCCCCUUUCCAUAGC
....(((((......(((((.(((((.((((....)))).))))........((((((((..(((....)))..)))))))).......).))))).......)))))............ ( -26.12)
>DroSec_CAF1 70930 120 + 1
CAAAGGGUGCAGUCUGUAAUUGGAAACUCAUGUUAAUGACUUUCACUCUCUCGCCAAAGCCAAAUGAAGGUUAUGCUUUGGCCUUCCGCACAUUACUUCCAUUUACCCCCUUUCCUUAGC
....(((((......(((((((((((.((((....)))).))))........((((((((..(((....)))..))))))))......)).))))).......)))))............ ( -26.22)
>DroSim_CAF1 84509 120 + 1
CAAAGGGUGCAGUCUGUAAUUGGAAACUCAUGUUAAUGACUUUCACUCUCUCGCCAAAGCCAAAUGAAGGUUAUGCUUUGGCCUUCCGCCCAUUACUUCCAUUUACCCCCUUUCCUUAGC
.((((((.(......((((.(((((..((((....)))).............((((((((..(((....)))..))))))))..............))))).)))))))))))....... ( -26.20)
>DroEre_CAF1 72327 114 + 1
UAAAGGCUGCAGUCUGUAAUUGGCAACUCAUGUUAAUGACUUUCACUC--UCGCCAAAGCCAAAUGAAGGUUAUGCCCUGGCCU----CCCAUUACUUCCAUUUACCCCCAUUCCUUAGC
...(((((((.....))....((((((....))).((((((((((...--..((....))....)))))))))))))..)))))----................................ ( -19.70)
>DroYak_CAF1 72543 118 + 1
CAAAGGGUGCAGUCCGUAAUUUGAAACUCAUGUUAAUGACUUACACUC--UCGCCAAAGCCAAAUGAAGGUUAUGCUUUGGCCUUCCACCCAUUACUUCCAUUUACCCCCAUUCCUUAGC
....(((((.((((..((((.((.....)).))))..)))).......--..((((((((..(((....)))..))))))))....)))))............................. ( -25.70)
>consensus
CAAAGGGUGCAGUCUGUAAUUGGAAACUCAUGUUAAUGACUUUCACUCU_UCGCCAAAGCCAAAUGAAGGUUAUGCUUUGGCCUUCCGCCCAUUACUUCCAUUUACCCCCUUUCCUUAGC
....(((((......(((((..((((.((((....)))).))))........((((((((..(((....)))..)))))))).........))))).......)))))............ (-21.10 = -22.10 +   1.00)

alignment

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secondary structure

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Window 0

Location 17,107,152 – 17,107,272
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 92.99
Mean single sequence MFE -19.39
Consensus MFE -17.28
Energy contribution -17.52
Covariance contribution 0.24
Combinations/Pair 1.06
Mean z-score -1.62
Structure conservation index 0.89
SVM decision value 1.54
SVM RNA-class probability 0.962438
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 17107152 120 + 22407834
UUUCACUCUUUCGCCAAAGCCAAAUGAAGGUUAUGCUUUGGCCUUCCGCCCAUUACUUCCAUUUACCCCCUUUCCAUAGCCUUACCACUUACAUAUAUCCAUGCAUAUUCAUGGGGCCGA
............((((((((..(((....)))..))))))))..((.((((..................((......))....................((((......)))))))).)) ( -20.50)
>DroSec_CAF1 70970 120 + 1
UUUCACUCUCUCGCCAAAGCCAAAUGAAGGUUAUGCUUUGGCCUUCCGCACAUUACUUCCAUUUACCCCCUUUCCUUAGCCUUACCACUUACAUAUAUCCAUGCAUAUUCAUGGGGCCGA
............(((...((.....((((((((.....)))))))).)).................................................(((((......))))))))... ( -19.50)
>DroSim_CAF1 84549 120 + 1
UUUCACUCUCUCGCCAAAGCCAAAUGAAGGUUAUGCUUUGGCCUUCCGCCCAUUACUUCCAUUUACCCCCUUUCCUUAGCCUUUCCACUUACAUAUAUCCAUGCAUAUUCAUGGGGCCGA
............((((((((..(((....)))..))))))))..((.((((..................((......))....................((((......)))))))).)) ( -20.50)
>DroEre_CAF1 72367 114 + 1
UUUCACUC--UCGCCAAAGCCAAAUGAAGGUUAUGCCCUGGCCU----CCCAUUACUUCCAUUUACCCCCAUUCCUUAGCCUUACCACUUACAUAUAGCCAUGCAUAUUCAUGGGGCCAG
........--..((...((((.......))))..)).((((((.----.......................................((.......))(((((......))))))))))) ( -17.70)
>DroYak_CAF1 72583 118 + 1
UUACACUC--UCGCCAAAGCCAAAUGAAGGUUAUGCUUUGGCCUUCCACCCAUUACUUCCAUUUACCCCCAUUCCUUAGCCUUACCACUUACAUAUACCUAUGCAUAUUCAUGGGGCCAA
........--..((((((((..(((....)))..))))))))........................((((((......((......................))......)))))).... ( -18.75)
>consensus
UUUCACUCU_UCGCCAAAGCCAAAUGAAGGUUAUGCUUUGGCCUUCCGCCCAUUACUUCCAUUUACCCCCUUUCCUUAGCCUUACCACUUACAUAUAUCCAUGCAUAUUCAUGGGGCCGA
............(((..........((((((((.....))))))))....................................................(((((......))))))))... (-17.28 = -17.52 +   0.24)

alignment

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secondary structure

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Window 1

Location 17,107,152 – 17,107,272
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 92.99
Mean single sequence MFE -31.04
Consensus MFE -26.98
Energy contribution -27.30
Covariance contribution 0.32
Combinations/Pair 1.06
Mean z-score -1.84
Structure conservation index 0.87
SVM decision value 1.90
SVM RNA-class probability 0.982061
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 17107152 120 - 22407834
UCGGCCCCAUGAAUAUGCAUGGAUAUAUGUAAGUGGUAAGGCUAUGGAAAGGGGGUAAAUGGAAGUAAUGGGCGGAAGGCCAAAGCAUAACCUUCAUUUGGCUUUGGCGAAAGAGUGAAA
...(((((.......((((((....)))))).((((.....))))......)))))........((..(((.(....).)))..))......(((((((.((....))....))))))). ( -29.80)
>DroSec_CAF1 70970 120 - 1
UCGGCCCCAUGAAUAUGCAUGGAUAUAUGUAAGUGGUAAGGCUAAGGAAAGGGGGUAAAUGGAAGUAAUGUGCGGAAGGCCAAAGCAUAACCUUCAUUUGGCUUUGGCGAGAGAGUGAAA
((.(((((((.....((((((....)))))).)))).(((((((((..((((..((................(....)((....))))..))))..))))))))))))..))........ ( -28.20)
>DroSim_CAF1 84549 120 - 1
UCGGCCCCAUGAAUAUGCAUGGAUAUAUGUAAGUGGAAAGGCUAAGGAAAGGGGGUAAAUGGAAGUAAUGGGCGGAAGGCCAAAGCAUAACCUUCAUUUGGCUUUGGCGAGAGAGUGAAA
((.(((((((.....((((((....)))))).)))).(((((((((..((((..((........((..(((.(....).)))..))))..))))..))))))))))))..))........ ( -32.90)
>DroEre_CAF1 72367 114 - 1
CUGGCCCCAUGAAUAUGCAUGGCUAUAUGUAAGUGGUAAGGCUAAGGAAUGGGGGUAAAUGGAAGUAAUGGG----AGGCCAGGGCAUAACCUUCAUUUGGCUUUGGCGA--GAGUGAAA
((.(((((((.....((((((....)))))).)))).((((((...((((((((((...((...((..(((.----...)))..)).))))))))))))))))))))).)--)....... ( -31.50)
>DroYak_CAF1 72583 118 - 1
UUGGCCCCAUGAAUAUGCAUAGGUAUAUGUAAGUGGUAAGGCUAAGGAAUGGGGGUAAAUGGAAGUAAUGGGUGGAAGGCCAAAGCAUAACCUUCAUUUGGCUUUGGCGA--GAGUGUAA
((((((((((..((((((....))))))....))))...))))))....(..((.((((((((.((.(((..(((....)))...))).)).)))))))).))..)((..--..)).... ( -32.80)
>consensus
UCGGCCCCAUGAAUAUGCAUGGAUAUAUGUAAGUGGUAAGGCUAAGGAAAGGGGGUAAAUGGAAGUAAUGGGCGGAAGGCCAAAGCAUAACCUUCAUUUGGCUUUGGCGA_AGAGUGAAA
...(((((((.....((((((....)))))).)))).(((((((((....((((((...((...((..(((.(....).)))..)).)))))))).))))))))))))............ (-26.98 = -27.30 +   0.32)

alignment

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secondary structure

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Window 2

Location 17,107,192 – 17,107,312
Length 120
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 95.42
Mean single sequence MFE -21.25
Consensus MFE -19.58
Energy contribution -19.82
Covariance contribution 0.25
Combinations/Pair 1.00
Mean z-score -2.58
Structure conservation index 0.92
SVM decision value 1.79
SVM RNA-class probability 0.977588
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 17107192 120 + 22407834
GCCUUCCGCCCAUUACUUCCAUUUACCCCCUUUCCAUAGCCUUACCACUUACAUAUAUCCAUGCAUAUUCAUGGGGCCGACUCACAUACGGCCCAAACGAAGUUGGCCCAAUCAUCAUCC
.......(((....(((((........................................((((......))))((((((.........))))))....))))).)))............. ( -22.70)
>DroSec_CAF1 71010 120 + 1
GCCUUCCGCACAUUACUUCCAUUUACCCCCUUUCCUUAGCCUUACCACUUACAUAUAUCCAUGCAUAUUCAUGGGGCCGACUCACAUACGGCCCAAACGAAGUUGGCCCAAUCAUCAUCC
(((...........(((((........................................((((......))))((((((.........))))))....))))).)))............. ( -20.70)
>DroSim_CAF1 84589 120 + 1
GCCUUCCGCCCAUUACUUCCAUUUACCCCCUUUCCUUAGCCUUUCCACUUACAUAUAUCCAUGCAUAUUCAUGGGGCCGACUCACAUACGGCCCAAACGAAGUUGGCCCAAUCAUCAUCC
.......(((....(((((........................................((((......))))((((((.........))))))....))))).)))............. ( -22.70)
>DroEre_CAF1 72405 116 + 1
GCCU----CCCAUUACUUCCAUUUACCCCCAUUCCUUAGCCUUACCACUUACAUAUAGCCAUGCAUAUUCAUGGGGCCAGCUCACAUACGGCCCAAACGAAGUUGGCCCAAUCAUCAUCC
(((.----......(((((........................................((((......))))(((((...........)))))....))))).)))............. ( -18.90)
>consensus
GCCUUCCGCCCAUUACUUCCAUUUACCCCCUUUCCUUAGCCUUACCACUUACAUAUAUCCAUGCAUAUUCAUGGGGCCGACUCACAUACGGCCCAAACGAAGUUGGCCCAAUCAUCAUCC
(((...........(((((........................................((((......))))((((((.........))))))....))))).)))............. (-19.58 = -19.82 +   0.25)

alignment

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secondary structure

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Window 3

Location 17,107,232 – 17,107,352
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 97.92
Mean single sequence MFE -21.18
Consensus MFE -20.22
Energy contribution -19.66
Covariance contribution -0.56
Combinations/Pair 1.15
Mean z-score -2.17
Structure conservation index 0.95
SVM decision value 3.16
SVM RNA-class probability 0.998605
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 17107232 120 + 22407834
CUUACCACUUACAUAUAUCCAUGCAUAUUCAUGGGGCCGACUCACAUACGGCCCAAACGAAGUUGGCCCAAUCAUCAUCCAAUUAGAACUGUAAAAUUAUACUAAUUACAACUUUGAAAU
...................((((......))))((((((.........))))))...(((((((((......).......((((((...((((....)))))))))).)))))))).... ( -22.10)
>DroSec_CAF1 71050 120 + 1
CUUACCACUUACAUAUAUCCAUGCAUAUUCAUGGGGCCGACUCACAUACGGCCCAAACGAAGUUGGCCCAAUCAUCAUCCAAUUAGAACUGUAAAAUUAUACUAAUUACAACUUUGAAAU
...................((((......))))((((((.........))))))...(((((((((......).......((((((...((((....)))))))))).)))))))).... ( -22.10)
>DroSim_CAF1 84629 120 + 1
CUUUCCACUUACAUAUAUCCAUGCAUAUUCAUGGGGCCGACUCACAUACGGCCCAAACGAAGUUGGCCCAAUCAUCAUCCAAUUAGAACUGUAAAAUUAUACUAAUUACAACUUUGAAAU
...................((((......))))((((((.........))))))...(((((((((......).......((((((...((((....)))))))))).)))))))).... ( -22.10)
>DroEre_CAF1 72441 120 + 1
CUUACCACUUACAUAUAGCCAUGCAUAUUCAUGGGGCCAGCUCACAUACGGCCCAAACGAAGUUGGCCCAAUCAUCAUCCAAUUAGAACUGUAAAAUUAUACUAAUUACAACUUUGAAAU
.............(((((.((((......))))(((((((((......((.......)).)))))))))...................)))))........................... ( -20.50)
>DroYak_CAF1 72661 120 + 1
CUUACCACUUACAUAUACCUAUGCAUAUUCAUGGGGCCAACUCACAUACGGCCCAAACGAAGUUGGCCCAAUCAUCAUCCAAUUAGAACUGUAAAAUUAUACUAAUUACAACUUUGAAAU
...........((((....))))....((((..(((((((((......((.......)).)))))))))...........((((((...((((....)))))))))).......)))).. ( -19.10)
>consensus
CUUACCACUUACAUAUAUCCAUGCAUAUUCAUGGGGCCGACUCACAUACGGCCCAAACGAAGUUGGCCCAAUCAUCAUCCAAUUAGAACUGUAAAAUUAUACUAAUUACAACUUUGAAAU
........(((((......((((......))))(((((((((......((.......)).)))))))))....................))))).......................... (-20.22 = -19.66 +  -0.56)

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 12:01:59 2006