Locus 5892

Sequence ID 3R_DroMel_CAF1
Location 15,475,119 – 15,475,430
Length 311
Max. P 0.938141
window9629 window9630 window9631 window9632

overview

Window 9

Location 15,475,119 – 15,475,230
Length 111
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 87.50
Mean single sequence MFE -28.30
Consensus MFE -25.01
Energy contribution -25.80
Covariance contribution 0.79
Combinations/Pair 1.10
Mean z-score -1.97
Structure conservation index 0.88
SVM decision value 0.72
SVM RNA-class probability 0.832987
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 15475119 111 - 27905053
UAAUAUAUGGGUCGGCAAUCCUUAAGUCGGAUGCACUCCUCAUCCGGUUCACACAGUUUAUCUAUUGAAAAGUAGAGAG-----UGUU----CAUAGUGUGUUCAUAAAUUGUUUUAAUC
.......((..(((((.........)))(((((.......)))))))..)).((((((((((((((....))))))(((-----..(.----......)..))).))))))))....... ( -23.70)
>DroSec_CAF1 7402 120 - 1
UUAUAUAUGUGUGGGCAAUCCUUAAGUUGGAUGCACUCCUCAUCCGAUUGACACAGUUUAUCUAUUGAAAAGUAGGGAAAUAAUUGUUAUAAGACAGUGUUUUCAUAAAUUGUAUUAAUC
......(((.(..((((.(((.......)))))).)..).)))..((((((.((((((((((((((....)))))(((((((.(((((....))))))))))))))))))))).)))))) ( -31.60)
>DroSim_CAF1 2684 120 - 1
UCAUAUAUGUGUGGGCAAUCCUUAAGUCGGAUGCACUUCUCAUCCGGUUGACACAGUUUAUCUAUUGAAAAGUAGAGAAAUAAUUGUUAUAAGACAGUGUUUUCAUAAAUUGUAUUAAUC
......(((.(.(((((.(((.......)))))).)).).)))..((((((.((((((((((((((....))))))((((..((((((....))))))..)))).)))))))).)))))) ( -29.60)
>consensus
UAAUAUAUGUGUGGGCAAUCCUUAAGUCGGAUGCACUCCUCAUCCGGUUGACACAGUUUAUCUAUUGAAAAGUAGAGAAAUAAUUGUUAUAAGACAGUGUUUUCAUAAAUUGUAUUAAUC
......(((.(..((((.(((.......)))))).)..).)))..((((((.((((((((((((((....))))))((((..((((((....))))))..)))).)))))))).)))))) (-25.01 = -25.80 +   0.79)

alignment

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secondary structure

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Window 0

Location 15,475,190 – 15,475,310
Length 120
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 77.50
Mean single sequence MFE -30.71
Consensus MFE -17.59
Energy contribution -20.53
Covariance contribution 2.94
Combinations/Pair 1.17
Mean z-score -2.31
Structure conservation index 0.57
SVM decision value 1.27
SVM RNA-class probability 0.938141
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 15475190 120 - 27905053
CUCGAACACUCACGCCACACAUUCUUGUCUGCGAUAUAUUCACUUUUGCGGACCCCGACAAUCUGUUUCUCCUCACAUUGUAAUAUAUGGGUCGGCAAUCCUUAAGUCGGAUGCACUCCU
............(((...(((....)))..)))...(((((((((((((.(((((..(((((.((........)).))))).......))))).)))).....)))).)))))....... ( -25.00)
>DroSec_CAF1 7482 120 - 1
AUCGAACAUUGUCGCCACAUAUUCUUGUCUGCAAUAUAUCUAAUUUUGCAGACCGCGACAAUCUUUUGCUCUUCAGAUCGUUAUAUAUGUGUGGGCAAUCCUUAAGUUGGAUGCACUCCU
(((.(((((((((((...........((((((((...........)))))))).))))))))...((((((..((.((........)).)).)))))).......))).)))........ ( -30.60)
>DroSim_CAF1 2764 120 - 1
AUCGAACAUUGUCGCCACAUAUUCUUGUCUGCAAUAUAUCUAAUUUUGCAGACCACGACAAUCUUUUGCUCUUCAGAUCGUCAUAUAUGUGUGGGCAAUCCUUAAGUCGGAUGCACUUCU
...(((........((((((((....((((((((...........))))))))...(((.((((..........)))).)))....))))))))(((.(((.......))))))..))). ( -31.10)
>DroYak_CAF1 2455 120 - 1
UACGAACACUGGAGCCACAUCGCCUGUUGUUCAAAAUUUCCCUUUUUGUGGCUCUGGACAUUCUGUUUGUCUUCACAGCGUCAUAAACUUGUGGGCAAUCCUGCAGUCUGACGCACGUCU
.((((((((..((((((((......(((......))).........))))))))..)......))))))).......((((((...(((.(..((....))..)))).))))))...... ( -36.16)
>consensus
AUCGAACACUGUCGCCACAUAUUCUUGUCUGCAAUAUAUCCAAUUUUGCAGACCACGACAAUCUGUUGCUCUUCACAUCGUCAUAUAUGUGUGGGCAAUCCUUAAGUCGGAUGCACUCCU
..............((((((((....((((((((...........))))))))...(((.(((((........))))).)))....))))))))(((.(((.......))))))...... (-17.59 = -20.53 +   2.94)

alignment

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secondary structure

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dotplot

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Window 1

Location 15,475,270 – 15,475,390
Length 120
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 77.78
Mean single sequence MFE -38.03
Consensus MFE -21.23
Energy contribution -24.86
Covariance contribution 3.63
Combinations/Pair 1.12
Mean z-score -2.11
Structure conservation index 0.56
SVM decision value 0.58
SVM RNA-class probability 0.787218
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 15475270 120 - 27905053
CUUCCCACAAUCCGGAUAGCUUGGCAAGGUGUUUGCCGGCUUGGGACAGCAGAUAUAAAUCCUUUUGUAACGUUUCCGGUCUCGAACACUCACGCCACACAUUCUUGUCUGCGAUAUAUU
.........((((((((((..((((..((((((((((((..((..((((.((.........)).))))..))...)))))...)))))))...)))).......))))))).)))..... ( -30.40)
>DroSec_CAF1 7562 120 - 1
CCGUCCACAAGCCGGAUAGCUUGGCAAGAUGGUUGCCGGCUUGGGACAGCAGAUAUAAAUCAUUUGGUUAAGAUUCUGGUAUCGAACAUUGUCGCCACAUAUUCUUGUCUGCAAUAUAUC
..((((.((((((((.(((((.........))))))))))))))))).(((((((..(((.((.((((...(((..((........))..))))))).)))))..)))))))........ ( -43.50)
>DroSim_CAF1 2844 120 - 1
CCGUCCACAAGCCGGAUAGCUUGGCAAGAUGGUUGCCGGCUUGGGACAGCAGAUAUAACUCAUUUGGUUAAGAUUCUGGUAUCGAACAUUGUCGCCACAUAUUCUUGUCUGCAAUAUAUC
..((((.((((((((.(((((.........))))))))))))))))).(((((((.........((((...(((..((........))..)))))))........)))))))........ ( -41.53)
>DroYak_CAF1 2535 117 - 1
UUGUCCGCAAGCCGAAAGUCUGGGCAAGAUGUCUGCGGGUUCGGGACAGCAGAUG---GUUCUAUGGUGAAGUUUCUGCUUACGAACACUGGAGCCACAUCGCCUGUUGUUCAAAAUUUC
((((((...((.(....).))))))))(((((((.((((((((....((((((.(---.(((......))).).))))))..))))).))).))..)))))................... ( -36.70)
>consensus
CCGUCCACAAGCCGGAUAGCUUGGCAAGAUGGUUGCCGGCUUGGGACAGCAGAUAUAAAUCAUUUGGUUAAGAUUCUGGUAUCGAACACUGUCGCCACAUAUUCUUGUCUGCAAUAUAUC
..((((.((((((((.(((((.........))))))))))))))))).(((((((.........((((...(((..((........))..)))))))........)))))))........ (-21.23 = -24.86 +   3.63)

alignment

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secondary structure

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dotplot

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Window 2

Location 15,475,310 – 15,475,430
Length 120
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 79.86
Mean single sequence MFE -38.30
Consensus MFE -26.51
Energy contribution -28.20
Covariance contribution 1.69
Combinations/Pair 1.15
Mean z-score -1.65
Structure conservation index 0.69
SVM decision value 0.21
SVM RNA-class probability 0.636426
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 15475310 120 + 27905053
ACCGGAAACGUUACAAAAGGAUUUAUAUCUGCUGUCCCAAGCCGGCAAACACCUUGCCAAGCUAUCCGGAUUGUGGGAAGCCACAAACGACUAACCGUGUUAUAGGCGGCACGGAGCCGA
.(((((...(..(((...((((....))))..)))..).(((.(((((.....)))))..))).))))).((((((....)))))).((.((..(((((((......))))))))).)). ( -40.00)
>DroSec_CAF1 7602 120 + 1
ACCAGAAUCUUAACCAAAUGAUUUAUAUCUGCUGUCCCAAGCCGGCAACCAUCUUGCCAAGCUAUCCGGCUUGUGGACGGCCACAAUUGAUUUACCGUGUUAUGGGUGGCACGGAGCCGA
....(((((..........(((....))).((((((((((((((((((.....)))))..(.....))))))).))))))).......))))).((((((((....))))))))...... ( -40.90)
>DroSim_CAF1 2884 120 + 1
ACCAGAAUCUUAACCAAAUGAGUUAUAUCUGCUGUCCCAAGCCGGCAACCAUCUUGCCAAGCUAUCCGGCUUGUGGACGGCCACAAUUGACUUACCGGGUUAUGGGUGGCACGGAGCCGA
......(((((((((...(((((((.....((((((((((((((((((.....)))))..(.....))))))).)))))))......)))))))...))))).))))(((.....))).. ( -45.30)
>DroYak_CAF1 2575 117 + 1
AGCAGAAACUUCACCAUAGAAC---CAUCUGCUGUCCCGAACCCGCAGACAUCUUGCCCAGACUUUCGGCUUGCGGACAAAUGAAAAUGACUUUCCGGAUUAUGGGUGGCACGGAGCCGG
((((((...(((......))).---..))))))(..(((...((((((.......(((.........)))))))))...........((.((.((((.....)))).)))))))..)... ( -27.01)
>consensus
ACCAGAAACUUAACCAAAGGAUUUAUAUCUGCUGUCCCAAGCCGGCAAACAUCUUGCCAAGCUAUCCGGCUUGUGGACAGCCACAAAUGACUUACCGGGUUAUGGGUGGCACGGAGCCGA
..............................((((((((((((((((((.....)))))..(.....))))))).))))))).............((((((((....))))))))...... (-26.51 = -28.20 +   1.69)

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 12:07:12 2006