Locus 9731

Sequence ID 3R_DroMel_CAF1
Location 25,747,865 – 25,748,177
Length 312
Max. P 0.942927
window15543 window15544 window15545 window15546 window15547

overview

Window 3

Location 25,747,865 – 25,747,980
Length 115
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 77.26
Mean single sequence MFE -26.75
Consensus MFE -16.66
Energy contribution -18.58
Covariance contribution 1.92
Combinations/Pair 1.30
Mean z-score -1.98
Structure conservation index 0.62
SVM decision value 1.21
SVM RNA-class probability 0.931651
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 25747865 115 - 27905053
AAUACGAACAGUUUCAUCUUGGUCAAGUCUUGCAAC---UCAAUGGUGUUCCGAUGUCGAAGCGCCUUUAUAUACAGAAGAA--GUCCCUUGUCUUAUCUUGACCAAGUGUCAAACUACC
.........(((((.((((((((((((....((...---.....((((((.((....)).))))))...........(((..--....))))).....)))))))))).)).)))))... ( -27.80)
>DroSec_CAF1 19150 115 - 1
AAUACGAACAGUUUCAUCUUGGUCAAGUCUUGCAAC---UCAAUGGUGUUCCGAGUCCGAAGCGCCUUUAUAUACAGAAGAA--GUCCCUUGUCUUAUCUUGACCAAGUGUCAAACUACC
.........(((((.((((((((((((....((...---.....((((((.((....)).))))))...........(((..--....))))).....)))))))))).)).)))))... ( -27.20)
>DroSim_CAF1 12924 115 - 1
AAUACGAACAGUUUCAUCUUGGUCAAGUCUUGCAAC---UCAAUGGUGUUCCGAAUCCGAAGCGCCUUUAUAUACAGAAGAA--GUCCCUUGUCUUAUCUUGACCAAGUGUCAAACUACC
.........(((((.((((((((((((....((...---.....((((((.((....)).))))))...........(((..--....))))).....)))))))))).)).)))))... ( -27.20)
>DroEre_CAF1 12921 115 - 1
AAUACGAAUAGUUUCAUCUUGGUCAAGUCUUGCAAC---UUAAUGGUGUUCUGAAACCAAGGCGCCCUUUUAUACAAAAGAA--AUCCGCUGUCUUAUCUUGGCCAAGAGCCAAACUACA
........((((((..(((((((((((....(((.(---.....(((((..((....))..)))))(((((....)))))..--....).))).....)))))))))))...)))))).. ( -32.10)
>DroWil_CAF1 28136 100 - 1
AAUAAGAACGAUUUCAUCUUGAGCAACUUGAACAACUACUCAUGGUUUUUCCUAAACUCUCCCACCUUUUUAUACAAAACAGUGAACGC-----UUAUCUC---UGAG------------
.............(((...(((((.....(((.(((((....))))).)))...........(((..((((....))))..)))...))-----)))....---))).------------ ( -11.40)
>DroYak_CAF1 13225 115 - 1
AAUACGAACAGUUUCAUCUUGGUCAAGUCUUGCAAC---UCAAUGGUGUUCCGAAACCGAAGCGCCUUUUUAUACCAAAGGA--AUCCGUUGUCUUAUCUUGACCAAGAGCUGAACUACG
.........(((((..(((((((((((....(((((---.....((((((.((....)).)))))).............((.--..))))))).....)))))))))))...)))))... ( -34.80)
>consensus
AAUACGAACAGUUUCAUCUUGGUCAAGUCUUGCAAC___UCAAUGGUGUUCCGAAACCGAAGCGCCUUUAUAUACAAAAGAA__AUCCCUUGUCUUAUCUUGACCAAGUGUCAAACUACC
.........(((((...((((((((((.................((((((.((....)).))))))...........((((...........))))..))))))))))....)))))... (-16.66 = -18.58 +   1.92)

alignment

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secondary structure

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dotplot

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Window 4

Location 25,747,980 – 25,748,100
Length 120
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 91.94
Mean single sequence MFE -48.87
Consensus MFE -42.17
Energy contribution -41.95
Covariance contribution -0.22
Combinations/Pair 1.29
Mean z-score -1.86
Structure conservation index 0.86
SVM decision value 0.81
SVM RNA-class probability 0.855705
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 25747980 120 + 27905053
CCUGGCCUUGGCCGUGGCCGCAGCUACUGCUGUGCCCGCUCCCGCCCAGAAGCUGACCCCGACGCCCAUCAAGGACAUUCAGGGUCGCAUCACCAACGGCUACCCAGCCUACGAGGGCAA
...(((....)))((((.((((((....)))))).))))....((((.((.((.(((((.((..((......))....)).))))))).))......((((....)))).....)))).. ( -50.90)
>DroSec_CAF1 19265 120 + 1
CCUGGCCUUGGCCGUGGCCGCAGCCACUGCUGUGCCCGCUCCCGCCCAGAAGCUGACCCCGACGCCCAUCAAGGACAUCCAGGGUCGCAUCACCAACGGCUACCCAGCCUGCGAGGGCAA
...(((....)))((((.((((((....)))))).))))....((((.((.((.(((((.((.(.((.....)).).))..))))))).))......((((....)))).....)))).. ( -49.30)
>DroSim_CAF1 13039 120 + 1
CCUGGCCUUGGCCGUGGCCGCAGCCACUGCUGUGCCCGCUCCCGCCCAGAAGCUGACCCCGACGCCCAUCAAGGACAUCCAGGGUCGCAUCACCAACGGCUACCCAGCCUACGAGGGCAA
...(((....)))((((.((((((....)))))).))))....((((.((.((.(((((.((.(.((.....)).).))..))))))).))......((((....)))).....)))).. ( -49.30)
>DroEre_CAF1 13036 120 + 1
CCUGGCCUUGGCCGUGGCCGCAGCCACCGCUGUGCCCGCUCCCACCCAGAAGCUGACCCCGACGCCCAUCAAGGACAUCCAGGGUCGCAUCACCAACGGCUACCCAGCCUACGAGGGCAA
..(((((((((..((((.((((((....)))))).)))).........((.((.(((((.((.(.((.....)).).))..))))))).)).)))).)))))....((((....)))).. ( -45.80)
>DroWil_CAF1 28236 117 + 1
CCUGGUCUUGGCUGUGGCCGCAGUCACCGCUGUCCCCACCC---UGCAGAAGCAGAAGCCGGUGCCCGUCAAGGACAUCGAGGGCCGUAUUACCAACGGCUACCCAGCCUAUGAGGGCAA
.......((((((((((..(((((....)))))..)))).(---(((....)))).))))))(((((.((((((........((((((.......))))))......))).)))))))). ( -45.44)
>DroYak_CAF1 13340 120 + 1
CCUGGCCUUGGCCGUGGCCGCAGCCACUGCUGUGCCCGCUCCCGCCCAGAAGCUGACCCCGACGCCCGUCAAGGACAUCCAGGGUCGCAUCACCAACGGCUACCCGGCCUACGAGGGCAA
...(((....)))((((.((((((....)))))).))))....((((.((.((.(((((.(((....)))..((....)).))))))).))......((((....)))).....)))).. ( -52.50)
>consensus
CCUGGCCUUGGCCGUGGCCGCAGCCACUGCUGUGCCCGCUCCCGCCCAGAAGCUGACCCCGACGCCCAUCAAGGACAUCCAGGGUCGCAUCACCAACGGCUACCCAGCCUACGAGGGCAA
...(((....)))((((.((((((....)))))).))))....((((.((.((.(((((.((.(.((.....)).).))..))))))).))......((((....)))).....)))).. (-42.17 = -41.95 +  -0.22)

alignment

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secondary structure

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dotplot

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Window 5

Location 25,747,980 – 25,748,100
Length 120
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 91.94
Mean single sequence MFE -60.77
Consensus MFE -53.61
Energy contribution -54.53
Covariance contribution 0.92
Combinations/Pair 1.15
Mean z-score -1.93
Structure conservation index 0.88
SVM decision value 1.33
SVM RNA-class probability 0.942927
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 25747980 120 - 27905053
UUGCCCUCGUAGGCUGGGUAGCCGUUGGUGAUGCGACCCUGAAUGUCCUUGAUGGGCGUCGGGGUCAGCUUCUGGGCGGGAGCGGGCACAGCAGUAGCUGCGGCCACGGCCAAGGCCAGG
....(((.((.((((..(((((..(((.((.(((((((((((.(((((.....))))))))))))).((((((....))))))..))))).)))..)))))))))))(((....)))))) ( -61.00)
>DroSec_CAF1 19265 120 - 1
UUGCCCUCGCAGGCUGGGUAGCCGUUGGUGAUGCGACCCUGGAUGUCCUUGAUGGGCGUCGGGGUCAGCUUCUGGGCGGGAGCGGGCACAGCAGUGGCUGCGGCCACGGCCAAGGCCAGG
.(((....)))((((..((((((((((.((.((((((((((.((((((.....))))))))))))).((((((....))))))..))))).))))))))))(((....)))..))))... ( -64.50)
>DroSim_CAF1 13039 120 - 1
UUGCCCUCGUAGGCUGGGUAGCCGUUGGUGAUGCGACCCUGGAUGUCCUUGAUGGGCGUCGGGGUCAGCUUCUGGGCGGGAGCGGGCACAGCAGUGGCUGCGGCCACGGCCAAGGCCAGG
....(((.((.((((..((((((((((.((.((((((((((.((((((.....))))))))))))).((((((....))))))..))))).))))))))))))))))(((....)))))) ( -63.90)
>DroEre_CAF1 13036 120 - 1
UUGCCCUCGUAGGCUGGGUAGCCGUUGGUGAUGCGACCCUGGAUGUCCUUGAUGGGCGUCGGGGUCAGCUUCUGGGUGGGAGCGGGCACAGCGGUGGCUGCGGCCACGGCCAAGGCCAGG
....(((.((.((((..(((((((..(.((.((((((((((.((((((.....))))))))))))).((((((....))))))..))))).)..)))))))))))))(((....)))))) ( -63.60)
>DroWil_CAF1 28236 117 - 1
UUGCCCUCAUAGGCUGGGUAGCCGUUGGUAAUACGGCCCUCGAUGUCCUUGACGGGCACCGGCUUCUGCUUCUGCA---GGGUGGGGACAGCGGUGACUGCGGCCACAGCCAAGACCAGG
...........((((((((.(((((((........((((((((.....)))).)))).((.(((.((((....)))---)))).))..))))))).......))).)))))......... ( -46.40)
>DroYak_CAF1 13340 120 - 1
UUGCCCUCGUAGGCCGGGUAGCCGUUGGUGAUGCGACCCUGGAUGUCCUUGACGGGCGUCGGGGUCAGCUUCUGGGCGGGAGCGGGCACAGCAGUGGCUGCGGCCACGGCCAAGGCCAGG
...........((((..((((((((((.((.((((((((((.((((((.....))))))))))))).((((((....))))))..))))).))))))))))(((....)))..))))... ( -65.20)
>consensus
UUGCCCUCGUAGGCUGGGUAGCCGUUGGUGAUGCGACCCUGGAUGUCCUUGAUGGGCGUCGGGGUCAGCUUCUGGGCGGGAGCGGGCACAGCAGUGGCUGCGGCCACGGCCAAGGCCAGG
...........((((..((((((((((.((.((((((((((.((((((.....))))))))))))).((((((....))))))..))))).))))))))))(((....)))..))))... (-53.61 = -54.53 +   0.92)

alignment

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secondary structure

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dotplot

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Window 6

Location 25,748,020 – 25,748,140
Length 120
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 92.22
Mean single sequence MFE -54.32
Consensus MFE -45.78
Energy contribution -47.75
Covariance contribution 1.97
Combinations/Pair 1.10
Mean z-score -1.56
Structure conservation index 0.84
SVM decision value -0.06
SVM RNA-class probability 0.505212
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 25748020 120 - 27905053
UCCGUUGCCGCUGAAGAGCAGACCCACGAUGUAAGGCACCUUGCCCUCGUAGGCUGGGUAGCCGUUGGUGAUGCGACCCUGAAUGUCCUUGAUGGGCGUCGGGGUCAGCUUCUGGGCGGG
.......(((((.(..(((.....(((.(.....(((((((.(((......))).)))).)))..).)))....((((((((.(((((.....))))))))))))).)))..).))))). ( -55.80)
>DroSec_CAF1 19305 120 - 1
UCCGUUGCCGCUGAAGAGCAGACCCACGAUGUAGGGAACCUUGCCCUCGCAGGCUGGGUAGCCGUUGGUGAUGCGACCCUGGAUGUCCUUGAUGGGCGUCGGGGUCAGCUUCUGGGCGGG
.......(((((.(..(((.(((((......(((((....((((..((((.((((....))))....)))).)))))))))(((((((.....))))))).))))).)))..).))))). ( -54.40)
>DroSim_CAF1 13079 120 - 1
UCCGUUGCCGCUGAAGAGCAGACCCACGAUGUAGGGAACCUUGCCCUCGUAGGCUGGGUAGCCGUUGGUGAUGCGACCCUGGAUGUCCUUGAUGGGCGUCGGGGUCAGCUUCUGGGCGGG
.......(((((.(..(((.(((((......(((((.((((.(((......))).))))...(((.......))).)))))(((((((.....))))))).))))).)))..).))))). ( -54.30)
>DroEre_CAF1 13076 120 - 1
UCCGUUGCCGCUGAAGAGCAGACCCACGAUGUAGGGCACCUUGCCCUCGUAGGCUGGGUAGCCGUUGGUGAUGCGACCCUGGAUGUCCUUGAUGGGCGUCGGGGUCAGCUUCUGGGUGGG
.......(((((.(..(((..(((.((.(((.(((((.....)))))))).((((....)))))).))).....(((((((.((((((.....))))))))))))).)))..).))))). ( -56.20)
>DroWil_CAF1 28276 117 - 1
ACCGUUGCCGCUGAAGCCCAGACCAACGAUGUAGGGCACUUUGCCCUCAUAGGCUGGGUAGCCGUUGGUAAUACGGCCCUCGAUGUCCUUGACGGGCACCGGCUUCUGCUUCUGCA---G
.....(((.((.((((((...((((((.(((.(((((.....)))))))).((((....))))))))))......((((((((.....)))).))))...)))))).))....)))---. ( -48.80)
>DroYak_CAF1 13380 120 - 1
UCCGUUGCCGCUGAAGAGCAGACCCACGAUGUAGGGCACCUUGCCCUCGUAGGCCGGGUAGCCGUUGGUGAUGCGACCCUGGAUGUCCUUGACGGGCGUCGGGGUCAGCUUCUGGGCGGG
.......(((((.(..(((..(((.((.(((.(((((.....)))))))).(((......))))).))).....(((((((.((((((.....))))))))))))).)))..).))))). ( -56.40)
>consensus
UCCGUUGCCGCUGAAGAGCAGACCCACGAUGUAGGGCACCUUGCCCUCGUAGGCUGGGUAGCCGUUGGUGAUGCGACCCUGGAUGUCCUUGAUGGGCGUCGGGGUCAGCUUCUGGGCGGG
.......(((((((((.(((.(((.((.(((.(((((.....)))))))).(((......))))).)))..)))(((((((.((((((.....)))))))))))))..))))..))))). (-45.78 = -47.75 +   1.97)

alignment

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secondary structure

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dotplot

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Window 7

Location 25,748,060 – 25,748,177
Length 117
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 93.62
Mean single sequence MFE -50.28
Consensus MFE -43.02
Energy contribution -42.88
Covariance contribution -0.14
Combinations/Pair 1.19
Mean z-score -1.99
Structure conservation index 0.86
SVM decision value 0.94
SVM RNA-class probability 0.885702
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 25748060 117 + 27905053
AGGGUCGCAUCACCAACGGCUACCCAGCCUACGAGGGCAAGGUGCCUUACAUCGUGGGUCUGCUCUUCAGCGGCAACGGAAAC---UGGUGGUGCGGUGGCUCGAUCAUCGGCAACACCU
.((((((((((((((..(((.(((..((((....))))..)))))).....((((..(.(((((....)))))).))))....---))))))))))((.((.((.....)))).)))))) ( -48.10)
>DroSec_CAF1 19345 117 + 1
AGGGUCGCAUCACCAACGGCUACCCAGCCUGCGAGGGCAAGGUUCCCUACAUCGUGGGUCUGCUCUUCAGCGGCAACGGAAAC---UGGUGGUGCGGUGGCUCGAUCAUCGGCAACACCU
.((((((((((((((..((..(((..((((....))))..)))..))....((((..(.(((((....)))))).))))....---))))))))))((.((.((.....)))).)))))) ( -45.70)
>DroSim_CAF1 13119 117 + 1
AGGGUCGCAUCACCAACGGCUACCCAGCCUACGAGGGCAAGGUUCCCUACAUCGUGGGUCUGCUCUUCAGCGGCAACGGAAAC---UGGUGGUGCGGUGGCUCGAUCAUCGGCAACACCU
.((((((((((((((..((..(((..((((....))))..)))..))....((((..(.(((((....)))))).))))....---))))))))))((.((.((.....)))).)))))) ( -45.40)
>DroEre_CAF1 13116 117 + 1
AGGGUCGCAUCACCAACGGCUACCCAGCCUACGAGGGCAAGGUGCCCUACAUCGUGGGUCUGCUCUUCAGCGGCAACGGAAAC---UGGUGGUGCGGUGGCUCGAUCAUCGGCAACACCU
.((((((((((((((...(((...((((((((((((((.....))))....))))))).)))......)))(....)(....)---))))))))))((.((.((.....)))).)))))) ( -49.10)
>DroWil_CAF1 28313 120 + 1
AGGGCCGUAUUACCAACGGCUACCCAGCCUAUGAGGGCAAAGUGCCCUACAUCGUUGGUCUGGGCUUCAGCGGCAACGGUGGCGGUUGGUGGUGCGGUGGUUCCAUCAUUGGCAACACCU
(((((((((((((((((.((..(((((((.((((((((.....))))).)))....)).)))))...((.((....)).)))).)))))))))))))).((((((....))).))).))) ( -61.30)
>DroYak_CAF1 13420 117 + 1
AGGGUCGCAUCACCAACGGCUACCCGGCCUACGAGGGCAAGGUGCCCUACAUCGUGGGUCUGCUCUUCAGCGGCAACGGAAAC---UGGUGGUGCGGUGGCUCGAUUAUCGGCAACACCU
.((((((((((((((...(((....(((((((((((((.....))))....))))))))).(((....))))))...(....)---))))))))))((.((.((.....)))).)))))) ( -52.10)
>consensus
AGGGUCGCAUCACCAACGGCUACCCAGCCUACGAGGGCAAGGUGCCCUACAUCGUGGGUCUGCUCUUCAGCGGCAACGGAAAC___UGGUGGUGCGGUGGCUCGAUCAUCGGCAACACCU
.((((((((((((((.........((((((((((((((.....))))....))))))).)))........((....))........))))))))))((.((.((.....)))).)))))) (-43.02 = -42.88 +  -0.14)

alignment

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secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:40:54 2006