Locus 1788

Sequence ID 3L_DroMel_CAF1
Location 5,068,754 – 5,069,050
Length 296
Max. P 0.999561
window2767 window2768 window2769 window2770 window2771

overview

Window 7

Location 5,068,754 – 5,068,860
Length 106
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 91.58
Mean single sequence MFE -40.66
Consensus MFE -34.36
Energy contribution -34.72
Covariance contribution 0.36
Combinations/Pair 1.03
Mean z-score -3.17
Structure conservation index 0.85
SVM decision value 3.72
SVM RNA-class probability 0.999561
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 5068754 106 + 23771897
AUCGGAAAAGCAGGCGGCCAGCCCCAAAACUGCUGUCUGCUGGUA--------------ACUGGUAACUGGUAACUGCCAGCGGAACAGAUGCAAUCAUAAAAUCUGUUCGAAGCACAGC
(((((...((((((((((.((........))))))))))))....--------------.)))))..(((((....)))))..((((((((...........)))))))).......... ( -35.70)
>DroSec_CAF1 275307 106 + 1
AUCGGAAAAGCAGGCGGCCAGCCCCAAAACUGCUGGCUGCUGGUG--------------ACUGGUAACUGGAAACUGCCAGCGGAACAGAUGCAAUCAUAAAAUCUGUUCGGAGCACAGC
.........((.((((((((((.........)))))))))).(((--------------.((((((...(....)))))))(.((((((((...........)))))))).)..))).)) ( -40.50)
>DroSim_CAF1 296584 106 + 1
AUCGGAAAAGCAGGCGGCCAGCCCCAAAACUGCUGGCUGCUGGUG--------------ACUGGUAACUGGAAACUGCCAGCGGAACAGAUGCAAUCAUAAAAUCUGUUCGGAGCACAGC
.........((.((((((((((.........)))))))))).(((--------------.((((((...(....)))))))(.((((((((...........)))))))).)..))).)) ( -40.50)
>DroEre_CAF1 282184 120 + 1
AUCGGAAAAGCAGGCGGCCAGCCCCAAAACUGCUGGCUGCUGGCUGCUGGCUGCUGGUAACUGGUAACUGGAAACUGCCAGCGGAACAGAUGCAAUCAUAAAAUCUGUUCGGAGCACAGC
........(((.((((((((((.........)))))))))).)))((((((((((((((...(....).(....)))))))).((((((((...........))))))))..))).)))) ( -51.80)
>DroYak_CAF1 286047 106 + 1
AUCGGAAAAGCAGGCGUCCAGCCCCAAAACUGCUGGCUACUGGCU--------------ACUGGUAACUGGAAACUGCCAGCGGAACAGAUGCAAUCAUAAAAUCUGUUCGGAGCAUAGC
...(((...(....).))).((.((.....((((((((((..(..--------------.)..)))...(....).)))))))((((((((...........)))))))))).))..... ( -34.80)
>consensus
AUCGGAAAAGCAGGCGGCCAGCCCCAAAACUGCUGGCUGCUGGUG______________ACUGGUAACUGGAAACUGCCAGCGGAACAGAUGCAAUCAUAAAAUCUGUUCGGAGCACAGC
..((.....((.((((((((((.........)))))))))).))................((((((...(....)))))))))((((((((...........)))))))).......... (-34.36 = -34.72 +   0.36)

alignment

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secondary structure

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Window 8

Location 5,068,794 – 5,068,899
Length 105
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 91.17
Mean single sequence MFE -35.16
Consensus MFE -29.24
Energy contribution -29.16
Covariance contribution -0.08
Combinations/Pair 1.07
Mean z-score -2.04
Structure conservation index 0.83
SVM decision value 1.77
SVM RNA-class probability 0.976663
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 5068794 105 + 23771897
UGGUA--------------ACUGGUAACUGGUAACUGCCAGCGGAACAGAUGCAAUCAUAAAAUCUGUUCGAAGCACAGCCAACUAACUCAGCCAUUAUCCCCAUGGGUAGUUGC-CGGG
.....--------------........((((((((((((.((.((((((((...........))))))))...))..................(((.......))))))))))))-))). ( -31.90)
>DroSec_CAF1 275347 105 + 1
UGGUG--------------ACUGGUAACUGGAAACUGCCAGCGGAACAGAUGCAAUCAUAAAAUCUGUUCGGAGCACAGCCAACUAACUCAGCCAUUAUCCCCAUGGGUAGUUGC-CGGG
((((.--------------.((((((...(....)))))))(.((((((((...........)))))))).)......)))).....(((.((.(((((((....))))))).))-.))) ( -33.50)
>DroSim_CAF1 296624 105 + 1
UGGUG--------------ACUGGUAACUGGAAACUGCCAGCGGAACAGAUGCAAUCAUAAAAUCUGUUCGGAGCACAGCCAACUAACUCAGCCAUUAUCCCCAUGGGUAGUUGC-CGGG
((((.--------------.((((((...(....)))))))(.((((((((...........)))))))).)......)))).....(((.((.(((((((....))))))).))-.))) ( -33.50)
>DroEre_CAF1 282224 119 + 1
UGGCUGCUGGCUGCUGGUAACUGGUAACUGGAAACUGCCAGCGGAACAGAUGCAAUCAUAAAAUCUGUUCGGAGCACAGCCAACUAACUCAGCCAUUAUCCCCAUGGGUAGCUGC-CAGG
((((.(((((((((((((..((((((...(....)))))))(.((((((((...........)))))))).).)).))))..........))))).(((((....))))))).))-)).. ( -42.00)
>DroYak_CAF1 286087 106 + 1
UGGCU--------------ACUGGUAACUGGAAACUGCCAGCGGAACAGAUGCAAUCAUAAAAUCUGUUCGGAGCAUAGCCAACUAACUCAGCCAUUAUCCCCAUGGGUAGCUGCCCAGG
(((((--------------(((((((...(....)))))))(.((((((((...........)))))))).)....))))))...................((.(((((....))))))) ( -34.90)
>consensus
UGGUG______________ACUGGUAACUGGAAACUGCCAGCGGAACAGAUGCAAUCAUAAAAUCUGUUCGGAGCACAGCCAACUAACUCAGCCAUUAUCCCCAUGGGUAGUUGC_CGGG
((((................((((((...(....)))))))..((((((((...........))))))))........)))).....((..((.(((((((....))))))).))..)). (-29.24 = -29.16 +  -0.08)

alignment

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secondary structure

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Window 9

Location 5,068,899 – 5,069,018
Length 119
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 93.18
Mean single sequence MFE -38.82
Consensus MFE -31.88
Energy contribution -32.56
Covariance contribution 0.68
Combinations/Pair 1.03
Mean z-score -2.22
Structure conservation index 0.82
SVM decision value 1.94
SVM RNA-class probability 0.983377
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 5068899 119 - 23771897
AAACGGAAGAACUUGUUCCCUGCCGACUCAAACUGGUUGUCCUUGAGUCGACAGUGGCAACAUUUGUCAUGAGCAGGGAUUUCUCGGUCACCUCGAACCCGACUGCC-CCCAUCCUUCCG
...((((((.......(((((((((((((((...((....)))))))))(((((((....)).)))))..).))))))).....(((((...........)))))..-......)))))) ( -43.30)
>DroSec_CAF1 275452 117 - 1
A-ACCGAAGACCUUGUUCACUGGCGACUCAAACUGGUUGUCCUUGAGUCGACAGUGGCAACAUUUGUCAUGAGCAGGGAUUUCUCGGCCACCUCGAACCCGACUGCC--CCAUCCUUCCG
.-...((((.((((((((((((.((((((((...((....)))))))))).))))((((.....))))..)))))))).......(((....(((....)))..)))--.....)))).. ( -39.40)
>DroSim_CAF1 296729 118 - 1
A-ACCGAAGACCUUGUUCACUGGCGACUCAAACUGGUUGUCCUUGAGUCGACAGUGGCAACAUUUGUCAUGAGCAGGGAUUUCUCGGCCACCUCGAACCCGACUGCC-CCCAUCCUUCCG
.-...((((.((((((((((((.((((((((...((....)))))))))).))))((((.....))))..)))))))).......(((....(((....)))..)))-......)))).. ( -39.40)
>DroEre_CAF1 282343 116 - 1
A-ACCGAAGACCUUGUCCACUGCCGACUCAAACUGGUUGUCCUUGAGUCGACAGUGGCAACAUUUGUCAUGAGCAGGGAUUUCUCGGCCACCUCAAACCCGACUGC---CCAUCCUUCCG
.-...((((...(((.((((((.((((((((...((....)))))))))).)))))))))...............(((.....((((...........))))...)---))...)))).. ( -35.20)
>DroYak_CAF1 286193 119 - 1
A-ACCGAAGACCUUGUUCGCUGCCGACUCAAACUAGUUGUCCUUGAGUAGACAGUGGCAACAUUUGUCAUGAGCAGGGAUUUCUCGGCCAGCUCAAGCCCGAGUGCCACCCAUCCCUCCC
.-...((((.(((((((((......((((((((.....))..)))))).(((((((....)).))))).))))))))).))))..(((..((((......)))))))............. ( -36.80)
>consensus
A_ACCGAAGACCUUGUUCACUGCCGACUCAAACUGGUUGUCCUUGAGUCGACAGUGGCAACAUUUGUCAUGAGCAGGGAUUUCUCGGCCACCUCGAACCCGACUGCC_CCCAUCCUUCCG
.....((((.((((((((((((.((((((((((.....))..)))))))).))))((((.....))))..)))))))).))))((((...........)))).................. (-31.88 = -32.56 +   0.68)

alignment

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secondary structure

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dotplot

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Window 0

Location 5,068,938 – 5,069,050
Length 112
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 87.38
Mean single sequence MFE -32.93
Consensus MFE -23.08
Energy contribution -24.36
Covariance contribution 1.28
Combinations/Pair 1.07
Mean z-score -1.76
Structure conservation index 0.70
SVM decision value 0.05
SVM RNA-class probability 0.560446
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 5068938 112 + 23771897
AUCCCUGCUCAUGACAAAUGUUGCCACUGUCGACUCAAGGACAACCAGUUUGAGUCGGCAGGGAACAAGUUCUUCCGUUUUCCGUUCC-AAAGAAGUGACC-------CAGUAAAUCUGA
...................((..(..((((((((((((((....))...))))))))))))(((((.................)))))-......)..)).-------(((.....))). ( -29.33)
>DroSec_CAF1 275490 112 + 1
AUCCCUGCUCAUGACAAAUGUUGCCACUGUCGACUCAAGGACAACCAGUUUGAGUCGCCAGUGAACAAGGUCUUCGGU-UUCCGUUCCGAAAGAAGUGACC-------CAGUAAAUCUGA
....(((.(((((((...((((..(((((.((((((((((....))...)))))))).)))))))))..)))(((((.-.......)))))....))))..-------)))......... ( -32.40)
>DroSim_CAF1 296768 112 + 1
AUCCCUGCUCAUGACAAAUGUUGCCACUGUCGACUCAAGGACAACCAGUUUGAGUCGCCAGUGAACAAGGUCUUCGGU-UUCCGUUCGAAAAGAAGUGACC-------CAGUAAAUCUGA
....(((.(((((((...((((..(((((.((((((((((....))...)))))))).)))))))))..)))(((((.-......))))).....))))..-------)))......... ( -29.90)
>DroEre_CAF1 282380 110 + 1
AUCCCUGCUCAUGACAAAUGUUGCCACUGUCGACUCAAGGACAACCAGUUUGAGUCGGCAGUGGACAAGGUCUUCGGU-UUCCGUUCUAAAC---------GCAGGGACAUUAAAUCUGA
.(((((((............((((((((((((((((((((....))...))))))))))))))).)))((.(....).-..)).........---------)))))))............ ( -45.40)
>DroYak_CAF1 286233 119 + 1
AUCCCUGCUCAUGACAAAUGUUGCCACUGUCUACUCAAGGACAACUAGUUUGAGUCGGCAGCGAACAAGGUCUUCGGU-UUCCGUUUCAAACAAAGUGACCGCAAUGACAGUAAAUCUGA
....(((.((((..(...(((((((..(((((......)))))(((......))).))))))).....((((....((-((.......)))).....)))))..)))))))......... ( -27.60)
>consensus
AUCCCUGCUCAUGACAAAUGUUGCCACUGUCGACUCAAGGACAACCAGUUUGAGUCGGCAGUGAACAAGGUCUUCGGU_UUCCGUUCCAAAAGAAGUGACC_______CAGUAAAUCUGA
............(((...((((..((((((((((((((((....))...))))))))))))))))))..)))..(((....)))........................(((.....))). (-23.08 = -24.36 +   1.28)

alignment

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secondary structure

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dotplot

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Window 1

Location 5,068,938 – 5,069,050
Length 112
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 87.38
Mean single sequence MFE -37.82
Consensus MFE -27.98
Energy contribution -28.86
Covariance contribution 0.88
Combinations/Pair 1.03
Mean z-score -2.33
Structure conservation index 0.74
SVM decision value 1.10
SVM RNA-class probability 0.915142
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 5068938 112 - 23771897
UCAGAUUUACUG-------GGUCACUUCUUU-GGAACGGAAAACGGAAGAACUUGUUCCCUGCCGACUCAAACUGGUUGUCCUUGAGUCGACAGUGGCAACAUUUGUCAUGAGCAGGGAU
.........(((-------..(((......)-))..)))....(....).......(((((((((((((((...((....)))))))))(((((((....)).)))))..).))))))). ( -37.20)
>DroSec_CAF1 275490 112 - 1
UCAGAUUUACUG-------GGUCACUUCUUUCGGAACGGAA-ACCGAAGACCUUGUUCACUGGCGACUCAAACUGGUUGUCCUUGAGUCGACAGUGGCAACAUUUGUCAUGAGCAGGGAU
((((.....)))-------)........((((((.......-.)))))).((((((((((((.((((((((...((....)))))))))).))))((((.....))))..)))))))).. ( -38.30)
>DroSim_CAF1 296768 112 - 1
UCAGAUUUACUG-------GGUCACUUCUUUUCGAACGGAA-ACCGAAGACCUUGUUCACUGGCGACUCAAACUGGUUGUCCUUGAGUCGACAGUGGCAACAUUUGUCAUGAGCAGGGAU
((((.....)))-------)....(((((((((....))))-)..)))).((((((((((((.((((((((...((....)))))))))).))))((((.....))))..)))))))).. ( -37.50)
>DroEre_CAF1 282380 110 - 1
UCAGAUUUAAUGUCCCUGC---------GUUUAGAACGGAA-ACCGAAGACCUUGUCCACUGCCGACUCAAACUGGUUGUCCUUGAGUCGACAGUGGCAACAUUUGUCAUGAGCAGGGAU
...........((((((((---------........(((..-.)))..(((..(((((((((.((((((((...((....)))))))))).))))))..)))...)))....)))))))) ( -43.20)
>DroYak_CAF1 286233 119 - 1
UCAGAUUUACUGUCAUUGCGGUCACUUUGUUUGAAACGGAA-ACCGAAGACCUUGUUCGCUGCCGACUCAAACUAGUUGUCCUUGAGUAGACAGUGGCAACAUUUGUCAUGAGCAGGGAU
((((((..(((((....)))))......))))))..(((..-.)))....(((((((((......((((((((.....))..)))))).(((((((....)).))))).))))))))).. ( -32.90)
>consensus
UCAGAUUUACUG_______GGUCACUUCUUUUGGAACGGAA_ACCGAAGACCUUGUUCACUGCCGACUCAAACUGGUUGUCCUUGAGUCGACAGUGGCAACAUUUGUCAUGAGCAGGGAU
....................................(((....)))....((((((((((((.((((((((((.....))..)))))))).))))((((.....))))..)))))))).. (-27.98 = -28.86 +   0.88)

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 10:16:25 2006