Locus 1360

Sequence ID 3R_DroMel_CAF1
Location 4,000,563 – 4,000,754
Length 191
Max. P 0.966437
window2235 window2236 window2237 window2238 window2239

overview

Window 5

Location 4,000,563 – 4,000,677
Length 114
Sequences 3
Columns 114
Reading direction forward
Mean pairwise identity 84.40
Mean single sequence MFE -39.17
Consensus MFE -32.65
Energy contribution -33.43
Covariance contribution 0.78
Combinations/Pair 1.04
Mean z-score -2.23
Structure conservation index 0.83
SVM decision value 1.03
SVM RNA-class probability 0.903541
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 4000563 114 + 27905053
GGAAUGCUGCUGAUGCAGUUGCUGCCGUAGCCGCUGCAGCGGACAAUGCACAUUGUGGCGGCACCUUUGGCACUGCGGCAUGCAAAGCAGCCAAGAGCAACAUCCACAGCAACA
(((..((((((..((((((((((((((..(((((..(((((.....)))....))..))))).....)))))..))))).)))).))))))...(.....).)))......... ( -44.10)
>DroSec_CAF1 6209 94 + 1
GGAAUGCUGUUG---------CU------GCUGCUGCAGCGGACAAUGCACAUUGUGGCGGCACCUUUGGCUCUGCGGCAUGC-----AGCCAAGAGCAACAUCCACAGCAACA
....((((((((---------((------((..(((((........))))....)..))))))......(((((..(((....-----.))).))))).......))))))... ( -36.70)
>DroSim_CAF1 6268 96 + 1
GGAAUGCUG------------CU------GCUGCUGCAGCGGACAAUGCACAUUGUGGCGGCACCUUUGGCUCUGCGGCAUGCAAAGCAGCCAAGAGCAACAUCCACAGCAACA
....(((((------------.(------(((((..(((((.....)))....))..))))))......(((((..(((.(((...)))))).)))))........)))))... ( -36.70)
>consensus
GGAAUGCUG_UG_________CU______GCUGCUGCAGCGGACAAUGCACAUUGUGGCGGCACCUUUGGCUCUGCGGCAUGCAAAGCAGCCAAGAGCAACAUCCACAGCAACA
....(((((....................(((((..(((((.....)))....))..))))).......(((((..(((.(((...)))))).)))))........)))))... (-32.65 = -33.43 +   0.78)

alignment

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secondary structure

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dotplot

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Window 6

Location 4,000,563 – 4,000,677
Length 114
Sequences 3
Columns 114
Reading direction reverse
Mean pairwise identity 84.40
Mean single sequence MFE -42.33
Consensus MFE -31.29
Energy contribution -32.07
Covariance contribution 0.78
Combinations/Pair 1.04
Mean z-score -2.57
Structure conservation index 0.74
SVM decision value 1.07
SVM RNA-class probability 0.909672
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 4000563 114 - 27905053
UGUUGCUGUGGAUGUUGCUCUUGGCUGCUUUGCAUGCCGCAGUGCCAAAGGUGCCGCCACAAUGUGCAUUGUCCGCUGCAGCGGCUACGGCAGCAACUGCAUCAGCAGCAUUCC
((((((((((.(.((((((((((((((((..(((.((.(((((((((...(((....)))..)).)))))).).))))))))))))).)).))))))).)).)))))))).... ( -50.30)
>DroSec_CAF1 6209 94 - 1
UGUUGCUGUGGAUGUUGCUCUUGGCU-----GCAUGCCGCAGAGCCAAAGGUGCCGCCACAAUGUGCAUUGUCCGCUGCAGCAGC------AG---------CAACAGCAUUCC
...((((((((((...(((((((((.-----....)))).)))))....(((((((......)).)))))))))(((((....))------))---------).)))))).... ( -37.90)
>DroSim_CAF1 6268 96 - 1
UGUUGCUGUGGAUGUUGCUCUUGGCUGCUUUGCAUGCCGCAGAGCCAAAGGUGCCGCCACAAUGUGCAUUGUCCGCUGCAGCAGC------AG------------CAGCAUUCC
(((((((((((((..(((.(.((((.(((((((.....)))))))....(....)))))....).)))..))))((....)).))------))------------))))).... ( -38.80)
>consensus
UGUUGCUGUGGAUGUUGCUCUUGGCUGCUUUGCAUGCCGCAGAGCCAAAGGUGCCGCCACAAUGUGCAUUGUCCGCUGCAGCAGC______AG_________CA_CAGCAUUCC
((((((.((((((..(((.(((((((...((((.....)))))))))).((.....)).....).)))..)))))).))))))............................... (-31.29 = -32.07 +   0.78)

alignment

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secondary structure

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dotplot

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Window 7

Location 4,000,603 – 4,000,714
Length 111
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 91.16
Mean single sequence MFE -36.95
Consensus MFE -30.10
Energy contribution -30.67
Covariance contribution 0.56
Combinations/Pair 1.03
Mean z-score -2.77
Structure conservation index 0.81
SVM decision value 1.57
SVM RNA-class probability 0.964725
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 4000603 111 + 27905053
GGACAAUGCACAUUGUGGCGGCACCUUUGGCACUGCGGCAUGCAAAGCAGCCAAGAGCAACAUCCACAGCAACA---------ACUGCAAGAACUGUUGCUGCAGUGCAAAUUAAUUGAA
...((((...((..(((....)))...))((((((((((.(((...))))))...(((((((......(((...---------..)))......))))))))))))))......)))).. ( -34.60)
>DroSec_CAF1 6234 103 + 1
GGACAAUGCACAUUGUGGCGGCACCUUUGGCUCUGCGGCAUGC-----AGCCAAGAGCAACAUCCACAGCAACA------------GCAAGAACUGUUGUUGCAGUGCAAAUUAAUUGAA
......(((((..(((((.(....)....(((((..(((....-----.))).))))).....)))))((((((------------(((.....))))))))).)))))........... ( -38.20)
>DroSim_CAF1 6290 108 + 1
GGACAAUGCACAUUGUGGCGGCACCUUUGGCUCUGCGGCAUGCAAAGCAGCCAAGAGCAACAUCCACAGCAACA------------GCAAGAACUGUUGCUGCAGUGCAAAUUAAUUGAA
......(((((...((((.(....)....(((((..(((.(((...)))))).))))).....))))(((((((------------(......))))))))...)))))........... ( -37.90)
>DroYak_CAF1 6073 120 + 1
GGACAAUGCACAUUGUGGCGGCACCUUUGGCUCUGCGGCAUGCAAAGCAGCCAAGAGCAACAUCCACAGCAACAUCCAGAGGAACGGCAAGAACUGUUGCUGCAGUGCAAAUUAAUUGAA
......(((((..((..((((((..(((.(((((..(((.(((...)))))).)))))..........((....(((...)))...)).)))..))))))..)))))))........... ( -37.10)
>consensus
GGACAAUGCACAUUGUGGCGGCACCUUUGGCUCUGCGGCAUGCAAAGCAGCCAAGAGCAACAUCCACAGCAACA____________GCAAGAACUGUUGCUGCAGUGCAAAUUAAUUGAA
......(((((..((..((((((..(((.(((((..(((.(((...)))))).)))))..........((................)).)))..))))))..)))))))........... (-30.10 = -30.67 +   0.56)

alignment

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secondary structure

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dotplot

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Window 8

Location 4,000,603 – 4,000,714
Length 111
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 91.16
Mean single sequence MFE -39.09
Consensus MFE -32.21
Energy contribution -32.77
Covariance contribution 0.56
Combinations/Pair 1.03
Mean z-score -2.67
Structure conservation index 0.82
SVM decision value 1.60
SVM RNA-class probability 0.966437
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 4000603 111 - 27905053
UUCAAUUAAUUUGCACUGCAGCAACAGUUCUUGCAGU---------UGUUGCUGUGGAUGUUGCUCUUGGCUGCUUUGCAUGCCGCAGUGCCAAAGGUGCCGCCACAAUGUGCAUUGUCC
...........(((((.((((((((.((....)).))---------))))))(((((.((..((..(((((....((((.....)))).)))))..))..)))))))..)))))...... ( -40.50)
>DroSec_CAF1 6234 103 - 1
UUCAAUUAAUUUGCACUGCAACAACAGUUCUUGC------------UGUUGCUGUGGAUGUUGCUCUUGGCU-----GCAUGCCGCAGAGCCAAAGGUGCCGCCACAAUGUGCAUUGUCC
...........(((((.....(((((((....))------------))))).(((((.((..((..((((((-----((.....))..))))))..))..)))))))..)))))...... ( -35.60)
>DroSim_CAF1 6290 108 - 1
UUCAAUUAAUUUGCACUGCAGCAACAGUUCUUGC------------UGUUGCUGUGGAUGUUGCUCUUGGCUGCUUUGCAUGCCGCAGAGCCAAAGGUGCCGCCACAAUGUGCAUUGUCC
...........(((((.(((((((((((....))------------)))))))))((.((..((..((((((...((((.....))))))))))..))..)))).....)))))...... ( -41.90)
>DroYak_CAF1 6073 120 - 1
UUCAAUUAAUUUGCACUGCAGCAACAGUUCUUGCCGUUCCUCUGGAUGUUGCUGUGGAUGUUGCUCUUGGCUGCUUUGCAUGCCGCAGAGCCAAAGGUGCCGCCACAAUGUGCAUUGUCC
...........(((((.((((((.(((..............)))..))))))(((((.((..((..((((((...((((.....))))))))))..))..)))))))..)))))...... ( -38.34)
>consensus
UUCAAUUAAUUUGCACUGCAGCAACAGUUCUUGC____________UGUUGCUGUGGAUGUUGCUCUUGGCUGCUUUGCAUGCCGCAGAGCCAAAGGUGCCGCCACAAUGUGCAUUGUCC
...........(((((.((((((.......................))))))(((((.((..((..((((((...((((.....))))))))))..))..)))))))..)))))...... (-32.21 = -32.77 +   0.56)

alignment

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secondary structure

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dotplot

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Window 9

Location 4,000,643 – 4,000,754
Length 111
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 91.59
Mean single sequence MFE -27.05
Consensus MFE -23.10
Energy contribution -22.91
Covariance contribution -0.19
Combinations/Pair 1.04
Mean z-score -1.68
Structure conservation index 0.85
SVM decision value 0.52
SVM RNA-class probability 0.769326
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 4000643 111 + 27905053
UGCAAAGCAGCCAAGAGCAACAUCCACAGCAACA---------ACUGCAAGAACUGUUGCUGCAGUGCAAAUUAAUUGAAGCAUCGCAAGGCAAUGUCAACGACAGCAACAUCACGUGUU
(((......(((...(((((((......(((...---------..)))......)))))))((.((((............)))).))..)))..((((...)))))))............ ( -26.70)
>DroSec_CAF1 6274 103 + 1
UGC-----AGCCAAGAGCAACAUCCACAGCAACA------------GCAAGAACUGUUGUUGCAGUGCAAAUUAAUUGAAGCAUCGCAAGGCAAUGUCAACGACAGCAACAUCACGUGUU
(((-----.(((..((((......(((.((((((------------(((.....))))))))).)))(((.....)))..)).))....)))..((((...)))))))............ ( -26.50)
>DroSim_CAF1 6330 108 + 1
UGCAAAGCAGCCAAGAGCAACAUCCACAGCAACA------------GCAAGAACUGUUGCUGCAGUGCAAAUUAAUUGAAGCAUCGCAAGGCAAUGUCAACGACAGCAACAUCACGUGUU
(((......(((..((((........((((((((------------(......)))))))))((((........))))..)).))....)))..((((...)))))))............ ( -27.60)
>DroYak_CAF1 6113 120 + 1
UGCAAAGCAGCCAAGAGCAACAUCCACAGCAACAUCCAGAGGAACGGCAAGAACUGUUGCUGCAGUGCAAAUUAAUUGAAGCAUCGCAAGGCAAUGUCAACGACAGCAACAUCACGUGUU
(((......(((...(((((((......((....(((...)))...))......)))))))((.((((............)))).))..)))..((((...)))))))............ ( -27.40)
>consensus
UGCAAAGCAGCCAAGAGCAACAUCCACAGCAACA____________GCAAGAACUGUUGCUGCAGUGCAAAUUAAUUGAAGCAUCGCAAGGCAAUGUCAACGACAGCAACAUCACGUGUU
(((......(((...(((((((......((................))......)))))))((.((((............)))).))..)))..((((...)))))))............ (-23.10 = -22.91 +  -0.19)

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 10:08:03 2006