Locus 4876

Sequence ID 2L_DroMel_CAF1
Location 13,894,178 – 13,894,303
Length 125
Max. P 0.816973
window7731 window7732 window7733

overview

Window 1

Location 13,894,178 – 13,894,278
Length 100
Sequences 6
Columns 113
Reading direction forward
Mean pairwise identity 82.41
Mean single sequence MFE -42.19
Consensus MFE -27.44
Energy contribution -27.17
Covariance contribution -0.28
Combinations/Pair 1.10
Mean z-score -2.60
Structure conservation index 0.65
SVM decision value 0.63
SVM RNA-class probability 0.806633
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 13894178 100 + 22407834
AGCAACGC--------AGACG--AGUGUCCUCG---UUGCCAGGACAUUCUAGCAGCCAGUUGUUUGUCGACUGGCGUCGCGUGCGGGCGGCUUUUUUUCCCAUUGCCGAAAG
.(((.(((--------.((((--((((((((..---.....))))))))).....((((((((.....)))))))))))))))))...((((.............)))).... ( -43.62)
>DroPse_CAF1 47018 96 + 1
AGCAACGA--------GGACGCCGUUGUCCUCGUCGUUGCCAGGACAUUCUCGAAGCCAGUUGUUUGUCGACUGGCGUCGCGUGCGGGCGGCUUUUUU--CC------G-AUU
....((((--------(((((....))))))))).((((((..(.(((...(((.((((((((.....)))))))).))).)))).))))))......--..------.-... ( -39.80)
>DroEre_CAF1 38051 98 + 1
AGCAACGC--------AGACG--AGUGUCCUCG---UCGCCAGGACAUUCUAGCAGCCAGUUGUUUGUCGACUGGCGUCGCGUGCGGGCGGCUUUUUU--CCAUCGCCGAACU
.(((.(((--------.((((--((((((((..---.....))))))))).....((((((((.....)))))))))))))))))(..((((......--.....))))..). ( -45.30)
>DroYak_CAF1 40112 98 + 1
AGCAACGC--------AGACG--AGUGUCCUCG---UCGCCAGGACAUUCUAGCAGCCAGUUGUUUGUCGACUGGCGUCGCGUGCGGGCGGCUUUUUU--CCAUUGCCGAACU
.(((.(((--------.((((--((((((((..---.....))))))))).....((((((((.....)))))))))))))))))(..((((......--.....))))..). ( -45.90)
>DroAna_CAF1 35316 100 + 1
AGCAACACAGGACAGCAGAC---UGUGUCCUCG---UUGCCAGGAUGUUCUGGCUGCCAGUUGUUUGUCGACUGGCGUCGCGUGCGGGCGGCUUUUUUCUCC------G-GGU
.(((((..((((((......---..)))))).)---))))........(((((..((((((((.....))))))))(((((......)))))........))------)-)). ( -38.70)
>DroPer_CAF1 48897 96 + 1
AGCAACGA--------GGACGCCGUUGUCCUCGUCGUUGCCAGGACAUUCUCGAAGCCAGUUGUUUGUCGACUGGCGUCGCGUGCGGGCGGCUUUUUU--CC------G-AUU
....((((--------(((((....))))))))).((((((..(.(((...(((.((((((((.....)))))))).))).)))).))))))......--..------.-... ( -39.80)
>consensus
AGCAACGC________AGACG__AGUGUCCUCG___UUGCCAGGACAUUCUAGCAGCCAGUUGUUUGUCGACUGGCGUCGCGUGCGGGCGGCUUUUUU__CC______G_ACU
.........................((((((.(......).))))))........((((((((.....))))))))(((((......)))))..................... (-27.44 = -27.17 +  -0.28)

alignment

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secondary structure

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dotplot

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Window 2

Location 13,894,178 – 13,894,278
Length 100
Sequences 6
Columns 113
Reading direction reverse
Mean pairwise identity 82.41
Mean single sequence MFE -37.17
Consensus MFE -24.58
Energy contribution -24.92
Covariance contribution 0.33
Combinations/Pair 1.00
Mean z-score -2.44
Structure conservation index 0.66
SVM decision value 0.57
SVM RNA-class probability 0.784712
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 13894178 100 - 22407834
CUUUCGGCAAUGGGAAAAAAAGCCGCCCGCACGCGACGCCAGUCGACAAACAACUGGCUGCUAGAAUGUCCUGGCAA---CGAGGACACU--CGUCU--------GCGUUGCU
....((((.............))))...(((((((((((((((.(.....).)))))).....((.(((((((....---).)))))).)--)))).--------))).))). ( -37.42)
>DroPse_CAF1 47018 96 - 1
AAU-C------GG--AAAAAAGCCGCCCGCACGCGACGCCAGUCGACAAACAACUGGCUUCGAGAAUGUCCUGGCAACGACGAGGACAACGGCGUCC--------UCGUUGCU
...-.------..--......((((...(((..(((.((((((.(.....).)))))).)))....)))..))))..((((((((((......))))--------)))))).. ( -36.20)
>DroEre_CAF1 38051 98 - 1
AGUUCGGCGAUGG--AAAAAAGCCGCCCGCACGCGACGCCAGUCGACAAACAACUGGCUGCUAGAAUGUCCUGGCGA---CGAGGACACU--CGUCU--------GCGUUGCU
.(..((((.....--......))))..)(((((((..((((((.(.....).)))))).(((((......)))))((---((((....))--)))))--------))).))). ( -39.80)
>DroYak_CAF1 40112 98 - 1
AGUUCGGCAAUGG--AAAAAAGCCGCCCGCACGCGACGCCAGUCGACAAACAACUGGCUGCUAGAAUGUCCUGGCGA---CGAGGACACU--CGUCU--------GCGUUGCU
.(..((((.....--......))))..)(((((((..((((((.(.....).)))))).(((((......)))))((---((((....))--)))))--------))).))). ( -39.10)
>DroAna_CAF1 35316 100 - 1
ACC-C------GGAGAAAAAAGCCGCCCGCACGCGACGCCAGUCGACAAACAACUGGCAGCCAGAACAUCCUGGCAA---CGAGGACACA---GUCUGCUGUCCUGUGUUGCU
...-(------((.(........)..)))...(((((((((((.(.....).)))))).(((((......))))).(---(.((((((..---......))))))))))))). ( -34.30)
>DroPer_CAF1 48897 96 - 1
AAU-C------GG--AAAAAAGCCGCCCGCACGCGACGCCAGUCGACAAACAACUGGCUUCGAGAAUGUCCUGGCAACGACGAGGACAACGGCGUCC--------UCGUUGCU
...-.------..--......((((...(((..(((.((((((.(.....).)))))).)))....)))..))))..((((((((((......))))--------)))))).. ( -36.20)
>consensus
AAU_C______GG__AAAAAAGCCGCCCGCACGCGACGCCAGUCGACAAACAACUGGCUGCUAGAAUGUCCUGGCAA___CGAGGACACU__CGUCU________GCGUUGCU
.....................((.....))..(((((((((((.(.....).))))))........((((((.(......).))))))...................))))). (-24.58 = -24.92 +   0.33)

alignment

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secondary structure

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dotplot

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Window 3

Location 13,894,205 – 13,894,303
Length 98
Sequences 6
Columns 100
Reading direction forward
Mean pairwise identity 81.14
Mean single sequence MFE -34.93
Consensus MFE -24.27
Energy contribution -24.27
Covariance contribution 0.00
Combinations/Pair 1.00
Mean z-score -1.96
Structure conservation index 0.69
SVM decision value 0.67
SVM RNA-class probability 0.816973
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 13894205 98 + 22407834
CAGGACAUUCUAGCAGCCAGUUGUUUGUCGACUGGCGUCGCGUGCGGGCGGCUUUUUUUCCCAUUGCCGAAAGGCUGCUCCUUU-UUGUGU-CAGGAUAA
(..(((((...((((((((((((.....))))))))(((((......))))).............(((....))))))).....-..))))-)..).... ( -36.30)
>DroPse_CAF1 47050 84 + 1
CAGGACAUUCUCGAAGCCAGUUGUUUGUCGACUGGCGUCGCGUGCGGGCGGCUUUUUU--CC------G-AUUGCUCCUCCU-----GCGA-CAUCG-AC
..........((((.((((((((.....))))))))((((((.(.(((.(((..((..--..------)-)..))).)))))-----))))-).)))-). ( -32.20)
>DroEre_CAF1 38078 96 + 1
CAGGACAUUCUAGCAGCCAGUUGUUUGUCGACUGGCGUCGCGUGCGGGCGGCUUUUUU--CCAUCGCCGAACUGCUGCUCCUUU-UUGGGG-CAGGAUAA
..(((..........((((((((.....))))))))(((((......))))).....)--))............(((((((...-..))))-)))..... ( -36.70)
>DroYak_CAF1 40139 97 + 1
CAGGACAUUCUAGCAGCCAGUUGUUUGUCGACUGGCGUCGCGUGCGGGCGGCUUUUUU--CCAUUGCCGAACUGCUGCUCCUUU-UUGGGGACAGGAUAA
......(((((....((((((((.....))))))))((((((.((((.((((......--.....))))..))))))).(((..-..))))))))))).. ( -36.00)
>DroAna_CAF1 35350 92 + 1
CAGGAUGUUCUGGCUGCCAGUUGUUUGUCGACUGGCGUCGCGUGCGGGCGGCUUUUUUCUCC------G-GGUACUAGUCCUCUGCUGUGA-CAGGAUAA
.....((((((....((((((((.....))))))))((((((.(((((.((((....((...------.-))....)))).))))))))))-))))))). ( -36.20)
>DroPer_CAF1 48929 84 + 1
CAGGACAUUCUCGAAGCCAGUUGUUUGUCGACUGGCGUCGCGUGCGGGCGGCUUUUUU--CC------G-AUUGCUCCUCCU-----GCGA-CAUCG-AC
..........((((.((((((((.....))))))))((((((.(.(((.(((..((..--..------)-)..))).)))))-----))))-).)))-). ( -32.20)
>consensus
CAGGACAUUCUAGCAGCCAGUUGUUUGUCGACUGGCGUCGCGUGCGGGCGGCUUUUUU__CC______G_ACUGCUGCUCCUUU_UUGCGA_CAGGAUAA
.((((..........((((((((.....))))))))(((((......)))))..........................)))).................. (-24.27 = -24.27 +   0.00)

alignment

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secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:29:55 2006