Locus 1901

Sequence ID 3L_DroMel_CAF1
Location 5,325,553 – 5,325,676
Length 123
Max. P 0.996705
window2958 window2959 window2960

overview

Window 8

Location 5,325,553 – 5,325,651
Length 98
Sequences 6
Columns 106
Reading direction reverse
Mean pairwise identity 83.38
Mean single sequence MFE -20.49
Consensus MFE -13.21
Energy contribution -14.07
Covariance contribution 0.86
Combinations/Pair 1.06
Mean z-score -2.17
Structure conservation index 0.64
SVM decision value 0.06
SVM RNA-class probability 0.563287
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 5325553 98 - 23771897
AUAAUUU-UCCCAAAUUA-----CCAAGUAGGAAAAUUUACCACAUACCCGUGAAUUUUUCAG--CUAGCGGGUAUGAAAAUUUCGCACGAUUUUCCCGCCAUCAU
.......-..........-----....(..((((((.......(((((((((...........--...)))))))))......((....))))))))..)...... ( -19.94)
>DroSec_CAF1 72813 98 - 1
AUAAUUU-UCCCAAAUUA-----CCAAGUGGGAAAAUUUACCACAUACCCGUGAACUUUUCAG--CUAGCGGGUAUGAAAAUUUCACACGAUUUUCCCGCCAUCGU
.......-..........-----....(((((((((.......(((((((((...((....))--...)))))))))......((....)))))))))))...... ( -25.80)
>DroSim_CAF1 74821 98 - 1
AUAAUUU-UUCCAAAUUA-----CCAAGUGGGAAAAUUUACCACAUACCCGUGAACUUUUCAG--CUAGCGGGUAUGAAAAUUUCACACGAUUUUCCCGCCAUCGU
.......-..........-----....(((((((((.......(((((((((...((....))--...)))))))))......((....)))))))))))...... ( -25.80)
>DroEre_CAF1 72737 98 - 1
AUAAUUU-UCCCAAAUUA-----UCGAAUAGGAAAAUUUACCGCAUACCCGUACACUUUUCUG--CUAGCGGGUAUGAACAUUUCGGACGCUUUUCCCGCCAUCGU
(((((((-....))))))-----)(((...((((((....((((((((((((...(......)--...))))))))).......)))....)))))).....))). ( -20.41)
>DroYak_CAF1 81371 98 - 1
CUAAUUU-UCCCAAAUUA-----UCAAAUAAGAAAAUUUACCGCAUACCCGUCAACUUUUCAG--CUAGCGGGUAUGAAAAUUUCGCACGAUUUUCCCGCCAUCGU
.......-....(((((.-----((......)).)))))...(((((((((..(.((....))--.)..)))))))(((((((......)))))))..))...... ( -16.60)
>DroAna_CAF1 71697 103 - 1
UUAUUUUUUCCCACCUUUCACCUUCAGAUA--CAAAUACAACAUAUACCCGUGAUAUUUUCGGGAAUAGCGGGUAUGAAAAUUU-GCACGAUUUUUCCGCUUUCUU
.......(((((.....((.......))..--.(((((..((........))..)))))..))))).(((((....(((((((.-....))))))))))))..... ( -14.40)
>consensus
AUAAUUU_UCCCAAAUUA_____CCAAAUAGGAAAAUUUACCACAUACCCGUGAACUUUUCAG__CUAGCGGGUAUGAAAAUUUCGCACGAUUUUCCCGCCAUCGU
..............................((((((((.....(((((((((................)))))))))............))))))))......... (-13.21 = -14.07 +   0.86)

alignment

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secondary structure

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dotplot

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Window 9

Location 5,325,579 – 5,325,676
Length 97
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 73.95
Mean single sequence MFE -25.37
Consensus MFE -12.86
Energy contribution -13.06
Covariance contribution 0.20
Combinations/Pair 1.25
Mean z-score -2.85
Structure conservation index 0.51
SVM decision value 2.74
SVM RNA-class probability 0.996705
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 5325579 97 + 23771897
UUUCAUACCCGCUAG--CUGAAAAAUUCACGGGUAUGUGGUAAAUUUUCCUACUUGG-----UAAUUUGGGA-AAAUUAUCU-------------UUGCUAUCUUAAUCAAAUAAAUU--
...((((((((....--.(((.....)))))))))))(((((((((((((((..(..-----..)..)))))-)))).....-------------)))))).................-- ( -20.90)
>DroSec_CAF1 72839 93 + 1
UUUCAUACCCGCUAG--CUGAAAAGUUCACGGGUAUGUGGUAAAUUUUCCCACUUGG-----UAAUUUGGGA-AAAUUAUCU-------------UAGCUAUCUUAAUCGAAUA------
...((((((((..((--((....))))..)))))))).(((((.((((((((..(..-----..)..)))))-)))))))).-------------...................------ ( -29.10)
>DroSim_CAF1 74847 97 + 1
UUUCAUACCCGCUAG--CUGAAAAGUUCACGGGUAUGUGGUAAAUUUUCCCACUUGG-----UAAUUUGGAA-AAAUUAUCU-------------UAGCUAUCUUAAUCAAAUAUCUU--
....(((((((..((--((....))))..)))))))((((.........))))..((-----((((((....-)))))))).-------------.......................-- ( -24.90)
>DroEre_CAF1 72763 97 + 1
GUUCAUACCCGCUAG--CAGAAAAGUGUACGGGUAUGCGGUAAAUUUUCCUAUUCGA-----UAAUUUGGGA-AAAUUAUCU-------------GUUCCAUCUUAAUCAAAUAAAUU--
...((((((((...(--(......))...))))))))(((..((((((((((.....-----.....)))))-)))))..))-------------)......................-- ( -23.50)
>DroYak_CAF1 81397 99 + 1
UUUCAUACCCGCUAG--CUGAAAAGUUGACGGGUAUGCGGUAAAUUUUCUUAUUUGA-----UAAUUUGGGA-AAAUUAGCU-------------GUGCAAUCUUAAUCAUGUGAAUUAU
.((((((((((.(((--((....))))).)))))))(((((.((((((((((..(..-----..)..)))))-))))).)))-------------))................))).... ( -30.30)
>DroAna_CAF1 71722 111 + 1
UUUCAUACCCGCUAUUCCCGAAAAUAUCACGGGUAUAUGUUGUAUUUG--UAUCUGAAGGUGAAAGGUGGGAAAAAAUAAGUGUUCCCAUUAUUUUAACAACCUUUAU-----GUUUU--
...((((((((((.(((((((.....)).((((((((.........))--))))))..)).))).))))))..(((((((.((....))))))))).........)))-----)....-- ( -23.50)
>consensus
UUUCAUACCCGCUAG__CUGAAAAGUUCACGGGUAUGUGGUAAAUUUUCCUACUUGA_____UAAUUUGGGA_AAAUUAUCU_____________UAGCUAUCUUAAUCAAAUAAAUU__
...((((((((..................)))))))).(((((.((.(((((...............))))).)).)))))....................................... (-12.86 = -13.06 +   0.20)

alignment

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secondary structure

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dotplot

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Window 0

Location 5,325,579 – 5,325,676
Length 97
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 73.95
Mean single sequence MFE -21.11
Consensus MFE -13.13
Energy contribution -12.99
Covariance contribution -0.14
Combinations/Pair 1.11
Mean z-score -2.20
Structure conservation index 0.62
SVM decision value 2.05
SVM RNA-class probability 0.986571
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 5325579 97 - 23771897
--AAUUUAUUUGAUUAAGAUAGCAA-------------AGAUAAUUU-UCCCAAAUUA-----CCAAGUAGGAAAAUUUACCACAUACCCGUGAAUUUUUCAG--CUAGCGGGUAUGAAA
--...((((((.....))))))...-------------....(((((-(((.......-----.......)))))))).....(((((((((...........--...)))))))))... ( -18.98)
>DroSec_CAF1 72839 93 - 1
------UAUUCGAUUAAGAUAGCUA-------------AGAUAAUUU-UCCCAAAUUA-----CCAAGUGGGAAAAUUUACCACAUACCCGUGAACUUUUCAG--CUAGCGGGUAUGAAA
------...................-------------....(((((-(((((.....-----.....)))))))))).....(((((((((...((....))--...)))))))))... ( -24.20)
>DroSim_CAF1 74847 97 - 1
--AAGAUAUUUGAUUAAGAUAGCUA-------------AGAUAAUUU-UUCCAAAUUA-----CCAAGUGGGAAAAUUUACCACAUACCCGUGAACUUUUCAG--CUAGCGGGUAUGAAA
--.((.(((((.....))))).)).-------------....(((((-(((((.....-----.....)))))))))).....(((((((((...((....))--...)))))))))... ( -22.90)
>DroEre_CAF1 72763 97 - 1
--AAUUUAUUUGAUUAAGAUGGAAC-------------AGAUAAUUU-UCCCAAAUUA-----UCGAAUAGGAAAAUUUACCGCAUACCCGUACACUUUUCUG--CUAGCGGGUAUGAAC
--..((((((((((......((((.-------------........)-)))......)-----)))))))))...........(((((((((...(......)--...)))))))))... ( -22.30)
>DroYak_CAF1 81397 99 - 1
AUAAUUCACAUGAUUAAGAUUGCAC-------------AGCUAAUUU-UCCCAAAUUA-----UCAAAUAAGAAAAUUUACCGCAUACCCGUCAACUUUUCAG--CUAGCGGGUAUGAAA
...............((((((((..-------------.)).)))))-)...(((((.-----((......)).)))))....((((((((..(.((....))--.)..))))))))... ( -15.20)
>DroAna_CAF1 71722 111 - 1
--AAAAC-----AUAAAGGUUGUUAAAAUAAUGGGAACACUUAUUUUUUCCCACCUUUCACCUUCAGAUA--CAAAUACAACAUAUACCCGUGAUAUUUUCGGGAAUAGCGGGUAUGAAA
--.....-----..((((((.(..(((((((((....)).)))))))..)..))))))............--...........(((((((((..(((((....))))))))))))))... ( -23.10)
>consensus
__AAUUUAUUUGAUUAAGAUAGCAA_____________AGAUAAUUU_UCCCAAAUUA_____CCAAAUAGGAAAAUUUACCACAUACCCGUGAACUUUUCAG__CUAGCGGGUAUGAAA
...................................................................................(((((((((................)))))))))... (-13.13 = -12.99 +  -0.14)

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 10:19:27 2006