Locus 1806

Sequence ID 2L_DroMel_CAF1
Location 4,985,512 – 4,985,620
Length 108
Max. P 0.999766
window2908 window2909

overview

Window 8

Location 4,985,512 – 4,985,620
Length 108
Sequences 5
Columns 110
Reading direction forward
Mean pairwise identity 75.14
Mean single sequence MFE -25.92
Consensus MFE -12.75
Energy contribution -12.99
Covariance contribution 0.24
Combinations/Pair 1.16
Mean z-score -3.25
Structure conservation index 0.49
SVM decision value 4.03
SVM RNA-class probability 0.999766
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 4985512 108 + 22407834
AAUUUUAUUAACUGAGCUUGUCGAAGA-UCUUCUCUUG-AAGUAAAAAAAAGGAAUACCUCAUUUUAAAACUCAGUUGGUAAAAGUGGGUCUUUAGCAUCCCCAACUAAU
..((((((((((((((...........-.((((....)-)))..((((..(((....)))..))))....)))))))))))))).((((...........))))...... ( -23.50)
>DroSec_CAF1 5833 86 + 1
AAUUUUAUUAACUGAGCUUGCAGAAGA------------------------GUAGAACCUCAUCUUAAAACUCAGUUGGUAAAAGUGCGUCUUCAGCAUUCCCAACUAAU
..((((((((((((((.((..(((.((------------------------(......))).)))..)).))))))))))))))((((.......))))........... ( -23.00)
>DroSim_CAF1 5875 86 + 1
AAUUUUGUUAACUGAGCUUGCAGAAGA------------------------GUAGAACCUCAUCUUAAAACUCAGUUGGUAAAAGUGCGUCUUCAGCAUUCCCAACUAAU
..(((((..(((((((.((..(((.((------------------------(......))).)))..)).)))))))..)))))((((.......))))........... ( -21.00)
>DroEre_CAF1 5767 108 + 1
AAUUUUAUUAGCUGAGCUUGUAGAAGAGUAUUCUGUCCAAAGUGACAA--UAGAAUCCCUCAUCUUAUAACUCAGUUGGUAAAAGUGGGUCUUCAGCAUUUCCAACUAAU
..((((((((((((((.(((((((.(((.((((((((......)))..--.)))))..))).)).))))))))))))))))))).((((...........))))...... ( -28.10)
>DroYak_CAF1 5805 107 + 1
AAAUAUAUUAGCUGAGCUUGUAGAAGAGUAUUCUCUUCAAAGUAAGAA--UAGAAUACAUCAUCUUAUAGCUCAGUUGGUAAUA-UGGGUCUUAAGCAUCCGCAACUAAU
.....(((((((((((((...(((.(((((((((.(((.......)))--.))))))).)).)))...)))))))))))))...-.(((((....).))))......... ( -34.00)
>consensus
AAUUUUAUUAACUGAGCUUGUAGAAGA_U_UUCU_U___AAGU_A_AA___GGAAUACCUCAUCUUAAAACUCAGUUGGUAAAAGUGGGUCUUCAGCAUUCCCAACUAAU
..((((((((((((((.....(((.((................................)).))).....)))))))))))))).......................... (-12.75 = -12.99 +   0.24)

alignment

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secondary structure

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dotplot

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Window 9

Location 4,985,512 – 4,985,620
Length 108
Sequences 5
Columns 110
Reading direction reverse
Mean pairwise identity 75.14
Mean single sequence MFE -23.74
Consensus MFE -10.50
Energy contribution -11.56
Covariance contribution 1.06
Combinations/Pair 1.21
Mean z-score -2.28
Structure conservation index 0.44
SVM decision value 1.72
SVM RNA-class probability 0.973717
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 4985512 108 - 22407834
AUUAGUUGGGGAUGCUAAAGACCCACUUUUACCAACUGAGUUUUAAAAUGAGGUAUUCCUUUUUUUUACUU-CAAGAGAAGA-UCUUCGACAAGCUCAGUUAAUAAAAUU
......((((..(.....)..)))).(((((..(((((((((((((((.((((....))))..)))))(((-(....)))).-........))))))))))..))))).. ( -25.60)
>DroSec_CAF1 5833 86 - 1
AUUAGUUGGGAAUGCUGAAGACGCACUUUUACCAACUGAGUUUUAAGAUGAGGUUCUAC------------------------UCUUCUGCAAGCUCAGUUAAUAAAAUU
.(((((.......)))))........(((((..((((((((((..(((.(((......)------------------------)).)))..))))))))))..))))).. ( -22.10)
>DroSim_CAF1 5875 86 - 1
AUUAGUUGGGAAUGCUGAAGACGCACUUUUACCAACUGAGUUUUAAGAUGAGGUUCUAC------------------------UCUUCUGCAAGCUCAGUUAACAAAAUU
....(.(((((.(((.......))).))))).)((((((((((..(((.(((......)------------------------)).)))..))))))))))......... ( -21.90)
>DroEre_CAF1 5767 108 - 1
AUUAGUUGGAAAUGCUGAAGACCCACUUUUACCAACUGAGUUAUAAGAUGAGGGAUUCUA--UUGUCACUUUGGACAGAAUACUCUUCUACAAGCUCAGCUAAUAAAAUU
((((((((((((.(.((......))).))).))))(((((((...(((.(((..(((((.--..(((......)))))))).))).)))...))))))))))))...... ( -23.60)
>DroYak_CAF1 5805 107 - 1
AUUAGUUGCGGAUGCUUAAGACCCA-UAUUACCAACUGAGCUAUAAGAUGAUGUAUUCUA--UUCUUACUUUGAAGAGAAUACUCUUCUACAAGCUCAGCUAAUAUAUUU
(((((....((...........)).-.........(((((((...(((.((.(((((((.--(((.......))).))))))))).)))...))))))))))))...... ( -25.50)
>consensus
AUUAGUUGGGAAUGCUGAAGACCCACUUUUACCAACUGAGUUUUAAGAUGAGGUAUUCC___UU_U_ACUU___A_AGAA_A_UCUUCUACAAGCUCAGUUAAUAAAAUU
.(((((.......)))))...............((((((((((......((((.........(((((......)))))......))))...))))))))))......... (-10.50 = -11.56 +   1.06)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:11:46 2006