Locus 4800

Sequence ID 2L_DroMel_CAF1
Location 13,703,436 – 13,703,590
Length 154
Max. P 0.999737
window7593 window7594 window7595

overview

Window 3

Location 13,703,436 – 13,703,538
Length 102
Sequences 5
Columns 109
Reading direction forward
Mean pairwise identity 79.38
Mean single sequence MFE -38.16
Consensus MFE -25.36
Energy contribution -26.24
Covariance contribution 0.88
Combinations/Pair 1.11
Mean z-score -2.11
Structure conservation index 0.66
SVM decision value 1.21
SVM RNA-class probability 0.930436
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 13703436 102 + 22407834
CAGGAGGCAGGAGGCAGGAGGCGAGGAUCCAGGUGCCC-------AGUGCCAGAAGCACGGAUUCAACAGAAGCGGAGGUGUUGGCCAGUUGUGGAUGGCCAAUGCUUU
......((.....((.....))..((((((.((...))-------.((((.....)))))))))).......)).(((((((((((((........))))))))))))) ( -34.80)
>DroSec_CAF1 59737 109 + 1
CAGGAGACGGGAGGCAGGAAGCGAGGAUCCAGGUGCCCGGUGCCCGGUGCCGGGAGCACGGAUUCAACAAAAGUGGAGGUGUUGGCCAUUUGUGGAUGGCCAAUGCUUU
..(....).....((.....))..((((((..((.(((((..(...)..))))).))..))))))..........(((((((((((((((....))))))))))))))) ( -46.50)
>DroSim_CAF1 58633 109 + 1
CAGGAGACGGGAGGCAGGAAGCGAGGAUCCAGGUGCCCGGUGCCCGGUGCCGGGAGCACGGAUUCUACAAAAGUGGAGGUGUUGGCCAUUUGUGGAUGGCCAAUGCUUU
..(....).....((.....)).(((((((..((.(((((..(...)..))))).))..))))))).........(((((((((((((((....))))))))))))))) ( -47.30)
>DroEre_CAF1 60009 87 + 1
CAG--------AGGCAGGAGGCGAGGAUC-------CA-------GGUGGCAGGAGCAGGGAUUCGACGAAAGUGGAGGUGUUGGCCAGCAUUGGAUGGUCGAUGCUUU
..(--------(((((.....(((..(((-------((-------(.((((...((((....(((.((....)).))).)))).)))).)..)))))..))).)))))) ( -30.70)
>DroYak_CAF1 60896 95 + 1
CAGG-------AGGCAGGAUGCGAGGAUCUAGGUGCCA-------GGUGCCAGGAGCAGGGAUUCCACGAGAGUGGAGGUGUUGGCCAGUCGUGGAUGGUCAAUGCUUU
....-------..((.....))..((((((..((.((.-------(....).)).))..))))))(((....)))(((((((((((((........))))))))))))) ( -31.50)
>consensus
CAGGAG_C_GGAGGCAGGAAGCGAGGAUCCAGGUGCCC_______GGUGCCAGGAGCACGGAUUCAACAAAAGUGGAGGUGUUGGCCAGUUGUGGAUGGCCAAUGCUUU
.............((.....))..((((((.((((((........))))))........))))))..........(((((((((((((........))))))))))))) (-25.36 = -26.24 +   0.88)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 4

Location 13,703,474 – 13,703,570
Length 96
Sequences 5
Columns 102
Reading direction forward
Mean pairwise identity 88.22
Mean single sequence MFE -36.76
Consensus MFE -31.16
Energy contribution -30.64
Covariance contribution -0.52
Combinations/Pair 1.15
Mean z-score -3.65
Structure conservation index 0.85
SVM decision value 3.97
SVM RNA-class probability 0.999737
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 13703474 96 + 22407834
------AGUGCCAGAAGCACGGAUUCAACAGAAGCGGAGGUGUUGGCCAGUUGUGGAUGGCCAAUGCUUUCACUGCUUCAAACUGAAACACACAAAUUGAAA
------.((((.....))))...((((...(((((((((((((((((((........))))))))))))...)))))))....))))............... ( -33.10)
>DroSec_CAF1 59776 102 + 1
GUGCCCGGUGCCGGGAGCACGGAUUCAACAAAAGUGGAGGUGUUGGCCAUUUGUGGAUGGCCAAUGCUUUCACUGCUUCAAACUGAAACACACAAAUUGAAA
(((((((....)))..))))...(((((....(((((((((((((((((((....)))))))))))))))))))(.(((.....))).).......))))). ( -40.80)
>DroSim_CAF1 58672 102 + 1
GUGCCCGGUGCCGGGAGCACGGAUUCUACAAAAGUGGAGGUGUUGGCCAUUUGUGGAUGGCCAAUGCUUUCACUGCUUCAAACUGAAACACACAAAUUGAAA
(((..((((....(((((..(.......)...(((((((((((((((((((....))))))))))))))))))))))))..))))...)))........... ( -40.30)
>DroEre_CAF1 60032 96 + 1
------GGUGGCAGGAGCAGGGAUUCGACGAAAGUGGAGGUGUUGGCCAGCAUUGGAUGGUCGAUGCUUUCACUGCUUCAAACUGAAACACACAAAUUGAAA
------.(((.(((((((((.......((....))((((((((((((((........)))))))))))))).))))))....)))...)))........... ( -34.60)
>DroYak_CAF1 60927 96 + 1
------GGUGCCAGGAGCAGGGAUUCCACGAGAGUGGAGGUGUUGGCCAGUCGUGGAUGGUCAAUGCUUUCACUGCUUCAAACUGAAACACACAAAUUGAAA
------.......((((((((((.(((((....)))))(((((((((((........)))))))))))))).)))))))....................... ( -35.00)
>consensus
______GGUGCCAGGAGCACGGAUUCAACAAAAGUGGAGGUGUUGGCCAGUUGUGGAUGGCCAAUGCUUUCACUGCUUCAAACUGAAACACACAAAUUGAAA
......(((....(((((..(.......)...(((((((((((((((((........))))))))))))))))))))))..))).................. (-31.16 = -30.64 +  -0.52)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 5

Location 13,703,498 – 13,703,590
Length 92
Sequences 6
Columns 102
Reading direction forward
Mean pairwise identity 81.75
Mean single sequence MFE -26.33
Consensus MFE -18.94
Energy contribution -20.48
Covariance contribution 1.54
Combinations/Pair 1.12
Mean z-score -2.28
Structure conservation index 0.72
SVM decision value 0.82
SVM RNA-class probability 0.859339
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 13703498 92 + 22407834
GAAGCGGAGGUGUUGGCCAGUUGUGGAUGGCCAAUGCUUUCACUGCUUCAAACUGAAACA--------CACAAAUUGAAAUAGAA--AACUUUUCCGAUGGA
(((((((((((((((((((........))))))))))))...)))))))...........--------.....((((.((.((..--..)).)).))))... ( -27.40)
>DroPse_CAF1 71755 93 + 1
AGCGUGGA-GUGGGGGCCAGCUGUGGAUGCC--------ACACUGCAUUGAGCUUAGUCAAGAAAUGCCAGAAAGUGAAAUAGAAGGAAGUUAGCGUGUGGA
.((((...-((((.(.(((....))).).))--------)).(((((((...(((....))).)))).)))......................))))..... ( -19.20)
>DroSec_CAF1 59806 92 + 1
AAAGUGGAGGUGUUGGCCAUUUGUGGAUGGCCAAUGCUUUCACUGCUUCAAACUGAAACA--------CACAAAUUGAAAUAGAA--AACUUUUCCGAUGGA
..(((((((((((((((((((....)))))))))))))))))))..(((((..((.....--------..))..)))))......--............... ( -29.90)
>DroSim_CAF1 58702 92 + 1
AAAGUGGAGGUGUUGGCCAUUUGUGGAUGGCCAAUGCUUUCACUGCUUCAAACUGAAACA--------CACAAAUUGAAAUAGAA--AACUUUUCCGAUGGA
..(((((((((((((((((((....)))))))))))))))))))..(((((..((.....--------..))..)))))......--............... ( -29.90)
>DroEre_CAF1 60056 92 + 1
AAAGUGGAGGUGUUGGCCAGCAUUGGAUGGUCGAUGCUUUCACUGCUUCAAACUGAAACA--------CACAAAUUGAAAUAGAA--AACUUUCCCGAUGGA
..(((((((((((((((((........)))))))))))))))))..(((((..((.....--------..))..)))))......--.....(((....))) ( -25.60)
>DroYak_CAF1 60951 92 + 1
AGAGUGGAGGUGUUGGCCAGUCGUGGAUGGUCAAUGCUUUCACUGCUUCAAACUGAAACA--------CACAAAUUGAAAUAGAA--AACUUUCCCGAUGGA
..(((((((((((((((((........)))))))))))))))))..(((((..((.....--------..))..)))))......--.....(((....))) ( -26.00)
>consensus
AAAGUGGAGGUGUUGGCCAGUUGUGGAUGGCCAAUGCUUUCACUGCUUCAAACUGAAACA________CACAAAUUGAAAUAGAA__AACUUUUCCGAUGGA
..(((((((((((((((((........))))))))))))))))).......................................................... (-18.94 = -20.48 +   1.54)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:27:38 2006