Locus 3964

Sequence ID X_DroMel_CAF1
Location 10,521,298 – 10,521,435
Length 137
Max. P 0.999775
window6517 window6518

overview

Window 7

Location 10,521,298 – 10,521,399
Length 101
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 74.86
Mean single sequence MFE -21.86
Consensus MFE -10.20
Energy contribution -10.52
Covariance contribution 0.32
Combinations/Pair 1.19
Mean z-score -3.24
Structure conservation index 0.47
SVM decision value 4.05
SVM RNA-class probability 0.999775
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 10521298 101 + 22224390
-------------------AAAGCCAAACCAAGCUGAAUUAAAAUUUUUUGCAUGAGCCCCCAGGAAAGUGAACUGUUGUUCGCUUUUUAUAAGUGCUCGCAAAAAACCAAAAAAAAAAA
-------------------..(((........))).........((((((((..(((((....(((((((((((....)))))))))))....).))))))))))))............. ( -24.80)
>DroSec_CAF1 52696 96 + 1
-------------------AAAGCCAAACCAAACUGAAUUAAAAUUUUUUGCAUGAGCCCGCAGGAAAGUGAACUGUUGUUCGCUUUUUAUAAGCAA---CAAAAAAACAAAA--AAAAA
-------------------...((.........................(((........)))(((((((((((....)))))))))))....))..---.............--..... ( -15.60)
>DroSim_CAF1 56283 89 + 1
-------------------AAAGCCAAACCAAACUGAAUUAAAAUUUUUUGCAUGAGCCCGCAGGAAAGUGAACUGUUGUUCGCUUUUUAUAAGUGC----------UCGCAA--AAAAA
-------------------.........................((((((((..((((.(...(((((((((((....)))))))))))....).))----------))))))--)))). ( -24.40)
>DroEre_CAF1 54706 98 + 1
-------------------AAAGCCAAACCAAACUGAAUUAAAAUUUUCUGCAUGAGCCCGCAGGAAAGUGAACAACAGU-CGCUU-UUAUAAGUGCUGGCAAAAAAAAAA-AAAAAAUA
-------------------...((((......((((........((((((((........))))))))........))))-(((((-....))))).))))..........-........ ( -20.89)
>DroYak_CAF1 54371 112 + 1
AAGAAAAAACCAAAAGAAAAAAGCCAAACCAAAGUGAAUUAAAAUUUUUUGCAUGAGCCCGCAGGAAAGUGAGGAACAGUACGCUU-UUCUAAGUGCUGGCAAAAA-------AGGCAUA
......................(((..((....)).........((((((((...(((.(..(((((((((..........)))))-))))..).))).)))))))-------))))... ( -23.60)
>consensus
___________________AAAGCCAAACCAAACUGAAUUAAAAUUUUUUGCAUGAGCCCGCAGGAAAGUGAACUGUUGUUCGCUUUUUAUAAGUGCU_GCAAAAAAACAAAAA_AAAAA
......................((....................((((((((........))))))))((((((....)))))).........))......................... (-10.20 = -10.52 +   0.32)

alignment

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secondary structure

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dotplot

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Window 8

Location 10,521,319 – 10,521,435
Length 116
Sequences 5
Columns 116
Reading direction forward
Mean pairwise identity 80.64
Mean single sequence MFE -22.64
Consensus MFE -11.34
Energy contribution -12.02
Covariance contribution 0.68
Combinations/Pair 1.11
Mean z-score -3.22
Structure conservation index 0.50
SVM decision value 2.34
SVM RNA-class probability 0.992583
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 10521319 116 + 22224390
AAAAUUUUUUGCAUGAGCCCCCAGGAAAGUGAACUGUUGUUCGCUUUUUAUAAGUGCUCGCAAAAAACCAAAAAAAAAAAAAAAAUGAAACACAAGAUGACACAAAAAAUUUAUCA
....((((((((..(((((....(((((((((((....)))))))))))....).))))))))))))............................(((((..........))))). ( -24.80)
>DroSec_CAF1 52717 111 + 1
AAAAUUUUUUGCAUGAGCCCGCAGGAAAGUGAACUGUUGUUCGCUUUUUAUAAGCAA---CAAAAAAACAAAA--AAAAAAAAAAUUAAACACAAGAUGACACAAAAAAUGUAUCA
..((((((((((....))..((.(((((((((((....)))))))))))....))..---.............--....))))))))..........(((.(((.....))).))) ( -17.50)
>DroSim_CAF1 56304 104 + 1
AAAAUUUUUUGCAUGAGCCCGCAGGAAAGUGAACUGUUGUUCGCUUUUUAUAAGUGC----------UCGCAA--AAAAAAGAAAUGAAACACAAGAUGACACAAAAAAUUUAUCA
....((((((((..((((.(...(((((((((((....)))))))))))....).))----------))))))--))))................(((((..........))))). ( -25.80)
>DroEre_CAF1 54727 113 + 1
AAAAUUUUCUGCAUGAGCCCGCAGGAAAGUGAACAACAGU-CGCUU-UUAUAAGUGCUGGCAAAAAAAAAA-AAAAAAUAACAAAUGAAACACAAGAUGACACAAAAAUGUUAUCA
....((((((((........))))))))(((.....(((.-(((((-....))))))))............-.........(....)...)))..(((((((......))))))). ( -24.10)
>DroYak_CAF1 54411 108 + 1
AAAAUUUUUUGCAUGAGCCCGCAGGAAAGUGAGGAACAGUACGCUU-UUCUAAGUGCUGGCAAAAA-------AGGCAUAACAACUGAAACACAAGAUGACAUACAAAAUUUAUCA
....((((((((...(((.(..(((((((((..........)))))-))))..).))).)))))))-------).....................(((((..........))))). ( -21.00)
>consensus
AAAAUUUUUUGCAUGAGCCCGCAGGAAAGUGAACUGUUGUUCGCUUUUUAUAAGUGCU_GCAAAAAAACAAAAA_AAAAAAAAAAUGAAACACAAGAUGACACAAAAAAUUUAUCA
....((((((((........))))))))((((((....))))))...................................................(((((..........))))). (-11.34 = -12.02 +   0.68)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:13:03 2006