Locus 1011

Sequence ID	3L_DroMel_CAF1
Location	3,001,632 – 3,001,851
Length	219
Max. P	0.917902

overview

Window 3

Location	3,001,632 – 3,001,744
Length	112
Sequences	6
Columns	117
Reading direction	reverse
Mean pairwise identity	74.85
Mean single sequence MFE	-41.88
Consensus MFE	-15.76
Energy contribution	-16.27
Covariance contribution	0.51
Combinations/Pair	1.26
Mean z-score	-2.36
Structure conservation index	0.38
SVM decision value	0.88
SVM RNA-class probability	0.873156
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 3001632 112 - 23771897
AUUCUCGCUCCGGCUACGGCU----CUUUGGCUUCAGCUUUG-GCUUUGGAGCCGGACAAGUGUCGGAUUUGGGGGGCCGAUGGAAAGGCGCUCCUUCAAAGCGACAGCGUUAUCAA
....((((((((((..(((((----((..((((........)-)))..))))))).......))))))...((((.(((........))).))))......))))............ ( -44.80)
>DroSec_CAF1 35893 116 - 1
AUUCUGGCUCCGGCUUCGGUUUUGGCUUUGGCUUCAGCUUUG-GCUUUGGAGCUGGACAAGUGUCGGAUUUGGGGAGCAGCUUAAAAGGCGCUCCUUCAAGGCGACAGCGUUAUCAA
..((..(((((((((..((((..(((....)))..))))..)-)))..)))))..))....(((((..((((((((((.(((.....)))))))).))))).))))).......... ( -47.10)
>DroSim_CAF1 36495 110 - 1
AUUCUGGCUCCGGCAUCG------GCUUUGGCUUCAGCUUUG-GCUUUGGAGCCGGACAAGUGUCGGAUUUGUGGGGCAGCUUAAAAGGCGCUCCUUCAAGGCGACAGCGUUAUCAA
..(((((((((((....(------(((..(((....)))..)-))))))))))))))....(((((..((((.(((((.(((.....))))))))..)))).))))).......... ( -45.80)
>DroEre_CAF1 38522 97 - 1
AUUCUGGCUCCGG------------------CUUUGGCUUUG-GCUUUGGAGCCGGACAAGUGUCGGAUUUGG-GGGCCGCUUGAAAGGCGCUCCUUCAAGGCGACCGCGUUAUCAA
..(((((((((((------------------((........)-)))..)))))))))...((((((..(((((-(((.((((.....))))..)))))))).))).)))........ ( -39.20)
>DroYak_CAF1 36344 109 - 1
AUUCUGGCUCCGGCUCCAGCU------ACGGCUUUGGCUCCA-GCUUUGCAGCUGGACAAGUGUCGGAUUUGG-GGGCCGCUUGAAAGACGCUUCUCCAAGGCGACAGCGUUAUCAA
.....((((((.(((..(((.------...)))..)))((((-(((....)))))))(((((.....))))))-)))))...(((..((((((((.(....).)).)))))).))). ( -41.60)
>DroAna_CAF1 33756 88 - 1
---------------------------GAGGAUUUUGCAUUGGUCUUUGGAGCCGGACAAGUGUCGGAUUUGG--GACGGCUGAAAAGAACCUGCUCGAAGGAGGCAACGUUGUCAA
---------------------------((.(((.((((...(((((((..(((((..(((((.....))))).--..)))))..)))).)))..(((....))))))).))).)).. ( -32.80)
>consensus
AUUCUGGCUCCGGCU_CG_________UUGGCUUCAGCUUUG_GCUUUGGAGCCGGACAAGUGUCGGAUUUGG_GGGCCGCUUAAAAGGCGCUCCUUCAAGGCGACAGCGUUAUCAA
....................................(((....((((((((((((.((....))))).......((((..((....))..)))))))))))))...)))........ (-15.76 = -16.27 +   0.51)

alignment

secondary structure

dotplot

Window 4

Location	3,001,744 – 3,001,851
Length	107
Sequences	5
Columns	107
Reading direction	forward
Mean pairwise identity	94.86
Mean single sequence MFE	-34.23
Consensus MFE	-29.54
Energy contribution	-30.14
Covariance contribution	0.60
Combinations/Pair	1.00
Mean z-score	-1.61
Structure conservation index	0.86
SVM decision value	1.12
SVM RNA-class probability	0.917902
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 3001744 107 + 23771897
CCCGGAUUGCGCCGCACCUUGACAUAAAUUCAUUAAAUCUCUUGUCCCUGCGGCACUUGCGCCGCGGGACAGUGAGCAUUUAACGGAUUUCCUUGGCUCUUUGGACG
.(((((..(.(((((.....).)..((((((.((((((((((((((((.(((((......)))))))))))).))).)))))).))))))....))).))))))... ( -38.20)
>DroSec_CAF1 36009 107 + 1
CCCGGAUUGCGCCGCACCUUGACAUAAAUUCAUUAAAUCUCUUGUCCCUGCGGCACUUGCGCCCCGGGACAGCGAGCAUUUAACGGAUUUCCCUGGCUCUUUGGACG
.(((((..(.(((((.....).)..((((((.((((((((((((((((.(.(((......)))).))))))).))).)))))).))))))....))).))))))... ( -32.90)
>DroSim_CAF1 36605 107 + 1
CCCGGAUUGCGCCGCACCUUGACAUAAAUUCAUUAAAUCUCUUGUCCCUGCGGCAACUGCGCCCCGGGACAGCGAGCAUUUAACGGAUUUCCCUGGCUCUUUGGACG
.(((((..(.(((((.....).)..((((((.((((((((((((((((.(.(((......)))).))))))).))).)))))).))))))....))).))))))... ( -32.90)
>DroEre_CAF1 38619 107 + 1
CCCGGAUUGUGCCGCACCUUGACAUAAAUUCAUUAAAUCUCUGUUCCCUGCGGCACUUUCGCCCCGGGACAGCGAGCAUUUAACGGAUUUCGCUGGCUCUUUGGACG
(((((...((((((((....((((.................))))...)))))))).......))))).(((((((.(((.....))))))))))............ ( -32.93)
>DroYak_CAF1 36453 107 + 1
CCCGGAUAGCGCCGCACCUUGGCAUAAAUUCAUUAAAUCUCUUAUCCCUGCGGCACUUUCGCCCCGGGACAGCGAGCAUUUAACGGAUUUCGCUGGCUCUUUGGACG
.(((((.(((((((.....))))..((((((.(((((((((((.((((.(.(((......)))).)))).)).))).)))))).)))))).....))).)))))... ( -34.20)
>consensus
CCCGGAUUGCGCCGCACCUUGACAUAAAUUCAUUAAAUCUCUUGUCCCUGCGGCACUUGCGCCCCGGGACAGCGAGCAUUUAACGGAUUUCCCUGGCUCUUUGGACG
.(((((..(.(((((.....).)..((((((.((((((((((((((((.(.(((......))).)))))))).))).)))))).))))))....))).))))))... (-29.54 = -30.14 +   0.60)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:56:49 2006