Locus 6538

Sequence ID	3L_DroMel_CAF1
Location	17,283,261 – 17,283,461
Length	200
Max. P	0.997771

overview

Window 7

Location	17,283,261 – 17,283,381
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	92.86
Mean single sequence MFE	-55.00
Consensus MFE	-49.18
Energy contribution	-50.98
Covariance contribution	1.80
Combinations/Pair	1.00
Mean z-score	-1.17
Structure conservation index	0.89
SVM decision value	0.12
SVM RNA-class probability	0.592373
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 17283261 120 - 23771897
CCGGGGCACGAGGCGAGUCCUGUAGCAACAGGAGCCCGAGGAGCGGAAUCACGUGGCUGGGGCGCGUGAGCUGCGCUCGAACUUUGUGCGGCCACGUUGCACGUCCACGACCCCCCCUGC
..((((..((.((((..((((((....))))))((((.((..(((......)))..)).))))(((((.(((((((.........))))))))))))....)).)).))..))))..... ( -55.20)
>DroSec_CAF1 166970 114 - 1
CCGGGGCACGAGGCGAGUCCUGUAGCAACAGGAGCCCGAGGAGCGGAAUCACGUGGCUGGGGCGCGUGAGCUGCGCUCGAACUUUGUGCGGCCACGUUGCACGUCCACGUCCCC------
..((((.(((.((((..((((((....))))))((((.((..(((......)))..)).))))(((((.(((((((.........))))))))))))....)).)).)))))))------ ( -57.00)
>DroSim_CAF1 163178 114 - 1
CCGGGGCACGAGGCGAGUCCUGUAGCAACAGGAGCCCGAGGAGCGGAAUCACGUGGCUGGGGCGCGUGAGCUGCGCUCGAACUUUGUGCGGCCACGUUGCACGUCCACGUCCCC------
..((((.(((.((((..((((((....))))))((((.((..(((......)))..)).))))(((((.(((((((.........))))))))))))....)).)).)))))))------ ( -57.00)
>DroEre_CAF1 170036 111 - 1
CCGGGGCACGAGGCGAGUCCUGUAGCAACAGG---------AGCGGAAUCACGUGGCUGGGGCGCGUGAGCUGCGCUCGAACUUUGUGCGGCCACGUUGCACGUCCACAUCCCCCCAUGC
..((((...((..((..((((((....)))))---------).))...))..((((.((..(((((((.(((((((.........))))))))))).))).)).))))....)))).... ( -47.30)
>DroYak_CAF1 175123 118 - 1
CCGGGGCACGAGGCGAGUCCUGUAGCAACAGGAGCCCGAGGAGCGGAAUCACGUGGCUGGGGCGCGUGAGCUGCGCUCGAACUUUGUGCGGCCACGUUGCACGUCCACGUCCCCCU--UC
..((((.(((.((((..((((((....))))))((((.((..(((......)))..)).))))(((((.(((((((.........))))))))))))....)).)).))).)))).--.. ( -58.50)
>consensus
CCGGGGCACGAGGCGAGUCCUGUAGCAACAGGAGCCCGAGGAGCGGAAUCACGUGGCUGGGGCGCGUGAGCUGCGCUCGAACUUUGUGCGGCCACGUUGCACGUCCACGUCCCCC____C
..((((.(((.((((..((((((....))))))((((.((..(((......)))..)).))))(((((.(((((((.........))))))))))))....)).)).)))))))...... (-49.18 = -50.98 +   1.80)

alignment

secondary structure

dotplot

Window 8

Location	17,283,301 – 17,283,421
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	96.33
Mean single sequence MFE	-50.04
Consensus MFE	-45.00
Energy contribution	-46.60
Covariance contribution	1.60
Combinations/Pair	1.00
Mean z-score	-2.22
Structure conservation index	0.90
SVM decision value	2.93
SVM RNA-class probability	0.997771
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 17283301 120 - 23771897
GCAAAAACGGCACCUUUGGGAAAUUAAUAUCCUUUUUGGGCCGGGGCACGAGGCGAGUCCUGUAGCAACAGGAGCCCGAGGAGCGGAAUCACGUGGCUGGGGCGCGUGAGCUGCGCUCGA
((.....((((.((...((((........))))....))))))..)).(((((((..((((((....))))))((((.((..(((......)))..)).))))((....))))).)))). ( -52.40)
>DroSec_CAF1 167004 120 - 1
GCAAAAACGGCACCUUUGGGAAAUUAAUAUGCUUUCUGGGCCGGGGCACGAGGCGAGUCCUGUAGCAACAGGAGCCCGAGGAGCGGAAUCACGUGGCUGGGGCGCGUGAGCUGCGCUCGA
((.....((((.((...(..(.((....))..)..).))))))..)).(((((((..((((((....))))))((((.((..(((......)))..)).))))((....))))).)))). ( -48.30)
>DroSim_CAF1 163212 120 - 1
GCAAAAACGGCACCUUUGGGAAAUUAAUAUCCUUUUUGGGCCGGGGCACGAGGCGAGUCCUGUAGCAACAGGAGCCCGAGGAGCGGAAUCACGUGGCUGGGGCGCGUGAGCUGCGCUCGA
((.....((((.((...((((........))))....))))))..)).(((((((..((((((....))))))((((.((..(((......)))..)).))))((....))))).)))). ( -52.40)
>DroEre_CAF1 170076 111 - 1
GCAAAAACGGCACCUUUGGGAAAUUAAUAUCCUUUUUGGGCCGGGGCACGAGGCGAGUCCUGUAGCAACAGG---------AGCGGAAUCACGUGGCUGGGGCGCGUGAGCUGCGCUCGA
((.....((((.((...((((........))))....))))))..)).((((.(...((((((....)))))---------)((((..(((((((.(...).))))))).))))))))). ( -44.70)
>DroYak_CAF1 175161 120 - 1
GCAAAAACGGCACCUUUGGGAAAUUAAUAUCCUUUUUGGGCCGGGGCACGAGGCGAGUCCUGUAGCAACAGGAGCCCGAGGAGCGGAAUCACGUGGCUGGGGCGCGUGAGCUGCGCUCGA
((.....((((.((...((((........))))....))))))..)).(((((((..((((((....))))))((((.((..(((......)))..)).))))((....))))).)))). ( -52.40)
>consensus
GCAAAAACGGCACCUUUGGGAAAUUAAUAUCCUUUUUGGGCCGGGGCACGAGGCGAGUCCUGUAGCAACAGGAGCCCGAGGAGCGGAAUCACGUGGCUGGGGCGCGUGAGCUGCGCUCGA
((.....((((.((...((((........))))....))))))..)).(((((((..((((((....))))))((((.((..(((......)))..)).))))((....))))).)))). (-45.00 = -46.60 +   1.60)

alignment

secondary structure

dotplot

Window 9

Location	17,283,341 – 17,283,461
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	95.50
Mean single sequence MFE	-37.48
Consensus MFE	-31.64
Energy contribution	-33.64
Covariance contribution	2.00
Combinations/Pair	1.00
Mean z-score	-1.40
Structure conservation index	0.84
SVM decision value	0.22
SVM RNA-class probability	0.638408
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 17283341 120 + 23771897
CUCGGGCUCCUGUUGCUACAGGACUCGCCUCGUGCCCCGGCCCAAAAAGGAUAUUAAUUUCCCAAAGGUGCCGUUUUUGCUGGCGAAAAUCACGCAAAAUGCGACCCGGCUUUCACGAGU
..((((.((((((....)))))))))).((((((...((((((.....(((........)))....)).)))).....(((((.(.....).(((.....)))..)))))...)))))). ( -40.90)
>DroSec_CAF1 167044 120 + 1
CUCGGGCUCCUGUUGCUACAGGACUCGCCUCGUGCCCCGGCCCAGAAAGCAUAUUAAUUUCCCAAAGGUGCCGUUUUUGCUGGCGAAAAUCACGCAAAAUUCGACCCGGCUUUCACGAGU
..((((.((((((....)))))))))).((((((...((((((.((((.........)))).....)).)))).....(((((((((............))))..)))))...)))))). ( -35.80)
>DroSim_CAF1 163252 120 + 1
CUCGGGCUCCUGUUGCUACAGGACUCGCCUCGUGCCCCGGCCCAAAAAGGAUAUUAAUUUCCCAAAGGUGCCGUUUUUGCUGGCGAAAAUCACGCAAAAUGCGACCCGGCUUUCACGAGU
..((((.((((((....)))))))))).((((((...((((((.....(((........)))....)).)))).....(((((.(.....).(((.....)))..)))))...)))))). ( -40.90)
>DroEre_CAF1 170115 112 + 1
--------CCUGUUGCUACAGGACUCGCCUCGUGCCCCGGCCCAAAAAGGAUAUUAAUUUCCCAAAGGUGCCGUUUUUGCUGGCGAAAAUCACGCAAAAUGCGACCCGGCUUUCAAGAGU
--------(((((....)))))(((((((....((..((((((.....(((........)))....)).)))).....)).)))((((..(.(((.....)))....)..))))..)))) ( -32.30)
>DroYak_CAF1 175201 120 + 1
CUCGGGCUCCUGUUGCUACAGGACUCGCCUCGUGCCCCGGCCCAAAAAGGAUAUUAAUUUCCCAAAGGUGCCGUUUUUGCUGGCAAAAAUCACGCAAAAUGCGACCCGGCUUUCAAGAGU
((((((.((((((....)))))))))(((((((....((((((.....(((........)))....)).)))).(((((((((......))).)))))).))))...)))......))). ( -37.50)
>consensus
CUCGGGCUCCUGUUGCUACAGGACUCGCCUCGUGCCCCGGCCCAAAAAGGAUAUUAAUUUCCCAAAGGUGCCGUUUUUGCUGGCGAAAAUCACGCAAAAUGCGACCCGGCUUUCACGAGU
..((((.((((((....)))))))))).((((((...((((((.....(((........)))....)).)))).....(((((.(.....).(((.....)))..)))))...)))))). (-31.64 = -33.64 +   2.00)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:23:34 2006