Locus 1819

Sequence ID	3L_DroMel_CAF1
Location	5,102,410 – 5,102,565
Length	155
Max. P	0.617433

overview

Window 9

Location	5,102,410 – 5,102,525
Length	115
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	90.66
Mean single sequence MFE	-33.55
Consensus MFE	-25.35
Energy contribution	-26.35
Covariance contribution	1.00
Combinations/Pair	1.09
Mean z-score	-1.71
Structure conservation index	0.76
SVM decision value	0.17
SVM RNA-class probability	0.617433
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 5102410 115 - 23771897
AACAGAGAUAGCAAACAUGGCGCAAAAAGUGUACUUUGUUUGCAUAUGUCUGACCUUUUGCA-UCGCACUCGGCACGUG--UUGCGACUAUCGAAAGAGGGCAGGUGACUA--AAACGAA
..((((.((((((((((..((((.....))))....))))))).))).)))).((..(((((-..((((.......)))--))))))...((....))))..((....)).--....... ( -34.40)
>DroSec_CAF1 295432 116 - 1
AACAGAGCUAGCAAACAUGGGGCAAAAGGCGUACUUUGUUUGCAUAUGUCUGUCCUUUUGAACUCGCACUCGGCACGUG--UUGCGACUAUCGAAAAAAGGCAGGUGACUA--AAACGAA
..........(((((((.((.((.....))...)).)))))))...(..(((((.((((((..((((((.((...)).)--.)))))...))))))...)))))..)....--....... ( -28.00)
>DroSim_CAF1 317042 115 - 1
AACAGAGAUAGCAAACAUGGCGCAAAAAGCGUACUUUGUUUGCAUAUGUCUGACCUUUUGCACUCGCACUCGGCACGUG--UUGCGACUAUCGAAA-AAGGCAGGUGACUA--AAAUGAA
..((((.((((((((((..((((.....))))....))))))).))).)))).((((((....((((((.((...)).)--.))))).......))-)))).((....)).--....... ( -35.20)
>DroYak_CAF1 307716 119 - 1
AAGAGAGAUAGCAAACAUGGCGCAAAAAGCGUACUUUGUUUGCAUAUGUGUGACCUUUCGCA-UCGCACUUGGCACGUGUGUGGCGACUAUCGAAAAAAGGCAGUUGCCUAUGAAACGAA
..........(((((((..((((.....))))....)))))))(((..((((.((....((.-..))....))))))..)))(((((((..(.......)..)))))))........... ( -36.60)
>consensus
AACAGAGAUAGCAAACAUGGCGCAAAAAGCGUACUUUGUUUGCAUAUGUCUGACCUUUUGCA_UCGCACUCGGCACGUG__UUGCGACUAUCGAAAAAAGGCAGGUGACUA__AAACGAA
..((((.((((((((((..((((.....))))....))))))).))).)))).((((((....((((.....)).(((.....)))......)).)))))).((....)).......... (-25.35 = -26.35 +   1.00)

alignment

secondary structure

dotplot

Window 0

Location	5,102,447 – 5,102,565
Length	118
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	86.73
Mean single sequence MFE	-37.28
Consensus MFE	-27.25
Energy contribution	-28.00
Covariance contribution	0.75
Combinations/Pair	1.09
Mean z-score	-1.41
Structure conservation index	0.73
SVM decision value	-0.02
SVM RNA-class probability	0.523243
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 5102447 118 - 23771897
UGGGCGGCUUAAAGGGGGUGUACAUAGUGGAUAAAGGGGGAACAGAGAUAGCAAACAUGGCGCAAAAAGUGUACUUUGUUUGCAUAUGUCUGACCUUUUGCA-UCGCACUCGGCACGUG-
...((((((......((((((.(.....)(((.((((((...((((.((((((((((..((((.....))))....))))))).))).)))).))))))..)-))))))))))).))).- ( -37.80)
>DroSec_CAF1 295469 119 - 1
UGGGCGGCUUAAAGGGGGUGUGCACAAUGGAUAAAGGGGGAACAGAGCUAGCAAACAUGGGGCAAAAGGCGUACUUUGUUUGCAUAUGUCUGUCCUUUUGAACUCGCACUCGGCACGUG-
...((((((......(((((((......(..(((((((...(((((..(((((((((.((.((.....))...)).))))))).))..))))))))))))..).)))))))))).))).- ( -34.00)
>DroSim_CAF1 317078 119 - 1
UGGGCGGCUUAAAGGGGGUGUGCACAAUGGAUAAGGGGGGAACAGAGAUAGCAAACAUGGCGCAAAAAGCGUACUUUGUUUGCAUAUGUCUGACCUUUUGCACUCGCACUCGGCACGUG-
...((((((......(((((((......(..(((((((....((((.((((((((((..((((.....))))....))))))).))).)))).)))))))..).)))))))))).))).- ( -40.60)
>DroYak_CAF1 307756 109 - 1
UGGGUG----------GUUGUACACCAUGGAUGGAGGGGGAAGAGAGAUAGCAAACAUGGCGCAAAAAGCGUACUUUGUUUGCAUAUGUGUGACCUUUCGCA-UCGCACUUGGCACGUGU
..((((----------......))))...((((((((((..(.(.(.((.(((((((..((((.....))))....))))))))).).).)..)))))).))-))((((.......)))) ( -36.70)
>consensus
UGGGCGGCUUAAAGGGGGUGUACACAAUGGAUAAAGGGGGAACAGAGAUAGCAAACAUGGCGCAAAAAGCGUACUUUGUUUGCAUAUGUCUGACCUUUUGCA_UCGCACUCGGCACGUG_
...................((((....((((..((((((...((((.((((((((((..((((.....))))....))))))).))).)))).))))))....)).))....)))).... (-27.25 = -28.00 +   0.75)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:17:33 2006