Locus 3919

Sequence ID	3R_DroMel_CAF1
Location	10,661,697 – 10,661,830
Length	133
Max. P	0.988138

overview

Window 6

Location	10,661,697 – 10,661,817
Length	120
Sequences	3
Columns	120
Reading direction	forward
Mean pairwise identity	93.22
Mean single sequence MFE	-37.08
Consensus MFE	-34.75
Energy contribution	-35.09
Covariance contribution	0.33
Combinations/Pair	1.00
Mean z-score	-3.25
Structure conservation index	0.94
SVM decision value	2.11
SVM RNA-class probability	0.988138
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 10661697 120 + 27905053
UUUAAAUUUCAUUCAGUUCAGCAGUUCAGUUUUCUCCUGUGUAGACCAGAAAACGACUUAACACACGUCGUAUGCGCAAUAUUCAUGAGCUGAGCUGCAUUACGCAUACGCCAGGUGUGC
...............((...((((((((((((.....((((((.........(((((.........))))).))))))........))))))))))))...))((((((.....)))))) ( -33.12)
>DroSec_CAF1 3362 114 + 1
UUUAAAUUUUGUUU------GCAGUUCAGUUUUCUCCUGUGUAGACCAGAAAACGACUUGACACAAGUCGUAUGCGCAAUAUUCAUGAGCUGAGCUGCAUUACGCAUACGCCAGGUGUGC
..........((.(------((((((((((((.....((((((.........((((((((...)))))))).))))))........)))))))))))))..))((((((.....)))))) ( -38.72)
>DroSim_CAF1 3412 114 + 1
UUUAAAUUUUGUUU------GCAGUUCAGUUUUCUUCUGUGUAGACCAGAAAACGACUUGACACAAGUCGUAUGCGCAAUAUUCAUGAGCUGAGCUGCAUUACGCAUACGCCAGGUGUGC
..........((.(------((((((((((((..(((((.(....)))))).((((((((...))))))))...............)))))))))))))..))((((((.....)))))) ( -39.40)
>consensus
UUUAAAUUUUGUUU______GCAGUUCAGUUUUCUCCUGUGUAGACCAGAAAACGACUUGACACAAGUCGUAUGCGCAAUAUUCAUGAGCUGAGCUGCAUUACGCAUACGCCAGGUGUGC
....................((((((((((((.....((((((.........(((((((.....))))))).))))))........)))))))))))).....((((((.....)))))) (-34.75 = -35.09 +   0.33)

alignment

secondary structure

dotplot

Window 7

Location	10,661,697 – 10,661,817
Length	120
Sequences	3
Columns	120
Reading direction	reverse
Mean pairwise identity	93.22
Mean single sequence MFE	-34.53
Consensus MFE	-32.39
Energy contribution	-32.17
Covariance contribution	-0.22
Combinations/Pair	1.03
Mean z-score	-2.75
Structure conservation index	0.94
SVM decision value	1.79
SVM RNA-class probability	0.977503
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 10661697 120 - 27905053
GCACACCUGGCGUAUGCGUAAUGCAGCUCAGCUCAUGAAUAUUGCGCAUACGACGUGUGUUAAGUCGUUUUCUGGUCUACACAGGAGAAAACUGAACUGCUGAACUGAAUGAAAUUUAAA
((((((....(((((((((((((....(((.....))).)))))))))))))..))))(((.(((..(((((((.......)))))))..))).))).)).................... ( -34.70)
>DroSec_CAF1 3362 114 - 1
GCACACCUGGCGUAUGCGUAAUGCAGCUCAGCUCAUGAAUAUUGCGCAUACGACUUGUGUCAAGUCGUUUUCUGGUCUACACAGGAGAAAACUGAACUGC------AAACAAAAUUUAAA
((((((..(((((((((((((((....(((.....))).))))))))))))).)).)))(((.((..(((((((.......)))))))..)))))..)))------.............. ( -34.20)
>DroSim_CAF1 3412 114 - 1
GCACACCUGGCGUAUGCGUAAUGCAGCUCAGCUCAUGAAUAUUGCGCAUACGACUUGUGUCAAGUCGUUUUCUGGUCUACACAGAAGAAAACUGAACUGC------AAACAAAAUUUAAA
((((((..(((((((((((((((....(((.....))).))))))))))))).)).)))(((.((..(((((((.......)))))))..)))))..)))------.............. ( -34.70)
>consensus
GCACACCUGGCGUAUGCGUAAUGCAGCUCAGCUCAUGAAUAUUGCGCAUACGACUUGUGUCAAGUCGUUUUCUGGUCUACACAGGAGAAAACUGAACUGC______AAACAAAAUUUAAA
((((((..(.(((((((((((((....(((.....))).))))))))))))).)..))))..(((..(((((((.......)))))))..))).....)).................... (-32.39 = -32.17 +  -0.22)

alignment

secondary structure

dotplot

Window 8

Location	10,661,737 – 10,661,830
Length	93
Sequences	3
Columns	93
Reading direction	reverse
Mean pairwise identity	98.57
Mean single sequence MFE	-29.40
Consensus MFE	-27.45
Energy contribution	-27.57
Covariance contribution	0.11
Combinations/Pair	1.03
Mean z-score	-1.67
Structure conservation index	0.93
SVM decision value	0.11
SVM RNA-class probability	0.588731
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 10661737 93 - 27905053
AUUGGCAGUCGCUGCACACCUGGCGUAUGCGUAAUGCAGCUCAGCUCAUGAAUAUUGCGCAUACGACGUGUGUUAAGUCGUUUUCUGGUCUAC
.....(((.((((((((((....(((((((((((((....(((.....))).)))))))))))))..))))))..)).))....)))...... ( -30.00)
>DroSec_CAF1 3396 93 - 1
AUUGGCAGUCGCUGCACACCUGGCGUAUGCGUAAUGCAGCUCAGCUCAUGAAUAUUGCGCAUACGACUUGUGUCAAGUCGUUUUCUGGUCUAC
....((((...))))..(((.(((((((((((((((....(((.....))).))))))))))))((((((...)))))))))....))).... ( -29.10)
>DroSim_CAF1 3446 93 - 1
AUUGGCAGUCGCUGCACACCUGGCGUAUGCGUAAUGCAGCUCAGCUCAUGAAUAUUGCGCAUACGACUUGUGUCAAGUCGUUUUCUGGUCUAC
....((((...))))..(((.(((((((((((((((....(((.....))).))))))))))))((((((...)))))))))....))).... ( -29.10)
>consensus
AUUGGCAGUCGCUGCACACCUGGCGUAUGCGUAAUGCAGCUCAGCUCAUGAAUAUUGCGCAUACGACUUGUGUCAAGUCGUUUUCUGGUCUAC
....((((...))))..(((.(((((((((((((((....(((.....))).))))))))))))((((((...)))))))))....))).... (-27.45 = -27.57 +   0.11)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:13:23 2006