Locus 1798

Sequence ID	3L_DroMel_CAF1
Location	5,076,305 – 5,076,542
Length	237
Max. P	0.969257

overview

Window 3

Location	5,076,305 – 5,076,423
Length	118
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	96.04
Mean single sequence MFE	-29.96
Consensus MFE	-28.26
Energy contribution	-29.18
Covariance contribution	0.92
Combinations/Pair	1.06
Mean z-score	-1.08
Structure conservation index	0.94
SVM decision value	-0.00
SVM RNA-class probability	0.531530
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 5076305 118 - 23771897
UUCGUGAUGGCAAUAGAGUGCAUCAUUGUGCCACUUGAAAAACUUUGAUUAAAAUCCUUUUGAAGUGCAAACAAAUAGCGCGGGACAAAAGUAUCUGCAGCUUGGAGCUGCCCAGAGA--
((((.(.(((((...((.....))....)))))).))))...(((((.........((((((..((((.........))))....)))))).....(((((.....))))).))))).-- ( -29.50)
>DroSec_CAF1 282701 118 - 1
UUCGAGAUGGCAAUAGAGUGCAUCAUUGUGCCACUUGAAAAACUUUGAUUAAAAUCCUUUUGAAGUGCAAACAAAUAGCGCGGGACAAAAGUAUCUGCAGCUUGGAGCUGCCCAGAGA--
((((((.(((((...((.....))....)))))))))))...(((((.........((((((..((((.........))))....)))))).....(((((.....))))).))))).-- ( -34.00)
>DroSim_CAF1 303979 118 - 1
UUCGAGAUGGCAAUAGAGUGCAUCAUUGUGCCACUUGAAAAACUUUGAUUAAAAUCCUUUUGAAGUGCAAACAAAUAGCGCGGGACAAAAGUAUCUGCAGCUUGGAGCUGCCCAGAGA--
((((((.(((((...((.....))....)))))))))))...(((((.........((((((..((((.........))))....)))))).....(((((.....))))).))))).-- ( -34.00)
>DroEre_CAF1 289754 118 - 1
UUCUAGAUGGCAAUAGAGUGCAUCAUUGUGCCACUUGAAAAACUUUGAUUAAAAUCCUUUUGAAGUGCAAACAAAUAGCGCGGGACAAAAGUAUCUGCAUCUUGGAGCUGCCCAGAGA--
(((.((.(((((...((.....))....))))))).)))...(((((.........((((((..((((.........))))....)))))).....(((.(.....).))).))))).-- ( -23.60)
>DroYak_CAF1 293915 120 - 1
UUGGGGAUGGCAAUAGAGUGCAUCAUUGUGCCACUUGAAAAACUUUGAUUAAAAUCCUUUUGAAGUGCAAACAAAUAGCGGGGGACAAAAGUAUCUGCAGCUCGGUGCUGGCCAAAGAGU
....((..((((...((((......((((..(((((.((((...((......))...)))).)))))...))))...(((((..((....)).))))).))))..))))..))....... ( -28.70)
>consensus
UUCGAGAUGGCAAUAGAGUGCAUCAUUGUGCCACUUGAAAAACUUUGAUUAAAAUCCUUUUGAAGUGCAAACAAAUAGCGCGGGACAAAAGUAUCUGCAGCUUGGAGCUGCCCAGAGA__
((((((.(((((...((.....))....)))))))))))...(((((.........((((((..((((.........))))....)))))).....(((((.....))))).)))))... (-28.26 = -29.18 +   0.92)

alignment

secondary structure

dotplot

Window 4

Location	5,076,343 – 5,076,462
Length	119
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	96.06
Mean single sequence MFE	-30.90
Consensus MFE	-25.28
Energy contribution	-25.56
Covariance contribution	0.28
Combinations/Pair	1.06
Mean z-score	-1.59
Structure conservation index	0.82
SVM decision value	0.22
SVM RNA-class probability	0.640015
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 5076343 119 + 23771897
CGCUAUUUGUUUGCACUUCAAAAGGAUUUUAAUCAAAGUUUUUCAAGUGGCACAAUGAUGCACUCUAUUGCCAUCACGAAAGUAGCUGG-UUUCCUUGGCGAAAAAUGCAGACAGAGUGA
((((...((((((((.(((..(((((....(((((....(((((..((((((....((.....))...))))))...)))))....)))-)))))))...)))...)))))))).)))). ( -30.70)
>DroSec_CAF1 282739 119 + 1
CGCUAUUUGUUUGCACUUCAAAAGGAUUUUAAUCAAAGUUUUUCAAGUGGCACAAUGAUGCACUCUAUUGCCAUCUCGAAAGUUGCUGG-UUUCCUUGGCGAAAAAUGCAGACAGAGUGA
((((...((((((((.(((..(((((....(((((....(((((.(((((((....((.....))...))))).)).)))))....)))-)))))))...)))...)))))))).)))). ( -31.70)
>DroSim_CAF1 304017 119 + 1
CGCUAUUUGUUUGCACUUCAAAAGGAUUUUAAUCAAAGUUUUUCAAGUGGCACAAUGAUGCACUCUAUUGCCAUCUCGAAAGUUGCUGG-UUUCCUUGGCGAAAAAUGCAGACAGAGUGA
((((...((((((((.(((..(((((....(((((....(((((.(((((((....((.....))...))))).)).)))))....)))-)))))))...)))...)))))))).)))). ( -31.70)
>DroEre_CAF1 289792 119 + 1
CGCUAUUUGUUUGCACUUCAAAAGGAUUUUAAUCAAAGUUUUUCAAGUGGCACAAUGAUGCACUCUAUUGCCAUCUAGAAAGUUGCUGG-UUUCCUUGGCGAAAACUGAGGACAGAGUGA
.((((((((...((.((.....))(((....)))...))....)))))))).........((((((...((((.(.........).)))-).((((..(......)..)))).)))))). ( -27.30)
>DroYak_CAF1 293955 120 + 1
CGCUAUUUGUUUGCACUUCAAAAGGAUUUUAAUCAAAGUUUUUCAAGUGGCACAAUGAUGCACUCUAUUGCCAUCCCCAAAGUUGCUGCCUUUCGUUGGCGAAAAACGCAGACAGAGUGA
((((...(((((((..........(((....)))...(((((((.((..((.....((((((......)).))))......))..))(((.......))))))))))))))))).)))). ( -33.10)
>consensus
CGCUAUUUGUUUGCACUUCAAAAGGAUUUUAAUCAAAGUUUUUCAAGUGGCACAAUGAUGCACUCUAUUGCCAUCUCGAAAGUUGCUGG_UUUCCUUGGCGAAAAAUGCAGACAGAGUGA
((((...(((((((..........(((....)))...(((((((..((((((....((.....))...))))))..........(((((......))))))))))))))))))).)))). (-25.28 = -25.56 +   0.28)

alignment

secondary structure

dotplot

Window 5

Location	5,076,423 – 5,076,542
Length	119
Sequences	4
Columns	119
Reading direction	reverse
Mean pairwise identity	91.35
Mean single sequence MFE	-21.72
Consensus MFE	-18.05
Energy contribution	-19.05
Covariance contribution	1.00
Combinations/Pair	1.00
Mean z-score	-2.67
Structure conservation index	0.83
SVM decision value	1.64
SVM RNA-class probability	0.969257
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 5076423 119 - 23771897
AAAACAAGAGCUGGGUAUAAAAAAAAAAAAAGAAAAACGAAAAUAAUAAUUAAAUCACUGUGAAUAACGGCAGAUAAAUCUCACUCUGUCUGCAUUUUUCGCCAAGGAAACCAGCUACU
........((((((.................(.....)................((...(((((.....(((((((..........)))))))....)))))....))..))))))... ( -21.40)
>DroSec_CAF1 282819 116 - 1
AAAACAAGAGCUGGGUAUAAAAA---AUAAAGAAAAAUGAAAAUGAUAAUUAAAUCACUGUGAAUAACGGCAGAUAAAUCUCACUCUGUCUGCAUUUUUCGCCAAGGAAACCAGCAACU
.........(((((.........---.................((((......))))..(((((.....(((((((..........)))))))....)))))........))))).... ( -23.60)
>DroSim_CAF1 304097 116 - 1
AAAACAAGAGCUGGGUAUAAAAA---AUAAAGAAAAAUGAAAAUGAUAAUUAAAUCACUGUGAAUAACGGCAGAUAAAUCUCACUCUGUCUGCAUUUUUCGCCAAGGAAACCAGCAACU
.........(((((.........---.................((((......))))..(((((.....(((((((..........)))))))....)))))........))))).... ( -23.60)
>DroEre_CAF1 289872 112 - 1
AAAACAAAAACUGGGUAGAA-------AAAUAAAAAAUGAAAAUGAUAAUUAAAUCACAGUGAAUAACGGCAGAUAAAUCUCACUCUGUCCUCAGUUUUCGCCAAGGAAACCAGCAACU
......(((((((((.....-------................((((......))))...........((((((..........))))))))))))))).((...(....)..)).... ( -18.30)
>consensus
AAAACAAGAGCUGGGUAUAAAAA___AAAAAGAAAAAUGAAAAUGAUAAUUAAAUCACUGUGAAUAACGGCAGAUAAAUCUCACUCUGUCUGCAUUUUUCGCCAAGGAAACCAGCAACU
.........(((((.............................((((......))))..(((((.....(((((((..........)))))))....)))))........))))).... (-18.05 = -19.05 +   1.00)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:16:50 2006