Locus 5024

Sequence ID	2L_DroMel_CAF1
Location	14,411,530 – 14,411,641
Length	111
Max. P	0.861162

overview

Window 6

Location	14,411,530 – 14,411,624
Length	94
Sequences	5
Columns	94
Reading direction	forward
Mean pairwise identity	91.70
Mean single sequence MFE	-18.82
Consensus MFE	-13.89
Energy contribution	-14.22
Covariance contribution	0.33
Combinations/Pair	1.08
Mean z-score	-2.43
Structure conservation index	0.74
SVM decision value	0.83
SVM RNA-class probability	0.861162
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 14411530 94 + 22407834
AUUAACCACACAAAAAGUAUAUGUCGUUUUCGCUCUCUGGGUAAACCACAAAAUUAAGUGGCUAACAGUAUUUUGUGGCCACAACACAUUACAA
................(((.((((.(((.........(((.....))).........(((((((.(((....)))))))))))))))))))).. ( -19.50)
>DroSec_CAF1 2089 94 + 1
AUUAACCACACAAAAAGUAUAUGUCGUUCUCGCUCUCCGGGUAAACCACAAAAUUAAGUGGCUAACAGUAUUUUGUGGCCACAACACAUUACAA
................(((.((((.(((..........((.....))..........(((((((.(((....)))))))))))))))))))).. ( -19.30)
>DroSim_CAF1 3169 94 + 1
AUUAACCACACAAAAAGUAUAUGUCGUUCUCGCUCUCCGGGUAAACCACAAAAUUAAGUGGCUAACAGUAUUUUGUGGCCACAACACAUUACAA
................(((.((((.(((..........((.....))..........(((((((.(((....)))))))))))))))))))).. ( -19.30)
>DroEre_CAF1 3324 93 + 1
AUUAACCACACAA-AAGUAUAUGUCGUUCUCGCUCUCUGGGCAAACCACAAAAUUAAGUGGCUAACAGUAUUUUGUGGCCACAACACAUUACAA
.............-..(((.((((.(((...(((.....)))...............(((((((.(((....)))))))))))))))))))).. ( -20.80)
>DroYak_CAF1 3405 84 + 1
AUUAACCACACAAAAAGUAUAUAUCGCUCCCGCUCUCUGGGUGAACCGCAAAAUUAAG----------UAUUUUGUGGCCACAACACAUUACAA
................(((....((((((.........)))))).(((((((((....----------.)))))))))...........))).. ( -15.20)
>consensus
AUUAACCACACAAAAAGUAUAUGUCGUUCUCGCUCUCUGGGUAAACCACAAAAUUAAGUGGCUAACAGUAUUUUGUGGCCACAACACAUUACAA
................(((.((((.(((...(((.....)))...(((((((((...((.....))...)))))))))....)))))))))).. (-13.89 = -14.22 +   0.33)

alignment

secondary structure

dotplot

Window 7

Location	14,411,549 – 14,411,641
Length	92
Sequences	6
Columns	95
Reading direction	forward
Mean pairwise identity	78.35
Mean single sequence MFE	-21.03
Consensus MFE	-11.38
Energy contribution	-12.70
Covariance contribution	1.32
Combinations/Pair	1.20
Mean z-score	-2.04
Structure conservation index	0.54
SVM decision value	0.59
SVM RNA-class probability	0.792177
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 14411549 92 + 22407834
UAUGUCGUUUUCGCUCUC-UGGGUAAACCACAAAAUUAAGUGGCUAACAGUAUUUUGUGGCCACAACACAUUACAAACCACACAAGCGAACUG--
.........((((((...-(((.....))).........(((((((.(((....))))))))))....................))))))...-- ( -21.60)
>DroVir_CAF1 14453 73 + 1
UAUAU---UUU-UGUGUGUUGUGCCGACCACAAAAUUAAGUGGCUAACUGAA-UUUGCGGCCACA---------------CACAUGUGGGCAG--
.....---...-(((((((.(.((((......(((((.(((.....))).))-))).))))))))---------------)))).........-- ( -19.10)
>DroSec_CAF1 2108 92 + 1
UAUGUCGUUCUCGCUCUC-CGGGUAAACCACAAAAUUAAGUGGCUAACAGUAUUUUGUGGCCACAACACAUUACAAACCACACAAGCGAACUG--
..........(((((...-.((.....))..........(((((((.(((....))))))))))....................)))))....-- ( -20.70)
>DroSim_CAF1 3188 92 + 1
UAUGUCGUUCUCGCUCUC-CGGGUAAACCACAAAAUUAAGUGGCUAACAGUAUUUUGUGGCCACAACACAUUACAAACCACACAAGCGAACUG--
..........(((((...-.((.....))..........(((((((.(((....))))))))))....................)))))....-- ( -20.70)
>DroEre_CAF1 3342 94 + 1
UAUGUCGUUCUCGCUCUC-UGGGCAAACCACAAAAUUAAGUGGCUAACAGUAUUUUGUGGCCACAACACAUUACAAACCCCACAAGCGAACUGUU
..........(((((...-((((....((((........))))......(((...((((.......)))).)))....))))..)))))...... ( -21.80)
>DroYak_CAF1 3424 82 + 1
UAUAUCGCUCCCGCUCUC-UGGGUGAACCGCAAAAUUAAG----------UAUUUUGUGGCCACAACACAUUACAAAACCCACAAGCGGACUG--
..........(((((...-(((((...(((((((((....----------.))))))))).................)))))..)))))....-- ( -22.25)
>consensus
UAUGUCGUUCUCGCUCUC_UGGGUAAACCACAAAAUUAAGUGGCUAACAGUAUUUUGUGGCCACAACACAUUACAAACCACACAAGCGAACUG__
....(((((...((((....))))...(((((((((...((.....))...)))))))))........................)))))...... (-11.38 = -12.70 +   1.32)

alignment

secondary structure

dotplot

Window 8

Location	14,411,549 – 14,411,641
Length	92
Sequences	6
Columns	95
Reading direction	reverse
Mean pairwise identity	78.35
Mean single sequence MFE	-25.62
Consensus MFE	-14.81
Energy contribution	-16.28
Covariance contribution	1.46
Combinations/Pair	1.24
Mean z-score	-1.99
Structure conservation index	0.58
SVM decision value	0.76
SVM RNA-class probability	0.843163
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 14411549 92 - 22407834
--CAGUUCGCUUGUGUGGUUUGUAAUGUGUUGUGGCCACAAAAUACUGUUAGCCACUUAAUUUUGUGGUUUACCCA-GAGAGCGAAAACGACAUA
--...(((((((.(((((.(..(((....)))..)))))).....(((..((((((........))))))....))-).)))))))......... ( -27.10)
>DroVir_CAF1 14453 73 - 1
--CUGCCCACAUGUG---------------UGUGGCCGCAAA-UUCAGUUAGCCACUUAAUUUUGUGGUCGGCACAACACACA-AAA---AUAUA
--.........((((---------------(((.((((....-........(((((........)))))))))...)))))))-...---..... ( -22.30)
>DroSec_CAF1 2108 92 - 1
--CAGUUCGCUUGUGUGGUUUGUAAUGUGUUGUGGCCACAAAAUACUGUUAGCCACUUAAUUUUGUGGUUUACCCG-GAGAGCGAGAACGACAUA
--...(((((((.(((((.(..(((....)))..)))))).....(((..((((((........))))))....))-).)))))))......... ( -26.10)
>DroSim_CAF1 3188 92 - 1
--CAGUUCGCUUGUGUGGUUUGUAAUGUGUUGUGGCCACAAAAUACUGUUAGCCACUUAAUUUUGUGGUUUACCCG-GAGAGCGAGAACGACAUA
--...(((((((.(((((.(..(((....)))..)))))).....(((..((((((........))))))....))-).)))))))......... ( -26.10)
>DroEre_CAF1 3342 94 - 1
AACAGUUCGCUUGUGGGGUUUGUAAUGUGUUGUGGCCACAAAAUACUGUUAGCCACUUAAUUUUGUGGUUUGCCCA-GAGAGCGAGAACGACAUA
.....(((((((...(((((..(((.((...(((((.(((......)))..)))))...)).)))..)...)))).-..)))))))......... ( -27.40)
>DroYak_CAF1 3424 82 - 1
--CAGUCCGCUUGUGGGUUUUGUAAUGUGUUGUGGCCACAAAAUA----------CUUAAUUUUGCGGUUCACCCA-GAGAGCGGGAGCGAUAUA
--...(((((((.(((((.((((((.(((((.((....)).))))----------)......))))))...)))))-..)))))))......... ( -24.70)
>consensus
__CAGUUCGCUUGUGUGGUUUGUAAUGUGUUGUGGCCACAAAAUACUGUUAGCCACUUAAUUUUGUGGUUUACCCA_GAGAGCGAGAACGACAUA
.....(((((((.((.(((..............(((((((((((...((.....))...))))))))))).)))))...)))))))......... (-14.81 = -16.28 +   1.46)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:33:47 2006