Locus 1022

Sequence ID	2L_DroMel_CAF1
Location	2,909,056 – 2,909,199
Length	143
Max. P	0.984176

overview

Window 7

Location	2,909,056 – 2,909,165
Length	109
Sequences	3
Columns	109
Reading direction	forward
Mean pairwise identity	86.03
Mean single sequence MFE	-30.07
Consensus MFE	-24.09
Energy contribution	-23.87
Covariance contribution	-0.22
Combinations/Pair	1.05
Mean z-score	-3.27
Structure conservation index	0.80
SVM decision value	1.63
SVM RNA-class probability	0.968815
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 2909056 109 + 22407834
UUGUUGUUGGCAUCAGCUCAUUUAGCUGAUGCUACAUUUUCUUCUUGUUGUUGUUGCUGUUUUCCCUCUCUUUGGGGCUUUGUGGAAUAUAGACACCGAAUAAAACCAA
....(((.((((((((((.....)))))))))))))..........(((.(((.((((((.(((((.(((....)))....).)))).)))).)).)))....)))... ( -28.00)
>DroEre_CAF1 28297 97 + 1
UUGUUUUUGGCAUCAGCUCAUUUAGCUGAUGCUACAUUUUG------------UUGUUGUUUUUCCCCUCUUUGGGGCUUUGAGGCAUAUAGACACCGAAUAAAACCGA
((((((.(((((((((((.....))))))))))).....((------------((..((((((.((((.....))))....))))))....))))..))))))...... ( -30.70)
>DroYak_CAF1 28580 96 + 1
UUGUUGUUGGCAUCAGCUCAUUUAGCUGAUGCUACAUUUUG------------UUGUUGUU-UUCCCCUCUUUGGGGCUUUGUGGAAUAUAGACAGCGAAUAAAACCGA
....(((.((((((((((.....)))))))))))))(((((------------((((((((-(.((((.....))))((....)).....))))))).))))))).... ( -31.50)
>consensus
UUGUUGUUGGCAUCAGCUCAUUUAGCUGAUGCUACAUUUUG____________UUGUUGUUUUUCCCCUCUUUGGGGCUUUGUGGAAUAUAGACACCGAAUAAAACCGA
.((((..(((((((((((.....)))))))))))..............................((((.....))))..............)))).............. (-24.09 = -23.87 +  -0.22)

alignment

secondary structure

dotplot

Window 8

Location	2,909,056 – 2,909,165
Length	109
Sequences	3
Columns	109
Reading direction	reverse
Mean pairwise identity	86.03
Mean single sequence MFE	-24.64
Consensus MFE	-19.69
Energy contribution	-19.80
Covariance contribution	0.11
Combinations/Pair	1.05
Mean z-score	-2.97
Structure conservation index	0.80
SVM decision value	1.41
SVM RNA-class probability	0.951587
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 2909056 109 - 22407834
UUGGUUUUAUUCGGUGUCUAUAUUCCACAAAGCCCCAAAGAGAGGGAAAACAGCAACAACAACAAGAAGAAAAUGUAGCAUCAGCUAAAUGAGCUGAUGCCAACAACAA
((((((((.(((..(((...............(((........)))...............))).))).)))))...(((((((((.....)))))))))...)))... ( -23.01)
>DroEre_CAF1 28297 97 - 1
UCGGUUUUAUUCGGUGUCUAUAUGCCUCAAAGCCCCAAAGAGGGGAAAAACAACAA------------CAAAAUGUAGCAUCAGCUAAAUGAGCUGAUGCCAAAAACAA
...(((((....(((((....)))))......((((.....)))).))))).....------------.........(((((((((.....)))))))))......... ( -27.10)
>DroYak_CAF1 28580 96 - 1
UCGGUUUUAUUCGCUGUCUAUAUUCCACAAAGCCCCAAAGAGGGGAA-AACAACAA------------CAAAAUGUAGCAUCAGCUAAAUGAGCUGAUGCCAACAACAA
...(((((......(((.........)))...((((.....))))))-))).....------------.....(((.(((((((((.....)))))))))..))).... ( -23.80)
>consensus
UCGGUUUUAUUCGGUGUCUAUAUUCCACAAAGCCCCAAAGAGGGGAAAAACAACAA____________CAAAAUGUAGCAUCAGCUAAAUGAGCUGAUGCCAACAACAA
.(((......))).(((...............((((.....))))................................(((((((((.....))))))))).....))). (-19.69 = -19.80 +   0.11)

alignment

secondary structure

dotplot

Window 9

Location	2,909,096 – 2,909,199
Length	103
Sequences	3
Columns	103
Reading direction	forward
Mean pairwise identity	83.84
Mean single sequence MFE	-24.48
Consensus MFE	-18.23
Energy contribution	-17.90
Covariance contribution	-0.33
Combinations/Pair	1.11
Mean z-score	-1.83
Structure conservation index	0.74
SVM decision value	0.21
SVM RNA-class probability	0.636108
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 2909096 103 + 22407834
CUUCUUGUUGUUGUUGCUGUUUUCCCUCUCUUUGGGGCUUUGUGGAAUAUAGACACCGAAUAAAACCAAAAAGAGGGAAAAUACCCAAAACUUAUCGAGUUUA
...((((..(((...(.((((((((((((.(((((.......(((..........))).......))))).)))))))))))).)...)))....)))).... ( -28.44)
>DroEre_CAF1 28337 91 + 1
G------------UUGUUGUUUUUCCCCUCUUUGGGGCUUUGAGGCAUAUAGACACCGAAUAAAACCGAAAAGAGGGAAAACACCCAAAACUUAUCGAGUUUA
(------------((..((((((.((((.....))))....))))))....)))........(((((((.(((.(((......)))....))).))).)))). ( -21.70)
>DroYak_CAF1 28620 90 + 1
G------------UUGUUGUU-UUCCCCUCUUUGGGGCUUUGUGGAAUAUAGACAGCGAAUAAAACCGAAAAGAGGGAGAAUACCCGAAACUUAUCGAGUUUA
.------------((((((((-(.((((.....))))((....)).....)))))))))...(((((((.(((.(((......)))....))).))).)))). ( -23.30)
>consensus
G____________UUGUUGUUUUUCCCCUCUUUGGGGCUUUGUGGAAUAUAGACACCGAAUAAAACCGAAAAGAGGGAAAAUACCCAAAACUUAUCGAGUUUA
.................(((((((((.((.(((((...((((..(........)..)))).....))))).)).)))))))))....((((((...)))))). (-18.23 = -17.90 +  -0.33)

alignment

secondary structure

dotplot

Window 0

Location	2,909,096 – 2,909,199
Length	103
Sequences	3
Columns	103
Reading direction	reverse
Mean pairwise identity	83.84
Mean single sequence MFE	-26.88
Consensus MFE	-20.25
Energy contribution	-20.92
Covariance contribution	0.67
Combinations/Pair	1.08
Mean z-score	-3.34
Structure conservation index	0.75
SVM decision value	1.97
SVM RNA-class probability	0.984176
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 2909096 103 - 22407834
UAAACUCGAUAAGUUUUGGGUAUUUUCCCUCUUUUUGGUUUUAUUCGGUGUCUAUAUUCCACAAAGCCCCAAAGAGAGGGAAAACAGCAACAACAACAAGAAG
...((((((......)))))).((((((((((((((((..((.....(((.........)))..))..))))))))))))))))................... ( -28.00)
>DroEre_CAF1 28337 91 - 1
UAAACUCGAUAAGUUUUGGGUGUUUUCCCUCUUUUCGGUUUUAUUCGGUGUCUAUAUGCCUCAAAGCCCCAAAGAGGGGAAAAACAACAA------------C
...((((((......)))))).((((((((((((..((((((....(((((....)))))..))))))..))))))))))))........------------. ( -28.40)
>DroYak_CAF1 28620 90 - 1
UAAACUCGAUAAGUUUCGGGUAUUCUCCCUCUUUUCGGUUUUAUUCGCUGUCUAUAUUCCACAAAGCCCCAAAGAGGGGAA-AACAACAA------------C
...((((((......)))))).(((.((((((((..((((((....................))))))..)))))))))))-........------------. ( -24.25)
>consensus
UAAACUCGAUAAGUUUUGGGUAUUUUCCCUCUUUUCGGUUUUAUUCGGUGUCUAUAUUCCACAAAGCCCCAAAGAGGGGAAAAACAACAA____________C
...((((((......)))))).((((((((((((..((((((....................))))))..))))))))))))..................... (-20.25 = -20.92 +   0.67)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:51:16 2006