Locus 1428

Sequence ID	3L_DroMel_CAF1
Location	4,147,497 – 4,147,630
Length	133
Max. P	0.992341

overview

Window 9

Location	4,147,497 – 4,147,596
Length	99
Sequences	6
Columns	99
Reading direction	forward
Mean pairwise identity	77.10
Mean single sequence MFE	-37.20
Consensus MFE	-22.19
Energy contribution	-23.75
Covariance contribution	1.56
Combinations/Pair	1.29
Mean z-score	-1.40
Structure conservation index	0.60
SVM decision value	-0.03
SVM RNA-class probability	0.520590
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 4147497 99 + 23771897
GGUGGUGGCGGUGGUGGAGAUGGCGAGUUCAGAGUGCUCUCCGCAAAGGAUAUGAUUUGAGAGAGGAAGUCACCACCUCCUCCGCCUCCAGAGGUCGAA
((.(((((.((.(((((.(((..((....)......(((((..((((........)))).))))))..))).))))).)).))))).)).......... ( -37.90)
>DroVir_CAF1 47701 96 + 1
GGCGGUGGAGCCGGUGCUGAGGGUGAGUUGAGCGUGCUCUCCGCAAAGGAUAUGAACUGGGAGAGCAGAUCCCCGCCAGAC---UGUGCAGGCGACGCG
....(((..(((.(..(....((((.(..((...((((((((....((........)).))))))))..)).)))))....---.)..).)))..))). ( -35.50)
>DroSim_CAF1 24776 99 + 1
GGUGGCGGCGGUGGUGGAGAUGGCGAGUUCAGAGUGCUCUCCGCAAAGGAUAUGAUUUGAGAGAGGAAGUCACCACCUCCUCCGCCUCCAGAGGACGAA
((.(((((.((.(((((.(((..((....)......(((((..((((........)))).))))))..))).))))).)).))))).)).......... ( -39.80)
>DroEre_CAF1 25719 99 + 1
GGUGGCUGUGGUGGUGAAGAUGGGGAGUUCAGAGUGCUCUCCGCAAAGGAUAUGAUUUGCGAGAGGAAGUCACCACCUCCUCCGCCUCCAGAGCUCGAA
(((((..(.((((((((....(((((((.......)))))))(((((........))))).........)))))))).)..)))))............. ( -39.60)
>DroYak_CAF1 24265 97 + 1
GGUGGCGGCGGUGGUGGAGAUGGCGAGUUCAGAGUGCUCUCCGCAAAGGAAAUGAUUUGGGAAAGGAAGUCCCCGCCUCCUCCGCCUCCAGAGGUCG--
((.(((((.((.(((((.(((..(((((.......))))(((.((((........)))))))...)..))).))))).)).))))).))........-- ( -41.10)
>DroAna_CAF1 26387 87 + 1
GGCGGGGGUGGUGGUGGAGCUGGCGAGUUCAGGGUGCUCUCGGCAAAGGAUAUGAUCUGGGAGAGGAGAUCU---------CCGCCCUGGG---UGGAU
..(.(((((((.......(((((.((((.......))))))))).........(((((........))))).---------))))))).).---..... ( -29.30)
>consensus
GGUGGCGGCGGUGGUGGAGAUGGCGAGUUCAGAGUGCUCUCCGCAAAGGAUAUGAUUUGGGAGAGGAAGUCACCACCUCCUCCGCCUCCAGAGGUCGAA
((.(((((.((.((((.....((.((((.......)))).))...........(((((........)))))..)))).)).))))).)).......... (-22.19 = -23.75 +   1.56)

alignment

secondary structure

dotplot

Window 0

Location	4,147,497 – 4,147,596
Length	99
Sequences	6
Columns	99
Reading direction	reverse
Mean pairwise identity	77.10
Mean single sequence MFE	-33.50
Consensus MFE	-18.74
Energy contribution	-20.97
Covariance contribution	2.23
Combinations/Pair	1.28
Mean z-score	-2.75
Structure conservation index	0.56
SVM decision value	2.06
SVM RNA-class probability	0.986945
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 4147497 99 - 23771897
UUCGACCUCUGGAGGCGGAGGAGGUGGUGACUUCCUCUCUCAAAUCAUAUCCUUUGCGGAGAGCACUCUGAACUCGCCAUCUCCACCACCGCCACCACC
.........(((.(((((.(((((((((((.(((((((((((((........)))).))))))......))).)))))))))))....))))).))).. ( -41.20)
>DroVir_CAF1 47701 96 - 1
CGCGUCGCCUGCACA---GUCUGGCGGGGAUCUGCUCUCCCAGUUCAUAUCCUUUGCGGAGAGCACGCUCAACUCACCCUCAGCACCGGCUCCACCGCC
.(((.....)))...---....((((((((.((((((((((((..........))).)))))))..(((............)))...)).))).))))) ( -31.10)
>DroSim_CAF1 24776 99 - 1
UUCGUCCUCUGGAGGCGGAGGAGGUGGUGACUUCCUCUCUCAAAUCAUAUCCUUUGCGGAGAGCACUCUGAACUCGCCAUCUCCACCACCGCCGCCACC
.........(((.(((((.(((((((((((.(((((((((((((........)))).))))))......))).)))))))))))....))))).))).. ( -41.70)
>DroEre_CAF1 25719 99 - 1
UUCGAGCUCUGGAGGCGGAGGAGGUGGUGACUUCCUCUCGCAAAUCAUAUCCUUUGCGGAGAGCACUCUGAACUCCCCAUCUUCACCACCACAGCCACC
........(((..((.((.((((((((.((.(((((((((((((........))))).)))))......))).)).)))))))).)).)).)))..... ( -32.40)
>DroYak_CAF1 24265 97 - 1
--CGACCUCUGGAGGCGGAGGAGGCGGGGACUUCCUUUCCCAAAUCAUUUCCUUUGCGGAGAGCACUCUGAACUCGCCAUCUCCACCACCGCCGCCACC
--.......(((.(((((.((((..((.((.(((((((((((((........)))).))))))......))).)).))..))))....))))).))).. ( -35.50)
>DroAna_CAF1 26387 87 - 1
AUCCA---CCCAGGGCGG---------AGAUCUCCUCUCCCAGAUCAUAUCCUUUGCCGAGAGCACCCUGAACUCGCCAGCUCCACCACCACCCCCGCC
.....---.....(((((---------.(((((........))))).......(((.((((..(.....)..)))).)))..............))))) ( -19.10)
>consensus
UUCGACCUCUGGAGGCGGAGGAGGUGGUGACUUCCUCUCCCAAAUCAUAUCCUUUGCGGAGAGCACUCUGAACUCGCCAUCUCCACCACCGCCGCCACC
.........(((.((.((.(((((.((.((.(((((((((((((........)))).))))))......))).)).)).))))).)).)).)))..... (-18.74 = -20.97 +   2.23)

alignment

secondary structure

dotplot

Window 1

Location	4,147,531 – 4,147,630
Length	99
Sequences	6
Columns	99
Reading direction	forward
Mean pairwise identity	75.02
Mean single sequence MFE	-41.12
Consensus MFE	-28.30
Energy contribution	-29.83
Covariance contribution	1.53
Combinations/Pair	1.36
Mean z-score	-1.90
Structure conservation index	0.69
SVM decision value	1.72
SVM RNA-class probability	0.973894
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 4147531 99 + 23771897
UGCUCUCCGCAAAGGAUAUGAUUUGAGAGAGGAAGUCACCACCUCCUCCGCCUCCAGAGGUCGAAGAUGGUGGUGCUGGCGGUGGAGACGCGGGACGAG
..((((((((...........(((....)))...(((.(((((.((..((((.(((...........))).))))..)).))))).))))))))..))) ( -37.00)
>DroVir_CAF1 47735 96 + 1
UGCUCUCCGCAAAGGAUAUGAACUGGGAGAGCAGAUCCCCGCCAGAC---UGUGCAGGCGACGCGGCUGCUGGUGCCGGAGCCGGCGCUGCGGGACGCG
((((((((....((........)).))))))))....(((((.....---...((((.((...)).)))).(((((((....))))))))))))..... ( -44.50)
>DroSim_CAF1 24810 99 + 1
UGCUCUCCGCAAAGGAUAUGAUUUGAGAGAGGAAGUCACCACCUCCUCCGCCUCCAGAGGACGAAGAUGGGGGUGGUGGCGGUGGGGACGCGGGACGAG
..((((((((...........(((....)))...(((.(((((.((.(((((((((...........))))))))).)).))))).))))))))..))) ( -44.20)
>DroEre_CAF1 25753 99 + 1
UGCUCUCCGCAAAGGAUAUGAUUUGCGAGAGGAAGUCACCACCUCCUCCGCCUCCAGAGCUCGAAGAUGGGGGUGGGGGCGGUGGAGAUGCGGGACGAG
..(((((((((.......((((((.(....).))))))(((((.((((((((((((...(.....).)))))))))))).)))))...))))))..))) ( -51.20)
>DroYak_CAF1 24299 96 + 1
UGCUCUCCGCAAAGGAAAUGAUUUGGGAAAGGAAGUCCCCGCCUCCUCCGCCUCCAGAGGUCG---AUGGGGGUGGUGGUGGGGGAGACGCGGGACGAG
..((((((.((((........)))))))......(((((((.((((((((((.(((.......---.......))).)))))))))).)).)))))))) ( -42.14)
>DroAna_CAF1 26421 87 + 1
UGCUCUCGGCAAAGGAUAUGAUCUGGGAGAGGAGAUCU---------CCGCCCUGGG---UGGAUGAGGAGGGCGGCGGCGGUGGAGAGGCUGGGCGGG
..(((((.((.........(((((........))))).---------(((((((...---.........))))))).....)).))))).......... ( -27.70)
>consensus
UGCUCUCCGCAAAGGAUAUGAUUUGGGAGAGGAAGUCACCACCUCCUCCGCCUCCAGAGGUCGAAGAUGGGGGUGGUGGCGGUGGAGACGCGGGACGAG
.(.((.((((.........(((((........))))).(((((.((.(((((((((...........))))))))).)).)))))....)))))))... (-28.30 = -29.83 +   1.53)

alignment

secondary structure

dotplot

Window 2

Location	4,147,531 – 4,147,630
Length	99
Sequences	6
Columns	99
Reading direction	reverse
Mean pairwise identity	75.02
Mean single sequence MFE	-35.60
Consensus MFE	-21.75
Energy contribution	-24.28
Covariance contribution	2.53
Combinations/Pair	1.28
Mean z-score	-2.55
Structure conservation index	0.61
SVM decision value	2.32
SVM RNA-class probability	0.992341
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 4147531 99 - 23771897
CUCGUCCCGCGUCUCCACCGCCAGCACCACCAUCUUCGACCUCUGGAGGCGGAGGAGGUGGUGACUUCCUCUCUCAAAUCAUAUCCUUUGCGGAGAGCA
........((.(((((......(((((((((..(((((.(((....))))))))..))))))).))........((((........)))).))))))). ( -35.60)
>DroVir_CAF1 47735 96 - 1
CGCGUCCCGCAGCGCCGGCUCCGGCACCAGCAGCCGCGUCGCCUGCACA---GUCUGGCGGGGAUCUGCUCUCCCAGUUCAUAUCCUUUGCGGAGAGCA
....((((((.((((((....))))....((((.((...)).))))...---))...))))))....((((((((((..........))).))))))). ( -40.30)
>DroSim_CAF1 24810 99 - 1
CUCGUCCCGCGUCCCCACCGCCACCACCCCCAUCUUCGUCCUCUGGAGGCGGAGGAGGUGGUGACUUCCUCUCUCAAAUCAUAUCCUUUGCGGAGAGCA
...(((((((.(((...(((((.(((.................))).))))).))).)))).)))...((((((((((........)))).)))))).. ( -35.43)
>DroEre_CAF1 25753 99 - 1
CUCGUCCCGCAUCUCCACCGCCCCCACCCCCAUCUUCGAGCUCUGGAGGCGGAGGAGGUGGUGACUUCCUCUCGCAAAUCAUAUCCUUUGCGGAGAGCA
...(((.(.(((((((.(((((.(((.................))).))))).)))))))).)))...((((((((((........))))).))))).. ( -38.43)
>DroYak_CAF1 24299 96 - 1
CUCGUCCCGCGUCUCCCCCACCACCACCCCCAU---CGACCUCUGGAGGCGGAGGAGGCGGGGACUUCCUUUCCCAAAUCAUUUCCUUUGCGGAGAGCA
...(((((.(((((((.((.((.(((.......---.......))).)).)).))))))))))))...((((((((((........)))).)))))).. ( -39.94)
>DroAna_CAF1 26421 87 - 1
CCCGCCCAGCCUCUCCACCGCCGCCGCCCUCCUCAUCCA---CCCAGGGCGG---------AGAUCUCCUCUCCCAGAUCAUAUCCUUUGCCGAGAGCA
........((.((((........(((((((.........---...)))))))---------.(((((........)))))............)))))). ( -23.90)
>consensus
CUCGUCCCGCGUCUCCACCGCCACCACCCCCAUCUUCGACCUCUGGAGGCGGAGGAGGUGGUGACUUCCUCUCCCAAAUCAUAUCCUUUGCGGAGAGCA
...(((((((..((((.(((((.(((.................))).))))).)))))))).)))...((((((((((........)))).)))))).. (-21.75 = -24.28 +   2.53)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:07:17 2006