Locus 5464

Sequence ID	3L_DroMel_CAF1
Location	14,942,639 – 14,942,904
Length	265
Max. P	0.888328

overview

Window 1

Location	14,942,639 – 14,942,749
Length	110
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	87.76
Mean single sequence MFE	-24.52
Consensus MFE	-21.73
Energy contribution	-21.49
Covariance contribution	-0.24
Combinations/Pair	1.04
Mean z-score	-1.66
Structure conservation index	0.89
SVM decision value	0.95
SVM RNA-class probability	0.888328
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 14942639 110 - 23771897
CACCCUCUACGUAAUUCUACGUAACUUUGGAUGGUACCGAAGCUUUAAAGACCGCUUGGCUCUC------CCAUUUUCCAACGCCCACCAAUCCACC----CACCACUCAAGUGGAAGAA
.......((((((....))))))....((((((((....((((..........))))(((....------............))).))).)))))..----..((((....))))..... ( -22.59)
>DroSec_CAF1 122965 110 - 1
CACCCUCUACGUAGUUCUACGUAACUUUGGAUGGUACCGAAGCUUUAAAGACCGCUUGGCCCUC------CCAUUUCCCAACGCCCAUCAUUCCACC----CACCACUCAAGUGGGAGAA
.......((((((....))))))....((((((((....((((..........))))(((....------............))).)))).))))((----(((.......))))).... ( -22.49)
>DroSim_CAF1 120727 110 - 1
CACCCUCUACGUAAUUCUACGUAACUUUGGAUGGUACCGAAGCUUUAAAGACCGCUUGGCUCUC------CCAUUUCCCAACGCCCACCAUUCCACC----CACCACUCAAGUGGGAGAA
.......((((((....))))))....((((((((....((((..........))))(((....------............))).)))).))))((----(((.......))))).... ( -24.89)
>DroEre_CAF1 117730 109 - 1
CACCCACUACGUAGACCUACGUAACUUUGGAUGGUACCGAAGCUUUAAAGACCGCUUGGCUCCCCAUU-------CCCCAACGCCCACCAGUCCACC----CGCCACUCAAGUGGGAGAA
..(((((((((((....))))))....((((((((....((((..........))))(((........-------.......))).)))).))))..----..........))))).... ( -27.36)
>DroYak_CAF1 118837 120 - 1
CACCCACUACGUAAUCCUACGUAACCUUGGAUGGUACCGAAGCUUUAAAGACCGCUUGGCUCCCCAUUACCCAUUACCCAACGCCCAUCAGUCCACCCACCCACCACUCAAGUGGGAGAG
..(((((((((((....))))))...(((..((((....((((..........))))(((......................))).................))))..)))))))).... ( -25.25)
>consensus
CACCCUCUACGUAAUUCUACGUAACUUUGGAUGGUACCGAAGCUUUAAAGACCGCUUGGCUCUC______CCAUUUCCCAACGCCCACCAGUCCACC____CACCACUCAAGUGGGAGAA
.......((((((....))))))....((((((((....((((..........))))(((......................))).)))).))))........((((....))))..... (-21.73 = -21.49 +  -0.24)

alignment

secondary structure

dotplot

Window 2

Location	14,942,709 – 14,942,824
Length	115
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	87.02
Mean single sequence MFE	-38.82
Consensus MFE	-29.20
Energy contribution	-29.44
Covariance contribution	0.24
Combinations/Pair	1.13
Mean z-score	-1.61
Structure conservation index	0.75
SVM decision value	0.11
SVM RNA-class probability	0.590762
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 14942709 115 - 23771897
UCU----CCCAAAAAAAUUAAAUGGGAU-GAGGGGGUGGCGCUCGAGGUGGUUUUUGCAGCUUUAAACGCGCUCCAAGCGCACCCUCUACGUAAUUCUACGUAACUUUGGAUGGUACCGA
(((----((((...........))))).-))(((((((.((((.(..(((((((..........)))).)))..).)))))))))))((((((....))))))...((((......)))) ( -37.50)
>DroSec_CAF1 123035 114 - 1
UCU----CCCAAAAUAA-AAAAUGGGAU-GAGGGGGUGGCGCUCGACGAGGUUGUUGCAGCUUUAAACGCGCUCCAAGCGCACCCUCUACGUAGUUCUACGUAACUUUGGAUGGUACCGA
(((----((((......-....))))).-))((((((...((((((((....))))).))).......((((.....))))))))))((((((....))))))...((((......)))) ( -36.30)
>DroSim_CAF1 120797 114 - 1
UCU----CCCAAAAUAA-AAAAUGGGAU-GAGGGGGUGGCGCUCGACGAGGUUGUUGCAGCUUUAAACGCGCUCCAAGCGCACCCUCUACGUAAUUCUACGUAACUUUGGAUGGUACCGA
(((----((((......-....))))).-))((((((...((((((((....))))).))).......((((.....))))))))))((((((....))))))...((((......)))) ( -35.60)
>DroEre_CAF1 117799 108 - 1
UCU----CCCGAA-----GAAUUGGGAGC---GGGGUGGCGAUCGAGGAGGCUGCUGCAGCUUUAAACGCGCUCCAAGCGCACCCACUACGUAGACCUACGUAACUUUGGAUGGUACCGA
...----.(((((-----(...((((.((---(.((.((((......(((((((...))))))).....))))))...))).)))).((((((....)))))).)))))).......... ( -38.70)
>DroYak_CAF1 118917 115 - 1
UCUCUCUUCCAAA-----GAAUUGGGAGAGAGGGGGUGGCGAUCGAGGAGGUUGUAGCAGCUUUAAACGCGCUCCAAGCGCACCCACUACGUAAUCCUACGUAACCUUGGAUGGUACCGA
((((((((((((.-----...)))))))))))).((((.((.((((((((((((...)))))).....((((.....))))......((((((....)))))).)))))).)).)))).. ( -46.00)
>consensus
UCU____CCCAAAA_AA_AAAAUGGGAU_GAGGGGGUGGCGCUCGAGGAGGUUGUUGCAGCUUUAAACGCGCUCCAAGCGCACCCUCUACGUAAUUCUACGUAACUUUGGAUGGUACCGA
.......((((...........))))........((((.((..(((((((((((...)))))).....((((.....))))......((((((....)))))).)))))..)).)))).. (-29.20 = -29.44 +   0.24)

alignment

secondary structure

dotplot

Window 3

Location	14,942,749 – 14,942,864
Length	115
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	87.53
Mean single sequence MFE	-39.08
Consensus MFE	-26.42
Energy contribution	-26.74
Covariance contribution	0.32
Combinations/Pair	1.12
Mean z-score	-2.15
Structure conservation index	0.68
SVM decision value	0.25
SVM RNA-class probability	0.652734
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 14942749 115 - 23771897
ACGAUCACAUCGCCUCAUCUCGUGAAACACCCACCCACUCUCU----CCCAAAAAAAUUAAAUGGGAU-GAGGGGGUGGCGCUCGAGGUGGUUUUUGCAGCUUUAAACGCGCUCCAAGCG
..........(((.((((((((.(......((((((.(.((((----((((...........))))).-))))))))))..).))))))))...(((.(((.........))).)))))) ( -36.70)
>DroSec_CAF1 123075 114 - 1
ACGAUCACAUCGCCUCAUCUCGUGAAACACCCACCCACUCUCU----CCCAAAAUAA-AAAAUGGGAU-GAGGGGGUGGCGCUCGACGAGGUUGUUGCAGCUUUAAACGCGCUCCAAGCG
...........((..((((((((((.....((((((.(.((((----((((......-....))))).-))))))))))...)).)))))).))..)).........(((.......))) ( -35.70)
>DroSim_CAF1 120837 114 - 1
ACGAUCACAUCGCCUCAUCUCGUAAAACACCCACCCACUCUCU----CCCAAAAUAA-AAAAUGGGAU-GAGGGGGUGGCGCUCGACGAGGUUGUUGCAGCUUUAAACGCGCUCCAAGCG
...........((..((((((((.......((((((.(.((((----((((......-....))))).-))))))))))......)))))).))..)).........(((.......))) ( -36.12)
>DroEre_CAF1 117839 107 - 1
ACGAUCACAUCGCCUCAUCUCGUGCAACAC-CACCCACUCUCU----CCCGAA-----GAAUUGGGAGC---GGGGUGGCGAUCGAGGAGGCUGCUGCAGCUUUAAACGCGCUCCAAGCG
...........(((((..((((.....(.(-(((((.....((----(((((.-----...))))))).---.)))))).)..))))))))).(((..(((.........)))...))). ( -39.40)
>DroYak_CAF1 118957 115 - 1
CCGAUCACAUCGCCUCAUCUCGUGAAAUACCCACCCACUCUCUCUCUUCCAAA-----GAAUUGGGAGAGAGGGGGUGGCGAUCGAGGAGGUUGUAGCAGCUUUAAACGCGCUCCAAGCG
.(((((...((((........)))).........((((((((((((((((((.-----...)))))))))))))))))).)))))....(.(((.(((.((.......))))).))).). ( -47.50)
>consensus
ACGAUCACAUCGCCUCAUCUCGUGAAACACCCACCCACUCUCU____CCCAAAA_AA_AAAAUGGGAU_GAGGGGGUGGCGCUCGAGGAGGUUGUUGCAGCUUUAAACGCGCUCCAAGCG
...........(((((.((..(((.......)))(((((((((....((((...........))))....))))))))).....)).)))))...............(((.......))) (-26.42 = -26.74 +   0.32)

alignment

secondary structure

dotplot

Window 4

Location	14,942,789 – 14,942,904
Length	115
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	87.88
Mean single sequence MFE	-42.34
Consensus MFE	-29.30
Energy contribution	-30.70
Covariance contribution	1.40
Combinations/Pair	1.00
Mean z-score	-2.18
Structure conservation index	0.69
SVM decision value	0.39
SVM RNA-class probability	0.718455
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 14942789 115 + 23771897
GCCACCCCCUC-AUCCCAUUUAAUUUUUUUGGG----AGAGAGUGGGUGGGUGUUUCACGAGAUGAGGCGAUGUGAUCGUUAACGGUUUACAUUGAGCACUGACUCGGCAAUCGGCGGAU
.((((((.(((-.(((((...........))))----)..))).))))))....(((.((((.(.((.(((((((((((....))).))))))))....)).)))))((.....))))). ( -41.60)
>DroSec_CAF1 123115 114 + 1
GCCACCCCCUC-AUCCCAUUUU-UUAUUUUGGG----AGAGAGUGGGUGGGUGUUUCACGAGAUGAGGCGAUGUGAUCGUUAACGGUUUACAUUGAGCACUGACUCGACGAUCGACGGAU
.((((((.(((-.(((((....-......))))----)..))).)))))).((((((.((((.(.((.(((((((((((....))).))))))))....)).)))))..))..))))... ( -40.30)
>DroSim_CAF1 120877 114 + 1
GCCACCCCCUC-AUCCCAUUUU-UUAUUUUGGG----AGAGAGUGGGUGGGUGUUUUACGAGAUGAGGCGAUGUGAUCGUUAACGGUUUACAUUGAGCACUGACUCGACGAUCGGCGGAU
.((((((.(((-.(((((....-......))))----)..))).))))))........((((.(.((.(((((((((((....))).))))))))....)).)))))............. ( -40.10)
>DroEre_CAF1 117879 107 + 1
GCCACCCC---GCUCCCAAUUC-----UUCGGG----AGAGAGUGGGUG-GUGUUGCACGAGAUGAGGCGAUGUGAUCGUUAACGGUUUACAUUGAGCACUGACUCGCCGAUCGCCGGAU
((((((((---.(((((.....-----...)))----))...).)))))-))......((.(((..(((((((((((((....))).)))))))(((......)))))).)))..))... ( -41.70)
>DroYak_CAF1 118997 115 + 1
GCCACCCCCUCUCUCCCAAUUC-----UUUGGAAGAGAGAGAGUGGGUGGGUAUUUCACGAGAUGAGGCGAUGUGAUCGGUAACGGUUUACAUUGAGCACUGACUCUGCCAUCGUCGGAU
.((((((((((((((((((...-----.))))..))))))).).))))))...........((((((((((((((((((....))).)))))))(((......))).))).))))).... ( -48.00)
>consensus
GCCACCCCCUC_AUCCCAUUUC_UU_UUUUGGG____AGAGAGUGGGUGGGUGUUUCACGAGAUGAGGCGAUGUGAUCGUUAACGGUUUACAUUGAGCACUGACUCGACGAUCGGCGGAU
.((((((((((...((((...........)))).....))).).))))))........((((.(.((.(((((((((((....))).))))))))....)).)))))............. (-29.30 = -30.70 +   1.40)

alignment

secondary structure

dotplot

Window 5

Location	14,942,789 – 14,942,904
Length	115
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	87.88
Mean single sequence MFE	-35.44
Consensus MFE	-24.62
Energy contribution	-25.18
Covariance contribution	0.56
Combinations/Pair	1.10
Mean z-score	-2.25
Structure conservation index	0.69
SVM decision value	0.50
SVM RNA-class probability	0.759304
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 14942789 115 - 23771897
AUCCGCCGAUUGCCGAGUCAGUGCUCAAUGUAAACCGUUAACGAUCACAUCGCCUCAUCUCGUGAAACACCCACCCACUCUCU----CCCAAAAAAAUUAAAUGGGAU-GAGGGGGUGGC
.......(((((..((((....))))((((.....))))..)))))...((((........)))).....((((((.(.((((----((((...........))))).-)))))))))). ( -31.20)
>DroSec_CAF1 123115 114 - 1
AUCCGUCGAUCGUCGAGUCAGUGCUCAAUGUAAACCGUUAACGAUCACAUCGCCUCAUCUCGUGAAACACCCACCCACUCUCU----CCCAAAAUAA-AAAAUGGGAU-GAGGGGGUGGC
....((.((((((.((((....))))((((.....)))).)))))))).((((........)))).....((((((.(.((((----((((......-....))))).-)))))))))). ( -35.10)
>DroSim_CAF1 120877 114 - 1
AUCCGCCGAUCGUCGAGUCAGUGCUCAAUGUAAACCGUUAACGAUCACAUCGCCUCAUCUCGUAAAACACCCACCCACUCUCU----CCCAAAAUAA-AAAAUGGGAU-GAGGGGGUGGC
..(((((((((((.((((....))))((((.....)))).))))))......(((((((((((....................----..........-...)))))))-)))).))))). ( -32.91)
>DroEre_CAF1 117879 107 - 1
AUCCGGCGAUCGGCGAGUCAGUGCUCAAUGUAAACCGUUAACGAUCACAUCGCCUCAUCUCGUGCAACAC-CACCCACUCUCU----CCCGAA-----GAAUUGGGAGC---GGGGUGGC
...(((.(((.(((((....(((.((((((.....))))...)).))).)))))..)))))).......(-(((((.....((----(((((.-----...))))))).---.)))))). ( -34.50)
>DroYak_CAF1 118997 115 - 1
AUCCGACGAUGGCAGAGUCAGUGCUCAAUGUAAACCGUUACCGAUCACAUCGCCUCAUCUCGUGAAAUACCCACCCACUCUCUCUCUUCCAAA-----GAAUUGGGAGAGAGGGGGUGGC
.(((((.((((((.((((....))))...((((....))))..........)))..)))))).)).........((((((((((((((((((.-----...)))))))))))))))))). ( -43.50)
>consensus
AUCCGCCGAUCGCCGAGUCAGUGCUCAAUGUAAACCGUUAACGAUCACAUCGCCUCAUCUCGUGAAACACCCACCCACUCUCU____CCCAAAA_AA_AAAAUGGGAU_GAGGGGGUGGC
.......(((((..((((....))))((((.....))))..)))))...((((........)))).........(((((((((....((((...........))))....))))))))). (-24.62 = -25.18 +   0.56)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:51:01 2006