Locus 4934

Sequence ID	2L_DroMel_CAF1
Location	14,134,983 – 14,135,143
Length	160
Max. P	0.999970

overview

Window 7

Location	14,134,983 – 14,135,103
Length	120
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	95.72
Mean single sequence MFE	-44.77
Consensus MFE	-42.63
Energy contribution	-43.13
Covariance contribution	0.50
Combinations/Pair	1.00
Mean z-score	-3.16
Structure conservation index	0.95
SVM decision value	5.04
SVM RNA-class probability	0.999970
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 14134983 120 + 22407834
CUGCCAAAAUUCCGAAGAAUCCGAGGAAAACACCAAAAACAUCGACACGUACCGCAUCGGCAACCGGUGGCGGUGGGGGAGGUGCUGGCGGAGGCGCCACCACCAGCACGAAAAUGGCAU
.(((((...((((...........((......)).............(.(((((((((((...))))).)))))).)))))(((((((.((.(....).)).))))))).....))))). ( -45.80)
>DroVir_CAF1 386935 120 + 1
UUGCCAAAAUUCCGAAAAAUCCGAGAAAAACACCAAAAACAUCGACACGUACCGCAUCGGCAACCGGUGGCGGUGGCGGAGGUGCUGGCGGAGGUGCCACCACCAGCACAAAAAUGGCAU
.(((((...(((((.......(((.................))).....(((((((((((...))))).)))))).)))))(((((((.((.(....).)).))))))).....))))). ( -44.93)
>DroPse_CAF1 278833 120 + 1
CUGCCAAAAUUCCGAAGAAUCCGAGAAAAACACCAAAAACAUCGACACGUACCGCAUCGGCAACCGGUGGCGGUGGCGGAGGUGCUGGCGGAGGCACCACCACCAGCACGAAAAUGGCAU
.(((((...(((((.......(((.................))).....(((((((((((...))))).)))))).)))))(((((((.((.(....).)).))))))).....))))). ( -44.83)
>DroGri_CAF1 265553 120 + 1
UUGCCAAAAUUCCGAAAAAUCCGAGAAAAACACCAAAAACUUCGACACGUACCGCAUCGGCAACCGGUGGCGGUGGCGGCGGUGCUGGCGGAGGUGCCACCACCAGCACGAAAAUGGCAU
.(((((...(((((.......)).)))...............((...(((((((((((((...))))).))))).))).))(((((((.((.(....).)).))))))).....))))). ( -43.60)
>DroWil_CAF1 317119 120 + 1
UUGCCAAAAUUCCGAAGAAUCCGAGAAAAACACCAAAAACAUCGACACGUACCGCAUCGGCAACCGGUGGCGGUGGCGGAGGUGCUGGCGGAGGUGCCACCACCAGCACAAAGAUGGCAU
.(((((...(((((.......(((.................))).....(((((((((((...))))).)))))).)))))(((((((.((.(....).)).))))))).....))))). ( -44.93)
>DroMoj_CAF1 345904 120 + 1
UUGCCAAAAUUCCGAAAAAUCCGAGAAAAACACCAAAAACAUCGACACGUACCGCAUCGGCAACCGGUGGCGGUGGCGGAGGUGCUGGCGGCGGUGCCACCACCAGCACAAAGAUGGCUU
..((((...(((((.......(((.................))).....(((((((((((...))))).)))))).)))))(((((((.((.(....).)).))))))).....)))).. ( -44.53)
>consensus
UUGCCAAAAUUCCGAAAAAUCCGAGAAAAACACCAAAAACAUCGACACGUACCGCAUCGGCAACCGGUGGCGGUGGCGGAGGUGCUGGCGGAGGUGCCACCACCAGCACAAAAAUGGCAU
.(((((...(((((.......(((.................))).....(((((((((((...))))).)))))).)))))(((((((.((.(....).)).))))))).....))))). (-42.63 = -43.13 +   0.50)

alignment

secondary structure

dotplot

Window 8

Location	14,134,983 – 14,135,103
Length	120
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	95.72
Mean single sequence MFE	-48.83
Consensus MFE	-46.19
Energy contribution	-46.44
Covariance contribution	0.25
Combinations/Pair	1.03
Mean z-score	-2.98
Structure conservation index	0.95
SVM decision value	4.74
SVM RNA-class probability	0.999944
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 14134983 120 - 22407834
AUGCCAUUUUCGUGCUGGUGGUGGCGCCUCCGCCAGCACCUCCCCCACCGCCACCGGUUGCCGAUGCGGUACGUGUCGAUGUUUUUGGUGUUUUCCUCGGAUUCUUCGGAAUUUUGGCAG
.(((((.....((((((((((.(....).))))))))))............((((((..(((((((((...)))))))..))..))))))........((((((....))))))))))). ( -47.60)
>DroVir_CAF1 386935 120 - 1
AUGCCAUUUUUGUGCUGGUGGUGGCACCUCCGCCAGCACCUCCGCCACCGCCACCGGUUGCCGAUGCGGUACGUGUCGAUGUUUUUGGUGUUUUUCUCGGAUUUUUCGGAAUUUUGGCAA
.(((((.((((((((((((((.(....).)))))))))).((((.......((((((..(((((((((...)))))))..))..)))))).......))))......))))...))))). ( -47.14)
>DroPse_CAF1 278833 120 - 1
AUGCCAUUUUCGUGCUGGUGGUGGUGCCUCCGCCAGCACCUCCGCCACCGCCACCGGUUGCCGAUGCGGUACGUGUCGAUGUUUUUGGUGUUUUUCUCGGAUUCUUCGGAAUUUUGGCAG
.(((((.((((((((((((((.(....).)))))))))).((((.......((((((..(((((((((...)))))))..))..)))))).......))))......))))...))))). ( -49.94)
>DroGri_CAF1 265553 120 - 1
AUGCCAUUUUCGUGCUGGUGGUGGCACCUCCGCCAGCACCGCCGCCACCGCCACCGGUUGCCGAUGCGGUACGUGUCGAAGUUUUUGGUGUUUUUCUCGGAUUUUUCGGAAUUUUGGCAA
.(((((.((((((((((((((.(....).))))))))))((((((.((((....)))).))(((((((...)))))))........)))).................))))...))))). ( -49.10)
>DroWil_CAF1 317119 120 - 1
AUGCCAUCUUUGUGCUGGUGGUGGCACCUCCGCCAGCACCUCCGCCACCGCCACCGGUUGCCGAUGCGGUACGUGUCGAUGUUUUUGGUGUUUUUCUCGGAUUCUUCGGAAUUUUGGCAA
.(((((.....((((((((((.(....).)))))))))).((((.......((((((..(((((((((...)))))))..))..)))))).......))))(((....)))...))))). ( -49.44)
>DroMoj_CAF1 345904 120 - 1
AAGCCAUCUUUGUGCUGGUGGUGGCACCGCCGCCAGCACCUCCGCCACCGCCACCGGUUGCCGAUGCGGUACGUGUCGAUGUUUUUGGUGUUUUUCUCGGAUUUUUCGGAAUUUUGGCAA
..((((.....((((((((((((....)))))))))))).((((.......((((((..(((((((((...)))))))..))..)))))).......)))).............)))).. ( -49.74)
>consensus
AUGCCAUUUUCGUGCUGGUGGUGGCACCUCCGCCAGCACCUCCGCCACCGCCACCGGUUGCCGAUGCGGUACGUGUCGAUGUUUUUGGUGUUUUUCUCGGAUUCUUCGGAAUUUUGGCAA
.(((((..(((((((((((((.(....).)))))))))).((((.......((((((..(((((((((...)))))))..))..)))))).......)))).......)))...))))). (-46.19 = -46.44 +   0.25)

alignment

secondary structure

dotplot

Window 9

Location	14,135,023 – 14,135,143
Length	120
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	95.89
Mean single sequence MFE	-46.97
Consensus MFE	-41.93
Energy contribution	-42.43
Covariance contribution	0.50
Combinations/Pair	1.00
Mean z-score	-1.60
Structure conservation index	0.89
SVM decision value	1.07
SVM RNA-class probability	0.910737
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 14135023 120 + 22407834
AUCGACACGUACCGCAUCGGCAACCGGUGGCGGUGGGGGAGGUGCUGGCGGAGGCGCCACCACCAGCACGAAAAUGGCAUCUAAAAGAAAAGCCUCGGUGUUGCUGCACAAGGUGAGUUU
...(((((.(((((((((((...))))).))))))((((..(((((((.((.(....).)).)))))))..........((.....))....)))).)))))(((.(((...)))))).. ( -42.90)
>DroVir_CAF1 386975 120 + 1
AUCGACACGUACCGCAUCGGCAACCGGUGGCGGUGGCGGAGGUGCUGGCGGAGGUGCCACCACCAGCACAAAAAUGGCAUCUAAAAGAAAAGCAUCGGUGUUGCUGCACAAGGUGAGUUC
...(((...((((.((((((...))))))((((..(((..((((((..(..((((((((...............))))))))....)...))))))..)))..))))....)))).))). ( -44.76)
>DroGri_CAF1 265593 120 + 1
UUCGACACGUACCGCAUCGGCAACCGGUGGCGGUGGCGGCGGUGCUGGCGGAGGUGCCACCACCAGCACGAAAAUGGCAUCUAAAAGAAAAGCAUCGGUGUUGCUGCACAAGGUGAGUUC
...(((...((((.((((((...))))))((((..(((.(((((((..(..((((((((...............))))))))....)...))))))).)))..))))....)))).))). ( -48.46)
>DroWil_CAF1 317159 120 + 1
AUCGACACGUACCGCAUCGGCAACCGGUGGCGGUGGCGGAGGUGCUGGCGGAGGUGCCACCACCAGCACAAAGAUGGCAUCUAAAAGAAAAGCCUCGGUGUUGCUGCACAAGGUGAGUGU
....((((.((((.((((((...))))))((((..(((...(((((((.((.(....).)).)))))))...((.(((.((.....))...)))))..)))..))))....)))).)))) ( -49.80)
>DroMoj_CAF1 345944 120 + 1
AUCGACACGUACCGCAUCGGCAACCGGUGGCGGUGGCGGAGGUGCUGGCGGCGGUGCCACCACCAGCACAAAGAUGGCUUCUAAAAGAAAAGCCUCGGUGUUGCUGCACAAGGUGAGUUC
...(((...((((.((((((...))))))((((..(((...(((((((.((.(....).)).)))))))...((.(((((.........)))))))..)))..))))....)))).))). ( -48.10)
>DroAna_CAF1 220008 120 + 1
AUCGACACGUACCGCAUCGGCAACCGGUGGCGGUGGCGGAGGUGCUGGCGGAGGCGCCACCACCAGCACGAAAAUGGCAUCUAAAAGAAAAGCCUCGGUGUUGCUGCACAAGGUGAGUGC
.....(((.((((.((((((...))))))((((..(((..((((((((.((.(....).)).)))))))......(((.((.....))...))).)..)))..))))....)))).))). ( -47.80)
>consensus
AUCGACACGUACCGCAUCGGCAACCGGUGGCGGUGGCGGAGGUGCUGGCGGAGGUGCCACCACCAGCACAAAAAUGGCAUCUAAAAGAAAAGCCUCGGUGUUGCUGCACAAGGUGAGUUC
......((.((((.((((((...))))))((((..(((..((((((((.((.(....).)).)))))))......(((.((.....))...))).)..)))..))))....)))).)).. (-41.93 = -42.43 +   0.50)

alignment

secondary structure

dotplot

Window 0

Location	14,135,023 – 14,135,143
Length	120
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	95.89
Mean single sequence MFE	-42.63
Consensus MFE	-38.27
Energy contribution	-38.93
Covariance contribution	0.67
Combinations/Pair	1.00
Mean z-score	-1.41
Structure conservation index	0.90
SVM decision value	0.76
SVM RNA-class probability	0.842688
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 14135023 120 - 22407834
AAACUCACCUUGUGCAGCAACACCGAGGCUUUUCUUUUAGAUGCCAUUUUCGUGCUGGUGGUGGCGCCUCCGCCAGCACCUCCCCCACCGCCACCGGUUGCCGAUGCGGUACGUGUCGAU
.......(((((((......)).)))))...........(((((.......((((((((((.(....).)))))))))).......(((((...(((...)))..)))))..)))))... ( -40.20)
>DroVir_CAF1 386975 120 - 1
GAACUCACCUUGUGCAGCAACACCGAUGCUUUUCUUUUAGAUGCCAUUUUUGUGCUGGUGGUGGCACCUCCGCCAGCACCUCCGCCACCGCCACCGGUUGCCGAUGCGGUACGUGUCGAU
...........(((......)))((((((...((.....))((((......((((((((((.(....).)))))))))).((.((.((((....)))).)).))...)))).)))))).. ( -39.10)
>DroGri_CAF1 265593 120 - 1
GAACUCACCUUGUGCAGCAACACCGAUGCUUUUCUUUUAGAUGCCAUUUUCGUGCUGGUGGUGGCACCUCCGCCAGCACCGCCGCCACCGCCACCGGUUGCCGAUGCGGUACGUGUCGAA
...........(((......)))((((((...((.....))((((......((((((((((.(....).)))))))))).((.((.((((....)))).))....)))))).)))))).. ( -39.30)
>DroWil_CAF1 317159 120 - 1
ACACUCACCUUGUGCAGCAACACCGAGGCUUUUCUUUUAGAUGCCAUCUUUGUGCUGGUGGUGGCACCUCCGCCAGCACCUCCGCCACCGCCACCGGUUGCCGAUGCGGUACGUGUCGAU
....((((..(((((.(((.....(((((...((.....)).))).))...((((((((((.(....).)))))))))).((.((.((((....)))).)).))))).))))).)).)). ( -42.50)
>DroMoj_CAF1 345944 120 - 1
GAACUCACCUUGUGCAGCAACACCGAGGCUUUUCUUUUAGAAGCCAUCUUUGUGCUGGUGGUGGCACCGCCGCCAGCACCUCCGCCACCGCCACCGGUUGCCGAUGCGGUACGUGUCGAU
....((((..(((((.(((.....(((((((((.....))))))).))...((((((((((((....)))))))))))).((.((.((((....)))).)).))))).))))).)).)). ( -48.90)
>DroAna_CAF1 220008 120 - 1
GCACUCACCUUGUGCAGCAACACCGAGGCUUUUCUUUUAGAUGCCAUUUUCGUGCUGGUGGUGGCGCCUCCGCCAGCACCUCCGCCACCGCCACCGGUUGCCGAUGCGGUACGUGUCGAU
((((.......)))).(((((.....(((...((.....)).))).....((.(.(((((((((((.....(....).....)))))))))))))))))))(((((((...))))))).. ( -45.80)
>consensus
GAACUCACCUUGUGCAGCAACACCGAGGCUUUUCUUUUAGAUGCCAUUUUCGUGCUGGUGGUGGCACCUCCGCCAGCACCUCCGCCACCGCCACCGGUUGCCGAUGCGGUACGUGUCGAU
....((((..(((((.(((.......(((...((.....)).)))......((((((((((.(....).)))))))))).((.((.((((....)))).)).))))).))))).)).)). (-38.27 = -38.93 +   0.67)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:31:26 2006