Locus 3049

Sequence ID	3R_DroMel_CAF1
Location	8,091,255 – 8,091,633
Length	378
Max. P	0.992315

overview

Window 9

Location	8,091,255 – 8,091,360
Length	105
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	88.35
Mean single sequence MFE	-34.12
Consensus MFE	-28.42
Energy contribution	-28.42
Covariance contribution	0.00
Combinations/Pair	1.00
Mean z-score	-1.37
Structure conservation index	0.83
SVM decision value	-0.01
SVM RNA-class probability	0.527955
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 8091255 105 + 27905053
CUUGGUCAGUCAUGCACUCAAUCAGUGGCAGGACACUCCGGCCAGGACAACAGGCGCAGUUCACCCCCUGCG-------ACAUGUAA-AGGGUACUCGCCCCCACCCUCGCC-------U
...((...(((.((((((.....))).))).)))...))(((.(((......((((.(((..((((..(((.-------....))).-.))))))))))).....))).)))-------. ( -33.40)
>DroSec_CAF1 43027 113 + 1
CUUGGUCAGUCAUGCACUCAAUCAGUGGCAGGACACUGCGGCCAGGACAACAGGCGCAGUUCACCCCCUGCG-------ACAUGUAAAAGGGUACUCGCCCUCACCCUCGCCCUCAUCCA
(((((((.......((((.....))))((((....)))))))))))......(((((((........)))).-------.........(((((....))))).......)))........ ( -35.00)
>DroSim_CAF1 15032 113 + 1
CUUGGUCAGUCAUGCACUCAAUCAGUGGCAGGACACUCCGGCCAGGACAACAGGCGCAGUUCACCCCCUGCG-------ACAUGUAAAAGGGUACUCGCCCUCACCCUCGCCCUCACCCA
...((...(((.((((((.....))).))).)))...))(((.(((...(((..(((((........)))))-------...)))...(((((....)))))...))).)))........ ( -33.90)
>DroEre_CAF1 18069 113 + 1
CUUGGUCAGUCAUGCACUCAAUCAGUGGCAGGACACUCCGGCCAGGACAACAGGCGCAGUUCACCCCCUGCUACCCUUCACAUGUAA-AGGGUACUCGCCCUCGCCAUC------GCCCU
(((((((.(((((...........))))).((.....)))))))))......(((((((........))))(((((((........)-)))))).........)))...------..... ( -34.20)
>consensus
CUUGGUCAGUCAUGCACUCAAUCAGUGGCAGGACACUCCGGCCAGGACAACAGGCGCAGUUCACCCCCUGCG_______ACAUGUAA_AGGGUACUCGCCCUCACCCUCGCC___ACCCA
(((((((.(((.((((((.....))).))).))).....)))))))......((((.(((..((((..(((............)))...))))))))))).................... (-28.42 = -28.42 +   0.00)

alignment

secondary structure

dotplot

Window 0

Location	8,091,328 – 8,091,440
Length	112
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	86.60
Mean single sequence MFE	-30.94
Consensus MFE	-27.46
Energy contribution	-27.98
Covariance contribution	0.52
Combinations/Pair	1.08
Mean z-score	-1.46
Structure conservation index	0.89
SVM decision value	0.24
SVM RNA-class probability	0.649791
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 8091328 112 + 27905053
CAUGUAA-AGGGUACUCGCCCCCACCCUCGCC-------UCUCCCUCCUUUAUGAAGUGCAGUUUUUAGUUCCGUUUCCCUCCGCCAGGAAGUCAGACUUCCUAAGCGGAACUCGCUGCA
((((...-((((.....((..........)).-------...))))....))))...((((((....((((((((((.........((((((.....)))))))))))))))).)))))) ( -32.00)
>DroSec_CAF1 43100 120 + 1
CAUGUAAAAGGGUACUCGCCCUCACCCUCGCCCUCAUCCACUCCAUCCUUCGUGAAGUGCAGUUUUUAGUUCUGUUUCCCCCCGCCAGGAAGUCAGACUUCCAAAGCGGAACUCGCUGCA
........(((((....))))).................(((.(((.....))).)))(((((....((((((((((..........(((((.....))))).)))))))))).))))). ( -28.40)
>DroSim_CAF1 15105 120 + 1
CAUGUAAAAGGGUACUCGCCCUCACCCUCGCCCUCACCCACUCCAUCCUUCGUGAAGUGCAGUUUUUAGUUCCUUUUCUCCCCGCCAGGAAGUCAGACUUCCAAAGCGGAACUCGCUGCA
........(((((....))))).................(((.(((.....))).)))(((((....((((((..........((..(((((.....)))))...)))))))).))))). ( -26.70)
>DroEre_CAF1 18149 113 + 1
CAUGUAA-AGGGUACUCGCCCUCGCCAUC------GCCCUCGCCCUCCUUCAUGGACUGCAGUUUGUAGUUCAGUUUCCCCCCGCCAGGAAGUCGGACUUCCUAAGCGGAACUCGCUGCA
..((((.-(((((....((....))....------))))).((.........((((((((.....))))))))........((((.((((((.....))))))..)))).....)))))) ( -33.40)
>DroYak_CAF1 11495 118 + 1
CAUGUAA-AGGGUACUCGCCCUCACCCUCACCCUCACCCUCGUCCUCCUUCAUGAAGUGCAGUUUGUAGUUCCGCUUCC-CUCGCCAGGAAGUCAGACUUCCUAAGCGGAACUCGCUGCA
.......-(((((....))))).................((((........))))..((((((..(.((((((((((..-......((((((.....))))))))))))))))))))))) ( -34.20)
>consensus
CAUGUAA_AGGGUACUCGCCCUCACCCUCGCCCUCACCCUCUCCCUCCUUCAUGAAGUGCAGUUUUUAGUUCCGUUUCCCCCCGCCAGGAAGUCAGACUUCCUAAGCGGAACUCGCUGCA
.........((((....))))....................................((((((....((((((((((.........((((((.....)))))))))))))))).)))))) (-27.46 = -27.98 +   0.52)

alignment

secondary structure

dotplot

Window 1

Location	8,091,360 – 8,091,480
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	91.92
Mean single sequence MFE	-45.20
Consensus MFE	-36.88
Energy contribution	-37.88
Covariance contribution	1.00
Combinations/Pair	1.10
Mean z-score	-2.48
Structure conservation index	0.82
SVM decision value	2.32
SVM RNA-class probability	0.992315
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 8091360 120 + 27905053
CUCCCUCCUUUAUGAAGUGCAGUUUUUAGUUCCGUUUCCCUCCGCCAGGAAGUCAGACUUCCUAAGCGGAACUCGCUGCAAUAUCCUUGCAUGGGAAUGCCAGGAUUCGCGGGGUGGCAA
..((((((.........((((((....((((((((((.........((((((.....)))))))))))))))).))))))..(((((.((((....)))).)))))....)))).))... ( -43.70)
>DroSec_CAF1 43140 119 + 1
CUCCAUCCUUCGUGAAGUGCAGUUUUUAGUUCUGUUUCCCCCCGCCAGGAAGUCAGACUUCCAAAGCGGAACUCGCUGCAUUAUCCUUGCAUGGGAAU-CCAGGACUCGCGGGGUGGCAA
..(((((((.(((((((......)))))((((((.(((((.((((..(((((.....)))))...)))).......((((.......)))).))))).-.)))))).)).)))))))... ( -42.00)
>DroSim_CAF1 15145 120 + 1
CUCCAUCCUUCGUGAAGUGCAGUUUUUAGUUCCUUUUCUCCCCGCCAGGAAGUCAGACUUCCAAAGCGGAACUCGCUGCAUUAUCCUUGCAUGGGAAUGCCAGGACUCGCGGGGUGGCAA
..((((((..(((((((((((((....((((((..........((..(((((.....)))))...)))))))).)))))))).((((.((((....)))).)))).)))))))))))... ( -45.30)
>DroEre_CAF1 18182 120 + 1
CGCCCUCCUUCAUGGACUGCAGUUUGUAGUUCAGUUUCCCCCCGCCAGGAAGUCGGACUUCCUAAGCGGAACUCGCUGCAUUAUCCUUGCAUGGGAAUGCCAGGACUCGCGGGGUGGCAA
.(((........((((((((.....))))))))......((((((.((((((.....))))))..((((......))))....((((.((((....)))).))))...)))))).))).. ( -48.80)
>DroYak_CAF1 11534 119 + 1
CGUCCUCCUUCAUGAAGUGCAGUUUGUAGUUCCGCUUCC-CUCGCCAGGAAGUCAGACUUCCUAAGCGGAACUCGCUGCAUUAUCCUUGCAUGGGAAUGCCAGGACUCGCGGGGUAGCAA
.((..((((.(....((((((((..(.((((((((((..-......((((((.....))))))))))))))))))))))))).((((.((((....)))).))))...).))))..)).. ( -46.20)
>consensus
CUCCCUCCUUCAUGAAGUGCAGUUUUUAGUUCCGUUUCCCCCCGCCAGGAAGUCAGACUUCCUAAGCGGAACUCGCUGCAUUAUCCUUGCAUGGGAAUGCCAGGACUCGCGGGGUGGCAA
..((.((((.(....((((((((....((((((((((.........((((((.....)))))))))))))))).)))))))).((((.((((....)))).))))...).)))).))... (-36.88 = -37.88 +   1.00)

alignment

secondary structure

dotplot

Window 2

Location	8,091,360 – 8,091,480
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	91.92
Mean single sequence MFE	-41.76
Consensus MFE	-33.24
Energy contribution	-33.88
Covariance contribution	0.64
Combinations/Pair	1.08
Mean z-score	-1.43
Structure conservation index	0.80
SVM decision value	0.07
SVM RNA-class probability	0.566769
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 8091360 120 - 27905053
UUGCCACCCCGCGAAUCCUGGCAUUCCCAUGCAAGGAUAUUGCAGCGAGUUCCGCUUAGGAAGUCUGACUUCCUGGCGGAGGGAAACGGAACUAAAAACUGCACUUCAUAAAGGAGGGAG
.......(((....(((((.((((....)))).)))))..(((((..(((((((((.((((((.....)))))))))....(....))))))).....)))))............))).. ( -42.90)
>DroSec_CAF1 43140 119 - 1
UUGCCACCCCGCGAGUCCUGG-AUUCCCAUGCAAGGAUAAUGCAGCGAGUUCCGCUUUGGAAGUCUGACUUCCUGGCGGGGGGAAACAGAACUAAAAACUGCACUUCACGAAGGAUGGAG
.(((.........(((.(((.-.(((((.((((.......)))).......(((((..(((((.....))))).))))))))))..))).))).......)))((((((....).))))) ( -38.49)
>DroSim_CAF1 15145 120 - 1
UUGCCACCCCGCGAGUCCUGGCAUUCCCAUGCAAGGAUAAUGCAGCGAGUUCCGCUUUGGAAGUCUGACUUCCUGGCGGGGAGAAAAGGAACUAAAAACUGCACUUCACGAAGGAUGGAG
...(((.((..((.(((((.((((....)))).)))))..(((((..(((((((((..(((((.....))))).)))..........)))))).....))))).....))..)).))).. ( -38.50)
>DroEre_CAF1 18182 120 - 1
UUGCCACCCCGCGAGUCCUGGCAUUCCCAUGCAAGGAUAAUGCAGCGAGUUCCGCUUAGGAAGUCCGACUUCCUGGCGGGGGGAAACUGAACUACAAACUGCAGUCCAUGAAGGAGGGCG
..(((..((..((.(((((.((((....)))).)))))..(((((..(((((((((.((((((.....))))))))))..((....))))))).....))))).....))..))..))). ( -46.20)
>DroYak_CAF1 11534 119 - 1
UUGCUACCCCGCGAGUCCUGGCAUUCCCAUGCAAGGAUAAUGCAGCGAGUUCCGCUUAGGAAGUCUGACUUCCUGGCGAG-GGAAGCGGAACUACAAACUGCACUUCAUGAAGGAGGACG
((((......))))(((((.((((....)))).)))))..(((((..((((((((((((((((.....))))))).....-...))))))))).....)))))((((......))))... ( -42.70)
>consensus
UUGCCACCCCGCGAGUCCUGGCAUUCCCAUGCAAGGAUAAUGCAGCGAGUUCCGCUUAGGAAGUCUGACUUCCUGGCGGGGGGAAACGGAACUAAAAACUGCACUUCAUGAAGGAGGGAG
...((..((..((.(((((.((((....)))).)))))..(((((..(((((((((.((((((.....))))))))))...(....).))))).....))))).....))..))..)).. (-33.24 = -33.88 +   0.64)

alignment

secondary structure

dotplot

Window 3

Location	8,091,400 – 8,091,520
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	96.00
Mean single sequence MFE	-43.42
Consensus MFE	-41.20
Energy contribution	-41.28
Covariance contribution	0.08
Combinations/Pair	1.05
Mean z-score	-1.41
Structure conservation index	0.95
SVM decision value	1.31
SVM RNA-class probability	0.940043
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 8091400 120 - 27905053
CCACAAAGACCGCUGAUUACAAAGUUUGGUGCUGCUGCAGUUGCCACCCCGCGAAUCCUGGCAUUCCCAUGCAAGGAUAUUGCAGCGAGUUCCGCUUAGGAAGUCUGACUUCCUGGCGGA
.........(((((.......((((..((.((((((((((((((......))))(((((.((((....)))).))))).))))))).))).))))))((((((.....))))))))))). ( -44.90)
>DroSec_CAF1 43180 119 - 1
CCACAAAGACCGCUGAUUACAAAGUUUGGUGCUGCUGCAGUUGCCACCCCGCGAGUCCUGG-AUUCCCAUGCAAGGAUAAUGCAGCGAGUUCCGCUUUGGAAGUCUGACUUCCUGGCGGG
.........(((((......(((((..((.(((((((((.((((......))))((((((.-((....)).).)))))..)))))).))).)))))))(((((.....))))).))))). ( -39.50)
>DroSim_CAF1 15185 120 - 1
CCACAAAGACCGCUGAUUACAAGGUUUGGUGCUGCUGCAGUUGCCACCCCGCGAGUCCUGGCAUUCCCAUGCAAGGAUAAUGCAGCGAGUUCCGCUUUGGAAGUCUGACUUCCUGGCGGG
.(((..(((((..((....)).))))).))).(((((((.((((......))))(((((.((((....)))).)))))..)))))))....(((((..(((((.....))))).))))). ( -44.40)
>DroEre_CAF1 18222 120 - 1
CCACAAGGACCGCUGAUUACAAAGUUCGGUGCUGCUGCAGUUGCCACCCCGCGAGUCCUGGCAUUCCCAUGCAAGGAUAAUGCAGCGAGUUCCGCUUAGGAAGUCCGACUUCCUGGCGGG
.....((.((((((........))..)))).))((((((.((((......))))(((((.((((....)))).)))))..)))))).....(((((.((((((.....))))))))))). ( -46.10)
>DroYak_CAF1 11573 120 - 1
CCACAAAGACCGCUGAUUACAAAGUUCGGUGCUGCUGCAGUUGCUACCCCGCGAGUCCUGGCAUUCCCAUGCAAGGAUAAUGCAGCGAGUUCCGCUUAGGAAGUCUGACUUCCUGGCGAG
..........((((.......(((..(((.(((((((((.((((......))))(((((.((((....)))).)))))..)))))).))).))))))((((((.....)))))))))).. ( -42.20)
>consensus
CCACAAAGACCGCUGAUUACAAAGUUUGGUGCUGCUGCAGUUGCCACCCCGCGAGUCCUGGCAUUCCCAUGCAAGGAUAAUGCAGCGAGUUCCGCUUAGGAAGUCUGACUUCCUGGCGGG
.........(((((.......((((..((.(((((((((.((((......))))(((((.((((....)))).)))))..)))))).))).)))))).(((((.....))))).))))). (-41.20 = -41.28 +   0.08)

alignment

secondary structure

dotplot

Window 4

Location	8,091,520 – 8,091,633
Length	113
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	92.36
Mean single sequence MFE	-33.42
Consensus MFE	-29.42
Energy contribution	-29.98
Covariance contribution	0.56
Combinations/Pair	1.03
Mean z-score	-1.21
Structure conservation index	0.88
SVM decision value	0.13
SVM RNA-class probability	0.600223
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 8091520 113 + 27905053
UUUAUGCUGGCAGCUCCUAAUUGAUGCAGUUAGUUGCGUGC-------UGCAACUGGAACCCUUUAAUUGAUGCUUCGGUUUGGGAAUAGAUUGCUGCUGCACUGAUAGCAACUUUGUGU
....(((((.((((..(((((((...)))))))..))((((-------.(((((((...(((...((((((....)))))).)))..))).))))....)))))).)))))......... ( -33.90)
>DroSec_CAF1 43299 113 + 1
UUUAUGCUGCCAGCUCCUAAUUGAUGCAGUUAGUUGCGUGC-------UGCAACUGGAACCCUUUAAUUGAUGCUUCGGUUUGGGAAUAGAUUGCUGCUGCACUGAUAGCAACUUUGUGU
....(((((.((((..(((((((...)))))))..))((((-------.(((((((...(((...((((((....)))))).)))..))).))))....)))))).)))))......... ( -33.90)
>DroSim_CAF1 15305 113 + 1
UUUAUGCUGGCAGCUCCUAAUUGAUGCAGUUAGUUGCGUGC-------UGCAACUGGAACCCUUUAAUUGAUGCUUCGGUUUGGGAAUAGAUUGCUGCUGCACUGAUAGCAACUUUGUGU
....(((((.((((..(((((((...)))))))..))((((-------.(((((((...(((...((((((....)))))).)))..))).))))....)))))).)))))......... ( -33.90)
>DroEre_CAF1 18342 119 + 1
UUUAUGCUGGCAGCUCCUAAUUGAUGCAGUUAGCUGCGUGCAGUGAGUUGCGACUGGAACCCUUUAAUUGAUGCUUCGG-UUGGGAAUAGAUUGCUGCAGCACUGAUAGCAACUUUGUUU
.........(((((((...((((((((((....)))))).)))))))))))........(((...((((((....))))-)))))((((((((((((((....)).)))))).)))))). ( -35.80)
>DroYak_CAF1 11693 118 + 1
UUUAUGCUGGCAGCUCCUAAUUGAUGCAGUUAGUUGCGUGCAGUUAGUUGCGACUGGAACCCUUUAAUUGAUGCUUCGC-UUGGGAAUAGAUUGGU-UGGCACUGAUAGCAACUUUGUGU
....(((..((.((..(((((((((((((....)))))).)))))))..))..(((...(((......(((....))).-..)))..)))....))-..))).................. ( -29.60)
>consensus
UUUAUGCUGGCAGCUCCUAAUUGAUGCAGUUAGUUGCGUGC_______UGCAACUGGAACCCUUUAAUUGAUGCUUCGGUUUGGGAAUAGAUUGCUGCUGCACUGAUAGCAACUUUGUGU
....(((((.((((..(((((((...)))))))..))((((........(((((((...(((...((((((....)))))).)))..))).))))....)))))).)))))......... (-29.42 = -29.98 +   0.56)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:51:33 2006