Locus 5492

Sequence ID	2R_DroMel_CAF1
Location	17,650,645 – 17,650,875
Length	230
Max. P	0.984607

overview

Window 2

Location	17,650,645 – 17,650,762
Length	117
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	95.09
Mean single sequence MFE	-38.98
Consensus MFE	-32.36
Energy contribution	-32.80
Covariance contribution	0.44
Combinations/Pair	1.03
Mean z-score	-2.28
Structure conservation index	0.83
SVM decision value	1.98
SVM RNA-class probability	0.984607
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 17650645 117 + 20766785
GUCUAAAGUAAAAGUAGCUGCAUUUACCUAGUUGCAACACCGCCAGAUGAAAGCUUCCGGGCAGGGGCGUUGCCCAUGGAAAUGGGAUGCAGCAGCU--UAAGACGGUGGAAAUUCCA-A
.((((..((..((((.((((((((.........(((((.(((((.((........))..)))...)).)))))((((....)))))))))))).)))--)...))..)))).......-. ( -39.40)
>DroSec_CAF1 4243 117 + 1
GUCUAAAGUAAAAGUAGCUGCAUUUACCCAGUUGCAACACCGCCAGAUGAAAGCUUCAGGGAAGGGGCGUUGCCCAUGGAAAUGGGAUGCAGCAGCU--UAAGACCGUGGAAAUUCCA-A
.((((..((..((((.((((((((.........(((((.((.((...(((.....))).....)))).)))))((((....)))))))))))).)))--)...))..)))).......-. ( -37.80)
>DroSim_CAF1 10161 117 + 1
GUCUAAAGUAAAAGUAGCUGCAUUUACCCAGUUGCAACACCGCCAGAUGAAAGCUUCCGGGCAGGGGCGUUGCCCAUGGAAAUGGGAUGCAGCAGCU--UAAGACCGUGGAAAUUCCA-A
.((((..((..((((.((((((((.........(((((.(((((.((........))..)))...)).)))))((((....)))))))))))).)))--)...))..)))).......-. ( -38.50)
>DroEre_CAF1 4306 117 + 1
GUCUAAAGUAAAAGUAGCUGCAUUUACCCAGUUGCAACACAGCCAGAUGAAAGCUUCCGGGCAGGGGCGUUGCCCAUGGAAAUGGGAUGCAGCAGCU--UAAGACCAAGGAAAUUCCA-A
((((.((((.......(((((((...((((((((.....))))...........((((((((((.....))))))..)))).))))))))))).)))--).))))...((.....)).-. ( -35.50)
>DroYak_CAF1 15580 120 + 1
GUCUAAAGUAAAAGUAGCUGCAUUUACCCAGUUGCAACACCGCCAGAUGAAAGCUUCCGGGCAGGGGCGUUGCCCAUGGAAAUGGGACGCUGCUGCUGCUUAGACCGAGGAAAUUCCAAA
((((((.(((...(((((((........)))))))....(((..((.(....)))..)))((((.(((((..(((((....)))))))))).)))))))))))))...((.....))... ( -43.70)
>consensus
GUCUAAAGUAAAAGUAGCUGCAUUUACCCAGUUGCAACACCGCCAGAUGAAAGCUUCCGGGCAGGGGCGUUGCCCAUGGAAAUGGGAUGCAGCAGCU__UAAGACCGUGGAAAUUCCA_A
((((........(((.(((((((...((((.((.((.....(((.((........))..)))..((((...)))).)).)).))))))))))).)))....))))...((.....))... (-32.36 = -32.80 +   0.44)

alignment

secondary structure

dotplot

Window 3

Location	17,650,645 – 17,650,762
Length	117
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	95.09
Mean single sequence MFE	-36.38
Consensus MFE	-31.26
Energy contribution	-31.90
Covariance contribution	0.64
Combinations/Pair	1.03
Mean z-score	-1.93
Structure conservation index	0.86
SVM decision value	1.82
SVM RNA-class probability	0.978902
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 17650645 117 - 20766785
U-UGGAAUUUCCACCGUCUUA--AGCUGCUGCAUCCCAUUUCCAUGGGCAACGCCCCUGCCCGGAAGCUUUCAUCUGGCGGUGUUGCAACUAGGUAAAUGCAGCUACUUUUACUUUAGAC
.-(((.....)))..((((.(--((..(((((((.((((....))))((((((((...(((.(((........))))))))))))))..........)))))))..))).......)))) ( -36.40)
>DroSec_CAF1 4243 117 - 1
U-UGGAAUUUCCACGGUCUUA--AGCUGCUGCAUCCCAUUUCCAUGGGCAACGCCCCUUCCCUGAAGCUUUCAUCUGGCGGUGUUGCAACUGGGUAAAUGCAGCUACUUUUACUUUAGAC
.-(((.....)))..((((.(--((..(((((((((((...(....)((((((((((.....(((.....)))...)).))))))))...))))...)))))))..))).......)))) ( -35.90)
>DroSim_CAF1 10161 117 - 1
U-UGGAAUUUCCACGGUCUUA--AGCUGCUGCAUCCCAUUUCCAUGGGCAACGCCCCUGCCCGGAAGCUUUCAUCUGGCGGUGUUGCAACUGGGUAAAUGCAGCUACUUUUACUUUAGAC
.-(((.....)))..((((.(--((..(((((((...........((((...)))).(((((((..((...((((....))))..))..))))))).)))))))..))).......)))) ( -37.60)
>DroEre_CAF1 4306 117 - 1
U-UGGAAUUUCCUUGGUCUUA--AGCUGCUGCAUCCCAUUUCCAUGGGCAACGCCCCUGCCCGGAAGCUUUCAUCUGGCUGUGUUGCAACUGGGUAAAUGCAGCUACUUUUACUUUAGAC
.-.((.....))...((((.(--((..(((((((...........((((...)))).(((((((..((...(((......)))..))..))))))).)))))))..))).......)))) ( -33.80)
>DroYak_CAF1 15580 120 - 1
UUUGGAAUUUCCUCGGUCUAAGCAGCAGCAGCGUCCCAUUUCCAUGGGCAACGCCCCUGCCCGGAAGCUUUCAUCUGGCGGUGUUGCAACUGGGUAAAUGCAGCUACUUUUACUUUAGAC
...((.....))..(((..(((.(((.((((((((((((....)))))..))))...(((((((..((...((((....))))..))..)))))))..))).))).)))..)))...... ( -38.20)
>consensus
U_UGGAAUUUCCACGGUCUUA__AGCUGCUGCAUCCCAUUUCCAUGGGCAACGCCCCUGCCCGGAAGCUUUCAUCUGGCGGUGUUGCAACUGGGUAAAUGCAGCUACUUUUACUUUAGAC
...((.....))...((((....((..(((((((((((...(....)((((((((.....(((((........))))).))))))))...))))...)))))))..))........)))) (-31.26 = -31.90 +   0.64)

alignment

secondary structure

dotplot

Window 4

Location	17,650,725 – 17,650,835
Length	110
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	89.56
Mean single sequence MFE	-34.18
Consensus MFE	-25.10
Energy contribution	-24.82
Covariance contribution	-0.28
Combinations/Pair	1.15
Mean z-score	-2.52
Structure conservation index	0.73
SVM decision value	1.11
SVM RNA-class probability	0.917222
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 17650725 110 - 20766785
AGAUAUAUGCUUUGUUUUAAGCGCA-------GCAGAUGGAAAUCCGAGGGGAUUUUCAUGAAAAUGUGUUCCAGUUACUU-UGGAAUUUCCACCGUCUUA--AGCUGCUGCAUCCCAUU
.(((....((((......))))(((-------((((((((((((((....))))))))))((...((.(((((((.....)-))))))...))...))...--..))))))))))..... ( -35.90)
>DroSec_CAF1 4323 110 - 1
AGAUAAAUGCUUUGUCUUAAGCGGA-------GGAGAUGGAAAUCCGAGGGGAUUUUCAUGAAAAUGUGUUCCAGUUACUU-UGGAAUUUCCACGGUCUUA--AGCUGCUGCAUCCCAUU
......((((...(.(((((((.(.-------((((((((((((((....))))))))))........(((((((.....)-)))))))))).).).))))--)))....))))...... ( -32.10)
>DroSim_CAF1 10241 110 - 1
AGAUAAAUGCUUUGUCUUAAGCGAA-------GCAGAUGGAAAUCCGAGGGGAUUUUCAUGAAAAUGUGUUCCAGUUACUU-UGGAAUUUCCACGGUCUUA--AGCUGCUGCAUCCCAUU
.......((((((((.....)))))-------))).((((((((((....))))))))))......((((..((((((((.-(((.....))).)))....--)))))..))))...... ( -32.10)
>DroEre_CAF1 4386 110 - 1
AGAUAAACGCUUUGUUUUAGGCGAG-------GCAGAUGGAAAUCCGAGGGGAUUUUCAUGAAAAUGAGUUCCAGUUACUU-UGGAAUUUCCUUGGUCUUA--AGCUGCUGCAUCCCAUU
........(((((((.....)))))-------)).(((((....((((((..(..(((((....)))))((((((.....)-))))))..)))))).....--.((....))...))))) ( -34.70)
>DroYak_CAF1 15660 120 - 1
AGAUAAAUGCUUUGUUUUAAGCCAGACAGAUGGCAGAUGGAAAUCCAAGGGGAUUUUCAUGAAAAUGAGUUCCAGUUACUUUUGGAAUUUCCUCGGUCUAAGCAGCAGCAGCGUCCCAUU
.(((...((((((((((...((((......))))((((((....))..(((((...((((....))))(((((((......))))))).))))).)))))))))).))))..)))..... ( -36.10)
>consensus
AGAUAAAUGCUUUGUUUUAAGCGAA_______GCAGAUGGAAAUCCGAGGGGAUUUUCAUGAAAAUGUGUUCCAGUUACUU_UGGAAUUUCCACGGUCUUA__AGCUGCUGCAUCCCAUU
.(((...(((((......))))).........((((((((((((((....))))))))))((...(((((((((........)))))....)))).))..........)))))))..... (-25.10 = -24.82 +  -0.28)

alignment

secondary structure

dotplot

Window 5

Location	17,650,762 – 17,650,875
Length	113
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	89.37
Mean single sequence MFE	-29.36
Consensus MFE	-22.74
Energy contribution	-22.82
Covariance contribution	0.08
Combinations/Pair	1.16
Mean z-score	-1.88
Structure conservation index	0.77
SVM decision value	0.73
SVM RNA-class probability	0.836535
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 17650762 113 - 20766785
AAAUUCGGUUGUAAACGCAUAUUUGCUGGAGAUAAAUGUAAGAUAUAUGCUUUGUUUUAAGCGCA-------GCAGAUGGAAAUCCGAGGGGAUUUUCAUGAAAAUGUGUUCCAGUUACU
......((.....(((((((((((((((.......(((((...)))))((((......)))).))-------))))))((((((((....))))))))......)))))))))....... ( -28.60)
>DroSec_CAF1 4360 112 - 1
-AACUCAAUUGUAAACGCAUAUUUGCUGGCGAUAAAUGUAAGAUAAAUGCUUUGUCUUAAGCGGA-------GGAGAUGGAAAUCCGAGGGGAUUUUCAUGAAAAUGUGUUCCAGUUACU
-.....(((((..(((((((.((((((...((((((.(((.......)))))))))...))))))-------....((((((((((....))))))))))....))))))).)))))... ( -30.00)
>DroSim_CAF1 10278 112 - 1
-AACUCGGUUGUAAACGCAUAUUUGCUGGCGAUAAAUGUAAGAUAAAUGCUUUGUCUUAAGCGAA-------GCAGAUGGAAAUCCGAGGGGAUUUUCAUGAAAAUGUGUUCCAGUUACU
-((((.((.....((((((((((((((.((........((((((((.....)))))))).))..)-------))))))((((((((....))))))))......)))))))))))))... ( -31.30)
>DroEre_CAF1 4423 113 - 1
AAACUCCGUUGAAAACGCGUAUUUGCUAGCGAUAAAUGUAAGAUAAACGCUUUGUUUUAGGCGAG-------GCAGAUGGAAAUCCGAGGGGAUUUUCAUGAAAAUGAGUUCCAGUUACU
.(((((.(((......((((..(((....)))...))))......)))(((((((.....)))))-------))..((((((((((....))))))))))......)))))......... ( -26.70)
>DroYak_CAF1 15700 120 - 1
GAACUCCGUUGAAAACGCAUAUUUGCUAGAGAUAAAUGUAAGAUAAAUGCUUUGUUUUAAGCCAGACAGAUGGCAGAUGGAAAUCCAAGGGGAUUUUCAUGAAAAUGAGUUCCAGUUACU
((((((..........(((....)))..((((((((.(((.......)))))))))))..((((......))))..((((((((((....))))))))))......))))))........ ( -30.20)
>consensus
_AACUCCGUUGUAAACGCAUAUUUGCUGGCGAUAAAUGUAAGAUAAAUGCUUUGUUUUAAGCGAA_______GCAGAUGGAAAUCCGAGGGGAUUUUCAUGAAAAUGUGUUCCAGUUACU
.............(((((((.((((((...((((((.(((.......)))))))))...))))))...........((((((((((....))))))))))....)))))))......... (-22.74 = -22.82 +   0.08)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:46:16 2006