Locus 3109

Sequence ID	3R_DroMel_CAF1
Location	8,198,898 – 8,199,058
Length	160
Max. P	0.892402

overview

Window 4

Location	8,198,898 – 8,199,018
Length	120
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	92.64
Mean single sequence MFE	-39.13
Consensus MFE	-35.40
Energy contribution	-34.90
Covariance contribution	-0.50
Combinations/Pair	1.14
Mean z-score	-1.81
Structure conservation index	0.90
SVM decision value	0.97
SVM RNA-class probability	0.892402
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 8198898 120 + 27905053
UACGCUGAAAGGGGAGCAAAUGAAUCCCGAUUUCAUCAAGAUCAACCCGCAGCACUCGAUUCCCACGCUGGUAGACAAUGGUUUCACCAUUUGGGAGUCGCGUGCCAUUCUCGUUUACCU
...((.....((((..(....)..))))(((((.....))))).....)).((((.(((((((((...((((((((....)))).))))..))))))))).))))............... ( -37.70)
>DroSim_CAF1 14586 120 + 1
UACGCUGGAGGGGGAGCAAAUGAAUCCGGAUUUCAUCAAGAUCAACCCGCAGCAUUCGAUUCCCACGCUGGUGGACAAUGGUUUCACCAUUUGGGAAUCGCGUGCCAUUCUCGUUUACCU
...((.(((((((((.........))).(((((.....)))))..)))...((((.(((((((((...(((((((.......)))))))..))))))))).))))...))).))...... ( -39.00)
>DroEre_CAF1 14258 120 + 1
UACCCUGGAGGGGGAGCAACUGAAUCCGGAUUUCAUCAAGAUCAAUCCCCAGCACUCGAUUCCCACGCUGGUGGACAAUGGCUUCACCAUUUGGGAGUCGCGUGCCAUUCUGGUUUACCU
....(..((((((((.....(((.((..(((...)))..))))).))))).((((.(((((((((...(((((((.......)))))))..))))))))).))))..)))..)....... ( -44.80)
>DroYak_CAF1 14303 120 + 1
UACCCUGGAAGGGGAGCAACUGAAUCCGGAUUUCAUCAAGAUCAACCCCCAGCACUCGAUUCCCACGCUGGUUGACAAUGGCUUUACCAUUUGGGAGUCUCGUGCCAUCCUGGUUUACCU
.(((..(((.((((.(....(((.((..(((...)))..))))).))))).((((..((((((((...((((.............))))..))))))))..))))..))).)))...... ( -35.02)
>consensus
UACCCUGGAAGGGGAGCAAAUGAAUCCGGAUUUCAUCAAGAUCAACCCCCAGCACUCGAUUCCCACGCUGGUGGACAAUGGCUUCACCAUUUGGGAGUCGCGUGCCAUUCUCGUUUACCU
.(((..(((.(((((.........))).(((((.....)))))...))...((((.(((((((((...(((((((.......)))))))..))))))))).))))..))).)))...... (-35.40 = -34.90 +  -0.50)

alignment

secondary structure

dotplot

Window 5

Location	8,198,898 – 8,199,018
Length	120
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	92.64
Mean single sequence MFE	-41.10
Consensus MFE	-33.46
Energy contribution	-34.40
Covariance contribution	0.94
Combinations/Pair	1.08
Mean z-score	-1.67
Structure conservation index	0.81
SVM decision value	0.21
SVM RNA-class probability	0.634602
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 8198898 120 - 27905053
AGGUAAACGAGAAUGGCACGCGACUCCCAAAUGGUGAAACCAUUGUCUACCAGCGUGGGAAUCGAGUGCUGCGGGUUGAUCUUGAUGAAAUCGGGAUUCAUUUGCUCCCCUUUCAGCGUA
........((((..(((((.(((.(((((..((((((........)).))))...))))).))).)))))((((((.(((((((((...))))))))).)))))).....))))...... ( -40.90)
>DroSim_CAF1 14586 120 - 1
AGGUAAACGAGAAUGGCACGCGAUUCCCAAAUGGUGAAACCAUUGUCCACCAGCGUGGGAAUCGAAUGCUGCGGGUUGAUCUUGAUGAAAUCCGGAUUCAUUUGCUCCCCCUCCAGCGUA
........(((...((((..(((((((((..(((((...........)))))...)))))))))..))))((((((.(((((.(((...))).))))).)))))).....)))....... ( -40.70)
>DroEre_CAF1 14258 120 - 1
AGGUAAACCAGAAUGGCACGCGACUCCCAAAUGGUGAAGCCAUUGUCCACCAGCGUGGGAAUCGAGUGCUGGGGAUUGAUCUUGAUGAAAUCCGGAUUCAGUUGCUCCCCCUCCAGGGUA
......(((.....(((((.(((.(((((..(((((...........)))))...))))).))).)))))((((((((((((.(((...))).))).))))....)))))......))). ( -42.30)
>DroYak_CAF1 14303 120 - 1
AGGUAAACCAGGAUGGCACGAGACUCCCAAAUGGUAAAGCCAUUGUCAACCAGCGUGGGAAUCGAGUGCUGGGGGUUGAUCUUGAUGAAAUCCGGAUUCAGUUGCUCCCCUUCCAGGGUA
......(((.(((.(((((..((.(((((..((((...((....))..))))...))))).))..)))))((((((.(((((.(((...))).))))).....))))))..)))..))). ( -40.50)
>consensus
AGGUAAACCAGAAUGGCACGCGACUCCCAAAUGGUGAAACCAUUGUCCACCAGCGUGGGAAUCGAGUGCUGCGGGUUGAUCUUGAUGAAAUCCGGAUUCAGUUGCUCCCCCUCCAGCGUA
......(((.....(((((.(((.(((((..(((((...........)))))...))))).))).)))))((((((((((((.(((...))).))).))))....)))))......))). (-33.46 = -34.40 +   0.94)

alignment

secondary structure

dotplot

Window 6

Location	8,198,938 – 8,199,058
Length	120
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	93.06
Mean single sequence MFE	-39.93
Consensus MFE	-33.44
Energy contribution	-33.62
Covariance contribution	0.19
Combinations/Pair	1.10
Mean z-score	-1.52
Structure conservation index	0.84
SVM decision value	0.05
SVM RNA-class probability	0.559796
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 8198938 120 + 27905053
AUCAACCCGCAGCACUCGAUUCCCACGCUGGUAGACAAUGGUUUCACCAUUUGGGAGUCGCGUGCCAUUCUCGUUUACCUGGUGGAAAAGUACGGAAAGGAUGACGCGCUGUACCCCAAG
........(((((....((((((((...((((((((....)))).))))..))))))))((((.((.(((.(((...((....))......)))))).))...)))))))))........ ( -39.90)
>DroSim_CAF1 14626 120 + 1
AUCAACCCGCAGCAUUCGAUUCCCACGCUGGUGGACAAUGGUUUCACCAUUUGGGAAUCGCGUGCCAUUCUCGUUUACCUGGUGGAAAAGUACGGAAAGGAUGACGCGCUGUACCCCAAG
........(((((....((((((((...(((((((.......)))))))..))))))))((((.((.(((.(((...((....))......)))))).))...)))))))))........ ( -41.70)
>DroEre_CAF1 14298 120 + 1
AUCAAUCCCCAGCACUCGAUUCCCACGCUGGUGGACAAUGGCUUCACCAUUUGGGAGUCGCGUGCCAUUCUGGUUUACCUGGUGGAAAAGUACGGAAAGGACGACUCCCUGUACCCCAAG
.....((((((((((.(((((((((...(((((((.......)))))))..))))))))).))))......((....))))).)))...((((((..((.....))..))))))...... ( -45.20)
>DroYak_CAF1 14343 120 + 1
AUCAACCCCCAGCACUCGAUUCCCACGCUGGUUGACAAUGGCUUUACCAUUUGGGAGUCUCGUGCCAUCCUGGUUUACCUGGUGGAAAAGUAUGGAAAGGACGACUCCCUGUACCCCAAG
.((((((...(((.............))))))))).(((((.....))))).(((((((((.(.((((.((..(((((...)))))..)).))))..).)).)))))))........... ( -32.92)
>consensus
AUCAACCCCCAGCACUCGAUUCCCACGCUGGUGGACAAUGGCUUCACCAUUUGGGAGUCGCGUGCCAUUCUCGUUUACCUGGUGGAAAAGUACGGAAAGGACGACGCCCUGUACCCCAAG
...........((((.(((((((((...(((((((.......)))))))..))))))))).)))).................(((....((((((...(.....)...)))))).))).. (-33.44 = -33.62 +   0.19)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:53:19 2006