Locus 3268

Sequence ID	2L_DroMel_CAF1
Location	9,464,668 – 9,464,768
Length	100
Max. P	0.696038

overview

Window 9

Location	9,464,668 – 9,464,768
Length	100
Sequences	5
Columns	104
Reading direction	forward
Mean pairwise identity	83.85
Mean single sequence MFE	-19.84
Consensus MFE	-14.34
Energy contribution	-15.22
Covariance contribution	0.88
Combinations/Pair	1.11
Mean z-score	-1.78
Structure conservation index	0.72
SVM decision value	0.34
SVM RNA-class probability	0.696038
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 9464668 100 + 22407834
AAAUUUUCUACAGCGAAAUUUCUAAUAUUU-UUCGACCAUAGCUUCGAAAAUGGUGUCCCUUGCAAAAUGGUUUUC---GAAUGAUAGAAUUUUGCAUUUCAUU
............((((((((.(((.(((((-...((((((.((...((........))....))...))))))...---))))).)))))))))))........ ( -18.10)
>DroSec_CAF1 29485 95 + 1
AAAUUUUCUACAGCGAAAUUUCUAUUAUUUUUUCGACCAUAGCUUCGAAAAUGGUGUCCCUUGCAAAAUGUUUUUCGGCGAAUAAUAGAAUUUCG---------
.............(((((((.(((((((((((((((........)))))).....(((....((.....)).....)))))))))))))))))))--------- ( -18.30)
>DroSim_CAF1 29313 95 + 1
AAAUUUUCUACAGCGAAAUUUCUAUUAUUUUUUCGACCAUAGAUUCGAAAAUGGUGUCCAUUGCAAAAUGGUUUUCGGCGAAUAAUAGAAUUUCG---------
.............(((((((.(((((((((((((((........)))))).(((...(((((....)))))...)))..))))))))))))))))--------- ( -22.20)
>DroEre_CAF1 29326 102 + 1
AAAUAUUCUACAGCGAAACUUCUAUUACUU-UUCGAACUUAGCUUCGAAAAUGGUGUCCUUCGCAAAAUGGAUUUCGGCAAAUAAUA-AAUUUCGCAUUUUAUU
............((((((....(((((.((-((((((......))))))))(((.((((..........)))).))).....)))))-..))))))........ ( -18.00)
>DroYak_CAF1 29484 103 + 1
AAAUAUUCUACAGCGAAAAUUCUAUCACUU-UUCGAUCACAGCUUCGAAAAUGAUGUCCUUUGCAAAAUCGUUUUCGGCAAAUAAUAGAAUUUCGCAUUUCAUU
............((((((.((((((((.((-(((((........)))))))))).....(((((..((.....))..)))))...)))))))))))........ ( -22.60)
>consensus
AAAUUUUCUACAGCGAAAUUUCUAUUAUUU_UUCGACCAUAGCUUCGAAAAUGGUGUCCCUUGCAAAAUGGUUUUCGGCGAAUAAUAGAAUUUCGCAUUU_AUU
............((((((.(((((((((((.(((((........))))).((..(((.....)))..))..........)))))))))))))))))........ (-14.34 = -15.22 +   0.88)

alignment

secondary structure

dotplot

Window 0

Location	9,464,668 – 9,464,768
Length	100
Sequences	5
Columns	104
Reading direction	reverse
Mean pairwise identity	83.85
Mean single sequence MFE	-20.81
Consensus MFE	-12.62
Energy contribution	-13.86
Covariance contribution	1.24
Combinations/Pair	1.08
Mean z-score	-1.90
Structure conservation index	0.61
SVM decision value	-0.02
SVM RNA-class probability	0.524384
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 9464668 100 - 22407834
AAUGAAAUGCAAAAUUCUAUCAUUC---GAAAACCAUUUUGCAAGGGACACCAUUUUCGAAGCUAUGGUCGAA-AAAUAUUAGAAAUUUCGCUGUAGAAAAUUU
..(((((((((((((....((....---)).....)))))))).((....))..)))))...((((((.((((-(...........)))))))))))....... ( -17.70)
>DroSec_CAF1 29485 95 - 1
---------CGAAAUUCUAUUAUUCGCCGAAAAACAUUUUGCAAGGGACACCAUUUUCGAAGCUAUGGUCGAAAAAAUAAUAGAAAUUUCGCUGUAGAAAAUUU
---------(((((((((((((((.((.(((.....))).))..((....)).(((((((........))))))))))))))).)))))))............. ( -19.60)
>DroSim_CAF1 29313 95 - 1
---------CGAAAUUCUAUUAUUCGCCGAAAACCAUUUUGCAAUGGACACCAUUUUCGAAUCUAUGGUCGAAAAAAUAAUAGAAAUUUCGCUGUAGAAAAUUU
---------(((((((((((((((.........(((((....)))))......(((((((........))))))))))))))).)))))))............. ( -20.30)
>DroEre_CAF1 29326 102 - 1
AAUAAAAUGCGAAAUU-UAUUAUUUGCCGAAAUCCAUUUUGCGAAGGACACCAUUUUCGAAGCUAAGUUCGAA-AAGUAAUAGAAGUUUCGCUGUAGAAUAUUU
........((((((((-((((((((..((((..........((((((......))))))........))))..-))))))))..))))))))............ ( -20.37)
>DroYak_CAF1 29484 103 - 1
AAUGAAAUGCGAAAUUCUAUUAUUUGCCGAAAACGAUUUUGCAAAGGACAUCAUUUUCGAAGCUGUGAUCGAA-AAGUGAUAGAAUUUUCGCUGUAGAAUAUUU
........(((((((((((((((((..(((..(((.(((((.(((........))).))))).)))..)))..-))))))))))).))))))............ ( -26.10)
>consensus
AAU_AAAUGCGAAAUUCUAUUAUUCGCCGAAAACCAUUUUGCAAAGGACACCAUUUUCGAAGCUAUGGUCGAA_AAAUAAUAGAAAUUUCGCUGUAGAAAAUUU
........((((((((((((((((.((.(((.....))).)).............(((((........)))))..)))))))))).))))))............ (-12.62 = -13.86 +   1.24)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:48:26 2006