Locus 361

Sequence ID	2R_DroMel_CAF1
Location	2,341,187 – 2,341,294
Length	107
Max. P	0.988589

overview

Window 1

Location	2,341,187 – 2,341,294
Length	107
Sequences	5
Columns	107
Reading direction	forward
Mean pairwise identity	90.09
Mean single sequence MFE	-34.38
Consensus MFE	-27.36
Energy contribution	-28.08
Covariance contribution	0.72
Combinations/Pair	1.10
Mean z-score	-2.58
Structure conservation index	0.80
SVM decision value	2.13
SVM RNA-class probability	0.988589
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 2341187 107 + 20766785
CGGAGGACGAAAGCCGAACGGCUGAAGGCCGGGGAAAGUGAAUCACAGUUGCGCCAUUAGGAGGCCGUGAAAUAAAUUCAAUAUAAGCGGGUCCUAAUGGCGGUAGU
....((.(....)))...((((.....))))......(((...))).....(((((((((((..((((...(((.......)))..)))).)))))))))))..... ( -35.20)
>DroSec_CAF1 113584 107 + 1
CGGAGGGCGAAAGCCGAACGACUGAAGGCCGGGGAAAGUGAAUCACAGUUGCGCCAUUAGGAGCCCGUGAAAUAAGUUCAAUAUAAGCGGGGCCUAAUGGCGGUAGU
((...(((....)))...)).......(((.(.((..(((...)))..)).)(((((((((..(((((...(((.......)))..))))).))))))))))))... ( -38.90)
>DroSim_CAF1 106530 107 + 1
CGGAGGGCGAAAGCCGAACGGCUGAAGGCCGGGGAAAGUGAAUCACAGUUGCGUCAUUAGGAGCCUGUGAAAUAAAUUCAAUAUAAGCGGGGCCUAAUGGCGGUAGU
.....(((....)))...((((.....))))......(((...))).....((((((((((..(((((...(((.......)))..))))).))))))))))..... ( -37.00)
>DroEre_CAF1 105078 107 + 1
CAGAAGGCGGAGGGCGUUAGGAUGAAGGCCGGGGAAAGUGAAUCACAGUUGCGCCAUUAGGAGCCCGUGAAAUAAAUUCAAUAUAAGCGGGGCCUAAUGGCGGUAGU
......((((..(((.((......)).))).......(((...)))..))))(((((((((..(((((...(((.......)))..))))).)))))))))...... ( -33.30)
>DroYak_CAF1 101839 103 + 1
-AGAGUUGGGAGGAC---AGGAUGAAGGGCGGGGAAAGUGAAUCACAGUUGCGCCAUUAGGAGCCCGUGAAAUAAAUUCAAUAUAAGCGGGGCCUAAUGGCGGUAGU
-...........(((---..(((.....((.......))..)))...))).((((((((((..(((((...(((.......)))..))))).))))))))))..... ( -27.50)
>consensus
CGGAGGGCGAAAGCCGAACGGCUGAAGGCCGGGGAAAGUGAAUCACAGUUGCGCCAUUAGGAGCCCGUGAAAUAAAUUCAAUAUAAGCGGGGCCUAAUGGCGGUAGU
.....(((....)))............(((.(.((..(((...)))..)).)(((((((((..(((((...(((.......)))..))))).))))))))))))... (-27.36 = -28.08 +   0.72)

alignment

secondary structure

dotplot

Window 2

Location	2,341,187 – 2,341,294
Length	107
Sequences	5
Columns	107
Reading direction	reverse
Mean pairwise identity	90.09
Mean single sequence MFE	-25.81
Consensus MFE	-20.25
Energy contribution	-22.45
Covariance contribution	2.20
Combinations/Pair	1.08
Mean z-score	-2.41
Structure conservation index	0.78
SVM decision value	1.71
SVM RNA-class probability	0.973412
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 2341187 107 - 20766785
ACUACCGCCAUUAGGACCCGCUUAUAUUGAAUUUAUUUCACGGCCUCCUAAUGGCGCAACUGUGAUUCACUUUCCCCGGCCUUCAGCCGUUCGGCUUUCGUCCUCCG
.....(((((((((((.(((.......((((.....)))))))..))))))))))).....................(((....((((....))))...)))..... ( -28.11)
>DroSec_CAF1 113584 107 - 1
ACUACCGCCAUUAGGCCCCGCUUAUAUUGAACUUAUUUCACGGGCUCCUAAUGGCGCAACUGUGAUUCACUUUCCCCGGCCUUCAGUCGUUCGGCUUUCGCCCUCCG
.....((((((((((.((((.......((((.....))))))))..)))))))))).....................(((....((((....))))...)))..... ( -29.21)
>DroSim_CAF1 106530 107 - 1
ACUACCGCCAUUAGGCCCCGCUUAUAUUGAAUUUAUUUCACAGGCUCCUAAUGACGCAACUGUGAUUCACUUUCCCCGGCCUUCAGCCGUUCGGCUUUCGCCCUCCG
........(((((((....((((....((((.....)))).)))).))))))).(((....))).............(((....((((....))))...)))..... ( -22.50)
>DroEre_CAF1 105078 107 - 1
ACUACCGCCAUUAGGCCCCGCUUAUAUUGAAUUUAUUUCACGGGCUCCUAAUGGCGCAACUGUGAUUCACUUUCCCCGGCCUUCAUCCUAACGCCCUCCGCCUUCUG
......(((((((((.((((.......((((.....))))))))..)))))))))((....(((...))).......(((.((......)).)))....))...... ( -26.01)
>DroYak_CAF1 101839 103 - 1
ACUACCGCCAUUAGGCCCCGCUUAUAUUGAAUUUAUUUCACGGGCUCCUAAUGGCGCAACUGUGAUUCACUUUCCCCGCCCUUCAUCCU---GUCCUCCCAACUCU-
.....((((((((((.((((.......((((.....))))))))..)))))))))).................................---..............- ( -23.21)
>consensus
ACUACCGCCAUUAGGCCCCGCUUAUAUUGAAUUUAUUUCACGGGCUCCUAAUGGCGCAACUGUGAUUCACUUUCCCCGGCCUUCAGCCGUUCGGCUUUCGCCCUCCG
.....((((((((((.((((.......((((.....))))))))..)))))))))).....................(((....((((....))))...)))..... (-20.25 = -22.45 +   2.20)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:36:24 2006