Locus 811

Sequence ID	2R_DroMel_CAF1
Location	3,824,974 – 3,825,108
Length	134
Max. P	0.998775

overview

Window 8

Location	3,824,974 – 3,825,077
Length	103
Sequences	5
Columns	105
Reading direction	reverse
Mean pairwise identity	88.67
Mean single sequence MFE	-30.18
Consensus MFE	-21.22
Energy contribution	-22.38
Covariance contribution	1.16
Combinations/Pair	1.13
Mean z-score	-2.97
Structure conservation index	0.70
SVM decision value	1.21
SVM RNA-class probability	0.931360
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 3824974 103 - 20766785
--CUUAUUGCUGCACUUCAAUGUCGGAUUUCCGUUCGGGGAUCCGACACUUCUUCACAAGAAAUCCUUGAAUGUAAUCCUCGUUGCAUAUUGCGGUCAUCGCUUC
--......((((((......((((((((..((....))..))))))))........((((.....)))).(((((((....)))))))..))))))......... ( -32.50)
>DroSec_CAF1 81003 105 - 1
CCCCUCCUGCUGCACUUCAAUGUCGGACUUCCGCUCGGGGAUCCGACACUUCUUCACAAGAAAUCCUUGAAUGUAAUCCUCGCUGCAUAUUGCGGUCAUCGCUUC
........((((((.((((((((((((..(((....)))..))))))).((((.....))))....)))))))))......(((((.....)))))....))... ( -27.90)
>DroSim_CAF1 98494 105 - 1
CCCCUCCUGCUACACUUCAAUGUCGGAUUUCCGCUCGGGGAUCCGACACUUCUUCGCAAGAAAUCCUUGAAUGUAAUCCUCGCUGCAUAUUGCGGUCAUCGCUUC
........((((((.(((((((((((((..((....))..))))))))....(((....)))....)))))))))......(((((.....)))))....))... ( -34.90)
>DroEre_CAF1 82364 105 - 1
CCUUUACAGCUGCACUUCAGUGUCGGAUUUCCGUUGGAGGAUCCAACCCUUCUGCACAAGAAAUCCUUGAACGUAAUCCUCGCUGCAUAUUGCGGUCAUCGCUUC
........((((((...(((((..(((((..((((.((((((.......((((.....)))))))))).)))).))))).))))).....))))))......... ( -30.71)
>DroYak_CAF1 78963 105 - 1
CUUAUUCAACUGCCCUUUAAUGACGGAUUUCCGGUCGAGGAUCCAACCCUUCUUCACAAGAAAUCCUUGAACGUAAUCCUCGCUGCAUAUUGCGGUCAUCGCUUC
...................((((((((((..((.((((((((.......((((.....)))))))))))).)).))))).(((........))))))))...... ( -24.91)
>consensus
CCCCUACUGCUGCACUUCAAUGUCGGAUUUCCGCUCGGGGAUCCGACACUUCUUCACAAGAAAUCCUUGAAUGUAAUCCUCGCUGCAUAUUGCGGUCAUCGCUUC
........((((((.(((((.(((((((((((....)))))))))))..((((.....))))....)))))))))......(((((.....)))))....))... (-21.22 = -22.38 +   1.16)

alignment

secondary structure

dotplot

Window 9

Location	3,825,011 – 3,825,108
Length	97
Sequences	5
Columns	101
Reading direction	reverse
Mean pairwise identity	77.72
Mean single sequence MFE	-21.61
Consensus MFE	-12.82
Energy contribution	-14.02
Covariance contribution	1.20
Combinations/Pair	1.00
Mean z-score	-3.06
Structure conservation index	0.59
SVM decision value	3.22
SVM RNA-class probability	0.998775
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 3825011 97 - 20766785
UCCACACUCGAAAAUAUUUUUCAGCACCACC----CUUAUUGCUGCACUUCAAUGUCGGAUUUCCGUUCGGGGAUCCGACACUUCUUCACAAGAAAUCCUU
.........(((.........(((((.....----.....)))))........((((((((..((....))..))))))))....)))............. ( -24.40)
>DroSec_CAF1 81040 101 - 1
UCCACUGCCGAACAUUGUUUUCAGCUCCACCUUCCCCUCCUGCUGCACUUCAAUGUCGGACUUCCGCUCGGGGAUCCGACACUUCUUCACAAGAAAUCCUU
....((...(((.((((....((((................)))).....))))((((((..(((....)))..)))))).....)))...))........ ( -20.39)
>DroSim_CAF1 98531 101 - 1
UCCACACGCGAAAAUUAUUUUCAGCUCCACCUUCCCCUCCUGCUACACUUCAAUGUCGGAUUUCCGCUCGGGGAUCCGACACUUCUUCGCAAGAAAUCCUU
.......(((((..........(((................))).........((((((((..((....))..))))))))....)))))........... ( -27.29)
>DroEre_CAF1 82401 101 - 1
UUCACACUCUCAAAUAGUUUUCAGCGCUACCAUCCUUUACAGCUGCACUUCAGUGUCGGAUUUCCGUUGGAGGAUCCAACCCUUCUGCACAAGAAAUCCUU
...(((((.......(((...((((................)))).)))..))))).(((((((.((.(((((.......))))).))....))))))).. ( -20.99)
>DroYak_CAF1 79000 90 - 1
UCCACACAUAAAAAU-----------CUACCAUCUUAUUCAACUGCCCUUUAAUGACGGAUUUCCGGUCGAGGAUCCAACCCUUCUUCACAAGAAAUCCUU
...............-----------...............................(((((((..((.(((((.........)))))))..))))))).. ( -15.00)
>consensus
UCCACACUCGAAAAUAGUUUUCAGCUCCACCAUCCCCUACUGCUGCACUUCAAUGUCGGAUUUCCGCUCGGGGAUCCGACACUUCUUCACAAGAAAUCCUU
......................................................(((((((((((....)))))))))))..((((.....))))...... (-12.82 = -14.02 +   1.20)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:47:59 2006