Locus 3878

Sequence ID	2L_DroMel_CAF1
Location	11,349,551 – 11,349,650
Length	99
Max. P	0.992491

overview

Window 8

Location	11,349,551 – 11,349,650
Length	99
Sequences	4
Columns	107
Reading direction	forward
Mean pairwise identity	89.03
Mean single sequence MFE	-34.08
Consensus MFE	-29.64
Energy contribution	-29.20
Covariance contribution	-0.44
Combinations/Pair	1.06
Mean z-score	-2.68
Structure conservation index	0.87
SVM decision value	2.17
SVM RNA-class probability	0.989491
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 11349551 99 + 22407834
CCGGCAAAGAUCUGAGGGUAAGCCGAAAUUGAUUUGCUCCUUAGCCGAGCAACUUCUCGGCUUCGAUCAAUAUGUGG--------AUCUAUAGAUCUGUAGAAUCGG
((((....(((((((((((((..((....))..)))).)))))((((((......))))))...))))....((..(--------(((....))))..))...)))) ( -32.10)
>DroSec_CAF1 66739 107 + 1
CCGGCAAAGAUCUGAGGGUAAGCCGAAAUUGAUUUGCUCCUUAGCCGAGCAACUUCUCGGCUUCGAUCAGUAUGUGGAUCUAUAGAUCUAUAGAUCUGUGGAAUCGG
((((....(((((((((((((..((....))..)))).)))))((((((......))))))...))))..........((((((((((....)))))))))).)))) ( -38.00)
>DroSim_CAF1 71503 91 + 1
CCGGCAAAGAUCUGAGGGUAAGCCGAAAUUGAUUUGCUCCUUAGCCGAGCAACUUCUCGGCUUCGAUC----------------GAUCUAUAGAUCUGUGGAAUCGG
((((....(((((((((((((..((....))..)))).)))))((((((......))))))...))))----------------..((((((....)))))).)))) ( -29.50)
>DroYak_CAF1 68208 99 + 1
CCGGCAAAGAUCUGAGGGUAAACCGAAAUUGAUUUGCUCCUUAGCCGAGCAACUUCUCGGCUUCGAUCGUUCUGUA--------GAUCUAUAGAUCUGUAGAAUCGG
(((.....((((((((((((((.((....)).))))).)))))((((((......))))))...))))((((((((--------((((....))))))))))))))) ( -36.70)
>consensus
CCGGCAAAGAUCUGAGGGUAAGCCGAAAUUGAUUUGCUCCUUAGCCGAGCAACUUCUCGGCUUCGAUCA_UAUGUG________GAUCUAUAGAUCUGUAGAAUCGG
((((....((((((((((((((.((....)).))))).)))))((((((......))))))...))))..................((((((....)))))).)))) (-29.64 = -29.20 +  -0.44)

alignment

secondary structure

dotplot

Window 9

Location	11,349,551 – 11,349,650
Length	99
Sequences	4
Columns	107
Reading direction	reverse
Mean pairwise identity	89.03
Mean single sequence MFE	-31.10
Consensus MFE	-27.78
Energy contribution	-27.59
Covariance contribution	-0.19
Combinations/Pair	1.07
Mean z-score	-2.67
Structure conservation index	0.89
SVM decision value	2.33
SVM RNA-class probability	0.992491
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 11349551 99 - 22407834
CCGAUUCUACAGAUCUAUAGAU--------CCACAUAUUGAUCGAAGCCGAGAAGUUGCUCGGCUAAGGAGCAAAUCAAUUUCGGCUUACCCUCAGAUCUUUGCCGG
(((....((.((((((...(((--------(........)))).(((((((((..((((((.......)))))).....)))))))))......)))))).)).))) ( -29.60)
>DroSec_CAF1 66739 107 - 1
CCGAUUCCACAGAUCUAUAGAUCUAUAGAUCCACAUACUGAUCGAAGCCGAGAAGUUGCUCGGCUAAGGAGCAAAUCAAUUUCGGCUUACCCUCAGAUCUUUGCCGG
(((........((((((((....))))))))......((((...(((((((((..((((((.......)))))).....)))))))))....))))........))) ( -35.00)
>DroSim_CAF1 71503 91 - 1
CCGAUUCCACAGAUCUAUAGAUC----------------GAUCGAAGCCGAGAAGUUGCUCGGCUAAGGAGCAAAUCAAUUUCGGCUUACCCUCAGAUCUUUGCCGG
(((........((((....))))----------------((((.(((((((((..((((((.......)))))).....))))))))).......)))).....))) ( -29.00)
>DroYak_CAF1 68208 99 - 1
CCGAUUCUACAGAUCUAUAGAUC--------UACAGAACGAUCGAAGCCGAGAAGUUGCUCGGCUAAGGAGCAAAUCAAUUUCGGUUUACCCUCAGAUCUUUGCCGG
(((.((((..(((((....))))--------)..)))).((((..(((((((......))))))).(((.(.(((((......))))).))))..)))).....))) ( -30.80)
>consensus
CCGAUUCCACAGAUCUAUAGAUC________CACAUA_UGAUCGAAGCCGAGAAGUUGCUCGGCUAAGGAGCAAAUCAAUUUCGGCUUACCCUCAGAUCUUUGCCGG
(((....((.((((((...((((................)))).(((((((((..((((((.......)))))).....)))))))))......)))))).)).))) (-27.78 = -27.59 +  -0.19)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:03:30 2006