Locus 3874

Sequence ID	X_DroMel_CAF1
Location	10,325,596 – 10,325,756
Length	160
Max. P	0.995417

overview

Window 9

Location	10,325,596 – 10,325,716
Length	120
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	90.20
Mean single sequence MFE	-33.15
Consensus MFE	-29.90
Energy contribution	-31.40
Covariance contribution	1.50
Combinations/Pair	1.00
Mean z-score	-2.46
Structure conservation index	0.90
SVM decision value	2.12
SVM RNA-class probability	0.988439
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 10325596 120 + 22224390
AACCAGGGUCAAAAAUGAAAAGGAUGAGAAGAAUGACAACGAUGAGACUGAUUCGCCGCAUGAGGCUGCCGAGAUCGAGGAGCCCGAUGAAGAGGUGGAUGAGGCUGAUCAGGAGACCAA
......((((.....(....)...................(((.((.((.(((((((.(((..((((.(((....)).).))))..)))....))))))).)).)).)))....)))).. ( -35.00)
>DroSec_CAF1 3768 114 + 1
------GGUAAAAAAUGAAAAGGAUGAGAAGAGUGACAACGAUGAGACUGAUUCGCCGCAUGAGGCUGCCGAGAUCGAGGAGCCCGAUGAAGAGGUGGAUGAGGCUGAUCAAGGGACCAA
------(((.......................((....))(((.((.((.(((((((.(((..((((.(((....)).).))))..)))....))))))).)).)).))).....))).. ( -33.30)
>DroSim_CAF1 3530 114 + 1
------GGUCAAAAAUGAAAAGGAUGAGAAGAGUGACAACGAUGAGACUGAUUCGCCGCAUGAGGCUGCCGAGAUCGAGGAGCCCGAUGAAGAGGUGGAUGAGGCUGAUCAAGGGACCAA
------((((......................((....))(((.((.((.(((((((.(((..((((.(((....)).).))))..)))....))))))).)).)).)))....)))).. ( -36.80)
>DroEre_CAF1 4043 120 + 1
AGACAAGGAGAAAAACGAUAAGGAGGAUAAGAGUGACAACGAUGAGACUGAUUCGCCGCAGGAGGCUGCCGAGAUCGAGGAGCCCGAUGAGGAGGUGGAUGAUGCUGAUCAGGAGGCCAA
........................((......((....))(((.((..(.(((((((.((...((((.(((....)).).))))...))....))))))).)..)).)))......)).. ( -27.50)
>consensus
______GGUCAAAAAUGAAAAGGAUGAGAAGAGUGACAACGAUGAGACUGAUUCGCCGCAUGAGGCUGCCGAGAUCGAGGAGCCCGAUGAAGAGGUGGAUGAGGCUGAUCAAGAGACCAA
......((((......................((....))(((.((.((.(((((((.(((..((((.(((....)).).))))..)))....))))))).)).)).)))....)))).. (-29.90 = -31.40 +   1.50)

alignment

secondary structure

dotplot

Window 0

Location	10,325,636 – 10,325,756
Length	120
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	94.72
Mean single sequence MFE	-40.85
Consensus MFE	-39.29
Energy contribution	-39.85
Covariance contribution	0.56
Combinations/Pair	1.03
Mean z-score	-3.06
Structure conservation index	0.96
SVM decision value	2.57
SVM RNA-class probability	0.995417
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 10325636 120 - 22224390
GCCCUCCUUCUGACUGCCGUAAGCAGGCUGCUUGGUGGUCUUGGUCUCCUGAUCAGCCUCAUCCACCUCUUCAUCGGGCUCCUCGAUCUCGGCAGCCUCAUGCGGCGAAUCAGUCUCAUC
.........((((.(((((((.(.((((((((.(((((..((((((....))))))......))))).....((((((...))))))...))))))))).)))))))..))))....... ( -44.70)
>DroSec_CAF1 3802 120 - 1
ACCCUCCUUCUGACUGUCGUAAACAGGCUGCUUGGUGGUCUUGGUCCCUUGAUCAGCCUCAUCCACCUCUUCAUCGGGCUCCUCGAUCUCGGCAGCCUCAUGCGGCGAAUCAGUCUCAUC
.........((((.(((((((...((((((((.(((((..((((((....))))))......))))).....((((((...))))))...))))))))..)))))))..))))....... ( -39.60)
>DroSim_CAF1 3564 120 - 1
ACCCUCCUUCUGACUGCCGUAAACAGGCUGCUUGGUGGUCUUGGUCCCUUGAUCAGCCUCAUCCACCUCUUCAUCGGGCUCCUCGAUCUCGGCAGCCUCAUGCGGCGAAUCAGUCUCAUC
.........((((.(((((((...((((((((.(((((..((((((....))))))......))))).....((((((...))))))...))))))))..)))))))..))))....... ( -42.30)
>DroEre_CAF1 4083 120 - 1
ACCCUCUUUCUUACUGCCGUUAACAGGCUGCUUGGUGGUCUUGGCCUCCUGAUCAGCAUCAUCCACCUCCUCAUCGGGCUCCUCGAUCUCGGCAGCCUCCUGCGGCGAAUCAGUCUCAUC
..............((((((....((((((((.(((((.....((..........)).....))))).....((((((...))))))...))))))))...))))))............. ( -36.80)
>consensus
ACCCUCCUUCUGACUGCCGUAAACAGGCUGCUUGGUGGUCUUGGUCCCCUGAUCAGCCUCAUCCACCUCUUCAUCGGGCUCCUCGAUCUCGGCAGCCUCAUGCGGCGAAUCAGUCUCAUC
.........((((.(((((((...((((((((.(((((..((((((....))))))......))))).....((((((...))))))...))))))))..)))))))..))))....... (-39.29 = -39.85 +   0.56)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:10:48 2006