Locus 632

Sequence ID	2R_DroMel_CAF1
Location	3,176,175 – 3,176,295
Length	120
Max. P	0.967781

overview

Window 8

Location	3,176,175 – 3,176,295
Length	120
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	83.61
Mean single sequence MFE	-37.85
Consensus MFE	-25.16
Energy contribution	-26.98
Covariance contribution	1.81
Combinations/Pair	1.18
Mean z-score	-2.28
Structure conservation index	0.66
SVM decision value	1.00
SVM RNA-class probability	0.897209
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 3176175 120 + 20766785
GAGCAGGAUAAGCUUCAUGUCCUGAUAAACAAUGCAGGAGUUAUGCACUGUCCCAGAACACUGACCAAGGAUGGCUUCGAAAUGCAGUUGGGAGUCAACCAUAUGGGACACUUCCUGCUC
((((((((...((......(((((..........))))).....))..((((((((....))......((.(((((((.((......)).))))))).))....))))))..)))))))) ( -40.90)
>DroSim_CAF1 2341 120 + 1
GAGCAGGAUAAGCUCCAUGUCCUGAUCAACAAUGCAGGAGUUAUGCACUGUCCCAAAACACUGACCAAGGAUGGCUUCGAAAUGCAGCUGGGAGUCAACCAUAUGGGACACUUUCUGCUC
((((((((..((((((.(((..((.....))..)))))))))......(((((((......(((((..((...((........))..))..).))))......)))))))..)))))))) ( -39.60)
>DroWil_CAF1 13527 120 + 1
GAACAGGAUAAGCUGCAUAUAUUGAUAAACAAUGCCGGGCAAAUGAAUUGUCCAAAAUCUCUAACUAAAGAUGGCUUUGAGAUGCAUCUUGGUGUGAAUCAUUUGGGGCAUUUUCUACUG
....((((...(((.((.....((((..(((..(((((((((.....))))))...((((........))))))).(..(((....)))..))))..))))..)).)))...)))).... ( -27.50)
>DroYak_CAF1 2374 120 + 1
GAGCAGGAUAAGCUCCAUGUCCUAGUCAACAAUGCAGGAGUUAUGCACUGUCCCAAAACACUGACGAAGGACGGCUUCGAAAUGCAGUUGGGAGUCAACCAUAUGGGACACUUCCUGCUC
((((((((...(..(((((((((.(((((((.((((.......)))).)))..........))))..)))))((((((.((......)).))))))......))))..)...)))))))) ( -43.40)
>consensus
GAGCAGGAUAAGCUCCAUGUCCUGAUAAACAAUGCAGGAGUUAUGCACUGUCCCAAAACACUGACCAAGGAUGGCUUCGAAAUGCAGCUGGGAGUCAACCAUAUGGGACACUUCCUGCUC
((((((((..((((((.(((..((.....))..)))))))))......(((((((......((((...((...((........))..))....))))......)))))))..)))))))) (-25.16 = -26.98 +   1.81)

alignment

secondary structure

dotplot

Window 9

Location	3,176,175 – 3,176,295
Length	120
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	83.61
Mean single sequence MFE	-39.35
Consensus MFE	-25.90
Energy contribution	-26.78
Covariance contribution	0.88
Combinations/Pair	1.23
Mean z-score	-2.77
Structure conservation index	0.66
SVM decision value	1.62
SVM RNA-class probability	0.967781
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 3176175 120 - 20766785
GAGCAGGAAGUGUCCCAUAUGGUUGACUCCCAACUGCAUUUCGAAGCCAUCCUUGGUCAGUGUUCUGGGACAGUGCAUAACUCCUGCAUUGUUUAUCAGGACAUGAAGCUUAUCCUGCUC
((((((((............(((((.....)))))((........((((....))))..((((((((((((((((((.......)))))))))..)))))))))...))...)))))))) ( -43.10)
>DroSim_CAF1 2341 120 - 1
GAGCAGAAAGUGUCCCAUAUGGUUGACUCCCAGCUGCAUUUCGAAGCCAUCCUUGGUCAGUGUUUUGGGACAGUGCAUAACUCCUGCAUUGUUGAUCAGGACAUGGAGCUUAUCCUGCUC
(((((....((((((....((((..((((((((..(((((.....((((....)))).))))).)))))).((((((.......))))))))..))))))))))(((.....)))))))) ( -40.80)
>DroWil_CAF1 13527 120 - 1
CAGUAGAAAAUGCCCCAAAUGAUUCACACCAAGAUGCAUCUCAAAGCCAUCUUUAGUUAGAGAUUUUGGACAAUUCAUUUGCCCGGCAUUGUUUAUCAAUAUAUGCAGCUUAUCCUGUUC
..(((((.((((((.(((((((......(((((((((........))..(((......))).))))))).....)))))))...)))))).)))))........((((......)))).. ( -25.00)
>DroYak_CAF1 2374 120 - 1
GAGCAGGAAGUGUCCCAUAUGGUUGACUCCCAACUGCAUUUCGAAGCCGUCCUUCGUCAGUGUUUUGGGACAGUGCAUAACUCCUGCAUUGUUGACUAGGACAUGGAGCUUAUCCUGCUC
((((((((...(..((((.((((..((((((((..(((((.(((((.....)))))..))))).)))))).((((((.......))))))))..))))....))))..)...)))))))) ( -48.50)
>consensus
GAGCAGAAAGUGUCCCAUAUGGUUGACUCCCAACUGCAUUUCGAAGCCAUCCUUGGUCAGUGUUUUGGGACAGUGCAUAACUCCUGCAUUGUUGAUCAGGACAUGGAGCUUAUCCUGCUC
((((((((...((.((((.((((..(((((((...((((..(.(((.....))).)...))))..))))).((((((.......))))))))..))))....)))).))...)))))))) (-25.90 = -26.78 +   0.88)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:43:16 2006