Locus 7219

Sequence ID	2L_DroMel_CAF1
Location	20,254,783 – 20,254,968
Length	185
Max. P	0.938460

overview

Window 7

Location	20,254,783 – 20,254,903
Length	120
Sequences	3
Columns	120
Reading direction	reverse
Mean pairwise identity	99.44
Mean single sequence MFE	-38.50
Consensus MFE	-37.32
Energy contribution	-37.10
Covariance contribution	-0.22
Combinations/Pair	1.03
Mean z-score	-2.34
Structure conservation index	0.97
SVM decision value	1.27
SVM RNA-class probability	0.938460
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 20254783 120 - 22407834
GCAGCGCAUAGUGAACAUUUGCGCCUACAAGCGGGCAAUAGAUUUUGCAAUCUGCUCUGUAUUUGCGCACAUGAUUUUUCUCACUCAACGUGCGUUGCUUCCUGUCCGCGUUGUUGUUCA
((((((((((((((.(((.(((((.(((((((((((((......))))...))))).))))...))))).))).......)))))....)))))))))...................... ( -37.30)
>DroSec_CAF1 16326 120 - 1
GCAGCGCAUAGUGAACAUUUGCGCCUACGAGCGGGCAAUAGAUUUUGCAAUCUGCUCUGUAUUUGCGCACAUGAUUUUUCUCACUCAACGUGCGUUGCUUCCUGUCCGCGUUGUUGUUCA
((((((((((((((.(((.(((((.(((((((((((((......))))...)))))).)))...))))).))).......)))))....)))))))))...................... ( -39.10)
>DroSim_CAF1 14744 120 - 1
GCAGCGCAUAGUGAACAUUUGCGCCUACGAGCGGGCAAUAGAUUUUGCAAUCUGCUCUGUAUUUGCGCACAUGAUUUUUCUCACUCAACGUGCGUUGCUUCCUGUCCGCGUUGUUGUUCA
((((((((((((((.(((.(((((.(((((((((((((......))))...)))))).)))...))))).))).......)))))....)))))))))...................... ( -39.10)
>consensus
GCAGCGCAUAGUGAACAUUUGCGCCUACGAGCGGGCAAUAGAUUUUGCAAUCUGCUCUGUAUUUGCGCACAUGAUUUUUCUCACUCAACGUGCGUUGCUUCCUGUCCGCGUUGUUGUUCA
((((((((((((((.(((.(((((.(((((((((((((......))))...))))).))))...))))).))).......)))))....)))))))))...................... (-37.32 = -37.10 +  -0.22)

alignment

secondary structure

dotplot

Window 8

Location	20,254,823 – 20,254,943
Length	120
Sequences	3
Columns	120
Reading direction	reverse
Mean pairwise identity	97.22
Mean single sequence MFE	-37.60
Consensus MFE	-34.41
Energy contribution	-34.63
Covariance contribution	0.23
Combinations/Pair	1.05
Mean z-score	-2.57
Structure conservation index	0.92
SVM decision value	1.16
SVM RNA-class probability	0.923721
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 20254823 120 - 22407834
AUUGUUUCAAGUGAACUGCACUUUCGACCCACUGUGCCGUGCAGCGCAUAGUGAACAUUUGCGCCUACAAGCGGGCAAUAGAUUUUGCAAUCUGCUCUGUAUUUGCGCACAUGAUUUUUC
...(((..(((((.....)))))..))).(((((((((.....).))))))))..(((.(((((.(((((((((((((......))))...))))).))))...))))).)))....... ( -37.90)
>DroSec_CAF1 16366 120 - 1
AUUGUUCCAAGUGAACUGCACUUUCGACCCACUGUGCCGUGCAGCGCAUAGUGAACAUUUGCGCCUACGAGCGGGCAAUAGAUUUUGCAAUCUGCUCUGUAUUUGCGCACAUGAUUUUUC
...(((..(((((.....)))))..))).(((((((((.....).))))))))..(((.(((((.(((((((((((((......))))...)))))).)))...))))).)))....... ( -39.70)
>DroSim_CAF1 14784 120 - 1
AUUAUUCCAAGUAAACUGCAUUUUCGACCCACUGUGCCGUGCAGCGCAUAGUGAACAUUUGCGCCUACGAGCGGGCAAUAGAUUUUGCAAUCUGCUCUGUAUUUGCGCACAUGAUUUUUC
.............................(((((((((.....).))))))))..(((.(((((.(((((((((((((......))))...)))))).)))...))))).)))....... ( -35.20)
>consensus
AUUGUUCCAAGUGAACUGCACUUUCGACCCACUGUGCCGUGCAGCGCAUAGUGAACAUUUGCGCCUACGAGCGGGCAAUAGAUUUUGCAAUCUGCUCUGUAUUUGCGCACAUGAUUUUUC
...(((..(((((.....)))))..))).(((((((((.....).))))))))..(((.(((((.(((((((((((((......))))...))))).))))...))))).)))....... (-34.41 = -34.63 +   0.23)

alignment

secondary structure

dotplot

Window 9

Location	20,254,863 – 20,254,968
Length	105
Sequences	3
Columns	120
Reading direction	forward
Mean pairwise identity	80.51
Mean single sequence MFE	-27.90
Consensus MFE	-25.78
Energy contribution	-24.90
Covariance contribution	-0.88
Combinations/Pair	1.15
Mean z-score	-0.54
Structure conservation index	0.92
SVM decision value	0.50
SVM RNA-class probability	0.761829
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 20254863 105 + 22407834
UAUUGCCCGCUUGUAGGCGCAAAUGUUCACUAUGCGCUGCACGGCACAGUGGGUCGAAAGUGCAGUUCACUUGAAACAAUUUUCAGUUUUAU-ACUCAUAUCAUCA--------------
....((((((((((.((((((...(....)..)))))).....))).))))))).((((((....(((....)))...))))))........-.............-------------- ( -26.60)
>DroSec_CAF1 16406 114 + 1
UAUUGCCCGCUCGUAGGCGCAAAUGUUCACUAUGCGCUGCACGGCACAGUGGGUCGAAAGUGCAGUUCACUUGGAACAAUUUUCAGUUUCCC-UCCUUUAAUAGCAAUUAA-----UUAC
.(((((..((.(((.((((((...(....)..))))))..)))))...(.(((.(((((((...((((.....)))).)))))).)...)))-.)........)))))...-----.... ( -28.90)
>DroSim_CAF1 14824 120 + 1
UAUUGCCCGCUCGUAGGCGCAAAUGUUCACUAUGCGCUGCACGGCACAGUGGGUCGAAAAUGCAGUUUACUUGGAAUAAUUUUCAAUUUCCCCCCCUUUGAUAGCAGUUGAAUGGAUAUC
....((((((((((.((((((...(....)..))))))..)))....))))))).((((((...((((.....)))).)))))).........((.((..((....))..)).))..... ( -28.20)
>consensus
UAUUGCCCGCUCGUAGGCGCAAAUGUUCACUAUGCGCUGCACGGCACAGUGGGUCGAAAGUGCAGUUCACUUGGAACAAUUUUCAGUUUCCC_ACCUUUAAUAGCA_UU_A_____U__C
....((((((((((.((((((...(....)..))))))..)))....))))))).((((((....(((....)))...)))))).................................... (-25.78 = -24.90 +  -0.88)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:30:40 2006