Locus 7720

Sequence ID	2L_DroMel_CAF1
Location	21,829,844 – 21,829,956
Length	112
Max. P	0.882083

overview

Window 4

Location	21,829,844 – 21,829,956
Length	112
Sequences	3
Columns	115
Reading direction	forward
Mean pairwise identity	82.80
Mean single sequence MFE	-50.33
Consensus MFE	-42.70
Energy contribution	-42.27
Covariance contribution	-0.44
Combinations/Pair	1.17
Mean z-score	-1.50
Structure conservation index	0.85
SVM decision value	0.35
SVM RNA-class probability	0.700239
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 21829844 112 + 22407834
GUU---UGAGCGGUGGUGGGGAGAGGGAGUUAUAUGUGGGGUUGCGGAAACGGGAUGUGGGGGCGCCACAUCAAGCGCACUGGCCGCUGGGGGCGUGGCAGCCACGGCCGCCGCC
...---...((((((((.(((..............(((.(.((.((....)).(((((((.....))))))))).).)))..(((((.......)))))..)).).)))))))). ( -47.50)
>DroEre_CAF1 78179 113 + 1
GUUCACUUGGCGGUGGCGGGGAGAAGGGGUU--UUGUGGGGCUGCGGAAAAGGGAUGUGGGGGCGCCACAUCAAGCGCACUGACCGCAGGGGGCGUGGCAGCCACUGCCACUGCC
........(((((((((((.((((.....))--))....((((((........(((((((.....)))))))..((((.(((....)))...)))).)))))).))))))))))) ( -52.40)
>DroYak_CAF1 67811 107 + 1
UGUGAAUAGGCAGUGGCGUGGA------GUU--UUCUGGGGUUGCGGAAACGGGAUGUGGGGGCGCCACAUCAAGCGCACUGACCGCUGGGGGCGUGGCAGCCACGGCCGCUGCC
........(((((((((((((.------(((--..(..(.(((.((....)).))).))..)))(((((..(.((((.......))))...)..)))))..)))).))))))))) ( -51.10)
>consensus
GUU_A_UAGGCGGUGGCGGGGAGA_GG_GUU__UUGUGGGGUUGCGGAAACGGGAUGUGGGGGCGCCACAUCAAGCGCACUGACCGCUGGGGGCGUGGCAGCCACGGCCGCUGCC
........(((((((((.(....................((((((........(((((((.....)))))))..((((.....((....)).)))).)))))).).))))))))) (-42.70 = -42.27 +  -0.44)

alignment

secondary structure

dotplot

Window 5

Location	21,829,844 – 21,829,956
Length	112
Sequences	3
Columns	115
Reading direction	reverse
Mean pairwise identity	82.80
Mean single sequence MFE	-37.33
Consensus MFE	-33.43
Energy contribution	-33.43
Covariance contribution	0.01
Combinations/Pair	1.12
Mean z-score	-1.57
Structure conservation index	0.90
SVM decision value	0.92
SVM RNA-class probability	0.882083
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 21829844 112 - 22407834
GGCGGCGGCCGUGGCUGCCACGCCCCCAGCGGCCAGUGCGCUUGAUGUGGCGCCCCCACAUCCCGUUUCCGCAACCCCACAUAUAACUCCCUCUCCCCACCACCGCUCA---AAC
(((((.(((((((((......)))....))))))..((((...(((((((.....))))))).......)))).............................)))))..---... ( -34.80)
>DroEre_CAF1 78179 113 - 1
GGCAGUGGCAGUGGCUGCCACGCCCCCUGCGGUCAGUGCGCUUGAUGUGGCGCCCCCACAUCCCUUUUCCGCAGCCCCACAA--AACCCCUUCUCCCCGCCACCGCCAAGUGAAC
(((.(((((.((((...)))).....((((((..((....)).(((((((.....)))))))......))))))........--..............))))).)))........ ( -38.00)
>DroYak_CAF1 67811 107 - 1
GGCAGCGGCCGUGGCUGCCACGCCCCCAGCGGUCAGUGCGCUUGAUGUGGCGCCCCCACAUCCCGUUUCCGCAACCCCAGAA--AAC------UCCACGCCACUGCCUAUUCACA
(((((.((((((((...)))))......((((.....(((...(((((((.....))))))).)))..))))..........--...------.....))).)))))........ ( -39.20)
>consensus
GGCAGCGGCCGUGGCUGCCACGCCCCCAGCGGUCAGUGCGCUUGAUGUGGCGCCCCCACAUCCCGUUUCCGCAACCCCACAA__AAC_CC_UCUCCCCGCCACCGCCAA_U_AAC
(((((.(((..(((((((..........))))))).((((...(((((((.....))))))).......)))).........................))).)))))........ (-33.43 = -33.43 +   0.01)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:43:29 2006