Locus 3589

Sequence ID	2R_DroMel_CAF1
Location	11,953,982 – 11,954,188
Length	206
Max. P	0.912332

overview

Window 0

Location	11,953,982 – 11,954,082
Length	100
Sequences	6
Columns	113
Reading direction	reverse
Mean pairwise identity	78.25
Mean single sequence MFE	-30.17
Consensus MFE	-20.82
Energy contribution	-22.43
Covariance contribution	1.61
Combinations/Pair	1.11
Mean z-score	-1.80
Structure conservation index	0.69
SVM decision value	1.08
SVM RNA-class probability	0.912332
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 11953982 100 - 20766785
AAGCGGGCAAAUAGCGCGAUAUAAAGUUGGGGCUUUUUGGCUUUGACGCACGUAGCUCCCGAUUUGAAAGUUUGUCGUGUGUGCUU---------CGUAU---AUGUUUA-UA
..(((((((....((((((((..(((((((((((...((((......)).)).))).)))))))).......)))))))).))).)---------)))..---.......-.. ( -32.10)
>DroVir_CAF1 5533 95 - 1
--------------AACGAUAUAAAGUUGGCGCUUUUUGGCUUAGACGCACGUAGCUGCCGAUUUCAAAGUUUUUCCUGUGAGUUCACGCGCGCGCGUGU---GUGUGUG-UG
--------------..........((((((((((...((((......)).)).))).)))))))(((.((......)).)))...((((((((((....)---)))))))-)) ( -27.40)
>DroSec_CAF1 5209 99 - 1
AAGCGGGCAUAUAGCGCGAUAUAAAGUUG-GGCUUUUUGGCUUUGACGCACGUAGCUCCCAAUUUGAAAGUUUGUCGUGUGUGCUG---------CGUAU---AUGUUUA-UA
....(((((((((.((((...((((((..-(.....)..))))))(((((((.((((..(.....)..))))...)))))))..))---------)))))---)))))).-.. ( -29.00)
>DroSim_CAF1 8382 100 - 1
AAGCGGGCAAAUAGCGCGAUAUAAAGUUGGGGCUUUUUGGCUUUGACGCACGUAGCUCCCGAUUUGAAAGUUUGUCGUGUGUGCUG---------CGUAU---AUGUUUA-UA
..(((((((....((((((((..(((((((((((...((((......)).)).))).)))))))).......)))))))).)))).---------)))..---.......-.. ( -32.10)
>DroYak_CAF1 5210 94 - 1
AAGCGGGCAAAUAGCGCGAUAUAAAGUUGGGGCUUUUUGGCUUUGACGCACGUAGCUCCCGAUUUGAAAGUUUGUCGUGUGUGCUC---------AGUAUACA----------
....(((((....((((((((..(((((((((((...((((......)).)).))).)))))))).......)))))))).)))))---------........---------- ( -32.50)
>DroAna_CAF1 6011 90 - 1
-----------GAGCGCGAUAUAAAGUUGGGGCUUUUUGGCUUUGACGCACGUAGCUCCCGAUUUGAAAGUUUGUCGUGUGUGCUC---------GCAAU---AUGUACACUA
-----------((((((........((..(((((....)))))..))(((((.((((..(.....)..))))...)))))))))))---------.....---.......... ( -27.90)
>consensus
AAGCGGGCAAAUAGCGCGAUAUAAAGUUGGGGCUUUUUGGCUUUGACGCACGUAGCUCCCGAUUUGAAAGUUUGUCGUGUGUGCUC_________CGUAU___AUGUUUA_UA
.....((((....((((((((..(((((((((((...((((......)).)).))).)))))))).......)))))))).))))............................ (-20.82 = -22.43 +   1.61)

alignment

secondary structure

dotplot

Window 1

Location	11,954,082 – 11,954,188
Length	106
Sequences	5
Columns	110
Reading direction	reverse
Mean pairwise identity	94.55
Mean single sequence MFE	-19.59
Consensus MFE	-15.84
Energy contribution	-15.84
Covariance contribution	-0.00
Combinations/Pair	1.00
Mean z-score	-1.90
Structure conservation index	0.81
SVM decision value	0.97
SVM RNA-class probability	0.891332
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 11954082 106 - 20766785
CG---GCAGCAGCAUCGAAAAGAAGGAGGGGACUUAAAAAAUAAGCUAAAAGUCUUUUGAAGUUGCCAAAGUAAAAGCAGGGGUAAAAAUG-GAACGGAGAGGUUGGGAA
..---.((((..(..((((((((......((.((((.....)))))).....))))))....(((((...((....))...))))).....-...))..)..)))).... ( -18.20)
>DroSec_CAF1 5308 108 - 1
CGGUAGCAGCAGCAUCGAAAAGAAAGAGGGGACUUAAAAAAUAAGCUAAAAGUCUUUUGAAGUUGCCAAAGUAAAAGCAGGGGUAAAAAUGGGAAAG--GAGGUUGGGAA
((((.((....))))))........(((....)))..........((((...((((((..(.(((((...((....))...)))))...)..)))))--)...))))... ( -19.90)
>DroSim_CAF1 8482 107 - 1
CGGCAGCAGCAGCAUCGAAAAGAAAGAGGGGACUUAAAAAAUAAGCUAAAAGUCUUUUGAAGUUGCCAAAGUAAAAGCAGGGGUAAAAAUG-GAAAG--GAGGUUGGGAA
...((((..((((.((.....))..(((....))).........)))......(((((.(..(((((...((....))...)))))...).-)))))--)..)))).... ( -19.70)
>DroEre_CAF1 5335 106 - 1
CAGCGGCAGCAGCAUCGAACAGAAA-AGGGGACUUAAAAAAUAAGCUAAAAGUCUUUUGAAGUUGCCAAAGUAAAAGCAGGGGUAAAAAUG-GAGCG--GAGGUUGGGAA
(((((((((((((.((.....)).(-((....))).........))).....((....)).)))))).........((.............-..)).--...)))).... ( -20.16)
>DroYak_CAF1 5304 107 - 1
CAGCGGCAGCAGCAUCGAAAAGAAAGAGGGGACUUAAAAAAUAAGCUAAAAGUCUUUUGAAGUUGCCAAAGUAAAAGCAGGGGUAAAAAUG-GAACG--GAGGUUGGGAA
(((((((((((((.((.....))..(((....))).........))).....((....)).))))))...((....)).............-.....--...)))).... ( -20.00)
>consensus
CGGCAGCAGCAGCAUCGAAAAGAAAGAGGGGACUUAAAAAAUAAGCUAAAAGUCUUUUGAAGUUGCCAAAGUAAAAGCAGGGGUAAAAAUG_GAACG__GAGGUUGGGAA
......((((..(.(((((.(((......((.((((.....)))))).....))))))))..(((((...((....))...))))).............)..)))).... (-15.84 = -15.84 +  -0.00)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:59:22 2006