Locus 2053

Sequence ID	2R_DroMel_CAF1
Location	7,724,063 – 7,724,194
Length	131
Max. P	0.927657

overview

Window 2

Location	7,724,063 – 7,724,164
Length	101
Sequences	6
Columns	119
Reading direction	reverse
Mean pairwise identity	81.56
Mean single sequence MFE	-30.30
Consensus MFE	-14.88
Energy contribution	-14.43
Covariance contribution	-0.44
Combinations/Pair	1.14
Mean z-score	-3.21
Structure conservation index	0.49
SVM decision value	0.82
SVM RNA-class probability	0.857799
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 7724063 101 - 20766785
AGAAGGCGCUACUCAAUGGGGCGUUAAUGAAAUAAUUAACGCAUAAAUACAAUUUGCUGGUCAGAGUUCAAGGAAACAAGAAGCGAACACAGCAAAC-----GGCC-------------
....(((.............((((((((......))))))))..........(((((((((..(..(((..(....)..))).)..)).))))))).-----.)))------------- ( -27.00)
>DroPse_CAF1 9787 116 - 1
GGAAGGCG-UAUCCAAUGGGGCGUUAAUGAAAUAAUUAACGCAUAAAUACGAUUCUCUGGUCAGAGUUCAAGGAAACAAGCAGCGAG--CAGCAAACAAGAAGGGCCAAAGGGCCAAAG
.....(((-(.(((......((((((((......))))))))........((..((((....)))).))..))).))..((.....)--).))..........((((....)))).... ( -31.10)
>DroEre_CAF1 7835 99 - 1
AGAAGGCGCCACUCAAUGGGGCGUUAAUGAAAUAAUUAACGCAUAAAUACAAUUUGCUAGUCAGAGUUCAAGGAAACAAGAAGCGAC--CAGCAAUC-----GGCC-------------
.......(((..........((((((((......))))))))...........(((((.(((.(..(((..(....)..))).))))--.)))))..-----))).------------- ( -26.20)
>DroYak_CAF1 7747 99 - 1
AGAAGGCGCUACUCAAUGGGGCGUUAAUGAAAUAAUUAACGCAUAAAUACAAUUUGCUGGUCAGAGUUCAAGGAAACAAGAAGCGAC--CAGCAAAC-----GGCC-------------
....(((.............((((((((......))))))))..........((((((((((.(..(((..(....)..))).))))--))))))).-----.)))------------- ( -32.40)
>DroAna_CAF1 7834 97 - 1
AGAAGGCG-UACUCAAUGGGGCGUUAAUGAAAUAAUUAACGCAUAAAUACAAUUUGCUGGUCAGAGUUCAAGGAAACAAGGAC-GUC--GGACCAGC-----CGCU-------------
....((((-...........((((((((......)))))))).............(((((((.((((((..(....)..))))-.))--.)))))))-----))))------------- ( -34.00)
>DroPer_CAF1 9304 116 - 1
GGAAGGCG-UAUCCAAUGGGGCGUUAAUGAAAUAAUUAACGCAUAAAUACGAUUCUCUGGUCAGAGUUCAAGGAAACAAGCAGCGAG--CAGCAAACAAGAAGGGCCAAAGGGCCAAAG
.....(((-(.(((......((((((((......))))))))........((..((((....)))).))..))).))..((.....)--).))..........((((....)))).... ( -31.10)
>consensus
AGAAGGCG_UACUCAAUGGGGCGUUAAUGAAAUAAUUAACGCAUAAAUACAAUUUGCUGGUCAGAGUUCAAGGAAACAAGAAGCGAC__CAGCAAAC_____GGCC_____________
....(((....((.....))((((((((......)))))))).................))).........(....).......................................... (-14.88 = -14.43 +  -0.44)

alignment

secondary structure

dotplot

Window 3

Location	7,724,085 – 7,724,194
Length	109
Sequences	6
Columns	114
Reading direction	reverse
Mean pairwise identity	79.87
Mean single sequence MFE	-23.21
Consensus MFE	-15.52
Energy contribution	-15.27
Covariance contribution	-0.25
Combinations/Pair	1.18
Mean z-score	-2.31
Structure conservation index	0.67
SVM decision value	1.18
SVM RNA-class probability	0.927657
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 7724085 109 - 20766785
AACCAAAACCGUAGCCAAAGCCAAAGCCC-----AAGAAGGCGCUACUCAAUGGGGCGUUAAUGAAAUAAUUAACGCAUAAAUACAAUUUGCUGGUCAGAGUUCAAGGAAACAA
.((((.....(((((....(((.......-----.....))))))))........((((((((......))))))))...............))))..........(....).. ( -23.30)
>DroPse_CAF1 9825 85 - 1
-----------------------UGGCCA-----AGGAAGGCG-UAUCCAAUGGGGCGUUAAUGAAAUAAUUAACGCAUAAAUACGAUUCUCUGGUCAGAGUUCAAGGAAACAA
-----------------------((((((-----..(((..((-(((((....))((((((((......))))))))....))))).)))..))))))........(....).. ( -29.10)
>DroSim_CAF1 11948 103 - 1
AUCCAAAGCCG------AAGCCAAAGCCC-----AAGAAGGCGCUACUCAAUGGGGCGUUAAUGAAAUAAUUAACGCAUAAAUACAAUUUGCUGGUCAGAGUUCAAGGAAACAA
.(((..((((.------..((((...(((-----(...((......))...))))((((((((......))))))))...............))))..).)))...)))..... ( -23.50)
>DroEre_CAF1 7855 82 - 1
---------------------------CC-----AAGAAGGCGCCACUCAAUGGGGCGUUAAUGAAAUAAUUAACGCAUAAAUACAAUUUGCUAGUCAGAGUUCAAGGAAACAA
---------------------------..-----..((.(((.(((.....))).((((((((......)))))))).............)))..)).........(....).. ( -16.80)
>DroYak_CAF1 7767 98 - 1
ACCCAAGAC-----------ACGAUGCCC-----AAGAAGGCGCUACUCAAUGGGGCGUUAAUGAAAUAAUUAACGCAUAAAUACAAUUUGCUGGUCAGAGUUCAAGGAAACAA
.((((....-----------....((((.-----.....))))........))))((((((((......)))))))).............................(....).. ( -21.39)
>DroAna_CAF1 7853 93 - 1
GG--------G------------UAGCCCCUUUGGAGAAGGCG-UACUCAAUGGGGCGUUAAUGAAAUAAUUAACGCAUAAAUACAAUUUGCUGGUCAGAGUUCAAGGAAACAA
((--------.------------(((((((....(((......-..)))...)))((((((((......)))))))).............)))).)).........(....).. ( -25.20)
>consensus
A______________________AAGCCC_____AAGAAGGCGCUACUCAAUGGGGCGUUAAUGAAAUAAUUAACGCAUAAAUACAAUUUGCUGGUCAGAGUUCAAGGAAACAA
....................................((.((((...((.....))((((((((......))))))))............))))..)).........(....).. (-15.52 = -15.27 +  -0.25)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:20:03 2006