Locus 5180

Sequence ID	2R_DroMel_CAF1
Location	16,848,028 – 16,848,216
Length	188
Max. P	0.593999

overview

Window 3

Location	16,848,028 – 16,848,148
Length	120
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	81.89
Mean single sequence MFE	-43.83
Consensus MFE	-27.28
Energy contribution	-27.82
Covariance contribution	0.53
Combinations/Pair	1.30
Mean z-score	-1.86
Structure conservation index	0.62
SVM decision value	0.12
SVM RNA-class probability	0.593999
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 16848028 120 + 20766785
CAAAACACAAAGGGACUAUCGAAUUCGGUGACCAUGCAGCAGAUUCAACAAGUUAUGCGAAGUGGCCAGCAGGGCACGUUAGCCACCACCAAUCUGGUGUUGGGUAAAACAAGCGUGGGA
................(((((....))))).((((((.(((((((.....)))).)))...(((.((....)).))).(((.(((.((((.....)))).))).))).....)))))).. ( -34.90)
>DroPse_CAF1 17647 120 + 1
CAAAACACCAAGACGCUGCCCAGCUCGGUGACGGUGCAGCAGUUCCAACAGGUCAUGCGCAGUGGGCAGCAGGGGACGUUGGCCACCACGAAUCUGGUGCUGGGCAAGACUAGUGUCGGA
.......((..(((((((((((((((((...((.(((.(((...((....))...))))))((((.((((.(....))))).))))..))...)))).)))))))......)))))))). ( -49.70)
>DroWil_CAF1 18172 117 + 1
CAAAACACGAAAGCUUUGCCCAGUUCGGUGACGGUUCAGCAAAUCCAACAGGUAAUGCGUAGUGGUCAACAGGGAACAUUGGCCAC---CAAUCUGGUGCUGGGCAAAACUAGUGUCGGA
....((((...((.(((((((((((((....))).((((((...((....))...)))...((((((((..(....).))))))))---.....))).)))))))))).)).)))).... ( -40.20)
>DroYak_CAF1 16276 120 + 1
CAAAACACAAAAGCACUGCCGAAUUCGGUCACCGUGCAGCAGAUUCAACAAGUGAUGCGUAGUGGCCAGCAGGGUACGUUAGCCACCACCAAUCUGGUGUUGGGUAAGACGAGCGUGGGA
.....(((.......((((.(....)((((((..((((.((...........)).))))..)))))).)))).((.(((((.(((.((((.....)))).))).)..)))).)))))... ( -37.70)
>DroAna_CAF1 16782 120 + 1
CAGAACACGAAGGCCUUGCCCAAUUCGGUGACUGUUCAGCAAAUCCAGCAGGUGAUGCGCAGUGGCCAACAGGGCACUCUGGCCACCACGAACCUGGUGCUGGGCAAGACCAGCGUGGGU
.....((((..((.((((((((....(.(((....))).).....((.(((((....((..(((((((..((....)).)))))))..)).))))).)).)))))))).))..))))... ( -50.80)
>DroPer_CAF1 17562 120 + 1
CAAAACACCAAGACGCUGCCCAGCUCGGUGACGGUGCAGCAGUUCCAACAGGUUAUGCGCAGUGGGCAGCAGGGGACGUUGGCCACCACGAAUCUGGUGCUGGGCAAGACUAGUGUCGGA
.......((..(((((((((((((((((...((.(((.(((...((....))...))))))((((.((((.(....))))).))))..))...)))).)))))))......)))))))). ( -49.70)
>consensus
CAAAACACAAAGGCACUGCCCAAUUCGGUGACGGUGCAGCAGAUCCAACAGGUGAUGCGCAGUGGCCAGCAGGGCACGUUGGCCACCACCAAUCUGGUGCUGGGCAAGACUAGCGUCGGA
................((((((((((((..........(((...((....))...)))...(((((((((.(....)))))))))).......)))).)))))))).............. (-27.28 = -27.82 +   0.53)

alignment

secondary structure

dotplot

Window 4

Location	16,848,108 – 16,848,216
Length	108
Sequences	6
Columns	109
Reading direction	forward
Mean pairwise identity	81.23
Mean single sequence MFE	-40.53
Consensus MFE	-27.40
Energy contribution	-27.40
Covariance contribution	0.00
Combinations/Pair	1.30
Mean z-score	-1.35
Structure conservation index	0.68
SVM decision value	0.00
SVM RNA-class probability	0.535447
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 16848108 108 + 20766785
AGCCACCACCAAUCUGGUGUUGGGUAAAACAAGCGUGGGACGGGUAAUCCCCGUGUCGGUGGCUUCACAGGCCAACCAGCGUCAAACCAUUCAGGUAGGUUU-CUUGUU
..(((.((((.....)))).)))....(((((((((((.(((((.....))))).))(((((((.....)))).))).)))..(((((.........)))))-)))))) ( -37.20)
>DroPse_CAF1 17727 108 + 1
GGCCACCACGAAUCUGGUGCUGGGCAAGACUAGUGUCGGACGGGUCAUACCCGUGUCGGUGGCCUCGCAGGCCAAUCAGCGGCAGACGAUCCAGGUAGGUUA-CCUAUC
((((((((((..(((((..((((......))))..)))))((((.....))))))).)))))))(((...(((.......)))...)))....((((((...-)))))) ( -46.90)
>DroWil_CAF1 18252 105 + 1
GGCCAC---CAAUCUGGUGCUGGGCAAAACUAGUGUCGGACGUGUAAUACCCGUUUCGGUGGCCUCGCAGGCCAAUCAACGUCAGACCAUACAGGUAAGAUC-CCCACA
((((((---(..(((((..((((......))))..)))))((.(.....).))....)))))))................(((..(((.....)))..))).-...... ( -33.00)
>DroYak_CAF1 16356 108 + 1
AGCCACCACCAAUCUGGUGUUGGGUAAGACGAGCGUGGGACGGGUGAUUCCCGUGUCGGUGGCUUCACAGGCCAACCAGCGUCAAACCAUUCAGGUGGGUUA-UUUGUU
..((((((((.....)))....(((..((((.....((.(((((.....))))).))(((((((.....)))).)))..))))..))).....)))))....-...... ( -41.10)
>DroAna_CAF1 16862 109 + 1
GGCCACCACGAACCUGGUGCUGGGCAAGACCAGCGUGGGUCGGGUGAUUCCCGUCUCCGUGGCAUCACAGGCCAACCAACGACAGACUAUUCAGGUGGGUUCUAUAGCU
..(((((.......(((((((((......)))))...((((..(((((.((((....)).)).))))).)))).))))..((........)).)))))........... ( -38.10)
>DroPer_CAF1 17642 108 + 1
GGCCACCACGAAUCUGGUGCUGGGCAAGACUAGUGUCGGACGGGUCAUACCCGUGUCGGUGGCCUCGCAGGCCAAUCAGCGGCAGACGAUCCAGGUAGGUUA-CCUAUC
((((((((((..(((((..((((......))))..)))))((((.....))))))).)))))))(((...(((.......)))...)))....((((((...-)))))) ( -46.90)
>consensus
GGCCACCACCAAUCUGGUGCUGGGCAAGACUAGCGUCGGACGGGUAAUACCCGUGUCGGUGGCCUCACAGGCCAACCAGCGUCAGACCAUUCAGGUAGGUUA_CCUAUU
....(((....((((((.(((((......)))))((((.(((((.....)))))...(((((((.....)))).))).........)))))))))).)))......... (-27.40 = -27.40 +   0.00)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:38:34 2006