Locus 7349

Sequence ID	2L_DroMel_CAF1
Location	20,488,599 – 20,488,718
Length	119
Max. P	0.865129

overview

Window 2

Location	20,488,599 – 20,488,718
Length	119
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	81.97
Mean single sequence MFE	-35.40
Consensus MFE	-22.70
Energy contribution	-22.31
Covariance contribution	-0.39
Combinations/Pair	1.18
Mean z-score	-2.15
Structure conservation index	0.64
SVM decision value	0.42
SVM RNA-class probability	0.730046
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 20488599 119 + 22407834
UUUUGGCCAUAAUCCGCGCCGCUUUU-GUCGGCAGCUGUUUGGCUCGGCUUGGAUGCAAGUUUAAAGCUGCAACUUUUCGCCAUUGCCCGGUUUAGAUGGCACUUUAUAUUUUAUCGCCA
...((((.((((.....(((((....-).)))).(((((((((((.(((.(((.((((.((.....))))))........)))..))).)).)))))))))..........)))).)))) ( -33.60)
>DroPse_CAF1 42936 98 + 1
UUUUGGCCAUAAUCUGGGCUGCCUUUUGUCGGCAGCUGUUUGGCUCGGCG-----GCAACUUUAAAGCUGCAACUUUUUGGCAUUGCC------AAGUGCCA-----------AACUCCA
...(((..........(((((((.......)))))))(((((((.(.(((-----((.........)))))......(((((...)))------))).))))-----------))).))) ( -36.70)
>DroSec_CAF1 5671 119 + 1
UUUUGGCCAUAAUCCGCGCCGCUUUU-GUCGGCAGCUGUUUGGCUCGGCUUGGAUGCAAGUUUAAAGCUGCAACUUUUCGCCAUUGCCCGGCUUAAAUGGCACUUUAUAUUUUAUCGCCA
...((((.((((.....(((((....-).)))).(((((((((((.(((.(((.((((.((.....))))))........)))..))).))).))))))))..........)))).)))) ( -36.00)
>DroEre_CAF1 5294 118 + 1
UUUUGGCCAUAAUCCGCGCCGCUUUUGGUCGGCAGCUGUUUGGCUCGGCU-GCAUGCAAGUUUAAAGCUGCAACUUUUCGCCAUUGC-CGGCUUAGAUGGCACUUUAUAUUCUAUCGCCA
...((((..........((((.(..(((.(((((((((.......)))))-)).((((.((.....))))))......)))))..).-))))...(((((...........))))))))) ( -36.10)
>DroYak_CAF1 4811 120 + 1
UUUUGGCCAUAAUCUGCGCCGCUUUUUGUCGGCAGUUGUUUGGCGCGGCUUGGAUGCAAGUUUAAAGCUGCAACUUUUCACCAUUGCCCGGCUUAGAUGGCACUUUAUAUUUUAUCGCCA
...((((.((((...(.((((.(((..(((((((((.((..(..(((((((((((....)))).)))))))..).....)).)))).)))))..))))))).)........)))).)))) ( -33.60)
>DroPer_CAF1 48726 98 + 1
UUUUGGCCAUAAUCUGGGCUGCCUUUUGUCGGCAGCUGUUUGGCUCGGCG-----GCAACUUUAAAGCUGCAACUUUUUGGCAUUGCC------AAAUGCCA-----------AACUCCA
...(((..........(((((((.......)))))))(((((((...(((-----((.........))))).....((((((...)))------))).))))-----------))).))) ( -36.40)
>consensus
UUUUGGCCAUAAUCCGCGCCGCUUUUUGUCGGCAGCUGUUUGGCUCGGCU_GGAUGCAAGUUUAAAGCUGCAACUUUUCGCCAUUGCCCGGCUUAAAUGGCACUUUAUAUUUUAUCGCCA
....(((((........(((((.....).)))).......))))).(((......(((..........)))........((((((..........))))))...............))). (-22.70 = -22.31 +  -0.39)

alignment

secondary structure

dotplot

Window 3

Location	20,488,599 – 20,488,718
Length	119
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	81.97
Mean single sequence MFE	-35.77
Consensus MFE	-21.92
Energy contribution	-21.57
Covariance contribution	-0.36
Combinations/Pair	1.17
Mean z-score	-2.88
Structure conservation index	0.61
SVM decision value	0.85
SVM RNA-class probability	0.865129
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 20488599 119 - 22407834
UGGCGAUAAAAUAUAAAGUGCCAUCUAAACCGGGCAAUGGCGAAAAGUUGCAGCUUUAAACUUGCAUCCAAGCCGAGCCAAACAGCUGCCGAC-AAAAGCGGCGCGGAUUAUGGCCAAAA
((((.((((.......((......))...((((((..((((.......(((((........))))).....)))).))).....(((((....-....))))).))).)))).))))... ( -33.40)
>DroPse_CAF1 42936 98 - 1
UGGAGUU-----------UGGCACUU------GGCAAUGCCAAAAAGUUGCAGCUUUAAAGUUGC-----CGCCGAGCCAAACAGCUGCCGACAAAAGGCAGCCCAGAUUAUGGCCAAAA
(((.(((-----------((((..((------(((...)))))...((.((((((....))))))-----.))...))))))).((((((.......))))))(((.....))))))... ( -39.40)
>DroSec_CAF1 5671 119 - 1
UGGCGAUAAAAUAUAAAGUGCCAUUUAAGCCGGGCAAUGGCGAAAAGUUGCAGCUUUAAACUUGCAUCCAAGCCGAGCCAAACAGCUGCCGAC-AAAAGCGGCGCGGAUUAUGGCCAAAA
((((.((((........(((((......((((.....)))).....(((((((((.....(((((......).))))......))))).))))-......)))))...)))).))))... ( -34.80)
>DroEre_CAF1 5294 118 - 1
UGGCGAUAGAAUAUAAAGUGCCAUCUAAGCCG-GCAAUGGCGAAAAGUUGCAGCUUUAAACUUGCAUGC-AGCCGAGCCAAACAGCUGCCGACCAAAAGCGGCGCGGAUUAUGGCCAAAA
((((.((((.........((((.........)-))).((((.....((((((((.........)).)))-)))...))))....((.((((........))))))...)))).))))... ( -37.00)
>DroYak_CAF1 4811 120 - 1
UGGCGAUAAAAUAUAAAGUGCCAUCUAAGCCGGGCAAUGGUGAAAAGUUGCAGCUUUAAACUUGCAUCCAAGCCGCGCCAAACAACUGCCGACAAAAAGCGGCGCAGAUUAUGGCCAAAA
((((.((((........((((.....((((...(((((........))))).)))).......))))....(((((......................))))).....)))).))))... ( -29.55)
>DroPer_CAF1 48726 98 - 1
UGGAGUU-----------UGGCAUUU------GGCAAUGCCAAAAAGUUGCAGCUUUAAAGUUGC-----CGCCGAGCCAAACAGCUGCCGACAAAAGGCAGCCCAGAUUAUGGCCAAAA
(((.(((-----------((((.(((------(((...))))))..((.((((((....))))))-----.))...))))))).((((((.......))))))(((.....))))))... ( -40.50)
>consensus
UGGCGAUAAAAUAUAAAGUGCCAUCUAAGCCGGGCAAUGGCGAAAAGUUGCAGCUUUAAACUUGCAUCC_AGCCGAGCCAAACAGCUGCCGACAAAAAGCGGCGCAGAUUAUGGCCAAAA
.(((..............((((((............)))))).......((((........))))......)))(.((((....(((((.........)))))........))))).... (-21.92 = -21.57 +  -0.36)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:34:23 2006