Locus 4470

Sequence ID	2R_DroMel_CAF1
Location	14,695,726 – 14,695,873
Length	147
Max. P	0.545334

overview

Window 0

Location	14,695,726 – 14,695,846
Length	120
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	81.79
Mean single sequence MFE	-26.59
Consensus MFE	-14.60
Energy contribution	-16.97
Covariance contribution	2.37
Combinations/Pair	1.13
Mean z-score	-2.20
Structure conservation index	0.55
SVM decision value	0.02
SVM RNA-class probability	0.545334
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 14695726 120 - 20766785
AAUUUCGUCAAAAUUAAUCGAAUGGAAAACGUUCGAAAAGCUGAUGAUUUAUAGAUUUUGGGUUGCCAACUAGAAUGCAAUAAAUCGAAUUGGGGAAAUCCCUCGAAUUCAAAGGCAUUC
.................(((((((.....)))))))...(((...(((((((.((((((((........))))))).).)))))))(((((((((....))))..)))))...))).... ( -31.00)
>DroSec_CAF1 1094 119 - 1
AAUUUCGUCAAAGUUAAUCGAAUGGAAAACGUUCGAAAAGCUGAUGAUUUAUAGAUUUC-GGUGGCCAACUAGAACGCAAUAAAUCGAAUUGAGGAAAUCCAUCGAAUUCAAAGGCAUUC
......(((..((((..(((((((.....)))))))..))))...(((((((.(..(((-(((.....))).)))..).)))))))(((((((((....)).)).)))))...))).... ( -27.50)
>DroSim_CAF1 3499 119 - 1
AAUUUCGUCAAAGUUAAUCGAAUGGAAAACGUUCGAAAAGCUGAUGAUUUAUAGAUUUC-GGUGGCCAACUAGAACGCAAUAAAUCGAAUUGAGGAAAUCCCUCGAAUUCAAAGGCAUUC
......(((..((((..(((((((.....)))))))..))))...(((((((.(..(((-(((.....))).)))..).)))))))(((((((((.....)))).)))))...))).... ( -30.70)
>DroEre_CAF1 1014 117 - 1
--UUUCGUCAAAAUUAAUCGAAUGGAAAGCGUUCGAAAAGCUGAUGAUUUAUAGAUUUC-AGUGGCCAACUAGAACGCAAUAAAUCCAAUUGGGGAAAUCCCUCGAAUGCAAAGGCAUUC
--................(((.((((..((((((.....(((((.((((....))))))-))).........))))))......)))).)))(((....)))..((((((....)))))) ( -28.04)
>DroYak_CAF1 1045 119 - 1
AAUUUCGUCAAAAUUAAUCGAAUGGAAAGCGUUCGAAAAGCUGAUGAUUUAUAGAUUUC-GGUGGCCAGCUAGAACGCAAUAAAUCCAAUUGAGGAAAUCCCCCGAAUGCAAAGGAAUUC
((((((...........((((.((((..((((((....(((((.(.((..(......).-.)).).))))).))))))......)))).))))((....))............)))))). ( -24.00)
>DroAna_CAF1 437 96 - 1
AAUC----------UAAUCACA-GGAAGACCU--GAAAAGCACACUUUUCAU------C-AAAAACCAACU----UGCCAUAAAUCGAAAAGCGGAAACCCCUCGAAAUCAAAGGCUUCC
....----------........-(((((.(((--((((((....))))))..------.-...........----.........((((...(.(....))..))))......)))))))) ( -18.30)
>consensus
AAUUUCGUCAAAAUUAAUCGAAUGGAAAACGUUCGAAAAGCUGAUGAUUUAUAGAUUUC_GGUGGCCAACUAGAACGCAAUAAAUCGAAUUGAGGAAAUCCCUCGAAUUCAAAGGCAUUC
.................(((((((.....)))))))...(((...(((((((.(..(((.(((.....))).)))..).)))))))...((((((.....)))))).......))).... (-14.60 = -16.97 +   2.37)

alignment

secondary structure

dotplot

Window 1

Location	14,695,766 – 14,695,873
Length	107
Sequences	5
Columns	107
Reading direction	reverse
Mean pairwise identity	87.78
Mean single sequence MFE	-21.49
Consensus MFE	-15.91
Energy contribution	-15.78
Covariance contribution	-0.13
Combinations/Pair	1.11
Mean z-score	-1.53
Structure conservation index	0.74
SVM decision value	-0.05
SVM RNA-class probability	0.510074
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 14695766 107 - 20766785
UGAGCAAUGUGAAAUUUAAUCAAUUUCAAUUUCGUCAAAAUUAAUCGAAUGGAAAACGUUCGAAAAGCUGAUGAUUUAUAGAUUUUGGGUUGCCAACUAGAAUGCAA
((.(((((.(((((((((.............((((((.......(((((((.....))))))).....))))))....))))))))).)))))))............ ( -22.73)
>DroSec_CAF1 1134 106 - 1
UGAGCAAUGUGAAAUUUAAUCAAUUUCAAUUUCGUCAAAGUUAAUCGAAUGGAAAACGUUCGAAAAGCUGAUGAUUUAUAGAUUUC-GGUGGCCAACUAGAACGCAA
...((....(((((((.....)))))))...((((((..(((..(((((((.....)))))))..)))))))))........(((.-.((.....))..))).)).. ( -21.90)
>DroSim_CAF1 3539 106 - 1
UGAGCAAUGUGAAAUUUAAUCAAUUUCAAUUUCGUCAAAGUUAAUCGAAUGGAAAACGUUCGAAAAGCUGAUGAUUUAUAGAUUUC-GGUGGCCAACUAGAACGCAA
...((....(((((((.....)))))))...((((((..(((..(((((((.....)))))))..)))))))))........(((.-.((.....))..))).)).. ( -21.90)
>DroEre_CAF1 1054 84 - 1
UGAGAAA----------------------UUUCGUCAAAAUUAAUCGAAUGGAAAGCGUUCGAAAAGCUGAUGAUUUAUAGAUUUC-AGUGGCCAACUAGAACGCAA
...((((----------------------((((((((.......(((((((.....))))))).....))))))......))))))-.(((..(.....)..))).. ( -16.90)
>DroYak_CAF1 1085 106 - 1
UGAGAAAUGUGAAAUUUAAUCAAUUUCAAUUUCGUCAAAAUUAAUCGAAUGGAAAGCGUUCGAAAAGCUGAUGAUUUAUAGAUUUC-GGUGGCCAGCUAGAACGCAA
((((((((.(((((((.....)))))))))))).)))..................((((((....(((((.(.((..(......).-.)).).))))).)))))).. ( -24.00)
>consensus
UGAGCAAUGUGAAAUUUAAUCAAUUUCAAUUUCGUCAAAAUUAAUCGAAUGGAAAACGUUCGAAAAGCUGAUGAUUUAUAGAUUUC_GGUGGCCAACUAGAACGCAA
.........(((((((.....)))))))...((((((.......(((((((.....))))))).....))))))......(..(((.(((.....))).)))..).. (-15.91 = -15.78 +  -0.13)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:20:33 2006