Locus 2817

Sequence ID	2R_DroMel_CAF1
Location	9,807,486 – 9,807,590
Length	104
Max. P	0.999941

overview

Window 7

Location	9,807,486 – 9,807,590
Length	104
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	69.21
Mean single sequence MFE	-21.36
Consensus MFE	-10.91
Energy contribution	-12.66
Covariance contribution	1.75
Combinations/Pair	1.31
Mean z-score	-3.04
Structure conservation index	0.51
SVM decision value	3.74
SVM RNA-class probability	0.999578
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 9807486 104 + 20766785
-AUUCACUUGAAUAUUU-UGGGGCUAAAAACAAUAGUUCAUAU--------------CGAACUAUUGUUAUAAACCCCUACAAAUUGCAUUGAAAAAUUUCUUUUCACAACUUUUUUUUU
-.((((..((...((((-.((((.....(((((((((((....--------------.))))))))))).....))))...))))..)).)))).......................... ( -23.00)
>DroSec_CAF1 45135 102 + 1
-AUACACUUCAGUAUUU-UUGGGCUGAAAACGAUAGUUCAUAU--------------CGAACUAUUGUUAAAAACCCAUAUAAAUUGCGUUUAA-AAUUUCUUUUCACAACUUUU-UUUU
-..........((((((-.((((.....(((((((((((....--------------.))))))))))).....))))...))).)))......-....................-.... ( -19.00)
>DroEre_CAF1 48706 117 + 1
UAUUCACUUGAAUUUGUUUAGGGCUUAAGACAAUAGUUCAUAUACCAUAUUUUACUAUGAACUAUUGCCUAAGGCUCAUGGAAUUCGCGAU-AA-AAUAUCGUUUCACAUCUUUU-UUUU
.........((((((.....((((((.((.((((((((((((.............)))))))))))).)).))))))...))))))(((((-(.-..))))))............-.... ( -28.42)
>DroYak_CAF1 47222 92 + 1
UAUUCACUUGAUUUUCCUUAGGGUUUA--ACAAUAGUUCAUA----------------------UUGCCUAAGACCCACGGAAAUUGCGAU-AA-AAUAUUGUUUCACACCUUU--UUUU
........(((.(((((...((((((.--.(((((.....))----------------------)))....))))))..)))))..(((((-(.-..)))))).))).......--.... ( -15.00)
>consensus
_AUUCACUUGAAUAUUU_UAGGGCUUAAAACAAUAGUUCAUAU______________CGAACUAUUGCCAAAAACCCAUAGAAAUUGCGAU_AA_AAUAUCGUUUCACAACUUUU_UUUU
....................(((((...(((((((((((...................)))))))))))...)))))........................................... (-10.91 = -12.66 +   1.75)

alignment

secondary structure

dotplot

Window 8

Location	9,807,486 – 9,807,590
Length	104
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	69.21
Mean single sequence MFE	-25.53
Consensus MFE	-13.55
Energy contribution	-16.30
Covariance contribution	2.75
Combinations/Pair	1.31
Mean z-score	-3.77
Structure conservation index	0.53
SVM decision value	4.71
SVM RNA-class probability	0.999941
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 9807486 104 - 20766785
AAAAAAAAAGUUGUGAAAAGAAAUUUUUCAAUGCAAUUUGUAGGGGUUUAUAACAAUAGUUCG--------------AUAUGAACUAUUGUUUUUAGCCCCA-AAAUAUUCAAGUGAAU-
.......((((((((((((....)))))....)))))))...((((((...(((((((((((.--------------....)))))))))))...)))))).-....((((....))))- ( -30.60)
>DroSec_CAF1 45135 102 - 1
AAAA-AAAAGUUGUGAAAAGAAAUU-UUAAACGCAAUUUAUAUGGGUUUUUAACAAUAGUUCG--------------AUAUGAACUAUCGUUUUCAGCCCAA-AAAUACUGAAGUGUAU-
....-..((((((((((((....))-))...))))))))...((((((...(((.(((((((.--------------....))))))).)))...)))))).-..((((....))))..- ( -25.20)
>DroEre_CAF1 48706 117 - 1
AAAA-AAAAGAUGUGAAACGAUAUU-UU-AUCGCGAAUUCCAUGAGCCUUAGGCAAUAGUUCAUAGUAAAAUAUGGUAUAUGAACUAUUGUCUUAAGCCCUAAACAAAUUCAAGUGAAUA
....-..(((((((......)))))-))-.(((((((((....(.((...(((((((((((((((.............)))))))))))))))...)).)......)))))..))))... ( -27.02)
>DroYak_CAF1 47222 92 - 1
AAAA--AAAGGUGUGAAACAAUAUU-UU-AUCGCAAUUUCCGUGGGUCUUAGGCAA----------------------UAUGAACUAUUGU--UAAACCCUAAGGAAAAUCAAGUGAAUA
....--.(((((((......)))))-))-.((((..(((((..((((.((((.(((----------------------((.....))))))--)))))))...))))).....))))... ( -19.30)
>consensus
AAAA_AAAAGUUGUGAAAAGAAAUU_UU_AACGCAAUUUCCAUGGGUCUUAAACAAUAGUUCG______________AUAUGAACUAUUGUUUUAAGCCCUA_AAAAAUUCAAGUGAAU_
.......((((((((................))))))))...((((((...((((((((((((.................))))))))))))...))))))................... (-13.55 = -16.30 +   2.75)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:40:11 2006