Locus 3801

Sequence ID	3R_DroMel_CAF1
Location	10,322,536 – 10,322,633
Length	97
Max. P	0.815790

overview

Window 5

Location	10,322,536 – 10,322,633
Length	97
Sequences	6
Columns	98
Reading direction	forward
Mean pairwise identity	78.77
Mean single sequence MFE	-19.12
Consensus MFE	-12.47
Energy contribution	-12.30
Covariance contribution	-0.17
Combinations/Pair	1.16
Mean z-score	-1.50
Structure conservation index	0.65
SVM decision value	0.41
SVM RNA-class probability	0.724621
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 10322536 97 + 27905053
UGCCGUAUGCUGUUUUAUUUUUACCUUUAGAA-UGCAAUUGGAACUGUCAAUUUGCAUUUAAUUCGGCGAAAAUAAAUUGCCGCCUGACUCACGACUU
....((..((.((((((((((..((....(((-(((((((((.....)))).)))))))).....))..))))))))..)).))...))......... ( -19.30)
>DroVir_CAF1 202485 74 + 1
-----------------------UUUUUAGAA-UGAAAUUGGAACUGUCAAUUUGCAUUUAAUUCGGCAAAAAUAAAUUGCCGACUGACUCACGACUU
-----------------------......(((-(((((((((.....))))))).)))))...(((((((.......))))))).............. ( -15.70)
>DroSim_CAF1 179470 92 + 1
UGCCGU-----GUUUUAUUUUUACCUUUAGAA-UGCAAUUGGAACUGUCAAUUUGCAUUUAAUUCGGCGAAAAUAAAUUGCCGCCUGACUCACGACUU
...(((-----(..(((............(((-(((((((((.....)))).))))))))....((((((.......))))))..)))..)))).... ( -20.70)
>DroWil_CAF1 202074 92 + 1
CA---UUUGUU---UAUUUCGUUUUUUUAGAAUUGCAAUUGGAACUGUCAAUUUGCAUUUAAUUCGGCGAAAAUAAAUUGCCGACUGACUCACGACUU
..---......---....((((....((((...(((((((((.....)))).)))))......(((((((.......)))))))))))...))))... ( -18.60)
>DroMoj_CAF1 206728 91 + 1
UG---UAUU-UCUUUUCUU--UUUUUUUAGAG-UGCAAUUGGAACUGUCAAUUUGCAUUUAAUUCGGCAAAAAUAAAUUGCCGAUUGACUCACGACUU
..---....-.........--........(((-(((((((((.....)))).)))).......(((((((.......)))))))...))))....... ( -18.40)
>DroAna_CAF1 158564 91 + 1
CGCCGUUUUGUGUC------UCUCCCACAGAA-UGCAAUUGGAACUGUCAAUUUGCAUUUAAUUCGGCGAAAAUAAAUUGCCGCCUGACUCACGACCG
....(((.((.(((------.........(((-(((((((((.....)))).))))))))....((((((.......))))))...))).)).))).. ( -22.00)
>consensus
UG___U_U__UGUUUU_UU_UUUCCUUUAGAA_UGCAAUUGGAACUGUCAAUUUGCAUUUAAUUCGGCGAAAAUAAAUUGCCGACUGACUCACGACUU
..........................((((...(((((((((.....)))).))))).......((((((.......)))))).)))).......... (-12.47 = -12.30 +  -0.17)

alignment

secondary structure

dotplot

Window 6

Location	10,322,536 – 10,322,633
Length	97
Sequences	6
Columns	98
Reading direction	reverse
Mean pairwise identity	78.77
Mean single sequence MFE	-21.02
Consensus MFE	-10.77
Energy contribution	-10.93
Covariance contribution	0.17
Combinations/Pair	1.00
Mean z-score	-2.25
Structure conservation index	0.51
SVM decision value	0.66
SVM RNA-class probability	0.815790
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 10322536 97 - 27905053
AAGUCGUGAGUCAGGCGGCAAUUUAUUUUCGCCGAAUUAAAUGCAAAUUGACAGUUCCAAUUGCA-UUCUAAAGGUAAAAAUAAAACAGCAUACGGCA
..((((((.(((....)))..((((((((..((......(((((((.(((.......))))))))-)).....))..))))))))......)))))). ( -25.30)
>DroVir_CAF1 202485 74 - 1
AAGUCGUGAGUCAGUCGGCAAUUUAUUUUUGCCGAAUUAAAUGCAAAUUGACAGUUCCAAUUUCA-UUCUAAAAA-----------------------
..(.(....).)..(((((((.......)))))))....((((.((((((.......))))))))-)).......----------------------- ( -16.50)
>DroSim_CAF1 179470 92 - 1
AAGUCGUGAGUCAGGCGGCAAUUUAUUUUCGCCGAAUUAAAUGCAAAUUGACAGUUCCAAUUGCA-UUCUAAAGGUAAAAAUAAAAC-----ACGGCA
..((((((.(((....)))..((((((((..((......(((((((.(((.......))))))))-)).....))..)))))))).)-----))))). ( -27.40)
>DroWil_CAF1 202074 92 - 1
AAGUCGUGAGUCAGUCGGCAAUUUAUUUUCGCCGAAUUAAAUGCAAAUUGACAGUUCCAAUUGCAAUUCUAAAAAAACGAAAUA---AACAAA---UG
...((((.......(((((...........)))))......(((((.(((.......))))))))...........))))....---......---.. ( -15.30)
>DroMoj_CAF1 206728 91 - 1
AAGUCGUGAGUCAAUCGGCAAUUUAUUUUUGCCGAAUUAAAUGCAAAUUGACAGUUCCAAUUGCA-CUCUAAAAAAA--AAGAAAAGA-AAUA---CA
.....(((..((..(((((((.......)))))))......(((((.(((.......))))))))-...........--.......))-..))---). ( -18.40)
>DroAna_CAF1 158564 91 - 1
CGGUCGUGAGUCAGGCGGCAAUUUAUUUUCGCCGAAUUAAAUGCAAAUUGACAGUUCCAAUUGCA-UUCUGUGGGAGA------GACACAAAACGGCG
..(((((.......)))))..........(((((.....(((((((.(((.......))))))))-)).((((.....------..))))...))))) ( -23.20)
>consensus
AAGUCGUGAGUCAGGCGGCAAUUUAUUUUCGCCGAAUUAAAUGCAAAUUGACAGUUCCAAUUGCA_UUCUAAAAAAAA_AA_AAAACA__A_A___CA
..(.(....).)...((((...........)))).......(((((.(((.......))))))))................................. (-10.77 = -10.93 +   0.17)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:10:28 2006