Locus 9639

Sequence ID	3R_DroMel_CAF1
Location	25,471,994 – 25,472,101
Length	107
Max. P	0.988138

overview

Window 1

Location	25,471,994 – 25,472,101
Length	107
Sequences	6
Columns	110
Reading direction	forward
Mean pairwise identity	77.52
Mean single sequence MFE	-29.25
Consensus MFE	-19.84
Energy contribution	-21.53
Covariance contribution	1.70
Combinations/Pair	1.17
Mean z-score	-2.90
Structure conservation index	0.68
SVM decision value	2.11
SVM RNA-class probability	0.988138
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 25471994 107 + 27905053
CACCCACUCAGGCGCUCAGUGGCGAUAAAUCGCCGCCUAAAAUCUUCAAAAUUGCUCUGCGAGCGUUUUUUUUUUUUUUGGCGCUUUUGGGGCUUCGAUCCU--UUU-UU
..((((...((((((...(((((((....))))))).(((((.....((((.(((((...))))).)))).....))))))))))).))))...........--...-.. ( -31.50)
>DroSec_CAF1 154880 103 + 1
CACCCACUCAGGCGCUCAGUGGCCAUAAAUCGCCGCCUAAAAUCUUCAAAAUUGCUCCCCGAGCGAUUU------UUUUGGCGCUUUUGGGGCUUCGCUCCAUUUUU-UU
.........((((((.(((((((........)))))...........((((((((((...)))))))))------)..)))))))).((((((...)))))).....-.. ( -31.80)
>DroSim_CAF1 156922 104 + 1
CACCCACUCAGCCGCUCAGUGGCGAUAAAUCGCCGCCUAAAAUCUUCAAAAUUGCUCCCCGAGCGAUUU------UUUUGGCGCUUUUGGGGCUUCGCUCCAUUUUUUUU
..........(((.....(((((((....)))))))...........((((((((((...)))))))))------)...))).....((((((...))))))........ ( -32.40)
>DroEre_CAF1 162133 88 + 1
CAGCCACUCAGCCGCUCAGCGGCGAUAAAUCGCCGCCUAAAGUCUUCAGAAUUGCUCCCCGAGCGUUU--------UUUGGCGCUU-UGGGGCU------------U-UU
.........((((.....(((((((....)))))))(((((((..((((((.(((((...)))))..)--------))))).))))-)))))))------------.-.. ( -33.50)
>DroYak_CAF1 167136 96 + 1
CACCCACUUAGGCGCUCAAUGGCGAUAAAUCGCCGCCUAAAAUCUUCCAAAUUGCUCCCUGAACAUUUUUU-UUUUUUUGGCGCUUUUGGGGCU------------U-UU
..((((...((((((.(((.(((((....)))))....(((((.(((.............))).)))))..-.....))))))))).))))...------------.-.. ( -24.32)
>DroAna_CAF1 164026 82 + 1
CACCCACUCAGGAGCUGAG---CGAUAAAUCGCUGCCUAAAAUCUUCCAAAUUGCUCCCAGAGCGUUUU---------CAGGGUUUUCGG--C-------------A-UU
...((.....)).....((---(((....)))))(((.((((((((..((((.((((...)))))))).---------.)))))))).))--)-------------.-.. ( -22.00)
>consensus
CACCCACUCAGGCGCUCAGUGGCGAUAAAUCGCCGCCUAAAAUCUUCAAAAUUGCUCCCCGAGCGUUUU______UUUUGGCGCUUUUGGGGCU____________U_UU
..((((...(((((((..(((((((....)))))))................(((((...)))))..............))))))).))))................... (-19.84 = -21.53 +   1.70)

alignment

secondary structure

dotplot

Window 2

Location	25,471,994 – 25,472,101
Length	107
Sequences	6
Columns	110
Reading direction	reverse
Mean pairwise identity	77.52
Mean single sequence MFE	-28.27
Consensus MFE	-17.36
Energy contribution	-18.28
Covariance contribution	0.92
Combinations/Pair	1.15
Mean z-score	-1.79
Structure conservation index	0.61
SVM decision value	0.81
SVM RNA-class probability	0.856240
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 25471994 107 - 27905053
AA-AAA--AGGAUCGAAGCCCCAAAAGCGCCAAAAAAAAAAAAAACGCUCGCAGAGCAAUUUUGAAGAUUUUAGGCGGCGAUUUAUCGCCACUGAGCGCCUGAGUGGGUG
..-...--.........(((((..(.((((................((((...)))).............((((..(((((....))))).)))))))).)..).)))). ( -27.30)
>DroSec_CAF1 154880 103 - 1
AA-AAAAAUGGAGCGAAGCCCCAAAAGCGCCAAAA------AAAUCGCUCGGGGAGCAAUUUUGAAGAUUUUAGGCGGCGAUUUAUGGCCACUGAGCGCCUGAGUGGGUG
..-.....(((.((............)).)))...------...(((((((((..((((((.....))))((((..(((........))).)))))).)))))))))... ( -27.40)
>DroSim_CAF1 156922 104 - 1
AAAAAAAAUGGAGCGAAGCCCCAAAAGCGCCAAAA------AAAUCGCUCGGGGAGCAAUUUUGAAGAUUUUAGGCGGCGAUUUAUCGCCACUGAGCGGCUGAGUGGGUG
........(((.((...)).)))....((((....------.(..(((((((...((.................))(((((....))))).)))))))..).....)))) ( -29.43)
>DroEre_CAF1 162133 88 - 1
AA-A------------AGCCCCA-AAGCGCCAAA--------AAACGCUCGGGGAGCAAUUCUGAAGACUUUAGGCGGCGAUUUAUCGCCGCUGAGCGGCUGAGUGGCUG
..-.------------..((((.-.((((.....--------...)))).))))(((.((((.(..(.(((..((((((((....))))))))))))..).)))).))). ( -34.30)
>DroYak_CAF1 167136 96 - 1
AA-A------------AGCCCCAAAAGCGCCAAAAAAA-AAAAAAUGUUCAGGGAGCAAUUUGGAAGAUUUUAGGCGGCGAUUUAUCGCCAUUGAGCGCCUAAGUGGGUG
..-.------------.(((((....(((((((.....-..(((((.(((..(((....))).))).)))))....(((((....))))).))).))))....).)))). ( -27.90)
>DroAna_CAF1 164026 82 - 1
AA-U-------------G--CCGAAAACCCUG---------AAAACGCUCUGGGAGCAAUUUGGAAGAUUUUAGGCAGCGAUUUAUCG---CUCAGCUCCUGAGUGGGUG
..-.-------------.--......((((..---------.....((((.((((((...(((((....)))))(.(((((....)))---))).)))))))))))))). ( -23.31)
>consensus
AA_A____________AGCCCCAAAAGCGCCAAAA______AAAACGCUCGGGGAGCAAUUUUGAAGAUUUUAGGCGGCGAUUUAUCGCCACUGAGCGCCUGAGUGGGUG
...................((((..(((((................((((...))))................((.(((((....))))).))..))).))...)))).. (-17.36 = -18.28 +   0.92)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:38:55 2006