Locus 2296

Sequence ID	3R_DroMel_CAF1
Location	6,522,274 – 6,522,427
Length	153
Max. P	0.926865

overview

Window 0

Location	6,522,274 – 6,522,394
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	75.11
Mean single sequence MFE	-23.31
Consensus MFE	-13.94
Energy contribution	-14.30
Covariance contribution	0.36
Combinations/Pair	1.17
Mean z-score	-1.95
Structure conservation index	0.60
SVM decision value	1.18
SVM RNA-class probability	0.926865
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 6522274 120 + 27905053
UUGGAAAGAAAAGCUGGCAAAUAGCUGACCAAUAUUUCGCUACAGCGUUUCAUACCAAAUGGGAACACACCCUUGUUAAUAGUAUCGAAUAACUAUCGACUGCUGUUCCACCUCCAGCAA
(((((..((((.((((.....((((.((........)))))))))).))))..........((((((((.....((..(((((........)))))..)))).))))))...)))))... ( -27.60)
>DroSec_CAF1 7408 101 + 1
----AAAAAAAACCUAGCAAAUAGCUGACCAAUAUC-------------UCAUCUCCAAUGGGAAC--ACCCUUGUUAAUAGUAUCGAAUAACUAUCGACUGCUGUUCCACCUCCAGCAA
----...................((((.........-------------.(((.....)))(((((--(.(...((..(((((........)))))..)).).)))))).....)))).. ( -19.30)
>DroSim_CAF1 8786 105 + 1
UUGUAAAGAAAACCUGGAAAAUAGCUGACCAAUAUC-------------UCAUCUCCAAUGGGAAC--ACCCUUGUUAAUAGUAUCGAAUAACUAUCGACUGCCCUUCCACCUCCAGCAA
.............(((((................((-------------((((.....))))))..--......((..(((((........)))))..))............)))))... ( -16.30)
>DroEre_CAF1 7374 118 + 1
UGGUGGAGAAUAGACAGCAAACUGCUGACAAAGUUUUAGCAACAGCAGUUUAUGCAUAAUGGGAAC--ACCCUUGUUAAUAAUAUCGAAUAACUAUCGACGAUUGUUCCACCCCCAGCAA
.((((((.....(((((((((((((((...............))))))))..))).....(((...--.))).)))).(((((.((((.......))))..)))))))))))........ ( -30.76)
>DroYak_CAF1 7552 115 + 1
UUCUGGAAAACAGCUAGCAAACAGCUGAUCAAAUUUUAGCAAGCGC---UCAUCCACAAUAGGAAC--ACCCUUACUAAUAGCAUCGAACAACUAUCGACUGCAGUUCCACCGCCAGCAA
............(((.((.....(((((.......)))))......---............(((((--.....((....))(((((((.......)))).))).)))))...)).))).. ( -22.60)
>consensus
UUGUAAAGAAAAGCUAGCAAAUAGCUGACCAAUAUUU_GC_A__GC___UCAUCCCCAAUGGGAAC__ACCCUUGUUAAUAGUAUCGAAUAACUAUCGACUGCUGUUCCACCUCCAGCAA
.......................((((.................................(((......))).....(((((((((((.......)))).))))))).......)))).. (-13.94 = -14.30 +   0.36)

alignment

secondary structure

dotplot

Window 1

Location	6,522,274 – 6,522,394
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	75.11
Mean single sequence MFE	-31.68
Consensus MFE	-16.28
Energy contribution	-15.48
Covariance contribution	-0.80
Combinations/Pair	1.33
Mean z-score	-1.73
Structure conservation index	0.51
SVM decision value	0.08
SVM RNA-class probability	0.571477
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 6522274 120 - 27905053
UUGCUGGAGGUGGAACAGCAGUCGAUAGUUAUUCGAUACUAUUAACAAGGGUGUGUUCCCAUUUGGUAUGAAACGCUGUAGCGAAAUAUUGGUCAGCUAUUUGCCAGCUUUUCUUUCCAA
....(((((..((((.(((.((..(((((........)))))..))..(((......)))...(((((......((((.(.(((....))).)))))....)))))))).))))))))). ( -32.70)
>DroSec_CAF1 7408 101 - 1
UUGCUGGAGGUGGAACAGCAGUCGAUAGUUAUUCGAUACUAUUAACAAGGGU--GUUCCCAUUGGAGAUGA-------------GAUAUUGGUCAGCUAUUUGCUAGGUUUUUUUU----
..((((.........))))(((.(((((((..(((((((((((..((((((.--...))).)))..))).)-------------).))))))..))))))).)))...........---- ( -26.60)
>DroSim_CAF1 8786 105 - 1
UUGCUGGAGGUGGAAGGGCAGUCGAUAGUUAUUCGAUACUAUUAACAAGGGU--GUUCCCAUUGGAGAUGA-------------GAUAUUGGUCAGCUAUUUUCCAGGUUUUCUUUACAA
...((((((((((...(((.(((((.......)))))..((((..((((((.--...))).)))..)))).-------------.......)))..))).)))))))............. ( -26.00)
>DroEre_CAF1 7374 118 - 1
UUGCUGGGGGUGGAACAAUCGUCGAUAGUUAUUCGAUAUUAUUAACAAGGGU--GUUCCCAUUAUGCAUAAACUGCUGUUGCUAAAACUUUGUCAGCAGUUUGCUGUCUAUUCUCCACCA
........((((((......(((((.......)))))...........(((.--...)))..((.(((((((((((((..((.........)))))))))))).))).))...)))))). ( -32.80)
>DroYak_CAF1 7552 115 - 1
UUGCUGGCGGUGGAACUGCAGUCGAUAGUUGUUCGAUGCUAUUAGUAAGGGU--GUUCCUAUUGUGGAUGA---GCGCUUGCUAAAAUUUGAUCAGCUGUUUGCUAGCUGUUUUCCAGAA
...((((....(((((.(((((.((((((((.((((.....((((((((.((--..(((......)))...---)).))))))))...)))).)))))))).))).)).))))))))).. ( -40.30)
>consensus
UUGCUGGAGGUGGAACAGCAGUCGAUAGUUAUUCGAUACUAUUAACAAGGGU__GUUCCCAUUGGGGAUGA___GC__U_GC_AAAUAUUGGUCAGCUAUUUGCUAGCUUUUCUUUACAA
..(((((.............((..(((((........)))))..))..(((......)))................................)))))....................... (-16.28 = -15.48 +  -0.80)

alignment

secondary structure

dotplot

Window 2

Location	6,522,314 – 6,522,427
Length	113
Sequences	5
Columns	113
Reading direction	forward
Mean pairwise identity	79.69
Mean single sequence MFE	-25.28
Consensus MFE	-16.96
Energy contribution	-17.44
Covariance contribution	0.48
Combinations/Pair	1.21
Mean z-score	-1.81
Structure conservation index	0.67
SVM decision value	0.56
SVM RNA-class probability	0.781134
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 6522314 113 + 27905053
UACAGCGUUUCAUACCAAAUGGGAACACACCCUUGUUAAUAGUAUCGAAUAACUAUCGACUGCUGUUCCACCUCCAGCAAAAACGUGUGUUUUUGUUGCGCUGCUAUUUGUUU
..((((((..((..((....))((((((((....((..(((((........)))))..))(((((.........))))).....)))))))).))..)))))).......... ( -31.90)
>DroSec_CAF1 7440 102 + 1
---------UCAUCUCCAAUGGGAAC--ACCCUUGUUAAUAGUAUCGAAUAACUAUCGACUGCUGUUCCACCUCCAGCAAAAACGUGUGUUUUUGUUGCGCUGCUAUUUGUUU
---------............(((((--(.(...((..(((((........)))))..)).).)))))).....((((((((((....))))))))))............... ( -23.10)
>DroSim_CAF1 8822 102 + 1
---------UCAUCUCCAAUGGGAAC--ACCCUUGUUAAUAGUAUCGAAUAACUAUCGACUGCCCUUCCACCUCCAGCAAAAACGUGUGUUUUUGUUGCGCUGCUAUUUGUUU
---------.......(((.(((...--.))))))..(((((((((((.......))))...............((((((((((....))))))))))...)))))))..... ( -19.80)
>DroEre_CAF1 7414 99 + 1
AACAGCAGUUUAUGCAUAAUGGGAAC--ACCCUUGUUAAUAAUAUCGAAUAACUAUCGACGAUUGUUCCACCCCCAGCAAGAACGUGUGUUGCUGCUGAGC------------
..(((((((..((((((...((....--.))((((((((((((.((((.......))))..))))))........))))))...)))))).)))))))...------------ ( -24.80)
>DroYak_CAF1 7592 108 + 1
AAGCGC---UCAUCCACAAUAGGAAC--ACCCUUACUAAUAGCAUCGAACAACUAUCGACUGCAGUUCCACCGCCAGCAAGAACGUGUGUUUUUGUUGCGCUGCUAUUUGUUU
.(((..---............(((((--.....((....))(((((((.......)))).))).)))))...((((((((((((....)))))))))).)).)))........ ( -26.80)
>consensus
_A__GC___UCAUCCCCAAUGGGAAC__ACCCUUGUUAAUAGUAUCGAAUAACUAUCGACUGCUGUUCCACCUCCAGCAAAAACGUGUGUUUUUGUUGCGCUGCUAUUUGUUU
....................(((......))).....(((((((((((.......)))).))))))).......((((((((((....))))))))))............... (-16.96 = -17.44 +   0.48)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:31:52 2006