Locus 796

Sequence ID	X_DroMel_CAF1
Location	2,202,451 – 2,202,597
Length	146
Max. P	0.908982

overview

Window 8

Location	2,202,451 – 2,202,561
Length	110
Sequences	6
Columns	110
Reading direction	forward
Mean pairwise identity	78.61
Mean single sequence MFE	-38.98
Consensus MFE	-21.20
Energy contribution	-20.53
Covariance contribution	-0.66
Combinations/Pair	1.36
Mean z-score	-1.69
Structure conservation index	0.54
SVM decision value	-0.08
SVM RNA-class probability	0.500000
Prediction	OTHER

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 2202451 110 + 22224390
CUCAUCCUUUAGUGGCUUAACCGUAAUGGGAACAUGAUACUCCUUUCCCUGCGGAAUACCCAUCCUCAAAAUGGGUGAAGCCACUCCGAUGGUGAGCUUGGAAGGCGGUG
.(((((.((.((((((((..(((((..(((((............))))))))))..(((((((.......)))))))))))))))..)).)))))(((.....))).... ( -37.60)
>DroPse_CAF1 892 110 + 1
GACAUCCCGCAGAGGCUUGACUGUUAUGGGUACAUGGUACUCCUUGCGCUGCGGUAUCCCCAUCCUAAGUAUGGGCGAGGCCACCUCGAUGGUCAGUUUGACUGGAGACG
..((((((((((..((..((.((..(((....)))..)).))...)).))))))....(((((.......))))).((((...))))))))(((.....))).(....). ( -33.80)
>DroEre_CAF1 781 110 + 1
CUCAUCUUUUAGCGGCUUAACCGUAAUGGGAACAUGGUAUUCCUUUCUCUGGGGAAUACCCAUUCUCAAAAUGGGUGAAGCCACUUCGAUGGUGAGCUUGGCAGGCGGUG
...........((.((((..((((..((((((...((((((((((.....))))))))))..))))))..))))((.((((((((.....)))).)))).)))))).)). ( -41.90)
>DroWil_CAF1 2471 107 + 1
--UAUCCGUUAAGGGCUUGACCGUAAUGGGCACAUGGUAGUCCUUGCGCUGUGAUAUACCCAUUCGGAGUAUGGGUGAGGCCACUUCGAUGGUCAGCUUGU-UGGAGUUG
--..((((....(((((.((((((....(((.((((((.((....))))))))...(((((((.......)))))))..)))......)))))))))))..-)))).... ( -36.40)
>DroYak_CAF1 799 110 + 1
CUCAUCUUUGAGUGGCUUUACCGUAAUGGGAACGUGGUAUUCCUUUCGCUGGGGAAUACCCAUUCUUAGAAUGGGUGAGGCCACUUCGAUGGUGAGCUUGGCAGGCGGUG
.(((((.(((((((((((((((((..((((((.(.((((((((((.....))))))))))).))))))..)).))))))))))).)))).)))))(((.....))).... ( -49.10)
>DroPer_CAF1 892 110 + 1
GACAUCUCGCAGAGGCUUGACUGUUAUGGGUACAUGGCACUCCUUGCGCUGCGGUAUCCCCAUCCUAAGUAUGGGCGAGGCCACCUCGAUGGUUAGUUUAACUGGAGACG
..((((..((((..((..((.(((((((....))))))).))...)).))))(((.(((((((.......))))).)).))).....))))............(....). ( -35.10)
>consensus
CUCAUCCUUUAGAGGCUUGACCGUAAUGGGAACAUGGUACUCCUUGCGCUGCGGAAUACCCAUCCUAAGAAUGGGUGAGGCCACUUCGAUGGUGAGCUUGGCAGGAGGUG
..(((((((....((((.((((((...(((((...((....)).))).....((..(((((((.......)))))))...)).))...))))))))))....))).)))) (-21.20 = -20.53 +  -0.66)

alignment

secondary structure

dotplot

Window 9

Location	2,202,481 – 2,202,597
Length	116
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	71.95
Mean single sequence MFE	-43.30
Consensus MFE	-14.18
Energy contribution	-14.13
Covariance contribution	-0.05
Combinations/Pair	1.42
Mean z-score	-1.99
Structure conservation index	0.33
SVM decision value	0.06
SVM RNA-class probability	0.564096
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 2202481 116 + 22224390
AACAUGAUACUCCUUUCCCUGCGGAAUACCCAUCCUCAAAAUGGGUGAAGCCACUCCGAUGGUGAGCUUGGAAGGCGGUGAAGUCAACUGUUG----CGACUUCCCUGCCCCGCCAAAGA
............((((....((((..(((((((.......)))))))((((((((.....)))).))))....(((((.((((((........----.)))))).))))))))).)))). ( -37.80)
>DroVir_CAF1 886 101 + 1
CACAUGGUAUUCCUUGCG---CGGAAUACCCAUGCGCAGUAUGGGCGAGGCCACCUCAAUGGUCAGCUUGGCCGGCGCUGCACU-------UG----CC-----CUGGCGCCGCCAUAGA
.....((((((((.....---.)))))))).(((.((......(((.((((.(((.....)))..)))).)))((((((((...-------.)----).-----..)))))))))))... ( -42.20)
>DroPse_CAF1 922 110 + 1
UACAUGGUACUCCUUGCGCUGCGGUAUCCCCAUCCUAAGUAUGGGCGAGGCCACCUCGAUGGUCAGUUUGACUGGAGACGGAGC-GGGGGUGG----CG-----CCGGCUCCCCCGAAUA
..((.((....)).))((((..(((.(((((((.......))))).)).))).((((..(((((.....)))))..)).)))))-)((((..(----(.-----...))..))))..... ( -39.40)
>DroEre_CAF1 811 116 + 1
AACAUGGUAUUCCUUUCUCUGGGGAAUACCCAUUCUCAAAAUGGGUGAAGCCACUUCGAUGGUGAGCUUGGCAGGCGGUGAAGUCACCUGUUG----GGACUUCCCUGCCCCGCCAAAGA
.....((((((((((.....))))))))))(((((.......)))))((((((((.....)))).))))(((.(((((.((((((.((....)----))))))).)))))..)))..... ( -49.80)
>DroWil_CAF1 2499 119 + 1
CACAUGGUAGUCCUUGCGCUGUGAUAUACCCAUUCGGAGUAUGGGUGAGGCCACUUCGAUGGUCAGCUUGU-UGGAGUUGGAGUUGGAAGUGGAUGUGGAAGUGGAGGAACCACCGAAGA
....((((..(((((.((((.(.((((((((((.......))))))....(((((((.(...(((((((..-..)))))))...).))))))))))).).)))))))))...)))).... ( -41.70)
>DroYak_CAF1 829 116 + 1
AACGUGGUAUUCCUUUCGCUGGGGAAUACCCAUUCUUAGAAUGGGUGAGGCCACUUCGAUGGUGAGCUUGGCAGGCGGUGAAGUCACCUGUUG----CGACUUGCCUGCCCCGCCAAAGA
...(((((.((((((.....))))))(((((((((...)))))))))..))))).((..(((((.(...(((((((((((....)))).((..----..))..)))))))))))))..)) ( -48.90)
>consensus
AACAUGGUAUUCCUUGCGCUGCGGAAUACCCAUUCUCAGAAUGGGUGAGGCCACUUCGAUGGUCAGCUUGGCAGGCGGUGAAGUCACCUGUUG____CGACUU_CCGGCCCCGCCAAAGA
....((((..................(((((((.......)))))))((((.(((.....)))..))))((((((.............................))))))..)))).... (-14.18 = -14.13 +  -0.05)

alignment

secondary structure

dotplot

Window 0

Location	2,202,481 – 2,202,597
Length	116
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	71.95
Mean single sequence MFE	-40.80
Consensus MFE	-16.56
Energy contribution	-16.73
Covariance contribution	0.17
Combinations/Pair	1.35
Mean z-score	-2.13
Structure conservation index	0.41
SVM decision value	1.06
SVM RNA-class probability	0.908982
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 2202481 116 - 22224390
UCUUUGGCGGGGCAGGGAAGUCG----CAACAGUUGACUUCACCGCCUUCCAAGCUCACCAUCGGAGUGGCUUCACCCAUUUUGAGGAUGGGUAUUCCGCAGGGAAAGGAGUAUCAUGUU
..(((((.(((((.(((((((((----(....).))))))).))))))))))))..((((.(((((((((......))))))))))).))((((((((.........))))))))..... ( -42.60)
>DroVir_CAF1 886 101 - 1
UCUAUGGCGGCGCCAG-----GG----CA-------AGUGCAGCGCCGGCCAAGCUGACCAUUGAGGUGGCCUCGCCCAUACUGCGCAUGGGUAUUCCG---CGCAAGGAAUACCAUGUG
.....((((((((...-----.(----(.-------...)).)))))(((((..((........)).)))))..))).......(((((((.((((((.---.....))))))))))))) ( -42.90)
>DroPse_CAF1 922 110 - 1
UAUUCGGGGGAGCCGG-----CG----CCACCCCC-GCUCCGUCUCCAGUCAAACUGACCAUCGAGGUGGCCUCGCCCAUACUUAGGAUGGGGAUACCGCAGCGCAAGGAGUACCAUGUA
.....(((((.((...-----.)----)..)))))-(((((.....(((.....))).....((..((((..((.(((((.(....))))))))..))))..))...)))))........ ( -37.50)
>DroEre_CAF1 811 116 - 1
UCUUUGGCGGGGCAGGGAAGUCC----CAACAGGUGACUUCACCGCCUGCCAAGCUCACCAUCGAAGUGGCUUCACCCAUUUUGAGAAUGGGUAUUCCCCAGAGAAAGGAAUACCAUGUU
(((((((.(((((((((((((((----(....)).))))))....))))))..(((((...(((((((((......)))))))))...)))))...)))))))))..((....))..... ( -48.50)
>DroWil_CAF1 2499 119 - 1
UCUUCGGUGGUUCCUCCACUUCCACAUCCACUUCCAACUCCAACUCCA-ACAAGCUGACCAUCGAAGUGGCCUCACCCAUACUCCGAAUGGGUAUAUCACAGCGCAAGGACUACCAUGUG
.....((((((.(((............(((((((......((.((...-...)).))......)))))))....((((((.......)))))).............)))))))))..... ( -27.90)
>DroYak_CAF1 829 116 - 1
UCUUUGGCGGGGCAGGCAAGUCG----CAACAGGUGACUUCACCGCCUGCCAAGCUCACCAUCGAAGUGGCCUCACCCAUUCUAAGAAUGGGUAUUCCCCAGCGAAAGGAAUACCACGUU
.....(((..(((((((((((((----(.....)))))))....)))))))..)))..........((((....((((((((...))))))))(((((.........))))).))))... ( -45.40)
>consensus
UCUUUGGCGGGGCAGG_AAGUCG____CAACAGCUGACUUCACCGCCUGCCAAGCUCACCAUCGAAGUGGCCUCACCCAUACUGAGAAUGGGUAUUCCGCAGCGAAAGGAAUACCAUGUU
.....(((((................................)))))...................((((....((((((.......))))))(((((.........))))).))))... (-16.56 = -16.73 +   0.17)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:54:00 2006