Locus 2060

Sequence ID	X_DroMel_CAF1
Location	5,658,817 – 5,658,959
Length	142
Max. P	0.987794

overview

Window 0

Location	5,658,817 – 5,658,920
Length	103
Sequences	4
Columns	117
Reading direction	reverse
Mean pairwise identity	71.47
Mean single sequence MFE	-31.62
Consensus MFE	-16.55
Energy contribution	-17.55
Covariance contribution	1.00
Combinations/Pair	1.29
Mean z-score	-1.84
Structure conservation index	0.52
SVM decision value	0.50
SVM RNA-class probability	0.759482
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 5658817 103 - 22224390
UGCCAAUCCCCCA-------UGCUGCCAGUGCUAAAUGGCCGCGUGCAAAC-------UUUGCUGCCGGCCAAAAGCAAACUGGCCAAGGAACCCAGUAACAAGUAACAAAAGUGCG
.(((......((.-------((..(((((((((...((((((.(((((...-------..))).))))))))..)))..)))))))).))......((........))....).)). ( -29.70)
>DroVir_CAF1 33632 110 - 1
UGCUGCUGCUGGUUGCCACCGGCAGCGCCAGCUAAAUGGCAGCCUGAUUACCUCUUUUUUCUUUGUUCGCCAAAGACAAACAAGC-----GGCUCGGGCAAAAGUAACAAAAGUA--
(((((((((((((....)))))))))((((......)))).((((((...((.((((((((((((.....)))))).))).))).-----)).))))))...)))).........-- ( -41.30)
>DroSec_CAF1 4603 102 - 1
UGGCAAUCCCCCA-------UGCUGCUAGUGCUAAAUGGCCGCGUGCAAAC-------UUUGCUGCCGGCCAAAACCAAACUGGCCAAGGAAC-CAGUAACAAGUAACAAAAGUGCG
(((((........-------...)))))(..((...((((((.(((((...-------..))).)))))))).......(((((........)-)))).............))..). ( -28.20)
>DroYak_CAF1 3494 102 - 1
UGCCAAUGCCCCA-------UGCUGCCGAUGCUAAAUGGCCGCGUGCAAAC-------UUUGCUGCCGGCCAAAAGCAAACUGGCCAAGGAAC-CAGUAACAAGUAACAAAAGUGCG
.......(((...-------((.(((...((((...((((((.(((((...-------..))).))))))))..)))).(((((........)-)))).....))).))...).)). ( -27.30)
>consensus
UGCCAAUCCCCCA_______UGCUGCCAGUGCUAAAUGGCCGCGUGCAAAC_______UUUGCUGCCGGCCAAAAGCAAACUGGCCAAGGAAC_CAGUAACAAGUAACAAAAGUGCG
........................((((((......((((((...(((((........)))))...)))))).......))))))................................ (-16.55 = -17.55 +   1.00)

alignment

secondary structure

dotplot

Window 1

Location	5,658,856 – 5,658,959
Length	103
Sequences	3
Columns	103
Reading direction	reverse
Mean pairwise identity	77.99
Mean single sequence MFE	-19.63
Consensus MFE	-17.58
Energy contribution	-17.13
Covariance contribution	-0.44
Combinations/Pair	1.06
Mean z-score	-1.67
Structure conservation index	0.90
SVM decision value	2.09
SVM RNA-class probability	0.987794
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 5658856 103 - 22224390
CACUCCCCACUCCCCACUGCCCACUACCCACAAUCCACUUGCCAAUCCCCCAUGCUGCCAGUGCUAAAUGGCCGCGUGCAAACUUUGCUGCCGGCCAAAAGCA
..................((...............((((.((((........))..)).)))).....((((((.(((((.....))).))))))))...)). ( -19.80)
>DroSec_CAF1 4641 98 - 1
-----CCCACUACCCACUACCCACUACCCAUAACCCACUUGGCAAUCCCCCAUGCUGCUAGUGCUAAAUGGCCGCGUGCAAACUUUGCUGCCGGCCAAAACCA
-----..............................((((.((((........))))...)))).....((((((.(((((.....))).))))))))...... ( -20.90)
>DroYak_CAF1 3532 89 - 1
CAUUCUCCAUUCUUCAUUCCCC--------------ACUUGCCAAUGCCCCAUGCUGCCGAUGCUAAAUGGCCGCGUGCAAACUUUGCUGCCGGCCAAAAGCA
......................--------------....((....((.....)).))...((((...((((((.(((((.....))).))))))))..)))) ( -18.20)
>consensus
CA_UCCCCACUCCCCACUACCCACUACCCA_AA_CCACUUGCCAAUCCCCCAUGCUGCCAGUGCUAAAUGGCCGCGUGCAAACUUUGCUGCCGGCCAAAAGCA
.......................................(((...........((.......))....((((((.(((((.....))).))))))))...))) (-17.58 = -17.13 +  -0.44)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:25:17 2006