Locus 1282

Sequence ID	3L_DroMel_CAF1
Location	3,705,748 – 3,705,847
Length	99
Max. P	0.971498

overview

Window 0

Location	3,705,748 – 3,705,847
Length	99
Sequences	6
Columns	111
Reading direction	forward
Mean pairwise identity	76.02
Mean single sequence MFE	-40.28
Consensus MFE	-21.86
Energy contribution	-20.70
Covariance contribution	-1.16
Combinations/Pair	1.28
Mean z-score	-1.70
Structure conservation index	0.54
SVM decision value	0.30
SVM RNA-class probability	0.676504
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 3705748 99 + 23771897
AUUGUUGGGCCGCAGCUGCGGCAGCUGCCGCCAUCGAGCCAAUACCGCCAUUGCUGUUUGCCAUGGCCGCUGCCGUUGCCGCACUUCCCGCUCC------------AUGUU
......(((..((.((.((((((((.((((....)).)).......(((((.((.....)).))))).)))))))).)).))....))).....------------..... ( -37.40)
>DroVir_CAF1 124604 93 + 1
ACUGUUGAGCCGCUGCAGCGGCUGCGGCCGCCAUGGAGCCAAUGCCGCCAUUGCUAUUGGAAAUGGCAGCAGCUGUUGCGGCGCUGU------G------------AUGCU
.......(((.((((((((((((((.(((.(((...(((.((((....)))))))..)))....))).)))))))))))))))))..------.------------..... ( -45.30)
>DroGri_CAF1 83416 93 + 1
ACUGUUGAGCGGCAGCAGCAGCUGCUGCUGCCAUGGAGCCGAUGCCACCAUUGCUAUUGGAAAUGGCAGCCGCUUGGGCGGCACUGU------G------------AUGCU
.......((((((((((((....)))))))))((((.(((..((((((((.......)))...)))))(((.....)))))).))))------.------------..))) ( -43.00)
>DroSim_CAF1 96584 99 + 1
AUUGUUGGGCCGCUGCUGCGGCAGCUGCCGCCAUCGAGCCAAUACCGCCAUUGCUGUUUGCCAUGGCCGCCGCCGUGGCCGCGCUUCCCGCUCC------------AUGUU
.......(((.(((((....))))).)))..(((.((((.......(((((.((.....)).)))))(((.((....)).)))......)))).------------))).. ( -39.10)
>DroYak_CAF1 83752 99 + 1
AUUGUUGGGCCGCUGCUGCGGCAGCUGCUGCCAUUGAACCAAUACCGCCAUUGCUGUUUGCCAUGGCCGCCGCCGUUGCCGCGCUGCCCGCUCC------------AUGUU
......((((.((....((((((((.((.((.((((...))))...(((((.((.....)).))))).)).)).)))))))))).)))).....------------..... ( -39.90)
>DroAna_CAF1 101112 111 + 1
ACUGCUGUGCUGCUGCUGCGGCAGCUGCCGCCAUUGAUCCGAUACCGCCAUUGCUAUUUGAAAUGGCCGCCGCACUGGCCGCACUUCCGGCCCCAGUUCCGCCCGAAUGCU
...((.((((.(((..((((((.((....))...............((((((.(.....).)))))).))))))..))).))))(((.(((.........))).))).)). ( -37.00)
>consensus
ACUGUUGGGCCGCUGCUGCGGCAGCUGCCGCCAUCGAGCCAAUACCGCCAUUGCUAUUUGAAAUGGCCGCCGCCGUGGCCGCACUGCCCGCUCC____________AUGCU
..(((.(.(((((....))))).((.((.(((((....(.((((.((....)).)))).)..))))).)).)).....).)))............................ (-21.86 = -20.70 +  -1.16)

alignment

secondary structure

dotplot

Window 1

Location	3,705,748 – 3,705,847
Length	99
Sequences	6
Columns	111
Reading direction	reverse
Mean pairwise identity	76.02
Mean single sequence MFE	-42.47
Consensus MFE	-24.25
Energy contribution	-23.83
Covariance contribution	-0.41
Combinations/Pair	1.16
Mean z-score	-2.28
Structure conservation index	0.57
SVM decision value	1.68
SVM RNA-class probability	0.971498
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 3705748 99 - 23771897
AACAU------------GGAGCGGGAAGUGCGGCAACGGCAGCGGCCAUGGCAAACAGCAAUGGCGGUAUUGGCUCGAUGGCGGCAGCUGCCGCAGCUGCGGCCCAACAAU
.....------------.....(((...((((((..(((((((.(((((.((.....)).))))).......((.((....)))).)))))))..)))))).)))...... ( -43.40)
>DroVir_CAF1 124604 93 - 1
AGCAU------------C------ACAGCGCCGCAACAGCUGCUGCCAUUUCCAAUAGCAAUGGCGGCAUUGGCUCCAUGGCGGCCGCAGCCGCUGCAGCGGCUCAACAGU
.....------------.------...(((((((...(((((((((((((.(.....).)))))))))...)))).....)))).)))((((((....))))))....... ( -40.00)
>DroGri_CAF1 83416 93 - 1
AGCAU------------C------ACAGUGCCGCCCAAGCGGCUGCCAUUUCCAAUAGCAAUGGUGGCAUCGGCUCCAUGGCAGCAGCAGCUGCUGCUGCCGCUCAACAGU
(((..------------.------...(.(((((....)).((..(((((.(.....).)))))..))...))).)...(((((((((....))))))))))))....... ( -39.70)
>DroSim_CAF1 96584 99 - 1
AACAU------------GGAGCGGGAAGCGCGGCCACGGCGGCGGCCAUGGCAAACAGCAAUGGCGGUAUUGGCUCGAUGGCGGCAGCUGCCGCAGCAGCGGCCCAACAAU
..(((------------.((((.((.(.(((.((((.(((....))).))))...((....))))).).)).)))).)))(.(((.(((((....))))).))))...... ( -44.50)
>DroYak_CAF1 83752 99 - 1
AACAU------------GGAGCGGGCAGCGCGGCAACGGCGGCGGCCAUGGCAAACAGCAAUGGCGGUAUUGGUUCAAUGGCAGCAGCUGCCGCAGCAGCGGCCCAACAAU
.....------------.....((((..(((.((..(((((((.(((((.((.....)).)))))(.(((((...))))).)....)))))))..)).)))))))...... ( -42.40)
>DroAna_CAF1 101112 111 - 1
AGCAUUCGGGCGGAACUGGGGCCGGAAGUGCGGCCAGUGCGGCGGCCAUUUCAAAUAGCAAUGGCGGUAUCGGAUCAAUGGCGGCAGCUGCCGCAGCAGCAGCACAGCAGU
.((..((((......))))(((((......))))).((((.((.((((((((..(((.(......).)))..))..)))))).)).(((((....))))).)))).))... ( -44.80)
>consensus
AACAU____________GGAGCGGGAAGCGCGGCAACGGCGGCGGCCAUGGCAAACAGCAAUGGCGGUAUUGGCUCAAUGGCGGCAGCUGCCGCAGCAGCGGCCCAACAAU
...........................(.((.((....((.((.(((((...........))))).))............(((((....))))).)).)).)).)...... (-24.25 = -23.83 +  -0.41)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:03:44 2006