Locus 2315

Sequence ID	2L_DroMel_CAF1
Location	6,285,159 – 6,285,258
Length	99
Max. P	0.998424

overview

Window 5

Location	6,285,159 – 6,285,258
Length	99
Sequences	6
Columns	114
Reading direction	forward
Mean pairwise identity	74.19
Mean single sequence MFE	-34.85
Consensus MFE	-20.11
Energy contribution	-20.86
Covariance contribution	0.75
Combinations/Pair	1.25
Mean z-score	-3.59
Structure conservation index	0.58
SVM decision value	3.10
SVM RNA-class probability	0.998424
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 6285159 99 + 22407834
GAAAAAGCGG---------------CCGGGAGAGCCAGAGGGCCGGGACGUGGCCGGGAGGGAUGCUUGGGUCGACGAGGAGUCGGCCAUUAGCGUUUUAUGGCCAAAAAGAAA
.......(((---------------((.((....))....))))).....((((((...((((((((..(((((((.....)))))))...)))))))).))))))........ ( -42.00)
>DroSec_CAF1 121419 93 + 1
GGAAAAACGG---------------CCGGGAAAGCCA-GGGGCCGGGAUGG-----GGAGGGAUGCUUGGGUCGACGAGGAGUCGGCCAUUAGCGUUUUAUGGCCAAAAAGAAA
.......(((---------------((.((....)).-..)))))...(((-----...((((((((..(((((((.....)))))))...))))))))....)))........ ( -34.50)
>DroSim_CAF1 136113 99 + 1
GGAAAAGCGG---------------CCGGGAAAGCCACGGGGCCGGGACGGGGCCGGGAGGGAUGCUUGGGUCGACGAGGAGUCGGCCAUUAGCGUUUUAUGGCCAAAAAGAAA
.......(((---------------((.((....))....)))))......(((((...((((((((..(((((((.....)))))))...)))))))).)))))......... ( -41.10)
>DroEre_CAF1 121094 106 + 1
GGAAGAGCGGGAGAGACCGGGAAACCCGGGAAAGCCAGGGGGCCGGGCC--------GAAGGAUGCUUGGGUCGACGAGCAGUCGGCCAUUAGCGUUUUAUGGCCAAAAAGAAA
.......(((......)))((...(((.((....)).)))..)).((((--------(.((((((((..(((((((.....)))))))...)))))))).)))))......... ( -46.10)
>DroYak_CAF1 134427 80 + 1
GGAAAAGCGG---------------CCGGGAAAACGAAGGG-------------------AGAUGCUUGGGUCGACGAGGAGUCGGCCAUUAGCGUUUUAUGGCCAAAAAGAAA
........((---------------(((......(....)(-------------------(((((((..(((((((.....)))))))...)))))))).)))))......... ( -31.50)
>DroAna_CAF1 72971 82 + 1
GCAAGA---------------------GUGAAAGU-AGGGUGCA--AAC--------GAAAGAGGUUUCGGCCGACGUGGAUUCGACCAUUAGCGUUUUAUGGUAAAAAGGAAA
......---------------------......((-((..(((.--..(--------....).((((((.((....)).))...))))....)))..))))............. ( -13.90)
>consensus
GGAAAAGCGG_______________CCGGGAAAGCCAGGGGGCCGGGAC________GAGGGAUGCUUGGGUCGACGAGGAGUCGGCCAUUAGCGUUUUAUGGCCAAAAAGAAA
........................................(((((..............((((((((..(((((((.....)))))))...)))))))).)))))......... (-20.11 = -20.86 +   0.75)

alignment

secondary structure

dotplot

Window 6

Location	6,285,159 – 6,285,258
Length	99
Sequences	6
Columns	114
Reading direction	reverse
Mean pairwise identity	74.19
Mean single sequence MFE	-22.33
Consensus MFE	-9.63
Energy contribution	-9.68
Covariance contribution	0.06
Combinations/Pair	1.11
Mean z-score	-2.02
Structure conservation index	0.43
SVM decision value	0.52
SVM RNA-class probability	0.765930
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 6285159 99 - 22407834
UUUCUUUUUGGCCAUAAAACGCUAAUGGCCGACUCCUCGUCGACCCAAGCAUCCCUCCCGGCCACGUCCCGGCCCUCUGGCUCUCCCGG---------------CCGCUUUUUC
.........((((.......(((...((.((((.....)))).))..)))...((....((((.......))))....)).......))---------------))........ ( -27.30)
>DroSec_CAF1 121419 93 - 1
UUUCUUUUUGGCCAUAAAACGCUAAUGGCCGACUCCUCGUCGACCCAAGCAUCCCUCC-----CCAUCCCGGCCCC-UGGCUUUCCCGG---------------CCGUUUUUCC
.........((((.......(((...((.((((.....)))).))..)))........-----.......((((..-.)))).....))---------------))........ ( -22.30)
>DroSim_CAF1 136113 99 - 1
UUUCUUUUUGGCCAUAAAACGCUAAUGGCCGACUCCUCGUCGACCCAAGCAUCCCUCCCGGCCCCGUCCCGGCCCCGUGGCUUUCCCGG---------------CCGCUUUUCC
.........((((.......(((...((.((((.....)))).))..)))........((....))....))))..((((((.....))---------------))))...... ( -27.70)
>DroEre_CAF1 121094 106 - 1
UUUCUUUUUGGCCAUAAAACGCUAAUGGCCGACUGCUCGUCGACCCAAGCAUCCUUC--------GGCCCGGCCCCCUGGCUUUCCCGGGUUUCCCGGUCUCUCCCGCUCUUCC
.........(((((......(((...((((((.((((.(......).))))....))--------)))).)))....)))))...(((((...)))))................ ( -28.30)
>DroYak_CAF1 134427 80 - 1
UUUCUUUUUGGCCAUAAAACGCUAAUGGCCGACUCCUCGUCGACCCAAGCAUCU-------------------CCCUUCGUUUUCCCGG---------------CCGCUUUUCC
.........((((..((((((((...((.((((.....)))).))..)))....-------------------......)))))...))---------------))........ ( -16.90)
>DroAna_CAF1 72971 82 - 1
UUUCCUUUUUACCAUAAAACGCUAAUGGUCGAAUCCACGUCGGCCGAAACCUCUUUC--------GUU--UGCACCCU-ACUUUCAC---------------------UCUUGC
....................((.(((((((((.......))))))((((....))))--------)))--.)).....-........---------------------...... ( -11.50)
>consensus
UUUCUUUUUGGCCAUAAAACGCUAAUGGCCGACUCCUCGUCGACCCAAGCAUCCCUC________GUCCCGGCCCCCUGGCUUUCCCGG_______________CCGCUUUUCC
.........((((((.........))))))(((.....)))......................................................................... ( -9.63 =  -9.68 +   0.06)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:24:56 2006