Locus 1350

Sequence ID	2R_DroMel_CAF1
Location	5,219,569 – 5,219,689
Length	120
Max. P	0.830492

overview

Window 2

Location	5,219,569 – 5,219,689
Length	120
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	81.06
Mean single sequence MFE	-45.58
Consensus MFE	-31.25
Energy contribution	-31.28
Covariance contribution	0.03
Combinations/Pair	1.32
Mean z-score	-2.03
Structure conservation index	0.69
SVM decision value	0.71
SVM RNA-class probability	0.830492
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 5219569 120 + 20766785
UCGGUAUCCUUAAGCCACGAUGCCAAGAUCCUGGCCAGUGGCGGUGCAGACUGCAAAGUGCGAGUCUGGGAUGCCCUGUUGGGGAAACAGCUGAAGAAGCUUAGACAUACCAAAACAGUG
..(((((((....(((((...((((......))))..)))))....((((((((.....)).)))))))))))))((((((((....)((((.....))))........)))..)))).. ( -48.10)
>DroSec_CAF1 95683 120 + 1
UCGGUAUCCUUAAGCCACGAUGCCAAGAUCCUGGCCAGUGGCGGUGCAGACUGCAAAGUGCGAGUCUGGGAUGCCCUGCUAGGGAAACAGCUGAAGAAGCUUAGGCAUACCAAAACAGUA
..(((((.(((((((..(...((.....(((((((.((.((((.(.((((((((.....)).)))))).).))))))))))))).....))....)..))))))).)))))......... ( -46.70)
>DroSim_CAF1 81492 120 + 1
UCGGUAUCCUUAAGCCACGAUGCCAAGAUCCUGGCCAGUGGCGGUGCAGACUGCAAAGUGCGAGUCUGGGAUGCCCUGCUGGGGAAACAGCUGAAGAAGCUUAGGCAUACAAAAACAGUG
..(((((((....(((((...((((......))))..)))))....((((((((.....)).)))))))))))))..((((.(....)((((.....))))..............)))). ( -46.30)
>DroEre_CAF1 96421 120 + 1
UCGGUGUCCUUGAGCCACGAUGCCAAGAUCCUGGCCAGUGGCGGUGCAGACUGCAAAGUUCGGGUCUGGGAUGCACUGCUGGGCAAACAGCUAAAGAAGCUAACGCACAGGAAUACAGUG
...((((.((((.(((((...((((......))))..)))))((((((..((...............))..))))))((((......)))).......((....)).)))).)))).... ( -40.06)
>DroYak_CAF1 94388 120 + 1
UCGGUGUCCUUAAGCCACGACGCCAAGAUCCUGGCCAGUGGCGGGGCGGAUUGCAAAGUCCGUGUCUGGGAUGCCCUGCUGGGGAAACAGCUGAAGAAGCUUACGCAUAACAAGACAGUG
..((((((((...(((((...((((......))))..)))))((.(((((((....))))))).)).))))))))..((((.(....)((((.....))))..............)))). ( -47.50)
>DroAna_CAF1 113544 120 + 1
AGCGUGACCUUGAAUGACGAGGCCACCAUGAUGGCCAGCGGCAGUGCAGAUCGGACGGCUCGCAUCUGGUGCGCCAUCACUGGCGAUGAGCUGGUGAAGUUUACGCUUCCGGAGGCAGUA
.(.(((.(((((.....))))).))))......(((.(((((.((.(.....).)).)).))).(((((.(((.(.((((..((.....))..)))).)....)))..)))))))).... ( -44.80)
>consensus
UCGGUAUCCUUAAGCCACGAUGCCAAGAUCCUGGCCAGUGGCGGUGCAGACUGCAAAGUGCGAGUCUGGGAUGCCCUGCUGGGGAAACAGCUGAAGAAGCUUACGCAUACCAAAACAGUG
..(((((((....(((((...((((......))))..)))))....((((((((.....))).)))))))))))).............((((.....))))................... (-31.25 = -31.28 +   0.03)

alignment

secondary structure

dotplot

Window 3

Location	5,219,569 – 5,219,689
Length	120
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	81.06
Mean single sequence MFE	-39.89
Consensus MFE	-27.28
Energy contribution	-27.65
Covariance contribution	0.37
Combinations/Pair	1.33
Mean z-score	-1.48
Structure conservation index	0.68
SVM decision value	0.20
SVM RNA-class probability	0.631258
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 5219569 120 - 20766785
CACUGUUUUGGUAUGUCUAAGCUUCUUCAGCUGUUUCCCCAACAGGGCAUCCCAGACUCGCACUUUGCAGUCUGCACCGCCACUGGCCAGGAUCUUGGCAUCGUGGCUUAAGGAUACCGA
..(((((..((........((((.....))))....))..)))))((.((((((((((.((.....))))))))....(((((..(((((....)))))...)))))....)))).)).. ( -41.60)
>DroSec_CAF1 95683 120 - 1
UACUGUUUUGGUAUGCCUAAGCUUCUUCAGCUGUUUCCCUAGCAGGGCAUCCCAGACUCGCACUUUGCAGUCUGCACCGCCACUGGCCAGGAUCUUGGCAUCGUGGCUUAAGGAUACCGA
.......(((((((.((((((((.(..((((((((.....)))))(((....((((((.((.....))))))))....))).)))(((((....)))))...).))))).)))))))))) ( -43.50)
>DroSim_CAF1 81492 120 - 1
CACUGUUUUUGUAUGCCUAAGCUUCUUCAGCUGUUUCCCCAGCAGGGCAUCCCAGACUCGCACUUUGCAGUCUGCACCGCCACUGGCCAGGAUCUUGGCAUCGUGGCUUAAGGAUACCGA
..(((((.......((...((((.....))))))......)))))((.((((((((((.((.....))))))))....(((((..(((((....)))))...)))))....)))).)).. ( -38.82)
>DroEre_CAF1 96421 120 - 1
CACUGUAUUCCUGUGCGUUAGCUUCUUUAGCUGUUUGCCCAGCAGUGCAUCCCAGACCCGAACUUUGCAGUCUGCACCGCCACUGGCCAGGAUCUUGGCAUCGUGGCUCAAGGACACCGA
...((((((.(((.(((.(((((.....)))))..))).))).))))))((((((((............)))))....(((((..(((((....)))))...)))))....)))...... ( -38.70)
>DroYak_CAF1 94388 120 - 1
CACUGUCUUGUUAUGCGUAAGCUUCUUCAGCUGUUUCCCCAGCAGGGCAUCCCAGACACGGACUUUGCAAUCCGCCCCGCCACUGGCCAGGAUCUUGGCGUCGUGGCUUAAGGACACCGA
...((((((.....((....)).......((((......)))).((((.((...))...(((........))))))).(((((..(((((....)))))...)))))...)))))).... ( -35.60)
>DroAna_CAF1 113544 120 - 1
UACUGCCUCCGGAAGCGUAAACUUCACCAGCUCAUCGCCAGUGAUGGCGCACCAGAUGCGAGCCGUCCGAUCUGCACUGCCGCUGGCCAUCAUGGUGGCCUCGUCAUUCAAGGUCACGCU
..(((....))).(((((...........((((...((((....))))(((.....))))))).....(((((....((.((..((((((....)))))).)).))....)))))))))) ( -41.10)
>consensus
CACUGUUUUGGUAUGCCUAAGCUUCUUCAGCUGUUUCCCCAGCAGGGCAUCCCAGACUCGCACUUUGCAGUCUGCACCGCCACUGGCCAGGAUCUUGGCAUCGUGGCUUAAGGACACCGA
.......(((((((.(.((((((.(..((((((((.....)))))(((....(((((............)))))....))).)))(((((....)))))...).)))))).).))))))) (-27.28 = -27.65 +   0.37)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:02:50 2006