Locus 3716

Sequence ID 2R_DroMel_CAF1
Location 12,319,662 – 12,319,825
Length 163
Max. P 0.862956
window6037 window6038

overview

Window 7

Location 12,319,662 – 12,319,762
Length 100
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 80.31
Mean single sequence MFE -32.18
Consensus MFE -15.72
Energy contribution -16.44
Covariance contribution 0.73
Combinations/Pair 1.19
Mean z-score -2.80
Structure conservation index 0.49
SVM decision value 0.84
SVM RNA-class probability 0.862956
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 12319662 100 + 20766785
AAUUAAUUACAGGCAAUAAGGUAAUUUCAGCC--------------AGGAGCUGUGCUUUUUGUGGCCCAAA----GGAU--ACGAUGGCCACGGAGCAUGUGCCAGUGUUGCCAAAAAC
...........(((((((.((((....((((.--------------....))))(((((..(((((((....----(...--.)...))))))))))))..))))..)))))))...... ( -34.30)
>DroSec_CAF1 18444 100 + 1
AAUUAAUUACAGGCAAUAAGGUAAUUUCAGCC--------------AAGAGCUGUGCUUUUUGUGGCCCAAA----GGAU--ACGAUGGCCAAGGCGUAUUCGCCAGUGUUGCCAAAAAC
...........((((((((((((....((((.--------------....)))))))))....(((((....----(...--.)...))))).((((....))))..)))))))...... ( -29.20)
>DroSim_CAF1 16551 102 + 1
AAUUAAUUACAGGCAAUAAGGUAAUUUCAGCC--------------AGGAGCUGUGCUUUUUGUGGCCCAAA----GGAUAUACGAUGGCCAAGGCGUAUUUGCCAGUGUUGCCAAAAAC
...........(((((((.(((((.....(((--------------((((((...))))))..(((((....----(......)...))))).)))....)))))..)))))))...... ( -31.60)
>DroEre_CAF1 18486 91 + 1
AAUUAAUUACAGGCAAUAAGGUAAUUUCAGCC--------------AGGAGCUGUGCUUUUUGUGGCCCAAA----GGAU--ACGAGGGCAA---------AGCGAGUAUUGCCAAAAAC
...........(((((((.(((.......)))--------------....(((.(((((((.(((.((....----)).)--))))))))).---------)))...)))))))...... ( -26.30)
>DroYak_CAF1 16851 99 + 1
AAUUAAUUACAGGCAAUAAGGUAAUUUCAGCC--------------AGUAGCUGUGCUUUUUGUGGCCCAAA----GGAU--ACGAUGGCCAAGGAGUA-GAGCCAGUGUUGCCGAAAAC
...........(((((((.(((.......)))--------------....(((.((((((...(((((....----(...--.)...))))).))))))-.)))...)))))))...... ( -30.80)
>DroAna_CAF1 16469 115 + 1
AAUUAAUUACAGGCAAUAACGUAAUUCCUGCCAAGGGCCACCAGGCAAGAGCUGUGCUUUUUGUGGCCAAAACAGGGAGU--GCGGUGGCAG--GACAA-CCUUUUGAUUUGCCAAAAAA
...........(((((.........(((((((....(((....)))....((((..((((((((.......)))))))).--.)))))))))--))(((-....)))..)))))...... ( -40.90)
>consensus
AAUUAAUUACAGGCAAUAAGGUAAUUUCAGCC______________AGGAGCUGUGCUUUUUGUGGCCCAAA____GGAU__ACGAUGGCCAAGGAGUA_GAGCCAGUGUUGCCAAAAAC
...........(((((((.(((........................((((((...))))))..(((((...................)))))..........)))..)))))))...... (-15.72 = -16.44 +   0.73)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 8

Location 12,319,724 – 12,319,825
Length 101
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 81.25
Mean single sequence MFE -25.90
Consensus MFE -16.36
Energy contribution -17.53
Covariance contribution 1.17
Combinations/Pair 1.19
Mean z-score -2.14
Structure conservation index 0.63
SVM decision value 0.57
SVM RNA-class probability 0.783646
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 12319724 101 + 20766785
--ACGAUGGCCACGGAGCAUGUGCCAGUGUUGCCAAAAACAA----------------CUGUUAAAUAGAGGAAACGAC-AGUGGCGACGCAGCGCCAAAGGAAAUAUAAAUGCGACAUA
--....((((.(((.....)))))))(((((((........(----------------(((((.......(....))))-)))((((......))))...............))))))). ( -26.91)
>DroSec_CAF1 18506 101 + 1
--ACGAUGGCCAAGGCGUAUUCGCCAGUGUUGCCAAAAACAA----------------CUGUUAAAUAGAGGAAACGAC-AGUGGCGACGCAGCGCCAAAGGAAAUAUAAAUGCGACAUA
--.(..(((((..((((....)))).(((((((((.......----------------((((...)))).(....)...-..))))))))).).))))..)................... ( -30.30)
>DroSim_CAF1 16613 103 + 1
AUACGAUGGCCAAGGCGUAUUUGCCAGUGUUGCCAAAAACAA----------------CUGUUAAAUAGAGGAAACGAC-AGUGGCGACGCAGCGCCAAAGGAAAUAUAAAUGCGACAUA
...(..(((((..((((....)))).(((((((((.......----------------((((...)))).(....)...-..))))))))).).))))..)................... ( -28.90)
>DroEre_CAF1 18548 92 + 1
--ACGAGGGCAA---------AGCGAGUAUUGCCAAAAACAA----------------UUGUUAAAUAGAGGAAACGAC-AGUGGCGACGCAGCGCCAAAGGAAAUAUAAAUGCGACAUA
--.(...(((..---------.((..(..((((((..(((..----------------..))).......(....)...-..))))))..).)))))...)................... ( -18.10)
>DroYak_CAF1 16913 100 + 1
--ACGAUGGCCAAGGAGUA-GAGCCAGUGUUGCCGAAAACAA----------------CUGUUAAAUAGAGGAAACGAC-AGUGGCGACGCAGCGCCAAAGGAAAUAUAAAUGCGACAUA
--....(((((........-).))))(((((((........(----------------(((((.......(....))))-)))((((......))))...............))))))). ( -25.11)
>DroAna_CAF1 16549 115 + 1
--GCGGUGGCAG--GACAA-CCUUUUGAUUUGCCAAAAAAAAAGGAGAGAAGAGGGAGCUGCUAAAUCGAGGAAACGAAAAACGGCGACGCAGCGCUAAAGGAAAUAUAAAUGCGACAUA
--...((.(((.--.....-((((((..(((.((.........)))))..)))))).(((((........(....).......(....)))))).................))).))... ( -26.10)
>consensus
__ACGAUGGCCAAGGAGUA_GAGCCAGUGUUGCCAAAAACAA________________CUGUUAAAUAGAGGAAACGAC_AGUGGCGACGCAGCGCCAAAGGAAAUAUAAAUGCGACAUA
...(..((((...((........)).(((((((((.......................((((...)))).(....)......)))))))))...))))..)................... (-16.36 = -17.53 +   1.17)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:02:36 2006