Locus 1038

Sequence ID 3R_DroMel_CAF1
Location 3,233,895 – 3,234,045
Length 150
Max. P 0.882425
window1681 window1682

overview

Window 1

Location 3,233,895 – 3,234,005
Length 110
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 76.53
Mean single sequence MFE -36.05
Consensus MFE -26.19
Energy contribution -26.58
Covariance contribution 0.39
Combinations/Pair 1.25
Mean z-score -1.38
Structure conservation index 0.73
SVM decision value 0.92
SVM RNA-class probability 0.882425
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 3233895 110 + 27905053
-------U--UAAUCAGAAUAUUAUCCCAU-CUUUUUGCCAGUGCAGCUUGGCCAUCAGCUUAACGGAUAAGUGGGGAGAGCUGCUGGACAAUGGCAGUUGGUCAGGUGUGAUGGGUCAG
-------.--......((.(((((..((..-((..((((((..(((((((..((....(((((.....))))).))..))))))).......))))))..))...))..)))))..)).. ( -34.70)
>DroVir_CAF1 402 89 + 1
---------------------UUACUACAA----------CUUGCAGCUUGGAAGUGCGCUUUCGCGAAACUUGGGGGCAGCUGCUGCCAAAUGGCAGCUGGACGGGUGUAAUGGGCCAC
---------------------....((((.----------(((((.((((..((((.(((....)))..))))..))))....((((((....))))))..).))))))))......... ( -27.50)
>DroSec_CAF1 1203 111 + 1
-------U--UAAUAAUAAUAUUUUCCCACCCUUUUUGCCAGUGCAGCUUGGCCAUCAGCUUAACGGAUAAGUGGGGCGAGCUGCUGGAGAAUGGCAGUUGGUCAGGUGUGAUGGGUCAG
-------.--..............((.((((((..((((((..((((((((.((....(((((.....))))).)).)))))))).......))))))..))...)))).))........ ( -36.50)
>DroSim_CAF1 1204 111 + 1
-------U--UAAUGAUAAUAUUUUCCCACCCUUUUUGCCAGUGCAGCUUGGCCAUCAGCUUAACGGAUAAGUGGGGCGAGCUGCUGGAGAAUGGCAGUUGGUCAGGUGUGAUGGGUCAG
-------.--...((((.......((.((((((..((((((..((((((((.((....(((((.....))))).)).)))))))).......))))))..))...)))).))...)))). ( -38.60)
>DroEre_CAF1 1261 115 + 1
GGAAUGAUUAUGAUCAGAAUAU----CCCC-CCUUUUUCCAGUGCAGCUUGGCCAUCAGCCUAACGGACAAGUGGGGCGAGCUGCUGGAGAACGGCAGUUGGUCAGGUGUGAUGGGUCAG
(((.((((....)))).....)----))..-......((((..(((.(((((((....((((.((......)).)))).((((((((.....))))))))))))))))))..)))).... ( -39.90)
>DroYak_CAF1 1282 110 + 1
-------U--UAAUCAGAAUAUUACACCAC-CUUUUUCCCAGUGCAGCUUGGCCAUAAGCUUAACGGAUAAGUGGGGCGAACUGCUGGAGAAUGGCAGUUGGUCAGGUGUGAUGGGUCAG
-------.--......((.(((((((((.(-(.(((..((.((..((((((....))))))..))))..))).))(((.((((((((.....)))))))).))).)))))))))..)).. ( -39.10)
>consensus
_______U__UAAUCAGAAUAUUAUCCCAC_CUUUUUGCCAGUGCAGCUUGGCCAUCAGCUUAACGGAUAAGUGGGGCGAGCUGCUGGAGAAUGGCAGUUGGUCAGGUGUGAUGGGUCAG
......................................(((.((((.(((((((....((((.((......)).)))).((((((((.....))))))))))))))))))).)))..... (-26.19 = -26.58 +   0.39)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 2

Location 3,233,925 – 3,234,045
Length 120
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 75.35
Mean single sequence MFE -48.40
Consensus MFE -28.14
Energy contribution -29.23
Covariance contribution 1.09
Combinations/Pair 1.42
Mean z-score -1.57
Structure conservation index 0.58
SVM decision value 0.41
SVM RNA-class probability 0.725550
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 3233925 120 + 27905053
AGUGCAGCUUGGCCAUCAGCUUAACGGAUAAGUGGGGAGAGCUGCUGGACAAUGGCAGUUGGUCAGGUGUGAUGGGUCAGGUGACGAGUCGCGAGGCGGACUUUGCCGUGUGUCCCAUUC
...(((((((..((....(((((.....))))).))..))))))).((((((((((((((.(((...((((((..(((....)))..)))))).))).)))..)))))).)))))..... ( -49.50)
>DroVir_CAF1 411 120 + 1
CUUGCAGCUUGGAAGUGCGCUUUCGCGAAACUUGGGGGCAGCUGCUGCCAAAUGGCAGCUGGACGGGUGUAAUGGGCCACGUUACAAGCGGCGAGGUACACUUUGCUGUAUGCCCCAUUA
......((..(((((....)))))))........((((((...((((((....))))))........(((((((.....))))))).(((((((((....))))))))).)))))).... ( -47.50)
>DroPse_CAF1 990 117 + 1
---UCAGCCUGGCCAUAAGCUUCACGGACAACUGGGGCCAGCAGCUGGCCAACGGCAGAUGGUCGGGUGUGAUGGGUCAGAUAACCAACGGGGAGGCCGACUUUGCCGUGUGUCCCAUUC
---...((((((((((..(((...(((....))).((((((...))))))...)))..))))))))))..((((((.((........((((.((((....)))).)))).)).)))))). ( -47.50)
>DroYak_CAF1 1312 120 + 1
AGUGCAGCUUGGCCAUAAGCUUAACGGAUAAGUGGGGCGAACUGCUGGAGAAUGGCAGUUGGUCAGGUGUGAUGGGUCAGGUGACAAGUCGCGCGGCGGACUUGGCCGUGUGUCCUAUUC
...((((.((.(((....(((((.....)))))..))).)))))).(((.((((((((((.(((..(((((((..(((....)))..)))))))))).))))..))))).).)))..... ( -46.60)
>DroMoj_CAF1 421 120 + 1
GCUACAGCUUGCAGGUGCUCUUUCGCGACACCUGGGGUCAGCUGCUGCCCAACGGCAGCUGGUCGGGCGUGAUUGGCCACAUAGUCAGCGGCGAGGCAGACUUCUCCGUGUGCCCCAUCC
((....))...((((((.((......)))))))).(..(((((((((.....)))))))))..)(((((((((((......))))))((((.((((....)))).)))).)))))..... ( -51.80)
>DroPer_CAF1 980 117 + 1
---UCAGCCUGGCCAUAAGCUUCACGGACAACUGGGGCCAGCAGCUGGCCAACGGCAGAUGGUCGGGUGUGAUGGGUCAGAUAACCAACGGGGAGGCCGACUUUGCCGUGUGUCCCAUUC
---...((((((((((..(((...(((....))).((((((...))))))...)))..))))))))))..((((((.((........((((.((((....)))).)))).)).)))))). ( -47.50)
>consensus
__UGCAGCUUGGCCAUAAGCUUAACGGACAACUGGGGCCAGCUGCUGGCCAACGGCAGAUGGUCGGGUGUGAUGGGUCAGAUAACCAGCGGCGAGGCAGACUUUGCCGUGUGUCCCAUUC
......((((((((.....((((((......))))))..((((((((.....))))))))))))))))..((((((.((........((((.((((....)))).)))).)).)))))). (-28.14 = -29.23 +   1.09)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:59:01 2006