Locus 1142

Sequence ID	2R_DroMel_CAF1
Location	4,558,485 – 4,558,745
Length	260
Max. P	0.916967

overview

Window 8

Location	4,558,485 – 4,558,602
Length	117
Sequences	6
Columns	119
Reading direction	reverse
Mean pairwise identity	72.12
Mean single sequence MFE	-28.22
Consensus MFE	-18.84
Energy contribution	-19.37
Covariance contribution	0.53
Combinations/Pair	1.05
Mean z-score	-1.18
Structure conservation index	0.67
SVM decision value	0.56
SVM RNA-class probability	0.780654
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 4558485 117 - 20766785
CCGUCAGCCCAUCAGUACAUUCAACAAUCCAC-CCA-UUUCAGGGUCUCCUGGCGGCCAUUCCCCUGGCCUACAUCCUGCCCGGCCUGGCCUACAUUCAGAUGGAGCCGCACGCCCUGC
.((((.(((((((.................((-((.-.....))))....((..(((((....((.(((.........))).))..)))))..))....))))).)).).)))...... ( -31.70)
>DroVir_CAF1 37440 105 - 1
-------------AUUUCAUGUAAAUUUUCUCAACA-ACUUAGGGCCUGCUGGCAGCCAUACCCCUGGCCUAUAUACUGCCCGGCCUGGCCUACAUACAAAUGGAACCGCAUGCCCUCU
-------------....(((((..............-.....(((((.(((((((((((......))))........)).)))))..))))).(((....))).....)))))...... ( -25.80)
>DroPse_CAF1 32148 90 - 1
----------------------------GCAC-GCAUUUUUAGGGUCUCCUGGCAGCCAUACCCCUGGCUUAUAUACUGCCCGGGCUGGCCUACAUCCGGAUGGAGCCGCACGCCCUCU
----------------------------....-........(((((....((((.((((...(((.(((.........))).))).)))).....(((....)))))))...))))).. ( -29.00)
>DroGri_CAF1 36304 104 - 1
-------------AUUUCAUGCAAAUUUCUUC-ACA-ACUUAGGGUCUGCUGGCAGCCAUACCACUGGCCUAUAUACUGCCCGGCCUGGCCUACAUACAAAUGGAACCGCAUGCGCUCU
-------------....(((((..........-...-.....(((((.(((((((((((......))))........)).)))))..))))).(((....))).....)))))...... ( -25.50)
>DroYak_CAF1 32228 109 - 1
CCAUCCGCC--------CAUUCACCAGUCCAC-CCA-UUUCAGGGUCUCCUGGCGGCCAUACCCCUGGCCUACAUCCUGCCCGGCCUGGCCUACAUCCAGAUGGAGCCGCACGCCCUGC
......(((--------((((..((((...((-((.-.....))))...)))).(((((....((.(((.........))).))..)))))........))))).)).(((.....))) ( -32.00)
>DroAna_CAF1 32333 91 - 1
--------------------------GUUGGA-ACA-UUUCAGGGUCUCCUGGCCGCCAUCCCACUGGCCUACAUCCUACCCGGCCUGGCCUACAUCCAGAUGGAGCCGCACGCCCUCC
--------------------------......-...-....(((((....((((..(((((.....((((.....((.....))...))))........))))).))))...))))).. ( -25.32)
>consensus
_________________CAU_CAA__GUCCAC_ACA_UUUCAGGGUCUCCUGGCAGCCAUACCCCUGGCCUACAUACUGCCCGGCCUGGCCUACAUCCAGAUGGAGCCGCACGCCCUCC
.........................................(((((....((((.((((..((...(((.........))).))..))))...(((....)))..))))...))))).. (-18.84 = -19.37 +   0.53)

alignment

secondary structure

dotplot

Window 9

Location	4,558,525 – 4,558,641
Length	116
Sequences	5
Columns	116
Reading direction	reverse
Mean pairwise identity	79.75
Mean single sequence MFE	-18.72
Consensus MFE	-15.00
Energy contribution	-15.00
Covariance contribution	0.00
Combinations/Pair	1.00
Mean z-score	-1.83
Structure conservation index	0.80
SVM decision value	1.02
SVM RNA-class probability	0.901974
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 4558525 116 - 20766785
UUAUGCCCCACCCAUCAGCCAGCCCAUCAGAACAUCAGCCCGUCAGCCCAUCAGUACAUUCAACAAUCCACCCAUUUCAGGGUCUCCUGGCGGCCAUUCCCCUGGCCUACAUCCUG
.................(((((...............((......))......................((((......))))...)))))(((((......)))))......... ( -22.20)
>DroSec_CAF1 31845 88 - 1
UUAUGCCCCACCCAUCA----------------------------GCACAUCAGUCCAUUCAACAAUCCACCCAUUUCAGGGUCUCCUGGCGGCCAUUCCCCUGGCCUACAUCCUG
....(((..........----------------------------(.((....)).)............((((......)))).....)))(((((......)))))......... ( -16.80)
>DroSim_CAF1 32265 88 - 1
UUAUGCCCCACCCAUCA----------------------------GCACAUCAGUCCAUUCAACAAUCCACCCAUUUCAGGGUCUCCUGGCGGCCAUUCCCCUGGCCUACAUCCUG
....(((..........----------------------------(.((....)).)............((((......)))).....)))(((((......)))))......... ( -16.80)
>DroEre_CAF1 32362 96 - 1
UUAUGCCCCACCCAUUAG--------------------CCCAUCAGCCCAUCAGUCCAUUUACGAGUCCACCCAUUUCAGGGUCUUCUGGCGGCCAUACCCCUGGCCUACAUCCUG
.................(--------------------((.....((((....((......))(((.........))).)))).....)))(((((......)))))......... ( -18.70)
>DroYak_CAF1 32268 88 - 1
UUAUGCCCCACCCAUUAG--------------------CCCAUCCGCC--------CAUUCACCAGUCCACCCAUUUCAGGGUCUCCUGGCGGCCAUACCCCUGGCCUACAUCCUG
..................--------------------..........--------......((((...((((......))))...)))).(((((......)))))......... ( -19.10)
>consensus
UUAUGCCCCACCCAUCAG____________________CCC_UC_GCCCAUCAGUCCAUUCAACAAUCCACCCAUUUCAGGGUCUCCUGGCGGCCAUUCCCCUGGCCUACAUCCUG
.............................................................................(((((((....)))(((((......))))).....)))) (-15.00 = -15.00 +   0.00)

alignment

secondary structure

dotplot

Window 0

Location	4,558,602 – 4,558,705
Length	103
Sequences	4
Columns	103
Reading direction	reverse
Mean pairwise identity	83.69
Mean single sequence MFE	-16.12
Consensus MFE	-14.93
Energy contribution	-15.17
Covariance contribution	0.25
Combinations/Pair	1.00
Mean z-score	-1.78
Structure conservation index	0.93
SVM decision value	1.11
SVM RNA-class probability	0.916967
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 4558602 103 - 20766785
CGCCAAUCCCAAACGGCAUCUACAAAUUCUGGCCGGAACCCGUCUUUGUAUUUGCCAUGCAAAUUUAUGCCCCACCCAUCAGCCAGCCCAUCAGAACAUCAGC
.((...........((((..((((((..(.((......)).)..))))))..))))..(((......)))...........)).................... ( -16.70)
>DroSim_CAF1 32336 81 - 1
CGCCAAUCCCAAACGGCAUCUACAAAUUCUGGCCCGAACCCGGCUUUGUAUUUGCCAUGCAAAUUUAUGCCCCACCCAUCA----------------------
..............((((..((((((..((((.......)))).))))))..))))..(((......)))...........---------------------- ( -16.60)
>DroEre_CAF1 32439 83 - 1
UGUCAAUCCCAAACGGCAUAUACAAAUUCUGGCCUGAACCCGGCUUUGUAUUUGCCAUGCAAAUUUAUGCCCCACCCAUUAG--------------------C
..............((((.(((((((..((((.......)))).))))))).))))..(((......)))............--------------------. ( -17.60)
>DroYak_CAF1 32337 82 - 1
UGCCAAUCCCAAACGGCAUCUACAAAUUCUGGCCCGAACCC-GCUUUGUAUUUGCCAUGCAAAUUUAUGCCCCACCCAUUAG--------------------C
..............((((..((((((..(.((......)).-).))))))..))))..(((......)))............--------------------. ( -13.60)
>consensus
CGCCAAUCCCAAACGGCAUCUACAAAUUCUGGCCCGAACCCGGCUUUGUAUUUGCCAUGCAAAUUUAUGCCCCACCCAUCAG____________________C
..............((((..((((((..(.((......)).)..))))))..))))..(((......)))................................. (-14.93 = -15.17 +   0.25)

alignment

secondary structure

dotplot

Window 1

Location	4,558,641 – 4,558,745
Length	104
Sequences	6
Columns	115
Reading direction	reverse
Mean pairwise identity	79.39
Mean single sequence MFE	-30.07
Consensus MFE	-13.45
Energy contribution	-14.12
Covariance contribution	0.67
Combinations/Pair	1.17
Mean z-score	-2.76
Structure conservation index	0.45
SVM decision value	0.85
SVM RNA-class probability	0.867021
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 4558641 104 - 20766785
CAUUUGCCCCUUGUAUUCCAGUCACGGGUAUUGGCCACAACGCCAAUCCCAAACGGCAUCUACAAAUUCUGGCCGGAACCCGUCUUUG-----------UAUUUGCCAUGCAAAU
.((((((..................(((.((((((......)))))))))....((((..((((((..(.((......)).)..))))-----------))..))))..)))))) ( -32.50)
>DroSec_CAF1 31933 91 - 1
CAUUUGGCUCUUGUAUUCCGGUCACGGGUAUUGGCCACAA-------------CGGCAUCUACAAAUUCAGGCCCGAACCCGGCUUUG-----------UAUUUGCCAUGCAAAU
....(((((...((((.(((....))))))).)))))...-------------.((((..((((((..(.((......)).)..))))-----------))..))))........ ( -27.30)
>DroSim_CAF1 32353 104 - 1
CAUUUGGCUCUUGUAUUCCGGUCACGGGUAUUGGCCACAACGCCAAUCCCAAACGGCAUCUACAAAUUCUGGCCCGAACCCGGCUUUG-----------UAUUUGCCAUGCAAAU
..........((((((.........(((.((((((......)))))))))....((((..((((((..((((.......)))).))))-----------))..)))))))))).. ( -32.20)
>DroEre_CAF1 32458 104 - 1
CAUUUGUCCCUUGUAUUCUGGUCACGGGUAUUGGCCACAAUGUCAAUCCCAAACGGCAUAUACAAAUUCUGGCCUGAACCCGGCUUUG-----------UAUUUGCCAUGCAAAU
..........((((((.........(((.((((((......)))))))))....((((.(((((((..((((.......)))).))))-----------))).)))))))))).. ( -30.40)
>DroYak_CAF1 32356 103 - 1
CAUUCGGCCCUUGUAUUCCGGUCACGGGUAUUGGCCACAAUGCCAAUCCCAAACGGCAUCUACAAAUUCUGGCCCGAACCC-GCUUUG-----------UAUUUGCCAUGCAAAU
.....((((..........))))..(((.((((((......)))))))))....((((..((((((..(.((......)).-).))))-----------))..))))........ ( -29.50)
>DroAna_CAF1 32434 108 - 1
UUUUUCCCCCUUGCAUUCUGGUCACGGGUAUCGGCCAAAAUGGCCUCCC-------CCUCCACACAUUUUCCCCCAUUUCGGCCUUUGUAGUUUGUGGGUAUUUGGCAUGCAAAU
..........((((((.(..(..(((((....((((.....))))...)-------)).(((((.(((.....((.....)).......))).)))))))..)..).)))))).. ( -28.50)
>consensus
CAUUUGGCCCUUGUAUUCCGGUCACGGGUAUUGGCCACAAUGCCAAUCCCAAACGGCAUCUACAAAUUCUGGCCCGAACCCGGCUUUG___________UAUUUGCCAUGCAAAU
..........((((((.........((((...(((((................................)))))...))))(((....................))))))))).. (-13.45 = -14.12 +   0.67)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:57:33 2006