Locus 376

Sequence ID 2R_DroMel_CAF1
Location 2,359,205 – 2,359,501
Length 296
Max. P 0.999822
window738 window739 window740 window741 window742

overview

Window 8

Location 2,359,205 – 2,359,325
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 97.17
Mean single sequence MFE -31.84
Consensus MFE -30.10
Energy contribution -29.70
Covariance contribution -0.40
Combinations/Pair 1.07
Mean z-score -1.44
Structure conservation index 0.95
SVM decision value 1.18
SVM RNA-class probability 0.927676
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 2359205 120 + 20766785
CAAUCUGUUAACGCGUUUGCAAAUAAAAAUUAUCAAAUUAUUUUGGCCCGAUUUCGGGCGGCUCCCGGCCAUGUGUGCUCGCUCAAUCAAUUAUUCUGCCGAUUUCGGGUAUUUGCAUGU
.................(((((((.........((((....))))((((((..((((..(((.....))).((.((....)).)).............))))..)))))))))))))... ( -32.30)
>DroSec_CAF1 8683 120 + 1
CAAUCUGUUAACGCGUUUGCAAAUAAAAAUUAUCAAAUUAUUUUGGCCCGAUUUCGGGCGGCUCCCGGCCAUGUGUGCUCGCUCAAUCAAUUAUUCUGCCGAUUUCGGGUAUUUGCAUGU
.................(((((((.........((((....))))((((((..((((..(((.....))).((.((....)).)).............))))..)))))))))))))... ( -32.30)
>DroSim_CAF1 8807 120 + 1
CAAUCUGUUAACGCGUUUGCAAAUAAAAAUUAUCAAAUUAUUUUGGCCCGAUUUCGGGCGGCUCCCGGCCAUGUGUGCUCGCUCAAUCAAUUAUUCUGCCGAUUUCGGGUAUUUGCAUGU
.................(((((((.........((((....))))((((((..((((..(((.....))).((.((....)).)).............))))..)))))))))))))... ( -32.30)
>DroEre_CAF1 8836 120 + 1
CAAUCUGUUAACGCGUUGGCAAAUAAAAAUUAUCAAAUUAUUUUGGCCCGAUUUCGGGUGGCUCCCGGCCAUGUGUGCUCGCUCAAUCAAUUAUUCUGCCGAUUUCGGGUAUUUGCAUGU
((((.((....)).))))((((((.........((((....))))((((((..(((((((((.....)))))(((....)))................))))..)))))))))))).... ( -35.30)
>DroYak_CAF1 8177 120 + 1
CAAUCUAUUAACGCGUUUGCAAAUAAAAAUUAUCAAAUUAUUUUGGCCCGAGUUCGUGUGGCUCCCGGCCAUGUGUGCCCGCUCAAUCAAUUAUUCUGCCGAUUUUGGGUAUUUGCGUGU
..........((((....((((((.........((((....))))(((((((.(((.(((((.....)))))(((....))).................))).))))))))))))))))) ( -27.00)
>consensus
CAAUCUGUUAACGCGUUUGCAAAUAAAAAUUAUCAAAUUAUUUUGGCCCGAUUUCGGGCGGCUCCCGGCCAUGUGUGCUCGCUCAAUCAAUUAUUCUGCCGAUUUCGGGUAUUUGCAUGU
..................((((((.........((((....))))((((((..(((.(((((.....))).((.((....)).))............)))))..)))))))))))).... (-30.10 = -29.70 +  -0.40)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 9

Location 2,359,245 – 2,359,365
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 97.83
Mean single sequence MFE -34.46
Consensus MFE -31.76
Energy contribution -32.16
Covariance contribution 0.40
Combinations/Pair 1.00
Mean z-score -2.25
Structure conservation index 0.92
SVM decision value 2.91
SVM RNA-class probability 0.997713
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 2359245 120 - 20766785
AGCAAUUUAAUAUUCAUUUGUGCGUGUAAAUCAGAUUUGCACAUGCAAAUACCCGAAAUCGGCAGAAUAAUUGAUUGAGCGAGCACACAUGGCCGGGAGCCGCCCGAAAUCGGGCCAAAA
..(((((...(((((((((((..((((((((...))))))))..))))))..(((....)))..)))))...))))).............(((.....)))(((((....)))))..... ( -35.40)
>DroSec_CAF1 8723 120 - 1
AGCAAUUUAAUAUUCAUUUGUGCGUGUAAAUCAGAUUUGCACAUGCAAAUACCCGAAAUCGGCAGAAUAAUUGAUUGAGCGAGCACACAUGGCCGGGAGCCGCCCGAAAUCGGGCCAAAA
..(((((...(((((((((((..((((((((...))))))))..))))))..(((....)))..)))))...))))).............(((.....)))(((((....)))))..... ( -35.40)
>DroSim_CAF1 8847 120 - 1
AGCAAUUUAAUAUUCAUUUGUGCGUGUAAAUCAGAUUUGCACAUGCAAAUACCCGAAAUCGGCAGAAUAAUUGAUUGAGCGAGCACACAUGGCCGGGAGCCGCCCGAAAUCGGGCCAAAA
..(((((...(((((((((((..((((((((...))))))))..))))))..(((....)))..)))))...))))).............(((.....)))(((((....)))))..... ( -35.40)
>DroEre_CAF1 8876 120 - 1
AGCAAUUUAAUAUUCAUUUGUGCGUGUAAAUCAGAUUUGCACAUGCAAAUACCCGAAAUCGGCAGAAUAAUUGAUUGAGCGAGCACACAUGGCCGGGAGCCACCCGAAAUCGGGCCAAAA
..(((((...(((((((((((..((((((((...))))))))..))))))..(((....)))..)))))...)))))............((((((((.....)))(....).)))))... ( -34.00)
>DroYak_CAF1 8217 120 - 1
AGCAAUUUAAUAUUCAUUUGUGCGUGUAAAUCAGAUUUGCACACGCAAAUACCCAAAAUCGGCAGAAUAAUUGAUUGAGCGGGCACACAUGGCCGGGAGCCACACGAACUCGGGCCAAAA
..(((((...((((((((((((.((((((((...)))))))).)))))))..((......))..)))))...)))))....(((.....((((.....))))..((....)).))).... ( -32.10)
>consensus
AGCAAUUUAAUAUUCAUUUGUGCGUGUAAAUCAGAUUUGCACAUGCAAAUACCCGAAAUCGGCAGAAUAAUUGAUUGAGCGAGCACACAUGGCCGGGAGCCGCCCGAAAUCGGGCCAAAA
..................(((((.(((.((((((((((((....))))))..(((....)))........))))))..))).)))))..((((((((.....)))(....).)))))... (-31.76 = -32.16 +   0.40)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 0

Location 2,359,285 – 2,359,389
Length 104
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 93.12
Mean single sequence MFE -27.74
Consensus MFE -25.10
Energy contribution -25.34
Covariance contribution 0.24
Combinations/Pair 1.03
Mean z-score -2.62
Structure conservation index 0.90
SVM decision value 4.17
SVM RNA-class probability 0.999822
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 2359285 104 - 20766785
----------------GUGUACUUGAACUCAAUUGAUUCAAGCAAUUUAAUAUUCAUUUGUGCGUGUAAAUCAGAUUUGCACAUGCAAAUACCCGAAAUCGGCAGAAUAAUUGAUUGAGC
----------------.....((((((.((....))))))))(((((...(((((((((((..((((((((...))))))))..))))))..(((....)))..)))))...)))))... ( -26.80)
>DroSec_CAF1 8763 104 - 1
----------------GUGUACUUGAACUCAAUUGAUUCAAGCAAUUUAAUAUUCAUUUGUGCGUGUAAAUCAGAUUUGCACAUGCAAAUACCCGAAAUCGGCAGAAUAAUUGAUUGAGC
----------------.....((((((.((....))))))))(((((...(((((((((((..((((((((...))))))))..))))))..(((....)))..)))))...)))))... ( -26.80)
>DroSim_CAF1 8887 104 - 1
----------------GUGUACUUGAACUCAAUUGAUUCAAGCAAUUUAAUAUUCAUUUGUGCGUGUAAAUCAGAUUUGCACAUGCAAAUACCCGAAAUCGGCAGAAUAAUUGAUUGAGC
----------------.....((((((.((....))))))))(((((...(((((((((((..((((((((...))))))))..))))))..(((....)))..)))))...)))))... ( -26.80)
>DroEre_CAF1 8916 104 - 1
----------------GUGUACUUGAACUCAAUUGAUUCAAGCAAUUUAAUAUUCAUUUGUGCGUGUAAAUCAGAUUUGCACAUGCAAAUACCCGAAAUCGGCAGAAUAAUUGAUUGAGC
----------------.....((((((.((....))))))))(((((...(((((((((((..((((((((...))))))))..))))))..(((....)))..)))))...)))))... ( -26.80)
>DroYak_CAF1 8257 120 - 1
GUGUUUGGGUGUAUGGGUGUACUCGAACUCAAUUGAUUCAAGCAAUUUAAUAUUCAUUUGUGCGUGUAAAUCAGAUUUGCACACGCAAAUACCCAAAAUCGGCAGAAUAAUUGAUUGAGC
(.(((((((((........))))))))).)......(((((.((((....((((((((((((.((((((((...)))))))).)))))))..((......))..))))))))).))))). ( -31.50)
>consensus
________________GUGUACUUGAACUCAAUUGAUUCAAGCAAUUUAAUAUUCAUUUGUGCGUGUAAAUCAGAUUUGCACAUGCAAAUACCCGAAAUCGGCAGAAUAAUUGAUUGAGC
.....................((((((.((....))))))))(((((...((((((((((((.((((((((...)))))))).)))))))..(((....)))..)))))...)))))... (-25.10 = -25.34 +   0.24)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 1

Location 2,359,389 – 2,359,501
Length 112
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 83.80
Mean single sequence MFE -33.14
Consensus MFE -21.64
Energy contribution -22.44
Covariance contribution 0.80
Combinations/Pair 1.09
Mean z-score -1.93
Structure conservation index 0.65
SVM decision value 0.28
SVM RNA-class probability 0.665205
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 2359389 112 + 20766785
--------UCCGCACUCACCCUGCACUCGCUGUAGAUUUUUGAGUUCGCAGUGCUCAAUCACAAUGGCAUAAAUCGCGCCACGAGUGCAAAGUGAAAUUUGGAAAGGUGCCUUCCCGCAC
--------...((..((((..((((((((.(((.(((...(((((.......))))))))))).((((.........))))))))))))..)))).....((.(((....))).)))).. ( -35.80)
>DroSec_CAF1 8867 96 + 1
--------CCCGCACUCACACUGCACUCGCUGUGGAUUUUUGAGUU----GUGCGCAGUCACAAUGGCAUAAAUCGCGCCACGAGUGCAAAGUGAAAUUUGGAAAGG-G-----------
--------(((.(..((((..((((((((..((((((((.((.(((----(((......))))))..)).))))).)))..))))))))..))))......)...))-)----------- ( -34.40)
>DroSim_CAF1 8991 97 + 1
--------CCCGCACUCACACUGCACUCGCUGUGGAUUUUUGAGUU----GUGCGCAGUCACAAUGGCAUAAAUCGCGCCACAAGUGCAAAGUGAAAUUUGGAAAGGUG-----------
--------.(((...((((..((((((...(((((.....(((.((----((((.((.......)))))))).)))..)))))))))))..))))....))).......----------- ( -28.60)
>DroEre_CAF1 9020 94 + 1
--------CCAGCGCCCACACUGCACUCACUG-GGAUUUUUGAGUU----GUGCGCAGUCACAAUGGCA-AAACCGCGCCACGAGUGCGAAGUGAAAUUG-GAAAGCUG-----------
--------.((((..(((((((((((((..((-((..(((((.(((----(((......))))))..))-)))...).))).))))))..))))....))-)...))))----------- ( -30.70)
>DroYak_CAF1 8377 105 + 1
CCAAAUACCCAGCGCUCACACUGCACUCACUGUGGAUUUUUGAGUU----GUGCGCAGUCACAAUGGCAUAAAUCGCGCCACGAGUGCAAAGUGAAAUUGGGAAAGGUG-----------
.......(((((...((((..(((((((...((((((((.((.(((----(((......))))))..)).))))).)))...)))))))..))))..))))).......----------- ( -36.20)
>consensus
________CCCGCACUCACACUGCACUCGCUGUGGAUUUUUGAGUU____GUGCGCAGUCACAAUGGCAUAAAUCGCGCCACGAGUGCAAAGUGAAAUUUGGAAAGGUG___________
...............((((..(((((((((((((.((.............)).)))))).....((((.........)))).)))))))..))))......................... (-21.64 = -22.44 +   0.80)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 2

Location 2,359,389 – 2,359,501
Length 112
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 83.80
Mean single sequence MFE -35.30
Consensus MFE -24.58
Energy contribution -24.42
Covariance contribution -0.16
Combinations/Pair 1.13
Mean z-score -2.37
Structure conservation index 0.70
SVM decision value 1.14
SVM RNA-class probability 0.921568
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 2359389 112 - 20766785
GUGCGGGAAGGCACCUUUCCAAAUUUCACUUUGCACUCGUGGCGCGAUUUAUGCCAUUGUGAUUGAGCACUGCGAACUCAAAAAUCUACAGCGAGUGCAGGGUGAGUGCGGA--------
(..(((((((....)))))).....(((((((((((((((((((.......))))..((((((((((.........))))...))).)))))))))))))))))))..)...-------- ( -45.50)
>DroSec_CAF1 8867 96 - 1
-----------C-CCUUUCCAAAUUUCACUUUGCACUCGUGGCGCGAUUUAUGCCAUUGUGACUGCGCAC----AACUCAAAAAUCCACAGCGAGUGCAGUGUGAGUGCGGG--------
-----------.-.....((....(((((.((((((((((.(.(.(((((.((...(((((......)))----))..)).)))))).).)))))))))).)))))....))-------- ( -32.90)
>DroSim_CAF1 8991 97 - 1
-----------CACCUUUCCAAAUUUCACUUUGCACUUGUGGCGCGAUUUAUGCCAUUGUGACUGCGCAC----AACUCAAAAAUCCACAGCGAGUGCAGUGUGAGUGCGGG--------
-----------.......((....(((((.((((((((((.(.(.(((((.((...(((((......)))----))..)).)))))).).)))))))))).)))))....))-------- ( -30.80)
>DroEre_CAF1 9020 94 - 1
-----------CAGCUUUC-CAAUUUCACUUCGCACUCGUGGCGCGGUUU-UGCCAUUGUGACUGCGCAC----AACUCAAAAAUCC-CAGUGAGUGCAGUGUGGGCGCUGG--------
-----------((((..((-((....((((..(((((((((.(((((((.-.........))))))))))----.(((.........-.))))))))))))))))).)))).-------- ( -32.50)
>DroYak_CAF1 8377 105 - 1
-----------CACCUUUCCCAAUUUCACUUUGCACUCGUGGCGCGAUUUAUGCCAUUGUGACUGCGCAC----AACUCAAAAAUCCACAGUGAGUGCAGUGUGAGCGCUGGGUAUUUGG
-----------..((...((((..(((((.(((((((((..(.(.(((((.((...(((((......)))----))..)).)))))).)..))))))))).)))))...)))).....)) ( -34.80)
>consensus
___________CACCUUUCCAAAUUUCACUUUGCACUCGUGGCGCGAUUUAUGCCAUUGUGACUGCGCAC____AACUCAAAAAUCCACAGCGAGUGCAGUGUGAGUGCGGG________
........................(((((.((((((((((((((.......))))..((((....)))).....................)))))))))).))))).............. (-24.58 = -24.42 +  -0.16)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:36:54 2006