Locus 8317

Sequence ID X_DroMel_CAF1
Location 20,665,006 – 20,665,229
Length 223
Max. P 0.992788
window13659 window13660 window13661 window13662 window13663

overview

Window 9

Location 20,665,006 – 20,665,126
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 94.47
Mean single sequence MFE -21.46
Consensus MFE -20.42
Energy contribution -20.10
Covariance contribution -0.32
Combinations/Pair 1.17
Mean z-score -1.35
Structure conservation index 0.95
SVM decision value 1.22
SVM RNA-class probability 0.932884
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 20665006 120 + 22224390
GCAUACAUAUAUCAUUUGCAUAGUUAGACAAAGAUGGCCGAUAAGUCGAUGCGAAAUUUAAUCCGCAUUAAACGCUUCUAACAAAUGCACUAAAUAAAAAUCGAAAUAAAUUGCUUAAUA
(((....(((.((((((((((.((((((.......(((......)))((((((..........)))))).......))))))..))))).........))).)).)))...)))...... ( -18.00)
>DroSec_CAF1 66649 116 + 1
GCA----UAUAUCAUUUGCAUAGUUAGACAAAGAUGGCCGAUAAGUCGAUGCGAAAUUUAAUCUGCAUUAAACGCUUCUAACAAAUGCACUAAAUAAAAAGCGAAAUAAAUUGCUUGAUA
...----..((((...(((((.((((((.......(((......)))((((((..........)))))).......))))))..))))).........((((((......)))))))))) ( -21.50)
>DroSim_CAF1 44112 116 + 1
GCA----UAUAUCAUUUGCAUAGUUAGACAAAGAUGGCCGAUAAGUCGAUGCGAAAUUUAAUCCGCAUUAAACGCUUCUAACAAAUGCACUAAAUAAAAAGCGAAAUAAAUUGCUUGAUA
...----..((((...(((((.((((((.......(((......)))((((((..........)))))).......))))))..))))).........((((((......)))))))))) ( -23.50)
>DroEre_CAF1 62328 116 + 1
GCA----UAUAUCAUUUGCAUAGUUAGACAAAGAUGGUUGAUAAGUCGAUGCGAAAUUUAAGCCGCAUUAAACGCUUCUAGCAAAUGCACUAAAUAAAAUGCGAAAUAAAUUGCGUGAUA
...----..((((((.(((((.((((((....(((.........)))((((((..........)))))).......))))))..)))))...........((((......)))))))))) ( -22.20)
>DroYak_CAF1 63645 116 + 1
GCA----UAUAUCAUUUGCAUAGUUAGACAAAGAUGGCCGAUAAGUCGAUGCGAAAUUAAAGCCGCAUCAAACGCUUCUACCAAAUGCACUAAAUAAAAAGCGAAAUAAAUUGCUUGAUA
...----..((((...(((((...((((.......(((......)))((((((..........)))))).......))))....))))).........((((((......)))))))))) ( -22.10)
>consensus
GCA____UAUAUCAUUUGCAUAGUUAGACAAAGAUGGCCGAUAAGUCGAUGCGAAAUUUAAUCCGCAUUAAACGCUUCUAACAAAUGCACUAAAUAAAAAGCGAAAUAAAUUGCUUGAUA
.........((((...(((((.((((((.......(((......)))((((((..........)))))).......))))))..))))).........((((((......)))))))))) (-20.42 = -20.10 +  -0.32)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 0

Location 20,665,046 – 20,665,164
Length 118
Sequences 5
Columns 118
Reading direction forward
Mean pairwise identity 92.53
Mean single sequence MFE -24.18
Consensus MFE -21.34
Energy contribution -21.10
Covariance contribution -0.24
Combinations/Pair 1.11
Mean z-score -1.37
Structure conservation index 0.88
SVM decision value 0.67
SVM RNA-class probability 0.818287
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 20665046 118 + 22224390
AUAAGUCGAUGCGAAAUUUAAUCCGCAUUAAACGCUUCUAACAAAUGCACUAAAUAAAAAUCGAAAUAAAUUGCUUAAUAGUGAAAGUGCUUUGGAUGGCUAAUUUAACUGAAUAGCU
....(((((((((..........))))))............((((.(((((........((....))...(..((....))..).))))))))))))(((((.((.....)).))))) ( -18.30)
>DroSec_CAF1 66685 116 + 1
AUAAGUCGAUGCGAAAUUUAAUCUGCAUUAAACGCUUCUAACAAAUGCACUAAAUAAAAAGCGAAAUAAAUUGCUUGAUAGUGGAAGUGCUUUGGAUGGGUAAUUUAACUGAAUGG--
((..(((((.(((...((((((....))))))))).))...((((.(((((...((..((((((......))))))..)).....))))))))))))..))...............-- ( -20.10)
>DroSim_CAF1 44148 118 + 1
AUAAGUCGAUGCGAAAUUUAAUCCGCAUUAAACGCUUCUAACAAAUGCACUAAAUAAAAAGCGAAAUAAAUUGCUUGAUAGUGGAAGUGCUUUGGAUGGCUAAUUUAACUGAAUGGCU
...((((((((((..........))))))....(((.....((((.(((((...((..((((((......))))))..)).....)))))))))...)))..............)))) ( -25.60)
>DroEre_CAF1 62364 113 + 1
AUAAGUCGAUGCGAAAUUUAAGCCGCAUUAAACGCUUCUAGCAAAUGCACUAAAUAAAAUGCGAAAUAAAUUGCGUGAUAGUGGAAGUGCUUUGGACGGCUAAUUUAACUGAA-----
...((((((((((..........)))))((((((((((((((....))..........((((((......)))))).....)))))))).))))..)))))............----- ( -25.80)
>DroYak_CAF1 63681 118 + 1
AUAAGUCGAUGCGAAAUUAAAGCCGCAUCAAACGCUUCUACCAAAUGCACUAAAUAAAAAGCGAAAUAAAUUGCUUGAUAGUGGAAGUGCUUUGGAUGGCUAAUUCAACAGAAUGGCU
...((((((((((..........))))))....(((....(((((.(((((...((..((((((......))))))..)).....))))))))))..)))..((((....)))))))) ( -31.10)
>consensus
AUAAGUCGAUGCGAAAUUUAAUCCGCAUUAAACGCUUCUAACAAAUGCACUAAAUAAAAAGCGAAAUAAAUUGCUUGAUAGUGGAAGUGCUUUGGAUGGCUAAUUUAACUGAAUGGCU
...((((((((((..........))))))............((((.(((((...((..((((((......))))))..)).....)))))))))...))))................. (-21.34 = -21.10 +  -0.24)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 1

Location 20,665,086 – 20,665,194
Length 108
Sequences 5
Columns 114
Reading direction forward
Mean pairwise identity 83.06
Mean single sequence MFE -22.40
Consensus MFE -14.66
Energy contribution -16.62
Covariance contribution 1.96
Combinations/Pair 1.08
Mean z-score -3.35
Structure conservation index 0.65
SVM decision value 2.35
SVM RNA-class probability 0.992788
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 20665086 108 + 22224390
ACAAAUGCACUAAAUAAAAAUCGAAAUAAAUUGCUUAAUAGUGAAAGUGCUUUGGAUGGCUAAUUUAACUGAAUAGCUAAAU----AAAAGCCAUUCAUAAAA--AAAACUAAA
......(((((........((....))...(..((....))..).)))))..(((((((((.(((((.((....)).)))))----...))))))))).....--......... ( -17.80)
>DroSec_CAF1 66725 102 + 1
ACAAAUGCACUAAAUAAAAAGCGAAAUAAAUUGCUUGAUAGUGGAAGUGCUUUGGAUGGGUAAUUUAACUGAAUGG-----A----AUAAGCCAUUCAUAAAA--AAAA-CAAA
.((((.(((((...((..((((((......))))))..)).....)))))))))..((..(..((((..(((((((-----.----.....))))))))))).--.)..-)).. ( -21.90)
>DroSim_CAF1 44188 109 + 1
ACAAAUGCACUAAAUAAAAAGCGAAAUAAAUUGCUUGAUAGUGGAAGUGCUUUGGAUGGCUAAUUUAACUGAAUGGCUAAAU----AUAAGCCAUUCAUAAAAAAAAAA-CAAA
.((((.(((((...((..((((((......))))))..)).....)))))))))...............(((((((((....----...)))))))))...........-.... ( -26.00)
>DroEre_CAF1 62404 96 + 1
GCAAAUGCACUAAAUAAAAUGCGAAAUAAAUUGCGUGAUAGUGGAAGUGCUUUGGACGGCUAAUUUAACUGAA--------------UAUGGCAAUC-UGAAA--AUAG-CAAA
((....(((((...((..((((((......))))))..)).....)))))((..((..((((((((....)))--------------).))))..))-..)).--...)-)... ( -21.40)
>DroYak_CAF1 63721 110 + 1
CCAAAUGCACUAAAUAAAAAGCGAAAUAAAUUGCUUGAUAGUGGAAGUGCUUUGGAUGGCUAAUUCAACAGAAUGGCUAAAUAUGUAUAAGCCGAAC-UAAAC--AUAA-CAGA
(((((.(((((...((..((((((......))))))..)).....)))))))))).((((((.(((....)))))))))..(((((.((........-)).))--))).-.... ( -24.90)
>consensus
ACAAAUGCACUAAAUAAAAAGCGAAAUAAAUUGCUUGAUAGUGGAAGUGCUUUGGAUGGCUAAUUUAACUGAAUGGCUAAAU____AUAAGCCAUUCAUAAAA__AAAA_CAAA
.((((.(((((...((..((((((......))))))..)).....)))))))))................((((((((...........))))))))................. (-14.66 = -16.62 +   1.96)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 2

Location 20,665,086 – 20,665,194
Length 108
Sequences 5
Columns 114
Reading direction reverse
Mean pairwise identity 83.06
Mean single sequence MFE -19.25
Consensus MFE -11.34
Energy contribution -13.82
Covariance contribution 2.48
Combinations/Pair 1.04
Mean z-score -2.55
Structure conservation index 0.59
SVM decision value 0.92
SVM RNA-class probability 0.881257
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 20665086 108 - 22224390
UUUAGUUUU--UUUUAUGAAUGGCUUUU----AUUUAGCUAUUCAGUUAAAUUAGCCAUCCAAAGCACUUUCACUAUUAAGCAAUUUAUUUCGAUUUUUAUUUAGUGCAUUUGU
.........--.....((.((((((...----((((((((....)))))))).)))))).))..(((..(.(((((.((((.((((......))))))))..))))).)..))) ( -20.20)
>DroSec_CAF1 66725 102 - 1
UUUG-UUUU--UUUUAUGAAUGGCUUAU----U-----CCAUUCAGUUAAAUUACCCAUCCAAAGCACUUCCACUAUCAAGCAAUUUAUUUCGCUUUUUAUUUAGUGCAUUUGU
...(-(..(--((...(((((((.....----.-----)))))))...)))..)).....(((((((((.....((..((((..........))))..))...))))).)))). ( -19.30)
>DroSim_CAF1 44188 109 - 1
UUUG-UUUUUUUUUUAUGAAUGGCUUAU----AUUUAGCCAUUCAGUUAAAUUAGCCAUCCAAAGCACUUCCACUAUCAAGCAAUUUAUUUCGCUUUUUAUUUAGUGCAUUUGU
...(-((..(((....(((((((((...----....)))))))))...)))..)))....(((((((((.....((..((((..........))))..))...))))).)))). ( -24.80)
>DroEre_CAF1 62404 96 - 1
UUUG-CUAU--UUUCA-GAUUGCCAUA--------------UUCAGUUAAAUUAGCCGUCCAAAGCACUUCCACUAUCACGCAAUUUAUUUCGCAUUUUAUUUAGUGCAUUUGC
...(-(((.--(((..-(((((.....--------------..)))))))).))))....(((((((((..........((.((.....))))..........))))).)))). ( -11.25)
>DroYak_CAF1 63721 110 - 1
UCUG-UUAU--GUUUA-GUUCGGCUUAUACAUAUUUAGCCAUUCUGUUGAAUUAGCCAUCCAAAGCACUUCCACUAUCAAGCAAUUUAUUUCGCUUUUUAUUUAGUGCAUUUGG
....-....--.....-....((((.......(((((((......))))))).))))..((((((((((.....((..((((..........))))..))...))))).))))) ( -20.70)
>consensus
UUUG_UUUU__UUUUAUGAAUGGCUUAU____AUUUAGCCAUUCAGUUAAAUUAGCCAUCCAAAGCACUUCCACUAUCAAGCAAUUUAUUUCGCUUUUUAUUUAGUGCAUUUGU
.................((((((((...........))))))))................(((((((((.....((..((((..........))))..))...))))).)))). (-11.34 = -13.82 +   2.48)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 3

Location 20,665,126 – 20,665,229
Length 103
Sequences 5
Columns 114
Reading direction reverse
Mean pairwise identity 71.22
Mean single sequence MFE -18.04
Consensus MFE -5.97
Energy contribution -9.16
Covariance contribution 3.19
Combinations/Pair 1.21
Mean z-score -1.77
Structure conservation index 0.33
SVM decision value 0.27
SVM RNA-class probability 0.662433
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 20665126 103 - 22224390
UGUUAGCAUUUCAU-----CUAAGCCAUUAGCGGCUUGUUUUUAGUUUU--UUUUAUGAAUGGCUUUU----AUUUAGCUAUUCAGUUAAAUUAGCCAUCCAAAGCACUUUCAC
.....((.......-----.((((((......))))))...........--.....((.((((((...----((((((((....)))))))).)))))).))..))........ ( -24.60)
>DroSec_CAF1 66765 97 - 1
UGUUGGCAUUUCAU-----CUAAGCCACUAGCGGUUUGAUUUUG-UUUU--UUUUAUGAAUGGCUUAU----U-----CCAUUCAGUUAAAUUACCCAUCCAAAGCACUUCCAC
..((((......((-----(.(((((......))))))))...(-(..(--((...(((((((.....----.-----)))))))...)))..))....))))........... ( -17.20)
>DroSim_CAF1 44228 104 - 1
UGUUGGCAUUUCAU-----CUAAGCCGUUAGCGGUUUGAUUUUG-UUUUUUUUUUAUGAAUGGCUUAU----AUUUAGCCAUUCAGUUAAAUUAGCCAUCCAAAGCACUUCCAC
...((((.....((-----(.((((((....)))))))))....-...........(((((((((...----....))))))))).........))))................ ( -27.30)
>DroEre_CAF1 62444 96 - 1
UUUGAGCAACCCAUAAAUUCUUACCCAUUAACAAUUUGUUUUUG-CUAU--UUUCA-GAUUGCCAUA--------------UUCAGUUAAAUUAGCCGUCCAAAGCACUUCCAC
(((((((((...(((((((.(((.....))).)))))))..)))-))..--.....-(((.((...(--------------((......)))..)).))))))).......... (  -9.30)
>DroYak_CAF1 63761 96 - 1
UGUUAGCAUCCCAUCAAUUCUAA--------------GUUUCUG-UUAU--GUUUA-GUUCGGCUUAUACAUAUUUAGCCAUUCUGUUGAAUUAGCCAUCCAAAGCACUUCCAC
(((((((((..((..(((.....--------------)))..))-..))--)))..-....((((.......(((((((......))))))).))))......))))....... ( -11.80)
>consensus
UGUUAGCAUUUCAU_____CUAAGCCAUUAGCGGUUUGUUUUUG_UUUU__UUUUAUGAAUGGCUUAU____AUUUAGCCAUUCAGUUAAAUUAGCCAUCCAAAGCACUUCCAC
..(((((.............((((((......))))))...................((((((((...........)))))))).)))))........................ ( -5.97 =  -9.16 +   3.19)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:01:03 2006