Locus 4281

Sequence ID 3L_DroMel_CAF1
Location 12,537,213 – 12,537,372
Length 159
Max. P 0.809713
window6613 window6614 window6615

overview

Window 3

Location 12,537,213 – 12,537,314
Length 101
Sequences 6
Columns 111
Reading direction forward
Mean pairwise identity 78.62
Mean single sequence MFE -26.16
Consensus MFE -17.27
Energy contribution -17.42
Covariance contribution 0.14
Combinations/Pair 1.17
Mean z-score -1.60
Structure conservation index 0.66
SVM decision value 0.62
SVM RNA-class probability 0.800632
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 12537213 101 + 23771897
CCUCAUGCCCA------UUCCCAUUC-CAGUUCCAAUUCGGA--AACGAAUCUCGAGAUGUCGCGAGCGUAGC-CAUAUUUCCAUGUCUCAUUUGUGGCGACCCCUCGAGA
...........------.........-.........((((..--..))))(((((((..(((((....)).((-((((...............)))))))))..))))))) ( -27.06)
>DroPse_CAF1 25639 108 + 1
CCUCACCCUCCCCCCC-A-ACCGUGCUCAGCUCC-GCAGCAAUCUCUGAAUUUUAAGAUGUCGCGAGCGUAACUCAUUUUUCUAUGUCUCAUUUGGGGCGACCCCUCGAGA
.(((........((((-(-(..(((....((((.-((.(((...(((........)))))).))))))......(((......)))...))))))))).((....))))). ( -22.20)
>DroSec_CAF1 25364 107 + 1
CCUCAUGCUCAUGCCCAUACCCACUC-CAGUUCCAAUUCGGA--ACCCAAUCUCGAGAUGUCGCGAGCGUAGC-CAUAUUUCCAUGUCUCAUUUGCGGCGACCCCUCGAGA
......((....))............-..(((((.....)))--))....(((((((..(((((..(((.((.-(((......))).))....))).)))))..))))))) ( -29.00)
>DroSim_CAF1 25906 106 + 1
CCUCAUGCUCAUGCCC-UACCCACUC-CAGUUCCAAUUCGGA--ACCCAAUCUCGAGAUGUCGCGAGCGUAGC-CAUAUUUCCAUGUCUCAUUUGCGGCGACCCCUCGAGA
......((....))..-.........-..(((((.....)))--))....(((((((..(((((..(((.((.-(((......))).))....))).)))))..))))))) ( -29.00)
>DroEre_CAF1 26576 89 + 1
CCUCAUGC------CCUUUCCCA-------------UUCCAA--UCCGAAUCUCGAGAUGUCGCGAGCGGAGC-CAUAUUUCCAUGUCUCAUUUGCGGCGACCCCUCGAGA
........------.........-------------......--......(((((((..(((((..((.(((.-(((......))).)))....)).)))))..))))))) ( -25.50)
>DroYak_CAF1 26091 107 + 1
CCUCCUGCCCCUGCCCUUUCCCAUUC-UCAGUCCAAUUCCAA--UCCGAAUCUGGAGAUGUCGCGAGCGGAGC-CAUAUUUCCAUGUCUCAUUUGCGGCGACCCCUCGAGA
........................((-((..((((((((...--...)))).))))..(((((((((..(((.-(((......))).))).))))))))).......)))) ( -24.20)
>consensus
CCUCAUGCUCAUGCCC_UUCCCAUUC_CAGUUCCAAUUCCAA__ACCGAAUCUCGAGAUGUCGCGAGCGUAGC_CAUAUUUCCAUGUCUCAUUUGCGGCGACCCCUCGAGA
..................................................(((((((..(((((..(((.....(((......))).......))).)))))..))))))) (-17.27 = -17.42 +   0.14)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 4

Location 12,537,241 – 12,537,346
Length 105
Sequences 6
Columns 114
Reading direction forward
Mean pairwise identity 82.23
Mean single sequence MFE -29.28
Consensus MFE -20.28
Energy contribution -20.87
Covariance contribution 0.59
Combinations/Pair 1.23
Mean z-score -1.99
Structure conservation index 0.69
SVM decision value 0.43
SVM RNA-class probability 0.733271
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 12537241 105 + 23771897
AUUCGGA--AACGAAUCUCGAGAUGUCGCGAGCGUAGC-CAUAUUUCCAUGUCUCAUUUGUGGCGACCCCUCGAGAAUUGGAGCUCGCUC-UUUCCCCUAUAUAUUUUU-----
.((((..--..))))(((((((..(((((....)).((-((((...............)))))))))..)))))))...((((....)))-).................----- ( -31.06)
>DroPse_CAF1 25671 109 + 1
GCAGCAAUCUCUGAAUUUUAAGAUGUCGCGAGCGUAACUCAUUUUUCUAUGUCUCAUUUGGGGCGACCCCUCGAGAAUCGCUCCUCGUUUAUUUUCUUCUG-----UUUUUUUU
((.(((...(((........)))))).))(((((...(((..........(((((....)))))((....)))))...)))))..................-----........ ( -21.20)
>DroSec_CAF1 25398 100 + 1
AUUCGGA--ACCCAAUCUCGAGAUGUCGCGAGCGUAGC-CAUAUUUCCAUGUCUCAUUUGCGGCGACCCCUCGAGAAUUGGAGCUCGCUC-UUUCCCCCAG-----UUU-----
....(((--(..((((((((((..(((((..(((.((.-(((......))).))....))).)))))..)))))).))))(((....)))-.)))).....-----...----- ( -30.60)
>DroSim_CAF1 25939 100 + 1
AUUCGGA--ACCCAAUCUCGAGAUGUCGCGAGCGUAGC-CAUAUUUCCAUGUCUCAUUUGCGGCGACCCCUCGAGAAUUGGAGCUCGCUC-UUUCCCCCAG-----UUU-----
....(((--(..((((((((((..(((((..(((.((.-(((......))).))....))).)))))..)))))).))))(((....)))-.)))).....-----...----- ( -30.60)
>DroEre_CAF1 26593 96 + 1
-UUCCAA--UCCGAAUCUCGAGAUGUCGCGAGCGGAGC-CAUAUUUCCAUGUCUCAUUUGCGGCGACCCCUCGAGAAUUGGAGCUCGCUC---UUCCCCAA-----UU------
-......--(((((.(((((((..(((((..((.(((.-(((......))).)))....)).)))))..))))))).)))))........---........-----..------ ( -33.00)
>DroYak_CAF1 26125 100 + 1
AUUCCAA--UCCGAAUCUGGAGAUGUCGCGAGCGGAGC-CAUAUUUCCAUGUCUCAUUUGCGGCGACCCCUCGAGAAUUGGAGCUCGAUC-UUUUCCCCAA-----UUU-----
.......--(((((.(((.(((..(((((..((.(((.-(((......))).)))....)).)))))..))).))).)))))........-..........-----...----- ( -29.20)
>consensus
AUUCCAA__ACCGAAUCUCGAGAUGUCGCGAGCGUAGC_CAUAUUUCCAUGUCUCAUUUGCGGCGACCCCUCGAGAAUUGGAGCUCGCUC_UUUCCCCCAG_____UUU_____
..........((((.(((((((..(((((..(((.....(((......))).......))).)))))..))))))).))))................................. (-20.28 = -20.87 +   0.59)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 5

Location 12,537,275 – 12,537,372
Length 97
Sequences 6
Columns 105
Reading direction reverse
Mean pairwise identity 85.32
Mean single sequence MFE -30.70
Consensus MFE -24.37
Energy contribution -24.82
Covariance contribution 0.45
Combinations/Pair 1.09
Mean z-score -2.47
Structure conservation index 0.79
SVM decision value 0.64
SVM RNA-class probability 0.809713
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 12537275 97 - 23771897
GACGUGCGUGUGACCCCACUCAAAAA-------AAAAAUAUAUAGGGGAAAGAGC-GAGCUCCAAUUCUCGAGGGGUCGCCACAAAUGAGACAUGGAAAUAUGGC
..(((..((((((((((.((......-------..........))(((((.(((.-...)))...)))))..))))))).)))..)))...((((....)))).. ( -23.99)
>DroSec_CAF1 25432 92 - 1
GACGUGCGUGUGACCCCACUCACAAA-------AAA-----CUGGGGGAAAGAGC-GAGCUCCAAUUCUCGAGGGGUCGCCGCAAAUGAGACAUGGAAAUAUGGC
....((((.((((((((.....((..-------...-----.)).(((((.(((.-...)))...)))))..)))))))))))).......((((....)))).. ( -30.40)
>DroSim_CAF1 25973 92 - 1
GACGUGCGUGUGACCCCACUCACAAA-------AAA-----CUGGGGGAAAGAGC-GAGCUCCAAUUCUCGAGGGGUCGCCGCAAAUGAGACAUGGAAAUAUGGC
....((((.((((((((.....((..-------...-----.)).(((((.(((.-...)))...)))))..)))))))))))).......((((....)))).. ( -30.40)
>DroEre_CAF1 26626 96 - 1
GACGUGCGUGUGACCCCACUCAAAAAACUCAAA-AA-----UUGGGGAA--GAGC-GAGCUCCAAUUCUCGAGGGGUCGCCGCAAAUGAGACAUGGAAAUAUGGC
....((((.((((((((.(((......((((..-..-----.))))...--)))(-(((........)))).)))))))))))).......((((....)))).. ( -31.00)
>DroYak_CAF1 26159 99 - 1
GACGUGCGUGUGACCCCACUCAAAAACCUCAAAAAA-----UUGGGGAAAAGAUC-GAGCUCCAAUUCUCGAGGGGUCGCCGCAAAUGAGACAUGGAAAUAUGGC
....((((.((((((((.........((((((....-----))))))......((-(((........))))))))))))))))).......((((....)))).. ( -35.90)
>DroAna_CAF1 22899 89 - 1
GACAUGCGUGCGACCCCACUCAAA----------UU-----UUGGGGAA-AAUGCAAAGCCCCAAUUCUCGAGGGGUCGCCGCAAAUGAGACAUGGAAAAAUUGU
....((((.((((((((..((...----------..-----((((((..-.........)))))).....))))))))))))))..................... ( -32.50)
>consensus
GACGUGCGUGUGACCCCACUCAAAAA_______AAA_____UUGGGGAAAAGAGC_GAGCUCCAAUUCUCGAGGGGUCGCCGCAAAUGAGACAUGGAAAUAUGGC
....((((.((((((((...((....................))(((((..((((...))))...)))))..))))))))))))..................... (-24.37 = -24.82 +   0.45)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:18:24 2006