Locus 777

Sequence ID X_DroMel_CAF1
Location 2,157,875 – 2,157,993
Length 118
Max. P 0.985645
window1263 window1264 window1265

overview

Window 3

Location 2,157,875 – 2,157,972
Length 97
Sequences 6
Columns 108
Reading direction forward
Mean pairwise identity 79.73
Mean single sequence MFE -22.03
Consensus MFE -13.36
Energy contribution -12.87
Covariance contribution -0.50
Combinations/Pair 1.22
Mean z-score -1.72
Structure conservation index 0.61
SVM decision value 0.29
SVM RNA-class probability 0.668496
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 2157875 97 + 22224390
--G-UUAUCAUUCUU--AUUUUCGUAUUUUGUUUUAUUGGCACUCGCGUGUGCUGCCAUUUAGCGCAUUUAAUUUAAUAAUUAAGUUGCUGAUGAAGACG------CG
--(-((.(((.....--.....................(((((......))))).....((((((.((((((((....))))))))))))))))).))).------.. ( -19.90)
>DroVir_CAF1 49483 96 + 1
GAGUUG---UUUUUG--GUUUUCAU-UAUUUUUUUAUUGCCACUUGCGUGUGCUGCCAUUUAGCGCAUUUAAUUUAAUAAUUAAGUCGCUGAUGAAGACG------CG
......---......--((((((((-(...........(((((....))).))........((((.((((((((....))))))))))))))))))))).------.. ( -22.80)
>DroWil_CAF1 38551 91 + 1
----GUGUG--------UUUUUUUUUUUGGGUUUUAUUGCCACUUGCGUGUGCUGCUAUUUAGCGCAUUUAAUUUAAUAAUUAAGUCGCUGAUGAAGACAA-----CG
----((.((--------(((((................(((((....))).))......((((((.((((((((....)))))))))))))).))))))))-----). ( -20.20)
>DroMoj_CAF1 50421 96 + 1
GAGUUG---UUUUUG--GUUUUCAU-UAUUUUUUUAUUGCCAUUUGCGUGUGCUGCCAUUUAGCGCAUUUAAUUUAAUAAUUAAGUCGCUGAUGGAGACG------CG
.....(---(...((--((......-............))))...))((((.((.(((((.((((.((((((((....))))))))))))))))))))))------). ( -24.97)
>DroAna_CAF1 45142 105 + 1
--A-UCAUCACUCUCCAUUUUUCGUAUUUUGUUUUAUUGGCACUUGCGUGUGCUGCCAUUUAGCGCAUUUAAUUUAAUAAUUAAGUUGAUGAUGAAGACGACGCGACG
--.-.................((((...(((((((((..((......((((((((.....))))))))((((((....))))))))..))))....))))).)))).. ( -20.30)
>DroPer_CAF1 51518 101 + 1
UGGUUUUUCUUCUUU--AUUUUCGUAUCUUGUUUUAUUAGCACUUGCGUGUGCUGCCAUUUAGCGCAUUUAAUUUAAUAAUUAAGUUGCUGAUGAAGACGA-----CG
.......((.(((((--(((...(((.((((..((((((((....))((((((((.....))))))))......)))))).)))).))).)))))))).))-----.. ( -24.00)
>consensus
__G_UU_UCUUUUUG__AUUUUCGUAUUUUGUUUUAUUGCCACUUGCGUGUGCUGCCAUUUAGCGCAUUUAAUUUAAUAAUUAAGUCGCUGAUGAAGACG______CG
..................((((((................(((......))).......((((((.((((((((....)))))))))))))))))))).......... (-13.36 = -12.87 +  -0.50) 

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 4

Location 2,157,875 – 2,157,972
Length 97
Sequences 6
Columns 108
Reading direction reverse
Mean pairwise identity 79.73
Mean single sequence MFE -17.65
Consensus MFE -9.39
Energy contribution -9.42
Covariance contribution 0.03
Combinations/Pair 1.07
Mean z-score -2.35
Structure conservation index 0.53
SVM decision value 0.69
SVM RNA-class probability 0.822691
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 2157875 97 - 22224390
CG------CGUCUUCAUCAGCAACUUAAUUAUUAAAUUAAAUGCGCUAAAUGGCAGCACACGCGAGUGCCAAUAAAACAAAAUACGAAAAU--AAGAAUGAUAA-C--
..------.((((((....(((..((((((....)))))).)))......(((((((....))...)))))....................--..))).)))..-.-- ( -14.00)
>DroVir_CAF1 49483 96 - 1
CG------CGUCUUCAUCAGCGACUUAAUUAUUAAAUUAAAUGCGCUAAAUGGCAGCACACGCAAGUGGCAAUAAAAAAAUA-AUGAAAAC--CAAAAA---CAACUC
.(------.((.(((((.((((..((((((....))))))...))))........((.(((....)))))............-))))).))--).....---...... ( -19.00)
>DroWil_CAF1 38551 91 - 1
CG-----UUGUCUUCAUCAGCGACUUAAUUAUUAAAUUAAAUGCGCUAAAUAGCAGCACACGCAAGUGGCAAUAAAACCCAAAAAAAAAAA--------CACAC----
.(-----(((.((.....((((..((((((....))))))...))))....)))))).(((....))).......................--------.....---- ( -17.00)
>DroMoj_CAF1 50421 96 - 1
CG------CGUCUCCAUCAGCGACUUAAUUAUUAAAUUAAAUGCGCUAAAUGGCAGCACACGCAAAUGGCAAUAAAAAAAUA-AUGAAAAC--CAAAAA---CAACUC
.(------(((((((((.((((..((((((....))))))...))))..)))).))...))))...................-........--......---...... ( -15.70)
>DroAna_CAF1 45142 105 - 1
CGUCGCGUCGUCUUCAUCAUCAACUUAAUUAUUAAAUUAAAUGCGCUAAAUGGCAGCACACGCAAGUGCCAAUAAAACAAAAUACGAAAAAUGGAGAGUGAUGA-U--
((((((....(((((((..((...((((((....)))))).((((((....))).)))(((....))).................))...))))))))))))).-.-- ( -22.30)
>DroPer_CAF1 51518 101 - 1
CG-----UCGUCUUCAUCAGCAACUUAAUUAUUAAAUUAAAUGCGCUAAAUGGCAGCACACGCAAGUGCUAAUAAAACAAGAUACGAAAAU--AAAGAAGAAAAACCA
.(-----(..(((((....(((..((((((....)))))).)))(((....)))(((((......))))).....................--...)))))...)).. ( -17.90)
>consensus
CG______CGUCUUCAUCAGCAACUUAAUUAUUAAAUUAAAUGCGCUAAAUGGCAGCACACGCAAGUGCCAAUAAAACAAAAUACGAAAAA__AAAAAAGA_AA_C__
............................(((((........((((((....))).)))(((....)))..)))))................................. ( -9.39 =  -9.42 +   0.03) 

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 5

Location 2,157,903 – 2,157,993
Length 90
Sequences 6
Columns 110
Reading direction forward
Mean pairwise identity 76.46
Mean single sequence MFE -27.17
Consensus MFE -19.06
Energy contribution -18.53
Covariance contribution -0.53
Combinations/Pair 1.16
Mean z-score -2.40
Structure conservation index 0.70
SVM decision value 2.01
SVM RNA-class probability 0.985645
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 2157903 90 + 22224390
UUAUUGGCACUCGCGUGUGCUGCCAUUUAGCGCAUUUAAUUUAAUAAUUAAGUUGCUGAUGAAGACG-CGCGUU----CUCUUUUGUCUG---CUGCG------------
.....((((..(((((((.((..((((.((((.((((((((....)))))))))))))))).)))))-))))..----..........))---))...------------ ( -24.14)
>DroVir_CAF1 49510 107 + 1
UUAUUGCCACUUGCGUGUGCUGCCAUUUAGCGCAUUUAAUUUAAUAAUUAAGUCGCUGAUGAAGACG-CGCGCGCGCACUCUUUA--ACGCCAAUGCGCAUAUACAUACA
............(((((((((..((((.((((.((((((((....)))))))))))))))).)).))-)))))(((((.......--.......)))))........... ( -32.64)
>DroEre_CAF1 39400 88 + 1
UUAUUGGCAUUCGCGUGUGCUGCCAUUUAGCGCAUUUAAUUUAAUAAUUAAGUUGCUGAUGAAGACG-CGCGUU----CUCUUUUGUCUGUCU-----------------
.....((((..(((((((.((..((((.((((.((((((((....)))))))))))))))).)))))-))))..----......)))).....----------------- ( -24.50)
>DroWil_CAF1 38572 93 + 1
UUAUUGCCACUUGCGUGUGCUGCUAUUUAGCGCAUUUAAUUUAAUAAUUAAGUCGCUGAUGAAGACAACGCGCU----GCUUUUCG-GUGUUAAUACG------------
.(((((.((((.(((((((.((((..((((((.((((((((....))))))))))))))...)).)).))))).----)).....)-))).)))))..------------ ( -26.40)
>DroMoj_CAF1 50448 99 + 1
UUAUUGCCAUUUGCGUGUGCUGCCAUUUAGCGCAUUUAAUUUAAUAAUUAAGUCGCUGAUGGAGACG-CGCGCGCG--CUCUUUA--ACGCCA----GCAUACAC--ACA
...........((.((((((((.(..((((((.((((((((....))))))))))))))((((((.(-((....))--)))))))--..).))----)))))).)--).. ( -34.20)
>DroPer_CAF1 51549 91 + 1
UUAUUAGCACUUGCGUGUGCUGCCAUUUAGCGCAUUUAAUUUAAUAAUUAAGUUGCUGAUGAAGACGACGCGGA----CUCUUACGGCUA---CUGCU------------
(((((((((...((((((((((.....))))))))((((((....))))))))))))))))).......((((.----............---)))).------------ ( -21.12)
>consensus
UUAUUGCCACUUGCGUGUGCUGCCAUUUAGCGCAUUUAAUUUAAUAAUUAAGUCGCUGAUGAAGACG_CGCGCU____CUCUUUAG_CUG_CA_UGCG____________
............(((((((((..((((.((((.((((((((....)))))))))))))))).)).)).)))))..................................... (-19.06 = -18.53 +  -0.53) 

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript


Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:53:37 2006