Locus 777

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

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

secondary structure

dotplot

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

secondary structure

dotplot

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

secondary structure

dotplot

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