Locus 8779

Sequence ID	3R_DroMel_CAF1
Location	23,446,113 – 23,446,214
Length	101
Max. P	0.957103

overview

Window 3

Location	23,446,113 – 23,446,214
Length	101
Sequences	6
Columns	115
Reading direction	forward
Mean pairwise identity	76.35
Mean single sequence MFE	-26.10
Consensus MFE	-15.70
Energy contribution	-15.70
Covariance contribution	0.00
Combinations/Pair	1.00
Mean z-score	-2.11
Structure conservation index	0.60
SVM decision value	1.47
SVM RNA-class probability	0.957103
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 23446113 101 + 27905053
------UCCUGCGAA---AUGUAACAAAAGAUGAGAUGCACUUGAGCAUGCUAAAAUGCGUUAUUAAGUGCAUAAAUAUGCAAUG--CUC--AACCUUU-UGCACUCGGCACCAC
------.........---...........(.((((((((((((((..((((......))))..)))))))))).....(((((..--...--......)-)))))))).)..... ( -24.10)
>DroVir_CAF1 49332 98 + 1
------U---AUGUG---CUGUAACAAAAGAUGAGUUGCACUUGAGCAUGCUAAAAUGCGUUAUUAAGUGCAUAAAUAUGCAAUG--CGCGCAGCCA-UACGCUCGCUCUAU--C
------(---(((.(---((((..............(((((((((..((((......))))..))))))))).......((....--.)))))))))-))............--. ( -26.70)
>DroPse_CAF1 41879 108 + 1
UUUUCUCUCUCUGUA---AUGUUACAAAAGAUGAGUUGCACUUGAGCAUGCUAAAAUGCGUUAUUAAGUGCAUAAAUAUGCAAUGUGUGC--AACCU-U-UGCACCUGCCCCUGC
....((((((.((((---....))))..))).))).(((((((((..((((......))))..))))))))).......(((..(.((((--(....-.-)))))))))...... ( -27.20)
>DroGri_CAF1 46263 101 + 1
--------CUCAUUCUGUAUGUAACAAAAGAUGAGUUGCACUUGAGCAUGCUAAAAUGCGUUAUUAAGUGCAUAAAUAUGCAAUG--AGCGGAGCUU-U-UGCCACCGCCCU--C
--------.((((..(((((((..((.....))...(((((((((..((((......))))..)))))))))...))))))))))--)((((.((..-.-.))..))))...--. ( -29.10)
>DroWil_CAF1 36398 96 + 1
------AUG-----U---CUGUAACAAAAGAUGAGCUGCACUUGAGCAUGCUAAAAUGCGUUAUUAAGUGCAUAAAUAUGCAAUG--UGC--AACCUCU-GCCCCUCAACACACA
------..(-----(---((........))))(((.(((((((((..((((......))))..)))))))))......(((....--.))--)......-....)))........ ( -22.30)
>DroPer_CAF1 41548 107 + 1
-UUUCUCUCUCUGUA---AUGUUACAAAAGAUGAGUUGCACUUGAGCAUGCUAAAAUGCGUUAUUAAGUGCAUAAAUAUGCAAUGUGUGC--AACCU-U-UGCACCUGCCCCUGC
-...((((((.((((---....))))..))).))).(((((((((..((((......))))..))))))))).......(((..(.((((--(....-.-)))))))))...... ( -27.20)
>consensus
______CUCUCUGUA___AUGUAACAAAAGAUGAGUUGCACUUGAGCAUGCUAAAAUGCGUUAUUAAGUGCAUAAAUAUGCAAUG__UGC__AACCU_U_UGCACCCGCCAC__C
....................................(((((((((..((((......))))..)))))))))........................................... (-15.70 = -15.70 +   0.00)

alignment

secondary structure

dotplot

Window 4

Location	23,446,113 – 23,446,214
Length	101
Sequences	6
Columns	115
Reading direction	reverse
Mean pairwise identity	76.35
Mean single sequence MFE	-28.20
Consensus MFE	-11.49
Energy contribution	-11.52
Covariance contribution	0.03
Combinations/Pair	1.20
Mean z-score	-2.20
Structure conservation index	0.41
SVM decision value	0.33
SVM RNA-class probability	0.692930
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 23446113 101 - 27905053
GUGGUGCCGAGUGCA-AAAGGUU--GAG--CAUUGCAUAUUUAUGCACUUAAUAACGCAUUUUAGCAUGCUCAAGUGCAUCUCAUCUUUUGUUACAU---UUCGCAGGA------
....(((.(((((((-((((((.--(((--...(((((....))))).........((((((.((....)).))))))..)))))))))))...)))---)).)))...------ ( -27.00)
>DroVir_CAF1 49332 98 - 1
G--AUAGAGCGAGCGUA-UGGCUGCGCG--CAUUGCAUAUUUAUGCACUUAAUAACGCAUUUUAGCAUGCUCAAGUGCAACUCAUCUUUUGUUACAG---CACAU---A------
.--...(((((.(((((-....))))).--...(((((....))))).........((......)).)))))..((((....((.....)).....)---)))..---.------ ( -23.00)
>DroPse_CAF1 41879 108 - 1
GCAGGGGCAGGUGCA-A-AGGUU--GCACACAUUGCAUAUUUAUGCACUUAAUAACGCAUUUUAGCAUGCUCAAGUGCAACUCAUCUUUUGUAACAU---UACAGAGAGAGAAAA
(((.(((((((((((-.-(((((--(((.....)))).)))).)))))))......((......))..))))...)))..(((.(((((.(((....---))))))))))).... ( -30.90)
>DroGri_CAF1 46263 101 - 1
G--AGGGCGGUGGCA-A-AAGCUCCGCU--CAUUGCAUAUUUAUGCACUUAAUAACGCAUUUUAGCAUGCUCAAGUGCAACUCAUCUUUUGUUACAUACAGAAUGAG--------
.--.((((((.(((.-.-..))))))))--)..(((((....))))).........((((((.((....)).))))))..(((((..(((((.....))))))))))-------- ( -30.90)
>DroWil_CAF1 36398 96 - 1
UGUGUGUUGAGGGGC-AGAGGUU--GCA--CAUUGCAUAUUUAUGCACUUAAUAACGCAUUUUAGCAUGCUCAAGUGCAGCUCAUCUUUUGUUACAG---A-----CAU------
(((.(((.(((((..-.(((.((--(((--(..(((((....))))).........((((......))))....))))))))).)))))....))).---)-----)).------ ( -26.50)
>DroPer_CAF1 41548 107 - 1
GCAGGGGCAGGUGCA-A-AGGUU--GCACACAUUGCAUAUUUAUGCACUUAAUAACGCAUUUUAGCAUGCUCAAGUGCAACUCAUCUUUUGUAACAU---UACAGAGAGAGAAA-
(((.(((((((((((-.-(((((--(((.....)))).)))).)))))))......((......))..))))...)))..(((.(((((.(((....---)))))))))))...- ( -30.90)
>consensus
G__GGGGCGGGUGCA_A_AGGUU__GCA__CAUUGCAUAUUUAUGCACUUAAUAACGCAUUUUAGCAUGCUCAAGUGCAACUCAUCUUUUGUUACAU___UACAGAGAA______
...........((((...(((............(((((....))))).........((((((.((....)).)))))).......))).))))...................... (-11.49 = -11.52 +   0.03)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:19:36 2006