Locus 3152

Sequence ID	2R_DroMel_CAF1
Location	10,759,186 – 10,759,301
Length	115
Max. P	0.796503

overview

Window 3

Location	10,759,186 – 10,759,301
Length	115
Sequences	6
Columns	119
Reading direction	forward
Mean pairwise identity	79.94
Mean single sequence MFE	-37.42
Consensus MFE	-19.79
Energy contribution	-20.02
Covariance contribution	0.22
Combinations/Pair	1.04
Mean z-score	-2.35
Structure conservation index	0.53
SVM decision value	0.60
SVM RNA-class probability	0.796503
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 10759186 115 + 20766785
AGGGGCUGCGGUGGAGCAAGCG--GCUCUGUGUGUAAUAGUCCGCUUAGGCUUGCCAUGCUGUCGGCACUUUACAUCAAAGUAA--AGCCAUUGCAAUUGGCUAGACAGCGCCUUAUAA
.(((((...((..(.((.((((--(..((((.....)))).)))))...)))..))..((((((...(((((.....)))))..--(((((.......))))).))))))))))).... ( -44.60)
>DroEre_CAF1 23198 115 + 1
AGGGGCUGUGGAGGGGCAAGCG--GAUCUGUGUGUAAUAGUCCGCUUAGGCUUGCCAUGCUGUCGGCACUUUACAUCAAAGUAA--AGCCAUUGCAAUUGGCUAGACAGCGCCUUAUAA
.(((((.((((..((.((((((--((.((((.....))))))))))).).))..))))((((((...(((((.....)))))..--(((((.......))))).))))))))))).... ( -49.00)
>DroWil_CAF1 30755 113 + 1
AGGGGUGGUG------UGCGUGGUCAUGGGUGAGUAAUAGUCCGCUUAGGCUUGUUCUGCUGUCGGCACUUUACAUCAAAGCAAAAAGCCAUUGCAAUUGGCUAGACAUCGCCUUAUAA
.(((((((((------(.(.((((((....(((((((.((((((....(((.......)))..))).))))))).)))..((((.......))))...))))))))))))))))).... ( -34.40)
>DroYak_CAF1 23873 109 + 1
UGG-----UGCAA-GGGAAGCG--GAUCUGUGUGUAAUAGUCCGCUUAGGCUUGCCAUGCUGUCGGCACUUUACAUCAAAGUAA--AGCCAUUGCAAUUGGCUAGACAGCGCCUUAUAA
.((-----(((((-(..(((((--((.((((.....)))))))))))...)))))...((((((...(((((.....)))))..--(((((.......))))).)))))))))...... ( -42.60)
>DroAna_CAF1 21404 99 + 1
UUU-----UG-----------U--CUUCUGUGUGUAAUAGUCCGCUUAGGCUUGCCAUGCUGUCGGCACUUUACAUCAAAGUAA--AGCCAUUGCAAUUGGCUAGACAGCGCCUUAUAA
..(-----((-----------(--((..((.((((((.((((((....(((.......)))..))).)))))))))))......--(((((.......))))))))))).......... ( -24.20)
>DroPer_CAF1 22199 97 + 1
-------------------CCG--GCCGUGUGUGGCACAGUCCGCUUAGGCUUUCUUGGCUGUCGGCACUUUACAUCAAAGUAA-AAGCCAUUGCGAUUGGCUAGACAGCGCUUUAUAA
-------------------..(--(((....((((......))))...))))......((((((.....(((((......))))-)(((((.......))))).))))))......... ( -29.70)
>consensus
AGG_____UG_______AAGCG__GAUCUGUGUGUAAUAGUCCGCUUAGGCUUGCCAUGCUGUCGGCACUUUACAUCAAAGUAA__AGCCAUUGCAAUUGGCUAGACAGCGCCUUAUAA
.............................((((((((.((((((....(((.......)))..))).)))))))......((....(((((.......)))))..)).))))....... (-19.79 = -20.02 +   0.22)

alignment

secondary structure

dotplot

Window 4

Location	10,759,186 – 10,759,301
Length	115
Sequences	6
Columns	119
Reading direction	reverse
Mean pairwise identity	79.94
Mean single sequence MFE	-30.61
Consensus MFE	-20.30
Energy contribution	-20.49
Covariance contribution	0.19
Combinations/Pair	1.05
Mean z-score	-1.66
Structure conservation index	0.66
SVM decision value	0.49
SVM RNA-class probability	0.756921
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 10759186 115 - 20766785
UUAUAAGGCGCUGUCUAGCCAAUUGCAAUGGCU--UUACUUUGAUGUAAAGUGCCGACAGCAUGGCAAGCCUAAGCGGACUAUUACACACAGAGC--CGCUUGCUCCACCGCAGCCCCU
......(((((((((..((.....))....(((--((((......)))))))...)))))).(((..(((..((((((.((...........)))--))))))))))).....)))... ( -36.10)
>DroEre_CAF1 23198 115 - 1
UUAUAAGGCGCUGUCUAGCCAAUUGCAAUGGCU--UUACUUUGAUGUAAAGUGCCGACAGCAUGGCAAGCCUAAGCGGACUAUUACACACAGAUC--CGCUUGCCCCUCCACAGCCCCU
......(((((((((..((.....))....(((--((((......)))))))...))))))..((((......((((((((.........)).))--))))))))........)))... ( -35.90)
>DroWil_CAF1 30755 113 - 1
UUAUAAGGCGAUGUCUAGCCAAUUGCAAUGGCUUUUUGCUUUGAUGUAAAGUGCCGACAGCAGAACAAGCCUAAGCGGACUAUUACUCACCCAUGACCACGCA------CACCACCCCU
.....((((....(((.((.....))..((((.((((((......)))))).)))).....)))....))))..(((......................))).------.......... ( -22.25)
>DroYak_CAF1 23873 109 - 1
UUAUAAGGCGCUGUCUAGCCAAUUGCAAUGGCU--UUACUUUGAUGUAAAGUGCCGACAGCAUGGCAAGCCUAAGCGGACUAUUACACACAGAUC--CGCUUCCC-UUGCA-----CCA
......((.((((((..((.....))....(((--((((......)))))))...))))))...(((((...(((((((((.........)).))--)))))..)-)))).-----)). ( -36.30)
>DroAna_CAF1 21404 99 - 1
UUAUAAGGCGCUGUCUAGCCAAUUGCAAUGGCU--UUACUUUGAUGUAAAGUGCCGACAGCAUGGCAAGCCUAAGCGGACUAUUACACACAGAAG--A-----------CA-----AAA
...........((((((((((.......)))))--...((.((.((((((((.(((.......((....))....)))))).))))))).)).))--)-----------))-----... ( -22.70)
>DroPer_CAF1 22199 97 - 1
UUAUAAAGCGCUGUCUAGCCAAUCGCAAUGGCUU-UUACUUUGAUGUAAAGUGCCGACAGCCAAGAAAGCCUAAGCGGACUGUGCCACACACGGC--CGG-------------------
.......(.((((((..((.....))...(((((-((((......)))))).)))))))))).............(((.(((((.....))))))--)).------------------- ( -30.40)
>consensus
UUAUAAGGCGCUGUCUAGCCAAUUGCAAUGGCU__UUACUUUGAUGUAAAGUGCCGACAGCAUGGCAAGCCUAAGCGGACUAUUACACACAGAUC__CGCUU_______CA_____CCU
.....((((((((((..((.....))...(((...((((......))))...))))))))).......))))............................................... (-20.30 = -20.49 +   0.19)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:48:45 2006