Locus 3154

Sequence ID	2R_DroMel_CAF1
Location	10,765,323 – 10,765,428
Length	105
Max. P	0.963953

overview

Window 8

Location	10,765,323 – 10,765,428
Length	105
Sequences	6
Columns	115
Reading direction	forward
Mean pairwise identity	76.71
Mean single sequence MFE	-20.61
Consensus MFE	-14.42
Energy contribution	-14.78
Covariance contribution	0.36
Combinations/Pair	1.06
Mean z-score	-1.95
Structure conservation index	0.70
SVM decision value	1.56
SVM RNA-class probability	0.963953
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 10765323 105 + 20766785
-CUGGAUGGGUAAUUUGGAACUUCCUCUACAGUUCCCGCUCUUCCCCCCCC-CCCUA--CAUUUU--UUUGUAUUACCAG---CACUUUGGAUC-CCAAAAUACCCAUGACUCUU
-....(((((((.(((((.................................-...((--((....--..))))...((((---....))))...-))))).)))))))....... ( -19.90)
>DroSec_CAF1 1086 98 + 1
-CUGGAUGGGUAAUUUGGAACUUCCUCUACAGUUCCCCCUC-------CCC-CGACA--CAAUUU--UUUUUAUUACCAG---CACUUUGGAGC-CCAAAAUACCCAUGACUCUU
-....(((((((.(((((((((........)))))).....-------...-.....--......--.........((((---....))))...-..))).)))))))....... ( -18.30)
>DroSim_CAF1 1164 101 + 1
-CUGGAUGGGUAAUUUGGAACUUCCUCUACAGUACCCGCUU-------CCCCUCUCC--CAAUUUUUUUUUUAUUACCAG---CACUUUGGAGC-CCAAAAUACCCAUGACUCUU
-....(((((((.(((((......(((((.(((....(((.-------.........--...................))---)))).))))).-))))).)))))))....... ( -18.75)
>DroEre_CAF1 1120 107 + 1
-CUGGAUGGGUAAUUUGGAACUUCCUCUACAGUUCCCGCCCCUGCCAACCC-UGCCGUCCGUUCU--UUUUUAUUACCAG---CACUUUGGAGG-CCAAAAUACCCAUGACUCUU
-....(((((((.(((((((((........)))))).(((....((((...-(((..........--............)---))..)))).))-).))).)))))))....... ( -23.45)
>DroYak_CAF1 1094 97 + 1
-CUGGAUGGGUAAUUUGGAACUUCCUCUACAGUUGCCGCUCC-------CC-UUCCACC---UUU--UUUUUAUUACCAG---CACUUUGGAGC-CCAAAAUACCCAUGACUCUU
-....(((((((.(((((((((........))))...(((((-------..-.......---...--.............---......)))))-))))).)))))))....... ( -21.88)
>DroAna_CAF1 14867 89 + 1
GAUGGAUGGGUAAUUUGGUACUUCCUCCACGUAUCCCC---------------------CAG-----UUUUAAUGGCCAGUAGUACUUGAAAGCCCCAAAAUGCCCAUGACUGUU
((((((((((((.(((((..(((....((.((((..((---------------------((.-----......)))...)..)))).)).)))..))))).)))))))..))))) ( -21.40)
>consensus
_CUGGAUGGGUAAUUUGGAACUUCCUCUACAGUUCCCGCUC_______CCC_UCCCA__CAAUUU__UUUUUAUUACCAG___CACUUUGGAGC_CCAAAAUACCCAUGACUCUU
.....(((((((.(((((...((((................................................................))))..))))).)))))))....... (-14.42 = -14.78 +   0.36)

alignment

secondary structure

dotplot

Window 9

Location	10,765,323 – 10,765,428
Length	105
Sequences	6
Columns	115
Reading direction	reverse
Mean pairwise identity	76.71
Mean single sequence MFE	-27.48
Consensus MFE	-15.34
Energy contribution	-15.73
Covariance contribution	0.39
Combinations/Pair	1.10
Mean z-score	-2.11
Structure conservation index	0.56
SVM decision value	1.17
SVM RNA-class probability	0.926243
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 10765323 105 - 20766785
AAGAGUCAUGGGUAUUUUGG-GAUCCAAAGUG---CUGGUAAUACAAA--AAAAUG--UAGGG-GGGGGGGGAAGAGCGGGAACUGUAGAGGAAGUUCCAAAUUACCCAUCCAG-
.......((.((((((((((-...))))))))---)).))..((((..--....))--))...-((..(((...((...((((((........))))))...)).)))..))..- ( -29.90)
>DroSec_CAF1 1086 98 - 1
AAGAGUCAUGGGUAUUUUGG-GCUCCAAAGUG---CUGGUAAUAAAAA--AAAUUG--UGUCG-GGG-------GAGGGGGAACUGUAGAGGAAGUUCCAAAUUACCCAUCCAG-
.......((.((((((((((-...))))))))---)).))........--....((--.(..(-((.-------.(...((((((........))))))...)..)))..))).- ( -27.20)
>DroSim_CAF1 1164 101 - 1
AAGAGUCAUGGGUAUUUUGG-GCUCCAAAGUG---CUGGUAAUAAAAAAAAAAUUG--GGAGAGGGG-------AAGCGGGUACUGUAGAGGAAGUUCCAAAUUACCCAUCCAG-
.......(((((((.(((((-(((((..((((---((.((................--.........-------..)).)))))).....)).)).)))))).)))))))....- ( -26.43)
>DroEre_CAF1 1120 107 - 1
AAGAGUCAUGGGUAUUUUGG-CCUCCAAAGUG---CUGGUAAUAAAAA--AGAACGGACGGCA-GGGUUGGCAGGGGCGGGAACUGUAGAGGAAGUUCCAAAUUACCCAUCCAG-
.......(((((((.(((.(-(((((((..((---(((..........--........)))))-...))))...)))).((((((........))))))))).)))))))....- ( -32.87)
>DroYak_CAF1 1094 97 - 1
AAGAGUCAUGGGUAUUUUGG-GCUCCAAAGUG---CUGGUAAUAAAAA--AAA---GGUGGAA-GG-------GGAGCGGCAACUGUAGAGGAAGUUCCAAAUUACCCAUCCAG-
.......(((((((.(((((-(((((.....(---((..(........--)..---)))....-..-------)))))...((((........))))))))).)))))))....- ( -26.10)
>DroAna_CAF1 14867 89 - 1
AACAGUCAUGGGCAUUUUGGGGCUUUCAAGUACUACUGGCCAUUAAAA-----CUG---------------------GGGGAUACGUGGAGGAAGUACCAAAUUACCCAUCCAUC
.......(((((...(((((..(((((..((((..(..(.........-----)..---------------------)..).))).....)))))..)))))...)))))..... ( -22.40)
>consensus
AAGAGUCAUGGGUAUUUUGG_GCUCCAAAGUG___CUGGUAAUAAAAA__AAAAUG__UGGCA_GGG_______GAGCGGGAACUGUAGAGGAAGUUCCAAAUUACCCAUCCAG_
.......(((((((.(((((.(((((..((.....)).........................................(....)......)).))).))))).)))))))..... (-15.34 = -15.73 +   0.39)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:48:49 2006