Locus 157

Sequence ID	2L_DroMel_CAF1
Location	456,137 – 456,278
Length	141
Max. P	0.919470

overview

Window 3

Location	456,137 – 456,251
Length	114
Sequences	6
Columns	117
Reading direction	reverse
Mean pairwise identity	77.13
Mean single sequence MFE	-34.50
Consensus MFE	-23.08
Energy contribution	-22.80
Covariance contribution	-0.28
Combinations/Pair	1.20
Mean z-score	-1.12
Structure conservation index	0.67
SVM decision value	0.03
SVM RNA-class probability	0.550206
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 456137 114 - 22407834
CGAGGGAACUCCG---AUGUAGUGGACUUACCUGAUGCUUGUCCAGAAUGGGAGUCCAUUUGGAGCGCACUAUUUUGCGCACCAGUCGGCUGUUAUCUCGCGAGCAGAGGAUUCUGA
((((..(((.(((---((..(((((((((.((...((......))....)))))))))))(((.(((((......))))).))))))))..)))..))))....(((......))). ( -40.00)
>DroPse_CAF1 2512 109 - 1
AGAGAAGA----G---AUGGGGAU-GCUCACCUGAUGCUUAUCCAAUAUAGGCGUCCAUUUGGAGCGCACUAUCUUGCGCACCAGCCGGCUGUUAUCACGCGAGCAGAGAAUCUUGA
......((----(---((.....(-((((.(.((((((((((.....))))))(((...((((.(((((......))))).))))..)))....)))).).)))))....))))).. ( -34.80)
>DroGri_CAF1 2923 105 - 1
----U-GUUUGCG---AUG----UCGCUUACCUGAUGCUUAUCCAAUAUGGGCGUCCACUUGGAGCGUACUAUCUUGCGGACCAGACGGCUGUUAUCUCGCGAGCAGAGUAACUUGA
----(-(((((((---(.(----((((((....(((((((((.....)))))))))......))))).))......((((.((....))))))....)))))))))........... ( -32.40)
>DroMoj_CAF1 2264 110 - 1
----U-AUCUGCUCCAAUC--GUGCACUUACCUGAUGCUUAUCCAAAAUGGGCGUCCACUUGGAGCGCACUAUCUUGCGCACCAGGCGGCUGUUAUCUCGCGAGCAGAGUAUCUUGA
----.-.(((((((.....--..((........(((((((((.....)))))))))(.(((((.(((((......))))).))))).))).((......)))))))))......... ( -36.70)
>DroAna_CAF1 2294 108 - 1
----UGAA--CAA---AAAGAGUGACAAUACCUGAUGCUUGUCCAGAAUUGGUGUCCAUUUGGAGCGCACUAUUUUGCGCACCAGCCGGCUGUUAUCUCGGGAACAGAGCAACCUCA
----....--...---...(((.(.((.....)).(((((.(((.((..((..(.((..((((.(((((......))))).))))..)).)..))..)).)))...))))).)))). ( -28.30)
>DroPer_CAF1 2664 109 - 1
AGAGAAGA----G---AUGGGGAU-GCUCACCUGAUGCUUAUCCAAUAUAGGCGUCCAUUUGGAGCGCACUAUCUUGCGCACCAGCCGGCUGUUAUCACGCGAGCAGAGAAUCUUGA
......((----(---((.....(-((((.(.((((((((((.....))))))(((...((((.(((((......))))).))))..)))....)))).).)))))....))))).. ( -34.80)
>consensus
____U_AA___CG___AUGG_GUG_GCUUACCUGAUGCUUAUCCAAAAUGGGCGUCCAUUUGGAGCGCACUAUCUUGCGCACCAGCCGGCUGUUAUCUCGCGAGCAGAGAAUCUUGA
..............................((.(((((((((.....)))))))))...((((.(((((......))))).))))..))(((((........))))).......... (-23.08 = -22.80 +  -0.28)

alignment

secondary structure

dotplot

Window 4

Location	456,177 – 456,278
Length	101
Sequences	6
Columns	101
Reading direction	forward
Mean pairwise identity	79.67
Mean single sequence MFE	-22.63
Consensus MFE	-15.70
Energy contribution	-16.62
Covariance contribution	0.92
Combinations/Pair	1.22
Mean z-score	-2.12
Structure conservation index	0.69
SVM decision value	1.13
SVM RNA-class probability	0.919470
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 456177 101 + 22407834
CAAAAUAGUGCGCUCCAAAUGGACUCCCAUUCUGGACAAGCAUCAGGUAAGUCCACUACAUCGGAGUUCCCUCGAUUCAAACCUGCCUUACCGAGACAAAU
.......((((..(((((((((....))))).))))...))))..((((((........(((((.......)))))..........))))))......... ( -21.97)
>DroGri_CAF1 2963 90 + 1
CAAGAUAGUACGCUCCAAGUGGACGCCCAUAUUGGAUAAGCAUCAGGUAAGCGA----CAUCGCAAAC-A----AAAUAAUUCAGAUUUAUACA--UUAUU
...((((((..(((((((((((....)))).)))))...)).........(((.----...)))....-.----...................)--))))) ( -15.50)
>DroSec_CAF1 2262 101 + 1
CAAAAUAGUGCGCUCCAAAUGGACUCCCAUUCUGGACAAGCAUCAGGUAAGUCCACUACAUCCGAGUUUCCUUGAUACAAGCCUUUCUUACCGAAACAAAU
.......((((..(((((((((....))))).))))...))))..((((((...........((((....))))............))))))......... ( -21.80)
>DroSim_CAF1 2163 101 + 1
CAAAAUAGUGCGCUCCAAAUGGACUCCCAUUCUGGACAAGCAUCAGGUAAGUCCACUACAUCCGAGUUUCCUUGAUACAAGCCUUUCUUACCGAAACAAAU
.......((((..(((((((((....))))).))))...))))..((((((...........((((....))))............))))))......... ( -21.80)
>DroEre_CAF1 2250 101 + 1
CAAAAUAGUGCGCUCCAAAUGGACUCCCAUUCUGGACAAGCAUCAGGUAAGGCCACUACAUCGGAGUUCCCUCUAUAUAAGCCUGCCUUACCUAAGCAAAU
........((((((((((((((....))))).))))...))...(((((((((..((.....((((....)))).....))...)))))))))..)))... ( -30.20)
>DroYak_CAF1 2277 101 + 1
CAAAAUAGUGCGCUCCAAAUGGACUCCCAUUCUGGACAAGCAUCAGGUAAGUCCACCACACGGCAGAUCCCUCUAUAUCAGCCUGCCAUACCUAAACUUGU
.......((((..(((((((((....))))).))))...)))).(((((.((.....))..(((((................))))).)))))........ ( -24.49)
>consensus
CAAAAUAGUGCGCUCCAAAUGGACUCCCAUUCUGGACAAGCAUCAGGUAAGUCCACUACAUCGGAGUUCCCUCGAUACAAGCCUGCCUUACCGAAACAAAU
.......((((..(((((((((....))))).))))...))))..((((((...........((((....))))............))))))......... (-15.70 = -16.62 +   0.92)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:27:39 2006