Locus 2029

Sequence ID	2L_DroMel_CAF1
Location	5,491,621 – 5,491,716
Length	95
Max. P	0.960614

overview

Window 5

Location	5,491,621 – 5,491,716
Length	95
Sequences	6
Columns	117
Reading direction	forward
Mean pairwise identity	76.44
Mean single sequence MFE	-20.23
Consensus MFE	-11.54
Energy contribution	-11.43
Covariance contribution	-0.11
Combinations/Pair	1.14
Mean z-score	-1.74
Structure conservation index	0.57
SVM decision value	0.55
SVM RNA-class probability	0.778309
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 5491621 95 + 22407834
CACACACAUACUAAUUACCUAGUUAAACUGUCAAAUUGACAGAUGACAGUUUUUGCCUGCC-------CAAUGGCAAGCAACACUUUG---GCUGUCAGUCAA------------AG
.........((((......))))....(((((.....))))).((((((((.((((.((((-------....)))).))))......)---))))))).....------------.. ( -25.50)
>DroVir_CAF1 162687 98 + 1
C----ACACACUAAUUACCUAGUUAAACUGUCAAAUUGACAGAUGACAGUUU-UGUCUGCUGCCGC-GCAAU-GCAAGUAACAUUUUGCCCCCUGUCAGUUUC------------UG
.----....((((......))))....(((((.....))))).((((((...-....(((......-)))..-(((((......)))))...)))))).....------------.. ( -20.40)
>DroGri_CAF1 172514 85 + 1
C----ACACACUAAUUACCUAGUUAAACUGUCAAAUUGACAGAUGACAGUUU-UGUCUGCCGC--------U-CCAAGUAACAUUUUGC--UCUGUCAGCU----------------
.----....((((......))))....(((((.....))))).((((((...-(((.(((...--------.-....))))))......--.))))))...---------------- ( -15.20)
>DroWil_CAF1 163018 106 + 1
UACACACAUACUAAUUACCUAGUUAAACUGUCAAAUUGACAGAUGACAGUU-UUGUCUGCC-------CAAUGGCAAGCAACACUUUG---CCUGUCACUCACAAAGAGGAAGAAAA
.(((.....((((......)))).....))).....((((((..((.(((.-(((..((((-------....))))..))).))))).---.))))))(((.....)))........ ( -23.80)
>DroYak_CAF1 119806 92 + 1
---ACACAUACUAAUUACCUAGUUAAACUGUCAAAUUGACAGAUGACAGUUUUUGCCUGCC-------CAAUGGCAAGCAACACUUUG---GUUGUCAGUCAA------------AG
---......(((.((.(((.(((.(((((((((..........)))))))))((((.((((-------....)))).)))).)))..)---)).)).)))...------------.. ( -23.20)
>DroMoj_CAF1 180172 96 + 1
C----ACACACUAAUUACCUAGUUAAACUGUCAAAUUGACAGAUGACAGUUU-UGUCUGCUGCCGCUGCUAA-CCAAGUAACAUUUU---CCCCGUCAGUUCA------------UG
.----....((((......))))....(((((.....))))).(((((((..-.....)))...(.((((..-...)))).).....---....)))).....------------.. ( -13.30)
>consensus
C____ACACACUAAUUACCUAGUUAAACUGUCAAAUUGACAGAUGACAGUUU_UGUCUGCC_______CAAU_GCAAGCAACACUUUG___CCUGUCAGUCAA____________AG
.........((((......))))....(((((.....))))).((((((....(((.(((.............))).)))............))))))................... (-11.54 = -11.43 +  -0.11)

alignment

secondary structure

dotplot

Window 6

Location	5,491,621 – 5,491,716
Length	95
Sequences	6
Columns	117
Reading direction	reverse
Mean pairwise identity	76.44
Mean single sequence MFE	-27.42
Consensus MFE	-14.87
Energy contribution	-14.95
Covariance contribution	0.08
Combinations/Pair	1.06
Mean z-score	-2.32
Structure conservation index	0.54
SVM decision value	1.52
SVM RNA-class probability	0.960614
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 5491621 95 - 22407834
CU------------UUGACUGACAGC---CAAAGUGUUGCUUGCCAUUG-------GGCAGGCAAAAACUGUCAUCUGUCAAUUUGACAGUUUAACUAGGUAAUUAGUAUGUGUGUG
..------------...(((((..((---(......(((((((((....-------)))))))))(((((((((..........))))))))).....)))..)))))......... ( -32.00)
>DroVir_CAF1 162687 98 - 1
CA------------GAAACUGACAGGGGGCAAAAUGUUACUUGC-AUUGC-GCGGCAGCAGACA-AAACUGUCAUCUGUCAAUUUGACAGUUUAACUAGGUAAUUAGUGUGU----G
..------------.((((((.(((((.(((..((((.....))-)))))-.)(((((..((((-....))))..)))))..)))).)))))).(((((....)))))....----. ( -25.20)
>DroGri_CAF1 172514 85 - 1
----------------AGCUGACAGA--GCAAAAUGUUACUUGG-A--------GCGGCAGACA-AAACUGUCAUCUGUCAAUUUGACAGUUUAACUAGGUAAUUAGUGUGU----G
----------------..........--(((....(((((((((-.--------..(((((...-...)))))..(((((.....))))).....)))))))))...)))..----. ( -23.00)
>DroWil_CAF1 163018 106 - 1
UUUUCUUCCUCUUUGUGAGUGACAGG---CAAAGUGUUGCUUGCCAUUG-------GGCAGACAA-AACUGUCAUCUGUCAAUUUGACAGUUUAACUAGGUAAUUAGUAUGUGUGUA
.......((.....(..((..(((..---.....)))..))..)....)-------)(((.((((-((((((((..........))))))))).(((((....))))).))).))). ( -28.90)
>DroYak_CAF1 119806 92 - 1
CU------------UUGACUGACAAC---CAAAGUGUUGCUUGCCAUUG-------GGCAGGCAAAAACUGUCAUCUGUCAAUUUGACAGUUUAACUAGGUAAUUAGUAUGUGU---
..------------...(((((..((---(......(((((((((....-------)))))))))(((((((((..........))))))))).....)))..)))))......--- ( -31.70)
>DroMoj_CAF1 180172 96 - 1
CA------------UGAACUGACGGGG---AAAAUGUUACUUGG-UUAGCAGCGGCAGCAGACA-AAACUGUCAUCUGUCAAUUUGACAGUUUAACUAGGUAAUUAGUGUGU----G
((------------((.((((......---.....(((((((((-((((..((....)).((((-....))))..(((((.....))))).))))))))))))))))).)))----) ( -23.70)
>consensus
CU____________UUAACUGACAGG___CAAAAUGUUACUUGC_AUUG_______GGCAGACA_AAACUGUCAUCUGUCAAUUUGACAGUUUAACUAGGUAAUUAGUAUGU____G
...................................((((((((.............(((((.......)))))..(((((.....)))))......))))))))............. (-14.87 = -14.95 +   0.08)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:17:31 2006