Locus 7998

Sequence ID	3R_DroMel_CAF1
Location	21,454,837 – 21,454,944
Length	107
Max. P	0.919321

overview

Window 4

Location	21,454,837 – 21,454,944
Length	107
Sequences	6
Columns	109
Reading direction	forward
Mean pairwise identity	71.47
Mean single sequence MFE	-28.60
Consensus MFE	-13.90
Energy contribution	-16.48
Covariance contribution	2.58
Combinations/Pair	1.19
Mean z-score	-1.57
Structure conservation index	0.49
SVM decision value	-0.00
SVM RNA-class probability	0.531546
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 21454837 107 + 27905053
AAGUGUCGUGAUCGACUCAUGCAACAGCAGCAGCUGCUCC-UCGGAAUCAGCCAUCCGAGGAUGGGUUAC-AAAUUAACCCAUUGAGGACACGGAGGGCGGGUAAUAUA
..(.((((....)))).).(((....)))....((((.((-((((......)).(((...(((((((((.-....)))))))))..)))....))))))))........ ( -35.30)
>DroSec_CAF1 61777 107 + 1
AAGUGUCGUGAUCGACUCACGCAACAGCAGCAGCUGCUCC-UCGGAAUCAGCCAUCCGAGUAUGGGUUAC-AAAUUAACCCAUUGAGGACACGGAGGGCGGGUAAUAUA
..(.((((....)))).).(((..((((....))))..((-((((......)).(((....((((((((.-....))))))))...)))....)))))))......... ( -34.90)
>DroSim_CAF1 46352 107 + 1
AAGUGUCGUGAUCGACUCACGCAACAGCAGCAGCUGCUCC-UCGGAAUCAGCCAUCCGAGGAUGGGUUAC-AAAUUAACCCAUUGAGGACACGGAGGGCGGGAAANNNN
..(((((((((.....))))....((((....))))((((-(((((........))))))(((((((((.-....)))))))))))))))))................. ( -37.10)
>DroWil_CAF1 158889 101 + 1
AAAUGUCAUGAUCAAGGCAUGGCACUGCAGCUGCUGCUCC-UCUUCAU---CC-UUUAAACCUCUUUUUU-AACUUAACCCAUG--UGACACUAAGGGGUCAAAAUAUA
...(((((((.......)))))))..((((...))))...-.......---..-.....(((((((....-.((.........)--)......)))))))......... ( -17.30)
>DroYak_CAF1 52901 94 + 1
AAAUGUCGUGAUCGACUCACGCAACAGCGGCAGCUGCUCC-UCGGAAUUAACCAUCUGAGGAUGGGUUAC-ACAUUAACCCAUUGAGGACUUUGAA-------------
...((.(((((.....))))))).((((....))))((((-(((((........))))))(((((((((.-....)))))))))))).........------------- ( -30.80)
>DroAna_CAF1 141899 96 + 1
AAAUGUCGUGAUCGACACACGCAACAACAGCAGCUGCUGUUUUGGAAUUAACUAUCUUCGGCCAGGCUUCAAAAUUAACCCAUUGACAACAUCCCA-------------
...(((((((.....)))..((...((((((....))))))..........((..(....)..)))).................))))........------------- ( -16.20)
>consensus
AAAUGUCGUGAUCGACUCACGCAACAGCAGCAGCUGCUCC_UCGGAAUCAGCCAUCCGAGGAUGGGUUAC_AAAUUAACCCAUUGAGGACACGGAGGGCGGG_AA____
..((((((((.......)))....((((....)))).....(((((........))))).(((((((((......)))))))))...)))))................. (-13.90 = -16.48 +   2.58)

alignment

secondary structure

dotplot

Window 5

Location	21,454,837 – 21,454,944
Length	107
Sequences	6
Columns	109
Reading direction	reverse
Mean pairwise identity	71.47
Mean single sequence MFE	-31.34
Consensus MFE	-18.49
Energy contribution	-19.13
Covariance contribution	0.64
Combinations/Pair	1.35
Mean z-score	-1.68
Structure conservation index	0.59
SVM decision value	1.13
SVM RNA-class probability	0.919321
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 21454837 107 - 27905053
UAUAUUACCCGCCCUCCGUGUCCUCAAUGGGUUAAUUU-GUAACCCAUCCUCGGAUGGCUGAUUCCGA-GGAGCAGCUGCUGCUGUUGCAUGAGUCGAUCACGACACUU
................((((((((((.(((((((....-.)))))))((((((((........)))))-)))(((((.......))))).))))..)).))))...... ( -37.50)
>DroSec_CAF1 61777 107 - 1
UAUAUUACCCGCCCUCCGUGUCCUCAAUGGGUUAAUUU-GUAACCCAUACUCGGAUGGCUGAUUCCGA-GGAGCAGCUGCUGCUGUUGCGUGAGUCGAUCACGACACUU
....((((..(((.((((.((.....((((((((....-.)))))))))).)))).))).........-(.((((((....)))))).)))))((((....)))).... ( -37.60)
>DroSim_CAF1 46352 107 - 1
NNNNUUUCCCGCCCUCCGUGUCCUCAAUGGGUUAAUUU-GUAACCCAUCCUCGGAUGGCUGAUUCCGA-GGAGCAGCUGCUGCUGUUGCGUGAGUCGAUCACGACACUU
.................(((((.....(((((((....-.)))))))((((((((........)))))-)))(((((.......)))))((((.....))))))))).. ( -39.50)
>DroWil_CAF1 158889 101 - 1
UAUAUUUUGACCCCUUAGUGUCA--CAUGGGUUAAGUU-AAAAAAGAGGUUUAAA-GG---AUGAAGA-GGAGCAGCAGCUGCAGUGCCAUGCCUUGAUCAUGACAUUU
......(((((((..........--...)))))))(((-(.....(((((.....-((---.......-(.(((....))).)....))..))))).....)))).... ( -18.32)
>DroYak_CAF1 52901 94 - 1
-------------UUCAAAGUCCUCAAUGGGUUAAUGU-GUAACCCAUCCUCAGAUGGUUAAUUCCGA-GGAGCAGCUGCCGCUGUUGCGUGAGUCGAUCACGACAUUU
-------------.......(((((.((((((((....-.))))))))........((......))))-)))(((((....)))))(((((((.....))))).))... ( -30.40)
>DroAna_CAF1 141899 96 - 1
-------------UGGGAUGUUGUCAAUGGGUUAAUUUUGAAGCCUGGCCGAAGAUAGUUAAUUCCAAAACAGCAGCUGCUGUUGUUGCGUGUGUCGAUCACGACAUUU
-------------((((((.(((((..((((((........))))))......)))))...))))))...(((((((....)))))))...((((((....)))))).. ( -24.70)
>consensus
____UU_CCCGCCCUCCGUGUCCUCAAUGGGUUAAUUU_GUAACCCAUCCUCAGAUGGCUGAUUCCGA_GGAGCAGCUGCUGCUGUUGCGUGAGUCGAUCACGACACUU
.................(((((.....(((((((......)))))))......................(.((((((....)))))).)((((.....))))))))).. (-18.49 = -19.13 +   0.64)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:59:55 2006