Locus 1082

Sequence ID	3R_DroMel_CAF1
Location	3,303,687 – 3,303,886
Length	199
Max. P	0.744059

overview

Window 1

Location	3,303,687 – 3,303,806
Length	119
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	93.06
Mean single sequence MFE	-28.32
Consensus MFE	-21.61
Energy contribution	-22.55
Covariance contribution	0.94
Combinations/Pair	1.07
Mean z-score	-1.80
Structure conservation index	0.76
SVM decision value	-0.04
SVM RNA-class probability	0.513573
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 3303687 119 - 27905053
CCU-CCCUUUAUUCGGAAGAAUAAAUCUCGGAGCCAAAUAAAAAAUGCAUUUUUAUUGCCCAUCGCCUUUGUAUGGCAUUGAAAAGUUCCGAUUGGCAAACUUAACAUGGCAAUGUUUAC
..(-((.(((((((....)))))))....)))((((((((((((.....))))))))(((.((((((.......)))(((....)))...))).)))..........))))......... ( -30.20)
>DroSec_CAF1 7737 120 - 1
CCUUGCCUUUAUUCGGAAGAAUAAAUCUGGGAGCCAAAUAAAAAAUGCAUUUUUAUUGCCCACGGCCUUUGUAUGGCAUUGAAAAGUUCCGAUUUGCAAACUUAACACGGCAAUGUUUAC
..((((((((((((....))))))).(((((.((..((((((((.....)))))))))))).)))..(((((((((.(((....))).)))...))))))........)))))....... ( -27.90)
>DroSim_CAF1 6159 120 - 1
CCUUGCCUUUAUUCGGAAGAAUAAAUCUGGGAGCCAAAUAAAAAAUGCAUUUUUAUUGCCCAGCGCCUUUGUAUGGCAUUGAAAAGUUCCGAUUGGCAAACUUAACACGGCAAUGUUUAC
..((((((((((((....))))))).(((((.....((((((((.....)))))))).))))).(((...((.(((.(((....))).))))).)))...........)))))....... ( -32.60)
>DroYak_CAF1 17951 118 - 1
CCUU--CUUUAUUCGGGAGAAUAAAUCACUGAGCCAAAUAAAAAAUGCAUUUUUAUUGCCCAGCGCCUUUUUAUGGCAUUGAAAAGUUCCGAUUGACAAACUUAACACGGCGGUGUUUAC
....--.(((((((....))))))).......(((.((((((((.....))))))))((((((.(((.......))).)))..(((((..........))))).....))))))...... ( -22.60)
>consensus
CCUUGCCUUUAUUCGGAAGAAUAAAUCUCGGAGCCAAAUAAAAAAUGCAUUUUUAUUGCCCAGCGCCUUUGUAUGGCAUUGAAAAGUUCCGAUUGGCAAACUUAACACGGCAAUGUUUAC
..((((((((((((....)))))))....(((((..((((((((.....))))))))...((..(((.......)))..))....)))))..................)))))....... (-21.61 = -22.55 +   0.94)

alignment

secondary structure

dotplot

Window 2

Location	3,303,727 – 3,303,846
Length	119
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	93.89
Mean single sequence MFE	-28.62
Consensus MFE	-24.92
Energy contribution	-26.30
Covariance contribution	1.38
Combinations/Pair	1.02
Mean z-score	-1.64
Structure conservation index	0.87
SVM decision value	0.34
SVM RNA-class probability	0.694279
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 3303727 119 - 27905053
AUCACGUAGUGUAAAGAAAUAGAAAUUCGCGUUUUGUGCCCCU-CCCUUUAUUCGGAAGAAUAAAUCUCGGAGCCAAAUAAAAAAUGCAUUUUUAUUGCCCAUCGCCUUUGUAUGGCAUU
.....((.((((((((.(((((((((.((..((((((....((-((.(((((((....)))))))....))))....))))))..)).)))))))))((.....)))))))))).))... ( -26.80)
>DroSec_CAF1 7777 120 - 1
AUCACGUAGUGCAAAGAAAUAGAAACUCGCGUUUUGUCCCCCUUGCCUUUAUUCGGAAGAAUAAAUCUGGGAGCCAAAUAAAAAAUGCAUUUUUAUUGCCCACGGCCUUUGUAUGGCAUU
.....((.((((((((.....(((((....))))).........((((((((((....)))))))..((((.....((((((((.....)))))))).)))).))))))))))).))... ( -31.70)
>DroSim_CAF1 6199 120 - 1
AUCACGUAGUGCAAAGAAAUAGAAAUUCGCGUUUUGUGCCCCUUGCCUUUAUUCGGAAGAAUAAAUCUGGGAGCCAAAUAAAAAAUGCAUUUUUAUUGCCCAGCGCCUUUGUAUGGCAUU
.....((.((((((((.(((((((((..(((((((..(((((.....(((((((....)))))))...))).)).......))))))))))))))))((.....)))))))))).))... ( -33.00)
>DroYak_CAF1 17991 118 - 1
AUCACGUAGUGCAAAGAAAUAGAAAUUCGCGUUUUGUGCCCCUU--CUUUAUUCGGGAGAAUAAAUCACUGAGCCAAAUAAAAAAUGCAUUUUUAUUGCCCAGCGCCUUUUUAUGGCAUU
.....(..(..(((((....(....).....)))))..)..)..--.(((((((....)))))))...(((.((..((((((((.....)))))))))).))).(((.......)))... ( -23.00)
>consensus
AUCACGUAGUGCAAAGAAAUAGAAAUUCGCGUUUUGUGCCCCUUGCCUUUAUUCGGAAGAAUAAAUCUCGGAGCCAAAUAAAAAAUGCAUUUUUAUUGCCCAGCGCCUUUGUAUGGCAUU
.....((.((((((((.(((((((((..(((((((..(((((.....(((((((....)))))))...))).)).......))))))))))))))))((.....)))))))))).))... (-24.92 = -26.30 +   1.38)

alignment

secondary structure

dotplot

Window 3

Location	3,303,767 – 3,303,886
Length	119
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	95.42
Mean single sequence MFE	-29.38
Consensus MFE	-26.84
Energy contribution	-26.65
Covariance contribution	-0.19
Combinations/Pair	1.03
Mean z-score	-1.68
Structure conservation index	0.91
SVM decision value	0.46
SVM RNA-class probability	0.744059
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 3303767 119 - 27905053
CAACUUUAUUUUCGGCUCUUGGGAAAUUGGAAAAUUGCAAAUCACGUAGUGUAAAGAAAUAGAAAUUCGCGUUUUGUGCCCCU-CCCUUUAUUCGGAAGAAUAAAUCUCGGAGCCAAAUA
.............((((((.((((((((....))))(((....(((((((....(....)....))).))))....)))...)-)))(((((((....)))))))....))))))..... ( -29.50)
>DroSec_CAF1 7817 120 - 1
CAACUUUAUUUUCGGCUCUUGGGAAAUUGGAAAAUUGCAAAUCACGUAGUGCAAAGAAAUAGAAACUCGCGUUUUGUCCCCCUUGCCUUUAUUCGGAAGAAUAAAUCUGGGAGCCAAAUA
.............((((((..((.....((......(((((..(((((((....(....)....))).)))))))))........))(((((((....)))))))))..))))))..... ( -30.74)
>DroSim_CAF1 6239 120 - 1
CAACUUUAUUUUCGGCUCUUGGGAAAUUGGAAAAUUGCAAAUCACGUAGUGCAAAGAAAUAGAAAUUCGCGUUUUGUGCCCCUUGCCUUUAUUCGGAAGAAUAAAUCUGGGAGCCAAAUA
.............((((((..((.((((....))))((((.....(..(..(((((....(....).....)))))..)..))))).(((((((....)))))))))..))))))..... ( -31.00)
>DroYak_CAF1 18031 118 - 1
CAACUUUAUUUUCGGCUCUUGGGAAAUUGGAAAAUUGCAAAUCACGUAGUGCAAAGAAAUAGAAAUUCGCGUUUUGUGCCCCUU--CUUUAUUCGGGAGAAUAAAUCACUGAGCCAAAUA
.............(((((..(((.((((....))))............(..(((((....(....).....)))))..))))..--.(((((((....))))))).....)))))..... ( -26.30)
>consensus
CAACUUUAUUUUCGGCUCUUGGGAAAUUGGAAAAUUGCAAAUCACGUAGUGCAAAGAAAUAGAAAUUCGCGUUUUGUGCCCCUUGCCUUUAUUCGGAAGAAUAAAUCUCGGAGCCAAAUA
.............(((((..(((.((((....))))(((((..(((((((....(....)....))).)))))))))..))).....(((((((....))))))).....)))))..... (-26.84 = -26.65 +  -0.19)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:00:09 2006